sampleID	chr	pos	ref	mut	r1_vaf	r2_vaf	r1_pval	r2_pval	vaf	context	gene	aachange	ntchange	codonsub	impact	pid	vaf_ref
CAMB-71A93	MN908947.3	10097	G	A	1	1	0	0	0.999947867792722	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	5.21322072776561e-05
CAMB-71A93	MN908947.3	11074	C	INS	0.022	0.044	0.00036	6.6e-10	0.0285238531346266	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.971243027225044
CAMB-71A93	MN908947.3	11075	T	-	0.039	0.06	9.2e-10	2.4e-15	0.0455146941208975	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954092687111925
CAMB-71A93	MN908947.3	12243	G	T	0.02	0.015	2.5e-10	3e-08	0.018651832460733	CGT	ORF1ab:nsp8	R51L	G152T	CGT>CTT	Missense	ORF1ab:nsp8	0.981086387434555
CAMB-71A93	MN908947.3	12308	C	A	0.013	0.006	1.6e-06	0.0018	0.010776785420031	ACA	ORF1ab:nsp8	Q73K	C217A	CAG>AAG	Missense	ORF1ab:nsp8	0.98902547539795
CAMB-71A93	MN908947.3	12502	AT	-	0.00655	0.0125	0.0027;0.0024	1.5e-05;1.3e-05	0.00945171215441486	CAT	ORF1ab:nsp8	.	411-412-delfrshift	.	no-SNV	ORF1ab:nsp8	0.990622076198351
CAMB-71A93	MN908947.3	13250	T	C	0.0046	0.0092	0.00065	5.1e-06	0.00654651440802432	GTA	ORF1ab:nsp10	Y76H	T226C	TAC>CAC	Missense	ORF1ab:nsp10	0.993430715107078
CAMB-71A93	MN908947.3	13536	C	T	1	1	0	0	0.999702911467617	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-71A93	MN908947.3	14408	C	T	1	1	0	0	0.997871333964049	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000387030188354692
CAMB-71A93	MN908947.3	15017	C	T	0.019	0.0079	5.2e-08	0.00016	0.011275415896488	GCA	ORF1ab:RNA-dependent-RNA-polymerase	A517V	C1550T	GCA>GTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.988724584103512
CAMB-71A93	MN908947.3	16075	G	T	0.01	0.0068	1.2e-06	4e-05	0.00927034060903098	TGA	ORF1ab:RNA-dependent-RNA-polymerase	D870Y	G2608T	GAT>TAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.988678026633233
CAMB-71A93	MN908947.3	16474	A	G	0.016	0.0098	2.4e-07	6.8e-06	0.0112207390210873	TAG	ORF1ab:helicase	S80G	A238G	AGT>GGT	Missense	ORF1ab:helicase	0.988779260978913
CAMB-71A93	MN908947.3	18651	GCGCACCTGTT	-	0.0129090909090909	0.00490909090909091	0.00025;0.00032;0.00028;0.00032;3.1e-05;2.7e-06;5.5e-06;7.5e-06;0.00011;0.00041;0.00022	5.6e-05;6.5e-05;6.4e-05;7.4e-05;NA;NA;NA;NA;NA;NA;NA	0.00662632326877325	AGC	ORF1ab:3'-to-5'-exonuclease	.	612-622-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.987453607908825
CAMB-71A93	MN908947.3	20480	C	T	0.011	0.022	0.00031	4.2e-05	0.0138461538461538	TCA	ORF1ab:endoRNAse	S287L	C860T	TCA>TTA	Missense	ORF1ab:endoRNAse	0.986153846153846
CAMB-71A93	MN908947.3	21980	T	-	0.024	0.018	3.1e-06	1e-04	0.0209050013231014	ATT	S	.	418-418-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.979094998676899
CAMB-71A93	MN908947.3	23403	A	G	0.99	1	0	0	0.991907364038512	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000130106687483737
CAMB-71A93	MN908947.3	23454	C	T	0.015	0.013	1.5e-08	3e-08	0.0142450142450142	CCT	S	P631L	C1892T	CCT>CTT	Missense	GU280_gp02, spike glycoprotein	0.983706854674597
CAMB-71A93	MN908947.3	23731	C	T	1	1	0	0	0.999813025864755	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000124649423496416
CAMB-71A93	MN908947.3	241	C	T	1	0.99	0	0	0.997348042855628	TCG	NA	NA	NA	NA	NA	NA	0.000132597857218627
CAMB-71A93	MN908947.3	26781	CTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0182222222222222	0.03225	0.0055;0.02;0.02;0.026;0.01;0.019;0.0053;0.0053;0.003;0.0043;0.0037;0.0051;0.0044;0.0048;0.0062;0.0039;0.0057;0.0047;0.0044;0.0048;0.0061;0.0047;0.0052;0.0044;0.0044;0.0057;0.0042;0.0033;0.0044;0.0055;0.005;0.0039;0.0056;0.0033;0.004;0.0035	0.00027;0.00052;0.00058;0.00097;2e-05;6.6e-05;1.4e-05;1.3e-05;9.3e-06;8.6e-06;6.8e-06;1.1e-05;9.5e-06;1.2e-05;1.9e-05;7.7e-06;1.5e-05;8.8e-06;1.1e-05;1.2e-05;1.8e-05;1.1e-05;1.3e-05;9.8e-06;7.1e-06;1.5e-05;1e-05;4.9e-06;9.9e-06;1.5e-05;1.3e-05;5.4e-06;1.5e-05;3e-06;8.7e-06;4.7e-06	0.0249693306603632	TCT	M	.	259-294-delinframe	.	no-SNV	GU280_gp05	0.980933906539443
CAMB-71A93	MN908947.3	28253	C	T	0.0041	0.014	0.0071	3.8e-07	0.00760227605668553	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.991688383783867
CAMB-71A93	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.997646267652993	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000689093528785316
CAMB-71A93	MN908947.3	28908	G	T	1	1	0	0	0.999892008639309	GGC	N	G212V	G635T	GGC>GTC	Missense	GU280_gp10	0
CAMB-71A93	MN908947.3	29470	T	C	0.0098	0.0038	8.6e-06	0.0018	0.0080533185226326	ATT	N	D399D	T1197C	GAT>GAC	Synonymous	GU280_gp10	0.991668980838656
CAMB-71A93	MN908947.3	29779	G	T	0.032	0.016	2.7e-10	1.5e-06	0.0210891617725574	GGA	NA	NA	NA	NA	NA	NA	0.978910838227443
CAMB-71A93	MN908947.3	2987	T	-	0.0087	0.0068	1.3e-05	5.1e-05	0.00742864590121204	ATT	ORF1ab:nsp3	.	268-268-delfrshift	.	no-SNV	ORF1ab:nsp3	0.992571354098788
CAMB-71A93	MN908947.3	3037	C	T	1	1	0	0	0.99938529628719	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000122940742562085
CAMB-71A93	MN908947.3	3403	G	A	0.0088	0.0095	6.1e-06	1.7e-06	0.00901101346089665	TGG	ORF1ab:nsp3	V228V	G684A	GTG>GTA	Synonymous	ORF1ab:nsp3	0.98473133830237
CAMB-71A93	MN908947.3	4002	C	T	1	0.99	0	0	0.998861588084622	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	9.48676596148373e-05
CAMB-71A93	MN908947.3	5822	C	T	0.02	0.019	3.2e-10	1.3e-09	0.0196287414512834	ACT	ORF1ab:nsp3	L1035F	C3103T	CTT>TTT	Missense	ORF1ab:nsp3	0.975575095479172
CAMB-71A93	MN908947.3	7431	C	T	0.036	0.013	3.2e-17	1.6e-07	0.0308084127505751	TCA	ORF1ab:nsp3	S1571L	C4712T	TCA>TTA	Missense	ORF1ab:nsp3	0.969191587249425
CAMB-71AA2	MN908947.3	11074	C	INS	0.095	0.039	2.4e-32	4.6e-09	0.0879984609888147	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.911534339187072
CAMB-71AA2	MN908947.3	11083	G	-	0.27	0.039	2.3e-130	7.7e-16	0.242954372343301	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-71AA2	MN908947.3	11083	G	T	0.73	0.96	6.9e-266	0	0.756922774515344	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-71AA2	MN908947.3	13617	G	A	1	1	0	6.4e-70	0.997181113460183	AGG	ORF1ab:RNA-dependent-RNA-polymerase	K50K	G150A	AAG>AAA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00281888653981677
CAMB-71AA2	MN908947.3	14805	C	T	1	1	0	0	0.999881136336622	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000118863663378105
CAMB-71AA2	MN908947.3	19983	C	T	0.98	1	2.1e-208	1.5e-35	0.983388704318937	TCT	ORF1ab:endoRNAse	V121V	C363T	GTC>GTT	Synonymous	ORF1ab:endoRNAse	0
CAMB-71AA2	MN908947.3	22713	C	T	1	1	0	0	0.999931101005925	CCT	S	P384L	C1151T	CCT>CTT	Missense	GU280_gp02, spike glycoprotein	3.44494970373433e-05
CAMB-71AA2	MN908947.3	2480	A	G	1	1	0	2.8e-168	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-71AA2	MN908947.3	2558	C	T	1	1	0	4.4e-184	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-71AA2	MN908947.3	26144	G	T	1	1	7.7e-189	1.8e-16	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-71AA2	MN908947.3	3330	C	T	1	1	0	0	0.998727825288006	ACT	ORF1ab:nsp3	T204I	C611T	ACT>ATT	Missense	ORF1ab:nsp3	0.00021202911866563
CAMB-71AA2	MN908947.3	6367	G	A	1	1	0	2.1e-172	0.999156553113725	AGG	ORF1ab:nsp3	Q1216Q	G3648A	CAG>CAA	Synonymous	ORF1ab:nsp3	0.000656014244880746
CAMB-71AC0	MN908947.3	11074	C	INS	0.03	0.023	4.8e-07	0.00026	0.027692944769398	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.971608261297169
CAMB-71AC0	MN908947.3	11075	T	-	0.036	0.04	7.3e-09	2.2e-10	0.0369797793087996	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958068671931888
CAMB-71AC0	MN908947.3	14408	C	T	1	1	0	0	0.998221783156335	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000802667325265498
CAMB-71AC0	MN908947.3	14786	C	T	1	1	0	0	0.999913228339624	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A440V	C1319T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	7.59252028287561e-05
CAMB-71AC0	MN908947.3	16965	A	C	0.0052	0.0069	0.00021	3e-05	0.00580032671228012	AAG	ORF1ab:helicase	Q243H	A729C	CAA>CAC	Missense	ORF1ab:helicase	0.994152323681905
CAMB-71AC0	MN908947.3	17646	A	C	0.026	0.017	6.3e-13	1e-09	0.0224548251352594	AAT	ORF1ab:helicase	Q470H	A1410C	CAA>CAC	Missense	ORF1ab:helicase	0.977527493900067
CAMB-71AC0	MN908947.3	23403	A	G	1	1	0	0	0.99780217767562	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000146521488292017
CAMB-71AC0	MN908947.3	241	C	T	1	1	0	0	0.999006597690808	TCG	NA	NA	NA	NA	NA	NA	5.62303193882141e-05
CAMB-71AC0	MN908947.3	26176	C	T	1	1	0	0	1	ACC	ORF3a	P262S	C784T	CCA>TCA	Missense	GU280_gp03	0
CAMB-71AC0	MN908947.3	26314	G	A	1	1	0	0	0.999786004707896	CGT	E	V24M	G70A	GTG>ATG	Missense	GU280_gp04	0.000187245880590627
CAMB-71AC0	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99872705621484	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000140739350722462
CAMB-71AC0	MN908947.3	3037	C	T	1	1	0	0	0.999680347781614	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000127860887354558
CAMB-71AC0	MN908947.3	643	C	T	0.023	0.025	1.3e-11	1.1e-12	0.0234933104210139	ACG	ORF1ab:leader-protein	N126N	C378T	AAC>AAT	Synonymous	ORF1ab:leader-protein	0.976212102614459
CAMB-71ADF	MN908947.3	10666	T	C	0.0096	0.0096	4.8e-06	2.7e-06	0.00963341120821436	TTT	ORF1ab:3C-like-proteinase	V204V	T612C	GTT>GTC	Synonymous	ORF1ab:3C-like-proteinase	0.990366588791786
CAMB-71ADF	MN908947.3	11074	C	INS	0.12	0.13	1.7e-59	1.6e-46	0.122159581821324	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.873174788318645
CAMB-71ADF	MN908947.3	11083	G	-	0.19	0.19	2.4e-85	4.6e-85	0.192264606470304	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.89715113471753e-05
CAMB-71ADF	MN908947.3	11083	G	T	0.81	0.81	0	0	0.807503621438918	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.89715113471753e-05
CAMB-71ADF	MN908947.3	11220	T	C	0.038	0.019	1.1e-17	1.6e-10	0.0326144682446293	ATG	ORF1ab:nsp6	M83T	T248C	ATG>ACG	Missense	ORF1ab:nsp6	0.967385531755371
CAMB-71ADF	MN908947.3	11224	C	T	0.13	0.15	3.1e-61	3.1e-71	0.139215569928203	TCT	ORF1ab:nsp6	V84V	C252T	GTC>GTT	Synonymous	ORF1ab:nsp6	0.860725093455171
CAMB-71ADF	MN908947.3	11824	C	T	0.0035	0.013	0.0052	1.6e-05	0.00677966101694915	TCA	ORF1ab:nsp6	I284I	C852T	ATC>ATT	Synonymous	ORF1ab:nsp6	0.993220338983051
CAMB-71ADF	MN908947.3	12406	C	T	0.029	0.038	2.3e-13	2.5e-15	0.0321573524820481	ACA	ORF1ab:nsp8	N105N	C315T	AAC>AAT	Synonymous	ORF1ab:nsp8	0.96721823290665
CAMB-71ADF	MN908947.3	12469	C	A	1	1	0	0	0.999710797893391	CCA	ORF1ab:nsp8	A126A	C378A	GCC>GCA	Synonymous	ORF1ab:nsp8	7.61058175286919e-05
CAMB-71ADF	MN908947.3	13483	A	G	0.0026	0.009	0.0045	6.7e-06	0.00499227386188042	AAG	ORF1ab:RNA-dependent-RNA-polymerase	S6G	A16G	AGT>GGT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994888862474742
CAMB-71ADF	MN908947.3	13506	C	T	0.014	0.011	7.5e-07	2.1e-05	0.0131473540360963	GCG	ORF1ab:RNA-dependent-RNA-polymerase	C13C	C39T	TGC>TGT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.985438951981528
CAMB-71ADF	MN908947.3	14805	C	T	1	1	0	0	0.999919659355668	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	3.01277416244878e-05
CAMB-71ADF	MN908947.3	23603	C	T	0.031	0.043	8.2e-15	8e-20	0.036431531490505	TCC	S	P681S	C2041T	CCT>TCT	Missense	GU280_gp02, spike glycoprotein	0.963568468509495
CAMB-71ADF	MN908947.3	2480	A	G	1	0.99	0	0	0.997504678727386	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000155957579538366
CAMB-71ADF	MN908947.3	24844	C	T	0.016	0.014	1.1e-08	2.6e-08	0.0152733882234852	TCT	S	V1094V	C3282T	GTC>GTT	Synonymous	GU280_gp02, spike glycoprotein	0.984672354624744
CAMB-71ADF	MN908947.3	25522	G	A	0.051	0.074	9.9e-24	3.9e-34	0.0603397473673422	CGG	ORF3a	G44R	G130A	GGA>AGA	Missense	GU280_gp03	0.939634630659253
CAMB-71ADF	MN908947.3	25553	C	A	0.068	0.068	2.9e-31	1.5e-31	0.0683900684762796	GCT	ORF3a	A54D	C161A	GCT>GAT	Missense	GU280_gp03	0.926695896349574
CAMB-71ADF	MN908947.3	2558	C	T	1	1	0	0	0.998162071846282	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000167084377610693
CAMB-71ADF	MN908947.3	26144	G	T	1	1	0	0	0.999719337636823	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-71ADF	MN908947.3	26333	C	T	0.015	0.02	9.5e-08	5.7e-10	0.0166074051993953	ACA	E	T30I	C89T	ACA>ATA	Missense	GU280_gp04	0.983328720165222
CAMB-71ADF	MN908947.3	29028	C	T	0.011	0.0032	1.1e-06	0.0028	0.00749037932930181	GCT	N	A252V	C755T	GCT>GTT	Missense	GU280_gp10	0.992028587135789
CAMB-71ADF	MN908947.3	29272	C	T	0.013	0.0079	1.1e-07	2.5e-05	0.0106514657980456	ACA	N	Y333Y	C999T	TAC>TAT	Synonymous	GU280_gp10	0.989348534201954
CAMB-71ADF	MN908947.3	29373	AGCCTAAAAAGGACAAAAAGAAGAAGGCTGATGAAACTCAAGCCTTACCGCAGAGAC	-	0.00281578947368421	0.0205964912280702	0.0027;0.0027;0.0024;0.0028;0.0019;0.081;0.012;0.0024;0.0024;0.0023;0.0026;0.0023;0.0027;0.005;0.037;0.0068;0.0023;0.0033;0.0037;0.0045;0.0036;0.0071;0.0057;0.0037;0.0023;0.0027;0.0022;0.0023;0.0039;0.0046;0.0038;0.042;0.039;0.0056;0.0023;0.0024;0.0023;0.0022;0.0023;0.0043;0.0023;0.0013;0.0023;0.0023;0.0027;0.0021;0.0025;0.0018;0.00027;0.00048;0.0023;0.01;0.0094;0.0039;0.0032;0.0062;0.0055	7.1e-09;4.6e-09;6.7e-09;9.1e-09;2.7e-09;6.2e-08;8.6e-09;3.1e-09;5.6e-09;2.1e-09;5e-09;5.4e-09;6.1e-09;7.8e-09;1.1e-08;6.8e-09;5.1e-09;5.7e-09;1.2e-09;2.9e-09;3.7e-09;1.1e-08;3.2e-09;5e-09;4.7e-09;3.3e-09;4.8e-09;6.2e-09;7e-09;6.6e-09;5.9e-09;6.8e-08;4.8e-08;6.3e-09;4.7e-09;9.6e-09;5.9e-09;3.6e-09;6.2e-09;6.7e-09;6.1e-09;3e-10;3.9e-09;5.5e-09;3.5e-09;4.3e-09;5.1e-09;3.6e-09;2.9e-09;5.1e-09;6.3e-09;9.4e-09;4.7e-09;5.5e-09;4.6e-09;7.4e-09;7e-09	0.008327706504614	GAG	N	.	1100-1156-delinframe	.	no-SNV	GU280_gp10	0.991896627244853
CAMB-71ADF	MN908947.3	3176	C	T	0.028	0.027	4.3e-14	5.7e-14	0.0280225862044808	ACC	ORF1ab:nsp3	P153S	C457T	CCT>TCT	Missense	ORF1ab:nsp3	0.971360916899021
CAMB-71ADF	MN908947.3	4285	G	A	0.024	0.032	3e-12	4.2e-16	0.0272213510074859	AGG	ORF1ab:nsp3	E522E	G1566A	GAG>GAA	Synonymous	ORF1ab:nsp3	0.972778648992514
CAMB-71ADF	MN908947.3	758	C	T	0.0029	0.0086	0.0025	4.9e-06	0.00448638838475499	ACA	ORF1ab:leader-protein	H165Y	C493T	CAT>TAT	Missense	ORF1ab:leader-protein	0.995470054446461
CAMB-71ADF	MN908947.3	7749	C	T	0.015	0.0088	9.2e-08	3.3e-05	0.012500913809489	ACA	ORF1ab:nsp3	T1677I	C5030T	ACA>ATA	Missense	ORF1ab:nsp3	0.987425981431391
CAMB-71ADF	MN908947.3	9474	C	T	0.0084	0.012	1.2e-05	2.1e-07	0.00936065797246331	GCT	ORF1ab:nsp4	A307V	C920T	GCT>GTT	Missense	ORF1ab:nsp4	0.989412459671923
CAMB-71ADF	MN908947.3	9737	A	G	0.0099	0.0051	2.9e-06	0.00024	0.00811596718892409	TAG	ORF1ab:nsp4	S395G	A1183G	AGT>GGT	Missense	ORF1ab:nsp4	0.991884032811076
CAMB-71ADF	MN908947.3	9835	T	C	1	1	0	0	0.999875896646727	ATC	ORF1ab:nsp4	Y427Y	T1281C	TAT>TAC	Synonymous	ORF1ab:nsp4	4.96413413090422e-05
CAMB-71AEE	MN908947.3	11075	T	-	0.012	0.032	0.00054	9.7e-09	0.0183466147575887	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.971263458847862
CAMB-71AEE	MN908947.3	14408	C	T	1	1	0	0	0.999640955059542	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000299204117048651
CAMB-71AEE	MN908947.3	16074	TG	-	0.00935	0.0075	3.5e-06;6.1e-06	NA;1.5e-08	0.00883918706264439	CTG	ORF1ab:RNA-dependent-RNA-polymerase	.	2607-2608-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.992857751640672
CAMB-71AEE	MN908947.3	16075	G	-	0.0092	0.015	6.1e-06	1.5e-08	0.0106739909871386	TGA	ORF1ab:RNA-dependent-RNA-polymerase	.	2608-2608-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.98927666853064
CAMB-71AEE	MN908947.3	17876	C	T	0.0076	0.0091	3.4e-05	6.3e-06	0.00804014259144451	ACT	ORF1ab:helicase	T547I	C1640T	ACT>ATT	Missense	ORF1ab:helicase	0.991901735895846
CAMB-71AEE	MN908947.3	18123	T	A	0.0027	0.011	0.0027	7.6e-07	0.00712250712250712	GTG	ORF1ab:3'-to-5'-exonuclease	S28R	T84A	AGT>AGA	Missense	ORF1ab:3'-to-5'-exonuclease	0.992830009496676
CAMB-71AEE	MN908947.3	22858	C	T	0.018	0.03	3.4e-09	1.5e-14	0.023121387283237	GCG	S	C432C	C1296T	TGC>TGT	Synonymous	GU280_gp02, spike glycoprotein	0.976878612716763
CAMB-71AEE	MN908947.3	22858	CG	TA	0.009037	0.0182	3.4e-09;0.49	1.5e-14;2.9e-05	0.0128317806292846	GCG	S	.	1296-1297-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.976878612716763
CAMB-71AEE	MN908947.3	23403	A	G	1	1	0	0	0.999907768930427	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.17352763345323e-05
CAMB-71AEE	MN908947.3	241	C	T	1	1	0	0	0.999612671749501	TCG	NA	NA	NA	NA	NA	NA	0.000244628368736494
CAMB-71AEE	MN908947.3	24130	C	T	0.0037	0.009	0.0045	1.8e-05	0.00552147239263804	ACG	S	N856N	C2568T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.994425180048013
CAMB-71AEE	MN908947.3	24173	G	-	0.0095	0.011	2.9e-06	5.3e-07	0.0104686965446459	TGC	S	.	2611-2611-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.989531303455354
CAMB-71AEE	MN908947.3	26028	C	T	0.024	0.035	1.3e-08	7.9e-09	0.0272511848341232	ACC	ORF3a	Y212Y	C636T	TAC>TAT	Synonymous	GU280_gp03	0.972748815165877
CAMB-71AEE	MN908947.3	28000	C	T	0.005	0.0093	0.00078	1.5e-05	0.00707018451457148	CCG	ORF8	P36L	C107T	CCG>CTG	Missense	GU280_gp09	0.992929815485428
CAMB-71AEE	MN908947.3	28253	C	T	0.014	0.0045	4e-07	0.0043	0.0110375821028199	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.988604375524717
CAMB-71AEE	MN908947.3	28793	G	C	0.0061	0.0087	9.7e-05	7.5e-06	0.0071497986949882	AGA	N	E174Q	G520C	GAA>CAA	Missense	GU280_gp10	0.991808968485353
CAMB-71AEE	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999701692892833	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-71AEE	MN908947.3	29642	C	T	0.01	0.0036	2.1e-05	0.0053	0.00634920634920635	ACA	ORF10	Q29*	C85T	CAA>TAA	Nonsense	GU280_gp11	0.993650793650794
CAMB-71AEE	MN908947.3	3037	C	T	1	1	0	0	0.999817817453088	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-71AEE	MN908947.3	3216	GTCAACAAACTGTTG	-	0.000933333333333333	0.0170666666666667	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;1.3e-06	5.3e-09;5.8e-09;9.3e-09;9.3e-09;1.9e-08;1.2e-08;1e-08;6.3e-09;5.1e-09;7e-09;6.7e-09;1.2e-08;3.5e-09;6e-09;6.1e-08	0.00537803780378038	AGT	ORF1ab:nsp3	.	497-511-delinframe	.	no-SNV	ORF1ab:nsp3	0.99452492300673
CAMB-71AEE	MN908947.3	3230	G	-	0.014	0.017	1.3e-06	6.1e-08	0.0146759531454932	TGG	ORF1ab:nsp3	.	511-511-delfrshift	.	no-SNV	ORF1ab:nsp3	0.985233594138664
CAMB-71AEE	MN908947.3	3361	A	T	0.012	0.0085	4.6e-07	1.1e-05	0.0109198727220133	TAA	ORF1ab:nsp3	L214F	A642T	TTA>TTT	Missense	ORF1ab:nsp3	0.988959598881496
CAMB-71AEE	MN908947.3	4782	C	T	0.0078	0.012	2.5e-05	2.7e-07	0.00975956895237127	TCA	ORF1ab:nsp3	S688L	C2063T	TCA>TTA	Missense	ORF1ab:nsp3	0.990240431047629
CAMB-71AEE	MN908947.3	6990	C	T	0.016	0.01	2.1e-05	0.0018	0.0138648180242634	TCT	ORF1ab:nsp3	S1424F	C4271T	TCT>TTT	Missense	ORF1ab:nsp3	0.986135181975737
CAMB-71AEE	MN908947.3	7553	G	T	0.012	0.015	7.2e-07	8.3e-08	0.0123293338849814	TGT	ORF1ab:nsp3	V1612F	G4834T	GTT>TTT	Missense	ORF1ab:nsp3	0.98444352503103
CAMB-71AEE	MN908947.3	8002	T	C	1	1	0	0	0.99996172395315	ATG	ORF1ab:nsp3	D1761D	T5283C	GAT>GAC	Synonymous	ORF1ab:nsp3	3.82760468498813e-05
CAMB-71AEE	MN908947.3	8377	A	-	0.023	0.0099	2.9e-07	0.0043	0.0150607038573844	CAA	ORF1ab:nsp3	.	5658-5658-delfrshift	.	no-SNV	ORF1ab:nsp3	0.984631934839404
CAMB-71AEE	MN908947.3	872	G	T	0.0074	0.0033	2.3e-05	0.00091	0.00605520459251881	AGA	ORF1ab:nsp2	D23Y	G67T	GAC>TAC	Missense	ORF1ab:nsp2	0.993879262890246
CAMB-71AEE	MN908947.3	9491	C	T	0.022	0.032	3.9e-11	3.4e-13	0.0238120776574064	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.976187922342594
CAMB-71AEE	MN908947.3	9511	T	C	0.0075	0.0095	3.3e-05	3.7e-06	0.00828910336319124	CTT	ORF1ab:nsp4	T319T	T957C	ACT>ACC	Synonymous	ORF1ab:nsp4	0.991685193990721
CAMB-71AEE	MN908947.3	9603	C	T	0.0073	0.0093	2.4e-05	2.6e-06	0.00811857948973522	ACA	ORF1ab:nsp4	T350I	C1049T	ACA>ATA	Missense	ORF1ab:nsp4	0.991849267720206
CAMB-71AEE	MN908947.3	9838	A	-	0.011	0.0053	2.1e-06	0.00071	0.00887902330743618	TAA	ORF1ab:nsp4	.	1284-1284-delfrshift	.	no-SNV	ORF1ab:nsp4	0.99107272113111
CAMB-71AFD	MN908947.3	10243	T	C	0.4	0.58	8.7e-208	0	0.498728253128497	ATC	ORF1ab:3C-like-proteinase	N63N	T189C	AAT>AAC	Synonymous	ORF1ab:3C-like-proteinase	0.501271746871503
CAMB-71AFD	MN908947.3	1059	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0
CAMB-71AFD	MN908947.3	11074	CT	-	0.065015	0.0345	NA;3.1e-31	1.4e-20;2.7e-10	0.0581185991133138	TCT	ORF1ab:nsp6	.	102-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.973031508361274
CAMB-71AFD	MN908947.3	11075	T	-	0.13	0.038	3.1e-31	2.7e-10	0.100314727055674	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.899540570849763
CAMB-71AFD	MN908947.3	14408	C	T	0.97	1	0	0	0.985908678560629	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000393105533716359
CAMB-71AFD	MN908947.3	23240	CTGC	TCTG	0.0137675	0.02475	0.5;0.48;6.3e-24;0.48	2.7e-11;6.7e-11;2.2e-11;1.8e-11	0.00817712177121771	TCT	S	.	1678-1681-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.991685202048097
CAMB-71AFD	MN908947.3	23403	A	G	1	1	0	0	0.999843202098241	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.97804829375374e-05
CAMB-71AFD	MN908947.3	241	C	T	1	1	0	0	0.999748420640689	TCG	NA	NA	NA	NA	NA	NA	0.000167719572874154
CAMB-71AFD	MN908947.3	25563	G	T	1	1	0	0	0.999900299102692	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	4.98504486540379e-05
CAMB-71AFD	MN908947.3	26724	G	T	0.049	0.014	3.5e-23	2.8e-08	0.0338216055075386	TGC	M	A68S	G202T	GCT>TCT	Missense	GU280_gp05	0.966156947691252
CAMB-71AFD	MN908947.3	27923	C	T	0.055	0.058	1.5e-18	2.5e-20	0.0566140446379967	TCA	ORF8	I10I	C30T	ATC>ATT	Synonymous	GU280_gp09	0.943385955362003
CAMB-71AFD	MN908947.3	3037	C	T	1	1	2.1999755078019e-319	0	0.999622213826974	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-71AFD	MN908947.3	8318	CC	-	0.0014	0.02	0.015;0.0061	9.2e-11;4e-11	0.00819814098493159	ACC	ORF1ab:nsp3	.	5599-5600-delfrshift	.	no-SNV	ORF1ab:nsp3	0.991710798986875
CAMB-71B09	MN908947.3	13914	T	G	0.0062	0.015	6.1e-05	6.9e-07	0.00873362445414847	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.98981077147016
CAMB-71B09	MN908947.3	14408	C	T	1	1	0	0	0.998362802881467	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00163719711853307
CAMB-71B09	MN908947.3	19140	C	T	1	1	0	3.2e-123	0.998630136986301	TCT	ORF1ab:3'-to-5'-exonuclease	F367F	C1101T	TTC>TTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.000684931506849315
CAMB-71B09	MN908947.3	23403	A	G	1	1	0	0	0.99986868885825	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.56555708751888e-05
CAMB-71B09	MN908947.3	241	C	T	1	1	0	0	1	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-71B09	MN908947.3	28881	GGG	AAC	1	1	2.8000182346761e-319;0;0	3.9e-148;1.2e-150;3.4e-173	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-71B09	MN908947.3	3037	C	T	1	1	2.1e-100	1.8e-217	0.997607655502392	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00239234449760766
CAMB-71B18	MN908947.3	11074	C	INS	0.025	0.026	2.7e-05	5.4e-05	0.0255079070290956	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.974295120715853
CAMB-71B18	MN908947.3	11075	T	-	0.029	0.025	1.7e-07	5.1e-07	0.0273464033916567	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.969514908767245
CAMB-71B18	MN908947.3	14408	C	T	1	1	0	0	0.998784086562107	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000396196513470681
CAMB-71B18	MN908947.3	16206	G	T	1	1	0	0	0.999597963012597	AGG	ORF1ab:RNA-dependent-RNA-polymerase	E913D	G2739T	GAG>GAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-71B18	MN908947.3	21931	T	C	0.0026	0.0071	0.0045	4.7e-05	0.0048384898459861	CTA	S	A123A	T369C	GCT>GCC	Synonymous	GU280_gp02, spike glycoprotein	0.995161510154014
CAMB-71B18	MN908947.3	23403	A	G	1	1	0	0	0.998737373737374	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000106837606837607
CAMB-71B18	MN908947.3	241	C	T	1	1	0	0	0.999901978082299	TCG	NA	NA	NA	NA	NA	NA	7.84175341606383e-05
CAMB-71B18	MN908947.3	26333	C	T	0.017	0.014	1.7e-08	1.2e-07	0.0156568733939121	ACA	E	T30I	C89T	ACA>ATA	Missense	GU280_gp04	0.984290142262961
CAMB-71B18	MN908947.3	28473	C	T	0.0088	0.0069	6.9e-06	4.1e-05	0.00782841394735791	CCT	N	P67L	C200T	CCT>CTT	Missense	GU280_gp10	0.992131645165156
CAMB-71B18	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999886602029824	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000124138787164049
CAMB-71B18	MN908947.3	3037	C	T	1	1	0	0	0.999478895257947	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000130276185513288
CAMB-71B18	MN908947.3	9165	C	T	0.035	0.011	1.3e-16	9e-07	0.0239470723941353	ACC	ORF1ab:nsp4	T204I	C611T	ACC>ATC	Missense	ORF1ab:nsp4	0.976033861465424
CAMB-71B18	MN908947.3	9479	G	T	0.0057	0.013	0.00024	2.1e-07	0.00777349069450749	TGG	ORF1ab:nsp4	G309C	G925T	GGT>TGT	Missense	ORF1ab:nsp4	0.992113027689514
CAMB-71B18	MN908947.3	9483	A	G	0.028	0.011	2.3e-13	1.6e-06	0.0228564994651804	GAA	ORF1ab:nsp4	E310G	A929G	GAA>GGA	Missense	ORF1ab:nsp4	0.97714350053482
CAMB-71B18	MN908947.3	9491	C	T	0.18	0.16	5.6e-84	3.9e-70	0.177943402818214	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.822056597181786
CAMB-71B18	MN908947.3	9634	A	C	0.099	0.13	1.5e-45	4.1e-60	0.112805154732734	TAG	ORF1ab:nsp4	L360F	A1080C	TTA>TTC	Missense	ORF1ab:nsp4	0.884459310541532
CAMB-71B18	MN908947.3	9924	C	T	0.11	0.12	3.4e-47	5.5e-56	0.113257308420935	GCA	ORF1ab:nsp4	A457V	C1370T	GCA>GTA	Missense	ORF1ab:nsp4	0.886742691579065
CAMB-71B18	MN908947.3	9962	C	T	0.0036	0.012	0.0023	3.6e-07	0.00721275947309607	TCA	ORF1ab:nsp4	H470Y	C1408T	CAT>TAT	Missense	ORF1ab:nsp4	0.992719515085842
CAMB-71B27	MN908947.3	10035	TCACCTCAGCTGTT	-	0.00802857142857143	0.000807857142857143	0.00031;0.00044;0.00018;0.00051;0.00043;0.00039;0.00047;0.00035;0.00048;0.00038;1.7e-06;5.8e-06;5.7e-11;2.7e-07	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0042;0.0014	0.00314619596306284	ATC	ORF1ab:nsp4	.	1481-1494-delfrshift	.	no-SNV	ORF1ab:nsp4	0.996564156945917
CAMB-71B27	MN908947.3	10516	TGACTGTGTCTCTTTTTGTT	-	0.0006583	0.0217	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0064;0.0058;NA;NA;NA;NA;NA;NA	1.3e-08;8.5e-09;6.4e-09;5e-09;3.5e-09;2.8e-08;1.1e-08;1.9e-09;4.4e-08;9.3e-08;1.3e-08;4.5e-09;1.1e-10;1.4e-06;5.8e-08;7.4e-10;2.2e-10;6.5e-11;4.8e-11;6.3e-11	0.00653960332143011	ATG	ORF1ab:3C-like-proteinase	.	462-481-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.993652102225886
CAMB-71B27	MN908947.3	11075	T	-	0.032	0.046	3.9e-08	8.7e-12	0.0364364536001666	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957868436845522
CAMB-71B27	MN908947.3	11075	TT	-	0.0197	0.0230385	3.9e-08;0.00068	8.7e-12;0.48	0.0208036372573114	CTT	ORF1ab:nsp6	.	103-104-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957868436845522
CAMB-71B27	MN908947.3	11893	GCA	TGC	0.00406666666666667	0.01	0.0044;0.00095;0.0011	6.9e-06;1.8e-06;1.9e-06	0.0067267362328016	TGC	ORF1ab:nsp7	.	51-53-mnv	.	no-SNV	ORF1ab:nsp7	0.992979825517993
CAMB-71B27	MN908947.3	11897	C	A	0.004	0.01	0.0012	2e-06	0.00664571171980242	ACA	ORF1ab:nsp7	Q19K	C55A	CAA>AAA	Missense	ORF1ab:nsp7	0.986315671306691
CAMB-71B27	MN908947.3	11897	CA	TC	0.002079	0.013	0.45;0.0011	4.2e-09;1.6e-06	0.00686408435598406	ACA	ORF1ab:nsp7	.	55-56-mnv	.	no-SNV	ORF1ab:nsp7	0.986315671306691
CAMB-71B27	MN908947.3	11900	CTCAGAGTAGA	ACTCAGAGTAG	0.00405454545454545	0.0100727272727273	0.0013;0.0018;0.0016;0.0012;0.0011;0.0016;0.0013;0.001;0.001;0.0013;0.0018	2.1e-06;2.7e-06;2.6e-06;1.8e-06;1.9e-06;2.9e-06;1.9e-06;1.7e-06;1.3e-06;2.1e-06;3.9e-06	0.00665245971879264	ACT	ORF1ab:nsp7	.	58-68-mnv	.	no-SNV	ORF1ab:nsp7	0.99333408399955
CAMB-71B27	MN908947.3	11912	TCATCATCTA	ATCATCATCT	0.00407	0.01016	0.0011;0.0021;0.00087;0.0013;0.0023;0.00083;0.0012;0.0019;0.0012;0.0012	1.8e-06;3.9e-06;6.5e-07;2.3e-06;4.4e-06;8.8e-07;2.2e-06;5.7e-06;1.3e-06;3.2e-06	0.00656205084705827	ATC	ORF1ab:nsp7	.	70-79-mnv	.	no-SNV	ORF1ab:nsp7	0.990872246286769
CAMB-71B27	MN908947.3	11924	T	A	0.0043	0.011	0.00096	1.2e-06	0.00704251093538679	ATT	ORF1ab:nsp7	L28M	T82A	TTG>ATG	Missense	ORF1ab:nsp7	0.992933120514664
CAMB-71B27	MN908947.3	11926	GTG	TGT	0.00406666666666667	0.01	0.0019;0.0012;0.0017	3.4e-06;2e-06;3.1e-06	0.00662743529680626	TGT	ORF1ab:nsp7	.	84-86-mnv	.	no-SNV	ORF1ab:nsp7	0.993131442855669
CAMB-71B27	MN908947.3	11931	CTCA	GCTC	0.004125	0.01025	0.0012;0.0018;0.0018;0.0011	1.9e-06;4.3e-06;3.1e-06;1.3e-06	0.00669138154647813	GCT	ORF1ab:nsp7	.	89-92-mnv	.	no-SNV	ORF1ab:nsp7	0.993234691764273
CAMB-71B27	MN908947.3	11936	TGTGTC	ATGTGT	0.00405	0.00998333333333333	0.0011;0.0024;0.0011;0.0018;0.0012;0.0037	2e-06;3.8e-06;2.1e-06;2.6e-06;2.4e-06;6.1e-06	0.00665301352586576	ATG	ORF1ab:nsp7	.	94-99-mnv	.	no-SNV	ORF1ab:nsp7	0.993177285609321
CAMB-71B27	MN908947.3	11943	AGT	CAG	0.0041	0.0103333333333333	0.0012;0.0016;0.001	2.1e-06;3e-06;1.2e-06	0.00665576833255488	CAG	ORF1ab:nsp7	.	101-103-mnv	.	no-SNV	ORF1ab:nsp7	0.993250817375058
CAMB-71B27	MN908947.3	11947	ACACA	TACAC	0.00414	0.0102	0.0013;0.0012;0.0012;0.0011;0.00086	2.5e-06;2e-06;2.2e-06;1.8e-06;9.9e-07	0.00674644326113047	TAC	ORF1ab:nsp7	.	105-109-mnv	.	no-SNV	ORF1ab:nsp7	0.993393379397131
CAMB-71B27	MN908947.3	11953	TGACAT	ATGACA	0.0041	0.0101166666666667	0.0013;0.0022;0.0016;0.0017;0.00089;0.001	4.5e-06;3.3e-06;2.3e-06;5.1e-06;9.5e-07;1.9e-06	0.00664182133500609	ATG	ORF1ab:nsp7	.	111-116-mnv	.	no-SNV	ORF1ab:nsp7	0.993713477271329
CAMB-71B27	MN908947.3	11960	C	T	0.01	0.01	4e-06	3.1e-06	0.0100630269490463	TCT	ORF1ab:nsp7	L40F	C118T	CTC>TTC	Missense	ORF1ab:nsp7	0.987098986602339
CAMB-71B27	MN908947.3	11960	CTCT	TCTC	0.005625	0.01025	4e-06;0.0019;0.0023;0.0013	3.1e-06;2.7e-06;4e-06;1.4e-06	0.00673035688759708	TCT	ORF1ab:nsp7	.	118-121-mnv	.	no-SNV	ORF1ab:nsp7	0.987098986602339
CAMB-71B27	MN908947.3	11965	AGCTA	TAGCT	0.00408	0.01	0.0011;0.0013;0.0012;0.0018;0.0011	2e-06;1.8e-06;1.7e-06;3.3e-06;1.6e-06	0.00668963165877	TAG	ORF1ab:nsp7	.	123-127-mnv	.	no-SNV	ORF1ab:nsp7	0.993293783853495
CAMB-71B27	MN908947.3	11972	GATACTACTGA	AGATACTACTG	0.00409090909090909	0.0101636363636364	0.0011;0.0013;0.0014;0.0013;0.0012;0.002;0.0011;0.0012;0.0028;0.0016;0.0014	2e-06;1.4e-06;2.8e-06;1.9e-06;2.3e-06;3e-06;1.8e-06;2.1e-06;4.9e-06;2.9e-06;2.3e-06	0.00668984219140116	AGA	ORF1ab:nsp7	.	130-140-mnv	.	no-SNV	ORF1ab:nsp7	0.993289317025652
CAMB-71B27	MN908947.3	11984	GC	AG	0.0042	0.01015	0.00081;0.0016	9.9e-07;4.1e-06	0.00675484418826072	AGC	ORF1ab:nsp7	.	142-143-mnv	.	no-SNV	ORF1ab:nsp7	0.992279132562653
CAMB-71B27	MN908947.3	11987	T	C	0.0044	0.011	0.0036	7.2e-06	0.00696630052122856	CTT	ORF1ab:nsp7	F49L	T145C	TTT>CTT	Missense	ORF1ab:nsp7	0.992784903031585
CAMB-71B27	MN908947.3	11990	GA	TG	0.00425	0.0105	0.0012;0.0036	2.1e-06;4e-06	0.00690896706076972	TGA	ORF1ab:nsp7	.	148-149-mnv	.	no-SNV	ORF1ab:nsp7	0.991290437255599
CAMB-71B27	MN908947.3	11997	TG	AT	0.00395	0.01	0.00096;0.0029	1.9e-06;3.8e-06	0.00653387061919229	ATG	ORF1ab:nsp7	.	155-156-mnv	.	no-SNV	ORF1ab:nsp7	0.993185399159664
CAMB-71B27	MN908947.3	12000	T	G	0.004	0.0099	0.0014	2.9e-06	0.00648096743826788	GTT	ORF1ab:nsp7	V53G	T158G	GTT>GGT	Missense	ORF1ab:nsp7	0.993519032561732
CAMB-71B27	MN908947.3	12003	CACTACT	TCACTAC	0.00411428571428571	0.0102428571428571	0.0014;9e-04;0.0012;0.0024;0.0012;0.0013;0.0025	1.5e-06;1.6e-06;3.5e-06;4.6e-06;9.8e-07;2.1e-06;3.3e-06	0.00677321836294756	TCA	ORF1ab:nsp7	.	161-167-mnv	.	no-SNV	ORF1ab:nsp7	0.993129009616924
CAMB-71B27	MN908947.3	12012	CTGT	TCTG	0.00425	0.01025	0.0016;0.0018;0.0018;0.00082	2.7e-06;2.6e-06;2.6e-06;9.7e-07	0.00675708345421139	TCT	ORF1ab:nsp7	.	170-173-mnv	.	no-SNV	ORF1ab:nsp7	0.993200252562048
CAMB-71B27	MN908947.3	12019	GCT	TGC	0.00416666666666667	0.0102333333333333	0.0013;0.00085;0.0035	1.5e-06;9.3e-07;2e-05	0.00666110536997149	TGC	ORF1ab:nsp7	.	177-179-mnv	.	no-SNV	ORF1ab:nsp7	0.992915572045769
CAMB-71B27	MN908947.3	12024	C	T	0.0044	0.017	0.0014	6.5e-09	0.00943093445253672	TCC	ORF1ab:nsp7	S61F	C182T	TCC>TTC	Missense	ORF1ab:nsp7	0.990544377237378
CAMB-71B27	MN908947.3	12026	ATGCAG	CATGCA	0.00398333333333333	0.01015	0.0015;0.0012;0.0014;0.001;0.0016;0.0016	3.3e-06;2.9e-06;1.9e-06;1.1e-06;2.9e-06;4.6e-06	0.00645507666183889	CAT	ORF1ab:nsp7	.	184-189-mnv	.	no-SNV	ORF1ab:nsp7	0.993750546827153
CAMB-71B27	MN908947.3	12034	TG	GT	0.0041	0.01	0.0011;0.002	1.9e-06;3.1e-06	0.00666940531135974	GTG	ORF1ab:nsp7	.	192-193-mnv	.	no-SNV	ORF1ab:nsp7	0.993189708355006
CAMB-71B27	MN908947.3	12037	TGTAGACATA	CTGTAGACAT	0.00411	0.00982	0.0027;0.002;0.0013;8e-04;0.0012;0.0021;0.0015;0.0013;0.0013;0.0011	6.3e-06;3.6e-06;2.6e-06;9.1e-07;3.3e-06;1.1e-05;5e-06;1.4e-06;7.8e-06;4.2e-06	0.00640954937068765	CTG	ORF1ab:nsp7	.	195-204-mnv	.	no-SNV	ORF1ab:nsp7	0.993293508364485
CAMB-71B27	MN908947.3	12049	CA	AC	0.0039	0.0091	0.0015;0.0012	9e-06;3.9e-06	0.00606244316459533	ACA	ORF1ab:nsp7	.	207-208-mnv	.	no-SNV	ORF1ab:nsp7	0.994120613522589
CAMB-71B27	MN908947.3	12052	GCT	AGC	0.00413333333333333	0.0103333333333333	0.0012;0.0016;0.0055	1.9e-06;5.6e-06;8.4e-06	0.00698704601668507	AGC	ORF1ab:nsp7	.	210-212-mnv	.	no-SNV	ORF1ab:nsp7	0.992971031707215
CAMB-71B27	MN908947.3	12057	GTGA	TGTG	0.003975	0.00985	0.003;0.0012;0.0026;0.0015	8.7e-06;2e-06;8.3e-06;2.4e-06	0.00641810424782044	TGT	ORF1ab:nsp7	.	215-218-mnv	.	no-SNV	ORF1ab:nsp7	0.993913852024489
CAMB-71B27	MN908947.3	12062	GA	AG	0.0037	0.0092	0.0024;0.0044	1.3e-05;7.2e-06	0.00600952258396603	AGA	ORF1ab:nsp7	.	220-221-mnv	.	no-SNV	ORF1ab:nsp7	0.993985372634095
CAMB-71B27	MN908947.3	12374	C	T	0.0076	0.011	4.6e-05	9.5e-07	0.00896989908863525	GCT	ORF1ab:nsp8	L95F	C283T	CTT>TTT	Missense	ORF1ab:nsp8	0.991001351234799
CAMB-71B27	MN908947.3	12473	C	T	0.0083	0.0047	1.3e-05	0.00049	0.00664716830630152	ACT	ORF1ab:nsp8	L128L	C382T	CTA>TTA	Synonymous	ORF1ab:nsp8	0.993333839784252
CAMB-71B27	MN908947.3	14171	TAT	-	0.00153333333333333	0.00573333333333333	NA;NA;0.0011	4.4e-05;4.7e-05;0.00026	0.00205933265683758	ATA	ORF1ab:RNA-dependent-RNA-polymerase	.	704-706-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.997866053841103
CAMB-71B27	MN908947.3	14408	C	T	0.99	1	0	0	0.995632845700409	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00274171121947398
CAMB-71B27	MN908947.3	15730	GTG	-	0.0072	0.0039	9.6e-05;3.1e-05;4.3e-05	0.0036;0.00072;0.00099	0.00575795644891122	TGT	ORF1ab:RNA-dependent-RNA-polymerase	.	2263-2265-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.9942645174746
CAMB-71B27	MN908947.3	16289	C	T	0.006	0.013	0.0019	8.1e-07	0.0114090131203651	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0.988590986879635
CAMB-71B27	MN908947.3	18037	C	T	0.0079	0.0029	1.2e-05	0.0021	0.00508052809843091	ACA	ORF1ab:helicase	Q601*	C1801T	CAA>TAA	Nonsense	ORF1ab:helicase	0.994884910485934
CAMB-71B27	MN908947.3	18123	T	A	0.0069	0.007	3.2e-05	3.2e-05	0.00693794823822887	GTG	ORF1ab:3'-to-5'-exonuclease	S28R	T84A	AGT>AGA	Missense	ORF1ab:3'-to-5'-exonuclease	0.992906142812597
CAMB-71B27	MN908947.3	19719	A	-	0.0097	0.036	1.9e-05	5.9e-16	0.0174588811412147	CAA	ORF1ab:endoRNAse	.	99-99-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.977005376057912
CAMB-71B27	MN908947.3	19719	AA	-	0.0085	0.018	1.9e-05;4.7e-05	5.9e-16;NA	0.0116477272727273	CAA	ORF1ab:endoRNAse	.	99-100-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.977005376057912
CAMB-71B27	MN908947.3	20649	A	-	0.0096	0.0091	7.5e-06	6.3e-06	0.0092255125284738	CAA	ORF1ab:endoRNAse	.	1029-1029-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.990660592255125
CAMB-71B27	MN908947.3	21575	C	T	0.014	0.02	0.00041	2.5e-05	0.0167310167310167	TCT	S	L5F	C13T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.983268983268983
CAMB-71B27	MN908947.3	22215	A	T	0.0088	0.018	4e-06	1.8e-09	0.0103387943375219	CAG	S	Q218L	A653T	CAG>CTG	Missense	GU280_gp02, spike glycoprotein	0.989581676475266
CAMB-71B27	MN908947.3	22760	T	-	0.0064	0.0081	8.6e-05	1.3e-05	0.00701894849212703	ATT	S	.	1198-1198-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.992954363490793
CAMB-71B27	MN908947.3	23403	A	G	1	1	0	0	0.999623766387868	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.64701569569454e-05
CAMB-71B27	MN908947.3	23439	C	T	0.0045	0.0099	0.0012	3.9e-06	0.00626582095729424	GCA	S	A626V	C1877T	GCA>GTA	Missense	GU280_gp02, spike glycoprotein	0.99368605445778
CAMB-71B27	MN908947.3	23575	C	T	1	0.95	0	0	0.977082168809391	GCG	S	C671C	C2013T	TGC>TGT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-71B27	MN908947.3	23587	G	C	1	1	0	0	0.999864434352335	AGA	S	Q675H	G2025C	CAG>CAC	Missense	GU280_gp02, spike glycoprotein	6.77828238324409e-05
CAMB-71B27	MN908947.3	23855	C	T	0.0075	0.0087	9.1e-05	3.6e-05	0.00781190458044356	CCG	S	R765C	C2293T	CGT>TGT	Missense	GU280_gp02, spike glycoprotein	0.992188095419556
CAMB-71B27	MN908947.3	24068	C	T	0.0069	0.0091	3.7e-05	4.2e-06	0.00744030672284857	ACA	S	Q836*	C2506T	CAA>TAA	Nonsense	GU280_gp02, spike glycoprotein	0.992521732528565
CAMB-71B27	MN908947.3	241	C	T	1	1	0	0	0.997212082313771	TCG	NA	NA	NA	NA	NA	NA	0.000100284808857154
CAMB-71B27	MN908947.3	24321	AA	-	0.00895	0.031	0.0029;0.00029	8.8e-12;6.4e-11	0.0210215636670281	CAA	S	.	2759-2760-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.978464702679814
CAMB-71B27	MN908947.3	2440	AG	-	0.00975	0.0135	0.00016;0.00014	1.6e-05;1e-05	0.0113236034222446	AAG	ORF1ab:nsp2	.	1635-1636-delfrshift	.	no-SNV	ORF1ab:nsp2	0.98818998716303
CAMB-71B27	MN908947.3	25951	G	T	0.014	0.0026	2e-08	0.0046	0.0125426205552849	TGG	ORF3a	G187C	G559T	GGT>TGT	Missense	GU280_gp03	0.987457379444715
CAMB-71B27	MN908947.3	26839	C	T	0.011	0.0071	3.3e-06	0.00012	0.00920924466483663	ACG	M	T106M	C317T	ACG>ATG	Missense	GU280_gp05	0.98733728858585
CAMB-71B27	MN908947.3	28445	C	T	0.012	0.015	5.8e-07	2.1e-08	0.0132481192996472	TCA	N	Q58*	C172T	CAA>TAA	Nonsense	GU280_gp10	0.986751880700353
CAMB-71B27	MN908947.3	29774	C	T	0.032	0.026	9.4e-08	2.1e-09	0.0274390243902439	GCT	NA	NA	NA	NA	NA	NA	0.972560975609756
CAMB-71B27	MN908947.3	3005	T	-	0.01	0.0089	6.6e-06	1.2e-05	0.00935101186322401	GTT	ORF1ab:nsp3	.	286-286-delfrshift	.	no-SNV	ORF1ab:nsp3	0.990648988136776
CAMB-71B27	MN908947.3	3037	C	T	0.99	1	0	0	0.995952547103978	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000418702023726448
CAMB-71B27	MN908947.3	479	A	-	0.018	0.011	5.9e-10	3.4e-07	0.0154129610601283	CAA	ORF1ab:leader-protein	.	214-214-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.984232717995961
CAMB-71B27	MN908947.3	4829	C	T	0.0088	0.0057	4.9e-06	0.00011	0.00734115264534638	ACA	ORF1ab:nsp3	Q704*	C2110T	CAA>TAA	Nonsense	ORF1ab:nsp3	0.992658847354654
CAMB-71B27	MN908947.3	6762	C	T	0.017	0.0019	1e-08	0.0097	0.00777373470062851	ACT	ORF1ab:nsp3	T1348I	C4043T	ACT>ATT	Missense	ORF1ab:nsp3	0.992226265299372
CAMB-71B27	MN908947.3	8123	C	T	0.0078	0.0078	2.9e-05	3.3e-05	0.00780850908560169	ACT	ORF1ab:nsp3	L1802F	C5404T	CTT>TTT	Missense	ORF1ab:nsp3	0.992191490914398
CAMB-71B27	MN908947.3	8180	C	T	0.0075	0.0098	2.1e-05	2e-06	0.00815027284175178	GCA	ORF1ab:nsp3	Q1821*	C5461T	CAA>TAA	Nonsense	ORF1ab:nsp3	0.991779767734714
CAMB-71B27	MN908947.3	8460	C	T	0.0087	0.006	3.6e-05	0.00037	0.00709309689677011	GCT	ORF1ab:nsp3	A1914V	C5741T	GCT>GTT	Missense	ORF1ab:nsp3	0.992780240658645
CAMB-71B27	MN908947.3	9167	T	C	0.0086	0.01	1.6e-05	3.8e-06	0.00927325581395349	CTA	ORF1ab:nsp4	Y205H	T613C	TAC>CAC	Missense	ORF1ab:nsp4	0.990697674418605
CAMB-71B36	MN908947.3	14408	C	T	1	1	0	0	0.999277456647399	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000578034682080925
CAMB-71B36	MN908947.3	23403	A	G	1	1	0	0	0.999910710299567	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.46448502165275e-05
CAMB-71B36	MN908947.3	23575	C	T	1	1	0	0	1	GCG	S	C671C	C2013T	TGC>TGT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-71B36	MN908947.3	23587	G	C	1	1	0	0	1	AGA	S	Q675H	G2025C	CAG>CAC	Missense	GU280_gp02, spike glycoprotein	0
CAMB-71B36	MN908947.3	241	C	T	1	1	3.10000000023388e-314	0	1	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-71B36	MN908947.3	3037	C	T	1	1	2.4e-126	6e-264	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-71B45	MN908947.3	11075	T	-	0.031	0.034	3.1e-08	2.9e-09	0.0324474707573126	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964109500607141
CAMB-71B45	MN908947.3	14408	C	T	1	1	0	0	0.99772714750124	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000523444817896303
CAMB-71B45	MN908947.3	16206	G	T	1	1	0	0	0.999449733120564	AGG	ORF1ab:RNA-dependent-RNA-polymerase	E913D	G2739T	GAG>GAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000440213503549221
CAMB-71B45	MN908947.3	22918	G	T	0.98	0.98	0	0	0.981143598747996	TGT	S	L452L	G1356T	CTG>CTT	Synonymous	GU280_gp02, spike glycoprotein	0.018589205282846
CAMB-71B45	MN908947.3	23403	A	G	1	1	0	0	0.999124420789595	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.90278119373912e-05
CAMB-71B45	MN908947.3	241	C	T	1	1	0	0	0.998796067152699	TCG	NA	NA	NA	NA	NA	NA	0.000183934185004348
CAMB-71B45	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999029871862242	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000134306307919595
CAMB-71B45	MN908947.3	3037	C	T	1	1	0	0	0.9991580880946	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000229612337836286
CAMB-71B54	MN908947.3	11074	C	INS	0.017	0.034	0.0031	2.3e-07	0.0231135783061505	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.976260070740814
CAMB-71B54	MN908947.3	11075	T	-	0.036	0.032	5.7e-09	1.5e-08	0.0347676234584523	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961236469384458
CAMB-71B54	MN908947.3	13571	G	T	0.025	0.026	5.1e-06	2.4e-06	0.0251980384760468	GGT	ORF1ab:RNA-dependent-RNA-polymerase	G35V	G104T	GGT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.971909971080096
CAMB-71B54	MN908947.3	14358	C	T	0.013	0.0094	2e-07	5.3e-06	0.0115280901522556	GCA	ORF1ab:RNA-dependent-RNA-polymerase	C297C	C891T	TGC>TGT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.988095097912226
CAMB-71B54	MN908947.3	14408	C	T	1	1	0	0	0.997799397729905	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000301135047486681
CAMB-71B54	MN908947.3	23403	A	G	1	1	0	0	0.998769009178	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000209352180612313
CAMB-71B54	MN908947.3	241	C	T	1	1	0	0	0.998321959950777	TCG	NA	NA	NA	NA	NA	NA	0.00026568967446023
CAMB-71B54	MN908947.3	24933	G	T	1	1	0	0	0.999705622608184	GGT	S	G1124V	G3371T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	3.09870938754009e-05
CAMB-71B54	MN908947.3	27353	A	T	0.024	0.026	6.5e-12	3.6e-13	0.0244874188836917	CAA	ORF6	Q51L	A152T	CAA>CTA	Missense	GU280_gp06	0.975457116973876
CAMB-71B54	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999418018157833	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000170524790041352
CAMB-71B54	MN908947.3	29420	C	T	1	1	0	0	0.999792874896437	ACC	N	P383S	C1147T	CCG>TCG	Missense	GU280_gp10	0.000207125103562552
CAMB-71B54	MN908947.3	3037	C	T	1	1	0	0	0.99899142713061	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000252143217347453
CAMB-71B54	MN908947.3	558	G	T	0.017	0.014	3e-05	0.00013	0.0156944744874661	GGT	ORF1ab:leader-protein	G98V	G293T	GGT>GTT	Missense	ORF1ab:leader-protein	0.983884923210037
CAMB-71B54	MN908947.3	6058	A	G	1	1	0	0	0.999790751203181	TAT	ORF1ab:nsp3	V1113V	A3339G	GTA>GTG	Synonymous	ORF1ab:nsp3	0
CAMB-71B54	MN908947.3	8860	C	A	1	1	0	0	0.999780855539972	TCG	ORF1ab:nsp4	V102V	C306A	GTC>GTA	Synonymous	ORF1ab:nsp4	2.1914446002805e-05
CAMB-71B54	MN908947.3	923	G	A	0.0041	0.0071	0.00064	2.1e-05	0.00508953609044139	GGA	ORF1ab:nsp2	D40N	G118A	GAC>AAC	Missense	ORF1ab:nsp2	0.994877343284241
CAMB-71B63	MN908947.3	11075	T	-	0.041	0.043	6.1e-10	4.7e-11	0.0413028192973304	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954727936673547
CAMB-71B63	MN908947.3	14408	C	T	1	1	0	0	0.999643292045413	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00027060603451457
CAMB-71B63	MN908947.3	16289	C	T	1	1	0	0	0.999784529196294	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0
CAMB-71B63	MN908947.3	23403	A	G	1	1	0	0	0.999707321534733	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000100608222435634
CAMB-71B63	MN908947.3	241	C	T	1	1	0	0	0.999048962576677	TCG	NA	NA	NA	NA	NA	NA	0.000158506237220435
CAMB-71B63	MN908947.3	25429	G	T	1	1	0	0	0.99992329759001	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	3.06809639958888e-05
CAMB-71B63	MN908947.3	3037	C	T	1	1	0	0	0.999518652226233	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.01684717208183e-05
CAMB-71B72	MN908947.3	11075	T	-	0.055	0.071	4.3e-13	1.5e-17	0.059778986142782	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.935403145646962
CAMB-71B72	MN908947.3	12445	C	T	0.0019	0.011	0.0048	4.8e-07	0.00511025010619537	ACA	ORF1ab:nsp8	N118N	C354T	AAC>AAT	Synonymous	ORF1ab:nsp8	0.994889749893805
CAMB-71B72	MN908947.3	14146	T	C	0.0026	0.0063	0.0026	4.2e-05	0.00391423188175039	TTC	ORF1ab:RNA-dependent-RNA-polymerase	S227P	T679C	TCT>CCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.99608576811825
CAMB-71B72	MN908947.3	14408	C	T	1	1	0	0	0.999699807877041	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000220140890169709
CAMB-71B72	MN908947.3	15485	C	T	0.002	0.015	0.0094	2.8e-08	0.00372866771834218	TCA	ORF1ab:RNA-dependent-RNA-polymerase	S673L	C2018T	TCA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.996242650222286
CAMB-71B72	MN908947.3	16289	C	T	1	1	0	0	0.999691928527418	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0.000308071472581639
CAMB-71B72	MN908947.3	17502	C	T	0.0031	0.011	0.0032	1.1e-06	0.00605048087777126	TCA	ORF1ab:helicase	F422F	C1266T	TTC>TTT	Synonymous	ORF1ab:helicase	0.993949519122229
CAMB-71B72	MN908947.3	19648	G	T	0.0028	0.0098	0.0022	2.6e-06	0.00472196772147438	TGT	ORF1ab:endoRNAse	V10L	G28T	GTA>TTA	Missense	ORF1ab:endoRNAse	0.994996123757841
CAMB-71B72	MN908947.3	22017	G	T	0.0066	0.015	0.0047	4.8e-05	0.00756702219659844	TGG	S	W152L	G455T	TGG>TTG	Missense	GU280_gp02, spike glycoprotein	0.992432977803402
CAMB-71B72	MN908947.3	22019	A	G	0.0078	0.015	7e-04	6.9e-06	0.00865488640461594	GAT	S	M153V	A457G	ATG>GTG	Missense	GU280_gp02, spike glycoprotein	0.991345113595384
CAMB-71B72	MN908947.3	22023	A	G	0.0073	0.015	0.0013	8.2e-06	0.00824814945364822	GAA	S	E154G	A461G	GAA>GGA	Missense	GU280_gp02, spike glycoprotein	0.991751850546352
CAMB-71B72	MN908947.3	22026	G	A	0.0068	0.014	0.0025	3.5e-05	0.0076867816091954	AGT	S	S155N	G464A	AGT>AAT	Missense	GU280_gp02, spike glycoprotein	0.992313218390805
CAMB-71B72	MN908947.3	22029	AG	GA	0.0076	0.016	0.0024;0.0029	4.1e-05;3.7e-05	0.00845090596576667	GAG	S	.	467-468-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.991323677040011
CAMB-71B72	MN908947.3	22033	C	T	0.0073	0.016	0.0032	3.6e-05	0.00825674899483056	TCA	S	F157F	C471T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.991743251005169
CAMB-71B72	MN908947.3	22036	A	G	0.0081	0.017	0.0027	4.5e-05	0.00908815510451378	GAG	S	R158R	A474G	AGA>AGG	Synonymous	GU280_gp02, spike glycoprotein	0.990911844895486
CAMB-71B72	MN908947.3	22041	AT	TC	0.003791	0.01245	0.0036;NA	4.7e-05;1e-05	0.00481667864845435	TAT	S	.	479-480-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.991524820169504
CAMB-71B72	MN908947.3	22052	A	G	0.0083	0.021	0.0012	4.5e-07	0.00971023427866831	GAA	S	N164D	A490G	AAT>GAT	Missense	GU280_gp02, spike glycoprotein	0.990289765721332
CAMB-71B72	MN908947.3	22063	T	C	0.0074	0.016	0.0036	4.8e-05	0.00833461954005248	CTT	S	T167T	T501C	ACT>ACC	Synonymous	GU280_gp02, spike glycoprotein	0.991665380459948
CAMB-71B72	MN908947.3	22068	A	G	0.0082	0.018	0.0015	8.2e-06	0.00920765689362733	GAA	S	E169G	A506G	GAA>GGA	Missense	GU280_gp02, spike glycoprotein	0.990792343106373
CAMB-71B72	MN908947.3	22078	TC	CT	0.00745	0.024	0.0013;0.0028	2e-05;8.7e-10	0.00924989160283278	CTC	S	.	516-517-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.991704537257448
CAMB-71B72	MN908947.3	22084	T	C	0.0074	0.015	0.003	2.8e-05	0.00824053452115813	CTT	S	P174P	T522C	CCT>CCC	Synonymous	GU280_gp02, spike glycoprotein	0.991536748329621
CAMB-71B72	MN908947.3	22089	T	C	0.0073	0.016	0.0027	4.2e-05	0.00820555325321177	CTT	S	L176P	T527C	CTT>CCT	Missense	GU280_gp02, spike glycoprotein	0.991711562370493
CAMB-71B72	MN908947.3	22095	A	G	0.0076	0.015	0.0012	1.5e-05	0.00849288534604783	GAC	S	D178G	A533G	GAC>GGC	Missense	GU280_gp02, spike glycoprotein	0.991507114653952
CAMB-71B72	MN908947.3	22098	T	C	0.0088	0.018	0.0016	2.5e-05	0.00978895374943871	CTT	S	L179P	T536C	CTT>CCT	Missense	GU280_gp02, spike glycoprotein	0.989851818590031
CAMB-71B72	MN908947.3	22103	G	A	0.0055	0.014	0.0039	1.1e-05	0.00646191272616695	AGG	S	G181R	G541A	GGA>AGA	Missense	GU280_gp02, spike glycoprotein	0.993538087273833
CAMB-71B72	MN908947.3	22105	A	G	0.0081	0.017	0.0013	8.9e-06	0.00911002102312544	GAA	S	G181G	A543G	GGA>GGG	Synonymous	GU280_gp02, spike glycoprotein	0.99065638869423
CAMB-71B72	MN908947.3	22109	CAG	ACA	0.00656666666666667	0.0143333333333333	0.0019;0.0027;0.0027	2.7e-05;3.9e-05;1.8e-05	0.00744	ACA	S	.	547-549-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.99368
CAMB-71B72	MN908947.3	22128	T	C	0.0067	0.016	0.003	2e-05	0.00769351546553619	CTT	S	L189P	T566C	CTT>CCT	Missense	GU280_gp02, spike glycoprotein	0.992227979274611
CAMB-71B72	MN908947.3	23029	C	T	0.017	0.015	9.9e-09	4e-08	0.0161159263271939	ACT	S	Y489Y	C1467T	TAC>TAT	Synonymous	GU280_gp02, spike glycoprotein	0.983884073672806
CAMB-71B72	MN908947.3	23403	A	G	1	1	0	0	0.99985040017952	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000102849876580148
CAMB-71B72	MN908947.3	241	C	T	1	1	0	0	0.999633087365975	TCG	NA	NA	NA	NA	NA	NA	0.000326144563577806
CAMB-71B72	MN908947.3	24672	C	T	0.0062	0.011	1e-04	1.2e-05	0.00716204118173679	TCA	S	S1037L	C3110T	TCA>TTA	Missense	GU280_gp02, spike glycoprotein	0.992837958818263
CAMB-71B72	MN908947.3	25429	G	T	0.99	1	0	0	0.994247824285122	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	6.63075010360547e-05
CAMB-71B72	MN908947.3	26724	G	T	0.002	0.0064	0.0049	4.5e-05	0.00386842070399958	TGC	M	A68S	G202T	GCT>TCT	Missense	GU280_gp05	0.996052091199343
CAMB-71B72	MN908947.3	28893	C	A	0.0047	0.0088	2e-04	3.4e-06	0.00554795014050004	CCT	N	P207H	C620A	CCT>CAT	Missense	GU280_gp10	0.9944520498595
CAMB-71B72	MN908947.3	29092	T	C	0.0022	0.014	0.0069	1.2e-07	0.00610702825794431	CTT	N	A273A	T819C	GCT>GCC	Synonymous	GU280_gp10	0.991408756857468
CAMB-71B72	MN908947.3	29269	C	T	0.02	0.037	5.7e-11	6.2e-17	0.0257312513745327	CCT	N	T332T	C996T	ACC>ACT	Synonymous	GU280_gp10	0.974268748625467
CAMB-71B72	MN908947.3	3037	C	T	1	1	0	0	0.997321244590975	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-71B72	MN908947.3	3104	T	A	0.0037	0.01	0.0027	2.8e-06	0.00825172288719623	ATA	ORF1ab:nsp3	Y129N	T385A	TAT>AAT	Missense	ORF1ab:nsp3	0.991748277112804
CAMB-71B72	MN908947.3	5672	C	T	0.0044	0.022	0.00057	2e-11	0.00797041906327034	ACC	ORF1ab:nsp3	P985S	C2953T	CCT>TCT	Missense	ORF1ab:nsp3	0.988578471651602
CAMB-71B72	MN908947.3	6402	C	T	0.0044	0.012	0.00051	3.2e-07	0.00561127867012696	CCA	ORF1ab:nsp3	P1228L	C3683T	CCA>CTA	Missense	ORF1ab:nsp3	0.994318580346496
CAMB-71B72	MN908947.3	741	A	-	0.0034	0.016	0.0027	8.6e-09	0.00654576430765092	GAA	ORF1ab:leader-protein	.	476-476-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.993364567688135
CAMB-71B81	MN908947.3	11075	T	-	0.029	0.029	2.1e-07	5.3e-08	0.0287834388883637	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.968144437092353
CAMB-71B81	MN908947.3	13778	AT	-	0.022	0.0245	2.1e-07;3.3e-07	2.9e-08;6.5e-08	0.0228865159257106	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.977649448464002
CAMB-71B81	MN908947.3	13780	A	T	0.02	0.02	2.4e-06	1.5e-06	0.0201808625753594	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I105L	A313T	ATA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.975467614778173
CAMB-71B81	MN908947.3	14408	C	T	1	1	0	0	0.999165931892381	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000512356123251436
CAMB-71B81	MN908947.3	1547	A	-	0.0065	0.01	8.4e-05	2.6e-06	0.00801345468935497	TAG	ORF1ab:nsp2	.	742-742-delfrshift	.	no-SNV	ORF1ab:nsp2	0.934408389394539
CAMB-71B81	MN908947.3	1547	A	G	0.019	0.02	2.6e-09	1.1e-09	0.019192718638702	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.934408389394539
CAMB-71B81	MN908947.3	1547	A	T	0.035	0.039	5.3e-16	2.4e-17	0.0369014641867827	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.934408389394539
CAMB-71B81	MN908947.3	17278	G	T	0.02	0.019	3.6e-10	5.2e-10	0.0193031457854996	AGT	ORF1ab:helicase	V348L	G1042T	GTG>TTG	Missense	ORF1ab:helicase	0.980637678415035
CAMB-71B81	MN908947.3	19943	C	T	0.0043	0.016	0.0022	2.9e-06	0.00614754098360656	GCC	ORF1ab:endoRNAse	A108V	C323T	GCC>GTC	Missense	ORF1ab:endoRNAse	0.988217213114754
CAMB-71B81	MN908947.3	23403	A	G	1	1	0	0	0.999516732014225	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000100300902708124
CAMB-71B81	MN908947.3	241	C	T	1	1	0	0	0.999033028967689	TCG	NA	NA	NA	NA	NA	NA	0.000207208078352281
CAMB-71B81	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999521883045237	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.04269081500647e-05
CAMB-71B81	MN908947.3	3037	C	T	1	1	0	0	0.99919545669664	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-71B81	MN908947.3	4285	G	T	0.011	0.011	9.7e-07	5e-07	0.0110842791596233	AGG	ORF1ab:nsp3	E522D	G1566T	GAG>GAT	Missense	ORF1ab:nsp3	0.988722530789664
CAMB-71B81	MN908947.3	5024	T	G	0.022	0.019	1.2e-09	1.9e-08	0.0210843373493976	GTC	ORF1ab:nsp3	S769A	T2305G	TCA>GCA	Missense	ORF1ab:nsp3	0.978641840087623
CAMB-71BBE	MN908947.3	14408	C	T	1	1	0	0	0.999519153710531	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000320564192979644
CAMB-71BBE	MN908947.3	1842	AG	-	0.0555	0.065	1.8e-24;8.6e-19	NA;1.2e-40	0.0590229312063809	CAG	ORF1ab:nsp2	.	1037-1038-delfrshift	.	no-SNV	ORF1ab:nsp2	0.961815273890444
CAMB-71BBE	MN908947.3	1843	G	-	0.055	0.13	8.6e-19	1.2e-40	0.0799840827695981	AGA	ORF1ab:nsp2	.	1038-1038-delfrshift	.	no-SNV	ORF1ab:nsp2	0.920015917230402
CAMB-71BBE	MN908947.3	21711	C	T	0.16	0.09	4e-64	4.4e-33	0.133472057074911	TCA	S	S50L	C149T	TCA>TTA	Missense	GU280_gp02, spike glycoprotein	0.866527942925089
CAMB-71BBE	MN908947.3	23403	A	G	1	1	0	0	0.999956031393585	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.19843032075098e-05
CAMB-71BBE	MN908947.3	23435	C	T	0.06	0.24	5.5e-28	1.8e-115	0.100961857379768	TCA	S	H625Y	C1873T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.899038142620232
CAMB-71BBE	MN908947.3	241	C	T	1	1	0	0	0.999824476721225	TCG	NA	NA	NA	NA	NA	NA	0.000131642459081136
CAMB-71BBE	MN908947.3	28064	A	-	0.024	0.01	1.4e-09	2.3e-05	0.0181543116490166	TAA	ORF8	.	171-171-delfrshift	.	no-SNV	GU280_gp09	0.981845688350983
CAMB-71BBE	MN908947.3	28064	AA	-	0.012	0.0105	1.4e-09;NA	2.3e-05;3.2e-05	0.0113981762917933	TAA	ORF8	.	171-172-delfrshift	.	no-SNV	GU280_gp09	0.981845688350983
CAMB-71BBE	MN908947.3	28253	C	T	0.085	0.09	9.3e-38	4.2e-40	0.0863090994275937	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.913589048909169
CAMB-71BBE	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999469777306469	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000303859009419629
CAMB-71BBE	MN908947.3	3037	C	T	1	1	1.1e-263	0	0.999410029498525	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-71BBE	MN908947.3	4815	C	T	0.07	0.26	7.4e-31	3.4e-121	0.165000427240878	TCT	ORF1ab:nsp3	S699F	C2096T	TCT>TTT	Missense	ORF1ab:nsp3	0.834999572759122
CAMB-71BBE	MN908947.3	5239	C	T	0.89	0.94	1e-187	1.4e-64	0.896551724137931	ACC	ORF1ab:nsp3	Y840Y	C2520T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.103448275862069
CAMB-71BBE	MN908947.3	635	C	T	0.18	0.22	1.4e-79	2.4e-95	0.190711761736497	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.809288238263503
CAMB-71BBE	MN908947.3	683	C	T	0.14	0.093	1.3e-64	1.7e-42	0.126760875834683	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.873216939902833
CAMB-71BCD	MN908947.3	11075	T	-	0.26	0.13	1.2e-67	1.3e-32	0.210809168866977	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.789074000514055
CAMB-71BCD	MN908947.3	15784	T	-	0.042	0.044	4e-20	5.2e-21	0.0433684490379183	CTT	ORF1ab:RNA-dependent-RNA-polymerase	.	2317-2317-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.955601342594131
CAMB-71BCD	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999719101123596	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	9.36329588014981e-05
CAMB-71BCD	MN908947.3	17516	G	C	0.027	0.046	3.5e-14	3.4e-22	0.037569573283859	AGA	ORF1ab:helicase	R427T	G1280C	AGA>ACA	Missense	ORF1ab:helicase	0.962430426716141
CAMB-71BDC	MN908947.3	11075	T	-	0.037	0.037	9.9e-10	3.4e-10	0.0373169766521567	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958092599920855
CAMB-71BDC	MN908947.3	14408	C	T	1	1	0	0	0.998159161710564	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.0005380911922968
CAMB-71BDC	MN908947.3	14599	C	T	0.021	0.02	9.3e-11	1.1e-10	0.0206674360453933	TCT	ORF1ab:RNA-dependent-RNA-polymerase	L378L	C1132T	CTA>TTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.979149836507021
CAMB-71BDC	MN908947.3	17826	T	A	0.0084	0.009	1.8e-05	3.9e-06	0.00860985778742361	CTC	ORF1ab:helicase	T530T	T1590A	ACT>ACA	Synonymous	ORF1ab:helicase	0.991061739676738
CAMB-71BDC	MN908947.3	217	C	T	0.033	0.035	1.7e-15	7.5e-17	0.0334314356663294	GCC	NA	NA	NA	NA	NA	NA	0.966476593396487
CAMB-71BDC	MN908947.3	21780	C	T	0.11	0.12	9.5e-47	3.7e-53	0.111490732013823	ACC	S	T73I	C218T	ACC>ATC	Missense	GU280_gp02, spike glycoprotein	0.88846999685831
CAMB-71BDC	MN908947.3	23403	A	G	1	1	0	0	0.99912648812204	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000108063325108514
CAMB-71BDC	MN908947.3	241	C	T	1	1	0	0	0.998709163346614	TCG	NA	NA	NA	NA	NA	NA	0.000223107569721116
CAMB-71BDC	MN908947.3	277	T	A	0.013	0.014	2.3e-07	7e-08	0.0134784046355635	TTG	ORF1ab:leader-protein	L4L	T12A	CTT>CTA	Synonymous	ORF1ab:leader-protein	0.986238170967894
CAMB-71BDC	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998961484625457	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000350578454449842
CAMB-71BDC	MN908947.3	3037	C	T	1	1	0	0	0.999116496276663	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000189322226429383
CAMB-71BDC	MN908947.3	6500	C	T	0.008	0.0077	2e-05	1.7e-05	0.00792073333531104	ACC	ORF1ab:nsp3	P1261S	C3781T	CCA>TCA	Missense	ORF1ab:nsp3	0.992025868462428
CAMB-71BEB	MN908947.3	11075	T	-	0.086	0.0056	1.9e-21	0.0064	0.0721087931226146	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.927668877607737
CAMB-71BEB	MN908947.3	13914	T	G	0.0057	0.0097	3.5e-05	6.9e-07	0.00746527777777778	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.992534722222222
CAMB-71BEB	MN908947.3	14408	C	T	1	1	0	0	0.999411129649622	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000392580233585239
CAMB-71BEB	MN908947.3	20578	G	T	1	1	2.5e-103	8.9e-178	1	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	0
CAMB-71BEB	MN908947.3	21137	A	G	0.21	0.44	1.6e-82	2.8e-174	0.260969976905312	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.739030023094688
CAMB-71BEB	MN908947.3	23403	A	G	1	1	0	0	0.999883172110846	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.33655778307398e-05
CAMB-71BEB	MN908947.3	241	C	T	1	0.92	0	0	0.975203332672089	TCG	NA	NA	NA	NA	NA	NA	6.6124446207763e-05
CAMB-71BEB	MN908947.3	2416	C	T	1	1	5.2e-253	3.9e-275	1	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0
CAMB-71BEB	MN908947.3	25563	G	T	1	1	0	0	0.999740663900415	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	8.64453665283541e-05
CAMB-71BEB	MN908947.3	26777	TTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCT	-	0.0737441860465116	0.0531860465116279	1.5e-13;5e-12;5.4e-11;7.1e-14;4.5e-18;3.7e-14;5.3e-14;1.6e-13;8.3e-16;4.4e-15;3.1e-13;3e-13;4.9e-14;1.5e-13;6e-14;2.8e-13;1.2e-13;1.7e-13;4.9e-13;6.2e-14;3.9e-13;1.9e-13;1.6e-13;6.6e-14;3.9e-13;7.5e-14;2.5e-13;1.4e-13;4.5e-14;1.8e-13;1e-13;1e-12;1e-13;3.1e-13;6.9e-14;2.4e-14;1.5e-13;1.5e-14;1e-13;6.2e-14;5.4e-10;2.3e-08;2.6e-09	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;1.7e-12;1.5e-12;9.6e-13;6.3e-13;3.1e-13;1.1e-12;6.6e-13;9.2e-13;2.6e-12;3.9e-13;1.8e-12;7.3e-13;1e-12;6.2e-13;2.4e-12;4.6e-13;1.3e-12;7.3e-13;1.6e-13;5.9e-13;8e-13;2.6e-12;6.3e-13;1.6e-12;3.8e-13;9.4e-14;1e-12;6.9e-14;8.1e-13;2.6e-13;1.6e-09;6.3e-08;7.1e-09	0.0701003286628611	CTT	M	.	255-297-delfrshift	.	no-SNV	GU280_gp05	0.961572927099257
CAMB-71BEB	MN908947.3	3037	C	T	1	1	6.4e-207	5.7e-283	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-71BEB	MN908947.3	3478	T	C	0.3	0.27	2.1e-139	5.7e-114	0.291489048948993	TTG	ORF1ab:nsp3	V253V	T759C	GTT>GTC	Synonymous	ORF1ab:nsp3	0.70836395707776
CAMB-71BEB	MN908947.3	5840	T	C	1	0.85	0	8e-301	0.954436450839328	ATA	ORF1ab:nsp3	Y1041H	T3121C	TAC>CAC	Missense	ORF1ab:nsp3	0.0455635491606715
CAMB-71BEB	MN908947.3	7927	A	-	0.085	0.11	4.7e-22	8.6e-27	0.0970149253731343	CAA	ORF1ab:nsp3	.	5208-5208-delfrshift	.	no-SNV	ORF1ab:nsp3	0.902985074626866
CAMB-71BEB	MN908947.3	7927	AA	-	0.0425	0.115	4.7e-22;NA	8.6e-27;1e-31	0.073541842772612	CAA	ORF1ab:nsp3	.	5208-5209-delfrshift	.	no-SNV	ORF1ab:nsp3	0.902985074626866
CAMB-71BFA	MN908947.3	11074	C	INS	0.023	0.029	5.7e-05	5.4e-06	0.0253355535935806	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.974049777042658
CAMB-71BFA	MN908947.3	11075	T	-	0.045	0.014	9.1e-11	0.00018	0.0332251451998633	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964639562692176
CAMB-71BFA	MN908947.3	11824	C	T	1	1	0	0	0.999363057324841	TCA	ORF1ab:nsp6	I284I	C852T	ATC>ATT	Synonymous	ORF1ab:nsp6	0.000636942675159236
CAMB-71BFA	MN908947.3	14408	C	T	1	1	0	0	0.997671428426797	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000546708108491187
CAMB-71BFA	MN908947.3	187	A	G	1	1	0	0	0.998560970157595	CAG	NA	NA	NA	NA	NA	NA	0.000530904213702917
CAMB-71BFA	MN908947.3	21575	C	T	0.072	0.038	5.1e-20	2.9e-10	0.0574904580152672	TCT	S	L5F	C13T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.942270992366412
CAMB-71BFA	MN908947.3	21610	TAATCTTACAACCAGAACTCAATTACCCCCTGCA	-	0.00110558823529412	0.0111176470588235	0.067;0.072;0.066;0.065;0.065;0.064;0.05;0.03;0.033;0.031;0.025;0.03;0.026;0.052;0.13;0.027;0.028;0.027;0.03;0.031;0.05;0.0089;0.0088;0.013;0.039;0.13;0.054;0.039;0.038;0.038;0.047;0.049;0.039;0.044	7.3e-06;7.7e-06;5.7e-06;6.5e-06;6.6e-06;5.5e-06;4.2e-06;1.1e-06;4.1e-06;3.2e-06;1.5e-06;3.5e-06;3.3e-06;5.9e-06;3e-05;3.2e-06;3e-06;3.4e-06;3.7e-06;3.7e-06;5.4e-06;1.1e-05;1.5e-05;6.1e-05;1.8e-05;1.8e-05;1.2e-05;1.8e-05;1.7e-05;1.7e-05;3e-06;4.4e-06;8.7e-06;4.9e-06	0.00485436893203883	TTA	S	.	48-81-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.994610667162237
CAMB-71BFA	MN908947.3	22101	A	T	0.021	0.017	7.7e-11	1.7e-09	0.0198119236738793	GAA	S	E180V	A539T	GAA>GTA	Missense	GU280_gp02, spike glycoprotein	0.976216561672601
CAMB-71BFA	MN908947.3	23403	A	G	1	1	0	0	0.999579386713473	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000113242038680245
CAMB-71BFA	MN908947.3	23555	CCCATTGGTGCAGGTATATGCGCTAGT	-	0.0294074074074074	0.0380740740740741	0.0031;0.0028;0.0032;0.0033;0.0011;0.002;0.0015;0.0023;0.0024;0.0025;0.0024;0.0024;0.0017;0.0016;0.00064;0.00026;0.0011;0.00066;0.00086;0.00061;0.0011;0.0018;0.0012;0.00088;7.5e-05;9.2e-05;0.00097	0.00039;4e-04;0.00052;6e-04;0.00024;0.00037;0.00023;0.00043;0.00044;0.00046;0.00042;0.00042;0.00027;0.00025;0.00011;3.9e-05;0.00013;5.7e-05;0.00013;6.3e-05;0.00014;3e-04;0.00016;0.00021;7.2e-06;1e-05;0.00026	0.03265178385145	ACC	S	.	1993-2019-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.966580176440062
CAMB-71BFA	MN908947.3	23712	A	G	0.038	0.045	8e-18	6.5e-21	0.0419501133786848	AAT	S	N717S	A2150G	AAT>AGT	Missense	GU280_gp02, spike glycoprotein	0.958049886621315
CAMB-71BFA	MN908947.3	241	C	T	1	1	0	0	0.998997335777924	TCG	NA	NA	NA	NA	NA	NA	0.000171885295212995
CAMB-71BFA	MN908947.3	26759	A	G	0.0048	0.011	0.00065	1.4e-06	0.00747864583984693	GAA	M	G79G	A237G	GGA>GGG	Synonymous	GU280_gp05	0.992483835869987
CAMB-71BFA	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0221891891891892	0.0372162162162162	0.023;0.0092;0.03;0.032;0.039;0.01;0.015;0.00078;0.00077;4e-04;0.00061;0.00055;0.00072;0.00061;0.00072;0.00091;6e-04;0.00083;0.00065;0.00064;0.00052;0.00091;0.00059;0.00072;0.00063;0.00055;0.00081;0.00055;0.00024;0.00063;0.00076;0.00073;0.00033;8e-04;0.00054;0.00074;0.00067	4.5e-05;3.1e-06;1.3e-05;1.5e-05;2.8e-05;4.4e-06;9.2e-06;2.4e-06;2.2e-06;1.6e-06;1.4e-06;1.3e-06;1.7e-06;1.6e-06;2.1e-06;3e-06;9.2e-07;2.5e-06;1.4e-06;1.9e-06;1.5e-06;3.2e-06;1.5e-06;2.1e-06;1.6e-06;9.9e-07;2.4e-06;1.6e-06;2.3e-07;1.7e-06;2.5e-06;2.2e-06;1.1e-06;2.6e-06;4.4e-07;1.5e-06;8.2e-07	0.0300824272597046	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.979809697907146
CAMB-71BFA	MN908947.3	27289	G	A	0.014	0.013	6.4e-08	8.1e-08	0.0135412319413243	TGA	ORF6	D30N	G88A	GAT>AAT	Missense	GU280_gp06	0.985579697919534
CAMB-71BFA	MN908947.3	27390	G	T	0.01	0.0086	2.2e-06	8.2e-06	0.00956636611077125	CGA	NA	NA	NA	NA	NA	NA	0.990353840288676
CAMB-71BFA	MN908947.3	29402	G	T	0.023	0.024	1.6e-09	1.6e-09	0.023444976076555	TGA	N	D377Y	G1129T	GAT>TAT	Missense	GU280_gp10	0.976555023923445
CAMB-71BFA	MN908947.3	3037	C	T	1	1	0	0	0.998602324554951	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000294247462115639
CAMB-71BFA	MN908947.3	3264	C	T	0.0049	0.0088	0.00061	1.1e-05	0.00639065508259315	ACT	ORF1ab:nsp3	T182I	C545T	ACT>ATT	Missense	ORF1ab:nsp3	0.99359316604378
CAMB-71BFA	MN908947.3	6654	T	C	0.0073	0.0037	3.9e-05	0.00095	0.00494315373208107	GTT	ORF1ab:nsp3	V1312A	T3935C	GTT>GCT	Missense	ORF1ab:nsp3	0.995056846267919
CAMB-71C06	MN908947.3	10047	TT	-	0.005	0.01125	0.0073;0.0021	4.6e-06;2.4e-05	0.00670620437956204	GTT	ORF1ab:nsp4	.	1493-1494-delfrshift	.	no-SNV	ORF1ab:nsp4	0.9925
CAMB-71C06	MN908947.3	10162	TTACTGTCCAAGACATGTG	-	0.00383157894736842	0.00957368421052632	NA;0.0018;0.0021;0.0029;0.0023;0.0026;0.0017;0.0019;0.0016;0.0026;0.0016;0.0018;0.0017;0.0017;0.0017;0.0023;0.0023;0.0011;0.0012	0.00065;4.4e-06;5.5e-06;1.3e-05;5.1e-06;6.7e-06;4.5e-06;4.5e-06;3.3e-06;6e-06;3.9e-06;6e-06;3.2e-06;4.2e-06;3.2e-06;5.1e-06;4.9e-06;2.4e-06;2.8e-06	0.00631763307687496	TTT	ORF1ab:3C-like-proteinase	.	108-126-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.998113246667081
CAMB-71C06	MN908947.3	11074	C	INS	0.018	0.031	0.002	2.4e-06	0.021312432931716	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.978538149119113
CAMB-71C06	MN908947.3	11075	T	-	0.012	0.027	0.00083	9.6e-08	0.0155270552633475	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.979009054446766
CAMB-71C06	MN908947.3	12162	A	G	0.011	0.0095	7.1e-07	1.9e-06	0.0105534441417783	CAG	ORF1ab:nsp8	Q24R	A71G	CAG>CGG	Missense	ORF1ab:nsp8	0.987285301841551
CAMB-71C06	MN908947.3	12263	AAGTTGGAAA	-	0.00863	0.00625	0.0059;7.2e-10;1e-08;2.1e-09;1.5e-09;0.013;0.0039;0.019;0.0055;0.0017	1e-04;1e-04;0.00026;0.00013;0.00014;0.00034;8.7e-05;0.00066;0.00013;1.5e-05	0.00361172467315384	TAA	ORF1ab:nsp8	.	172-181-delfrshift	.	no-SNV	ORF1ab:nsp8	0.993662191695286
CAMB-71C06	MN908947.3	14408	C	T	1	0.99	0	0	0.995703758065009	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000336360578540195
CAMB-71C06	MN908947.3	16375	C	T	0.0081	0.012	0.00068	1.5e-05	0.0108527131782946	TCC	ORF1ab:helicase	P47S	C139T	CCG>TCG	Missense	ORF1ab:helicase	0.989147286821705
CAMB-71C06	MN908947.3	17331	G	T	1	1	0	0	0.999027250872	AGA	ORF1ab:helicase	E365D	G1095T	GAG>GAT	Missense	ORF1ab:helicase	5.55856644571365e-05
CAMB-71C06	MN908947.3	18202	A	C	0.0081	0.013	6.9e-06	6.1e-08	0.0103979921118681	CAT	ORF1ab:3'-to-5'-exonuclease	I55L	A163C	ATC>CTC	Missense	ORF1ab:3'-to-5'-exonuclease	0.989458587307279
CAMB-71C06	MN908947.3	21137	A	G	1	1	0	0	0.99993446347431	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	4.36910171268787e-05
CAMB-71C06	MN908947.3	21818	T	-	0.0045	0.0079	0.00078	2.7e-05	0.00621192211205352	ATT	S	.	256-256-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.990921036913153
CAMB-71C06	MN908947.3	22952	TTTGAGAGAG	-	0.00301	0.00611	0.0078;0.0074;0.0087;0.014;0.012;0.0087;0.0087;0.0089;0.0093;0.0085	0.00036;0.00044;0.00074;1.5e-05;7.5e-06;0.00085;8e-04;0.00089;9e-04;0.00089	0.0041758496694119	TTT	S	.	1390-1399-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.994229844526366
CAMB-71C06	MN908947.3	23403	A	G	1	1	0	0	0.999879321788451	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.0282588145377e-05
CAMB-71C06	MN908947.3	23675	GTTG	-	0.00085	0.005525	NA;NA;NA;0.0012	0.00012;4.2e-05;0.00013;0.00015	0.00246513136555303	AGT	S	.	2113-2116-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.997408507679666
CAMB-71C06	MN908947.3	241	C	T	1	1	0	0	0.999775827283544	TCG	NA	NA	NA	NA	NA	NA	0.000172440551120001
CAMB-71C06	MN908947.3	26526	G	T	0.013	0.012	1.9e-05	3e-05	0.0123334977799704	GGC	M	A2S	G4T	GCA>TCA	Missense	GU280_gp05	0.987365016718741
CAMB-71C06	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0271842105263158	0.0405789473684211	0.027;0.0075;0.0032;0.0032;0.0054;0.0011;0.0032;2e-04;2e-04;9.4e-05;5.4e-05;4.3e-05;8.1e-05;5.9e-05;7e-05;1e-04;4.9e-05;9.2e-05;6.4e-05;6.5e-05;6.3e-05;9.7e-05;6.5e-05;7.8e-05;6.2e-05;4.7e-05;8.4e-05;5.4e-05;1.8e-05;6.4e-05;8.3e-05;7.9e-05;0.00014;0.00021;8.2e-05;0.00013;0.00011;0.002	5.5e-05;4.1e-06;3e-05;3.2e-05;8.7e-05;7.3e-06;3.2e-05;2.4e-07;2.2e-07;1.5e-07;1.1e-07;8.3e-08;1.9e-07;1.5e-07;2e-07;3.5e-07;1.2e-07;2.8e-07;1.2e-07;2e-07;1.9e-07;3.5e-07;1.7e-07;2.3e-07;1.5e-07;8.1e-08;2.3e-07;1.6e-07;8.9e-09;1.7e-07;2.6e-07;2.5e-07;8.6e-08;2.8e-07;3.2e-08;1.4e-07;6.8e-08;2e-04	0.0342640975397344	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.981469135634498
CAMB-71C06	MN908947.3	26882	C	T	1	1	0	0	0.999870070811408	TCA	M	L120L	C360T	CTC>CTT	Synonymous	GU280_gp05	8.35259069521396e-05
CAMB-71C06	MN908947.3	27467	G	A	0.0083	0.012	8.8e-06	1.6e-07	0.00963273826349779	AGA	ORF7a	R25K	G74A	AGA>AAA	Missense	GU280_gp07	0.99032377307617
CAMB-71C06	MN908947.3	29737	GCCACGCGGAGTAC	-	0.999285714285714	1	0;0;0;0;0;0;0;0;0;0;0;0;0;0	0;0;0;0;0;0;0;0;0;0;0;0;0;0	0.999571183533448	GGC	NA	NA	NA	NA	NA	NA	0.00515463917525773
CAMB-71C06	MN908947.3	29751	GA	-	0.01055	0.0155	0.0074;0.002	0.00035;2.1e-05	0.0138532580810672	CGA	NA	NA	NA	NA	NA	NA	0.986589181940098
CAMB-71C06	MN908947.3	3037	C	T	1	1	0	0	0.999743392353092	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000128303823453939
CAMB-71C06	MN908947.3	307	C	T	0.083	0.074	1.3e-37	4.8e-34	0.0802643397921211	TCC	ORF1ab:leader-protein	V14V	C42T	GTC>GTT	Synonymous	ORF1ab:leader-protein	0.919719620171949
CAMB-71C06	MN908947.3	3881	A	G	0.11	0.12	2.1e-48	6.3e-45	0.108677879000234	GAT	ORF1ab:nsp3	I388V	A1162G	ATT>GTT	Missense	ORF1ab:nsp3	0.891322120999766
CAMB-71C06	MN908947.3	4480	AT	-	0.0135	0.0092	9e-07;1.8e-06	5.2e-05;9.2e-05	0.012453766562105	AAT	ORF1ab:nsp3	.	1761-1762-delfrshift	.	no-SNV	ORF1ab:nsp3	0.98764863121025
CAMB-71C06	MN908947.3	522	TT	-	0.0405	0.05	4.5e-07;9e-04	3e-08;1.6e-05	0.0427926901517568	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.942681895093063
CAMB-71C06	MN908947.3	7042	G	T	1	1	0	4.59999819560493e-319	1	TGC	ORF1ab:nsp3	M1441I	G4323T	ATG>ATT	Missense	ORF1ab:nsp3	0
CAMB-71C06	MN908947.3	7824	A	G	0.0016	0.0079	0.0047	1.6e-05	0.00381242851696531	CAT	ORF1ab:nsp3	H1702R	A5105G	CAT>CGT	Missense	ORF1ab:nsp3	0.996187571483035
CAMB-71C15	MN908947.3	1059	C	T	1	1	0	0	0.999936361129378	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	4.24259137481174e-05
CAMB-71C15	MN908947.3	10790	C	T	0.0059	0.043	0.00017	9.3e-20	0.01768882360142	CCA	ORF1ab:3C-like-proteinase	H246Y	C736T	CAT>TAT	Missense	ORF1ab:3C-like-proteinase	0.98231117639858
CAMB-71C15	MN908947.3	11071	G	INS	0.013	0.017	5.5e-05	3.3e-06	0.0141033340436661	TGT	ORF1ab:nsp6	.	98-99-insfrshift	.	no-SNV	ORF1ab:nsp6	0.985761056975145
CAMB-71C15	MN908947.3	11074	C	INS	0.02	0.026	0.00036	4.3e-05	0.0218080616830531	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.976036225106645
CAMB-71C15	MN908947.3	11074	CT	-	0.0174	0.016022	0.00011;7.3e-08	NA;9.6e-09	0.0178368406375357	TCT	ORF1ab:nsp6	.	102-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.976036225106645
CAMB-71C15	MN908947.3	11075	T	-	0.032	0.032	7.3e-08	9.6e-09	0.0318440391116869	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.965291414458368
CAMB-71C15	MN908947.3	1194	A	G	0.011	0.019	5.3e-07	1.5e-10	0.01454554344106	AAT	ORF1ab:nsp2	N130S	A389G	AAT>AGT	Missense	ORF1ab:nsp2	0.985381117684447
CAMB-71C15	MN908947.3	13636	A	G	0.003	0.013	8e-04	2.5e-08	0.00548669197263372	AAT	ORF1ab:RNA-dependent-RNA-polymerase	I57V	A169G	ATT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.99450211069681
CAMB-71C15	MN908947.3	13754	G	A	0.002	0.0083	0.0078	7e-06	0.00363509029364193	AGA	ORF1ab:RNA-dependent-RNA-polymerase	R96K	G287A	AGA>AAA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.996314885528005
CAMB-71C15	MN908947.3	14408	C	T	1	1	0	0	0.998896487636306	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000174238794267544
CAMB-71C15	MN908947.3	17766	C	T	0.0064	0.013	0.00012	1.4e-07	0.00788350698293061	TCT	ORF1ab:helicase	V510V	C1530T	GTC>GTT	Synonymous	ORF1ab:helicase	0.99210263799601
CAMB-71C15	MN908947.3	1840	A	G	0.007	0.0063	4.5e-05	4.4e-05	0.00681864441278241	AAC	ORF1ab:nsp2	E345E	A1035G	GAA>GAG	Synonymous	ORF1ab:nsp2	0.993181355587218
CAMB-71C15	MN908947.3	18457	C	T	0.0059	0.0081	0.00013	9.4e-06	0.00639356368300361	ACC	ORF1ab:3'-to-5'-exonuclease	P140S	C418T	CCA>TCA	Missense	ORF1ab:3'-to-5'-exonuclease	0.993528703019939
CAMB-71C15	MN908947.3	2033	T	C	0.01	0.0067	1.1e-06	3.5e-05	0.00931719570678237	TTT	ORF1ab:nsp2	L410L	T1228C	TTG>CTG	Synonymous	ORF1ab:nsp2	0.990637131765243
CAMB-71C15	MN908947.3	21137	A	G	0.0056	0.01	0.0023	3.4e-05	0.00684248324289818	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.993157516757102
CAMB-71C15	MN908947.3	23403	A	G	1	1	0	0	0.999906932670017	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.92246645345787e-05
CAMB-71C15	MN908947.3	23484	A	G	1	1	0	0	0.998887545703331	AAT	S	N641S	A1922G	AAT>AGT	Missense	GU280_gp02, spike glycoprotein	2.96654479111817e-05
CAMB-71C15	MN908947.3	241	C	T	1	1	0	0	0.999862945640815	TCG	NA	NA	NA	NA	NA	NA	6.85271795926059e-05
CAMB-71C15	MN908947.3	24368	G	T	1	1	0	0	1	AGA	S	D936Y	G2806T	GAC>TAC	Missense	GU280_gp02, spike glycoprotein	0
CAMB-71C15	MN908947.3	25523	G	C	0.011	0.011	2.2e-06	6e-07	0.0109282571202914	GGA	ORF3a	G44A	G131C	GGA>GCA	Missense	GU280_gp03	0.988958914266372
CAMB-71C15	MN908947.3	25563	G	T	1	1	0	0	0.999875650613753	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	3.55283960705594e-05
CAMB-71C15	MN908947.3	26333	C	T	0.0076	0.019	0.00012	2.7e-09	0.0101010101010101	ACA	E	T30I	C89T	ACA>ATA	Missense	GU280_gp04	0.989809600429069
CAMB-71C15	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0343243243243243	0.0358918918918919	9.5e-05;9.1e-06;0.00012;0.00013;0.00026;1.8e-06;8.9e-06;1e-05;9.9e-06;4.2e-06;6.5e-06;5.3e-06;9.7e-06;6.8e-06;8.5e-06;1.3e-05;2.2e-06;1.1e-05;7.9e-06;7.6e-06;7.4e-06;1.2e-05;6.8e-06;9.4e-06;7.4e-06;5.5e-06;9.6e-06;6.3e-06;2e-06;7.5e-06;1e-05;9.5e-06;6.7e-06;1.1e-05;2.8e-06;6e-06;4.8e-06	0.0051;0.0012;0.0041;0.0044;0.048;0.0011;0.0025;1.1e-06;1e-06;6.9e-07;5.9e-07;4.8e-07;8.2e-07;6.6e-07;8.9e-07;1.4e-06;5.8e-07;1.2e-06;6.1e-07;8.8e-07;8.7e-07;1.5e-06;6.7e-07;9.8e-07;7.5e-07;4.1e-07;9.7e-07;7.4e-07;7.4e-08;7.9e-07;1.1e-06;1e-06;4.7e-07;1.2e-06;1.6e-07;6.4e-07;3.4e-07	0.0365415048194504	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.976641323578635
CAMB-71C15	MN908947.3	27267	TAAAGTTTCCATTTGGAATCTTGATTACATCATA	-	0.0821764705882353	0.153823529411765	1.1e-20;9.9e-23;1e-21;1.7e-21;2.3e-21;4.2e-23;7.3e-21;9.1e-21;2.3e-21;8.6e-22;1.5e-21;2.1e-22;1.5e-20;7.7e-21;3e-21;7.8e-20;1.6e-21;8.7e-21;3e-21;4.7e-21;3.4e-23;4.4e-21;9.5e-24;1.5e-23;4.8e-35;1.4e-25;3.8e-35;5.7e-34;3.2e-32;4.2e-33;6.1e-32;1.6e-36;8.7e-37;4.5e-35	5e-39;3.8e-43;7.8e-41;2.1e-40;2.3e-40;5.9e-44;2.5e-39;4.8e-39;9.5e-41;1.7e-41;3.5e-41;9.5e-42;4.1e-39;1.7e-39;2.3e-40;4e-37;6.1e-41;4.1e-40;3.9e-40;7.5e-40;3.3e-44;5.1e-40;5.5e-45;4e-45;1.8e-68;1e-49;1.7e-68;9.8e-66;2.5e-63;4.2e-65;2e-62;4.8e-71;5e-71;5.6e-68	0.106200030170463	TTA	ORF6	.	66-99-delfrshift	.	no-SNV	GU280_gp06	0.897666217197386
CAMB-71C15	MN908947.3	3037	C	T	1	1	0	0	0.999582681272822	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-71C15	MN908947.3	522	T	-	0.047	0.045	5.5e-06	5.4e-06	0.0466793469646537	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.953142336344904
CAMB-71C15	MN908947.3	522	TT	-	0.0405	0.0345	5.5e-06;8e-05	5.4e-06;0.0016	0.0387723060427357	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.953142336344904
CAMB-71C15	MN908947.3	5489	G	T	0.027	0.03	8e-12	1.4e-12	0.0282009724473258	AGA	ORF1ab:nsp3	D924Y	G2770T	GAT>TAT	Missense	ORF1ab:nsp3	0.971799027552674
CAMB-71C15	MN908947.3	57	A	G	0.0025	0.013	0.0027	2.9e-08	0.00513128187315471	GAT	NA	NA	NA	NA	NA	NA	0.994868718126845
CAMB-71C15	MN908947.3	7427	G	T	0.01	0.02	1.7e-06	3.2e-10	0.0121057661675693	TGC	ORF1ab:nsp3	A1570S	G4708T	GCA>TCA	Missense	ORF1ab:nsp3	0.987788042901136
CAMB-71C15	MN908947.3	7735	CGT	TTC	0.00101	0.0163333333333333	NA;NA;0.0022	1.7e-05;1e-08;3.4e-09	0.00543872371283539	TCG	ORF1ab:nsp3	.	5016-5018-mnv	.	no-SNV	ORF1ab:nsp3	0.995562655307064
CAMB-71C15	MN908947.3	7837	AGACAACCTGAGAGCTAATA	-	0.000245	0.007215	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00074;NA;NA;NA	0.00029;2.3e-05;2.5e-05;3.6e-05;0.00033;4.7e-05;8.5e-05;8.8e-05;2.1e-05;3.2e-05;8e-05;7.9e-05;8.2e-05;6.1e-05;5e-05;3.5e-05;7.3e-05;3.7e-05;1.8e-05;2.6e-05	0.0023961661341853	TAG	ORF1ab:nsp3	.	5118-5137-delfrshift	.	no-SNV	ORF1ab:nsp3	0.998483556061037
CAMB-71C15	MN908947.3	7936	G	A	0.0065	0.0093	6.7e-05	4.6e-06	0.00740160222918844	CGT	ORF1ab:nsp3	A1739A	G5217A	GCG>GCA	Synonymous	ORF1ab:nsp3	0.992424242424242
CAMB-71C24	MN908947.3	11075	T	-	0.026	0.041	6.1e-07	1.2e-10	0.0314943657417941	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962721688002203
CAMB-71C24	MN908947.3	14408	C	T	1	1	0	0	0.999152605366833	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000713595480561956
CAMB-71C24	MN908947.3	1547	A	-	0.0075	0.0043	2.8e-05	0.00045	0.00616468516072215	TAG	ORF1ab:nsp2	.	742-742-delfrshift	.	no-SNV	ORF1ab:nsp2	0.960369881109643
CAMB-71C24	MN908947.3	1547	A	G	0.011	0.0097	5e-06	2.1e-05	0.0103478643769265	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.960369881109643
CAMB-71C24	MN908947.3	1547	A	T	0.024	0.022	3.3e-11	3.3e-10	0.0231175693527081	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.960369881109643
CAMB-71C24	MN908947.3	16138	T	C	0.017	0.016	1.6e-09	2e-09	0.0169157340803089	GTT	ORF1ab:RNA-dependent-RNA-polymerase	L891L	T2671C	TTA>CTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.98302987449178
CAMB-71C24	MN908947.3	1820	G	-	0.008	0.0042	1e-05	2e-04	0.00655229602240287	AGG	ORF1ab:nsp2	.	1015-1015-delfrshift	.	no-SNV	ORF1ab:nsp2	0
CAMB-71C24	MN908947.3	1820	G	A	0.99	1	0	0	0.993420516027297	AGG	ORF1ab:nsp2	G339S	G1015A	GGT>AGT	Missense	ORF1ab:nsp2	0
CAMB-71C24	MN908947.3	18583	G	A	0.0076	0.015	3.8e-05	2.7e-08	0.0101381989469267	CGT	ORF1ab:3'-to-5'-exonuclease	V182I	G544A	GTA>ATA	Missense	ORF1ab:3'-to-5'-exonuclease	0.989848265406949
CAMB-71C24	MN908947.3	23152	T	C	0.012	0.0056	3.3e-05	0.0042	0.00915774187692866	CTA	S	S530S	T1590C	TCT>TCC	Synonymous	GU280_gp02, spike glycoprotein	0.990842258123071
CAMB-71C24	MN908947.3	23161	G	T	0.014	0.0055	4e-05	0.0093	0.0104268402966178	TGG	S	L533F	G1599T	TTG>TTT	Missense	GU280_gp02, spike glycoprotein	0.989536986796889
CAMB-71C24	MN908947.3	23189	T	C	0.012	0.0055	3e-05	0.0039	0.00908903699266137	CTT	S	F543L	T1627C	TTC>CTC	Missense	GU280_gp02, spike glycoprotein	0.990892242024861
CAMB-71C24	MN908947.3	23194	TG	AT	0.0115	0.0061	8.3e-06;1.2e-05	0.0011;0.0023	0.00934878657872831	ATG	S	.	1632-1633-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.990208118963056
CAMB-71C24	MN908947.3	23197	T	G	0.012	0.0064	6.8e-06	0.0015	0.00989954718159579	GTT	S	G545G	T1635G	GGT>GGG	Synonymous	GU280_gp02, spike glycoprotein	0.990037995107479
CAMB-71C24	MN908947.3	23200	A	T	0.012	0.0063	6.5e-06	0.0014	0.00978532201697454	TAA	S	L546F	A1638T	TTA>TTT	Missense	GU280_gp02, spike glycoprotein	0.990134797803295
CAMB-71C24	MN908947.3	23202	CAG	ACA	0.012	0.00643333333333333	9.4e-06;5.7e-06;7.8e-06	0.0014;0.0012;0.0014	0.00976468541131434	ACA	S	.	1640-1642-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.98944071497072
CAMB-71C24	MN908947.3	23206	CACAG	GCACA	0.0118	0.00636	8e-06;4.5e-06;1e-05;4.4e-06;7.8e-06	0.0015;0.0011;0.0017;0.0012;0.0012	0.00976476716750253	GCA	S	.	1644-1648-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.990388226338493
CAMB-71C24	MN908947.3	23212	TGT	GTG	0.0123333333333333	0.00646666666666667	6.5e-06;8.5e-06;3.9e-06	0.0014;0.0016;0.00096	0.00982639352855924	GTG	S	.	1650-1652-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.990122213199848
CAMB-71C24	MN908947.3	23216	CT	TC	0.012	0.0064	1.2e-05;8.8e-06	0.0019;0.0013	0.00970513309749482	TCT	S	.	1654-1655-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.990300848547184
CAMB-71C24	MN908947.3	23219	ACTGAGTCTA	TACTGAGTCT	0.012	0.00643	8.6e-06;6.8e-06;8.9e-06;6.7e-06;9.1e-06;6.4e-06;6.9e-06;8.6e-06;6.9e-06;6.5e-06	0.0014;0.001;0.0015;0.0014;0.0018;0.0012;0.0013;0.0015;0.0016;0.0012	0.00983278138926367	TAC	S	.	1657-1666-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.990130871004438
CAMB-71C24	MN908947.3	23230	CA	AC	0.0115	0.0062	1.6e-05;5.9e-06	0.0015;0.0013	0.00940461109703572	ACA	S	.	1668-1669-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.990125783586676
CAMB-71C24	MN908947.3	23236	GT	AG	0.0115	0.0062	1.1e-05;8e-06	0.0016;0.0013	0.00945129955368863	AGT	S	.	1674-1675-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.990666301877262
CAMB-71C24	MN908947.3	23240	CTGC	TCTG	0.012	0.006475	5.4e-06;1.1e-05;6.8e-06;6e-06	0.0015;0.0017;0.0015;0.001	0.00989853228659199	TCT	S	.	1678-1681-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.989745945889503
CAMB-71C24	MN908947.3	23245	T	C	0.012	0.0064	1.1e-05	0.0019	0.00981511775054786	CTT	S	P561P	T1683C	CCT>CCC	Synonymous	GU280_gp02, spike glycoprotein	0.990112863565748
CAMB-71C24	MN908947.3	23248	C	T	0.012	0.0066	1.1e-05	0.002	0.0100475717496994	TCC	S	F562F	C1686T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.989910606931883
CAMB-71C24	MN908947.3	23250	A	C	0.012	0.0064	6.7e-06	0.0012	0.00975187720966002	CAA	S	Q563P	A1688C	CAA>CCA	Missense	GU280_gp02, spike glycoprotein	0.990023818933382
CAMB-71C24	MN908947.3	23252	CA	AC	0.0125	0.0068	6.6e-06;2.4e-06	0.0013;0.00077	0.0103657650202954	ACA	S	.	1690-1691-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.990234436792761
CAMB-71C24	MN908947.3	23255	T	A	0.013	0.0071	2.6e-06	0.0011	0.0110503460272567	ATT	S	F565I	T1693A	TTT>ATT	Missense	GU280_gp02, spike glycoprotein	0.987860888282629
CAMB-71C24	MN908947.3	23258	G	T	0.012	0.0067	6.2e-06	0.0014	0.0102389810337618	TGG	S	G566C	G1696T	GGC>TGC	Missense	GU280_gp02, spike glycoprotein	0.989707411735695
CAMB-71C24	MN908947.3	23260	CAGAGACAT	GCAGAGACA	0.0122222222222222	0.00661111111111111	6.9e-06;4.8e-06;1.2e-05;4.3e-06;6.6e-06;1.2e-05;4.7e-06;1.5e-06;6.2e-06	0.0013;0.0011;0.0017;0.0012;0.0017;0.0016;0.0011;0.00066;0.0012	0.0100716743747671	GCA	S	.	1698-1706-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.990076732857158
CAMB-71C24	MN908947.3	23270	GCTGACACTACTGATGCTGTC	TGCTGACACTACTGATGCTGT	0.012	0.00661904761904762	8.6e-06;6.6e-06;9.1e-06;6.3e-06;4.3e-06;6.7e-06;4.5e-06;1.2e-05;1.8e-06;1.3e-05;1.1e-05;6.4e-06;1.8e-05;5.6e-06;7.2e-06;9.5e-06;6.8e-06;7.1e-06;6.7e-06;6.2e-06;8.8e-06	0.0017;0.0013;0.0019;0.001;0.0012;0.00098;0.0011;0.0021;0.00012;0.0011;0.0016;0.0015;0.0022;0.001;0.0011;0.0016;0.0013;0.0014;0.0014;0.0014;0.0016	0.00989662805441534	TGC	S	.	1708-1728-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.989997512895098
CAMB-71C24	MN908947.3	23292	GTGATC	CGTGAT	0.012	0.00646666666666667	6.1e-06;4.8e-06;1.1e-05;4.9e-06;6.3e-06;1e-05	0.0012;0.00097;0.002;0.0013;0.0015;0.0016	0.00989438929924443	CGT	S	.	1730-1735-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.98982778148254
CAMB-71C24	MN908947.3	23299	ACAGACACT	CACAGACAC	0.0123333333333333	0.00647777777777778	1.2e-05;8.2e-06;4.6e-06;5.7e-06;1.9e-05;7.2e-06;3.1e-05;1.6e-05;1.6e-06	0.0013;0.0016;0.0012;0.0015;0.0019;0.0014;0.0042;0.0019;0.00078	0.00957546326953195	CAC	S	.	1737-1745-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.989074026419626
CAMB-71C24	MN908947.3	23309	GAGAT	TGAGA	0.012	0.00642	1.9e-05;7.7e-06;7e-06;6.5e-06;2.2e-06	0.0022;0.0014;0.0016;0.0013;7e-04	0.00984272914937539	TGA	S	.	1747-1751-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.991297903874656
CAMB-71C24	MN908947.3	23315	CT	TC	0.012	0.00635	8.2e-06;7.2e-06	0.0016;0.0015	0.00982808848480968	TCT	S	.	1753-1754-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.990105323569736
CAMB-71C24	MN908947.3	23318	GACAT	TGACA	0.0118	0.00628	5.2e-06;1.6e-05;1.3e-05;5.2e-06;4.3e-06	0.0015;0.0015;0.0016;0.0014;0.0016	0.00986723487952795	TGA	S	.	1756-1760-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.989909865908889
CAMB-71C24	MN908947.3	23403	A	G	1	1	0	0	0.999939856256453	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.0095829031385e-05
CAMB-71C24	MN908947.3	241	C	T	1	1	0	0	0.999613750482812	TCG	NA	NA	NA	NA	NA	NA	0.000302282230842864
CAMB-71C24	MN908947.3	27265	TTTAAAGTTTCCATTTGGAATC	-	1	1	0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0	0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0	1	TTT	ORF6	.	64-85-delfrshift	.	no-SNV	GU280_gp06	0.00100321253452066
CAMB-71C24	MN908947.3	28090	G	A	0.0022	0.0096	0.0043	3.7e-06	0.00502718785267262	GGT	ORF8	G66D	G197A	GGT>GAT	Missense	GU280_gp09	0.994870216476865
CAMB-71C24	MN908947.3	28514	G	T	1	1	0	0	0.999879539842197	AGA	N	D81Y	G241T	GAT>TAT	Missense	GU280_gp10	0
CAMB-71C24	MN908947.3	29433	A	G	0.0098	0.035	2e-05	2.8e-11	0.0180940892641737	AAG	N	K387R	A1160G	AAG>AGG	Missense	GU280_gp10	0.981905910735826
CAMB-71C24	MN908947.3	3021	AT	-	0.0024	0.00685	0.011;0.0068	0.00027;3.3e-05	0.00406317080650107	CAT	ORF1ab:nsp3	.	302-303-delfrshift	.	no-SNV	ORF1ab:nsp3	0.996663729069621
CAMB-71C24	MN908947.3	3037	C	T	1	1	0	0	0.999334176709501	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.65823290498702e-05
CAMB-71C24	MN908947.3	6369	GAAT	-	0.002125	0.006	0.0042;0.0058;0.0035;0.0056	0.00038;4.5e-05;1.1e-05;5.1e-05	0.00311564919640929	GGA	ORF1ab:nsp3	.	3650-3653-delfrshift	.	no-SNV	ORF1ab:nsp3	0.997388509441543
CAMB-71C33	MN908947.3	11074	CT	-	0.00975	0.01608	0.00054;4.2e-05	0.047;4.6e-09	0.0121692064587609	TCT	ORF1ab:nsp6	.	102-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.971861729570981
CAMB-71C33	MN908947.3	11075	T	-	0.017	0.032	4.2e-05	4.6e-09	0.0208141462516117	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.978968167584856
CAMB-71C33	MN908947.3	11595	A	G	0.0078	0.015	0.00021	7.2e-06	0.0101465614430665	CAG	ORF1ab:nsp6	Q208R	A623G	CAG>CGG	Missense	ORF1ab:nsp6	0.989853438556934
CAMB-71C33	MN908947.3	14359	A	T	0.012	0.019	2.3e-07	1.2e-10	0.014954954954955	CAT	ORF1ab:RNA-dependent-RNA-polymerase	I298F	A892T	ATT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.984894894894895
CAMB-71C33	MN908947.3	14408	C	T	1	1	0	0	0.999647183347054	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000352816652946019
CAMB-71C33	MN908947.3	15197	CTGTAGTAATT	-	0.0072	0.00190909090909091	2.9e-05;2.4e-05;0.00016;0.00013;0.00019;0.00011;6.5e-05;9.7e-05;7.8e-05;0.00011;0.00011	NA;NA;NA;0.0062;0.0081;0.0048;0.0033;0.0041;NA;NA;NA	0.00635745480678866	ACT	ORF1ab:RNA-dependent-RNA-polymerase	.	1730-1740-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.993643138974134
CAMB-71C33	MN908947.3	17252	G	T	0.063	0.034	4.2e-29	3.2e-17	0.0571872935476767	CGT	ORF1ab:helicase	R339L	G1016T	CGT>CTT	Missense	ORF1ab:helicase	0.942688835058357
CAMB-71C33	MN908947.3	1820	G	A	1	1	0	0	0.998736140633079	AGG	ORF1ab:nsp2	G339S	G1015A	GGT>AGT	Missense	ORF1ab:nsp2	0.000114896306083759
CAMB-71C33	MN908947.3	18828	C	T	0.052	0.076	6.7e-24	1.2e-34	0.0600406692590346	TCC	ORF1ab:3'-to-5'-exonuclease	V263V	C789T	GTC>GTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.939923655952339
CAMB-71C33	MN908947.3	23403	A	G	1	1	0	0	0.999875060907807	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000112445182973301
CAMB-71C33	MN908947.3	241	C	T	1	1	0	0	0.999762877091292	TCG	NA	NA	NA	NA	NA	NA	0.000184428928994862
CAMB-71C33	MN908947.3	24579	C	T	1	1	0	1.5e-302	0.999665551839465	ACA	S	T1006I	C3017T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0
CAMB-71C33	MN908947.3	25430	TAACTT	-	0.0263333333333333	0.00207366666666667	9.8e-07;7.3e-08;9e-07;8.3e-07;8.6e-07;7.9e-08	NA;0.00018;0.47;0.47;NA;NA	0.0168191880234601	GTA	ORF3a	.	38-43-delinframe	.	no-SNV	GU280_gp03	0.983599644917887
CAMB-71C33	MN908947.3	256	G	A	0.064	0.097	4.2e-29	1.3e-43	0.0712696016986007	CGA	NA	NA	NA	NA	NA	NA	0.928704816965542
CAMB-71C33	MN908947.3	25688	C	T	0.026	0.012	1e-11	0.00072	0.0245851259987707	GCT	ORF3a	A99V	C296T	GCT>GTT	Missense	GU280_gp03	0.975107559926245
CAMB-71C33	MN908947.3	26774	GG	-	0.007	0.0175	NA;0.0047	7.3e-09;0.00094	0.0104264627713947	TGG	M	.	252-253-delfrshift	.	no-SNV	GU280_gp05	0.993893780176086
CAMB-71C33	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0444594594594595	0.0519189189189189	4e-06;5.5e-08;3.1e-06;4.1e-06;6.3e-06;1.2e-06;1.8e-06;6.4e-08;6.6e-08;2.6e-08;4.2e-08;3.2e-08;5.9e-08;3.8e-08;5.3e-08;8.7e-08;3.3e-08;7.4e-08;4.8e-08;4.7e-08;1.8e-08;8.2e-08;3e-08;5.4e-08;4.1e-08;2.7e-08;6.7e-08;3.3e-08;1.7e-08;3.9e-08;6.6e-08;5.2e-08;3.8e-08;6.3e-08;1.1e-08;3.3e-08;2.6e-08	1.1e-09;3.6e-12;4.5e-13;8.7e-13;3.1e-12;5.3e-14;1.4e-13;1.6e-08;1.5e-08;8.9e-09;9.2e-09;6.7e-09;1.2e-08;9.2e-09;1.4e-08;2.3e-08;7.5e-09;1.9e-08;9.2e-09;1.2e-08;5.6e-09;2.2e-08;7e-09;1.3e-08;9.6e-09;5.5e-09;1.6e-08;1.1e-08;1.7e-09;1.1e-08;1.8e-08;1.5e-08;7.1e-09;1.7e-08;1.7e-09;9.5e-09;4.8e-09	0.0467643770960129	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.960003281782008
CAMB-71C33	MN908947.3	28514	G	T	1	1	0	0	1	AGA	N	D81Y	G241T	GAT>TAT	Missense	GU280_gp10	0
CAMB-71C33	MN908947.3	28887	C	T	0.0076	0.021	8.9e-05	2.1e-09	0.0111898016997167	ACT	N	T205I	C614T	ACT>ATT	Missense	GU280_gp10	0.988810198300283
CAMB-71C33	MN908947.3	28899	G	A	0.014	0.0081	5e-08	3.3e-05	0.0125215889464594	AGA	N	R209K	G626A	AGA>AAA	Missense	GU280_gp10	0.885866436384571
CAMB-71C33	MN908947.3	28899	G	T	0.12	0.034	6.8e-54	1.3e-14	0.100316637881405	AGA	N	R209I	G626T	AGA>ATA	Missense	GU280_gp10	0.885866436384571
CAMB-71C33	MN908947.3	3037	C	T	1	1	0	0	0.999724137931034	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-71C33	MN908947.3	4340	A	G	0.017	0.035	6.2e-10	9.1e-18	0.0215847110058771	TAT	ORF1ab:nsp3	I541V	A1621G	ATT>GTT	Missense	ORF1ab:nsp3	0.978415288994123
CAMB-71C33	MN908947.3	9558	ACTCATTCTTACCTGG	-	0.0047600625	0.0205625	NA;0.00019;0.00016;0.00015;8.7e-05;4.3e-05;0.00011;NA;NA;NA;NA;NA;NA;NA;0.5;NA	1.8e-06;3.1e-06;2.9e-06;2.2e-06;7.9e-07;3.4e-07;1.3e-11;2.2e-11;1e-07;4.2e-07;1.1e-06;8.5e-07;5.3e-06;1.1e-06;5.2e-08;6.3e-07	0.0063537038229549	TAC	ORF1ab:nsp4	.	1004-1019-delfrshift	.	no-SNV	ORF1ab:nsp4	0.993696903261167
CAMB-71C42	MN908947.3	1059	C	T	1	1	0	0	0.999620320449541	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.000379679550459412
CAMB-71C42	MN908947.3	11075	T	-	0.045	0.028	4.3e-11	4.8e-08	0.0409314493602758	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95413606573013
CAMB-71C42	MN908947.3	11916	C	T	1	1	0	0	0.999157010387347	TCA	ORF1ab:nsp7	S25L	C74T	TCA>TTA	Missense	ORF1ab:nsp7	0.000414350826558459
CAMB-71C42	MN908947.3	13780	A	T	0.019	0.015	2.6e-06	1.2e-05	0.0177678178398495	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I105L	A313T	ATA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.977770218896314
CAMB-71C42	MN908947.3	14408	C	T	1	1	0	0	0.997517469657963	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00150790731886723
CAMB-71C42	MN908947.3	14772	G	T	0.0061	0.0085	7.9e-05	4.1e-06	0.00674523865506701	AGG	ORF1ab:RNA-dependent-RNA-polymerase	Q435H	G1305T	CAG>CAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993225370326828
CAMB-71C42	MN908947.3	1546	TA	-	0.002345	0.009	0.063;0.00059	0.00045;4.1e-06	0.0040842999509884	CTA	ORF1ab:nsp2	.	741-742-delfrshift	.	no-SNV	ORF1ab:nsp2	0.995560867338228
CAMB-71C42	MN908947.3	1547	A	G	0.012	0.017	1.3e-06	4.7e-08	0.0133166222779257	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.961930126899577
CAMB-71C42	MN908947.3	1547	A	T	0.017	0.02	6.4e-09	1.7e-09	0.0180166066113113	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.961930126899577
CAMB-71C42	MN908947.3	17807	A	G	0.016	0.02	9e-09	7.1e-11	0.0168210214152021	AAG	ORF1ab:helicase	K524R	A1571G	AAG>AGG	Missense	ORF1ab:helicase	0.982401127883517
CAMB-71C42	MN908947.3	21727	C	T	0.0085	0.0051	2.4e-05	0.00076	0.00706455542021924	TCT	S	F55F	C165T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.992935444579781
CAMB-71C42	MN908947.3	23403	A	G	1	1	0	0	0.999731159801058	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000232180171813327
CAMB-71C42	MN908947.3	23893	C	T	0.0069	0.0063	2.7e-05	4.2e-05	0.0067859543548542	ACA	S	N777N	C2331T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.993182036426491
CAMB-71C42	MN908947.3	241	C	T	1	0.99	0	0	0.99822629687644	TCG	NA	NA	NA	NA	NA	NA	0.00110568506403759
CAMB-71C42	MN908947.3	24781	G	C	0.21	0.2	3.4e-101	5.6e-94	0.208149641012722	AGA	S	K1073N	G3219C	AAG>AAC	Missense	GU280_gp02, spike glycoprotein	0.791787378763068
CAMB-71C42	MN908947.3	25563	G	T	1	1	0	0	0.999215453446704	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000636118826996883
CAMB-71C42	MN908947.3	27561	G	T	0.0038	0.023	0.006	1.4e-05	0.00855920114122682	TGA	ORF7a	L56L	G168T	CTG>CTT	Synonymous	GU280_gp07	0.991440798858773
CAMB-71C42	MN908947.3	27987	G	A	0.12	0.11	1.4e-50	1.5e-45	0.1157982791587	TGT	ORF8	V32I	G94A	GTA>ATA	Missense	GU280_gp09	0.8842017208413
CAMB-71C42	MN908947.3	29240	GAA	-	0.0038	0.00786666666666667	0.004;0.00044;0.0011	0.00051;1.2e-06;5.7e-05	0.00592602921183811	GGA	N	.	967-969-delinframe	.	no-SNV	GU280_gp10	0.997400192314541
CAMB-71C42	MN908947.3	29242	A	G	0.0066	0.0098	9.1e-05	3.5e-06	0.00775945683802134	AAG	N	E323E	A969G	GAA>GAG	Synonymous	GU280_gp10	0.979700706664819
CAMB-71C42	MN908947.3	29242	A	T	0.0078	0.0045	2.7e-05	0.00084	0.00665096300401829	AAG	N	E323D	A969T	GAA>GAT	Missense	GU280_gp10	0.979700706664819
CAMB-71C42	MN908947.3	3037	C	T	1	1	0	0	0.998146813548852	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00113250283125708
CAMB-71C42	MN908947.3	3120	A	G	0.0093	0.0058	3.5e-06	9.8e-05	0.00740410347903657	GAA	ORF1ab:nsp3	E134G	A401G	GAA>GGA	Missense	ORF1ab:nsp3	0.992595896520963
CAMB-71C42	MN908947.3	3527	G	A	0.013	0.0018	1.8e-06	0.0062	0.0065756196256955	TGA	ORF1ab:nsp3	D270N	G808A	GAT>AAT	Missense	ORF1ab:nsp3	0.991906929691452
CAMB-71C42	MN908947.3	3738	C	T	0.018	0.0048	1e-07	0.0011	0.0107584722969338	CCT	ORF1ab:nsp3	P340L	C1019T	CCT>CTT	Missense	ORF1ab:nsp3	0.989241527703066
CAMB-71C42	MN908947.3	4071	C	T	0.0048	0.0086	0.00024	4e-06	0.00552385577273279	ACT	ORF1ab:nsp3	T451I	C1352T	ACT>ATT	Missense	ORF1ab:nsp3	0.994476144227267
CAMB-71C42	MN908947.3	4454	G	T	0.0081	0.0055	1.1e-05	0.00016	0.00747287762688719	AGC	ORF1ab:nsp3	A579S	G1735T	GCC>TCC	Missense	ORF1ab:nsp3	0.992527122373113
CAMB-71C42	MN908947.3	635	C	T	0.0096	0.0053	9.7e-06	0.00076	0.00849983886561392	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.991480019336126
CAMB-71C51	MN908947.3	14408	C	T	1	1	0	0	0.999682085518995	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00031791448100461
CAMB-71C51	MN908947.3	18657	C	T	1	1	0	0	0.999865174598894	CCT	ORF1ab:3'-to-5'-exonuclease	T206T	C618T	ACC>ACT	Synonymous	ORF1ab:3'-to-5'-exonuclease	8.98836007370455e-05
CAMB-71C51	MN908947.3	23403	A	G	1	1	0	0	1	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-71C51	MN908947.3	23466	T	C	1	1	0	0	0.999922296903532	GTT	S	V635A	T1904C	GTT>GCT	Missense	GU280_gp02, spike glycoprotein	3.88515482341971e-05
CAMB-71C51	MN908947.3	241	C	T	1	1	0	0	1	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-71C51	MN908947.3	28253	C	T	0.28	0.11	1.9e-137	2.9e-49	0.236291431189858	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.763708568810142
CAMB-71C51	MN908947.3	28514	G	T	1	1	2.3e-254	0	1	AGA	N	D81Y	G241T	GAT>TAT	Missense	GU280_gp10	0
CAMB-71C51	MN908947.3	3037	C	T	1	1	7.9e-124	7.6e-230	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-71C60	MN908947.3	10202	C	T	0.0082	0.01	1.6e-05	1.6e-06	0.00929030670317163	GCT	ORF1ab:3C-like-proteinase	L50F	C148T	CTT>TTT	Missense	ORF1ab:3C-like-proteinase	0.990617405481896
CAMB-71C60	MN908947.3	11075	T	-	0.055	0.042	2.1e-13	5.1e-11	0.0508138094165353	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.94666591574679
CAMB-71C60	MN908947.3	1191	C	T	0.0074	0.0091	3.9e-05	6.8e-06	0.00823755413017289	CCA	ORF1ab:nsp2	P129L	C386T	CCA>CTA	Missense	ORF1ab:nsp2	0.991729886367336
CAMB-71C60	MN908947.3	14408	C	T	0.99	1	0	0	0.994982746995598	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000535438067663507
CAMB-71C60	MN908947.3	15493	G	C	0.01	0.011	5.3e-06	4.3e-06	0.0102433313822226	TGC	ORF1ab:RNA-dependent-RNA-polymerase	A676P	G2026C	GCC>CCC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.989380382975165
CAMB-71C60	MN908947.3	17158	G	T	0.025	0.058	1.2e-12	1.9e-27	0.0350225428313796	AGC	ORF1ab:helicase	A308S	G922T	GCT>TCT	Missense	ORF1ab:helicase	0.96497745716862
CAMB-71C60	MN908947.3	18687	C	T	0.017	0.033	1.1e-08	6.6e-16	0.023180882484561	GCT	ORF1ab:3'-to-5'-exonuclease	C216C	C648T	TGC>TGT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.976774366777052
CAMB-71C60	MN908947.3	18924	A	G	0.15	0.16	1.1e-69	2.2e-77	0.154492609949531	AAT	ORF1ab:3'-to-5'-exonuclease	E295E	A885G	GAA>GAG	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.84547359408796
CAMB-71C60	MN908947.3	21431	C	T	0.013	0.035	3.4e-06	4.3e-10	0.0200308166409861	GCT	ORF1ab:2'-O-ribose-methyltransferase	A258V	C773T	GCT>GTT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.979969183359014
CAMB-71C60	MN908947.3	22208	C	T	0.02	0.0037	9.7e-11	0.003	0.018019884009942	TCT	S	L216F	C646T	CTC>TTC	Missense	GU280_gp02, spike glycoprotein	0.981980115990058
CAMB-71C60	MN908947.3	22351	A	G	1	0.97	2.4e-111	1e-242	0.976973684210526	CAG	S	A263A	A789G	GCA>GCG	Synonymous	GU280_gp02, spike glycoprotein	0.0230263157894737
CAMB-71C60	MN908947.3	23403	A	G	1	1	0	0	0.999803211131304	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000162061421278665
CAMB-71C60	MN908947.3	241	C	T	1	0.99	0	0	0.997793864184764	TCG	NA	NA	NA	NA	NA	NA	0.000229805814087096
CAMB-71C60	MN908947.3	25429	G	T	1	1	0	0	0.999882214369847	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	7.85237534354142e-05
CAMB-71C60	MN908947.3	25710	C	T	0.0055	0.044	0.00025	1.5e-13	0.00992501102779003	TCT	ORF3a	L106L	C318T	CTC>CTT	Synonymous	GU280_gp03	0.99007498897221
CAMB-71C60	MN908947.3	26461	C	T	0.98	1	0	0	0.987360901222695	TCT	E	L73F	C217T	CTT>TTT	Missense	GU280_gp04	9.15876722993085e-05
CAMB-71C60	MN908947.3	26906	T	C	0.0076	0.0078	3.1e-05	2.7e-05	0.00767424305963264	TTC	M	I128I	T384C	ATT>ATC	Synonymous	GU280_gp05	0.992283821185943
CAMB-71C60	MN908947.3	28292	C	A	0.021	0.044	3.5e-11	3.3e-21	0.0294014405863439	CCA	N	Q7K	C19A	CAA>AAA	Missense	GU280_gp10	0.97050027379565
CAMB-71C60	MN908947.3	28703	G	C	0.022	0.019	1.2e-11	2.4e-10	0.0204555506413092	AGA	N	D144H	G430C	GAT>CAT	Missense	GU280_gp10	0.979433878814684
CAMB-71C60	MN908947.3	29716	A	G	0.092	0.1	2.2e-24	4.7e-35	0.0987012987012987	GAG	NA	NA	NA	NA	NA	NA	0.901298701298701
CAMB-71C60	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-71C60	MN908947.3	4931	C	T	0.042	0.0087	1.9e-20	3.6e-06	0.0271459059913591	TCT	ORF1ab:nsp3	L738F	C2212T	CTT>TTT	Missense	ORF1ab:nsp3	0.972854094008641
CAMB-71C60	MN908947.3	5622	C	T	0.022	0.095	2.3e-11	1.4e-40	0.0382022471910112	CCT	ORF1ab:nsp3	P968L	C2903T	CCT>CTT	Missense	ORF1ab:nsp3	0.961640972040763
CAMB-71C7F	MN908947.3	10097	G	A	1	1	0	0	0.999715261958998	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000284738041002278
CAMB-71C7F	MN908947.3	13536	C	T	1	1	0	3e-86	1	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-71C7F	MN908947.3	13963	T	-	0.00045	0.0078	0.0097	4.6e-05	0.00079370805974457	ATA	ORF1ab:RNA-dependent-RNA-polymerase	.	496-496-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.999206291940255
CAMB-71C7F	MN908947.3	13965	C	A	0.00045	0.0078	0.0086	2.5e-05	0.000787796318842656	ACG	ORF1ab:RNA-dependent-RNA-polymerase	Y166*	C498A	TAC>TAA	Nonsense	ORF1ab:RNA-dependent-RNA-polymerase	0.99885411444532
CAMB-71C7F	MN908947.3	14184	C	T	1	1	0	0	0.999925600773752	CCA	ORF1ab:RNA-dependent-RNA-polymerase	T239T	C717T	ACC>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	7.4399226248047e-05
CAMB-71C7F	MN908947.3	14408	C	T	1	1	0	0	0.999859550561798	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000140449438202247
CAMB-71C7F	MN908947.3	1684	C	T	1	1	0	0	0.999876130310913	TCG	ORF1ab:nsp2	I293I	C879T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.00012386968908708
CAMB-71C7F	MN908947.3	21058	C	T	1	1	0	0	1	CCC	ORF1ab:2'-O-ribose-methyltransferase	P134S	C400T	CCT>TCT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0
CAMB-71C7F	MN908947.3	23403	A	G	1	1	0	0	0.999799931405053	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000171487367097291
CAMB-71C7F	MN908947.3	23731	C	T	1	1	0	0	1	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-71C7F	MN908947.3	26978	T	C	0.0033	0.28	0.0051	6.1e-92	0.0572882105728821	CTG	M	A152A	T456C	GCT>GCC	Synonymous	GU280_gp05	0.942711789427118
CAMB-71C7F	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999556147359077	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-71C7F	MN908947.3	3037	C	T	1	1	3.8e-191	1e-246	0.997097242380261	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-71C7F	MN908947.3	4002	C	T	1	1	0	3.5e-59	1	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-71C8E	MN908947.3	10097	G	A	1	1	0	0	0.999734439834025	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000199170124481328
CAMB-71C8E	MN908947.3	11075	T	-	0.035	0.031	4e-09	7.5e-09	0.0342051913980204	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961581269626744
CAMB-71C8E	MN908947.3	11083	G	T	0.023	0.024	4e-05	1.8e-05	0.0229461096443547	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.97091939742196
CAMB-71C8E	MN908947.3	1346	C	A	0.19	0.18	1.1e-83	8.8e-78	0.185082872928177	ACC	ORF1ab:nsp2	P181T	C541A	CCC>ACC	Missense	ORF1ab:nsp2	0.814522494080505
CAMB-71C8E	MN908947.3	13536	C	T	1	1	0	0	0.99973591936738	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	8.80268775399422e-05
CAMB-71C8E	MN908947.3	14408	C	T	1	1	0	0	0.997899257737734	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000451270560042326
CAMB-71C8E	MN908947.3	21137	A	G	0.036	0.038	7.8e-15	1e-15	0.036668960770819	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.963331039229181
CAMB-71C8E	MN908947.3	23403	A	G	1	1	0	0	0.999492954175734	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.5071092049944e-05
CAMB-71C8E	MN908947.3	23595	C	T	0.0079	0.0088	1.9e-05	5.9e-06	0.00814062709665877	ACT	S	T678I	C2033T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.991367356979917
CAMB-71C8E	MN908947.3	23731	C	T	1	1	0	0	0.999705869994538	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000210092861044582
CAMB-71C8E	MN908947.3	241	C	T	1	1	0	0	0.998664143381944	TCG	NA	NA	NA	NA	NA	NA	9.27678206983562e-05
CAMB-71C8E	MN908947.3	25617	G	T	0.0097	0.0081	2.4e-06	6.1e-06	0.00928190413834274	AGG	ORF3a	K75N	G225T	AAG>AAT	Missense	GU280_gp03	0.99052552523638
CAMB-71C8E	MN908947.3	26501	G	T	0.0078	0.009	3.7e-05	6.1e-06	0.00806550378781252	TGT	NA	NA	NA	NA	NA	NA	0.991619574155397
CAMB-71C8E	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999178082191781	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-71C8E	MN908947.3	3037	C	T	1	1	0	0	0.999581852393895	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.3629521220991e-05
CAMB-71C8E	MN908947.3	4002	C	T	1	1	0	0	0.999868863924466	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-71C8E	MN908947.3	5339	C	T	0.0087	0.0073	1.2e-05	3.6e-05	0.00818452380952381	TCC	ORF1ab:nsp3	P874S	C2620T	CCA>TCA	Missense	ORF1ab:nsp3	0.991650132275132
CAMB-71C8E	MN908947.3	5713	T	C	0.19	0.2	6.9e-91	1.6e-91	0.195459897587557	TTA	ORF1ab:nsp3	L998L	T2994C	CTT>CTC	Synonymous	ORF1ab:nsp3	0.804457953394124
CAMB-71C8E	MN908947.3	7083	C	T	0.0091	0.012	7e-05	5.1e-06	0.010221592180855	TCT	ORF1ab:nsp3	S1455F	C4364T	TCT>TTT	Missense	ORF1ab:nsp3	0.989778407819145
CAMB-71C8E	MN908947.3	9600	T	G	0.01	0.011	6.3e-07	2.3e-07	0.0102139295480135	TTG	ORF1ab:nsp4	L349W	T1046G	TTG>TGG	Missense	ORF1ab:nsp4	0.98942415956249
CAMB-71C9D	MN908947.3	11075	T	-	0.03	0.044	1.4e-07	1.3e-11	0.0336922004492293	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.96152782234418
CAMB-71C9D	MN908947.3	14408	C	T	1	1	0	0	0.999056346354996	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000397926235845195
CAMB-71C9D	MN908947.3	21801	A	C	1	1	0	0	0.999518459069021	GAT	S	D80A	A239C	GAT>GCT	Missense	GU280_gp02, spike glycoprotein	0.000107009095773141
CAMB-71C9D	MN908947.3	22972	T	C	0.12	0.11	7.7e-52	1.8e-48	0.112463509969818	CTG	S	T470T	T1410C	ACT>ACC	Synonymous	GU280_gp02, spike glycoprotein	0.88743753401613
CAMB-71C9D	MN908947.3	23403	A	G	1	1	0	0	0.999335377417011	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000106339613278273
CAMB-71C9D	MN908947.3	241	C	T	1	1	0	0	0.99858274159142	TCG	NA	NA	NA	NA	NA	NA	0.000102276380000584
CAMB-71C9D	MN908947.3	2416	C	T	1	1	0	0	0.998519103564024	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	9.87264290650607e-05
CAMB-71C9D	MN908947.3	25563	G	T	1	1	0	0	0.999827705031013	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	7.8315894994048e-05
CAMB-71C9D	MN908947.3	26052	T	C	0.067	0.064	2.6e-29	5.1e-28	0.0662049861495845	GTA	ORF3a	S220S	T660C	AGT>AGC	Synonymous	GU280_gp03	0.933564173591874
CAMB-71C9D	MN908947.3	3037	C	T	1	1	0	0	0.998894602777911	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000192242995145864
CAMB-71C9D	MN908947.3	355	C	T	0.011	0.011	1.3e-06	5.5e-07	0.0107371426497453	GCT	ORF1ab:leader-protein	G30G	C90T	GGC>GGT	Synonymous	ORF1ab:leader-protein	0.989232611878002
CAMB-71C9D	MN908947.3	4755	C	T	1	1	0	0	0.999481092300707	CCT	ORF1ab:nsp3	P679L	C2036T	CCT>CTT	Missense	ORF1ab:nsp3	0.000492962314328339
CAMB-71CAC	MN908947.3	13730	C	T	1	1	0	0	0.999831337493675	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A88V	C263T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000168662506324844
CAMB-71CAC	MN908947.3	14408	C	T	1	1	0	0	0.999570188257543	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000343849393965443
CAMB-71CAC	MN908947.3	23403	A	G	1	1	0	0	0.999735262972114	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000176491351923756
CAMB-71CAC	MN908947.3	241	C	T	1	1	0	0	0.999719442626017	TCG	NA	NA	NA	NA	NA	NA	0.000187038249321986
CAMB-71CAC	MN908947.3	25429	G	T	1	1	0	0	1	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0
CAMB-71CBB	MN908947.3	11075	T	-	0.043	0.041	9.2e-11	1e-10	0.0418899096734347	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953956612367791
CAMB-71CBB	MN908947.3	11842	G	T	1	1	0	0	0.999854693403081	AGT	ORF1ab:nsp6	Q290H	G870T	CAG>CAT	Missense	ORF1ab:nsp6	0
CAMB-71CBB	MN908947.3	14408	C	T	1	1	0	0	0.997925820801834	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00043666930487705
CAMB-71CBB	MN908947.3	23403	A	G	1	1	0	0	0.998668552024523	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000144498229896684
CAMB-71CBB	MN908947.3	241	C	T	1	1	0	0	0.998681466944683	TCG	NA	NA	NA	NA	NA	NA	0.000275972034833804
CAMB-71CBB	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99906160897968	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000200064020486556
CAMB-71CBB	MN908947.3	3037	C	T	1	1	0	0	0.999262962250849	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.61353585848875e-05
CAMB-71CBB	MN908947.3	4207	GA	TC	1	1	0;0	0;0	0.99898490338877	CGA	ORF1ab:nsp3	.	1488-1489-mnv	.	no-SNV	ORF1ab:nsp3	0
CAMB-71CCA	MN908947.3	11074	C	INS	0.02	0.026	0.00073	3.4e-05	0.0222924068956442	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.975365179628899
CAMB-71CCA	MN908947.3	11075	T	-	0.04	0.036	9.5e-10	1.9e-09	0.038375288556667	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95778828185116
CAMB-71CCA	MN908947.3	12400	C	T	0.023	0.019	2.1e-11	3.1e-10	0.0215221193635084	TCA	ORF1ab:nsp8	L103L	C309T	CTC>CTT	Synonymous	ORF1ab:nsp8	0.978413890192398
CAMB-71CCA	MN908947.3	1440	G	A	1	1	0	0	0.99984375	GGC	ORF1ab:nsp2	G212D	G635A	GGC>GAC	Missense	ORF1ab:nsp2	0.00015625
CAMB-71CCA	MN908947.3	14937	C	T	0.0084	0.0056	1e-05	0.00018	0.00698740486893053	ACA	ORF1ab:RNA-dependent-RNA-polymerase	D490D	C1470T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.992923583604077
CAMB-71CCA	MN908947.3	16391	C	T	0.013	0.0037	2e-07	0.0012	0.00680631731976475	GCT	ORF1ab:helicase	A52V	C155T	GCT>GTT	Missense	ORF1ab:helicase	0.993193682680235
CAMB-71CCA	MN908947.3	16967	A	G	0.013	0.0086	1.3e-07	6e-06	0.0112056273515459	GAG	ORF1ab:helicase	E244G	A731G	GAG>GGG	Missense	ORF1ab:helicase	0.988761655488304
CAMB-71CCA	MN908947.3	17505	T	C	0.028	0.033	4.6e-14	2e-16	0.030405200170099	ATT	ORF1ab:helicase	N423N	T1269C	AAT>AAC	Synonymous	ORF1ab:helicase	0.969579612417229
CAMB-71CCA	MN908947.3	19137	A	T	0.0045	0.0062	0.00038	4.4e-05	0.00515692580680936	TAT	ORF1ab:3'-to-5'-exonuclease	L366F	A1098T	TTA>TTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.994787623378064
CAMB-71CCA	MN908947.3	20275	G	T	0.025	0.0069	3.1e-07	0.002	0.0172910662824208	GGA	ORF1ab:endoRNAse	D219Y	G655T	GAT>TAT	Missense	ORF1ab:endoRNAse	0.979827089337176
CAMB-71CCA	MN908947.3	20486	A	C	0.011	0.02	0.00039	2.7e-05	0.0145867098865478	AAG	ORF1ab:endoRNAse	K289T	A866C	AAG>ACG	Missense	ORF1ab:endoRNAse	0.983792544570502
CAMB-71CCA	MN908947.3	23086	C	T	0.0077	0.0061	2.2e-05	1e-04	0.00693756194251734	ACA	S	Y508Y	C1524T	TAC>TAT	Synonymous	GU280_gp02, spike glycoprotein	0.993062438057483
CAMB-71CCA	MN908947.3	24193	G	T	1	1	0	0	0.998891922909494	TGT	S	L877L	G2631T	CTG>CTT	Synonymous	GU280_gp02, spike glycoprotein	0.000237445090822747
CAMB-71CCA	MN908947.3	26681	C	T	0.0074	0.0092	0.00018	2.7e-05	0.00808928665995869	TCC	M	F53F	C159T	TTC>TTT	Synonymous	GU280_gp05	0.99151353068898
CAMB-71CCA	MN908947.3	27341	A	G	0.013	0.013	1.2e-07	7.7e-08	0.0130666343216928	AAT	ORF6	N47S	A140G	AAT>AGT	Missense	GU280_gp06	0.986812072026376
CAMB-71CCA	MN908947.3	27669	A	G	1	1	0	0	1	AAG	ORF7a	E92E	A276G	GAA>GAG	Synonymous	GU280_gp07	0
CAMB-71CCA	MN908947.3	27792	TT	-	0.0275	0.04	1.8e-07;2.4e-08	1.3e-09;1.8e-09	0.0324324324324324	CTT	NA	NA	NA	NA	NA	NA	0.966117216117216
CAMB-71CCA	MN908947.3	28223	G	A	0.0083	0.0058	1.2e-05	7.2e-05	0.0074101686491127	AGT	ORF8	E110E	G330A	GAG>GAA	Synonymous	GU280_gp09	0.99218317575429
CAMB-71CCA	MN908947.3	28253	C	T	0.038	0.04	4e-17	2.4e-18	0.0390137399693651	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.960449006652797
CAMB-71CCA	MN908947.3	2891	G	A	1	1	0	0	0.99906425452277	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	0.000249532127261385
CAMB-71CCA	MN908947.3	4071	C	A	0.017	0.011	3e-09	2.7e-07	0.0151686197192056	ACT	ORF1ab:nsp3	T451N	C1352A	ACT>AAT	Missense	ORF1ab:nsp3	0.984799580239454
CAMB-71CCA	MN908947.3	635	C	T	0.025	0.028	3.8e-12	1.2e-13	0.0260630154575535	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.973924638253741
CAMB-71CCA	MN908947.3	8977	G	T	0.052	0.063	5.2e-24	3.6e-29	0.0567477145353421	AGT	ORF1ab:nsp4	E141D	G423T	GAG>GAT	Missense	ORF1ab:nsp4	0.943209666077098
CAMB-71CD9	MN908947.3	11075	T	-	0.038	0.04	2.9e-09	2.3e-10	0.0382803955268856	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957244257940671
CAMB-71CD9	MN908947.3	12845	G	T	0.019	0.018	6.7e-10	6.1e-10	0.0185948548217241	GGC	ORF1ab:nsp9	A54S	G160T	GCT>TCT	Missense	ORF1ab:nsp9	0.981224612607191
CAMB-71CD9	MN908947.3	1440	G	A	1	1	0	0	0.999786142001711	GGC	ORF1ab:nsp2	G212D	G635A	GGC>GAC	Missense	ORF1ab:nsp2	0
CAMB-71CD9	MN908947.3	20527	G	T	0.017	0.015	4.4e-09	1.8e-08	0.0158946522892681	TGT	ORF1ab:endoRNAse	V303F	G907T	GTT>TTT	Missense	ORF1ab:endoRNAse	0.984032324805881
CAMB-71CD9	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0231875	0.025625	0.0022;0.0043;0.0013;0.0013;0.00065;0.00087;0.00076;0.0011;8e-04;0.00092;0.0013;7e-04;0.0012;0.00092;0.00091;0.00085;0.0013;0.00085;0.0011;9e-04;0.00069;0.0011;0.00082;0.00026;0.00093;0.0011;9e-04;0.00063;0.0011;0.00058;0.00083;0.00074	0.00035;8e-04;4e-04;0.00036;0.00026;0.00025;0.00022;0.00029;0.00027;3e-04;0.00045;0.00023;4e-04;0.00026;0.00033;0.00032;0.00044;0.00029;0.00037;0.00031;2e-04;4e-04;0.00032;4.4e-05;0.00034;0.00043;4e-04;0.00018;0.00042;0.00015;0.00033;0.00021	0.0237252704353411	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.977086919104991
CAMB-71CD9	MN908947.3	28362	G	T	1	1	0	0	0.99967233168771	GGA	N	G30V	G89T	GGA>GTA	Missense	GU280_gp10	4.36891083052995e-05
CAMB-71CD9	MN908947.3	28708	C	T	1	1	0	0	0.998969650135612	ACA	N	H145H	C435T	CAC>CAT	Synonymous	GU280_gp10	0.000515174932193888
CAMB-71CD9	MN908947.3	2891	G	A	1	1	0	0	0.999691820022893	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	0.000264154266091397
CAMB-71CD9	MN908947.3	3877	T	G	0.027	0.033	3.1e-13	1.4e-15	0.028585916207137	CTG	ORF1ab:nsp3	A386A	T1158G	GCT>GCG	Synonymous	ORF1ab:nsp3	0.970590099511948
CAMB-71CD9	MN908947.3	4668	C	T	1	1	0	0	0.998763471936666	TCT	ORF1ab:nsp3	S650F	C1949T	TCT>TTT	Missense	ORF1ab:nsp3	0.000439004046153959
CAMB-71CD9	MN908947.3	7768	C	T	0.02	0.029	3.5e-10	1.6e-13	0.0234954657873042	TCC	ORF1ab:nsp3	I1683I	C5049T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.976504534212696
CAMB-71CE8	MN908947.3	11074	C	INS	0.12	0.084	1.2e-52	4.2e-23	0.113112514939389	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.886392351032952
CAMB-71CE8	MN908947.3	11083	G	-	0.18	0.13	7.6e-82	1.6e-55	0.166240093743254	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-71CE8	MN908947.3	11083	G	T	0.82	0.87	0	0	0.833621141570816	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-71CE8	MN908947.3	14805	C	T	1	1	0	0	0.999866128204556	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	6.69358977219483e-05
CAMB-71CE8	MN908947.3	15759	A	G	0.016	0.019	3.5e-09	1.5e-10	0.0176927387719158	AAG	ORF1ab:RNA-dependent-RNA-polymerase	Q764Q	A2292G	CAA>CAG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.982267232407333
CAMB-71CE8	MN908947.3	16247	CT	GC	0.0145	0.0135	1.2e-06;2.6e-06	NA;1.2e-11	0.0129819040125885	GCT	ORF1ab:helicase	.	11-12-mnv	.	no-SNV	ORF1ab:helicase	0.996336996336996
CAMB-71CE8	MN908947.3	16248	T	C	0.016	0.027	2.6e-06	1.2e-11	0.0242243943901402	CTT	ORF1ab:helicase	A4A	T12C	GCT>GCC	Synonymous	ORF1ab:helicase	0.97577560560986
CAMB-71CE8	MN908947.3	16325	G	T	0.0058	0.019	0.00092	2e-09	0.0158618258724004	TGT	ORF1ab:helicase	C30F	G89T	TGT>TTT	Missense	ORF1ab:helicase	0.9841381741276
CAMB-71CE8	MN908947.3	18634	G	T	0.014	0.012	6e-08	1.1e-07	0.013140990346144	TGT	ORF1ab:3'-to-5'-exonuclease	V199L	G595T	GTG>TTG	Missense	ORF1ab:3'-to-5'-exonuclease	0.986803949638439
CAMB-71CE8	MN908947.3	22205	G	T	0.035	0.1	2.1e-16	1.3e-31	0.0456095481670929	TGA	S	D215Y	G643T	GAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.954390451832907
CAMB-71CE8	MN908947.3	25123	T	C	0.089	0.33	1.2e-39	5.7e-156	0.173809198853555	ATG	S	N1187N	T3561C	AAT>AAC	Synonymous	GU280_gp02, spike glycoprotein	0.826122560393067
CAMB-71CE8	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-71CE8	MN908947.3	26144	G	T	1	1	0	5.5e-253	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-71CE8	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.0146411666666667	0.0380555555555556	NA;NA;0.018;0.018;0.012;0.015;0.014;0.018;0.016;0.016;0.021;0.014;0.019;0.016;0.016;0.014;0.021;0.016;0.017;0.016;0.015;0.019;0.015;0.0091;0.015;0.018;0.018;0.014;0.019;0.013;0.014;0.013;0.019;0.028;0.021;0.022	6.6e-08;2.5e-07;2.2e-06;2.2e-06;1.5e-06;1.3e-06;9.6e-07;1.8e-06;1.4e-06;1.8e-06;3.1e-06;1.2e-06;2.5e-06;1.5e-06;1.8e-06;1.4e-06;3e-06;1.8e-06;2.1e-06;1.5e-06;9.4e-07;2.2e-06;1.6e-06;5.3e-07;1.4e-06;2.4e-06;2.2e-06;9.5e-07;2.3e-06;4.3e-07;1.4e-06;6.8e-07;2.9e-05;0.00014;5.3e-05;8.2e-05	0.0253440115036648	GTA	M	.	263-298-delinframe	.	no-SNV	GU280_gp05	0.979105348933376
CAMB-71CE8	MN908947.3	26940	ATCGGAGCTGTGATCCTTCGTGGACATCTTCGTATT	-	0.000388888888888889	0.0143333333333333	NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00015;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	1.7e-07;1.6e-07;1.9e-07;1.8e-07;2.8e-07;3.2e-07;2.2e-07;2.3e-07;6.7e-05;0.00019;2.6e-07;3.2e-07;3.7e-07;3e-07;3.6e-07;2.3e-07;3.5e-07;3.4e-07;6.1e-07;4.1e-07;2e-07;2.6e-07;1.7e-07;1.8e-07;2.3e-07;1.4e-07;1.1e-07;1.5e-07;4.3e-08;1.6e-08;1e-07;1.3e-07;2.4e-08;4.7e-08;5.1e-08;7.3e-08	0.00412630068173663	AAT	M	.	418-453-delinframe	.	no-SNV	GU280_gp05	0.995808997280307
CAMB-71CE8	MN908947.3	28851	G	T	1	1	0	0	0.998905459023122	AGT	N	S193I	G578T	AGT>ATT	Missense	GU280_gp10	0.000273635244219455
CAMB-71CE8	MN908947.3	29543	G	C	0.021	0.0042	8.9e-10	0.00088	0.0131474103585657	AGA	NA	NA	NA	NA	NA	NA	0.986852589641434
CAMB-71CF7	MN908947.3	11074	C	INS	0.11	0.12	1.1e-48	3.3e-38	0.112273117817635	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.88263881430566
CAMB-71CF7	MN908947.3	11083	G	-	0.16	0.16	2.2e-71	8.5e-73	0.163194529847259	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-71CF7	MN908947.3	11083	G	T	0.84	0.84	0	0	0.836694788105369	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-71CF7	MN908947.3	13458	C	T	1	1	0	0	0.997778941854374	TCG	ORF1ab:nsp11	S6L	C17T	TCG>TTG	Missense	ORF1ab:nsp11	0.000293347302252488
CAMB-71CF7	MN908947.3	14805	C	T	1	1	0	0	0.998656809552517	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000507662531332297
CAMB-71CF7	MN908947.3	17247	T	C	1	1	0	0	0.99941668286992	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000349990278047832
CAMB-71CF7	MN908947.3	17288	C	T	0.026	0.024	5e-13	9.2e-13	0.0255127703571229	ACA	ORF1ab:helicase	T351I	C1052T	ACA>ATA	Missense	ORF1ab:helicase	0.974473257698541
CAMB-71CF7	MN908947.3	26144	G	T	1	1	0	0	0.999743194658449	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000192604006163328
CAMB-71CF7	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0195	0.02728125	0.0089;0.015;0.0042;0.0042;0.0023;0.0033;0.0032;0.004;0.0036;0.0038;0.0047;0.0034;0.0045;0.0036;0.0035;0.0033;0.005;0.0037;0.0041;0.0036;0.0035;0.0045;0.0032;0.0013;0.0035;0.0042;0.004;0.0031;0.0043;0.0025;0.0032;0.0027	0.00029;0.00071;2e-04;0.00019;0.00012;0.00012;0.00012;0.00015;0.00014;0.00016;2e-04;0.00012;0.00017;0.00011;0.00015;0.00015;0.00023;0.00015;0.00017;0.00013;0.00011;0.00018;0.00014;2e-05;0.00014;0.00018;0.00017;8e-05;0.00017;4.6e-05;0.00011;7.2e-05	0.0218676718122833	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.979766495852924
CAMB-71CF7	MN908947.3	28332	C	T	0.087	0.093	1.4e-39	5.4e-43	0.0886338585229852	CCC	N	P20L	C59T	CCC>CTC	Missense	GU280_gp10	0.911314270894119
CAMB-71CF7	MN908947.3	29000	G	T	0.041	0.041	2.2e-18	1.4e-18	0.0408502300221503	AGG	N	G243C	G727T	GGC>TGC	Missense	GU280_gp10	0.959107173283353
CAMB-71CF7	MN908947.3	29392	G	T	0.0044	0.0078	0.0012	4.2e-05	0.00525177633611369	AGA	N	K373N	G1119T	AAG>AAT	Missense	GU280_gp10	0.994645247657296
CAMB-71CF7	MN908947.3	8293	C	T	1	1	0	0	0.999895684829097	CCT	ORF1ab:nsp3	T1858T	C5574T	ACC>ACT	Synonymous	ORF1ab:nsp3	8.11340218134613e-05
CAMB-71CF7	MN908947.3	9866	C	T	0.037	0.037	2.4e-17	1.8e-17	0.037072722096919	TCT	ORF1ab:nsp4	L438F	C1312T	CTT>TTT	Missense	ORF1ab:nsp4	0.962795892000788
CAMB-71D03	MN908947.3	11074	C	INS	0.02	0.027	0.00087	3.1e-05	0.0218322208779109	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.977433694484849
CAMB-71D03	MN908947.3	11075	T	-	0.034	0.027	1.6e-08	1.2e-07	0.0320877102347741	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.963607140807072
CAMB-71D03	MN908947.3	14408	C	T	1	1	0	0	0.997007616974973	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000457513107132258
CAMB-71D03	MN908947.3	20679	G	T	1	1	0	0	0.999671313922594	CGG	ORF1ab:2'-O-ribose-methyltransferase	P7P	G21T	CCG>CCT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	5.47810129009285e-05
CAMB-71D03	MN908947.3	23403	A	G	1	1	0	0	0.999173583414178	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.28795228342496e-05
CAMB-71D03	MN908947.3	241	C	T	1	1	0	0	0.999331483771769	TCG	NA	NA	NA	NA	NA	NA	5.0138717117358e-05
CAMB-71D03	MN908947.3	24262	G	T	0.68	0.7	0	0	0.683806631648063	TGC	S	M900I	G2700T	ATG>ATT	Missense	GU280_gp02, spike glycoprotein	0.316070256073539
CAMB-71D03	MN908947.3	25361	G	T	0.016	0.016	4.7e-09	3.2e-09	0.0163473053892216	AGG	S	G1267*	G3799T	GGA>TGA	Nonsense	GU280_gp02, spike glycoprotein	0.983473053892216
CAMB-71D03	MN908947.3	26031	G	T	0.67	0.68	0	0	0.670039215686275	AGC	ORF3a	Q213H	G639T	CAG>CAT	Missense	GU280_gp03	0.329725490196078
CAMB-71D03	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999135396852845	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	3.79333889689705e-05
CAMB-71D03	MN908947.3	3037	C	T	1	1	0	0	0.999718468468468	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.63063063063063e-05
CAMB-71D03	MN908947.3	522	TT	-	0.024	0.034	0.00085;0.0074	1.9e-05;6e-04	0.0268021604071056	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.967237708091367
CAMB-71D12	MN908947.3	11075	T	-	0.04	0.041	1.2e-10	2.3e-11	0.0401178143408491	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955413365833841
CAMB-71D12	MN908947.3	14408	C	T	1	1	0	0	0.998559982276705	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000480005907765019
CAMB-71D12	MN908947.3	23403	A	G	1	1	0	0	0.998919304684712	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000142733343528572
CAMB-71D12	MN908947.3	241	C	T	1	1	0	0	0.999167399047134	TCG	NA	NA	NA	NA	NA	NA	0.000185022433970119
CAMB-71D12	MN908947.3	24872	G	T	0.097	0.1	5e-44	2.8e-45	0.0980425824175824	TGT	S	V1104L	G3310T	GTA>TTA	Missense	GU280_gp02, spike glycoprotein	0.901757097069597
CAMB-71D12	MN908947.3	28050	A	G	0.0082	0.0099	1.4e-05	3.3e-06	0.00910855606988204	AAA	ORF8	K53E	A157G	AAA>GAA	Missense	GU280_gp09	0.990816783634463
CAMB-71D12	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999400479616307	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-71D12	MN908947.3	29179	G	T	0.015	0.014	2.3e-08	4e-08	0.0144187249450407	CGC	N	P302P	G906T	CCG>CCT	Synonymous	GU280_gp10	0.984546747704642
CAMB-71D12	MN908947.3	29311	C	T	0.097	0.091	5e-44	8.9e-41	0.0948944614829515	TCA	N	F346F	C1038T	TTC>TTT	Synonymous	GU280_gp10	0.904925130795598
CAMB-71D12	MN908947.3	3037	C	T	1	1	0	0	0.999473360835601	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.85154627110214e-05
CAMB-71D12	MN908947.3	3395	G	T	0.032	0.029	2e-15	1.2e-14	0.0307457169261392	AGA	ORF1ab:nsp3	D226Y	G676T	GAC>TAC	Missense	ORF1ab:nsp3	0.969183194711026
CAMB-71D12	MN908947.3	392	C	T	0.99	0.99	0	0	0.992794804140451	ACG	ORF1ab:leader-protein	R43C	C127T	CGT>TGT	Missense	ORF1ab:leader-protein	0.0071600929120718
CAMB-71D21	MN908947.3	11075	T	-	0.04	0.036	1e-09	1.5e-09	0.0384552535541152	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957622964213737
CAMB-71D21	MN908947.3	14120	C	T	1	1	0	0	0.999598302570864	CCA	ORF1ab:RNA-dependent-RNA-polymerase	P218L	C653T	CCA>CTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	9.2699406723797e-05
CAMB-71D21	MN908947.3	14384	T	G	0.007	0.0054	3.8e-05	0.00012	0.00638944886732497	GTT	ORF1ab:RNA-dependent-RNA-polymerase	V306G	T917G	GTT>GGT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993337205726586
CAMB-71D21	MN908947.3	14408	C	T	1	1	0	0	0.998429848255265	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000384302874585502
CAMB-71D21	MN908947.3	23403	A	G	1	1	0	0	0.99925438948128	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.6207808867153e-05
CAMB-71D21	MN908947.3	241	C	T	1	1	0	0	0.999453426154997	TCG	NA	NA	NA	NA	NA	NA	4.31505667107761e-05
CAMB-71D21	MN908947.3	24404	C	T	0.0073	0.0041	2.7e-05	0.00051	0.0058214509413802	ACT	S	L948F	C2842T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.994141704432409
CAMB-71D21	MN908947.3	25000	C	T	0.19	0.2	9.5e-91	1.9e-92	0.194467682682865	ACT	S	D1146D	C3438T	GAC>GAT	Synonymous	GU280_gp02, spike glycoprotein	0.805495944422217
CAMB-71D21	MN908947.3	26370	C	T	0.0085	0.0066	1.5e-05	6.9e-05	0.00779400328350471	ACT	E	Y42Y	C126T	TAC>TAT	Synonymous	GU280_gp04	0.992136870301564
CAMB-71D21	MN908947.3	26735	C	T	0.018	0.019	1.9e-09	7.1e-10	0.018253326572842	ACA	M	Y71Y	C213T	TAC>TAT	Synonymous	GU280_gp05	0.981705562331273
CAMB-71D21	MN908947.3	28077	G	T	0.025	0.025	4.6e-11	5.2e-11	0.0251823660006343	CGT	ORF8	V62L	G184T	GTG>TTG	Missense	GU280_gp09	0.974627339042182
CAMB-71D21	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999354251665737	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	6.57981313330701e-05
CAMB-71D21	MN908947.3	29412	A	C	0.014	0.011	3.5e-07	3.8e-06	0.0124326108482781	CAA	N	Q380P	A1139C	CAA>CCA	Missense	GU280_gp10	0.986577181208054
CAMB-71D21	MN908947.3	3037	C	T	1	1	0	0	0.999440805240454	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000119827448474197
CAMB-71D21	MN908947.3	3695	C	T	0.18	0.17	1.2e-72	2.4e-73	0.173184357541899	TCT	ORF1ab:nsp3	L326L	C976T	CTA>TTA	Synonymous	ORF1ab:nsp3	0.826696778794722
CAMB-71D21	MN908947.3	6982	C	T	0.067	0.055	2.4e-25	3.8e-20	0.0616348916166101	GCC	ORF1ab:nsp3	C1421C	C4263T	TGC>TGT	Synonymous	ORF1ab:nsp3	0.938103943588404
CAMB-71D30	MN908947.3	11074	C	INS	0.022	0.038	0.00041	3.4e-08	0.0258824610155479	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.97402567576878
CAMB-71D30	MN908947.3	14408	C	T	1	1	0	0	0.999637580150544	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000223027599665459
CAMB-71D30	MN908947.3	15784	T	C	0.0043	0.0085	0.002	2.6e-05	0.00604969542190869	CTT	ORF1ab:RNA-dependent-RNA-polymerase	F773L	T2317C	TTT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993929371375939
CAMB-71D30	MN908947.3	22335	G	-	0.033	0.036	3e-05	5.5e-08	0.0349206349206349	TGG	S	.	773-773-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.965079365079365
CAMB-71D30	MN908947.3	23403	A	G	1	1	0	0	0.999922807739811	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.43268834911486e-05
CAMB-71D30	MN908947.3	23896	C	T	0.11	0.16	3e-51	1.7e-61	0.121570627231005	CCC	S	T778T	C2334T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.878429372768995
CAMB-71D30	MN908947.3	241	C	T	1	1	0	0	0.999938563617374	TCG	NA	NA	NA	NA	NA	NA	6.1436382625791e-05
CAMB-71D30	MN908947.3	24155	C	T	0.014	0.038	5.7e-08	2.8e-17	0.0260325770796975	GCT	S	L865F	C2593T	CTC>TTC	Missense	GU280_gp02, spike glycoprotein	0.973821989528796
CAMB-71D30	MN908947.3	26164	C	A	0.025	0.017	8.3e-11	1.3e-06	0.0231175693527081	TCC	ORF3a	P258T	C772A	CCA>ACA	Missense	GU280_gp03	0.976882430647292
CAMB-71D30	MN908947.3	27147	G	A	0.0051	0.0087	0.00012	3.3e-06	0.00653466319461504	AGA	M	D209N	G625A	GAC>AAC	Missense	GU280_gp05	0.99341620399941
CAMB-71D30	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000201816347124117
CAMB-71D30	MN908947.3	29640	CA	-	0.0535	0.0205	3.2e-22;1.6e-22	2e-10;1e-10	0.0331286360698125	GCA	ORF10	.	83-84-delfrshift	.	no-SNV	GU280_gp11	0.967424122040362
CAMB-71D30	MN908947.3	3037	C	T	1	1	0	0	0.999717753316399	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-71D30	MN908947.3	392	C	T	0.93	0.9	0	0	0.92371597394071	ACG	ORF1ab:leader-protein	R43C	C127T	CGT>TGT	Missense	ORF1ab:leader-protein	0.0762840260592899
CAMB-71D30	MN908947.3	6762	C	T	0.077	0.0026	9.4e-24	0.0062	0.0249094202898551	ACT	ORF1ab:nsp3	T1348I	C4043T	ACT>ATT	Missense	ORF1ab:nsp3	0.975090579710145
CAMB-71D4F	MN908947.3	11074	C	INS	0.11	0.13	2.1e-52	6.1e-47	0.118487129361911	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.874173270745783
CAMB-71D4F	MN908947.3	11083	G	-	0.16	0.14	2.6e-68	1.2e-62	0.152143090849602	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.09063147562439e-05
CAMB-71D4F	MN908947.3	11083	G	T	0.84	0.86	0	0	0.847715127058567	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.09063147562439e-05
CAMB-71D4F	MN908947.3	11343	T	C	0.026	0.017	5.1e-13	1.8e-09	0.0227056750348289	ATC	ORF1ab:nsp6	I124T	T371C	ATC>ACC	Missense	ORF1ab:nsp6	0.977285098766457
CAMB-71D4F	MN908947.3	12398	C	A	0.011	0.0062	8.3e-07	4.6e-05	0.00952925481227368	ACT	ORF1ab:nsp8	L103I	C307A	CTC>ATC	Missense	ORF1ab:nsp8	0.990446922050696
CAMB-71D4F	MN908947.3	1283	A	G	1	1	0	0	0.999182461292045	CAC	ORF1ab:nsp2	T160A	A478G	ACT>GCT	Missense	ORF1ab:nsp2	0.000166844634276562
CAMB-71D4F	MN908947.3	13968	C	A	0.014	0.01	3.8e-08	4.9e-07	0.0128699358299013	CCA	ORF1ab:RNA-dependent-RNA-polymerase	A167A	C501A	GCC>GCA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.987046259936788
CAMB-71D4F	MN908947.3	14805	C	T	1	1	0	0	0.999965548129263	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	2.29679138243873e-05
CAMB-71D4F	MN908947.3	1514	C	T	0.03	0.048	3.4e-13	1.1e-16	0.0351713859910581	CCA	ORF1ab:nsp2	H237Y	C709T	CAT>TAT	Missense	ORF1ab:nsp2	0.964828614008942
CAMB-71D4F	MN908947.3	1515	A	G	1	0.99	0	0	0.993928881179532	CAT	ORF1ab:nsp2	H237R	A710G	CAT>CGT	Missense	ORF1ab:nsp2	0.00549291702804279
CAMB-71D4F	MN908947.3	15350	T	C	0.014	0.023	1e-07	4.4e-12	0.0158247903075489	GTT	ORF1ab:RNA-dependent-RNA-polymerase	V628A	T1883C	GTT>GCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.984156570363467
CAMB-71D4F	MN908947.3	16438	A	G	0.0086	0.013	2.9e-05	2.6e-07	0.0116164383561644	TAT	ORF1ab:helicase	M68V	A202G	ATG>GTG	Missense	ORF1ab:helicase	0.987835616438356
CAMB-71D4F	MN908947.3	17247	T	C	0.99	0.99	0	0	0.988884855214829	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.0110831126676347
CAMB-71D4F	MN908947.3	17551	G	A	0.026	0.02	4.9e-13	1.1e-10	0.0230355039542319	CGG	ORF1ab:helicase	G439R	G1315A	GGA>AGA	Missense	ORF1ab:helicase	0.976897189971395
CAMB-71D4F	MN908947.3	21137	A	G	0.087	0.11	4.4e-34	5.9e-46	0.0960867020525137	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.903893115905467
CAMB-71D4F	MN908947.3	21777	G	A	0.0071	0.0042	2.6e-05	0.00044	0.00563290466574556	GGG	S	G72E	G215A	GGG>GAG	Missense	GU280_gp02, spike glycoprotein	0.993835689233712
CAMB-71D4F	MN908947.3	23895	C	T	0.011	0.0061	9.9e-07	8.1e-05	0.00954502644352677	ACC	S	T778I	C2333T	ACC>ATC	Missense	GU280_gp02, spike glycoprotein	0.988770557125263
CAMB-71D4F	MN908947.3	24138	C	T	0.021	0.024	2e-10	3.5e-12	0.0217611336032389	ACT	S	T859I	C2576T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.975006900993743
CAMB-71D4F	MN908947.3	25775	G	T	0.0022	0.0073	0.0036	2.1e-05	0.00299564270152505	TGG	ORF3a	W128L	G383T	TGG>TTG	Missense	GU280_gp03	0.996895424836601
CAMB-71D4F	MN908947.3	26144	G	T	1	1	0	0	0.999813866914844	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-71D4F	MN908947.3	27384	T	C	0.058	0.058	3.9e-26	1.5e-26	0.0576166039024483	ATT	ORF6	D61D	T183C	GAT>GAC	Synonymous	GU280_gp06	0.941928078845771
CAMB-71D4F	MN908947.3	27836	C	A	0.017	0.014	6e-09	6.8e-08	0.0159415476585852	TCT	NA	NA	NA	NA	NA	NA	0.984058452341415
CAMB-71D4F	MN908947.3	29567	A	G	0.022	0.019	3e-11	6.4e-10	0.020524864699275	TAT	ORF10	I4V	A10G	ATA>GTA	Missense	GU280_gp11	0.979475135300725
CAMB-71D4F	MN908947.3	29700	A	G	0.0045	0.014	0.0026	2.1e-07	0.0112858464384829	TAG	NA	NA	NA	NA	NA	NA	0.988529139685476
CAMB-71D4F	MN908947.3	29746	A	T	0.0075	0.0065	4e-05	5.8e-05	0.00679420704451994	GAG	NA	NA	NA	NA	NA	NA	0.991417843733238
CAMB-71D4F	MN908947.3	5869	C	T	0.017	0.011	3.4e-09	6.6e-07	0.0155333764151169	ACA	ORF1ab:nsp3	Y1050Y	C3150T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.98439482061224
CAMB-71D4F	MN908947.3	7528	C	T	0.0026	0.0096	0.0091	7.8e-06	0.00443562014193984	TCG	ORF1ab:nsp3	V1603V	C4809T	GTC>GTT	Synonymous	ORF1ab:nsp3	0.995522135856708
CAMB-71D4F	MN908947.3	7764	C	T	0.53	0.55	5.3e-171	1.1e-177	0.540885703785373	TCC	ORF1ab:nsp3	S1682F	C5045T	TCC>TTC	Missense	ORF1ab:nsp3	0.458471150312385
CAMB-71D4F	MN908947.3	9223	C	T	1	1	0	0	0.998072662826761	ACG	ORF1ab:nsp4	H223H	C669T	CAC>CAT	Synonymous	ORF1ab:nsp4	0.000221533008418254
CAMB-71D4F	MN908947.3	9565	C	T	0.0078	0.013	2.7e-05	7.9e-08	0.00993610824015785	TCT	ORF1ab:nsp4	F337F	C1011T	TTC>TTT	Synonymous	ORF1ab:nsp4	0.990052146951048
CAMB-71D6D	MN908947.3	12734	G	-	0.03	0.032	1.6e-15	1.7e-16	0.0309380414157248	CGG	ORF1ab:nsp9	.	49-49-delfrshift	.	no-SNV	ORF1ab:nsp9	0.968759453290433
CAMB-71D6D	MN908947.3	12734	GG	-	0.03	0.016	1.6e-15;2.7e-15	1.7e-16;NA	0.02443285741585	CGG	ORF1ab:nsp9	.	49-50-delfrshift	.	no-SNV	ORF1ab:nsp9	0.968759453290433
CAMB-71D6D	MN908947.3	14408	C	T	1	1	0	0	0.99970915436632	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000290845633679924
CAMB-71D6D	MN908947.3	18624	G	C	0.029	0.022	8.7e-15	4e-12	0.0267812111226926	TGA	ORF1ab:3'-to-5'-exonuclease	M195I	G585C	ATG>ATC	Missense	ORF1ab:3'-to-5'-exonuclease	0.973185165260079
CAMB-71D6D	MN908947.3	21046	G	C	0.063	0.067	5.5e-29	1.4e-28	0.0639143318965517	TGA	ORF1ab:2'-O-ribose-methyltransferase	D130H	G388C	GAT>CAT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.936085668103448
CAMB-71D6D	MN908947.3	23403	A	G	1	1	0	0	0.99987030504254	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000103755965968043
CAMB-71D6D	MN908947.3	24007	G	C	0.17	0.11	2.4e-69	4.2e-30	0.157878879180476	GGT	S	R815S	G2445C	AGG>AGC	Missense	GU280_gp02, spike glycoprotein	0.842121120819524
CAMB-71D6D	MN908947.3	241	C	T	1	1	0	0	0.999857428001141	TCG	NA	NA	NA	NA	NA	NA	4.7523999619808e-05
CAMB-71D6D	MN908947.3	28253	C	T	0.054	0.033	3e-24	2.3e-15	0.048494874083103	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.951222166597741
CAMB-71D6D	MN908947.3	28436	G	T	0.0047	0.016	0.00057	6.3e-09	0.00807076446280992	CGC	N	A55S	G163T	GCT>TCT	Missense	GU280_gp10	0.989895402892562
CAMB-71D6D	MN908947.3	28725	CTG	-	0.013	0.00153333333333333	9.6e-08;1.4e-07;1.6e-07	NA;NA;0.00065	0.00809044149164166	CCT	N	.	452-454-delinframe	.	no-SNV	GU280_gp10	0.991402787419234
CAMB-71D6D	MN908947.3	28793	G	C	0.0035	0.021	0.0014	6.9e-10	0.00788781770376862	AGA	N	E174Q	G520C	GAA>CAA	Missense	GU280_gp10	0.975314052001169
CAMB-71D6D	MN908947.3	28793	G	T	0.0056	0.038	0.00018	1.2e-15	0.0135845749342682	AGA	N	E174*	G520T	GAA>TAA	Nonsense	GU280_gp10	0.975314052001169
CAMB-71D6D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-71D6D	MN908947.3	29553	GG	CC	0.0082	0.0065	2.6e-05;2.2e-05	NA;8.8e-07	0.0069889341875364	AGG	NA	NA	NA	NA	NA	NA	0.994545454545455
CAMB-71D6D	MN908947.3	29554	G	C	0.0084	0.013	2.2e-05	8.8e-07	0.0106561974200785	GGC	NA	NA	NA	NA	NA	NA	0.989343802579921
CAMB-71D6D	MN908947.3	3018	C	T	1	1	0	0	0.999094202898551	TCA	ORF1ab:nsp3	S100L	C299T	TCA>TTA	Missense	ORF1ab:nsp3	0.000905797101449275
CAMB-71D6D	MN908947.3	3037	C	T	1	1	8e-219	2.5e-306	0.999003984063745	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00099601593625498
CAMB-71D6D	MN908947.3	635	C	T	0.055	0.063	7.8e-25	2.7e-27	0.0580890336590662	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.941910966340934
CAMB-71D6D	MN908947.3	683	C	T	0.014	0.016	6.1e-08	8.5e-09	0.0147656494240435	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.985210302286992
CAMB-71D7C	MN908947.3	11075	T	-	0.061	0.046	1.1e-14	3.7e-12	0.0572301636627305	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.94266625233064
CAMB-71D7C	MN908947.3	14408	C	T	1	1	0	0	0.997477712546206	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000231934478509821
CAMB-71D7C	MN908947.3	19178	GT	-	0.00425	0.0065	4e-04;0.00038	3.1e-05;2.8e-05	0.00496976724923383	GGT	ORF1ab:3'-to-5'-exonuclease	.	1139-1140-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.995000819537781
CAMB-71D7C	MN908947.3	23403	A	G	0.99	1	0	0	0.995941393725395	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000111611672551646
CAMB-71D7C	MN908947.3	241	C	T	1	1	0	0	0.999849611137369	TCG	NA	NA	NA	NA	NA	NA	0.000107420616164654
CAMB-71D7C	MN908947.3	24196	A	-	0.0036	0.017	0.0067	3.8e-07	0.00858802727961606	TAG	S	.	2634-2634-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.991411972720384
CAMB-71D7C	MN908947.3	25613	C	T	0.019	0.0047	4e-10	0.00026	0.0134206105944898	TCC	ORF3a	S74F	C221T	TCC>TTC	Missense	GU280_gp03	0.986544755571718
CAMB-71D7C	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998928430432576	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000321605454428507
CAMB-71D7C	MN908947.3	3037	C	T	1	1	0	0	0.999824253075571	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-71D8B	MN908947.3	11075	T	-	0.044	0.044	8.3e-11	3.1e-11	0.0439339122045345	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952906415822479
CAMB-71D8B	MN908947.3	13730	C	T	1	1	0	0	0.997527692530944	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A88V	C263T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000118240791998323
CAMB-71D8B	MN908947.3	14408	C	T	1	1	0	0	0.9988755453605	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000314847299059956
CAMB-71D8B	MN908947.3	23403	A	G	1	1	0	0	0.999209526052003	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000159776649063204
CAMB-71D8B	MN908947.3	23525	C	T	0.037	0.037	5.5e-17	4.4e-17	0.0367649559568752	ACA	S	H655Y	C1963T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.962792912287862
CAMB-71D8B	MN908947.3	241	C	T	1	1	0	0	0.998917623410259	TCG	NA	NA	NA	NA	NA	NA	0.000154625227105802
CAMB-71D8B	MN908947.3	25342	C	T	0.024	0.024	4.8e-12	1.7e-12	0.0237659334897673	ACT	S	D1260D	C3780T	GAC>GAT	Synonymous	GU280_gp02, spike glycoprotein	0.976139518492733
CAMB-71D8B	MN908947.3	25429	G	T	1	1	0	0	0.99849901497858	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	9.38115638387692e-05
CAMB-71D8B	MN908947.3	28153	C	T	0.009	0.009	8.9e-06	6.1e-06	0.00902624254017709	ACA	ORF8	T87I	C260T	ACA>ATA	Missense	GU280_gp09	0.990870665857207
CAMB-71D8B	MN908947.3	28826	C	T	0.013	0.011	2.3e-06	1.4e-05	0.0125830402500977	TCG	N	R185C	C553T	CGT>TGT	Missense	GU280_gp10	0.987286700534063
CAMB-71D8B	MN908947.3	3037	C	T	1	1	0	0	0.999436196203721	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000150347679007705
CAMB-71D9A	MN908947.3	11075	T	-	0.064	0.028	7.4e-16	8.9e-08	0.0469309003421394	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.949054039275727
CAMB-71D9A	MN908947.3	1270	T	-	0.0083	0.0071	1.5e-05	4.6e-05	0.00782816229116945	ATT	ORF1ab:nsp2	.	465-465-delfrshift	.	no-SNV	ORF1ab:nsp2	0.992028639618138
CAMB-71D9A	MN908947.3	13778	AT	-	0.0415	0.0088	6e-13;1.2e-12	0.00044;0.00056	0.0281277694293531	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.972790127128095
CAMB-71D9A	MN908947.3	13780	A	T	0.031	0.038	3.8e-09	8.1e-11	0.0337775023241401	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I105L	A313T	ATA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.966145026340254
CAMB-71D9A	MN908947.3	14408	C	T	1	1	0	0	0.999473263231823	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000429192922218537
CAMB-71D9A	MN908947.3	15202	GTAATT	-	0.00913333333333333	0.0047	1.8e-05;1e-05;1.4e-05;1.3e-05;1.6e-05;1.6e-05	0.0015;0.00094;0.0013;0.0013;0.0015;0.0014	0.00651009765146477	AGT	ORF1ab:RNA-dependent-RNA-polymerase	.	1735-1740-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.993592818474611
CAMB-71D9A	MN908947.3	1547	A	G	0.023	0.0097	2.4e-08	8.4e-05	0.0156569094622192	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.962559564329476
CAMB-71D9A	MN908947.3	1547	A	T	0.028	0.0036	4.3e-10	0.0024	0.0142954390742001	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.962559564329476
CAMB-71D9A	MN908947.3	16289	C	T	1	1	0	0	0.999811320754717	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0.000188679245283019
CAMB-71D9A	MN908947.3	17938	G	A	0.0087	0.0037	5.4e-06	9e-04	0.00633694737363236	AGC	ORF1ab:helicase	A568T	G1702A	GCA>ACA	Missense	ORF1ab:helicase	0.993613545225011
CAMB-71D9A	MN908947.3	22069	AT	-	0.0085	0.0165	1.2e-05;3.2e-05	7.5e-09;1.6e-08	0.0118580179048217	AAT	S	.	507-508-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.987733032039383
CAMB-71D9A	MN908947.3	23403	A	G	1	1	0	0	0.999951492808809	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.85071911910941e-05
CAMB-71D9A	MN908947.3	241	C	T	1	1	0	0	0.999790527660822	TCG	NA	NA	NA	NA	NA	NA	8.37889356710446e-05
CAMB-71D9A	MN908947.3	24642	C	T	0.029	0.061	8.6e-13	2.5e-23	0.0422794117647059	ACT	S	T1027I	C3080T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.957720588235294
CAMB-71D9A	MN908947.3	25429	G	T	1	1	0	0	0.999798374901708	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0.000100812549146118
CAMB-71D9A	MN908947.3	25936	C	T	1	1	0	0	0.999374843710928	ACA	ORF3a	H182Y	C544T	CAT>TAT	Missense	GU280_gp03	0.000375093773443361
CAMB-71D9A	MN908947.3	28330	A	G	0.03	0.059	3e-15	2.5e-27	0.0469012834607081	GAC	N	G19G	A57G	GGA>GGG	Synonymous	GU280_gp10	0.953098716539292
CAMB-71D9A	MN908947.3	28794	AA	-	0.011	0.0105	1.4e-06;5.9e-07	2e-06;5.7e-07	0.0108786610878661	GAA	N	.	521-522-delfrshift	.	no-SNV	GU280_gp10	0.989155514536225
CAMB-71D9A	MN908947.3	28795	A	G	0.016	0.015	2.3e-08	6.9e-08	0.0155067609477732	AAG	N	E174E	A522G	GAA>GAG	Synonymous	GU280_gp10	0.972956208907083
CAMB-71D9A	MN908947.3	29241	A	-	0.0088	0.0047	1.7e-05	0.00076	0.00683082686057401	GAA	N	.	968-968-delfrshift	.	no-SNV	GU280_gp10	0.993003911199251
CAMB-71D9A	MN908947.3	29700	A	G	1	1	0	0	1	TAG	NA	NA	NA	NA	NA	NA	0
CAMB-71D9A	MN908947.3	3037	C	T	1	1	0	0	0.999589592054502	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00016416317819913
CAMB-71D9A	MN908947.3	3103	AT	-	0.012	0.011	2e-06;2.8e-06	6.7e-06;9.1e-06	0.0115071359187028	AAT	ORF1ab:nsp3	.	384-385-delfrshift	.	no-SNV	ORF1ab:nsp3	0.988526300104306
CAMB-71D9A	MN908947.3	462	A	T	0.011	0.016	9.1e-05	5.2e-06	0.012817578393225	CAG	ORF1ab:leader-protein	Q66L	A197T	CAG>CTG	Missense	ORF1ab:leader-protein	0.987004399684647
CAMB-71D9A	MN908947.3	9165	C	T	0.018	0.006	7.3e-10	0.00016	0.0110864203560353	ACC	ORF1ab:nsp4	T204I	C611T	ACC>ATC	Missense	ORF1ab:nsp4	0.988913579643965
CAMB-71D9A	MN908947.3	9479	G	T	0.077	0.097	3.9e-31	5.1e-42	0.0905660377358491	TGG	ORF1ab:nsp4	G309C	G925T	GGT>TGT	Missense	ORF1ab:nsp4	0.909433962264151
CAMB-71D9A	MN908947.3	9491	C	T	0.016	0.014	4.8e-08	1.8e-07	0.0143626570915619	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.985637342908438
CAMB-71D9A	MN908947.3	9603	C	T	0.011	0.012	7.6e-07	3.5e-07	0.0113477701426342	ACA	ORF1ab:nsp4	T350I	C1049T	ACA>ATA	Missense	ORF1ab:nsp4	0.988624852848578
CAMB-71DA9	MN908947.3	11075	T	-	0.033	0.032	1.2e-08	7.2e-09	0.0328788968450017	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.963431412401113
CAMB-71DA9	MN908947.3	12410	A	G	1	1	0	0	0.999898915872735	TAT	ORF1ab:nsp8	I107V	A319G	ATC>GTC	Missense	ORF1ab:nsp8	7.58130954486872e-05
CAMB-71DA9	MN908947.3	13778	AT	-	0.022	0.022	1.8e-07;2.7e-07	1.2e-07;2.1e-07	0.0218901335420437	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.978836726998492
CAMB-71DA9	MN908947.3	13780	A	T	0.021	0.018	1.5e-06	2.8e-06	0.0200204642676628	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I105L	A313T	ATA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.975849698583528
CAMB-71DA9	MN908947.3	14408	C	T	1	1	0	0	0.997830401291668	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000386827676679337
CAMB-71DA9	MN908947.3	14928	C	T	0.11	0.1	8e-49	6.1e-46	0.105886097928001	ACA	ORF1ab:RNA-dependent-RNA-polymerase	N487N	C1461T	AAC>AAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.894084963537446
CAMB-71DA9	MN908947.3	1547	A	-	0.014	0.0076	1.1e-07	2.9e-05	0.0117545375972342	TAG	ORF1ab:nsp2	.	742-742-delfrshift	.	no-SNV	ORF1ab:nsp2	0.930682800345722
CAMB-71DA9	MN908947.3	1547	A	G	0.019	0.018	2.2e-09	1.6e-08	0.0188418323249784	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.930682800345722
CAMB-71DA9	MN908947.3	1547	A	T	0.039	0.033	2.9e-17	4.6e-14	0.0369922212618842	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.930682800345722
CAMB-71DA9	MN908947.3	18788	C	T	1	1	0	0	0.999517251892881	ACA	ORF1ab:3'-to-5'-exonuclease	T250I	C749T	ACA>ATA	Missense	ORF1ab:3'-to-5'-exonuclease	0.000203262360892322
CAMB-71DA9	MN908947.3	19839	T	C	1	1	0	0	0.998030341128154	ATA	ORF1ab:endoRNAse	N73N	T219C	AAT>AAC	Synonymous	ORF1ab:endoRNAse	0.000586706897996815
CAMB-71DA9	MN908947.3	21093	T	C	1	1	0	0	0.998558014755198	CTA	ORF1ab:2'-O-ribose-methyltransferase	S145S	T435C	TCT>TCC	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.000100603621730382
CAMB-71DA9	MN908947.3	22432	C	T	0.17	0.18	8.8e-60	4.8e-60	0.176786451879389	ACT	S	D290D	C870T	GAC>GAT	Synonymous	GU280_gp02, spike glycoprotein	0.822387443205287
CAMB-71DA9	MN908947.3	23403	A	G	1	1	0	0	0.99897174409105	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000126771276445897
CAMB-71DA9	MN908947.3	241	C	T	1	1	0	0	0.998901857985441	TCG	NA	NA	NA	NA	NA	NA	8.85598398838095e-05
CAMB-71DA9	MN908947.3	2453	C	T	0.013	0.011	2.4e-07	1.1e-06	0.0124775905342417	ACT	ORF1ab:nsp2	L550F	C1648T	CTC>TTC	Missense	ORF1ab:nsp2	0.987378988884905
CAMB-71DA9	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999376280851822	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	5.06842372022301e-05
CAMB-71DA9	MN908947.3	29241	AA	-	0.0118	0.012	2e-07;4.6e-05	1.7e-07;1.4e-05	0.0120532688538404	GAA	N	.	968-969-delfrshift	.	no-SNV	GU280_gp10	0.985043988269795
CAMB-71DA9	MN908947.3	29242	A	G	0.013	0.01	1.7e-07	1.8e-06	0.0124313438300989	AAG	N	E323E	A969G	GAA>GAG	Synonymous	GU280_gp10	0.963639692420359
CAMB-71DA9	MN908947.3	29242	A	T	0.014	0.013	9.8e-08	1.5e-07	0.0136213841083852	AAG	N	E323D	A969T	GAA>GAT	Missense	GU280_gp10	0.963639692420359
CAMB-71DA9	MN908947.3	3037	C	T	1	1	0	0	0.999264435454211	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.17293939765437e-05
CAMB-71DA9	MN908947.3	9499	T	C	0.0058	0.0078	0.00015	1.8e-05	0.00650027084461853	TTG	ORF1ab:nsp4	V315V	T945C	GTT>GTC	Synonymous	ORF1ab:nsp4	0.993333055543981
CAMB-71DB8	MN908947.3	10084	TG	-	0.00855	0.006	3.3e-06;1.4e-05	NA;5.9e-07	0.00726952307522855	CTG	ORF1ab:3C-like-proteinase	.	30-31-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.995437262357414
CAMB-71DB8	MN908947.3	10085	G	-	0.0088	0.012	1.4e-05	5.9e-07	0.0103875795822629	TGG	ORF1ab:3C-like-proteinase	.	31-31-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.989612420417737
CAMB-71DB8	MN908947.3	11075	T	-	0.034	0.023	3.5e-09	5.5e-07	0.0299333007971368	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.969996978781752
CAMB-71DB8	MN908947.3	11595	A	G	0.0035	0.021	0.0097	2.5e-07	0.0101522842639594	CAG	ORF1ab:nsp6	Q208R	A623G	CAG>CGG	Missense	ORF1ab:nsp6	0.989847715736041
CAMB-71DB8	MN908947.3	11954	G	T	0.012	0.016	3.6e-07	6.5e-09	0.0139199602286851	TGA	ORF1ab:nsp7	D38Y	G112T	GAC>TAC	Missense	ORF1ab:nsp7	0.986080039771315
CAMB-71DB8	MN908947.3	12142	TGCTCAAGAAGCTT	-	0.0113571428571429	0.000945214285714286	0.00051;0.00034;0.00054;0.00043;0.00033;9.9e-05;0.00027;0.00044;0.00037;0.00021;0.00016;0.00011;1e-06;2e-06	NA;NA;NA;NA;NA;0.081;NA;NA;0.00049;NA;NA;NA;NA;NA	0.00676213206046142	CTG	ORF1ab:nsp8	.	51-64-delfrshift	.	no-SNV	ORF1ab:nsp8	0.993219734142207
CAMB-71DB8	MN908947.3	12758	G	T	0.0066	0.012	4.8e-05	1.2e-07	0.00848472151557777	TGA	ORF1ab:nsp9	D25Y	G73T	GAT>TAT	Missense	ORF1ab:nsp9	0.991395564600605
CAMB-71DB8	MN908947.3	12793	G	T	0.012	0.012	1.7e-07	1.9e-07	0.0121009497322406	AGG	ORF1ab:nsp9	K36N	G108T	AAG>AAT	Missense	ORF1ab:nsp9	0.987869463593597
CAMB-71DB8	MN908947.3	14901	TATTAATGC	-	0.015	0.00517111111111111	5.3e-05;5.3e-05;0.00033;2e-05;5.9e-05;7.5e-05;4.5e-05;4.9e-05;4.1e-05	NA;NA;NA;NA;NA;NA;NA;7.1e-07;6.3e-07	0.00954877363789552	GTA	ORF1ab:RNA-dependent-RNA-polymerase	.	1434-1442-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.990465507571509
CAMB-71DB8	MN908947.3	15714	C	T	1	1	0	0	0.999477988515747	TCT	ORF1ab:RNA-dependent-RNA-polymerase	L749L	C2247T	CTC>CTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000174003828084218
CAMB-71DB8	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999625948487763	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.00010687757174157
CAMB-71DB8	MN908947.3	16133	ACATGTTAG	-	0.0141111111111111	0.00401333333333333	2.5e-08;2.7e-08;2.2e-08;3e-08;3e-08;3.1e-08;3.5e-08;6.5e-08;5.1e-08	NA;NA;NA;NA;NA;NA;NA;1.3e-09;9.5e-10	0.00792769938163945	CAC	ORF1ab:RNA-dependent-RNA-polymerase	.	2666-2674-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.991784290485939
CAMB-71DB8	MN908947.3	17140	G	T	0.011	0.0094	1.1e-06	7e-06	0.0105166895290352	TGC	ORF1ab:helicase	A302S	G904T	GCT>TCT	Missense	ORF1ab:helicase	0.989417989417989
CAMB-71DB8	MN908947.3	17140	GC	TT	0.0105	0.004855	1.1e-06;2.1e-06	7e-06;0.2	0.00824587706146927	TGC	ORF1ab:helicase	.	904-905-mnv	.	no-SNV	ORF1ab:helicase	0.989417989417989
CAMB-71DB8	MN908947.3	17320	G	C	0.0088	0.01	4e-06	9.7e-07	0.00933676754668384	TGC	ORF1ab:helicase	A362P	G1084C	GCA>CCA	Missense	ORF1ab:helicase	0.985901650455824
CAMB-71DB8	MN908947.3	18322	C	T	0.0037	0.019	0.0017	2.4e-10	0.00962384751900962	TCA	ORF1ab:3'-to-5'-exonuclease	H95Y	C283T	CAT>TAT	Missense	ORF1ab:3'-to-5'-exonuclease	0.99036172392399
CAMB-71DB8	MN908947.3	19577	A	C	0.89	0.94	0	0	0.911126279863481	CAA	ORF1ab:3'-to-5'-exonuclease	Q513P	A1538C	CAA>CCA	Missense	ORF1ab:3'-to-5'-exonuclease	0.0888737201365188
CAMB-71DB8	MN908947.3	21031	G	C	0.039	0.014	9.1e-17	9e-08	0.029945999018164	GGA	ORF1ab:2'-O-ribose-methyltransferase	D125H	G373C	GAT>CAT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.939304681572723
CAMB-71DB8	MN908947.3	21031	G	T	0.037	0.019	6.7e-18	4.6e-10	0.0307493194091132	GGA	ORF1ab:2'-O-ribose-methyltransferase	D125Y	G373T	GAT>TAT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.939304681572723
CAMB-71DB8	MN908947.3	22620	GG	TC	0.016	0.000305	1.1e-09;1e-08	NA;0.0071	0.0093029237760439	TGG	S	.	1058-1059-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.990111301369863
CAMB-71DB8	MN908947.3	24145	G	T	0.017	0.0085	1e-09	7.3e-06	0.0137909627067536	TGC	S	L861F	G2583T	TTG>TTT	Missense	GU280_gp02, spike glycoprotein	0.986031661567115
CAMB-71DB8	MN908947.3	25302	G	T	0.0089	0.016	9.2e-06	4.1e-09	0.0116138623060485	TGT	S	C1247F	G3740T	TGT>TTT	Missense	GU280_gp02, spike glycoprotein	0.988237480256434
CAMB-71DB8	MN908947.3	25521	C	T	0.056	0.012	1.2e-25	7e-07	0.0407820961326496	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.95921790386735
CAMB-71DB8	MN908947.3	27165	G	C	0.0028	0.0097	0.00074	6.1e-07	0.00542412549813397	TGA	M	D215H	G643C	GAC>CAC	Missense	GU280_gp05	0.991175912454931
CAMB-71DB8	MN908947.3	27222	T	-	0.016	0.011	3.8e-07	2.5e-05	0.0138134144024321	TTC	ORF6	.	21-21-delfrshift	.	no-SNV	GU280_gp06	0.986072582177465
CAMB-71DB8	MN908947.3	27222	TC	-	0.008	0.011	3.8e-07;NA	2.5e-05;1.5e-06	0.00895471310696224	TTC	ORF6	.	21-22-delfrshift	.	no-SNV	GU280_gp06	0.986072582177465
CAMB-71DB8	MN908947.3	27942	C	T	0.022	0.0096	6.6e-10	1.9e-05	0.015758547008547	TCA	ORF8	H17Y	C49T	CAC>TAC	Missense	GU280_gp09	0.984241452991453
CAMB-71DB8	MN908947.3	28253	C	T	0.0069	0.038	0.00043	1.8e-17	0.0184867840265877	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.981374738190442
CAMB-71DB8	MN908947.3	28603	C	T	0.025	0.011	1.9e-08	0.00011	0.0201273169818386	TCT	N	F110F	C330T	TTC>TTT	Synonymous	GU280_gp10	0.979779067590339
CAMB-71DB8	MN908947.3	2863	AG	-	0.0405	0.015	4.9e-18;4.1e-18	NA;3.4e-13	0.0310916312833858	CAG	ORF1ab:nsp3	.	144-145-delfrshift	.	no-SNV	ORF1ab:nsp3	0.974626865671642
CAMB-71DB8	MN908947.3	2864	G	-	0.041	0.03	4.1e-18	3.4e-13	0.0369294605809129	AGA	ORF1ab:nsp3	.	145-145-delfrshift	.	no-SNV	ORF1ab:nsp3	0.963070539419087
CAMB-71DB8	MN908947.3	28895	G	C	0.0024	0.0078	0.0048	1.9e-05	0.00515685431886549	TGC	N	A208P	G622C	GCT>CCT	Missense	GU280_gp10	0.994843145681135
CAMB-71DB8	MN908947.3	28975	G	C	0.0039	0.008	0.00044	8.9e-06	0.00603483747085448	TGT	N	M234I	G702C	ATG>ATC	Missense	GU280_gp10	0.993828007132081
CAMB-71DB8	MN908947.3	29140	G	T	0.0076	0.0075	2.2e-05	2.7e-05	0.00756593169044531	AGG	N	Q289H	G867T	CAG>CAT	Missense	GU280_gp10	0.992380025940337
CAMB-71DB8	MN908947.3	29260	GTG	-	0.0193333333333333	0.00166666666666667	1.8e-10;2.3e-10;6e-11	NA;NA;0.00022	0.0119329117404454	CGT	N	.	987-989-delinframe	.	no-SNV	GU280_gp10	0.98801209788287
CAMB-71DB8	MN908947.3	29315	G	T	0.0084	0.0071	7.1e-06	2.7e-05	0.00790244923592213	AGA	N	D348Y	G1042T	GAT>TAT	Missense	GU280_gp10	0.991940548461377
CAMB-71DB8	MN908947.3	29321	G	C	0.0077	4e-04	5.9e-06	0.0098	0.00497017892644135	AGT	N	V350L	G1048C	GTC>CTC	Missense	GU280_gp10	0.994980119284294
CAMB-71DB8	MN908947.3	29548	C	T	0.05	0.046	5.1e-20	2.4e-18	0.048106765983861	ACA	NA	NA	NA	NA	NA	NA	0.951893234016139
CAMB-71DB8	MN908947.3	3062	G	C	0.014	0.024	3.1e-08	7.4e-12	0.0176785973047384	AGA	ORF1ab:nsp3	E115Q	G343C	GAA>CAA	Missense	ORF1ab:nsp3	0.948558179973917
CAMB-71DB8	MN908947.3	4117	AT	-	0.0245	0.0475	1.8e-06;1.3e-06	7.4e-12;1.1e-11	0.0346869415927963	CAT	ORF1ab:nsp3	.	1398-1399-delfrshift	.	no-SNV	ORF1ab:nsp3	0.967114650738344
CAMB-71DB8	MN908947.3	4360	AG	-	0.0072	0.024	0.0016;0.0018	8.2e-08;1e-07	0.014836941763152	AAG	ORF1ab:nsp3	.	1641-1642-delfrshift	.	no-SNV	ORF1ab:nsp3	0.985003103662322
CAMB-71DB8	MN908947.3	8003	G	T	0.022	0.025	2.1e-11	2e-12	0.0235922330097087	TGT	ORF1ab:nsp3	V1762F	G5284T	GTT>TTT	Missense	ORF1ab:nsp3	0.967669902912621
CAMB-71DB8	MN908947.3	9236	AG	-	0.0024	0.02	0.0026;0.0029	2.9e-11;3.7e-11	0.00976187985915002	AAG	ORF1ab:nsp4	.	682-683-delfrshift	.	no-SNV	ORF1ab:nsp4	0.989996138860613
CAMB-71DB8	MN908947.3	9475	T	C	0.023	0.017	4.1e-09	3.4e-07	0.0196822385582167	CTT	ORF1ab:nsp4	A307A	T921C	GCT>GCC	Synonymous	ORF1ab:nsp4	0.97936921982452
CAMB-71DC7	MN908947.3	1348	C	T	0.003	0.014	0.0093	3.1e-06	0.00744960560911481	CCC	ORF1ab:nsp2	P181P	C543T	CCC>CCT	Synonymous	ORF1ab:nsp2	0.992550394390885
CAMB-71DC7	MN908947.3	14408	C	T	1	0.99	0	0	0.996572556215271	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000225034187886237
CAMB-71DC7	MN908947.3	20268	A	G	1	1	1.1e-212	3.2e-165	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-71DC7	MN908947.3	23403	A	G	1	1	0	0	0.999832883710937	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000131305655692697
CAMB-71DC7	MN908947.3	23571	TATGCGCTAGTT	-	0.0436666666666667	0.0215	1.1e-05;3.1e-06;9.9e-06;2.1e-06;6.6e-06;2.1e-05;8.8e-06;0.00013;2.7e-06;5.2e-06;0.00088;0.00066	0.0033;0.0027;0.0075;0.004;0.006;0.008;0.0063;0.0065;0.0014;0.002;0.0062;0.0051	0.0399538771980398	ATA	S	.	2009-2020-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.956875113725966
CAMB-71DC7	MN908947.3	241	C	T	1	1	0	0	0.999692437814771	TCG	NA	NA	NA	NA	NA	NA	0.00013455845603783
CAMB-71DC7	MN908947.3	2458	G	T	0.016	0.0027	1.8e-08	0.0049	0.0107497984412792	TGC	ORF1ab:nsp2	M551I	G1653T	ATG>ATT	Missense	ORF1ab:nsp2	0.989250201558721
CAMB-71DC7	MN908947.3	26230	G	T	1	1	0	0	0.99987002296261	TGA	NA	NA	NA	NA	NA	NA	0
CAMB-71DC7	MN908947.3	27484	T	C	0.0067	0.0047	3.5e-05	0.00017	0.00618245170441405	TTT	ORF7a	L31L	T91C	TTA>CTA	Synonymous	GU280_gp07	0.993802130710288
CAMB-71DC7	MN908947.3	28926	C	T	1	1	0	0	0.999638565103461	GCT	N	A218V	C653T	GCT>GTT	Missense	GU280_gp10	0.00018071744826963
CAMB-71DC7	MN908947.3	29545	C	A	1	1	0	0	0.999807247494217	ACC	NA	NA	NA	NA	NA	NA	0
CAMB-71DC7	MN908947.3	29759	G	T	0.99	0.99	0	0	0.993857493857494	TGT	NA	NA	NA	NA	NA	NA	0
CAMB-71DC7	MN908947.3	3037	C	T	1	1	0	0	0.999563763268867	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00014541224371092
CAMB-71DC7	MN908947.3	3216	GTCAACAAACTGTTG	-	0.0112666666666667	0.00058	1.3e-06;1.3e-06;1.9e-06;1.7e-06;3.4e-06;2.5e-06;1.9e-06;1.4e-06;1.1e-06;1.4e-06;1.5e-06;2.5e-06;8.9e-07;1.3e-06;1.1e-05	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00014	0.00750646888530218	AGT	ORF1ab:nsp3	.	497-511-delinframe	.	no-SNV	ORF1ab:nsp3	0.99238178860109
CAMB-71DC7	MN908947.3	3873	T	C	0.0054	0.0069	0.00018	4.2e-05	0.00591884760750196	ATC	ORF1ab:nsp3	I385T	T1154C	ATC>ACC	Missense	ORF1ab:nsp3	0.994081152392498
CAMB-71DC7	MN908947.3	4399	G	T	0.013	0.0051	1.2e-06	0.0026	0.00976071771530801	TGC	ORF1ab:nsp3	M560I	G1680T	ATG>ATT	Missense	ORF1ab:nsp3	0.986516528762546
CAMB-71DC7	MN908947.3	541	CGAAGG	-	0.00885	0.0013305	0.00018;4.8e-06;1.3e-06;4e-07;2.8e-06;8.9e-06	NA;5.3e-06;NA;NA;NA;NA	0.00695792472332165	TCG	ORF1ab:leader-protein	.	276-281-delinframe	.	no-SNV	ORF1ab:leader-protein	0.996383282729059
CAMB-71DC7	MN908947.3	6525	C	T	0.012	0.013	1.3e-07	6.3e-08	0.0127264126470633	ACA	ORF1ab:nsp3	T1269I	C3806T	ACA>ATA	Missense	ORF1ab:nsp3	0.987227808890177
CAMB-71DC7	MN908947.3	664	C	T	1	1	0	0	0.999759720401922	GCC	ORF1ab:leader-protein	G133G	C399T	GGC>GGT	Synonymous	ORF1ab:leader-protein	0.000196592398427261
CAMB-71DD6	MN908947.3	11075	T	-	0.04	0.04	2.2e-10	1.1e-10	0.0398209284735992	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955784051186655
CAMB-71DD6	MN908947.3	1150	C	T	1	1	0	0	0.999232453023282	GCT	ORF1ab:nsp2	G115G	C345T	GGC>GGT	Synonymous	ORF1ab:nsp2	0.000170565994826165
CAMB-71DD6	MN908947.3	14408	C	T	1	1	0	0	0.998425639583919	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00035610533220879
CAMB-71DD6	MN908947.3	18606	C	T	0.0064	0.0074	5.2e-05	2.2e-05	0.00690198670446023	GCT	ORF1ab:3'-to-5'-exonuclease	G189G	C567T	GGC>GGT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.992970904884776
CAMB-71DD6	MN908947.3	20268	A	G	1	1	0	0	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-71DD6	MN908947.3	22295	C	T	1	1	0	0	0.996468495260349	ACA	S	H245Y	C733T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.000212421337723374
CAMB-71DD6	MN908947.3	23403	A	G	1	1	0	0	0.999435807422267	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.26880641925777e-05
CAMB-71DD6	MN908947.3	241	C	T	1	1	0	0	0.998867214499654	TCG	NA	NA	NA	NA	NA	NA	0.000153598033945166
CAMB-71DD6	MN908947.3	25318	C	T	1	1	0	0	0.999715712951306	CCT	S	S1252S	C3756T	TCC>TCT	Synonymous	GU280_gp02, spike glycoprotein	0.000203062177638793
CAMB-71DD6	MN908947.3	29734	G	C	1	1	0	0	0.998781540336092	CGA	NA	NA	NA	NA	NA	NA	0
CAMB-71DD6	MN908947.3	3037	C	T	1	1	0	0	0.999324193859819	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.43624895410955e-05
CAMB-71DE5	MN908947.3	11075	T	-	0.039	0.037	2.2e-10	3.5e-10	0.0383975302091122	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957019849979499
CAMB-71DE5	MN908947.3	14408	C	T	1	1	0	0	0.996814734561213	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000606717226435536
CAMB-71DE5	MN908947.3	23403	A	G	1	1	0	0	0.998933750355417	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000142166619277794
CAMB-71DE5	MN908947.3	241	C	T	1	1	0	0	0.998605515959095	TCG	NA	NA	NA	NA	NA	NA	0.000180766449746927
CAMB-71DE5	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998575295626158	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	8.0638658172728e-05
CAMB-71DE5	MN908947.3	3037	C	T	1	1	0	0	0.999355189031426	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000135749677594516
CAMB-71DF4	MN908947.3	14408	C	T	1	1	0	0	0.999446596568899	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000368935620734182
CAMB-71DF4	MN908947.3	23403	A	G	1	1	0	0	0.999874694568009	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.39790739928576e-05
CAMB-71DF4	MN908947.3	24745	C	A	1	1	0	0	1	TCT	S	V1061V	C3183A	GTC>GTA	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-71DF4	MN908947.3	25429	G	T	1	1	0	0	1	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0
CAMB-71DF4	MN908947.3	3037	C	T	1	1	0	3e-228	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-71DF4	MN908947.3	6270	C	T	1	1	0	0	0.999785683669096	ACG	ORF1ab:nsp3	T1184M	C3551T	ACG>ATG	Missense	ORF1ab:nsp3	0.000214316330904415
CAMB-71E00	MN908947.3	11074	C	INS	0.11	0.11	7.5e-31	2.3e-33	0.108935921952484	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.890804783975626
CAMB-71E00	MN908947.3	14408	C	T	0.94	1	0	0	0.969810418989963	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000238967659710053
CAMB-71E00	MN908947.3	23403	A	G	1	1	0	0	0.999855918161516	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.8027279494753e-05
CAMB-71E00	MN908947.3	241	C	T	1	1	0	0	0.999877700774562	TCG	NA	NA	NA	NA	NA	NA	4.0766408479413e-05
CAMB-71E00	MN908947.3	24127	TAACGGCCTTACTG	-	0.0821428571428571	0.0362142857142857	NA;NA;6.9e-17;1.4e-16;9.5e-17;7.8e-17;8.3e-17;7.7e-17;8.1e-16;5.5e-14;9.9e-15;2.1e-13;3.6e-12;1.3e-07	2.1e-10;1.3e-07;1.1e-06;1.5e-06;1.3e-06;1.3e-06;1.4e-06;1.3e-06;2.7e-06;1.1e-05;8.6e-06;2.6e-05;5.2e-05;1.2e-05	0.0696412021713226	TTA	S	.	2565-2578-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.983396176490044
CAMB-71E00	MN908947.3	28877	A	T	0.23	0.18	2e-92	1.2e-70	0.205767350928641	CAG	N	S202C	A604T	AGT>TGT	Missense	GU280_gp10	0.793499511241447
CAMB-71E00	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99897066392177	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000571591883395256
CAMB-71E00	MN908947.3	29392	G	T	0.058	0.023	3.5e-15	2.5e-07	0.0410396716826265	AGA	N	K373N	G1119T	AAG>AAT	Missense	GU280_gp10	0.958960328317373
CAMB-71E00	MN908947.3	3037	C	T	1	1	0	0	0.998540856031128	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000972762645914397
CAMB-71E00	MN908947.3	522	T	-	0.039	0.084	2.8e-05	3.9e-11	0.0492251595259799	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.950354112614824
CAMB-71E00	MN908947.3	522	TT	-	0.0195	0.082	2.8e-05;NA	3.9e-11;1.1e-11	0.0328472127572577	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.950354112614824
CAMB-71E00	MN908947.3	9542	TGTTTAACACCAGTTTACTCATTCTTACCTGG	-	0.03146875	0.029625	1.6e-06;7.4e-07;1.8e-07;2.2e-05;4.6e-05;2.3e-05;4.6e-05;4.7e-05;2.1e-05;3.9e-06;3.5e-05;2.8e-05;2.1e-05;2.2e-07;7.6e-05;9.3e-05;7.9e-11;3.5e-10;1.6e-10;1.2e-10;5.6e-11;1.3e-11;5.8e-11;9.2e-11;3.9e-13;6.6e-12;4.3e-11;1.3e-11;9e-11;6.9e-12;5.5e-14;8.2e-12	3.4e-06;1.6e-06;4.2e-07;3.9e-05;7.5e-05;4e-05;7.6e-05;7.7e-05;3.4e-05;7.1e-06;5.7e-05;3.8e-05;3.5e-05;4.3e-07;0.00011;0.00014;5.3e-10;1.6e-09;1.2e-09;7.7e-10;1.3e-10;3.8e-11;3.7e-10;6.2e-10;4.7e-12;6.2e-11;3e-10;8.8e-11;3.2e-10;1.6e-11;8.6e-13;8.1e-11	0.0296654345559663	CTG	ORF1ab:nsp4	.	988-1019-delfrshift	.	no-SNV	ORF1ab:nsp4	0.971510488495318
CAMB-71E2E	MN908947.3	14407	CC	TT	1	1	0;0	0;0	0.998901501281582	ACC	ORF1ab:RNA-dependent-RNA-polymerase	.	940-941-mnv	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.00114649681528662
CAMB-71E2E	MN908947.3	23403	A	G	1	1	0	0	0.999665327978581	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000334672021419009
CAMB-71E2E	MN908947.3	241	C	T	1	1	0	0	0.999420625724218	TCG	NA	NA	NA	NA	NA	NA	0.000579374275782155
CAMB-71E2E	MN908947.3	25019	G	T	0.65	0.19	0	1.1e-85	0.330386649041639	AGA	S	D1153Y	G3457T	GAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.669530733641771
CAMB-71E2E	MN908947.3	25350	C	T	1	1	0	0	0.99887986558387	CCA	S	P1263L	C3788T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	0.00112013441612994
CAMB-71E2E	MN908947.3	3037	C	T	0.99	1	2.4e-299	0	0.996078431372549	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00326797385620915
CAMB-71E3D	MN908947.3	11074	C	INS	0.11	0.11	2.8e-47	3.9e-37	0.110507489981981	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.883306887556141
CAMB-71E3D	MN908947.3	11083	G	-	0.17	0.15	7.6e-73	2.4e-67	0.161352519013104	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.19017864581474e-05
CAMB-71E3D	MN908947.3	11083	G	T	0.83	0.85	0	0	0.838528463122315	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.19017864581474e-05
CAMB-71E3D	MN908947.3	14012	A	G	0.013	0.013	9.3e-08	4e-08	0.0132426066474745	CAA	ORF1ab:RNA-dependent-RNA-polymerase	Q182R	A545G	CAA>CGA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.986746924888773
CAMB-71E3D	MN908947.3	14805	C	T	1	1	0	0	0.999342398573339	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	3.34373606776638e-05
CAMB-71E3D	MN908947.3	17474	C	T	0.73	0.73	0	0	0.727996323831093	ACT	ORF1ab:helicase	T413I	C1238T	ACT>ATT	Missense	ORF1ab:helicase	0.271970853232239
CAMB-71E3D	MN908947.3	17615	A	G	0.0079	0.0096	1.3e-05	1.9e-06	0.00861248572516178	AAG	ORF1ab:helicase	K460R	A1379G	AAG>AGG	Missense	ORF1ab:helicase	0.991371653343484
CAMB-71E3D	MN908947.3	224	T	C	0.044	0.041	1.1e-20	8.8e-20	0.0432187157123463	ATC	NA	NA	NA	NA	NA	NA	0.956669704126606
CAMB-71E3D	MN908947.3	25139	T	C	0.014	0.019	7.9e-08	2.4e-10	0.0156220232425224	TTT	S	L1193L	T3577C	TTA>CTA	Synonymous	GU280_gp02, spike glycoprotein	0.984330348637836
CAMB-71E3D	MN908947.3	26144	G	T	1	1	0	0	0.999743677375256	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-71E3D	MN908947.3	27499	T	C	0.0083	0.0056	1.2e-05	0.00014	0.00728777027092334	CTC	ORF7a	S36P	T106C	TCT>CCT	Missense	GU280_gp07	0.992567247561883
CAMB-71E3D	MN908947.3	28842	G	T	1	1	0	0	0.998181458786321	AGT	N	S190I	G569T	AGT>ATT	Missense	GU280_gp10	7.90670092903736e-05
CAMB-71E3D	MN908947.3	3447	C	T	0.033	0.033	1e-15	5.1e-16	0.0327460473712759	GCC	ORF1ab:nsp3	A243V	C728T	GCC>GTC	Missense	ORF1ab:nsp3	0.967213773429496
CAMB-71E3D	MN908947.3	7869	C	T	0.018	0.015	1.8e-09	5.2e-08	0.0169503496009605	TCA	ORF1ab:nsp3	S1717L	C5150T	TCA>TTA	Missense	ORF1ab:nsp3	0.982484638745674
CAMB-71E4C	MN908947.3	11075	T	-	0.036	0.039	1.3e-09	1e-10	0.0374474673744747	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958504755585048
CAMB-71E4C	MN908947.3	14408	C	T	1	1	0	0	0.998405295106142	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000394389382351932
CAMB-71E4C	MN908947.3	14805	C	T	0.037	0.04	2e-17	3e-19	0.0381928057553957	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.961565467625899
CAMB-71E4C	MN908947.3	1547	A	T	0.013	0.014	1.1e-06	1.3e-07	0.0131099507907291	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.973329326471583
CAMB-71E4C	MN908947.3	18465	T	G	0.0063	0.0049	3.3e-05	9.8e-05	0.00578509969753032	CTG	ORF1ab:3'-to-5'-exonuclease	P142P	T426G	CCT>CCG	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.993803776466097
CAMB-71E4C	MN908947.3	23403	A	G	1	1	0	0	0.996140729733486	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000117595492885473
CAMB-71E4C	MN908947.3	241	C	T	1	1	0	0	0.998543664071846	TCG	NA	NA	NA	NA	NA	NA	6.93493299120997e-05
CAMB-71E4C	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999151823579305	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000238530651188678
CAMB-71E4C	MN908947.3	3037	C	T	1	1	0	0	0.9993111818152	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.84025978285827e-05
CAMB-71E4C	MN908947.3	851	T	C	0.05	0.049	7.7e-23	8e-23	0.0492562465997001	CTA	ORF1ab:nsp2	Y16H	T46C	TAC>CAC	Missense	ORF1ab:nsp2	0.950279322195831
CAMB-71E5B	MN908947.3	11075	T	-	0.029	0.027	7e-08	6.7e-08	0.0284022961014111	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.971458183847564
CAMB-71E5B	MN908947.3	12316	A	G	0.0048	0.014	0.0065	2.1e-05	0.00744021257750221	GAT	ORF1ab:nsp8	R75R	A225G	AGA>AGG	Synonymous	ORF1ab:nsp8	0.992500738116327
CAMB-71E5B	MN908947.3	14408	C	T	1	1	0	0	0.999450473966204	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000377799148234648
CAMB-71E5B	MN908947.3	18011	TTCCACGTAGGAATGTGGCAACTTT	-	0.01396	0.0003764	1.4e-09;2e-08;2.5e-08;3.1e-08;3.1e-08;1.8e-08;2.4e-08;2.5e-08;5.6e-08;0.00033;0.00011;1.7e-07;1.2e-07;1.5e-07;1.7e-07;1.3e-07;2.9e-07;8.6e-08;9.8e-08;8.5e-08;6.7e-08;6.8e-08;1.4e-07;7.3e-08;5.5e-08	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.48;NA;NA;1.3e-05;NA;NA	0.00779354459230939	ATT	ORF1ab:helicase	.	1775-1799-delfrshift	.	no-SNV	ORF1ab:helicase	0.990768083947361
CAMB-71E5B	MN908947.3	18400	C	T	0.082	0.08	5e-37	1e-34	0.0810111797096613	ACC	ORF1ab:3'-to-5'-exonuclease	P121S	C361T	CCT>TCT	Missense	ORF1ab:3'-to-5'-exonuclease	0.918738528282997
CAMB-71E5B	MN908947.3	21716	C	T	0.0073	0.0038	3.4e-05	0.00078	0.00539755034253685	TCA	S	Q52*	C154T	CAG>TAG	Nonsense	GU280_gp02, spike glycoprotein	0.994602449657463
CAMB-71E5B	MN908947.3	21992	TA	-	0.022	0.0495	0.0026;0.003	1.1e-05;9.7e-06	0.0312806539509537	TTA	S	.	430-431-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.968824679556811
CAMB-71E5B	MN908947.3	23403	A	G	1	1	0	0	0.99983662800196	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000133667998395984
CAMB-71E5B	MN908947.3	23468	TA	-	0.0295	0.00335	3.4e-12;2.9e-15	0.0031;0.0011	0.0191215730915694	TTA	S	.	1906-1907-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.981117303609342
CAMB-71E5B	MN908947.3	241	C	T	1	1	0	0	0.999747811362899	TCG	NA	NA	NA	NA	NA	NA	0.000252188637100551
CAMB-71E5B	MN908947.3	28822	T	C	0.018	0.011	3e-08	3.5e-05	0.0160250506538957	CTT	N	S183S	T549C	TCT>TCC	Synonymous	GU280_gp10	0.983974949346104
CAMB-71E5B	MN908947.3	28849	C	T	0.0026	0.012	0.008	2.3e-06	0.00557006092254134	ACA	N	N192N	C576T	AAC>AAT	Synonymous	GU280_gp10	0.9940818102698
CAMB-71E5B	MN908947.3	28881	GGG	AAC	1	0.996666666666667	0;0;0	0;0;0	0.998451712792723	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000424088210347752
CAMB-71E5B	MN908947.3	3037	C	T	1	1	3.7e-292	0	0.999588477366255	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000411522633744856
CAMB-71E5B	MN908947.3	8182	A	G	0.034	0.028	1.5e-16	1.4e-13	0.0318514241724403	AAG	ORF1ab:nsp3	Q1821Q	A5463G	CAA>CAG	Synonymous	ORF1ab:nsp3	0.96814857582756
CAMB-71E5B	MN908947.3	9724	C	T	0.033	0.022	4.1e-16	1.3e-11	0.0278895582796399	TCT	ORF1ab:nsp4	F390F	C1170T	TTC>TTT	Synonymous	ORF1ab:nsp4	0.972040659672955
CAMB-71E6A	MN908947.3	11074	C	INS	0.11	0.14	1.7e-36	2.2e-43	0.116169166224623	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.883469161402324
CAMB-71E6A	MN908947.3	11083	G	-	0.15	0.1	2.1e-66	1.2e-43	0.135882417946734	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.21018897115703e-05
CAMB-71E6A	MN908947.3	11083	G	T	0.85	0.9	0	0	0.863962868825285	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.21018897115703e-05
CAMB-71E6A	MN908947.3	13497	TACACCGTGCGGCACAGGCACTAGTACTGATGTCG	-	0.000862	0.0185714285714286	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;2.9e-08;2e-08;NA;NA;NA;NA;NA	2e-06;8.4e-05;1.9e-06;3.7e-06;1.6e-06;3.3e-06;1.8e-06;1.8e-06;8.2e-07;5.8e-08;9.3e-07;2e-06;7.5e-09;2.2e-09;5.1e-09;1.5e-09;3.1e-09;2.7e-09;4.7e-09;1.8e-10;2.7e-09;1.1e-09;1.5e-09;2.5e-09;1.4e-09;9.6e-10;1.5e-09;1.5e-16;1.2e-16;6.7e-17;4.9e-10;1.5e-09;1.6e-09;1.1e-09;1.2e-09	0.00901667233752977	TTA	ORF1ab:RNA-dependent-RNA-polymerase	.	30-64-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.995297170193789
CAMB-71E6A	MN908947.3	14805	C	T	1	1	0	0	0.999871732382443	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	7.69605705343629e-05
CAMB-71E6A	MN908947.3	15004	G	T	0.013	0.0093	5.6e-06	2e-05	0.0103513174404015	TGA	ORF1ab:RNA-dependent-RNA-polymerase	E513*	G1537T	GAG>TAG	Nonsense	ORF1ab:RNA-dependent-RNA-polymerase	0.989648682559598
CAMB-71E6A	MN908947.3	18739	GATTACGTCTA	-	0.04373	0.0230909090909091	NA;5.9e-08;1.5e-09;6.6e-08;9.8e-08;9.1e-09;3.6e-08;8.1e-09;1.1e-08;8.9e-10;5.5e-10	8.8e-08;0.00016;2.9e-05;0.00015;0.00022;5.6e-05;0.00011;5.6e-05;5.9e-05;2.2e-05;1.5e-05	0.03785090567944	TGA	ORF1ab:3'-to-5'-exonuclease	.	700-710-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.990619103243778
CAMB-71E6A	MN908947.3	23540	TATGAGTGTGACATACCCATTGGTGCAGG	-	0.0453793103448276	0.0106551724137931	4.7e-06;8.2e-06;3.9e-06;4.9e-06;6.4e-06;5.7e-06;6e-06;6.2e-06;1.6e-05;1.5e-05;1e-04;5e-05;6.3e-05;0.00061;0.00037;1.1e-05;8.6e-06;1.1e-05;2e-05;3.8e-06;8.3e-06;2e-06;5.7e-06;6.2e-06;6.2e-06;5.9e-06;6.2e-06;2.5e-06;2.3e-06	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0087;0.0071;0.008;0.0091;0.0059;0.0074;0.0062;0.008;0.0081;0.0084;0.0079;0.0081;0.0067;0.0063	0.0112044817927171	ATA	S	.	1978-2006-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.988562714449104
CAMB-71E6A	MN908947.3	23569	TA	-	0.0315	0.052	0.0018;0.00086	2.6e-05;7.3e-06	0.0437388987566607	GTA	S	.	2007-2008-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.961959654178674
CAMB-71E6A	MN908947.3	24460	T	C	0.0024	0.022	0.0095	9.5e-08	0.00587467362924282	TTA	S	L966L	T2898C	CTT>CTC	Synonymous	GU280_gp02, spike glycoprotein	0.994125326370757
CAMB-71E6A	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-71E6A	MN908947.3	25013	G	T	0.017	0.0093	1.2e-09	2e-06	0.013162982784489	GGA	S	E1151*	G3451T	GAG>TAG	Nonsense	GU280_gp02, spike glycoprotein	0.986821549550664
CAMB-71E6A	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-71E6A	MN908947.3	26144	G	T	1	1	0	6.00000000077142e-315	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-71E6A	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.023027027027027	0.0297297297297297	0.025;0.0072;0.023;0.024;0.031;0.014;0.023;0.00043;0.00044;0.00023;0.00031;0.00027;0.00043;0.00034;0.00038;0.00053;3e-04;0.00047;0.00037;0.00035;0.00033;5e-04;0.00034;0.00041;0.00035;3e-04;0.00045;0.00031;0.00019;0.00033;0.00045;0.00042;0.00033;0.00045;0.00021;3e-04;0.00024	3e-05;1.9e-06;2e-05;2.1e-05;4.9e-05;6.1e-06;1.5e-05;7.6e-05;7.6e-05;5.6e-05;4.9e-05;4.1e-05;6.4e-05;5.8e-05;6.7e-05;9.5e-05;4.9e-05;8.5e-05;5.4e-05;6.3e-05;6.3e-05;9.6e-05;6e-05;7.1e-05;5.8e-05;3.9e-05;7.8e-05;5.9e-05;1.7e-05;5.7e-05;8.2e-05;7.6e-05;3.9e-05;8e-05;2.4e-05;5.1e-05;2.8e-05	0.0268518139801219	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.979260410701137
CAMB-71E6A	MN908947.3	28081	A	G	0.48	0.51	2.5e-129	5.9e-171	0.501795332136445	GAT	ORF8	D63G	A188G	GAT>GGT	Missense	GU280_gp09	0.498204667863555
CAMB-71E6A	MN908947.3	28198	G	INS	0.0081	0.0096	1.7e-05	2.7e-06	0.00855821458930655	TGT	ORF8	.	304-305-insfrshift	.	no-SNV	GU280_gp09	0.991427377642025
CAMB-71E6A	MN908947.3	2904	T	INS	0.016	0.0099	8.2e-06	4.6e-05	0.0109536082474227	ATA	ORF1ab:nsp3	.	184-185-insfrshift	.	no-SNV	ORF1ab:nsp3	0.989046391752577
CAMB-71E6A	MN908947.3	29082	TAACACAAGCTT	-	0.00133125	0.0113916666666667	0.0046;0.0043;NA;NA;NA;NA;NA;NA;NA;NA;0.5;NA	7.3e-06;6.7e-06;0.00012;0.00016;0.00017;9.1e-05;7.7e-05;7.8e-05;0.00025;7e-05;8.4e-05;5.6e-05	0.00349791906203948	GTA	N	.	809-820-delinframe	.	no-SNV	GU280_gp10	0.988192037318993
CAMB-71E6A	MN908947.3	29688	G	T	0.99	1	2.70006875452241e-320	0	0.996354799513973	AGT	NA	NA	NA	NA	NA	NA	0.00364520048602673
CAMB-71E6A	MN908947.3	6762	C	T	0.047	0.039	4.5e-15	2.9e-15	0.0417344173441734	ACT	ORF1ab:nsp3	T1348I	C4043T	ACT>ATT	Missense	ORF1ab:nsp3	0.958265582655827
CAMB-71E6A	MN908947.3	9460	G	A	1	1	0	0	1	TGA	ORF1ab:nsp4	M302I	G906A	ATG>ATA	Missense	ORF1ab:nsp4	0
CAMB-71E79	MN908947.3	101	G	A	0.031	0.036	3.4e-15	1.1e-17	0.0326809340893848	CGG	NA	NA	NA	NA	NA	NA	0.967273336991647
CAMB-71E79	MN908947.3	11074	C	INS	0.087	0.11	1.5e-36	1.7e-35	0.0938083424976343	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.903378430219176
CAMB-71E79	MN908947.3	11083	G	-	0.16	0.19	1.3e-71	4.2e-86	0.170543270862842	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	8.19413066126634e-05
CAMB-71E79	MN908947.3	11083	G	T	0.84	0.81	0	0	0.829199199316375	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	8.19413066126634e-05
CAMB-71E79	MN908947.3	14805	C	T	1	1	0	0	0.999462746622162	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000320065842116092
CAMB-71E79	MN908947.3	23559	TTGGTGCAGGTATATGCGCTAGTT	-	0.0367083333333333	0.048875	0.00018;0.00037;0.00024;0.00046;0.00048;0.00049;0.00047;0.00049;0.00028;0.00027;8.4e-05;2.7e-05;0.00018;8.3e-05;0.00016;8.5e-05;0.00019;0.00034;2e-04;0.00027;9.9e-06;1.4e-05;0.00078;0.0082	3.8e-05;6.7e-05;1.9e-05;4.5e-05;4.5e-05;4.9e-05;4.4e-05;4.5e-05;2.2e-05;1.9e-05;1.2e-06;1.7e-07;9.1e-06;2.9e-06;9e-06;2.6e-06;8.6e-06;2e-05;9.6e-06;1.1e-05;4.2e-08;1.1e-07;0.00025;0.00082	0.0403422290214743	ATT	S	.	1997-2020-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.945880452342488
CAMB-71E79	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-71E79	MN908947.3	2558	C	T	1	1	0	0	0.99852209085252	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000388923459863099
CAMB-71E79	MN908947.3	25720	G	T	1	1	0	0	0.999847638395124	TGC	ORF3a	A110S	G328T	GCT>TCT	Missense	GU280_gp03	0
CAMB-71E79	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-71E79	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCT	-	0.034	0.0462	0.00088;7.4e-05;0.00031;0.00031;0.00054;1.8e-06;7.3e-06;5e-06;5.2e-06;2e-06;3.2e-06;2.2e-06;4.9e-06;3.3e-06;3.9e-06;6.3e-06;2.3e-06;5.6e-06;3.9e-06;3.7e-06;2e-06;6.2e-06;3.7e-06;4.8e-06;3.4e-06;2.7e-06;5.1e-06;3e-06;1.3e-06;3.7e-06;4.9e-06;4.7e-06;2.9e-06;5.4e-06;1.3e-06;2.8e-06;2.7e-06;0.0063;0.01;0.0057	7.1e-06;2.7e-07;1.3e-06;1.5e-06;3.9e-06;9.7e-09;6e-08;1.5e-08;1.4e-08;7.6e-09;7.1e-09;4e-09;1.1e-08;8.1e-09;1.1e-08;2.2e-08;5.2e-09;1.7e-08;7.1e-09;1.1e-08;9.7e-09;1.8e-08;8.5e-09;1.1e-08;8.7e-09;4.3e-09;1.4e-08;8.8e-09;5.1e-10;9.7e-09;1.6e-08;1.4e-08;3.4e-09;1.4e-08;7.9e-10;5.6e-09;3.1e-09;0.00024;0.00093;0.00067	0.0402410996921209	GTC	M	.	258-297-delfrshift	.	no-SNV	GU280_gp05	0.974980217250558
CAMB-71E79	MN908947.3	28303	A	G	0.14	0.13	3.9e-63	4.5e-61	0.136791311919505	GAA	N	R10R	A30G	CGA>CGG	Synonymous	GU280_gp10	0.862991002321981
CAMB-71E79	MN908947.3	5222	AC	GG	0.013	0.00585	3.1e-06;1.2e-05	0.0036;0.0045	0.011402810925484	CAC	ORF1ab:nsp3	.	2503-2504-mnv	.	no-SNV	ORF1ab:nsp3	0.987958555026603
CAMB-71E79	MN908947.3	5225	A	C	0.014	0.006	7.4e-06	0.0047	0.0118502558577969	TAA	ORF1ab:nsp3	K836Q	A2506C	AAA>CAA	Missense	ORF1ab:nsp3	0.986533800161594
CAMB-71E79	MN908947.3	5229	AG	-	0.0155	0.0064	8.5e-06;6e-06	0.0054;0.0051	0.0135759676487579	AAG	ORF1ab:nsp3	.	2510-2511-delfrshift	.	no-SNV	ORF1ab:nsp3	0.986003573555688
CAMB-71E88	MN908947.3	10219	A	G	0.014	0.028	3.5e-08	3.9e-14	0.0192696876374835	AAG	ORF1ab:3C-like-proteinase	E55E	A165G	GAA>GAG	Synonymous	ORF1ab:3C-like-proteinase	0.980642322921249
CAMB-71E88	MN908947.3	11074	C	INS	0.041	0.024	1.3e-10	0.00017	0.0357120101943294	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.922061165976426
CAMB-71E88	MN908947.3	11074	C	T	0.024	0.063	1.9e-18	3.6e-36	0.0355527237973877	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.922061165976426
CAMB-71E88	MN908947.3	11074	CT	-	0.0119	0.0315	0.00023;6.7e-06	2.2e-12;2.5e-12	0.0188217113032322	TCT	ORF1ab:nsp6	.	102-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.922061165976426
CAMB-71E88	MN908947.3	11606	C	T	0.04	0.094	4.5e-17	1.9e-33	0.0587889476778366	GCT	ORF1ab:nsp6	L212L	C634T	CTA>TTA	Synonymous	ORF1ab:nsp6	0.93885949441505
CAMB-71E88	MN908947.3	14048	GT	-	0.0011	0.014	NA;0.0094	2.9e-08;3.3e-08	0.00508025814992553	GGT	ORF1ab:RNA-dependent-RNA-polymerase	.	581-582-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.995622979358369
CAMB-71E88	MN908947.3	14408	C	T	1	1	0	0	0.996203750920732	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000358849415453189
CAMB-71E88	MN908947.3	15579	C	T	0.043	0.061	2.9e-20	3.1e-28	0.0496822559079368	ACA	ORF1ab:RNA-dependent-RNA-polymerase	N704N	C2112T	AAC>AAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.950272674008083
CAMB-71E88	MN908947.3	1727	G	T	0.014	0.0086	4.7e-08	2.8e-06	0.0121318707523548	TGT	ORF1ab:nsp2	V308L	G922T	GTG>TTG	Missense	ORF1ab:nsp2	0.987778705138905
CAMB-71E88	MN908947.3	18910	G	A	0.0055	0.015	0.00017	1.5e-08	0.00919125481226827	TGA	ORF1ab:3'-to-5'-exonuclease	D291N	G871A	GAC>AAC	Missense	ORF1ab:3'-to-5'-exonuclease	0.990808745187732
CAMB-71E88	MN908947.3	20268	A	G	1	1	1.5e-228	2.2e-161	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-71E88	MN908947.3	2094	C	T	0.0058	0.0082	0.00019	2.9e-05	0.00644442676426128	TCG	ORF1ab:nsp2	S430L	C1289T	TCG>TTG	Missense	ORF1ab:nsp2	0.993555573235739
CAMB-71E88	MN908947.3	21994	TT	-	0.0185	0.00875	2.2e-05;5e-05	0.0039;0.0049	0.0157540199913081	ATT	S	.	432-433-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.98404807429664
CAMB-71E88	MN908947.3	22289	G	T	0.016	0.01	8.8e-09	1.4e-05	0.0151065093779173	TGC	S	A243S	G727T	GCT>TCT	Missense	GU280_gp02, spike glycoprotein	0.978443520325893
CAMB-71E88	MN908947.3	22682	TTTTCCACTTTTAAGTG	-	0.0104521764705882	0.00813529411764706	0.48;NA;NA;NA;3.6e-09;5.3e-09;4.7e-09;3.9e-09;4.1e-14;2.5e-10;1.3e-08;4.3e-07;4.6e-07;NA;NA;NA;NA	0.00011;2.3e-05;3.6e-05;4.7e-05;3.4e-05;4.4e-05;3.7e-05;3.1e-05;0.00012;1.5e-05;4.6e-05;0.00024;0.00026;4e-05;8.9e-05;4.1e-05;4.9e-05	0.0145031078088162	ATT	S	.	1120-1136-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.997445145776976
CAMB-71E88	MN908947.3	2306	CTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGC	-	0.0123692307692308	0.000186615384615385	1.6e-06;1.7e-06;7.9e-06;1e-05;1.9e-06;4.3e-06;2e-06;2.7e-06;3.4e-06;2.8e-06;1.5e-06;1.5e-06;1.4e-05;1.5e-06;1.4e-06;1.6e-06;1.7e-06;9.6e-07;8.2e-07;1.7e-06;5.8e-06;1.5e-06;2.9e-06;3.2e-06;1.6e-06;1.9e-06;2.2e-06;2.2e-06;1.8e-06;1.5e-06;2e-06;1.5e-06;7.4e-07;1.1e-06;1.4e-06;1.1e-06;5e-07;9.3e-07;1.4e-06;1.8e-06;2.2e-07;2.5e-06;1.6e-06;8.7e-07;1.4e-06;1.5e-06;1.2e-06;1.4e-06;1.7e-06;1e-06;1.5e-06;8.3e-07;1.3e-06;9.4e-07;4.7e-07;1.3e-06;4.7e-07;8.8e-07;1.3e-06;8e-07;1.4e-06;8.5e-07;2.1e-07;3.5e-07;6.1e-07	NA;NA;NA;NA;NA;0.0021;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00048;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00684931506849315	GCT	ORF1ab:nsp2	.	1501-1565-delfrshift	.	no-SNV	ORF1ab:nsp2	0.993415145166118
CAMB-71E88	MN908947.3	23403	A	G	1	1	0	0	0.996488764044944	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.16076058772688e-05
CAMB-71E88	MN908947.3	23561	GGTGCAGGTATATGCGCTAG	-	0.0274	0.04085	0.002;0.0029;0.0031;0.0031;0.0031;0.0031;0.0023;0.0021;0.0014;0.00049;0.0014;0.00088;0.0013;0.00082;0.0014;0.0022;0.0015;0.0015;0.00017;0.00022	0.00049;0.00086;0.00088;9e-04;0.00084;0.00087;0.00058;0.00053;0.00028;9.9e-05;1.4e-05;4.2e-06;1.4e-05;3.9e-06;1.1e-05;3.2e-05;1.4e-05;1.6e-05;9.2e-08;2.1e-07	0.0331782673571491	TGG	S	.	1999-2018-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.970115344285215
CAMB-71E88	MN908947.3	241	C	T	0.99	1	0	0	0.995142047484105	TCG	NA	NA	NA	NA	NA	NA	9.52539708999119e-05
CAMB-71E88	MN908947.3	25552	G	T	0.017	0.007	3.1e-09	5.5e-05	0.012553750840653	TGC	ORF3a	A54S	G160T	GCT>TCT	Missense	GU280_gp03	0.987364731296745
CAMB-71E88	MN908947.3	2569	ACCTACTAGTGAAGCTGTTG	-	0.00997	0.000245	5.3e-05;5.2e-05;0.00011;0.00014;0.00016;5.9e-05;3.7e-05;4.9e-05;4.6e-05;4.1e-05;4.1e-05;5.2e-05;2.2e-05;2.1e-05;2.8e-05;6.9e-05;1e-04;7.9e-05;3.2e-05;8.9e-05	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0066	0.00624442462087422	AAC	ORF1ab:nsp2	.	1764-1783-delfrshift	.	no-SNV	ORF1ab:nsp2	0.993928881179532
CAMB-71E88	MN908947.3	26638	A	-	0.0079	0.0076	1.7e-05	1.8e-05	0.00779572556403396	TAT	M	.	116-116-delfrshift	.	no-SNV	GU280_gp05	0.992138208965084
CAMB-71E88	MN908947.3	26638	ATG	-	0.0077	0.00253333333333333	1.7e-05;1.6e-05;1.7e-05	1.8e-05;NA;NA	0.0045611125287063	TAT	M	.	116-118-delinframe	.	no-SNV	GU280_gp05	0.992138208965084
CAMB-71E88	MN908947.3	26787	GGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.034	0.0298	1.4e-05;1.5e-05;6.4e-06;9.3e-06;7e-06;1.4e-05;1e-05;1.3e-05;1.8e-05;9e-06;1.6e-05;1.1e-05;1.1e-05;8.2e-06;1.8e-05;9.9e-06;1.3e-05;1.1e-05;9e-06;1.5e-05;8.8e-06;4.6e-06;1e-05;1.4e-05;1.3e-05;1.1e-05;1.5e-05;4.4e-06;8.7e-06;6.7e-06	7.2e-05;6.8e-05;4.6e-05;4.5e-05;3.9e-05;5.9e-05;5e-05;6.6e-05;9.2e-05;4.7e-05;7.7e-05;5e-05;5.9e-05;5e-05;9.1e-05;5.2e-05;6.4e-05;5.3e-05;4.1e-05;7.2e-05;5.3e-05;1.2e-05;5.1e-05;7.4e-05;7e-05;4.3e-05;7.6e-05;2.2e-05;4.7e-05;2.9e-05	0.0317610845096698	AGG	M	.	265-294-delinframe	.	no-SNV	GU280_gp05	0.96886238448582
CAMB-71E88	MN908947.3	27692	TTTTTC	-	0.168333333333333	0.0315	5.4e-23;1.3e-22;1.5e-23;9.8e-23;1.4e-22;7.5e-23	0.00074;0.00068;0.00067;0.00087;0.001;0.00098	0.123152709359606	ATT	ORF7a	.	299-304-delinframe	.	no-SNV	GU280_gp07	0.874371859296482
CAMB-71E88	MN908947.3	29574	TTTTCGCT	-	0.0026475	0.042875	0.0097;0.0058;0.006;0.0064;0.01;0.012;0.0074;0.49	2.4e-18;2.8e-18;2.5e-18;8e-18;1.7e-17;1.2e-17;1.4e-17;1.7e-15	0.0233463035019455	GTT	ORF10	.	17-24-delfrshift	.	no-SNV	GU280_gp11	0.975210708973723
CAMB-71E88	MN908947.3	3037	C	T	1	1	0	0	0.999635435654393	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.0001822821728035
CAMB-71E88	MN908947.3	7735	C	T	0.025	0.0059	1.7e-08	0.003	0.017640832647301	TCG	ORF1ab:nsp3	I1672I	C5016T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.982359167352699
CAMB-71E88	MN908947.3	9891	C	T	0.0052	0.0086	0.00029	9.9e-06	0.00626235992089651	GCT	ORF1ab:nsp4	A446V	C1337T	GCT>GTT	Missense	ORF1ab:nsp4	0.993596383840286
CAMB-71E88	MN908947.3	9951	C	A	0.0061	0.0076	6.7e-05	1.1e-05	0.00652836210648484	GCT	ORF1ab:nsp4	A466D	C1397A	GCT>GAT	Missense	ORF1ab:nsp4	0.993326563180038
CAMB-71E88	MN908947.3	9996	C	T	0.0088	0.0067	1.2e-05	9.9e-05	0.00814784469024535	TCA	ORF1ab:nsp4	S481L	C1442T	TCA>TTA	Missense	ORF1ab:nsp4	0.991852155309755
CAMB-71E97	MN908947.3	1059	C	T	1	1	0	0	0.99969777984424	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.000139486225735209
CAMB-71E97	MN908947.3	11075	T	-	0.035	0.035	4e-09	1.3e-09	0.0351857885080334	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960253090759444
CAMB-71E97	MN908947.3	14408	C	T	1	1	0	0	0.998802326907722	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000342192312079389
CAMB-71E97	MN908947.3	20148	C	T	0.95	0.96	0	1.8e-303	0.954570333880679	TCA	ORF1ab:endoRNAse	F176F	C528T	TTC>TTT	Synonymous	ORF1ab:endoRNAse	0.0454296661193213
CAMB-71E97	MN908947.3	23403	A	G	1	1	0	0	0.999251895880303	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.14880098380816e-05
CAMB-71E97	MN908947.3	241	C	T	1	1	0	0	0.999008303607111	TCG	NA	NA	NA	NA	NA	NA	0.000118411509598733
CAMB-71E97	MN908947.3	24368	G	T	1	1	0	0	0.999912705687224	AGA	S	D936Y	G2806T	GAC>TAC	Missense	GU280_gp02, spike glycoprotein	4.36471563877613e-05
CAMB-71E97	MN908947.3	25563	G	T	1	1	0	0	0.999901246272047	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	1.9750745590646e-05
CAMB-71E97	MN908947.3	29762	C	G	0.065	0.044	2.7e-27	1.8e-19	0.0536403567150273	ACA	NA	NA	NA	NA	NA	NA	0.945561027552243
CAMB-71E97	MN908947.3	3037	C	T	1	1	0	0	0.999359765857228	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.14620203960306e-05
CAMB-71EA6	MN908947.3	1059	C	T	1	1	0	0	0.999645176170032	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.000248376680977894
CAMB-71EA6	MN908947.3	11075	T	-	0.039	0.041	8.8e-10	5.8e-11	0.0397639152162674	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956617266930898
CAMB-71EA6	MN908947.3	11083	G	T	0.023	0.021	3.1e-05	9.6e-05	0.0224492691925642	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.971647509578544
CAMB-71EA6	MN908947.3	14408	C	T	1	1	0	0	0.996264292363879	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000489341894827298
CAMB-71EA6	MN908947.3	16375	C	T	0.016	0.017	3.9e-07	1.8e-07	0.0166090679321195	TCC	ORF1ab:helicase	P47S	C139T	CCG>TCG	Missense	ORF1ab:helicase	0.983390932067881
CAMB-71EA6	MN908947.3	23403	A	G	1	1	0	0	0.999619957652424	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.23890185858805e-05
CAMB-71EA6	MN908947.3	23559	TTGGTGCAGGTATATGCGCTAG	-	0.0361818181818182	0.0352727272727273	0.00054;0.00087;0.00024;4e-04;0.00049;0.00049;0.00047;0.00045;0.00029;0.00027;0.00011;6.8e-05;0.00042;0.00017;0.00039;0.00012;0.00027;0.00049;3e-04;0.00041;1.9e-05;4.1e-05	0.00053;0.00076;0.00038;0.00053;0.00057;0.00058;0.00052;5e-04;0.00033;0.00031;0.00014;9.9e-05;5e-04;0.00018;0.00046;0.00013;0.00026;0.00052;0.00032;0.00043;2e-05;3.9e-05	0.034072249589491	ATT	S	.	1997-2018-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.956658511010136
CAMB-71EA6	MN908947.3	241	C	T	1	1	0	0	0.99813520657566	TCG	NA	NA	NA	NA	NA	NA	0.000217257486330883
CAMB-71EA6	MN908947.3	24368	G	T	1	1	0	0	0.999730676003232	AGA	S	D936Y	G2806T	GAC>TAC	Missense	GU280_gp02, spike glycoprotein	0
CAMB-71EA6	MN908947.3	25563	G	T	1	1	0	0	0.999598645866052	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.00013960143789481
CAMB-71EA6	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0422105263157895	0.0429736842105263	5.7e-05;3.1e-06;2.7e-05;2.3e-05;4.8e-05;3.1e-07;1.1e-06;1.8e-07;1.8e-07;6.9e-08;9.5e-08;6.8e-08;1.5e-07;8.9e-08;1.3e-07;2.1e-07;7.5e-08;1.8e-07;1.2e-07;1.1e-07;8.2e-08;1.9e-07;8.3e-08;1.3e-07;1e-07;7.3e-08;1.5e-07;8.3e-08;8.4e-08;9.5e-08;1.6e-07;1.4e-07;8.9e-08;1.5e-07;3.1e-08;8.7e-08;5e-08;0.00071	5e-05;4e-06;1.4e-05;1.1e-05;2.7e-05;2.7e-07;9.1e-07;1e-07;9.3e-08;5.3e-08;3.6e-08;3e-08;6.2e-08;4.2e-08;5.9e-08;1.1e-07;3.4e-08;8.3e-08;4.2e-08;5.5e-08;4.6e-08;1.1e-07;3.9e-08;6.6e-08;4.5e-08;2.4e-08;7.2e-08;4.6e-08;1.3e-08;3.9e-08;7.8e-08;7.2e-08;2.6e-08;7.8e-08;1.2e-08;4.6e-08;1.6e-08;0.00057	0.0447861370431387	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.972021247366975
CAMB-71EA6	MN908947.3	3037	C	T	1	1	0	0	0.998858323366315	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00021746221593998
CAMB-71EA6	MN908947.3	522	TT	-	0.04	0.042	3.8e-06;0.00022	9.3e-07;1e-04	0.0405508409980182	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.949405428183889
CAMB-71EA6	MN908947.3	790	T	G	0.012	0.0079	2.1e-07	1.1e-05	0.0106916817359855	GTG	ORF1ab:leader-protein	R175R	T525G	CGT>CGG	Synonymous	ORF1ab:leader-protein	0.988494575045208
CAMB-71EA6	MN908947.3	8334	C	T	1	1	0	0	0.998110602427149	GCT	ORF1ab:nsp3	A1872V	C5615T	GCT>GTT	Missense	ORF1ab:nsp3	0.00109003706126008
CAMB-71EB5	MN908947.3	11075	T	-	0.038	0.039	3.2e-10	7.5e-11	0.0384956275112267	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957338690616875
CAMB-71EB5	MN908947.3	14408	C	T	1	1	0	0	0.998631896359169	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000293165065892339
CAMB-71EB5	MN908947.3	23403	A	G	1	1	0	0	0.999266820822289	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.4597597428233e-05
CAMB-71EB5	MN908947.3	241	C	T	1	1	0	0	0.999230045341774	TCG	NA	NA	NA	NA	NA	NA	5.13303105483788e-05
CAMB-71EB5	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99917462563377	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-71EB5	MN908947.3	3037	C	T	1	1	0	0	0.99927115473385	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000121474211024999
CAMB-71EB5	MN908947.3	3340	G	T	1	1	0	0	0.999208927814663	TGA	ORF1ab:nsp3	V207V	G621T	GTG>GTT	Synonymous	ORF1ab:nsp3	0.000141262890238734
CAMB-71EC4	MN908947.3	106	C	T	0.012	0.011	7.9e-07	1.7e-06	0.0119820828667413	GCA	NA	NA	NA	NA	NA	NA	0.9880039193729
CAMB-71EC4	MN908947.3	1066	T	C	1	1	0	0	0.998975199836032	ATG	ORF1ab:nsp2	N87N	T261C	AAT>AAC	Synonymous	ORF1ab:nsp2	0.00040992006558721
CAMB-71EC4	MN908947.3	11074	C	INS	0.1	0.12	3e-46	2.1e-37	0.104917603040883	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.891746005266733
CAMB-71EC4	MN908947.3	11083	G	-	0.15	0.16	4.7e-65	3.3e-69	0.151973684210526	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.26860254083485e-05
CAMB-71EC4	MN908947.3	11083	G	T	0.85	0.84	0	0	0.847822141560799	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.26860254083485e-05
CAMB-71EC4	MN908947.3	14805	C	T	1	1	0	0	0.999555922096048	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	9.515955084692e-05
CAMB-71EC4	MN908947.3	15966	T	C	0.008	0.0097	1.9e-05	1.6e-06	0.00838838987454532	GTT	ORF1ab:RNA-dependent-RNA-polymerase	C833C	T2499C	TGT>TGC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.991113184936955
CAMB-71EC4	MN908947.3	2480	A	G	1	1	0	0	0.999884739511296	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000115260488704472
CAMB-71EC4	MN908947.3	2558	C	T	1	1	0	0	0.998969175007482	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000166262095567453
CAMB-71EC4	MN908947.3	25728	C	T	0.012	0.015	3.4e-07	2.4e-08	0.0128796749087403	TCT	ORF3a	V112V	C336T	GTC>GTT	Synonymous	GU280_gp03	0.987085887457814
CAMB-71EC4	MN908947.3	26144	G	T	1	1	0	0	0.999729418927146	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000135290536426977
CAMB-71EC4	MN908947.3	27518	G	A	0.023	0.022	6.4e-09	3.3e-07	0.022673031026253	GGC	ORF7a	G42D	G125A	GGC>GAC	Missense	GU280_gp07	0.977326968973747
CAMB-71EC4	MN908947.3	3164	G	A	0.041	0.043	1.6e-19	2.2e-20	0.0425095896169408	TGC	ORF1ab:nsp3	A149T	G445A	GCT>ACT	Missense	ORF1ab:nsp3	0.957227681151805
CAMB-71EC4	MN908947.3	5157	C	T	0.0042	0.011	0.001	5e-06	0.00556263761733689	GCT	ORF1ab:nsp3	A813V	C2438T	GCT>GTT	Missense	ORF1ab:nsp3	0.994437362382663
CAMB-71EC4	MN908947.3	9559	C	T	0.099	0.1	1.1e-44	1.2e-47	0.10013074312278	ACT	ORF1ab:nsp4	Y335Y	C1005T	TAC>TAT	Synonymous	ORF1ab:nsp4	0.89835052363281
CAMB-71ED3	MN908947.3	11075	T	-	0.043	0.046	1.4e-10	8.5e-12	0.0442314824784944	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951461421580943
CAMB-71ED3	MN908947.3	12032	G	A	0.0061	0.0069	8.9e-05	2.9e-05	0.00641337346072466	GGG	ORF1ab:nsp7	G64S	G190A	GGT>AGT	Missense	ORF1ab:nsp7	0.993481489269427
CAMB-71ED3	MN908947.3	14408	C	T	1	1	0	0	0.998954946586159	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000429633070134696
CAMB-71ED3	MN908947.3	1588	A	G	0.024	0.022	1.3e-11	1.3e-10	0.0231956743201943	AAG	ORF1ab:nsp2	E261E	A783G	GAA>GAG	Synonymous	ORF1ab:nsp2	0.976412506856829
CAMB-71ED3	MN908947.3	23403	A	G	1	1	0	0	0.998772425161777	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000184136225733476
CAMB-71ED3	MN908947.3	241	C	T	1	1	0	0	0.997697002264614	TCG	NA	NA	NA	NA	NA	NA	0.000211108125743676
CAMB-71ED3	MN908947.3	25071	C	T	0.0066	0.0079	9.3e-05	1.9e-05	0.00707884140797506	TCT	S	S1170F	C3509T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.992877862925921
CAMB-71ED3	MN908947.3	26397	T	A	0.016	0.014	1.3e-08	4.5e-08	0.0151734834946218	TTG	E	L51L	T153A	CTT>CTA	Synonymous	GU280_gp04	0.984489327983275
CAMB-71ED3	MN908947.3	2710	C	T	0.0078	0.0061	3.4e-05	0.00012	0.00717797146907139	TCA	ORF1ab:nsp2	L635L	C1905T	CTC>CTT	Synonymous	ORF1ab:nsp2	0.992761709442953
CAMB-71ED3	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999466467481193	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000246305418719212
CAMB-71ED3	MN908947.3	29738	CCACGCGGAGTACGATCGAGTGT	-	0.0132608695652174	0.0215217391304348	9.5e-06;1.1e-05;8.1e-06;1.3e-05;1.4e-05;9.5e-06;1.4e-05;1.6e-05;1.5e-05;3.3e-05;8.1e-05;8.9e-05;0.00021;0.00018;3.9e-05;4.2e-05;4.8e-05;4.9e-05;2e-05;0.00011;5.9e-05;9.3e-05;5.2e-06	4e-09;4.8e-09;1.9e-09;5.2e-09;5.4e-09;3.9e-09;4.8e-09;6e-09;5.8e-09;2.3e-08;1.4e-07;7.2e-08;1.1e-06;1.1e-06;9.3e-08;7.3e-08;6.2e-08;7.6e-08;1.5e-08;3.1e-07;6.6e-08;2.7e-07;1.5e-09	0.0184605419410558	GCC	NA	NA	NA	NA	NA	NA	0.981759656652361
CAMB-71ED3	MN908947.3	3037	C	T	1	1	0	0	0.999545764251647	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-71ED3	MN908947.3	3994	G	A	0.017	0.015	8.4e-09	1.2e-08	0.0162290637649942	TGG	ORF1ab:nsp3	L425L	G1275A	CTG>CTA	Synonymous	ORF1ab:nsp3	0.983548111560887
CAMB-71EE2	MN908947.3	10097	G	A	1	1	0	0	0.999701095981402	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000199269345732315
CAMB-71EE2	MN908947.3	11075	T	-	0.039	0.04	5.7e-10	5.8e-11	0.0393568916429409	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956437596531383
CAMB-71EE2	MN908947.3	13536	C	T	1	1	0	0	0.999718431164701	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000149065853981715
CAMB-71EE2	MN908947.3	14184	C	T	1	1	0	0	0.99980916713381	CCA	ORF1ab:RNA-dependent-RNA-polymerase	T239T	C717T	ACC>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000143124649642785
CAMB-71EE2	MN908947.3	14408	C	T	1	1	0	0	0.998927767793769	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000347342827370615
CAMB-71EE2	MN908947.3	21058	C	T	1	1	0	0	0.999592739120317	CCC	ORF1ab:2'-O-ribose-methyltransferase	P134S	C400T	CCT>TCT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.000145450314172679
CAMB-71EE2	MN908947.3	23403	A	G	1	1	0	0	0.99786039946678	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.60104851628225e-05
CAMB-71EE2	MN908947.3	23731	C	T	1	1	0	0	0.999901185770751	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	9.88142292490119e-05
CAMB-71EE2	MN908947.3	241	C	T	1	1	0	0	0.999123936208253	TCG	NA	NA	NA	NA	NA	NA	0.000143030823142387
CAMB-71EE2	MN908947.3	2582	G	A	0.96	0.96	0	0	0.963857302698342	AGC	ORF1ab:nsp2	A593T	G1777A	GCT>ACT	Missense	ORF1ab:nsp2	0.0358564700372095
CAMB-71EE2	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999559451958236	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-71EE2	MN908947.3	3037	C	T	1	1	0	0	0.999380311614731	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.42634560906516e-05
CAMB-71EE2	MN908947.3	4002	C	T	1	1	0	0	0.999503049469166	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0.000180709283939462
CAMB-71EE2	MN908947.3	583	C	T	1	1	0	0	0.999534753884805	TCC	ORF1ab:leader-protein	V106V	C318T	GTC>GTT	Synonymous	ORF1ab:leader-protein	0.000199391192226402
CAMB-71EF1	MN908947.3	10387	T	C	0.029	0.03	4.1e-14	1.5e-14	0.0296989365139574	CTT	ORF1ab:3C-like-proteinase	T111T	T333C	ACT>ACC	Synonymous	ORF1ab:3C-like-proteinase	0.96969696969697
CAMB-71EF1	MN908947.3	11075	T	-	0.039	0.043	1.5e-10	6e-12	0.040145839176249	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955286670139028
CAMB-71EF1	MN908947.3	1514	C	T	1	1	0	0	0.999086869178791	CCA	ORF1ab:nsp2	H237Y	C709T	CAT>TAT	Missense	ORF1ab:nsp2	0.000365252328483594
CAMB-71EF1	MN908947.3	15982	G	T	0.019	0.018	6.8e-10	3.5e-10	0.0184527449781249	CGT	ORF1ab:RNA-dependent-RNA-polymerase	V839L	G2515T	GTA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.981076821752834
CAMB-71EF1	MN908947.3	1601	C	T	0.018	0.015	4e-10	4.8e-09	0.0168461831949051	TCT	ORF1ab:nsp2	L266F	C796T	CTT>TTT	Missense	ORF1ab:nsp2	0.982860329292989
CAMB-71EF1	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999457756661847	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000258211113406321
CAMB-71EF1	MN908947.3	20270	C	T	1	1	0	0	1	GCT	ORF1ab:endoRNAse	A217V	C650T	GCT>GTT	Missense	ORF1ab:endoRNAse	0
CAMB-71EF1	MN908947.3	25453	A	G	0.026	0.025	2.6e-13	6.6e-13	0.0256671117610903	CAA	ORF3a	K21E	A61G	AAG>GAG	Missense	GU280_gp03	0.973675844089782
CAMB-71EF1	MN908947.3	26882	C	T	0.023	0.022	1.3e-11	1.4e-11	0.0224279345199605	TCA	M	L120L	C360T	CTC>CTT	Synonymous	GU280_gp05	0.977538032195487
CAMB-71EF1	MN908947.3	27393	C	T	0.0073	0.0062	3.7e-05	0.00011	0.00686336383717261	ACA	NA	NA	NA	NA	NA	NA	0.993105080467024
CAMB-71EF1	MN908947.3	28657	C	A	0.0069	0.0082	3.7e-05	1.3e-05	0.00755494505494505	ACG	N	D128E	C384A	GAC>GAA	Missense	GU280_gp10	0.992445054945055
CAMB-71EF1	MN908947.3	29683	A	T	0.96	0.98	0	0	0.969885773624091	TAA	NA	NA	NA	NA	NA	NA	0.0282104534440983
CAMB-71EF1	MN908947.3	5806	C	T	0.0096	0.01	7.9e-06	2.4e-06	0.00982233502538071	GCA	ORF1ab:nsp3	C1029C	C3087T	TGC>TGT	Synonymous	ORF1ab:nsp3	0.99010152284264
CAMB-71F0D	MN908947.3	11075	T	-	0.03	0.037	1.4e-07	1.2e-09	0.0322275068579661	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964940498509996
CAMB-71F0D	MN908947.3	11083	G	T	0.029	0.032	2.5e-06	3.6e-07	0.0301366389357573	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.964782070162777
CAMB-71F0D	MN908947.3	1260	A	T	0.048	0.035	2.2e-22	5.4e-17	0.0431531323843006	CAG	ORF1ab:nsp2	Q152L	A455T	CAG>CTG	Missense	ORF1ab:nsp2	0.956789234049911
CAMB-71F0D	MN908947.3	14217	T	G	0.26	0.21	4.1e-130	5.7e-101	0.245065209728587	CTG	ORF1ab:RNA-dependent-RNA-polymerase	T250T	T750G	ACT>ACG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.754376688990718
CAMB-71F0D	MN908947.3	14408	C	T	0.95	0.95	0	0	0.951000238900555	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.0488991713922873
CAMB-71F0D	MN908947.3	14805	C	T	0.034	0.024	4.3e-16	2.9e-12	0.0309804779247454	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.969019522075255
CAMB-71F0D	MN908947.3	17010	C	T	0.97	0.97	0	0	0.971096677130499	TCT	ORF1ab:helicase	I258I	C774T	ATC>ATT	Synonymous	ORF1ab:helicase	0.0289033228695011
CAMB-71F0D	MN908947.3	23403	A	G	0.97	0.97	0	0	0.971904061043094	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.0262376766788084
CAMB-71F0D	MN908947.3	23707	C	T	0.029	0.037	3.7e-14	1.3e-17	0.0324491263696747	CCA	S	P715P	C2145T	CCC>CCT	Synonymous	GU280_gp02, spike glycoprotein	0.967212421204044
CAMB-71F0D	MN908947.3	241	C	T	0.97	0.97	0	0	0.971411039522495	TCG	NA	NA	NA	NA	NA	NA	0.0277522104147491
CAMB-71F0D	MN908947.3	26144	G	T	0.019	0.03	1.3e-09	1.9e-13	0.0220653133274493	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.977383053839365
CAMB-71F0D	MN908947.3	28881	GGG	AAC	0.973333333333333	0.973333333333333	0;0;0	0;0;0	0.973883065779852	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.0281511636838467
CAMB-71F0D	MN908947.3	29020	A	G	0.027	0.029	2.5e-13	1.2e-14	0.027772278316725	AAT	N	K249K	A747G	AAA>AAG	Synonymous	GU280_gp10	0.972216722761169
CAMB-71F0D	MN908947.3	29281	C	T	0.97	0.97	0	0	0.970736941360082	CCA	N	A336A	C1008T	GCC>GCT	Synonymous	GU280_gp10	0.0291167433467185
CAMB-71F0D	MN908947.3	3037	C	T	0.95	0.96	0	0	0.956183258697899	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.0436100585601102
CAMB-71F0D	MN908947.3	8169	C	T	0.088	0.084	6.8e-40	9.1e-39	0.086706990702783	TCA	ORF1ab:nsp3	S1817L	C5450T	TCA>TTA	Missense	ORF1ab:nsp3	0.913215661401853
CAMB-71F1C	MN908947.3	11075	T	-	0.035	0.035	1.1e-08	1.9e-09	0.0348535683122565	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961422654819403
CAMB-71F1C	MN908947.3	13469	G	-	0.0083	0.012	5.3e-05	1.6e-06	0.00930190279966065	CGG	ORF1ab:nsp11	.	28-28-delfrshift	.	no-SNV	ORF1ab:nsp11	0.986622833595928
CAMB-71F1C	MN908947.3	14408	C	T	1	1	0	0	0.998251256527216	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000366869260024703
CAMB-71F1C	MN908947.3	14966	G	-	0.0098	0.0074	1.1e-05	0.00011	0.00875312086943751	TGG	ORF1ab:RNA-dependent-RNA-polymerase	.	1499-1499-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.990835658687032
CAMB-71F1C	MN908947.3	18315	G	-	0.018	0.017	2.8e-06	3.6e-06	0.0178867311770944	AGG	ORF1ab:3'-to-5'-exonuclease	.	276-276-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.980862274655355
CAMB-71F1C	MN908947.3	19996	AG	-	0.018	0.012	1.6e-06;7e-06	0.00032;0.00044	0.01669449081803	TAG	ORF1ab:endoRNAse	.	376-377-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.980861244019139
CAMB-71F1C	MN908947.3	23403	A	-	0.012	0.01	2.3e-06	5.1e-06	0.0117355785559786	GAT	S	.	1841-1841-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.00021451171770258
CAMB-71F1C	MN908947.3	23403	A	G	0.99	0.99	0	0	0.988032033749844	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00021451171770258
CAMB-71F1C	MN908947.3	241	C	T	1	1	0	0	0.999156743868219	TCG	NA	NA	NA	NA	NA	NA	0.000159927887061834
CAMB-71F1C	MN908947.3	25350	C	T	1	1	0	0	0.999115044247788	CCA	S	P1263L	C3788T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	0.000742730720606827
CAMB-71F1C	MN908947.3	29196	CCC	-	0.0117666666666667	0.0085	1e-05;5.8e-05;0.00013	0.00031;0.00095;0.00087	0.0109472403831534	GCC	N	.	923-925-delinframe	.	no-SNV	GU280_gp10	0.987073470642484
CAMB-71F1C	MN908947.3	3037	C	T	1	1	0	0	0.999575256776585	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.86130203104487e-05
CAMB-71F1C	MN908947.3	4261	G	-	0.0088	0.0081	1.4e-05	2.1e-05	0.0085247182362335	AGG	ORF1ab:nsp3	.	1542-1542-delfrshift	.	no-SNV	ORF1ab:nsp3	0.991188060798934
CAMB-71F1C	MN908947.3	7064	AG	-	0.0069	0.0205	0.0018;0.0019	2.4e-07;2.4e-07	0.0135947712418301	CAG	ORF1ab:nsp3	.	4345-4346-delfrshift	.	no-SNV	ORF1ab:nsp3	0.986269125147117
CAMB-71F2B	MN908947.3	11074	C	INS	0.062	0.047	2.4e-17	9.6e-11	0.0576717184934929	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.903832885251362
CAMB-71F2B	MN908947.3	11075	T	-	0.11	0.08	3.8e-27	1.4e-20	0.102530865509254	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.897362884889182
CAMB-71F2B	MN908947.3	12164	G	T	0.025	0.0045	1.5e-09	0.0065	0.0178789706145998	GGC	ORF1ab:nsp8	A25S	G73T	GCT>TCT	Missense	ORF1ab:nsp8	0.98197434685529
CAMB-71F2B	MN908947.3	12506	A	-	0.025	0.03	2.7e-10	3.1e-12	0.0269193305587532	TAA	ORF1ab:nsp8	.	415-415-delfrshift	.	no-SNV	ORF1ab:nsp8	0.972947843797042
CAMB-71F2B	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999432977999546	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0
CAMB-71F2B	MN908947.3	17676	C	T	0.032	0.02	9.1e-16	2.2e-10	0.0262958280657396	TCA	ORF1ab:helicase	I480I	C1440T	ATC>ATT	Synonymous	ORF1ab:helicase	0.97370417193426
CAMB-71F2B	MN908947.3	27874	C	T	1	1	0	0	1	ACT	NA	NA	NA	NA	NA	NA	0
CAMB-71F2B	MN908947.3	5392	C	T	1	1	3.7e-295	6.6e-303	1	ACT	ORF1ab:nsp3	N891N	C2673T	AAC>AAT	Synonymous	ORF1ab:nsp3	0
CAMB-71F3A	MN908947.3	11075	T	-	0.034	0.037	8e-10	6.8e-10	0.0369553226696084	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959216118879984
CAMB-71F3A	MN908947.3	14408	C	T	1	1	0	0	0.998021322465373	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00103363751808866
CAMB-71F3A	MN908947.3	16431	A	G	0.01	0.0071	3.7e-05	3.3e-05	0.00728134046846215	TAG	ORF1ab:helicase	L65L	A195G	TTA>TTG	Synonymous	ORF1ab:helicase	0.992543205544346
CAMB-71F3A	MN908947.3	21561	CA	TT	0.024	0.013	2.4e-07;2.4e-07	3.7e-07;7.9e-07	0.013975726369989	ACA	NA	NA	NA	NA	NA	NA	0.985362370581935
CAMB-71F3A	MN908947.3	2189	C	T	0.031	0.034	5.4e-15	1.3e-16	0.0332496863237139	TCT	ORF1ab:nsp2	L462F	C1384T	CTT>TTT	Missense	ORF1ab:nsp2	0.966645754914262
CAMB-71F3A	MN908947.3	23403	A	G	1	1	0	0	0.998965524521291	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000190005700171005
CAMB-71F3A	MN908947.3	23427	T	C	0.0065	0.0069	3.9e-05	3.2e-05	0.00680982322932732	GTT	S	V622A	T1865C	GTT>GCT	Missense	GU280_gp02, spike glycoprotein	0.992810535057539
CAMB-71F3A	MN908947.3	241	C	T	1	1	0	0	0.9987549891977	TCG	NA	NA	NA	NA	NA	NA	0.000109853894320554
CAMB-71F3A	MN908947.3	24355	T	C	0.019	0.01	1.1e-07	1.6e-06	0.0108843537414966	TTG	S	I931I	T2793C	ATT>ATC	Synonymous	GU280_gp02, spike glycoprotein	0.988532555879495
CAMB-71F3A	MN908947.3	25184	C	G	0.032	0.03	5.5e-13	1.2e-14	0.0302033240529824	GCA	S	Q1208E	C3622G	CAG>GAG	Missense	GU280_gp02, spike glycoprotein	0.968193706234708
CAMB-71F3A	MN908947.3	25587	C	T	0.012	0.0076	6.7e-07	2.4e-05	0.00803168665419738	TCA	ORF3a	L65L	C195T	CTC>CTT	Synonymous	GU280_gp03	0.991968313345803
CAMB-71F3A	MN908947.3	28705	T	C	0.0055	0.0085	0.00018	7.1e-06	0.00810344827586207	ATC	N	D144D	T432C	GAT>GAC	Synonymous	GU280_gp10	0.991637931034483
CAMB-71F3A	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999106272343191	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-71F3A	MN908947.3	29769	C	T	0.47	0.46	4e-140	1.4e-236	0.456733662293898	ACA	NA	NA	NA	NA	NA	NA	0.542905283427609
CAMB-71F3A	MN908947.3	3037	C	T	1	1	0	0	0.999475262368816	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000149925037481259
CAMB-71F3A	MN908947.3	6770	A	G	0.012	0.0082	6.1e-06	9.8e-06	0.00850844398607709	TAT	ORF1ab:nsp3	M1351V	A4051G	ATG>GTG	Missense	ORF1ab:nsp3	0.991491556013923
CAMB-71F49	MN908947.3	10986	G	C	0.011	0.0032	1.3e-06	0.00088	0.0091853685547702	AGA	ORF1ab:nsp6	R5T	G14C	AGA>ACA	Missense	ORF1ab:nsp6	0.987166541806456
CAMB-71F49	MN908947.3	11074	C	INS	0.019	0.032	0.00024	1.2e-06	0.0212723105771234	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.972150843808598
CAMB-71F49	MN908947.3	11074	CT	-	0.0141	0.0155205	1e-05;4.2e-06	NA;2.4e-08	0.015094241922121	TCT	ORF1ab:nsp6	.	102-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.972150843808598
CAMB-71F49	MN908947.3	11075	T	-	0.025	0.031	4.2e-06	2.4e-08	0.0259636363636364	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.968884848484848
CAMB-71F49	MN908947.3	14408	C	T	1	1	0	0	0.999672416617098	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000241377229506642
CAMB-71F49	MN908947.3	14718	G	-	0.0024	0.011	0.0096	1.1e-06	0.00399825379556935	AGG	ORF1ab:RNA-dependent-RNA-polymerase	.	1251-1251-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.994532717080235
CAMB-71F49	MN908947.3	18979	C	T	0.045	0.022	1.8e-20	8.4e-12	0.0413941962922728	ACA	ORF1ab:3'-to-5'-exonuclease	H314Y	C940T	CAC>TAC	Missense	ORF1ab:3'-to-5'-exonuclease	0.958023586881661
CAMB-71F49	MN908947.3	20016	C	T	0.022	0.0059	1.3e-09	0.0024	0.0214083510261854	ACT	ORF1ab:endoRNAse	D132D	C396T	GAC>GAT	Synonymous	ORF1ab:endoRNAse	0.978591648973815
CAMB-71F49	MN908947.3	20850	T	C	0.018	0.016	6.3e-09	2.8e-09	0.0172500173425107	ATA	ORF1ab:2'-O-ribose-methyltransferase	N64N	T192C	AAT>AAC	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.981339458451198
CAMB-71F49	MN908947.3	23403	A	G	1	1	0	0	0.995931524426501	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.8671903524969e-05
CAMB-71F49	MN908947.3	241	C	T	1	1	0	0	0.999743480119709	TCG	NA	NA	NA	NA	NA	NA	0.000195443718316741
CAMB-71F49	MN908947.3	25688	C	T	0.012	0.0088	1.2e-06	7e-05	0.0116493462956755	GCT	ORF3a	A99V	C296T	GCT>GTT	Missense	GU280_gp03	0.988224941334227
CAMB-71F49	MN908947.3	26078	C	T	0.0082	0.008	2.1e-05	0.00015	0.00816326530612245	ACC	ORF3a	T229I	C686T	ACC>ATC	Missense	GU280_gp03	0.991836734693878
CAMB-71F49	MN908947.3	26150	C	T	0.012	0.011	2.6e-07	9.1e-06	0.0121666666666667	TCC	ORF3a	S253F	C758T	TCC>TTC	Missense	GU280_gp03	0.985833333333333
CAMB-71F49	MN908947.3	26408	C	T	0.019	0.0073	2.2e-09	3.4e-05	0.0165959984099642	TCT	E	S55F	C164T	TCT>TTT	Missense	GU280_gp04	0.983271498608719
CAMB-71F49	MN908947.3	27281	G	T	0.01	0.0047	7e-06	5e-04	0.00883751387979387	TGG	ORF6	W27L	G80T	TGG>TTG	Missense	GU280_gp06	0.990228625117444
CAMB-71F49	MN908947.3	28253	C	T	0.011	0.01	1e-05	1.6e-05	0.0111692281803904	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.987736986762396
CAMB-71F49	MN908947.3	28556	C	T	0.0098	0.0081	1.5e-05	2.7e-05	0.00944747744608356	TCG	N	R95C	C283T	CGT>TGT	Missense	GU280_gp10	0.990126611685445
CAMB-71F49	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999074614254964	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.45692383117172e-05
CAMB-71F49	MN908947.3	29750	C	T	0.011	0.0081	9e-06	0.00012	0.00966386554621849	ACG	NA	NA	NA	NA	NA	NA	0.989975990396158
CAMB-71F49	MN908947.3	3037	C	T	1	1	0	0	0.999749084157174	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.01831685652632e-05
CAMB-71F49	MN908947.3	8222	G	T	0.003	0.0063	0.0023	3e-05	0.00351318324951826	TGA	ORF1ab:nsp3	E1835*	G5503T	GAA>TAA	Nonsense	ORF1ab:nsp3	0.996451567420219
CAMB-71F49	MN908947.3	8851	G	-	0.012	0.0071	1.3e-06	0.00018	0.01148473874806	TGG	ORF1ab:nsp4	.	297-297-delfrshift	.	no-SNV	ORF1ab:nsp4	0.988473874806001
CAMB-71F58	MN908947.3	10993	C	T	0.39	0.18	5.9e-89	4.4e-28	0.328125	TCA	ORF1ab:nsp6	I7I	C21T	ATC>ATT	Synonymous	ORF1ab:nsp6	0.671875
CAMB-71F58	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999249249249249	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0
CAMB-71F58	MN908947.3	21986	G	T	1	0.55	3.7e-131	3.1e-182	0.598923283983849	GGG	S	G142C	G424T	GGT>TGT	Missense	GU280_gp02, spike glycoprotein	0.401076716016151
CAMB-71F58	MN908947.3	26527	C	T	1	1	0	0	0.999673788941445	GCA	M	A2V	C5T	GCA>GTA	Missense	GU280_gp05	0.000326211058554885
CAMB-71F58	MN908947.3	29032	G	A	1	1	0	0	0.9998204882719	AGG	N	E253E	G759A	GAG>GAA	Synonymous	GU280_gp10	0.000119674485399713
CAMB-71F67	MN908947.3	11075	T	-	0.055	0.038	3e-14	1.5e-10	0.0405707721143963	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954954954954955
CAMB-71F67	MN908947.3	14408	C	T	1	1	0	0	0.998147418210485	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000394166338194718
CAMB-71F67	MN908947.3	23403	A	G	1	1	0	0	0.999302632562078	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000149435879554681
CAMB-71F67	MN908947.3	23533	C	T	0.018	0.014	4.4e-08	5e-08	0.014407527197883	ACA	S	N657N	C1971T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.985102420856611
CAMB-71F67	MN908947.3	241	C	T	1	1	0	0	0.999140506691769	TCG	NA	NA	NA	NA	NA	NA	0.000327426022183113
CAMB-71F67	MN908947.3	27214	G	T	0.01	0.01	2.4e-06	2.1e-06	0.0101653725327485	CGT	ORF6	V5F	G13T	GTT>TTT	Missense	GU280_gp06	0.987404421788868
CAMB-71F67	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999498495486459	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000184128153194623
CAMB-71F67	MN908947.3	3037	C	T	1	1	0	0	0.999331327315279	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000200601805416249
CAMB-71F76	MN908947.3	11075	T	-	0.046	0.029	1.8e-11	3.8e-08	0.0398321408915795	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960013070996148
CAMB-71F76	MN908947.3	11839	A	G	0.89	0.91	9.4e-207	6.5e-139	0.894285714285714	TAC	ORF1ab:nsp6	V289V	A867G	GTA>GTG	Synonymous	ORF1ab:nsp6	0.105714285714286
CAMB-71F76	MN908947.3	14399	T	A	0.0093	0.0087	1.2e-06	2.3e-06	0.00900874378072835	GTG	ORF1ab:RNA-dependent-RNA-polymerase	V311E	T932A	GTG>GAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.990873494862661
CAMB-71F76	MN908947.3	14408	C	T	1	0.99	0	0	0.995233778765461	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000321646831778707
CAMB-71F76	MN908947.3	16289	C	T	0.15	0.1	5.1e-27	2.5e-37	0.107482185273159	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0.892517814726841
CAMB-71F76	MN908947.3	17769	T	G	0.073	0.059	2.8e-33	3.3e-27	0.0679168452636091	TTA	ORF1ab:helicase	F511L	T1533G	TTT>TTG	Missense	ORF1ab:helicase	0.931997428204029
CAMB-71F76	MN908947.3	17797	G	A	0.0049	0.01	0.00036	1.6e-06	0.00676404066879452	TGT	ORF1ab:helicase	V521I	G1561A	GTA>ATA	Missense	ORF1ab:helicase	0.993193684077025
CAMB-71F76	MN908947.3	18928	C	T	0.016	0.018	5e-09	1.1e-09	0.0167799464495572	TCC	ORF1ab:3'-to-5'-exonuclease	P297S	C889T	CCT>TCT	Missense	ORF1ab:3'-to-5'-exonuclease	0.983195822580841
CAMB-71F76	MN908947.3	19839	T	C	0.87	0.83	0	0	0.855538922155689	ATA	ORF1ab:endoRNAse	N73N	T219C	AAT>AAC	Synonymous	ORF1ab:endoRNAse	0.144461077844311
CAMB-71F76	MN908947.3	22069	AT	-	0.0125	0.0074	3.1e-07;6.8e-07	0.00014;0.00026	0.0114750445632799	AAT	S	.	507-508-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.988298114064985
CAMB-71F76	MN908947.3	22703	G	T	0.035	0.046	2.3e-17	5.9e-22	0.0392314156925663	TGG	S	G381*	G1141T	GGA>TGA	Nonsense	GU280_gp02, spike glycoprotein	0.960768584307434
CAMB-71F76	MN908947.3	23403	A	G	1	1	0	0	0.99702043309688	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.23340356301348e-05
CAMB-71F76	MN908947.3	241	C	T	1	0.98	0	0	0.994227194155442	TCG	NA	NA	NA	NA	NA	NA	0.000130458889142559
CAMB-71F76	MN908947.3	25868	C	T	0.011	0.0085	2.7e-06	0.00029	0.0107597716293368	CCT	ORF3a	P159L	C476T	CCT>CTT	Missense	GU280_gp03	0.989240228370663
CAMB-71F76	MN908947.3	28783	C	T	0.042	0.12	1.2e-19	1.5e-52	0.0675328599486327	GCT	N	G170G	C510T	GGC>GGT	Synonymous	GU280_gp10	0.931661378858841
CAMB-71F76	MN908947.3	28881	GGG	AAC	0.833333333333333	0.88	0;0;0	0;0;0	0.848722648642456	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.164376748523469
CAMB-71F76	MN908947.3	29645	G	T	0.01	0.0095	2.9e-06	5e-06	0.00975542731519648	AGT	ORF10	V30L	G88T	GTA>TTA	Missense	GU280_gp11	0.989145369607035
CAMB-71F76	MN908947.3	3037	C	T	1	1	0	0	0.999651203348448	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000174398325776073
CAMB-71F76	MN908947.3	344	C	T	0.0047	0.012	0.00086	2.6e-07	0.0074371225096908	GCT	ORF1ab:leader-protein	L27F	C79T	CTC>TTC	Missense	ORF1ab:leader-protein	0.992502779530635
CAMB-71F76	MN908947.3	4261	G	-	0.0076	0.0079	3.3e-05	2.3e-05	0.0077134545066325	AGG	ORF1ab:nsp3	.	1542-1542-delfrshift	.	no-SNV	ORF1ab:nsp3	0.992179784877359
CAMB-71F76	MN908947.3	4320	C	T	0.013	0.024	7.5e-08	1.9e-12	0.0178451087689031	GCC	ORF1ab:nsp3	A534V	C1601T	GCC>GTC	Missense	ORF1ab:nsp3	0.98212793487344
CAMB-71F76	MN908947.3	8293	C	T	0.83	0.89	0	0	0.852943956147812	CCT	ORF1ab:nsp3	T1858T	C5574T	ACC>ACT	Synonymous	ORF1ab:nsp3	0.147056043852188
CAMB-71F76	MN908947.3	9234	AAAGATCA	-	0.0042875	0.03225	0.00042;0.00014;0.00015;0.00017;8.8e-05;8.1e-05;1e-04;NA	8.3e-16;1.9e-16;3e-16;4.2e-16;3.9e-16;1.7e-16;3.3e-16;3.3e-16	0.0178253808676823	GAA	ORF1ab:nsp4	.	680-687-delfrshift	.	no-SNV	ORF1ab:nsp4	0.982172359472855
CAMB-71F76	MN908947.3	9962	C	T	0.0089	0.0043	9.8e-06	0.0012	0.00740108169655565	TCA	ORF1ab:nsp4	H470Y	C1408T	CAT>TAT	Missense	ORF1ab:nsp4	0.992598918303444
CAMB-71F85	MN908947.3	11001	C	T	1	1	0	0	0.99927196246562	ACA	ORF1ab:nsp6	T10I	C29T	ACA>ATA	Missense	ORF1ab:nsp6	0.000687591004691797
CAMB-71F85	MN908947.3	11074	C	INS	0.033	0.031	8.9e-08	1.7e-06	0.0321183292437182	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.967127719365584
CAMB-71F85	MN908947.3	11075	T	-	0.039	0.031	1e-09	2.2e-08	0.0360996196902681	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960812599101086
CAMB-71F85	MN908947.3	11083	G	-	0.0059	0.016	0.0058	4.7e-07	0.00967871391138075	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.929487028162697
CAMB-71F85	MN908947.3	11083	G	T	0.062	0.059	3e-13	9.8e-13	0.0607988479969784	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.929487028162697
CAMB-71F85	MN908947.3	11714	A	G	0.0086	0.021	0.00026	5.7e-06	0.0128388017118402	TAC	ORF1ab:nsp6	T248A	A742G	ACA>GCA	Missense	ORF1ab:nsp6	0.98716119828816
CAMB-71F85	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999613057548895	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	8.79430129276229e-05
CAMB-71F85	MN908947.3	17640	A	G	0.031	0.031	2.6e-15	2.2e-15	0.030731592881799	CAG	ORF1ab:helicase	S468S	A1404G	TCA>TCG	Synonymous	ORF1ab:helicase	0.969234893930762
CAMB-71F85	MN908947.3	18877	C	T	0.0093	0.005	8e-06	0.00053	0.00753136717038095	TCT	ORF1ab:3'-to-5'-exonuclease	L280L	C838T	CTA>TTA	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.992419938645328
CAMB-71F85	MN908947.3	25562	A	G	0.0099	0.016	3.1e-06	8.1e-09	0.0124306540203461	CAG	ORF3a	Q57R	A170G	CAG>CGG	Missense	GU280_gp03	0.987555580028358
CAMB-71F85	MN908947.3	27697	C	T	0.013	0.041	0.00024	1.5e-08	0.0262529832935561	TCT	ORF7a	L102F	C304T	CTT>TTT	Missense	GU280_gp07	0.973747016706444
CAMB-71F85	MN908947.3	28985	G	T	1	1	0	0	0.999916184728858	AGG	N	G238C	G712T	GGC>TGC	Missense	GU280_gp10	0
CAMB-71F85	MN908947.3	29298	A	G	0.011	0.013	8.9e-07	6.9e-08	0.0116639598405433	AAA	N	K342R	A1025G	AAA>AGA	Missense	GU280_gp10	0.988317584526798
CAMB-71F85	MN908947.3	6696	C	T	1	1	0	0	0.999872220802453	CCT	ORF1ab:nsp3	P1326L	C3977T	CCT>CTT	Missense	ORF1ab:nsp3	0.000127779197546639
CAMB-71F85	MN908947.3	9438	C	T	0.052	0.062	2.5e-23	1.2e-27	0.0549186066865045	ACA	ORF1ab:nsp4	T295I	C884T	ACA>ATA	Missense	ORF1ab:nsp4	0.945081393313495
CAMB-71F85	MN908947.3	9737	A	G	0.013	0.021	1.8e-07	5.6e-11	0.0158045630857446	TAG	ORF1ab:nsp4	S395G	A1183G	AGT>GGT	Missense	ORF1ab:nsp4	0.984195436914255
CAMB-71F85	MN908947.3	9741	A	G	0.11	0.1	1e-48	1.4e-46	0.104056892727635	AAT	ORF1ab:nsp4	N396S	A1187G	AAT>AGT	Missense	ORF1ab:nsp4	0.895943107272365
CAMB-71F85	MN908947.3	9924	C	T	0.02	0.027	3.1e-10	2.3e-13	0.0222438531977792	GCA	ORF1ab:nsp4	A457V	C1370T	GCA>GTA	Missense	ORF1ab:nsp4	0.977647991924436
CAMB-71F94	MN908947.3	11075	T	-	0.023	0.035	3.3e-07	2.4e-09	0.0327989410207383	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962715105162524
CAMB-71F94	MN908947.3	14408	C	T	1	1	0	0	0.999545339732256	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000429401363980803
CAMB-71F94	MN908947.3	14790	C	T	0.0031	0.012	0.0041	4.3e-07	0.0093470604172311	TCA	ORF1ab:RNA-dependent-RNA-polymerase	I441I	C1323T	ATC>ATT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.990562629820284
CAMB-71F94	MN908947.3	15944	C	T	0.016	0.0099	1.3e-08	4e-06	0.0122371283538796	TCA	ORF1ab:RNA-dependent-RNA-polymerase	S826L	C2477T	TCA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.98776287164612
CAMB-71F94	MN908947.3	17167	C	T	0.038	0.034	9.2e-18	2.9e-16	0.0346032021521239	TCA	ORF1ab:helicase	H311Y	C931T	CAT>TAT	Missense	ORF1ab:helicase	0.965396797847876
CAMB-71F94	MN908947.3	18050	T	C	0.013	0.024	8.9e-07	1.5e-12	0.0234457469859437	GTA	ORF1ab:3'-to-5'-exonuclease	V4A	T11C	GTA>GCA	Missense	ORF1ab:3'-to-5'-exonuclease	0.976554253014056
CAMB-71F94	MN908947.3	18232	C	T	0.014	0.011	2.3e-07	4.5e-07	0.0116959064327485	TCA	ORF1ab:3'-to-5'-exonuclease	Q65*	C193T	CAA>TAA	Nonsense	ORF1ab:3'-to-5'-exonuclease	0.988192703982178
CAMB-71F94	MN908947.3	18747	C	T	0.0071	0.0057	3.7e-05	0.00014	0.00582709002259484	TCT	ORF1ab:3'-to-5'-exonuclease	V236V	C708T	GTC>GTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.994143179926269
CAMB-71F94	MN908947.3	20217	T	G	0.079	0.077	1.8e-12	1.6e-19	0.0770547945205479	ATT	ORF1ab:endoRNAse	N199K	T597G	AAT>AAG	Missense	ORF1ab:endoRNAse	0.922945205479452
CAMB-71F94	MN908947.3	203	C	T	0.015	0.014	7.6e-08	1.5e-07	0.0144573465164406	TCG	NA	NA	NA	NA	NA	NA	0.985513911243964
CAMB-71F94	MN908947.3	21651	A	G	0.033	0.053	5.9e-09	2.2e-18	0.0485519591141397	AAT	S	N30S	A89G	AAT>AGT	Missense	GU280_gp02, spike glycoprotein	0.95144804088586
CAMB-71F94	MN908947.3	21984	TGGGTGT	-	0.0632857142857143	0.0478571428571429	1.9e-09;1.6e-10;2.6e-09;4.8e-09;3.5e-09;1.2e-09;9.2e-10	2.7e-08;3.1e-09;3.4e-08;7.3e-08;4.6e-08;1.9e-08;1.7e-08	0.0493323963457484	TTG	S	.	422-428-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.949000289771081
CAMB-71F94	MN908947.3	23403	A	G	1	1	0	0	0.999862637362637	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.10500610500611e-05
CAMB-71F94	MN908947.3	241	C	T	1	1	0	0	0.999628018770745	TCG	NA	NA	NA	NA	NA	NA	0.000343367288542978
CAMB-71F94	MN908947.3	24213	C	T	0.017	0.024	2e-06	1.2e-10	0.0233023848534498	TCT	S	S884F	C2651T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.976606590205716
CAMB-71F94	MN908947.3	24707	C	T	0.016	0.0087	1e-05	7.7e-05	0.0101285547331515	TCT	S	L1049F	C3145T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.989871445266848
CAMB-71F94	MN908947.3	25093	AA	-	0.0016	0.0091	0.002;NA	3.5e-06;1e-05	0.00780686216624024	TAA	S	.	3531-3532-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.991650099403579
CAMB-71F94	MN908947.3	25521	C	T	0.016	0.0072	2.7e-08	0.00012	0.00846721058681695	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.991532789413183
CAMB-71F94	MN908947.3	26958	C	T	0.017	0.0055	7.3e-08	0.00033	0.007104631850895	TCG	M	R146C	C436T	CGT>TGT	Missense	GU280_gp05	0.992434028418527
CAMB-71F94	MN908947.3	28253	C	T	0.33	0.35	3.8e-164	2e-179	0.346639069584073	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.651734673763059
CAMB-71F94	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999528153507392	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000173913043478261
CAMB-71F94	MN908947.3	3037	C	T	1	1	7.60000000000019e-311	0	0.999233814327672	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-71F94	MN908947.3	313	C	T	0.011	0.0048	1.7e-06	0.00074	0.00690659903955107	TCA	ORF1ab:leader-protein	L16L	C48T	CTC>CTT	Synonymous	ORF1ab:leader-protein	0.993093400960449
CAMB-71F94	MN908947.3	635	C	T	0.074	0.076	1.5e-33	1e-34	0.0755138814735718	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.924419380672718
CAMB-71F94	MN908947.3	6539	C	T	0.42	0.28	9.2e-105	2.7e-124	0.298148148148148	CCA	ORF1ab:nsp3	H1274Y	C3820T	CAC>TAC	Missense	ORF1ab:nsp3	0.701322751322751
CAMB-71F94	MN908947.3	6629	C	T	0.047	0.052	2.2e-12	5.2e-22	0.0515406162464986	CCT	ORF1ab:nsp3	L1304F	C3910T	CTT>TTT	Missense	ORF1ab:nsp3	0.948459383753501
CAMB-71F94	MN908947.3	683	C	T	0.016	0.021	1.1e-08	1e-10	0.0192118481694371	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.980762259851898
CAMB-71F94	MN908947.3	7714	T	C	0.069	0.055	3.2e-18	2.6e-24	0.0562204724409449	CTA	ORF1ab:nsp3	P1665P	T4995C	CCT>CCC	Synonymous	ORF1ab:nsp3	0.943779527559055
CAMB-71F94	MN908947.3	9430	C	T	0.011	0.025	0.00011	1e-10	0.0208227526663281	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.979177247333672
CAMB-71FA3	MN908947.3	10096	G	-	0.013	0.0081	8.6e-07	0.00011	0.0115569123419102	AGG	ORF1ab:3C-like-proteinase	.	42-42-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.98844308765809
CAMB-71FA3	MN908947.3	10714	C	T	0.0047	0.024	0.00023	2.1e-12	0.0123375638367801	TCA	ORF1ab:3C-like-proteinase	L220L	C660T	CTC>CTT	Synonymous	ORF1ab:3C-like-proteinase	0.98766243616322
CAMB-71FA3	MN908947.3	11074	C	INS	0.11	0.17	1.1e-43	5.7e-65	0.135854510417921	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.863784174394797
CAMB-71FA3	MN908947.3	11083	G	-	0.14	0.2	3.1e-59	1.5e-90	0.15845387335262	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.60720025715204e-05
CAMB-71FA3	MN908947.3	11083	G	T	0.86	0.8	0	0	0.841417550626808	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.60720025715204e-05
CAMB-71FA3	MN908947.3	13269	A	G	0.014	0.014	5.4e-08	1.7e-08	0.0139178754043619	GAT	ORF1ab:nsp10	D82G	A245G	GAT>GGT	Missense	ORF1ab:nsp10	0.98604299279975
CAMB-71FA3	MN908947.3	14407	C	A	0.011	0.012	3.6e-07	1.7e-07	0.0113484843995378	ACC	ORF1ab:RNA-dependent-RNA-polymerase	P314T	C940A	CCT>ACT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.988592254585321
CAMB-71FA3	MN908947.3	1457	C	T	1	1	0	0	1	TCG	ORF1ab:nsp2	R218C	C652T	CGT>TGT	Missense	ORF1ab:nsp2	0
CAMB-71FA3	MN908947.3	14805	C	T	1	1	0	0	0.99993234863006	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	4.51009132934942e-05
CAMB-71FA3	MN908947.3	20270	C	T	0.041	0.039	6.5e-08	7.6e-07	0.0402684563758389	GCT	ORF1ab:endoRNAse	A217V	C650T	GCT>GTT	Missense	ORF1ab:endoRNAse	0.959731543624161
CAMB-71FA3	MN908947.3	20742	A	G	1	1	0	0	1	AAA	ORF1ab:2'-O-ribose-methyltransferase	Q28Q	A84G	CAA>CAG	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0
CAMB-71FA3	MN908947.3	20759	C	T	0.057	0.041	2.4e-16	1.9e-16	0.0447227191413238	GCA	ORF1ab:2'-O-ribose-methyltransferase	A34V	C101T	GCA>GTA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.955277280858676
CAMB-71FA3	MN908947.3	20762	C	T	0.028	0.018	3.9e-09	1.7e-08	0.0206140350877193	ACA	ORF1ab:2'-O-ribose-methyltransferase	T35I	C104T	ACA>ATA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.979385964912281
CAMB-71FA3	MN908947.3	20925	G	T	1	1	0	0	0.999971049736553	TGC	ORF1ab:2'-O-ribose-methyltransferase	L89F	G267T	TTG>TTT	Missense	ORF1ab:2'-O-ribose-methyltransferase	2.89502634473974e-05
CAMB-71FA3	MN908947.3	23385	T	C	0.013	0.013	1.3e-07	4.8e-08	0.0128239514533812	GTT	S	V608A	T1823C	GTT>GCT	Missense	GU280_gp02, spike glycoprotein	0.987058705199987
CAMB-71FA3	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-71FA3	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-71FA3	MN908947.3	26144	G	T	1	1	1.2e-284	1.6e-284	0.998137802607076	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.00186219739292365
CAMB-71FA3	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTT	-	0.0277505769230769	0.036575	4.3e-06;6.4e-08;2.9e-06;3.2e-06;7.3e-06;5.6e-07;1.8e-06;1.3e-05;1.2e-05;4.8e-06;8.1e-06;6.3e-06;1.2e-05;5e-05;5.9e-05;8.4e-05;4.9e-05;7.6e-05;5.6e-05;5.1e-05;4.6e-05;8.4e-05;5.4e-05;6.4e-05;5.2e-05;4.2e-05;7.2e-05;4.5e-05;4.5e-05;4.5e-05;7e-05;5.9e-05;3.8e-05;7.1e-05;2.7e-05;4.3e-05;3.6e-05;0.0019;0.004;0.0025;0.0031;0.00044;0.00026;0.00028;0.00038;0.00039;0.00039;0.007;0.0065;NA;NA;NA	5e-05;3.7e-06;3.5e-05;3.5e-05;8e-05;1.1e-05;2.8e-05;5.9e-07;5.5e-07;3.5e-07;3.1e-07;2.5e-07;4.5e-07;3.7e-07;5.1e-07;7.8e-07;3.6e-07;6.6e-07;3.7e-07;4.4e-07;3.9e-07;8e-07;4.6e-07;5.1e-07;3.7e-07;2.2e-07;5.6e-07;4e-07;2.6e-07;3.5e-07;6.4e-07;5e-07;1.9e-07;6.1e-07;1e-07;3.3e-07;1.6e-07;3.1e-05;0.00015;5.9e-05;9.3e-05;4.5e-05;2.5e-05;3.2e-05;4.2e-05;4.1e-05;4.4e-05;4.3e-05;2.5e-05;8.1e-06;4.2e-06;0.00037	0.0347551593407465	GTC	M	.	258-309-delfrshift	.	no-SNV	GU280_gp05	0.968808385319358
CAMB-71FA3	MN908947.3	27208	C	T	0.0048	0.017	0.00075	3.9e-09	0.0105585533031938	TCA	ORF6	H3Y	C7T	CAT>TAT	Missense	GU280_gp06	0.984774682805892
CAMB-71FA3	MN908947.3	2723	C	T	1	1	6.7e-217	1.5e-173	1	ACC	ORF1ab:nsp3	P2S	C4T	CCA>TCA	Missense	ORF1ab:nsp3	0
CAMB-71FA3	MN908947.3	27382	GATTA	-	0.25	0.2	5.3e-123;2.1e-97;4.3e-126;1.8e-94;4.7e-121	8e-95;2.1e-74;2.3e-96;9.8e-75;1.1e-94	0.224488249821967	TGA	ORF6	.	181-185-delfrshift	.	no-SNV	GU280_gp06	0.773106669729688
CAMB-71FA3	MN908947.3	29144	C	T	0.027	0.03	7.5e-13	1.1e-14	0.0290076335877863	ACT	N	L291L	C871T	CTA>TTA	Synonymous	GU280_gp10	0.970907548770144
CAMB-71FA3	MN908947.3	3096	C	T	0.017	0.02	1.8e-06	3.4e-08	0.0190548780487805	TCA	ORF1ab:nsp3	S126L	C377T	TCA>TTA	Missense	ORF1ab:nsp3	0.980754573170732
CAMB-71FA3	MN908947.3	425	GTAGAAGTTGAAAAAGGCG	-	0.0124734736842105	0.0144736842105263	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.5;NA;NA;7.3e-12;1.3e-11;2.5e-12;2.4e-12;3.6e-12;3.9e-12	1.9e-05;7.2e-08;7.9e-07;8.2e-05;1.6e-06;1.7e-06;3e-06;2.5e-06;3.1e-06;1.7e-06;7.3e-06;3.6e-06;5.7e-06;1.7e-05;2.4e-05;1.4e-05;1.4e-05;1.7e-05;1.8e-05	0.00482676811060662	AGT	ORF1ab:leader-protein	.	160-178-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.995223952480334
CAMB-71FA3	MN908947.3	445	TTTGCCTCAACTT	-	0.00623561538461538	0.0141538461538462	1.3e-09;1.8e-12;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00023;1.2e-05;3.3e-07;8.7e-08;2.5e-07;2.9e-07;1e-07;3.3e-07;2.7e-07;2.4e-07;3.2e-07;6.7e-08;2.6e-07	0.00482499182204776	TTT	ORF1ab:leader-protein	.	180-192-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.967069649945868
CAMB-71FA3	MN908947.3	4854	G	T	0.013	0.012	6e-08	2.2e-07	0.0121315274860578	AGA	ORF1ab:nsp3	R712I	G2135T	AGA>ATA	Missense	ORF1ab:nsp3	0.987868472513942
CAMB-71FA3	MN908947.3	6428	C	T	0.016	0.04	2.8e-09	1.5e-19	0.0221000470213766	TCC	ORF1ab:nsp3	P1237S	C3709T	CCT>TCT	Missense	ORF1ab:nsp3	0.977899952978623
CAMB-71FA3	MN908947.3	6428	CC	TT	0.0165	0.02	2.8e-09;9.3e-10	1.5e-19;NA	0.017259470999023	TCC	ORF1ab:nsp3	.	3709-3710-mnv	.	no-SNV	ORF1ab:nsp3	0.977899952978623
CAMB-71FA3	MN908947.3	7735	C	T	0.03	0.038	1.1e-09	1.3e-11	0.0333476456275941	TCG	ORF1ab:nsp3	I1672I	C5016T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.966509231429798
CAMB-71FA3	MN908947.3	8782	C	T	0.0076	0.015	7.9e-05	1e-06	0.00937431872683671	GCC	ORF1ab:nsp4	S76S	C228T	AGC>AGT	Synonymous	ORF1ab:nsp4	0.990625681273163
CAMB-71FB2	MN908947.3	11074	C	INS	0.032	0.04	5.2e-07	1.1e-08	0.0322888589398023	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.967402291105121
CAMB-71FB2	MN908947.3	11075	T	-	0.061	0.036	7.1e-15	1.1e-09	0.0598974706195289	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.940029985007496
CAMB-71FB2	MN908947.3	11083	G	T	0.069	0.033	8.7e-15	1.3e-06	0.0671396981994022	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.92987145530095
CAMB-71FB2	MN908947.3	13914	T	G	0.00095	0.012	0.0086	4.6e-08	0.00647116032019152	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993454028577841
CAMB-71FB2	MN908947.3	14408	C	T	1	0.99	0	0	0.993969849246231	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00027162841233193
CAMB-71FB2	MN908947.3	17977	C	T	0.027	0.0071	2.5e-13	0.00038	0.0259611992945326	CCT	ORF1ab:helicase	L581F	C1741T	CTT>TTT	Missense	ORF1ab:helicase	0.974003527336861
CAMB-71FB2	MN908947.3	18747	C	T	0.018	0.044	1.1e-09	5.8e-21	0.0293740402854304	TCT	ORF1ab:3'-to-5'-exonuclease	V236V	C708T	GTC>GTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.970607894499142
CAMB-71FB2	MN908947.3	20279	AATTCATTGAACGGTATAAATTAGAAGGCTATGCCTTCGAACATATCGTTTATGGAGATTTTA	-	0.0503492063492064	0.060015873015873	1.5e-06;3.5e-06;5.3e-06;4.9e-06;6.6e-06;1.2e-05;7.3e-06;1.1e-05;1.1e-05;9.7e-06;1.1e-05;8.3e-06;6.9e-06;7.7e-06;3.1e-06;3.5e-06;1.4e-05;1.3e-05;2.2e-05;1.9e-05;2.5e-05;2.9e-05;3.6e-05;6.9e-06;1.8e-05;3.3e-05;9.8e-06;2.8e-05;3.2e-05;4.7e-05;3.3e-05;2.5e-05;2.7e-05;1.5e-05;2.7e-06;3.8e-07;1.1e-05;2.9e-05;3.3e-05;1.4e-05;9.8e-06;2.9e-05;1.5e-05;1.2e-05;2.7e-05;9.7e-06;1.7e-05;1.9e-05;5.6e-07;9.1e-08;2.7e-06;2.2e-06;4.9e-06;1.4e-05;5.4e-06;3e-06;1e-05;8.8e-06;1.5e-08;1.8e-06;5.7e-06;2.5e-07;2.7e-07	0.0023;0.0023;0.0024;0.0027;0.003;0.0031;0.0035;0.0017;0.0018;0.0017;0.0018;0.0015;0.0016;0.0017;0.0017;0.0013;0.0021;0.0021;0.0022;0.0028;0.0032;0.0033;0.0027;0.002;0.0019;0.0028;0.002;0.0029;0.0028;0.0029;0.0024;0.0026;0.0028;0.002;0.0012;0.0011;0.0018;0.0029;0.0027;0.0021;0.0022;0.0025;0.0021;0.0023;0.0024;0.0017;0.0024;0.0026;0.001;0.00099;0.0015;0.0016;0.0017;0.0021;0.0018;0.0016;0.0023;0.002;0.0019;0.0015;NA;NA;NA	0.050761421319797	GAA	ORF1ab:endoRNAse	.	659-721-delinframe	.	no-SNV	ORF1ab:endoRNAse	0.95049504950495
CAMB-71FB2	MN908947.3	23403	A	G	1	1	0	0	0.999865379437671	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00013462056232932
CAMB-71FB2	MN908947.3	241	C	T	1	1	0	0	0.999730146491904	TCG	NA	NA	NA	NA	NA	NA	0.00023130300693909
CAMB-71FB2	MN908947.3	25429	G	T	1	1	0	0	0.999906725118925	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	6.21832540496844e-05
CAMB-71FB2	MN908947.3	25614	C	T	1	1	0	0	0.999888817855852	CCA	ORF3a	S74S	C222T	TCC>TCT	Synonymous	GU280_gp03	0.00011118214414765
CAMB-71FB2	MN908947.3	26775	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.0336617173913044	0.0507826086956522	NA;NA;0.5;0.5;NA;1.8e-07;9.5e-10;1.1e-07;1.2e-07;2.8e-07;9.4e-09;4.6e-08;4.8e-07;4.8e-07;1.7e-07;3.5e-07;2.6e-07;4.5e-07;3e-07;4.2e-07;6.2e-07;2.5e-07;5.5e-07;3.4e-07;3.5e-07;2.9e-07;6e-07;3.7e-07;4.3e-07;3.2e-07;2.3e-07;4.8e-07;2.6e-07;8e-08;3.3e-07;4.7e-07;4.4e-07;3.5e-07;5.5e-07;8.9e-08;2.4e-07;1.8e-07;NA;NA;0.5;NA	4.7e-06;2.3e-05;4e-06;2.5e-05;7.4e-05;1.6e-05;7.1e-07;9.8e-06;1.2e-05;2.3e-05;2.6e-06;7.2e-06;4.8e-10;4.2e-10;2.6e-10;2.5e-10;1.7e-10;3e-10;2.7e-10;4.4e-10;6.9e-10;2.2e-10;5.4e-10;1.9e-10;3.8e-10;3e-10;7.1e-10;3.1e-10;4.3e-10;2.6e-10;1.1e-10;4.5e-10;2.6e-10;1.4e-11;3.3e-10;5e-10;4.3e-10;1.6e-10;6.1e-10;2.2e-11;2.3e-10;8.5e-11;9e-08;1.4e-06;3.5e-07;8.8e-07	0.0471919855776911	GGC	M	.	253-298-delfrshift	.	no-SNV	GU280_gp05	0.987161590040506
CAMB-71FB2	MN908947.3	28748	C	T	0.0048	0.0069	0.00029	3.5e-05	0.00575010604703775	GCT	N	L159L	C475T	CTA>TTA	Synonymous	GU280_gp10	0.994155629919404
CAMB-71FB2	MN908947.3	29310	TCAAAGATCAAGTCATTT	-	0.0071	0.00217222222222222	4.3e-06;1.6e-05;6.4e-05;2.5e-05;2.2e-05;2.5e-05;1.7e-05;8.3e-05;8.6e-05;0.00014;7.9e-05;8e-05;8.9e-05;8.3e-05;8.8e-05;0.00042;0.00013;0.00037	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;5.9e-06;2.6e-05;1.1e-05;1.6e-05	0.00324777842933827	TTC	N	.	1037-1054-delinframe	.	no-SNV	GU280_gp10	0.995307483329217
CAMB-71FB2	MN908947.3	29784	C	T	0.007	0.013	0.0024	3e-06	0.0115040477204942	GCT	NA	NA	NA	NA	NA	NA	0.988495952279506
CAMB-71FB2	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-71FB2	MN908947.3	4531	TTACTTTTACACCAGTAAAACAACTG	-	0.0501923076923077	0.00530769230769231	7.9e-07;4e-06;5.8e-06;5.7e-06;8.9e-07;7.2e-07;4.1e-06;2.4e-06;2.2e-06;3.5e-06;3.1e-06;2.9e-06;1.1e-06;3.3e-06;2.9e-06;3.4e-06;3.7e-07;3.5e-07;3.3e-07;4.2e-07;4.1e-07;4e-07;3.2e-07;3.6e-07;3.2e-07;2.6e-08	0.0014;0.0032;0.0039;0.0037;0.0019;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0464046822742475	TTT	ORF1ab:nsp3	.	1812-1837-delfrshift	.	no-SNV	ORF1ab:nsp3	0.948424687095382
CAMB-71FD0	MN908947.3	10028	A	G	0.016	0.015	8.4e-09	2.2e-08	0.0149704908593638	AAC	ORF1ab:nsp4	T492A	A1474G	ACC>GCC	Missense	ORF1ab:nsp4	0.984669641571902
CAMB-71FD0	MN908947.3	11075	T	-	0.034	0.044	9.3e-10	2.3e-11	0.0429487179487179	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952857905982906
CAMB-71FD0	MN908947.3	14120	C	T	1	1	0	0	0.999182078429591	CCA	ORF1ab:RNA-dependent-RNA-polymerase	P218L	C653T	CCA>CTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000136320261734903
CAMB-71FD0	MN908947.3	14408	C	T	1	1	0	0	0.998460591133005	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000923645320197044
CAMB-71FD0	MN908947.3	15264	T	C	0.053	0.048	6.8e-24	1.2e-22	0.0487502140044513	ATG	ORF1ab:RNA-dependent-RNA-polymerase	D599D	T1797C	GAT>GAC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.95120698510529
CAMB-71FD0	MN908947.3	19011	C	T	0.0083	0.0098	1.5e-05	2.5e-06	0.00957339603627813	ACA	ORF1ab:3'-to-5'-exonuclease	D324D	C972T	GAC>GAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.990359422237151
CAMB-71FD0	MN908947.3	19269	C	T	0.093	0.088	2.5e-40	1.8e-40	0.0890524200084287	ACT	ORF1ab:3'-to-5'-exonuclease	N410N	C1230T	AAC>AAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.910753071611502
CAMB-71FD0	MN908947.3	20762	C	T	0.016	0.016	1.1e-08	1.5e-08	0.0159839357429719	ACA	ORF1ab:2'-O-ribose-methyltransferase	T35I	C104T	ACA>ATA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.983534136546185
CAMB-71FD0	MN908947.3	23329	A	G	0.0069	0.0035	1.7e-05	0.00079	0.00425258266605817	CAT	S	P589P	A1767G	CCA>CCG	Synonymous	GU280_gp02, spike glycoprotein	0.995021366634859
CAMB-71FD0	MN908947.3	23403	A	G	1	1	0	0	0.999160789215249	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.92777430586555e-05
CAMB-71FD0	MN908947.3	241	C	T	1	1	0	0	0.999659226444028	TCG	NA	NA	NA	NA	NA	NA	0.000204464133583234
CAMB-71FD0	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999506033448592	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-71FD0	MN908947.3	3037	C	T	1	1	0	0	0.998687185471519	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000291736561884618
CAMB-71FD0	MN908947.3	9603	C	T	0.0088	0.0074	4.2e-06	1.9e-05	0.00758658924455079	ACA	ORF1ab:nsp4	T350I	C1049T	ACA>ATA	Missense	ORF1ab:nsp4	0.992209156429634
CAMB-71FEF	MN908947.3	11074	C	INS	0.031	0.018	1.8e-08	0.0015	0.0300588523200707	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.935417636595877
CAMB-71FEF	MN908947.3	11083	G	-	0.25	0.51	4.5e-111	1.2e-287	0.273386901439599	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-71FEF	MN908947.3	11083	G	T	0.75	0.49	1.7e-282	9.3e-137	0.726476194488031	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-71FEF	MN908947.3	11319	A	G	0.036	0.11	7.4e-17	9.3e-49	0.043478698254615	TAT	ORF1ab:nsp6	Y116C	A347G	TAT>TGT	Missense	ORF1ab:nsp6	0.956501182033097
CAMB-71FEF	MN908947.3	1440	G	A	1	1	0	6.3e-255	1	GGC	ORF1ab:nsp2	G212D	G635A	GGC>GAC	Missense	ORF1ab:nsp2	0
CAMB-71FEF	MN908947.3	2143	C	T	1	1	0	0	0.999749498997996	CCG	ORF1ab:nsp2	P446P	C1338T	CCC>CCT	Synonymous	ORF1ab:nsp2	0.000250501002004008
CAMB-71FEF	MN908947.3	21742	C	T	1	1	0	0	1	CCA	S	S60S	C180T	TCC>TCT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-71FEF	MN908947.3	2891	G	A	1	1	0	0	1	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	0
CAMB-71FEF	MN908947.3	29051	C	INS	0.022	0.019	4.2e-05	0.00032	0.0208512370527839	GCA	N	.	777-778-insfrshift	.	no-SNV	GU280_gp10	0.979013071599801
CAMB-71FEF	MN908947.3	29348	G	T	0.024	0.064	5.3e-12	4.5e-29	0.0389818256918629	CGC	N	A359S	G1075T	GCA>TCA	Missense	GU280_gp10	0.960243700950021
CAMB-71FEF	MN908947.3	4668	C	T	1	1	0	0	0.999908159985306	TCT	ORF1ab:nsp3	S650F	C1949T	TCT>TTT	Missense	ORF1ab:nsp3	9.18400146944024e-05
CAMB-71FFE	MN908947.3	1440	G	A	1	1	2.8e-228	1.3e-118	1	GGC	ORF1ab:nsp2	G212D	G635A	GGC>GAC	Missense	ORF1ab:nsp2	0
CAMB-72009	MN908947.3	11075	T	-	0.035	0.039	6.1e-10	1.6e-10	0.0387306346826587	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957354656005331
CAMB-72009	MN908947.3	14408	C	T	1	1	0	0	0.99860582538905	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000527525528467538
CAMB-72009	MN908947.3	23403	A	G	1	1	0	0	0.999492411552713	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.0758844728694e-05
CAMB-72009	MN908947.3	241	C	T	1	1	0	0	0.999432865447327	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-72009	MN908947.3	25561	C	T	0.056	0.057	1.1e-23	1.3e-26	0.0565240833932423	TCA	ORF3a	Q57*	C169T	CAG>TAG	Nonsense	GU280_gp03	0.943475916606758
CAMB-72009	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99950490964601	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-72009	MN908947.3	3037	C	T	1	1	0	0	0.999401824435472	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.47719455660236e-05
CAMB-72009	MN908947.3	5629	G	T	0.055	0.048	4.1e-19	3.3e-22	0.0482925843604769	CGT	ORF1ab:nsp3	T970T	G2910T	ACG>ACT	Synonymous	ORF1ab:nsp3	0.951606385128309
CAMB-72018	MN908947.3	10373	C	T	0.0095	0.0061	2.4e-06	8.3e-05	0.00773718297325357	TCA	ORF1ab:3C-like-proteinase	Q107*	C319T	CAA>TAA	Nonsense	ORF1ab:3C-like-proteinase	0.992238097592327
CAMB-72018	MN908947.3	10647	C	T	0.018	0.0075	1.1e-09	1.5e-05	0.0136769861255123	ACA	ORF1ab:3C-like-proteinase	T198I	C593T	ACA>ATA	Missense	ORF1ab:3C-like-proteinase	0.986323013874488
CAMB-72018	MN908947.3	10818	C	T	0.011	0.0064	3.5e-06	0.00016	0.00801282051282051	GCT	ORF1ab:3C-like-proteinase	A255V	C764T	GCT>GTT	Missense	ORF1ab:3C-like-proteinase	0.991880341880342
CAMB-72018	MN908947.3	10946	A	T	0.0064	0.0088	4.2e-05	4e-06	0.00784467542655423	TAG	ORF1ab:3C-like-proteinase	R298*	A892T	AGA>TGA	Nonsense	ORF1ab:3C-like-proteinase	0.992057266130614
CAMB-72018	MN908947.3	10946	AG	TT	0.0032	0.0089	4.2e-05;NA	4e-06;3.5e-06	0.00662703440210506	TAG	ORF1ab:3C-like-proteinase	.	892-893-mnv	.	no-SNV	ORF1ab:3C-like-proteinase	0.992057266130614
CAMB-72018	MN908947.3	11074	C	INS	0.11	0.12	3.1e-45	2.1e-40	0.109524177153298	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.890218482204895
CAMB-72018	MN908947.3	11083	G	-	0.1	0.24	3.6e-43	2.8e-111	0.149951485252686	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-72018	MN908947.3	11083	G	T	0.9	0.76	0	8.6e-295	0.849966682643411	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-72018	MN908947.3	1131	AA	-	0.00755	0.00585	2.5e-05;1.9e-05	0.00018;1e-04	0.00656439357506973	GAA	ORF1ab:nsp2	.	326-327-delfrshift	.	no-SNV	ORF1ab:nsp2	0.993221000268234
CAMB-72018	MN908947.3	11450	C	T	0.0058	0.011	0.00038	2e-06	0.00895316804407714	TCA	ORF1ab:nsp6	Q160*	C478T	CAA>TAA	Nonsense	ORF1ab:nsp6	0.991046831955923
CAMB-72018	MN908947.3	13572	T	-	0.009	0.0068	2.2e-05	0.00018	0.00789033767970578	GTT	ORF1ab:RNA-dependent-RNA-polymerase	.	105-105-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.992042795051822
CAMB-72018	MN908947.3	13572	TT	-	0.0045	0.00665	2.2e-05;NA	0.00018;4.2e-05	0.00552881488226877	GTT	ORF1ab:RNA-dependent-RNA-polymerase	.	105-106-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.992042795051822
CAMB-72018	MN908947.3	13762	G	-	0.02	0.0079	2.5e-10	4.1e-05	0.0146647502136586	CGG	ORF1ab:RNA-dependent-RNA-polymerase	.	295-295-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.985257555745474
CAMB-72018	MN908947.3	13762	GGTGACAT	-	0.00965	0.0009875	2.5e-10;6.2e-06;7.8e-06;1.3e-05;1e-05;1.7e-05;3.8e-07;5.1e-06	4.1e-05;NA;NA;NA;NA;NA;NA;NA	0.00433302383163107	CGG	ORF1ab:RNA-dependent-RNA-polymerase	.	295-302-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.985257555745474
CAMB-72018	MN908947.3	14184	C	T	0.0036	0.0079	0.002	1.9e-05	0.00516293861691794	CCA	ORF1ab:RNA-dependent-RNA-polymerase	T239T	C717T	ACC>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.994837061383082
CAMB-72018	MN908947.3	14805	C	T	1	1	0	0	0.998723516252138	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	1.3159626266614e-05
CAMB-72018	MN908947.3	1515	A	G	1	1	0	0	1	CAT	ORF1ab:nsp2	H237R	A710G	CAT>CGT	Missense	ORF1ab:nsp2	0
CAMB-72018	MN908947.3	17247	T	C	1	1	0	0	0.997596972379776	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000136203994668587
CAMB-72018	MN908947.3	17949	C	T	0.56	0.55	0	0	0.554695328915468	GCA	ORF1ab:helicase	G571G	C1713T	GGC>GGT	Synonymous	ORF1ab:helicase	0.445272345240019
CAMB-72018	MN908947.3	18895	T	-	0.0046	0.013	0.0013	3.2e-07	0.00826981517461266	CTT	ORF1ab:3'-to-5'-exonuclease	.	856-856-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.991605639416131
CAMB-72018	MN908947.3	19009	GACA	-	0.0079	0.001775	0.00011;2.6e-05;1.8e-05;2.1e-05	NA;NA;NA;3.2e-05	0.0049675816909132	AGA	ORF1ab:3'-to-5'-exonuclease	.	970-973-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.994966171376776
CAMB-72018	MN908947.3	19012	A	-	0.0077	0.0071	2.1e-05	3.2e-05	0.00750297226952861	CAA	ORF1ab:3'-to-5'-exonuclease	.	973-973-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.992256032903827
CAMB-72018	MN908947.3	19801	CG	TC	0.0074	0.00295	1.8e-05;4.2e-05	0.00029;NA	0.00609707815345633	GCG	ORF1ab:endoRNAse	.	181-182-mnv	.	no-SNV	ORF1ab:endoRNAse	0.992291961617115
CAMB-72018	MN908947.3	20612	T	-	0.004	0.0083	0.0024	2.6e-05	0.00663949513541941	CTT	ORF1ab:endoRNAse	.	992-992-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.993229029713384
CAMB-72018	MN908947.3	20620	A	-	0.0082	0.011	4e-05	2e-06	0.00997559925362423	TAA	ORF1ab:endoRNAse	.	1000-1000-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.989737333141955
CAMB-72018	MN908947.3	20844	C	T	0.0081	0.0054	1.7e-05	0.00025	0.0068724851333547	CCT	ORF1ab:2'-O-ribose-methyltransferase	P62P	C186T	CCC>CCT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.992967275575971
CAMB-72018	MN908947.3	22037	G	INS	0.0046	0.011	0.00032	2.2e-06	0.00559558485359497	AGT	S	.	474-475-insfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.991568296795953
CAMB-72018	MN908947.3	23992	AA	-	0.0095	0.0037	1.8e-05;6.7e-06	0.00013;NA	0.00764321757197982	CAA	S	.	2430-2431-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.991070456277905
CAMB-72018	MN908947.3	24035	A	-	0.014	0.009	1.2e-07	1.5e-05	0.0122147454651843	CAA	S	.	2473-2473-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.987638970157987
CAMB-72018	MN908947.3	24423	AA	-	0.0087	0.0029	3.8e-05;8.1e-06	0.00067;NA	0.00559499741407683	CAA	S	.	2861-2862-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.992686108264232
CAMB-72018	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-72018	MN908947.3	4421	C	T	0.065	0.039	2.8e-24	1.9e-15	0.0559184821679742	ACG	ORF1ab:nsp3	R568C	C1702T	CGC>TGC	Missense	ORF1ab:nsp3	0.944081517832026
CAMB-72018	MN908947.3	6131	A	-	0.0072	0.01	0.00038	7e-06	0.0094876660341556	TAA	ORF1ab:nsp3	.	3412-3412-delfrshift	.	no-SNV	ORF1ab:nsp3	0.990512333965844
CAMB-72018	MN908947.3	6170	G	C	0.0097	0.0083	2.1e-05	1.7e-05	0.00868167202572347	GGC	ORF1ab:nsp3	A1151P	G3451C	GCT>CCT	Missense	ORF1ab:nsp3	0.990675241157556
CAMB-72018	MN908947.3	6539	CA	-	0.0033	0.0093	NA;0.00048	1.8e-05;5.8e-06	0.00761819403988349	CCA	ORF1ab:nsp3	.	3820-3821-delfrshift	.	no-SNV	ORF1ab:nsp3	0.993363749481543
CAMB-72018	MN908947.3	6813	C	T	0.0088	0.0043	3.6e-05	0.0011	0.00562851782363977	ACT	ORF1ab:nsp3	T1365I	C4094T	ACT>ATT	Missense	ORF1ab:nsp3	0.993518676445506
CAMB-72018	MN908947.3	7463	GTTGTAGACG	-	0.0013	0.0106	NA;NA;NA;NA;NA;NA;NA;NA;NA;3.2e-06	4.6e-06;1.4e-06;2.7e-06;2.6e-06;1.2e-06;1.9e-06;3.5e-07;7.8e-07;1.1e-06;2.8e-05	0.00275536311749656	TGT	ORF1ab:nsp3	.	4744-4753-delfrshift	.	no-SNV	ORF1ab:nsp3	0.997086530057298
CAMB-72018	MN908947.3	7472	G	-	0.013	0.011	3.2e-06	2.8e-05	0.0121212121212121	CGG	ORF1ab:nsp3	.	4753-4753-delfrshift	.	no-SNV	ORF1ab:nsp3	0.987570621468927
CAMB-72018	MN908947.3	8024	GCAGTTAAAATGTTTGATGCTTACGTTAATACGTTTTCATCAACTTTTAACGTACCAATG	-	0.00852333333333333	0.000189333333333333	4.8e-06;1.1e-05;8.6e-06;6.4e-06;6e-06;1.4e-05;7.4e-06;5.6e-06;1.4e-05;6.4e-06;6e-06;4.7e-06;1e-05;1.1e-05;2.2e-05;1.3e-05;2.1e-05;1.5e-05;1e-05;9e-06;6.5e-06;6.7e-06;7.8e-06;6.5e-06;7.3e-06;4.2e-06;4.9e-06;5.6e-06;4.8e-06;1.4e-05;7e-06;7.1e-06;4.9e-06;6.8e-06;4.2e-06;1.2e-05;1.1e-05;6.6e-06;9.5e-06;1.1e-05;1.4e-05;1.1e-05;5.9e-05;5.6e-05;1.1e-05;2.6e-06;3.7e-05;2.1e-05;5.9e-06;3.9e-06;1.2e-05;3.9e-06;6.8e-06;5e-06;4.5e-06;4.5e-06;3.2e-06;2.8e-06;6e-04;0.00043	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;7.8e-07;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00555674289378072	TGC	ORF1ab:nsp3	.	5305-5364-delinframe	.	no-SNV	ORF1ab:nsp3	0.994354420336293
CAMB-72018	MN908947.3	9223	C	T	1	0.99	0	0	0.994819792302993	ACG	ORF1ab:nsp4	H223H	C669T	CAC>CAT	Synonymous	ORF1ab:nsp4	0.000146609651802077
CAMB-72018	MN908947.3	932	G	T	0.0089	0.0062	4.6e-06	5.3e-05	0.0078510648300503	TGA	ORF1ab:nsp2	D43Y	G127T	GAC>TAC	Missense	ORF1ab:nsp2	0.99207058122953
CAMB-72027	MN908947.3	10163	T	C	0.0093	0.0091	5.8e-06	6.1e-06	0.00919980833732631	TTA	ORF1ab:3C-like-proteinase	Y37H	T109C	TAC>CAC	Missense	ORF1ab:3C-like-proteinase	0.990184133068656
CAMB-72027	MN908947.3	11074	C	INS	0.026	0.024	2.6e-05	0.00013	0.024978317432784	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.974298930326684
CAMB-72027	MN908947.3	11075	T	-	0.034	0.042	1.5e-08	7.6e-11	0.0369376246644832	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959491738284617
CAMB-72027	MN908947.3	12116	C	T	0.0081	0.0089	3.5e-05	1.4e-05	0.0084638003655726	CCT	ORF1ab:nsp8	L9F	C25T	CTT>TTT	Missense	ORF1ab:nsp8	0.991297782722721
CAMB-72027	MN908947.3	14126	G	A	0.012	0.011	3.2e-07	6.6e-07	0.0116040395194176	AGT	ORF1ab:RNA-dependent-RNA-polymerase	S220N	G659A	AGT>AAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.988313856427379
CAMB-72027	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999336141963488	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000178731009830206
CAMB-72027	MN908947.3	25596	A	G	1	1	0	0	0.999687812187812	GAT	ORF3a	R68R	A204G	AGA>AGG	Synonymous	GU280_gp03	0.000140484515484515
CAMB-72027	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.02834375	0.02953125	2e-04;0.00042;0.00015;0.00015;5.5e-05;9.9e-05;8.1e-05;0.00013;9.3e-05;0.00011;0.00016;8.3e-05;0.00015;1e-04;1e-04;0.00011;0.00016;9.8e-05;0.00013;9.7e-05;8.4e-05;0.00013;8.5e-05;3.6e-05;9.9e-05;0.00013;0.00012;8.3e-05;0.00014;5.2e-05;8.9e-05;8.6e-05	0.00012;0.00024;8.4e-05;8e-05;4.7e-05;5.2e-05;4.6e-05;6.6e-05;5.4e-05;6.8e-05;9.7e-05;5.1e-05;8.1e-05;4.9e-05;6.2e-05;6.9e-05;9.6e-05;5.5e-05;6.8e-05;5.6e-05;4.1e-05;7.4e-05;5.7e-05;1.1e-05;5.8e-05;7.6e-05;7.6e-05;3.6e-05;8e-05;2.1e-05;4.6e-05;3.4e-05	0.0285268967884005	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.972319814442133
CAMB-72027	MN908947.3	29771	A	G	1	1	0	0	0.998976574937457	AAT	NA	NA	NA	NA	NA	NA	0.000113713895838071
CAMB-72036	MN908947.3	11075	T	-	0.037	0.045	4.1e-09	1.8e-11	0.0398518259501279	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956279913455865
CAMB-72036	MN908947.3	13818	C	T	0.059	0.078	6.6e-28	2.7e-36	0.066299672111422	ACC	ORF1ab:RNA-dependent-RNA-polymerase	D117D	C351T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.933670246367656
CAMB-72036	MN908947.3	14408	C	T	1	1	0	0	0.996926963292837	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00166673177337656
CAMB-72036	MN908947.3	21801	A	C	1	1	0	0	0.999763853904282	GAT	S	D80A	A239C	GAT>GCT	Missense	GU280_gp02, spike glycoprotein	0.000236146095717884
CAMB-72036	MN908947.3	23403	A	G	1	1	0	0	0.999304138495246	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.82106015440603e-05
CAMB-72036	MN908947.3	241	C	T	1	1	0	0	0.998391445554262	TCG	NA	NA	NA	NA	NA	NA	0.000153195661498866
CAMB-72036	MN908947.3	2416	C	T	1	1	0	0	0.999854756717502	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0
CAMB-72036	MN908947.3	25563	G	T	1	1	0	0	0.999858068789327	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	6.30805380769898e-05
CAMB-72036	MN908947.3	27213	C	T	0.38	0.39	2.7e-202	2.8e-209	0.38844232022594	TCG	ORF6	L4L	C12T	CTC>CTT	Synonymous	GU280_gp06	0.608903456158082
CAMB-72036	MN908947.3	3037	C	T	1	1	0	0	0.999730845146241	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.97182845863987e-05
CAMB-72036	MN908947.3	4755	C	T	1	1	0	0	0.998373119957502	CCT	ORF1ab:nsp3	P679L	C2036T	CCT>CTT	Missense	ORF1ab:nsp3	0.00159367840897772
CAMB-72036	MN908947.3	763	C	T	0.035	0.04	8.4e-17	2.6e-19	0.0366960965482627	GCA	ORF1ab:leader-protein	S166S	C498T	AGC>AGT	Synonymous	ORF1ab:leader-protein	0.963246868797481
CAMB-72045	MN908947.3	11074	C	INS	0.11	0.11	4.8e-43	1.7e-33	0.109260447988108	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.889523294705902
CAMB-72045	MN908947.3	11083	G	-	0.19	0.2	4.7e-87	5.5e-90	0.19483684684405	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.55236114129591e-05
CAMB-72045	MN908947.3	11083	G	T	0.81	0.8	0	0	0.805070011487472	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.55236114129591e-05
CAMB-72045	MN908947.3	14805	C	T	1	1	0	0	0.998657638919621	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	4.42536619905297e-05
CAMB-72045	MN908947.3	1541	C	T	1	1	0	0	0.997441300421433	ACG	ORF1ab:nsp2	R246C	C736T	CGT>TGT	Missense	ORF1ab:nsp2	0
CAMB-72045	MN908947.3	2480	A	G	1	1	0	0	0.999138376701706	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000861623298293986
CAMB-72045	MN908947.3	2558	C	T	1	1	0	0	0.99821579491032	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000657338717250446
CAMB-72045	MN908947.3	25672	C	T	0.0072	0.005	2.8e-05	0.00049	0.00682170542635659	CCT	ORF3a	L94F	C280T	CTT>TTT	Missense	GU280_gp03	0.993178294573643
CAMB-72045	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-72045	MN908947.3	27390	G	C	0.047	0.033	3.9e-22	3.2e-16	0.0406321535481599	CGA	NA	NA	NA	NA	NA	NA	0.95932382461701
CAMB-72045	MN908947.3	4068	C	T	0.037	0.022	3.9e-17	2.8e-10	0.0344910903050438	GCC	ORF1ab:nsp3	A450V	C1349T	GCC>GTC	Missense	ORF1ab:nsp3	0.965206886137119
CAMB-72054	MN908947.3	11074	C	INS	0.12	0.099	9.7e-50	3.2e-27	0.115224015348155	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.884080051160516
CAMB-72054	MN908947.3	11083	G	-	0.15	0.45	1.7e-63	1.4e-239	0.211274793318137	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	5.10325587724969e-05
CAMB-72054	MN908947.3	11083	G	T	0.85	0.55	0	7.5e-166	0.788555098152621	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	5.10325587724969e-05
CAMB-72054	MN908947.3	13914	T	G	0.00097	0.012	0.0083	1.5e-07	0.0031223167590352	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.996643509484037
CAMB-72054	MN908947.3	1457	C	T	1	1	0	4.6e-238	1	TCG	ORF1ab:nsp2	R218C	C652T	CGT>TGT	Missense	ORF1ab:nsp2	0
CAMB-72054	MN908947.3	14805	C	T	1	1	0	0	0.999929498025945	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	7.05019740552736e-05
CAMB-72054	MN908947.3	1547	A	G	0.034	0.055	1.2e-12	2.3e-11	0.037953795379538	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.935643564356436
CAMB-72054	MN908947.3	17206	TATTTGCCTATAGA	-	0.0207857142857143	0.00371428571428571	1e-05;1.1e-05;1.2e-07;4.1e-07;3e-10;2.9e-10;2.6e-10;1.7e-10;1.5e-11;2.3e-11;1.3e-11;9e-11;1e-10;2.1e-10	0.00053;0.00042;2.1e-05;3.9e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0161959201972652	ATA	ORF1ab:helicase	.	970-983-delfrshift	.	no-SNV	ORF1ab:helicase	0.982098982098982
CAMB-72054	MN908947.3	19831	A	G	0.088	0.19	1.4e-38	1e-65	0.104959630911188	AAT	ORF1ab:endoRNAse	I71V	A211G	ATA>GTA	Missense	ORF1ab:endoRNAse	0.895040369088812
CAMB-72054	MN908947.3	20742	A	G	1	1	6.3e-145	7.1e-228	1	AAA	ORF1ab:2'-O-ribose-methyltransferase	Q28Q	A84G	CAA>CAG	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0
CAMB-72054	MN908947.3	20759	C	T	0.13	0.48	2.1e-15	1.6e-85	0.366548042704626	GCA	ORF1ab:2'-O-ribose-methyltransferase	A34V	C101T	GCA>GTA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.633451957295374
CAMB-72054	MN908947.3	20925	G	T	1	1	0	0	1	TGC	ORF1ab:2'-O-ribose-methyltransferase	L89F	G267T	TTG>TTT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0
CAMB-72054	MN908947.3	2480	A	G	1	1	0	1.4e-273	0.998542274052478	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.00145772594752187
CAMB-72054	MN908947.3	2558	C	T	0.99	1	0	9.79999999999999e-305	0.994553376906318	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.00544662309368192
CAMB-72054	MN908947.3	26144	G	T	1	1	1.4e-198	1e-76	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-72054	MN908947.3	26774	GGCTTGTCTTG	-	0.0151818181818182	0.0409090909090909	NA;NA;0.0023;0.0019;0.0032;0.0077;0.0064;0.0013;0.0062;0.0061;0.0089	2.1e-17;3.2e-07;2.2e-06;2.2e-07;1.4e-06;7.1e-06;5.6e-07;1.8e-08;3.1e-07;3.4e-07;1.1e-06	0.0250582535044569	TGG	M	.	252-262-delfrshift	.	no-SNV	GU280_gp05	0.987173969183094
CAMB-72054	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.0325555555555556	0.0442777777777778	0.003;0.0055;9.5e-06;9.6e-06;4.6e-06;6.8e-06;4.9e-06;9.1e-06;6.8e-06;8.2e-06;1.2e-05;5.9e-06;1.1e-05;8e-06;7.5e-06;5.1e-06;1.2e-05;7.1e-06;8.7e-06;7e-06;7.2e-06;9.9e-06;6e-06;4.8e-06;6.3e-06;9.7e-06;8.9e-06;7e-06;9.6e-06;3.1e-06;5.6e-06;3.7e-06;8.1e-05;0.015;0.011;0.012	7.6e-18;9.5e-17;3.9e-07;3.7e-07;2.6e-07;2e-07;1.5e-07;3.2e-07;2.5e-07;3e-07;5.2e-07;2e-07;4.4e-07;2.6e-07;3e-07;2.4e-07;5.3e-07;2.7e-07;3.4e-07;2.4e-07;2.1e-07;3.8e-07;2.6e-07;6.4e-08;2.6e-07;4.3e-07;3.6e-07;1.6e-07;3.9e-07;6.7e-08;2.2e-07;8.7e-08;8.3e-06;5.3e-05;1.9e-05;3e-05	0.0367752797166006	GTA	M	.	263-298-delinframe	.	no-SNV	GU280_gp05	0.953952108497563
CAMB-72054	MN908947.3	2723	C	T	0.97	1	5e-165	3.5e-44	0.972789115646258	ACC	ORF1ab:nsp3	P2S	C4T	CCA>TCA	Missense	ORF1ab:nsp3	0.0272108843537415
CAMB-72054	MN908947.3	29616	G	T	0.012	0.022	1.4e-06	6e-09	0.0152855993563958	AGA	ORF10	R20I	G59T	AGA>ATA	Missense	GU280_gp11	0.984714400643604
CAMB-72054	MN908947.3	3096	C	T	0.13	0.071	1.6e-37	5e-23	0.0921232876712329	TCA	ORF1ab:nsp3	S126L	C377T	TCA>TTA	Missense	ORF1ab:nsp3	0.907876712328767
CAMB-72054	MN908947.3	508	T	-	0.035	0.13	0.00023	2.1e-13	0.0517825257065452	ATG	ORF1ab:leader-protein	.	243-243-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.947786466350594
CAMB-72054	MN908947.3	513	ATG	-	0.046	0.183333333333333	0.025;0.0087;0.03	0.00025;2.2e-07;0.00014	0.0688243872606671	CAT	ORF1ab:leader-protein	.	248-250-delinframe	.	no-SNV	ORF1ab:leader-protein	0.93058445243049
CAMB-72054	MN908947.3	516	TTATGGT	-	0.0475714285714286	0.215714285714286	0.02;0.024;0.026;0.031;0.038;0.021;1.5e-06	4.2e-06;1.3e-05;1.4e-05;0.00018;4e-04;7.3e-05;2.9e-27	0.080975271321671	GTT	ORF1ab:leader-protein	.	251-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.913644032053986
CAMB-72054	MN908947.3	522	T	-	0.05	0.19	1.5e-06	2.9e-27	0.0742665036674817	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.925580684596577
CAMB-72063	MN908947.3	11071	G	INS	0.24	0.24	3.2e-66	4.9e-66	0.237909654561559	TGT	ORF1ab:nsp6	.	98-99-insfrshift	.	no-SNV	ORF1ab:nsp6	0.761275465013286
CAMB-72063	MN908947.3	11073	T	-	0.019	0.022	3.1e-10	7.1e-12	0.021041923221074	TTC	ORF1ab:nsp6	.	101-101-delfrshift	.	no-SNV	ORF1ab:nsp6	0.97858328425336
CAMB-72063	MN908947.3	11074	C	-	0.17	0.22	1.3e-81	1.2e-137	0.202998790810157	TCT	ORF1ab:nsp6	.	102-102-delfrshift	.	no-SNV	ORF1ab:nsp6	0.000290205562273277
CAMB-72063	MN908947.3	11074	C	T	0.83	0.78	0	0	0.796469165659008	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.000290205562273277
CAMB-72063	MN908947.3	11083	G	T	1	1	0	0	0.999328118251188	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-72063	MN908947.3	14805	C	T	1	1	0	0	0.999952821287035	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	4.71787129647103e-05
CAMB-72063	MN908947.3	15017	C	T	0.015	0.017	0.00079	1.5e-06	0.016295025728988	GCA	ORF1ab:RNA-dependent-RNA-polymerase	A517V	C1550T	GCA>GTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.983704974271012
CAMB-72063	MN908947.3	18046	A	C	0.0099	0.0047	1.7e-06	0.00032	0.00523611934400316	AAA	ORF1ab:3'-to-5'-exonuclease	N3H	A7C	AAT>CAT	Missense	ORF1ab:3'-to-5'-exonuclease	0.994665085951393
CAMB-72063	MN908947.3	18804	C	T	1	1	0	0	0.999808199472549	GCA	ORF1ab:3'-to-5'-exonuclease	S255S	C765T	AGC>AGT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.000143850395588588
CAMB-72063	MN908947.3	18999	A	C	0.28	0.23	4.4e-106	2.8e-94	0.246239113222486	CAT	ORF1ab:3'-to-5'-exonuclease	A320A	A960C	GCA>GCC	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.753760886777514
CAMB-72063	MN908947.3	19610	C	T	0.28	0.11	1.4e-70	9e-43	0.140016920473773	ACA	ORF1ab:3'-to-5'-exonuclease	T524I	C1571T	ACA>ATA	Missense	ORF1ab:3'-to-5'-exonuclease	0.859983079526227
CAMB-72063	MN908947.3	20987	CT	AC	0.0085	0.047	NA;4.7e-07	7.9e-23;1.6e-19	0.0409518539014942	ACT	ORF1ab:2'-O-ribose-methyltransferase	.	329-330-mnv	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.95763300458397
CAMB-72063	MN908947.3	20988	T	C	0.017	0.044	4.7e-07	1.6e-19	0.039696760854583	CTT	ORF1ab:2'-O-ribose-methyltransferase	T110T	T330C	ACT>ACC	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.960303239145417
CAMB-72063	MN908947.3	23308	T	G	0.0069	0.0064	3.7e-05	5.8e-05	0.00663716814159292	TTG	S	L582L	T1746G	CTT>CTG	Synonymous	GU280_gp02, spike glycoprotein	0.993080399171531
CAMB-72063	MN908947.3	2480	A	G	1	1	6.7e-273	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-72063	MN908947.3	25406	T	G	0.0074	0.0085	4.4e-06	3e-06	0.00834683954619125	ATG	ORF3a	M5R	T14G	ATG>AGG	Missense	GU280_gp03	0.991572123176661
CAMB-72063	MN908947.3	2558	C	T	1	1	0	0	0.996363636363636	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-72063	MN908947.3	27264	TTTTAAAGTTTCCATTTGGAATCTTGA	-	0.357407407407407	0.179259259259259	2.2e-174;1.3e-127;1.1e-112;7.2e-101;5.9e-112;1.4e-105;4e-104;1.3e-103;9.1e-113;1.6e-101;1.4e-100;1.2e-103;5.7e-106;6.9e-105;1.2e-105;3e-98;2.2e-101;5e-103;1.8e-95;2.2e-104;6.1e-100;5.2e-103;4.6e-102;1.6e-113;3.7e-102;1.5e-115;2.4e-115	3.5e-81;5.9e-59;1.1e-51;5.2e-46;5.8e-51;1.9e-48;6e-48;1.5e-47;8.7e-52;1.6e-46;3.4e-46;3.9e-48;5.7e-49;6.7e-49;1e-49;8.5e-46;1.2e-46;1.2e-47;1.1e-43;1.4e-48;1.5e-47;1.6e-47;3.6e-47;1.6e-52;4e-47;3.7e-53;1.2e-53	0.225098342230964	CTT	ORF6	.	63-89-delinframe	.	no-SNV	GU280_gp06	0.777163520044505
CAMB-72063	MN908947.3	28913	G	A	0.0093	0.024	6.3e-06	5.9e-11	0.0158134548378451	TGG	N	G214S	G640A	GGC>AGC	Missense	GU280_gp10	0.984186545162155
CAMB-72063	MN908947.3	6016	C	T	1	1	7.2e-128	0	1	ACC	ORF1ab:nsp3	N1099N	C3297T	AAC>AAT	Synonymous	ORF1ab:nsp3	0
CAMB-72072	MN908947.3	10427	G	-	0.0099	0.0019	6.9e-07	0.0034	0.00453350258409647	TGT	ORF1ab:3C-like-proteinase	.	373-373-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.99528515731254
CAMB-72072	MN908947.3	11075	T	-	0.039	0.024	5.5e-11	4.3e-07	0.0288912614448866	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.968714613866511
CAMB-72072	MN908947.3	1125	G	-	0.01	0.0043	1e-05	0.0019	0.00533180995905932	AGG	ORF1ab:nsp2	.	320-320-delfrshift	.	no-SNV	ORF1ab:nsp2	0.992716366752356
CAMB-72072	MN908947.3	1190	C	T	0.064	0.098	4.3e-28	7.3e-45	0.0923127157384084	ACC	ORF1ab:nsp2	P129S	C385T	CCA>TCA	Missense	ORF1ab:nsp2	0.907687284261592
CAMB-72072	MN908947.3	12513	C	T	0.013	0.007	5.1e-07	0.00015	0.00822429906542056	ACG	ORF1ab:nsp8	T141M	C422T	ACG>ATG	Missense	ORF1ab:nsp8	0.991775700934579
CAMB-72072	MN908947.3	13615	A	G	0.0072	0.011	7.3e-05	7.4e-06	0.00880572372041827	AAA	ORF1ab:RNA-dependent-RNA-polymerase	K50E	A148G	AAG>GAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.991194276279582
CAMB-72072	MN908947.3	14408	C	T	1	1	0	0	0.998751393534002	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00102564102564103
CAMB-72072	MN908947.3	15187	A	G	0.023	0.013	4.3e-08	1.3e-07	0.0145379023883697	TAG	ORF1ab:RNA-dependent-RNA-polymerase	R574G	A1720G	AGA>GGA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.98546209761163
CAMB-72072	MN908947.3	1830	AT	-	0.0033	0.013	NA;0.00019	1e-07;1.7e-07	0.011039886039886	AAT	ORF1ab:nsp2	.	1025-1026-delfrshift	.	no-SNV	ORF1ab:nsp2	0.989316432775011
CAMB-72072	MN908947.3	20626	G	A	0.0028	0.014	0.0045	6.3e-08	0.010467706013363	TGG	ORF1ab:endoRNAse	G336S	G1006A	GGC>AGC	Missense	ORF1ab:endoRNAse	0.989309576837416
CAMB-72072	MN908947.3	23403	A	G	1	1	0	0	0.99982432854466	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000117114303560275
CAMB-72072	MN908947.3	241	C	T	1	1	0	0	0.999753086419753	TCG	NA	NA	NA	NA	NA	NA	0.000123456790123457
CAMB-72072	MN908947.3	24239	G	-	0.0071	0.012	0.00057	5.9e-07	0.0113718151720167	TGC	S	.	2677-2677-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.988628184827983
CAMB-72072	MN908947.3	25424	G	T	0.0073	0.0096	2.3e-05	2e-06	0.00918325883787078	GGA	ORF3a	G11V	G32T	GGA>GTA	Missense	GU280_gp03	0.990816741162129
CAMB-72072	MN908947.3	26907	C	T	0.0041	0.013	0.0029	2.1e-07	0.0111874915756841	TCT	M	L129L	C385T	CTG>TTG	Synonymous	GU280_gp05	0.98625151637687
CAMB-72072	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999366458503032	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-72072	MN908947.3	3037	C	T	1	1	6.6e-309	0	0.999449035812672	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-72081	MN908947.3	11075	T	-	0.045	0.04	1.6e-10	1.7e-10	0.0437729947849399	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952429156863703
CAMB-72081	MN908947.3	1191	C	T	1	1	0	0	0.999031881155066	CCA	ORF1ab:nsp2	P129L	C386T	CCA>CTA	Missense	ORF1ab:nsp2	0.000367217492906026
CAMB-72081	MN908947.3	12817	G	T	0.018	0.015	7.5e-09	6.9e-09	0.0173853945147217	TGT	ORF1ab:nsp9	L44L	G132T	CTG>CTT	Synonymous	ORF1ab:nsp9	0.982453832606201
CAMB-72081	MN908947.3	13009	C	T	0.096	0.1	7.2e-43	1.3e-47	0.0969918183871367	CCA	ORF1ab:nsp9	A108A	C324T	GCC>GCT	Synonymous	ORF1ab:nsp9	0.902877042671155
CAMB-72081	MN908947.3	14408	C	T	1	1	0	0	0.999454110700199	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000330609012555454
CAMB-72081	MN908947.3	15016	G	T	0.012	0.0089	4.6e-07	4.8e-06	0.0106016851932434	TGC	ORF1ab:RNA-dependent-RNA-polymerase	A517S	G1549T	GCA>TCA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.989240080699395
CAMB-72081	MN908947.3	16887	C	T	0.042	0.05	1.2e-16	1.3e-20	0.0438075347743217	ACA	ORF1ab:helicase	Y217Y	C651T	TAC>TAT	Synonymous	ORF1ab:helicase	0.955695689200697
CAMB-72081	MN908947.3	18877	C	T	0.024	0.017	2e-11	2.4e-09	0.0229653226225308	TCT	ORF1ab:3'-to-5'-exonuclease	L280L	C838T	CTA>TTA	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.977008708297987
CAMB-72081	MN908947.3	23403	A	G	1	1	0	0	0.999731223122312	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.37543754375438e-05
CAMB-72081	MN908947.3	241	C	T	1	1	0	0	0.999893718779892	TCG	NA	NA	NA	NA	NA	NA	0.000106281220108407
CAMB-72081	MN908947.3	24382	C	T	0.0028	0.0075	0.0063	3.4e-05	0.00378165077277211	CCA	S	S940S	C2820T	TCC>TCT	Synonymous	GU280_gp02, spike glycoprotein	0.996218349227228
CAMB-72081	MN908947.3	26882	C	T	1	1	0	0	0.99988755978792	TCA	M	L120L	C360T	CTC>CTT	Synonymous	GU280_gp05	9.94663414549763e-05
CAMB-72081	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999487484368273	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	9.06043308870164e-05
CAMB-72081	MN908947.3	29206	T	C	0.038	0.042	4.8e-17	1.1e-19	0.0386435058880409	CTT	N	A311A	T933C	GCT>GCC	Synonymous	GU280_gp10	0.960285941223193
CAMB-72081	MN908947.3	3037	C	T	1	1	0	0	0.99935149156939	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000176865935620799
CAMB-72081	MN908947.3	4698	C	T	0.013	0.0078	6.8e-07	3.6e-05	0.0113931053559697	TCT	ORF1ab:nsp3	S660F	C1979T	TCT>TTT	Missense	ORF1ab:nsp3	0.988166038518723
CAMB-72090	MN908947.3	13914	T	G	0.0051	0.0079	6.7e-05	3.6e-06	0.00652346857597454	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993476531424025
CAMB-72090	MN908947.3	14408	C	T	1	1	0	0	0.999578896709379	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00036094567767551
CAMB-72090	MN908947.3	20578	G	T	1	1	2.47032822920623e-323	6.3e-217	1	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	0
CAMB-72090	MN908947.3	20868	T	C	0.0052	0.069	0.00043	3.6e-30	0.0319778918278721	TTG	ORF1ab:2'-O-ribose-methyltransferase	F70F	T210C	TTT>TTC	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.968022108172128
CAMB-72090	MN908947.3	22321	TTC	-	0.00223333333333333	0.0183333333333333	0.0067;0.025;0.036	3.8e-05;0.00015;0.00022	0.00471253534401508	ATT	S	.	759-761-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.995327102803738
CAMB-72090	MN908947.3	23403	A	G	1	1	0	0	1	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-72090	MN908947.3	241	C	T	1	1	0	0	0.999124562281141	TCG	NA	NA	NA	NA	NA	NA	0.000500250125062531
CAMB-72090	MN908947.3	2416	C	T	1	1	6.7e-209	1.6e-288	0.997737556561086	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0
CAMB-72090	MN908947.3	25563	G	T	1	1	0	0	0.999929922915207	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0
CAMB-72090	MN908947.3	3037	C	T	1	1	4.5e-164	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-72090	MN908947.3	5840	T	C	1	1	0	0	1	ATA	ORF1ab:nsp3	Y1041H	T3121C	TAC>CAC	Missense	ORF1ab:nsp3	0
CAMB-720AF	MN908947.3	11074	C	INS	0.098	0.11	9e-41	7.8e-34	0.100795792112937	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.890633090780258
CAMB-720AF	MN908947.3	11074	C	T	0.0076	0.0067	1.7e-05	0.00095	0.00735835172921266	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.890633090780258
CAMB-720AF	MN908947.3	11083	G	-	0.17	0.18	2.2e-75	1e-81	0.174276949490614	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-720AF	MN908947.3	11083	G	T	0.83	0.82	0	0	0.825558936033227	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-720AF	MN908947.3	147	C	T	0.21	0.21	4.3e-101	4.9e-99	0.212752363915155	ACT	NA	NA	NA	NA	NA	NA	0.787105659198682
CAMB-720AF	MN908947.3	14805	C	T	1	1	0	0	0.99802336229424	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00102740490920867
CAMB-720AF	MN908947.3	15405	A	G	1	1	0	0	0.999630332058247	TAG	ORF1ab:RNA-dependent-RNA-polymerase	L646L	A1938G	TTA>TTG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	4.82175576199814e-05
CAMB-720AF	MN908947.3	23555	CCCATTGGTGCAGGTATATGCGCTAGT	-	0.0383703703703704	0.0414814814814815	0.0018;0.0016;0.0018;0.0019;0.00028;0.00059;0.00011;2e-04;0.00022;0.00021;0.00021;2e-04;0.00012;0.00011;4.1e-05;1.6e-05;0.00019;8.6e-05;0.00024;6.1e-05;0.00015;0.00026;0.00017;0.00029;9.4e-06;1.3e-05;0.00092	0.00076;0.00059;0.00074;0.00077;7e-05;0.00013;5.1e-05;1e-04;1e-04;0.00011;1e-04;1e-04;5.3e-05;5.1e-05;8.6e-06;3.4e-06;0.00011;4.7e-05;0.00014;4.2e-05;9.4e-05;0.00019;1e-04;0.00015;3.7e-06;7.4e-06;0.00064	0.0372665872069925	ACC	S	.	1993-2019-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.967523520843995
CAMB-720AF	MN908947.3	2480	A	G	1	1	0	0	0.999900586539417	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	9.94134605825629e-05
CAMB-720AF	MN908947.3	2558	C	T	1	1	0	0	0.998702772823091	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-720AF	MN908947.3	26144	G	T	1	1	0	0	0.999872797812122	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	6.36010939388158e-05
CAMB-720AF	MN908947.3	26435	A	G	0.27	0.27	1.7e-135	7.3e-132	0.273633703920421	AAT	E	N64S	A191G	AAT>AGT	Missense	GU280_gp04	0.72592159157402
CAMB-720AF	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0345526315789474	0.0391842105263158	0.0014;0.00016;0.00081;0.00068;0.00084;1.2e-05;4.2e-05;4.9e-06;4.5e-06;2.1e-06;2.7e-06;2e-06;3.8e-06;2.8e-06;3.6e-06;5.2e-06;2.3e-06;4.5e-06;3e-06;3.1e-06;2.3e-06;5.1e-06;3e-06;3.6e-06;2.9e-06;2.1e-06;4.2e-06;2.4e-06;9.7e-07;3e-06;4e-06;3.6e-06;2.6e-06;4.5e-06;1.1e-06;2.9e-06;2.4e-06;0.0024	0.00018;1.7e-05;8.5e-05;9.2e-05;0.00021;2.5e-06;9.3e-06;4.2e-07;4.1e-07;2.7e-07;2.1e-07;1.5e-07;2.7e-07;2.4e-07;3.4e-07;5.3e-07;2.1e-07;4.3e-07;1.9e-07;3e-07;2.2e-07;5e-07;2.9e-07;3.4e-07;2.4e-07;1.3e-07;3.8e-07;2.6e-07;1.9e-08;2.8e-07;4.1e-07;3.7e-07;1.6e-07;5.2e-07;5.9e-08;2.8e-07;1.4e-07;0.00063	0.0383964274247687	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.977932078547826
CAMB-720AF	MN908947.3	27331	C	T	1	1	0	0	0.999939044832526	ACT	ORF6	L44L	C130T	CTA>TTA	Synonymous	GU280_gp06	5.07959728952689e-05
CAMB-720AF	MN908947.3	3015	C	T	0.0089	0.0066	4.1e-06	4.4e-05	0.0076201096552365	GCT	ORF1ab:nsp3	A99V	C296T	GCT>GTT	Missense	ORF1ab:nsp3	0.992286962178236
CAMB-720AF	MN908947.3	583	C	T	1	1	0	0	0.99963839948129	TCC	ORF1ab:leader-protein	V106V	C318T	GTC>GTT	Synonymous	ORF1ab:leader-protein	0.000174565767652963
CAMB-720AF	MN908947.3	700	A	G	1	1	0	0	0.99963636153744	TAG	ORF1ab:leader-protein	L145L	A435G	TTA>TTG	Synonymous	ORF1ab:leader-protein	8.08085472354819e-05
CAMB-720AF	MN908947.3	7273	G	INS	0.024	0.011	3.3e-05	2e-05	0.0130010834236186	GGT	ORF1ab:nsp3	.	4553-4554-insfrshift	.	no-SNV	ORF1ab:nsp3	0.985915492957746
CAMB-720AF	MN908947.3	7279	C	T	1	0.99	2.7e-173	0	0.99455930359086	TCT	ORF1ab:nsp3	F1520F	C4560T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00108813928182807
CAMB-720BE	MN908947.3	10097	G	A	1	1	0	0	0.99984502130957	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000116234017822549
CAMB-720BE	MN908947.3	10937	GATGTTGTT	-	0.0107555555555556	0.00384444444444444	6.6e-05;9.2e-05;0.00017;0.00019;0.00015;3.9e-05;8.6e-05;0.00067;0.00092	0.0084;0.01;0.013;0.015;0.012;0.0075;0.01;NA;NA	0.0081764308754032	TGA	ORF1ab:3C-like-proteinase	.	883-891-delinframe	.	no-SNV	ORF1ab:3C-like-proteinase	0.991759065028469
CAMB-720BE	MN908947.3	11075	T	-	0.035	0.033	9.6e-09	8.5e-09	0.0343112026076514	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956882255389718
CAMB-720BE	MN908947.3	12263	AAGTTGG	-	0.00141428571428571	0.0058	NA;NA;NA;NA;0.00051;0.0011;NA	0.00027;0.00029;6e-04;0.00036;0.00032;3.1e-05;0.00022	0.00176239454524442	TAA	ORF1ab:nsp8	.	172-178-delfrshift	.	no-SNV	ORF1ab:nsp8	0.998064199243015
CAMB-720BE	MN908947.3	13536	C	T	0.99	1	0	0	0.997228256798262	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-720BE	MN908947.3	14178	C	T	0.004	0.014	0.0018	5.5e-08	0.0076507164098405	CCT	ORF1ab:RNA-dependent-RNA-polymerase	T237T	C711T	ACC>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.99234928359016
CAMB-720BE	MN908947.3	14184	C	T	1	1	0	0	0.999920837016611	CCA	ORF1ab:RNA-dependent-RNA-polymerase	T239T	C717T	ACC>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	7.91629833889673e-05
CAMB-720BE	MN908947.3	14408	C	T	1	0.99	0	0	0.993570729737704	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00034165204292392
CAMB-720BE	MN908947.3	1684	C	T	1	1	0	0	0.999756186760941	TCG	ORF1ab:nsp2	I293I	C879T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.000243813239058881
CAMB-720BE	MN908947.3	17012	C	T	0.011	0.0025	1e-06	0.0047	0.0067390240647658	TCA	ORF1ab:helicase	S259L	C776T	TCA>TTA	Missense	ORF1ab:helicase	0.993216493928206
CAMB-720BE	MN908947.3	17167	C	T	0.0028	0.023	0.0095	1.9e-11	0.00949679468996426	TCA	ORF1ab:helicase	H311Y	C931T	CAT>TAT	Missense	ORF1ab:helicase	0.990503205310036
CAMB-720BE	MN908947.3	18415	G	T	0.0075	0.0059	2.5e-05	9.1e-05	0.00693472552010441	TGA	ORF1ab:3'-to-5'-exonuclease	D126Y	G376T	GAT>TAT	Missense	ORF1ab:3'-to-5'-exonuclease	0.993033824477537
CAMB-720BE	MN908947.3	18538	G	T	0.012	0.0057	1.9e-07	8e-05	0.0101054619864631	TGT	ORF1ab:3'-to-5'-exonuclease	V167L	G499T	GTA>TTA	Missense	ORF1ab:3'-to-5'-exonuclease	0.989863056823548
CAMB-720BE	MN908947.3	203	C	T	0.0064	0.019	0.00039	2.2e-09	0.0109313821022979	TCG	NA	NA	NA	NA	NA	NA	0.989033183920061
CAMB-720BE	MN908947.3	21058	C	T	1	1	0	0	0.999913543422816	CCC	ORF1ab:2'-O-ribose-methyltransferase	P134S	C400T	CCT>TCT	Missense	ORF1ab:2'-O-ribose-methyltransferase	4.32282885920546e-05
CAMB-720BE	MN908947.3	21084	AAATGACTCT	-	0.0007332	0.00552	NA;NA;NA;NA;NA;NA;0.0022;0.0025;NA;NA	0.00018;8.3e-05;4.2e-05;0.00014;0.00019;0.00045;0.00052;0.00055;0.00051;0.00051	0.00175665883489603	AAA	ORF1ab:2'-O-ribose-methyltransferase	.	426-435-delfrshift	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.9981195767915
CAMB-720BE	MN908947.3	21663	G	C	0.0083	0.0049	1.6e-05	0.00022	0.00699790062981106	CGT	S	R34P	G101C	CGT>CCT	Missense	GU280_gp02, spike glycoprotein	0.992768836015862
CAMB-720BE	MN908947.3	22205	G	C	0.0066	0.0055	3.8e-05	9e-05	0.00638541723516891	TGA	S	D215H	G643C	GAT>CAT	Missense	GU280_gp02, spike glycoprotein	0.993560006549146
CAMB-720BE	MN908947.3	23114	C	T	0.0034	0.023	0.001	6.7e-12	0.0190373913892414	TCT	S	L518L	C1552T	CTA>TTA	Synonymous	GU280_gp02, spike glycoprotein	0.980864980962609
CAMB-720BE	MN908947.3	23403	A	G	1	1	0	0	0.999898949998622	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.18636376163223e-05
CAMB-720BE	MN908947.3	23427	TTGCTA	-	0.00993333333333333	0.00161666666666667	0.00017;0.00013;8.3e-06;5.8e-06;3e-05;8.8e-06	0.0055;0.0047;NA;NA;NA;NA	0.00639039863473631	GTT	S	.	1865-1870-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.991179925469864
CAMB-720BE	MN908947.3	23481	C	T	0.011	0.015	1.8e-06	3.6e-08	0.0123307503742823	TCT	S	S640F	C1919T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.986262606320846
CAMB-720BE	MN908947.3	23492	C	T	0.0087	0.0028	1.5e-05	0.0065	0.00651932826362484	TCA	S	Q644*	C1930T	CAA>TAA	Nonsense	GU280_gp02, spike glycoprotein	0.993290557667934
CAMB-720BE	MN908947.3	23731	C	T	1	1	0	0	0.999936220422221	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	6.37795777791951e-05
CAMB-720BE	MN908947.3	241	C	T	1	1	0	0	0.999823723316117	TCG	NA	NA	NA	NA	NA	NA	0.000105766010329814
CAMB-720BE	MN908947.3	24213	C	T	0.0091	0.011	4.1e-05	8.5e-06	0.0101404056162246	TCT	S	S884F	C2651T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.989807592303692
CAMB-720BE	MN908947.3	25416	CACA	TCAC	0.00175825	0.01075	6.4e-05;NA;NA;NA	1.3e-06;1.1e-06;1.6e-06;9.8e-07	0.00510273506599537	TCA	ORF3a	.	24-27-mnv	.	no-SNV	GU280_gp03	0.991077075605545
CAMB-720BE	MN908947.3	25521	C	T	0.0033	0.025	0.007	3.1e-12	0.0135554836622452	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.985134260757037
CAMB-720BE	MN908947.3	25624	C	T	0.012	0.0046	2.3e-07	0.00034	0.00873068250563713	TCA	ORF3a	H78Y	C232T	CAC>TAC	Missense	GU280_gp03	0.991214321069131
CAMB-720BE	MN908947.3	26768	C	T	0.026	0.029	7.9e-13	3.8e-14	0.0271315888318518	TCG	M	I82I	C246T	ATC>ATT	Synonymous	GU280_gp05	0.972868411168148
CAMB-720BE	MN908947.3	2764	G	-	0.018	0.003	3e-08	0.0087	0.0126074498567335	TGC	ORF1ab:nsp3	.	45-45-delfrshift	.	no-SNV	ORF1ab:nsp3	0.987392550143266
CAMB-720BE	MN908947.3	28253	C	T	0.11	0.13	1.4e-47	3.8e-57	0.114668225402143	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.884927102887782
CAMB-720BE	MN908947.3	28443	CTCA	ACTC	0.0081	0.00065	1.6e-05;1.1e-05;2.7e-05;9e-06	NA;NA;0.0042;NA	0.00381144309121178	ACT	N	.	170-173-mnv	.	no-SNV	GU280_gp10	0.996274314430533
CAMB-720BE	MN908947.3	28561	TG	GT	0.00775	0.001595	2e-05;2e-05	NA;0.0016	0.00459985709181851	GTG	N	.	288-289-mnv	.	no-SNV	GU280_gp10	0.995939595784479
CAMB-720BE	MN908947.3	28603	CTACTAC	TCTACTA	0.00951428571428571	0.00104014285714286	2.1e-07;2.3e-05;2.9e-05;2.7e-05;9.3e-06;1.4e-05;4.3e-05	0.0017;NA;NA;NA;NA;NA;NA	0.00363042294427301	TCT	N	.	330-336-mnv	.	no-SNV	GU280_gp10	0.985958516036853
CAMB-720BE	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998789091291987	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000889205050684688
CAMB-720BE	MN908947.3	28896	C	T	0.005	0.0091	0.00048	8.2e-06	0.00661436702045839	GCT	N	A208V	C623T	GCT>GTT	Missense	GU280_gp10	0.986514895144337
CAMB-720BE	MN908947.3	29406	AAACTCAAGCCTTACCGCAGAGACAGAAGAAACA	-	0.00591764705882353	0.00678235294117647	0.00036;0.00019;0.00023;0.00021;0.00018;0.00021;0.00029;0.00021;5.5e-05;2e-04;0.00021;0.00017;0.00019;0.00021;2e-04;0.00027;4.1e-05;0.00022;0.00068;0.00048;0.00028;0.00022;0.00043;0.00038;0.00035;0.00043;0.00044;0.00023;0.00015;4e-04;0.00019;0.00018;0.00023;0.00025	0.00053;0.00016;0.00016;0.00016;0.00016;0.00015;4e-04;0.00015;9.3e-05;0.00015;0.00016;0.00021;0.00015;0.00018;0.00016;0.00035;0.00058;0.00016;0.00042;0.00033;0.00036;0.00029;0.00061;0.00053;0.00059;0.00064;0.00068;0.00029;0.00028;0.00061;0.00018;0.00017;0.00029;0.00033	0.00594648166501487	GAA	N	.	1133-1166-delfrshift	.	no-SNV	GU280_gp10	0.99412148922273
CAMB-720BE	MN908947.3	29585	C	T	0.0026	0.0089	0.0082	1.5e-05	0.00603836135448733	TCC	ORF10	P10S	C28T	CCG>TCG	Missense	GU280_gp11	0.993961638645513
CAMB-720BE	MN908947.3	29614	C	T	0.025	0.03	2.6e-11	1.5e-13	0.027939602900963	GCA	ORF10	C19C	C57T	TGC>TGT	Synonymous	GU280_gp11	0.972060397099037
CAMB-720BE	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-720BE	MN908947.3	313	C	T	0.009	0.0039	1.2e-05	0.002	0.00708240900501191	TCA	ORF1ab:leader-protein	L16L	C48T	CTC>CTT	Synonymous	ORF1ab:leader-protein	0.992917590994988
CAMB-720BE	MN908947.3	4002	C	T	1	1	0	0	0.999755759993487	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0.000244240006513067
CAMB-720BE	MN908947.3	4200	TGCTAGCGAAAGCTT	-	0.00052	0.00778666666666667	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;4.8e-05;NA	2e-05;2.4e-05;1.9e-05;1.9e-05;2.9e-06;3.2e-05;2.8e-05;2.6e-05;3.6e-05;1.3e-05;1.4e-05;1.9e-05;1.9e-05;2.8e-05;5.8e-06	0.00313568985176739	ATG	ORF1ab:nsp3	.	1481-1495-delinframe	.	no-SNV	ORF1ab:nsp3	0.996804789452442
CAMB-720BE	MN908947.3	4556	G	T	0.0069	0.0047	4.3e-05	0.00041	0.00619556751398428	TGT	ORF1ab:nsp3	V613L	G1837T	GTA>TTA	Missense	ORF1ab:nsp3	0.987962897401402
CAMB-720BE	MN908947.3	4817	G	C	0.0094	0.00076	2.3e-06	0.0089	0.00565147413856171	TGG	ORF1ab:nsp3	G700R	G2098C	GGA>CGA	Missense	ORF1ab:nsp3	0.994330236301119
CAMB-720BE	MN908947.3	635	C	T	0.097	0.089	5e-44	1.9e-40	0.0937797181637417	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.906220281836258
CAMB-720BE	MN908947.3	683	C	T	0.029	0.019	5.7e-14	3.3e-10	0.0252460094609294	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.974382973699965
CAMB-720BE	MN908947.3	9070	T	C	0.04	0.038	4e-19	5.5e-18	0.0390505359877489	ATA	ORF1ab:nsp4	D172D	T516C	GAT>GAC	Synonymous	ORF1ab:nsp4	0.96090006421973
CAMB-720BE	MN908947.3	9430	C	T	0.014	0.016	4.3e-07	2.2e-07	0.0145772594752187	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.985422740524781
CAMB-720BE	MN908947.3	9515	C	T	0.024	0.027	1.5e-12	4.7e-14	0.0255440846702993	ACT	ORF1ab:nsp4	L321L	C961T	CTA>TTA	Synonymous	ORF1ab:nsp4	0.974445082384548
CAMB-720BE	MN908947.3	9561	C	T	0.011	0.024	1.1e-06	2.3e-12	0.0164008939055339	TCA	ORF1ab:nsp4	S336L	C1007T	TCA>TTA	Missense	ORF1ab:nsp4	0.98137696804414
CAMB-720BE	MN908947.3	9661	C	T	0.0052	0.019	0.00026	2.6e-10	0.011092558795739	TCA	ORF1ab:nsp4	F369F	C1107T	TTC>TTT	Synonymous	ORF1ab:nsp4	0.986487011221994
CAMB-720CD	MN908947.3	11075	T	-	0.036	0.039	2.5e-09	2e-10	0.0373369250285822	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958074266652049
CAMB-720CD	MN908947.3	11455	C	T	1	1	0	0	0.999903966196101	CCA	ORF1ab:nsp6	A161A	C483T	GCC>GCT	Synonymous	ORF1ab:nsp6	4.80169019494862e-05
CAMB-720CD	MN908947.3	14408	C	T	1	1	0	0	0.999267753320739	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000322188538874976
CAMB-720CD	MN908947.3	2305	G	T	0.013	0.015	3.3e-07	3.4e-08	0.0140862100235778	AGC	ORF1ab:nsp2	K500N	G1500T	AAG>AAT	Missense	ORF1ab:nsp2	0.9857928783024
CAMB-720CD	MN908947.3	23202	C	T	0.015	0.016	4.1e-08	1.7e-08	0.0152870487040373	ACA	S	T547I	C1640T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0.983879869622718
CAMB-720CD	MN908947.3	23403	A	G	1	1	0	0	0.999198042818423	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.09081403729608e-05
CAMB-720CD	MN908947.3	241	C	T	1	1	0	0	0.999089162692104	TCG	NA	NA	NA	NA	NA	NA	0.000149046104928458
CAMB-720CD	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999512836751595	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000165152766308836
CAMB-720CD	MN908947.3	3037	C	T	1	1	0	0	0.999686793109448	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000243605359317905
CAMB-720DC	MN908947.3	11074	CT	-	0.0105	0.0225	NA;1e-06	6.3e-09;3.1e-09	0.0196531381050537	TCT	ORF1ab:nsp6	.	102-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.976285970172501
CAMB-720DC	MN908947.3	11075	T	-	0.021	0.034	1e-06	3.1e-09	0.0299395326033666	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.965876777251185
CAMB-720DC	MN908947.3	13459	G	T	1	0.99	0	0	0.995044864068568	CGT	ORF1ab:nsp11	S6S	G18T	TCG>TCT	Synonymous	ORF1ab:nsp11	0
CAMB-720DC	MN908947.3	14408	C	T	1	0.99	0	0	0.994648341289871	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000456107276431417
CAMB-720DC	MN908947.3	16260	C	T	0.054	0.027	1.9e-08	3.4e-12	0.0277576635288438	GCA	ORF1ab:helicase	C8C	C24T	TGC>TGT	Synonymous	ORF1ab:helicase	0.972242336471156
CAMB-720DC	MN908947.3	16410	AG	-	0.0225	0.0088	8.8e-05;9.4e-05	1.9e-05;2e-05	0.00921658986175115	CAG	ORF1ab:helicase	.	174-175-delfrshift	.	no-SNV	ORF1ab:helicase	0.990531177829099
CAMB-720DC	MN908947.3	17999	C	T	0.047	0.032	2.7e-22	8.1e-16	0.0354425077377766	ACA	ORF1ab:helicase	T588I	C1763T	ACA>ATA	Missense	ORF1ab:helicase	0.964510949244839
CAMB-720DC	MN908947.3	1870	A	T	0.01	0.011	1.1e-05	1.6e-06	0.0104918520723268	CAT	ORF1ab:nsp2	A355A	A1065T	GCA>GCT	Synonymous	ORF1ab:nsp2	0.989508147927673
CAMB-720DC	MN908947.3	19109	G	T	0.011	0.0068	1.1e-06	3.9e-05	0.00760814889336016	AGT	ORF1ab:3'-to-5'-exonuclease	S357I	G1070T	AGT>ATT	Missense	ORF1ab:3'-to-5'-exonuclease	0.987550301810865
CAMB-720DC	MN908947.3	21123	G	T	1	1	0	0	0.999869867915935	GGT	ORF1ab:2'-O-ribose-methyltransferase	G155G	G465T	GGG>GGT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0
CAMB-720DC	MN908947.3	23403	A	G	1	1	0	0	0.99988358556461	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.76096235933256e-05
CAMB-720DC	MN908947.3	241	C	T	1	1	0	0	0.999585312523562	TCG	NA	NA	NA	NA	NA	NA	0.000376988614943829
CAMB-720DC	MN908947.3	24489	T	-	0.0077	0.013	0.0026	3.7e-06	0.0117302052785924	GTT	S	.	2927-2927-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.987781036168133
CAMB-720DC	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999878758486906	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000282406099971759
CAMB-720DC	MN908947.3	3037	C	T	1	1	1.1e-225	0	0.999598447329675	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000133850890108419
CAMB-720DC	MN908947.3	4117	AT	-	0.015	0.0225	0.00027;0.00024	5.5e-06;3.2e-06	0.0205786842777393	CAT	ORF1ab:nsp3	.	1398-1399-delfrshift	.	no-SNV	ORF1ab:nsp3	0.980641857289177
CAMB-720DC	MN908947.3	5203	C	T	0.05	0.078	6.9e-10	5e-18	0.0677618069815195	ACA	ORF1ab:nsp3	Y828Y	C2484T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.932238193018481
CAMB-720DC	MN908947.3	6003	A	G	0.016	0.026	0.00013	1.9e-11	0.0253968253968254	GAT	ORF1ab:nsp3	D1095G	A3284G	GAT>GGT	Missense	ORF1ab:nsp3	0.974603174603175
CAMB-720DC	MN908947.3	7798	G	T	0.059	0.0079	1.2e-13	4e-05	0.0107379929714955	AGA	ORF1ab:nsp3	K1693N	G5079T	AAG>AAT	Missense	ORF1ab:nsp3	0.988871534556814
CAMB-720EB	MN908947.3	10138	C	T	0.017	0.0094	6.9e-09	1.1e-05	0.0115338406087305	ACG	ORF1ab:3C-like-proteinase	N28N	C84T	AAC>AAT	Synonymous	ORF1ab:3C-like-proteinase	0.988439460686157
CAMB-720EB	MN908947.3	11075	T	-	0.03	0.007	7.2e-09	0.0035	0.0130740864901106	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.986791820315119
CAMB-720EB	MN908947.3	14371	G	T	1	1	0	0	0.99988720108287	TGC	ORF1ab:RNA-dependent-RNA-polymerase	A302S	G904T	GCA>TCA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-720EB	MN908947.3	14645	C	T	0.007	0.014	4.5e-05	4.2e-08	0.0116367624211777	ACT	ORF1ab:RNA-dependent-RNA-polymerase	T393I	C1178T	ACT>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.988363237578822
CAMB-720EB	MN908947.3	1565	A	G	1	1	0	0	0.9994708994709	TAA	ORF1ab:nsp2	N254D	A760G	AAC>GAC	Missense	ORF1ab:nsp2	0.000529100529100529
CAMB-720EB	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999384064057338	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000168001344010752
CAMB-720EB	MN908947.3	16247	C	T	0.026	0.017	0.00075	7.8e-07	0.0169293636894337	GCT	ORF1ab:helicase	A4V	C11T	GCT>GTT	Missense	ORF1ab:helicase	0.983070636310566
CAMB-720EB	MN908947.3	1740	A	G	1	1	0	0	0.999858996051889	AAA	ORF1ab:nsp2	K312R	A935G	AAA>AGA	Missense	ORF1ab:nsp2	7.05019740552736e-05
CAMB-720EB	MN908947.3	23035	T	C	0.0093	0.0083	0.0032	4.7e-05	0.00836699365262551	CTT	S	P491P	T1473C	CCT>CCC	Synonymous	GU280_gp02, spike glycoprotein	0.99134448932487
CAMB-720EB	MN908947.3	2459	C	T	0.012	0.0079	0.00012	4.1e-05	0.00839416058394161	GCC	ORF1ab:nsp2	P552S	C1654T	CCT>TCT	Missense	ORF1ab:nsp2	0.991605839416058
CAMB-720EB	MN908947.3	24893	G	C	0.022	0.0062	5.4e-11	5.4e-05	0.00775120072281136	TGA	S	E1111Q	G3331C	GAA>CAA	Missense	GU280_gp02, spike glycoprotein	0.992106139141186
CAMB-720EB	MN908947.3	25586	T	C	0.0043	0.013	0.001	2.2e-07	0.0112678003594636	CTC	ORF3a	L65P	T194C	CTC>CCC	Missense	GU280_gp03	0.988697635835753
CAMB-720EB	MN908947.3	26325	G	T	1	1	0	0	0.999902190923318	TGC	E	L27F	G81T	TTG>TTT	Missense	GU280_gp04	9.78090766823161e-05
CAMB-720EB	MN908947.3	26877	C	-	0.0016	0.0068	0.0083	2.7e-05	0.00597609561752988	TCT	M	.	355-355-delfrshift	.	no-SNV	GU280_gp05	0.994000189717321
CAMB-720EB	MN908947.3	27925	C	T	0.31	0.23	5.3e-101	4.1e-99	0.242053307008884	ACA	ORF8	T11I	C32T	ACA>ATA	Missense	GU280_gp09	0.75538005923001
CAMB-720EB	MN908947.3	28360	T	C	0.0033	0.012	0.00063	1.4e-07	0.00977198697068404	ATG	N	N29N	T87C	AAT>AAC	Synonymous	GU280_gp10	0.990201092955017
CAMB-720FA	MN908947.3	11074	C	INS	0.13	0.11	2.5e-39	2e-34	0.111645152430651	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.885985992859105
CAMB-720FA	MN908947.3	11083	G	-	0.17	0.15	2e-74	7e-65	0.151179826065272	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	6.23421963155762e-05
CAMB-720FA	MN908947.3	11083	G	T	0.83	0.85	0	0	0.848664318443939	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	6.23421963155762e-05
CAMB-720FA	MN908947.3	14805	C	T	1	1	0	0	0.995857375351383	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000887705281846427
CAMB-720FA	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-720FA	MN908947.3	2558	C	T	1	1	0	0	0.999647204092433	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-720FA	MN908947.3	25975	T	G	0.84	0.9	2.9e-95	0	0.897740784780024	ATC	ORF3a	S195A	T583G	TCT>GCT	Missense	GU280_gp03	0.102259215219976
CAMB-720FA	MN908947.3	26144	G	T	1	1	9.1e-119	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-720FA	MN908947.3	26447	C	T	0.011	0.0075	2.8e-06	3.6e-05	0.00836311651179414	TCT	E	S68F	C203T	TCT>TTT	Missense	GU280_gp04	0.990135811293781
CAMB-720FA	MN908947.3	28378	G	T	0.0047	0.01	0.00081	2.4e-06	0.00903347700301116	CGC	N	A35A	G105T	GCG>GCT	Synonymous	GU280_gp10	0.990523705496841
CAMB-720FA	MN908947.3	29013	C	T	1	1	0	0	0.999416399182959	ACT	N	T247I	C740T	ACT>ATT	Missense	GU280_gp10	8.3371545291592e-05
CAMB-720FA	MN908947.3	4185	G	A	1	1	0	0	0.999897526984561	GGT	ORF1ab:nsp3	G489D	G1466A	GGT>GAT	Missense	ORF1ab:nsp3	0.000102473015439268
CAMB-720FA	MN908947.3	8407	C	T	0.91	0.92	0	0	0.922772277227723	ACG	ORF1ab:nsp3	N1896N	C5688T	AAC>AAT	Synonymous	ORF1ab:nsp3	0.0772277227722772
CAMB-72106	MN908947.3	11075	T	-	0.023	0.023	6.8e-06	1.4e-06	0.0232709308372335	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.974044844146707
CAMB-72106	MN908947.3	130	T	C	0.013	0.041	2.4e-07	5.7e-20	0.0193046884563594	ATA	NA	NA	NA	NA	NA	NA	0.980695311543641
CAMB-72106	MN908947.3	13613	A	-	0.0046	0.013	0.0025	2.1e-06	0.00559870876626652	GAA	ORF1ab:RNA-dependent-RNA-polymerase	.	146-146-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.994199535962877
CAMB-72106	MN908947.3	14408	C	T	0.99	1	0	0	0.995582659484398	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.0028958121157834
CAMB-72106	MN908947.3	17373	C	T	0.027	0.014	9e-13	3.7e-08	0.0241898744576136	CCA	ORF1ab:helicase	A379A	C1137T	GCC>GCT	Synonymous	ORF1ab:helicase	0.975757847332691
CAMB-72106	MN908947.3	1912	C	T	0.011	0.005	2.3e-06	0.00073	0.00967299921036741	CCC	ORF1ab:nsp2	S369S	C1107T	TCC>TCT	Synonymous	ORF1ab:nsp2	0.990292164057783
CAMB-72106	MN908947.3	19269	C	T	0.016	0.03	2.2e-08	7.2e-15	0.018828947085279	ACT	ORF1ab:3'-to-5'-exonuclease	N410N	C1230T	AAC>AAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.981171052914721
CAMB-72106	MN908947.3	20148	C	T	0.011	0.011	1.9e-05	0.00065	0.0112359550561798	TCA	ORF1ab:endoRNAse	F176F	C528T	TTC>TTT	Synonymous	ORF1ab:endoRNAse	0.98876404494382
CAMB-72106	MN908947.3	20931	G	T	0.048	0.051	1.3e-21	1.1e-23	0.0488271778248551	CGG	ORF1ab:2'-O-ribose-methyltransferase	T91T	G273T	ACG>ACT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.951147298297557
CAMB-72106	MN908947.3	21606	G	C	0.014	0.011	2.1e-07	2.3e-06	0.0137922763252579	TGT	S	C15S	G44C	TGT>TCT	Missense	GU280_gp02, spike glycoprotein	0.986087790837131
CAMB-72106	MN908947.3	23403	A	G	1	1	0	0	0.999916754181501	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.48246714991932e-05
CAMB-72106	MN908947.3	23758	C	T	0.081	0.064	4.7e-36	1.2e-28	0.0760670123653769	CCA	S	T732T	C2196T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.923893099321899
CAMB-72106	MN908947.3	241	C	T	1	1	0	0	0.99982146728388	TCG	NA	NA	NA	NA	NA	NA	0.000102018694925845
CAMB-72106	MN908947.3	27503	C	T	0.0091	0.0072	8.7e-06	3e-05	0.00854807375096221	TCT	ORF7a	S37F	C110T	TCT>TTT	Missense	GU280_gp07	0.991415270701221
CAMB-72106	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.996564371604996	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-72106	MN908947.3	28907	G	A	0.027	0.022	3.7e-13	4.9e-11	0.0260463445302676	TGG	N	G212S	G634A	GGC>AGC	Missense	GU280_gp10	0.970720316148734
CAMB-72106	MN908947.3	29737	G	A	0.024	0.014	3.9e-11	7.7e-08	0.018431292238378	GGC	NA	NA	NA	NA	NA	NA	0.981568707761622
CAMB-72106	MN908947.3	29750	C	T	0.011	0.0083	3.3e-05	0.00016	0.00922625288320403	ACG	NA	NA	NA	NA	NA	NA	0.990773747116796
CAMB-72106	MN908947.3	3037	C	T	1	0.99	0	0	0.992957746478873	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000110035211267606
CAMB-72106	MN908947.3	3199	T	C	0.024	0.043	1.3e-11	4.7e-20	0.0273701298701299	ATT	ORF1ab:nsp3	D160D	T480C	GAT>GAC	Synonymous	ORF1ab:nsp3	0.972597402597403
CAMB-72106	MN908947.3	3267	C	T	0.0027	0.0077	0.0061	1.9e-05	0.00355181205840194	ACT	ORF1ab:nsp3	T183I	C548T	ACT>ATT	Missense	ORF1ab:nsp3	0.996410132812401
CAMB-72106	MN908947.3	3728	G	T	0.023	0.037	3.5e-08	1.2e-11	0.0296762589928058	TGG	ORF1ab:nsp3	G337C	G1009T	GGT>TGT	Missense	ORF1ab:nsp3	0.970323741007194
CAMB-72106	MN908947.3	4021	C	T	0.0085	0.0034	2.1e-05	0.0045	0.00817972350230415	ACT	ORF1ab:nsp3	N434N	C1302T	AAC>AAT	Synonymous	ORF1ab:nsp3	0.991781874039939
CAMB-72106	MN908947.3	772	T	C	0.0087	0.0035	1.3e-05	0.0013	0.00755911131143539	TTA	ORF1ab:leader-protein	V169V	T507C	GTT>GTC	Synonymous	ORF1ab:leader-protein	0.992440888688565
CAMB-72106	MN908947.3	8257	A	G	0.033	0.027	6.2e-16	1e-13	0.0319166984773296	AAG	ORF1ab:nsp3	E1846E	A5538G	GAA>GAG	Synonymous	ORF1ab:nsp3	0.96808330152267
CAMB-72106	MN908947.3	9111	G	A	0.026	0.07	1.6e-12	7.6e-32	0.0380706374932469	CGC	ORF1ab:nsp4	R186H	G557A	CGC>CAC	Missense	ORF1ab:nsp4	0.958957995678012
CAMB-72106	MN908947.3	9474	C	T	0.0044	0.0099	0.00059	5.7e-06	0.00491424640031451	GCT	ORF1ab:nsp4	A307V	C920T	GCT>GTT	Missense	ORF1ab:nsp4	0.995036611135682
CAMB-72115	MN908947.3	11075	T	-	0.04	0.045	9e-10	1.5e-11	0.041589254062827	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955709313003182
CAMB-72115	MN908947.3	11195	C	T	1	1	0	0	0.998663593340036	TCT	ORF1ab:nsp6	L75F	C223T	CTT>TTT	Missense	ORF1ab:nsp6	0.000147127338711655
CAMB-72115	MN908947.3	12322	G	A	1	1	0	0	0.999865479900455	AGG	ORF1ab:nsp8	E77E	G231A	GAG>GAA	Synonymous	ORF1ab:nsp8	6.72600497724368e-05
CAMB-72115	MN908947.3	13768	A	G	0.0035	0.0076	0.003	3.6e-05	0.00485017606803535	CAT	ORF1ab:RNA-dependent-RNA-polymerase	M101V	A301G	ATG>GTG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994850840475716
CAMB-72115	MN908947.3	14408	C	T	1	1	0	0	0.998434224144794	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000252116451261909
CAMB-72115	MN908947.3	16474	A	G	0.0086	0.0049	3.9e-05	0.00066	0.00588686972101357	TAG	ORF1ab:helicase	S80G	A238G	AGT>GGT	Missense	ORF1ab:helicase	0.994113130278986
CAMB-72115	MN908947.3	16887	C	T	0.013	0.01	1.9e-06	2.3e-05	0.0122068054179055	ACA	ORF1ab:helicase	Y217Y	C651T	TAC>TAT	Synonymous	ORF1ab:helicase	0.987528906508094
CAMB-72115	MN908947.3	20874	T	A	0.0073	0.0034	4.2e-05	0.00054	0.0061556910162886	CTG	ORF1ab:2'-O-ribose-methyltransferase	A72A	T216A	GCT>GCA	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.993764364944539
CAMB-72115	MN908947.3	22987	C	T	1	1	0	0	0.999037613280937	CCG	S	A475A	C1425T	GCC>GCT	Synonymous	GU280_gp02, spike glycoprotein	0.000320795573021092
CAMB-72115	MN908947.3	23182	TTTCAACT	-	0.0094625	0.0041875	5e-06;2.5e-05;0.00074;0.00047;0.00067;0.00092;0.00093;0.00096	0.0011;0.0018;0.009;0.0079;0.0059;0.0096;0.0096;0.01	0.00760135135135135	ATT	S	.	1620-1627-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.990482428141503
CAMB-72115	MN908947.3	23191	CAATGG	-	0.0103833333333333	0.005	0.00047;0.00067;1e-04;9.1e-05;0.00014;1e-05	0.0078;0.011;0.0025;0.0024;0.0031;0.00068	0.00876548043044429	TCA	S	.	1629-1634-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.990588752053881
CAMB-72115	MN908947.3	23403	A	G	1	1	0	0	0.999917565809962	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.49561266921907e-05
CAMB-72115	MN908947.3	241	C	T	1	1	0	0	0.999574779310462	TCG	NA	NA	NA	NA	NA	NA	0.000136070620652118
CAMB-72115	MN908947.3	25452	C	T	0.0087	0.0036	2e-05	0.0034	0.00664929615592853	TCA	ORF3a	I20I	C60T	ATC>ATT	Synonymous	GU280_gp03	0.993316865186789
CAMB-72115	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998969395528073	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00020632382524372
CAMB-72115	MN908947.3	3037	C	T	1	1	0	0	0.999730312837109	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.98957209636821e-05
CAMB-72115	MN908947.3	3373	C	A	1	1	0	0	0.998809733733028	ACA	ORF1ab:nsp3	D218E	C654A	GAC>GAA	Missense	ORF1ab:nsp3	2.20419679068947e-05
CAMB-72115	MN908947.3	427	A	T	0.0052	0.0084	0.00017	4.3e-06	0.00618741672053721	TAG	ORF1ab:leader-protein	V54V	A162T	GTA>GTT	Synonymous	ORF1ab:leader-protein	0.993298064618267
CAMB-72115	MN908947.3	5133	ATG	-	0.0173333333333333	0.0043	3.5e-08;1.5e-08;2e-08	0.0057;0.0059;0.0064	0.0149847094801223	AAT	ORF1ab:nsp3	.	2414-2416-delinframe	.	no-SNV	ORF1ab:nsp3	0.985804416403785
CAMB-72115	MN908947.3	7135	T	C	1	1	3.4e-132	5.89998372294241e-319	1	TTT	ORF1ab:nsp3	V1472V	T4416C	GTT>GTC	Synonymous	ORF1ab:nsp3	0
CAMB-72124	MN908947.3	13914	T	G	0.0062	0.0039	2.5e-05	0.00023	0.00482794042116076	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.995172059578839
CAMB-72124	MN908947.3	14408	C	T	1	1	0	0	0.999577479666209	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000316890250343298
CAMB-72124	MN908947.3	23403	A	G	1	1	0	0	0.999909035089714	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.82236827143929e-05
CAMB-72124	MN908947.3	241	C	T	1	1	0	0	0.999732405673	TCG	NA	NA	NA	NA	NA	NA	0.000267594327000268
CAMB-72124	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-72124	MN908947.3	29739	C	T	1	1	6.5e-103	0	1	CCA	NA	NA	NA	NA	NA	NA	0
CAMB-72124	MN908947.3	3037	C	T	1	1	1.2e-225	0	0.999544626593807	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-72124	MN908947.3	4794	C	T	0.071	0.11	8.8e-32	1.8e-47	0.0884395424836601	TCC	ORF1ab:nsp3	S692F	C2075T	TCC>TTC	Missense	ORF1ab:nsp3	0.91156045751634
CAMB-72133	MN908947.3	1063	C	T	0.066	0.077	1.8e-30	2.2e-35	0.071445911374204	TCA	ORF1ab:nsp2	F86F	C258T	TTC>TTT	Synonymous	ORF1ab:nsp2	0.928516741050587
CAMB-72133	MN908947.3	11075	T	-	0.041	0.045	3.4e-10	1.5e-11	0.0427280895602127	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95619126253673
CAMB-72133	MN908947.3	11195	C	T	1	1	0	0	0.999766400622932	TCT	ORF1ab:nsp6	L75F	C223T	CTT>TTT	Missense	ORF1ab:nsp6	3.8933229511388e-05
CAMB-72133	MN908947.3	14408	C	T	1	1	0	0	0.999372393143395	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000353028856840261
CAMB-72133	MN908947.3	15216	C	T	1	1	0	0	0.999752388720578	GCA	ORF1ab:RNA-dependent-RNA-polymerase	S583S	C1749T	AGC>AGT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	5.82614775110697e-05
CAMB-72133	MN908947.3	23114	C	T	0.0083	0.0081	6e-06	8.4e-06	0.00820079522862823	TCT	S	L518L	C1552T	CTA>TTA	Synonymous	GU280_gp02, spike glycoprotein	0.991737077534791
CAMB-72133	MN908947.3	23403	A	G	1	1	0	0	0.997669552454903	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.92511825781692e-05
CAMB-72133	MN908947.3	241	C	T	1	1	0	0	0.998810853662931	TCG	NA	NA	NA	NA	NA	NA	0.000738712118482217
CAMB-72133	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999480496991212	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000142396050882856
CAMB-72133	MN908947.3	3037	C	T	1	1	0	0	0.997963488253691	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00138191868499527
CAMB-72133	MN908947.3	3373	C	A	1	1	0	0	0.999815306475817	ACA	ORF1ab:nsp3	D218E	C654A	GAC>GAA	Missense	ORF1ab:nsp3	2.30866905229135e-05
CAMB-72133	MN908947.3	678	C	T	0.0078	0.0091	1.4e-05	2.8e-06	0.00828668751618494	GCC	ORF1ab:leader-protein	A138V	C413T	GCC>GTC	Missense	ORF1ab:leader-protein	0.991441073550992
CAMB-72133	MN908947.3	7851	C	T	0.012	0.021	6e-07	2.2e-10	0.0161772956798205	GCT	ORF1ab:nsp3	A1711V	C5132T	GCT>GTT	Missense	ORF1ab:nsp3	0.983542173181223
CAMB-72142	MN908947.3	11074	C	INS	0.11	0.11	7e-45	1.4e-39	0.108336175642046	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.884261189221965
CAMB-72142	MN908947.3	11083	G	-	0.16	0.16	4.7e-72	1.6e-69	0.161311385270972	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-72142	MN908947.3	11083	G	T	0.84	0.84	0	0	0.838619883844806	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-72142	MN908947.3	14805	C	T	1	1	0	0	0.999134401922646	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000112018574716389
CAMB-72142	MN908947.3	16348	T	C	0.044	0.04	4.8e-20	1.3e-18	0.0411626758824981	ATC	ORF1ab:helicase	S38P	T112C	TCA>CCA	Missense	ORF1ab:helicase	0.958837324117502
CAMB-72142	MN908947.3	16485	G	T	0.033	0.022	8.6e-16	4.3e-11	0.0249273418287503	TGT	ORF1ab:helicase	L83F	G249T	TTG>TTT	Missense	ORF1ab:helicase	0.974793203666443
CAMB-72142	MN908947.3	17553	A	C	0.12	0.11	6.1e-55	2.4e-51	0.115518865311098	GAA	ORF1ab:helicase	G439G	A1317C	GGA>GGC	Synonymous	ORF1ab:helicase	0.884301069311319
CAMB-72142	MN908947.3	18110	C	T	0.017	0.019	3.9e-09	3e-10	0.0180175555669627	CCT	ORF1ab:3'-to-5'-exonuclease	P24L	C71T	CCT>CTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.981982444433037
CAMB-72142	MN908947.3	20284	AT	TC	1	1	0;0	0;0	0.995759717314488	CAT	ORF1ab:endoRNAse	.	664-665-mnv	.	no-SNV	ORF1ab:endoRNAse	0
CAMB-72142	MN908947.3	21876	TTTTTGGTACTA	-	0.0103583333333333	0.0130333333333333	0.00014;0.00036;1.8e-06;2.2e-06;1.1e-06;2.7e-05;2.8e-07;9e-04;0.0011;0.00065;0.00019;0.00043	2.2e-05;9.7e-05;1.9e-07;2.1e-07;8e-08;3.4e-06;2.1e-08;0.00041;0.00052;0.00025;3.2e-05;7.4e-05	0.0126207729468599	ATT	S	.	314-325-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.991538209248934
CAMB-72142	MN908947.3	21980	TTT	-	0.0186666666666667	0.0153333333333333	2.1e-05;0.00041;0.00069	0.00017;0.002;0.0025	0.0165133547600576	ATT	S	.	418-420-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.981742491822777
CAMB-72142	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-72142	MN908947.3	2558	C	T	1	1	0	0	0.999239006359733	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000135891721476328
CAMB-72142	MN908947.3	26144	G	T	1	1	0	0	0.999432069161355	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000378620559096359
CAMB-72142	MN908947.3	26486	TA	-	0.012	0.00975	7.2e-07;6.8e-07	4.5e-06;3.8e-06	0.0109762627164019	TTA	NA	NA	NA	NA	NA	NA	0.988954924635709
CAMB-72142	MN908947.3	4162	G	T	0.24	0.24	1.1e-113	1.1e-115	0.237646549465073	TGG	ORF1ab:nsp3	V481V	G1443T	GTG>GTT	Synonymous	ORF1ab:nsp3	0.761897708758218
CAMB-72142	MN908947.3	635	C	T	0.011	0.011	2.3e-06	3.3e-06	0.0110044858327182	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.988859235704957
CAMB-72142	MN908947.3	884	C	T	0.058	0.058	1.1e-26	5.9e-27	0.058374893291998	ACG	ORF1ab:nsp2	R27C	C79T	CGT>TGT	Missense	ORF1ab:nsp2	0.941231971963877
CAMB-72142	MN908947.3	9928	G	T	0.035	0.032	9.7e-17	1.5e-15	0.0341092189088025	TGG	ORF1ab:nsp4	M458I	G1374T	ATG>ATT	Missense	ORF1ab:nsp4	0.965865992414665
CAMB-72151	MN908947.3	10097	G	A	1	1	0	0	0.999739306555437	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000100266709447129
CAMB-72151	MN908947.3	11075	T	-	0.04	0.043	1.1e-09	1.4e-11	0.04062438618586	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95518145790246
CAMB-72151	MN908947.3	13216	T	G	1	1	0	0	0.999755846335788	ATC	ORF1ab:nsp10	D64E	T192G	GAT>GAG	Missense	ORF1ab:nsp10	6.86682180597414e-05
CAMB-72151	MN908947.3	14408	C	T	1	1	0	0	0.997517533679802	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000615570916797013
CAMB-72151	MN908947.3	18329	C	T	0.0064	0.0084	0.00012	6.8e-06	0.00676326522247044	ACT	ORF1ab:3'-to-5'-exonuclease	T97I	C290T	ACT>ATT	Missense	ORF1ab:3'-to-5'-exonuclease	0.993134261062038
CAMB-72151	MN908947.3	23403	A	G	1	1	0	0	0.999264659866074	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.04049064397021e-05
CAMB-72151	MN908947.3	23731	C	T	1	1	0	0	0.999702358806459	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.00022323089515589
CAMB-72151	MN908947.3	241	C	T	1	1	0	0	0.997542906531671	TCG	NA	NA	NA	NA	NA	NA	0.000197555253735029
CAMB-72151	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99914743316485	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000100894598775812
CAMB-72151	MN908947.3	3037	C	T	1	1	0	0	0.999204391757499	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000132601373750232
CAMB-72160	MN908947.3	11069	T	INS	0.0076	0.0014	4.4e-06	0.0013	0.00387508547982676	TTT	ORF1ab:nsp6	.	96-97-insfrshift	.	no-SNV	ORF1ab:nsp6	0.995061165564927
CAMB-72160	MN908947.3	11070	T	INS	0.027	0.011	6.3e-14	3e-07	0.0172393777571395	TTG	ORF1ab:nsp6	.	97-98-insfrshift	.	no-SNV	ORF1ab:nsp6	0.981773856512654
CAMB-72160	MN908947.3	11071	G	C	0.1	0.13	5e-45	1.1e-57	0.115519320204398	TGT	ORF1ab:nsp6	L33F	G99C	TTG>TTC	Missense	ORF1ab:nsp6	0.865935580180284
CAMB-72160	MN908947.3	11071	G	T	0.029	0.01	1.9e-14	1.2e-06	0.0175116265717403	TGT	ORF1ab:nsp6	L33F	G99T	TTG>TTT	Missense	ORF1ab:nsp6	0.865935580180284
CAMB-72160	MN908947.3	11074	C	-	0.013	0.092	2.7e-08	1.5e-51	0.0579291976473199	TCT	ORF1ab:nsp6	.	102-102-delfrshift	.	no-SNV	ORF1ab:nsp6	0.651148596160249
CAMB-72160	MN908947.3	11074	C	INS	0.23	0.14	2.6e-79	3.1e-41	0.178615026079236	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.651148596160249
CAMB-72160	MN908947.3	11074	C	T	0.14	0.095	6.6e-63	9e-47	0.112307180113195	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.651148596160249
CAMB-72160	MN908947.3	11083	G	-	0.16	0.023	2e-70	6.8e-10	0.0782637841461371	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	5.58628009608402e-05
CAMB-72160	MN908947.3	11083	G	T	0.84	0.98	0	0	0.92156862745098	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	5.58628009608402e-05
CAMB-72160	MN908947.3	14805	C	T	1	1	0	0	0.999944909651829	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-72160	MN908947.3	23707	C	T	1	1	0	0	1	CCA	S	P715P	C2145T	CCC>CCT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-72160	MN908947.3	27833	T	C	0.2	0.02	5.9e-29	2.3e-08	0.0466883821932682	TTA	NA	NA	NA	NA	NA	NA	0.953311617806732
CAMB-72160	MN908947.3	29737	GCCACGCGGAGTAC	-	0.0497857142857143	0.0915714285714286	1.6e-06;2.2e-06;2.3e-06;1.9e-06;2.5e-06;2.3e-06;1.9e-06;2.5e-06;3.1e-06;3.2e-06;4e-06;6.2e-06;5.4e-06;1.3e-05	9.6e-22;1.2e-21;1.5e-21;2.5e-22;2.2e-21;1.7e-21;7.5e-22;1.8e-21;1.9e-21;3.7e-21;3.8e-20;1e-18;5e-19;8.4e-17	0.0826771653543307	GGC	NA	NA	NA	NA	NA	NA	0.917808219178082
CAMB-72160	MN908947.3	29745	GAGT	-	0.049	0.09075	3.1e-06;3.2e-06;4e-06;6.2e-06	1.9e-21;3.7e-21;3.8e-20;1e-18	0.0823529411764706	GGA	NA	NA	NA	NA	NA	NA	0.917322834645669
CAMB-72160	MN908947.3	29750	C	-	0.05	0.091	1.3e-05	8.4e-17	0.0828402366863905	ACG	NA	NA	NA	NA	NA	NA	0.917159763313609
CAMB-72160	MN908947.3	6720	C	T	0.13	0.11	4.9e-21	1.9e-35	0.11	ACA	ORF1ab:nsp3	T1334I	C4001T	ACA>ATA	Missense	ORF1ab:nsp3	0.89
CAMB-72160	MN908947.3	9603	C	T	0.92	0.82	0	0	0.860495838654278	ACA	ORF1ab:nsp4	T350I	C1049T	ACA>ATA	Missense	ORF1ab:nsp4	0.139504161345722
CAMB-7217F	MN908947.3	10252	C	T	0.36	0.21	3.8e-187	1.8e-96	0.327534161347559	TCT	ORF1ab:3C-like-proteinase	F66F	C198T	TTC>TTT	Synonymous	ORF1ab:3C-like-proteinase	0.672074106505058
CAMB-7217F	MN908947.3	11075	T	-	0.026	0.051	1.2e-06	2.4e-13	0.030992692207034	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.965222555513055
CAMB-7217F	MN908947.3	11077	TTTTTTGTATG	-	0.0446363636363636	0.0485454545454545	5.1e-21;8.4e-21;1.1e-20;2.1e-20;2.1e-18;1.1e-06;4.4e-18;8.4e-18;9.4e-18;2.4e-14;1.2e-14	1.5e-23;2e-23;3.2e-23;6e-23;1.2e-20;1.6e-07;1.1e-21;4.7e-20;5.6e-20;3.5e-16;1.5e-16	0.0449723931843819	TTT	ORF1ab:nsp6	.	105-115-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952938012639505
CAMB-7217F	MN908947.3	11271	TGGTTGATACTAGTTTGTCTGGTT	-	0.021	0.000708333333333333	1.4e-06;4.8e-07;2.1e-06;1.9e-06;6.1e-06;2.6e-06;6.9e-06;5.7e-06;2e-05;7.5e-06;5.5e-06;7.3e-06;9.8e-06;4.7e-05;9.3e-06;2.4e-05;1.4e-05;8.4e-06;7.1e-06;2.7e-06;3.1e-06;8.3e-06;1.3e-07;1e-05	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;2.6e-06;NA	0.0168297681937588	ATG	ORF1ab:nsp6	.	299-322-delinframe	.	no-SNV	ORF1ab:nsp6	0.982547975975389
CAMB-7217F	MN908947.3	1440	G	A	0.28	0.27	9.1e-110	1e-62	0.278273111215392	GGC	ORF1ab:nsp2	G212D	G635A	GGC>GAC	Missense	ORF1ab:nsp2	0.721726888784608
CAMB-7217F	MN908947.3	14408	C	T	0.72	0.74	0	0	0.72709408376335	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.272860914436577
CAMB-7217F	MN908947.3	15017	C	T	0.011	0.0087	9.7e-06	8.1e-05	0.00987284966342558	GCA	ORF1ab:RNA-dependent-RNA-polymerase	A517V	C1550T	GCA>GTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.990127150336574
CAMB-7217F	MN908947.3	15324	C	T	0.6	0.65	0	4.30000000384662e-316	0.600008398773779	ACA	ORF1ab:RNA-dependent-RNA-polymerase	N619N	C1857T	AAC>AAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.399991601226221
CAMB-7217F	MN908947.3	1572	C	T	0.12	0.14	1.8e-44	9.8e-35	0.120615911035073	ACA	ORF1ab:nsp2	T256I	C767T	ACA>ATA	Missense	ORF1ab:nsp2	0.878956372968349
CAMB-7217F	MN908947.3	17013	A	C	0.011	0.0065	5.3e-07	5.2e-05	0.0100630765304262	CAG	ORF1ab:helicase	S259S	A777C	TCA>TCC	Synonymous	ORF1ab:helicase	0.989681700514092
CAMB-7217F	MN908947.3	18880	GCTGTCCACGAGTGCTTTGTTAAGCGTGTTGACTGGACTATT	-	0.0146785714285714	0.00059647619047619	1.4e-05;5.8e-08;4e-08;7.1e-08;7.7e-08;5.1e-08;6.3e-08;4.8e-08;5.4e-08;6.5e-08;4.5e-08;6.6e-08;7.3e-08;5.9e-08;2.1e-08;5.5e-08;6.5e-08;5.6e-06;5.8e-06;7.1e-08;7.4e-08;4.5e-08;5.6e-08;6.2e-08;5.3e-08;7.3e-08;8.4e-08;5e-06;8e-08;6.6e-08;7.2e-08;6.8e-08;4.5e-08;3.2e-07;6.5e-08;3.1e-07;7e-08;5.2e-08;7.7e-08;3.1e-06;3.7e-06;1.2e-05	NA;NA;NA;9.3e-13;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0117205518513859	AGC	ORF1ab:3'-to-5'-exonuclease	.	841-882-delinframe	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.988033573648492
CAMB-7217F	MN908947.3	21004	G	T	0.54	0.67	2.29999909780246e-318	0	0.559440272477328	TGC	ORF1ab:2'-O-ribose-methyltransferase	A116S	G346T	GCA>TCA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.439923673519636
CAMB-7217F	MN908947.3	23403	A	G	0.73	0.68	0	0	0.72032699775189	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.279664827304312
CAMB-7217F	MN908947.3	23555	CCCATTGGTGCAGGTA	-	0.0295	0.0764375	NA;NA;NA;NA;0.00076;0.0014;0.00079;0.0013;0.0014;0.0014;0.0014;0.0013;0.00094;0.00088;1e-07;1.8e-08	9e-05;6.9e-05;9e-05;7.7e-07;1.2e-07;3e-07;3.7e-08;1.6e-07;1.9e-07;2e-07;1.8e-07;1.9e-07;5.6e-08;4.3e-08;5.3e-12;2.2e-13	0.0477218743251997	ACC	S	.	1993-2008-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.982199481118478
CAMB-7217F	MN908947.3	241	C	T	0.66	0.63	0	0	0.651628548001605	TCG	NA	NA	NA	NA	NA	NA	0.348336560771794
CAMB-7217F	MN908947.3	25318	C	T	0.24	0.33	1.4e-115	3e-171	0.260005621952756	CCT	S	S1252S	C3756T	TCC>TCT	Synonymous	GU280_gp02, spike glycoprotein	0.73995560595927
CAMB-7217F	MN908947.3	25433	C	T	0.8	0.65	0	0	0.765471458540355	ACT	ORF3a	T14I	C41T	ACT>ATT	Missense	GU280_gp03	0.234349122225903
CAMB-7217F	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0605	0.0925	8.8e-09;3.2e-11;5.9e-09;6.5e-09;1.6e-08;3.9e-10;1.9e-09;1.5e-10;1.6e-10;5e-11;8.1e-11;4.9e-11;1.6e-10;8e-11;1.1e-10;3.3e-13;5.5e-11;1.9e-10;1.1e-10;1e-10;8.7e-11;2.1e-10;1.3e-10;1.5e-10;9e-11;5.8e-11;1.5e-10;6.8e-11;5.1e-11;9.3e-11;1.4e-10;1.4e-10;1.3e-10;1.9e-10;1.1e-11;6.2e-11;5.8e-11;0.00082	1.3e-14;2.9e-18;3.8e-15;5.1e-15;3.3e-14;5e-17;6e-16;4.3e-18;3.5e-18;2e-18;1.1e-18;4.3e-19;2.3e-18;1.2e-18;2.6e-18;8.4e-18;8.1e-19;5.4e-18;1.3e-18;2.4e-18;2.5e-18;6.9e-18;2.9e-18;3.4e-18;1.3e-18;3.5e-19;2.9e-18;1.4e-18;6.2e-20;2e-18;5.1e-18;3.9e-18;1.3e-18;7e-18;9.8e-21;1.1e-18;4e-19;1.2e-05	0.0700964414126819	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.944968833481745
CAMB-7217F	MN908947.3	26817	T	-	0.027	0.04	0.00082	1.2e-05	0.0303481473189298	TTC	M	.	295-295-delfrshift	.	no-SNV	GU280_gp05	0.969607074890854
CAMB-7217F	MN908947.3	26894	C	T	0.047	0.13	7.8e-22	9.3e-57	0.0585255865629697	TCC	M	L124L	C372T	CTC>CTT	Synonymous	GU280_gp05	0.941441735834259
CAMB-7217F	MN908947.3	2891	G	A	0.29	0.24	3.1e-115	4.8e-106	0.258614232209738	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	0.741385767790262
CAMB-7217F	MN908947.3	29109	C	T	0.16	0.19	9.8e-75	1.6e-87	0.170588235294118	CCA	N	P279L	C836T	CCA>CTA	Missense	GU280_gp10	0.829411764705882
CAMB-7217F	MN908947.3	29546	C	T	0.77	0.77	0	0	0.767094017094017	CCA	NA	NA	NA	NA	NA	NA	0.232905982905983
CAMB-7217F	MN908947.3	3037	C	T	0.71	0.74	3.9e-172	2.1e-203	0.729083665338645	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.270030987162461
CAMB-7217F	MN908947.3	514	T	-	0.12	0.16	8.2e-05	4e-06	0.131037335815493	ATG	ORF1ab:leader-protein	.	249-249-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.867204467887062
CAMB-7217F	MN908947.3	522	T	-	0.089	0.12	1e-11	3.6e-16	0.0954124976401737	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.904474230696621
CAMB-7217F	MN908947.3	522	TT	-	0.0805	0.087	1e-11;1.6e-10	3.6e-16;7e-08	0.081365212630042	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.904474230696621
CAMB-7217F	MN908947.3	523	T	-	0.072	0.054	1.6e-10	7e-08	0.0682589033352176	TTG	ORF1ab:leader-protein	.	258-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.931741096664782
CAMB-7217F	MN908947.3	5906	ACTTA	-	0.0174	0.01582	8e-08;8.1e-08;1.4e-08;1.7e-06;2.6e-05	4.3e-15;4.4e-15;0.022;0.082;NA	0.0155522465669243	TAC	ORF1ab:nsp3	.	3187-3191-delfrshift	.	no-SNV	ORF1ab:nsp3	0.981080062202535
CAMB-7217F	MN908947.3	6654	TTAATAGTGTCCCTTGGGATACTATAGCTA	-	0.00206666666666667	0.0180333333333333	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;3.9e-06;3.4e-09;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	1.5e-08;2.4e-08;5.6e-08;6.7e-06;2.9e-05;2.6e-05;8.5e-06;2.6e-05;5.3e-06;2.2e-05;6.7e-06;5.1e-06;5.6e-06;3.8e-07;1.2e-08;4.1e-08;9.7e-09;2.1e-08;2.9e-08;2.5e-08;4.8e-08;3.9e-08;3.3e-08;1.7e-08;1.2e-08;5.5e-08;9.2e-09;2e-08;4.9e-08;4.6e-08	0.00846325167037862	GTT	ORF1ab:nsp3	.	3935-3964-delinframe	.	no-SNV	ORF1ab:nsp3	0.992273281821879
CAMB-7217F	MN908947.3	686	AAGTCATTT	-	0.33	0.312222222222222	5.4e-50;4.6e-51;4.5e-44;2.3e-50;1.8e-43;1.4e-46;2.4e-55;7.6e-50;5e-42	1.8e-48;2.4e-49;7.8e-43;2.5e-49;3.5e-42;2.1e-45;4.2e-51;3.5e-46;2.6e-38	0.316007642372711	AAA	ORF1ab:leader-protein	.	421-429-delinframe	.	no-SNV	ORF1ab:leader-protein	0.685668241178105
CAMB-7217F	MN908947.3	7011	C	T	0.25	0.11	4.8e-73	1.3e-12	0.231362467866324	GCT	ORF1ab:nsp3	A1431V	C4292T	GCT>GTT	Missense	ORF1ab:nsp3	0.768637532133676
CAMB-7217F	MN908947.3	8254	A	T	0.32	0.26	6.3e-161	5.7e-112	0.311116200946709	TAG	ORF1ab:nsp3	I1845I	A5535T	ATA>ATT	Synonymous	ORF1ab:nsp3	0.688807451519316
CAMB-7218E	MN908947.3	11075	T	-	0.038	0.038	1.6e-10	3.1e-10	0.0378475798146241	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957775489186406
CAMB-7218E	MN908947.3	14408	C	T	1	1	0	0	0.997317866362691	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000569953397928052
CAMB-7218E	MN908947.3	20031	C	A	1	1	3.3e-209	0	1	CCC	ORF1ab:endoRNAse	A137A	C411A	GCC>GCA	Synonymous	ORF1ab:endoRNAse	0
CAMB-7218E	MN908947.3	23403	A	G	1	1	0	0	0.998663222765996	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.79717237629146e-05
CAMB-7218E	MN908947.3	23548	T	C	0.012	0.0099	2.4e-06	2.5e-06	0.0100891205649908	GTG	S	C662C	T1986C	TGT>TGC	Synonymous	GU280_gp02, spike glycoprotein	0.988229359340844
CAMB-7218E	MN908947.3	2382	G	A	0.013	0.0037	4.1e-06	0.00077	0.00475194829880251	GGT	ORF1ab:nsp2	G526D	G1577A	GGT>GAT	Missense	ORF1ab:nsp2	0.994867895837293
CAMB-7218E	MN908947.3	241	C	T	1	1	0	0	0.998621279832652	TCG	NA	NA	NA	NA	NA	NA	0.000142626224208424
CAMB-7218E	MN908947.3	25663	T	A	1	1	0	0	0.999361249112846	TTA	ORF3a	Y91N	T271A	TAC>AAC	Missense	GU280_gp03	0.00035486160397445
CAMB-7218E	MN908947.3	27046	C	T	1	1	0	0	0.999934857663996	ACG	M	T175M	C524T	ACG>ATG	Missense	GU280_gp05	0
CAMB-7218E	MN908947.3	28116	G	A	0.012	0.013	1.5e-07	3.7e-08	0.0132033857892227	CGA	ORF8	D75N	G223A	GAT>AAT	Missense	GU280_gp09	0.986647591797806
CAMB-7218E	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998052879688461	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000227272727272727
CAMB-7218E	MN908947.3	3037	C	T	1	1	0	0	0.999332542272323	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7218E	MN908947.3	3222	A	T	0.02	0.022	5.9e-10	1.7e-11	0.0217915849796411	CAA	ORF1ab:nsp3	Q168L	A503T	CAA>CTA	Missense	ORF1ab:nsp3	0.977982204795657
CAMB-7219D	MN908947.3	11075	T	-	0.042	0.03	3.6e-10	2.6e-08	0.0378396731176753	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958999215576083
CAMB-7219D	MN908947.3	11207	G	T	0.0096	0.0058	3.8e-06	7.8e-05	0.00832148887836049	AGC	ORF1ab:nsp6	A79S	G235T	GCT>TCT	Missense	ORF1ab:nsp6	0.991654214803746
CAMB-7219D	MN908947.3	1305	A	G	0.0078	0.02	1.6e-05	9.4e-11	0.0134822606341973	GAG	ORF1ab:nsp2	E167G	A500G	GAG>GGG	Missense	ORF1ab:nsp2	0.986449214534117
CAMB-7219D	MN908947.3	14408	C	T	1	1	0	0	0.999643922197	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000252221777124968
CAMB-7219D	MN908947.3	2164	G	A	1	1	0	0	0.99986907567426	AGA	ORF1ab:nsp2	E453E	G1359A	GAG>GAA	Synonymous	ORF1ab:nsp2	0.000130924325739722
CAMB-7219D	MN908947.3	21741	C	T	0.013	0.0064	2e-07	8.7e-05	0.00929183581416328	TCC	S	S60F	C179T	TCC>TTC	Missense	GU280_gp02, spike glycoprotein	0.990708164185837
CAMB-7219D	MN908947.3	21781	C	T	0.004	0.017	0.00055	3.2e-09	0.0111249640356766	CCA	S	T73T	C219T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.988779131101947
CAMB-7219D	MN908947.3	23403	A	G	1	1	0	0	0.99929900708675	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000134436997061591
CAMB-7219D	MN908947.3	241	C	T	1	1	0	0	0.999801038218749	TCG	NA	NA	NA	NA	NA	NA	0.000126612042613996
CAMB-7219D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999216569553934	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7219D	MN908947.3	3037	C	T	1	1	0	0	0.999803883114336	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7219D	MN908947.3	7160	G	A	1	1	3e-78	5.8e-246	1	AGA	ORF1ab:nsp3	D1481N	G4441A	GAC>AAC	Missense	ORF1ab:nsp3	0
CAMB-721AC	MN908947.3	11075	T	-	0.027	0.043	3.9e-07	2e-11	0.0316033093027586	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.967864648453087
CAMB-721AC	MN908947.3	14075	TCAATGGTAACTGGTAT	-	0.000527647058823529	0.00577058823529412	NA;0.12;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.19;0.39;4.8e-05	4.5e-05;3.7e-05;3.9e-05;4.3e-05;4e-05;4.8e-05;4.1e-05;5.4e-05;4.2e-05;4.5e-05;4.5e-05;5.8e-05;0.00028;4.1e-05;5.9e-05;2.2e-05;6e-04	0.00180206155842284	CTC	ORF1ab:RNA-dependent-RNA-polymerase	.	608-624-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.997248416406317
CAMB-721AC	MN908947.3	14408	C	T	1	1	0	0	0.996643281527978	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000218186700681414
CAMB-721AC	MN908947.3	14617	A	-	0.004	0.0062	0.00048	3.7e-05	0.00476616406848965	CAC	ORF1ab:RNA-dependent-RNA-polymerase	.	1150-1150-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.995208280092001
CAMB-721AC	MN908947.3	15613	C	T	0.0076	0.018	1.8e-05	4.1e-10	0.0121335878427369	ACA	ORF1ab:RNA-dependent-RNA-polymerase	H716Y	C2146T	CAC>TAC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.987792426865539
CAMB-721AC	MN908947.3	17105	A	G	0.091	0.086	3.4e-42	4.4e-40	0.0892649083783497	CAT	ORF1ab:helicase	H290R	A869G	CAT>CGT	Missense	ORF1ab:helicase	0.909499346820605
CAMB-721AC	MN908947.3	22747	C	T	0.0045	0.0089	0.00078	7.8e-06	0.00557941167878947	TCT	S	V395V	C1185T	GTC>GTT	Synonymous	GU280_gp02, spike glycoprotein	0.99442058832121
CAMB-721AC	MN908947.3	23403	A	G	1	1	0	0	0.999832525618347	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000125605786239886
CAMB-721AC	MN908947.3	241	C	T	0.99	1	0	0	0.993270472995122	TCG	NA	NA	NA	NA	NA	NA	7.71292493395808e-05
CAMB-721AC	MN908947.3	24321	A	-	0.016	0.016	8.2e-06	9.8e-06	0.0159421952058722	CAA	S	.	2759-2759-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.983656382612685
CAMB-721AC	MN908947.3	25101	AAA	-	0.00763333333333333	0.00233333333333333	3e-04;2.8e-05;1.6e-05	0.00055;NA;NA	0.00527363184079602	CAA	S	.	3539-3541-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.992537313432836
CAMB-721AC	MN908947.3	25244	G	C	0.013	0.0058	5.4e-06	0.00027	0.0103712319472715	AGT	S	V1228L	G3682C	GTA>CTA	Missense	GU280_gp02, spike glycoprotein	0.989531840651352
CAMB-721AC	MN908947.3	25429	G	T	1	1	0	0	0.999915093058008	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	1.69813883983154e-05
CAMB-721AC	MN908947.3	27804	C	T	0.13	0.18	2.5e-23	6.9e-21	0.143312101910828	TCT	NA	NA	NA	NA	NA	NA	0.856687898089172
CAMB-721AC	MN908947.3	28253	C	T	0.013	0.007	8.4e-07	0.00035	0.011338874989912	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.988472816291394
CAMB-721AC	MN908947.3	28311	C	T	0.015	0.0036	5.9e-08	0.0033	0.011106723898562	CCC	N	P13L	C38T	CCC>CTC	Missense	GU280_gp10	0.986791659767421
CAMB-721AC	MN908947.3	3037	C	T	1	1	0	0	0.998939273402281	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000265181649429859
CAMB-721AC	MN908947.3	4886	C	T	0.0057	0.0066	0.00011	3.7e-05	0.00606434371466749	TCC	ORF1ab:nsp3	P723S	C2167T	CCT>TCT	Missense	ORF1ab:nsp3	0.993915099187995
CAMB-721AC	MN908947.3	614	G	C	0.0053	0.0079	4e-04	2.7e-05	0.00612114113981393	GGC	ORF1ab:leader-protein	A117P	G349C	GCT>CCT	Missense	ORF1ab:leader-protein	0.993812564912823
CAMB-721AC	MN908947.3	6383	G	C	0.0075	0.01	1.6e-05	7.9e-07	0.00818751003371328	TGC	ORF1ab:nsp3	A1222P	G3664C	GCC>CCC	Missense	ORF1ab:nsp3	0.991629016352086
CAMB-721AC	MN908947.3	6813	C	T	0.0061	0.011	0.00017	1.6e-06	0.00814159292035398	ACT	ORF1ab:nsp3	T1365I	C4094T	ACT>ATT	Missense	ORF1ab:nsp3	0.991858407079646
CAMB-721BB	MN908947.3	13914	T	G	0.0077	0.0034	6.4e-06	0.00079	0.00635997456010176	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993640025439898
CAMB-721BB	MN908947.3	14408	C	T	1	1	0	0	0.999718389186145	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000281610813855252
CAMB-721BB	MN908947.3	15540	C	T	1	1	0	0	0.999721642310369	TCA	ORF1ab:RNA-dependent-RNA-polymerase	V691V	C2073T	GTC>GTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000278357689631176
CAMB-721BB	MN908947.3	23403	A	G	1	1	0	0	0.999896800825593	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000103199174406605
CAMB-721BB	MN908947.3	241	C	T	1	1	0	0	0.999859154929577	TCG	NA	NA	NA	NA	NA	NA	0.000140845070422535
CAMB-721BB	MN908947.3	3037	C	T	1	1	1.1e-37	8.4e-257	0.997938144329897	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00206185567010309
CAMB-721BB	MN908947.3	751	C	T	1	0.99	0	0	0.998585572842999	ACA	ORF1ab:leader-protein	N162N	C486T	AAC>AAT	Synonymous	ORF1ab:leader-protein	0.00141442715700141
CAMB-721CA	MN908947.3	105	G	T	1	1	0	0	0.999887569706782	TGC	NA	NA	NA	NA	NA	NA	2.24860586436409e-05
CAMB-721CA	MN908947.3	10567	T	G	0.03	0.054	1.1e-14	2.6e-24	0.0375084772288591	TTC	ORF1ab:3C-like-proteinase	V171V	T513G	GTT>GTG	Synonymous	ORF1ab:3C-like-proteinase	0.962439355208931
CAMB-721CA	MN908947.3	11074	C	INS	0.036	0.02	6.2e-09	0.0014	0.0317634357815188	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.968017273371344
CAMB-721CA	MN908947.3	11075	T	-	0.03	0.098	7.2e-08	1.3e-24	0.0493430120371221	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.9415602315538
CAMB-721CA	MN908947.3	11273	GTTGATACTAGTTTGTCTGGTTTT	-	0.01325	0.0125875	8.8e-05;9.5e-05;0.00019;0.00012;0.00022;2e-04;0.00044;0.00024;0.00021;0.00024;3e-04;0.00091;0.00039;0.00061;0.00041;0.00024;0.00022;0.00012;0.00013;0.00024;3.2e-05;3e-04;0.00011;4e-05	0.47;3.5e-05;8.5e-05;4.7e-05;9.9e-05;7.9e-05;2e-04;0.00011;9.1e-05;0.00011;0.00013;0.00043;0.00016;0.00028;0.00019;0.00011;1e-04;5.1e-05;5.4e-05;0.00011;8.5e-06;0.00014;NA;NA	0.0135177979535956	GGT	ORF1ab:nsp6	.	301-324-delinframe	.	no-SNV	ORF1ab:nsp6	0.990420849754049
CAMB-721CA	MN908947.3	12599	AGTG	-	0.03	0.02175	5.8e-10;2.1e-10;7.6e-15;1.7e-14	6.9e-08;6.3e-08;1e-11;2.9e-11	0.026224566691786	TAG	ORF1ab:nsp8	.	508-511-delfrshift	.	no-SNV	ORF1ab:nsp8	0.973766051364366
CAMB-721CA	MN908947.3	14408	C	T	1	1	0	0	0.999665446941976	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000250914793518035
CAMB-721CA	MN908947.3	15442	A	T	0.11	0.15	2.1e-49	1.5e-60	0.113863744640305	CAT	ORF1ab:RNA-dependent-RNA-polymerase	M659L	A1975T	ATG>TTG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.886136255359695
CAMB-721CA	MN908947.3	17013	A	C	0.043	0.03	1.4e-20	5e-15	0.0375477554918816	CAG	ORF1ab:helicase	S259S	A777C	TCA>TCC	Synonymous	ORF1ab:helicase	0.958273638968481
CAMB-721CA	MN908947.3	203	C	T	0.044	0.022	5.6e-20	1.1e-10	0.0361292256952252	TCG	NA	NA	NA	NA	NA	NA	0.963845788671514
CAMB-721CA	MN908947.3	21575	C	T	0.057	0.049	1.9e-15	5.2e-12	0.0543478260869565	TCT	S	L5F	C13T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.945301542776999
CAMB-721CA	MN908947.3	21994	TTA	-	0.0173333333333333	0.0055	3.8e-05;8.2e-05;1.5e-09	0.0052;0.0063;NA	0.0151424694708277	ATT	S	.	432-434-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.984617911101379
CAMB-721CA	MN908947.3	23403	A	G	1	1	0	0	0.999905452998322	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.27286264684331e-05
CAMB-721CA	MN908947.3	23435	C	T	0.042	0.038	6.5e-20	1.2e-18	0.0408542576742314	TCA	S	H625Y	C1873T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.959145742325769
CAMB-721CA	MN908947.3	241	C	T	1	1	0	0	0.999804286133673	TCG	NA	NA	NA	NA	NA	NA	0.000122321166454643
CAMB-721CA	MN908947.3	24213	C	T	0.014	0.014	5.2e-07	4.8e-07	0.0141987829614604	TCT	S	S884F	C2651T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.98580121703854
CAMB-721CA	MN908947.3	25521	C	T	0.02	0.036	3.8e-10	3.5e-17	0.026349111764925	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.973613645674277
CAMB-721CA	MN908947.3	26284	GTT	-	0.00813333333333333	0.0123333333333333	0.0044;0.0036;0.00068	0.00062;0.00038;4.2e-05	0.00911625911625912	AGT	E	.	40-42-delinframe	.	no-SNV	GU280_gp04	0.991072669167709
CAMB-721CA	MN908947.3	27208	C	T	0.0076	0.0093	4.6e-05	7.4e-06	0.0082473676484326	TCA	ORF6	H3Y	C7T	CAT>TAT	Missense	GU280_gp06	0.991699251331189
CAMB-721CA	MN908947.3	28253	C	T	0.052	0.022	5.4e-23	1.3e-10	0.0416253427454641	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.957966279680299
CAMB-721CA	MN908947.3	28445	C	T	0.005	0.01	0.00036	1.9e-06	0.00749081315367945	TCA	N	Q58*	C172T	CAA>TAA	Nonsense	GU280_gp10	0.992509186846321
CAMB-721CA	MN908947.3	28706	C	T	0.021	0.022	1.7e-10	5.1e-11	0.0216694168560665	TCA	N	H145Y	C433T	CAC>TAC	Missense	GU280_gp10	0.978330583143934
CAMB-721CA	MN908947.3	28744	C	T	0.012	0.0083	2.3e-06	7.1e-05	0.0101911222624911	TCG	N	I157I	C471T	ATC>ATT	Synonymous	GU280_gp10	0.988322027073072
CAMB-721CA	MN908947.3	28881	GGG	AAC	0.99	1	0;0;0	0;0;0	0.99638141809291	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000109397221310579
CAMB-721CA	MN908947.3	29274	C	T	0.041	0.012	3e-19	7.2e-07	0.027075183018941	ACA	N	T334I	C1001T	ACA>ATA	Missense	GU280_gp10	0.972924816981059
CAMB-721CA	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-721CA	MN908947.3	505	TCA	-	0.0113333333333333	0.013	1.5e-06;3e-06;0.00018	5.2e-07;9.5e-07;6.5e-05	0.0118099231306778	CTC	ORF1ab:leader-protein	.	240-242-delinframe	.	no-SNV	ORF1ab:leader-protein	0.987939134703036
CAMB-721CA	MN908947.3	519	T	G	0.0043	0.014	0.0059	5.5e-07	0.00736126840317101	ATG	ORF1ab:leader-protein	M85R	T254G	ATG>AGG	Missense	ORF1ab:leader-protein	0.936579841449604
CAMB-721CA	MN908947.3	522	TTGA	-	0.0335	0.02875	5.3e-08;2.3e-06;0.00024;3.2e-06	6.1e-07;4.9e-07;0.00077;NA	0.0313632290489734	GTT	ORF1ab:leader-protein	.	257-260-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.941760566420585
CAMB-721CA	MN908947.3	635	C	T	0.019	0.034	9.3e-10	6.2e-16	0.0233994695672609	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.976600530432739
CAMB-721CA	MN908947.3	6683	AATTATGCTAAGCCTTTTCTTAACAAAGTTGTTAGTACAACTACTAACATAGTTACACGGTGTT	-	0.00033828125	0.008825	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;3.9e-06;5.5e-06;NA;NA;NA	3e-05;2.2e-05;0.00017;8.6e-05;2.7e-06;1.1e-05;3.1e-05;7.3e-06;5.9e-06;5.1e-06;9.6e-06;1.1e-05;3.2e-06;1.1e-05;3.5e-05;5.4e-06;4.8e-06;5.3e-06;5.1e-06;4.8e-06;1e-05;3.9e-06;2.5e-05;6.8e-05;5.3e-05;1.2e-06;4e-06;6.5e-06;8.3e-06;1.2e-05;9e-06;5.3e-06;0.00015;2.9e-05;7.4e-05;7.2e-06;1e-05;8.9e-06;7.8e-06;7.7e-06;1.1e-05;7.9e-06;6.9e-06;6.8e-06;7.8e-06;8.7e-06;4.5e-06;7e-06;7.3e-06;5.9e-06;7.9e-06;7.6e-06;7.5e-06;8.3e-06;8.1e-06;7.8e-06;4.3e-06;7e-06;6e-06;1.2e-05;1.8e-05;1.4e-05;1.7e-05;8.9e-06	0.00551823416506718	TAA	ORF1ab:nsp3	.	3964-4027-delfrshift	.	no-SNV	ORF1ab:nsp3	0.992693110647182
CAMB-721CA	MN908947.3	9430	C	T	0.0083	0.011	0.00012	3.3e-05	0.00888248709638699	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.991117512903613
CAMB-721D9	MN908947.3	11075	T	-	0.041	0.035	1.2e-10	4.8e-10	0.0361550119073393	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959839792162806
CAMB-721D9	MN908947.3	11195	C	T	1	1	0	0	0.99912739965096	TCT	ORF1ab:nsp6	L75F	C223T	CTT>TTT	Missense	ORF1ab:nsp6	0.00024931438544004
CAMB-721D9	MN908947.3	13170	C	A	0.0048	0.0066	6.5e-05	2.8e-05	0.00644961879249949	ACT	ORF1ab:nsp10	T49N	C146A	ACT>AAT	Missense	ORF1ab:nsp10	0.993529775396662
CAMB-721D9	MN908947.3	14408	C	T	1	1	0	0	0.997662347953564	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000673560759142597
CAMB-721D9	MN908947.3	20956	C	T	0.01	0.0054	2.3e-05	0.00024	0.00586831111995226	TCT	ORF1ab:2'-O-ribose-methyltransferase	L100F	C298T	CTT>TTT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.993733837278695
CAMB-721D9	MN908947.3	23403	A	G	1	1	0	0	0.999069197795468	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000122473974280465
CAMB-721D9	MN908947.3	241	C	T	1	1	0	0	0.998937255568781	TCG	NA	NA	NA	NA	NA	NA	0.000212548886243836
CAMB-721D9	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999276061776062	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000539519827353655
CAMB-721D9	MN908947.3	3037	C	T	1	1	0	0	0.999319033026898	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000113494495516967
CAMB-721D9	MN908947.3	3373	C	A	1	1	0	0	0.998728470697029	ACA	ORF1ab:nsp3	D218E	C654A	GAC>GAA	Missense	ORF1ab:nsp3	0
CAMB-721D9	MN908947.3	4246	C	T	1	1	0	0	0.999702496738907	CCA	ORF1ab:nsp3	T509T	C1527T	ACC>ACT	Synonymous	ORF1ab:nsp3	0.000137309197427741
CAMB-721D9	MN908947.3	4780	C	T	1	1	0	0	0.998910987562332	TCT	ORF1ab:nsp3	I687I	C2061T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.000114632888175618
CAMB-721D9	MN908947.3	6597	A	G	0.017	0.014	1.2e-07	6.5e-08	0.0145392345520633	AAT	ORF1ab:nsp3	N1293S	A3878G	AAT>AGT	Missense	ORF1ab:nsp3	0.985460765447937
CAMB-721D9	MN908947.3	9246	C	T	1	1	0	0	0.998942172073343	GCT	ORF1ab:nsp4	A231V	C692T	GCT>GTT	Missense	ORF1ab:nsp4	0.000235072872590503
CAMB-721F7	MN908947.3	14408	C	T	1	1	0	0	0.999673561444639	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000326438555361011
CAMB-721F7	MN908947.3	15576	TAACAAAATTGCCGATAAGTATGTCCGCAATT	-	0.0007203125	0.03653125	NA;NA;NA;NA;6.6e-11;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	1.5e-17;4.3e-18;2e-17;2.5e-17;1.7e-16;2.7e-17;3.4e-17;2.9e-17;8.6e-18;9.2e-18;8.8e-18;8.3e-18;8.6e-18;1.4e-17;7.7e-18;5e-19;2.2e-19;3.3e-19;5.3e-18;1.7e-18;1.5e-18;1.6e-17;8.8e-18;1e-17;1.5e-17;6.9e-18;9.5e-18;1.1e-17;1.3e-17;6.8e-19;4.7e-18;7.3e-18	0.0106861134677521	GTA	ORF1ab:RNA-dependent-RNA-polymerase	.	2109-2140-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.989377086643695
CAMB-721F7	MN908947.3	1758	C	T	0.043	0.012	2e-20	1.1e-06	0.0383163265306122	GCA	ORF1ab:nsp2	A318V	C953T	GCA>GTA	Missense	ORF1ab:nsp2	0.961632653061224
CAMB-721F7	MN908947.3	22671	A	G	1	1	0	0	0.999951573849879	AAT	S	N370S	A1109G	AAT>AGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-721F7	MN908947.3	23403	A	G	1	1	0	0	0.999881169722045	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000108027525413475
CAMB-721F7	MN908947.3	241	C	T	1	1	0	0	0.999758821117623	TCG	NA	NA	NA	NA	NA	NA	0.000144707329426235
CAMB-721F7	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-72203	MN908947.3	14408	C	T	1	1	0	0	0.999884384152921	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	7.70772313858486e-05
CAMB-72203	MN908947.3	23403	A	G	1	1	0	0	0.999857416142869	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.50559047539834e-05
CAMB-72203	MN908947.3	241	C	T	1	1	0	0	0.99972581873572	TCG	NA	NA	NA	NA	NA	NA	0.000213252094440213
CAMB-72203	MN908947.3	28881	GGG	AAC	1	1	0;0;0	3e-265;1.4e-270;4.1e-282	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-72203	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-72221	MN908947.3	10951	A	G	0.013	0.02	1.2e-07	1.3e-10	0.0161832926095117	AAT	ORF1ab:3C-like-proteinase	Q299Q	A897G	CAA>CAG	Synonymous	ORF1ab:3C-like-proteinase	0.983816707390488
CAMB-72221	MN908947.3	11075	T	-	0.037	0.038	2.1e-09	5.9e-10	0.037552889128953	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957418624689739
CAMB-72221	MN908947.3	14408	C	T	1	1	0	0	0.998269711973593	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000585635947399244
CAMB-72221	MN908947.3	16163	C	T	0.0075	0.0056	2.6e-05	0.00016	0.00663210307479082	ACT	ORF1ab:RNA-dependent-RNA-polymerase	T899I	C2696T	ACT>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993111236589497
CAMB-72221	MN908947.3	171	C	T	0.0089	0.012	4.4e-06	2.3e-07	0.0100032619332391	ACT	NA	NA	NA	NA	NA	NA	0.989931499401979
CAMB-72221	MN908947.3	19086	G	T	0.0052	0.007	0.00029	3.8e-05	0.00592117436624931	AGT	ORF1ab:3'-to-5'-exonuclease	K349N	G1047T	AAG>AAT	Missense	ORF1ab:3'-to-5'-exonuclease	0.99392462838463
CAMB-72221	MN908947.3	20991	G	A	0.089	0.088	3.6e-40	7.9e-40	0.0883024034073623	TGA	ORF1ab:2'-O-ribose-methyltransferase	L111L	G333A	TTG>TTA	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.911418720210932
CAMB-72221	MN908947.3	23403	A	G	1	1	0	0	0.998731704323456	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.11409546993423e-05
CAMB-72221	MN908947.3	241	C	T	1	1	0	0	0.998438903383089	TCG	NA	NA	NA	NA	NA	NA	0.000235233736794833
CAMB-72221	MN908947.3	27493	C	T	0.15	0.14	2e-67	2.4e-65	0.144211952431131	ACC	ORF7a	P34S	C100T	CCT>TCT	Missense	GU280_gp07	0.85568769130413
CAMB-72221	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999128751210068	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000107553866561503
CAMB-72221	MN908947.3	3037	C	T	1	1	0	0	0.998829754757301	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000203520911773685
CAMB-72221	MN908947.3	3510	C	T	0.011	0.01	7.9e-06	7.2e-06	0.0104029304029304	GCC	ORF1ab:nsp3	A264V	C791T	GCC>GTC	Missense	ORF1ab:nsp3	0.989157509157509
CAMB-72221	MN908947.3	5698	T	C	0.014	0.013	5.9e-08	1.3e-07	0.0138212077170785	CTG	ORF1ab:nsp3	P993P	T2979C	CCT>CCC	Synonymous	ORF1ab:nsp3	0.986150294947422
CAMB-72230	MN908947.3	11074	C	INS	0.035	0.039	8.9e-09	7.8e-09	0.0365293683548801	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.963361303195124
CAMB-72230	MN908947.3	11075	T	-	0.01	0.023	0.0013	9e-07	0.0149084485187042	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.981976175129509
CAMB-72230	MN908947.3	13858	G	T	1	1	0	0	0.999580676159692	TGA	ORF1ab:RNA-dependent-RNA-polymerase	D131Y	G391T	GAC>TAC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	1.74718266794793e-05
CAMB-72230	MN908947.3	14408	C	T	1	1	0	0	0.99837404822335	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000264382402707276
CAMB-72230	MN908947.3	15004	G	T	0.0036	0.0098	0.0028	5e-06	0.00731452455590387	TGA	ORF1ab:RNA-dependent-RNA-polymerase	E513*	G1537T	GAG>TAG	Nonsense	ORF1ab:RNA-dependent-RNA-polymerase	0.985475444096134
CAMB-72230	MN908947.3	15487	G	T	0.0033	0.0087	0.0016	5.5e-06	0.00431202359094197	AGG	ORF1ab:RNA-dependent-RNA-polymerase	G674*	G2020T	GGA>TGA	Nonsense	ORF1ab:RNA-dependent-RNA-polymerase	0.995632337394981
CAMB-72230	MN908947.3	19638	T	-	0.014	0.017	6.2e-07	9.7e-08	0.015056717025281	CTT	ORF1ab:endoRNAse	.	18-18-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.984943282974719
CAMB-72230	MN908947.3	21641	G	-	0.0052	0.011	0.00054	8.7e-06	0.00688791484032561	TGC	S	.	79-79-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.992694635775412
CAMB-72230	MN908947.3	23403	A	G	1	0.99	0	0	0.997952050411067	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.90754689115345e-05
CAMB-72230	MN908947.3	241	C	T	1	1	0	0	0.999856836077308	TCG	NA	NA	NA	NA	NA	NA	7.15819613457409e-05
CAMB-72230	MN908947.3	2410	A	G	0.0074	0.01	3.1e-05	3.5e-06	0.00862068965517241	GAT	ORF1ab:nsp2	G535G	A1605G	GGA>GGG	Synonymous	ORF1ab:nsp2	0.991379310344828
CAMB-72230	MN908947.3	25734	C	T	1	1	0	0	0.999903855398519	TCT	ORF3a	F114F	C342T	TTC>TTT	Synonymous	GU280_gp03	9.61446014806269e-05
CAMB-72230	MN908947.3	27115	G	-	0.0031	0.0065	0.0016	4.5e-05	0.00458052814411756	CGC	M	.	593-593-delfrshift	.	no-SNV	GU280_gp05	0.995327246457008
CAMB-72230	MN908947.3	2857	C	T	0.0093	0.026	3.8e-06	1.8e-13	0.0205725291079401	TCG	ORF1ab:nsp3	L46L	C138T	CTC>CTT	Synonymous	ORF1ab:nsp3	0.979339928215005
CAMB-72230	MN908947.3	28706	C	T	1	1	0	0	0.999261771747805	TCA	N	H145Y	C433T	CAC>TAC	Missense	GU280_gp10	7.98084596967278e-05
CAMB-72230	MN908947.3	28881	GGG	AAC	0.996666666666667	1	0;0;0	0;0;0	0.998211091234347	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-72230	MN908947.3	29315	G	T	0.0039	0.0082	9e-04	1.1e-05	0.00576149581476247	AGA	N	D348Y	G1042T	GAT>TAT	Missense	GU280_gp10	0.99422038627387
CAMB-72230	MN908947.3	3037	C	T	0.99	1	0	0	0.995606443882306	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000133138064172547
CAMB-72230	MN908947.3	4136	G	T	0.0077	0.0065	3.2e-05	8.9e-05	0.00723852668898956	TGT	ORF1ab:nsp3	V473F	G1417T	GTT>TTT	Missense	ORF1ab:nsp3	0.992675300374237
CAMB-72230	MN908947.3	6254	G	T	0.0068	0.0085	5.9e-05	8.1e-06	0.00723362314759407	TGC	ORF1ab:nsp3	A1179S	G3535T	GCA>TCA	Missense	ORF1ab:nsp3	0.992713576683445
CAMB-72230	MN908947.3	6337	G	T	0.0075	0.0061	3.1e-05	0.00011	0.00714800243807835	CGT	ORF1ab:nsp3	S1206S	G3618T	TCG>TCT	Synonymous	ORF1ab:nsp3	0.992851997561922
CAMB-72230	MN908947.3	6374	G	T	0.0073	0.007	3.5e-05	4.5e-05	0.0072420688536994	GGA	ORF1ab:nsp3	D1219Y	G3655T	GAT>TAT	Missense	ORF1ab:nsp3	0.99273991604965
CAMB-72230	MN908947.3	6684	ATT	-	0.00793333333333333	0.0273333333333333	0.00092;0.00014;6.5e-05	6e-10;3.3e-10;3.5e-11	0.0235856836549563	AAT	ORF1ab:nsp3	.	3965-3967-delinframe	.	no-SNV	ORF1ab:nsp3	0.984886649874055
CAMB-72230	MN908947.3	8178	GG	TT	0.005	0.009	NA;1.8e-06	2.2e-06;4.9e-06	0.00630643144881233	CGG	ORF1ab:nsp3	.	5459-5460-mnv	.	no-SNV	ORF1ab:nsp3	0.989546557811121
CAMB-72230	MN908947.3	8179	G	T	0.01	0.0092	1.8e-06	4.9e-06	0.00996333715820996	GGC	ORF1ab:nsp3	R1820R	G5460T	CGG>CGT	Synonymous	ORF1ab:nsp3	0.989952702135401
CAMB-72230	MN908947.3	9290	G	T	0.0075	0.0047	2.9e-05	0.00055	0.00681749622926094	TGA	ORF1ab:nsp4	D246Y	G736T	GAT>TAT	Missense	ORF1ab:nsp4	0.988114630467572
CAMB-7224F	MN908947.3	11071	G	C	0.023	0.016	1e-11	3.4e-09	0.0203896186710879	TGT	ORF1ab:nsp6	L33F	G99C	TTG>TTC	Missense	ORF1ab:nsp6	0.979482846575692
CAMB-7224F	MN908947.3	11074	C	INS	0.066	0.03	1.8e-20	4.9e-06	0.0550638950736243	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.938424981757629
CAMB-7224F	MN908947.3	11075	T	-	0.025	0.11	8.4e-07	2.1e-26	0.050958173637727	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.938393601066489
CAMB-7224F	MN908947.3	12053	C	T	0.01	0.016	1.2e-06	4e-09	0.0127395334768607	GCT	ORF1ab:nsp7	L71F	C211T	CTT>TTT	Missense	ORF1ab:nsp7	0.987207088589577
CAMB-7224F	MN908947.3	13965	C	T	1	1	0	0	0.999751681324366	ACG	ORF1ab:RNA-dependent-RNA-polymerase	Y166Y	C498T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000206932229694775
CAMB-7224F	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999489916032332	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	7.84744565643883e-05
CAMB-7224F	MN908947.3	18367	GGTTTTTCTACAGGTGTTAACCTAGTTGCTGTACCTACAGGTTATG	-	0.00393478260869565	0.0177173913043478	0.00077;0.0011;0.00028;0.00065;0.00032;0.0011;0.002;0.0022;0.0022;0.0025;0.0021;0.0019;0.0016;0.0024;0.0013;0.0021;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	4.2e-05;7.2e-05;4.1e-06;2.2e-05;9.8e-06;6.3e-05;0.00015;0.00016;0.00016;0.00019;0.00016;0.00014;0.00011;0.00021;7.8e-05;2e-04;2.7e-06;5.9e-06;3.7e-09;1.4e-08;4.8e-09;6.6e-09;1e-07;2.9e-08;3.7e-05;1.1e-05;1.3e-05;3.2e-05;5e-05;2.9e-05;3.1e-05;5.9e-06;3.4e-06;3.4e-07;2.9e-06;8.7e-07;9.5e-07;1.1e-06;9.6e-07;3.9e-06;2.3e-06;2.9e-08;1.7e-06;7.9e-09;6.7e-07;6.8e-07	0.00618568401937046	AGG	ORF1ab:3'-to-5'-exonuclease	.	328-373-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.986621015611916
CAMB-7224F	MN908947.3	20270	C	T	0.99	1	0	2.7e-172	0.995675675675676	GCT	ORF1ab:endoRNAse	A217V	C650T	GCT>GTT	Missense	ORF1ab:endoRNAse	0
CAMB-7224F	MN908947.3	26333	C	T	0.0072	0.014	0.00016	1.6e-07	0.00949663572097777	ACA	E	T30I	C89T	ACA>ATA	Missense	GU280_gp04	0.990418192658206
CAMB-7224F	MN908947.3	28233	G	T	0.004	0.0064	0.00054	3.8e-05	0.00490693739424704	CGT	ORF8	V114F	G340T	GTT>TTT	Missense	GU280_gp09	0.994940778341794
CAMB-7224F	MN908947.3	29683	AATCAGTGTG	-	0.00092	0.0151	NA;NA;NA;NA;NA;NA;NA;NA;NA;4.8e-05	2.3e-07;2.1e-06;2.2e-07;4.6e-07;2.1e-07;4.3e-06;1.1e-06;1.1e-06;2.1e-07;6.6e-07	0.00905432595573441	TAA	NA	NA	NA	NA	NA	NA	0.990712074303406
CAMB-7224F	MN908947.3	561	G	-	0.0036	0.012	0.00096	1.8e-07	0.00651335903230094	CGT	ORF1ab:leader-protein	.	296-296-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.993353715273162
CAMB-7224F	MN908947.3	6516	TA	-	0.00935	0.0036	4.8e-06;1.8e-05	0.0023;0.0074	0.00815597967870383	TTA	ORF1ab:nsp3	.	3797-3798-delfrshift	.	no-SNV	ORF1ab:nsp3	0.991805314129625
CAMB-7224F	MN908947.3	7981	A	G	0.0041	0.02	0.00039	5.6e-11	0.00855265445190001	TAG	ORF1ab:nsp3	L1754L	A5262G	CTA>CTG	Synonymous	ORF1ab:nsp3	0.9914473455481
CAMB-7225E	MN908947.3	11074	C	INS	0.12	0.12	2.2e-55	2.5e-41	0.12273942551587	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.874545828477411
CAMB-7225E	MN908947.3	11083	G	-	0.14	0.14	2.1e-61	2.9e-63	0.142317083751658	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-7225E	MN908947.3	11083	G	T	0.86	0.86	0	0	0.857484599462066	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-7225E	MN908947.3	14805	C	T	1	1	0	0	0.999683449544424	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000136886683492322
CAMB-7225E	MN908947.3	18086	C	T	1	1	0	0	0.999538546729834	ACT	ORF1ab:3'-to-5'-exonuclease	T16I	C47T	ACT>ATT	Missense	ORF1ab:3'-to-5'-exonuclease	0.000123054205377469
CAMB-7225E	MN908947.3	26144	G	T	1	1	0	0	0.999239956568947	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000325732899022801
CAMB-7225E	MN908947.3	28842	G	T	1	1	0	0	0.999000847765532	AGT	N	S190I	G569T	AGT>ATT	Missense	GU280_gp10	0.000181664042630495
CAMB-7225E	MN908947.3	835	C	T	0.019	0.019	7.2e-10	3.9e-10	0.019252109731864	TCT	ORF1ab:nsp2	F10F	C30T	TTC>TTT	Synonymous	ORF1ab:nsp2	0.980541433327312
CAMB-7226D	MN908947.3	11074	C	INS	0.4	0.41	0	1.1e-238	0.400929672381829	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.594875299403223
CAMB-7226D	MN908947.3	11083	G	-	0.083	0.086	5.6e-34	6.3e-37	0.0835068155898698	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	4.52562408356112e-05
CAMB-7226D	MN908947.3	11083	G	T	0.92	0.91	0	0	0.916113031987111	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	4.52562408356112e-05
CAMB-7226D	MN908947.3	14805	C	T	1	1	0	0	0.999535850215294	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000128533786533944
CAMB-7226D	MN908947.3	15653	A	G	0.019	0.019	5.6e-10	1.8e-10	0.0193093538102295	GAC	ORF1ab:RNA-dependent-RNA-polymerase	D729G	A2186G	GAC>GGC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.980679419821276
CAMB-7226D	MN908947.3	18086	C	T	1	1	0	0	0.999643349659993	ACT	ORF1ab:3'-to-5'-exonuclease	T16I	C47T	ACT>ATT	Missense	ORF1ab:3'-to-5'-exonuclease	0.000142660136002663
CAMB-7226D	MN908947.3	26144	G	T	1	1	0	0	0.999731155694458	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000134422152770777
CAMB-7226D	MN908947.3	26912	C	T	0.043	0.041	1.7e-19	1.5e-19	0.0426871840701539	CCA	M	T130T	C390T	ACC>ACT	Synonymous	GU280_gp05	0.957242997179322
CAMB-7226D	MN908947.3	28842	G	T	1	1	0	0	0.999085329161151	AGT	N	S190I	G569T	AGT>ATT	Missense	GU280_gp10	0.0002407028523288
CAMB-7226D	MN908947.3	3773	C	T	0.015	0.019	5.1e-08	1.9e-09	0.0166390372689875	TCG	ORF1ab:nsp3	R352C	C1054T	CGC>TGC	Missense	ORF1ab:nsp3	0.983360962731012
CAMB-7226D	MN908947.3	950	T	C	0.26	0.26	5.9e-126	9.2e-126	0.258335223406668	ATA	ORF1ab:nsp2	Y49H	T145C	TAC>CAC	Missense	ORF1ab:nsp2	0.741649656006653
CAMB-7227C	MN908947.3	11075	T	-	0.031	0.031	9.8e-09	5.8e-09	0.0313020099859173	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964089105108181
CAMB-7227C	MN908947.3	14408	C	T	1	1	0	0	0.998370289890859	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000493851548224604
CAMB-7227C	MN908947.3	23403	A	G	1	1	0	0	0.9989110820733	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.11119407628648e-05
CAMB-7227C	MN908947.3	241	C	T	1	1	0	0	0.998614541292693	TCG	NA	NA	NA	NA	NA	NA	0.000301186675501476
CAMB-7227C	MN908947.3	25317	C	T	0.32	0.34	1.8e-131	1.2e-172	0.33482482863671	TCC	S	S1252F	C3755T	TCC>TTC	Missense	GU280_gp02, spike glycoprotein	0.665127570449353
CAMB-7227C	MN908947.3	25350	C	T	1	1	0	0	0.998364429367579	CCA	S	P1263L	C3788T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	0.000726920281075842
CAMB-7227C	MN908947.3	3037	C	T	1	1	0	0	0.999043311880327	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000260914941728996
CAMB-7227C	MN908947.3	635	C	T	1	1	0	0	0.999432512659333	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.000174611489436005
CAMB-7228B	MN908947.3	14408	C	T	1	1	0	0	0.999195112135514	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00051220136830937
CAMB-7228B	MN908947.3	21575	C	T	0.42	0.074	7.9e-133	1.8e-12	0.373435996150144	TCT	S	L5F	C13T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.624639076034649
CAMB-7228B	MN908947.3	23403	A	G	1	1	0	0	0.99991333831638	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.41635522624116e-05
CAMB-7228B	MN908947.3	241	C	T	1	1	0	0	0.999747511181648	TCG	NA	NA	NA	NA	NA	NA	0.00014427932477276
CAMB-7228B	MN908947.3	28310	C	T	0.13	0.097	2.7e-57	9.5e-45	0.120639906152143	ACC	N	P13S	C37T	CCC>TCC	Missense	GU280_gp10	0.879256028684143
CAMB-7228B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7228B	MN908947.3	29420	C	T	0.065	0.028	5.5e-22	1.3e-05	0.0608465608465608	ACC	N	P383S	C1147T	CCG>TCG	Missense	GU280_gp10	0.939153439153439
CAMB-7228B	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7229A	MN908947.3	10097	G	A	1	1	0	0	0.999885242139086	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000114757860913473
CAMB-7229A	MN908947.3	11991	A	-	0.018	0.025	4.2e-07	7.5e-10	0.0209972801450589	GAA	ORF1ab:nsp7	.	149-149-delfrshift	.	no-SNV	ORF1ab:nsp7	0.978912058023572
CAMB-7229A	MN908947.3	14408	C	T	1	1	0	0	0.999663893790438	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000252079657171666
CAMB-7229A	MN908947.3	17083	C	T	0.012	0.013	3e-07	1.3e-07	0.0126450718863676	ACC	ORF1ab:helicase	P283S	C847T	CCA>TCA	Missense	ORF1ab:helicase	0.987311623072926
CAMB-7229A	MN908947.3	17083	CC	TT	0.0115	0.0065	3e-07;7.2e-07	1.3e-07;NA	0.00882391106881786	ACC	ORF1ab:helicase	.	847-848-mnv	.	no-SNV	ORF1ab:helicase	0.987311623072926
CAMB-7229A	MN908947.3	1814	A	-	0.017	0.02	2.5e-06	5.5e-07	0.0182184917691457	TAA	ORF1ab:nsp2	.	1009-1009-delfrshift	.	no-SNV	ORF1ab:nsp2	0.981586310104756
CAMB-7229A	MN908947.3	1814	AAA	-	0.00566666666666667	0.0193333333333333	2.5e-06;NA;NA	5.5e-07;7e-10;1.2e-10	0.00666311300639659	TAA	ORF1ab:nsp2	.	1009-1011-delinframe	.	no-SNV	ORF1ab:nsp2	0.981586310104756
CAMB-7229A	MN908947.3	23403	A	G	1	1	0	0	0.999912481584667	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.91728051110755e-05
CAMB-7229A	MN908947.3	23417	G	T	0.015	0.017	3e-08	4.2e-09	0.0157070347154554	AGA	S	E619*	G1855T	GAA>TAA	Nonsense	GU280_gp02, spike glycoprotein	0.984234791081895
CAMB-7229A	MN908947.3	23731	C	T	1	1	0	0	0.99983280387895	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-7229A	MN908947.3	241	C	T	1	1	0	0	0.999753625228777	TCG	NA	NA	NA	NA	NA	NA	0.000175981979445305
CAMB-7229A	MN908947.3	26526	G	T	0.04	0.036	6.3e-14	2.3e-12	0.0387770320656227	GGC	M	A2S	G4T	GCA>TCA	Missense	GU280_gp05	0.960850111856823
CAMB-7229A	MN908947.3	28350	G	T	1	1	0	0	0.999864212432106	AGT	N	S26I	G77T	AGT>ATT	Missense	GU280_gp10	6.03500301750151e-05
CAMB-7229A	MN908947.3	28580	G	T	1	1	0	0	0.999763723714263	AGA	N	D103Y	G307T	GAT>TAT	Missense	GU280_gp10	7.87587619122627e-05
CAMB-7229A	MN908947.3	28836	C	T	0.016	0.0095	7.3e-08	4.9e-05	0.013510101010101	TCA	N	S188L	C563T	TCA>TTA	Missense	GU280_gp10	0.986489898989899
CAMB-7229A	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999588984792437	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000451263537906137
CAMB-7229A	MN908947.3	3037	C	T	1	1	0	0	0.999640287769784	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7229A	MN908947.3	6701	C	T	0.066	0.016	8.6e-17	3.7e-07	0.0280678851174935	TCT	ORF1ab:nsp3	L1328F	C3982T	CTT>TTT	Missense	ORF1ab:nsp3	0.971932114882507
CAMB-7229A	MN908947.3	672	ACGGCGCCGATC	-	0.013	0.00366666666666667	5.8e-07;1.9e-07;8.6e-07;8.2e-07;8.9e-07;6.6e-07;2.1e-07;6.1e-07;6.9e-07;2.4e-06;1.1e-06;3.3e-06	2.4e-06;1.1e-06;4e-06;3.8e-06;NA;NA;NA;NA;NA;NA;NA;NA	0.00866493506493506	TAC	ORF1ab:leader-protein	.	407-418-delinframe	.	no-SNV	ORF1ab:leader-protein	0.987645687645688
CAMB-7229A	MN908947.3	9417	G	T	0.027	0.022	8.1e-13	1.7e-07	0.0264288074000661	GGT	ORF1ab:nsp4	G288V	G863T	GGT>GTT	Missense	ORF1ab:nsp4	0.973571192599934
CAMB-722A9	MN908947.3	11075	T	-	0.031	0.037	4.8e-08	8.5e-10	0.0328298236475928	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960860183049334
CAMB-722A9	MN908947.3	14408	C	T	1	1	0	0	0.998273501220456	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000198448135579766
CAMB-722A9	MN908947.3	16289	C	T	1	1	0	0	1	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0
CAMB-722A9	MN908947.3	2307	TTG	-	0.012	0.0126666666666667	NA;6.3e-08;8.8e-08	1.5e-06;5.8e-06;9.5e-06	0.0154689010634869	CTT	ORF1ab:nsp2	.	1502-1504-delinframe	.	no-SNV	ORF1ab:nsp2	0.993392798149983
CAMB-722A9	MN908947.3	23403	A	G	1	1	0	0	0.999930467029783	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.31776567389037e-05
CAMB-722A9	MN908947.3	23425	T	C	0.0072	0.0081	4.8e-05	1.7e-05	0.0075085888339256	CTG	S	P621P	T1863C	CCT>CCC	Synonymous	GU280_gp02, spike glycoprotein	0.992467799251502
CAMB-722A9	MN908947.3	241	C	T	1	1	0	0	0.99981220657277	TCG	NA	NA	NA	NA	NA	NA	0.000125195618153365
CAMB-722A9	MN908947.3	25429	G	T	1	0.99	0	0	0.997438206744721	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	8.00560392274592e-05
CAMB-722A9	MN908947.3	27264	TTTTAAAGTTTCCATTTGGAATCTTGA	-	0.921111111111111	0.885925925925926	0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0	0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0	0.903932752927049	CTT	ORF6	.	63-89-delinframe	.	no-SNV	GU280_gp06	0.0982928091050181
CAMB-722A9	MN908947.3	29466	C	T	0.024	0.016	5.8e-09	4e-05	0.021551724137931	GCA	N	A398V	C1193T	GCA>GTA	Missense	GU280_gp10	0.977586206896552
CAMB-722A9	MN908947.3	29538	A	C	0.02	0.0056	9.7e-09	0.00021	0.0115495668912416	CAT	NA	NA	NA	NA	NA	NA	0.988450433108758
CAMB-722A9	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-722A9	MN908947.3	435	A	G	0.013	0.0085	1.9e-07	1e-05	0.0110699017581609	GAA	ORF1ab:leader-protein	E57G	A170G	GAA>GGA	Missense	ORF1ab:leader-protein	0.98825061578098
CAMB-722A9	MN908947.3	6061	T	C	0.0063	0.012	0.00034	1.4e-06	0.0102315562735595	GTG	ORF1ab:nsp3	C1114C	T3342C	TGT>TGC	Synonymous	ORF1ab:nsp3	0.98976844372644
CAMB-722B8	MN908947.3	14408	C	T	1	1	0	0	0.999000499750125	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000999500249875062
CAMB-722B8	MN908947.3	17835	T	C	1	1	0	0	1	TTG	ORF1ab:helicase	V533V	T1599C	GTT>GTC	Synonymous	ORF1ab:helicase	0
CAMB-722B8	MN908947.3	23403	A	G	1	1	0	0	0.999868126071476	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000131873928524331
CAMB-722B8	MN908947.3	241	C	T	1	1	0	0	0.999089667728721	TCG	NA	NA	NA	NA	NA	NA	0.000910332271279017
CAMB-722B8	MN908947.3	3037	C	T	1	1	9.3e-31	8.5e-236	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-722C7	MN908947.3	10097	G	A	1	1	0	0	0.999773806831034	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000135715901379778
CAMB-722C7	MN908947.3	11075	T	-	0.042	0.042	2.8e-11	1.3e-11	0.0418205696462284	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953911187720594
CAMB-722C7	MN908947.3	1141	G	A	0.0088	0.009	2.2e-06	1.9e-06	0.00892805041722589	AGC	ORF1ab:nsp2	K112K	G336A	AAG>AAA	Synonymous	ORF1ab:nsp2	0.990955243041373
CAMB-722C7	MN908947.3	13536	C	T	1	1	0	0	0.999736378394128	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	5.54992854466999e-05
CAMB-722C7	MN908947.3	14408	C	T	1	1	0	0	0.998278756454663	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00055249792813277
CAMB-722C7	MN908947.3	23403	A	G	1	1	0	0	0.999414526761982	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.19662533225606e-05
CAMB-722C7	MN908947.3	23731	C	T	1	1	0	0	0.999627282892285	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000106490602204355
CAMB-722C7	MN908947.3	241	C	T	1	1	0	0	0.998913220670543	TCG	NA	NA	NA	NA	NA	NA	0.000163016899418573
CAMB-722C7	MN908947.3	26765	T	C	0.028	0.025	9e-14	1.3e-12	0.0264227642276423	CTA	M	A81A	T243C	GCT>GCC	Synonymous	GU280_gp05	0.973397895743663
CAMB-722C7	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998732113747509	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000201491033649003
CAMB-722C7	MN908947.3	28908	G	T	1	1	0	0	0.99936170212766	GGC	N	G212V	G635T	GGC>GTC	Missense	GU280_gp10	0.000212765957446809
CAMB-722C7	MN908947.3	3037	C	T	1	1	0	0	0.999500665778961	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000166444740346205
CAMB-722C7	MN908947.3	4002	C	T	1	1	0	0	0.999794913863823	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0.000102543068088597
CAMB-722C7	MN908947.3	4138	T	C	1	1	0	0	0.999432850297137	TTC	ORF1ab:nsp3	V473V	T1419C	GTT>GTC	Synonymous	ORF1ab:nsp3	0.000304123753709077
CAMB-722C7	MN908947.3	4547	A	G	1	1	0	0	0.996753490623513	TAA	ORF1ab:nsp3	K610E	A1828G	AAA>GAA	Missense	ORF1ab:nsp3	0.00022533612638853
CAMB-722C7	MN908947.3	683	C	T	0.012	0.012	8.3e-07	8.1e-07	0.0119300996975468	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.987690277933361
CAMB-722D6	MN908947.3	1091	C	T	0.02	0.0084	1.1e-07	5.9e-06	0.00942148760330578	TCC	ORF1ab:nsp2	P96S	C286T	CCC>TCC	Missense	ORF1ab:nsp2	0.990413223140496
CAMB-722D6	MN908947.3	11074	C	INS	0.15	0.14	1e-46	1.4e-57	0.143439340400471	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.843533568904594
CAMB-722D6	MN908947.3	11074	C	T	0.0078	0.012	0.00077	6.7e-08	0.0114016489988221	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.843533568904594
CAMB-722D6	MN908947.3	11083	G	-	0.16	0.17	7e-69	2.9e-77	0.170142676382041	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-722D6	MN908947.3	11083	G	T	0.84	0.83	0	0	0.829748243815175	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-722D6	MN908947.3	1314	C	T	1	1	0	0	0.99669093315685	ACT	ORF1ab:nsp2	T170I	C509T	ACT>ATT	Missense	ORF1ab:nsp2	0
CAMB-722D6	MN908947.3	14805	C	T	1	1	0	0	0.999456468989615	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	3.88236435989518e-05
CAMB-722D6	MN908947.3	17247	T	C	1	1	0	0	0.998881014546811	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000497326868084048
CAMB-722D6	MN908947.3	18613	T	C	0.13	0.17	2.9e-59	4e-80	0.163593818303376	GTT	ORF1ab:3'-to-5'-exonuclease	L192L	T574C	TTG>CTG	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.836406181696624
CAMB-722D6	MN908947.3	2306	CTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGC	-	0.0127076923076923	8.21538461538462e-05	1.6e-05;2.4e-05;8.5e-05;0.00011;1.7e-05;5.1e-05;2e-05;3e-05;3.8e-05;2.8e-05;1.4e-05;1.5e-05;0.00013;1.8e-05;1.4e-05;1.5e-05;1.6e-05;1.4e-05;1.1e-05;1.7e-05;5.8e-05;1.9e-05;3.3e-05;3.6e-05;1.5e-05;1.8e-05;2.1e-05;2.2e-05;2.3e-05;1.7e-05;1.9e-05;2e-05;1e-05;1.5e-05;1.5e-05;1.7e-05;1.4e-05;1.3e-05;1.7e-05;2.1e-05;1e-05;3.5e-05;2.9e-05;1.7e-05;1.8e-05;2.1e-05;1.7e-05;1.8e-05;1.7e-05;1.2e-05;1.7e-05;1.2e-05;1.4e-05;1.3e-05;1.2e-05;1.6e-05;8.3e-06;1e-05;1.5e-05;1.2e-05;2.1e-05;1.2e-05;5.9e-06;8.3e-06;9.4e-06	NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0061;NA;NA;0.051;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00155004428697963	GCT	ORF1ab:nsp2	.	1501-1565-delfrshift	.	no-SNV	ORF1ab:nsp2	0.99765708200213
CAMB-722D6	MN908947.3	23125	A	C	0.0043	0.0075	0.00014	1.8e-05	0.00712496085186345	CAG	S	P521P	A1563C	CCA>CCC	Synonymous	GU280_gp02, spike glycoprotein	0.991700595051676
CAMB-722D6	MN908947.3	24213	C	T	0.03	0.022	5.2e-11	5.9e-10	0.0227725956899325	TCT	S	S884F	C2651T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.977163074943712
CAMB-722D6	MN908947.3	25481	G	A	0.0051	0.01	0.00026	1.6e-06	0.00943368062811595	CGC	ORF3a	R30H	G89A	CGC>CAC	Missense	GU280_gp03	0.990387198853629
CAMB-722D6	MN908947.3	26144	G	T	1	1	8.5e-257	0	0.997612225405922	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000477554918815664
CAMB-722D6	MN908947.3	29284	C	T	0.0091	0.0071	4.3e-06	3.3e-05	0.00749063670411985	TCA	N	I337I	C1011T	ATC>ATT	Synonymous	GU280_gp10	0.99250936329588
CAMB-722D6	MN908947.3	3267	C	T	0.028	0.017	3.1e-13	3.4e-09	0.0181378988854515	ACT	ORF1ab:nsp3	T183I	C548T	ACT>ATT	Missense	ORF1ab:nsp3	0.981777344577701
CAMB-722D6	MN908947.3	3727	T	A	0.017	0.017	3.3e-06	1.5e-08	0.0170940170940171	TTG	ORF1ab:nsp3	F336L	T1008A	TTT>TTA	Missense	ORF1ab:nsp3	0.982905982905983
CAMB-722D6	MN908947.3	6459	A	G	1	1	0	0	0.999967020645076	AAT	ORF1ab:nsp3	N1247S	A3740G	AAT>AGT	Missense	ORF1ab:nsp3	3.29793549238177e-05
CAMB-722D6	MN908947.3	9491	C	T	0.0042	0.0075	0.0024	4.7e-05	0.00686400686400686	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.993135993135993
CAMB-722E5	MN908947.3	11074	C	INS	0.11	0.12	1.9e-29	1.1e-46	0.119368808800836	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.875777788839664
CAMB-722E5	MN908947.3	11083	G	-	0.17	0.16	3e-74	3.9e-69	0.158572370965174	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-722E5	MN908947.3	11083	G	T	0.83	0.84	0	0	0.841177407247333	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-722E5	MN908947.3	11222	G	A	1	1	0	0	0.999788225328251	GGT	ORF1ab:nsp6	V84I	G250A	GTC>ATC	Missense	ORF1ab:nsp6	7.05915572497529e-05
CAMB-722E5	MN908947.3	14805	C	T	1	1	0	0	0.998940256987681	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00060556743561115
CAMB-722E5	MN908947.3	21658	C	G	1	1	0	0	0.998983739837398	TCA	S	F32L	C96G	TTC>TTG	Missense	GU280_gp02, spike glycoprotein	0
CAMB-722E5	MN908947.3	2480	A	G	1	1	0	0	0.99978646166987	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-722E5	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-722E5	MN908947.3	26144	G	T	1	1	4e-226	0	0.999551569506726	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000448430493273543
CAMB-722E5	MN908947.3	28744	C	T	1	1	0	0	0.998866657948651	TCG	N	I157I	C471T	ATC>ATT	Synonymous	GU280_gp10	0.000479490867878471
CAMB-722E5	MN908947.3	4633	C	T	0.0066	0.0056	2.8e-05	8.7e-05	0.00579106737320212	GCT	ORF1ab:nsp3	G638G	C1914T	GGC>GGT	Synonymous	ORF1ab:nsp3	0.994208932626798
CAMB-722F4	MN908947.3	11074	C	INS	0.025	0.026	2e-05	5.9e-05	0.0256410256410256	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.973551383000202
CAMB-722F4	MN908947.3	11075	T	-	0.026	0.03	6.2e-08	2.2e-08	0.0295297372060858	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.965387275242047
CAMB-722F4	MN908947.3	14408	C	T	1	1	0	0	0.998159330900636	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00054897148577518
CAMB-722F4	MN908947.3	19629	A	G	0.013	0.0074	1.6e-06	1.8e-05	0.00787229389897223	AAA	ORF1ab:endoRNAse	E3E	A9G	GAA>GAG	Synonymous	ORF1ab:endoRNAse	0.991909031270501
CAMB-722F4	MN908947.3	21063	G	C	0.0068	0.0042	1.7e-05	0.00031	0.004476676515355	AGA	ORF1ab:2'-O-ribose-methyltransferase	K135N	G405C	AAG>AAC	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.995523323484645
CAMB-722F4	MN908947.3	23403	A	G	1	1	0	0	0.999167822468793	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.4013656246666e-05
CAMB-722F4	MN908947.3	24010	A	C	0.0071	0.01	6e-06	7.4e-07	0.00931506849315068	CAT	S	S816S	A2448C	TCA>TCC	Synonymous	GU280_gp02, spike glycoprotein	0.99054794520548
CAMB-722F4	MN908947.3	241	C	T	1	1	0	0	0.999512528029638	TCG	NA	NA	NA	NA	NA	NA	0.000146241591108511
CAMB-722F4	MN908947.3	25889	C	T	0.0078	0.0045	2.5e-05	0.00041	0.00539025442000862	TCA	ORF3a	S166L	C497T	TCA>TTA	Missense	GU280_gp03	0.994609745579991
CAMB-722F4	MN908947.3	27318	T	C	0.006	0.0058	4.2e-05	6.9e-05	0.0058656330749354	ATT	ORF6	N39N	T117C	AAT>AAC	Synonymous	GU280_gp06	0.993565891472868
CAMB-722F4	MN908947.3	27754	G	T	0.038	0.036	1.5e-07	7e-12	0.0359712230215827	AGA	ORF7a	E121*	G361T	GAA>TAA	Nonsense	GU280_gp07	0.964028776978417
CAMB-722F4	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998547567175018	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000176740897843761
CAMB-722F4	MN908947.3	29581	TT	-	0.013	0.018	7e-05;4.2e-06	5.4e-08;2.3e-09	0.0174972517405643	CTT	ORF10	.	24-25-delfrshift	.	no-SNV	GU280_gp11	0.98184472219688
CAMB-722F4	MN908947.3	3037	C	T	1	1	0	0	0.999198477106502	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-72300	MN908947.3	10039	C	T	0.61	0.6	0	0	0.60770291668795	CCT	ORF1ab:nsp4	T495T	C1485T	ACC>ACT	Synonymous	ORF1ab:nsp4	0.39229708331205
CAMB-72300	MN908947.3	10118	TG	CT	0.004859	0.0135	NA;1.9e-06	3.8e-08;2.7e-08	0.00708467615822897	TTG	ORF1ab:3C-like-proteinase	.	64-65-mnv	.	no-SNV	ORF1ab:3C-like-proteinase	0.996482872822324
CAMB-72300	MN908947.3	10119	G	T	0.0097	0.013	1.9e-06	2.7e-08	0.0106344165934734	TGT	ORF1ab:3C-like-proteinase	C22F	G65T	TGT>TTT	Missense	ORF1ab:3C-like-proteinase	0.989298020404027
CAMB-72300	MN908947.3	10770	A	G	0.0067	0.012	2.7e-05	2.6e-07	0.00841346153846154	TAT	ORF1ab:3C-like-proteinase	Y239C	A716G	TAT>TGT	Missense	ORF1ab:3C-like-proteinase	0.991586538461538
CAMB-72300	MN908947.3	11074	C	INS	0.12	0.033	1.6e-66	6.4e-07	0.103738749134549	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.895972767135934
CAMB-72300	MN908947.3	11083	G	-	0.22	0.2	1.7e-95	2.1e-90	0.211501705874998	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.0494525123698266
CAMB-72300	MN908947.3	11083	G	T	0.74	0.75	7.2e-268	4.6e-283	0.738920743797224	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.0494525123698266
CAMB-72300	MN908947.3	11322	C	T	0.032	0.026	2.9e-15	1.7e-13	0.0308455065576723	GCA	ORF1ab:nsp6	A117V	C350T	GCA>GTA	Missense	ORF1ab:nsp6	0.969120182534032
CAMB-72300	MN908947.3	13486	G	T	0.014	0.0089	6.4e-08	2.5e-05	0.0130153597413096	TGC	ORF1ab:RNA-dependent-RNA-polymerase	A7S	G19T	GCA>TCA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.986661277283751
CAMB-72300	MN908947.3	14805	C	T	0.91	0.96	0	0	0.923159221131214	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.0767694538884002
CAMB-72300	MN908947.3	1551	C	T	0.66	0.55	0	5.6e-173	0.638305446778213	GCT	ORF1ab:nsp2	A249V	C746T	GCT>GTT	Missense	ORF1ab:nsp2	0.361694553221787
CAMB-72300	MN908947.3	1605	ATG	-	0.0913333333333333	0.03	6.2e-42;2.5e-41;2.4e-41	6.3e-15;8.6e-15;8.7e-15	0.076154094212785	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.922666129276034
CAMB-72300	MN908947.3	16852	G	T	0.0077	0.0079	2.7e-05	1.6e-05	0.00772899834517668	TGG	ORF1ab:helicase	G206C	G616T	GGT>TGT	Missense	ORF1ab:helicase	0.984619877348389
CAMB-72300	MN908947.3	17898	C	T	0.044	0.04	2.7e-20	2e-19	0.0428601769911504	ACT	ORF1ab:helicase	H554H	C1662T	CAC>CAT	Synonymous	ORF1ab:helicase	0.957125663716814
CAMB-72300	MN908947.3	18687	C	T	0.93	0.88	0	0	0.920602278213909	GCT	ORF1ab:3'-to-5'-exonuclease	C216C	C648T	TGC>TGT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.0787807800289694
CAMB-72300	MN908947.3	18812	A	G	0.16	0.099	4.1e-72	4.2e-45	0.143501705733465	GAT	ORF1ab:3'-to-5'-exonuclease	D258G	A773G	GAT>GGT	Missense	ORF1ab:3'-to-5'-exonuclease	0.856470782436448
CAMB-72300	MN908947.3	1940	G	C	0.0076	0.0081	8.4e-06	2.7e-06	0.00768766015958666	TGT	ORF1ab:nsp2	V379L	G1135C	GTG>CTG	Missense	ORF1ab:nsp2	0.992187337236192
CAMB-72300	MN908947.3	21082	G	A	0.014	0.015	1.8e-07	1.5e-08	0.013879648111185	AGA	ORF1ab:2'-O-ribose-methyltransferase	E142K	G424A	GAA>AAA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.980261698824573
CAMB-72300	MN908947.3	21746	G	A	0.015	0.012	2.2e-08	4.3e-07	0.0135989879822897	TGT	S	V62I	G184A	GTT>ATT	Missense	GU280_gp02, spike glycoprotein	0.98629559350622
CAMB-72300	MN908947.3	23282	G	T	0.011	0.01	3.7e-05	3.9e-05	0.010677410828	TGA	S	D574Y	G1720T	GAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.98921845838373
CAMB-72300	MN908947.3	2480	A	G	0.97	0.98	0	0	0.975076156189421	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.0249238438105788
CAMB-72300	MN908947.3	24834	G	T	0.012	0.015	1.1e-06	1.1e-08	0.0125858246125173	CGT	S	R1091L	G3272T	CGT>CTT	Missense	GU280_gp02, spike glycoprotein	0.987382041367195
CAMB-72300	MN908947.3	25498	CCGATACAAGCCTCACTCCCTTTCGGATGGCTTATTG	-	0.000704648648648649	0.0136486486486486	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;8.9e-12;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.45;NA;NA	3.3e-05;2.3e-05;1.4e-05;5.4e-08;2.4e-08;5.6e-08;1.9e-07;2.5e-07;5.8e-08;1.4e-07;1.5e-07;2.7e-06;2.9e-06;1.1e-06;2.3e-06;1.8e-07;7.7e-08;1.1e-11;1.2e-07;5.6e-07;3.4e-07;7.9e-05;0.00029;0.00019;0.00013;7.1e-05;6.9e-05;8e-05;0.00014;6e-05;9.1e-05;4.1e-05;8.3e-05;3.9e-05;0.00016;0.00034;3e-05	0.00311941474894817	ACC	ORF3a	.	106-142-delfrshift	.	no-SNV	GU280_gp03	0.996702454839175
CAMB-72300	MN908947.3	2558	C	T	0.97	0.97	0	0	0.970330568858778	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.0296694311412218
CAMB-72300	MN908947.3	26144	G	T	0.93	0.98	0	2.6e-277	0.93509234828496	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.0649076517150396
CAMB-72300	MN908947.3	26296	C	A	0.028	0.045	6.7e-14	8e-21	0.0313826841425143	ACT	E	L18I	C52A	CTT>ATT	Missense	GU280_gp04	0.968586548520091
CAMB-72300	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0335675675675676	0.0187432432432432	1.2e-05;3.2e-07;9.5e-06;1.1e-05;1.8e-05;4.2e-06;6.3e-06;3.5e-05;3.4e-05;2e-05;2.7e-05;2.5e-05;3.2e-05;2.6e-05;3.2e-05;4.2e-05;2.3e-05;3.7e-05;2.9e-05;2.8e-05;2.1e-05;4.2e-05;2.2e-05;3.2e-05;2.7e-05;2.2e-05;3.5e-05;2.4e-05;1.4e-05;2.7e-05;3.4e-05;3.2e-05;2.6e-05;3.5e-05;1.2e-05;2.3e-05;1.7e-05	0.093;0.049;0.09;0.096;0.11;0.079;0.095;0.13;0.13;0.0021;0.0023;0.0021;0.0024;0.0023;0.00089;0.0012;0.0022;0.003;0.0022;0.0025;0.0023;0.0034;0.0021;0.0027;0.0024;0.0019;0.003;0.0024;0.00065;0.0024;0.003;0.0028;6.1e-05;0.0029;0.0014;0.00013;7.7e-05	0.0297378986782154	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.972879684418146
CAMB-72300	MN908947.3	26950	TGATCCTTCGTGGACATCTTCGTATT	-	0.00965384615384615	0.000357692307692308	8e-05;8.6e-05;1e-04;9.9e-05;9.9e-05;7.7e-05;8.1e-05;1e-04;2.4e-08;1.5e-08;5.9e-09;1.1e-08;5.8e-05;6.1e-05;6.7e-05;5.9e-05;5.1e-05;6e-05;2.6e-05;1.3e-05;4.6e-05;4.8e-05;2.7e-05;3.6e-05;3.7e-05;4.2e-05	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;2e-05;NA;NA;NA;NA;NA;NA;NA	0.00691753631112273	GTG	M	.	428-453-delfrshift	.	no-SNV	GU280_gp05	0.992939575905423
CAMB-72300	MN908947.3	27235	G	A	0.65	0.6	0	0	0.632912491808197	AGC	ORF6	A12T	G34A	GCA>ACA	Missense	GU280_gp06	0.367055925338134
CAMB-72300	MN908947.3	27895	T	G	0.007	0.011	4.6e-05	3.2e-06	0.00808580858085809	ATG	ORF8	M1R	T2G	ATG>AGG	Missense	GU280_gp09	0.991749174917492
CAMB-72300	MN908947.3	27897	AAATT	-	0.258	0.306	2.4e-100;3e-37;3e-30;7.2e-113;2.4e-36	6.6e-111;1.3e-43;1.7e-35;7.5e-123;2.5e-43	0.272003745318352	GAA	ORF8	.	4-8-delfrshift	.	no-SNV	GU280_gp09	0.733730522456462
CAMB-72300	MN908947.3	28253	C	T	0.037	0.04	4.9e-16	3.1e-18	0.0372589075382803	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.96235460836278
CAMB-7231F	MN908947.3	11075	T	-	0.038	0.043	2.6e-09	4e-11	0.0394589647106682	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957772579861464
CAMB-7231F	MN908947.3	14408	C	T	1	1	0	0	0.999277137464359	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000455135670588865
CAMB-7231F	MN908947.3	22363	G	T	1	1	5.8e-230	0	1	TGG	S	V267V	G801T	GTG>GTT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-7231F	MN908947.3	23403	A	G	1	1	0	0	0.999027049938348	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.88995067817509e-05
CAMB-7231F	MN908947.3	23663	G	T	1	1	0	0	0.999890793928142	TGC	S	A701S	G2101T	GCA>TCA	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7231F	MN908947.3	241	C	T	1	1	0	0	0.998754975382468	TCG	NA	NA	NA	NA	NA	NA	0.000245232121635132
CAMB-7231F	MN908947.3	24368	G	T	1	1	0	0	0.999953716560215	AGA	S	D936Y	G2806T	GAC>TAC	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7231F	MN908947.3	27046	C	T	1	1	0	0	0.999927639354543	ACG	M	T175M	C524T	ACG>ATG	Missense	GU280_gp05	7.23606454569575e-05
CAMB-7231F	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999531244365918	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000159464200287036
CAMB-7231F	MN908947.3	28903	G	T	1	1	0	0	0.9971277614269	TGG	N	M210I	G630T	ATG>ATT	Missense	GU280_gp10	0.00010637920641112
CAMB-7231F	MN908947.3	3037	C	T	1	1	0	0	0.999843088027616	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000156911972383493
CAMB-7231F	MN908947.3	376	G	T	1	1	0	0	0.9998877926408	AGG	ORF1ab:leader-protein	E37D	G111T	GAG>GAT	Missense	ORF1ab:leader-protein	4.80888682284862e-05
CAMB-7232E	MN908947.3	11075	T	-	0.15	0.0063	2.2e-37	0.0042	0.0967557335915834	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.903112206717436
CAMB-7232E	MN908947.3	13914	T	G	0.0014	0.0075	0.0045	8.2e-06	0.00371366372134716	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.996158278908951
CAMB-7232E	MN908947.3	14408	C	T	1	1	0	0	0.999727505586135	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000163496648318709
CAMB-7232E	MN908947.3	14419	G	T	0.045	0.059	9.7e-21	3.4e-27	0.0531344932339133	TGG	ORF1ab:RNA-dependent-RNA-polymerase	G318*	G952T	GGA>TGA	Nonsense	ORF1ab:RNA-dependent-RNA-polymerase	0.946589339961337
CAMB-7232E	MN908947.3	23403	A	G	1	1	0	0	1	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7232E	MN908947.3	241	C	T	1	1	0	0	0.999521492942021	TCG	NA	NA	NA	NA	NA	NA	0.000478507057979105
CAMB-7232E	MN908947.3	28690	G	T	1	1	0	0	0.999823633156967	TGA	N	L139F	G417T	TTG>TTT	Missense	GU280_gp10	0.00017636684303351
CAMB-7232E	MN908947.3	28881	GGG	AAC	1	1	2.5e-158;1.6e-170;3.8e-174	1.2e-127;1.2e-133;8.5e-137	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7232E	MN908947.3	3037	C	T	1	1	1.4e-145	2.7e-297	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7234C	MN908947.3	11075	T	-	0.037	0.042	3.5e-09	8.2e-11	0.03835334304516	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957301451750641
CAMB-7234C	MN908947.3	12513	C	T	0.014	0.012	2.2e-07	1.6e-06	0.0128491453754988	ACG	ORF1ab:nsp8	T141M	C422T	ACG>ATG	Missense	ORF1ab:nsp8	0.987016854267167
CAMB-7234C	MN908947.3	14408	C	T	1	1	0	0	0.997296464059573	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000486162164725971
CAMB-7234C	MN908947.3	20268	A	G	1	1	0	0	0.999340804218853	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-7234C	MN908947.3	23403	A	G	1	1	0	0	0.999545911016024	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00012225472645505
CAMB-7234C	MN908947.3	23929	C	T	0.021	0.022	1.3e-10	3.1e-11	0.0211429292292166	ACA	S	Y789Y	C2367T	TAC>TAT	Synonymous	GU280_gp02, spike glycoprotein	0.978793995206257
CAMB-7234C	MN908947.3	241	C	T	1	1	0	0	0.998607979906493	TCG	NA	NA	NA	NA	NA	NA	0.000181567838283579
CAMB-7234C	MN908947.3	28854	C	T	1	1	0	0	0.999381972126943	TCA	N	S194L	C581T	TCA>TTA	Missense	GU280_gp10	6.18027873057075e-05
CAMB-7234C	MN908947.3	3037	C	T	1	1	0	0	0.999405204460967	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.71747211895911e-05
CAMB-7234C	MN908947.3	6606	C	T	1	1	0	0	0.999524601854053	TCT	ORF1ab:nsp3	S1296F	C3887T	TCT>TTT	Missense	ORF1ab:nsp3	5.94247682434038e-05
CAMB-7236A	MN908947.3	11075	T	-	0.04	0.039	6.9e-10	4.1e-10	0.0395873235961129	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955442228828596
CAMB-7236A	MN908947.3	14097	C	T	1	1	0	0	0.998412681036465	TCG	ORF1ab:RNA-dependent-RNA-polymerase	F210F	C630T	TTC>TTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000153258382686182
CAMB-7236A	MN908947.3	14408	C	T	1	1	0	0	0.999202444339601	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000336995349464177
CAMB-7236A	MN908947.3	23403	A	G	1	1	0	0	0.998658287455421	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000147155569405492
CAMB-7236A	MN908947.3	241	C	T	1	1	0	0	0.998748358502955	TCG	NA	NA	NA	NA	NA	NA	6.15561391989494e-05
CAMB-7236A	MN908947.3	2416	C	T	1	1	0	0	0.998676248108926	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0
CAMB-7236A	MN908947.3	25563	G	T	1	1	0	0	0.999816277787985	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	6.12407373384775e-05
CAMB-7236A	MN908947.3	27944	C	T	0.0074	0.013	6.7e-05	3.9e-07	0.0102573018080668	ACC	ORF8	H17H	C51T	CAC>CAT	Synonymous	GU280_gp09	0.989568845618915
CAMB-7236A	MN908947.3	3037	C	T	1	1	0	0	0.998491419950971	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000188572506128606
CAMB-7236A	MN908947.3	686	AAGTCATTT	-	0.203333333333333	0.214444444444444	1.7e-28;8.8e-29;1.3e-24;3.4e-28;2.4e-24;1e-26;9.7e-31;1.1e-26;2.7e-22	5.2e-31;3.4e-31;1.8e-26;9.1e-31;4.6e-26;8.4e-29;3.1e-34;3.2e-29;6.3e-24	0.202849840324646	AAA	ORF1ab:leader-protein	.	421-429-delinframe	.	no-SNV	ORF1ab:leader-protein	0.7975055539978
CAMB-7236A	MN908947.3	860	G	A	1	1	0	0	0.999607950292849	TGA	ORF1ab:nsp2	E19K	G55A	GAG>AAG	Missense	ORF1ab:nsp2	0.00010692264740475
CAMB-72379	MN908947.3	10450	C	T	1	1	0	0	0.998794167134044	CCA	ORF1ab:3C-like-proteinase	P132P	C396T	CCC>CCT	Synonymous	ORF1ab:3C-like-proteinase	0.000560852495793606
CAMB-72379	MN908947.3	11074	C	INS	0.1	0.11	4.5e-40	2.7e-38	0.106571936056838	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.88854351687389
CAMB-72379	MN908947.3	11083	G	-	0.16	0.14	1.5e-70	1.4e-59	0.150976557338055	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-72379	MN908947.3	11083	G	T	0.84	0.86	0	0	0.848798794830457	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-72379	MN908947.3	14805	C	T	1	1	0	0	0.99863154293534	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000397293986514076
CAMB-72379	MN908947.3	17339	C	T	0.0073	0.0076	7.2e-05	4.7e-05	0.00740519720067271	GCA	ORF1ab:helicase	A368V	C1103T	GCA>GTA	Missense	ORF1ab:helicase	0.992472739109206
CAMB-72379	MN908947.3	246	G	A	0.047	0.048	9.8e-22	1.7e-22	0.0470370965151758	CGG	NA	NA	NA	NA	NA	NA	0.952705957925165
CAMB-72379	MN908947.3	2558	C	T	1	1	0	0	0.99910839383518	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	6.36861546299834e-05
CAMB-72379	MN908947.3	26144	G	T	1	1	0	0	0.999927436325376	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	7.2563674624483e-05
CAMB-72379	MN908947.3	26408	C	T	0.15	0.15	1.5e-70	2.1e-66	0.151383952611739	TCT	E	S55F	C164T	TCT>TTT	Missense	GU280_gp04	0.844760366182014
CAMB-72379	MN908947.3	3016	T	G	0.014	0.012	2.4e-05	7.9e-05	0.0124730833299476	CTT	ORF1ab:nsp3	A99A	T297G	GCT>GCG	Synonymous	ORF1ab:nsp3	0.98736440092634
CAMB-72379	MN908947.3	3874	C	T	0.063	0.068	2.3e-28	2.8e-30	0.0646434237825963	TCG	ORF1ab:nsp3	I385I	C1155T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.93507180342541
CAMB-72379	MN908947.3	5542	G	A	0.0081	0.0051	1.7e-05	0.00029	0.00656530753282654	AGA	ORF1ab:nsp3	Q941Q	G2823A	CAG>CAA	Synonymous	ORF1ab:nsp3	0.993434692467173
CAMB-72388	MN908947.3	14408	C	T	1	1	0	0	0.99958272480701	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000347729327491481
CAMB-72388	MN908947.3	16289	C	T	1	1	1.7e-205	0	1	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0
CAMB-72388	MN908947.3	22095	A	G	1	1	0	0	1	GAC	S	D178G	A533G	GAC>GGC	Missense	GU280_gp02, spike glycoprotein	0
CAMB-72388	MN908947.3	23403	A	G	1	1	0	0	0.999890093786635	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.1588511137163e-05
CAMB-72388	MN908947.3	241	C	T	1	0.95	0	0	0.97734763274915	TCG	NA	NA	NA	NA	NA	NA	0.000156944807742611
CAMB-72388	MN908947.3	25429	G	T	1	1	0	0	0.999919617378723	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	4.01913106386399e-05
CAMB-72388	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0569815135135135	0.0472432432432432	NA;NA;NA;0.5;0.5;7.6e-15;2.1e-13;1.1e-11;1e-11;1.8e-12;4.1e-12;2.6e-12;9.2e-12;4.5e-12;7.2e-12;1.6e-11;2.9e-12;1.4e-11;5.5e-12;5.7e-12;3.5e-12;1.4e-11;5e-12;8.6e-12;5e-12;2.3e-12;9.3e-12;3.7e-12;1.4e-13;6.2e-12;9.6e-12;8.1e-12;4.2e-12;1.1e-11;5.2e-13;3.4e-12;2.6e-12	1.6e-08;8.5e-11;4.9e-09;5e-09;2.9e-08;3.6e-10;3.8e-09;4.9e-08;4.4e-08;2.4e-08;2.4e-08;1.8e-08;2.9e-08;2.6e-08;4e-08;6.9e-08;2.1e-08;5.6e-08;2e-08;3.4e-08;3.3e-08;6.7e-08;3.2e-08;4.2e-08;2.9e-08;1.4e-08;4e-08;2.8e-08;3.9e-10;3.5e-08;5.4e-08;3.9e-08;1.4e-08;5.6e-08;4e-09;2.4e-08;1.2e-08	0.0553343314962887	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.977833370277716
CAMB-72388	MN908947.3	27030	G	T	0.028	0.069	2e-13	1.9e-27	0.0342708579532026	TGT	M	V170F	G508T	GTT>TTT	Missense	GU280_gp05	0.965729142046797
CAMB-72388	MN908947.3	29070	AAGCATACAATGTAACACAAGCTT	-	0.00108333333333333	0.0352916666666667	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;8.7e-11;NA;NA;NA;NA;NA	4.7e-08;4.3e-08;3.4e-08;4.3e-08;4.3e-08;2.5e-07;6.5e-08;2.5e-08;4.9e-08;4.8e-09;4.3e-08;2.2e-08;3e-10;3.3e-10;1.1e-13;1.9e-13;1.6e-12;1.3e-13;7.7e-14;1.2e-13;4.6e-12;8.5e-14;5.7e-14;2.7e-14	0.00709874352239654	AAA	N	.	797-820-delinframe	.	no-SNV	GU280_gp10	0.992979637455904
CAMB-72388	MN908947.3	2919	C	T	1	1	0	0	1	CCA	ORF1ab:nsp3	P67L	C200T	CCA>CTA	Missense	ORF1ab:nsp3	0
CAMB-72388	MN908947.3	3037	C	T	1	1	3.3e-246	0	0.998411016949153	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-723A6	MN908947.3	1059	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0
CAMB-723A6	MN908947.3	11075	T	-	0.09	0.0053	1.2e-22	0.0078	0.0575610097685655	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.942263926333112
CAMB-723A6	MN908947.3	14408	C	T	1	1	0	0	0.999613955508372	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000337788930174203
CAMB-723A6	MN908947.3	23403	A	G	1	1	0	0	0.999937202694004	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.70979794966796e-05
CAMB-723A6	MN908947.3	241	C	T	1	1	0	0	0.999714357125004	TCG	NA	NA	NA	NA	NA	NA	0.000178526796872211
CAMB-723A6	MN908947.3	25563	G	T	1	1	0	0	0.999891583245998	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	3.61389180007951e-05
CAMB-723A6	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.0583658536585366	0.0293170731707317	6.9e-11;4.7e-14;3e-11;2.8e-11;1.7e-10;6.8e-13;8.2e-12;3.3e-10;3.3e-10;9.9e-11;1.5e-10;7e-11;3.2e-10;1.6e-10;2.4e-10;4.8e-10;1.3e-10;4e-10;2.4e-10;2.2e-10;1.3e-10;4.5e-10;1.3e-10;2.8e-10;2.1e-10;8.6e-11;3.2e-10;1.6e-10;2.3e-10;1.4e-10;3.4e-10;2.6e-10;1.4e-10;3.3e-10;3e-11;1.3e-10;6.7e-11;6.4e-08;1.1e-06;2.5e-07;5.9e-07	8.8e-06;4.1e-07;5.4e-06;5.7e-06;1.5e-05;1.1e-06;4e-06;2.3e-05;2.4e-05;1.8e-05;1.5e-05;1.1e-05;2.2e-05;1.7e-05;2.1e-05;3.2e-05;1.5e-05;2.7e-05;1.7e-05;2e-05;1.7e-05;3.1e-05;1.5e-05;2.2e-05;1.8e-05;1.1e-05;2.5e-05;1.8e-05;7.6e-06;1.6e-05;2.6e-05;2.3e-05;1.1e-05;2.6e-05;6.8e-06;1.6e-05;8.2e-06;NA;NA;NA;NA	0.0452240067624683	GTC	M	.	258-298-delfrshift	.	no-SNV	GU280_gp05	0.954668916958941
CAMB-723A6	MN908947.3	28197	TG	-	0.0325	0.0275	2e-06;5.7e-20	6.2e-11;2.3e-11	0.0308400129398656	TTG	ORF8	.	304-305-delfrshift	.	no-SNV	GU280_gp09	0.97961530038689
CAMB-723A6	MN908947.3	3037	C	T	1	1	6.2e-307	0	0.99917593737124	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-723A6	MN908947.3	3564	G	T	0.034	0.03	5e-06	1.2e-06	0.0317460317460317	GGT	ORF1ab:nsp3	G282V	G845T	GGT>GTT	Missense	ORF1ab:nsp3	0.968253968253968
CAMB-723A6	MN908947.3	9438	C	T	0.026	0.036	1.7e-10	6e-12	0.0293814432989691	ACA	ORF1ab:nsp4	T295I	C884T	ACA>ATA	Missense	ORF1ab:nsp4	0.970618556701031
CAMB-723B5	MN908947.3	1434	AATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCGCACTA	-	0.011047619047619	0.00544761904761905	3.4e-06;6.1e-06;5.6e-06;6.9e-06;6.9e-06;2.6e-05;7.8e-06;4e-06;2.7e-06;4.9e-06;8.2e-06;1.9e-05;7.2e-06;6.1e-06;5.9e-06;7.1e-06;6.6e-06;4e-06;4e-06;1.2e-05;1.1e-05;2.4e-06;5.1e-06;1.3e-05;2.9e-05;4.7e-06;3.3e-06;2.5e-06;8.9e-06;1.3e-05;1.8e-05;1.5e-05;8.8e-06;7.9e-06;7.5e-06;1.6e-05;1.4e-05;8e-06;6.5e-06;1.1e-05;1.7e-05;1.3e-05	0.00087;0.00051;0.00092;0.0018;0.0015;0.0082;0.002;0.00053;7.5e-06;1e-06;0.0026;0.0083;0.0022;0.0021;0.002;0.0027;0.0021;0.0024;0.0028;0.0041;0.0054;0.0027;0.0021;0.0051;0.01;0.003;0.0035;0.002;0.0035;0.0042;0.0066;0.0087;0.0037;0.0025;0.003;1.1e-06;5.2e-07;0.0028;0.003;0.0049;0.0081;0.0085	0.00866089273817455	GAA	ORF1ab:nsp2	.	629-670-delinframe	.	no-SNV	ORF1ab:nsp2	0.990889978976875
CAMB-723B5	MN908947.3	14408	C	T	1	1	0	0	0.999474071736615	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000455804494933558
CAMB-723B5	MN908947.3	1469	CG	-	0.011	0.0195	1.6e-05;1.4e-05	1.1e-06;5.2e-07	0.0136518771331058	TCG	ORF1ab:nsp2	.	664-665-delfrshift	.	no-SNV	ORF1ab:nsp2	0.98674618952949
CAMB-723B5	MN908947.3	1781	TG	-	0.0092	0.0045	4.1e-06;1.6e-05	NA;1.5e-05	0.00728744939271255	CTG	ORF1ab:nsp2	.	976-977-delfrshift	.	no-SNV	ORF1ab:nsp2	0.994169271459485
CAMB-723B5	MN908947.3	1782	G	-	0.0088	0.009	1.6e-05	1.5e-05	0.00886188830676625	TGT	ORF1ab:nsp2	.	977-977-delfrshift	.	no-SNV	ORF1ab:nsp2	0.9909151711069
CAMB-723B5	MN908947.3	18289	C	T	0.016	0.0054	1.6e-08	0.00088	0.0112875422661274	ACG	ORF1ab:3'-to-5'-exonuclease	R84C	C250T	CGT>TGT	Missense	ORF1ab:3'-to-5'-exonuclease	0.988712457733873
CAMB-723B5	MN908947.3	18825	A	G	0.017	0.029	4.1e-09	1.7e-14	0.0220067626893833	AAG	ORF1ab:3'-to-5'-exonuclease	Q262Q	A786G	CAA>CAG	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.977955874385847
CAMB-723B5	MN908947.3	23242	GC	TG	0.01	0.011755	3.1e-05;2.6e-05	0.48;8.5e-11	0.0108991123536156	TGC	S	.	1680-1681-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.993210500070324
CAMB-723B5	MN908947.3	23243	C	G	0.01	0.023	2.6e-05	8.5e-11	0.0151884930937792	GCC	S	P561A	C1681G	CCT>GCT	Missense	GU280_gp02, spike glycoprotein	0.984616782635788
CAMB-723B5	MN908947.3	23281	TG	GT	0.0048	0.012	NA;9.1e-05	7.2e-08;2.7e-05	0.00748742885561143	CTG	S	.	1719-1720-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.987970182015137
CAMB-723B5	MN908947.3	23285	G	T	0.01	0.012	3.5e-05	7.9e-06	0.0110556683837474	TGC	S	A575S	G1723T	GCT>TCT	Missense	GU280_gp02, spike glycoprotein	0.983416497424379
CAMB-723B5	MN908947.3	23285	GC	TG	0.0105	0.006255	3.5e-05;2.7e-05	7.9e-06;0.48	0.00893821559732124	TGC	S	.	1723-1724-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.983416497424379
CAMB-723B5	MN908947.3	23403	A	G	1	1	0	0	0.99990091038583	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.6703412398588e-05
CAMB-723B5	MN908947.3	241	C	T	1	1	0	0	0.99974358974359	TCG	NA	NA	NA	NA	NA	NA	0.000230769230769231
CAMB-723B5	MN908947.3	25350	C	T	1	1	0	0	0.999763235154844	CCA	S	P1263L	C3788T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	0.000189411876124633
CAMB-723B5	MN908947.3	29485	C	T	0.011	0.036	2.9e-05	1.3e-08	0.0172811059907834	CCA	N	S404S	C1212T	TCC>TCT	Synonymous	GU280_gp10	0.982718894009217
CAMB-723B5	MN908947.3	3037	C	T	1	1	0	0	0.999750499001996	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-723B5	MN908947.3	3293	C	T	0.011	0.023	8.5e-07	5.1e-12	0.0150912458628124	ACC	ORF1ab:nsp3	P192S	C574T	CCT>TCT	Missense	ORF1ab:nsp3	0.984878389457383
CAMB-723B5	MN908947.3	5222	AC	GG	0.0165	0.028	2.2e-05;3.6e-05	4e-07;9.3e-07	0.0208333333333333	CAC	ORF1ab:nsp3	.	2503-2504-mnv	.	no-SNV	ORF1ab:nsp3	0.978288633461047
CAMB-723B5	MN908947.3	5225	A	C	0.016	0.036	3.6e-05	4.2e-08	0.0240506329113924	TAA	ORF1ab:nsp3	K836Q	A2506C	AAA>CAA	Missense	ORF1ab:nsp3	0.973417721518987
CAMB-723B5	MN908947.3	5229	AG	-	0.017	0.036	6e-05;5.8e-05	1.9e-07;1.3e-07	0.0244845360824742	AAG	ORF1ab:nsp3	.	2510-2511-delfrshift	.	no-SNV	ORF1ab:nsp3	0.974598930481283
CAMB-723C4	MN908947.3	10313	C	T	0.14	0.15	2.2e-66	2.6e-70	0.146897765608957	ACT	ORF1ab:3C-like-proteinase	L87F	C259T	CTT>TTT	Missense	ORF1ab:3C-like-proteinase	0.85302889551655
CAMB-723C4	MN908947.3	11074	C	INS	0.09	0.11	1.7e-33	6.1e-37	0.0974915917206229	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.89733750166684
CAMB-723C4	MN908947.3	11083	G	-	0.16	0.17	2.9e-72	5.6e-76	0.166144691512684	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.60987576991335e-05
CAMB-723C4	MN908947.3	11083	G	T	0.84	0.83	0	0	0.833711765319971	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.60987576991335e-05
CAMB-723C4	MN908947.3	12476	A	G	0.035	0.019	3.8e-17	2.8e-10	0.0280199746353836	AAT	ORF1ab:nsp8	M129V	A385G	ATG>GTG	Missense	ORF1ab:nsp8	0.971960209258085
CAMB-723C4	MN908947.3	13348	G	T	1	1	0	0	0.999828197945845	TGG	ORF1ab:nsp10	V108V	G324T	GTG>GTT	Synonymous	ORF1ab:nsp10	1.49393090569561e-05
CAMB-723C4	MN908947.3	14805	C	T	1	1	0	0	0.999934524978721	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	3.92850127676292e-05
CAMB-723C4	MN908947.3	18877	C	T	0.018	0.0056	2.2e-09	0.00028	0.0131105807478123	TCT	ORF1ab:3'-to-5'-exonuclease	L280L	C838T	CTA>TTA	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.986873508353222
CAMB-723C4	MN908947.3	1917	C	T	0.0093	0.0064	2.4e-06	3.5e-05	0.0083285554784393	ACT	ORF1ab:nsp2	T371I	C1112T	ACT>ATT	Missense	ORF1ab:nsp2	0.991671444521561
CAMB-723C4	MN908947.3	21622	C	T	0.056	0.036	8.3e-20	3.7e-10	0.0503505417463352	CCA	S	T20T	C60T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.949649458253665
CAMB-723C4	MN908947.3	22846	T	C	1	1	0	0	0.999640783092858	ATT	S	D428D	T1284C	GAT>GAC	Synonymous	GU280_gp02, spike glycoprotein	1.99564948412461e-05
CAMB-723C4	MN908947.3	23566	AGGTA	-	0.01332	0.0388	0.29;0.3;0.29;0.0036;0.0039	0.00096;0.00069;0.00062;5e-05;1e-05	0.0170654468684025	CAG	S	.	2004-2008-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.982846586910626
CAMB-723C4	MN908947.3	2370	C	T	1	1	0	0	1	GCC	ORF1ab:nsp2	A522V	C1565T	GCC>GTC	Missense	ORF1ab:nsp2	0
CAMB-723C4	MN908947.3	24459	TTAGCTCCAA	-	0.00305	0.00688	0.0068;0.0067;0.0083;0.01;0.01;0.01;0.011;0.01;0.014;0.0098	0.00044;0.00042;0.00057;0.00069;0.00066;0.00072;2.3e-05;2e-05;0.00095;0.00062	0.00375344065393277	CTT	S	.	2897-2906-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.996187732971874
CAMB-723C4	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-723C4	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-723C4	MN908947.3	26144	G	T	1	1	0	0	0.999774774774775	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-723C4	MN908947.3	28085	G	T	0.01	0.011	4.8e-06	2.6e-06	0.0108585858585859	AGG	ORF8	E64D	G192T	GAG>GAT	Missense	GU280_gp09	0.988888888888889
CAMB-723C4	MN908947.3	522	T	-	0.042	0.028	2.2e-05	9e-04	0.0369235657225853	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.962985657225853
CAMB-723C4	MN908947.3	664	C	T	0.14	0.11	9.3e-64	8.4e-53	0.130037383818637	GCC	ORF1ab:leader-protein	G133G	C399T	GGC>GGT	Synonymous	ORF1ab:leader-protein	0.869911170559385
CAMB-723C4	MN908947.3	9925	A	T	0.0011	0.0062	0.0068	3.4e-05	0.00268343815513627	CAA	ORF1ab:nsp4	A457A	A1371T	GCA>GCT	Synonymous	ORF1ab:nsp4	0.997232704402516
CAMB-723E2	MN908947.3	11074	C	INS	0.022	0.026	0.00036	1.9e-05	0.0225264823524241	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.976880137136829
CAMB-723E2	MN908947.3	11075	T	-	0.03	0.029	5.5e-08	1.9e-08	0.0301203670144784	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.96593098449154
CAMB-723E2	MN908947.3	14408	C	T	1	1	0	0	0.997898735879505	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000470683162990855
CAMB-723E2	MN908947.3	15720	C	T	0.021	0.019	1.6e-10	7.8e-10	0.0203613157955145	ACG	ORF1ab:RNA-dependent-RNA-polymerase	D751D	C2253T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.979432086862705
CAMB-723E2	MN908947.3	162	C	T	0.82	0.81	0	0	0.816960945683076	ACA	NA	NA	NA	NA	NA	NA	0.182945533443064
CAMB-723E2	MN908947.3	1820	G	A	1	0.99	0	0	0.995398208369125	AGG	ORF1ab:nsp2	G339S	G1015A	GGT>AGT	Missense	ORF1ab:nsp2	0.000122714443489999
CAMB-723E2	MN908947.3	23403	A	G	1	1	0	0	0.999404991074866	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000105001575023625
CAMB-723E2	MN908947.3	241	C	T	1	1	0	0	0.998473563218391	TCG	NA	NA	NA	NA	NA	NA	0.000220689655172414
CAMB-723E2	MN908947.3	24383	A	G	0.0034	0.0063	0.00096	4.7e-05	0.00408910588953311	CAC	S	T941A	A2821G	ACA>GCA	Missense	GU280_gp02, spike glycoprotein	0.995666768385719
CAMB-723E2	MN908947.3	26163	T	C	0.013	0.013	3.2e-07	3.9e-07	0.0130252576735757	ATC	ORF3a	N257N	T771C	AAT>AAC	Synonymous	GU280_gp03	0.986238532110092
CAMB-723E2	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.02425	0.0279375	0.00068;0.0019;0.00067;0.00066;0.00035;0.00045;0.00039;0.00063;5e-04;0.00053;0.00071;0.00043;0.00068;0.00057;0.00053;0.00048;0.00076;0.00055;0.00062;0.00053;0.00047;0.00066;0.00048;0.00041;0.00048;0.00066;0.00059;0.00038;0.00066;0.00031;0.00044;0.00037	5.7e-05;0.00018;0.00014;0.00014;9.7e-05;8.3e-05;7e-05;0.00011;9.9e-05;0.00011;0.00016;8.7e-05;0.00014;9.5e-05;0.00011;0.00011;0.00017;0.00012;0.00012;1e-04;7.5e-05;0.00013;1e-04;4.1e-05;9.5e-05;0.00014;0.00013;5.8e-05;0.00016;5e-05;9e-05;5.2e-05	0.0247445335677398	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.974836520155616
CAMB-723E2	MN908947.3	28514	G	T	1	1	0	0	0.998325782942683	AGA	N	D81Y	G241T	GAT>TAT	Missense	GU280_gp10	0.000393933425251133
CAMB-723E2	MN908947.3	29040	A	T	0.13	0.14	4.2e-61	2.2e-62	0.132810131698609	AAG	N	K256M	A767T	AAG>ATG	Missense	GU280_gp10	0.866903566977668
CAMB-723E2	MN908947.3	29700	A	G	0.019	0.016	4.1e-09	4.7e-07	0.0180203708540089	TAG	NA	NA	NA	NA	NA	NA	0.981979629145991
CAMB-723E2	MN908947.3	3037	C	T	1	1	0	0	0.999318986652138	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000136202669572324
CAMB-723E2	MN908947.3	3425	C	T	0.022	0.024	2.3e-11	3.6e-12	0.0223449739412664	ACC	ORF1ab:nsp3	P236S	C706T	CCA>TCA	Missense	ORF1ab:nsp3	0.977655026058734
CAMB-723F1	MN908947.3	13914	T	G	0.0068	0.017	5e-05	3.2e-07	0.00988947062245491	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.990110529377545
CAMB-723F1	MN908947.3	14408	C	T	1	1	0	0	0.998918918918919	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000810810810810811
CAMB-723F1	MN908947.3	14562	T	C	0.0085	0.0038	2e-05	0.00068	0.0053394355453852	ATG	ORF1ab:RNA-dependent-RNA-polymerase	Y365Y	T1095C	TAT>TAC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.994660564454615
CAMB-723F1	MN908947.3	23403	A	G	1	1	0	0	0.999741294562012	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000206964350390645
CAMB-723F1	MN908947.3	241	C	T	1	1	0	0	0.999820515121601	TCG	NA	NA	NA	NA	NA	NA	8.97424391994974e-05
CAMB-723F1	MN908947.3	28881	GGG	AAC	1	0.996666666666667	0;0;0	1.5e-222;1.2e-236;1.3e-251	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-723F1	MN908947.3	3037	C	T	1	1	4.6e-91	1.6e-241	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-723F1	MN908947.3	683	C	T	1	0.97	0	0	0.993655254641458	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	4.25821836143757e-05
CAMB-7240D	MN908947.3	11075	T	-	0.034	0.029	1.2e-08	4.4e-08	0.0321242804632776	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.965240307927041
CAMB-7240D	MN908947.3	14408	C	T	1	1	0	0	0.997574236721037	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000376411543287328
CAMB-7240D	MN908947.3	23403	A	G	1	1	0	0	0.999115214054238	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.39604298140884e-05
CAMB-7240D	MN908947.3	241	C	T	1	1	0	0	0.99903862153118	TCG	NA	NA	NA	NA	NA	NA	0.000221856569727671
CAMB-7240D	MN908947.3	25728	C	T	0.44	0.45	2e-240	4.5e-241	0.446178413297525	TCT	ORF3a	V112V	C336T	GTC>GTT	Synonymous	GU280_gp03	0.553603832474414
CAMB-7240D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999498688878606	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7240D	MN908947.3	3037	C	T	1	1	0	0	0.999800981823006	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.63393923311662e-05
CAMB-7240D	MN908947.3	6883	C	T	0.43	0.4	3.2e-151	2e-120	0.414648910411622	TCG	ORF1ab:nsp3	V1388V	C4164T	GTC>GTT	Synonymous	ORF1ab:nsp3	0.585351089588378
CAMB-7241C	MN908947.3	11075	T	-	0.033	0.032	1.5e-08	1.1e-08	0.0325963596661351	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.963898346478185
CAMB-7241C	MN908947.3	14408	C	T	1	1	0	0	0.998706047819972	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000618846694796062
CAMB-7241C	MN908947.3	15451	G	A	0.0077	0.0061	2e-05	6.1e-05	0.00723087139378735	CGG	ORF1ab:RNA-dependent-RNA-polymerase	G662S	G1984A	GGT>AGT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.992732236405224
CAMB-7241C	MN908947.3	17118	C	T	0.0071	0.0072	2.9e-05	2.1e-05	0.00717956406220068	GCC	ORF1ab:helicase	G294G	C882T	GGC>GGT	Synonymous	ORF1ab:helicase	0.992787120095283
CAMB-7241C	MN908947.3	21898	G	T	0.0094	0.009	3.8e-06	5.1e-06	0.00918576652100241	CGA	S	S112S	G336T	TCG>TCT	Synonymous	GU280_gp02, spike glycoprotein	0.990635869080531
CAMB-7241C	MN908947.3	23403	A	G	1	1	0	0	0.999024813089175	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.58478708419114e-05
CAMB-7241C	MN908947.3	241	C	T	1	1	0	0	0.998966038336117	TCG	NA	NA	NA	NA	NA	NA	0.000198838781515947
CAMB-7241C	MN908947.3	25251	T	C	0.0062	0.0073	8.4e-05	2.4e-05	0.00662830504770923	GTG	S	V1230A	T3689C	GTG>GCG	Missense	GU280_gp02, spike glycoprotein	0.993371694952291
CAMB-7241C	MN908947.3	26270	C	T	0.028	0.031	1.9e-13	1.4e-14	0.029123364292373	ACA	E	T9I	C26T	ACA>ATA	Missense	GU280_gp04	0.970652211442185
CAMB-7241C	MN908947.3	28093	C	T	0.019	0.015	5.8e-09	1.4e-07	0.0172058823529412	TCT	ORF8	S67F	C200T	TCT>TTT	Missense	GU280_gp09	0.981470588235294
CAMB-7241C	MN908947.3	28514	G	T	1	1	0	0	0.998301613467206	AGA	N	D81Y	G241T	GAT>TAT	Missense	GU280_gp10	0.000149857635246516
CAMB-7241C	MN908947.3	28868	C	T	0.015	0.016	1.3e-07	5e-08	0.0156751373879689	TCC	N	P199S	C595T	CCA>TCA	Missense	GU280_gp10	0.984140449230996
CAMB-7241C	MN908947.3	3037	C	T	1	1	0	0	0.999334995843724	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7241C	MN908947.3	3602	C	T	1	1	0	0	0.999471039407564	ACA	ORF1ab:nsp3	H295Y	C883T	CAC>TAC	Missense	ORF1ab:nsp3	0
CAMB-7242B	MN908947.3	10202	C	T	0.083	0.084	1.8e-37	3.5e-38	0.0831082688459439	GCT	ORF1ab:3C-like-proteinase	L50F	C148T	CTT>TTT	Missense	ORF1ab:3C-like-proteinase	0.916863743860287
CAMB-7242B	MN908947.3	11074	C	INS	0.25	0.26	3.5e-159	6.3e-132	0.249854034101592	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.746078712729216
CAMB-7242B	MN908947.3	11083	G	-	0.15	0.13	8.8e-64	1.5e-54	0.139532153757497	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.06716752395791e-05
CAMB-7242B	MN908947.3	11083	G	T	0.85	0.87	0	0	0.860275756088191	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.06716752395791e-05
CAMB-7242B	MN908947.3	14805	C	T	1	1	0	0	0.999256520316821	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000128869811750944
CAMB-7242B	MN908947.3	17247	T	C	1	1	0	0	0.998417276308385	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000691708872631776
CAMB-7242B	MN908947.3	1782	G	T	0.011	0.0093	1.2e-06	3.5e-06	0.0103223119599006	TGT	ORF1ab:nsp2	C326F	G977T	TGT>TTT	Missense	ORF1ab:nsp2	0.98903812116074
CAMB-7242B	MN908947.3	18555	C	T	0.017	0.016	5.7e-09	7.2e-09	0.0163017907060419	ACA	ORF1ab:3'-to-5'-exonuclease	D172D	C516T	GAC>GAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.983615178101907
CAMB-7242B	MN908947.3	19696	A	G	0.011	0.0053	8.2e-07	0.00012	0.00915802638479848	TAT	ORF1ab:endoRNAse	I26V	A76G	ATC>GTC	Missense	ORF1ab:endoRNAse	0.990841973615202
CAMB-7242B	MN908947.3	25000	C	T	0.011	0.0089	1.4e-06	4.8e-06	0.00986520804844696	ACT	S	D1146D	C3438T	GAC>GAT	Synonymous	GU280_gp02, spike glycoprotein	0.989988278960734
CAMB-7242B	MN908947.3	26144	G	T	1	1	0	0	0.999640649705333	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000143740117866897
CAMB-7242B	MN908947.3	2745	A	T	0.019	0.019	1.1e-09	4.6e-10	0.0189728875095157	GAT	ORF1ab:nsp3	D9V	A26T	GAT>GTT	Missense	ORF1ab:nsp3	0.980734321016572
CAMB-7242B	MN908947.3	27493	C	T	0.01	0.0075	3.1e-06	4e-05	0.009222906654031	ACC	ORF7a	P34S	C100T	CCT>TCT	Missense	GU280_gp07	0.990633249847695
CAMB-7242B	MN908947.3	27503	C	T	0.026	0.024	6.2e-13	2.9e-12	0.0250812027383013	TCT	ORF7a	S37F	C110T	TCT>TTT	Missense	GU280_gp07	0.974893221596092
CAMB-7242B	MN908947.3	28389	A	G	0.0069	0.0074	7e-05	3.1e-05	0.00705052878965922	CAA	N	Q39R	A116G	CAA>CGA	Missense	GU280_gp10	0.992655699177438
CAMB-7242B	MN908947.3	29151	G	A	0.13	0.14	1.8e-60	4.1e-64	0.134604824061167	AGA	N	R293K	G878A	AGA>AAA	Missense	GU280_gp10	0.865120601529168
CAMB-7242B	MN908947.3	3539	G	A	0.0096	0.0099	1.2e-05	1e-05	0.0097442143727162	AGC	ORF1ab:nsp3	A274T	G820A	GCT>ACT	Missense	ORF1ab:nsp3	0.990255785627284
CAMB-7242B	MN908947.3	9180	C	T	0.034	0.027	3.2e-16	2.1e-13	0.0309265043756615	TCT	ORF1ab:nsp4	S209F	C626T	TCT>TTT	Missense	ORF1ab:nsp4	0.969047680512172
CAMB-7242B	MN908947.3	9438	C	T	0.17	0.18	9.8e-75	3.9e-81	0.169894566098946	ACA	ORF1ab:nsp4	T295I	C884T	ACA>ATA	Missense	ORF1ab:nsp4	0.830105433901054
CAMB-7242B	MN908947.3	9491	C	T	0.026	0.015	1.3e-12	5.2e-08	0.0229155707522357	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.977018674381904
CAMB-7242B	MN908947.3	9519	T	C	0.092	0.098	5.6e-42	4.2e-45	0.0941768169141659	TTC	ORF1ab:nsp4	F322S	T965C	TTC>TCC	Missense	ORF1ab:nsp4	0.905799346888184
CAMB-7242B	MN908947.3	9603	C	T	0.0096	0.011	3.4e-06	5.9e-07	0.0101444170482564	ACA	ORF1ab:nsp4	T350I	C1049T	ACA>ATA	Missense	ORF1ab:nsp4	0.989832100504873
CAMB-7242B	MN908947.3	9634	A	T	0.082	0.076	1.6e-37	7.4e-35	0.0796334607844199	TAG	ORF1ab:nsp4	L360F	A1080T	TTA>TTT	Missense	ORF1ab:nsp4	0.919034260151858
CAMB-7242B	MN908947.3	9636	C	T	0.023	0.026	9.1e-12	3e-13	0.0244312108718888	GCA	ORF1ab:nsp4	A361V	C1082T	GCA>GTA	Missense	ORF1ab:nsp4	0.975204670119924
CAMB-7242B	MN908947.3	9737	A	G	0.17	0.17	6.7e-80	4.1e-80	0.171492806727412	TAG	ORF1ab:nsp4	S395G	A1183G	AGT>GGT	Missense	ORF1ab:nsp4	0.828496384448264
CAMB-7242B	MN908947.3	9744	A	G	0.012	0.0066	4e-07	3.1e-05	0.0098263421154308	TAC	ORF1ab:nsp4	Y397C	A1190G	TAC>TGC	Missense	ORF1ab:nsp4	0.990017021187724
CAMB-7242B	MN908947.3	9917	A	C	0.021	0.024	2.1e-10	6.2e-12	0.0219070778368375	TAG	ORF1ab:nsp4	S455R	A1363C	AGT>CGT	Missense	ORF1ab:nsp4	0.977189093804472
CAMB-7243A	MN908947.3	14408	C	T	1	1	0	0	0.999454595036815	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000545404963185165
CAMB-7243A	MN908947.3	18723	T	C	0.1	0.17	1.9e-45	1.6e-76	0.133815683695096	ATC	ORF1ab:3'-to-5'-exonuclease	H228H	T684C	CAT>CAC	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.866184316304904
CAMB-7243A	MN908947.3	23403	A	G	1	1	0	0	0.999901189025394	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.88109746055795e-05
CAMB-7243A	MN908947.3	241	C	T	1	1	0	0	0.999903044405662	TCG	NA	NA	NA	NA	NA	NA	9.69555943377933e-05
CAMB-7243A	MN908947.3	28005	CCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAG	-	0.00119230769230769	0.0775769230769231	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;4e-13;NA;NA;NA;NA;NA;NA;NA	2.3e-09;1.5e-15;8.4e-16;1.4e-15;1.8e-16;1.9e-15;1.4e-15;7e-16;4.7e-16;4.1e-17;1.4e-15;4.4e-16;6.9e-16;7.2e-16;6.3e-16;1.8e-15;1.9e-15;1.3e-15;1.5e-15;1.8e-16;4.3e-16;5.2e-16;7.9e-16;1.9e-15;6.7e-15;5.2e-15;1.1e-15;1.6e-15;1.3e-15;5.1e-16;1.6e-15;1.9e-15;9e-16;2.4e-15;5.3e-16;9.7e-16;1.9e-15;1.7e-15;2.3e-15;8.4e-16;9.8e-16;1.5e-15;3.6e-15;1.2e-14;5.9e-15;1.9e-15;3.4e-16;4.7e-16;1.8e-15;8.2e-15;2.4e-15;2.3e-15	0.0376470588235294	TCC	ORF8	.	112-163-delfrshift	.	no-SNV	GU280_gp09	0.981351981351981
CAMB-7243A	MN908947.3	28849	C	T	1	1	0	4.7e-260	1	ACA	N	N192N	C576T	AAC>AAT	Synonymous	GU280_gp10	0
CAMB-7243A	MN908947.3	28881	GGG	AAC	1	1	0;0;0	6e-244;3e-256;3.5e-273	0.997923875432526	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7243A	MN908947.3	3037	C	T	1	1	5.2e-140	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-72458	MN908947.3	11074	C	INS	0.082	0.16	4.1e-30	2.2e-56	0.1051116124436	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.872580740916647
CAMB-72458	MN908947.3	11074	C	T	0.022	0.014	1.1e-16	1.2e-07	0.0194579672286868	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.872580740916647
CAMB-72458	MN908947.3	11083	G	-	0.15	0.13	5.5e-66	7.3e-57	0.144620407228157	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-72458	MN908947.3	11083	G	T	0.85	0.87	0	0	0.855265041954237	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-72458	MN908947.3	13914	T	G	0.0019	0.0086	0.0023	1.8e-06	0.00449092950422502	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.995509070495775
CAMB-72458	MN908947.3	14805	C	T	1	1	0	0	0.999918164260696	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	3.27342957216275e-05
CAMB-72458	MN908947.3	15028	T	C	0.016	0.014	6.4e-06	3.1e-06	0.0144991212653779	ATA	ORF1ab:RNA-dependent-RNA-polymerase	Y521H	T1561C	TAT>CAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.985500878734622
CAMB-72458	MN908947.3	17247	T	C	1	0.99	0	0	0.99750171311101	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.00245545911375057
CAMB-72458	MN908947.3	17410	C	T	0.039	0.046	4.1e-18	1.9e-21	0.0416845449482823	ACG	ORF1ab:helicase	R392C	C1174T	CGT>TGT	Missense	ORF1ab:helicase	0.958251549704666
CAMB-72458	MN908947.3	1820	G	A	0.0091	0.0054	8.1e-06	0.00038	0.00788208680899194	AGG	ORF1ab:nsp2	G339S	G1015A	GGT>AGT	Missense	ORF1ab:nsp2	0.992011876148735
CAMB-72458	MN908947.3	20099	C	T	0.083	0.09	4e-17	6.8e-13	0.0850480109739369	GCT	ORF1ab:endoRNAse	A160V	C479T	GCT>GTT	Missense	ORF1ab:endoRNAse	0.914951989026063
CAMB-72458	MN908947.3	21534	T	C	1	1	0	0	0.999475065616798	GTG	ORF1ab:2'-O-ribose-methyltransferase	S292S	T876C	AGT>AGC	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0
CAMB-72458	MN908947.3	22284	TACTTGCTTTACATAGAAGTTA	-	0.0150454545454545	0.00159090909090909	3.5e-07;1.2e-06;1.7e-06;1.3e-05;4e-06;2.6e-05;2.5e-06;6e-04;2.1e-06;2.4e-05;8.2e-05;1.4e-06;4.3e-07;1.5e-06;2.9e-07;1.5e-08;1.3e-08;8.4e-09;1e-08;1.5e-08;4.1e-08;2.2e-07	NA;NA;NA;NA;NA;NA;NA;0.00058;NA;NA;3.5e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0126015586138286	TTA	S	.	722-743-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.987084870848708
CAMB-72458	MN908947.3	23191	C	T	1	1	0	0	0.999804113614104	TCA	S	F543F	C1629T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.000163238654913484
CAMB-72458	MN908947.3	24026	CTTT	-	0.0095	0.0435	0.014;0.0028;NA;NA	0.00012;1.6e-06;8.9e-06;2.2e-07	0.0182806324110672	ACT	S	.	2464-2467-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.975191646043339
CAMB-72458	MN908947.3	26144	G	T	1	1	2.5e-272	3.1e-145	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-72458	MN908947.3	26209	G	-	0.021	0.025	2.4e-06	3.2e-05	0.0220588235294118	CGT	ORF3a	.	817-817-delfrshift	.	no-SNV	GU280_gp03	0.977941176470588
CAMB-72458	MN908947.3	26858	C	T	0.032	0.023	6.6e-16	3.2e-12	0.0284409895736936	TCA	M	F112F	C336T	TTC>TTT	Synonymous	GU280_gp05	0.971534332778086
CAMB-72458	MN908947.3	27190	A	-	0.0048	0.0076	0.00068	3.1e-05	0.00591037718952609	TAA	M	.	668-668-delfrshift	.	no-SNV	GU280_gp05	0.994006041718905
CAMB-72458	MN908947.3	27393	C	T	0.01	0.037	2.1e-06	7e-18	0.0214612007593735	ACA	NA	NA	NA	NA	NA	NA	0.978479473184623
CAMB-72458	MN908947.3	28868	C	T	0.03	0.015	9.6e-14	7.2e-07	0.026503164556962	TCC	N	P199S	C595T	CCA>TCA	Missense	GU280_gp10	0.973496835443038
CAMB-72458	MN908947.3	5204	ATG	-	0.00433333333333333	0.018	NA;NA;4e-06	3e-06;6.7e-06;9.1e-06	0.00442477876106195	CAT	ORF1ab:nsp3	.	2485-2487-delinframe	.	no-SNV	ORF1ab:nsp3	0.995475113122172
CAMB-72458	MN908947.3	5206	G	-	0.013	0.018	4e-06	9.1e-06	0.0141592920353982	TGT	ORF1ab:nsp3	.	2487-2487-delfrshift	.	no-SNV	ORF1ab:nsp3	0.985840707964602
CAMB-72458	MN908947.3	5570	A	G	0.0068	0.014	0.00029	3.2e-07	0.0116455696202532	TAT	ORF1ab:nsp3	M951V	A2851G	ATG>GTG	Missense	ORF1ab:nsp3	0.988354430379747
CAMB-72458	MN908947.3	6320	GTT	-	0.00983333333333333	0.0323333333333333	1.4e-06;8.1e-07;1.3e-06	1.1e-15;3.1e-16;7.2e-16	0.0122009065036366	AGT	ORF1ab:nsp3	.	3601-3603-delinframe	.	no-SNV	ORF1ab:nsp3	0.987825631627176
CAMB-72458	MN908947.3	8084	G	A	0.018	0.01	2.9e-09	1.5e-05	0.0162697350816163	GGA	ORF1ab:nsp3	E1789K	G5365A	GAA>AAA	Missense	ORF1ab:nsp3	0.983676746052984
CAMB-72458	MN908947.3	9707	A	-	0.0088	0.01	5.6e-06	1e-06	0.00941694438499404	TAT	ORF1ab:nsp4	.	1153-1153-delfrshift	.	no-SNV	ORF1ab:nsp4	0.990537193872871
CAMB-72467	MN908947.3	11074	C	INS	0.11	0.11	3.2e-43	2.7e-37	0.107733603159211	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.887150947903931
CAMB-72467	MN908947.3	11083	G	-	0.14	0.14	1.9e-62	1.1e-59	0.140729179672868	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.00053689599200899
CAMB-72467	MN908947.3	11083	G	T	0.86	0.86	0	0	0.858484205269072	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.00053689599200899
CAMB-72467	MN908947.3	1191	C	T	0.037	0.039	2e-17	1e-18	0.0378705792493383	CCA	ORF1ab:nsp2	P129L	C386T	CCA>CTA	Missense	ORF1ab:nsp2	0.962093894878946
CAMB-72467	MN908947.3	12067	G	T	0.009	0.012	1.4e-05	6.3e-07	0.0102955692037728	TGC	ORF1ab:nsp7	M75I	G225T	ATG>ATT	Missense	ORF1ab:nsp7	0.989498793595087
CAMB-72467	MN908947.3	14805	C	T	1	1	0	0	0.998927711574645	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000606955712464847
CAMB-72467	MN908947.3	24734	C	T	0.0082	0.0089	1.3e-05	5.1e-06	0.00851296932370011	TCA	S	H1058Y	C3172T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.991442615184176
CAMB-72467	MN908947.3	2480	A	G	1	1	0	0	0.998953610045344	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.00104638995465644
CAMB-72467	MN908947.3	2558	C	T	1	1	0	0	0.99878704777977	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000817424322328868
CAMB-72467	MN908947.3	26144	G	T	1	1	0	0	0.99955240104866	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000383656244005371
CAMB-72467	MN908947.3	26801	C	T	0.054	0.048	1.2e-23	1.4e-21	0.0513655798260667	TCA	M	L93L	C279T	CTC>CTT	Synonymous	GU280_gp05	0.938832494691836
CAMB-72467	MN908947.3	28868	C	T	1	1	0	0	0.999158826095084	TCC	N	P199S	C595T	CCA>TCA	Missense	GU280_gp10	0.000685400959561343
CAMB-72467	MN908947.3	4185	G	A	1	1	0	0	0.999378835689617	GGT	ORF1ab:nsp3	G489D	G1466A	GGT>GAT	Missense	ORF1ab:nsp3	0.000608741024175715
CAMB-72467	MN908947.3	7478	A	G	0.043	0.045	8e-20	8e-21	0.0438218782362239	TAA	ORF1ab:nsp3	N1587D	A4759G	AAT>GAT	Missense	ORF1ab:nsp3	0.956096364528261
CAMB-72467	MN908947.3	9848	A	G	0.0072	0.0088	3.8e-05	6.3e-06	0.00783976531283193	TAG	ORF1ab:nsp4	S432G	A1294G	AGT>GGT	Missense	ORF1ab:nsp4	0.99188204946639
CAMB-72476	MN908947.3	11075	T	-	0.089	0.072	9.6e-22	1.5e-18	0.0836754683950566	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.916178646604006
CAMB-72476	MN908947.3	1135	G	A	0.019	0.0024	3.7e-10	0.0054	0.0107370864770749	AGA	ORF1ab:nsp2	K110K	G330A	AAG>AAA	Synonymous	ORF1ab:nsp2	0.973483749274521
CAMB-72476	MN908947.3	14275	A	C	0.041	0.058	1.8e-19	1.4e-26	0.0479552248298671	GAG	ORF1ab:RNA-dependent-RNA-polymerase	R270R	A808C	AGG>CGG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.951599567512561
CAMB-72476	MN908947.3	14408	C	T	1	1	0	0	0.999867250763308	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000132749236691889
CAMB-72476	MN908947.3	23403	A	G	1	1	0	0	0.999889750975015	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.89056406157408e-05
CAMB-72476	MN908947.3	241	C	T	1	1	0	0	0.999635191828297	TCG	NA	NA	NA	NA	NA	NA	0.000152003404876269
CAMB-72476	MN908947.3	28424	T	C	0.0075	0.0031	2.1e-05	0.0015	0.00572232190485427	GTC	N	S51P	T151C	TCT>CCT	Missense	GU280_gp10	0.99426797924446
CAMB-72476	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999644465513155	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000406945198046663
CAMB-72476	MN908947.3	29320	A	T	0.03	0.012	3.3e-13	1.4e-06	0.0242623107875072	AAG	N	Q349H	A1047T	CAA>CAT	Missense	GU280_gp10	0.959810308488216
CAMB-72476	MN908947.3	3037	C	T	1	1	4.3e-254	0	0.999055266887104	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000472366556447804
CAMB-72476	MN908947.3	3748	T	C	1	1	1.2e-81	5.8e-231	1	CTT	ORF1ab:nsp3	S343S	T1029C	TCT>TCC	Synonymous	ORF1ab:nsp3	0
CAMB-72476	MN908947.3	4207	G	T	0.058	0.041	1.9e-27	5.8e-20	0.0504841216081603	CGA	ORF1ab:nsp3	A496A	G1488T	GCG>GCT	Synonymous	ORF1ab:nsp3	0.949476032991991
CAMB-72476	MN908947.3	6670	G	T	0.046	0.088	9.6e-12	2.6e-27	0.075046904315197	GGG	ORF1ab:nsp3	W1317C	G3951T	TGG>TGT	Missense	ORF1ab:nsp3	0.924953095684803
CAMB-72485	MN908947.3	10296	C	T	0.049	0.011	3.1e-23	2.5e-07	0.0324861000794281	TCT	ORF1ab:3C-like-proteinase	S81F	C242T	TCT>TTT	Missense	ORF1ab:3C-like-proteinase	0.967355043685465
CAMB-72485	MN908947.3	10424	G	T	0.004	0.0071	0.00054	1.8e-05	0.00523843179644951	TGG	ORF1ab:3C-like-proteinase	G124C	G370T	GGT>TGT	Missense	ORF1ab:3C-like-proteinase	0.994636843636968
CAMB-72485	MN908947.3	10793	G	T	1	1	0	0	0.999740932642487	TGT	ORF1ab:3C-like-proteinase	V247F	G739T	GTT>TTT	Missense	ORF1ab:3C-like-proteinase	0
CAMB-72485	MN908947.3	11073	TC	CT	0.01765	0.019	2.2e-05;3e-19	2.8e-09;1.8e-11	0.018125032898777	TTC	ORF1ab:nsp6	.	101-102-mnv	.	no-SNV	ORF1ab:nsp6	0.987492804437699
CAMB-72485	MN908947.3	11074	C	-	0.0045	0.0035	9.9e-06	0.00027	0.00416534293480179	TCT	ORF1ab:nsp6	.	102-102-delfrshift	.	no-SNV	ORF1ab:nsp6	0.887924035440714
CAMB-72485	MN908947.3	11074	C	INS	0.069	0.11	2.3e-21	8.6e-34	0.0829538635320696	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.887924035440714
CAMB-72485	MN908947.3	11083	G	-	0.25	0.19	2.5e-114	2.2e-84	0.22461325468007	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.50484560284115e-05
CAMB-72485	MN908947.3	11083	G	T	0.75	0.81	1.9e-287	0	0.775341599951845	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.50484560284115e-05
CAMB-72485	MN908947.3	11090	A	T	0.99	1	0	0	0.994924021464138	AAA	ORF1ab:nsp6	N40Y	A118T	AAT>TAT	Missense	ORF1ab:nsp6	0.00505986431828803
CAMB-72485	MN908947.3	11152	C	T	0.0082	0.0087	1.3e-05	6.1e-06	0.00839939771057453	TCA	ORF1ab:nsp6	V60V	C180T	GTC>GTT	Synonymous	ORF1ab:nsp6	0.991528037298405
CAMB-72485	MN908947.3	11939	G	T	0.005	0.018	0.00068	1.8e-09	0.0103199565475514	TGT	ORF1ab:nsp7	V33F	G97T	GTC>TTC	Missense	ORF1ab:nsp7	0.989541096669067
CAMB-72485	MN908947.3	12025	C	T	0.0061	0.0077	0.00024	3.8e-05	0.00675519296418446	CCA	ORF1ab:nsp7	S61S	C183T	TCC>TCT	Synonymous	ORF1ab:nsp7	0.993158016548053
CAMB-72485	MN908947.3	12114	C	T	0.028	0.013	3.9e-14	1.3e-07	0.0218823741795722	TCC	ORF1ab:nsp8	S8F	C23T	TCC>TTC	Missense	ORF1ab:nsp8	0.978117625820428
CAMB-72485	MN908947.3	13458	C	T	0.0063	0.027	0.00036	5.5e-12	0.0115326493279249	TCG	ORF1ab:nsp11	S6L	C17T	TCG>TTG	Missense	ORF1ab:nsp11	0.988467350672075
CAMB-72485	MN908947.3	14790	C	T	0.03	0.02	1.2e-14	1.1e-10	0.0260861331607935	TCA	ORF1ab:RNA-dependent-RNA-polymerase	I441I	C1323T	ATC>ATT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.973850742500039
CAMB-72485	MN908947.3	14805	C	T	1	1	0	0	0.999934666143996	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	3.26669280020907e-05
CAMB-72485	MN908947.3	14931	C	T	0.005	0.0076	0.00024	1.8e-05	0.00638977635782748	ACC	ORF1ab:RNA-dependent-RNA-polymerase	N488N	C1464T	AAC>AAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.993610223642173
CAMB-72485	MN908947.3	15738	C	T	0.01	0.023	3.8e-06	5.6e-12	0.0155516431924883	TCA	ORF1ab:RNA-dependent-RNA-polymerase	F757F	C2271T	TTC>TTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.982082599765258
CAMB-72485	MN908947.3	15842	C	A	0.026	0.017	5.1e-13	1.8e-09	0.0218887021022166	ACT	ORF1ab:RNA-dependent-RNA-polymerase	T792N	C2375A	ACT>AAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.974055908909724
CAMB-72485	MN908947.3	1623	T	C	0.0054	0.016	0.00014	5e-09	0.00880724030798325	ATA	ORF1ab:nsp2	I273T	T818C	ATA>ACA	Missense	ORF1ab:nsp2	0.991192759692017
CAMB-72485	MN908947.3	1627	C	T	0.034	0.037	2e-16	5.5e-18	0.0347208296330249	TCC	ORF1ab:nsp2	L274L	C822T	CTC>CTT	Synonymous	ORF1ab:nsp2	0.965279170366975
CAMB-72485	MN908947.3	16399	TGTG	-	0.0018	0.009525	0.00072;NA;NA;NA	2.5e-05;5e-09;0.00045;0.00044	0.00487144790257104	TTG	ORF1ab:helicase	.	163-166-delfrshift	.	no-SNV	ORF1ab:helicase	0.990998363338789
CAMB-72485	MN908947.3	1653	TTG	-	0.0015	0.00683333333333333	0.00044;NA;NA	0.00038;1e-05;6.7e-06	0.00265643447461629	ATT	ORF1ab:nsp2	.	848-850-delinframe	.	no-SNV	ORF1ab:nsp2	0.995407366583999
CAMB-72485	MN908947.3	17167	C	T	0.015	0.013	4.4e-08	1.8e-07	0.0143528950720094	TCA	ORF1ab:helicase	H311Y	C931T	CAT>TAT	Missense	ORF1ab:helicase	0.985598118937984
CAMB-72485	MN908947.3	18744	C	T	0.013	0.0083	3.4e-07	5e-05	0.011434804025051	ACG	ORF1ab:3'-to-5'-exonuclease	Y235Y	C705T	TAC>TAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.984413482513546
CAMB-72485	MN908947.3	203	C	T	0.022	0.046	9.6e-11	4.7e-21	0.0312277169581813	TCG	NA	NA	NA	NA	NA	NA	0.96870936621786
CAMB-72485	MN908947.3	21882	G	T	0.006	0.01	0.00029	6.3e-06	0.00814619110523998	GGT	S	G107V	G320T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.99185380889476
CAMB-72485	MN908947.3	23997	C	T	0.007	0.0064	4e-05	7.3e-05	0.0067449956483899	CCA	S	P812L	C2435T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	0.99325500435161
CAMB-72485	MN908947.3	24213	C	T	0.012	0.018	4.5e-06	2.3e-08	0.014041514041514	TCT	S	S884F	C2651T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.985911524373063
CAMB-72485	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-72485	MN908947.3	24904	C	T	0.0044	0.0088	0.00071	8.1e-06	0.00625599024135227	TCA	S	I1114I	C3342T	ATC>ATT	Synonymous	GU280_gp02, spike glycoprotein	0.993726583601987
CAMB-72485	MN908947.3	25006	C	T	0.012	0.013	4.7e-07	7.7e-08	0.0121485668487546	TCA	S	F1148F	C3444T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.98779870499652
CAMB-72485	MN908947.3	25521	C	T	0.034	0.046	7.1e-16	3.5e-21	0.0387326318629435	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.96125050586807
CAMB-72485	MN908947.3	2558	C	T	1	1	0	0	0.997291102312982	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.00270889768701813
CAMB-72485	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-72485	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0245945945945946	0.0401891891891892	0.0013;2e-05;0.00022;0.00022;9.8e-05;6.7e-05;2e-04;0.00068;7e-04;0.00038;5e-04;0.00044;0.00067;0.00052;0.00059;0.00083;0.00047;0.00075;0.00058;0.00056;0.00044;0.00082;0.00054;0.00064;0.00055;0.00048;0.00073;5e-04;0.00034;0.00054;7e-04;0.00066;0.00049;0.00072;0.00034;0.002;0.002	3.3e-05;2.4e-06;2e-05;2.2e-05;5.8e-05;5.1e-07;2.1e-06;4.4e-07;3.9e-07;3e-07;2.2e-07;1.7e-07;3.6e-07;2.7e-07;3.6e-07;6.2e-07;2.3e-07;5e-07;2.5e-07;3.6e-07;2.5e-07;6.1e-07;2.8e-07;3.8e-07;3e-07;1.7e-07;4.6e-07;3.2e-07;1.1e-07;3e-07;4.7e-07;4.4e-07;1.7e-07;4.8e-07;6e-08;2.7e-07;1.7e-07	0.0312791593979472	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.975797713852321
CAMB-72485	MN908947.3	27343	A	T	0.0026	0.0068	0.0025	2.9e-05	0.00429876410531972	TAA	ORF6	K48*	A142T	AAA>TAA	Nonsense	GU280_gp06	0.994223535733477
CAMB-72485	MN908947.3	27467	G	A	0.0016	0.0072	0.0044	1.5e-05	0.00388419578044743	AGA	ORF7a	R25K	G74A	AGA>AAA	Missense	GU280_gp07	0.996083966549221
CAMB-72485	MN908947.3	28253	C	T	0.11	0.095	3.3e-49	1.5e-42	0.105031215571061	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.894696753308578
CAMB-72485	MN908947.3	29221	A	G	1	1	0	0	0.996898632648384	GAA	N	G316G	A948G	GGA>GGG	Synonymous	GU280_gp10	9.16660300970132e-05
CAMB-72485	MN908947.3	29284	C	T	0.0096	0.015	4.3e-06	1.3e-08	0.0115884680610514	TCA	N	I337I	C1011T	ATC>ATT	Synonymous	GU280_gp10	0.988352027610009
CAMB-72485	MN908947.3	29633	T	C	0.011	0.0074	1.6e-06	3.3e-05	0.00914682226778111	CTA	ORF10	Y26H	T76C	TAC>CAC	Missense	GU280_gp11	0.990853177732219
CAMB-72485	MN908947.3	29743	C	T	0.053	0.035	2.6e-19	5.1e-14	0.0431654676258993	GCG	NA	NA	NA	NA	NA	NA	0.956834532374101
CAMB-72485	MN908947.3	29754	C	T	0.12	0.13	5.6e-42	7.2e-48	0.123860951738103	TCG	NA	NA	NA	NA	NA	NA	0.876139048261897
CAMB-72485	MN908947.3	3096	C	T	0.025	0.0085	4.1e-09	0.00021	0.0136765888978278	TCA	ORF1ab:nsp3	S126L	C377T	TCA>TTA	Missense	ORF1ab:nsp3	0.986323411102172
CAMB-72485	MN908947.3	3120	A	T	0.0047	0.017	0.00012	3.4e-09	0.0128497409326425	GAA	ORF1ab:nsp3	E134V	A401T	GAA>GTA	Missense	ORF1ab:nsp3	0.986735751295337
CAMB-72485	MN908947.3	313	C	T	0.016	0.05	7.7e-09	2.4e-23	0.0292474210690841	TCA	ORF1ab:leader-protein	L16L	C48T	CTC>CTT	Synonymous	ORF1ab:leader-protein	0.970733041575492
CAMB-72485	MN908947.3	5183	C	T	0.02	0.011	3.5e-07	0.00039	0.0172413793103448	TCC	ORF1ab:nsp3	P822S	C2464T	CCT>TCT	Missense	ORF1ab:nsp3	0.982758620689655
CAMB-72485	MN908947.3	522	TT	-	0.049	0.032	4.5e-07;3.3e-06	9.2e-05;0.00029	0.0428549833719641	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.951778534661579
CAMB-72485	MN908947.3	635	C	T	0.054	0.059	9.4e-25	5.9e-27	0.0554390109778203	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.94456098902218
CAMB-72485	MN908947.3	6374	G	T	0.0066	0.0073	7.8e-05	3.3e-05	0.00673164952339921	GGA	ORF1ab:nsp3	D1219Y	G3655T	GAT>TAT	Missense	ORF1ab:nsp3	0.981438598380814
CAMB-72485	MN908947.3	683	C	T	0.016	0.041	1e-08	1.4e-19	0.0253778181517879	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.971541828392105
CAMB-72485	MN908947.3	7675	G	T	0.0087	0.0069	1.4e-05	8.5e-05	0.00789650537634409	CGA	ORF1ab:nsp3	A1652A	G4956T	GCG>GCT	Synonymous	ORF1ab:nsp3	0.990255376344086
CAMB-72485	MN908947.3	815	C	T	0.0037	0.013	0.0029	2.6e-07	0.00697654870975876	TCG	ORF1ab:nsp2	R4C	C10T	CGC>TGC	Missense	ORF1ab:nsp2	0.991538483090975
CAMB-72485	MN908947.3	8964	C	T	0.035	0.0075	4.5e-17	1.8e-05	0.0211850270234203	TCA	ORF1ab:nsp4	S137L	C410T	TCA>TTA	Missense	ORF1ab:nsp4	0.97881497297658
CAMB-72485	MN908947.3	8968	A	G	0.025	0.026	1.3e-12	4.5e-13	0.0252216891990115	AAC	ORF1ab:nsp4	K138K	A414G	AAA>AAG	Synonymous	ORF1ab:nsp4	0.974778310800989
CAMB-72485	MN908947.3	9430	C	T	0.024	0.017	3.7e-11	6.7e-08	0.0225007785736531	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.97454064154469
CAMB-72494	MN908947.3	11074	CT	-	0.0163	0.0255435	0.00032;1.2e-07	0.077;6.2e-13	0.0204945711465531	TCT	ORF1ab:nsp6	.	102-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.977436241986507
CAMB-72494	MN908947.3	11075	T	-	0.03	0.051	1.2e-07	6.2e-13	0.0367059165576392	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955492561903377
CAMB-72494	MN908947.3	14408	C	T	1	1	0	0	0.996841431702768	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000381206518631469
CAMB-72494	MN908947.3	153	T	G	0.015	0.024	2.8e-08	2.8e-12	0.0180290145072536	GTT	NA	NA	NA	NA	NA	NA	0.981890945472736
CAMB-72494	MN908947.3	23403	A	G	1	1	0	0	0.999888340743448	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.0603366019043e-05
CAMB-72494	MN908947.3	23457	C	A	0.0084	0.007	8.7e-06	1.7e-05	0.00787096905578918	ACT	S	T632N	C1895A	ACT>AAT	Missense	GU280_gp02, spike glycoprotein	0.989736174892321
CAMB-72494	MN908947.3	241	C	T	1	1	0	0	0.999898908208653	TCG	NA	NA	NA	NA	NA	NA	4.04367165386171e-05
CAMB-72494	MN908947.3	25710	C	T	0.004	0.0096	0.001	6.6e-06	0.00511434207642288	TCT	ORF3a	L106L	C318T	CTC>CTT	Synonymous	GU280_gp03	0.994885657923577
CAMB-72494	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0363684210526316	0.0335	0.00011;5.8e-06;5.2e-05;5.4e-05;7.7e-05;1.3e-06;7.1e-06;3.6e-06;3.5e-06;1.4e-06;2.2e-06;1.7e-06;3.1e-06;2.3e-06;3.1e-06;4.4e-06;2e-06;3.8e-06;2.5e-06;2.5e-06;2.6e-06;4.1e-06;2.6e-06;3.2e-06;2.4e-06;2.1e-06;3.3e-06;2e-06;6.8e-07;2.5e-06;3.4e-06;3.2e-06;1.1e-06;1.8e-06;9.6e-07;2.3e-06;1.6e-06;0.00055	0.00052;5.6e-05;0.00034;0.00038;7e-04;1.7e-05;6.5e-05;9e-06;8.1e-06;5.4e-06;5.2e-06;1.9e-06;3e-06;2.7e-06;3.6e-06;5.3e-06;5.4e-06;9.3e-06;5.1e-06;7.2e-06;7.6e-06;1.1e-05;6.6e-06;7.8e-06;6.1e-06;4.5e-06;8.6e-06;6.1e-06;6.3e-07;6.9e-06;9.1e-06;8.6e-06;2.2e-06;5.3e-06;7.7e-07;2.7e-06;2.7e-06;0.0028	0.0361514164445761	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.974930328069232
CAMB-72494	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999656313098767	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	9.54152950718e-05
CAMB-72494	MN908947.3	3037	C	T	1	1	0	0	0.999511897498475	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-72494	MN908947.3	518	ATG	-	0.273333333333333	0.28	1.3e-05;0.00052;0.00057	4.2e-06;0.00019;0.00025	0.277585449433266	TAT	ORF1ab:leader-protein	.	253-255-delinframe	.	no-SNV	ORF1ab:leader-protein	0.706995569654871
CAMB-72494	MN908947.3	522	T	-	0.078	0.1	7.2e-10	3.2e-13	0.0853248523398455	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.914547932757837
CAMB-72494	MN908947.3	522	TT	-	0.0615	0.069	7.2e-10;1.9e-06	3.2e-13;1.5e-05	0.0635847410862097	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.914547932757837
CAMB-72494	MN908947.3	523	T	-	0.045	0.038	1.9e-06	1.5e-05	0.0427372791180421	TTG	ORF1ab:leader-protein	.	258-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.957123170582797
CAMB-72494	MN908947.3	5512	C	T	0.045	0.031	7.9e-18	1.1e-12	0.0381081081081081	ACG	ORF1ab:nsp3	N931N	C2793T	AAC>AAT	Synonymous	ORF1ab:nsp3	0.961891891891892
CAMB-72494	MN908947.3	870	AAGACCTTCTAGCACGTGCTGGTA	-	0.000390125	0.0059375	NA;NA;0.036;NA;NA;NA;NA;NA;0.0093;NA;NA;NA;NA;NA;NA;NA;NA;0.0033;0.01;NA;NA;NA;NA;NA	0.00071;0.00076;0.00084;0.00082;0.00074;0.00075;0.00086;0.00097;0.00091;0.00061;1.6e-05;2.9e-05;5.1e-05;9.5e-05;4.8e-05;0.00018;4.8e-05;5e-05;0.00015;8e-04;0.00022;0.00022;1e-04;0.00025	0.00199697600775968	AAA	ORF1ab:nsp2	.	65-88-delinframe	.	no-SNV	ORF1ab:nsp2	0.99838427156318
CAMB-72494	MN908947.3	8717	C	T	0.014	0.0094	9.1e-08	1.1e-05	0.0128440366972477	TCG	ORF1ab:nsp4	R55C	C163T	CGT>TGT	Missense	ORF1ab:nsp4	0.987106372427473
CAMB-72494	MN908947.3	8961	C	T	0.0025	0.0067	0.0031	3.7e-05	0.00434098294069862	CCA	ORF1ab:nsp4	P136L	C407T	CCA>CTA	Missense	ORF1ab:nsp4	0.995633631194151
CAMB-724A3	MN908947.3	11074	C	INS	0.12	0.11	1.3e-52	1.8e-35	0.112884034918528	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.883847049835302
CAMB-724A3	MN908947.3	11083	G	-	0.14	0.13	7.1e-60	1.4e-57	0.136185461798952	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.15971610149835e-05
CAMB-724A3	MN908947.3	11083	G	T	0.86	0.87	0	0	0.863710163751914	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.15971610149835e-05
CAMB-724A3	MN908947.3	14805	C	T	1	1	0	0	0.999937719538626	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	2.49121845494631e-05
CAMB-724A3	MN908947.3	2558	C	T	1	1	0	0	0.999562107721501	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-724A3	MN908947.3	26144	G	T	1	1	0	0	0.999685929648241	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000314070351758794
CAMB-724A3	MN908947.3	28851	G	T	1	1	0	0	0.999528413110116	AGT	N	S193I	G578T	AGT>ATT	Missense	GU280_gp10	0.000353690167413346
CAMB-724B2	MN908947.3	11074	CTTTTT	-	0.00751016666666667	0.0107833333333333	0.13;3e-09;0.00044;NA;NA;NA	5.5e-06;1.5e-09;2e-04;0.00062;0.00067;0.00075	0.00161904761904762	TCT	ORF1ab:nsp6	.	102-107-delinframe	.	no-SNV	ORF1ab:nsp6	0.978863918751013
CAMB-724B2	MN908947.3	14408	C	T	1	1	0	0	0.997762893866262	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000244047941862357
CAMB-724B2	MN908947.3	1651	T	C	0.0081	0.013	1.3e-05	6.1e-08	0.00975693994732979	ATA	ORF1ab:nsp2	N282N	T846C	AAT>AAC	Synonymous	ORF1ab:nsp2	0.990221473902344
CAMB-724B2	MN908947.3	187	A	G	1	1	0	0	0.997707951325221	CAG	NA	NA	NA	NA	NA	NA	0.00222259265433128
CAMB-724B2	MN908947.3	23403	A	G	1	1	0	0	0.999904510573284	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.94468557936039e-05
CAMB-724B2	MN908947.3	2397	C	T	0.15	0.14	3.8e-65	7.3e-58	0.148224661071659	ACG	ORF1ab:nsp2	T531M	C1592T	ACG>ATG	Missense	ORF1ab:nsp2	0.851775338928341
CAMB-724B2	MN908947.3	241	C	T	1	1	0	0	0.999138868105651	TCG	NA	NA	NA	NA	NA	NA	5.6467665203213e-05
CAMB-724B2	MN908947.3	3037	C	T	1	1	0	0	0.998927569707969	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-724B2	MN908947.3	5222	AC	GG	0.013	0.0083	3e-06;1.4e-05	0.00067;0.00061	0.0116279069767442	CAC	ORF1ab:nsp3	.	2503-2504-mnv	.	no-SNV	ORF1ab:nsp3	0.987612903225806
CAMB-724B2	MN908947.3	5225	A	C	0.013	0.012	1e-05	9.8e-05	0.0126582278481013	TAA	ORF1ab:nsp3	K836Q	A2506C	AAA>CAA	Missense	ORF1ab:nsp3	0.987098344693281
CAMB-724B2	MN908947.3	5229	AG	-	0.0155	0.013	8.3e-06;5.6e-06	0.00014;8.9e-05	0.0150497178177909	AAG	ORF1ab:nsp3	.	2510-2511-delfrshift	.	no-SNV	ORF1ab:nsp3	0.984581497797357
CAMB-724C1	MN908947.3	11075	T	-	0.031	0.032	5.5e-08	1.3e-08	0.031045662598082	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964799476896251
CAMB-724C1	MN908947.3	14408	C	T	1	1	0	0	0.997390052602548	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000390146775907764
CAMB-724C1	MN908947.3	1528	C	T	0.013	0.014	1.9e-07	1.3e-07	0.0135418120899065	CCT	ORF1ab:nsp2	A241A	C723T	GCC>GCT	Synonymous	ORF1ab:nsp2	0.986039368979478
CAMB-724C1	MN908947.3	187	A	G	1	1	0	0	0.999249968083748	CAG	NA	NA	NA	NA	NA	NA	0.000175539384654666
CAMB-724C1	MN908947.3	22684	T	C	0.0085	0.0095	8.5e-06	2.6e-06	0.00891346903092157	TTT	S	F374F	T1122C	TTT>TTC	Synonymous	GU280_gp02, spike glycoprotein	0.990668415150997
CAMB-724C1	MN908947.3	23403	A	G	1	1	0	0	0.999659914978745	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.00225056264066e-05
CAMB-724C1	MN908947.3	241	C	T	1	1	0	0	0.998822105159834	TCG	NA	NA	NA	NA	NA	NA	0.000147236855020777
CAMB-724C1	MN908947.3	27484	T	C	0.012	0.01	3.3e-07	1.4e-06	0.010982445158904	TTT	ORF7a	L31L	T91C	TTA>CTA	Synonymous	GU280_gp07	0.989017554841096
CAMB-724C1	MN908947.3	3037	C	T	1	1	0	0	0.999144616788321	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000114051094890511
CAMB-724C1	MN908947.3	8389	C	T	0.033	0.039	1.1e-15	4.1e-18	0.036322360953462	ACA	ORF1ab:nsp3	N1890N	C5670T	AAC>AAT	Synonymous	ORF1ab:nsp3	0.963614579392105
CAMB-724D0	MN908947.3	11074	C	INS	0.23	0.12	9.2e-106	1.3e-34	0.193181818181818	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.806475214925919
CAMB-724D0	MN908947.3	11083	G	-	0.16	0.15	3.1e-72	6.4e-69	0.159452718924085	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	6.99251800573386e-05
CAMB-724D0	MN908947.3	11083	G	T	0.84	0.84	0	0	0.840267580355686	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	6.99251800573386e-05
CAMB-724D0	MN908947.3	12781	C	T	0.019	0.023	5.7e-10	6e-12	0.0200840972603097	ACA	ORF1ab:nsp9	Y32Y	C96T	TAC>TAT	Synonymous	ORF1ab:nsp9	0.97991590273969
CAMB-724D0	MN908947.3	14805	C	T	1	1	0	0	0.999946344735077	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-724D0	MN908947.3	14853	TGTA	-	0.0355	0.0355	0.00071;9.2e-08;7.3e-07;8.8e-07	7.3e-05;3.4e-05;5.6e-08;8.4e-08	0.0316707270162841	TTG	ORF1ab:RNA-dependent-RNA-polymerase	.	1386-1389-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.970384842798015
CAMB-724D0	MN908947.3	17247	T	C	1	1	0	0	0.999828976997406	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000114015335062566
CAMB-724D0	MN908947.3	1843	G	-	0.02	0.024	1e-07	6.4e-09	0.0211379529561348	AGA	ORF1ab:nsp2	.	1038-1038-delfrshift	.	no-SNV	ORF1ab:nsp2	0.978862047043865
CAMB-724D0	MN908947.3	1843	GAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCGTGTT	-	0.0200961538461538	0.000461538461538462	1e-07;9.8e-11;2.1e-11;2.4e-11;2.7e-11;5.2e-11;4.5e-11;1.8e-12;3.6e-12;5.2e-12;1.1e-10;1.8e-11;9.1e-11;3.9e-11;4.7e-11;7.6e-11;9.4e-11;1e-10;3.8e-11;3.2e-11;1.7e-10;2.5e-10;3.7e-10;3.7e-10;5.8e-09;6.5e-09;6.4e-09;4.7e-09;1.9e-09;7.1e-09;1.3e-10;9.8e-11;8.4e-11;9.3e-11;9.8e-11;9.4e-11;1e-10;2.1e-10;8.2e-11;4.5e-10;1.6e-10;1.7e-10;1.8e-10;1.2e-10;5e-11;9.5e-11;9.5e-11;1.9e-10;1.2e-09;2e-09;1.1e-09;1.3e-09	6.4e-09;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0139516448672216	AGA	ORF1ab:nsp2	.	1038-1089-delfrshift	.	no-SNV	ORF1ab:nsp2	0.978862047043865
CAMB-724D0	MN908947.3	24015	TTGAAGATCTACTTT	-	0.0474666666666667	0.0461333333333333	2.6e-06;3.3e-06;4.1e-06;3.3e-06;9.6e-06;9.9e-06;9.4e-06;1.1e-05;1e-05;3.5e-06;4.7e-06;4.7e-05;2.6e-07;2.7e-06;3.7e-08	1.7e-06;2.1e-06;2.7e-06;2.4e-06;6.8e-06;7.1e-06;6.8e-06;8.6e-06;1e-05;2.2e-06;3.5e-06;3.9e-05;2.4e-07;1.9e-06;NA	0.0474780826596835	ATT	S	.	2453-2467-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.951364590622813
CAMB-724D0	MN908947.3	26144	G	T	1	1	2.5e-272	2.8e-146	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-724D0	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0268666216216216	0.161081081081081	NA;NA;NA;NA;NA;3.1e-06;8.5e-06;4.1e-05;4.1e-05;1.5e-05;2.8e-05;2.5e-05;4e-05;2.8e-05;3.4e-05;5.1e-05;2.5e-05;4.5e-05;3.2e-05;3.2e-05;2.6e-05;4.9e-05;2.7e-05;3.8e-05;3.1e-05;2.6e-05;4.4e-05;2.6e-05;6.6e-06;3e-05;4.2e-05;3.8e-05;2.5e-05;4.4e-05;1.4e-05;2.5e-05;2.2e-05	1.6e-33;2.1e-41;3.1e-35;4.9e-35;1.5e-32;2.4e-38;1e-36;5e-32;3.2e-32;2e-32;5.8e-33;9.9e-34;1.4e-32;4.2e-33;2.3e-32;1.4e-31;2.2e-33;7e-32;5e-33;2.4e-32;8.8e-33;9.5e-32;3.8e-33;3.3e-32;6.7e-33;6.3e-34;2.8e-32;9e-33;2.9e-35;1.4e-32;5.3e-32;3.1e-32;2.3e-33;5.7e-32;9.7e-37;7.8e-33;6.3e-34	0.0883853921604112	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.928194183186225
CAMB-724D0	MN908947.3	5817	CTTTA	-	0.0196	0.027	NA;NA;5.6e-06;1.8e-05;9.4e-06	2.2e-06;4.6e-07;5.5e-05;0.00013;8.9e-05	0.0313035352748793	GCT	ORF1ab:nsp3	.	3098-3102-delfrshift	.	no-SNV	ORF1ab:nsp3	0.992142740219348
CAMB-724D0	MN908947.3	686	AAGTCATTTG	-	0.0139	0.0346	0.022;0.02;0.029;0.02;0.03;0.023;0.02;0.025;0.032;1.9e-06	2.2e-05;1.9e-05;7e-05;2e-05;8e-05;3.4e-05;1.3e-05;4e-05;0.00013;1.2e-06	0.0202311597324991	AAA	ORF1ab:leader-protein	.	421-430-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.979706834902746
CAMB-724D0	MN908947.3	695	G	-	0.013	0.014	1.9e-06	1.2e-06	0.0136540010249652	TGA	ORF1ab:leader-protein	.	430-430-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.986254484222857
CAMB-724D0	MN908947.3	9812	T	C	0.0043	0.037	0.0048	4.4e-17	0.0148130680843766	CTT	ORF1ab:nsp4	F420L	T1258C	TTT>CTT	Missense	ORF1ab:nsp4	0.984500943234437
CAMB-724EF	MN908947.3	17410	C	T	0.065	0.099	1.2e-29	4.7e-44	0.0760751933945248	ACG	ORF1ab:helicase	R392C	C1174T	CGT>TGT	Missense	ORF1ab:helicase	0.923884724838671
CAMB-724EF	MN908947.3	23403	A	G	1	1	0	0	0.999810417555334	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000189582444665624
CAMB-724FE	MN908947.3	11071	G	INS	0.0091	0.016	3e-04	5.9e-06	0.0115538990825688	TGT	ORF1ab:nsp6	.	98-99-insfrshift	.	no-SNV	ORF1ab:nsp6	0.988302752293578
CAMB-724FE	MN908947.3	11074	C	-	0.0099	0.021	1.7e-08	2.1e-13	0.0139395385297025	TCT	ORF1ab:nsp6	.	102-102-delfrshift	.	no-SNV	ORF1ab:nsp6	0.865955488906309
CAMB-724FE	MN908947.3	11074	C	T	0.091	0.16	1.6e-54	2e-80	0.115026754371017	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.865955488906309
CAMB-724FE	MN908947.3	11074	CT	-	0.02545	0.0128	1.7e-08;7.5e-11	2.1e-13;0.012	0.0210706692476121	TCT	ORF1ab:nsp6	.	102-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.865955488906309
CAMB-724FE	MN908947.3	12270	A	G	0.021	0.052	5.3e-05	1.9e-10	0.0310718754344502	GAA	ORF1ab:nsp8	E60G	A179G	GAA>GGA	Missense	ORF1ab:nsp8	0.940150145975254
CAMB-724FE	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999538212883861	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0
CAMB-724FE	MN908947.3	17742	T	C	0.21	0.22	1.1e-100	9e-102	0.212972631681197	GTA	ORF1ab:helicase	R502R	T1506C	CGT>CGC	Synonymous	ORF1ab:helicase	0.787027368318803
CAMB-724FE	MN908947.3	22102	AGG	-	0.0366666666666667	0.0253333333333333	4.2e-19;3.3e-09;5e-10	NA;1.3e-08;2.7e-09	0.0342232574807382	AAG	S	.	540-542-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.963235294117647
CAMB-724FE	MN908947.3	27395	TG	-	0.037	0.021	2.8e-14;7.2e-16	8.1e-09;9.7e-10	0.0286268392428011	ATG	ORF7a	.	2-3-delfrshift	.	no-SNV	GU280_gp07	0.971459749853102
CAMB-724FE	MN908947.3	27906	G	T	0.01	0.012	1.8e-05	5.6e-06	0.010998680158381	TGT	ORF8	V5F	G13T	GTT>TTT	Missense	GU280_gp09	0.989001319841619
CAMB-724FE	MN908947.3	29318	C	T	0.015	0.0019	9.9e-09	0.0082	0.00847039473684211	TCA	N	Q349*	C1045T	CAA>TAA	Nonsense	GU280_gp10	0.991529605263158
CAMB-724FE	MN908947.3	29355	A	C	0.24	0.24	1.1e-111	2.1e-112	0.242444370640983	AAA	N	K361T	A1082C	AAA>ACA	Missense	GU280_gp10	0.756559282630355
CAMB-724FE	MN908947.3	29723	ACATTTTCACCGAGGCCACGCGGAGTACGATCGAGTGTACAGTG	-	0.0311818181818182	0.0375681818181818	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;1.2e-09;1.2e-09;1.6e-09;1.7e-09;2.2e-09;1.8e-09;2.2e-09;1.5e-09;2.2e-09;2.8e-09;1.8e-09;4.4e-09;1.3e-08;1.2e-08;6.7e-08;6.2e-08;1.1e-08;1.3e-08;1.2e-08;1.1e-08;7.4e-09;2.5e-08;1.2e-08;1.8e-08;NA;NA;NA;NA;NA;NA;NA	9.3e-09;7.8e-09;7.6e-09;7.5e-08;1.4e-08;2.1e-08;4.6e-08;8.8e-08;2.1e-08;6.9e-08;6.8e-08;9.7e-08;8.9e-08;1.1e-07;1.4e-07;1.8e-07;2.2e-07;1.7e-07;2.2e-07;2.4e-07;1.8e-07;2.4e-07;3.3e-07;5.1e-09;1.2e-08;2.6e-08;1.8e-08;1.2e-07;9.5e-08;2.9e-08;1.8e-08;1.7e-08;1.9e-08;2.7e-08;5.3e-08;3e-08;4.1e-08;1.7e-09;1e-09;1.2e-09;1e-09;8.1e-10;8.4e-10;5.6e-10	0.0413223140495868	CAC	NA	NA	NA	NA	NA	NA	0.978768577494692
CAMB-724FE	MN908947.3	3528	ATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAGTTGTGTTTT	-	0.0543269230769231	0.000848076923076923	6e-10;1.5e-10;2.3e-10;2.3e-09;2.7e-09;2.2e-09;2.7e-09;2.9e-09;3.1e-09;2.7e-09;2.8e-09;2.5e-09;2.5e-09;3.6e-09;2.8e-09;2.9e-09;7.1e-09;8.3e-09;6.4e-05;5.1e-05;3e-05;4.8e-08;5.7e-08;1.5e-07;5.1e-08;6e-08;3.2e-08;3.6e-08;1.7e-08;1.8e-08;5.9e-09;3.3e-09;4.9e-09;5e-09;8.3e-09;7.5e-09;5.5e-09;6.6e-09;6.3e-09;5.2e-09;6.3e-09;4.8e-09;6.1e-09;5.8e-09;7.2e-09;6.7e-09;4.4e-09;4.4e-09;9.4e-09;4e-09;3.4e-09;1.9e-09	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;6.3e-10;0.0062;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0138888888888889	GAT	ORF1ab:nsp3	.	809-860-delfrshift	.	no-SNV	ORF1ab:nsp3	0.986230636833046
CAMB-724FE	MN908947.3	4531	TTACTTTTACACCAGTAAAACAACTG	-	0.0411153846153846	0.0448076923076923	NA;3.4e-05;3.9e-05;3.9e-05;8.5e-06;6e-06;2.2e-05;1.7e-05;1.2e-05;2.3e-05;1.8e-05;1.9e-05;8.3e-06;1.8e-05;1.6e-05;2e-05;3.6e-06;3.2e-06;2.7e-06;3.4e-06;3.4e-06;3.3e-06;2.7e-06;3e-06;2.3e-06;3.2e-07	4.7e-06;2.1e-05;3.1e-05;2.6e-05;4.9e-06;4.4e-06;1.2e-05;1.1e-05;8e-06;1.6e-05;1.1e-05;1.4e-05;5.2e-06;1.3e-05;1.1e-05;1.4e-05;2.6e-06;2.1e-06;2.1e-06;2.3e-06;2.5e-06;2.2e-06;1.7e-06;2e-06;1.5e-06;2.1e-07	0.0428888536546694	TTT	ORF1ab:nsp3	.	1812-1837-delfrshift	.	no-SNV	ORF1ab:nsp3	0.986219195849546
CAMB-724FE	MN908947.3	686	AAGTCATTT	-	0.0597777777777778	0.0226666666666667	2.3e-08;1.7e-08;1.2e-07;1.7e-08;1.4e-07;4.8e-08;1.8e-08;6.8e-08;4.3e-07	0.0017;0.0015;0.003;0.0015;0.0032;0.002;0.0013;0.0022;0.004	0.0465668866304221	AAA	ORF1ab:leader-protein	.	421-429-delinframe	.	no-SNV	ORF1ab:leader-protein	0.953980765796791
CAMB-724FE	MN908947.3	9751	GAGACGTGTAGTCTTT	-	0.027625	0.001568375	6.4e-14;3.3e-14;6.5e-14;1.6e-14;3.8e-14;1.3e-13;9.9e-14;3.6e-09;3e-12;4.1e-11;7.5e-14;5.8e-14;2.3e-15;6.1e-14;3.6e-14;4.4e-14	NA;NA;NA;NA;NA;NA;NA;1.4e-08;NA;NA;NA;NA;NA;NA;NA;NA	0.0154657221112461	AGA	ORF1ab:nsp4	.	1197-1212-delfrshift	.	no-SNV	ORF1ab:nsp4	0.984692841771895
CAMB-7250A	MN908947.3	11074	C	INS	0.028	0.029	4.8e-06	9.7e-06	0.0282783026525113	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.970828869192559
CAMB-7250A	MN908947.3	11075	T	-	0.032	0.034	2.4e-08	3.6e-09	0.0328635221881105	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.96208484510187
CAMB-7250A	MN908947.3	11083	G	T	0.024	0.019	2.3e-05	0.00017	0.0225134408602151	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.973884408602151
CAMB-7250A	MN908947.3	14408	C	T	0.97	0.97	0	0	0.973896292801824	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.022617971196813
CAMB-7250A	MN908947.3	14805	C	T	0.02	0.023	1.9e-10	9.6e-12	0.0211351351351351	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.978745945945946
CAMB-7250A	MN908947.3	18265	C	T	0.0084	0.0078	7.2e-06	9.6e-06	0.00815469372170403	CCG	ORF1ab:3'-to-5'-exonuclease	R76C	C226T	CGC>TGC	Missense	ORF1ab:3'-to-5'-exonuclease	0.991818033055146
CAMB-7250A	MN908947.3	21602	C	T	0.017	0.015	9.4e-09	5.7e-08	0.0164372710169324	TCA	S	Q14*	C40T	CAG>TAG	Nonsense	GU280_gp02, spike glycoprotein	0.983463709278146
CAMB-7250A	MN908947.3	23403	A	G	0.98	0.98	0	0	0.979925151326638	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.0199069822555322
CAMB-7250A	MN908947.3	241	C	T	0.97	0.97	0	0	0.971610743036261	TCG	NA	NA	NA	NA	NA	NA	0.0273206525610886
CAMB-7250A	MN908947.3	2480	A	G	0.024	0.025	1.2e-11	1.2e-11	0.0244013891427527	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.975598610857247
CAMB-7250A	MN908947.3	24865	C	T	0.018	0.023	1.1e-09	7e-12	0.0196568452443455	ACT	S	H1101H	C3303T	CAC>CAT	Synonymous	GU280_gp02, spike glycoprotein	0.980175147531344
CAMB-7250A	MN908947.3	2558	C	T	0.024	0.026	9.2e-12	4.2e-13	0.0245347931995681	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.975289420155194
CAMB-7250A	MN908947.3	26144	G	T	0.013	0.015	2.8e-07	2.7e-08	0.013977547875853	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.9859674224081
CAMB-7250A	MN908947.3	26994	C	T	0.016	0.013	8.2e-09	1.1e-07	0.0153488163959368	ACG	M	R158C	C472T	CGC>TGC	Missense	GU280_gp05	0.984449814292746
CAMB-7250A	MN908947.3	28881	GGG	AAC	0.98	0.98	0;0;0	0;0;0	0.980085298368052	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.0214269078487695
CAMB-7250A	MN908947.3	3037	C	T	0.97	0.97	0	0	0.971536296532314	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.0279857681482662
CAMB-7250A	MN908947.3	4788	C	T	0.0079	0.0074	1.9e-05	2.5e-05	0.00769641566927402	GCT	ORF1ab:nsp3	A690V	C2069T	GCT>GTT	Missense	ORF1ab:nsp3	0.992193635535451
CAMB-72519	MN908947.3	10097	G	A	1	1	0	0	0.9996255996256	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.00014040014040014
CAMB-72519	MN908947.3	11075	T	-	0.039	0.034	1.3e-09	3.4e-09	0.037434857452779	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958603532435683
CAMB-72519	MN908947.3	13536	C	T	1	1	0	0	0.999608055394838	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000111984172903563
CAMB-72519	MN908947.3	14408	C	T	1	1	0	0	0.998204923976747	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000677611478976212
CAMB-72519	MN908947.3	17122	G	T	0.13	0.12	3.4e-58	1.1e-56	0.12509845018258	AGC	ORF1ab:helicase	A296S	G886T	GCT>TCT	Missense	ORF1ab:helicase	0.873371910616998
CAMB-72519	MN908947.3	22661	G	T	0.031	0.034	6.3e-15	3.3e-16	0.0321111788205024	TGT	S	V367F	G1099T	GTC>TTC	Missense	GU280_gp02, spike glycoprotein	0.966856252962286
CAMB-72519	MN908947.3	23403	A	G	1	1	0	0	0.999113649793185	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.95303239207119e-05
CAMB-72519	MN908947.3	23731	C	T	1	1	0	0	0.999715069273783	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000142465363108594
CAMB-72519	MN908947.3	241	C	T	1	1	0	0	0.998262032085562	TCG	NA	NA	NA	NA	NA	NA	2.22816399286988e-05
CAMB-72519	MN908947.3	25366	C	T	0.13	0.13	2.9e-59	6e-61	0.130930056816592	TCA	S	V1268V	C3804T	GTC>GTT	Synonymous	GU280_gp02, spike glycoprotein	0.868902012370903
CAMB-72519	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99928265894418	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	2.98694704142896e-05
CAMB-72519	MN908947.3	3037	C	T	1	1	0	0	0.999226818357541	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.52272601756227e-05
CAMB-72519	MN908947.3	4002	C	T	1	1	0	0	0.999730594376158	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	6.73514059605994e-05
CAMB-72519	MN908947.3	5869	C	T	0.11	0.11	1.3e-47	6.2e-48	0.106513632405154	ACA	ORF1ab:nsp3	Y1050Y	C3150T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.893084429359355
CAMB-72519	MN908947.3	884	C	T	1	1	0	0	0.998489868068319	ACG	ORF1ab:nsp2	R27C	C79T	CGT>TGT	Missense	ORF1ab:nsp2	0.000234128981655994
CAMB-72537	MN908947.3	11075	T	-	0.039	0.042	5.5e-10	5e-11	0.0403136531365314	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954858548585486
CAMB-72537	MN908947.3	13685	A	T	0.0088	0.012	5.8e-06	1.2e-07	0.0101223647603021	CAT	ORF1ab:RNA-dependent-RNA-polymerase	H73L	A218T	CAT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.989632398332389
CAMB-72537	MN908947.3	14408	C	T	1	1	0	0	0.998179154160206	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000512112892442067
CAMB-72537	MN908947.3	23403	A	G	1	1	0	0	0.998900217665254	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000217665253751862
CAMB-72537	MN908947.3	241	C	T	1	1	0	0	0.998718062063478	TCG	NA	NA	NA	NA	NA	NA	0.000176819025727168
CAMB-72537	MN908947.3	24919	C	T	0.027	0.023	2.1e-13	3.3e-12	0.0252818140353163	ACA	S	N1119N	C3357T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.974196911448492
CAMB-72537	MN908947.3	25429	G	T	1	1	0	0	0.998328088119591	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	1.9669551534225e-05
CAMB-72537	MN908947.3	3037	C	T	1	1	0	0	0.998332638599416	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000104210087536474
CAMB-72546	MN908947.3	10252	C	T	0.15	0.16	3e-69	7.1e-73	0.154012898602651	TCT	ORF1ab:3C-like-proteinase	F66F	C198T	TTC>TTT	Synonymous	ORF1ab:3C-like-proteinase	0.845485489072017
CAMB-72546	MN908947.3	11074	C	INS	0.11	0.12	6.1e-49	8.8e-43	0.115788924537653	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.882998148003235
CAMB-72546	MN908947.3	11083	G	-	0.16	0.14	1.1e-71	3.8e-63	0.155971896955504	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.40196961508437e-05
CAMB-72546	MN908947.3	11083	G	T	0.84	0.86	0	0	0.843932024259893	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.40196961508437e-05
CAMB-72546	MN908947.3	13680	C	T	0.4	0.4	6.5e-218	7.8e-213	0.399414776883687	ACC	ORF1ab:RNA-dependent-RNA-polymerase	Y71Y	C213T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.600565972355908
CAMB-72546	MN908947.3	14805	C	T	1	1	0	0	0.999783434938441	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	1.08282530779309e-05
CAMB-72546	MN908947.3	1515	A	G	1	1	0	0	0.999128160418483	CAT	ORF1ab:nsp2	H237R	A710G	CAT>CGT	Missense	ORF1ab:nsp2	0.000726532984597501
CAMB-72546	MN908947.3	15436	A	G	0.021	0.015	5.2e-11	1.4e-08	0.0192581743329903	AAT	ORF1ab:RNA-dependent-RNA-polymerase	M657V	A1969G	ATG>GTG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.980583485076399
CAMB-72546	MN908947.3	16375	C	T	0.03	0.044	5.4e-11	1.4e-16	0.0415958404159584	TCC	ORF1ab:helicase	P47S	C139T	CCG>TCG	Missense	ORF1ab:helicase	0.958404159584042
CAMB-72546	MN908947.3	16428	C	T	0.007	0.0079	0.00013	2.5e-05	0.00768851651059635	ACT	ORF1ab:helicase	Y64Y	C192T	TAC>TAT	Synonymous	ORF1ab:helicase	0.992311483489404
CAMB-72546	MN908947.3	16573	G	T	0.047	0.037	5.8e-09	5e-06	0.0434782608695652	TGA	ORF1ab:helicase	D113Y	G337T	GAC>TAC	Missense	ORF1ab:helicase	0.956521739130435
CAMB-72546	MN908947.3	16949	C	T	0.037	0.047	1.5e-17	5e-22	0.0410781651509905	CCT	ORF1ab:helicase	P238L	C713T	CCT>CTT	Missense	ORF1ab:helicase	0.958903610285943
CAMB-72546	MN908947.3	17247	T	C	1	1	0	0	0.999254461581473	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000232980755789572
CAMB-72546	MN908947.3	20762	C	T	0.038	0.038	5.1e-18	9.7e-18	0.0381097088281807	ACA	ORF1ab:2'-O-ribose-methyltransferase	T35I	C104T	ACA>ATA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.961859282458371
CAMB-72546	MN908947.3	23874	C	A	0.0098	0.0089	3.1e-06	5.5e-06	0.00944803580308304	GCT	S	A771D	C2312A	GCT>GAT	Missense	GU280_gp02, spike glycoprotein	0.990170727664512
CAMB-72546	MN908947.3	24834	G	A	0.13	0.12	1.5e-61	4.6e-56	0.129223752241352	CGT	S	R1091H	G3272A	CGT>CAT	Missense	GU280_gp02, spike glycoprotein	0.870741430635587
CAMB-72546	MN908947.3	25626	C	T	0.065	0.06	9.5e-30	6.7e-28	0.0631813197445656	ACT	ORF3a	H78H	C234T	CAC>CAT	Synonymous	GU280_gp03	0.93657141628502
CAMB-72546	MN908947.3	26144	G	T	1	1	0	0	0.998889985199803	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000986679822397632
CAMB-72546	MN908947.3	29218	C	T	0.052	0.055	6.1e-24	1.3e-25	0.0531389467420411	TCG	N	F315F	C945T	TTC>TTT	Synonymous	GU280_gp10	0.946742041059209
CAMB-72546	MN908947.3	29528	G	T	0.0089	0.0091	1.4e-05	1.1e-05	0.00900313152400835	GGC	N	A419S	G1255T	GCC>TCC	Missense	GU280_gp10	0.990735908141962
CAMB-72546	MN908947.3	29736	G	T	0.028	0.031	1.3e-11	1.3e-13	0.029771520886222	AGG	NA	NA	NA	NA	NA	NA	0.96976690514655
CAMB-72546	MN908947.3	6673	T	C	0.048	0.031	2.3e-20	1.7e-14	0.0374267247858109	ATA	ORF1ab:nsp3	D1318D	T3954C	GAT>GAC	Synonymous	ORF1ab:nsp3	0.962573275214189
CAMB-72546	MN908947.3	9223	C	T	1	1	0	0	0.999841709537	ACG	ORF1ab:nsp4	H223H	C669T	CAC>CAT	Synonymous	ORF1ab:nsp4	0.000131908719166337
CAMB-72546	MN908947.3	9951	C	T	0.055	0.044	5.9e-25	1.2e-20	0.0511293403753231	GCT	ORF1ab:nsp4	A466V	C1397T	GCT>GTT	Missense	ORF1ab:nsp4	0.948617822227217
CAMB-72555	MN908947.3	14408	C	T	1	1	0	0	0.999765515085196	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000234484914803814
CAMB-72555	MN908947.3	23403	A	G	1	1	0	0	0.999772764832259	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000185919682697075
CAMB-72555	MN908947.3	23885	G	C	0.17	0.19	6.3e-69	2.7e-49	0.17343976777939	AGA	S	D775H	G2323C	GAC>CAC	Missense	GU280_gp02, spike glycoprotein	0.825471698113208
CAMB-72555	MN908947.3	241	C	T	1	1	0	0	1	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-72555	MN908947.3	25429	G	T	1	1	0	0	0.999953505672308	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	4.64943276920216e-05
CAMB-72555	MN908947.3	3037	C	T	1	1	3.1e-111	4.4e-257	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-72555	MN908947.3	6558	C	T	1	1	8.7e-162	3.3e-269	1	GCT	ORF1ab:nsp3	A1280V	C3839T	GCT>GTT	Missense	ORF1ab:nsp3	0
CAMB-72564	MN908947.3	11074	C	INS	0.025	0.021	2.4e-05	0.00084	0.0234682566983909	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.97614952413714
CAMB-72564	MN908947.3	11075	T	-	0.044	0.052	1.4e-10	4.5e-13	0.0464500760934295	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.949601887999294
CAMB-72564	MN908947.3	14408	C	T	1	1	0	0	0.997933908972568	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000238854454038432
CAMB-72564	MN908947.3	23403	A	G	1	1	0	0	0.999614943539004	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.20787189338958e-05
CAMB-72564	MN908947.3	241	C	T	1	1	0	0	0.998949441891005	TCG	NA	NA	NA	NA	NA	NA	6.56598818122127e-05
CAMB-72564	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999134922292158	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	6.54857404800105e-05
CAMB-72564	MN908947.3	3037	C	T	1	1	0	0	0.999601865544307	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-72573	MN908947.3	11075	T	-	0.031	0.028	2.5e-08	5e-08	0.030029864966379	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.965701093827296
CAMB-72573	MN908947.3	14408	C	T	1	1	0	0	0.998777127390716	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000456539107466045
CAMB-72573	MN908947.3	16365	G	T	1	1	0	0	0.999525680986584	TGT	ORF1ab:helicase	L43F	G129T	TTG>TTT	Missense	ORF1ab:helicase	6.77598590594932e-05
CAMB-72573	MN908947.3	20268	A	G	1	1	0	0	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-72573	MN908947.3	23403	A	G	1	1	0	0	0.999589543924664	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.03638986290767e-05
CAMB-72573	MN908947.3	241	C	T	1	1	0	0	0.999190162606824	TCG	NA	NA	NA	NA	NA	NA	0.000213115103467383
CAMB-72573	MN908947.3	27577	C	T	0.064	0.054	2.2e-23	1e-18	0.0598461100028498	TCA	ORF7a	Q62*	C184T	CAA>TAA	Nonsense	GU280_gp07	0.94015388999715
CAMB-72573	MN908947.3	29734	G	C	1	1	0	0	0.998811096433289	CGA	NA	NA	NA	NA	NA	NA	0
CAMB-72573	MN908947.3	3037	C	T	1	1	0	0	0.999554477501114	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.90049997524875e-05
CAMB-72582	MN908947.3	11074	C	INS	0.065	0.086	6.5e-21	2.9e-25	0.0724923964506318	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.92728811965008
CAMB-72582	MN908947.3	11083	G	-	0.22	0.21	3e-98	5.7e-96	0.213768813801833	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.37578075557879e-05
CAMB-72582	MN908947.3	11083	G	T	0.78	0.79	2.6000000000049e-313	6.17582057301558e-322	0.786148639352833	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.37578075557879e-05
CAMB-72582	MN908947.3	12881	TA	-	0.0033	0.00605	0.0016;0.0012	8.1e-05;4.4e-05	0.00417377754693181	CTA	ORF1ab:nsp9	.	196-197-delfrshift	.	no-SNV	ORF1ab:nsp9	0.995982392397988
CAMB-72582	MN908947.3	14805	C	T	1	1	0	0	0.999925183300913	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	2.99266796348945e-05
CAMB-72582	MN908947.3	17561	G	A	0.014	0.0067	3.2e-08	2.4e-05	0.010484897035955	CGG	ORF1ab:helicase	R442Q	G1325A	CGG>CAG	Missense	ORF1ab:helicase	0.989491541397672
CAMB-72582	MN908947.3	22859	GTTATAGCTTGGAA	-	0.00540214285714286	0.0113928571428571	0.019;0.011;0.012;0.0072;0.0037;0.0037;0.0034;0.0039;0.0036;0.003;0.0027;0.003;0.0025;0.2	0.00073;0.00035;0.00042;0.00013;5.2e-05;5.6e-05;5.1e-05;7.9e-05;5.1e-05;3.7e-05;2.6e-05;4.1e-05;2.5e-05;9.5e-05	0.00775822139879574	CGT	S	.	1297-1310-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.992155329085095
CAMB-72582	MN908947.3	23378	AACCAGGTTGCTGTTCTTTATC	-	0.000407045454545455	0.00527272727272727	0.45;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;4e-04;0.00063;NA;NA	8.3e-05;4.2e-05;0.00015;0.00012;7.9e-05;0.00017;0.00012;6e-05;0.00018;0.00017;0.00016;0.00024;0.00039;0.00014;0.00015;0.00013;0.00028;0.00017;0.00011;2e-04;0.00015;0.00015	0.00189110393192026	TAA	S	.	1816-1837-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.997869692182488
CAMB-72582	MN908947.3	23555	CCCATTGGTGCAGGTATATGCGCTAGTT	-	0.0204928571428571	0.0765357142857143	0.16;0.14;0.15;0.14;0.13;0.16;0.029;0.0086;0.0088;0.009;0.0088;0.0088;0.0071;0.007;3e-04;9.6e-05;0.00056;0.00034;0.0025;0.0017;0.0028;0.004;0.0029;0.0029;5e-04;0.0081;0.017;0.014	5.5e-07;3.9e-07;6.6e-07;1.1e-06;9.9e-08;2.2e-07;5.5e-08;2.3e-07;2.5e-07;2.7e-07;2.2e-07;2.6e-07;7e-08;6.3e-08;8.7e-09;9.6e-10;1.3e-08;2.3e-09;1.2e-08;1.4e-09;8.8e-09;5.7e-08;1.2e-08;1.5e-08;1.9e-12;5.1e-12;3.9e-08;2.8e-08	0.0450710479573712	ACC	S	.	1993-2020-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.962733606104169
CAMB-72582	MN908947.3	24321	A	-	0.008	0.016	0.0067	8.3e-06	0.0112256586483391	CAA	S	.	2759-2759-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.988316151202749
CAMB-72582	MN908947.3	24382	C	T	0.016	0.036	1.4e-08	9.1e-17	0.0234444116779711	CCA	S	S940S	C2820T	TCC>TCT	Synonymous	GU280_gp02, spike glycoprotein	0.976555588322029
CAMB-72582	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-72582	MN908947.3	24865	C	T	1	1	0	0	0.999915962855582	ACT	S	H1101H	C3303T	CAC>CAT	Synonymous	GU280_gp02, spike glycoprotein	4.20185722089163e-05
CAMB-72582	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-72582	MN908947.3	26144	G	T	1	1	0	3.1e-270	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-72582	MN908947.3	26994	C	T	1	1	0	0	0.999899684004614	ACG	M	R158C	C472T	CGC>TGC	Missense	GU280_gp05	5.01579976927321e-05
CAMB-72582	MN908947.3	522	T	-	0.051	0.035	1.1e-06	0.00011	0.0457208500861574	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.954078116025273
CAMB-72582	MN908947.3	8700	TT	-	0.00615	0.0175	0.00012;9e-05	8.3e-09;4.3e-09	0.00844688819826281	ATT	ORF1ab:nsp4	.	146-147-delfrshift	.	no-SNV	ORF1ab:nsp4	0.991568828303522
CAMB-72582	MN908947.3	9006	TTT	-	0.0131666666666667	0.0126666666666667	9.6e-08;8.5e-09;1.8e-05	3.7e-11;4.7e-08;NA	0.0149351651744366	GTT	ORF1ab:nsp4	.	452-454-delinframe	.	no-SNV	ORF1ab:nsp4	0.98061297758966
CAMB-72591	MN908947.3	1059	C	T	1	1	0	0	0.999723331777075	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	6.91670557313552e-05
CAMB-72591	MN908947.3	11075	T	-	0.034	0.033	1.7e-08	7.5e-09	0.0336352752490456	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962287379430301
CAMB-72591	MN908947.3	12789	C	T	0.016	0.013	1.1e-08	8e-08	0.0151196199470884	ACA	ORF1ab:nsp9	T35I	C104T	ACA>ATA	Missense	ORF1ab:nsp9	0.984411003328308
CAMB-72591	MN908947.3	12924	C	T	0.0082	0.0092	1.6e-05	4e-06	0.00856108489866168	CCT	ORF1ab:nsp9	P80L	C239T	CCT>CTT	Missense	ORF1ab:nsp9	0.991320217217128
CAMB-72591	MN908947.3	14120	C	T	0.022	0.025	3.5e-11	6.4e-13	0.023207119176409	CCA	ORF1ab:RNA-dependent-RNA-polymerase	P218L	C653T	CCA>CTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.976695942146998
CAMB-72591	MN908947.3	14408	C	T	1	1	0	0	0.996328761225978	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00057400475945613
CAMB-72591	MN908947.3	16554	T	C	1	1	4.94065645841247e-324	7.7e-249	1	TTA	ORF1ab:helicase	F106F	T318C	TTT>TTC	Synonymous	ORF1ab:helicase	0
CAMB-72591	MN908947.3	23403	A	G	1	1	0	0	0.998748424355662	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000134097390464782
CAMB-72591	MN908947.3	241	C	T	1	1	0	0	0.998383879562628	TCG	NA	NA	NA	NA	NA	NA	0.000276633228018578
CAMB-72591	MN908947.3	25563	G	T	1	1	0	0	0.999711893705725	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	8.47371453750466e-05
CAMB-72591	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0276216216216216	0.0336756756756757	0.0039;0.00069;0.0022;0.0018;0.0019;7.1e-05;0.00021;0.00014;0.00013;6.6e-05;9.8e-05;8e-05;0.00012;8.4e-05;1e-04;0.00016;7.7e-05;0.00014;1e-04;1e-04;1e-04;0.00015;0.00011;0.00012;8.6e-05;7.5e-05;0.00011;7.8e-05;4e-05;8.6e-05;0.00012;0.00012;9.8e-05;0.00013;5.9e-05;8.3e-05;8.2e-05	2e-04;2.1e-05;6.7e-05;5.6e-05;0.00011;2.9e-06;1.1e-05;9.5e-06;8.9e-06;6.3e-06;4.8e-06;4.8e-06;7.9e-06;6.1e-06;7e-06;1.1e-05;5.4e-06;1.1e-05;6e-06;7.8e-06;8.6e-06;1.2e-05;8e-06;8.9e-06;6.5e-06;4.6e-06;9.3e-06;6.3e-06;1.1e-06;6.5e-06;9.4e-06;9.2e-06;4.5e-06;1.1e-05;1.9e-06;6.4e-06;3.9e-06	0.0305891688157112	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.979124934106484
CAMB-72591	MN908947.3	29813	A	G	0.021	0.02	3.5e-10	2.8e-10	0.0207417823870628	AAA	NA	NA	NA	NA	NA	NA	0.979082439796098
CAMB-72591	MN908947.3	3037	C	T	1	1	0	0	0.999461844796039	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.38155203960822e-05
CAMB-72591	MN908947.3	3902	C	T	0.084	0.09	2.3e-37	8.1e-40	0.0856992119233686	GCC	ORF1ab:nsp3	P395S	C1183T	CCA>TCA	Missense	ORF1ab:nsp3	0.914135918488476
CAMB-72591	MN908947.3	635	C	T	0.044	0.048	4.4e-20	2.7e-22	0.0453552554315913	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.95460951262478
CAMB-72591	MN908947.3	8713	C	A	1	1	0	0	0.99759067357513	TCA	ORF1ab:nsp4	V53V	C159A	GTC>GTA	Synonymous	ORF1ab:nsp4	5.18134715025907e-05
CAMB-72591	MN908947.3	944	G	A	0.009	0.0093	5.3e-06	2.2e-06	0.00912649495015031	GGG	ORF1ab:nsp2	G47S	G139A	GGT>AGT	Missense	ORF1ab:nsp2	0.990862691667207
CAMB-72591	MN908947.3	9979	C	T	0.023	0.029	2.3e-11	8e-14	0.0249472351203039	TCA	ORF1ab:nsp4	L475L	C1425T	CTC>CTT	Synonymous	ORF1ab:nsp4	0.974926129168425
CAMB-725A0	MN908947.3	11418	T	C	0.019	0.054	5.7e-08	7.1e-13	0.0282485875706215	GTT	ORF1ab:nsp6	V149A	T446C	GTT>GCT	Missense	ORF1ab:nsp6	0.971751412429379
CAMB-725A0	MN908947.3	12125	T	C	0.012	0.019	4.9e-06	6e-09	0.014529757531227	ATA	ORF1ab:nsp8	Y12H	T34C	TAT>CAT	Missense	ORF1ab:nsp8	0.985470242468773
CAMB-725A0	MN908947.3	14408	C	T	1	1	0	0	0.999632055338877	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00022076679667378
CAMB-725A0	MN908947.3	15821	TGTCTGAAGCAAAATGTTGGACTGAGACTG	-	0.000336666666666667	0.0101333333333333	NA;3.8e-06;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	1.1e-06;3.9e-06;1.1e-06;1.2e-06;7.6e-07;9.7e-07;8.7e-07;6.8e-06;2.4e-06;2.3e-06;1.2e-05;3.2e-06;4.4e-07;2.6e-07;6.3e-07;9.7e-07;4.8e-07;4.4e-07;8.5e-06;1.4e-06;1.7e-06;1.4e-06;1.6e-06;1.7e-06;1.4e-06;1.4e-06;1.4e-06;1.4e-06;1.1e-06;2.1e-06	0.00419311630073962	ATG	ORF1ab:RNA-dependent-RNA-polymerase	.	2354-2383-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.995761727821644
CAMB-725A0	MN908947.3	17502	C	T	1	1	0	0	0.999908604853082	TCA	ORF1ab:helicase	F422F	C1266T	TTC>TTT	Synonymous	ORF1ab:helicase	0
CAMB-725A0	MN908947.3	22104	G	C	0.022	0.016	7.1e-08	2.5e-06	0.0205621301775148	GGA	S	G181A	G542C	GGA>GCA	Missense	GU280_gp02, spike glycoprotein	0.979437869822485
CAMB-725A0	MN908947.3	222	C	T	0.018	0.037	1.8e-09	1.2e-17	0.0250870685505564	TCA	NA	NA	NA	NA	NA	NA	0.974856301497862
CAMB-725A0	MN908947.3	23165	A	-	0.0085	0.01	2.7e-05	3.5e-06	0.0092135854255594	TAA	S	.	1603-1603-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.990405077927989
CAMB-725A0	MN908947.3	23403	A	G	1	1	0	0	0.99986833789762	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000118495892142406
CAMB-725A0	MN908947.3	23417	G	T	0.013	0.013	2.8e-07	1.5e-07	0.0130407375305334	AGA	S	E619*	G1855T	GAA>TAA	Nonsense	GU280_gp02, spike glycoprotein	0.986919864470885
CAMB-725A0	MN908947.3	241	C	T	1	0.98	0	0	0.993866605808182	TCG	NA	NA	NA	NA	NA	NA	0.000114109659382667
CAMB-725A0	MN908947.3	25429	G	T	1	1	0	0	0.999837358705375	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0
CAMB-725A0	MN908947.3	28146	C	T	0.082	0.078	2.6e-37	5.4e-36	0.0805112262521589	ACC	ORF8	P85S	C253T	CCT>TCT	Missense	GU280_gp09	0.919474956822107
CAMB-725A0	MN908947.3	28436	G	T	0.011	0.011	1.4e-06	8.9e-07	0.0107303325363549	CGC	N	A55S	G163T	GCT>TCT	Missense	GU280_gp10	0.988830751816302
CAMB-725A0	MN908947.3	3037	C	T	1	1	9.99999999963881e-315	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-725A0	MN908947.3	9165	C	T	0.022	0.04	3.1e-11	6.7e-19	0.0298514754739105	ACC	ORF1ab:nsp4	T204I	C611T	ACC>ATC	Missense	ORF1ab:nsp4	0.970099667774086
CAMB-725BF	MN908947.3	11075	T	-	0.033	0.035	9.6e-09	1.7e-09	0.0339286311494599	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961924350356175
CAMB-725BF	MN908947.3	14408	C	T	1	1	0	0	0.998831250561899	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000389583146033744
CAMB-725BF	MN908947.3	16662	G	A	0.028	0.0065	1.3e-05	0.0062	0.0192061459667093	AGG	ORF1ab:helicase	E142E	G426A	GAG>GAA	Synonymous	ORF1ab:helicase	0.980793854033291
CAMB-725BF	MN908947.3	21700	A	T	0.31	0.3	2.3e-153	6.4e-149	0.304735970354566	CAG	S	S46S	A138T	TCA>TCT	Synonymous	GU280_gp02, spike glycoprotein	0.695095589680245
CAMB-725BF	MN908947.3	23403	A	G	1	1	0	0	0.999619486883828	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000103776304410493
CAMB-725BF	MN908947.3	241	C	T	1	1	0	0	0.999139212770952	TCG	NA	NA	NA	NA	NA	NA	0.000130422307431463
CAMB-725BF	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999480271990991	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	9.79192166462668e-05
CAMB-725BF	MN908947.3	3037	C	T	1	1	0	0	0.999248779266308	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000292141396435875
CAMB-725DD	MN908947.3	11074	C	INS	0.1	0.11	1.1e-39	7.6e-35	0.105550766828761	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.889147299429148
CAMB-725DD	MN908947.3	11083	G	-	0.16	0.14	3e-69	1.2e-62	0.151845747706489	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.4585126088415e-05
CAMB-725DD	MN908947.3	11083	G	T	0.84	0.86	0	0	0.848052156410892	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.4585126088415e-05
CAMB-725DD	MN908947.3	14805	C	T	1	1	0	0	0.997429615647215	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00124502992088036
CAMB-725DD	MN908947.3	18646	C	T	0.0065	0.013	6.1e-05	6.4e-08	0.00903321443461342	ACC	ORF1ab:3'-to-5'-exonuclease	P203S	C607T	CCT>TCT	Missense	ORF1ab:3'-to-5'-exonuclease	0.990661045999907
CAMB-725DD	MN908947.3	19900	G	T	1	1	0	0	0.999872983614886	AGC	ORF1ab:endoRNAse	A94S	G280T	GCA>TCA	Missense	ORF1ab:endoRNAse	4.23387950378932e-05
CAMB-725DD	MN908947.3	2480	A	G	1	1	0	0	0.999710270896712	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000144864551644213
CAMB-725DD	MN908947.3	2558	C	T	1	1	0	0	0.999038197306952	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	6.87001923605386e-05
CAMB-725DD	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-725DD	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0304210526315789	0.0347105263157895	0.0015;0.00014;0.0011;0.0012;0.0014;0.00022;0.00043;2.8e-05;2.9e-05;7.7e-06;1.7e-05;1.4e-05;2.1e-05;1.6e-05;1.4e-05;1.9e-05;1.4e-05;2.4e-05;1.6e-05;1.7e-05;1.9e-05;2.6e-05;1.7e-05;2.1e-05;1.6e-05;1.6e-05;2.3e-05;1.4e-05;8.1e-06;1.6e-05;2.2e-05;2.1e-05;1.5e-05;2.5e-05;1.5e-05;2.7e-05;2.4e-05;0.0055	0.00047;5.6e-05;7.1e-05;7.8e-05;0.00014;2e-05;4.6e-05;5.2e-06;4.9e-06;2.9e-06;3.5e-06;2.8e-06;3.9e-06;3.5e-06;4.7e-06;6.8e-06;3e-06;5.5e-06;3.1e-06;4.1e-06;4.8e-06;6.7e-06;4e-06;4.7e-06;3.4e-06;2.9e-06;5.1e-06;3.6e-06;5e-07;3.7e-06;5.4e-06;5.1e-06;1.1e-06;2.9e-06;3.5e-07;1e-06;5.6e-07;0.00011	0.033613171938045	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.978668997216288
CAMB-725DD	MN908947.3	6070	C	T	1	1	0	0	1	TCA	ORF1ab:nsp3	I1117I	C3351T	ATC>ATT	Synonymous	ORF1ab:nsp3	0
CAMB-725EC	MN908947.3	10534	TTACATGCACCATATGGAA	-	0.00668947368421053	0.000363157894736842	9.1e-05;9.2e-05;9.4e-05;6.5e-05;1e-04;8.2e-05;6.5e-05;8.1e-05;8.6e-05;9.7e-05;5.8e-05;5.5e-05;3.8e-05;6.2e-05;6.3e-05;9.9e-05;0.00017;0.00034;0.00034	NA;NA;4.3e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00470938158383939	GTT	ORF1ab:3C-like-proteinase	.	480-498-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.995355337251839
CAMB-725EC	MN908947.3	1059	C	T	1	1	0	0	0.999926801595725	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	3.65992021373934e-05
CAMB-725EC	MN908947.3	11025	TTTTGACTTCACTTTTAGT	-	0.000453421052631579	0.00938947368421053	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0018;NA;NA;NA;NA;NA;0.0074	7.2e-06;4.1e-06;4.5e-06;4.4e-06;4.5e-06;4.9e-06;1.1e-05;3.7e-06;5.2e-06;5.4e-06;4.6e-06;6.7e-06;7.6e-06;7.9e-07;1.8e-06;3.6e-06;4.6e-06;4.4e-06;1.4e-05	0.00298671158158619	ATT	ORF1ab:nsp6	.	53-71-delfrshift	.	no-SNV	ORF1ab:nsp6	0.996915447557649
CAMB-725EC	MN908947.3	11074	C	INS	0.018	0.031	0.0021	1.8e-06	0.0223038054634454	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.97755145007632
CAMB-725EC	MN908947.3	11075	T	-	0.033	0.05	2.2e-08	8.6e-13	0.0387484459179445	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954413593037712
CAMB-725EC	MN908947.3	13126	G	A	0.016	0.011	4.7e-09	6e-07	0.0141457811383555	GGG	ORF1ab:nsp10	G34G	G102A	GGG>GGA	Synonymous	ORF1ab:nsp10	0.985772817307779
CAMB-725EC	MN908947.3	14408	C	T	1	1	0	0	0.999610092115738	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000308677075041022
CAMB-725EC	MN908947.3	20620	AA	-	0.0032	0.0063	0.0076;0.00066	0.00036;2.3e-05	0.00449315528680608	TAA	ORF1ab:endoRNAse	.	1000-1001-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.99561062771908
CAMB-725EC	MN908947.3	23403	A	G	1	1	0	0	0.998617712219045	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.78708981083486e-05
CAMB-725EC	MN908947.3	23841	G	T	0.0082	0.0046	7.6e-06	0.00022	0.00718757245536749	TGT	S	C760F	G2279T	TGT>TTT	Missense	GU280_gp02, spike glycoprotein	0.992667516809645
CAMB-725EC	MN908947.3	241	C	T	1	0.99	0	0	0.996690346844964	TCG	NA	NA	NA	NA	NA	NA	0.00148767237776849
CAMB-725EC	MN908947.3	25563	G	T	1	1	0	0	0.999750650645971	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	9.35060077609986e-05
CAMB-725EC	MN908947.3	26526	G	T	1	1	0	0	0.999754581151832	GGC	M	A2S	G4T	GCA>TCA	Missense	GU280_gp05	0.000163612565445026
CAMB-725EC	MN908947.3	3037	C	T	1	1	0	0	0.999877450980392	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-725EC	MN908947.3	4836	G	T	0.0069	0.0093	4.3e-05	3.6e-06	0.00787128139830999	GGT	ORF1ab:nsp3	G706V	G2117T	GGT>GTT	Missense	ORF1ab:nsp3	0.992109426245322
CAMB-725EC	MN908947.3	5384	GCT	-	0.00876666666666667	0.00186666666666667	0.00066;7e-04;6.3e-06	NA;NA;0.0024	0.00354039266173157	AGC	ORF1ab:nsp3	.	2665-2667-delinframe	.	no-SNV	ORF1ab:nsp3	0.995215311004785
CAMB-725EC	MN908947.3	9365	C	T	0.088	0.074	1.1e-39	8.3e-31	0.0855727470141151	ACT	ORF1ab:nsp4	L271L	C811T	CTA>TTA	Synonymous	ORF1ab:nsp4	0.914359391965255
CAMB-725FB	MN908947.3	11074	C	INS	0.021	0.028	0.00029	1.2e-05	0.0237563930200003	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.975744639565344
CAMB-725FB	MN908947.3	11075	T	-	0.037	0.037	3.5e-09	1e-09	0.0368115768701788	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959433116067691
CAMB-725FB	MN908947.3	14408	C	T	1	1	0	0	0.997925070709881	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000452079566003617
CAMB-725FB	MN908947.3	23403	A	G	1	1	0	0	0.999017130019657	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	1.7551249648975e-05
CAMB-725FB	MN908947.3	241	C	T	1	1	0	0	0.998419368518447	TCG	NA	NA	NA	NA	NA	NA	0.000115655962064844
CAMB-725FB	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0231875	0.0304375	0.0023;0.0055;0.0011;0.0012;0.00062;0.00085;0.00068;0.00098;0.00082;0.00098;0.0012;0.00078;0.001;0.00086;0.00082;0.00082;0.0012;0.00093;0.00099;0.00082;0.00081;0.001;0.00075;0.00046;0.00087;0.001;0.001;0.00079;0.0011;0.00053;0.00069;0.00059	9.6e-05;0.00031;4.9e-05;4.6e-05;3.2e-05;3.3e-05;2.6e-05;3.7e-05;3.7e-05;4.6e-05;5.8e-05;3.1e-05;5.2e-05;3.1e-05;3.9e-05;4.2e-05;6.2e-05;4.2e-05;4.5e-05;3.4e-05;2.7e-05;4.6e-05;3.6e-05;8.6e-06;3.8e-05;5e-05;4.8e-05;2.2e-05;5.1e-05;1.2e-05;3.2e-05;1.3e-05	0.0255948888454267	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.976195971118658
CAMB-725FB	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998989032534771	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000210245987805733
CAMB-725FB	MN908947.3	3037	C	T	1	1	0	0	0.999558087007758	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.82028871648826e-05
CAMB-725FB	MN908947.3	5175	C	T	0.0083	0.0086	3.8e-05	2.3e-05	0.0083373527182526	ACA	ORF1ab:nsp3	T819I	C2456T	ACA>ATA	Missense	ORF1ab:nsp3	0.991662647281747
CAMB-725FB	MN908947.3	8228	C	T	0.0058	0.0082	0.00013	6.3e-06	0.00658168313282381	TCT	ORF1ab:nsp3	L1837F	C5509T	CTT>TTT	Missense	ORF1ab:nsp3	0.993346620972483
CAMB-72607	MN908947.3	11941	C	T	0.27	0.15	4.4e-133	3.7e-67	0.207031411662459	TCC	ORF1ab:nsp7	V33V	C99T	GTC>GTT	Synonymous	ORF1ab:nsp7	0.792906509953234
CAMB-72607	MN908947.3	14408	C	T	0.98	1	0	0	0.990183498011036	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00032080071859361
CAMB-72607	MN908947.3	23403	A	G	1	1	0	0	0.999909222948439	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.56475429678044e-05
CAMB-72607	MN908947.3	241	C	T	1	1	0	0	0.99980564598416	TCG	NA	NA	NA	NA	NA	NA	9.71770079199261e-05
CAMB-72607	MN908947.3	28737	C	T	0.029	0.011	2.9e-14	1.7e-06	0.0209666605717072	GCT	N	A155V	C464T	GCT>GTT	Missense	GU280_gp10	0.979033339428293
CAMB-72607	MN908947.3	28881	GGG	AAC	0.99	1	0;0;0	0;0;0	0.994711233340385	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00292540224280839
CAMB-72607	MN908947.3	28897	TAGAATGGCTGGCAATGGCGGTG	-	0.00320434782608696	0.0202173913043478	0.0065;0.00074;4.9e-05;2.6e-05;2.1e-05;9.4e-05;8.9e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00098;1.3e-05;1.6e-07;6.7e-08;4.8e-08;2.8e-07;2.7e-07;5.8e-08;5.8e-08;4.6e-08;4e-08;2.6e-08;6e-08;1.9e-08;8.1e-08;6e-08;3.6e-08;3.1e-08;3.1e-08;2e-08;3.1e-08;2.3e-08;2.9e-08	0.00505561172901921	CTA	N	.	624-646-delfrshift	.	no-SNV	GU280_gp10	0.987236628849271
CAMB-72607	MN908947.3	29618	ATG	-	0.00653333333333333	0.0183666666666667	NA;0.00097;9e-04	0.00088;9.3e-07;7.9e-07	0.0152616279069767	AAT	ORF10	.	61-63-delinframe	.	no-SNV	GU280_gp11	0.996223564954683
CAMB-72607	MN908947.3	3037	C	T	1	1	4.1e-277	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-72607	MN908947.3	346	C	T	0.052	0.1	6.9e-25	1.1e-47	0.0677169850498339	TCG	ORF1ab:leader-protein	L27L	C81T	CTC>CTT	Synonymous	ORF1ab:leader-protein	0.932283014950166
CAMB-72607	MN908947.3	514	T	-	0.081	0.16	0.00093	2e-06	0.101490178369835	ATG	ORF1ab:leader-protein	.	249-249-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.896026191013773
CAMB-72607	MN908947.3	522	TT	-	0.067	0.0575	4.8e-09;1.1e-09	8.8e-08;4.7e-08	0.0646681888487884	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.933919711321606
CAMB-72616	MN908947.3	11075	T	-	0.04	0.037	4.2e-10	5.5e-10	0.0392753182430378	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957292436025546
CAMB-72616	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999435046487603	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000322830578512397
CAMB-72616	MN908947.3	27785	T	C	1	1	0	0	0.997905027932961	ATT	NA	NA	NA	NA	NA	NA	0.00209497206703911
CAMB-72616	MN908947.3	29032	G	A	1	1	0	0	0.999850483436887	AGG	N	E253E	G759A	GAG>GAA	Synonymous	GU280_gp10	9.13712330132571e-05
CAMB-72625	MN908947.3	11074	C	INS	0.023	0.027	0.00012	2.7e-05	0.024781250966206	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.974801348050583
CAMB-72625	MN908947.3	11075	T	-	0.032	0.036	2.3e-08	1.7e-09	0.0337543868873145	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961237660852535
CAMB-72625	MN908947.3	14408	C	T	1	1	0	0	0.996792373260406	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000383381682023233
CAMB-72625	MN908947.3	14481	C	T	1	1	0	0	0.999738662949873	ACT	ORF1ab:RNA-dependent-RNA-polymerase	H338H	C1014T	CAC>CAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000161780078650007
CAMB-72625	MN908947.3	15427	T	C	0.0056	0.0075	0.00013	1.2e-05	0.00624703174661162	ATT	ORF1ab:RNA-dependent-RNA-polymerase	L654L	T1960C	TTG>CTG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.993625105030504
CAMB-72625	MN908947.3	20268	A	G	1	1	0	1.9e-277	0.998714652956298	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-72625	MN908947.3	23403	A	G	1	1	0	0	0.99946523005011	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.92251777614926e-05
CAMB-72625	MN908947.3	241	C	T	1	1	0	0	0.998051968454457	TCG	NA	NA	NA	NA	NA	NA	0.000141389386370063
CAMB-72625	MN908947.3	2706	C	T	0.0059	0.0079	0.00022	3.3e-05	0.00672351590685471	ACA	ORF1ab:nsp2	T634I	C1901T	ACA>ATA	Missense	ORF1ab:nsp2	0.99319448999672
CAMB-72625	MN908947.3	27881	C	T	0.016	0.015	5.1e-08	1e-07	0.0155774185992036	ACG	NA	NA	NA	NA	NA	NA	0.984422581400796
CAMB-72625	MN908947.3	3037	C	T	1	1	0	0	0.999675934927733	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-72625	MN908947.3	5230	G	T	0.99	0.99	0	0	0.990504826713087	AGT	ORF1ab:nsp3	K837N	G2511T	AAG>AAT	Missense	ORF1ab:nsp3	0.000633011552460832
CAMB-72625	MN908947.3	6330	C	T	1	1	0	0	0.999627143922446	TCA	ORF1ab:nsp3	S1204L	C3611T	TCA>TTA	Missense	ORF1ab:nsp3	9.3214019388516e-05
CAMB-72625	MN908947.3	9518	T	C	1	1	0	0	0.999765595241583	ATT	ORF1ab:nsp4	F322L	T964C	TTC>CTC	Missense	ORF1ab:nsp4	0.000224637893482571
CAMB-72634	MN908947.3	11074	C	INS	0.1	0.1	8.1e-37	8.4e-32	0.102033098629594	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.883758621310619
CAMB-72634	MN908947.3	11074	C	T	0.013	0.0099	2.8e-08	2.9e-05	0.0116331418486971	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.883758621310619
CAMB-72634	MN908947.3	11083	G	-	0.16	0.15	3.7e-73	1.7e-65	0.158834663813678	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.64595506542671e-05
CAMB-72634	MN908947.3	11083	G	T	0.83	0.85	0	0	0.840967821578471	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.64595506542671e-05
CAMB-72634	MN908947.3	14805	C	T	1	1	0	0	0.998287996956439	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000672119713398009
CAMB-72634	MN908947.3	20309	A	G	0.023	0.013	4.6e-07	0.00011	0.0181268882175227	TAT	ORF1ab:endoRNAse	Y230C	A689G	TAT>TGT	Missense	ORF1ab:endoRNAse	0.974823766364552
CAMB-72634	MN908947.3	22000	C	T	0.047	0.048	8.1e-22	2.1e-22	0.0470203380309614	ACA	S	H146H	C438T	CAC>CAT	Synonymous	GU280_gp02, spike glycoprotein	0.950782295504486
CAMB-72634	MN908947.3	23559	TTGGTGCAGGTATATGCGCTAGT	-	0.033304347826087	0.0409565217391304	0.00078;0.0013;0.00043;0.00073;0.00078;0.00079;0.00076;0.00072;0.00048;0.00046;0.00019;9.6e-05;0.00064;0.00034;0.00053;0.00027;0.00057;0.00095;0.00057;0.00082;5.9e-05;8.6e-05;0.0029	0.00026;0.00039;7.7e-05;0.00016;0.00017;0.00018;0.00016;0.00015;9e-05;8.1e-05;2e-05;7.2e-06;1e-04;4.1e-05;0.00012;3.8e-05;8.3e-05;0.00019;1e-04;0.00014;2.9e-06;6.3e-06;0.00045	0.034337899543379	ATT	S	.	1997-2019-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.956260570362162
CAMB-72634	MN908947.3	2480	A	G	1	1	0	0	0.999812751615017	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	9.36241924913398e-05
CAMB-72634	MN908947.3	2558	C	T	1	1	0	0	0.998839330127674	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000138174984800752
CAMB-72634	MN908947.3	26144	G	T	1	1	0	0	0.999786678043838	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000106660978081169
CAMB-72634	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0388421052631579	0.0471842105263158	0.00019;1e-05;7.6e-05;7.1e-05;0.00013;2.3e-06;8.7e-06;6.1e-07;6.2e-07;1.9e-07;3.2e-07;2.4e-07;4.8e-07;3.1e-07;4.1e-07;6.4e-07;2.6e-07;5e-07;3.7e-07;3.4e-07;3.3e-07;6.2e-07;3.3e-07;4.8e-07;3.4e-07;2.7e-07;5.1e-07;2.8e-07;2.2e-07;3.3e-07;5e-07;4.6e-07;3.2e-07;6.1e-07;1.3e-07;3.7e-07;3e-07;0.0018	1.3e-05;6.4e-07;4e-06;3.7e-06;8.8e-06;2e-08;9.4e-08;1.2e-08;1e-08;5.8e-09;4.8e-09;3.8e-09;7.3e-09;6.1e-09;8.5e-09;1.4e-08;4.6e-09;1.2e-08;5.3e-09;7.6e-09;7.8e-09;1.4e-08;7.1e-09;9.2e-09;6.2e-09;3.7e-09;9.4e-09;6e-09;1e-09;7.2e-09;1.1e-08;9.9e-09;2.9e-09;1.2e-08;7e-10;5.4e-09;2.7e-09;0.00018	0.0444599841740123	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.97242808922806
CAMB-72634	MN908947.3	28077	G	T	0.053	0.05	3.9e-22	1.3e-20	0.0515139973338412	CGT	ORF8	V62L	G184T	GTG>TTG	Missense	GU280_gp09	0.948009902875643
CAMB-72634	MN908947.3	28313	C	T	0.0087	0.0071	1.4e-05	5.9e-05	0.00811713174257972	CCG	N	R14C	C40T	CGC>TGC	Missense	GU280_gp10	0.991775660857047
CAMB-72634	MN908947.3	522	TT	-	0.032	0.0315	5.5e-05;0.0012	4.5e-05;0.00091	0.0317185302089409	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.961140751811752
CAMB-72634	MN908947.3	7531	A	G	0.039	0.041	4.1e-18	4e-19	0.0394978464825882	AAT	ORF1ab:nsp3	E1604E	A4812G	GAA>GAG	Synonymous	ORF1ab:nsp3	0.960268438449467
CAMB-72652	MN908947.3	10634	G	A	0.0073	0.0057	3.3e-05	0.00012	0.00678185597927956	AGC	ORF1ab:3C-like-proteinase	A194T	G580A	GCT>ACT	Missense	ORF1ab:3C-like-proteinase	0.993115904985857
CAMB-72652	MN908947.3	11074	C	INS	0.082	0.12	1.4e-31	7.3e-45	0.0969620221733895	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.900368728816716
CAMB-72652	MN908947.3	11083	G	-	0.16	0.13	8e-69	6.1e-59	0.149454764400241	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-72652	MN908947.3	11083	G	T	0.84	0.87	0	0	0.850377985415784	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-72652	MN908947.3	11833	C	T	1	1	0	0	1	CCA	ORF1ab:nsp6	A287A	C861T	GCC>GCT	Synonymous	ORF1ab:nsp6	0
CAMB-72652	MN908947.3	13778	AT	-	0.0165	0.0185	4e-06;6.2e-06	1.1e-06;2e-06	0.0170373876005679	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.983133867004835
CAMB-72652	MN908947.3	14805	C	T	1	1	0	0	0.998596325742263	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000696222431837578
CAMB-72652	MN908947.3	1547	A	T	0.013	0.022	2.6e-07	2e-10	0.0161316604204008	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.972625061104774
CAMB-72652	MN908947.3	15960	C	G	0.0022	0.0063	0.0033	3.7e-05	0.0036288099298601	CCG	ORF1ab:RNA-dependent-RNA-polymerase	A831A	C2493G	GCC>GCG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.992088424993909
CAMB-72652	MN908947.3	17247	T	C	1	1	0	0	0.999788692712246	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.00016435011269722
CAMB-72652	MN908947.3	23856	G	A	1	1	0	0	0.997716844368586	CGT	S	R765H	G2294A	CGT>CAT	Missense	GU280_gp02, spike glycoprotein	2.21665595282956e-05
CAMB-72652	MN908947.3	25791	C	T	1	1	0	0	0.997924865831843	GCC	ORF3a	C133C	C399T	TGC>TGT	Synonymous	GU280_gp03	7.15563506261181e-05
CAMB-72652	MN908947.3	26144	G	T	1	1	0	0	0.999189298743413	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-72652	MN908947.3	5222	AC	GG	0.015	0.0115	5.3e-07;3.3e-06	6.9e-05;0.00012	0.0138445154419595	CAC	ORF1ab:nsp3	.	2503-2504-mnv	.	no-SNV	ORF1ab:nsp3	0.985228539576366
CAMB-72652	MN908947.3	5225	A	C	0.015	0.011	2.9e-06	0.00012	0.0138666666666667	TAA	ORF1ab:nsp3	K836Q	A2506C	AAA>CAA	Missense	ORF1ab:nsp3	0.985866666666667
CAMB-72652	MN908947.3	5229	AG	-	0.0165	0.012	4.9e-06;3.3e-06	0.00019;0.00017	0.0153278455861482	AAG	ORF1ab:nsp3	.	2510-2511-delfrshift	.	no-SNV	ORF1ab:nsp3	0.984187408491947
CAMB-72652	MN908947.3	5833	C	T	1	1	0	0	0.999938172375417	CCT	ORF1ab:nsp3	S1038S	C3114T	TCC>TCT	Synonymous	ORF1ab:nsp3	6.18276245826635e-05
CAMB-72661	MN908947.3	14408	C	T	1	1	0	0	0.99981220657277	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-72661	MN908947.3	23403	A	G	1	1	0	0	0.999957024367184	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-72661	MN908947.3	241	C	T	1	1	0	0	0.999821141119657	TCG	NA	NA	NA	NA	NA	NA	0.000178858880343409
CAMB-72661	MN908947.3	28881	GGG	AAC	1	1	0;0;0	5.8e-266;1.6e-277;7.7e-287	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-72661	MN908947.3	3037	C	T	1	1	5.6e-81	8e-143	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-72661	MN908947.3	824	G	A	0.0033	0.034	0.0013	4.2e-13	0.00652366209641751	CGA	ORF1ab:nsp2	D7N	G19A	GAT>AAT	Missense	ORF1ab:nsp2	0.993476337903582
CAMB-72670	MN908947.3	11074	C	INS	0.019	0.029	0.0013	9.7e-06	0.0223505415266167	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.977448361056049
CAMB-72670	MN908947.3	11075	T	-	0.032	0.02	3.3e-08	4.6e-06	0.0281741400298684	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.968236637676794
CAMB-72670	MN908947.3	11195	C	T	1	1	0	0	0.999783973731206	TCT	ORF1ab:nsp6	L75F	C223T	CTT>TTT	Missense	ORF1ab:nsp6	0.000100812258770667
CAMB-72670	MN908947.3	13115	C	T	0.0073	0.0048	4.3e-05	0.00052	0.0061768998335012	TCT	ORF1ab:nsp10	L31L	C91T	CTA>TTA	Synonymous	ORF1ab:nsp10	0.993781989352299
CAMB-72670	MN908947.3	13469	G	-	0.0057	0.018	0.00055	6.6e-08	0.00705557171952284	CGG	ORF1ab:nsp11	.	28-28-delfrshift	.	no-SNV	ORF1ab:nsp11	0.989743962758219
CAMB-72670	MN908947.3	14408	C	T	1	1	0	0	0.998987535062823	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000846487078623712
CAMB-72670	MN908947.3	15216	C	T	1	1	0	0	0.999937989623597	GCA	ORF1ab:RNA-dependent-RNA-polymerase	S583S	C1749T	AGC>AGT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	4.13402509353232e-05
CAMB-72670	MN908947.3	23403	A	G	1	1	0	0	0.99844523782103	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.75837844063112e-05
CAMB-72670	MN908947.3	241	C	T	1	1	0	0	0.999005574019313	TCG	NA	NA	NA	NA	NA	NA	0.000209352838039411
CAMB-72670	MN908947.3	2551	T	C	0.0063	0.01	4.9e-05	1.4e-06	0.00744840781741151	ATT	ORF1ab:nsp2	D582D	T1746C	GAT>GAC	Synonymous	ORF1ab:nsp2	0.992278256115894
CAMB-72670	MN908947.3	26333	C	T	0.068	0.044	2.3e-30	5.2e-20	0.0620900026239832	ACA	E	T30I	C89T	ACA>ATA	Missense	GU280_gp04	0.93774599842561
CAMB-72670	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999472752607992	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000289699126764061
CAMB-72670	MN908947.3	3037	C	T	1	1	0	0	0.999297629499561	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-72670	MN908947.3	3373	C	A	1	1	0	0	0.999919390592882	ACA	ORF1ab:nsp3	D218E	C654A	GAC>GAA	Missense	ORF1ab:nsp3	0
CAMB-72670	MN908947.3	9491	C	T	0.012	0.0096	5.3e-07	1.4e-05	0.0118609892064998	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.9881390107935
CAMB-7268F	MN908947.3	10455	TCACTATTAAGGGTTCATTCCTTAATGGTTCATGTGGTAGTGTTGGTTTTAACATAGATTA	-	0.00957377049180328	0.0411475409836066	NA;NA;NA;NA;1.9e-14;6.5e-13;1.7e-15;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;1.2e-11;1.4e-11;3.4e-10;7.4e-10;3.7e-10;5.1e-10;1.5e-09;1.9e-09;1.3e-10;3.6e-10;3.4e-10;1.2e-11;7.7e-13;8e-12;7.8e-12	1.9e-17;2.3e-17;1.4e-16;1.2e-17;1.8e-17;8e-16;8.6e-19;9.8e-18;2e-17;1.1e-17;3.2e-17;2e-17;2.6e-17;2e-17;3.4e-17;9e-16;4e-17;2.2e-17;2.6e-17;2e-17;1.4e-17;1.2e-17;6.6e-16;5.8e-17;6e-16;2.1e-17;1.5e-17;1.5e-17;2.7e-18;1.5e-17;1.3e-17;4.6e-18;3.3e-19;1.8e-17;9.8e-19;1.3e-17;1.1e-17;2e-18;8.9e-17;7.3e-16;5.6e-15;1.1e-15;1.3e-15;6.1e-15;6.4e-16;9.2e-15;2e-14;2.6e-14;9.3e-13;3.4e-12;1.1e-12;2.5e-12;7.8e-12;6.7e-12;4.6e-13;1.4e-12;3.9e-12;2.2e-14;8.1e-16;1.3e-14;1.1e-14	0.0125591730267607	TTC	ORF1ab:3C-like-proteinase	.	401-461-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.987221056646958
CAMB-7268F	MN908947.3	10501	TTTTAACATAGATTATGACTGTGTCTCTT	-	0.0316896551724138	0.0221486206896552	1.2e-11;1.4e-11;3.4e-10;7.4e-10;3.7e-10;5.1e-10;1.5e-09;1.9e-09;1.3e-10;3.6e-10;3.4e-10;1.2e-11;7.7e-13;8e-12;7.8e-12;8e-12;4.3e-12;2.8e-12;2.7e-12;7.2e-13;1.7e-11;7.3e-12;5.4e-13;6.3e-11;1.8e-10;7.3e-12;2.3e-12;3.5e-10;6.2e-09	2e-14;2.6e-14;9.3e-13;3.4e-12;1.1e-12;2.5e-12;7.8e-12;6.7e-12;4.6e-13;1.4e-12;3.9e-12;2.2e-14;8.1e-16;1.3e-14;1.1e-14;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0343322087715817	GTT	ORF1ab:3C-like-proteinase	.	447-475-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.961156379060163
CAMB-7268F	MN908947.3	10653	TTACAGTTAATGTTTTAGCTT	-	0.0012452380952381	0.0413809523809524	NA;NA;NA;NA;NA;NA;NA;NA;9.2e-06;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	1.3e-10;1e-09;1e-09;2.2e-09;6e-09;1.5e-09;2.2e-09;2.5e-09;1.3e-08;3.1e-09;4.8e-09;3.3e-09;1.1e-12;3.7e-10;5.6e-10;2.3e-11;5.2e-12;4.3e-12;1.7e-11;3e-13;5.7e-12	0.0129007413112545	ATT	ORF1ab:3C-like-proteinase	.	599-619-delinframe	.	no-SNV	ORF1ab:3C-like-proteinase	0.986342338749875
CAMB-7268F	MN908947.3	11075	T	-	0.047	0.075	7.3e-12	7.2e-19	0.0569082779092925	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.933716604666892
CAMB-7268F	MN908947.3	12772	A	G	0.01	0.0092	9.8e-07	1.6e-06	0.00967278666366299	TAG	ORF1ab:nsp9	L29L	A87G	TTA>TTG	Synonymous	ORF1ab:nsp9	0.990327213336337
CAMB-7268F	MN908947.3	13385	G	-	0.016	0.016	7.4e-08	2.6e-06	0.0156152404747033	CGG	ORF1ab:nsp10	.	361-361-delfrshift	.	no-SNV	ORF1ab:nsp10	0.984072454715803
CAMB-7268F	MN908947.3	14408	C	T	1	1	0	0	0.999908600676355	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	9.1399323645005e-05
CAMB-7268F	MN908947.3	162	C	T	0.51	0.69	2.2e-297	0	0.578950145080454	ACA	NA	NA	NA	NA	NA	NA	0.421023476655236
CAMB-7268F	MN908947.3	18005	TTGAAATTCCACGTAGGAATGTGGCAACT	-	0.00682965517241379	0.00882068965517241	NA;NA;NA;0.48;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00028;8.6e-05;1.1e-07;9.5e-08;9.8e-08;1.1e-07;8.7e-08;1.9e-07;6e-08;6.6e-08;5.9e-08;4.3e-08;4.8e-08;1e-07	2.7e-06;3.1e-06;4.6e-06;7.4e-06;4.4e-06;4e-06;1.2e-06;5.6e-06;9e-06;9.5e-08;9.9e-08;6.7e-06;8.5e-06;8e-06;2.7e-05;9e-05;2.4e-05;6.1e-05;4.1e-05;5.5e-05;5.9e-05;4.3e-05;9.3e-05;3.1e-05;3.6e-05;3.1e-05;2.4e-05;2.6e-05;5.6e-05	0.00340347603745551	CTT	ORF1ab:helicase	.	1769-1797-delfrshift	.	no-SNV	ORF1ab:helicase	0.996114233975931
CAMB-7268F	MN908947.3	1820	G	-	0.01	0.0012	8.8e-07	0.0037	0.0070879450411646	AGG	ORF1ab:nsp2	.	1015-1015-delfrshift	.	no-SNV	ORF1ab:nsp2	5.45226541628046e-05
CAMB-7268F	MN908947.3	1820	G	A	0.99	1	0	0	0.992857532304673	AGG	ORF1ab:nsp2	G339S	G1015A	GGT>AGT	Missense	ORF1ab:nsp2	5.45226541628046e-05
CAMB-7268F	MN908947.3	23403	A	G	1	1	0	0	0.999968560874008	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.14391259922974e-05
CAMB-7268F	MN908947.3	241	C	T	1	1	0	0	0.999844147747935	TCG	NA	NA	NA	NA	NA	NA	0.000103901501376695
CAMB-7268F	MN908947.3	24120	A	-	0.012	0.0085	1.1e-06	2.6e-05	0.0102575061438188	CAA	S	.	2558-2558-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.98963564483385
CAMB-7268F	MN908947.3	28514	G	T	1	1	0	0	0.999753208292201	AGA	N	D81Y	G241T	GAT>TAT	Missense	GU280_gp10	0
CAMB-7268F	MN908947.3	28899	G	T	0.012	0.037	3.2e-07	3.8e-16	0.0212734082397004	AGA	N	R209I	G626T	AGA>ATA	Missense	GU280_gp10	0.9787265917603
CAMB-7268F	MN908947.3	29040	A	T	0.3	0.33	1.4e-151	3.2e-162	0.309206186322656	AAG	N	K256M	A767T	AAG>ATG	Missense	GU280_gp10	0.690647218353735
CAMB-7268F	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7268F	MN908947.3	3425	C	T	0.028	0.023	4.1e-14	3.7e-12	0.0263174848601984	ACC	ORF1ab:nsp3	P236S	C706T	CCA>TCA	Missense	ORF1ab:nsp3	0.973650302796031
CAMB-7268F	MN908947.3	427	AG	-	0.0065	0.014	NA;0.00025	1.5e-06;0.00012	0.00844193736627115	TAG	ORF1ab:leader-protein	.	162-163-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.99594393944881
CAMB-7269E	MN908947.3	14408	C	T	1	1	0	0	0.999585864163446	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000276090557702927
CAMB-7269E	MN908947.3	17126	T	C	0.96	1	0	0	0.972879684418146	CTC	ORF1ab:helicase	L297P	T890C	CTC>CCC	Missense	ORF1ab:helicase	0.0270943631267518
CAMB-7269E	MN908947.3	23403	A	G	0.95	1	0	0	0.970125316008372	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.0298475004757115
CAMB-7269E	MN908947.3	23804	G	A	0.072	0.042	7.6e-21	7.5e-16	0.0505725190839695	TGA	S	E748K	G2242A	GAA>AAA	Missense	GU280_gp02, spike glycoprotein	0.949427480916031
CAMB-7269E	MN908947.3	241	C	T	1	1	0	0	0.999855553950599	TCG	NA	NA	NA	NA	NA	NA	7.22230247002744e-05
CAMB-7269E	MN908947.3	28325	G	-	0.015	0.013	1.2e-08	4.3e-08	0.0143063645253178	TGG	N	.	52-52-delfrshift	.	no-SNV	GU280_gp10	0.985587347476723
CAMB-7269E	MN908947.3	28426	TTGG	-	0.01125	0.001125	2.8e-07;3.2e-07;7.9e-07;3.4e-07	0.00029;NA;NA;NA	0.00694156320811923	CTT	N	.	153-156-delfrshift	.	no-SNV	GU280_gp10	0.991132354834556
CAMB-7269E	MN908947.3	28541	G	C	0.027	0.018	8.7e-13	4.5e-09	0.0235302905804138	AGC	N	A90P	G268C	GCT>CCT	Missense	GU280_gp10	0.968551579890939
CAMB-7269E	MN908947.3	28557	G	C	0.013	0.019	1.6e-07	3.8e-10	0.0151885208365135	CGT	N	R95P	G284C	CGT>CCT	Missense	GU280_gp10	0.984811479163486
CAMB-7269E	MN908947.3	28793	G	T	0.011	0.01	1.4e-06	1.2e-05	0.010737948366461	AGA	N	E174*	G520T	GAA>TAA	Nonsense	GU280_gp10	0.943111720356408
CAMB-7269E	MN908947.3	28793	GA	CG	0.031	0.00426	7.1e-20;1.1e-07	6e-05;NA	0.0223082176189392	AGA	N	.	520-521-mnv	.	no-SNV	GU280_gp10	0.943111720356408
CAMB-7269E	MN908947.3	29000	G	T	0.014	0.007	3.6e-07	0.00054	0.0119047619047619	AGG	N	G243C	G727T	GGC>TGC	Missense	GU280_gp10	0.988095238095238
CAMB-7269E	MN908947.3	29245	C	T	0.012	0.023	2e-07	4.2e-12	0.0144898437238564	TCA	N	V324V	C972T	GTC>GTT	Synonymous	GU280_gp10	0.985443228591507
CAMB-7269E	MN908947.3	3037	C	T	1	1	1e-82	1.6e-304	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7269E	MN908947.3	3229	TGG	-	0.011	0.0313333333333333	NA;1.1e-14;NA	2.1e-14;4.4e-13;6.6e-15	0.0100820842255532	TTG	ORF1ab:nsp3	.	510-512-delinframe	.	no-SNV	ORF1ab:nsp3	0.989480483528652
CAMB-726AD	MN908947.3	10908	C	T	0.011	0.004	2e-06	0.0013	0.00776780121110879	GCT	ORF1ab:3C-like-proteinase	A285V	C854T	GCT>GTT	Missense	ORF1ab:3C-like-proteinase	0.992148674044686
CAMB-726AD	MN908947.3	11075	T	-	0.033	0.037	2e-08	9.3e-10	0.0345670347299685	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960908418664695
CAMB-726AD	MN908947.3	11283	GTTTGTCTG	-	0.0165555555555556	0.0115555555555556	7e-05;0.00018;7.4e-05;0.00015;9.1e-05;6.7e-05;6.4e-05;2.8e-05;3.5e-05	0.00071;0.0015;0.00056;0.0011;0.00093;0.00061;0.00062;0.00032;0.00037	0.0141218317158202	AGT	ORF1ab:nsp6	.	311-319-delinframe	.	no-SNV	ORF1ab:nsp6	0.985870684008609
CAMB-726AD	MN908947.3	14408	C	T	1	1	0	0	0.997067116459393	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000553849252303509
CAMB-726AD	MN908947.3	14931	C	T	0.0061	0.0074	6.4e-05	2e-05	0.00681571521597569	ACC	ORF1ab:RNA-dependent-RNA-polymerase	N488N	C1464T	AAC>AAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.993184284784024
CAMB-726AD	MN908947.3	2263	C	T	0.0062	0.0074	1e-04	3.5e-05	0.00677736360555744	CCT	ORF1ab:nsp2	T486T	C1458T	ACC>ACT	Synonymous	ORF1ab:nsp2	0.993222636394443
CAMB-726AD	MN908947.3	23403	A	G	1	1	0	0	0.999490702926056	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000105703166290299
CAMB-726AD	MN908947.3	23466	T	C	0.26	0.27	7.9e-128	7.9e-132	0.263149129595705	GTT	S	V635A	T1904C	GTT>GCT	Missense	GU280_gp02, spike glycoprotein	0.734774047551406
CAMB-726AD	MN908947.3	241	C	T	1	1	0	0	0.997951569244275	TCG	NA	NA	NA	NA	NA	NA	0.00010973736191382
CAMB-726AD	MN908947.3	25521	C	T	0.73	0.74	0	0	0.732142004678325	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.263911652849164
CAMB-726AD	MN908947.3	25614	C	T	0.0098	0.01	5.1e-06	3.9e-06	0.00991189427312775	CCA	ORF3a	S74S	C222T	TCC>TCT	Synonymous	GU280_gp03	0.989969043933802
CAMB-726AD	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0298108108108108	0.0338378378378378	0.00066;6.8e-05;0.00051;0.00061;0.0011;4.7e-05;0.00013;6e-05;5.8e-05;2.7e-05;3e-05;2.7e-05;4.5e-05;3.7e-05;4.3e-05;6.4e-05;3.3e-05;5.6e-05;3.1e-05;2.9e-05;2.4e-05;4.5e-05;2.8e-05;3.9e-05;3e-05;2.4e-05;4.2e-05;2.7e-05;2.4e-05;2.9e-05;4e-05;3.8e-05;3.3e-05;5.3e-05;2.2e-05;4e-05;3.7e-05	0.00045;5.6e-05;0.00018;0.00019;0.00038;9.9e-06;2.8e-05;7.5e-06;7.2e-06;5e-06;4.3e-06;3.8e-06;6.2e-06;4.5e-06;5.3e-06;7.5e-06;3.7e-06;7.1e-06;4.1e-06;4.7e-06;4.4e-06;7.7e-06;5.6e-06;5.9e-06;4.5e-06;3e-06;5.3e-06;4.7e-06;2.1e-06;4.4e-06;6.7e-06;6.3e-06;2.9e-06;7.2e-06;1.6e-06;4.9e-06;3.4e-06	0.0325757045947269	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.97741539491672
CAMB-726AD	MN908947.3	27688	C	T	0.02	0.0054	2.9e-07	0.0026	0.0147347740667976	TCC	ORF7a	P99S	C295T	CCA>TCA	Missense	GU280_gp07	0.985265225933202
CAMB-726AD	MN908947.3	28514	G	T	1	1	0	0	0.999053578000946	AGA	N	D81Y	G241T	GAT>TAT	Missense	GU280_gp10	0.000210315999789684
CAMB-726AD	MN908947.3	28851	G	T	0.011	0.012	9e-07	4.1e-07	0.0116786727788692	AGT	N	S193I	G578T	AGT>ATT	Missense	GU280_gp10	0.988066652113803
CAMB-726AD	MN908947.3	28854	C	T	0.075	0.077	1.4e-32	2.2e-33	0.0759319580166486	TCA	N	S194L	C581T	TCA>TTA	Missense	GU280_gp10	0.92399565689468
CAMB-726AD	MN908947.3	28887	C	T	0.29	0.3	1.2e-139	2.4e-146	0.295602926138598	ACT	N	T205I	C614T	ACT>ATT	Missense	GU280_gp10	0.704082435302446
CAMB-726AD	MN908947.3	28923	C	T	0.016	0.018	1.5e-08	2.2e-09	0.0165130417728966	GCT	N	A217V	C650T	GCT>GTT	Missense	GU280_gp10	0.983408511472838
CAMB-726AD	MN908947.3	28932	C	T	0.019	0.013	8.9e-10	2.3e-07	0.0168184723553851	GCT	N	A220V	C659T	GCT>GTT	Missense	GU280_gp10	0.98310162991371
CAMB-726AD	MN908947.3	29449	G	T	0.0071	0.0099	0.00018	4.1e-05	0.00810898475510866	TGA	N	V392V	G1176T	GTG>GTT	Synonymous	GU280_gp10	0.991891015244891
CAMB-726AD	MN908947.3	3037	C	T	1	1	0	0	0.998875363852871	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000264620269912675
CAMB-726AD	MN908947.3	522	TT	-	0.0375	0.0355	1.1e-05;0.00027	2.3e-05;0.00024	0.0364133711781402	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.956201299190643
CAMB-726AD	MN908947.3	9246	C	T	0.0063	0.01	0.00016	3.4e-06	0.00763283758107842	GCT	ORF1ab:nsp4	A231V	C692T	GCT>GTT	Missense	ORF1ab:nsp4	0.992301644499771
CAMB-726AD	MN908947.3	9891	C	T	0.12	0.12	5.3e-53	2.4e-52	0.117354633301681	GCT	ORF1ab:nsp4	A446V	C1337T	GCT>GTT	Missense	ORF1ab:nsp4	0.882589510137966
CAMB-726AD	MN908947.3	9967	C	T	0.032	0.024	3.3e-15	2.4e-12	0.0287582051006134	TCG	ORF1ab:nsp4	L471L	C1413T	CTC>CTT	Synonymous	ORF1ab:nsp4	0.971241794899387
CAMB-726BC	MN908947.3	10323	A	G	0.04	0.037	4.7e-11	2.8e-10	0.0384460637489383	AAG	ORF1ab:3C-like-proteinase	K90R	A269G	AAG>AGG	Missense	ORF1ab:3C-like-proteinase	0.961449625225386
CAMB-726BC	MN908947.3	11074	C	INS	0.027	0.029	7.7e-06	7.7e-06	0.027708844619329	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.971290291621536
CAMB-726BC	MN908947.3	11075	T	-	0.036	0.027	4.4e-09	1.5e-07	0.032567727455692	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.9647243940817
CAMB-726BC	MN908947.3	12854	C	T	0.078	0.076	1.5e-35	7.6e-35	0.0772549755273974	CCC	ORF1ab:nsp9	P57S	C169T	CCT>TCT	Missense	ORF1ab:nsp9	0.922676808158671
CAMB-726BC	MN908947.3	1288	C	T	0.0084	0.0097	3.4e-05	9.6e-06	0.00901104488573769	GCG	ORF1ab:nsp2	C161C	C483T	TGC>TGT	Synonymous	ORF1ab:nsp2	0.990777096692184
CAMB-726BC	MN908947.3	14016	C	A	0.0053	0.0063	0.00018	4.1e-05	0.00570522979397781	TCT	ORF1ab:RNA-dependent-RNA-polymerase	F183L	C549A	TTC>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994169908274504
CAMB-726BC	MN908947.3	1405	T	C	0.011	0.013	5.2e-06	5.6e-07	0.0117018859350148	CTG	ORF1ab:nsp2	P200P	T600C	CCT>CCC	Synonymous	ORF1ab:nsp2	0.988298114064985
CAMB-726BC	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999587687495557	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000227489229806776
CAMB-726BC	MN908947.3	1913	C	T	0.0052	0.0076	0.00019	1.3e-05	0.0061955096057403	CCG	ORF1ab:nsp2	R370C	C1108T	CGC>TGC	Missense	ORF1ab:nsp2	0.993750482215878
CAMB-726BC	MN908947.3	21034	C	A	0.016	0.015	1.2e-08	1.6e-08	0.0153979503390608	TCT	ORF1ab:2'-O-ribose-methyltransferase	L126I	C376A	CTC>ATC	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.984245143527252
CAMB-726BC	MN908947.3	22327	T	G	0.073	0.093	5.4e-18	1.3e-29	0.0871177015755329	CTT	S	S255S	T765G	TCT>TCG	Synonymous	GU280_gp02, spike glycoprotein	0.912882298424467
CAMB-726BC	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.025875	0.02940625	0.00037;0.00068;0.00039;0.00039;2e-04;0.00032;0.00026;0.00038;0.00027;3e-04;0.00041;0.00024;0.00036;0.00029;0.00028;0.00026;0.00042;0.00028;0.00033;0.00028;0.00023;0.00036;0.00025;0.00015;0.00028;0.00035;0.00033;0.00024;0.00036;0.00018;0.00026;0.00022	9.7e-05;0.00018;8.2e-05;7.7e-05;5.4e-05;5.8e-05;4.6e-05;6.9e-05;5.8e-05;7e-05;1e-04;5.1e-05;9.2e-05;5.4e-05;6.2e-05;6.6e-05;9.1e-05;5.5e-05;7.3e-05;6.2e-05;4.1e-05;8.1e-05;6.2e-05;1.8e-05;6.3e-05;8.4e-05;7.9e-05;4.1e-05;8.4e-05;2.5e-05;5.6e-05;3.2e-05	0.0271589163619558	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.97301359016208
CAMB-726BC	MN908947.3	27785	T	C	0.99	1	0	3.2e-208	0.996275605214153	ATT	NA	NA	NA	NA	NA	NA	0.0037243947858473
CAMB-726BC	MN908947.3	27999	C	T	0.0077	0.01	8.7e-05	9.5e-06	0.00884205426356589	CCC	ORF8	P36S	C106T	CCG>TCG	Missense	GU280_gp09	0.991157945736434
CAMB-726BC	MN908947.3	29032	G	A	1	1	0	0	0.999675472636129	AGG	N	E253E	G759A	GAG>GAA	Synonymous	GU280_gp10	6.21435377625564e-05
CAMB-726BC	MN908947.3	5072	G	A	0.022	0.027	1.1e-10	1.1e-10	0.0233930453108535	TGA	ORF1ab:nsp3	D785N	G2353A	GAT>AAT	Missense	ORF1ab:nsp3	0.976606954689146
CAMB-726CB	MN908947.3	11075	T	-	0.036	0.035	1.6e-09	9.3e-10	0.0360849149666575	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959673282563232
CAMB-726CB	MN908947.3	14408	C	T	1	1	0	0	0.997878154637518	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000337566307667578
CAMB-726CB	MN908947.3	23311	G	T	0.015	0.014	1.6e-08	3.7e-08	0.0145336643653142	AGA	S	E583D	G1749T	GAG>GAT	Missense	GU280_gp02, spike glycoprotein	0.98418528721559
CAMB-726CB	MN908947.3	23403	A	G	1	1	0	0	0.999451609841494	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.43677166932073e-05
CAMB-726CB	MN908947.3	241	C	T	1	1	0	0	0.9986612559093	TCG	NA	NA	NA	NA	NA	NA	0.000292850269840606
CAMB-726CB	MN908947.3	26466	G	INS	0.02	0.021	8.9e-05	2.9e-05	0.0200875393821496	TGG	E	.	221-222-insfrshift	.	no-SNV	GU280_gp04	0.970143573044637
CAMB-726CB	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998581157775255	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	8.0450522928399e-05
CAMB-726CB	MN908947.3	3037	C	T	1	1	0	0	0.999386620663216	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000153344834195898
CAMB-726CB	MN908947.3	5321	A	G	0.034	0.037	1.6e-15	1.2e-16	0.0350216380830261	AAT	ORF1ab:nsp3	I868V	A2602G	ATA>GTA	Missense	ORF1ab:nsp3	0.964898220868729
CAMB-726DA	MN908947.3	11074	C	INS	0.021	0.025	0.00056	3.6e-05	0.022468594553579	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.976899081021836
CAMB-726DA	MN908947.3	11075	T	-	0.033	0.037	3.2e-09	2.1e-10	0.0343262826612018	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962197174851789
CAMB-726DA	MN908947.3	1113	C	T	1	1	0	0	0.999803985625613	ACT	ORF1ab:nsp2	T103I	C308T	ACT>ATT	Missense	ORF1ab:nsp2	6.53381247958184e-05
CAMB-726DA	MN908947.3	11861	A	C	0.015	0.011	2.3e-07	9.1e-06	0.013723247835321	AAA	ORF1ab:nsp7	K7Q	A19C	AAG>CAG	Missense	ORF1ab:nsp7	0.986113380166639
CAMB-726DA	MN908947.3	14183	C	T	0.013	0.013	7.2e-08	5.8e-08	0.0133502958217099	ACC	ORF1ab:RNA-dependent-RNA-polymerase	T239I	C716T	ACC>ATC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.986542411330125
CAMB-726DA	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999392651078044	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000121469784391133
CAMB-726DA	MN908947.3	17523	G	T	0.01	0.012	8e-07	1.7e-07	0.0108672235919286	TGA	ORF1ab:helicase	M429I	G1287T	ATG>ATT	Missense	ORF1ab:helicase	0.989013093328865
CAMB-726DA	MN908947.3	20233	C	T	0.036	0.045	4.4e-13	8.6e-14	0.0389016018306636	ACC	ORF1ab:endoRNAse	P205S	C613T	CCC>TCC	Missense	ORF1ab:endoRNAse	0.960717009916095
CAMB-726DA	MN908947.3	23506	C	T	0.0073	0.0054	4.4e-05	0.00029	0.00638256087981147	GCT	S	G648G	C1944T	GGC>GGT	Synonymous	GU280_gp02, spike glycoprotein	0.993617439120189
CAMB-726DA	MN908947.3	26228	C	T	0.0082	0.0084	2e-05	1.4e-05	0.00826353992183138	GCT	NA	NA	NA	NA	NA	NA	0.991624790619765
CAMB-726DA	MN908947.3	28380	G	A	0.011	0.009	3.3e-06	2.6e-05	0.010476346374202	CGA	N	R36Q	G107A	CGA>CAA	Missense	GU280_gp10	0.989298575871665
CAMB-726DA	MN908947.3	29311	C	T	0.073	0.065	1.9e-33	1e-29	0.0700848583989367	TCA	N	F346F	C1038T	TTC>TTT	Synonymous	GU280_gp10	0.929403946426746
CAMB-726DA	MN908947.3	29640	C	T	0.0073	0.0084	5.7e-05	2.1e-05	0.00784832451499118	GCA	ORF10	A28V	C83T	GCA>GTA	Missense	GU280_gp11	0.991975308641975
CAMB-726DA	MN908947.3	29771	A	G	1	1	0	0	0.99894641782059	AAT	NA	NA	NA	NA	NA	NA	0
CAMB-726DA	MN908947.3	3569	A	G	1	1	0	0	0.999093760892297	TAG	ORF1ab:nsp3	S284G	A850G	AGT>GGT	Missense	ORF1ab:nsp3	0.000139421401185082
CAMB-726DA	MN908947.3	4149	T	G	0.015	0.016	1.1e-08	5.9e-09	0.0155143607287771	GTT	ORF1ab:nsp3	V477G	T1430G	GTT>GGT	Missense	ORF1ab:nsp3	0.983801416182672
CAMB-726E9	MN908947.3	10033	TATCACCTCAGCTGTTTTGCAGAGTGGTTT	-	0.0139666666666667	0.000607	9.1e-09;8.4e-10;4.4e-08;1.4e-07;2.1e-08;1.5e-07;1.4e-07;5.1e-08;1.4e-07;3.8e-09;6.3e-08;1.1e-07;2.8e-07;1.3e-09;2.3e-06;6.9e-07;5.6e-07;1.3e-07;9.9e-08;8.1e-08;1.2e-07;1.4e-07;4.1e-08;1.2e-07;1.3e-07;2e-07;1.1e-07;2.3e-07;1.3e-07;1e-07	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;1.7e-08;NA;NA	0.00848713458170551	CTA	ORF1ab:nsp4	.	1479-1500-delfrshift	.	no-SNV	ORF1ab:nsp4	0.989854255576133
CAMB-726E9	MN908947.3	10065	G	A	0.014	0.015	5e-08	1.8e-08	0.0143326758711374	AGA	ORF1ab:3C-like-proteinase	R4K	G11A	AGA>AAA	Missense	ORF1ab:3C-like-proteinase	0.985404339250493
CAMB-726E9	MN908947.3	10388	T	C	0.0095	0.0084	2.5e-06	7.5e-06	0.00903240374844756	TTT	ORF1ab:3C-like-proteinase	F112L	T334C	TTT>CTT	Missense	ORF1ab:3C-like-proteinase	0.990967596251552
CAMB-726E9	MN908947.3	10429	T	C	0.036	0.018	8.5e-18	4e-10	0.0279527908421333	TTT	ORF1ab:3C-like-proteinase	V125V	T375C	GTT>GTC	Synonymous	ORF1ab:3C-like-proteinase	0.972047209157867
CAMB-726E9	MN908947.3	11075	T	-	0.015	0.061	0.00014	1.4e-15	0.0290259807780864	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.946330159390365
CAMB-726E9	MN908947.3	14408	C	T	1	0.99	0	0	0.994068526741335	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000231957054808138
CAMB-726E9	MN908947.3	15878	G	T	0.015	0.016	2.7e-08	8.7e-09	0.014798297182242	TGC	ORF1ab:RNA-dependent-RNA-polymerase	C804F	G2411T	TGC>TTC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.985111606640088
CAMB-726E9	MN908947.3	19983	C	INS	0.067	0.074	5.2e-10	8.6e-08	0.0695067264573991	TCT	ORF1ab:endoRNAse	.	362-363-insfrshift	.	no-SNV	ORF1ab:endoRNAse	0.930493273542601
CAMB-726E9	MN908947.3	20031	C	A	1	1	3.6e-284	6.1e-174	1	CCC	ORF1ab:endoRNAse	A137A	C411A	GCC>GCA	Synonymous	ORF1ab:endoRNAse	0
CAMB-726E9	MN908947.3	21732	C	T	0.023	0.033	1.3e-09	3.7e-13	0.0287865367581931	CCT	S	P57L	C170T	CCT>CTT	Missense	GU280_gp02, spike glycoprotein	0.971213463241807
CAMB-726E9	MN908947.3	22559	AC	-	0.014	0.0055	4.8e-08;2.5e-08	NA;2.2e-07	0.0111822526828388	TAC	S	.	997-998-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.990530359429439
CAMB-726E9	MN908947.3	22560	C	-	0.014	0.011	2.5e-08	2.2e-07	0.0130496798276228	ACA	S	.	998-998-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.98685927589451
CAMB-726E9	MN908947.3	23403	A	G	0.99	1	0	0	0.993301969539909	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.9738457858225e-05
CAMB-726E9	MN908947.3	241	C	T	1	1	0	0	0.999853907962016	TCG	NA	NA	NA	NA	NA	NA	3.65230094959825e-05
CAMB-726E9	MN908947.3	24793	T	-	0.018	0.03	6e-10	4.3e-15	0.0232014428536439	CTG	S	.	3231-3231-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.976664959586738
CAMB-726E9	MN908947.3	24793	TG	-	0.0090375	0.03	6e-10;0.46	4.3e-15;3e-13	0.0177621075039915	CTG	S	.	3231-3232-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.976664959586738
CAMB-726E9	MN908947.3	26865	G	-	0.019	0.011	4.1e-07	0.00013	0.0157594081526174	AGA	M	.	343-343-delfrshift	.	no-SNV	GU280_gp05	0.979732170330038
CAMB-726E9	MN908947.3	27046	C	T	1	1	0	0	1	ACG	M	T175M	C524T	ACG>ATG	Missense	GU280_gp05	0
CAMB-726E9	MN908947.3	27059	C	T	0.021	0.047	5.4e-11	1.8e-20	0.0275936360623136	ACA	M	Y179Y	C537T	TAC>TAT	Synonymous	GU280_gp05	0.972406363937686
CAMB-726E9	MN908947.3	28193	GCGTTGTTCGTTCTATGAAGACTTTTTAGAGTATCATG	-	0.000596052631578947	0.0148157894736842	NA;NA;0.46;0.46;NA;NA;NA;NA;NA;0.46;0.46;0.46;0.46;0.46;0.46;0.5;0.5;0.46;0.46;0.46;0.46;0.46;1e-04;2.1e-05;0.46;0.46;0.46;0.46;0.46;0.46;0.46;0.46;0.46;0.46;0.46;0.46;0.46;0.46	2.7e-08;1.9e-08;1.1e-07;2.1e-08;2.9e-06;2.8e-06;1.2e-08;1.9e-08;2.4e-08;8.3e-08;3.2e-08;4.4e-08;7.6e-08;8.7e-08;7e-08;4e-07;4.4e-07;6.2e-08;4.8e-08;1.5e-08;4.5e-08;6.4e-08;3.7e-07;2.8e-08;3.4e-08;1.8e-08;4.3e-08;1e-07;7.4e-08;6.6e-08;6.9e-08;7.9e-08;2.4e-08;6e-08;6.6e-08;4.1e-08;6.5e-08;6.1e-08	0.0049542110794175	TGC	ORF8	.	300-337-delfrshift	.	no-SNV	GU280_gp09	0.995158437943931
CAMB-726E9	MN908947.3	28859	A	C	0.0093	0.0062	4.2e-05	0.0021	0.00858594708253023	AAA	N	N196H	A586C	AAT>CAT	Missense	GU280_gp10	0.991238829507622
CAMB-726E9	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999559729967714	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000164446637066272
CAMB-726E9	MN908947.3	3037	C	T	1	1	0	0	0.999461206896552	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000269396551724138
CAMB-726E9	MN908947.3	3291	A	G	0.07	0.035	3.9e-32	3.7e-17	0.0606167231782995	CAA	ORF1ab:nsp3	Q191R	A572G	CAA>CGA	Missense	ORF1ab:nsp3	0.9393832768217
CAMB-726E9	MN908947.3	6285	C	T	0.016	0.019	5.5e-09	2.3e-09	0.016716463068719	ACC	ORF1ab:nsp3	T1189I	C3566T	ACC>ATC	Missense	ORF1ab:nsp3	0.983245716879089
CAMB-726E9	MN908947.3	6285	CC	TT	0.0225	0.0095	5.5e-09;7.4e-15	2.3e-09;NA	0.020958198129414	ACC	ORF1ab:nsp3	.	3566-3567-mnv	.	no-SNV	ORF1ab:nsp3	0.983245716879089
CAMB-726E9	MN908947.3	6962	T	-	0.034	0.032	3.7e-09	1.6e-06	0.0330578512396694	GTT	ORF1ab:nsp3	.	4243-4243-delfrshift	.	no-SNV	ORF1ab:nsp3	0.966942148760331
CAMB-726F8	MN908947.3	11075	T	-	0.036	0.028	4.7e-09	9.8e-08	0.0330620931397096	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964096144216325
CAMB-726F8	MN908947.3	13568	C	T	1	1	0	0	0.999334900013302	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A34V	C101T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	6.65099986698e-05
CAMB-726F8	MN908947.3	14408	C	T	1	1	0	0	0.999094921815169	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000431652672765501
CAMB-726F8	MN908947.3	20355	A	G	1	1	0	1.2e-281	1	TAG	ORF1ab:endoRNAse	L245L	A735G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-726F8	MN908947.3	23403	A	G	1	1	0	0	0.999503533672099	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.73463388041976e-06
CAMB-726F8	MN908947.3	241	C	T	1	1	0	0	0.997148288973384	TCG	NA	NA	NA	NA	NA	NA	0.000249329925824347
CAMB-726F8	MN908947.3	26530	A	G	1	1	0	0	0.999363983281846	GAT	M	D3G	A8G	GAT>GGT	Missense	GU280_gp05	0.000345266218426313
CAMB-726F8	MN908947.3	2775	A	G	1	1	0	0	0.999604569420035	AAG	ORF1ab:nsp3	K19R	A56G	AAG>AGG	Missense	ORF1ab:nsp3	0.000175746924428823
CAMB-726F8	MN908947.3	3037	C	T	1	1	0	0	0.998606190835705	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.80753818456356e-05
CAMB-726F8	MN908947.3	3564	G	T	0.0047	0.011	0.0044	2.1e-05	0.00831633453632512	GGT	ORF1ab:nsp3	G282V	G845T	GGT>GTT	Missense	ORF1ab:nsp3	0.991056017574141
CAMB-726F8	MN908947.3	4255	G	T	1	1	0	0	0.999491459511203	CGG	ORF1ab:nsp3	P512P	G1536T	CCG>CCT	Synonymous	ORF1ab:nsp3	0.000344012683598074
CAMB-72704	MN908947.3	11075	T	-	0.031	0.034	4.1e-08	4.2e-09	0.0322720439864032	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.963434948064084
CAMB-72704	MN908947.3	14120	C	T	1	1	0	0	0.999498282582687	CCA	ORF1ab:RNA-dependent-RNA-polymerase	P218L	C653T	CCA>CTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000250858708656555
CAMB-72704	MN908947.3	14408	C	T	1	1	0	0	0.997048077941332	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000423594196759504
CAMB-72704	MN908947.3	23403	A	G	1	1	0	0	0.999468986037995	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.4087891966125e-05
CAMB-72704	MN908947.3	241	C	T	1	1	0	0	0.998196504288099	TCG	NA	NA	NA	NA	NA	NA	0.000422094741083249
CAMB-72704	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998892311952646	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000151234451207985
CAMB-72704	MN908947.3	3037	C	T	1	1	0	0	0.999228602092836	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.35390394419104e-05
CAMB-72704	MN908947.3	6539	C	T	0.0092	0.0093	1.7e-05	1.5e-05	0.00927950824516815	CCA	ORF1ab:nsp3	H1274Y	C3820T	CAC>TAC	Missense	ORF1ab:nsp3	0.990484071162598
CAMB-72713	MN908947.3	11075	T	-	0.044	0.0053	2.9e-11	0.0091	0.0294167402868367	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.970376496682393
CAMB-72713	MN908947.3	14952	T	C	0.011	0.0034	2.2e-05	0.0037	0.00600461893764434	TTC	ORF1ab:RNA-dependent-RNA-polymerase	F495F	T1485C	TTT>TTC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.993995381062356
CAMB-72713	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.99942354806168	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000288239815526518
CAMB-72713	MN908947.3	26262	G	A	1	1	0	0	0.999799237100984	CGG	E	S6S	G18A	TCG>TCA	Synonymous	GU280_gp04	0.000200762899016262
CAMB-72713	MN908947.3	26735	C	T	1	1	0	0	0.999582432697976	ACA	M	Y71Y	C213T	TAC>TAT	Synonymous	GU280_gp05	7.36883474159953e-05
CAMB-72713	MN908947.3	29683	A	T	1	1	3e-211	0	1	TAA	NA	NA	NA	NA	NA	NA	0
CAMB-72713	MN908947.3	425	GTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTT	-	0.0279393939393939	0.031	7.3e-07;2.2e-11;1.1e-09;8.1e-06;3.6e-12;2.7e-12;5.2e-12;7.5e-12;3.5e-11;3.8e-12;1.3e-12;2.4e-11;9.6e-11;8.1e-10;1.9e-09;3.7e-10;3.8e-10;5.3e-10;5.8e-10;8.4e-06;8.3e-08;3.2e-10;1.8e-13;7.2e-15;1.2e-13;1.5e-13;9.9e-15;2.1e-13;3e-09;2.6e-09;3.6e-09;4.4e-10;2.9e-09	7.8e-10;6.2e-17;2.2e-14;2.8e-08;4.7e-12;3e-12;5.2e-12;1e-11;4.8e-11;6e-12;3.3e-12;2.8e-11;1e-10;1.1e-09;2.7e-09;5.4e-10;4.4e-10;6.6e-10;7.6e-10;7.4e-06;8.6e-08;3.5e-10;2.5e-13;1.4e-14;1.4e-13;2.4e-13;1.6e-14;2.7e-13;1.9e-13;1.5e-13;2.7e-13;1e-14;1.9e-13	0.0302189959626443	AGT	ORF1ab:leader-protein	.	160-192-delinframe	.	no-SNV	ORF1ab:leader-protein	0.977538867351425
CAMB-72713	MN908947.3	518	ATG	-	0.486666666666667	0.41	2.8e-10;2.5e-07;3.9e-07	3.6e-09;1.7e-06;4.4e-06	0.470420107068324	TAT	ORF1ab:leader-protein	.	253-255-delinframe	.	no-SNV	ORF1ab:leader-protein	0.530251592801005
CAMB-72713	MN908947.3	522	TT	-	0.0375	0.031	4.1e-05;2e-05	0.00023;2e-04	0.0353024240997882	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.963758001636425
CAMB-72722	MN908947.3	11074	C	INS	0.11	0.11	1.5e-35	1.1e-32	0.111726819078566	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.881832424277591
CAMB-72722	MN908947.3	11083	G	-	0.15	0.15	1.2e-67	1.8e-64	0.149825601216858	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-72722	MN908947.3	11083	G	T	0.85	0.85	0	0	0.849990821116677	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-72722	MN908947.3	11590	A	G	1	1	0	0	0.999576952364836	CAC	ORF1ab:nsp6	T206T	A618G	ACA>ACG	Synonymous	ORF1ab:nsp6	8.46095270327439e-05
CAMB-72722	MN908947.3	14805	C	T	1	1	0	0	0.999141618621153	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000343352551538649
CAMB-72722	MN908947.3	23593	G	C	0.4	0.4	3.2e-202	3.7e-209	0.402471823770492	AGA	S	Q677H	G2031C	CAG>CAC	Missense	GU280_gp02, spike glycoprotein	0.597143954918033
CAMB-72722	MN908947.3	2480	A	G	1	1	0	0	0.999529153260614	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000156948913128777
CAMB-72722	MN908947.3	2558	C	T	1	1	0	0	0.999666136412734	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	3.92780690901235e-05
CAMB-72722	MN908947.3	26144	G	T	1	1	0	0	0.999679230152366	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	8.01924619085806e-05
CAMB-72722	MN908947.3	29013	C	T	1	1	0	0	0.999681551199491	ACT	N	T247I	C740T	ACT>ATT	Missense	GU280_gp10	3.53832000566131e-05
CAMB-72722	MN908947.3	4185	G	A	1	1	0	0	0.9997535640795	GGT	ORF1ab:nsp3	G489D	G1466A	GGT>GAT	Missense	ORF1ab:nsp3	7.39307761499316e-05
CAMB-72722	MN908947.3	6119	T	C	0.44	0.43	8.2e-208	1.2e-213	0.434674556213018	TTC	ORF1ab:nsp3	S1134P	T3400C	TCA>CCA	Missense	ORF1ab:nsp3	0.565325443786982
CAMB-72731	MN908947.3	11074	C	INS	0.11	0.11	3e-61	4.4e-35	0.108209584233675	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.888143073881661
CAMB-72731	MN908947.3	11083	G	-	0.16	0.16	1.2e-65	7.6e-72	0.157276634940129	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.09339325090016e-05
CAMB-72731	MN908947.3	11083	G	T	0.84	0.84	0	0	0.842611717419823	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.09339325090016e-05
CAMB-72731	MN908947.3	14805	C	T	1	1	0	0	0.998821563392566	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000472706209761716
CAMB-72731	MN908947.3	1856	A	G	0.0057	0.0072	0.00045	2e-05	0.00596297913797158	GAG	ORF1ab:nsp2	S351G	A1051G	AGT>GGT	Missense	ORF1ab:nsp2	0.993919440991702
CAMB-72731	MN908947.3	21575	C	T	0.04	0.037	1.4e-11	3.7e-10	0.0393237082066869	TCT	S	L5F	C13T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.960106382978723
CAMB-72731	MN908947.3	2480	A	G	1	1	0	0	0.999728911579994	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	9.03628066687751e-05
CAMB-72731	MN908947.3	2558	C	T	1	1	0	0	0.999156677308596	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000195771339075959
CAMB-72731	MN908947.3	26144	G	T	1	1	0	0	0.999314217930421	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000296554408466628
CAMB-72731	MN908947.3	26167	G	T	0.041	0.047	1.4e-17	8.4e-21	0.0420834832673624	AGT	ORF3a	V259L	G775T	GTA>TTA	Missense	GU280_gp03	0.957610651313422
CAMB-72731	MN908947.3	29013	C	T	1	1	0	0	0.999637202488928	ACT	N	T247I	C740T	ACT>ATT	Missense	GU280_gp10	0.000102678540869482
CAMB-72731	MN908947.3	4185	G	A	1	1	0	0	0.999798237460098	GGT	ORF1ab:nsp3	G489D	G1466A	GGT>GAT	Missense	ORF1ab:nsp3	0.000115292879944083
CAMB-72731	MN908947.3	6394	T	G	0.098	0.11	3.7e-47	2.3e-48	0.0988702813294443	ATC	ORF1ab:nsp3	D1225E	T3675G	GAT>GAG	Missense	ORF1ab:nsp3	0.900961173821239
CAMB-72740	MN908947.3	11074	C	INS	0.11	0.12	2.4e-59	5.8e-37	0.110941745048284	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.883803921920252
CAMB-72740	MN908947.3	11083	G	-	0.16	0.15	2.3e-67	1.1e-67	0.157644273739643	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-72740	MN908947.3	11083	G	T	0.84	0.85	0	0	0.84217857976826	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-72740	MN908947.3	14805	C	T	1	1	0	0	0.999295518457994	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000294496382314049
CAMB-72740	MN908947.3	1515	A	G	1	1	0	0	0.999179628535801	CAT	ORF1ab:nsp2	H237R	A710G	CAT>CGT	Missense	ORF1ab:nsp2	0.000492222878519394
CAMB-72740	MN908947.3	17247	T	C	1	1	0	0	0.999145709484743	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000247108826727291
CAMB-72740	MN908947.3	26144	G	T	1	1	0	0	0.999602709521066	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000238374287360203
CAMB-72740	MN908947.3	9223	C	T	1	1	0	0	0.999112358263658	ACG	ORF1ab:nsp4	H223H	C669T	CAC>CAT	Synonymous	ORF1ab:nsp4	0.00034360325277746
CAMB-7275F	MN908947.3	11074	C	INS	0.21	0.018	5.9e-100	0.0012	0.196396209806866	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.803267229327396
CAMB-7275F	MN908947.3	11083	G	-	0.33	0.52	2.1e-160	9.1e-253	0.339527742481999	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.64718339686573e-05
CAMB-7275F	MN908947.3	11083	G	T	0.67	0.48	1.7e-230	1.1e-124	0.660392842016095	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.64718339686573e-05
CAMB-7275F	MN908947.3	14805	C	T	1	1	0	0	0.999869848156182	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000130151843817787
CAMB-7275F	MN908947.3	17247	T	C	1	1	0	0	0.999854054166754	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000104247023747472
CAMB-7275F	MN908947.3	19763	C	T	0.19	0.37	5.8e-67	1.2e-81	0.227459016393443	ACA	ORF1ab:endoRNAse	T48I	C143T	ACA>ATA	Missense	ORF1ab:endoRNAse	0.772540983606557
CAMB-7275F	MN908947.3	28507	CAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGGTGGTGACGGTAAAATGAAAGATCT	-	0.0679358974358974	0.00396153846153846	1.1e-27;1.4e-27;1.6e-27;5e-28;2.7e-27;7.4e-28;2.1e-27;1.4e-27;4.7e-28;1.1e-28;3.3e-28;5.4e-28;1.2e-27;6.9e-28;2.9e-31;1.2e-28;1.4e-29;8.9e-30;2.4e-28;4.5e-28;5.4e-28;1.7e-27;5.7e-28;2.5e-30;1.9e-27;5.7e-28;2.1e-30;1.2e-27;1.8e-27;2e-27;4.4e-28;1e-30;2.8e-29;8.2e-28;3e-27;1.1e-27;1.5e-27;5e-27;5.6e-27;6.2e-27;8.3e-24;8.4e-29;1e-31;2.6e-27;1.7e-27;2.7e-28;7.1e-33;8.1e-33;2.2e-29;1.1e-27;2.9e-27;2.4e-29;3.4e-27;1.3e-27;6.5e-29;2.2e-27;8.8e-28;5.2e-29;6.4e-28;3.3e-28;7.7e-28;5.5e-28;6.4e-28;1.7e-29;1.9e-33;3.5e-30;6.9e-31;6.6e-30;2.3e-28;6e-28;3.1e-29;5.7e-32;4.4e-30;2.7e-28;1.3e-28;3.9e-28;5.6e-28;7.6e-28	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;2.7e-35;4e-32;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;7.7e-57;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0362891425226807	GCA	N	.	234-311-delinframe	.	no-SNV	GU280_gp10	0.964797728885735
CAMB-7275F	MN908947.3	28571	A	-	0.083	0.14	1.9e-33	7.7e-57	0.110356224752112	TAA	N	.	298-298-delfrshift	.	no-SNV	GU280_gp10	0.886889460154242
CAMB-7276E	MN908947.3	11074	C	-	0.0018	0.0056	0.0047	2.4e-06	0.00397128455781274	TCT	ORF1ab:nsp6	.	102-102-delfrshift	.	no-SNV	ORF1ab:nsp6	0.84187414082786
CAMB-7276E	MN908947.3	11074	C	INS	0.1	0.16	1.9e-32	2e-64	0.135176416679395	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.84187414082786
CAMB-7276E	MN908947.3	11074	C	T	0.014	0.023	1.6e-07	7.2e-15	0.018978157934932	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.84187414082786
CAMB-7276E	MN908947.3	11083	G	-	0.16	0.16	2.8e-69	3.3e-70	0.157019473204227	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-7276E	MN908947.3	11083	G	T	0.84	0.84	0	0	0.842694419111993	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-7276E	MN908947.3	1368	T	C	1	1	0	0	0.998565051020408	ATT	ORF1ab:nsp2	I188T	T563C	ATT>ACT	Missense	ORF1ab:nsp2	0
CAMB-7276E	MN908947.3	14805	C	T	1	1	0	0	0.999890740234909	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	9.10498042429209e-05
CAMB-7276E	MN908947.3	16325	G	-	0.028	0.0047	2.7e-08	0.006	0.00812127774769897	TGT	ORF1ab:helicase	.	89-89-delfrshift	.	no-SNV	ORF1ab:helicase	0.991878722252301
CAMB-7276E	MN908947.3	17413	G	A	0.0021	0.0067	0.0035	2.6e-05	0.00470962677820669	TGC	ORF1ab:helicase	A393T	G1177A	GCT>ACT	Missense	ORF1ab:helicase	0.992731260954183
CAMB-7276E	MN908947.3	18731	TTGGATTTG	-	0.0041	0.00825555555555556	0.00028;0.00035;0.00061;0.00076;0.00081;0.0013;0.0041;0.0051;0.018	1.8e-05;3.5e-05;4.6e-05;5.2e-05;5.6e-05;1.8e-08;0.00032;7.5e-05;0.00079	0.00602475627122357	ATT	ORF1ab:3'-to-5'-exonuclease	.	692-700-delinframe	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.993220753046081
CAMB-7276E	MN908947.3	18741	T	C	0.011	0.011	3e-07	4.7e-07	0.0111750295890562	ATT	ORF1ab:3'-to-5'-exonuclease	D234D	T702C	GAT>GAC	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.98186122044535
CAMB-7276E	MN908947.3	18743	ACGTCTATAATCCGTT	-	0.00499375	0.0121125	0.06;0.034;0.039;0.033;0.034;0.027;0.028;0.0066;0.0044;0.00054;6e-04;0.00077;0.00049;0.00068;0.0026;0.00053	0.00048;0.00013;0.00025;0.00013;0.00015;8e-04;0.00074;0.00084;3e-04;3.7e-05;4.6e-05;4.7e-05;3.1e-05;4.5e-05;0.00014;4.1e-05	0.00610687022900763	TAC	ORF1ab:3'-to-5'-exonuclease	.	704-719-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.983115616022549
CAMB-7276E	MN908947.3	19872	G	T	1	1	0	0	0.999868178223042	TGA	ORF1ab:endoRNAse	V84V	G252T	GTG>GTT	Synonymous	ORF1ab:endoRNAse	0
CAMB-7276E	MN908947.3	19983	C	T	0.23	0.16	2.2e-22	4.3e-18	0.187713310580205	TCT	ORF1ab:endoRNAse	V121V	C363T	GTC>GTT	Synonymous	ORF1ab:endoRNAse	0.798634812286689
CAMB-7276E	MN908947.3	20178	C	T	1	1	6e-148	7.3e-186	1	TCC	ORF1ab:endoRNAse	V186V	C558T	GTC>GTT	Synonymous	ORF1ab:endoRNAse	0
CAMB-7276E	MN908947.3	2065	C	T	0.004	0.0089	0.00071	3.9e-06	0.00608403574370999	ACA	ORF1ab:nsp2	Y420Y	C1260T	TAC>TAT	Synonymous	ORF1ab:nsp2	0.99385258888396
CAMB-7276E	MN908947.3	22586	TTTA	-	0.03	0.02975	1e-08;3.8e-08;9.8e-08;1.9e-08	7.2e-07;2.9e-09;2e-08;3.9e-08	0.0305047143649473	TTT	S	.	1024-1027-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.974302006961416
CAMB-7276E	MN908947.3	23555	CCCATTGGTGCAGGTATATGCGCTAG	-	0.0396153846153846	0.0418461538461538	0.011;0.0095;0.01;0.011;0.00013;0.00023;0.00051;0.00085;0.00093;0.00091;0.00091;0.00096;0.00061;0.00056;6.3e-09;1.2e-09;6.4e-05;2.4e-05;4.2e-05;2.2e-05;5.3e-05;0.00011;6.1e-05;6.1e-05;1.5e-06;2.2e-06	0.00056;0.00046;0.00058;0.00067;4.9e-05;6.2e-05;5.2e-05;0.00011;0.00012;0.00012;1e-04;0.00012;6e-05;5.5e-05;1.3e-06;1.6e-07;0.00017;9.4e-05;0.00018;9e-05;0.00018;0.00038;0.00021;0.00023;7.9e-06;1.2e-05	0.0367425611372124	ACC	S	.	1993-2018-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.968828677616593
CAMB-7276E	MN908947.3	23571	TATGCGCTAG	-	0.0417	0.0359	6.4e-05;2.4e-05;4.2e-05;2.2e-05;5.3e-05;0.00011;6.1e-05;6.1e-05;1.5e-06;2.2e-06	0.00017;9.4e-05;0.00018;9e-05;0.00018;0.00038;0.00021;0.00023;7.9e-06;1.2e-05	0.037050668629616	ATA	S	.	2009-2018-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.959845765190799
CAMB-7276E	MN908947.3	23707	C	T	1	1	0	0	0.999878271454656	CCA	S	P715P	C2145T	CCC>CCT	Synonymous	GU280_gp02, spike glycoprotein	0.000121728545343883
CAMB-7276E	MN908947.3	25527	GCTTATT	-	0.0119428571428571	0.00228571428571429	0.00082;0.00089;0.00069;1e-05;3.7e-06;0.00021;4e-04	NA;NA;NA;NA;NA;0.0019;0.0031	0.00385473168314106	GGC	ORF3a	.	135-141-delfrshift	.	no-SNV	GU280_gp03	0.997122859435084
CAMB-7276E	MN908947.3	25958	A	G	0.0062	0.012	3.8e-05	1.1e-06	0.00757575757575758	TAT	ORF3a	Y189C	A566G	TAT>TGT	Missense	GU280_gp03	0.992424242424242
CAMB-7276E	MN908947.3	26144	G	T	1	1	4e-268	0	0.998516320474777	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.00148367952522255
CAMB-7276E	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.0577073170731707	0.0683170731707317	1.7e-05;4e-07;1.5e-07;1.5e-07;4.9e-07;1.9e-10;2.1e-09;1.8e-11;1.7e-11;3.3e-12;6.2e-12;3.7e-12;1.5e-11;8.9e-12;1.3e-11;2.6e-11;6.5e-12;2.1e-11;9.7e-12;9.4e-12;7.6e-12;2.3e-11;1.2e-11;1.4e-11;8.4e-12;5.7e-12;1.6e-11;5.4e-12;6.8e-12;8.4e-12;1.6e-11;1.4e-11;2.7e-12;8.2e-12;3.6e-13;2.4e-12;1.7e-12;3.2e-06;2e-04;0.00014;0.00055	2.8e-07;4.7e-09;2.3e-08;2.8e-08;1.1e-07;1.4e-10;8e-10;3e-12;2.8e-12;3.4e-13;2e-13;1.6e-13;4e-13;8e-15;1.6e-14;3.1e-14;6.6e-15;2e-14;5.2e-15;1.1e-14;1.3e-14;3e-14;1.4e-14;1.5e-14;8.1e-15;4.1e-15;1.5e-14;8.3e-15;4e-15;8.3e-15;1.5e-13;4e-14;3.5e-14;1.7e-13;1.2e-14;2.7e-13;8.7e-14;4.5e-07;9.6e-05;3.7e-05;4e-04	0.0709071495500207	GTC	M	.	258-298-delfrshift	.	no-SNV	GU280_gp05	0.963439079658358
CAMB-7276E	MN908947.3	28695	CAC	-	0.00123333333333333	0.00876666666666667	NA;NA;0.0057	2e-05;1.6e-05;1.9e-05	0.00722712296737167	ACA	N	.	422-424-delinframe	.	no-SNV	GU280_gp10	0.992725355824987
CAMB-7276E	MN908947.3	29572	CGTTTTCGCTTTTC	-	0.056	0.00482142857142857	5.1e-19;3.8e-19;1.1e-19;1.2e-19;7.5e-20;2.2e-19;1.1e-18;1.9e-19;2.4e-19;5.1e-17;9.9e-19;3.2e-20;7.2e-19;7.6e-19	0.00019;0.00025;0.0014;0.00089;0.00097;0.001;0.0016;0.0019;0.0011;0.012;0.0014;0.00071;0.00086;0.0011	0.0200657894736842	ACG	ORF10	.	15-28-delfrshift	.	no-SNV	GU280_gp11	0.980462390100944
CAMB-7276E	MN908947.3	29640	C	T	0.64	0.63	1.1e-254	1.4999981227434e-318	0.633728590250329	GCA	ORF10	A28V	C83T	GCA>GTA	Missense	GU280_gp11	0.365942028985507
CAMB-7276E	MN908947.3	2973	C	T	0.0069	0.0097	0.00011	4.8e-06	0.00907935355002724	GCT	ORF1ab:nsp3	A85V	C254T	GCT>GTT	Missense	ORF1ab:nsp3	0.990920646449973
CAMB-7276E	MN908947.3	522	TT	-	0.0385	0.0295	8.9e-06;7.2e-05	8.1e-05;0.0018	0.0344834483448345	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.959257806856412
CAMB-7276E	MN908947.3	5490	A	G	0.049	0.04	2.4e-19	1.6e-17	0.0435879788942418	GAT	ORF1ab:nsp3	D924G	A2771G	GAT>GGT	Missense	ORF1ab:nsp3	0.956412021105758
CAMB-7276E	MN908947.3	6990	C	T	1	1	0	0	0.998641304347826	TCT	ORF1ab:nsp3	S1424F	C4271T	TCT>TTT	Missense	ORF1ab:nsp3	0
CAMB-7276E	MN908947.3	7432	ATTTT	-	0.00766	0.0226	NA;0.14;0.043;0.0014;0.002	6.1e-08;6e-09;3.1e-06;8.1e-05;0.00024	0.0142372138867594	CAT	ORF1ab:nsp3	.	4713-4717-delfrshift	.	no-SNV	ORF1ab:nsp3	0.990627253064167
CAMB-7277D	MN908947.3	11074	C	INS	0.12	0.11	9.3e-33	1.8e-33	0.113723934723481	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.879703082502267
CAMB-7277D	MN908947.3	11083	G	-	0.15	0.15	2.3e-60	3.8e-66	0.149071865601991	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-7277D	MN908947.3	11083	G	T	0.85	0.85	0	0	0.850928134398009	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-7277D	MN908947.3	12896	C	A	0.0081	0.0099	4.4e-06	9.8e-07	0.00957056431617574	ACC	ORF1ab:nsp9	P71T	C211A	CCA>ACA	Missense	ORF1ab:nsp9	0.990379847267678
CAMB-7277D	MN908947.3	14805	C	T	1	1	0	0	0.998504296747525	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000516697487218536
CAMB-7277D	MN908947.3	2480	A	G	1	1	0	0	0.999659574468085	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-7277D	MN908947.3	2558	C	T	1	1	0	0	0.99899709156554	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	5.01454217229967e-05
CAMB-7277D	MN908947.3	26144	G	T	1	1	0	0	0.99986013986014	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7278C	MN908947.3	11074	C	INS	0.027	0.019	8.9e-06	0.0022	0.0208411838024291	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.978781993680976
CAMB-7278C	MN908947.3	11075	T	-	0.033	0.031	1.6e-09	2.3e-08	0.0315260358206042	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.963056951832512
CAMB-7278C	MN908947.3	12624	C	A	0.0065	0.0044	3.2e-05	0.00034	0.00478802992518703	CCT	ORF1ab:nsp8	P178H	C533A	CCT>CAT	Missense	ORF1ab:nsp8	0.995112219451372
CAMB-7278C	MN908947.3	14408	C	T	1	1	0	0	0.99759585898977	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000515173073620685
CAMB-7278C	MN908947.3	22987	C	T	0.0053	0.01	0.0019	8.5e-06	0.00940813030962578	CCG	S	A475A	C1425T	GCC>GCT	Synonymous	GU280_gp02, spike glycoprotein	0.990240820051955
CAMB-7278C	MN908947.3	23042	T	C	0.0045	0.0081	0.00043	1e-05	0.00767803442318766	ATC	S	S494P	T1480C	TCA>CCA	Missense	GU280_gp02, spike glycoprotein	0.992002047475846
CAMB-7278C	MN908947.3	23403	A	G	1	1	0	0	0.998480958818794	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.11424708723854e-05
CAMB-7278C	MN908947.3	241	C	T	1	1	0	0	0.998493349958437	TCG	NA	NA	NA	NA	NA	NA	7.7930174563591e-05
CAMB-7278C	MN908947.3	25429	G	T	1	1	0	0	0.99875229612172	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	3.4658441063321e-05
CAMB-7278C	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0368421052631579	0.0348157894736842	0.00027;1.7e-05;0.00018;0.00015;0.00025;2e-05;5.7e-05;1.5e-06;1.4e-06;3.2e-07;7.8e-07;5.4e-07;1.1e-06;7.5e-07;7e-07;1.2e-06;5.9e-07;1.2e-06;8e-07;7.6e-07;5.5e-07;1.4e-06;7.9e-07;1e-06;7.1e-07;5.3e-07;1.2e-06;6.1e-07;3.1e-07;6.9e-07;1.1e-06;9.4e-07;5.8e-07;1.3e-06;3.7e-07;8e-07;9.3e-07;0.00049	0.00019;1.7e-05;4.7e-05;4.3e-05;8.8e-05;1.3e-05;2.5e-05;5.5e-06;5.1e-06;3.8e-06;2.9e-06;2.4e-06;3.2e-06;2.9e-06;2.8e-06;4.4e-06;2.4e-06;4.6e-06;2.5e-06;3.5e-06;2.7e-06;5.5e-06;3.2e-06;3.8e-06;2.9e-06;2.1e-06;4.2e-06;3.1e-06;1.5e-06;2.7e-06;4.5e-06;3.8e-06;1.7e-06;4.8e-06;9.8e-07;3.6e-06;2.7e-06;0.0013	0.0366036523322444	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.97512424517715
CAMB-7278C	MN908947.3	2927	G	A	0.026	0.029	6.5e-12	3.4e-14	0.0284992551331045	TGA	ORF1ab:nsp3	E70K	G208A	GAA>AAA	Missense	ORF1ab:nsp3	0.971176889694928
CAMB-7278C	MN908947.3	3037	C	T	1	1	0	0	0.99907228449942	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000309238500193274
CAMB-7278C	MN908947.3	4039	C	T	0.0081	0.0037	3.9e-05	0.0015	0.00480034911629937	ACA	ORF1ab:nsp3	D440D	C1320T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.995199650883701
CAMB-7278C	MN908947.3	6336	C	T	0.0075	0.0054	2.4e-05	0.00023	0.00582849486377847	TCG	ORF1ab:nsp3	S1206L	C3617T	TCG>TTG	Missense	ORF1ab:nsp3	0.994104510942385
CAMB-7279B	MN908947.3	11075	T	-	0.054	0.045	1.3e-14	1.1e-11	0.0468234384754883	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.949787436453905
CAMB-7279B	MN908947.3	12663	C	T	0.026	0.031	1.5e-12	2.2e-15	0.0303556625745076	GCC	ORF1ab:nsp8	A191V	C572T	GCC>GTC	Missense	ORF1ab:nsp8	0.969604863221885
CAMB-7279B	MN908947.3	13011	C	T	0.0097	0.0058	8.2e-06	0.00027	0.00643415953791036	ACA	ORF1ab:nsp9	T109I	C326T	ACA>ATA	Missense	ORF1ab:nsp9	0.993529282737442
CAMB-7279B	MN908947.3	14408	C	T	1	1	0	0	0.997532276023955	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000270847753468356
CAMB-7279B	MN908947.3	17117	G	T	0.0045	0.009	0.00013	2.5e-06	0.00836424957841484	GGC	ORF1ab:helicase	G294V	G881T	GGC>GTC	Missense	ORF1ab:helicase	0.991298482293423
CAMB-7279B	MN908947.3	19660	C	T	0.011	0.011	5.5e-06	8.5e-07	0.0105922002888782	ACA	ORF1ab:endoRNAse	H14Y	C40T	CAC>TAC	Missense	ORF1ab:endoRNAse	0.989407799711122
CAMB-7279B	MN908947.3	20099	C	T	0.083	0.031	3.9e-06	5.1e-06	0.039647577092511	GCT	ORF1ab:endoRNAse	A160V	C479T	GCT>GTT	Missense	ORF1ab:endoRNAse	0.960352422907489
CAMB-7279B	MN908947.3	21614	C	T	0.32	0.3	1.1e-67	1.6e-110	0.302786377708978	TCT	S	L18F	C52T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.697213622291022
CAMB-7279B	MN908947.3	22104	G	C	0.98	0.97	0	0	0.976378868978357	GGA	S	G181A	G542C	GGA>GCA	Missense	GU280_gp02, spike glycoprotein	0.023621131021643
CAMB-7279B	MN908947.3	23403	A	G	1	1	0	0	0.99969850571897	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000169590533079576
CAMB-7279B	MN908947.3	241	C	T	1	1	0	0	0.997303509857661	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-7279B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999232009830274	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7279B	MN908947.3	3037	C	T	1	1	9.9e-307	0	0.997705036840198	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7279B	MN908947.3	931	T	A	0.036	0.038	1.8e-17	3.4e-18	0.0374940673943996	TTG	ORF1ab:nsp2	I42I	T126A	ATT>ATA	Synonymous	ORF1ab:nsp2	0.962411010915994
CAMB-727AA	MN908947.3	1059	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0
CAMB-727AA	MN908947.3	14408	C	T	1	1	0	0	0.999576629974598	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000317527519051651
CAMB-727AA	MN908947.3	23403	A	G	1	1	0	0	0.999858300742504	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.66797029983563e-05
CAMB-727AA	MN908947.3	241	C	T	1	1	0	0	0.999915390472967	TCG	NA	NA	NA	NA	NA	NA	8.46095270327439e-05
CAMB-727AA	MN908947.3	25563	G	T	1	1	0	0	0.99990136121523	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	9.86387847701716e-05
CAMB-727AA	MN908947.3	3037	C	T	1	1	7.6e-43	1.9e-173	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-727C8	MN908947.3	11075	T	-	0.041	0.029	6.2e-10	3.2e-08	0.0381242129428415	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961742056991296
CAMB-727C8	MN908947.3	14408	C	T	1	1	0	0	0.999707217098521	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000230043708304578
CAMB-727C8	MN908947.3	23403	A	G	1	1	0	0	0.999895430304298	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.97131304681237e-05
CAMB-727C8	MN908947.3	241	C	T	1	1	0	0	0.99982414631027	TCG	NA	NA	NA	NA	NA	NA	0.000175853689730145
CAMB-727C8	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99977596056906	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-727C8	MN908947.3	29051	C	INS	0.048	0.016	3.5e-14	0.0029	0.0311496648453782	GCA	N	.	777-778-insfrshift	.	no-SNV	GU280_gp10	0.968737678138906
CAMB-727C8	MN908947.3	3037	C	T	1	1	0	0	0.99976213130352	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-727C8	MN908947.3	9685	A	G	0.0028	0.017	0.0025	8.7e-10	0.00774262075134168	TAA	ORF1ab:nsp4	I377M	A1131G	ATA>ATG	Missense	ORF1ab:nsp4	0.992257379248658
CAMB-727E6	MN908947.3	11075	T	-	0.078	0.0063	7e-20	0.0045	0.0450486636799011	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954889541171018
CAMB-727E6	MN908947.3	1426	C	T	0.069	0.042	4.5e-17	6.4e-08	0.0612244897959184	ACC	ORF1ab:nsp2	Y207Y	C621T	TAC>TAT	Synonymous	ORF1ab:nsp2	0.938775510204082
CAMB-727E6	MN908947.3	14408	C	T	1	1	0	0	0.999577301067315	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000317024199513896
CAMB-727E6	MN908947.3	15348	TG	-	0.0325	0.0545	3.4e-12;1.7e-11	5.9e-14;1.9e-13	0.0358877495952509	TTG	ORF1ab:RNA-dependent-RNA-polymerase	.	1881-1882-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.962311557788945
CAMB-727E6	MN908947.3	21990	T	-	0.11	0.14	1.6e-14	1.9e-20	0.127690802348337	GTT	S	.	428-428-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.872309197651663
CAMB-727E6	MN908947.3	23403	A	G	1	1	0	0	0.999877079406703	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.19470621978202e-05
CAMB-727E6	MN908947.3	241	C	T	1	1	0	0	0.999760501987834	TCG	NA	NA	NA	NA	NA	NA	4.78996024332998e-05
CAMB-727E6	MN908947.3	27509	C	T	0.056	0.045	2.7e-26	1.6e-21	0.0492232441183562	ACA	ORF7a	T39I	C116T	ACA>ATA	Missense	GU280_gp07	0.946264338121319
CAMB-727E6	MN908947.3	28662	T	C	0.015	0.03	3e-07	2.9e-14	0.02723125178215	ATC	N	I130T	T389C	ATC>ACC	Missense	GU280_gp10	0.97276874821785
CAMB-727E6	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-727E6	MN908947.3	29685	T	INS	0.38	0.37	6.5e-74	4.8e-151	0.368589743589744	ATC	NA	NA	NA	NA	NA	NA	0.629807692307692
CAMB-727E6	MN908947.3	29687	A	C	0.33	0.31	1.1e-53	1e-116	0.312703583061889	CAG	NA	NA	NA	NA	NA	NA	0.686644951140065
CAMB-727E6	MN908947.3	3037	C	T	1	1	8.5e-236	0	0.99843137254902	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000784313725490196
CAMB-727E6	MN908947.3	4398	TG	-	0.0075	0.00855	NA;4.4e-06	3.6e-06;0.00031	0.00794609665427509	ATG	ORF1ab:nsp3	.	1679-1680-delfrshift	.	no-SNV	ORF1ab:nsp3	0.995653380190511
CAMB-727E6	MN908947.3	4399	G	-	0.015	0.0086	4.4e-06	0.00031	0.0117691014384457	TGC	ORF1ab:nsp3	.	1680-1680-delfrshift	.	no-SNV	ORF1ab:nsp3	0.988137492994582
CAMB-727F5	MN908947.3	11075	T	-	0.018	0.038	2.1e-05	4.9e-10	0.0260019435201272	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.96691598692541
CAMB-727F5	MN908947.3	12164	G	T	0.022	0.0049	2.6e-08	0.0051	0.0139833422480324	GGC	ORF1ab:nsp8	A25S	G73T	GCT>TCT	Missense	ORF1ab:nsp8	0.982938357584953
CAMB-727F5	MN908947.3	13548	C	-	0.014	0.014	3.2e-05	9.4e-05	0.0143188854489164	ACA	ORF1ab:RNA-dependent-RNA-polymerase	.	81-81-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.985681114551084
CAMB-727F5	MN908947.3	13571	G	T	0.01	0.027	0.0038	7.8e-06	0.0132100396301189	GGT	ORF1ab:RNA-dependent-RNA-polymerase	G35V	G104T	GGT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.979807510851104
CAMB-727F5	MN908947.3	14091	TGATTTCGG	-	0.000855555555555556	0.00974444444444444	NA;NA;NA;NA;NA;NA;NA;0.0012;NA	1.3e-05;4.9e-05;6.7e-06;5.2e-06;4.9e-06;7.7e-06;5.8e-06;0.00019;9e-06	0.00278114964428942	ATG	ORF1ab:RNA-dependent-RNA-polymerase	.	624-632-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.997121073112088
CAMB-727F5	MN908947.3	14408	C	T	1	1	0	0	0.999731327243418	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000223893963818735
CAMB-727F5	MN908947.3	20922	G	T	0.0082	0.011	8.1e-05	9.1e-06	0.00952032222629074	GGT	ORF1ab:2'-O-ribose-methyltransferase	W88C	G264T	TGG>TGT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.990398307498271
CAMB-727F5	MN908947.3	22014	G	T	0.0046	0.01	0.00071	8.8e-06	0.00542888165038002	AGT	S	S151I	G452T	AGT>ATT	Missense	GU280_gp02, spike glycoprotein	0.99457111834962
CAMB-727F5	MN908947.3	2255	A	T	0.012	0.012	7.1e-06	3.9e-06	0.0120343839541547	AAT	ORF1ab:nsp2	I484F	A1450T	ATT>TTT	Missense	ORF1ab:nsp2	0.987965616045845
CAMB-727F5	MN908947.3	23403	A	G	1	1	0	0	0.999877543166034	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.74691671185907e-05
CAMB-727F5	MN908947.3	23444	C	T	0.0058	0.0081	0.00016	9.2e-06	0.00650654671057916	TCA	S	Q628*	C1882T	CAA>TAA	Nonsense	GU280_gp02, spike glycoprotein	0.993439901464642
CAMB-727F5	MN908947.3	23625	C	T	0.017	0.016	1.3e-05	3.6e-05	0.0164952454880652	GCT	S	A688V	C2063T	GCT>GTT	Missense	GU280_gp02, spike glycoprotein	0.983504754511935
CAMB-727F5	MN908947.3	241	C	T	0.99	1	0	0	0.991377913779138	TCG	NA	NA	NA	NA	NA	NA	9.00009000090001e-05
CAMB-727F5	MN908947.3	28881	G	A	1	1	0	0	0.999853843905291	AGG	N	R203K	G608A	AGG>AAG	Missense	GU280_gp10	0
CAMB-727F5	MN908947.3	28881	GGG	AAC	1	0.996666666666667	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-727F5	MN908947.3	28883	G	C	1	0.99	0	0	0.997016706443914	GGG	N	G204R	G610C	GGA>CGA	Missense	GU280_gp10	0.000119331742243437
CAMB-727F5	MN908947.3	2975	A	G	0.0082	0.0087	0.00016	4.4e-05	0.00854820627802691	TAC	ORF1ab:nsp3	T86A	A256G	ACA>GCA	Missense	ORF1ab:nsp3	0.991451793721973
CAMB-727F5	MN908947.3	29781	G	T	0.015	0.011	3.4e-05	3.9e-05	0.0119445771619685	AGA	NA	NA	NA	NA	NA	NA	0.988055422838031
CAMB-727F5	MN908947.3	3037	C	T	1	1	0	0	0.999843627834246	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000156372165754496
CAMB-727F5	MN908947.3	4488	G	T	0.013	0.015	4.4e-08	5.4e-09	0.0137330957123388	GGT	ORF1ab:nsp3	G590V	G1769T	GGT>GTT	Missense	ORF1ab:nsp3	0.986162071495964
CAMB-727F5	MN908947.3	5706	ATG	-	0.0084	0.0146666666666667	1.1e-05;2.8e-05;3.6e-05	NA;7.6e-11;9.7e-11	0.0135612722939098	TAT	ORF1ab:nsp3	.	2987-2989-delinframe	.	no-SNV	ORF1ab:nsp3	0.988943173052198
CAMB-727F5	MN908947.3	6151	C	T	0.012	0.021	5.9e-06	1.1e-09	0.0181818181818182	ACT	ORF1ab:nsp3	D1144D	C3432T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.981818181818182
CAMB-727F5	MN908947.3	6808	T	C	0.015	0.014	1.4e-06	1.7e-06	0.0142209398186315	CTT	ORF1ab:nsp3	T1363T	T4089C	ACT>ACC	Synonymous	ORF1ab:nsp3	0.985366859027205
CAMB-727F5	MN908947.3	9787	TT	-	0.0018	0.0092	0.0026;NA	7.9e-06;2.5e-06	0.00514025554413277	CTT	ORF1ab:nsp4	.	1233-1234-delfrshift	.	no-SNV	ORF1ab:nsp4	0.993744817654161
CAMB-72801	MN908947.3	10042	A	C	0.057	0.052	2e-19	5.9e-22	0.0533567868660217	CAG	ORF1ab:nsp4	S496S	A1488C	TCA>TCC	Synonymous	ORF1ab:nsp4	0.94283201407212
CAMB-72801	MN908947.3	11074	C	INS	0.081	0.09	2.9e-21	2.5e-27	0.0879801324503311	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.904867549668874
CAMB-72801	MN908947.3	11083	G	-	0.15	0.19	1.2e-65	1.6e-86	0.182587947740565	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-72801	MN908947.3	11083	G	T	0.85	0.81	0	0	0.81732475921669	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-72801	MN908947.3	1376	C	T	0.0086	0.01	0.00074	2.3e-05	0.00975609756097561	TCC	ORF1ab:nsp2	P191S	C571T	CCA>TCA	Missense	ORF1ab:nsp2	0.990243902439024
CAMB-72801	MN908947.3	14123	G	T	0.0024	0.0079	0.0056	1.5e-05	0.00600740568114141	GGT	ORF1ab:RNA-dependent-RNA-polymerase	G219V	G656T	GGT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.991454983298376
CAMB-72801	MN908947.3	14805	C	T	1	1	0	0	0.999911777679753	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-72801	MN908947.3	15684	T	-	0.0082	0.0043	3.4e-05	0.0015	0.00501199188241806	ATT	ORF1ab:RNA-dependent-RNA-polymerase	.	2217-2217-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.994926511284669
CAMB-72801	MN908947.3	16801	AA	-	0.0029	0.0094	0.039;0.0036	3.4e-05;4e-06	0.00854860559630028	TAA	ORF1ab:helicase	.	565-566-delfrshift	.	no-SNV	ORF1ab:helicase	0.990566037735849
CAMB-72801	MN908947.3	17486	TAG	-	0.00176666666666667	0.0123333333333333	NA;NA;7.7e-05	1.1e-07;1.7e-07;4.9e-08	0.00873884980781783	CTA	ORF1ab:helicase	.	1250-1252-delinframe	.	no-SNV	ORF1ab:helicase	0.991188628617014
CAMB-72801	MN908947.3	18243	T	C	0.069	0.095	2.4e-25	2.9e-43	0.0933268523019235	GTT	ORF1ab:3'-to-5'-exonuclease	G68G	T204C	GGT>GGC	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.906603708075828
CAMB-72801	MN908947.3	21562	AA	-	0.0495	0.0068	3.2e-10;2.6e-10	0.00057;0.00028	0.0191693290734824	CAA	S	.	1-1-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.979865771812081
CAMB-72801	MN908947.3	22573	T	-	0.014	0.0099	4.9e-06	8.2e-05	0.0110247071562162	CTT	S	.	1011-1011-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.987892509105227
CAMB-72801	MN908947.3	22573	TTTTGGTGAAG	-	0.00127272727272727	0.00655454545454545	4.9e-06;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	8.2e-05;3e-06;6.9e-06;3.4e-05;6.5e-05;5.4e-05;2.9e-05;6.3e-05;4.1e-05;2.7e-05;5.1e-05	0.00415876704788698	CTT	S	.	1011-1021-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.987892509105227
CAMB-72801	MN908947.3	23525	C	T	0.0039	0.01	0.0064	6.1e-06	0.00908086881825991	ACA	S	H655Y	C1963T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.99079641673825
CAMB-72801	MN908947.3	24772	A	T	0.033	0.046	2.2e-15	1e-21	0.0449777842523126	CAC	S	A1070A	A3210T	GCA>GCT	Synonymous	GU280_gp02, spike glycoprotein	0.95494937723068
CAMB-72801	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-72801	MN908947.3	25186	G	-	0.0071	0.009	1e-04	4.7e-06	0.00870582120582121	AGT	S	.	3624-3624-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.990904365904366
CAMB-72801	MN908947.3	25464	T	C	0.0048	0.016	0.00087	8.1e-09	0.0146286439423314	CTC	ORF3a	T24T	T72C	ACT>ACC	Synonymous	GU280_gp03	0.985371356057669
CAMB-72801	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-72801	MN908947.3	26144	G	T	1	1	4e-98	9.2e-251	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-72801	MN908947.3	27283	AATCTTGATTACATC	-	0.00570666666666667	0.01038	0.013;0.014;0.013;0.013;0.012;0.013;0.011;0.011;0.00065;0.0021;0.00067;0.00036;0.00045;0.00046;0.00034	0.00082;0.00084;0.00091;0.00088;0.00062;0.00089;0.00056;0.00053;6.1e-06;6.7e-05;5.5e-06;3.5e-06;5.3e-06;4.9e-06;4.8e-06	0.00924772501741866	GAA	ORF6	.	82-96-delinframe	.	no-SNV	GU280_gp06	0.990643720497026
CAMB-72801	MN908947.3	29160	C	T	0.024	0.015	3.5e-11	1.9e-08	0.0158701092595984	ACT	N	T296I	C887T	ACT>ATT	Missense	GU280_gp10	0.984068851858634
CAMB-72801	MN908947.3	29756	AGTGTAC	-	0.0192857142857143	0.02	0.0016;0.0023;0.0019;0.002;0.00069;0.00073;0.00069	5.7e-07;3.2e-06;1.3e-06;2.7e-06;4.6e-08;4.3e-08;4.8e-08	0.0194373401534527	GAG	NA	NA	NA	NA	NA	NA	0.9764121663563
CAMB-72801	MN908947.3	445	TTTGCCTCAACTTG	-	0.000669285714285714	0.00928571428571429	0.042;0.009;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	8.4e-05;0.00041;3.6e-05;1.6e-05;2.9e-05;3.3e-05;1.7e-05;3.5e-05;3e-05;3e-05;3.4e-05;1.4e-05;2.9e-05;4.3e-06	0.00604674796747967	TTT	ORF1ab:leader-protein	.	180-193-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.985865528518375
CAMB-72801	MN908947.3	4806	GG	TT	0.0125	0.003026	2.1e-06;5.1e-08	0.00022;NA	0.00526729559748428	TGG	ORF1ab:nsp3	.	2087-2088-mnv	.	no-SNV	ORF1ab:nsp3	0.992881055912572
CAMB-72801	MN908947.3	6699	T	G	0.012	0.03	0.00013	1.1e-13	0.0286806883365201	TTT	ORF1ab:nsp3	F1327C	T3980G	TTT>TGT	Missense	ORF1ab:nsp3	0.97131931166348
CAMB-72801	MN908947.3	8664	C	T	0.01	0.012	9.7e-06	8.1e-07	0.0113207547169811	ACT	ORF1ab:nsp4	T37I	C110T	ACT>ATT	Missense	ORF1ab:nsp4	0.988515176374077
CAMB-72801	MN908947.3	9479	G	T	0.031	0.032	1.1e-11	7.5e-14	0.0317294281729428	TGG	ORF1ab:nsp4	G309C	G925T	GGT>TGT	Missense	ORF1ab:nsp4	0.968270571827057
CAMB-72801	MN908947.3	9491	C	T	0.013	0.017	4.6e-06	3e-08	0.0160349854227405	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.983965014577259
CAMB-72801	MN908947.3	9737	A	G	0.013	0.0057	8.6e-08	0.00013	0.00699300699300699	TAG	ORF1ab:nsp4	S395G	A1183G	AGT>GGT	Missense	ORF1ab:nsp4	0.993006993006993
CAMB-72801	MN908947.3	9924	C	T	0.0028	0.013	0.0033	1.3e-07	0.0101660939289805	GCA	ORF1ab:nsp4	A457V	C1370T	GCA>GTA	Missense	ORF1ab:nsp4	0.98983390607102
CAMB-72810	MN908947.3	11075	T	-	0.037	0.034	1.6e-10	5.3e-09	0.0345687722038852	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959888130212401
CAMB-72810	MN908947.3	14408	C	T	1	1	0	0	0.998553637968229	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000588350656991567
CAMB-72810	MN908947.3	18132	T	C	0.018	0.019	3e-09	5.2e-10	0.01860282958829	CTA	ORF1ab:3'-to-5'-exonuclease	T31T	T93C	ACT>ACC	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.98090762226465
CAMB-72810	MN908947.3	18657	C	T	0.042	0.041	7.8e-18	2.3e-19	0.0413968747302081	CCT	ORF1ab:3'-to-5'-exonuclease	T206T	C618T	ACC>ACT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.958430458430458
CAMB-72810	MN908947.3	23086	C	T	0.035	0.044	4.1e-15	1.7e-20	0.0426546562458604	ACA	S	Y508Y	C1524T	TAC>TAT	Synonymous	GU280_gp02, spike glycoprotein	0.9565505364949
CAMB-72810	MN908947.3	23403	A	G	1	1	0	0	0.997876156314895	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000188786105342647
CAMB-72810	MN908947.3	241	C	T	1	1	0	0	0.998411409609207	TCG	NA	NA	NA	NA	NA	NA	0.000176510043421471
CAMB-72810	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999513470777839	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	6.74946004319654e-05
CAMB-72810	MN908947.3	3037	C	T	1	1	0	0	0.999416531604538	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000194489465153971
CAMB-7282F	MN908947.3	106	C	T	0.0058	0.0091	0.00038	1.3e-05	0.00709447873799726	GCA	NA	NA	NA	NA	NA	NA	0.992798353909465
CAMB-7282F	MN908947.3	11074	C	INS	0.03	0.032	5.9e-06	1.5e-06	0.0306236773310096	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.968795385700651
CAMB-7282F	MN908947.3	11075	T	-	0.037	0.035	8.7e-10	2.1e-09	0.0360410662824208	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961041066282421
CAMB-7282F	MN908947.3	11085	A	G	0.0037	0.0066	0.00078	4.1e-05	0.00526797984425103	TAT	ORF1ab:nsp6	Y38C	A113G	TAT>TGT	Missense	ORF1ab:nsp6	0.994732020155749
CAMB-7282F	MN908947.3	14408	C	T	1	1	0	0	0.999223734782362	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000473332449779427
CAMB-7282F	MN908947.3	18167	C	T	0.0057	0.013	0.00023	1.7e-07	0.0107299039718678	CCT	ORF1ab:3'-to-5'-exonuclease	P43L	C128T	CCT>CTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.989270096028132
CAMB-7282F	MN908947.3	22858	C	T	0.0091	0.0046	2.6e-05	0.0026	0.0067245637797785	GCG	S	C432C	C1296T	TGC>TGT	Synonymous	GU280_gp02, spike glycoprotein	0.992223727193052
CAMB-7282F	MN908947.3	23403	A	G	1	1	0	0	0.998326157214894	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000126327757366487
CAMB-7282F	MN908947.3	241	C	T	1	1	0	0	0.999464854929151	TCG	NA	NA	NA	NA	NA	NA	0.000139603061960492
CAMB-7282F	MN908947.3	26078	C	T	0.029	0.025	1.1e-11	1e-11	0.0260454002389486	ACC	ORF3a	T229I	C686T	ACC>ATC	Missense	GU280_gp03	0.973954599761051
CAMB-7282F	MN908947.3	26873	C	T	0.011	0.0053	2e-06	0.00045	0.00738197677845229	ACA	M	N117N	C351T	AAC>AAT	Synonymous	GU280_gp05	0.992529616314021
CAMB-7282F	MN908947.3	28253	C	T	0.011	0.0087	6.4e-06	6.8e-05	0.0098804352004921	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.989427549882742
CAMB-7282F	MN908947.3	2869	A	G	1	1	0	0	0.999765456421803	TAA	ORF1ab:nsp3	V50V	A150G	GTA>GTG	Synonymous	ORF1ab:nsp3	0.000140726146918097
CAMB-7282F	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99928744477697	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	5.24246395806029e-05
CAMB-7282F	MN908947.3	29095	C	T	1	1	0	0	0.99911451477803	TCG	N	F274F	C822T	TTC>TTT	Synonymous	GU280_gp10	0.000263252363288261
CAMB-7282F	MN908947.3	3037	C	T	1	1	0	0	0.998293515358362	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7282F	MN908947.3	3802	T	A	0.01	0.0094	6.9e-07	1.5e-06	0.00978366553232863	ATA	ORF1ab:nsp3	D361E	T1083A	GAT>GAA	Missense	ORF1ab:nsp3	0.989608653378707
CAMB-7282F	MN908947.3	635	C	T	0.0097	0.01	8.8e-06	4.9e-06	0.00993320181358807	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.990066798186412
CAMB-7283E	MN908947.3	10475	C	A	0.04	0.038	1e-18	1.1e-17	0.0396908501620543	CCT	ORF1ab:3C-like-proteinase	L141I	C421A	CTT>ATT	Missense	ORF1ab:3C-like-proteinase	0.960159561206682
CAMB-7283E	MN908947.3	10795	TGAC	GTTG	7e-05	0.03325	NA;NA;NA;0.0078	7.4e-15;5.6e-15;1.2e-14;1.1e-14	0.00733153638814016	TTG	ORF1ab:3C-like-proteinase	.	741-744-mnv	.	no-SNV	ORF1ab:3C-like-proteinase	0.992438154909798
CAMB-7283E	MN908947.3	11071	G	INS	0.17	0.23	8.1e-43	3.1e-63	0.176467414760466	TGT	ORF1ab:nsp6	.	98-99-insfrshift	.	no-SNV	ORF1ab:nsp6	0.769005487391331
CAMB-7283E	MN908947.3	11073	T	-	0.016	0.015	1.1e-08	1.1e-08	0.0161749848454233	TTC	ORF1ab:nsp6	.	101-101-delfrshift	.	no-SNV	ORF1ab:nsp6	0.983713881592241
CAMB-7283E	MN908947.3	11074	C	-	0.17	0.14	3.6e-196	1.6e-92	0.162953106272944	TCT	ORF1ab:nsp6	.	102-102-delfrshift	.	no-SNV	ORF1ab:nsp6	0.000169870615214745
CAMB-7283E	MN908947.3	11074	C	T	0.83	0.86	0	0	0.836792087804234	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.000169870615214745
CAMB-7283E	MN908947.3	11083	G	T	1	1	0	0	0.999532036405658	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-7283E	MN908947.3	14805	C	T	1	1	0	0	0.99990515146126	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	2.3712134684925e-05
CAMB-7283E	MN908947.3	20543	C	T	0.029	0.051	2.7e-14	3.4e-21	0.0346456692913386	TCC	ORF1ab:endoRNAse	S308F	C923T	TCC>TTC	Missense	ORF1ab:endoRNAse	0.965354330708661
CAMB-7283E	MN908947.3	21137	A	G	0.017	0.027	1.5e-07	1.1e-11	0.0190906954887218	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.980894619360902
CAMB-7283E	MN908947.3	24099	C	T	0.071	0.099	1.2e-32	2.5e-40	0.0735807393689009	GCT	S	A846V	C2537T	GCT>GTT	Missense	GU280_gp02, spike glycoprotein	0.926348030486502
CAMB-7283E	MN908947.3	2480	A	G	1	1	0	0	0.999790751203181	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000209248796819418
CAMB-7283E	MN908947.3	2558	C	T	1	1	0	0	0.999659458539077	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000340541460922867
CAMB-7283E	MN908947.3	26144	G	T	1	1	0	2.8e-246	0.999589827727646	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000410172272354389
CAMB-7283E	MN908947.3	26270	C	T	0.066	0.13	8.8e-30	8.8e-58	0.0769365536228257	ACA	E	T9I	C26T	ACA>ATA	Missense	GU280_gp04	0.922988361907146
CAMB-7283E	MN908947.3	28376	GC	-	0.0055	0.03	0.0066;0.0074	2.2e-12;4.3e-13	0.0101950821398484	GGC	N	.	103-104-delfrshift	.	no-SNV	GU280_gp10	0.989744701538623
CAMB-7283E	MN908947.3	4665	G	A	0.0065	0.023	5.3e-05	2.6e-12	0.00987892743073609	AGA	ORF1ab:nsp3	R649K	G1946A	AGA>AAA	Missense	ORF1ab:nsp3	0.990078628197918
CAMB-7283E	MN908947.3	5020	C	T	0.071	0.037	9.7e-19	9.1e-06	0.0659133709981168	ACA	ORF1ab:nsp3	D767D	C2301T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.934086629001883
CAMB-7283E	MN908947.3	7410	G	-	0.036	0.05	7.5e-17	1.9e-18	0.0375579086697551	AGA	ORF1ab:nsp3	.	4691-4691-delfrshift	.	no-SNV	ORF1ab:nsp3	0.962442091330245
CAMB-7283E	MN908947.3	9165	C	T	0.059	0.065	1.2e-26	6.8e-30	0.0606909037323958	ACC	ORF1ab:nsp4	T204I	C611T	ACC>ATC	Missense	ORF1ab:nsp4	0.939288044965581
CAMB-7283E	MN908947.3	9438	C	T	0.23	0.19	1.2e-106	1.3e-50	0.228311711234666	ACA	ORF1ab:nsp4	T295I	C884T	ACA>ATA	Missense	ORF1ab:nsp4	0.771688288765334
CAMB-7283E	MN908947.3	9483	A	G	0.32	0.29	9.9e-159	2.8e-84	0.322417285617826	GAA	ORF1ab:nsp4	E310G	A929G	GAA>GGA	Missense	ORF1ab:nsp4	0.677582714382174
CAMB-7284D	MN908947.3	11075	T	-	0.036	0.039	2.8e-10	3.3e-10	0.0383937891440501	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957202505219207
CAMB-7284D	MN908947.3	14408	C	T	1	1	0	0	0.998671194448546	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000885870367636203
CAMB-7284D	MN908947.3	23403	A	G	1	1	0	0	0.999400851204496	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.1980909879757e-05
CAMB-7284D	MN908947.3	241	C	T	1	1	0	0	0.999009639508781	TCG	NA	NA	NA	NA	NA	NA	0.000495180245609402
CAMB-7284D	MN908947.3	25429	G	T	1	1	0	0	0.998961103723404	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0.000166223404255319
CAMB-7284D	MN908947.3	25614	C	T	1	1	0	0	0.999963291975626	CCA	ORF3a	S74S	C222T	TCC>TCT	Synonymous	GU280_gp03	3.67080243741282e-05
CAMB-7284D	MN908947.3	3037	C	T	1	1	0	0	0.999298393320704	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7284D	MN908947.3	9223	C	T	0.0085	0.0074	9.9e-05	4e-05	0.00742486741308191	ACG	ORF1ab:nsp4	H223H	C669T	CAC>CAT	Synonymous	ORF1ab:nsp4	0.992516205067767
CAMB-7285C	MN908947.3	10323	A	G	0.13	0.087	2.6e-35	7.8e-23	0.115250228457776	AAG	ORF1ab:3C-like-proteinase	K90R	A269G	AAG>AGG	Missense	ORF1ab:3C-like-proteinase	0.884696016771488
CAMB-7285C	MN908947.3	10726	C	T	0.17	0.02	1.1e-67	1.1e-09	0.0989259468626343	CCA	ORF1ab:3C-like-proteinase	T224T	C672T	ACC>ACT	Synonymous	ORF1ab:3C-like-proteinase	0.901074053137366
CAMB-7285C	MN908947.3	11398	T	C	1	1	7.89999999999999e-292	9.2e-237	1	TTA	ORF1ab:nsp6	L142L	T426C	CTT>CTC	Synonymous	ORF1ab:nsp6	0
CAMB-7285C	MN908947.3	14408	C	T	1	1	0	0	0.99954691676861	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000362466585111685
CAMB-7285C	MN908947.3	23403	A	G	1	1	0	0	0.999881644799134	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000101447315027729
CAMB-7285C	MN908947.3	241	C	T	1	1	0	0	0.999766682221185	TCG	NA	NA	NA	NA	NA	NA	5.83294447036864e-05
CAMB-7285C	MN908947.3	29353	C	T	1	1	0	0	0.999086201644837	ACA	N	Y360Y	C1080T	TAC>TAT	Synonymous	GU280_gp10	0
CAMB-7285C	MN908947.3	3037	C	T	1	1	1.4e-267	0	0.998939554612937	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000530222693531283
CAMB-7286B	MN908947.3	11071	G	INS	0.093	0.097	2.3e-25	3.3e-26	0.0955693229853951	TGT	ORF1ab:nsp6	.	98-99-insfrshift	.	no-SNV	ORF1ab:nsp6	0.904117554964103
CAMB-7286B	MN908947.3	11073	T	-	0.0064	0.0063	3.8e-05	5.2e-05	0.00631128446828105	TTC	ORF1ab:nsp6	.	101-101-delfrshift	.	no-SNV	ORF1ab:nsp6	0.992794842624194
CAMB-7286B	MN908947.3	11074	C	-	0.065	0.061	2.3e-39	1.2e-46	0.0621305696185756	TCT	ORF1ab:nsp6	.	102-102-delfrshift	.	no-SNV	ORF1ab:nsp6	0.540620775571872
CAMB-7286B	MN908947.3	11074	C	INS	0.063	0.076	2.2e-15	5.8e-22	0.0714872637633525	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.540620775571872
CAMB-7286B	MN908947.3	11074	C	T	0.33	0.32	2.8e-197	7e-238	0.325734884830493	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.540620775571872
CAMB-7286B	MN908947.3	11083	G	-	0.1	0.11	1.8e-44	7e-47	0.10617507806991	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	5.03676840938854e-05
CAMB-7286B	MN908947.3	11083	G	T	0.9	0.89	0	0	0.893598267351667	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	5.03676840938854e-05
CAMB-7286B	MN908947.3	14805	C	T	1	1	0	0	0.999302892994075	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000275173818128451
CAMB-7286B	MN908947.3	20401	T	G	1	1	1.2e-272	0	1	ATC	ORF1ab:endoRNAse	S261A	T781G	TCA>GCA	Missense	ORF1ab:endoRNAse	0
CAMB-7286B	MN908947.3	23868	G	T	1	1	0	0	0.999874071275658	GGA	S	G769V	G2306T	GGA>GTA	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7286B	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-7286B	MN908947.3	2558	C	T	1	1	0	0	0.999026763990268	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000608272506082725
CAMB-7286B	MN908947.3	26144	G	T	1	1	0	0	0.999776386404293	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7287A	MN908947.3	11075	T	-	0.033	0.034	2.3e-09	2e-09	0.0339057043073341	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.963086922778425
CAMB-7287A	MN908947.3	14408	C	T	1	1	0	0	0.997660674710662	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000533530329147172
CAMB-7287A	MN908947.3	23403	A	G	1	1	0	0	0.99942390279669	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000157117419084529
CAMB-7287A	MN908947.3	241	C	T	1	1	0	0	0.999120879120879	TCG	NA	NA	NA	NA	NA	NA	0.000175824175824176
CAMB-7287A	MN908947.3	25552	G	T	1	1	0	0	0.999092849519744	TGC	ORF3a	A54S	G160T	GCT>TCT	Missense	GU280_gp03	5.33617929562433e-05
CAMB-7287A	MN908947.3	27373	A	INS	0.0054	0.0024	2.1e-05	0.001	0.00270453008789723	AAT	ORF6	.	171-172-insfrshift	.	no-SNV	GU280_gp06	0.996659109891421
CAMB-7287A	MN908947.3	27380	T	INS	0.0046	0.0021	4.1e-05	0.0013	0.00234022782806208	ATT	ORF6	.	178-179-insfrshift	.	no-SNV	GU280_gp06	0.997418866366108
CAMB-7287A	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998908826382153	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7287A	MN908947.3	3037	C	T	1	1	0	0	0.999292185730464	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000141562853907135
CAMB-7287A	MN908947.3	6513	GTT	-	0.0123333333333333	0.00806666666666667	3e-05;5.6e-05;4.7e-05	4e-04;0.00078;0.00059	0.00865711398916139	AGT	ORF1ab:nsp3	.	3794-3796-delinframe	.	no-SNV	ORF1ab:nsp3	0.990920222720237
CAMB-7287A	MN908947.3	8683	C	T	1	1	0	0	0.999804372279552	TCA	ORF1ab:nsp4	I43I	C129T	ATC>ATT	Synonymous	ORF1ab:nsp4	9.78138602239937e-05
CAMB-72889	MN908947.3	11074	C	INS	0.11	0.11	1.7e-65	7.9e-34	0.107117718706582	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.88826118092067
CAMB-72889	MN908947.3	11083	G	-	0.17	0.17	4.8e-69	1.2e-75	0.166357769689391	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.90773284505281e-05
CAMB-72889	MN908947.3	11083	G	T	0.83	0.83	0	0	0.833391018913427	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.90773284505281e-05
CAMB-72889	MN908947.3	11392	G	T	0.0029	0.007	0.006	4.4e-05	0.00374662528237433	GGA	ORF1ab:nsp6	W140C	G420T	TGG>TGT	Missense	ORF1ab:nsp6	0.996032984995133
CAMB-72889	MN908947.3	13665	C	T	0.014	0.016	4.6e-07	4.8e-09	0.0142830143361696	ACA	ORF1ab:RNA-dependent-RNA-polymerase	H66H	C198T	CAC>CAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.985628393569395
CAMB-72889	MN908947.3	14805	C	T	1	1	0	0	0.998824264067363	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000443950082447872
CAMB-72889	MN908947.3	17247	T	C	1	1	0	0	0.998393574297189	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000661802138129985
CAMB-72889	MN908947.3	18083	T	A	0.67	0.68	0	0	0.673252037846387	ATC	ORF1ab:3'-to-5'-exonuclease	I15N	T44A	ATC>AAC	Missense	ORF1ab:3'-to-5'-exonuclease	0.326345540134577
CAMB-72889	MN908947.3	2036	G	T	0.0061	0.0073	0.00061	4.3e-05	0.00631551923323777	GGC	ORF1ab:nsp2	A411S	G1231T	GCT>TCT	Missense	ORF1ab:nsp2	0.993384964271961
CAMB-72889	MN908947.3	22878	AC	-	0.0052	0.0069	0.0044;0.00018	0.00069;1.4e-05	0.00552312081204803	AAC	S	.	1316-1317-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.996641617343885
CAMB-72889	MN908947.3	22899	G	T	0.014	0.016	4.8e-05	4.8e-06	0.0141659583687482	GGT	S	G446V	G1337T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.984934086629002
CAMB-72889	MN908947.3	23505	G	T	0.0068	0.0065	0.00022	4.4e-05	0.006778898218078	GGC	S	G648V	G1943T	GGC>GTC	Missense	GU280_gp02, spike glycoprotein	0.99286949917725
CAMB-72889	MN908947.3	25563	G	T	0.66	0.65	0	0	0.658586797240788	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.340884234604525
CAMB-72889	MN908947.3	26144	G	T	1	1	0	0	0.999691626251016	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000182220851672227
CAMB-72889	MN908947.3	29443	A	G	0.016	0.015	2e-07	1.1e-07	0.0156439312949897	AAA	N	Q390Q	A1170G	CAA>CAG	Synonymous	GU280_gp10	0.98417789181099
CAMB-72889	MN908947.3	29523	CTC	-	0.0111333333333333	0.0126666666666667	0.0016;0.00074;2.2e-10	0.00017;1e-04;1.5e-12	0.00587653702079069	ACT	N	.	1250-1252-delinframe	.	no-SNV	GU280_gp10	0.994095612092855
CAMB-72889	MN908947.3	29525	C	T	0.0087	0.011	6e-05	2.2e-06	0.00909560582988906	TCA	N	Q418*	C1252T	CAG>TAG	Nonsense	GU280_gp10	0.967709919512726
CAMB-72889	MN908947.3	29614	C	T	0.07	0.071	8.9e-29	1.3e-30	0.0703812316715543	GCA	ORF10	C19C	C57T	TGC>TGT	Synonymous	GU280_gp11	0.929457343485162
CAMB-72889	MN908947.3	29781	G	T	0.0081	0.0095	2e-04	3.1e-05	0.00845717047239338	AGA	NA	NA	NA	NA	NA	NA	0.991277032741331
CAMB-72889	MN908947.3	3564	G	T	0.016	0.018	3.7e-07	4.9e-08	0.0168426802621996	GGT	ORF1ab:nsp3	G282V	G845T	GGT>GTT	Missense	ORF1ab:nsp3	0.982277251760136
CAMB-72889	MN908947.3	5375	G	T	0.0048	0.0074	0.0016	4.1e-05	0.00537032893264713	GGC	ORF1ab:nsp3	A886S	G2656T	GCT>TCT	Missense	ORF1ab:nsp3	0.994132418388404
CAMB-72889	MN908947.3	558	G	T	0.013	0.016	0.00043	3.7e-05	0.0133329635894734	GGT	ORF1ab:leader-protein	G98V	G293T	GGT>GTT	Missense	ORF1ab:leader-protein	0.98608468983112
CAMB-72889	MN908947.3	7038	G	T	0.013	0.014	2.1e-05	4e-06	0.0131877729257642	GGC	ORF1ab:nsp3	G1440V	G4319T	GGC>GTC	Missense	ORF1ab:nsp3	0.986375545851528
CAMB-72898	MN908947.3	11074	C	INS	0.11	0.11	2.9e-32	4.1e-32	0.111097964978703	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.883045433033602
CAMB-72898	MN908947.3	11083	G	-	0.16	0.16	1.9e-64	8.6e-70	0.156887553376562	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.000105435183720808
CAMB-72898	MN908947.3	11083	G	T	0.84	0.84	0	0	0.842796141072276	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.000105435183720808
CAMB-72898	MN908947.3	11962	C	T	1	1	0	0	0.999511748550504	TCT	ORF1ab:nsp7	L40L	C120T	CTC>CTT	Synonymous	ORF1ab:nsp7	0.000183094293561184
CAMB-72898	MN908947.3	12088	A	G	0.37	0.37	6e-165	5.3e-192	0.368191385594743	TAC	ORF1ab:nsp7	L82L	A246G	TTA>TTG	Synonymous	ORF1ab:nsp7	0.63165460239232
CAMB-72898	MN908947.3	14805	C	T	1	1	0	0	0.999453916631272	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00012135185971725
CAMB-72898	MN908947.3	17013	A	C	0.012	0.0062	2.2e-06	6.7e-05	0.00701792269488232	CAG	ORF1ab:helicase	S259S	A777C	TCA>TCC	Synonymous	ORF1ab:helicase	0.992766141222198
CAMB-72898	MN908947.3	23926	T	C	0.011	0.009	5.5e-07	3.6e-06	0.00950280543573444	TTT	S	I788I	T2364C	ATT>ATC	Synonymous	GU280_gp02, spike glycoprotein	0.990497194564266
CAMB-72898	MN908947.3	2480	A	G	1	1	0	0	0.999853694220922	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-72898	MN908947.3	2558	C	T	1	1	0	0	0.999620333263025	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	8.43703859945159e-05
CAMB-72898	MN908947.3	26144	G	T	1	1	0	0	0.999843038769424	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-72898	MN908947.3	28887	C	T	1	1	0	0	0.999431414356788	ACT	N	T205I	C614T	ACT>ATT	Missense	GU280_gp10	0.000142146410803127
CAMB-72898	MN908947.3	29664	A	G	0.012	0.014	9.5e-07	5.4e-08	0.0138951649344781	AAT	ORF10	N36S	A107G	AAT>AGT	Missense	GU280_gp11	0.9856529597831
CAMB-728A7	MN908947.3	11074	C	INS	0.021	0.026	0.00066	3.5e-05	0.0245301998079649	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.975172602990261
CAMB-728A7	MN908947.3	11075	T	-	0.039	0.033	8.7e-11	8.3e-09	0.0351169561289027	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956831643409296
CAMB-728A7	MN908947.3	11288	TCTGGTTTT	-	0.0236666666666667	0.0186666666666667	8.6e-07;7.9e-07;2.4e-07;2.8e-07;9.3e-07;7.9e-09;1.3e-06;2.2e-07;5.3e-08	1.3e-05;1.3e-05;5.1e-06;5.8e-06;1.5e-05;2.9e-07;2e-05;4.9e-06;1.1e-06	0.0199056408714122	GTC	ORF1ab:nsp6	.	316-324-delinframe	.	no-SNV	ORF1ab:nsp6	0.979863236238619
CAMB-728A7	MN908947.3	13571	G	T	0.025	0.037	3.9e-06	2.5e-08	0.030407429598562	GGT	ORF1ab:RNA-dependent-RNA-polymerase	G35V	G104T	GGT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.969442780107849
CAMB-728A7	MN908947.3	14408	C	T	1	1	0	0	0.99773125477335	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000516644952603441
CAMB-728A7	MN908947.3	23403	A	G	1	1	0	0	0.99965953798043	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000113487339856754
CAMB-728A7	MN908947.3	23432	ATTC	-	0.00945	0.0107	1.3e-05;3.3e-06;2.2e-06;2.3e-06	6.7e-06;6.9e-07;5.6e-07;6.2e-07	0.0105311825747457	TAT	S	.	1870-1873-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.990430683467561
CAMB-728A7	MN908947.3	241	C	T	1	1	0	0	0.998303481126228	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-728A7	MN908947.3	25518	T	C	0.0034	0.0094	0.0029	6.3e-06	0.00816577644788725	CTT	ORF3a	P42P	T126C	CCT>CCC	Synonymous	GU280_gp03	0.991750328588607
CAMB-728A7	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.02409375	0.02925	0.00025;7e-04;0.00063;0.00062;0.00027;0.00033;0.00036;0.00062;0.00048;0.00053;0.00075;4e-04;0.00069;5e-04;0.00049;5e-04;0.00072;0.00047;0.00057;0.00048;0.00046;0.00063;0.00045;0.00043;0.00043;0.00065;0.00055;0.00035;0.00063;0.00032;0.00043;0.00036	7.7e-05;0.00021;9.2e-05;8.6e-05;6.1e-05;5.6e-05;4.4e-05;7.7e-05;6.8e-05;8e-05;0.00012;6e-05;1e-04;6.2e-05;7.7e-05;8.4e-05;0.00012;7e-05;8.8e-05;6.9e-05;6.1e-05;7.7e-05;7.4e-05;6.2e-05;6.4e-05;1e-04;8.4e-05;4.2e-05;9.8e-05;3.2e-05;6.6e-05;2.8e-05	0.0280320013162495	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.971281611658808
CAMB-728A7	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998642943305187	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000326797385620915
CAMB-728A7	MN908947.3	3037	C	T	1	1	0	0	0.997781907559499	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-728B6	MN908947.3	11074	C	INS	0.023	0.023	1.1e-05	0.00031	0.0226744272152367	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.976629493046608
CAMB-728B6	MN908947.3	11075	T	-	0.038	0.037	5.4e-09	6.2e-10	0.0378250902479513	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957557113119549
CAMB-728B6	MN908947.3	1288	C	T	0.022	0.021	2.3e-10	1e-10	0.0218585302303547	GCG	ORF1ab:nsp2	C161C	C483T	TGC>TGT	Synonymous	ORF1ab:nsp2	0.977978622609108
CAMB-728B6	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999399795051969	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000197628458498024
CAMB-728B6	MN908947.3	17013	A	C	0.013	0.0069	2.2e-07	3.4e-05	0.0121879300176922	CAG	ORF1ab:helicase	S259S	A777C	TCA>TCC	Synonymous	ORF1ab:helicase	0.98747939695453
CAMB-728B6	MN908947.3	20104	C	T	0.18	0.21	1.7e-52	1.4e-38	0.176854876341577	TCT	ORF1ab:endoRNAse	L162F	C484T	CTT>TTT	Missense	ORF1ab:endoRNAse	0.822678488100793
CAMB-728B6	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0327837837837838	0.0363243243243243	0.0013;0.00018;0.00076;0.00072;0.001;6.3e-05;0.00012;3e-05;3e-05;1.8e-05;2.1e-05;1.7e-05;2.7e-05;1.9e-05;2.4e-05;3.2e-05;1.8e-05;2.9e-05;2.3e-05;2.2e-05;1.5e-05;3.3e-05;2.2e-05;2.5e-05;2.1e-05;1.8e-05;2.7e-05;1.8e-05;3.5e-05;1.8e-05;2.7e-05;2.1e-05;1.5e-05;2.4e-05;1.1e-05;2e-05;1.4e-05	0.00026;3.3e-05;0.00014;0.00013;0.00019;5.7e-06;1.3e-05;2e-06;1.9e-06;1.2e-06;1e-06;8.7e-07;1.4e-06;1.1e-06;1.5e-06;2.2e-06;9.3e-07;1.9e-06;1e-06;1.4e-06;1e-06;2.2e-06;1.2e-06;1.5e-06;1.1e-06;8.4e-07;1.7e-06;1.2e-06;8.2e-07;1e-06;1.8e-06;1.4e-06;5.4e-07;1.6e-06;3.9e-07;1.1e-06;4.8e-07	0.0349438934564615	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.977986334720804
CAMB-728B6	MN908947.3	29771	A	G	1	1	0	0	0.998933712457793	AAT	NA	NA	NA	NA	NA	NA	0
CAMB-728B6	MN908947.3	593	C	T	1	1	0	0	0.99900525792241	TCA	ORF1ab:leader-protein	H110Y	C328T	CAT>TAT	Missense	ORF1ab:leader-protein	0.000307896357349249
CAMB-728C5	MN908947.3	11455	C	T	1	1	0	0	0.997213779128673	CCA	ORF1ab:nsp6	A161A	C483T	GCC>GCT	Synonymous	ORF1ab:nsp6	0
CAMB-728C5	MN908947.3	13264	C	T	0.0093	0.026	1.3e-05	1.6e-13	0.01254174284894	ACA	ORF1ab:nsp10	H80H	C240T	CAC>CAT	Synonymous	ORF1ab:nsp10	0.987428036083954
CAMB-728C5	MN908947.3	14408	C	T	1	1	0	0	0.996136817432069	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00233527215904158
CAMB-728C5	MN908947.3	16222	C	T	0.062	0.051	3.7e-27	2.1e-20	0.0591287938355087	GCA	ORF1ab:RNA-dependent-RNA-polymerase	H919Y	C2755T	CAT>TAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.940871206164491
CAMB-728C5	MN908947.3	16393	C	T	0.0086	0.039	1.2e-05	6.3e-16	0.0161912104857363	TCC	ORF1ab:helicase	P53S	C157T	CCA>TCA	Missense	ORF1ab:helicase	0.983808789514264
CAMB-728C5	MN908947.3	17012	C	T	0.0051	0.021	0.00062	2.5e-11	0.00667666696079296	TCA	ORF1ab:helicase	S259L	C776T	TCA>TTA	Missense	ORF1ab:helicase	0.993303724619352
CAMB-728C5	MN908947.3	203	C	T	0.057	0.033	2e-24	2.4e-15	0.0557930051932534	TCG	NA	NA	NA	NA	NA	NA	0.943260260122248
CAMB-728C5	MN908947.3	22388	C	T	0.03	0.097	9.2e-11	1.5e-13	0.0376610505450942	TCT	S	L276L	C826T	CTA>TTA	Synonymous	GU280_gp02, spike glycoprotein	0.962338949454906
CAMB-728C5	MN908947.3	22452	C	T	0.031	0.068	1.5e-05	8.1e-07	0.0349586016559338	TCA	S	S297L	C890T	TCA>TTA	Missense	GU280_gp02, spike glycoprotein	0.965041398344066
CAMB-728C5	MN908947.3	23403	A	G	1	1	0	0	0.997251482043996	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.36911469305766e-05
CAMB-728C5	MN908947.3	23435	C	T	0.011	0.011	2.4e-06	8.6e-07	0.0113034298200388	TCA	S	H625Y	C1873T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.988686749650144
CAMB-728C5	MN908947.3	23444	C	T	0.003	0.023	0.0041	2.1e-12	0.00565320331467325	TCA	S	Q628*	C1882T	CAA>TAA	Nonsense	GU280_gp02, spike glycoprotein	0.994321715925279
CAMB-728C5	MN908947.3	23638	C	T	0.0088	0.046	0.00012	2.1e-18	0.0116654495137795	TCA	S	I692I	C2076T	ATC>ATT	Synonymous	GU280_gp02, spike glycoprotein	0.988296114079256
CAMB-728C5	MN908947.3	241	C	T	1	1	0	0	0.998839434423615	TCG	NA	NA	NA	NA	NA	NA	9.74520712994791e-05
CAMB-728C5	MN908947.3	24707	C	T	0.021	0.078	7.9e-09	6.5e-18	0.0216754162774969	TCT	S	L1049F	C3145T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.978292376566073
CAMB-728C5	MN908947.3	26753	C	T	0.011	0.021	3e-06	4.2e-11	0.01266662245507	CCG	M	T77T	C231T	ACC>ACT	Synonymous	GU280_gp05	0.98729117556626
CAMB-728C5	MN908947.3	26958	C	T	0.0077	0.072	8.7e-05	4.7e-31	0.011189275285373	TCG	M	R146C	C436T	CGT>TGT	Missense	GU280_gp05	0.988731085744624
CAMB-728C5	MN908947.3	27297	C	T	0.0039	0.039	0.0025	6.1e-19	0.00749723080510698	TCA	ORF6	I32I	C96T	ATC>ATT	Synonymous	GU280_gp06	0.992485279542937
CAMB-728C5	MN908947.3	28253	C	T	0.11	0.29	5.4e-46	1e-140	0.129064389445435	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.867084551989291
CAMB-728C5	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999832631981637	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	8.18754946644469e-05
CAMB-728C5	MN908947.3	28925	G	T	0.018	0.006	4.9e-09	7.3e-05	0.0175524475524476	TGC	N	A218S	G652T	GCT>TCT	Missense	GU280_gp10	0.981864801864802
CAMB-728C5	MN908947.3	29520	C	T	0.011	0.009	1.9e-06	1.6e-05	0.010679509998953	TCA	N	S416L	C1247T	TCA>TTA	Missense	GU280_gp10	0.989268139461836
CAMB-728C5	MN908947.3	29686	C	T	0.0042	0.012	0.0016	1.9e-06	0.00676788000731663	TCA	NA	NA	NA	NA	NA	NA	0.993232119992683
CAMB-728C5	MN908947.3	29743	C	T	0.034	0.068	2.9e-15	1.8e-28	0.04581482449264	GCG	NA	NA	NA	NA	NA	NA	0.95209476526435
CAMB-728C5	MN908947.3	29754	C	T	0.012	0.0074	7.8e-07	7e-05	0.0104765993988836	TCG	NA	NA	NA	NA	NA	NA	0.98866466294547
CAMB-728C5	MN908947.3	3037	C	T	1	1	0	0	0.999713745920879	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.72508158241255e-05
CAMB-728C5	MN908947.3	3096	C	T	0.066	0.12	7.1e-24	3.9e-43	0.0776419841840403	TCA	ORF1ab:nsp3	S126L	C377T	TCA>TTA	Missense	ORF1ab:nsp3	0.92235801581596
CAMB-728C5	MN908947.3	4263	G	T	0.0041	0.083	0.0024	9.1e-38	0.0104965650636964	GGT	ORF1ab:nsp3	G515V	G1544T	GGT>GTT	Missense	ORF1ab:nsp3	0.989461748816114
CAMB-728C5	MN908947.3	635	C	T	0.12	0.16	4e-54	1.4e-71	0.125571619530041	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.874358027297031
CAMB-728C5	MN908947.3	683	C	T	0.055	0.032	7.6e-24	6.2e-16	0.0526180944755805	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.946456720932301
CAMB-728C5	MN908947.3	7735	C	T	0.012	0.029	0.00023	2.6e-09	0.0127642276422764	TCG	ORF1ab:nsp3	I1672I	C5016T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.987235772357724
CAMB-728C5	MN908947.3	9700	C	T	0.032	0.04	6.4e-15	1.5e-19	0.0332624644014856	TCA	ORF1ab:nsp4	I382I	C1146T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.966717849784112
CAMB-728E3	MN908947.3	10507	C	T	0.011	0.0051	2.1e-06	0.00029	0.00940623162845385	ACA	ORF1ab:3C-like-proteinase	N151N	C453T	AAC>AAT	Synonymous	ORF1ab:3C-like-proteinase	0.990542647547478
CAMB-728E3	MN908947.3	11074	C	INS	0.11	0.11	3e-57	8.5e-40	0.111237835948566	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.88075090598039
CAMB-728E3	MN908947.3	11083	G	-	0.11	0.15	1.8e-46	2.5e-66	0.121865236496082	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	8.35380014368536e-06
CAMB-728E3	MN908947.3	11083	G	T	0.88	0.85	0	0	0.874459091440696	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	8.35380014368536e-06
CAMB-728E3	MN908947.3	11557	G	T	0.052	0.063	3.2e-23	8.1e-27	0.0565198983911939	AGT	ORF1ab:nsp6	E195D	G585T	GAG>GAT	Missense	ORF1ab:nsp6	0.943480101608806
CAMB-728E3	MN908947.3	14411	C	T	0.12	0.12	1.5e-55	3.5e-53	0.120660296526068	ACA	ORF1ab:RNA-dependent-RNA-polymerase	T315I	C944T	ACA>ATA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.876259476578345
CAMB-728E3	MN908947.3	14641	C	A	0.015	0.029	4.9e-08	2.2e-14	0.01880451308314	ACT	ORF1ab:RNA-dependent-RNA-polymerase	L392I	C1174A	CTT>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.981163479235016
CAMB-728E3	MN908947.3	14805	C	T	0.99	1	0	0	0.994537324051019	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00138895946609753
CAMB-728E3	MN908947.3	18600	A	T	0.014	0.011	9.7e-08	4.3e-07	0.0135263086703639	CAC	ORF1ab:3'-to-5'-exonuclease	A187A	A561T	GCA>GCT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.986396398137234
CAMB-728E3	MN908947.3	21627	C	T	0.021	0.045	2.5e-10	6.5e-19	0.0285977859778598	ACT	S	T22I	C65T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.97140221402214
CAMB-728E3	MN908947.3	23559	TTGGTGCAGGTATATGCGCTAGT	-	0.0443478260869565	0.0363913043478261	0.00029;4e-04;0.00017;0.00031;0.00034;0.00034;0.00033;0.00034;0.00019;0.00018;1e-05;2.9e-06;4.9e-05;1.2e-05;1.6e-05;4.4e-06;1.4e-05;3.5e-05;1.5e-05;1.7e-05;1.2e-07;2.1e-07;0.00019	0.00061;0.0012;0.00055;0.00096;0.00099;0.001;0.00095;0.00098;0.00065;0.00061;9.8e-05;2.8e-05;0.00013;4.2e-05;0.00012;4.1e-05;9.1e-05;0.00021;0.00011;0.00021;5.7e-06;1.1e-05;0.00034	0.0401986370885892	ATT	S	.	1997-2019-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.954455183370846
CAMB-728E3	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-728E3	MN908947.3	2558	C	T	1	1	0	0	0.998131244160138	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000143750449220154
CAMB-728E3	MN908947.3	25983	A	G	0.0062	0.0086	8.4e-05	2e-05	0.0068308181096108	TAA	ORF3a	V197V	A591G	GTA>GTG	Synonymous	GU280_gp03	0.993169181890389
CAMB-728E3	MN908947.3	26144	G	T	1	1	0	0	0.99980959634425	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-728E3	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0419210526315789	0.0518157894736842	2e-05;7.8e-07;7e-06;7e-06;1.7e-05;3.3e-07;1.4e-06;8.3e-07;8.4e-07;4.4e-07;4.9e-07;3.2e-07;8.8e-07;2.5e-07;3.2e-07;5.1e-07;2.2e-07;4.5e-07;3.3e-07;3e-07;2.2e-07;5e-07;2.5e-07;3.8e-07;3.1e-07;1.9e-07;3.8e-07;2.5e-07;5.7e-07;2.3e-07;3.9e-07;3.5e-07;2.6e-07;4.2e-07;1.9e-07;4.9e-07;4.6e-07;0.0057	4.1e-07;1.8e-08;3.4e-08;3.2e-08;1.4e-07;2.9e-10;2.3e-09;6.1e-09;5.9e-09;2.2e-09;1.1e-09;7.3e-10;2.4e-09;1.5e-09;2.2e-09;4.4e-09;1.3e-09;3.4e-09;1.5e-09;2.2e-09;1.7e-09;4.1e-09;1.5e-09;2.5e-09;1.7e-09;7.4e-10;2.6e-09;1.8e-09;1.7e-09;1.3e-09;3.2e-09;2.8e-09;8.6e-10;3.2e-09;2.2e-10;7.5e-10;3.9e-10;0.00022	0.0470021505376344	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.966291749537069
CAMB-728E3	MN908947.3	28092	T	C	0.011	0.0064	1.2e-06	6.6e-05	0.00904877510483337	TTC	ORF8	S67P	T199C	TCT>CCT	Missense	GU280_gp09	0.990656955786066
CAMB-728E3	MN908947.3	28253	C	T	0.017	0.0064	4.9e-08	0.00067	0.0139986306693066	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.98477082215355
CAMB-728E3	MN908947.3	28898	AGA	-	0.996666666666667	0.996666666666667	0;0;0	0;0;0	0.996860028486339	TAG	N	.	625-627-delinframe	.	no-SNV	GU280_gp10	0.00605903509056151
CAMB-728E3	MN908947.3	29723	ACATTTTCACCGAGGCCACGCGGAGTACGATCGAGT	-	0.596388888888889	0.635833333333333	5.3e-271;1.9e-270;5e-275;1.3e-276;8.9e-275;4.8e-277;2.7e-267;2.3e-266;7.8e-282;1.8e-267;7.9e-267;1.5e-265;1.9e-270;1.3e-269;5.4e-266;3.4e-267;7.6e-267;4.1e-276;3.7e-267;3.2e-264;1.6e-268;1.1e-266;1.1e-264;1.4e-268;2e-245;4.4e-223;4.2e-226;2.5e-188;9.3e-190;3.6e-217;6.3e-224;4.9e-226;5.3e-223;5.4e-226;1.2e-204;9.89999999999999e-225	0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;1.20000146258859e-318;5.7e-288;6.79999999999999e-291;1.3e-238;6e-240;3.3e-275;5.7e-290;6.79999999999999e-291;3.9e-290;7.8e-289;1.2e-260;9.99999999999999e-290	0.62024873007532	CAC	NA	NA	NA	NA	NA	NA	0.374292786421499
CAMB-728E3	MN908947.3	522	T	-	0.04	0.052	4e-05	6.6e-07	0.043888834523926	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.955948070587468
CAMB-728E3	MN908947.3	522	TT	-	0.0325	0.0435	4e-05;0.0014	6.6e-07;3.9e-05	0.0356265748094281	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.955948070587468
CAMB-728F2	MN908947.3	11074	C	INS	0.15	0.022	3e-47	0.00032	0.0781281082156356	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.921623234533519
CAMB-728F2	MN908947.3	14408	C	T	1	1	0	0	0.999628712871287	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000371287128712871
CAMB-728F2	MN908947.3	23403	A	G	1	1	0	0	0.999932438138671	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.37809306646398e-05
CAMB-728F2	MN908947.3	241	C	T	1	1	0	0	0.999712695277429	TCG	NA	NA	NA	NA	NA	NA	0.000215478541928533
CAMB-728F2	MN908947.3	26778	TG	-	0.11	0.025	9.8e-18;9.6e-16	0.00029;0.001	0.0455487202371466	TTG	M	.	256-257-delfrshift	.	no-SNV	GU280_gp05	0.947867298578199
CAMB-728F2	MN908947.3	27813	C	T	1	1	0	0	0.998576174655909	CCT	NA	NA	NA	NA	NA	NA	0.000474608448030375
CAMB-728F2	MN908947.3	28436	G	T	0.013	0.041	9.3e-08	1.6e-19	0.0292896794305433	CGC	N	A55S	G163T	GCT>TCT	Missense	GU280_gp10	0.969960158034241
CAMB-728F2	MN908947.3	29000	G	C	0.0035	0.02	0.0011	1.1e-09	0.0106640814348037	AGG	N	G243R	G727C	GGC>CGC	Missense	GU280_gp10	0.989335918565196
CAMB-728F2	MN908947.3	3037	C	T	1	1	1.5e-298	0	0.999391171993912	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-728F2	MN908947.3	8313	T	INS	0.0012	0.0067	0.0069	1.8e-05	0.0042636347486232	ATG	ORF1ab:nsp3	.	5593-5594-insfrshift	.	no-SNV	ORF1ab:nsp3	0.995736365251377
CAMB-728F2	MN908947.3	8315	ACACC	-	0.0012	0.00676	0.011;0.011;0.012;0.024;0.0095	2.6e-05;2.7e-05;2.7e-05;5.7e-05;2.1e-05	0.00426970289983989	GAC	ORF1ab:nsp3	.	5596-5600-delfrshift	.	no-SNV	ORF1ab:nsp3	0.98830616583983
CAMB-7291D	MN908947.3	11075	T	-	0.035	0.04	2.6e-08	1.2e-10	0.0356044139775957	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960240762414312
CAMB-7291D	MN908947.3	14408	C	T	1	1	0	0	0.998134527673912	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000493076385750092
CAMB-7291D	MN908947.3	23403	A	G	1	1	0	0	0.997737466756639	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.93871313460088e-05
CAMB-7291D	MN908947.3	241	C	T	1	1	0	0	0.998843974694479	TCG	NA	NA	NA	NA	NA	NA	8.89250235016134e-05
CAMB-7291D	MN908947.3	28086	G	T	1	1	0	0	0.99510281230311	GGC	ORF8	A65S	G193T	GCT>TCT	Missense	GU280_gp09	0.000400939343605017
CAMB-7291D	MN908947.3	28337	G	T	0.25	0.25	6.9e-124	1.2e-122	0.254060194889355	AGA	N	D22Y	G64T	GAT>TAT	Missense	GU280_gp10	0.745739795510184
CAMB-7291D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999162321207933	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00019466614755694
CAMB-7291D	MN908947.3	3037	C	T	1	1	0	0	0.999263137483033	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000116346713205352
CAMB-7292C	MN908947.3	11075	T	-	0.037	0.032	2.6e-10	7.5e-09	0.0328982656892544	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962846415161809
CAMB-7292C	MN908947.3	15368	C	T	0.0091	0.01	3e-06	1.3e-06	0.00988172453262114	ACA	ORF1ab:RNA-dependent-RNA-polymerase	T634I	C1901T	ACA>ATA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.989965661961084
CAMB-7292C	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999373082126241	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000164978387831194
CAMB-7292C	MN908947.3	29742	G	A	0.047	0.053	1.6e-14	2.5e-23	0.0525715589006728	CGC	NA	NA	NA	NA	NA	NA	0.945831907857224
CAMB-7292C	MN908947.3	29771	A	G	1	1	0	0	0.998771635957566	AAT	NA	NA	NA	NA	NA	NA	0.000111669458403127
CAMB-7292C	MN908947.3	6148	T	G	0.17	0.15	2.5e-33	9.6e-63	0.148709545268333	CTG	ORF1ab:nsp3	P1143P	T3429G	CCT>CCG	Synonymous	ORF1ab:nsp3	0.850880786562884
CAMB-7293B	MN908947.3	11075	T	-	0.26	0.05	5.5e-71	3.3e-13	0.129454355127143	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.870414794783443
CAMB-7293B	MN908947.3	14408	C	T	1	1	0	0	0.999737684276796	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000157389433922669
CAMB-7293B	MN908947.3	23403	A	G	1	1	0	0	0.999963121404337	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.68785956630772e-05
CAMB-7293B	MN908947.3	241	C	T	1	1	0	0	0.999834947183099	TCG	NA	NA	NA	NA	NA	NA	0.000110035211267606
CAMB-7293B	MN908947.3	25350	C	T	1	1	0	0	0.999956188389923	CCA	S	P1263L	C3788T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	4.38116100766703e-05
CAMB-7293B	MN908947.3	28407	TACCCAATA	-	0.00269322222222222	0.0281111111111111	NA;4.4e-06;0.5;NA;NA;NA;NA;NA;NA	2.2e-09;7.6e-07;1.1e-08;1.7e-07;1.7e-07;6.1e-08;5.2e-08;5.6e-08;2.1e-07	0.0132547405189621	TTA	N	.	134-142-delinframe	.	no-SNV	GU280_gp10	0.986359869972592
CAMB-7293B	MN908947.3	3037	C	T	1	1	1.2e-220	0	0.999285459092533	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7294A	MN908947.3	11074	C	INS	0.03	0.022	4.1e-08	0.00045	0.028178854215184	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.971718677224033
CAMB-7294A	MN908947.3	11075	T	-	0.041	0.042	1.1e-09	6.7e-11	0.0411746848387045	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95427165385783
CAMB-7294A	MN908947.3	11083	G	T	0.043	0.041	6.6e-09	6.7e-09	0.0424815151634969	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.948108022616741
CAMB-7294A	MN908947.3	12621	C	T	0.0084	0.0051	1.4e-05	0.00013	0.00740425645047656	TCA	ORF1ab:nsp8	S177L	C530T	TCA>TTA	Missense	ORF1ab:nsp8	0.992542571151315
CAMB-7294A	MN908947.3	14307	T	C	0.011	0.019	2.5e-06	1.4e-10	0.0131055525926962	ATT	ORF1ab:RNA-dependent-RNA-polymerase	Y280Y	T840C	TAT>TAC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.986876961680029
CAMB-7294A	MN908947.3	14408	C	T	1	1	0	0	0.99686501052335	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000255378356244001
CAMB-7294A	MN908947.3	15575	G	T	0.0079	0.012	3e-05	1.8e-07	0.00898884751460223	GGT	ORF1ab:RNA-dependent-RNA-polymerase	G703V	G2108T	GGT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.990974008487404
CAMB-7294A	MN908947.3	16393	C	T	0.031	0.031	1.2e-14	8.6e-15	0.0308655456067555	TCC	ORF1ab:helicase	P53S	C157T	CCA>TCA	Missense	ORF1ab:helicase	0.968988862196986
CAMB-7294A	MN908947.3	1784	G	A	1	1	0	0	0.998960813459439	TGG	ORF1ab:nsp2	G327S	G979A	GGT>AGT	Missense	ORF1ab:nsp2	2.63085200142066e-05
CAMB-7294A	MN908947.3	18086	C	T	0.036	0.027	6.3e-17	2.8e-13	0.0328950242453366	ACT	ORF1ab:3'-to-5'-exonuclease	T16I	C47T	ACT>ATT	Missense	ORF1ab:3'-to-5'-exonuclease	0.967083133109082
CAMB-7294A	MN908947.3	23403	A	G	1	1	0	0	0.999912715211557	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.81898589623293e-05
CAMB-7294A	MN908947.3	23555	CCCATTGGTGCAGGTATATGCGCTAGT	-	0.0252851851851852	0.0457407407407407	0.0064;0.0056;0.0063;0.0063;0.00066;0.0011;0.00037;0.00066;7e-04;0.00071;0.00067;0.00068;0.00042;4e-04;0.0029;0.0013;0.016;0.014;0.015;0.014;0.018;0.022;0.018;0.018;0.007;0.016;0.17	2e-04;0.00016;2e-04;0.00024;7.7e-06;1.8e-05;8.2e-06;2.1e-05;2.2e-05;2.3e-05;2.1e-05;2.1e-05;9.9e-06;9.4e-06;1.8e-05;4.7e-06;7.7e-05;4e-05;6.8e-05;2.8e-05;6.4e-05;0.00015;7.4e-05;0.00013;3.2e-06;5.7e-06;0.00086	0.0289054588971739	ACC	S	.	1993-2019-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.971169271668882
CAMB-7294A	MN908947.3	241	C	T	1	1	0	0	0.998681998520611	TCG	NA	NA	NA	NA	NA	NA	6.72449734382355e-05
CAMB-7294A	MN908947.3	25228	T	C	0.1	0.14	6.2e-46	2.4e-63	0.11298773690078	CTG	S	A1222A	T3666C	GCT>GCC	Synonymous	GU280_gp02, spike glycoprotein	0.886900780379041
CAMB-7294A	MN908947.3	25421	TTG	-	0.011	0.0068	2.7e-05;3.6e-05;0.00082	0.0011;0.001;0.002	0.009454051903681	ATT	ORF3a	.	29-31-delinframe	.	no-SNV	GU280_gp03	0.989385094631031
CAMB-7294A	MN908947.3	25451	TCAAGGATGCTACTCCT	-	0.0108823529411765	0.0198823529411765	0.0026;0.00019;3.9e-06;2.6e-06;4.9e-07;3.3e-06;4.4e-06;3.6e-06;2.1e-06;2e-06;1.6e-06;1.9e-07;2.5e-06;2.8e-06;4e-06;4.2e-06;1.5e-06	8.5e-05;3.4e-07;3.7e-10;1.8e-10;2.2e-11;1.3e-10;2.5e-10;2.3e-10;1.4e-10;7.2e-11;7.3e-11;2.8e-12;1.5e-10;1.7e-10;2.1e-10;1.8e-10;7.8e-11	0.0129018784299621	ATC	ORF3a	.	59-75-delfrshift	.	no-SNV	GU280_gp03	0.987205379478117
CAMB-7294A	MN908947.3	26787	GGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0248	0.0297666666666667	8e-04;0.00078;0.00044;0.00066;0.00056;0.00077;0.00064;0.00073;0.00093;0.00058;0.00085;0.00065;0.00066;0.00058;0.00094;7e-04;0.00075;0.00065;0.00059;0.00083;6e-04;0.00051;0.00064;0.00081;0.00079;0.00066;0.00083;0.00039;0.00058;5e-04	0.00012;0.00012;7.8e-05;3.8e-05;3.3e-05;4.5e-05;4.1e-05;4.9e-05;7.4e-05;3.5e-05;6.1e-05;3.6e-05;4.7e-05;4.3e-05;7e-05;4.8e-05;5.1e-05;4.2e-05;3.1e-05;5.9e-05;4.3e-05;1.4e-05;4.4e-05;6.1e-05;5.9e-05;2.9e-05;0.00014;3.8e-05;8.6e-05;5.4e-05	0.025713348638898	AGG	M	.	265-294-delinframe	.	no-SNV	GU280_gp05	0.975273894109558
CAMB-7294A	MN908947.3	28046	T	C	0.059	0.067	6.9e-25	3.6e-28	0.0634153942038018	CTA	ORF8	A51A	T153C	GCT>GCC	Synonymous	GU280_gp09	0.936584605796198
CAMB-7294A	MN908947.3	2881	C	T	0.019	0.017	1.4e-10	1.1e-09	0.0184086815166293	CCT	ORF1ab:nsp3	A54A	C162T	GCC>GCT	Synonymous	ORF1ab:nsp3	0.981151970475814
CAMB-7294A	MN908947.3	28913	G	T	0.0073	0.0074	5.4e-05	2.2e-05	0.00730120410987135	TGG	N	G214C	G640T	GGC>TGC	Missense	GU280_gp10	0.992639915211823
CAMB-7294A	MN908947.3	29756	AGTGTAC	-	0.00634285714285714	0.0101	0.0099;0.011;0.0098;0.0096;0.0024;0.0025;0.0025	0.00042;6e-04;0.00039;0.00053;4e-05;3.7e-05;4.1e-05	0.00902552531377803	GAG	NA	NA	NA	NA	NA	NA	0.98973954222573
CAMB-7294A	MN908947.3	3037	C	T	1	1	0	0	0.999657973492946	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.55066267635742e-05
CAMB-7294A	MN908947.3	375	A	C	0.03	0.03	4.1e-14	1.2e-14	0.0300360730149837	GAG	ORF1ab:leader-protein	E37A	A110C	GAG>GCG	Missense	ORF1ab:leader-protein	0.969758122145172
CAMB-7294A	MN908947.3	5298	C	A	0.0062	0.0077	5.9e-05	1.7e-05	0.00688330398591324	ACT	ORF1ab:nsp3	T860N	C2579A	ACT>AAT	Missense	ORF1ab:nsp3	0.993116696014087
CAMB-7294A	MN908947.3	6336	C	T	0.013	0.022	2.3e-07	8.6e-12	0.0146132306615331	TCG	ORF1ab:nsp3	S1206L	C3617T	TCG>TTG	Missense	ORF1ab:nsp3	0.985360518025901
CAMB-7294A	MN908947.3	6525	C	T	0.0037	0.0089	0.0016	4.1e-06	0.00467692971506942	ACA	ORF1ab:nsp3	T1269I	C3806T	ACA>ATA	Missense	ORF1ab:nsp3	0.995292250319757
CAMB-7294A	MN908947.3	6627	C	T	0.0019	0.0084	0.0076	1.3e-05	0.00514908394204287	ACC	ORF1ab:nsp3	T1303I	C3908T	ACC>ATC	Missense	ORF1ab:nsp3	0.994850916057957
CAMB-7294A	MN908947.3	8318	C	T	0.014	0.0056	5e-08	7.3e-05	0.0123073045742849	ACC	ORF1ab:nsp3	P1867S	C5599T	CCC>TCC	Missense	ORF1ab:nsp3	0.987335657579703
CAMB-7294A	MN908947.3	8845	A	G	0.054	0.079	7.3e-25	3.8e-35	0.0586061754972207	GAG	ORF1ab:nsp4	R97R	A291G	AGA>AGG	Synonymous	ORF1ab:nsp4	0.941393824502779
CAMB-7294A	MN908947.3	9928	G	T	0.011	0.0041	2.7e-06	0.00049	0.00923766613082165	TGG	ORF1ab:nsp4	M458I	G1374T	ATG>ATT	Missense	ORF1ab:nsp4	0.990739692530622
CAMB-72959	MN908947.3	11074	C	INS	0.025	0.018	1.1e-06	0.0038	0.0237298582372105	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.976079363681723
CAMB-72959	MN908947.3	11075	T	-	0.03	0.036	3.3e-07	2.7e-09	0.0312651385737233	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.966580403355345
CAMB-72959	MN908947.3	1440	G	A	1	1	0	0	1	GGC	ORF1ab:nsp2	G212D	G635A	GGC>GAC	Missense	ORF1ab:nsp2	0
CAMB-72959	MN908947.3	17079	G	A	1	1	0	0	0.999649395755497	AGG	ORF1ab:helicase	Q281Q	G843A	CAG>CAA	Synonymous	ORF1ab:helicase	0.000306778713939806
CAMB-72959	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0169459459459459	0.0346216216216216	0.048;0.019;0.036;0.038;0.029;0.024;0.037;0.011;0.011;0.0068;0.0098;0.009;0.011;0.0098;0.011;0.0073;0.009;0.012;0.0099;0.0097;0.0099;0.013;0.01;0.011;0.0098;0.0094;0.012;0.0092;0.004;0.01;0.011;0.011;0.009;0.012;0.0074;0.0088;0.0086	0.00026;2.4e-05;5.9e-05;6.8e-05;0.00013;7.9e-06;2.2e-05;7.3e-06;6.6e-06;4.2e-06;4.2e-06;3.6e-06;5.3e-06;5.1e-06;6.4e-06;9.5e-06;4.2e-06;7.8e-06;4.1e-06;5.8e-06;5.9e-06;9.5e-06;2.7e-06;6.8e-06;4.9e-06;3.4e-06;7.1e-06;5.2e-06;3.6e-07;5.9e-06;7.8e-06;6.8e-06;2.8e-06;8.5e-06;1.3e-06;1.8e-06;1.1e-06	0.0221757708906569	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.984792857293861
CAMB-72959	MN908947.3	2891	G	A	1	1	0	0	0.999554962171785	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	0.000445037828215398
CAMB-72959	MN908947.3	29743	C	T	0.0085	0.023	0.00011	2.1e-10	0.0174893120870579	GCG	NA	NA	NA	NA	NA	NA	0.981927710843373
CAMB-72959	MN908947.3	527	C	T	0.0087	0.014	2.4e-05	4.8e-08	0.0100467678429488	GCT	ORF1ab:leader-protein	L88L	C262T	CTG>TTG	Synonymous	ORF1ab:leader-protein	0.989907018873505
CAMB-72959	MN908947.3	7863	A	G	0.027	0.012	2.4e-12	7.1e-07	0.0244570664884731	AAA	ORF1ab:nsp3	K1715R	A5144G	AAA>AGA	Missense	ORF1ab:nsp3	0.975542933511527
CAMB-72959	MN908947.3	823	C	T	0.015	0.031	8.5e-08	2.8e-15	0.0189202968333994	TCG	ORF1ab:nsp2	V6V	C18T	GTC>GTT	Synonymous	ORF1ab:nsp2	0.98105846031836
CAMB-72959	MN908947.3	9133	C	T	1	0.99	0	0	0.996072103176092	TCA	ORF1ab:nsp4	L193L	C579T	CTC>CTT	Synonymous	ORF1ab:nsp4	6.25461277692298e-05
CAMB-72959	MN908947.3	9239	T	A	0.02	0.026	5.6e-10	2.7e-13	0.0214577684915719	ATC	ORF1ab:nsp4	S229T	T685A	TCA>ACA	Missense	ORF1ab:nsp4	0.978492483977149
CAMB-72959	MN908947.3	9968	G	A	0.0075	0.014	0.00014	1.4e-07	0.00891326059509676	CGC	ORF1ab:nsp4	A472T	G1414A	GCA>ACA	Missense	ORF1ab:nsp4	0.990276442987167
CAMB-72968	MN908947.3	14408	C	T	1	1	0	0	0.999736252142951	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000263747857048661
CAMB-72968	MN908947.3	19839	T	C	1	1	0	0	1	ATA	ORF1ab:endoRNAse	N73N	T219C	AAT>AAC	Synonymous	ORF1ab:endoRNAse	0
CAMB-72968	MN908947.3	23403	A	G	1	1	0	0	0.999880265332024	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000119734667975766
CAMB-72968	MN908947.3	241	C	T	1	0.85	0	0	0.940584287406238	TCG	NA	NA	NA	NA	NA	NA	0.0594157125937623
CAMB-72968	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999280575539568	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-72968	MN908947.3	3037	C	T	1	1	5.5e-136	1.1e-263	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-72977	MN908947.3	11074	C	INS	0.12	0.11	2.7e-33	1.6e-34	0.111864846180436	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.884116833736606
CAMB-72977	MN908947.3	11083	G	-	0.18	0.16	3.6e-77	2.9e-72	0.165006790402897	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.77244605402143e-05
CAMB-72977	MN908947.3	11083	G	T	0.82	0.84	2.69999998058451e-316	0	0.834766862833861	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.77244605402143e-05
CAMB-72977	MN908947.3	11590	A	G	0.79	0.8	0	0	0.794563662374821	CAC	ORF1ab:nsp6	T206T	A618G	ACA>ACG	Synonymous	ORF1ab:nsp6	0.205340963280877
CAMB-72977	MN908947.3	11793	A	G	0.037	0.04	1.5e-08	1.1e-14	0.0392927308447937	AAA	ORF1ab:nsp6	K274R	A821G	AAA>AGA	Missense	ORF1ab:nsp6	0.960707269155206
CAMB-72977	MN908947.3	12459	C	T	0.009	0.0056	2.9e-05	0.00056	0.00604854343836431	ACA	ORF1ab:nsp8	T123I	C368T	ACA>ATA	Missense	ORF1ab:nsp8	0.993822214180474
CAMB-72977	MN908947.3	1354	T	C	0.027	0.027	7.2e-11	1.4e-12	0.0270090768208988	ATG	ORF1ab:nsp2	N183N	T549C	AAT>AAC	Synonymous	ORF1ab:nsp2	0.972990923179101
CAMB-72977	MN908947.3	14805	C	T	1	1	0	0	0.9988469218438	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000140619287341452
CAMB-72977	MN908947.3	21855	C	T	0.0053	0.0074	0.0012	4.1e-05	0.00714626012386851	TCT	S	S98F	C293T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.992734635540734
CAMB-72977	MN908947.3	2480	A	G	1	1	0	0	0.999792315680166	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000207684319833853
CAMB-72977	MN908947.3	2558	C	T	1	1	0	0	0.999684303573684	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000126278570526582
CAMB-72977	MN908947.3	26144	G	T	1	1	0	0	0.999641705481906	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000358294518093873
CAMB-72977	MN908947.3	29013	C	T	1	1	0	0	0.999780185272413	ACT	N	T247I	C740T	ACT>ATT	Missense	GU280_gp10	6.28042078819281e-05
CAMB-72977	MN908947.3	4185	G	A	1	1	0	0	0.999678580611983	GGT	ORF1ab:nsp3	G489D	G1466A	GGT>GAT	Missense	ORF1ab:nsp3	9.64258164052456e-05
CAMB-72986	MN908947.3	11074	C	INS	0.027	0.025	6.9e-06	6.6e-05	0.0254699988742542	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.974276708319261
CAMB-72986	MN908947.3	11075	T	-	0.041	0.043	1.6e-11	6.8e-11	0.0426324600910184	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954160673441958
CAMB-72986	MN908947.3	14408	C	T	1	1	0	0	0.997207877245435	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000321217662029601
CAMB-72986	MN908947.3	14583	C	T	0.016	0.011	4.1e-09	6.9e-07	0.0122256717696178	ACG	ORF1ab:RNA-dependent-RNA-polymerase	H372H	C1116T	CAC>CAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.987710095278878
CAMB-72986	MN908947.3	15360	C	T	0.0098	0.0047	1.4e-06	0.00021	0.00591623851782656	GCA	ORF1ab:RNA-dependent-RNA-polymerase	R631R	C1893T	CGC>CGT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.993512896362032
CAMB-72986	MN908947.3	1594	C	T	0.041	0.043	2.1e-12	3.5e-17	0.0427061310782241	CCG	ORF1ab:nsp2	S263S	C789T	TCC>TCT	Synonymous	ORF1ab:nsp2	0.957293868921776
CAMB-72986	MN908947.3	1643	A	G	0.0096	0.01	7.2e-06	1.9e-06	0.0100073112776458	CAA	ORF1ab:nsp2	N280D	A838G	AAC>GAC	Missense	ORF1ab:nsp2	0.989992688722354
CAMB-72986	MN908947.3	18555	C	T	0.0082	0.0085	1.7e-05	1e-05	0.00845278652696535	ACA	ORF1ab:3'-to-5'-exonuclease	D172D	C516T	GAC>GAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.991515073600309
CAMB-72986	MN908947.3	18744	C	T	0.018	0.016	3.8e-08	1.8e-08	0.0164884294860331	ACG	ORF1ab:3'-to-5'-exonuclease	Y235Y	C705T	TAC>TAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.982867770664187
CAMB-72986	MN908947.3	23403	A	G	1	1	0	0	0.999423061073106	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000115387785378719
CAMB-72986	MN908947.3	241	C	T	1	1	0	0	0.998303874308159	TCG	NA	NA	NA	NA	NA	NA	0.000119026364339701
CAMB-72986	MN908947.3	25324	C	T	0.012	0.024	2.2e-07	1.9e-12	0.0227146558105107	GCA	S	C1254C	C3762T	TGC>TGT	Synonymous	GU280_gp02, spike glycoprotein	0.977192820133235
CAMB-72986	MN908947.3	28514	G	T	1	1	0	0	0.99736170212766	AGA	N	D81Y	G241T	GAT>TAT	Missense	GU280_gp10	0
CAMB-72986	MN908947.3	28900	A	G	0.0038	0.0083	0.0015	1.4e-05	0.0071876151861408	GAA	N	R209R	A627G	AGA>AGG	Synonymous	GU280_gp10	0.992812384813859
CAMB-72986	MN908947.3	3037	C	T	1	1	9e-279	0	0.999392782789729	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.67453157529493e-05
CAMB-72986	MN908947.3	6196	C	T	0.014	0.014	0.00036	9.3e-08	0.0144150184378143	CCT	ORF1ab:nsp3	P1159P	C3477T	CCC>CCT	Synonymous	ORF1ab:nsp3	0.98524974857526
CAMB-72995	MN908947.3	11074	C	INS	0.1	0.11	1.9e-28	1.6e-32	0.104724935303448	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.890892395024626
CAMB-72995	MN908947.3	11083	G	-	0.14	0.14	5.7e-58	2.1e-63	0.143136803316444	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.83847689236911e-05
CAMB-72995	MN908947.3	11083	G	T	0.86	0.86	0	0	0.85659450330109	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.83847689236911e-05
CAMB-72995	MN908947.3	12715	A	C	0.0055	0.0013	1.8e-05	0.003	0.00176552187986044	GAC	ORF1ab:nsp9	R10R	A30C	CGA>CGC	Synonymous	ORF1ab:nsp9	0.998108369414435
CAMB-72995	MN908947.3	14805	C	T	1	1	0	0	0.999284397104561	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000302755071147442
CAMB-72995	MN908947.3	21626	A	G	1	1	0	0	0.998967653131452	AAC	S	T22A	A64G	ACT>GCT	Missense	GU280_gp02, spike glycoprotein	0.000344115622849277
CAMB-72995	MN908947.3	2480	A	G	1	1	0	0	0.99983716007165	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-72995	MN908947.3	2558	C	T	1	1	0	0	0.999659383971583	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	4.86594326310155e-05
CAMB-72995	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-72995	MN908947.3	28695	C	T	0.1	0.05	6.1e-16	8.7e-22	0.0518890483022477	ACA	N	T141I	C422T	ACA>ATA	Missense	GU280_gp10	0.948110951697752
CAMB-72995	MN908947.3	6026	C	T	0.032	0.0031	9.5e-09	0.0058	0.00494868035190616	TCC	ORF1ab:nsp3	P1103S	C3307T	CCA>TCA	Missense	ORF1ab:nsp3	0.994868035190616
CAMB-72995	MN908947.3	9923	G	A	1	1	0	0	0.999122293739029	AGC	ORF1ab:nsp4	A457T	G1369A	GCA>ACA	Missense	ORF1ab:nsp4	0.000292568753657109
CAMB-729A4	MN908947.3	11075	T	-	0.038	0.052	5.1e-09	5.1e-13	0.0411928412088271	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953161218128047
CAMB-729A4	MN908947.3	11518	C	T	0.014	0.024	1.1e-07	1.1e-11	0.0162414713734797	TCA	ORF1ab:nsp6	V182V	C546T	GTC>GTT	Synonymous	ORF1ab:nsp6	0.981237021655295
CAMB-729A4	MN908947.3	11824	C	T	0.012	0.044	3.1e-06	2.9e-11	0.0169270833333333	TCA	ORF1ab:nsp6	I284I	C852T	ATC>ATT	Synonymous	ORF1ab:nsp6	0.983072916666667
CAMB-729A4	MN908947.3	12073	C	T	0.015	0.0033	8.7e-08	0.0026	0.0115507567611064	ACA	ORF1ab:nsp7	D77D	C231T	GAC>GAT	Synonymous	ORF1ab:nsp7	0.988434612768012
CAMB-729A4	MN908947.3	12400	C	T	0.014	0.0082	2.5e-07	1.5e-05	0.0127591482671982	TCA	ORF1ab:nsp8	L103L	C309T	CTC>CTT	Synonymous	ORF1ab:nsp8	0.987226815266061
CAMB-729A4	MN908947.3	14253	A	-	0.0077	0.0064	3.4e-05	6.7e-05	0.00740357065045363	TAA	ORF1ab:RNA-dependent-RNA-polymerase	.	786-786-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.992485437451955
CAMB-729A4	MN908947.3	14408	C	T	1	1	0	0	0.999537818860546	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000408852546440316
CAMB-729A4	MN908947.3	1650	A	T	0.062	0.067	9.4e-28	7.3e-31	0.0627501129987102	AAT	ORF1ab:nsp2	N282I	A845T	AAT>ATT	Missense	ORF1ab:nsp2	0.937227838472478
CAMB-729A4	MN908947.3	21137	A	G	0.0057	0.01	0.0028	3.4e-05	0.00647952932345766	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.993520470676542
CAMB-729A4	MN908947.3	23403	A	G	1	1	0	0	0.999936489387377	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.44574288363586e-05
CAMB-729A4	MN908947.3	241	C	T	1	1	0	0	0.999846497183814	TCG	NA	NA	NA	NA	NA	NA	0.000141694907248875
CAMB-729A4	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99974764203022	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-729A4	MN908947.3	3037	C	T	1	1	0	0	0.999665253291676	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-729A4	MN908947.3	4113	C	T	0.0078	0.008	4.7e-05	1.6e-05	0.00782247765006386	GCT	ORF1ab:nsp3	A465V	C1394T	GCT>GTT	Missense	ORF1ab:nsp3	0.992139208173691
CAMB-729A4	MN908947.3	7039	C	T	0.015	0.0095	2.8e-07	0.00071	0.0146147032772365	GCA	ORF1ab:nsp3	G1440G	C4320T	GGC>GGT	Synonymous	ORF1ab:nsp3	0.985385296722764
CAMB-729A4	MN908947.3	875	C	T	0.0058	0.0064	0.00018	4.4e-05	0.00594108035098656	CCT	ORF1ab:nsp2	L24F	C70T	CTT>TTT	Missense	ORF1ab:nsp2	0.994030583812681
CAMB-729C2	MN908947.3	11074	C	INS	0.024	0.019	4.6e-06	0.0022	0.0227258250585662	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.977125547620901
CAMB-729C2	MN908947.3	11075	T	-	0.028	0.041	1.2e-06	1.7e-10	0.0303610138907391	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.966005837259152
CAMB-729C2	MN908947.3	14408	C	T	1	1	0	0	0.998189335405457	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000234580028442828
CAMB-729C2	MN908947.3	21008	C	T	1	1	0	0	0.999378025646076	ACT	ORF1ab:2'-O-ribose-methyltransferase	T117I	C350T	ACT>ATT	Missense	ORF1ab:2'-O-ribose-methyltransferase	2.0732478464138e-05
CAMB-729C2	MN908947.3	23403	A	G	1	1	0	0	0.999243868761917	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.4792118701646e-05
CAMB-729C2	MN908947.3	241	C	T	1	1	0	0	0.99936056270482	TCG	NA	NA	NA	NA	NA	NA	0.00014209717670672
CAMB-729C2	MN908947.3	25350	C	T	1	1	0	0	0.998706889217838	CCA	S	P1263L	C3788T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	7.65657699964269e-05
CAMB-729C2	MN908947.3	3037	C	T	1	1	0	0	0.999165930723187	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.90628986360514e-05
CAMB-729C2	MN908947.3	5956	C	T	0.036	0.028	3.2e-16	9.9e-13	0.0330744174392383	ACA	ORF1ab:nsp3	D1079D	C3237T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.966675018792283
CAMB-729D1	MN908947.3	11075	T	-	0.029	0.032	1.5e-08	1.3e-08	0.0317776285495011	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964217191097467
CAMB-729D1	MN908947.3	14408	C	T	1	1	0	0	0.99865664254908	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000353515118663241
CAMB-729D1	MN908947.3	1441	C	T	0.0046	0.01	0.0027	4.7e-06	0.00917711838482716	GCT	ORF1ab:nsp2	G212G	C636T	GGC>GGT	Synonymous	ORF1ab:nsp2	0.990516977669012
CAMB-729D1	MN908947.3	23403	A	G	1	1	0	0	0.998093104909498	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.54022640595678e-05
CAMB-729D1	MN908947.3	241	C	T	1	1	0	0	0.999360744604684	TCG	NA	NA	NA	NA	NA	NA	0.000102280863250486
CAMB-729D1	MN908947.3	27946	A	T	0.012	0.002	1.9e-06	0.0028	0.00325581395348837	CAA	ORF8	Q18L	A53T	CAA>CTA	Missense	GU280_gp09	0.996434108527132
CAMB-729D1	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.997613030047739	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-729D1	MN908947.3	3037	C	T	1	1	0	0	0.999490662139219	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000254668930390492
CAMB-729D1	MN908947.3	6539	C	T	0.017	0.0034	1.2e-05	0.0054	0.00434346809221517	CCA	ORF1ab:nsp3	H1274Y	C3820T	CAC>TAC	Missense	ORF1ab:nsp3	0.995656531907785
CAMB-729E0	MN908947.3	11075	T	-	0.034	0.06	1.3e-09	9.5e-16	0.0476442002957955	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952214944714416
CAMB-729E0	MN908947.3	14408	C	T	1	1	0	0	0.999505709060353	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000346003657752953
CAMB-729E0	MN908947.3	14773	G	A	1	1	0	0	1	GGA	ORF1ab:RNA-dependent-RNA-polymerase	D436N	G1306A	GAT>AAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-729E0	MN908947.3	17138	C	T	0.031	0.039	9.3e-16	7.5e-19	0.03547051989544	TCT	ORF1ab:helicase	S301F	C902T	TCT>TTT	Missense	ORF1ab:helicase	0.964493174557072
CAMB-729E0	MN908947.3	21736	C	T	0.055	0.083	3.2e-18	2e-31	0.0736245954692557	TCT	S	F58F	C174T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.925970873786408
CAMB-729E0	MN908947.3	23403	A	G	1	1	0	0	0.999864369998644	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000118676251186763
CAMB-729E0	MN908947.3	241	C	T	1	1	0	0	0.998745469751882	TCG	NA	NA	NA	NA	NA	NA	0.0012545302481182
CAMB-729E0	MN908947.3	25521	C	T	0.05	0.073	3.3e-22	4.8e-33	0.068586387434555	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.931378708551483
CAMB-729E0	MN908947.3	27267	T	A	0.032	0.022	1.9e-16	8.2e-12	0.025417439703154	TTA	ORF6	F22L	T66A	TTT>TTA	Missense	GU280_gp06	0.974512987012987
CAMB-729E0	MN908947.3	28253	C	T	0.13	0.21	1.7e-59	3.2e-96	0.171087131908027	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.828685962081484
CAMB-729E0	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999629903774982	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-729E0	MN908947.3	2925	C	T	0.015	0.018	3.1e-06	1.6e-09	0.0174956260934766	TCT	ORF1ab:nsp3	S69F	C206T	TCT>TTT	Missense	ORF1ab:nsp3	0.982504373906523
CAMB-729E0	MN908947.3	3037	C	T	1	1	5.8e-259	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-729E0	MN908947.3	522	TTGA	-	0.04925	0.0175	1.5e-09;5.7e-10;3.3e-06;5.9e-14	7.2e-05;6e-05;NA;NA	0.0320694838817438	GTT	ORF1ab:leader-protein	.	257-260-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.94592150479291
CAMB-729E0	MN908947.3	635	C	T	0.081	0.027	6.2e-36	3.7e-13	0.053471548959654	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.946528451040346
CAMB-729E0	MN908947.3	683	C	T	0.019	0.011	4.1e-10	1.1e-06	0.0154550658271322	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.984490418949492
CAMB-729E0	MN908947.3	9430	C	T	0.079	0.036	5.2e-21	8.6e-10	0.0590717299578059	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.940928270042194
CAMB-729FF	MN908947.3	10492	T	C	0.0042	0.0076	0.0011	2.2e-05	0.00707802481472229	GTA	ORF1ab:3C-like-proteinase	G146G	T438C	GGT>GGC	Synonymous	ORF1ab:3C-like-proteinase	0.992838704305104
CAMB-729FF	MN908947.3	11074	C	INS	0.028	0.038	3.2e-06	2.9e-08	0.036284412755001	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.962606456724104
CAMB-729FF	MN908947.3	11075	T	-	0.025	0.026	1.6e-07	1.8e-07	0.0258673158855752	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.968147697301684
CAMB-729FF	MN908947.3	11875	A	G	0.99	0.99	1.2e-162	0	0.988269794721408	TAG	ORF1ab:nsp7	V11V	A33G	GTA>GTG	Synonymous	ORF1ab:nsp7	0.0117302052785924
CAMB-729FF	MN908947.3	14408	C	T	1	1	0	0	0.999037420286367	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000360967392612201
CAMB-729FF	MN908947.3	14773	G	A	1	1	0	0	0.999529411764706	GGA	ORF1ab:RNA-dependent-RNA-polymerase	D436N	G1306A	GAT>AAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000171122994652406
CAMB-729FF	MN908947.3	18508	C	T	0.0087	0.0043	1.4e-05	0.0012	0.00516973978976392	ACT	ORF1ab:3'-to-5'-exonuclease	L157F	C469T	CTT>TTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.994514331667528
CAMB-729FF	MN908947.3	19029	C	T	0.0057	0.0087	4e-04	1.6e-05	0.00818538485421547	ACG	ORF1ab:3'-to-5'-exonuclease	H330H	C990T	CAC>CAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.99178638968077
CAMB-729FF	MN908947.3	20946	C	T	0.012	0.0075	2.8e-06	4.8e-05	0.00798522461839318	TCG	ORF1ab:2'-O-ribose-methyltransferase	V96V	C288T	GTC>GTT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.992014775381607
CAMB-729FF	MN908947.3	23403	A	G	1	1	0	0	0.999531517560014	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.46182675842461e-05
CAMB-729FF	MN908947.3	241	C	T	1	1	0	0	0.99934358974359	TCG	NA	NA	NA	NA	NA	NA	0.000369230769230769
CAMB-729FF	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99947309490878	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-729FF	MN908947.3	29128	T	C	0.0058	0.0016	4e-05	0.0049	0.0022113967053394	ATT	N	N285N	T855C	AAT>AAC	Synonymous	GU280_gp10	0.996955323376707
CAMB-729FF	MN908947.3	3037	C	T	1	1	0	0	0.999001633690325	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-729FF	MN908947.3	6659	A	G	0.019	0.019	3.9e-06	1.4e-09	0.0190809968847352	TAG	ORF1ab:nsp3	S1314G	A3940G	AGT>GGT	Missense	ORF1ab:nsp3	0.980919003115265
CAMB-72A0B	MN908947.3	11075	T	-	0.034	0.041	1.2e-09	1.1e-10	0.040123944730768	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955133272204129
CAMB-72A0B	MN908947.3	11195	C	T	0.018	0.023	1.9e-09	5.2e-12	0.0227460848260107	TCT	ORF1ab:nsp6	L75F	C223T	CTT>TTT	Missense	ORF1ab:nsp6	0.976955931529981
CAMB-72A0B	MN908947.3	14408	C	T	1	1	0	0	0.995630289285912	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000497815144642956
CAMB-72A0B	MN908947.3	14741	C	T	1	1	0	0	0.999387226019326	TCT	ORF1ab:RNA-dependent-RNA-polymerase	S425F	C1274T	TCT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	7.07046900777752e-05
CAMB-72A0B	MN908947.3	187	A	G	1	1	0	0	0.999439077594266	CAG	NA	NA	NA	NA	NA	NA	9.34870676223122e-05
CAMB-72A0B	MN908947.3	22132	G	A	0.014	0.013	4.2e-08	8.4e-08	0.0134165975508611	GGG	S	R190R	G570A	AGG>AGA	Synonymous	GU280_gp02, spike glycoprotein	0.986485827194224
CAMB-72A0B	MN908947.3	23403	A	G	1	1	0	0	0.999344751642671	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.28053730365301e-05
CAMB-72A0B	MN908947.3	23559	TTGGTGCAGGTATATGCGCTAGT	-	0.0382173913043478	0.0416086956521739	3e-04;0.00061;0.00018;0.00032;0.00034;0.00036;0.00035;0.00032;0.00021;0.00021;9.3e-05;7.3e-05;0.00027;0.00012;0.00019;1e-04;0.00018;0.00035;0.00022;0.00031;2.2e-05;2.8e-05;0.00095	2e-04;0.00034;1e-04;0.00017;0.00018;0.00019;0.00017;0.00017;9.3e-05;9.2e-05;1.1e-05;4.9e-06;7.1e-05;2.7e-05;7.4e-05;3.1e-05;7.1e-05;0.00016;8.5e-05;0.00012;2.3e-06;5.5e-06;0.00072	0.0386414972571797	ATT	S	.	1997-2019-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.951101002791275
CAMB-72A0B	MN908947.3	241	C	T	1	1	0	0	0.998678671296439	TCG	NA	NA	NA	NA	NA	NA	0.00027655717051286
CAMB-72A0B	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0443421052631579	0.0449210526315789	5.5e-05;2.7e-06;1.9e-05;1.7e-05;5.8e-05;4.9e-07;1.9e-06;1.3e-07;1.4e-07;3.5e-08;3.4e-08;2.1e-08;7.4e-08;3.6e-08;5.1e-08;1e-07;2.9e-08;8.2e-08;5.1e-08;4.9e-08;2.4e-08;9.5e-08;4.2e-08;6.5e-08;4.6e-08;3.2e-08;7.8e-08;4.2e-08;1.1e-08;4.6e-08;6.7e-08;6.4e-08;2.7e-08;5.8e-08;9.4e-09;2.9e-08;2.2e-08;0.00028	4.5e-05;2.9e-06;1.3e-05;1.2e-05;3.1e-05;1.8e-07;7.6e-07;3.3e-08;3.2e-08;2.1e-08;1.2e-08;8.6e-09;2.4e-08;1.5e-08;2.2e-08;4.1e-08;1.4e-08;3.3e-08;1.4e-08;2.1e-08;1.4e-08;3.9e-08;1.5e-08;2.3e-08;1.7e-08;9.3e-09;2.8e-08;1.8e-08;2.4e-09;1.7e-08;3.1e-08;2.7e-08;1.2e-08;2.9e-08;2.8e-09;1.8e-08;1e-08;0.00021	0.0474453834554827	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.971586728795151
CAMB-72A0B	MN908947.3	3037	C	T	1	1	0	0	0.999330855018587	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000148698884758364
CAMB-72A0B	MN908947.3	3611	C	T	0.022	0.027	3.3e-08	9e-13	0.0263311027058481	TCA	ORF1ab:nsp3	H298Y	C892T	CAT>TAT	Missense	ORF1ab:nsp3	0.973523421588595
CAMB-72A0B	MN908947.3	522	TT	-	0.044	0.0435	9e-07;2.3e-05	1e-06;4.5e-05	0.0433108495589721	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.947938465018947
CAMB-72A1A	MN908947.3	11074	C	INS	0.16	0.096	9.8e-52	9.8e-29	0.122271575333134	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.8757119110554
CAMB-72A1A	MN908947.3	11083	G	-	0.13	0.17	1.2e-58	1.2e-75	0.153793790873508	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.43113801570515e-05
CAMB-72A1A	MN908947.3	11083	G	T	0.87	0.83	0	0	0.846084652225707	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.43113801570515e-05
CAMB-72A1A	MN908947.3	14805	C	T	1	0.99	0	0	0.995070806650371	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00486858851336337
CAMB-72A1A	MN908947.3	1778	TC	CG	0.00295	0.00625	7.5e-05;NA	3.6e-05;4e-05	0.00536058895003931	ATC	ORF1ab:nsp2	.	973-974-mnv	.	no-SNV	ORF1ab:nsp2	0.993615827136242
CAMB-72A1A	MN908947.3	18740	ATTA	-	0.016	0.0305	0.0015;0.00048;0.0015;0.0021	5.6e-06;2.4e-06;2.1e-05;3.2e-05	0.02647412755716	GAT	ORF1ab:3'-to-5'-exonuclease	.	701-704-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.970061355740088
CAMB-72A1A	MN908947.3	22286	CTTGCTTTACATA	-	0.0184615384615385	0.00615384615384615	8.7e-06;3.3e-07;6.2e-08;3.9e-10;1.7e-07;0.00014;3.5e-05;3e-04;7e-08;1.1e-06;3e-07;1.1e-06;1.6e-07	NA;0.00034;4.7e-08;4.8e-07;0.00015;0.0054;NA;NA;NA;NA;NA;NA;NA	0.010938323668951	ACT	S	.	724-736-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.990387256248283
CAMB-72A1A	MN908947.3	24027	TT	-	0.0295	0.0325	1e-04;0.00027	4.7e-05;0.00014	0.0307199145184987	CTT	S	.	2465-2466-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.96881328473066
CAMB-72A1A	MN908947.3	25065	A	G	0.014	0.0087	5.5e-08	1e-05	0.0103617298504684	GAC	S	D1168G	A3503G	GAC>GGC	Missense	GU280_gp02, spike glycoprotein	0.989638270149532
CAMB-72A1A	MN908947.3	26144	G	T	1	1	1.5e-66	7.9e-259	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-72A1A	MN908947.3	26795	G	-	0.025	0.039	0.00029	1.1e-06	0.0353194245269926	TGT	M	.	273-273-delfrshift	.	no-SNV	GU280_gp05	0.964541795808854
CAMB-72A1A	MN908947.3	28842	G	T	1	1	0	0	0.999597585513078	AGT	N	S190I	G569T	AGT>ATT	Missense	GU280_gp10	0.000402414486921529
CAMB-72A1A	MN908947.3	29474	G	T	1	1	8.19999999999999e-277	6e-300	1	GGA	N	D401Y	G1201T	GAT>TAT	Missense	GU280_gp10	0
CAMB-72A1A	MN908947.3	29554	G	T	0.007	0.0096	0.00061	1.2e-05	0.00893388921977368	GGC	NA	NA	NA	NA	NA	NA	0.991066110780226
CAMB-72A1A	MN908947.3	4827	C	T	0.018	0.019	1.3e-09	4.8e-10	0.0183096484667165	ACA	ORF1ab:nsp3	T703I	C2108T	ACA>ATA	Missense	ORF1ab:nsp3	0.981660433807031
CAMB-72A1A	MN908947.3	508	T	-	0.086	0.074	2e-09	3.5e-08	0.0789871715870259	ATG	ORF1ab:leader-protein	.	243-243-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.919892443000392
CAMB-72A1A	MN908947.3	513	AT	-	0.2	0.14	0.00044;1.9e-08	0.0024;6.1e-06	0.163563053742904	CAT	ORF1ab:leader-protein	.	248-249-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.85661884199285
CAMB-72A1A	MN908947.3	514	T	-	0.23	0.16	1.9e-08	6.1e-06	0.190779702970297	ATG	ORF1ab:leader-protein	.	249-249-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.807178217821782
CAMB-72A1A	MN908947.3	516	TTA	-	0.203333333333333	0.12	2.2e-05;7.7e-05;0.00012	8e-04;0.0016;0.002	0.158647844041102	GTT	ORF1ab:leader-protein	.	251-253-delinframe	.	no-SNV	ORF1ab:leader-protein	0.830327868852459
CAMB-72A1A	MN908947.3	521	GT	-	0.155	0.103	0.00021;6.2e-23	0.0019;1.3e-14	0.126067558954748	GGT	ORF1ab:leader-protein	.	256-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.877363759674459
CAMB-72A1A	MN908947.3	522	T	-	0.16	0.11	6.2e-23	1.3e-14	0.134072626460028	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.865245648320684
CAMB-72A1A	MN908947.3	6565	A	G	0.99	1	1.1e-280	0	0.999138673557278	TAG	ORF1ab:nsp3	V1282V	A3846G	GTA>GTG	Synonymous	ORF1ab:nsp3	0.000861326442721792
CAMB-72A29	MN908947.3	11074	C	INS	0.032	0.045	7.1e-08	3.4e-10	0.0348136319825069	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.964927423647375
CAMB-72A29	MN908947.3	11075	T	-	0.053	0.048	1.3e-12	1.1e-12	0.0517841764331449	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.948066050099225
CAMB-72A29	MN908947.3	14408	C	T	1	1	0	0	0.999623257566244	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000251161622504081
CAMB-72A29	MN908947.3	1547	A	T	0.064	0.015	4.7e-24	3.5e-06	0.0525210084033613	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.878676470588235
CAMB-72A29	MN908947.3	15580	A	-	0.01	0.01	9.7e-06	9.4e-06	0.0102239820341587	CAA	ORF1ab:RNA-dependent-RNA-polymerase	.	2113-2113-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.9895987234797
CAMB-72A29	MN908947.3	15580	AA	-	0.01	0.005	9.7e-06;1.5e-06	9.4e-06;NA	0.00810624692572553	CAA	ORF1ab:RNA-dependent-RNA-polymerase	.	2113-2114-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.9895987234797
CAMB-72A29	MN908947.3	23403	A	G	1	1	0	0	0.999915886278248	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.47677526682742e-05
CAMB-72A29	MN908947.3	23562	GT	-	0.0565	0.033	6.8e-06;7.3e-06	0.00081;0.00083	0.0459157787924911	GGT	S	.	2000-2001-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.953850076491586
CAMB-72A29	MN908947.3	241	C	T	1	1	0	0	0.999773202630849	TCG	NA	NA	NA	NA	NA	NA	0.000100798830733563
CAMB-72A29	MN908947.3	25624	C	T	0.15	0.036	3.2e-72	4.9e-18	0.114461392928935	TCA	ORF3a	H78Y	C232T	CAC>TAC	Missense	GU280_gp03	0.8855048227166
CAMB-72A29	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999786757650069	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-72A29	MN908947.3	29051	C	INS	0.026	0.031	7.9e-06	1.3e-07	0.0287568392925309	GCA	N	.	777-778-insfrshift	.	no-SNV	GU280_gp10	0.970861432752259
CAMB-72A29	MN908947.3	29242	A	T	0.019	0.012	1.4e-09	6.3e-07	0.0152766308835673	AAG	N	E323D	A969T	GAA>GAT	Missense	GU280_gp10	0.980319295348197
CAMB-72A29	MN908947.3	29679	C	T	0.0085	0.011	0.00028	3.2e-06	0.010697911360163	TCT	NA	NA	NA	NA	NA	NA	0.989302088639837
CAMB-72A29	MN908947.3	3037	C	T	1	1	0	0	0.999551267668836	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-72A47	MN908947.3	10115	A	G	0.0027	0.0066	0.0019	2.2e-05	0.00385811727568925	AAC	ORF1ab:3C-like-proteinase	T21A	A61G	ACT>GCT	Missense	ORF1ab:3C-like-proteinase	0.996114192887404
CAMB-72A47	MN908947.3	1059	C	T	1	1	0	0	0.999952210845749	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	3.5841865688582e-05
CAMB-72A47	MN908947.3	11074	C	INS	0.025	0.028	4.7e-06	1.3e-05	0.0256440019643734	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.974213134514934
CAMB-72A47	MN908947.3	11075	T	-	0.035	0.035	2e-08	3.6e-09	0.0351227100162484	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.963722190991768
CAMB-72A47	MN908947.3	13006	T	C	1	1	0	0	0.998761719441005	CTG	ORF1ab:nsp9	A107A	T321C	GCT>GCC	Synonymous	ORF1ab:nsp9	0.000363622068911296
CAMB-72A47	MN908947.3	1437	C	T	1	1	0	0	1	TCT	ORF1ab:nsp2	S211F	C632T	TCT>TTT	Missense	ORF1ab:nsp2	0
CAMB-72A47	MN908947.3	14408	C	T	1	1	0	0	0.998830096269197	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000287518713502474
CAMB-72A47	MN908947.3	15960	C	T	1	1	0	0	0.999899152884227	CCG	ORF1ab:RNA-dependent-RNA-polymerase	A831A	C2493T	GCC>GCT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	6.05082694634933e-05
CAMB-72A47	MN908947.3	21018	A	C	0.0043	0.012	0.0051	1.2e-06	0.00587181398511776	CAG	ORF1ab:2'-O-ribose-methyltransferase	T120T	A360C	ACA>ACC	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.994102030941452
CAMB-72A47	MN908947.3	21631	A	G	0.011	0.0079	1.2e-06	3.8e-05	0.0107167710508003	AAT	S	Q23Q	A69G	CAA>CAG	Synonymous	GU280_gp02, spike glycoprotein	0.989144050104384
CAMB-72A47	MN908947.3	23403	A	G	1	1	0	0	0.99985270487413	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000113818960899839
CAMB-72A47	MN908947.3	24033	A	G	0.01	0.013	2.1e-06	3.2e-08	0.011014948859166	AAC	S	N824S	A2471G	AAC>AGC	Missense	GU280_gp02, spike glycoprotein	0.987858522280238
CAMB-72A47	MN908947.3	241	C	T	0.99	0.99	0	0	0.992811973479793	TCG	NA	NA	NA	NA	NA	NA	0.00141134767291744
CAMB-72A47	MN908947.3	24624	C	T	1	1	0	0	0.999870792686866	TCT	S	S1021F	C3062T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-72A47	MN908947.3	25563	G	T	1	1	0	0	0.999874772313297	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	2.27686703096539e-05
CAMB-72A47	MN908947.3	25688	C	T	1	1	0	0	0.998010346199761	GCT	ORF3a	A99V	C296T	GCT>GTT	Missense	GU280_gp03	0.000113694502870786
CAMB-72A47	MN908947.3	26029	C	A	0.029	0.043	2.1e-13	2.5e-16	0.0331331999110518	CCA	ORF3a	Q213K	C637A	CAG>AAG	Missense	GU280_gp03	0.966866800088948
CAMB-72A47	MN908947.3	26151	C	T	0.0086	0.004	3.3e-05	0.0048	0.00730735163861825	CCG	ORF3a	S253S	C759T	TCC>TCT	Synonymous	GU280_gp03	0.992692648361382
CAMB-72A47	MN908947.3	28435	C	T	0.0034	0.013	0.004	2.8e-07	0.00598202445852365	CCG	N	T54T	C162T	ACC>ACT	Synonymous	GU280_gp10	0.993970826580227
CAMB-72A47	MN908947.3	29597	T	C	0.0042	0.0096	0.00029	2.4e-06	0.00661843927966754	ATA	ORF10	Y14H	T40C	TAT>CAT	Missense	GU280_gp11	0.993381560720332
CAMB-72A47	MN908947.3	3037	C	T	1	1	0	0	0.999687597625742	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-72A47	MN908947.3	3093	C	T	0.0061	0.011	6.7e-05	4.3e-07	0.00943000838222967	CCA	ORF1ab:nsp3	P125L	C374T	CCA>CTA	Missense	ORF1ab:nsp3	0.99056999161777
CAMB-72A56	MN908947.3	11075	T	-	0.032	0.046	1e-07	8.6e-12	0.0350248424889808	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964782376291415
CAMB-72A56	MN908947.3	11075	TT	-	0.0160465	0.02645	1e-07;0.46	8.6e-12;0.00096	0.0184387795535596	CTT	ORF1ab:nsp6	.	103-104-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964782376291415
CAMB-72A56	MN908947.3	14408	C	T	1	1	0	0	0.998145939371036	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000318851190968245
CAMB-72A56	MN908947.3	18651	G	T	0.015	0.024	8.6e-08	2e-12	0.0170242031975731	AGC	ORF1ab:3'-to-5'-exonuclease	E204D	G612T	GAG>GAT	Missense	ORF1ab:3'-to-5'-exonuclease	0.982938111792582
CAMB-72A56	MN908947.3	1912	C	T	0.0092	0.014	1.2e-05	9.2e-08	0.0102333514225909	CCC	ORF1ab:nsp2	S369S	C1107T	TCC>TCT	Synonymous	ORF1ab:nsp2	0.989740806780887
CAMB-72A56	MN908947.3	23403	A	G	1	1	0	0	0.999947184958276	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.01800238422188e-05
CAMB-72A56	MN908947.3	241	C	T	1	1	0	0	0.996231064724215	TCG	NA	NA	NA	NA	NA	NA	0.00371095165615714
CAMB-72A56	MN908947.3	24817	A	-	0.005	0.014	0.001	8.3e-08	0.00724318126695037	GAA	S	.	3255-3255-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.992613498555774
CAMB-72A56	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999297670607515	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	6.76452682134885e-05
CAMB-72A56	MN908947.3	29627	C	T	0.0044	0.011	0.0013	1.6e-06	0.00823858955346845	TCG	ORF10	R24C	C70T	CGT>TGT	Missense	GU280_gp11	0.991761410446532
CAMB-72A56	MN908947.3	3037	C	T	1	1	0	0	0.999320915793558	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-72A56	MN908947.3	443	G	-	0.0052	0.012	0.0061	4.1e-05	0.00691152022658703	CGT	ORF1ab:leader-protein	.	178-178-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.993088479773413
CAMB-72A56	MN908947.3	6850	G	T	0.084	0.096	4.4e-25	3.8e-17	0.086322869955157	CGA	ORF1ab:nsp3	P1377P	G4131T	CCG>CCT	Synonymous	ORF1ab:nsp3	0.913677130044843
CAMB-72A56	MN908947.3	7424	TTTGCATCAT	-	0.0114	0.0015	7.6e-07;5.9e-07;6e-07;4.4e-07;4.2e-07;6.1e-07;6e-07;5.4e-07;7.2e-06;8.3e-05	NA;NA;NA;NA;NA;NA;NA;NA;NA;5.2e-05	0.0094382906206987	CTT	ORF1ab:nsp3	.	4705-4714-delfrshift	.	no-SNV	ORF1ab:nsp3	0.990610328638498
CAMB-72A56	MN908947.3	9431	G	A	0.087	0.081	4.3e-39	1.6e-31	0.0867390033136248	CGT	ORF1ab:nsp4	V293I	G877A	GTA>ATA	Missense	ORF1ab:nsp4	0.913260996686375
CAMB-72A65	MN908947.3	11074	C	INS	0.027	0.02	5.9e-06	0.0014	0.0208201892744479	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.978474670625348
CAMB-72A65	MN908947.3	11075	T	-	0.03	0.033	9.4e-09	7e-09	0.0324860081918519	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.963292999405934
CAMB-72A65	MN908947.3	11195	C	T	0.0072	0.0081	6.4e-05	1.7e-05	0.00801935248699341	TCT	ORF1ab:nsp6	L75F	C223T	CTT>TTT	Missense	ORF1ab:nsp6	0.991881234052424
CAMB-72A65	MN908947.3	14408	C	T	1	1	0	0	0.998175182481752	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000492411076352682
CAMB-72A65	MN908947.3	20268	A	G	1	1	2.7e-84	1.1e-270	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-72A65	MN908947.3	23403	A	G	1	1	0	0	0.99873051136589	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.95072797238862e-05
CAMB-72A65	MN908947.3	241	C	T	1	1	0	0	0.998466513317999	TCG	NA	NA	NA	NA	NA	NA	6.66733340000667e-05
CAMB-72A65	MN908947.3	26787	GGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0301333333333333	0.0260333333333333	8.3e-05;8.3e-05;3.3e-05;6.8e-05;5.4e-05;7.8e-05;5.9e-05;4.6e-05;7e-05;4.6e-05;9.1e-05;7e-05;6.4e-05;6.5e-05;8.3e-05;6e-05;6.9e-05;6.2e-05;5e-05;6.9e-05;4.2e-05;5e-05;5.1e-05;8.4e-05;7e-05;4.4e-05;8.2e-05;5.5e-05;0.00011;0.00011	0.00033;0.00031;0.00021;0.00026;0.00023;0.00029;0.00025;0.00027;0.00036;0.00022;0.00036;0.00023;0.00028;0.00028;4e-04;0.00028;0.00031;0.00025;0.00019;0.00034;0.00025;0.00015;0.00023;0.00034;3e-04;0.00014;3e-04;0.00011;0.00022;0.00016	0.0258669415167736	AGG	M	.	265-294-delinframe	.	no-SNV	GU280_gp05	0.974628571428571
CAMB-72A65	MN908947.3	28296	A	T	0.0092	0.013	1.2e-06	7.8e-08	0.0121257282211083	AAT	N	N8I	A23T	AAT>ATT	Missense	GU280_gp10	0.987366210540577
CAMB-72A65	MN908947.3	29144	C	T	0.0088	0.0066	2.8e-05	0.00013	0.00680272108843537	ACT	N	L291L	C871T	CTA>TTA	Synonymous	GU280_gp10	0.993197278911565
CAMB-72A65	MN908947.3	3037	C	T	1	1	3e-303	0	0.999584855529724	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000166057788110262
CAMB-72A74	MN908947.3	11074	C	INS	0.021	0.028	0.00026	1.1e-05	0.0268913155267854	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.971354245439971
CAMB-72A74	MN908947.3	11075	T	-	0.02	0.026	1.8e-06	3.5e-07	0.0245310982777125	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.972223641845965
CAMB-72A74	MN908947.3	11195	C	T	1	1	0	0	0.999883081959546	TCT	ORF1ab:nsp6	L75F	C223T	CTT>TTT	Missense	ORF1ab:nsp6	2.92295101134105e-05
CAMB-72A74	MN908947.3	12116	C	T	0.034	0.028	2.7e-16	1.2e-13	0.028983795530779	CCT	ORF1ab:nsp8	L9F	C25T	CTT>TTT	Missense	ORF1ab:nsp8	0.970992582793972
CAMB-72A74	MN908947.3	13778	AT	-	0.0057	0.0155	0.0036;0.0042	7e-06;1.1e-05	0.0126225745879407	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.98774062816616
CAMB-72A74	MN908947.3	14408	C	T	1	1	0	0	0.998755074424899	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00054127198917456
CAMB-72A74	MN908947.3	15216	C	T	1	1	0	0	0.999848490587478	GCA	ORF1ab:RNA-dependent-RNA-polymerase	S583S	C1749T	AGC>AGT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00011363205939169
CAMB-72A74	MN908947.3	1547	A	G	0.016	0.0095	7.2e-06	2.9e-05	0.0110153256704981	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.962164750957854
CAMB-72A74	MN908947.3	1547	A	T	0.0078	0.015	0.00024	1.7e-07	0.0129310344827586	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.962164750957854
CAMB-72A74	MN908947.3	15842	C	T	0.0079	0.0055	3.3e-05	0.00036	0.00591715976331361	ACT	ORF1ab:RNA-dependent-RNA-polymerase	T792I	C2375T	ACT>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.99282683934353
CAMB-72A74	MN908947.3	18594	A	G	0.038	0.038	1.4e-18	1.1e-18	0.0384484864938238	TAT	ORF1ab:3'-to-5'-exonuclease	L185L	A555G	TTA>TTG	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.961517578390118
CAMB-72A74	MN908947.3	23403	A	G	1	1	0	0	0.999010222294337	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.49034561090378e-05
CAMB-72A74	MN908947.3	241	C	T	1	1	0	0	0.997282889079966	TCG	NA	NA	NA	NA	NA	NA	0.000103181427343078
CAMB-72A74	MN908947.3	25521	C	T	0.0039	0.0092	0.0045	1.5e-05	0.0085602150869928	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.991038041966686
CAMB-72A74	MN908947.3	28294	A	G	0.0047	0.0074	0.00033	2.4e-05	0.00679772619611559	AAA	N	Q7Q	A21G	CAA>CAG	Synonymous	GU280_gp10	0.993083846518238
CAMB-72A74	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999763649255495	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000171703296703297
CAMB-72A74	MN908947.3	29241	AA	-	0.00645	0.013	0.00014;0.00038	1.1e-07;1e-05	0.0118891551014873	GAA	N	.	968-969-delfrshift	.	no-SNV	GU280_gp10	0.986257256894049
CAMB-72A74	MN908947.3	29242	A	G	0.0066	0.0094	0.00016	5.4e-06	0.00901185058351732	AAG	N	E323E	A969G	GAA>GAG	Synonymous	GU280_gp10	0.970981841121074
CAMB-72A74	MN908947.3	29242	A	T	0.0079	0.0099	4.7e-05	3.4e-06	0.00964268012436354	AAG	N	E323D	A969T	GAA>GAT	Missense	GU280_gp10	0.970981841121074
CAMB-72A74	MN908947.3	3037	C	T	1	1	6.4e-304	0	0.999782182531039	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-72A74	MN908947.3	3131	C	A	0.0077	0.0072	3.2e-05	1.7e-05	0.00723742277140335	CCA	ORF1ab:nsp3	Q138K	C412A	CAA>AAA	Missense	ORF1ab:nsp3	0.992762577228597
CAMB-72A74	MN908947.3	3373	C	A	1	1	0	0	0.999288489956762	ACA	ORF1ab:nsp3	D218E	C654A	GAC>GAA	Missense	ORF1ab:nsp3	0
CAMB-72A83	MN908947.3	11075	T	-	0.035	0.037	1.7e-08	8.9e-10	0.0357382341984354	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95819363384246
CAMB-72A83	MN908947.3	11471	C	T	0.015	0.029	3.9e-08	2.5e-13	0.0198427102238354	TCT	ORF1ab:nsp6	L167F	C499T	CTT>TTT	Missense	ORF1ab:nsp6	0.980157289776165
CAMB-72A83	MN908947.3	14408	C	T	1	1	0	0	0.999194027745595	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00035261286130225
CAMB-72A83	MN908947.3	23403	A	-	0.0069	0.011	0.00049	2.8e-06	0.00808669567900019	GAT	S	.	1841-1841-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	7.8766516353898e-05
CAMB-72A83	MN908947.3	23403	A	G	0.99	0.99	0	0	0.991808282299195	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.8766516353898e-05
CAMB-72A83	MN908947.3	241	C	T	1	1	0	0	0.999202233745513	TCG	NA	NA	NA	NA	NA	NA	0.000177281389886097
CAMB-72A83	MN908947.3	28829	T	C	0.0038	0.011	0.0017	8.4e-07	0.00546577244659793	TTC	N	S186P	T556C	TCC>CCC	Missense	GU280_gp10	0.994504682837475
CAMB-72A83	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999350669428898	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	3.4348916291691e-05
CAMB-72A83	MN908947.3	3037	C	T	1	1	0	0	0.998394249885304	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000764642911760208
CAMB-72A83	MN908947.3	3587	C	T	1	1	0	0	1	ACA	ORF1ab:nsp3	H290Y	C868T	CAC>TAC	Missense	ORF1ab:nsp3	0
CAMB-72A83	MN908947.3	5222	A	G	0.012	0.0085	1.4e-05	0.0034	0.0113466706479546	CAC	ORF1ab:nsp3	T835A	A2503G	ACT>GCT	Missense	ORF1ab:nsp3	0.988653329352045
CAMB-72AA1	MN908947.3	11074	C	INS	0.15	0.039	3e-44	1.7e-08	0.0815137350323366	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.864634692962797
CAMB-72AA1	MN908947.3	11083	G	-	0.065	0.12	3.5e-27	5.9e-51	0.098458364376182	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-72AA1	MN908947.3	11083	G	T	0.93	0.88	0	0	0.901255086251361	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-72AA1	MN908947.3	13923	C	T	0.29	0.14	3.3e-138	7.6e-62	0.215282623866015	ACT	ORF1ab:RNA-dependent-RNA-polymerase	D152D	C456T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.784717376133985
CAMB-72AA1	MN908947.3	14805	C	T	1	1	0	0	1	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-72AA1	MN908947.3	2480	A	G	1	1	3.2e-200	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-72AA1	MN908947.3	2558	C	T	1	1	5.2e-218	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-72AA1	MN908947.3	28302	G	A	0.18	0.11	2.1e-84	2.7e-48	0.138516418766124	CGA	N	R10Q	G29A	CGA>CAA	Missense	GU280_gp10	0.861451731057107
CAMB-72AA1	MN908947.3	3199	T	C	0.075	0.065	2.3e-27	1.5e-27	0.067858892699657	ATT	ORF1ab:nsp3	D160D	T480C	GAT>GAC	Synonymous	ORF1ab:nsp3	0.932141107300343
CAMB-72AB0	MN908947.3	11075	T	-	0.039	0.031	1.4e-09	2e-08	0.035823316161038	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.96018174012593
CAMB-72AB0	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999627330973096	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	4.30008886850328e-05
CAMB-72AB0	MN908947.3	18486	C	T	1	1	0	0	0.999809509854202	TCA	ORF1ab:3'-to-5'-exonuclease	L149L	C447T	CTC>CTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	8.79185288299509e-05
CAMB-72AB0	MN908947.3	27240	G	A	0.018	0.015	2.4e-09	1.3e-08	0.0166818111680697	AGA	ORF6	E13E	G39A	GAG>GAA	Synonymous	GU280_gp06	0.983275327035507
CAMB-72AB0	MN908947.3	29032	G	A	1	1	0	0	0.999865066171549	AGG	N	E253E	G759A	GAG>GAA	Synonymous	GU280_gp10	7.01655907942745e-05
CAMB-72AB0	MN908947.3	3196	A	G	0.0062	0.0067	9.3e-05	3.8e-05	0.0063663854846411	AAG	ORF1ab:nsp3	E159E	A477G	GAA>GAG	Synonymous	ORF1ab:nsp3	0.993588140333326
CAMB-72AB0	MN908947.3	6253	T	A	0.0044	0.0064	5e-04	3.5e-05	0.00510507577708132	ATG	ORF1ab:nsp3	N1178K	T3534A	AAT>AAA	Missense	ORF1ab:nsp3	0.994761748333082
CAMB-72ACF	MN908947.3	11074	C	INS	0.025	0.016	2.3e-05	0.0091	0.0172580126487298	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.981812984599993
CAMB-72ACF	MN908947.3	11075	T	-	0.037	0.027	1.8e-10	2e-07	0.027882797731569	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.968838610586011
CAMB-72ACF	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999412628487518	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000293707320654967
CAMB-72ACF	MN908947.3	18486	C	T	1	1	0	0	0.999582419876814	TCA	ORF1ab:3'-to-5'-exonuclease	L149L	C447T	CTC>CTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0
CAMB-72ACF	MN908947.3	24771	C	T	0.0099	0.012	1e-05	2.8e-07	0.0117780294450736	GCA	S	A1070V	C3209T	GCA>GTA	Missense	GU280_gp02, spike glycoprotein	0.988221970554926
CAMB-72ACF	MN908947.3	27914	A	G	0.013	0.014	6.9e-06	1.2e-07	0.0134858313417549	TAG	ORF8	L7L	A21G	TTA>TTG	Synonymous	GU280_gp09	0.986514168658245
CAMB-72ACF	MN908947.3	27954	A	G	0.005	0.0092	0.0012	6.1e-06	0.00873129009265859	TAG	ORF8	S21G	A61G	AGT>GGT	Missense	GU280_gp09	0.991090520313614
CAMB-72ACF	MN908947.3	29032	G	A	1	1	0	0	0.999929773308239	AGG	N	E253E	G759A	GAG>GAA	Synonymous	GU280_gp10	2.80906767044018e-05
CAMB-72ADE	MN908947.3	10063	TAGAAAAATG	-	0.00045	0.00874	NA;NA;NA;0.0048;NA;NA;NA;NA;NA;NA	1.2e-05;1.4e-05;1.4e-05;7.2e-05;8.7e-06;2.6e-06;1.7e-06;2e-06;2.3e-06;4.4e-06	0.00600905981325691	TTA	ORF1ab:3C-like-proteinase	.	9-18-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.994089199355185
CAMB-72ADE	MN908947.3	11075	T	-	0.03	0.041	9.7e-09	1.1e-10	0.0376035845056851	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959433416843322
CAMB-72ADE	MN908947.3	11083	GTATGAAAATGCCT	-	0.00872142857142857	0.00115285714285714	0.00054;6.5e-05;7.1e-05;3e-04;0.00029;4.1e-05;2.2e-05;1.7e-05;1.1e-05;2e-05;1.6e-05;0.00016;0.00019;1e-04	0.48;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;1.3e-06	0.00266860747210092	TGT	ORF1ab:nsp6	.	111-124-delfrshift	.	no-SNV	ORF1ab:nsp6	0.980808889535871
CAMB-72ADE	MN908947.3	11096	T	-	0.011	0.015	1e-04	1.3e-06	0.0135950005481855	CTT	ORF1ab:nsp6	.	124-124-delfrshift	.	no-SNV	ORF1ab:nsp6	0.986350180901217
CAMB-72ADE	MN908947.3	14408	C	T	0.99	1	0	0	0.994382982880309	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00173394876303514
CAMB-72ADE	MN908947.3	14539	AG	-	0.00675	0.00525	2e-05;1.9e-05	0.00012;0.00014	0.0055452865064695	TAG	ORF1ab:RNA-dependent-RNA-polymerase	.	1072-1073-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.99404915912031
CAMB-72ADE	MN908947.3	18449	G	T	0.011	0.005	3.4e-07	0.00022	0.00693218060570916	AGT	ORF1ab:3'-to-5'-exonuclease	S137I	G410T	AGT>ATT	Missense	ORF1ab:3'-to-5'-exonuclease	0.993015103191966
CAMB-72ADE	MN908947.3	20605	T	-	0.0077	0.015	3e-05	1.9e-08	0.0124458544323104	ATT	ORF1ab:endoRNAse	.	985-985-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.98755414556769
CAMB-72ADE	MN908947.3	22247	T	C	0.015	0.02	2.1e-08	6.2e-10	0.0172381132790301	TTT	S	L229L	T685C	TTG>CTG	Synonymous	GU280_gp02, spike glycoprotein	0.98276188672097
CAMB-72ADE	MN908947.3	23403	A	G	1	1	0	0	0.999893598627422	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.65008578610664e-05
CAMB-72ADE	MN908947.3	24038	G	T	0.0053	0.0066	9.7e-05	2.6e-05	0.00594134961299466	AGT	S	V826L	G2476T	GTG>TTG	Missense	GU280_gp02, spike glycoprotein	0.994058650387005
CAMB-72ADE	MN908947.3	241	C	T	1	1	0	0	0.999645241397104	TCG	NA	NA	NA	NA	NA	NA	0.000161253910407327
CAMB-72ADE	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0376486486486486	0.0283513513513514	8.9e-06;1.6e-07;6e-06;5.7e-06;1.5e-05;6.7e-07;4e-06;1.7e-06;1.7e-06;6e-07;9e-07;5.7e-07;1.7e-06;1.1e-06;1.3e-06;2.3e-06;9.3e-07;1.9e-06;1.3e-06;1.2e-06;1.2e-06;2.2e-06;1.2e-06;1.6e-06;1.3e-06;9e-07;1.5e-06;9.5e-07;7.1e-07;8.7e-07;1.7e-06;1.6e-06;9.6e-07;1.9e-06;4.1e-07;9.1e-07;5.6e-07	0.0013;0.00024;0.001;0.001;0.0019;0.00036;0.001;2.7e-05;2.7e-05;1.8e-05;1.6e-05;1.2e-05;2.5e-05;2e-05;2.4e-05;3.6e-05;1.7e-05;3e-05;1.8e-05;2.3e-05;2.4e-05;3.7e-05;2.3e-05;2.7e-05;2.1e-05;1.4e-05;2.5e-05;2.1e-05;1.2e-05;1.7e-05;3e-05;0.0021;0.0012;0.0022;0.001;0.0016;0.0011	0.0330296694544006	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.977044261065266
CAMB-72ADE	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998834196891192	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.0002862458852154
CAMB-72ADE	MN908947.3	29013	C	T	0.0039	0.011	5e-04	4.1e-07	0.00944170771756979	ACT	N	T247I	C740T	ACT>ATT	Missense	GU280_gp10	0.990528970208773
CAMB-72ADE	MN908947.3	29620	GA	-	0.014	0.00345	0.00013;1.3e-05	0.0026;NA	0.00556328233657858	TGA	ORF10	.	63-64-delfrshift	.	no-SNV	GU280_gp11	0.991300366300366
CAMB-72ADE	MN908947.3	3037	C	T	1	1	4.59481050632359e-322	0	0.999470806138649	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000176397953783736
CAMB-72ADE	MN908947.3	3079	AG	-	0.016	0.00445	6e-07;7.6e-07	0.00076;0.00096	0.00602017572404816	AAG	ORF1ab:nsp3	.	360-361-delfrshift	.	no-SNV	ORF1ab:nsp3	0.993747943402435
CAMB-72ADE	MN908947.3	3431	G	C	0.0087	0.0036	6.6e-06	0.001	0.00465926204819277	AGT	ORF1ab:nsp3	V238L	G712C	GTG>CTG	Missense	ORF1ab:nsp3	0.995340737951807
CAMB-72ADE	MN908947.3	522	TT	-	0.0185	0.0385	0.0031;0.028	3.4e-06;0.00019	0.0301578496142014	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.96279995808446
CAMB-72ADE	MN908947.3	557	G	-	0.01	0.0056	8.8e-07	9e-05	0.00740091964090212	CGG	ORF1ab:leader-protein	.	292-292-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.992292533391723
CAMB-72ADE	MN908947.3	8377	A	-	0.021	0.012	2.4e-05	0.0013	0.0136830102622577	CAA	ORF1ab:nsp3	.	5658-5658-delfrshift	.	no-SNV	ORF1ab:nsp3	0.986088939566705
CAMB-72ADE	MN908947.3	858	TTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTA	-	0.000120888888888889	0.0115555555555556	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0012;NA;NA;NA;NA;NA;NA	1.8e-07;1.7e-07;5.3e-07;5.5e-07;7.7e-07;7.1e-07;3.4e-07;5.4e-07;3e-07;9.5e-08;2.5e-07;9.1e-07;3.6e-07;6.5e-07;9.9e-07;9.1e-07;7.6e-07;8.2e-07;3.2e-07;9.5e-07;1.1e-06;3e-07;2.8e-07;7.2e-07;1.5e-06;2.7e-06;1.5e-06;8.3e-06;1.1e-06;1.3e-06;8.2e-07;2.7e-08;1.5e-06;1.4e-06;3.2e-07;1.9e-06	0.00627806600688843	CTT	ORF1ab:nsp2	.	53-88-delinframe	.	no-SNV	ORF1ab:nsp2	0.993169054441261
CAMB-72AED	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.998326826547685	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.00167317345231456
CAMB-72AED	MN908947.3	17898	C	T	1	1	0	0	0.99988417882789	ACT	ORF1ab:helicase	H554H	C1662T	CAC>CAT	Synonymous	ORF1ab:helicase	0
CAMB-72AFC	MN908947.3	11074	C	INS	0.17	0.11	1.6e-66	4.5e-30	0.152233389972065	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.822855168044236
CAMB-72AFC	MN908947.3	11083	G	-	0.067	0.19	1.4e-28	3.1e-85	0.106686332350049	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.73134491423577e-05
CAMB-72AFC	MN908947.3	11083	G	T	0.93	0.81	0	0	0.893122473505954	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.73134491423577e-05
CAMB-72AFC	MN908947.3	12826	T	C	0.18	0.056	1.4e-86	6.8e-26	0.15748497399645	ATT	ORF1ab:nsp9	D47D	T141C	GAT>GAC	Synonymous	ORF1ab:nsp9	0.84251502600355
CAMB-72AFC	MN908947.3	14674	C	T	0.15	0.13	2.4e-71	2.5e-60	0.146246854906346	ACC	ORF1ab:RNA-dependent-RNA-polymerase	P403S	C1207T	CCC>TCC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.853718199608611
CAMB-72AFC	MN908947.3	14805	C	T	1	1	0	0	0.99996760818865	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	3.23918113500907e-05
CAMB-72AFC	MN908947.3	1515	A	G	1	1	3.2e-287	1.8e-160	1	CAT	ORF1ab:nsp2	H237R	A710G	CAT>CGT	Missense	ORF1ab:nsp2	0
CAMB-72AFC	MN908947.3	17247	T	C	1	1	0	0	0.99978488146969	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.0001075592651551
CAMB-72AFC	MN908947.3	17799	A	G	1	1	0	0	0.999838553438812	TAG	ORF1ab:helicase	V521V	A1563G	GTA>GTG	Synonymous	ORF1ab:helicase	8.07232805941233e-05
CAMB-72AFC	MN908947.3	22845	ATTTTACAGGCTGCGTTATAGCTTGGA	-	0.0332592592592593	0.0194074074074074	7.9e-30;3e-31;4.9e-24;2.5e-11;4.5e-11;1.9e-11;5.9e-12;6.9e-12;5.5e-12;5.2e-11;3.1e-11;6.3e-11;7.1e-12;5.5e-11;7e-12;3.5e-12;5.5e-12;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	1.5e-07;2.4e-07;4.4e-06;1.2e-05;1.6e-05;1.2e-05;8e-06;8.7e-06;7.6e-06;1.8e-05;1.7e-05;2.1e-05;9.3e-06;1.8e-05;9.4e-06;3.7e-06;5.1e-06;4.2e-05;2.2e-07;2.4e-07;2.1e-07;4.4e-07;2e-07;1.4e-07;7e-08;1.7e-07;6.8e-08	0.0338290570354633	GAT	S	.	1283-1309-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.938437055029735
CAMB-72AFC	MN908947.3	23188	CT	AC	0.015665	0.028	0.47;5.2e-12	7.1e-08;2.4e-11	0.0203325261354911	ACT	S	.	1626-1627-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.989396387134675
CAMB-72AFC	MN908947.3	23189	T	C	0.031	0.029	5.2e-12	2.4e-11	0.0302278969638483	CTT	S	F543L	T1627C	TTC>CTC	Missense	GU280_gp02, spike glycoprotein	0.969772103036152
CAMB-72AFC	MN908947.3	28580	G	A	1	1	0	0	1	AGA	N	D103N	G307A	GAT>AAT	Missense	GU280_gp10	0
CAMB-72AFC	MN908947.3	29051	C	INS	0.053	0.046	7.9e-13	8.6e-12	0.0483022477283596	GCA	N	.	777-778-insfrshift	.	no-SNV	GU280_gp10	0.950980392156863
CAMB-72AFC	MN908947.3	3877	T	G	0.016	0.034	1.4e-08	5.6e-10	0.0184381778741865	CTG	ORF1ab:nsp3	A386A	T1158G	GCT>GCG	Synonymous	ORF1ab:nsp3	0.980838756326826
CAMB-72AFC	MN908947.3	5810	GACGGTGCTTTACTT	-	0.118	0.013	1.5e-36;1.8e-37;7.2e-37;1e-37;7.5e-37;7e-38;1.4e-37;1.6e-25;3.6e-29;2.5e-19;1.8e-17;9.7e-19;1.2e-21;8.9e-34;1.6e-30	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;1e-11;1.2e-17;4.1e-16	0.0913635396724101	AGA	ORF1ab:nsp3	.	3091-3105-delinframe	.	no-SNV	ORF1ab:nsp3	0.911287824021481
CAMB-72AFC	MN908947.3	9223	C	T	1	1	0	0	0.999933466400532	ACG	ORF1ab:nsp4	H223H	C669T	CAC>CAT	Synonymous	ORF1ab:nsp4	6.65335994677312e-05
CAMB-72B17	MN908947.3	11075	T	-	0.02	0.033	4.2e-06	4.9e-09	0.0258587417985334	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.97407314913615
CAMB-72B17	MN908947.3	11117	A	G	0.026	0.047	3.2e-13	2.3e-22	0.0354443943153621	TAT	ORF1ab:nsp6	I49V	A145G	ATT>GTT	Missense	ORF1ab:nsp6	0.964414617640424
CAMB-72B17	MN908947.3	11176	T	-	0.0074	0.013	2e-04	1.5e-06	0.0101191009223605	GTT	ORF1ab:nsp6	.	204-204-delfrshift	.	no-SNV	ORF1ab:nsp6	0.984925823109758
CAMB-72B17	MN908947.3	11237	AG	-	0.0103	0.0175	0.00013;0.00021	6.4e-07;1.2e-06	0.0135321671833631	TAG	ORF1ab:nsp6	.	265-266-delfrshift	.	no-SNV	ORF1ab:nsp6	0.985722376929249
CAMB-72B17	MN908947.3	11298	A	G	0.0089	0.038	5.8e-06	1.4e-18	0.0226568592324067	AAG	ORF1ab:nsp6	K109R	A326G	AAG>AGG	Missense	ORF1ab:nsp6	0.97732206461947
CAMB-72B17	MN908947.3	12770	TTAGCTTACTACAACACAACAAAGGGAGGTAGGTTTGTACTTGCACTGTTATCCGATTTACAGGATT	-	0.00853731343283582	0.00146537313432836	0.00024;0.00018;0.00032;0.00034;0.00033;0.00029;0.00029;0.00026;2e-04;0.00019;3e-05;3.1e-05;3.2e-05;8.2e-05;8.5e-05;2.5e-05;2.6e-05;1e-04;5e-05;7.7e-05;4.5e-05;1.3e-05;2.2e-05;9e-11;1.6e-08;2.7e-08;3.1e-08;3.1e-08;2.3e-08;8.3e-09;9.2e-10;2.3e-08;1.8e-08;1.4e-09;7.8e-06;2.9e-05;4.9e-05;2.5e-05;3.1e-05;1.4e-05;1.6e-05;1.6e-05;2.9e-05;1.5e-05;1.2e-05;1.2e-05;9.6e-06;3.2e-05;3e-05;3.1e-05;2.7e-05;3e-05;3.8e-05;3.1e-05;4.5e-05;3.9e-05;8e-05;2.8e-05;4.1e-05;4.4e-05;2.4e-05;2.5e-05;3.1e-05;2.2e-05;1.7e-05;3.5e-05;1.1e-05	NA;NA;NA;NA;NA;0.47;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;9.3e-07;1.1e-06;8.3e-07;1e-06;1.3e-06;1.1e-06;1.6e-06;1.5e-06;2.3e-06;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00372758787788422	GTT	ORF1ab:nsp9	.	85-151-delfrshift	.	no-SNV	ORF1ab:nsp9	0.998120883731961
CAMB-72B17	MN908947.3	14408	C	-	0.012	0.0049	4.5e-07	0.00096	0.00712806141099062	CCT	ORF1ab:RNA-dependent-RNA-polymerase	.	941-941-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.000487388814426709
CAMB-72B17	MN908947.3	14408	C	T	0.99	0.99	0	0	0.992262702570976	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000487388814426709
CAMB-72B17	MN908947.3	14600	TATTACTAGA	-	0.00738	0.0162	9e-04;0.00068;8.1e-05;0.00067;0.00039;0.00054;0.00022;0.00076;0.00073;0.00043	2.2e-06;9.7e-07;1.1e-08;2e-06;4.8e-07;1.1e-06;1.3e-07;2e-06;2.1e-06;7.1e-07	0.0110720770506039	CTA	ORF1ab:RNA-dependent-RNA-polymerase	.	1133-1142-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.988732114467409
CAMB-72B17	MN908947.3	14854	GTAGTTGAAGTT	-	0.00282225	0.0102416666666667	0.0012;0.052;0.052;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00027;4.3e-05;5e-05;6.7e-05;4.9e-05;5.3e-05;3.9e-05;4.2e-05;3.1e-05;5.1e-05;6.1e-05;0.00013	0.00250616828240048	TGT	ORF1ab:RNA-dependent-RNA-polymerase	.	1387-1398-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.974554256700909
CAMB-72B17	MN908947.3	15598	G	T	0.0062	0.004	3.7e-05	0.00039	0.00486039035009999	TGT	ORF1ab:RNA-dependent-RNA-polymerase	V711F	G2131T	GTC>TTC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.995114295116827
CAMB-72B17	MN908947.3	16375	C	T	0.0089	0.016	0.0051	7.1e-07	0.0154039610185476	TCC	ORF1ab:helicase	P47S	C139T	CCG>TCG	Missense	ORF1ab:helicase	0.984596038981452
CAMB-72B17	MN908947.3	17104	C	T	0.16	0.17	5.7e-76	4.4e-83	0.168980249899234	TCA	ORF1ab:helicase	H290Y	C868T	CAT>TAT	Missense	ORF1ab:helicase	0.829923417976622
CAMB-72B17	MN908947.3	17330	AGACGACAGCAGATA	-	0.000690666666666667	0.00846	NA;NA;NA;NA;NA;NA;0.0043;0.0034;0.0045;NA;NA;NA;NA;NA;NA	6.9e-06;1.4e-05;8.1e-06;1.8e-05;8.6e-06;4.7e-06;2.2e-05;9.2e-06;1.8e-05;9.7e-06;1.9e-05;2.2e-05;3.8e-05;2.3e-05;8.6e-06	0.00413976782560866	GAG	ORF1ab:helicase	.	1094-1108-delinframe	.	no-SNV	ORF1ab:helicase	0.995678660384719
CAMB-72B17	MN908947.3	17505	T	C	0.0079	0.0075	6.6e-06	9.6e-06	0.00771757502312083	ATT	ORF1ab:helicase	N423N	T1269C	AAT>AAC	Synonymous	ORF1ab:helicase	0.992282424976879
CAMB-72B17	MN908947.3	1843	GAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCGTGTT	-	0.00903269230769231	0.000894615384615385	2.7e-05;4.1e-06;1.1e-06;1.1e-06;1.2e-06;1.6e-06;2e-06;4.3e-07;6.7e-07;1.2e-06;4.1e-06;1.5e-06;3.2e-06;2.1e-06;2.4e-06;2.7e-06;3.7e-06;3.7e-06;2.8e-06;1.9e-06;1.2e-05;1.2e-05;1.7e-05;1.7e-05;8.9e-05;9.7e-05;9.4e-05;7.8e-05;6.6e-05;4.7e-05;7.6e-06;3.2e-06;2.5e-06;2.5e-06;2.5e-06;2.7e-06;5.4e-06;7.4e-06;3.1e-06;1.9e-05;6.4e-06;7.9e-06;7.4e-06;4e-06;2.6e-06;3.6e-06;3.7e-06;7e-06;7.8e-05;0.00014;6.8e-05;6.4e-05	0.0015;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0012;0.0013;0.0013;0.0012;0.001;5e-04;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00358327803583278	AGA	ORF1ab:nsp2	.	1038-1089-delfrshift	.	no-SNV	ORF1ab:nsp2	0.988736336976806
CAMB-72B17	MN908947.3	2155	GCTTGAAGAGAAGTT	-	0.0103266666666667	0.00156266666666667	0.00012;0.00012;6.7e-06;7.2e-06;8.1e-05;8.6e-06;1.6e-05;1.5e-05;5.6e-06;7.4e-06;4.9e-06;3.2e-06;3e-06;2.5e-06;4.1e-07	NA;NA;NA;4.5e-06;5.5e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00666304052216481	GGC	ORF1ab:nsp2	.	1350-1364-delinframe	.	no-SNV	ORF1ab:nsp2	0.993113896157554
CAMB-72B17	MN908947.3	22284	TACTTGCTTTACA	-	0.00854615384615385	0.0260769230769231	0.00014;0.00028;0.00039;0.00098;0.00082;0.0027;0.00057;0.0089;0.00028;0.0017;0.0051;0.00031;2e-04	2.3e-10;1.1e-09;1.9e-09;2.4e-08;4.3e-09;5.2e-08;3.2e-09;4.8e-05;4.1e-08;6.1e-07;3e-06;3e-08;8.4e-09	0.0131401617250674	TTA	S	.	722-734-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.986896666113783
CAMB-72B17	MN908947.3	22675	C	T	0.0096	0.0098	2.9e-06	2.5e-06	0.00966269488410694	CCG	S	S371S	C1113T	TCC>TCT	Synonymous	GU280_gp02, spike glycoprotein	0.990337305115893
CAMB-72B17	MN908947.3	23403	A	G	1	0.99	0	0	0.996114396357737	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000130828405463394
CAMB-72B17	MN908947.3	23523	AACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGT	-	0.0227457627118644	0.0351186440677966	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00038;0.00036;0.0013;0.00085;0.0011;0.00068;0.00041;0.0014;0.0012;0.0014;0.0016;0.00072;0.0012;0.00076;0.0012;0.0012;0.0012;0.0012;0.0012;0.00083;8e-04;1.7e-05;4e-06;2.5e-06;7.5e-07;2.1e-06;5.8e-07;2.3e-06;6e-06;2.4e-06;2.4e-06;9.9e-09;2.1e-08;3.8e-06	5.7e-08;8e-08;7.9e-08;7.7e-08;7.2e-08;5.5e-08;7e-08;1.1e-07;1.3e-07;1.5e-07;9.3e-08;8.2e-08;1.5e-07;5.8e-08;6.3e-06;3.4e-06;0.00037;1.3e-07;2.4e-07;6.8e-08;1.2e-07;1.8e-07;1.4e-07;1.4e-07;1.7e-07;7e-07;6.9e-07;8.1e-06;2.9e-06;3.7e-06;8.2e-05;3.9e-05;0.00021;0.00015;0.00021;0.00026;6.5e-06;1.2e-05;7.4e-05;0.00015;0.00015;0.00017;0.00014;0.00015;8.9e-05;7.9e-05;3.1e-05;7.5e-06;3.2e-05;1.4e-05;3.8e-05;1.2e-05;3.2e-05;7.6e-05;3.6e-05;4e-05;4.3e-07;9.5e-07;5.5e-05	0.0349704693814113	GAA	S	.	1961-2019-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.989668127739512
CAMB-72B17	MN908947.3	241	C	T	1	1	0	0	0.999529234535354	TCG	NA	NA	NA	NA	NA	NA	0.000258921005555032
CAMB-72B17	MN908947.3	26610	A	G	0.009	0.0053	1.8e-06	9e-05	0.0066901802709663	TAC	M	T30A	A88G	ACA>GCA	Missense	GU280_gp05	0.993225842570821
CAMB-72B17	MN908947.3	26679	TTCCTCTGGCTGTTATGGCCAGTA	-	0.00237333333333333	0.00852083333333333	NA;NA;NA;NA;NA;1.5e-05;1.5e-05;2.9e-05;8.6e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.19;NA;5.8e-07;3.3e-06;2.9e-06;NA	6.6e-06;7.1e-06;6.8e-06;6.1e-06;9.6e-06;1.1e-05;1.1e-05;1.8e-05;5.8e-05;7.3e-06;5.3e-05;0.00016;4.7e-06;4.1e-07;1.8e-07;3.8e-06;8.7e-06;5.8e-06;8.3e-06;7.4e-06;2.8e-06;1e-05;8.1e-06;2.7e-06	0.00516325434250582	TTT	M	.	157-180-delinframe	.	no-SNV	GU280_gp05	0.994769905040175
CAMB-72B17	MN908947.3	26699	AGT	-	0.00903333333333333	0.0082	5.8e-07;3.3e-06;2.9e-06	2.8e-06;1e-05;8.1e-06	0.00814495155897231	CAG	M	.	177-179-delinframe	.	no-SNV	GU280_gp05	0.99020889917178
CAMB-72B17	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCT	-	0.058	0.018145	3.9e-09;7.1e-12;2.5e-10;2.7e-10;1.5e-09;7.2e-12;1.1e-10;5.9e-11;6.2e-11;1.4e-11;2.2e-11;1.4e-11;5.6e-11;2.8e-11;4.3e-11;8.4e-11;2.1e-11;7.3e-11;3.3e-11;3.5e-11;2.5e-11;7.4e-11;3.4e-11;5.2e-11;3e-11;1.9e-11;5.6e-11;2.1e-11;3.9e-12;3e-11;5.7e-11;4.8e-11;3.4e-11;6.6e-11;3.2e-12;2e-11;1.7e-11;0.00013;0.00047;0.00021	0.1;0.055;0.095;0.099;0.12;0.073;0.11;0.0034;0.0034;0.0026;0.0025;0.0025;0.0031;0.0029;0.0032;0.0042;0.0027;0.0038;0.0027;0.003;0.0031;0.0043;0.0031;0.0033;0.0029;0.0026;0.0037;0.0029;0.00066;0.003;0.0037;0.0035;0.0023;0.0039;0.0017;0.0027;0.0021;0.0058;0.01;0.0066	0.0347265656867811	GTC	M	.	258-297-delfrshift	.	no-SNV	GU280_gp05	0.975945578231292
CAMB-72B17	MN908947.3	26970	C	-	0.0048	0.0081	0.0012	3.8e-05	0.0067157712305026	TCG	M	.	448-448-delfrshift	.	no-SNV	GU280_gp05	0.993284228769497
CAMB-72B17	MN908947.3	29068	TAAAGCATACAATGTAACACAAGCTT	-	0.0295384615384615	0.00728846153846154	1.5e-09;9.7e-09;3.3e-09;3.2e-09;2.2e-09;3.5e-09;3.2e-09;1.8e-08;5.8e-09;1.6e-09;3.5e-09;4.2e-10;3e-09;1.5e-09;6.8e-05;6.2e-05;3.2e-06;4.1e-06;5e-06;2.3e-06;1.7e-06;2e-06;3.3e-06;1.9e-06;2.1e-06;1.2e-06	1.4e-06;3.4e-06;0.00034;0.00032;0.00031;0.00036;0.00036;0.044;0.042;0.041;0.043;0.031;0.046;0.042;0.00016;0.00017;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0117890131259115	CTA	N	.	795-820-delfrshift	.	no-SNV	GU280_gp10	0.981125226860254
CAMB-72B17	MN908947.3	29734	G	C	0.98	1	4.3e-165	0	0.996969696969697	CGA	NA	NA	NA	NA	NA	NA	0.00101010101010101
CAMB-72B17	MN908947.3	3037	C	T	1	1	0	0	0.999634436117712	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-72B17	MN908947.3	315	G	T	0.005	0.01	0.00048	2.1e-06	0.00678638316624435	AGT	ORF1ab:leader-protein	S17I	G50T	AGT>ATT	Missense	ORF1ab:leader-protein	0.988828908229591
CAMB-72B17	MN908947.3	387	A	C	0.0084	0.0086	6.1e-06	3.1e-06	0.00846883468834688	GAG	ORF1ab:leader-protein	E41A	A122C	GAG>GCG	Missense	ORF1ab:leader-protein	0.991377186499138
CAMB-72B17	MN908947.3	5818	TTTACTT	-	0.00472857142857143	0.0227142857142857	0.0081;0.041;0.051;0.052;NA;NA;NA	0.00086;1.8e-05;4.4e-05;2.9e-05;3.4e-06;1e-04;0.00024	0.0210919770391136	CTT	ORF1ab:nsp3	.	3099-3105-delfrshift	.	no-SNV	ORF1ab:nsp3	0.988791032826261
CAMB-72B17	MN908947.3	583	C	T	0.032	0.055	4e-16	4.8e-26	0.0417409917945059	TCC	ORF1ab:leader-protein	V106V	C318T	GTC>GTT	Synonymous	ORF1ab:leader-protein	0.958226575422437
CAMB-72B17	MN908947.3	8025	C	T	1	1	0	0	0.999913073713491	GCA	ORF1ab:nsp3	A1769V	C5306T	GCA>GTA	Missense	ORF1ab:nsp3	8.69262865090403e-05
CAMB-72B17	MN908947.3	929	A	G	0.014	0.011	2.7e-08	5e-07	0.0129577121253697	TAT	ORF1ab:nsp2	I42V	A124G	ATT>GTT	Missense	ORF1ab:nsp2	0.987011799140218
CAMB-73CC8	MN908947.3	11075	T	-	0.045	0.04	1.2e-11	2e-10	0.0427302900238066	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953186091368794
CAMB-73CC8	MN908947.3	12998	A	G	1	1	0	0	0.999448050094212	TAG	ORF1ab:nsp9	S105G	A313G	AGT>GGT	Missense	ORF1ab:nsp9	9.5163776859976e-05
CAMB-73CC8	MN908947.3	13378	C	T	0.63	0.63	0	0	0.630658915981402	CCG	ORF1ab:nsp10	T118T	C354T	ACC>ACT	Synonymous	ORF1ab:nsp10	0.369299529510626
CAMB-73CC8	MN908947.3	14408	C	T	1	1	0	0	0.998115397746671	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000655513827244793
CAMB-73CC8	MN908947.3	17303	T	C	0.011	0.0088	9.2e-07	6e-06	0.00979303224191606	GTC	ORF1ab:helicase	V356A	T1067C	GTC>GCC	Missense	ORF1ab:helicase	0.990144392472193
CAMB-73CC8	MN908947.3	23403	A	G	1	1	0	0	0.99949075026197	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000137105698700434
CAMB-73CC8	MN908947.3	241	C	T	1	1	0	0	0.998432902091205	TCG	NA	NA	NA	NA	NA	NA	0.00010447319391966
CAMB-73CC8	MN908947.3	24386	G	A	0.0076	0.0053	3.3e-05	0.00031	0.00658898857164129	AGC	S	A942T	G2824A	GCA>ACA	Missense	GU280_gp02, spike glycoprotein	0.993187655883557
CAMB-73CC8	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999330058061635	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.0001511868165096
CAMB-73CC8	MN908947.3	3037	C	T	1	1	0	0	0.999026089009562	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000118049817022784
CAMB-73CC8	MN908947.3	4582	C	T	1	1	0	0	0.998479605746042	ACG	ORF1ab:nsp3	N621N	C1863T	AAC>AAT	Synonymous	ORF1ab:nsp3	2.62136940337632e-05
CAMB-73CC8	MN908947.3	6720	C	T	0.0053	0.0084	0.00029	1.4e-05	0.00663285212641436	ACA	ORF1ab:nsp3	T1334I	C4001T	ACA>ATA	Missense	ORF1ab:nsp3	0.993318376902068
CAMB-7591A	MN908947.3	11074	C	INS	0.13	0.13	1.6e-47	7.5e-43	0.125927566729427	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.87381400671909
CAMB-7591A	MN908947.3	11083	G	-	0.15	0.21	9.3e-67	2.2e-96	0.175903403622364	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	5.24980313238254e-05
CAMB-7591A	MN908947.3	11083	G	T	0.85	0.79	0	4.90113120674517e-321	0.823939102283664	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	5.24980313238254e-05
CAMB-7591A	MN908947.3	1263	C	G	0.014	0.0088	2.9e-08	4.2e-06	0.0126743766813656	ACG	ORF1ab:nsp2	T153R	C458G	ACG>AGG	Missense	ORF1ab:nsp2	0.987186953989517
CAMB-7591A	MN908947.3	13163	AC	-	0.014	0.025	1.7e-05;1.8e-05	7.3e-09;8.5e-09	0.0151687258619786	TAC	ORF1ab:nsp10	.	139-140-delfrshift	.	no-SNV	ORF1ab:nsp10	0.984613761451757
CAMB-7591A	MN908947.3	1350	A	T	1	1	0	0	1	CAA	ORF1ab:nsp2	Q182L	A545T	CAA>CTA	Missense	ORF1ab:nsp2	0
CAMB-7591A	MN908947.3	13780	A	T	0.017	0.029	5.1e-06	1.2e-08	0.0208333333333333	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I105L	A313T	ATA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.979045189504373
CAMB-7591A	MN908947.3	14183	C	T	0.074	0.032	2.1e-34	4.5e-16	0.0483628152051186	ACC	ORF1ab:RNA-dependent-RNA-polymerase	T239I	C716T	ACC>ATC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.951543093714716
CAMB-7591A	MN908947.3	14805	C	T	1	1	0	0	0.999801767104667	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000141594925237879
CAMB-7591A	MN908947.3	1535	G	A	1	1	0	0	1	GGT	ORF1ab:nsp2	V244I	G730A	GTT>ATT	Missense	ORF1ab:nsp2	0
CAMB-7591A	MN908947.3	1547	A	T	0.014	0.053	2.3e-06	5.3e-15	0.0283748925193465	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.964746345657782
CAMB-7591A	MN908947.3	16963	C	T	0.01	0.018	2.2e-06	5.8e-10	0.0147836538461538	ACA	ORF1ab:helicase	Q243*	C727T	CAA>TAA	Nonsense	ORF1ab:helicase	0.985186298076923
CAMB-7591A	MN908947.3	17676	C	T	0.015	0.011	1.5e-08	1.4e-06	0.0133354334015856	TCA	ORF1ab:helicase	I480I	C1440T	ATC>ATT	Synonymous	ORF1ab:helicase	0.986533312332651
CAMB-7591A	MN908947.3	18875	G	-	0.015	0.012	2e-08	1.5e-07	0.0142688948635493	TGT	ORF1ab:3'-to-5'-exonuclease	.	836-836-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.98567838754459
CAMB-7591A	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-7591A	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-7591A	MN908947.3	26144	G	T	0.99	1	1.1e-182	6.3e-120	0.995305164319249	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7591A	MN908947.3	28810	CAGTCA	GCAGTC	0.012	0.0029	8.7e-06;6.6e-06;2.4e-05;1e-05;1.3e-07;1.4e-05	0.074;0.18;0.21;0.18;4.6e-05;0.2	0.0068976580044915	GCA	N	.	537-542-mnv	.	no-SNV	GU280_gp10	0.992620505573873
CAMB-7591A	MN908947.3	28826	C	T	0.01	0.012	5.4e-05	1.6e-05	0.0112522102555859	TCG	N	R185C	C553T	CGT>TGT	Missense	GU280_gp10	0.988747789744414
CAMB-7591A	MN908947.3	29240	GAA	-	0.0153333333333333	0.0121666666666667	3e-09;4.9e-08;6.2e-07	NA;3.6e-12;2.3e-05	0.0131839606530501	GGA	N	.	967-969-delinframe	.	no-SNV	GU280_gp10	0.990132960111966
CAMB-7591A	MN908947.3	29242	A	G	0.0041	0.008	0.0013	2.6e-05	0.00552081947585473	AAG	N	E323E	A969G	GAA>GAG	Synonymous	GU280_gp10	0.965212185712385
CAMB-7591A	MN908947.3	4388	T	C	0.0044	0.0091	0.00033	2.4e-06	0.00690223361406078	TTT	ORF1ab:nsp3	L557L	T1669C	TTG>CTG	Synonymous	ORF1ab:nsp3	0.993097766385939
CAMB-7591A	MN908947.3	4440	GTGTGGAAACTAAAGCCATAGTTTCAACTATACAGCGTAAATATAAGGGTATTAAAATACAAGAGG	-	0.00743030303030303	0.00138845454545455	0.00015;5.7e-05;7.9e-05;7.8e-05;0.00017;6.4e-05;6.6e-05;2.1e-05;6.4e-05;7.9e-05;0.00012;0.00022;0.00039;1e-04;9.5e-05;9e-05;0.00012;6.4e-05;5.3e-05;6.5e-05;0.00011;0.00011;5.8e-05;7.7e-05;8.9e-05;5.4e-05;2.9e-05;5.2e-05;0.00011;6.4e-05;3.8e-05;2.8e-05;2.8e-05;1.6e-05;5.1e-05;5e-05;1e-04;1.2e-05;3.5e-05;3.5e-06;5.8e-05;9.9e-05;4.1e-06;2.7e-06;7.5e-06;4.1e-06;7.3e-06;6.1e-06;9.9e-06;1.1e-05;1e-06;4.1e-06;9.9e-06;2.2e-05;6.5e-06;3.1e-05;1.3e-05;2.1e-05;2.3e-05;1.5e-05;2.1e-05;2.1e-05;1.5e-05;3.1e-05;0.00016;3.5e-05	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.48;0.14;1.1e-18;3.3e-17;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.002917534980649	TGT	ORF1ab:nsp3	.	1721-1786-delinframe	.	no-SNV	ORF1ab:nsp3	0.997191303443254
CAMB-7591A	MN908947.3	9438	C	T	0.046	0.016	1.6e-18	6.7e-08	0.0282331511839709	ACA	ORF1ab:nsp4	T295I	C884T	ACA>ATA	Missense	ORF1ab:nsp4	0.971766848816029
CAMB-75929	MN908947.3	10097	G	A	1	1	0	0	0.999842484957313	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000157515042686577
CAMB-75929	MN908947.3	11075	T	-	0.043	0.028	9e-11	7e-08	0.0379641279222869	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958671036076894
CAMB-75929	MN908947.3	13536	C	T	1	1	0	0	0.999880074353901	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-75929	MN908947.3	14408	C	T	1	1	0	0	0.99851118343605	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000727096461463887
CAMB-75929	MN908947.3	23403	A	G	1	1	0	0	0.999292093225877	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000231431060771074
CAMB-75929	MN908947.3	23731	C	T	1	1	0	0	0.999895211149534	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.00010478885046631
CAMB-75929	MN908947.3	241	C	T	1	1	0	0	0.999718011984491	TCG	NA	NA	NA	NA	NA	NA	0.000117495006462225
CAMB-75929	MN908947.3	27384	T	C	0.016	0.02	1e-08	2.1e-10	0.0170009848131447	ATT	ORF6	D61D	T183C	GAT>GAC	Synonymous	GU280_gp06	0.982947182916084
CAMB-75929	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999385155906895	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.87044613286577e-05
CAMB-75929	MN908947.3	2914	G	A	0.086	0.072	1.6e-38	2.1e-32	0.0808992962570841	TGC	ORF1ab:nsp3	L65L	G195A	TTG>TTA	Synonymous	ORF1ab:nsp3	0.918758174005107
CAMB-75929	MN908947.3	3037	C	T	1	1	0	0	0.999343017738521	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000218994087159647
CAMB-75929	MN908947.3	4002	C	T	1	1	0	0	0.999909551374819	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-75929	MN908947.3	6196	C	T	0.034	0.021	2.9e-15	3.4e-10	0.0274983232729712	CCT	ORF1ab:nsp3	P1159P	C3477T	CCC>CCT	Synonymous	ORF1ab:nsp3	0.972278113123184
CAMB-75938	MN908947.3	11074	C	INS	0.073	0.12	3.2e-21	4.9e-39	0.0928915321438686	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.892778249787596
CAMB-75938	MN908947.3	11074	C	T	0.012	0.013	2.2e-07	2.4e-07	0.0124988199754555	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.892778249787596
CAMB-75938	MN908947.3	11083	G	-	0.18	0.11	4.7e-83	1.2e-47	0.149581481864214	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.44459371017189e-05
CAMB-75938	MN908947.3	11083	G	T	0.82	0.89	0	0	0.850263511418828	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.44459371017189e-05
CAMB-75938	MN908947.3	11753	C	T	1	1	5.3e-217	2.5e-200	1	CCC	ORF1ab:nsp6	P261S	C781T	CCA>TCA	Missense	ORF1ab:nsp6	0
CAMB-75938	MN908947.3	11983	A	G	0.0084	0.016	9.7e-06	4.2e-09	0.0119815165682974	AAG	ORF1ab:nsp7	E47E	A141G	GAA>GAG	Synonymous	ORF1ab:nsp7	0.987936698335673
CAMB-75938	MN908947.3	12410	A	G	0.066	0.028	3.7e-30	6.4e-14	0.0453974086250242	TAT	ORF1ab:nsp8	I107V	A319G	ATC>GTC	Missense	ORF1ab:nsp8	0.954602591374976
CAMB-75938	MN908947.3	14805	C	T	1	1	0	0	0.999828064745904	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000122810895782674
CAMB-75938	MN908947.3	16466	C	T	0.0062	0.019	0.004	2e-06	0.0134878090956251	CCA	ORF1ab:helicase	P77L	C230T	CCA>CTA	Missense	ORF1ab:helicase	0.986339270274944
CAMB-75938	MN908947.3	17065	T	C	0.031	0.025	1.1e-15	5.7e-13	0.0278939715915446	GTA	ORF1ab:helicase	Y277H	T829C	TAT>CAT	Missense	ORF1ab:helicase	0.972061290683369
CAMB-75938	MN908947.3	19032	C	T	0.032	0.068	4.8e-16	2.4e-31	0.0518774703557312	ACA	ORF1ab:3'-to-5'-exonuclease	D331D	C993T	GAC>GAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.948101943346509
CAMB-75938	MN908947.3	19684	G	T	1	1	0	0	0.999779638607316	AGT	ORF1ab:endoRNAse	V22L	G64T	GTA>TTA	Missense	ORF1ab:endoRNAse	0.000110180696342001
CAMB-75938	MN908947.3	2164	G	A	0.011	0.031	5.6e-07	2e-15	0.0212414444182204	AGA	ORF1ab:nsp2	E453E	G1359A	GAG>GAA	Synonymous	ORF1ab:nsp2	0.97875855558178
CAMB-75938	MN908947.3	23086	C	T	0.0059	0.0078	0.00015	1.9e-05	0.00712538551526109	ACA	S	Y508Y	C1524T	TAC>TAT	Synonymous	GU280_gp02, spike glycoprotein	0.992768265447198
CAMB-75938	MN908947.3	24374	C	T	0.048	0.029	7.1e-22	4.1e-13	0.0433578537429684	ACT	S	L938F	C2812T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.956642146257032
CAMB-75938	MN908947.3	24374	CT	TC	0.0289	0.0145	7.1e-22;6.4e-06	4.1e-13;NA	0.0259255970878096	ACT	S	.	2812-2813-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.956642146257032
CAMB-75938	MN908947.3	26144	G	T	1	1	0	1.7e-205	0.998080614203455	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-75938	MN908947.3	28842	G	T	1	0.99	0	0	0.996898834967731	AGT	N	S190I	G569T	AGT>ATT	Missense	GU280_gp10	0
CAMB-75938	MN908947.3	3709	A	G	0.2	0.2	5.1e-59	3.3e-68	0.201559688062388	TAT	ORF1ab:nsp3	L330L	A990G	TTA>TTG	Synonymous	ORF1ab:nsp3	0.798440311937612
CAMB-75938	MN908947.3	4073	C	T	0.055	0.12	3.1e-25	4.1e-53	0.0862437633642195	TCT	ORF1ab:nsp3	L452F	C1354T	CTT>TTT	Missense	ORF1ab:nsp3	0.913561847988077
CAMB-75938	MN908947.3	583	C	T	0.0069	0.0097	4e-05	2.4e-06	0.00769230769230769	TCC	ORF1ab:leader-protein	V106V	C318T	GTC>GTT	Synonymous	ORF1ab:leader-protein	0.992307692307692
CAMB-75938	MN908947.3	8655	C	T	0.046	0.019	7.1e-21	9.6e-10	0.0303787878787879	TCT	ORF1ab:nsp4	S34F	C101T	TCT>TTT	Missense	ORF1ab:nsp4	0.969621212121212
CAMB-75947	MN908947.3	11075	T	-	0.035	0.03	8.6e-09	2.5e-08	0.033140239795231	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962602721271723
CAMB-75947	MN908947.3	13288	A	G	0.018	0.018	1.1e-09	1.7e-10	0.0180999061975664	GAT	ORF1ab:nsp10	G88G	A264G	GGA>GGG	Synonymous	ORF1ab:nsp10	0.981847247360981
CAMB-75947	MN908947.3	14408	C	T	1	1	0	0	0.999122571149573	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000283041564653769
CAMB-75947	MN908947.3	17687	T	C	0.033	0.036	4.6e-16	1.8e-17	0.0339894272223363	GTT	ORF1ab:helicase	V484A	T1451C	GTT>GCT	Missense	ORF1ab:helicase	0.965433175939232
CAMB-75947	MN908947.3	23403	A	G	1	1	0	0	0.99864979746962	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.50112516877532e-05
CAMB-75947	MN908947.3	241	C	T	1	1	0	0	0.999140231779183	TCG	NA	NA	NA	NA	NA	NA	0.000125382865535833
CAMB-75947	MN908947.3	2624	G	A	0.0074	0.0065	2.2e-05	4.6e-05	0.00712896953985742	CGG	ORF1ab:nsp2	G607R	G1819A	GGG>AGG	Missense	ORF1ab:nsp2	0.992582991286815
CAMB-75947	MN908947.3	27384	T	C	0.031	0.03	1.1e-14	8.3e-15	0.0307029496113469	ATT	ORF6	D61D	T183C	GAT>GAC	Synonymous	GU280_gp06	0.969271096923217
CAMB-75947	MN908947.3	27923	C	T	0.019	0.017	1.6e-09	9.4e-09	0.0184729802674983	TCA	ORF8	I10I	C30T	ATC>ATT	Synonymous	GU280_gp09	0.981467042523841
CAMB-75947	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999462437844376	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	7.55144421370587e-05
CAMB-75947	MN908947.3	3037	C	T	1	1	0	0	0.999316083437821	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.7995364565523e-05
CAMB-75947	MN908947.3	6780	T	C	0.12	0.12	2.6e-53	2.5e-53	0.120415249945743	TTC	ORF1ab:nsp3	F1354S	T4061C	TTC>TCC	Missense	ORF1ab:nsp3	0.879584750054257
CAMB-75956	MN908947.3	14408	C	T	1	1	0	0	0.999605878047407	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.0002815156804234
CAMB-75956	MN908947.3	23403	A	G	1	1	0	0	0.999947116062615	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.28839373854181e-05
CAMB-75956	MN908947.3	241	C	T	1	1	0	0	1	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-75956	MN908947.3	27128	C	T	1	1	0	0	0.999800039992002	GCA	M	G202G	C606T	GGC>GGT	Synonymous	GU280_gp05	0
CAMB-75956	MN908947.3	28881	G	A	1	1	0	0	0.99969960949234	AGG	N	R203K	G608A	AGG>AAG	Missense	GU280_gp10	0
CAMB-75956	MN908947.3	28881	GGG	AAC	0.996666666666667	1	0;0;0	0;0;0	0.999730603448276	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-75956	MN908947.3	28883	G	C	0.99	1	0	0	0.997730711043873	GGG	N	G204R	G610C	GGA>CGA	Missense	GU280_gp10	0
CAMB-75956	MN908947.3	3037	C	T	1	1	0	0	0.999286478772743	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75956	MN908947.3	313	C	T	1	1	0	0	0.999574014909478	TCA	ORF1ab:leader-protein	L16L	C48T	CTC>CTT	Synonymous	ORF1ab:leader-protein	0
CAMB-75956	MN908947.3	6813	C	T	0.79	0.011	4.6e-135	0.00049	0.287058823529412	ACT	ORF1ab:nsp3	T1365I	C4094T	ACT>ATT	Missense	ORF1ab:nsp3	0.712941176470588
CAMB-75974	MN908947.3	11071	G	INS	0.03	0.031	3e-09	1.2e-09	0.0306728193265906	TGT	ORF1ab:nsp6	.	98-99-insfrshift	.	no-SNV	ORF1ab:nsp6	0.968583668700506
CAMB-75974	MN908947.3	11074	C	-	0.018	0.017	1.9e-18	1.7e-15	0.0175054126841633	TCT	ORF1ab:nsp6	.	102-102-delfrshift	.	no-SNV	ORF1ab:nsp6	0.783413423456725
CAMB-75974	MN908947.3	11074	C	INS	0.095	0.092	1.9e-37	1e-29	0.0936130326873317	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.783413423456725
CAMB-75974	MN908947.3	11074	C	T	0.1	0.11	5.4e-90	9.8e-78	0.105441727834398	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.783413423456725
CAMB-75974	MN908947.3	11083	G	-	0.15	0.12	7.7e-64	3.2e-52	0.13676521395785	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.46779527170426e-05
CAMB-75974	MN908947.3	11083	G	T	0.85	0.88	0	0	0.862975667538621	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.46779527170426e-05
CAMB-75974	MN908947.3	12529	A	G	0.13	0.14	7.4e-61	6.4e-62	0.133190057933097	CAT	ORF1ab:nsp8	T146T	A438G	ACA>ACG	Synonymous	ORF1ab:nsp8	0.866772565875537
CAMB-75974	MN908947.3	14805	C	T	1	1	0	0	0.999271303652055	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000114305309481625
CAMB-75974	MN908947.3	17750	C	T	0.82	0.83	0	0	0.821942247562994	GCT	ORF1ab:helicase	A505V	C1514T	GCT>GTT	Missense	ORF1ab:helicase	0.177873827478389
CAMB-75974	MN908947.3	18555	C	T	0.092	0.089	1.9e-41	2.8e-40	0.09030002027164	ACA	ORF1ab:3'-to-5'-exonuclease	D172D	C516T	GAC>GAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.909112102169065
CAMB-75974	MN908947.3	21575	C	T	0.019	0.016	1.6e-05	0.00029	0.0177339901477833	TCT	S	L5F	C13T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.981609195402299
CAMB-75974	MN908947.3	2480	A	G	1	1	0	0	0.999870951090463	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000129048909536714
CAMB-75974	MN908947.3	2558	C	T	1	1	0	0	0.999673861480076	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000266840607210626
CAMB-75974	MN908947.3	26144	G	T	1	1	0	0	0.999497627686296	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000446553167736534
CAMB-75974	MN908947.3	28883	G	A	0.15	0.14	2.2e-65	8e-63	0.143959234798451	GGG	N	G204R	G610A	GGA>AGA	Missense	GU280_gp10	0.855983830562514
CAMB-75974	MN908947.3	29013	C	T	0.83	0.84	0	0	0.832095589760611	ACT	N	T247I	C740T	ACT>ATT	Missense	GU280_gp10	0.167748827946729
CAMB-75974	MN908947.3	29414	G	A	0.2	0.15	1e-78	8.8e-51	0.1854031783402	AGC	N	A381T	G1141A	GCC>ACC	Missense	GU280_gp10	0.81430253090053
CAMB-75974	MN908947.3	3728	G	A	0.0079	0.0082	2.4e-05	1.6e-05	0.00803180269349343	TGG	ORF1ab:nsp3	G337S	G1009A	GGT>AGT	Missense	ORF1ab:nsp3	0.991968197306507
CAMB-75974	MN908947.3	4185	G	A	0.87	0.86	0	0	0.864681699264981	GGT	ORF1ab:nsp3	G489D	G1466A	GGT>GAT	Missense	ORF1ab:nsp3	0.135231095054192
CAMB-75983	MN908947.3	11074	C	INS	0.024	0.03	6.9e-05	2.3e-06	0.0266311938809445	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.970522115064849
CAMB-75983	MN908947.3	11074	CT	-	0.0218	0.014795	3.8e-05;7.1e-10	0.036;7.4e-08	0.0199268398536797	TCT	ORF1ab:nsp6	.	102-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.970522115064849
CAMB-75983	MN908947.3	11075	T	-	0.04	0.029	7.1e-10	7.4e-08	0.035290428966254	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959751027707458
CAMB-75983	MN908947.3	11893	G	T	1	1	0	0	0.999785539514344	TGC	ORF1ab:nsp7	L17F	G51T	TTG>TTT	Missense	ORF1ab:nsp7	9.74820389343264e-06
CAMB-75983	MN908947.3	12114	C	T	0.013	0.012	1.6e-07	2.7e-07	0.0124866788651398	TCC	ORF1ab:nsp8	S8F	C23T	TCC>TTC	Missense	ORF1ab:nsp8	0.987442945328052
CAMB-75983	MN908947.3	14408	C	T	1	0.99	0	0	0.996769688505677	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000510049183314105
CAMB-75983	MN908947.3	16118	A	C	0.013	0.01	2.7e-07	4e-06	0.0113650956722743	GAT	ORF1ab:RNA-dependent-RNA-polymerase	D884A	A2651C	GAT>GCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.988579867544809
CAMB-75983	MN908947.3	23403	A	G	1	1	0	0	0.999349451299498	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.39883967707189e-05
CAMB-75983	MN908947.3	241	C	T	1	1	0	0	0.998443579766537	TCG	NA	NA	NA	NA	NA	NA	0.000181582360570687
CAMB-75983	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0302972972972973	0.0303243243243243	0.0042;4e-04;0.0022;0.0019;0.0023;0.00023;0.00043;3.6e-05;3.5e-05;7.5e-06;2.9e-05;2.5e-05;3.6e-05;2.7e-05;2.6e-05;3.7e-05;2.6e-05;3.8e-05;2.3e-05;2.8e-05;2.1e-05;4.8e-05;2.2e-05;3e-05;2.7e-05;1.9e-05;3.9e-05;2.2e-05;7.1e-06;2.8e-05;3.9e-05;3.5e-05;2.4e-05;3.3e-05;1.1e-05;2.2e-05;2e-05	0.00063;1e-04;5e-04;0.00049;0.00086;3.3e-05;0.00011;4.1e-05;4.2e-05;2.2e-05;2.7e-05;2.2e-05;3.8e-05;2.8e-05;2.6e-05;4.3e-05;2.4e-05;4.8e-05;3.4e-05;3.1e-05;3.1e-05;5.3e-05;3.4e-05;4.1e-05;3.3e-05;2e-05;4.7e-05;3.3e-05;2.3e-05;2.9e-05;4.6e-05;4.3e-05;1.8e-05;3.9e-05;1.3e-05;3.5e-05;2.3e-05	0.0314235722569225	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.979978774643863
CAMB-75983	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99901902243453	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000187327307638271
CAMB-75983	MN908947.3	29332	G	T	1	1	0	0	0.997765040366108	TGA	N	L353L	G1059T	CTG>CTT	Synonymous	GU280_gp10	1.52038070332811e-05
CAMB-75983	MN908947.3	29744	G	A	0.47	0.47	2.7e-243	2.6e-230	0.468552174800899	CGG	NA	NA	NA	NA	NA	NA	0.530937308556259
CAMB-75983	MN908947.3	3037	C	T	1	1	0	0	0.999247809244424	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000150438151115123
CAMB-75983	MN908947.3	522	TT	-	0.039	0.0385	5.9e-06;0.00018	6.3e-06;1e-04	0.0388815518539031	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.952784361923156
CAMB-75992	MN908947.3	11074	C	INS	0.11	0.12	2.8e-41	3.5e-39	0.115111728778847	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.880920162381597
CAMB-75992	MN908947.3	11083	G	-	0.16	0.13	8.5e-70	2e-57	0.146644106034969	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	5.12741629492899e-05
CAMB-75992	MN908947.3	11083	G	T	0.84	0.87	0	0	0.853219162863833	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	5.12741629492899e-05
CAMB-75992	MN908947.3	14805	C	T	1	1	0	0	0.998424221959593	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000600296396345696
CAMB-75992	MN908947.3	15535	G	T	0.024	0.024	3.5e-12	1.8e-12	0.0237172446969766	AGC	ORF1ab:RNA-dependent-RNA-polymerase	A690S	G2068T	GCT>TCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.976064916086518
CAMB-75992	MN908947.3	2480	A	G	1	1	0	0	0.999687226323033	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000312773676967346
CAMB-75992	MN908947.3	2558	C	T	1	1	0	0	0.999171585378482	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000103551827689759
CAMB-75992	MN908947.3	26144	G	T	1	1	0	0	0.999705674593831	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000294325406169061
CAMB-75992	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.02696875	0.0285625	0.00026;0.00055;0.00026;0.00026;6e-05;0.00015;0.00013;0.00022;0.00018;2e-04;0.00029;0.00015;0.00025;0.00017;0.00018;0.00017;3e-04;0.00017;0.00021;0.00017;0.00013;0.00024;0.00015;6.9e-05;0.00019;0.00025;0.00024;0.00018;0.00026;1e-04;0.00015;0.00011	0.00014;0.00043;0.00011;0.00011;5.2e-05;6.9e-05;5.6e-05;9.6e-05;7.8e-05;8.2e-05;0.00013;6.7e-05;0.00012;7.4e-05;7.8e-05;6.9e-05;0.00013;8.1e-05;9.9e-05;8e-05;5.4e-05;0.00012;7.8e-05;1.9e-05;8e-05;0.00011;0.00011;4.2e-05;9.3e-05;3.3e-05;6.8e-05;4.3e-05	0.0272386375473074	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.9731552189913
CAMB-75992	MN908947.3	29013	C	T	1	1	0	0	0.999149541525568	ACT	N	T247I	C740T	ACT>ATT	Missense	GU280_gp10	0.000170091694886425
CAMB-75992	MN908947.3	4185	G	A	1	1	0	0	0.999711496850507	GGT	ORF1ab:nsp3	G489D	G1466A	GGT>GAT	Missense	ORF1ab:nsp3	8.01397637479765e-05
CAMB-75992	MN908947.3	6777	A	INS	0.012	0.014	3.2e-07	1.4e-07	0.0130298941986793	TAT	ORF1ab:nsp3	.	4057-4058-insfrshift	.	no-SNV	ORF1ab:nsp3	0.986402045018817
CAMB-75992	MN908947.3	6781	C	T	1	1	0	0	0.997488893181379	TCT	ORF1ab:nsp3	F1354F	C4062T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000579486188912498
CAMB-759A1	MN908947.3	11074	C	-	0.0018	0.012	0.0032	1.4e-09	0.00538702607484484	TCT	ORF1ab:nsp6	.	102-102-delfrshift	.	no-SNV	ORF1ab:nsp6	0.888777370393888
CAMB-759A1	MN908947.3	11074	C	INS	0.089	0.11	1.7e-29	5.6e-35	0.0982364146576268	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.888777370393888
CAMB-759A1	MN908947.3	11083	G	-	0.097	0.13	6.6e-42	4.9e-57	0.108641466294346	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	7.49639236117618e-05
CAMB-759A1	MN908947.3	11083	G	T	0.9	0.87	0	0	0.891096159973013	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	7.49639236117618e-05
CAMB-759A1	MN908947.3	14805	C	T	1	1	0	0	0.999916821471151	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	2.77261762830288e-05
CAMB-759A1	MN908947.3	15193	G	A	0.0051	0.0082	0.00015	1.4e-05	0.0063006300630063	AGC	ORF1ab:RNA-dependent-RNA-polymerase	A576T	G1726A	GCT>ACT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993699369936994
CAMB-759A1	MN908947.3	15222	C	T	0.008	0.0013	4.7e-06	0.0077	0.00529277131413313	TCT	ORF1ab:RNA-dependent-RNA-polymerase	F585F	C1755T	TTC>TTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.994611863436964
CAMB-759A1	MN908947.3	17029	A	G	0.056	0.048	2.6e-26	1.3e-22	0.0518332966306981	CAA	ORF1ab:helicase	N265D	A793G	AAT>GAT	Missense	ORF1ab:helicase	0.948139176392865
CAMB-759A1	MN908947.3	18591	C	A	0.017	0.0088	1.5e-09	3.6e-06	0.0122784599144397	TCT	ORF1ab:3'-to-5'-exonuclease	V184V	C552A	GTC>GTA	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.98772154008556
CAMB-759A1	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-759A1	MN908947.3	25228	T	C	0.0098	0.0044	2.6e-06	0.00048	0.00738481297158452	CTG	S	A1222A	T3666C	GCT>GCC	Synonymous	GU280_gp02, spike glycoprotein	0.99245464761599
CAMB-759A1	MN908947.3	2558	C	T	1	1	0	0	0.999746386000507	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000253613999492772
CAMB-759A1	MN908947.3	25906	G	T	1	1	0	0	0.999821300929235	AGG	ORF3a	G172C	G514T	GGT>TGT	Missense	GU280_gp03	0.000178699070764832
CAMB-759A1	MN908947.3	26144	G	T	1	1	1.3e-280	4.6e-142	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-759A1	MN908947.3	26822	C	T	0.019	0.013	2e-10	4.7e-08	0.017008087101545	TCA	M	F100F	C300T	TTC>TTT	Synonymous	GU280_gp05	0.982960445577268
CAMB-759A1	MN908947.3	27047	G	A	0.0022	0.012	0.008	4.1e-07	0.00533725247524753	CGC	M	T175T	G525A	ACG>ACA	Synonymous	GU280_gp05	0.994662747524752
CAMB-759A1	MN908947.3	28076	C	T	0.017	0.037	6.1e-08	1.4e-13	0.023046357615894	GCG	ORF8	C61C	C183T	TGC>TGT	Synonymous	GU280_gp09	0.976953642384106
CAMB-759A1	MN908947.3	28331	C	T	0.0034	0.021	0.0013	2.4e-11	0.0105714472736794	ACC	N	P20S	C58T	CCC>TCC	Missense	GU280_gp10	0.989395823787393
CAMB-759A1	MN908947.3	29013	C	T	1	1	0	0	0.999821098455483	ACT	N	T247I	C740T	ACT>ATT	Missense	GU280_gp10	0.000119267696344445
CAMB-759A1	MN908947.3	4185	G	A	1	1	0	0	0.999903781391321	GGT	ORF1ab:nsp3	G489D	G1466A	GGT>GAT	Missense	ORF1ab:nsp3	9.62186086789185e-05
CAMB-759B0	MN908947.3	11074	C	INS	0.58	0.58	0	0	0.578915565238853	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.416539715231619
CAMB-759B0	MN908947.3	11083	G	T	1	1	0	0	0.996023947717198	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	4.57017503770394e-05
CAMB-759B0	MN908947.3	13627	G	T	1	1	0	0	0.999658384385889	TGA	ORF1ab:RNA-dependent-RNA-polymerase	D54Y	G160T	GAC>TAC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	1.13871871370334e-05
CAMB-759B0	MN908947.3	14805	C	T	1	1	0	0	0.999961852445258	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	1.90737773708705e-05
CAMB-759B0	MN908947.3	15540	C	T	1	1	0	0	0.999843854909982	TCA	ORF1ab:RNA-dependent-RNA-polymerase	V691V	C2073T	GTC>GTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	4.68435270052933e-05
CAMB-759B0	MN908947.3	18395	C	T	0.21	0.21	8.7e-99	1.8e-98	0.209206922387216	GCT	ORF1ab:3'-to-5'-exonuclease	A119V	C356T	GCT>GTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.790092978124962
CAMB-759B0	MN908947.3	18559	C	T	0.01	0.0065	1.4e-06	5.6e-05	0.008247321461445	ACT	ORF1ab:3'-to-5'-exonuclease	L174F	C520T	CTT>TTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.991691314539586
CAMB-759B0	MN908947.3	19704	T	C	1	1	0	0	0.999693796313308	ATA	ORF1ab:endoRNAse	N28N	T84C	AAT>AAC	Synonymous	ORF1ab:endoRNAse	0.000306203686692388
CAMB-759B0	MN908947.3	25681	G	A	1	1	0	0	0.999967646963668	CGT	ORF3a	V97I	G289A	GTT>ATT	Missense	GU280_gp03	0
CAMB-759B0	MN908947.3	26144	G	T	1	1	0	0	0.99978072579761	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-759B0	MN908947.3	28338	A	G	1	1	0	0	0.999795165915608	GAT	N	D22G	A65G	GAT>GGT	Missense	GU280_gp10	8.19336337566571e-05
CAMB-759B0	MN908947.3	29723	ACATTTTCACCGAGGCCACGCGGAGTACGATCGAGTGTACAGTGAACAATGCT	-	1	1	0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0	0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0	1	CAC	NA	NA	NA	NA	NA	NA	0.000387259173201665
CAMB-759B0	MN908947.3	4182	C	T	0.097	0.12	1e-44	3.5e-56	0.106919452618715	GCT	ORF1ab:nsp3	A488V	C1463T	GCT>GTT	Missense	ORF1ab:nsp3	0.893064466849985
CAMB-759CF	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999360341151386	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0
CAMB-759CF	MN908947.3	17310	T	C	0.037	0.0018	5.4e-18	0.0092	0.0183945422086202	GTA	ORF1ab:helicase	C358C	T1074C	TGT>TGC	Synonymous	ORF1ab:helicase	0.98160545779138
CAMB-759CF	MN908947.3	20270	C	T	1	1	1.8e-24	0	1	GCT	ORF1ab:endoRNAse	A217V	C650T	GCT>GTT	Missense	ORF1ab:endoRNAse	0
CAMB-759CF	MN908947.3	24904	C	T	1	1	0	0	0.999930201717038	TCA	S	I1114I	C3342T	ATC>ATT	Synonymous	GU280_gp02, spike glycoprotein	6.97982829622391e-05
CAMB-759CF	MN908947.3	29683	A	T	1	1	4.3e-295	1.8e-271	1	TAA	NA	NA	NA	NA	NA	NA	0
CAMB-759DE	MN908947.3	12473	C	T	0.035	0.03	3.4e-17	1.3e-14	0.0336902956785444	ACT	ORF1ab:nsp8	L128L	C382T	CTA>TTA	Synonymous	ORF1ab:nsp8	0.966262319939348
CAMB-759DE	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999495662699213	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000201755270856451
CAMB-759DE	MN908947.3	18486	C	T	1	1	0	0	0.999806744613006	TCA	ORF1ab:3'-to-5'-exonuclease	L149L	C447T	CTC>CTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	9.66276934969562e-05
CAMB-759DE	MN908947.3	23245	TTTCCAACAA	-	0.0383	0.0092189	4.6e-18;1.6e-18;8e-18;2.4e-18;2.5e-19;3e-18;2.6e-18;2e-18;1.9e-20;8e-19	NA;NA;NA;0.47;1.4e-15;8.8e-15;1.2e-14;0.47;NA;NA	0.0221440151844676	CTT	S	.	1683-1692-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.978177002360799
CAMB-759DE	MN908947.3	25770	G	C	0.18	0.12	4.6e-53	1.8e-43	0.143901068015739	GGC	ORF3a	R126S	G378C	AGG>AGC	Missense	GU280_gp03	0.856098931984261
CAMB-759DE	MN908947.3	29032	G	A	1	1	0	0	0.999851841874874	AGG	N	E253E	G759A	GAG>GAA	Synonymous	GU280_gp10	0.000107751363728197
CAMB-759DE	MN908947.3	7691	C	T	0.037	0.1	3.8e-16	5.3e-30	0.0479274611398964	ACA	ORF1ab:nsp3	Q1658*	C4972T	CAG>TAG	Nonsense	ORF1ab:nsp3	0.952072538860104
CAMB-759DE	MN908947.3	9228	C	T	0.039	0.0063	7.6e-19	5.2e-05	0.0293410293410293	ACT	ORF1ab:nsp4	T225I	C674T	ACT>ATT	Missense	ORF1ab:nsp4	0.970615243342516
CAMB-759ED	MN908947.3	11075	T	-	0.047	0.046	2.2e-11	4.2e-12	0.0466376162996114	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.947997225820804
CAMB-759ED	MN908947.3	14408	C	T	0.99	0.99	0	0	0.994095793059859	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000292897994419522
CAMB-759ED	MN908947.3	18788	C	T	1	1	0	0	0.999555536742296	ACA	ORF1ab:3'-to-5'-exonuclease	T250I	C749T	ACA>ATA	Missense	ORF1ab:3'-to-5'-exonuclease	0.000232814087368778
CAMB-759ED	MN908947.3	19839	T	C	1	1	0	0	0.998971810470397	ATA	ORF1ab:endoRNAse	N73N	T219C	AAT>AAC	Synonymous	ORF1ab:endoRNAse	0.000171364921600548
CAMB-759ED	MN908947.3	23403	A	G	1	1	0	0	0.999239131836529	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.15842822691926e-05
CAMB-759ED	MN908947.3	241	C	T	1	1	0	0	0.997998089920658	TCG	NA	NA	NA	NA	NA	NA	0.000808110490743462
CAMB-759ED	MN908947.3	25183	G	T	0.012	0.015	3.8e-07	1.2e-08	0.0130314121385191	AGC	S	E1207D	G3621T	GAG>GAT	Missense	GU280_gp02, spike glycoprotein	0.986847926637976
CAMB-759ED	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0335789473684211	0.0458947368421053	0.00061;3e-05;0.00045;0.00046;0.00074;6.2e-05;0.00014;9.4e-06;9e-06;1.8e-06;6e-06;5.2e-06;8e-06;6.8e-06;6e-06;9.2e-06;5.6e-06;1e-05;6.2e-06;7.6e-06;5.7e-06;1.3e-05;4.7e-06;8.1e-06;7.1e-06;4.7e-06;1e-05;5.7e-06;2.8e-06;7.2e-06;1e-05;8.9e-06;4.8e-06;7.4e-06;1.8e-06;5.2e-06;4.4e-06;0.0024	3.1e-05;5.5e-07;5.2e-06;5.3e-06;1e-05;3.3e-08;1.9e-07;1.7e-08;1.8e-08;6.7e-09;9e-09;7.4e-09;1.8e-08;1.1e-08;1.4e-08;2.6e-08;8.5e-09;2.2e-08;1.2e-08;1.1e-08;8.9e-09;2.5e-08;1.2e-08;1.7e-08;1.2e-08;6.6e-09;2e-08;1.1e-08;1.7e-08;9.8e-09;2.1e-08;1.4e-08;2.6e-09;1.1e-08;2.1e-09;1.8e-08;1.1e-08;2e-04	0.0389243876464324	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.975437991538574
CAMB-759ED	MN908947.3	27359	A	T	0.012	0.014	4.8e-07	7.5e-09	0.0121404787678647	GAT	ORF6	D53V	A158T	GAT>GTT	Missense	GU280_gp06	0.987818413516217
CAMB-759ED	MN908947.3	28001	G	T	0.0086	0.0083	1.9e-05	4.8e-05	0.00851121318562551	CGT	ORF8	P36P	G108T	CCG>CCT	Synonymous	GU280_gp09	0.990813293704404
CAMB-759ED	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998308009881222	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	3.8125738686187e-05
CAMB-759ED	MN908947.3	2973	C	A	0.0066	0.01	4.3e-05	9.1e-07	0.00756975618343456	GCT	ORF1ab:nsp3	A85D	C254A	GCT>GAT	Missense	ORF1ab:nsp3	0.990449784349969
CAMB-759ED	MN908947.3	3037	C	T	1	1	0	0	0.99967516647718	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000108277840939852
CAMB-759ED	MN908947.3	3871	G	T	0.0021	0.0073	0.008	3.2e-05	0.00351353509542442	AGA	ORF1ab:nsp3	K384N	G1152T	AAG>AAT	Missense	ORF1ab:nsp3	0.99636668529905
CAMB-759ED	MN908947.3	522	TT	-	0.057	0.055	1.4e-08;2.1e-06	9e-09;2.1e-06	0.0564932347607756	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.931256057723373
CAMB-759ED	MN908947.3	6828	C	T	0.0083	0.011	1.1e-05	1.5e-06	0.00946848678478071	TCT	ORF1ab:nsp3	S1370F	C4109T	TCT>TTT	Missense	ORF1ab:nsp3	0.990531513215219
CAMB-759FC	MN908947.3	1059	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0
CAMB-759FC	MN908947.3	13914	T	G	0.0098	0.0016	1.8e-06	0.0036	0.00413683373110581	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.995704057279236
CAMB-759FC	MN908947.3	14408	C	T	1	1	0	0	0.999670157499794	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000247381875154614
CAMB-759FC	MN908947.3	23403	A	G	1	1	0	0	1	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-759FC	MN908947.3	241	C	T	1	1	0	0	0.999704032556419	TCG	NA	NA	NA	NA	NA	NA	7.39918608953015e-05
CAMB-759FC	MN908947.3	25563	G	T	1	1	0	0	0.999928031666067	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0
CAMB-759FC	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-759FC	MN908947.3	688	G	A	0.13	0.33	2e-61	2.2e-162	0.204535683576956	AGT	ORF1ab:leader-protein	K141K	G423A	AAG>AAA	Synonymous	ORF1ab:leader-protein	0.789552880481513
CAMB-759FC	MN908947.3	8313	T	INS	0.0022	0.0071	0.0036	1.7e-05	0.00564794477565108	ATG	ORF1ab:nsp3	.	5593-5594-insfrshift	.	no-SNV	ORF1ab:nsp3	0.994352055224349
CAMB-759FC	MN908947.3	8315	ACACC	-	0.00218	0.0071	0.0058;0.0059;0.0063;0.013;0.005	2.5e-05;2.6e-05;2.6e-05;5.8e-05;2.3e-05	0.00563380281690141	GAC	ORF1ab:nsp3	.	5596-5600-delfrshift	.	no-SNV	ORF1ab:nsp3	0.994051346274264
CAMB-75A08	MN908947.3	10282	G	A	1	1	0	0	0.999875628520157	GGG	ORF1ab:3C-like-proteinase	R76R	G228A	AGG>AGA	Synonymous	ORF1ab:3C-like-proteinase	5.330206278983e-05
CAMB-75A08	MN908947.3	11075	T	-	0.055	0.017	3e-13	5.3e-05	0.0362180506946654	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.963580443313183
CAMB-75A08	MN908947.3	12237	T	G	0.024	0.018	4.9e-12	1.3e-09	0.0212360906287706	TTT	ORF1ab:nsp8	F49C	T146G	TTT>TGT	Missense	ORF1ab:nsp8	0.978629843142512
CAMB-75A08	MN908947.3	14408	C	T	1	1	0	0	0.99960974169119	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000326973177651911
CAMB-75A08	MN908947.3	1676	G	T	0.01	0.0081	8.9e-07	8.6e-06	0.00930584328039196	TGA	ORF1ab:nsp2	E291*	G871T	GAA>TAA	Nonsense	ORF1ab:nsp2	0.990694156719608
CAMB-75A08	MN908947.3	20268	A	G	1	1	1.4e-259	2.6e-214	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-75A08	MN908947.3	21982	TTTGGGTGT	-	0.0373333333333333	0.033	3.6e-07;1.3e-06;1.1e-06;2.1e-07;1.2e-06;2.3e-06;1.6e-06;8.2e-07;8.6e-07	4.3e-06;1.3e-05;1.2e-05;1.5e-09;1.3e-05;2e-05;1.7e-05;8.8e-06;1.2e-05	0.0339473498482603	TTT	S	.	420-428-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.965903452186858
CAMB-75A08	MN908947.3	23403	A	G	1	1	0	0	0.999826726629754	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000126016996542409
CAMB-75A08	MN908947.3	23855	C	T	0.016	0.011	2.2e-08	2.8e-06	0.0132412204951065	CCG	S	R765C	C2293T	CGT>TGT	Missense	GU280_gp02, spike glycoprotein	0.986726795880509
CAMB-75A08	MN908947.3	241	C	T	1	1	0	0	0.999600473285493	TCG	NA	NA	NA	NA	NA	NA	0.000107564884675077
CAMB-75A08	MN908947.3	24138	C	T	0.0086	0.0065	1.9e-05	0.00015	0.00753165649370008	ACT	S	T859I	C2576T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.992452652555271
CAMB-75A08	MN908947.3	25855	G	T	0.0072	0.0098	0.00012	9.6e-06	0.00863092027187399	CGA	ORF3a	D155Y	G463T	GAC>TAC	Missense	GU280_gp03	0.991045420217931
CAMB-75A08	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0313243243243243	0.0406756756756757	0.0017;0.00011;0.0014;0.0013;0.0022;3.2e-06;6.5e-06;3e-05;2.8e-05;4.6e-06;2.3e-05;1.9e-05;2.9e-05;2.1e-05;2.4e-05;4e-05;1.6e-05;3.2e-05;2e-05;2.4e-05;2.7e-05;4.2e-05;2e-05;2.9e-05;2.4e-05;1.8e-05;3.6e-05;1.9e-05;8.7e-06;2.3e-05;3.4e-05;3.2e-05;2.9e-05;3.6e-05;8.1e-06;1.7e-05;1.8e-05	1.7e-05;6.1e-07;9.3e-06;1.1e-05;2.6e-05;4.6e-06;9.9e-06;5.4e-07;5.4e-07;2.5e-07;3.2e-07;2.9e-07;5.2e-07;3.8e-07;4.3e-07;7.7e-07;2.7e-07;6.4e-07;3.8e-07;3.8e-07;3.5e-07;7.4e-07;3.1e-07;5.1e-07;3.9e-07;2.1e-07;5.9e-07;3.7e-07;5.1e-08;4.3e-07;6.1e-07;5.6e-07;1.9e-07;5.7e-07;1e-07;3.8e-07;2.6e-07	0.0366127802646754	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.974723045716961
CAMB-75A08	MN908947.3	28411	C	T	0.059	0.016	1.4e-26	1.4e-08	0.0393234562335827	CCA	N	P46P	C138T	CCC>CCT	Synonymous	GU280_gp10	0.952874270704199
CAMB-75A08	MN908947.3	28763	G	C	0.015	0.0066	2.2e-08	3.1e-05	0.0108114601477566	AGG	N	G164R	G490C	GGA>CGA	Missense	GU280_gp10	0.988888221514806
CAMB-75A08	MN908947.3	3037	C	T	1	1	0	0	0.999647266313933	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.81834215167549e-05
CAMB-75A08	MN908947.3	3176	C	T	1	1	0	0	0.999763909656095	ACC	ORF1ab:nsp3	P153S	C457T	CCT>TCT	Missense	ORF1ab:nsp3	9.44361375619737e-05
CAMB-75A08	MN908947.3	522	TT	-	0.018	0.0385	0.0032;0.038	1.4e-05;3.9e-05	0.0274821286735504	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.967883091149273
CAMB-75A08	MN908947.3	7252	G	-	0.031	0.024	2.3e-07	1.9e-06	0.0276381909547739	TGG	ORF1ab:nsp3	.	4533-4533-delfrshift	.	no-SNV	ORF1ab:nsp3	0.972361809045226
CAMB-75A08	MN908947.3	9365	C	T	0.022	0.0085	2.4e-11	5e-06	0.0151014961017068	ACT	ORF1ab:nsp4	L271L	C811T	CTA>TTA	Synonymous	ORF1ab:nsp4	0.984758024864789
CAMB-75A08	MN908947.3	9430	C	T	0.012	0.013	4.2e-06	1.9e-06	0.0122294693151497	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.98777053068485
CAMB-75A17	MN908947.3	11074	C	INS	0.097	0.098	6.9e-40	4e-35	0.0975373482726424	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.898366013071895
CAMB-75A17	MN908947.3	11083	G	-	0.18	0.18	1.2e-80	1.5e-79	0.180444587628866	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.14776632302406e-05
CAMB-75A17	MN908947.3	11083	G	T	0.82	0.82	0	0	0.819372852233677	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.14776632302406e-05
CAMB-75A17	MN908947.3	12928	A	G	0.012	0.011	3.9e-07	8.7e-07	0.0116044242838501	AAG	ORF1ab:nsp9	K81K	A243G	AAA>AAG	Synonymous	ORF1ab:nsp9	0.988193624557261
CAMB-75A17	MN908947.3	13348	G	T	1	1	0	0	0.999582463465553	TGG	ORF1ab:nsp10	V108V	G324T	GTG>GTT	Synonymous	ORF1ab:nsp10	0.000144690878273631
CAMB-75A17	MN908947.3	14805	C	T	1	1	0	0	0.999539261502008	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000205686829460936
CAMB-75A17	MN908947.3	22846	T	C	1	1	0	0	0.999510847291813	ATT	S	D428D	T1284C	GAT>GAC	Synonymous	GU280_gp02, spike glycoprotein	0.000118983091180709
CAMB-75A17	MN908947.3	2370	C	T	1	1	0	0	0.999764949229033	GCC	ORF1ab:nsp2	A522V	C1565T	GCC>GTC	Missense	ORF1ab:nsp2	0.000141030462579917
CAMB-75A17	MN908947.3	2480	A	G	1	1	0	0	0.999442119944212	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000325430032543003
CAMB-75A17	MN908947.3	2558	C	T	1	1	0	0	0.999851170543674	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	5.95317825303984e-05
CAMB-75A17	MN908947.3	26144	G	T	1	1	0	0	0.999778693739799	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	5.53265650502089e-05
CAMB-75A17	MN908947.3	5481	C	T	0.029	0.026	2e-13	4.6e-12	0.0272279076716217	GCC	ORF1ab:nsp3	A921V	C2762T	GCC>GTC	Missense	ORF1ab:nsp3	0.972772092328378
CAMB-75A26	MN908947.3	11074	C	INS	0.092	0.1	2.8e-31	4.5e-39	0.0977949956955206	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.899289066622233
CAMB-75A26	MN908947.3	11083	G	-	0.18	0.17	2.4e-78	1.5e-73	0.170513353227817	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.77743361160428e-05
CAMB-75A26	MN908947.3	11083	G	T	0.82	0.83	0	0	0.829297775091603	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.77743361160428e-05
CAMB-75A26	MN908947.3	14189	C	T	0.84	0.83	0	0	0.830723488602577	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A241V	C722T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.168768582755203
CAMB-75A26	MN908947.3	14805	C	T	1	1	0	0	0.999882337714292	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	3.52986857122686e-05
CAMB-75A26	MN908947.3	19688	C	T	0.0091	0.0095	4e-06	3.1e-06	0.00934662631297846	CCA	ORF1ab:endoRNAse	P23L	C68T	CCA>CTA	Missense	ORF1ab:endoRNAse	0.990608865942674
CAMB-75A26	MN908947.3	19955	C	T	0.9	0.82	2.59878529712496e-321	5.1e-280	0.858858858858859	ACT	ORF1ab:endoRNAse	T112I	C335T	ACT>ATT	Missense	ORF1ab:endoRNAse	0.141141141141141
CAMB-75A26	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-75A26	MN908947.3	2558	C	T	1	1	0	0	0.999666822149664	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000133271140134604
CAMB-75A26	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-75A26	MN908947.3	27384	T	C	0.15	0.16	1.7e-70	1.9e-73	0.156163551351175	ATT	ORF6	D61D	T183C	GAT>GAC	Synonymous	GU280_gp06	0.843771357901474
CAMB-75A26	MN908947.3	28059	C	T	0.84	0.84	0	0	0.843920595533499	ACC	ORF8	P56S	C166T	CCT>TCT	Missense	GU280_gp09	0.155955334987593
CAMB-75A26	MN908947.3	28900	A	T	0.087	0.11	1.5e-38	5.6e-49	0.0995380945129689	GAA	N	R209S	A627T	AGA>AGT	Missense	GU280_gp10	0.899649763971372
CAMB-75A26	MN908947.3	6026	C	T	0.0035	0.0085	0.0044	3.3e-05	0.00628688734924301	TCC	ORF1ab:nsp3	P1103S	C3307T	CCA>TCA	Missense	ORF1ab:nsp3	0.993713112650757
CAMB-75A26	MN908947.3	7675	G	C	0.019	0.0076	1.2e-09	2.6e-05	0.0145114724206048	CGA	ORF1ab:nsp3	A1652A	G4956C	GCG>GCC	Synonymous	ORF1ab:nsp3	0.985336574988604
CAMB-75A35	MN908947.3	11075	T	-	0.0062	0.035	0.0049	1.7e-09	0.0222647058823529	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.977441176470588
CAMB-75A35	MN908947.3	12085	C	T	0.37	0.4	1e-191	4.4e-215	0.389989241432829	CCT	ORF1ab:nsp7	T81T	C243T	ACC>ACT	Synonymous	ORF1ab:nsp7	0.609975484576448
CAMB-75A35	MN908947.3	14408	C	T	1	1	0	0	0.999529101525711	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000282539084573366
CAMB-75A35	MN908947.3	1813	T	INS	0.043	0.017	6.8e-16	5e-06	0.0292477746258437	CTA	ORF1ab:nsp2	.	1007-1008-insfrshift	.	no-SNV	ORF1ab:nsp2	0.970654406729923
CAMB-75A35	MN908947.3	23403	A	G	1	1	0	0	0.999918003214274	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.19967857259995e-05
CAMB-75A35	MN908947.3	23575	C	T	1	1	0	0	0.999727148703956	GCG	S	C671C	C2013T	TGC>TGT	Synonymous	GU280_gp02, spike glycoprotein	0.000272851296043656
CAMB-75A35	MN908947.3	23587	G	C	1	1	0	0	0.999865735767991	AGA	S	Q675H	G2025C	CAG>CAC	Missense	GU280_gp02, spike glycoprotein	0
CAMB-75A35	MN908947.3	241	C	T	1	1	0	0	0.999770246984492	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-75A35	MN908947.3	28209	G	T	0.14	0.025	1.7e-63	9e-13	0.0635160843998616	TGA	ORF8	E106*	G316T	GAA>TAA	Nonsense	GU280_gp09	0.936267727429955
CAMB-75A35	MN908947.3	29555	C	T	0.0083	0.011	0.00042	8.4e-06	0.0103806228373702	GCA	NA	NA	NA	NA	NA	NA	0.989186851211073
CAMB-75A35	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75A44	MN908947.3	11074	C	INS	0.1	0.1	1.7e-39	3.9e-31	0.10366814980906	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.892197736748064
CAMB-75A44	MN908947.3	11083	G	-	0.18	0.18	8.2e-81	2.1e-82	0.181448608726637	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.23928606135208e-05
CAMB-75A44	MN908947.3	11083	G	T	0.82	0.82	0	0	0.818373230539989	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.23928606135208e-05
CAMB-75A44	MN908947.3	14805	C	T	1	1	0	0	0.998781091011871	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000282645562464669
CAMB-75A44	MN908947.3	23948	G	A	0.0053	0.0073	0.00021	2.6e-05	0.006194966819243	AGA	S	D796N	G2386A	GAT>AAT	Missense	GU280_gp02, spike glycoprotein	0.993621206272174
CAMB-75A44	MN908947.3	2480	A	G	1	1	0	0	0.999606531575841	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000196734212079481
CAMB-75A44	MN908947.3	25519	T	C	0.022	0.028	2.6e-11	2.3e-14	0.0231505148616081	TTT	ORF3a	F43L	T127C	TTC>CTC	Missense	GU280_gp03	0.97536454149322
CAMB-75A44	MN908947.3	2558	C	T	1	1	0	0	0.999434953134348	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	9.9714152762082e-05
CAMB-75A44	MN908947.3	26144	G	T	1	1	0	0	0.999685798072895	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000157100963552576
CAMB-75A44	MN908947.3	26494	T	G	1	1	0	0	0.999236379914159	GTT	NA	NA	NA	NA	NA	NA	0.000289648998077784
CAMB-75A44	MN908947.3	28921	T	C	0.23	0.22	1.5e-105	6.2e-100	0.223487855215114	ATG	N	D216D	T648C	GAT>GAC	Synonymous	GU280_gp10	0.776274011747896
CAMB-75A44	MN908947.3	6868	T	C	0.082	0.098	7.3e-30	9.7e-34	0.0891355533131517	ATA	ORF1ab:nsp3	N1383N	T4149C	AAT>AAC	Synonymous	ORF1ab:nsp3	0.910864446686848
CAMB-75A44	MN908947.3	9163	C	A	0.12	0.13	8.5e-56	1e-59	0.125497314501691	ACA	ORF1ab:nsp4	N203K	C609A	AAC>AAA	Missense	ORF1ab:nsp4	0.873980505271534
CAMB-75A53	MN908947.3	14408	C	T	1	1	0	0	0.999752658916646	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000247341083353945
CAMB-75A53	MN908947.3	16289	C	T	1	1	3.9e-244	2e-279	1	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0
CAMB-75A53	MN908947.3	23403	A	G	1	1	0	0	0.999927031267102	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.29687328979532e-05
CAMB-75A53	MN908947.3	241	C	T	1	1	0	0	0.99986710080404	TCG	NA	NA	NA	NA	NA	NA	0.000132899195959864
CAMB-75A53	MN908947.3	25429	G	T	1	1	0	0	0.99970903800691	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	3.63702491362066e-05
CAMB-75A53	MN908947.3	25521	C	T	0.26	0.099	1.5e-125	5.5e-45	0.181468364775591	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.818531635224409
CAMB-75A53	MN908947.3	2918	C	T	0.21	0.16	7.7e-60	3.6e-49	0.18140243902439	ACC	ORF1ab:nsp3	P67S	C199T	CCA>TCA	Missense	ORF1ab:nsp3	0.81859756097561
CAMB-75A53	MN908947.3	29520	C	T	0.049	0.017	5e-13	1.7e-06	0.0301455301455301	TCA	N	S416L	C1247T	TCA>TTA	Missense	GU280_gp10	0.96985446985447
CAMB-75A53	MN908947.3	29810	G	T	1	1	6.2e-251	9.88131291682493e-324	0.998185117967332	TGT	NA	NA	NA	NA	NA	NA	0
CAMB-75A53	MN908947.3	3037	C	T	1	1	6.5e-255	5.6e-299	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75A62	MN908947.3	11083	G	-	0.7	0.033	0	4.2e-14	0.263571428571429	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	5.49450549450549e-05
CAMB-75A62	MN908947.3	11083	G	T	0.3	0.97	5.8e-72	0	0.736153846153846	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	5.49450549450549e-05
CAMB-75A62	MN908947.3	13914	T	G	0.0063	0.0017	2.1e-05	0.0031	0.00335985853227233	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.996640141467728
CAMB-75A62	MN908947.3	14805	C	T	1	1	0	0	0.9998445998446	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000155400155400155
CAMB-75A62	MN908947.3	23707	C	T	1	1	0	0	1	CCA	S	P715P	C2145T	CCC>CCT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-75A62	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.123783783783784	0.0944864864864865	NA;NA;NA;NA;NA;NA;NA;2.9e-30;2.6e-30;3.2e-34;2.5e-31;9.3e-32;1.6e-30;6.7e-31;1.3e-30;9.5e-30;2.9e-31;4.7e-30;1.5e-31;1.4e-30;3.9e-31;9.1e-30;6.2e-31;1.9e-30;6.2e-31;7.2e-32;4e-30;1.6e-31;6.3e-32;1.5e-30;4.8e-30;2.5e-30;1e-30;5.9e-30;2.2e-34;1.9e-31;4.6e-32	2.8e-18;1.7e-23;2.3e-19;2.9e-19;5.9e-18;3.4e-22;4.7e-20;1.6e-17;1.6e-17;4.9e-18;4e-18;2.3e-18;1.3e-17;6.3e-18;1.1e-17;3.1e-17;3e-18;2.2e-17;5.8e-18;7.3e-18;6.6e-18;2.8e-17;5.4e-18;1.5e-17;7.2e-18;1.7e-18;1.5e-17;5.9e-18;2.5e-19;7.7e-18;2e-17;2e-17;2.1e-18;1.9e-17;1.5e-19;6.4e-18;1.3e-18	0.116893701245779	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.947486552378004
CAMB-75A62	MN908947.3	28824	C	A	0.11	0.069	1.6e-36	1.5e-26	0.0834586466165414	TCT	N	S184Y	C551A	TCT>TAT	Missense	GU280_gp10	0.916165413533835
CAMB-75A71	MN908947.3	10097	G	A	1	1	0	0	0.999710345134912	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000200530291214545
CAMB-75A71	MN908947.3	11075	T	-	0.043	0.033	1.2e-10	1.8e-08	0.038512854966455	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957607471683116
CAMB-75A71	MN908947.3	13536	C	T	1	1	0	0	0.999720586338821	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000214933585522074
CAMB-75A71	MN908947.3	14408	C	T	0.99	1	0	0	0.994896625100309	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00217299178591072
CAMB-75A71	MN908947.3	16246	G	T	0.0086	0.0064	1.1e-05	8.2e-05	0.00749704473340385	GGC	ORF1ab:helicase	A4S	G10T	GCT>TCT	Missense	ORF1ab:helicase	0.992471847197163
CAMB-75A71	MN908947.3	23403	A	G	1	1	0	0	0.999215804554366	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000226210224702157
CAMB-75A71	MN908947.3	23731	C	T	1	1	0	0	0.999161274862209	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000748861730170141
CAMB-75A71	MN908947.3	241	C	T	1	1	0	0	0.999072832331661	TCG	NA	NA	NA	NA	NA	NA	0.000215235351578669
CAMB-75A71	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998711079660332	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000448531060775959
CAMB-75A71	MN908947.3	3037	C	T	1	1	0	0	0.997956875478857	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00134992155861213
CAMB-75A71	MN908947.3	4002	C	T	1	1	0	0	0.999237688672054	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0.000396401890532093
CAMB-75A80	MN908947.3	11074	C	INS	0.1	0.099	2.7e-33	1.3e-27	0.100599566271208	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.895905089934941
CAMB-75A80	MN908947.3	11083	G	-	0.18	0.17	1.1e-79	2.6e-77	0.175697406138572	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	4.66102682420937e-05
CAMB-75A80	MN908947.3	11083	G	T	0.82	0.83	0	0	0.824092847654338	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	4.66102682420937e-05
CAMB-75A80	MN908947.3	13896	T	C	0.014	0.013	4.6e-08	4.5e-08	0.0140112953703371	GTG	ORF1ab:RNA-dependent-RNA-polymerase	C143C	T429C	TGT>TGC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.985916759595669
CAMB-75A80	MN908947.3	14805	C	T	1	1	0	0	0.999508616161445	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000186386973244997
CAMB-75A80	MN908947.3	1514	C	T	1	1	0	0	0.999543054427295	CCA	ORF1ab:nsp2	H237Y	C709T	CAT>TAT	Missense	ORF1ab:nsp2	0.000304630381803412
CAMB-75A80	MN908947.3	19904	A	G	0.99	0.99	0	0	0.987746847489888	CAT	ORF1ab:endoRNAse	H95R	A284G	CAT>CGT	Missense	ORF1ab:endoRNAse	0.0121341898643826
CAMB-75A80	MN908947.3	20515	C	T	0.017	0.019	2e-09	3.2e-10	0.0180701026651457	ACT	ORF1ab:endoRNAse	L299F	C895T	CTT>TTT	Missense	ORF1ab:endoRNAse	0.981929897334854
CAMB-75A80	MN908947.3	2480	A	G	1	1	0	0	0.99987866286477	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000121337135230237
CAMB-75A80	MN908947.3	2558	C	T	1	1	0	0	0.999583766909469	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	7.5678743732854e-05
CAMB-75A80	MN908947.3	26144	G	T	1	1	0	0	0.999675640609796	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000162179695102173
CAMB-75A80	MN908947.3	26951	G	T	0.31	0.3	3e-151	2.7e-150	0.304972023655443	TGA	M	V143V	G429T	GTG>GTT	Synonymous	GU280_gp05	0.694370880707274
CAMB-75A80	MN908947.3	29140	G	T	1	1	0	0	0.999556111537065	AGG	N	Q289H	G867T	CAG>CAT	Missense	GU280_gp10	0.000282474476413381
CAMB-75A80	MN908947.3	6245	G	T	0.023	0.024	1e-11	1.6e-12	0.0230297471313982	TGT	ORF1ab:nsp3	V1176F	G3526T	GTT>TTT	Missense	ORF1ab:nsp3	0.976637531024064
CAMB-75A9F	MN908947.3	11075	T	-	0.074	0.043	5.8e-18	4.8e-11	0.0593913537238532	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.940347754024647
CAMB-75A9F	MN908947.3	14408	C	T	1	1	0	0	0.999554069119286	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000350374263417742
CAMB-75A9F	MN908947.3	1781	TG	-	0.0145	0.0086	2e-08;1.1e-07	8.1e-06;2.5e-05	0.0119642387588746	CTG	ORF1ab:nsp2	.	976-977-delfrshift	.	no-SNV	ORF1ab:nsp2	0.987368229734642
CAMB-75A9F	MN908947.3	19185	C	T	0.008	0.015	4.3e-05	2.8e-08	0.0117113819993806	GCC	ORF1ab:3'-to-5'-exonuclease	C382C	C1146T	TGC>TGT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.988288618000619
CAMB-75A9F	MN908947.3	20480	C	T	0.99	0.99	2.8e-156	8.9e-279	0.9923273657289	TCA	ORF1ab:endoRNAse	S287L	C860T	TCA>TTA	Missense	ORF1ab:endoRNAse	0.00255754475703325
CAMB-75A9F	MN908947.3	21137	A	G	0.013	0.016	4.4e-06	3.3e-07	0.0139706928439323	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.985972400056907
CAMB-75A9F	MN908947.3	23403	A	G	1	1	0	0	0.999892719977686	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.43680133885468e-05
CAMB-75A9F	MN908947.3	241	C	T	1	1	0	0	0.999795635686551	TCG	NA	NA	NA	NA	NA	NA	0.000181657167510616
CAMB-75A9F	MN908947.3	25429	G	T	1	1	0	0	0.999789905780823	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	6.46443751313089e-05
CAMB-75A9F	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0206486486486487	0.0357837837837838	0.055;0.013;0.049;0.051;0.066;0.034;0.054;0.084;0.082;0.042;0.071;0.067;0.00049;0.00044;0.00049;0.00067;4e-04;6e-04;0.00036;0.00043;0.00042;7e-04;0.00044;5e-04;0.00042;0.00035;0.00059;0.00035;0.00017;0.00045;0.00059;0.00056;0.00042;6e-04;0.00021;0.00034;0.00031	1e-04;7.3e-06;7.7e-05;1.2e-06;3.2e-06;1.4e-07;7.6e-07;5.7e-06;5.8e-06;3.3e-06;3.2e-06;2.6e-06;5.7e-06;4.3e-06;4.7e-06;7.5e-06;3.5e-06;6.6e-06;4.5e-06;4.3e-06;3.8e-06;7.6e-06;4.4e-06;5.7e-06;4.3e-06;3.1e-06;6.5e-06;4.1e-06;1.2e-06;4.2e-06;6.4e-06;6.3e-06;3e-06;6.2e-06;1.5e-06;4.1e-06;2.4e-06	0.030410577592206	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.980385079889501
CAMB-75A9F	MN908947.3	3037	C	T	1	1	0	0	0.999311226999902	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75A9F	MN908947.3	4527	GAT	-	0.0233333333333333	0.00833333333333333	1.9e-06;1.9e-06;0.00036	NA;NA;0.00024	0.00972978983653953	AGA	ORF1ab:nsp3	.	1808-1810-delinframe	.	no-SNV	ORF1ab:nsp3	0.990270210163461
CAMB-75A9F	MN908947.3	4548	AAACAACTGTAGCGTCACTTATCAACACAC	-	0.00670466666666667	0.0163333333333333	0.00087;0.00082;0.00088;0.00094;0.00087;0.00075;0.00083;0.00071;0.00031;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00067;0.00063;0.00071;0.00068;0.00067;0.00057;0.00063;0.00056;0.00022;4.1e-05;5.2e-05;2e-06;4.4e-06;7.5e-06;2.2e-06;2.6e-06;8.7e-07;1.4e-06;1.8e-07;1.6e-07;1.6e-07;1.4e-07;1.4e-07;1.7e-07;2.5e-06;2.3e-06;1.6e-07;1.4e-07;1.4e-07;1.1e-07	0.00771823024241765	AAA	ORF1ab:nsp3	.	1829-1858-delinframe	.	no-SNV	ORF1ab:nsp3	0.976727552816901
CAMB-75ABD	MN908947.3	11075	T	-	0.038	0.039	1.3e-10	9.4e-11	0.0381848367459878	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955569610245869
CAMB-75ABD	MN908947.3	14408	C	T	1	1	0	0	0.999321735001865	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000271305999253909
CAMB-75ABD	MN908947.3	20372	T	A	0.021	0.029	6.6e-08	2.3e-07	0.022083805209513	CTG	ORF1ab:endoRNAse	L251Q	T752A	CTG>CAG	Missense	ORF1ab:endoRNAse	0.977916194790487
CAMB-75ABD	MN908947.3	2246	G	A	0.051	0.033	1.6e-23	2.3e-16	0.0462599487107135	CGG	ORF1ab:nsp2	G481S	G1441A	GGT>AGT	Missense	ORF1ab:nsp2	0.953540869594084
CAMB-75ABD	MN908947.3	23403	A	G	1	1	0	0	0.999656372148963	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-75ABD	MN908947.3	241	C	T	1	1	0	0	0.999190837794099	TCG	NA	NA	NA	NA	NA	NA	8.29909954769907e-05
CAMB-75ABD	MN908947.3	25571	C	T	0.053	0.055	5.9e-25	1e-25	0.0535692679975802	TCC	ORF3a	S60F	C179T	TCC>TTC	Missense	GU280_gp03	0.946249243799153
CAMB-75ABD	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999366487171365	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-75ABD	MN908947.3	3037	C	T	1	1	0	0	0.999328010119377	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000197644082536169
CAMB-75ABD	MN908947.3	6627	C	T	1	1	0	0	0.999833721316927	ACC	ORF1ab:nsp3	T1303I	C3908T	ACC>ATC	Missense	ORF1ab:nsp3	8.3139341536415e-05
CAMB-75ACC	MN908947.3	11075	T	-	0.11	0.17	7.8e-27	1.8e-42	0.136897044646122	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.863069711778199
CAMB-75ACC	MN908947.3	14408	C	T	1	1	0	0	0.999316005471956	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000521138688033353
CAMB-75ACC	MN908947.3	1498	C	T	0.3	0.15	3.4e-64	2.1e-35	0.210374639769452	TCT	ORF1ab:nsp2	F231F	C693T	TTC>TTT	Synonymous	ORF1ab:nsp2	0.789625360230548
CAMB-75ACC	MN908947.3	1912	C	T	0.25	0.32	1.6e-110	2.6e-153	0.291620111731844	CCC	ORF1ab:nsp2	S369S	C1107T	TCC>TCT	Synonymous	ORF1ab:nsp2	0.708379888268156
CAMB-75ACC	MN908947.3	22373	C	T	0.051	0.05	6.9e-09	1.2e-07	0.0506329113924051	TCA	S	Q271*	C811T	CAA>TAA	Nonsense	GU280_gp02, spike glycoprotein	0.949367088607595
CAMB-75ACC	MN908947.3	23403	A	G	1	1	0	0	0.999899680650069	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.35994582755104e-05
CAMB-75ACC	MN908947.3	241	C	T	1	1	0	0	0.999762819600588	TCG	NA	NA	NA	NA	NA	NA	0.000237180399411793
CAMB-75ACC	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999782466826191	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000246487552378605
CAMB-75ACC	MN908947.3	29253	C	T	0.018	0.013	3.1e-09	2.3e-07	0.0156228492773572	TCG	N	S327L	C980T	TCG>TTG	Missense	GU280_gp10	0.984377150722643
CAMB-75ACC	MN908947.3	3037	C	T	1	1	0	0	0.999266593325999	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000366703337000367
CAMB-75ADB	MN908947.3	10097	G	A	1	1	0	0	0.998639847244383	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000104627135047475
CAMB-75ADB	MN908947.3	11075	T	-	0.039	0.037	1.3e-09	2.2e-09	0.0376776395680856	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958569912588751
CAMB-75ADB	MN908947.3	13536	C	T	1	1	0	0	1	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-75ADB	MN908947.3	14184	C	T	1	1	0	0	0.999867747359671	CCA	ORF1ab:RNA-dependent-RNA-polymerase	T239T	C717T	ACC>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00010391278883032
CAMB-75ADB	MN908947.3	14408	C	T	1	1	0	0	0.999542150746867	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000331940708521719
CAMB-75ADB	MN908947.3	1684	C	T	1	1	0	0	0.999790087953148	TCG	ORF1ab:nsp2	I293I	C879T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.000167929637481895
CAMB-75ADB	MN908947.3	21058	C	T	1	1	0	0	0.999910094580501	CCC	ORF1ab:2'-O-ribose-methyltransferase	P134S	C400T	CCT>TCT	Missense	ORF1ab:2'-O-ribose-methyltransferase	8.99054194986874e-05
CAMB-75ADB	MN908947.3	21608	G	T	0.0096	0.016	5.6e-06	2.6e-08	0.0128950428073142	TGT	S	V16F	G46T	GTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.986999260120495
CAMB-75ADB	MN908947.3	22243	A	C	1	1	0	0	0.999881849760155	TAG	S	V227V	A681C	GTA>GTC	Synonymous	GU280_gp02, spike glycoprotein	4.72600959379948e-05
CAMB-75ADB	MN908947.3	23403	A	G	1	1	0	0	0.999784399120348	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000198352809279462
CAMB-75ADB	MN908947.3	23731	C	T	1	1	0	0	0.99990538665321	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	3.15377822631513e-05
CAMB-75ADB	MN908947.3	241	C	T	1	1	0	0	0.998837323150732	TCG	NA	NA	NA	NA	NA	NA	0.000110148333088559
CAMB-75ADB	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998905231091437	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	5.20156046814044e-05
CAMB-75ADB	MN908947.3	3037	C	T	1	1	0	0	0.999596383597029	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000121084920891185
CAMB-75ADB	MN908947.3	4002	C	T	1	1	0	0	0.999954580551392	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-75AEA	MN908947.3	11074	C	INS	0.11	0.1	2.7e-33	4e-29	0.105446637029456	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.894233536955896
CAMB-75AEA	MN908947.3	11083	G	-	0.23	0.12	3e-105	2.3e-53	0.194504655777744	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	6.10593802472905e-05
CAMB-75AEA	MN908947.3	11083	G	T	0.77	0.88	3.6e-305	0	0.805128987940772	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	6.10593802472905e-05
CAMB-75AEA	MN908947.3	14805	C	T	1	1	0	0	0.99994590208277	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-75AEA	MN908947.3	22696	G	T	1	1	0	0	0.998543689320388	AGT	S	K378N	G1134T	AAG>AAT	Missense	GU280_gp02, spike glycoprotein	0.00145631067961165
CAMB-75AEA	MN908947.3	2480	A	G	1	1	0	5.99999999998091e-313	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-75AEA	MN908947.3	2513	G	A	1	1	0	1.99997773436537e-319	1	AGA	ORF1ab:nsp2	E570K	G1708A	GAA>AAA	Missense	ORF1ab:nsp2	0
CAMB-75AEA	MN908947.3	2558	C	T	1	1	0	0	0.999111111111111	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000888888888888889
CAMB-75AEA	MN908947.3	8537	A	G	1	1	0	0	1	GAT	ORF1ab:nsp3	I1940V	A5818G	ATA>GTA	Missense	ORF1ab:nsp3	0
CAMB-75AEA	MN908947.3	8824	G	A	1	1	0	0	0.999623493975904	TGA	ORF1ab:nsp4	L90L	G270A	TTG>TTA	Synonymous	ORF1ab:nsp4	0.000376506024096386
CAMB-75AF9	MN908947.3	11075	T	-	0.043	0.036	1.3e-10	1.4e-09	0.0402629186770156	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954576603034753
CAMB-75AF9	MN908947.3	14408	C	T	1	1	0	0	0.998287345385347	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00045987947986045
CAMB-75AF9	MN908947.3	16049	C	T	0.56	0.59	0	0	0.573807450526642	ACT	ORF1ab:RNA-dependent-RNA-polymerase	T861I	C2582T	ACT>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.426109050135388
CAMB-75AF9	MN908947.3	23403	A	G	1	1	0	0	0.997938802377691	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000146278540938044
CAMB-75AF9	MN908947.3	241	C	T	1	1	0	0	0.998687381649165	TCG	NA	NA	NA	NA	NA	NA	0.000279738337063178
CAMB-75AF9	MN908947.3	27948	G	T	1	1	0	0	0.999755067050395	AGA	ORF8	E19*	G55T	GAA>TAA	Nonsense	GU280_gp09	0
CAMB-75AF9	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999500665778961	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	7.37517516041006e-05
CAMB-75AF9	MN908947.3	3037	C	T	1	1	0	0	0.999160675838412	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.29847097033172e-05
CAMB-75AF9	MN908947.3	4345	C	T	0.038	0.042	3.2e-18	4.8e-20	0.0394693591500816	TCT	ORF1ab:nsp3	I542I	C1626T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.960468621115239
CAMB-75B14	MN908947.3	11074	C	INS	0.14	0.14	1e-67	9.1e-56	0.139473192165662	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.858154536530641
CAMB-75B14	MN908947.3	11083	G	-	0.15	0.16	4.9e-66	6.1e-70	0.154028541532159	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.22632856156912e-05
CAMB-75B14	MN908947.3	11083	G	T	0.85	0.84	0	0	0.845804483825723	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.22632856156912e-05
CAMB-75B14	MN908947.3	11651	C	INS	0.023	0.027	5.7e-11	1.8e-12	0.024852652259332	CCT	ORF1ab:nsp6	.	678-679-insfrshift	.	no-SNV	ORF1ab:nsp6	0.968958742632613
CAMB-75B14	MN908947.3	11651	C	T	0.007	0.0051	4.1e-05	0.00022	0.00618860510805501	CCT	ORF1ab:nsp6	L227F	C679T	CTC>TTC	Missense	ORF1ab:nsp6	0.968958742632613
CAMB-75B14	MN908947.3	11653	C	T	1	1	0	0	0.997190293742018	TCT	ORF1ab:nsp6	L227L	C681T	CTC>CTT	Synonymous	ORF1ab:nsp6	0.000102171136653895
CAMB-75B14	MN908947.3	14805	C	T	1	1	0	0	0.998531124285412	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000158797374550074
CAMB-75B14	MN908947.3	16017	C	T	0.059	0.061	4.8e-27	3.9e-28	0.0598976870438389	TCG	ORF1ab:RNA-dependent-RNA-polymerase	F850F	C2550T	TTC>TTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.940054857967218
CAMB-75B14	MN908947.3	16913	T	A	0.045	0.04	5e-21	1.4e-18	0.0422849005466489	GTG	ORF1ab:helicase	V226E	T677A	GTG>GAG	Missense	ORF1ab:helicase	0.956957140888419
CAMB-75B14	MN908947.3	21137	A	G	1	1	0	0	0.999051040466346	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0
CAMB-75B14	MN908947.3	21987	G	A	1	1	0	0	0.997134670487106	GGT	S	G142D	G425A	GGT>GAT	Missense	GU280_gp02, spike glycoprotein	0.000232324014558972
CAMB-75B14	MN908947.3	23559	TTGGTGCAGGTATATGCGCTAG	-	0.0297272727272727	0.0390909090909091	0.0011;0.0017;0.00053;0.00091;0.00095;0.00099;0.00091;0.00089;0.00062;0.00058;0.00038;0.0015;0.0037;0.0026;0.0029;0.0015;0.0023;0.0038;0.0026;0.0027;0.00031;0.00027	0.00022;0.00036;5.2e-05;8.8e-05;9.5e-05;1e-04;9.4e-05;8.6e-05;5.1e-05;4.3e-05;8.6e-06;4.1e-05;0.00034;0.00021;0.00035;0.00022;0.00044;0.00076;0.00048;0.00047;2.6e-05;0.00014	0.0299051787016776	ATT	S	.	1997-2018-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.959382716049383
CAMB-75B14	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-75B14	MN908947.3	2558	C	T	1	1	0	0	0.999694868238558	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	2.77392510402219e-05
CAMB-75B14	MN908947.3	25584	C	T	0.03	0.028	9.4e-15	2.2e-14	0.0297598035453918	CCC	ORF3a	T64T	C192T	ACC>ACT	Synonymous	GU280_gp03	0.97020950042207
CAMB-75B14	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-75B14	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0293421052631579	0.0389473684210526	0.0029;0.00024;0.0014;0.0015;0.0027;0.00018;0.00045;6.2e-05;6e-05;1.3e-05;3.5e-05;2.7e-05;5.8e-05;4.6e-05;4.9e-05;7.9e-05;3.7e-05;7e-05;3.1e-05;4.9e-05;5.1e-05;8.3e-05;4.2e-05;5.8e-05;4.8e-05;3.6e-05;6.1e-05;4.1e-05;4.6e-05;3.4e-05;6.9e-05;2.7e-05;2e-05;4.7e-05;2.5e-05;1.4e-05;7.3e-06;0.0019	0.00042;4.3e-05;0.00023;0.00024;4e-04;1.1e-06;5.5e-06;5.2e-07;5.4e-07;1.9e-07;1.8e-07;1.4e-07;3.5e-07;2.3e-07;2.7e-07;4.9e-07;1.8e-07;4.2e-07;2.5e-07;2.4e-07;1.8e-07;4.8e-07;2.1e-07;3.3e-07;2.5e-07;1.3e-07;3.9e-07;2.3e-07;4.1e-08;2.4e-07;4e-07;3.7e-07;1.5e-07;4.3e-07;8.8e-08;4.3e-07;1.9e-07;0.00059	0.0339473204283146	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.979954299958455
CAMB-75B14	MN908947.3	2764	G	A	0.0042	0.0076	0.00089	2.9e-05	0.00553035481265146	TGC	ORF1ab:nsp3	V15V	G45A	GTG>GTA	Synonymous	ORF1ab:nsp3	0.994407506369229
CAMB-75B14	MN908947.3	6312	C	T	0.98	0.98	0	0	0.979218153223995	ACA	ORF1ab:nsp3	T1198I	C3593T	ACA>ATA	Missense	ORF1ab:nsp3	0.0198045383059987
CAMB-75B14	MN908947.3	9724	C	T	1	1	0	0	0.999192850965696	TCT	ORF1ab:nsp4	F390F	C1170T	TTC>TTT	Synonymous	ORF1ab:nsp4	6.72624195253195e-05
CAMB-75B23	MN908947.3	10097	G	A	1	1	0	0	1	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0
CAMB-75B23	MN908947.3	11939	G	C	0.015	0.0076	3.1e-08	2.2e-05	0.0108980889753327	TGT	ORF1ab:nsp7	V33L	G97C	GTC>CTC	Missense	ORF1ab:nsp7	0.988957838082595
CAMB-75B23	MN908947.3	13469	G	-	0.021	0.0055	3.7e-10	0.00084	0.0128998968008256	CGG	ORF1ab:nsp11	.	28-28-delfrshift	.	no-SNV	ORF1ab:nsp11	0.982585139318885
CAMB-75B23	MN908947.3	13968	C	T	0.032	0.008	8.3e-16	1.4e-05	0.0175542496165702	CCA	ORF1ab:RNA-dependent-RNA-polymerase	A167A	C501T	GCC>GCT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.982415379709353
CAMB-75B23	MN908947.3	14371	G	T	0.017	0.0073	2e-09	4.2e-05	0.0125553223067563	TGC	ORF1ab:RNA-dependent-RNA-polymerase	A302S	G904T	GCA>TCA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.986749388279025
CAMB-75B23	MN908947.3	14408	C	T	1	1	0	0	0.999551014299514	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00031292942761126
CAMB-75B23	MN908947.3	16363	TTG	-	0.006	0.00906666666666667	NA;NA;1.3e-09	2.7e-06;5.2e-06;6.9e-06	0.0053043697903511	CTT	ORF1ab:helicase	.	127-129-delinframe	.	no-SNV	ORF1ab:helicase	0.994054054054054
CAMB-75B23	MN908947.3	16365	G	-	0.018	0.0087	1.3e-09	6.9e-06	0.0127365356622999	TGT	ORF1ab:helicase	.	129-129-delfrshift	.	no-SNV	ORF1ab:helicase	0.987142163998059
CAMB-75B23	MN908947.3	16476	T	C	0.014	0.01	6e-08	1.3e-06	0.0115434963703439	GTT	ORF1ab:helicase	S80S	T240C	AGT>AGC	Synonymous	ORF1ab:helicase	0.988456503629656
CAMB-75B23	MN908947.3	20875	GG	-	0.017	0.00535	1.1e-08;5.7e-09	0.00094;0.00051	0.0117534239838698	TGG	ORF1ab:2'-O-ribose-methyltransferase	.	217-218-delfrshift	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.988221465827558
CAMB-75B23	MN908947.3	21952	C	T	0.1	0.042	1.9e-42	2.7e-19	0.066974358974359	TCT	S	V130V	C390T	GTC>GTT	Synonymous	GU280_gp02, spike glycoprotein	0.933025641025641
CAMB-75B23	MN908947.3	23403	A	G	1	1	0	0	0.999924538268531	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.602901503575e-05
CAMB-75B23	MN908947.3	23731	C	T	1	1	0	0	0.999927599189111	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	7.2400810889082e-05
CAMB-75B23	MN908947.3	23868	G	T	0.014	0.011	2.7e-08	5.1e-07	0.0120846949891068	GGA	S	G769V	G2306T	GGA>GTA	Missense	GU280_gp02, spike glycoprotein	0.987813180827887
CAMB-75B23	MN908947.3	241	C	T	1	1	0	0	0.999826709796673	TCG	NA	NA	NA	NA	NA	NA	5.77634011090573e-05
CAMB-75B23	MN908947.3	25947	G	T	1	1	0	0	0.999898662342927	AGA	ORF3a	Q185H	G555T	CAG>CAT	Missense	GU280_gp03	0
CAMB-75B23	MN908947.3	26350	GC	-	0.0165	0.00835	1.8e-08;7.7e-09	4.2e-05;3e-05	0.0122659780503551	TGC	E	.	106-107-delfrshift	.	no-SNV	GU280_gp04	0.987808295964126
CAMB-75B23	MN908947.3	26353	C	T	0.015	0.0073	1.5e-06	0.0011	0.0110274244116905	GCT	E	L37F	C109T	CTT>TTT	Missense	GU280_gp04	0.988900500918952
CAMB-75B23	MN908947.3	26383	G	-	0.016	0.0056	8.3e-08	0.001	0.0106638899859969	TGT	E	.	139-139-delfrshift	.	no-SNV	GU280_gp04	0.989228393953538
CAMB-75B23	MN908947.3	26951	G	T	0.0077	0.005	2.6e-05	0.00042	0.00664451827242525	TGA	M	V143V	G429T	GTG>GTT	Synonymous	GU280_gp05	0.993311767791572
CAMB-75B23	MN908947.3	27227	TTACTATAGCAGAGATA	-	0.00786470588235294	0.00199411764705882	1.5e-05;1.3e-05;1.2e-05;1.6e-05;1.5e-05;1.4e-05;1.2e-05;1.1e-05;1.3e-05;1.6e-05;3.1e-05;2.6e-05;1.7e-05;1.8e-05;5.3e-05;3.2e-05;1.2e-05	NA;3.1e-05;2.6e-05;3e-05;NA;NA;NA;NA;NA;NA;4.6e-05;4.1e-05;NA;NA;NA;NA;NA	0.00496574936594847	GTT	ORF6	.	26-42-delfrshift	.	no-SNV	GU280_gp06	0.995003130426565
CAMB-75B23	MN908947.3	27237	AG	-	0.0076	0.00695	3.1e-05;2.6e-05	4.6e-05;4.1e-05	0.00736974405850091	CAG	ORF6	.	36-37-delfrshift	.	no-SNV	GU280_gp06	0.992623516500922
CAMB-75B23	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999698613622664	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	6.66400106624017e-05
CAMB-75B23	MN908947.3	29688	G	T	0.0089	0.0039	1.6e-05	0.0011	0.00570852921423774	AGT	NA	NA	NA	NA	NA	NA	0.994291470785762
CAMB-75B23	MN908947.3	3037	C	T	1	1	0	0	0.999660479855138	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000113173381620643
CAMB-75B23	MN908947.3	3100	T	G	1	1	0	0	0.999416796267496	CTC	ORF1ab:nsp3	T127T	T381G	ACT>ACG	Synonymous	ORF1ab:nsp3	9.72006220839813e-05
CAMB-75B23	MN908947.3	7851	C	T	0.013	0.011	2.2e-07	3.1e-06	0.0128249970852279	GCT	ORF1ab:nsp3	A1711V	C5132T	GCT>GTT	Missense	ORF1ab:nsp3	0.987175002914772
CAMB-75B32	MN908947.3	11075	T	-	0.038	0.038	1.6e-09	2.9e-10	0.0376258113065563	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957592575173235
CAMB-75B32	MN908947.3	11083	G	-	0.013	0.013	8.6e-06	5.8e-06	0.0129962338704698	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.928520713712416
CAMB-75B32	MN908947.3	11083	G	T	0.058	0.059	1.9e-12	4.9e-13	0.058421312588751	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.928520713712416
CAMB-75B32	MN908947.3	11831	G	A	1	1	0	0	1	AGC	ORF1ab:nsp6	A287T	G859A	GCC>ACC	Missense	ORF1ab:nsp6	0
CAMB-75B32	MN908947.3	1554	A	G	0.0087	0.014	1.9e-05	8.8e-08	0.0111665478736042	AAC	ORF1ab:nsp2	N250S	A749G	AAC>AGC	Missense	ORF1ab:nsp2	0.988774055595153
CAMB-75B32	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999357644697223	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000227500836400134
CAMB-75B32	MN908947.3	16887	C	T	1	1	0	0	0.999805975941017	ACA	ORF1ab:helicase	Y217Y	C651T	TAC>TAT	Synonymous	ORF1ab:helicase	7.46246380705054e-05
CAMB-75B32	MN908947.3	18651	G	A	1	1	0	0	0.998794885796599	AGC	ORF1ab:3'-to-5'-exonuclease	E204E	G612A	GAG>GAA	Synonymous	ORF1ab:3'-to-5'-exonuclease	1.88299094281357e-05
CAMB-75B32	MN908947.3	25276	C	T	0.021	0.021	1.3e-10	7.1e-11	0.0206273731741525	CCA	S	T1238T	C3714T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.979270003078712
CAMB-75B32	MN908947.3	25494	G	T	1	1	0	0	0.996649940126589	CGA	ORF3a	T34T	G102T	ACG>ACT	Synonymous	GU280_gp03	0.00019957803501169
CAMB-75B32	MN908947.3	26158	GTTA	-	0.0105	0.009875	0.00025;1.1e-05;2.9e-05;0.00026	0.00034;2.8e-05;4.8e-05;3e-04	0.0110648665110141	TGT	ORF3a	.	766-769-delfrshift	.	no-SNV	GU280_gp03	0.992167367421674
CAMB-75B32	MN908947.3	28826	C	T	0.055	0.055	1.6e-23	1.5e-23	0.0548503659779487	TCG	N	R185C	C553T	CGT>TGT	Missense	GU280_gp10	0.945026097161741
CAMB-75B32	MN908947.3	29179	G	T	0.017	0.018	5.7e-09	9.8e-10	0.0169993400046378	CGC	N	P302P	G906T	CCG>CCT	Synonymous	GU280_gp10	0.981698506983464
CAMB-75B32	MN908947.3	4949	T	C	1	1	0	0	0.998155764893194	TTT	ORF1ab:nsp3	L744L	T2230C	TTG>CTG	Synonymous	ORF1ab:nsp3	0.00173809207907656
CAMB-75B32	MN908947.3	811	C	T	1	1	0	0	0.999259513923783	ACA	ORF1ab:nsp2	Y2Y	C6T	TAC>TAT	Synonymous	ORF1ab:nsp2	0.000149860277329666
CAMB-75B41	MN908947.3	11074	C	INS	0.054	0.12	3.9e-14	1.2e-38	0.0824694324413355	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.917162400449551
CAMB-75B41	MN908947.3	11083	G	-	0.15	0.21	4.4e-66	1.4e-94	0.174258073400813	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	5.16422226812642e-05
CAMB-75B41	MN908947.3	11083	G	T	0.85	0.79	0	0	0.825569785856917	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	5.16422226812642e-05
CAMB-75B41	MN908947.3	1314	C	T	1	0.97	0	0	0.982065553494125	ACT	ORF1ab:nsp2	T170I	C509T	ACT>ATT	Missense	ORF1ab:nsp2	0
CAMB-75B41	MN908947.3	14805	C	T	1	1	0	0	0.999890027713016	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	8.79778295869441e-05
CAMB-75B41	MN908947.3	17247	T	C	1	1	0	0	0.99981368484792	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	9.31575760398714e-05
CAMB-75B41	MN908947.3	24745	C	-	0.0018	0.019	0.0034	1.3e-10	0.00982008588045586	TCT	S	.	3183-3183-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.990089322921385
CAMB-75B41	MN908947.3	26144	G	T	1	1	2.3e-302	7.2e-264	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-75B41	MN908947.3	26746	G	T	1	1	0	0	0.998434936737503	TGG	M	W75L	G224T	TGG>TTG	Missense	GU280_gp05	0.000169705654969547
CAMB-75B41	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0157577567567568	0.0353513513513514	NA;NA;NA;NA;NA;NA;NA;0.0044;0.0045;0.0014;0.0032;0.0028;0.0043;0.0037;0.004;0.0054;0.0035;0.0049;0.0035;0.0038;0.0037;0.0055;0.0034;0.0042;0.0037;0.0034;0.005;0.0033;0.0016;0.0038;0.0048;0.0046;0.0036;0.0048;0.0025;0.0032;0.0027	2.8e-06;6e-08;1.5e-06;1.6e-06;4.8e-06;2.1e-07;1.2e-06;8.5e-06;8.6e-06;3.9e-06;4.6e-06;4.4e-06;8.4e-06;6.2e-06;6.9e-06;1.1e-05;4.8e-06;9.9e-06;6.6e-06;6.1e-06;5.2e-06;1.1e-05;6.3e-06;8.1e-06;6.2e-06;3.7e-06;9.5e-06;5.9e-06;2e-06;6.4e-06;9.6e-06;9.1e-06;4.1e-06;9.3e-06;2.3e-06;6.1e-06;4.2e-06	0.0269688442892498	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.982261228354978
CAMB-75B41	MN908947.3	28045	C	T	0.0063	0.016	0.00074	3.3e-07	0.011354079058032	GCT	ORF8	A51V	C152T	GCT>GTT	Missense	GU280_gp09	0.988645920941968
CAMB-75B41	MN908947.3	28243	T	C	0.013	0.0091	1e-07	3.2e-06	0.0109093615121298	GTT	ORF8	V117A	T350C	GTT>GCT	Missense	GU280_gp09	0.988882274147939
CAMB-75B41	MN908947.3	522	TTG	-	0.0493333333333333	0.04	4.7e-08;1.6e-08;1.2e-06	3.6e-08;1.9e-06;0.0013	0.0524721483625593	GTT	ORF1ab:leader-protein	.	257-259-delinframe	.	no-SNV	ORF1ab:leader-protein	0.938527062999113
CAMB-75B41	MN908947.3	6459	A	G	1	1	0	0	0.999939074542297	AAT	ORF1ab:nsp3	N1247S	A3740G	AAT>AGT	Missense	ORF1ab:nsp3	6.0925457702501e-05
CAMB-75B41	MN908947.3	7435	TTATTA	-	0.0126666666666667	0.0248333333333333	1.6e-05;6.1e-05;0.00015;NA;NA;NA	2.9e-05;7.1e-05;0.00016;2.5e-07;1.4e-06;3.9e-07	0.0178317816001262	TTT	ORF1ab:nsp3	.	4716-4721-delinframe	.	no-SNV	ORF1ab:nsp3	0.974015226746111
CAMB-75B50	MN908947.3	11074	C	INS	0.099	0.1	4.1e-44	4.5e-29	0.0994515079602068	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.898269656917443
CAMB-75B50	MN908947.3	11083	G	-	0.19	0.17	1.2e-81	5e-68	0.184304867385602	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.9146021568056e-05
CAMB-75B50	MN908947.3	11083	G	T	0.81	0.83	0	0	0.815622267560478	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.9146021568056e-05
CAMB-75B50	MN908947.3	14805	C	T	1	1	0	0	0.998020032611228	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00115174573595258
CAMB-75B50	MN908947.3	19868	C	T	0.016	0.016	1.4e-08	1.2e-08	0.0158718733129386	ACT	ORF1ab:endoRNAse	T83I	C248T	ACT>ATT	Missense	ORF1ab:endoRNAse	0.984128126687061
CAMB-75B50	MN908947.3	2480	A	G	1	1	0	0	0.999716553287982	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000283446712018141
CAMB-75B50	MN908947.3	2558	C	T	1	1	0	0	0.998555826338117	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-75B50	MN908947.3	26144	G	T	1	1	0	4e-226	0.99984735931617	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	5.08802279434212e-05
CAMB-75B50	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0385135135135135	0.031	0.00026;8.1e-06;7.3e-05;6.1e-05;0.00011;3.2e-06;9.1e-06;1.7e-06;1.6e-06;2.8e-07;7.6e-07;5.3e-07;1.6e-06;1.1e-06;1.2e-06;2.2e-06;7.9e-07;1.8e-06;9.5e-07;1.2e-06;1e-06;2.1e-06;1.1e-06;1.4e-06;1e-06;7.2e-07;1.6e-06;8.9e-07;1.5e-06;1e-06;1.7e-06;1.6e-06;1.2e-06;1.9e-06;3.4e-07;9.7e-07;8.9e-07	0.00034;3.7e-05;0.00012;0.00013;0.00032;8e-06;4.1e-05;3.2e-05;3.3e-05;1.5e-05;1.7e-05;1.4e-05;3e-05;2.3e-05;2.2e-05;4.3e-05;2e-05;3.7e-05;2.3e-05;2.5e-05;2.4e-05;4.1e-05;2.2e-05;3.2e-05;2.6e-05;1.4e-05;3.7e-05;2.5e-05;7.9e-06;2.5e-05;3.6e-05;3e-05;7.4e-06;2.4e-05;8.9e-06;1.8e-05;1.1e-05	0.0392070549221581	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.975100717017904
CAMB-75B50	MN908947.3	28081	A	G	0.66	0.65	0	1.9e-158	0.657223796033994	GAT	ORF8	D63G	A188G	GAT>GGT	Missense	GU280_gp09	0.34264130581411
CAMB-75B50	MN908947.3	28089	GGTTCTA	-	0.01492	0.0317142857142857	0.084;6.5e-09;7e-09;7.8e-09;1.5e-08;6e-08;2.6e-07	0.00032;1.1e-08;1.3e-08;1.3e-08;1.5e-08;9.7e-09;3.9e-08	0.0177873601940439	TGG	ORF8	.	196-202-delfrshift	.	no-SNV	GU280_gp09	0.9988749824216
CAMB-75B50	MN908947.3	28834	A	T	0.021	0.018	1.7e-10	4e-09	0.0209067151460061	CAT	N	S187S	A561T	TCA>TCT	Synonymous	GU280_gp10	0.977616179979548
CAMB-75B50	MN908947.3	29688	G	T	1	1	0	2.2e-123	0.996937573616019	AGT	NA	NA	NA	NA	NA	NA	0.0016489988221437
CAMB-75B50	MN908947.3	9460	G	A	1	1	0	3.5e-282	0.999771240334904	TGA	ORF1ab:nsp4	M302I	G906A	ATG>ATA	Missense	ORF1ab:nsp4	0.00013725579905751
CAMB-75B6F	MN908947.3	10317	A	G	0.017	0.021	5.1e-09	7.1e-10	0.0167414290291573	AAG	ORF1ab:3C-like-proteinase	K88R	A263G	AAG>AGG	Missense	ORF1ab:3C-like-proteinase	0.983038289009933
CAMB-75B6F	MN908947.3	11074	C	INS	0.11	0.11	3.3e-44	7.8e-32	0.110434802067715	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.884440665070378
CAMB-75B6F	MN908947.3	11083	G	-	0.16	0.16	9.1e-71	6.7e-64	0.160430357179875	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.07301146375339e-05
CAMB-75B6F	MN908947.3	11083	G	T	0.84	0.84	0	0	0.839383071788387	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.07301146375339e-05
CAMB-75B6F	MN908947.3	14805	C	T	1	1	0	0	0.998260962149309	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000692066083438326
CAMB-75B6F	MN908947.3	20823	C	T	0.016	0.015	4.4e-09	2.1e-08	0.0160017862459065	ACA	ORF1ab:2'-O-ribose-methyltransferase	N55N	C165T	AAC>AAT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.98384935992855
CAMB-75B6F	MN908947.3	23086	C	T	0.0082	0.0076	1.8e-05	0.00077	0.00818021646111251	ACA	S	Y508Y	C1524T	TAC>TAT	Synonymous	GU280_gp02, spike glycoprotein	0.991777833710882
CAMB-75B6F	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-75B6F	MN908947.3	2558	C	T	1	1	0	0	0.998429442713923	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	5.23519095359003e-05
CAMB-75B6F	MN908947.3	26144	G	T	1	0.99	0	9.8e-191	0.99967450035805	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000130199856780158
CAMB-75B6F	MN908947.3	26724	G	T	0.02	0.02	1.5e-10	6.9e-11	0.019982181494209	TGC	M	A68S	G202T	GCT>TCT	Missense	GU280_gp05	0.97980569343685
CAMB-75B6F	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0352702702702703	0.0292162162162162	0.00039;1.8e-05;0.00019;0.00022;0.00036;1.1e-05;2e-05;5e-06;5.1e-06;8.6e-07;2.7e-06;2.2e-06;4.5e-06;3.3e-06;3.3e-06;5.8e-06;2.7e-06;5.3e-06;3.1e-06;3.7e-06;2.8e-06;6.6e-06;3.3e-06;3.4e-06;3.5e-06;2.1e-06;5.4e-06;2.7e-06;6.7e-06;2.7e-06;5.3e-06;1.5e-06;1.4e-06;2.6e-06;1.4e-06;2.6e-06;1.4e-06	0.00043;5.3e-05;0.00028;0.00028;0.00043;1.4e-05;4.9e-05;7e-05;7.6e-05;3.5e-05;4.5e-05;3.7e-05;7.1e-05;5.6e-05;6.3e-05;9.5e-05;4.8e-05;7.6e-05;5.1e-05;5.6e-05;4.5e-05;9e-05;5.5e-05;6.9e-05;5.3e-05;3.7e-05;7.9e-05;5.1e-05;3.1e-05;5.4e-05;7.7e-05;6.4e-05;3.5e-05;7.3e-05;3.1e-05;5.8e-05;3.7e-05	0.0359371201685439	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.976453482501666
CAMB-75B6F	MN908947.3	29688	G	T	1	1	0	1.2e-125	0.997051539096592	AGT	NA	NA	NA	NA	NA	NA	0.0022408302865904
CAMB-75B6F	MN908947.3	4851	A	G	0.022	0.034	2.4e-11	2.2e-08	0.0222323318234864	AAG	ORF1ab:nsp3	K711R	A2132G	AAG>AGG	Missense	ORF1ab:nsp3	0.977589651284689
CAMB-75B7E	MN908947.3	10755	C	T	0.0081	0.0033	3.7e-05	0.0053	0.00592577190976193	GCT	ORF1ab:3C-like-proteinase	A234V	C701T	GCT>GTT	Missense	ORF1ab:3C-like-proteinase	0.994074228090238
CAMB-75B7E	MN908947.3	11074	C	INS	0.024	0.028	6.2e-05	4.3e-06	0.0260665740064548	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.973850974110109
CAMB-75B7E	MN908947.3	11075	T	-	0.025	0.048	1.2e-06	7.8e-12	0.0356266501009474	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95751928353264
CAMB-75B7E	MN908947.3	11195	C	T	1	1	0	0	0.99977114224112	TCT	ORF1ab:nsp6	L75F	C223T	CTT>TTT	Missense	ORF1ab:nsp6	2.40902904084509e-05
CAMB-75B7E	MN908947.3	12578	G	T	0.005	0.014	0.0051	5.2e-06	0.00923411189570885	AGA	ORF1ab:nsp8	D163Y	G487T	GAT>TAT	Missense	ORF1ab:nsp8	0.989123993876846
CAMB-75B7E	MN908947.3	13571	G	T	0.022	0.043	1.5e-05	8.8e-10	0.0321301428507052	GGT	ORF1ab:RNA-dependent-RNA-polymerase	G35V	G104T	GGT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.966022261277094
CAMB-75B7E	MN908947.3	13726	G	T	0.0033	0.0077	0.0032	2.7e-05	0.00524587119761382	TGT	ORF1ab:RNA-dependent-RNA-polymerase	V87F	G259T	GTT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.992769518238687
CAMB-75B7E	MN908947.3	14229	G	C	0.0095	0.005	7.7e-06	0.00079	0.00712548662470102	AGC	ORF1ab:RNA-dependent-RNA-polymerase	K254N	G762C	AAG>AAC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.992864505669365
CAMB-75B7E	MN908947.3	14408	C	T	0.99	0.99	0	0	0.991955694440147	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00107257407464703
CAMB-75B7E	MN908947.3	15216	C	T	1	1	0	0	0.999738763188831	GCA	ORF1ab:RNA-dependent-RNA-polymerase	S583S	C1749T	AGC>AGT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	8.70789370564417e-05
CAMB-75B7E	MN908947.3	18034	T	C	0.0018	0.0075	0.0053	1.8e-05	0.00448274885275622	TTT	ORF1ab:helicase	L600L	T1798C	TTA>CTA	Synonymous	ORF1ab:helicase	0.994695767945159
CAMB-75B7E	MN908947.3	18137	TC	AA	0.008	0.00145	1.5e-05;1.5e-05	NA;0.0023	0.00509904696384128	TTC	ORF1ab:3'-to-5'-exonuclease	.	98-99-mnv	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.995431227957679
CAMB-75B7E	MN908947.3	20925	G	T	0.0033	0.01	0.0028	2.5e-06	0.00620209575295294	TGC	ORF1ab:2'-O-ribose-methyltransferase	L89F	G267T	TTG>TTT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.993649794497723
CAMB-75B7E	MN908947.3	22014	G	T	0.003	0.0073	0.0042	4.7e-05	0.00516185476815398	AGT	S	S151I	G452T	AGT>ATT	Missense	GU280_gp02, spike glycoprotein	0.994750656167979
CAMB-75B7E	MN908947.3	22679	T	C	0.012	0.022	3.2e-07	1.3e-11	0.0171490790309409	ATC	S	S373P	T1117C	TCA>CCA	Missense	GU280_gp02, spike glycoprotein	0.982850920969059
CAMB-75B7E	MN908947.3	22747	C	T	0.018	0.0048	7.6e-10	0.00054	0.011317818490486	TCT	S	V395V	C1185T	GTC>GTT	Synonymous	GU280_gp02, spike glycoprotein	0.988658602720992
CAMB-75B7E	MN908947.3	22878	AC	-	0.00725	0.0049	0.00035;1.3e-05	0.0056;8.6e-05	0.00594290565637271	AAC	S	.	1316-1317-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.996378098146439
CAMB-75B7E	MN908947.3	22899	G	T	0.096	0.12	4.8e-28	8.5e-34	0.107025305255707	GGT	S	G446V	G1337T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.892974694744293
CAMB-75B7E	MN908947.3	23403	A	G	1	1	0	0	0.999971221158204	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.1584131346634e-05
CAMB-75B7E	MN908947.3	241	C	T	1	1	0	0	0.997467958292437	TCG	NA	NA	NA	NA	NA	NA	9.9574673892943e-05
CAMB-75B7E	MN908947.3	24933	G	T	0.031	0.027	9.7e-06	2.8e-05	0.02942115411628	GGT	S	G1124V	G3371T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.96903372450869
CAMB-75B7E	MN908947.3	25556	T	-	0.0051	0.015	0.007	7.7e-07	0.0092604947826319	GTT	ORF3a	.	164-164-delfrshift	.	no-SNV	GU280_gp03	0.990579381388274
CAMB-75B7E	MN908947.3	25780	TGC	-	0.00833333333333333	0.003	2.3e-05;6.4e-05;1.8e-05	NA;0.0026;0.00071	0.00610287707061901	TTG	ORF3a	.	388-390-delinframe	.	no-SNV	GU280_gp03	0.99611234528721
CAMB-75B7E	MN908947.3	27075	C	T	0.0076	0.0033	3.8e-05	0.0029	0.00590232858990944	GCA	M	Q185*	C553T	CAG>TAG	Nonsense	GU280_gp05	0.99407072013799
CAMB-75B7E	MN908947.3	28328	G	-	0.014	0.0099	2.3e-06	5.1e-05	0.0120891075060304	TGG	N	.	55-55-delfrshift	.	no-SNV	GU280_gp10	0.986491983162276
CAMB-75B7E	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999528524280999	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.78080030597122e-05
CAMB-75B7E	MN908947.3	29166	ACAAAC	-	0.00635	0.00295	0.00026;0.00044;1.2e-05;0.00029;0.00039;3e-04	0.0051;0.0081;0.0099;0.0056;0.0068;0.0059	0.00450736414423565	TAC	N	.	893-898-delinframe	.	no-SNV	GU280_gp10	0.995124525116083
CAMB-75B7E	MN908947.3	29635	C	T	0.014	0.013	6.1e-08	1.6e-07	0.0134328358208955	ACA	ORF10	Y26Y	C78T	TAC>TAT	Synonymous	GU280_gp11	0.985914179104478
CAMB-75B7E	MN908947.3	29781	G	T	0.011	0.0054	8.7e-06	0.002	0.00844194312796209	AGA	NA	NA	NA	NA	NA	NA	0.991558056872038
CAMB-75B7E	MN908947.3	3035	TTCTA	-	0.00492	0.00042	0.00092;2.1e-05;8e-05;7e-04;0.00092	NA;NA;0.0067;NA;NA	0.00166213357509822	TTT	ORF1ab:nsp3	.	316-320-delfrshift	.	no-SNV	ORF1ab:nsp3	0.997329224447869
CAMB-75B7E	MN908947.3	3211	T	-	0.0037	0.01	0.0017	2e-06	0.00659966435992684	ATG	ORF1ab:nsp3	.	492-492-delfrshift	.	no-SNV	ORF1ab:nsp3	0.993249486168989
CAMB-75B7E	MN908947.3	3259	G	T	0.019	0.0072	2.1e-07	0.00097	0.0140852911702483	AGA	ORF1ab:nsp3	Q180H	G540T	CAG>CAT	Missense	ORF1ab:nsp3	0.985877593437999
CAMB-75B7E	MN908947.3	3373	C	A	1	1	0	0	0.998333498660847	ACA	ORF1ab:nsp3	D218E	C654A	GAC>GAA	Missense	ORF1ab:nsp3	5.95179049697451e-05
CAMB-75B7E	MN908947.3	3564	G	T	0.0061	0.013	0.005	2e-05	0.0103680663556247	GGT	ORF1ab:nsp3	G282V	G845T	GGT>GTT	Missense	ORF1ab:nsp3	0.987039917055469
CAMB-75B7E	MN908947.3	3920	A	-	0.0095	0.003	3.6e-06	0.002	0.00659130101552021	TAA	ORF1ab:nsp3	.	1201-1201-delfrshift	.	no-SNV	ORF1ab:nsp3	0.993063805326691
CAMB-75B7E	MN908947.3	506	C	T	0.004	0.0082	0.00083	1.1e-05	0.00586005655496059	TCA	ORF1ab:leader-protein	H81Y	C241T	CAT>TAT	Missense	ORF1ab:leader-protein	0.994115877504362
CAMB-75B7E	MN908947.3	558	G	T	0.034	0.01	5.3e-09	0.00075	0.0233883623124725	GGT	ORF1ab:leader-protein	G98V	G293T	GGT>GTT	Missense	ORF1ab:leader-protein	0.976473542150524
CAMB-75B7E	MN908947.3	7472	G	-	0.014	0.0063	1e-06	0.00078	0.0101860053144376	CGG	ORF1ab:nsp3	.	4753-4753-delfrshift	.	no-SNV	ORF1ab:nsp3	0.988169049727951
CAMB-75B7E	MN908947.3	8466	A	G	0.0051	0.016	0.00016	7e-09	0.0101783546549631	AAA	ORF1ab:nsp3	K1916R	A5747G	AAA>AGA	Missense	ORF1ab:nsp3	0.989728265944533
CAMB-75B7E	MN908947.3	8793	G	T	0.01	0.0059	3.4e-06	0.00033	0.00800971965981191	GGT	ORF1ab:nsp4	G80V	G239T	GGT>GTT	Missense	ORF1ab:nsp4	0.990190343337983
CAMB-75B7E	MN908947.3	9451	C	T	0.0043	0.0072	0.00037	2.6e-05	0.00588897992625973	ACT	ORF1ab:nsp4	Y299Y	C897T	TAC>TAT	Synonymous	ORF1ab:nsp4	0.99411102007374
CAMB-75B8D	MN908947.3	11074	C	INS	0.18	0.072	3.3e-67	4.1e-22	0.112861655330116	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.87107338720617
CAMB-75B8D	MN908947.3	11083	G	-	0.18	0.19	9.5e-84	1.6e-84	0.186676252096813	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.68670390237608e-05
CAMB-75B8D	MN908947.3	11083	G	T	0.81	0.81	0	0	0.813084112149533	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.68670390237608e-05
CAMB-75B8D	MN908947.3	14184	C	T	0.026	0.04	2.2e-13	2.3e-19	0.0354278575890069	CCA	ORF1ab:RNA-dependent-RNA-polymerase	T239T	C717T	ACC>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.964547158026234
CAMB-75B8D	MN908947.3	14805	C	T	1	1	0	0	0.999948591404483	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	2.57042977585852e-05
CAMB-75B8D	MN908947.3	15673	T	-	0.023	0.012	1.2e-11	5.6e-07	0.0157366808817346	GTT	ORF1ab:RNA-dependent-RNA-polymerase	.	2206-2206-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.984063106893307
CAMB-75B8D	MN908947.3	22261	T	C	1	1	0	0	0.999648135116115	TTA	S	I233I	T699C	ATT>ATC	Synonymous	GU280_gp02, spike glycoprotein	0.000234576589256392
CAMB-75B8D	MN908947.3	24126	TTAACGGCCTTA	-	0.0215833333333333	0.0126666666666667	2.1e-07;7.7e-07;4.7e-05;0.00022;0.00027;0.00027;0.00025;0.00025;0.00025;0.00038;0.00085;0.00089	NA;NA;0.00059;0.0021;0.0024;0.0024;0.0023;0.0023;0.0023;0.0048;0.0064;0.0068	0.0171995688880905	TTT	S	.	2564-2575-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.992221223021583
CAMB-75B8D	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-75B8D	MN908947.3	25508	C	T	0.045	0.019	1.9e-21	2.2e-10	0.0302733356962659	GCC	ORF3a	A39V	C116T	GCC>GTC	Missense	GU280_gp03	0.969684965494235
CAMB-75B8D	MN908947.3	2558	C	T	1	1	0	0	0.999477806788512	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000522193211488251
CAMB-75B8D	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-75B8D	MN908947.3	28098	T	C	0.011	0.063	5e-05	2.9e-21	0.0449612403100775	ATC	ORF8	S69P	T205C	TCA>CCA	Missense	GU280_gp09	0.955038759689922
CAMB-75B8D	MN908947.3	5368	A	G	1	1	0	0	1	GAG	ORF1ab:nsp3	R883R	A2649G	AGA>AGG	Synonymous	ORF1ab:nsp3	0
CAMB-75B8D	MN908947.3	6362	G	A	0.064	0.03	4.1e-30	2.7e-15	0.0441894138467314	CGC	ORF1ab:nsp3	A1215T	G3643A	GCG>ACG	Missense	ORF1ab:nsp3	0.955622888400279
CAMB-75B8D	MN908947.3	6928	T	C	0.033	0.067	0.00018	1.1e-10	0.0567010309278351	CTA	ORF1ab:nsp3	P1403P	T4209C	CCT>CCC	Synonymous	ORF1ab:nsp3	0.943298969072165
CAMB-75B8D	MN908947.3	8377	A	-	0.034	0.026	2e-09	5.5e-08	0.0287966050318278	CAA	ORF1ab:nsp3	.	5658-5658-delfrshift	.	no-SNV	ORF1ab:nsp3	0.971203394968172
CAMB-75B9C	MN908947.3	10674	G	-	0.025	0.027	4.1e-12	2.3e-12	0.0260945709281961	TGG	ORF1ab:3C-like-proteinase	.	620-620-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.973905429071804
CAMB-75B9C	MN908947.3	11074	C	INS	0.039	0.029	1.1e-08	1.1e-05	0.0339806808286588	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.965816812134222
CAMB-75B9C	MN908947.3	11152	C	T	0.18	0.1	2.2e-82	8.5e-48	0.143978383942357	TCA	ORF1ab:nsp6	V60V	C180T	GTC>GTT	Synonymous	ORF1ab:nsp6	0.855984854054849
CAMB-75B9C	MN908947.3	11271	TGGTTGATACTAGTTTGTCTGGTTTT	-	0.0261923076923077	0.000769230769230769	3.3e-08;7e-09;5.5e-08;6.2e-08;2.7e-07;6.6e-08;3.1e-07;2e-07;1.1e-06;3.1e-07;2e-07;3.1e-07;4.2e-07;4.1e-06;7.4e-07;2e-06;6.7e-07;3.6e-07;2.8e-07;8.2e-08;7.8e-08;3.6e-07;1.2e-09;4.6e-07;7.9e-08;1.1e-08	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;4.3e-07	0.0145727074008535	ATG	ORF1ab:nsp6	.	299-324-delfrshift	.	no-SNV	ORF1ab:nsp6	0.984871569664271
CAMB-75B9C	MN908947.3	11296	TAAGC	-	0.0052	0.0198	1.1e-08;NA;NA;NA;NA	4.3e-07;2.6e-07;1.8e-08;1.4e-08;2.6e-09	0.00870386266094421	TTA	ORF1ab:nsp6	.	324-328-delfrshift	.	no-SNV	ORF1ab:nsp6	0.9768049207931
CAMB-75B9C	MN908947.3	12754	C	T	0.0096	0.0093	3.6e-06	3.9e-06	0.00949100650593188	GCA	ORF1ab:nsp9	C23C	C69T	TGC>TGT	Synonymous	ORF1ab:nsp9	0.990508993494068
CAMB-75B9C	MN908947.3	13019	C	T	0.13	0.13	1.6e-58	8.6e-61	0.129592483108108	TCT	ORF1ab:nsp9	L112L	C334T	CTA>TTA	Synonymous	ORF1ab:nsp9	0.870407516891892
CAMB-75B9C	MN908947.3	1405	T	-	0.011	0.011	3.4e-06	4.3e-06	0.0107784431137725	CTG	ORF1ab:nsp2	.	600-600-delfrshift	.	no-SNV	ORF1ab:nsp2	0.989221556886228
CAMB-75B9C	MN908947.3	1405	TG	-	0.0105	0.0055	3.4e-06;4.8e-06	4.3e-06;NA	0.00823206585652685	CTG	ORF1ab:nsp2	.	600-601-delfrshift	.	no-SNV	ORF1ab:nsp2	0.989221556886228
CAMB-75B9C	MN908947.3	14289	TG	-	0.0075	0.017	NA;5.7e-09	7.9e-10;1.2e-09	0.0108311017597552	TTG	ORF1ab:RNA-dependent-RNA-polymerase	.	822-823-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.993996220728586
CAMB-75B9C	MN908947.3	14290	G	-	0.015	0.017	5.7e-09	1.2e-09	0.0157747556107938	TGA	ORF1ab:RNA-dependent-RNA-polymerase	.	823-823-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.984153540954612
CAMB-75B9C	MN908947.3	14408	C	T	1	1	0	0	0.999322374200025	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000527042288869369
CAMB-75B9C	MN908947.3	17167	C	T	0.032	0.023	9.7e-16	1.7e-11	0.0269580784723258	TCA	ORF1ab:helicase	H311Y	C931T	CAT>TAT	Missense	ORF1ab:helicase	0.972997165448307
CAMB-75B9C	MN908947.3	17410	C	T	0.013	0.014	6.9e-07	2.1e-07	0.0134698174571842	ACG	ORF1ab:helicase	R392C	C1174T	CGT>TGT	Missense	ORF1ab:helicase	0.986464384411483
CAMB-75B9C	MN908947.3	17410	CG	TT	0.01145	0.007017	6.9e-07;1e-06	2.1e-07;0.46	0.00896818831315334	ACG	ORF1ab:helicase	.	1174-1175-mnv	.	no-SNV	ORF1ab:helicase	0.986464384411483
CAMB-75B9C	MN908947.3	18377	C	T	0.032	0.018	1.6e-15	1.2e-09	0.0232342187227951	ACA	ORF1ab:3'-to-5'-exonuclease	T113I	C338T	ACA>ATA	Missense	ORF1ab:3'-to-5'-exonuclease	0.976746435549709
CAMB-75B9C	MN908947.3	186	CAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGAT	-	0.0211666666666667	0.00114405555555556	5.2e-11;2.8e-11;1.3e-11;5e-11;5.5e-11;2.2e-11;6.3e-11;4.6e-11;5.2e-12;4.7e-11;1.3e-11;1.1e-11;4.5e-11;8e-11;7.7e-12;1.9e-11;5.7e-11;1.9e-11;6.2e-11;3.1e-11;2.1e-11;1.8e-11;6.2e-11;6.9e-14;1.7e-10;2.1e-12;4.3e-11;1.4e-11;6.6e-11;6.7e-12;3.6e-11;4.7e-11;9.4e-11;7.5e-11;2.4e-12;4.3e-12	NA;NA;NA;NA;NA;NA;NA;NA;0.39;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;7.4e-10;6.1e-12;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00856651876170202	GCA	NA	NA	NA	NA	NA	NA	0.991300554300965
CAMB-75B9C	MN908947.3	208	GT	-	0.0235	0.0205	6.2e-11;6.9e-14	7.4e-10;6.1e-12	0.0212705695754383	CGT	NA	NA	NA	NA	NA	NA	0.981210959858647
CAMB-75B9C	MN908947.3	23335	T	C	0.0091	0.013	0.00012	4.5e-06	0.0103705266118259	CTT	S	S591S	T1773C	TCT>TCC	Synonymous	GU280_gp02, spike glycoprotein	0.98954158756943
CAMB-75B9C	MN908947.3	23403	A	G	1	1	0	0	0.999820800208523	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000162908901342369
CAMB-75B9C	MN908947.3	241	C	T	1	1	0	0	0.99981714643958	TCG	NA	NA	NA	NA	NA	NA	0.000104487748811452
CAMB-75B9C	MN908947.3	25100	C	T	0.021	0.019	4e-11	3e-10	0.020492480581722	TCA	S	Q1180*	C3538T	CAA>TAA	Nonsense	GU280_gp02, spike glycoprotein	0.979507519418278
CAMB-75B9C	MN908947.3	25169	C	T	0.058	0.11	2.6e-26	5.6e-47	0.079214000614062	ACT	S	L1203F	C3607T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.920734827550916
CAMB-75B9C	MN908947.3	25429	G	T	1	1	0	0	0.999901756109542	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0
CAMB-75B9C	MN908947.3	25521	C	T	0.029	0.019	5.3e-14	1.3e-09	0.0251427077432568	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.967689223931326
CAMB-75B9C	MN908947.3	25916	C	T	1	1	0	0	0.999847514486124	ACA	ORF3a	T175I	C524T	ACA>ATA	Missense	GU280_gp03	0.000152485513876182
CAMB-75B9C	MN908947.3	27503	C	T	0.16	0.083	7.5e-75	1.5e-38	0.13667921371811	TCT	ORF7a	S37F	C110T	TCT>TTT	Missense	GU280_gp07	0.86332078628189
CAMB-75B9C	MN908947.3	28086	G	T	0.011	0.0094	6.7e-06	3.1e-05	0.0102269095557686	GGC	ORF8	A65S	G193T	GCT>TCT	Missense	GU280_gp09	0.985937999360818
CAMB-75B9C	MN908947.3	28253	C	T	0.088	0.14	2.4e-39	4.1e-62	0.113976913258227	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.885773350352406
CAMB-75B9C	MN908947.3	28603	C	T	0.025	0.021	2.7e-08	4.1e-07	0.0229823419006397	TCT	N	F110F	C330T	TTC>TTT	Synonymous	GU280_gp10	0.974987551231471
CAMB-75B9C	MN908947.3	29094	TCGGCAGACGTGGTCCAGAA	-	0.00121545	0.006505	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00015;0.00017;0.00035;0.00017;0.0015	3.2e-05;4.9e-05;5e-07;3.3e-05;3.5e-05;2.5e-05;3.4e-05;2.6e-05;3.6e-05;3.8e-05;3.5e-05;6.3e-05;3.4e-05;3.4e-05;3.6e-05;3.2e-05;2.7e-05;7.8e-05;3.2e-05;0.00031	0.00278643336529243	TTC	N	.	821-840-delfrshift	.	no-SNV	GU280_gp10	0.997056208027966
CAMB-75B9C	MN908947.3	29123	GGAAATT	-	0.000751428571428571	0.00617142857142857	NA;NA;NA;NA;0.0015;0.022;NA	0.00038;0.00026;0.00037;6.3e-06;3.4e-05;0.00043;4.7e-05	0.00262303682087937	AGG	N	.	850-856-delfrshift	.	no-SNV	GU280_gp10	0.99734873591516
CAMB-75B9C	MN908947.3	29686	C	T	0.023	0.0081	3.9e-10	5.4e-05	0.0138952164009112	TCA	NA	NA	NA	NA	NA	NA	0.985876993166287
CAMB-75B9C	MN908947.3	3037	C	T	1	1	0	0	0.999307718933887	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75B9C	MN908947.3	3096	C	T	0.019	0.016	7.2e-08	6.3e-07	0.017554571821096	TCA	ORF1ab:nsp3	S126L	C377T	TCA>TTA	Missense	ORF1ab:nsp3	0.982445428178904
CAMB-75B9C	MN908947.3	4669	T	G	0.015	0.01	9.8e-09	1.9e-06	0.0125036707315188	CTC	ORF1ab:nsp3	S650S	T1950G	TCT>TCG	Synonymous	ORF1ab:nsp3	0.987357227863557
CAMB-75B9C	MN908947.3	635	C	T	0.21	0.076	4.9e-99	2.5e-34	0.164601769911504	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.835357069355835
CAMB-75B9C	MN908947.3	683	C	T	0.021	0.041	9.6e-11	1.9e-19	0.0311515954211885	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.968848404578811
CAMB-75B9C	MN908947.3	9430	C	T	0.016	0.01	8.6e-08	3.4e-05	0.0134563212154097	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.98654367878459
CAMB-75BAB	MN908947.3	11074	C	INS	0.035	0.032	1.1e-08	1.3e-06	0.0344833203023195	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.964604508730779
CAMB-75BAB	MN908947.3	11075	T	-	0.035	0.037	8.2e-09	3.6e-10	0.0355628427658732	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959716175722282
CAMB-75BAB	MN908947.3	11083	G	-	0.031	0.027	4e-13	1.2e-11	0.0301833840058331	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.840814978882637
CAMB-75BAB	MN908947.3	11083	G	T	0.13	0.13	7.9e-28	4.5e-29	0.128877821953803	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.840814978882637
CAMB-75BAB	MN908947.3	13730	C	T	1	1	0	0	0.996327135523687	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A88V	C263T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000136032017641205
CAMB-75BAB	MN908947.3	14408	C	T	1	1	0	0	0.996297923907688	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000519355998561783
CAMB-75BAB	MN908947.3	23403	A	G	1	1	0	0	0.998269636739073	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.0750285509938e-05
CAMB-75BAB	MN908947.3	241	C	T	1	1	0	0	0.998420651345169	TCG	NA	NA	NA	NA	NA	NA	8.16904476636532e-05
CAMB-75BAB	MN908947.3	25429	G	T	1	1	0	0	0.997646675476548	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0.000235332452345178
CAMB-75BAB	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0354594594594595	0.0348918918918919	0.00053;2.5e-05;0.00017;0.00015;0.00033;9.4e-06;3e-05;5.9e-06;5.7e-06;9e-07;2.6e-06;1.6e-06;5e-06;3.2e-06;3.6e-06;6.7e-06;2.7e-06;5.8e-06;3.4e-06;3.9e-06;3.8e-06;6.9e-06;3.3e-06;4.7e-06;3.8e-06;2.9e-06;5.7e-06;3e-06;2.1e-06;3.8e-06;5.5e-06;5.3e-06;3.4e-06;5.6e-06;1.3e-06;3.9e-06;3.2e-06	0.00056;6e-05;0.00024;0.00023;0.00036;2.4e-06;1.2e-05;3.5e-06;3.8e-06;1.8e-06;1.8e-06;1.6e-06;3.4e-06;2.3e-06;2.2e-06;4.1e-06;1.8e-06;3.9e-06;2.5e-06;2.4e-06;2e-06;4.2e-06;2.2e-06;3.1e-06;2.4e-06;1.5e-06;3.6e-06;2.2e-06;6.3e-07;2.4e-06;3.9e-06;3.6e-06;1.2e-06;3.3e-06;8.3e-07;2.6e-06;1.5e-06	0.0366616258634079	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.977052760903693
CAMB-75BAB	MN908947.3	27769	C	T	1	1	0	7.8e-136	0.999352331606218	TCA	NA	NA	NA	NA	NA	NA	0
CAMB-75BAB	MN908947.3	28462	C	T	0.0069	0.0076	5.3e-05	1.2e-05	0.00706448812060936	ACC	N	D63D	C189T	GAC>GAT	Synonymous	GU280_gp10	0.992856579051227
CAMB-75BAB	MN908947.3	3037	C	T	1	1	0	0	0.999190310718262	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000168685267028778
CAMB-75BBA	MN908947.3	11075	T	-	0.04	0.038	5.8e-10	3.6e-10	0.0391022973496535	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956836803512749
CAMB-75BBA	MN908947.3	11460	C	T	0.043	0.037	1.6e-19	7.8e-17	0.039787969876208	TCC	ORF1ab:nsp6	S163F	C488T	TCC>TTC	Missense	ORF1ab:nsp6	0.960147386793368
CAMB-75BBA	MN908947.3	12325	C	T	0.0082	0.0069	1.3e-05	3e-05	0.00769096650458165	ACA	ORF1ab:nsp8	D78D	C234T	GAC>GAT	Synonymous	ORF1ab:nsp8	0.991398516050292
CAMB-75BBA	MN908947.3	13778	AT	-	0.0345	0.034	1.7e-10;3.5e-10	7.2e-11;1.5e-10	0.0340725064409275	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.967010144580238
CAMB-75BBA	MN908947.3	13780	A	T	0.029	0.025	3.6e-08	8.4e-08	0.0282090187443332	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I105L	A313T	ATA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.964250689265955
CAMB-75BBA	MN908947.3	14408	C	T	1	1	0	0	0.997434394944808	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000237556023628906
CAMB-75BBA	MN908947.3	1547	A	-	0.016	0.019	6.1e-08	1.1e-09	0.0170621518487653	TAG	ORF1ab:nsp2	.	742-742-delfrshift	.	no-SNV	ORF1ab:nsp2	0.895916487565244
CAMB-75BBA	MN908947.3	1547	A	G	0.034	0.031	2.6e-15	4.8e-14	0.0331154875213825	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.895916487565244
CAMB-75BBA	MN908947.3	1547	A	T	0.054	0.048	1.8e-23	2.4e-21	0.0517127944208079	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.895916487565244
CAMB-75BBA	MN908947.3	15842	C	T	0.0072	0.0078	6.5e-05	3e-05	0.00747483272047742	ACT	ORF1ab:RNA-dependent-RNA-polymerase	T792I	C2375T	ACT>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.989269998191573
CAMB-75BBA	MN908947.3	23403	A	G	1	1	0	0	0.998216091695696	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000294976963703787
CAMB-75BBA	MN908947.3	241	C	T	1	1	0	0	0.997636290484812	TCG	NA	NA	NA	NA	NA	NA	0.0002682223563334
CAMB-75BBA	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0318648648648649	0.0327027027027027	0.00089;5e-05;4e-04;0.00036;6e-04;2.9e-05;6.9e-05;2.3e-05;2.2e-05;3.6e-06;1.3e-05;1.1e-05;2e-05;1.5e-05;1.7e-05;2.6e-05;1.3e-05;2.3e-05;1.3e-05;1.5e-05;1.5e-05;2.5e-05;1.4e-05;1.8e-05;1.5e-05;1.1e-05;2.2e-05;1.2e-05;5.9e-06;1.6e-05;2.2e-05;2.1e-05;1.4e-05;2.1e-05;5.6e-06;1.2e-05;1e-05	0.00039;5.6e-05;2e-04;0.00023;0.00039;1.3e-05;3.4e-05;1.1e-05;1.1e-05;5.6e-06;6.3e-06;5.6e-06;9.5e-06;6.9e-06;7.4e-06;1.3e-05;5.7e-06;1.1e-05;7.3e-06;7.4e-06;6.6e-06;1.3e-05;6.9e-06;9.5e-06;7.8e-06;6e-06;1.2e-05;7.6e-06;5.8e-06;6.4e-06;1.1e-05;8e-06;3.1e-06;9.7e-06;3.8e-06;8.6e-06;6.2e-06	0.0332236648845544	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.97777516462841
CAMB-75BBA	MN908947.3	28334	T	C	0.19	0.19	1.1e-89	9.5e-89	0.190684232663528	CTC	N	S21P	T61C	TCA>CCA	Missense	GU280_gp10	0.808881592336811
CAMB-75BBA	MN908947.3	28514	G	T	1	1	0	0	0.997768458312493	AGA	N	D81Y	G241T	GAT>TAT	Missense	GU280_gp10	0.000192374283405794
CAMB-75BBA	MN908947.3	28795	A	G	0.009	0.0086	1.6e-05	1.9e-05	0.00889345569216596	AAG	N	E174E	A522G	GAA>GAG	Synonymous	GU280_gp10	0.986394075753818
CAMB-75BBA	MN908947.3	3037	C	T	1	1	0	0	0.998974326100196	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00016026154684445
CAMB-75BBA	MN908947.3	3602	C	T	1	1	0	0	0.999788655000423	ACA	ORF1ab:nsp3	H295Y	C883T	CAC>TAC	Missense	ORF1ab:nsp3	8.4537999830924e-05
CAMB-75BBA	MN908947.3	4554	C	T	0.0096	0.0092	6.1e-06	9.6e-06	0.00937482026801633	ACT	ORF1ab:nsp3	T612I	C1835T	ACT>ATT	Missense	ORF1ab:nsp3	0.979620789478729
CAMB-75BBA	MN908947.3	522	TT	-	0.0295	0.0335	0.00016;0.0019	2.3e-05;0.00046	0.0300741288539081	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.96324870504122
CAMB-75BC9	MN908947.3	10928	A	G	0.028	0.036	1.2e-13	5.4e-17	0.0302275189599133	TAC	ORF1ab:3C-like-proteinase	T292A	A874G	ACA>GCA	Missense	ORF1ab:3C-like-proteinase	0.969772481040087
CAMB-75BC9	MN908947.3	11075	T	-	0.032	0.034	2.7e-08	3.3e-09	0.0326051321789408	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964801955115787
CAMB-75BC9	MN908947.3	13620	C	T	0.015	0.015	2e-08	3.6e-08	0.0150301125949201	ACG	ORF1ab:RNA-dependent-RNA-polymerase	D51D	C153T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.983451165226499
CAMB-75BC9	MN908947.3	14241	G	A	0.016	0.014	3.2e-09	1.6e-08	0.0154113137173643	AGT	ORF1ab:RNA-dependent-RNA-polymerase	K258K	G774A	AAG>AAA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.984096560298384
CAMB-75BC9	MN908947.3	1440	G	A	1	1	0	0	1	GGC	ORF1ab:nsp2	G212D	G635A	GGC>GAC	Missense	ORF1ab:nsp2	0
CAMB-75BC9	MN908947.3	2137	C	T	0.0064	0.0072	2.4e-05	1.1e-05	0.00677810151817206	TCA	ORF1ab:nsp2	L444L	C1332T	CTC>CTT	Synonymous	ORF1ab:nsp2	0.993160558196596
CAMB-75BC9	MN908947.3	25889	C	T	0.018	0.016	9.9e-10	6.1e-09	0.0169148740577312	TCA	ORF3a	S166L	C497T	TCA>TTA	Missense	GU280_gp03	0.983085125942269
CAMB-75BC9	MN908947.3	28332	C	T	0.0089	0.0084	4.8e-06	6.2e-06	0.00869872331519464	CCC	N	P20L	C59T	CCC>CTC	Missense	GU280_gp10	0.991235872750105
CAMB-75BC9	MN908947.3	28708	C	T	1	1	0	0	0.999020756129875	ACA	N	H145H	C435T	CAC>CAT	Synonymous	GU280_gp10	0.000710431827345865
CAMB-75BC9	MN908947.3	2891	G	A	1	1	0	0	0.999387978142076	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	0.000612021857923497
CAMB-75BC9	MN908947.3	4668	C	T	1	1	0	0	0.998898579680076	TCT	ORF1ab:nsp3	S650F	C1949T	TCT>TTT	Missense	ORF1ab:nsp3	0.000192108195335613
CAMB-75BD8	MN908947.3	11075	T	-	0.051	0.066	1.8e-12	5.6e-16	0.0585421044124778	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.941307041646463
CAMB-75BD8	MN908947.3	13778	ATA	-	0.0103333333333333	0.0243333333333333	5.7e-06;7.1e-06;NA	3.1e-11;1.1e-10;0.00059	0.0259889519148778	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-313-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.975079373525603
CAMB-75BD8	MN908947.3	13780	A	G	0.011	0.0032	4.6e-07	0.0011	0.00683801864240313	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I105V	A313G	ATA>GTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.959620480699739
CAMB-75BD8	MN908947.3	13780	A	T	0.04	0.025	4.9e-11	1.1e-07	0.0319478160962141	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I105L	A313T	ATA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.959620480699739
CAMB-75BD8	MN908947.3	14408	C	T	1	1	0	0	0.998664164274674	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000331198940163391
CAMB-75BD8	MN908947.3	1546	TA	-	0.01565	0.017705	0.00058;2e-11	NA;2.8e-15	0.0170154840905224	CTA	ORF1ab:nsp2	.	741-742-delfrshift	.	no-SNV	ORF1ab:nsp2	0.995519713261649
CAMB-75BD8	MN908947.3	1547	A	-	0.024	0.035	2e-11	2.8e-15	0.0288352502834926	TAG	ORF1ab:nsp2	.	742-742-delfrshift	.	no-SNV	ORF1ab:nsp2	0.856957719099303
CAMB-75BD8	MN908947.3	1547	A	G	0.046	0.034	1.2e-19	8.7e-15	0.0409849343917058	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.856957719099303
CAMB-75BD8	MN908947.3	1547	A	T	0.078	0.067	3.4e-32	1.8e-27	0.0732220962254981	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.856957719099303
CAMB-75BD8	MN908947.3	15936	A	G	0.0099	0.0024	1.8e-06	0.0042	0.00597902056830062	CAG	ORF1ab:RNA-dependent-RNA-polymerase	P823P	A2469G	CCA>CCG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.994009232829404
CAMB-75BD8	MN908947.3	18058	C	INS	0.0051	0.0062	2.5e-05	8.6e-06	0.00570125427594071	ACT	ORF1ab:3'-to-5'-exonuclease	.	18-19-insfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.994277629967482
CAMB-75BD8	MN908947.3	18060	C	T	0.99	1	0	0	0.996797185131721	TCT	ORF1ab:3'-to-5'-exonuclease	L7L	C21T	CTC>CTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.000202995308552869
CAMB-75BD8	MN908947.3	18315	GG	-	0.0103	0.0056	1.5e-05;0.00048	0.0017;0.0046	0.00779202973615258	AGG	ORF1ab:3'-to-5'-exonuclease	.	276-277-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.987808130453004
CAMB-75BD8	MN908947.3	19071	TGA	-	0.0096	0.0023	1.3e-06;3.1e-06;2.7e-06	NA;0.00082;0.00082	0.00657710214842654	CTG	ORF1ab:3'-to-5'-exonuclease	.	1032-1034-delinframe	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.994609366788294
CAMB-75BD8	MN908947.3	1912	C	T	0.12	0.091	7.5e-56	4.2e-42	0.105410393110317	CCC	ORF1ab:nsp2	S369S	C1107T	TCC>TCT	Synonymous	ORF1ab:nsp2	0.894501728279337
CAMB-75BD8	MN908947.3	21034	C	T	0.016	0.0088	9.3e-09	1.1e-05	0.0127871362940276	TCT	ORF1ab:2'-O-ribose-methyltransferase	L126F	C376T	CTC>TTC	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.987193721286371
CAMB-75BD8	MN908947.3	2109	A	T	0.0067	0.0011	1.2e-05	0.0052	0.0030880382217561	AAC	ORF1ab:nsp2	N435I	A1304T	AAC>ATC	Missense	ORF1ab:nsp2	0.996853696906135
CAMB-75BD8	MN908947.3	23403	A	G	1	1	0	0	0.997919632103361	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000151605757649774
CAMB-75BD8	MN908947.3	241	C	T	1	1	0	0	0.999717577948486	TCG	NA	NA	NA	NA	NA	NA	9.41406838379274e-05
CAMB-75BD8	MN908947.3	26535	A	G	0.031	0.038	3.6e-15	3.9e-18	0.0343938896958905	CAA	M	N5D	A13G	AAC>GAC	Missense	GU280_gp05	0.965442106742889
CAMB-75BD8	MN908947.3	27512	A	-	0.12	0.0076	1.2e-27	0.0012	0.073094867807154	TAC	ORF7a	.	119-119-delfrshift	.	no-SNV	GU280_gp07	0.926905132192846
CAMB-75BD8	MN908947.3	27809	A	T	0.0088	0.0022	9.3e-06	0.0058	0.00508025327639523	TAT	NA	NA	NA	NA	NA	NA	0.994625239287292
CAMB-75BD8	MN908947.3	28311	C	T	0.0066	0.011	0.00016	1.3e-06	0.00887691695491138	CCC	N	P13L	C38T	CCC>CTC	Missense	GU280_gp10	0.990612915404002
CAMB-75BD8	MN908947.3	28514	G	T	1	1	0	0	0.999480721796703	AGA	N	D81Y	G241T	GAT>TAT	Missense	GU280_gp10	3.24548877060885e-05
CAMB-75BD8	MN908947.3	28795	A	G	0.0096	0.0039	7.7e-06	0.0023	0.00675850193715024	AAG	N	E174E	A522G	GAA>GAG	Synonymous	GU280_gp10	0.989754627636677
CAMB-75BD8	MN908947.3	29413	A	G	0.0085	0.0031	3e-05	0.0043	0.00614692653673163	AAG	N	Q380Q	A1140G	CAA>CAG	Synonymous	GU280_gp10	0.992053973013493
CAMB-75BD8	MN908947.3	3037	C	T	1	1	0	0	0.999482426010446	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.0002823130852115
CAMB-75BD8	MN908947.3	3763	A	G	0.012	0.004	1.4e-06	0.00091	0.0067789197463372	TAG	ORF1ab:nsp3	V348V	A1044G	GTA>GTG	Synonymous	ORF1ab:nsp3	0.993221080253663
CAMB-75BD8	MN908947.3	4554	C	A	0.0072	0.0031	1.3e-05	0.00082	0.00508542512149907	ACT	ORF1ab:nsp3	T612N	C1835A	ACT>AAT	Missense	ORF1ab:nsp3	0.979382734605942
CAMB-75BD8	MN908947.3	4554	C	T	0.011	0.0063	5.6e-07	0.00011	0.0087679743474122	ACT	ORF1ab:nsp3	T612I	C1835T	ACT>ATT	Missense	ORF1ab:nsp3	0.979382734605942
CAMB-75BD8	MN908947.3	462	A	G	0.0079	0.0066	2.1e-05	7.8e-05	0.00724181360201511	CAG	ORF1ab:leader-protein	Q66R	A197G	CAG>CGG	Missense	ORF1ab:leader-protein	0.982292791171884
CAMB-75BD8	MN908947.3	462	A	T	0.015	0.006	1.5e-05	0.0013	0.0104653952261005	CAG	ORF1ab:leader-protein	Q66L	A197T	CAG>CTG	Missense	ORF1ab:leader-protein	0.982292791171884
CAMB-75BD8	MN908947.3	6133	A	G	0.0056	0.0087	0.00029	1.5e-05	0.0072151751425579	AAG	ORF1ab:nsp3	K1138K	A3414G	AAA>AAG	Synonymous	ORF1ab:nsp3	0.989759106249273
CAMB-75BD8	MN908947.3	6629	C	T	0.011	0.0039	3.4e-06	0.0025	0.00704763522119385	CCT	ORF1ab:nsp3	L1304F	C3910T	CTT>TTT	Missense	ORF1ab:nsp3	0.992952364778806
CAMB-75BD8	MN908947.3	7869	C	T	0.025	0.0081	4.4e-12	2e-05	0.0182110337439743	TCA	ORF1ab:nsp3	S1717L	C5150T	TCA>TTA	Missense	ORF1ab:nsp3	0.981788966256026
CAMB-75BD8	MN908947.3	8415	A	T	0.015	0.0065	1.7e-05	0.0017	0.0107311256842448	GAT	ORF1ab:nsp3	D1899V	A5696T	GAT>GTT	Missense	ORF1ab:nsp3	0.989268874315755
CAMB-75BD8	MN908947.3	875	C	A	0.0097	0.0064	2.3e-06	4.7e-05	0.00804705131419974	CCT	ORF1ab:nsp2	L24I	C70A	CTT>ATT	Missense	ORF1ab:nsp2	0.99194155059612
CAMB-75BD8	MN908947.3	9052	A	T	0.022	0.0067	3.2e-09	0.00023	0.0146958657557432	CAG	ORF1ab:nsp4	P166P	A498T	CCA>CCT	Synonymous	ORF1ab:nsp4	0.979689983281389
CAMB-75BD8	MN908947.3	9255	GTGTATCTACTAGT	TGTGTATCTACTAG	0.00683571428571429	0.0002405	3.6e-05;2.7e-05;3.1e-05;2.5e-05;2.3e-05;3.2e-05;2.7e-05;3.8e-05;2.8e-05;2.9e-05;3.5e-05;3.1e-05;3.5e-05;3.2e-05	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0021;NA;NA;NA	0.00345379496251369	TGT	ORF1ab:nsp4	.	701-714-mnv	.	no-SNV	ORF1ab:nsp4	0.996446574663251
CAMB-75BD8	MN908947.3	9396	CAGCAT	TCAGCA	0.00786666666666667	0.000563833333333333	4e-05;3.2e-05;3.8e-07;1.9e-05;3.2e-05;3.4e-05	NA;NA;0.0024;NA;NA;NA	0.00352829420545529	TCA	ORF1ab:nsp4	.	842-847-mnv	.	no-SNV	ORF1ab:nsp4	0.996340919232485
CAMB-75BE7	MN908947.3	10277	C	T	0.013	0.013	9.8e-08	8.2e-08	0.0134223603545143	ACT	ORF1ab:3C-like-proteinase	L75F	C223T	CTC>TTC	Missense	ORF1ab:3C-like-proteinase	0.986560562851142
CAMB-75BE7	MN908947.3	10909	T	C	0.29	0.31	6.5e-142	7.8e-148	0.297218893863909	CTT	ORF1ab:3C-like-proteinase	A285A	T855C	GCT>GCC	Synonymous	ORF1ab:3C-like-proteinase	0.702718042504887
CAMB-75BE7	MN908947.3	11075	T	-	0.042	0.039	1.3e-10	2.2e-10	0.0410550315447561	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954338184771066
CAMB-75BE7	MN908947.3	1440	G	A	0.3	0.32	1.1e-126	2.5e-131	0.308886971527179	GGC	ORF1ab:nsp2	G212D	G635A	GGC>GAC	Missense	ORF1ab:nsp2	0.691113028472821
CAMB-75BE7	MN908947.3	14408	C	T	0.68	0.68	0	0	0.676964558360134	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.321768508592405
CAMB-75BE7	MN908947.3	23403	A	G	0.66	0.66	0	0	0.66048702274777	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.338811504158733
CAMB-75BE7	MN908947.3	23501	G	T	0.022	0.027	1.2e-10	1.5e-12	0.0232767547611544	TGC	S	A647S	G1939T	GCA>TCA	Missense	GU280_gp02, spike glycoprotein	0.976092926928099
CAMB-75BE7	MN908947.3	241	C	T	0.67	0.66	0	0	0.667889547643225	TCG	NA	NA	NA	NA	NA	NA	0.331291558845688
CAMB-75BE7	MN908947.3	27669	A	G	0.3	0.38	5.5e-57	8.5e-32	0.314569536423841	AAG	ORF7a	E92E	A276G	GAA>GAG	Synonymous	GU280_gp07	0.685430463576159
CAMB-75BE7	MN908947.3	28881	GGG	AAC	0.656666666666667	0.653333333333333	0;0;0	0;0;0	0.653475048997437	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.371164031860268
CAMB-75BE7	MN908947.3	2891	G	A	0.32	0.32	2.5e-157	8e-156	0.318825834652197	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	0.681174165347803
CAMB-75BE7	MN908947.3	3037	C	T	0.65	0.66	2e-171	1.4e-173	0.657115305138449	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.342655094824815
CAMB-75BE7	MN908947.3	3096	C	T	0.12	0.12	8.8e-43	5e-44	0.120246659815005	TCA	ORF1ab:nsp3	S126L	C377T	TCA>TTA	Missense	ORF1ab:nsp3	0.879753340184995
CAMB-75BE7	MN908947.3	6113	C	T	0.3	0.33	4.7e-133	1.3e-149	0.316070475173518	ACC	ORF1ab:nsp3	P1132S	C3394T	CCT>TCT	Missense	ORF1ab:nsp3	0.68379604911906
CAMB-75BF6	MN908947.3	13778	AT	-	0.0215	0.0315	3e-07;4.4e-07	6e-05;7.3e-05	0.0213605789240498	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.979354155637904
CAMB-75BF6	MN908947.3	14408	C	T	1	1	0	0	0.99907356574252	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000188718089486687
CAMB-75BF6	MN908947.3	17504	A	T	0.0089	0.012	6.2e-05	7.6e-06	0.00900430892895098	AAT	ORF1ab:helicase	N423I	A1268T	AAT>ATT	Missense	ORF1ab:helicase	0.990783143006203
CAMB-75BF6	MN908947.3	23403	A	G	1	1	0	5.9e-08	0.998903017474468	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.72522905304142e-05
CAMB-75BF6	MN908947.3	241	C	T	1	1	0	5.7e-11	0.998501376642387	TCG	NA	NA	NA	NA	NA	NA	6.97034119820165e-05
CAMB-75BF6	MN908947.3	28001	G	T	0.29	0.31	3e-136	5.3e-45	0.287462733406559	CGT	ORF8	P36P	G108T	CCG>CCT	Synonymous	GU280_gp09	0.711674250745332
CAMB-75BF6	MN908947.3	28881	GGG	AAC	1	1	0;0;0	6.6e-42;5.3e-46;1.3e-49	0.998740730376382	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000273298715496037
CAMB-75BF6	MN908947.3	29241	AA	-	0.00535	0.0135	0.00023;0.0021	5.7e-06;0.00017	0.00540836297060123	GAA	N	.	968-969-delfrshift	.	no-SNV	GU280_gp10	0.992658041443147
CAMB-75BF6	MN908947.3	29242	A	T	0.0078	0.0083	4.1e-05	0.00069	0.00781036188711817	AAG	N	E323D	A969T	GAA>GAT	Missense	GU280_gp10	0.980716195448517
CAMB-75BF6	MN908947.3	3037	C	T	1	1	0	9e-170	0.99922815683853	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000308737264587836
CAMB-75BF6	MN908947.3	313	C	T	1	1	0	5.5e-16	0.996991043930759	TCA	ORF1ab:leader-protein	L16L	C48T	CTC>CTT	Synonymous	ORF1ab:leader-protein	0
CAMB-75C02	MN908947.3	11075	T	-	0.038	0.055	5.4e-10	4.5e-14	0.0457189283010506	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.948224606237421
CAMB-75C02	MN908947.3	11083	G	T	0.028	0.011	3.5e-06	0.0098	0.0201451161463997	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.979248747615567
CAMB-75C02	MN908947.3	14408	C	T	1	1	0	0	0.999550340456511	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000256948310564858
CAMB-75C02	MN908947.3	14589	T	-	0.014	0.0086	2.7e-08	4.6e-06	0.0113761266212354	CTT	ORF1ab:RNA-dependent-RNA-polymerase	.	1122-1122-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.988596394812047
CAMB-75C02	MN908947.3	15613	C	T	0.01	0.0072	9.3e-07	1.6e-05	0.00893106936105193	ACA	ORF1ab:RNA-dependent-RNA-polymerase	H716Y	C2146T	CAC>TAC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.991068930638948
CAMB-75C02	MN908947.3	17163	CT	-	0.0095	0.0063	2.5e-06;2.5e-06	6.6e-05;6.7e-05	0.00776247871259027	GCT	ORF1ab:helicase	.	927-928-delfrshift	.	no-SNV	ORF1ab:helicase	0.991965005484412
CAMB-75C02	MN908947.3	18021	G	A	0.0074	0.0075	3.5e-05	3.2e-05	0.00746858303860336	GGA	ORF1ab:helicase	R595R	G1785A	AGG>AGA	Synonymous	ORF1ab:helicase	0.992493791857928
CAMB-75C02	MN908947.3	21405	A	G	0.11	0.032	5.6e-22	1.2e-08	0.0694736842105263	AAT	ORF1ab:2'-O-ribose-methyltransferase	K249K	A747G	AAA>AAG	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.930526315789474
CAMB-75C02	MN908947.3	23403	A	G	1	1	0	0	0.999950215731829	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.31895121141719e-05
CAMB-75C02	MN908947.3	241	C	T	1	1	0	0	0.999731194838941	TCG	NA	NA	NA	NA	NA	NA	0.000201603870794319
CAMB-75C02	MN908947.3	24128	AACGGCCTTA	-	0.0861	0.0644	2.1e-16;1e-14;2.3e-14;1.7e-14;1.6e-14;1.5e-14;1.5e-14;6.2e-14;2.9e-12;8.4e-13	1.2e-12;3e-11;5.2e-11;4.7e-11;4.4e-11;4.5e-11;4.3e-11;2.6e-10;3.5e-09;9.3e-10	0.0744633206938763	TAA	S	.	2566-2575-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.92627476453394
CAMB-75C02	MN908947.3	24391	T	C	0.0021	0.016	0.0056	1.5e-08	0.0060516846581616	GTG	S	S943S	T2829C	AGT>AGC	Synonymous	GU280_gp02, spike glycoprotein	0.993866535819431
CAMB-75C02	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999413214411454	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000132065504490227
CAMB-75C02	MN908947.3	3037	C	T	1	1	0	0	0.999667939565001	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75C02	MN908947.3	6199	T	C	0.015	0.012	6.2e-08	2.5e-06	0.0134846351362545	CTT	ORF1ab:nsp3	S1160S	T3480C	TCT>TCC	Synonymous	ORF1ab:nsp3	0.98065103950965
CAMB-75C02	MN908947.3	7204	T	C	0.028	0.016	2.1e-05	0.00014	0.019790454016298	CTT	ORF1ab:nsp3	S1495S	T4485C	TCT>TCC	Synonymous	ORF1ab:nsp3	0.980209545983702
CAMB-75C02	MN908947.3	7420	C	T	0.11	0.16	6.5e-46	9.8e-67	0.132644272179156	TCT	ORF1ab:nsp3	I1567I	C4701T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.867355727820844
CAMB-75C11	MN908947.3	14408	C	T	1	1	0	0	0.999487704918033	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.0003725782414307
CAMB-75C11	MN908947.3	23403	A	G	1	1	0	0	0.999971721856177	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-75C11	MN908947.3	23455	TA	-	0.115	0.0455	1.3e-25;6.3e-34	5.8e-11;3.7e-14	0.0831334247201279	CTA	S	.	1893-1894-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.915329018025602
CAMB-75C11	MN908947.3	241	C	T	1	1	0	0	0.999583035501549	TCG	NA	NA	NA	NA	NA	NA	0.000297831784608053
CAMB-75C11	MN908947.3	2940	C	T	1	1	0	0	0.998670212765957	CCA	ORF1ab:nsp3	P74L	C221T	CCA>CTA	Missense	ORF1ab:nsp3	0.00132978723404255
CAMB-75C11	MN908947.3	29742	G	C	0.011	0.035	1.5e-05	1.6e-11	0.02321083172147	CGC	NA	NA	NA	NA	NA	NA	0.97678916827853
CAMB-75C11	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75C11	MN908947.3	3241	C	T	0.22	0.21	7.9e-104	8.5e-93	0.216265181507079	ACG	ORF1ab:nsp3	D174D	C522T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.783734818492921
CAMB-75C11	MN908947.3	9805	G	A	0.12	0.11	1.4e-53	2.8e-50	0.112116333154438	TGT	ORF1ab:nsp4	L417L	G1251A	CTG>CTA	Synonymous	ORF1ab:nsp4	0.887832553860308
CAMB-75C20	MN908947.3	1087	A	G	0.12	0.33	1.3e-55	1.7e-157	0.212752613240418	TAT	ORF1ab:nsp2	V94V	A282G	GTA>GTG	Synonymous	ORF1ab:nsp2	0.787247386759582
CAMB-75C20	MN908947.3	14805	C	T	1	1	0	0	1	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-75C20	MN908947.3	28144	T	C	1	1	0	0	0.999909993024459	TTA	ORF8	L84S	T251C	TTA>TCA	Missense	GU280_gp09	6.75052316554533e-05
CAMB-75C20	MN908947.3	28657	C	T	1	1	0	0	0.999573196756295	ACG	N	D128D	C384T	GAC>GAT	Synonymous	GU280_gp10	0.000142267747901551
CAMB-75C20	MN908947.3	28863	C	T	1	1	0	0	1	TCA	N	S197L	C590T	TCA>TTA	Missense	GU280_gp10	0
CAMB-75C20	MN908947.3	29051	C	INS	0.024	0.099	1.5e-05	1.4e-33	0.0593673524879906	GCA	N	.	777-778-insfrshift	.	no-SNV	GU280_gp10	0.940542010332638
CAMB-75C20	MN908947.3	8782	C	T	1	1	0	0	0.999421965317919	GCC	ORF1ab:nsp4	S76S	C228T	AGC>AGT	Synonymous	ORF1ab:nsp4	0.000289017341040462
CAMB-75C20	MN908947.3	9477	T	A	1	1	0	0	1	TTT	ORF1ab:nsp4	F308Y	T923A	TTT>TAT	Missense	ORF1ab:nsp4	0
CAMB-75C3F	MN908947.3	12005	C	T	1	1	0	0	0.999813762920197	ACT	ORF1ab:nsp7	L55L	C163T	CTA>TTA	Synonymous	ORF1ab:nsp7	0.000155197566502157
CAMB-75C3F	MN908947.3	13914	T	G	0.0092	0.00095	1.7e-06	0.0088	0.00363131474954609	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.996261881875467
CAMB-75C3F	MN908947.3	14408	C	T	1	1	0	0	0.999311017970948	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00057415169087673
CAMB-75C3F	MN908947.3	21069	A	G	1	1	0	0	0.999914288163195	AAA	ORF1ab:2'-O-ribose-methyltransferase	K137K	A411G	AAA>AAG	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	8.57118368046627e-05
CAMB-75C3F	MN908947.3	23403	A	G	1	1	0	0	0.999686028257457	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000285428856857428
CAMB-75C3F	MN908947.3	241	C	T	1	1	0	0	0.999763593380615	TCG	NA	NA	NA	NA	NA	NA	0.000236406619385343
CAMB-75C3F	MN908947.3	28086	G	T	1	1	0	0	0.997639653815893	GGC	ORF8	A65S	G193T	GCT>TCT	Missense	GU280_gp09	0.002360346184107
CAMB-75C3F	MN908947.3	28881	GGG	AAC	0.99	1	0;0;0	0;0;0	0.997055359246172	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00266311584553928
CAMB-75C3F	MN908947.3	3037	C	T	1	1	0	0	0.998223801065719	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00118413262285376
CAMB-75C3F	MN908947.3	313	C	T	1	1	0	0	0.999757751937985	TCA	ORF1ab:leader-protein	L16L	C48T	CTC>CTT	Synonymous	ORF1ab:leader-protein	0.000242248062015504
CAMB-75C3F	MN908947.3	6048	TTAAGTTTGTATGTGATA	-	0.191111111111111	0.0191111111111111	1e-37;6.5e-45;2.9e-49;9.5e-48;3.6e-46;4.9e-47;2.9e-49;1e-47;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00029;1.6e-05;4.7e-06;4.7e-06;4.9e-06;8.8e-06;3.8e-06;3.1e-06;3.3e-06;2.1e-06;1.4e-06;1.7e-06;2.1e-06;9.7e-07;6.1e-07;8.6e-07;4.8e-06;6.6e-07	0.016025641025641	TTT	ORF1ab:nsp3	.	3329-3346-delinframe	.	no-SNV	ORF1ab:nsp3	0.922480620155039
CAMB-75C3F	MN908947.3	922	G	T	1	1	0	0	0.999110772357724	TGG	ORF1ab:nsp2	L39L	G117T	CTG>CTT	Synonymous	ORF1ab:nsp2	0.000889227642276423
CAMB-75C4E	MN908947.3	11075	T	-	0.038	0.037	8.7e-10	8.3e-10	0.0378328850530547	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957275441137351
CAMB-75C4E	MN908947.3	14408	C	T	1	1	0	0	0.99746192893401	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000478671297533173
CAMB-75C4E	MN908947.3	14612	A	G	0.026	0.025	8.1e-13	1e-12	0.0253730298948694	AAA	ORF1ab:RNA-dependent-RNA-polymerase	K382R	A1145G	AAA>AGA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.974548253362954
CAMB-75C4E	MN908947.3	23403	A	G	1	1	0	0	0.998976646759248	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.59646303536165e-05
CAMB-75C4E	MN908947.3	241	C	T	1	1	0	0	0.998671301453516	TCG	NA	NA	NA	NA	NA	NA	0.00012079077695312
CAMB-75C4E	MN908947.3	26013	C	T	1	1	0	0	0.999712772068679	TCA	ORF3a	F207F	C621T	TTC>TTT	Synonymous	GU280_gp03	0.000127656858364716
CAMB-75C4E	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99932157394844	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000239205836622414
CAMB-75C4E	MN908947.3	3037	C	T	1	1	0	0	0.998821897007618	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000157080398984213
CAMB-75C4E	MN908947.3	4999	C	T	0.02	0.018	9.4e-09	3.5e-08	0.0191053122087605	ACC	ORF1ab:nsp3	N760N	C2280T	AAC>AAT	Synonymous	ORF1ab:nsp3	0.980661696178938
CAMB-75C4E	MN908947.3	8991	C	T	0.026	0.025	2.6e-12	6.1e-12	0.0253843726047162	GCA	ORF1ab:nsp4	A146V	C437T	GCA>GTA	Missense	ORF1ab:nsp4	0.974525452004148
CAMB-75C5D	MN908947.3	12452	C	T	0.034	0.025	4.6e-17	2.3e-13	0.0302427650528048	ACC	ORF1ab:nsp8	P121S	C361T	CCT>TCT	Missense	ORF1ab:nsp8	0.969757234947195
CAMB-75C5D	MN908947.3	14408	C	T	1	1	0	0	0.999717434303476	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000242199168449522
CAMB-75C5D	MN908947.3	15277	C	T	1	1	0	0	1	TCA	ORF1ab:RNA-dependent-RNA-polymerase	H604Y	C1810T	CAC>TAC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-75C5D	MN908947.3	23403	A	G	1	1	0	0	0.999895273858859	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.97652638350713e-05
CAMB-75C5D	MN908947.3	241	C	T	1	1	0	0	0.999824139750278	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-75C5D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999809523809524	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-75C5D	MN908947.3	3037	C	T	1	1	0	0	0.999733404425487	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75C6C	MN908947.3	11075	T	-	0.036	0.035	3.8e-09	2.1e-09	0.0357247071574472	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960106715577973
CAMB-75C6C	MN908947.3	14408	C	T	1	1	0	0	0.998837361629659	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00026200301303465
CAMB-75C6C	MN908947.3	16438	A	G	1	1	0	0	0.998691484837581	TAT	ORF1ab:helicase	M68V	A202G	ATG>GTG	Missense	ORF1ab:helicase	0.00114495076711701
CAMB-75C6C	MN908947.3	20578	G	T	1	1	0	0	0.999882300322497	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	2.35399355005767e-05
CAMB-75C6C	MN908947.3	23403	A	G	1	1	0	0	0.998701932963191	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.42607443964631e-05
CAMB-75C6C	MN908947.3	241	C	T	1	1	0	0	0.999299542467101	TCG	NA	NA	NA	NA	NA	NA	0.000119226814110493
CAMB-75C6C	MN908947.3	2416	C	T	1	1	0	0	0.998550124275062	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0.000103562551781276
CAMB-75C6C	MN908947.3	25563	G	T	1	1	0	0	0.999792056560616	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	8.3177375753795e-05
CAMB-75C6C	MN908947.3	29032	G	A	0.0073	0.011	0.00015	5.4e-06	0.00822207564764482	AGG	N	E253E	G759A	GAG>GAA	Synonymous	GU280_gp10	0.991425387222235
CAMB-75C6C	MN908947.3	3037	C	T	1	1	0	0	0.999349567055571	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000162608236107159
CAMB-75C6C	MN908947.3	8139	C	T	1	1	0	0	0.999616679244379	TCC	ORF1ab:nsp3	S1807F	C5420T	TCC>TTC	Missense	ORF1ab:nsp3	0.00014374528335789
CAMB-75C6C	MN908947.3	9430	C	T	1	1	0	0	0.999566536627655	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	3.33433363342336e-05
CAMB-75C7B	MN908947.3	1059	C	T	1	1	0	0	0.999930353629446	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	6.96463705535145e-05
CAMB-75C7B	MN908947.3	11075	T	-	0.068	0.048	1.4e-16	6.6e-12	0.0576489198931563	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.937021861466248
CAMB-75C7B	MN908947.3	11075	TT	-	0.0340135	0.02775	1.4e-16;NA	6.6e-12;0.00062	0.0310061279002776	CTT	ORF1ab:nsp6	.	103-104-delfrshift	.	no-SNV	ORF1ab:nsp6	0.937021861466248
CAMB-75C7B	MN908947.3	11270	ATGGT	-	0.00944	0.002245	3.2e-05;0.00059;0.00041;0.00083;0.00094	NA;NA;NA;0.0074;0.0087	0.0045766295379538	TAT	ORF1ab:nsp6	.	298-302-delfrshift	.	no-SNV	ORF1ab:nsp6	0.994924000618681
CAMB-75C7B	MN908947.3	11295	TTAAGCTA	-	0.0091375	0.0013745	0.00093;0.00044;0.00028;8.7e-05;8e-05;3.8e-05;8.2e-06;4.6e-05	0.0084;0.0052;NA;NA;NA;NA;NA;0.5	0.00439981108155808	TTT	ORF1ab:nsp6	.	323-330-delfrshift	.	no-SNV	ORF1ab:nsp6	0.992835171894109
CAMB-75C7B	MN908947.3	11992	AAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAA	-	0.000120964285714286	0.00498571428571429	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.46;NA;NA;NA;NA;NA;6.4e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00066;0.00025;0.00024;0.00023;0.00019;0.00023;0.00024;0.00026;0.00033;0.00028;0.00029;0.00024;0.00026;0.00021;0.00027;0.00023;0.00027;0.00035;0.00016;3e-04;0.00029;0.00031;7.3e-06;0.00087;0.00027;3e-04;0.00034;0.00024;0.00018;0.00046;0.00025;0.00029;0.00028;0.00019;0.00025;0.00028;0.00024;2e-04;0.00018;1.6e-05;0.00025;0.00027;0.00031;0.00038;0.00025;0.00028;5e-04;0.00028;0.00018;0.00014;0.00027;0.00032;0.00016;0.00022;0.00041;3e-04	0.00253578459177205	AAA	ORF1ab:nsp7	.	150-205-delfrshift	.	no-SNV	ORF1ab:nsp7	0.995309661436829
CAMB-75C7B	MN908947.3	12506	AA	-	0.0098	0.00705	1.2e-05;8.1e-05	0.00034;0.00068	0.00834521367224173	TAA	ORF1ab:nsp8	.	415-416-delfrshift	.	no-SNV	ORF1ab:nsp8	0.988701553099202
CAMB-75C7B	MN908947.3	13171	T	C	0.0066	0.0074	8.2e-05	3.3e-05	0.00694010189750792	CTG	ORF1ab:nsp10	T49T	T147C	ACT>ACC	Synonymous	ORF1ab:nsp10	0.992967636777414
CAMB-75C7B	MN908947.3	13778	AT	-	0.0325	0.00445	1.8e-10;3e-10	0.0089;0.0097	0.017665555026203	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.982640927774516
CAMB-75C7B	MN908947.3	13780	A	T	0.016	0.012	8.3e-06	6.7e-05	0.0141354123301669	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I105L	A313T	ATA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.983461378344624
CAMB-75C7B	MN908947.3	14106	C	T	0.021	0.0034	3e-11	0.00093	0.0103126714207351	TCA	ORF1ab:RNA-dependent-RNA-polymerase	F213F	C639T	TTC>TTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.98960504662644
CAMB-75C7B	MN908947.3	14408	C	T	1	1	0	0	0.997979903296016	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000286723403146138
CAMB-75C7B	MN908947.3	1547	A	G	0.013	0.0057	2e-06	0.00058	0.00870053325849004	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.964355879876509
CAMB-75C7B	MN908947.3	1547	A	T	0.014	0.026	4e-07	9e-12	0.0210496772382823	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.964355879876509
CAMB-75C7B	MN908947.3	15840	GAC	-	0.00513333333333333	0.0026	0.001;1.8e-05;0.00055	0.0027;0.0033;0.0028	0.00339116398312557	GGA	ORF1ab:RNA-dependent-RNA-polymerase	.	2373-2375-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.996852999823659
CAMB-75C7B	MN908947.3	23403	A	G	1	1	0	0	0.99985936357329	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000121884903148381
CAMB-75C7B	MN908947.3	241	C	T	1	1	0	0	0.999905759951749	TCG	NA	NA	NA	NA	NA	NA	3.76960193003619e-05
CAMB-75C7B	MN908947.3	25563	G	T	1	1	0	0	0.999851754241476	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	4.9415252841377e-05
CAMB-75C7B	MN908947.3	29240	GAA	-	0.00383333333333333	0.0156	NA;0.00015;9e-04	0.00016;6.7e-11;3.3e-08	0.0120253742241694	GGA	N	.	967-969-delinframe	.	no-SNV	GU280_gp10	0.997549835862791
CAMB-75C7B	MN908947.3	3037	C	T	1	1	0	0	0.999755879241598	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75C7B	MN908947.3	4021	C	T	0.0077	0.0055	3.1e-05	0.00027	0.00653635849412356	ACT	ORF1ab:nsp3	N434N	C1302T	AAC>AAT	Synonymous	ORF1ab:nsp3	0.993400791904971
CAMB-75C7B	MN908947.3	4197	A	G	0.0033	0.0092	0.0031	7.3e-06	0.0067598631000017	GAA	ORF1ab:nsp3	E493G	A1478G	GAA>GGA	Missense	ORF1ab:nsp3	0.993206082174054
CAMB-75C7B	MN908947.3	682	T	C	1	1	0	0	0.999923271694928	ATC	ORF1ab:leader-protein	D139D	T417C	GAT>GAC	Synonymous	ORF1ab:leader-protein	6.13826440573928e-05
CAMB-75C7B	MN908947.3	8090	C	T	0.05	0.063	7.4e-24	3.1e-29	0.0568243610657966	ACT	ORF1ab:nsp3	L1791F	C5371T	CTC>TTC	Missense	ORF1ab:nsp3	0.943175638934203
CAMB-75C8A	MN908947.3	11075	T	-	0.049	0.041	4.2e-12	6.6e-11	0.0466034985422741	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.947944606413994
CAMB-75C8A	MN908947.3	11124	C	T	0.019	0.015	8.4e-10	2.2e-08	0.0172435415099072	GCT	ORF1ab:nsp6	A51V	C152T	GCT>GTT	Missense	ORF1ab:nsp6	0.982458615500376
CAMB-75C8A	MN908947.3	14408	C	T	1	1	0	0	0.997377417693064	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000265380352487551
CAMB-75C8A	MN908947.3	160	G	T	0.0082	0.0031	8.9e-06	0.001	0.00591548297970316	GGA	NA	NA	NA	NA	NA	NA	0.994013672912755
CAMB-75C8A	MN908947.3	23403	A	G	1	1	0	0	0.99792697888903	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.64087377134718e-05
CAMB-75C8A	MN908947.3	241	C	T	1	1	0	0	0.997801385681293	TCG	NA	NA	NA	NA	NA	NA	0.000166281755196305
CAMB-75C8A	MN908947.3	24138	C	T	0.025	0.027	2.5e-12	2.2e-13	0.0255755189792129	ACT	S	T859I	C2576T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.966383269813349
CAMB-75C8A	MN908947.3	2440	A	G	1	1	0	0	0.999271756281102	AAG	ORF1ab:nsp2	E545E	A1635G	GAA>GAG	Synonymous	ORF1ab:nsp2	0.000485495812598616
CAMB-75C8A	MN908947.3	24400	A	C	0.0082	0.011	4.4e-05	4.9e-07	0.00870812416760578	GAA	S	G946G	A2838C	GGA>GGC	Synonymous	GU280_gp02, spike glycoprotein	0.990882081753919
CAMB-75C8A	MN908947.3	25500	G	T	0.14	0.13	1.4e-62	5.5e-62	0.135552486683286	CGA	ORF3a	P36P	G108T	CCG>CCT	Synonymous	GU280_gp03	0.863335545312696
CAMB-75C8A	MN908947.3	26895	C	T	0.011	0.014	4e-06	2.4e-07	0.0114542786037904	CCA	M	H125Y	C373T	CAT>TAT	Missense	GU280_gp05	0.988450003190607
CAMB-75C8A	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998245538961873	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	9.38438438438438e-05
CAMB-75C8A	MN908947.3	3037	C	T	1	1	0	0	0.998665982555156	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00025654181631606
CAMB-75C8A	MN908947.3	3271	T	C	0.033	0.034	4.5e-16	9.2e-17	0.0335717613527364	TTC	ORF1ab:nsp3	I184I	T552C	ATT>ATC	Synonymous	ORF1ab:nsp3	0.966346022088849
CAMB-75C8A	MN908947.3	522	TT	-	0.0305	0.034	0.00013;0.0012	1.8e-05;0.00047	0.031118124756197	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.962660700203569
CAMB-75C8A	MN908947.3	6016	C	T	0.15	0.16	6.7e-62	2.7e-66	0.150464198057838	ACC	ORF1ab:nsp3	N1099N	C3297T	AAC>AAT	Synonymous	ORF1ab:nsp3	0.84921566535055
CAMB-75C8A	MN908947.3	6633	C	T	0.0075	0.009	3.5e-05	8.8e-06	0.00821018062397373	GCT	ORF1ab:nsp3	A1305V	C3914T	GCT>GTT	Missense	ORF1ab:nsp3	0.991789819376026
CAMB-75C8A	MN908947.3	8782	C	T	0.055	0.059	2.9e-25	1e-26	0.0572310977237198	GCC	ORF1ab:nsp4	S76S	C228T	AGC>AGT	Synonymous	ORF1ab:nsp4	0.942616387692073
CAMB-75CB7	MN908947.3	11075	T	-	0.045	0.044	5.1e-11	1.5e-11	0.0443512829779545	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.950328876039031
CAMB-75CB7	MN908947.3	1263	C	T	0.0086	0.0085	2.6e-05	3.2e-05	0.00856461655980186	ACG	ORF1ab:nsp2	T153M	C458T	ACG>ATG	Missense	ORF1ab:nsp2	0.990717807458161
CAMB-75CB7	MN908947.3	14408	C	T	1	1	0	0	0.997820835515313	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000287176715036235
CAMB-75CB7	MN908947.3	14805	C	T	0.037	0.042	1.1e-17	4.3e-20	0.0381760169314884	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.961743815036316
CAMB-75CB7	MN908947.3	1547	A	G	0.005	0.01	0.00082	7.9e-06	0.00690925840626439	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.971902349147858
CAMB-75CB7	MN908947.3	1547	A	T	0.019	0.013	1.8e-09	4.8e-07	0.0165822201750345	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.971902349147858
CAMB-75CB7	MN908947.3	23403	A	G	1	1	0	0	0.997245179063361	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000431836795473159
CAMB-75CB7	MN908947.3	241	C	T	1	1	0	0	0.999291496449945	TCG	NA	NA	NA	NA	NA	NA	0.00015074543618192
CAMB-75CB7	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999591670069416	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000153241048168769
CAMB-75CB7	MN908947.3	3037	C	T	1	1	0	0	0.999027651169857	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.07718018839259e-05
CAMB-75CB7	MN908947.3	851	T	C	0.055	0.053	2.6e-25	1e-24	0.054099795739714	CTA	ORF1ab:nsp2	Y16H	T46C	TAC>CAC	Missense	ORF1ab:nsp2	0.945156113218559
CAMB-75CC6	MN908947.3	10085	GG	-	0.00555	0.0112	0.00028;6.9e-05	1.9e-07;1.6e-06	0.00811372627908536	TGG	ORF1ab:3C-like-proteinase	.	31-32-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.990949615020937
CAMB-75CC6	MN908947.3	11001	C	T	0.011	0.012	4.2e-06	2.3e-06	0.0113889773813316	ACA	ORF1ab:nsp6	T10I	C29T	ACA>ATA	Missense	ORF1ab:nsp6	0.988611022618668
CAMB-75CC6	MN908947.3	11075	TT	-	0.01745	0.0286	2.8e-07;0.00041	7.4e-13;0.00071	0.0221421967005694	CTT	ORF1ab:nsp6	.	103-104-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957531380753138
CAMB-75CC6	MN908947.3	13730	C	T	1	0.99	0	0	0.997742426628865	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A88V	C263T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000131254265763637
CAMB-75CC6	MN908947.3	14408	C	T	1	1	0	0	0.998837467731182	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000307729129981365
CAMB-75CC6	MN908947.3	16468	C	T	0.07	0.051	6.2e-31	6.9e-23	0.061336032388664	ACC	ORF1ab:helicase	P78S	C232T	CCC>TCC	Missense	ORF1ab:helicase	0.938663967611336
CAMB-75CC6	MN908947.3	16949	C	T	0.012	0.0087	5.3e-07	1e-05	0.0100772312394168	CCT	ORF1ab:helicase	P238L	C713T	CCT>CTT	Missense	ORF1ab:helicase	0.989902118696568
CAMB-75CC6	MN908947.3	17532	A	G	0.0068	0.0037	4.2e-05	0.001	0.00529703634169237	TAG	ORF1ab:helicase	I432M	A1296G	ATA>ATG	Missense	ORF1ab:helicase	0.994613562201064
CAMB-75CC6	MN908947.3	21137	A	G	0.0099	0.0049	4.3e-05	0.0039	0.00812614544071372	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.991873854559286
CAMB-75CC6	MN908947.3	21812	C	T	0.024	0.005	1.3e-11	0.00073	0.0145510469655744	CCT	S	L84L	C250T	CTA>TTA	Synonymous	GU280_gp02, spike glycoprotein	0.985448953034426
CAMB-75CC6	MN908947.3	23403	A	G	1	1	0	0	0.999945020960759	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.12342794309669e-05
CAMB-75CC6	MN908947.3	241	C	T	1	1	0	0	0.99856524427953	TCG	NA	NA	NA	NA	NA	NA	0.000173160173160173
CAMB-75CC6	MN908947.3	25419	AATT	-	0.007325	0.0055	4.9e-05;2.3e-05;0.00026;0.00046	0.00025;0.00011;0.0013;0.0015	0.0066690780847312	CAA	ORF3a	.	27-30-delfrshift	.	no-SNV	GU280_gp03	0.993535608566951
CAMB-75CC6	MN908947.3	25429	G	T	0.99	0.99	0	0	0.993246534697312	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	6.64275275674239e-05
CAMB-75CC6	MN908947.3	26211	G	T	0.0051	0.02	0.0011	3.1e-08	0.0113748763600396	TGC	ORF3a	V273V	G819T	GTG>GTT	Synonymous	GU280_gp03	0.98862512363996
CAMB-75CC6	MN908947.3	26681	C	T	0.021	0.07	4.2e-10	1.5e-31	0.0441659450008987	TCC	M	F53F	C159T	TTC>TTT	Synonymous	GU280_gp05	0.955817715396807
CAMB-75CC6	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.0543414634146341	0.0598048780487805	5.6e-06;4e-08;2e-07;2.1e-07;8.6e-07;4.5e-11;2.8e-10;3.4e-10;3.5e-10;1.9e-11;1.2e-10;7.5e-11;2.9e-10;1.8e-10;2.2e-10;5.5e-10;1.2e-10;4.4e-10;1.9e-10;2.4e-10;1.5e-10;5.7e-10;1.3e-10;2.9e-10;1.9e-10;7.3e-11;3.6e-10;1.3e-10;7.2e-11;1.9e-10;4e-10;3.3e-10;2.2e-10;3.5e-10;2.6e-11;1.3e-10;5.6e-11;6.9e-06;0.00017;7e-05;0.00045	1.2e-07;1.1e-09;6.5e-08;6.7e-08;2.2e-07;2.7e-11;1.5e-10;2.5e-11;2.5e-11;9.3e-12;9.6e-12;7.8e-12;2.2e-11;1.4e-11;1.7e-11;4e-11;9.4e-12;3.2e-11;1.5e-11;1.4e-11;7.4e-12;3.7e-11;1.3e-11;2.4e-11;1.5e-11;5.7e-12;2.7e-11;1.3e-11;1.9e-11;1.3e-11;2.9e-11;2.2e-11;3.8e-12;2.3e-11;1.5e-12;1.4e-11;7.7e-12;1.7e-06;1.5e-05;3.8e-06;6.8e-06	0.0606273653348491	GTC	M	.	258-298-delfrshift	.	no-SNV	GU280_gp05	0.962806627510478
CAMB-75CC6	MN908947.3	2880	C	T	0.0083	0.006	8.4e-06	1e-04	0.00737478234149339	GCC	ORF1ab:nsp3	A54V	C161T	GCC>GTC	Missense	ORF1ab:nsp3	0.992522790125986
CAMB-75CC6	MN908947.3	28854	C	T	0.0048	0.028	0.0051	2.2e-12	0.0158086409534845	TCA	N	S194L	C581T	TCA>TTA	Missense	GU280_gp10	0.984191359046515
CAMB-75CC6	MN908947.3	2911	T	C	0.01	0.0082	7.6e-06	6.3e-05	0.00938811574994478	CTT	ORF1ab:nsp3	T64T	T192C	ACT>ACC	Synonymous	ORF1ab:nsp3	0.990501435829468
CAMB-75CC6	MN908947.3	2933	C	T	0.037	0.031	2e-17	1.4e-14	0.0347245409015025	ACT	ORF1ab:nsp3	L72F	C214T	CTT>TTT	Missense	ORF1ab:nsp3	0.965275459098498
CAMB-75CC6	MN908947.3	3037	C	T	1	1	0	0	0.99949012109624	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000127469725940089
CAMB-75CC6	MN908947.3	3722	A	G	0.045	0.035	1.7e-15	4e-13	0.0398773006134969	TAT	ORF1ab:nsp3	I335V	A1003G	ATT>GTT	Missense	ORF1ab:nsp3	0.960122699386503
CAMB-75CC6	MN908947.3	4112	G	T	0.0038	0.028	0.0024	9.1e-14	0.0149301841731257	TGC	ORF1ab:nsp3	A465S	G1393T	GCT>TCT	Missense	ORF1ab:nsp3	0.984981905027033
CAMB-75CC6	MN908947.3	522	TT	-	0.0495	0.043	7.1e-07;1.2e-06	4.3e-07;7.3e-05	0.0470115891682565	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.946851377981705
CAMB-75CC6	MN908947.3	5679	T	C	0.008	0.0034	8.7e-06	0.00068	0.00616085745632543	GTT	ORF1ab:nsp3	V987A	T2960C	GTT>GCT	Missense	ORF1ab:nsp3	0.993839142543675
CAMB-75CD5	MN908947.3	11075	T	-	0.21	0.0052	8.4e-55	0.009	0.0883115088276958	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.911584839166638
CAMB-75CD5	MN908947.3	13914	T	G	0.012	0.017	5.5e-08	7.4e-10	0.0146448937273199	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.985225505443235
CAMB-75CD5	MN908947.3	14408	C	T	1	0.85	0	0	0.94521050315388	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	7.33460466480857e-05
CAMB-75CD5	MN908947.3	23403	A	G	1	1	0	0	0.999895864067897	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.94239547355815e-05
CAMB-75CD5	MN908947.3	241	C	T	1	1	0	0	0.999900681983712	TCG	NA	NA	NA	NA	NA	NA	3.31060054293849e-05
CAMB-75CD5	MN908947.3	28408	ACCCAATA	-	0.0365	0.05275	1.7e-08;5.4e-11;2.2e-09;2.3e-09;5.2e-10;4e-10;3.9e-10;3e-09	1e-11;1.8e-15;5.2e-13;5.6e-13;5.4e-14;3.3e-14;4.4e-14;8.1e-13	0.0455467927145683	TAC	N	.	135-142-delfrshift	.	no-SNV	GU280_gp10	0.954438294382944
CAMB-75CD5	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-75CD5	MN908947.3	29051	C	INS	0.12	0.027	9e-30	1.7e-05	0.06232741617357	GCA	N	.	777-778-insfrshift	.	no-SNV	GU280_gp10	0.93767258382643
CAMB-75CD5	MN908947.3	29075	TACAATG	-	0.0107142857142857	0.0345714285714286	NA;NA;NA;1.5e-13;NA;NA;NA	1.2e-06;4.8e-07;2.4e-07;3.4e-07;5.7e-08;4.2e-07;2.2e-07	0.0214961306964746	ATA	N	.	802-808-delfrshift	.	no-SNV	GU280_gp10	0.978641606151217
CAMB-75CD5	MN908947.3	3037	C	T	1	1	0	0	0.99958686221855	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75CE4	MN908947.3	11074	C	INS	0.021	0.026	5e-04	4.6e-05	0.0228616534858436	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.976363880076851
CAMB-75CE4	MN908947.3	11075	T	-	0.032	0.028	3.9e-08	8.8e-08	0.030255869163809	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.966657873911897
CAMB-75CE4	MN908947.3	14408	C	T	1	1	0	0	0.998435649644001	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00061404406497171
CAMB-75CE4	MN908947.3	23403	A	G	1	1	0	0	0.999174295458625	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.37671273858673e-05
CAMB-75CE4	MN908947.3	241	C	T	1	1	0	0	0.999249949691748	TCG	NA	NA	NA	NA	NA	NA	0.000164645189616377
CAMB-75CE4	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99942764475818	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000140272127928181
CAMB-75CE4	MN908947.3	29825	G	T	0.0086	0.0087	2.4e-05	1e-05	0.00860501757362744	AGT	NA	NA	NA	NA	NA	NA	0.991314184139296
CAMB-75CE4	MN908947.3	3037	C	T	1	1	0	0	0.999396098798237	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000150975300440848
CAMB-75CE4	MN908947.3	835	C	T	0.045	0.04	8.5e-21	6.5e-19	0.0423372670744858	TCT	ORF1ab:nsp2	F10F	C30T	TTC>TTT	Synonymous	ORF1ab:nsp2	0.957279772642527
CAMB-75CF3	MN908947.3	11075	T	-	0.063	0.026	1.7e-15	5.1e-07	0.0424373152826771	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954440366097817
CAMB-75CF3	MN908947.3	13914	T	G	0.0096	0.0078	7e-07	4.6e-06	0.00857723690439723	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.991394914923835
CAMB-75CF3	MN908947.3	14408	C	T	1	1	0	0	0.999534533506742	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000342254774454104
CAMB-75CF3	MN908947.3	1547	A	G	0.0096	0.016	1.5e-05	3.4e-08	0.0130941704035874	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.960717488789238
CAMB-75CF3	MN908947.3	1547	A	T	0.03	0.016	1.6e-13	2.9e-08	0.022780269058296	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.960717488789238
CAMB-75CF3	MN908947.3	15952	C	T	0.014	0.0044	1.3e-06	0.0061	0.00851164790841823	CCT	ORF1ab:RNA-dependent-RNA-polymerase	L829L	C2485T	CTA>TTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.991458694781796
CAMB-75CF3	MN908947.3	1604	AATG	-	0.012	0.003525	5.1e-07;2.4e-07;2.9e-07;2.9e-07	0.0037;0.002;0.0019;0.0018	0.00689243460327798	TAA	ORF1ab:nsp2	.	799-802-delfrshift	.	no-SNV	ORF1ab:nsp2	0.992431667211151
CAMB-75CF3	MN908947.3	17005	A	-	0.0077	0.0053	1.3e-05	0.00016	0.00624574420625044	CAA	ORF1ab:helicase	.	769-769-delfrshift	.	no-SNV	ORF1ab:helicase	0.993495973138604
CAMB-75CF3	MN908947.3	1944	G	T	0.0059	0.0048	3.3e-05	1e-04	0.00521362312952807	CGT	ORF1ab:nsp2	R380L	G1139T	CGT>CTT	Missense	ORF1ab:nsp2	0.994718667479179
CAMB-75CF3	MN908947.3	23403	A	G	1	1	0	0	0.999893182105089	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.73964594723196e-05
CAMB-75CF3	MN908947.3	23709	C	T	0.022	0.0095	3.9e-11	6e-06	0.0134878819810327	ACA	S	T716I	C2147T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0.98640674394099
CAMB-75CF3	MN908947.3	241	C	T	1	1	0	0	0.998476145821123	TCG	NA	NA	NA	NA	NA	NA	0.00148478099480327
CAMB-75CF3	MN908947.3	24453	AACAACTT	-	0.00155	0.0088	NA;NA;NA;NA;NA;NA;0.00028;3e-04	1.2e-05;8.9e-06;1.5e-05;1.2e-05;1.2e-05;1.2e-05;2.3e-05;2.4e-05	0.00448086032518244	AAA	S	.	2891-2898-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.995462388956349
CAMB-75CF3	MN908947.3	25587	C	T	0.015	0.014	2e-08	7.8e-08	0.0141512822354716	TCA	ORF3a	L65L	C195T	CTC>CTT	Synonymous	GU280_gp03	0.985791250628547
CAMB-75CF3	MN908947.3	28622	CCAGAAGCTGGA	-	0.00954166666666667	0.000573583333333333	2.9e-06;4.9e-06;2.7e-06;2.6e-06;2.8e-06;3.9e-06;2e-06;3.7e-06;2.5e-06;2.7e-06;3.1e-06;4.6e-06	NA;NA;NA;NA;0.0011;0.001;NA;NA;NA;NA;NA;NA	0.00376479912815178	GCC	N	.	349-360-delinframe	.	no-SNV	GU280_gp10	0.99606416899163
CAMB-75CF3	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999728467470403	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	5.95983074080696e-05
CAMB-75CF3	MN908947.3	3037	C	T	1	1	0	0	0.999244712990937	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000137324910738808
CAMB-75CF3	MN908947.3	9059	TAT	-	0.00833333333333333	0.0100666666666667	NA;NA;8.4e-09	5.8e-06;1.3e-06;0.00015	0.00596715557227028	ATA	ORF1ab:nsp4	.	505-507-delinframe	.	no-SNV	ORF1ab:nsp4	0.994439721526549
CAMB-75CF3	MN908947.3	9061	TT	-	0.024	0.00502	8.4e-09;1.8e-07	0.00015;NA	0.0127362266805754	ATT	ORF1ab:nsp4	.	507-508-delfrshift	.	no-SNV	ORF1ab:nsp4	0.983579021259527
CAMB-75CF3	MN908947.3	9983	G	A	1	1	0	0	0.999850069342929	TGA	ORF1ab:nsp4	D477N	G1429A	GAC>AAC	Missense	ORF1ab:nsp4	0.000149930657071105
CAMB-75D0F	MN908947.3	10148	C	T	0.0033	0.012	0.0079	7.5e-07	0.00807169789870588	GCT	ORF1ab:3C-like-proteinase	L32F	C94T	CTT>TTT	Missense	ORF1ab:3C-like-proteinase	0.991890406805995
CAMB-75D0F	MN908947.3	11075	T	-	0.043	0.057	9.1e-11	4e-14	0.0489559296926189	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.947938922599208
CAMB-75D0F	MN908947.3	13813	GCAGACCTCGTCTAT	-	0.00894	0.000233333333333333	7.5e-06;1.6e-05;3.4e-05;3.2e-05;1.2e-05;1.1e-05;5.6e-06;1.1e-05;7.4e-05;0.00011;5.2e-06;1.9e-08;2.5e-07;1.7e-07;0.00095	NA;NA;NA;NA;NA;NA;NA;0.001;NA;NA;NA;NA;NA;NA;NA	0.00437288306961225	GGC	ORF1ab:RNA-dependent-RNA-polymerase	.	346-360-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.995469760652354
CAMB-75D0F	MN908947.3	14408	C	T	1	1	0	0	0.998008761449622	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000117999321503901
CAMB-75D0F	MN908947.3	14993	C	T	0.0045	0.0067	0.00036	4.1e-05	0.00551102204408818	TCA	ORF1ab:RNA-dependent-RNA-polymerase	S509L	C1526T	TCA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994488977955912
CAMB-75D0F	MN908947.3	16838	AA	-	0.00405	0.0085	0.039;0.004	0.00068;4.8e-05	0.00640158027581666	GAA	ORF1ab:helicase	.	602-603-delfrshift	.	no-SNV	ORF1ab:helicase	0.993113174716559
CAMB-75D0F	MN908947.3	20611	C	T	0.0068	0.013	0.00012	3.3e-07	0.0100098934993889	GCT	ORF1ab:endoRNAse	L331F	C991T	CTT>TTT	Missense	ORF1ab:endoRNAse	0.989408135948321
CAMB-75D0F	MN908947.3	21891	TA	-	0.0092	0.0255	0.024;0.0078	0.00014;1.9e-05	0.0172431489274351	TTA	S	.	329-330-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.981011235955056
CAMB-75D0F	MN908947.3	22286	CTTGCTTT	-	0.017625	0.0056375	7.3e-07;2.9e-08;6e-08;6.9e-07;2.1e-06;8e-04;5e-05;1.1e-05	0.0094;0.018;0.017;0.039;0.014;0.056;0.0059;4.7e-05	0.0110176431176952	ACT	S	.	724-731-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.98946909724744
CAMB-75D0F	MN908947.3	22293	TA	-	0.0135	0.0135	1.1e-05;0.001	4.7e-05;2e-04	0.013630989637666	TTA	S	.	731-732-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.984586014282684
CAMB-75D0F	MN908947.3	23403	A	G	1	1	0	0	0.99991223707691	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.85086153936167e-05
CAMB-75D0F	MN908947.3	241	C	T	1	1	0	0	0.999793908861919	TCG	NA	NA	NA	NA	NA	NA	0.000114495076711701
CAMB-75D0F	MN908947.3	24321	A	-	0.016	0.02	5.3e-06	2.8e-07	0.0178998973891232	CAA	S	.	2759-2759-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.981872078440315
CAMB-75D0F	MN908947.3	24321	AA	-	0.008	0.01415	5.3e-06;NA	2.8e-07;4e-04	0.0105871029836381	CAA	S	.	2759-2760-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.981872078440315
CAMB-75D0F	MN908947.3	25613	C	T	0.003	0.011	0.0019	4.2e-07	0.0066798721859954	TCC	ORF3a	S74F	C221T	TCC>TTC	Missense	GU280_gp03	0.993233376227173
CAMB-75D0F	MN908947.3	25867	C	T	0.0024	0.0079	0.0066	2.4e-05	0.00526981450252951	ACC	ORF3a	P159S	C475T	CCT>TCT	Missense	GU280_gp03	0.99473018549747
CAMB-75D0F	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0308918918918919	0.0420540540540541	0.0011;5e-05;0.00079;0.00087;0.0047;0.00012;0.00031;2.8e-05;2.7e-05;4.2e-06;1.8e-05;1.4e-05;2.4e-05;2.2e-05;2.5e-05;3.6e-05;1.9e-05;3.2e-05;1.6e-05;2.2e-05;2.1e-05;3.8e-05;2.3e-05;2.6e-05;2e-05;1.6e-05;3e-05;1.6e-05;6.2e-06;2.3e-05;1.1e-05;2.9e-05;2.2e-05;3.3e-05;6.9e-06;1.6e-05;1.4e-05	2e-07;2.2e-09;9.7e-08;1.2e-07;3.2e-07;9.5e-09;5.7e-08;6.5e-07;6.4e-07;3.3e-07;4.1e-07;3.7e-07;6e-07;5e-07;5.8e-07;8.6e-07;3.8e-07;7.6e-07;4.7e-07;4.6e-07;4.5e-07;8.7e-07;5e-07;6.4e-07;4.4e-07;1.9e-07;6.3e-07;4.6e-07;4.7e-07;4.9e-07;7.5e-07;6e-07;1.9e-07;6.4e-07;1.4e-07;4.5e-07;2.1e-07	0.0366806840482198	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.968647971733977
CAMB-75D0F	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999621236033079	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	6.90417011875173e-05
CAMB-75D0F	MN908947.3	28912	T	A	0.0023	0.012	0.0014	5.8e-07	0.00709643188751824	ATG	N	N213K	T639A	AAT>AAA	Missense	GU280_gp10	0.989255869478711
CAMB-75D0F	MN908947.3	3037	C	T	0.99	1	0	0	0.997218259629101	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75D0F	MN908947.3	4557	TAGCGTCACTTATCAACACAC	-	0.000228238095238095	0.00904285714285714	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00093;NA	7e-04;0.00086;7.1e-05;0.00012;0.00018;7.7e-05;8.6e-05;4e-05;5.5e-05;1.4e-05;1.2e-05;1.2e-05;1.1e-05;1.2e-05;1.2e-05;7.8e-05;7.8e-05;1.1e-05;1e-05;1e-05;9.2e-06	0.00508003064145466	GTA	ORF1ab:nsp3	.	1838-1858-delinframe	.	no-SNV	ORF1ab:nsp3	0.994284229670044
CAMB-75D0F	MN908947.3	5808	TAGACGGTG	-	0.00871111111111111	0.00434444444444444	3.9e-06;7.3e-06;0.00063;0.00059;0.00068;0.00047;0.00056;0.00048;0.00046	NA;NA;0.0053;0.0053;0.0057;0.0046;0.0046;0.0044;0.0043	0.0072662462297779	ATA	ORF1ab:nsp3	.	3089-3097-delinframe	.	no-SNV	ORF1ab:nsp3	0.994931802936573
CAMB-75D0F	MN908947.3	682	TC	-	0.0145	0.0365	1.6e-06;4.1e-07	3.7e-14;8e-16	0.0248846561506328	ATC	ORF1ab:leader-protein	.	417-418-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.977972931751409
CAMB-75D0F	MN908947.3	683	C	T	0.98	0.96	0	0	0.97219214079622	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.000113594196093874
CAMB-75D0F	MN908947.3	685	A	T	0.0098	0.024	1.3e-06	1.6e-12	0.0163878257700018	TAA	ORF1ab:leader-protein	L140L	A420T	CTA>CTT	Synonymous	ORF1ab:leader-protein	0.980419172589758
CAMB-75D0F	MN908947.3	9475	T	C	0.0077	0.011	5e-04	2.3e-05	0.00936160613579968	CTT	ORF1ab:nsp4	A307A	T921C	GCT>GCC	Synonymous	ORF1ab:nsp4	0.990412812993458
CAMB-75D1E	MN908947.3	11075	T	-	0.043	0.043	5.5e-11	7.8e-12	0.0431283487310652	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952131060789804
CAMB-75D1E	MN908947.3	14408	C	T	1	1	0	0	0.998575397108056	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000534226084478951
CAMB-75D1E	MN908947.3	15625	G	C	0.0065	0.0076	6.1e-05	7.2e-06	0.00683803248544284	TGA	ORF1ab:RNA-dependent-RNA-polymerase	E720Q	G2158C	GAG>CAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993066196751456
CAMB-75D1E	MN908947.3	17691	A	G	0.29	0.29	1.6e-145	1.1e-141	0.288901561052106	CAT	ORF1ab:helicase	S485S	A1455G	TCA>TCG	Synonymous	ORF1ab:helicase	0.710927364744458
CAMB-75D1E	MN908947.3	23403	A	G	1	1	0	0	0.999262235689349	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000118569264211844
CAMB-75D1E	MN908947.3	241	C	T	1	1	0	0	0.998757023667632	TCG	NA	NA	NA	NA	NA	NA	0.000136216584369147
CAMB-75D1E	MN908947.3	27441	G	T	0.28	0.29	3.1e-140	2.4e-139	0.282812450524049	AGC	ORF7a	E16D	G48T	GAG>GAT	Missense	GU280_gp07	0.717124220259016
CAMB-75D1E	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999214057149273	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000190888266734538
CAMB-75D1E	MN908947.3	29568	T	C	1	1	0	0	0.999630006474887	ATA	ORF10	I4T	T11C	ATA>ACA	Missense	GU280_gp11	0
CAMB-75D1E	MN908947.3	3037	C	T	1	1	0	0	0.999618053345216	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75D1E	MN908947.3	3457	C	T	0.02	0.016	1e-10	2.9e-09	0.0193417509006331	ACC	ORF1ab:nsp3	Y246Y	C738T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.98051834493372
CAMB-75D1E	MN908947.3	4232	G	T	0.0082	0.008	1.3e-05	8e-06	0.00812427086508245	AGA	ORF1ab:nsp3	D505Y	G1513T	GAC>TAC	Missense	ORF1ab:nsp3	0.991791648711993
CAMB-75D1E	MN908947.3	6027	C	T	0.0094	0.0081	9.9e-06	2.8e-05	0.00879833294744154	CCA	ORF1ab:nsp3	P1103L	C3308T	CCA>CTA	Missense	ORF1ab:nsp3	0.990970131974994
CAMB-75D2D	MN908947.3	11075	T	-	0.012	0.062	0.00026	3.3e-15	0.0407141181826962	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956291993763883
CAMB-75D2D	MN908947.3	13469	G	-	0.027	0.0074	3e-12	0.00013	0.0154632587859425	CGG	ORF1ab:nsp11	.	28-28-delfrshift	.	no-SNV	ORF1ab:nsp11	0.976613418530351
CAMB-75D2D	MN908947.3	14408	C	T	1	1	0	0	0.999512818951343	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000258814932099141
CAMB-75D2D	MN908947.3	14966	G	-	0.0086	0.012	9.1e-05	2.3e-06	0.01074016563147	TGG	ORF1ab:RNA-dependent-RNA-polymerase	.	1499-1499-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.98925983436853
CAMB-75D2D	MN908947.3	15952	C	T	0.019	0.0069	1.1e-08	0.00064	0.0117977891266404	CCT	ORF1ab:RNA-dependent-RNA-polymerase	L829L	C2485T	CTA>TTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.98812140409852
CAMB-75D2D	MN908947.3	21761	G	T	0.011	0.013	6.7e-07	1.5e-07	0.0121269640409153	TGC	S	A67S	G199T	GCT>TCT	Missense	GU280_gp02, spike glycoprotein	0.975218812612043
CAMB-75D2D	MN908947.3	23403	A	G	1	1	0	0	0.999900354737136	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.97162102913628e-05
CAMB-75D2D	MN908947.3	241	C	T	1	1	0	0	0.999837989631336	TCG	NA	NA	NA	NA	NA	NA	9.00057603686636e-05
CAMB-75D2D	MN908947.3	27281	G	T	1	1	0	0	0.999940084600544	TGG	ORF6	W27L	G80T	TGG>TTG	Missense	GU280_gp06	2.39661597823873e-05
CAMB-75D2D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999907381680096	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-75D2D	MN908947.3	3037	C	T	1	1	0	0	0.999363636363636	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75D2D	MN908947.3	4439	TG	-	0.0086	0.00665	8.2e-06;2e-05	5.6e-05;0.00014	0.00745095102590984	CTG	ORF1ab:nsp3	.	1720-1721-delfrshift	.	no-SNV	ORF1ab:nsp3	0.992097617664149
CAMB-75D2D	MN908947.3	5922	GT	-	0.011	0.00715	7.6e-07;1.4e-06	3.4e-05;5.9e-05	0.00884355746838428	GGT	ORF1ab:nsp3	.	3203-3204-delfrshift	.	no-SNV	ORF1ab:nsp3	0.991035092892952
CAMB-75D3C	MN908947.3	11074	C	INS	0.053	0.035	5.3e-13	3.9e-08	0.0414830572861267	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.958364990123082
CAMB-75D3C	MN908947.3	11083	G	-	0.038	0.19	9.9e-15	6.6e-84	0.138598118457665	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-75D3C	MN908947.3	11083	G	T	0.96	0.8	0	2.40000000001213e-313	0.861269378561018	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-75D3C	MN908947.3	14805	C	T	1	1	0	0	0.999866684442074	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-75D3C	MN908947.3	2480	A	G	1	1	3.8043054729776e-322	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-75D3C	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-75D3C	MN908947.3	29759	G	T	0.07	0.078	1.6e-11	1.7e-12	0.0739299610894942	TGT	NA	NA	NA	NA	NA	NA	0.926070038910506
CAMB-75D4B	MN908947.3	11075	T	-	0.014	0.043	0.00013	1.2e-10	0.0319561657639501	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.967817105428895
CAMB-75D4B	MN908947.3	12846	C	T	0.013	0.007	1.2e-07	3.7e-05	0.00955437563782113	GCT	ORF1ab:nsp9	A54V	C161T	GCT>GTT	Missense	ORF1ab:nsp9	0.990430834307012
CAMB-75D4B	MN908947.3	13155	TGT	-	0.00393333333333333	0.016	0.00066;0.0012;0.00063	1e-08;1.1e-08;7.2e-09	0.0109208483441612	ATG	ORF1ab:nsp10	.	131-133-delinframe	.	no-SNV	ORF1ab:nsp10	0.988814609239639
CAMB-75D4B	MN908947.3	13897	G	T	0.024	0.016	7.9e-13	3.1e-09	0.0193923723335488	TGA	ORF1ab:RNA-dependent-RNA-polymerase	D144Y	G430T	GAT>TAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.975478032404029
CAMB-75D4B	MN908947.3	14408	C	T	1	1	0	0	0.999611683997066	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00021573111274108
CAMB-75D4B	MN908947.3	15208	G	T	0.0031	0.01	0.0012	6e-07	0.00759605476225526	TGG	ORF1ab:RNA-dependent-RNA-polymerase	G581*	G1741T	GGA>TGA	Nonsense	ORF1ab:RNA-dependent-RNA-polymerase	0.988635359929339
CAMB-75D4B	MN908947.3	16392	T	C	0.0085	0.012	3.7e-05	5.2e-07	0.0111014744145707	CTC	ORF1ab:helicase	A52A	T156C	GCT>GCC	Synonymous	ORF1ab:helicase	0.988898525585429
CAMB-75D4B	MN908947.3	21101	G	T	0.058	0.0095	1.3e-26	6e-06	0.0304461371055495	GGT	ORF1ab:2'-O-ribose-methyltransferase	G148V	G443T	GGT>GTT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.963547334058759
CAMB-75D4B	MN908947.3	23269	TGC	-	0.00466666666666667	0.0072	NA;NA;2.4e-08	3.9e-05;3e-05;2.7e-05	0.00405297408379952	TTG	S	.	1707-1709-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.993731881971242
CAMB-75D4B	MN908947.3	23271	CTGACACTA	-	0.0144444444444444	8e-04	2.4e-08;3.8e-08;4e-08;2.7e-08;3.2e-08;2.5e-08;3.8e-08;2e-09;1.5e-08	2.7e-05;NA;NA;NA;NA;NA;NA;NA;NA	0.0061815513153438	GCT	S	.	1709-1717-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.989130640789948
CAMB-75D4B	MN908947.3	23403	A	G	0.99	1	0	0	0.994323931887183	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000413604963259559
CAMB-75D4B	MN908947.3	241	C	T	1	1	0	0	0.999728131584313	TCG	NA	NA	NA	NA	NA	NA	0.00011327850653617
CAMB-75D4B	MN908947.3	24833	C	T	0.016	0.01	1.1e-08	4.5e-06	0.0126812747482207	TCG	S	R1091C	C3271T	CGT>TGT	Missense	GU280_gp02, spike glycoprotein	0.987267796437529
CAMB-75D4B	MN908947.3	24899	C	T	0.019	0.0096	4.4e-10	4e-06	0.0134731541377047	ACA	S	Q1113*	C3337T	CAA>TAA	Nonsense	GU280_gp02, spike glycoprotein	0.986526845862295
CAMB-75D4B	MN908947.3	25011	A	C	0.01	0.012	2.3e-06	6.7e-07	0.0113539369798705	GAG	S	E1150A	A3449C	GAG>GCG	Missense	GU280_gp02, spike glycoprotein	0.98853047869692
CAMB-75D4B	MN908947.3	26266	G	A	0.014	0.0097	1.6e-08	1.5e-06	0.0114224385756449	AGA	E	E8K	G22A	GAG>AAG	Missense	GU280_gp04	0.988577561424355
CAMB-75D4B	MN908947.3	26266	GAGACAG	AGAGACA	0.00201428571428571	0.0101428571428571	1.6e-08;NA;NA;NA;NA;NA;NA	1.5e-06;7.2e-07;1.4e-06;1.2e-06;9e-07;5e-07;2.2e-06	0.00629027308990488	AGA	E	.	22-28-mnv	.	no-SNV	GU280_gp04	0.988577561424355
CAMB-75D4B	MN908947.3	26332	ACACTAGCCATC	TACACTAGTCAT	0.00152	0.0107666666666667	NA;NA;NA;NA;9.5e-10;NA;NA;NA;NA;NA;NA;NA	5.9e-07;6.2e-07;7.5e-07;8.8e-07;1.4e-06;4.2e-07;4.1e-07;1.9e-06;2.8e-06;3.8e-07;1.9e-06;1e-06	0.00671849911265106	TAC	E	.	88-99-mnv	.	no-SNV	GU280_gp04	0.993021870479108
CAMB-75D4B	MN908947.3	26589	G	T	0.0078	0.011	1.4e-05	1.2e-06	0.00952013915651984	AGT	M	V23L	G67T	GTA>TTA	Missense	GU280_gp05	0.986063516201944
CAMB-75D4B	MN908947.3	26885	C	T	0.022	0.0045	2.9e-11	0.0011	0.0120492364879232	ACG	M	N121N	C363T	AAC>AAT	Synonymous	GU280_gp05	0.987935012876145
CAMB-75D4B	MN908947.3	27030	G	T	0.0084	0.0067	2.5e-05	0.00014	0.00756960342663023	TGT	M	V170F	G508T	GTT>TTT	Missense	GU280_gp05	0.988885606676021
CAMB-75D4B	MN908947.3	28093	C	T	0.02	0.017	9.9e-09	3.3e-08	0.0181818181818182	TCT	ORF8	S67F	C200T	TCT>TTT	Missense	GU280_gp09	0.981616161616162
CAMB-75D4B	MN908947.3	28362	GAGAACGCAGTGGG	-	0.00721428571428571	0.000765571428571429	3.1e-05;3.3e-05;2.5e-05;2.4e-05;2e-05;2.5e-05;2.1e-05;2.4e-05;2.1e-05;3e-05;2.9e-05;0.00011;2.3e-05;2.4e-05	0.0014;0.0017;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0042;NA;NA	0.00318420474735981	GGA	N	.	89-102-delfrshift	.	no-SNV	GU280_gp10	0.994267559914359
CAMB-75D4B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999762456202862	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-75D4B	MN908947.3	29232	TT	-	0.003	0.008	4.5e-05;NA	1.1e-05;7.8e-06	0.00605765590351019	ATT	N	.	959-960-delfrshift	.	no-SNV	GU280_gp10	0.992808210189244
CAMB-75D4B	MN908947.3	3037	C	T	1	1	0	0	0.999662769784173	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000224820143884892
CAMB-75D4B	MN908947.3	345	TCG	-	0.00693333333333333	0.00286666666666667	1.4e-05;2e-05;2.1e-05	NA;0.00034;0.00034	0.00549964772810919	CTC	ORF1ab:leader-protein	.	80-82-delinframe	.	no-SNV	ORF1ab:leader-protein	0.996534232332462
CAMB-75D4B	MN908947.3	3546	ATGGACCACTT	-	0.0589090909090909	0.00627272727272727	1.3e-05;1.5e-05;6.4e-06;3.1e-09;3.1e-09;1.1e-08;3e-09;3.1e-09;1.6e-09;1.5e-09;9.7e-10	0.0037;0.0034;0.0029;NA;NA;NA;NA;NA;NA;NA;NA	0.0175131348511384	AAT	ORF1ab:nsp3	.	827-837-delfrshift	.	no-SNV	ORF1ab:nsp3	0.965641952983725
CAMB-75D4B	MN908947.3	4059	C	T	0.024	0.012	7.4e-12	3.9e-07	0.0165031222123104	CCA	ORF1ab:nsp3	P447L	C1340T	CCA>CTA	Missense	ORF1ab:nsp3	0.98349687778769
CAMB-75D4B	MN908947.3	5886	C	T	0.046	0.0072	1.8e-21	2.8e-05	0.022956633886829	ACA	ORF1ab:nsp3	T1056I	C3167T	ACA>ATA	Missense	ORF1ab:nsp3	0.976914396259874
CAMB-75D4B	MN908947.3	5895	TAAAACCAGTTACT	-	0.0305	0.00214664285714286	5.8e-12;2.1e-14;3.2e-15;7.4e-17;3e-19;2e-13;1.9e-13;6.2e-17;1.7e-15;1.5e-15;4.7e-14;8.2e-12;1e-11;4.4e-13	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;1.9e-05;2.1e-05;5.6e-06	0.0115703521548599	ATA	ORF1ab:nsp3	.	3176-3189-delfrshift	.	no-SNV	ORF1ab:nsp3	0.988714501557152
CAMB-75D4B	MN908947.3	5925	T	G	0.026	0.00094	4.6e-13	0.0075	0.0107475181717906	GTT	ORF1ab:nsp3	V1069G	T3206G	GTT>GGT	Missense	ORF1ab:nsp3	0.989167633000537
CAMB-75D4B	MN908947.3	8128	A	-	0.0077	0.032	3.6e-05	1.9e-15	0.0205364425891272	CAA	ORF1ab:nsp3	.	5409-5409-delfrshift	.	no-SNV	ORF1ab:nsp3	0.979127681013387
CAMB-75D4B	MN908947.3	8128	AAAG	-	0.001925	0.03325	3.6e-05;NA;NA;NA	1.9e-15;4.8e-12;1.3e-09;2.4e-09	0.0176108740946522	CAA	ORF1ab:nsp3	.	5409-5412-delfrshift	.	no-SNV	ORF1ab:nsp3	0.979127681013387
CAMB-75D4B	MN908947.3	842	C	T	0.01	0.0069	9.2e-07	2.3e-05	0.00838293555857528	CCC	ORF1ab:nsp2	P13S	C37T	CCT>TCT	Missense	ORF1ab:nsp2	0.991444812340906
CAMB-75D4B	MN908947.3	8921	C	T	0.0038	0.011	0.00065	7.2e-07	0.00800418910831837	ACC	ORF1ab:nsp4	P123S	C367T	CCT>TCT	Missense	ORF1ab:nsp4	0.991995810891682
CAMB-75D4B	MN908947.3	9558	ACTCATTCTTACCTGG	-	0.0146875	0.0079325	3.2e-05;6e-05;3.9e-05;3.8e-05;2.7e-05;1.5e-05;2.6e-05;3.1e-05;3.1e-06;9e-06;2e-05;1.3e-05;3.2e-05;9e-06;1.7e-06;1.1e-05	NA;0.004;0.0032;0.0031;0.0026;1e-05;2.1e-05;0.0051;0.0019;0.0027;0.0037;0.0031;0.0045;0.0026;0.0014;0.003	0.00991592247767433	TAC	ORF1ab:nsp4	.	1004-1019-delfrshift	.	no-SNV	ORF1ab:nsp4	0.994226166964846
CAMB-75D5A	MN908947.3	10946	AG	-	0.00985	0.0037	0.00018;1.7e-06	0.0011;NA	0.00651669344759864	TAG	ORF1ab:3C-like-proteinase	.	892-893-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.991352909385696
CAMB-75D5A	MN908947.3	11075	T	-	0.061	0.032	9.2e-15	1.7e-08	0.048457258472433	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.947799696509863
CAMB-75D5A	MN908947.3	11075	TT	-	0.0365	0.016015	9.2e-15;2.1e-05	1.7e-08;NA	0.0277296581240128	CTT	ORF1ab:nsp6	.	103-104-delfrshift	.	no-SNV	ORF1ab:nsp6	0.947799696509863
CAMB-75D5A	MN908947.3	14408	C	T	1	1	0	0	0.999578661230037	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000326197757390418
CAMB-75D5A	MN908947.3	15138	G	T	0.0087	0.0024	6.9e-06	0.0042	0.00544259601560895	TGA	ORF1ab:RNA-dependent-RNA-polymerase	M557I	G1671T	ATG>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994557403984391
CAMB-75D5A	MN908947.3	20268	A	G	1	1	4e-219	8.99999999999999e-281	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-75D5A	MN908947.3	20865	T	-	0.017	0.0045	1.8e-08	0.0035	0.0110084912517062	ATT	ORF1ab:2'-O-ribose-methyltransferase	.	207-207-delfrshift	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.988920600592083
CAMB-75D5A	MN908947.3	23403	A	G	1	1	0	0	0.999910061428045	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.19508575642836e-05
CAMB-75D5A	MN908947.3	241	C	T	1	1	0	0	0.999734536766658	TCG	NA	NA	NA	NA	NA	NA	0.000123882842226352
CAMB-75D5A	MN908947.3	24436	T	-	0.0067	0.011	0.00012	1.2e-06	0.0090124157055524	CTT	S	.	2874-2874-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.987489758618516
CAMB-75D5A	MN908947.3	29366	C	T	1	1	0	0	1	ACC	N	P365S	C1093T	CCA>TCA	Missense	GU280_gp10	0
CAMB-75D5A	MN908947.3	2937	C	T	1	1	0	0	0.999801232359372	ACA	ORF1ab:nsp3	T73I	C218T	ACA>ATA	Missense	ORF1ab:nsp3	0.000198767640628106
CAMB-75D5A	MN908947.3	3037	C	T	1	1	0	0	0.999361888809125	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000319055595437505
CAMB-75D5A	MN908947.3	3825	T	-	0.0082	0.0021	6.8e-06	0.0037	0.00543881334981459	GTT	ORF1ab:nsp3	.	1106-1106-delfrshift	.	no-SNV	ORF1ab:nsp3	0.994437577255871
CAMB-75D5A	MN908947.3	4322	T	C	0.0068	0.011	0.00019	2.4e-06	0.0089494992542084	CTT	ORF1ab:nsp3	F535L	T1603C	TTT>CTT	Missense	ORF1ab:nsp3	0.990925157618982
CAMB-75D5A	MN908947.3	5312	C	T	0.0088	0.0043	1.3e-05	0.00052	0.00625339858618815	ACT	ORF1ab:nsp3	L865F	C2593T	CTC>TTC	Missense	ORF1ab:nsp3	0.993746601413812
CAMB-75D5A	MN908947.3	7834	C	T	0.013	0.0088	3e-07	1.3e-05	0.0113736554399577	ACT	ORF1ab:nsp3	N1705N	C5115T	AAC>AAT	Synonymous	ORF1ab:nsp3	0.988626344560042
CAMB-75D69	MN908947.3	11074	C	INS	0.1	0.12	2.3e-40	1.8e-48	0.110684666142018	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.886010049034445
CAMB-75D69	MN908947.3	11083	G	-	0.18	0.15	2.1e-79	5.3e-66	0.164943960845225	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-75D69	MN908947.3	11083	G	T	0.82	0.85	0	0	0.83487725022628	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-75D69	MN908947.3	14116	A	G	0.11	0.11	5.2e-50	1.9e-48	0.106806535821328	CAC	ORF1ab:RNA-dependent-RNA-polymerase	T217A	A649G	ACG>GCG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.892884076186793
CAMB-75D69	MN908947.3	14805	C	T	1	1	0	0	0.998678625770802	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000490510130535757
CAMB-75D69	MN908947.3	21800	G	T	1	1	0	0	0.999930565199278	TGA	S	D80Y	G238T	GAT>TAT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-75D69	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-75D69	MN908947.3	2558	C	T	1	1	0	0	0.998492759864348	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-75D69	MN908947.3	26144	G	T	1	1	0	0	0.999910176951406	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	8.98230485942693e-05
CAMB-75D69	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.02575	0.03078125	0.002;0.0048;0.00047;0.00048;0.00013;0.00019;0.00015;3e-04;0.00024;0.00026;0.00039;0.00021;0.00034;0.00022;0.00025;0.00025;4e-04;0.00018;3e-04;0.00025;0.00019;0.00031;0.00022;0.00019;0.00021;0.00034;0.00031;0.00035;0.00051;0.00031;0.00045;0.00034	5.7e-05;0.00018;5.3e-05;5.4e-05;3e-05;3.4e-05;3.1e-05;5.1e-05;4.1e-05;4.5e-05;6.7e-05;3.5e-05;6e-05;4.2e-05;4.1e-05;3.8e-05;6.7e-05;4.3e-05;5.3e-05;4.3e-05;3e-05;5.7e-05;4.2e-05;2.5e-05;4e-05;5.9e-05;5.4e-05;2.3e-05;5.3e-05;1.9e-05;4e-05;1.7e-05	0.0283173029468859	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.974023480359886
CAMB-75D69	MN908947.3	27679	C	T	0.027	0.029	1.2e-06	2.6e-08	0.0284757118927973	ACT	ORF7a	L96F	C286T	CTT>TTT	Missense	GU280_gp07	0.969849246231156
CAMB-75D69	MN908947.3	29109	C	T	0.11	0.1	1.9e-48	2.3e-47	0.10595537357141	CCA	N	P279L	C836T	CCA>CTA	Missense	GU280_gp10	0.893928006841682
CAMB-75D69	MN908947.3	860	G	A	1	1	0	0	0.999712524722874	TGA	ORF1ab:nsp2	E19K	G55A	GAG>AAG	Missense	ORF1ab:nsp2	5.74950554252334e-05
CAMB-75D78	MN908947.3	13914	T	G	0.0074	0.013	8.1e-06	3.7e-08	0.0103190767141887	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.989545145960625
CAMB-75D78	MN908947.3	14408	C	T	1	1	0	0	0.999772429879957	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	5.68925300108096e-05
CAMB-75D78	MN908947.3	23403	A	G	1	1	0	0	0.999945229488443	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-75D78	MN908947.3	241	C	T	1	1	0	0	0.999866488651535	TCG	NA	NA	NA	NA	NA	NA	0.000133511348464619
CAMB-75D78	MN908947.3	27046	C	T	1	1	0	0	0.999664091367148	ACG	M	T175M	C524T	ACG>ATG	Missense	GU280_gp05	0.000335908632851864
CAMB-75D78	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998521803399852	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-75D78	MN908947.3	3037	C	T	1	1	2.6e-201	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75D87	MN908947.3	11074	C	INS	0.036	0.14	6e-08	5.8e-41	0.096638189282148	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.903139909020304
CAMB-75D87	MN908947.3	11083	G	-	0.21	0.16	5.5e-94	1e-72	0.182959319602418	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.000102469515319193
CAMB-75D87	MN908947.3	11083	G	T	0.79	0.84	2.50000000000851e-313	0	0.816835741366943	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.000102469515319193
CAMB-75D87	MN908947.3	14805	C	T	1	1	0	0	0.999849488260084	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	7.52558699578567e-05
CAMB-75D87	MN908947.3	15654	C	T	0.036	0.032	1.4e-17	5.9e-16	0.0341423282599753	ACA	ORF1ab:RNA-dependent-RNA-polymerase	D729D	C2187T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.965857671740025
CAMB-75D87	MN908947.3	17247	T	C	1	1	0	0	0.999929251123138	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	3.53744384307899e-05
CAMB-75D87	MN908947.3	18060	C	T	0.069	0.045	9.7e-30	9e-20	0.0569324898890387	TCT	ORF1ab:3'-to-5'-exonuclease	L7L	C21T	CTC>CTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.943067510110961
CAMB-75D87	MN908947.3	26787	GGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.173029411764706	0.0412058823529412	9.5e-38;7.8e-38;2e-41;4.3e-39;7.5e-40;6.1e-38;7.7e-39;2.7e-38;3.8e-37;4.2e-39;1.7e-37;9.6e-39;3.2e-38;4.5e-39;4e-37;9.7e-39;4.9e-38;1.4e-38;5.3e-40;7.1e-38;2.9e-39;3.9e-39;4.1e-38;1.5e-37;8.2e-38;4.4e-38;9.6e-38;1.4e-42;2.8e-39;7.9e-41;1.2e-12;1.8e-10;1.4e-11;6.7e-11	5e-07;5.1e-07;2.5e-07;2.5e-07;2.1e-07;5.1e-07;3.6e-07;3.9e-07;7.1e-07;2.5e-07;6.1e-07;3.9e-07;3.7e-07;3.1e-07;6.8e-07;3.9e-07;5.1e-07;3.6e-07;2.1e-07;5.4e-07;3.4e-07;2.3e-07;3.3e-07;5.6e-07;5e-07;1.5e-07;5.1e-07;1.1e-07;3.4e-07;1.7e-07;1.1e-05;6.3e-05;2.2e-05;3.6e-05	0.0885605642797016	AGG	M	.	265-298-delfrshift	.	no-SNV	GU280_gp05	0.91291453990704
CAMB-75D87	MN908947.3	28975	G	T	1	1	0	0	1	TGT	N	M234I	G702T	ATG>ATT	Missense	GU280_gp10	0
CAMB-75D87	MN908947.3	8313	T	INS	0.0049	0.0087	0.00019	1.3e-05	0.00649614291514413	ATG	ORF1ab:nsp3	.	5593-5594-insfrshift	.	no-SNV	ORF1ab:nsp3	0.993503857084856
CAMB-75D87	MN908947.3	8315	ACACC	-	0.0049	0.00872	0.00031;0.00032;0.00032;0.00072;0.00027	2.1e-05;2.1e-05;1.9e-05;4.6e-05;1.8e-05	0.0064464141821112	GAC	ORF1ab:nsp3	.	5596-5600-delfrshift	.	no-SNV	ORF1ab:nsp3	0.993158953722334
CAMB-75D96	MN908947.3	10870	G	T	0.0085	0.0097	2e-05	1e-05	0.00899463223560133	TGC	ORF1ab:3C-like-proteinase	L272L	G816T	CTG>CTT	Synonymous	ORF1ab:3C-like-proteinase	0.990715218337444
CAMB-75D96	MN908947.3	11075	T	-	0.033	0.052	6.4e-09	1.9e-13	0.0414817082504209	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954500229603551
CAMB-75D96	MN908947.3	11075	TT	-	0.02065	0.026	6.4e-09;0.00029	1.9e-13;NA	0.0232025703676626	CTT	ORF1ab:nsp6	.	103-104-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954500229603551
CAMB-75D96	MN908947.3	1170	C	T	0.0081	0.013	1.4e-05	1.5e-07	0.00934058274083368	TCT	ORF1ab:nsp2	S122F	C365T	TCT>TTT	Missense	ORF1ab:nsp2	0.990659417259166
CAMB-75D96	MN908947.3	1288	C	T	0.011	0.007	2.9e-06	0.00014	0.00971553877078638	GCG	ORF1ab:nsp2	C161C	C483T	TGC>TGT	Synonymous	ORF1ab:nsp2	0.990101723822867
CAMB-75D96	MN908947.3	14408	C	T	1	1	0	0	0.999653859466944	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000197794590317955
CAMB-75D96	MN908947.3	16375	C	T	0.012	0.0034	1.3e-05	0.0092	0.0070041779306955	TCC	ORF1ab:helicase	P47S	C139T	CCG>TCG	Missense	ORF1ab:helicase	0.992995822069304
CAMB-75D96	MN908947.3	16774	TATGTC	-	0.004	0.000566666666666667	0.00078;2.7e-05;0.00061;0.00075;0.00072;0.00069	0.0038;0.0035;NA;NA;NA;NA	0.00129931064351969	TTA	ORF1ab:helicase	.	538-543-delinframe	.	no-SNV	ORF1ab:helicase	0.997806898301706
CAMB-75D96	MN908947.3	17124	T	C	0.13	0.11	2.4e-61	1.5e-52	0.121217775289984	CTC	ORF1ab:helicase	A296A	T888C	GCT>GCC	Synonymous	ORF1ab:helicase	0.87835463507168
CAMB-75D96	MN908947.3	17440	C	T	0.0095	0.0036	4.7e-06	0.0023	0.00660989554435143	CCC	ORF1ab:helicase	P402S	C1204T	CCT>TCT	Missense	ORF1ab:helicase	0.993365980749282
CAMB-75D96	MN908947.3	18508	C	T	0.011	0.0058	1.8e-06	0.00026	0.00764808541217534	ACT	ORF1ab:3'-to-5'-exonuclease	L157F	C469T	CTT>TTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.992334804777059
CAMB-75D96	MN908947.3	20823	C	T	0.043	0.031	2e-20	1.3e-15	0.0378743330066427	ACA	ORF1ab:2'-O-ribose-methyltransferase	N55N	C165T	AAC>AAT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.962060328868562
CAMB-75D96	MN908947.3	23403	A	G	1	1	0	0	0.99990770309933	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.38375205360604e-05
CAMB-75D96	MN908947.3	241	C	T	1	1	0	0	0.999811813904862	TCG	NA	NA	NA	NA	NA	NA	6.27286983795086e-05
CAMB-75D96	MN908947.3	25350	C	T	0.99	1	0	0	0.995229279407576	CCA	S	P1263L	C3788T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	0.000189879426564132
CAMB-75D96	MN908947.3	26873	C	T	0.017	0.0067	2.7e-09	9.8e-05	0.012792266806202	ACA	M	N117N	C351T	AAC>AAT	Synonymous	GU280_gp05	0.987180193329845
CAMB-75D96	MN908947.3	27384	T	C	0.0075	0.0085	5.5e-05	2e-05	0.00777895186492502	ATT	ORF6	D61D	T183C	GAT>GAC	Synonymous	GU280_gp06	0.990287551428764
CAMB-75D96	MN908947.3	28374	G	A	0.012	0.0091	1.9e-07	2.9e-06	0.0106059373729158	GGG	N	G34E	G101A	GGG>GAG	Missense	GU280_gp10	0.989377795851972
CAMB-75D96	MN908947.3	29700	A	G	0.0057	0.012	0.00087	5.7e-06	0.00872545964474914	TAG	NA	NA	NA	NA	NA	NA	0.99096291679651
CAMB-75D96	MN908947.3	3037	C	T	1	1	0	0	0.999785292538916	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75D96	MN908947.3	344	C	T	0.0077	0.0045	3.5e-05	0.0011	0.00615535813580582	GCT	ORF1ab:leader-protein	L27F	C79T	CTC>TTC	Missense	ORF1ab:leader-protein	0.993779984740919
CAMB-75D96	MN908947.3	3712	A	G	0.012	0.0065	1.1e-05	0.00013	0.00834824090638044	TAT	ORF1ab:nsp3	L331L	A993G	TTA>TTG	Synonymous	ORF1ab:nsp3	0.99165175909362
CAMB-75D96	MN908947.3	4331	C	T	0.0059	0.0066	1e-04	4.8e-05	0.00628902155584925	TCT	ORF1ab:nsp3	L538L	C1612T	CTA>TTA	Synonymous	ORF1ab:nsp3	0.993665405824181
CAMB-75D96	MN908947.3	4991	A	T	0.01	0.0073	1.1e-06	1.6e-05	0.00852279115788527	CAA	ORF1ab:nsp3	N758Y	A2272T	AAC>TAC	Missense	ORF1ab:nsp3	0.991319795812813
CAMB-75D96	MN908947.3	561	G	-	0.0069	0.0086	2.8e-05	5.1e-06	0.00746296503600881	CGT	ORF1ab:leader-protein	.	296-296-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.992462405313631
CAMB-75D96	MN908947.3	6172	TATTGAT	-	0.000685714285714286	0.00827142857142857	NA;NA;NA;NA;0.00035;NA;NA	2e-05;1.9e-05;1.9e-05;1.6e-05;1.7e-05;1.6e-05;2.3e-05	0.00420244838297095	CTA	ORF1ab:nsp3	.	3453-3459-delfrshift	.	no-SNV	ORF1ab:nsp3	0.995457023441759
CAMB-75D96	MN908947.3	7666	TGAAG	-	0.00148	0.00778	NA;NA;3.4e-05;NA;NA	1.5e-05;2.3e-05;5.6e-05;6.3e-05;8e-05	0.00216463603191292	ATG	ORF1ab:nsp3	.	4947-4951-delfrshift	.	no-SNV	ORF1ab:nsp3	0.99735531090473
CAMB-75D96	MN908947.3	8162	T	C	0.0086	0.0064	1.3e-05	0.00012	0.00720897496054259	TTT	ORF1ab:nsp3	F1815L	T5443C	TTT>CTT	Missense	ORF1ab:nsp3	0.992791025039457
CAMB-75D96	MN908947.3	8655	C	T	0.02	0.026	3.4e-10	7.9e-13	0.0240072394336208	TCT	ORF1ab:nsp4	S34F	C101T	TCT>TTT	Missense	ORF1ab:nsp4	0.975939529436815
CAMB-75D96	MN908947.3	9654	TTATGTTCACACCTTTAGTACCTTTCTGGATAACAAT	-	0.00590540540540541	0.000432702702702703	0.00017;0.00011;0.00012;5.3e-05;0.00012;8.2e-05;5.8e-05;6.5e-05;6.1e-05;7.2e-05;6e-05;7.7e-05;3.1e-05;0.00013;4.9e-05;9.6e-05;0.00022;0.00016;3.1e-05;6.6e-05;4.4e-05;3.7e-05;8.2e-05;6e-05;7.6e-05;9.6e-05;6e-05;6.6e-05;4.9e-05;7.5e-05;5e-05;6.6e-05;6.8e-05;6.3e-05;6.4e-05;6.2e-05;0.00076	0.0015;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.46;NA;0.00088;0.0017;0.0014;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00256327110452278	GTT	ORF1ab:nsp4	.	1100-1136-delfrshift	.	no-SNV	ORF1ab:nsp4	0.994380860452289
CAMB-75DA5	MN908947.3	11075	T	-	0.039	0.036	2e-10	1.2e-09	0.0375244272587418	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95738222942913
CAMB-75DA5	MN908947.3	14408	C	T	1	1	0	0	0.999386522876239	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000274450292208841
CAMB-75DA5	MN908947.3	14786	C	T	1	1	0	0	0.999609574840464	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A440V	C1319T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000161555238428606
CAMB-75DA5	MN908947.3	20578	G	T	1	1	0	0	0.999697329515029	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	4.65646899955764e-05
CAMB-75DA5	MN908947.3	23403	A	G	1	1	0	0	0.998499379442627	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000112828613336342
CAMB-75DA5	MN908947.3	241	C	T	1	1	0	0	0.999213737577054	TCG	NA	NA	NA	NA	NA	NA	7.86262422946283e-05
CAMB-75DA5	MN908947.3	2416	C	T	1	1	0	0	0.999925556465421	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0
CAMB-75DA5	MN908947.3	25563	G	T	1	1	0	0	0.999824229907281	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	4.3942523179681e-05
CAMB-75DA5	MN908947.3	26042	C	T	1	1	0	0	0.999712726228095	ACT	ORF3a	T217I	C650T	ACT>ATT	Missense	GU280_gp03	0.000172364263142775
CAMB-75DA5	MN908947.3	29502	C	T	0.012	0.011	9.6e-07	3e-06	0.0115696770851321	TCC	N	S410F	C1229T	TCC>TTC	Missense	GU280_gp10	0.988257641167329
CAMB-75DA5	MN908947.3	3037	C	T	1	1	0	0	0.999274814926726	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000151080223598731
CAMB-75DA5	MN908947.3	9505	T	C	1	1	0	0	0.99977833518054	TTA	ORF1ab:nsp4	F317F	T951C	TTT>TTC	Synonymous	ORF1ab:nsp4	0.000174998541678819
CAMB-75DB4	MN908947.3	1059	C	T	1	1	0	0	0.99953170992775	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.000361252341450361
CAMB-75DB4	MN908947.3	11075	T	-	0.033	0.024	2.6e-08	1.1e-06	0.0287678922256525	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.967119324683175
CAMB-75DB4	MN908947.3	14408	C	T	1	1	0	0	0.998525871881473	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000391856841633856
CAMB-75DB4	MN908947.3	16348	T	C	0.043	0.056	5e-20	3.7e-25	0.0496670105993809	ATC	ORF1ab:helicase	S38P	T112C	TCA>CCA	Missense	ORF1ab:helicase	0.950286089485039
CAMB-75DB4	MN908947.3	16375	C	T	0.035	0.048	2.4e-13	8.9e-18	0.0415799454234309	TCC	ORF1ab:helicase	P47S	C139T	CCG>TCG	Missense	ORF1ab:helicase	0.958096295268489
CAMB-75DB4	MN908947.3	18041	C	T	0.0076	0.0042	2.2e-05	0.00065	0.00588194588609785	GCT	ORF1ab:3'-to-5'-exonuclease	A1V	C2T	GCT>GTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.994014255068853
CAMB-75DB4	MN908947.3	23298	C	G	0.0083	0.0031	9.3e-06	0.0016	0.00576395335788539	CCA	S	P579R	C1736G	CCA>CGA	Missense	GU280_gp02, spike glycoprotein	0.993562735276415
CAMB-75DB4	MN908947.3	23403	A	G	1	1	0	0	0.999639616912778	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.00957718054292e-05
CAMB-75DB4	MN908947.3	23623	A	G	0.0072	0.0051	3.7e-05	0.00027	0.00614694822100087	TAG	S	V687V	A2061G	GTA>GTG	Synonymous	GU280_gp02, spike glycoprotein	0.993563783627423
CAMB-75DB4	MN908947.3	241	C	T	1	1	0	0	0.999066992964209	TCG	NA	NA	NA	NA	NA	NA	0.000183542367696543
CAMB-75DB4	MN908947.3	24368	G	T	1	1	0	0	0.999924179240276	AGA	S	D936Y	G2806T	GAC>TAC	Missense	GU280_gp02, spike glycoprotein	7.58207597240124e-05
CAMB-75DB4	MN908947.3	25563	G	T	1	1	0	0	0.998856736363405	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	1.27029292954955e-05
CAMB-75DB4	MN908947.3	26521	C	G	1	1	0	0	0.999770934079919	GCC	NA	NA	NA	NA	NA	NA	0.000127258844489692
CAMB-75DB4	MN908947.3	3037	C	T	1	1	0	0	0.998739085206317	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000315228698420704
CAMB-75DB4	MN908947.3	5069	G	T	0.0043	0.0086	6e-04	2e-05	0.00634115409004439	AGC	ORF1ab:nsp3	A784S	G2350T	GCT>TCT	Missense	ORF1ab:nsp3	0.993447474106954
CAMB-75DB4	MN908947.3	6693	A	G	0.0081	0.0085	1.5e-05	9.4e-06	0.00830744292854248	AAG	ORF1ab:nsp3	K1325R	A3974G	AAG>AGG	Missense	ORF1ab:nsp3	0.991692557071458
CAMB-75DC3	MN908947.3	11020	C	T	0.0079	0.0052	3.1e-05	0.00056	0.00702521270782921	TCA	ORF1ab:nsp6	L16L	C48T	CTC>CTT	Synonymous	ORF1ab:nsp6	0.992896729373195
CAMB-75DC3	MN908947.3	11074	C	INS	0.026	0.019	9.6e-06	0.0017	0.0243727808057045	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.975422651489691
CAMB-75DC3	MN908947.3	11075	T	-	0.05	0.077	4.2e-12	3.2e-19	0.0576199926881496	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.934101948085862
CAMB-75DC3	MN908947.3	11846	A	-	0.013	0.0095	3.1e-05	0.001	0.0115303983228512	TAA	ORF1ab:nsp7	.	4-4-delfrshift	.	no-SNV	ORF1ab:nsp7	0.988469601677149
CAMB-75DC3	MN908947.3	13217	C	T	0.0069	0.002	3.8e-05	0.0035	0.00650890837884053	TCA	ORF1ab:nsp10	Q65*	C193T	CAA>TAA	Nonsense	ORF1ab:nsp10	0.99346351150091
CAMB-75DC3	MN908947.3	14408	C	T	1	1	0	0	0.999120979294179	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000244172418283631
CAMB-75DC3	MN908947.3	16111	C	T	0.0093	0.0032	4.5e-06	0.0021	0.00675225741150148	GCT	ORF1ab:RNA-dependent-RNA-polymerase	L882L	C2644T	CTA>TTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.993221106464587
CAMB-75DC3	MN908947.3	16792	C	T	0.0078	0.0027	4.2e-05	0.0085	0.00549186417469081	TCG	ORF1ab:helicase	R186C	C556T	CGT>TGT	Missense	ORF1ab:helicase	0.994479001267353
CAMB-75DC3	MN908947.3	16838	AA	-	0.0058	0.0135	0.0087;0.00069	1.3e-06;2.7e-06	0.00918215780708466	GAA	ORF1ab:helicase	.	602-603-delfrshift	.	no-SNV	ORF1ab:helicase	0.987230838729107
CAMB-75DC3	MN908947.3	207	C	T	0.0035	0.011	0.0014	8.5e-07	0.00671370699328629	CCG	NA	NA	NA	NA	NA	NA	0.993267274006733
CAMB-75DC3	MN908947.3	21855	C	T	0.0083	0.0045	1.8e-05	0.00078	0.00668019617791307	TCT	S	S98F	C293T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.993319803822087
CAMB-75DC3	MN908947.3	23403	A	G	1	1	0	0	0.999956348080407	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.27389396948731e-05
CAMB-75DC3	MN908947.3	241	C	T	1	0.99	0	0	0.997646875790047	TCG	NA	NA	NA	NA	NA	NA	1.94473075202738e-05
CAMB-75DC3	MN908947.3	25429	G	T	1	1	0	0	0.999785568778814	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	1.78692684321504e-05
CAMB-75DC3	MN908947.3	25855	G	T	0.99	0.96	0	0	0.974591988130564	CGA	ORF3a	D155Y	G463T	GAC>TAC	Missense	GU280_gp03	0.0254080118694362
CAMB-75DC3	MN908947.3	27539	T	A	0.024	0.091	8.4e-06	5.5e-06	0.0320855614973262	CTA	ORF7a	L49Q	T146A	CTA>CAA	Missense	GU280_gp07	0.967914438502674
CAMB-75DC3	MN908947.3	29041	G	T	0.023	0.011	6.8e-09	4.3e-05	0.0192769561370244	AGA	N	K256N	G768T	AAG>AAT	Missense	GU280_gp10	0.9806598407281
CAMB-75DC3	MN908947.3	3037	C	T	1	1	0	0	0.999664519592056	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75DC3	MN908947.3	4304	AA	-	0.0149	0.0022	5.1e-10;2.6e-06	0.0035;NA	0.0107642841451481	TAA	ORF1ab:nsp3	.	1585-1586-delfrshift	.	no-SNV	ORF1ab:nsp3	0.985014215763702
CAMB-75DC3	MN908947.3	4586	C	T	0.0075	0.0044	2.6e-05	0.00068	0.00609860554356392	TCT	ORF1ab:nsp3	L623L	C1867T	CTA>TTA	Synonymous	ORF1ab:nsp3	0.99386713262754
CAMB-75DC3	MN908947.3	5779	T	C	0.012	0.0053	1.8e-05	0.0084	0.0102966101694915	ATA	ORF1ab:nsp3	H1020H	T3060C	CAT>CAC	Synonymous	ORF1ab:nsp3	0.989661016949153
CAMB-75DC3	MN908947.3	6170	G	C	0.016	0.0023	2.4e-08	0.0037	0.0107088220295767	GGC	ORF1ab:nsp3	A1151P	G3451C	GCT>CCT	Missense	ORF1ab:nsp3	0.988781234064253
CAMB-75DC3	MN908947.3	6280	A	-	0.01	0.004	2e-06	0.0013	0.00817654450622278	CAA	ORF1ab:nsp3	.	3561-3561-delfrshift	.	no-SNV	ORF1ab:nsp3	0.991582462603067
CAMB-75DC3	MN908947.3	6941	C	T	0.98	0.96	0	0	0.97242497972425	ACT	ORF1ab:nsp3	L1408L	C4222T	CTG>TTG	Synonymous	ORF1ab:nsp3	0.0275750202757502
CAMB-75DC3	MN908947.3	830	A	-	0.0018	0.0058	0.003	4.6e-05	0.00354300871542251	CAA	ORF1ab:nsp2	.	25-25-delfrshift	.	no-SNV	ORF1ab:nsp2	0.995585449033725
CAMB-75DC3	MN908947.3	8862	TGCCTGGTT	-	0.00641111111111111	0.0012	3.6e-05;4.4e-05;4.8e-05;3.7e-05;7e-05;0.00014;8.7e-05;1e-04;2.5e-05	NA;NA;NA;NA;0.0026;0.0058;0.0034;0.012;NA	0.00341195035612232	GTG	ORF1ab:nsp4	.	308-316-delinframe	.	no-SNV	ORF1ab:nsp4	0.996452366531107
CAMB-75DC3	MN908947.3	9207	C	T	0.012	0.0036	3e-07	0.00057	0.0090797204096324	TCT	ORF1ab:nsp4	S218F	C653T	TCT>TTT	Missense	ORF1ab:nsp4	0.990897057799039
CAMB-75DC3	MN908947.3	9665	C	T	0.007	0.0025	3.9e-05	0.0027	0.00522562734744979	ACC	ORF1ab:nsp4	P371S	C1111T	CCT>TCT	Missense	ORF1ab:nsp4	0.994741712481629
CAMB-75DD2	MN908947.3	10507	C	T	0.12	0.035	9e-53	1.2e-16	0.0753393459050742	ACA	ORF1ab:3C-like-proteinase	N151N	C453T	AAC>AAT	Synonymous	ORF1ab:3C-like-proteinase	0.924660654094926
CAMB-75DD2	MN908947.3	11075	T	-	0.0094	0.066	0.00099	2.5e-16	0.0411569521068202	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958623171024226
CAMB-75DD2	MN908947.3	13914	T	G	0.003	0.0094	6e-04	8e-07	0.00637285012285012	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993588759213759
CAMB-75DD2	MN908947.3	14335	G	A	0.02	0.056	5.6e-11	2.5e-26	0.0383363924578675	TGT	ORF1ab:RNA-dependent-RNA-polymerase	V290I	G868A	GTT>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.961663607542133
CAMB-75DD2	MN908947.3	14408	C	T	1	1	0	0	0.999486631016043	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000363636363636364
CAMB-75DD2	MN908947.3	16183	TA	-	0.0215	0.017	1.6e-11;5.1e-12	1e-09;7.6e-10	0.018914230101976	GTA	ORF1ab:RNA-dependent-RNA-polymerase	.	2716-2717-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.981387829547339
CAMB-75DD2	MN908947.3	18696	T	-	0.013	0.029	7.1e-08	3.2e-14	0.0211452204811557	CTG	ORF1ab:3'-to-5'-exonuclease	.	657-657-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.946685501252403
CAMB-75DD2	MN908947.3	18696	T	A	0.049	0.015	6.2e-23	2.1e-08	0.0321110269703501	CTG	ORF1ab:3'-to-5'-exonuclease	T219T	T657A	ACT>ACA	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.946685501252403
CAMB-75DD2	MN908947.3	18696	TG	-	0.013	0.0145145	7.1e-08;9.2e-08	3.2e-14;NA	0.0138657712292484	CTG	ORF1ab:3'-to-5'-exonuclease	.	657-658-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.946685501252403
CAMB-75DD2	MN908947.3	21994	TT	-	0.0235	0.0092	1.9e-06;5.5e-06	0.0028;0.0037	0.0138064596738927	ATT	S	.	432-433-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.981426682616634
CAMB-75DD2	MN908947.3	22010	A	-	0.016	0.01	5.3e-08	1.2e-05	0.0121727748691099	CAA	S	.	448-448-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.982918848167539
CAMB-75DD2	MN908947.3	22450	C	A	0.16	0.094	3.6e-26	3.2e-17	0.124668435013263	TCT	S	L296L	C888A	CTC>CTA	Synonymous	GU280_gp02, spike glycoprotein	0.875331564986737
CAMB-75DD2	MN908947.3	23099	C	T	0.02	0.013	6.4e-10	1.5e-07	0.0152467567206099	ACT	S	L513F	C1537T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.984619499799385
CAMB-75DD2	MN908947.3	23403	A	G	1	1	0	0	0.999840082243418	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000148495059683591
CAMB-75DD2	MN908947.3	23633	TCCATCAT	ATTCATCA	0.01725	0.0019075	1.4e-08;1.7e-10;5.9e-08;4.2e-09;4.8e-09;1.1e-07;1.3e-09;1e-09	0.16;0.34;8.7e-08;NA;NA;NA;NA;NA	0.00838898843459847	ATC	S	.	2071-2078-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.992142857142857
CAMB-75DD2	MN908947.3	241	C	T	1	1	0	0	0.999849424802747	TCG	NA	NA	NA	NA	NA	NA	3.01150394507017e-05
CAMB-75DD2	MN908947.3	25625	A	G	0.073	0.04	4.4e-34	1.3e-19	0.0554539098873964	CAC	ORF3a	H78R	A233G	CAC>CGC	Missense	GU280_gp03	0.944456840257635
CAMB-75DD2	MN908947.3	26044	C	T	0.013	0.025	3.7e-05	1.5e-07	0.0181058495821727	TCA	ORF3a	Q218*	C652T	CAA>TAA	Nonsense	GU280_gp03	0.981894150417827
CAMB-75DD2	MN908947.3	26574	GAACAATGGAACCTAGTAATAGGTTTCCTATT	-	0.011625	0.02033125	0.0051;0.0029;0.0042;0.0044;0.0035;0.0036;0.0039;0.0028;0.0039;0.0042;0.0036;0.0035;0.0039;0.0039;0.0031;0.0039;0.003;0.0031;0.0033;0.003;0.0025;0.0031;0.0032;0.0033;0.0028;0.0034;0.0033;0.0031;0.0033;0.0025;NA;NA	6.5e-05;7e-05;0.00014;0.00016;0.00011;0.00011;0.00017;7.1e-05;0.00014;0.00015;0.00013;0.00012;0.00019;0.00017;9.1e-05;0.00014;1e-04;8.1e-05;0.00012;0.00017;7.4e-05;1e-04;0.00011;0.00011;9.7e-05;0.00012;0.00011;0.00011;0.00012;5.8e-05;1.6e-05;1.6e-05	0.0166222695791156	TGA	M	.	52-83-delfrshift	.	no-SNV	GU280_gp05	0.982356490133467
CAMB-75DD2	MN908947.3	27920	C	-	0.013	0.005	3.8e-07	0.00022	0.00788342092689919	TCA	ORF8	.	27-27-delfrshift	.	no-SNV	GU280_gp09	0.992116579073101
CAMB-75DD2	MN908947.3	28090	GTTCTA	-	0.014	0.00981666666666667	3.2e-06;3.9e-06;4e-06;3.8e-06;3.1e-06;1.2e-05	3e-05;3.3e-05;4e-05;3.9e-05;2.9e-05;0.00011	0.0111214087117702	GGT	ORF8	.	197-202-delinframe	.	no-SNV	GU280_gp09	0.988891460310113
CAMB-75DD2	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999634235552304	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-75DD2	MN908947.3	29103	GTG	-	0.0186666666666667	0.0113333333333333	1.7e-10;1.2e-10;3.2e-10	1.1e-09;8.9e-10;NA	0.017737465356513	CGT	N	.	830-832-delinframe	.	no-SNV	GU280_gp10	0.982010582010582
CAMB-75DD2	MN908947.3	29469	ATTTGGATGATTTCTCCAAACA	-	0.000590909090909091	0.0100090909090909	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;1.2e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	2.5e-05;7.4e-05;1.9e-05;3.7e-05;5.7e-05;7.3e-05;8.1e-05;8.5e-05;3.2e-05;1.6e-05;3e-05;1.6e-05;1.9e-05;1.7e-05;1.8e-05;1.8e-05;1.7e-05;3.1e-05;3.9e-05;5.3e-05;0.00011;2.1e-05	0.00537995965030262	GAT	N	.	1196-1217-delfrshift	.	no-SNV	GU280_gp10	0.994659546061415
CAMB-75DD2	MN908947.3	29810	G	T	0.0024	0.0096	0.009	2.1e-05	0.00636942675159236	TGT	NA	NA	NA	NA	NA	NA	0.993630573248408
CAMB-75DD2	MN908947.3	3037	C	T	1	1	0	0	0.999448504067282	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000137873983179374
CAMB-75DD2	MN908947.3	6787	TT	-	0.019	0.0145	NA;5.4e-16	1.7e-07;7.6e-08	0.0163234555499749	CTT	ORF1ab:nsp3	.	4068-4069-delfrshift	.	no-SNV	ORF1ab:nsp3	0.992267398353704
CAMB-75DD2	MN908947.3	6788	TTA	-	0.0376666666666667	0.005	5.4e-16;5e-16;1.1e-15	7.6e-08;NA;NA	0.0173323285606631	TTT	ORF1ab:nsp3	.	4069-4071-delinframe	.	no-SNV	ORF1ab:nsp3	0.974709155285786
CAMB-75DE1	MN908947.3	13914	T	G	0.0061	0.025	5.2e-05	2.2e-10	0.0118956254796623	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.988104374520338
CAMB-75DE1	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999691643539932	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0
CAMB-75DE1	MN908947.3	18795	C	T	1	1	0	0	0.999834443938579	ACC	ORF1ab:3'-to-5'-exonuclease	N252N	C756T	AAC>AAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0
CAMB-75DE1	MN908947.3	2059	G	A	1	1	3.1e-174	1.6e-238	1	TGG	ORF1ab:nsp2	M418I	G1254A	ATG>ATA	Missense	ORF1ab:nsp2	0
CAMB-75DE1	MN908947.3	29032	G	A	1	1	0	0	0.999937673993435	AGG	N	E253E	G759A	GAG>GAA	Synonymous	GU280_gp10	4.15506710433374e-05
CAMB-75DE1	MN908947.3	8313	T	INS	0.0042	0.013	0.00044	2e-07	0.00896336710833983	ATG	ORF1ab:nsp3	.	5593-5594-insfrshift	.	no-SNV	ORF1ab:nsp3	0.99103663289166
CAMB-75DE1	MN908947.3	8315	ACACC	-	0.00422	0.0132	0.00069;0.00072;0.00071;0.0016;0.00061	3.1e-07;3.3e-07;2.5e-07;7e-07;2.7e-07	0.00895638629283489	GAC	ORF1ab:nsp3	.	5596-5600-delfrshift	.	no-SNV	ORF1ab:nsp3	0.991047100038926
CAMB-75DF0	MN908947.3	11075	T	-	0.04	0.038	5.3e-10	8.5e-10	0.0391407609462446	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955932841085454
CAMB-75DF0	MN908947.3	14408	C	T	1	1	0	0	0.999022025682456	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000393315758142699
CAMB-75DF0	MN908947.3	23403	A	G	1	1	0	0	0.997949277699222	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.78832907477694e-05
CAMB-75DF0	MN908947.3	241	C	T	1	1	0	0	0.998555414307177	TCG	NA	NA	NA	NA	NA	NA	0.000158904426210563
CAMB-75DF0	MN908947.3	25477	G	T	0.015	0.015	6.6e-08	7.7e-08	0.0149317406143345	TGT	ORF3a	V29F	G85T	GTT>TTT	Missense	GU280_gp03	0.984570534698521
CAMB-75DF0	MN908947.3	25606	G	A	0.011	0.0099	3.7e-06	6.9e-06	0.0102655091565807	AGC	ORF3a	A72T	G214A	GCA>ACA	Missense	GU280_gp03	0.989354286800583
CAMB-75DF0	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99961495172087	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000132815353454859
CAMB-75DF0	MN908947.3	3037	C	T	1	1	0	0	0.998982731242557	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000223302897975387
CAMB-75E0C	MN908947.3	12439	C	T	0.054	0.044	1.1e-24	8.1e-20	0.0507876792852104	CCT	ORF1ab:nsp8	P116P	C348T	CCC>CCT	Synonymous	ORF1ab:nsp8	0.94921232071479
CAMB-75E0C	MN908947.3	13914	T	G	0.0093	0.0037	8.8e-07	0.00035	0.00800985828712261	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.991990141712877
CAMB-75E0C	MN908947.3	14408	C	T	1	1	0	0	0.999645923696557	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000265557227582544
CAMB-75E0C	MN908947.3	20846	ATAATATGAGAGTTATACATTTTGGTGCTGGTTCTG	-	0.00547541666666667	0.0300555555555556	NA;NA;NA;4.9e-10;2.8e-09;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;5.4e-35;2e-34;NA;NA	1.4e-11;3.4e-11;5.2e-11;1.9e-10;1.9e-09;1.7e-11;2.5e-11;1.2e-09;4e-10;5.5e-11;2.9e-10;2e-10;2.1e-11;9.5e-12;3e-11;4.8e-12;2.5e-11;2.2e-11;1.5e-11;4.1e-11;1.5e-11;8.8e-12;1.1e-18;9.8e-19;6.2e-19;9.3e-19;1.4e-18;5e-19;1.4e-18;1.2e-17;4e-18;1.8e-19;3e-19;8.1e-19;3.5e-19;1.5e-18	0.00591137194862635	TAT	ORF1ab:2'-O-ribose-methyltransferase	.	188-223-delinframe	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.993998628257888
CAMB-75E0C	MN908947.3	20878	TC	-	0.0765	0.042	5.4e-35;2e-34	3e-19;8.1e-19	0.0687225840755018	TTC	ORF1ab:2'-O-ribose-methyltransferase	.	220-221-delfrshift	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.93057140938696
CAMB-75E0C	MN908947.3	21891	TA	-	0.0475	0.069	2.4e-07;7.9e-09	5e-10;9.6e-12	0.0565053607649957	TTA	S	.	329-330-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.938271604938272
CAMB-75E0C	MN908947.3	23403	A	G	1	1	0	0	0.999938409739473	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-75E0C	MN908947.3	241	C	T	1	1	0	0	0.999663053855225	TCG	NA	NA	NA	NA	NA	NA	5.61576907957545e-05
CAMB-75E0C	MN908947.3	28657	C	T	1	1	0	0	1	ACG	N	D128D	C384T	GAC>GAT	Synonymous	GU280_gp10	0
CAMB-75E0C	MN908947.3	2940	C	T	1	1	0	0	0.99936628643853	CCA	ORF1ab:nsp3	P74L	C221T	CCA>CTA	Missense	ORF1ab:nsp3	0.000316856780735108
CAMB-75E0C	MN908947.3	3037	C	T	1	1	0	6.4e-308	0.999331997327989	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75E0C	MN908947.3	3776	A	G	1	1	1.7e-161	1e-253	1	CAC	ORF1ab:nsp3	T353A	A1057G	ACA>GCA	Missense	ORF1ab:nsp3	0
CAMB-75E1B	MN908947.3	10159	A	G	1	1	0	0	0.999375786362883	TAG	ORF1ab:3C-like-proteinase	V35V	A105G	GTA>GTG	Synonymous	ORF1ab:3C-like-proteinase	0.00032186015663861
CAMB-75E1B	MN908947.3	11075	T	-	0.034	0.034	1.2e-08	6.9e-09	0.0339468587267898	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961147257692263
CAMB-75E1B	MN908947.3	14408	C	T	1	1	0	0	0.99939649969825	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000316590322229587
CAMB-75E1B	MN908947.3	1547	A	G	0.013	0.011	5.6e-07	2.8e-06	0.0121181772658988	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.961692538808212
CAMB-75E1B	MN908947.3	1547	A	T	0.021	0.02	4.4e-10	1.1e-09	0.0200801201802704	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.961692538808212
CAMB-75E1B	MN908947.3	19170	C	T	1	1	0	0	0.999857172535577	TCA	ORF1ab:3'-to-5'-exonuclease	F377F	C1131T	TTC>TTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.000129843149475434
CAMB-75E1B	MN908947.3	23403	A	G	1	1	0	0	0.997613456434106	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.11934247665088e-05
CAMB-75E1B	MN908947.3	241	C	T	1	1	0	0	0.998828813932981	TCG	NA	NA	NA	NA	NA	NA	0.000220458553791887
CAMB-75E1B	MN908947.3	28854	C	T	0.87	0.87	0	0	0.867713314353631	TCA	N	S194L	C581T	TCA>TTA	Missense	GU280_gp10	0.131761519113298
CAMB-75E1B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999453701174542	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000101895251681272
CAMB-75E1B	MN908947.3	29776	A	G	1	1	0	0	0.998418507975238	TAG	NA	NA	NA	NA	NA	NA	0.000135556459265284
CAMB-75E1B	MN908947.3	29818	A	G	1	1	0	0	0.999866250557289	TAA	NA	NA	NA	NA	NA	NA	8.91662951404369e-05
CAMB-75E1B	MN908947.3	29824	A	G	1	1	0	0	0.999686126804771	TAG	NA	NA	NA	NA	NA	NA	0.000224195139449377
CAMB-75E1B	MN908947.3	3037	C	T	1	1	0	0	0.999313627809144	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.42820768294033e-05
CAMB-75E1B	MN908947.3	534	C	T	1	1	0	0	0.999567125801899	GCA	ORF1ab:leader-protein	A90V	C269T	GCA>GTA	Missense	ORF1ab:leader-protein	0.000112547291506142
CAMB-75E2A	MN908947.3	10323	A	G	0.035	0.028	5.1e-10	3.7e-08	0.0320495310935082	AAG	ORF1ab:3C-like-proteinase	K90R	A269G	AAG>AGG	Missense	ORF1ab:3C-like-proteinase	0.96790494400437
CAMB-75E2A	MN908947.3	11074	C	INS	0.11	0.11	1.2e-40	1.4e-36	0.110912215380209	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.88710081626808
CAMB-75E2A	MN908947.3	11083	G	-	0.16	0.14	1.7e-68	4.3e-63	0.150721324145038	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.22019707606105e-05
CAMB-75E2A	MN908947.3	11083	G	T	0.84	0.86	0	0	0.849085464030399	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.22019707606105e-05
CAMB-75E2A	MN908947.3	13197	C	T	0.014	0.016	4.9e-08	5.1e-09	0.0139981429247184	ACA	ORF1ab:nsp10	T58I	C173T	ACA>ATA	Missense	ORF1ab:nsp10	0.985966817919025
CAMB-75E2A	MN908947.3	1350	A	T	1	1	0	0	0.999514327343371	CAA	ORF1ab:nsp2	Q182L	A545T	CAA>CTA	Missense	ORF1ab:nsp2	0
CAMB-75E2A	MN908947.3	14805	C	T	1	1	0	0	0.999943143052081	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	1.89523159730119e-05
CAMB-75E2A	MN908947.3	1535	G	A	1	1	0	0	1	GGT	ORF1ab:nsp2	V244I	G730A	GTT>ATT	Missense	ORF1ab:nsp2	0
CAMB-75E2A	MN908947.3	23553	TACCCATTGGTGCAGGTATATGCGCTAG	-	0.0400357142857143	0.0437	7e-04;4e-04;0.00029;0.00023;0.00028;0.00034;4.4e-05;7.3e-05;2.6e-05;5.7e-05;6.1e-05;6.7e-05;5.8e-05;6.1e-05;3e-05;2.8e-05;7.8e-05;2.1e-05;4e-04;0.00022;0.00039;0.00022;0.00042;8e-04;0.00049;0.00051;2.4e-05;4.2e-05	0.078;0.074;0.0022;0.0017;0.0021;0.0021;3.9e-05;5.6e-05;2.9e-05;5.4e-05;6.3e-05;6.2e-05;5.6e-05;5.5e-05;3.2e-05;2.9e-05;1.1e-05;2.1e-06;1.4e-05;4.8e-06;1.1e-05;3.2e-06;1.1e-05;2.8e-05;1.3e-05;1.3e-05;8.8e-08;3e-07	0.0405320953486296	ATA	S	.	1991-2018-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.973087071240106
CAMB-75E2A	MN908947.3	24216	G	A	0.014	0.007	5.2e-08	6e-05	0.0130761159092744	GGT	S	G885D	G2654A	GGT>GAT	Missense	GU280_gp02, spike glycoprotein	0.986843167325854
CAMB-75E2A	MN908947.3	24381	C	T	0.023	0.028	6.2e-12	1.4e-12	0.0240531859266453	TCC	S	S940F	C2819T	TCC>TTC	Missense	GU280_gp02, spike glycoprotein	0.975946814073355
CAMB-75E2A	MN908947.3	2480	A	G	1	1	0	0	0.999620709273658	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.00018964536317087
CAMB-75E2A	MN908947.3	2558	C	T	0.99	1	0	0	0.9950882782424	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000132749236691889
CAMB-75E2A	MN908947.3	26144	G	T	1	1	0	1.5e-278	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-75E2A	MN908947.3	29196	C	-	0.0073	0.012	0.0035	4.1e-05	0.0087937187723055	GCC	N	.	923-923-delfrshift	.	no-SNV	GU280_gp10	0.990663811563169
CAMB-75E2A	MN908947.3	29748	T	C	0.01	0.003	3.7e-06	0.0057	0.00857927247769389	GTA	NA	NA	NA	NA	NA	NA	0.991420727522306
CAMB-75E2A	MN908947.3	4633	C	T	0.017	0.0026	1.3e-09	0.0019	0.00922367409684858	GCT	ORF1ab:nsp3	G638G	C1914T	GGC>GGT	Synonymous	ORF1ab:nsp3	0.990701941434628
CAMB-75E39	MN908947.3	11074	C	INS	0.11	0.099	2e-44	6.2e-30	0.103283125274538	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.887733269097247
CAMB-75E39	MN908947.3	11074	C	T	0.0075	0.0066	2.4e-05	0.0012	0.00724072945744123	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.887733269097247
CAMB-75E39	MN908947.3	11083	G	-	0.18	0.17	3.3e-78	5.5e-78	0.17609242766049	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.91200594624904e-05
CAMB-75E39	MN908947.3	11083	G	T	0.82	0.83	0	0	0.823581571843989	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.91200594624904e-05
CAMB-75E39	MN908947.3	14805	C	T	1	1	0	0	0.998877118930693	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000473504065370618
CAMB-75E39	MN908947.3	2480	A	G	1	1	0	0	0.999917566564999	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-75E39	MN908947.3	2558	C	T	1	1	0	0	0.999615046194457	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.00010998680158381
CAMB-75E39	MN908947.3	26144	G	T	1	1	0	0	0.99963503649635	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	9.12408759124088e-05
CAMB-75E39	MN908947.3	27230	C	T	0.13	0.13	6.8e-59	3.5e-59	0.127776773338155	ACT	ORF6	T10I	C29T	ACT>ATT	Missense	GU280_gp06	0.872054480805159
CAMB-75E39	MN908947.3	27307	A	G	0.35	0.36	7.4e-186	3.7e-186	0.354891608174421	CAT	ORF6	I36V	A106G	ATA>GTA	Missense	GU280_gp06	0.644984160506864
CAMB-75E39	MN908947.3	418	T	C	0.0072	0.0073	4.4e-05	2.2e-05	0.00717147435897436	GTG	ORF1ab:leader-protein	C51C	T153C	TGT>TGC	Synonymous	ORF1ab:leader-protein	0.992708333333333
CAMB-75E48	MN908947.3	13585	C	T	1	1	0	0	1	CCT	ORF1ab:RNA-dependent-RNA-polymerase	L40L	C118T	CTA>TTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-75E48	MN908947.3	14408	C	T	1	1	0	0	0.999728587491761	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000116319646388275
CAMB-75E48	MN908947.3	17002	C	T	0.023	0.054	3.6e-12	2.4e-25	0.0425470748886014	ACT	ORF1ab:helicase	L256F	C766T	CTC>TTC	Missense	ORF1ab:helicase	0.957452925111399
CAMB-75E48	MN908947.3	23403	A	G	1	1	0	0	0.999879901519246	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000100082067295182
CAMB-75E48	MN908947.3	241	C	T	1	1	0	0	0.999683488658344	TCG	NA	NA	NA	NA	NA	NA	0.000211007561104273
CAMB-75E48	MN908947.3	25100	C	A	0.11	0.047	4.2e-47	3.5e-21	0.0842023194620407	TCA	S	Q1180K	C3538A	CAA>AAA	Missense	GU280_gp02, spike glycoprotein	0.915797680537959
CAMB-75E48	MN908947.3	25816	G	T	0.0035	0.018	0.007	9.7e-08	0.011154489682097	TGA	ORF3a	D142Y	G424T	GAT>TAT	Missense	GU280_gp03	0.988845510317903
CAMB-75E48	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999796126401631	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000228571428571429
CAMB-75E48	MN908947.3	3037	C	T	1	1	0	0	0.99926226484692	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000368867576540022
CAMB-75E48	MN908947.3	4106	A	-	0.067	0.046	6.2e-31	8.7e-22	0.0579053858753252	GAA	ORF1ab:nsp3	.	1387-1387-delfrshift	.	no-SNV	ORF1ab:nsp3	0.941998265728876
CAMB-75E48	MN908947.3	5694	C	T	0.072	0.046	3.6e-32	1.9e-20	0.0633824913711955	CCA	ORF1ab:nsp3	P992L	C2975T	CCA>CTA	Missense	ORF1ab:nsp3	0.936617508628805
CAMB-75E57	MN908947.3	11075	T	-	0.074	0.034	2.3e-18	2.2e-09	0.0577638895271357	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.941914434079316
CAMB-75E57	MN908947.3	11075	TT	-	0.0370195	0.032	2.3e-18;NA	2.2e-09;1.3e-11	0.0349533877720974	CTT	ORF1ab:nsp6	.	103-104-delfrshift	.	no-SNV	ORF1ab:nsp6	0.941914434079316
CAMB-75E57	MN908947.3	1440	G	A	1	1	0	0	0.999567286888793	GGC	ORF1ab:nsp2	G212D	G635A	GGC>GAC	Missense	ORF1ab:nsp2	0.00043271311120727
CAMB-75E57	MN908947.3	17964	G	T	0.021	0.014	3.3e-11	2.5e-08	0.0189153632509867	TGT	ORF1ab:helicase	M576I	G1728T	ATG>ATT	Missense	ORF1ab:helicase	0.981055401257126
CAMB-75E57	MN908947.3	21982	TTTGGGTG	-	0.004125	0.0295	NA;NA;NA;1.2e-06;NA;NA;NA;NA	8e-06;2.2e-05;2e-05;5.8e-06;2.1e-05;3e-05;2.6e-05;1.5e-05	0.0168401356566483	TTT	S	.	420-427-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.983056830215319
CAMB-75E57	MN908947.3	23533	C	T	1	1	0	0	0.999892553991619	ACA	S	N657N	C1971T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-75E57	MN908947.3	28087	C	T	0.0089	0.011	8.3e-05	1.7e-05	0.00994275384151853	GCT	ORF8	A65V	C194T	GCT>GTT	Missense	GU280_gp09	0.990057246158481
CAMB-75E57	MN908947.3	28486	C	T	0.014	0.06	1.1e-07	4.8e-27	0.0330273175100761	GCG	N	G71G	C213T	GGC>GGT	Synonymous	GU280_gp10	0.966972682489924
CAMB-75E57	MN908947.3	2891	G	A	1	1	0	0	0.999724593775819	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	0.000275406224180667
CAMB-75E57	MN908947.3	4412	G	T	0.017	0.012	6.4e-08	4.9e-06	0.0140735881686445	AGA	ORF1ab:nsp3	E565*	G1693T	GAA>TAA	Nonsense	ORF1ab:nsp3	0.985926411831355
CAMB-75E57	MN908947.3	4720	G	T	1	1	0	0	0.999857053004746	CGT	ORF1ab:nsp3	A667A	G2001T	GCG>GCT	Synonymous	ORF1ab:nsp3	5.71787981016639e-05
CAMB-75E57	MN908947.3	4963	G	T	0.028	0.02	4.7e-14	7e-11	0.0239351142873348	GGA	ORF1ab:nsp3	R748S	G2244T	AGG>AGT	Missense	ORF1ab:nsp3	0.965004821053826
CAMB-75E66	MN908947.3	11071	G	T	0.056	0.039	7.1e-26	6.4e-19	0.0495818249906379	TGT	ORF1ab:nsp6	L33F	G99T	TTG>TTT	Missense	ORF1ab:nsp6	0.944613656222694
CAMB-75E66	MN908947.3	11074	C	INS	0.11	0.12	6.6e-43	1.6e-43	0.110969030969031	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.886193806193806
CAMB-75E66	MN908947.3	11083	G	-	0.17	0.15	3.8e-77	5.9e-68	0.166274075100457	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.51930416818875e-05
CAMB-75E66	MN908947.3	11083	G	T	0.83	0.85	0	0	0.833637749253656	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.51930416818875e-05
CAMB-75E66	MN908947.3	12076	C	T	1	1	0	0	0.998848046915907	ACA	ORF1ab:nsp7	N78N	C234T	AAC>AAT	Synonymous	ORF1ab:nsp7	0.000602157293957482
CAMB-75E66	MN908947.3	14805	C	T	1	1	0	0	0.997592912141293	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00236358627089889
CAMB-75E66	MN908947.3	17247	T	C	1	1	0	0	0.998998433720819	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000287683931254195
CAMB-75E66	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-75E66	MN908947.3	28093	C	T	0.0068	0.014	0.00033	1.2e-06	0.00923550538737814	TCT	ORF8	S67F	C200T	TCT>TTT	Missense	GU280_gp09	0.989567299469814
CAMB-75E66	MN908947.3	5098	T	C	0.0085	0.0095	6e-05	3.5e-05	0.00898371701291409	ATT	ORF1ab:nsp3	N793N	T2379C	AAT>AAC	Synonymous	ORF1ab:nsp3	0.991016282987086
CAMB-75E66	MN908947.3	593	C	T	0.0078	0.0033	3.7e-05	0.0036	0.00653481127291169	TCA	ORF1ab:leader-protein	H110Y	C328T	CAT>TAT	Missense	ORF1ab:leader-protein	0.993450699123379
CAMB-75E66	MN908947.3	9180	C	T	0.0081	0.01	2.5e-05	2.4e-06	0.00907567147704509	TCT	ORF1ab:nsp4	S209F	C626T	TCT>TTT	Missense	ORF1ab:nsp4	0.99090388782143
CAMB-75E66	MN908947.3	9474	C	T	0.0026	0.0076	0.0041	2e-05	0.00429813110891783	GCT	ORF1ab:nsp4	A307V	C920T	GCT>GTT	Missense	ORF1ab:nsp4	0.995701868891082
CAMB-75E66	MN908947.3	9491	C	T	0.029	0.039	8.5e-14	5.2e-18	0.0323708403470154	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.967596788812638
CAMB-75E75	MN908947.3	11075	T	-	0.036	0.037	2.9e-09	2.1e-09	0.0364869886247857	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958358804703513
CAMB-75E75	MN908947.3	14408	C	T	0.99	1	0	0	0.994599135861738	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000370968445860429
CAMB-75E75	MN908947.3	20312	CCTT	-	0.01475	0.02125	0.014;0.0064;0.0042;0.012	0.00065;9.2e-05;3.4e-05;3e-04	0.0194518125552608	GCC	ORF1ab:endoRNAse	.	692-695-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.978902953586498
CAMB-75E75	MN908947.3	20327	TTTATGGAGAT	-	0.0163636363636364	0.0219090909090909	0.0029;0.0022;0.0052;0.0062;0.0083;0.012;0.0084;0.0058;0.012;0.0094;0.0024	2.4e-05;7.7e-06;0.00016;0.00012;0.00023;0.00079;0.00017;0.00016;0.00084;0.00048;0.00013	0.0191780821917808	GTT	ORF1ab:endoRNAse	.	707-717-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.975528364849833
CAMB-75E75	MN908947.3	23403	A	G	1	1	0	0	0.998924856423535	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.16762384310071e-05
CAMB-75E75	MN908947.3	23567	GGTATATGCGCTAG	-	0.035	0.0345714285714286	0.00088;0.00084;0.00022;8.7e-05;0.00031;0.00016;0.00027;0.00014;0.00031;6e-04;0.00036;0.00045;1.8e-05;3.4e-05	0.00071;0.00064;0.00015;6.3e-05;0.00045;0.00022;0.00053;0.00021;0.00041;0.00073;0.00046;0.00051;2.4e-05;6.8e-05	0.0332909630167665	AGG	S	.	2005-2018-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.968178524851471
CAMB-75E75	MN908947.3	241	C	T	1	1	0	0	0.998362834727355	TCG	NA	NA	NA	NA	NA	NA	0.000275562471633275
CAMB-75E75	MN908947.3	25350	C	T	1	1	0	0	0.996342656982434	CCA	S	P1263L	C3788T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	0.00328388193478597
CAMB-75E75	MN908947.3	25821	C	T	0.015	0.013	2.1e-08	1.4e-07	0.0139778499984224	CCA	ORF3a	A143A	C429T	GCC>GCT	Synonymous	GU280_gp03	0.985895939166377
CAMB-75E75	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.0524878048780488	0.054780487804878	1.2e-06;4.4e-09;1.3e-07;1.5e-07;3.7e-07;4.9e-10;3.4e-09;1.5e-09;1.3e-09;4.8e-11;3.6e-10;2.7e-10;8.2e-10;5.1e-10;4.9e-10;1.3e-09;3.5e-10;1.1e-09;3.8e-10;5.5e-10;5.9e-10;1.4e-09;5.4e-10;8e-10;4.5e-10;3.6e-10;9.1e-10;3.5e-10;5.1e-10;5.6e-10;1e-09;8.2e-10;5.5e-10;1.1e-09;6.6e-11;4.4e-10;3.4e-10;2.8e-05;0.00042;0.00019;0.00048	5.6e-07;1e-08;1e-07;9.8e-08;3.5e-07;3e-10;4.3e-09;4e-10;4.5e-10;1.6e-10;1.8e-10;1.4e-10;3.4e-10;1.5e-10;2e-10;3.8e-10;1.4e-10;3.5e-10;1.5e-10;1.5e-10;1.3e-10;3.7e-10;1.7e-10;2.7e-10;1.7e-10;7e-11;3e-10;1.6e-10;2.1e-10;1.6e-10;3.1e-10;2.9e-10;4.7e-11;2.3e-10;2.4e-11;1.9e-10;6.3e-11;9.5e-06;0.00026;0.00015;0.00031	0.0573992570707009	GTC	M	.	258-298-delfrshift	.	no-SNV	GU280_gp05	0.961984567749545
CAMB-75E75	MN908947.3	3037	C	T	1	1	0	0	0.998395932326503	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.0530855603644e-05
CAMB-75E75	MN908947.3	522	TT	-	0.0545	0.0565	1.1e-08;9.5e-06	3.1e-09;1e-05	0.0551448678120839	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.928711412750398
CAMB-75E75	MN908947.3	5284	C	T	0.0052	0.0072	0.00025	4.6e-05	0.00637713029136888	ACT	ORF1ab:nsp3	N855N	C2565T	AAC>AAT	Synonymous	ORF1ab:nsp3	0.993622869708631
CAMB-75E75	MN908947.3	5944	C	A	0.0061	0.0098	0.00016	5.6e-06	0.00806338521946431	ACC	ORF1ab:nsp3	D1075E	C3225A	GAC>GAA	Missense	ORF1ab:nsp3	0.991726265600897
CAMB-75E75	MN908947.3	597	T	A	0.028	0.031	1e-13	6.8e-15	0.0296076559374432	GTG	ORF1ab:leader-protein	V111E	T332A	GTG>GAG	Missense	ORF1ab:leader-protein	0.970187761411166
CAMB-75E75	MN908947.3	635	C	T	1	1	0	0	0.996772795144743	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.00290207600789943
CAMB-75E75	MN908947.3	686	AAGTCATT	-	0.032625	0.030375	0.00011;7.6e-05;0.00037;0.00011;0.00042;0.00016;3.4e-05;0.00023	0.00021;0.00018;0.00059;2e-04;6e-04;0.00033;9.8e-05;0.00042	0.0305611166411292	AAA	ORF1ab:leader-protein	.	421-428-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.969412763011718
CAMB-75E75	MN908947.3	9118	C	T	0.036	0.031	4.5e-17	5.8e-15	0.0330161196348806	ACA	ORF1ab:nsp4	D188D	C564T	GAC>GAT	Synonymous	ORF1ab:nsp4	0.966465980449278
CAMB-75E93	MN908947.3	10369	C	T	0.17	0.2	1.1e-76	1.5e-93	0.180191884869079	GCA	ORF1ab:3C-like-proteinase	R105R	C315T	CGC>CGT	Synonymous	ORF1ab:3C-like-proteinase	0.819774801785595
CAMB-75E93	MN908947.3	10714	C	T	0.081	0.11	3.7e-37	7.7e-50	0.0874574894675397	TCA	ORF1ab:3C-like-proteinase	L220L	C660T	CTC>CTT	Synonymous	ORF1ab:3C-like-proteinase	0.911908024973352
CAMB-75E93	MN908947.3	11074	C	INS	0.022	0.027	0.00036	3.7e-05	0.0232949572476941	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.97655355820373
CAMB-75E93	MN908947.3	11075	T	-	0.049	0.043	6.1e-12	2.3e-11	0.0469090227407098	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.946385568229339
CAMB-75E93	MN908947.3	12082	A	G	0.047	0.047	7.9e-22	2e-22	0.0467293691039406	CAA	ORF1ab:nsp7	A80A	A240G	GCA>GCG	Synonymous	ORF1ab:nsp7	0.952675713193008
CAMB-75E93	MN908947.3	1281	C	T	0.015	0.016	1.6e-08	7e-09	0.0153188789789902	GCC	ORF1ab:nsp2	A159V	C476T	GCC>GTC	Missense	ORF1ab:nsp2	0.98464380341083
CAMB-75E93	MN908947.3	13096	T	C	0.015	0.026	2.1e-08	3.2e-13	0.0155840174404742	CTA	ORF1ab:nsp10	A24A	T72C	GCT>GCC	Synonymous	ORF1ab:nsp10	0.984364887420377
CAMB-75E93	MN908947.3	13119	C	T	0.014	0.021	3.6e-08	2.9e-11	0.0146388689512427	GCT	ORF1ab:nsp10	A32V	C95T	GCT>GTT	Missense	ORF1ab:nsp10	0.985327747083076
CAMB-75E93	MN908947.3	14408	C	T	1	1	0	0	0.999241095520777	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000421613599568268
CAMB-75E93	MN908947.3	23403	A	G	1	1	0	0	0.999551828827526	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.67428075755385e-05
CAMB-75E93	MN908947.3	241	C	T	1	1	0	0	0.998792406653034	TCG	NA	NA	NA	NA	NA	NA	3.22024892524192e-05
CAMB-75E93	MN908947.3	25429	G	T	1	0.99	0	0	0.996703513620213	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	7.89577575996842e-05
CAMB-75E93	MN908947.3	25889	C	T	0.67	0.67	0	0	0.669250281848929	TCA	ORF3a	S166L	C497T	TCA>TTA	Missense	GU280_gp03	0.330749718151071
CAMB-75E93	MN908947.3	26518	T	C	0.0085	0.0044	1.4e-05	0.00092	0.00763049496927544	TTA	NA	NA	NA	NA	NA	NA	0.992301978526572
CAMB-75E93	MN908947.3	3037	C	T	1	1	0	0	0.997274397108491	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000177756710315814
CAMB-75E93	MN908947.3	3267	C	T	0.012	0.015	6.4e-07	2e-08	0.0123219411796566	ACT	ORF1ab:nsp3	T183I	C548T	ACT>ATT	Missense	ORF1ab:nsp3	0.987678058820343
CAMB-75E93	MN908947.3	6558	C	T	1	1	0	0	0.999928881302894	GCT	ORF1ab:nsp3	A1280V	C3839T	GCT>GTT	Missense	ORF1ab:nsp3	0
CAMB-75E93	MN908947.3	8240	C	T	0.65	0.65	0	0	0.649987998744484	ACA	ORF1ab:nsp3	H1841Y	C5521T	CAT>TAT	Missense	ORF1ab:nsp3	0.350012001255516
CAMB-75E93	MN908947.3	8843	A	G	0.0059	0.01	6.8e-05	1.3e-06	0.00801898125901009	AAG	ORF1ab:nsp4	R97G	A289G	AGA>GGA	Missense	ORF1ab:nsp4	0.991920951465642
CAMB-75EA2	MN908947.3	1059	C	T	1	1	0	0	0.999799277398635	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.000200722601364914
CAMB-75EA2	MN908947.3	11075	T	-	0.0049	0.14	0.0099	3.9e-36	0.062600579336981	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.937158030254265
CAMB-75EA2	MN908947.3	13914	T	G	0.015	0.0095	9.8e-07	1.4e-05	0.0118483412322275	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.987361769352291
CAMB-75EA2	MN908947.3	14408	C	T	1	1	0	0	1	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-75EA2	MN908947.3	23403	A	G	1	1	0	0	0.999809940131141	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000142544901644018
CAMB-75EA2	MN908947.3	25563	G	T	1	1	0	0	1	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0
CAMB-75EA2	MN908947.3	28857	G	A	1	1	0	0	0.997825141365811	AGA	N	R195K	G584A	AGA>AAA	Missense	GU280_gp10	0
CAMB-75EA2	MN908947.3	3037	C	T	1	1	2e-275	3.5e-290	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75EB1	MN908947.3	11074	C	INS	0.035	0.027	6.2e-08	3.2e-05	0.0319282478578056	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.967926210271618
CAMB-75EB1	MN908947.3	11075	T	-	0.038	0.027	1.1e-09	9e-08	0.0342502218278616	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.965556182947487
CAMB-75EB1	MN908947.3	12133	T	-	0.0084	0.013	0.00057	5.3e-06	0.010673104831262	CTT	ORF1ab:nsp8	.	42-42-delfrshift	.	no-SNV	ORF1ab:nsp8	0.989221351486847
CAMB-75EB1	MN908947.3	12506	AA	-	0.0088	0.0064	0.00058;9.8e-06	0.0063;9.9e-05	0.00829490645041607	TAA	ORF1ab:nsp8	.	415-416-delfrshift	.	no-SNV	ORF1ab:nsp8	0.991547117487067
CAMB-75EB1	MN908947.3	13469	G	-	0.01	0.004	1.1e-05	0.0055	0.00778919456413656	CGG	ORF1ab:nsp11	.	28-28-delfrshift	.	no-SNV	ORF1ab:nsp11	0.988233344381836
CAMB-75EB1	MN908947.3	14408	C	T	1	1	0	0	0.999740370528346	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000185449622610018
CAMB-75EB1	MN908947.3	1520	A	-	0.014	0.0078	2.7e-06	2e-04	0.0104675505931612	CAA	ORF1ab:nsp2	.	715-715-delfrshift	.	no-SNV	ORF1ab:nsp2	0.989183531053733
CAMB-75EB1	MN908947.3	23403	A	G	1	1	0	0	0.999886255924171	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000113744075829384
CAMB-75EB1	MN908947.3	241	C	T	1	1	0	0	0.999712623033264	TCG	NA	NA	NA	NA	NA	NA	0.00019757166463108
CAMB-75EB1	MN908947.3	25036	T	C	0.06	0.041	1.3e-27	5.1e-20	0.053273606720361	ATC	S	N1158N	T3474C	AAT>AAC	Synonymous	GU280_gp02, spike glycoprotein	0.946715222466739
CAMB-75EB1	MN908947.3	25182	AGC	-	0.0136333333333333	0.012	4.6e-06;4e-06;5.4e-09	1.1e-06;7.8e-07;8.9e-06	0.0107427120464866	GAG	S	.	3620-3622-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.988102791878173
CAMB-75EB1	MN908947.3	25429	G	T	1	1	0	0	0.999850456108868	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	9.34649319575295e-05
CAMB-75EB1	MN908947.3	3037	C	T	1	1	0	0	0.999794976934905	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75EB1	MN908947.3	5498	AA	-	0.00345	0.012	0.0017;NA	1.6e-05;2.3e-06	0.00779162956366874	CAA	ORF1ab:nsp3	.	2779-2780-delfrshift	.	no-SNV	ORF1ab:nsp3	0.990297542043984
CAMB-75EDF	MN908947.3	13914	T	G	0.0074	0.0056	5.9e-06	3.8e-05	0.00647642177696823	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993523578223032
CAMB-75EDF	MN908947.3	14805	C	T	1	1	0	0	0.999939990398464	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-75EDF	MN908947.3	22102	A	G	0.45	0.51	1.7e-141	2e-192	0.486570893191755	AAG	S	E180E	A540G	GAA>GAG	Synonymous	GU280_gp02, spike glycoprotein	0.513429106808245
CAMB-75EDF	MN908947.3	27504	T	C	0.51	0.17	2.4e-294	1.7e-78	0.270271016172656	CTG	ORF7a	S37S	T111C	TCT>TCC	Synonymous	GU280_gp07	0.72970138543909
CAMB-75EDF	MN908947.3	28144	T	C	1	1	0	0	0.999809010461982	TTA	ORF8	L84S	T251C	TTA>TCA	Missense	GU280_gp09	0.000148547418458078
CAMB-75EDF	MN908947.3	28657	C	T	1	1	0	0	0.999556639326092	ACG	N	D128D	C384T	GAC>GAT	Synonymous	GU280_gp10	0
CAMB-75EDF	MN908947.3	28863	C	T	1	1	0	0	1	TCA	N	S197L	C590T	TCA>TTA	Missense	GU280_gp10	0
CAMB-75EDF	MN908947.3	8782	C	T	1	1	0	0	1	GCC	ORF1ab:nsp4	S76S	C228T	AGC>AGT	Synonymous	ORF1ab:nsp4	0
CAMB-75EDF	MN908947.3	9477	T	A	1	1	5.6e-308	0	1	TTT	ORF1ab:nsp4	F308Y	T923A	TTT>TAT	Missense	ORF1ab:nsp4	0
CAMB-75EEE	MN908947.3	11083	G	-	0.012	0.14	2e-05	3.4e-60	0.093733275567675	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.696271566553684
CAMB-75EEE	MN908947.3	11083	G	T	0.33	0.14	2e-84	2e-32	0.209944188180127	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.696271566553684
CAMB-75EEE	MN908947.3	14408	C	T	0.74	0.55	0	4.5000000000845e-314	0.663007997388608	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.336747184592786
CAMB-75EEE	MN908947.3	14805	C	T	0.19	0.18	5.6e-88	5e-82	0.181607174257078	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.818357657816072
CAMB-75EEE	MN908947.3	1707	C	T	0.28	0.14	3.6e-118	3.6e-60	0.191330110712615	TCT	ORF1ab:nsp2	S301F	C902T	TCT>TTT	Missense	ORF1ab:nsp2	0.779198503040699
CAMB-75EEE	MN908947.3	17247	T	C	0.3	0.14	7.3e-147	3e-62	0.199216454456415	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.800744368266405
CAMB-75EEE	MN908947.3	23403	A	G	0.7	0.65	0	0	0.665564179455518	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.334435820544482
CAMB-75EEE	MN908947.3	241	C	T	0.46	0.46	1.2e-239	1.8e-249	0.46377161626896	TCG	NA	NA	NA	NA	NA	NA	0.536083470196116
CAMB-75EEE	MN908947.3	27920	C	A	0.35	0.12	1.9e-110	1.1e-42	0.213973799126638	TCA	ORF8	I9I	C27A	ATC>ATA	Synonymous	GU280_gp09	0.786026200873362
CAMB-75EEE	MN908947.3	28473	C	T	0.31	0.3	5.4e-143	9.7e-138	0.307588574230722	CCT	N	P67L	C200T	CCT>CTT	Missense	GU280_gp10	0.692411425769278
CAMB-75EEE	MN908947.3	28854	C	T	0.65	0.67	1.09999763521387e-318	0	0.658843252305113	TCA	N	S194L	C581T	TCA>TTA	Missense	GU280_gp10	0.341156747694887
CAMB-75EEE	MN908947.3	3037	C	T	0.68	0.84	1.7e-159	1.6e-260	0.779883750315896	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.220116249684104
CAMB-75EFD	MN908947.3	11075	T	-	0.048	0.041	1.3e-11	1.6e-10	0.0455344659577172	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.949084862093802
CAMB-75EFD	MN908947.3	1350	A	G	0.013	0.0084	3.8e-07	3.3e-05	0.0111889692585895	CAA	ORF1ab:nsp2	Q182R	A545G	CAA>CGA	Missense	ORF1ab:nsp2	0.98869801084991
CAMB-75EFD	MN908947.3	1426	C	T	0.057	0.07	1.6e-24	2.3e-29	0.062804736475505	ACC	ORF1ab:nsp2	Y207Y	C621T	TAC>TAT	Synonymous	ORF1ab:nsp2	0.937195263524495
CAMB-75EFD	MN908947.3	14408	C	T	1	1	0	0	0.999540364365703	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000386511783386261
CAMB-75EFD	MN908947.3	17157	A	G	0.0073	0.0023	3.7e-05	0.0041	0.00509976144917519	CAG	ORF1ab:helicase	T307T	A921G	ACA>ACG	Synonymous	ORF1ab:helicase	0.994891809193058
CAMB-75EFD	MN908947.3	18568	C	T	0.013	0.0044	1.4e-07	0.00068	0.00917350095761921	TCT	ORF1ab:3'-to-5'-exonuclease	L177F	C529T	CTC>TTC	Missense	ORF1ab:3'-to-5'-exonuclease	0.990787212100378
CAMB-75EFD	MN908947.3	23403	A	G	1	1	0	0	0.997158392977054	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.73234846127389e-05
CAMB-75EFD	MN908947.3	241	C	T	1	1	0	0	0.999671299774606	TCG	NA	NA	NA	NA	NA	NA	0.000156523916854495
CAMB-75EFD	MN908947.3	25528	C	T	1	1	0	0	0.999845153298235	GCT	ORF3a	L46F	C136T	CTT>TTT	Missense	GU280_gp03	8.44618373265013e-05
CAMB-75EFD	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999643836592229	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	7.84282969295322e-05
CAMB-75EFD	MN908947.3	29541	C	T	0.013	0.019	6.2e-07	1.9e-09	0.0161210725448265	GCA	NA	NA	NA	NA	NA	NA	0.983673301529857
CAMB-75EFD	MN908947.3	3037	C	T	1	1	0	0	0.997877108149546	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.93128120454456e-05
CAMB-75EFD	MN908947.3	6515	TTAAAAA	-	0.00291428571428571	0.01	0.02;0.0053;0.015;0.0083;0.0046;0.0055;0.0054	0.00013;2.7e-06;8.7e-06;4e-06;2.2e-06;5.4e-06;5.3e-06	0.00587638930609793	TTT	ORF1ab:nsp3	.	3796-3802-delfrshift	.	no-SNV	ORF1ab:nsp3	0.994085737964288
CAMB-75EFD	MN908947.3	6573	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	S1285F	C3854T	TCT>TTT	Missense	ORF1ab:nsp3	0
CAMB-75F27	MN908947.3	10976	G	A	0.0078	0.0085	1.7e-05	8.4e-06	0.00797110474529829	TGC	ORF1ab:nsp6	A2T	G4A	GCA>ACA	Missense	ORF1ab:nsp6	0.991904346743056
CAMB-75F27	MN908947.3	11074	C	INS	0.069	0.08	1.7e-21	1.1e-22	0.0733120220412921	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.922855477649635
CAMB-75F27	MN908947.3	11075	T	-	0.017	0.012	3.5e-05	0.00032	0.0149639816633923	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.980451866404715
CAMB-75F27	MN908947.3	11083	G	-	0.082	0.11	6.2e-35	2.5e-46	0.0912348576140039	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.43112196359485
CAMB-75F27	MN908947.3	11083	G	T	0.47	0.49	1.9e-129	1e-139	0.477405340267648	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.43112196359485
CAMB-75F27	MN908947.3	1315	T	C	0.008	0.0033	3.7e-05	0.0034	0.00605788647072022	CTA	ORF1ab:nsp2	T170T	T510C	ACT>ACC	Synonymous	ORF1ab:nsp2	0.99394211352928
CAMB-75F27	MN908947.3	1328	A	C	0.0076	0.0026	3.6e-05	0.0042	0.00553191489361702	CAC	ORF1ab:nsp2	T175P	A523C	ACT>CCT	Missense	ORF1ab:nsp2	0.994468085106383
CAMB-75F27	MN908947.3	1354	T	A	0.0072	0.002	4.3e-05	0.0068	0.00511352014726938	ATG	ORF1ab:nsp2	N183K	T549A	AAT>AAA	Missense	ORF1ab:nsp2	0.99468193904684
CAMB-75F27	MN908947.3	1356	C	G	0.0082	0.0023	2.5e-05	0.0064	0.00581530588508956	GCT	ORF1ab:nsp2	A184G	C551G	GCT>GGT	Missense	ORF1ab:nsp2	0.99418469411491
CAMB-75F27	MN908947.3	1428	ATA	CAT	0.0079	0.00139333333333333	2.8e-05;3.9e-05;4.1e-05	0.017;NA;0.0098	0.00523684836943585	CAT	ORF1ab:nsp2	.	623-625-mnv	.	no-SNV	ORF1ab:nsp2	0.990954534634611
CAMB-75F27	MN908947.3	14408	C	T	1	1	0	0	0.998880706921944	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000157093765341188
CAMB-75F27	MN908947.3	14741	C	T	1	1	0	0	0.999661368072985	TCT	ORF1ab:RNA-dependent-RNA-polymerase	S425F	C1274T	TCT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000159356200948169
CAMB-75F27	MN908947.3	187	A	G	1	1	0	0	0.99982957773149	CAG	NA	NA	NA	NA	NA	NA	0.000132550653285363
CAMB-75F27	MN908947.3	23403	A	G	1	1	0	0	0.999333855146802	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.99608639898746e-05
CAMB-75F27	MN908947.3	23416	A	T	0.011	0.0068	9.1e-07	3.1e-05	0.00972263843105917	CAG	S	T618T	A1854T	ACA>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.990060932973729
CAMB-75F27	MN908947.3	2388	C	T	0.022	0.011	1.1e-10	2.4e-06	0.0174350377200335	ACA	ORF1ab:nsp2	T528I	C1583T	ACA>ATA	Missense	ORF1ab:nsp2	0.982564962279966
CAMB-75F27	MN908947.3	241	C	T	1	1	0	0	0.997620920550258	TCG	NA	NA	NA	NA	NA	NA	9.59306229734656e-05
CAMB-75F27	MN908947.3	26985	C	A	0.0099	0.0034	1.4e-06	0.00062	0.00851020198913155	CCA	M	H155N	C463A	CAT>AAT	Missense	GU280_gp05	0.991387265456783
CAMB-75F27	MN908947.3	27227	T	C	0.014	0.0078	3.4e-08	7.4e-06	0.0123526013524994	GTT	ORF6	V9A	T26C	GTT>GCT	Missense	GU280_gp06	0.98746049546335
CAMB-75F27	MN908947.3	27849	C	T	0.012	0.0089	4.5e-06	0.00015	0.0108130588479933	ACT	NA	NA	NA	NA	NA	NA	0.989186941152007
CAMB-75F27	MN908947.3	27920	C	T	0.0088	0.011	3.7e-05	2.2e-05	0.00941124972641716	TCA	ORF8	I9I	C27T	ATC>ATT	Synonymous	GU280_gp09	0.990588750273583
CAMB-75F27	MN908947.3	29767	AACAATGCTA	-	0.0143	0.0173	8e-07;1.4e-06;1.5e-06;3.7e-07;9.5e-08;4.5e-07;5.7e-07;3.7e-07;3.5e-07;5.1e-07	1.4e-07;2.5e-07;1.5e-07;8.2e-08;2.1e-08;3e-07;4.7e-07;5.8e-08;2e-07;2.5e-07	0.0154171066525871	GAA	NA	NA	NA	NA	NA	NA	0.984624974028672
CAMB-75F27	MN908947.3	3037	C	T	1	1	0	0	0.999365884590996	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.92644261255549e-05
CAMB-75F27	MN908947.3	5649	A	G	0.0091	0.014	4.4e-06	1.8e-08	0.0103462157809984	AAA	ORF1ab:nsp3	K977R	A2930G	AAA>AGA	Missense	ORF1ab:nsp3	0.989653784219002
CAMB-75F27	MN908947.3	5650	A	G	1	1	0	0	0.999920194724871	AAT	ORF1ab:nsp3	K977K	A2931G	AAA>AAG	Synonymous	ORF1ab:nsp3	3.9902637564343e-05
CAMB-75F27	MN908947.3	8078	C	A	0.013	0.01	6.5e-08	1.1e-06	0.0114486307517402	ACC	ORF1ab:nsp3	P1787T	C5359A	CCA>ACA	Missense	ORF1ab:nsp3	0.988471587849293
CAMB-75F27	MN908947.3	8841	C	T	0.0028	0.01	0.0022	1.5e-06	0.00701279157261099	ACA	ORF1ab:nsp4	T96I	C287T	ACA>ATA	Missense	ORF1ab:nsp4	0.992987208427389
CAMB-75F27	MN908947.3	8937	C	T	0.028	0.02	9.7e-14	2.3e-10	0.0236756986054404	GCA	ORF1ab:nsp4	A128V	C383T	GCA>GTA	Missense	ORF1ab:nsp4	0.976271276313696
CAMB-75F27	MN908947.3	9479	G	T	0.014	0.0032	4.4e-08	0.0032	0.0104529616724739	TGG	ORF1ab:nsp4	G309C	G925T	GGT>TGT	Missense	ORF1ab:nsp4	0.986748157879705
CAMB-75F27	MN908947.3	9541	C	T	0.0084	0.0081	7.2e-06	9.4e-06	0.00828191303991308	TCT	ORF1ab:nsp4	L329L	C987T	CTC>CTT	Synonymous	ORF1ab:nsp4	0.991677087390582
CAMB-75F36	MN908947.3	11075	T	-	0.13	0.1	1.3e-32	3e-26	0.113994478657889	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.885793162030155
CAMB-75F36	MN908947.3	14408	C	T	1	1	0	0	0.999663526244953	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000336473755047106
CAMB-75F36	MN908947.3	23403	A	G	1	1	0	0	0.999900968037434	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.42739719244386e-05
CAMB-75F36	MN908947.3	241	C	T	1	1	0	0	0.999880139038715	TCG	NA	NA	NA	NA	NA	NA	5.99304806424548e-05
CAMB-75F36	MN908947.3	27389	C	T	0.024	0.013	2.9e-12	9.6e-08	0.0196645285632547	ACG	NA	NA	NA	NA	NA	NA	0.980335471436745
CAMB-75F36	MN908947.3	27890	G	T	0.023	0.014	1.2e-09	2.4e-07	0.0180722891566265	CGA	NA	NA	NA	NA	NA	NA	0.981464318813716
CAMB-75F36	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999699744783066	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-75F36	MN908947.3	29321	G	T	0.027	0.0025	8.3e-14	0.0026	0.014456630109671	AGT	N	V350F	G1048T	GTC>TTC	Missense	GU280_gp10	0.985543369890329
CAMB-75F36	MN908947.3	29600	A	G	0.012	0.011	1.5e-06	2.6e-06	0.0113072255929399	TAG	ORF10	S15G	A43G	AGT>GGT	Missense	GU280_gp11	0.98869277440706
CAMB-75F36	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75F45	MN908947.3	11075	T	-	0.043	0.043	4e-11	1.6e-11	0.0427274010634794	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952402239894593
CAMB-75F45	MN908947.3	14408	C	T	1	1	0	0	0.997840872287596	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000287883694987225
CAMB-75F45	MN908947.3	23403	A	G	1	1	0	0	0.998332073701493	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000130306742070835
CAMB-75F45	MN908947.3	241	C	T	1	1	0	0	0.998846739981054	TCG	NA	NA	NA	NA	NA	NA	0.000164751431278059
CAMB-75F45	MN908947.3	27559	C	T	0.024	0.021	3.7e-10	9.8e-09	0.0227351016190148	ACT	ORF7a	L56L	C166T	CTG>TTG	Synonymous	GU280_gp07	0.976575955907682
CAMB-75F45	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999164098009508	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000117598635855824
CAMB-75F45	MN908947.3	3037	C	T	1	1	0	0	0.999216417120227	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000127067494017239
CAMB-75F54	MN908947.3	10755	C	T	1	1	0	0	0.999821990150122	GCT	ORF1ab:3C-like-proteinase	A234V	C701T	GCT>GTT	Missense	ORF1ab:3C-like-proteinase	0.00017800984987836
CAMB-75F54	MN908947.3	11074	C	INS	0.019	0.031	0.0013	3.5e-06	0.0219054186244167	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.977244663961898
CAMB-75F54	MN908947.3	11075	T	-	0.039	0.022	1.3e-09	1e-06	0.0348819518402235	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961895409468749
CAMB-75F54	MN908947.3	14408	C	T	1	1	0	0	0.999542998906462	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00031010788490101
CAMB-75F54	MN908947.3	20644	T	C	0.056	0.025	3.1e-25	1.2e-12	0.0457890433360589	TTA	ORF1ab:endoRNAse	Y342H	T1024C	TAC>CAC	Missense	ORF1ab:endoRNAse	0.954179508145166
CAMB-75F54	MN908947.3	20833	T	C	0.0037	0.0066	0.00083	1.6e-05	0.00425729969473382	ATT	ORF1ab:2'-O-ribose-methyltransferase	L59L	T175C	TTA>CTA	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.995715322172181
CAMB-75F54	MN908947.3	21957	A	C	1	1	0	0	1	GAA	S	E132A	A395C	GAA>GCA	Missense	GU280_gp02, spike glycoprotein	0
CAMB-75F54	MN908947.3	222	C	T	0.073	0.061	6e-33	4.9e-28	0.0689084991210207	TCA	NA	NA	NA	NA	NA	NA	0.931074095347501
CAMB-75F54	MN908947.3	23271	C	A	0.015	0.014	1.3e-08	1.2e-08	0.0152361390526301	GCT	S	A570D	C1709A	GCT>GAT	Missense	GU280_gp02, spike glycoprotein	0.984144848834428
CAMB-75F54	MN908947.3	23403	A	G	1	1	0	0	0.996238546438984	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.80924614743857e-05
CAMB-75F54	MN908947.3	241	C	T	1	1	0	0	0.999751146503608	TCG	NA	NA	NA	NA	NA	NA	0.000106651498453553
CAMB-75F54	MN908947.3	28606	C	T	0.046	0.038	8e-21	2.5e-17	0.0443376289727759	ACT	N	Y111Y	C333T	TAC>TAT	Synonymous	GU280_gp10	0.955662371027224
CAMB-75F54	MN908947.3	28631	G	A	0.022	0.033	5e-11	1.9e-15	0.0240937983164405	TGG	N	G120R	G358A	GGA>AGA	Missense	GU280_gp10	0.975863253736471
CAMB-75F54	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999700209853103	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00121275121275121
CAMB-75F54	MN908947.3	3037	C	T	1	1	0	0	0.999862750480373	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75F54	MN908947.3	4331	C	T	0.0075	0.0046	2.7e-05	0.00042	0.00657444185727982	TCT	ORF1ab:nsp3	L538L	C1612T	CTA>TTA	Synonymous	ORF1ab:nsp3	0.99342555814272
CAMB-75F63	MN908947.3	10097	G	A	1	1	0	0	0.999726938734982	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	9.92950054612253e-05
CAMB-75F63	MN908947.3	11075	T	-	0.04	0.043	5e-10	9.6e-11	0.0415343427883938	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952363403821767
CAMB-75F63	MN908947.3	13536	C	T	1	1	0	0	0.999886456105823	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	3.78479647256969e-05
CAMB-75F63	MN908947.3	14184	C	T	1	1	0	0	0.999608288987188	CCA	ORF1ab:RNA-dependent-RNA-polymerase	T239T	C717T	ACC>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000391711012811816
CAMB-75F63	MN908947.3	14408	C	T	1	1	0	0	0.99838023891476	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000273334683134238
CAMB-75F63	MN908947.3	21058	C	T	1	1	0	0	0.999915964621105	CCC	ORF1ab:2'-O-ribose-methyltransferase	P134S	C400T	CCT>TCT	Missense	ORF1ab:2'-O-ribose-methyltransferase	6.30265341708859e-05
CAMB-75F63	MN908947.3	23403	A	G	1	1	0	0	0.999642400209792	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.74132820508745e-05
CAMB-75F63	MN908947.3	23731	C	T	1	1	0	0	0.999668532704773	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000294637595757219
CAMB-75F63	MN908947.3	241	C	T	1	1	0	0	0.998655263299446	TCG	NA	NA	NA	NA	NA	NA	0.000268947340110806
CAMB-75F63	MN908947.3	25643	TGT	-	0.015	0.015	3.5e-08;4.5e-08;4.2e-08	6.6e-08;8.7e-08;7.5e-08	0.0149412931343383	CTG	ORF3a	.	251-253-delinframe	.	no-SNV	GU280_gp03	0.98493552704871
CAMB-75F63	MN908947.3	28087	C	T	0.019	0.019	3.4e-09	3.2e-09	0.0194120909595119	GCT	ORF8	A65V	C194T	GCT>GTT	Missense	GU280_gp09	0.980310593455352
CAMB-75F63	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999593076032178	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	3.43973582828839e-05
CAMB-75F63	MN908947.3	3037	C	T	1	1	0	0	0.999534840450274	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75F63	MN908947.3	4002	C	T	1	1	0	0	0.999856938483548	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	7.15307582260372e-05
CAMB-75F63	MN908947.3	583	C	T	1	1	0	0	0.999867762542214	TCC	ORF1ab:leader-protein	V106V	C318T	GTC>GTT	Synonymous	ORF1ab:leader-protein	0.000101721121373642
CAMB-75F72	MN908947.3	11846	A	G	0.056	0.033	1.1e-07	1.2e-06	0.0416666666666667	TAA	ORF1ab:nsp7	K2E	A4G	AAA>GAA	Missense	ORF1ab:nsp7	0.958333333333333
CAMB-75F72	MN908947.3	15984	A	-	0.041	0.02	1.7e-18	1.6e-09	0.0261556814792723	TAA	ORF1ab:RNA-dependent-RNA-polymerase	.	2517-2517-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.973695198329854
CAMB-75F72	MN908947.3	1605	ATG	-	1	0.99	0;0;0	0;0;0	0.996384671005061	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.00298345538378085
CAMB-75F72	MN908947.3	16438	A	G	0.13	0.011	6.2e-43	9.6e-06	0.0563258232235702	TAT	ORF1ab:helicase	M68V	A202G	ATG>GTG	Missense	ORF1ab:helicase	0.94367417677643
CAMB-75F72	MN908947.3	25096	C	T	0.042	0.084	2.1e-19	9.1e-38	0.06763836646964	ACA	S	N1178N	C3534T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.93236163353036
CAMB-75F72	MN908947.3	27235	G	A	0.12	0.1	3.5e-55	9e-48	0.109458714150646	AGC	ORF6	A12T	G34A	GCA>ACA	Missense	GU280_gp06	0.890462496060511
CAMB-75F72	MN908947.3	27367	C	T	0.024	0.054	1.6e-12	2.5e-25	0.041909290564365	GCA	ORF6	Q56*	C166T	CAA>TAA	Nonsense	GU280_gp06	0.958030263343475
CAMB-75F72	MN908947.3	27921	ATCACAACTGTAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGT	-	0.0679791666666667	0.0515208333333333	3.1e-25;3e-25;9.2e-26;2.8e-25;2.9e-25;2.1e-25;8.4e-26;3.9e-26;7.4e-27;1.7e-25;1.5e-20;7e-27;6.3e-27;1.7e-26;5.6e-26;1.4e-25;2.7e-26;6.7e-26;1.3e-26;5.5e-19;3.9e-11;1.3e-23;1.9e-27;1.1e-21;5.3e-09;2.5e-24;2.4e-24;1.7e-23;1.8e-10;4.1e-07;6e-08;1.6e-08;4.2e-09;3.3e-16;1.9e-09;9.6e-24;1.7e-06;8e-08;2.5e-11;4.3e-08;9.6e-10;1.3e-11;8.3e-10;2.3e-08;1e-08;1.1e-19;4.2e-24;1.9e-13	4.4e-20;2.2e-20;7.2e-21;3.4e-20;3.3e-20;3.1e-20;2.1e-20;1e-20;5.5e-21;1.3e-20;4.5e-16;5.9e-21;1.5e-21;2e-21;1.5e-20;2e-20;4.9e-21;1.5e-20;3.7e-21;3.8e-15;3.6e-09;7.3e-19;1.3e-21;3.2e-17;2.3e-07;4.1e-19;3.1e-19;1.4e-18;1.4e-08;5.8e-06;1.2e-06;3.3e-07;1.4e-07;5.9e-13;8.3e-08;2.4e-19;1.2e-05;1.4e-06;2.7e-09;6.3e-07;4.4e-08;1.5e-09;3.9e-08;5e-07;3.3e-07;1.4e-15;2.7e-19;4.9e-11	0.059064807219032	CAT	ORF8	.	28-75-delinframe	.	no-SNV	GU280_gp09	0.939180370660402
CAMB-75F72	MN908947.3	2821	A	G	0.17	0.12	1.6e-09	1.5e-19	0.128654970760234	TAC	ORF1ab:nsp3	V34V	A102G	GTA>GTG	Synonymous	ORF1ab:nsp3	0.871345029239766
CAMB-75F72	MN908947.3	29555	C	T	0.059	0.048	9.4e-22	2.4e-20	0.0515536723163842	GCA	NA	NA	NA	NA	NA	NA	0.948446327683616
CAMB-75F72	MN908947.3	6051	A	C	1	0.92	4.6e-219	1.9e-171	0.963963963963964	AAG	ORF1ab:nsp3	K1111T	A3332C	AAG>ACG	Missense	ORF1ab:nsp3	0.036036036036036
CAMB-75F81	MN908947.3	11074	C	INS	0.036	0.19	1.4e-07	2.7e-74	0.128899207866703	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.870554493307839
CAMB-75F81	MN908947.3	11083	G	-	0.28	0.21	4.2e-135	2.8e-96	0.241108961960026	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-75F81	MN908947.3	11083	G	T	0.72	0.79	8.8e-261	3.20154538505128e-321	0.758762088974855	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-75F81	MN908947.3	13914	T	G	0.007	0.0089	8.8e-06	1.3e-06	0.00780068078668684	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.99215204236006
CAMB-75F81	MN908947.3	14805	C	T	1	1	0	0	0.999877845189136	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	8.14365405757563e-05
CAMB-75F81	MN908947.3	15158	A	-	0.049	0.029	1.2e-13	4.4e-07	0.0405844155844156	CAA	ORF1ab:RNA-dependent-RNA-polymerase	.	1691-1691-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.957251082251082
CAMB-75F81	MN908947.3	15493	G	C	0.091	0.019	5.4e-38	2.3e-09	0.0467559455091203	TGC	ORF1ab:RNA-dependent-RNA-polymerase	A676P	G2026C	GCC>CCC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.95278226737474
CAMB-75F81	MN908947.3	17247	T	C	1	1	0	0	0.999816782704287	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000160315133748626
CAMB-75F81	MN908947.3	1801	A	-	0.053	0.058	1.1e-22	1.2e-25	0.0560237388724036	CAA	ORF1ab:nsp2	.	996-996-delfrshift	.	no-SNV	ORF1ab:nsp2	0.943857566765579
CAMB-75F81	MN908947.3	1801	AA	-	0.0265	0.0605	1.1e-22;NA	1.2e-25;4.3e-28	0.0465547048653989	CAA	ORF1ab:nsp2	.	996-997-delfrshift	.	no-SNV	ORF1ab:nsp2	0.943857566765579
CAMB-75F81	MN908947.3	27877	G	INS	0.21	0.16	6.9e-68	6.8e-53	0.186421173762946	TGT	NA	NA	NA	NA	NA	NA	0.804372842347526
CAMB-75F81	MN908947.3	27880	ACG	-	0.266666666666667	0.216666666666667	6e-78;2.3e-79;2.3e-80	3.7e-65;1.4e-67;4e-69	0.238525730180807	CAC	NA	NA	NA	NA	NA	NA	0.769491525423729
CAMB-75F81	MN908947.3	27883	C	T	0.25	0.2	5.3e-76	1.1e-63	0.22739916550765	GCC	NA	NA	NA	NA	NA	NA	0.770514603616134
CAMB-75F81	MN908947.3	8313	T	INS	0.0024	0.0084	0.0014	5.3e-06	0.00473415877640204	ATG	ORF1ab:nsp3	.	5593-5594-insfrshift	.	no-SNV	ORF1ab:nsp3	0.995265841223598
CAMB-75F81	MN908947.3	8315	ACACC	-	0.0024	0.0085	0.0022;0.0023;0.0024;0.005;0.0019	7.5e-06;8.1e-06;7.5e-06;1.8e-05;6.5e-06	0.00475667764361508	GAC	ORF1ab:nsp3	.	5596-5600-delfrshift	.	no-SNV	ORF1ab:nsp3	0.994873672647382
CAMB-75F90	MN908947.3	14408	C	T	1	1	0	1.4e-124	0.999210991701809	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000353693375051013
CAMB-75F90	MN908947.3	241	C	T	1	1	0	2.9e-08	0.99930537689735	TCG	NA	NA	NA	NA	NA	NA	5.14535631592488e-05
CAMB-75F90	MN908947.3	3037	C	T	1	1	0	4.2e-16	0.999468085106383	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000265957446808511
CAMB-75FBE	MN908947.3	11075	T	-	0.058	0.04	6.2e-14	4.1e-10	0.0495196526199744	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.946700564717529
CAMB-75FBE	MN908947.3	11502	G	T	0.0086	0.0033	3e-05	0.0047	0.00574300071787509	GGT	ORF1ab:nsp6	G177V	G530T	GGT>GTT	Missense	ORF1ab:nsp6	0.994256999282125
CAMB-75FBE	MN908947.3	14408	C	T	1	1	0	0	0.998341606498195	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000203068592057762
CAMB-75FBE	MN908947.3	14576	C	T	0.0098	0.011	5.6e-06	2.6e-06	0.0101514342825448	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A370V	C1109T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.989759609850031
CAMB-75FBE	MN908947.3	16458	A	-	0.0074	0.002	1.3e-05	0.0021	0.0043792576115668	CAC	ORF1ab:helicase	.	222-222-delfrshift	.	no-SNV	ORF1ab:helicase	0.995551230362853
CAMB-75FBE	MN908947.3	18318	G	T	0.0077	0.004	3.7e-05	0.0018	0.0059100015410695	GGT	ORF1ab:3'-to-5'-exonuclease	G93G	G279T	GGG>GGT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.994051471721375
CAMB-75FBE	MN908947.3	23403	A	G	1	1	0	0	0.999886229734671	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.93909227581163e-05
CAMB-75FBE	MN908947.3	23593	G	T	0.007	0.02	3.1e-05	2.4e-10	0.0131472818196483	AGA	S	Q677H	G2031T	CAG>CAT	Missense	GU280_gp02, spike glycoprotein	0.986852718180352
CAMB-75FBE	MN908947.3	241	C	T	0.99	1	0	0	0.995939086294416	TCG	NA	NA	NA	NA	NA	NA	8.82807327300817e-05
CAMB-75FBE	MN908947.3	25626	C	T	0.056	0.07	9.6e-26	6.2e-32	0.0628623970276407	ACT	ORF3a	H78H	C234T	CAC>CAT	Synonymous	GU280_gp03	0.936931189131373
CAMB-75FBE	MN908947.3	27923	C	T	1	1	0	0	0.999816412704241	TCA	ORF8	I10I	C30T	ATC>ATT	Synonymous	GU280_gp09	0.000122391530506089
CAMB-75FBE	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999771875509206	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	7.29022380987096e-05
CAMB-75FBE	MN908947.3	3037	C	T	1	1	0	0	0.999091270517408	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.67955926620094e-05
CAMB-75FBE	MN908947.3	7359	T	C	0.0068	0.0019	4.1e-05	0.0069	0.00414245749946202	ATG	ORF1ab:nsp3	M1547T	T4640C	ATG>ACG	Missense	ORF1ab:nsp3	0.994404992468259
CAMB-75FCD	MN908947.3	10456	C	T	0.77	0.78	0	0	0.767863973017142	TCA	ORF1ab:3C-like-proteinase	F134F	C402T	TTC>TTT	Synonymous	ORF1ab:3C-like-proteinase	0.231649222851977
CAMB-75FCD	MN908947.3	11075	T	-	0.044	0.042	1.2e-10	3.6e-11	0.0432537949811214	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953651144273496
CAMB-75FCD	MN908947.3	14408	C	T	1	1	0	0	0.998832901325878	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000122138233338309
CAMB-75FCD	MN908947.3	15951	C	T	0.0094	0.0099	4.5e-06	1.7e-06	0.00962202394296731	TCC	ORF1ab:RNA-dependent-RNA-polymerase	I828I	C2484T	ATC>ATT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.990351073846568
CAMB-75FCD	MN908947.3	23403	A	G	1	1	0	0	0.998519006088531	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000120673577971587
CAMB-75FCD	MN908947.3	23525	C	T	0.025	0.024	6.2e-12	1.6e-11	0.0248680970805487	ACA	S	H655Y	C1963T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.974885684136476
CAMB-75FCD	MN908947.3	241	C	T	1	1	0	0	0.998528285149792	TCG	NA	NA	NA	NA	NA	NA	0.000241925728801258
CAMB-75FCD	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999344638322274	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	2.98454008237331e-05
CAMB-75FCD	MN908947.3	3037	C	T	1	1	0	0	0.99876687835255	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000184968247117578
CAMB-75FCD	MN908947.3	4874	T	C	0.029	0.026	4.3e-14	3.5e-13	0.0280710233776805	TTA	ORF1ab:nsp3	Y719H	T2155C	TAC>CAC	Missense	ORF1ab:nsp3	0.971865381191015
CAMB-75FCD	MN908947.3	6606	C	T	0.011	0.0082	1.2e-06	2.2e-05	0.00999302811991634	TCT	ORF1ab:nsp3	S1296F	C3887T	TCT>TTT	Missense	ORF1ab:nsp3	0.989852041211558
CAMB-75FDC	MN908947.3	11074	C	INS	0.11	0.11	1.1e-30	9.2e-30	0.105958132045089	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.887869028448739
CAMB-75FDC	MN908947.3	11083	G	-	0.17	0.17	7.1e-78	8.2e-72	0.172636886922601	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-75FDC	MN908947.3	11083	G	T	0.83	0.83	0	0	0.827077684220541	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-75FDC	MN908947.3	1140	A	G	0.016	0.011	5.3e-09	2e-06	0.0155464640561075	AAG	ORF1ab:nsp2	K112R	A335G	AAG>AGG	Missense	ORF1ab:nsp2	0.98416130917592
CAMB-75FDC	MN908947.3	12274	G	A	0.13	0.12	1.1e-55	5.1e-55	0.125866401568497	AGA	ORF1ab:nsp8	K61K	G183A	AAG>AAA	Synonymous	ORF1ab:nsp8	0.873111865904509
CAMB-75FDC	MN908947.3	12278	G	T	0.14	0.14	4.3e-64	1.2e-63	0.140277586917686	GGC	ORF1ab:nsp8	A63S	G187T	GCT>TCT	Missense	ORF1ab:nsp8	0.859667445375842
CAMB-75FDC	MN908947.3	14805	C	T	1	1	0	0	0.99935585168485	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000140907443938967
CAMB-75FDC	MN908947.3	22103	G	A	0.021	0.019	2.7e-09	3.6e-08	0.0204701416265148	AGG	S	G181R	G541A	GGA>AGA	Missense	GU280_gp02, spike glycoprotein	0.978537012702584
CAMB-75FDC	MN908947.3	2480	A	G	1	1	0	0	0.999840823473232	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-75FDC	MN908947.3	2558	C	T	1	1	0	0	0.999835161816151	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	3.66307075221158e-05
CAMB-75FDC	MN908947.3	25728	C	T	0.012	0.011	6.2e-07	7.5e-07	0.0115696389093589	TCT	ORF3a	V112V	C336T	GTC>GTT	Synonymous	GU280_gp03	0.988184721198723
CAMB-75FDC	MN908947.3	25996	G	T	0.021	0.029	3.8e-08	3.8e-10	0.0227448953217886	TGT	ORF3a	V202L	G604T	GTA>TTA	Missense	GU280_gp03	0.976867407598863
CAMB-75FDC	MN908947.3	26144	G	T	1	1	0	0	0.999765166340509	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000234833659491194
CAMB-75FDC	MN908947.3	26681	C	T	0.029	0.028	1.3e-13	1.3e-12	0.0284158375301969	TCC	M	F53F	C159T	TTC>TTT	Synonymous	GU280_gp05	0.971543217458953
CAMB-75FDC	MN908947.3	29247	C	T	0.055	0.062	2.3e-25	1.6e-26	0.0562198447661003	ACA	N	T325I	C974T	ACA>ATA	Missense	GU280_gp10	0.943570379693728
CAMB-75FDC	MN908947.3	4788	C	T	0.046	0.049	5.8e-22	4.6e-23	0.047077203489129	GCT	ORF1ab:nsp3	A690V	C2069T	GCT>GTT	Missense	ORF1ab:nsp3	0.952844681682073
CAMB-75FEB	MN908947.3	11074	C	INS	0.43	0.13	8.6e-197	4.2e-37	0.306156124391792	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.693251533742331
CAMB-75FEB	MN908947.3	11083	G	-	0.014	0.13	3.5e-06	5.6e-57	0.0730744560122366	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-75FEB	MN908947.3	11083	G	T	0.99	0.87	0	0	0.926580154931662	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-75FEB	MN908947.3	14707	G	T	0.046	0.011	3.4e-15	1.9e-05	0.032251249911978	TGC	ORF1ab:RNA-dependent-RNA-polymerase	A414S	G1240T	GCT>TCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.889726075628477
CAMB-75FEB	MN908947.3	14805	C	T	1	1	0	0	0.999925794004155	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-75FEB	MN908947.3	14931	C	T	1	1	0	0	0.999190938511327	ACC	ORF1ab:RNA-dependent-RNA-polymerase	N488N	C1464T	AAC>AAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000809061488673139
CAMB-75FEB	MN908947.3	15732	G	T	0.48	0.3	2.1e-268	1.7e-143	0.409804352604968	TGT	ORF1ab:RNA-dependent-RNA-polymerase	V755V	G2265T	GTG>GTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.590063750274786
CAMB-75FEB	MN908947.3	16793	G	-	0.051	0.016	9.2e-23	2.6e-08	0.0285479694309354	CGT	ORF1ab:helicase	.	557-557-delfrshift	.	no-SNV	ORF1ab:helicase	0.971452030569065
CAMB-75FEB	MN908947.3	16793	GTG	-	0.017	0.0153333333333333	9.2e-23;NA;NA	2.6e-08;2.8e-08;5.2e-08	0.00970023155391451	CGT	ORF1ab:helicase	.	557-559-delinframe	.	no-SNV	ORF1ab:helicase	0.971452030569065
CAMB-75FEB	MN908947.3	28857	G	T	1	1	0	0	1	AGA	N	R195I	G584T	AGA>ATA	Missense	GU280_gp10	0
CAMB-75FEB	MN908947.3	3763	A	G	1	1	2.2e-148	2e-166	1	TAG	ORF1ab:nsp3	V348V	A1044G	GTA>GTG	Synonymous	ORF1ab:nsp3	0
CAMB-75FEB	MN908947.3	3931	T	C	1	1	0	0	1	TTG	ORF1ab:nsp3	V404V	T1212C	GTT>GTC	Synonymous	ORF1ab:nsp3	0
CAMB-75FEB	MN908947.3	692	TTTGAC	-	0.23	0.0706666666666667	5.4e-42;6e-36;1e-30;1.3e-74;2e-92;9.8e-93	5.2e-10;1.7e-09;2.3e-08;7.3e-26;2.4e-32;3.6e-32	0.149518014630478	ATT	ORF1ab:leader-protein	.	427-432-delinframe	.	no-SNV	ORF1ab:leader-protein	0.807107961561175
CAMB-75FEB	MN908947.3	9646	G	T	0.18	0.15	8.9e-86	1.9e-71	0.168566615740197	AGT	ORF1ab:nsp4	Q364H	G1092T	CAG>CAT	Missense	ORF1ab:nsp4	0.8313550358444
CAMB-75FFA	MN908947.3	13914	T	G	0.0065	0.0037	1.6e-05	0.00028	0.0050314465408805	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994894561598224
CAMB-75FFA	MN908947.3	14408	C	T	1	1	0	0	0.99949485136973	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000427433456382359
CAMB-75FFA	MN908947.3	23403	A	G	1	1	0	0	0.999876555909886	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000123444090114186
CAMB-75FFA	MN908947.3	241	C	T	1	1	0	0	0.999855606093423	TCG	NA	NA	NA	NA	NA	NA	7.21969532885712e-05
CAMB-75FFA	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-75FFA	MN908947.3	29110	A	G	0.71	0.58	0	0	0.628057512745604	CAG	N	P279P	A837G	CCA>CCG	Synonymous	GU280_gp10	0.371942487254396
CAMB-75FFA	MN908947.3	3037	C	T	1	1	0	0	0.998791175581747	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-75FFA	MN908947.3	522	T	-	0.08	0.043	1.1e-10	1.1e-05	0.0618661257606491	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.938133874239351
CAMB-75FFA	MN908947.3	522	TT	-	0.04	0.0415	1.1e-10;NA	1.1e-05;7.6e-06	0.0400471142520612	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.938133874239351
CAMB-75FFA	MN908947.3	683	C	T	0.064	0.12	6.6e-30	6.8e-54	0.0917723032767281	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.908227696723272
CAMB-75FFA	MN908947.3	8016	C	T	1	1	0	0	0.999286606028179	GCG	ORF1ab:nsp3	A1766V	C5297T	GCG>GTG	Missense	ORF1ab:nsp3	0.000535045478865704
CAMB-76005	MN908947.3	12070	G	T	0.029	0.0069	1.4e-14	5.5e-05	0.0173918793810343	TGG	ORF1ab:nsp7	L76L	G228T	CTG>CTT	Synonymous	ORF1ab:nsp7	0.982528766036239
CAMB-76005	MN908947.3	14099	G	T	0.031	0.016	5.4e-15	1.7e-08	0.0208672212669052	GGT	ORF1ab:RNA-dependent-RNA-polymerase	G211V	G632T	GGT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.978993354092113
CAMB-76005	MN908947.3	14408	C	T	1	1	0	0	0.999635797098517	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000303502417902596
CAMB-76005	MN908947.3	21618	C	T	0.068	0.073	6.6e-20	1.8e-26	0.0711422845691383	ACA	S	T19I	C56T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0.928857715430862
CAMB-76005	MN908947.3	21648	C	T	0.071	0.097	3.7e-21	3.7e-35	0.0894552723638181	ACT	S	T29I	C86T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.910544727636182
CAMB-76005	MN908947.3	23403	A	G	1	0.98	0	0	0.9909677126894	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.2665714706649e-05
CAMB-76005	MN908947.3	241	C	T	1	1	0	0	0.99971729051227	TCG	NA	NA	NA	NA	NA	NA	0.000113083795092163
CAMB-76005	MN908947.3	26404	C	T	0.036	0.031	3.6e-17	2.9e-15	0.0335437330928765	ACC	E	P54S	C160T	CCT>TCT	Missense	GU280_gp04	0.966456266907123
CAMB-76005	MN908947.3	26854	CATTCAATCCAGAAACTAA	-	0.00273684210526316	0.0151052631578947	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;9.9e-14;4.9e-09;NA;NA;NA;NA;NA;NA;NA	2.8e-09;3e-09;2.1e-09;8.3e-09;2.4e-08;1.4e-08;3.8e-08;5.1e-08;1.5e-08;3.7e-08;9.3e-09;2.9e-06;1.2e-08;1.4e-08;3.2e-08;1.1e-07;2.8e-08;1.3e-08;7e-09	0.00744736125887622	TCA	M	.	332-350-delfrshift	.	no-SNV	GU280_gp05	0.991111566677893
CAMB-76005	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99951658126269	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000213857998289136
CAMB-76005	MN908947.3	29000	G	T	0.007	0.098	0.00013	4.1e-41	0.0426555148980659	AGG	N	G243C	G727T	GGC>TGC	Missense	GU280_gp10	0.957135389440669
CAMB-76005	MN908947.3	29095	C	T	0.015	0.0093	1.9e-07	3.4e-05	0.0120181051974403	TCG	N	F274F	C822T	TTC>TTT	Synonymous	GU280_gp10	0.98798189480256
CAMB-76005	MN908947.3	3037	C	T	1	1	0	0	0.999076638965836	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00015389350569406
CAMB-76005	MN908947.3	7504	C	T	0.055	0.032	8.4e-24	1.1e-14	0.0437510598609462	ACA	ORF1ab:nsp3	Y1595Y	C4785T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.956248940139054
CAMB-76005	MN908947.3	843	C	T	0.018	0.02	1.8e-09	1.5e-10	0.0189676106717422	CCT	ORF1ab:nsp2	P13L	C38T	CCT>CTT	Missense	ORF1ab:nsp2	0.980835493715748
CAMB-76005	MN908947.3	843	CT	TC	0.0135	0.01016	1.8e-09;1.7e-05	1.5e-10;0.48	0.0120123671628174	CCT	ORF1ab:nsp2	.	38-39-mnv	.	no-SNV	ORF1ab:nsp2	0.980835493715748
CAMB-76005	MN908947.3	9542	TGTTTAACACCAGTTTACTCATTCTTACCTGG	-	0.02603125	0.0156875	1.2e-05;7.9e-06;2.5e-06;0.00011;2e-04;0.00011;0.00019;2e-04;1e-04;2.7e-05;0.00015;0.00013;0.00011;3.4e-06;3e-04;0.00036;3.9e-09;1e-08;9.5e-09;7.3e-09;1.7e-09;6e-10;4.7e-09;6.9e-09;9e-11;8.5e-10;2.7e-09;9.8e-10;3.7e-09;7.3e-10;1.8e-11;1e-09	5e-04;4e-04;2e-04;0.0015;0.002;0.0015;0.0022;0.0022;0.0015;7e-04;0.0018;0.0016;0.0015;8.2e-05;0.0028;0.003;7.5e-06;1.6e-05;9.9e-06;8.8e-06;4.5e-06;2.9e-06;6.5e-06;8.4e-06;6.4e-07;2.1e-06;4.8e-06;2.7e-06;5.2e-06;1e-06;2.5e-07;2.3e-06	0.0199427946274401	CTG	ORF1ab:nsp4	.	988-1019-delfrshift	.	no-SNV	ORF1ab:nsp4	0.980850716054971
CAMB-76023	MN908947.3	11075	T	-	0.045	0.036	5.9e-11	2.1e-09	0.0413712256581269	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953495783207949
CAMB-76023	MN908947.3	12076	C	T	0.0079	0.0075	3e-05	3.5e-05	0.00770422476238328	ACA	ORF1ab:nsp7	N78N	C234T	AAC>AAT	Synonymous	ORF1ab:nsp7	0.992128292090608
CAMB-76023	MN908947.3	14408	C	T	1	1	0	0	0.99890330657919	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000553199336160797
CAMB-76023	MN908947.3	23403	A	G	1	1	0	0	0.999550061389929	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.91390157783557e-05
CAMB-76023	MN908947.3	241	C	T	1	1	0	0	0.997655905140265	TCG	NA	NA	NA	NA	NA	NA	0.000289206508668585
CAMB-76023	MN908947.3	27923	C	T	1	1	0	0	0.999439519005401	TCA	ORF8	I10I	C30T	ATC>ATT	Synonymous	GU280_gp09	0.000458575359217365
CAMB-76023	MN908947.3	28344	C	T	0.038	0.038	6.9e-18	3.2e-18	0.0381416832694004	ACT	N	T24I	C71T	ACT>ATT	Missense	GU280_gp10	0.961818668411193
CAMB-76023	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99963059711338	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	8.83080183680678e-05
CAMB-76023	MN908947.3	3037	C	T	1	1	0	0	0.999307199353386	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	2.8866693608914e-05
CAMB-76041	MN908947.3	11074	C	INS	0.094	0.12	7.3e-35	2e-04	0.0944917603185002	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.868215491609132
CAMB-76041	MN908947.3	11083	G	T	0.9	0.96	0	2.1e-38	0.897170446368469	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.32120888558761e-05
CAMB-76041	MN908947.3	11950	C	T	0.013	0.038	1.2e-07	6.4e-09	0.0130044400592008	ACA	ORF1ab:nsp7	H36H	C108T	CAC>CAT	Synonymous	ORF1ab:nsp7	0.986975826344351
CAMB-76041	MN908947.3	1314	C	T	1	1	0	4.9e-75	1	ACT	ORF1ab:nsp2	T170I	C509T	ACT>ATT	Missense	ORF1ab:nsp2	0
CAMB-76041	MN908947.3	14805	C	T	1	1	0	9.4e-46	0.999915492957747	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	5.63380281690141e-05
CAMB-76041	MN908947.3	17247	T	C	1	1	0	9.3e-70	0.999876923076923	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	7.03296703296703e-05
CAMB-76041	MN908947.3	9627	C	INS	0.013	0.019	3.5e-05	0.0027	0.0126243413080847	TCT	ORF1ab:nsp4	.	1072-1073-insfrshift	.	no-SNV	ORF1ab:nsp4	0.987291120692084
CAMB-76050	MN908947.3	11075	T	-	0.055	0.037	1.4e-13	6.1e-10	0.0472755105364297	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.94321401817412
CAMB-76050	MN908947.3	13462	TTTA	-	0.033	0.0055	2.4e-14;2.1e-13;5.2e-13;1.9e-13	NA;NA;1.6e-05;1.2e-05	0.0180521506574549	TTT	ORF1ab:nsp11	.	21-24-delfrshift	.	no-SNV	ORF1ab:nsp11	0.982632771205638
CAMB-76050	MN908947.3	14408	C	T	1	1	0	0	0.999424108267646	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000359932332721448
CAMB-76050	MN908947.3	1495	G	-	0.017	0.0084	1.8e-06	0.00014	0.0122086570477248	TGT	ORF1ab:nsp2	.	690-690-delfrshift	.	no-SNV	ORF1ab:nsp2	0.975582685904551
CAMB-76050	MN908947.3	18027	GG	TT	0.0105	0.00635	1.8e-06;7e-06	0.00012;0.00047	0.00825984082598408	TGG	ORF1ab:helicase	.	1791-1792-mnv	.	no-SNV	ORF1ab:helicase	0.991565336530228
CAMB-76050	MN908947.3	23403	A	G	1	1	0	0	0.999776678146194	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00014104538135145
CAMB-76050	MN908947.3	23426	G	T	0.02	0.012	2.1e-10	6.9e-07	0.0158040253989081	TGT	S	V622F	G1864T	GTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.984125682419925
CAMB-76050	MN908947.3	24026	CTT	-	0.033	0.0166666666666667	0.00086;3.5e-05;1e-04	0.026;0.0052;0.0071	0.0232518183380104	ACT	S	.	2464-2466-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.961157114839834
CAMB-76050	MN908947.3	241	C	T	1	1	0	0	0.998849521699299	TCG	NA	NA	NA	NA	NA	NA	0.000980037070967467
CAMB-76050	MN908947.3	25429	G	T	0.98	1	0	0	0.988744964139252	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0.000126461077087059
CAMB-76050	MN908947.3	26777	TTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.03975	0.0644772727272727	NA;NA;NA;1e-06;3.1e-09;4e-07;6.3e-07;1.4e-06;1e-07;3.9e-07;5.8e-08;5.5e-08;1e-08;3.1e-08;2.2e-08;4.5e-08;3.1e-08;4.7e-08;9.1e-08;2.4e-08;7.2e-08;3.6e-08;3.5e-08;3.5e-08;8.3e-08;3.1e-08;5e-08;3.3e-08;1.5e-08;7e-08;2.5e-08;2.7e-09;5e-08;6.4e-08;5.8e-08;2.3e-08;6.5e-08;6.2e-09;2.7e-08;2e-08;0.047;0.057;0.047;0.048	1e-05;7.2e-05;0.00024;3.3e-10;7.2e-13;9.7e-11;1e-10;7.3e-10;3.2e-12;6.2e-11;3.6e-13;3.9e-13;1.3e-13;9.8e-14;6.5e-14;3.5e-13;1.8e-13;2e-13;6.2e-13;7.2e-14;4.8e-13;2.3e-13;2.1e-13;1.9e-13;5.8e-13;2.2e-13;3.8e-13;2e-13;5.3e-14;4.1e-13;1.9e-13;1e-14;2.2e-13;4.4e-13;4.1e-13;2.4e-11;1.1e-10;6.7e-12;5.8e-11;2.2e-11;3.5e-06;2.5e-05;7.7e-06;1.2e-05	0.0589165853514297	CTT	M	.	255-298-delfrshift	.	no-SNV	GU280_gp05	0.981842758286763
CAMB-76050	MN908947.3	28086	GC	TT	0.00965	0.0041	2.5e-05;2.8e-05	8.8e-05;NA	0.00715912788805727	GGC	ORF8	.	193-194-mnv	.	no-SNV	GU280_gp09	0.990828693088765
CAMB-76050	MN908947.3	28727	G	T	0.0086	0.0061	3.7e-05	0.00045	0.00747045268713298	TGC	N	A152S	G454T	GCT>TCT	Missense	GU280_gp10	0.991042890061696
CAMB-76050	MN908947.3	3037	C	T	1	1	0	0	0.998967475477543	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00086043710204784
CAMB-76050	MN908947.3	7092	TCACTAT	GTCACTA	0.0371428571428571	0.001	3.1e-06;6.5e-08;4.4e-08;4.4e-08;4.2e-08;4.8e-08;3.8e-08	NA;NA;NA;NA;0.009;NA;NA	0.0164948453608247	GTC	ORF1ab:nsp3	.	4373-4379-mnv	.	no-SNV	ORF1ab:nsp3	0.991256830601093
CAMB-7606F	MN908947.3	11075	T	-	0.034	0.034	8.9e-09	8.2e-09	0.033968215455538	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960718185126774
CAMB-7606F	MN908947.3	15815	T	C	1	1	0	0	0.999177191218149	GTT	ORF1ab:RNA-dependent-RNA-polymerase	V783A	T2348C	GTT>GCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000261209137095616
CAMB-7606F	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999399114484503	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000105422956903095
CAMB-7606F	MN908947.3	1908	T	C	1	1	0	0	0.999757881893838	TTC	ORF1ab:nsp2	F368S	T1103C	TTC>TCC	Missense	ORF1ab:nsp2	0.000166159484620753
CAMB-7606F	MN908947.3	22441	T	C	1	1	0	0	0.999840357598978	TTG	S	L293L	T879C	CTT>CTC	Synonymous	GU280_gp02, spike glycoprotein	0.000159642401021711
CAMB-7606F	MN908947.3	29771	A	G	1	1	0	0	0.9989510342802	AAT	NA	NA	NA	NA	NA	NA	0.000167834515168044
CAMB-7607E	MN908947.3	10097	G	A	1	1	0	0	0.999782107949947	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000124509742887381
CAMB-7607E	MN908947.3	11075	T	-	0.047	0.033	2.2e-11	5e-09	0.042018643522983	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952812600450016
CAMB-7607E	MN908947.3	13536	C	T	1	1	0	0	0.9999302211988	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-7607E	MN908947.3	1385	C	T	0.054	0.055	7.4e-22	9.4e-22	0.0542759407069555	TCA	ORF1ab:nsp2	H194Y	C580T	CAC>TAC	Missense	ORF1ab:nsp2	0.945724059293044
CAMB-7607E	MN908947.3	14408	C	T	1	0.99	0	0	0.995112761426309	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000832741768142849
CAMB-7607E	MN908947.3	15666	G	T	0.011	0.011	1e-06	5.1e-07	0.0108971144332552	TGA	ORF1ab:RNA-dependent-RNA-polymerase	V733V	G2199T	GTG>GTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.989075778316911
CAMB-7607E	MN908947.3	1912	C	T	0.082	0.084	2e-37	1.3e-38	0.0821685856782218	CCC	ORF1ab:nsp2	S369S	C1107T	TCC>TCT	Synonymous	ORF1ab:nsp2	0.917800628040145
CAMB-7607E	MN908947.3	23403	A	G	1	1	0	0	0.998028530699316	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.0220197955738e-05
CAMB-7607E	MN908947.3	23731	C	T	1	1	0	0	0.999952269581404	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-7607E	MN908947.3	241	C	T	1	1	0	0	0.998317816158958	TCG	NA	NA	NA	NA	NA	NA	3.33105711097417e-05
CAMB-7607E	MN908947.3	26780	TCTTGTAGGCTTGAT	-	0.0246666666666667	0.0186666666666667	4e-04;1.8e-05;0.00025;0.00033;0.00054;0.00015;0.00029;0.00086;0.00086;0.00041;0.00061;0.00055;0.00079;0.00066;0.00077	0.032;0.013;0.018;0.01;0.015;0.0036;0.0064;0.0019;0.002;0.0014;0.0014;0.0014;0.0019;0.0016;0.0017	0.0229818026016686	GTC	M	.	258-272-delinframe	.	no-SNV	GU280_gp05	0.98062015503876
CAMB-7607E	MN908947.3	2721	C	T	0.0093	0.007	2.5e-05	0.00023	0.00827586206896552	GCA	ORF1ab:nsp3	A1V	C2T	GCA>GTA	Missense	ORF1ab:nsp3	0.991379310344828
CAMB-7607E	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99942354806168	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	5.32850215804337e-05
CAMB-7607E	MN908947.3	3037	C	T	1	1	0	0	0.999230134726423	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000109980753368161
CAMB-7607E	MN908947.3	4002	C	T	1	1	0	0	0.999802045529528	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0.000131969646981194
CAMB-7607E	MN908947.3	522	TT	-	0.042	0.024	5.1e-06;2.8e-05	0.00087;0.0042	0.0375218467812409	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.957296639520734
CAMB-7607E	MN908947.3	6286	C	T	0.088	0.084	3.1e-40	5.1e-39	0.0864124660606776	CCT	ORF1ab:nsp3	T1189T	C3567T	ACC>ACT	Synonymous	ORF1ab:nsp3	0.913548184000315
CAMB-7607E	MN908947.3	8809	C	T	0.12	0.089	2.5e-54	2.8e-40	0.103453925809411	ACA	ORF1ab:nsp4	D85D	C255T	GAC>GAT	Synonymous	ORF1ab:nsp4	0.896447765106829
CAMB-7608D	MN908947.3	11075	T	-	0.037	0.041	3.5e-09	3.9e-10	0.0392615615820753	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956477559942619
CAMB-7608D	MN908947.3	11956	C	T	0.0068	0.0075	8.2e-05	4.1e-05	0.00714889192175213	ACA	ORF1ab:nsp7	D38D	C114T	GAC>GAT	Synonymous	ORF1ab:nsp7	0.992704880743485
CAMB-7608D	MN908947.3	14408	C	T	1	1	0	0	0.998556350933884	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00040392253663353
CAMB-7608D	MN908947.3	1594	C	T	0.24	0.23	3.7e-107	9.4e-106	0.234967622571693	CCG	ORF1ab:nsp2	S263S	C789T	TCC>TCT	Synonymous	ORF1ab:nsp2	0.764788938117727
CAMB-7608D	MN908947.3	16289	C	T	1	1	0	0	0.998784989952802	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	9.3462311322959e-05
CAMB-7608D	MN908947.3	16580	C	A	0.043	0.053	5.4e-13	6.5e-17	0.0489038785834739	ACA	ORF1ab:helicase	T115K	C344A	ACA>AAA	Missense	ORF1ab:helicase	0.951096121416526
CAMB-7608D	MN908947.3	17123	C	T	0.0079	0.008	2e-05	1.7e-05	0.00795385786504792	GCT	ORF1ab:helicase	A296V	C887T	GCT>GTT	Missense	ORF1ab:helicase	0.991763121425644
CAMB-7608D	MN908947.3	23403	A	G	1	1	0	0	0.999339411663513	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.88112850507483e-05
CAMB-7608D	MN908947.3	241	C	T	1	1	0	0	0.998922777417262	TCG	NA	NA	NA	NA	NA	NA	0.000376378974691759
CAMB-7608D	MN908947.3	25096	C	T	0.008	0.0085	2.9e-05	2.3e-05	0.00825885576358536	ACA	S	N1178N	C3534T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.991597625415878
CAMB-7608D	MN908947.3	25429	G	T	1	1	0	0	0.999255858903117	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	5.79850205363614e-05
CAMB-7608D	MN908947.3	26801	C	T	0.012	0.011	2.7e-06	9.1e-06	0.0112245137741155	TCA	M	L93L	C279T	CTC>CTT	Synonymous	GU280_gp05	0.981443912679079
CAMB-7608D	MN908947.3	28166	G	T	0.03	0.028	1.4e-14	7.2e-14	0.0289667830921662	AGG	ORF8	Q91H	G273T	CAG>CAT	Missense	GU280_gp09	0.970765913464965
CAMB-7608D	MN908947.3	28193	G	A	0.077	0.071	2.5e-35	1.4e-32	0.0739933545321376	TGC	ORF8	V100V	G300A	GTG>GTA	Synonymous	GU280_gp09	0.925640430168995
CAMB-7608D	MN908947.3	2880	C	T	0.0099	0.0079	3.5e-06	3e-05	0.00880949134051548	GCC	ORF1ab:nsp3	A54V	C161T	GCC>GTC	Missense	ORF1ab:nsp3	0.991099595436156
CAMB-7608D	MN908947.3	28844	C	T	0.013	0.015	1.9e-06	1.5e-07	0.0140366595736738	TCG	N	R191C	C571T	CGC>TGC	Missense	GU280_gp10	0.9857206854071
CAMB-7608D	MN908947.3	3037	C	T	1	1	0	0	0.999278105123503	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000195106723377688
CAMB-7608D	MN908947.3	3145	G	A	0.015	0.017	4.1e-08	9.8e-09	0.015783371977476	TGG	ORF1ab:nsp3	L142L	G426A	TTG>TTA	Synonymous	ORF1ab:nsp3	0.983736336535277
CAMB-7608D	MN908947.3	3293	C	T	0.019	0.021	6.4e-10	1.9e-10	0.0199023512784273	ACC	ORF1ab:nsp3	P192S	C574T	CCT>TCT	Missense	ORF1ab:nsp3	0.980033406141591
CAMB-7608D	MN908947.3	3412	T	C	1	1	0	0	0.997941439713592	CTA	ORF1ab:nsp3	A231A	T693C	GCT>GCC	Synonymous	ORF1ab:nsp3	0.000230149597238205
CAMB-7609C	MN908947.3	10961	G	A	0.042	0.037	5.2e-19	1.7e-17	0.0392874572962421	TGT	ORF1ab:3C-like-proteinase	V303I	G907A	GTT>ATT	Missense	ORF1ab:3C-like-proteinase	0.960590531966813
CAMB-7609C	MN908947.3	11075	T	-	0.016	0.037	4.2e-05	1e-09	0.0263490663137774	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.968651668872225
CAMB-7609C	MN908947.3	11104	TTTTGCTATGGGTATTA	-	0.0102882352941176	0.00127770588235294	3.9e-05;0.00022;7.6e-05;1e-04;0.00017;0.00019;8.5e-05;0.00017;1.9e-05;6.9e-05;2.4e-05;1.4e-05;3.4e-05;2.1e-05;2.9e-06;6.3e-06;4e-06	9.8e-05;0.00039;0.46;0.46;0.46;0.45;0.46;0.46;0.46;0.46;0.46;0.46;NA;NA;NA;NA;NA	0.00539443729585272	CTT	ORF1ab:nsp6	.	132-148-delfrshift	.	no-SNV	ORF1ab:nsp6	0.988268188086827
CAMB-7609C	MN908947.3	11283	GTTTGTCTGGTT	-	1	1	0;0;0;0;0;0;0;0;0;0;0;0	0;0;0;0;0;0;0;0;0;0;0;0	0.998191631036658	AGT	ORF1ab:nsp6	.	311-322-delinframe	.	no-SNV	ORF1ab:nsp6	0.00190657769304099
CAMB-7609C	MN908947.3	14408	C	T	1	1	0	0	0.999566755722435	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000306881363275327
CAMB-7609C	MN908947.3	1547	A	G	0.02	0.021	4.4e-08	8.7e-09	0.0202858460119871	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.944213923467035
CAMB-7609C	MN908947.3	1547	A	T	0.02	0.036	1.5e-08	5.1e-14	0.0285846011987091	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.944213923467035
CAMB-7609C	MN908947.3	16012	C	G	0.01	0.0063	4.5e-06	0.00015	0.00824894641180818	ACG	ORF1ab:RNA-dependent-RNA-polymerase	R849G	C2545G	CGG>GGG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.991571294465416
CAMB-7609C	MN908947.3	18855	T	C	0.023	0.034	9.4e-12	1.1e-16	0.0279054916985951	GTG	ORF1ab:3'-to-5'-exonuclease	C272C	T816C	TGT>TGC	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.972078544061303
CAMB-7609C	MN908947.3	20268	A	G	1	1	1.5e-118	6.6e-246	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-7609C	MN908947.3	21481	CTTAGTAAAG	-	0.0157	0.0201	0.00065;0.00069;0.00084;0.00093;0.001;0.00088;0.0011;7e-04;0.00046;0.00081	3.8e-05;3.7e-05;5.2e-05;5.8e-05;5.4e-05;5.3e-05;6.4e-05;2.9e-05;1.4e-05;3.8e-05	0.0177347843611447	TCT	ORF1ab:2'-O-ribose-methyltransferase	.	823-832-delfrshift	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.981900452488688
CAMB-7609C	MN908947.3	21496	CTTATAATTAGAGAAAACAACAGAGTTGTTATT	-	0.0170606060606061	0.0238787878787879	0.00046;0.00042;0.00043;0.00067;0.00056;0.00072;0.00075;0.00069;0.00071;0.00087;0.00052;7e-04;0.00067;0.00066;0.00065;6e-04;0.00059;0.00062;0.00072;0.00068;0.00056;0.00093;0.00069;0.00071;0.00081;0.00042;0.00053;7e-04;0.00065;8e-04;0.00098;0.00086;0.00097	1.8e-06;3.5e-06;4.8e-06;8.1e-06;5.8e-06;1.1e-05;9.1e-06;1.1e-05;1.1e-05;1.3e-05;7.4e-06;9.8e-06;5.9e-06;1.2e-05;7e-06;9e-06;7.2e-06;7.2e-06;1.1e-05;8.9e-06;8.9e-06;1.4e-05;8.3e-06;1.2e-05;1.2e-05;2.7e-06;5.1e-06;1.1e-05;9.6e-06;1.2e-05;1.4e-05;1.5e-05;1.6e-05	0.0205450733752621	ACT	ORF1ab:2'-O-ribose-methyltransferase	.	838-870-delinframe	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.976120857699805
CAMB-7609C	MN908947.3	21531	TAGTGA	-	0.017	0.0235	0.00091;0.00073;0.00097;0.0011;0.00098;0.00092	1.8e-05;1.4e-05;2.1e-05;2e-05;1.7e-05;1.9e-05	0.020090200902009	CTA	ORF1ab:2'-O-ribose-methyltransferase	.	873-878-delinframe	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.979901558654635
CAMB-7609C	MN908947.3	21543	TGTTAACAA	-	0.0217777777777778	0.0245555555555556	0.00014;2e-04;9.3e-05;8.8e-05;0.00015;4.4e-05;6.6e-05;0.00018;0.00012	1.6e-05;3.2e-05;1e-05;1.1e-05;2.1e-05;9.9e-06;8.9e-06;3.5e-05;2.1e-05	0.0228310502283105	TTG	ORF1ab:2'-O-ribose-methyltransferase	.	885-893-delinframe	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.974700399467377
CAMB-7609C	MN908947.3	21928	C	T	0.097	0.097	1.5e-42	9.6e-43	0.097317619839491	ACG	S	N122N	C366T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.896464463885475
CAMB-7609C	MN908947.3	22120	C	T	0.034	0.071	2.8e-10	3.8e-20	0.0530341662417134	TCA	S	F186F	C558T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.946965833758287
CAMB-7609C	MN908947.3	23117	C	A	0.06	0.04	1.2e-26	1.4e-18	0.0484620886981402	ACA	S	H519N	C1555A	CAT>AAT	Missense	GU280_gp02, spike glycoprotein	0.95153791130186
CAMB-7609C	MN908947.3	23403	A	G	0.99	1	0	0	0.99689370406849	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00309547260073815
CAMB-7609C	MN908947.3	241	C	T	0.99	1	0	0	0.992988430911003	TCG	NA	NA	NA	NA	NA	NA	0.00696148645264687
CAMB-7609C	MN908947.3	24374	C	T	1	1	0	0	0.999817126137247	ACT	S	L938F	C2812T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	4.57184656882915e-05
CAMB-7609C	MN908947.3	24635	G	T	0.049	0.029	2.7e-21	1.2e-13	0.0386020457866537	TGC	S	A1025S	G3073T	GCT>TCT	Missense	GU280_gp02, spike glycoprotein	0.961397954213346
CAMB-7609C	MN908947.3	29311	C	T	0.67	0.72	0	0	0.688592250182779	TCA	N	F346F	C1038T	TTC>TTT	Synonymous	GU280_gp10	0.311289828070093
CAMB-7609C	MN908947.3	29734	G	C	1	1	0	0	0.999920496104309	CGA	NA	NA	NA	NA	NA	NA	0
CAMB-7609C	MN908947.3	3037	C	T	1	1	0	0	0.999901980003921	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7609C	MN908947.3	3130	C	T	0.027	0.034	1.4e-13	2e-16	0.0310897965933521	ACC	ORF1ab:nsp3	Y137Y	C411T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.968910203406648
CAMB-7609C	MN908947.3	462	A	G	0.011	0.011	1.2e-06	7.9e-07	0.0107546481954065	CAG	ORF1ab:leader-protein	Q66R	A197G	CAG>CGG	Missense	ORF1ab:leader-protein	0.983928788431158
CAMB-7609C	MN908947.3	702	G	A	0.23	0.19	8.9e-110	2.9e-92	0.209893126892667	GGC	ORF1ab:leader-protein	G146D	G437A	GGC>GAC	Missense	ORF1ab:leader-protein	0.79005974053519
CAMB-7609C	MN908947.3	7626	ATT	-	0.0103	0.0166666666666667	0.0047;0.0018;0.0019	0.00024;4.7e-05;4.5e-05	0.0127017178552837	AAT	ORF1ab:nsp3	.	4907-4909-delinframe	.	no-SNV	ORF1ab:nsp3	0.986523501698258
CAMB-7609C	MN908947.3	8072	A	G	0.23	0.2	2.3e-110	1e-90	0.218552237148884	TAA	ORF1ab:nsp3	N1785D	A5353G	AAC>GAC	Missense	ORF1ab:nsp3	0.781447762851116
CAMB-760AB	MN908947.3	11075	T	-	0.04	0.035	7.4e-10	1.5e-08	0.0374670294294793	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.9587253456285
CAMB-760AB	MN908947.3	14408	C	T	1	1	0	0	0.997006830741771	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000226547214499022
CAMB-760AB	MN908947.3	21859	C	T	0.013	0.018	1.4e-07	3e-09	0.0159722694215999	ACA	S	N99N	C297T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.983993747026439
CAMB-760AB	MN908947.3	23403	A	G	1	1	0	0	0.998706398440779	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.6240103948072e-05
CAMB-760AB	MN908947.3	241	C	T	1	1	0	0	0.998590266968193	TCG	NA	NA	NA	NA	NA	NA	8.81083144879438e-05
CAMB-760AB	MN908947.3	26125	C	A	0.014	0.018	3.9e-06	1.3e-07	0.0161512027491409	CCA	ORF3a	Q245K	C733A	CAA>AAA	Missense	GU280_gp03	0.983848797250859
CAMB-760AB	MN908947.3	28380	G	A	0.99	0.99	0	0	0.994096637239706	CGA	N	R36Q	G107A	CGA>CAA	Missense	GU280_gp10	0.00578206078576723
CAMB-760AB	MN908947.3	28677	C	T	1	1	0	0	0.999950108928839	ACT	N	T135I	C404T	ACT>ATT	Missense	GU280_gp10	4.98910711612978e-05
CAMB-760AB	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999358033749083	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000103571132653907
CAMB-760AB	MN908947.3	29392	G	T	1	1	0	0	0.9995189574496	AGA	N	K373N	G1119T	AAG>AAT	Missense	GU280_gp10	0
CAMB-760AB	MN908947.3	3037	C	T	1	1	0	0	0.999046165585654	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.15375810759252e-05
CAMB-760AB	MN908947.3	353	G	T	0.012	0.0078	3.6e-07	1.7e-05	0.00977943727915626	TGG	ORF1ab:leader-protein	G30C	G88T	GGC>TGC	Missense	ORF1ab:leader-protein	0.990196126345833
CAMB-760AB	MN908947.3	5031	C	T	0.044	0.034	1.1e-16	1.8e-14	0.0369769704832955	ACA	ORF1ab:nsp3	T771I	C2312T	ACA>ATA	Missense	ORF1ab:nsp3	0.962860849821602
CAMB-760AB	MN908947.3	6099	C	T	0.0093	0.004	7e-06	0.00084	0.00644545237526856	ACT	ORF1ab:nsp3	T1127I	C3380T	ACT>ATT	Missense	ORF1ab:nsp3	0.993554547624731
CAMB-760AB	MN908947.3	6404	G	T	1	1	0	0	0.998969379498318	AGT	ORF1ab:nsp3	V1229F	G3685T	GTC>TTC	Missense	ORF1ab:nsp3	0.00042587624036455
CAMB-760C9	MN908947.3	11074	C	INS	0.11	0.11	1.4e-44	1.1e-39	0.111291564578229	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.884298214910746
CAMB-760C9	MN908947.3	11083	G	-	0.16	0.16	3.9e-69	1.1e-72	0.159733427788054	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.62374224356199e-05
CAMB-760C9	MN908947.3	11083	G	T	0.84	0.84	0	0	0.840056672832461	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.62374224356199e-05
CAMB-760C9	MN908947.3	13627	G	T	1	1	0	0	0.999780004806049	TGA	ORF1ab:RNA-dependent-RNA-polymerase	D54Y	G160T	GAC>TAC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	3.04608730086204e-05
CAMB-760C9	MN908947.3	14805	C	T	1	1	0	0	0.998058436330918	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000558791495004025
CAMB-760C9	MN908947.3	14937	C	T	0.59	0.59	0	0	0.587582655726166	ACA	ORF1ab:RNA-dependent-RNA-polymerase	D490D	C1470T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.412287688232788
CAMB-760C9	MN908947.3	15540	C	T	1	1	0	0	0.999495679197448	TCA	ORF1ab:RNA-dependent-RNA-polymerase	V691V	C2073T	GTC>GTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000218084671373661
CAMB-760C9	MN908947.3	26144	G	T	1	1	0	0	0.999667301817742	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000120981157184768
CAMB-760C9	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0313783783783784	0.0338378378378378	0.00089;6.1e-05;0.00035;0.00039;0.00066;3.1e-05;9.8e-05;2.8e-05;2.9e-05;9e-06;1.7e-05;1.5e-05;2.4e-05;2e-05;2.3e-05;3.6e-05;1.4e-05;3.1e-05;1.9e-05;1.3e-05;1.6e-05;8.7e-06;1.1e-05;2.3e-05;1.9e-05;1.4e-05;3.2e-05;1.1e-05;3e-06;2.7e-05;3.1e-05;2.8e-05;1.1e-05;2.8e-05;8.5e-06;1.9e-05;1.5e-05	0.00047;3.3e-05;2e-04;0.00023;0.00043;1.5e-05;5e-05;8.8e-06;8.6e-06;2.1e-06;4.5e-06;3.9e-06;6.7e-06;4.9e-06;6.2e-06;9.8e-06;3.5e-06;8.5e-06;5.3e-06;3.7e-06;3.9e-06;2.2e-06;2.9e-06;6.7e-06;5.5e-06;4.3e-06;8e-06;2.7e-06;1.5e-06;6.4e-06;8.2e-06;6.9e-06;4.4e-06;8.9e-06;2.7e-06;5.4e-06;4.9e-06	0.0335783020017053	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.977813968389577
CAMB-760C9	MN908947.3	28338	A	G	1	1	0	0	0.999453647195583	GAT	N	D22G	A65G	GAT>GGT	Missense	GU280_gp10	9.29962220284801e-05
CAMB-760C9	MN908947.3	3484	A	G	1	1	0	0	0.999328204858001	GAG	ORF1ab:nsp3	G255G	A765G	GGA>GGG	Synonymous	ORF1ab:nsp3	9.2207176352811e-05
CAMB-760C9	MN908947.3	522	TT	-	0.0395	0.035	9.8e-06;0.00011	2.5e-05;0.00036	0.0378639118927687	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.955253237174234
CAMB-760D8	MN908947.3	14408	C	T	1	1	0	0	0.999763257575758	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000197285353535354
CAMB-760D8	MN908947.3	16289	C	T	1	1	0	0	0.999376169681847	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0
CAMB-760D8	MN908947.3	17321	C	T	0.038	0.05	6.4e-18	3.3e-23	0.0442545454545455	GCA	ORF1ab:helicase	A362V	C1085T	GCA>GTA	Missense	ORF1ab:helicase	0.955672727272727
CAMB-760D8	MN908947.3	22012	A	C	0.86	0.85	0	0	0.853887399463807	AAA	S	K150N	A450C	AAA>AAC	Missense	GU280_gp02, spike glycoprotein	0.146112600536193
CAMB-760D8	MN908947.3	23403	A	G	1	1	0	0	0.999835951277529	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.15182709264652e-05
CAMB-760D8	MN908947.3	241	C	T	1	1	0	0	0.99989727786338	TCG	NA	NA	NA	NA	NA	NA	5.13610683102209e-05
CAMB-760D8	MN908947.3	25429	G	T	1	1	0	0	0.999917848732132	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	2.73837559559669e-05
CAMB-760D8	MN908947.3	2590	A	T	1	1	6.6e-61	4.8e-162	1	AAG	ORF1ab:nsp2	E595D	A1785T	GAA>GAT	Missense	ORF1ab:nsp2	0
CAMB-760D8	MN908947.3	28090	GTTCTA	-	0.0666666666666667	0.0261666666666667	9.1e-21;1.5e-20;1.7e-20;6.7e-21;1.2e-20;6.2e-20	8.9e-11;1.1e-10;1.1e-10;8e-11;9.2e-11;3.8e-10	0.0386317907444668	GGT	ORF8	.	197-202-delinframe	.	no-SNV	GU280_gp09	0.961352657004831
CAMB-760D8	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-760D8	MN908947.3	6532	G	T	1	1	0	0	0.999597909127463	AGG	ORF1ab:nsp3	E1271D	G3813T	GAG>GAT	Missense	ORF1ab:nsp3	0
CAMB-760D8	MN908947.3	686	AAGTCATTT	-	0.0737777777777778	0.0641111111111111	2.3e-10;9.9e-11;5e-09;2.3e-10;6.7e-09;6.7e-10;1.2e-11;9.6e-10;2.4e-08	4.7e-09;3.6e-09;5e-08;4.5e-09;5.5e-08;1.4e-08;1.6e-09;1.5e-08;1.7e-07	0.0673486786018755	AAA	ORF1ab:leader-protein	.	421-429-delinframe	.	no-SNV	ORF1ab:leader-protein	0.932476835118617
CAMB-760E7	MN908947.3	11074	C	INS	0.12	0.12	1.4e-56	4.6e-44	0.119007751250291	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.877343949256479
CAMB-760E7	MN908947.3	11083	G	-	0.14	0.15	2.4e-58	7.8e-64	0.139664402634635	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.000123305829283079
CAMB-760E7	MN908947.3	11083	G	T	0.86	0.85	0	0	0.860027332792158	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.000123305829283079
CAMB-760E7	MN908947.3	12973	C	T	0.0062	0.0066	7.5e-05	4.1e-05	0.00634842590851904	ACC	ORF1ab:nsp9	N96N	C288T	AAC>AAT	Synonymous	ORF1ab:nsp9	0.993550346343509
CAMB-760E7	MN908947.3	14805	C	T	1	1	0	0	0.998696430016272	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000314654823658447
CAMB-760E7	MN908947.3	17247	T	C	1	1	0	0	0.998381644986172	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.00107548909146779
CAMB-760E7	MN908947.3	232	T	C	0.037	0.036	1.2e-17	2.5e-17	0.0365274857314509	ATC	NA	NA	NA	NA	NA	NA	0.963352358065485
CAMB-760E7	MN908947.3	23277	C	T	0.009	0.0095	1.3e-05	5.9e-06	0.00920335624496873	ACT	S	T572I	C1715T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.989310483621277
CAMB-760E7	MN908947.3	26144	G	T	1	1	0	0	0.999661068012352	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000225954658431875
CAMB-760E7	MN908947.3	28117	A	G	1	1	0	0	0.99954850965593	GAT	ORF8	D75G	A224G	GAT>GGT	Missense	GU280_gp09	0.000161855029006125
CAMB-760E7	MN908947.3	28843	T	C	1	1	0	0	0.997085096379878	GTC	N	S190S	T570C	AGT>AGC	Synonymous	GU280_gp10	0.00119887165021157
CAMB-760E7	MN908947.3	28881	GG	TT	1	1	0;0	0;0	0.997449755504083	AGG	N	.	608-609-mnv	.	no-SNV	GU280_gp10	0.000515173073620685
CAMB-760E7	MN908947.3	6449	C	T	1	1	0	0	0.998678254199796	TCT	ORF1ab:nsp3	L1244F	C3730T	CTT>TTT	Missense	ORF1ab:nsp3	9.58779336935604e-05
CAMB-760F6	MN908947.3	11074	C	INS	0.03	0.02	8.5e-07	0.001	0.0274253731343284	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.972405020352782
CAMB-760F6	MN908947.3	11075	T	-	0.031	0.032	5.3e-08	5.8e-09	0.0313620071684588	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.965776390334143
CAMB-760F6	MN908947.3	13019	C	T	1	1	0	0	0.998658520581502	TCT	ORF1ab:nsp9	L112L	C334T	CTA>TTA	Synonymous	ORF1ab:nsp9	0.000656158411221767
CAMB-760F6	MN908947.3	14408	C	T	1	1	0	0	0.997652823464912	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000274122807017544
CAMB-760F6	MN908947.3	15779	A	G	0.034	0.023	2.8e-16	6.1e-12	0.0289172686618507	AAG	ORF1ab:RNA-dependent-RNA-polymerase	K771R	A2312G	AAG>AGG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.971071981424149
CAMB-760F6	MN908947.3	16329	C	T	0.0085	0.0071	2.8e-05	0.00011	0.00775882215470904	ACG	ORF1ab:helicase	Y31Y	C93T	TAC>TAT	Synonymous	ORF1ab:helicase	0.992100958167796
CAMB-760F6	MN908947.3	20268	A	G	1	1	6.4e-216	4.2e-248	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-760F6	MN908947.3	23403	A	G	1	1	0	0	0.998127227081309	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.07385811467444e-05
CAMB-760F6	MN908947.3	241	C	T	1	1	0	0	0.99933216168717	TCG	NA	NA	NA	NA	NA	NA	0.000597539543057996
CAMB-760F6	MN908947.3	24123	A	G	0.0046	0.0083	0.00033	7.8e-06	0.00637630100110407	AAG	S	K854R	A2561G	AAG>AGG	Missense	GU280_gp02, spike glycoprotein	0.993623698998896
CAMB-760F6	MN908947.3	26787	GGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.0385882352941176	0.0221441176470588	2.1e-06;2e-06;2.5e-07;1.1e-06;8.5e-07;1.9e-06;1.5e-06;1.7e-06;2.8e-06;1.5e-06;2.4e-06;1.2e-06;1.5e-06;1.2e-06;3e-06;1.4e-06;1.8e-06;1.5e-06;1.1e-06;2.3e-06;1.2e-06;1.9e-06;1.3e-06;2.3e-06;1.9e-06;1.2e-06;2.2e-06;4.3e-07;1.1e-06;8.5e-07;0.00011;4e-04;0.00019;0.00026	0.00087;0.00087;0.00059;0.00062;0.00058;0.00088;0.00073;0.00077;0.0011;0.00064;0.00098;0.00074;0.00072;0.00058;0.0011;7e-04;0.00084;0.00074;0.00056;0.00097;0.00074;0.00043;0.00072;0.00094;0.00091;0.00054;9e-04;0.00044;0.00072;0.00059;0.099;0.22;0.2;0.18	0.0303143678423142	AGG	M	.	265-298-delfrshift	.	no-SNV	GU280_gp05	0.970247874848203
CAMB-760F6	MN908947.3	27499	T	G	0.014	0.0049	1.1e-07	0.00041	0.00945752490024672	CTC	ORF7a	S36A	T106G	TCT>GCT	Missense	GU280_gp07	0.98966677834973
CAMB-760F6	MN908947.3	27577	C	T	0.014	0.04	0.0013	1.2e-08	0.0294117647058824	TCA	ORF7a	Q62*	C184T	CAA>TAA	Nonsense	GU280_gp07	0.970588235294118
CAMB-760F6	MN908947.3	29108	C	T	1	1	0	0	0.999861508051418	TCC	N	P279S	C835T	CCA>TCA	Missense	GU280_gp10	7.55410628627545e-05
CAMB-760F6	MN908947.3	29734	G	C	1	1	0	0	0.998675496688742	CGA	NA	NA	NA	NA	NA	NA	0
CAMB-760F6	MN908947.3	3037	C	T	1	1	0	0	0.999266154262099	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.72469197790738e-05
CAMB-760F6	MN908947.3	3172	T	C	0.1	0.088	4.2e-46	1.8e-40	0.0961368636901109	TTC	ORF1ab:nsp3	L151L	T453C	CTT>CTC	Synonymous	ORF1ab:nsp3	0.903848168714733
CAMB-760F6	MN908947.3	8025	C	T	1	1	0	0	0.999002968434887	GCA	ORF1ab:nsp3	A1769V	C5306T	GCA>GTA	Missense	ORF1ab:nsp3	0.000181278466384174
CAMB-76102	MN908947.3	11075	T	-	0.033	0.044	3.1e-08	4.5e-11	0.0370781934957692	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957447242328474
CAMB-76102	MN908947.3	14120	C	T	1	1	0	0	0.999184700731997	CCA	ORF1ab:RNA-dependent-RNA-polymerase	P218L	C653T	CCA>CTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000372201839740522
CAMB-76102	MN908947.3	14408	C	T	1	1	0	0	0.997319825005756	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000460511167395809
CAMB-76102	MN908947.3	17666	A	G	0.2	0.2	4.4e-94	3e-94	0.200286337878697	AAG	ORF1ab:helicase	K477R	A1430G	AAG>AGG	Missense	ORF1ab:helicase	0.79963356760978
CAMB-76102	MN908947.3	17886	T	A	0.0087	0.0072	8.6e-06	2.4e-05	0.00813422855803565	CTG	ORF1ab:helicase	T550T	T1650A	ACT>ACA	Synonymous	ORF1ab:helicase	0.99172790316132
CAMB-76102	MN908947.3	23403	A	G	1	1	0	0	0.999753609987009	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.71972762704018e-05
CAMB-76102	MN908947.3	241	C	T	1	1	0	0	0.998625651118991	TCG	NA	NA	NA	NA	NA	NA	0.000152705431223171
CAMB-76102	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999463794990952	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000150225338007011
CAMB-76102	MN908947.3	3037	C	T	1	1	0	0	0.999094650205761	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000109739368998628
CAMB-76102	MN908947.3	61	G	T	0.05	0.06	5.1e-23	9e-28	0.0543094719401062	TGT	NA	NA	NA	NA	NA	NA	0.945537111472492
CAMB-76111	MN908947.3	11075	T	-	0.044	0.026	9.3e-11	5.4e-07	0.0356560242367746	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960925969082576
CAMB-76111	MN908947.3	14408	C	T	1	1	0	0	0.997005047437535	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00171738538546924
CAMB-76111	MN908947.3	1547	A	T	0.0072	0.015	4.7e-05	6.5e-08	0.0111550917596258	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.984166966534725
CAMB-76111	MN908947.3	22158	G	T	0.011	0.014	2.3e-06	1.5e-07	0.0124343076975921	GGT	S	G199V	G596T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.986432178064782
CAMB-76111	MN908947.3	23403	A	G	1	1	0	0	0.999868666033173	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000123608439366198
CAMB-76111	MN908947.3	241	C	T	1	1	0	0	0.998891930647895	TCG	NA	NA	NA	NA	NA	NA	0.000195541650371529
CAMB-76111	MN908947.3	26776	CTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.0592666666666667	0.0493777777777778	6.6e-05;7.5e-05;0.00015;0.00039;6.3e-09;4.5e-12;4.7e-10;2e-10;1.2e-09;3e-12;1.5e-11;5.3e-11;5e-11;2.6e-12;9.7e-12;6.2e-12;2.2e-11;1.6e-11;2.2e-11;4e-11;1.2e-11;3.2e-11;1.2e-11;1.8e-11;1.3e-11;4.4e-11;1.6e-11;2.2e-11;1.5e-11;8.3e-12;2.7e-11;9.7e-12;1.1e-11;1.7e-11;3.2e-11;2.8e-11;3.9e-11;6.4e-11;2.7e-12;1.9e-11;9.5e-12;1.3e-05;0.00027;0.00013;0.00043	0.019;0.0051;0.011;0.015;6.5e-07;3.6e-08;3.8e-07;5e-07;1.1e-06;3.9e-09;8.1e-09;6e-10;6.3e-10;3.7e-10;2.7e-10;2.6e-10;5.9e-10;4e-10;4.6e-10;8.9e-10;2.6e-10;7.7e-10;4.3e-10;2.9e-10;2.1e-10;9e-10;3e-10;5.7e-10;4.2e-10;1.3e-10;6.1e-10;3.8e-10;6.4e-10;3e-10;7.2e-10;5.3e-10;1.3e-10;6e-10;6.2e-11;4.3e-10;1.8e-10;0.00011;0.0014;0.00093;0.0019	0.0612006128418218	GCT	M	.	254-298-delinframe	.	no-SNV	GU280_gp05	0.973068545459435
CAMB-76111	MN908947.3	28522	A	G	1	1	0	0	0.99974203836593	AAA	N	Q83Q	A249G	CAA>CAG	Synonymous	GU280_gp10	2.34510576426997e-05
CAMB-76111	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998666634342651	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	8.10723165063236e-05
CAMB-76111	MN908947.3	2919	C	T	0.46	0.44	1.1e-252	1.2e-238	0.453688980760057	CCA	ORF1ab:nsp3	P67L	C200T	CCA>CTA	Missense	ORF1ab:nsp3	0.546231515344252
CAMB-76111	MN908947.3	3037	C	T	1	1	0	0	0.999436857665775	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.38570557041626e-05
CAMB-76111	MN908947.3	6145	C	T	1	1	0	0	0.999150072850899	TCC	ORF1ab:nsp3	F1142F	C3426T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76111	MN908947.3	9135	T	C	0.0079	0.0018	2e-05	0.0088	0.00518978130146693	ATG	ORF1ab:nsp4	M194T	T581C	ATG>ACG	Missense	ORF1ab:nsp4	0.994733616760504
CAMB-76120	MN908947.3	10389	TTTCAGTGTTA	-	7e-04	0.00845454545454545	NA;NA;NA;NA;NA;NA;NA;1.7e-05;NA;NA;NA	3.6e-06;3.6e-06;3.4e-06;4.5e-06;3.5e-06;4.4e-06;4.4e-06;7.1e-06;3.9e-06;2.8e-06;3.9e-06	0.00345939261898102	TTT	ORF1ab:3C-like-proteinase	.	335-345-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.996422715754956
CAMB-76120	MN908947.3	11075	T	-	0.052	0.063	1.3e-12	1.2e-15	0.0564261462117435	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.943467008571361
CAMB-76120	MN908947.3	14408	C	T	0.99	1	0	0	0.994932139262036	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000295046686799264
CAMB-76120	MN908947.3	16801	AA	-	0.00295	0.0175	0.0016;NA	7.4e-10;2.4e-08	0.00876075183179357	TAA	ORF1ab:helicase	.	565-566-delfrshift	.	no-SNV	ORF1ab:helicase	0.987879770201884
CAMB-76120	MN908947.3	22121	A	-	0.0072	0.012	0.0016	1.8e-05	0.00916890982503365	CAA	S	.	559-559-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.978970390309556
CAMB-76120	MN908947.3	23403	A	G	1	0.99	0	0	0.997053362768915	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.46597511523291e-05
CAMB-76120	MN908947.3	23475	C	T	0.0078	0.0091	1.9e-05	3.3e-06	0.00822804116428789	ACA	S	T638I	C1913T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0.991739849406778
CAMB-76120	MN908947.3	241	C	T	1	1	0	0	0.999854199066874	TCG	NA	NA	NA	NA	NA	NA	7.2900466562986e-05
CAMB-76120	MN908947.3	2533	TG	-	0.0093	0.0105	3.2e-05;3.6e-05	1.4e-05;1.8e-05	0.00979083222073876	TTG	ORF1ab:nsp2	.	1728-1729-delfrshift	.	no-SNV	ORF1ab:nsp2	0.990100494975251
CAMB-76120	MN908947.3	26244	TA	CT	0.0029	0.019	NA;0.0015	2.5e-11;3.6e-08	0.00873808443032229	TTA	E	.	1-1-mnv	.	no-SNV	GU280_gp04	0.992269974040958
CAMB-76120	MN908947.3	26775	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	-	0.0115186964285714	0.04925	NA;0.0041;0.0039;0.0087;0.019;0.021;0.0042;0.017;0.018;0.026;0.0091;0.019;0.034;0.034;0.02;0.028;0.026;0.032;0.03;0.033;0.04;0.029;0.037;0.03;0.03;0.029;0.04;0.028;0.033;0.029;0.026;0.038;0.028;0.011;0.032;0.036;0.036;0.025;0.036;0.025;0.00022;0.00014;0.0011;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	1.1e-06;8e-07;3.8e-07;3e-06;1.8e-05;4.9e-10;2.6e-13;1.6e-10;4.3e-14;5.7e-13;6.4e-12;8.4e-11;2.5e-09;2.5e-09;3.6e-10;1e-09;7e-10;2.3e-09;1.2e-09;1.9e-09;3.9e-09;1.1e-09;3.1e-09;1.7e-09;1.4e-09;8.4e-10;3.4e-09;1.1e-09;2.1e-09;1.3e-09;6.5e-10;2.3e-09;9.7e-10;4.2e-10;1.2e-09;2.6e-09;2e-09;1.2e-09;2.6e-09;2.5e-10;9.3e-10;5.9e-10;6.1e-05;0.00026;0.00011;0.00017;1.2e-05;5.2e-06;6.8e-06;1.1e-05;1.1e-05;1.1e-05;9.9e-06;5.5e-06;1.3e-07;6.7e-08	0.0294646368181563	GGC	M	.	253-308-delfrshift	.	no-SNV	GU280_gp05	0.985667688049817
CAMB-76120	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999720857525681	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000125258345337258
CAMB-76120	MN908947.3	29750	CGATCGAGTG	-	0.0169	0.0206	3e-05;2.9e-05;3.5e-06;4.4e-06;3.8e-06;4.6e-06;2.6e-07;1.3e-05;4.8e-06;1e-05	4.9e-06;5.2e-06;4.7e-07;5.8e-07;4.8e-07;6e-07;1.6e-08;2e-06;5.8e-07;1.5e-06	0.0176546576718817	ACG	NA	NA	NA	NA	NA	NA	0.981983280484289
CAMB-76120	MN908947.3	3022	T	C	0.013	0.0059	7e-06	0.006	0.0103251954067355	ATA	ORF1ab:nsp3	H101H	T303C	CAT>CAC	Synonymous	ORF1ab:nsp3	0.987841358679919
CAMB-76120	MN908947.3	3037	C	T	1	1	0	0	0.999543914516549	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000130310138128746
CAMB-76120	MN908947.3	6105	A	T	0.0095	0.021	5.8e-06	7.1e-10	0.0149511213341001	TAT	ORF1ab:nsp3	Y1129F	A3386T	TAT>TTT	Missense	ORF1ab:nsp3	0.9850488786659
CAMB-76120	MN908947.3	6219	TG	-	0.014	0.001	2.1e-08;1.8e-08	0.0029;0.0033	0.00994568408690546	TTG	ORF1ab:nsp3	.	3500-3501-delfrshift	.	no-SNV	ORF1ab:nsp3	0.989875318112745
CAMB-76120	MN908947.3	6422	G	A	0.013	0.015	8e-08	5.6e-09	0.013777917584146	GGA	ORF1ab:nsp3	E1235K	G3703A	GAA>AAA	Missense	ORF1ab:nsp3	0.986138198594946
CAMB-76120	MN908947.3	8345	TG	-	0.007605	0.02	NA;2.1e-06	6.5e-10;1.2e-07	0.0124729540537101	CTG	ORF1ab:nsp3	.	5626-5627-delfrshift	.	no-SNV	ORF1ab:nsp3	0.991769547325103
CAMB-76120	MN908947.3	8346	G	-	0.015	0.019	2.1e-06	1.2e-07	0.0166259168704156	TGT	ORF1ab:nsp3	.	5627-5627-delfrshift	.	no-SNV	ORF1ab:nsp3	0.983251833740831
CAMB-7614E	MN908947.3	14408	C	T	1	1	0	0	0.999694796276515	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00022890279261407
CAMB-7614E	MN908947.3	21774	C	T	1	1	0	0	0.998697492673396	TCT	S	S71F	C212T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.00130250732660371
CAMB-7614E	MN908947.3	23403	A	G	1	1	0	0	0.999794372123187	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000173992818841841
CAMB-7614E	MN908947.3	241	C	T	1	1	0	0	0.999595647698868	TCG	NA	NA	NA	NA	NA	NA	0.000294074400823408
CAMB-7614E	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7614E	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7615D	MN908947.3	13914	T	G	0.0089	0.014	1.6e-06	1.1e-08	0.0115892139988526	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.988066551921974
CAMB-7615D	MN908947.3	14408	C	T	1	1	0	0	0.999602332979852	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000265111346765642
CAMB-7615D	MN908947.3	20665	C	T	0.044	0.082	7.6e-11	1.4e-22	0.068	TCA	ORF1ab:2'-O-ribose-methyltransferase	Q3*	C7T	CAA>TAA	Nonsense	ORF1ab:2'-O-ribose-methyltransferase	0.932
CAMB-7615D	MN908947.3	2164	G	A	1	1	3.1e-268	0	1	AGA	ORF1ab:nsp2	E453E	G1359A	GAG>GAA	Synonymous	ORF1ab:nsp2	0
CAMB-7615D	MN908947.3	23403	A	G	1	1	0	0	0.999955023837366	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7615D	MN908947.3	241	C	T	1	1	0	0	0.99979398434281	TCG	NA	NA	NA	NA	NA	NA	0.000137343771459964
CAMB-7615D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7615D	MN908947.3	29051	C	INS	0.054	0.026	2.3e-12	1.3e-05	0.0342987804878049	GCA	N	.	777-778-insfrshift	.	no-SNV	GU280_gp10	0.965701219512195
CAMB-7615D	MN908947.3	29533	A	G	0.029	0.037	2.3e-11	2.7e-14	0.0335758254057079	AAA	N	*420*	A1260G	TAA>TAG	Synonymous	GU280_gp10	0.966424174594292
CAMB-7615D	MN908947.3	29781	G	T	0.092	0.024	3.5e-25	1.9e-07	0.0578661844484629	AGA	NA	NA	NA	NA	NA	NA	0.942133815551537
CAMB-7615D	MN908947.3	3037	C	T	1	1	5.4e-225	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7616C	MN908947.3	11074	C	INS	0.1	0.13	8.1e-39	6.3e-63	0.118029759281412	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.879556758798716
CAMB-7616C	MN908947.3	11083	G	-	0.17	0.19	1.4e-73	4e-86	0.181597097248028	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-7616C	MN908947.3	11083	G	T	0.83	0.81	0	0	0.818256986935671	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-7616C	MN908947.3	14805	C	T	0.99	1	0	0	0.996032181203705	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.002302930004885
CAMB-7616C	MN908947.3	1548	G	A	0.18	0.15	1.3e-74	9.4e-60	0.165100904662491	AGC	ORF1ab:nsp2	S248N	G743A	AGC>AAC	Missense	ORF1ab:nsp2	0.834899095337509
CAMB-7616C	MN908947.3	17247	T	C	1	1	0	0	0.999859444678703	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000114999808333653
CAMB-7616C	MN908947.3	17466	A	G	0.0032	0.0082	0.0014	1.2e-05	0.00611100611100611	CAT	ORF1ab:helicase	T410T	A1230G	ACA>ACG	Synonymous	ORF1ab:helicase	0.993876393876394
CAMB-7616C	MN908947.3	18814	C	T	0.0021	0.01	0.0056	2.4e-06	0.00670929338024794	TCT	ORF1ab:3'-to-5'-exonuclease	L259L	C775T	CTG>TTG	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.993252872258585
CAMB-7616C	MN908947.3	2144	G	T	0.032	0.027	4.7e-16	6.3e-14	0.0292775790199232	CGT	ORF1ab:nsp2	V447F	G1339T	GTC>TTC	Missense	ORF1ab:nsp2	0.970459841796042
CAMB-7616C	MN908947.3	21616	T	C	0.0041	0.019	0.0029	4.1e-09	0.0128617363344051	TTA	S	L18L	T54C	CTT>CTC	Synonymous	GU280_gp02, spike glycoprotein	0.987138263665595
CAMB-7616C	MN908947.3	21886	TACTT	-	0.0202	0.034	1.1e-05;3.7e-05;0.00019;0.00022;0.00011	5.6e-09;3.9e-08;6.3e-07;9e-07;5.4e-07	0.030578434156963	CTA	S	.	324-328-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.975582055650199
CAMB-7616C	MN908947.3	21983	TTGGGTGT	-	0.023875	0.027625	0.00015;0.00014;6.5e-05;0.00015;0.00023;2e-04;0.00013;0.00021	3.9e-05;3.7e-05;1.2e-05;3.9e-05;5.7e-05;5e-05;2.8e-05;6.6e-05	0.0261797848004745	TTT	S	.	421-428-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.973650658733532
CAMB-7616C	MN908947.3	22713	C	T	0.012	0.0066	2.5e-07	5.2e-05	0.00887053418698988	CCT	S	P384L	C1151T	CCT>CTT	Missense	GU280_gp02, spike glycoprotein	0.99093397194663
CAMB-7616C	MN908947.3	26144	G	T	1	1	0	0	0.999802683504341	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7616C	MN908947.3	26295	A	T	0.016	0.018	7.4e-09	1.5e-09	0.0171426831496255	TAC	E	V17V	A51T	GTA>GTT	Synonymous	GU280_gp04	0.98273552158821
CAMB-7616C	MN908947.3	26748	A	G	0.082	0.071	1.8e-37	7.3e-32	0.0748052572352536	GAT	M	I76V	A226G	ATC>GTC	Missense	GU280_gp05	0.92497623755886
CAMB-7616C	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.035	0.0201891891891892	0.00022;1.7e-05;2e-04;0.00024;6.9e-05;1.4e-06;4.8e-06;6.7e-06;6.9e-06;2.5e-06;4.3e-06;3.2e-06;6e-06;4.5e-06;6.1e-06;9.4e-06;3.6e-06;8.2e-06;5.2e-06;4.8e-06;4.8e-06;9.1e-06;4e-06;6.3e-06;4.5e-06;2.4e-06;8e-06;3.9e-06;1.1e-06;5.6e-06;7.4e-06;6.8e-06;2.8e-06;7.2e-06;2e-06;1.7e-06;7.6e-07	0.0033;0.00022;0.0017;0.002;0.0053;0.00093;0.0015;0.0041;0.004;0.0019;0.0035;0.0031;0.0038;0.0034;0.0039;0.0048;0.0032;0.0045;0.0035;0.0035;0.0031;0.0048;0.0032;0.0039;0.0034;0.0028;0.0044;0.0031;0.0017;0.0033;0.0042;0.004;0.0031;0.0043;0.0025;0.0045;0.0037	0.0260468031374139	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.978942352628541
CAMB-7616C	MN908947.3	27792	TT	-	0.023	0.0245	0.00017;2.9e-05	0.00012;2.3e-05	0.0235294117647059	CTT	NA	NA	NA	NA	NA	NA	0.97609561752988
CAMB-7616C	MN908947.3	28119	A	G	0.0057	0.0087	0.00011	8.2e-06	0.00749206461794904	TAT	ORF8	I76V	A226G	ATC>GTC	Missense	GU280_gp09	0.99248133633607
CAMB-7616C	MN908947.3	29200	C	T	0.014	0.012	5.1e-08	3.5e-07	0.013020293289883	CCA	N	P309P	C927T	CCC>CCT	Synonymous	GU280_gp10	0.986905643608354
CAMB-7616C	MN908947.3	29614	C	T	0.0068	0.009	0.00037	4.1e-05	0.00811237136633366	GCA	ORF10	C19C	C57T	TGC>TGT	Synonymous	GU280_gp11	0.991887628633666
CAMB-7616C	MN908947.3	3531	ATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAGTTGTGTTT	-	0.0149854166666667	0.00234583333333333	0.00013;5.9e-06;5.9e-06;6.6e-06;6.5e-06;7.5e-06;7.1e-06;6.3e-06;5.4e-06;7.5e-06;8.4e-06;7.5e-06;7.2e-06;1.7e-05;1.3e-05;1.5e-05;1.4e-05;4.2e-06;9.9e-05;0.00011;0.00027;9.9e-05;0.00012;7.7e-05;8.1e-05;4.1e-05;3.2e-05;1.3e-05;9e-06;1.4e-05;9.1e-06;2.2e-05;1.5e-05;1.6e-05;7.6e-06;1.8e-05;1.5e-05;1.2e-05;9.4e-06;1.3e-05;1e-05;1.7e-05;1.6e-05;8.2e-06;1.1e-05;2.6e-05;0.00029;0.00024	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.13;0.14;0.0013;0.0011;0.00066;0.27;0.28;0.36;0.28;0.28;0.29;0.29;0.22;0.24;0.12;0.11;0.11;0.12;0.15;0.12;0.12;0.13;0.13;0.12;0.12;0.13;0.11;0.1;0.12;0.12;0.099;0.1;0.17;0.11;0.091	0.00590219224283305	GAT	ORF1ab:nsp3	.	812-859-delinframe	.	no-SNV	ORF1ab:nsp3	0.99670510708402
CAMB-7616C	MN908947.3	6333	A	C	0.0073	0.0063	1.7e-05	5.4e-05	0.00671482924177915	AAT	ORF1ab:nsp3	N1205T	A3614C	AAT>ACT	Missense	ORF1ab:nsp3	0.993228553310988
CAMB-7616C	MN908947.3	8214	A	G	0.013	0.0038	1.2e-07	0.00037	0.00851405009163103	GAT	ORF1ab:nsp3	D1832G	A5495G	GAT>GGT	Missense	ORF1ab:nsp3	0.991466860109957
CAMB-7617B	MN908947.3	11075	T	-	0.035	0.034	4.1e-09	6.9e-09	0.0345701308678248	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960173591924202
CAMB-7617B	MN908947.3	14408	C	T	1	1	0	0	0.998588124558789	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000347366179980503
CAMB-7617B	MN908947.3	14786	C	T	1	1	0	0	0.999793950830161	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A440V	C1319T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	7.59128520458514e-05
CAMB-7617B	MN908947.3	20578	G	T	1	1	0	0	0.999763983950909	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	0
CAMB-7617B	MN908947.3	23403	A	G	1	1	0	0	0.998985753594471	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.57381929509875e-05
CAMB-7617B	MN908947.3	241	C	T	1	1	0	0	0.998769302897999	TCG	NA	NA	NA	NA	NA	NA	0.000205116183666891
CAMB-7617B	MN908947.3	2416	C	T	1	1	0	0	0.998500119990401	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0.000359971202303816
CAMB-7617B	MN908947.3	25563	G	T	1	1	0	0	0.999831451205124	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	7.6613088580053e-05
CAMB-7617B	MN908947.3	26042	C	T	1	1	0	0	0.999733084211931	ACT	ORF3a	T217I	C650T	ACT>ATT	Missense	GU280_gp03	4.4485964678144e-05
CAMB-7617B	MN908947.3	26679	T	C	0.014	0.015	3.5e-08	2.8e-08	0.0145109880892468	TTT	M	F53L	T157C	TTC>CTC	Missense	GU280_gp05	0.98546105239613
CAMB-7617B	MN908947.3	29502	C	T	0.016	0.012	2.3e-08	1.2e-06	0.0145985401459854	TCC	N	S410F	C1229T	TCC>TTC	Missense	GU280_gp10	0.985401459854015
CAMB-7617B	MN908947.3	3037	C	T	1	1	0	0	0.999237223493516	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.534706331045e-05
CAMB-7617B	MN908947.3	9505	T	C	1	1	0	0	0.999797383819882	TTA	ORF1ab:nsp4	F317F	T951C	TTT>TTC	Synonymous	ORF1ab:nsp4	0.000186406885708265
CAMB-7618A	MN908947.3	10265	G	A	0.016	0.016	4.9e-09	5.2e-09	0.0160817881924696	TGG	ORF1ab:3C-like-proteinase	G71S	G211A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.983804459105904
CAMB-7618A	MN908947.3	11074	C	INS	0.087	0.08	8.5e-31	1.2e-26	0.0834527456058475	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.914259797283973
CAMB-7618A	MN908947.3	11083	G	-	0.19	0.15	4.7e-86	1.2e-63	0.169850121993726	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	4.64738003950273e-05
CAMB-7618A	MN908947.3	11083	G	T	0.81	0.85	0	0	0.829929127454398	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	4.64738003950273e-05
CAMB-7618A	MN908947.3	12053	C	T	0.01	0.0066	2.2e-06	6e-05	0.00816766836184312	GCT	ORF1ab:nsp7	L71F	C211T	CTT>TTT	Missense	ORF1ab:nsp7	0.991698772281297
CAMB-7618A	MN908947.3	13778	AT	-	0.0145	0.00895	1e-05;1.5e-05	0.00041;0.00051	0.011812234686135	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.988445503275759
CAMB-7618A	MN908947.3	14805	C	T	1	1	0	0	0.997828460968783	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	2.51044974707219e-05
CAMB-7618A	MN908947.3	1547	A	G	0.014	0.016	6.1e-07	1.7e-07	0.0151661826395611	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.968699580509842
CAMB-7618A	MN908947.3	1547	A	T	0.012	0.018	1.7e-06	8.5e-09	0.0151661826395611	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.968699580509842
CAMB-7618A	MN908947.3	17074	C	T	0.0074	0.015	2.9e-05	2.5e-08	0.0118993319202597	ACT	ORF1ab:helicase	L280F	C838T	CTC>TTC	Missense	ORF1ab:helicase	0.988073837568082
CAMB-7618A	MN908947.3	17247	T	C	1	1	0	0	0.999856619861017	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000124262787118728
CAMB-7618A	MN908947.3	18176	C	T	0.027	0.011	2.1e-13	6.6e-07	0.0179623741925032	CCT	ORF1ab:3'-to-5'-exonuclease	P46L	C137T	CCT>CTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.982017375103785
CAMB-7618A	MN908947.3	19011	C	T	0.013	0.0038	1.6e-07	0.0014	0.00791734096850492	ACA	ORF1ab:3'-to-5'-exonuclease	D324D	C972T	GAC>GAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.992057761732852
CAMB-7618A	MN908947.3	21138	G	A	0.044	0.035	1.2e-20	1.1e-16	0.0396367477957011	AGC	ORF1ab:2'-O-ribose-methyltransferase	K160K	G480A	AAG>AAA	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.96034293608549
CAMB-7618A	MN908947.3	21812	C	T	0.0044	0.0079	0.0012	3.6e-05	0.00641238253178552	CCT	S	L84L	C250T	CTA>TTA	Synonymous	GU280_gp02, spike glycoprotein	0.993532338308458
CAMB-7618A	MN908947.3	23148	A	T	0.016	0.0035	1.5e-06	0.0055	0.00911083448523403	AAG	S	K529M	A1586T	AAG>ATG	Missense	GU280_gp02, spike glycoprotein	0.990423313961036
CAMB-7618A	MN908947.3	23439	C	T	0.017	0.011	6.6e-09	1.9e-06	0.0135396683292834	GCA	S	A626V	C1877T	GCA>GTA	Missense	GU280_gp02, spike glycoprotein	0.986400647994202
CAMB-7618A	MN908947.3	24198	C	T	0.0069	0.01	0.00044	1.7e-05	0.00841536995871705	GCG	S	A879V	C2636T	GCG>GTG	Missense	GU280_gp02, spike glycoprotein	0.991425849476024
CAMB-7618A	MN908947.3	24700	C	T	0.0027	0.0096	0.0043	5.5e-06	0.00607337630143778	GCT	S	G1046G	C3138T	GGC>GGT	Synonymous	GU280_gp02, spike glycoprotein	0.993926623698562
CAMB-7618A	MN908947.3	2496	GA	-	0.00875	0.00155	0.00018;5.1e-06	NA;0.0078	0.00485386760301559	GGA	ORF1ab:nsp2	.	1691-1692-delfrshift	.	no-SNV	ORF1ab:nsp2	0.996911991765311
CAMB-7618A	MN908947.3	25483	GCTACT	-	0.00768333333333333	0.00115	1.8e-05;1.8e-05;1.9e-05;3.4e-05;2.3e-05;1.9e-05	NA;0.0048;0.0058;0.0093;NA;NA	0.0044494595253055	CGC	ORF3a	.	91-96-delinframe	.	no-SNV	GU280_gp03	0.99568790915862
CAMB-7618A	MN908947.3	26125	C	A	0.041	0.071	3.6e-11	1.3e-20	0.0580945003872967	CCA	ORF3a	Q245K	C733A	CAA>AAA	Missense	GU280_gp03	0.941905499612703
CAMB-7618A	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7618A	MN908947.3	26927	A	G	0.019	0.011	5.2e-10	8.2e-07	0.0150111511408475	AAA	M	E135E	A405G	GAA>GAG	Synonymous	GU280_gp05	0.984988848859152
CAMB-7618A	MN908947.3	27213	C	T	0.25	0.22	3.8e-122	3.8e-104	0.237042372615953	TCG	ORF6	L4L	C12T	CTC>CTT	Synonymous	GU280_gp06	0.761287359201612
CAMB-7618A	MN908947.3	27925	C	A	0.017	0.036	1.8e-07	1.1e-13	0.0281607509533588	ACA	ORF8	T11K	C32A	ACA>AAA	Missense	GU280_gp09	0.971741468661387
CAMB-7618A	MN908947.3	28762	A	G	0.0019	0.0077	0.0089	2.1e-05	0.0049344424080079	AAG	N	Q163Q	A489G	CAA>CAG	Synonymous	GU280_gp10	0.994995065557592
CAMB-7618A	MN908947.3	28887	C	T	0.22	0.19	1e-98	2.5e-87	0.206214275245493	ACT	N	T205I	C614T	ACT>ATT	Missense	GU280_gp10	0.793639161659094
CAMB-7618A	MN908947.3	28919	G	T	0.023	0.02	1e-11	1.7e-10	0.0215582724444766	TGA	N	D216Y	G646T	GAT>TAT	Missense	GU280_gp10	0.977935325182667
CAMB-7618A	MN908947.3	28975	G	T	0.017	0.015	2.5e-09	2e-08	0.0162532683202601	TGT	N	M234I	G702T	ATG>ATT	Missense	GU280_gp10	0.98374673167974
CAMB-7618A	MN908947.3	29247	C	T	1	1	0	0	0.999885242139086	ACA	N	T325I	C974T	ACA>ATA	Missense	GU280_gp10	2.86894652283681e-05
CAMB-7618A	MN908947.3	29543	G	C	0.0043	0.009	0.00039	4.7e-06	0.00699382212379065	AGA	NA	NA	NA	NA	NA	NA	0.993006177876209
CAMB-7618A	MN908947.3	29747	G	T	1	1	0	0	0.998276109754346	AGT	NA	NA	NA	NA	NA	NA	0
CAMB-7618A	MN908947.3	5240	C	T	0.012	0.0026	2.9e-06	0.0019	0.00594985125371866	CCC	ORF1ab:nsp3	P841S	C2521T	CCA>TCA	Missense	ORF1ab:nsp3	0.994050148746281
CAMB-7618A	MN908947.3	586	TGTCCCT	-	0.0024	0.00408571428571429	NA;NA;0.00027;0.00047;0.00032;0.00038;NA	0.00073;4.6e-05;0.00046;0.00089;0.00052;0.00073;0.00094	0.00378434011558863	TTG	ORF1ab:leader-protein	.	321-327-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.99784133837021
CAMB-7618A	MN908947.3	6270	C	T	0.005	0.017	0.00021	1.9e-09	0.0115168895184788	ACG	ORF1ab:nsp3	T1184M	C3551T	ACG>ATG	Missense	ORF1ab:nsp3	0.988483110481521
CAMB-7618A	MN908947.3	6539	C	T	0.028	0.025	3.7e-13	1e-11	0.026212865107764	CCA	ORF1ab:nsp3	H1274Y	C3820T	CAC>TAC	Missense	ORF1ab:nsp3	0.973703919447449
CAMB-7618A	MN908947.3	775	C	A	0.068	0.073	1.3e-31	1.5e-33	0.071024347444615	CCC	ORF1ab:leader-protein	T170T	C510A	ACC>ACA	Synonymous	ORF1ab:leader-protein	0.928898881333626
CAMB-7618A	MN908947.3	8178	G	A	0.026	0.042	1.8e-13	5.5e-20	0.0346802749427203	CGG	ORF1ab:nsp3	R1820Q	G5459A	CGG>CAG	Missense	ORF1ab:nsp3	0.962403665902937
CAMB-7618A	MN908947.3	9926	A	C	0.017	0.02	4.1e-09	1.8e-10	0.0186166717771256	AAT	ORF1ab:nsp4	M458L	A1372C	ATG>CTG	Missense	ORF1ab:nsp4	0.981251916422095
CAMB-761A8	MN908947.3	11075	T	-	0.041	0.033	2.4e-10	3.5e-09	0.0386692413431957	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956928716371015
CAMB-761A8	MN908947.3	14408	C	T	1	1	0	0	0.997177099004378	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000287361179195051
CAMB-761A8	MN908947.3	14501	T	C	0.0098	0.0063	3.8e-06	9.6e-05	0.00917076775786486	GTA	ORF1ab:RNA-dependent-RNA-polymerase	V345A	T1034C	GTA>GCA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.990795639686246
CAMB-761A8	MN908947.3	20679	G	T	0.011	0.012	1.1e-06	5e-07	0.0114333779868532	CGG	ORF1ab:2'-O-ribose-methyltransferase	P7P	G21T	CCG>CCT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.988473161157668
CAMB-761A8	MN908947.3	20759	C	T	1	1	0	0	0.998802505526898	GCA	ORF1ab:2'-O-ribose-methyltransferase	A34V	C101T	GCA>GTA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.000245639891918448
CAMB-761A8	MN908947.3	23403	A	G	1	1	0	0	0.999112925936356	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.85637848493382e-05
CAMB-761A8	MN908947.3	241	C	T	1	1	0	0	0.999092488396816	TCG	NA	NA	NA	NA	NA	NA	0.000233360126533046
CAMB-761A8	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0344864864864865	0.0336756756756757	0.00026;1e-05;1e-04;1e-04;0.00016;4.1e-06;1.2e-05;8.8e-06;8.5e-06;1.4e-06;4.5e-06;3.3e-06;6.7e-06;5.4e-06;5.8e-06;9.7e-06;4.3e-06;8.5e-06;5.2e-06;5.7e-06;3.9e-06;1e-05;4.4e-06;6.7e-06;5.5e-06;3.7e-06;8.1e-06;4.6e-06;3e-06;5.5e-06;7.8e-06;7.5e-06;5.6e-06;8.6e-06;2e-06;4.5e-06;2.8e-06	0.00066;9.7e-05;0.00034;0.00033;0.00033;1.1e-05;3.9e-05;7.2e-06;7.1e-06;3.1e-06;3.9e-06;3.3e-06;6.7e-06;4.2e-06;4.5e-06;8e-06;3.3e-06;7.2e-06;4.6e-06;4.5e-06;3.5e-06;7.3e-06;4.3e-06;5e-06;3.8e-06;2.1e-06;5.8e-06;3.7e-06;9.1e-07;4.6e-06;6.9e-06;6.3e-06;3.2e-06;6.9e-06;2e-06;4.6e-06;3.2e-06	0.0352659245516388	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.976211099424612
CAMB-761A8	MN908947.3	27265	TTTAAAGTTTCCATTTGGAATCTTGA	-	0.0160384615384615	0.0150384615384615	6.1e-06;1.5e-05;4.5e-05;2.1e-05;2.9e-05;3.1e-05;3.2e-05;1.9e-05;3.9e-05;4.1e-05;3.1e-05;2.3e-05;2.8e-05;1.5e-05;3.8e-05;4.1e-05;3.7e-05;6e-05;2.8e-05;3.8e-05;3.3e-05;3.8e-05;1.9e-05;4.1e-05;1.7e-05;1.8e-05	8.9e-06;1.9e-05;6.5e-05;3.6e-05;5.3e-05;4.7e-05;5.1e-05;3.3e-05;6.5e-05;7.1e-05;4.5e-05;3.9e-05;4.2e-05;2.6e-05;4.5e-05;6.5e-05;5.9e-05;8.6e-05;3.9e-05;3.6e-05;4.8e-05;6.5e-05;2.8e-05;5.7e-05;3e-05;2.5e-05	0.0156965336821452	TTT	ORF6	.	64-89-delfrshift	.	no-SNV	GU280_gp06	0.985152426767222
CAMB-761A8	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998716067498166	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.11776816965205e-05
CAMB-761A8	MN908947.3	29466	C	T	0.012	0.013	2.6e-06	1.6e-06	0.0120011163829193	GCA	N	A398V	C1193T	GCA>GTA	Missense	GU280_gp10	0.987859335752163
CAMB-761A8	MN908947.3	3037	C	T	1	1	0	0	0.99919507244348	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.49968502834745e-05
CAMB-761B7	MN908947.3	13914	T	G	0.0088	0.03	4.4e-05	1.8e-14	0.0260922330097087	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.973907766990291
CAMB-761B7	MN908947.3	14408	C	T	1	1	0	0	0.999484713156991	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000515286843009275
CAMB-761B7	MN908947.3	22323	C	T	1	1	5.2e-261	2.6e-239	1	TCT	S	S254F	C761T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-761B7	MN908947.3	23403	A	G	0.51	1	4.6e-224	0	0.751390849456116	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-761B7	MN908947.3	241	C	T	1	1	0	0	1	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-761B7	MN908947.3	28253	C	T	1	0.15	0	2.6e-67	0.29709373720835	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.70290626279165
CAMB-761B7	MN908947.3	28881	GGG	AAC	1	1	2.8e-236;4.3e-248;9.99999999999999e-265	2.8000182346761e-319;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-761B7	MN908947.3	3037	C	T	1	1	1.4e-136	2e-258	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-761B7	MN908947.3	635	C	T	0.19	0.61	3e-76	5.8e-208	0.278422273781903	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.721577726218097
CAMB-761B7	MN908947.3	997	T	G	0.51	0.38	9.19999999999999e-292	8.5e-188	0.471970802919708	GTT	ORF1ab:nsp2	R64R	T192G	CGT>CGG	Synonymous	ORF1ab:nsp2	0.527810218978102
CAMB-761C6	MN908947.3	14408	C	T	1	1	0	0	0.999396074484147	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000301962757926522
CAMB-761C6	MN908947.3	16289	C	T	1	1	0	0	0.9975	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0.0025
CAMB-761C6	MN908947.3	23403	A	G	1	1	0	0	0.999883022693597	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000116977306402558
CAMB-761C6	MN908947.3	241	C	T	1	1	0	0	1	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-761C6	MN908947.3	25429	G	T	1	1	0	0	0.999660518275433	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0
CAMB-761C6	MN908947.3	3037	C	T	1	1	7.6e-230	1.6e-229	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-761D5	MN908947.3	11075	T	-	0.042	0.037	1.3e-10	6.2e-10	0.0398542961217056	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95505266107366
CAMB-761D5	MN908947.3	13778	AT	-	0.0135	0.0125	2.7e-05;3.5e-05	5.5e-05;8.1e-05	0.0132694302371329	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.987027445665327
CAMB-761D5	MN908947.3	14408	C	T	1	1	0	0	0.99730185015989	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000513933302878027
CAMB-761D5	MN908947.3	14805	C	T	1	1	0	0	0.998741784791658	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000642492872344697
CAMB-761D5	MN908947.3	1547	A	G	0.012	0.01	7.7e-07	6.2e-06	0.0114184029065026	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.961815081189293
CAMB-761D5	MN908947.3	1547	A	T	0.02	0.019	9e-10	1.3e-09	0.0192778230889004	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.961815081189293
CAMB-761D5	MN908947.3	17722	G	T	0.025	0.026	1.3e-12	2.2e-13	0.025542300490227	GGT	ORF1ab:helicase	V496L	G1486T	GTA>TTA	Missense	ORF1ab:helicase	0.974317434268201
CAMB-761D5	MN908947.3	23403	A	G	1	1	0	0	0.998041036325754	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.92644261255549e-05
CAMB-761D5	MN908947.3	241	C	T	1	1	0	0	0.99846010808298	TCG	NA	NA	NA	NA	NA	NA	0.000145272822360393
CAMB-761D5	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998942014242116	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00013934045517882
CAMB-761D5	MN908947.3	3037	C	T	1	1	0	0	0.998946317657498	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000166370896184561
CAMB-761D5	MN908947.3	4672	C	T	0.0073	0.0078	2.5e-05	1.1e-05	0.00745767606396419	TCA	ORF1ab:nsp3	L651L	C1953T	CTC>CTT	Synonymous	ORF1ab:nsp3	0.992376276937516
CAMB-761D5	MN908947.3	9802	G	T	0.023	0.024	4.4e-12	1.7e-12	0.0234751877880649	CGC	ORF1ab:nsp4	A416A	G1248T	GCG>GCT	Synonymous	ORF1ab:nsp4	0.97632325078273
CAMB-761E4	MN908947.3	11074	C	INS	0.3	0.29	9e-171	4.2e-127	0.298234128982442	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.698509416859704
CAMB-761E4	MN908947.3	11083	G	-	0.12	0.11	2.4e-53	1.5e-49	0.119785836877845	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.000130587269606746
CAMB-761E4	MN908947.3	11083	G	T	0.88	0.89	0	0	0.879729124692187	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.000130587269606746
CAMB-761E4	MN908947.3	14805	C	T	1	1	0	0	0.999221443665888	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000259518778037297
CAMB-761E4	MN908947.3	15653	A	G	0.0072	0.0064	2.4e-05	3.6e-05	0.00690488520628345	GAC	ORF1ab:RNA-dependent-RNA-polymerase	D729G	A2186G	GAC>GGC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.992884132190191
CAMB-761E4	MN908947.3	16887	C	T	0.016	0.018	1.5e-07	3.2e-08	0.017004827965532	ACA	ORF1ab:helicase	Y217Y	C651T	TAC>TAT	Synonymous	ORF1ab:helicase	0.982918780174785
CAMB-761E4	MN908947.3	18086	C	T	1	1	0	0	0.99932136018808	ACT	ORF1ab:3'-to-5'-exonuclease	T16I	C47T	ACT>ATT	Missense	ORF1ab:3'-to-5'-exonuclease	0.000290845633679924
CAMB-761E4	MN908947.3	26144	G	T	1	1	0	0	0.999521588326755	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.00017940437746681
CAMB-761E4	MN908947.3	26912	C	T	0.0077	0.0077	2.2e-05	1.5e-05	0.00767794148163519	CCA	M	T130T	C390T	ACC>ACT	Synonymous	GU280_gp05	0.99229241395666
CAMB-761E4	MN908947.3	28842	G	T	1	1	0	0	0.9993789784195	AGT	N	S190I	G569T	AGT>ATT	Missense	GU280_gp10	0.000310510790249961
CAMB-761E4	MN908947.3	3773	C	T	0.017	0.015	1.3e-08	3.5e-08	0.0164192949907236	TCG	ORF1ab:nsp3	R352C	C1054T	CGC>TGC	Missense	ORF1ab:nsp3	0.983487940630798
CAMB-761E4	MN908947.3	8760	C	T	0.01	0.0089	3e-06	1.3e-05	0.00969532223354853	GCT	ORF1ab:nsp4	A69V	C206T	GCT>GTT	Missense	ORF1ab:nsp4	0.990236719900328
CAMB-761E4	MN908947.3	950	T	C	0.48	0.48	9.99999999999999e-276	2.1e-274	0.480719411976152	ATA	ORF1ab:nsp2	Y49H	T145C	TAC>CAC	Missense	ORF1ab:nsp2	0.519243402704612
CAMB-761F3	MN908947.3	10523	G	C	1	1	0	0	1	TGT	ORF1ab:3C-like-proteinase	V157L	G469C	GTC>CTC	Missense	ORF1ab:3C-like-proteinase	0
CAMB-761F3	MN908947.3	13914	T	G	0.0063	0.0077	1.8e-05	1.2e-05	0.00657115156738123	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993428848432619
CAMB-761F3	MN908947.3	14408	C	T	1	1	0	0	0.999397392352361	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000493042620795442
CAMB-761F3	MN908947.3	23403	A	G	1	1	0	0	0.999912739965096	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.8173356602676e-05
CAMB-761F3	MN908947.3	241	C	T	1	1	0	0	1	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-761F3	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-761F3	MN908947.3	28957	C	T	1	1	0	0	0.998323554065381	ACC	N	N228N	C684T	AAC>AAT	Synonymous	GU280_gp10	0
CAMB-761F3	MN908947.3	29081	G	T	0.14	0.046	1.7e-59	8.6e-17	0.118915314514337	TGT	N	V270L	G808T	GTA>TTA	Missense	GU280_gp10	0.881084685485663
CAMB-761F3	MN908947.3	3037	C	T	1	1	9.79999999999999e-274	3.7e-292	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7620F	MN908947.3	10530	TTT	-	0.0086	0.00596666666666667	0.00025;4.3e-05;2.8e-05	0.0018;0.00061;0.00046	0.00795438547092778	TTT	ORF1ab:3C-like-proteinase	.	476-478-delinframe	.	no-SNV	ORF1ab:3C-like-proteinase	0.991547416030251
CAMB-7620F	MN908947.3	11074	C	INS	0.022	0.029	0.00033	7.9e-06	0.0249279491171696	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.973266637956736
CAMB-7620F	MN908947.3	11075	T	-	0.019	0.064	1.3e-05	5.1e-16	0.0374933522425102	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962358919813272
CAMB-7620F	MN908947.3	14408	C	T	1	1	0	0	0.996888312650491	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000277829227634747
CAMB-7620F	MN908947.3	2051	GT	TC	0.00355	0.0065	0.00082;0.0011	3.9e-05;4.4e-05	0.00493159401845371	AGT	ORF1ab:nsp2	.	1246-1247-mnv	.	no-SNV	ORF1ab:nsp2	0.99481658692185
CAMB-7620F	MN908947.3	2116	T	A	0.0067	0.012	9.5e-06	8.5e-08	0.00936960631215583	TTG	ORF1ab:nsp2	F437L	T1311A	TTT>TTA	Missense	ORF1ab:nsp2	0.99054820415879
CAMB-7620F	MN908947.3	21633	T	C	0.009	0.031	5.5e-05	4.2e-12	0.0184426229508197	TTA	S	L24S	T71C	TTA>TCA	Missense	GU280_gp02, spike glycoprotein	0.98155737704918
CAMB-7620F	MN908947.3	23403	A	G	1	1	0	0	0.999921254675504	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.8745324496358e-05
CAMB-7620F	MN908947.3	241	C	T	1	1	0	0	0.999750223015165	TCG	NA	NA	NA	NA	NA	NA	0.000124888492417484
CAMB-7620F	MN908947.3	27367	C	T	0.003	0.011	0.0032	7.6e-07	0.0048327631447836	GCA	ORF6	Q56*	C166T	CAA>TAA	Nonsense	GU280_gp06	0.995100807121267
CAMB-7620F	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999402494585107	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7620F	MN908947.3	29719	C	T	0.013	0.018	2.4e-07	4.1e-09	0.0148883374689826	CCA	NA	NA	NA	NA	NA	NA	0.981389578163772
CAMB-7620F	MN908947.3	3037	C	T	1	0.99	0	0	0.996600216349869	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00108174934322361
CAMB-7620F	MN908947.3	4183	TGG	-	0.0093	0.00246666666666667	3e-06;8.8e-06;2.7e-06	NA;5.2e-05;NA	0.00520560106533231	CTG	ORF1ab:nsp3	.	1464-1466-delinframe	.	no-SNV	ORF1ab:nsp3	0.994592631451515
CAMB-7620F	MN908947.3	4200	TGCTAGCGAAAGCTT	-	0.00968	0.00150313333333333	3.5e-06;4.6e-06;3.3e-06;3.3e-06;9.7e-08;5.1e-06;4.6e-06;4.2e-06;6.4e-06;1.9e-06;2.3e-06;3.3e-06;3.4e-06;3.3e-06;7e-07	NA;NA;NA;NA;5.5e-07;NA;NA;NA;NA;NA;NA;NA;NA;0.00041;0.00013	0.00522943365026871	ATG	ORF1ab:nsp3	.	1481-1495-delinframe	.	no-SNV	ORF1ab:nsp3	0.994735972916065
CAMB-7620F	MN908947.3	4876	C	T	1	1	0	0	0.999960650835186	ACA	ORF1ab:nsp3	Y719Y	C2157T	TAC>TAT	Synonymous	ORF1ab:nsp3	0
CAMB-7620F	MN908947.3	7438	TTATGTA	-	0.00654285714285714	0.0109571428571429	0.0067;0.01;0.0069;3e-04;0.00039;0.00014;0.00016	0.00013;0.00036;0.00017;5.8e-07;6.9e-07;0.00049;0.00051	0.00975149418055992	ATT	ORF1ab:nsp3	.	4719-4725-delfrshift	.	no-SNV	ORF1ab:nsp3	0.989414433336134
CAMB-7620F	MN908947.3	8964	C	T	0.008	0.01	1.5e-05	1.4e-06	0.00895226229205602	TCA	ORF1ab:nsp4	S137L	C410T	TCA>TTA	Missense	ORF1ab:nsp4	0.991001592026026
CAMB-7620F	MN908947.3	9109	ACGCCCTGACACACGTTATGTGCTCATGGATGGCTCTATTATTC	-	0.00842045454545455	0.00390659090909091	0.00034;1.2e-05;1.9e-05;1.6e-05;1.2e-05;1.2e-05;5.9e-06;1.1e-05;5.7e-05;7.5e-05;4.3e-06;1.2e-05;7.5e-06;1e-05;1.2e-05;1.2e-05;1.2e-05;3.4e-05;1e-05;1.7e-05;1.4e-05;1.5e-05;3.2e-05;3.3e-05;1.3e-05;1.5e-05;1.7e-05;5.9e-05;1.3e-05;1.4e-05;1e-05;1.9e-05;1.1e-05;0.00011;7.2e-05;5.1e-06;0.00066;0.00046;1.5e-05;1.5e-05;2.7e-08;7.7e-05;6.7e-05;9.3e-05	0.36;0.47;0.46;0.46;0.48;0.49;0.47;0.49;0.46;0.46;0.48;0.49;0.48;0.49;0.47;0.46;0.46;5.4e-08;8.1e-09;1.4e-08;9.8e-09;1.2e-08;6.1e-08;6e-08;1.1e-08;1.2e-08;1.4e-08;1e-07;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00472186754679708	TAC	ORF1ab:nsp4	.	555-598-delfrshift	.	no-SNV	ORF1ab:nsp4	0.995073646496815
CAMB-7620F	MN908947.3	9474	C	T	0.0073	0.0043	2.5e-05	0.00052	0.00596287897875199	GCT	ORF1ab:nsp4	A307V	C920T	GCT>GTT	Missense	ORF1ab:nsp4	0.99395313681028
CAMB-7620F	MN908947.3	9491	C	T	0.015	0.014	2.7e-08	1.2e-07	0.0147133866303793	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.985286613369621
CAMB-7620F	MN908947.3	9636	C	T	0.012	0.017	4e-07	2.3e-09	0.0144803174943688	GCA	ORF1ab:nsp4	A361V	C1082T	GCA>GTA	Missense	ORF1ab:nsp4	0.985466051700096
CAMB-7621E	MN908947.3	14408	C	T	1	1	0	0	0.999513665985799	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000145900204260286
CAMB-7621E	MN908947.3	17278	G	T	0.061	0.18	1.4e-28	3.3e-82	0.116636808790159	AGT	ORF1ab:helicase	V348L	G1042T	GTG>TTG	Missense	ORF1ab:helicase	0.883315418607429
CAMB-7621E	MN908947.3	187	A	G	1	1	0	0	0.999444367273232	CAG	NA	NA	NA	NA	NA	NA	0.000277816363383803
CAMB-7621E	MN908947.3	23403	A	G	1	1	0	0	0.999891880203265	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.10898475510866e-05
CAMB-7621E	MN908947.3	241	C	T	1	1	0	0	0.999928479473609	TCG	NA	NA	NA	NA	NA	NA	7.15205263910742e-05
CAMB-7621E	MN908947.3	25549	C	T	1	1	0	0	0.99960259637038	TCT	ORF3a	L53F	C157T	CTT>TTT	Missense	GU280_gp03	4.41559588466464e-05
CAMB-7621E	MN908947.3	28476	G	T	1	1	0	0	1	CGA	N	R68L	G203T	CGA>CTA	Missense	GU280_gp10	0
CAMB-7621E	MN908947.3	3037	C	T	1	1	1.7e-229	1e-242	0.998706338939198	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7622D	MN908947.3	11287	G	T	0.0065	0.01	0.00012	2.1e-06	0.00784609246863779	TGT	ORF1ab:nsp6	L105F	G315T	TTG>TTT	Missense	ORF1ab:nsp6	0.992109579325325
CAMB-7622D	MN908947.3	12056	TG	-	0.00425	0.00735	0.0038;0.00061	3.9e-05;8.1e-05	0.00561715689529248	TTG	ORF1ab:nsp7	.	214-215-delfrshift	.	no-SNV	ORF1ab:nsp7	0.994522223921476
CAMB-7622D	MN908947.3	14408	C	T	1	1	0	0	0.999510266270043	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000362765725894218
CAMB-7622D	MN908947.3	15960	CGG	-	0.00713333333333333	0.00303333333333333	3.3e-05;3e-05;2.1e-05	NA;4e-06;NA	0.00357050215908571	CCG	ORF1ab:RNA-dependent-RNA-polymerase	.	2493-2495-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.996277724797736
CAMB-7622D	MN908947.3	2040	C	T	0.05	0.032	1.2e-22	2.8e-15	0.0413439771237936	ACT	ORF1ab:nsp2	T412I	C1235T	ACT>ATT	Missense	ORF1ab:nsp2	0.958536875968069
CAMB-7622D	MN908947.3	22093	G	C	0.043	0.049	2.5e-20	2.7e-22	0.0451553650696464	TGG	S	M177I	G531C	ATG>ATC	Missense	GU280_gp02, spike glycoprotein	0.954538496862085
CAMB-7622D	MN908947.3	22988	G	A	0.0039	0.013	0.0018	1.7e-07	0.0092443729903537	CGG	S	G476S	G1426A	GGT>AGT	Missense	GU280_gp02, spike glycoprotein	0.987942122186495
CAMB-7622D	MN908947.3	23403	A	G	1	1	0	0	0.99986772136829	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000105822905367867
CAMB-7622D	MN908947.3	241	C	T	1	1	0	0	0.999780360209257	TCG	NA	NA	NA	NA	NA	NA	0.000159738029631404
CAMB-7622D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999687890137328	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00011568718186025
CAMB-7622D	MN908947.3	28960	G	T	0.012	0.026	2.5e-07	1e-12	0.0180329466809631	AGC	N	Q229H	G687T	CAG>CAT	Missense	GU280_gp10	0.981967053319037
CAMB-7622D	MN908947.3	3037	C	T	1	0.99	0	0	0.997401331817444	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00243625142114666
CAMB-7622D	MN908947.3	3467	G	-	0.015	0.011	2.6e-08	1.7e-06	0.0137892450470611	TGG	ORF1ab:nsp3	.	748-748-delfrshift	.	no-SNV	ORF1ab:nsp3	0.986112025274798
CAMB-7622D	MN908947.3	5989	A	C	0.0082	0.018	2.4e-05	1.1e-08	0.0123376623376623	CAG	ORF1ab:nsp3	T1090T	A3270C	ACA>ACC	Synonymous	ORF1ab:nsp3	0.987445887445887
CAMB-7622D	MN908947.3	8586	TTAAAGTTACACTTGTGTTCCTTT	-	0.0122083333333333	0.00775	6.2e-07;7.1e-07;1.2e-06;9.7e-07;9.7e-07;1.1e-06;1.4e-06;1.2e-06;1.5e-06;1.6e-06;1.3e-06;6.4e-07;1.6e-06;4.1e-06;3.1e-05;1.8e-06;1.9e-06;1.8e-06;1.9e-06;1.7e-06;1.4e-06;1.4e-06;1.2e-06;5.1e-07	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;1.3e-07;4e-07;3.6e-06;1.4e-07;1.5e-07;1e-07;1.5e-07;1.2e-07;1.1e-07;1.3e-07;1.1e-07;4.2e-08	0.0102658392706657	ATT	ORF1ab:nsp4	.	32-55-delinframe	.	no-SNV	ORF1ab:nsp4	0.99184249745078
CAMB-7624B	MN908947.3	10097	G	A	1	1	0	0	0.999400726618974	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	3.74545863140942e-05
CAMB-7624B	MN908947.3	11074	C	INS	0.022	0.026	0.00025	1.9e-05	0.0237733391228832	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.974544072948328
CAMB-7624B	MN908947.3	11075	T	-	0.038	0.032	2.1e-10	2.5e-09	0.0355505107832009	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960272417707151
CAMB-7624B	MN908947.3	13536	C	T	1	1	0	0	0.999719788533747	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	5.60422932506398e-05
CAMB-7624B	MN908947.3	14097	C	T	0.018	0.017	1.1e-09	2.4e-09	0.0173985465083114	TCG	ORF1ab:RNA-dependent-RNA-polymerase	F210F	C630T	TTC>TTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.982202142588219
CAMB-7624B	MN908947.3	14408	C	T	1	1	0	0	0.997861011241069	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000477859190825104
CAMB-7624B	MN908947.3	23403	A	G	1	1	0	0	0.998382923673997	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000102131136379111
CAMB-7624B	MN908947.3	23731	C	T	1	1	0	0	0.999646095996461	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.00013271400132714
CAMB-7624B	MN908947.3	241	C	T	1	1	0	0	0.998548188958791	TCG	NA	NA	NA	NA	NA	NA	0.000204742582734616
CAMB-7624B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999385560675883	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000577367205542725
CAMB-7624B	MN908947.3	3037	C	T	1	1	0	0	0.999306480248558	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000110963160230803
CAMB-7624B	MN908947.3	4002	C	T	1	1	0	0	0.999936106319085	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-76269	MN908947.3	11074	C	INS	0.11	0.1	2.6e-33	1e-28	0.109640998500485	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.880259327864514
CAMB-76269	MN908947.3	11083	G	-	0.17	0.16	9.4e-77	3.7e-72	0.168455064023296	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-76269	MN908947.3	11083	G	T	0.83	0.84	0	0	0.831385376361243	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-76269	MN908947.3	14805	C	T	1	1	0	0	0.998408910103421	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000574560240431362
CAMB-76269	MN908947.3	1514	C	T	1	1	0	0	0.999573612718524	CCA	ORF1ab:nsp2	H237Y	C709T	CAT>TAT	Missense	ORF1ab:nsp2	0.000121824937564719
CAMB-76269	MN908947.3	20759	C	T	0.51	0.51	1.1e-291	3.1e-285	0.508151104615212	GCA	ORF1ab:2'-O-ribose-methyltransferase	A34V	C101T	GCA>GTA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.491286750238912
CAMB-76269	MN908947.3	2480	A	G	1	1	0	0	0.999708126589668	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000125088604428137
CAMB-76269	MN908947.3	2558	C	T	1	1	0	0	0.999229853672198	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	5.25099768956102e-05
CAMB-76269	MN908947.3	26144	G	T	1	1	0	0	0.99957660756814	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.00021169621593014
CAMB-76269	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.02871875	0.0301875	0.00012;0.00039;0.00011;0.00011;1.9e-05;6.2e-05;4.5e-05;9.7e-05;7.9e-05;7.9e-05;0.00013;5.8e-05;0.00012;7.5e-05;8.9e-05;8.6e-05;0.00014;8.3e-05;1e-04;8e-05;5.8e-05;0.00012;6.9e-05;1.9e-05;8.8e-05;0.00012;0.00011;6.7e-05;0.00012;3.4e-05;6.5e-05;5.4e-05	2.9e-05;0.00012;5e-05;5e-05;2.7e-05;3e-05;2.4e-05;4.9e-05;3.6e-05;3.9e-05;6.5e-05;2.6e-05;5.5e-05;4e-05;3.9e-05;3.3e-05;6.3e-05;3.8e-05;4.9e-05;3.9e-05;1.9e-05;5.3e-05;3.7e-05;1.4e-05;3.7e-05;5.4e-05;5e-05;1.9e-05;4.7e-05;1.7e-05;3.6e-05;2.1e-05	0.0288945303484883	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.970555155010815
CAMB-76269	MN908947.3	28544	A	C	0.014	0.0077	2.8e-05	0.0068	0.0115793866054663	TAC	N	T91P	A271C	ACC>CCC	Missense	GU280_gp10	0.986751512622575
CAMB-76269	MN908947.3	29140	G	T	1	1	0	0	0.999384046812442	AGG	N	Q289H	G867T	CAG>CAT	Missense	GU280_gp10	0.000307976593778873
CAMB-76278	MN908947.3	10606	T	C	0.01	0.01	4.6e-05	4.3e-05	0.0102853745541023	CTT	ORF1ab:3C-like-proteinase	P184P	T552C	CCT>CCC	Synonymous	ORF1ab:3C-like-proteinase	0.988941736028537
CAMB-76278	MN908947.3	1102	C	T	0.011	0.0033	1.2e-06	0.0021	0.00789869608826479	CCA	ORF1ab:nsp2	S99S	C297T	TCC>TCT	Synonymous	ORF1ab:nsp2	0.99205951186894
CAMB-76278	MN908947.3	11074	C	INS	0.033	0.027	2.9e-07	3.6e-05	0.0302167649883386	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.969663191109892
CAMB-76278	MN908947.3	11075	T	-	0.026	0.045	3.4e-07	1e-11	0.0343300278147297	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959063973878341
CAMB-76278	MN908947.3	14408	C	T	1	1	0	0	0.999230855513003	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000352524556540132
CAMB-76278	MN908947.3	14594	GTAATCTATTACTAGATA	-	0.00894444444444444	0.000157555555555556	6e-06;8.1e-06;6.1e-06;5.7e-06;7.9e-06;6e-06;3e-04;0.00022;1.8e-05;0.00025;0.00012;2e-04;6.2e-05;0.00026;0.00026;0.00014;3.8e-06;5.3e-06	0.0028;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0050258207303578	GGT	ORF1ab:RNA-dependent-RNA-polymerase	.	1127-1144-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.993718117554456
CAMB-76278	MN908947.3	1723	T	-	0.01	0.0034	5.8e-06	0.0074	0.00780520346897932	CTT	ORF1ab:nsp2	.	918-918-delfrshift	.	no-SNV	ORF1ab:nsp2	0.9920613742495
CAMB-76278	MN908947.3	20268	A	G	1	0.99	2.4e-141	1.2e-191	0.995983935742972	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-76278	MN908947.3	20487	GT	-	0.057	0.014	4.6e-07;4e-07	0.0084;0.0087	0.0323886639676113	AGT	ORF1ab:endoRNAse	.	867-868-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.967871485943775
CAMB-76278	MN908947.3	22952	T	C	0.025	0.021	4.4e-12	1.8e-10	0.0225394440270473	TTT	S	F464L	T1390C	TTT>CTT	Missense	GU280_gp02, spike glycoprotein	0.977043158861341
CAMB-76278	MN908947.3	23403	A	G	1	0.99	0	0	0.997456518579526	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.05590814398527e-05
CAMB-76278	MN908947.3	23555	CCCATTGGTGCAGGTATATGCGCTAGTT	-	0.0577857142857143	0.0292142857142857	2.5e-05;1.7e-05;2.5e-05;3.6e-05;2.4e-06;5.2e-06;2.8e-08;6.2e-07;6.9e-07;7.6e-07;5.8e-07;6.8e-07;2.1e-07;1.7e-07;3.1e-08;4.5e-09;2.2e-05;7.7e-06;1.9e-05;5.2e-06;1.5e-05;4.2e-05;1.9e-05;2e-05;1.3e-07;3.2e-07;0.00012;9.3e-05	0.015;0.04;0.043;0.042;0.0029;0.004;0.0012;0.001;0.0011;0.0011;0.001;0.00045;0.00071;0.00063;0.00035;0.00027;0.00072;5e-04;0.00021;0.00013;0.00026;0.00049;3e-04;3e-04;1e-05;5.9e-05;0.0066;0.015	0.0432559130620072	ACC	S	.	1993-2020-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.963432678080744
CAMB-76278	MN908947.3	24056	GG	TT	0.0042	0.0061	NA;3.7e-06	2.6e-05;4e-05	0.00496793424261584	TGG	S	.	2494-2495-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.997251385572027
CAMB-76278	MN908947.3	24057	G	T	0.0084	0.0058	3.7e-06	4e-05	0.0072883657763694	GGC	S	G832V	G2495T	GGC>GTC	Missense	GU280_gp02, spike glycoprotein	0.992666364870982
CAMB-76278	MN908947.3	241	C	T	1	1	0	0	0.999888362954363	TCG	NA	NA	NA	NA	NA	NA	6.69822273823345e-05
CAMB-76278	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGT	-	0.04452	0.05144	2.1e-07;2.6e-10;9.3e-08;9.5e-08;3.6e-07;1.1e-08;6e-08;8.5e-10;7.9e-10;3.2e-11;3.4e-10;2.3e-10;6.4e-10;4.9e-10;6.3e-10;1.3e-09;3.9e-10;1e-09;3.7e-10;5.8e-10;5.1e-10;1.4e-09;5.5e-10;7.5e-10;5.1e-10;2.5e-10;9.4e-10;3.6e-10;4.2e-10;5.5e-10;1e-09;8.2e-10;4.6e-10;1e-09;5.6e-11;3e-10;2e-10;0.00063;0.0016;0.0039;0.0043;0.017;0.013;0.013;0.013;0.013;0.014;0.012;0.012;0.0032	1.6e-07;1.7e-09;1.6e-08;1.6e-08;7.6e-09;6.1e-12;7.8e-11;4.4e-11;4.5e-11;1.5e-11;1.9e-11;1.3e-11;4.4e-11;2.4e-11;2.8e-11;6.9e-11;1.5e-11;5.6e-11;2.5e-11;2.6e-11;3.2e-11;6e-11;2.8e-11;4.8e-11;2.4e-11;1.2e-11;5.2e-11;2.4e-11;2.1e-12;2.5e-11;5.1e-11;4.9e-11;1.5e-11;5.1e-11;2.6e-12;2.5e-11;1.1e-11;3.5e-05;0.00016;6.7e-05;1e-04;4e-04;0.00023;0.00031;0.00035;0.00035;0.00036;0.00032;0.00023;0.00052	0.058029513179612	GTC	M	.	258-307-delfrshift	.	no-SNV	GU280_gp05	0.959357293316569
CAMB-76278	MN908947.3	29734	G	C	1	1	0	0	0.998121712997746	CGA	NA	NA	NA	NA	NA	NA	0
CAMB-76278	MN908947.3	3037	C	T	1	1	0	0	0.999070891015516	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000278732695345164
CAMB-76278	MN908947.3	316	TTTGCCTGTT	-	0.003385	0.01054	8e-04;0.016;0.0039;0.0026;0.0026;0.0023;0.002;NA;0.47;NA	0.00023;0.00022;1.4e-05;6e-06;5.5e-06;5.2e-06;2.4e-06;1.7e-06;7.6e-06;4.7e-05	0.00685003688481399	GTT	ORF1ab:leader-protein	.	51-60-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.989266206546132
CAMB-76278	MN908947.3	522	TT	-	0.0765	0.037	3.5e-11;9.7e-10	9.2e-06;0.00013	0.0609249808287278	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.930541535943255
CAMB-76278	MN908947.3	6429	C	T	0.024	0.018	1.2e-12	2.5e-10	0.0216832990901086	CCT	ORF1ab:nsp3	P1237L	C3710T	CCT>CTT	Missense	ORF1ab:nsp3	0.978243322571177
CAMB-76278	MN908947.3	8025	C	T	0.99	1	0	0	0.993212026441112	GCA	ORF1ab:nsp3	A1769V	C5306T	GCA>GTA	Missense	ORF1ab:nsp3	0.00678797355888834
CAMB-76278	MN908947.3	929	A	G	0.01	0.016	1.4e-06	3.2e-09	0.012803344547147	TAT	ORF1ab:nsp2	I42V	A124G	ATT>GTT	Missense	ORF1ab:nsp2	0.987147663063004
CAMB-76287	MN908947.3	11075	T	-	0.041	0.034	1.8e-10	4.9e-09	0.0380846660910798	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957105072016884
CAMB-76287	MN908947.3	14408	C	T	1	1	0	0	0.99900434467777	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00033619530361022
CAMB-76287	MN908947.3	1572	C	T	0.009	0.011	1.2e-05	1.5e-06	0.0101019819126419	ACA	ORF1ab:nsp2	T256I	C767T	ACA>ATA	Missense	ORF1ab:nsp2	0.989801808735809
CAMB-76287	MN908947.3	23403	A	G	1	1	0	0	0.999413600492973	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.95117975629634e-05
CAMB-76287	MN908947.3	241	C	T	1	1	0	0	0.999085517205341	TCG	NA	NA	NA	NA	NA	NA	0.000169832519008178
CAMB-76287	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999380737286901	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-76287	MN908947.3	29160	C	T	0.013	0.011	2.4e-07	9.4e-07	0.0118784753001853	ACT	N	T296I	C887T	ACT>ATT	Missense	GU280_gp10	0.988057055363043
CAMB-76287	MN908947.3	3037	C	T	1	1	0	0	0.999531217954352	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76287	MN908947.3	347	G	A	0.042	0.038	8.3e-20	3.7e-18	0.0399297652337907	CGT	ORF1ab:leader-protein	V28I	G82A	GTA>ATA	Missense	ORF1ab:leader-protein	0.959956428432074
CAMB-762A5	MN908947.3	10377	C	T	0.052	0.1	1.5e-24	2.5e-47	0.0760228612900299	CCA	ORF1ab:3C-like-proteinase	P108L	C323T	CCA>CTA	Missense	ORF1ab:3C-like-proteinase	0.923886419305089
CAMB-762A5	MN908947.3	1059	C	T	1	1	0	0	0.999675219227022	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.000270650644148533
CAMB-762A5	MN908947.3	11075	T	-	0.032	0.039	1.6e-08	1.6e-10	0.0348757098966577	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957098966576669
CAMB-762A5	MN908947.3	12820	A	G	0.0035	0.0073	0.0017	2.7e-05	0.00477582337282739	TAT	ORF1ab:nsp9	L45L	A135G	TTA>TTG	Synonymous	ORF1ab:nsp9	0.995198079231693
CAMB-762A5	MN908947.3	14408	C	T	0.99	1	0	0	0.99504613890238	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00381253035454104
CAMB-762A5	MN908947.3	15682	T	C	0.02	0.01	1.9e-10	3.2e-06	0.0166083065849626	ATA	ORF1ab:RNA-dependent-RNA-polymerase	Y739H	T2215C	TAT>CAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.983294426612197
CAMB-762A5	MN908947.3	16224	T	C	0.036	0.029	1.1e-16	8.6e-14	0.0320499259572668	ATA	ORF1ab:RNA-dependent-RNA-polymerase	H919H	T2757C	CAT>CAC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.967950074042733
CAMB-762A5	MN908947.3	18318	G	T	0.0057	0.012	0.00026	3.5e-07	0.00904094255413803	GGT	ORF1ab:3'-to-5'-exonuclease	G93G	G279T	GGG>GGT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.990786849016259
CAMB-762A5	MN908947.3	20579	T	C	0.012	0.017	6.1e-06	3e-08	0.0151441133365901	GTG	ORF1ab:endoRNAse	V320A	T959C	GTG>GCG	Missense	ORF1ab:endoRNAse	0.98485588666341
CAMB-762A5	MN908947.3	23380	C	T	0.078	0.044	8.3e-36	2.3e-21	0.0653102778077712	ACC	S	N606N	C1818T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.9346588718012
CAMB-762A5	MN908947.3	23403	A	G	1	1	0	0	0.998282822196783	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.51888895583539e-05
CAMB-762A5	MN908947.3	23565	CAGGTATATGCGCTAG	-	0.0194375	0.0339375	0.0039;0.0039;0.003;0.0028;0.0019;0.00081;0.028;0.024;0.027;0.023;0.028;0.034;0.03;0.029;0.014;0.017	0.00091;0.00098;0.00066;6e-04;0.00036;1e-04;0.00036;0.00023;0.00036;0.00017;0.00035;0.00059;0.00038;0.00038;1.9e-05;3.3e-05	0.0205942293253245	GCA	S	.	2003-2018-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.972421808960271
CAMB-762A5	MN908947.3	241	C	T	1	0.99	0	0	0.996164574616457	TCG	NA	NA	NA	NA	NA	NA	6.97350069735007e-05
CAMB-762A5	MN908947.3	24135	TTACTGTT	-	0.02525	0.0077875	0.00052;0.00094;0.00091;1e-04;0.00021;5.5e-05;1.8e-06;9.6e-05	0.038;0.046;0.053;0.063;0.069;0.06;0.0062;NA	0.0177718165814402	CTT	S	.	2573-2580-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.982091852926509
CAMB-762A5	MN908947.3	25459	G	T	1	1	0	0	0.999908073449314	TGC	ORF3a	A23S	G67T	GCT>TCT	Missense	GU280_gp03	4.59632753430009e-05
CAMB-762A5	MN908947.3	25563	G	T	1	1	0	0	0.999807298566783	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	7.22630374563411e-05
CAMB-762A5	MN908947.3	26382	TG	-	0.0039	0.00875	NA;0.00013	2.2e-05;8e-05	0.0056483300589391	TTG	E	.	138-139-delfrshift	.	no-SNV	GU280_gp04	0.996717171717172
CAMB-762A5	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0249131578947368	0.0483157894736842	0.0038;0.044;0.11;0.12;0.14;0.013;0.023;0.00018;0.00017;3.7e-05;0.00011;9.2e-05;0.00016;0.00013;0.00014;0.00022;0.00011;0.00019;0.00012;0.00014;0.00015;0.00023;0.00015;0.00017;0.00014;9.8e-05;0.00019;0.00012;8.8e-05;0.00013;0.00019;0.00017;0.00011;0.00019;6.3e-05;0.00011;9.1e-05;0.00069	4.3e-06;1.3e-07;2.2e-06;2.6e-06;7e-06;9.2e-10;9.9e-09;8.7e-09;8.7e-09;3.8e-09;4.3e-09;3.4e-09;8.3e-09;5.4e-09;6.1e-09;1.3e-08;4e-09;1e-08;5.8e-09;5.5e-09;6.5e-09;1.2e-08;6.4e-09;8.4e-09;5.8e-09;4.5e-09;9.9e-09;5.5e-09;7e-09;5.2e-09;9.9e-09;7.3e-09;1.7e-09;8.8e-09;1.2e-09;5.2e-10;2.6e-10;0.00018	0.0370487334618709	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.975330836454432
CAMB-762A5	MN908947.3	26940	ATCGGAGCTGTGATCCTTCGTGGACATCTTCGTATT	-	0.0116666666666667	0.000766666666666667	1.4e-06;1.6e-06;2e-06;2e-06;3e-06;2.8e-06;2.2e-06;2.3e-06;0.00027;1.9e-05;2.7e-06;3.2e-06;3.3e-06;2.8e-06;3.5e-06;1.9e-06;1.7e-06;2.5e-06;5.7e-06;4.2e-06;1.9e-06;2.7e-06;1.9e-06;1.9e-06;2.3e-06;1.5e-06;1.1e-06;1.5e-06;2.6e-07;1.8e-07;1.3e-06;1.4e-06;6.6e-07;7.3e-07;6.8e-07;1.1e-06	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0034;0.0031;0.0035;0.0035;0.0041;0.0045;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00786353738204694	AAT	M	.	418-453-delinframe	.	no-SNV	GU280_gp05	0.992036753445636
CAMB-762A5	MN908947.3	27205	TTTCATCTCGTTGAC	-	0.0139333333333333	0.0265333333333333	0.0043;0.0049;0.0052;0.0051;0.005;0.0051;0.005;0.005;0.0054;0.005;0.0042;0.0049;0.0048;0.0048;0.005	4.1e-05;6.7e-05;7.5e-05;7.7e-05;7.1e-05;7.3e-05;7e-05;7.4e-05;7.7e-05;7.1e-05;4.8e-05;6.7e-05;6.5e-05;6.5e-05;6.8e-05	0.0169673498341609	GTT	ORF6	.	4-18-delinframe	.	no-SNV	GU280_gp06	0.982928455749262
CAMB-762A5	MN908947.3	2919	C	T	0.012	0.017	3.5e-07	1.5e-09	0.0143712574850299	CCA	ORF1ab:nsp3	P67L	C200T	CCA>CTA	Missense	ORF1ab:nsp3	0.985469061876247
CAMB-762A5	MN908947.3	3037	C	T	1	0.99	0	0	0.994066679223959	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.41796948577887e-05
CAMB-762A5	MN908947.3	3116	A	G	1	1	0	0	0.999671835261301	TAC	ORF1ab:nsp3	T133A	A397G	ACT>GCT	Missense	ORF1ab:nsp3	0.000328164738698827
CAMB-762A5	MN908947.3	3645	A	G	0.0077	0.021	0.0014	5.1e-07	0.015527950310559	GAC	ORF1ab:nsp3	D309G	A926G	GAC>GGC	Missense	ORF1ab:nsp3	0.984472049689441
CAMB-762A5	MN908947.3	3992	C	A	0.026	0.0081	4.7e-13	6.6e-06	0.0172567447136029	TCT	ORF1ab:nsp3	L425M	C1273A	CTG>ATG	Missense	ORF1ab:nsp3	0.982743255286397
CAMB-762A5	MN908947.3	4504	G	A	0.039	0.011	7.3e-19	4.1e-07	0.0215329402717252	AGG	ORF1ab:nsp3	E595E	G1785A	GAG>GAA	Synonymous	ORF1ab:nsp3	0.978467059728275
CAMB-762A5	MN908947.3	522	TT	-	0.0295	0.0385	6.2e-05;0.0031	1.6e-06;0.00037	0.0318184583561477	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.959204726624777
CAMB-762A5	MN908947.3	6219	TG	-	0.0058	0.0013	2.8e-05;2.8e-05	0.002;0.0023	0.00364100185528757	TTG	ORF1ab:nsp3	.	3500-3501-delfrshift	.	no-SNV	ORF1ab:nsp3	0.996172936865055
CAMB-762A5	MN908947.3	6606	C	T	0.009	0.0079	1e-05	2.5e-05	0.00838517717067893	TCT	ORF1ab:nsp3	S1296F	C3887T	TCT>TTT	Missense	ORF1ab:nsp3	0.991614822829321
CAMB-762A5	MN908947.3	6896	C	T	0.033	0.013	5.6e-07	0.001	0.0221729490022173	TCT	ORF1ab:nsp3	L1393L	C4177T	CTA>TTA	Synonymous	ORF1ab:nsp3	0.977827050997783
CAMB-762A5	MN908947.3	8933	AGTGCAGTTGGTAACATCTG	-	0.000855	0.005515	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;3.8e-05;4.9e-05;4.6e-05;NA;NA;NA;NA;NA	5e-05;4.5e-05;4e-05;1e-04;6.5e-05;9.1e-05;0.00011;1e-04;4.5e-05;0.00012;6.1e-05;4.6e-05;4.7e-05;4.6e-05;4.5e-05;4.2e-05;5.9e-05;8.2e-05;4.2e-05;4.3e-05	0.00252901714407411	TAG	ORF1ab:nsp4	.	379-398-delfrshift	.	no-SNV	ORF1ab:nsp4	0.997367502081822
CAMB-762A5	MN908947.3	9996	C	T	0.016	0.033	7e-09	6.9e-16	0.0237968483816014	TCA	ORF1ab:nsp4	S481L	C1442T	TCA>TTA	Missense	ORF1ab:nsp4	0.976149914821124
CAMB-762B4	MN908947.3	14408	C	T	1	1	0	0	0.999372680223744	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000418213184170631
CAMB-762B4	MN908947.3	23403	A	G	1	1	0	0	0.999801621742257	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000148783693307214
CAMB-762B4	MN908947.3	241	C	T	1	1	0	0	0.999894286167345	TCG	NA	NA	NA	NA	NA	NA	5.28569163275015e-05
CAMB-762B4	MN908947.3	24780	A	C	1	1	0	0	0.999694179210982	AAG	S	K1073T	A3218C	AAG>ACG	Missense	GU280_gp02, spike glycoprotein	6.79601753372524e-05
CAMB-762B4	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999659052165019	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-762B4	MN908947.3	3037	C	T	1	1	0	0	0.999518999518999	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-762C3	MN908947.3	11075	T	-	0.035	0.048	5e-09	1.4e-12	0.0395236844409421	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956256019612994
CAMB-762C3	MN908947.3	13458	C	T	0.022	0.02	3.2e-10	9.9e-09	0.0212047288421843	TCG	ORF1ab:nsp11	S6L	C17T	TCG>TTG	Missense	ORF1ab:nsp11	0.978795271157816
CAMB-762C3	MN908947.3	1401	G	A	1	1	0	0	0.99890590809628	GGA	ORF1ab:nsp2	G199E	G596A	GGA>GAA	Missense	ORF1ab:nsp2	0
CAMB-762C3	MN908947.3	14408	C	T	1	1	0	0	0.999693794973863	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000240589663393189
CAMB-762C3	MN908947.3	15743	G	A	0.0041	0.0075	0.00058	1.4e-05	0.00537190875429273	AGC	ORF1ab:RNA-dependent-RNA-polymerase	S759N	G2276A	AGC>AAC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994628091245707
CAMB-762C3	MN908947.3	17352	C	T	0.0049	0.0068	0.00026	3.4e-05	0.00566773987744625	TCT	ORF1ab:helicase	V372V	C1116T	GTC>GTT	Synonymous	ORF1ab:helicase	0.994317423107168
CAMB-762C3	MN908947.3	17708	C	T	0.0059	0.018	8.1e-05	1.8e-10	0.00971627534936244	CCA	ORF1ab:helicase	P491L	C1472T	CCA>CTA	Missense	ORF1ab:helicase	0.990201383334118
CAMB-762C3	MN908947.3	18804	C	T	0.0055	0.014	0.00019	2.2e-08	0.00842796660467693	GCA	ORF1ab:3'-to-5'-exonuclease	S255S	C765T	AGC>AGT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.991492897558659
CAMB-762C3	MN908947.3	19168	T	A	0.0042	0.029	0.00047	1.9e-14	0.0140482828675787	ATT	ORF1ab:3'-to-5'-exonuclease	F377I	T1129A	TTC>ATC	Missense	ORF1ab:3'-to-5'-exonuclease	0.985886878903802
CAMB-762C3	MN908947.3	20611	C	T	0.0093	0.009	9.8e-06	1.4e-05	0.00915569632782342	GCT	ORF1ab:endoRNAse	L331F	C991T	CTT>TTT	Missense	ORF1ab:endoRNAse	0.990695832920915
CAMB-762C3	MN908947.3	22326	C	T	0.016	0.008	5.2e-06	0.001	0.0132547864506627	TCT	S	S255F	C764T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.986745213549337
CAMB-762C3	MN908947.3	23403	A	G	1	1	0	0	0.999855935459086	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00014406454091433
CAMB-762C3	MN908947.3	241	C	T	1	1	0	0	0.999691323380851	TCG	NA	NA	NA	NA	NA	NA	0.000112246043326973
CAMB-762C3	MN908947.3	24932	GG	-	0.00285	0.014	0.00019;NA	7.8e-10;8e-07	0.00684335202769735	TGG	S	.	3370-3371-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.989828997487641
CAMB-762C3	MN908947.3	26211	G	T	0.012	0.014	2e-05	2.4e-05	0.0125448028673835	TGC	ORF3a	V273V	G819T	GTG>GTT	Synonymous	GU280_gp03	0.987455197132617
CAMB-762C3	MN908947.3	26461	C	T	0.012	0.023	3.4e-07	1.2e-11	0.0149442464651109	TCT	E	L73F	C217T	CTT>TTT	Missense	GU280_gp04	0.98327393953328
CAMB-762C3	MN908947.3	26529	G	T	0.0036	0.0072	0.00078	1.8e-05	0.00459812396542211	AGA	M	D3Y	G7T	GAT>TAT	Missense	GU280_gp05	0.990573845870885
CAMB-762C3	MN908947.3	26720	G	C	0.0074	0.0035	2.1e-05	0.00071	0.00598354525056096	TGC	M	V66V	G198C	GTG>GTC	Synonymous	GU280_gp05	0.992115432560459
CAMB-762C3	MN908947.3	27920	C	T	0.0085	0.01	3.9e-05	1.7e-05	0.00893426930440332	TCA	ORF8	I9I	C27T	ATC>ATT	Synonymous	GU280_gp09	0.991065730695597
CAMB-762C3	MN908947.3	28000	C	T	0.042	0.05	1.3e-18	1.8e-20	0.0440708190039485	CCG	ORF8	P36L	C107T	CCG>CTG	Missense	GU280_gp09	0.955929180996052
CAMB-762C3	MN908947.3	28375	G	A	1	1	0	0	0.999907853917744	GGG	N	G34G	G102A	GGG>GGA	Synonymous	GU280_gp10	7.67884018797801e-05
CAMB-762C3	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998263495658739	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000416944629753169
CAMB-762C3	MN908947.3	29730	C	T	0.011	0.0066	2.4e-06	0.00013	0.00918091809180918	TCA	NA	NA	NA	NA	NA	NA	0.990819081908191
CAMB-762C3	MN908947.3	29754	C	T	0.057	0.022	5.6e-24	7.7e-10	0.0441928414901388	TCG	NA	NA	NA	NA	NA	NA	0.955441928414901
CAMB-762C3	MN908947.3	3037	C	T	1	1	0	0	0.999433855444423	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.43574259294206e-05
CAMB-762C3	MN908947.3	3272	C	T	0.0045	0.0067	0.00031	2.7e-05	0.00520501380922031	TCA	ORF1ab:nsp3	Q185*	C553T	CAA>TAA	Nonsense	ORF1ab:nsp3	0.994759577933574
CAMB-762C3	MN908947.3	5670	C	T	0.0064	0.008	1e-04	2e-05	0.00683319757444113	TCA	ORF1ab:nsp3	S984L	C2951T	TCA>TTA	Missense	ORF1ab:nsp3	0.993166802425559
CAMB-762C3	MN908947.3	7805	G	T	0.0071	0.0099	4.5e-05	1.2e-05	0.00759734093067426	TGA	ORF1ab:nsp3	E1696*	G5086T	GAA>TAA	Nonsense	ORF1ab:nsp3	0.987496043051599
CAMB-762D2	MN908947.3	11075	T	-	0.027	0.055	1.6e-07	8.2e-14	0.0409375093481708	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957342427233839
CAMB-762D2	MN908947.3	11842	G	T	1	1	5.6e-299	0	1	AGT	ORF1ab:nsp6	Q290H	G870T	CAG>CAT	Missense	ORF1ab:nsp6	0
CAMB-762D2	MN908947.3	14408	C	T	1	1	0	0	0.999669207989415	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00023628000756096
CAMB-762D2	MN908947.3	14757	C	T	1	1	0	0	0.999851447458823	ACT	ORF1ab:RNA-dependent-RNA-polymerase	H430H	C1290T	CAC>CAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	5.57072029413403e-05
CAMB-762D2	MN908947.3	16072	G	T	1	1	0	0	0.999854423699822	TGC	ORF1ab:RNA-dependent-RNA-polymerase	A869S	G2605T	GCT>TCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-762D2	MN908947.3	19743	A	C	1	1	0	0	0.999817861696315	AAT	ORF1ab:endoRNAse	E41D	A123C	GAA>GAC	Missense	ORF1ab:endoRNAse	0.000121425535790177
CAMB-762D2	MN908947.3	22498	C	T	1	1	0	0	1	TCT	S	I312I	C936T	ATC>ATT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-762D2	MN908947.3	23403	A	G	1	1	0	0	0.999938743506812	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.67538959129668e-05
CAMB-762D2	MN908947.3	241	C	T	0.99	1	0	0	0.996918475551729	TCG	NA	NA	NA	NA	NA	NA	6.79748040059818e-05
CAMB-762D2	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999183873337142	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	9.03179190751445e-05
CAMB-762D2	MN908947.3	3037	C	T	1	1	0	0	0.999568562594377	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000143812468541023
CAMB-762D2	MN908947.3	4207	GA	TC	1	1	0;0	0;0	0.999811312843306	CGA	ORF1ab:nsp3	.	1488-1489-mnv	.	no-SNV	ORF1ab:nsp3	2.12336766111052e-05
CAMB-762E1	MN908947.3	10810	T	C	0.012	0.008	4.7e-07	3.3e-05	0.0111157067521456	CTC	ORF1ab:3C-like-proteinase	P252P	T756C	CCT>CCC	Synonymous	ORF1ab:3C-like-proteinase	0.988780891324579
CAMB-762E1	MN908947.3	11074	C	INS	0.11	0.11	1.7e-40	1.4e-34	0.107072919778287	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.88924292210163
CAMB-762E1	MN908947.3	11083	G	-	0.19	0.16	2.5e-84	4.1e-72	0.178186213736672	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.09942970493429e-05
CAMB-762E1	MN908947.3	11083	G	T	0.81	0.84	0	0	0.821147408876767	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.09942970493429e-05
CAMB-762E1	MN908947.3	11651	C	INS	0.016	0.037	5.7e-08	1.2e-16	0.0259403372243839	CCT	ORF1ab:nsp6	.	678-679-insfrshift	.	no-SNV	ORF1ab:nsp6	0.96717983420741
CAMB-762E1	MN908947.3	11653	C	T	1	1	0	0	0.99639199255121	TCT	ORF1ab:nsp6	L227L	C681T	CTC>CTT	Synonymous	ORF1ab:nsp6	0.000698324022346369
CAMB-762E1	MN908947.3	14805	C	T	1	1	0	0	0.999193624003751	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000731364275668073
CAMB-762E1	MN908947.3	21137	A	G	1	1	0	0	0.999817111086726	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	7.31555653096309e-05
CAMB-762E1	MN908947.3	21987	G	A	1	1	0	0	0.997724638303353	GGT	S	G142D	G425A	GGT>GAT	Missense	GU280_gp02, spike glycoprotein	0.000257588116601554
CAMB-762E1	MN908947.3	2480	A	G	1	1	0	0	0.999404812515942	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.00034010713374713
CAMB-762E1	MN908947.3	2558	C	T	1	1	0	0	0.999636439181469	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000103874519580347
CAMB-762E1	MN908947.3	26144	G	T	1	1	0	0	0.999582753824757	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000139082058414465
CAMB-762E1	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0205945945945946	0.0299459459459459	0.0092;0.0016;0.0055;0.0056;0.0086;0.0014;0.0031;0.0023;0.0023;0.00078;0.0016;0.0014;0.0022;0.0019;0.002;0.0028;0.0017;0.0026;0.0018;0.0019;0.002;0.0029;0.002;0.0022;0.0019;0.0016;0.0025;0.0017;0.0015;0.0017;0.0025;0.0022;0.0013;0.0024;0.0013;0.0016;0.0013	0.00082;9.9e-05;0.00039;0.00038;0.00071;5.3e-05;0.00019;3.6e-05;3.8e-05;1.8e-05;2e-05;1.7e-05;3.7e-05;2.7e-05;2.9e-05;5e-05;2.3e-05;4.4e-05;2.9e-05;2e-05;2.1e-05;4.9e-05;2.5e-05;3.6e-05;2.2e-05;1.8e-05;3.3e-05;2.9e-05;2.9e-05;2.4e-05;4.1e-05;3.6e-05;1.4e-05;3.6e-05;1.4e-05;2.4e-05;1.6e-05	0.024467863939486	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.982135139028958
CAMB-762E1	MN908947.3	6347	C	T	0.0069	0.0056	4e-05	0.00014	0.00635826128294263	ACT	ORF1ab:nsp3	L1210L	C3628T	CTG>TTG	Synonymous	ORF1ab:nsp3	0.993612027215735
CAMB-762E1	MN908947.3	885	G	A	0.018	0.017	1e-09	2.1e-09	0.0171894937044081	CGT	ORF1ab:nsp2	R27H	G80A	CGT>CAT	Missense	ORF1ab:nsp2	0.982425307557118
CAMB-762E1	MN908947.3	9724	C	T	1	1	0	0	0.999437776528392	TCT	ORF1ab:nsp4	F390F	C1170T	TTC>TTT	Synonymous	ORF1ab:nsp4	7.33334962966584e-05
CAMB-762F0	MN908947.3	10076	T	C	0.017	0.0061	3.6e-09	8.4e-05	0.0126163645271926	ATT	ORF1ab:3C-like-proteinase	F8L	T22C	TTC>CTC	Missense	ORF1ab:3C-like-proteinase	0.987261146496815
CAMB-762F0	MN908947.3	10232	C	T	1	1	0	0	0.999953334266648	TCG	ORF1ab:3C-like-proteinase	R60C	C178T	CGT>TGT	Missense	ORF1ab:3C-like-proteinase	2.33328666759998e-05
CAMB-762F0	MN908947.3	11075	T	-	0.027	0.041	2.5e-07	8.2e-11	0.0327399726141206	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.96578303614013
CAMB-762F0	MN908947.3	11750	C	T	0.94	1	2.9e-220	1.5e-282	0.973469387755102	ACT	ORF1ab:nsp6	L260F	C778T	CTC>TTC	Missense	ORF1ab:nsp6	0.0244897959183673
CAMB-762F0	MN908947.3	12818	T	C	0.018	0.017	7.3e-10	2.3e-09	0.0176515732924021	GTT	ORF1ab:nsp9	L45L	T133C	TTA>CTA	Synonymous	ORF1ab:nsp9	0.98231005372218
CAMB-762F0	MN908947.3	14408	C	T	1	1	0	0	0.99616481599424	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00107994351064714
CAMB-762F0	MN908947.3	15360	C	T	0.011	0.0069	4.3e-07	2.4e-05	0.00965414810099724	GCA	ORF1ab:RNA-dependent-RNA-polymerase	R631R	C1893T	CGC>CGT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.99028219817526
CAMB-762F0	MN908947.3	1592	T	A	0.95	0.99	0	0	0.971823204419889	TTC	ORF1ab:nsp2	S263T	T787A	TCC>ACC	Missense	ORF1ab:nsp2	0.0281767955801105
CAMB-762F0	MN908947.3	19014	A	G	0.97	1	0	0	0.98156879554222	AAT	ORF1ab:3'-to-5'-exonuclease	K325K	A975G	AAA>AAG	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.0184312044577797
CAMB-762F0	MN908947.3	23403	A	G	1	1	0	0	0.999899618550492	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.78337683196145e-05
CAMB-762F0	MN908947.3	241	C	T	1	1	0	0	0.998818611414031	TCG	NA	NA	NA	NA	NA	NA	0.00111323155216285
CAMB-762F0	MN908947.3	25463	C	T	0.0054	0.0079	0.00019	1.3e-05	0.00637211693844572	ACT	ORF3a	T24I	C71T	ACT>ATT	Missense	GU280_gp03	0.993554429263993
CAMB-762F0	MN908947.3	29587	G	A	0.015	0.016	3e-08	6.7e-09	0.0156555772994129	CGT	ORF10	P10P	G30A	CCG>CCA	Synonymous	GU280_gp11	0.984158046780356
CAMB-762F0	MN908947.3	29783	G	A	0.008	0.011	2.1e-05	2e-06	0.00922387666359204	AGC	NA	NA	NA	NA	NA	NA	0.990512584003162
CAMB-762F0	MN908947.3	3037	C	T	1	1	0	0	0.999177105239097	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000182865502422968
CAMB-762F0	MN908947.3	6633	C	T	0.0023	0.013	0.0063	2.2e-07	0.00716392751790982	GCT	ORF1ab:nsp3	A1305V	C3914T	GCT>GTT	Missense	ORF1ab:nsp3	0.99283607248209
CAMB-762F0	MN908947.3	8590	A	G	0.0071	0.0051	3.6e-05	0.00023	0.00606366851945427	AAG	ORF1ab:nsp4	K12K	A36G	AAA>AAG	Synonymous	ORF1ab:nsp4	0.993936331480546
CAMB-762F0	MN908947.3	9851	GATGTGCTA	-	0.0902222222222222	0.11	2.5e-40;5.4e-40;1e-40;1.7e-40;7.3e-36;1e-39;1e-32;9.6e-29;1.3e-32	3.5e-48;5.3e-48;1.1e-48;2.9e-48;9.1e-43;1.5e-47;6.4e-39;1.4e-34;5.4e-39	0.0971111004647152	TGA	ORF1ab:nsp4	.	1297-1305-delinframe	.	no-SNV	ORF1ab:nsp4	0.903184226858261
CAMB-7630C	MN908947.3	14097	C	T	0.071	0.061	9.6e-33	1.7e-28	0.0658028455284553	TCG	ORF1ab:RNA-dependent-RNA-polymerase	F210F	C630T	TTC>TTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.934197154471545
CAMB-7630C	MN908947.3	14408	C	T	0.97	1	0	0	0.97909813046618	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000401187515044532
CAMB-7630C	MN908947.3	19782	A	G	1	1	0	0	1	CAT	ORF1ab:endoRNAse	A54A	A162G	GCA>GCG	Synonymous	ORF1ab:endoRNAse	0
CAMB-7630C	MN908947.3	23403	A	G	1	1	0	0	0.9998497660643	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000128771944885608
CAMB-7630C	MN908947.3	241	C	T	1	1	0	0	0.99977143901993	TCG	NA	NA	NA	NA	NA	NA	9.1424392027793e-05
CAMB-7630C	MN908947.3	28820	TCT	CTC	0.00302333333333333	0.036	NA;0.00051;NA	2.3e-13;1.4e-13;9.7e-14	0.0152880152880153	CTC	N	.	547-549-mnv	.	no-SNV	GU280_gp10	0.9847453010079
CAMB-7630C	MN908947.3	3037	C	T	1	1	0	0	0.999234596249522	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000765403750478377
CAMB-7630C	MN908947.3	686	AAGTCATTT	-	0.0376666666666667	0.0425555555555556	9.4e-06;8.7e-06;7.1e-05;1.9e-05;8.1e-05;3.5e-05;9e-06;4.1e-05;0.00013	8.4e-07;7.7e-07;3.4e-06;7.3e-07;3.6e-06;1.8e-06;7.9e-07;1.3e-06;NA	0.0414403540535104	AAA	ORF1ab:leader-protein	.	421-429-delinframe	.	no-SNV	ORF1ab:leader-protein	0.95722641509434
CAMB-7630C	MN908947.3	8928	T	-	0.044	0.04	1.3e-19	8.7e-17	0.0431944444444444	GTT	ORF1ab:nsp4	.	374-374-delfrshift	.	no-SNV	ORF1ab:nsp4	0.956805555555556
CAMB-7630C	MN908947.3	8928	TT	-	0.022	0.0395	1.3e-19;NA	8.7e-17;2e-18	0.0264709980030651	GTT	ORF1ab:nsp4	.	374-375-delfrshift	.	no-SNV	ORF1ab:nsp4	0.956805555555556
CAMB-7631B	MN908947.3	11074	C	INS	0.13	0.13	8.3e-59	1.5e-56	0.129514524993457	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.865142196632644
CAMB-7631B	MN908947.3	11083	G	-	0.16	0.14	7.9e-69	3.2e-59	0.148476401242712	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	4.2558624505256e-05
CAMB-7631B	MN908947.3	11083	G	T	0.84	0.86	0	0	0.851300165978636	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	4.2558624505256e-05
CAMB-7631B	MN908947.3	1440	G	A	1	1	0	0	0.999812030075188	GGC	ORF1ab:nsp2	G212D	G635A	GGC>GAC	Missense	ORF1ab:nsp2	0
CAMB-7631B	MN908947.3	16388	A	G	0.006	0.0085	9.3e-05	8.8e-06	0.00723602341337512	AAT	ORF1ab:helicase	N51S	A152G	AAT>AGT	Missense	ORF1ab:helicase	0.992533529981103
CAMB-7631B	MN908947.3	20555	C	T	0.033	0.033	3.7e-16	5.8e-16	0.0329713635169454	TCT	ORF1ab:endoRNAse	S312F	C935T	TCT>TTT	Missense	ORF1ab:endoRNAse	0.966984849811717
CAMB-7631B	MN908947.3	21587	C	T	0.022	0.017	2.7e-09	2.2e-07	0.019578313253012	GCC	S	P9S	C25T	CCA>TCA	Missense	GU280_gp02, spike glycoprotein	0.980421686746988
CAMB-7631B	MN908947.3	21742	C	T	1	1	0	0	0.999309604173059	CCA	S	S60S	C180T	TCC>TCT	Synonymous	GU280_gp02, spike glycoprotein	0.000613685179502915
CAMB-7631B	MN908947.3	2891	G	A	1	1	0	0	0.99991087741188	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	8.9122588119959e-05
CAMB-7631B	MN908947.3	4668	C	T	1	1	0	0	0.998891191472115	TCT	ORF1ab:nsp3	S650F	C1949T	TCT>TTT	Missense	ORF1ab:nsp3	0.000818224224025204
CAMB-7631B	MN908947.3	6121	A	G	0.014	0.019	8.7e-08	2e-09	0.0165606979151264	CAA	ORF1ab:nsp3	S1134S	A3402G	TCA>TCG	Synonymous	ORF1ab:nsp3	0.983439302084874
CAMB-7632A	MN908947.3	11378	G	-	0.021	0.015	4.4e-09	8.5e-07	0.0185013876040703	TGC	ORF1ab:nsp6	.	406-406-delfrshift	.	no-SNV	ORF1ab:nsp6	0.98149861239593
CAMB-7632A	MN908947.3	11871	C	T	0.022	0.026	1.7e-05	2e-04	0.0235294117647059	TCA	ORF1ab:nsp7	S10L	C29T	TCA>TTA	Missense	ORF1ab:nsp7	0.976470588235294
CAMB-7632A	MN908947.3	11938	TGTCCAGTTACACAATGACATT	-	0.0258181818181818	0.000945454545454545	2e-12;1.9e-12;2.4e-12;1.9e-12;1.8e-10;1.4e-12;1.9e-12;6.7e-13;2.5e-12;1.1e-12;1.4e-12;4e-12;2.4e-12;2.7e-13;2.1e-13;1.2e-23;7.8e-13;7.1e-13;1.4e-12;8.5e-13;2.4e-13;2.4e-12	NA;1.2e-06;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;3.2e-07;NA;NA;NA;NA;NA;NA;NA;NA	0.0142693720272142	GTG	ORF1ab:nsp7	.	96-117-delfrshift	.	no-SNV	ORF1ab:nsp7	0.985881308272902
CAMB-7632A	MN908947.3	11951	A	-	0.026	0.011	2.7e-13	3.2e-07	0.0198748443536286	CAA	ORF1ab:nsp7	.	109-109-delfrshift	.	no-SNV	ORF1ab:nsp7	0.979981482072731
CAMB-7632A	MN908947.3	13049	G	C	0.0028	0.0082	0.00094	1.7e-06	0.00385222533751149	TGC	ORF1ab:nsp10	A9P	G25C	GCC>CCC	Missense	ORF1ab:nsp10	0.996006408595057
CAMB-7632A	MN908947.3	13571	G	T	0.0094	0.039	0.0095	3.4e-08	0.0279965004374453	GGT	ORF1ab:RNA-dependent-RNA-polymerase	G35V	G104T	GGT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.967629046369204
CAMB-7632A	MN908947.3	14408	C	T	1	1	0	0	0.999596358254474	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000358792662690048
CAMB-7632A	MN908947.3	15618	ACT	GTC	0.00368033333333333	0.0076	NA;NA;9e-07	7.8e-06;1.7e-05;1.4e-05	0.00266059575401832	GAC	ORF1ab:RNA-dependent-RNA-polymerase	.	2151-2153-mnv	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.997258304940375
CAMB-7632A	MN908947.3	15620	T	C	0.011	0.0083	9e-07	1.4e-05	0.0101362731587812	CTT	ORF1ab:RNA-dependent-RNA-polymerase	L718P	T2153C	CTT>CCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.989802480477722
CAMB-7632A	MN908947.3	1579	TG	-	0.00965	0.02	0.00026;0.00027	1.5e-06;1.6e-06	0.0137763371150729	TTG	ORF1ab:nsp2	.	774-775-delfrshift	.	no-SNV	ORF1ab:nsp2	0.985353946297803
CAMB-7632A	MN908947.3	17211	G	T	0.0092	0.0053	3.7e-06	2e-04	0.00703954050362484	TGC	ORF1ab:helicase	L325F	G975T	TTG>TTT	Missense	ORF1ab:helicase	0.992960459496375
CAMB-7632A	MN908947.3	17455	G	T	0.017	0.015	2.4e-09	1.1e-08	0.0161680458306811	TGC	ORF1ab:helicase	A407S	G1219T	GCA>TCA	Missense	ORF1ab:helicase	0.983609166136219
CAMB-7632A	MN908947.3	17455	GC	TT	0.008555	0.0135	2.4e-09;0.47	1.1e-08;2.7e-07	0.0106927903700858	TGC	ORF1ab:helicase	.	1219-1220-mnv	.	no-SNV	ORF1ab:helicase	0.983609166136219
CAMB-7632A	MN908947.3	1757	G	T	0.0086	0.0069	1.5e-05	0.00013	0.00817355435031701	AGC	ORF1ab:nsp2	A318S	G952T	GCA>TCA	Missense	ORF1ab:nsp2	0.991826445649683
CAMB-7632A	MN908947.3	17644	C	T	0.013	0.0062	1.2e-07	8.6e-05	0.00997055674518201	TCA	ORF1ab:helicase	Q470*	C1408T	CAA>TAA	Nonsense	ORF1ab:helicase	0.989929068522484
CAMB-7632A	MN908947.3	18025	GTG	-	0.011	0.00261433333333333	1.8e-06;1.4e-06;3.1e-06	NA;NA;9.8e-05	0.00630178764996601	TGT	ORF1ab:helicase	.	1789-1791-delinframe	.	no-SNV	ORF1ab:helicase	0.993654472217624
CAMB-7632A	MN908947.3	1814	A	-	0.011	0.017	0.00055	7.9e-06	0.0123901637271635	TAA	ORF1ab:nsp2	.	1009-1009-delfrshift	.	no-SNV	ORF1ab:nsp2	0.987230545546495
CAMB-7632A	MN908947.3	18486	CA	TG	0.048	0.0285	3e-20;4.2e-24	NA;1.3e-26	0.0326345878989995	TCA	ORF1ab:3'-to-5'-exonuclease	.	447-448-mnv	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.986945312928528
CAMB-7632A	MN908947.3	18487	A	G	0.053	0.057	4.2e-24	1.3e-26	0.0560187597707139	CAT	ORF1ab:3'-to-5'-exonuclease	I150V	A448G	ATA>GTA	Missense	ORF1ab:3'-to-5'-exonuclease	0.943850964043773
CAMB-7632A	MN908947.3	21099	G	-	0.0066	0.018	0.00019	4.4e-09	0.0108076242876793	AGG	ORF1ab:2'-O-ribose-methyltransferase	.	441-441-delfrshift	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.989126874959062
CAMB-7632A	MN908947.3	2155	G	C	0.012	0.011	5.8e-07	6.5e-07	0.0118223760092272	GGC	ORF1ab:nsp2	W450C	G1350C	TGG>TGC	Missense	ORF1ab:nsp2	0.987024221453287
CAMB-7632A	MN908947.3	2235	GTGA	TGTG	0.0015025	0.007825	NA;NA;6.3e-05;NA	1.3e-05;4.6e-06;1e-05;2.6e-05	0.00370967741935484	TGT	ORF1ab:nsp2	.	1430-1433-mnv	.	no-SNV	ORF1ab:nsp2	0.996120898658477
CAMB-7632A	MN908947.3	23067	GT	-	0.018	0.0185	7e-09;8.8e-09	7.7e-10;7.9e-10	0.018210197710718	GGT	S	.	1505-1506-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.981896551724138
CAMB-7632A	MN908947.3	2329	G	T	0.019	0.025	9.5e-09	8.9e-10	0.0211267605633803	TGT	ORF1ab:nsp2	L508F	G1524T	TTG>TTT	Missense	ORF1ab:nsp2	0.978458989229495
CAMB-7632A	MN908947.3	2329	GTGTGCTGACTCTATCAT	TGTGTGCTGACTCTATCA	0.00204333333333333	0.0255555555555556	9.5e-09;NA;NA;NA;NA;NA;NA;4.8e-08;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	8.9e-10;2.4e-10;1.5e-10;4.8e-10;3.9e-10;7.5e-10;1.1e-09;3.3e-10;5e-10;3.4e-10;4.5e-08;8.8e-09;4.4e-10;6.8e-09;8e-10;4.8e-10;3.3e-10;2.2e-10	0.00943800943800944	TGT	ORF1ab:nsp2	.	1524-1541-mnv	.	no-SNV	ORF1ab:nsp2	0.978458989229495
CAMB-7632A	MN908947.3	23403	A	G	1	1	0	0	0.999920590804415	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.97045977924244e-05
CAMB-7632A	MN908947.3	2383	TGA	GTG	0.00633333333333333	0.0236666666666667	NA;1.2e-08;NA	5.5e-10;5.8e-10;1e-07	0.00873362445414847	GTG	ORF1ab:nsp2	.	1578-1580-mnv	.	no-SNV	ORF1ab:nsp2	0.989864864864865
CAMB-7632A	MN908947.3	2393	GTCACGCACTC	TGTCACGCACT	0.000718181818181818	0.0179090909090909	5.4e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	1.9e-08;2.9e-08;8e-08;7e-08;1e-07;1.6e-08;3.5e-06;3.5e-08;4.3e-07;5.6e-08;2.4e-07	0.00692340977931631	TGT	ORF1ab:nsp2	.	1588-1598-mnv	.	no-SNV	ORF1ab:nsp2	0.987455197132617
CAMB-7632A	MN908947.3	24011	TTTATTGAAGATCTACTTTTCA	-	0.0108636363636364	0.0434090909090909	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;9.7e-07;1.7e-07;4.4e-07;NA;7.7e-08;NA;NA;NA;NA;NA	7.6e-09;2.1e-07;3.6e-06;1.2e-05;2e-04;0.00023;2.7e-07;2.8e-07;8.9e-07;9.7e-07;9.1e-07;1.2e-06;1.1e-06;2.6e-07;4.2e-07;6.2e-06;1.1e-08;0.00045;3e-05;2.2e-13;8.9e-13;2.1e-13	0.0317560132054708	ATT	S	.	2449-2470-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.977837581130283
CAMB-7632A	MN908947.3	24027	T	-	0.056	0.06	7.7e-08	1.1e-08	0.058546105057733	CTT	S	.	2465-2465-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.941453894942267
CAMB-7632A	MN908947.3	241	C	T	1	1	0	0	0.999940747763228	TCG	NA	NA	NA	NA	NA	NA	5.92522367719381e-05
CAMB-7632A	MN908947.3	28403	G	T	0.012	0.007	2.2e-07	5.1e-05	0.00995714906742294	AGG	N	G44C	G130T	GGT>TGT	Missense	GU280_gp10	0.990001449065353
CAMB-7632A	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999791666666667	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00023121387283237
CAMB-7632A	MN908947.3	2905	A	-	0.02	0.011	4.3e-09	2.5e-05	0.0164873550370267	TAA	ORF1ab:nsp3	.	186-186-delfrshift	.	no-SNV	ORF1ab:nsp3	0.983512644962973
CAMB-7632A	MN908947.3	29442	A	-	0.014	0.0056	4.3e-05	0.0096	0.0102974828375286	CAA	N	.	1169-1169-delfrshift	.	no-SNV	GU280_gp10	0.989702517162471
CAMB-7632A	MN908947.3	3037	C	T	1	1	0	0	0.999832551908908	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7632A	MN908947.3	313	C	T	1	1	0	0	0.999820035992801	TCA	ORF1ab:leader-protein	L16L	C48T	CTC>CTT	Synonymous	ORF1ab:leader-protein	5.99880023995201e-05
CAMB-7632A	MN908947.3	3211	T	-	0.011	0.012	7.1e-07	5.2e-07	0.0114123581336696	ATG	ORF1ab:nsp3	.	492-492-delfrshift	.	no-SNV	ORF1ab:nsp3	0.988461538461539
CAMB-7632A	MN908947.3	3410	G	T	0.01	0.012	1.7e-06	2.7e-07	0.0108667859882383	AGC	ORF1ab:nsp3	A231S	G691T	GCT>TCT	Missense	ORF1ab:nsp3	0.988941447200205
CAMB-7632A	MN908947.3	3410	GC	TT	0.0105	0.006	1.7e-06;7.8e-07	2.7e-07;NA	0.00879897238278741	AGC	ORF1ab:nsp3	.	691-692-mnv	.	no-SNV	ORF1ab:nsp3	0.988941447200205
CAMB-7632A	MN908947.3	4399	G	T	0.02	0.015	3e-09	4.1e-07	0.0175064047822374	TGC	ORF1ab:nsp3	M560I	G1680T	ATG>ATT	Missense	ORF1ab:nsp3	0.975021349274125
CAMB-7632A	MN908947.3	9542	TG	CT	0.0155	0.006145	5.3e-09;4.5e-09	0.12;1.7e-07	0.0108078538056656	CTG	ORF1ab:nsp4	.	988-989-mnv	.	no-SNV	ORF1ab:nsp4	0.992323568278668
CAMB-7632A	MN908947.3	9543	G	T	0.016	0.012	4.5e-09	1.7e-07	0.0139426686886235	TGT	ORF1ab:nsp4	C330F	G989T	TGT>TTT	Missense	ORF1ab:nsp4	0.985085614169403
CAMB-7632A	MN908947.3	9841	G	T	0.0085	0.015	6.9e-06	1.3e-08	0.011994288434079	AGT	ORF1ab:nsp4	K429N	G1287T	AAG>AAT	Missense	ORF1ab:nsp4	0.988005711565921
CAMB-76339	MN908947.3	10138	C	T	0.0085	0.013	3e-05	3.8e-07	0.01072904757717	ACG	ORF1ab:3C-like-proteinase	N28N	C84T	AAC>AAT	Synonymous	ORF1ab:3C-like-proteinase	0.989253363820245
CAMB-76339	MN908947.3	11074	C	INS	0.065	0.083	1.5e-18	9e-25	0.0733769926439565	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.926274466640985
CAMB-76339	MN908947.3	12130	AGCT	-	0.00895	0.0040105	7.2e-05;3.7e-05;7.4e-05;0.00025	NA;NA;NA;3.2e-07	0.00407779527202293	CAG	ORF1ab:nsp8	.	39-42-delfrshift	.	no-SNV	ORF1ab:nsp8	0.995509100575785
CAMB-76339	MN908947.3	12133	T	-	0.0093	0.016	0.00025	3.2e-07	0.0132336422353272	CTT	ORF1ab:nsp8	.	42-42-delfrshift	.	no-SNV	ORF1ab:nsp8	0.986672751099878
CAMB-76339	MN908947.3	12142	TGCTCAAGAAGCTTATGAGCAGGCTG	-	0.00239834615384615	0.013	0.0043;0.0036;0.0044;0.004;0.0034;0.002;0.0036;0.005;0.0039;NA;NA;NA;0.47;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00024;0.00014;0.00025;0.00022;0.00014;4.1e-05;0.00014;2e-04;0.00016;1e-04;6.5e-05;4.8e-05;2e-07;4.1e-07;7.6e-07;1.5e-07;1.6e-07;1.5e-07;1.3e-07;1.4e-07;1.3e-07;1.8e-07;1.2e-07;1.2e-07;2.3e-07;2.8e-07	0.00677151209890458	CTG	ORF1ab:nsp8	.	51-76-delfrshift	.	no-SNV	ORF1ab:nsp8	0.989933989001128
CAMB-76339	MN908947.3	12263	AAGTTGGA	-	0.01128375	0.010875	2.1e-07;4.6e-08;4.7e-07;2.2e-07;2.8e-07;7.6e-07;2e-07;0.47	9.1e-07;6.9e-07;2.5e-06;9.6e-07;1.2e-06;3.2e-06;8.8e-07;6.6e-06	0.0116459993399029	TAA	ORF1ab:nsp8	.	172-179-delfrshift	.	no-SNV	ORF1ab:nsp8	0.987766549006334
CAMB-76339	MN908947.3	13469	G	-	0.019	0.019	1e-08	6.3e-09	0.0190806591500434	CGG	ORF1ab:nsp11	.	28-28-delfrshift	.	no-SNV	ORF1ab:nsp11	0.977016478751084
CAMB-76339	MN908947.3	13469	GG	-	0.0095	0.019	1e-08;NA	6.3e-09;1.1e-09	0.0140905209222886	CGG	ORF1ab:nsp11	.	28-29-delfrshift	.	no-SNV	ORF1ab:nsp11	0.977016478751084
CAMB-76339	MN908947.3	14408	C	T	1	0.99	0	0	0.995080370189966	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000487092060399416
CAMB-76339	MN908947.3	14653	G	T	0.026	0.0079	3.4e-13	1.7e-05	0.016341369370031	TGT	ORF1ab:RNA-dependent-RNA-polymerase	V396F	G1186T	GTT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.98356682518407
CAMB-76339	MN908947.3	15004	G	T	0.0086	0.0037	2.9e-05	0.0027	0.00576701268742791	TGA	ORF1ab:RNA-dependent-RNA-polymerase	E513*	G1537T	GAG>TAG	Nonsense	ORF1ab:RNA-dependent-RNA-polymerase	0.993903443730433
CAMB-76339	MN908947.3	15672	G	T	0.0071	0.0062	4.3e-05	1e-04	0.00668654102032911	AGT	ORF1ab:RNA-dependent-RNA-polymerase	E735D	G2205T	GAG>GAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993262930961885
CAMB-76339	MN908947.3	17074	C	T	0.03	0.0093	4.6e-15	4.3e-06	0.0172993432038295	ACT	ORF1ab:helicase	L280F	C838T	CTC>TTC	Missense	ORF1ab:helicase	0.982656128242235
CAMB-76339	MN908947.3	17721	G	C	0.0069	0.0049	3.6e-05	0.00029	0.0058869658379262	TGG	ORF1ab:helicase	V495V	G1485C	GTG>GTC	Synonymous	ORF1ab:helicase	0.993991539557539
CAMB-76339	MN908947.3	18630	T	-	0.0098	0.0095	3.3e-06	4.6e-06	0.00964252298508386	ATT	ORF1ab:3'-to-5'-exonuclease	.	591-591-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.990311081555485
CAMB-76339	MN908947.3	22188	C	A	0.056	0.031	2.3e-24	8e-15	0.0404061551345127	CCT	S	P209H	C626A	CCT>CAT	Missense	GU280_gp02, spike glycoprotein	0.959593844865487
CAMB-76339	MN908947.3	23403	A	G	1	1	0	0	0.999843120849239	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000104586100507243
CAMB-76339	MN908947.3	241	C	T	0.99	1	0	0	0.994711945632191	TCG	NA	NA	NA	NA	NA	NA	8.26258494970151e-05
CAMB-76339	MN908947.3	24387	C	T	0.23	0.17	3.7e-103	6.8e-77	0.200356606606607	GCA	S	A942V	C2825T	GCA>GTA	Missense	GU280_gp02, spike glycoprotein	0.79954954954955
CAMB-76339	MN908947.3	27188	G	T	0.0055	0.008	8.3e-05	5.6e-06	0.00655741664352048	AGT	M	Q222H	G666T	CAG>CAT	Missense	GU280_gp05	0.9933942782615
CAMB-76339	MN908947.3	28028	G	T	0.0078	0.0096	6.2e-05	1.3e-05	0.00875715729201751	GGT	ORF8	W45C	G135T	TGG>TGT	Missense	GU280_gp09	0.991242842707982
CAMB-76339	MN908947.3	28253	C	T	0.024	0.014	1.9e-11	6.2e-07	0.0188367437423585	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.980706445068455
CAMB-76339	MN908947.3	3037	C	T	1	1	0	0	0.999390020739295	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76339	MN908947.3	4540	C	T	0.23	0.16	5.8e-106	1e-73	0.186944014162425	ACA	ORF1ab:nsp3	Y607Y	C1821T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.805886258021686
CAMB-76348	MN908947.3	11075	T	-	0.083	0.0052	1.3e-20	0.0093	0.0491711903838697	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95070763861962
CAMB-76348	MN908947.3	11990	G	INS	0.028	0.031	1e-12	6.9e-14	0.0295136297136715	TGA	ORF1ab:nsp7	.	147-148-insfrshift	.	no-SNV	ORF1ab:nsp7	0.970426656316245
CAMB-76348	MN908947.3	14408	C	T	1	1	0	0	0.999844840961986	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	7.75795190069822e-05
CAMB-76348	MN908947.3	23403	A	G	1	1	0	0	0.999893409672311	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.13631380192472e-05
CAMB-76348	MN908947.3	241	C	T	1	1	0	0	0.999866879659212	TCG	NA	NA	NA	NA	NA	NA	3.32800851970181e-05
CAMB-76348	MN908947.3	24137	ACTG	-	0.05975	0.0185	3.8e-09;2.2e-08;9.1e-08;5.1e-09	0.0023;0.0035;0.0049;0.0027	0.0453107855160395	TAC	S	.	2575-2578-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.954371389628091
CAMB-76348	MN908947.3	27923	C	T	1	1	0	0	0.99953906430053	TCA	ORF8	I10I	C30T	ATC>ATT	Synonymous	GU280_gp09	0.000230467849734962
CAMB-76348	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999777827149522	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-76348	MN908947.3	3037	C	T	1	1	0	0	0.999571917808219	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000428082191780822
CAMB-76366	MN908947.3	11075	T	-	0.043	0.041	1.6e-10	1.3e-10	0.042005739914771	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954913093714669
CAMB-76366	MN908947.3	127	G	T	0.18	0.18	5.4e-82	3.2e-83	0.176261974944731	AGT	NA	NA	NA	NA	NA	NA	0.823569147629575
CAMB-76366	MN908947.3	14408	C	T	1	1	0	0	0.997535454250989	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000521075386933683
CAMB-76366	MN908947.3	22484	G	T	1	1	0	0	0.998300283286119	TGT	S	V308L	G922T	GTA>TTA	Missense	GU280_gp02, spike glycoprotein	0.00113314447592068
CAMB-76366	MN908947.3	22564	C	T	0.0082	0.007	1.1e-05	3.5e-05	0.00754457254040317	ACT	S	N334N	C1002T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.992230413892602
CAMB-76366	MN908947.3	23403	A	G	1	1	0	0	0.999231223468853	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.45667554287879e-05
CAMB-76366	MN908947.3	241	C	T	1	1	0	0	0.997549735501249	TCG	NA	NA	NA	NA	NA	NA	0.000162269172102684
CAMB-76366	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999170152028148	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000258207303578015
CAMB-76366	MN908947.3	3037	C	T	1	1	0	0	0.999030269446561	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.46332340513957e-05
CAMB-76366	MN908947.3	4180	G	T	1	1	0	0	0.999923406862745	AGG	ORF1ab:nsp3	K487N	G1461T	AAG>AAT	Missense	ORF1ab:nsp3	1.2765522875817e-05
CAMB-76375	MN908947.3	11075	T	-	0.059	0.017	2.6e-14	4.2e-05	0.0386975162625665	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961179282475853
CAMB-76375	MN908947.3	11273	GTTGATACTAGTTTGTCTGGTTTT	-	0.000926375	0.0214166666666667	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;2.9e-05;NA;NA;0.5;NA;NA;NA;NA;NA;0.5;NA;NA;NA	7.7e-07;8.1e-07;2.8e-06;1.1e-06;3.3e-06;2.4e-06;9.5e-06;3.3e-06;2.3e-06;3.5e-06;4.5e-06;2.5e-05;7.4e-06;1.5e-05;6.5e-06;3.5e-06;3.4e-06;1.1e-06;1.3e-06;3.7e-06;5.1e-08;4.6e-06;1e-06;2e-07	0.010018367006178	GGT	ORF1ab:nsp6	.	301-324-delinframe	.	no-SNV	ORF1ab:nsp6	0.989910887437389
CAMB-76375	MN908947.3	11991	A	-	0.017	0.009	1.3e-06	0.0016	0.0127367547975867	GAA	ORF1ab:nsp7	.	149-149-delfrshift	.	no-SNV	ORF1ab:nsp7	0.987195073455058
CAMB-76375	MN908947.3	13768	A	G	0.025	0.02	1e-12	1.1e-10	0.0224215246636771	CAT	ORF1ab:RNA-dependent-RNA-polymerase	M101V	A301G	ATG>GTG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.976909763197231
CAMB-76375	MN908947.3	14408	C	T	1	1	0	0	0.999655250142541	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000212153758436427
CAMB-76375	MN908947.3	16852	G	T	0.0074	0.0048	3e-05	0.00043	0.00597504326441388	TGG	ORF1ab:helicase	G206C	G616T	GGT>TGT	Missense	ORF1ab:helicase	0.993915657163676
CAMB-76375	MN908947.3	18740	ATTACGTCTATA	-	0.0188333333333333	0.00325208333333333	0.00075;0.00018;0.00074;0.00099;0.00032;0.00057;0.00032;0.00034;0.00013;1e-04;2.1e-07;5.4e-09	0.0048;0.0018;0.0046;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0092166467198855	GAT	ORF1ab:3'-to-5'-exonuclease	.	701-712-delinframe	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.984295039323179
CAMB-76375	MN908947.3	19269	C	T	0.12	0.12	1.2e-56	6.4e-57	0.123616276766654	ACT	ORF1ab:3'-to-5'-exonuclease	N410N	C1230T	AAC>AAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.876383723233346
CAMB-76375	MN908947.3	21101	G	INS	0.018	0.01	2.3e-06	0.001	0.0141473437041385	GGT	ORF1ab:2'-O-ribose-methyltransferase	.	442-443-insfrshift	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.985754818510909
CAMB-76375	MN908947.3	23403	A	G	1	1	0	0	0.999904827001445	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.92167262218915e-05
CAMB-76375	MN908947.3	241	C	T	1	1	0	0	0.999669196699318	TCG	NA	NA	NA	NA	NA	NA	0.000165401650340911
CAMB-76375	MN908947.3	26530	A	G	0.95	1	0	0	0.979949874686717	GAT	M	D3G	A8G	GAT>GGT	Missense	GU280_gp05	0.0200045568466621
CAMB-76375	MN908947.3	3037	C	T	1	1	0	0	0.99923639834553	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000190900413617563
CAMB-76375	MN908947.3	4969	TAA	-	0.0193333333333333	0.003321	3.8e-10;5.8e-11;6.9e-10	0.017;NA;7.2e-06	0.00793934490997686	TTA	ORF1ab:nsp3	.	2250-2252-delinframe	.	no-SNV	ORF1ab:nsp3	0.991853705341185
CAMB-76375	MN908947.3	4971	AG	-	0.0095235	0.00995	6.9e-10;NA	7.2e-06;1.3e-06	0.0098731135971169	AAG	ORF1ab:nsp3	.	2252-2253-delfrshift	.	no-SNV	ORF1ab:nsp3	0.986223074488485
CAMB-76375	MN908947.3	5382	AAGCTGCTAACTTTT	-	0.016	0.000573333333333333	8.6e-08;2.7e-08;1.6e-07;4.9e-07;6e-07;3.1e-07;1.6e-07;1.3e-07;8e-08;3.8e-07;2.9e-07;1.1e-06;3.7e-07;1.5e-07;1.6e-07	NA;NA;7.5e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00487408610885459	GAA	ORF1ab:nsp3	.	2663-2677-delinframe	.	no-SNV	ORF1ab:nsp3	0.994892747701736
CAMB-76375	MN908947.3	635	C	T	0.013	0.0085	3.9e-07	2.8e-05	0.0106937291729779	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.989275976976674
CAMB-76375	MN908947.3	9811	C	INS	0.0031	0.0092	0.0028	4.9e-06	0.00624792289797275	CCT	ORF1ab:nsp4	.	1256-1257-insfrshift	.	no-SNV	ORF1ab:nsp4	0.99360964724873
CAMB-76384	MN908947.3	11074	C	INS	0.028	0.018	9.4e-06	0.0026	0.0232227824728357	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.976620978623677
CAMB-76384	MN908947.3	11075	T	-	0.044	0.055	6.2e-11	1.3e-13	0.0491435712710432	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.944424024112328
CAMB-76384	MN908947.3	14408	C	T	1	1	0	0	0.997868434154842	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000373412994772218
CAMB-76384	MN908947.3	20290	C	T	0.1	0.032	4.9e-22	8.6e-07	0.0770750988142292	ACG	ORF1ab:endoRNAse	R224W	C670T	CGG>TGG	Missense	ORF1ab:endoRNAse	0.920948616600791
CAMB-76384	MN908947.3	23403	A	G	1	1	0	0	0.997764087438453	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.94657596156133e-05
CAMB-76384	MN908947.3	24071	T	C	1	1	0	0	0.999974783134961	ATA	S	Y837H	T2509C	TAT>CAT	Missense	GU280_gp02, spike glycoprotein	2.52168650393383e-05
CAMB-76384	MN908947.3	241	C	T	1	1	0	0	0.999832514515409	TCG	NA	NA	NA	NA	NA	NA	8.37427422956677e-05
CAMB-76384	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0387567567567568	0.0280540540540541	0.00028;8e-06;2e-04;0.00022;0.00064;3.5e-06;9.9e-06;1.1e-06;1e-06;1.3e-07;6.9e-07;5.5e-07;9.1e-07;7.8e-07;9.5e-07;1.4e-06;6.7e-07;1.2e-06;6.2e-07;8.2e-07;7.4e-07;1.5e-06;7.6e-07;9.7e-07;7.5e-07;4.8e-07;1.1e-06;5.9e-07;2.3e-07;8.3e-07;1.2e-06;6.2e-07;4.6e-07;7.1e-07;8.9e-08;2.9e-07;1.2e-07	0.0026;0.00054;0.0021;0.0021;0.0037;3.3e-05;0.00012;0.00011;0.00011;7.3e-05;6.7e-05;5.8e-05;0.00011;8.2e-05;4.6e-05;7.3e-05;7e-05;0.00012;9.1e-05;8.6e-05;7.5e-05;0.00014;7.6e-05;1e-04;8.8e-05;5.4e-05;0.00011;8.7e-05;7e-05;7.4e-05;0.00012;0.00011;5e-05;0.00011;4.4e-05;8.4e-05;6.1e-05	0.0344939926747159	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.978297834697909
CAMB-76384	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998757834114392	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000442254233004802
CAMB-76384	MN908947.3	3037	C	T	1	1	0	0	0.999796095223531	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.09761941173472e-05
CAMB-76384	MN908947.3	522	TT	-	0.063	0.0325	5.1e-09;4e-08	3.8e-05;0.00067	0.0512956431323778	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.941828254847645
CAMB-76393	MN908947.3	11071	G	INS	0.22	0.22	6.8e-61	6.9e-60	0.222158579494313	TGT	ORF1ab:nsp6	.	98-99-insfrshift	.	no-SNV	ORF1ab:nsp6	0.775141150478684
CAMB-76393	MN908947.3	11073	T	-	0.021	0.021	5.3e-11	1.8e-11	0.0210250565601238	TTC	ORF1ab:nsp6	.	101-101-delfrshift	.	no-SNV	ORF1ab:nsp6	0.978600711041557
CAMB-76393	MN908947.3	11074	C	-	0.16	0.16	4.4e-146	1.5e-115	0.158929292301959	TCT	ORF1ab:nsp6	.	102-102-delfrshift	.	no-SNV	ORF1ab:nsp6	0.00843089153184486
CAMB-76393	MN908947.3	11074	C	T	0.83	0.84	0	0	0.83177033195665	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.00843089153184486
CAMB-76393	MN908947.3	11083	G	T	1	1	0	0	0.996733486386959	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.5408083080384e-05
CAMB-76393	MN908947.3	1314	C	T	1	1	0	0	0.996411176621379	ACT	ORF1ab:nsp2	T170I	C509T	ACT>ATT	Missense	ORF1ab:nsp2	0.00187985986499188
CAMB-76393	MN908947.3	14805	C	T	1	1	0	0	0.998740864779262	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00070096187546244
CAMB-76393	MN908947.3	17247	T	C	0.98	1	0	0	0.989368132293911	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.0101204221750384
CAMB-76393	MN908947.3	26144	G	T	1	1	0	0	0.999428680251381	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000444359804481686
CAMB-76393	MN908947.3	26781	CTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0320833333333333	0.0291111111111111	6.1e-05;0.00053;0.00046;0.00077;1.7e-05;4.4e-05;2.2e-05;2.1e-05;3e-06;1.4e-05;1.1e-05;1.8e-05;1.6e-05;1.8e-05;2.7e-05;1.3e-05;2.4e-05;1.5e-05;1.6e-05;1.7e-05;2.8e-05;1.7e-05;2e-05;1.6e-05;1.1e-05;2e-05;1.3e-05;1.9e-05;1.7e-05;2.4e-05;1.6e-05;8.7e-06;2e-05;6.5e-06;1.1e-05;7.1e-06	0.00044;0.0014;0.0011;0.0016;6.6e-05;0.00023;4.6e-05;4.5e-05;2.4e-05;2.2e-05;2e-05;4.5e-05;3.3e-05;3.5e-05;5.6e-05;2.6e-05;5e-05;3.5e-05;3.2e-05;3.3e-05;5.8e-05;3.9e-05;4.5e-05;3.4e-05;2.5e-05;4.9e-05;3.3e-05;3e-05;3.1e-05;4.8e-05;4e-05;1.8e-05;4.9e-05;2e-05;4.2e-05;2.7e-05	0.0319054318472162	TCT	M	.	259-294-delinframe	.	no-SNV	GU280_gp05	0.975269372987158
CAMB-763A2	MN908947.3	11074	C	INS	0.12	0.12	6.5e-49	4.8e-45	0.119382863990413	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.875265537338635
CAMB-763A2	MN908947.3	11083	G	-	0.16	0.14	9.1e-70	4.9e-63	0.151894303963601	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	4.99981250703099e-05
CAMB-763A2	MN908947.3	11083	G	T	0.84	0.86	0	0	0.847793207754709	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	4.99981250703099e-05
CAMB-763A2	MN908947.3	1186	G	A	0.022	0.017	2.2e-11	9e-10	0.021108232011162	CGT	ORF1ab:nsp2	A127A	G381A	GCG>GCA	Synonymous	ORF1ab:nsp2	0.978712377915089
CAMB-763A2	MN908947.3	14805	C	T	1	1	0	0	0.999327820418627	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000281377499179316
CAMB-763A2	MN908947.3	1528	C	T	0.013	0.014	3.8e-07	7.8e-08	0.0133800287356322	CCT	ORF1ab:nsp2	A241A	C723T	GCC>GCT	Synonymous	ORF1ab:nsp2	0.986170977011494
CAMB-763A2	MN908947.3	15957	G	T	0.0062	0.0078	6.5e-05	1.7e-05	0.00708790990919545	GGG	ORF1ab:RNA-dependent-RNA-polymerase	G830G	G2490T	GGG>GGT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.992723740037273
CAMB-763A2	MN908947.3	2480	A	G	1	1	0	0	0.999880153403643	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	5.99232981783317e-05
CAMB-763A2	MN908947.3	2558	C	T	1	1	0	0	0.998954535023077	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	7.64974373358493e-05
CAMB-763A2	MN908947.3	25672	C	T	0.0069	0.0078	5.2e-05	2.7e-05	0.00743638031773625	CCT	ORF3a	L94F	C280T	CTT>TTT	Missense	GU280_gp03	0.992153170119272
CAMB-763A2	MN908947.3	26144	G	T	1	1	0	0	0.99877800407332	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.00046552225778295
CAMB-763A2	MN908947.3	459	A	G	0.0089	0.0075	6e-06	1.3e-05	0.00853287278262397	GAA	ORF1ab:leader-protein	E65G	A194G	GAA>GGA	Missense	ORF1ab:leader-protein	0.991467127217376
CAMB-763B1	MN908947.3	11074	C	INS	0.039	0.13	4.4e-09	1.8e-38	0.095906432748538	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.903785780240074
CAMB-763B1	MN908947.3	14408	C	T	1	1	0	0	0.999314967950286	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000538239467632236
CAMB-763B1	MN908947.3	23403	A	G	1	1	0	0	0.999756323407573	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000194941273941225
CAMB-763B1	MN908947.3	241	C	T	1	1	0	0	0.999681680725768	TCG	NA	NA	NA	NA	NA	NA	0.000159159637116027
CAMB-763B1	MN908947.3	27813	C	T	1	1	1.5e-168	1.9e-57	1	CCT	NA	NA	NA	NA	NA	NA	0
CAMB-763B1	MN908947.3	3037	C	T	1	1	0	1.5e-172	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-763C0	MN908947.3	11074	C	INS	0.1	0.1	3.7e-38	5.4e-36	0.10069156669067	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.896183475767992
CAMB-763C0	MN908947.3	11083	G	-	0.17	0.14	1.9e-73	1.2e-61	0.154916108841172	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-763C0	MN908947.3	11083	G	T	0.83	0.86	0	0	0.844959699954049	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-763C0	MN908947.3	14805	C	T	1	1	0	0	0.999446928875053	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000395050803533334
CAMB-763C0	MN908947.3	21633	T	C	0.019	0.016	3.1e-09	5.9e-08	0.0180122907395635	TTA	S	L24S	T71C	TTA>TCA	Missense	GU280_gp02, spike glycoprotein	0.981987709260437
CAMB-763C0	MN908947.3	2480	A	G	1	1	0	0	0.999936455487069	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-763C0	MN908947.3	2558	C	T	1	1	0	0	0.9997913064218	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000119253473257409
CAMB-763C0	MN908947.3	26144	G	T	1	1	0	0	0.999861782999309	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000138217000691085
CAMB-763C0	MN908947.3	26994	C	T	1	1	0	0	0.999864438946691	ACG	M	R158C	C472T	CGC>TGC	Missense	GU280_gp05	0.000101670789982038
CAMB-763C0	MN908947.3	27881	C	T	1	1	0	0	1	ACG	NA	NA	NA	NA	NA	NA	0
CAMB-763C0	MN908947.3	9634	A	T	0.99	1	0	0	0.994901424154883	TAG	ORF1ab:nsp4	L360F	A1080T	TTA>TTT	Missense	ORF1ab:nsp4	2.027266737621e-05
CAMB-763EE	MN908947.3	10035	TCACCTCAGCTGTTTTGCAGAGTGGTTT	-	0.00107142857142857	0.0107142857142857	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;7e-04;0.0023;0.0023;7e-04;0.00029;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	6.8e-07;1.8e-06;1.1e-07;1.9e-06;1.8e-06;1.1e-06;1.8e-06;2.8e-07;1.2e-06;1.4e-06;3.2e-06;1.2e-05;1.3e-05;3e-06;1.6e-06;1.3e-06;1.1e-06;9.2e-07;1.5e-06;1.8e-06;6.2e-07;1.4e-06;1.5e-06;2.7e-06;1.5e-06;4.3e-06;1.6e-06;1.2e-06	0.00579390260725617	ATC	ORF1ab:nsp4	.	1481-1500-delfrshift	.	no-SNV	ORF1ab:nsp4	0.993202474604751
CAMB-763EE	MN908947.3	11075	T	-	0.11	0.082	3.3e-27	2e-20	0.0972373369990645	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.902629016553067
CAMB-763EE	MN908947.3	13860	C	T	0.0075	0.0075	3.1e-05	3.9e-05	0.00750800032821859	ACA	ORF1ab:RNA-dependent-RNA-polymerase	D131D	C393T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.992491999671781
CAMB-763EE	MN908947.3	14408	C	T	1	1	0	0	0.999783970620004	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00016202203499676
CAMB-763EE	MN908947.3	14786	C	T	1	1	0	0	0.999854907745508	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A440V	C1319T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	7.25461272459072e-05
CAMB-763EE	MN908947.3	15017	C	T	0.01	0.0078	3.8e-05	0.00021	0.00883466554480438	GCA	ORF1ab:RNA-dependent-RNA-polymerase	A517V	C1550T	GCA>GTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.991165334455196
CAMB-763EE	MN908947.3	15474	T	C	0.078	0.14	7.3e-36	5.3e-63	0.108889814429173	GTG	ORF1ab:RNA-dependent-RNA-polymerase	G669G	T2007C	GGT>GGC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.89106390855662
CAMB-763EE	MN908947.3	15492	T	C	0.007	0.0066	3.4e-05	4.6e-05	0.00679403583967899	ATG	ORF1ab:RNA-dependent-RNA-polymerase	D675D	T2025C	GAT>GAC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.993205964160321
CAMB-763EE	MN908947.3	16997	C	T	0.01	0.027	9.5e-07	1.6e-13	0.0201321720863057	CCA	ORF1ab:helicase	P254L	C761T	CCA>CTA	Missense	ORF1ab:helicase	0.979802179526456
CAMB-763EE	MN908947.3	17440	C	T	0.0094	0.034	5.2e-06	1.3e-16	0.0217753152290398	CCC	ORF1ab:helicase	P402S	C1204T	CCT>TCT	Missense	ORF1ab:helicase	0.978201883393757
CAMB-763EE	MN908947.3	17456	C	T	0.017	0.01	3.6e-09	1.6e-06	0.0134379776870252	GCA	ORF1ab:helicase	A407V	C1220T	GCA>GTA	Missense	ORF1ab:helicase	0.986516392507586
CAMB-763EE	MN908947.3	17578	A	G	0.01	0.035	7.6e-07	3.7e-17	0.0225114854517611	AAT	ORF1ab:helicase	I448V	A1342G	ATT>GTT	Missense	ORF1ab:helicase	0.97736089841756
CAMB-763EE	MN908947.3	17731	T	C	0.059	0.06	9.7e-28	1.5e-28	0.0593407716984267	ATT	ORF1ab:helicase	F499L	T1495C	TTC>CTC	Missense	ORF1ab:helicase	0.940659228301573
CAMB-763EE	MN908947.3	17741	G	T	0.013	0.017	4e-08	9.3e-10	0.0151453235940134	CGT	ORF1ab:helicase	R502L	G1505T	CGT>CTT	Missense	ORF1ab:helicase	0.984675895183123
CAMB-763EE	MN908947.3	17795	C	T	0.0091	0.0067	1e-05	0.00012	0.00800518134715026	GCT	ORF1ab:helicase	A520V	C1559T	GCT>GTT	Missense	ORF1ab:helicase	0.99199481865285
CAMB-763EE	MN908947.3	20578	G	T	1	1	0	0	1	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	0
CAMB-763EE	MN908947.3	2105	A	G	0.0092	0.021	2.7e-06	7.1e-11	0.0155339805825243	AAC	ORF1ab:nsp2	T434A	A1300G	ACT>GCT	Missense	ORF1ab:nsp2	0.984466019417476
CAMB-763EE	MN908947.3	22014	GT	AG	0.024	0.036	9.2e-07;7e-08	3.9e-09;4.4e-11	0.0291172106824926	AGT	S	.	452-453-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.976538592315539
CAMB-763EE	MN908947.3	22017	G	T	0.021	0.033	3.5e-07	1.5e-10	0.0271554650373388	TGG	S	W152L	G455T	TGG>TTG	Missense	GU280_gp02, spike glycoprotein	0.972844534962661
CAMB-763EE	MN908947.3	22019	ATG	GAT	0.0253333333333333	0.0363333333333333	2.8e-10;4.5e-08;3.9e-07	2.9e-14;3.1e-11;1.9e-09	0.0293609671848014	GAT	S	.	457-459-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.969257340241796
CAMB-763EE	MN908947.3	22023	A	G	0.024	0.036	1.5e-09	5.8e-14	0.0295937134258485	GAA	S	E154G	A461G	GAA>GGA	Missense	GU280_gp02, spike glycoprotein	0.970239090453102
CAMB-763EE	MN908947.3	22026	GTGAGT	AGTGAG	0.0241666666666667	0.0343333333333333	1.1e-08;1.7e-07;1.4e-07;9.2e-08;6.1e-08;7.3e-07	9.6e-11;3.7e-10;1.2e-09;6.8e-11;3.6e-11;9.1e-10	0.0291525423728814	AGT	S	.	464-469-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.972514421445538
CAMB-763EE	MN908947.3	22033	CAGAGT	TCAGAG	0.0245	0.0353333333333333	4.6e-08;2.5e-07;1.4e-07;4.8e-07;4e-08;5.4e-07	3.1e-11;3.2e-09;3e-10;1.2e-10;9.3e-11;1.2e-09	0.0298609919340999	TCA	S	.	471-476-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.969619823489477
CAMB-763EE	MN908947.3	22041	AT	TA	0.025	0.035	1.1e-07;4.2e-07	3.7e-10;1.8e-09	0.0298532923916752	TAT	S	.	479-480-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.970078204692282
CAMB-763EE	MN908947.3	22044	CTAGTGCGA	TCTAGTGCG	0.0245555555555556	0.0362222222222222	1.1e-07;1.8e-07;3.1e-07;1.1e-07;2.2e-07;2.2e-07;2.5e-07;5.5e-07;1.8e-09	2e-10;3.3e-10;7.8e-10;2.2e-10;2.2e-10;1.8e-10;7e-10;5.2e-10;1.4e-13	0.0301215129214445	TCT	S	.	482-490-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.96943156448566
CAMB-763EE	MN908947.3	22054	TA	AT	0.024	0.0325	1.1e-07;1.4e-07	2e-09;1.9e-10	0.0279917339845952	ATA	S	.	492-493-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.974121647147714
CAMB-763EE	MN908947.3	22057	T	A	0.023	0.034	3.4e-07	6.5e-10	0.028523800703834	ATT	S	N165K	T495A	AAT>AAA	Missense	GU280_gp02, spike glycoprotein	0.971290979811076
CAMB-763EE	MN908947.3	22059	GCACT	TGCAC	0.0242	0.0354	2.1e-07;2.5e-07;1.7e-06;1.8e-07;6.8e-08	2.6e-10;8.9e-10;2.8e-09;4.7e-10;1.3e-10	0.029337196667874	TGC	S	.	497-501-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.969823826966684
CAMB-763EE	MN908947.3	22067	GA	TG	0.0255	0.0355	5.2e-08;3.9e-09	2.9e-10;1.2e-12	0.029940119760479	TGA	S	.	505-506-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.972054510953942
CAMB-763EE	MN908947.3	22070	TATGTCTCTCAGC	ATATGTCTCTCAG	0.0242307692307692	0.0349230769230769	4.2e-07;2e-07;8.6e-08;1.3e-07;5.8e-07;2.3e-07;8.1e-08;1.9e-07;3.2e-09;6.1e-08;2.1e-07;3.7e-09;2.9e-07	6.8e-10;2.1e-09;1.7e-09;6.9e-10;1.6e-09;3.2e-10;4e-11;2e-10;8e-13;4.7e-11;8.3e-10;1.1e-12;2.5e-10	0.030054167394723	ATA	S	.	508-520-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.971523668639053
CAMB-763EE	MN908947.3	22084	T	C	0.025	0.033	2.7e-09	3.2e-12	0.0287089871611983	CTT	S	P174P	T522C	CCT>CCC	Synonymous	GU280_gp02, spike glycoprotein	0.970221112696148
CAMB-763EE	MN908947.3	22088	CT	TC	0.0265	0.0355	1.5e-07;2.9e-08	1.3e-09;2.8e-10	0.0307782787688688	TCT	S	.	526-527-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.967177672955975
CAMB-763EE	MN908947.3	22091	ATG	TAT	0.0233333333333333	0.033	2.3e-07;1.4e-07;2e-07	1.1e-09;4.9e-10;1.2e-10	0.0293553338449731	TAT	S	.	529-531-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.974290099769762
CAMB-763EE	MN908947.3	22095	AC	GA	0.025	0.0355	2.3e-09;4.5e-07	9.1e-13;1.4e-09	0.0300284292821606	GAC	S	.	533-534-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.970159733192909
CAMB-763EE	MN908947.3	22098	T	C	0.028	0.036	1.1e-08	1.2e-10	0.0318376068376068	CTT	S	L179P	T536C	CTT>CCT	Missense	GU280_gp02, spike glycoprotein	0.967948717948718
CAMB-763EE	MN908947.3	22100	GA	TG	0.0255	0.0365	4e-08;3.7e-08	2.6e-10;1.4e-11	0.0300037979491075	TGA	S	.	538-539-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.974349964862966
CAMB-763EE	MN908947.3	22103	G	A	0.02	0.031	2.6e-08	1.8e-12	0.0251091703056769	AGG	S	G181R	G541A	GGA>AGA	Missense	GU280_gp02, spike glycoprotein	0.974890829694323
CAMB-763EE	MN908947.3	22105	A	G	0.026	0.037	1.8e-09	5.3e-13	0.0313479623824451	GAA	S	G181G	A543G	GGA>GGG	Synonymous	GU280_gp02, spike glycoprotein	0.968652037617555
CAMB-763EE	MN908947.3	22109	CAG	ACA	0.022	0.0303333333333333	1e-08;9.6e-08;5.2e-08	4.1e-10;2.3e-10;2e-11	0.0267153565250817	ACA	S	.	547-549-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.978089563713242
CAMB-763EE	MN908947.3	22113	GTA	TGT	0.023	0.0263333333333333	5.7e-08;6.6e-08;8e-08	NA;7.5e-11;2.6e-10	0.0287226001511716	GGT	S	.	551-553-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.992862241256246
CAMB-763EE	MN908947.3	22117	T	A	0.025	0.032	2.9e-08	4.6e-10	0.0283336635625124	ATT	S	N185K	T555A	AAT>AAA	Missense	GU280_gp02, spike glycoprotein	0.971666336437488
CAMB-763EE	MN908947.3	22120	CA	TC	0.026	0.0355	9.7e-08;2.7e-07	3.4e-10;2.8e-09	0.0302641232575202	TCA	S	.	558-559-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.968990825688073
CAMB-763EE	MN908947.3	22126	TCT	ATC	0.0233333333333333	0.034	7.2e-08;1.9e-07;7.7e-08	8.9e-11;8.1e-10;1.5e-11	0.028169014084507	ATC	S	.	564-566-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.974018794914317
CAMB-763EE	MN908947.3	22130	AG	TA	0.0245	0.0325	1.2e-06;8.4e-07	2.1e-08;1.8e-08	0.0282398452611219	TAG	S	.	568-569-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.970535890844374
CAMB-763EE	MN908947.3	22134	A	G	0.025	0.036	2.3e-07	3.1e-10	0.0302338847689675	GAA	S	E191G	A572G	GAA>GGA	Missense	GU280_gp02, spike glycoprotein	0.960448754516068
CAMB-763EE	MN908947.3	22136	T	A	0.016	0.023	1.3e-06	8.5e-09	0.0191427382438618	ATT	S	F192I	T574A	TTT>ATT	Missense	GU280_gp02, spike glycoprotein	0.980649188514357
CAMB-763EE	MN908947.3	22139	GTGT	TGTG	0.02375	0.03325	1.7e-06;1.7e-05;4.1e-07;5.5e-06	1.3e-08;2.7e-07;5.4e-09;5.3e-08	0.0278476464247215	TGT	S	.	577-580-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.97
CAMB-763EE	MN908947.3	22145	A	T	0.025	0.035	3.4e-06	4.1e-08	0.029839749493461	TAA	S	K195*	A583T	AAG>TAG	Nonsense	GU280_gp02, spike glycoprotein	0.970160250506539
CAMB-763EE	MN908947.3	22147	GA	AG	0.022	0.0295	1.5e-06;3e-07	2.5e-08;2.7e-09	0.025414156626506	AGA	S	.	585-586-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.976571216065452
CAMB-763EE	MN908947.3	22150	TAT	ATA	0.0223333333333333	0.0296666666666667	3e-05;2.4e-07;6.6e-06	8.4e-07;6.9e-10;9.5e-07	0.0256410256410256	ATA	S	.	588-590-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.97438105489774
CAMB-763EE	MN908947.3	22154	GATG	TGAT	0.022	0.02875	2.4e-06;4.2e-05;4.5e-05;4.1e-06	9.9e-08;9.2e-07;1.3e-05;4e-08	0.023567733282238	TGA	S	.	592-595-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.974990805443178
CAMB-763EE	MN908947.3	22157	G	T	0.013	0.018	4.1e-06	4e-08	0.0155402963498374	TGG	S	G199C	G595T	GGT>TGT	Missense	GU280_gp02, spike glycoprotein	0.984459703650163
CAMB-763EE	MN908947.3	22159	T	G	0.021	0.031	1.4e-05	2e-07	0.0257127864264474	GTT	S	G199G	T597G	GGT>GGG	Synonymous	GU280_gp02, spike glycoprotein	0.974112296659087
CAMB-763EE	MN908947.3	22161	AT	TA	0.0215	0.028	3.9e-05;2.2e-06	4.1e-06;4.1e-08	0.0243346007604563	TAT	S	.	599-600-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.973638637675582
CAMB-763EE	MN908947.3	22166	A	T	0.01	0.029	0.0036	6.9e-06	0.0192857142857143	TAA	S	K202*	A604T	AAA>TAA	Nonsense	GU280_gp02, spike glycoprotein	0.980714285714286
CAMB-763EE	MN908947.3	22170	T	A	0.011	0.015	3e-05	1.4e-06	0.0127245508982036	ATA	S	I203K	T608A	ATA>AAA	Missense	GU280_gp02, spike glycoprotein	0.987275449101796
CAMB-763EE	MN908947.3	22170	TATA	ATAT	0.01125	0.01675	3e-05;0.00016;0.00072;0.00016	1.4e-06;7.9e-06;4.1e-05;8e-06	0.0144292237442922	ATA	S	.	608-611-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.987275449101796
CAMB-763EE	MN908947.3	22177	TA	CT	0.0101	0.0155	0.00012;0.00055	2.4e-06;4.2e-05	0.0126430890141808	CTA	S	.	615-616-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.988293179504581
CAMB-763EE	MN908947.3	22180	G	A	0.0089	0.014	0.00045	2e-05	0.0114285714285714	AGC	S	K206K	G618A	AAG>AAA	Synonymous	GU280_gp02, spike glycoprotein	0.988571428571429
CAMB-763EE	MN908947.3	22860	TTATAGCTTGGA	-	0.0113833333333333	0.00601666666666667	0.00075;0.00084;1.2e-06;0.00013;0.00013;0.00011;0.00014;0.00011;9.4e-05;6.8e-05;9.9e-05;6.4e-05	0.0077;0.0089;0.03;0.0024;0.0026;0.0024;0.0029;0.0025;0.0021;0.0019;0.0021;0.0017	0.00735383052323472	GTT	S	.	1298-1309-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.992337069735145
CAMB-763EE	MN908947.3	23403	A	G	1	1	0	0	0.999876784696659	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000107813390423091
CAMB-763EE	MN908947.3	241	C	T	1	1	0	0	0.999837894793721	TCG	NA	NA	NA	NA	NA	NA	8.10526031394375e-05
CAMB-763EE	MN908947.3	2416	C	T	0.99	1	0	0	0.995855913292955	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0.000318775900541919
CAMB-763EE	MN908947.3	2470	C	T	0.011	0.045	2.5e-06	4.6e-18	0.0254574383452665	CCC	ORF1ab:nsp2	A555A	C1665T	GCC>GCT	Synonymous	ORF1ab:nsp2	0.974277380005304
CAMB-763EE	MN908947.3	25433	C	T	0.034	0.0088	1.8e-16	5e-06	0.0232684966369751	ACT	ORF3a	T14I	C41T	ACT>ATT	Missense	GU280_gp03	0.954553717505908
CAMB-763EE	MN908947.3	25460	C	T	1	1	0	0	0.999539891414374	GCT	ORF3a	A23V	C68T	GCT>GTT	Missense	GU280_gp03	0.000299070580657035
CAMB-763EE	MN908947.3	25563	G	T	1	1	0	0	0.999859343132428	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	9.37712450477061e-05
CAMB-763EE	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0572631578947368	0.0477105263157895	1.2e-07;1.4e-10;1.4e-10;1.6e-10;9.9e-10;8.1e-13;8.5e-12;3.4e-10;3.2e-10;1.2e-11;1.5e-10;7.2e-11;2.8e-10;1.8e-10;2.2e-10;5e-10;1.2e-10;4.3e-10;1.5e-10;2.1e-10;2.5e-10;5.3e-10;1.9e-10;3e-10;1.9e-10;9.6e-11;3.8e-10;1.2e-10;2.7e-10;2.1e-10;3.8e-10;2.9e-10;1.6e-10;3.6e-10;1.9e-11;1.1e-10;6.2e-11;0.00067	2e-05;1.2e-06;1.3e-05;1.3e-05;3.1e-05;6.3e-11;4.8e-10;1.1e-08;1.1e-08;5.4e-09;5e-09;3.5e-09;1.2e-08;6.8e-09;7.4e-09;1.6e-08;4.3e-09;1.4e-08;8.1e-09;7.3e-09;8.3e-09;1.6e-08;5.1e-09;1.1e-08;7.5e-09;3.3e-09;1.3e-08;7.5e-09;1.5e-08;4.4e-09;1.3e-08;6.4e-09;1.7e-09;9e-09;1.7e-09;7.4e-09;3e-09;0.0053	0.0536999280402974	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.96432859115193
CAMB-763EE	MN908947.3	27382	GAT	CTC	0.0286	0.0103583333333333	4.9e-18;8.6e-19;5.3e-06	9.1e-09;4e-09;NA	0.0296847325540205	TGA	ORF6	.	181-183-mnv	.	no-SNV	GU280_gp06	0.970207743153919
CAMB-763EE	MN908947.3	27919	T	C	0.02	0.031	1.1e-09	1.7e-13	0.0257656781720953	ATC	ORF8	I9T	T26C	ATC>ACC	Missense	GU280_gp09	0.974234321827905
CAMB-763EE	MN908947.3	28523	A	G	0.015	0.0045	1.4e-08	0.00028	0.0101729925122644	AAT	N	I84V	A250G	ATT>GTT	Missense	GU280_gp10	0.989775367931836
CAMB-763EE	MN908947.3	28711	T	A	0.026	0.017	3.1e-13	2.8e-09	0.0214074957624459	TTG	N	I146I	T438A	ATT>ATA	Synonymous	GU280_gp10	0.978404168497709
CAMB-763EE	MN908947.3	29068	TAAAGCATACAATG	-	0.0247142857142857	0.00972142857142857	2.1e-05;5e-05;2.8e-06;2.3e-06;2e-06;2.7e-06;2.7e-06;1e-05;3.6e-06;2.1e-06;2.3e-06;4.6e-07;2.1e-06;2.3e-06	0.0046;0.0062;0.0054;0.0053;0.0054;0.0055;0.0056;0.01;0.0082;0.0076;0.0081;0.0042;0.0085;0.0075	0.0189587721938008	CTA	N	.	795-808-delfrshift	.	no-SNV	GU280_gp10	0.990237308501051
CAMB-763EE	MN908947.3	29750	C	T	0.014	0.011	3.3e-06	2.3e-05	0.0123111359820929	ACG	NA	NA	NA	NA	NA	NA	0.983771684387241
CAMB-763EE	MN908947.3	3037	C	T	1	0.99	0	0	0.993251363594342	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-763EE	MN908947.3	522	T	-	0.11	0.052	2.5e-14	5.7e-07	0.0870352949374586	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.912929863070973
CAMB-763EE	MN908947.3	522	TT	-	0.0985	0.0385	2.5e-14;6.8e-13	5.7e-07;0.0011	0.0752046384720327	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.912929863070973
CAMB-763EE	MN908947.3	5382	AAGCTGCTAACTTTTGTGCACTTATCTT	-	0.00125357142857143	0.016	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;1.2e-11;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	1.2e-07;5.4e-08;4.3e-07;6e-07;8.7e-07;6.6e-07;2.4e-07;1.7e-07;1e-07;4.6e-07;4.4e-07;8.7e-07;2.4e-07;1.3e-07;2.1e-07;3.9e-07;2.5e-07;4e-07;1.8e-07;1.2e-07;1.5e-07;7.7e-08;6e-08;7.2e-08;6.4e-08;8e-08;7.2e-08;2.6e-07	0.00934579439252336	GAA	ORF1ab:nsp3	.	2663-2690-delfrshift	.	no-SNV	ORF1ab:nsp3	0.990783410138249
CAMB-763EE	MN908947.3	7918	A	C	0.028	0.11	7.9e-13	4.3e-36	0.0396674172873722	AAT	ORF1ab:nsp3	E1733D	A5199C	GAA>GAC	Missense	ORF1ab:nsp3	0.960332582712628
CAMB-763EE	MN908947.3	8482	T	C	0.029	0.014	5.5e-11	1.1e-05	0.0208471944998891	CTT	ORF1ab:nsp3	P1921P	T5763C	CCT>CCC	Synonymous	ORF1ab:nsp3	0.979152805500111
CAMB-763FD	MN908947.3	10097	G	A	0.95	1	0	0	0.971352294896807	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.0285450251565869
CAMB-763FD	MN908947.3	10198	C	A	1	0.52	0	1.6e-146	0.723785166240409	ACA	ORF1ab:3C-like-proteinase	D48E	C144A	GAC>GAA	Missense	ORF1ab:3C-like-proteinase	0.276214833759591
CAMB-763FD	MN908947.3	11075	T	-	0.02	0.087	5.6e-06	5.5e-22	0.0456676729398163	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.94900122037382
CAMB-763FD	MN908947.3	13536	C	T	1	1	0	0	1	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-763FD	MN908947.3	14184	C	T	1	1	0	0	0.999916208138983	CCA	ORF1ab:RNA-dependent-RNA-polymerase	T239T	C717T	ACC>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	5.58612406781555e-05
CAMB-763FD	MN908947.3	14408	C	T	0.99	1	0	0	0.993631436314363	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00636856368563686
CAMB-763FD	MN908947.3	15540	C	T	0.0084	0.0057	1.8e-05	0.00029	0.00749994549458216	TCA	ORF1ab:RNA-dependent-RNA-polymerase	V691V	C2073T	GTC>GTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.992391043669741
CAMB-763FD	MN908947.3	1684	C	T	0.99	1	0	0	0.992928660826033	TCG	ORF1ab:nsp2	I293I	C879T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.00707133917396746
CAMB-763FD	MN908947.3	17167	C	T	0.028	0.025	8.9e-14	1.8e-12	0.0267095854731307	TCA	ORF1ab:helicase	H311Y	C931T	CAT>TAT	Missense	ORF1ab:helicase	0.973290414526869
CAMB-763FD	MN908947.3	18684	ATGCTTTTCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTT	-	0.000218605263157895	0.0216052631578947	NA;NA;NA;NA;0.47;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.5;NA;0.0022;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	4.1e-08;2.3e-11;1.6e-07;1.7e-07;3.5e-10;2.1e-11;2.9e-11;4.5e-11;3e-11;2.2e-11;3e-11;3.6e-11;2.5e-11;2.9e-11;7.1e-12;3e-11;3.8e-11;3.8e-11;2.4e-11;2.9e-11;2.7e-11;4.4e-11;2e-11;3.9e-11;1.8e-11;2.5e-11;1.9e-11;2.9e-11;1.5e-11;2.2e-11;3.6e-11;2.4e-11;4.3e-11;1.8e-11;3.6e-11;3.2e-11;2.5e-11;4.1e-11;2.4e-11;2.3e-11;3.3e-11;7.9e-12;3.3e-13;9.9e-12;1.3e-11;2.9e-12;5.4e-13;2.2e-12;2e-11;2.1e-11;1.8e-11;1.6e-11;2.3e-12;4.4e-10;9.7e-10;1.7e-07;0.00024;4.8e-05;0.00025;0.00033;9.1e-05;0.00017;9.1e-05;9.5e-05;3.6e-05;2.8e-05;2.1e-08;2.9e-10;9.6e-12;1.7e-11;1.9e-11;5.4e-12;1.6e-11;4.2e-11;1.1e-11;2.8e-11	0.0072851473810981	CAT	ORF1ab:3'-to-5'-exonuclease	.	645-720-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.992668966598714
CAMB-763FD	MN908947.3	19752	AAAT	-	0.0035	0.013	NA;NA;NA;7.9e-08	1.7e-07;1e-07;2e-07;3.4e-07	0.00509943906170321	AAA	ORF1ab:endoRNAse	.	132-135-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.994943536153716
CAMB-763FD	MN908947.3	19755	T	-	0.014	0.013	7.9e-08	3.4e-07	0.0135731252120801	ATA	ORF1ab:endoRNAse	.	135-135-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.98642687478792
CAMB-763FD	MN908947.3	21058	C	T	1	1	0	0	0.999917379270459	CCC	ORF1ab:2'-O-ribose-methyltransferase	P134S	C400T	CCT>TCT	Missense	ORF1ab:2'-O-ribose-methyltransferase	8.26207295410419e-05
CAMB-763FD	MN908947.3	21962	C	T	0.043	0.012	2.7e-19	5.4e-07	0.0304787592717465	TCA	S	Q134*	C400T	CAA>TAA	Nonsense	GU280_gp02, spike glycoprotein	0.969521240728254
CAMB-763FD	MN908947.3	22573	T	C	0.031	0.038	2.1e-12	9e-15	0.0333424682561432	CTT	S	P337P	T1011C	CCT>CCC	Synonymous	GU280_gp02, spike glycoprotein	0.96546999177857
CAMB-763FD	MN908947.3	23403	A	G	1	1	0	0	0.999913724678193	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.90202574455603e-05
CAMB-763FD	MN908947.3	23731	C	T	0.98	0.97	0	0	0.978464801370422	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.0215351986295783
CAMB-763FD	MN908947.3	241	C	T	1	1	0	0	0.999841425898322	TCG	NA	NA	NA	NA	NA	NA	0.000126859281342171
CAMB-763FD	MN908947.3	24707	C	T	0.04	0.014	5.4e-15	4.3e-06	0.0296864576384256	TCT	S	L1049F	C3145T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.970313542361574
CAMB-763FD	MN908947.3	28253	C	T	0.059	0.051	2.9e-26	7.1e-23	0.0561136262070841	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.943692074533196
CAMB-763FD	MN908947.3	28435	C	T	0.027	0.015	2.5e-13	2.5e-08	0.0226990096339691	CCG	N	T54T	C162T	ACC>ACT	Synonymous	GU280_gp10	0.977271024676745
CAMB-763FD	MN908947.3	28881	GGG	AAC	0.986666666666667	0.99	0;0;0	0;0;0	0.992785793562708	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00776143790849673
CAMB-763FD	MN908947.3	29585	C	T	0.58	0.51	1.2e-251	1e-176	0.556513409961686	TCC	ORF10	P10S	C28T	CCG>TCG	Missense	GU280_gp11	0.443486590038314
CAMB-763FD	MN908947.3	29627	C	T	0.0052	0.022	0.001	1.4e-08	0.0114285714285714	TCG	ORF10	R24C	C70T	CGT>TGT	Missense	GU280_gp11	0.988571428571429
CAMB-763FD	MN908947.3	3037	C	T	1	1	0	0	0.999156402901974	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-763FD	MN908947.3	4002	C	T	0.95	1	0	0	0.963508941517641	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0.0364910584823586
CAMB-763FD	MN908947.3	635	C	T	0.7	0.5	0	5.8e-270	0.63765026083012	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.36234973916988
CAMB-763FD	MN908947.3	683	C	T	0.018	0.018	1.1e-09	1.1e-09	0.0182365221662778	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.981722542879365
CAMB-763FD	MN908947.3	9724	C	T	0.013	0.0095	7.4e-08	3.4e-06	0.011980563002681	TCT	ORF1ab:nsp4	F390F	C1170T	TTC>TTT	Synonymous	ORF1ab:nsp4	0.988019436997319
CAMB-76409	MN908947.3	11075	T	-	0.026	0.041	6.5e-07	2.1e-10	0.03256117607284	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964396050223253
CAMB-76409	MN908947.3	11379	C	T	0.39	0.4	4.3e-189	3.7e-200	0.393709412409045	GCT	ORF1ab:nsp6	A136V	C407T	GCT>GTT	Missense	ORF1ab:nsp6	0.606290587590955
CAMB-76409	MN908947.3	1170	C	T	0.36	0.34	1.3e-185	3e-172	0.353981238874332	TCT	ORF1ab:nsp2	S122F	C365T	TCT>TTT	Missense	ORF1ab:nsp2	0.64593875632538
CAMB-76409	MN908947.3	14408	C	T	1	1	0	0	0.999769668178219	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000129561649751674
CAMB-76409	MN908947.3	23403	A	G	1	1	0	0	0.999612829850818	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.25944029715309e-05
CAMB-76409	MN908947.3	241	C	T	1	1	0	0	0.999009410599307	TCG	NA	NA	NA	NA	NA	NA	0.000136206042595344
CAMB-76409	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999737704918033	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.85578323783626e-05
CAMB-76409	MN908947.3	3037	C	T	1	1	0	0	0.999862580733819	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76418	MN908947.3	10097	G	A	1	1	0	0	1	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0
CAMB-76418	MN908947.3	10979	G	A	0.42	0.47	2.2e-173	1.5e-143	0.42921146953405	AGT	ORF1ab:nsp6	V3M	G7A	GTG>ATG	Missense	ORF1ab:nsp6	0.57078853046595
CAMB-76418	MN908947.3	1099	T	C	1	1	0	0	0.999953406019942	ATT	ORF1ab:nsp2	N98N	T294C	AAT>AAC	Synonymous	ORF1ab:nsp2	4.65939800577765e-05
CAMB-76418	MN908947.3	11075	T	-	0.058	0.048	1.2e-14	9.6e-13	0.0546755577217041	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.945147211945324
CAMB-76418	MN908947.3	12377	A	-	0.078	0.029	3.4e-35	4e-14	0.0569439071566731	TAG	ORF1ab:nsp8	.	286-286-delfrshift	.	no-SNV	ORF1ab:nsp8	0.943056092843327
CAMB-76418	MN908947.3	12377	AG	-	0.0785	0.0145	3.4e-35;9.5e-35	4e-14;NA	0.0507201486758557	TAG	ORF1ab:nsp8	.	286-287-delfrshift	.	no-SNV	ORF1ab:nsp8	0.943056092843327
CAMB-76418	MN908947.3	13536	C	T	1	1	0	0	1	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-76418	MN908947.3	14408	C	T	1	1	0	0	0.999583293265378	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000320543642016861
CAMB-76418	MN908947.3	18457	C	T	0.33	0.23	1.2e-170	3.8e-109	0.289020161808142	ACC	ORF1ab:3'-to-5'-exonuclease	P140S	C418T	CCA>TCA	Missense	ORF1ab:3'-to-5'-exonuclease	0.707717991524335
CAMB-76418	MN908947.3	19032	C	T	0.0018	0.073	0.0096	1.6e-33	0.0306709037026458	ACA	ORF1ab:3'-to-5'-exonuclease	D331D	C993T	GAC>GAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.969329096297354
CAMB-76418	MN908947.3	23403	A	G	1	1	0	0	0.999853795825871	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.31020870645857e-05
CAMB-76418	MN908947.3	23731	C	T	1	1	0	0	0.999836734693878	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000163265306122449
CAMB-76418	MN908947.3	241	C	T	1	1	0	0	0.999923783392401	TCG	NA	NA	NA	NA	NA	NA	7.62166075987958e-05
CAMB-76418	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999735799207398	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-76418	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76418	MN908947.3	4002	C	T	1	1	0	0	0.999481462276381	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-76418	MN908947.3	6592	A	G	0.17	0.14	2.9e-51	1.5e-51	0.146750524109015	AAC	ORF1ab:nsp3	K1291K	A3873G	AAA>AAG	Synonymous	ORF1ab:nsp3	0.853249475890985
CAMB-76418	MN908947.3	8733	C	T	0.034	0.026	1e-13	9.9e-12	0.0287134180011044	ACA	ORF1ab:nsp4	T60I	C179T	ACA>ATA	Missense	ORF1ab:nsp4	0.971010491441193
CAMB-76427	MN908947.3	11074	C	INS	0.025	0.025	3.7e-05	5.9e-05	0.0252585521081941	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.974258438458916
CAMB-76427	MN908947.3	11075	T	-	0.04	0.035	5.8e-10	3.7e-09	0.0375031430726678	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958926326376666
CAMB-76427	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999341755132909	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000126046889442873
CAMB-76427	MN908947.3	19951	C	T	1	1	0	0	0.999368886083938	ACC	ORF1ab:endoRNAse	P111S	C331T	CCA>TCA	Missense	ORF1ab:endoRNAse	0.000631113916061849
CAMB-76427	MN908947.3	20915	G	A	1	1	0	0	0.999751977975644	AGA	ORF1ab:2'-O-ribose-methyltransferase	R86K	G257A	AGA>AAA	Missense	ORF1ab:2'-O-ribose-methyltransferase	2.48022024355763e-05
CAMB-76427	MN908947.3	24454	A	G	0.0077	0.008	3e-05	1.8e-05	0.00783180026281209	AAC	S	K964K	A2892G	AAA>AAG	Synonymous	GU280_gp02, spike glycoprotein	0.991852825229961
CAMB-76427	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.028	0.02803125	0.00023;0.00057;0.00016;0.00016;2.8e-05;0.00012;1e-04;0.00015;0.00012;0.00014;0.00019;0.00011;0.00018;1e-04;0.00013;0.00016;2e-04;0.00013;0.00014;0.00012;9e-05;0.00018;9.9e-05;0.00012;0.00012;0.00017;0.00015;0.00012;2e-04;7.4e-05;0.00012;7.1e-05	0.00016;0.00035;0.00016;0.00016;8.8e-05;0.00011;1e-04;0.00015;0.00011;0.00011;0.00018;8.1e-05;0.00016;0.00012;0.00011;0.00012;0.00018;0.00011;0.00014;0.00012;8.6e-05;0.00016;0.00011;3.4e-05;0.00011;0.00016;0.00016;9.7e-05;0.00016;6.6e-05;0.00012;9.8e-05	0.0278359705816804	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.972562834496308
CAMB-76427	MN908947.3	27467	G	T	0.03	0.03	5.6e-15	1.2e-15	0.0303256173478543	AGA	ORF7a	R25I	G74T	AGA>ATA	Missense	GU280_gp07	0.968873797396718
CAMB-76427	MN908947.3	28188	G	T	0.012	0.011	3.9e-07	8.7e-07	0.01121327375897	TGT	ORF8	V99L	G295T	GTA>TTA	Missense	GU280_gp09	0.98872518247726
CAMB-76427	MN908947.3	4158	C	T	0.0058	0.0077	0.00022	3e-05	0.0066899946622383	GCT	ORF1ab:nsp3	A480V	C1439T	GCT>GTT	Missense	ORF1ab:nsp3	0.992645750548603
CAMB-76427	MN908947.3	6968	C	T	0.0061	0.01	0.00041	1.3e-05	0.00858860578299456	ACT	ORF1ab:nsp3	L1417L	C4249T	CTA>TTA	Synonymous	ORF1ab:nsp3	0.991411394217005
CAMB-76427	MN908947.3	7936	G	T	1	1	0	0	0.999516479974212	CGT	ORF1ab:nsp3	A1739A	G5217T	GCG>GCT	Synonymous	ORF1ab:nsp3	0
CAMB-76445	MN908947.3	10570	T	C	0.019	0.0025	7.4e-10	0.0059	0.0125	ATG	ORF1ab:3C-like-proteinase	H172H	T516C	CAT>CAC	Synonymous	ORF1ab:3C-like-proteinase	0.9875
CAMB-76445	MN908947.3	1059	C	T	1	1	0	0	0.999955253266512	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0
CAMB-76445	MN908947.3	11083	G	T	0.035	0.029	1.1e-07	1.7e-06	0.0318504190844616	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.966967547818612
CAMB-76445	MN908947.3	11396	C	T	0.017	0.012	6.3e-08	1.7e-06	0.0142366224840452	ACT	ORF1ab:nsp6	L142F	C424T	CTT>TTT	Missense	ORF1ab:nsp6	0.985763377515955
CAMB-76445	MN908947.3	13006	T	C	1	1	0	0	0.999483713507932	CTG	ORF1ab:nsp9	A107A	T321C	GCT>GCC	Synonymous	ORF1ab:nsp9	0.000445883788604149
CAMB-76445	MN908947.3	13914	T	G	0.0059	0.0033	2.9e-05	0.00042	0.00483017118126666	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.995092546079833
CAMB-76445	MN908947.3	1437	C	T	1	1	0	0	1	TCT	ORF1ab:nsp2	S211F	C632T	TCT>TTT	Missense	ORF1ab:nsp2	0
CAMB-76445	MN908947.3	14408	C	T	1	1	0	0	0.999554069119286	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000297287253808993
CAMB-76445	MN908947.3	1549	C	T	0.014	0.0052	5.9e-06	0.0019	0.00926585887384177	GCG	ORF1ab:nsp2	S248S	C744T	AGC>AGT	Synonymous	ORF1ab:nsp2	0.990734141126158
CAMB-76445	MN908947.3	16161	T	C	0.011	0.011	4.1e-07	6.8e-07	0.0106667265500438	TTA	ORF1ab:RNA-dependent-RNA-polymerase	L898L	T2694C	CTT>CTC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.989310817183535
CAMB-76445	MN908947.3	21078	A	-	0.019	0.016	2.3e-09	7.7e-08	0.0173881449185093	CAA	ORF1ab:2'-O-ribose-methyltransferase	.	420-420-delfrshift	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.982404235440673
CAMB-76445	MN908947.3	23403	A	G	1	1	0	0	0.999916833000665	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.99001996007984e-05
CAMB-76445	MN908947.3	241	C	T	1	1	0	0	0.999875828842476	TCG	NA	NA	NA	NA	NA	NA	2.48342315047061e-05
CAMB-76445	MN908947.3	25563	G	T	1	1	0	0	0.99984544845706	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	7.72757714697852e-05
CAMB-76445	MN908947.3	25688	C	T	1	1	0	0	0.99977421539851	GCT	ORF3a	A99V	C296T	GCT>GTT	Missense	GU280_gp03	0.000225784601490178
CAMB-76445	MN908947.3	25994	TT	-	0.04	0.00655	3.8e-10;1.4e-09	0.00084;0.0023	0.0216216216216216	GTT	ORF3a	.	602-603-delfrshift	.	no-SNV	GU280_gp03	0.977443609022556
CAMB-76445	MN908947.3	26520	G	A	0.013	0.014	8.5e-08	2.5e-08	0.0132218715345901	AGC	NA	NA	NA	NA	NA	NA	0.98677812846541
CAMB-76445	MN908947.3	29744	G	A	0.0048	0.02	0.00063	1.2e-09	0.0121225983531565	CGG	NA	NA	NA	NA	NA	NA	0.986276303751144
CAMB-76445	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76445	MN908947.3	9491	C	T	0.013	0.014	5.5e-07	1.9e-07	0.0134091240343973	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.986590875965603
CAMB-76454	MN908947.3	10505	A	T	0.0039	0.0088	0.00054	5.3e-06	0.00599581015675793	TAA	ORF1ab:3C-like-proteinase	N151Y	A451T	AAC>TAC	Missense	ORF1ab:3C-like-proteinase	0.991475836162682
CAMB-76454	MN908947.3	11075	T	-	0.047	0.035	1e-11	4.5e-09	0.0416951553037703	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955630982613792
CAMB-76454	MN908947.3	14408	C	T	1	1	0	0	0.996773567512493	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000218330017951579
CAMB-76454	MN908947.3	14741	C	T	0.99	1	0	0	0.995798487455484	TCT	ORF1ab:RNA-dependent-RNA-polymerase	S425F	C1274T	TCT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00233417363584224
CAMB-76454	MN908947.3	187	A	G	1	1	0	0	0.999864642753553	CAG	NA	NA	NA	NA	NA	NA	9.66837474620516e-05
CAMB-76454	MN908947.3	23403	A	G	1	1	0	0	0.998885496923002	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000116295973251926
CAMB-76454	MN908947.3	241	C	T	1	1	0	0	0.998926099753401	TCG	NA	NA	NA	NA	NA	NA	5.96611248110731e-05
CAMB-76454	MN908947.3	25473	T	C	0.0089	0.011	5.7e-06	7.1e-07	0.00974709858612002	ATT	ORF3a	D27D	T81C	GAT>GAC	Synonymous	GU280_gp03	0.989908724203918
CAMB-76454	MN908947.3	27222	T	C	0.01	0.019	1.8e-06	2e-10	0.0140678411780174	TTC	ORF6	F7F	T21C	TTT>TTC	Synonymous	GU280_gp06	0.985230958015602
CAMB-76454	MN908947.3	27881	C	T	0.63	0.64	0	0	0.634193862640039	ACG	NA	NA	NA	NA	NA	NA	0.365611300535801
CAMB-76454	MN908947.3	29659	C	T	0.0063	0.0091	9.5e-05	6.8e-06	0.00765400906591365	ACT	ORF10	N34N	C102T	AAC>AAT	Synonymous	GU280_gp11	0.992197369398826
CAMB-76454	MN908947.3	3037	C	T	1	1	0	0	0.999710348822775	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76454	MN908947.3	5650	A	G	1	1	0	0	0.99909200968523	AAT	ORF1ab:nsp3	K977K	A2931G	AAA>AAG	Synonymous	ORF1ab:nsp3	0.000467752586396654
CAMB-76463	MN908947.3	11074	C	INS	0.028	0.025	3.6e-06	6e-05	0.0268335620162063	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.971380122712093
CAMB-76463	MN908947.3	11075	T	-	0.033	0.034	2.3e-08	4.5e-09	0.0335162186359358	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962799292945525
CAMB-76463	MN908947.3	11083	G	-	0.021	0.021	5.1e-09	6e-09	0.0208752600880035	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.887437323054883
CAMB-76463	MN908947.3	11083	G	T	0.091	0.092	1.7e-19	4.8e-20	0.0915964571181681	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.887437323054883
CAMB-76463	MN908947.3	13019	C	T	1	1	0	0	0.998797802565702	TCT	ORF1ab:nsp9	L112L	C334T	CTA>TTA	Synonymous	ORF1ab:nsp9	0.000989149787713238
CAMB-76463	MN908947.3	14408	C	T	1	1	0	0	0.997097625329815	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000823218997361478
CAMB-76463	MN908947.3	20268	A	G	1	1	0	0	0.999261992619926	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-76463	MN908947.3	23403	A	G	1	1	0	0	0.998210766021777	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00018179382666437
CAMB-76463	MN908947.3	24023	C	T	0.012	0.012	7.7e-07	9.1e-07	0.0119169434692946	TCT	S	L821L	C2461T	CTA>TTA	Synonymous	GU280_gp02, spike glycoprotein	0.983927081529525
CAMB-76463	MN908947.3	241	C	T	1	1	0	0	0.998709457023021	TCG	NA	NA	NA	NA	NA	NA	0.00022774287829041
CAMB-76463	MN908947.3	26499	C	T	0.0083	0.0098	1.6e-05	2.6e-06	0.00885231230179575	TCT	NA	NA	NA	NA	NA	NA	0.990894764489581
CAMB-76463	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0326216216216216	0.0355405405405405	7e-04;2.8e-05;0.00035;0.00041;0.00081;2.9e-05;6.3e-05;1.9e-05;1.8e-05;2.2e-06;1.3e-05;1.1e-05;1.5e-05;1.4e-05;1.5e-05;2.3e-05;1.1e-05;2.2e-05;9.8e-06;1.5e-05;1.2e-05;2.5e-05;1.3e-05;1.8e-05;1.4e-05;9.9e-06;2e-05;1.1e-05;3.6e-06;1.6e-05;2.1e-05;1.8e-05;1.2e-05;2e-05;4.3e-06;1e-05;8.6e-06	0.00045;5.6e-05;0.00014;0.00014;0.00026;6.5e-06;2.5e-05;3.5e-06;3.6e-06;1.9e-06;2.1e-06;1.7e-06;3.4e-06;2.6e-06;2.4e-06;3.8e-06;2e-06;3.6e-06;2.6e-06;2.4e-06;2e-06;4.4e-06;2.4e-06;3.1e-06;2.4e-06;1.6e-06;3.6e-06;2.3e-06;2.1e-06;2.3e-06;3.5e-06;3.7e-06;1.6e-06;3.3e-06;1e-06;2.6e-06;1.5e-06	0.0350247958723639	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.977216433850443
CAMB-76463	MN908947.3	27673	CAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAG	-	0.010974358974359	0.0115128205128205	3.8e-05;2.6e-05;3e-05;2.5e-05;6.4e-05;5.4e-05;1.6e-05;5.1e-05;0.00046;3.2e-05;0.00036;0.00088;0.00013;0.00015;7.4e-05;2.7e-05;0.00015;2.8e-05;2e-04;2.9e-05;3.2e-05;1.7e-05;2.7e-05;4.6e-05;3.4e-05;6.7e-05;4.8e-05;3.5e-05;1.8e-05;3.5e-05;4.4e-05;2e-05;2.3e-05;3.5e-05;3.8e-05;2.6e-05;1.8e-05;1.8e-05;2.9e-05;2.7e-05;3.1e-06;1.5e-05;4.5e-05;4.8e-05;3.1e-05;4.9e-05;3.9e-05;1.1e-05;1.3e-05;3.4e-05;3.1e-05;3.1e-05;3.9e-05;3.1e-05;1.8e-05;3.7e-05;1.2e-05;3.6e-05;1.4e-05;1.9e-05;3.4e-05;3.2e-05;3.4e-05;4.1e-05;3.7e-05;3.9e-05;3.4e-05;3.3e-05;3.1e-05;1e-04;3.7e-05;2.6e-05;3.6e-05;3.4e-05;3.2e-05;3e-05;3.7e-06;3.4e-05	8.1e-05;8.2e-05;0.00015;0.00014;0.00012;0.00011;7.8e-05;3e-04;0.00051;0.00018;0.00089;0.0012;5e-04;0.00042;0.00035;0.00022;0.00048;0.00023;7e-04;6e-04;0.00057;0.00046;0.00062;0.00083;0.00081;0.00064;0.00062;0.00062;0.00024;3e-04;0.00038;0.00022;0.00019;0.00026;0.00026;0.00021;2e-04;0.00022;0.00025;2e-04;0.00013;0.00023;0.00033;0.00033;0.00024;0.00054;0.00028;0.00041;0.00046;0.00024;0.00025;0.00022;0.00026;0.00022;2e-04;0.00024;0.00015;0.00022;0.00017;2e-04;0.00022;0.00023;0.00023;0.00025;0.00026;0.00024;0.00021;0.00023;0.00022;0.00079;0.00025;0.00019;0.00022;0.00027;0.00023;0.00019;0.00014;0.00021	0.0108303249097473	TCA	ORF7a	.	280-357-delinframe	.	no-SNV	GU280_gp07	0.988333333333333
CAMB-76463	MN908947.3	29108	C	T	1	1	0	0	0.999713067716019	TCC	N	P279S	C835T	CCA>TCA	Missense	GU280_gp10	9.56440946603268e-05
CAMB-76463	MN908947.3	29734	G	C	1	1	0	0	0.996337281795511	CGA	NA	NA	NA	NA	NA	NA	0
CAMB-76463	MN908947.3	3037	C	T	1	1	0	0	0.999029884933574	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.08429222021612e-05
CAMB-76463	MN908947.3	4622	G	A	0.0084	0.0077	9.6e-06	2.1e-05	0.00804666294492463	TGT	ORF1ab:nsp3	V635I	G1903A	GTA>ATA	Missense	ORF1ab:nsp3	0.991741582767051
CAMB-76463	MN908947.3	6308	A	INS	0.026	0.028	4.9e-15	8e-16	0.0270926000808734	GAG	ORF1ab:nsp3	.	3588-3589-insfrshift	.	no-SNV	ORF1ab:nsp3	0.97250303275374
CAMB-76463	MN908947.3	8025	C	T	1	1	0	0	0.999908893165849	GCA	ORF1ab:nsp3	A1769V	C5306T	GCA>GTA	Missense	ORF1ab:nsp3	5.6941771344623e-05
CAMB-76463	MN908947.3	9050	C	T	0.023	0.019	3.7e-11	7.8e-10	0.0210070139408601	GCC	ORF1ab:nsp4	P166S	C496T	CCA>TCA	Missense	ORF1ab:nsp4	0.978958177419636
CAMB-76472	MN908947.3	11075	T	-	0.069	0.056	1e-16	1.8e-14	0.0641751346927641	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.931289640591966
CAMB-76472	MN908947.3	13393	GA	AG	0.017	0.013	1.4e-06;9.7e-11	NA;4.1e-11	0.0152857775808595	GGA	ORF1ab:nsp10	.	369-370-mnv	.	no-SNV	ORF1ab:nsp10	0.993109579906646
CAMB-76472	MN908947.3	13394	A	G	0.023	0.026	9.7e-11	4.1e-11	0.0238463236917642	GAA	ORF1ab:nsp10	K124E	A370G	AAA>GAA	Missense	ORF1ab:nsp10	0.975712077721351
CAMB-76472	MN908947.3	14408	C	T	1	0.98	0	0	0.99367481786864	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00039532388321003
CAMB-76472	MN908947.3	17167	C	T	0.0094	0.031	9.7e-06	6.4e-15	0.0190681824094066	TCA	ORF1ab:helicase	H311Y	C931T	CAT>TAT	Missense	ORF1ab:helicase	0.980853775916339
CAMB-76472	MN908947.3	17766	C	T	0.015	0.027	1.2e-08	1.3e-13	0.0194326435521447	TCT	ORF1ab:helicase	V510V	C1530T	GTC>GTT	Synonymous	ORF1ab:helicase	0.980567356447855
CAMB-76472	MN908947.3	18554	A	-	0.034	0.028	3.3e-16	6.7e-14	0.0308371980570147	GAC	ORF1ab:3'-to-5'-exonuclease	.	515-515-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.96885508934655
CAMB-76472	MN908947.3	18554	AC	-	0.0170225	0.028	3.3e-16;NA	6.7e-14;6.7e-14	0.0226021060051989	GAC	ORF1ab:3'-to-5'-exonuclease	.	515-516-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.96885508934655
CAMB-76472	MN908947.3	23403	A	G	1	1	0	0	0.99990622985407	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.20488776885659e-05
CAMB-76472	MN908947.3	241	C	T	1	1	0	0	0.999766211753704	TCG	NA	NA	NA	NA	NA	NA	8.76705923609691e-05
CAMB-76472	MN908947.3	2455	C	T	0.41	0.18	7.6e-164	3.3e-49	0.344320486815416	TCA	ORF1ab:nsp2	L550L	C1650T	CTC>CTT	Synonymous	ORF1ab:nsp2	0.655679513184584
CAMB-76472	MN908947.3	26768	C	T	0.038	0.031	2.2e-18	3.6e-15	0.0346737350228429	TCG	M	I82I	C246T	ATC>ATT	Synonymous	GU280_gp05	0.965304715110766
CAMB-76472	MN908947.3	26895	C	T	0.29	0.22	2.1e-140	8.8e-97	0.266480223731522	CCA	M	H125Y	C373T	CAT>TAT	Missense	GU280_gp05	0.733519776268478
CAMB-76472	MN908947.3	28253	C	T	0.08	0.15	2.3e-35	1.1e-68	0.111990848059728	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.887798416473492
CAMB-76472	MN908947.3	28603	C	T	0.0092	0.018	0.00044	1.4e-06	0.0127681902985075	TCT	N	F110F	C330T	TTC>TTT	Synonymous	GU280_gp10	0.987115205223881
CAMB-76472	MN908947.3	28724	C	T	0.0068	0.015	0.00026	8.6e-08	0.00972402930904609	TCC	N	P151S	C451T	CCT>TCT	Missense	GU280_gp10	0.990207491611313
CAMB-76472	MN908947.3	28810	CAGTCA	GCAGTC	0.017	0.00283333333333333	2.2e-07;1.8e-07;2.8e-07;1.2e-07;3.1e-11;1.5e-07	NA;NA;NA;NA;1.3e-07;NA	0.0106254792419761	GCA	N	.	537-542-mnv	.	no-SNV	GU280_gp10	0.989505571784053
CAMB-76472	MN908947.3	28824	CTCGT	TCTCG	0.015	0.0026	5.2e-07;1.8e-07;2e-07;1.9e-07;2e-07	NA;NA;6.3e-06;NA;NA	0.0105018792836613	TCT	N	.	551-555-mnv	.	no-SNV	GU280_gp10	0.990184446122317
CAMB-76472	MN908947.3	28881	G	A	0.99	0.98	0	0	0.989930691774552	AGG	N	R203K	G608A	AGG>AAG	Missense	GU280_gp10	0
CAMB-76472	MN908947.3	28881	GGGGAACTT	-	0.00581111111111111	0.0167777777777778	0.00014;7.9e-05;9.4e-05;6e-04;0.00018;0.00013;0.00016;0.00069;0.0013	8.8e-09;8.5e-09;2.1e-08;3.3e-07;1.5e-08;4.5e-09;1.7e-08;7.2e-07;7.6e-07	0.00870178739416745	AGG	N	.	608-616-delinframe	.	no-SNV	GU280_gp10	0
CAMB-76472	MN908947.3	28883	G	C	0.99	0.98	0	0	0.985386459641512	GGG	N	G204R	G610C	GGA>CGA	Missense	GU280_gp10	0
CAMB-76472	MN908947.3	28895	G	T	0.0075	0.017	1e-04	4.4e-08	0.0102086605339915	TGC	N	A208S	G622T	GCT>TCT	Missense	GU280_gp10	0.705407224590532
CAMB-76472	MN908947.3	29686	C	T	0.0049	0.013	0.0023	6e-06	0.00881742738589212	TCA	NA	NA	NA	NA	NA	NA	0.991182572614108
CAMB-76472	MN908947.3	29722	CACATTTT	-	0.03575	0.03175	4.9e-13;3.3e-13;2e-13;1.3e-13;2.5e-12;3.1e-13;3.5e-13;2.5e-12	3e-06;2.5e-06;2.6e-13;1e-13;1.5e-12;2.2e-13;4.3e-13;2e-12	0.0364741641337386	CCA	NA	NA	NA	NA	NA	NA	0.975586404978459
CAMB-76472	MN908947.3	3037	C	T	1	1	0	0	0.99918995544755	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000202511138112596
CAMB-76472	MN908947.3	4064	TC	-	0.013	0.012	NA;9e-13	2e-07;3.5e-07	0.0126212302378105	TTC	ORF1ab:nsp3	.	1345-1346-delfrshift	.	no-SNV	ORF1ab:nsp3	0.995141700404858
CAMB-76472	MN908947.3	4065	C	-	0.026	0.012	9e-13	3.5e-07	0.0204108334423656	TCT	ORF1ab:nsp3	.	1346-1346-delfrshift	.	no-SNV	ORF1ab:nsp3	0.979458327881722
CAMB-76472	MN908947.3	4134	TT	-	0.0022	0.044	0.00029;NA	1e-21;2.6e-18	0.0185466322554527	GTT	ORF1ab:nsp3	.	1415-1416-delfrshift	.	no-SNV	ORF1ab:nsp3	0.979592885781844
CAMB-76472	MN908947.3	635	C	T	0.51	0.54	2.8e-298	5.19999999999997e-310	0.520371603411649	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.479628396588351
CAMB-76472	MN908947.3	7561	G	T	0.067	0.034	5.4e-28	1.1e-14	0.0541724296911019	GGT	ORF1ab:nsp3	R1614S	G4842T	AGG>AGT	Missense	ORF1ab:nsp3	0.945827570308898
CAMB-76472	MN908947.3	9255	GTGTATCTACTAGTG	TGTGTATCTACTAGT	0.0501333333333333	0.00498066666666667	4.8e-20;9.1e-21;2.5e-20;3.5e-21;2.7e-21;3.2e-20;5.4e-21;4.7e-21;1.1e-20;6.1e-21;4.1e-21;2.1e-20;3.3e-20;6.2e-19;1.2e-20	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;1.2e-15;8.7e-15	0.0282208588957055	TGT	ORF1ab:nsp4	.	701-715-mnv	.	no-SNV	ORF1ab:nsp4	0.972677595628415
CAMB-76472	MN908947.3	9271	TAGATG	GTAGAT	0.0491666666666667	0.000266666666666667	7.4e-21;2.4e-20;2.1e-20;1.4e-20;3.3e-21;3.7e-18	NA;NA;NA;NA;0.0049;NA	0.027588344699318	GTA	ORF1ab:nsp4	.	717-722-mnv	.	no-SNV	ORF1ab:nsp4	0.971741112123975
CAMB-76472	MN908947.3	9430	C	T	0.64	0.49	1.3e-304	1.2e-199	0.574720433751271	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.425279566248729
CAMB-76472	MN908947.3	9587	A	G	0.13	0.1	1.7e-61	2.6e-46	0.117870444752793	TAT	ORF1ab:nsp4	I345V	A1033G	ATT>GTT	Missense	ORF1ab:nsp4	0.882114949244139
CAMB-76481	MN908947.3	1059	C	T	1	1	0	0	0.999709503698241	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.000134075216196286
CAMB-76481	MN908947.3	11075	T	-	0.034	0.034	4.8e-09	2.6e-09	0.034396444565532	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961516849149454
CAMB-76481	MN908947.3	13006	T	C	1	1	0	0	0.998932717649365	CTG	ORF1ab:nsp9	A107A	T321C	GCT>GCC	Synonymous	ORF1ab:nsp9	0.000435625449238745
CAMB-76481	MN908947.3	1437	C	T	1	1	0	0	0.999500392548712	TCT	ORF1ab:nsp2	S211F	C632T	TCT>TTT	Missense	ORF1ab:nsp2	7.13724930411819e-05
CAMB-76481	MN908947.3	14408	C	T	1	1	0	0	0.999134480147138	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000342601608424393
CAMB-76481	MN908947.3	20941	C	T	1	1	0	0	0.999391357273281	GCT	ORF1ab:2'-O-ribose-methyltransferase	L95F	C283T	CTT>TTT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.000214815080018617
CAMB-76481	MN908947.3	23403	A	G	1	1	0	0	0.999580760114162	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.67476659625587e-05
CAMB-76481	MN908947.3	241	C	T	1	1	0	0	0.999300376842474	TCG	NA	NA	NA	NA	NA	NA	0.000222607368303891
CAMB-76481	MN908947.3	25563	G	T	1	1	0	0	0.999650938359821	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	8.21321506303643e-05
CAMB-76481	MN908947.3	25688	C	T	1	1	0	0	0.999597619602279	GCT	ORF3a	A99V	C296T	GCT>GTT	Missense	GU280_gp03	0.000211779156695398
CAMB-76481	MN908947.3	3037	C	T	1	1	0	0	0.999198557403326	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.67868830561678e-05
CAMB-76481	MN908947.3	6431	A	G	1	1	0	0	0.999634922290602	TAC	ORF1ab:nsp3	T1238A	A3712G	ACC>GCC	Missense	ORF1ab:nsp3	0.000177323458850527
CAMB-76490	MN908947.3	11075	T	-	0.041	0.036	2.2e-10	1.1e-09	0.0387660754812138	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956274691098596
CAMB-76490	MN908947.3	14408	C	T	1	1	0	0	0.998155114512619	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000432395036104986
CAMB-76490	MN908947.3	16541	A	G	1	1	2.6e-288	0	1	AAT	ORF1ab:helicase	N102S	A305G	AAT>AGT	Missense	ORF1ab:helicase	0
CAMB-76490	MN908947.3	17730	A	G	1	1	0	0	0.999667500554166	AAT	ORF1ab:helicase	E498E	A1494G	GAA>GAG	Synonymous	ORF1ab:helicase	4.74999208334653e-05
CAMB-76490	MN908947.3	23403	A	G	1	1	0	0	0.999607048566341	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.59581261128507e-05
CAMB-76490	MN908947.3	241	C	T	1	1	0	0	0.999070813771518	TCG	NA	NA	NA	NA	NA	NA	0.000220070422535211
CAMB-76490	MN908947.3	25996	G	T	0.019	0.015	2.7e-07	2.2e-06	0.0175224123879381	TGT	ORF3a	V202L	G604T	GTA>TTA	Missense	GU280_gp03	0.982324775876121
CAMB-76490	MN908947.3	27128	C	T	1	1	0	0	0.999734536766658	GCA	M	G202G	C606T	GGC>GGT	Synonymous	GU280_gp05	0.000176975488894788
CAMB-76490	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99936148476077	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000141790339351546
CAMB-76490	MN908947.3	3037	C	T	1	1	0	0	0.999320336254695	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.57717760686818e-05
CAMB-76490	MN908947.3	313	C	T	1	1	0	0	0.997804691546829	TCA	ORF1ab:leader-protein	L16L	C48T	CTC>CTT	Synonymous	ORF1ab:leader-protein	4.93327742285587e-05
CAMB-76490	MN908947.3	8171	G	A	0.93	0.92	0	0	0.924481433515212	AGC	ORF1ab:nsp3	A1818T	G5452A	GCA>ACA	Missense	ORF1ab:nsp3	0.0754124116260801
CAMB-764CD	MN908947.3	11074	C	INS	0.1	0.11	1.2e-37	3.3e-36	0.103201449713078	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.890048323769254
CAMB-764CD	MN908947.3	11083	G	-	0.18	0.16	5.2e-81	6e-70	0.170974155069582	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-764CD	MN908947.3	11083	G	T	0.82	0.84	0	0	0.828914624143252	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-764CD	MN908947.3	14805	C	T	1	1	0	0	0.999297412134696	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000250924237608525
CAMB-764CD	MN908947.3	18322	C	T	0.034	0.043	1.2e-16	5.4e-20	0.0390063867298708	TCA	ORF1ab:3'-to-5'-exonuclease	H95Y	C283T	CAT>TAT	Missense	ORF1ab:3'-to-5'-exonuclease	0.960966172969932
CAMB-764CD	MN908947.3	2480	A	G	1	1	0	0	0.999675877157443	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-764CD	MN908947.3	2558	C	T	1	1	0	0	0.999794436069618	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	6.85213101274496e-05
CAMB-764CD	MN908947.3	25927	A	G	0.046	0.046	2.5e-21	2.1e-21	0.0461220939157726	TAT	ORF3a	I179V	A535G	ATT>GTT	Missense	GU280_gp03	0.953639108260699
CAMB-764CD	MN908947.3	26144	G	T	1	1	0	0	0.999806248486316	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	9.68757568418503e-05
CAMB-764CD	MN908947.3	26182	T	C	0.014	0.015	1.6e-07	4.3e-08	0.0143203550350002	TTA	ORF3a	Y264H	T790C	TAT>CAT	Missense	GU280_gp03	0.985450885299904
CAMB-764CD	MN908947.3	713	G	T	1	1	0	0	0.99876332118162	TGG	ORF1ab:leader-protein	G150C	G448T	GGC>TGC	Missense	ORF1ab:leader-protein	0.000247335763676055
CAMB-764CD	MN908947.3	9419	A	G	0.012	0.0099	9.2e-07	4e-06	0.0109431614390806	TAT	ORF1ab:nsp4	I289V	A865G	ATT>GTT	Missense	ORF1ab:nsp4	0.988690846539545
CAMB-764DC	MN908947.3	12513	C	T	0.035	0.062	2.7e-16	4.3e-28	0.0482646318141367	ACG	ORF1ab:nsp8	T141M	C422T	ACG>ATG	Missense	ORF1ab:nsp8	0.951697498721906
CAMB-764DC	MN908947.3	12513	CG	TT	0.034	0.0365	2.7e-16;2.7e-16	4.3e-28;6.1e-07	0.0351665936410569	ACG	ORF1ab:nsp8	.	422-423-mnv	.	no-SNV	ORF1ab:nsp8	0.951697498721906
CAMB-764DC	MN908947.3	12514	G	T	0.033	0.011	2.7e-16	6.1e-07	0.0219462173921377	CGT	ORF1ab:nsp8	T141T	G423T	ACG>ACT	Synonymous	ORF1ab:nsp8	0.978015448603684
CAMB-764DC	MN908947.3	14408	C	T	1	1	0	0	0.999362024024352	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000236962505240517
CAMB-764DC	MN908947.3	14904	TAATGC	-	0.005	0.017	3.6e-05;8.7e-05;NA;NA;NA;NA	1.3e-05;3.4e-05;4.8e-05;2.7e-05;2.9e-05;2.6e-05	0.00831889081455806	TTA	ORF1ab:RNA-dependent-RNA-polymerase	.	1437-1442-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.983832129342965
CAMB-764DC	MN908947.3	19839	T	C	1	1	0	0	0.999869041382923	ATA	ORF1ab:endoRNAse	N73N	T219C	AAT>AAC	Synonymous	ORF1ab:endoRNAse	0
CAMB-764DC	MN908947.3	21883	TACTACTT	-	0.03275	0.015125	1.3e-06;2.2e-06;2.9e-07;7.7e-10;6.3e-09;2.6e-06;5.2e-06;2.9e-06	NA;NA;NA;2.6e-07;9.8e-07;8.1e-05;0.00012;6.5e-05	0.0279614585301341	GTA	S	.	321-328-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.983792846497765
CAMB-764DC	MN908947.3	23270	GCTGACACTACTGATGCTGTC	TGCTGACACTACTGATGCTGT	0.00115809523809524	0.010952380952381	0.5;0.5;0.29;0.48;0.5;0.5;0.5;0.5;2.3e-08;0.5;0.5;0.5;0.5;0.5;0.5;0.5;0.5;0.5;0.5;0.5;0.5	2.7e-05;1.2e-05;3.3e-05;1.7e-05;1.5e-05;2e-05;1.3e-05;2.1e-05;8.5e-06;2.2e-05;2.9e-05;1.9e-05;4.1e-05;1.5e-05;1.9e-05;2.1e-05;1.6e-05;2.4e-05;1.8e-05;1.6e-05;1.9e-05	0.00563810348143874	TGC	S	.	1708-1728-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.994280348301178
CAMB-764DC	MN908947.3	23403	A	G	1	1	0	0	0.999888932081968	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.99611262286888e-05
CAMB-764DC	MN908947.3	241	C	T	1	1	0	0	0.999870429396978	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-764DC	MN908947.3	24621	C	T	1	1	0	0	1	GCT	S	A1020V	C3059T	GCT>GTT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-764DC	MN908947.3	26574	GAACAATGGAAC	-	0.012	0.017	NA;0.0019;0.0028;0.0029;0.0023;0.0023;0.0027;0.0018;0.0025;0.0027;0.0022;0.0024	8.9e-06;5e-04;0.00083;9e-04;0.00072;0.00068;0.00096;5e-04;8e-04;0.00083;0.00071;0.00075	0.0141645326504481	TGA	M	.	52-63-delinframe	.	no-SNV	GU280_gp05	0.985525512776289
CAMB-764DC	MN908947.3	26681	C	T	1	1	0	0	0.99976198976556	TCC	M	F53F	C159T	TTC>TTT	Synonymous	GU280_gp05	0.000163632036177556
CAMB-764DC	MN908947.3	27134	TAAATT	-	0.0203333333333333	0.0306666666666667	0.00049;0.00029;0.00079;0.00032;0.00079;4.9e-05	1.2e-05;4.4e-06;2.1e-05;8.1e-06;2.2e-05;4.4e-07	0.0246165498958531	ATA	M	.	612-617-delinframe	.	no-SNV	GU280_gp05	0.976651378879028
CAMB-764DC	MN908947.3	28881	GGG	AAC	1	0.99	0;0;0	0;0;0	0.996634739839503	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-764DC	MN908947.3	3037	C	T	1	1	0	0	0.999605678233438	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-764DC	MN908947.3	8359	T	C	0.013	0.02	2.4e-06	5.6e-09	0.0160444307312558	ATA	ORF1ab:nsp3	H1880H	T5640C	CAT>CAC	Synonymous	ORF1ab:nsp3	0.983955569268744
CAMB-764EB	MN908947.3	10702	C	T	0.026	0.0061	1.9e-13	0.00011	0.018485421028443	ACA	ORF1ab:3C-like-proteinase	D216D	C648T	GAC>GAT	Synonymous	ORF1ab:3C-like-proteinase	0.981514578971557
CAMB-764EB	MN908947.3	11074	C	INS	0.092	0.083	1.9e-29	2.9e-25	0.0873140315052509	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.912175466744457
CAMB-764EB	MN908947.3	11083	G	-	0.16	0.16	3.9e-71	1.1e-70	0.159456159456159	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.3000033000033e-05
CAMB-764EB	MN908947.3	11083	G	T	0.84	0.84	0	0	0.84034584034584	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.3000033000033e-05
CAMB-764EB	MN908947.3	12738	C	T	0.0092	0.0047	3.4e-06	0.00032	0.00733496332518337	ACT	ORF1ab:nsp9	T18I	C53T	ACT>ATT	Missense	ORF1ab:nsp9	0.992650483176156
CAMB-764EB	MN908947.3	1457	C	T	0.011	0.012	1.8e-05	1.3e-05	0.0116331096196868	TCG	ORF1ab:nsp2	R218C	C652T	CGT>TGT	Missense	ORF1ab:nsp2	0.988366890380313
CAMB-764EB	MN908947.3	14805	C	T	1	1	0	0	0.999907616979999	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	4.61915100004619e-05
CAMB-764EB	MN908947.3	1593	C	T	0.27	0.15	6.6e-96	1.6e-51	0.209331131296449	TCC	ORF1ab:nsp2	S263F	C788T	TCC>TTC	Missense	ORF1ab:nsp2	0.790668868703551
CAMB-764EB	MN908947.3	1835	G	A	1	1	0	0	0.999941873982795	TGG	ORF1ab:nsp2	G344S	G1030A	GGT>AGT	Missense	ORF1ab:nsp2	5.81260172053011e-05
CAMB-764EB	MN908947.3	19884	C	T	0.0097	0.0065	2.4e-06	5.2e-05	0.0080813911537629	ACA	ORF1ab:endoRNAse	Y88Y	C264T	TAC>TAT	Synonymous	ORF1ab:endoRNAse	0.991918608846237
CAMB-764EB	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-764EB	MN908947.3	25568	C	T	1	1	0	0	0.999922543666008	GCT	ORF3a	A59V	C176T	GCT>GTT	Missense	GU280_gp03	3.87281669958561e-05
CAMB-764EB	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-764EB	MN908947.3	26144	G	T	1	1	5.5e-253	7.6e-219	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-764EB	MN908947.3	28253	C	T	0.01	0.0048	1.3e-05	0.0035	0.00709624184232241	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.992678718775786
CAMB-764EB	MN908947.3	29774	C	T	0.051	0.013	5e-17	8.2e-06	0.0273181993074259	GCT	NA	NA	NA	NA	NA	NA	0.972681800692574
CAMB-764EB	MN908947.3	3052	G	A	0.14	0.15	2.8e-61	5.8e-64	0.144966587626644	AGG	ORF1ab:nsp3	E111E	G333A	GAG>GAA	Synonymous	ORF1ab:nsp3	0.85492563052382
CAMB-764EB	MN908947.3	4118	T	C	0.012	0.012	3.8e-06	3.8e-06	0.0116128501839558	ATA	ORF1ab:nsp3	Y467H	T1399C	TAT>CAT	Missense	ORF1ab:nsp3	0.988366596098905
CAMB-764EB	MN908947.3	5797	T	C	0.0061	0.0085	0.00027	2.5e-05	0.00716768027801911	CTT	ORF1ab:nsp3	T1026T	T3078C	ACT>ACC	Synonymous	ORF1ab:nsp3	0.992723718505647
CAMB-764FA	MN908947.3	10188	C	T	0.039	0.026	9.1e-19	2.3e-13	0.0337826654651783	ACC	ORF1ab:3C-like-proteinase	T45I	C134T	ACC>ATC	Missense	ORF1ab:3C-like-proteinase	0.966180554278463
CAMB-764FA	MN908947.3	11075	T	-	0.049	0.052	5.2e-12	4.6e-13	0.0501087651951376	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.945770953294946
CAMB-764FA	MN908947.3	1142	C	T	0.048	0.046	2.3e-22	7.6e-22	0.0473266909907381	GCT	ORF1ab:nsp2	L113F	C337T	CTT>TTT	Missense	ORF1ab:nsp2	0.952620684816166
CAMB-764FA	MN908947.3	14408	C	T	1	1	0	0	0.999306578833319	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000260032937505417
CAMB-764FA	MN908947.3	14649	C	T	0.007	0.0036	3.1e-05	8e-04	0.00568942017931052	ACA	ORF1ab:RNA-dependent-RNA-polymerase	N394N	C1182T	AAC>AAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.994310579820689
CAMB-764FA	MN908947.3	17822	C	T	0.069	0.078	1.4e-31	1.3e-35	0.0727617074315684	CCA	ORF1ab:helicase	P529L	C1586T	CCA>CTA	Missense	ORF1ab:helicase	0.927173543551807
CAMB-764FA	MN908947.3	2019	T	C	0.0082	0.0067	7.5e-06	3.2e-05	0.0075133301017935	ATG	ORF1ab:nsp2	M405T	T1214C	ATG>ACG	Missense	ORF1ab:nsp2	0.99161415414445
CAMB-764FA	MN908947.3	2164	G	A	1	1	0	0	0.998182625903639	AGA	ORF1ab:nsp2	E453E	G1359A	GAG>GAA	Synonymous	ORF1ab:nsp2	0.000646177456483987
CAMB-764FA	MN908947.3	21866	A	G	0.2	0.16	5.4e-90	7.8e-69	0.176326412918108	AAG	S	R102G	A304G	AGA>GGA	Missense	GU280_gp02, spike glycoprotein	0.823673587081892
CAMB-764FA	MN908947.3	22006	C	T	0.0071	0.016	2.2e-05	2.8e-09	0.0112656397986142	ACA	S	N148N	C444T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.987313693235631
CAMB-764FA	MN908947.3	23403	A	G	1	1	0	0	0.999850961299617	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000109295046947191
CAMB-764FA	MN908947.3	2388	C	T	0.034	0.039	4e-15	1.3e-17	0.0368402817877353	ACA	ORF1ab:nsp2	T528I	C1583T	ACA>ATA	Missense	ORF1ab:nsp2	0.963159718212265
CAMB-764FA	MN908947.3	24014	A	G	0.0052	0.0072	0.00015	1.6e-05	0.00595018842263338	TAT	S	I818V	A2452G	ATT>GTT	Missense	GU280_gp02, spike glycoprotein	0.99300144504576
CAMB-764FA	MN908947.3	241	C	T	1	1	0	0	0.999847214529898	TCG	NA	NA	NA	NA	NA	NA	9.54909188136208e-05
CAMB-764FA	MN908947.3	24198	C	T	0.0067	0.015	0.00052	1.2e-07	0.0106440361034198	GCG	S	A879V	C2636T	GCG>GTG	Missense	GU280_gp02, spike glycoprotein	0.98935596389658
CAMB-764FA	MN908947.3	24334	C	T	0.029	0.0084	4.3e-14	1e-05	0.0199287271217521	CCA	S	A924A	C2772T	GCC>GCT	Synonymous	GU280_gp02, spike glycoprotein	0.980071272878248
CAMB-764FA	MN908947.3	26437	C	T	0.0074	0.0062	2.4e-05	6.3e-05	0.0069052102950408	TCT	E	L65L	C193T	CTG>TTG	Synonymous	GU280_gp04	0.993037721851281
CAMB-764FA	MN908947.3	28295	A	T	0.064	0.064	2.5e-29	1.8e-29	0.0638734142816557	AAA	N	N8Y	A22T	AAT>TAT	Missense	GU280_gp10	0.935706609681683
CAMB-764FA	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999050852407549	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000201979398101394
CAMB-764FA	MN908947.3	29735	AGGCCACGCGGAGT	-	0.00606428571428571	0.00937857142857143	0.0013;0.001;0.002;0.0015;0.0029;0.0024;0.0031;0.0032;0.0026;0.0032;0.0028;0.0032;0.0046;0.0081	4.8e-05;6.4e-05;7.5e-05;0.00012;0.00014;9.4e-05;0.00015;0.00017;9.1e-05;0.00016;0.00018;0.00022;0.00024;0.00048	0.00744372895374254	GAG	NA	NA	NA	NA	NA	NA	0.991905585763717
CAMB-764FA	MN908947.3	3037	C	T	1	1	0	0	0.999677610015582	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.37316640696362e-05
CAMB-764FA	MN908947.3	7267	C	T	0.01	0.019	0.00041	1.6e-06	0.0148741418764302	TCA	ORF1ab:nsp3	F1516F	C4548T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.98512585812357
CAMB-764FA	MN908947.3	8158	T	C	0.0072	0.0052	2.3e-05	0.00013	0.00644482103425255	CTA	ORF1ab:nsp3	S1813S	T5439C	TCT>TCC	Synonymous	ORF1ab:nsp3	0.993529502387922
CAMB-764FA	MN908947.3	9608	T	C	0.11	0.089	1.3e-50	4.3e-41	0.10237011497104	TTA	ORF1ab:nsp4	Y352H	T1054C	TAT>CAT	Missense	ORF1ab:nsp4	0.89762988502896
CAMB-764FA	MN908947.3	9629	T	C	0.036	0.042	5.4e-17	9.1e-20	0.0381271200248848	TTT	ORF1ab:nsp4	F359L	T1075C	TTT>CTT	Missense	ORF1ab:nsp4	0.961798817970405
CAMB-764FA	MN908947.3	9924	C	T	0.011	0.015	9e-07	2.3e-08	0.0124862903906184	GCA	ORF1ab:nsp4	A457V	C1370T	GCA>GTA	Missense	ORF1ab:nsp4	0.9874715261959
CAMB-76506	MN908947.3	11075	T	-	0.038	0.034	3.8e-10	1.1e-09	0.0366980817600533	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959392708869966
CAMB-76506	MN908947.3	13730	C	T	1	1	0	0	0.999553626546874	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A88V	C263T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00012346499767316
CAMB-76506	MN908947.3	14408	C	T	1	1	0	0	0.999272757495792	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000249340287156897
CAMB-76506	MN908947.3	23403	A	G	1	1	0	0	0.99928085578162	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.4946513648758e-05
CAMB-76506	MN908947.3	241	C	T	1	1	0	0	0.999339361658202	TCG	NA	NA	NA	NA	NA	NA	0.000165159585449441
CAMB-76506	MN908947.3	25429	G	T	1	1	0	0	0.999232624424468	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	8.22188116641087e-05
CAMB-76506	MN908947.3	3037	C	T	1	1	0	0	0.999746780494863	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76506	MN908947.3	516	TTA	-	0.996666666666667	0.996666666666667	1.4e-62;2.2e-85;8.1e-77	8.7e-60;8.1e-86;5e-83	0.999387161023441	GTT	ORF1ab:leader-protein	.	251-253-delinframe	.	no-SNV	ORF1ab:leader-protein	0.011488794595671
CAMB-76506	MN908947.3	6419	G	A	1	1	0	0	0.999786822996469	AGT	ORF1ab:nsp3	V1234M	G3700A	GTG>ATG	Missense	ORF1ab:nsp3	6.66178136033575e-05
CAMB-76515	MN908947.3	11074	C	INS	0.026	0.019	3.6e-05	0.0022	0.0232763538005778	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.976429241724474
CAMB-76515	MN908947.3	11075	T	-	0.043	0.056	6.9e-11	2.9e-14	0.0477085856332462	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951829307157881
CAMB-76515	MN908947.3	11291	G	A	0.018	0.05	8.9e-10	7.4e-24	0.0295246116414	TGG	ORF1ab:nsp6	G107S	G319A	GGT>AGT	Missense	ORF1ab:nsp6	0.970459791627675
CAMB-76515	MN908947.3	11839	A	G	0.16	0.12	5e-47	5.8e-34	0.144230769230769	TAC	ORF1ab:nsp6	V289V	A867G	GTA>GTG	Synonymous	ORF1ab:nsp6	0.854967948717949
CAMB-76515	MN908947.3	14408	C	T	1	1	0	0	0.998995968427069	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000200806314586262
CAMB-76515	MN908947.3	16289	C	T	0.86	0.87	0	0	0.866900341038272	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0.133004926108374
CAMB-76515	MN908947.3	16575	C	T	0.063	0.11	6.1e-09	1.1e-14	0.087719298245614	ACT	ORF1ab:helicase	D113D	C339T	GAC>GAT	Synonymous	ORF1ab:helicase	0.912280701754386
CAMB-76515	MN908947.3	19232	T	C	0.0097	0.0041	1.7e-06	0.00026	0.00771101488819028	GTT	ORF1ab:3'-to-5'-exonuclease	V398A	T1193C	GTT>GCT	Missense	ORF1ab:3'-to-5'-exonuclease	0.992269213278763
CAMB-76515	MN908947.3	19839	T	C	0.15	0.14	4.6e-66	1.4e-60	0.143280196584966	ATA	ORF1ab:endoRNAse	N73N	T219C	AAT>AAC	Synonymous	ORF1ab:endoRNAse	0.856656795413017
CAMB-76515	MN908947.3	22078	T	C	0.053	0.026	1.7e-20	2.3e-10	0.0420247875017807	CTC	S	S172S	T516C	TCT>TCC	Synonymous	GU280_gp02, spike glycoprotein	0.957975212498219
CAMB-76515	MN908947.3	22964	A	G	0.015	0.018	1.1e-08	7e-10	0.0163770887023028	TAT	S	I468V	A1402G	ATT>GTT	Missense	GU280_gp02, spike glycoprotein	0.982625322138166
CAMB-76515	MN908947.3	23403	A	G	1	1	0	0	0.997768746513666	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.31250830079422e-05
CAMB-76515	MN908947.3	241	C	T	1	1	0	0	0.999741682165737	TCG	NA	NA	NA	NA	NA	NA	0.000103327133705311
CAMB-76515	MN908947.3	25298	G	A	0.0041	0.01	0.00041	1.2e-06	0.00632932929526661	GGG	S	G1246S	G3736A	GGC>AGC	Missense	GU280_gp02, spike glycoprotein	0.993670670704733
CAMB-76515	MN908947.3	26333	C	T	0.0091	0.015	2.5e-05	8.8e-08	0.0112363545852149	ACA	E	T30I	C89T	ACA>ATA	Missense	GU280_gp04	0.988550296910003
CAMB-76515	MN908947.3	26681	C	T	0.0091	0.0073	3.2e-05	0.00017	0.00851399417378849	TCC	M	F53F	C159T	TTC>TTT	Synonymous	GU280_gp05	0.991469911319267
CAMB-76515	MN908947.3	28305	A	T	0.0089	0.013	5.6e-06	7.4e-08	0.0102936301620811	AAT	N	N11I	A32T	AAT>ATT	Missense	GU280_gp10	0.98960168885322
CAMB-76515	MN908947.3	28307	G	A	0.0094	0.013	6.6e-06	1.1e-07	0.0107776804903287	TGC	N	A12T	G34A	GCA>ACA	Missense	GU280_gp10	0.989190479980896
CAMB-76515	MN908947.3	28337	G	A	0.026	0.03	6.4e-13	4e-15	0.0271399076423584	AGA	N	D22N	G64A	GAT>AAT	Missense	GU280_gp10	0.972828570978266
CAMB-76515	MN908947.3	28881	GGG	AAC	0.11	0.12	1.1e-43;1.5e-48;5.4e-52	4.3e-46;1.1e-50;1.1e-55	0.114116450242355	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.897071179930381
CAMB-76515	MN908947.3	29062	T	A	0.0014	0.0074	0.0048	8.3e-06	0.0030713728549142	CTG	N	T263T	T789A	ACT>ACA	Synonymous	GU280_gp10	0.99683112324493
CAMB-76515	MN908947.3	3037	C	T	1	1	0	0	0.999583130688529	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76515	MN908947.3	4683	C	T	0.033	0.047	2e-16	1.1e-22	0.0383723972935591	GCT	ORF1ab:nsp3	A655V	C1964T	GCT>GTT	Missense	ORF1ab:nsp3	0.957590370453441
CAMB-76515	MN908947.3	5549	C	T	0.0084	0.013	1.5e-05	4e-07	0.0101665205959684	CCT	ORF1ab:nsp3	L944F	C2830T	CTT>TTT	Missense	ORF1ab:nsp3	0.989833479404032
CAMB-76515	MN908947.3	5730	C	T	0.0089	0.0059	8.7e-06	0.00015	0.00780940727678411	ACT	ORF1ab:nsp3	T1004I	C3011T	ACT>ATT	Missense	ORF1ab:nsp3	0.992190592723216
CAMB-76515	MN908947.3	8293	C	T	0.12	0.11	2.6e-54	7.8e-51	0.114823529411765	CCT	ORF1ab:nsp3	T1858T	C5574T	ACC>ACT	Synonymous	ORF1ab:nsp3	0.885176470588235
CAMB-76524	MN908947.3	10996	G	T	0.1	0.072	5.9e-41	1.4e-26	0.0909847434119279	AGG	ORF1ab:nsp6	K8N	G24T	AAG>AAT	Missense	ORF1ab:nsp6	0.909015256588072
CAMB-76524	MN908947.3	11083	G	T	0.028	0.047	2.5e-06	2.1e-10	0.0348933678200185	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.964545410180079
CAMB-76524	MN908947.3	14318	C	T	0.048	0.022	5.1e-23	8.9e-12	0.0394628439611139	ACA	ORF1ab:RNA-dependent-RNA-polymerase	T284I	C851T	ACA>ATA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.960454770143351
CAMB-76524	MN908947.3	14408	C	T	1	1	0	0	0.99968654717465	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000199469979768045
CAMB-76524	MN908947.3	14851	TTT	-	0.0373333333333333	0.0116666666666667	1.6e-05;1.7e-05;6.5e-05	0.006;0.0049;NA	0.0299058945788349	ATT	ORF1ab:RNA-dependent-RNA-polymerase	.	1384-1386-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.968531362631372
CAMB-76524	MN908947.3	160	G	T	1	1	0	0	1	GGA	NA	NA	NA	NA	NA	NA	0
CAMB-76524	MN908947.3	16860	TG	-	0.00815	0.025	1.1e-05;1.4e-05	1.1e-12;1e-12	0.0154578519469405	CTG	ORF1ab:helicase	.	624-625-delfrshift	.	no-SNV	ORF1ab:helicase	0.984321853741497
CAMB-76524	MN908947.3	16934	TGCCATTAAGTGCACCTACACTAG	-	0.013875	0.00320833333333333	5.6e-08;1.1e-07;3.6e-08;8.3e-08;2.6e-08;8.5e-09;7.2e-08;2.2e-06;1.8e-06;8.6e-06;4.7e-05;4.2e-05;1.1e-05;7e-05;1.9e-05;2e-06;7.1e-08;8.5e-08;1.7e-07;1.7e-07;1.4e-07;7.8e-09;4.1e-08;8.2e-08	2.7e-07;2.9e-07;1.3e-07;2.7e-07;1.1e-07;4.9e-08;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00782356927246966	ATG	ORF1ab:helicase	.	698-721-delinframe	.	no-SNV	ORF1ab:helicase	0.986824925816024
CAMB-76524	MN908947.3	1738	G	T	0.053	0.043	2.9e-24	2.2e-19	0.0490298898793917	TGA	ORF1ab:nsp2	V311V	G933T	GTG>GTT	Synonymous	ORF1ab:nsp2	0.950970110120608
CAMB-76524	MN908947.3	18982	ATGGTTGTT	-	0.0144444444444444	0.0265555555555556	NA;NA;NA;2.1e-19;5.6e-21;7.3e-17;NA;NA;NA	2.8e-13;1.4e-12;4.6e-10;2.7e-12;3.5e-13;1.2e-10;1.4e-12;2.4e-13;1.9e-13	0.00971867007672634	CAT	ORF1ab:3'-to-5'-exonuclease	.	943-951-delinframe	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.989849071724322
CAMB-76524	MN908947.3	19147	T	C	0.042	0.025	3.1e-20	7e-13	0.0355397601066193	TTA	ORF1ab:3'-to-5'-exonuclease	Y370H	T1108C	TAT>CAT	Missense	ORF1ab:3'-to-5'-exonuclease	0.964333312178714
CAMB-76524	MN908947.3	203	C	T	0.029	0.042	9.7e-14	2.5e-19	0.0339442377474622	TCG	NA	NA	NA	NA	NA	NA	0.966055762252538
CAMB-76524	MN908947.3	21707	C	T	0.15	0.11	6.7e-57	2.3e-41	0.128498001142204	ACA	S	H49Y	C145T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.871501998857796
CAMB-76524	MN908947.3	21777	G	T	0.07	0.1	1.2e-26	5e-37	0.0845972362655881	GGG	S	G72V	G215T	GGG>GTG	Missense	GU280_gp02, spike glycoprotein	0.915402763734412
CAMB-76524	MN908947.3	23403	A	G	1	1	0	0	0.999773128308545	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000151247794303
CAMB-76524	MN908947.3	241	C	T	1	0.95	0	0	0.982422133133618	TCG	NA	NA	NA	NA	NA	NA	4.40548041763954e-05
CAMB-76524	MN908947.3	25429	G	T	1	1	0	0	0.999780461031833	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	3.65898280278083e-05
CAMB-76524	MN908947.3	28253	C	T	0.16	0.073	3e-71	1.4e-32	0.126041104067768	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.873560931237386
CAMB-76524	MN908947.3	28744	C	T	0.076	0.059	7e-34	1.5e-25	0.0708021851638873	TCG	N	I157I	C471T	ATC>ATT	Synonymous	GU280_gp10	0.929125934445083
CAMB-76524	MN908947.3	3037	C	T	1	1	0	0	0.999553172475425	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76524	MN908947.3	518	ATG	-	0.213333333333333	0.112666666666667	2.7e-05;0.00043;0.00078	0.0013;0.004;0.006	0.183219463422763	TAT	ORF1ab:leader-protein	.	253-255-delinframe	.	no-SNV	ORF1ab:leader-protein	0.809301924238502
CAMB-76524	MN908947.3	522	TT	-	0.0095	0.071	0.0099;NA	1.5e-09;3.3e-10	0.0308296943231441	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.962176628010705
CAMB-76524	MN908947.3	635	C	T	0.12	0.022	2.7e-55	9.4e-11	0.0890450243762547	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.910954975623745
CAMB-76524	MN908947.3	6587	A	G	0.11	0.069	1.3e-38	2e-26	0.086924219910847	TAA	ORF1ab:nsp3	K1290E	A3868G	AAG>GAG	Missense	ORF1ab:nsp3	0.913075780089153
CAMB-76524	MN908947.3	857	C	A	0.014	0.026	1.3e-08	8.8e-14	0.0182762601000385	TCT	ORF1ab:nsp2	L18I	C52A	CTT>ATT	Missense	ORF1ab:nsp2	0.98162754905733
CAMB-76524	MN908947.3	9114	C	A	0.0071	0.0015	1.8e-05	0.0061	0.00512820512820513	CCT	ORF1ab:nsp4	P187H	C560A	CCT>CAT	Missense	ORF1ab:nsp4	0.994814174589456
CAMB-76524	MN908947.3	9858	TAT	-	0.0706666666666667	0.0913333333333333	9.3e-22;1.7e-24;1.5e-21	4.6e-27;2.3e-30;6.6e-27	0.0789955097289207	CTA	ORF1ab:nsp4	.	1304-1306-delinframe	.	no-SNV	ORF1ab:nsp4	0.921481481481481
CAMB-76533	MN908947.3	11083	G	T	0.23	0.18	7.2e-55	1.8e-42	0.209621310008945	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.783222343703409
CAMB-76533	MN908947.3	14408	C	T	1	1	0	0	0.999286811498793	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000603467193328944
CAMB-76533	MN908947.3	23403	A	G	1	1	0	0	0.99974001494914	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000227486919502129
CAMB-76533	MN908947.3	241	C	T	1	1	0	0	0.999725123694338	TCG	NA	NA	NA	NA	NA	NA	0.000274876305662452
CAMB-76533	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99852652259332	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000544365813826892
CAMB-76533	MN908947.3	3037	C	T	1	0.99	8.4e-293	0	0.996309963099631	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.003690036900369
CAMB-76533	MN908947.3	6740	C	T	1	0.63	1.4e-136	3.3e-186	0.685816876122083	ACG	ORF1ab:nsp3	R1341W	C4021T	CGG>TGG	Missense	ORF1ab:nsp3	0.314183123877917
CAMB-76533	MN908947.3	8932	T	C	0.0028	0.011	0.0053	9.3e-07	0.00682358353139615	TTA	ORF1ab:nsp4	F126F	T378C	TTT>TTC	Synonymous	ORF1ab:nsp4	0.993099746990723
CAMB-76542	MN908947.3	13914	T	G	0.0015	0.0098	0.0047	2.3e-06	0.00466635557629491	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.995333644423705
CAMB-76542	MN908947.3	14408	C	T	1	1	0	0	0.999473268369766	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00043894302519533
CAMB-76542	MN908947.3	21981	TTTTGGGTG	-	0.172222222222222	0.174444444444444	1.8e-29;7.7e-29;3.2e-26;2.2e-26;1.5e-30;1.7e-26;2e-25;8.3e-26;1.5e-27	6.4e-29;2.8e-28;1e-25;6.2e-26;2.2e-29;1.7e-25;4.7e-25;3.8e-25;5.5e-27	0.173526660430309	TTT	S	.	419-427-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.822742474916388
CAMB-76542	MN908947.3	21991	TTA	-	0.0776666666666667	0.39	1.4e-05;4.6e-08;3.8e-08	2.8e-21;9.6e-41;7.2e-41	0.232490272373541	TTT	S	.	429-431-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.765762822606991
CAMB-76542	MN908947.3	22002	A	C	0.46	0.067	4.1e-196	1.3e-26	0.263630916716597	AAA	S	K147T	A440C	AAA>ACA	Missense	GU280_gp02, spike glycoprotein	0.736369083283403
CAMB-76542	MN908947.3	23403	A	G	1	1	0	0	0.999956468744559	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.35312554414069e-05
CAMB-76542	MN908947.3	241	C	T	1	1	0	0	0.999889356052224	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-76542	MN908947.3	28881	GGG	AAC	1	1	2.3e-239;6.5e-265;7.69999999999999e-291	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-76542	MN908947.3	3037	C	T	1	1	5.1e-293	8.6e-269	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76542	MN908947.3	6448	T	C	0.65	0.11	0	2.1e-46	0.325141365811222	TTC	ORF1ab:nsp3	V1243V	T3729C	GTT>GTC	Synonymous	ORF1ab:nsp3	0.674858634188778
CAMB-76551	MN908947.3	10097	G	A	1	1	0	0	0.999617922889892	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.00024313997915943
CAMB-76551	MN908947.3	1060	C	T	0.0056	0.0079	0.00021	1.9e-05	0.006783703472005	CCT	ORF1ab:nsp2	T85T	C255T	ACC>ACT	Synonymous	ORF1ab:nsp2	0.993177197372537
CAMB-76551	MN908947.3	11074	C	INS	0.027	0.02	3e-05	0.0011	0.0233302667893284	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.976044158233671
CAMB-76551	MN908947.3	11075	T	-	0.039	0.04	2.8e-10	2.4e-10	0.0397388000127726	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955407606092538
CAMB-76551	MN908947.3	13008	C	T	0.009	0.014	3.7e-06	2.8e-08	0.0115924092409241	GCC	ORF1ab:nsp9	A108V	C323T	GCC>GTC	Missense	ORF1ab:nsp9	0.988201320132013
CAMB-76551	MN908947.3	13536	C	T	1	1	0	0	0.999369028303588	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000135208220659816
CAMB-76551	MN908947.3	14184	C	T	1	1	0	0	0.999896147055769	CCA	ORF1ab:RNA-dependent-RNA-polymerase	T239T	C717T	ACC>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	5.93445395605537e-05
CAMB-76551	MN908947.3	14408	C	T	1	1	0	0	0.996546921246591	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000797980384191283
CAMB-76551	MN908947.3	14788	A	G	0.01	0.0055	9.3e-07	8.4e-05	0.00748632306363375	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I441V	A1321G	ATC>GTC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.991892342431085
CAMB-76551	MN908947.3	1684	C	T	1	1	0	0	0.999691065163184	TCG	ORF1ab:nsp2	I293I	C879T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.000264801288699605
CAMB-76551	MN908947.3	17472	A	G	0.032	0.029	4.7e-16	1e-14	0.0307632791738151	TAA	ORF1ab:helicase	L412L	A1236G	CTA>CTG	Synonymous	ORF1ab:helicase	0.96921990110001
CAMB-76551	MN908947.3	18714	C	T	0.0047	0.0067	0.00028	3.6e-05	0.00564555202123402	CCT	ORF1ab:3'-to-5'-exonuclease	A225A	C675T	GCC>GCT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.994333382486149
CAMB-76551	MN908947.3	21058	C	T	1	1	0	0	0.999569204258724	CCC	ORF1ab:2'-O-ribose-methyltransferase	P134S	C400T	CCT>TCT	Missense	ORF1ab:2'-O-ribose-methyltransferase	6.15422487537695e-05
CAMB-76551	MN908947.3	23403	A	G	1	1	0	0	0.999535467671061	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.78844946641557e-05
CAMB-76551	MN908947.3	23731	C	T	1	1	0	0	0.999875714640815	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000124285359184688
CAMB-76551	MN908947.3	24095	G	T	0.016	0.012	6e-09	4.3e-07	0.0134498664724448	TGC	S	A845S	G2533T	GCT>TCT	Missense	GU280_gp02, spike glycoprotein	0.985894634620053
CAMB-76551	MN908947.3	241	C	T	1	1	0	0	0.998151627174111	TCG	NA	NA	NA	NA	NA	NA	0.000151505969335192
CAMB-76551	MN908947.3	25572	C	T	0.0081	0.013	9.5e-06	1.2e-07	0.0103084115292772	CCA	ORF3a	S60S	C180T	TCC>TCT	Synonymous	GU280_gp03	0.989657955806679
CAMB-76551	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998482549317147	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000192363181687025
CAMB-76551	MN908947.3	3037	C	T	1	1	0	0	0.999299915989919	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.66722673387473e-05
CAMB-76551	MN908947.3	3096	C	T	0.011	0.014	2.7e-05	2.6e-06	0.0123063615632618	TCA	ORF1ab:nsp3	S126L	C377T	TCA>TTA	Missense	ORF1ab:nsp3	0.987654320987654
CAMB-76551	MN908947.3	4002	C	T	1	1	0	0	0.999938141779042	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-76551	MN908947.3	4582	C	T	0.0067	0.0096	0.00017	9.3e-06	0.0082745129140561	ACG	ORF1ab:nsp3	N621N	C1863T	AAC>AAT	Synonymous	ORF1ab:nsp3	0.99077378592011
CAMB-76551	MN908947.3	5365	C	T	0.0067	0.0095	0.00022	1.4e-05	0.0083786231884058	ACA	ORF1ab:nsp3	Y882Y	C2646T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.991621376811594
CAMB-76551	MN908947.3	7732	C	T	0.011	0.016	2.7e-06	2.8e-08	0.0138241308793456	ACA	ORF1ab:nsp3	Y1671Y	C5013T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.986094069529652
CAMB-76551	MN908947.3	9208	T	C	0.0093	0.0047	4.3e-06	0.00043	0.00711139415167436	CTG	ORF1ab:nsp4	S218S	T654C	TCT>TCC	Synonymous	ORF1ab:nsp4	0.992835535742716
CAMB-76560	MN908947.3	11075	T	-	0.044	0.048	5.2e-11	1.8e-12	0.0455576234341033	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95253436762015
CAMB-76560	MN908947.3	12020	C	T	1	1	0	0	0.999601511684706	GCT	ORF1ab:nsp7	L60F	C178T	CTT>TTT	Missense	ORF1ab:nsp7	0.000141399079620536
CAMB-76560	MN908947.3	1218	C	T	0.072	0.075	1.3e-32	1.2e-34	0.0728790447409155	TCA	ORF1ab:nsp2	S138L	C413T	TCA>TTA	Missense	ORF1ab:nsp2	0.92710252819341
CAMB-76560	MN908947.3	13225	C	T	1	1	0	0	0.997009331399453	CCT	ORF1ab:nsp10	S67S	C201T	TCC>TCT	Synonymous	ORF1ab:nsp10	0.00195099410851121
CAMB-76560	MN908947.3	14408	C	T	1	1	0	0	0.997766148362888	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000263544294266029
CAMB-76560	MN908947.3	23403	A	G	1	1	0	0	0.998882353605256	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.51574300906535e-05
CAMB-76560	MN908947.3	241	C	T	1	1	0	0	0.999397436788802	TCG	NA	NA	NA	NA	NA	NA	0.000231755081230156
CAMB-76560	MN908947.3	26606	C	T	0.0063	0.0064	6.6e-05	3.9e-05	0.00638266489668396	TCC	M	F28F	C84T	TTC>TTT	Synonymous	GU280_gp05	0.993577108223715
CAMB-76560	MN908947.3	26873	C	T	0.18	0.19	2.4e-86	2.7e-89	0.186232153834166	ACA	M	N117N	C351T	AAC>AAT	Synonymous	GU280_gp05	0.813724556497346
CAMB-76560	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99831836084436	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.99201277955272e-05
CAMB-76560	MN908947.3	3037	C	T	1	1	0	0	0.999163553225896	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000167289354820722
CAMB-76560	MN908947.3	354	G	A	0.071	0.079	1.6e-32	1.9e-36	0.073738680465718	GGC	ORF1ab:leader-protein	G30D	G89A	GGC>GAC	Missense	ORF1ab:leader-protein	0.926261319534282
CAMB-76560	MN908947.3	3990	C	T	0.078	0.082	6e-35	5.2e-36	0.0795660923771659	ACT	ORF1ab:nsp3	T424I	C1271T	ACT>ATT	Missense	ORF1ab:nsp3	0.920433907622834
CAMB-7657F	MN908947.3	10097	G	A	1	1	0	0	0.999620031917319	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000227980849608633
CAMB-7657F	MN908947.3	11074	C	INS	0.12	0.14	2.8e-46	7.1e-56	0.131471977651176	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.868010107192743
CAMB-7657F	MN908947.3	11083	G	-	0.098	0.19	4.7e-42	2.3e-87	0.142310030395137	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	7.59878419452888e-05
CAMB-7657F	MN908947.3	11083	G	T	0.9	0.81	0	0	0.857462006079027	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	7.59878419452888e-05
CAMB-7657F	MN908947.3	11152	C	T	0.025	0.036	8e-13	1.3e-17	0.0304686483371442	TCA	ORF1ab:nsp6	V60V	C180T	GTC>GTT	Synonymous	ORF1ab:nsp6	0.969456992545498
CAMB-7657F	MN908947.3	1189	A	G	0.023	0.047	6e-12	1.8e-22	0.03437849677404	CAC	ORF1ab:nsp2	S128S	A384G	TCA>TCG	Synonymous	ORF1ab:nsp2	0.965573887579459
CAMB-7657F	MN908947.3	13536	C	T	1	1	0	0	0.999265785609398	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-7657F	MN908947.3	14184	C	T	1	1	0	0	0.999767382845542	CCA	ORF1ab:RNA-dependent-RNA-polymerase	T239T	C717T	ACC>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000232617154457791
CAMB-7657F	MN908947.3	14408	C	T	1	1	0	0	0.999154877203658	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000456366310024847
CAMB-7657F	MN908947.3	15265	G	-	0.026	0.012	3.3e-13	2.7e-07	0.0188920714242184	TGT	ORF1ab:RNA-dependent-RNA-polymerase	.	1798-1798-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.981107928575782
CAMB-7657F	MN908947.3	1684	C	T	1	1	0	0	0.999716593453309	TCG	ORF1ab:nsp2	I293I	C879T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.00023617212224269
CAMB-7657F	MN908947.3	21058	C	T	1	1	0	0	0.999904876656732	CCC	ORF1ab:2'-O-ribose-methyltransferase	P134S	C400T	CCT>TCT	Missense	ORF1ab:2'-O-ribose-methyltransferase	6.34155621789587e-05
CAMB-7657F	MN908947.3	22452	C	T	0.065	0.054	3e-07	1.1e-06	0.0589812332439678	TCA	S	S297L	C890T	TCA>TTA	Missense	GU280_gp02, spike glycoprotein	0.941018766756032
CAMB-7657F	MN908947.3	22993	C	T	0.76	0.75	0	0	0.757056808787056	GCA	S	S477S	C1431T	AGC>AGT	Synonymous	GU280_gp02, spike glycoprotein	0.242943191212944
CAMB-7657F	MN908947.3	23164	T	C	0.72	0.81	0	0	0.766250349519992	TTA	S	V534V	T1602C	GTT>GTC	Synonymous	GU280_gp02, spike glycoprotein	0.2336937272812
CAMB-7657F	MN908947.3	23403	A	G	1	1	0	0	0.999874876179553	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.34158802982118e-05
CAMB-7657F	MN908947.3	23731	C	T	1	1	0	0	0.999687108886108	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000312891113892365
CAMB-7657F	MN908947.3	241	C	T	1	1	0	0	0.999855553950599	TCG	NA	NA	NA	NA	NA	NA	5.77784197602196e-05
CAMB-7657F	MN908947.3	28253	C	T	0.063	0.14	3.9e-28	3.3e-65	0.103501925003955	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.896260745741258
CAMB-7657F	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999830795262267	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7657F	MN908947.3	29272	C	T	0.077	0.052	3.8e-35	3.7e-24	0.0657232852240139	ACA	N	Y333Y	C999T	TAC>TAT	Synonymous	GU280_gp10	0.934229702411734
CAMB-7657F	MN908947.3	3037	C	T	1	1	0	0	0.999790400335359	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7657F	MN908947.3	4002	C	T	1	1	0	0	1	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-7657F	MN908947.3	635	C	T	0.13	0.07	8.2e-58	4.8e-32	0.106471876440756	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.893499308437068
CAMB-7658E	MN908947.3	10428	T	C	0.012	0.0035	8.8e-08	0.00075	0.00740089604718426	GTT	ORF1ab:3C-like-proteinase	V125A	T374C	GTT>GCT	Missense	ORF1ab:3C-like-proteinase	0.992542392105711
CAMB-7658E	MN908947.3	11074	C	INS	0.15	0.053	1e-58	7.2e-13	0.111113571934798	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.888598511693834
CAMB-7658E	MN908947.3	11083	G	-	0.068	0.19	3.3e-29	9.3e-85	0.123714363518297	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	8.37889356710446e-05
CAMB-7658E	MN908947.3	11083	G	T	0.93	0.81	0	0	0.876118058610361	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	8.37889356710446e-05
CAMB-7658E	MN908947.3	14805	C	T	1	1	0	0	0.999911992490026	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-7658E	MN908947.3	15720	C	T	1	1	0	0	0.999896568665477	ACG	ORF1ab:RNA-dependent-RNA-polymerase	D751D	C2253T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	2.58578336306984e-05
CAMB-7658E	MN908947.3	18027	GG	TT	0.016	0.007055	1e-08;4.9e-08	0.47;2.1e-07	0.0108099187193134	TGG	ORF1ab:helicase	.	1791-1792-mnv	.	no-SNV	ORF1ab:helicase	0.985229736917475
CAMB-7658E	MN908947.3	18028	G	T	0.016	0.014	4.9e-08	2.1e-07	0.0147517789521868	GGC	ORF1ab:helicase	A598S	G1792T	GCA>TCA	Missense	ORF1ab:helicase	0.985019350006242
CAMB-7658E	MN908947.3	25006	C	T	1	1	0	0	0.99992145651047	TCA	S	F1148F	C3444T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	4.71260937180917e-05
CAMB-7658E	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-7658E	MN908947.3	26144	G	T	1	1	1.7e-162	6.2e-140	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7658E	MN908947.3	29353	C	T	0.091	0.062	1.7e-41	9.4e-29	0.0783428802869872	ACA	N	Y360Y	C1080T	TAC>TAT	Synonymous	GU280_gp10	0.921657119713013
CAMB-7658E	MN908947.3	6367	G	T	0.03	0.039	1.6e-15	4.7e-19	0.0346579462174078	AGG	ORF1ab:nsp3	Q1216H	G3648T	CAG>CAT	Missense	ORF1ab:nsp3	0.965254459984233
CAMB-7659D	MN908947.3	10078	C	T	1	1	0	0	0.999565635568242	TCC	ORF1ab:3C-like-proteinase	F8F	C24T	TTC>TTT	Synonymous	ORF1ab:3C-like-proteinase	0.00040333840091837
CAMB-7659D	MN908947.3	10796	G	A	0.02	0.01	2.5e-10	1.3e-06	0.0152088162335814	TGA	ORF1ab:3C-like-proteinase	D248N	G742A	GAC>AAC	Missense	ORF1ab:3C-like-proteinase	0.984750518482372
CAMB-7659D	MN908947.3	11075	T	-	0.028	0.034	1.8e-07	5.4e-09	0.0309798364555843	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.963248007696208
CAMB-7659D	MN908947.3	12988	G	T	1	1	0	0	0.999709930060915	TGG	ORF1ab:nsp9	M101I	G303T	ATG>ATT	Missense	ORF1ab:nsp9	3.22299932317014e-05
CAMB-7659D	MN908947.3	1421	G	A	1	1	0	0	0.998728342075982	CGA	ORF1ab:nsp2	E206K	G616A	GAA>AAA	Missense	ORF1ab:nsp2	0.00063582896200922
CAMB-7659D	MN908947.3	14408	C	T	1	1	0	0	0.99767323853018	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000841594574190275
CAMB-7659D	MN908947.3	1648	C	A	0.0079	0.0089	1.3e-05	4.4e-06	0.00837419101784664	TCA	ORF1ab:nsp2	I281I	C843A	ATC>ATA	Synonymous	ORF1ab:nsp2	0.991586585605021
CAMB-7659D	MN908947.3	19819	C	T	0.023	0.028	1.5e-11	1.7e-13	0.025119772109284	ACC	ORF1ab:endoRNAse	P67S	C199T	CCA>TCA	Missense	ORF1ab:endoRNAse	0.974837066770253
CAMB-7659D	MN908947.3	23403	A	G	1	1	0	0	0.999861356995073	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.59836187957255e-05
CAMB-7659D	MN908947.3	241	C	-	0.0089	0.003	2.9e-05	0.0044	0.0058945356061813	TCG	NA	NA	NA	NA	NA	NA	0.00031862354628007
CAMB-7659D	MN908947.3	241	C	T	0.99	1	0	0	0.993667357017684	TCG	NA	NA	NA	NA	NA	NA	0.00031862354628007
CAMB-7659D	MN908947.3	25242	TAG	-	0.0263333333333333	0.035	2.1e-06;5.3e-08;1.5e-08	1e-08;5.2e-09;4.5e-11	0.028458942632171	ATA	S	.	3680-3682-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.975489415884132
CAMB-7659D	MN908947.3	26029	C	A	0.0082	0.0056	3.3e-05	0.00051	0.00723504106374658	CCA	ORF3a	Q213K	C637A	CAG>AAG	Missense	GU280_gp03	0.992178333985139
CAMB-7659D	MN908947.3	26182	T	C	0.02	0.021	8.8e-10	1.2e-09	0.0201959608078384	TTA	ORF3a	Y264H	T790C	TAT>CAT	Missense	GU280_gp03	0.979804039192162
CAMB-7659D	MN908947.3	28079	G	T	0.021	0.023	3.3e-09	7.9e-10	0.0220780922431866	TGG	ORF8	V62V	G186T	GTG>GTT	Synonymous	GU280_gp09	0.977856394129979
CAMB-7659D	MN908947.3	28833	C	T	0.067	0.075	3.9e-29	1.2e-32	0.0704202823209501	TCA	N	S187L	C560T	TCA>TTA	Missense	GU280_gp10	0.92957971767905
CAMB-7659D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999231603688302	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7659D	MN908947.3	29164	T	C	0.0081	0.01	1.4e-05	1.4e-06	0.00907785119218615	ATT	N	D297D	T891C	GAT>GAC	Synonymous	GU280_gp10	0.990318873886814
CAMB-7659D	MN908947.3	29738	CCACGCGGAGTACGATCGAGTGT	-	1	1	0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0	0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0	0.999937535136486	GCC	NA	NA	NA	NA	NA	NA	6.25078134766846e-05
CAMB-7659D	MN908947.3	3037	C	T	1	1	0	0	0.99957921312855	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000126236061434883
CAMB-7659D	MN908947.3	5310	C	T	0.0085	0.0049	2.9e-05	0.00085	0.0065550743298607	ACA	ORF1ab:nsp3	T864I	C2591T	ACA>ATA	Missense	ORF1ab:nsp3	0.993444925670139
CAMB-765AC	MN908947.3	1059	C	T	1	1	0	0	0.999863893728223	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.000108885017421603
CAMB-765AC	MN908947.3	11074	C	INS	0.025	0.027	4.7e-05	2.2e-05	0.0255452964003747	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.973451090592801
CAMB-765AC	MN908947.3	11075	T	-	0.029	0.028	1.3e-07	1.3e-07	0.0287325705285589	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.966947700004632
CAMB-765AC	MN908947.3	13006	T	C	1	1	0	0	0.997664390945023	CTG	ORF1ab:nsp9	A107A	T321C	GCT>GCC	Synonymous	ORF1ab:nsp9	0.000389268175829441
CAMB-765AC	MN908947.3	1437	C	T	1	1	0	0	0.999056192827065	TCT	ORF1ab:nsp2	S211F	C632T	TCT>TTT	Missense	ORF1ab:nsp2	7.26005517641934e-05
CAMB-765AC	MN908947.3	14408	C	T	1	1	0	0	0.996843453443459	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000655512863179338
CAMB-765AC	MN908947.3	23403	A	G	1	1	0	0	0.999311621361154	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.05946061709321e-05
CAMB-765AC	MN908947.3	241	C	T	1	1	0	0	0.998858363947719	TCG	NA	NA	NA	NA	NA	NA	0.000307363552537213
CAMB-765AC	MN908947.3	25552	G	A	1	1	0	0	0.998810490078088	TGC	ORF3a	A54T	G160A	GCT>ACT	Missense	GU280_gp03	8.39654062526239e-05
CAMB-765AC	MN908947.3	25563	G	T	1	1	0	0	0.999641912736889	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	8.26355222565007e-05
CAMB-765AC	MN908947.3	25688	C	T	1	1	0	0	0.999685551071747	GCT	ORF3a	A99V	C296T	GCT>GTT	Missense	GU280_gp03	0
CAMB-765AC	MN908947.3	25797	C	T	0.031	0.028	8.6e-15	1.2e-13	0.0294009451314412	CCA	ORF3a	S135S	C405T	TCC>TCT	Synonymous	GU280_gp03	0.969014403350406
CAMB-765AC	MN908947.3	27383	A	G	0.27	0.27	2.1e-136	3.7e-135	0.273829896666199	GAT	ORF6	D61G	A182G	GAT>GGT	Missense	GU280_gp06	0.72591761350353
CAMB-765AC	MN908947.3	28863	C	T	0.26	0.27	7.2e-125	5.8e-129	0.26836303698362	TCA	N	S197L	C590T	TCA>TTA	Missense	GU280_gp10	0.730967343154425
CAMB-765AC	MN908947.3	3037	C	T	1	1	0	0	0.998975013097055	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.83324601963419e-05
CAMB-765BB	MN908947.3	11075	T	-	0.018	0.098	1.5e-05	1.2e-24	0.0481004495191852	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951766781101227
CAMB-765BB	MN908947.3	11309	T	C	0.0022	0.021	0.0084	4.6e-11	0.00905406885473331	CTG	ORF1ab:nsp6	C113R	T337C	TGT>CGT	Missense	ORF1ab:nsp6	0.99081815194772
CAMB-765BB	MN908947.3	11416	C	T	0.016	0.012	1.4e-07	7.7e-06	0.0141003948110547	TCG	ORF1ab:nsp6	L148L	C444T	CTC>CTT	Synonymous	ORF1ab:nsp6	0.985899605188945
CAMB-765BB	MN908947.3	12061	AG	-	0.0131	0.0123	5.8e-06;9.8e-07	7.8e-06;1.5e-06	0.012864657357617	AAG	ORF1ab:nsp7	.	219-220-delfrshift	.	no-SNV	ORF1ab:nsp7	0.990808125091334
CAMB-765BB	MN908947.3	12141	C	-	0.016	0.024	0.00043	1.7e-05	0.0190745134266938	ACT	ORF1ab:nsp8	.	50-50-delfrshift	.	no-SNV	ORF1ab:nsp8	0.980820508513721
CAMB-765BB	MN908947.3	12164	G	T	0.017	0.012	8.7e-07	1.8e-05	0.0150243552706493	GGC	ORF1ab:nsp8	A25S	G73T	GCT>TCT	Missense	ORF1ab:nsp8	0.984880754064483
CAMB-765BB	MN908947.3	12459	C	T	0.1	0.09	6.6e-47	6.1e-41	0.0989323993585957	ACA	ORF1ab:nsp8	T123I	C368T	ACA>ATA	Missense	ORF1ab:nsp8	0.901004304160689
CAMB-765BB	MN908947.3	12578	G	T	0.056	0.053	9.3e-19	1.3e-17	0.0552198960236054	AGA	ORF1ab:nsp8	D163Y	G487T	GAT>TAT	Missense	ORF1ab:nsp8	0.940845862020514
CAMB-765BB	MN908947.3	12747	CTG	-	0.0113333333333333	0.00303333333333333	2.7e-07;2.9e-07;2e-07	NA;1.1e-06;NA	0.00882438405187575	ACT	ORF1ab:nsp9	.	62-64-delinframe	.	no-SNV	ORF1ab:nsp9	0.991142319519023
CAMB-765BB	MN908947.3	13571	G	T	0.12	0.1	3.1e-22	2.8e-17	0.113297872340426	GGT	ORF1ab:RNA-dependent-RNA-polymerase	G35V	G104T	GGT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.871808510638298
CAMB-765BB	MN908947.3	14408	C	T	1	1	0	0	0.999397914884178	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000475330354596445
CAMB-765BB	MN908947.3	15836	G	T	0.012	0.012	2.4e-07	1.1e-07	0.0122302013557822	TGT	ORF1ab:RNA-dependent-RNA-polymerase	C790F	G2369T	TGT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.987769798644218
CAMB-765BB	MN908947.3	1681	G	T	0.044	0.02	4.5e-21	4.8e-10	0.03998096144693	AGA	ORF1ab:nsp2	E292D	G876T	GAG>GAT	Missense	ORF1ab:nsp2	0.96001903855307
CAMB-765BB	MN908947.3	1709	G	T	0.016	0.018	4e-09	7.9e-09	0.0166444217633666	TGC	ORF1ab:nsp2	A302S	G904T	GCT>TCT	Missense	ORF1ab:nsp2	0.983355578236633
CAMB-765BB	MN908947.3	17119	CTAG	-	0.0068	0.004325	3.5e-05;3.5e-05;7.1e-05;7.5e-05	NA;NA;8.8e-06;9.8e-06	0.00567880395466602	CCT	ORF1ab:helicase	.	883-886-delfrshift	.	no-SNV	ORF1ab:helicase	0.996163421410273
CAMB-765BB	MN908947.3	17211	G	T	0.018	0.0087	9.3e-10	6.2e-06	0.0137518303940918	TGC	ORF1ab:helicase	L325F	G975T	TTG>TTT	Missense	ORF1ab:helicase	0.986226947645424
CAMB-765BB	MN908947.3	17425	G	T	0.0064	0.0069	4.4e-05	2e-05	0.00658090167493088	TGT	ORF1ab:helicase	V397L	G1189T	GTG>TTG	Missense	ORF1ab:helicase	0.990562804195325
CAMB-765BB	MN908947.3	17443	G	T	0.017	0.011	1.5e-09	6.2e-07	0.015105573625889	TGC	ORF1ab:helicase	A403S	G1207T	GCT>TCT	Missense	ORF1ab:helicase	0.961905286950769
CAMB-765BB	MN908947.3	17443	GC	TT	0.02	0.005585	1.5e-09;4.6e-12	6.2e-07;0.49	0.0154443343244136	TGC	ORF1ab:helicase	.	1207-1208-mnv	.	no-SNV	ORF1ab:helicase	0.961905286950769
CAMB-765BB	MN908947.3	17564	G	T	0.014	0.017	7.3e-08	3.4e-09	0.0151220627751415	CGT	ORF1ab:helicase	R443L	G1328T	CGT>CTT	Missense	ORF1ab:helicase	0.984563489794752
CAMB-765BB	MN908947.3	17675	T	C	0.0016	0.021	0.0079	1.7e-11	0.00772853185595568	ATC	ORF1ab:helicase	I480T	T1439C	ATC>ACC	Missense	ORF1ab:helicase	0.992271468144044
CAMB-765BB	MN908947.3	20922	G	T	0.013	0.042	7.6e-07	1.6e-17	0.0226324862370016	GGT	ORF1ab:2'-O-ribose-methyltransferase	W88C	G264T	TGG>TGT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.977256297614414
CAMB-765BB	MN908947.3	20925	G	T	0.032	0.021	2.1e-15	6.3e-11	0.0283394007280874	TGC	ORF1ab:2'-O-ribose-methyltransferase	L89F	G267T	TTG>TTT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.9715485858303
CAMB-765BB	MN908947.3	21137	A	G	0.39	0.48	2.6e-180	3.5e-224	0.417426487348986	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.582573512651014
CAMB-765BB	MN908947.3	22870	G	T	0.028	0.0054	1.7e-14	0.00018	0.0147306705753023	GGA	S	W436C	G1308T	TGG>TGT	Missense	GU280_gp02, spike glycoprotein	0.982044705020154
CAMB-765BB	MN908947.3	22899	G	T	0.04	0.032	4.4e-12	3.2e-10	0.0348494554772582	GGT	S	G446V	G1337T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.965150544522742
CAMB-765BB	MN908947.3	23403	A	G	1	1	0	0	0.999904567404043	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.72595575744851e-05
CAMB-765BB	MN908947.3	241	C	T	1	1	0	0	0.999573180195561	TCG	NA	NA	NA	NA	NA	NA	0.00031041440322831
CAMB-765BB	MN908947.3	24129	AC	GT	0.0205	0.0225	NA;4.4e-19	3.3e-13;1.8e-09	0.0215412820009167	AAC	S	.	2567-2568-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.978964941569282
CAMB-765BB	MN908947.3	24130	C	T	0.041	0.019	4.4e-19	1.8e-09	0.0310251798561151	ACG	S	N856N	C2568T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.960110483042138
CAMB-765BB	MN908947.3	24473	G	-	0.026	0.029	7.1e-12	1.5e-10	0.0269671222755818	TGG	S	.	2911-2911-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.973032877724418
CAMB-765BB	MN908947.3	24933	G	T	0.083	0.025	2.6e-13	4.9e-05	0.0605004044517587	GGT	S	G1124V	G3371T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.939415915874034
CAMB-765BB	MN908947.3	26011	T	C	0.093	0.031	2.4e-19	1.6e-05	0.075801749271137	CTT	ORF3a	F207L	T619C	TTC>CTC	Missense	GU280_gp03	0.924198250728863
CAMB-765BB	MN908947.3	26151	C	T	0.1	0.14	2.8e-20	3.6e-17	0.11377245508982	CCG	ORF3a	S253S	C759T	TCC>TCT	Synonymous	GU280_gp03	0.88622754491018
CAMB-765BB	MN908947.3	26574	GAACAATGGAACCTAGTAATAGGTTTCCTA	-	0.0634666666666667	0.000768466666666667	1.6e-11;8.8e-13;1.1e-11;1.4e-11;4.5e-12;5.7e-12;1.7e-11;8e-13;1.1e-11;1.6e-11;5.7e-12;6.4e-12;2.1e-11;8.9e-12;1.3e-12;7.6e-12;3.4e-12;6.9e-13;8e-12;7.5e-12;1.4e-12;4.8e-12;6e-12;4.1e-12;3.6e-12;9.2e-12;6.8e-12;5.4e-12;5.9e-12;4.8e-13	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;4.4e-05;NA	0.0289591567852437	TGA	M	.	52-81-delinframe	.	no-SNV	GU280_gp05	0.971850413814243
CAMB-765BB	MN908947.3	28881	GGG	AAC	0.986666666666667	1	0;0;0	0;0;0	0.990288962576978	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.0100625509926571
CAMB-765BB	MN908947.3	29096	G	T	0.035	0.023	7.4e-17	1.7e-11	0.0304231664224769	CGG	N	G275C	G823T	GGC>TGC	Missense	GU280_gp10	0.969490648970094
CAMB-765BB	MN908947.3	3037	C	T	1	1	0	0	0.999111505997335	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-765BB	MN908947.3	3062	G	T	0.012	0.02	2.1e-07	7.6e-10	0.0152083333333333	AGA	ORF1ab:nsp3	E115*	G343T	GAA>TAA	Nonsense	ORF1ab:nsp3	0.984791666666667
CAMB-765BB	MN908947.3	3155	G	T	0.037	0.024	8.8e-17	3.2e-11	0.0321269595509967	TGC	ORF1ab:nsp3	A146S	G436T	GCC>TCC	Missense	ORF1ab:nsp3	0.967679504548094
CAMB-765BB	MN908947.3	4208	A	-	0.038	0.026	2e-18	2.9e-13	0.0337536303747255	GAA	ORF1ab:nsp3	.	1489-1489-delfrshift	.	no-SNV	ORF1ab:nsp3	0.966175533045265
CAMB-765BB	MN908947.3	4208	AA	-	0.0395	0.013	2e-18;8.6e-20	2.9e-13;NA	0.0300314580437486	GAA	ORF1ab:nsp3	.	1489-1490-delfrshift	.	no-SNV	ORF1ab:nsp3	0.966175533045265
CAMB-765BB	MN908947.3	519	T	G	0.021	0.018	8.5e-10	6.5e-08	0.0206029060941227	ATG	ORF1ab:leader-protein	M85R	T254G	ATG>AGG	Missense	ORF1ab:leader-protein	0.944408298995157
CAMB-765BB	MN908947.3	522	TT	-	0.049	0.0755	7.9e-07;7.4e-07	3.5e-10;1.7e-10	0.0535184034251778	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.943806428313471
CAMB-765BB	MN908947.3	5655	TAG	-	0.0253333333333333	0.0303333333333333	NA;7.3e-18;5.3e-18	3.6e-11;7.2e-11;5.3e-21	0.0330176383699713	CTA	ORF1ab:nsp3	.	2936-2938-delinframe	.	no-SNV	ORF1ab:nsp3	0.963684676705049
CAMB-765BB	MN908947.3	6052	G	T	0.069	0.032	4.8e-21	3.3e-12	0.0473751600512164	AGT	ORF1ab:nsp3	K1111N	G3333T	AAG>AAT	Missense	ORF1ab:nsp3	0.951984635083227
CAMB-765BB	MN908947.3	7830	T	C	0.0031	0.031	0.002	1.3e-08	0.00563733166301284	GTT	ORF1ab:nsp3	V1704A	T5111C	GTT>GCT	Missense	ORF1ab:nsp3	0.994049483244598
CAMB-765BB	MN908947.3	8901	G	T	0.03	0.04	8.5e-14	4.4e-18	0.0359337181158071	GGT	ORF1ab:nsp4	G116V	G347T	GGT>GTT	Missense	ORF1ab:nsp4	0.964066281884193
CAMB-765BB	MN908947.3	9249	G	T	0.051	0.051	2.8e-21	3.6e-19	0.0507876154263987	GGT	ORF1ab:nsp4	G232V	G695T	GGT>GTT	Missense	ORF1ab:nsp4	0.918794133623031
CAMB-765BB	MN908947.3	9536	G	T	0.021	0.013	1.8e-11	7.3e-08	0.0171119395257326	TGT	ORF1ab:nsp4	V328L	G982T	GTA>TTA	Missense	ORF1ab:nsp4	0.982771564668116
CAMB-765BB	MN908947.3	9609	ATCTTACTAATGATGTTTCTTTTTTAGCACATATTCAGTGGATGGTTATG	-	0.00362656	0.01542	4.2e-13;2.3e-13;5.6e-13;5.2e-13;1e-12;1.1e-12;7.3e-12;0.46;0.46;0.46;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.5;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	2.4e-08;1.8e-08;2.4e-08;2.6e-08;4.3e-08;4.6e-08;1.2e-07;3.9e-08;9.6e-09;1.3e-07;6.9e-08;1.1e-07;2.5e-07;9.4e-08;3.8e-08;2.8e-07;1e-07;4.9e-08;8.9e-09;2.1e-06;4.6e-08;2.1e-08;1.1e-07;4.8e-08;2e-07;1.9e-07;8.8e-08;7.8e-08;2.9e-07;1e-06;4.8e-06;1.3e-06;9.7e-08;1.1e-08;1.6e-07;9.9e-08;7.8e-08;2.9e-08;1.5e-06;6.4e-08;3.1e-07;3.2e-07;5.9e-07;4.1e-08;2.1e-08;6.4e-09;5.5e-09;5.2e-09;5.8e-09;1.8e-08	0.00763795475980642	TAT	ORF1ab:nsp4	.	1055-1104-delfrshift	.	no-SNV	ORF1ab:nsp4	0.979391473553865
CAMB-765BB	MN908947.3	9945	G	T	0.02	0.027	3.4e-10	7.5e-13	0.0233333333333333	AGA	ORF1ab:nsp4	R464I	G1391T	AGA>ATA	Missense	ORF1ab:nsp4	0.976666666666667
CAMB-765CA	MN908947.3	11074	C	INS	0.11	0.11	1.4e-38	5.4e-31	0.109551833408782	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.874855389567929
CAMB-765CA	MN908947.3	11074	C	T	0.014	0.014	2.3e-08	2e-06	0.0136562547155576	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.874855389567929
CAMB-765CA	MN908947.3	11083	G	-	0.16	0.13	2.9e-70	7.1e-59	0.152742399102615	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-765CA	MN908947.3	11083	G	T	0.84	0.86	0	0	0.847140753896848	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-765CA	MN908947.3	14805	C	T	1	1	0	0	0.998523173605656	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000785545954438335
CAMB-765CA	MN908947.3	1514	C	T	1	1	0	0	0.999585749792875	CCA	ORF1ab:nsp2	H237Y	C709T	CAT>TAT	Missense	ORF1ab:nsp2	0.000138083402375035
CAMB-765CA	MN908947.3	20759	C	T	0.27	0.27	2.9e-127	3e-131	0.268226230740323	GCA	ORF1ab:2'-O-ribose-methyltransferase	A34V	C101T	GCA>GTA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.731280533633972
CAMB-765CA	MN908947.3	2480	A	G	1	1	0	0	0.999892767143853	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	5.36164280735617e-05
CAMB-765CA	MN908947.3	2558	C	T	1	1	0	0	0.998510125627679	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000110361064616403
CAMB-765CA	MN908947.3	26144	G	T	1	1	0	0	0.999769452449568	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	3.84245917387128e-05
CAMB-765CA	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.03184375	0.02840625	6.4e-05;2e-04;3.9e-05;4e-05;1.6e-05;2.2e-05;1.6e-05;3.5e-05;2.4e-05;3e-05;5e-05;2.2e-05;4.4e-05;2.7e-05;2.7e-05;1.9e-05;4.8e-05;2.2e-05;3.2e-05;2.6e-05;1.6e-05;4.2e-05;2.3e-05;1e-05;2.9e-05;4e-05;3.8e-05;1.7e-05;3.7e-05;1.2e-05;2.2e-05;1.6e-05	0.00014;0.00039;9.9e-05;1e-04;4.9e-05;6.9e-05;5.9e-05;9.8e-05;7.6e-05;8.4e-05;0.00013;6.5e-05;0.00011;7.6e-05;7.4e-05;7.3e-05;0.00012;7.7e-05;9.7e-05;7.2e-05;5.2e-05;0.00011;7.4e-05;3.2e-05;7.4e-05;0.00011;1e-04;4.4e-05;1e-04;3.9e-05;8.1e-05;5e-05	0.0308570684971615	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.970212593969768
CAMB-765CA	MN908947.3	29140	G	T	1	1	0	0	0.999645662316187	AGG	N	Q289H	G867T	CAG>CAT	Missense	GU280_gp10	0.000147640701588614
CAMB-765CA	MN908947.3	5310	C	T	0.027	0.028	1.7e-12	6e-13	0.0271181805751789	ACA	ORF1ab:nsp3	T864I	C2591T	ACA>ATA	Missense	ORF1ab:nsp3	0.972790665876669
CAMB-765CA	MN908947.3	6539	C	T	0.034	0.028	2.2e-15	6.1e-13	0.0318346520742439	CCA	ORF1ab:nsp3	H1274Y	C3820T	CAC>TAC	Missense	ORF1ab:nsp3	0.967906529616209
CAMB-765E8	MN908947.3	11074	C	INS	0.025	0.023	4.3e-05	0.00027	0.0243885927054244	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.975222137598375
CAMB-765E8	MN908947.3	11075	T	-	0.042	0.043	1.9e-10	2.8e-11	0.0421608544285124	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95339883165162
CAMB-765E8	MN908947.3	14408	C	T	1	1	0	0	0.998155520169851	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000490976645435244
CAMB-765E8	MN908947.3	1973	C	T	0.0091	0.0078	2.9e-06	7.8e-06	0.00860862262038074	ACT	ORF1ab:nsp2	L390L	C1168T	CTA>TTA	Synonymous	ORF1ab:nsp2	0.991204740574841
CAMB-765E8	MN908947.3	19862	C	T	0.026	0.023	1e-12	1.4e-11	0.025275088938529	GCT	ORF1ab:endoRNAse	A81V	C242T	GCT>GTT	Missense	ORF1ab:endoRNAse	0.974559444030777
CAMB-765E8	MN908947.3	23403	A	G	1	1	0	0	0.999617086932528	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000112621490432804
CAMB-765E8	MN908947.3	241	C	T	1	1	0	0	0.9987009496506	TCG	NA	NA	NA	NA	NA	NA	8.95896792689482e-05
CAMB-765E8	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999497875627655	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	8.41928015154704e-05
CAMB-765E8	MN908947.3	29692	G	T	0.014	0.011	1.9e-07	2.1e-06	0.0127345082433201	TGT	NA	NA	NA	NA	NA	NA	0.987208641273451
CAMB-765E8	MN908947.3	3037	C	T	1	1	0	0	0.999363310783924	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000198965380023876
CAMB-765E8	MN908947.3	4432	G	T	0.0089	0.0072	5.7e-06	2e-05	0.00829140098193004	TGC	ORF1ab:nsp3	M571I	G1713T	ATG>ATT	Missense	ORF1ab:nsp3	0.991036323262778
CAMB-765F7	MN908947.3	11074	C	INS	0.04	0.026	1.2e-08	5.5e-05	0.0334889618998213	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.966251657156032
CAMB-765F7	MN908947.3	11075	T	-	0.05	0.057	5.9e-13	8.3e-15	0.0529682502535299	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.942845255740177
CAMB-765F7	MN908947.3	13458	C	T	0.021	0.035	1.5e-09	1.8e-13	0.0253285543608124	TCG	ORF1ab:nsp11	S6L	C17T	TCG>TTG	Missense	ORF1ab:nsp11	0.974671445639188
CAMB-765F7	MN908947.3	14408	C	T	0.98	1	0	0	0.989318445850007	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00070995223957661
CAMB-765F7	MN908947.3	1518	ACAAGTGTGCCTATTGGGTTCCACGTG	-	0.0010037037037037	0.00844814814814815	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00012;0.00014;0.00015;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00025;0.00024;0.00025;0.00022;3e-04;0.00027;0.00026;0.00015;0.00021;0.00018;0.00017;0.00031;3e-04;0.00018;0.00022;0.00024;8.3e-05;6.6e-05;4.2e-05;6.7e-05;9.8e-05;8.4e-05;7.5e-05;6.6e-05;7.2e-05;6.3e-05;5.4e-05	0.00401606425702811	AAC	ORF1ab:nsp2	.	713-739-delinframe	.	no-SNV	ORF1ab:nsp2	0.995983935742972
CAMB-765F7	MN908947.3	15339	G	A	0.0055	0.017	8.8e-05	1.6e-09	0.00956641431520991	TGG	ORF1ab:RNA-dependent-RNA-polymerase	M624I	G1872A	ATG>ATA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.99036476256022
CAMB-765F7	MN908947.3	15372	G	T	0.0048	0.0088	0.00052	1.1e-05	0.00623139237000623	CGT	ORF1ab:RNA-dependent-RNA-polymerase	T635T	G1905T	ACG>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.993630132243994
CAMB-765F7	MN908947.3	16466	C	T	0.024	0.038	3.5e-07	2.5e-10	0.0309278350515464	CCA	ORF1ab:helicase	P77L	C230T	CCA>CTA	Missense	ORF1ab:helicase	0.969072164948454
CAMB-765F7	MN908947.3	17125	C	T	0.007	0.007	3.4e-05	3e-05	0.00701696860398393	TCT	ORF1ab:helicase	L297F	C889T	CTC>TTC	Missense	ORF1ab:helicase	0.992933847036642
CAMB-765F7	MN908947.3	17144	G	A	0.018	0.0044	1.4e-09	0.0021	0.0132720465130437	CGC	ORF1ab:helicase	R303H	G908A	CGC>CAC	Missense	ORF1ab:helicase	0.986697513013302
CAMB-765F7	MN908947.3	2192	AG	-	0.0025	0.012	0.005;0.0051	4.1e-07;4.3e-07	0.00670578373847443	TAG	ORF1ab:nsp2	.	1387-1388-delfrshift	.	no-SNV	ORF1ab:nsp2	0.993284566494784
CAMB-765F7	MN908947.3	23352	TTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGATGTT	-	0.00509642857142857	0.000110446428571429	0.00017;0.00026;0.00028;9.6e-05;8.3e-05;9.6e-05;0.00016;0.00013;0.00016;0.00014;1e-04;0.00012;0.00013;6.1e-05;8.2e-05;0.00014;0.00026;8.3e-05;5.2e-05;8.3e-05;7.3e-05;0.00014;7.6e-05;0.00013;0.00021;6e-05;0.00012;5.6e-05;0.00023;0.00017;7.6e-05;0.00022;0.00016;8.5e-05;0.00023;0.00024;0.00023;0.00031;0.00055;0.00019;0.00021;0.00016;4e-04;0.00023;0.00015;0.00026;2e-04;0.00021;0.00013;0.00017;0.00016;1.6e-05;0.00031;0.00028;0.00015;0.00017	NA;NA;NA;NA;NA;NA;NA;NA;0.19;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00014;NA;NA;NA;NA	0.00292089389723293	GTT	S	.	1790-1845-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.997051266575848
CAMB-765F7	MN908947.3	241	C	T	1	1	0	0	0.999778888250122	TCG	NA	NA	NA	NA	NA	NA	0.000176889399902711
CAMB-765F7	MN908947.3	24544	T	C	0.033	0.044	2.1e-14	9.1e-17	0.0370588235294118	ATA	S	D994D	T2982C	GAT>GAC	Synonymous	GU280_gp02, spike glycoprotein	0.962352941176471
CAMB-765F7	MN908947.3	25977	T	C	0.01	0.0082	1.1e-05	0.00025	0.00948991696322657	CTG	ORF3a	S195S	T585C	TCT>TCC	Synonymous	GU280_gp03	0.990510083036773
CAMB-765F7	MN908947.3	27925	C	T	0.015	0.011	2.4e-07	4.7e-06	0.0126972610194087	ACA	ORF8	T11I	C32T	ACA>ATA	Missense	GU280_gp09	0.987302738980591
CAMB-765F7	MN908947.3	28253	C	A	0.023	0.0071	3.3e-12	1.7e-05	0.0167238001958864	TCA	ORF8	F120L	C360A	TTC>TTA	Missense	GU280_gp09	0.976322233104799
CAMB-765F7	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999002493765586	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000244061178001952
CAMB-765F7	MN908947.3	29449	G	T	0.011	0.0045	6.8e-06	0.0019	0.00789330430048993	TGA	N	V392V	G1176T	GTG>GTT	Synonymous	GU280_gp10	0.99210669569951
CAMB-765F7	MN908947.3	2998	T	C	0.0022	0.0094	0.0051	3.7e-06	0.00568310979768129	CTG	ORF1ab:nsp3	S93S	T279C	TCT>TCC	Synonymous	ORF1ab:nsp3	0.994203228006365
CAMB-765F7	MN908947.3	3037	C	T	1	1	0	0	0.998770441411533	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000491823435386696
CAMB-765F7	MN908947.3	8994	C	T	0.054	0.047	3e-25	6.5e-22	0.0517261088248743	ACA	ORF1ab:nsp4	T147I	C440T	ACA>ATA	Missense	ORF1ab:nsp4	0.948273891175126
CAMB-765F7	MN908947.3	9661	C	T	0.011	0.0084	4.6e-07	7.2e-06	0.0101156443225623	TCA	ORF1ab:nsp4	F369F	C1107T	TTC>TTT	Synonymous	ORF1ab:nsp4	0.989858484464337
CAMB-76612	MN908947.3	11074	C	INS	0.36	0.27	1e-131	8.5e-104	0.287265494812665	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.712035693167769
CAMB-76612	MN908947.3	11083	G	-	0.019	0.024	9.4e-08	1.8e-10	0.0232173486890468	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.000122518990443519
CAMB-76612	MN908947.3	11083	G	T	0.98	0.98	0	0	0.976292575349179	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.000122518990443519
CAMB-76612	MN908947.3	11109	C	T	1	1	0	0	0.99985121261717	GCT	ORF1ab:nsp6	A46V	C137T	GCT>GTT	Missense	ORF1ab:nsp6	0.000148787382829936
CAMB-76612	MN908947.3	13077	C	T	0.34	0.37	7.8e-175	3.4e-195	0.355349863609894	GCT	ORF1ab:nsp10	A18V	C53T	GCT>GTT	Missense	ORF1ab:nsp10	0.644435590155393
CAMB-76612	MN908947.3	14411	C	T	0.2	0.12	1.2e-87	1.5e-52	0.156174782447695	ACA	ORF1ab:RNA-dependent-RNA-polymerase	T315I	C944T	ACA>ATA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.843825217552305
CAMB-76612	MN908947.3	14805	C	T	1	1	0	0	0.999829336974145	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	8.53315129277242e-05
CAMB-76612	MN908947.3	16949	C	T	0.21	0.13	1.2e-74	5.4e-55	0.150591845681719	CCT	ORF1ab:helicase	P238L	C713T	CCT>CTT	Missense	ORF1ab:helicase	0.848750548005261
CAMB-76612	MN908947.3	17536	C	T	0.18	0.077	9.2e-80	5.1e-35	0.114546283629731	TCC	ORF1ab:helicase	P434S	C1300T	CCA>TCA	Missense	ORF1ab:helicase	0.885362517099863
CAMB-76612	MN908947.3	17871	A	G	0.44	0.2	1.1e-223	1.5e-87	0.323575866062967	TAT	ORF1ab:helicase	I545M	A1635G	ATA>ATG	Missense	ORF1ab:helicase	0.67631883752764
CAMB-76612	MN908947.3	23707	C	T	1	1	0	0	1	CCA	S	P715P	C2145T	CCC>CCT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-76621	MN908947.3	10038	C	T	0.0041	0.0063	0.00038	3.2e-05	0.00484002227266887	ACC	ORF1ab:nsp4	T495I	C1484T	ACC>ATC	Missense	ORF1ab:nsp4	0.995117145671821
CAMB-76621	MN908947.3	11075	T	-	0.041	0.029	1.4e-10	2.3e-08	0.0375448339696864	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955474565158703
CAMB-76621	MN908947.3	12634	A	G	0.0049	0.0084	0.00021	4.6e-06	0.00603272928994083	CAT	ORF1ab:nsp8	A181A	A543G	GCA>GCG	Synonymous	ORF1ab:nsp8	0.993944156804734
CAMB-76621	MN908947.3	1440	G	A	1	1	0	0	1	GGC	ORF1ab:nsp2	G212D	G635A	GGC>GAC	Missense	ORF1ab:nsp2	0
CAMB-76621	MN908947.3	23589	C	T	0.19	0.2	7e-85	4.9e-90	0.191605154510196	ACT	S	T676I	C2027T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.808207181283623
CAMB-76621	MN908947.3	23895	C	A	0.01	0.0081	1.1e-06	6.6e-06	0.00947274939973029	ACC	S	T778N	C2333A	ACC>AAC	Missense	GU280_gp02, spike glycoprotein	0.99052725060027
CAMB-76621	MN908947.3	25324	C	T	0.03	0.033	5e-15	2.3e-16	0.0311927170782051	GCA	S	C1254C	C3762T	TGC>TGT	Synonymous	GU280_gp02, spike glycoprotein	0.968653244812767
CAMB-76621	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0378918918918919	0.0237567567567568	0.00017;4.5e-06;4.3e-05;6.9e-06;2.3e-05;1.2e-06;4.1e-06;1.6e-06;1.6e-06;2.1e-07;8.1e-07;5.6e-07;1.5e-06;1.1e-06;1.3e-06;2.3e-06;9.2e-07;1.9e-06;9.8e-07;1.2e-06;8e-07;2.3e-06;9.2e-07;1.4e-06;1.1e-06;6.6e-07;1.7e-06;8.7e-07;3.8e-07;1.2e-06;1.9e-06;1.7e-06;1.1e-06;1.7e-06;3.5e-07;8e-07;4.9e-07	0.0074;0.002;0.0074;0.0034;0.0053;6e-04;0.0015;0.00042;0.00043;0.00023;0.00027;0.00025;0.00042;0.00034;0.00034;0.00054;0.00029;0.00048;0.00035;0.00027;0.00024;0.00053;0.00032;0.00042;0.00034;0.00027;0.00047;0.00034;8.8e-05;0.00033;0.00046;0.00046;4e-04;0.00083;0.00038;0.00062;0.00046	0.0345767846998674	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.977366917094033
CAMB-76621	MN908947.3	27209	A	G	0.0046	0.011	0.00024	3.2e-07	0.0066859312142331	CAT	ORF6	H3R	A8G	CAT>CGT	Missense	GU280_gp06	0.989956938070146
CAMB-76621	MN908947.3	27669	A	G	1	1	3.9e-162	8.4e-190	1	AAG	ORF7a	E92E	A276G	GAA>GAG	Synonymous	GU280_gp07	0
CAMB-76621	MN908947.3	2891	G	A	1	1	0	0	0.999866515384102	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	0.000133484615898018
CAMB-76621	MN908947.3	522	T	-	0.039	0.034	4.2e-05	0.00013	0.0375065244948177	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.962418909850123
CAMB-7664F	MN908947.3	11074	C	INS	0.11	0.1	7.9e-37	7.5e-28	0.105548314549311	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.889365943417925
CAMB-7664F	MN908947.3	11083	G	-	0.17	0.17	3.3e-76	6.9e-74	0.169121251021123	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	4.66798926362469e-05
CAMB-7664F	MN908947.3	11083	G	T	0.83	0.83	0	0	0.830808729139923	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	4.66798926362469e-05
CAMB-7664F	MN908947.3	14805	C	T	1	1	0	0	0.998370131144077	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000482924105458552
CAMB-7664F	MN908947.3	15894	G	T	1	1	0	0	0.999698436176171	TGC	ORF1ab:RNA-dependent-RNA-polymerase	M809I	G2427T	ATG>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	1.43601820871089e-05
CAMB-7664F	MN908947.3	17528	C	T	0.0093	0.0083	4e-06	4.1e-06	0.00898585884380886	ACT	ORF1ab:helicase	T431I	C1292T	ACT>ATT	Missense	ORF1ab:helicase	0.990918377118779
CAMB-7664F	MN908947.3	17678	C	T	0.025	0.025	2e-12	2.4e-12	0.0250865051903114	ACG	ORF1ab:helicase	T481M	C1442T	ACG>ATG	Missense	ORF1ab:helicase	0.974792084016269
CAMB-7664F	MN908947.3	20434	G	A	0.0046	0.016	0.00093	4e-06	0.00993788819875776	GGA	ORF1ab:endoRNAse	D272N	G814A	GAC>AAC	Missense	ORF1ab:endoRNAse	0.990062111801242
CAMB-7664F	MN908947.3	2480	A	G	1	1	0	0	0.999769602949082	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000153598033945166
CAMB-7664F	MN908947.3	25036	T	C	0.021	0.019	4.7e-11	9.1e-11	0.0202513222817791	ATC	S	N1158N	T3474C	AAT>AAC	Synonymous	GU280_gp02, spike glycoprotein	0.979624436477228
CAMB-7664F	MN908947.3	2558	C	T	1	1	0	0	0.998651413690476	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000162760416666667
CAMB-7664F	MN908947.3	26144	G	T	1	1	0	0	0.999802498395299	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7664F	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0288108108108108	0.0332972972972973	0.0016;9.2e-05;0.00079;0.00081;0.0014;0.00011;0.00029;7.5e-05;7.1e-05;1.1e-05;4.5e-05;3.6e-05;6.4e-05;5e-05;5.6e-05;8.6e-05;4.5e-05;7.7e-05;4.4e-05;5.2e-05;4.7e-05;8.8e-05;4.3e-05;6.2e-05;5e-05;4.2e-05;7.4e-05;4.2e-05;4.4e-05;5.2e-05;7.6e-05;6.7e-05;4.4e-05;7.3e-05;2.3e-05;4.1e-05;3.5e-05	0.00051;4.7e-05;0.00015;0.00014;0.00024;6.6e-06;3.1e-05;8.4e-06;9e-06;3.8e-06;4.4e-06;3.8e-06;6.9e-06;5.2e-06;5.2e-06;9.1e-06;3.6e-06;8e-06;5.1e-06;4.8e-06;5.5e-06;9e-06;4.9e-06;6.9e-06;4.9e-06;3.1e-06;7.5e-06;5.1e-06;1.2e-06;5e-06;8.3e-06;7.7e-06;3.8e-06;1e-05;2.4e-06;7.3e-06;4.3e-06	0.0310036337363735	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.979214780600462
CAMB-7664F	MN908947.3	29269	C	T	1	1	0	0	0.999388233694729	CCT	N	T332T	C996T	ACC>ACT	Synonymous	GU280_gp10	0.000169935084797607
CAMB-7664F	MN908947.3	522	TT	-	0.0385	0.0355	8.2e-06;0.00017	1.6e-05;0.00026	0.0374017961859165	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.955067798588989
CAMB-7666D	MN908947.3	10870	G	T	1	1	0	0	0.999656902689025	TGC	ORF1ab:3C-like-proteinase	L272L	G816T	CTG>CTT	Synonymous	ORF1ab:3C-like-proteinase	8.57743277437063e-05
CAMB-7666D	MN908947.3	11074	C	INS	0.073	0.072	9.4e-22	2e-19	0.0726101831354397	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.925316965184142
CAMB-7666D	MN908947.3	11075	T	-	0.017	0.013	2.4e-05	0.00013	0.015609173780929	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.978548690493416
CAMB-7666D	MN908947.3	11083	G	-	0.093	0.077	3.5e-40	6.5e-33	0.0864880092967567	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.425044899109061
CAMB-7666D	MN908947.3	11083	G	T	0.49	0.49	4.8e-137	2.7e-139	0.488291016656689	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.425044899109061
CAMB-7666D	MN908947.3	14408	C	T	1	1	0	0	0.998502102817199	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000844967641580089
CAMB-7666D	MN908947.3	21614	C	T	1	1	0	0	0.999662009914376	TCT	S	L18F	C52T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7666D	MN908947.3	23403	A	G	1	1	0	0	0.998203030344283	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00147024790013205
CAMB-7666D	MN908947.3	241	C	T	1	1	0	0	0.998628390698875	TCG	NA	NA	NA	NA	NA	NA	0.000500233980410192
CAMB-7666D	MN908947.3	26487	A	G	0.025	0.028	1.4e-12	3.6e-14	0.0260552496860813	TAT	NA	NA	NA	NA	NA	NA	0.973727422003284
CAMB-7666D	MN908947.3	27281	G	T	1	1	0	0	0.998272038314489	TGG	ORF6	W27L	G80T	TGG>TTG	Missense	GU280_gp06	0.00104766180932555
CAMB-7666D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999222898588266	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000293527713908322
CAMB-7666D	MN908947.3	3037	C	T	1	1	0	0	0.99922738159623	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000115892760565557
CAMB-7666D	MN908947.3	8692	C	T	0.029	0.032	3.5e-14	2.6e-15	0.030644070034159	ACA	ORF1ab:nsp4	Y46Y	C138T	TAC>TAT	Synonymous	ORF1ab:nsp4	0.969190910741101
CAMB-7667C	MN908947.3	11075	T	-	0.047	0.0062	3.5e-12	0.0068	0.023791707765042	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.976072242440733
CAMB-7667C	MN908947.3	1108	C	T	0.04	0.066	3.2e-19	1.5e-30	0.0542865446091253	TCA	ORF1ab:nsp2	I101I	C303T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.945713455390875
CAMB-7667C	MN908947.3	14408	C	T	1	1	0	0	0.999444984043291	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000455905964439335
CAMB-7667C	MN908947.3	15022	TTCGCATATACAAAACGTA	-	0.0188421052631579	0.00621052631578947	1.8e-05;0.00019;0.00033;0.00045;0.00052;1.2e-05;7e-06;0.00053;0.00017;0.00023;0.00013;0.00012;0.00016;0.00017;2e-04;0.00011;0.00015;2e-04;0.00017	8.2e-05;0.00062;0.00053;0.00067;0.0015;0.0019;0.0016;0.0016;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00789692435577722	TTT	ORF1ab:RNA-dependent-RNA-polymerase	.	1555-1573-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.983746792130026
CAMB-7667C	MN908947.3	21714	C	T	1	1	0	0	0.999814643188137	ACT	S	T51I	C152T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7667C	MN908947.3	21724	G	T	1	1	0	0	0.999392466585662	TGT	S	L54F	G162T	TTG>TTT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7667C	MN908947.3	22739	ACTA	-	0.02075	0.01775	2.3e-06;2.7e-06;1.1e-07;2e-07	8.2e-06;1.2e-05;8.3e-07;1.6e-06	0.018771543668757	TAC	S	.	1177-1180-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.981473150382397
CAMB-7667C	MN908947.3	23403	A	G	1	1	0	0	0.999873056172644	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.46292182375965e-05
CAMB-7667C	MN908947.3	241	C	T	1	1	0	0	0.99974632166413	TCG	NA	NA	NA	NA	NA	NA	7.24795245343191e-05
CAMB-7667C	MN908947.3	24872	G	T	1	1	0	0	0.999564846003836	TGT	S	V1104L	G3310T	GTA>TTA	Missense	GU280_gp02, spike glycoprotein	1.61168146727481e-05
CAMB-7667C	MN908947.3	28770	C	T	0.0035	0.02	0.0012	1.2e-10	0.0133023648648649	ACA	N	T166I	C497T	ACA>ATA	Missense	GU280_gp10	0.986697635135135
CAMB-7667C	MN908947.3	28776	C	INS	0.0082	0.0059	1e-05	9e-05	0.00684638425331622	CCA	N	.	502-503-insfrshift	.	no-SNV	GU280_gp10	0.987056054771074
CAMB-7667C	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99988045427376	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7667C	MN908947.3	29585	C	-	0.012	0.0034	1.2e-06	0.0032	0.00762910798122066	TCC	ORF10	.	28-28-delfrshift	.	no-SNV	GU280_gp11	0.992370892018779
CAMB-7667C	MN908947.3	29787	C	-	0.0055	0.0085	5e-04	3.6e-05	0.00702576112412178	GCC	NA	NA	NA	NA	NA	NA	0.992974238875878
CAMB-7667C	MN908947.3	3037	C	T	1	1	0	0	0.999878256635013	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000121743364986608
CAMB-7667C	MN908947.3	9251	G	T	0.021	0.013	2.1e-09	2.9e-07	0.0158789463852046	TGT	ORF1ab:nsp4	V233F	G697T	GTT>TTT	Missense	ORF1ab:nsp4	0.984121053614795
CAMB-7667C	MN908947.3	9438	C	T	0.026	0.023	5.4e-11	5.2e-11	0.0240890688259109	ACA	ORF1ab:nsp4	T295I	C884T	ACA>ATA	Missense	ORF1ab:nsp4	0.975708502024291
CAMB-7668B	MN908947.3	11075	T	-	0.039	0.04	7.4e-10	2.5e-10	0.0392636862187333	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956920720449666
CAMB-7668B	MN908947.3	1108	C	T	0.041	0.04	3.7e-19	3.7e-19	0.0403430644895266	TCA	ORF1ab:nsp2	I101I	C303T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.9596404420254
CAMB-7668B	MN908947.3	1302	C	T	0.0083	0.008	1.4e-05	1.7e-05	0.00817959848073793	ACT	ORF1ab:nsp2	T166I	C497T	ACT>ATT	Missense	ORF1ab:nsp2	0.991779706999457
CAMB-7668B	MN908947.3	14408	C	T	1	1	0	0	0.998622140942456	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00020041586291555
CAMB-7668B	MN908947.3	21714	C	T	1	1	0	0	0.999251683711649	ACT	S	T51I	C152T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.000124719381391868
CAMB-7668B	MN908947.3	21724	G	T	1	1	0	0	0.999595523796683	TGT	S	L54F	G162T	TTG>TTT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7668B	MN908947.3	23403	A	G	1	1	0	0	0.998409555307451	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.42619704661794e-05
CAMB-7668B	MN908947.3	23987	C	T	0.024	0.017	4.1e-12	1.4e-09	0.0206840102645784	TCC	S	P809S	C2425T	CCA>TCA	Missense	GU280_gp02, spike glycoprotein	0.979028404565968
CAMB-7668B	MN908947.3	241	C	T	1	1	0	0	0.998640890451084	TCG	NA	NA	NA	NA	NA	NA	0.000234329232571763
CAMB-7668B	MN908947.3	24872	G	T	1	1	0	0	0.999076461307577	TGT	S	V1104L	G3310T	GTA>TTA	Missense	GU280_gp02, spike glycoprotein	3.84807788509639e-05
CAMB-7668B	MN908947.3	28770	C	T	0.011	0.012	1.2e-06	3.1e-07	0.0115452930728242	ACA	N	T166I	C497T	ACA>ATA	Missense	GU280_gp10	0.987084496320731
CAMB-7668B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99917066524495	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000163730434213112
CAMB-7668B	MN908947.3	3037	C	T	1	1	0	0	0.998888106445276	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000222378710944739
CAMB-7668B	MN908947.3	5861	G	A	0.0085	0.0084	7.9e-06	6.3e-06	0.00847102490421456	TGT	ORF1ab:nsp3	V1048I	G3142A	GTT>ATT	Missense	ORF1ab:nsp3	0.990720785440613
CAMB-7668B	MN908947.3	6855	C	T	0.0031	0.016	0.0022	5.2e-07	0.010406811731315	ACT	ORF1ab:nsp3	T1379I	C4136T	ACT>ATT	Missense	ORF1ab:nsp3	0.989593188268685
CAMB-7668B	MN908947.3	7765	C	T	0.01	0.012	3.2e-06	1.3e-06	0.0109214464849122	CCA	ORF1ab:nsp3	S1682S	C5046T	TCC>TCT	Synonymous	ORF1ab:nsp3	0.988674055497128
CAMB-766B8	MN908947.3	10201	G	T	0.0075	0.0032	2.2e-05	0.0019	0.00540673384123863	TGC	ORF1ab:3C-like-proteinase	M49I	G147T	ATG>ATT	Missense	ORF1ab:3C-like-proteinase	0.994396657655444
CAMB-766B8	MN908947.3	10986	G	T	0.021	0.02	2.5e-06	4.1e-06	0.0208652265124454	AGA	ORF1ab:nsp6	R5I	G14T	AGA>ATA	Missense	ORF1ab:nsp6	0.976129727277882
CAMB-766B8	MN908947.3	11074	C	INS	0.13	0.14	1.2e-63	9.5e-54	0.136360834021775	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.859755120158814
CAMB-766B8	MN908947.3	11083	G	-	0.22	0.17	6e-98	5.3e-75	0.198619962623988	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.19794911112176e-05
CAMB-766B8	MN908947.3	11083	G	T	0.78	0.83	2.09999999999826e-312	0	0.801176386027122	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.19794911112176e-05
CAMB-766B8	MN908947.3	11271	TGGTTGATACTAGTTTGTCTGGTTT	-	0.00023744	0.014	0.46;0.0089;0.47;0.48;0.47;0.48;0.48;0.48;0.48;0.49;0.49;0.5;0.5;0.5;0.5;NA;NA;NA;NA;NA;NA;0.47;0.5;0.5;0.47	3.7e-05;2e-05;5.5e-05;6.2e-05;0.00013;7.5e-05;0.00015;0.00012;0.00031;0.00016;0.00012;0.00016;2e-04;0.00062;0.00023;0.00043;0.00028;0.00015;0.00016;7.6e-05;8.8e-05;0.00016;1.9e-05;0.00021;6.9e-05	0.00502285816066022	ATG	ORF1ab:nsp6	.	299-323-delfrshift	.	no-SNV	ORF1ab:nsp6	0.994773348964439
CAMB-766B8	MN908947.3	11939	G	T	0.014	0.0056	1.5e-07	0.00038	0.0103321591606487	TGT	ORF1ab:nsp7	V33F	G97T	GTC>TTC	Missense	ORF1ab:nsp7	0.987692204221977
CAMB-766B8	MN908947.3	12164	G	T	0.0089	0.013	0.00028	1.5e-05	0.0106625902292362	GGC	ORF1ab:nsp8	A25S	G73T	GCT>TCT	Missense	ORF1ab:nsp8	0.989001230542834
CAMB-766B8	MN908947.3	1252	T	C	0.0071	0.0035	3.6e-05	0.001	0.00611431103234382	CTT	ORF1ab:nsp2	T149T	T447C	ACT>ACC	Synonymous	ORF1ab:nsp2	0.993797075764289
CAMB-766B8	MN908947.3	12577	AG	-	0.00365	0.00705	0.00054;0.0053	9.1e-05;1.6e-05	0.0044539531265195	CAG	ORF1ab:nsp8	.	486-487-delfrshift	.	no-SNV	ORF1ab:nsp8	0.994781718291554
CAMB-766B8	MN908947.3	12578	G	T	0.0099	0.015	0.00014	2.1e-06	0.0112404888171547	AGA	ORF1ab:nsp8	D163Y	G487T	GAT>TAT	Missense	ORF1ab:nsp8	0.984858965490739
CAMB-766B8	MN908947.3	12809	C	T	0.0056	0.0097	0.00026	3.1e-06	0.00691023202120222	ACT	ORF1ab:nsp9	L42F	C124T	CTT>TTT	Missense	ORF1ab:nsp9	0.993040989870413
CAMB-766B8	MN908947.3	13462	TTTA	-	0.0059	0.0165	0.00063;0.00069;0.00099;0.00077	2.7e-07;1.5e-08;2.8e-08;1.6e-08	0.00982357658380112	TTT	ORF1ab:nsp11	.	21-24-delfrshift	.	no-SNV	ORF1ab:nsp11	0.990408735428656
CAMB-766B8	MN908947.3	13476	C	T	0.016	0.011	6.2e-08	1.9e-05	0.0144664288031138	GCG	ORF1ab:nsp11	A12V	C35T	GCG>GTG	Missense	ORF1ab:nsp11	0.985533571196886
CAMB-766B8	MN908947.3	13571	G	T	0.015	0.021	0.00043	2.8e-05	0.0167447231667415	GGT	ORF1ab:RNA-dependent-RNA-polymerase	G35V	G104T	GGT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.9831911208058
CAMB-766B8	MN908947.3	13993	G	T	0.0027	0.0073	0.0043	3.3e-05	0.00505499877780494	AGC	ORF1ab:RNA-dependent-RNA-polymerase	A176S	G526T	GCT>TCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994876558298704
CAMB-766B8	MN908947.3	14512	G	C	0.0037	0.0062	0.00085	4.5e-05	0.00453402376026659	GGA	ORF1ab:RNA-dependent-RNA-polymerase	D349H	G1045C	GAT>CAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.995404036024429
CAMB-766B8	MN908947.3	14805	C	T	1	1	0	0	0.997817409034778	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	4.30774532609632e-05
CAMB-766B8	MN908947.3	14931	C	T	1	1	0	0	0.999895985021843	ACC	ORF1ab:RNA-dependent-RNA-polymerase	N488N	C1464T	AAC>AAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000104014978156855
CAMB-766B8	MN908947.3	15732	G	T	0.0037	0.0087	0.00084	4.3e-06	0.00554677316471143	TGT	ORF1ab:RNA-dependent-RNA-polymerase	V755V	G2265T	GTG>GTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.994328424439083
CAMB-766B8	MN908947.3	20627	G	T	0.015	0.0072	1.1e-06	0.00043	0.0102958425648377	GGC	ORF1ab:endoRNAse	G336V	G1007T	GGC>GTC	Missense	ORF1ab:endoRNAse	0.989573830314088
CAMB-766B8	MN908947.3	20931	G	T	0.0082	0.0023	1.3e-05	0.0045	0.00612719205577858	CGG	ORF1ab:2'-O-ribose-methyltransferase	T91T	G273T	ACG>ACT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.993687935770125
CAMB-766B8	MN908947.3	2182	AGAGT	-	0.00548	0.00092	7e-04;0.00046;2.1e-05;2.5e-05;5.8e-05	0.00059;NA;NA;NA;NA	0.00349293352678811	TAG	ORF1ab:nsp2	.	1377-1381-delfrshift	.	no-SNV	ORF1ab:nsp2	0.995478522984175
CAMB-766B8	MN908947.3	23371	T	C	0.013	0.017	8e-08	1.3e-09	0.0146928980552851	ATA	S	N603N	T1809C	AAT>AAC	Synonymous	GU280_gp02, spike glycoprotein	0.985182585859501
CAMB-766B8	MN908947.3	23927	T	C	0.0017	0.0084	0.009	6.5e-06	0.00470613119001666	TTA	S	Y789H	T2365C	TAC>CAC	Missense	GU280_gp02, spike glycoprotein	0.995214551992174
CAMB-766B8	MN908947.3	24933	G	T	0.036	0.025	2.2e-06	4.9e-05	0.0312785388127854	GGT	S	G1124V	G3371T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.96455098934551
CAMB-766B8	MN908947.3	25420	AT	-	0.0048	0.00885	NA;0.00012	6.3e-06;0.00013	0.00600048003840307	AAT	ORF3a	.	28-29-delfrshift	.	no-SNV	GU280_gp03	0.997148126908353
CAMB-766B8	MN908947.3	25550	TTGCTGT	-	0.0134285714285714	0.000763857142857143	9.6e-05;0.00015;6.2e-05;0.00018;0.00021;0.00039;4.1e-07	NA;NA;NA;NA;NA;NA;0.0053	0.00857534246575343	CTT	ORF3a	.	158-164-delfrshift	.	no-SNV	GU280_gp03	0.99010329015424
CAMB-766B8	MN908947.3	25660	G	T	0.0045	0.0095	0.00056	3.8e-06	0.00720305409493625	AGT	ORF3a	V90F	G268T	GTT>TTT	Missense	GU280_gp03	0.984585464236836
CAMB-766B8	MN908947.3	26144	G	T	1	1	0	0	0.999426605504587	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000573394495412844
CAMB-766B8	MN908947.3	26227	G	T	0.0041	0.0068	0.00055	3.1e-05	0.00498909944658729	AGC	NA	NA	NA	NA	NA	NA	0.994843199731679
CAMB-766B8	MN908947.3	26781	CTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0324444444444444	0.02375	8.9e-05;0.00018;4.7e-05;3.1e-05;1.9e-06;1.1e-05;3.1e-05;3e-05;1e-05;2.1e-05;1.6e-05;2.7e-05;2.2e-05;3e-05;4e-05;2.1e-05;3.6e-05;2.2e-05;2.2e-05;2.2e-05;4e-05;2.2e-05;2.8e-05;2.1e-05;1.5e-05;3.7e-05;1.9e-05;8.1e-06;2.7e-05;3.4e-05;3.3e-05;1.4e-05;3.5e-05;1.8e-06;4.4e-06;2.1e-06	0.003;0.0096;0.00059;0.001;0.0011;0.0021;0.00059;0.00058;0.00038;0.00043;0.00041;0.00057;5e-04;0.00052;0.00071;0.00045;0.00064;0.00048;0.00047;4e-04;0.00072;0.00043;0.00057;0.00048;0.00036;0.00065;0.00049;0.00015;0.00048;0.00063;0.00061;0.00035;6e-04;0.0012;0.0018;0.0014	0.0285854313384971	TCT	M	.	259-294-delinframe	.	no-SNV	GU280_gp05	0.976313664125991
CAMB-766B8	MN908947.3	27115	G	T	0.003	0.011	0.002	4.6e-07	0.00551684088269454	CGC	M	R198L	G593T	CGC>CTC	Missense	GU280_gp05	0.994265389082462
CAMB-766B8	MN908947.3	28079	G	T	0.012	0.0082	1.5e-05	0.00033	0.0102412380518889	TGG	ORF8	V62V	G186T	GTG>GTT	Synonymous	GU280_gp09	0.988848429676832
CAMB-766B8	MN908947.3	28792	AG	-	0.00435	0.0066	9e-04;0.00098	4.5e-05;0.00021	0.00521587945523037	CAG	N	.	519-520-delfrshift	.	no-SNV	GU280_gp10	0.994015917659027
CAMB-766B8	MN908947.3	28857	G	T	1	1	0	0	0.999502796768179	AGA	N	R195I	G584T	AGA>ATA	Missense	GU280_gp10	0.000310752019888129
CAMB-766B8	MN908947.3	29113	AC	-	0.0155	0.0044	4.2e-07;1.2e-05	0.034;0.0017	0.0116720729712495	AAC	N	.	840-841-delfrshift	.	no-SNV	GU280_gp10	0.989210959548448
CAMB-766B8	MN908947.3	3763	A	G	1	1	0	0	1	TAG	ORF1ab:nsp3	V348V	A1044G	GTA>GTG	Synonymous	ORF1ab:nsp3	0
CAMB-766B8	MN908947.3	3931	T	C	1	1	0	0	1	TTG	ORF1ab:nsp3	V404V	T1212C	GTT>GTC	Synonymous	ORF1ab:nsp3	0
CAMB-766B8	MN908947.3	553	G	T	0.0081	0.0027	1.3e-05	0.0024	0.00652699198491278	AGT	ORF1ab:leader-protein	Q96H	G288T	CAG>CAT	Missense	ORF1ab:leader-protein	0.993369872701556
CAMB-766B8	MN908947.3	6762	C	T	0.047	0.021	1.1e-20	8.6e-11	0.0315599639314698	ACT	ORF1ab:nsp3	T1348I	C4043T	ACT>ATT	Missense	ORF1ab:nsp3	0.96844003606853
CAMB-766B8	MN908947.3	692	TTTGAC	-	0.0685	0.0573333333333333	4.9e-12;2.2e-09;6.7e-08;4.6e-22;3.5e-27;1.8e-27	4e-10;1e-08;1.4e-07;1e-17;1.4e-21;1.6e-21	0.0591772285148848	ATT	ORF1ab:leader-protein	.	427-432-delinframe	.	no-SNV	ORF1ab:leader-protein	0.909907086085302
CAMB-766B8	MN908947.3	8790	G	T	0.003	0.0091	0.0061	1.2e-05	0.00582880868732035	GGT	ORF1ab:nsp4	G79V	G236T	GGT>GTT	Missense	ORF1ab:nsp4	0.994091344618333
CAMB-766B8	MN908947.3	9180	C	T	0.011	0.0045	1.5e-06	0.00081	0.00789638511095204	TCT	ORF1ab:nsp4	S209F	C626T	TCT>TTT	Missense	ORF1ab:nsp4	0.992036506800286
CAMB-766B8	MN908947.3	9491	C	T	0.0059	0.0084	0.00024	2.3e-05	0.00695410292072323	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.993045897079277
CAMB-766B8	MN908947.3	9634	A	T	0.006	0.01	9.7e-05	1.3e-06	0.00813325162943569	TAG	ORF1ab:nsp4	L360F	A1080T	TTA>TTT	Missense	ORF1ab:nsp4	0.991773903032329
CAMB-766C7	MN908947.3	11195	C	T	1	1	0	0	0.999792584910552	TCT	ORF1ab:nsp6	L75F	C223T	CTT>TTT	Missense	ORF1ab:nsp6	5.18537723619393e-05
CAMB-766C7	MN908947.3	14408	C	T	1	1	0	0	0.999610858890021	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000315018993792273
CAMB-766C7	MN908947.3	15216	C	T	1	1	0	0	0.998963674048216	GCA	ORF1ab:RNA-dependent-RNA-polymerase	S583S	C1749T	AGC>AGT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000218173884586015
CAMB-766C7	MN908947.3	19219	GC	CT	0.0305	0.043	NA;2.3e-28	3.2e-14;2e-27	0.0363062536528346	TGC	ORF1ab:3'-to-5'-exonuclease	.	1180-1181-mnv	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.986519465427077
CAMB-766C7	MN908947.3	19220	C	T	0.061	0.058	2.3e-28	2e-27	0.0596133947888251	GCT	ORF1ab:3'-to-5'-exonuclease	A394V	C1181T	GCT>GTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.940339572947042
CAMB-766C7	MN908947.3	2110	C	T	1	1	0	0	1	ACA	ORF1ab:nsp2	N435N	C1305T	AAC>AAT	Synonymous	ORF1ab:nsp2	0
CAMB-766C7	MN908947.3	2130	A	-	0.024	0.039	2.1e-10	7.2e-17	0.0331554878048781	GAA	ORF1ab:nsp2	.	1325-1325-delfrshift	.	no-SNV	ORF1ab:nsp2	0.966653963414634
CAMB-766C7	MN908947.3	2130	AA	-	0.024	0.0195	2.1e-10;2.2e-11	7.2e-17;NA	0.0212601468882876	GAA	ORF1ab:nsp2	.	1325-1326-delfrshift	.	no-SNV	ORF1ab:nsp2	0.966653963414634
CAMB-766C7	MN908947.3	23403	A	G	1	1	0	0	0.999901427116305	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.85728836949498e-05
CAMB-766C7	MN908947.3	241	C	T	1	1	0	0	0.999622030237581	TCG	NA	NA	NA	NA	NA	NA	0.000188984881209503
CAMB-766C7	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999432785025525	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000249003984063745
CAMB-766C7	MN908947.3	3037	C	T	1	1	0	0	0.999623103740695	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000188448129652313
CAMB-766C7	MN908947.3	3373	C	A	1	1	0	0	0.999826774836158	ACA	ORF1ab:nsp3	D218E	C654A	GAC>GAA	Missense	ORF1ab:nsp3	2.88708606403557e-05
CAMB-766D6	MN908947.3	11074	C	INS	0.1	0.11	2.7e-38	7.4e-34	0.103033506310462	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.889390736113781
CAMB-766D6	MN908947.3	11083	G	-	0.16	0.14	1.5e-70	7.5e-64	0.153998157667964	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.97150328351113e-05
CAMB-766D6	MN908947.3	11083	G	T	0.84	0.86	0	0	0.845764122069355	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.97150328351113e-05
CAMB-766D6	MN908947.3	11835	C	T	0.021	0.031	3.2e-09	2e-11	0.0235644637053088	ACT	ORF1ab:nsp6	T288I	C863T	ACT>ATT	Missense	ORF1ab:nsp6	0.976435536294691
CAMB-766D6	MN908947.3	140	C	T	0.0063	0.007	5.8e-05	2.5e-05	0.00661813368630046	ACT	NA	NA	NA	NA	NA	NA	0.993266048974189
CAMB-766D6	MN908947.3	14448	T	A	0.024	0.022	4e-12	4.5e-12	0.024051754696916	ATG	ORF1ab:RNA-dependent-RNA-polymerase	D327E	T981A	GAT>GAA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.975735554767813
CAMB-766D6	MN908947.3	14805	C	T	1	1	0	0	0.999193362525928	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000345701774602443
CAMB-766D6	MN908947.3	18471	T	C	0.046	0.043	9.5e-22	2.5e-20	0.0447602131438721	ATC	ORF1ab:3'-to-5'-exonuclease	D144D	T432C	GAT>GAC	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.955083481349911
CAMB-766D6	MN908947.3	18692	C	T	0.018	0.019	1.2e-09	1.8e-10	0.0183083703954847	TCC	ORF1ab:3'-to-5'-exonuclease	S218F	C653T	TCC>TTC	Missense	ORF1ab:3'-to-5'-exonuclease	0.981671685845914
CAMB-766D6	MN908947.3	20930	C	T	0.0093	0.011	1.3e-05	2.6e-06	0.00969548775980211	ACG	ORF1ab:2'-O-ribose-methyltransferase	T91M	C272T	ACG>ATG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.990105484632225
CAMB-766D6	MN908947.3	21800	G	T	1	1	0	0	0.99964930738208	TGA	S	D80Y	G238T	GAT>TAT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-766D6	MN908947.3	23193	ATGGTTTAACAGGCACAGGTGTTC	-	0.00500833333333333	0.00661666666666667	0.0025;0.0023;0.0029;0.00076;0.00041;0.00016;2e-04;0.00016;0.00034;0.00028;3e-04;0.00023;2e-04;0.00018;0.00018;0.00062;0.00022;0.00019;0.00025;0.00034;0.00045;0.00019;0.00024;0.00029	0.00066;0.00055;8e-04;0.00011;6.6e-05;1.6e-05;2e-05;2e-05;1.6e-05;1.3e-05;1.3e-05;1.2e-05;1.3e-05;2.7e-05;1.6e-05;2.3e-05;1.4e-05;2.3e-05;3.7e-05;4.4e-05;6.6e-05;1.9e-05;2.8e-05;4e-05	0.00524053920356171	AAT	S	.	1631-1654-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.993888439773646
CAMB-766D6	MN908947.3	2480	A	G	1	1	0	0	0.999864480281881	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	6.77598590594932e-05
CAMB-766D6	MN908947.3	25359	A	G	1	1	0	0	0.999114120912652	AAA	S	K1266R	A3797G	AAA>AGA	Missense	GU280_gp02, spike glycoprotein	0.000590586058231785
CAMB-766D6	MN908947.3	2558	C	T	1	1	0	0	0.999040675364543	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	2.74092752987611e-05
CAMB-766D6	MN908947.3	26144	G	T	1	1	0	0	0.999713417779561	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000171949332263426
CAMB-766D6	MN908947.3	27264	TTT	-	0.009	0.00936666666666667	5.5e-05;0.00032;0.00076	3.3e-05;0.00019;0.00058	0.00911232861157635	CTT	ORF6	.	63-65-delinframe	.	no-SNV	GU280_gp06	0.99054702358986
CAMB-766D6	MN908947.3	27336	T	C	0.0086	0.0085	6.3e-06	3.5e-06	0.0086109022279235	CTG	ORF6	T45T	T135C	ACT>ACC	Synonymous	GU280_gp06	0.991330118989693
CAMB-766D6	MN908947.3	29234	G	A	0.0085	0.0071	9.1e-06	1.9e-05	0.00811483178012952	TGG	N	G321S	G961A	GGC>AGC	Missense	GU280_gp10	0.991786447638604
CAMB-766D6	MN908947.3	6513	GTT	-	0.0263333333333333	0.0276666666666667	4.3e-09;5.2e-09;1.1e-08	1.7e-09;3e-09;3.3e-09	0.0270620124059562	AGT	ORF1ab:nsp3	.	3794-3796-delinframe	.	no-SNV	ORF1ab:nsp3	0.972215225604725
CAMB-766D6	MN908947.3	860	G	A	1	1	0	0	0.999420717257359	TGA	ORF1ab:nsp2	E19K	G55A	GAG>AAG	Missense	ORF1ab:nsp2	0.000144820685660119
CAMB-766E5	MN908947.3	11075	T	-	0.041	0.038	2.5e-10	3.4e-10	0.0398474972328127	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955432911081048
CAMB-766E5	MN908947.3	12862	T	C	0.19	0.21	3.4e-90	6.2e-96	0.195063492429306	GTG	ORF1ab:nsp9	S59S	T177C	AGT>AGC	Synonymous	ORF1ab:nsp9	0.804844322555369
CAMB-766E5	MN908947.3	13296	A	C	0.0087	0.0082	4.5e-05	1.3e-05	0.00858548936397839	GAC	ORF1ab:nsp10	D91A	A272C	GAC>GCC	Missense	ORF1ab:nsp10	0.991262949556907
CAMB-766E5	MN908947.3	14408	C	T	1	1	0	0	0.998766084963864	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000320497411983398
CAMB-766E5	MN908947.3	16349	C	T	0.21	0.21	2.8e-99	6.6e-100	0.212882523284026	TCA	ORF1ab:helicase	S38L	C113T	TCA>TTA	Missense	ORF1ab:helicase	0.786960945448853
CAMB-766E5	MN908947.3	17766	C	T	0.015	0.014	3.6e-08	2.6e-08	0.0144631896203183	TCT	ORF1ab:helicase	V510V	C1530T	GTC>GTT	Synonymous	ORF1ab:helicase	0.98537141176903
CAMB-766E5	MN908947.3	21707	C	T	1	1	0	0	0.999846934870788	ACA	S	H49Y	C145T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.000102043419474987
CAMB-766E5	MN908947.3	22070	T	C	0.013	0.012	1.9e-07	2.7e-07	0.0125912190453404	ATA	S	Y170H	T508C	TAT>CAT	Missense	GU280_gp02, spike glycoprotein	0.98627228137337
CAMB-766E5	MN908947.3	23403	A	G	1	1	0	0	0.999342547000895	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.99418084153984e-05
CAMB-766E5	MN908947.3	241	C	T	1	1	0	0	0.998840421540875	TCG	NA	NA	NA	NA	NA	NA	0.00020463149278674
CAMB-766E5	MN908947.3	2940	C	T	1	1	0	0	0.999323501555946	CCA	ORF1ab:nsp3	P74L	C221T	CCA>CTA	Missense	ORF1ab:nsp3	0.000541198755242863
CAMB-766E5	MN908947.3	3037	C	T	1	1	0	0	0.998446087882363	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000172656901959656
CAMB-766E5	MN908947.3	3286	G	A	0.013	0.013	2.4e-07	1.3e-07	0.0131132366553533	AGG	ORF1ab:nsp3	E189E	G567A	GAG>GAA	Synonymous	ORF1ab:nsp3	0.986501079913607
CAMB-766E5	MN908947.3	3768	C	T	0.0099	0.0092	8.4e-06	1.2e-05	0.00965242417533761	ACT	ORF1ab:nsp3	T350I	C1049T	ACT>ATT	Missense	ORF1ab:nsp3	0.990303298649546
CAMB-766E5	MN908947.3	3951	A	G	1	1	0	0	0.99968028419183	GAT	ORF1ab:nsp3	D411G	A1232G	GAT>GGT	Missense	ORF1ab:nsp3	7.10479573712256e-05
CAMB-766E5	MN908947.3	6712	T	A	0.0089	0.0076	2.8e-05	9e-05	0.00822318121580754	TTG	ORF1ab:nsp3	V1331V	T3993A	GTT>GTA	Synonymous	ORF1ab:nsp3	0.991437017907506
CAMB-766F4	MN908947.3	11075	T	-	0.0059	0.083	0.0065	9.8e-21	0.0438608809624116	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.936689603520105
CAMB-766F4	MN908947.3	14408	C	T	1	1	0	0	0.999584740601296	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000304523559049886
CAMB-766F4	MN908947.3	17307	T	C	1	1	0	0	0.999853937835943	TTT	ORF1ab:helicase	F357F	T1071C	TTT>TTC	Synonymous	ORF1ab:helicase	0.000146062164057023
CAMB-766F4	MN908947.3	22468	G	T	1	0.99	3.2e-171	1.2e-188	0.996336996336996	CGT	S	T302T	G906T	ACG>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.00366300366300366
CAMB-766F4	MN908947.3	23403	A	G	1	1	0	0	0.999935019575353	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.49804246470751e-05
CAMB-766F4	MN908947.3	241	C	T	1	1	0	0	0.999719672016259	TCG	NA	NA	NA	NA	NA	NA	0.000175204989838111
CAMB-766F4	MN908947.3	25234	GATTGCCATAGTAATGGTGACAATTA	-	0.00161538461538462	0.0544615384615385	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;8.6e-19;NA;NA;NA;NA;NA	5.5e-25;4.4e-27;1.2e-21;3.4e-23;8.3e-13;2.4e-15;5e-25;1.3e-24;1.1e-13;4.7e-14;5.4e-18;2.4e-18;8.8e-22;4.9e-16;5.4e-26;8.7e-16;5.2e-12;2.6e-24;3.6e-23;7.3e-13;1.4e-25;5.8e-17;8e-32;3.9e-20;1.1e-12;2.3e-26	0.0314679063114608	TGA	S	.	3672-3697-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.96433998581704
CAMB-766F4	MN908947.3	25429	G	T	1	1	0	0	0.999716697829905	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0.000141651085047311
CAMB-766F4	MN908947.3	27434	C	T	0.027	0.025	2.9e-13	2.2e-12	0.025953609776354	ACT	ORF7a	T14I	C41T	ACT>ATT	Missense	GU280_gp07	0.974046390223646
CAMB-766F4	MN908947.3	27925	C	T	0.034	0.016	1e-12	5.5e-07	0.0254865616311399	ACA	ORF8	T11I	C32T	ACA>ATA	Missense	GU280_gp09	0.97451343836886
CAMB-766F4	MN908947.3	3037	C	T	1	1	0	0	0.999776935088111	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7672E	MN908947.3	12400	C	T	1	1	0	0	0.999928815489749	TCA	ORF1ab:nsp8	L103L	C309T	CTC>CTT	Synonymous	ORF1ab:nsp8	7.11845102505695e-05
CAMB-7672E	MN908947.3	14408	C	T	1	1	0	0	0.99946685065546	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000376340713792887
CAMB-7672E	MN908947.3	21532	A	G	0.008	0.04	0.00037	4.5e-11	0.023448275862069	TAG	ORF1ab:2'-O-ribose-methyltransferase	S292G	A874G	AGT>GGT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.973793103448276
CAMB-7672E	MN908947.3	23403	A	G	1	1	0	0	0.999925943754281	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.40562457186233e-05
CAMB-7672E	MN908947.3	241	C	T	1	1	0	0	0.999745787332946	TCG	NA	NA	NA	NA	NA	NA	0.00018158047646717
CAMB-7672E	MN908947.3	26564	A	G	1	1	0	0	0.999870451404883	AAA	M	K14K	A42G	AAA>AAG	Synonymous	GU280_gp05	8.63657300783049e-05
CAMB-7672E	MN908947.3	28985	G	T	1	1	0	0	1	AGG	N	G238C	G712T	GGC>TGC	Missense	GU280_gp10	0
CAMB-7672E	MN908947.3	29586	C	T	1	1	0	0	0.99953531598513	CCG	ORF10	P10L	C29T	CCG>CTG	Missense	GU280_gp11	0.000464684014869888
CAMB-7672E	MN908947.3	3037	C	T	1	1	0	0	0.99923273657289	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7672E	MN908947.3	6317	C	T	0.22	0.2	3.8e-104	1.6e-92	0.206992163954189	ACC	ORF1ab:nsp3	P1200S	C3598T	CCA>TCA	Missense	ORF1ab:nsp3	0.793007836045811
CAMB-7672E	MN908947.3	8650	C	T	1	1	0	0	1	TCA	ORF1ab:nsp4	V32V	C96T	GTC>GTT	Synonymous	ORF1ab:nsp4	0
CAMB-7673D	MN908947.3	11075	T	-	0.033	0.035	1.2e-08	3.3e-09	0.0338789332580782	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960815577818541
CAMB-7673D	MN908947.3	14408	C	T	1	0.99	0	0	0.994344957587182	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000314169022934339
CAMB-7673D	MN908947.3	18096	T	C	0.0088	0.0078	7.1e-06	1.9e-05	0.00830576993752297	ATC	ORF1ab:3'-to-5'-exonuclease	H19H	T57C	CAT>CAC	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.991694230062477
CAMB-7673D	MN908947.3	18951	G	T	0.013	0.022	8.1e-08	1.8e-11	0.0173494234763303	AGA	ORF1ab:3'-to-5'-exonuclease	K304N	G912T	AAG>AAT	Missense	ORF1ab:3'-to-5'-exonuclease	0.982641624292774
CAMB-7673D	MN908947.3	19645	G	T	0.046	0.027	2.4e-20	1e-12	0.0357063155545637	TGT	ORF1ab:endoRNAse	V9F	G25T	GTT>TTT	Missense	ORF1ab:endoRNAse	0.964144908130626
CAMB-7673D	MN908947.3	20852	TGAGAGTT	-	0.011125	0.0015625	8.8e-07;1.2e-05;7.9e-06;1.9e-06;6.1e-06;1.4e-05;2.4e-06;1.7e-06	0.00022;0.00089;NA;NA;NA;NA;NA;NA	0.00546850587027365	ATG	ORF1ab:2'-O-ribose-methyltransferase	.	194-201-delfrshift	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.990758345166181
CAMB-7673D	MN908947.3	22156	TGGTTATTT	-	0.0107333333333333	0.00265444444444444	6.6e-06;2.1e-05;0.00015;5.1e-08;2.8e-08;1.8e-08;0.00026;9.1e-05;1.8e-05	NA;0.18;0.17;0.00014;8.8e-05;8.6e-05;NA;NA;NA	0.00398512221041445	ATG	S	.	594-602-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.995684423465947
CAMB-7673D	MN908947.3	22643	TG	-	0.00725	0.0106	0.00013;0.0063	4.6e-06;0.00096	0.00869485908855988	CTG	S	.	1081-1082-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.989542574188857
CAMB-7673D	MN908947.3	23403	A	G	1	1	0	0	0.999920321899526	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.97183379148241e-05
CAMB-7673D	MN908947.3	241	C	T	1	1	0	0	0.999439932791935	TCG	NA	NA	NA	NA	NA	NA	0.000330948804765663
CAMB-7673D	MN908947.3	24893	GAACCACAAATCATTACTACAGACAACACATT	-	0.01096875	0.00040625	8.2e-06;6.2e-05;0.00028;0.00063;6.9e-06;2.7e-06;1.6e-06;2.1e-06;7.6e-07;1.2e-07;4.6e-07;1.1e-06;1.5e-06;8.1e-07;9.5e-07;1.6e-06;1.3e-06;1.1e-06;2.1e-06;1.7e-06;8.9e-07;1.4e-05;4.8e-06;4.9e-06;8.8e-07;1.2e-06;3.5e-06;5.3e-07;1.3e-06;3.3e-07;7.3e-07;3e-07	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;3.5e-07;NA	0.00532898793270501	TGA	S	.	3331-3362-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.990078742510497
CAMB-7673D	MN908947.3	27395	TG	CA	0.00478	0.00755	0.46;4.9e-06	2.2e-05;3.1e-05	0.00609935902410256	ATG	ORF7a	.	2-3-mnv	.	no-SNV	GU280_gp07	0.991215204335274
CAMB-7673D	MN908947.3	27396	G	A	0.0095	0.0076	4.9e-06	3.1e-05	0.00856581164575922	TGA	ORF7a	M1I	G3A	ATG>ATA	Missense	GU280_gp07	0.991402983211633
CAMB-7673D	MN908947.3	28160	T	C	0.024	0.042	1.8e-12	7.5e-20	0.0334479095056559	ATT	ORF8	N89N	T267C	AAT>AAC	Synonymous	GU280_gp09	0.966539591275545
CAMB-7673D	MN908947.3	29347	C	T	0.078	0.032	1.5e-35	1e-15	0.057964542490957	ACG	N	D358D	C1074T	GAC>GAT	Synonymous	GU280_gp10	0.942035457509043
CAMB-7673D	MN908947.3	29726	T	-	0.014	0.0056	2.2e-05	0.0055	0.00850546780072904	ATT	NA	NA	NA	NA	NA	NA	0.991190765492102
CAMB-7673D	MN908947.3	3037	C	T	1	1	0	0	0.999526776559666	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.88705733890685e-05
CAMB-7673D	MN908947.3	3792	C	T	1	1	0	0	1	GCT	ORF1ab:nsp3	A358V	C1073T	GCT>GTT	Missense	ORF1ab:nsp3	0
CAMB-7673D	MN908947.3	5784	C	T	0.012	0.0092	3.7e-06	2.9e-05	0.010319532512744	ACT	ORF1ab:nsp3	T1022I	C3065T	ACT>ATT	Missense	ORF1ab:nsp3	0.989639023581582
CAMB-7673D	MN908947.3	826	T	C	0.075	0.039	1.6e-34	8.8e-19	0.0538137927580508	ATA	ORF1ab:nsp2	D7D	T21C	GAT>GAC	Synonymous	ORF1ab:nsp2	0.945760504832974
CAMB-7673D	MN908947.3	9105	GTTTACGCCCTGACACAC	-	0.00956666666666667	0.00133333333333333	0.00027;5e-06;1.1e-05;5.1e-05;1.9e-06;3e-06;4.5e-06;3.8e-06;2.8e-06;2.9e-06;1.1e-06;2.6e-06;1.6e-05;2.1e-05;7.5e-07;3e-06;1.7e-06;2.3e-06	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;1.7e-06;2.4e-06;NA;NA;NA;NA	0.00495918999896684	AGT	ORF1ab:nsp4	.	551-568-delinframe	.	no-SNV	ORF1ab:nsp4	0.997733902896437
CAMB-7673D	MN908947.3	9994	C	A	0.0036	0.012	0.00042	1.9e-07	0.00801305119715945	ACT	ORF1ab:nsp4	N480K	C1440A	AAC>AAA	Missense	ORF1ab:nsp4	0.991938966460343
CAMB-7674C	MN908947.3	13914	T	G	0.0039	0.0065	0.00023	1.6e-05	0.00489173440759658	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994964391051004
CAMB-7674C	MN908947.3	14408	C	T	0.96	1	0	0	0.972416877888773	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.0275458476218876
CAMB-7674C	MN908947.3	23171	A	-	0.021	0.025	1.6e-11	4.5e-13	0.0229346331708536	CAA	S	.	1609-1609-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.976377952755906
CAMB-7674C	MN908947.3	23403	A	G	1	0.97	0	0	0.987976020164861	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.0119899175693167
CAMB-7674C	MN908947.3	241	C	T	0.95	0.97	0	0	0.959177409453653	TCG	NA	NA	NA	NA	NA	NA	0.0406471981057616
CAMB-7674C	MN908947.3	25531	A	G	0.058	0.045	5.8e-27	1e-21	0.0535147392290249	TAT	ORF3a	I47V	A139G	ATT>GTT	Missense	GU280_gp03	0.946424792139078
CAMB-7674C	MN908947.3	26735	C	T	0.052	0.025	4.8e-24	1.2e-12	0.0383097630170005	ACA	M	Y71Y	C213T	TAC>TAT	Synonymous	GU280_gp05	0.961626245173951
CAMB-7674C	MN908947.3	27849	C	T	0.038	0.013	1.1e-14	8.7e-06	0.0261617900172117	ACT	NA	NA	NA	NA	NA	NA	0.973838209982788
CAMB-7674C	MN908947.3	28377	C	T	0.015	0.0077	2.4e-08	3.4e-05	0.0109277395235889	GCG	N	A35V	C104T	GCG>GTG	Missense	GU280_gp10	0.988976403112169
CAMB-7674C	MN908947.3	28881	GGG	AAC	0.87	0.933333333333333	0;0;0	0;0;0	0.909524892020914	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.0970039292730845
CAMB-7674C	MN908947.3	29095	C	T	0.018	0.01	9.8e-09	1.8e-05	0.0143777592172772	TCG	N	F274F	C822T	TTC>TTT	Synonymous	GU280_gp10	0.985622240782723
CAMB-7674C	MN908947.3	29167	C	T	0.084	0.043	5.8e-38	3.8e-20	0.0660959335263754	ACA	N	Y298Y	C894T	TAC>TAT	Synonymous	GU280_gp10	0.928805237315876
CAMB-7674C	MN908947.3	3037	C	T	0.94	1	0	0	0.964038128249567	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.0357452339688042
CAMB-7675B	MN908947.3	14408	C	T	1	1	0	0	0.999670029225983	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000282832092014707
CAMB-7675B	MN908947.3	20031	C	A	1	1	3.6e-170	9.09999999999999e-201	1	CCC	ORF1ab:endoRNAse	A137A	C411A	GCC>GCA	Synonymous	ORF1ab:endoRNAse	0
CAMB-7675B	MN908947.3	23403	A	G	1	1	0	0	0.999977341218589	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7675B	MN908947.3	241	C	T	1	1	0	0	0.999873348250095	TCG	NA	NA	NA	NA	NA	NA	0.000126651749905011
CAMB-7675B	MN908947.3	2445	C	T	1	1	0	0	1	ACT	ORF1ab:nsp2	T547I	C1640T	ACT>ATT	Missense	ORF1ab:nsp2	0
CAMB-7675B	MN908947.3	27046	C	T	1	1	0	0	1	ACG	M	T175M	C524T	ACG>ATG	Missense	GU280_gp05	0
CAMB-7675B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7675B	MN908947.3	3037	C	T	1	1	0	0	0.999164578111946	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000417710944026733
CAMB-7675B	MN908947.3	8670	T	C	0.29	0.16	2.4e-83	5.3e-59	0.191608391608392	TTT	ORF1ab:nsp4	F39S	T116C	TTT>TCT	Missense	ORF1ab:nsp4	0.807925407925408
CAMB-7675B	MN908947.3	9972	A	G	0.25	0.12	1.4e-104	1.6e-50	0.187114038699053	AAG	ORF1ab:nsp4	K473R	A1418G	AAG>AGG	Missense	ORF1ab:nsp4	0.812885961300947
CAMB-7676A	MN908947.3	10097	G	A	1	1	0	0	0.999601763618262	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000142227279192149
CAMB-7676A	MN908947.3	11075	T	-	0.04	0.04	4.8e-10	1.9e-10	0.0395642201834862	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956361661033317
CAMB-7676A	MN908947.3	1170	C	T	0.83	0.84	0	0	0.832395737545302	TCT	ORF1ab:nsp2	S122F	C365T	TCT>TTT	Missense	ORF1ab:nsp2	0.167171525937145
CAMB-7676A	MN908947.3	11962	C	T	1	1	0	0	0.999614082481099	TCT	ORF1ab:nsp7	L40L	C120T	CTC>CTT	Synonymous	ORF1ab:nsp7	0.000228042170259793
CAMB-7676A	MN908947.3	13536	C	T	1	1	0	0	0.999659346994392	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000131020386772182
CAMB-7676A	MN908947.3	14408	C	T	1	1	0	0	0.998009547127935	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00044036567966039
CAMB-7676A	MN908947.3	16887	C	T	0.018	0.02	2.2e-08	8.4e-09	0.0191141957102875	ACA	ORF1ab:helicase	Y217Y	C651T	TAC>TAT	Synonymous	ORF1ab:helicase	0.980772851064898
CAMB-7676A	MN908947.3	21622	C	T	0.015	0.015	1.1e-07	2.3e-07	0.014967925873129	CCA	S	T20T	C60T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.984889522451889
CAMB-7676A	MN908947.3	23191	C	T	0.027	0.013	5.9e-06	0.00087	0.0216919927088643	TCA	S	F543F	C1629T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.978126592776247
CAMB-7676A	MN908947.3	23403	A	G	1	1	0	0	0.999607652348593	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.41634363376701e-05
CAMB-7676A	MN908947.3	23731	C	T	1	1	0	0	0.9998670507423	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000132949257699978
CAMB-7676A	MN908947.3	241	C	T	1	1	0	0	0.998809584545006	TCG	NA	NA	NA	NA	NA	NA	0.000136047480570719
CAMB-7676A	MN908947.3	25002	C	T	0.016	0.02	7.9e-09	1.8e-10	0.0172417458596424	TCA	S	S1147L	C3440T	TCA>TTA	Missense	GU280_gp02, spike glycoprotein	0.982651954844059
CAMB-7676A	MN908947.3	25440	G	T	0.031	0.032	4.8e-15	8.4e-16	0.0309692260948826	AGC	ORF3a	K16N	G48T	AAG>AAT	Missense	GU280_gp03	0.968358001649377
CAMB-7676A	MN908947.3	2669	C	T	0.034	0.036	8.5e-16	1.2e-16	0.0345392764341395	CCT	ORF1ab:nsp2	L622F	C1864T	CTT>TTT	Missense	ORF1ab:nsp2	0.96514091545073
CAMB-7676A	MN908947.3	27219	C	T	0.0052	0.0066	0.00023	3.9e-05	0.00560803637056598	ACT	ORF6	D6D	C18T	GAC>GAT	Synonymous	GU280_gp06	0.992077968039637
CAMB-7676A	MN908947.3	27944	C	T	0.039	0.046	1.1e-17	4.3e-20	0.0411334552102377	ACC	ORF8	H17H	C51T	CAC>CAT	Synonymous	GU280_gp09	0.958866544789762
CAMB-7676A	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999301261223492	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000232937339855579
CAMB-7676A	MN908947.3	3037	C	T	1	1	0	0	0.99915872125631	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7676A	MN908947.3	3121	A	T	0.0087	0.01	7.9e-06	8.2e-07	0.00922546227588143	AAG	ORF1ab:nsp3	E134D	A402T	GAA>GAT	Missense	ORF1ab:nsp3	0.990293209257551
CAMB-7676A	MN908947.3	4002	C	T	1	1	0	0	0.999877335732101	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	4.0888089299587e-05
CAMB-7676A	MN908947.3	5548	C	T	1	1	0	0	0.999677973379133	CCC	ORF1ab:nsp3	T943T	C2829T	ACC>ACT	Synonymous	ORF1ab:nsp3	0.000322026620867325
CAMB-7676A	MN908947.3	5879	A	G	0.017	0.017	4.2e-09	2.4e-09	0.0166745206075325	CAG	ORF1ab:nsp3	S1054G	A3160G	AGT>GGT	Missense	ORF1ab:nsp3	0.983325479392468
CAMB-7676A	MN908947.3	6638	C	T	0.0061	0.0092	0.00023	1.4e-05	0.0078883966736613	TCA	ORF1ab:nsp3	H1307Y	C3919T	CAT>TAT	Missense	ORF1ab:nsp3	0.992111603326339
CAMB-7676A	MN908947.3	7119	C	T	0.038	0.037	4.2e-15	5e-15	0.0376609442060086	TCT	ORF1ab:nsp3	S1467F	C4400T	TCT>TTT	Missense	ORF1ab:nsp3	0.962124463519313
CAMB-76779	MN908947.3	10367	CG	-	0.014	0.0055	4.2e-08;2.5e-08	NA;7.9e-07	0.00945300576042538	TCG	ORF1ab:3C-like-proteinase	.	313-314-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.993391379850944
CAMB-76779	MN908947.3	10368	G	-	0.014	0.011	2.5e-08	7.9e-07	0.0126187723090845	CGC	ORF1ab:3C-like-proteinase	.	314-314-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.987129857724599
CAMB-76779	MN908947.3	1059	C	T	1	1	0	0	0.99989118015126	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	2.72049621851026e-05
CAMB-76779	MN908947.3	11074	C	INS	0.045	0.047	8.9e-11	4.9e-11	0.0456611899824533	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.954139416174829
CAMB-76779	MN908947.3	11075	T	-	0.027	0.018	1.5e-07	1.4e-05	0.0233258355324915	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.973185030374949
CAMB-76779	MN908947.3	11083	G	T	0.032	0.014	5e-07	0.0024	0.0242358155404692	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.970136128601076
CAMB-76779	MN908947.3	13462	TTTA	-	0.014	0.004825	3.1e-06;3.6e-06;5.9e-06;4.5e-06	NA;NA;7.3e-05;5.6e-05	0.00851688693098385	TTT	ORF1ab:nsp11	.	21-24-delfrshift	.	no-SNV	ORF1ab:nsp11	0.993273542600897
CAMB-76779	MN908947.3	14408	C	T	1	1	0	0	0.999719252275226	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000280747724773647
CAMB-76779	MN908947.3	15285	G	C	0.0067	0.0066	1.3e-05	1.3e-05	0.00664350582068629	TGG	ORF1ab:RNA-dependent-RNA-polymerase	M606I	G1818C	ATG>ATC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993356494179314
CAMB-76779	MN908947.3	23196	GTT	-	0.011	0.012	5.2e-06;1.6e-06;7.2e-07	1.6e-06;4.6e-07;1.6e-07	0.0110984591879387	GGT	S	.	1634-1636-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.988938941811087
CAMB-76779	MN908947.3	23403	A	G	1	1	0	0	0.9979276670641	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000212910918071879
CAMB-76779	MN908947.3	241	C	T	1	1	0	0	0.999651557826882	TCG	NA	NA	NA	NA	NA	NA	0.000290368477598072
CAMB-76779	MN908947.3	24368	G	T	1	1	0	0	0.999500898382911	AGA	S	D936Y	G2806T	GAC>TAC	Missense	GU280_gp02, spike glycoprotein	9.98203234178479e-05
CAMB-76779	MN908947.3	25563	G	T	1	1	0	0	0.999879419283268	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	2.41161433463561e-05
CAMB-76779	MN908947.3	25634	G	T	0.014	0.0027	2.8e-08	0.0022	0.00944641761347788	TGC	ORF3a	C81F	G242T	TGC>TTC	Missense	GU280_gp03	0.990497796455734
CAMB-76779	MN908947.3	26787	GGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.0409411764705882	0.0148823529411765	4.9e-06;4.6e-06;4.7e-07;3.3e-06;2.4e-06;4.1e-06;1.5e-07;1.9e-07;3.2e-07;1.2e-07;2.7e-07;1.3e-07;1.6e-07;1.8e-07;3.4e-07;1.7e-07;2.1e-07;1.5e-07;1.2e-07;2.5e-07;1.2e-07;1.1e-07;1.6e-07;2.6e-07;2.2e-07;1.1e-07;2.5e-07;1.1e-06;2.4e-06;1.8e-06;5.3e-05;0.00022;1e-04;0.00016	0.011;0.012;0.0077;0.009;0.0089;0.011;0.01;0.01;0.013;0.0091;0.012;0.01;0.0099;0.0094;0.013;0.01;0.011;0.01;0.0078;0.012;0.01;0.0071;0.0097;0.012;0.011;0.0064;0.011;0.008;0.0097;0.0081;NA;NA;NA;NA	0.0304126807401005	AGG	M	.	265-298-delfrshift	.	no-SNV	GU280_gp05	0.973808396804223
CAMB-76779	MN908947.3	28513	AG	-	0.012	0.00505	7.8e-07;9.5e-07	0.00093;0.0011	0.00926829268292683	CAG	N	.	240-241-delfrshift	.	no-SNV	GU280_gp10	0.990533562822719
CAMB-76779	MN908947.3	3037	C	T	1	1	0	0	0.999727111474963	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76779	MN908947.3	4338	C	T	0.012	0.0056	9.9e-08	8.8e-05	0.00879240448570576	TCT	ORF1ab:nsp3	S540F	C1619T	TCT>TTT	Missense	ORF1ab:nsp3	0.991137396676085
CAMB-76779	MN908947.3	4441	TGTGGAAACTAAAGCCATAGTTTCAACTA	-	0.00651724137931034	0.000413793103448276	8.4e-05;0.00012;0.00012;0.00025;9.9e-05;0.00011;3.8e-05;0.00011;0.00013;2e-04;0.00042;0.00059;0.00016;0.00015;0.00016;0.00019;0.00011;9.4e-05;0.00011;0.00018;0.00017;9.2e-05;0.00012;0.00014;9.1e-05;5e-05;8.8e-05;0.00018;0.00012	NA;3.7e-07;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00264648528182747	GTG	ORF1ab:nsp3	.	1722-1750-delfrshift	.	no-SNV	ORF1ab:nsp3	0.997391030542936
CAMB-76779	MN908947.3	4591	TG	-	0.012	0.0135	3e-05;3.1e-05	8.8e-06;9.1e-06	0.0127890913952141	ATG	ORF1ab:nsp3	.	1872-1873-delfrshift	.	no-SNV	ORF1ab:nsp3	0.987066246056782
CAMB-76779	MN908947.3	9860	TT	-	0.015	0.0094	1e-05;7.3e-06	0.00061;0.00045	0.0123586826767783	ATT	ORF1ab:nsp4	.	1306-1307-delfrshift	.	no-SNV	ORF1ab:nsp4	0.98760737924236
CAMB-76797	MN908947.3	11074	C	INS	0.15	0.039	2.3e-45	2e-08	0.0920137398024903	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.907857449549163
CAMB-76797	MN908947.3	11083	G	-	0.16	0.11	7e-72	1.5e-48	0.135376856703834	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.93995508451204e-05
CAMB-76797	MN908947.3	11083	G	T	0.84	0.89	0	0	0.864386745991096	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.93995508451204e-05
CAMB-76797	MN908947.3	14408	C	T	1	1	0	0	0.999722145040289	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	6.94637399277577e-05
CAMB-76797	MN908947.3	23403	A	G	1	1	0	0	0.999929153382926	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.54233085370174e-05
CAMB-76797	MN908947.3	241	C	T	1	1	0	0	0.9995115995116	TCG	NA	NA	NA	NA	NA	NA	0.000244200244200244
CAMB-76797	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998769230769231	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000676132521974307
CAMB-76797	MN908947.3	3037	C	T	1	1	1.90000000000005e-311	0	0.999410029498525	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-767A6	MN908947.3	10684	T	C	0.083	0.12	1.7e-36	1.3e-49	0.0943755958055291	CTG	ORF1ab:3C-like-proteinase	A210A	T630C	GCT>GCC	Synonymous	ORF1ab:3C-like-proteinase	0.905624404194471
CAMB-767A6	MN908947.3	11052	AG	-	0.0285	0.0395	6.8e-11;3.9e-09	7.8e-14;8.3e-13	0.0303454093411472	CAG	ORF1ab:nsp6	.	80-81-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956279482065407
CAMB-767A6	MN908947.3	11075	T	-	0.097	0.017	1.1e-23	1.8e-05	0.0613740880329173	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.924812420040801
CAMB-767A6	MN908947.3	14408	C	T	1	1	0	0	0.999748254949079	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000160201396040737
CAMB-767A6	MN908947.3	1472	A	G	0.01	0.011	7.7e-05	1.3e-05	0.0107962213225371	CAC	ORF1ab:nsp2	T223A	A667G	ACT>GCT	Missense	ORF1ab:nsp2	0.989203778677463
CAMB-767A6	MN908947.3	15004	G	T	0.0098	0.0044	9.3e-06	0.0017	0.00732818379877203	TGA	ORF1ab:RNA-dependent-RNA-polymerase	E513*	G1537T	GAG>TAG	Nonsense	ORF1ab:RNA-dependent-RNA-polymerase	0.992671816201228
CAMB-767A6	MN908947.3	15839	G	-	0.0088	0.007	3.3e-05	2e-04	0.00799984905945171	TGG	ORF1ab:RNA-dependent-RNA-polymerase	.	2372-2372-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.99188694552933
CAMB-767A6	MN908947.3	16438	A	G	0.047	0.049	7.6e-19	4.6e-20	0.0483066421632975	TAT	ORF1ab:helicase	M68V	A202G	ATG>GTG	Missense	ORF1ab:helicase	0.951168285639275
CAMB-767A6	MN908947.3	18859	G	T	1	1	0	0	0.999838138593829	TGC	ORF1ab:3'-to-5'-exonuclease	A274S	G820T	GCA>TCA	Missense	ORF1ab:3'-to-5'-exonuclease	2.02326757713708e-05
CAMB-767A6	MN908947.3	19679	G	T	0.015	0.014	3.3e-07	9.4e-07	0.0147021864790148	GGT	ORF1ab:endoRNAse	G20V	G59T	GGT>GTT	Missense	ORF1ab:endoRNAse	0.985297813520985
CAMB-767A6	MN908947.3	21624	G	T	1	1	0	0	0.999615975422427	AGA	S	R21I	G62T	AGA>ATA	Missense	GU280_gp02, spike glycoprotein	0.000384024577572965
CAMB-767A6	MN908947.3	21985	G	-	0.025	0.019	3.7e-05	0.00043	0.0211973942715334	TGG	S	.	423-423-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.978595801881915
CAMB-767A6	MN908947.3	2295	C	T	0.019	0.025	3e-09	5.7e-11	0.0218860637270679	ACA	ORF1ab:nsp2	T497I	C1490T	ACA>ATA	Missense	ORF1ab:nsp2	0.978113936272932
CAMB-767A6	MN908947.3	23403	A	G	1	1	0	0	0.999910174261932	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.98838253787652e-05
CAMB-767A6	MN908947.3	241	C	T	1	1	0	0	0.999725802029065	TCG	NA	NA	NA	NA	NA	NA	0.000189829364493472
CAMB-767A6	MN908947.3	24132	G	T	0.007	0.0022	1.6e-05	0.0032	0.00448038465741449	GGC	S	G857V	G2570T	GGC>GTC	Missense	GU280_gp02, spike glycoprotein	0.995483189451062
CAMB-767A6	MN908947.3	24321	AA	-	0.02	0.00855	2.9e-07;1.6e-07	0.0064;0.00045	0.0159562343286984	CAA	S	.	2759-2760-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.983365836870483
CAMB-767A6	MN908947.3	27849	C	T	0.0048	0.012	0.003	6.1e-06	0.00799467021985343	ACT	NA	NA	NA	NA	NA	NA	0.992005329780147
CAMB-767A6	MN908947.3	28338	A	T	0.0046	0.0098	0.00023	1.6e-06	0.00713903517418119	GAT	N	D22V	A65T	GAT>GTT	Missense	GU280_gp10	0.992832802951364
CAMB-767A6	MN908947.3	28650	ACAA	-	0.001	0.008575	0.0089;0.011;NA;NA	0.00017;0.00023;4.7e-06;2.8e-07	0.004164738546969	AAC	N	.	377-380-delfrshift	.	no-SNV	GU280_gp10	0.99635099913119
CAMB-767A6	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999879022501815	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000263887056339887
CAMB-767A6	MN908947.3	29462	G	C	0.0074	0.011	0.0014	2.5e-05	0.0099626400996264	TGC	N	A397P	G1189C	GCT>CCT	Missense	GU280_gp10	0.990037359900374
CAMB-767A6	MN908947.3	29670	C	T	0.0094	0.0098	1.5e-05	1.7e-05	0.00958126330731015	ACA	ORF10	T38I	C113T	ACA>ATA	Missense	GU280_gp11	0.99041873669269
CAMB-767A6	MN908947.3	3037	C	T	1	1	0	0	0.998766447368421	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000548245614035088
CAMB-767A6	MN908947.3	3231	G	T	0.0088	0.017	7.6e-06	1.4e-09	0.0122109638867238	GGT	ORF1ab:nsp3	G171V	G512T	GGT>GTT	Missense	ORF1ab:nsp3	0.98771480532977
CAMB-767A6	MN908947.3	9474	C	T	0.014	0.006	1.1e-07	0.00011	0.00920559154449369	GCT	ORF1ab:nsp4	A307V	C920T	GCT>GTT	Missense	ORF1ab:nsp4	0.990794408455506
CAMB-767A6	MN908947.3	9661	C	T	0.0068	0.0086	3.9e-05	8e-06	0.00789352385342245	TCA	ORF1ab:nsp4	F369F	C1107T	TTC>TTT	Synonymous	ORF1ab:nsp4	0.992077667665361
CAMB-767B5	MN908947.3	11074	C	INS	0.026	0.033	2.7e-05	4.8e-07	0.0291910599346638	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.970582527412103
CAMB-767B5	MN908947.3	11075	T	-	0.035	0.037	5e-09	9.1e-10	0.0358842862809543	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962132373774579
CAMB-767B5	MN908947.3	14408	C	T	1	1	0	0	0.999633795448601	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000209259743656814
CAMB-767B5	MN908947.3	14724	C	T	0.0046	0.0078	0.0011	3.7e-05	0.00573343261355175	TCT	ORF1ab:RNA-dependent-RNA-polymerase	F419F	C1257T	TTC>TTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.994173492181683
CAMB-767B5	MN908947.3	21575	C	T	0.075	0.031	2.1e-19	3.4e-08	0.0547736782046405	TCT	S	L5F	C13T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.944465576264739
CAMB-767B5	MN908947.3	23403	A	G	1	1	0	0	0.999824438202247	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00013504753673293
CAMB-767B5	MN908947.3	24026	CTTT	-	0.05325	0.03625	1.8e-05;5.4e-08;5.3e-07;1.3e-08	0.00025;1.8e-05;6.4e-05;2.7e-06	0.0435233832781994	ACT	S	.	2464-2467-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.955804213289992
CAMB-767B5	MN908947.3	241	C	T	1	1	0	0	0.997168803418803	TCG	NA	NA	NA	NA	NA	NA	0.000195868945868946
CAMB-767B5	MN908947.3	25889	C	T	0.046	0.036	7e-21	3.6e-17	0.0399022215831476	TCA	ORF3a	S166L	C497T	TCA>TTA	Missense	GU280_gp03	0.960097778416852
CAMB-767B5	MN908947.3	28253	C	INS	0.028	0.029	8.5e-13	4.6e-13	0.0284273390842734	TCA	ORF8	.	359-360-insfrshift	.	no-SNV	GU280_gp09	0.966901128069011
CAMB-767B5	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998664886515354	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	7.36702519522617e-05
CAMB-767B5	MN908947.3	29711	G	-	0.094	0.13	8.3e-39	7.9e-49	0.106183290393817	TGA	NA	NA	NA	NA	NA	NA	0.893448656606551
CAMB-767B5	MN908947.3	3037	C	T	1	1	0	0	0.999646668079994	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.06663840011307e-05
CAMB-767B5	MN908947.3	3345	G	-	0.64	0.6	0	0	0.62425578831312	AGT	ORF1ab:nsp3	.	626-626-delfrshift	.	no-SNV	ORF1ab:nsp3	2.4500796275879e-05
CAMB-767B5	MN908947.3	3345	G	T	0.36	0.4	4.5e-185	2.7e-210	0.375646208501776	AGT	ORF1ab:nsp3	S209I	G626T	AGT>ATT	Missense	ORF1ab:nsp3	2.4500796275879e-05
CAMB-767B5	MN908947.3	3346	TT	-	0.995	0.99	0;0	0;0	0.99222300304521	GTT	ORF1ab:nsp3	.	627-628-delfrshift	.	no-SNV	ORF1ab:nsp3	0.0153016988869361
CAMB-767B5	MN908947.3	3709	ATTATCAGCTGGTA	-	0.0167857142857143	0.00045	8.7e-08;8.8e-08;1.1e-07;5.3e-08;1.7e-07;2.4e-07;1.4e-07;3.7e-07;1.4e-07;1.9e-07;2.6e-07;1.2e-07;1.1e-07;1.9e-07	NA;NA;NA;NA;NA;NA;0.008;0.011;NA;NA;NA;NA;NA;NA	0.00626370184779204	TAT	ORF1ab:nsp3	.	990-1003-delfrshift	.	no-SNV	ORF1ab:nsp3	0.993788819875776
CAMB-767B5	MN908947.3	515	G	-	0.54	0.54	2.8e-10	6e-11	0.53743622196733	TGT	ORF1ab:leader-protein	.	250-250-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.46256377803267
CAMB-767B5	MN908947.3	516	TT	-	0.705	0.7	4.3e-17;3.5e-15	1.9e-18;3.1e-16	0.701213283141382	GTT	ORF1ab:leader-protein	.	251-252-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.294169847731466
CAMB-767B5	MN908947.3	518	A	G	0.017	0.018	2.8e-08	3.3e-09	0.0175941977005998	TAT	ORF1ab:leader-protein	M85V	A253G	ATG>GTG	Missense	ORF1ab:leader-protein	0.000159403829677008
CAMB-767B5	MN908947.3	518	ATG	-	0.993333333333333	0.993333333333333	4e-50;1.7e-68;1.3e-57	1.5e-51;4.2e-63;1.4e-52	0.999800407169374	TAT	ORF1ab:leader-protein	.	253-255-delinframe	.	no-SNV	ORF1ab:leader-protein	0.000159403829677008
CAMB-767B5	MN908947.3	5587	T	C	0.01	0.016	1.4e-06	5.6e-09	0.0124504643047259	TTT	ORF1ab:nsp3	L956L	T2868C	CTT>CTC	Synonymous	ORF1ab:nsp3	0.987490388596439
CAMB-767B5	MN908947.3	8118	C	T	0.26	0.27	2.1e-123	1.7e-130	0.262301359372008	GCT	ORF1ab:nsp3	A1800V	C5399T	GCT>GTT	Missense	ORF1ab:nsp3	0.737634820345906
CAMB-767C4	MN908947.3	11074	C	INS	0.031	0.029	2.4e-06	2.4e-06	0.0301884527667747	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.968251110310887
CAMB-767C4	MN908947.3	11075	T	-	0.039	0.037	1.3e-10	1.7e-10	0.0381759831393399	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956794558605164
CAMB-767C4	MN908947.3	11083	G	T	0.031	0.038	7e-07	2.4e-08	0.0329041487839771	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.960702789699571
CAMB-767C4	MN908947.3	11379	C	T	0.97	0.98	0	0	0.973689475790316	GCT	ORF1ab:nsp6	A136V	C407T	GCT>GTT	Missense	ORF1ab:nsp6	0.0259103641456583
CAMB-767C4	MN908947.3	1170	C	T	0.98	0.97	0	0	0.974652190067291	TCT	ORF1ab:nsp2	S122F	C365T	TCT>TTT	Missense	ORF1ab:nsp2	0.0246047145275152
CAMB-767C4	MN908947.3	14408	C	T	0.98	0.98	0	0	0.977476940203562	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.0197996183206107
CAMB-767C4	MN908947.3	14805	C	T	0.018	0.017	8.6e-10	2.4e-09	0.0178970500595948	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.981953963051251
CAMB-767C4	MN908947.3	23403	A	G	0.98	0.98	0	0	0.979338291698629	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.0203615382049828
CAMB-767C4	MN908947.3	241	C	T	0.98	0.98	0	0	0.976107298814722	TCG	NA	NA	NA	NA	NA	NA	0.022707423580786
CAMB-767C4	MN908947.3	2480	A	G	0.024	0.02	2.4e-11	6.4e-10	0.022143584794381	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.977749182349472
CAMB-767C4	MN908947.3	2558	C	T	0.021	0.022	1.2e-10	4.1e-11	0.0215356464212823	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.978165247378422
CAMB-767C4	MN908947.3	26144	G	T	0.022	0.02	1.1e-10	6.1e-10	0.0215573556310426	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.978268443515373
CAMB-767C4	MN908947.3	28881	GGG	AAC	0.97	0.976666666666667	0;0;0	0;0;0	0.973196138211382	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.0296697810427216
CAMB-767C4	MN908947.3	3037	C	T	0.98	0.98	0	0	0.976624443251098	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.0225858419938718
CAMB-767C4	MN908947.3	6485	G	T	0.021	0.021	3.8e-11	2e-11	0.0211927697802793	AGA	ORF1ab:nsp3	D1256Y	G3766T	GAC>TAC	Missense	ORF1ab:nsp3	0.978720640761987
CAMB-767D3	MN908947.3	11074	C	INS	0.11	0.1	5.4e-39	5.1e-34	0.106022896963664	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.889548754741594
CAMB-767D3	MN908947.3	11083	G	-	0.18	0.17	2.1e-80	2e-75	0.174306671546087	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.1822304253051e-05
CAMB-767D3	MN908947.3	11083	G	T	0.82	0.83	0	0	0.825327371955003	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.1822304253051e-05
CAMB-767D3	MN908947.3	14805	C	T	1	1	0	0	0.99881052940061	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000603354651864366
CAMB-767D3	MN908947.3	15405	A	G	1	1	0	0	0.999630948942589	TAG	ORF1ab:RNA-dependent-RNA-polymerase	L646L	A1938G	TTA>TTG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	6.41827925933057e-05
CAMB-767D3	MN908947.3	17623	G	A	0.0078	0.0075	2.8e-05	3.3e-05	0.00765517877455652	AGC	ORF1ab:helicase	A463T	G1387A	GCA>ACA	Missense	ORF1ab:helicase	0.992160359086298
CAMB-767D3	MN908947.3	2480	A	G	1	1	0	0	0.999808831963296	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	4.77920091760658e-05
CAMB-767D3	MN908947.3	2558	C	T	1	1	0	0	0.999440285454418	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	3.49821590988596e-05
CAMB-767D3	MN908947.3	26144	G	T	1	1	0	0	0.999565274094683	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000260835543190019
CAMB-767D3	MN908947.3	27331	C	T	1	1	0	0	0.999617116427237	ACT	ORF6	L44L	C130T	CTA>TTA	Synonymous	GU280_gp06	0.000183784114926333
CAMB-767D3	MN908947.3	28087	C	T	0.02	0.018	9.8e-10	5.7e-09	0.0194136291600634	GCT	ORF8	A65V	C194T	GCT>GTT	Missense	GU280_gp09	0.980256207078711
CAMB-767D3	MN908947.3	583	C	T	1	1	0	0	0.999700041047015	TCC	ORF1ab:leader-protein	V106V	C318T	GTC>GTT	Synonymous	ORF1ab:leader-protein	0.000205235073095261
CAMB-767D3	MN908947.3	6998	T	C	0.016	0.016	1.9e-07	1.3e-07	0.0156968447756461	CTA	ORF1ab:nsp3	Y1427H	T4279C	TAC>CAC	Missense	ORF1ab:nsp3	0.984303155224354
CAMB-767D3	MN908947.3	700	A	G	1	1	0	0	0.999317683181479	TAG	ORF1ab:leader-protein	L145L	A435G	TTA>TTG	Synonymous	ORF1ab:leader-protein	0.000252927786176026
CAMB-767D3	MN908947.3	7273	G	INS	0.012	0.012	3e-06	3.1e-06	0.0122492455174862	GGT	ORF1ab:nsp3	.	4553-4554-insfrshift	.	no-SNV	ORF1ab:nsp3	0.986863127995739
CAMB-767D3	MN908947.3	7279	C	T	0.99	0.99	0	0	0.992553382379329	TCT	ORF1ab:nsp3	F1520F	C4560T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000269154853759196
CAMB-767D3	MN908947.3	8637	C	T	0.011	0.01	6.2e-07	3e-06	0.0107061246367817	ACA	ORF1ab:nsp4	T28I	C83T	ACA>ATA	Missense	ORF1ab:nsp4	0.989265664231106
CAMB-767E2	MN908947.3	11075	T	-	0.033	0.059	4.9e-09	5.4e-15	0.0447304940941607	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.948407087007154
CAMB-767E2	MN908947.3	14408	C	T	1	1	0	0	0.999612261654959	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000296505793267038
CAMB-767E2	MN908947.3	15101	C	T	0.47	0.45	5.4e-207	3.5e-186	0.457510729613734	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A545V	C1634T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.542489270386266
CAMB-767E2	MN908947.3	16466	C	T	0.11	0.11	2.3e-26	8.5e-28	0.109753116597409	CCA	ORF1ab:helicase	P77L	C230T	CCA>CTA	Missense	ORF1ab:helicase	0.890246883402591
CAMB-767E2	MN908947.3	18859	G	T	1	1	0	0	0.999863051218844	TGC	ORF1ab:3'-to-5'-exonuclease	A274S	G820T	GCA>TCA	Missense	ORF1ab:3'-to-5'-exonuclease	3.91282231873851e-05
CAMB-767E2	MN908947.3	21624	G	T	1	1	0	0	1	AGA	S	R21I	G62T	AGA>ATA	Missense	GU280_gp02, spike glycoprotein	0
CAMB-767E2	MN908947.3	22121	AA	-	0.0325	0.0055	5.6e-16;4.1e-12	9.3e-05;NA	0.0212694125590817	CAA	S	.	559-560-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.97192151556157
CAMB-767E2	MN908947.3	23403	A	G	1	1	0	0	0.999856647266263	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000114682186989306
CAMB-767E2	MN908947.3	241	C	T	1	1	0	0	0.999684193904942	TCG	NA	NA	NA	NA	NA	NA	9.47418285172904e-05
CAMB-767E2	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999532448101739	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000210703750526759
CAMB-767E2	MN908947.3	29751	G	T	0.37	0.5	4.6e-150	1.5e-200	0.422897196261682	CGA	NA	NA	NA	NA	NA	NA	0.577102803738318
CAMB-767E2	MN908947.3	3037	C	T	1	1	0	0	0.999481865284974	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-767E2	MN908947.3	3747	C	T	0.03	0.019	3e-07	3.6e-06	0.02321083172147	TCT	ORF1ab:nsp3	S343F	C1028T	TCT>TTT	Missense	ORF1ab:nsp3	0.97678916827853
CAMB-767F1	MN908947.3	10262	G	A	1	1	0	0	0.999879179108342	GGC	ORF1ab:3C-like-proteinase	A70T	G208A	GCT>ACT	Missense	ORF1ab:3C-like-proteinase	8.63006368987003e-05
CAMB-767F1	MN908947.3	11075	T	-	0.031	0.048	5.4e-08	3.1e-12	0.03707616066771	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959428794992175
CAMB-767F1	MN908947.3	11452	A	G	0.0051	0.016	0.00036	1.8e-08	0.00969869390922022	AAG	ORF1ab:nsp6	Q160Q	A480G	CAA>CAG	Synonymous	ORF1ab:nsp6	0.99030130609078
CAMB-767F1	MN908947.3	11695	TTATGATTACTTAG	-	0.0190714285714286	0.00205	8.7e-05;0.00011;0.00015;1.6e-05;1.6e-05;7.3e-06;8.4e-06;1.3e-05;2e-05;1.3e-05;1.4e-05;1.4e-05;0.00022;0.00055	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0087	0.0128676470588235	TTT	ORF1ab:nsp6	.	723-736-delfrshift	.	no-SNV	ORF1ab:nsp6	0.990458015267176
CAMB-767F1	MN908947.3	1263	C	T	0.98	0.98	0	0	0.978483547925608	ACG	ORF1ab:nsp2	T153M	C458T	ACG>ATG	Missense	ORF1ab:nsp2	0.0214592274678112
CAMB-767F1	MN908947.3	13301	AAAGGT	-	0.000383333333333333	0.00468333333333333	0.0026;NA;NA;NA;NA;NA	8.5e-05;1.7e-05;3.2e-05;6.6e-05;8.6e-05;0.00055	0.000575391888529485	AAA	ORF1ab:nsp10	.	277-282-delinframe	.	no-SNV	ORF1ab:nsp10	0.997339438188343
CAMB-767F1	MN908947.3	14408	C	T	1	0.99	0	0	0.995735116131635	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000288167828943577
CAMB-767F1	MN908947.3	19839	T	C	1	1	0	0	1	ATA	ORF1ab:endoRNAse	N73N	T219C	AAT>AAC	Synonymous	ORF1ab:endoRNAse	0
CAMB-767F1	MN908947.3	2163	AGAAGTTT	-	0.005725	0.000375	0.00073;0.00094;8.5e-05;0.00041;0.00042;2.7e-05;6.2e-05;4.5e-05	NA;NA;NA;NA;NA;0.0067;NA;NA	0.00262064873417722	GAG	ORF1ab:nsp2	.	1358-1365-delfrshift	.	no-SNV	ORF1ab:nsp2	0.997331392527899
CAMB-767F1	MN908947.3	22995	C	T	1	1	0	0	0.999699085219066	ACA	S	T478I	C1433T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0.000120365912373616
CAMB-767F1	MN908947.3	23403	A	G	1	1	0	0	0.998454115332365	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.51337424462454e-05
CAMB-767F1	MN908947.3	241	C	T	1	0.99	0	0	0.994845265588915	TCG	NA	NA	NA	NA	NA	NA	0.00218013856812933
CAMB-767F1	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.03778125	0.02784375	1.9e-05;4.7e-05;2.8e-06;2.8e-06;3.5e-07;1.6e-06;1.2e-06;2.5e-06;2e-06;2.5e-06;3.7e-06;1.9e-06;3.3e-06;1.7e-06;2.1e-06;1.8e-06;4e-06;2e-06;2.5e-06;2e-06;1.3e-06;3e-06;1.6e-06;2.5e-06;1.8e-06;3.2e-06;2.4e-06;1.6e-06;3e-06;1.3e-06;2.8e-06;2.1e-06	0.00021;0.00039;3.3e-05;3.3e-05;1.8e-05;2e-05;1.9e-05;0.00021;0.00016;0.00018;0.00027;0.00014;0.00025;0.00018;0.00016;0.00012;0.00027;0.00017;0.00021;0.00017;9.6e-05;0.00024;0.00017;7.2e-05;0.00016;0.00023;0.00022;1e-04;0.00021;9.6e-05;0.00017;0.00012	0.0332065360415321	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.969416550874529
CAMB-767F1	MN908947.3	28826	C	T	0.085	0.096	2e-36	7.3e-41	0.0899067005937235	TCG	N	R185C	C553T	CGT>TGT	Missense	GU280_gp10	0.910028055066223
CAMB-767F1	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999422799422799	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000159782695534074
CAMB-767F1	MN908947.3	3037	C	T	1	1	0	0	0.999568885877933	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000184763195171522
CAMB-767F1	MN908947.3	522	TT	-	0.061	0.0355	2e-09;7.5e-07	1.7e-05;0.00018	0.0524704215964006	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.935111225629133
CAMB-767F1	MN908947.3	7434	TTTA	-	0.021	0.01575	4.6e-05;4.4e-05;0.00013;0.00082	0.0019;0.00024;0.00065;0.0039	0.0195277335364587	TTT	ORF1ab:nsp3	.	4715-4718-delfrshift	.	no-SNV	ORF1ab:nsp3	0.983052112886367
CAMB-767F1	MN908947.3	9438	C	T	1	1	0	0	0.999732656062024	ACA	ORF1ab:nsp4	T295I	C884T	ACA>ATA	Missense	ORF1ab:nsp4	0.000200507953482155
CAMB-7680D	MN908947.3	10097	G	A	1	1	0	0	0.999796479088226	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000203520911773685
CAMB-7680D	MN908947.3	11075	T	-	0.0054	0.067	0.0086	9.6e-17	0.0389262621644569	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.947597587790913
CAMB-7680D	MN908947.3	13536	C	T	1	1	0	0	0.999752352649827	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000247647350173353
CAMB-7680D	MN908947.3	13728	T	C	0.028	0.018	2.3e-14	5.4e-10	0.022007625994695	TTG	ORF1ab:RNA-dependent-RNA-polymerase	V87V	T261C	GTT>GTC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.977992374005305
CAMB-7680D	MN908947.3	14408	C	T	1	1	0	0	0.999531731361676	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000295748613678373
CAMB-7680D	MN908947.3	17550	C	T	0.02	0.017	1.5e-10	6e-09	0.0182229443435598	TCG	ORF1ab:helicase	L438L	C1314T	CTC>CTT	Synonymous	ORF1ab:helicase	0.981713339067826
CAMB-7680D	MN908947.3	21597	C	T	0.35	0.2	2.5e-78	8e-65	0.234290147401086	TCT	S	S12F	C35T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.765709852598914
CAMB-7680D	MN908947.3	21996	A	G	0.0082	0.0022	9.4e-06	0.0046	0.00423312883435583	TAC	S	Y145C	A434G	TAC>TGC	Missense	GU280_gp02, spike glycoprotein	0.995705521472393
CAMB-7680D	MN908947.3	23403	A	G	1	1	0	0	0.999882853684252	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00011714631574837
CAMB-7680D	MN908947.3	23731	C	T	1	1	0	0	1	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-7680D	MN908947.3	24011	TTTATTGA	-	0.026625	0.026125	6.5e-08;1.1e-06;1.4e-05;4.9e-05;0.00057;0.00065;0.00069;0.00074	7.3e-08;1.4e-06;1.6e-05;5.2e-05;0.00063;0.00069;0.00073;8e-04	0.0265661153483589	ATT	S	.	2449-2456-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.973512772158409
CAMB-7680D	MN908947.3	241	C	T	0.97	1	0	0	0.987774581589958	TCG	NA	NA	NA	NA	NA	NA	3.26882845188284e-05
CAMB-7680D	MN908947.3	28881	GGG	AAC	0.98	1	0;0;0	0;0;0	0.99201198202696	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7680D	MN908947.3	29411	C	T	0.025	0.011	1e-05	0.00043	0.0158730158730159	TCA	N	Q380*	C1138T	CAA>TAA	Nonsense	GU280_gp10	0.984126984126984
CAMB-7680D	MN908947.3	29555	C	T	0.51	0.55	8.7e-153	9.99999999999999e-229	0.538288288288288	GCA	NA	NA	NA	NA	NA	NA	0.461711711711712
CAMB-7680D	MN908947.3	3037	C	T	1	1	0	0	0.999658353262726	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00017082336863683
CAMB-7680D	MN908947.3	4002	C	T	1	1	0	0	1	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-7680D	MN908947.3	522	TT	-	0.0305	0.0945	0.00033;0.00022	5.6e-13;8.7e-14	0.0595293226118806	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.938887212860406
CAMB-7680D	MN908947.3	7340	A	T	0.0067	0.0085	3.5e-05	4.4e-06	0.00789265982636148	TAT	ORF1ab:nsp3	I1541F	A4621T	ATT>TTT	Missense	ORF1ab:nsp3	0.992107340173639
CAMB-7681C	MN908947.3	14408	C	T	1	1	0	0	0.999856754046698	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000143245953301819
CAMB-7681C	MN908947.3	23403	A	G	1	1	0	0	0.999667571610616	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000304726023602416
CAMB-7681C	MN908947.3	241	C	T	1	1	0	0	1	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-7681C	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7681C	MN908947.3	3037	C	T	1	1	7.9e-242	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7681C	MN908947.3	313	C	T	1	1	0	0	0.999816950393557	TCA	ORF1ab:leader-protein	L16L	C48T	CTC>CTT	Synonymous	ORF1ab:leader-protein	9.15248032216731e-05
CAMB-7682B	MN908947.3	10369	C	T	0.013	0.0057	4.2e-07	0.00055	0.00921871398939848	GCA	ORF1ab:3C-like-proteinase	R105R	C315T	CGC>CGT	Synonymous	ORF1ab:3C-like-proteinase	0.990781286010602
CAMB-7682B	MN908947.3	10523	G	C	0.014	0.0045	1e-07	0.0013	0.0114176974310181	TGT	ORF1ab:3C-like-proteinase	V157L	G469C	GTC>CTC	Missense	ORF1ab:3C-like-proteinase	0.988582302568982
CAMB-7682B	MN908947.3	10626	C	T	0.011	0.023	1.9e-06	6.4e-11	0.0146307798481712	GCA	ORF1ab:3C-like-proteinase	A191V	C572T	GCA>GTA	Missense	ORF1ab:3C-like-proteinase	0.985369220151829
CAMB-7682B	MN908947.3	10684	T	C	0.037	0.015	1.1e-17	2.6e-08	0.0312075061191188	CTG	ORF1ab:3C-like-proteinase	A210A	T630C	GCT>GCC	Synonymous	ORF1ab:3C-like-proteinase	0.968656513462061
CAMB-7682B	MN908947.3	11074	C	INS	0.022	0.029	3e-04	7.9e-06	0.0252207957752891	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.974597104616225
CAMB-7682B	MN908947.3	11075	T	-	0.048	0.031	5.2e-12	1.7e-08	0.0412868289087909	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954980213723825
CAMB-7682B	MN908947.3	14408	C	T	1	1	0	0	0.997112865910786	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000382401866121107
CAMB-7682B	MN908947.3	17104	C	T	0.0079	0.012	1.4e-05	1.8e-07	0.0100147447407991	TCA	ORF1ab:helicase	H290Y	C868T	CAT>TAT	Missense	ORF1ab:helicase	0.989956057752668
CAMB-7682B	MN908947.3	18859	G	T	1	1	0	0	0.999829740865597	TGC	ORF1ab:3'-to-5'-exonuclease	A274S	G820T	GCA>TCA	Missense	ORF1ab:3'-to-5'-exonuclease	3.40518268805121e-05
CAMB-7682B	MN908947.3	19002	A	G	0.0063	0.011	3.9e-05	6.2e-07	0.00865529145537735	TAT	ORF1ab:3'-to-5'-exonuclease	L321L	A963G	TTA>TTG	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.991328190812838
CAMB-7682B	MN908947.3	195	T	A	0.011	0.0055	4.5e-07	8.8e-05	0.00810943070864307	TTA	NA	NA	NA	NA	NA	NA	0.991657539673293
CAMB-7682B	MN908947.3	1968	C	T	0.022	0.029	1.8e-11	2.3e-14	0.0256693348054099	ACA	ORF1ab:nsp2	T388I	C1163T	ACA>ATA	Missense	ORF1ab:nsp2	0.97433066519459
CAMB-7682B	MN908947.3	21624	G	T	1	1	0	0	0.999671268902038	AGA	S	R21I	G62T	AGA>ATA	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7682B	MN908947.3	2174	G	A	0.0064	0.012	1.7e-05	1e-07	0.00912515696944328	GGA	ORF1ab:nsp2	E457K	G1369A	GAA>AAA	Missense	ORF1ab:nsp2	0.990874843030557
CAMB-7682B	MN908947.3	2197	C	T	0.02	0.0039	2e-10	0.0016	0.0118505013673655	ACG	ORF1ab:nsp2	D464D	C1392T	GAC>GAT	Synonymous	ORF1ab:nsp2	0.988149498632634
CAMB-7682B	MN908947.3	23403	A	G	1	1	0	0	0.999893539157629	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.65380264821345e-05
CAMB-7682B	MN908947.3	24010	A	G	0.0052	0.0058	8e-05	4.8e-05	0.00551111791496039	CAT	S	S816S	A2448G	TCA>TCG	Synonymous	GU280_gp02, spike glycoprotein	0.994412338780665
CAMB-7682B	MN908947.3	241	C	T	1	1	0	0	0.999807812424927	TCG	NA	NA	NA	NA	NA	NA	7.20703406524768e-05
CAMB-7682B	MN908947.3	27112	G	A	0.014	0.0032	2.3e-08	0.00072	0.0102959437086093	AGT	M	S197N	G590A	AGT>AAT	Missense	GU280_gp05	0.989704056291391
CAMB-7682B	MN908947.3	27134	T	C	0.011	0.017	2.8e-07	2e-09	0.0132032451349488	ATA	M	Y204Y	T612C	TAT>TAC	Synonymous	GU280_gp05	0.986796754865051
CAMB-7682B	MN908947.3	27920	C	T	0.011	0.023	7.4e-06	7.4e-10	0.0160042678047479	TCA	ORF8	I9I	C27T	ATC>ATT	Synonymous	GU280_gp09	0.983995732195252
CAMB-7682B	MN908947.3	28338	A	T	0.0087	0.0033	5.1e-06	0.00077	0.0062728555188802	GAT	N	D22V	A65T	GAT>GTT	Missense	GU280_gp10	0.993658663525674
CAMB-7682B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000132432790358893
CAMB-7682B	MN908947.3	29420	C	T	0.017	0.024	3.7e-05	8.1e-07	0.0204724409448819	ACC	N	P383S	C1147T	CCG>TCG	Missense	GU280_gp10	0.979527559055118
CAMB-7682B	MN908947.3	3037	C	T	1	1	0	0	0.999384236453202	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7682B	MN908947.3	352	T	C	0.048	0.029	4.7e-23	7e-15	0.0402311763531056	GTG	ORF1ab:leader-protein	R29R	T87C	CGT>CGC	Synonymous	ORF1ab:leader-protein	0.959718893549031
CAMB-7682B	MN908947.3	4719	C	A	0.038	0.041	1.8e-18	8.8e-20	0.0396268097360843	GCG	ORF1ab:nsp3	A667E	C2000A	GCG>GAG	Missense	ORF1ab:nsp3	0.960274567044065
CAMB-7682B	MN908947.3	5392	C	T	0.0053	0.013	0.00082	8.4e-07	0.00956080071706005	ACT	ORF1ab:nsp3	N891N	C2673T	AAC>AAT	Synonymous	ORF1ab:nsp3	0.99043919928294
CAMB-7682B	MN908947.3	9085	A	G	0.028	0.03	7.6e-14	1e-14	0.0288032791425485	AAG	ORF1ab:nsp4	E177E	A531G	GAA>GAG	Synonymous	ORF1ab:nsp4	0.971030548093168
CAMB-7682B	MN908947.3	9180	C	T	0.0068	0.022	7.8e-05	2.8e-11	0.0133403413926015	TCT	ORF1ab:nsp4	S209F	C626T	TCT>TTT	Missense	ORF1ab:nsp4	0.986609601041197
CAMB-7682B	MN908947.3	9474	C	T	0.0036	0.008	0.0012	1.6e-05	0.00553709856035437	GCT	ORF1ab:nsp4	A307V	C920T	GCT>GTT	Missense	ORF1ab:nsp4	0.991017595668758
CAMB-7682B	MN908947.3	9491	C	T	0.0071	0.0092	8.7e-05	1.4e-05	0.00803818136146697	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.991961818638533
CAMB-7683A	MN908947.3	11074	C	INS	0.1	0.098	2.9e-32	3.6e-27	0.100442180678384	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.895891637747677
CAMB-7683A	MN908947.3	11083	G	-	0.16	0.17	1.7e-73	1.1e-74	0.16539019363375	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.5444645174423e-05
CAMB-7683A	MN908947.3	11083	G	T	0.84	0.83	0	0	0.834406249204855	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.5444645174423e-05
CAMB-7683A	MN908947.3	14805	C	T	1	1	0	0	0.998812492578079	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000458038577026821
CAMB-7683A	MN908947.3	15600	C	A	0.0073	0.01	1.7e-05	4.6e-07	0.00835546969331079	TCC	ORF1ab:RNA-dependent-RNA-polymerase	V711V	C2133A	GTC>GTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.991523786524994
CAMB-7683A	MN908947.3	19947	G	T	1	1	0	0	0.999489274770174	AGA	ORF1ab:endoRNAse	K109N	G327T	AAG>AAT	Missense	ORF1ab:endoRNAse	0
CAMB-7683A	MN908947.3	22661	G	T	0.01	0.0092	3.3e-06	8.3e-06	0.00991478394130076	TGT	S	V367F	G1099T	GTC>TTC	Missense	GU280_gp02, spike glycoprotein	0.989876239347993
CAMB-7683A	MN908947.3	2445	C	T	1	1	0	0	0.999560400914366	ACT	ORF1ab:nsp2	T547I	C1640T	ACT>ATT	Missense	ORF1ab:nsp2	0
CAMB-7683A	MN908947.3	24766	C	T	1	1	0	0	0.999577464788732	TCC	S	V1068V	C3204T	GTC>GTT	Synonymous	GU280_gp02, spike glycoprotein	0.00028169014084507
CAMB-7683A	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-7683A	MN908947.3	2558	C	T	1	1	0	0	0.999301874595992	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	5.17129928894635e-05
CAMB-7683A	MN908947.3	26144	G	T	1	1	0	0	0.999800505386355	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7683A	MN908947.3	677	G	A	0.01	0.0096	1.4e-06	2e-06	0.0100781207991827	CGC	ORF1ab:leader-protein	A138T	G412A	GCC>ACC	Missense	ORF1ab:leader-protein	0.989514759991704
CAMB-76849	MN908947.3	11071	G	INS	0.037	0.0039	3.3e-11	0.0084	0.02281618399979	TGT	ORF1ab:nsp6	.	98-99-insfrshift	.	no-SNV	ORF1ab:nsp6	0.976973770577887
CAMB-76849	MN908947.3	11074	C	INS	0.58	0.58	0	0	0.576945591469299	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.409748920214533
CAMB-76849	MN908947.3	11083	G	T	1	1	0	0	0.999214718420462	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.80457706977788e-05
CAMB-76849	MN908947.3	14028	G	T	0.14	0.33	2.9e-66	1.2e-166	0.254082479933573	TGC	ORF1ab:RNA-dependent-RNA-polymerase	M187I	G561T	ATG>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.745892358402738
CAMB-76849	MN908947.3	1437	C	T	0.037	0.011	1.8e-10	9.3e-05	0.0220125786163522	TCT	ORF1ab:nsp2	S211F	C632T	TCT>TTT	Missense	ORF1ab:nsp2	0.977987421383648
CAMB-76849	MN908947.3	14805	C	T	1	1	0	0	0.99985517216409	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	3.62069589775155e-05
CAMB-76849	MN908947.3	1578	TT	-	0.0425	0.00465	7e-12;8.6e-12	NA;0.00062	0.0213414634146341	GTT	ORF1ab:nsp2	.	773-774-delfrshift	.	no-SNV	ORF1ab:nsp2	0.980808080808081
CAMB-76849	MN908947.3	16838	AA	-	0.0094	0.0125	0.00028;2.1e-05	2.5e-05;9e-07	0.0110963304240615	GAA	ORF1ab:helicase	.	602-603-delfrshift	.	no-SNV	ORF1ab:helicase	0.988362265132306
CAMB-76849	MN908947.3	22084	T	C	0.032	0.024	1.5e-12	6.6e-09	0.0288836846213895	CTT	S	P174P	T522C	CCT>CCC	Synonymous	GU280_gp02, spike glycoprotein	0.970465781941192
CAMB-76849	MN908947.3	23559	TTGGTGCAGGTATATGCGCTAG	-	0.0219090909090909	0.0415	0.028;0.036;0.032;0.037;0.038;0.039;0.037;0.038;0.035;0.033;3.5e-09;2.5e-10;0.027;0.022;0.027;0.023;0.029;0.034;0.03;0.03;0.014;0.018	0.00038;0.00053;0.00035;0.00059;0.00063;0.00065;6e-04;0.00059;0.00039;0.00035;0.00019;5.8e-05;0.00023;0.00011;9.5e-06;1.9e-06;5.9e-06;1.7e-05;7.2e-06;7.3e-06;3.9e-08;8.4e-08	0.0225005542008424	ATT	S	.	1997-2018-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.971304591265398
CAMB-76849	MN908947.3	2480	A	G	1	1	0	0	0.999014292755052	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.00098570724494825
CAMB-76849	MN908947.3	25006	C	T	0.002	0.01	0.0066	1.2e-06	0.0056559736963151	TCA	S	F1148F	C3444T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.994344026303685
CAMB-76849	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-76849	MN908947.3	26144	G	T	1	1	2.6e-229	3.1e-122	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-76849	MN908947.3	27242	T	C	0.051	0.067	4.9e-24	2.9e-31	0.0555131017822368	ATA	ORF6	I14T	T41C	ATA>ACA	Missense	GU280_gp06	0.944462247639707
CAMB-76849	MN908947.3	29155	A	G	0.36	0.36	2.2e-183	2.3e-176	0.359463554233769	AAG	N	Q294Q	A882G	CAA>CAG	Synonymous	GU280_gp10	0.64019976432299
CAMB-76849	MN908947.3	29555	C	T	0.057	0.063	1.8e-22	6.3e-25	0.0603626943005181	GCA	NA	NA	NA	NA	NA	NA	0.939637305699482
CAMB-76849	MN908947.3	4616	GGCTATGTAACACATGGCTTA	-	0.00134047619047619	0.0185714285714286	NA;NA;NA;NA;NA;NA;NA;NA;NA;6.9e-08;9.3e-08;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	2.1e-10;2e-10;2.3e-11;2.8e-10;2.5e-10;2.8e-10;1.9e-12;3.1e-10;2.9e-10;1.1e-09;1.3e-09;3.5e-10;4.9e-10;1.1e-10;4.4e-10;2.7e-10;4.3e-10;2.9e-10;3.3e-10;3.6e-10;7.7e-10	0.010479434110558	TGG	ORF1ab:nsp3	.	1897-1917-delinframe	.	no-SNV	ORF1ab:nsp3	0.989368064323211
CAMB-76849	MN908947.3	686	AAGTCATTT	-	0.0147777777777778	0.0462222222222222	0.0066;0.0055;0.012;0.0064;0.012;0.057;0.044;0.062;0.076	7.8e-07;6.7e-07;3.5e-06;6.8e-07;3.7e-06;1.7e-06;6.9e-07;1.8e-06;0.00021	0.0307795421736441	AAA	ORF1ab:leader-protein	.	421-429-delinframe	.	no-SNV	ORF1ab:leader-protein	0.969087619539933
CAMB-76849	MN908947.3	8344	C	T	0.014	0.019	2e-07	3.1e-09	0.016122098022356	ACT	ORF1ab:nsp3	D1875D	C5625T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.983877901977644
CAMB-76849	MN908947.3	9561	C	T	0.01	0.02	1.3e-06	9.2e-11	0.0154481289119723	TCA	ORF1ab:nsp4	S336L	C1007T	TCA>TTA	Missense	ORF1ab:nsp4	0.976611399653749
CAMB-76858	MN908947.3	10714	C	T	0.0077	0.0043	1.6e-05	0.00038	0.00647067390716351	TCA	ORF1ab:3C-like-proteinase	L220L	C660T	CTC>CTT	Synonymous	ORF1ab:3C-like-proteinase	0.993529326092837
CAMB-76858	MN908947.3	11075	T	-	0.045	0.026	3.3e-11	2.3e-07	0.0386215334420881	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95899945622621
CAMB-76858	MN908947.3	14408	C	T	1	1	0	0	0.999445014845853	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000194244803951494
CAMB-76858	MN908947.3	15026	C	T	0.0051	0.0084	0.00031	1.2e-05	0.006486117432863	GCA	ORF1ab:RNA-dependent-RNA-polymerase	A520V	C1559T	GCA>GTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.991238051888939
CAMB-76858	MN908947.3	21899	A	C	0.0048	0.0072	0.00023	2.4e-05	0.00582868727825646	GAA	S	K113Q	A337C	AAG>CAG	Missense	GU280_gp02, spike glycoprotein	0.994044602128738
CAMB-76858	MN908947.3	23403	A	G	1	1	0	0	0.997914818101153	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.54569653948536e-05
CAMB-76858	MN908947.3	241	C	T	1	1	0	0	0.998716096934681	TCG	NA	NA	NA	NA	NA	NA	0.000114634202260586
CAMB-76858	MN908947.3	25546	C	T	0.011	0.0082	1.1e-06	1e-05	0.0098773488365195	ACT	ORF3a	L52F	C154T	CTT>TTT	Missense	GU280_gp03	0.988951013688878
CAMB-76858	MN908947.3	26333	C	T	0.011	0.0087	6.1e-06	3.8e-05	0.00983193277310924	ACA	E	T30I	C89T	ACA>ATA	Missense	GU280_gp04	0.990140056022409
CAMB-76858	MN908947.3	26492	A	G	0.047	0.043	4.6e-22	2.2e-20	0.0454814257297995	TAG	NA	NA	NA	NA	NA	NA	0.953954088489866
CAMB-76858	MN908947.3	27661	C	T	0.039	0.032	9.7e-10	4.9e-07	0.0362173038229376	ACA	ORF7a	Q90*	C268T	CAA>TAA	Nonsense	GU280_gp07	0.963782696177062
CAMB-76858	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998384164815189	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-76858	MN908947.3	3037	C	T	1	1	0	0	0.999591073723566	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000116836078981189
CAMB-76858	MN908947.3	3587	C	T	0.047	0.073	1.3e-19	5.4e-29	0.0588853838065195	ACA	ORF1ab:nsp3	H290Y	C868T	CAC>TAC	Missense	ORF1ab:nsp3	0.941114616193481
CAMB-76858	MN908947.3	683	C	T	1	0.99	0	0	0.994002071707822	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	4.17683028703178e-05
CAMB-76858	MN908947.3	8818	C	T	0.019	0.017	1.8e-09	1.5e-08	0.0178376251475539	GCC	ORF1ab:nsp4	C88C	C264T	TGC>TGT	Synonymous	ORF1ab:nsp4	0.982074935513488
CAMB-76867	MN908947.3	14408	C	T	1	1	0	0	1	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-76867	MN908947.3	23403	A	G	1	1	0	0	1	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-76867	MN908947.3	241	C	T	1	1	0	0	0.999638858793788	TCG	NA	NA	NA	NA	NA	NA	0.000120380402070543
CAMB-76867	MN908947.3	24289	T	C	1	1	0	0	1	TTG	S	I909I	T2727C	ATT>ATC	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-76867	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-76867	MN908947.3	3037	C	T	1	1	1.7e-302	2.4e-126	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76876	MN908947.3	11075	T	-	0.035	0.044	1.7e-09	1.4e-11	0.039044289044289	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960731576116192
CAMB-76876	MN908947.3	11674	C	T	0.11	0.054	9.5e-16	4.3e-06	0.092896174863388	ACT	ORF1ab:nsp6	Y234Y	C702T	TAC>TAT	Synonymous	ORF1ab:nsp6	0.907103825136612
CAMB-76876	MN908947.3	11903	AG	TC	0.000245	0.01	0.0092;NA	9e-07;8.7e-07	0.00437720194610094	CAG	ORF1ab:nsp7	.	61-62-mnv	.	no-SNV	ORF1ab:nsp7	0.995343883140597
CAMB-76876	MN908947.3	12720	TG	-	0.019	0.026	5.9e-11;3.2e-10	9.1e-14;8e-13	0.0226109689620647	ATG	ORF1ab:nsp9	.	35-36-delfrshift	.	no-SNV	ORF1ab:nsp9	0.97623213764946
CAMB-76876	MN908947.3	14408	C	T	1	1	0	0	0.999636891793755	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000317719680464778
CAMB-76876	MN908947.3	16931	T	C	0.025	0.0078	5.7e-13	7.9e-06	0.0162183701932656	GTA	ORF1ab:helicase	V232A	T695C	GTA>GCA	Missense	ORF1ab:helicase	0.983741781231321
CAMB-76876	MN908947.3	18648	TGAGCGCACCTGT	-	0.00559230769230769	0.0270769230769231	8.8e-05;6e-05;7e-04;0.00012;0.00015;0.00014;0.00016;NA;NA;NA;NA;NA;NA	3.4e-08;9.1e-09;4.2e-06;5.5e-09;7e-09;7.1e-09;8.8e-09;1.4e-11;3.4e-14;4.3e-13;1.3e-09;1e-07;1.5e-06	0.0199453597707122	CTG	ORF1ab:3'-to-5'-exonuclease	.	609-621-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.987533762725951
CAMB-76876	MN908947.3	23403	A	G	1	1	0	0	0.999874367913565	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000109928075630516
CAMB-76876	MN908947.3	241	C	T	1	1	0	0	0.999607489107823	TCG	NA	NA	NA	NA	NA	NA	0.000274757624524081
CAMB-76876	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0165135135135135	0.0334864864864865	NA;NA;NA;NA;NA;0.001;0.002;0.0051;0.0049;0.0016;0.004;0.0036;0.0046;0.0044;0.0046;0.0059;0.0039;0.0055;0.0039;0.0043;0.0044;0.0061;0.0042;0.0048;0.0041;0.004;0.0056;0.0039;0.0032;0.004;0.0054;0.004;0.0029;0.0049;0.0031;0.0036;0.0032	6.1e-06;2.1e-07;3.6e-06;4.1e-06;9.8e-06;6.8e-07;2.7e-06;1.6e-05;1.6e-05;7.9e-06;9.7e-06;8.7e-06;1.6e-05;1.3e-05;1.3e-05;2.1e-05;9.8e-06;1.9e-05;1.2e-05;1.2e-05;9.9e-06;2.1e-05;1.3e-05;1.6e-05;1.2e-05;7.7e-06;1.8e-05;1.2e-05;5.9e-06;1.1e-05;1.8e-05;1.7e-05;8e-06;1.7e-05;5.2e-06;1.2e-05;8.2e-06	0.0250867845321708	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.985017218116278
CAMB-76876	MN908947.3	27053	TTA	-	0.0456666666666667	0.004	6.6e-11;4e-10;8.9e-08	NA;NA;0.0059	0.0192914766748509	CTT	M	.	531-533-delinframe	.	no-SNV	GU280_gp05	0.980424528301887
CAMB-76876	MN908947.3	27264	TT	-	0.021	0.0085	1.9e-10;3.9e-08	NA;1.1e-06	0.0149595212953185	CTT	ORF6	.	63-64-delfrshift	.	no-SNV	GU280_gp06	0.989016991475
CAMB-76876	MN908947.3	27265	TTTAAAGTTTCCATTTGGAATC	-	0.000954545454545455	0.017	3.9e-08;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	1.1e-06;6.5e-06;2.3e-05;1.4e-05;1.5e-05;1.5e-05;1.4e-05;9e-06;1.9e-05;2e-05;1.3e-05;1.1e-05;1.5e-05;1.2e-05;1.8e-05;2e-05;1.7e-05;2.8e-05;1.7e-05;1.4e-05;1.6e-05;1.8e-05	0.00832224362921326	TTT	ORF6	.	64-85-delfrshift	.	no-SNV	GU280_gp06	0.980711177323872
CAMB-76876	MN908947.3	28514	G	T	1	1	0	0	0.999730458221024	AGA	N	D81Y	G241T	GAT>TAT	Missense	GU280_gp10	0.000179694519317161
CAMB-76876	MN908947.3	29070	AAGCATACAATGTAACACAAGCTT	-	0.00316666666666667	0.018375	NA;NA;NA;NA;NA;NA;NA;NA;0.001;4e-04;0.00082;0.00083;7.8e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00014;0.00014;0.00013;0.00014;0.00015;0.00038;0.00023;0.00016;0.00022;6.8e-05;0.00022;0.00015;1.1e-05;9.5e-06;1.6e-07;2.5e-07;4.1e-07;1.4e-07;1e-07;1e-07;5.3e-07;9.9e-08;9.1e-08;5.6e-08	0.00687037885231957	AAA	N	.	797-820-delinframe	.	no-SNV	GU280_gp10	0.993211792086889
CAMB-76876	MN908947.3	3037	C	T	1	1	0	0	0.999684642068748	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76876	MN908947.3	522	T	-	0.034	0.045	0.00012	5.5e-06	0.0384248535222782	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.96150701730481
CAMB-76885	MN908947.3	10323	A	G	1	1	0	0	1	AAG	ORF1ab:3C-like-proteinase	K90R	A269G	AAG>AGG	Missense	ORF1ab:3C-like-proteinase	0
CAMB-76885	MN908947.3	11074	C	INS	0.11	0.075	2.7e-32	1.9e-19	0.0939582071471835	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.905587522713507
CAMB-76885	MN908947.3	11083	G	-	0.063	0.27	5.6e-27	3.4e-126	0.160119805831928	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.44269631975763e-05
CAMB-76885	MN908947.3	11083	G	T	0.94	0.73	0	4.2e-271	0.839742486315282	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.44269631975763e-05
CAMB-76885	MN908947.3	11482	TGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCA	-	0.0903684210526316	0.00128947368421053	1.4e-12;3.3e-17;1.5e-09;2.6e-09;6.2e-09;4.5e-07;3.4e-07;2.7e-07;1.3e-07;6.1e-08;4.3e-07;2.9e-08;4.3e-08;9.9e-08;5.5e-08;1.1e-08;2.1e-08;1.9e-08;2.3e-07;4.6e-08;7.6e-09;5e-09;1.4e-08;5.4e-09;2.8e-16;2.5e-16;3.4e-16;2.4e-16;2.4e-17;2.9e-17;5.3e-17;1.3e-17;3.8e-17;1.8e-17;5.3e-17;3.2e-17;7.9e-18;1.5e-17	NA;NA;NA;NA;1.2e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0443458980044346	CTG	ORF1ab:nsp6	.	510-547-delfrshift	.	no-SNV	ORF1ab:nsp6	0.97198275862069
CAMB-76885	MN908947.3	12758	G	C	0.024	0.02	4.2e-13	3e-11	0.0225973680712482	TGA	ORF1ab:nsp9	D25H	G73C	GAT>CAT	Missense	ORF1ab:nsp9	0.977203243386947
CAMB-76885	MN908947.3	13405	C	A	0.84	0.88	0	0	0.859751037344398	GCT	ORF1ab:nsp10	G127G	C381A	GGC>GGA	Synonymous	ORF1ab:nsp10	0.140248962655602
CAMB-76885	MN908947.3	14805	C	T	1	1	0	0	0.999859845830413	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	7.00770847932726e-05
CAMB-76885	MN908947.3	1721	G	C	0.021	0.02	8.9e-11	1.3e-09	0.0207030407591115	TGC	ORF1ab:nsp2	A306P	G916C	GCT>CCT	Missense	ORF1ab:nsp2	0.979296959240889
CAMB-76885	MN908947.3	1735	TG	-	0.0215	0.009	2.2e-11;3.8e-10	NA;1.1e-08	0.0181063314496598	CTG	ORF1ab:nsp2	.	930-931-delfrshift	.	no-SNV	ORF1ab:nsp2	0.983173667403586
CAMB-76885	MN908947.3	1736	G	-	0.02	0.018	3.8e-10	1.1e-08	0.0197826086956522	TGT	ORF1ab:nsp2	.	931-931-delfrshift	.	no-SNV	ORF1ab:nsp2	0.98
CAMB-76885	MN908947.3	18652	C	T	1	1	0	0	0.999961562115621	GCG	ORF1ab:3'-to-5'-exonuclease	R205C	C613T	CGC>TGC	Missense	ORF1ab:3'-to-5'-exonuclease	0
CAMB-76885	MN908947.3	21097	G	T	0.079	0.051	5.4e-35	6.1e-23	0.0674114021571649	AGA	ORF1ab:2'-O-ribose-methyltransferase	E147*	G439T	GAG>TAG	Nonsense	ORF1ab:2'-O-ribose-methyltransferase	0.932588597842835
CAMB-76885	MN908947.3	24350	G	-	0.044	0.12	3.2e-19	9.4e-42	0.0629716981132075	TGC	S	.	2788-2788-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.937028301886792
CAMB-76885	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-76885	MN908947.3	2513	G	T	0.043	0.057	7.7e-15	1.1e-17	0.0489051094890511	AGA	ORF1ab:nsp2	E570*	G1708T	GAA>TAA	Nonsense	ORF1ab:nsp2	0.951094890510949
CAMB-76885	MN908947.3	2558	C	T	1	1	0	0	0.999329758713137	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000670241286863271
CAMB-76885	MN908947.3	28832	TCATCACGTAGTCGCA	CTCATCACGTAGTCGC	0.018	0.0006875	2.8e-07;3.3e-07;2.2e-08;6.7e-08;1.8e-07;2.9e-08;2.5e-08;3.3e-08;4.6e-08;6e-08;5.6e-07;4.7e-08;1.9e-07;4.8e-08;2.6e-08;3.1e-08	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;2.7e-05;NA;NA	0.00907571053260091	CTC	N	.	559-574-mnv	.	no-SNV	GU280_gp10	0.99131862975129
CAMB-76885	MN908947.3	29543	G	T	0.031	0.0042	6.1e-11	0.0061	0.0165148063781321	AGA	NA	NA	NA	NA	NA	NA	0.983485193621868
CAMB-76885	MN908947.3	29581	TT	-	0.00875	0.013	0.0027;0.00018	0.00012;6.6e-06	0.0109953703703704	CTT	ORF10	.	24-25-delfrshift	.	no-SNV	GU280_gp11	0.989080459770115
CAMB-76885	MN908947.3	29781	G	T	0.0087	0.018	0.0013	6.5e-06	0.013170272812794	AGA	NA	NA	NA	NA	NA	NA	0.975540921919097
CAMB-76885	MN908947.3	3230	GG	TT	0.0345	0.017225	1.7e-16;2.8e-16	0.24;2.4e-16	0.0254651529485967	TGG	ORF1ab:nsp3	.	511-512-mnv	.	no-SNV	ORF1ab:nsp3	0.982984086970222
CAMB-76885	MN908947.3	3231	G	T	0.034	0.034	2.8e-16	2.4e-16	0.0340066277418337	GGT	ORF1ab:nsp3	G171V	G512T	GGT>GTT	Missense	ORF1ab:nsp3	0.96591447056967
CAMB-76885	MN908947.3	370	G	C	0.026	0.018	5.6e-14	1.6e-10	0.0221470601862577	TGG	ORF1ab:leader-protein	V35V	G105C	GTG>GTC	Synonymous	ORF1ab:leader-protein	0.977690775147107
CAMB-76885	MN908947.3	6596	A	G	0.052	0.0028	1e-17	0.009	0.0246331236897275	TAA	ORF1ab:nsp3	N1293D	A3877G	AAT>GAT	Missense	ORF1ab:nsp3	0.974842767295597
CAMB-76885	MN908947.3	984	G	-	0.014	0.028	1.5e-08	8.2e-15	0.020912978682045	TGG	ORF1ab:nsp2	.	179-179-delfrshift	.	no-SNV	ORF1ab:nsp2	0.978989826994104
CAMB-76885	MN908947.3	9848	A	G	0.14	0.11	4.7e-55	1.6e-41	0.123643704264446	TAG	ORF1ab:nsp4	S432G	A1294G	AGT>GGT	Missense	ORF1ab:nsp4	0.876356295735554
CAMB-76894	MN908947.3	11075	T	-	0.03	0.036	8e-08	2.1e-09	0.0323836905384213	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962401986408782
CAMB-76894	MN908947.3	1346	C	T	0.55	0.56	5.2e-294	2.5e-286	0.553076228556688	ACC	ORF1ab:nsp2	P181S	C541T	CCC>TCC	Missense	ORF1ab:nsp2	0.446923771443312
CAMB-76894	MN908947.3	14408	C	T	1	1	0	0	0.998795767249994	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00024340874734172
CAMB-76894	MN908947.3	23403	A	G	1	1	0	0	0.999464624833327	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000242434037738899
CAMB-76894	MN908947.3	241	C	T	1	1	0	0	0.998647407531101	TCG	NA	NA	NA	NA	NA	NA	0.000100192034733239
CAMB-76894	MN908947.3	25521	C	T	0.44	0.43	3.8e-240	1.5e-233	0.435296807132515	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.563575401966014
CAMB-76894	MN908947.3	25844	C	T	0.0083	0.0099	1.2e-05	2.5e-06	0.00900181810119285	ACT	ORF3a	T151I	C452T	ACT>ATT	Missense	GU280_gp03	0.990998181898807
CAMB-76894	MN908947.3	26529	G	T	0.02	0.024	1e-10	1.5e-12	0.0221600034726744	AGA	M	D3Y	G7T	GAT>TAT	Missense	GU280_gp05	0.97777488388245
CAMB-76894	MN908947.3	28514	G	T	1	1	0	0	0.999108778531465	AGA	N	D81Y	G241T	GAT>TAT	Missense	GU280_gp10	9.90246076149923e-05
CAMB-76894	MN908947.3	29179	G	T	0.11	0.12	1.6e-51	1.9e-54	0.116080215542971	CGC	N	P302P	G906T	CCG>CCT	Synonymous	GU280_gp10	0.882112837390898
CAMB-76894	MN908947.3	29316	A	C	0.59	0.61	0	0	0.597853627047527	GAT	N	D348A	A1043C	GAT>GCT	Missense	GU280_gp10	0.40156539982248
CAMB-76894	MN908947.3	3037	C	T	1	1	0	0	0.999405948996478	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-768A3	MN908947.3	11074	C	INS	0.03	0.03	2.2e-06	4.3e-06	0.029818794774547	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.9700800674252
CAMB-768A3	MN908947.3	11075	T	-	0.028	0.036	1.7e-07	1e-09	0.0311187363189966	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964784357806307
CAMB-768A3	MN908947.3	14408	C	T	1	1	0	0	0.998762057048538	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000395453998383797
CAMB-768A3	MN908947.3	14790	C	T	0.0082	0.01	1.9e-05	1.7e-06	0.00880137615444996	TCA	ORF1ab:RNA-dependent-RNA-polymerase	I441I	C1323T	ATC>ATT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.991148521134993
CAMB-768A3	MN908947.3	17167	C	T	0.0079	0.013	4.3e-05	3.7e-07	0.0101214574898785	TCA	ORF1ab:helicase	H311Y	C931T	CAT>TAT	Missense	ORF1ab:helicase	0.989760162890357
CAMB-768A3	MN908947.3	17277	A	C	0.007	0.0061	3.1e-05	7.1e-05	0.00655209598820623	AAG	ORF1ab:helicase	K347N	A1041C	AAA>AAC	Missense	ORF1ab:helicase	0.993393303211892
CAMB-768A3	MN908947.3	17550	C	T	0.015	0.015	5.1e-08	3.4e-08	0.014706919658602	TCG	ORF1ab:helicase	L438L	C1314T	CTC>CTT	Synonymous	ORF1ab:helicase	0.985010933201665
CAMB-768A3	MN908947.3	17690	C	T	0.035	0.035	6.9e-17	1.9e-17	0.0348518111964874	TCA	ORF1ab:helicase	S485L	C1454T	TCA>TTA	Missense	ORF1ab:helicase	0.965062431394072
CAMB-768A3	MN908947.3	18651	G	T	1	1	0	0	0.999023306585978	AGC	ORF1ab:3'-to-5'-exonuclease	E204D	G612T	GAG>GAT	Missense	ORF1ab:3'-to-5'-exonuclease	1.91508512553383e-05
CAMB-768A3	MN908947.3	203	C	T	0.017	0.018	9.2e-09	5.2e-09	0.0174167088038654	TCG	NA	NA	NA	NA	NA	NA	0.98256456355226
CAMB-768A3	MN908947.3	22452	C	T	0.015	0.032	0.0011	1.4e-05	0.0217391304347826	TCA	S	S297L	C890T	TCA>TTA	Missense	GU280_gp02, spike glycoprotein	0.978260869565217
CAMB-768A3	MN908947.3	23403	A	G	1	1	0	0	0.999342806653718	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.30214829202751e-05
CAMB-768A3	MN908947.3	23435	C	T	0.0058	0.0072	0.00016	2.9e-05	0.0061470656460218	TCA	S	H625Y	C1873T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.993548480630944
CAMB-768A3	MN908947.3	23672	T	C	0.009	0.0078	1.4e-05	5.2e-05	0.0087216939000683	TTC	S	S704P	T2110C	TCA>CCA	Missense	GU280_gp02, spike glycoprotein	0.991278306099932
CAMB-768A3	MN908947.3	241	C	T	1	1	0	0	0.999761773868426	TCG	NA	NA	NA	NA	NA	NA	0.000109950522264981
CAMB-768A3	MN908947.3	24213	C	T	0.016	0.019	1.2e-07	4.9e-08	0.0162931716319536	TCT	S	S884F	C2651T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.983706828368046
CAMB-768A3	MN908947.3	25521	C	T	0.02	0.02	4.5e-10	2.7e-10	0.0200890041979713	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.979622723096049
CAMB-768A3	MN908947.3	25528	C	A	0.0052	0.0086	0.00024	5.4e-06	0.00606614591989363	GCT	ORF3a	L46I	C136A	CTT>ATT	Missense	GU280_gp03	0.993829981718464
CAMB-768A3	MN908947.3	28253	C	T	0.041	0.035	1.2e-18	4.1e-16	0.0388032156151272	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.960586818480403
CAMB-768A3	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999384207285302	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	5.17946858652302e-05
CAMB-768A3	MN908947.3	3037	C	T	1	1	0	0	0.999421597547574	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.78402452426398e-05
CAMB-768A3	MN908947.3	4058	C	T	0.011	0.0091	1.2e-06	6.8e-06	0.0102319837699568	TCC	ORF1ab:nsp3	P447S	C1339T	CCA>TCA	Missense	ORF1ab:nsp3	0.989768016230043
CAMB-768A3	MN908947.3	6271	G	A	0.17	0.17	2.3e-79	4.9e-81	0.170565059099297	CGT	ORF1ab:nsp3	T1184T	G3552A	ACG>ACA	Synonymous	ORF1ab:nsp3	0.829110767542766
CAMB-768A3	MN908947.3	635	C	T	0.068	0.091	1.2e-30	1.8e-41	0.0727657772130453	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.927234222786955
CAMB-768A3	MN908947.3	683	C	T	0.012	0.016	5.3e-07	1.9e-08	0.0136447357729083	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.985732278772448
CAMB-768A3	MN908947.3	7688	C	T	1	1	0	0	0.999904030710173	ACT	ORF1ab:nsp3	L1657L	C4969T	CTA>TTA	Synonymous	ORF1ab:nsp3	9.59692898272553e-05
CAMB-768A3	MN908947.3	815	C	T	0.0046	0.01	0.0011	2.9e-06	0.0075496963960012	TCG	ORF1ab:nsp2	R4C	C10T	CGC>TGC	Missense	ORF1ab:nsp2	0.992392584212592
CAMB-768B2	MN908947.3	11075	T	-	0.043	0.041	2.8e-11	3.4e-11	0.0421680416163102	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953155378067364
CAMB-768B2	MN908947.3	14408	C	T	1	1	0	0	0.998918595554737	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000483180709585385
CAMB-768B2	MN908947.3	14785	G	T	0.0078	0.0082	8.6e-06	4.8e-06	0.00799186283057251	TGC	ORF1ab:RNA-dependent-RNA-polymerase	A440S	G1318T	GCT>TCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.991717523975589
CAMB-768B2	MN908947.3	15720	C	T	0.44	0.45	1.1e-239	2e-243	0.442885893761054	ACG	ORF1ab:RNA-dependent-RNA-polymerase	D751D	C2253T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.556992132707202
CAMB-768B2	MN908947.3	16474	A	G	0.013	0.011	3.3e-07	1.3e-06	0.0119040902679831	TAG	ORF1ab:helicase	S80G	A238G	AGT>GGT	Missense	ORF1ab:helicase	0.988095909732017
CAMB-768B2	MN908947.3	1820	G	A	1	1	0	0	0.995069173465768	AGG	ORF1ab:nsp2	G339S	G1015A	GGT>AGT	Missense	ORF1ab:nsp2	0
CAMB-768B2	MN908947.3	23403	A	G	1	1	0	0	0.999749310604161	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-768B2	MN908947.3	23842	T	C	0.039	0.038	1e-18	1.6e-18	0.0385876550982398	GTA	S	C760C	T2280C	TGT>TGC	Synonymous	GU280_gp02, spike glycoprotein	0.96141234490176
CAMB-768B2	MN908947.3	241	C	T	1	1	0	0	0.999148832684825	TCG	NA	NA	NA	NA	NA	NA	0.0001215953307393
CAMB-768B2	MN908947.3	28514	G	T	1	1	0	0	0.998887859128823	AGA	N	D81Y	G241T	GAT>TAT	Missense	GU280_gp10	0.000185356811862836
CAMB-768B2	MN908947.3	29031	A	T	0.012	0.016	1.6e-07	2e-09	0.0136608481572663	GAG	N	E253V	A758T	GAG>GTG	Missense	GU280_gp10	0.985820854080669
CAMB-768B2	MN908947.3	29700	A	G	0.15	0.15	2.4e-62	1.6e-61	0.147566909975669	TAG	NA	NA	NA	NA	NA	NA	0.852433090024331
CAMB-768B2	MN908947.3	3037	C	T	1	1	0	0	0.998979360399183	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000226808800181447
CAMB-768B2	MN908947.3	3653	C	T	0.053	0.059	6.8e-23	2.4e-25	0.0564669121749805	ACT	ORF1ab:nsp3	L312F	C934T	CTT>TTT	Missense	ORF1ab:nsp3	0.94353308782502
CAMB-768B2	MN908947.3	5144	C	T	0.022	0.017	4.2e-10	4e-08	0.0195719773184562	TCT	ORF1ab:nsp3	L809L	C2425T	CTA>TTA	Synonymous	ORF1ab:nsp3	0.980428022681544
CAMB-768B2	MN908947.3	683	C	T	0.14	0.14	2.4e-64	2.1e-63	0.137642229957916	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.859843092429989
CAMB-768B2	MN908947.3	977	A	C	0.0055	0.006	6.7e-05	2.8e-05	0.00571413695705937	AAT	ORF1ab:nsp2	I58L	A172C	ATT>CTT	Missense	ORF1ab:nsp2	0.994181732984498
CAMB-768C1	MN908947.3	10993	C	T	0.037	0.039	1.5e-17	2e-18	0.037952945217242	TCA	ORF1ab:nsp6	I7I	C21T	ATC>ATT	Synonymous	ORF1ab:nsp6	0.962012708226
CAMB-768C1	MN908947.3	11075	T	-	0.042	0.037	9.2e-11	4.3e-10	0.0403686702832157	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954678229947203
CAMB-768C1	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999467499081895	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000348879911861917
CAMB-768C1	MN908947.3	2069	A	G	1	1	0	0	0.999735986144553	TAC	ORF1ab:nsp2	T422A	A1264G	ACA>GCA	Missense	ORF1ab:nsp2	7.39238795251975e-05
CAMB-768C1	MN908947.3	21525	T	C	0.036	0.031	3.5e-15	5.9e-12	0.0347469220246238	TTA	ORF1ab:2'-O-ribose-methyltransferase	V289V	T867C	GTT>GTC	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.960601915184679
CAMB-768C1	MN908947.3	21691	C	T	0.013	0.015	3.7e-07	5.2e-08	0.0135062491600591	TCA	S	F43F	C129T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.986359360301035
CAMB-768C1	MN908947.3	21711	C	T	0.013	0.018	1.8e-07	1.2e-09	0.0149425287356322	TCA	S	S50L	C149T	TCA>TTA	Missense	GU280_gp02, spike glycoprotein	0.98498985801217
CAMB-768C1	MN908947.3	21752	T	A	0.044	0.038	9.5e-20	2.6e-17	0.0415942769545222	TTG	S	W64R	T190A	TGG>AGG	Missense	GU280_gp02, spike glycoprotein	0.938988247317322
CAMB-768C1	MN908947.3	21752	T	C	0.022	0.013	7e-11	2.7e-07	0.0180889115993868	TTG	S	W64R	T190C	TGG>CGG	Missense	GU280_gp02, spike glycoprotein	0.938988247317322
CAMB-768C1	MN908947.3	21846	C	T	0.011	0.0077	1.8e-06	5.6e-05	0.00966424230347713	ACT	S	T95I	C284T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.990136494968616
CAMB-768C1	MN908947.3	21986	G	T	0.98	0.98	0	0	0.982473913483943	GGG	S	G142C	G424T	GGT>TGT	Missense	GU280_gp02, spike glycoprotein	0.0143855739033533
CAMB-768C1	MN908947.3	22032	T	C	0.35	0.29	1.3e-124	2.8e-40	0.347145488029466	TTC	S	F157S	T470C	TTC>TCC	Missense	GU280_gp02, spike glycoprotein	0.652854511970534
CAMB-768C1	MN908947.3	22035	G	C	0.11	0.16	2.4e-35	5e-22	0.111217641418984	AGA	S	R158T	G473C	AGA>ACA	Missense	GU280_gp02, spike glycoprotein	0.884947267497603
CAMB-768C1	MN908947.3	22036	A	C	0.03	0.051	2.6e-12	1.2e-09	0.0324427480916031	GAG	S	R158S	A474C	AGA>AGC	Missense	GU280_gp02, spike glycoprotein	0.963740458015267
CAMB-768C1	MN908947.3	22206	A	G	0.092	0.065	8.2e-33	2.7e-14	0.0872727272727273	GAT	S	D215G	A644G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.912727272727273
CAMB-768C1	MN908947.3	23280	C	T	0.092	0.09	3.9e-42	1.6e-41	0.0915319400630915	ACT	S	T573I	C1718T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.907400105152471
CAMB-768C1	MN908947.3	23403	A	G	0.019	0.023	2.1e-07	2.7e-09	0.0197550560743278	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.979916475059828
CAMB-768C1	MN908947.3	23525	C	T	0.088	0.089	5.3e-39	1.1e-37	0.088262572135202	ACA	S	H655Y	C1963T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.911376751854905
CAMB-768C1	MN908947.3	26527	C	T	1	1	0	0	0.999309153713299	GCA	M	A2V	C5T	GCA>GTA	Missense	GU280_gp05	0.000439629455173497
CAMB-768C1	MN908947.3	27384	T	C	0.0083	0.0076	2.8e-05	5.2e-05	0.008186852877438	ATT	ORF6	D61D	T183C	GAT>GAC	Synonymous	GU280_gp06	0.991107977021774
CAMB-768C1	MN908947.3	29032	G	A	1	1	0	0	0.999752466494572	AGG	N	E253E	G759A	GAG>GAA	Synonymous	GU280_gp10	0.000106085788040595
CAMB-768C1	MN908947.3	5844	A	G	0.0099	0.011	3e-06	7.2e-07	0.0102148321194631	AAA	ORF1ab:nsp3	K1042R	A3125G	AAA>AGA	Missense	ORF1ab:nsp3	0.989647748614356
CAMB-768C1	MN908947.3	753	C	T	0.011	0.011	5.9e-07	4.5e-07	0.0111982881597718	ACT	ORF1ab:leader-protein	T163I	C488T	ACT>ATT	Missense	ORF1ab:leader-protein	0.98876604850214
CAMB-768C1	MN908947.3	8858	G	A	0.12	0.12	3.6e-56	2.3e-56	0.123279509026992	TGT	ORF1ab:nsp4	V102I	G304A	GTC>ATC	Missense	ORF1ab:nsp4	0.876660906870047
CAMB-768D0	MN908947.3	11075	T	-	0.035	0.041	2.2e-09	7.9e-11	0.0376768485680509	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957823284902566
CAMB-768D0	MN908947.3	13562	A	C	0.0068	0.0058	4.3e-05	1e-04	0.00636597589055939	AAA	ORF1ab:RNA-dependent-RNA-polymerase	K32T	A95C	AAA>ACA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993634024109441
CAMB-768D0	MN908947.3	14408	C	T	1	1	0	0	0.997538855736489	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00070800040457166
CAMB-768D0	MN908947.3	14786	C	T	0.85	0.85	0	0	0.851785850277968	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A440V	C1319T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.14807706953012
CAMB-768D0	MN908947.3	20268	A	G	0.15	0.15	4.4e-34	2e-27	0.147798742138365	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0.852201257861635
CAMB-768D0	MN908947.3	20578	G	T	0.86	0.85	0	0	0.853363103544516	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	0.146413619871616
CAMB-768D0	MN908947.3	23403	A	G	1	1	0	0	0.99957965531736	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	1.27377176557504e-05
CAMB-768D0	MN908947.3	241	C	T	1	1	0	0	0.998658828262959	TCG	NA	NA	NA	NA	NA	NA	0.000268234347408186
CAMB-768D0	MN908947.3	2416	C	T	0.83	0.84	0	0	0.834784575370349	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0.162840664932715
CAMB-768D0	MN908947.3	25563	G	T	0.84	0.83	0	0	0.835793481912868	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.164004927763467
CAMB-768D0	MN908947.3	29085	C	T	0.057	0.06	2.1e-26	9e-28	0.0586133237507736	ACA	N	T271I	C812T	ACA>ATA	Missense	GU280_gp10	0.940288674612206
CAMB-768D0	MN908947.3	29120	C	A	0.3	0.32	2.5e-150	1e-161	0.308246647449555	CCA	N	Q283K	C847A	CAA>AAA	Missense	GU280_gp10	0.691502694573255
CAMB-768D0	MN908947.3	2937	C	T	0.14	0.15	5.5e-63	7.5e-70	0.146579302370399	ACA	ORF1ab:nsp3	T73I	C218T	ACA>ATA	Missense	ORF1ab:nsp3	0.853227982270187
CAMB-768D0	MN908947.3	29614	C	T	0.053	0.051	2.9e-23	3.2e-22	0.0519747235387046	GCA	ORF10	C19C	C57T	TGC>TGT	Synonymous	GU280_gp11	0.948025276461295
CAMB-768D0	MN908947.3	3037	C	T	1	1	0	0	0.99914694922103	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000224487047097382
CAMB-768D0	MN908947.3	6354	C	T	0.34	0.34	4.3e-178	6.7e-174	0.34104597607173	TCA	ORF1ab:nsp3	S1212L	C3635T	TCA>TTA	Missense	ORF1ab:nsp3	0.658790505000954
CAMB-768EF	MN908947.3	10097	G	A	1	1	0	0	0.999762383081675	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000151210766206554
CAMB-768EF	MN908947.3	11075	T	-	0.039	0.035	1.2e-09	3.4e-09	0.0370606214977076	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958532857870606
CAMB-768EF	MN908947.3	13536	C	T	1	1	0	0	0.999728697067667	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000113042888471886
CAMB-768EF	MN908947.3	14408	C	T	1	1	0	0	0.999364055844771	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000266209181258874
CAMB-768EF	MN908947.3	186	C	T	0.083	0.09	5.7e-37	3e-40	0.0861968477573443	GCA	NA	NA	NA	NA	NA	NA	0.913679145843926
CAMB-768EF	MN908947.3	18905	G	A	0.3	0.32	5.4e-147	2.1e-159	0.303024520561015	CGT	ORF1ab:3'-to-5'-exonuclease	R289H	G866A	CGT>CAT	Missense	ORF1ab:3'-to-5'-exonuclease	0.696880068695735
CAMB-768EF	MN908947.3	23403	A	G	1	1	0	0	0.999320255202433	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000107328125931668
CAMB-768EF	MN908947.3	23731	C	T	1	1	0	0	0.999959497772377	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	4.05022276225192e-05
CAMB-768EF	MN908947.3	241	C	T	1	1	0	0	0.999362587644199	TCG	NA	NA	NA	NA	NA	NA	3.74948444588869e-05
CAMB-768EF	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999680296684677	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000105995830830654
CAMB-768EF	MN908947.3	3037	C	T	1	1	0	0	0.999369641956631	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000157589510842158
CAMB-768EF	MN908947.3	4002	C	T	1	1	0	0	0.999778858911986	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0.000221141088014153
CAMB-768FE	MN908947.3	11075	T	-	0.029	0.033	1.5e-07	6.6e-09	0.0305399274628664	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.963449486729293
CAMB-768FE	MN908947.3	14408	C	T	1	1	0	0	0.998605249552117	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000408806165758877
CAMB-768FE	MN908947.3	23403	A	G	1	1	0	0	0.999589703511943	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.81517120109412e-05
CAMB-768FE	MN908947.3	241	C	T	1	1	0	0	0.99947546611988	TCG	NA	NA	NA	NA	NA	NA	0.00012715972851398
CAMB-768FE	MN908947.3	25395	G	T	0.17	0.15	1.6e-76	4.2e-67	0.158341228773413	TGG	ORF3a	M1I	G3T	ATG>ATT	Missense	GU280_gp03	0.841585890241236
CAMB-768FE	MN908947.3	25521	C	T	1	1	0	0	0.99690518195138	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.000164458930119906
CAMB-768FE	MN908947.3	28254	A	G	0.0079	0.0058	2.4e-05	0.00012	0.00710479573712256	CAT	ORF8	I121V	A361G	ATC>GTC	Missense	GU280_gp09	0.991685551540393
CAMB-768FE	MN908947.3	28514	G	T	1	1	0	0	0.99901768172888	AGA	N	D81Y	G241T	GAT>TAT	Missense	GU280_gp10	5.45732372844357e-05
CAMB-768FE	MN908947.3	3037	C	T	1	1	0	0	0.999375130181212	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000208289939595918
CAMB-7690A	MN908947.3	11075	T	-	0.044	0.035	8.5e-11	3.9e-09	0.0402974999397285	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955085706019914
CAMB-7690A	MN908947.3	14554	C	T	0.01	0.012	5.5e-06	6.7e-07	0.0108272029149275	ACT	ORF1ab:RNA-dependent-RNA-polymerase	L363F	C1087T	CTT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.988942185734382
CAMB-7690A	MN908947.3	1547	A	T	0.012	0.011	6.6e-07	2.1e-06	0.0116574819838915	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.980288257736329
CAMB-7690A	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999485558903506	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000411528682079396
CAMB-7690A	MN908947.3	16375	C	T	0.0089	0.0098	9.8e-05	4.6e-05	0.00931137882055868	TCC	ORF1ab:helicase	P47S	C139T	CCG>TCG	Missense	ORF1ab:helicase	0.990636014519438
CAMB-7690A	MN908947.3	17441	C	T	0.044	0.042	1.1e-20	8.1e-20	0.0431639737849588	CCT	ORF1ab:helicase	P402L	C1205T	CCT>CTT	Missense	ORF1ab:helicase	0.95679709298553
CAMB-7690A	MN908947.3	19065	T	G	0.0079	0.004	1.5e-05	0.00049	0.00611564121571534	CTC	ORF1ab:3'-to-5'-exonuclease	P342P	T1026G	CCT>CCG	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.993686681492464
CAMB-7690A	MN908947.3	20480	C	T	0.049	0.024	3e-10	1e-05	0.0377777777777778	TCA	ORF1ab:endoRNAse	S287L	C860T	TCA>TTA	Missense	ORF1ab:endoRNAse	0.962222222222222
CAMB-7690A	MN908947.3	23868	G	T	0.011	0.013	8.8e-07	8.9e-08	0.0118567146182573	GGA	S	G769V	G2306T	GGA>GTA	Missense	GU280_gp02, spike glycoprotein	0.988109791837623
CAMB-7690A	MN908947.3	27804	C	T	0.039	0.065	3.6e-10	1.5e-11	0.0472589792060491	TCT	NA	NA	NA	NA	NA	NA	0.952741020793951
CAMB-7690A	MN908947.3	27900	TTTC	-	0.06625	0.06875	2.9e-28;3.4e-10;1.8e-08;1.1e-13	1.1e-28;7.2e-11;5.5e-09;6.8e-14	0.0668996505242137	ATT	ORF8	.	7-10-delfrshift	.	no-SNV	GU280_gp09	0.932595473127929
CAMB-7690A	MN908947.3	29771	A	G	1	1	0	0	0.999451052150046	AAT	NA	NA	NA	NA	NA	NA	0
CAMB-7690A	MN908947.3	4704	C	T	0.011	0.0093	7e-07	4.8e-06	0.0105017115131105	CCT	ORF1ab:nsp3	P662L	C1985T	CCT>CTT	Missense	ORF1ab:nsp3	0.98916595584407
CAMB-7690A	MN908947.3	5541	A	T	0.01	0.0054	1.8e-06	0.00015	0.00818112633181126	CAG	ORF1ab:nsp3	Q941L	A2822T	CAG>CTG	Missense	ORF1ab:nsp3	0.991533485540335
CAMB-7690A	MN908947.3	6573	C	T	0.016	0.019	1.6e-08	9.9e-10	0.017434391631492	TCT	ORF1ab:nsp3	S1285F	C3854T	TCT>TTT	Missense	ORF1ab:nsp3	0.982320915152627
CAMB-7690A	MN908947.3	6588	A	G	0.011	0.0048	9e-07	0.00039	0.00839558875844895	AAG	ORF1ab:nsp3	K1290R	A3869G	AAG>AGG	Missense	ORF1ab:nsp3	0.991248665955176
CAMB-7690A	MN908947.3	7086	C	T	0.044	0.036	1.1e-17	1.2e-14	0.0404380791912384	ACT	ORF1ab:nsp3	T1456I	C4367T	ACT>ATT	Missense	ORF1ab:nsp3	0.959281100814378
CAMB-7690A	MN908947.3	9893	C	T	0.0083	0.01	1.1e-05	1.2e-06	0.0092972972972973	TCT	ORF1ab:nsp4	L447F	C1339T	CTT>TTT	Missense	ORF1ab:nsp4	0.990378378378378
CAMB-76919	MN908947.3	10097	G	A	1	1	0	0	0.999664692075556	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000223538616295965
CAMB-76919	MN908947.3	11075	T	-	0.077	0.059	2.4e-19	5.6e-15	0.0674645349105864	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.932419943625526
CAMB-76919	MN908947.3	14408	C	-	0.0045	0.0085	0.00094	3.8e-05	0.00657708809701205	CCT	ORF1ab:RNA-dependent-RNA-polymerase	.	941-941-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.000256917503789533
CAMB-76919	MN908947.3	14408	C	T	1	0.99	0	0	0.993114610898441	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000256917503789533
CAMB-76919	MN908947.3	167	G	T	0.13	0.021	2.9e-58	1.7e-11	0.0719950378804661	AGT	NA	NA	NA	NA	NA	NA	0.927783438926056
CAMB-76919	MN908947.3	18573	T	G	0.027	0.045	7.6e-14	1.9e-21	0.0376433285403532	CTG	ORF1ab:3'-to-5'-exonuclease	S178S	T534G	TCT>TCG	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.962319802381742
CAMB-76919	MN908947.3	20032	C	T	1	1	5.8e-199	0	1	CCG	ORF1ab:endoRNAse	R138C	C412T	CGT>TGT	Missense	ORF1ab:endoRNAse	0
CAMB-76919	MN908947.3	21089	ACTCTAAAGAGGGTTT	-	0.01625	0.000955625	6.7e-09;1.2e-08;1e-08;1.2e-08;9.9e-09;2.7e-08;5.4e-09;2.9e-09;2.3e-08;2.5e-07;2e-08;8.2e-09;1.4e-08;1.3e-07;5.4e-08;8.9e-09	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;5.1e-08;NA;NA;0.5;NA;NA	0.0080540640622107	GAC	ORF1ab:2'-O-ribose-methyltransferase	.	431-446-delfrshift	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.991545951080503
CAMB-76919	MN908947.3	21561	CA	TT	0.0225	0.0215	1.5e-07;3.4e-09	1e-07;2.3e-08	0.0211210398050366	ACA	NA	NA	NA	NA	NA	NA	0.98046875
CAMB-76919	MN908947.3	23403	A	G	1	1	0	0	0.999851318310976	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000115641313685323
CAMB-76919	MN908947.3	23731	C	T	1	1	0	0	0.999809414903755	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000190585096245474
CAMB-76919	MN908947.3	241	C	T	1	1	0	0	0.999630359783144	TCG	NA	NA	NA	NA	NA	NA	0.000123213405618531
CAMB-76919	MN908947.3	24145	G	T	0.0077	0.0061	1.7e-05	9.3e-05	0.00686825439300687	TGC	S	L861F	G2583T	TTG>TTT	Missense	GU280_gp02, spike glycoprotein	0.992462759789492
CAMB-76919	MN908947.3	28580	G	T	1	1	0	0	0.999846098599497	AGA	N	D103Y	G307T	GAT>TAT	Missense	GU280_gp10	0.000153901400502745
CAMB-76919	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999791122715405	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000116225011622501
CAMB-76919	MN908947.3	3037	C	T	1	1	0	0	0.99971169093268	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76919	MN908947.3	522	TTG	-	0.0583333333333333	0.0243333333333333	4.2e-12;9.7e-07;1.4e-08	0.00037;0.00031;0.0018	0.0382018771612053	GTT	ORF1ab:leader-protein	.	257-259-delinframe	.	no-SNV	ORF1ab:leader-protein	0.936186317321689
CAMB-76928	MN908947.3	11074	C	INS	0.019	0.027	0.0021	2.2e-05	0.0221383165440038	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.976991489801035
CAMB-76928	MN908947.3	11075	T	-	0.048	0.036	8.6e-12	1.9e-09	0.0431212801867997	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952132587149909
CAMB-76928	MN908947.3	1108	C	T	0.045	0.035	4.6e-21	4.2e-17	0.0421700932886514	TCA	ORF1ab:nsp2	I101I	C303T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.957793678108867
CAMB-76928	MN908947.3	11430	A	G	0.0069	0.0017	3.1e-05	0.0051	0.00421974522292994	TAT	ORF1ab:nsp6	Y153C	A458G	TAT>TGT	Missense	ORF1ab:nsp6	0.99578025477707
CAMB-76928	MN908947.3	14408	C	T	1	1	0	0	0.998285444010879	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00110854913089748
CAMB-76928	MN908947.3	21714	C	T	1	1	0	0	0.998798704690275	ACT	S	T51I	C152T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-76928	MN908947.3	21724	G	T	1	1	0	0	0.998747865680137	TGT	S	L54F	G162T	TTG>TTT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-76928	MN908947.3	23403	A	G	1	1	0	0	0.998886479517084	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.68850729648948e-05
CAMB-76928	MN908947.3	23987	C	T	0.018	0.016	1.1e-09	5e-09	0.0168613028797557	TCC	S	P809S	C2425T	CCA>TCA	Missense	GU280_gp02, spike glycoprotein	0.983074176828613
CAMB-76928	MN908947.3	241	C	T	1	1	0	0	0.997193447976731	TCG	NA	NA	NA	NA	NA	NA	0.000119065843411407
CAMB-76928	MN908947.3	24872	G	T	1	1	0	0	0.99931729776931	TGT	S	V1104L	G3310T	GTA>TTA	Missense	GU280_gp02, spike glycoprotein	1.58767960625546e-05
CAMB-76928	MN908947.3	28770	C	T	0.0096	0.012	3.7e-06	3.8e-07	0.0106200420916302	ACA	N	T166I	C497T	ACA>ATA	Missense	GU280_gp10	0.988505747126437
CAMB-76928	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998653675819309	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000115718418514947
CAMB-76928	MN908947.3	3037	C	T	1	1	0	0	0.999288022345145	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.47675119119338e-05
CAMB-76928	MN908947.3	5861	G	A	0.012	0.012	3.7e-07	2.1e-07	0.0119380942124858	TGT	ORF1ab:nsp3	V1048I	G3142A	GTT>ATT	Missense	ORF1ab:nsp3	0.987692686378881
CAMB-76928	MN908947.3	6855	C	T	0.033	0.011	3.6e-10	2.6e-05	0.0197512801755669	ACT	ORF1ab:nsp3	T1379I	C4136T	ACT>ATT	Missense	ORF1ab:nsp3	0.980248719824433
CAMB-76928	MN908947.3	7765	C	T	0.011	0.013	1.3e-06	2.8e-06	0.0116559907592145	CCA	ORF1ab:nsp3	S1682S	C5046T	TCC>TCT	Synonymous	ORF1ab:nsp3	0.988344009240785
CAMB-76937	MN908947.3	11075	T	-	0.04	0.037	4.4e-10	6e-10	0.0386937389021848	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95806376901104
CAMB-76937	MN908947.3	1108	C	T	0.043	0.042	2.8e-20	4.5e-20	0.0426676991578744	TCA	ORF1ab:nsp2	I101I	C303T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.957119349530539
CAMB-76937	MN908947.3	11430	A	G	0.0055	0.0072	0.00013	2.4e-05	0.00625363583478767	TAT	ORF1ab:nsp6	Y153C	A458G	TAT>TGT	Missense	ORF1ab:nsp6	0.993673647469459
CAMB-76937	MN908947.3	14408	C	T	1	1	0	0	0.998960742410492	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000234198893410229
CAMB-76937	MN908947.3	21714	C	T	1	1	0	0	0.999545247839927	ACT	S	T51I	C152T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.00045475216007276
CAMB-76937	MN908947.3	21724	G	T	1	1	0	0	0.999497436928334	TGT	S	L54F	G162T	TTG>TTT	Missense	GU280_gp02, spike glycoprotein	0.000100512614333099
CAMB-76937	MN908947.3	23403	A	G	1	1	0	0	0.998492026873432	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.37605923858611e-05
CAMB-76937	MN908947.3	23987	C	T	0.0098	0.012	2.4e-06	3.6e-07	0.0105587438821396	TCC	S	P809S	C2425T	CCA>TCA	Missense	GU280_gp02, spike glycoprotein	0.989341879704852
CAMB-76937	MN908947.3	241	C	T	1	1	0	0	0.998859112535198	TCG	NA	NA	NA	NA	NA	NA	0.000291290416545296
CAMB-76937	MN908947.3	24872	G	T	1	1	0	0	0.99937306786	TGT	S	V1104L	G3310T	GTA>TTA	Missense	GU280_gp02, spike glycoprotein	0
CAMB-76937	MN908947.3	24899	C	A	0.011	0.01	1e-06	8.4e-07	0.0105213673300351	ACA	S	Q1113K	C3337A	CAA>AAA	Missense	GU280_gp02, spike glycoprotein	0.989165230238857
CAMB-76937	MN908947.3	28770	C	T	0.0075	0.0076	3e-05	2.2e-05	0.00753039375793867	ACA	N	T166I	C497T	ACA>ATA	Missense	GU280_gp10	0.992046210609085
CAMB-76937	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999116607773852	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000114613180515759
CAMB-76937	MN908947.3	3037	C	T	1	1	0	0	0.998850281042412	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76937	MN908947.3	5861	G	A	0.009	0.015	5.1e-06	1e-08	0.0112137853924825	TGT	ORF1ab:nsp3	V1048I	G3142A	GTT>ATT	Missense	ORF1ab:nsp3	0.988260054589102
CAMB-76937	MN908947.3	895	A	G	0.0077	0.0054	1.3e-05	9.9e-05	0.00680596803846698	AAG	ORF1ab:nsp2	K30K	A90G	AAA>AAG	Synonymous	ORF1ab:nsp2	0.992981897892802
CAMB-76955	MN908947.3	11075	T	-	0.048	0.053	4.9e-12	2.6e-13	0.0501495390497333	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.936037369346036
CAMB-76955	MN908947.3	11962	C	T	0.034	0.035	3.3e-16	6.8e-17	0.0344805076115623	TCT	ORF1ab:nsp7	L40L	C120T	CTC>CTT	Synonymous	ORF1ab:nsp7	0.965519492388438
CAMB-76955	MN908947.3	12049	C	T	0.008	0.0054	1.5e-05	2e-04	0.00682427830824612	ACA	ORF1ab:nsp7	N69N	C207T	AAC>AAT	Synonymous	ORF1ab:nsp7	0.9930367343535
CAMB-76955	MN908947.3	13862	C	T	1	1	0	0	0.999920108652233	ACA	ORF1ab:RNA-dependent-RNA-polymerase	T132I	C395T	ACA>ATA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	2.66304492556789e-05
CAMB-76955	MN908947.3	14408	C	T	1	1	0	0	0.999620026142201	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00027358117761498
CAMB-76955	MN908947.3	14917	G	T	0.0082	0.0053	1.3e-05	0.00022	0.00637685667625787	AGT	ORF1ab:RNA-dependent-RNA-polymerase	V484F	G1450T	GTC>TTC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993623143323742
CAMB-76955	MN908947.3	16045	C	T	0.014	0.015	5.1e-08	1.7e-08	0.0142960774252906	ACT	ORF1ab:RNA-dependent-RNA-polymerase	L860F	C2578T	CTT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.985668536244449
CAMB-76955	MN908947.3	16117	G	T	0.0085	0.0057	6.6e-06	0.00012	0.00721014862429004	TGA	ORF1ab:RNA-dependent-RNA-polymerase	D884Y	G2650T	GAT>TAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.9927728463082
CAMB-76955	MN908947.3	17104	C	T	0.06	0.069	3.4e-28	5.5e-32	0.064278755138736	TCA	ORF1ab:helicase	H290Y	C868T	CAT>TAT	Missense	ORF1ab:helicase	0.935681639959761
CAMB-76955	MN908947.3	21786	G	T	0.01	0.0076	5.8e-06	7.5e-05	0.00890405876678786	GGT	S	G75V	G224T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.990947540253766
CAMB-76955	MN908947.3	23403	A	G	1	1	0	0	0.999871280293013	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.36143323542834e-05
CAMB-76955	MN908947.3	241	C	T	1	0.99	0	0	0.99549887471868	TCG	NA	NA	NA	NA	NA	NA	2.58685360995421e-05
CAMB-76955	MN908947.3	24672	C	INS	0.0074	0.0073	2.3e-05	2.4e-05	0.00738409393535892	TCA	S	.	3109-3110-insfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.988015978695073
CAMB-76955	MN908947.3	25347	A	T	0.0072	0.0053	2.1e-05	9.2e-05	0.0063817550379366	GAG	S	E1262V	A3785T	GAG>GTG	Missense	GU280_gp02, spike glycoprotein	0.993529763089787
CAMB-76955	MN908947.3	28687	C	T	1	1	0	0	0.999774397318551	CCT	N	A138A	C414T	GCC>GCT	Synonymous	GU280_gp10	0.000161144772463581
CAMB-76955	MN908947.3	28836	C	T	1	1	0	0	0.999365079365079	TCA	N	S188L	C563T	TCA>TTA	Missense	GU280_gp10	0.000634920634920635
CAMB-76955	MN908947.3	3037	C	T	1	1	0	0	0.99900922185809	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76955	MN908947.3	448	G	T	0.0084	0.0058	8.4e-06	0.00012	0.00730104648332928	TGC	ORF1ab:leader-protein	L61F	G183T	TTG>TTT	Missense	ORF1ab:leader-protein	0.992607690435629
CAMB-76964	MN908947.3	13914	T	G	0.0032	0.0081	0.00071	8.5e-06	0.00522489777373921	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994547932757837
CAMB-76964	MN908947.3	14408	C	T	1	1	0	0	0.999733735688293	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	8.87547705689181e-05
CAMB-76964	MN908947.3	14786	C	T	1	1	0	0	0.999858996051889	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A440V	C1319T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000141003948110547
CAMB-76964	MN908947.3	20578	G	T	1	1	0	0	1	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	0
CAMB-76964	MN908947.3	23403	A	G	1	1	0	0	0.999969984391884	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.00156081162204e-05
CAMB-76964	MN908947.3	241	C	T	1	1	0	0	0.999841709537	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-76964	MN908947.3	2416	C	T	1	1	3.4e-281	4.2e-174	0.997448979591837	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0.00255102040816327
CAMB-76964	MN908947.3	25563	G	T	1	1	0	0	0.999792681662693	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000207318337306935
CAMB-76964	MN908947.3	28706	C	T	0.083	0.16	9.7e-36	1.1e-64	0.109340007904097	TCA	N	H145Y	C433T	CAC>TAC	Missense	GU280_gp10	0.890659992095903
CAMB-76964	MN908947.3	29302	T	C	0.12	0.1	4.5e-47	3.5e-39	0.110203070827142	ATC	N	D343D	T1029C	GAT>GAC	Synonymous	GU280_gp10	0.889796929172858
CAMB-76964	MN908947.3	3037	C	T	1	1	0	2.4e-212	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76964	MN908947.3	510	GTCATGTTA	-	0.168888888888889	0.563333333333333	0.00036;0.0016;0.0016;0.00031;4.2e-09;0.00057;4e-05;0.00012;0.00013	1.8e-11;7.1e-08;5.7e-08;3.6e-10;2.8e-23;1.6e-10;3.8e-14;7.5e-13;3.6e-12	0.206896551724138	GGT	ORF1ab:leader-protein	.	245-253-delinframe	.	no-SNV	ORF1ab:leader-protein	0.830750407830343
CAMB-76973	MN908947.3	11075	T	-	0.0065	0.029	0.0038	2.1e-08	0.0181848445757563	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.981648703757646
CAMB-76973	MN908947.3	13426	C	T	0.27	0.078	7.1e-79	4.9e-22	0.180385288966725	GCG	ORF1ab:nsp10	R134R	C402T	CGC>CGT	Synonymous	ORF1ab:nsp10	0.819614711033275
CAMB-76973	MN908947.3	14408	C	T	1	1	0	0	0.999439890014767	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00035643362696675
CAMB-76973	MN908947.3	23403	A	G	1	1	0	0	0.999852526018624	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000147473981376143
CAMB-76973	MN908947.3	241	C	T	1	1	0	0	0.999933840555739	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-76973	MN908947.3	24816	G	A	0.78	0.92	0	0	0.836302398246967	GGA	S	G1085E	G3254A	GGA>GAA	Missense	GU280_gp02, spike glycoprotein	0.163697601753033
CAMB-76973	MN908947.3	25831	C	T	0.04	0.25	3.6e-13	1.7e-54	0.101408450704225	TCT	ORF3a	L147F	C439T	CTT>TTT	Missense	GU280_gp03	0.897652582159624
CAMB-76973	MN908947.3	26828	G	-	0.07	0.015	1.1e-11	0.0035	0.0447395833333333	TGT	M	.	306-306-delfrshift	.	no-SNV	GU280_gp05	0.955260416666667
CAMB-76973	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999744702578504	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-76973	MN908947.3	3037	C	T	1	1	0	0	0.999637089457449	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76973	MN908947.3	8810	A	-	0.052	0.035	3.4e-15	1.2e-10	0.0436432637571157	CAA	ORF1ab:nsp4	.	256-256-delfrshift	.	no-SNV	ORF1ab:nsp4	0.956356736242884
CAMB-76973	MN908947.3	8810	AA	-	0.026	0.0365	3.4e-15;NA	1.2e-10;5.6e-12	0.0322255790533736	CAA	ORF1ab:nsp4	.	256-257-delfrshift	.	no-SNV	ORF1ab:nsp4	0.956356736242884
CAMB-76982	MN908947.3	11075	T	-	0.043	0.042	8.9e-11	2.9e-11	0.0427599139951824	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952665017702119
CAMB-76982	MN908947.3	14408	C	T	1	1	0	0	0.996086139716115	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000574032841636515
CAMB-76982	MN908947.3	22993	C	T	0.39	0.37	1.7e-200	3.1e-190	0.378085235840322	GCA	S	S477S	C1431T	AGC>AGT	Synonymous	GU280_gp02, spike glycoprotein	0.621676675220232
CAMB-76982	MN908947.3	23403	A	G	1	1	0	0	0.998488018693587	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.10901537944622e-05
CAMB-76982	MN908947.3	241	C	T	1	1	0	0	0.997762271904307	TCG	NA	NA	NA	NA	NA	NA	0.000284801757633704
CAMB-76982	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0302972972972973	0.0316216216216216	0.0018;0.00015;0.0011;0.00094;0.0016;6.9e-05;0.00019;4.4e-05;4.2e-05;7.4e-06;2.4e-05;1.9e-05;3.6e-05;2.5e-05;2.7e-05;4.5e-05;2.2e-05;3.8e-05;2.2e-05;2.8e-05;2.7e-05;4.3e-05;2.4e-05;3.2e-05;2.8e-05;2.1e-05;4e-05;2.4e-05;2.8e-05;2.4e-05;4.2e-05;2.9e-05;1.7e-05;3.8e-05;1.3e-05;2.4e-05;2e-05	0.00082;0.00014;4e-04;0.00045;0.00077;3.2e-05;8e-05;1.9e-05;2e-05;1e-05;1e-05;9e-06;1.5e-05;1.2e-05;1e-05;1.7e-05;8.2e-06;1.8e-05;1.2e-05;1e-05;8.3e-06;1.5e-05;9.3e-06;1.5e-05;1.2e-05;6.4e-06;1.7e-05;1.2e-05;3.3e-06;1.1e-05;1.7e-05;1.5e-05;6e-06;1.6e-05;5.8e-06;1.2e-05;6.9e-06	0.0318246110325318	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.979586059386009
CAMB-76982	MN908947.3	27923	C	T	1	1	0	0	0.999503031507802	TCA	ORF8	I10I	C30T	ATC>ATT	Synonymous	GU280_gp09	0.000397574793758076
CAMB-76982	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999243513125047	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.17815659730927e-05
CAMB-76982	MN908947.3	3037	C	T	1	1	0	0	0.999388728147031	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000203757284322915
CAMB-76982	MN908947.3	522	TT	-	0.0395	0.04	7e-06;0.00013	4.1e-06;5.2e-05	0.039409490079867	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.953227626783104
CAMB-76991	MN908947.3	11075	T	-	0.033	0.034	1.3e-08	4.8e-09	0.0332277061971242	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961346447041942
CAMB-76991	MN908947.3	14408	C	T	1	1	0	0	0.999412447714841	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000307765482702181
CAMB-76991	MN908947.3	17396	T	C	0.022	0.021	2.5e-11	5.3e-11	0.0214698833220913	GTC	ORF1ab:helicase	V387A	T1160C	GTC>GCC	Missense	ORF1ab:helicase	0.978530116677909
CAMB-76991	MN908947.3	18006	T	C	0.015	0.013	8.7e-08	4.6e-07	0.0140600235185848	TTG	ORF1ab:helicase	L590L	T1770C	CTT>CTC	Synonymous	ORF1ab:helicase	0.985858172708216
CAMB-76991	MN908947.3	18859	G	T	1	1	0	0	0.999418867437205	TGC	ORF1ab:3'-to-5'-exonuclease	A274S	G820T	GCA>TCA	Missense	ORF1ab:3'-to-5'-exonuclease	2.15234282516519e-05
CAMB-76991	MN908947.3	19002	A	G	0.0055	0.0062	0.00011	4e-05	0.00577634754625905	TAT	ORF1ab:3'-to-5'-exonuclease	L321L	A963G	TTA>TTG	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.994111021721641
CAMB-76991	MN908947.3	21624	G	T	1	1	0	0	0.99965433805738	AGA	S	R21I	G62T	AGA>ATA	Missense	GU280_gp02, spike glycoprotein	0
CAMB-76991	MN908947.3	2197	C	T	0.042	0.046	6.9e-20	1.2e-21	0.0436745198970501	ACG	ORF1ab:nsp2	D464D	C1392T	GAC>GAT	Synonymous	ORF1ab:nsp2	0.956246287863789
CAMB-76991	MN908947.3	23403	A	G	1	1	0	0	0.999093249748125	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.83611328780925e-05
CAMB-76991	MN908947.3	241	C	T	1	1	0	0	0.998073579852464	TCG	NA	NA	NA	NA	NA	NA	0.000352393929427242
CAMB-76991	MN908947.3	27002	C	T	0.017	0.02	2.1e-09	9.9e-11	0.0185065754423352	ACA	M	D160D	C480T	GAC>GAT	Synonymous	GU280_gp05	0.981241062165269
CAMB-76991	MN908947.3	28338	A	T	0.024	0.025	2.7e-12	6.3e-13	0.0242926155969634	GAT	N	D22V	A65T	GAT>GTT	Missense	GU280_gp10	0.975462004447512
CAMB-76991	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999193027759845	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00013641944431813
CAMB-76991	MN908947.3	28909	C	T	0.019	0.02	5.1e-10	2.2e-10	0.0197233308792188	GCA	N	G212G	C636T	GGC>GGT	Synonymous	GU280_gp10	0.979036695470221
CAMB-76991	MN908947.3	29813	A	G	0.0093	0.0068	4.7e-06	4.5e-05	0.00798384876571533	AAA	NA	NA	NA	NA	NA	NA	0.992016151234285
CAMB-76991	MN908947.3	3037	C	T	1	1	0	0	0.999679852020489	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.11439954467843e-05
CAMB-76991	MN908947.3	352	T	C	0.025	0.024	1.1e-12	1.8e-12	0.0242830869831755	GTG	ORF1ab:leader-protein	R29R	T87C	CGT>CGC	Synonymous	ORF1ab:leader-protein	0.975691369797698
CAMB-76991	MN908947.3	4719	C	A	0.081	0.084	3.4e-37	1.6e-38	0.0822038133603913	GCG	ORF1ab:nsp3	A667E	C2000A	GCG>GAG	Missense	ORF1ab:nsp3	0.917538731807787
CAMB-76991	MN908947.3	614	G	A	0.0084	0.0088	8.9e-06	4.4e-06	0.00856124950894732	GGC	ORF1ab:leader-protein	A117T	G349A	GCT>ACT	Missense	ORF1ab:leader-protein	0.990720797605018
CAMB-76991	MN908947.3	9085	A	G	0.05	0.037	3.7e-23	6e-18	0.0448389405869721	AAG	ORF1ab:nsp4	E177E	A531G	GAA>GAG	Synonymous	ORF1ab:nsp4	0.95478883321403
CAMB-76991	MN908947.3	9166	C	T	0.016	0.02	9.9e-09	1.1e-10	0.0172965079684786	CCT	ORF1ab:nsp4	T204T	C612T	ACC>ACT	Synonymous	ORF1ab:nsp4	0.982502077091568
CAMB-769A0	MN908947.3	11075	T	-	0.051	0.045	1.5e-12	1e-11	0.0487635410415943	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.947383381233617
CAMB-769A0	MN908947.3	14408	C	T	1	1	0	0	0.998495640983814	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00081561633407645
CAMB-769A0	MN908947.3	20290	C	T	0.41	0.33	1.3e-47	1.9e-36	0.369230769230769	ACG	ORF1ab:endoRNAse	R224W	C670T	CGG>TGG	Missense	ORF1ab:endoRNAse	0.630769230769231
CAMB-769A0	MN908947.3	23403	A	G	1	1	0	0	0.99915674918857	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.36415706739642e-05
CAMB-769A0	MN908947.3	24071	T	C	1	1	0	0	0.997976286225774	ATA	S	Y837H	T2509C	TAT>CAT	Missense	GU280_gp02, spike glycoprotein	0.00150481280647588
CAMB-769A0	MN908947.3	241	C	T	1	1	0	0	0.997647411082833	TCG	NA	NA	NA	NA	NA	NA	0.000299420407639498
CAMB-769A0	MN908947.3	26593	T	C	0.015	0.0081	2.1e-08	7.3e-06	0.0124401387130511	ATA	M	I24T	T71C	ATA>ACA	Missense	GU280_gp05	0.978404065980441
CAMB-769A0	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.02771875	0.02784375	0.00018;0.00039;0.00024;0.00024;5.1e-05;8.5e-05;9.2e-05;0.00019;0.00015;0.00016;0.00024;0.00014;0.00022;0.00014;0.00016;0.00015;0.00025;0.00016;0.00018;0.00016;0.00012;0.00021;0.00013;9.2e-05;0.00015;0.00021;2e-04;1e-04;0.00014;4.8e-05;7.7e-05;6e-05	0.00013;0.00037;0.00013;0.00014;8.5e-05;8.9e-05;8.4e-05;0.00013;0.00011;0.00011;0.00017;8.8e-05;0.00015;0.00011;0.00011;7.6e-05;0.00017;1e-04;0.00013;0.00011;7.1e-05;0.00015;0.00011;3.8e-05;1e-04;0.00015;0.00014;6.9e-05;0.00014;5.8e-05;0.00011;6.4e-05	0.0273764031526152	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.972367220295674
CAMB-769A0	MN908947.3	28881	GGG	AAC	1	0.996666666666667	0;0;0	0;0;0	0.997491800115763	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000978952520802741
CAMB-769A0	MN908947.3	3037	C	T	1	1	0	0	0.997778892312101	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000143297270187003
CAMB-769A0	MN908947.3	522	TT	-	0.0275	0.0385	0.00045;0.0018	6.1e-06;6.4e-05	0.0295561313699467	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.966042078294288
CAMB-769BF	MN908947.3	10232	C	T	1	1	0	0	0.999669067242385	TCG	ORF1ab:3C-like-proteinase	R60C	C178T	CGT>TGT	Missense	ORF1ab:3C-like-proteinase	9.45522164615409e-05
CAMB-769BF	MN908947.3	11075	T	-	0.041	0.039	1.8e-10	1.1e-10	0.0403351034257999	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954603837969442
CAMB-769BF	MN908947.3	14408	C	T	1	1	0	0	0.99833147942158	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000429048148736692
CAMB-769BF	MN908947.3	21614	C	T	0.0047	0.0086	0.0011	3.7e-05	0.0058987558987559	TCT	S	L18F	C52T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.994101244101244
CAMB-769BF	MN908947.3	22713	C	T	0.026	0.028	7.3e-13	5.3e-14	0.0263123445477157	CCT	S	P384L	C1151T	CCT>CTT	Missense	GU280_gp02, spike glycoprotein	0.973600383994415
CAMB-769BF	MN908947.3	23403	A	G	1	1	0	0	0.999311116851804	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.92059391568562e-05
CAMB-769BF	MN908947.3	241	C	T	1	1	0	0	0.998697889320592	TCG	NA	NA	NA	NA	NA	NA	0.000294024992124331
CAMB-769BF	MN908947.3	3037	C	T	1	1	0	0	0.999140129277116	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.93014291644429e-05
CAMB-769CE	MN908947.3	11074	C	INS	0.11	0.11	8.6e-46	2.4e-37	0.111545025890248	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.88227892042003
CAMB-769CE	MN908947.3	11083	G	-	0.16	0.13	6.4e-69	2.2e-56	0.145452574819471	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	6.77405806722575e-05
CAMB-769CE	MN908947.3	11083	G	T	0.84	0.87	0	0	0.854330655322377	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	6.77405806722575e-05
CAMB-769CE	MN908947.3	14805	C	T	1	1	0	0	0.99833088023307	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000652474090709072
CAMB-769CE	MN908947.3	15894	G	T	1	1	0	0	0.999341540794541	TGC	ORF1ab:RNA-dependent-RNA-polymerase	M809I	G2427T	ATG>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	2.99299638845102e-05
CAMB-769CE	MN908947.3	17678	C	T	0.016	0.019	1e-08	9e-10	0.017505527376772	ACG	ORF1ab:helicase	T481M	C1442T	ACG>ATG	Missense	ORF1ab:helicase	0.982338405514371
CAMB-769CE	MN908947.3	2480	A	G	1	1	0	0	0.999921777221527	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	7.82227784730914e-05
CAMB-769CE	MN908947.3	25036	T	C	0.037	0.034	1.1e-17	7.2e-17	0.0357297203854963	ATC	S	N1158N	T3474C	AAT>AAC	Synonymous	GU280_gp02, spike glycoprotein	0.964248671074809
CAMB-769CE	MN908947.3	2558	C	T	1	1	0	0	0.999466061536408	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000100113461923513
CAMB-769CE	MN908947.3	26144	G	T	1	1	0	0	0.999934162881032	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-769CE	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0288421052631579	0.034	0.0011;8.3e-05;0.00054;0.00048;0.00087;7.8e-05;0.00021;9.3e-05;9.3e-05;2e-05;4.9e-05;3.8e-05;6.7e-05;5.3e-05;5.5e-05;8.3e-05;4.4e-05;7.6e-05;4.5e-05;5.1e-05;5.2e-05;9.1e-05;5.2e-05;6.5e-05;5.1e-05;4.4e-05;7.3e-05;4.2e-05;4.8e-05;4.8e-05;7.3e-05;6e-05;4.6e-05;7.8e-05;3e-05;5.9e-05;4.4e-05;0.0041	0.00019;1.8e-05;9.2e-05;8.9e-05;0.00017;3.1e-06;1.7e-05;7.3e-06;7.5e-06;4.1e-06;4e-06;3.4e-06;7.5e-06;5.2e-06;4.9e-06;8.3e-06;4.3e-06;8.7e-06;5.6e-06;5.3e-06;5.3e-06;9.3e-06;5.3e-06;7.5e-06;5.4e-06;3.4e-06;7.1e-06;5.5e-06;4.3e-06;4.6e-06;8.4e-06;7.3e-06;2.9e-06;7.2e-06;2.2e-06;5.4e-06;2.9e-06;0.00088	0.0321281678693693	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.97714777688949
CAMB-769CE	MN908947.3	29269	C	T	1	1	0	0	0.999826695781775	CCT	N	T332T	C996T	ACC>ACT	Synonymous	GU280_gp10	3.46608436449343e-05
CAMB-769CE	MN908947.3	5129	C	T	0.026	0.032	3.6e-12	1.8e-14	0.0293847566574839	ACC	ORF1ab:nsp3	P804S	C2410T	CCT>TCT	Missense	ORF1ab:nsp3	0.969926538108356
CAMB-769CE	MN908947.3	522	TT	-	0.041	0.0375	6.3e-06;6.2e-05	8.1e-06;0.00017	0.0394460377589988	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.95365141805723
CAMB-769DD	MN908947.3	10262	G	A	1	1	0	0	0.999345121152587	GGC	ORF1ab:3C-like-proteinase	A70T	G208A	GCT>ACT	Missense	ORF1ab:3C-like-proteinase	0.000587711786140077
CAMB-769DD	MN908947.3	11074	C	INS	0.024	0.028	0.00014	1.2e-05	0.0258651158307361	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.973733251935867
CAMB-769DD	MN908947.3	11075	T	-	0.042	0.037	8e-11	1.2e-09	0.039829322887521	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955721880246223
CAMB-769DD	MN908947.3	1263	C	T	1	1	0	0	0.997514233020608	ACG	ORF1ab:nsp2	T153M	C458T	ACG>ATG	Missense	ORF1ab:nsp2	0.00178012990137118
CAMB-769DD	MN908947.3	14408	C	T	1	0.99	0	0	0.994022976264959	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000878582553480385
CAMB-769DD	MN908947.3	19839	T	C	1	1	0	0	0.99920601312725	ATA	ORF1ab:endoRNAse	N73N	T219C	AAT>AAC	Synonymous	ORF1ab:endoRNAse	5.2932458183358e-05
CAMB-769DD	MN908947.3	22995	C	T	1	1	0	0	0.999200900802731	ACA	S	T478I	C1433T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0.000472194980204134
CAMB-769DD	MN908947.3	23403	A	G	1	1	0	0	0.999730974183869	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.1388587097108e-05
CAMB-769DD	MN908947.3	241	C	T	1	1	0	0	0.99918355683465	TCG	NA	NA	NA	NA	NA	NA	0.000102055395668769
CAMB-769DD	MN908947.3	25471	G	T	0.019	0.017	3.4e-10	1.9e-09	0.0179670734190698	AGA	ORF3a	D27Y	G79T	GAT>TAT	Missense	GU280_gp03	0.981970268957847
CAMB-769DD	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.02115625	0.03253125	0.0011;0.0025;0.0026;0.0026;0.00081;0.0014;0.0013;0.0023;0.0019;0.002;0.0029;0.0018;0.0026;0.0018;0.002;0.0017;0.003;0.0018;0.0022;0.002;0.0016;0.0027;0.0017;0.0012;0.002;0.0026;0.0024;0.0023;0.0032;0.0016;0.0011;0.0011	6.9e-05;0.00023;2.4e-05;2.4e-05;1.2e-05;1.4e-05;1.2e-05;2e-05;1.7e-05;1.8e-05;2.8e-05;1.2e-05;2.4e-05;1.6e-05;1.6e-05;1.6e-05;2.7e-05;1.8e-05;2.1e-05;1.6e-05;1.1e-05;2.3e-05;1.6e-05;4.2e-06;1.7e-05;2.3e-05;2.3e-05;1.2e-05;2.6e-05;7e-06;1.7e-05;1e-05	0.0265507767092888	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.973541339612768
CAMB-769DD	MN908947.3	27669	A	G	1	1	3.2e-147	1.2e-228	1	AAG	ORF7a	E92E	A276G	GAA>GAG	Synonymous	GU280_gp07	0
CAMB-769DD	MN908947.3	28826	C	T	0.011	0.014	2.6e-05	7.6e-07	0.0124117013209881	TCG	N	R185C	C553T	CGT>TGT	Missense	GU280_gp10	0.987508480664086
CAMB-769DD	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999275887038378	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000191570881226054
CAMB-769DD	MN908947.3	3037	C	T	1	1	0	0	0.999285850314226	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.76099790516092e-05
CAMB-769DD	MN908947.3	9438	C	T	1	1	0	0	1	ACA	ORF1ab:nsp4	T295I	C884T	ACA>ATA	Missense	ORF1ab:nsp4	0
CAMB-769EC	MN908947.3	1059	C	T	1	1	0	0	0.999821339950372	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.000158808933002481
CAMB-769EC	MN908947.3	11075	T	-	0.04	0.035	4.8e-10	2.7e-09	0.0377842941927518	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951762939682629
CAMB-769EC	MN908947.3	1181	G	A	0.01	0.0096	1.3e-06	1.3e-06	0.0102636666201646	AGT	ORF1ab:nsp2	V126I	G376A	GTT>ATT	Missense	ORF1ab:nsp2	0.989377603284373
CAMB-769EC	MN908947.3	14408	C	T	1	1	0	0	0.99790548298011	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000232724113321128
CAMB-769EC	MN908947.3	20268	A	G	1	1	4.3e-108	1.7e-157	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-769EC	MN908947.3	23403	A	G	1	1	0	0	0.999909943521723	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.00564782770909e-05
CAMB-769EC	MN908947.3	241	C	T	1	1	0	0	0.999914245532192	TCG	NA	NA	NA	NA	NA	NA	5.14526806846637e-05
CAMB-769EC	MN908947.3	27358	G	T	1	1	0	0	0.999843527738265	AGA	ORF6	D53Y	G157T	GAT>TAT	Missense	GU280_gp06	0.000142247510668563
CAMB-769EC	MN908947.3	28854	C	T	1	1	0	0	0.999558571980356	TCA	N	S194L	C581T	TCA>TTA	Missense	GU280_gp10	5.51785024554434e-05
CAMB-769EC	MN908947.3	29485	C	T	1	1	0	0	1	CCA	N	S404S	C1212T	TCC>TCT	Synonymous	GU280_gp10	0
CAMB-769EC	MN908947.3	3037	C	T	1	1	0	0	0.999666866546739	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-769FB	MN908947.3	11075	T	-	0.035	0.034	4.5e-09	3.4e-09	0.0348775711488157	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961420260438257
CAMB-769FB	MN908947.3	11083	G	T	0.027	0.022	4.7e-06	4.9e-05	0.0250817884405671	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.969069098840091
CAMB-769FB	MN908947.3	14408	C	T	1	1	0	0	0.997782057241517	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000424995019589614
CAMB-769FB	MN908947.3	23403	A	G	1	1	0	0	0.99641111317369	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.28160386114721e-05
CAMB-769FB	MN908947.3	241	C	T	1	1	0	0	0.999004149377593	TCG	NA	NA	NA	NA	NA	NA	0.00012448132780083
CAMB-769FB	MN908947.3	27877	G	T	1	1	0	0	0.998555840821566	TGT	NA	NA	NA	NA	NA	NA	0.000561617458279846
CAMB-769FB	MN908947.3	28086	G	T	0.99	1	0	0	0.995526604928583	GGC	ORF8	A65S	G193T	GCT>TCT	Missense	GU280_gp09	0.000784806152880239
CAMB-769FB	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999442068067696	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000126358352287086
CAMB-769FB	MN908947.3	3037	C	T	1	1	0	0	0.999227705064629	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.06471018616373e-05
CAMB-769FB	MN908947.3	3787	C	T	1	1	0	0	0.996730083234245	ACT	ORF1ab:nsp3	Y356Y	C1068T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.00267538644470868
CAMB-769FB	MN908947.3	3903	C	T	1	1	0	0	0.998598949211909	CCA	ORF1ab:nsp3	P395L	C1184T	CCA>CTA	Missense	ORF1ab:nsp3	0.0010507880910683
CAMB-76A16	MN908947.3	11075	T	-	0.027	0.053	2.9e-07	2.6e-13	0.0382463593075396	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954631904821401
CAMB-76A16	MN908947.3	1148	G	T	0.071	0.077	2e-32	2.3e-35	0.0735334382914642	TGG	ORF1ab:nsp2	G115C	G343T	GGC>TGC	Missense	ORF1ab:nsp2	0.926380998014922
CAMB-76A16	MN908947.3	14408	C	T	1	1	0	0	0.998930910062809	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000296969426997491
CAMB-76A16	MN908947.3	18877	C	T	1	1	0	0	0.999903969270166	TCT	ORF1ab:3'-to-5'-exonuclease	L280L	C838T	CTA>TTA	Synonymous	ORF1ab:3'-to-5'-exonuclease	6.40204865556978e-05
CAMB-76A16	MN908947.3	21622	C	T	0.01	0.0068	2.1e-05	0.00066	0.00890782339271882	CCA	S	T20T	C60T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.991092176607281
CAMB-76A16	MN908947.3	23403	A	G	1	1	0	0	0.99840215654518	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.60877835628648e-05
CAMB-76A16	MN908947.3	23422	C	T	0.0076	0.0021	2.2e-05	0.0076	0.00519809548770366	TCC	S	V620V	C1860T	GTC>GTT	Synonymous	GU280_gp02, spike glycoprotein	0.99475822303761
CAMB-76A16	MN908947.3	241	C	T	1	1	0	0	0.999912767875316	TCG	NA	NA	NA	NA	NA	NA	5.8154749789189e-05
CAMB-76A16	MN908947.3	24197	G	T	0.99	1	0	0	0.996274276654776	AGC	S	A879S	G2635T	GCG>TCG	Missense	GU280_gp02, spike glycoprotein	7.92707094728498e-05
CAMB-76A16	MN908947.3	25563	G	T	1	1	0	0	0.999914179296614	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	5.1492422031891e-05
CAMB-76A16	MN908947.3	26735	C	T	1	1	0	0	0.999460615642146	ACA	M	Y71Y	C213T	TAC>TAT	Synonymous	GU280_gp05	5.57983818469264e-05
CAMB-76A16	MN908947.3	3037	C	T	1	1	0	0	0.999333155508136	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76A16	MN908947.3	4173	C	T	0.0044	0.0072	0.00046	2.4e-05	0.00561425343957575	ACT	ORF1ab:nsp3	T485I	C1454T	ACT>ATT	Missense	ORF1ab:nsp3	0.994385746560424
CAMB-76A16	MN908947.3	6255	C	T	0.014	0.0096	3.5e-08	3.3e-06	0.0121840127533591	GCA	ORF1ab:nsp3	A1179V	C3536T	GCA>GTA	Missense	ORF1ab:nsp3	0.987787519927124
CAMB-76A16	MN908947.3	934	C	T	0.036	0.049	1.2e-17	3.6e-23	0.0412912573006746	ACA	ORF1ab:nsp2	D43D	C129T	GAC>GAT	Synonymous	ORF1ab:nsp2	0.958708742699325
CAMB-76A25	MN908947.3	10653	TTACAGTTAATGTTTTAGCTT	-	0.0376190476190476	0.00611904761904762	3.1e-06;8.2e-06;1.7e-10;4.5e-10;1.3e-09;2.6e-10;3.1e-10;4e-10;4.5e-09;5.4e-10;8.6e-10;6e-10;6.9e-14;6.4e-11;8.1e-11;2.2e-12;3.6e-13;3.7e-07;6e-07;9e-08;4.5e-07	0.0018;0.0028;0.0027;0.0038;0.0044;0.0036;0.0048;0.0041;0.011;0.0055;0.0053;0.0052;0.0023;0.0036;0.0029;NA;NA;NA;NA;NA;NA	0.0277515192437542	ATT	ORF1ab:3C-like-proteinase	.	599-619-delinframe	.	no-SNV	ORF1ab:3C-like-proteinase	0.983896251959527
CAMB-76A25	MN908947.3	10887	G	T	0.02	0.0072	5e-10	7.2e-05	0.0136263736263736	GGA	ORF1ab:3C-like-proteinase	G278V	G833T	GGA>GTA	Missense	ORF1ab:3C-like-proteinase	0.986373626373626
CAMB-76A25	MN908947.3	11075	T	-	0.068	0.052	6.7e-17	2.8e-13	0.0605350484075126	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.939293900311313
CAMB-76A25	MN908947.3	11080	TTTGTATGAAAATGCCTTTTTA	-	0.0186363636363636	0.001245	8e-10;8.3e-09;0.00096;5.5e-08;1.3e-08;1.4e-08;3.5e-07;3e-07;2.7e-09;1.7e-09;1.3e-09;5.1e-10;1.4e-09;8.6e-10;6.2e-08;7.4e-08;5.4e-09;8.6e-06;9.7e-05;0.00013;0.00014;0.00013	1e-04;0.00034;0.034;0.0024;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.5;NA;NA;NA;NA;NA	0.00934172637782093	TTT	ORF1ab:nsp6	.	108-129-delfrshift	.	no-SNV	ORF1ab:nsp6	0.986938817764588
CAMB-76A25	MN908947.3	12236	T	A	0.015	0.011	4.3e-07	1.4e-05	0.0133912414042707	ATT	ORF1ab:nsp8	F49I	T145A	TTT>ATT	Missense	ORF1ab:nsp8	0.986557054960964
CAMB-76A25	MN908947.3	12239	GAC	TGA	0.015	0.012	4.1e-07;4.5e-07;9.3e-07	6.8e-06;1.9e-05;1.3e-05	0.0133306705277348	TGA	ORF1ab:nsp8	.	148-150-mnv	.	no-SNV	ORF1ab:nsp8	0.985870487792701
CAMB-76A25	MN908947.3	12243	GTGATGCAGC	CGTGATGCAG	0.0145	0.0122	8.1e-07;9.5e-07;1e-06;7e-07;4.7e-07;2.5e-06;6.3e-07;1.3e-06;5.8e-07;4.4e-07	1e-05;1.2e-05;1e-05;6.3e-06;4.6e-06;1.5e-05;9.6e-06;1e-05;7e-06;9.1e-06	0.0132590694006309	CGT	ORF1ab:nsp8	.	152-161-mnv	.	no-SNV	ORF1ab:nsp8	0.986713218892445
CAMB-76A25	MN908947.3	12254	ATGCA	CATGC	0.0152	0.0122	3.2e-07;6.2e-07;2e-06;5.4e-07;3.1e-07	4.5e-06;1.1e-05;3.1e-05;7e-06;3.4e-06	0.0136134799136957	CAT	ORF1ab:nsp8	.	163-167-mnv	.	no-SNV	ORF1ab:nsp8	0.985524920466596
CAMB-76A25	MN908947.3	12260	CGTA	ACGT	0.01375	0.0114	9.8e-06;1.3e-06;1.9e-07;1.2e-06	8.7e-05;8.4e-06;1.6e-06;2.3e-05	0.0129296751813308	ACG	ORF1ab:nsp8	.	169-172-mnv	.	no-SNV	ORF1ab:nsp8	0.990155360713736
CAMB-76A25	MN908947.3	12265	GT	AG	0.0145	0.0125	1.8e-06;3.7e-07	2e-05;2.9e-06	0.0131708581799326	AGT	ORF1ab:nsp8	.	174-175-mnv	.	no-SNV	ORF1ab:nsp8	0.983137757617592
CAMB-76A25	MN908947.3	12268	G	T	0.014	0.011	7.3e-07	1.8e-05	0.0126904796903327	TGG	ORF1ab:nsp8	L59F	G177T	TTG>TTT	Missense	ORF1ab:nsp8	0.987309520309667
CAMB-76A25	MN908947.3	12274	GATG	AGAT	0.01375	0.01175	1.3e-06;9.6e-07;8.6e-07;2.5e-06	2.7e-05;1.3e-05;4.3e-06;1.9e-05	0.0126089740432448	AGA	ORF1ab:nsp8	.	183-186-mnv	.	no-SNV	ORF1ab:nsp8	0.987659176950686
CAMB-76A25	MN908947.3	12279	CTGATCA	GCTGATC	0.014	0.0117142857142857	1.2e-06;1e-06;9.2e-07;6.1e-07;2.2e-06;1.7e-06;7.6e-07	1.7e-05;1.1e-05;8.3e-06;8.5e-06;1.3e-05;1.4e-05;9.2e-06	0.0128518373729476	GCT	ORF1ab:nsp8	.	188-194-mnv	.	no-SNV	ORF1ab:nsp8	0.987181977082929
CAMB-76A25	MN908947.3	12287	GCTATGAC	AGCTATGA	0.0145	0.011825	3.4e-07;4e-07;9.5e-06;2.6e-07;2e-06;3e-06;1.5e-06;1.1e-06	5.8e-06;8e-06;3.2e-05;3e-06;9.5e-05;3.4e-05;1.6e-05;1.4e-05	0.012816089121112	AGC	ORF1ab:nsp8	.	196-203-mnv	.	no-SNV	ORF1ab:nsp8	0.985637626262626
CAMB-76A25	MN908947.3	12297	A	C	0.015	0.012	5.9e-07	9.3e-06	0.0137759251728345	CAA	ORF1ab:nsp8	Q69P	A206C	CAA>CCA	Missense	ORF1ab:nsp8	0.986020740138268
CAMB-76A25	MN908947.3	12300	TGTATA	ATGTAT	0.0143333333333333	0.0115	5.7e-07;1.3e-06;8.7e-07;5.3e-06;3.1e-06;1.9e-06	1.4e-05;1.6e-05;1e-05;2.2e-05;3e-05;1.3e-05	0.0130572751391562	ATG	ORF1ab:nsp8	.	209-214-mnv	.	no-SNV	ORF1ab:nsp8	0.986634589681903
CAMB-76A25	MN908947.3	12308	CAG	ACA	0.013	0.0113333333333333	1.4e-06;1.9e-06;1.6e-06	1.6e-05;1.2e-05;1.3e-05	0.0123946698020772	ACA	ORF1ab:nsp8	.	217-219-mnv	.	no-SNV	ORF1ab:nsp8	0.987761120668469
CAMB-76A25	MN908947.3	12788	AC	-	0.0115	0.0047	1.1e-06;2.6e-06	0.0014;0.0021	0.00841478744965238	AAC	ORF1ab:nsp9	.	103-104-delfrshift	.	no-SNV	ORF1ab:nsp9	0.99116442207288
CAMB-76A25	MN908947.3	14398	G	T	0.065	0.077	2e-30	9.5e-36	0.0709317759490311	AGT	ORF1ab:RNA-dependent-RNA-polymerase	V311L	G931T	GTG>TTG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.92903282895319
CAMB-76A25	MN908947.3	14408	C	T	1	0.99	0	0	0.996187724123525	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000348153048079936
CAMB-76A25	MN908947.3	17561	G	A	0.04	0.084	2.3e-19	5.4e-39	0.0639438759551365	CGG	ORF1ab:helicase	R442Q	G1325A	CGG>CAG	Missense	ORF1ab:helicase	0.936056124044863
CAMB-76A25	MN908947.3	18119	T	C	0.023	0.026	1.4e-11	5.3e-13	0.0246814261809757	CTC	ORF1ab:3'-to-5'-exonuclease	L27P	T80C	CTC>CCC	Missense	ORF1ab:3'-to-5'-exonuclease	0.975189857124469
CAMB-76A25	MN908947.3	20627	G	T	0.0067	0.011	0.00066	1.8e-05	0.00865757786844462	GGC	ORF1ab:endoRNAse	G336V	G1007T	GGC>GTC	Missense	ORF1ab:endoRNAse	0.991043884963678
CAMB-76A25	MN908947.3	22951	T	C	0.013	0.0057	1.4e-05	0.0046	0.00875196919306844	CTT	S	P463P	T1389C	CCT>CCC	Synonymous	GU280_gp02, spike glycoprotein	0.99107299142307
CAMB-76A25	MN908947.3	23403	A	G	1	0.99	0	0	0.996523013388397	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000119896090055285
CAMB-76A25	MN908947.3	23423	C	T	0.032	0.0032	6.3e-16	0.0026	0.0182890696546894	CCC	S	P621S	C1861T	CCT>TCT	Missense	GU280_gp02, spike glycoprotein	0.981670527393201
CAMB-76A25	MN908947.3	241	C	T	0.96	1	0	0	0.985408890397014	TCG	NA	NA	NA	NA	NA	NA	0.000101798439090601
CAMB-76A25	MN908947.3	24138	C	T	0.0067	0.019	0.00013	8.4e-10	0.0128615492056102	ACT	S	T859I	C2576T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.980853168829657
CAMB-76A25	MN908947.3	24673	A	-	0.017	0.0072	4.1e-06	0.0097	0.0128909047505371	CAA	S	.	3111-3111-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.987109095249463
CAMB-76A25	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0428684210526316	0.0370263157894737	4.9e-06;2.7e-08;2.6e-06;3.9e-06;1.7e-07;3.6e-10;5.7e-10;4.4e-07;4e-07;4.5e-08;2.4e-07;2.1e-07;3.6e-07;3.1e-07;3.4e-07;6.1e-07;2.5e-07;5.2e-07;2.6e-07;3.3e-07;2.1e-07;6.3e-07;2.2e-07;3.9e-07;3e-07;1.6e-07;4.6e-07;2.5e-07;3e-07;2.5e-07;5e-07;3.5e-07;1.9e-07;4.3e-07;7.8e-08;1.4e-10;8.5e-11;9.3e-05	3e-05;1.3e-06;2.1e-05;2.1e-05;0.00046;5.1e-05;2e-04;1.3e-06;1.4e-06;6.9e-07;6.9e-07;5.9e-07;1.3e-06;9.4e-07;1e-06;1.9e-06;7e-07;1.6e-06;9e-07;9.7e-07;8.2e-07;1.8e-06;1.1e-06;1.4e-06;9.8e-07;5.3e-07;1.4e-06;9.5e-07;6.9e-07;8.1e-07;1.5e-06;1.4e-06;4.7e-07;1.4e-06;2.9e-07;9.3e-07;5.5e-07;0.0043	0.0402206320810972	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.968674196764737
CAMB-76A25	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998936547323644	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-76A25	MN908947.3	29735	A	C	0.0057	0.011	0.00011	9.1e-07	0.00909233422166484	GAG	NA	NA	NA	NA	NA	NA	0.990907665778335
CAMB-76A25	MN908947.3	3037	C	T	1	1	0	0	0.99939107931192	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.61150860100472e-05
CAMB-76A25	MN908947.3	3350	AGTG	-	0.0023	0.007025	NA;NA;NA;9.5e-06	0.00036;0.00016;2.2e-06;0.00021	0.00287867516253194	TAG	ORF1ab:nsp3	.	631-634-delfrshift	.	no-SNV	ORF1ab:nsp3	0.997037085273337
CAMB-76A25	MN908947.3	3353	G	-	0.0092	0.0061	9.5e-06	0.00021	0.00770252324037185	TGG	ORF1ab:nsp3	.	634-634-delfrshift	.	no-SNV	ORF1ab:nsp3	0.992231075697211
CAMB-76A25	MN908947.3	522	T	-	0.14	0.027	2e-18	0.001	0.0840200422377738	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.915814319433517
CAMB-76A25	MN908947.3	593	C	T	0.023	0.0061	9.7e-12	0.00018	0.0148909115245616	TCA	ORF1ab:leader-protein	H110Y	C328T	CAT>TAT	Missense	ORF1ab:leader-protein	0.985109088475438
CAMB-76A34	MN908947.3	11075	T	-	0.054	0.04	1.9e-13	1.6e-10	0.0480162483139273	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.943347958883083
CAMB-76A34	MN908947.3	13026	C	T	0.19	0.17	1.3e-87	5.7e-80	0.180538060950161	GCT	ORF1ab:nsp10	A1V	C2T	GCT>GTT	Missense	ORF1ab:nsp10	0.819405538530954
CAMB-76A34	MN908947.3	14408	C	T	1	1	0	0	0.997698022391964	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000191831467336333
CAMB-76A34	MN908947.3	14786	C	T	1	1	0	0	0.999875495793536	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A440V	C1319T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	3.55726304181563e-05
CAMB-76A34	MN908947.3	16247	C	T	0.0084	0.014	0.00065	3.4e-06	0.0115550851195202	GCT	ORF1ab:helicase	A4V	C11T	GCT>GTT	Missense	ORF1ab:helicase	0.988356708123842
CAMB-76A34	MN908947.3	16440	G	A	0.031	0.016	9.1e-15	4e-09	0.0231033917745371	TGA	ORF1ab:helicase	M68I	G204A	ATG>ATA	Missense	ORF1ab:helicase	0.976896608225463
CAMB-76A34	MN908947.3	17460	A	G	0.0028	0.0076	0.0014	1.1e-05	0.00504751627388868	CAC	ORF1ab:helicase	P408P	A1224G	CCA>CCG	Synonymous	ORF1ab:helicase	0.994952483726111
CAMB-76A34	MN908947.3	17884	A	G	0.0021	0.011	0.0041	4.2e-07	0.00601481544013676	CAC	ORF1ab:helicase	T550A	A1648G	ACT>GCT	Missense	ORF1ab:helicase	0.993900766097546
CAMB-76A34	MN908947.3	20578	G	T	1	1	0	0	0.999857326294764	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	0.000142673705236125
CAMB-76A34	MN908947.3	22858	C	T	0.0048	0.01	0.0021	7.4e-06	0.00702550078925721	GCG	S	C432C	C1296T	TGC>TGT	Synonymous	GU280_gp02, spike glycoprotein	0.991507147780075
CAMB-76A34	MN908947.3	23403	A	G	1	1	0	0	0.997036871730021	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.43881574053411e-05
CAMB-76A34	MN908947.3	23567	GGTATATGCGCTAGT	-	0.0234666666666667	0.0322666666666667	0.0063;0.006;0.0042;0.0019;0.0042;0.0029;0.0045;0.0027;0.004;0.0061;0.0044;0.0046;0.00076;0.0011;0.0046	0.00096;0.00091;0.00056;0.00017;0.00058;0.00029;0.00059;0.00025;5e-04;0.00085;0.00057;0.00056;2.9e-05;5e-05;0.00063	0.0264299404821951	AGG	S	.	2005-2019-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.974546688645399
CAMB-76A34	MN908947.3	23623	A	G	0.0041	0.01	0.00071	1.6e-06	0.00682068206820682	TAG	S	V687V	A2061G	GTA>GTG	Synonymous	GU280_gp02, spike glycoprotein	0.993124312431243
CAMB-76A34	MN908947.3	241	C	T	1	1	0	0	0.999833356478267	TCG	NA	NA	NA	NA	NA	NA	8.33217608665463e-05
CAMB-76A34	MN908947.3	2416	C	T	1	1	0	0	0.997513513513513	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0.000108108108108108
CAMB-76A34	MN908947.3	25096	C	T	0.0025	0.01	0.006	2.5e-06	0.00537283647388418	ACA	S	N1178N	C3534T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.994627163526116
CAMB-76A34	MN908947.3	25354	G	T	0.012	0.013	5.4e-07	1.7e-07	0.0125013224247981	TGC	S	V1264V	G3792T	GTG>GTT	Synonymous	GU280_gp02, spike glycoprotein	0.98735761893007
CAMB-76A34	MN908947.3	25485	T	C	1	1	0	0	0.99992902893845	CTA	ORF3a	A31A	T93C	GCT>GCC	Synonymous	GU280_gp03	3.54855307748266e-05
CAMB-76A34	MN908947.3	25563	G	T	1	1	0	0	0.99984165940939	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	5.93777214789011e-05
CAMB-76A34	MN908947.3	25627	T	C	0.0038	0.01	0.0038	5.7e-06	0.00651043775406093	CTT	ORF3a	F79L	T235C	TTT>CTT	Missense	GU280_gp03	0.993408586651983
CAMB-76A34	MN908947.3	28248	G	A	0.039	0.035	9.7e-19	5.7e-17	0.0376036455834989	AGA	ORF8	D119N	G355A	GAT>AAT	Missense	GU280_gp09	0.962087987391215
CAMB-76A34	MN908947.3	3037	C	T	1	1	0	0	0.999182301367374	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000272566210875392
CAMB-76A34	MN908947.3	5184	C	T	0.014	0.012	3.5e-06	6.6e-05	0.0131313131313131	CCT	ORF1ab:nsp3	P822L	C2465T	CCT>CTT	Missense	ORF1ab:nsp3	0.986868686868687
CAMB-76A34	MN908947.3	6060	G	T	0.0098	0.0092	1.3e-05	2.2e-05	0.00952743902439024	TGT	ORF1ab:nsp3	C1114F	G3341T	TGT>TTT	Missense	ORF1ab:nsp3	0.99047256097561
CAMB-76A34	MN908947.3	6608	A	-	0.0094	0.0041	1.5e-05	0.002	0.00632911392405063	TAG	ORF1ab:nsp3	.	3889-3889-delfrshift	.	no-SNV	ORF1ab:nsp3	0.993670886075949
CAMB-76A34	MN908947.3	9409	A	G	0.022	0.013	1.5e-11	8.9e-08	0.0191825869088631	TAG	ORF1ab:nsp4	V285V	A855G	GTA>GTG	Synonymous	ORF1ab:nsp4	0.980739116818039
CAMB-76A61	MN908947.3	11075	T	-	0.025	0.031	7.8e-07	1.5e-08	0.0275912170677104	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.96896914705926
CAMB-76A61	MN908947.3	11908	A	G	0.0017	0.0066	0.0069	3.6e-05	0.00375137618419801	TAG	ORF1ab:nsp7	V22V	A66G	GTA>GTG	Synonymous	ORF1ab:nsp7	0.996221439930409
CAMB-76A61	MN908947.3	14408	C	T	1	1	0	0	0.997031931354621	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00021100014066676
CAMB-76A61	MN908947.3	21752	T	A	0.37	0.38	5.1e-178	2.3e-193	0.375673652694611	TTG	S	W64R	T190A	TGG>AGG	Missense	GU280_gp02, spike glycoprotein	0.62312874251497
CAMB-76A61	MN908947.3	22846	TTTTACAGGCTGCG	-	0.0358571428571429	0.0443571428571429	4.8e-12;2e-09;7.6e-09;3.3e-09;2e-09;6.2e-10;6.6e-10;5.2e-10;3.5e-09;2e-09;4e-09;3.4e-10;2e-09;7e-10	4.3e-16;2.3e-12;2.6e-11;4.8e-11;2.5e-11;6.2e-12;1.1e-11;5.4e-12;4.4e-11;3.4e-11;5.2e-11;6.7e-12;5.8e-11;7.7e-12	0.0392081785810009	ATT	S	.	1284-1297-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.96209723396308
CAMB-76A61	MN908947.3	23403	A	G	1	1	0	0	0.99995337995338	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.33100233100233e-05
CAMB-76A61	MN908947.3	241	C	T	1	1	0	0	0.999261852539227	TCG	NA	NA	NA	NA	NA	NA	0.000168719419605197
CAMB-76A61	MN908947.3	26781	CTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0343888888888889	0.016175	1e-04;0.00028;0.00031;0.00061;5.7e-07;3.5e-06;9.6e-06;9.1e-06;1.3e-06;5.4e-06;4.4e-06;7.9e-06;7.1e-06;4.2e-06;6.7e-06;6e-06;1.1e-05;5e-06;7.4e-06;7.2e-06;1.3e-05;6.4e-06;8.1e-06;6.9e-06;5.2e-06;9.9e-06;5.3e-06;1.7e-06;7.6e-06;1.1e-05;9.9e-06;6.7e-06;1.1e-05;2e-06;2.7e-06;8.7e-07	0.18;0.26;0.27;0.3;0.12;0.18;0.0088;0.0088;0.0059;0.0071;0.0037;0.0048;0.0043;0.0078;0.01;0.0065;0.0094;0.0075;0.0074;0.0069;0.01;0.0074;0.0085;0.0075;0.0058;0.0094;0.0076;0.002;0.0076;0.0094;0.0092;0.0054;0.0091;0.0056;0.0036;0.0026	0.0272832788170211	TCT	M	.	259-294-delinframe	.	no-SNV	GU280_gp05	0.982645155409717
CAMB-76A61	MN908947.3	3037	C	T	1	1	0	0	0.999604091059056	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76A61	MN908947.3	751	C	T	1	1	0	0	0.999920074171169	ACA	ORF1ab:leader-protein	N162N	C486T	AAC>AAT	Synonymous	ORF1ab:leader-protein	6.3940663064676e-05
CAMB-76A61	MN908947.3	9598	C	T	0.039	0.048	1.3e-18	8.5e-23	0.0426016966238117	ACT	ORF1ab:nsp4	Y348Y	C1044T	TAC>TAT	Synonymous	ORF1ab:nsp4	0.956948558490098
CAMB-76A70	MN908947.3	11074	C	INS	0.091	0.1	3.9e-29	2.8e-32	0.0963183040912193	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.903260127674951
CAMB-76A70	MN908947.3	11083	G	-	0.19	0.23	4.2e-84	1.6e-105	0.203865336658354	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-76A70	MN908947.3	11083	G	T	0.81	0.77	0	7.3e-305	0.796061317294998	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-76A70	MN908947.3	12396	C	T	0.012	0.028	2.5e-07	9.3e-14	0.0182832068744858	GCA	ORF1ab:nsp8	A102V	C305T	GCA>GTA	Missense	ORF1ab:nsp8	0.981671085108328
CAMB-76A70	MN908947.3	12677	AA	-	0.00705	0.0033	4e-05;1.9e-05	5.4e-05;NA	0.00546141655491893	CAA	ORF1ab:nsp8	.	586-587-delfrshift	.	no-SNV	ORF1ab:nsp8	0.992981437111256
CAMB-76A70	MN908947.3	1368	T	C	1	1	0	0	1	ATT	ORF1ab:nsp2	I188T	T563C	ATT>ACT	Missense	ORF1ab:nsp2	0
CAMB-76A70	MN908947.3	14117	C	T	0.007	0.017	2.4e-05	8.7e-10	0.0119742518976536	ACG	ORF1ab:RNA-dependent-RNA-polymerase	T217M	C650T	ACG>ATG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.98800267632605
CAMB-76A70	MN908947.3	14411	C	T	0.011	0.0065	8.1e-07	0.00012	0.00967462039045553	ACA	ORF1ab:RNA-dependent-RNA-polymerase	T315I	C944T	ACA>ATA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.990281995661605
CAMB-76A70	MN908947.3	14805	C	T	1	1	0	0	0.999937321103984	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-76A70	MN908947.3	14880	T	C	0.36	0.42	5.3e-191	8.1e-226	0.386964058225257	TTG	ORF1ab:RNA-dependent-RNA-polymerase	F471F	T1413C	TTT>TTC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.613015057536078
CAMB-76A70	MN908947.3	16375	C	T	0.28	0.33	1.2e-96	1.1e-117	0.303417124901807	TCC	ORF1ab:helicase	P47S	C139T	CCG>TCG	Missense	ORF1ab:helicase	0.696582875098193
CAMB-76A70	MN908947.3	16466	C	T	0.0053	0.014	0.0068	3.7e-05	0.00982986767485822	CCA	ORF1ab:helicase	P77L	C230T	CCA>CTA	Missense	ORF1ab:helicase	0.989981096408318
CAMB-76A70	MN908947.3	17111	C	T	0.018	0.03	3.9e-10	2.4e-15	0.0237080738555665	GCT	ORF1ab:helicase	A292V	C875T	GCT>GTT	Missense	ORF1ab:helicase	0.976231229590784
CAMB-76A70	MN908947.3	17456	C	T	0.1	0.11	4.4e-46	3.9e-49	0.103476151980598	GCA	ORF1ab:helicase	A407V	C1220T	GCA>GTA	Missense	ORF1ab:helicase	0.896496901104823
CAMB-76A70	MN908947.3	17488	G	A	0.093	0.026	1.4e-42	1.5e-13	0.0606050790360197	AGA	ORF1ab:helicase	E418K	G1252A	GAA>AAA	Missense	ORF1ab:helicase	0.935410728167919
CAMB-76A70	MN908947.3	18110	C	T	0.0088	0.02	7.2e-06	1.8e-10	0.0135453922836923	CCT	ORF1ab:3'-to-5'-exonuclease	P24L	C71T	CCT>CTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.986340461152119
CAMB-76A70	MN908947.3	19602	C	T	0.0074	0.032	4.3e-05	6.1e-15	0.0179073033707865	ACA	ORF1ab:3'-to-5'-exonuclease	N521N	C1563T	AAC>AAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.982092696629214
CAMB-76A70	MN908947.3	23707	C	T	1	1	0	0	0.99938418905396	CCA	S	P715P	C2145T	CCC>CCT	Synonymous	GU280_gp02, spike glycoprotein	0.000461858209529674
CAMB-76A70	MN908947.3	25047	C	T	0.016	0.012	1.2e-08	2.5e-07	0.0144196106705119	CCA	S	P1162L	C3485T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	0.985516302170953
CAMB-76A70	MN908947.3	26144	G	T	1	1	0	1.9e-239	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-76A70	MN908947.3	27366	GC	CT	0.01265	0.024	1.8e-05;7e-10	NA;9.7e-23	0.0172734093101354	AGC	ORF6	.	165-166-mnv	.	no-SNV	GU280_gp06	0.995473556517173
CAMB-76A70	MN908947.3	27367	C	T	0.018	0.048	7e-10	9.7e-23	0.0298602175177593	GCA	ORF6	Q56*	C166T	CAA>TAA	Nonsense	GU280_gp06	0.970104528388359
CAMB-76A70	MN908947.3	27925	C	T	0.0087	0.015	7.5e-05	1.3e-07	0.0127982646420824	ACA	ORF8	T11I	C32T	ACA>ATA	Missense	GU280_gp09	0.987201735357918
CAMB-76A70	MN908947.3	28887	C	T	0.02	0.016	4.2e-10	5.5e-08	0.018538248455146	ACT	N	T205I	C614T	ACT>ATT	Missense	GU280_gp10	0.981355209887066
CAMB-76A70	MN908947.3	29367	C	T	0.0042	0.015	0.0034	7.2e-06	0.00851063829787234	CCA	N	P365L	C1094T	CCA>CTA	Missense	GU280_gp10	0.991489361702128
CAMB-76A70	MN908947.3	6990	C	T	1	1	5.9e-306	4.5e-237	1	TCT	ORF1ab:nsp3	S1424F	C4271T	TCT>TTT	Missense	ORF1ab:nsp3	0
CAMB-76A70	MN908947.3	8802	C	T	0.013	0.013	1.3e-07	1.4e-07	0.0129490392648287	ACT	ORF1ab:nsp4	T83I	C248T	ACT>ATT	Missense	ORF1ab:nsp4	0.987050960735171
CAMB-76A70	MN908947.3	8833	A	G	0.34	0.27	7.4e-157	2.7e-119	0.30842628678941	CAG	ORF1ab:nsp4	A93A	A279G	GCA>GCG	Synonymous	ORF1ab:nsp4	0.69157371321059
CAMB-76A8F	MN908947.3	10499	G	-	0.0045	0.013	0.0033	1.8e-06	0.00803627805522071	TGG	ORF1ab:3C-like-proteinase	.	445-445-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.991906319958671
CAMB-76A8F	MN908947.3	11075	T	-	0.034	0.039	8.7e-09	1.9e-10	0.0359330857378662	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95970225057931
CAMB-76A8F	MN908947.3	11083	G	T	0.033	0.033	2.5e-07	2e-07	0.0333667797473999	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.957300078041633
CAMB-76A8F	MN908947.3	11475	TAATCTCTG	-	0.00187777777777778	0.00666666666666667	0.0017;0.0029;0.0014;0.0023;0.0027;0.0019;0.0016;0.006;0.026	2.8e-05;3.3e-05;2.9e-05;3e-05;2.8e-05;3e-05;2.8e-05;6.3e-05;0.00023	0.00397511234013135	ATA	ORF1ab:nsp6	.	503-511-delinframe	.	no-SNV	ORF1ab:nsp6	0.996085106382979
CAMB-76A8F	MN908947.3	1197	A	G	0.003	0.008	0.0022	1.1e-05	0.00468721419425645	GAA	ORF1ab:nsp2	E131G	A392G	GAA>GGA	Missense	ORF1ab:nsp2	0.995289921346259
CAMB-76A8F	MN908947.3	13530	C	T	0.01	0.0079	2.3e-06	2e-05	0.00931321823430096	TCG	ORF1ab:RNA-dependent-RNA-polymerase	V21V	C63T	GTC>GTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.990577855236643
CAMB-76A8F	MN908947.3	14195	C	T	0.0042	0.0085	0.00039	4.2e-06	0.00606702971382625	ACT	ORF1ab:RNA-dependent-RNA-polymerase	T243I	C728T	ACT>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993878147728519
CAMB-76A8F	MN908947.3	14408	C	T	1	1	0	0	0.998902683722097	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000344870830198144
CAMB-76A8F	MN908947.3	15981	C	T	0.047	0.084	2e-22	1.1e-38	0.0617586780060355	TCG	ORF1ab:RNA-dependent-RNA-polymerase	I838I	C2514T	ATC>ATT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.938112221020866
CAMB-76A8F	MN908947.3	17074	C	T	0.011	0.0044	1.2e-06	0.00057	0.00823341141545098	ACT	ORF1ab:helicase	L280F	C838T	CTC>TTC	Missense	ORF1ab:helicase	0.991766588584549
CAMB-76A8F	MN908947.3	18047	A	G	0.071	0.057	1.6e-32	2.2e-26	0.0650514061082552	AAT	ORF1ab:3'-to-5'-exonuclease	N3S	A8G	AAT>AGT	Missense	ORF1ab:3'-to-5'-exonuclease	0.934948593891745
CAMB-76A8F	MN908947.3	19145	C	T	0.0087	0.041	9.6e-06	1.1e-19	0.0216985049833887	TCT	ORF1ab:3'-to-5'-exonuclease	S369F	C1106T	TCT>TTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.978218438538206
CAMB-76A8F	MN908947.3	203	C	T	0.0039	0.01	0.0048	6.5e-06	0.00655005943572451	TCG	NA	NA	NA	NA	NA	NA	0.993401421605492
CAMB-76A8F	MN908947.3	23403	A	G	1	1	0	0	0.999947037404833	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.29625951671632e-05
CAMB-76A8F	MN908947.3	23567	GGTATATGCGCTAGT	-	0.0310666666666667	0.0332666666666667	0.00022;0.00021;0.00082;0.00028;0.00072;0.00047;0.00071;0.00045;0.00087;0.0015;0.001;0.001;7.4e-05;0.00012;0.0026	0.00081;0.00074;0.00045;0.00013;0.00044;0.00023;0.00032;2e-04;4e-04;0.00072;0.00045;0.00048;2.3e-05;4e-05;0.00052	0.030180608365019	AGG	S	.	2005-2019-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.966010189339214
CAMB-76A8F	MN908947.3	23611	G	A	1	1	0	0	1	GGG	S	R683R	G2049A	CGG>CGA	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-76A8F	MN908947.3	240	TCG	-	0.00246666666666667	0.00653333333333333	0.0023;0.0024;NA	0.00012;0.00012;3.8e-05	0.00488012887330617	TTC	NA	NA	NA	NA	NA	NA	0.994994068801898
CAMB-76A8F	MN908947.3	25350	C	T	1	1	0	0	0.999736028358096	CCA	S	P1263L	C3788T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	0.000188551172788295
CAMB-76A8F	MN908947.3	26787	GGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0288666666666667	0.0212	0.00012;0.00012;2.4e-05;7.5e-05;6.5e-05;0.00011;8.7e-05;9.5e-05;0.00015;7.6e-05;0.00014;8.1e-05;9.6e-05;0.00011;0.00016;9.7e-05;0.00011;9.3e-05;7.2e-05;0.00013;7.7e-05;4.1e-05;9.7e-05;0.00013;0.00012;9e-05;0.00014;4.1e-05;6.9e-05;6.6e-05	0.0022;0.0022;0.0012;0.0016;0.0016;0.0021;0.0018;0.00067;0.001;0.0015;0.0024;0.0018;0.0017;0.0018;0.0027;0.0017;0.0021;0.0018;0.0014;0.0024;0.0018;0.00047;0.0019;0.0024;0.0023;0.0011;0.0024;0.0012;0.0018;0.0014	0.0255265144821604	AGG	M	.	265-294-delinframe	.	no-SNV	GU280_gp05	0.974988995786958
CAMB-76A8F	MN908947.3	28233	G	T	0.0073	0.011	2.4e-05	6.8e-07	0.00857079952192238	CGT	ORF8	V114F	G340T	GTT>TTT	Missense	GU280_gp09	0.991161854437944
CAMB-76A8F	MN908947.3	28253	C	T	0.013	0.015	9.8e-07	1.9e-07	0.0137088584911296	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.98541007108297
CAMB-76A8F	MN908947.3	3037	C	T	1	1	0	0	0.999754510862894	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000122744568552842
CAMB-76A8F	MN908947.3	635	C	T	0.017	0.018	3.8e-09	2.5e-09	0.0175983657140425	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.982401634285958
CAMB-76A8F	MN908947.3	6582	C	T	0.0051	0.01	5e-04	5.1e-06	0.00761010362694301	ACT	ORF1ab:nsp3	T1288I	C3863T	ACT>ATT	Missense	ORF1ab:nsp3	0.992227979274611
CAMB-76A8F	MN908947.3	6815	AG	-	0.0037	0.0079	0.00023;NA	0.00011;2.9e-05	0.00577264653641208	TAG	ORF1ab:nsp3	.	4096-4097-delfrshift	.	no-SNV	ORF1ab:nsp3	0.992213740458015
CAMB-76A9E	MN908947.3	10252	C	T	0.027	0.0054	1.7e-13	0.00042	0.017351879320478	TCT	ORF1ab:3C-like-proteinase	F66F	C198T	TTC>TTT	Synonymous	ORF1ab:3C-like-proteinase	0.982592146875262
CAMB-76A9E	MN908947.3	11074	C	INS	0.15	0.099	1.6e-58	5.4e-30	0.126917395750483	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.872779608377836
CAMB-76A9E	MN908947.3	11083	G	-	0.13	0.16	5.9e-59	1.7e-70	0.144098531365579	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	5.38618980932888e-05
CAMB-76A9E	MN908947.3	11083	G	T	0.87	0.84	0	0	0.85572192897411	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	5.38618980932888e-05
CAMB-76A9E	MN908947.3	12260	CGTA	ACGT	0.0165	0.001675	1.7e-06;6.2e-08;1.4e-08;5.6e-08	NA;0.0015;NA;NA	0.0114653094026252	ACG	ORF1ab:nsp8	.	169-172-mnv	.	no-SNV	ORF1ab:nsp8	0.991470092670598
CAMB-76A9E	MN908947.3	13728	TG	-	0.01	0.0023	0.00045;3.5e-07	NA;0.0059	0.00730503993240112	TTG	ORF1ab:RNA-dependent-RNA-polymerase	.	261-262-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.996610076066586
CAMB-76A9E	MN908947.3	13735	C	A	0.012	0.0051	1.2e-07	5.7e-05	0.00922976394674508	ACA	ORF1ab:RNA-dependent-RNA-polymerase	H90N	C268A	CAT>AAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.990688556726293
CAMB-76A9E	MN908947.3	14805	C	T	0.98	1	0	0	0.987868016382042	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00216366586817093
CAMB-76A9E	MN908947.3	15950	T	C	0.0077	0.0073	1.3e-05	1.8e-05	0.0075685903500473	ATC	ORF1ab:RNA-dependent-RNA-polymerase	I828T	T2483C	ATC>ACC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.992363832950399
CAMB-76A9E	MN908947.3	17749	G	T	0.0077	0.0052	2.8e-05	0.00036	0.00676253205289356	TGC	ORF1ab:helicase	A505S	G1513T	GCT>TCT	Missense	ORF1ab:helicase	0.993162049374026
CAMB-76A9E	MN908947.3	23021	A	-	0.0073	0.0093	2.5e-05	4.8e-06	0.00807940904893813	TAA	S	.	1459-1459-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.991805170821791
CAMB-76A9E	MN908947.3	23021	AATTGTTACTTTCCTTTA	-	0.000417222222222222	0.00956666666666667	2.5e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	4.8e-06;1.4e-06;1.9e-06;1.3e-05;1.8e-05;1.7e-06;1.8e-06;3.5e-06;4e-06;3.1e-06;4.4e-07;1.7e-06;2.7e-06;2.1e-06;3.8e-06;1.8e-06;1.7e-06;3.1e-06	0.00352567869314843	TAA	S	.	1459-1476-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.991805170821791
CAMB-76A9E	MN908947.3	24030	TCAACAAA	-	0.0078875	0.002875	2.8e-05;3.9e-05;1.6e-05;3e-05;3e-05;5.5e-05;2.7e-06;9.1e-06	1.1e-06;1.7e-06;NA;NA;NA;NA;NA;NA	0.00504525894049562	TTC	S	.	2468-2475-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.990581332509843
CAMB-76A9E	MN908947.3	24918	AC	-	0.0073	0.006	3.9e-05;0.00011	0.00015;0.00029	0.006773122813313	AAC	S	.	3356-3357-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.992444854727432
CAMB-76A9E	MN908947.3	26144	G	T	1	1	0	9e-179	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-76A9E	MN908947.3	27134	TAAATT	-	0.0182833333333333	0.021	0.00044;0.00024;0.00074;0.00034;0.00063;0.03	0.00035;0.00021;0.00061;0.00035;0.00064;2.9e-05	0.0205133545061696	ATA	M	.	612-617-delinframe	.	no-SNV	GU280_gp05	0.980481296634877
CAMB-76A9E	MN908947.3	27386	AAACGAACATG	-	0.000518181818181818	0.00983636363636364	0.00029;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	4.5e-06;7e-07;1.1e-06;1.1e-06;1.2e-06;1.4e-06;1e-06;1e-06;1.1e-06;5.7e-05;2.1e-05	0.00382157815891651	TAA	ORF6	.	185-186-delfrshift	.	no-SNV	GU280_gp06	0.992649060713313
CAMB-76A9E	MN908947.3	28842	G	T	0.99	1	0	0	0.995540276874477	AGT	N	S190I	G569T	AGT>ATT	Missense	GU280_gp10	0.00185821796896776
CAMB-76A9E	MN908947.3	522	T	-	0.042	0.059	1.6e-05	6.5e-08	0.0470741847919458	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.952650929457444
CAMB-76A9E	MN908947.3	522	TT	-	0.0405	0.03365	1.6e-05;1e-05	6.5e-08;0.17	0.0382426360459311	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.952650929457444
CAMB-76A9E	MN908947.3	527	C	T	0.027	0.029	1.3e-13	2.2e-14	0.0278068340306834	GCT	ORF1ab:leader-protein	L88L	C262T	CTG>TTG	Synonymous	ORF1ab:leader-protein	0.972193165969317
CAMB-76A9E	MN908947.3	683	C	T	0.011	0.0071	2e-06	9.2e-05	0.00956781597649481	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.989590919364155
CAMB-76AAD	MN908947.3	11075	T	-	0.041	0.038	2.2e-10	4.9e-10	0.0397559735638027	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956002614568959
CAMB-76AAD	MN908947.3	1185	C	T	1	1	0	0	0.999586044740284	GCG	ORF1ab:nsp2	A127V	C380T	GCG>GTG	Missense	ORF1ab:nsp2	0.000149023893497591
CAMB-76AAD	MN908947.3	14408	C	T	1	1	0	0	0.998764669549104	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00039076779569147
CAMB-76AAD	MN908947.3	15720	C	T	1	1	0	0	0.999532085561497	ACG	ORF1ab:RNA-dependent-RNA-polymerase	D751D	C2253T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000167112299465241
CAMB-76AAD	MN908947.3	16289	C	T	1	1	0	0	0.999711339124045	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	7.87256934421497e-05
CAMB-76AAD	MN908947.3	23403	A	G	1	1	0	0	0.999430199430199	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.74833808167141e-05
CAMB-76AAD	MN908947.3	241	C	T	1	1	0	0	0.998620575037394	TCG	NA	NA	NA	NA	NA	NA	8.30978893136114e-05
CAMB-76AAD	MN908947.3	25429	G	T	1	1	0	0	0.998977156495056	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0.000102284350494374
CAMB-76AAD	MN908947.3	3037	C	T	1	1	0	0	0.99914322855117	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.90876861262113e-05
CAMB-76AAD	MN908947.3	4686	C	T	0.015	0.015	2.3e-08	3e-08	0.0149749808247197	ACA	ORF1ab:nsp3	T656I	C1967T	ACA>ATA	Missense	ORF1ab:nsp3	0.98495197048833
CAMB-76ABC	MN908947.3	11074	C	INS	0.11	0.11	9.2e-33	2e-29	0.108306355775929	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.887431873130353
CAMB-76ABC	MN908947.3	11083	G	-	0.16	0.15	3.3e-72	1e-64	0.15756372062231	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.00077237117952113
CAMB-76ABC	MN908947.3	11083	G	T	0.84	0.85	0	0	0.841590349038214	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.00077237117952113
CAMB-76ABC	MN908947.3	14805	C	T	1	1	0	0	0.998421392978052	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00133135531971547
CAMB-76ABC	MN908947.3	26144	G	T	1	1	0	0	0.998079812990483	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.0018367006177993
CAMB-76ABC	MN908947.3	26256	C	T	0.012	0.011	5.4e-07	1.4e-06	0.0113701839972343	TCG	E	F4F	C12T	TTC>TTT	Synonymous	GU280_gp04	0.988610609610879
CAMB-76ABC	MN908947.3	26793	A	G	0.014	0.017	8.1e-08	3.7e-09	0.0147725307040304	GAT	M	M91V	A271G	ATG>GTG	Missense	GU280_gp05	0.983532260854523
CAMB-76ABC	MN908947.3	28842	G	T	1	1	0	0	0.996521273748997	AGT	N	S190I	G569T	AGT>ATT	Missense	GU280_gp10	0.00303273570600303
CAMB-76ABC	MN908947.3	29642	C	T	0.58	0.57	0	3.19999994771109e-317	0.574114000808516	ACA	ORF10	Q29*	C85T	CAA>TAA	Nonsense	GU280_gp11	0.425414364640884
CAMB-76ACB	MN908947.3	11075	T	-	0.0049	0.62	0.01	3e-217	0.322054103622192	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.677945896377808
CAMB-76ACB	MN908947.3	14408	C	T	1	1	0	0	0.999725450718404	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000183032854397364
CAMB-76ACB	MN908947.3	23403	A	G	1	1	0	0	0.999874204342466	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000125795657533902
CAMB-76ACB	MN908947.3	241	C	T	1	1	0	0	0.999613003095975	TCG	NA	NA	NA	NA	NA	NA	0.000128998968008256
CAMB-76ACB	MN908947.3	26782	TTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGT	-	0.0584166666666667	0.0614041666666667	1.5e-11;1.8e-11;1.3e-10;8.4e-13;7.2e-12;2.4e-10;2.1e-10;7.4e-12;8.1e-11;5.7e-11;1.8e-10;1.2e-10;1.7e-10;3.8e-10;1e-10;3.2e-10;1e-10;1.6e-10;8.4e-11;3.9e-10;1.2e-10;1.9e-10;1.3e-10;4.8e-11;2.7e-10;9e-11;3.8e-11;1.6e-10;2.9e-10;2.2e-10;1.4e-10;2.9e-10;1.1e-11;7.6e-11;6.5e-11;6.1e-08;9.8e-07;2e-07;4.3e-07;7.8e-09;2.3e-09;3.1e-09;9.3e-09;9.1e-09;9.7e-09;7.6e-09;2.4e-09;4.7e-12	1.4e-16;1.6e-16;3.1e-15;7e-19;3.8e-17;6.3e-15;5.9e-15;1.3e-15;1.2e-15;1.1e-15;4.9e-15;2.5e-15;3.5e-15;1e-14;1.6e-15;7.9e-15;3e-15;2.7e-15;2e-15;8.6e-15;2.6e-15;5.7e-15;2.6e-15;7.4e-16;5.9e-15;2.1e-15;5.3e-17;3.3e-15;7.6e-15;6.7e-15;7.5e-16;7.3e-15;1.2e-16;2.3e-15;5.3e-16;4.9e-11;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0663252963470688	CTT	M	.	260-307-delinframe	.	no-SNV	GU280_gp05	0.929228652506664
CAMB-76ACB	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-76ACB	MN908947.3	29409	C	T	0.0081	0.028	0.0098	1.3e-06	0.0192982456140351	ACT	N	T379I	C1136T	ACT>ATT	Missense	GU280_gp10	0.980701754385965
CAMB-76ACB	MN908947.3	3037	C	T	0.97	1	0	0	0.982253771073647	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76ADA	MN908947.3	11075	T	-	0.049	0.051	1.8e-12	2.9e-13	0.0497303774715398	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.944980475610008
CAMB-76ADA	MN908947.3	14408	C	T	1	1	0	0	0.998286989084535	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000338618436777946
CAMB-76ADA	MN908947.3	15438	G	T	1	1	0	0	0.99967902423367	TGG	ORF1ab:RNA-dependent-RNA-polymerase	M657I	G1971T	ATG>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000160487883164821
CAMB-76ADA	MN908947.3	23403	A	G	1	1	0	0	0.998801394167836	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.73133881117227e-05
CAMB-76ADA	MN908947.3	24026	C	T	0.0033	0.0071	0.0022	4e-05	0.00464482253748675	ACT	S	L822F	C2464T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.99429494623113
CAMB-76ADA	MN908947.3	241	C	T	1	0.99	0	0	0.994960938821063	TCG	NA	NA	NA	NA	NA	NA	0.000101457607629612
CAMB-76ADA	MN908947.3	26542	C	T	0.01	0.006	2.4e-06	2e-04	0.0085573476702509	ACT	M	T7I	C20T	ACT>ATT	Missense	GU280_gp05	0.991039426523297
CAMB-76ADA	MN908947.3	3037	C	T	1	1	0	0	0.998737904922171	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.01163932127331e-05
CAMB-76ADA	MN908947.3	3215	A	G	1	1	0	0	0.996751289436667	TAG	ORF1ab:nsp3	S166G	A496G	AGT>GGT	Missense	ORF1ab:nsp3	6.69837229553219e-05
CAMB-76ADA	MN908947.3	7119	C	T	0.029	0.013	1.8e-05	0.00045	0.0181818181818182	TCT	ORF1ab:nsp3	S1467F	C4400T	TCT>TTT	Missense	ORF1ab:nsp3	0.981818181818182
CAMB-76AE9	MN908947.3	11075	T	-	0.045	0.041	1.4e-11	3.8e-11	0.043470442796134	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952416273319847
CAMB-76AE9	MN908947.3	13813	G	T	0.028	0.029	1.5e-13	2.1e-14	0.0281454576777306	GGC	ORF1ab:RNA-dependent-RNA-polymerase	A116S	G346T	GCA>TCA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.971359251177214
CAMB-76AE9	MN908947.3	14408	C	T	1	1	0	0	0.997442374982348	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000517801383941881
CAMB-76AE9	MN908947.3	16912	G	T	0.025	0.022	2e-12	2.9e-11	0.0235096557514694	TGT	ORF1ab:helicase	V226L	G676T	GTG>TTG	Missense	ORF1ab:helicase	0.976130502578865
CAMB-76AE9	MN908947.3	20268	A	G	1	1	0	0	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-76AE9	MN908947.3	21600	G	T	0.029	0.031	2.2e-13	3.5e-14	0.0300807823129252	AGT	S	S13I	G38T	AGT>ATT	Missense	GU280_gp02, spike glycoprotein	0.969812925170068
CAMB-76AE9	MN908947.3	21608	G	T	0.014	0.017	1.1e-07	6.7e-09	0.0156014633096621	TGT	S	V16F	G46T	GTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.984398536690338
CAMB-76AE9	MN908947.3	21748	TACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGG	-	0.0667435897435898	0.0761538461538462	1.4e-11;5.8e-12;3.1e-11;2.1e-11;2.9e-12;3.4e-12;4.1e-12;5.9e-12;6.7e-12;4.2e-12;2.2e-12;5.2e-12;1.9e-12;3.7e-12;2.8e-12;3.6e-13;6.7e-14;1.3e-11;6.5e-13;5e-12;7.1e-12;2.8e-12;5.4e-13;3.7e-13;2.7e-13;2.5e-12;5.2e-12;3.5e-12;4.6e-13;3.5e-12;5.2e-12;5.2e-12;1.5e-28;7.2e-30;1.9e-28;4.2e-29;9.6e-30;1.7e-29;2.8e-29	3.6e-13;1.2e-13;1.2e-12;5.8e-13;7.4e-14;8.2e-14;8.1e-14;1.1e-13;1.7e-13;1.2e-13;6.5e-14;9.8e-14;4.9e-14;8.4e-14;7.8e-14;4.3e-15;5.6e-16;4.7e-13;9.3e-15;9.2e-14;1.5e-13;1e-13;2.1e-14;6.1e-15;3.4e-15;3.8e-14;7.6e-14;7.7e-14;5.6e-15;5.9e-14;1.1e-13;1e-13;2e-32;8e-34;4.1e-32;6.3e-33;5.6e-33;7.4e-33;1.4e-33	0.071161460624725	TTA	S	.	186-224-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.924933286924237
CAMB-76AE9	MN908947.3	21867	G	T	0.0084	0.0059	8.7e-06	8.3e-05	0.00710984713828653	AGA	S	R102I	G305T	AGA>ATA	Missense	GU280_gp02, spike glycoprotein	0.992890152861713
CAMB-76AE9	MN908947.3	21991	TTA	-	0.0676666666666667	0.0863333333333333	5.8e-05;2.3e-07;2.4e-07	7.8e-06;4.4e-09;4.6e-09	0.0755645763344532	TTT	S	.	429-431-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.92314865737309
CAMB-76AE9	MN908947.3	22016	T	C	0.7	0.7	0	0	0.697857017829012	TTG	S	W152R	T454C	TGG>CGG	Missense	GU280_gp02, spike glycoprotein	0.301842914655798
CAMB-76AE9	MN908947.3	22022	G	A	0.0084	0.0086	1.4e-05	9.9e-06	0.00851324828263003	GGA	S	E154K	G460A	GAA>AAA	Missense	GU280_gp02, spike glycoprotein	0.991192345436703
CAMB-76AE9	MN908947.3	22026	G	T	0.019	0.022	6e-10	3.7e-11	0.0203711865236766	AGT	S	S155I	G464T	AGT>ATT	Missense	GU280_gp02, spike glycoprotein	0.978967729298271
CAMB-76AE9	MN908947.3	22319	G	T	0.011	0.012	1.3e-06	2.1e-07	0.0112150758602597	TGA	S	D253Y	G757T	GAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.988653753661842
CAMB-76AE9	MN908947.3	22326	C	T	0.073	0.073	2.3e-27	9.5e-27	0.0733176224142446	TCT	S	S255F	C764T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.926420528934276
CAMB-76AE9	MN908947.3	22335	G	T	0.15	0.14	2.8e-54	7.5e-51	0.144054478784704	TGG	S	W258L	G773T	TGG>TTG	Missense	GU280_gp02, spike glycoprotein	0.855945521215296
CAMB-76AE9	MN908947.3	23403	A	G	1	1	0	0	0.999476670195178	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.37877184009896e-05
CAMB-76AE9	MN908947.3	241	C	T	1	1	0	0	0.998998038714079	TCG	NA	NA	NA	NA	NA	NA	8.5273300929479e-05
CAMB-76AE9	MN908947.3	25590	A	T	0.0081	0.0076	1.4e-05	1.2e-05	0.00789726356216995	AAA	ORF3a	K66N	A198T	AAA>AAT	Missense	GU280_gp03	0.991958713394143
CAMB-76AE9	MN908947.3	27145	C	T	0.025	0.026	1.9e-12	3.9e-13	0.0255543324422079	ACA	M	T208I	C623T	ACA>ATA	Missense	GU280_gp05	0.974367038842585
CAMB-76AE9	MN908947.3	27784	A	G	0.013	0.024	9.5e-06	8.2e-09	0.0187927107061503	TAT	NA	NA	NA	NA	NA	NA	0.98120728929385
CAMB-76AE9	MN908947.3	27797	A	G	0.014	0.02	6.8e-06	6.8e-08	0.0172117039586919	TAG	NA	NA	NA	NA	NA	NA	0.982788296041308
CAMB-76AE9	MN908947.3	28655	G	T	0.76	0.77	0	0	0.76617033948779	AGA	N	D128Y	G382T	GAC>TAC	Missense	GU280_gp10	0.233710541989279
CAMB-76AE9	MN908947.3	28812	G	C	0.61	0.6	0	0	0.608220415537489	AGT	N	S180T	G539C	AGT>ACT	Missense	GU280_gp10	0.391102077687444
CAMB-76AE9	MN908947.3	29311	C	T	0.078	0.083	1.6e-35	9.2e-38	0.0798766095674324	TCA	N	F346F	C1038T	TTC>TTT	Synonymous	GU280_gp10	0.919562524829988
CAMB-76AE9	MN908947.3	2937	C	T	1	1	0	0	0.999759665935651	ACA	ORF1ab:nsp3	T73I	C218T	ACA>ATA	Missense	ORF1ab:nsp3	0.000210292306305765
CAMB-76AE9	MN908947.3	3037	C	T	1	1	0	0	0.999081195126931	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000102089430340979
CAMB-76AE9	MN908947.3	3743	C	T	0.83	0.82	0	0	0.82560522121879	ACA	ORF1ab:nsp3	H342Y	C1024T	CAT>TAT	Missense	ORF1ab:nsp3	0.173711770509221
CAMB-76AE9	MN908947.3	3838	G	T	0.076	0.079	3.8e-34	4.6e-35	0.0770075908909309	TGG	ORF1ab:nsp3	L373F	G1119T	TTG>TTT	Missense	ORF1ab:nsp3	0.922542948461846
CAMB-76AE9	MN908947.3	4300	G	T	0.028	0.027	8.2e-14	8.3e-14	0.0276186790505676	TGC	ORF1ab:nsp3	V527V	G1581T	GTG>GTT	Synonymous	ORF1ab:nsp3	0.972278121775026
CAMB-76AE9	MN908947.3	6533	G	T	0.0093	0.0092	8.6e-06	8.2e-06	0.00925435002650986	GGT	ORF1ab:nsp3	V1272F	G3814T	GTT>TTT	Missense	ORF1ab:nsp3	0.990649250494047
CAMB-76AE9	MN908947.3	9802	G	T	0.048	0.045	1.3e-22	1.5e-21	0.0464474845542807	CGC	ORF1ab:nsp4	A416A	G1248T	GCG>GCT	Synonymous	ORF1ab:nsp4	0.953063926364897
CAMB-76AF8	MN908947.3	10186	C	T	0.87	0.54	0	2.9e-292	0.712594541269319	GCA	ORF1ab:3C-like-proteinase	C44C	C132T	TGC>TGT	Synonymous	ORF1ab:3C-like-proteinase	0.287405458730681
CAMB-76AF8	MN908947.3	11074	C	INS	0.044	0.033	2.5e-10	6.9e-07	0.0428845232390992	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.957115476760901
CAMB-76AF8	MN908947.3	11083	G	-	0.022	0.047	2e-09	6.2e-16	0.0253560965754117	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.232952823517527
CAMB-76AF8	MN908947.3	11083	G	T	0.71	0.95	7.2e-250	0	0.741691079907061	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.232952823517527
CAMB-76AF8	MN908947.3	13914	T	G	0.0026	0.0091	0.0011	4.5e-06	0.00481822163819536	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994962768287341
CAMB-76AF8	MN908947.3	14805	C	T	0.65	1	0	0	0.807825700311249	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.192085371276123
CAMB-76AF8	MN908947.3	28857	G	T	0.4	1	4.1e-135	2.4e-246	0.529	AGA	N	R195I	G584T	AGA>ATA	Missense	GU280_gp10	0.471
CAMB-76AF8	MN908947.3	29068	TAAAGCATACAATG	-	0.0279285714285714	0.00621428571428571	7.2e-09;2.3e-08;6.7e-06;6.4e-06;4.2e-06;6.5e-06;7.9e-06;2.3e-05;1.2e-05;6e-06;1.2e-05;2.3e-06;5.7e-06;6e-06	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;1.1e-10;NA;NA;NA	0.0231716147719044	CTA	N	.	795-808-delfrshift	.	no-SNV	GU280_gp10	0.976693372177713
CAMB-76AF8	MN908947.3	3931	T	C	0.45	1	7.2e-158	1e-82	0.475663716814159	TTG	ORF1ab:nsp3	V404V	T1212C	GTT>GTC	Synonymous	ORF1ab:nsp3	0.524336283185841
CAMB-76B04	MN908947.3	11074	C	INS	0.025	0.02	4.1e-05	0.0011	0.0233823993096467	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.975256808111651
CAMB-76B04	MN908947.3	11075	T	-	0.038	0.037	1e-09	8.1e-10	0.0377681785457163	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958027357811375
CAMB-76B04	MN908947.3	11083	G	T	0.034	0.035	1.9e-07	1e-07	0.0343494020606787	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.957530610497474
CAMB-76B04	MN908947.3	11322	C	T	0.046	0.044	1.6e-21	5.2e-21	0.0449584406617628	GCA	ORF1ab:nsp6	A117V	C350T	GCA>GTA	Missense	ORF1ab:nsp6	0.954988448362854
CAMB-76B04	MN908947.3	11812	C	T	0.033	0.018	4.2e-13	4.8e-08	0.0261829652996845	GCA	ORF1ab:nsp6	G280G	C840T	GGC>GGT	Synonymous	ORF1ab:nsp6	0.973501577287066
CAMB-76B04	MN908947.3	1346	C	T	1	1	0	0	0.999361770024465	ACC	ORF1ab:nsp2	P181S	C541T	CCC>TCC	Missense	ORF1ab:nsp2	0.000425486650356345
CAMB-76B04	MN908947.3	14408	C	T	1	1	0	0	0.997529787852368	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000343451956355182
CAMB-76B04	MN908947.3	16375	C	T	0.025	0.024	6.2e-10	7.8e-10	0.0243585142652072	TCC	ORF1ab:helicase	P47S	C139T	CCG>TCG	Missense	ORF1ab:helicase	0.975641485734793
CAMB-76B04	MN908947.3	2325	C	T	0.087	0.087	2.4e-37	4.6e-37	0.0868725868725869	GCT	ORF1ab:nsp2	A507V	C1520T	GCT>GTT	Missense	ORF1ab:nsp2	0.912951912951913
CAMB-76B04	MN908947.3	23277	C	T	0.035	0.035	1.1e-16	7.9e-17	0.0346828172406605	ACT	S	T572I	C1715T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.964471825277347
CAMB-76B04	MN908947.3	23403	A	G	1	1	0	0	0.999010444116983	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000225876886340902
CAMB-76B04	MN908947.3	241	C	T	1	1	0	0	0.998040775154701	TCG	NA	NA	NA	NA	NA	NA	0.000271575721130531
CAMB-76B04	MN908947.3	26108	A	G	0.014	0.018	1.2e-07	4.2e-09	0.0153526970954357	GAG	ORF3a	E239G	A716G	GAG>GGG	Missense	GU280_gp03	0.984647302904564
CAMB-76B04	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0281891891891892	0.0302702702702703	0.0027;0.00019;0.001;0.00091;0.0017;0.00011;0.00036;0.00011;0.00011;1.7e-05;6.4e-05;5.4e-05;9.5e-05;7.2e-05;8e-05;0.00013;6.1e-05;0.00011;6.9e-05;8e-05;6.7e-05;0.00013;6.3e-05;9.2e-05;7.6e-05;6.1e-05;0.00011;6.3e-05;1.8e-05;8.5e-05;0.00011;9.7e-05;6.8e-05;0.00012;3.7e-05;6.9e-05;6.2e-05	0.00044;5.7e-05;0.00029;0.00021;0.00039;1.5e-05;6.4e-05;4.1e-05;4.1e-05;1.8e-05;2.3e-05;2.2e-05;3.6e-05;2.8e-05;2.9e-05;4.9e-05;2.1e-05;4.2e-05;2.8e-05;2.7e-05;3.2e-05;4.7e-05;2.9e-05;3.6e-05;2.8e-05;2.2e-05;4e-05;2.6e-05;1.2e-05;2.7e-05;4.1e-05;4e-05;2.2e-05;4.1e-05;1.2e-05;2.7e-05;2.1e-05	0.0295632900017972	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.979472622693658
CAMB-76B04	MN908947.3	28514	G	T	1	1	0	0	0.997984726347051	AGA	N	D81Y	G241T	GAT>TAT	Missense	GU280_gp10	0.000106067034365719
CAMB-76B04	MN908947.3	3037	C	T	1	1	0	0	0.998885644020904	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000307408545957578
CAMB-76B04	MN908947.3	4099	C	T	0.01	0.0095	1.7e-06	2.4e-06	0.00992609270226616	TCT	ORF1ab:nsp3	F460F	C1380T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.990054329205619
CAMB-76B04	MN908947.3	522	TT	-	0.0375	0.0345	1.5e-05;0.00018	2e-05;0.00046	0.0362357180649497	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.95673069813525
CAMB-76B04	MN908947.3	7387	G	T	0.034	0.036	3.2e-16	3.1e-17	0.034666395305451	TGG	ORF1ab:nsp3	M1556I	G4668T	ATG>ATT	Missense	ORF1ab:nsp3	0.96475696211119
CAMB-76B13	MN908947.3	11919	C	T	1	1	0	0	0.999832971438116	TCT	ORF1ab:nsp7	S26F	C77T	TCT>TTT	Missense	ORF1ab:nsp7	5.56761872946941e-05
CAMB-76B13	MN908947.3	14408	C	T	1	1	0	0	0.999357876712329	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000642123287671233
CAMB-76B13	MN908947.3	23403	A	G	1	1	0	0	0.999750137424417	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000199890060466743
CAMB-76B13	MN908947.3	241	C	T	1	1	0	0	0.999561082662765	TCG	NA	NA	NA	NA	NA	NA	0.000292611558156547
CAMB-76B13	MN908947.3	28881	GGG	AAC	1	1	1.99999996731943e-317;0;0	3.3e-306;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-76B13	MN908947.3	3037	C	T	1	1	1.7e-302	8.19999999999999e-300	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76B22	MN908947.3	11075	T	-	0.04	0.035	1.8e-10	1.1e-09	0.0382446927601718	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957236775152144
CAMB-76B22	MN908947.3	14408	C	T	1	1	0	0	0.998085876036141	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000421756127629893
CAMB-76B22	MN908947.3	16289	C	T	1	1	0	0	0.999331941544885	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0.000125260960334029
CAMB-76B22	MN908947.3	16607	A	G	0.025	0.047	2.2e-08	2.6e-12	0.0349740932642487	AAC	ORF1ab:helicase	N124S	A371G	AAC>AGC	Missense	ORF1ab:helicase	0.965025906735751
CAMB-76B22	MN908947.3	17497	T	C	0.013	0.012	1.1e-07	2.6e-07	0.0121809475103445	ATA	ORF1ab:helicase	Y421H	T1261C	TAT>CAT	Missense	ORF1ab:helicase	0.987447115161095
CAMB-76B22	MN908947.3	19170	C	T	0.0074	0.0083	2.4e-05	7.5e-06	0.00774785890550152	TCA	ORF1ab:3'-to-5'-exonuclease	F377F	C1131T	TTC>TTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.992088837276818
CAMB-76B22	MN908947.3	21762	C	T	0.0083	0.0084	1.3e-05	1.1e-05	0.00838425465397186	GCT	S	A67V	C200T	GCT>GTT	Missense	GU280_gp02, spike glycoprotein	0.989863104542655
CAMB-76B22	MN908947.3	23403	A	G	1	1	0	0	0.999454694174316	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.79008322405578e-05
CAMB-76B22	MN908947.3	241	C	T	1	1	0	0	0.999009031328123	TCG	NA	NA	NA	NA	NA	NA	0.000135132091619558
CAMB-76B22	MN908947.3	2485	C	T	0.0071	0.0086	7.5e-05	1.9e-05	0.00784769655573318	TCT	ORF1ab:nsp2	I560I	C1680T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.992006975730272
CAMB-76B22	MN908947.3	25201	A	G	0.017	0.0098	1.8e-08	7.9e-06	0.0135410599883518	CAT	S	P1213P	A3639G	CCA>CCG	Synonymous	GU280_gp02, spike glycoprotein	0.98573092603378
CAMB-76B22	MN908947.3	25429	G	T	1	1	0	0	0.998868633394527	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0.000106732698629552
CAMB-76B22	MN908947.3	29755	G	T	0.021	0.024	1.4e-10	6.1e-12	0.0227452105905145	CGA	NA	NA	NA	NA	NA	NA	0.976609026332783
CAMB-76B22	MN908947.3	3037	C	T	1	1	0	0	0.999096908648836	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000138937130948246
CAMB-76B22	MN908947.3	6317	C	T	0.016	0.017	4.4e-09	1.6e-09	0.0164009930464283	ACC	ORF1ab:nsp3	P1200S	C3598T	CCA>TCA	Missense	ORF1ab:nsp3	0.983441737157236
CAMB-76B22	MN908947.3	673	C	T	0.023	0.022	9.2e-12	2.8e-11	0.0225200049075071	ACG	ORF1ab:leader-protein	Y136Y	C408T	TAC>TAT	Synonymous	ORF1ab:leader-protein	0.977036956255027
CAMB-76B31	MN908947.3	10712	C	A	0.076	0.077	1.2e-34	3.8e-35	0.0761056159568381	TCT	ORF1ab:3C-like-proteinase	L220I	C658A	CTC>ATC	Missense	ORF1ab:3C-like-proteinase	0.923698193411265
CAMB-76B31	MN908947.3	11074	C	INS	0.11	0.11	1.7e-43	2.3e-34	0.111641037330575	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.882958391050481
CAMB-76B31	MN908947.3	11083	G	-	0.17	0.16	1.5e-73	2.1e-71	0.164044761595848	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.012017515407071
CAMB-76B31	MN908947.3	11083	G	T	0.82	0.84	0	0	0.823710671423938	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.012017515407071
CAMB-76B31	MN908947.3	1346	C	T	0.97	1	0	0	0.982495599452376	ACC	ORF1ab:nsp2	P181S	C541T	CCC>TCC	Missense	ORF1ab:nsp2	0.0170154508116566
CAMB-76B31	MN908947.3	13627	G	T	0.99	1	0	0	0.995790733145416	TGA	ORF1ab:RNA-dependent-RNA-polymerase	D54Y	G160T	GAC>TAC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00398829381868354
CAMB-76B31	MN908947.3	14805	C	T	1	1	0	0	0.998500490989676	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000544069640914037
CAMB-76B31	MN908947.3	15540	C	T	1	1	0	0	0.999558041102177	TCA	ORF1ab:RNA-dependent-RNA-polymerase	V691V	C2073T	GTC>GTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000101990514882116
CAMB-76B31	MN908947.3	21137	A	G	0.017	0.018	7.3e-08	2.8e-08	0.0176926533363289	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.982166928780049
CAMB-76B31	MN908947.3	21569	G	INS	0.053	0.045	4.3e-22	1.4e-18	0.0498115873763542	TGT	S	.	6-7-insfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.948068770607631
CAMB-76B31	MN908947.3	21575	C	-	0.017	0.018	1.1e-08	5.5e-09	0.0178200903210057	TCT	S	.	13-13-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.00390577322104235
CAMB-76B31	MN908947.3	21575	C	T	0.98	0.98	0	0	0.978152081044794	TCT	S	L5F	C13T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.00390577322104235
CAMB-76B31	MN908947.3	22225	G	T	0.98	1	0	0	0.988634236354398	CGG	S	S221S	G663T	TCG>TCT	Synonymous	GU280_gp02, spike glycoprotein	0.011151819859332
CAMB-76B31	MN908947.3	24026	C	T	0.13	0.13	9.4e-58	9.5e-62	0.129854954186297	ACT	S	L822F	C2464T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.860982305152651
CAMB-76B31	MN908947.3	26144	G	T	1	1	0	0	0.999544257646344	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000303828235770711
CAMB-76B31	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.02696875	0.0288125	0.00023;0.00052;0.00028;0.00029;5.6e-05;0.00017;0.00015;0.00024;0.00017;0.00019;0.00029;0.00015;0.00025;0.00017;0.00019;0.00019;3e-04;0.00019;0.00023;0.00019;0.00017;0.00027;0.00016;0.00011;0.00019;0.00027;0.00024;0.00019;0.00026;9.3e-05;0.00015;0.00016	0.00011;0.00036;9.7e-05;9.4e-05;5.3e-05;5.6e-05;4.4e-05;8.6e-05;6.7e-05;7.2e-05;0.00011;5.7e-05;1e-04;7.2e-05;6.5e-05;6.8e-05;0.00011;7.5e-05;8.5e-05;6.3e-05;5.5e-05;9.1e-05;6.6e-05;1.3e-05;7e-05;1e-04;9.9e-05;4.8e-05;1e-04;3.7e-05;7.5e-05;4.2e-05	0.0272419378589309	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.972654773979277
CAMB-76B31	MN908947.3	28338	A	G	0.98	1	0	0	0.98720228111372	GAT	N	D22G	A65G	GAT>GGT	Missense	GU280_gp10	0.0124119423012412
CAMB-76B31	MN908947.3	29274	C	T	0.0096	0.011	1.2e-05	1.9e-06	0.0100986219940557	ACA	N	T334I	C1001T	ACA>ATA	Missense	GU280_gp10	0.989715617400702
CAMB-76B31	MN908947.3	29350	A	G	0.0053	0.0061	0.00018	4.8e-05	0.0055336461272271	CAT	N	A359A	A1077G	GCA>GCG	Synonymous	GU280_gp10	0.994341651988216
CAMB-76B31	MN908947.3	29585	C	T	0.049	0.048	5.8e-22	9.2e-22	0.0484906228061378	TCC	ORF10	P10S	C28T	CCG>TCG	Missense	GU280_gp11	0.95130879550697
CAMB-76B31	MN908947.3	29728	TTCACCGAGGCCACGCGGAGTACGATCGAGTGTACAGTGAACAATGCTA	-	0.0151428571428571	0.0124897959183673	1.1e-07;2.6e-07;2.8e-07;5.1e-08;2.5e-07;2.4e-07;3.5e-07;2.1e-07;3.1e-07;2.3e-07;2.5e-07;3e-07;1e-07;4.6e-07;6.8e-07;4.4e-07;6e-07;7.2e-07;6.2e-07;2.1e-06;7.4e-06;7.2e-06;4.1e-05;4.5e-05;9.5e-06;8.1e-06;7.3e-06;8.7e-06;4.2e-06;2.2e-05;9e-06;1.6e-05;2.5e-07;4.3e-07;5.1e-07;3.3e-07;3.4e-07;3.5e-07;2.7e-07;3.4e-07;6.3e-07;6.1e-07;1.4e-07;6.5e-08;2.5e-07;3e-07;2.2e-07;1.4e-07;2.3e-07	2.3e-06;3.9e-06;5.4e-06;2.2e-06;4.2e-06;4.2e-06;6.3e-06;6.3e-06;6.3e-06;8.1e-06;4.8e-06;6.1e-06;2.8e-06;5.7e-06;6.1e-06;6.1e-06;7.7e-06;9.2e-06;1.1e-05;1.4e-05;3.8e-05;3.3e-05;0.00014;0.00014;3.8e-05;3.1e-05;3.3e-05;3.7e-05;3.5e-05;5.6e-05;2.6e-05;5.9e-05;2.2e-06;4e-06;4.6e-06;5.3e-06;5.8e-06;6.1e-06;4.4e-06;4.8e-06;5.8e-06;6.4e-06;2.4e-06;1.4e-06;3.8e-06;3.4e-06;2.2e-06;2.8e-06;3.7e-06	0.013769846845581	TTT	NA	NA	NA	NA	NA	NA	0.986142322097378
CAMB-76B31	MN908947.3	4924	T	C	0.76	0.77	0	0	0.761385121555433	TTG	ORF1ab:nsp3	F735F	T2205C	TTT>TTC	Synonymous	ORF1ab:nsp3	0.238451117297643
CAMB-76B31	MN908947.3	5622	C	T	0.8	0.82	0	0	0.809027256062746	CCT	ORF1ab:nsp3	P968L	C2903T	CCT>CTT	Missense	ORF1ab:nsp3	0.190912642365598
CAMB-76B40	MN908947.3	1030	T	C	1	1	0	0	0.999978853433145	TTG	ORF1ab:nsp2	F75F	T225C	TTT>TTC	Synonymous	ORF1ab:nsp2	0
CAMB-76B40	MN908947.3	11074	C	INS	0.12	0.12	5e-44	1.1e-45	0.121396503807002	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.869904126033975
CAMB-76B40	MN908947.3	11083	G	-	0.081	0.15	6.1e-35	7e-68	0.121838615908349	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.10892104894996e-05
CAMB-76B40	MN908947.3	11083	G	T	0.92	0.85	0	0	0.878005938039203	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.10892104894996e-05
CAMB-76B40	MN908947.3	14805	C	T	1	1	0	0	0.999944724914324	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	3.68500571175885e-05
CAMB-76B40	MN908947.3	16247	C	T	0.013	0.0059	3.9e-05	0.0068	0.0079734219269103	GCT	ORF1ab:helicase	A4V	C11T	GCT>GTT	Missense	ORF1ab:helicase	0.99202657807309
CAMB-76B40	MN908947.3	17247	T	C	1	1	0	0	0.999699539293583	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000250383922013754
CAMB-76B40	MN908947.3	26144	G	T	1	0.99	4.4e-308	1.1e-296	0.996644295302013	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-76B40	MN908947.3	27945	C	T	0.96	0.93	0	0	0.941430020283976	CCA	ORF8	Q18*	C52T	CAA>TAA	Nonsense	GU280_gp09	0.0585699797160243
CAMB-76B40	MN908947.3	28373	G	-	0.014	0.0097	2.2e-07	1.1e-05	0.0115302019226612	TGG	N	.	100-100-delfrshift	.	no-SNV	GU280_gp10	0.988368908810516
CAMB-76B40	MN908947.3	28373	GG	-	0.007	0.00955	2.2e-07;NA	1.1e-05;2.5e-06	0.00824132435497997	TGG	N	.	100-101-delfrshift	.	no-SNV	GU280_gp10	0.988368908810516
CAMB-76B5F	MN908947.3	11041	A	G	0.047	0.04	8.9e-23	1.5e-19	0.0444612362097627	TAG	ORF1ab:nsp6	L23L	A69G	TTA>TTG	Synonymous	ORF1ab:nsp6	0.955478313435091
CAMB-76B5F	MN908947.3	11075	T	-	0.061	0.0055	1.2e-15	0.0071	0.0428098469203789	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956403448388894
CAMB-76B5F	MN908947.3	1440	G	A	0.34	1	2.7e-111	0	0.53537936913896	GGC	ORF1ab:nsp2	G212D	G635A	GGC>GAC	Missense	ORF1ab:nsp2	0.46462063086104
CAMB-76B5F	MN908947.3	16114	C	T	0.1	0.11	5.7e-47	3e-48	0.10352819984548	ACA	ORF1ab:RNA-dependent-RNA-polymerase	H883Y	C2647T	CAT>TAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.896385955876041
CAMB-76B5F	MN908947.3	16438	A	G	0.037	0.065	1.6e-13	2e-19	0.0471171729696218	TAT	ORF1ab:helicase	M68V	A202G	ATG>GTG	Missense	ORF1ab:helicase	0.952882827030378
CAMB-76B5F	MN908947.3	20611	C	T	1	1	0	0	1	GCT	ORF1ab:endoRNAse	L331F	C991T	CTT>TTT	Missense	ORF1ab:endoRNAse	0
CAMB-76B5F	MN908947.3	22299	G	C	0.03	0.037	1.9e-14	4.5e-16	0.0327679259830378	AGA	S	R246T	G737C	AGA>ACA	Missense	GU280_gp02, spike glycoprotein	0.96703932151118
CAMB-76B5F	MN908947.3	27382	GATTA	-	0.058	0.057	7.1e-37;3.7e-20;1.3e-25;1.7e-20;1.6e-24	3.3e-27;6.4e-22;2e-27;5.3e-22;2e-26	0.054329864030383	TGA	ORF6	.	181-185-delfrshift	.	no-SNV	GU280_gp06	0.929241162425019
CAMB-76B5F	MN908947.3	27669	A	G	0.16	1	4e-25	8.4e-40	0.231578947368421	AAG	ORF7a	E92E	A276G	GAA>GAG	Synonymous	GU280_gp07	0.768421052631579
CAMB-76B5F	MN908947.3	27873	A	INS	0.024	0.0099	8.4e-11	5.2e-06	0.0176730486008837	AAC	NA	NA	NA	NA	NA	NA	0.981958762886598
CAMB-76B5F	MN908947.3	27876	TG	GT	0.024	0.01	7.9e-11;3.2e-10	6.2e-06;2.3e-05	0.0175038051750381	TTG	NA	NA	NA	NA	NA	NA	0.982244049867775
CAMB-76B5F	MN908947.3	27880	ACG	-	0.025	0.0099	1e-10;8.3e-11;4.6e-11	1.6e-05;1.3e-05;1.5e-05	0.0180654873917953	CAC	NA	NA	NA	NA	NA	NA	0.982261640798226
CAMB-76B5F	MN908947.3	28166	G	T	0.032	0.032	6.5e-16	2.9e-16	0.0320659866269706	AGG	ORF8	Q91H	G273T	CAG>CAT	Missense	GU280_gp09	0.967909610034653
CAMB-76B5F	MN908947.3	28603	C	T	0.033	0.0099	2.4e-10	0.00036	0.0258086329313648	TCT	N	F110F	C330T	TTC>TTT	Synonymous	GU280_gp10	0.974191367068635
CAMB-76B5F	MN908947.3	2891	G	A	1	1	0	0	0.999790268456376	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	0.000209731543624161
CAMB-76B5F	MN908947.3	4665	G	A	0.79	1	0	0	0.855606123293339	AGA	ORF1ab:nsp3	R649K	G1946A	AGA>AAA	Missense	ORF1ab:nsp3	0.144393876706661
CAMB-76B6E	MN908947.3	10519	C	T	0.0039	0.0074	0.00084	2.2e-05	0.0053304492255398	ACT	ORF1ab:3C-like-proteinase	D155D	C465T	GAC>GAT	Synonymous	ORF1ab:3C-like-proteinase	0.994515044999807
CAMB-76B6E	MN908947.3	11074	C	INS	0.029	0.022	4.8e-06	0.00045	0.0257082141658811	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.973109431671114
CAMB-76B6E	MN908947.3	11075	T	-	0.028	0.028	1.4e-07	1.3e-07	0.0279454817969155	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.967403941783748
CAMB-76B6E	MN908947.3	14408	C	T	1	1	0	0	0.997834214570049	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000520272477585936
CAMB-76B6E	MN908947.3	23403	A	G	1	1	0	0	0.999354200302068	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.16644966408e-05
CAMB-76B6E	MN908947.3	241	C	T	1	1	0	0	0.999433287287925	TCG	NA	NA	NA	NA	NA	NA	0.000177097722523288
CAMB-76B6E	MN908947.3	25563	G	T	1	1	0	0	0.999763078089462	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	6.31791761435431e-05
CAMB-76B6E	MN908947.3	27128	C	T	0.46	0.45	3.4e-251	4.7e-244	0.453948320263897	GCA	M	G202G	C606T	GGC>GGT	Synonymous	GU280_gp05	0.546022743713649
CAMB-76B6E	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999484004127967	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000141817150420724
CAMB-76B6E	MN908947.3	3037	C	T	1	1	0	0	0.999479458636983	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.00416433090414e-05
CAMB-76B7D	MN908947.3	14408	C	T	1	1	0	0	0.999462018506563	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00035865432895775
CAMB-76B7D	MN908947.3	23403	A	G	1	1	0	0	0.999877750611247	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.07497962510187e-05
CAMB-76B7D	MN908947.3	241	C	T	1	1	0	0	1	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-76B7D	MN908947.3	25429	G	T	1	1	0	0	0.999773465226912	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0
CAMB-76B7D	MN908947.3	3037	C	T	1	1	2.7e-260	1.1e-291	0.999072356215213	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76B7D	MN908947.3	4527	GATTTTACTT	-	0.015	0.0908	NA;NA;NA;NA;NA;NA;NA;NA;1.9e-18;NA	6.6e-20;8.6e-20;1.2e-14;7.4e-12;2.4e-11;4e-10;7.6e-10;5.5e-10;2.7e-11;2.6e-11	0.0478539713862852	AGA	ORF1ab:nsp3	.	1808-1817-delfrshift	.	no-SNV	ORF1ab:nsp3	0.951741293532338
CAMB-76B8C	MN908947.3	1060	C	G	0.019	0.02	7.5e-10	1.7e-10	0.0193954475591012	CCT	ORF1ab:nsp2	T85T	C255G	ACC>ACG	Synonymous	ORF1ab:nsp2	0.980458171704604
CAMB-76B8C	MN908947.3	11075	T	-	0.038	0.042	4.4e-10	3e-11	0.0398908523908524	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955994455994456
CAMB-76B8C	MN908947.3	14408	C	T	1	1	0	0	0.997573662896243	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000541125541125541
CAMB-76B8C	MN908947.3	20766	A	G	0.015	0.016	1.2e-08	4.7e-09	0.0157749405364027	TAC	ORF1ab:2'-O-ribose-methyltransferase	L36L	A108G	TTA>TTG	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.984170380293627
CAMB-76B8C	MN908947.3	21823	T	A	0.022	0.02	4.8e-11	2.7e-10	0.0212187996514787	ATG	S	N87K	T261A	AAT>AAA	Missense	GU280_gp02, spike glycoprotein	0.978524934652247
CAMB-76B8C	MN908947.3	23403	A	G	1	1	0	0	0.998778559214164	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000115715442868714
CAMB-76B8C	MN908947.3	241	C	T	1	1	0	0	0.998534286422982	TCG	NA	NA	NA	NA	NA	NA	9.01977585856991e-05
CAMB-76B8C	MN908947.3	28310	C	T	0.01	0.0096	2.5e-06	3.3e-06	0.00984315846403461	ACC	N	P13S	C37T	CCC>TCC	Missense	GU280_gp10	0.989850369569137
CAMB-76B8C	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998788911814838	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	9.87800661826443e-05
CAMB-76B8C	MN908947.3	3037	C	T	1	1	0	0	0.999221104676758	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.77300281079617e-05
CAMB-76B8C	MN908947.3	5869	C	T	0.058	0.052	9.9e-27	4.1e-24	0.055846766247586	ACA	ORF1ab:nsp3	Y1050Y	C3150T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.943798525992196
CAMB-76B8C	MN908947.3	7081	C	T	0.069	0.069	2.6e-29	2.4e-29	0.0691200925457306	ACT	ORF1ab:nsp3	N1454N	C4362T	AAC>AAT	Synonymous	ORF1ab:nsp3	0.930807606102234
CAMB-76B8C	MN908947.3	7271	A	C	0.07	0.071	4.7e-28	2.6e-28	0.0707561970505177	TAG	ORF1ab:nsp3	R1518R	A4552C	AGG>CGG	Synonymous	ORF1ab:nsp3	0.928773140884845
CAMB-76B9B	MN908947.3	10976	G	A	0.029	0.01	2.7e-14	1.6e-06	0.0189711016699617	TGC	ORF1ab:nsp6	A2T	G4A	GCA>ACA	Missense	ORF1ab:nsp6	0.980986833803054
CAMB-76B9B	MN908947.3	11074	C	-	0.0063	0.008	1.2e-07	8.8e-09	0.00710546467981471	TCT	ORF1ab:nsp6	.	102-102-delfrshift	.	no-SNV	ORF1ab:nsp6	0.853911144030029
CAMB-76B9B	MN908947.3	11074	C	INS	0.12	0.11	1.8e-51	2.2e-40	0.115018140276435	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.853911144030029
CAMB-76B9B	MN908947.3	11074	C	T	0.031	0.016	2e-23	7.7e-11	0.0239275895401534	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.853911144030029
CAMB-76B9B	MN908947.3	11083	G	-	0.17	0.14	2.7e-74	5.8e-60	0.153756316140719	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.00183525598245781
CAMB-76B9B	MN908947.3	11083	G	T	0.83	0.86	0	0	0.844241586423873	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.00183525598245781
CAMB-76B9B	MN908947.3	14805	C	T	1	1	0	0	0.997971478498894	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00199186147397749
CAMB-76B9B	MN908947.3	19106	G	A	0.078	0.069	1.2e-35	5.4e-32	0.0739116545174687	TGT	ORF1ab:3'-to-5'-exonuclease	C356Y	G1067A	TGT>TAT	Missense	ORF1ab:3'-to-5'-exonuclease	0.926030261667586
CAMB-76B9B	MN908947.3	23707	C	T	1	1	0	0	0.999729382315134	CCA	S	P715P	C2145T	CCC>CCT	Synonymous	GU280_gp02, spike glycoprotein	0.000270617684865706
CAMB-76B9B	MN908947.3	24034	C	T	0.97	1	0	0	0.986068263062534	ACA	S	N824N	C2472T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.0139072523382792
CAMB-76B9B	MN908947.3	25916	C	T	0.016	0.024	1.5e-08	5.7e-12	0.0197775030902349	ACA	ORF3a	T175I	C524T	ACA>ATA	Missense	GU280_gp03	0.980160692212608
CAMB-76B9B	MN908947.3	26124	C	T	0.039	0.052	1.4e-16	3.6e-21	0.0454437869822485	TCC	ORF3a	V244V	C732T	GTC>GTT	Synonymous	GU280_gp03	0.954556213017752
CAMB-76B9B	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-76B9B	MN908947.3	29735	AGGCCACGCGGAGT	-	0.110714285714286	0.0977142857142857	3.3e-46;4.4e-45;3.9e-44;7.3e-44;9.3e-44;3.4e-48;9.8e-44;7.9e-44;1.4e-44;2.3e-44;1.2e-43;2.2e-44;6.4e-40;7.7e-36	6.4e-42;5.1e-41;5.8e-40;4e-40;8.5e-40;1.8e-41;7.2e-40;1.3e-39;2e-40;3.9e-40;9.6e-40;5.5e-40;6.3e-36;2.4e-32	0.102369050206477	GAG	NA	NA	NA	NA	NA	NA	0.892853110534041
CAMB-76B9B	MN908947.3	8090	C	A	0.97	1	0	0	0.981757681597206	ACT	ORF1ab:nsp3	L1791I	C5371A	CTC>ATC	Missense	ORF1ab:nsp3	0.0154575919195733
CAMB-76BB9	MN908947.3	11074	C	INS	0.093	0.14	1.5e-26	6.1e-46	0.116042547897487	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.883428713610351
CAMB-76BB9	MN908947.3	11083	G	-	0.16	0.097	3.3e-72	5.1e-42	0.133976543994454	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.0013287884915362
CAMB-76BB9	MN908947.3	11083	G	T	0.84	0.9	0	0	0.864608007394997	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.0013287884915362
CAMB-76BB9	MN908947.3	14805	C	T	1	1	0	0	0.998661596958175	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00127756653992395
CAMB-76BB9	MN908947.3	16957	G	A	0.018	0.0075	7.7e-10	1.8e-05	0.0137053054760309	AGT	ORF1ab:helicase	V241M	G721A	GTG>ATG	Missense	ORF1ab:helicase	0.982152646646769
CAMB-76BB9	MN908947.3	17125	C	T	0.021	0.022	2.6e-11	7.6e-12	0.0213847739058462	TCT	ORF1ab:helicase	L297F	C889T	CTC>TTC	Missense	ORF1ab:helicase	0.978598334487593
CAMB-76BB9	MN908947.3	2480	A	G	1	1	0	0	0.999578237030789	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000421762969211303
CAMB-76BB9	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-76BB9	MN908947.3	26239	GA	AT	0.00855	0.018	0.00018;9.9e-05	3.5e-08;1.6e-08	0.0130211182842762	CGA	NA	NA	NA	NA	NA	NA	0.987246566383257
CAMB-76BB9	MN908947.3	26242	CT	AG	0.00895	0.019	0.00016;7.2e-05	1.9e-08;5.1e-09	0.0138855922145739	ACT	NA	NA	NA	NA	NA	NA	0.986582568807339
CAMB-76BB9	MN908947.3	26245	AT	TC	0.00825	0.0175	0.00029;0.00017	5.8e-08;2.4e-08	0.0128645891094599	TAT	E	.	1-2-mnv	.	no-SNV	GU280_gp04	0.98742907998665
CAMB-76BB9	MN908947.3	28507	CAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGGTGGTGACGGTAAAATGAAAGATCT	-	0.0151025641025641	0.00058974358974359	4.2e-08;5.5e-08;5.5e-08;4.2e-08;6.4e-08;4.1e-08;1.3e-07;1.6e-07;4.7e-08;2.3e-08;3.7e-08;4.3e-08;6e-08;4.7e-08;1.1e-08;2.7e-08;1.6e-08;1.7e-08;3.5e-08;6.1e-08;5.5e-08;1.3e-07;9.5e-08;5.5e-08;1.9e-07;1.3e-07;2.7e-08;1.3e-07;1.4e-07;2e-07;1.5e-07;1.9e-08;5.6e-08;1.4e-07;2.3e-07;8.5e-08;9.2e-08;1.1e-07;3.6e-07;3.5e-07;4.5e-07;1.2e-07;1.5e-09;1.7e-07;1.8e-07;3.9e-08;1.5e-09;3.4e-09;4.2e-08;1.3e-07;2.1e-07;3.2e-08;1.4e-07;7e-08;2.5e-08;9.5e-08;6.6e-08;3.7e-08;6.7e-08;4.8e-08;6.1e-08;6.2e-08;5.5e-08;2.7e-08;7.2e-09;2e-08;8.9e-09;1.8e-08;1.2e-07;1.3e-07;2.9e-08;3.5e-09;1.4e-08;2.8e-08;2.2e-08;3.1e-08;3.6e-08;3.6e-08	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;3.7e-10;3.5e-10;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0104753322820455	GCA	N	.	234-311-delinframe	.	no-SNV	GU280_gp10	0.989702015775635
CAMB-76BB9	MN908947.3	4433	C	T	0.0039	0.01	0.003	1.2e-05	0.00656077348066298	GCC	ORF1ab:nsp3	P572S	C1714T	CCT>TCT	Missense	ORF1ab:nsp3	0.993439226519337
CAMB-76BB9	MN908947.3	9071	A	G	0.011	0.0035	6.7e-07	0.0011	0.00883778390192911	TAC	ORF1ab:nsp4	T173A	A517G	ACC>GCC	Missense	ORF1ab:nsp4	0.991067186163642
CAMB-76BB9	MN908947.3	9423	T	C	0.0098	0.0033	1.4e-05	0.0075	0.00747149036570979	GTA	ORF1ab:nsp4	V290A	T869C	GTA>GCA	Missense	ORF1ab:nsp4	0.99252850963429
CAMB-76BC8	MN908947.3	10660	TAA	-	0.013	0.0216666666666667	NA;6.4e-08;NA	8.8e-06;5.2e-05;1.4e-05	0.0112320417936439	TTA	ORF1ab:3C-like-proteinase	.	606-608-delinframe	.	no-SNV	ORF1ab:3C-like-proteinase	0.988761130803147
CAMB-76BC8	MN908947.3	10719	GATT	-	0.01225	8e-04	1.5e-07;1.3e-07;2.4e-07;2.9e-08	NA;NA;0.0021;NA	0.00534608891389983	CGA	ORF1ab:3C-like-proteinase	.	665-668-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.994605244640428
CAMB-76BC8	MN908947.3	13860	C	T	0.013	0.015	8.2e-08	1.9e-08	0.0140572101467053	ACA	ORF1ab:RNA-dependent-RNA-polymerase	D131D	C393T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.985869191894411
CAMB-76BC8	MN908947.3	14408	C	T	1	1	0	0	0.999460079638253	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000388067760005399
CAMB-76BC8	MN908947.3	15352	C	T	0.0091	0.015	4.5e-06	2.1e-08	0.0117432279074357	TCT	ORF1ab:RNA-dependent-RNA-polymerase	L629F	C1885T	CTT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.988256772092564
CAMB-76BC8	MN908947.3	16294	A	-	0.017	0.0097	1.1e-08	3.3e-06	0.011957015286817	CAT	ORF1ab:helicase	.	58-58-delfrshift	.	no-SNV	ORF1ab:helicase	0.987891630089299
CAMB-76BC8	MN908947.3	16294	AT	-	0.0085	0.0095	1.1e-08;NA	3.3e-06;5.4e-06	0.00905985444824001	CAT	ORF1ab:helicase	.	58-59-delfrshift	.	no-SNV	ORF1ab:helicase	0.987891630089299
CAMB-76BC8	MN908947.3	17037	A	-	0.011	0.0097	6e-07	2.2e-06	0.0102991915134662	CAA	ORF1ab:helicase	.	801-801-delfrshift	.	no-SNV	ORF1ab:helicase	0.989546320613832
CAMB-76BC8	MN908947.3	17037	AA	-	0.0055	0.0098	6e-07;NA	2.2e-06;1.1e-06	0.00772050222256882	CAA	ORF1ab:helicase	.	801-802-delfrshift	.	no-SNV	ORF1ab:helicase	0.989546320613832
CAMB-76BC8	MN908947.3	19145	C	T	0.037	0.022	7.8e-18	2.2e-11	0.0282416429320941	TCT	ORF1ab:3'-to-5'-exonuclease	S369F	C1106T	TCT>TTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.971698396042572
CAMB-76BC8	MN908947.3	22530	C	T	0.013	0.025	0.0017	1.1e-07	0.021978021978022	ACA	S	T323I	C968T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0.978021978021978
CAMB-76BC8	MN908947.3	23403	A	G	1	1	0	0	0.999887466239872	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.75262578773632e-05
CAMB-76BC8	MN908947.3	23540	TATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTT	-	0.0703255813953488	0.0224186046511628	4e-05;6.4e-05;3.5e-09;4.1e-09;6e-09;4.7e-09;4.2e-09;5.6e-09;3.2e-08;3.1e-08;6.9e-07;1.9e-07;2.1e-07;1.2e-05;4.1e-06;1.8e-07;1.1e-07;1.8e-07;3.1e-07;4.5e-08;9.7e-08;1.3e-08;6.1e-08;6.4e-08;7.1e-08;5.4e-08;5e-08;1.7e-08;1.5e-08;1.1e-09;1.1e-10;1.3e-09;2.7e-10;2.4e-09;1.5e-10;1.7e-09;1.2e-08;2.3e-09;2.6e-09;5.7e-14;4.1e-13;5.6e-09;1.5e-06	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.012;0.0093;0.0012;0.001;0.0012;0.0012;0.00067;0.00098;0.00059;0.00099;0.001;0.001;0.001;0.00099;0.00066;0.00061;0.00034;8.7e-05;0.00031;0.00017;3e-04;0.00016;0.00034;6e-04;0.00037;0.00037;1.3e-05;2.6e-05;0.00042;0.018	0.0493480296808587	ATA	S	.	1978-2020-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.982687131737834
CAMB-76BC8	MN908947.3	23611	G	A	1	1	0	0	0.999633672796542	GGG	S	R683R	G2049A	CGG>CGA	Synonymous	GU280_gp02, spike glycoprotein	0.000366327203458129
CAMB-76BC8	MN908947.3	241	C	T	1	1	0	0	0.999772631305421	TCG	NA	NA	NA	NA	NA	NA	6.49624841653945e-05
CAMB-76BC8	MN908947.3	24125	T	-	0.014	0.0077	1.2e-07	4.8e-05	0.010379746835443	GTT	S	.	2563-2563-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.989588607594937
CAMB-76BC8	MN908947.3	25319	TGCTGCA	CTGCTGC	0.000395571428571429	0.00962857142857143	0.49;NA;NA;0.01;NA;NA;NA	3.8e-06;2.2e-06;1.5e-06;4.6e-06;2.3e-06;1.6e-06;1.3e-06	0.00494054116160165	CTG	S	.	3757-3763-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.99495727959506
CAMB-76BC8	MN908947.3	25350	C	T	1	0.99	0	0	0.99475489609509	CCA	S	P1263L	C3788T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	0.00520521718319971
CAMB-76BC8	MN908947.3	25704	T	-	0.017	0.017	3.2e-07	9.9e-07	0.0170990566037736	CTT	ORF3a	.	312-312-delfrshift	.	no-SNV	GU280_gp03	0.982606132075472
CAMB-76BC8	MN908947.3	26333	C	T	0.022	0.017	1.1e-10	9.6e-09	0.019853045075597	ACA	E	T30I	C89T	ACA>ATA	Missense	GU280_gp04	0.980146954924403
CAMB-76BC8	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	-	0.0157647058823529	0.0683529411764706	0.0017;8.5e-05;0.0013;0.0014;0.0023;0.00053;0.0012;0.0032;0.0031;0.00095;0.0024;0.0022;0.0029;0.0027;1e-07;1.7e-07;0.0025;0.0034;0.0024;0.0027;0.0028;0.0039;0.0022;0.003;0.0026;0.0024;0.0034;0.0023;0.0021;0.0028;0.0035;0.0031;0.0023;0.0034;0.0017;0.0022;0.0018;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	4.5e-06;1e-07;1.1e-09;1e-09;3e-09;4.5e-11;2.8e-10;9.9e-16;1.1e-15;3.7e-16;4e-16;2.2e-16;1e-15;4.2e-16;5.3e-16;1.8e-15;2.1e-16;1.4e-15;5.3e-16;5.2e-16;7e-16;1.6e-15;5.7e-16;1.1e-15;5e-16;1.2e-16;9.8e-16;3.8e-16;5.4e-17;5.9e-16;1.2e-15;1.1e-15;2.5e-16;1.3e-15;1.5e-17;4.5e-16;1.3e-16;3.3e-09;9.4e-08;1.5e-08;4.3e-08;1.9e-05;8.9e-06;1.4e-05;1.8e-05;1.8e-05;1.8e-05;1.6e-05;8.9e-06;0.00053;0.00041	0.0532685414434056	GTC	M	.	258-308-delinframe	.	no-SNV	GU280_gp05	0.973027323210892
CAMB-76BC8	MN908947.3	27203	TGTTTCATCTCGTTGACTT	-	0.0375263157894737	0.0154210526315789	2e-06;2.4e-07;8.9e-07;2.2e-06;2.5e-06;2.4e-06;2.3e-06;2.3e-06;2.2e-06;2.4e-06;2.5e-06;2.1e-06;1.5e-06;2.2e-06;1.9e-06;1.9e-06;2e-06;6.2e-07;1.2e-06	0.0025;0.0014;0.0022;0.0027;0.0028;0.0028;0.0027;0.0028;0.0027;0.0028;0.0029;0.0027;0.0023;0.0027;0.0027;0.0027;0.0027;0.0018;0.0022	0.0259417934702319	ATG	ORF6	.	2-20-delfrshift	.	no-SNV	GU280_gp06	0.973728256321358
CAMB-76BC8	MN908947.3	28146	C	T	0.025	0.0072	8.3e-13	2.9e-05	0.0158508391131514	ACC	ORF8	P85S	C253T	CCT>TCT	Missense	GU280_gp09	0.984149160886849
CAMB-76BC8	MN908947.3	28322	T	-	0.013	0.0055	1.3e-07	0.00031	0.00918532435676635	GTT	N	.	49-49-delfrshift	.	no-SNV	GU280_gp10	0.99067550406207
CAMB-76BC8	MN908947.3	28809	GCAGTCAAGCCT	CGGCAGTCAAGC	0.0153333333333333	0.000948333333333333	1e-08;1.9e-07;1.7e-08;1.3e-08;1.1e-08;5.7e-09;6.6e-09;1.8e-08;4.3e-08;3.2e-08;1.6e-07;4.4e-07	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;2e-05	0.00847319537233176	GGC	N	.	536-547-mnv	.	no-SNV	GU280_gp10	0.991503687079192
CAMB-76BC8	MN908947.3	28820	T	C	0.015	0.011	4.4e-07	2e-05	0.0134434726271461	CTC	N	S183P	T547C	TCT>CCT	Missense	GU280_gp10	0.986394557823129
CAMB-76BC8	MN908947.3	28861	TTCA	AATT	0.01425	0.000475	5.8e-07;1e-07;7.9e-07;1.5e-08	NA;NA;NA;0.0065	0.0077814283243991	ATT	N	.	588-591-mnv	.	no-SNV	GU280_gp10	0.991678726483357
CAMB-76BC8	MN908947.3	29320	A	T	0.0096	0.01	2.1e-05	8.8e-06	0.00994770043672831	AAG	N	Q349H	A1047T	CAA>CAT	Missense	GU280_gp10	0.973931093977463
CAMB-76BC8	MN908947.3	3037	C	T	0.97	1	0	0	0.990975554032442	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76BC8	MN908947.3	3386	A	-	0.012	0.013	5.4e-06	1.1e-06	0.0125922023182297	TAA	ORF1ab:nsp3	.	667-667-delfrshift	.	no-SNV	ORF1ab:nsp3	0.978292939936776
CAMB-76BC8	MN908947.3	3386	AA	-	0.012	0.0065	5.4e-06;2.6e-07	1.1e-06;NA	0.0095181759518176	TAA	ORF1ab:nsp3	.	667-668-delfrshift	.	no-SNV	ORF1ab:nsp3	0.978292939936776
CAMB-76BC8	MN908947.3	3587	C	T	0.014	0.027	6.4e-05	1.5e-11	0.025	ACA	ORF1ab:nsp3	H290Y	C868T	CAC>TAC	Missense	ORF1ab:nsp3	0.975
CAMB-76BC8	MN908947.3	4527	GAT	-	0.0206666666666667	0.0153606666666667	5.5e-06;6.3e-06;0.00096	NA;NA;5.4e-08	0.00921028633959511	AGA	ORF1ab:nsp3	.	1808-1810-delinframe	.	no-SNV	ORF1ab:nsp3	0.990702148124399
CAMB-76BC8	MN908947.3	4529	TT	-	0.0215	0.039	0.00096;0.0029	5.4e-08;0.00018	0.0313128008599336	ATT	ORF1ab:nsp3	.	1810-1811-delfrshift	.	no-SNV	ORF1ab:nsp3	0.964831455548967
CAMB-76BC8	MN908947.3	522	TT	-	0.025	0.064	0.0013;0.0014	5.8e-10;1e-07	0.0424571324334185	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.951368070425886
CAMB-76BC8	MN908947.3	635	C	T	0.02	0.015	3.1e-10	3.4e-08	0.017866874270144	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.982133125729856
CAMB-76BC8	MN908947.3	8937	C	T	0.84	0.81	0	0	0.823435378618666	GCA	ORF1ab:nsp4	A128V	C383T	GCA>GTA	Missense	ORF1ab:nsp4	0.176455130731835
CAMB-76BC8	MN908947.3	9427	TATCGTAG	-	0.0024625	0.0098375	2.2e-05;1.6e-05;NA;NA;NA;NA;NA;NA	2.7e-05;1.9e-05;3.6e-05;3.3e-05;3.1e-05;3e-06;5.2e-06;1.8e-06	0.00481996030620924	CTA	ORF1ab:nsp4	.	873-880-delfrshift	.	no-SNV	ORF1ab:nsp4	0.990224828934506
CAMB-76BC8	MN908947.3	9849	GTGATGTGCTATT	-	0.00282307692307692	0.0246923076923077	NA;NA;NA;NA;NA;NA;0.00028;0.00021;0.00048;0.0016;0.0011;NA;NA	3.9e-11;1.4e-11;1.8e-11;3.1e-11;2.2e-11;2.8e-11;9.7e-10;1.7e-10;5.4e-09;5.7e-08;1.1e-08;8.8e-13;8.5e-13	0.0104540738967361	AGT	ORF1ab:nsp4	.	1295-1307-delfrshift	.	no-SNV	ORF1ab:nsp4	0.989530887876608
CAMB-76BD7	MN908947.3	100	C	T	0.028	0.031	5.6e-14	2.4e-15	0.0292583243178267	TCG	NA	NA	NA	NA	NA	NA	0.97059742757543
CAMB-76BD7	MN908947.3	11075	T	-	0.037	0.034	9.7e-10	9.2e-10	0.0360816788396256	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959289167781093
CAMB-76BD7	MN908947.3	14408	C	T	1	1	0	0	0.997170907183273	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000449657136433469
CAMB-76BD7	MN908947.3	16852	G	T	1	1	0	0	0.99966585271816	TGG	ORF1ab:helicase	G206C	G616T	GGT>TGT	Missense	ORF1ab:helicase	0
CAMB-76BD7	MN908947.3	22041	A	G	0.011	0.011	1.7e-06	3.3e-07	0.0108523972079279	TAT	S	Y160C	A479G	TAT>TGT	Missense	GU280_gp02, spike glycoprotein	0.986421765934682
CAMB-76BD7	MN908947.3	2271	A	C	0.015	0.015	1.4e-07	2.1e-07	0.0151525355242777	AAG	ORF1ab:nsp2	K489T	A1466C	AAG>ACG	Missense	ORF1ab:nsp2	0.984443396861742
CAMB-76BD7	MN908947.3	23403	A	G	1	1	0	0	0.998893714660329	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000109262749597094
CAMB-76BD7	MN908947.3	241	C	T	1	1	0	0	0.99875828908087	TCG	NA	NA	NA	NA	NA	NA	0.000264193812580909
CAMB-76BD7	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0288378378378378	0.0309189189189189	0.0025;0.00023;0.0012;0.0012;0.0022;5.6e-05;0.00018;6.1e-05;6.3e-05;1.2e-05;3.4e-05;2.8e-05;5.8e-05;4.2e-05;4.8e-05;7.9e-05;3.8e-05;6.7e-05;4.1e-05;4.8e-05;3.8e-05;7.8e-05;3.9e-05;5e-05;4.6e-05;3.8e-05;6.6e-05;3.8e-05;1.7e-05;4.6e-05;6.7e-05;6.1e-05;3.7e-05;5.9e-05;1.8e-05;3.5e-05;2.6e-05	0.00071;0.00011;0.00039;0.00036;0.00067;1.2e-05;5e-05;2.4e-05;2.5e-05;1.3e-05;1.4e-05;1.2e-05;2.3e-05;1.8e-05;1.7e-05;2.9e-05;1.4e-05;2.7e-05;1.8e-05;1.8e-05;1.5e-05;3.2e-05;1.6e-05;2.3e-05;1.7e-05;1.1e-05;2.6e-05;1.7e-05;2.8e-06;1.7e-05;2.7e-05;2.5e-05;9.4e-06;2.4e-05;7e-06;1.6e-05;9.1e-06	0.0305369289401322	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.980098660347246
CAMB-76BD7	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998825885765592	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-76BD7	MN908947.3	3037	C	T	1	1	0	0	0.999321389793703	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000101791530944625
CAMB-76BE6	MN908947.3	13914	T	G	0.0045	0.0081	0.00019	3e-06	0.00715892820617713	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.992738801390877
CAMB-76BE6	MN908947.3	14408	C	T	1	1	0	0	0.999610709805787	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000302781262165319
CAMB-76BE6	MN908947.3	23403	A	G	1	1	0	0	0.999838618575002	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000161381424997983
CAMB-76BE6	MN908947.3	241	C	T	1	1	0	0	0.999758434656575	TCG	NA	NA	NA	NA	NA	NA	0.000161043562283598
CAMB-76BE6	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999418942475305	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-76BE6	MN908947.3	3037	C	T	1	1	7.2e-235	0	0.999072642967543	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000309119010819165
CAMB-76BE6	MN908947.3	6196	C	T	1	1	0	0	1	CCT	ORF1ab:nsp3	P1159P	C3477T	CCC>CCT	Synonymous	ORF1ab:nsp3	0
CAMB-76C01	MN908947.3	10323	A	G	1	1	0	0	0.999905408728882	AAG	ORF1ab:3C-like-proteinase	K90R	A269G	AAG>AGG	Missense	ORF1ab:3C-like-proteinase	7.5673016894001e-05
CAMB-76C01	MN908947.3	11074	C	INS	0.11	0.12	1.5e-42	1.1e-37	0.114244087912869	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.881989232983316
CAMB-76C01	MN908947.3	11083	G	-	0.17	0.16	2.5e-74	8.1e-74	0.166316584069054	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.64101217631035e-05
CAMB-76C01	MN908947.3	11083	G	T	0.83	0.83	0	0	0.833552134956841	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.64101217631035e-05
CAMB-76C01	MN908947.3	14805	C	T	1	1	0	0	0.999329191356152	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000590950471961796
CAMB-76C01	MN908947.3	18652	C	T	1	1	0	0	0.999051367443738	GCG	ORF1ab:3'-to-5'-exonuclease	R205C	C613T	CGC>TGC	Missense	ORF1ab:3'-to-5'-exonuclease	4.03673428196589e-05
CAMB-76C01	MN908947.3	2480	A	G	1	1	0	0	0.999883882954018	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.00011611704598235
CAMB-76C01	MN908947.3	2558	C	T	1	1	0	0	0.999850157334798	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	4.99475550671795e-05
CAMB-76C01	MN908947.3	26144	G	T	1	1	0	0	0.999632285346571	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-76C01	MN908947.3	3695	C	T	0.05	0.05	1.6e-20	1.5e-20	0.0501462599247806	TCT	ORF1ab:nsp3	L326L	C976T	CTA>TTA	Synonymous	ORF1ab:nsp3	0.949853740075219
CAMB-76C2F	MN908947.3	1059	C	T	1	1	0	0	0.999421965317919	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.00023121387283237
CAMB-76C2F	MN908947.3	11074	C	INS	0.022	0.027	0.00041	2.3e-05	0.0245327102803738	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.975122567795312
CAMB-76C2F	MN908947.3	11075	T	-	0.035	0.045	3.6e-09	1.9e-11	0.0396204560239912	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955032289798962
CAMB-76C2F	MN908947.3	13006	T	C	1	1	0	0	0.996252465483235	CTG	ORF1ab:nsp9	A107A	T321C	GCT>GCC	Synonymous	ORF1ab:nsp9	0.000394477317554241
CAMB-76C2F	MN908947.3	13653	A	G	0.065	0.067	2.9e-30	2e-31	0.0659555083137195	TAG	ORF1ab:RNA-dependent-RNA-polymerase	V62V	A186G	GTA>GTG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.934006529496621
CAMB-76C2F	MN908947.3	14121	A	G	0.14	0.14	7.1e-63	4.9e-65	0.138196570926522	CAG	ORF1ab:RNA-dependent-RNA-polymerase	P218P	A654G	CCA>CCG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.86154502112485
CAMB-76C2F	MN908947.3	1437	C	T	1	1	0	0	0.999722453510963	TCT	ORF1ab:nsp2	S211F	C632T	TCT>TTT	Missense	ORF1ab:nsp2	0.000138773244518457
CAMB-76C2F	MN908947.3	14408	C	T	1	1	0	0	0.997036403789984	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000584170406782076
CAMB-76C2F	MN908947.3	18550	A	G	0.028	0.027	4.9e-14	1.7e-13	0.0271395679224024	AAG	ORF1ab:3'-to-5'-exonuclease	S171G	A511G	AGT>GGT	Missense	ORF1ab:3'-to-5'-exonuclease	0.972811443687846
CAMB-76C2F	MN908947.3	19146	T	C	0.0093	0.01	2.9e-06	8.9e-07	0.0098828570441273	CTT	ORF1ab:3'-to-5'-exonuclease	S369S	T1107C	TCT>TCC	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.990082587511662
CAMB-76C2F	MN908947.3	21036	C	T	0.008	0.0085	9.7e-06	5.9e-06	0.00821792227351603	TCA	ORF1ab:2'-O-ribose-methyltransferase	L126L	C378T	CTC>CTT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.991683855547916
CAMB-76C2F	MN908947.3	23403	A	G	1	1	0	0	0.999188469407583	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.85800500634365e-05
CAMB-76C2F	MN908947.3	23854	C	T	0.059	0.058	1.5e-27	6.5e-27	0.0586919493525416	ACC	S	N764N	C2292T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.941287528986846
CAMB-76C2F	MN908947.3	241	C	T	1	1	0	0	0.998145689782329	TCG	NA	NA	NA	NA	NA	NA	0.000168573656151885
CAMB-76C2F	MN908947.3	25096	C	T	0.15	0.13	2.3e-68	5.8e-60	0.14144344518583	ACA	S	N1178N	C3534T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.858459852367598
CAMB-76C2F	MN908947.3	25563	G	T	1	1	0	0	0.999863720432201	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	7.78740387423343e-05
CAMB-76C2F	MN908947.3	25688	C	T	1	1	0	0	0.998636256759934	GCT	ORF3a	A99V	C296T	GCT>GTT	Missense	GU280_gp03	0.000752410063484599
CAMB-76C2F	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.03403125	0.02996875	9.4e-06;2.4e-05;1.3e-05;1.2e-05;1.6e-06;8e-06;6e-06;1e-05;8.6e-06;1e-05;1.5e-05;7.3e-06;1.3e-05;7.3e-06;9.3e-06;1e-05;1.6e-05;8.2e-06;1.1e-05;8.3e-06;7e-06;1.3e-05;6.7e-06;3.4e-06;9.5e-06;1.3e-05;1.2e-05;8.9e-06;1.5e-05;3e-06;7e-06;5.4e-06	0.00013;0.00036;6.3e-05;6.4e-05;4.1e-05;3.6e-05;3.6e-05;6.3e-05;4.8e-05;5e-05;8.2e-05;3.8e-05;6.6e-05;5e-05;4.7e-05;3.5e-05;7.6e-05;4.2e-05;5.6e-05;3.9e-05;2.9e-05;6.2e-05;4.4e-05;1.3e-05;4.5e-05;6.7e-05;6.5e-05;2.8e-05;5.5e-05;2.2e-05;4.3e-05;2.4e-05	0.0316407821678603	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.968911306941964
CAMB-76C2F	MN908947.3	3037	C	T	1	1	0	0	0.998714386430556	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.0006635424874549
CAMB-76C2F	MN908947.3	313	C	T	0.0085	0.0097	1.6e-05	5.2e-06	0.00910607398685114	TCA	ORF1ab:leader-protein	L16L	C48T	CTC>CTT	Synonymous	ORF1ab:leader-protein	0.99085467569424
CAMB-76C2F	MN908947.3	4057	T	C	0.095	0.075	1.3e-42	2e-33	0.085436797475843	ATC	ORF1ab:nsp3	H446H	T1338C	CAT>CAC	Synonymous	ORF1ab:nsp3	0.914563202524157
CAMB-76C2F	MN908947.3	6363	C	T	0.014	0.015	2.3e-08	9.3e-09	0.0149613091789306	GCG	ORF1ab:nsp3	A1215V	C3644T	GCG>GTG	Missense	ORF1ab:nsp3	0.984987188896185
CAMB-76C2F	MN908947.3	6761	A	G	0.01	0.016	1.3e-06	5.9e-09	0.0137647381409378	TAC	ORF1ab:nsp3	T1348A	A4042G	ACT>GCT	Missense	ORF1ab:nsp3	0.986180422264875
CAMB-76C2F	MN908947.3	7092	T	C	0.99	0.99	0	0	0.994131455399061	GTC	ORF1ab:nsp3	V1458A	T4373C	GTC>GCC	Missense	ORF1ab:nsp3	0.00586854460093897
CAMB-76C3E	MN908947.3	11075	T	-	0.049	0.042	3.1e-12	3.4e-11	0.0461479931519878	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.949648088263268
CAMB-76C3E	MN908947.3	1108	C	T	0.059	0.062	3.4e-27	5.5e-29	0.0601933924254633	TCA	ORF1ab:nsp2	I101I	C303T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.939665592264303
CAMB-76C3E	MN908947.3	14408	C	T	1	1	0	0	0.998509348514317	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000312326977952555
CAMB-76C3E	MN908947.3	21714	C	T	1	1	0	0	0.999667553191489	ACT	S	T51I	C152T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	9.49848024316109e-05
CAMB-76C3E	MN908947.3	21724	G	T	1	1	0	0	0.99907431216251	TGT	S	L54F	G162T	TTG>TTT	Missense	GU280_gp02, spike glycoprotein	0.000102854204165595
CAMB-76C3E	MN908947.3	23403	A	G	1	1	0	0	0.999191980059711	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.84762661261607e-05
CAMB-76C3E	MN908947.3	23987	C	T	0.01	0.012	1.4e-06	2.4e-07	0.0110091743119266	TCC	S	P809S	C2425T	CCA>TCA	Missense	GU280_gp02, spike glycoprotein	0.988623853211009
CAMB-76C3E	MN908947.3	241	C	T	1	1	0	0	0.99835913959247	TCG	NA	NA	NA	NA	NA	NA	0.0002685044303231
CAMB-76C3E	MN908947.3	24872	G	T	1	1	0	0	0.999170124481328	TGT	S	V1104L	G3310T	GTA>TTA	Missense	GU280_gp02, spike glycoprotein	2.24290680722216e-05
CAMB-76C3E	MN908947.3	24899	C	A	0.014	0.013	4.6e-08	4.9e-08	0.0136964041135641	ACA	S	Q1113K	C3337A	CAA>AAA	Missense	GU280_gp02, spike glycoprotein	0.985862525245491
CAMB-76C3E	MN908947.3	28770	C	T	0.0085	0.0082	1.1e-05	1.1e-05	0.00840927365317609	ACA	N	T166I	C497T	ACA>ATA	Missense	GU280_gp10	0.990652640042884
CAMB-76C3E	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998900062853551	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000131602035444815
CAMB-76C3E	MN908947.3	3037	C	T	1	1	0	0	0.999235500573375	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000173749869687598
CAMB-76C3E	MN908947.3	5861	G	A	0.015	0.015	1.9e-08	1.2e-08	0.014906414615011	TGT	ORF1ab:nsp3	V1048I	G3142A	GTT>ATT	Missense	ORF1ab:nsp3	0.984570553293234
CAMB-76C3E	MN908947.3	6855	C	T	0.0096	0.0099	4.6e-05	4.1e-05	0.0097165991902834	ACT	ORF1ab:nsp3	T1379I	C4136T	ACT>ATT	Missense	ORF1ab:nsp3	0.990283400809717
CAMB-76C3E	MN908947.3	895	A	G	0.0095	0.0082	2.2e-06	5.8e-06	0.00904186611959578	AAG	ORF1ab:nsp2	K30K	A90G	AAA>AAG	Synonymous	ORF1ab:nsp2	0.990787174226882
CAMB-76C4D	MN908947.3	11074	C	INS	0.14	0.12	6.9e-56	6e-37	0.129882109846318	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.866538752467576
CAMB-76C4D	MN908947.3	11083	G	-	0.14	0.18	3.3e-59	2.4e-80	0.151469204224616	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.48565652340618e-05
CAMB-76C4D	MN908947.3	11083	G	T	0.86	0.82	0	0	0.848356512949214	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.48565652340618e-05
CAMB-76C4D	MN908947.3	12137	G	T	0.009	0.0066	1.7e-05	0.00018	0.00815504600424997	TGC	ORF1ab:nsp8	A16S	G46T	GCT>TCT	Missense	ORF1ab:nsp8	0.991800451698319
CAMB-76C4D	MN908947.3	14805	C	T	1	1	0	0	0.999157283224557	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000842716775442875
CAMB-76C4D	MN908947.3	17440	C	T	0.0048	0.011	0.00064	9.3e-07	0.00745943116384575	CCC	ORF1ab:helicase	P402S	C1204T	CCT>TCT	Missense	ORF1ab:helicase	0.992496946431687
CAMB-76C4D	MN908947.3	18744	C	T	0.01	0.0043	1e-05	0.003	0.00792713779726767	ACG	ORF1ab:3'-to-5'-exonuclease	Y235Y	C705T	TAC>TAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.992072862202732
CAMB-76C4D	MN908947.3	2068	T	C	0.0069	0.0021	2.7e-05	0.0047	0.00472274244768341	TTA	ORF1ab:nsp2	I421I	T1263C	ATT>ATC	Synonymous	ORF1ab:nsp2	0.994951551176614
CAMB-76C4D	MN908947.3	218	C	T	0.018	0.018	5.3e-10	6.4e-10	0.0180396145091772	CCG	NA	NA	NA	NA	NA	NA	0.981887742747833
CAMB-76C4D	MN908947.3	2306	C	T	0.027	0.021	1.7e-12	3.4e-10	0.0239190432382705	GCT	ORF1ab:nsp2	L501F	C1501T	CTT>TTT	Missense	ORF1ab:nsp2	0.97608095676173
CAMB-76C4D	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-76C4D	MN908947.3	25572	C	T	0.046	0.027	1.5e-21	1.2e-13	0.0385479378201096	CCA	ORF3a	S60S	C180T	TCC>TCT	Synonymous	GU280_gp03	0.961398148980142
CAMB-76C4D	MN908947.3	2558	C	T	1	1	0	0	0.99989113868931	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000108861310690181
CAMB-76C4D	MN908947.3	26144	G	T	0.99	1	0	0	0.994618834080717	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.00224215246636771
CAMB-76C4D	MN908947.3	27384	T	C	1	1	0	0	0.999308696027883	ATT	ORF6	D61D	T183C	GAT>GAC	Synonymous	GU280_gp06	0.000676901806031627
CAMB-76C5C	MN908947.3	11074	C	INS	0.31	0.076	5.9e-116	1.2e-19	0.175780536790214	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.823945590651817
CAMB-76C5C	MN908947.3	11083	G	-	0.035	0.032	6e-15	1.4e-13	0.0330449149963042	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.0750032610113483
CAMB-76C5C	MN908947.3	11083	G	T	0.76	0.97	2.6e-287	0	0.891734423235793	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.0750032610113483
CAMB-76C5C	MN908947.3	14805	C	T	1	1	0	0	0.999893650962459	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00010634903754121
CAMB-76C5C	MN908947.3	18623	T	C	1	1	0	0	0.999977566906701	ATG	ORF1ab:3'-to-5'-exonuclease	M195T	T584C	ATG>ACG	Missense	ORF1ab:3'-to-5'-exonuclease	0
CAMB-76C5C	MN908947.3	2480	A	G	1	1	3.5e-291	4.80000002037976e-316	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-76C5C	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-76C5C	MN908947.3	282	C	T	1	1	0	0	0.999371266897202	CCT	ORF1ab:leader-protein	P6L	C17T	CCT>CTT	Missense	ORF1ab:leader-protein	0.000471549827098397
CAMB-76C6B	MN908947.3	11075	T	-	0.04	0.039	3.3e-10	1.9e-10	0.0394966794826984	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956169171618315
CAMB-76C6B	MN908947.3	14408	C	T	1	1	0	0	0.998740515467084	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000353270051915338
CAMB-76C6B	MN908947.3	14786	C	T	1	1	0	0	0.999762294279682	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A440V	C1319T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	5.59307577219402e-05
CAMB-76C6B	MN908947.3	20578	G	T	1	1	0	0	0.999773229774931	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	0
CAMB-76C6B	MN908947.3	23403	A	G	1	1	0	0	0.999566567940475	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-76C6B	MN908947.3	241	C	T	1	1	0	0	0.998474164836435	TCG	NA	NA	NA	NA	NA	NA	0.000161831002196278
CAMB-76C6B	MN908947.3	2416	C	T	1	1	0	0	0.998178137651822	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0.000101214574898785
CAMB-76C6B	MN908947.3	25563	G	T	1	1	0	0	0.999852451414359	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	6.32351081320349e-05
CAMB-76C6B	MN908947.3	26858	C	T	0.014	0.013	4.8e-08	5.5e-08	0.0134370146325513	TCA	M	F112F	C336T	TTC>TTT	Synonymous	GU280_gp05	0.986471021008747
CAMB-76C6B	MN908947.3	27317	A	G	0.027	0.026	1.7e-13	2.8e-13	0.0265604603457922	AAT	ORF6	N39S	A116G	AAT>AGT	Missense	GU280_gp06	0.973332978128247
CAMB-76C6B	MN908947.3	3037	C	T	1	1	0	0	0.999318801089918	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76C6B	MN908947.3	4301	C	T	0.0069	0.0069	3.8e-05	2.6e-05	0.00688933997662545	GCT	ORF1ab:nsp3	L528F	C1582T	CTT>TTT	Missense	ORF1ab:nsp3	0.993095282032355
CAMB-76C6B	MN908947.3	5680	T	C	0.0084	0.012	1.1e-05	3.1e-07	0.00959017524492894	TTA	ORF1ab:nsp3	V987V	T2961C	GTT>GTC	Synonymous	ORF1ab:nsp3	0.990271836622051
CAMB-76C7A	MN908947.3	1059	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0
CAMB-76C7A	MN908947.3	14408	C	T	1	1	0	0	0.999687000069556	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000139111080197538
CAMB-76C7A	MN908947.3	1547	A	G	0.012	0.022	0.00018	3.4e-06	0.0170068027210884	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.947278911564626
CAMB-76C7A	MN908947.3	1547	A	T	0.053	0.015	1.9e-13	2.9e-05	0.0357142857142857	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.947278911564626
CAMB-76C7A	MN908947.3	21137	A	G	0.032	0.031	2.1e-13	4.1e-13	0.0317884405670665	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.968211559432933
CAMB-76C7A	MN908947.3	23148	A	G	0.002	0.015	0.0064	5.7e-09	0.00759629992884479	AAG	S	K529R	A1586G	AAG>AGG	Missense	GU280_gp02, spike glycoprotein	0.977326487047828
CAMB-76C7A	MN908947.3	23403	A	G	1	1	0	0	0.999692898272553	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000268714011516315
CAMB-76C7A	MN908947.3	241	C	T	1	1	0	0	0.999878419452888	TCG	NA	NA	NA	NA	NA	NA	6.0790273556231e-05
CAMB-76C7A	MN908947.3	24368	G	T	1	1	0	0	0.999844454814124	AGA	S	D936Y	G2806T	GAC>TAC	Missense	GU280_gp02, spike glycoprotein	0
CAMB-76C7A	MN908947.3	25563	G	T	1	1	0	0	0.99975200170056	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000106284985474385
CAMB-76C7A	MN908947.3	3037	C	T	1	1	0	0	0.999574377527133	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76C7A	MN908947.3	8675	A	G	0.0064	0.021	9.1e-05	1.5e-09	0.0123456790123457	AAG	ORF1ab:nsp4	S41G	A121G	AGT>GGT	Missense	ORF1ab:nsp4	0.968253968253968
CAMB-76C89	MN908947.3	10323	A	G	0.8	0.8	0	0	0.795130602325225	AAG	ORF1ab:3C-like-proteinase	K90R	A269G	AAG>AGG	Missense	ORF1ab:3C-like-proteinase	0.204716134258752
CAMB-76C89	MN908947.3	11075	T	-	0.043	0.039	7.2e-11	1.4e-10	0.0414838372046214	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954470431947184
CAMB-76C89	MN908947.3	14408	C	T	1	1	0	0	0.996446951521034	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00031134960898152
CAMB-76C89	MN908947.3	20578	G	T	1	1	0	0	0.99941197224509	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	0
CAMB-76C89	MN908947.3	22341	C	T	0.019	0.01	1.7e-07	5e-04	0.0165837479270315	GCT	S	A260V	C779T	GCT>GTT	Missense	GU280_gp02, spike glycoprotein	0.983416252072968
CAMB-76C89	MN908947.3	23403	A	G	1	1	0	0	0.999275496362067	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000200394623258108
CAMB-76C89	MN908947.3	23559	TTGGTGCAGGTATATGCGCTAG	-	0.034	0.0337727272727273	0.00055;0.001;5e-04;0.00085;0.00089;0.00093;0.00085;0.00089;0.00055;0.00055;0.00017;0.00013;0.00041;0.00023;0.00045;0.00022;0.00044;0.00083;0.00051;6e-04;3e-05;5.8e-05	0.00054;0.00073;0.00027;0.00051;0.00054;0.00055;5e-04;5e-04;0.00033;0.00029;3e-04;3e-04;0.00086;6e-04;0.00052;0.00028;0.00055;0.00093;6e-04;0.00061;2.9e-05;7.1e-05	0.0320744081172492	ATT	S	.	1997-2018-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.957220032121478
CAMB-76C89	MN908947.3	241	C	T	1	0.99	0	0	0.995012977922949	TCG	NA	NA	NA	NA	NA	NA	0.000145819358978098
CAMB-76C89	MN908947.3	2416	C	T	1	1	0	0	0.995861281575567	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0.000428143285286142
CAMB-76C89	MN908947.3	25563	G	T	1	1	0	0	0.999773926149209	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	5.02386335091685e-05
CAMB-76C89	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0457105263157895	0.0417368421052632	1.5e-05;1.3e-07;6.6e-06;5.7e-06;1.3e-05;1.2e-07;4.9e-07;4.2e-08;4e-08;2e-09;1.6e-08;1.1e-08;2.6e-08;1.8e-08;2.3e-08;4.1e-08;1.4e-08;3.3e-08;1.5e-08;2e-08;1.7e-08;4.3e-08;1.6e-08;2.4e-08;1.8e-08;9.8e-09;3.3e-08;1.3e-08;3.8e-09;2e-08;3.2e-08;2.8e-08;2e-08;3.5e-08;3.8e-09;1.8e-08;1.1e-08;0.00027	9e-05;7.1e-06;2.8e-05;2.9e-05;7e-05;1.7e-07;1.1e-06;1.3e-07;1.2e-07;5.2e-08;5.6e-08;4.1e-08;1e-07;6.9e-08;8.3e-08;1.5e-07;5e-08;1.2e-07;6.7e-08;6.8e-08;7.3e-08;1.4e-07;7.2e-08;9.2e-08;6.6e-08;3.5e-08;7.2e-08;6.8e-08;2.7e-08;6.6e-08;9.8e-08;9e-08;3.8e-08;1.4e-07;2.2e-08;7.3e-08;4.1e-08;0.00043	0.0469130617387652	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.970309855623577
CAMB-76C89	MN908947.3	27447	TCACTACCAAGAGTGTG	-	0.0177058823529412	0.0164705882352941	2.8e-09;1.6e-09;1e-09;1.8e-09;1.6e-09;1.5e-09;1.2e-09;2.3e-09;7.4e-10;9.2e-10;1.1e-09;3e-10;1e-09;1.3e-09;9.4e-10;2.4e-09;1.1e-09	2.1e-09;1.5e-09;1.1e-09;1.7e-09;1.5e-09;1.3e-09;1.3e-09;2e-09;7.7e-10;9.9e-10;1.2e-09;7.4e-10;1.4e-09;1.7e-09;1.2e-09;2e-09;1.5e-09	0.017264337205565	ATC	ORF7a	.	54-70-delfrshift	.	no-SNV	GU280_gp07	0.982824398703159
CAMB-76C89	MN908947.3	3037	C	T	1	1	0	0	0.99902589961036	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.73000229200092e-05
CAMB-76C89	MN908947.3	522	TT	-	0.039	0.0355	5.8e-06;0.00019	1.5e-05;0.00028	0.0373995384737805	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.954676022815873
CAMB-76C98	MN908947.3	11005	C	T	0.0041	0.019	0.00041	3.3e-10	0.0110880110880111	ACC	ORF1ab:nsp6	H11H	C33T	CAC>CAT	Synonymous	ORF1ab:nsp6	0.988773388773389
CAMB-76C98	MN908947.3	11075	T	-	0.062	0.031	2.9e-15	3.3e-08	0.0457509665183456	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951900211539864
CAMB-76C98	MN908947.3	14408	C	T	1	0.99	0	0	0.99677714175766	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00222874276460308
CAMB-76C98	MN908947.3	23403	A	G	1	1	0	0	0.999797416464083	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000166833500166834
CAMB-76C98	MN908947.3	2389	A	T	0.01	0.0024	4.2e-06	0.0043	0.00577445652173913	CAT	ORF1ab:nsp2	T528T	A1584T	ACA>ACT	Synonymous	ORF1ab:nsp2	0.994225543478261
CAMB-76C98	MN908947.3	241	C	T	1	1	0	0	0.99975943138327	TCG	NA	NA	NA	NA	NA	NA	0.000109349371241115
CAMB-76C98	MN908947.3	29508	G	T	0.02	0.0098	1.3e-07	1.9e-05	0.0132947976878613	AGC	N	S412I	G1235T	AGC>ATC	Missense	GU280_gp10	0.986705202312139
CAMB-76C98	MN908947.3	3037	C	T	1	1	0	0	0.99961068286226	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.78634275480807e-05
CAMB-76C98	MN908947.3	8169	CAG	-	0.00393333333333333	0.0163333333333333	6e-04;0.00032;0.00044	6.1e-09;7.3e-10;2.5e-09	0.00934108527131783	TCA	ORF1ab:nsp3	.	5450-5452-delinframe	.	no-SNV	ORF1ab:nsp3	0.991367625026753
CAMB-76CA7	MN908947.3	10097	G	A	1	1	0	0	1	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0
CAMB-76CA7	MN908947.3	13536	C	T	0.99	1	9.3e-186	1.1e-152	0.995934959349594	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-76CA7	MN908947.3	14408	C	T	1	1	0	0	0.999083333333333	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000583333333333333
CAMB-76CA7	MN908947.3	23403	A	G	1	1	0	0	0.999900955776754	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.95221116228396e-05
CAMB-76CA7	MN908947.3	23731	C	T	1	1	2.4e-180	0	1	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-76CA7	MN908947.3	241	C	T	1	1	0	0	0.999853049228508	TCG	NA	NA	NA	NA	NA	NA	0.00014695077149155
CAMB-76CA7	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-76CA7	MN908947.3	3037	C	T	1	1	0	2.39999996078331e-317	0.99934554973822	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76CA7	MN908947.3	4002	C	T	1	1	1.6e-291	7.3e-238	1	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-76CB6	MN908947.3	11075	T	-	0.039	0.031	6.2e-10	1.2e-08	0.035997701892348	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958598154332292
CAMB-76CB6	MN908947.3	14408	C	T	1	1	0	0	0.998040168702278	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000329251658017278
CAMB-76CB6	MN908947.3	15738	C	T	1	1	0	0	0.997490437352007	TCA	ORF1ab:RNA-dependent-RNA-polymerase	F757F	C2271T	TTC>TTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	8.09536338062375e-05
CAMB-76CB6	MN908947.3	23403	A	G	1	1	0	0	0.999016360243596	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.78611621414416e-05
CAMB-76CB6	MN908947.3	241	C	T	1	1	0	0	0.998821641678785	TCG	NA	NA	NA	NA	NA	NA	0.000100285814571529
CAMB-76CB6	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999522343700244	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-76CB6	MN908947.3	3037	C	T	1	1	0	0	0.999476115635567	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000142877553936277
CAMB-76CB6	MN908947.3	9241	A	C	0.02	0.022	1.7e-10	1.2e-11	0.020519563921041	CAG	ORF1ab:nsp4	S229S	A687C	TCA>TCC	Synonymous	ORF1ab:nsp4	0.97925108178774
CAMB-76CC5	MN908947.3	11075	T	-	0.022	0.067	1.6e-06	1.1e-16	0.0472831519586579	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.920465475943494
CAMB-76CC5	MN908947.3	11075	T	C	0.049	0.019	4.4e-06	0.0056	0.0321759302917712	CTT	ORF1ab:nsp6	F35L	T103C	TTT>CTT	Missense	ORF1ab:nsp6	0.920465475943494
CAMB-76CC5	MN908947.3	14408	C	T	1	1	0	0	0.999474069331382	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000434464465380042
CAMB-76CC5	MN908947.3	16206	G	T	1	1	0	0	0.99927797833935	AGG	ORF1ab:RNA-dependent-RNA-polymerase	E913D	G2739T	GAG>GAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-76CC5	MN908947.3	21178	C	T	0.069	0.038	5e-05	2.6e-06	0.0440251572327044	ACA	ORF1ab:2'-O-ribose-methyltransferase	H174Y	C520T	CAT>TAT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.955974842767296
CAMB-76CC5	MN908947.3	23403	A	G	1	1	0	0	0.999935744210553	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.57023157786517e-05
CAMB-76CC5	MN908947.3	241	C	T	1	1	0	0	0.999831498539654	TCG	NA	NA	NA	NA	NA	NA	5.61671534486632e-05
CAMB-76CC5	MN908947.3	27506	G	C	0.014	0.024	1.9e-08	2.1e-12	0.0195879822975753	GGA	ORF7a	G38A	G113C	GGA>GCA	Missense	GU280_gp07	0.98024060337842
CAMB-76CC5	MN908947.3	28881	GGG	AAC	1	0.996666666666667	0;0;0	0;0;0	0.999480249480249	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-76CC5	MN908947.3	3037	C	T	1	1	0	0	0.999891209747607	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76CC5	MN908947.3	3227	GTTG	-	0.003	0.00955	NA;NA;NA;8.5e-06	1.7e-05;7.8e-06;1.1e-05;7.6e-05	0.00521621037686348	TGT	ORF1ab:nsp3	.	508-511-delfrshift	.	no-SNV	ORF1ab:nsp3	0.994803625377644
CAMB-76CC5	MN908947.3	3230	G	-	0.012	0.0093	8.5e-06	7.6e-05	0.0103787327021122	TGG	ORF1ab:nsp3	.	511-511-delfrshift	.	no-SNV	ORF1ab:nsp3	0.989439184268026
CAMB-76CD4	MN908947.3	10186	C	T	0.62	0.72	0	0	0.640124954305274	GCA	ORF1ab:3C-like-proteinase	C44C	C132T	TGC>TGT	Synonymous	ORF1ab:3C-like-proteinase	0.359841813166728
CAMB-76CD4	MN908947.3	11071	G	INS	0.015	0.033	1.4e-05	3.5e-10	0.0168791605551168	TGT	ORF1ab:nsp6	.	98-99-insfrshift	.	no-SNV	ORF1ab:nsp6	0.983008010831547
CAMB-76CD4	MN908947.3	11073	T	-	0.0016	0.0073	0.0089	1.8e-05	0.0022751978158101	TTC	ORF1ab:nsp6	.	101-101-delfrshift	.	no-SNV	ORF1ab:nsp6	0.997370882523953
CAMB-76CD4	MN908947.3	11074	C	-	0.016	0.083	3.4e-15	1.5e-38	0.0235273216415827	TCT	ORF1ab:nsp6	.	102-102-delfrshift	.	no-SNV	ORF1ab:nsp6	0.823050176391462
CAMB-76CD4	MN908947.3	11074	C	INS	0.088	0.028	8.2e-30	4.9e-06	0.0806324712570747	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.823050176391462
CAMB-76CD4	MN908947.3	11074	C	T	0.048	0.26	3.3e-35	8.9e-117	0.0727392705768889	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.823050176391462
CAMB-76CD4	MN908947.3	11083	G	-	0.16	0.022	7.2e-73	3.1e-09	0.147589662691969	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	9.27945065652113e-05
CAMB-76CD4	MN908947.3	11083	G	T	0.84	0.98	0	0	0.852039159281771	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	9.27945065652113e-05
CAMB-76CD4	MN908947.3	14805	C	T	1	1	0	0	0.999953815956587	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	2.30920217065004e-05
CAMB-76CD4	MN908947.3	26144	G	T	1	1	0	3.6e-23	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-76CD4	MN908947.3	28539	G	A	0.094	0.036	1e-41	1.1e-13	0.0889115520118672	AGA	N	R89K	G266A	AGA>AAA	Missense	GU280_gp10	0.911088447988133
CAMB-76CD4	MN908947.3	28857	G	T	1	1	0	0	0.9998821866164	AGA	N	R195I	G584T	AGA>ATA	Missense	GU280_gp10	0.000117813383600377
CAMB-76CD4	MN908947.3	3931	T	C	1	1	0	6.99999998443113e-316	0.999893435635124	TTG	ORF1ab:nsp3	V404V	T1212C	GTT>GTC	Synonymous	ORF1ab:nsp3	0
CAMB-76CE3	MN908947.3	11074	C	INS	0.1	0.12	4.4e-30	2.6e-36	0.11202971919729	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.887387551444076
CAMB-76CE3	MN908947.3	11083	G	-	0.14	0.21	2.1e-60	6.5e-95	0.166543574593796	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.35705653283201e-05
CAMB-76CE3	MN908947.3	11083	G	T	0.86	0.79	0	1.69998107421056e-319	0.833389284275547	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.35705653283201e-05
CAMB-76CE3	MN908947.3	13059	C	A	1	1	0	0	0.99991945551931	ACT	ORF1ab:nsp10	T12N	C35A	ACT>AAT	Missense	ORF1ab:nsp10	0
CAMB-76CE3	MN908947.3	14805	C	T	1	1	0	0	1	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-76CE3	MN908947.3	15193	G	T	1	1	0	0	1	AGC	ORF1ab:RNA-dependent-RNA-polymerase	A576S	G1726T	GCT>TCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-76CE3	MN908947.3	522	T	-	0.088	0.058	8.2e-12	1.4e-07	0.0764838824788866	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.923397169025812
CAMB-76CE3	MN908947.3	522	TTG	-	0.0826666666666667	0.0193333333333333	8.2e-12;2.2e-12;8.4e-16	1.4e-07;NA;NA	0.0514382402707276	GTT	ORF1ab:leader-protein	.	257-259-delinframe	.	no-SNV	ORF1ab:leader-protein	0.923397169025812
CAMB-76CF2	MN908947.3	1059	C	T	0.69	1	0	0	0.886352829291488	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.113647170708512
CAMB-76CF2	MN908947.3	13914	T	G	0.0064	0.0069	0.00019	1.9e-05	0.006765899864682	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993234100135318
CAMB-76CF2	MN908947.3	14408	C	T	1	1	0	0	0.999358666025333	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000481000481000481
CAMB-76CF2	MN908947.3	23403	A	G	1	1	0	0	0.99990375360924	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.62463907603465e-05
CAMB-76CF2	MN908947.3	241	C	T	1	1	0	0	1	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-76CF2	MN908947.3	25563	G	T	1	1	0	0	0.999705275567345	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	5.89448865310934e-05
CAMB-76CF2	MN908947.3	3037	C	T	1	1	7.5e-190	0	0.999455634186173	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76D0E	MN908947.3	11075	T	-	0.034	0.05	9.4e-09	8.3e-13	0.0401256052098319	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951985397620926
CAMB-76D0E	MN908947.3	14408	C	T	1	1	0	0	0.998553535619185	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000394490285676715
CAMB-76D0E	MN908947.3	16206	G	T	1	1	0	0	0.998818718764198	AGG	ORF1ab:RNA-dependent-RNA-polymerase	E913D	G2739T	GAG>GAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00109041344843253
CAMB-76D0E	MN908947.3	23403	A	G	0.99	1	0	0	0.99531877820111	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.90101816574126e-05
CAMB-76D0E	MN908947.3	241	C	T	1	1	0	0	0.998419848588477	TCG	NA	NA	NA	NA	NA	NA	7.07530482771633e-05
CAMB-76D0E	MN908947.3	25506	A	G	0.023	0.012	8.1e-12	4.4e-07	0.0186860538730165	AAG	ORF3a	Q38Q	A114G	CAA>CAG	Synonymous	GU280_gp03	0.981109726958972
CAMB-76D0E	MN908947.3	25947	G	C	0.094	0.069	2.3e-42	8e-31	0.0851390809897034	AGA	ORF3a	Q185H	G555C	CAG>CAC	Missense	GU280_gp03	0.91340095282004
CAMB-76D0E	MN908947.3	2695	C	T	0.0093	0.0068	3.2e-05	2e-04	0.008	ACA	ORF1ab:nsp2	N630N	C1890T	AAC>AAT	Synonymous	ORF1ab:nsp2	0.992
CAMB-76D0E	MN908947.3	27331	C	T	0.0039	0.0061	0.00052	4.7e-05	0.00477320604783872	ACT	ORF6	L44L	C130T	CTA>TTA	Synonymous	GU280_gp06	0.995213460974374
CAMB-76D0E	MN908947.3	28006	C	T	0.0082	0.014	3.5e-05	1.7e-07	0.0115790997249964	CCT	ORF8	P38L	C113T	CCT>CTT	Missense	GU280_gp09	0.988276161528441
CAMB-76D0E	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999696348591817	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-76D0E	MN908947.3	3037	C	T	1	1	0	0	0.999447399323064	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.90750846169787e-05
CAMB-76D0E	MN908947.3	7224	C	T	0.96	0.95	9.79999999999999e-291	0	0.951838879159369	GCT	ORF1ab:nsp3	A1502V	C4505T	GCT>GTT	Missense	ORF1ab:nsp3	0.0446584938704028
CAMB-76D2C	MN908947.3	10396	G	T	0.0094	0.0044	2.9e-06	0.00046	0.00676650027731559	TGT	ORF1ab:3C-like-proteinase	V114V	G342T	GTG>GTT	Synonymous	ORF1ab:3C-like-proteinase	0.993171874037099
CAMB-76D2C	MN908947.3	11074	C	INS	0.035	0.029	2e-08	4e-06	0.0319129379756609	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.967731656801108
CAMB-76D2C	MN908947.3	11075	T	-	0.024	0.02	1.7e-06	8.8e-06	0.0220481994154304	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.974124524347874
CAMB-76D2C	MN908947.3	11084	TATGAAAATGCCT	-	0.00275484615384615	0.00887692307692308	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00025;3e-04;1.1e-07	0.00023;0.00024;1.5e-05;1.3e-05;1.3e-07;8.4e-05;7.2e-05;5.4e-05;8.4e-05;6.2e-05;0.00039;0.00047;6e-04	0.00352332286549004	GTA	ORF1ab:nsp6	.	112-124-delfrshift	.	no-SNV	ORF1ab:nsp6	0.996334930927544
CAMB-76D2C	MN908947.3	11104	TT	-	0.0195	0.00865	2.1e-08;3.6e-06	0.00039;0.001	0.0142128802597436	CTT	ORF1ab:nsp6	.	132-133-delfrshift	.	no-SNV	ORF1ab:nsp6	0.978770040943493
CAMB-76D2C	MN908947.3	11224	C	T	0.014	0.03	4.4e-08	9.4e-15	0.0222535334020888	TCT	ORF1ab:nsp6	V84V	C252T	GTC>GTT	Synonymous	ORF1ab:nsp6	0.977383321470592
CAMB-76D2C	MN908947.3	11506	AGTT	-	0.004975	0.013	NA;0.002;0.0016;0.0016	6.8e-06;5.4e-06;6e-06;6.4e-06	0.0100352112676056	TAG	ORF1ab:nsp6	.	534-537-delfrshift	.	no-SNV	ORF1ab:nsp6	0.992530515576608
CAMB-76D2C	MN908947.3	12167	G	-	0.0033	0.0076	0.0037	4.7e-05	0.00549566400272063	TGT	ORF1ab:nsp8	.	76-76-delfrshift	.	no-SNV	ORF1ab:nsp8	0.992470668253698
CAMB-76D2C	MN908947.3	13201	G	T	0.0054	0.01	0.00019	1.3e-06	0.00732551172275161	CGG	ORF1ab:nsp10	P59P	G177T	CCG>CCT	Synonymous	ORF1ab:nsp10	0.992500531534492
CAMB-76D2C	MN908947.3	13721	CAG	-	0.0055	0.00593333333333333	5.9e-05;8.6e-05;7.5e-05	3.7e-05;5.4e-05;5.2e-05	0.00576816587706885	CCA	ORF1ab:RNA-dependent-RNA-polymerase	.	254-256-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.994075755691006
CAMB-76D2C	MN908947.3	13939	G	T	0.0047	0.0059	0.00012	3.8e-05	0.00534640561594739	AGA	ORF1ab:RNA-dependent-RNA-polymerase	E158*	G472T	GAA>TAA	Nonsense	ORF1ab:RNA-dependent-RNA-polymerase	0.992343236278546
CAMB-76D2C	MN908947.3	14408	C	T	1	1	0	0	0.999433119178356	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00028899806593602
CAMB-76D2C	MN908947.3	14908	G	T	0.011	0.0045	7.9e-07	0.00045	0.00797577726903478	TGC	ORF1ab:RNA-dependent-RNA-polymerase	A481S	G1441T	GCT>TCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.98486079314674
CAMB-76D2C	MN908947.3	1564	T	C	0.012	0.013	2.2e-06	4e-06	0.0124223602484472	GTA	ORF1ab:nsp2	C253C	T759C	TGT>TGC	Synonymous	ORF1ab:nsp2	0.987577639751553
CAMB-76D2C	MN908947.3	16887	C	T	0.065	0.057	2.4e-26	6.2e-23	0.0604946779998468	ACA	ORF1ab:helicase	Y217Y	C651T	TAC>TAT	Synonymous	ORF1ab:helicase	0.939382801133318
CAMB-76D2C	MN908947.3	17676	C	T	0.11	0.06	4.9e-48	6.9e-28	0.0836845966825395	TCA	ORF1ab:helicase	I480I	C1440T	ATC>ATT	Synonymous	ORF1ab:helicase	0.916257858468444
CAMB-76D2C	MN908947.3	19006	G	T	0.0094	0.0067	4.2e-06	6.6e-05	0.00791964162857186	AGC	ORF1ab:3'-to-5'-exonuclease	A323S	G967T	GCA>TCA	Missense	ORF1ab:3'-to-5'-exonuclease	0.992003913954164
CAMB-76D2C	MN908947.3	21622	C	T	0.037	0.018	1.6e-13	3.2e-08	0.0254988913525499	CCA	S	T20T	C60T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.97450110864745
CAMB-76D2C	MN908947.3	21707	C	T	1	1	0	0	0.999739668076798	ACA	S	H49Y	C145T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	6.50829808005207e-05
CAMB-76D2C	MN908947.3	21882	G	T	0.0044	0.011	0.00087	1.9e-06	0.00748876684972541	GGT	S	G107V	G320T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.992511233150275
CAMB-76D2C	MN908947.3	23403	A	G	1	1	0	0	0.997533387082612	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000103773358983979
CAMB-76D2C	MN908947.3	236	G	-	0.0086	0.0074	8.6e-06	3.2e-05	0.0079728658267994	AGG	NA	NA	NA	NA	NA	NA	0.990059612956274
CAMB-76D2C	MN908947.3	23804	G	T	0.0069	0.0097	4.8e-05	3.4e-06	0.00829929047516663	TGA	S	E748*	G2242T	GAA>TAA	Nonsense	GU280_gp02, spike glycoprotein	0.991571705009675
CAMB-76D2C	MN908947.3	241	C	T	1	1	0	0	0.999642159567013	TCG	NA	NA	NA	NA	NA	NA	0.000104370126287853
CAMB-76D2C	MN908947.3	25784	G	-	0.0089	0.003	1.5e-05	0.0056	0.00574712643678161	TGG	ORF3a	.	392-392-delfrshift	.	no-SNV	GU280_gp03	0.990001574555188
CAMB-76D2C	MN908947.3	26926	AA	-	0.0024	0.0067	0.00028;NA	5.4e-05;3.5e-05	0.00457937584803256	GAA	M	.	404-405-delfrshift	.	no-SNV	GU280_gp05	0.994276743957877
CAMB-76D2C	MN908947.3	27505	G	-	0.0037	0.0074	0.0014	3.1e-05	0.00554745707806932	TGG	ORF7a	.	112-112-delfrshift	.	no-SNV	GU280_gp07	0.994314868804665
CAMB-76D2C	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999877164967449	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-76D2C	MN908947.3	3037	C	T	1	1	0	0	0.999162268576694	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000335092569322275
CAMB-76D2C	MN908947.3	3556	T	A	0.0061	0.013	0.00025	4.9e-07	0.0105922002888782	TTA	ORF1ab:nsp3	L279L	T837A	CTT>CTA	Synonymous	ORF1ab:nsp3	0.989407799711122
CAMB-76D2C	MN908947.3	3737	C	T	0.018	0.012	1.7e-07	2.5e-06	0.014572864321608	CCC	ORF1ab:nsp3	P340S	C1018T	CCT>TCT	Missense	ORF1ab:nsp3	0.984924623115578
CAMB-76D2C	MN908947.3	4834	AGGTATAGAATTTCTTAAGAGAGGTGATAAAAGTGTA	-	0.00888648648648649	7.64594594594595e-05	3.4e-05;1.5e-05;3.1e-06;6.4e-06;4.7e-06;7.2e-06;1.7e-08;1.8e-09;8e-06;0.00029;0.00046;5.3e-06;9.4e-06;6.1e-06;5.1e-05;2.3e-05;1e-05;5.3e-06;4.8e-06;5.7e-06;1.4e-05;8.4e-06;2.4e-05;1.7e-05;7.7e-06;7.9e-06;7.2e-06;7.5e-06;2.9e-05;7.6e-06;5.5e-06;8.5e-06;3.1e-05;1.6e-05;5.8e-06;2.4e-05;2.6e-05	NA;0.003;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00352524653933233	TAG	ORF1ab:nsp3	.	2115-2151-delfrshift	.	no-SNV	ORF1ab:nsp3	0.99550143751057
CAMB-76D2C	MN908947.3	6374	G	T	0.0079	0.0064	1.9e-05	9.6e-05	0.00708472605725912	GGA	ORF1ab:nsp3	D1219Y	G3655T	GAT>TAT	Missense	ORF1ab:nsp3	0.992866831371409
CAMB-76D2C	MN908947.3	7336	T	C	0.0043	0.0085	0.00042	6.5e-06	0.00621316935690494	ATT	ORF1ab:nsp3	H1539H	T4617C	CAT>CAC	Synonymous	ORF1ab:nsp3	0.993722777350756
CAMB-76D2C	MN908947.3	7646	G	-	0.0076	0.0095	1.7e-05	2.5e-06	0.00843440251185126	TGG	ORF1ab:nsp3	.	4927-4927-delfrshift	.	no-SNV	ORF1ab:nsp3	0.990334297851382
CAMB-76D2C	MN908947.3	8359	T	C	0.012	0.0075	4.6e-06	0.00024	0.00952979369567494	ATA	ORF1ab:nsp3	H1880H	T5640C	CAT>CAC	Synonymous	ORF1ab:nsp3	0.984082102837993
CAMB-76D4A	MN908947.3	11074	C	INS	0.023	0.026	0.00035	4.7e-05	0.0241935483870968	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.975198690977092
CAMB-76D4A	MN908947.3	11075	T	-	0.04	0.032	1.3e-10	9.2e-09	0.0364763380617475	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958695911312433
CAMB-76D4A	MN908947.3	11379	C	T	1	0.99	0	0	0.994726411608612	GCT	ORF1ab:nsp6	A136V	C407T	GCT>GTT	Missense	ORF1ab:nsp6	0.00456820395687078
CAMB-76D4A	MN908947.3	1170	C	T	1	1	0	0	0.999376414203503	TCT	ORF1ab:nsp2	S122F	C365T	TCT>TTT	Missense	ORF1ab:nsp2	0.000124717159299446
CAMB-76D4A	MN908947.3	14408	C	T	1	1	0	0	0.998876666454717	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000434496937326466
CAMB-76D4A	MN908947.3	22838	C	T	0.01	0.011	1.5e-06	5e-07	0.0108963208507007	ACC	S	P426S	C1276T	CCA>TCA	Missense	GU280_gp02, spike glycoprotein	0.989013423479602
CAMB-76D4A	MN908947.3	23403	A	G	1	1	0	0	0.999498110070735	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00014115654260575
CAMB-76D4A	MN908947.3	241	C	T	1	1	0	0	0.99876859545251	TCG	NA	NA	NA	NA	NA	NA	0.000261207025225136
CAMB-76D4A	MN908947.3	24368	G	T	0.042	0.038	1.7e-19	7.1e-18	0.0403249016660804	AGA	S	D936Y	G2806T	GAC>TAC	Missense	GU280_gp02, spike glycoprotein	0.959547184292156
CAMB-76D4A	MN908947.3	25757	G	T	0.063	0.059	1.9e-28	1.4e-26	0.0611092420819916	AGA	ORF3a	R122I	G365T	AGA>ATA	Missense	GU280_gp03	0.938794636420435
CAMB-76D4A	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999633766709394	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000101619131495156
CAMB-76D4A	MN908947.3	3037	C	T	1	1	0	0	0.99931766489765	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.58150113722517e-05
CAMB-76D68	MN908947.3	14408	C	T	1	1	0	0	0.999387942466592	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000340031963004522
CAMB-76D68	MN908947.3	16435	G	T	0.054	0.033	5.7e-22	1.2e-13	0.0450505669629176	AGG	ORF1ab:helicase	G67C	G199T	GGT>TGT	Missense	ORF1ab:helicase	0.954949433037082
CAMB-76D68	MN908947.3	17350	G	T	0.028	0.0089	2.2e-14	2e-06	0.0214540795463839	TGT	ORF1ab:helicase	V372F	G1114T	GTC>TTC	Missense	ORF1ab:helicase	0.978545920453616
CAMB-76D68	MN908947.3	17909	T	C	0.22	0.16	1.6e-106	1.1e-69	0.210982898887598	GTA	ORF1ab:helicase	V558A	T1673C	GTA>GCA	Missense	ORF1ab:helicase	0.789017101112402
CAMB-76D68	MN908947.3	23403	A	G	1	1	0	0	0.999800848690963	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000107235320250624
CAMB-76D68	MN908947.3	241	C	T	1	1	0	0	0.999875616733695	TCG	NA	NA	NA	NA	NA	NA	8.29221775363821e-05
CAMB-76D68	MN908947.3	26158	GTTA	-	0.19	0.145	1.3e-30;8.5e-31;6.5e-29;2.8e-26	1.4e-13;1.1e-13;3.9e-13;5.6e-12	0.172	TGT	ORF3a	.	766-769-delfrshift	.	no-SNV	GU280_gp03	0.824
CAMB-76D68	MN908947.3	26309	C	T	0.033	0.04	1.5e-15	1.2e-14	0.0339168490153173	GCT	E	A22V	C65T	GCT>GTT	Missense	GU280_gp04	0.965926852141294
CAMB-76D68	MN908947.3	27132	TA	-	0.0205	0.016	2e-05;4.2e-05	0.00039;0.00063	0.0195280039886987	CTA	M	.	610-611-delfrshift	.	no-SNV	GU280_gp05	0.980615359234513
CAMB-76D68	MN908947.3	28724	C	T	0.016	0.0094	2.4e-08	2.7e-05	0.0144269052414633	TCC	N	P151S	C451T	CCT>TCT	Missense	GU280_gp10	0.985573094758537
CAMB-76D68	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999793303017776	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-76D68	MN908947.3	28892	C	T	0.12	0.11	7.9e-51	2.4e-41	0.118367346938776	TCC	N	P207S	C619T	CCT>TCT	Missense	GU280_gp10	0.881632653061225
CAMB-76D68	MN908947.3	29635	C	T	0.021	0.033	1.5e-09	1.4e-11	0.0248538011695906	ACA	ORF10	Y26Y	C78T	TAC>TAT	Synonymous	GU280_gp11	0.975146198830409
CAMB-76D68	MN908947.3	3037	C	T	1	1	0	0	0.999739447628973	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000260552371026576
CAMB-76D68	MN908947.3	466	C	T	0.033	0.034	1.2e-16	2.6e-16	0.0333658627259631	CCT	ORF1ab:leader-protein	P67P	C201T	CCC>CCT	Synonymous	ORF1ab:leader-protein	0.966494725591338
CAMB-76D68	MN908947.3	9844	G	A	0.063	0.041	1.4e-27	7e-19	0.052699560836993	TGC	ORF1ab:nsp4	L430L	G1290A	TTG>TTA	Synonymous	ORF1ab:nsp4	0.947300439163007
CAMB-76D86	MN908947.3	11075	T	-	0.045	0.028	4.9e-11	1.4e-07	0.0383938933489669	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958519280697766
CAMB-76D86	MN908947.3	12410	A	G	1	1	0	0	0.999944260193417	TAT	ORF1ab:nsp8	I107V	A319G	ATC>GTC	Missense	ORF1ab:nsp8	5.57398065828712e-05
CAMB-76D86	MN908947.3	14408	C	T	0.99	1	0	0	0.993977181151122	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000311037593134552
CAMB-76D86	MN908947.3	14928	C	T	0.11	0.12	4.5e-49	6.1e-54	0.114788908318761	ACA	ORF1ab:RNA-dependent-RNA-polymerase	N487N	C1461T	AAC>AAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.885148638521109
CAMB-76D86	MN908947.3	18788	C	T	1	1	0	0	0.999546674403423	ACA	ORF1ab:3'-to-5'-exonuclease	T250I	C749T	ACA>ATA	Missense	ORF1ab:3'-to-5'-exonuclease	7.25320954522376e-05
CAMB-76D86	MN908947.3	19734	T	C	0.0097	0.0051	3.2e-06	0.00028	0.00755517826825127	TTG	ORF1ab:endoRNAse	V38V	T114C	GTT>GTC	Synonymous	ORF1ab:endoRNAse	0.992444821731749
CAMB-76D86	MN908947.3	19839	T	C	1	1	0	0	0.999843100337334	ATA	ORF1ab:endoRNAse	N73N	T219C	AAT>AAC	Synonymous	ORF1ab:endoRNAse	0.000156899662665725
CAMB-76D86	MN908947.3	21093	T	C	1	1	0	0	0.996906836872468	CTA	ORF1ab:2'-O-ribose-methyltransferase	S145S	T435C	TCT>TCC	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.000687369583895913
CAMB-76D86	MN908947.3	22432	C	T	0.16	0.15	9e-36	3e-31	0.155905511811024	ACT	S	D290D	C870T	GAC>GAT	Synonymous	GU280_gp02, spike glycoprotein	0.844094488188976
CAMB-76D86	MN908947.3	23403	A	G	1	1	0	0	0.999467660367314	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.80242594775467e-05
CAMB-76D86	MN908947.3	241	C	T	1	1	0	0	0.999737846261396	TCG	NA	NA	NA	NA	NA	NA	0.00010194867612362
CAMB-76D86	MN908947.3	2453	C	T	0.034	0.039	4.4e-15	1.7e-16	0.0356113277937935	ACT	ORF1ab:nsp2	L550F	C1648T	CTC>TTC	Missense	ORF1ab:nsp2	0.964388672206206
CAMB-76D86	MN908947.3	25627	T	-	0.0073	0.0023	4e-05	0.0078	0.00554760200429492	CTT	ORF3a	.	235-235-delfrshift	.	no-SNV	GU280_gp03	0.994297303746123
CAMB-76D86	MN908947.3	28681	G	T	0.01	0.0052	3.6e-06	0.00023	0.00847504416961131	AGG	N	E136D	G408T	GAG>GAT	Missense	GU280_gp10	0.991469743816254
CAMB-76D86	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999236433051541	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	5.98730690935217e-05
CAMB-76D86	MN908947.3	3037	C	T	1	1	0	0	0.999230236317451	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76D86	MN908947.3	4137	TTCAAGAGGGTGTTTTAACTGC	-	0.00186363636363636	0.0062	0.0045;0.0031;0.0035;0.0052;0.0057;0.0059;0.0032;0.013;0.0023;0.0074;0.03;0.0087;0.00017;4.8e-06;NA;NA;NA;NA;NA;NA;NA;NA	0.00016;0.00016;0.00016;0.00016;0.00016;2e-04;4e-05;0.00015;3.8e-05;8.7e-05;0.00092;0.00011;4.3e-05;3e-05;3.1e-05;6.6e-05;0.00016;5.1e-05;0.00089;0.00075;0.00091;0.00012	0.00405104028456088	GTT	ORF1ab:nsp3	.	1418-1439-delfrshift	.	no-SNV	ORF1ab:nsp3	0.99684288589893
CAMB-76D86	MN908947.3	6120	C	T	0.011	0.0039	3.4e-05	0.0043	0.00776119402985075	TCA	ORF1ab:nsp3	S1134L	C3401T	TCA>TTA	Missense	ORF1ab:nsp3	0.992238805970149
CAMB-76D86	MN908947.3	6606	C	T	0.0094	0.0046	6.2e-06	0.00056	0.0069204152249135	TCT	ORF1ab:nsp3	S1296F	C3887T	TCT>TTT	Missense	ORF1ab:nsp3	0.993079584775087
CAMB-76D86	MN908947.3	7357	TATG	-	0.000975	0.0066	NA;NA;NA;0.0025	9.2e-05;0.00016;4.7e-05;0.00024	0.00287638098973655	TTA	ORF1ab:nsp3	.	4638-4641-delfrshift	.	no-SNV	ORF1ab:nsp3	0.996855766657747
CAMB-76D86	MN908947.3	7395	T	-	0.0074	0.0073	3.2e-05	3.8e-05	0.00736556064073227	ATT	ORF1ab:nsp3	.	4676-4676-delfrshift	.	no-SNV	ORF1ab:nsp3	0.992562929061785
CAMB-76D86	MN908947.3	9499	T	C	0.012	0.0024	3.7e-07	0.0043	0.00794789052228995	TTG	ORF1ab:nsp4	V315V	T945C	GTT>GTC	Synonymous	ORF1ab:nsp4	0.991992350902354
CAMB-76DA4	MN908947.3	101	G	A	0.012	0.015	2.8e-07	1.2e-08	0.0134796869605248	CGG	NA	NA	NA	NA	NA	NA	0.986362066981241
CAMB-76DA4	MN908947.3	10262	G	A	1	1	0	0	0.999593551009348	GGC	ORF1ab:3C-like-proteinase	A70T	G208A	GCT>ACT	Missense	ORF1ab:3C-like-proteinase	0.000184749541205306
CAMB-76DA4	MN908947.3	10986	G	T	0.017	0.016	2.7e-05	3.9e-05	0.0165180152622597	AGA	ORF1ab:nsp6	R5I	G14T	AGA>ATA	Missense	ORF1ab:nsp6	0.98158225198828
CAMB-76DA4	MN908947.3	11075	T	-	0.033	0.027	1.2e-08	1.2e-07	0.0303613084744555	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964510212440123
CAMB-76DA4	MN908947.3	11939	G	T	0.007	0.0085	8.8e-05	1.7e-05	0.00758621671244965	TGT	ORF1ab:nsp7	V33F	G97T	GTC>TTC	Missense	ORF1ab:nsp7	0.992057956987717
CAMB-76DA4	MN908947.3	12140	AC	-	0.019	0.019	0.00073;1.3e-05	0.00075;9.2e-06	0.0190342328306648	TAC	ORF1ab:nsp8	.	49-50-delfrshift	.	no-SNV	ORF1ab:nsp8	0.986340463729824
CAMB-76DA4	MN908947.3	12164	G	T	0.026	0.027	1.1e-09	7.5e-10	0.0265322231558577	GGC	ORF1ab:nsp8	A25S	G73T	GCT>TCT	Missense	ORF1ab:nsp8	0.971948497271238
CAMB-76DA4	MN908947.3	12536	TAT	-	0.00803333333333333	0.00923333333333333	0.0013;0.00087;2e-08	0.00022;0.00016;6.3e-09	0.00406308249732967	TTA	ORF1ab:nsp8	.	445-447-delinframe	.	no-SNV	ORF1ab:nsp8	0.996200865947873
CAMB-76DA4	MN908947.3	12578	G	T	0.048	0.048	5.2e-16	1.8e-16	0.0476742152662411	AGA	ORF1ab:nsp8	D163Y	G487T	GAT>TAT	Missense	ORF1ab:nsp8	0.946402028503978
CAMB-76DA4	MN908947.3	13548	C	-	0.027	0.029	1.2e-07	2.6e-08	0.027658559847401	ACA	ORF1ab:RNA-dependent-RNA-polymerase	.	81-81-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.97068122008513
CAMB-76DA4	MN908947.3	13569	TGG	-	0.0142333333333333	0.0149666666666667	0.0013;1.2e-08;4.6e-08	0.00029;9.9e-09;2.2e-08	0.0175001717386824	CTG	ORF1ab:RNA-dependent-RNA-polymerase	.	102-104-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.995660270976781
CAMB-76DA4	MN908947.3	13571	G	T	0.1	0.1	2.2e-21	1.3e-21	0.104182496373558	GGT	ORF1ab:RNA-dependent-RNA-polymerase	G35V	G104T	GGT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.87746079988948
CAMB-76DA4	MN908947.3	13726	G	T	0.0089	0.0089	1.3e-05	8.3e-06	0.00892754621655758	TGT	ORF1ab:RNA-dependent-RNA-polymerase	V87F	G259T	GTT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.989443391893444
CAMB-76DA4	MN908947.3	14187	GG	TT	0.0087	0.00955	8.9e-06;5.4e-06	3.2e-06;3.1e-06	0.00912661945690758	GGG	ORF1ab:RNA-dependent-RNA-polymerase	.	720-721-mnv	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.99009299886856
CAMB-76DA4	MN908947.3	14277	G	T	0.017	0.018	4.8e-08	1.1e-08	0.0171524842780997	GGT	ORF1ab:RNA-dependent-RNA-polymerase	R270S	G810T	AGG>AGT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.982527994422901
CAMB-76DA4	MN908947.3	1440	G	T	0.009	0.0088	1.8e-05	2.1e-05	0.00891464229997771	GGC	ORF1ab:nsp2	G212V	G635T	GGC>GTC	Missense	ORF1ab:nsp2	0.990862491642523
CAMB-76DA4	MN908947.3	14408	C	T	1	1	0	0	0.997282944300358	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000710139557860936
CAMB-76DA4	MN908947.3	1547	A	G	0.012	0.014	1.3e-06	1.9e-07	0.0129446317850538	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.960295877297944
CAMB-76DA4	MN908947.3	1547	A	T	0.022	0.017	8.4e-11	1e-08	0.0194713368867617	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.960295877297944
CAMB-76DA4	MN908947.3	16508	G	T	0.026	0.021	5.9e-06	3.2e-05	0.0237226277372263	GGT	ORF1ab:helicase	G91V	G272T	GGT>GTT	Missense	ORF1ab:helicase	0.976277372262774
CAMB-76DA4	MN908947.3	18263	C	-	0.0067	0.0072	4.2e-05	2.5e-05	0.00695987834834484	ACC	ORF1ab:3'-to-5'-exonuclease	.	224-224-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.991850898740593
CAMB-76DA4	MN908947.3	18318	G	T	0.015	0.015	2.3e-08	1.9e-08	0.0153419303832872	GGT	ORF1ab:3'-to-5'-exonuclease	G93G	G279T	GGG>GGT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.983942063142821
CAMB-76DA4	MN908947.3	19679	G	T	0.02	0.019	4.4e-09	6.7e-09	0.019677221359714	GGT	ORF1ab:endoRNAse	G20V	G59T	GGT>GTT	Missense	ORF1ab:endoRNAse	0.979997833700401
CAMB-76DA4	MN908947.3	19687	C	-	0.0058	0.007	0.00014	4.2e-05	0.00636076182072211	ACC	ORF1ab:endoRNAse	.	67-67-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.992609750716964
CAMB-76DA4	MN908947.3	19816	G	T	0.038	0.037	1.4e-17	2.4e-17	0.0373650107991361	AGT	ORF1ab:endoRNAse	V66L	G196T	GTA>TTA	Missense	ORF1ab:endoRNAse	0.96231101511879
CAMB-76DA4	MN908947.3	19839	T	C	1	1	0	0	0.998304545936209	ATA	ORF1ab:endoRNAse	N73N	T219C	AAT>AAC	Synonymous	ORF1ab:endoRNAse	0.000600473314259475
CAMB-76DA4	MN908947.3	20578	G	T	0.017	0.016	3.7e-08	1.2e-07	0.0167274147357459	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	0.98288206196303
CAMB-76DA4	MN908947.3	20627	G	T	0.017	0.016	8.1e-08	1.3e-07	0.0166925159696117	GGC	ORF1ab:endoRNAse	G336V	G1007T	GGC>GTC	Missense	ORF1ab:endoRNAse	0.982650298362293
CAMB-76DA4	MN908947.3	20922	G	T	0.023	0.024	3.1e-10	6.2e-11	0.0231334749223983	GGT	ORF1ab:2'-O-ribose-methyltransferase	W88C	G264T	TGG>TGT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.975428851494854
CAMB-76DA4	MN908947.3	20925	G	T	0.017	0.017	2.2e-09	3.7e-09	0.0171920712665593	TGC	ORF1ab:2'-O-ribose-methyltransferase	L89F	G267T	TTG>TTT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.981328687419874
CAMB-76DA4	MN908947.3	20936	C	-	0.0074	0.011	0.00011	4.7e-06	0.00868195226602306	ACG	ORF1ab:2'-O-ribose-methyltransferase	.	278-278-delfrshift	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.98994368463395
CAMB-76DA4	MN908947.3	2219	A	G	0.0089	0.0072	8.2e-06	2.8e-05	0.00815912834156848	TAT	ORF1ab:nsp2	I472V	A1414G	ATC>GTC	Missense	ORF1ab:nsp2	0.991655053000549
CAMB-76DA4	MN908947.3	22878	AC	-	0.0083	0.0091	0.00054;2.3e-06	0.00035;1e-06	0.00866860223973455	AAC	S	.	1316-1317-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.994785955184043
CAMB-76DA4	MN908947.3	22899	G	T	0.028	0.026	4.7e-09	1.9e-08	0.026638486649368	GGT	S	G446V	G1337T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.971310789319494
CAMB-76DA4	MN908947.3	22995	C	T	1	1	0	0	0.99970289109816	ACA	S	T478I	C1433T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	6.85635927322592e-05
CAMB-76DA4	MN908947.3	2320	T	G	0.0073	0.0051	3.7e-05	0.00023	0.00622454468608315	TTT	ORF1ab:nsp2	F505L	T1515G	TTT>TTG	Missense	ORF1ab:nsp2	0.993391224160455
CAMB-76DA4	MN908947.3	23403	A	G	1	1	0	0	0.998920297262839	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.29723986630064e-05
CAMB-76DA4	MN908947.3	241	C	T	1	1	0	0	0.99867363534446	TCG	NA	NA	NA	NA	NA	NA	0.000142110498807851
CAMB-76DA4	MN908947.3	24911	A	G	0.0074	0.0069	2.2e-05	3.4e-05	0.00720137066980779	TAC	S	T1117A	A3349G	ACA>GCA	Missense	GU280_gp02, spike glycoprotein	0.991834877121593
CAMB-76DA4	MN908947.3	24933	G	T	0.036	0.033	1.6e-06	3.5e-06	0.034548151029637	GGT	S	G1124V	G3371T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.963944470107705
CAMB-76DA4	MN908947.3	26158	GTTA	-	0.13	0.12	1.1e-54;1.8e-56;4.8e-53;7.6e-43	1.3e-49;1.6e-51;1.4e-48;2.2e-39	0.122918182985829	TGT	ORF3a	.	766-769-delfrshift	.	no-SNV	GU280_gp03	0.876471847570113
CAMB-76DA4	MN908947.3	27669	A	G	1	0.99	0	8.6e-155	0.997765363128492	AAG	ORF7a	E92E	A276G	GAA>GAG	Synonymous	GU280_gp07	0
CAMB-76DA4	MN908947.3	28079	G	T	0.021	0.018	2.3e-09	3.8e-08	0.0204187575705139	TGG	ORF8	V62V	G186T	GTG>GTT	Synonymous	GU280_gp09	0.978889081155909
CAMB-76DA4	MN908947.3	28086	G	T	0.014	0.014	1.2e-07	2.3e-07	0.0138960814776454	GGC	ORF8	A65S	G193T	GCT>TCT	Missense	GU280_gp09	0.985327118936648
CAMB-76DA4	MN908947.3	28089	G	T	0.015	0.012	2.5e-08	7.4e-07	0.0141130810620094	TGG	ORF8	G66C	G196T	GGT>TGT	Missense	GU280_gp09	0.985093058128253
CAMB-76DA4	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998674393061394	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000126273255324522
CAMB-76DA4	MN908947.3	29543	G	T	0.04	0.035	4.4e-18	6.3e-16	0.0380782918149466	AGA	NA	NA	NA	NA	NA	NA	0.960231316725979
CAMB-76DA4	MN908947.3	29779	G	T	0.013	0.013	9.8e-06	8.8e-06	0.012996859092386	GGA	NA	NA	NA	NA	NA	NA	0.98483699772555
CAMB-76DA4	MN908947.3	29781	G	T	0.015	0.014	2.9e-07	5.9e-07	0.0145407890516412	AGA	NA	NA	NA	NA	NA	NA	0.985352293381803
CAMB-76DA4	MN908947.3	3037	C	T	1	1	0	0	0.999328479536297	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.06863646002686e-05
CAMB-76DA4	MN908947.3	3211	T	-	0.013	0.014	1.6e-07	6.3e-08	0.0132236262121657	ATG	ORF1ab:nsp3	.	492-492-delfrshift	.	no-SNV	ORF1ab:nsp3	0.985836027034969
CAMB-76DA4	MN908947.3	3259	G	T	0.024	0.027	5.9e-09	8.9e-10	0.0250940665701881	AGA	ORF1ab:nsp3	Q180H	G540T	CAG>CAT	Missense	ORF1ab:nsp3	0.973342981186686
CAMB-76DA4	MN908947.3	3551	C	-	0.01	0.017	0.00032	2.6e-06	0.0136030069804904	ACC	ORF1ab:nsp3	.	832-832-delfrshift	.	no-SNV	ORF1ab:nsp3	0.986039019151602
CAMB-76DA4	MN908947.3	3564	G	T	0.017	0.025	8e-08	1.4e-10	0.0211754797569632	GGT	ORF1ab:nsp3	G282V	G845T	GGT>GTT	Missense	ORF1ab:nsp3	0.976658846176984
CAMB-76DA4	MN908947.3	4505	G	T	0.025	0.027	1.5e-12	4.1e-13	0.0261749108818602	GGG	ORF1ab:nsp3	G596C	G1786T	GGT>TGT	Missense	ORF1ab:nsp3	0.972389121918654
CAMB-76DA4	MN908947.3	4595	AC	-	0.00625	0.0061	0.00029;2e-05	0.00054;1.5e-05	0.00629521299004562	AAC	ORF1ab:nsp3	.	1876-1877-delfrshift	.	no-SNV	ORF1ab:nsp3	0.995288757733427
CAMB-76DA4	MN908947.3	481	AC	-	0.01995	0.02115	0.00012;3.4e-09	0.00013;4.1e-10	0.0207833459016019	AAC	ORF1ab:leader-protein	.	216-217-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.994127200828547
CAMB-76DA4	MN908947.3	5230	G	T	0.0089	0.0061	2e-05	0.00027	0.00738482384823848	AGT	ORF1ab:nsp3	K837N	G2511T	AAG>AAT	Missense	ORF1ab:nsp3	0.992344173441734
CAMB-76DA4	MN908947.3	558	G	T	0.046	0.049	2e-11	2e-12	0.0466938852128209	GGT	ORF1ab:leader-protein	G98V	G293T	GGT>GTT	Missense	ORF1ab:leader-protein	0.952132901590877
CAMB-76DA4	MN908947.3	6307	G	T	0.0098	0.0094	4e-06	4.5e-06	0.00963359705645125	GGA	ORF1ab:nsp3	W1196C	G3588T	TGG>TGT	Missense	ORF1ab:nsp3	0.989206383730731
CAMB-76DA4	MN908947.3	6513	G	T	0.013	0.014	2.3e-07	6.2e-08	0.0134873702760916	AGT	ORF1ab:nsp3	S1265I	G3794T	AGT>ATT	Missense	ORF1ab:nsp3	0.985925200704915
CAMB-76DA4	MN908947.3	7194	C	-	0.014	0.017	1e-06	8e-08	0.0154715858375483	ACC	ORF1ab:nsp3	.	4475-4475-delfrshift	.	no-SNV	ORF1ab:nsp3	0.98318952692651
CAMB-76DA4	MN908947.3	7214	G	T	0.023	0.029	3.5e-10	3.1e-12	0.0263563898174338	GGA	ORF1ab:nsp3	D1499Y	G4495T	GAT>TAT	Missense	ORF1ab:nsp3	0.97261506814091
CAMB-76DA4	MN908947.3	8018	G	T	0.0065	0.0079	7.1e-05	1.7e-05	0.00720372583401275	GGA	ORF1ab:nsp3	E1767*	G5299T	GAA>TAA	Nonsense	ORF1ab:nsp3	0.99250589141919
CAMB-76DA4	MN908947.3	8790	G	T	0.014	0.014	8.4e-08	1.2e-07	0.0140896720773581	GGT	ORF1ab:nsp4	G79V	G236T	GGT>GTT	Missense	ORF1ab:nsp4	0.984211846905097
CAMB-76DA4	MN908947.3	9249	G	T	0.018	0.018	1.5e-09	1.8e-09	0.0181144742172579	GGT	ORF1ab:nsp4	G232V	G695T	GGT>GTT	Missense	ORF1ab:nsp4	0.977718617975577
CAMB-76DA4	MN908947.3	9438	C	T	1	1	0	0	0.999665812632282	ACA	ORF1ab:nsp4	T295I	C884T	ACA>ATA	Missense	ORF1ab:nsp4	0.000111395789239167
CAMB-76DA4	MN908947.3	9649	G	T	0.0063	0.007	6.7e-05	3e-05	0.00661273754494093	GGA	ORF1ab:nsp4	W365C	G1095T	TGG>TGT	Missense	ORF1ab:nsp4	0.992526964560863
CAMB-76DC2	MN908947.3	11074	C	INS	0.094	0.098	3e-34	6.5e-37	0.0958911028613279	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.896696719448443
CAMB-76DC2	MN908947.3	11083	G	-	0.18	0.17	1.2e-82	3.5e-76	0.178158453277044	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	5.79905127521138e-05
CAMB-76DC2	MN908947.3	11083	G	T	0.82	0.83	0	0	0.821621182774498	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	5.79905127521138e-05
CAMB-76DC2	MN908947.3	13442	T	G	0.028	0.028	3.1e-13	3.6e-13	0.0276213160504176	GTC	ORF1ab:nsp11	S1A	T1G	TCA>GCA	Missense	ORF1ab:nsp11	0.972153787963976
CAMB-76DC2	MN908947.3	14805	C	T	1	1	0	0	0.999119437130401	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000276255017913411
CAMB-76DC2	MN908947.3	16141	G	A	0.0069	0.0059	4.1e-05	9.2e-05	0.00642613351037118	AGA	ORF1ab:RNA-dependent-RNA-polymerase	D892N	G2674A	GAC>AAC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.992578028581399
CAMB-76DC2	MN908947.3	16375	C	T	0.013	0.015	7.1e-06	1.6e-06	0.0135309788199298	TCC	ORF1ab:helicase	P47S	C139T	CCG>TCG	Missense	ORF1ab:helicase	0.986416268825996
CAMB-76DC2	MN908947.3	16466	C	T	0.018	0.019	5.2e-06	3.7e-06	0.0183506522219766	CCA	ORF1ab:helicase	P77L	C230T	CCA>CTA	Missense	ORF1ab:helicase	0.981551084580048
CAMB-76DC2	MN908947.3	16949	C	T	0.026	0.027	5.2e-13	2e-13	0.0267246031069836	CCT	ORF1ab:helicase	P238L	C713T	CCT>CTT	Missense	ORF1ab:helicase	0.973104995597967
CAMB-76DC2	MN908947.3	17400	T	A	0.11	0.1	2.3e-49	3.9e-48	0.10583419062669	ATG	ORF1ab:helicase	N388K	T1164A	AAT>AAA	Missense	ORF1ab:helicase	0.894080963845199
CAMB-76DC2	MN908947.3	18290	G	A	0.13	0.13	1.8e-59	7.6e-61	0.131075727087525	CGT	ORF1ab:3'-to-5'-exonuclease	R84H	G251A	CGT>CAT	Missense	ORF1ab:3'-to-5'-exonuclease	0.868355601104848
CAMB-76DC2	MN908947.3	18412	G	T	0.0085	0.0078	1.2e-05	2.4e-05	0.00814754627516891	TGT	ORF1ab:3'-to-5'-exonuclease	V125F	G373T	GTT>TTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.991451754727692
CAMB-76DC2	MN908947.3	23996	C	T	0.0066	0.0072	8.5e-05	4.1e-05	0.0068477846562307	ACC	S	P812S	C2434T	CCA>TCA	Missense	GU280_gp02, spike glycoprotein	0.992981349315879
CAMB-76DC2	MN908947.3	2480	A	G	1	1	0	0	0.999737136097785	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	6.57159755536571e-05
CAMB-76DC2	MN908947.3	2526	A	T	0.2	0.19	1.7e-89	8.5e-87	0.195163856188355	GAG	ORF1ab:nsp2	E574V	A1721T	GAG>GTG	Missense	ORF1ab:nsp2	0.804772510340439
CAMB-76DC2	MN908947.3	2558	CC	TT	1	1	0;0	0;0	0.998631750320413	ACC	ORF1ab:nsp2	.	1753-1754-mnv	.	no-SNV	ORF1ab:nsp2	0.000127858551910572
CAMB-76DC2	MN908947.3	26144	G	T	1	1	0	0	0.999563374855528	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000128419160138693
CAMB-76DC2	MN908947.3	27925	C	T	0.0088	0.0091	2.6e-05	1.9e-05	0.00897115602997956	ACA	ORF8	T11I	C32T	ACA>ATA	Missense	GU280_gp09	0.990574608221667
CAMB-76DC2	MN908947.3	28239	G	T	0.028	0.028	2.7e-13	4.9e-13	0.0282577575256568	TGT	ORF8	V116F	G346T	GTT>TTT	Missense	GU280_gp09	0.970552654394419
CAMB-76DC2	MN908947.3	28242	G	T	0.0075	0.0086	5.5e-05	2e-05	0.00807020455582756	TGT	ORF8	V117F	G349T	GTT>TTT	Missense	GU280_gp09	0.990788763951703
CAMB-76DC2	MN908947.3	3874	C	T	0.0092	0.0092	8.4e-06	1.1e-05	0.0092384008009648	TCG	ORF1ab:nsp3	I385I	C1155T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.990670580471932
CAMB-76DC2	MN908947.3	4965	C	T	0.0082	0.0087	1.4e-05	7e-06	0.00842260201161174	ACT	ORF1ab:nsp3	T749I	C2246T	ACT>ATT	Missense	ORF1ab:nsp3	0.991448897819002
CAMB-76DC2	MN908947.3	6659	A	G	0.0058	0.0079	0.00035	4.4e-05	0.00687285223367698	TAG	ORF1ab:nsp3	S1314G	A3940G	AGT>GGT	Missense	ORF1ab:nsp3	0.99274532264223
CAMB-76DE0	MN908947.3	11075	T	-	0.035	0.036	7.5e-09	2.8e-09	0.0351388620089026	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960688020127734
CAMB-76DE0	MN908947.3	11195	C	T	1	1	0	0	0.998678977272727	TCT	ORF1ab:nsp6	L75F	C223T	CTT>TTT	Missense	ORF1ab:nsp6	0.000454545454545455
CAMB-76DE0	MN908947.3	14408	C	T	1	1	0	0	0.998577000644957	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000511870271598366
CAMB-76DE0	MN908947.3	17363	T	C	0.011	0.011	8e-07	7.1e-07	0.0108839501665678	ATT	ORF1ab:helicase	I376T	T1127C	ATT>ACT	Missense	ORF1ab:helicase	0.988705334732807
CAMB-76DE0	MN908947.3	23403	A	G	1	1	0	0	0.999085462732606	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.87515791268494e-05
CAMB-76DE0	MN908947.3	241	C	T	1	1	0	0	0.998169548944076	TCG	NA	NA	NA	NA	NA	NA	0.000259541567631068
CAMB-76DE0	MN908947.3	25457	A	G	0.015	0.013	1.9e-08	8.3e-08	0.0143719305758139	GAT	ORF3a	D22G	A65G	GAT>GGT	Missense	GU280_gp03	0.985614687738361
CAMB-76DE0	MN908947.3	26801	C	T	0.011	0.01	3e-06	5.8e-06	0.0108581516910331	TCA	M	L93L	C279T	CTC>CTT	Synonymous	GU280_gp05	0.982887737558127
CAMB-76DE0	MN908947.3	28305	A	T	0.013	0.011	1.4e-07	7e-07	0.0122227365418538	AAT	N	N11I	A32T	AAT>ATT	Missense	GU280_gp10	0.987489522475073
CAMB-76DE0	MN908947.3	28307	G	A	0.014	0.012	1.2e-07	7.5e-07	0.0125945147868104	TGC	N	A12T	G34A	GCA>ACA	Missense	GU280_gp10	0.987137040848284
CAMB-76DE0	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998882713573598	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	9.62278675904542e-05
CAMB-76DE0	MN908947.3	29159	A	G	0.092	0.1	2.4e-41	4.4e-47	0.0974604521486151	AAC	N	T296A	A886G	ACT>GCT	Missense	GU280_gp10	0.900499020142635
CAMB-76DE0	MN908947.3	3037	C	T	1	1	0	0	0.999290066852038	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000147902739158729
CAMB-76DE0	MN908947.3	3373	C	A	1	1	0	0	0.999363402730295	ACA	ORF1ab:nsp3	D218E	C654A	GAC>GAA	Missense	ORF1ab:nsp3	2.35776766557423e-05
CAMB-76DE0	MN908947.3	3923	C	A	1	1	0	0	0.999775306145377	ACC	ORF1ab:nsp3	P402T	C1204A	CCT>ACT	Missense	ORF1ab:nsp3	0
CAMB-76E0B	MN908947.3	1059	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0
CAMB-76E0B	MN908947.3	11916	C	T	1	1	0	0	0.999930089485459	TCA	ORF1ab:nsp7	S25L	C74T	TCA>TTA	Missense	ORF1ab:nsp7	6.9910514541387e-05
CAMB-76E0B	MN908947.3	14408	C	T	1	1	0	0	0.999512127125732	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000313632562029551
CAMB-76E0B	MN908947.3	15205	ATT	-	0.0466666666666667	0.00753333333333333	1.9e-21;8.1e-21;2.9e-20	9.3e-05;0.00011;1e-04	0.0252245712730242	AAT	ORF1ab:RNA-dependent-RNA-polymerase	.	1738-1740-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.973795833726082
CAMB-76E0B	MN908947.3	23403	A	G	1	1	0	0	0.999929457244036	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.2325653578634e-05
CAMB-76E0B	MN908947.3	241	C	T	1	1	0	0	0.999335516635816	TCG	NA	NA	NA	NA	NA	NA	0.00052209407185913
CAMB-76E0B	MN908947.3	24781	G	C	0.042	0.12	1e-19	3.8e-53	0.0725060827250608	AGA	S	K1073N	G3219C	AAG>AAC	Missense	GU280_gp02, spike glycoprotein	0.927291159772912
CAMB-76E0B	MN908947.3	25563	G	T	1	1	0	0	0.999549985374525	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000135004387642598
CAMB-76E0B	MN908947.3	26787	GGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.0514117647058824	0.0828529411764706	6.9e-09;7.3e-09;1.3e-09;2.8e-09;1.7e-09;6.4e-09;3e-09;4.9e-09;1.1e-08;2.3e-09;9.6e-09;3.8e-09;4.3e-09;2.4e-19;7e-19;1.5e-19;3.5e-19;3.8e-09;1.6e-09;8.3e-09;2.9e-09;5.2e-10;5.3e-09;8.2e-09;7.8e-09;3e-09;8.9e-09;6.9e-10;3.1e-09;1.7e-09;NA;NA;NA;NA	4.2e-15;4.3e-15;9.7e-16;1.3e-15;9.2e-16;3.7e-15;2.2e-15;3e-15;7.6e-15;1.2e-15;5.8e-15;1.9e-15;1.9e-15;2.1e-15;7.1e-15;2.7e-15;4.1e-15;2.1e-15;5.2e-16;4.6e-15;1.7e-15;1.4e-16;2.7e-15;5.1e-15;4.9e-15;8.9e-16;5.4e-15;6.4e-17;2e-15;6.2e-16;4.1e-11;2.7e-09;2.9e-10;1e-09	0.0655231371683856	AGG	M	.	265-298-delfrshift	.	no-SNV	GU280_gp05	0.935490869643826
CAMB-76E0B	MN908947.3	27987	G	A	0.18	0.13	1.4e-55	1.2e-31	0.162574089754445	TGT	ORF8	V32I	G94A	GTA>ATA	Missense	GU280_gp09	0.837425910245555
CAMB-76E0B	MN908947.3	3037	C	T	1	1	0	0	0.999550561797753	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-76E0B	MN908947.3	6347	C	T	0.085	0.0022	3.4e-39	0.0056	0.0441556602103325	ACT	ORF1ab:nsp3	L1210L	C3628T	CTG>TTG	Synonymous	ORF1ab:nsp3	0.955808930278673
CAMB-76E29	MN908947.3	10986	G	T	0.017	0.022	2.4e-05	1.9e-06	0.0201213669754072	AGA	ORF1ab:nsp6	R5I	G14T	AGA>ATA	Missense	ORF1ab:nsp6	0.979878633024593
CAMB-76E29	MN908947.3	11074	C	INS	0.16	0.11	8.9e-68	8.1e-42	0.135959755317091	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.860765899179925
CAMB-76E29	MN908947.3	11083	G	-	0.13	0.25	2.6e-58	5.3e-119	0.194754304673646	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.4301241347749e-05
CAMB-76E29	MN908947.3	11083	G	T	0.87	0.75	0	8.79999999999999e-282	0.805074080430181	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.4301241347749e-05
CAMB-76E29	MN908947.3	12138	CTAC	-	0.009425	0.0405	0.035;0.03;8.7e-05;0.00072	1.5e-06;3.6e-07;1.1e-12;1.2e-09	0.0255472986543483	GCT	ORF1ab:nsp8	.	47-50-delfrshift	.	no-SNV	ORF1ab:nsp8	0.9849936499873
CAMB-76E29	MN908947.3	12164	G	T	0.016	0.027	1.9e-06	8.2e-10	0.0216475229376077	GGC	ORF1ab:nsp8	A25S	G73T	GCT>TCT	Missense	ORF1ab:nsp8	0.978133312080972
CAMB-76E29	MN908947.3	12578	G	T	0.034	0.028	2.9e-12	3.7e-10	0.0305894611491515	AGA	ORF1ab:nsp8	D163Y	G487T	GAT>TAT	Missense	ORF1ab:nsp8	0.969385729879925
CAMB-76E29	MN908947.3	12578	GA	TT	0.0295	0.014	2.9e-12;8.1e-13	3.7e-10;NA	0.0205226671986435	AGA	ORF1ab:nsp8	.	487-488-mnv	.	no-SNV	ORF1ab:nsp8	0.969385729879925
CAMB-76E29	MN908947.3	13394	A	-	0.016	0.014	8.3e-07	1.8e-06	0.015	GAA	ORF1ab:nsp10	.	370-370-delfrshift	.	no-SNV	ORF1ab:nsp10	0.985
CAMB-76E29	MN908947.3	13394	AA	-	0.0165	0.007	8.3e-07;4.1e-08	1.8e-06;NA	0.0120329322355921	GAA	ORF1ab:nsp10	.	370-371-delfrshift	.	no-SNV	ORF1ab:nsp10	0.985
CAMB-76E29	MN908947.3	13571	G	T	0.077	0.16	3.7e-15	1.2e-31	0.12018779342723	GGT	ORF1ab:RNA-dependent-RNA-polymerase	G35V	G104T	GGT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.852895148669797
CAMB-76E29	MN908947.3	14277	G	T	0.051	0.018	1.7e-21	9.2e-09	0.032688363514953	GGT	ORF1ab:RNA-dependent-RNA-polymerase	R270S	G810T	AGG>AGT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.967263939456572
CAMB-76E29	MN908947.3	14805	C	T	1	1	0	0	0.999921465454617	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	7.85345453831504e-05
CAMB-76E29	MN908947.3	16064	A	T	0.088	0.1	1.9e-40	3.2e-47	0.0950930996714129	CAG	ORF1ab:RNA-dependent-RNA-polymerase	Q866L	A2597T	CAG>CTG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.904753559693319
CAMB-76E29	MN908947.3	16127	C	A	0.068	0.02	1.3e-31	1e-10	0.0440693025322079	ACA	ORF1ab:RNA-dependent-RNA-polymerase	T887K	C2660A	ACA>AAA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.955788538427366
CAMB-76E29	MN908947.3	16280	G	T	0.013	0.011	8.4e-07	3.1e-06	0.0117281821317696	AGA	ORF1ab:helicase	R15I	G44T	AGA>ATA	Missense	ORF1ab:helicase	0.98827181786823
CAMB-76E29	MN908947.3	17096	G	T	0.008	0.014	1.5e-05	5.2e-08	0.0111856823266219	GGT	ORF1ab:helicase	G287V	G860T	GGT>GTT	Missense	ORF1ab:helicase	0.9887615905513
CAMB-76E29	MN908947.3	18097	C	A	0.022	0.016	1.1e-11	5.7e-09	0.0185979442431413	TCC	ORF1ab:3'-to-5'-exonuclease	P20T	C58A	CCT>ACT	Missense	ORF1ab:3'-to-5'-exonuclease	0.981291133624196
CAMB-76E29	MN908947.3	18484	C	T	0.016	0.017	3.6e-09	2.6e-09	0.0166141102273262	CCT	ORF1ab:3'-to-5'-exonuclease	L149F	C445T	CTC>TTC	Missense	ORF1ab:3'-to-5'-exonuclease	0.983354512793963
CAMB-76E29	MN908947.3	1899	G	T	0.0019	0.02	0.0069	4.8e-11	0.0104800422015122	CGA	ORF1ab:nsp2	R365L	G1094T	CGA>CTA	Missense	ORF1ab:nsp2	0.989344118164234
CAMB-76E29	MN908947.3	20578	G	T	0.016	0.013	1.2e-07	8.6e-07	0.014371850995292	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	0.985586850582308
CAMB-76E29	MN908947.3	20578	GTG	TCT	0.00533333333333333	0.0156666666666667	1.2e-07;NA;NA	8.6e-07;3.7e-09;6.9e-10	0.00997890637676456	AGT	ORF1ab:endoRNAse	.	958-960-mnv	.	no-SNV	ORF1ab:endoRNAse	0.985586850582308
CAMB-76E29	MN908947.3	22380	G	T	0.031	0.014	1.7e-07	8.2e-05	0.0212765957446809	AGG	S	R273M	G818T	AGG>ATG	Missense	GU280_gp02, spike glycoprotein	0.978723404255319
CAMB-76E29	MN908947.3	22498	C	T	0.0099	0.038	0.0015	4.5e-09	0.0259179265658747	TCT	S	I312I	C936T	ATC>ATT	Synonymous	GU280_gp02, spike glycoprotein	0.974082073434125
CAMB-76E29	MN908947.3	22899	G	T	0.039	0.033	1.3e-11	1.5e-10	0.0346358792184725	GGT	S	G446V	G1337T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.965364120781528
CAMB-76E29	MN908947.3	23029	C	T	0.0095	0.012	1.6e-05	1e-06	0.0109559354683361	ACT	S	Y489Y	C1467T	TAC>TAT	Synonymous	GU280_gp02, spike glycoprotein	0.989044064531664
CAMB-76E29	MN908947.3	23402	G	A	1	1	0	0	0.999814659461147	GGA	S	D614N	G1840A	GAT>AAT	Missense	GU280_gp02, spike glycoprotein	0.00012681194763642
CAMB-76E29	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-76E29	MN908947.3	24868	G	T	0.024	0.034	4e-12	5.1e-16	0.0291861919327377	GGT	S	W1102C	G3306T	TGG>TGT	Missense	GU280_gp02, spike glycoprotein	0.970693266231712
CAMB-76E29	MN908947.3	24933	G	T	0.055	0.03	3.8e-09	1.1e-05	0.0418301058931146	GGT	S	G1124V	G3371T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.958061365292485
CAMB-76E29	MN908947.3	25337	GACGACTCTGAGC	AGACGACTCTGAG	0.00806923076923077	0.000385923076923077	7.3e-06;3.8e-05;2.4e-05;1.5e-05;2.1e-05;1.7e-05;3.1e-05;1.8e-05;3e-05;2.8e-05;2.4e-05;1.2e-06;1.4e-06	NA;0.45;NA;NA;0.45;NA;0.47;0.45;0.46;0.00076;NA;0.45;NA	0.00364909735837083	AGA	S	.	3775-3787-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.996107170383143
CAMB-76E29	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-76E29	MN908947.3	25893	T	A	0.02	0.018	4.2e-10	2.5e-09	0.0192732383055611	TTG	ORF3a	I167I	T501A	ATT>ATA	Synonymous	GU280_gp03	0.980726761694439
CAMB-76E29	MN908947.3	26144	G	T	1	1	4.2e-222	9.2e-251	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-76E29	MN908947.3	26526	G	T	0.015	0.007	2.1e-06	0.00094	0.011240632805995	GGC	M	A2S	G4T	GCA>TCA	Missense	GU280_gp05	0.979415302063096
CAMB-76E29	MN908947.3	27000	G	T	0.013	0.0088	1.4e-07	7.5e-06	0.010792753436978	TGA	M	D160Y	G478T	GAC>TAC	Missense	GU280_gp05	0.98914300398304
CAMB-76E29	MN908947.3	28077	G	T	0.0052	0.019	0.0073	1.1e-07	0.0108017282765242	CGT	ORF8	V62L	G184T	GTG>TTG	Missense	GU280_gp09	0.989198271723476
CAMB-76E29	MN908947.3	28079	G	T	0.0081	0.054	0.00026	1.1e-18	0.0260721247563353	TGG	ORF8	V62V	G186T	GTG>GTT	Synonymous	GU280_gp09	0.970760233918129
CAMB-76E29	MN908947.3	28086	G	T	0.022	0.015	2.8e-10	2.7e-07	0.0191881918819188	GGC	ORF8	A65S	G193T	GCT>TCT	Missense	GU280_gp09	0.980811808118081
CAMB-76E29	MN908947.3	28086	GC	TT	0.016	0.0075	2.8e-10;2.2e-05	2.7e-07;NA	0.0124908155767818	GGC	ORF8	.	193-194-mnv	.	no-SNV	GU280_gp09	0.980811808118081
CAMB-76E29	MN908947.3	28326	G	T	0.0063	0.017	0.00016	2.7e-09	0.0119955376140036	GGT	N	G18V	G53T	GGT>GTT	Missense	GU280_gp10	0.98793545641698
CAMB-76E29	MN908947.3	28377	C	T	0.43	0.46	2.6e-233	1.5e-255	0.443043595106505	GCG	N	A35V	C104T	GCG>GTG	Missense	GU280_gp10	0.556874612948833
CAMB-76E29	MN908947.3	28460	G	T	0.0073	0.018	4.2e-05	2e-09	0.0122454002830595	AGA	N	D63Y	G187T	GAC>TAC	Missense	GU280_gp10	0.98775459971694
CAMB-76E29	MN908947.3	29210	G	T	0.0075	0.017	1.4e-05	1.5e-09	0.0123761490860965	AGC	N	A313S	G937T	GCG>TCG	Missense	GU280_gp10	0.987445004828844
CAMB-76E29	MN908947.3	29320	AG	-	0.0097	0.005	2.7e-06;3.3e-06	0.00036;0.00037	0.00730581476438747	AAG	N	.	1047-1048-delfrshift	.	no-SNV	GU280_gp10	0.992410381513858
CAMB-76E29	MN908947.3	29529	CCTAAACTCATGCAG	-	0.000466666666666667	0.0123	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;6e-05;NA	4e-07;2.5e-07;3.7e-07;2.1e-06;3e-07;2.4e-07;3.1e-07;3.4e-07;3.5e-07;4.8e-07;5.6e-07;4e-07;3.5e-07;1.6e-08;0.00047	0.00661594442606682	GCC	N	.	1256-1260-delfrshift	.	no-SNV	GU280_gp10	0.993344425956739
CAMB-76E29	MN908947.3	29543	G	C	0.012	0.0019	9.8e-07	0.0063	0.00679347826086957	AGA	NA	NA	NA	NA	NA	NA	0.964673913043478
CAMB-76E29	MN908947.3	29543	G	T	0.026	0.026	1.2e-10	4.8e-11	0.0261548913043478	AGA	NA	NA	NA	NA	NA	NA	0.964673913043478
CAMB-76E29	MN908947.3	29779	G	T	0.025	0.0069	4.9e-08	0.0023	0.0148609779482263	GGA	NA	NA	NA	NA	NA	NA	0.985139022051774
CAMB-76E29	MN908947.3	29781	G	T	0.0064	0.026	0.0027	1.2e-09	0.0170616113744076	AGA	NA	NA	NA	NA	NA	NA	0.980094786729858
CAMB-76E29	MN908947.3	29782	A	T	0.17	0.19	2.6e-54	1.2e-67	0.180997624703088	GAG	NA	NA	NA	NA	NA	NA	0.819002375296912
CAMB-76E29	MN908947.3	3211	T	-	0.018	0.051	7e-10	7.7e-24	0.037772397094431	ATG	ORF1ab:nsp3	.	492-492-delfrshift	.	no-SNV	ORF1ab:nsp3	0.96219301279834
CAMB-76E29	MN908947.3	3211	TG	-	0.018	0.0255285	7e-10;7.3e-10	7.7e-24;NA	0.0223068552774755	ATG	ORF1ab:nsp3	.	492-493-delfrshift	.	no-SNV	ORF1ab:nsp3	0.96219301279834
CAMB-76E29	MN908947.3	3259	G	T	0.032	0.013	2.4e-11	9.7e-06	0.0210605234460196	AGA	ORF1ab:nsp3	Q180H	G540T	CAG>CAT	Missense	ORF1ab:nsp3	0.978905398037077
CAMB-76E29	MN908947.3	3564	G	T	0.025	0.015	6.2e-07	1.7e-05	0.0183406113537118	GGT	ORF1ab:nsp3	G282V	G845T	GGT>GTT	Missense	ORF1ab:nsp3	0.981659388646288
CAMB-76E29	MN908947.3	4505	G	T	0.015	0.03	3.7e-08	7.2e-15	0.024718965308836	GGG	ORF1ab:nsp3	G596C	G1786T	GGT>TGT	Missense	ORF1ab:nsp3	0.97516015955518
CAMB-76E29	MN908947.3	4593	A	-	0.026	0.032	1.6e-13	3.2e-16	0.0301539165760714	GAA	ORF1ab:nsp3	.	1874-1874-delfrshift	.	no-SNV	ORF1ab:nsp3	0.955713223093208
CAMB-76E29	MN908947.3	481	AC	-	0.0155	0.039	3.4e-09;2.7e-05	3.3e-09;8.1e-16	0.0254752431476569	AAC	ORF1ab:leader-protein	.	216-217-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.984125177809388
CAMB-76E29	MN908947.3	558	G	T	0.023	0.041	1.2e-06	1e-10	0.0301657860158238	GGT	ORF1ab:leader-protein	G98V	G293T	GGT>GTT	Missense	ORF1ab:leader-protein	0.969666470966479
CAMB-76E29	MN908947.3	558	GT	TC	0.0195	0.0205	1.2e-06;1.7e-09	1e-10;NA	0.0198790458058013	GGT	ORF1ab:leader-protein	.	293-294-mnv	.	no-SNV	ORF1ab:leader-protein	0.969666470966479
CAMB-76E29	MN908947.3	6483	G	T	0.017	0.017	1.1e-09	8e-10	0.017130226561061	GGA	ORF1ab:nsp3	G1255V	G3764T	GGA>GTA	Missense	ORF1ab:nsp3	0.982851353840486
CAMB-76E29	MN908947.3	6513	G	T	0.026	0.041	4.6e-13	1.4e-19	0.0345391520753711	AGT	ORF1ab:nsp3	S1265I	G3794T	AGT>ATT	Missense	ORF1ab:nsp3	0.965389743133944
CAMB-76E29	MN908947.3	663	G	T	0.014	0.017	3.4e-08	1.8e-09	0.0157183684073785	GGC	ORF1ab:leader-protein	G133V	G398T	GGC>GTC	Missense	ORF1ab:leader-protein	0.984151727721486
CAMB-76E65	MN908947.3	11074	C	INS	0.11	0.12	1.4e-47	3.1e-49	0.115958287068304	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.867443537586282
CAMB-76E65	MN908947.3	11074	C	T	0.015	0.013	2.9e-11	6.8e-09	0.0141485136047803	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.867443537586282
CAMB-76E65	MN908947.3	11083	G	-	0.15	0.13	1.9e-64	2.8e-54	0.136949903723067	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.15143985112036e-05
CAMB-76E65	MN908947.3	11083	G	T	0.85	0.87	0	0	0.862856466690333	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.15143985112036e-05
CAMB-76E65	MN908947.3	12731	G	A	0.03	0.035	1.7e-14	1.2e-16	0.0320495755316946	TGC	ORF1ab:nsp9	A16T	G46A	GCC>ACC	Missense	ORF1ab:nsp9	0.967920844795457
CAMB-76E65	MN908947.3	1314	C	T	0.0079	0.0079	4e-05	3.9e-05	0.00788977861516722	ACT	ORF1ab:nsp2	T170I	C509T	ACT>ATT	Missense	ORF1ab:nsp2	0.991756947715497
CAMB-76E65	MN908947.3	14805	C	T	1	1	0	0	0.998951312386732	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.0002138100959091
CAMB-76E65	MN908947.3	18902	A	G	0.0045	0.0086	0.00038	6.6e-06	0.00638804041353383	AAG	ORF1ab:3'-to-5'-exonuclease	K288R	A863G	AAG>AGG	Missense	ORF1ab:3'-to-5'-exonuclease	0.99359727443609
CAMB-76E65	MN908947.3	2083	T	C	0.01	0.016	1.7e-06	7e-09	0.013330693592028	TTC	ORF1ab:nsp2	V426V	T1278C	GTT>GTC	Synonymous	ORF1ab:nsp2	0.98662531071955
CAMB-76E65	MN908947.3	21538	G	T	1	0.99	0	0	0.996108261100301	TGT	ORF1ab:2'-O-ribose-methyltransferase	V294F	G880T	GTT>TTT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.00389173889969927
CAMB-76E65	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-76E65	MN908947.3	25578	C	T	0.0039	0.011	0.0011	8.4e-07	0.00736903629508234	TCA	ORF3a	I62I	C186T	ATC>ATT	Synonymous	GU280_gp03	0.99259658250914
CAMB-76E65	MN908947.3	2558	C	T	1	1	0	0	0.999920306024864	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	3.98469875677399e-05
CAMB-76E65	MN908947.3	25868	C	T	0.024	0.031	6.2e-12	1.1e-14	0.0279170720754435	CCT	ORF3a	P159L	C476T	CCT>CTT	Missense	GU280_gp03	0.972008083227303
CAMB-76E65	MN908947.3	26144	G	T	1	1	0	0	0.999851279000595	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000148720999405116
CAMB-76E65	MN908947.3	27384	T	C	0.99	1	0	0	0.995122910152959	ATT	ORF6	D61D	T183C	GAT>GAC	Synonymous	GU280_gp06	9.3610169808848e-05
CAMB-76E65	MN908947.3	27920	C	T	0.018	0.013	7e-09	7.3e-07	0.0153483910351443	TCA	ORF8	I9I	C27T	ATC>ATT	Synonymous	GU280_gp09	0.984477195430365
CAMB-76E65	MN908947.3	29460	C	G	0.0042	0.0087	0.00063	2.5e-05	0.00648172154524242	CCT	N	P396R	C1187G	CCT>CGT	Missense	GU280_gp10	0.993259009592948
CAMB-76E65	MN908947.3	29560	G	T	0.025	0.025	2.8e-12	2.2e-12	0.0247490371866911	TGG	ORF10	M1I	G3T	ATG>ATT	Missense	GU280_gp11	0.975124692215418
CAMB-76E65	MN908947.3	337	C	T	0.018	0.018	6e-09	5.2e-09	0.017756909898646	GCG	ORF1ab:leader-protein	R24R	C72T	CGC>CGT	Synonymous	ORF1ab:leader-protein	0.982243090101354
CAMB-76E83	MN908947.3	10262	G	A	1	1	0	0	0.999904185715459	GGC	ORF1ab:3C-like-proteinase	A70T	G208A	GCT>ACT	Missense	ORF1ab:3C-like-proteinase	1.36877549344357e-05
CAMB-76E83	MN908947.3	11075	T	-	0.033	0.031	4.9e-09	1.2e-08	0.03169992100502	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.963560380195194
CAMB-76E83	MN908947.3	14408	C	T	1	1	0	0	0.998655395226653	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000498001767906276
CAMB-76E83	MN908947.3	1547	A	T	0.0082	0.0089	2.8e-05	1.7e-05	0.00853612525938502	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.983305036785512
CAMB-76E83	MN908947.3	19839	T	C	1	1	0	0	0.999303912014479	ATA	ORF1ab:endoRNAse	N73N	T219C	AAT>AAC	Synonymous	ORF1ab:endoRNAse	0.00030163812705926
CAMB-76E83	MN908947.3	22995	C	T	1	1	0	0	0.999361090405708	ACA	S	T478I	C1433T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0.000133106165477585
CAMB-76E83	MN908947.3	23403	A	G	1	1	0	0	0.999394693863566	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000102787834488745
CAMB-76E83	MN908947.3	241	C	T	1	1	0	0	0.999181209937772	TCG	NA	NA	NA	NA	NA	NA	0.000116970008889721
CAMB-76E83	MN908947.3	25485	T	G	0.0075	0.007	2.6e-05	4.3e-05	0.00728164288611142	CTA	ORF3a	A31A	T93G	GCT>GCG	Synonymous	GU280_gp03	0.99222062456218
CAMB-76E83	MN908947.3	27669	A	G	1	1	0	0	0.999815668202765	AAG	ORF7a	E92E	A276G	GAA>GAG	Synonymous	GU280_gp07	0
CAMB-76E83	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999018249018249	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-76E83	MN908947.3	3037	C	T	1	1	0	0	0.999436340270106	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.76391675873109e-05
CAMB-76E83	MN908947.3	9438	C	T	1	1	0	0	0.999753390875462	ACA	ORF1ab:nsp4	T295I	C884T	ACA>ATA	Missense	ORF1ab:nsp4	8.2203041512536e-05
CAMB-76EA1	MN908947.3	11075	T	-	0.037	0.032	3e-10	3.8e-09	0.0350025939149806	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958588910250542
CAMB-76EA1	MN908947.3	13592	C	T	1	1	0	0	0.999892074684318	ACT	ORF1ab:RNA-dependent-RNA-polymerase	T42I	C125T	ACT>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	3.59751052271828e-05
CAMB-76EA1	MN908947.3	14408	C	T	1	1	0	0	0.996641465750096	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000385874147861257
CAMB-76EA1	MN908947.3	17502	C	T	1	1	0	0	0.999135107084554	TCA	ORF1ab:helicase	F422F	C1266T	TTC>TTT	Synonymous	ORF1ab:helicase	0.000108111614430738
CAMB-76EA1	MN908947.3	23403	A	G	1	1	0	0	0.999303000968054	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00010648596321394
CAMB-76EA1	MN908947.3	241	C	T	1	1	0	0	0.998686949112294	TCG	NA	NA	NA	NA	NA	NA	0.000195560770509436
CAMB-76EA1	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99835771105979	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000352961938937585
CAMB-76EA1	MN908947.3	3037	C	T	1	1	0	0	0.999210217528658	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000135391280801516
CAMB-76EA1	MN908947.3	683	C	T	0.012	0.011	8e-07	1.6e-06	0.0117701784556398	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.98713033182036
CAMB-76ECF	MN908947.3	11075	T	-	0.033	0.028	1.4e-08	2.3e-07	0.0303947591348054	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.9650985485966
CAMB-76ECF	MN908947.3	11195	C	T	1	1	0	0	0.99928439459783	TCT	ORF1ab:nsp6	L75F	C223T	CTT>TTT	Missense	ORF1ab:nsp6	0.000156132087746233
CAMB-76ECF	MN908947.3	13778	AT	-	0.031	0.0255	1.4e-09;2.1e-09	1.9e-08;5.2e-08	0.0284807075062334	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.972369284185556
CAMB-76ECF	MN908947.3	13780	A	T	0.021	0.023	1.5e-06	5.5e-07	0.0218191323249207	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I105L	A313T	ATA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.972636661920386
CAMB-76ECF	MN908947.3	14408	C	T	1	1	0	0	0.998122327236138	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000583965213641427
CAMB-76ECF	MN908947.3	1547	A	-	0.012	0.012	1e-06	9.6e-07	0.0118498191343395	TAG	ORF1ab:nsp2	.	742-742-delfrshift	.	no-SNV	ORF1ab:nsp2	0.922352500935512
CAMB-76ECF	MN908947.3	1547	A	G	0.022	0.022	1e-10	1.2e-10	0.0222651864787327	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.922352500935512
CAMB-76ECF	MN908947.3	1547	A	T	0.041	0.042	3e-18	1.2e-18	0.0414119995010602	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.922352500935512
CAMB-76ECF	MN908947.3	18244	T	C	0.013	0.015	1.2e-07	4.3e-08	0.0139676113360324	TTA	ORF1ab:3'-to-5'-exonuclease	Y69H	T205C	TAC>CAC	Missense	ORF1ab:3'-to-5'-exonuclease	0.985914304993252
CAMB-76ECF	MN908947.3	20067	A	G	0.012	0.011	3.8e-05	3.4e-05	0.010998680158381	AAG	ORF1ab:endoRNAse	K149K	A447G	AAA>AAG	Synonymous	ORF1ab:endoRNAse	0.988561372635284
CAMB-76ECF	MN908947.3	23050	T	C	0.0088	0.007	5.8e-06	3.5e-05	0.00786838340486409	GTT	S	G496G	T1488C	GGT>GGC	Synonymous	GU280_gp02, spike glycoprotein	0.991982594182165
CAMB-76ECF	MN908947.3	23403	A	G	1	1	0	0	0.999616729746563	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.58935786262955e-05
CAMB-76ECF	MN908947.3	24022	T	C	0.0091	0.0098	6.1e-06	2.4e-06	0.00938681793625067	ATC	S	D820D	T2460C	GAT>GAC	Synonymous	GU280_gp02, spike glycoprotein	0.985926526202053
CAMB-76ECF	MN908947.3	241	C	T	1	1	0	0	0.998687503815396	TCG	NA	NA	NA	NA	NA	NA	0.000167877418960991
CAMB-76ECF	MN908947.3	25521	C	T	0.011	0.011	2.4e-06	2.2e-06	0.0112988079646607	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.985504672689738
CAMB-76ECF	MN908947.3	26447	C	G	0.015	0.017	3.4e-08	3.8e-09	0.015637112671377	TCT	E	S68C	C203G	TCT>TGT	Missense	GU280_gp04	0.982613125429135
CAMB-76ECF	MN908947.3	27591	T	C	0.0058	0.0098	0.00087	4.6e-05	0.00808720112517581	CTT	ORF7a	A66A	T198C	GCT>GCC	Synonymous	GU280_gp07	0.991209563994374
CAMB-76ECF	MN908947.3	27923	C	T	0.011	0.0098	1.5e-06	5.8e-06	0.010540404885394	TCA	ORF8	I10I	C30T	ATC>ATT	Synonymous	GU280_gp09	0.989292287100552
CAMB-76ECF	MN908947.3	28253	C	T	0.05	0.052	2.1e-22	3.8e-23	0.0513730658051352	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.945906308450944
CAMB-76ECF	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999213943024422	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000120845921450151
CAMB-76ECF	MN908947.3	29311	C	T	0.014	0.014	1.3e-07	8.1e-08	0.013924749974631	TCA	N	F346F	C1038T	TTC>TTT	Synonymous	GU280_gp10	0.9858271977991
CAMB-76ECF	MN908947.3	29741	C	T	0.0089	0.008	2.3e-05	5.4e-05	0.00842646267853941	ACG	NA	NA	NA	NA	NA	NA	0.991214964441523
CAMB-76ECF	MN908947.3	3037	C	T	1	1	0	0	0.999014755213587	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.38328368012386e-05
CAMB-76ECF	MN908947.3	3373	C	A	1	1	0	0	0.999326694780113	ACA	ORF1ab:nsp3	D218E	C654A	GAC>GAA	Missense	ORF1ab:nsp3	1.77185584180871e-05
CAMB-76ECF	MN908947.3	3923	C	A	1	1	0	0	0.999605649076972	ACC	ORF1ab:nsp3	P402T	C1204A	CCT>ACT	Missense	ORF1ab:nsp3	4.92938653784537e-05
CAMB-76ECF	MN908947.3	5826	C	T	0.017	0.018	2.8e-07	1.3e-07	0.0174202183278263	ACA	ORF1ab:nsp3	T1036I	C3107T	ACA>ATA	Missense	ORF1ab:nsp3	0.981910577606759
CAMB-76ECF	MN908947.3	635	C	T	0.02	0.025	7.8e-10	2.9e-12	0.0224575041125052	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.9772683288714
CAMB-76ECF	MN908947.3	9900	A	G	0.0073	0.0079	3.1e-05	2.2e-05	0.00763409306533107	AAT	ORF1ab:nsp4	N449S	A1346G	AAT>AGT	Missense	ORF1ab:nsp4	0.992145268406769
CAMB-76EED	MN908947.3	11074	C	INS	0.024	0.03	5.7e-05	1e-06	0.0268408814084819	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.9729155132322
CAMB-76EED	MN908947.3	11075	T	-	0.034	0.028	1.5e-08	2e-07	0.031240518717886	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961526792268167
CAMB-76EED	MN908947.3	12138	C	T	0.066	0.063	6.1e-30	4.5e-29	0.0644877520638787	GCT	ORF1ab:nsp8	A16V	C47T	GCT>GTT	Missense	ORF1ab:nsp8	0.934417254149288
CAMB-76EED	MN908947.3	14408	C	T	1	1	0	0	0.99825828257247	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000772004481391868
CAMB-76EED	MN908947.3	14485	A	C	0.0039	0.0076	0.00095	3.6e-05	0.00568926642546274	CAG	ORF1ab:RNA-dependent-RNA-polymerase	R340R	A1018C	AGA>CGA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.994188383758936
CAMB-76EED	MN908947.3	1547	A	G	0.0069	0.0081	0.00013	4.4e-05	0.00746661057945105	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.971185192975076
CAMB-76EED	MN908947.3	1547	A	T	0.02	0.016	8.3e-10	1.4e-08	0.0179829635082553	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.971185192975076
CAMB-76EED	MN908947.3	18744	C	T	0.0089	0.0035	3.1e-05	0.0068	0.00643659463476883	ACG	ORF1ab:3'-to-5'-exonuclease	Y235Y	C705T	TAC>TAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.99209098175597
CAMB-76EED	MN908947.3	23403	A	G	1	1	0	0	0.999699166060335	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.99613813175127e-05
CAMB-76EED	MN908947.3	241	C	T	1	1	0	0	0.99907263521981	TCG	NA	NA	NA	NA	NA	NA	0.000150383477868565
CAMB-76EED	MN908947.3	25521	C	T	1	1	0	0	0.995495919279347	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.000129360020697603
CAMB-76EED	MN908947.3	28329	G	A	0.003	0.0073	0.0018	2.7e-05	0.0052090722986805	GGA	N	G19E	G56A	GGA>GAA	Missense	GU280_gp10	0.994649046354663
CAMB-76EED	MN908947.3	28514	G	T	1	1	0	0	0.998281975362796	AGA	N	D81Y	G241T	GAT>TAT	Missense	GU280_gp10	0.000109661147055598
CAMB-76EED	MN908947.3	28851	G	C	0.19	0.18	4.7e-89	3.4e-84	0.187965795873539	AGT	N	S193T	G578C	AGT>ACT	Missense	GU280_gp10	0.811328155644465
CAMB-76EED	MN908947.3	29200	C	T	0.0095	0.013	5e-06	1.2e-07	0.0111741809925397	CCA	N	P309P	C927T	CCC>CCT	Synonymous	GU280_gp10	0.988371715861174
CAMB-76EED	MN908947.3	29659	C	T	0.059	0.049	2.3e-26	2.4e-22	0.0535580308189531	ACT	ORF10	N34N	C102T	AAC>AAT	Synonymous	GU280_gp11	0.946441969181047
CAMB-76EED	MN908947.3	29722	C	T	0.0075	0.0069	3.2e-05	6.2e-05	0.00714008537058595	CCA	NA	NA	NA	NA	NA	NA	0.992627085758634
CAMB-76EED	MN908947.3	3037	C	T	1	1	0	0	0.998734067957534	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	2.87711827833242e-05
CAMB-76EED	MN908947.3	3340	G	T	0.018	0.023	1.9e-07	6.3e-09	0.0202699060180776	TGA	ORF1ab:nsp3	V207V	G621T	GTG>GTT	Synonymous	ORF1ab:nsp3	0.979712124207084
CAMB-76F26	MN908947.3	11071	G	INS	0.056	0.054	6.2e-16	2.2e-15	0.0549584000826831	TGT	ORF1ab:nsp6	.	98-99-insfrshift	.	no-SNV	ORF1ab:nsp6	0.944318123094414
CAMB-76F26	MN908947.3	11073	TC	-	0.019	0.01895	0.00048;1.7e-24	0.00054;1.4e-22	0.0190763944429634	TTC	ORF1ab:nsp6	.	101-102-delfrshift	.	no-SNV	ORF1ab:nsp6	0.994669222245515
CAMB-76F26	MN908947.3	11074	C	INS	0.076	0.087	1.3e-20	8.8e-24	0.0805837191584129	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.690206880384458
CAMB-76F26	MN908947.3	11074	C	T	0.2	0.19	1.6e-126	1.4e-112	0.195217722557581	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.690206880384458
CAMB-76F26	MN908947.3	11083	G	-	0.13	0.12	9.1e-57	1e-52	0.12541263358138	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-76F26	MN908947.3	11083	G	T	0.87	0.88	0	0	0.874195714205785	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-76F26	MN908947.3	12529	A	G	0.21	0.21	5.3e-101	6.2e-101	0.212220108553378	CAT	ORF1ab:nsp8	T146T	A438G	ACA>ACG	Synonymous	ORF1ab:nsp8	0.787605368331035
CAMB-76F26	MN908947.3	12661	G	A	0.0067	0.0069	4.4e-05	2.1e-05	0.00681066355322047	GGG	ORF1ab:nsp8	R190R	G570A	AGG>AGA	Synonymous	ORF1ab:nsp8	0.993065506200357
CAMB-76F26	MN908947.3	14805	C	T	1	1	0	0	0.999389164526665	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000224388541225161
CAMB-76F26	MN908947.3	2480	A	G	1	1	0	0	0.999878394811512	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-76F26	MN908947.3	25540	G	A	0.027	0.029	2.2e-13	8e-15	0.0276906748998987	CGT	ORF3a	V50I	G148A	GTT>ATT	Missense	GU280_gp03	0.972212841912297
CAMB-76F26	MN908947.3	2558	C	T	1	1	0	0	0.99962793927969	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000124020240103185
CAMB-76F26	MN908947.3	26144	G	T	1	1	0	0	0.999374095372218	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	7.82380784727927e-05
CAMB-76F26	MN908947.3	28883	G	A	0.23	0.23	4.8e-107	1.9e-104	0.230649031754004	GGG	N	G204R	G610A	GGA>AGA	Missense	GU280_gp10	0.769127741503432
CAMB-76F26	MN908947.3	29013	C	T	0.72	0.73	0	0	0.722977181360059	ACT	N	T247I	C740T	ACT>ATT	Missense	GU280_gp10	0.27679633089859
CAMB-76F26	MN908947.3	29414	G	A	0.29	0.24	3.6e-119	1.5e-98	0.265854123024186	AGC	N	A381T	G1141A	GCC>ACC	Missense	GU280_gp10	0.733764997143401
CAMB-76F26	MN908947.3	4185	G	A	0.76	0.76	0	0	0.759804227412322	GGT	ORF1ab:nsp3	G489D	G1466A	GGT>GAT	Missense	ORF1ab:nsp3	0.240036326075051
CAMB-770D7	MN908947.3	11075	T	-	0.036	0.032	5.2e-09	1.7e-08	0.0346181818181818	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95933986013986
CAMB-770D7	MN908947.3	1190	C	T	1	1	0	0	0.999734813955416	ACC	ORF1ab:nsp2	P129S	C385T	CCA>TCA	Missense	ORF1ab:nsp2	0.000248611916797879
CAMB-770D7	MN908947.3	14805	C	T	1	1	0	0	0.999471500376697	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000157425419707414
CAMB-770D7	MN908947.3	2445	C	T	1	1	0	0	0.999544211485871	ACT	ORF1ab:nsp2	T547I	C1640T	ACT>ATT	Missense	ORF1ab:nsp2	9.11577028258888e-05
CAMB-770D7	MN908947.3	25979	G	T	1	1	0	0	0.999795165915608	GGA	ORF3a	G196V	G587T	GGA>GTA	Missense	GU280_gp03	0.000102417042195821
CAMB-770D7	MN908947.3	28144	T	C	1	1	0	0	0.999777913040617	TTA	ORF8	L84S	T251C	TTA>TCA	Missense	GU280_gp09	0.000131607087041637
CAMB-770D7	MN908947.3	28657	C	T	1	1	0	0	0.999804847585965	ACG	N	D128D	C384T	GAC>GAT	Synonymous	GU280_gp10	0.000156121931228289
CAMB-770D7	MN908947.3	28863	C	T	1	1	0	0	0.998071268220192	TCA	N	S197L	C590T	TCA>TTA	Missense	GU280_gp10	0.000189711322604104
CAMB-770D7	MN908947.3	3157	C	T	0.18	0.18	2.5e-81	1.1e-84	0.178867184118648	CCA	ORF1ab:nsp3	A146A	C438T	GCC>GCT	Synonymous	ORF1ab:nsp3	0.821075107481894
CAMB-770D7	MN908947.3	8782	C	T	1	1	0	0	0.999699767319673	GCC	ORF1ab:nsp4	S76S	C228T	AGC>AGT	Synonymous	ORF1ab:nsp4	0.000200155120218169
CAMB-770D7	MN908947.3	9477	T	A	1	1	0	0	0.999856687327577	TTT	ORF1ab:nsp4	F308Y	T923A	TTT>TAT	Missense	ORF1ab:nsp4	0.000107484504317294
CAMB-770E6	MN908947.3	11074	C	INS	0.18	0.034	9e-74	4.9e-07	0.119391586584357	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.880099280850251
CAMB-770E6	MN908947.3	11083	G	-	0.11	0.2	1.7e-49	2.3e-93	0.156106556555553	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.00444987873078e-05
CAMB-770E6	MN908947.3	11083	G	T	0.89	0.8	0	0	0.843733087454148	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.00444987873078e-05
CAMB-770E6	MN908947.3	12405	A	G	1	1	0	0	0.999822222222222	AAC	ORF1ab:nsp8	N105S	A314G	AAC>AGC	Missense	ORF1ab:nsp8	0.000177777777777778
CAMB-770E6	MN908947.3	14805	C	T	1	1	0	0	1	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-770E6	MN908947.3	17144	G	A	0.38	0.33	8.3e-199	3.3e-166	0.355648741376554	CGC	ORF1ab:helicase	R303H	G908A	CGC>CAC	Missense	ORF1ab:helicase	0.64431436687613
CAMB-770E6	MN908947.3	22676	G	A	1	1	0	0	0.999874600288419	CGC	S	A372T	G1114A	GCA>ACA	Missense	GU280_gp02, spike glycoprotein	6.26998557903317e-05
CAMB-770E6	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-770E6	MN908947.3	25519	T	A	1	1	0	0	0.999683577681679	TTT	ORF3a	F43I	T127A	TTC>ATC	Missense	GU280_gp03	3.51580353689836e-05
CAMB-770E6	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-770E6	MN908947.3	9474	C	T	0.13	0.42	1.6e-44	1.4e-113	0.212915601023018	GCT	ORF1ab:nsp4	A307V	C920T	GCT>GTT	Missense	ORF1ab:nsp4	0.786445012787724
CAMB-770E6	MN908947.3	9634	A	T	0.37	0.79	7.4e-196	0	0.601870811615786	TAG	ORF1ab:nsp4	L360F	A1080T	TTA>TTT	Missense	ORF1ab:nsp4	0.397617274758004
CAMB-770F5	MN908947.3	11075	T	-	0.034	0.026	1.1e-08	7.6e-07	0.0296547362596099	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.966481551018795
CAMB-770F5	MN908947.3	14408	C	T	1	1	0	0	0.998678414096916	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000440528634361233
CAMB-770F5	MN908947.3	23403	A	G	1	1	0	0	0.999294436906377	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.75344058926149e-05
CAMB-770F5	MN908947.3	241	C	T	1	1	0	0	0.99925705794948	TCG	NA	NA	NA	NA	NA	NA	8.91530460624071e-05
CAMB-770F5	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99946008804718	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-770F5	MN908947.3	3037	C	T	1	1	0	0	0.999369399269831	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00016594756057086
CAMB-77101	MN908947.3	10097	G	A	1	1	0	0	1	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0
CAMB-77101	MN908947.3	11075	T	-	0.0051	0.083	0.0087	1.6e-20	0.0618508927354505	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.937958293580482
CAMB-77101	MN908947.3	13536	C	T	1	1	0	1.1e-247	1	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-77101	MN908947.3	14184	C	T	1	1	0	0	0.999910233393178	CCA	ORF1ab:RNA-dependent-RNA-polymerase	T239T	C717T	ACC>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	4.48833034111311e-05
CAMB-77101	MN908947.3	14408	C	T	1	1	0	0	0.999626228107646	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000320375907731739
CAMB-77101	MN908947.3	1684	C	T	1	1	0	0	0.999770220588235	TCG	ORF1ab:nsp2	I293I	C879T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.000229779411764706
CAMB-77101	MN908947.3	21058	C	T	1	1	0	0	0.999896114689383	CCC	ORF1ab:2'-O-ribose-methyltransferase	P134S	C400T	CCT>TCT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.000103885310617079
CAMB-77101	MN908947.3	23403	A	G	1	1	0	0	0.999888923857304	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.4050761797212e-05
CAMB-77101	MN908947.3	23731	C	T	1	1	0	0	0.999814849102018	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000185150897981855
CAMB-77101	MN908947.3	241	C	T	1	1	0	0	0.999795102960762	TCG	NA	NA	NA	NA	NA	NA	0.000102448519618892
CAMB-77101	MN908947.3	24368	G	T	1	1	0	0	0.999095677337674	AGA	S	D936Y	G2806T	GAC>TAC	Missense	GU280_gp02, spike glycoprotein	0
CAMB-77101	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999047013977128	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-77101	MN908947.3	3037	C	T	1	1	0	0	0.998974884674526	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77101	MN908947.3	4002	C	T	1	1	0	7.8e-295	1	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-77110	MN908947.3	10449	C	T	0.0057	0.022	0.00024	2.8e-11	0.0138081664383815	CCC	ORF1ab:3C-like-proteinase	P132L	C395T	CCC>CTC	Missense	ORF1ab:3C-like-proteinase	0.986117795135675
CAMB-77110	MN908947.3	10626	C	T	0.021	0.015	2.2e-10	3.7e-08	0.0181217874160507	GCA	ORF1ab:3C-like-proteinase	A191V	C572T	GCA>GTA	Missense	ORF1ab:3C-like-proteinase	0.981728135669531
CAMB-77110	MN908947.3	11074	C	INS	0.12	0.11	5e-49	2.5e-47	0.112907134803637	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.874901212842857
CAMB-77110	MN908947.3	11074	C	T	0.016	0.0055	4.8e-12	0.00082	0.0107585799938884	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.874901212842857
CAMB-77110	MN908947.3	11083	G	-	0.15	0.11	1e-63	1.2e-48	0.129733247848303	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	6.7999456004352e-05
CAMB-77110	MN908947.3	11083	G	T	0.85	0.89	0	0	0.870082182199685	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	6.7999456004352e-05
CAMB-77110	MN908947.3	13329	C	T	0.012	0.014	5e-07	1.1e-07	0.0127127420241828	ACT	ORF1ab:nsp10	T102I	C305T	ACT>ATT	Missense	ORF1ab:nsp10	0.987272973996015
CAMB-77110	MN908947.3	14805	C	T	1	1	0	0	0.999923502284003	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	4.37129805695801e-05
CAMB-77110	MN908947.3	17939	C	T	0.15	0.11	4.8e-69	2.9e-48	0.128314588293244	GCA	ORF1ab:helicase	A568V	C1703T	GCA>GTA	Missense	ORF1ab:helicase	0.871616999151684
CAMB-77110	MN908947.3	20262	A	G	1	1	1.5e-290	2.1e-202	1	TAG	ORF1ab:endoRNAse	L214L	A642G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-77110	MN908947.3	23280	C	T	0.19	0.19	9.5e-90	1.3e-87	0.188937918954424	ACT	S	T573I	C1718T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.809529423653451
CAMB-77110	MN908947.3	24408	AAG	-	0.00496666666666667	0.001	3.7e-05;0.00051;0.00088	NA;NA;0.0018	0.00169842365054933	CAA	S	.	2846-2848-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.996629690568441
CAMB-77110	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-77110	MN908947.3	2558	C	T	1	1	0	0	0.999448326590658	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-77110	MN908947.3	25762	A	C	0.0041	0.012	3e-04	3.3e-07	0.00826895219700628	AAT	ORF3a	I124L	A370C	ATA>CTA	Missense	GU280_gp03	0.991731047802994
CAMB-77110	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-77110	MN908947.3	26533	C	T	0.93	0.92	0	0	0.924319101950681	TCC	M	S4F	C11T	TCC>TTC	Missense	GU280_gp05	0.0756118881118881
CAMB-77110	MN908947.3	3310	A	C	0.0039	0.0073	0.00099	3.5e-05	0.00568386863948033	AAC	ORF1ab:nsp3	E197D	A591C	GAA>GAC	Missense	ORF1ab:nsp3	0.994225911223385
CAMB-77110	MN908947.3	490	T	C	1	1	0	0	0.999656112285707	ATG	ORF1ab:leader-protein	D75D	T225C	GAT>GAC	Synonymous	ORF1ab:leader-protein	0.000331151132282141
CAMB-77110	MN908947.3	5950	G	T	0.01	0.003	3.8e-06	0.0032	0.00672116257947321	AGT	ORF1ab:nsp3	K1077N	G3231T	AAG>AAT	Missense	ORF1ab:nsp3	0.993278837420527
CAMB-77110	MN908947.3	9438	C	T	0.024	0.0054	7.4e-12	0.00051	0.0145678410337681	ACA	ORF1ab:nsp4	T295I	C884T	ACA>ATA	Missense	ORF1ab:nsp4	0.985371205656467
CAMB-77110	MN908947.3	9491	C	T	0.95	0.93	0	0	0.941246220430426	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.0569751585937037
CAMB-7712F	MN908947.3	11074	C	INS	0.11	0.11	1.6e-38	2.1e-34	0.106771480285339	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.888650317634951
CAMB-7712F	MN908947.3	11083	G	-	0.14	0.18	2.2e-62	1.1e-79	0.157525006580679	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	8.22584890760726e-05
CAMB-7712F	MN908947.3	11083	G	T	0.86	0.82	0	0	0.842228217952093	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	8.22584890760726e-05
CAMB-7712F	MN908947.3	14805	C	T	1	1	0	0	0.99954526024756	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000136421925731904
CAMB-7712F	MN908947.3	1515	A	G	1	1	0	0	0.999480986817065	CAT	ORF1ab:nsp2	H237R	A710G	CAT>CGT	Missense	ORF1ab:nsp2	0.000276807030898585
CAMB-7712F	MN908947.3	15205	A	G	0.049	0.048	9.2e-23	2.3e-22	0.0487821726095906	AAT	ORF1ab:RNA-dependent-RNA-polymerase	I580V	A1738G	ATT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.950996781012116
CAMB-7712F	MN908947.3	17247	T	C	1	1	0	0	0.999137001078749	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000408788962698007
CAMB-7712F	MN908947.3	17799	A	G	1	1	0	0	0.999475228394915	TAG	ORF1ab:helicase	V521V	A1563G	GTA>GTG	Synonymous	ORF1ab:helicase	0.000119266273883071
CAMB-7712F	MN908947.3	20271	T	C	1	1	0	0	1	CTA	ORF1ab:endoRNAse	A217A	T651C	GCT>GCC	Synonymous	ORF1ab:endoRNAse	0
CAMB-7712F	MN908947.3	2541	A	G	0.04	0.042	4.2e-18	6e-19	0.0405928902883659	AAA	ORF1ab:nsp2	K579R	A1736G	AAA>AGA	Missense	ORF1ab:nsp2	0.959396751740139
CAMB-7712F	MN908947.3	26144	G	T	1	1	0	0	0.999611076540137	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000233354075917859
CAMB-7712F	MN908947.3	28184	T	C	0.012	0.013	2.6e-07	1.6e-07	0.0126208472490772	GTC	ORF8	S97S	T291C	AGT>AGC	Synonymous	GU280_gp09	0.98732056014531
CAMB-7712F	MN908947.3	29085	C	A	0.0074	0.0091	1.6e-05	2.4e-06	0.00804650363667602	ACA	N	T271K	C812A	ACA>AAA	Missense	GU280_gp10	0.991237615256858
CAMB-7712F	MN908947.3	9223	C	T	1	1	0	0	0.99864485043164	ACG	ORF1ab:nsp4	H223H	C669T	CAC>CAT	Synonymous	ORF1ab:nsp4	0.000501907247540655
CAMB-7714D	MN908947.3	11075	T	-	0.08	0.056	4.7e-19	3e-14	0.0718084098573937	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.928103171695992
CAMB-7714D	MN908947.3	12844	G	T	0.016	0.001	6.8e-09	0.0087	0.0115639518994261	GGG	ORF1ab:nsp9	W53C	G159T	TGG>TGT	Missense	ORF1ab:nsp9	0.988401885761137
CAMB-7714D	MN908947.3	13214	G	T	0.018	0.018	8.5e-10	5.7e-10	0.0181024697639829	GGA	ORF1ab:nsp10	D64Y	G190T	GAT>TAT	Missense	ORF1ab:nsp10	0.981838819523269
CAMB-7714D	MN908947.3	13344	C	T	0.019	0.016	4.5e-10	3.4e-09	0.0179020953691798	CCT	ORF1ab:nsp10	P107L	C320T	CCT>CTT	Missense	ORF1ab:nsp10	0.982079794266259
CAMB-7714D	MN908947.3	14408	C	T	1	0.99	0	0	0.994322046429099	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000384444773029721
CAMB-7714D	MN908947.3	17385	T	-	0.016	0.016	7.4e-09	9.7e-09	0.0160165187789497	ATT	ORF1ab:helicase	.	1149-1149-delfrshift	.	no-SNV	ORF1ab:helicase	0.983927674535409
CAMB-7714D	MN908947.3	17385	TT	-	0.0145	0.008	7.4e-09;8.6e-07	9.7e-09;NA	0.0113278587425752	ATT	ORF1ab:helicase	.	1149-1150-delfrshift	.	no-SNV	ORF1ab:helicase	0.983927674535409
CAMB-7714D	MN908947.3	17407	TTACGTGCTAAGCACTATG	-	0.000313210526315789	0.00664210526315789	0.45;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00037;NA;NA;NA;NA;NA	0.00011;0.00013;0.001;0.00094;9e-04;0.00077;0.00096;0.00085;0.00089;3.3e-06;7e-04;0.00071;0.00083;0.00087;0.00067;2.3e-06;1.7e-06;5.4e-07;7.2e-07	0.0019974600199746	ATT	ORF1ab:helicase	.	1171-1189-delfrshift	.	no-SNV	ORF1ab:helicase	0.997919577899902
CAMB-7714D	MN908947.3	20297	AATT	-	0.06525	0.105	5.4e-06;6.6e-06;7.9e-06;9.5e-06	1.7e-08;4e-08;4.4e-08;5.6e-08	0.0824742268041237	AAA	ORF1ab:endoRNAse	.	677-680-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.911602209944751
CAMB-7714D	MN908947.3	203	C	T	1	1	0	0	0.999193570065321	TCG	NA	NA	NA	NA	NA	NA	0.000188166984758474
CAMB-7714D	MN908947.3	23403	A	G	1	1	0	0	0.999828137005136	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000151643818997938
CAMB-7714D	MN908947.3	23539	ATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTA	-	0.0526666666666667	0.0183555555555556	7.3e-07;7.9e-06;1.1e-05;4.4e-06;8.5e-06;1e-05;9.3e-06;9.5e-06;9.7e-06;2.7e-05;2.6e-05;0.00016;7.9e-05;9.7e-05;0.00092;0.00054;3.6e-06;2.4e-06;3.7e-06;4.8e-06;5.4e-07;1.7e-06;4.9e-07;1.6e-06;2.2e-06;2e-06;1.6e-06;1.8e-06;6.2e-07;5.6e-07;1.3e-07;1.3e-08;1.9e-07;3.4e-08;2.2e-07;1.8e-08;1.1e-07;4.6e-07;1.5e-07;1.7e-07;3.6e-11;1.6e-10;3.7e-07;2.4e-07;9.6e-06	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0083;0.0068;0.0081;0.008;0.0043;0.0065;0.0058;0.0078;0.0083;0.0081;0.00011;1e-04;5.5e-05;5e-05;2e-05;0.0022;0.0048;0.0034;0.0053;0.0028;0.0045;0.001;0.0048;0.0046;0.00083;1.1e-07;1.6e-05;1.3e-05;NA	0.04177612066774	CAT	S	.	1977-2021-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.986198964922369
CAMB-7714D	MN908947.3	23579	AGTT	-	0.06575	0.041	3.6e-11;1.6e-10;3.7e-07;2.4e-07	0.00083;1.1e-07;1.6e-05;1.3e-05	0.0554555584126168	TAG	S	.	2017-2020-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.954802259887006
CAMB-7714D	MN908947.3	241	C	T	1	1	0	0	0.999218413109099	TCG	NA	NA	NA	NA	NA	NA	0.000134756360500216
CAMB-7714D	MN908947.3	24794	G	T	0.016	0.043	1.1e-08	4.2e-20	0.0274614594039054	TGC	S	A1078S	G3232T	GCT>TCT	Missense	GU280_gp02, spike glycoprotein	0.972442617334704
CAMB-7714D	MN908947.3	26158	GTTA	-	0.01125	0.04175	0.00038;0.00056;8e-04;0.003	6.8e-12;5.9e-12;2e-11;8.6e-10	0.0253475061324612	TGT	ORF3a	.	766-769-delfrshift	.	no-SNV	GU280_gp03	0.974735126324368
CAMB-7714D	MN908947.3	28243	T	-	0.011	0.0067	1.6e-05	0.00077	0.00919175566879258	GTT	ORF8	.	350-350-delfrshift	.	no-SNV	GU280_gp09	0.990775649452949
CAMB-7714D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999419953596288	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00016260162601626
CAMB-7714D	MN908947.3	29160	C	T	0.014	0.0059	5.5e-08	0.00012	0.0108398253931786	ACT	N	T296I	C887T	ACT>ATT	Missense	GU280_gp10	0.989160174606821
CAMB-7714D	MN908947.3	29207	T	C	0.0078	0.0081	2.1e-05	1.3e-05	0.00790685948708546	TTC	N	S312P	T934C	TCA>CCA	Missense	GU280_gp10	0.991703527146884
CAMB-7714D	MN908947.3	29281	C	T	0.0075	0.0081	2.6e-05	1.1e-05	0.007714758046411	CCA	N	A336A	C1008T	GCC>GCT	Synonymous	GU280_gp10	0.992264832540768
CAMB-7714D	MN908947.3	29752	ATCGAGTGT	-	0.0158888888888889	0.0203333333333333	8.3e-06;1.2e-05;1.2e-05;1.3e-05;3.3e-06;3.2e-05;1.5e-05;2.5e-05;6.6e-07	8.9e-07;1.2e-06;9.8e-07;1.8e-06;3.3e-07;4.9e-06;2.1e-06;3.7e-06;7.2e-08	0.0166112956810631	GAT	NA	NA	NA	NA	NA	NA	0.980492813141684
CAMB-7714D	MN908947.3	3037	C	T	1	1	0	0	0.99941141848146	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000147145379635079
CAMB-7714D	MN908947.3	370	G	T	0.016	0.03	4.7e-09	2.1e-15	0.0208358957959214	TGG	ORF1ab:leader-protein	V35V	G105T	GTG>GTT	Synonymous	ORF1ab:leader-protein	0.979114904922388
CAMB-7714D	MN908947.3	5365	C	T	0.017	0.035	8e-08	6.2e-13	0.023320570831883	ACA	ORF1ab:nsp3	Y882Y	C2646T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.976679429168117
CAMB-7714D	MN908947.3	5833	C	T	0.023	0.02	6.2e-12	9.2e-11	0.0222834973868992	CCT	ORF1ab:nsp3	S1038S	C3114T	TCC>TCT	Synonymous	ORF1ab:nsp3	0.977652377440764
CAMB-7715C	MN908947.3	14408	C	T	1	1	0	0	0.999492976229533	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000417548987443705
CAMB-7715C	MN908947.3	18636	G	A	1	1	0	0	0.999880732303656	TGA	ORF1ab:3'-to-5'-exonuclease	V199V	G597A	GTG>GTA	Synonymous	ORF1ab:3'-to-5'-exonuclease	5.96338481722226e-05
CAMB-7715C	MN908947.3	23403	A	G	1	1	0	0	0.999968751464775	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.12485352249113e-05
CAMB-7715C	MN908947.3	241	C	T	1	1	0	0	0.999860237596087	TCG	NA	NA	NA	NA	NA	NA	9.31749359422315e-05
CAMB-7715C	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7715C	MN908947.3	3037	C	T	1	1	0	0	0.999599839935974	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7715C	MN908947.3	521	GTT	-	0.09	0.15	0.003;5.6e-13;1.5e-13	0.00018;1.5e-21;6.4e-23	0.11233121848056	GGT	ORF1ab:leader-protein	.	256-258-delinframe	.	no-SNV	ORF1ab:leader-protein	0.901094968868532
CAMB-7715C	MN908947.3	683	C	T	0.087	0.13	3.2e-40	3.2e-58	0.101627993476581	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.898372006523419
CAMB-7716B	MN908947.3	10097	G	A	1	1	0	0	0.999823297272888	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	9.8168181728938e-05
CAMB-7716B	MN908947.3	11075	T	-	0.038	0.037	1.8e-09	1.4e-09	0.0372342424735965	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958393364988286
CAMB-7716B	MN908947.3	14408	C	T	1	1	0	0	0.995695839311334	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000631705175699694
CAMB-7716B	MN908947.3	23403	A	G	1	1	0	0	0.999136699441529	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000129877075168267
CAMB-7716B	MN908947.3	23731	C	T	1	1	0	0	0.999914775148433	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	5.68165677111446e-05
CAMB-7716B	MN908947.3	241	C	T	1	1	0	0	0.997911832946636	TCG	NA	NA	NA	NA	NA	NA	0.000232018561484919
CAMB-7716B	MN908947.3	27059	C	T	0.023	0.022	1.2e-11	2.6e-11	0.0228033104419792	ACA	M	Y179Y	C537T	TAC>TAT	Synonymous	GU280_gp05	0.976369079063215
CAMB-7716B	MN908947.3	28580	G	T	1	1	0	0	0.999345911949686	AGA	N	D103Y	G307T	GAT>TAT	Missense	GU280_gp10	0.000352201257861635
CAMB-7716B	MN908947.3	28872	G	T	0.014	0.014	6.7e-08	4.6e-08	0.0143538353544889	GGC	N	G200V	G599T	GGC>GTC	Missense	GU280_gp10	0.985597753733692
CAMB-7716B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998837362927732	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000208221785948004
CAMB-7716B	MN908947.3	3037	C	T	1	1	0	0	0.999225860936474	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.38350380031904e-05
CAMB-7717A	MN908947.3	11074	C	INS	0.1	0.11	6.6e-31	9.3e-32	0.105014081235665	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.891443834741457
CAMB-7717A	MN908947.3	11083	G	-	0.18	0.16	1.6e-80	9.6e-73	0.171736425489106	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	7.94218092288142e-05
CAMB-7717A	MN908947.3	11083	G	T	0.82	0.84	0	0	0.828078256956027	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	7.94218092288142e-05
CAMB-7717A	MN908947.3	14805	C	T	1	1	0	0	0.999160267089242	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000270881584115504
CAMB-7717A	MN908947.3	1514	C	T	1	1	0	0	0.99845513963161	CCA	ORF1ab:nsp2	H237Y	C709T	CAT>TAT	Missense	ORF1ab:nsp2	0.00142602495543672
CAMB-7717A	MN908947.3	2480	A	G	1	1	0	0	0.999861217125807	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-7717A	MN908947.3	2558	C	T	1	1	0	0	0.999458571712177	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000162428486346983
CAMB-7717A	MN908947.3	25785	G	T	0.012	0.015	3.9e-07	2.8e-08	0.0135347465336163	GGA	ORF3a	W131C	G393T	TGG>TGT	Missense	GU280_gp03	0.986189596714172
CAMB-7717A	MN908947.3	26144	G	T	1	1	0	0	0.999612252811167	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.00014540519581233
CAMB-7717A	MN908947.3	28487	G	C	0.99	0.99	0	0	0.994103442466446	CGT	N	V72L	G214C	GTT>CTT	Missense	GU280_gp10	0.00550345369798394
CAMB-7717A	MN908947.3	29140	G	T	1	1	0	0	0.998309172048674	AGG	N	Q289H	G867T	CAG>CAT	Missense	GU280_gp10	0.00144136153227818
CAMB-77189	MN908947.3	11074	C	INS	0.031	0.025	5.4e-07	1.8e-05	0.0271527052033097	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.972061093586707
CAMB-77189	MN908947.3	11075	T	-	0.042	0.03	2.1e-10	1.6e-07	0.0349851296443681	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958924307795417
CAMB-77189	MN908947.3	11160	A	G	0.0082	0.0054	1.1e-05	0.00023	0.00656515178238972	AAG	ORF1ab:nsp6	K63R	A188G	AAG>AGG	Missense	ORF1ab:nsp6	0.99329766594156
CAMB-77189	MN908947.3	13335	C	T	0.0099	0.0087	3.7e-06	1.5e-05	0.0091698428685217	GCT	ORF1ab:nsp10	A104V	C311T	GCT>GTT	Missense	ORF1ab:nsp10	0.990816991527934
CAMB-77189	MN908947.3	14408	C	T	1	1	0	0	0.997924612529075	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000971124703376225
CAMB-77189	MN908947.3	14599	C	T	0.012	0.0062	4.7e-07	0.00015	0.00865519763934211	TCT	ORF1ab:RNA-dependent-RNA-polymerase	L378L	C1132T	CTA>TTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.99089272651055
CAMB-77189	MN908947.3	19842	T	C	0.0089	0.01	4.1e-06	1.6e-06	0.00969906906256766	ATT	ORF1ab:endoRNAse	N74N	T222C	AAT>AAC	Synonymous	ORF1ab:endoRNAse	0.988828750811864
CAMB-77189	MN908947.3	20268	A	G	1	1	1.8e-238	1.5e-153	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-77189	MN908947.3	2040	C	T	0.012	0.0069	2.1e-07	4.5e-05	0.00889863830139481	ACT	ORF1ab:nsp2	T412I	C1235T	ACT>ATT	Missense	ORF1ab:nsp2	0.991039278175572
CAMB-77189	MN908947.3	23403	A	G	1	1	0	0	0.999114694705874	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.85305294125659e-05
CAMB-77189	MN908947.3	23997	C	T	0.0077	0.013	2.2e-05	1.9e-07	0.0105028364683773	CCA	S	P812L	C2435T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	0.989479600259936
CAMB-77189	MN908947.3	241	C	T	1	1	0	0	0.998871559263289	TCG	NA	NA	NA	NA	NA	NA	6.71690914708688e-05
CAMB-77189	MN908947.3	24232	A	G	0.015	0.0075	5.4e-08	7.5e-05	0.0106214756690635	CAG	S	A890A	A2670G	GCA>GCG	Synonymous	GU280_gp02, spike glycoprotein	0.989318853119313
CAMB-77189	MN908947.3	26099	T	C	0.0091	0.0055	6e-06	0.00017	0.00726327116212339	ATT	ORF3a	I236T	T707C	ATT>ACT	Missense	GU280_gp03	0.992467718794835
CAMB-77189	MN908947.3	26645	C	T	0.0097	0.011	4.6e-06	1.6e-06	0.0105076591973668	ACA	M	N41N	C123T	AAC>AAT	Synonymous	GU280_gp05	0.989399502046673
CAMB-77189	MN908947.3	29366	C	T	0.99	1	0	1.5e-287	0.991724137931035	ACC	N	P365S	C1093T	CCA>TCA	Missense	GU280_gp10	0.00827586206896552
CAMB-77189	MN908947.3	2937	C	T	1	1	0	0	0.999836984872196	ACA	ORF1ab:nsp3	T73I	C218T	ACA>ATA	Missense	ORF1ab:nsp3	6.52060511215441e-05
CAMB-77189	MN908947.3	29690	G	T	0.76	0.73	0	0	0.74527714345028	TGT	NA	NA	NA	NA	NA	NA	0.253892464189329
CAMB-77189	MN908947.3	3037	C	T	1	1	0	0	0.999044086720453	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.82365311818912e-05
CAMB-77189	MN908947.3	5183	C	T	0.0071	0.01	0.00024	1.1e-05	0.0090293453724605	TCC	ORF1ab:nsp3	P822S	C2464T	CCT>TCT	Missense	ORF1ab:nsp3	0.990594431903687
CAMB-77189	MN908947.3	6393	A	G	0.12	0.12	6.5e-56	4.6e-55	0.1202968950375	GAT	ORF1ab:nsp3	D1225G	A3674G	GAT>GGT	Missense	ORF1ab:nsp3	0.879695332841099
CAMB-77189	MN908947.3	8660	C	T	0.019	0.0084	5e-10	1.2e-05	0.0134142073953109	ACA	ORF1ab:nsp4	H36Y	C106T	CAT>TAT	Missense	ORF1ab:nsp4	0.985710952991951
CAMB-77198	MN908947.3	10323	A	G	1	1	0	0	0.99913895608676	AAG	ORF1ab:3C-like-proteinase	K90R	A269G	AAG>AGG	Missense	ORF1ab:3C-like-proteinase	2.7334727404431e-05
CAMB-77198	MN908947.3	11074	C	INS	0.11	0.12	6.7e-50	2.4e-39	0.115460476407222	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.880139584281596
CAMB-77198	MN908947.3	11083	G	-	0.15	0.12	2.5e-66	1.6e-54	0.14362987081189	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.31288730175402e-05
CAMB-77198	MN908947.3	11083	G	T	0.85	0.88	0	0	0.856238840457935	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.31288730175402e-05
CAMB-77198	MN908947.3	14805	C	T	1	1	0	0	0.998911924716953	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000264666960741067
CAMB-77198	MN908947.3	18652	C	T	1	1	0	0	0.999382716049383	GCG	ORF1ab:3'-to-5'-exonuclease	R205C	C613T	CGC>TGC	Missense	ORF1ab:3'-to-5'-exonuclease	6.17283950617284e-05
CAMB-77198	MN908947.3	21194	A	G	0.032	0.043	6.8e-09	1.9e-07	0.0344827586206897	GAT	ORF1ab:2'-O-ribose-methyltransferase	D179G	A536G	GAT>GGT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.96551724137931
CAMB-77198	MN908947.3	2480	A	G	1	1	0	0	0.999548247199133	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000180701120346946
CAMB-77198	MN908947.3	2558	C	T	1	1	0	0	0.998902348190835	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	3.92018503273355e-05
CAMB-77198	MN908947.3	26144	G	T	1	1	0	0	0.999904607459697	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-77198	MN908947.3	26152	G	A	0.3	0.27	8.8e-143	1.3e-113	0.293326299129517	CGG	ORF3a	G254R	G760A	GGA>AGA	Missense	GU280_gp03	0.706585773322782
CAMB-77198	MN908947.3	26529	G	T	0.83	0.83	0	0	0.828450959723482	AGA	M	D3Y	G7T	GAT>TAT	Missense	GU280_gp05	0.17096070404236
CAMB-77198	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.02603125	0.02184375	0.00018;0.00088;0.00035;0.00036;9.3e-05;0.00022;0.00016;4e-04;0.00025;0.00033;0.00055;0.00021;0.00048;0.00032;0.00031;0.00039;0.00052;0.00024;0.00041;0.00031;0.00022;0.00048;0.00018;2.3e-05;0.00024;3e-04;0.00031;0.00015;0.00031;0.00017;0.00032;0.00025	0.00049;0.0015;0.0016;0.0017;0.001;0.0011;0.00099;0.0016;0.0013;0.0013;0.0021;0.0011;0.0019;0.0012;0.0014;0.0013;0.0021;0.0013;0.0016;0.0014;0.001;0.0017;0.0014;0.00056;0.0012;0.0018;0.0017;0.00082;0.0017;0.00095;0.0012;0.00083	0.0243415719126115	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.972904478175299
CAMB-77198	MN908947.3	27809	A	T	0.86	0.86	0	0	0.856982274102897	TAT	NA	NA	NA	NA	NA	NA	0.142844790315607
CAMB-77198	MN908947.3	4347	C	T	0.033	0.039	3.7e-16	4.2e-19	0.0356481324422431	TCT	ORF1ab:nsp3	S543F	C1628T	TCT>TTT	Missense	ORF1ab:nsp3	0.964243308342097
CAMB-77198	MN908947.3	5924	G	A	0.022	0.024	3.7e-11	2e-12	0.0221948795608348	TGT	ORF1ab:nsp3	V1069I	G3205A	GTT>ATT	Missense	ORF1ab:nsp3	0.977237234394965
CAMB-77198	MN908947.3	689	T	G	0.042	0.042	1.1e-19	4.2e-20	0.0422059716835662	GTC	ORF1ab:leader-protein	S142A	T424G	TCA>GCA	Missense	ORF1ab:leader-protein	0.948781598990701
CAMB-77198	MN908947.3	9693	C	T	0.042	0.044	8.5e-20	1.1e-20	0.0428463983307858	GCT	ORF1ab:nsp4	A380V	C1139T	GCT>GTT	Missense	ORF1ab:nsp4	0.956328699323095
CAMB-771A7	MN908947.3	1059	C	T	1	1	0	4.5e-33	0.999887514060742	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.000112485939257593
CAMB-771A7	MN908947.3	14408	C	T	1	1	0	0	0.99960390156954	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000297073822844977
CAMB-771A7	MN908947.3	21137	A	G	1	1	0	0	1	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0
CAMB-771A7	MN908947.3	23403	A	G	1	1	0	1.2e-23	0.999935001624959	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.4998375040624e-05
CAMB-771A7	MN908947.3	241	C	T	1	1	0	9.7e-27	0.999909297052154	TCG	NA	NA	NA	NA	NA	NA	9.0702947845805e-05
CAMB-771A7	MN908947.3	24368	G	T	1	1	0	0	1	AGA	S	D936Y	G2806T	GAC>TAC	Missense	GU280_gp02, spike glycoprotein	0
CAMB-771A7	MN908947.3	25563	G	T	1	1	0	2.5e-258	0.999574024990534	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000141991669822037
CAMB-771A7	MN908947.3	26858	C	T	0.022	0.043	8e-12	1.3e-07	0.0221646303838085	TCA	M	F112F	C336T	TTC>TTT	Synonymous	GU280_gp05	0.977810687399729
CAMB-771A7	MN908947.3	3037	C	T	1	1	0	1.3e-75	0.999566536627655	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-771B6	MN908947.3	11075	T	-	0.042	0.018	2.9e-10	1.1e-05	0.0340845908168147	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961790604755809
CAMB-771B6	MN908947.3	11674	C	T	1	1	0	1.1e-231	0.998260869565217	ACT	ORF1ab:nsp6	Y234Y	C702T	TAC>TAT	Synonymous	ORF1ab:nsp6	0.00173913043478261
CAMB-771B6	MN908947.3	14408	C	T	1	1	0	0	0.999415066002687	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000347798592996601
CAMB-771B6	MN908947.3	1615	T	C	0.019	0.016	9.5e-10	4e-09	0.0179730951532919	TTC	ORF1ab:nsp2	L270L	T810C	CTT>CTC	Synonymous	ORF1ab:nsp2	0.981972108824899
CAMB-771B6	MN908947.3	18861	A	-	0.0094	0.0086	1.6e-05	2.5e-05	0.00917600602264172	CAA	ORF1ab:3'-to-5'-exonuclease	.	822-822-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.990696154884164
CAMB-771B6	MN908947.3	22458	C	T	0.03	0.019	3.8e-07	3.5e-05	0.0252808988764045	ACA	S	T299I	C896T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0.974719101123595
CAMB-771B6	MN908947.3	23248	C	T	0.012	0.0062	9.6e-06	0.0029	0.0104612008626234	TCC	S	F562F	C1686T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.98833755817033
CAMB-771B6	MN908947.3	23403	A	G	1	1	0	0	0.99989160087442	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.2266083720258e-05
CAMB-771B6	MN908947.3	241	C	T	1	1	0	0	0.997756784359498	TCG	NA	NA	NA	NA	NA	NA	0.000145900204260286
CAMB-771B6	MN908947.3	2449	C	T	0.02	0.024	4.6e-10	3.2e-11	0.0215015443098123	GCC	ORF1ab:nsp2	G548G	C1644T	GGC>GGT	Synonymous	ORF1ab:nsp2	0.978379662627703
CAMB-771B6	MN908947.3	25101	AA	-	0.00245	0.0082	0.0041;NA	0.00011;2.1e-05	0.00447106115919439	CAA	S	.	3539-3540-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.993600787595373
CAMB-771B6	MN908947.3	26211	G	T	0.0061	0.0095	0.00016	7.9e-06	0.00738728951656708	TGC	ORF3a	V273V	G819T	GTG>GTT	Synonymous	GU280_gp03	0.992612710483433
CAMB-771B6	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998100500777068	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000664577992974461
CAMB-771B6	MN908947.3	3037	C	T	1	1	0	0	0.998526896027371	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000142558448964075
CAMB-771B6	MN908947.3	4625	AC	-	0.011	0.0045	1.2e-06;1.4e-06	0.00084;0.001	0.00800326407632917	AAC	ORF1ab:nsp3	.	1906-1907-delfrshift	.	no-SNV	ORF1ab:nsp3	0.991991709063501
CAMB-771B6	MN908947.3	5211	C	T	0.038	0.04	2.2e-09	6.2e-10	0.0388170055452865	GCA	ORF1ab:nsp3	A831V	C2492T	GCA>GTA	Missense	ORF1ab:nsp3	0.961182994454713
CAMB-771B6	MN908947.3	6568	C	T	0.038	0.023	3.7e-13	5.3e-09	0.0304317055909413	ACA	ORF1ab:nsp3	D1283D	C3849T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.969568294409059
CAMB-771C5	MN908947.3	11075	T	-	0.02	0.15	6.6e-06	5e-39	0.0655600529306453	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.934323188292987
CAMB-771C5	MN908947.3	12133	T	C	0.048	0.026	1.3e-21	3.6e-12	0.0381249754011256	CTT	ORF1ab:nsp8	A14A	T42C	GCT>GCC	Synonymous	ORF1ab:nsp8	0.961809427600593
CAMB-771C5	MN908947.3	14408	C	T	1	1	0	0	0.999658594874046	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000268246884678226
CAMB-771C5	MN908947.3	17722	G	T	0.014	0.01	5.2e-08	1.3e-06	0.012119503945885	GGT	ORF1ab:helicase	V496L	G1486T	GTA>TTA	Missense	ORF1ab:helicase	0.987849179506451
CAMB-771C5	MN908947.3	18649	G	T	0.037	0.01	3.2e-18	1.3e-06	0.0288425504577333	TGA	ORF1ab:3'-to-5'-exonuclease	E204*	G610T	GAG>TAG	Nonsense	ORF1ab:3'-to-5'-exonuclease	0.971144065528133
CAMB-771C5	MN908947.3	23030	T	C	0.034	0.03	1.9e-15	2.3e-13	0.0320823244552058	CTT	S	F490L	T1468C	TTT>CTT	Missense	GU280_gp02, spike glycoprotein	0.967917675544794
CAMB-771C5	MN908947.3	23403	A	G	1	1	0	0	0.999857553546917	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.06477428712025e-05
CAMB-771C5	MN908947.3	241	C	T	1	1	0	0	0.999777307649482	TCG	NA	NA	NA	NA	NA	NA	0.00011134617525888
CAMB-771C5	MN908947.3	26753	C	T	0.39	0.38	1.4e-205	1.2e-200	0.38413924698655	CCG	M	T77T	C231T	ACC>ACT	Synonymous	GU280_gp05	0.615674593940522
CAMB-771C5	MN908947.3	28550	C	T	0.0076	0.0072	3.1e-05	4.4e-05	0.00737078240168475	ACG	N	R93*	C277T	CGA>TGA	Nonsense	GU280_gp10	0.992629217598315
CAMB-771C5	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999510823040235	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000139703827884884
CAMB-771C5	MN908947.3	3037	C	T	1	1	0	0	0.999354734634618	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000322632682690757
CAMB-771C5	MN908947.3	4109	G	T	0.037	0.025	2.9e-18	1.8e-13	0.0310863008624795	AGA	ORF1ab:nsp3	D464Y	G1390T	GAT>TAT	Missense	ORF1ab:nsp3	0.96891369913752
CAMB-771C5	MN908947.3	8313	T	INS	0.0022	0.007	0.0015	1.2e-05	0.00348045023696682	ATG	ORF1ab:nsp3	.	5593-5594-insfrshift	.	no-SNV	ORF1ab:nsp3	0.99637144549763
CAMB-771C5	MN908947.3	8315	ACACC	-	0.00222	0.00714	0.0023;0.0024;0.0024;0.005;0.002	1.7e-05;1.8e-05;1.5e-05;3.8e-05;1.5e-05	0.00348612965435395	GAC	ORF1ab:nsp3	.	5596-5600-delfrshift	.	no-SNV	ORF1ab:nsp3	0.996154699401021
CAMB-771E3	MN908947.3	14408	C	T	1	1	0	0	0.999614985932178	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000266548200799645
CAMB-771E3	MN908947.3	15540	C	T	0.2	0.15	1.8e-92	1.8e-70	0.176167413431406	TCA	ORF1ab:RNA-dependent-RNA-polymerase	V691V	C2073T	GTC>GTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.823806687213488
CAMB-771E3	MN908947.3	23403	A	G	1	1	0	0	0.999854893709642	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.67375269051247e-05
CAMB-771E3	MN908947.3	241	C	T	1	1	0	0	0.999550499636942	TCG	NA	NA	NA	NA	NA	NA	0.000414923412053525
CAMB-771E3	MN908947.3	24257	G	T	0.12	0.084	2.4e-47	3e-35	0.0992546809670969	TGC	S	A899S	G2695T	GCT>TCT	Missense	GU280_gp02, spike glycoprotein	0.900745319032903
CAMB-771E3	MN908947.3	25350	C	T	1	1	0	0	0.99986050080212	CCA	S	P1263L	C3788T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	9.29994652530748e-05
CAMB-771E3	MN908947.3	28356	AGA	-	0.0153333333333333	0.0236666666666667	3.5e-12;1e-11;NA	2.8e-12;4.7e-12;3.6e-12	0.0231282065351587	CAG	N	.	83-85-delinframe	.	no-SNV	GU280_gp10	0.976241384160923
CAMB-771E3	MN908947.3	3037	C	T	1	1	0	0	0.999136442141623	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000863557858376511
CAMB-771E3	MN908947.3	4438	C	T	0.26	0.072	1.1e-100	3.3e-30	0.144353369763206	TCT	ORF1ab:nsp3	V573V	C1719T	GTC>GTT	Synonymous	ORF1ab:nsp3	0.855646630236794
CAMB-771E3	MN908947.3	9371	C	T	0.0032	0.22	0.0094	2.6e-55	0.0703918722786647	TCA	ORF1ab:nsp4	Q273*	C817T	CAA>TAA	Nonsense	ORF1ab:nsp4	0.929608127721335
CAMB-771F2	MN908947.3	11075	T	-	0.039	0.032	1.2e-09	4.8e-08	0.0352750241249232	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960935169751733
CAMB-771F2	MN908947.3	12235	A	G	0.025	0.02	1.1e-12	2e-10	0.0226290476296017	AAT	ORF1ab:nsp8	E48E	A144G	GAA>GAG	Synonymous	ORF1ab:nsp8	0.977304461535052
CAMB-771F2	MN908947.3	14120	C	T	1	1	0	0	0.99963413231866	CCA	ORF1ab:RNA-dependent-RNA-polymerase	P218L	C653T	CCA>CTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	7.31735362679406e-05
CAMB-771F2	MN908947.3	14408	C	T	1	1	0	0	0.998770733350173	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00101877578513093
CAMB-771F2	MN908947.3	23403	A	G	1	1	0	0	0.99993684919588	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.80670240534396e-05
CAMB-771F2	MN908947.3	241	C	T	1	1	0	0	0.999691200765822	TCG	NA	NA	NA	NA	NA	NA	0.00015439961708895
CAMB-771F2	MN908947.3	25687	G	T	0.022	0.022	3.7e-11	2.7e-11	0.0216805644644003	TGC	ORF3a	A99S	G295T	GCT>TCT	Missense	GU280_gp03	0.977592473807997
CAMB-771F2	MN908947.3	26535	AACGGTACT	-	0.0160666666666667	0.0122666666666667	1.1e-09;4e-10;4e-09;2.9e-09;5.3e-09;2.6e-09;3e-09;1.6e-09;0.00013	4.9e-08;2.3e-08;1.1e-07;7.7e-08;1.4e-07;7.3e-08;8.1e-08;6e-08;0.0012	0.0154149305199204	CAA	M	.	13-21-delinframe	.	no-SNV	GU280_gp05	0.983613999437947
CAMB-771F2	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999767084362044	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-771F2	MN908947.3	29212	G	A	0.011	0.0099	8.4e-07	4.4e-06	0.0106187401644287	CGT	N	A313A	G939A	GCG>GCA	Synonymous	GU280_gp10	0.989351845042872
CAMB-771F2	MN908947.3	3037	C	T	1	1	0	0	0.999637506041566	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.02771064926696e-05
CAMB-7720E	MN908947.3	1059	C	T	1	1	0	0	0.99989994196634	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	8.0046426927618e-05
CAMB-7720E	MN908947.3	10872	A	-	0.0078	0.012	9.2e-05	1.7e-06	0.00960189083388729	CAA	ORF1ab:3C-like-proteinase	.	818-818-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.990398109166113
CAMB-7720E	MN908947.3	11074	C	INS	0.045	0.02	3.5e-12	0.00078	0.0332277679250063	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.966607550038004
CAMB-7720E	MN908947.3	11075	T	-	0.029	0.037	1.2e-07	2.2e-09	0.0330085261875761	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95983833462518
CAMB-7720E	MN908947.3	11083	G	T	0.034	0.055	1.6e-07	8.3e-12	0.0448250728862974	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.94741143210531
CAMB-7720E	MN908947.3	1288	C	T	0.021	0.0077	9e-11	6.8e-05	0.0139884656511298	GCG	ORF1ab:nsp2	C161C	C483T	TGC>TGT	Synonymous	ORF1ab:nsp2	0.985994004943292
CAMB-7720E	MN908947.3	13006	T	C	1	0.99	0	0	0.992996232059137	CTG	ORF1ab:nsp9	A107A	T321C	GCT>GCC	Synonymous	ORF1ab:nsp9	0.000287629073546754
CAMB-7720E	MN908947.3	1437	C	T	1	1	0	0	1	TCT	ORF1ab:nsp2	S211F	C632T	TCT>TTT	Missense	ORF1ab:nsp2	0
CAMB-7720E	MN908947.3	14408	C	T	1	0.99	0	0	0.994796815651179	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000364222904417503
CAMB-7720E	MN908947.3	14849	TATTTG	-	0.0038	0.0343333333333333	NA;NA;NA;NA;0.13;0.008	3.3e-05;1.5e-05;5e-05;4.5e-05;1.1e-05;2.2e-05	0.0156032396327695	CTA	ORF1ab:RNA-dependent-RNA-polymerase	.	1382-1387-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.98723700598642
CAMB-7720E	MN908947.3	15200	TAGTAATTGGAACAAGCAAATT	-	0.00670454545454545	0.000318181818181818	0.00024;0.00032;0.00018;0.00012;0.00015;0.00014;0.00017;0.00017;6.2e-05;2e-05;3.1e-05;1.6e-05;2.7e-05;3.4e-05;2.3e-05;2.6e-05;2.5e-05;1e-04;1.7e-05;1.5e-05;1.1e-05;1.8e-05	0.0071;0.0095;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00351356133565886	GTA	ORF1ab:RNA-dependent-RNA-polymerase	.	1733-1754-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.994631842465223
CAMB-7720E	MN908947.3	17795	C	T	0.078	0.11	1.8e-35	2.8e-49	0.0924947435780236	GCT	ORF1ab:helicase	A520V	C1559T	GCT>GTT	Missense	ORF1ab:helicase	0.907468690008227
CAMB-7720E	MN908947.3	18022	AATGTGGCAACTT	-	0.00887692307692308	0.00148784615384615	2.5e-05;1.3e-05;2.1e-05;2.4e-05;1.8e-05;4.1e-05;1.3e-05;1.5e-05;1.4e-05;9.9e-06;1.1e-05;2.2e-05;1.1e-05	NA;NA;8.6e-06;1.1e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00440863163667813	GAA	ORF1ab:helicase	.	1786-1798-delfrshift	.	no-SNV	ORF1ab:helicase	0.995461168356062
CAMB-7720E	MN908947.3	1912	C	T	0.15	0.22	5.7e-71	9.2e-104	0.180867607939431	CCC	ORF1ab:nsp2	S369S	C1107T	TCC>TCT	Synonymous	ORF1ab:nsp2	0.819111929609167
CAMB-7720E	MN908947.3	19984	T	-	0.023	0.04	0.00039	1.7e-07	0.0321285140562249	CTT	ORF1ab:endoRNAse	.	364-364-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.966532797858099
CAMB-7720E	MN908947.3	21994	TT	-	0.013	0.024	0.00034;0.00057	1.2e-06;3.9e-06	0.0188480534572923	ATT	S	.	432-433-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.977351022502382
CAMB-7720E	MN908947.3	22939	TAATCTCAAACCTTTTGAGAGAGA	-	0.01035	0.000175	7.2e-06;8.1e-06;5.1e-06;1e-05;9.4e-06;1e-05;1e-05;1.2e-05;8e-06;4.7e-07;3.4e-06;7.5e-07;9e-06;4.8e-07;1.4e-06;3.6e-06;1.1e-05;5.8e-06;6.8e-06;6.4e-06;7.3e-06;7.9e-06;7e-06;2.1e-05	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0076;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00376146070057206	CTA	S	.	1377-1400-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.996436525612472
CAMB-7720E	MN908947.3	23403	A	G	1	1	0	0	0.999949160125269	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.06718997844389e-05
CAMB-7720E	MN908947.3	23555	CCCATTGGTGCAGGTATATGCGCTAGTT	-	0.0463571428571429	0.04125	0.00012;1e-04;0.00013;0.00014;3.3e-05;8.1e-05;3.8e-05;8.6e-05;9.6e-05;9.6e-05;8.3e-05;8.6e-05;4.6e-05;4e-05;1.4e-05;3.3e-06;1.5e-05;6.7e-06;1.1e-05;4.5e-06;1.5e-05;4e-05;1.9e-05;2e-05;1.1e-07;2.4e-07;3e-05;0.00026	NA;NA;NA;NA;0.00041;0.00073;4.4e-05;9.8e-05;1e-04;1e-04;1e-04;1e-04;5.1e-05;4.9e-05;1.7e-05;4.2e-06;1.6e-06;4.2e-07;1.3e-06;3e-07;1.4e-06;4.3e-06;1.7e-06;1.7e-06;2.4e-09;5.1e-09;0.0052;0.0042	0.0446924419527159	ACC	S	.	1993-2020-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.980591205554387
CAMB-7720E	MN908947.3	24070	A	T	1	1	0	0	1	AAT	S	Q836H	A2508T	CAA>CAT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7720E	MN908947.3	241	C	T	1	1	0	0	0.999729999169228	TCG	NA	NA	NA	NA	NA	NA	0.00014538506272327
CAMB-7720E	MN908947.3	25563	G	T	1	1	0	0	0.999845100529756	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	7.74497351219059e-05
CAMB-7720E	MN908947.3	25688	C	T	1	1	0	0	0.999836921069798	GCT	ORF3a	A99V	C296T	GCT>GTT	Missense	GU280_gp03	0.000163078930202218
CAMB-7720E	MN908947.3	26787	GGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTT	-	0.0517714285714286	0.037	6.2e-09;6.7e-09;1.4e-09;2e-09;1e-09;6.2e-09;2.9e-09;4.4e-09;1.1e-08;2e-09;8.3e-09;4.4e-09;4e-09;2.2e-09;9.7e-09;1.9e-09;5.2e-09;3.4e-09;1.3e-09;8.5e-09;2.7e-09;3.3e-10;4.8e-09;7.2e-09;7.6e-09;2.6e-09;7.6e-09;8.5e-10;2.9e-09;1.1e-09;6e-07;5.8e-06;1.5e-06;3e-06;0.00059	1.3e-06;1.3e-06;3.1e-07;6.7e-07;5.6e-07;1.1e-06;7.8e-07;1.1e-06;1.7e-06;6.3e-07;1.5e-06;8.7e-07;8.5e-07;6.8e-07;1.6e-06;8.4e-07;1.1e-06;7.9e-07;5.8e-07;1.2e-06;6.7e-07;6.4e-07;6.2e-07;1.3e-06;1e-06;5.1e-07;1.2e-06;3e-07;6.7e-07;5.4e-07;0.00027;0.0089;0.0059;0.0067;NA	0.0453557882332724	AGG	M	.	265-299-delfrshift	.	no-SNV	GU280_gp05	0.955581944894263
CAMB-7720E	MN908947.3	27945	C	T	1	1	0	0	1	CCA	ORF8	Q18*	C52T	CAA>TAA	Nonsense	GU280_gp09	0
CAMB-7720E	MN908947.3	28405	TTT	-	0.00297366666666667	0.0087	NA;NA;0.00081	0.00063;7.2e-05;4.7e-05	0.00329847405020169	GTT	N	.	132-134-delinframe	.	no-SNV	GU280_gp10	0.99667656169334
CAMB-7720E	MN908947.3	29079	ATGTAACACA	-	0.01212	0.0039964	0.00025;0.00054;0.00055;2e-05;2e-04;0.00042;0.00052;0.00049;0.00031;0.00024	0.24;0.28;0.29;6.8e-05;6.3e-05;NA;NA;NA;NA;NA	0.00603008628155371	AAT	N	.	806-815-delfrshift	.	no-SNV	GU280_gp10	0.989903195586551
CAMB-7720E	MN908947.3	3037	C	T	1	1	0	0	0.999743545905283	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7720E	MN908947.3	444	T	-	0.043	0.019	3e-07	0.0023	0.0334181749622926	GTT	ORF1ab:leader-protein	.	179-179-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.966275452488688
CAMB-7720E	MN908947.3	514	T	-	0.11	0.13	0.00021	4.3e-05	0.117980304931371	ATG	ORF1ab:leader-protein	.	249-249-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.878369643739782
CAMB-7720E	MN908947.3	522	TT	-	0.0845	0.041	1.5e-11;6.2e-12	2e-07;0.00073	0.0674920127795527	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.924087834091161
CAMB-7720E	MN908947.3	5822	CTT	-	0.028	0.01	7.4e-06;8.2e-09;5.7e-08	0.0086;0.00059;0.00082	0.0188679245283019	ACT	ORF1ab:nsp3	.	3103-3105-delinframe	.	no-SNV	ORF1ab:nsp3	0.981241030547393
CAMB-7720E	MN908947.3	5911	T	-	0.0062	0.015	0.0014	8.3e-07	0.0109042250313176	ATA	ORF1ab:nsp3	.	3192-3192-delfrshift	.	no-SNV	ORF1ab:nsp3	0.989067304407243
CAMB-7720E	MN908947.3	9696	ATATCAT	-	0.0182571428571429	0.00611428571428571	6.4e-05;0.00036;1e-06;9.2e-05;8.9e-05;1.6e-05;3.2e-06	0.024;0.023;0.0098;0.00071;0.00073;2e-04;NA	0.00884654644436883	TAT	ORF1ab:nsp4	.	1142-1148-delfrshift	.	no-SNV	ORF1ab:nsp4	0.982616419236138
CAMB-7721D	MN908947.3	14408	C	T	1	1	0	0	0.99959331224582	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000180750112968821
CAMB-7721D	MN908947.3	14786	C	T	1	1	0	0	1	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A440V	C1319T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-7721D	MN908947.3	20578	G	T	1	1	0	0	1	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	0
CAMB-7721D	MN908947.3	23403	A	G	1	1	0	0	0.999830508474576	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.77966101694915e-05
CAMB-7721D	MN908947.3	241	C	T	1	1	0	0	0.999775078722447	TCG	NA	NA	NA	NA	NA	NA	7.49737591842855e-05
CAMB-7721D	MN908947.3	2416	C	T	1	1	4e-230	0	1	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0
CAMB-7721D	MN908947.3	25563	G	T	1	1	0	0	1	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0
CAMB-7721D	MN908947.3	28153	C	T	1	1	0	0	0.999765368371657	ACA	ORF8	T87I	C260T	ACA>ATA	Missense	GU280_gp09	2.93289535429376e-05
CAMB-7721D	MN908947.3	28325	G	T	0.17	0.15	4e-78	1.6e-71	0.159242059396858	TGG	N	G18C	G52T	GGT>TGT	Missense	GU280_gp10	0.840614608416466
CAMB-7721D	MN908947.3	3037	C	T	1	1	2.6e-309	0	0.999332443257677	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7721D	MN908947.3	3096	C	T	0.18	0.25	2.8e-49	6.7e-72	0.218430034129693	TCA	ORF1ab:nsp3	S126L	C377T	TCA>TTA	Missense	ORF1ab:nsp3	0.781569965870307
CAMB-7721D	MN908947.3	683	C	T	0.1	0.036	2.1e-48	1.8e-17	0.0746662621359223	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.925303398058252
CAMB-7721D	MN908947.3	9430	C	T	0.27	0.36	1.2e-75	9.4e-76	0.303506650544135	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.696493349455865
CAMB-7724A	MN908947.3	13036	A	G	0.0022	0.0096	0.0091	2.7e-06	0.00403308496821382	CAA	ORF1ab:nsp10	A4A	A12G	GCA>GCG	Synonymous	ORF1ab:nsp10	0.9959498256887
CAMB-7724A	MN908947.3	14408	C	T	1	1	0	0	0.999736321687541	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.0001318391562294
CAMB-7724A	MN908947.3	23403	A	G	1	1	0	0	0.999770167777522	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000183865777982073
CAMB-7724A	MN908947.3	241	C	T	1	1	0	0	0.999407512738476	TCG	NA	NA	NA	NA	NA	NA	0.000473989809219102
CAMB-7724A	MN908947.3	28854	C	T	1	1	0	0	0.99956766104626	TCA	N	S194L	C581T	TCA>TTA	Missense	GU280_gp10	0
CAMB-77259	MN908947.3	11075	T	-	0.035	0.037	7.2e-09	1.2e-09	0.0356093192224731	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960530797078598
CAMB-77259	MN908947.3	11651	C	INS	0.027	0.027	1.3e-12	2.2e-12	0.0271820519341075	CCT	ORF1ab:nsp6	.	678-679-insfrshift	.	no-SNV	ORF1ab:nsp6	0.963889124353649
CAMB-77259	MN908947.3	11651	C	T	0.0089	0.0081	1.4e-05	1.7e-05	0.00861801022858919	CCT	ORF1ab:nsp6	L227F	C679T	CTC>TTC	Missense	ORF1ab:nsp6	0.963889124353649
CAMB-77259	MN908947.3	11653	C	T	1	1	0	0	0.995963023636789	TCT	ORF1ab:nsp6	L227L	C681T	CTC>CTT	Synonymous	ORF1ab:nsp6	0.000321787970980576
CAMB-77259	MN908947.3	14408	C	T	1	1	0	0	0.998644850888123	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000536602668461406
CAMB-77259	MN908947.3	22450	C	T	0.03	0.029	1.8e-12	3e-12	0.0296213808463252	TCT	S	L296L	C888T	CTC>CTT	Synonymous	GU280_gp02, spike glycoprotein	0.969933184855234
CAMB-77259	MN908947.3	23403	A	G	1	1	0	0	0.997966894122102	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.93871873173703e-05
CAMB-77259	MN908947.3	241	C	T	1	1	0	0	0.9988058056219	TCG	NA	NA	NA	NA	NA	NA	0.000165349990813889
CAMB-77259	MN908947.3	27297	C	T	0.022	0.022	3.8e-11	3.1e-11	0.0218385835989986	TCA	ORF6	I32I	C96T	ATC>ATT	Synonymous	GU280_gp06	0.978017326777256
CAMB-77259	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999111257406188	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-77259	MN908947.3	3037	C	T	1	1	0	0	0.999145094552543	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000102588653694901
CAMB-77259	MN908947.3	8151	T	C	0.07	0.075	2.7e-31	3.2e-34	0.0714227554011508	GTC	ORF1ab:nsp3	V1811A	T5432C	GTC>GCC	Missense	ORF1ab:nsp3	0.928210834871349
CAMB-77268	MN908947.3	14408	C	T	1	1	0	6.7e-180	0.99818943971031	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000590400094464015
CAMB-77268	MN908947.3	28881	GGG	AAC	1	1	0;0;0	4.5e-11;3.3e-14;8.3e-15	0.999232486742953	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000154059466954244
CAMB-77268	MN908947.3	3037	C	T	1	1	0	1.3e-33	0.999518149694828	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00016061676839062
CAMB-77277	MN908947.3	11071	G	INS	0.22	0.26	9.1e-59	6.4e-73	0.229261929097854	TGT	ORF1ab:nsp6	.	98-99-insfrshift	.	no-SNV	ORF1ab:nsp6	0.770119425466674
CAMB-77277	MN908947.3	11072	TT	-	0.052	0.05885	2.6e-14;9.1e-27	0.00072;7.3e-53	0.0548385807895157	GTT	ORF1ab:nsp6	.	100-101-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964197330520508
CAMB-77277	MN908947.3	11073	T	-	0.058	0.11	9.1e-27	7.3e-53	0.0738014642210501	TTC	ORF1ab:nsp6	.	101-101-delfrshift	.	no-SNV	ORF1ab:nsp6	0.925962371093442
CAMB-77277	MN908947.3	11074	C	-	0.16	0.19	8.4e-148	1.8e-120	0.170648464163823	TCT	ORF1ab:nsp6	.	102-102-delfrshift	.	no-SNV	ORF1ab:nsp6	0.000144464308286834
CAMB-77277	MN908947.3	11074	C	T	0.84	0.81	0	0	0.829008433103996	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.000144464308286834
CAMB-77277	MN908947.3	11083	G	T	1	1	0	0	0.999425844188467	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.79423691104173e-05
CAMB-77277	MN908947.3	14805	C	T	1	1	0	0	0.999923399039935	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	2.55336533551221e-05
CAMB-77277	MN908947.3	17523	G	T	0.79	0.77	0	0	0.779853143643873	TGA	ORF1ab:helicase	M429I	G1287T	ATG>ATT	Missense	ORF1ab:helicase	0.219963285910968
CAMB-77277	MN908947.3	241	C	T	1	1	0	0	0.999806170247133	TCG	NA	NA	NA	NA	NA	NA	3.23049588111775e-05
CAMB-77277	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-77277	MN908947.3	25317	C	T	1	1	0	0	0.999897983473323	TCC	S	S1252F	C3755T	TCC>TTC	Missense	GU280_gp02, spike glycoprotein	0.000102016526677322
CAMB-77277	MN908947.3	2558	C	T	1	1	0	0	0.999781945050153	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000218054949847362
CAMB-77277	MN908947.3	26144	G	T	1	1	3.1e-270	5.5e-284	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-77286	MN908947.3	11074	C	INS	0.11	0.1	1.2e-45	4e-47	0.103990598157654	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.885855757764297
CAMB-77286	MN908947.3	11074	C	T	0.0086	0.0086	2.6e-06	1.1e-06	0.00861547501771487	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.885855757764297
CAMB-77286	MN908947.3	11083	G	-	0.14	0.15	2.9e-59	3.5e-62	0.141677758762756	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.000570450656018254
CAMB-77286	MN908947.3	11083	G	T	0.86	0.85	0	0	0.857601254991443	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.000570450656018254
CAMB-77286	MN908947.3	14805	C	T	1	1	0	0	0.998146767642284	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00105202287975588
CAMB-77286	MN908947.3	19021	G	T	0.028	0.032	7.7e-14	4.5e-15	0.0300582331805229	AGT	ORF1ab:3'-to-5'-exonuclease	V328F	G982T	GTT>TTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.969826126460992
CAMB-77286	MN908947.3	21606	G	T	0.013	0.012	3e-07	1.6e-06	0.0124343093093093	TGT	S	C15F	G44T	TGT>TTT	Missense	GU280_gp02, spike glycoprotein	0.987424924924925
CAMB-77286	MN908947.3	22550	C	T	0.032	0.031	3.3e-15	1.4e-14	0.0310006383657836	TCC	S	P330S	C988T	CCT>TCT	Missense	GU280_gp02, spike glycoprotein	0.96896943823811
CAMB-77286	MN908947.3	2480	A	G	1	1	0	0	0.99945125297238	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000228644594841778
CAMB-77286	MN908947.3	25519	T	A	1	1	0	0	0.997852339541598	TTT	ORF3a	F43I	T127A	TTC>ATC	Missense	GU280_gp03	0.000844981163961553
CAMB-77286	MN908947.3	2558	C	T	1	1	0	0	0.99898829887781	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000479226847352937
CAMB-77286	MN908947.3	26144	G	T	1	1	0	0	0.998507280813989	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.00137086455858161
CAMB-77286	MN908947.3	29747	G	T	0.05	0.055	5.2e-22	3.2e-24	0.0528202300299354	AGT	NA	NA	NA	NA	NA	NA	0.946510162281393
CAMB-77286	MN908947.3	29752	ATCGAGTGT	-	0.019	0.0168888888888889	5.3e-07;7.4e-07;7e-07;8.4e-07;1.2e-07;3e-06;8.1e-07;2.3e-06;1.5e-08	2.9e-06;3.8e-06;3.5e-06;4e-06;4.3e-07;1.3e-05;4.9e-06;1.1e-05;1.8e-07	0.0171894803548796	GAT	NA	NA	NA	NA	NA	NA	0.980108991825613
CAMB-77286	MN908947.3	713	G	T	1	1	0	0	0.99901057537193	TGG	ORF1ab:leader-protein	G150C	G448T	GGC>TGC	Missense	ORF1ab:leader-protein	0.000638107187668041
CAMB-77295	MN908947.3	11074	C	INS	0.24	0.16	2e-128	1.5e-51	0.217903773922375	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.781774280093007
CAMB-77295	MN908947.3	11083	G	-	0.086	0.13	6e-37	3.9e-56	0.0995232759111888	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.89929915861047e-05
CAMB-77295	MN908947.3	11083	G	T	0.91	0.87	0	0	0.90028679417295	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.89929915861047e-05
CAMB-77295	MN908947.3	14805	C	T	1	1	0	0	0.99991540001692	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	5.63999887200023e-05
CAMB-77295	MN908947.3	23707	C	T	1	1	0	0	0.999576331026691	CCA	S	P715P	C2145T	CCC>CCT	Synonymous	GU280_gp02, spike glycoprotein	0.000423668973308855
CAMB-772A4	MN908947.3	10449	C	T	0.0078	0.0031	3.6e-05	0.0045	0.0051529049280187	CCC	ORF1ab:3C-like-proteinase	P132L	C395T	CCC>CTC	Missense	ORF1ab:3C-like-proteinase	0.994723142032476
CAMB-772A4	MN908947.3	11075	T	-	0.021	0.041	1.2e-05	7.3e-10	0.0326859339785231	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962428741879889
CAMB-772A4	MN908947.3	11270	A	G	1	1	0	0	0.999875211360758	TAT	ORF1ab:nsp6	M100V	A298G	ATG>GTG	Missense	ORF1ab:nsp6	8.11126155074842e-05
CAMB-772A4	MN908947.3	14408	C	T	1	1	0	0	0.999590209253465	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000273193831023111
CAMB-772A4	MN908947.3	14790	C	T	0.013	0.0052	1.7e-07	6e-04	0.00856634162722475	TCA	ORF1ab:RNA-dependent-RNA-polymerase	I441I	C1323T	ATC>ATT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.99137663390928
CAMB-772A4	MN908947.3	21255	G	T	0.079	0.1	3.3e-13	4.5e-19	0.0932835820895522	CGT	ORF1ab:2'-O-ribose-methyltransferase	A199A	G597T	GCG>GCT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.906716417910448
CAMB-772A4	MN908947.3	21682	C	T	0.054	0.046	4e-23	4.1e-20	0.0487101426053517	ACA	S	D40D	C120T	GAC>GAT	Synonymous	GU280_gp02, spike glycoprotein	0.951289857394648
CAMB-772A4	MN908947.3	22201	G	T	1	1	0	0	0.99969747631558	TGC	S	V213V	G639T	GTG>GTT	Synonymous	GU280_gp02, spike glycoprotein	1.59222991800016e-05
CAMB-772A4	MN908947.3	23403	A	G	1	1	0	0	0.998712211112235	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000723716069157456
CAMB-772A4	MN908947.3	241	C	T	1	1	0	0	0.998913126175182	TCG	NA	NA	NA	NA	NA	NA	0.000130424858978121
CAMB-772A4	MN908947.3	25521	C	T	0.011	0.016	3.4e-06	3.3e-08	0.0139197340707521	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.985456994254438
CAMB-772A4	MN908947.3	28253	C	T	0.022	0.018	2.9e-10	1.9e-08	0.0195541510567106	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.978465410243944
CAMB-772A4	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999056408368047	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000130497194310322
CAMB-772A4	MN908947.3	3037	C	T	1	1	0	0	0.999689994574905	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.16675708491565e-05
CAMB-772A4	MN908947.3	635	C	T	0.018	0.023	2.4e-09	3e-11	0.020763597010042	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.979194456329332
CAMB-772A4	MN908947.3	9430	C	T	0.012	0.005	3.7e-06	0.0029	0.00805242149465864	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.991924505664383
CAMB-772B3	MN908947.3	14408	C	T	1	1	0	3.3e-175	0.99884505220364	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000300286427053497
CAMB-772B3	MN908947.3	241	C	T	1	1	0	5.7e-11	0.998971775230065	TCG	NA	NA	NA	NA	NA	NA	0.000205644953986942
CAMB-772B3	MN908947.3	3037	C	T	1	0.8	0	1.6e-17	0.999142918362974	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000178558674380401
CAMB-772C2	MN908947.3	11075	T	C	0.066	0.053	1.5e-07	1.4e-06	0.0616345510389677	CTT	ORF1ab:nsp6	F35L	T103C	TTT>CTT	Missense	ORF1ab:nsp6	0.933114844111944
CAMB-772C2	MN908947.3	14408	C	T	1	1	0	0	0.999527074958619	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000291030794695964
CAMB-772C2	MN908947.3	23403	A	G	1	1	0	0	0.999926599347783	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.24290372980171e-05
CAMB-772C2	MN908947.3	241	C	T	1	1	0	0	0.999654448969517	TCG	NA	NA	NA	NA	NA	NA	0.000271504381093422
CAMB-772C2	MN908947.3	25429	G	T	1	1	0	0	0.999805474994695	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0.00012378863973969
CAMB-772C2	MN908947.3	25916	C	T	1	1	0	0	0.999691833590139	ACA	ORF3a	T175I	C524T	ACA>ATA	Missense	GU280_gp03	0.000308166409861325
CAMB-772C2	MN908947.3	28708	C	T	0.07	0.028	4.6e-32	1.3e-13	0.0565912518853695	ACA	N	H145H	C435T	CAC>CAT	Synonymous	GU280_gp10	0.943227752639517
CAMB-772C2	MN908947.3	3037	C	T	1	0.95	0	0	0.979806550144239	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-772C2	MN908947.3	4331	C	T	0.086	0.037	3.9e-40	1.4e-18	0.0681797264711838	TCT	ORF1ab:nsp3	L538L	C1612T	CTA>TTA	Synonymous	ORF1ab:nsp3	0.93178345942165
CAMB-772C2	MN908947.3	5544	C	T	0.072	0.013	7.3e-27	4.5e-06	0.0486373165618449	ACA	ORF1ab:nsp3	T942I	C2825T	ACA>ATA	Missense	ORF1ab:nsp3	0.951362683438155
CAMB-772C2	MN908947.3	686	AAGTCATTTGACTT	-	0.0137867142857143	0.0736428571428571	0.0027;0.0023;0.005;0.0025;0.0052;0.0029;0.0017;0.0032;0.0061;NA;NA;NA;NA;NA	1.2e-12;6.5e-13;2.1e-11;7.7e-13;3.2e-11;3.1e-12;2.4e-13;2.7e-12;1.8e-10;5.7e-17;4.3e-21;4.5e-21;2e-21;3.2e-21	0.0414709185915906	AAA	ORF1ab:leader-protein	.	421-434-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.95748319731157
CAMB-772D1	MN908947.3	14408	C	T	1	1	0	0	0.999385692213183	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000390923137065098
CAMB-772D1	MN908947.3	23231	A	-	0.021	0.027	4.6e-09	1.1e-11	0.0237691889404777	CAA	S	.	1669-1669-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.975760237587318
CAMB-772D1	MN908947.3	23231	AA	-	0.010509	0.027	4.6e-09;NA	1.1e-11;1.3e-13	0.0176411977555194	CAA	S	.	1669-1670-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.975760237587318
CAMB-772D1	MN908947.3	23403	A	G	1	1	0	0	0.999863608703863	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000115408019808213
CAMB-772D1	MN908947.3	241	C	T	1	1	0	0	0.999764792849703	TCG	NA	NA	NA	NA	NA	NA	6.72020429421054e-05
CAMB-772D1	MN908947.3	26776	CTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0382142857142857	0.0602142857142857	0.0047;0.0042;0.0095;0.022;3.7e-07;9.4e-10;1.2e-07;1.4e-07;5.5e-07;9.3e-09;1.2e-07;1.1e-06;1.1e-06;2.8e-07;6.5e-07;4.7e-07;9.1e-07;7.1e-07;1e-06;1.6e-06;5.7e-07;1.4e-06;6.6e-07;7.3e-07;6.4e-07;1.5e-06;7.7e-07;9.6e-07;6.8e-07;5.3e-07;1.4e-06;5.8e-07;9e-07;8.3e-07;1.2e-06;6.8e-07;2.4e-07;1.1e-06;2.6e-07;5.8e-07;3.1e-07;0.04	1.4e-10;1.4e-11;3.5e-10;1e-08;6.7e-11;2.6e-14;1.9e-11;2.2e-11;2.1e-10;4.3e-13;8.9e-12;4.3e-10;4.3e-10;7.2e-11;1.5e-10;9.5e-11;4.3e-10;2e-10;3.3e-10;6.9e-10;1.7e-10;5.7e-10;2.8e-10;2.4e-10;1.5e-10;6e-10;2e-10;3.7e-10;2.3e-10;1.5e-10;4.4e-10;1.6e-10;3.1e-10;2e-10;4.5e-10;3.6e-10;1.8e-10;4.4e-10;3.9e-11;1.4e-10;1e-10;7.7e-08	0.0476655034832964	GCT	M	.	254-295-delinframe	.	no-SNV	GU280_gp05	0.952138341390852
CAMB-772D1	MN908947.3	27264	TTTTAAAGTTTCCATTTGGAATCTTGA	-	0.014	0.00852244444444444	4.2e-07;1.1e-05;4.9e-05;0.00014;9.8e-05;9.4e-05;9.5e-05;8.4e-05;6.9e-05;0.00012;0.00012;9.3e-05;7.4e-05;8.4e-05;7.1e-05;0.00012;0.00012;9.9e-05;0.00015;9.4e-05;9.1e-05;1e-04;1e-04;5.8e-05;0.00011;4.1e-05;4.7e-05	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;6.4e-07;1.3e-06;5.1e-07;7.4e-07;6.5e-07;7.1e-07;2.2e-07;7.2e-07;1.6e-07;1.6e-07	0.00760503677845655	CTT	ORF6	.	63-89-delinframe	.	no-SNV	GU280_gp06	0.992477276262862
CAMB-772D1	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999487232078761	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000116171003717472
CAMB-772D1	MN908947.3	29253	C	T	0.92	0.92	0	0	0.917491569672577	TCG	N	S327L	C980T	TCG>TTG	Missense	GU280_gp10	0.0823996519090612
CAMB-772D1	MN908947.3	29274	C	T	0.0052	0.0098	0.00086	7.9e-06	0.00727437448373258	ACA	N	T334I	C1001T	ACA>ATA	Missense	GU280_gp10	0.992645687335127
CAMB-772D1	MN908947.3	3037	C	T	1	1	0	0	0.99970242523434	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-772D1	MN908947.3	6123	G	A	1	1	0	0	1	AGA	ORF1ab:nsp3	R1135K	G3404A	AGA>AAA	Missense	ORF1ab:nsp3	0
CAMB-772D1	MN908947.3	6512	AGTTTAAAAATTAC	-	0.0283571428571429	0.00450321428571429	7.2e-11;3.8e-10;8.1e-10;9.7e-10;3.7e-14;1.8e-13;7e-14;4.1e-14;3.7e-13;4.4e-13;2e-14;1.6e-14;2.6e-14;2e-14	NA;NA;NA;NA;NA;4.3e-15;1.6e-15;NA;NA;NA;NA;NA;NA;NA	0.0163287859157076	TAG	ORF1ab:nsp3	.	3793-3806-delfrshift	.	no-SNV	ORF1ab:nsp3	0.981789658900596
CAMB-772D1	MN908947.3	683	C	T	0.0088	0.02	1.5e-05	1.4e-10	0.0124560979424688	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.987515463477754
CAMB-772D1	MN908947.3	7434	TTTA	-	0.0655	0.0385	NA;1.9e-16;2.8e-15;5.6e-13	1.5e-08;3.1e-07;1.1e-06;5e-06	0.0701438848920863	TTT	ORF1ab:nsp3	.	4715-4718-delfrshift	.	no-SNV	ORF1ab:nsp3	0.985218033998522
CAMB-772E0	MN908947.3	11074	C	INS	0.025	0.018	2.4e-05	0.0031	0.0225574619617999	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.977300097118809
CAMB-772E0	MN908947.3	11075	T	-	0.032	0.034	3.9e-08	5.2e-09	0.0328826198283994	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964354701046674
CAMB-772E0	MN908947.3	12070	G	T	0.021	0.022	1e-10	2.6e-11	0.0212472988592392	TGG	ORF1ab:nsp7	L76L	G228T	CTG>CTT	Synonymous	ORF1ab:nsp7	0.978220011055832
CAMB-772E0	MN908947.3	14120	C	T	1	1	0	0	0.999645663547116	CCA	ORF1ab:RNA-dependent-RNA-polymerase	P218L	C653T	CCA>CTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	6.25299622735894e-05
CAMB-772E0	MN908947.3	14408	C	T	1	1	0	0	0.999289887350311	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000268982064275954
CAMB-772E0	MN908947.3	16965	A	C	0.014	0.0069	4.6e-08	3.7e-05	0.0106472716366431	AAG	ORF1ab:helicase	Q243H	A729C	CAA>CAC	Missense	ORF1ab:helicase	0.989277747577183
CAMB-772E0	MN908947.3	23403	A	G	1	1	0	0	0.998741867664344	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.13859320939626e-05
CAMB-772E0	MN908947.3	241	C	T	1	1	0	0	0.998444682062463	TCG	NA	NA	NA	NA	NA	NA	0.000180527974892725
CAMB-772E0	MN908947.3	2872	T	C	0.0089	0.0054	4.3e-06	0.00015	0.00729810185333376	ATG	ORF1ab:nsp3	N51N	T153C	AAT>AAC	Synonymous	ORF1ab:nsp3	0.992669888928011
CAMB-772E0	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999433213678443	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000107215610592902
CAMB-772E0	MN908947.3	28961	C	T	0.0096	0.011	6.7e-06	1.6e-06	0.0101655619296733	GCT	N	L230F	C688T	CTT>TTT	Missense	GU280_gp10	0.989745266474452
CAMB-772E0	MN908947.3	3037	C	T	1	1	0	0	0.999614364907207	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.82043865991805e-05
CAMB-772E0	MN908947.3	7765	C	T	0.0049	0.0092	0.00065	1.5e-05	0.00626994984040128	CCA	ORF1ab:nsp3	S1682S	C5046T	TCC>TCT	Synonymous	ORF1ab:nsp3	0.993730050159599
CAMB-772FF	MN908947.3	11075	T	-	0.043	0.036	2.4e-10	7.1e-09	0.0398357787254672	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954331639107085
CAMB-772FF	MN908947.3	11417	G	T	0.0076	0.0043	3.9e-05	0.00078	0.00628726726970348	CGT	ORF1ab:nsp6	V149F	G445T	GTT>TTT	Missense	ORF1ab:nsp6	0.993388228613151
CAMB-772FF	MN908947.3	14408	C	T	1	1	0	0	0.999410482444716	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000342742764700237
CAMB-772FF	MN908947.3	20268	A	G	1	1	0	1.9e-252	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-772FF	MN908947.3	20313	C	A	0.03	0.011	7.6e-10	0.00025	0.024745269286754	CCT	ORF1ab:endoRNAse	A231A	C693A	GCC>GCA	Synonymous	ORF1ab:endoRNAse	0.975254730713246
CAMB-772FF	MN908947.3	23403	A	G	1	1	0	0	0.999312106918239	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.68514150943396e-05
CAMB-772FF	MN908947.3	241	C	T	1	1	0	0	0.997220249875365	TCG	NA	NA	NA	NA	NA	NA	0.000105751363437221
CAMB-772FF	MN908947.3	28027	G	C	0.2	0.19	1.6e-90	2.1e-85	0.192490962865593	TGG	ORF8	W45S	G134C	TGG>TCG	Missense	GU280_gp09	0.80697502464673
CAMB-772FF	MN908947.3	2937	C	T	1	1	0	0	0.999825901503776	ACA	ORF1ab:nsp3	T73I	C218T	ACA>ATA	Missense	ORF1ab:nsp3	6.52869360840896e-05
CAMB-772FF	MN908947.3	3037	C	T	1	1	0	0	0.999353788094192	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	2.58484762323261e-05
CAMB-772FF	MN908947.3	4571	A	G	0.0082	0.0039	1.4e-05	0.00078	0.00640087018365895	CAA	ORF1ab:nsp3	N618D	A1852G	AAC>GAC	Missense	ORF1ab:nsp3	0.993445732055948
CAMB-772FF	MN908947.3	8083	G	C	0.017	0.013	6.3e-09	2.4e-07	0.0154974511518069	TGG	ORF1ab:nsp3	M1788I	G5364C	ATG>ATC	Missense	ORF1ab:nsp3	0.982243213478809
CAMB-772FF	MN908947.3	8296	T	C	0.016	0.014	6.5e-09	3.8e-08	0.0154173456454825	ATA	ORF1ab:nsp3	Y1859Y	T5577C	TAT>TAC	Synonymous	ORF1ab:nsp3	0.984501176896614
CAMB-772FF	MN908947.3	9741	A	C	0.015	0.019	4.7e-08	1.5e-09	0.0167930620493203	AAT	ORF1ab:nsp4	N396T	A1187C	AAT>ACT	Missense	ORF1ab:nsp4	0.982916116716255
CAMB-7730B	MN908947.3	10277	C	T	0.0037	0.0082	0.0016	1.3e-05	0.0055167852978542	ACT	ORF1ab:3C-like-proteinase	L75F	C223T	CTC>TTC	Missense	ORF1ab:3C-like-proteinase	0.994465811593951
CAMB-7730B	MN908947.3	11075	T	-	0.032	0.016	3.2e-08	4.5e-05	0.0266196316882695	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.971953073325829
CAMB-7730B	MN908947.3	14408	C	T	1	1	0	0	0.998666902613107	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000377514304252935
CAMB-7730B	MN908947.3	19648	G	T	0.0036	0.008	0.00099	1.2e-05	0.00534380282458149	TGT	ORF1ab:endoRNAse	V10L	G28T	GTA>TTA	Missense	ORF1ab:endoRNAse	0.994492611374666
CAMB-7730B	MN908947.3	20275	G	A	1	1	7.1e-302	3.5e-274	0.998214285714286	GGA	ORF1ab:endoRNAse	D219N	G655A	GAT>AAT	Missense	ORF1ab:endoRNAse	0.00178571428571429
CAMB-7730B	MN908947.3	23403	A	G	1	1	0	0	0.999886969299123	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.08626850877727e-05
CAMB-7730B	MN908947.3	241	C	T	1	1	0	0	0.998368475845673	TCG	NA	NA	NA	NA	NA	NA	6.21533011172056e-05
CAMB-7730B	MN908947.3	24933	G	T	0.085	0.094	3.8e-13	1e-14	0.0885609897163171	GGT	S	G1124V	G3371T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.911439010283683
CAMB-7730B	MN908947.3	27219	C	T	0.0022	0.0093	0.0064	2.9e-06	0.00435763997742805	ACT	ORF6	D6D	C18T	GAC>GAT	Synonymous	GU280_gp06	0.995631910046607
CAMB-7730B	MN908947.3	27999	C	T	0.013	0.0075	4.3e-07	0.00013	0.0110568269478015	CCC	ORF8	P36S	C106T	CCG>TCG	Missense	GU280_gp09	0.988943173052198
CAMB-7730B	MN908947.3	3037	C	T	1	1	0	0	0.99957005097967	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00012284257723727
CAMB-7730B	MN908947.3	6672	A	G	1	1	0	0	0.999901195534038	GAT	ORF1ab:nsp3	D1318G	A3953G	GAT>GGT	Missense	ORF1ab:nsp3	9.88044659618615e-05
CAMB-7730B	MN908947.3	890	G	A	0.014	0.011	7.3e-08	4.7e-07	0.0126013724266999	TGG	ORF1ab:nsp2	G29S	G85A	GGT>AGT	Missense	ORF1ab:nsp2	0.987357038885423
CAMB-7730B	MN908947.3	9712	C	T	0.11	0.11	4.6e-49	2.6e-52	0.109829136870781	CCA	ORF1ab:nsp4	S386S	C1158T	TCC>TCT	Synonymous	ORF1ab:nsp4	0.890170863129219
CAMB-7731A	MN908947.3	11075	T	-	0.074	0.018	1.1e-17	3.8e-05	0.0459233000322269	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953906087088396
CAMB-7731A	MN908947.3	11075	TTTTTTTTGTATGAAAATGCCTTTTTACC	-	0.0410689655172414	0.000629655172413793	1.1e-17;2.6e-14;1.3e-18;1.1e-18;1.8e-18;2.4e-18;1.8e-16;3.9e-06;4.1e-16;5.5e-16;7.6e-16;6.9e-13;3.2e-13;1.5e-17;1.2e-17;5.9e-18;1.3e-18;1.3e-17;2.6e-18;2.3e-14;3.3e-14;2.8e-21;1.8e-10;3.2e-08;5.9e-08;7e-08;5.2e-08;8.3e-08;5.6e-08	3.8e-05;NA;NA;NA;NA;NA;NA;NA;0.5;NA;NA;NA;NA;0.5;NA;NA;NA;NA;NA;NA;NA;0.5;NA;NA;NA;NA;NA;NA;NA	0.0190609241486216	CTT	ORF1ab:nsp6	.	103-131-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953906087088396
CAMB-7731A	MN908947.3	11567	ATT	CCC	0.0033	0.0153333333333333	NA;2.7e-06;NA	3.5e-08;3.7e-08;2e-07	0.0063391442155309	TAT	ORF1ab:nsp6	.	595-597-mnv	.	no-SNV	ORF1ab:nsp6	0.993699133630874
CAMB-7731A	MN908947.3	12557	A	G	0.7	0.69	0	0	0.692508359617711	AAT	ORF1ab:nsp8	I156V	A466G	ATC>GTC	Missense	ORF1ab:nsp8	0.304479806483743
CAMB-7731A	MN908947.3	12775	TTACTACAACACAACAAAGGGAGGTAGGTTT	-	0.00105835483870968	0.00718064516129032	0.44;NA;NA;NA;NA;8.4e-07;NA;NA;NA;NA;NA;NA;NA;5.8e-06;1.3e-05;0.49;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00089;0.00094;0.00087;0.00076;0.00077;5.6e-05;6.2e-05;5.9e-05;0.00013;0.00014;4.9e-05;5.3e-05;0.00015;7e-05;0.00012;5.8e-05;2.5e-05;4.8e-05;9.9e-05;4.6e-05;6.3e-05;7.6e-05;6.9e-05;5.7e-05;3.1e-05;1e-05;5.6e-05;4.8e-05;2.4e-05;1.2e-05;4.1e-05	0.00386944100967893	CTT	ORF1ab:nsp9	.	90-120-delfrshift	.	no-SNV	ORF1ab:nsp9	0.997656004872557
CAMB-7731A	MN908947.3	12788	AC	-	0.01035	0.00775	5.8e-06;1.3e-05	7e-05;0.00012	0.00885063717933077	AAC	ORF1ab:nsp9	.	103-104-delfrshift	.	no-SNV	ORF1ab:nsp9	0.990666558452852
CAMB-7731A	MN908947.3	13994	C	T	0.036	0.068	1.5e-17	2.2e-31	0.0523010794001465	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A176V	C527T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.947686913924142
CAMB-7731A	MN908947.3	14408	C	T	1	1	0	0	0.999547225439612	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000263241023481099
CAMB-7731A	MN908947.3	15022	TTCGCATATACAAAACGTA	-	0.0224210526315789	0.0092421052631579	1.4e-07;6.5e-06;1.5e-05;2.4e-05;4.1e-05;3.3e-05;1.9e-05;2.8e-05;5.4e-06;6.9e-06;2.5e-06;1.4e-06;3.6e-06;4.9e-06;8.5e-06;3.6e-06;4.7e-06;1.2e-05;7.6e-06	0.0016;0.0069;0.0099;0.011;0.012;0.015;0.014;0.013;0.0074;0.008;0.0043;3.1e-05;0.0058;0.0061;0.007;0.0063;0.0064;0.0058;0.0052	0.0163588390501319	TTT	ORF1ab:RNA-dependent-RNA-polymerase	.	1555-1573-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.983121597096189
CAMB-7731A	MN908947.3	15219	A	G	0.14	0.08	5.1e-63	4.5e-37	0.111218206157965	AAT	ORF1ab:RNA-dependent-RNA-polymerase	K584K	A1752G	AAA>AAG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.888781793842035
CAMB-7731A	MN908947.3	16289	C	T	1	1	0	0	1	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0
CAMB-7731A	MN908947.3	18499	T	C	0.0024	0.016	0.0032	7.3e-09	0.00864387502508865	GTA	ORF1ab:3'-to-5'-exonuclease	Y154H	T460C	TAC>CAC	Missense	ORF1ab:3'-to-5'-exonuclease	0.991329363751923
CAMB-7731A	MN908947.3	2152	TTGGC	-	0.0128	0.004662	7.3e-06;7.5e-06;8.9e-05;2.4e-05;1.9e-05	NA;NA;NA;6.1e-05;5.7e-05	0.00650113574058119	ATT	ORF1ab:nsp2	.	1347-1351-delfrshift	.	no-SNV	ORF1ab:nsp2	0.993341260404281
CAMB-7731A	MN908947.3	21575	C	T	0.035	0.038	1.7e-08	1.2e-07	0.036319612590799	TCT	S	L5F	C13T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.963680387409201
CAMB-7731A	MN908947.3	22860	TTA	-	0.0153333333333333	0.00806666666666667	0.00069;7.3e-06;6.1e-05	0.002;0.0027;0.01	0.0135073305615787	GTT	S	.	1298-1300-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.990496760259179
CAMB-7731A	MN908947.3	23403	A	G	1	1	0	0	0.999863366365114	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000107868659120655
CAMB-7731A	MN908947.3	23423	C	T	0.014	0.008	6e-08	2.3e-05	0.0107544059661174	CCC	S	P621S	C1861T	CCT>TCT	Missense	GU280_gp02, spike glycoprotein	0.989194762945589
CAMB-7731A	MN908947.3	241	C	T	1	1	0	0	0.999782061216583	TCG	NA	NA	NA	NA	NA	NA	0.000193723363037582
CAMB-7731A	MN908947.3	25169	C	T	0.63	0.71	0	0	0.66900264066626	ACT	S	L1203F	C3607T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.330743449116392
CAMB-7731A	MN908947.3	25429	G	T	1	1	0	0	0.999890582828799	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	4.86298538672891e-05
CAMB-7731A	MN908947.3	26533	C	T	0.11	0.14	3.7e-50	1.8e-61	0.122214503286485	TCC	M	S4F	C11T	TCC>TTC	Missense	GU280_gp05	0.877785496713515
CAMB-7731A	MN908947.3	29034	C	T	0.13	0.11	2.3e-25	3.6e-22	0.122600709461101	GCT	N	A254V	C761T	GCT>GTT	Missense	GU280_gp10	0.877399290538899
CAMB-7731A	MN908947.3	3037	C	T	1	1	0	0	0.999550662772411	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000112334306897326
CAMB-77329	MN908947.3	11074	C	INS	0.13	0.14	1.1e-42	2.4e-48	0.136223223780827	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.863346331088267
CAMB-77329	MN908947.3	11083	G	-	0.02	0.024	1.1e-08	2.1e-10	0.0220700515365528	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.327567283832793
CAMB-77329	MN908947.3	11083	G	T	0.6	0.69	1.2e-190	2.2e-242	0.650195648024432	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.327567283832793
CAMB-77329	MN908947.3	14408	C	T	1	1	0	0	0.999540945142945	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000357042666598659
CAMB-77329	MN908947.3	19170	C	T	1	1	0	0	0.99992388491399	TCA	ORF1ab:3'-to-5'-exonuclease	F377F	C1131T	TTC>TTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	7.61150860100472e-05
CAMB-77329	MN908947.3	23403	A	G	1	1	0	0	0.999905404553194	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.88295390048559e-05
CAMB-77329	MN908947.3	23416	A	T	0.99	0.73	0	0	0.857091109536184	CAG	S	T618T	A1854T	ACA>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.142861642649027
CAMB-77329	MN908947.3	241	C	T	1	1	0	0	0.999610812340787	TCG	NA	NA	NA	NA	NA	NA	0.000247664874044721
CAMB-77329	MN908947.3	261	G	T	0.38	0.14	5.1e-201	9.7e-63	0.286694239887017	GGT	NA	NA	NA	NA	NA	NA	0.713305760112983
CAMB-77329	MN908947.3	28881	G	A	1	1	0	0	0.99811106913487	AGG	N	R203K	G608A	AGG>AAG	Missense	GU280_gp10	0
CAMB-77329	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998987512656092	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-77329	MN908947.3	28883	G	C	1	1	0	0	1	GGG	N	G204R	G610C	GGA>CGA	Missense	GU280_gp10	0
CAMB-77329	MN908947.3	3037	C	T	1	1	0	0	0.999505317833292	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77338	MN908947.3	13499	C	T	1	0.79	0	3.8e-141	0.936594202898551	ACA	ORF1ab:RNA-dependent-RNA-polymerase	T11I	C32T	ACA>ATA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.0634057971014493
CAMB-77338	MN908947.3	13536	C	T	1	1	0	1.2e-201	0.998073217726397	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00192678227360308
CAMB-77338	MN908947.3	14408	C	T	1	1	0	0	1	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-77338	MN908947.3	23403	A	G	1	1	0	0	0.99989503516322	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.29789020678073e-05
CAMB-77338	MN908947.3	23731	C	T	1	1	0	0	0.999713467048711	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000286532951289398
CAMB-77338	MN908947.3	241	C	T	1	1	0	0	0.999368985644423	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-77338	MN908947.3	27970	C	T	0.99	1	5.8e-242	4.7e-168	0.994029850746269	ACT	ORF8	T26I	C77T	ACT>ATT	Missense	GU280_gp09	0.00597014925373134
CAMB-77338	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-77338	MN908947.3	3037	C	T	1	1	2.4e-281	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77338	MN908947.3	4002	C	T	1	1	0	0	1	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-77347	MN908947.3	11074	C	INS	0.045	0.19	6.7e-12	7.3e-93	0.119265940122761	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.880320681448077
CAMB-77347	MN908947.3	11083	G	-	0.1	0.076	5.5e-44	2.6e-32	0.0894219040344737	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.28000775202636e-05
CAMB-77347	MN908947.3	11083	G	T	0.9	0.92	0	0	0.910361495229084	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.28000775202636e-05
CAMB-77347	MN908947.3	14805	C	T	1	1	0	0	0.999927843420222	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	1.80391449445296e-05
CAMB-77347	MN908947.3	18391	G	T	0.049	0.029	3.5e-23	1.7e-14	0.0394030878005287	AGT	ORF1ab:3'-to-5'-exonuclease	V118F	G352T	GTT>TTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.960581269846236
CAMB-77347	MN908947.3	22651	T	A	0.073	0.078	4.5e-33	4.3e-35	0.0754632274916333	CTG	S	A363A	T1089A	GCT>GCA	Synonymous	GU280_gp02, spike glycoprotein	0.924006203575218
CAMB-77347	MN908947.3	24729	C	T	0.018	0.066	2.2e-09	7.8e-30	0.0421792946487702	GCA	S	A1056V	C3167T	GCA>GTA	Missense	GU280_gp02, spike glycoprotein	0.957792722625899
CAMB-77347	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-77347	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-77347	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-77347	MN908947.3	28893	CTG	AAA	1	1	0;0;0	0;0;0	0.999913919256262	CCT	N	.	620-622-mnv	.	no-SNV	GU280_gp10	0.000162482736209278
CAMB-77347	MN908947.3	28899	G	A	1	1	0	0	0.999650471862985	AGA	N	R209K	G626A	AGA>AAA	Missense	GU280_gp10	8.73820342537574e-05
CAMB-77347	MN908947.3	28904	G	T	1	1	0	0	1	GGC	N	A211S	G631T	GCT>TCT	Missense	GU280_gp10	0
CAMB-77347	MN908947.3	398	C	T	0.033	0.017	1.7e-16	1.1e-09	0.0267364518591211	ACA	ORF1ab:leader-protein	H45Y	C133T	CAT>TAT	Missense	ORF1ab:leader-protein	0.973241740268237
CAMB-77347	MN908947.3	4300	G	T	0.04	0.023	2.2e-19	6e-12	0.0307897378511363	TGC	ORF1ab:nsp3	V527V	G1581T	GTG>GTT	Synonymous	ORF1ab:nsp3	0.969144436947685
CAMB-77347	MN908947.3	4966	T	A	1	1	0	0	0.99988923963006	CTA	ORF1ab:nsp3	T749T	T2247A	ACT>ACA	Synonymous	ORF1ab:nsp3	0
CAMB-77347	MN908947.3	8914	T	C	0.052	0.0019	9.7e-25	0.0048	0.0267845362184985	ATT	ORF1ab:nsp4	H120H	T360C	CAT>CAC	Synonymous	ORF1ab:nsp4	0.97319897084048
CAMB-77365	MN908947.3	14408	C	T	1	1	0	0	0.999721581417548	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000238644499244292
CAMB-77365	MN908947.3	17401	GCCAGATTACGTGCTAA	-	0.00894117647058824	0.0382941176470588	NA;NA;NA;5.9e-35;5.7e-35;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	9.8e-24;5.5e-25;1.9e-23;6.1e-25;6.4e-25;1.2e-25;5.1e-16;8e-16;6e-15;8.7e-15;8.4e-15;4.2e-15;8e-15;6.4e-15;8.4e-15;9.1e-15;5.2e-15	0.0153982824992597	TGC	ORF1ab:helicase	.	1165-1181-delfrshift	.	no-SNV	ORF1ab:helicase	0.974111801242236
CAMB-77365	MN908947.3	18624	G	A	1	1	0	0	0.999840208793843	TGA	ORF1ab:3'-to-5'-exonuclease	M195I	G585A	ATG>ATA	Missense	ORF1ab:3'-to-5'-exonuclease	0.000133159338464407
CAMB-77365	MN908947.3	23403	A	G	1	1	0	0	0.999908475196778	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.86436024162548e-05
CAMB-77365	MN908947.3	241	C	T	1	1	0	3.5e-293	0.999687451164244	TCG	NA	NA	NA	NA	NA	NA	0.000312548835755587
CAMB-77365	MN908947.3	25422	TGGAACTGTAACTTTGAAGCAAGG	-	0.225	0.100583333333333	4.8e-81;1.3e-54;7.1e-48;1.3e-51;3e-59;2.6e-48;2.1e-48;9.6e-53;1.3e-46;1.1e-59;3.2e-49;1.8e-50;3.8e-50;1.8e-58;1.6e-42;5.4e-57;7.9e-57;1.2e-42;1e-56;4.8e-36;2.6e-43;3.3e-43;3.8e-52;2.2e-35	3.2e-35;9.5e-24;4.4e-21;9.3e-23;9.5e-26;5.1e-21;1.4e-21;3.9e-23;9.2e-21;2.4e-25;3.1e-21;4.5e-21;4e-21;1e-24;5.9e-19;2e-25;3.9e-26;3.3e-19;1.1e-24;5e-16;2.1e-19;6e-21;1e-22;8.3e-16	0.145445813990716	TTG	ORF3a	.	30-53-delinframe	.	no-SNV	GU280_gp03	0.858437392956124
CAMB-77365	MN908947.3	26226	A	G	1	1	0	0	1	AAG	NA	NA	NA	NA	NA	NA	0
CAMB-77365	MN908947.3	28028	G	INS	0.49	0.51	4e-164	9.9e-181	0.501953125	GGT	ORF8	.	134-135-insfrshift	.	no-SNV	GU280_gp09	0.496744791666667
CAMB-77365	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-77365	MN908947.3	3037	C	T	1	1	5.7e-226	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77374	MN908947.3	10523	G	C	1	1	0	0	0.999950455806579	TGT	ORF1ab:3C-like-proteinase	V157L	G469C	GTC>CTC	Missense	ORF1ab:3C-like-proteinase	0
CAMB-77374	MN908947.3	11075	T	-	0.023	0.035	2.7e-06	1e-08	0.0290912195168221	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960626784410066
CAMB-77374	MN908947.3	12854	C	T	0.15	0.19	1.7e-71	1.2e-91	0.175871548975825	CCC	ORF1ab:nsp9	P57S	C169T	CCT>TCT	Missense	ORF1ab:nsp9	0.824115543967887
CAMB-77374	MN908947.3	14408	C	T	1	1	0	0	0.998008099661047	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000253114407712286
CAMB-77374	MN908947.3	21663	G	T	0.0052	0.036	0.0018	9.1e-15	0.0222222222222222	CGT	S	R34L	G101T	CGT>CTT	Missense	GU280_gp02, spike glycoprotein	0.977260981912145
CAMB-77374	MN908947.3	23403	A	G	1	1	0	0	0.999891407855389	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.51791770386087e-05
CAMB-77374	MN908947.3	23950	T	C	0.035	0.019	2.7e-17	2.1e-10	0.0284562374009657	ATT	S	D796D	T2388C	GAT>GAC	Synonymous	GU280_gp02, spike glycoprotein	0.963527260794149
CAMB-77374	MN908947.3	241	C	T	1	1	0	0	0.999756736526946	TCG	NA	NA	NA	NA	NA	NA	0.000112275449101796
CAMB-77374	MN908947.3	27641	C	T	0.14	0.12	3.2e-20	2e-20	0.126099706744868	TCA	ORF7a	S83L	C248T	TCA>TTA	Missense	GU280_gp07	0.873900293255132
CAMB-77374	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99800908673235	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000170881749829118
CAMB-77374	MN908947.3	28957	C	T	1	1	0	0	0.999857617465591	ACC	N	N228N	C684T	AAC>AAT	Synonymous	GU280_gp10	9.4921689606075e-05
CAMB-77374	MN908947.3	3037	C	T	1	1	0	0	0.999580360889635	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.99398517275143e-05
CAMB-77374	MN908947.3	4669	T	G	0.014	0.014	6.7e-08	6.9e-08	0.0141305617190237	CTC	ORF1ab:nsp3	S650S	T1950G	TCT>TCG	Synonymous	ORF1ab:nsp3	0.985720807278673
CAMB-77374	MN908947.3	8682	T	C	0.019	0.0086	2.5e-10	4.6e-06	0.0153836039708106	ATC	ORF1ab:nsp4	I43T	T128C	ATC>ACC	Missense	ORF1ab:nsp4	0.984616396029189
CAMB-77383	MN908947.3	11075	T	-	0.036	0.036	5.5e-09	2.9e-09	0.0355751055935407	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959979464681586
CAMB-77383	MN908947.3	11130	C	T	0.03	0.029	1.4e-14	1.9e-14	0.0294653818966479	TCT	ORF1ab:nsp6	S53F	C158T	TCT>TTT	Missense	ORF1ab:nsp6	0.970398204298275
CAMB-77383	MN908947.3	1186	G	T	1	1	0	0	0.999555733262251	CGT	ORF1ab:nsp2	A127A	G381T	GCG>GCT	Synonymous	ORF1ab:nsp2	0.000177706695099738
CAMB-77383	MN908947.3	14408	C	T	1	1	0	0	0.998826791808874	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000426621160409556
CAMB-77383	MN908947.3	18972	G	T	1	1	0	0	0.999295955550058	AGG	ORF1ab:3'-to-5'-exonuclease	K311N	G933T	AAG>AAT	Missense	ORF1ab:3'-to-5'-exonuclease	0.000237852854709962
CAMB-77383	MN908947.3	23403	A	G	1	1	0	0	0.9993361006981	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.03544819908932e-05
CAMB-77383	MN908947.3	241	C	T	1	1	0	0	0.998660482984343	TCG	NA	NA	NA	NA	NA	NA	0.000227465153602163
CAMB-77383	MN908947.3	26137	A	C	0.022	0.018	2.1e-05	0.00029	0.0206461348514987	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.979148089718088
CAMB-77383	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999453834655628	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000128250344672801
CAMB-77383	MN908947.3	3037	C	T	1	1	0	0	0.999288421122309	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.3096691985636e-05
CAMB-77383	MN908947.3	7423	C	T	1	1	0	0	0.997980929111948	TCT	ORF1ab:nsp3	F1568F	C4704T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000169669822525366
CAMB-77392	MN908947.3	11074	C	INS	0.051	0.028	7.9e-15	1.4e-05	0.0430855481727575	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.956751305173232
CAMB-77392	MN908947.3	14408	C	T	1	1	0	0	0.999636140794362	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000287257267608871
CAMB-77392	MN908947.3	19231	G	T	0.017	0.033	3.6e-09	4.3e-16	0.0229724718803524	TGT	ORF1ab:3'-to-5'-exonuclease	V398F	G1192T	GTT>TTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.976992213020677
CAMB-77392	MN908947.3	23403	A	G	1	1	0	0	0.999890793928142	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.94947730002879e-05
CAMB-77392	MN908947.3	241	C	T	1	1	0	0	0.999823255197402	TCG	NA	NA	NA	NA	NA	NA	0.00015465170227338
CAMB-77392	MN908947.3	25350	C	T	1	1	0	0	0.999785241817713	CCA	S	P1263L	C3788T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	0.000200440970134295
CAMB-77392	MN908947.3	26239	G	A	0.016	0.0047	4e-08	0.0046	0.0117664148750726	CGA	NA	NA	NA	NA	NA	NA	0.988185163664536
CAMB-77392	MN908947.3	3037	C	T	1	1	0	0	0.999247365780231	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77392	MN908947.3	4965	C	T	0.038	0.015	2.1e-18	9.7e-09	0.0291383246640149	ACT	ORF1ab:nsp3	T749I	C2246T	ACT>ATT	Missense	ORF1ab:nsp3	0.970838138724786
CAMB-773A1	MN908947.3	10755	C	T	0.053	0.1	6.8e-24	5.6e-46	0.0764806401867211	GCT	ORF1ab:3C-like-proteinase	A234V	C701T	GCT>GTT	Missense	ORF1ab:3C-like-proteinase	0.923519359813279
CAMB-773A1	MN908947.3	11074	C	INS	0.025	0.04	3.8e-05	7.2e-10	0.0319319192175791	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.964575130191795
CAMB-773A1	MN908947.3	11075	T	-	0.038	0.051	1.2e-09	1.1e-12	0.0445004291749808	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95533235979355
CAMB-773A1	MN908947.3	11083	G	-	0.015	0.011	8.5e-07	3.9e-05	0.0134788684352409	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.9522903073182
CAMB-773A1	MN908947.3	11083	G	T	0.028	0.041	3e-06	7.4e-09	0.0341648052991208	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.9522903073182
CAMB-773A1	MN908947.3	14220	C	T	0.0092	0.011	7.1e-06	9.5e-07	0.0100577549610031	ACT	ORF1ab:RNA-dependent-RNA-polymerase	D251D	C753T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.989892881824464
CAMB-773A1	MN908947.3	14408	C	T	1	1	0	0	0.998039215686275	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000295298842428538
CAMB-773A1	MN908947.3	20268	A	G	1	1	5.2e-251	8.5e-113	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-773A1	MN908947.3	23403	A	G	1	1	0	0	0.998691695659337	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00010660257590588
CAMB-773A1	MN908947.3	241	C	T	1	1	0	0	0.999737868213244	TCG	NA	NA	NA	NA	NA	NA	0.000131065893377896
CAMB-773A1	MN908947.3	26316	G	-	0.0045	0.0079	0.00038	1.1e-05	0.00568160991166013	TGG	E	.	72-72-delfrshift	.	no-SNV	GU280_gp04	0.994171767897071
CAMB-773A1	MN908947.3	28090	GTTCTA	-	0.0391666666666667	0.0235	6.2e-17;1.2e-16;8.7e-17;2.1e-17;7.6e-17;1e-16	1e-10;1.4e-10;1.1e-10;6.3e-11;1e-10;4.5e-10	0.0319442909251686	GGT	ORF8	.	197-202-delinframe	.	no-SNV	GU280_gp09	0.968034509456918
CAMB-773A1	MN908947.3	28201	C	T	0.036	0.043	2.9e-17	5.3e-20	0.0393489104751903	TCG	ORF8	S103L	C308T	TCG>TTG	Missense	GU280_gp09	0.960640588080861
CAMB-773A1	MN908947.3	29734	G	C	1	1	0	0	0.997560678131479	CGA	NA	NA	NA	NA	NA	NA	0
CAMB-773A1	MN908947.3	3037	C	T	1	1	0	0	0.999372529334254	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-773A1	MN908947.3	3076	A	C	0.0041	0.037	0.00035	6.2e-17	0.0209760273972603	AAG	ORF1ab:nsp3	E119D	A357C	GAA>GAC	Missense	ORF1ab:nsp3	0.978916952054795
CAMB-773A1	MN908947.3	3233	CAA	-	0.0069	0.00363333333333333	4.1e-05;5.4e-05;8.1e-05	0.0015;0.002;0.0016	0.00521022399692511	TCA	ORF1ab:nsp3	.	514-516-delinframe	.	no-SNV	ORF1ab:nsp3	0.994717672367889
CAMB-773A1	MN908947.3	6651	C	T	0.0096	0.0057	1.6e-05	0.00054	0.0076095947063689	GCT	ORF1ab:nsp3	A1311V	C3932T	GCT>GTT	Missense	ORF1ab:nsp3	0.992059553349876
CAMB-773A1	MN908947.3	8025	C	T	1	1	0	0	0.999824515223304	GCA	ORF1ab:nsp3	A1769V	C5306T	GCA>GTA	Missense	ORF1ab:nsp3	0.000146237313913018
CAMB-773B0	MN908947.3	11075	T	-	0.035	0.037	1.4e-08	2.3e-09	0.0355723297961565	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953807023301608
CAMB-773B0	MN908947.3	11979	C	T	0.016	0.011	1.1e-08	9.2e-07	0.0138670197537933	ACT	ORF1ab:nsp7	T46I	C137T	ACT>ATT	Missense	ORF1ab:nsp7	0.986132980246207
CAMB-773B0	MN908947.3	14408	C	T	1	1	0	0	0.998723769070397	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000272782183426534
CAMB-773B0	MN908947.3	17440	C	T	0.032	0.046	1.9e-15	1.5e-21	0.0375968191048261	CCC	ORF1ab:helicase	P402S	C1204T	CCT>TCT	Missense	ORF1ab:helicase	0.962354543354288
CAMB-773B0	MN908947.3	1989	A	G	0.014	0.013	2.2e-08	8.2e-08	0.013916287077221	CAG	ORF1ab:nsp2	Q395R	A1184G	CAG>CGG	Missense	ORF1ab:nsp2	0.986011979484237
CAMB-773B0	MN908947.3	20268	A	G	1	1	0	0	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-773B0	MN908947.3	22331	G	A	0.0069	0.028	0.00032	5.6e-10	0.0170109356014581	AGG	S	G257S	G769A	GGT>AGT	Missense	GU280_gp02, spike glycoprotein	0.982989064398542
CAMB-773B0	MN908947.3	23403	A	G	1	1	0	0	0.998149574719855	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000135009569795977
CAMB-773B0	MN908947.3	23934	C	T	0.0081	0.016	2.6e-05	1.1e-08	0.0107537393684622	ACA	S	T791I	C2372T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0.989168051617949
CAMB-773B0	MN908947.3	241	C	T	0.99	1	0	0	0.996788492853266	TCG	NA	NA	NA	NA	NA	NA	0.000120619986731801
CAMB-773B0	MN908947.3	26447	C	T	0.0089	0.011	1e-05	1.9e-06	0.00961639516552811	TCT	E	S68F	C203T	TCT>TTT	Missense	GU280_gp04	0.989464004203889
CAMB-773B0	MN908947.3	27213	C	T	0.019	0.014	1.6e-09	2.2e-07	0.0169349417247657	TCG	ORF6	L4L	C12T	CTC>CTT	Synonymous	GU280_gp06	0.982241727031702
CAMB-773B0	MN908947.3	27415	G	T	0.008	0.0036	1.6e-05	0.00074	0.00627432292907632	GGC	ORF7a	A8S	G22T	GCA>TCA	Missense	GU280_gp07	0.993646255261695
CAMB-773B0	MN908947.3	28703	G	C	0.0076	0.0083	2.5e-05	7.9e-06	0.00786314911098273	AGA	N	D144H	G430C	GAT>CAT	Missense	GU280_gp10	0.991864047756595
CAMB-773B0	MN908947.3	29734	G	C	1	1	0	0	0.998886414253898	CGA	NA	NA	NA	NA	NA	NA	0
CAMB-773B0	MN908947.3	3037	C	T	1	1	0	0	0.999349925705795	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000232169390787519
CAMB-773B0	MN908947.3	3530	G	A	0.0069	0.009	4.1e-05	7e-06	0.00784313725490196	TGA	ORF1ab:nsp3	D271N	G811A	GAT>AAT	Missense	ORF1ab:nsp3	0.992156862745098
CAMB-773B0	MN908947.3	6616	A	G	0.0072	0.018	0.00011	3.6e-09	0.0125838231641692	TAG	ORF1ab:nsp3	L1299L	A3897G	TTA>TTG	Synonymous	ORF1ab:nsp3	0.987416176835831
CAMB-773B0	MN908947.3	6701	C	T	0.022	0.0028	8e-11	0.0054	0.0126108888502348	TCT	ORF1ab:nsp3	L1328F	C3982T	CTT>TTT	Missense	ORF1ab:nsp3	0.987389111149765
CAMB-773B0	MN908947.3	9969	C	T	0.033	0.025	1.2e-15	1.2e-12	0.0294834437086093	GCA	ORF1ab:nsp4	A472V	C1415T	GCA>GTA	Missense	ORF1ab:nsp4	0.970145695364238
CAMB-773CF	MN908947.3	11074	C	INS	0.11	0.12	5.7e-50	1.8e-49	0.115217803229678	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.875918479061836
CAMB-773CF	MN908947.3	11074	C	T	0.0075	0.0076	1.6e-05	4.7e-05	0.00756889908836348	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.875918479061836
CAMB-773CF	MN908947.3	11083	G	-	0.16	0.16	1.9e-67	5.8e-69	0.155827789337944	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.93074646112365e-05
CAMB-773CF	MN908947.3	11083	G	T	0.84	0.84	0	0	0.843957289254907	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.93074646112365e-05
CAMB-773CF	MN908947.3	1440	G	A	1	1	0	0	0.999724061810154	GGC	ORF1ab:nsp2	G212D	G635A	GGC>GAC	Missense	ORF1ab:nsp2	0.000197098707032482
CAMB-773CF	MN908947.3	14411	C	T	0.0093	0.0081	1.1e-05	3.1e-05	0.00873862072396239	ACA	ORF1ab:RNA-dependent-RNA-polymerase	T315I	C944T	ACA>ATA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.990788797320377
CAMB-773CF	MN908947.3	16129	G	A	0.023	0.025	1.9e-11	1.6e-12	0.0235816841592941	AGG	ORF1ab:RNA-dependent-RNA-polymerase	G888R	G2662A	GGA>AGA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.976253463854239
CAMB-773CF	MN908947.3	16375	C	T	0.014	0.014	3.5e-06	2.5e-06	0.0141704930437325	TCC	ORF1ab:helicase	P47S	C139T	CCG>TCG	Missense	ORF1ab:helicase	0.985760718155084
CAMB-773CF	MN908947.3	16438	A	G	0.015	0.015	9.9e-08	5.1e-08	0.0151496933990622	TAT	ORF1ab:helicase	M68V	A202G	ATG>GTG	Missense	ORF1ab:helicase	0.984781600508425
CAMB-773CF	MN908947.3	16466	C	T	0.091	0.091	7.2e-23	2.8e-23	0.0909859065110643	CCA	ORF1ab:helicase	P77L	C230T	CCA>CTA	Missense	ORF1ab:helicase	0.908902493463427
CAMB-773CF	MN908947.3	16877	C	T	0.061	0.063	1.1e-27	1.6e-28	0.0618898445064647	ACA	ORF1ab:helicase	T214I	C641T	ACA>ATA	Missense	ORF1ab:helicase	0.937973457880048
CAMB-773CF	MN908947.3	17795	C	T	0.013	0.013	3.7e-07	2.5e-07	0.0131300921782297	GCT	ORF1ab:helicase	A520V	C1559T	GCT>GTT	Missense	ORF1ab:helicase	0.986851453721731
CAMB-773CF	MN908947.3	21742	C	T	1	1	0	0	0.999703549988883	CCA	S	S60S	C180T	TCC>TCT	Synonymous	GU280_gp02, spike glycoprotein	0.000271745843523802
CAMB-773CF	MN908947.3	24718	C	T	0.013	0.013	5.3e-07	2.3e-07	0.0129574163302513	TCC	S	F1052F	C3156T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.986977471024873
CAMB-773CF	MN908947.3	28087	C	T	0.038	0.041	1.3e-16	3.8e-18	0.0394691966638762	GCT	ORF8	A65V	C194T	GCT>GTT	Missense	GU280_gp09	0.960251759526246
CAMB-773CF	MN908947.3	28253	C	T	0.013	0.012	9.4e-07	2.2e-06	0.0128501386488767	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.986195394446007
CAMB-773CF	MN908947.3	2891	G	A	1	1	0	0	0.999633219806131	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	0.000353680901231334
CAMB-773CF	MN908947.3	4668	C	T	1	1	0	0	0.999406614329197	TCT	ORF1ab:nsp3	S650F	C1949T	TCT>TTT	Missense	ORF1ab:nsp3	0.000239061852985498
CAMB-773DE	MN908947.3	10288	T	A	0.038	0.037	4.3e-18	1.2e-17	0.0374105568806388	TTG	ORF1ab:3C-like-proteinase	I78I	T234A	ATT>ATA	Synonymous	ORF1ab:3C-like-proteinase	0.962291299388157
CAMB-773DE	MN908947.3	10327	T	C	0.013	0.015	2e-07	1.1e-08	0.0137590450536101	TTG	ORF1ab:3C-like-proteinase	V91V	T273C	GTT>GTC	Synonymous	ORF1ab:3C-like-proteinase	0.986227750488565
CAMB-773DE	MN908947.3	10956	C	T	0.0073	0.0088	3.6e-05	7.6e-06	0.00797303755124626	TCA	ORF1ab:3C-like-proteinase	S301L	C902T	TCA>TTA	Missense	ORF1ab:3C-like-proteinase	0.992026962448754
CAMB-773DE	MN908947.3	11074	C	INS	0.11	0.13	1.3e-52	3.1e-52	0.117877324875287	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.869636350861697
CAMB-773DE	MN908947.3	11074	C	T	0.013	0.006	1.2e-10	6e-04	0.0104387276796917	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.869636350861697
CAMB-773DE	MN908947.3	11083	G	-	0.16	0.19	2.4e-68	2.1e-87	0.17284904688305	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-773DE	MN908947.3	11083	G	T	0.84	0.81	0	0	0.826994553617428	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-773DE	MN908947.3	11096	T	G	0.017	0.025	5e-09	1.6e-12	0.0201918863442423	CTT	ORF1ab:nsp6	F42V	T124G	TTT>GTT	Missense	ORF1ab:nsp6	0.977513319034111
CAMB-773DE	MN908947.3	12921	C	T	0.025	0.024	1.8e-12	3.1e-12	0.0246752805553354	ACA	ORF1ab:nsp9	T79I	C236T	ACA>ATA	Missense	ORF1ab:nsp9	0.975268098791715
CAMB-773DE	MN908947.3	13984	G	A	0.034	0.039	1.4e-16	7.1e-19	0.0361649298023759	TGT	ORF1ab:RNA-dependent-RNA-polymerase	V173I	G517A	GTA>ATA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.963825839740809
CAMB-773DE	MN908947.3	14805	C	T	1	1	0	0	0.999899523191874	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	4.56712764208334e-05
CAMB-773DE	MN908947.3	1633	A	G	0.039	0.032	3.8e-18	1.3e-15	0.0361510592181246	AAG	ORF1ab:nsp2	K276K	A828G	AAA>AAG	Synonymous	ORF1ab:nsp2	0.963817298716914
CAMB-773DE	MN908947.3	19947	G	T	0.014	0.009	2.9e-06	9.4e-05	0.0117647058823529	AGA	ORF1ab:endoRNAse	K109N	G327T	AAG>AAT	Missense	ORF1ab:endoRNAse	0.988235294117647
CAMB-773DE	MN908947.3	21575	C	T	0.02	0.016	6.9e-06	6.8e-05	0.0174658098533531	TCT	S	L5F	C13T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.982369418355578
CAMB-773DE	MN908947.3	21796	G	T	0.06	0.056	4.6e-27	4.5e-25	0.0582827561585148	GGT	S	R78S	G234T	AGG>AGT	Missense	GU280_gp02, spike glycoprotein	0.941717243841485
CAMB-773DE	MN908947.3	22320	A	G	0.013	0.0069	8.5e-08	2.9e-05	0.0107275910049823	GAT	S	D253G	A758G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.989182638358993
CAMB-773DE	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-773DE	MN908947.3	2558	C	T	1	1	0	0	0.999953475388481	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-773DE	MN908947.3	26144	G	T	1	1	0	0	0.999092109607131	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000825354902608122
CAMB-773DE	MN908947.3	27371	C	T	0.0097	0.0078	3.7e-06	2e-05	0.00887641823908988	CCA	ORF6	P57L	C170T	CCA>CTA	Missense	GU280_gp06	0.991062417810942
CAMB-773DE	MN908947.3	27384	T	C	1	1	0	0	0.999361546161789	ATT	ORF6	D61D	T183C	GAT>GAC	Synonymous	GU280_gp06	1.57642923015079e-05
CAMB-773DE	MN908947.3	28904	G	A	0.017	0.019	8.7e-09	1.3e-09	0.0177807486631016	GGC	N	A211T	G631A	GCT>ACT	Missense	GU280_gp10	0.982118983957219
CAMB-773DE	MN908947.3	6352	GTCAGAGGACGCGCAGGGAATGGATAATCTTGCCTGCGAAGATCTA	-	0.0124782608695652	0.0224130434782609	5.5e-08;1.3e-05;3.7e-07;7.2e-07;2e-05;1.2e-05;4e-05;0.00025;0.00026;8.9e-05;5.6e-05;0.00047;0.00028;0.00019;0.00016;4.5e-05;0.00017;2.5e-07;2e-07;6e-09;2.3e-07;2.6e-07;2.9e-06;1.2e-06;3.5e-06;2.1e-06;6.2e-07;3e-07;2.4e-07;4.1e-08;2.1e-07;2.1e-07;2e-07;2.3e-06;1.4e-07;1.2e-06;5.9e-06;2.8e-07;3e-07;3.5e-07;2e-07;3.2e-07;2.3e-07;6.2e-08;4e-07;6.2e-07	1.4e-12;1.2e-08;2.5e-11;6.3e-11;4e-08;1.2e-08;1.8e-07;4.5e-06;4.3e-06;7e-07;3.2e-07;1.5e-05;5.5e-06;2.6e-06;1.8e-06;1.9e-07;2.2e-06;1.3e-11;1e-11;9.2e-15;1.3e-11;1.6e-11;4.8e-10;8.1e-11;6.6e-10;2.4e-10;7.9e-11;1.6e-11;1.6e-11;8.1e-13;1e-11;1.1e-11;1.2e-11;9.1e-10;3.8e-12;2.3e-10;4.3e-09;1.8e-11;1.2e-11;1.6e-11;9e-12;1.5e-11;6.2e-12;1e-12;2.1e-11;3.2e-11	0.0164166331930352	AGT	ORF1ab:nsp3	.	3633-3678-delfrshift	.	no-SNV	ORF1ab:nsp3	0.981366704051315
CAMB-773DE	MN908947.3	6402	C	T	0.0047	0.011	0.00049	5.5e-07	0.00736917173226475	CCA	ORF1ab:nsp3	P1228L	C3683T	CCA>CTA	Missense	ORF1ab:nsp3	0.992596868950997
CAMB-773DE	MN908947.3	7666	T	C	0.0069	0.012	4.9e-05	4.3e-07	0.00892170435317644	ATG	ORF1ab:nsp3	D1649D	T4947C	GAT>GAC	Synonymous	ORF1ab:nsp3	0.991044112871524
CAMB-773DE	MN908947.3	9235	A	T	0.01	0.021	2.2e-06	6.9e-11	0.015043629358214	AAA	ORF1ab:nsp4	E227D	A681T	GAA>GAT	Missense	ORF1ab:nsp4	0.984833604049409
CAMB-773DE	MN908947.3	9429	T	C	0.033	0.028	1.5e-15	1.4e-13	0.0308154529260057	ATC	ORF1ab:nsp4	I292T	T875C	ATC>ACC	Missense	ORF1ab:nsp4	0.969157959107708
CAMB-773DE	MN908947.3	9479	G	T	0.0072	0.012	6.6e-05	5.2e-07	0.009186762710095	TGG	ORF1ab:nsp4	G309C	G925T	GGT>TGT	Missense	ORF1ab:nsp4	0.990500052197515
CAMB-773DE	MN908947.3	9600	T	G	0.016	0.015	3.3e-09	5.3e-09	0.0159255283579988	TTG	ORF1ab:nsp4	L349W	T1046G	TTG>TGG	Missense	ORF1ab:nsp4	0.983740123532828
CAMB-773ED	MN908947.3	11075	T	-	0.046	0.046	2.5e-11	9e-12	0.0462217957235304	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.950616372628626
CAMB-773ED	MN908947.3	1243	T	C	0.0026	0.0072	0.0055	3.7e-05	0.00383586083853702	GTG	ORF1ab:nsp2	C146C	T438C	TGT>TGC	Synonymous	ORF1ab:nsp2	0.996097234611954
CAMB-773ED	MN908947.3	14408	C	T	1	1	0	0	0.998501751549448	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000549717057396928
CAMB-773ED	MN908947.3	15931	T	C	0.019	0.023	4e-10	2.4e-12	0.0202213147147938	TTA	ORF1ab:RNA-dependent-RNA-polymerase	Y822H	T2464C	TAC>CAC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.979778685285206
CAMB-773ED	MN908947.3	16289	C	T	1	1	0	0	0.999801888661428	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	6.60371128574259e-05
CAMB-773ED	MN908947.3	17413	G	A	0.0067	0.005	4e-05	0.00017	0.00603205242171031	TGC	ORF1ab:helicase	A393T	G1177A	GCT>ACT	Missense	ORF1ab:helicase	0.993567927259797
CAMB-773ED	MN908947.3	23403	A	G	1	1	0	0	0.999519896386941	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.81564021258541e-05
CAMB-773ED	MN908947.3	241	C	T	1	1	0	0	0.996894658813159	TCG	NA	NA	NA	NA	NA	NA	8.01378370797772e-05
CAMB-773ED	MN908947.3	25429	G	T	1	1	0	0	0.999172658623906	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	6.01702818977707e-05
CAMB-773ED	MN908947.3	26408	C	T	0.032	0.025	2.9e-15	1.7e-12	0.0303123794832241	TCT	E	S55F	C164T	TCT>TTT	Missense	GU280_gp04	0.969379097570382
CAMB-773ED	MN908947.3	3037	C	T	1	1	0	0	0.998963372494817	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000153574445212317
CAMB-773ED	MN908947.3	5575	C	T	0.0076	0.0073	3.9e-05	7.8e-05	0.00752935171005615	ACA	ORF1ab:nsp3	Y952Y	C2856T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.992470648289944
CAMB-77426	MN908947.3	12213	C	T	0.99	0.98	0	1.6e-150	0.992210310473176	TCT	ORF1ab:nsp8	S41F	C122T	TCT>TTT	Missense	ORF1ab:nsp8	0.00673100497024539
CAMB-77426	MN908947.3	2480	A	G	1	1	0	4.4e-09	0.999496981891348	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	7.18597298074159e-05
CAMB-77426	MN908947.3	2558	C	T	1	1	0	1.8e-31	0.998614365766684	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.0011207335710647
CAMB-77444	MN908947.3	14408	C	T	1	1	0	0	0.999493619607049	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000303828235770711
CAMB-77444	MN908947.3	21123	G	T	1	1	0	0	1	GGT	ORF1ab:2'-O-ribose-methyltransferase	G155G	G465T	GGG>GGT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0
CAMB-77444	MN908947.3	23403	A	G	1	1	0	0	0.997094722670021	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.08604226824213e-05
CAMB-77444	MN908947.3	241	C	T	1	1	0	0	0.999845774213448	TCG	NA	NA	NA	NA	NA	NA	0.000154225786551511
CAMB-77444	MN908947.3	28881	GGG	AAC	1	0.97	0;0;0	0;0;0	0.98266253869969	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000340831629175187
CAMB-77444	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77444	MN908947.3	8313	T	INS	0.0015	0.01	0.004	4e-06	0.0033563672260612	ATG	ORF1ab:nsp3	.	5593-5594-insfrshift	.	no-SNV	ORF1ab:nsp3	0.996248766041461
CAMB-77444	MN908947.3	8315	ACACC	-	0.0015	0.01	0.0064;0.0065;0.0071;0.014;0.0056	5.7e-06;6e-06;5.5e-06;1.4e-05;5.2e-06	0.00334382376081825	GAC	ORF1ab:nsp3	.	5596-5600-delfrshift	.	no-SNV	ORF1ab:nsp3	0.996061441512406
CAMB-77453	MN908947.3	10528	T	-	0.026	0.025	7.4e-09	1.3e-08	0.0258359841725502	CTT	ORF1ab:3C-like-proteinase	.	474-474-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.974125223058422
CAMB-77453	MN908947.3	10528	TT	-	0.013	0.028	7.4e-09;NA	1.3e-08;3.1e-08	0.0192766046414384	CTT	ORF1ab:3C-like-proteinase	.	474-475-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.974125223058422
CAMB-77453	MN908947.3	11075	T	-	0.021	0.037	1.2e-05	1.4e-09	0.0272519878201273	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.967106707520785
CAMB-77453	MN908947.3	14408	C	T	1	1	0	0	0.999243530610744	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000388741213923239
CAMB-77453	MN908947.3	23403	A	G	1	1	0	0	0.999870743023525	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.80299876185423e-05
CAMB-77453	MN908947.3	241	C	T	1	1	0	0	0.999805295950156	TCG	NA	NA	NA	NA	NA	NA	9.73520249221184e-05
CAMB-77453	MN908947.3	26705	T	-	0.0081	0.0073	2.7e-05	5.5e-05	0.00775405514522526	CTT	M	.	183-183-delfrshift	.	no-SNV	GU280_gp05	0.991806587978246
CAMB-77453	MN908947.3	26917	C	T	0.0095	0.0042	2.7e-06	0.00061	0.00711970363510072	CCG	M	P132L	C395T	CCG>CTG	Missense	GU280_gp05	0.992880296364899
CAMB-77453	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999746428873299	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-77453	MN908947.3	3037	C	T	1	1	0	0	0.999356381022435	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000183891136447223
CAMB-77462	MN908947.3	10802	C	T	0.0072	0.007	2.6e-05	3.4e-05	0.00711014316369343	ACT	ORF1ab:3C-like-proteinase	L250L	C748T	CTA>TTA	Synonymous	ORF1ab:3C-like-proteinase	0.992889856836307
CAMB-77462	MN908947.3	11071	G	C	0.03	0.021	1.8e-14	7.7e-11	0.025234438762763	TGT	ORF1ab:nsp6	L33F	G99C	TTG>TTC	Missense	ORF1ab:nsp6	0.972641870846311
CAMB-77462	MN908947.3	11074	C	INS	0.14	0.12	1.6e-69	6.2e-55	0.129055290285153	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.861894774420992
CAMB-77462	MN908947.3	11083	G	-	0.15	0.15	2.8e-64	1.4e-65	0.150028793910714	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	8.34606107647496e-06
CAMB-77462	MN908947.3	11083	G	T	0.85	0.85	0	0	0.84979593880668	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	8.34606107647496e-06
CAMB-77462	MN908947.3	11546	A	G	1	1	0	0	0.998372271160475	TAT	ORF1ab:nsp6	M192V	A574G	ATG>GTG	Missense	ORF1ab:nsp6	0
CAMB-77462	MN908947.3	11595	A	G	0.0099	0.015	6e-06	6.7e-08	0.0119359797450041	CAG	ORF1ab:nsp6	Q208R	A623G	CAG>CGG	Missense	ORF1ab:nsp6	0.987973596166019
CAMB-77462	MN908947.3	13665	C	T	0.015	0.016	1.8e-08	3.9e-09	0.0156077925037026	ACA	ORF1ab:RNA-dependent-RNA-polymerase	H66H	C198T	CAC>CAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.983373207255788
CAMB-77462	MN908947.3	13713	G	A	0.15	0.11	3.2e-71	7.1e-51	0.13097882422627	AGG	ORF1ab:RNA-dependent-RNA-polymerase	K82K	G246A	AAG>AAA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.868956389752703
CAMB-77462	MN908947.3	1439	G	-	0.013	0.0041	2.1e-06	0.0035	0.00920245398773006	TGG	ORF1ab:nsp2	.	634-634-delfrshift	.	no-SNV	ORF1ab:nsp2	0.99079754601227
CAMB-77462	MN908947.3	14805	C	T	1	1	0	0	0.999934300061007	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	2.81571167112488e-05
CAMB-77462	MN908947.3	15848	C	T	0.028	0.022	8.3e-14	3.9e-11	0.0250960087124324	ACT	ORF1ab:RNA-dependent-RNA-polymerase	T794I	C2381T	ACT>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.974091977301821
CAMB-77462	MN908947.3	16194	T	C	0.016	0.0038	2e-08	0.0041	0.0102078831681693	CTG	ORF1ab:RNA-dependent-RNA-polymerase	P909P	T2727C	CCT>CCC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.989792116831831
CAMB-77462	MN908947.3	16289	C	T	0.16	0.13	3.9e-69	1.9e-56	0.143930767478934	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0.855917406816974
CAMB-77462	MN908947.3	17475	T	C	0.0018	0.01	0.0062	1.2e-06	0.00609288044521205	CTA	ORF1ab:helicase	T413T	T1239C	ACT>ACC	Synonymous	ORF1ab:helicase	0.993895125695644
CAMB-77462	MN908947.3	2480	A	G	1	1	0	0	0.999813153961136	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000186846038863976
CAMB-77462	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-77462	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-77462	MN908947.3	26464	C	T	0.013	0.025	9.2e-08	9e-13	0.0196897053278026	TCT	E	L74L	C220T	CTG>TTG	Synonymous	GU280_gp04	0.980014006356731
CAMB-77462	MN908947.3	26538	G	A	0.077	0.06	3.6e-35	7.7e-28	0.0684495007907097	CGG	M	G6S	G16A	GGT>AGT	Missense	GU280_gp05	0.931526895933156
CAMB-77462	MN908947.3	4990	C	T	0.009	0.0018	5.3e-06	0.0068	0.00520190264143305	ACA	ORF1ab:nsp3	D757D	C2271T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.994787976925412
CAMB-77462	MN908947.3	6730	C	T	0.0093	0.0034	7.1e-06	0.0022	0.00633726111496188	ACA	ORF1ab:nsp3	N1337N	C4011T	AAC>AAT	Synonymous	ORF1ab:nsp3	0.993662738885038
CAMB-77462	MN908947.3	851	T	C	0.0077	0.0028	4.1e-05	0.0065	0.00526333623230966	CTA	ORF1ab:nsp2	Y16H	T46C	TAC>CAC	Missense	ORF1ab:nsp2	0.994522064221738
CAMB-77462	MN908947.3	8762	G	T	0.11	0.12	1.4e-51	7.4e-55	0.117337360215493	TGA	ORF1ab:nsp4	D70Y	G208T	GAT>TAT	Missense	ORF1ab:nsp4	0.882540200799935
CAMB-77462	MN908947.3	9188	G	A	0.019	0.0059	7e-10	0.00012	0.0123723949757727	AGT	ORF1ab:nsp4	V212M	G634A	GTG>ATG	Missense	ORF1ab:nsp4	0.987627605024227
CAMB-77462	MN908947.3	9737	A	G	0.0078	0.0047	2.1e-05	0.00047	0.00618395934718899	TAG	ORF1ab:nsp4	S395G	A1183G	AGT>GGT	Missense	ORF1ab:nsp4	0.993789153873041
CAMB-77480	MN908947.3	11074	C	INS	0.12	0.12	9.3e-59	5.3e-53	0.121661162700989	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.875431614402514
CAMB-77480	MN908947.3	11083	G	-	0.2	0.13	5.9e-87	1.4e-56	0.165744502031097	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.75094551057571e-05
CAMB-77480	MN908947.3	11083	G	T	0.8	0.87	0	0	0.831891721529626	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.75094551057571e-05
CAMB-77480	MN908947.3	1368	T	C	1	1	0	0	1	ATT	ORF1ab:nsp2	I188T	T563C	ATT>ACT	Missense	ORF1ab:nsp2	0
CAMB-77480	MN908947.3	14805	C	T	0.99	1	0	0	0.997139697886301	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00279633369582103
CAMB-77480	MN908947.3	1951	ACAGA	TACAG	0.00085	0.00782	0.00039;NA;NA;NA;0.37	7.8e-06;9.3e-06;7.4e-06;5.6e-06;3.3e-05	0.00334835801674179	TAC	ORF1ab:nsp2	.	1146-1150-mnv	.	no-SNV	ORF1ab:nsp2	0.99411739447808
CAMB-77480	MN908947.3	1971	TACTAGATG	ATACTAGAT	0.000404111111111111	0.00775555555555556	NA;NA;NA;0.0018;NA;NA;NA;NA;NA	5.8e-06;1.4e-05;1.2e-05;1.7e-05;4e-06;1.1e-05;3.1e-05;7.5e-06;1.8e-05	0.00326624293785311	ATA	ORF1ab:nsp2	.	1166-1174-mnv	.	no-SNV	ORF1ab:nsp2	0.996285979572888
CAMB-77480	MN908947.3	20594	C	T	0.18	0.21	2.8e-81	2.3e-96	0.190745869247285	ACA	ORF1ab:endoRNAse	T325I	C974T	ACA>ATA	Missense	ORF1ab:endoRNAse	0.809191897190155
CAMB-77480	MN908947.3	21952	C	T	0.0078	0.0032	2.3e-05	0.0021	0.00540197013028281	TCT	S	V130V	C390T	GTC>GTT	Synonymous	GU280_gp02, spike glycoprotein	0.994518589132507
CAMB-77480	MN908947.3	23559	TTGGTGCAGGTATATGCGCTAGT	-	0.0213478260869565	0.053695652173913	0.0052;0.0078;0.0088;0.011;0.012;0.012;0.011;0.012;0.0095;0.0092;0.0063;0.003;0.0059;0.004;0.0053;0.0042;0.0066;0.009;0.0071;0.0072;0.0013;0.0019;0.023	9.9e-06;1.9e-05;1.4e-05;1.6e-05;1.9e-05;1.8e-05;1.6e-05;1.7e-05;7.3e-06;6.7e-06;3.5e-06;8.5e-07;4.7e-06;1.4e-06;4.3e-06;1.2e-06;4.9e-06;1.4e-05;5.9e-06;5.8e-06;1.7e-08;3.9e-08;0.00053	0.0372284671269021	ATT	S	.	1997-2019-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.948872626582278
CAMB-77480	MN908947.3	23707	C	T	1	1	0	0	0.999609610675374	CCA	S	P715P	C2145T	CCC>CCT	Synonymous	GU280_gp02, spike glycoprotein	0.000212939631614437
CAMB-77480	MN908947.3	24383	A	G	1	1	0	0	0.999579334823189	CAC	S	T941A	A2821G	ACA>GCA	Missense	GU280_gp02, spike glycoprotein	0.000341790456158801
CAMB-77480	MN908947.3	26022	C	T	0.17	0.14	6.6e-69	4.8e-55	0.158346162304816	ACT	ORF3a	D210D	C630T	GAC>GAT	Synonymous	GU280_gp03	0.841653837695184
CAMB-77480	MN908947.3	26144	G	T	1	1	0	0	0.999291951852726	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-77480	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.0552439024390244	0.021780487804878	1.7e-05;2.2e-07;4.4e-07;5.6e-07;1.8e-06;3.5e-09;1.8e-08;3.7e-10;3.6e-10;5.3e-11;1.8e-10;1.2e-10;2.8e-10;1.9e-10;3.4e-10;6.3e-10;1.6e-10;4.8e-10;1.9e-10;2.2e-10;1.8e-10;5.8e-10;1.7e-10;3.2e-10;2e-10;6.5e-11;4.8e-10;1.3e-10;1.9e-11;3.2e-10;4.1e-10;4e-10;1.4e-10;4.6e-10;2.5e-11;1.5e-10;8.9e-11;1.8e-05;0.00017;7.3e-05;0.00022	0.0025;0.0034;0.015;0.016;0.044;0.021;0.032;0.0017;0.0017;0.00076;0.00055;0.00046;0.00073;0.00059;0.00068;0.00093;0.00055;0.00084;0.00062;6e-04;0.00053;0.00091;0.00058;7e-04;0.00057;0.00042;0.00066;0.00054;0.00058;0.00056;0.00077;7e-04;0.0011;0.0017;0.00026;0.0012;0.00097;0.017;0.025;0.019;0.034	0.0424404732108592	GTC	M	.	258-298-delfrshift	.	no-SNV	GU280_gp05	0.974498802429948
CAMB-77480	MN908947.3	26985	C	T	1	1	0	0	0.999756353093098	CCA	M	H155Y	C463T	CAT>TAT	Missense	GU280_gp05	0.000121823453451258
CAMB-77480	MN908947.3	28887	C	T	0.036	0.03	7.6e-17	4.8e-14	0.0333333333333333	ACT	N	T205I	C614T	ACT>ATT	Missense	GU280_gp10	0.966666666666667
CAMB-77480	MN908947.3	28975	G	T	0.17	0.16	1.2e-79	1.6e-74	0.170389821732377	TGT	N	M234I	G702T	ATG>ATT	Missense	GU280_gp10	0.829610178267623
CAMB-77480	MN908947.3	29708	C	T	0.042	0.084	1.1e-17	4.9e-32	0.0591026747195859	ACT	NA	NA	NA	NA	NA	NA	0.940681622088007
CAMB-77480	MN908947.3	475	C	T	0.022	0.026	1.8e-11	1.6e-13	0.0237419794723193	TCA	ORF1ab:leader-protein	F70F	C210T	TTC>TTT	Synonymous	ORF1ab:leader-protein	0.976172792909062
CAMB-77480	MN908947.3	5206	G	T	0.0045	0.018	0.0052	4.8e-07	0.0113798008534851	TGT	ORF1ab:nsp3	M829I	G2487T	ATG>ATT	Missense	ORF1ab:nsp3	0.988620199146515
CAMB-77480	MN908947.3	522	TT	-	0.0655	0.0143	5.8e-09;1.4e-08	0.0087;0.16	0.0457718708923616	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.948322259893877
CAMB-77480	MN908947.3	5897	AAACCAGTTACT	-	0.00815833333333333	0.00415	4.2e-05;2.1e-05;6.3e-06;1e-04;9.4e-05;4.8e-07;6.7e-07;7.7e-07;0.00019;0.00076;0.00072;0.00033	0.00075;0.00047;0.00026;0.0013;0.0012;0.0011;0.0013;0.0021;0.0027;0.0077;0.0075;0.0042	0.00532978014656895	AAA	ORF1ab:nsp3	.	3178-3189-delinframe	.	no-SNV	ORF1ab:nsp3	0.994101830167404
CAMB-77480	MN908947.3	5950	G	T	0.17	0.18	2.1e-70	8.3e-73	0.176193068408637	AGT	ORF1ab:nsp3	K1077N	G3231T	AAG>AAT	Missense	ORF1ab:nsp3	0.823806931591363
CAMB-77480	MN908947.3	6693	A	G	0.042	0.026	8.1e-19	1.6e-12	0.0347222222222222	AAG	ORF1ab:nsp3	K1325R	A3974G	AAG>AGG	Missense	ORF1ab:nsp3	0.965144230769231
CAMB-77480	MN908947.3	6987	G	INS	0.0071	0.0077	8e-05	4.6e-05	0.00740740740740741	GGT	ORF1ab:nsp3	.	4267-4268-insfrshift	.	no-SNV	ORF1ab:nsp3	0.990476190476191
CAMB-77480	MN908947.3	6990	C	T	0.99	0.99	0	0	0.992565055762082	TCT	ORF1ab:nsp3	S1424F	C4271T	TCT>TTT	Missense	ORF1ab:nsp3	0
CAMB-77480	MN908947.3	8879	A	T	0.021	0.035	5.8e-11	9.3e-17	0.0266793514228987	CAC	ORF1ab:nsp4	T109S	A325T	ACG>TCG	Missense	ORF1ab:nsp4	0.973320648577101
CAMB-77480	MN908947.3	9333	C	T	1	0.99	0	0	0.997088210105624	GCT	ORF1ab:nsp4	A260V	C779T	GCT>GTT	Missense	ORF1ab:nsp4	0.00251213245789323
CAMB-7749F	MN908947.3	11075	T	-	0.046	0.044	4.9e-11	2.1e-11	0.0452435682079392	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954712227035629
CAMB-7749F	MN908947.3	14408	C	T	1	1	0	0	0.999363597793806	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000503818413237166
CAMB-7749F	MN908947.3	17148	A	G	0.013	0.0062	2.3e-07	9.6e-05	0.0100740055504163	TAG	ORF1ab:helicase	I304M	A912G	ATA>ATG	Missense	ORF1ab:helicase	0.989916743755782
CAMB-7749F	MN908947.3	17762	C	T	0.058	0.044	1.7e-26	4.4e-21	0.0546101880591565	GCT	ORF1ab:helicase	A509V	C1526T	GCT>GTT	Missense	ORF1ab:helicase	0.94533503742925
CAMB-7749F	MN908947.3	18273	A	G	0.038	0.038	6.6e-18	3.2e-18	0.0380846515604959	AAG	ORF1ab:3'-to-5'-exonuclease	E78E	A234G	GAA>GAG	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.96182984181274
CAMB-7749F	MN908947.3	21123	G	T	1	1	0	0	0.999877024700467	GGT	ORF1ab:2'-O-ribose-methyltransferase	G155G	G465T	GGG>GGT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	7.02715997329679e-05
CAMB-7749F	MN908947.3	21687	T	-	0.016	0.013	1.1e-08	4.4e-07	0.0148591625491398	GTT	S	.	125-125-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.985068705593826
CAMB-7749F	MN908947.3	21741	CCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGA	-	0.0151794871794872	0.0288461538461538	0.0011;0.0016;0.0018;0.0018;0.0026;0.0028;0.0021;0.0024;0.0022;0.0028;0.0024;0.0017;0.0018;0.0018;0.0019;0.0019;0.0017;0.0016;0.0019;0.0016;0.0018;0.0017;0.0015;0.001;0.0023;0.0015;0.0019;0.0021;0.0019;0.0014;0.0013;0.0011;0.0016;0.0018;0.0017;0.0013;0.0017;0.0018;0.0018	3.4e-06;7.3e-06;9.8e-06;8.5e-06;2.6e-05;2.8e-05;1.3e-05;1.5e-05;1.1e-05;2.3e-05;1.7e-05;8.7e-06;9.1e-06;9.5e-06;1e-05;1.1e-05;1e-05;8.1e-06;9.8e-06;7.5e-06;9.7e-06;8.8e-06;4.2e-06;2.1e-06;1.5e-05;4.7e-06;1e-05;1.2e-05;1.1e-05;7.1e-06;3.9e-06;3.4e-06;7.2e-06;9.1e-06;8.5e-06;4.1e-06;8.3e-06;9.8e-06;9.5e-06	0.0213584136397331	TCC	S	.	179-217-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.978410571375395
CAMB-7749F	MN908947.3	23403	A	G	1	1	0	0	0.999871154182427	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.20327268376635e-05
CAMB-7749F	MN908947.3	241	C	T	1	1	0	0	0.999899517684887	TCG	NA	NA	NA	NA	NA	NA	8.37352625937835e-05
CAMB-7749F	MN908947.3	28044	G	T	0.051	0.039	1.9e-22	7.5e-17	0.0477055449330784	AGC	ORF8	A51S	G151T	GCT>TCT	Missense	GU280_gp09	0.952198852772467
CAMB-7749F	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999658392165794	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7749F	MN908947.3	29077	C	T	0.0047	0.028	0.00048	6.4e-14	0.0120679494734684	ACA	N	Y268Y	C804T	TAC>TAT	Synonymous	GU280_gp10	0.987880806579723
CAMB-7749F	MN908947.3	3037	C	T	1	1	0	0	0.999514432155382	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000161855948206097
CAMB-7749F	MN908947.3	3282	T	C	0.019	0.033	7.5e-10	3.1e-16	0.0227995427621324	GTT	ORF1ab:nsp3	V188A	T563C	GTT>GCT	Missense	ORF1ab:nsp3	0.977158890158994
CAMB-7749F	MN908947.3	8605	C	T	0.064	0.034	1.2e-28	5.4e-16	0.0552157381385353	TCC	ORF1ab:nsp4	F17F	C51T	TTC>TTT	Synonymous	ORF1ab:nsp4	0.94472915633438
CAMB-7749F	MN908947.3	9565	C	T	0.0095	0.021	6.1e-06	6.6e-11	0.0142592316004955	TCT	ORF1ab:nsp4	F337F	C1011T	TTC>TTT	Synonymous	ORF1ab:nsp4	0.985696839774734
CAMB-7749F	MN908947.3	9611	C	T	0.01	0.011	2.4e-06	1.4e-06	0.0104734090763442	TCT	ORF1ab:nsp4	L353F	C1057T	CTT>TTT	Missense	ORF1ab:nsp4	0.989499125690064
CAMB-7749F	MN908947.3	9714	C	T	0.0054	0.0076	0.00019	1.6e-05	0.0063037954651357	ACA	ORF1ab:nsp4	T387I	C1160T	ACA>ATA	Missense	ORF1ab:nsp4	0.99360828549072
CAMB-774AE	MN908947.3	11074	C	INS	0.03	0.023	4.8e-07	0.00011	0.0267194508287181	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.973088177225187
CAMB-774AE	MN908947.3	11075	T	-	0.022	0.035	7.2e-06	9.7e-09	0.0279625879857294	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964840771031109
CAMB-774AE	MN908947.3	14408	C	T	1	1	0	0	0.996878992221737	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00029916395802002
CAMB-774AE	MN908947.3	18859	G	-	0.0046	0.0079	0.00072	2.6e-05	0.00611949870110107	TGC	ORF1ab:3'-to-5'-exonuclease	.	820-820-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.993673981804546
CAMB-774AE	MN908947.3	20268	A	G	1	1	1.1e-243	1.6e-148	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-774AE	MN908947.3	21624	G	T	0.0049	0.012	0.00085	2.6e-06	0.00796685787125558	AGA	S	R21I	G62T	AGA>ATA	Missense	GU280_gp02, spike glycoprotein	0.992033142128744
CAMB-774AE	MN908947.3	23403	A	G	1	1	0	0	0.999878519148419	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.50365961065387e-05
CAMB-774AE	MN908947.3	23599	T	A	0.026	0.0032	9.9e-13	0.0028	0.0140808050465605	ATT	S	N679K	T2037A	AAT>AAA	Missense	GU280_gp02, spike glycoprotein	0.985881646139982
CAMB-774AE	MN908947.3	241	C	T	1	1	0	0	0.999885718203947	TCG	NA	NA	NA	NA	NA	NA	4.57127184210827e-05
CAMB-774AE	MN908947.3	28253	C	T	0.015	0.0054	2.6e-07	0.0021	0.00987397368032908	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.989921172093938
CAMB-774AE	MN908947.3	28321	G	A	0.05	0.052	2.9e-23	5.6e-24	0.0513734339740098	CGT	N	T16T	G48A	ACG>ACA	Synonymous	GU280_gp10	0.947046922418489
CAMB-774AE	MN908947.3	29734	G	C	1	1	0	0	0.997964335151861	CGA	NA	NA	NA	NA	NA	NA	0
CAMB-774AE	MN908947.3	3037	C	T	1	1	0	0	0.999618964672582	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.44336182026019e-05
CAMB-774AE	MN908947.3	4331	C	T	0.0072	0.0063	3.4e-05	0.00011	0.00666517069265618	TCT	ORF1ab:nsp3	L538L	C1612T	CTA>TTA	Synonymous	ORF1ab:nsp3	0.99332269978834
CAMB-774AE	MN908947.3	5371	A	T	0.0076	0.0041	2.1e-05	0.00045	0.0057063002212647	CAA	ORF1ab:nsp3	A884A	A2652T	GCA>GCT	Synonymous	ORF1ab:nsp3	0.994177244672179
CAMB-774AE	MN908947.3	5530	TGGACAACAGCAGACAAC	-	0.000344444444444444	0.00534444444444444	NA;NA;NA;NA;NA;NA;NA;NA;0.0017;0.0017;NA;NA;NA;NA;NA;NA;NA;NA	0.00024;0.00073;0.00037;1.8e-05;2.1e-05;1.7e-05;0.00031;0.00037;0.00036;0.00036;0.00042;0.00049;0.00029;0.00028;0.00028;0.00027;0.00019;0.00026	0.00252303641948223	GTG	ORF1ab:nsp3	.	2811-2828-delinframe	.	no-SNV	ORF1ab:nsp3	0.997208263539922
CAMB-774AE	MN908947.3	6449	C	T	0.02	0.013	1.7e-10	9.5e-08	0.0163719711853307	TCT	ORF1ab:nsp3	L1244F	C3730T	CTT>TTT	Missense	ORF1ab:nsp3	0.983570245386956
CAMB-774AE	MN908947.3	8025	C	T	1	1	0	0	0.999550669502441	GCA	ORF1ab:nsp3	A1769V	C5306T	GCA>GTA	Missense	ORF1ab:nsp3	0.000389419764550819
CAMB-774AE	MN908947.3	8318	C	A	0.0035	0.012	8e-04	2.3e-07	0.00727926897554118	ACC	ORF1ab:nsp3	P1867T	C5599A	CCC>ACC	Missense	ORF1ab:nsp3	0.992673076235748
CAMB-774BD	MN908947.3	11074	C	INS	0.11	0.11	1.7e-51	2.2e-39	0.106543599988474	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.888826992710124
CAMB-774BD	MN908947.3	11083	G	-	0.15	0.13	1.6e-63	7.1e-58	0.14363995031782	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.000146124059326368
CAMB-774BD	MN908947.3	11083	G	T	0.85	0.87	0	0	0.856113465332067	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.000146124059326368
CAMB-774BD	MN908947.3	12797	G	A	1	1	0	0	0.998821607988257	AGG	ORF1ab:nsp9	G38S	G112A	GGT>AGT	Missense	ORF1ab:nsp9	0.000392797337247524
CAMB-774BD	MN908947.3	14805	C	T	1	1	0	0	0.999159402810518	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000137053889589387
CAMB-774BD	MN908947.3	17750	C	T	0.01	0.013	3.7e-06	5.6e-08	0.0107460750547927	GCT	ORF1ab:helicase	A505V	C1514T	GCT>GTT	Missense	ORF1ab:helicase	0.989130920964351
CAMB-774BD	MN908947.3	20844	C	T	1	1	0	0	0.999605169857539	CCT	ORF1ab:2'-O-ribose-methyltransferase	P62P	C186T	CCC>CCT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.000128924128150583
CAMB-774BD	MN908947.3	21108	C	T	0.99	1	0	0	0.994498075334045	TCA	ORF1ab:2'-O-ribose-methyltransferase	F150F	C450T	TTC>TTT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.000261996412664503
CAMB-774BD	MN908947.3	2480	A	G	1	1	0	0	0.999689211763335	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000271939707082087
CAMB-774BD	MN908947.3	2558	C	T	1	1	0	0	0.999522186474692	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	9.55627050616379e-05
CAMB-774BD	MN908947.3	26144	G	T	1	1	0	0	0.999601037303012	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000199481348493916
CAMB-774CC	MN908947.3	11075	T	-	0.044	0.13	9.2e-11	1e-32	0.0707134911806769	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.915938344191959
CAMB-774CC	MN908947.3	11824	C	T	0.039	0.036	1.7e-10	2.8e-06	0.0386266094420601	TCA	ORF1ab:nsp6	I284I	C852T	ATC>ATT	Synonymous	ORF1ab:nsp6	0.96137339055794
CAMB-774CC	MN908947.3	14408	C	T	1	1	0	0	0.999546750493457	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000380144747423057
CAMB-774CC	MN908947.3	14922	C	T	0.021	0.0028	2.3e-10	0.0081	0.0141704817963811	TCG	ORF1ab:RNA-dependent-RNA-polymerase	I485I	C1455T	ATC>ATT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.985829518203619
CAMB-774CC	MN908947.3	15981	C	T	0.24	0.24	8.4e-115	2.1e-117	0.239434661723818	TCG	ORF1ab:RNA-dependent-RNA-polymerase	I838I	C2514T	ATC>ATT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.760542168674699
CAMB-774CC	MN908947.3	16466	C	T	0.29	0.15	5.5e-73	7.4e-37	0.219725013220518	CCA	ORF1ab:helicase	P77L	C230T	CCA>CTA	Missense	ORF1ab:helicase	0.780274986779482
CAMB-774CC	MN908947.3	16779	C	T	0.14	0.26	1.7e-65	2e-125	0.187292024239028	TCT	ORF1ab:helicase	V181V	C543T	GTC>GTT	Synonymous	ORF1ab:helicase	0.808679813653718
CAMB-774CC	MN908947.3	20480	C	T	0.29	0.14	6.4e-41	3.1e-12	0.248730964467005	TCA	ORF1ab:endoRNAse	S287L	C860T	TCA>TTA	Missense	ORF1ab:endoRNAse	0.751269035532995
CAMB-774CC	MN908947.3	21998	C	T	0.017	0.027	7.4e-10	1.3e-13	0.0210778043490351	CCA	S	H146Y	C436T	CAC>TAC	Missense	GU280_gp02, spike glycoprotein	0.978866581391469
CAMB-774CC	MN908947.3	23185	C	T	0.047	0.017	7.3e-12	2.2e-05	0.035131865473022	TCA	S	F541F	C1623T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.964868134526978
CAMB-774CC	MN908947.3	23185	CA	TC	0.0475	0.00945	7.3e-12;2.2e-09	2.2e-05;0.1	0.0325139013718654	TCA	S	.	1623-1624-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.964868134526978
CAMB-774CC	MN908947.3	23403	A	G	1	1	0	0	0.999907961343764	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.06795520785397e-05
CAMB-774CC	MN908947.3	241	C	T	1	1	0	0	0.999767858327253	TCG	NA	NA	NA	NA	NA	NA	0.00013265238442661
CAMB-774CC	MN908947.3	24213	C	T	0.075	0.026	9.8e-30	1.7e-11	0.0450243302497193	TCT	S	S884F	C2651T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.954922196673975
CAMB-774CC	MN908947.3	25429	G	T	1	1	0	0	0.999897871347077	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	2.91796151208766e-05
CAMB-774CC	MN908947.3	27434	C	T	0.22	0.29	1.1e-102	2.4e-142	0.250223983721319	ACT	ORF7a	T14I	C41T	ACT>ATT	Missense	GU280_gp07	0.749760830941643
CAMB-774CC	MN908947.3	28253	C	T	0.084	0.082	8.2e-37	1.2e-36	0.0830712429919322	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.916819362778613
CAMB-774CC	MN908947.3	3037	C	T	1	1	0	0	0.999318026824278	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-774CC	MN908947.3	635	C	T	0.023	0.012	1.5e-11	9.2e-07	0.019903206291591	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.980066545674531
CAMB-774CC	MN908947.3	6696	C	INS	0.025	0.037	6.1e-05	1.4e-06	0.0288905074047099	CCT	ORF1ab:nsp3	.	3976-3977-insfrshift	.	no-SNV	ORF1ab:nsp3	0.97110949259529
CAMB-774CC	MN908947.3	888	C	A	0.049	0.023	2.8e-23	2.6e-12	0.0399550321593778	GCT	ORF1ab:nsp2	A28D	C83A	GCT>GAT	Missense	ORF1ab:nsp2	0.959805385083209
CAMB-774DB	MN908947.3	10076	T	C	0.14	0.42	1.1e-51	2.8e-161	0.251188051595384	ATT	ORF1ab:3C-like-proteinase	F8L	T22C	TTC>CTC	Missense	ORF1ab:3C-like-proteinase	0.748811948404616
CAMB-774DB	MN908947.3	11074	C	INS	0.12	0.039	6.6e-35	4.2e-09	0.100855818376322	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.898549863306787
CAMB-774DB	MN908947.3	11083	G	-	0.31	0.042	1.8e-149	5.9e-17	0.245887207702889	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	5.50206327372765e-05
CAMB-774DB	MN908947.3	11083	G	T	0.69	0.96	2.8e-242	0	0.7539477303989	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	5.50206327372765e-05
CAMB-774DB	MN908947.3	14805	C	T	0.71	1	0	0	0.833200838332008	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.0002890800028908
CAMB-774DB	MN908947.3	210	G	T	1	1	0	0	0.999047981721249	TGT	NA	NA	NA	NA	NA	NA	0.000698146737750698
CAMB-774DB	MN908947.3	2558	C	T	1	1	1.7e-27	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-774DB	MN908947.3	9165	C	T	0.13	0.3	1.7e-57	3.2e-141	0.169181929181929	ACC	ORF1ab:nsp4	T204I	C611T	ACC>ATC	Missense	ORF1ab:nsp4	0.830769230769231
CAMB-774F9	MN908947.3	10226	C	T	0.0059	0.007	0.00013	4.8e-05	0.00650984257073942	ACT	ORF1ab:3C-like-proteinase	L58F	C172T	CTC>TTC	Missense	ORF1ab:3C-like-proteinase	0.993438286173717
CAMB-774F9	MN908947.3	11075	T	-	0.045	0.042	5.4e-11	4.5e-10	0.0431484468709931	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955941597385945
CAMB-774F9	MN908947.3	11083	G	T	0.028	0.022	3.8e-06	7.3e-05	0.0245414325785269	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.964762068316937
CAMB-774F9	MN908947.3	13730	C	T	1	1	0	0	0.99793505756027	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A88V	C263T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	2.58117804966187e-05
CAMB-774F9	MN908947.3	14408	C	T	1	1	0	0	0.998885733195935	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00041889729476127
CAMB-774F9	MN908947.3	15101	C	T	0.0094	0.0065	9e-06	0.00016	0.00783278702481801	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A545V	C1634T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.992124643480482
CAMB-774F9	MN908947.3	2022	T	G	0.0063	0.017	1.2e-05	9.8e-10	0.013018020578705	TTC	ORF1ab:nsp2	F406C	T1217G	TTC>TGC	Missense	ORF1ab:nsp2	0.98692513216986
CAMB-774F9	MN908947.3	2189	C	T	0.019	0.0076	3.9e-10	2e-05	0.0118609185441941	TCT	ORF1ab:nsp2	L462F	C1384T	CTT>TTT	Missense	ORF1ab:nsp2	0.988139081455806
CAMB-774F9	MN908947.3	23403	A	G	1	1	0	0	0.999878469526234	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.77720088312144e-05
CAMB-774F9	MN908947.3	241	C	T	1	0.99	0	0	0.996286639804061	TCG	NA	NA	NA	NA	NA	NA	0.00368175713044165
CAMB-774F9	MN908947.3	2462	C	T	0.0072	0.0016	3.9e-05	0.0087	0.00438942037141249	TCT	ORF1ab:nsp2	L553L	C1657T	CTA>TTA	Synonymous	ORF1ab:nsp2	0.995610579628587
CAMB-774F9	MN908947.3	25429	G	T	1	1	0	0	0.999723843714588	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	8.57036747831221e-05
CAMB-774F9	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0359189189189189	0.0163081081081081	0.00058;3.4e-05;5.7e-05;6.1e-05;0.00015;1.3e-06;8e-06;4.5e-06;4.5e-06;1.6e-06;2.4e-06;1.8e-06;4e-06;2.9e-06;3.9e-06;6.5e-06;2.5e-06;5.4e-06;3.1e-06;3.3e-06;2.3e-06;6.1e-06;3e-06;4e-06;3e-06;2.1e-06;5.4e-06;2.5e-06;2.8e-06;3.1e-06;4.9e-06;4e-06;2.1e-06;4.4e-06;1.3e-06;2.7e-06;1.3e-06	0.13;0.073;0.13;0.13;0.37;0.29;0.36;0.0035;0.0035;0.0022;0.0028;0.0027;0.0092;0.0085;0.0087;0.011;0.0075;0.01;0.0081;0.0083;0.008;0.011;0.0084;0.0095;0.0084;0.007;0.01;0.0084;0.0026;0.0088;0.01;0.01;0.0061;0.01;0.0061;0.0082;0.0069	0.0258923832271762	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.985147287334281
CAMB-774F9	MN908947.3	27885	TAAACGAA	-	0.0012625	0.0082625	0.0071;0.016;0.01;0.013;0.014;0.013;0.03;0.03	1.3e-05;1.7e-05;1.4e-05;3.2e-05;1.6e-05;1.4e-05;0.00023;0.00097	0.00433809123985446	CTA	NA	NA	NA	NA	NA	NA	0.99578231292517
CAMB-774F9	MN908947.3	27900	TT	-	0.011	0.0105	6.2e-06;0.00094	8.5e-06;0.00093	0.0105812641083521	ATT	ORF8	.	7-8-delfrshift	.	no-SNV	GU280_gp09	0.989560133630289
CAMB-774F9	MN908947.3	27903	CTTGT	-	0.00322	0.00852	0.00032;0.035;0.047;0.051;0.052	0.00034;3.6e-05;4.5e-05;4.6e-05;5.5e-05	0.00433142378091379	TCT	ORF8	.	10-14-delfrshift	.	no-SNV	GU280_gp09	0.989360192935168
CAMB-774F9	MN908947.3	28251	T	C	0.011	0.0025	1.7e-06	0.0065	0.00631552803846086	TTT	ORF8	F120L	T358C	TTC>CTC	Missense	GU280_gp09	0.9934804591176
CAMB-774F9	MN908947.3	28253	C	T	0.013	0.0062	1.8e-06	0.00088	0.00917262082404368	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.990616716113969
CAMB-774F9	MN908947.3	28464	T	C	0.0043	0.0083	0.00096	2.1e-05	0.00659568453783096	CTT	N	L64P	T191C	CTT>CCT	Missense	GU280_gp10	0.992964603159647
CAMB-774F9	MN908947.3	28564	TGACG	GTGAC	0.000513	0.00818	NA;NA;NA;NA;0.002	1.9e-05;3.1e-05;1.4e-05;1.9e-05;1.9e-05	0.00477046234275445	GTG	N	.	291-295-mnv	.	no-SNV	GU280_gp10	0.994735531604596
CAMB-774F9	MN908947.3	28575	TGA	ATG	0.0012	0.00813333333333333	NA;NA;0.0017	2.2e-05;2.9e-05;1.3e-05	0.00468489727928928	ATG	N	.	302-304-mnv	.	no-SNV	GU280_gp10	0.995275645256539
CAMB-774F9	MN908947.3	28887	C	T	0.012	0.019	1e-06	1.4e-09	0.015748031496063	ACT	N	T205I	C614T	ACT>ATT	Missense	GU280_gp10	0.983635741184526
CAMB-774F9	MN908947.3	29700	A	G	0.007	0.013	0.00036	7e-06	0.00953206239168111	TAG	NA	NA	NA	NA	NA	NA	0.990467937608319
CAMB-774F9	MN908947.3	2979	A	G	0.0081	0.015	8.6e-06	2.3e-08	0.0118525359809128	TAC	ORF1ab:nsp3	Y87C	A260G	TAC>TGC	Missense	ORF1ab:nsp3	0.987955052720696
CAMB-774F9	MN908947.3	3037	C	T	1	1	0	0	0.998040385106927	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00170401295049842
CAMB-774F9	MN908947.3	5249	A	C	0.0045	0.011	5.8e-05	3.7e-07	0.0077319587628866	TAA	ORF1ab:nsp3	N844H	A2530C	AAT>CAT	Missense	ORF1ab:nsp3	0.991981672394044
CAMB-774F9	MN908947.3	6196	C	T	0.017	0.037	5.5e-09	1.2e-16	0.0277388187626617	CCT	ORF1ab:nsp3	P1159P	C3477T	CCC>CCT	Synonymous	ORF1ab:nsp3	0.972261181237338
CAMB-774F9	MN908947.3	6419	G	A	1	1	0	0	0.999947585664679	AGT	ORF1ab:nsp3	V1234M	G3700A	GTG>ATG	Missense	ORF1ab:nsp3	2.62071676603551e-05
CAMB-774F9	MN908947.3	7071	G	A	0.048	0.056	6.2e-18	1.6e-20	0.0521361332367849	GGC	ORF1ab:nsp3	G1451D	G4352A	GGC>GAC	Missense	ORF1ab:nsp3	0.947863866763215
CAMB-77505	MN908947.3	14408	C	T	1	1	0	2.1e-171	0.999577323400433	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000184921012310456
CAMB-77505	MN908947.3	19717	A	G	0.051	0.044	3.5e-23	1.4e-18	0.0508147372554152	CAC	ORF1ab:endoRNAse	T33A	A97G	ACA>GCA	Missense	ORF1ab:endoRNAse	0.94866173679733
CAMB-77505	MN908947.3	22858	C	T	0.098	0.25	1.7e-43	6.6e-06	0.0984281842818428	GCG	S	C432C	C1296T	TGC>TGT	Synonymous	GU280_gp02, spike glycoprotein	0.900560072267389
CAMB-77505	MN908947.3	241	C	T	1	1	0	5.7e-11	0.999008282676168	TCG	NA	NA	NA	NA	NA	NA	0.000128555949385686
CAMB-77505	MN908947.3	28739	G	T	1	1	0	3.6e-162	0.999545727109189	TGC	N	A156S	G466T	GCA>TCA	Missense	GU280_gp10	0
CAMB-77505	MN908947.3	3037	C	T	1	1	0	2.6e-40	0.999633580327335	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.14265939255761e-05
CAMB-77505	MN908947.3	3298	A	C	0.021	0.077	2.3e-10	9.5e-06	0.0205692866346492	AAT	ORF1ab:nsp3	Q193H	A579C	CAA>CAC	Missense	ORF1ab:nsp3	0.979407285931826
CAMB-77505	MN908947.3	9474	C	T	0.035	0.29	7.2e-16	6.6e-07	0.0345580640401358	GCT	ORF1ab:nsp4	A307V	C920T	GCT>GTT	Missense	ORF1ab:nsp4	0.965323889626678
CAMB-77505	MN908947.3	9519	T	C	0.17	0.23	1.1e-80	1.2e-12	0.173708754949406	TTC	ORF1ab:nsp4	F322S	T965C	TTC>TCC	Missense	ORF1ab:nsp4	0.826273647162341
CAMB-77505	MN908947.3	9603	C	T	0.069	0.15	4.6e-31	8e-08	0.0685922185922186	ACA	ORF1ab:nsp4	T350I	C1049T	ACA>ATA	Missense	ORF1ab:nsp4	0.93013068013068
CAMB-77523	MN908947.3	11074	C	INS	0.4	0.4	4.3e-199	8.3e-93	0.395956932542298	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.601669962645572
CAMB-77523	MN908947.3	11083	G	-	0.02	0.14	5.9e-09	3.2e-32	0.0231918008784773	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.000234260614934114
CAMB-77523	MN908947.3	11083	G	T	0.98	0.86	0	6.5e-182	0.976046852122987	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.000234260614934114
CAMB-77523	MN908947.3	14805	C	T	1	1	0	1.5e-189	1	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-77523	MN908947.3	17247	T	C	0.99	1	0	3.9e-135	0.986082824168364	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.0139171758316361
CAMB-77523	MN908947.3	1772	G	A	0.41	0.27	9.4e-218	6.1e-50	0.407892892191224	TGT	ORF1ab:nsp2	V323I	G967A	GTT>ATT	Missense	ORF1ab:nsp2	0.591756624141315
CAMB-77523	MN908947.3	26144	G	T	1	1	1.4e-198	4.7e-14	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-77523	MN908947.3	28867	T	C	0.015	0.15	1.6e-06	3.3e-05	0.0154241645244216	CTC	N	T198T	T594C	ACT>ACC	Synonymous	GU280_gp10	0.983290488431877
CAMB-77523	MN908947.3	29332	G	T	0.45	0.4	3.5e-202	2.2e-27	0.447733580018501	TGA	N	L353L	G1059T	CTG>CTT	Synonymous	GU280_gp10	0.551341350601295
CAMB-77523	MN908947.3	9519	T	C	0.15	0.15	2.2e-69	4.2e-40	0.148251192368839	TTC	ORF1ab:nsp4	F322S	T965C	TTC>TCC	Missense	ORF1ab:nsp4	0.85170906200318
CAMB-77523	MN908947.3	9741	A	G	0.27	0.32	1.2e-130	4.7e-84	0.266122252912213	AAT	ORF1ab:nsp4	N396S	A1187G	AAT>AGT	Missense	ORF1ab:nsp4	0.733877747087787
CAMB-77532	MN908947.3	1059	C	T	1	1	0	0	0.999946752808789	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	5.32471912106636e-05
CAMB-77532	MN908947.3	11075	T	-	0.04	0.023	5.3e-10	1.9e-06	0.0327146045397638	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959512274780905
CAMB-77532	MN908947.3	12559	C	T	0.0078	0.0077	1.4e-05	1.4e-05	0.00774451097804391	TCC	ORF1ab:nsp8	I156I	C468T	ATC>ATT	Synonymous	ORF1ab:nsp8	0.992255489021956
CAMB-77532	MN908947.3	13006	T	C	1	1	0	0	0.999846284987633	CTG	ORF1ab:nsp9	A107A	T321C	GCT>GCC	Synonymous	ORF1ab:nsp9	0.000111792736266961
CAMB-77532	MN908947.3	1437	C	T	1	1	0	0	1	TCT	ORF1ab:nsp2	S211F	C632T	TCT>TTT	Missense	ORF1ab:nsp2	0
CAMB-77532	MN908947.3	14408	C	T	1	0.99	0	0	0.995766588826526	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00411050568779275
CAMB-77532	MN908947.3	15763	C	T	0.0096	0.007	3.5e-06	4.2e-05	0.00834771582543764	TCT	ORF1ab:RNA-dependent-RNA-polymerase	L766L	C2296T	CTA>TTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.991617061744919
CAMB-77532	MN908947.3	16111	C	T	0.0076	0.0041	2.2e-05	0.00083	0.00598503740648379	GCT	ORF1ab:RNA-dependent-RNA-polymerase	L882L	C2644T	CTA>TTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.994001482779538
CAMB-77532	MN908947.3	18981	C	T	0.15	0.27	9.6e-72	1.8e-131	0.211065242026874	ACA	ORF1ab:3'-to-5'-exonuclease	H314H	C942T	CAC>CAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.788914521612433
CAMB-77532	MN908947.3	22320	A	C	0.0061	0.0072	4.6e-05	1.3e-05	0.00652976672971269	GAT	S	D253A	A758C	GAT>GCT	Missense	GU280_gp02, spike glycoprotein	0.993380167522291
CAMB-77532	MN908947.3	23403	A	G	1	0.99	0	0	0.997016125429937	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.36025371867602e-05
CAMB-77532	MN908947.3	241	C	T	1	1	0	0	0.999759557585958	TCG	NA	NA	NA	NA	NA	NA	7.21327242125511e-05
CAMB-77532	MN908947.3	24556	A	G	0.0081	0.0087	2.3e-05	1.3e-05	0.00832099287779423	CAG	S	T998T	A2994G	ACA>ACG	Synonymous	GU280_gp02, spike glycoprotein	0.991679007122206
CAMB-77532	MN908947.3	25563	G	T	1	1	0	0	0.999811754581759	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	9.41227091204905e-05
CAMB-77532	MN908947.3	25688	C	T	1	1	0	0	0.999898590406653	GCT	ORF3a	A99V	C296T	GCT>GTT	Missense	GU280_gp03	0
CAMB-77532	MN908947.3	2855	C	T	0.0018	0.0066	0.0038	2.3e-05	0.00403506330875191	ACT	ORF1ab:nsp3	L46F	C136T	CTC>TTC	Missense	ORF1ab:nsp3	0.995964936691248
CAMB-77532	MN908947.3	3037	C	T	1	1	0	0	0.999712119758181	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77532	MN908947.3	3732	C	T	0.011	0.12	8.3e-05	2.1e-32	0.0619765494137353	GCT	ORF1ab:nsp3	A338V	C1013T	GCT>GTT	Missense	ORF1ab:nsp3	0.938023450586265
CAMB-77532	MN908947.3	6031	C	T	0.01	0.0037	9.9e-06	0.0034	0.00713775874375446	ACG	ORF1ab:nsp3	N1104N	C3312T	AAC>AAT	Synonymous	ORF1ab:nsp3	0.992862241256246
CAMB-77541	MN908947.3	14805	C	T	1	1	0	2.8e-16	0.999532787335789	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000233606332105755
CAMB-77541	MN908947.3	23868	G	T	1	1	0	6.4e-41	0.999893730074389	GGA	S	G769V	G2306T	GGA>GTA	Missense	GU280_gp02, spike glycoprotein	4.5544253833308e-05
CAMB-77541	MN908947.3	2480	A	G	1	1	0	4.4e-09	0.999569839611627	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	6.14514840533399e-05
CAMB-77541	MN908947.3	2558	C	T	1	1	0	3.6e-14	0.99977732181769	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	7.95279222535032e-05
CAMB-77541	MN908947.3	6449	C	T	0.0075	0.037	4.4e-05	2e-06	0.00755051931434368	TCT	ORF1ab:nsp3	L1244F	C3730T	CTT>TTT	Missense	ORF1ab:nsp3	0.992115182883953
CAMB-77541	MN908947.3	8733	C	T	1	1	0	1.1e-222	0.999809487521433	ACA	ORF1ab:nsp4	T60I	C179T	ACA>ATA	Missense	ORF1ab:nsp4	9.52562392836731e-05
CAMB-7756F	MN908947.3	11074	C	INS	0.5	0.46	9.30000021858458e-317	6.5e-265	0.477021987110466	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.520590484215783
CAMB-7756F	MN908947.3	11083	G	-	0.014	0.099	2.7e-06	9.9e-43	0.0556626284875184	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-7756F	MN908947.3	11083	G	T	0.99	0.9	0	0	0.943832599118943	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-7756F	MN908947.3	14805	C	T	1	1	0	0	1	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-7756F	MN908947.3	17247	T	C	0.99	1	0	0	0.996075191076224	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.00392480892377608
CAMB-7756F	MN908947.3	1772	G	A	0.53	0.32	7.5e-299	5.2e-156	0.422699828283388	TGT	ORF1ab:nsp2	V323I	G967A	GTT>ATT	Missense	ORF1ab:nsp2	0.577023209438874
CAMB-7756F	MN908947.3	26144	G	T	1	1	3.7e-263	3e-252	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7756F	MN908947.3	28867	T	C	0.04	0.022	3.3e-15	4.5e-08	0.0334624867911236	CTC	N	T198T	T594C	ACT>ACC	Synonymous	GU280_gp10	0.965833039802747
CAMB-7756F	MN908947.3	29332	G	T	0.35	0.25	2.5e-131	1.5e-106	0.279507785032647	TGA	N	L353L	G1059T	CTG>CTT	Synonymous	GU280_gp10	0.720492214967353
CAMB-7756F	MN908947.3	3176	C	T	0.011	0.024	4.2e-07	1.5e-12	0.0179788147724019	ACC	ORF1ab:nsp3	P153S	C457T	CCT>TCT	Missense	ORF1ab:nsp3	0.981963927855711
CAMB-7756F	MN908947.3	7623	T	A	0.042	0.0017	7.7e-19	0.002	0.0274633123689727	GTT	ORF1ab:nsp3	V1635D	T4904A	GTT>GAT	Missense	ORF1ab:nsp3	0.972536687631027
CAMB-7756F	MN908947.3	9519	T	C	0.064	0.18	3.5e-30	9.7e-87	0.12773951158422	TTC	ORF1ab:nsp4	F322S	T965C	TTC>TCC	Missense	ORF1ab:nsp4	0.872164153942488
CAMB-7756F	MN908947.3	9741	A	G	0.36	0.17	3.3e-191	2.5e-81	0.261535904255319	AAT	ORF1ab:nsp4	N396S	A1187G	AAT>AGT	Missense	ORF1ab:nsp4	0.738464095744681
CAMB-7757E	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999376234535814	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000207921821395155
CAMB-7757E	MN908947.3	24443	A	G	1	1	0	0	0.999841143764893	CAC	S	T961A	A2881G	ACG>GCG	Missense	GU280_gp02, spike glycoprotein	0.000158856235107228
CAMB-7757E	MN908947.3	25596	A	G	1	1	0	0	1	GAT	ORF3a	R68R	A204G	AGA>AGG	Synonymous	GU280_gp03	0
CAMB-7757E	MN908947.3	25671	C	T	0.12	0.0091	6.4e-33	0.00042	0.0851612903225806	ACC	ORF3a	H93H	C279T	CAC>CAT	Synonymous	GU280_gp03	0.914838709677419
CAMB-7757E	MN908947.3	29771	A	G	1	1	0	0	1	AAT	NA	NA	NA	NA	NA	NA	0
CAMB-7758D	MN908947.3	14408	C	T	1	1	0	5.2e-89	0.998204987224684	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000468967301659174
CAMB-7758D	MN908947.3	241	C	T	1	1	0	2.9e-08	0.998527590155888	TCG	NA	NA	NA	NA	NA	NA	0.000280459017926006
CAMB-7758D	MN908947.3	25275	C	T	0.05	0.042	5.3e-23	2.2e-14	0.0501705164715396	ACC	S	T1238I	C3713T	ACC>ATC	Missense	GU280_gp02, spike glycoprotein	0.949618535316247
CAMB-7758D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	1.3e-13;3.3e-14;8.3e-15	0.998838848801526	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000233470302577512
CAMB-7758D	MN908947.3	3037	C	T	1	1	0	1e-07	0.999589995899959	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000111819300011182
CAMB-775AB	MN908947.3	1059	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0
CAMB-775AB	MN908947.3	14408	C	T	1	1	0	0	0.999834874504623	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000165125495376486
CAMB-775AB	MN908947.3	23403	A	G	1	1	0	0	0.999967283910227	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-775AB	MN908947.3	241	C	T	1	1	0	0	0.999794196336695	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-775AB	MN908947.3	25459	G	T	1	1	0	0	0.999789340636191	TGC	ORF3a	A23S	G67T	GCT>TCT	Missense	GU280_gp03	0
CAMB-775AB	MN908947.3	25563	G	T	1	1	0	0	0.999890752171301	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	5.46239143497023e-05
CAMB-775AB	MN908947.3	28254	A	-	0.37	0.17	1e-22	2.6e-10	0.265422159605515	CAT	ORF8	.	361-361-delfrshift	.	no-SNV	GU280_gp09	0.734477206400322
CAMB-775AB	MN908947.3	3037	C	T	1	1	5e-296	1.9e-197	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-775AB	MN908947.3	3116	A	G	1	1	0	6.09999977680785e-317	0.999047619047619	TAC	ORF1ab:nsp3	T133A	A397G	ACT>GCT	Missense	ORF1ab:nsp3	0.000952380952380952
CAMB-775BA	MN908947.3	1059	C	T	1	1	0	0	0.99971306624583	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.000197266955991535
CAMB-775BA	MN908947.3	11074	C	INS	0.024	0.026	7.4e-05	3.9e-05	0.0247861244579866	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.974378881987578
CAMB-775BA	MN908947.3	11075	T	-	0.031	0.03	6.1e-08	2.4e-08	0.0306012068448696	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964719988531064
CAMB-775BA	MN908947.3	13006	T	C	1	1	0	0	0.997199185217518	CTG	ORF1ab:nsp9	A107A	T321C	GCT>GCC	Synonymous	ORF1ab:nsp9	0.000618361705223338
CAMB-775BA	MN908947.3	1437	C	T	1	1	0	0	0.999455115106934	TCT	ORF1ab:nsp2	S211F	C632T	TCT>TTT	Missense	ORF1ab:nsp2	0
CAMB-775BA	MN908947.3	14408	C	T	1	1	0	0	0.996422013393822	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000445560596241089
CAMB-775BA	MN908947.3	20941	C	T	1	1	0	0	0.999355452564378	GCT	ORF1ab:2'-O-ribose-methyltransferase	L95F	C283T	CTT>TTT	Missense	ORF1ab:2'-O-ribose-methyltransferase	3.06927350296185e-05
CAMB-775BA	MN908947.3	23403	A	G	1	1	0	0	0.999702545361832	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.37402796073599e-05
CAMB-775BA	MN908947.3	241	C	T	1	1	0	0	0.99861455017097	TCG	NA	NA	NA	NA	NA	NA	0.000176865935620799
CAMB-775BA	MN908947.3	25563	G	T	1	1	0	0	0.999688828959651	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000103723680116171
CAMB-775BA	MN908947.3	25688	C	T	1	1	0	0	0.999610112451777	GCT	ORF3a	A99V	C296T	GCT>GTT	Missense	GU280_gp03	0.000307805959123369
CAMB-775BA	MN908947.3	3037	C	T	1	1	0	0	0.998988743114139	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00010644809324853
CAMB-775BA	MN908947.3	6431	A	G	1	1	0	0	0.999717550391578	TAC	ORF1ab:nsp3	T1238A	A3712G	ACC>GCC	Missense	ORF1ab:nsp3	0.000145504343732614
CAMB-775D8	MN908947.3	11075	T	-	0.036	0.03	4.1e-09	4.5e-08	0.0333630640762141	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962086839622032
CAMB-775D8	MN908947.3	12488	C	T	0.01	0.006	2e-06	6.9e-05	0.00922936616507068	ACC	ORF1ab:nsp8	P133S	C397T	CCA>TCA	Missense	ORF1ab:nsp8	0.990661194710442
CAMB-775D8	MN908947.3	13730	C	T	1	1	0	0	0.997427063800096	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A88V	C263T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000174436352535868
CAMB-775D8	MN908947.3	14408	C	T	1	1	0	0	0.998269963708261	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000637381791693224
CAMB-775D8	MN908947.3	2185	G	T	0.013	0.012	1.6e-07	1.4e-07	0.0125080610490112	AGT	ORF1ab:nsp2	E460D	G1380T	GAG>GAT	Missense	ORF1ab:nsp2	0.987236672398968
CAMB-775D8	MN908947.3	23403	A	G	1	1	0	0	0.99917780906671	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.16643199967112e-05
CAMB-775D8	MN908947.3	241	C	T	1	1	0	0	0.998880046379256	TCG	NA	NA	NA	NA	NA	NA	0.000171287024349109
CAMB-775D8	MN908947.3	25429	G	T	1	1	0	0	0.998518009795594	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	7.22922050929859e-05
CAMB-775D8	MN908947.3	25777	C	T	0.017	0.015	3.1e-09	4.8e-08	0.0159386068476978	GCT	ORF3a	L129F	C385T	CTT>TTT	Missense	GU280_gp03	0.983555405633328
CAMB-775D8	MN908947.3	27059	C	T	0.0083	0.0064	1.4e-05	8.7e-05	0.00760656100461926	ACA	M	Y179Y	C537T	TAC>TAT	Synonymous	GU280_gp05	0.991950875446021
CAMB-775D8	MN908947.3	29171	C	T	0.0094	0.0077	7e-06	2.8e-05	0.0087489367611575	ACA	N	H300Y	C898T	CAT>TAT	Missense	GU280_gp10	0.991025396219209
CAMB-775D8	MN908947.3	3037	C	T	1	1	0	0	0.999114828154569	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.0001831390025029
CAMB-775D8	MN908947.3	3141	C	T	0.16	0.16	3.2e-73	3e-75	0.161935056328695	CCT	ORF1ab:nsp3	P141L	C422T	CCT>CTT	Missense	ORF1ab:nsp3	0.838038436050364
CAMB-775D8	MN908947.3	5031	C	T	0.0085	0.015	5.6e-05	6.4e-07	0.0114055686011406	ACA	ORF1ab:nsp3	T771I	C2312T	ACA>ATA	Missense	ORF1ab:nsp3	0.988594431398859
CAMB-775E7	MN908947.3	11074	C	INS	0.025	0.019	2.8e-05	0.0014	0.022138399142623	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.977777544287305
CAMB-775E7	MN908947.3	11075	T	-	0.014	0.023	0.00029	3.2e-06	0.0179315174523608	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.979165898787365
CAMB-775E7	MN908947.3	14408	C	T	1	1	0	0	0.99807304092494	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000367039823820885
CAMB-775E7	MN908947.3	15729	T	G	0.5	0.47	2.2e-293	9.99999999999999e-270	0.485337163028821	TTG	ORF1ab:RNA-dependent-RNA-polymerase	V754V	T2262G	GTT>GTG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.513752918863808
CAMB-775E7	MN908947.3	22441	T	A	0.029	0.031	9e-10	7.5e-10	0.0302267002518892	TTG	S	L293L	T879A	CTT>CTA	Synonymous	GU280_gp02, spike glycoprotein	0.969773299748111
CAMB-775E7	MN908947.3	23198	T	C	0.011	0.0019	1.1e-06	0.0048	0.00610562807315434	TTT	S	L546L	T1636C	TTA>CTA	Synonymous	GU280_gp02, spike glycoprotein	0.993887297039159
CAMB-775E7	MN908947.3	23403	A	G	1	1	0	0	0.999910620363431	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.87535665912669e-05
CAMB-775E7	MN908947.3	241	C	T	1	1	0	0	0.998927470170264	TCG	NA	NA	NA	NA	NA	NA	2.97924952704414e-05
CAMB-775E7	MN908947.3	28310	C	A	0.013	0.0055	2e-07	0.00015	0.00913535090650113	ACC	N	P13T	C37A	CCC>ACC	Missense	GU280_gp10	0.990600875727575
CAMB-775E7	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999730470329275	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-775E7	MN908947.3	29110	A	T	0.012	0.0068	4.7e-07	3.8e-05	0.00954324470319909	CAG	N	P279P	A837T	CCA>CCT	Synonymous	GU280_gp10	0.99032170938119
CAMB-775E7	MN908947.3	3037	C	T	1	1	0	0	0.999633094844983	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-775E7	MN908947.3	6451	T	C	0.0027	0.0088	0.0041	8.2e-06	0.00583611556560372	TTG	ORF1ab:nsp3	L1244L	T3732C	CTT>CTC	Synonymous	ORF1ab:nsp3	0.994155121498112
CAMB-775F6	MN908947.3	11075	T	-	0.035	0.043	5.9e-09	1.9e-10	0.03984375	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95726943597561
CAMB-775F6	MN908947.3	14408	C	T	0.99	1	0	0	0.996175253053778	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000555653309378502
CAMB-775F6	MN908947.3	18636	G	A	0.016	0.016	4.7e-09	5.7e-09	0.0163413109812139	TGA	ORF1ab:3'-to-5'-exonuclease	V199V	G597A	GTG>GTA	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.983634180115927
CAMB-775F6	MN908947.3	18698	C	T	0.019	0.021	3.2e-10	8.1e-11	0.0205643686413699	GCT	ORF1ab:3'-to-5'-exonuclease	A220V	C659T	GCT>GTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.979394990313884
CAMB-775F6	MN908947.3	19032	C	T	0.025	0.038	1e-12	4.3e-18	0.0333698512837948	ACA	ORF1ab:3'-to-5'-exonuclease	D331D	C993T	GAC>GAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.966604963922783
CAMB-775F6	MN908947.3	21752	T	G	0.035	0.033	4.9e-16	3.2e-15	0.0336002512168315	TTG	S	W64G	T190G	TGG>GGG	Missense	GU280_gp02, spike glycoprotein	0.961637096352122
CAMB-775F6	MN908947.3	23403	A	G	1	1	0	0	0.997370177022412	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.06519605919064e-05
CAMB-775F6	MN908947.3	23555	CCCATTGGTGCAGGTATATGCGCTAG	-	0.0618076923076923	0.0332692307692308	4e-04;0.00028;0.00042;0.00026;1.4e-06;2e-06;7e-08;4.2e-07;3.9e-07;4.7e-07;3.5e-07;1.1e-07;1.3e-07;1.2e-07;4e-09;1.6e-07;1.2e-06;2.6e-07;6.2e-06;3.3e-07;1.1e-06;6.5e-06;1.7e-06;5.6e-06;3.6e-09;3.1e-07	0.0024;0.0018;0.0024;0.0022;0.00063;0.00073;0.00015;0.00019;0.00021;0.00021;0.00014;9.4e-05;9e-05;8.2e-05;2.8e-05;0.00031;0.0034;0.0022;0.0069;0.003;0.004;0.0043;0.0027;0.0022;0.00033;0.0017	0.0416560347027303	ACC	S	.	1993-2018-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.962960625946492
CAMB-775F6	MN908947.3	23575	C	T	0.94	0.97	0	0	0.958787720954458	GCG	S	C671C	C2013T	TGC>TGT	Synonymous	GU280_gp02, spike glycoprotein	0.00130212572023829
CAMB-775F6	MN908947.3	23587	G	C	1	0.99	0	0	0.996417910447761	AGA	S	Q675H	G2025C	CAG>CAC	Missense	GU280_gp02, spike glycoprotein	0
CAMB-775F6	MN908947.3	241	C	T	0.99	1	0	0	0.995972627519241	TCG	NA	NA	NA	NA	NA	NA	0.00131401559753579
CAMB-775F6	MN908947.3	25488	T	A	0.015	0.0092	1.7e-08	8.6e-06	0.0114087739429782	CTG	ORF3a	T32T	T96A	ACT>ACA	Synonymous	GU280_gp03	0.987940241857181
CAMB-775F6	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0426842105263158	0.0294210526315789	7e-06;1.3e-07;2.3e-06;1.3e-06;5.8e-06;1.4e-08;3.9e-07;3e-07;3.2e-07;9.3e-08;5.8e-08;2.7e-08;2.1e-07;7.7e-08;1.2e-07;3.3e-07;6.7e-08;2.7e-07;1.4e-07;1.3e-07;1.3e-07;3.1e-07;1.2e-07;2e-07;1.2e-07;5.7e-08;2.5e-07;1e-07;1.2e-08;1.4e-07;2.4e-07;2.4e-07;1e-07;3.5e-07;6e-08;1.5e-07;8.8e-08;0.00021	0.00044;7.6e-05;0.00028;0.00029;0.00052;6e-06;2.3e-05;8.7e-05;8.8e-05;5.1e-05;5.7e-05;5.4e-05;8.7e-05;7.2e-05;7.8e-05;0.00011;5.9e-05;9.9e-05;7.1e-05;6.7e-05;6e-05;0.00011;6.9e-05;8.6e-05;6.9e-05;5e-05;9.7e-05;6.8e-05;2.5e-05;7.1e-05;9.6e-05;9.5e-05;3.5e-05;9.5e-05;4e-05;8.5e-05;5.9e-05;0.0017	0.0349455208795543	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.973136273435417
CAMB-775F6	MN908947.3	28603	C	T	0.15	0.14	5.5e-43	2.7e-40	0.144703489281803	TCT	N	F110F	C330T	TTC>TTT	Synonymous	GU280_gp10	0.853982162415897
CAMB-775F6	MN908947.3	28890	C	T	0.012	0.018	1.2e-06	4.2e-09	0.015083657258746	TCT	N	S206F	C617T	TCT>TTT	Missense	GU280_gp10	0.98419807334798
CAMB-775F6	MN908947.3	3037	C	T	1	1	0	0	0.999275391489876	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.05120566804879e-05
CAMB-775F6	MN908947.3	522	TT	-	0.04	0.0355	9.4e-07;0.00057	1.1e-05;8e-04	0.0370773807030039	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.951764604366209
CAMB-775F6	MN908947.3	7042	G	A	0.051	0.049	1.7e-17	1.5e-17	0.0498652291105121	TGC	ORF1ab:nsp3	M1441I	G4323A	ATG>ATA	Missense	ORF1ab:nsp3	0.949236298292902
CAMB-77602	MN908947.3	13730	C	T	1	1	0	5.7e-157	0.999932079982612	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A88V	C263T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	4.07520104325147e-05
CAMB-77602	MN908947.3	14408	C	T	1	1	0	6.5e-62	0.999442496178401	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000377663879147559
CAMB-77602	MN908947.3	23403	A	G	1	1	0	5.9e-08	0.999079825166782	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	1.43777317690361e-05
CAMB-77602	MN908947.3	25429	G	T	1	1	0	5.3e-54	0.997413380863366	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	6.52088857975047e-05
CAMB-77602	MN908947.3	3037	C	T	1	1	0	1e-07	0.99952397953112	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77602	MN908947.3	516	TTA	-	0.993333333333333	1	5.7e-51;1e-85;2.7e-65	2.1e-05;2.4e-05;2.2e-05	0.998997284956189	GTT	ORF1ab:leader-protein	.	251-253-delinframe	.	no-SNV	ORF1ab:leader-protein	0.021280861103829
CAMB-77602	MN908947.3	6419	G	A	1	1	0	4.3e-178	0.999941233508653	AGT	ORF1ab:nsp3	V1234M	G3700A	GTG>ATG	Missense	ORF1ab:nsp3	4.40748685099756e-05
CAMB-77620	MN908947.3	11001	C	T	0.0093	0.014	2e-05	1.6e-07	0.0119266859598351	ACA	ORF1ab:nsp6	T10I	C29T	ACA>ATA	Missense	ORF1ab:nsp6	0.988029465930018
CAMB-77620	MN908947.3	11071	G	INS	0.0059	0.015	0.0028	1.9e-05	0.0107264708329866	TGT	ORF1ab:nsp6	.	98-99-insfrshift	.	no-SNV	ORF1ab:nsp6	0.989223599900141
CAMB-77620	MN908947.3	11074	C	INS	0.25	0.24	5.2e-153	2.1e-155	0.244884488448845	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.742419427127898
CAMB-77620	MN908947.3	11074	C	T	0.0054	0.017	0.00056	1.1e-14	0.0118241453775007	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.742419427127898
CAMB-77620	MN908947.3	11083	G	-	0.15	0.12	1.2e-66	2.6e-49	0.133011586315483	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.71142030771337e-05
CAMB-77620	MN908947.3	11083	G	T	0.85	0.88	0	0	0.866714586435283	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.71142030771337e-05
CAMB-77620	MN908947.3	11790	T	C	0.028	0.012	5.2e-06	0.00085	0.0207885304659498	ATT	ORF1ab:nsp6	I273T	T818C	ATT>ACT	Missense	ORF1ab:nsp6	0.97921146953405
CAMB-77620	MN908947.3	12068	C	T	0.016	0.0074	3.4e-08	0.00012	0.0109098394400988	GCT	ORF1ab:nsp7	L76L	C226T	CTG>TTG	Synonymous	ORF1ab:nsp7	0.989050574785445
CAMB-77620	MN908947.3	1264	G	T	1	1	0	0	0.999868894011734	CGG	ORF1ab:nsp2	T153T	G459T	ACG>ACT	Synonymous	ORF1ab:nsp2	0
CAMB-77620	MN908947.3	14805	C	T	0.99	1	0	0	0.993919984233346	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	5.91249507292077e-05
CAMB-77620	MN908947.3	16799	C	T	0.0024	0.013	0.0033	9.5e-08	0.0085610879315113	ACT	ORF1ab:helicase	T188I	C563T	ACT>ATT	Missense	ORF1ab:helicase	0.991390816068873
CAMB-77620	MN908947.3	17247	T	C	1	1	0	0	0.998742576977535	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	9.50992201863945e-05
CAMB-77620	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-77620	MN908947.3	26984	C	T	1	1	0	0	0.999750499001996	ACC	M	H154H	C462T	CAC>CAT	Synonymous	GU280_gp05	0.00017821499857428
CAMB-77620	MN908947.3	27208	C	T	0.0033	0.0089	0.0043	1.6e-05	0.00655668803194284	TCA	ORF6	H3Y	C7T	CAT>TAT	Missense	GU280_gp06	0.993415291933733
CAMB-77620	MN908947.3	9474	C	T	0.0059	0.012	0.00012	4e-07	0.00840009711094926	GCT	ORF1ab:nsp4	A307V	C920T	GCT>GTT	Missense	ORF1ab:nsp4	0.991599902889051
CAMB-77620	MN908947.3	9609	A	G	0.012	0.021	2.6e-07	1.3e-10	0.0171155277218037	TAT	ORF1ab:nsp4	Y352C	A1055G	TAT>TGT	Missense	ORF1ab:nsp4	0.982867749730349
CAMB-7763F	MN908947.3	13730	C	T	0.32	0.59	1.3e-160	0	0.453147555388188	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A88V	C263T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.546852444611812
CAMB-7763F	MN908947.3	14408	C	T	0.49	0.47	2.8e-270	6.6e-262	0.480068370125732	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.519815748305232
CAMB-7763F	MN908947.3	14805	C	T	0.6	0.69	0	0	0.625425232953705	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.374500813489129
CAMB-7763F	MN908947.3	23403	A	G	0.2	0.37	2.1e-73	3.3e-148	0.27962193103274	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.720365432972365
CAMB-7763F	MN908947.3	241	C	T	0.088	0.47	2.4e-38	1.1e-253	0.269343224961815	TCG	NA	NA	NA	NA	NA	NA	0.730569495963343
CAMB-7763F	MN908947.3	25429	G	T	0.32	0.63	1.2e-159	0	0.53119717227601	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0.468572306746581
CAMB-7763F	MN908947.3	28144	T	C	0.5	0.63	8.4e-290	0	0.558930965922227	TTA	ORF8	L84S	T251C	TTA>TCA	Missense	GU280_gp09	0.441053621245049
CAMB-7763F	MN908947.3	28657	C	T	0.37	0.63	1.7e-176	0	0.495037521181312	ACG	N	D128D	C384T	GAC>GAT	Synonymous	GU280_gp10	0.504841442749939
CAMB-7763F	MN908947.3	28863	C	T	0.54	0.57	6.7e-252	3e-246	0.555116914667476	TCA	N	S197L	C590T	TCA>TTA	Missense	GU280_gp10	0.444579410871546
CAMB-7763F	MN908947.3	3037	C	T	0.25	0.47	1.7e-45	7.1e-100	0.385122045718714	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.614684230918249
CAMB-7763F	MN908947.3	4331	C	T	0.68	0.51	0	5.7e-295	0.587924752769723	TCT	ORF1ab:nsp3	L538L	C1612T	CTA>TTA	Synonymous	ORF1ab:nsp3	0.412075247230277
CAMB-7763F	MN908947.3	8782	C	T	0.63	0.6	2.1e-216	1.1e-217	0.612880396319887	GCC	ORF1ab:nsp4	S76S	C228T	AGC>AGT	Synonymous	ORF1ab:nsp4	0.387119603680113
CAMB-7763F	MN908947.3	9477	T	A	0.48	0.76	7.6e-146	3.10000000023388e-314	0.646464646464647	TTT	ORF1ab:nsp4	F308Y	T923A	TTT>TAT	Missense	ORF1ab:nsp4	0.353535353535354
CAMB-7764E	MN908947.3	2480	A	G	1	1	0	9.5e-17	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-7764E	MN908947.3	2558	C	T	1	1	0	3.6e-14	0.99860983679484	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	2.78032641032057e-05
CAMB-7764E	MN908947.3	28251	T	G	0.033	0.057	4.8e-16	2e-05	0.0330106553381155	TTT	ORF8	F120V	T358G	TTC>GTC	Missense	GU280_gp09	0.966200060357035
CAMB-7764E	MN908947.3	28253	CA	TC	0.035	0.059	1.8e-15;9.3e-17	0.00024;9.3e-06	0.0347347442346019	TCA	ORF8	.	360-361-mnv	.	no-SNV	GU280_gp09	0.964976873691235
CAMB-7765D	MN908947.3	11075	T	-	0.023	0.024	2.8e-06	1.5e-06	0.0232389092030486	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.969899555046478
CAMB-7765D	MN908947.3	13730	C	T	0.99	1	0	0	0.991411978384196	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A88V	C263T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	8.96921317577416e-05
CAMB-7765D	MN908947.3	14179	T	C	0.011	0.0042	5.2e-07	0.00059	0.00747632097697005	CTT	ORF1ab:RNA-dependent-RNA-polymerase	L238L	T712C	TTG>CTG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.992499639405741
CAMB-7765D	MN908947.3	14408	C	T	1	1	0	0	0.999393718928095	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000363768643142961
CAMB-7765D	MN908947.3	23403	A	G	1	1	0	0	0.99768860506124	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000222402262148724
CAMB-7765D	MN908947.3	241	C	T	1	1	0	0	0.999849071791518	TCG	NA	NA	NA	NA	NA	NA	8.38490047123141e-05
CAMB-7765D	MN908947.3	25429	G	T	1	1	0	0	0.999798797816956	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	5.03005457609215e-05
CAMB-7765D	MN908947.3	2922	T	C	0.0055	0.0072	0.00019	3.6e-05	0.00632281482348809	GTA	ORF1ab:nsp3	V68A	T203C	GTA>GCA	Missense	ORF1ab:nsp3	0.993618640594813
CAMB-7765D	MN908947.3	3037	C	T	1	1	0	0	0.999643722388485	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.12555223029785e-05
CAMB-7765D	MN908947.3	9832	G	A	0.14	0.08	1.4e-64	4.6e-37	0.109595793624712	TGT	ORF1ab:nsp4	M426I	G1278A	ATG>ATA	Missense	ORF1ab:nsp4	0.890322050607953
CAMB-7766C	MN908947.3	11075	T	-	0.03	0.071	5.6e-08	2.3e-17	0.0509752592866594	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.948854016987011
CAMB-7766C	MN908947.3	11270	A	G	1	1	0	0	0.999866344110453	TAT	ORF1ab:nsp6	M100V	A298G	ATG>GTG	Missense	ORF1ab:nsp6	6.68279447733864e-05
CAMB-7766C	MN908947.3	13459	G	INS	0.013	0.016	4.4e-06	6.6e-07	0.0143127194166892	CGT	ORF1ab:nsp11	.	17-18-insfrshift	.	no-SNV	ORF1ab:nsp11	0.985147177963813
CAMB-7766C	MN908947.3	14408	C	T	1	1	0	0	0.999520515103774	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000342489211589835
CAMB-7766C	MN908947.3	17795	C	T	0.013	0.0066	1.8e-07	0.00013	0.0102598889218637	GCT	ORF1ab:helicase	A520V	C1559T	GCT>GTT	Missense	ORF1ab:helicase	0.989697714842922
CAMB-7766C	MN908947.3	18683	C	T	0.06	0.011	1.3e-27	6.7e-07	0.0361354909489852	ACA	ORF1ab:3'-to-5'-exonuclease	T215I	C644T	ACA>ATA	Missense	ORF1ab:3'-to-5'-exonuclease	0.963850795392211
CAMB-7766C	MN908947.3	23403	A	G	1	1	0	0	0.999924230944082	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.41207542268309e-05
CAMB-7766C	MN908947.3	241	C	T	1	1	0	0	0.999780545344818	TCG	NA	NA	NA	NA	NA	NA	0.000164590991386405
CAMB-7766C	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999172337686224	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000620989443179466
CAMB-7766C	MN908947.3	3037	C	T	1	1	0	0	0.999320190346703	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00030213762368759
CAMB-7766C	MN908947.3	9319	C	T	0.024	0.027	1.2e-11	1.4e-11	0.0251822398939695	TCT	ORF1ab:nsp4	F255F	C765T	TTC>TTT	Synonymous	ORF1ab:nsp4	0.97481776010603
CAMB-7767B	MN908947.3	1063	C	T	0.061	0.061	7.4e-28	3.5e-28	0.0608461323241397	TCA	ORF1ab:nsp2	F86F	C258T	TTC>TTT	Synonymous	ORF1ab:nsp2	0.939065514143928
CAMB-7767B	MN908947.3	11075	T	-	0.039	0.031	8.5e-10	1.6e-08	0.0355932942698867	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95886706311703
CAMB-7767B	MN908947.3	14408	C	T	1	1	0	0	0.997843572768637	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000452849718586246
CAMB-7767B	MN908947.3	2144	G	T	0.013	0.015	2.3e-07	2.4e-08	0.0142185615612323	CGT	ORF1ab:nsp2	V447F	G1339T	GTC>TTC	Missense	ORF1ab:nsp2	0.985514198004605
CAMB-7767B	MN908947.3	23403	A	G	1	1	0	0	0.999385252531789	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.66214773352315e-05
CAMB-7767B	MN908947.3	23802	C	T	1	1	0	0	0.999611055184406	ACT	S	T747I	C2240T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.000183032854397364
CAMB-7767B	MN908947.3	241	C	T	1	1	0	0	0.998655515007595	TCG	NA	NA	NA	NA	NA	NA	0.000174608440572017
CAMB-7767B	MN908947.3	26749	T	C	0.035	0.035	5.4e-17	4.7e-17	0.0351704329919254	ATC	M	I76T	T227C	ATC>ACC	Missense	GU280_gp05	0.964721183547391
CAMB-7767B	MN908947.3	28045	C	T	1	1	0	0	0.999930743126255	GCT	ORF8	A51V	C152T	GCT>GTT	Missense	GU280_gp09	0
CAMB-7767B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999286197310091	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000341938792956061
CAMB-7767B	MN908947.3	3037	C	T	1	1	0	0	0.999057117713615	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.19058793948791e-05
CAMB-7767B	MN908947.3	3195	A	G	0.065	0.069	1e-29	2.2e-31	0.0665884836402017	GAA	ORF1ab:nsp3	E159G	A476G	GAA>GGA	Missense	ORF1ab:nsp3	0.93334115163598
CAMB-7767B	MN908947.3	9430	C	T	1	1	0	0	0.99876421156698	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	3.53082409434362e-05
CAMB-7768A	MN908947.3	14408	C	T	1	1	0	7.2e-81	0.998822184501334	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000519624484705719
CAMB-7768A	MN908947.3	27428	T	C	1	1	0	1.8e-11	0.999866639994666	CTC	ORF7a	L12P	T35C	CTC>CCC	Missense	GU280_gp07	0.00010668800426752
CAMB-776A8	MN908947.3	11195	C	T	1	1	0	0	0.999924913650698	TCT	ORF1ab:nsp6	L75F	C223T	CTT>TTT	Missense	ORF1ab:nsp6	7.50863493016969e-05
CAMB-776A8	MN908947.3	14408	C	T	1	1	0	0	0.999680015753071	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000172299209885052
CAMB-776A8	MN908947.3	23403	A	G	1	1	0	0	0.999908684138435	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.60902461614725e-05
CAMB-776A8	MN908947.3	241	C	T	1	1	0	0	1	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-776A8	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999200639488409	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-776A8	MN908947.3	29051	C	INS	0.11	0.056	3.6e-40	1.3e-17	0.0824521765326103	GCA	N	.	777-778-insfrshift	.	no-SNV	GU280_gp10	0.917367073354421
CAMB-776A8	MN908947.3	3037	C	T	1	1	0	9.6e-295	0.999487442337263	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-776A8	MN908947.3	3373	C	A	1	1	0	0	0.999880038387716	ACA	ORF1ab:nsp3	D218E	C654A	GAC>GAA	Missense	ORF1ab:nsp3	0.000119961612284069
CAMB-776A8	MN908947.3	4246	C	T	1	1	0	0	0.999831961014955	CCA	ORF1ab:nsp3	T509T	C1527T	ACC>ACT	Synonymous	ORF1ab:nsp3	0
CAMB-776B7	MN908947.3	10097	G	A	1	1	0	0	0.999667243444696	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000199653933182484
CAMB-776B7	MN908947.3	11075	T	-	0.031	0.033	6.4e-08	6.7e-09	0.0318151373074347	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964501004688547
CAMB-776B7	MN908947.3	11109	C	T	0.0098	0.0096	9.9e-06	9.6e-06	0.00973982296122905	GCT	ORF1ab:nsp6	A46V	C137T	GCT>GTT	Missense	ORF1ab:nsp6	0.989923857185137
CAMB-776B7	MN908947.3	13536	C	T	1	1	0	0	0.999481641468682	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	8.63930885529158e-05
CAMB-776B7	MN908947.3	14408	C	T	1	1	0	0	0.999027365211219	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000486317394390263
CAMB-776B7	MN908947.3	18118	C	T	0.0099	0.01	2.7e-06	2e-06	0.0100043649061545	CCT	ORF1ab:3'-to-5'-exonuclease	L27F	C79T	CTC>TTC	Missense	ORF1ab:3'-to-5'-exonuclease	0.989943256219991
CAMB-776B7	MN908947.3	18180	G	A	0.078	0.084	1.8e-35	3.7e-38	0.0811648410366017	AGG	ORF1ab:3'-to-5'-exonuclease	K47K	G141A	AAG>AAA	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.918692670763202
CAMB-776B7	MN908947.3	1968	C	T	0.0074	0.0096	3.1e-05	3.2e-06	0.00832526621490804	ACA	ORF1ab:nsp2	T388I	C1163T	ACA>ATA	Missense	ORF1ab:nsp2	0.991376870950927
CAMB-776B7	MN908947.3	20703	C	T	0.022	0.019	5.3e-11	6.8e-10	0.0203291384317522	ACA	ORF1ab:2'-O-ribose-methyltransferase	Y15Y	C45T	TAC>TAT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.979409225294995
CAMB-776B7	MN908947.3	2207	A	G	0.085	0.091	7.6e-39	8.1e-42	0.087416124943308	AAT	ORF1ab:nsp2	I468V	A1402G	ATT>GTT	Missense	ORF1ab:nsp2	0.912479212940889
CAMB-776B7	MN908947.3	22987	C	T	0.026	0.029	1.3e-12	8.8e-14	0.0281581827324085	CCG	S	A475A	C1425T	GCC>GCT	Synonymous	GU280_gp02, spike glycoprotein	0.9716939276524
CAMB-776B7	MN908947.3	23403	A	G	1	1	0	0	0.999504147598731	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.2311808518331e-05
CAMB-776B7	MN908947.3	23731	C	T	1	1	0	0	0.99978253778406	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.00010873110796999
CAMB-776B7	MN908947.3	241	C	T	1	1	0	0	0.998687775865301	TCG	NA	NA	NA	NA	NA	NA	0.000289711821946523
CAMB-776B7	MN908947.3	24106	C	T	0.0091	0.0095	6.1e-06	2.7e-06	0.00924684578795614	ACC	S	D848D	C2544T	GAC>GAT	Synonymous	GU280_gp02, spike glycoprotein	0.990734789076417
CAMB-776B7	MN908947.3	25606	G	A	0.1	0.11	5.5e-47	1.1e-49	0.106126017815181	AGC	ORF3a	A72T	G214A	GCA>ACA	Missense	GU280_gp03	0.893846658287338
CAMB-776B7	MN908947.3	26566	A	G	0.0088	0.007	1e-05	4.1e-05	0.00819575102185766	AAG	M	K15R	A44G	AAG>AGG	Missense	GU280_gp05	0.991658020625161
CAMB-776B7	MN908947.3	27386	AAACGAACATG	-	0.00852727272727273	0.0069	2.5e-05;6.1e-06;1e-05;1e-05;1e-05;1.2e-05;6.2e-06;9.3e-06;9.1e-06;0.00022;8.7e-05	1e-04;1.5e-05;1.9e-05;2.7e-05;2.8e-05;1.4e-05;9.9e-06;2.2e-05;1e-05;0.00059;0.00034	0.00811650437750955	TAA	ORF6	.	185-186-delfrshift	.	no-SNV	GU280_gp06	0.991753225552909
CAMB-776B7	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999358426005133	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	8.82456759618779e-05
CAMB-776B7	MN908947.3	29200	C	T	0.0099	0.0088	4.1e-06	7.6e-06	0.00953488006785944	CCA	N	P309P	C927T	CCC>CCT	Synonymous	GU280_gp10	0.990040998413471
CAMB-776B7	MN908947.3	29247	C	T	0.023	0.027	1.3e-11	1.8e-13	0.024465906659739	ACA	N	T325I	C974T	ACA>ATA	Missense	GU280_gp10	0.97548824841835
CAMB-776B7	MN908947.3	3037	C	T	1	1	0	0	0.99939170693792	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.3794059004427e-05
CAMB-776B7	MN908947.3	4002	C	T	1	1	0	0	0.999163529903806	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0.000266149576061747
CAMB-776B7	MN908947.3	6396	TAAAACCAGTCTCTGAAGAAG	-	0.00435714285714286	0.00702380952380952	0.00044;0.00078;0.00043;0.0048;0.0016;0.00042;0.00085;0.00039;0.00041;0.00039;3e-04;0.00049;0.00043;0.0019;0.00052;0.00046;0.00064;0.0013;0.00043;0.00044;0.00048	2.4e-05;7.2e-05;2.1e-05;0.00022;8.6e-05;1.3e-05;4.2e-05;1.9e-05;2.6e-05;2.5e-05;1.8e-05;2.4e-05;2.1e-05;9.7e-05;2.1e-05;2e-05;2.9e-05;6.9e-05;2.2e-05;2.2e-05;2.3e-05	0.0052842514290005	CTA	ORF1ab:nsp3	.	3677-3697-delinframe	.	no-SNV	ORF1ab:nsp3	0.994514113857664
CAMB-776B7	MN908947.3	66	C	T	0.014	0.017	5.8e-08	2e-09	0.0155759385005646	TCT	NA	NA	NA	NA	NA	NA	0.984377658504896
CAMB-776B7	MN908947.3	9857	C	T	0.0082	0.0063	3.1e-05	0.00018	0.00738583907392941	GCT	ORF1ab:nsp4	L435L	C1303T	CTA>TTA	Synonymous	ORF1ab:nsp4	0.992495798120399
CAMB-776C6	MN908947.3	14408	C	T	1	1	0	1.3e-18	0.997115535350368	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00062705753252861
CAMB-776C6	MN908947.3	26439	G	T	0.82	0.75	0	7.6e-17	0.824257786324039	TGA	E	L65L	G195T	CTG>CTT	Synonymous	GU280_gp04	0.175596538764094
CAMB-776C6	MN908947.3	27882	G	A	1	1	0	1.3e-41	1	CGC	NA	NA	NA	NA	NA	NA	0
CAMB-776C6	MN908947.3	3037	C	T	1	1	0	6.1e-18	0.999005384641767	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000102891243955139
CAMB-776D5	MN908947.3	10097	G	A	1	1	0	0	0.999774673276251	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0
CAMB-776D5	MN908947.3	14408	C	T	1	1	0	0	0.99941551050543	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000461439074660842
CAMB-776D5	MN908947.3	17749	G	T	1	1	0	0	0.999785767843753	TGC	ORF1ab:helicase	A505S	G1513T	GCT>TCT	Missense	ORF1ab:helicase	3.57053593744421e-05
CAMB-776D5	MN908947.3	23161	G	T	0.033	0.021	1.7e-10	4.7e-07	0.0266826511388936	TGG	S	L533F	G1599T	TTG>TTT	Missense	GU280_gp02, spike glycoprotein	0.951407204429982
CAMB-776D5	MN908947.3	23403	A	G	1	1	0	0	0.999926879204446	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.87471970361704e-05
CAMB-776D5	MN908947.3	23731	C	T	1	1	0	0	1	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-776D5	MN908947.3	241	C	T	1	1	0	0	0.99958932238193	TCG	NA	NA	NA	NA	NA	NA	0.00027378507871321
CAMB-776D5	MN908947.3	25006	C	T	0.045	0.034	1.6e-21	7.4e-17	0.0392714673956231	TCA	S	F1148F	C3444T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.960680853769012
CAMB-776D5	MN908947.3	25521	C	T	0.22	0.04	6.2e-105	1.3e-18	0.126869562831033	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.873102994044842
CAMB-776D5	MN908947.3	27973	A	G	0.0097	0.021	3.6e-05	7.3e-09	0.0157266811279826	CAA	ORF8	Q27R	A80G	CAA>CGA	Missense	GU280_gp09	0.984273318872017
CAMB-776D5	MN908947.3	28580	G	T	1	1	0	0	0.999540229885057	AGA	N	D103Y	G307T	GAT>TAT	Missense	GU280_gp10	0.000275862068965517
CAMB-776D5	MN908947.3	28730	A	-	0.025	0.0023	9.9e-13	0.0069	0.0138946618371831	TAA	N	.	457-457-delfrshift	.	no-SNV	GU280_gp10	0.986045959266077
CAMB-776D5	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999528746465599	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-776D5	MN908947.3	3037	C	T	1	1	0	0	0.998793727382388	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-776E4	MN908947.3	10286	A	G	0.026	0.015	5.9e-13	2.6e-08	0.0212318374103366	TAT	ORF1ab:3C-like-proteinase	I78V	A232G	ATT>GTT	Missense	ORF1ab:3C-like-proteinase	0.978411807982343
CAMB-776E4	MN908947.3	11074	C	INS	0.035	0.02	5.9e-10	0.00089	0.0290683021087121	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.97074687053684
CAMB-776E4	MN908947.3	11075	T	-	0.034	0.035	2.8e-08	1.1e-08	0.0342692968426041	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962361530715005
CAMB-776E4	MN908947.3	14408	C	T	1	1	0	0	0.997744626696833	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000304015837104072
CAMB-776E4	MN908947.3	14730	G	A	0.006	0.014	0.00016	4.2e-08	0.00966744567505189	AGG	ORF1ab:RNA-dependent-RNA-polymerase	K421K	G1263A	AAG>AAA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.990230944535571
CAMB-776E4	MN908947.3	16289	C	T	1	1	0	0	0.999350558983161	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0.000139165932179802
CAMB-776E4	MN908947.3	18391	G	T	0.013	0.0058	1.8e-07	0.00014	0.00984013731895808	AGT	ORF1ab:3'-to-5'-exonuclease	V118F	G352T	GTT>TTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.990120312289889
CAMB-776E4	MN908947.3	23403	A	G	1	1	0	0	0.998950756993122	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000104374958799358
CAMB-776E4	MN908947.3	241	C	T	1	1	0	0	0.99775074370571	TCG	NA	NA	NA	NA	NA	NA	0.000604638788787578
CAMB-776E4	MN908947.3	25429	G	T	1	1	0	0	0.996065885608058	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	8.6464052570144e-06
CAMB-776E4	MN908947.3	28221	G	C	1	1	0	0	0.998994895956027	AGA	ORF8	E110Q	G328C	GAG>CAG	Missense	GU280_gp09	6.28190027483314e-05
CAMB-776E4	MN908947.3	29810	G	T	1	1	0	0	0.99888212644392	TGT	NA	NA	NA	NA	NA	NA	0.00074524903738666
CAMB-776E4	MN908947.3	3037	C	T	1	1	0	0	0.999837672878385	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.49308486461918e-05
CAMB-776F3	MN908947.3	11074	C	INS	0.095	0.097	2.9e-33	3.6e-36	0.0960900361607324	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.899725070086813
CAMB-776F3	MN908947.3	11083	G	-	0.12	0.1	3.6e-51	5.1e-45	0.111140314647242	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.222505913716067
CAMB-776F3	MN908947.3	11083	G	T	0.66	0.67	8.5e-221	8.6e-229	0.666266161028298	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.222505913716067
CAMB-776F3	MN908947.3	14408	C	T	1	1	0	0	0.998182619231193	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000504827991335316
CAMB-776F3	MN908947.3	16852	G	T	1	1	0	0	0.999445053532031	TGG	ORF1ab:helicase	G206C	G616T	GGT>TGT	Missense	ORF1ab:helicase	5.41411188262205e-05
CAMB-776F3	MN908947.3	23403	A	G	1	1	0	0	0.999238402778307	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.33118055185335e-05
CAMB-776F3	MN908947.3	241	C	T	1	1	0	0	0.998761335311119	TCG	NA	NA	NA	NA	NA	NA	0.000198798036487086
CAMB-776F3	MN908947.3	26166	AG	-	0.0115	0.0077	3.2e-06;8.5e-05	0.00017;0.0011	0.0092985708305926	CAG	ORF3a	.	774-775-delfrshift	.	no-SNV	GU280_gp03	0.989548798585457
CAMB-776F3	MN908947.3	28253	C	T	0.023	0.021	6.6e-11	6.1e-10	0.0218804113132522	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.977424802787695
CAMB-776F3	MN908947.3	28603	C	T	0.023	0.025	7.3e-08	2.8e-08	0.0241409610137354	TCT	N	F110F	C330T	TTC>TTT	Synonymous	GU280_gp10	0.975211580261758
CAMB-776F3	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998935604044705	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000100704934541793
CAMB-776F3	MN908947.3	29750	CGATCGAGTG	-	0.428	0.396	1.1e-137;4.9e-139;4.4e-168;3.8e-171;1e-170;7.9e-168;5.3e-179;4.4e-151;3.2e-169;2.4e-152	3.9e-125;4.3e-126;1.4e-150;7.4e-157;1.2e-155;6.4e-153;2.6e-155;3.4e-137;5.6e-154;5.2e-139	0.405521262002743	ACG	NA	NA	NA	NA	NA	NA	0.592944310759711
CAMB-776F3	MN908947.3	3037	C	T	1	1	0	0	0.999399283015212	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-776F3	MN908947.3	560	C	T	0.0094	0.01	9.1e-06	3.7e-06	0.00990202629269746	TCG	ORF1ab:leader-protein	R99C	C295T	CGT>TGT	Missense	ORF1ab:leader-protein	0.989904763438177
CAMB-776F3	MN908947.3	635	C	T	0.015	0.015	1e-07	8e-08	0.0147427438057831	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.985132317687388
CAMB-776F3	MN908947.3	683	C	T	0.01	0.01	5.6e-06	4.6e-06	0.0103129969995573	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.98924021576954
CAMB-776F3	MN908947.3	9430	C	T	0.033	0.031	1.1e-14	4.2e-14	0.0318045632634248	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.967465621879081
CAMB-7772D	MN908947.3	11074	C	INS	0.031	0.11	1.8e-06	3.8e-36	0.0699061065040093	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.929705526237635
CAMB-7772D	MN908947.3	11083	G	-	0.29	0.13	1e-140	8.4e-56	0.216381766381766	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-7772D	MN908947.3	11083	G	T	0.71	0.87	3.9e-254	0	0.783577533577534	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-7772D	MN908947.3	1440	G	A	1	1	0	3.5e-211	1	GGC	ORF1ab:nsp2	G212D	G635A	GGC>GAC	Missense	ORF1ab:nsp2	0
CAMB-7772D	MN908947.3	21742	C	T	1	1	0	0	1	CCA	S	S60S	C180T	TCC>TCT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-7772D	MN908947.3	24912	C	T	0.027	0.041	4e-13	2.6e-19	0.032154482921153	ACA	S	T1117I	C3350T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0.96781605809312
CAMB-7772D	MN908947.3	25931	C	A	0.89	0.84	0	0	0.8691917219836	TCT	ORF3a	S180Y	C539A	TCT>TAT	Missense	GU280_gp03	0.1308082780164
CAMB-7772D	MN908947.3	26756	T	C	0.064	0.03	1.5e-29	8.8e-15	0.0491777579206446	GTG	M	G78G	T234C	GGT>GGC	Synonymous	GU280_gp05	0.950618445186474
CAMB-7772D	MN908947.3	2891	G	A	1	1	0	0	0.999549803038829	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	0.000450196961170512
CAMB-7772D	MN908947.3	29751	GATCGAGT	-	0.01775	0.0115	1.9e-05;4.6e-06;3e-06;2.8e-06;3.1e-06;2.2e-06;9.3e-06;4e-06	0.0012;0.00034;0.00042;0.00041;4e-04;0.00031;0.00076;0.00049	0.0149144254278729	CGA	NA	NA	NA	NA	NA	NA	0.984856007944389
CAMB-7772D	MN908947.3	29774	C	T	0.02	0.033	8e-09	1e-12	0.0251107828655835	GCT	NA	NA	NA	NA	NA	NA	0.974889217134417
CAMB-7772D	MN908947.3	3809	C	T	0.004	0.046	0.00051	3e-20	0.0174717368961973	TCT	ORF1ab:nsp3	L364F	C1090T	CTC>TTC	Missense	ORF1ab:nsp3	0.982528263103803
CAMB-7772D	MN908947.3	4668	C	T	1	1	0	0	0.999893778049234	TCT	ORF1ab:nsp3	S650F	C1949T	TCT>TTT	Missense	ORF1ab:nsp3	0.000106221950766126
CAMB-7772D	MN908947.3	4790	G	A	0.02	0.069	5.8e-11	6.6e-32	0.04107666015625	TGG	ORF1ab:nsp3	G691S	G2071A	GGT>AGT	Missense	ORF1ab:nsp3	0.95892333984375
CAMB-7772D	MN908947.3	875	C	T	0.047	0.081	2.1e-22	1.3e-37	0.0596402769416014	CCT	ORF1ab:nsp2	L24F	C70T	CTT>TTT	Missense	ORF1ab:nsp2	0.940340909090909
CAMB-7774B	MN908947.3	11962	C	T	0.028	0.021	1.8e-13	0.00014	0.0278570594028007	TCT	ORF1ab:nsp7	L40L	C120T	CTC>CTT	Synonymous	ORF1ab:nsp7	0.972142940597199
CAMB-7774B	MN908947.3	14408	C	T	0.99	1	0	1.99999999999999e-310	0.993882935257174	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000373561205668791
CAMB-7774B	MN908947.3	21123	G	T	1	1	0	0	0.999806036154861	GGT	ORF1ab:2'-O-ribose-methyltransferase	G155G	G465T	GGG>GGT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.000193963845139266
CAMB-7774B	MN908947.3	241	C	T	1	1	0	2.9e-08	0.999782970411633	TCG	NA	NA	NA	NA	NA	NA	0.000180857990306012
CAMB-7774B	MN908947.3	25452	C	T	0.012	0.013	9.9e-07	0.0018	0.0117760718575383	TCA	ORF3a	I20I	C60T	ATC>ATT	Synonymous	GU280_gp03	0.988171706094313
CAMB-7774B	MN908947.3	28253	C	T	0.39	0.39	1.7e-203	9.6e-107	0.389081560885698	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.610263623796474
CAMB-7774B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	5.2e-16;6.1e-19;3.4e-17	0.999692276130885	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7774B	MN908947.3	3037	C	T	1	1	0	1.1e-37	0.999361124421019	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000319437789490497
CAMB-7774B	MN908947.3	635	C	T	0.085	0.29	2.7e-38	3.2e-06	0.0848199012755975	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.915180098724403
CAMB-7774B	MN908947.3	683	C	T	0.059	0.22	1.9e-27	5.2e-06	0.0593956234803751	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.940589903901818
CAMB-7775A	MN908947.3	11075	T	-	0.083	0.024	1.8e-20	6.4e-07	0.0539589547573544	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.945844571061139
CAMB-7775A	MN908947.3	14408	C	T	1	1	0	0	0.999296524450529	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000494334169898852
CAMB-7775A	MN908947.3	16795	G	-	0.0098	0.0094	1.2e-05	1.8e-05	0.00956948993916706	TGT	ORF1ab:helicase	.	559-559-delfrshift	.	no-SNV	ORF1ab:helicase	0.990336920917174
CAMB-7775A	MN908947.3	1812	C	T	0.0087	0.0096	4.5e-06	1.7e-06	0.00910209102091021	GCT	ORF1ab:nsp2	A336V	C1007T	GCT>GTT	Missense	ORF1ab:nsp2	0.990792479353365
CAMB-7775A	MN908947.3	2101	G	C	0.014	0.014	2.1e-07	9.3e-08	0.0139514917364241	GGC	ORF1ab:nsp2	W432C	G1296C	TGG>TGC	Missense	ORF1ab:nsp2	0.985404593260356
CAMB-7775A	MN908947.3	21123	G	T	1	1	0	0	0.999932727884292	GGT	ORF1ab:2'-O-ribose-methyltransferase	G155G	G465T	GGG>GGT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	6.7272115708039e-05
CAMB-7775A	MN908947.3	23403	A	G	1	1	0	0	0.999917492600118	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.15671249265168e-05
CAMB-7775A	MN908947.3	241	C	T	1	1	0	0	0.999748593695987	TCG	NA	NA	NA	NA	NA	NA	0.000125703152006537
CAMB-7775A	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0166504324324324	0.048027027027027	NA;NA;NA;NA;NA;NA;NA;0.0031;0.0031;0.0014;0.0021;0.0018;0.003;0.0024;0.0028;0.0038;0.0021;0.0035;0.0024;0.0025;0.0031;0.0037;0.0024;0.003;0.0024;0.0021;0.0034;0.0022;0.0015;0.0026;0.0033;0.0028;0.0017;0.0033;0.0019;0.0022;0.0015	8.7e-07;1.8e-08;5.3e-07;5.1e-07;1.6e-06;6.5e-08;3.2e-07;1.6e-08;1.7e-08;8.3e-09;6.9e-09;5.9e-09;1.7e-08;1.1e-08;1.2e-08;2.4e-08;8e-09;2.1e-08;1.2e-08;1.1e-08;7.8e-09;2.3e-08;9.2e-09;1.6e-08;1.1e-08;5.6e-09;1.9e-08;1e-08;3.1e-09;1.1e-08;1.9e-08;1.8e-08;6.5e-09;1.8e-08;2.3e-09;1.1e-08;4.9e-09	0.0355249131259432	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.980385684025199
CAMB-7775A	MN908947.3	27879	C	T	0.023	0.045	1.8e-10	2e-18	0.0328209389281263	TCA	NA	NA	NA	NA	NA	NA	0.967179061071874
CAMB-7775A	MN908947.3	28881	G	A	1	1	0	0	0.999046938289254	AGG	N	R203K	G608A	AGG>AAG	Missense	GU280_gp10	0.000238265427686443
CAMB-7775A	MN908947.3	28881	GGG	AAC	0.996666666666667	1	0;0;0	0;0;0	0.999782135076253	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000238265427686443
CAMB-7775A	MN908947.3	28883	G	C	0.99	1	0	0	0.993666360200225	GGG	N	G204R	G610C	GGA>CGA	Missense	GU280_gp10	0.000102155480641536
CAMB-7775A	MN908947.3	29187	C	T	0.01	0.0062	1.5e-05	0.00091	0.00826504662333993	GCA	N	A305V	C914T	GCA>GTA	Missense	GU280_gp10	0.991664311952529
CAMB-7775A	MN908947.3	29413	A	G	0.018	0.0094	4.9e-08	8.8e-05	0.014894709809964	AAG	N	Q380Q	A1140G	CAA>CAG	Synonymous	GU280_gp10	0.985105290190036
CAMB-7775A	MN908947.3	3037	C	T	1	1	0	0	0.99963816186226	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7775A	MN908947.3	3546	ATG	-	0.0263333333333333	0.048	0.0044;0.0033;0.0029	3.9e-05;3.6e-05;1.5e-05	0.0372670807453416	AAT	ORF1ab:nsp3	.	827-829-delinframe	.	no-SNV	ORF1ab:nsp3	0.963114754098361
CAMB-7775A	MN908947.3	4176	AAAAGGCTGGTGGCACTACTGAAATGCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATT	-	0.0181746031746032	0.00349296825396825	1.5e-09;6.3e-10;5.5e-10;4.4e-10;7.2e-10;3.4e-10;7.6e-10;1.2e-09;4e-09;7.1e-10;9.3e-10;1.2e-09;5.3e-10;8.9e-10;4.6e-10;5.6e-10;1.4e-10;1e-10;4.7e-10;3.2e-10;9e-10;1.4e-09;3e-10;2.4e-10;9.2e-10;1.3e-09;8.4e-10;1e-09;4.7e-13;1.1e-09;1.2e-09;8.6e-10;1.1e-09;2.6e-10;3.7e-10;7.4e-10;8.4e-10;3.2e-10;1.9e-11;2.2e-10;6.1e-10;3.6e-10;3.5e-09;3.6e-09;9.7e-11;1.9e-10;3.2e-10;3.5e-10;2.4e-10;6.1e-10;2.5e-10;2.5e-07;2.9e-10;9.4e-08;7.7e-10;3.5e-10;3.6e-10;7e-10;5e-10;2.1e-11;3.6e-12;4.5e-12;2.1e-10	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;2.4e-12;2.7e-12;1e-15;2.2e-12;2.8e-12;2.6e-12;5.4e-12;1.1e-12;2.4e-12;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0083968556455455	AAA	ORF1ab:nsp3	.	1457-1519-delinframe	.	no-SNV	ORF1ab:nsp3	0.991735537190083
CAMB-7775A	MN908947.3	6025	TCCAAACGCAAGCTTCGATAATT	-	0.0427391304347826	0.00931739130434783	5.8e-15;7.3e-15;5.6e-15;2.8e-15;1.3e-14;1.6e-14;7.8e-15;2.5e-13;1.7e-14;1.2e-14;1.5e-15;4.1e-16;3.8e-15;1.5e-16;2.2e-15;1.1e-14;1e-14;5.1e-15;3.4e-15;2.7e-14;5.4e-08;1.8e-07;2e-07	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;1.5e-11;9.3e-11;7.5e-11	0.0248675091724419	ATC	ORF1ab:nsp3	.	3306-3328-delfrshift	.	no-SNV	ORF1ab:nsp3	0.976246105919003
CAMB-77769	MN908947.3	10541	C	T	0.0088	0.0064	1.1e-05	0.00012	0.00766889835666464	GCA	ORF1ab:3C-like-proteinase	H163Y	C487T	CAC>TAC	Missense	ORF1ab:3C-like-proteinase	0.992249949279773
CAMB-77769	MN908947.3	1059	C	T	1	1	0	0	0.999955711712776	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	2.95255248162036e-05
CAMB-77769	MN908947.3	10604	C	T	0.0071	0.0065	2.8e-05	4.7e-05	0.00678019552191738	ACC	ORF1ab:3C-like-proteinase	P184S	C550T	CCT>TCT	Missense	ORF1ab:3C-like-proteinase	0.993219804478083
CAMB-77769	MN908947.3	11075	T	-	0.04	0.012	6.4e-10	0.00058	0.025416381939274	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.97437963425704
CAMB-77769	MN908947.3	11593	T	C	0.0085	0.0046	1.4e-05	0.00072	0.00700029788501638	TTC	ORF1ab:nsp6	L207L	T621C	CTT>CTC	Synonymous	ORF1ab:nsp6	0.992999702114984
CAMB-77769	MN908947.3	12357	C	T	0.0075	0.0047	4.1e-05	0.00073	0.0061534987438959	ACA	ORF1ab:nsp8	T89I	C266T	ACA>ATA	Missense	ORF1ab:nsp8	0.993846501256104
CAMB-77769	MN908947.3	1259	C	T	0.0098	0.0047	3.1e-06	0.00048	0.00735183590920893	GCA	ORF1ab:nsp2	Q152*	C454T	CAG>TAG	Nonsense	ORF1ab:nsp2	0.992620833845775
CAMB-77769	MN908947.3	14408	C	T	1	1	0	0	0.996291718170581	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000211298109938407
CAMB-77769	MN908947.3	16115	ATG	-	0.0113333333333333	0.00533333333333333	1.8e-05;5.8e-05;2.6e-05	0.0029;0.005;0.0034	0.00859456230781143	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	2648-2650-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.991104110241039
CAMB-77769	MN908947.3	18195	A	T	0.0069	0.006	2.9e-05	7e-05	0.00639742149728964	GAA	ORF1ab:3'-to-5'-exonuclease	R52S	A156T	AGA>AGT	Missense	ORF1ab:3'-to-5'-exonuclease	0.99360257850271
CAMB-77769	MN908947.3	21781	C	INS	0.013	0.0069	3.8e-07	0.00015	0.0099913654866165	CCA	S	.	218-219-insfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.989885284322191
CAMB-77769	MN908947.3	23202	C	T	0.053	0.054	4.5e-24	2e-24	0.0530844535690294	ACA	S	T547I	C1640T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0.944122819597394
CAMB-77769	MN908947.3	23403	A	G	1	1	0	0	0.999903444075551	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.17011668412101e-05
CAMB-77769	MN908947.3	23929	C	T	0.0085	0.0064	8.3e-06	6.5e-05	0.00752483194541989	ACA	S	Y789Y	C2367T	TAC>TAT	Synonymous	GU280_gp02, spike glycoprotein	0.992450085281429
CAMB-77769	MN908947.3	241	C	T	1	1	0	0	0.999756147124568	TCG	NA	NA	NA	NA	NA	NA	8.12842918106076e-05
CAMB-77769	MN908947.3	25544	C	-	0.017	0.0049	3.4e-06	0.0041	0.0105821250811513	GCA	ORF3a	.	152-152-delfrshift	.	no-SNV	GU280_gp03	0.989201471542956
CAMB-77769	MN908947.3	25563	G	T	1	1	0	0	0.999752527314798	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000111362708341067
CAMB-77769	MN908947.3	25631	T	C	0.0013	0.011	0.0076	5e-07	0.0066270715407709	GTT	ORF3a	V80A	T239C	GTT>GCT	Missense	GU280_gp03	0.993345044567753
CAMB-77769	MN908947.3	2623	C	T	1	1	0	0	1	ACG	ORF1ab:nsp2	N606N	C1818T	AAC>AAT	Synonymous	ORF1ab:nsp2	0
CAMB-77769	MN908947.3	29753	T	C	0.01	0.0079	4.2e-06	3.8e-05	0.00912951167728238	ATC	NA	NA	NA	NA	NA	NA	0.990658174097665
CAMB-77769	MN908947.3	3037	C	T	1	1	0	0	0.999221032132425	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.73709834469328e-05
CAMB-77769	MN908947.3	3604	C	T	0.0053	0.015	0.0014	5.5e-06	0.00960614793467819	ACT	ORF1ab:nsp3	H295H	C885T	CAC>CAT	Synonymous	ORF1ab:nsp3	0.990393852065322
CAMB-77769	MN908947.3	4328	A	G	1	1	0	0	0.999919821683424	CAT	ORF1ab:nsp3	I537V	A1609G	ATT>GTT	Missense	ORF1ab:nsp3	7.21604849184586e-05
CAMB-77769	MN908947.3	4455	CC	TT	0.021	0.011	1.8e-06;1.2e-15	NA;1e-11	0.0168386217636753	GCC	ORF1ab:nsp3	.	1736-1737-mnv	.	no-SNV	ORF1ab:nsp3	0.994959991686584
CAMB-77769	MN908947.3	4456	C	T	0.032	0.022	1.2e-15	1e-11	0.0272546282523628	CCA	ORF1ab:nsp3	A579A	C1737T	GCC>GCT	Synonymous	ORF1ab:nsp3	0.972699604109934
CAMB-77769	MN908947.3	4721	TA	-	0.0084	0.00415	4.9e-06;5.4e-06	0.00038;0.00037	0.00601845454685029	GTA	ORF1ab:nsp3	.	2002-2003-delfrshift	.	no-SNV	ORF1ab:nsp3	0.989978348283328
CAMB-77769	MN908947.3	4737	C	T	0.0093	0.0063	2.4e-06	5.1e-05	0.00759710438234607	ACT	ORF1ab:nsp3	T673I	C2018T	ACT>ATT	Missense	ORF1ab:nsp3	0.988588775589632
CAMB-77769	MN908947.3	4833	T	C	0.013	0.0077	1.6e-07	2.4e-05	0.00983179815778935	CTA	ORF1ab:nsp3	L705P	T2114C	CTA>CCA	Missense	ORF1ab:nsp3	0.989587505006007
CAMB-77769	MN908947.3	5434	T	C	0.0068	0.011	0.00011	5.3e-06	0.00858778625954199	GTG	ORF1ab:nsp3	G905G	T2715C	GGT>GGC	Synonymous	ORF1ab:nsp3	0.990776081424936
CAMB-77769	MN908947.3	6517	A	-	0.0087	0.0069	3.4e-05	0.00021	0.00781711195323063	TAA	ORF1ab:nsp3	.	3798-3798-delfrshift	.	no-SNV	ORF1ab:nsp3	0.992116237883953
CAMB-77769	MN908947.3	6823	A	-	0.013	0.0026	2.4e-07	0.0033	0.00760582010582011	CAA	ORF1ab:nsp3	.	4104-4104-delfrshift	.	no-SNV	ORF1ab:nsp3	0.99239417989418
CAMB-77769	MN908947.3	7926	C	T	0.061	0.058	2.4e-26	1.5e-25	0.0591358206754166	GCA	ORF1ab:nsp3	A1736V	C5207T	GCA>GTA	Missense	ORF1ab:nsp3	0.940864179324583
CAMB-77778	MN908947.3	10138	C	T	0.11	0.056	8.4e-50	6.2e-26	0.0849855170280379	ACG	ORF1ab:3C-like-proteinase	N28N	C84T	AAC>AAT	Synonymous	ORF1ab:3C-like-proteinase	0.914944177282826
CAMB-77778	MN908947.3	11074	C	INS	0.025	0.028	2.9e-05	1e-05	0.0265442993293329	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.973314507589128
CAMB-77778	MN908947.3	11075	T	-	0.087	0.03	8.5e-21	4.1e-08	0.0634607511073064	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.936315926601407
CAMB-77778	MN908947.3	11312	G	A	0.054	0.019	3.7e-25	3.6e-10	0.0387433702428585	TGT	ORF1ab:nsp6	V114I	G340A	GTT>ATT	Missense	ORF1ab:nsp6	0.961210105145622
CAMB-77778	MN908947.3	12419	G	C	0.0057	0.0094	1e-04	2.3e-06	0.0072791720732981	TGC	ORF1ab:nsp8	A110P	G328C	GCA>CCA	Missense	ORF1ab:nsp8	0.992562585055543
CAMB-77778	MN908947.3	12459	C	T	0.006	0.015	0.00042	3.3e-08	0.00990693801840161	ACA	ORF1ab:nsp8	T123I	C368T	ACA>ATA	Missense	ORF1ab:nsp8	0.99007198339007
CAMB-77778	MN908947.3	14408	C	T	0.99	1	0	0	0.994754712847911	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000438121432657085
CAMB-77778	MN908947.3	15023	TCGCATATACAAAACGTA	-	0.0273333333333333	0.00416666666666667	3.6e-07;1.1e-06;2.1e-06;3.8e-06;3.8e-06;2.9e-06;2.9e-06;3e-07;4e-07;7.5e-08;2.9e-08;1.5e-07;2.1e-07;3e-07;1.7e-07;2.2e-07;2.9e-07;3.9e-07	0.0018;0.0031;0.0032;0.0042;0.0055;0.0048;0.0044;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0151813880126183	TTC	ORF1ab:RNA-dependent-RNA-polymerase	.	1556-1573-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.980897713371601
CAMB-77778	MN908947.3	17353	TTTGATGAAA	-	0.0149	0.0046147	4.7e-06;0.00012;0.00022;0.00016;4.2e-06;1.8e-06;2.4e-06;5e-06;1.2e-06;3.4e-06	0.0064;0.023;0.0013;0.0011;0.0015;NA;NA;0.042;0.028;0.038	0.0112705996253657	CTT	ORF1ab:helicase	.	1117-1126-delfrshift	.	no-SNV	ORF1ab:helicase	0.991824112513768
CAMB-77778	MN908947.3	17676	C	T	0.055	0.091	1.2e-25	9.8e-42	0.0718103022409844	TCA	ORF1ab:helicase	I480I	C1440T	ATC>ATT	Synonymous	ORF1ab:helicase	0.928159758087454
CAMB-77778	MN908947.3	214	C	T	0.013	0.0067	1.2e-07	7.5e-05	0.0104082084594375	GCA	NA	NA	NA	NA	NA	NA	0.989499520188972
CAMB-77778	MN908947.3	22150	TAT	ATA	0.00609333333333333	0.0236666666666667	NA;5.7e-07;0.47	8.8e-06;8.3e-09;5.9e-06	0.011219368172424	ATA	S	.	588-590-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.988535124872207
CAMB-77778	MN908947.3	22326	C	T	0.088	0.077	5.5e-23	3.5e-17	0.0839793281653747	TCT	S	S255F	C764T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.916020671834625
CAMB-77778	MN908947.3	23403	A	G	0.99	1	0	0	0.996190278421162	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.99341884574222e-05
CAMB-77778	MN908947.3	23427	TTGCTA	-	0.00891666666666667	0.00145	0.00028;0.00026;2e-05;1.4e-05;7e-05;2.4e-05	0.008;0.0079;NA;NA;NA;NA	0.00488869136600541	GTT	S	.	1865-1870-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.992327551725392
CAMB-77778	MN908947.3	241	C	T	1	1	0	0	0.999744265648975	TCG	NA	NA	NA	NA	NA	NA	0.000157374985246095
CAMB-77778	MN908947.3	26360	TG	-	0.0091	0.00755	9.8e-06;1.5e-05	5.6e-05;6.1e-05	0.00849037067715883	TTG	E	.	116-117-delfrshift	.	no-SNV	GU280_gp04	0.99120748239745
CAMB-77778	MN908947.3	26581	G	T	0.0081	0.0028	1.9e-05	0.0035	0.00582779609687092	TGG	M	W20L	G59T	TGG>TTG	Missense	GU280_gp05	0.983562626393441
CAMB-77778	MN908947.3	26784	GTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.0521621621621622	0.0171972972972973	0.00053;7.5e-05;0.00025;3.1e-09;3e-09;6.5e-10;1.5e-09;9.4e-10;2.7e-09;1.7e-09;2.9e-09;5e-09;1.5e-09;4.1e-09;1.8e-09;1.9e-09;1.4e-09;4.5e-09;1.8e-09;2.7e-09;1.7e-09;6.8e-10;3.9e-09;1.3e-09;2.8e-10;2.5e-09;3.5e-09;3.3e-09;1.2e-09;3.7e-09;2.9e-10;1.3e-09;5.3e-10;3.7e-07;2.5e-05;8.2e-06;1.5e-05	0.11;0.056;0.091;0.0071;0.0073;0.005;0.0047;0.0045;0.0073;0.006;0.006;0.0086;0.0053;0.0078;0.0063;0.006;0.0048;0.0084;0.0056;0.007;0.0063;0.005;0.0078;0.0062;0.0036;0.0058;0.0078;0.0074;0.0045;0.0074;0.0046;0.0061;0.0053;0.026;0.037;0.026;0.026	0.0388072858475384	TGT	M	.	262-298-delfrshift	.	no-SNV	GU280_gp05	0.982573753407087
CAMB-77778	MN908947.3	27005	C	T	0.0083	0.021	1.2e-05	3.1e-11	0.0137710561908275	TCA	M	I161I	C483T	ATC>ATT	Synonymous	GU280_gp05	0.986146973236608
CAMB-77778	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999267594380451	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	7.37680731779286e-05
CAMB-77778	MN908947.3	3037	C	T	1	1	0	0	0.999269005847953	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000162443144899285
CAMB-77778	MN908947.3	3490	A	-	0.012	0.0055	3.9e-07	0.00017	0.0089966662099831	TAA	ORF1ab:nsp3	.	771-771-delfrshift	.	no-SNV	ORF1ab:nsp3	0.990843494542631
CAMB-77778	MN908947.3	5674	T	-	0.013	0.0083	8.6e-07	0.00013	0.0113915944861986	CTT	ORF1ab:nsp3	.	2955-2955-delfrshift	.	no-SNV	ORF1ab:nsp3	0.9883050790334
CAMB-77778	MN908947.3	688	G	T	0.012	0.0048	3.7e-07	0.00015	0.00887639249741965	AGT	ORF1ab:leader-protein	K141N	G423T	AAG>AAT	Missense	ORF1ab:leader-protein	0.985962914190127
CAMB-77778	MN908947.3	7067	G	A	0.3	0.47	8.5e-102	7.4e-164	0.381239714755897	AGA	ORF1ab:nsp3	E1450K	G4348A	GAA>AAA	Missense	ORF1ab:nsp3	0.555128908392759
CAMB-77796	MN908947.3	11074	C	INS	0.023	0.033	1e-04	9.7e-07	0.0261099642369087	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.973701043817056
CAMB-77796	MN908947.3	11075	T	-	0.056	0.033	1.5e-13	6.8e-09	0.0489808998846302	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.949365465965902
CAMB-77796	MN908947.3	1230	A	G	0.026	0.0088	3.6e-13	5.3e-06	0.0238235926085088	AAG	ORF1ab:nsp2	K142R	A425G	AAG>AGG	Missense	ORF1ab:nsp2	0.976149548775247
CAMB-77796	MN908947.3	13778	AT	-	0.015	0.0145	9.1e-06;8.9e-06	1.6e-05;1.8e-05	0.0150767037203285	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.985511968918411
CAMB-77796	MN908947.3	14408	C	T	1	1	0	0	0.999250621435882	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000438660622898085
CAMB-77796	MN908947.3	14786	C	T	1	1	0	0	0.999882825577503	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A440V	C1319T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	8.36960160696351e-05
CAMB-77796	MN908947.3	15351	T	C	0.011	0.0038	1.5e-06	0.002	0.00854071072110393	TTC	ORF1ab:RNA-dependent-RNA-polymerase	V628V	T1884C	GTT>GTC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.991291824362796
CAMB-77796	MN908947.3	1547	A	-	0.011	0.0023	2.1e-06	0.0032	0.00770456960680128	TAG	ORF1ab:nsp2	.	742-742-delfrshift	.	no-SNV	ORF1ab:nsp2	0.944739638682253
CAMB-77796	MN908947.3	1547	A	G	0.015	0.016	1.4e-07	2.6e-07	0.0154091392136026	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.944739638682253
CAMB-77796	MN908947.3	1547	A	T	0.037	0.024	8.1e-16	2.9e-10	0.0321466524973433	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.944739638682253
CAMB-77796	MN908947.3	15842	C	T	0.0089	0.0051	1.4e-05	0.00053	0.00774860732487851	ACT	ORF1ab:RNA-dependent-RNA-polymerase	T792I	C2375T	ACT>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.990829086168069
CAMB-77796	MN908947.3	16111	C	T	0.029	0.014	1.4e-14	2.5e-08	0.0226894471316378	GCT	ORF1ab:RNA-dependent-RNA-polymerase	L882L	C2644T	CTA>TTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.977258542674364
CAMB-77796	MN908947.3	16887	C	T	0.012	0.0081	6.4e-06	0.00017	0.0100058004640371	ACA	ORF1ab:helicase	Y217Y	C651T	TAC>TAT	Synonymous	ORF1ab:helicase	0.989950696055684
CAMB-77796	MN908947.3	18166	C	T	0.042	0.026	1.8e-19	3.9e-13	0.0344941591359929	ACC	ORF1ab:3'-to-5'-exonuclease	P43S	C127T	CCT>TCT	Missense	ORF1ab:3'-to-5'-exonuclease	0.963940930130042
CAMB-77796	MN908947.3	18730	A	G	0.0037	0.0066	0.00083	2e-05	0.00437434007800547	TAT	ORF1ab:3'-to-5'-exonuclease	I231V	A691G	ATT>GTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.995367078242506
CAMB-77796	MN908947.3	19895	C	T	0.0094	0.011	3.8e-06	8.2e-07	0.00988869012124826	GCT	ORF1ab:endoRNAse	A92V	C275T	GCT>GTT	Missense	ORF1ab:endoRNAse	0.990111309878752
CAMB-77796	MN908947.3	20483	C	T	1	1	5e-209	1.4e-99	1	TCT	ORF1ab:endoRNAse	S288F	C863T	TCT>TTT	Missense	ORF1ab:endoRNAse	0
CAMB-77796	MN908947.3	21707	C	T	0.013	0.0094	1e-07	4.8e-06	0.0116144018583043	ACA	S	H49Y	C145T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.988385598141696
CAMB-77796	MN908947.3	23403	A	G	1	1	0	0	0.997053251946958	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.42877660430621e-05
CAMB-77796	MN908947.3	23996	C	T	0.012	0.011	2e-07	6e-07	0.0117114303560275	ACC	S	P812S	C2434T	CCA>TCA	Missense	GU280_gp02, spike glycoprotein	0.988194878201124
CAMB-77796	MN908947.3	241	C	T	1	1	0	0	0.999881043014846	TCG	NA	NA	NA	NA	NA	NA	7.1374191092501e-05
CAMB-77796	MN908947.3	25818	T	C	0.024	0.012	5.4e-12	4.5e-07	0.0168840521725214	ATG	ORF3a	D142D	T426C	GAT>GAC	Synonymous	GU280_gp03	0.983035928622869
CAMB-77796	MN908947.3	27422	T	C	0.016	0.017	6e-09	9.9e-10	0.0161994566995207	ATA	ORF7a	I10T	T29C	ATA>ACA	Missense	GU280_gp07	0.983786320774843
CAMB-77796	MN908947.3	28514	G	T	1	1	0	0	0.998678207478787	AGA	N	D81Y	G241T	GAT>TAT	Missense	GU280_gp10	4.26384684262141e-05
CAMB-77796	MN908947.3	29241	A	-	0.0094	0.0052	1.3e-05	0.00051	0.00834088848594742	GAA	N	.	968-968-delfrshift	.	no-SNV	GU280_gp10	0.991218754047403
CAMB-77796	MN908947.3	3037	C	T	1	1	0	0	0.999555226093403	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.41289844329133e-05
CAMB-77796	MN908947.3	367	C	A	0.007	0.0062	2.5e-05	2.1e-05	0.00675649133833523	CCG	ORF1ab:leader-protein	S34S	C102A	TCC>TCA	Synonymous	ORF1ab:leader-protein	0.993125662882508
CAMB-77796	MN908947.3	462	A	G	0.0099	0.0027	3.2e-06	0.0053	0.00884219662586117	CAG	ORF1ab:leader-protein	Q66R	A197G	CAG>CGG	Missense	ORF1ab:leader-protein	0.988228486700541
CAMB-77796	MN908947.3	6826	T	C	0.021	0.035	5.9e-11	2.5e-16	0.0283547047137439	ATT	ORF1ab:nsp3	N1369N	T4107C	AAT>AAC	Synonymous	ORF1ab:nsp3	0.971645295286256
CAMB-77796	MN908947.3	816	G	A	1	1	0	0	0.999768257450523	CGC	ORF1ab:nsp2	R4H	G11A	CGC>CAC	Missense	ORF1ab:nsp2	0.000139045529686221
CAMB-77796	MN908947.3	8187	T	C	1	1	0	0	0.999811168060426	TTT	ORF1ab:nsp3	F1823S	T5468C	TTT>TCT	Missense	ORF1ab:nsp3	2.69759913676828e-05
CAMB-777A5	MN908947.3	11075	T	-	0.035	0.042	5.7e-09	3.3e-10	0.0386105035018362	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95756657502358
CAMB-777A5	MN908947.3	11842	G	T	1	1	0	0	0.999631404349429	AGT	ORF1ab:nsp6	Q290H	G870T	CAG>CAT	Missense	ORF1ab:nsp6	0
CAMB-777A5	MN908947.3	14408	C	T	1	1	0	0	0.998124609293603	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00063381259984719
CAMB-777A5	MN908947.3	16072	G	T	1	1	0	0	0.999692727893479	TGC	ORF1ab:RNA-dependent-RNA-polymerase	A869S	G2605T	GCT>TCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	1.70706725844998e-05
CAMB-777A5	MN908947.3	19743	A	C	1	1	0	0	0.999712980458753	AAT	ORF1ab:endoRNAse	E41D	A123C	GAA>GAC	Missense	ORF1ab:endoRNAse	0.00014350977062355
CAMB-777A5	MN908947.3	23403	A	G	1	1	0	0	0.99913659722606	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.83505553406642e-05
CAMB-777A5	MN908947.3	241	C	T	1	1	0	0	0.998411077062762	TCG	NA	NA	NA	NA	NA	NA	0.000170241743275451
CAMB-777A5	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998830688461997	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	2.69759913676828e-05
CAMB-777A5	MN908947.3	3037	C	T	1	1	0	0	0.999182935521444	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.21530518227492e-05
CAMB-777A5	MN908947.3	4207	GA	TC	1	1	0;0	0;0	0.999338668631128	CGA	ORF1ab:nsp3	.	1488-1489-mnv	.	no-SNV	ORF1ab:nsp3	2.56081946222791e-05
CAMB-777A5	MN908947.3	4524	C	T	0.0088	0.0071	7.9e-06	4.6e-05	0.00784164446136277	GCT	ORF1ab:nsp3	A602V	C1805T	GCT>GTT	Missense	ORF1ab:nsp3	0.991676183225479
CAMB-777A5	MN908947.3	9207	C	T	0.012	0.011	2.1e-07	8.9e-07	0.0116520639508626	TCT	ORF1ab:nsp4	S218F	C653T	TCT>TTT	Missense	ORF1ab:nsp4	0.988257609971999
CAMB-777C3	MN908947.3	23403	A	G	1	1	0	1.2e-21	0.99995340819084	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.65918091599497e-05
CAMB-777C3	MN908947.3	241	C	T	1	1	0	2.9e-08	0.999861840287372	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-777D2	MN908947.3	10886	G	-	0.0093	0.0049	1.2e-05	0.00062	0.00715358120639407	TGG	ORF1ab:3C-like-proteinase	.	832-832-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.992581471341517
CAMB-777D2	MN908947.3	11058	C	T	0.018	0.012	9e-10	3.1e-07	0.0151777051666648	ACT	ORF1ab:nsp6	T29I	C86T	ACT>ATT	Missense	ORF1ab:nsp6	0.984799991078498
CAMB-777D2	MN908947.3	11074	C	INS	0.047	0.022	5.6e-13	0.00043	0.0361602854398243	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.963675037738438
CAMB-777D2	MN908947.3	11075	T	-	0.036	0.062	3.5e-09	4.7e-15	0.0479490344972165	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951864619971582
CAMB-777D2	MN908947.3	11665	C	T	0.0084	0.0013	8.2e-06	0.0093	0.00542986425339366	TCA	ORF1ab:nsp6	L231L	C693T	CTC>CTT	Synonymous	ORF1ab:nsp6	0.994389140271493
CAMB-777D2	MN908947.3	14408	C	T	1	1	0	0	0.999411480062252	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000340033741809764
CAMB-777D2	MN908947.3	14676	C	T	0.018	0.028	9.9e-10	3e-14	0.0231087098974284	CCG	ORF1ab:RNA-dependent-RNA-polymerase	P403P	C1209T	CCC>CCT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.976797678430533
CAMB-777D2	MN908947.3	15324	C	T	1	1	0	0	0.999804847585965	ACA	ORF1ab:RNA-dependent-RNA-polymerase	N619N	C1857T	AAC>AAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-777D2	MN908947.3	23403	A	G	1	1	0	0	0.999857168702806	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.56987783163047e-05
CAMB-777D2	MN908947.3	241	C	T	1	1	0	0	0.999420115976805	TCG	NA	NA	NA	NA	NA	NA	0.00013997200559888
CAMB-777D2	MN908947.3	27459	G	T	0.0066	0.0074	4.7e-05	2.3e-05	0.00701727664389225	AGT	ORF7a	E22D	G66T	GAG>GAT	Missense	GU280_gp07	0.992939205361417
CAMB-777D2	MN908947.3	29730	CACCGAGGCCACGCGGAGTACGATCGAGTG	-	1	1	0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0	0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0	1	TCA	NA	NA	NA	NA	NA	NA	0
CAMB-777D2	MN908947.3	3037	C	T	1	1	0	0	0.999660441426146	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-777D2	MN908947.3	6286	C	T	0.012	0.0069	2.3e-07	4.6e-05	0.0098471675665782	CCT	ORF1ab:nsp3	T1189T	C3567T	ACC>ACT	Synonymous	ORF1ab:nsp3	0.990079619291663
CAMB-777E1	MN908947.3	11074	C	INS	0.034	0.02	2.6e-08	0.0012	0.028701239696242	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.971117024729019
CAMB-777E1	MN908947.3	11075	T	-	0.04	0.046	7.7e-10	1.3e-11	0.0421256258534365	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953231679563041
CAMB-777E1	MN908947.3	14408	C	T	1	1	0	0	0.998531680587328	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000297919880832048
CAMB-777E1	MN908947.3	18853	T	G	0.015	0.03	2e-08	6.5e-15	0.0213005943343022	TTG	ORF1ab:3'-to-5'-exonuclease	C272G	T814G	TGT>GGT	Missense	ORF1ab:3'-to-5'-exonuclease	0.978598180845372
CAMB-777E1	MN908947.3	18935	T	A	0.01	0.0077	1.8e-06	1.3e-05	0.00916073706777499	ATT	ORF1ab:3'-to-5'-exonuclease	I299N	T896A	ATT>AAT	Missense	ORF1ab:3'-to-5'-exonuclease	0.990826110402336
CAMB-777E1	MN908947.3	21883	T	C	0.0036	0.0076	0.0016	3e-05	0.00542678440029433	GTA	S	G107G	T321C	GGT>GGC	Synonymous	GU280_gp02, spike glycoprotein	0.994573215599706
CAMB-777E1	MN908947.3	23403	A	G	1	1	0	0	0.999089939936036	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.80051483397904e-05
CAMB-777E1	MN908947.3	241	C	T	1	1	0	0	0.999463413995733	TCG	NA	NA	NA	NA	NA	NA	9.16122446308681e-05
CAMB-777E1	MN908947.3	25429	G	T	1	1	0	0	0.997221826471007	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	4.27411312152728e-05
CAMB-777E1	MN908947.3	2907	A	G	0.011	0.0079	7.2e-07	9e-06	0.00942598972892154	AAA	ORF1ab:nsp3	K63R	A188G	AAA>AGA	Missense	ORF1ab:nsp3	0.990574010271078
CAMB-777E1	MN908947.3	3037	C	T	1	1	0	0	0.998765241549622	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000848896434634975
CAMB-777E1	MN908947.3	6285	C	T	0.024	0.0046	6.4e-12	0.0011	0.0152552648055575	ACC	ORF1ab:nsp3	T1189I	C3566T	ACC>ATC	Missense	ORF1ab:nsp3	0.984704982061399
CAMB-777F0	MN908947.3	1605	ATG	-	1	1	0;0;0	7.7e-23;6.8e-23;6.5e-23	0.999392617972278	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000249182370347298
CAMB-7780C	MN908947.3	11074	C	INS	0.025	0.023	1.1e-05	0.00022	0.0243301347595826	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.975523045461696
CAMB-7780C	MN908947.3	11075	T	-	0.039	0.036	2.2e-09	3.2e-09	0.0375869859918662	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958535924084953
CAMB-7780C	MN908947.3	14408	C	T	1	1	0	0	0.998959101357505	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000329617903456651
CAMB-7780C	MN908947.3	1973	C	T	0.025	0.022	6e-13	1.1e-11	0.0239343845832804	ACT	ORF1ab:nsp2	L390L	C1168T	CTA>TTA	Synonymous	ORF1ab:nsp2	0.975702698288846
CAMB-7780C	MN908947.3	21005	C	T	0.83	0.84	0	0	0.833097436227362	GCA	ORF1ab:2'-O-ribose-methyltransferase	A116V	C347T	GCA>GTA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.166741724836748
CAMB-7780C	MN908947.3	23403	A	G	1	1	0	0	0.999384715483953	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00013437248051599
CAMB-7780C	MN908947.3	241	C	T	1	1	0	0	0.99839722362042	TCG	NA	NA	NA	NA	NA	NA	0.000185445200943121
CAMB-7780C	MN908947.3	25471	G	C	0.47	0.47	9.29999999999999e-266	1.3e-268	0.468689213085765	AGA	ORF3a	D27H	G79C	GAT>CAT	Missense	GU280_gp03	0.531156056587091
CAMB-7780C	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999358582773366	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7780C	MN908947.3	3037	C	T	1	1	0	0	0.999328959141068	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.45600954369222e-05
CAMB-7780C	MN908947.3	8062	A	G	0.025	0.032	2.7e-12	8.9e-16	0.0274633580031926	CAT	ORF1ab:nsp3	S1781S	A5343G	TCA>TCG	Synonymous	ORF1ab:nsp3	0.972500362792048
CAMB-7781B	MN908947.3	10186	C	T	0.073	0.07	4.2e-33	8.5e-32	0.0715026330868509	GCA	ORF1ab:3C-like-proteinase	C44C	C132T	TGC>TGT	Synonymous	ORF1ab:3C-like-proteinase	0.928401866353789
CAMB-7781B	MN908947.3	11074	C	INS	0.026	0.021	3.9e-05	0.00083	0.0240190722161518	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.974788914274362
CAMB-7781B	MN908947.3	11075	T	-	0.03	0.035	4.8e-08	1.4e-09	0.0319376554699323	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.96468766851636
CAMB-7781B	MN908947.3	11651	C	INS	0.044	0.027	1.3e-19	1e-12	0.0364985945186226	CCT	ORF1ab:nsp6	.	678-679-insfrshift	.	no-SNV	ORF1ab:nsp6	0.952565003513703
CAMB-7781B	MN908947.3	11651	C	T	0.014	0.0064	4.6e-08	6.7e-05	0.0108924806746311	CCT	ORF1ab:nsp6	L227F	C679T	CTC>TTC	Missense	ORF1ab:nsp6	0.952565003513703
CAMB-7781B	MN908947.3	11653	C	T	1	1	0	0	0.997021764032073	TCT	ORF1ab:nsp6	L227L	C681T	CTC>CTT	Synonymous	ORF1ab:nsp6	0.000183276059564719
CAMB-7781B	MN908947.3	14408	C	T	1	1	0	0	0.997352676444115	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.0003706252978239
CAMB-7781B	MN908947.3	23403	A	G	1	1	0	0	0.998982777018739	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.98094202826284e-05
CAMB-7781B	MN908947.3	241	C	T	1	1	0	0	0.998501007942935	TCG	NA	NA	NA	NA	NA	NA	0.000223987318871793
CAMB-7781B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998656205297152	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000145638137773678
CAMB-7781B	MN908947.3	29521	AA	TG	0.285	0.285	1.1e-135;1.1e-138	2.8e-135;1.2e-138	0.285312684947721	CAA	N	.	1248-1249-mnv	.	no-SNV	GU280_gp10	0.718096540941958
CAMB-7781B	MN908947.3	3037	C	T	1	1	0	0	0.999488870147461	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000127782463134759
CAMB-7781B	MN908947.3	9565	C	T	0.42	0.43	7.9e-232	7.9e-232	0.424863072931681	TCT	ORF1ab:nsp4	F337F	C1011T	TTC>TTT	Synonymous	ORF1ab:nsp4	0.572931680599596
CAMB-7782A	MN908947.3	11075	T	-	0.035	0.034	1.2e-08	1.2e-08	0.0343706978094533	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961808254586662
CAMB-7782A	MN908947.3	11083	G	T	0.033	0.035	3.5e-07	1e-07	0.0341304831061055	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.958163529934795
CAMB-7782A	MN908947.3	14408	C	T	1	1	0	0	0.997374774196816	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000455826988334206
CAMB-7782A	MN908947.3	23403	A	G	1	1	0	0	0.999730416979359	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.55742482641039e-05
CAMB-7782A	MN908947.3	241	C	T	1	1	0	0	0.999025997450759	TCG	NA	NA	NA	NA	NA	NA	6.01236141506938e-05
CAMB-7782A	MN908947.3	25690	G	T	1	1	0	0	0.99967337339953	TGG	ORF3a	G100C	G298T	GGC>TGC	Missense	GU280_gp03	0.00015242574688616
CAMB-7782A	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0310625	0.02765625	0.00012;0.00044;6.7e-05;6.7e-05;2.2e-05;3.9e-05;3.2e-05;5.1e-05;3.8e-05;4.9e-05;7.3e-05;3.3e-05;6.4e-05;4e-05;4.2e-05;4.5e-05;7.2e-05;3.8e-05;5.2e-05;3.9e-05;2.4e-05;6.4e-05;3.5e-05;1.2e-05;4.8e-05;6.5e-05;6.4e-05;3e-05;6.7e-05;2e-05;4.2e-05;3.4e-05	0.00014;0.00044;2e-04;2e-04;7.2e-05;0.00013;0.00012;2e-04;0.00013;0.00015;0.00023;0.00011;2e-04;0.00014;0.00014;0.00014;0.00022;0.00014;0.00017;0.00013;9.7e-05;0.00019;0.00012;7.6e-05;0.00013;0.00018;0.00016;0.00013;0.00023;0.00011;0.00017;0.00016	0.0294505536210708	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.971246955385255
CAMB-7782A	MN908947.3	3037	C	T	1	1	0	0	0.999109849396141	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000240581244286195
CAMB-7782A	MN908947.3	9752	A	C	0.029	0.032	9e-14	2.5e-15	0.0302989234014078	GAG	ORF1ab:nsp4	R400R	A1198C	AGA>CGA	Synonymous	ORF1ab:nsp4	0.969480843999085
CAMB-77839	MN908947.3	10440	C	T	0.0078	0.0083	3.3e-05	1.9e-05	0.00804259429829488	GCT	ORF1ab:3C-like-proteinase	A129V	C386T	GCT>GTT	Missense	ORF1ab:3C-like-proteinase	0.991934940354503
CAMB-77839	MN908947.3	10525	C	T	0.035	0.031	2.2e-16	7e-15	0.0331552162849873	TCT	ORF1ab:3C-like-proteinase	V157V	C471T	GTC>GTT	Synonymous	ORF1ab:3C-like-proteinase	0.965038167938931
CAMB-77839	MN908947.3	11074	C	INS	0.12	0.13	1.8e-60	3.5e-54	0.126678330214013	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.867767922532346
CAMB-77839	MN908947.3	11083	G	-	0.14	0.17	2.8e-62	2.4e-74	0.153818650558425	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.88180389721587e-05
CAMB-77839	MN908947.3	11083	G	T	0.86	0.83	0	0	0.846021396110311	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.88180389721587e-05
CAMB-77839	MN908947.3	11307	A	C	0.0086	0.0087	3.8e-05	1.8e-05	0.00864654543489421	GAC	ORF1ab:nsp6	D112A	A335C	GAC>GCC	Missense	ORF1ab:nsp6	0.991272393201654
CAMB-77839	MN908947.3	14805	C	T	1	1	0	0	0.999252249697032	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	5.15689864115721e-05
CAMB-77839	MN908947.3	16014	G	A	0.046	0.051	1.8e-21	8.3e-24	0.0480800478919011	GGT	ORF1ab:RNA-dependent-RNA-polymerase	R849R	G2547A	CGG>CGA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.951885743607286
CAMB-77839	MN908947.3	17247	T	C	1	1	0	0	0.999262805259278	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000485242107817064
CAMB-77839	MN908947.3	1762	C	T	0.029	0.029	5.2e-14	1.9e-14	0.0290935018454312	TCA	ORF1ab:nsp2	F319F	C957T	TTC>TTT	Synonymous	ORF1ab:nsp2	0.9708645565373
CAMB-77839	MN908947.3	23267	A	T	0.0059	0.0064	0.00012	4.6e-05	0.00609908850904746	CAT	S	I569F	A1705T	ATT>TTT	Missense	GU280_gp02, spike glycoprotein	0.992908484766732
CAMB-77839	MN908947.3	241	C	T	0.065	0.066	2.9e-27	7.9e-28	0.065296460231546	TCG	NA	NA	NA	NA	NA	NA	0.934666551592341
CAMB-77839	MN908947.3	25169	C	T	0.0092	0.0067	1.2e-05	0.00013	0.00809672657810194	ACT	S	L1203F	C3607T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.991881566380134
CAMB-77839	MN908947.3	25521	C	T	0.27	0.28	1.4e-129	1.6e-139	0.275667608336443	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.721763232237088
CAMB-77839	MN908947.3	2564	GAACAACCTACT	-	0.0628333333333333	0.04575	1e-21;5e-21;2.4e-21;5.2e-21;2.5e-21;7.2e-33;4.2e-33;1.7e-33;1.6e-33;6.2e-33;4.3e-33;1.1e-33	3e-16;8.3e-16;5.4e-16;9.3e-16;6e-16;2.2e-24;1.5e-24;1.1e-24;7.8e-25;1.9e-24;1.4e-24;4.4e-25	0.0646508431569488	AGA	ORF1ab:nsp2	.	1759-1770-delinframe	.	no-SNV	ORF1ab:nsp2	0.959395718573738
CAMB-77839	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-77839	MN908947.3	4148	G	T	0.065	0.062	1.3e-29	1.5e-28	0.0640961442163245	TGT	ORF1ab:nsp3	V477F	G1429T	GTT>TTT	Missense	ORF1ab:nsp3	0.935087816910551
CAMB-77839	MN908947.3	5541	A	T	0.064	0.075	6.6e-28	1.7e-32	0.0688421353943037	CAG	ORF1ab:nsp3	Q941L	A2822T	CAG>CTG	Missense	ORF1ab:nsp3	0.931086303134392
CAMB-77839	MN908947.3	8626	C	T	0.056	0.057	1.1e-25	1.6e-26	0.0563297778141049	TCT	ORF1ab:nsp4	F24F	C72T	TTC>TTT	Synonymous	ORF1ab:nsp4	0.943642976827823
CAMB-77839	MN908947.3	9634	A	T	0.0074	0.004	2.9e-05	0.00055	0.00589157004073958	TAG	ORF1ab:nsp4	L360F	A1080T	TTA>TTT	Missense	ORF1ab:nsp4	0.993508528450553
CAMB-77848	MN908947.3	11074	C	INS	0.023	0.016	3.7e-05	0.0094	0.0205864248795787	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.9785049194423
CAMB-77848	MN908947.3	11075	T	-	0.042	0.048	4e-10	9.2e-12	0.0442284112804344	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952355929234542
CAMB-77848	MN908947.3	11124	C	T	1	1	0	0	0.999834087620171	GCT	ORF1ab:nsp6	A51V	C152T	GCT>GTT	Missense	ORF1ab:nsp6	5.53041266095805e-05
CAMB-77848	MN908947.3	14408	C	T	1	1	0	0	0.998686522503088	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000556705694055427
CAMB-77848	MN908947.3	16111	C	T	0.051	0.044	1.5e-23	4.9e-21	0.0487445780583277	GCT	ORF1ab:RNA-dependent-RNA-polymerase	L882L	C2644T	CTA>TTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.951237789611031
CAMB-77848	MN908947.3	20030	C	T	1	1	0	0	1	GCC	ORF1ab:endoRNAse	A137V	C410T	GCC>GTC	Missense	ORF1ab:endoRNAse	0
CAMB-77848	MN908947.3	22793	G	A	0.0099	0.0061	2.7e-06	0.00011	0.00827428502655293	CGC	S	A411T	G1231A	GCT>ACT	Missense	GU280_gp02, spike glycoprotein	0.990808021543229
CAMB-77848	MN908947.3	23403	A	G	1	1	0	0	0.998721583013729	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.72708576510478e-05
CAMB-77848	MN908947.3	241	C	T	1	1	0	0	0.997539476187456	TCG	NA	NA	NA	NA	NA	NA	0.000164880461665293
CAMB-77848	MN908947.3	27393	C	T	0.0071	0.0079	6.9e-05	2.5e-05	0.00742026920736684	ACA	NA	NA	NA	NA	NA	NA	0.992572310523426
CAMB-77848	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999495608829812	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	9.61538461538462e-05
CAMB-77848	MN908947.3	3037	C	T	1	1	0	0	0.999340831376426	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.23960779466897e-05
CAMB-77848	MN908947.3	3877	T	G	0.033	0.026	1e-15	5.6e-13	0.0304705215419501	CTG	ORF1ab:nsp3	A386A	T1158G	GCT>GCG	Synonymous	ORF1ab:nsp3	0.969246031746032
CAMB-77848	MN908947.3	4839	T	C	0.012	0.0057	3.6e-07	1e-04	0.00961999353465093	ATA	ORF1ab:nsp3	I707T	T2120C	ATA>ACA	Missense	ORF1ab:nsp3	0.990212799161734
CAMB-77866	MN908947.3	1059	C	T	1	1	0	0	0.999560375146542	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.000188410651482164
CAMB-77866	MN908947.3	11075	T	-	0.029	0.033	8.8e-08	4e-09	0.030523378709732	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.965265916969646
CAMB-77866	MN908947.3	14408	C	T	1	1	0	0	0.998765956317508	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000451155754889732
CAMB-77866	MN908947.3	23403	A	G	1	1	0	0	0.999569244023261	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.4766314882619e-05
CAMB-77866	MN908947.3	241	C	T	1	1	0	0	0.999119351652406	TCG	NA	NA	NA	NA	NA	NA	7.14039200752121e-05
CAMB-77866	MN908947.3	24368	G	T	1	1	0	0	0.999606283711957	AGA	S	D936Y	G2806T	GAC>TAC	Missense	GU280_gp02, spike glycoprotein	7.87432576085673e-05
CAMB-77866	MN908947.3	25463	C	A	1	1	0	0	0.999731639681546	ACT	ORF3a	T24N	C71A	ACT>AAT	Missense	GU280_gp03	0.000143125503175597
CAMB-77866	MN908947.3	25563	G	T	1	1	0	0	0.999679692504805	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000106769165065129
CAMB-77866	MN908947.3	26446	T	C	0.17	0.17	9.2e-78	2.1e-79	0.170354485492413	TTC	E	S68P	T202C	TCT>CCT	Missense	GU280_gp04	0.82867076063294
CAMB-77866	MN908947.3	27998	C	T	0.026	0.022	1.8e-12	8.5e-11	0.0247236478484011	ACC	ORF8	D35D	C105T	GAC>GAT	Synonymous	GU280_gp09	0.9750789577576
CAMB-77866	MN908947.3	3037	C	T	1	1	0	0	0.999438908340066	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000112218331986713
CAMB-77866	MN908947.3	5554	G	T	1	1	0	0	0.999419560801006	AGG	ORF1ab:nsp3	K945N	G2835T	AAG>AAT	Missense	ORF1ab:nsp3	0.000241849666247461
CAMB-77875	MN908947.3	1060	C	T	0.015	0.0055	2.8e-08	0.00022	0.0118044891184637	CCT	ORF1ab:nsp2	T85T	C255T	ACC>ACT	Synonymous	ORF1ab:nsp2	0.988164487257046
CAMB-77875	MN908947.3	11075	T	-	0.031	0.025	5.4e-08	3.3e-07	0.0293847676040388	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956787106464649
CAMB-77875	MN908947.3	12506	AA	-	0.009	0.005	0.00051;9.2e-06	0.019;0.00041	0.00770923074078867	TAA	ORF1ab:nsp8	.	415-416-delfrshift	.	no-SNV	ORF1ab:nsp8	0.992186046511628
CAMB-77875	MN908947.3	13202	G	T	0.01	0.011	3e-06	1.3e-06	0.0103260810116059	GGA	ORF1ab:nsp10	E60*	G178T	GAA>TAA	Nonsense	ORF1ab:nsp10	0.989564532537
CAMB-77875	MN908947.3	14087	G	C	0.0084	0.005	5.5e-06	0.00011	0.00693793103448276	TGG	ORF1ab:RNA-dependent-RNA-polymerase	W207S	G620C	TGG>TCG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.989420689655172
CAMB-77875	MN908947.3	14129	G	C	0.0051	0.0065	0.00012	2.5e-05	0.00573273223131296	GGA	ORF1ab:RNA-dependent-RNA-polymerase	G221A	G662C	GGA>GCA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994211610174208
CAMB-77875	MN908947.3	14408	C	T	1	0.99	0	0	0.997289231534444	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000410345685152947
CAMB-77875	MN908947.3	15911	A	G	1	0.99	0	0	0.998096032085802	GAT	ORF1ab:RNA-dependent-RNA-polymerase	D815G	A2444G	GAT>GGT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	1.12660823325297e-05
CAMB-77875	MN908947.3	19178	G	T	0.0068	0.0056	3.9e-05	9.5e-05	0.00627943485086342	GGT	ORF1ab:3'-to-5'-exonuclease	G380V	G1139T	GGT>GTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.993691221995628
CAMB-77875	MN908947.3	21776	G	A	0.0054	0.021	0.00012	7.9e-11	0.0114851199075412	TGG	S	G72R	G214A	GGG>AGG	Missense	GU280_gp02, spike glycoprotein	0.983603004911875
CAMB-77875	MN908947.3	21914	C	T	0.0063	0.01	9.9e-05	2.9e-06	0.00779594308204662	ACT	S	L118F	C352T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.992204056917953
CAMB-77875	MN908947.3	21982	TTTGGGTGT	-	0.0442222222222222	0.0468888888888889	2.2e-08;1.2e-07;1e-07;1.3e-08;1.4e-07;2.5e-07;1.7e-07;6.5e-08;8.1e-08	9.7e-09;5.4e-08;4.6e-08;5.1e-09;5.7e-08;1.2e-07;7.6e-08;2.7e-08;1.8e-08	0.0450508988520684	TTT	S	.	420-428-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.954535519125683
CAMB-77875	MN908947.3	23029	C	T	0.041	0.016	6.1e-19	8e-09	0.0281807262311744	ACT	S	Y489Y	C1467T	TAC>TAT	Synonymous	GU280_gp02, spike glycoprotein	0.971819273768826
CAMB-77875	MN908947.3	23403	A	G	1	1	0	0	0.999938273237921	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.29086532102325e-05
CAMB-77875	MN908947.3	241	C	T	1	1	0	0	0.99981224183252	TCG	NA	NA	NA	NA	NA	NA	0.000136551394531117
CAMB-77875	MN908947.3	24153	T	C	0.025	0.069	1.6e-12	9e-31	0.0391908403855727	TTG	S	L864S	T2591C	TTG>TCG	Missense	GU280_gp02, spike glycoprotein	0.958591664026791
CAMB-77875	MN908947.3	24169	G	T	0.0042	0.007	7e-04	3.8e-05	0.00511088396071286	TGA	S	M869I	G2607T	ATG>ATT	Missense	GU280_gp02, spike glycoprotein	0.99480023110084
CAMB-77875	MN908947.3	25244	G	T	0.013	0.019	2.6e-07	7e-10	0.0145050812553163	AGT	S	V1228L	G3682T	GTA>TTA	Missense	GU280_gp02, spike glycoprotein	0.985494918744684
CAMB-77875	MN908947.3	25459	G	T	0.0089	0.0065	1.4e-05	0.00012	0.00814353813559322	TGC	ORF3a	A23S	G67T	GCT>TCT	Missense	GU280_gp03	0.991790254237288
CAMB-77875	MN908947.3	25782	C	T	1	1	0	0	0.99991811333115	GCT	ORF3a	C130C	C390T	TGC>TGT	Synonymous	GU280_gp03	8.18866688503112e-05
CAMB-77875	MN908947.3	26530	A	G	1	1	0	0	0.999916569330886	GAT	M	D3G	A8G	GAT>GGT	Missense	GU280_gp05	8.34306691139663e-05
CAMB-77875	MN908947.3	28739	G	T	1	1	0	0	0.999745581600461	TGC	N	A156S	G466T	GCA>TCA	Missense	GU280_gp10	1.69612266359103e-05
CAMB-77875	MN908947.3	3037	C	T	1	1	0	0	0.999707709170625	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.30727073438071e-05
CAMB-77875	MN908947.3	4559	G	A	0.11	0.074	2.4e-51	6.3e-34	0.098630330415137	AGC	ORF1ab:nsp3	A614T	G1840A	GCG>ACG	Missense	ORF1ab:nsp3	0.90129906805987
CAMB-77875	MN908947.3	5869	CA	-	0.00725	0.00235	3e-05;9.3e-05	NA;0.00073	0.00532785747981241	ACA	ORF1ab:nsp3	.	3150-3151-delfrshift	.	no-SNV	ORF1ab:nsp3	0.995247568523431
CAMB-77875	MN908947.3	686	AAGTCATTT	-	1	1	0;0;0;0;0;0;0;0;0	0;0;0;0;0;0;0;0;0	0.999962695754031	AAA	ORF1ab:leader-protein	.	421-429-delinframe	.	no-SNV	ORF1ab:leader-protein	6.71476427446972e-05
CAMB-77875	MN908947.3	7165	C	T	0.0086	0.02	0.0016	9e-06	0.0144329896907217	CCT	ORF1ab:nsp3	T1482T	C4446T	ACC>ACT	Synonymous	ORF1ab:nsp3	0.985567010309278
CAMB-77875	MN908947.3	7768	C	T	0.016	0.017	1.4e-08	1.1e-08	0.0162180425723618	TCC	ORF1ab:nsp3	I1683I	C5049T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.983781957427638
CAMB-77875	MN908947.3	9165	C	T	0.025	0.032	2.7e-12	2.2e-15	0.0274809499477929	ACC	ORF1ab:nsp4	T204I	C611T	ACC>ATC	Missense	ORF1ab:nsp4	0.972474618443561
CAMB-77875	MN908947.3	9180	C	T	0.046	0.057	2.6e-21	2.7e-26	0.0507563416336979	TCT	ORF1ab:nsp4	S209F	C626T	TCT>TTT	Missense	ORF1ab:nsp4	0.949220386316034
CAMB-77875	MN908947.3	934	C	T	0.031	0.029	1.7e-15	8.6e-15	0.0305839652237525	ACA	ORF1ab:nsp2	D43D	C129T	GAC>GAT	Synonymous	ORF1ab:nsp2	0.969401966714967
CAMB-77875	MN908947.3	9438	C	T	0.091	0.064	2.1e-40	2e-27	0.083497828661666	ACA	ORF1ab:nsp4	T295I	C884T	ACA>ATA	Missense	ORF1ab:nsp4	0.916436373207001
CAMB-77875	MN908947.3	9474	C	T	0.044	0.016	1.5e-20	6.7e-09	0.0364905809511263	GCT	ORF1ab:nsp4	A307V	C920T	GCT>GTT	Missense	ORF1ab:nsp4	0.963509419048874
CAMB-77875	MN908947.3	9479	G	A	0.0045	0.0073	3e-04	1.6e-05	0.0052661633145105	TGG	ORF1ab:nsp4	G309S	G925A	GGT>AGT	Missense	ORF1ab:nsp4	0.981282913520716
CAMB-77875	MN908947.3	9479	G	T	0.016	0.0059	7.6e-09	2e-04	0.0134509231647738	TGG	ORF1ab:nsp4	G309C	G925T	GGT>TGT	Missense	ORF1ab:nsp4	0.981282913520716
CAMB-77875	MN908947.3	9491	C	T	0.041	0.049	6.7e-19	2e-21	0.0430100422832981	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.956857822410148
CAMB-77875	MN908947.3	9737	A	G	0.0059	0.011	0.00013	6.3e-07	0.00802480189819582	TAG	ORF1ab:nsp4	S395G	A1183G	AGT>GGT	Missense	ORF1ab:nsp4	0.991941621524824
CAMB-77875	MN908947.3	9924	C	T	0.0059	0.011	1e-04	4.3e-07	0.00816938173732296	GCA	ORF1ab:nsp4	A457V	C1370T	GCA>GTA	Missense	ORF1ab:nsp4	0.991830618262677
CAMB-77893	MN908947.3	1059	C	T	0.25	0.3	2.9e-119	1.2e-149	0.269432670193785	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.730567329806215
CAMB-77893	MN908947.3	11074	C	INS	0.033	0.042	3.2e-08	1.1e-09	0.0360225426482535	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.963913992688871
CAMB-77893	MN908947.3	12781	C	T	0.017	0.0075	3.8e-09	4.5e-05	0.0135385385385385	ACA	ORF1ab:nsp9	Y32Y	C96T	TAC>TAT	Synonymous	ORF1ab:nsp9	0.986461461461461
CAMB-77893	MN908947.3	13006	T	C	0.52	0.51	6.1e-307	2.7e-297	0.517734157611775	CTG	ORF1ab:nsp9	A107A	T321C	GCT>GCC	Synonymous	ORF1ab:nsp9	0.482240660765773
CAMB-77893	MN908947.3	13408	TA	CT	0.0026325	0.0145	NA;0.00012	1.1e-07;3.2e-08	0.00408626560726447	GTA	ORF1ab:nsp10	.	384-385-mnv	.	no-SNV	ORF1ab:nsp10	0.998138957816377
CAMB-77893	MN908947.3	1437	C	T	0.28	0.3	6.6e-125	3e-121	0.290136411332634	TCT	ORF1ab:nsp2	S211F	C632T	TCT>TTT	Missense	ORF1ab:nsp2	0.709863588667366
CAMB-77893	MN908947.3	1440	G	A	0.7	0.68	0	0	0.691358024691358	GGC	ORF1ab:nsp2	G212D	G635A	GGC>GAC	Missense	ORF1ab:nsp2	0.308641975308642
CAMB-77893	MN908947.3	14408	C	T	0.6	0.47	0	8e-260	0.550796714982168	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.449017875644843
CAMB-77893	MN908947.3	16438	A	G	0.0082	0.0067	2.5e-05	0.00015	0.00775267088966626	TAT	ORF1ab:helicase	M68V	A202G	ATG>GTG	Missense	ORF1ab:helicase	0.992152784343387
CAMB-77893	MN908947.3	16466	C	T	0.028	0.0067	1.1e-08	0.0027	0.0216880534971986	CCA	ORF1ab:helicase	P77L	C230T	CCA>CTA	Missense	ORF1ab:helicase	0.978311946502801
CAMB-77893	MN908947.3	17456	C	T	0.012	0.012	4.5e-07	3.1e-07	0.0121701669359181	GCA	ORF1ab:helicase	A407V	C1220T	GCA>GTA	Missense	ORF1ab:helicase	0.987793932866631
CAMB-77893	MN908947.3	21741	CCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGA	-	0.0109230769230769	0.0317948717948718	0.0082;0.0093;0.011;0.0098;0.012;0.014;0.011;0.012;0.012;0.013;0.012;0.0095;0.011;0.01;0.011;0.011;0.0099;0.0099;0.01;0.0097;0.01;0.0098;0.01;0.0084;0.011;0.0094;0.011;0.012;0.011;0.0087;0.0086;0.008;0.0089;0.011;0.0096;0.0087;0.01;0.01;0.0098	1.3e-06;2.5e-06;3.5e-06;2.4e-06;7.2e-06;1e-05;3.6e-06;5.6e-06;4.3e-06;8.4e-06;4.6e-06;2.8e-06;3.8e-06;3.9e-06;4.2e-06;4.5e-06;4e-06;3.5e-06;3.9e-06;2.5e-06;3.7e-06;3.5e-06;1.6e-06;7.2e-07;5.3e-06;1.8e-06;4.2e-06;5e-06;3.5e-06;2.4e-06;1.5e-06;1.4e-06;3.1e-06;4e-06;2.7e-06;1.7e-06;3.5e-06;3.8e-06;4e-06	0.0198207297058452	TCC	S	.	179-217-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.97999493542669
CAMB-77893	MN908947.3	22661	G	T	0.026	0.019	7.3e-13	7.2e-10	0.0232642927828608	TGT	S	V367F	G1099T	GTC>TTC	Missense	GU280_gp02, spike glycoprotein	0.976648900154517
CAMB-77893	MN908947.3	23403	A	G	0.58	0.62	8.4e-284	5.89999999998452e-313	0.595244426127072	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.404742279006076
CAMB-77893	MN908947.3	241	C	T	0.24	0.23	5.2e-115	4.9e-107	0.240378594480035	TCG	NA	NA	NA	NA	NA	NA	0.759609363710804
CAMB-77893	MN908947.3	25552	G	A	0.42	0.4	4.1e-229	4.9e-214	0.411668784011832	TGC	ORF3a	A54T	G160A	GCT>ACT	Missense	GU280_gp03	0.588312254688181
CAMB-77893	MN908947.3	25563	G	T	0.43	0.4	7.3e-232	8.49999999999999e-216	0.417766807188817	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.582196213297833
CAMB-77893	MN908947.3	25688	C	T	0.55	0.53	4.94065645841247e-324	3.7e-286	0.545431705887279	GCT	ORF3a	A99V	C296T	GCT>GTT	Missense	GU280_gp03	0.454568294112721
CAMB-77893	MN908947.3	27486	A	-	0.0039	0.0086	0.0011	7.1e-06	0.00553994801375798	TAA	ORF7a	.	93-93-delfrshift	.	no-SNV	GU280_gp07	0.994433796308452
CAMB-77893	MN908947.3	2891	G	A	0.71	0.71	0	0	0.712483795241933	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	0.287481167443327
CAMB-77893	MN908947.3	3037	C	T	0.28	0.28	1.1e-54	7.4e-54	0.283280392723072	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.716472092735448
CAMB-77893	MN908947.3	9502	C	T	0.0089	0.023	0.00027	3.1e-09	0.0120203789205541	CCT	ORF1ab:nsp4	A316A	C948T	GCC>GCT	Synonymous	ORF1ab:nsp4	0.987900015921032
CAMB-778A2	MN908947.3	11074	C	INS	0.022	0.047	0.00012	2.6e-11	0.0304194192656322	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.969426947303733
CAMB-778A2	MN908947.3	11083	G	-	0.47	0.038	5.7e-240	9.8e-15	0.319709702062643	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-778A2	MN908947.3	11083	G	T	0.53	0.96	3.2e-152	0	0.680290297937357	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-778A2	MN908947.3	14805	C	T	1	1	0	0	1	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-778A2	MN908947.3	17247	T	C	1	1	0	0	0.99993082217841	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	6.91778215903981e-05
CAMB-778A2	MN908947.3	22845	ATTTTACAGGCTGCGTT	-	0.00588235294117647	0.120588235294118	NA;9.6e-34;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	2.6e-37;1.7e-39;2.1e-30;3.8e-27;1.1e-26;1.4e-27;6.8e-29;2.8e-28;2.3e-29;1.1e-26;1.6e-27;5.6e-27;5.1e-29;2.1e-26;6e-29;1.3e-29;4.1e-29	0.0484401943878351	GAT	S	.	1283-1299-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.950756972111554
CAMB-778A2	MN908947.3	6120	C	T	1	1	2.3e-147	5.4e-38	1	TCA	ORF1ab:nsp3	S1134L	C3401T	TCA>TTA	Missense	ORF1ab:nsp3	0
CAMB-778A2	MN908947.3	9223	C	T	1	1	0	0	1	ACG	ORF1ab:nsp4	H223H	C669T	CAC>CAT	Synonymous	ORF1ab:nsp4	0
CAMB-778B1	MN908947.3	11074	C	INS	0.028	0.025	3.8e-06	2.8e-05	0.02634996439194	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.971963889237987
CAMB-778B1	MN908947.3	11075	T	-	0.043	0.039	1.4e-10	1.3e-09	0.0410282477670467	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953834144216106
CAMB-778B1	MN908947.3	1191	C	T	0.036	0.038	8.7e-17	1.3e-17	0.0366248000272303	CCA	ORF1ab:nsp2	P129L	C386T	CCA>CTA	Missense	ORF1ab:nsp2	0.963068858708601
CAMB-778B1	MN908947.3	14408	C	T	1	1	0	0	0.997532268790411	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000681029716932001
CAMB-778B1	MN908947.3	17518	C	T	0.023	0.017	1.3e-10	3.2e-08	0.0199166236398753	ACT	ORF1ab:helicase	L428F	C1282T	CTT>TTT	Missense	ORF1ab:helicase	0.979949515231484
CAMB-778B1	MN908947.3	18021	G	A	0.26	0.26	1.2e-125	3e-126	0.259005457853244	GGA	ORF1ab:helicase	R595R	G1785A	AGG>AGA	Synonymous	ORF1ab:helicase	0.739787750151607
CAMB-778B1	MN908947.3	18029	C	T	1	1	0	0	0.998996366362554	GCA	ORF1ab:helicase	A598V	C1793T	GCA>GTA	Missense	ORF1ab:helicase	0.000259977388013229
CAMB-778B1	MN908947.3	20268	A	G	1	1	0	7.1e-231	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-778B1	MN908947.3	23403	A	G	1	1	0	0	0.999554309539214	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.90741140104953e-05
CAMB-778B1	MN908947.3	241	C	T	1	1	0	0	0.997423938391453	TCG	NA	NA	NA	NA	NA	NA	0.000149140408915885
CAMB-778B1	MN908947.3	26176	C	T	0.013	0.016	2.4e-07	3.5e-08	0.0145761532867487	ACC	ORF3a	P262S	C784T	CCA>TCA	Missense	GU280_gp03	0.985265753944415
CAMB-778B1	MN908947.3	29734	G	C	1	1	0	0	0.99762537993921	CGA	NA	NA	NA	NA	NA	NA	0
CAMB-778B1	MN908947.3	3037	C	T	1	1	0	0	0.999615169325497	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.49846067730199e-05
CAMB-778B1	MN908947.3	3569	A	G	1	1	0	0	0.998817407757805	TAG	ORF1ab:nsp3	S284G	A850G	AGT>GGT	Missense	ORF1ab:nsp3	0.000236518448438978
CAMB-778B1	MN908947.3	5386	T	C	0.019	0.016	1.6e-09	1.6e-08	0.017452278924815	CTG	ORF1ab:nsp3	A889A	T2667C	GCT>GCC	Synonymous	ORF1ab:nsp3	0.981456953642384
CAMB-778B1	MN908947.3	9508	T	C	0.026	0.025	5.7e-13	1e-12	0.0257302869487625	ATA	ORF1ab:nsp4	N318N	T954C	AAT>AAC	Synonymous	ORF1ab:nsp4	0.974246231155779
CAMB-778C0	MN908947.3	14408	C	T	1	1	0	6e-35	0.997650195440475	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000429291217605459
CAMB-778C0	MN908947.3	241	C	T	1	1	0	6.7e-16	0.999250509653436	TCG	NA	NA	NA	NA	NA	NA	0.000179877683175441
CAMB-778C0	MN908947.3	25563	G	T	1	1	0	6.5e-23	0.999669947191551	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000180028804608737
CAMB-778C0	MN908947.3	3037	C	T	1	1	0	2e-21	0.999253285543608	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000149342891278375
CAMB-778C0	MN908947.3	4900	C	T	1	1	0	9.5e-12	0.999712056960369	ACC	ORF1ab:nsp3	H727H	C2181T	CAC>CAT	Synonymous	ORF1ab:nsp3	0.00013088319983247
CAMB-778DF	MN908947.3	11074	C	INS	0.033	0.047	5.5e-07	7.7e-11	0.0391856500469437	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.960468448880763
CAMB-778DF	MN908947.3	11083	G	-	0.33	0.034	2.1e-159	1.5e-14	0.192583425791585	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-778DF	MN908947.3	11083	G	T	0.67	0.97	6.8e-231	0	0.807288555090894	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-778DF	MN908947.3	11981	G	A	1	1	0	0	0.999766622820045	TGA	ORF1ab:nsp7	E47K	G139A	GAA>AAA	Missense	ORF1ab:nsp7	6.36483218059151e-05
CAMB-778DF	MN908947.3	14198	C	T	1	1	0	0	0.99979913628603	GCA	ORF1ab:RNA-dependent-RNA-polymerase	A244V	C731T	GCA>GTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000200863713970071
CAMB-778DF	MN908947.3	14805	C	T	1	1	0	0	0.999854953343325	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	9.66977711163758e-05
CAMB-778DF	MN908947.3	22846	T	-	0.031	0.019	5.7e-11	6.5e-07	0.0265459088069956	ATT	S	.	1284-1284-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.973454091193004
CAMB-778DF	MN908947.3	22846	TTTTACAGGCTGCG	-	0.00221428571428571	0.0189285714285714	5.7e-11;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	6.5e-07;6.7e-06;2.1e-05;2.9e-05;2.5e-05;1.4e-05;1.6e-05;1.3e-05;3.1e-05;2.7e-05;2.9e-05;1.6e-05;3.1e-05;1.7e-05	0.00678105414568992	ATT	S	.	1284-1297-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.973454091193004
CAMB-778DF	MN908947.3	23127	C	T	1	1	0	0	1	GCA	S	A522V	C1565T	GCA>GTA	Missense	GU280_gp02, spike glycoprotein	0
CAMB-778DF	MN908947.3	241	C	T	1	1	0	0	0.999726850587271	TCG	NA	NA	NA	NA	NA	NA	0.000204862059546572
CAMB-778DF	MN908947.3	2480	A	G	1	1	0	2.49999999999863e-312	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-778DF	MN908947.3	25317	C	T	1	1	0	0	0.999940522214953	TCC	S	S1252F	C3755T	TCC>TTC	Missense	GU280_gp02, spike glycoprotein	5.94777850472848e-05
CAMB-778DF	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-778DF	MN908947.3	28628	G	T	0.053	0.42	6.1e-23	1.1e-198	0.249147769378983	AGC	N	A119S	G355T	GCT>TCT	Missense	GU280_gp10	0.750852230621017
CAMB-778EE	MN908947.3	11075	T	-	0.022	0.045	6.8e-06	1.1e-10	0.0345427547209431	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961902476339038
CAMB-778EE	MN908947.3	12889	A	G	0.0061	0.0089	1e-04	1.2e-05	0.0077533375460135	AAC	ORF1ab:nsp9	E68E	A204G	GAA>GAG	Synonymous	ORF1ab:nsp9	0.992086179399994
CAMB-778EE	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999477584740615	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000121499301379017
CAMB-778EE	MN908947.3	17898	C	T	1	1	0	0	0.999926469043467	ACT	ORF1ab:helicase	H554H	C1662T	CAC>CAT	Synonymous	ORF1ab:helicase	4.20176894472573e-05
CAMB-778EE	MN908947.3	20611	C	T	0.019	0.03	1e-09	2.6e-14	0.0250660708933875	GCT	ORF1ab:endoRNAse	L331F	C991T	CTT>TTT	Missense	ORF1ab:endoRNAse	0.974824946189685
CAMB-778EE	MN908947.3	25870	T	C	0.047	0.02	8.6e-22	3.3e-10	0.0315552983626647	TTA	ORF3a	Y160H	T478C	TAC>CAC	Missense	GU280_gp03	0.968410661401777
CAMB-778EE	MN908947.3	26137	A	C	0.016	0.023	0.0027	4.2e-05	0.0189266890273119	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.98083373263057
CAMB-778EE	MN908947.3	27046	C	T	1	1	0	0	0.999940405244338	ACG	M	T175M	C524T	ACG>ATG	Missense	GU280_gp05	2.97973778307509e-05
CAMB-778EE	MN908947.3	27595	C	T	0.99	1	1.1e-232	6.7e-261	0.995475113122172	TCC	ORF7a	P68S	C202T	CCT>TCT	Missense	GU280_gp07	0
CAMB-778EE	MN908947.3	28524	T	C	0.011	0.0087	3.5e-06	2e-05	0.0095856524427953	ATT	N	I84T	T251C	ATT>ACT	Missense	GU280_gp10	0.99037999037999
CAMB-778EE	MN908947.3	952	C	T	0.0064	0.0098	9e-05	3.5e-06	0.0082022752398274	ACT	ORF1ab:nsp2	Y49Y	C147T	TAC>TAT	Synonymous	ORF1ab:nsp2	0.991744231660782
CAMB-778FD	MN908947.3	11074	C	INS	0.027	0.034	2.1e-05	2.3e-07	0.030110635076309	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.969596861611521
CAMB-778FD	MN908947.3	14408	C	T	1	1	0	0	0.999725964832153	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000228362639872117
CAMB-778FD	MN908947.3	14593	GGTAATCTATTACTAGATA	-	0.00285457894736842	0.0195789473684211	NA;NA;NA;NA;NA;1.3e-13;1e-13;NA;NA;0.47;NA;NA;NA;NA;NA;NA;NA;NA;NA	1.5e-10;1.2e-10;1.8e-10;1.2e-10;9.7e-11;1.6e-10;1.2e-10;2.3e-07;8.2e-08;3.1e-10;2e-07;3.7e-08;1.1e-07;7.1e-09;2e-07;2.1e-07;6e-08;8.5e-11;1.1e-10	0.00803117520226297	TGG	ORF1ab:RNA-dependent-RNA-polymerase	.	1126-1144-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.992064262015173
CAMB-778FD	MN908947.3	17169	TG	CT	0.009	0.00695	2.5e-06;4.2e-06	1.6e-05;2.6e-05	0.00826386019492988	ATG	ORF1ab:helicase	.	933-934-mnv	.	no-SNV	ORF1ab:helicase	0.99143916581639
CAMB-778FD	MN908947.3	17919	TA	-	0.0315	0.00945	1.1e-12;1.8e-13	4.6e-05;2.7e-05	0.0222361185190635	TTA	ORF1ab:helicase	.	1683-1684-delfrshift	.	no-SNV	ORF1ab:helicase	0.97730679859081
CAMB-778FD	MN908947.3	18353	TACCTTTACAGCTAGGTTTTTCTACA	-	0.00762865384615385	0.0366538461538462	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;2.3e-07;2.5e-07;2.5e-07;3e-07;2.3e-07;2.1e-07	3.9e-06;4e-06;8.7e-06;8.8e-06;1.6e-10;6.8e-10;3.7e-08;8.6e-09;8.5e-09;8.2e-10;1.2e-09;3.2e-08;3.2e-08;1.2e-11;8.5e-09;2.9e-08;6.5e-11;2.7e-09;6.1e-10;2.3e-08;7.2e-08;9.6e-08;8.9e-08;1.1e-07;8.5e-08;7e-08	0.0101661438364122	TTA	ORF1ab:3'-to-5'-exonuclease	.	314-339-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.989765580331618
CAMB-778FD	MN908947.3	18740	ATTACGTCTATA	-	0.0373555833333333	0.0265833333333333	NA;0.5;8e-09;1.1e-08;5.5e-10;2.8e-09;7.6e-10;8.9e-10;5.1e-11;1.7e-11;NA;0.45	5.6e-05;7.6e-06;6e-05;8.6e-05;1.9e-05;4.1e-05;1.6e-05;2.1e-05;5.9e-06;4.5e-06;1e-09;4.3e-12	0.043320494326547	GAT	ORF1ab:3'-to-5'-exonuclease	.	701-712-delinframe	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.988863816194356
CAMB-778FD	MN908947.3	23403	A	G	1	1	0	0	0.999842292341473	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.06567917409712e-05
CAMB-778FD	MN908947.3	23561	GGTGCAGGTATATGCGCTAGTTA	-	0.0151739130434783	0.0336086956521739	4.3e-05;9e-05;1e-04;9.7e-05;8.4e-05;8.5e-05;4.9e-05;4.3e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00055;9e-04;0.00098;0.00096;0.00092;0.00097;0.00061;0.00058;0.00029;9.6e-05;0.00034;2e-04;0.00028;0.00015;0.00032;0.00057;0.00037;0.00037;1.8e-05;2.7e-05;0.00045;0.00037;5e-06	0.0165354330708661	TGG	S	.	1999-2021-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.96182783801726
CAMB-778FD	MN908947.3	241	C	T	1	1	0	0	0.999952414941708	TCG	NA	NA	NA	NA	NA	NA	4.75850582916964e-05
CAMB-778FD	MN908947.3	24137	ACTG	-	0.24	0.19	5.1e-37;3.4e-33;4.8e-30;1.3e-36	9.4e-29;9.9e-26;1.3e-23;1.4e-28	0.217858314201377	TAC	S	.	2575-2578-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.780889621087315
CAMB-778FD	MN908947.3	27870	G	A	0.0084	0.012	8.8e-05	5.7e-06	0.0100671140939597	TGA	NA	NA	NA	NA	NA	NA	0.98993288590604
CAMB-778FD	MN908947.3	3037	C	T	1	1	0	0	0.999573014517506	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-778FD	MN908947.3	3405	A	-	0.0099	0.011	2.3e-06	6.5e-07	0.0103010301030103	GAA	ORF1ab:nsp3	.	686-686-delfrshift	.	no-SNV	ORF1ab:nsp3	0.98956562322899
CAMB-778FD	MN908947.3	3405	AA	-	0.00995	0.0055	2.3e-06;2.1e-06	6.5e-07;NA	0.00842658756909802	GAA	ORF1ab:nsp3	.	686-687-delfrshift	.	no-SNV	ORF1ab:nsp3	0.98956562322899
CAMB-778FD	MN908947.3	514	T	-	0.13	0.12	6.5e-05	4.6e-05	0.126539278131635	ATG	ORF1ab:leader-protein	.	249-249-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.870382165605096
CAMB-778FD	MN908947.3	521	GTT	-	0.17	0.041	0.00023;3.4e-25;5.4e-27	0.022;8.3e-06;6.2e-06	0.149265785609398	GGT	ORF1ab:leader-protein	.	256-258-delinframe	.	no-SNV	ORF1ab:leader-protein	0.86849925705795
CAMB-778FD	MN908947.3	684	TAAAGTCATTT	-	0.0327272727272727	0.00364536363636364	0.00068;2e-04;9.2e-06;8.7e-06;0.00015;3.9e-05;0.00016;7.1e-05;1e-05;9.6e-05;0.00025	0.00041;0.00011;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0254743805489468	CTA	ORF1ab:leader-protein	.	419-429-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.980752788280671
CAMB-778FD	MN908947.3	9624	TTTCTT	-	0.00419233333333333	0.0163333333333333	NA;NA;NA;0.46;1.5e-10;NA	1.4e-07;3.8e-08;2e-08;3.5e-09;9.9e-07;1.6e-08	0.00724938139503778	GTT	ORF1ab:nsp4	.	1070-1075-delinframe	.	no-SNV	ORF1ab:nsp4	0.992877529839128
CAMB-77909	MN908947.3	1030	T	C	1	1	0	0	0.999451058427969	TTG	ORF1ab:nsp2	F75F	T225C	TTT>TTC	Synonymous	ORF1ab:nsp2	0.000257316361889731
CAMB-77909	MN908947.3	11074	C	INS	0.11	0.1	1.7e-37	1.1e-34	0.105845629965948	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.889383513053349
CAMB-77909	MN908947.3	11083	G	-	0.15	0.16	4.6e-65	9.7e-71	0.153364084619055	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.59058374423413e-05
CAMB-77909	MN908947.3	11083	G	T	0.85	0.84	0	0	0.846508668681406	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.59058374423413e-05
CAMB-77909	MN908947.3	14242	T	C	0.0075	0.0073	2.4e-05	3.1e-05	0.00738438771735109	GTG	ORF1ab:RNA-dependent-RNA-polymerase	W259R	T775C	TGG>CGG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.992487359723764
CAMB-77909	MN908947.3	14805	C	T	1	1	0	0	0.999477901162674	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000170686158356594
CAMB-77909	MN908947.3	17247	T	C	1	1	0	0	0.999522863705463	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000199731472131912
CAMB-77909	MN908947.3	26144	G	T	1	1	0	0	0.99976403964134	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000101125867997034
CAMB-77909	MN908947.3	5114	A	G	0.013	0.013	8.9e-07	5.3e-07	0.0128979840552481	AAC	ORF1ab:nsp3	T799A	A2395G	ACA>GCA	Missense	ORF1ab:nsp3	0.986898898085614
CAMB-77909	MN908947.3	7849	A	G	0.01	0.012	3.3e-06	6.8e-07	0.0106046772947538	GAG	ORF1ab:nsp3	R1710R	A5130G	AGA>AGG	Synonymous	ORF1ab:nsp3	0.989395322705246
CAMB-77918	MN908947.3	11075	T	-	0.04	0.04	1.1e-09	8.8e-10	0.0398993157613847	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95455667869461
CAMB-77918	MN908947.3	13335	C	T	1	1	0	0	0.999656493394965	GCT	ORF1ab:nsp10	A104V	C311T	GCT>GTT	Missense	ORF1ab:nsp10	5.22727442443975e-05
CAMB-77918	MN908947.3	14408	C	T	1	1	0	0	0.99902550874176	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000229292060762396
CAMB-77918	MN908947.3	21974	G	T	0.71	0.68	0	0	0.692587012786341	TGA	S	D138Y	G412T	GAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.306910804650983
CAMB-77918	MN908947.3	23403	A	G	1	1	0	0	0.999446613969224	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.80386867143333e-05
CAMB-77918	MN908947.3	241	C	T	1	1	0	0	0.99879914911137	TCG	NA	NA	NA	NA	NA	NA	0.000320226903634575
CAMB-77918	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99793301358592	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000110771412113962
CAMB-77918	MN908947.3	3037	C	T	1	1	0	0	0.9995473201352	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.01786576533076e-05
CAMB-77927	MN908947.3	14408	C	T	1	1	0	2.8e-16	0.997619047619048	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000421245421245421
CAMB-77927	MN908947.3	23403	A	G	1	1	0	5.9e-08	0.999493725261575	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000107391611181001
CAMB-77927	MN908947.3	241	C	T	1	1	0	1.7e-13	0.998977702870721	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-77927	MN908947.3	28881	GGG	AAC	1	1	0;0;0	4.4e-52;5.3e-46;6.2e-48	0.998681156362102	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000119431506031291
CAMB-77927	MN908947.3	29230	C	T	1	1	0	1.2e-18	0.999209586945436	GCA	N	R319R	C957T	CGC>CGT	Synonymous	GU280_gp10	0.00012748597654258
CAMB-77927	MN908947.3	3037	C	T	1	1	0	3.4e-14	0.999298056155508	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000107991360691145
CAMB-77927	MN908947.3	6312	C	A	1	0.97	0	2.5e-96	0.995923294957483	ACA	ORF1ab:nsp3	T1198K	C3593A	ACA>AAA	Missense	ORF1ab:nsp3	0.000944815760926619
CAMB-77936	MN908947.3	13914	T	G	0.0081	0.0053	3.6e-06	7.4e-05	0.00697167755991285	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993028322440087
CAMB-77936	MN908947.3	14408	C	T	1	1	0	0	0.999381341252165	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000371195248700817
CAMB-77936	MN908947.3	23403	A	G	1	1	0	0	0.999909763580581	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.51182097094387e-05
CAMB-77936	MN908947.3	241	C	T	1	1	0	0	0.999644886363636	TCG	NA	NA	NA	NA	NA	NA	0.000118371212121212
CAMB-77936	MN908947.3	2440	A	G	1	1	1.1e-303	6.1e-223	1	AAG	ORF1ab:nsp2	E545E	A1635G	GAA>GAG	Synonymous	ORF1ab:nsp2	0
CAMB-77936	MN908947.3	28881	GGG	AAC	1	1	4.4e-132;3.6e-140;2.6e-145	3.6e-149;1.1e-151;1.7e-165	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-77936	MN908947.3	3037	C	T	1	1	7.6e-301	1.1e-222	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77954	MN908947.3	11075	T	-	0.035	0.039	7.7e-09	1.5e-09	0.0372531986134422	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957365877520727
CAMB-77954	MN908947.3	13249	G	T	0.15	0.17	2.6e-69	1e-81	0.160204768961336	TGT	ORF1ab:nsp10	L75L	G225T	CTG>CTT	Synonymous	ORF1ab:nsp10	0.838924064843504
CAMB-77954	MN908947.3	14408	C	T	1	1	0	0	0.998337521160547	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000630071888925158
CAMB-77954	MN908947.3	18651	G	T	0.26	0.27	2.1e-125	1.3e-131	0.262884393310808	AGC	ORF1ab:3'-to-5'-exonuclease	E204D	G612T	GAG>GAT	Missense	ORF1ab:3'-to-5'-exonuclease	0.735351353663231
CAMB-77954	MN908947.3	21575	C	T	0.11	0.09	2e-30	1.2e-25	0.0977611940298507	TCT	S	L5F	C13T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.900559701492537
CAMB-77954	MN908947.3	23403	A	G	1	1	0	0	0.999493614689336	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.32414209310553e-05
CAMB-77954	MN908947.3	241	C	T	1	1	0	0	0.997187908004419	TCG	NA	NA	NA	NA	NA	NA	0.000100431856985036
CAMB-77954	MN908947.3	2764	G	T	0.02	0.021	2.7e-10	1.6e-10	0.0203607214428858	TGC	ORF1ab:nsp3	V15V	G45T	GTG>GTT	Synonymous	ORF1ab:nsp3	0.979438877755511
CAMB-77954	MN908947.3	28881	GGG	AAC	0.996666666666667	1	0;0;0	0;0;0	0.997274449115351	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00228150683155739
CAMB-77954	MN908947.3	29077	C	T	0.017	0.02	4.3e-09	4.3e-10	0.0187350721314608	ACA	N	Y268Y	C804T	TAC>TAT	Synonymous	GU280_gp10	0.97896245342505
CAMB-77954	MN908947.3	3037	C	T	1	1	0	0	0.999381103011965	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000114610553339752
CAMB-77954	MN908947.3	4540	C	T	0.13	0.14	8.2e-61	2.1e-63	0.135473531326689	ACA	ORF1ab:nsp3	Y607Y	C1821T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.862072419492162
CAMB-77963	MN908947.3	11075	T	-	0.038	0.069	9.7e-10	9e-17	0.0534753499695679	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.946415094339623
CAMB-77963	MN908947.3	14184	C	T	0.089	0.045	2.8e-41	2.6e-21	0.0653613928131778	CCA	ORF1ab:RNA-dependent-RNA-polymerase	T239T	C717T	ACC>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.934619067159075
CAMB-77963	MN908947.3	14408	C	T	1	1	0	0	0.999548378054288	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00026474389921044
CAMB-77963	MN908947.3	19839	T	C	1	1	0	0	0.999887247716766	ATA	ORF1ab:endoRNAse	N73N	T219C	AAT>AAC	Synonymous	ORF1ab:endoRNAse	0.000112752283233735
CAMB-77963	MN908947.3	22452	C	T	0.077	0.032	1.3e-07	3.2e-05	0.0441176470588235	TCA	S	S297L	C890T	TCA>TTA	Missense	GU280_gp02, spike glycoprotein	0.955882352941177
CAMB-77963	MN908947.3	23403	A	G	1	1	0	0	0.999869880615465	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.75895384014834e-05
CAMB-77963	MN908947.3	241	C	T	1	1	0	0	0.999716625577375	TCG	NA	NA	NA	NA	NA	NA	0.000141687211312307
CAMB-77963	MN908947.3	27411	C	A	0.11	0.047	2.8e-52	2.8e-22	0.0740200026849241	TCT	ORF7a	F6L	C18A	TTC>TTA	Missense	GU280_gp07	0.92594643576319
CAMB-77963	MN908947.3	28253	C	T	0.24	0.35	1.2e-114	3.4e-178	0.294745020483119	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.705160804256722
CAMB-77963	MN908947.3	28308	C	T	0.011	0.052	2.4e-06	9.6e-24	0.0305129270181977	GCA	N	A12V	C35T	GCA>GTA	Missense	GU280_gp10	0.969464620496874
CAMB-77963	MN908947.3	28744	C	T	0.038	0.0088	3.2e-17	4e-05	0.020997375328084	TCG	N	I157I	C471T	ATC>ATT	Synonymous	GU280_gp10	0.979002624671916
CAMB-77963	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999633475870495	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-77963	MN908947.3	29084	A	G	1	1	0	0	0.999681950702359	AAC	N	T271A	A811G	ACA>GCA	Missense	GU280_gp10	0.000318049297641134
CAMB-77963	MN908947.3	29616	G	-	0.013	0.0062	1.3e-05	0.0038	0.00982727814175104	AGA	ORF10	.	59-59-delfrshift	.	no-SNV	GU280_gp11	0.990172721858249
CAMB-77963	MN908947.3	3037	C	T	1	1	0	0	0.999875575463481	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000124424536518601
CAMB-77963	MN908947.3	5907	C	T	0.11	0.089	7.7e-49	3.2e-40	0.0989338482202821	ACT	ORF1ab:nsp3	T1063I	C3188T	ACT>ATT	Missense	ORF1ab:nsp3	0.900898253861652
CAMB-77963	MN908947.3	635	C	T	0.17	0.2	1.3e-76	4.7e-91	0.177031995619182	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.822968004380818
CAMB-77963	MN908947.3	683	C	T	0.09	0.18	1.8e-41	1.4e-87	0.134321900566394	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.86566826620516
CAMB-77963	MN908947.3	9561	C	T	0.058	0.034	3.5e-27	1.6e-16	0.0457541206936757	TCA	ORF1ab:nsp4	S336L	C1007T	TCA>TTA	Missense	ORF1ab:nsp4	0.954209060003191
CAMB-77963	MN908947.3	9917	AG	TT	0.0345	0.0265	2.1e-16;1.4e-14	NA;2.1e-21	0.0305619226227686	TAG	ORF1ab:nsp4	.	1363-1364-mnv	.	no-SNV	ORF1ab:nsp4	0.981920750356827
CAMB-77963	MN908947.3	9918	G	T	0.035	0.053	1.4e-14	2.1e-21	0.0436048576095448	AGT	ORF1ab:nsp4	S455I	G1364T	AGT>ATT	Missense	ORF1ab:nsp4	0.956395142390455
CAMB-77972	MN908947.3	1437	C	T	1	1	0	2.3e-38	0.999483577773187	TCT	ORF1ab:nsp2	S211F	C632T	TCT>TTT	Missense	ORF1ab:nsp2	0.000103284445362528
CAMB-77972	MN908947.3	14408	C	T	1	1	0	1.4e-08	0.997929722470904	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000522232169501641
CAMB-77972	MN908947.3	25563	G	T	1	1	0	3.4e-16	0.999603220912592	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000163379624226864
CAMB-77972	MN908947.3	25688	C	T	1	1	0	1.1e-28	0.999700789168568	GCT	ORF3a	A99V	C296T	GCT>GTT	Missense	GU280_gp03	0.000187006769645061
CAMB-77972	MN908947.3	26882	C	G	1	1	0	2.7e-22	0.999751176502407	TCA	M	L120L	C360G	CTC>CTG	Synonymous	GU280_gp05	2.16368258776437e-05
CAMB-77972	MN908947.3	6431	A	G	1	1	0	4.1e-67	0.999676173570966	TAC	ORF1ab:nsp3	T1238A	A3712G	ACC>GCC	Missense	ORF1ab:nsp3	0.000167910000239871
CAMB-77981	MN908947.3	11071	G	INS	0.14	0.27	3.9e-37	2.7e-69	0.183398950131234	TGT	ORF1ab:nsp6	.	98-99-insfrshift	.	no-SNV	ORF1ab:nsp6	0.816437007874016
CAMB-77981	MN908947.3	11073	T	-	0.016	0.011	6.9e-09	3.6e-06	0.0145719489981785	TTC	ORF1ab:nsp6	.	101-101-delfrshift	.	no-SNV	ORF1ab:nsp6	0.985428051001822
CAMB-77981	MN908947.3	11074	C	-	0.14	0.085	3.2e-60	2.8e-31	0.122293256341514	TCT	ORF1ab:nsp6	.	102-102-delfrshift	.	no-SNV	ORF1ab:nsp6	0.000206228088265622
CAMB-77981	MN908947.3	11074	C	T	0.86	0.92	0	0	0.877500515570221	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.000206228088265622
CAMB-77981	MN908947.3	11083	G	T	1	1	0	0	0.999590331831217	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-77981	MN908947.3	14805	C	T	1	1	0	0	1	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-77981	MN908947.3	18202	A	C	0.02	0.021	1.4e-09	5.4e-08	0.0202702702702703	CAT	ORF1ab:3'-to-5'-exonuclease	I55L	A163C	ATC>CTC	Missense	ORF1ab:3'-to-5'-exonuclease	0.97972972972973
CAMB-77981	MN908947.3	2480	A	G	1	1	0	3.6e-103	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-77981	MN908947.3	2558	C	T	1	1	0	4.4e-118	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-77981	MN908947.3	25907	G	T	1	1	5e-185	1.3e-29	1	GGT	ORF3a	G172V	G515T	GGT>GTT	Missense	GU280_gp03	0
CAMB-77981	MN908947.3	29348	G	T	1	1	0	7.1e-247	1	CGC	N	A359S	G1075T	GCA>TCA	Missense	GU280_gp10	0
CAMB-77990	MN908947.3	11075	T	-	0.057	0.017	1.4e-13	6.5e-05	0.0368984337499333	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955545876371136
CAMB-77990	MN908947.3	13610	A	-	0.0077	0.004	2.5e-05	0.0014	0.00652210740301542	CAA	ORF1ab:RNA-dependent-RNA-polymerase	.	143-143-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.993393189903439
CAMB-77990	MN908947.3	14408	C	T	1	1	0	0	0.999650465075635	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000271860496727965
CAMB-77990	MN908947.3	18040	G	T	0.029	0.058	4.1e-14	1.8e-26	0.0435704569096583	AGC	ORF1ab:3'-to-5'-exonuclease	A1S	G1T	GCT>TCT	Missense	ORF1ab:3'-to-5'-exonuclease	0.956409538289189
CAMB-77990	MN908947.3	19164	C	T	0.069	0.069	1.5e-31	6e-32	0.0688291003750578	ACA	ORF1ab:3'-to-5'-exonuclease	D375D	C1125T	GAC>GAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.931102395917179
CAMB-77990	MN908947.3	2023	CACATC	TCACAT	0.0067	0.000433333333333333	4.1e-05;2.2e-05;3.6e-05;1.8e-05;3.7e-05;3.1e-05	0.0043;NA;NA;NA;NA;NA	0.003762050317423	TCA	ORF1ab:nsp2	.	1218-1223-mnv	.	no-SNV	ORF1ab:nsp2	0.994809790622235
CAMB-77990	MN908947.3	21614	C	T	0.061	0.011	3.9e-24	2.9e-06	0.0328273244781784	TCT	S	L18F	C52T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.967172675521822
CAMB-77990	MN908947.3	23403	A	G	1	1	0	0	0.999883792096313	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.52191293703856e-05
CAMB-77990	MN908947.3	241	C	T	1	1	0	0	0.999571113471122	TCG	NA	NA	NA	NA	NA	NA	0.000224654848460093
CAMB-77990	MN908947.3	25132	C	T	0.0045	0.0092	0.00047	5.2e-06	0.0068762074911191	CCA	S	A1190A	C3570T	GCC>GCT	Synonymous	GU280_gp02, spike glycoprotein	0.993103018468122
CAMB-77990	MN908947.3	2764	G	-	0.013	0.0066	6.5e-07	0.00012	0.00933660933660934	TGC	ORF1ab:nsp3	.	45-45-delfrshift	.	no-SNV	ORF1ab:nsp3	0.990663390663391
CAMB-77990	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.997983096427199	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00103074462413364
CAMB-77990	MN908947.3	3037	C	T	1	1	0	0	0.999767297548868	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.75674837108284e-05
CAMB-77990	MN908947.3	805	G	T	0.0051	0.0068	0.00018	3.2e-05	0.00586071184120465	GGG	ORF1ab:leader-protein	G180G	G540T	GGG>GGT	Synonymous	ORF1ab:leader-protein	0.994096509240246
CAMB-77990	MN908947.3	85	T	C	0.0098	0.002	2.7e-06	0.0084	0.00648950440488707	CTG	NA	NA	NA	NA	NA	NA	0.993456114273284
CAMB-77990	MN908947.3	936	C	T	0.88	0.88	0	0	0.87937646141855	ACT	ORF1ab:nsp2	T44I	C131T	ACT>ATT	Missense	ORF1ab:nsp2	0.120607950116913
CAMB-779AF	MN908947.3	11075	T	-	0.034	0.04	2.3e-08	3.6e-10	0.0360255037381249	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.9587578225545
CAMB-779AF	MN908947.3	119	C	T	1	1	0	0	0.999880374189535	ACT	NA	NA	NA	NA	NA	NA	7.17754862789195e-05
CAMB-779AF	MN908947.3	13694	C	T	1	1	0	0	0.999852844309279	ACA	ORF1ab:RNA-dependent-RNA-polymerase	T76I	C227T	ACA>ATA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	7.00741384384679e-05
CAMB-779AF	MN908947.3	14408	C	T	1	1	0	0	0.997656760880622	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000508610041415389
CAMB-779AF	MN908947.3	17608	G	T	1	1	0	0	0.999368626703517	TGA	ORF1ab:helicase	D458Y	G1372T	GAT>TAT	Missense	ORF1ab:helicase	5.9563518536167e-05
CAMB-779AF	MN908947.3	23403	A	G	1	1	0	0	0.999296608914557	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.14452835776692e-05
CAMB-779AF	MN908947.3	241	C	T	1	1	0	0	0.999747105017969	TCG	NA	NA	NA	NA	NA	NA	5.32410488486623e-05
CAMB-779AF	MN908947.3	25429	G	T	1	1	0	0	0.999137290613243	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	7.18924488964509e-05
CAMB-779AF	MN908947.3	26166	AG	-	0.0092	0.005	3.2e-05;0.00031	0.0021;0.0077	0.00757967269595177	CAG	ORF3a	.	774-775-delfrshift	.	no-SNV	GU280_gp03	0.991341991341991
CAMB-779AF	MN908947.3	26173	G	T	1	1	0	0	0.996885176270706	GGA	ORF3a	E261*	G781T	GAA>TAA	Nonsense	GU280_gp03	0
CAMB-779AF	MN908947.3	26781	CTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0213611111111111	0.0311666666666667	0.0031;0.012;0.012;0.017;0.001;0.0026;0.0021;0.0021;0.001;0.0013;0.0011;0.0018;0.0014;0.0017;0.0023;0.0013;0.0021;0.0016;0.0015;0.0013;0.0023;0.0012;0.0017;0.0015;0.001;0.0022;0.0014;5e-04;0.0016;0.002;0.002;0.0013;0.0022;0.0015;0.0018;0.0013	0.00013;0.00043;0.00048;0.00088;3.8e-05;0.00012;3.3e-05;3.3e-05;1.1e-05;1.7e-05;1.4e-05;3.3e-05;2.2e-05;2.6e-05;4.4e-05;1.8e-05;3.9e-05;2.7e-05;2.5e-05;1.6e-05;4.2e-05;1.9e-05;2.9e-05;2.4e-05;1.5e-05;3.5e-05;2e-05;1.1e-05;2.1e-05;3.4e-05;2.9e-05;1.8e-05;2.8e-05;1e-05;1.6e-05;1e-05	0.0262083653789268	TCT	M	.	259-294-delinframe	.	no-SNV	GU280_gp05	0.97918181926576
CAMB-779AF	MN908947.3	28805	G	A	0.012	0.015	2.1e-06	1.4e-07	0.0133856653290765	AGG	N	G178S	G532A	GGC>AGC	Missense	GU280_gp10	0.986526463782549
CAMB-779AF	MN908947.3	3037	C	T	1	1	0	0	0.999658766596352	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.10212185134632e-05
CAMB-779AF	MN908947.3	9977	C	A	1	1	0	0	0.998927567316889	TCT	ORF1ab:nsp4	L475I	C1423A	CTC>ATC	Missense	ORF1ab:nsp4	0.00049273934088867
CAMB-779BE	MN908947.3	11075	T	-	0.023	0.035	2.1e-06	1.2e-08	0.0299461581402049	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.969945797993986
CAMB-779BE	MN908947.3	11595	A	G	0.015	0.014	1e-07	5.3e-07	0.0144191714053615	CAG	ORF1ab:nsp6	Q208R	A623G	CAG>CGG	Missense	ORF1ab:nsp6	0.985580828594638
CAMB-779BE	MN908947.3	12745	A	C	0.0097	0.0048	2.1e-06	0.00031	0.00685001533585523	AAA	ORF1ab:nsp9	Q20H	A60C	CAA>CAC	Missense	ORF1ab:nsp9	0.993088641243227
CAMB-779BE	MN908947.3	15759	A	C	0.012	0.012	3.4e-07	7.2e-07	0.0118383277958776	AAG	ORF1ab:RNA-dependent-RNA-polymerase	Q764H	A2292C	CAA>CAC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.988000387084288
CAMB-779BE	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999632352941176	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	2.29784691743836e-05
CAMB-779BE	MN908947.3	17020	T	-	0.008	0.0041	2.8e-05	0.0018	0.00574862061992663	GTT	ORF1ab:helicase	.	784-784-delfrshift	.	no-SNV	ORF1ab:helicase	0.994179160528064
CAMB-779BE	MN908947.3	17336	CAG	-	0.00816666666666667	0.00346666666666667	4.4e-05;3.3e-05;3.4e-05	0.0046;0.0039;0.0049	0.00569834594419374	ACA	ORF1ab:helicase	.	1100-1102-delinframe	.	no-SNV	ORF1ab:helicase	0.994505449911941
CAMB-779BE	MN908947.3	17454	T	C	1	1	0	0	0.999696422117817	CTG	ORF1ab:helicase	P406P	T1218C	CCT>CCC	Synonymous	ORF1ab:helicase	0.000159016985905313
CAMB-779BE	MN908947.3	17766	C	T	1	1	0	0	0.999843676723464	TCT	ORF1ab:helicase	V510V	C1530T	GTC>GTT	Synonymous	ORF1ab:helicase	3.9080819133969e-05
CAMB-779BE	MN908947.3	1862	C	T	0.014	0.0063	3.1e-08	4.1e-05	0.0097913769123783	TCT	ORF1ab:nsp2	L353F	C1057T	CTT>TTT	Missense	ORF1ab:nsp2	0.990208623087622
CAMB-779BE	MN908947.3	20016	C	T	1	1	2.5e-266	6.5e-225	1	ACT	ORF1ab:endoRNAse	D132D	C396T	GAC>GAT	Synonymous	ORF1ab:endoRNAse	0
CAMB-779BE	MN908947.3	20270	C	T	1	1	1.6e-168	4.4e-175	1	GCT	ORF1ab:endoRNAse	A217V	C650T	GCT>GTT	Missense	ORF1ab:endoRNAse	0
CAMB-779BE	MN908947.3	2132	AA	GC	0.115	0.082	1.1e-46;6.5e-51	4.1e-35;1.1e-38	0.0938491454303551	AAA	ORF1ab:nsp2	.	1327-1328-mnv	.	no-SNV	ORF1ab:nsp2	0.910643083529291
CAMB-779BE	MN908947.3	24495	A	G	0.016	0.012	1.4e-08	7.1e-07	0.0134263914355001	AAT	S	N978S	A2933G	AAT>AGT	Missense	GU280_gp02, spike glycoprotein	0.9865736085645
CAMB-779BE	MN908947.3	25582	A	G	0.019	0.0091	4.1e-10	6.2e-06	0.0134008184807595	AAC	ORF3a	T64A	A190G	ACC>GCC	Missense	GU280_gp03	0.986568256553516
CAMB-779BE	MN908947.3	25710	C	A	0.4	0.5	1.1e-188	1.4e-274	0.465489292722464	TCT	ORF3a	L106L	C318A	CTC>CTA	Synonymous	GU280_gp03	0.527855984984216
CAMB-779BE	MN908947.3	25890	A	G	0.036	0.021	9e-17	6.3e-11	0.0258075542642283	CAA	ORF3a	S166S	A498G	TCA>TCG	Synonymous	GU280_gp03	0.974021534780379
CAMB-779BE	MN908947.3	26334	A	G	0.04	0.011	2.6e-15	2.4e-05	0.0227435140593444	CAC	E	T30T	A90G	ACA>ACG	Synonymous	GU280_gp04	0.977225415566258
CAMB-779BE	MN908947.3	28961	C	T	0.015	0.0081	2.8e-08	2.2e-05	0.0110162310149273	GCT	N	L230F	C688T	CTT>TTT	Missense	GU280_gp10	0.988983768985073
CAMB-779BE	MN908947.3	29683	A	T	1	1	0	0	0.996628029504742	TAA	NA	NA	NA	NA	NA	NA	0.00316122233930453
CAMB-779BE	MN908947.3	8219	G	A	0.069	0.022	7.5e-32	5.9e-12	0.0459068811380469	TGT	ORF1ab:nsp3	V1834I	G5500A	GTT>ATT	Missense	ORF1ab:nsp3	0.954060491370028
CAMB-779BE	MN908947.3	9180	C	T	0.17	0.12	2.2e-76	3.8e-56	0.143159006867406	TCT	ORF1ab:nsp4	S209F	C626T	TCT>TTT	Missense	ORF1ab:nsp4	0.856788166930798
CAMB-779BE	MN908947.3	9657	T	C	0.21	0.23	8.8e-102	6.3e-113	0.225079456804392	ATG	ORF1ab:nsp4	M368T	T1103C	ATG>ACG	Missense	ORF1ab:nsp4	0.774864978996733
CAMB-779CD	MN908947.3	11075	T	-	0.035	0.039	1.1e-09	1.6e-10	0.0370513102840784	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958214049768773
CAMB-779CD	MN908947.3	14408	C	T	1	1	0	0	0.997738626792657	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000496117591406782
CAMB-779CD	MN908947.3	23403	A	G	1	1	0	0	0.999641191245066	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.50995068465717e-05
CAMB-779CD	MN908947.3	241	C	T	1	1	0	0	0.998928114518862	TCG	NA	NA	NA	NA	NA	NA	9.22052026785611e-05
CAMB-779CD	MN908947.3	26137	A	C	0.024	0.02	8e-06	8.4e-05	0.0217370208636584	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.977971858321203
CAMB-779CD	MN908947.3	2676	C	T	1	1	0	0	0.999856975995805	CCT	ORF1ab:nsp2	P624L	C1871T	CCT>CTT	Missense	ORF1ab:nsp2	0.000119186670162809
CAMB-779CD	MN908947.3	28544	A	C	0.014	0.008	3e-05	0.005	0.0112164780258999	TAC	N	T91P	A271C	ACC>CCC	Missense	GU280_gp10	0.988171714081778
CAMB-779CD	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998774244718437	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000168790615241793
CAMB-779CD	MN908947.3	3037	C	T	1	1	0	0	0.99929634097306	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.35075727114328e-05
CAMB-779CD	MN908947.3	3587	C	T	1	1	0	0	0.999827207425144	ACA	ORF1ab:nsp3	H290Y	C868T	CAC>TAC	Missense	ORF1ab:nsp3	0.000172792574856212
CAMB-779CD	MN908947.3	8598	TTGTGTTCCTTT	-	0.0219166666666667	0.0211666666666667	3e-10;8.1e-10;3.3e-08;5.7e-10;4.4e-10;2.2e-10;5.5e-10;3.1e-10;3.1e-10;2.1e-11;2.2e-10;1.8e-10	7.8e-10;1.3e-09;4.9e-08;1.2e-09;1e-09;6.5e-10;1e-09;7.5e-10;7.6e-10;3.2e-11;6.7e-10;4.5e-10	0.0207685910622839	CTT	ORF1ab:nsp4	.	44-55-delinframe	.	no-SNV	ORF1ab:nsp4	0.978901362204375
CAMB-779DC	MN908947.3	14408	C	T	1	1	0	0	0.999410102003195	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00036868624800295
CAMB-779DC	MN908947.3	14919	C	T	0.045	0.0041	4.9e-19	0.0048	0.0374517374517375	TCA	ORF1ab:RNA-dependent-RNA-polymerase	V484V	C1452T	GTC>GTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.962548262548263
CAMB-779DC	MN908947.3	17749	G	C	0.058	0.064	1.2e-26	2.8e-29	0.0607521342360907	TGC	ORF1ab:helicase	A505P	G1513C	GCT>CCT	Missense	ORF1ab:helicase	0.939174271415955
CAMB-779DC	MN908947.3	23403	A	G	1	1	0	0	0.99991391036347	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.44358546118218e-05
CAMB-779DC	MN908947.3	241	C	T	1	1	0	0	0.998552069797661	TCG	NA	NA	NA	NA	NA	NA	0.00144793020233896
CAMB-779DC	MN908947.3	27471	TA	-	0.014	0.031	NA;2.3e-14	2e-15;9.7e-16	0.0214182225745606	GTA	ORF7a	.	78-79-delfrshift	.	no-SNV	GU280_gp07	0.986640724552293
CAMB-779DC	MN908947.3	27472	ACA	-	0.0286666666666667	0.0103443333333333	2.3e-14;9.8e-15;2e-14	9.7e-16;NA;NA	0.0164556095557533	TAC	ORF7a	.	79-81-delinframe	.	no-SNV	GU280_gp07	0.970316334878647
CAMB-779DC	MN908947.3	28452	G	C	0.02	0.016	2e-10	6.1e-09	0.0186877219597973	GGC	N	G60A	G179C	GGC>GCC	Missense	GU280_gp10	0.981001965313933
CAMB-779DC	MN908947.3	28881	GGG	AAC	0.983333333333333	1	0;0;0	0;0;0	0.991518467852257	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00403406544150605
CAMB-779DC	MN908947.3	29581	TTTTCCGT	-	0.0037375	0.012375	0.031;0.0054;0.0023;0.0029;0.0038;0.0021;0.0028;0.0031	5.6e-05;1.4e-05;3e-06;7.1e-06;9.3e-06;5.1e-06;7.1e-06;5.5e-06	0.0066815144766147	CTT	ORF10	.	24-31-delfrshift	.	no-SNV	GU280_gp11	0.991074748977315
CAMB-779DC	MN908947.3	3037	C	T	1	1	0	0	0.999362041467305	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-779DC	MN908947.3	4399	G	T	0.051	0.038	3.2e-21	3.4e-16	0.0447136138135429	TGC	ORF1ab:nsp3	M560I	G1680T	ATG>ATT	Missense	ORF1ab:nsp3	0.955157528509761
CAMB-779EB	MN908947.3	11075	T	-	0.051	0.022	1.2e-12	6.5e-07	0.0483377913641574	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951471150171953
CAMB-779EB	MN908947.3	14244	G	T	1	1	0	0	0.999951445311236	GGG	ORF1ab:RNA-dependent-RNA-polymerase	W259C	G777T	TGG>TGT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-779EB	MN908947.3	14408	C	T	1	1	0	0	0.99949492115158	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00047701891239688
CAMB-779EB	MN908947.3	15842	C	T	0.034	0.029	3.2e-16	2.7e-13	0.0336416394631846	ACT	ORF1ab:RNA-dependent-RNA-polymerase	T792I	C2375T	ACT>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.966290351831701
CAMB-779EB	MN908947.3	23403	A	G	1	1	0	0	0.999849721985673	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.34877857369467e-05
CAMB-779EB	MN908947.3	241	C	T	1	1	0	0	0.998966693073399	TCG	NA	NA	NA	NA	NA	NA	0.000861089105500637
CAMB-779EB	MN908947.3	27263	CTTTTAAAGTTTCCATTTGGAATCTTGA	-	0.0116428571428571	0.000292857142857143	1.3e-06;3.9e-06;5.5e-05;2e-04;0.00048;0.00038;0.00035;0.00035;0.00032;0.00027;0.00041;0.00043;0.00034;0.00028;0.00033;3e-04;0.00043;0.00044;0.00038;0.00051;0.00037;0.00036;0.00037;0.00037;0.00024;0.00041;0.00019;0.00021	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0064;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0104435345682798	ACT	ORF6	.	62-89-delfrshift	.	no-SNV	GU280_gp06	0.990729929589923
CAMB-779EB	MN908947.3	28214	C	INS	0.013	0.0043	1.3e-06	0.0088	0.0120106247834623	ACT	ORF8	.	320-321-insfrshift	.	no-SNV	GU280_gp09	0.986900499892762
CAMB-779EB	MN908947.3	28881	G	A	0.99	0.99	0	0	0.98771012854923	AGG	N	R203K	G608A	AGG>AAG	Missense	GU280_gp10	0
CAMB-779EB	MN908947.3	28881	GG	-	0.0115	0.00305	6e-07;8.5e-07	0.0011;NA	0.0107600108962136	AGG	N	.	608-609-delfrshift	.	no-SNV	GU280_gp10	0
CAMB-779EB	MN908947.3	28883	G	C	0.99	1	0	0	0.990825688073395	GGG	N	G204R	G610C	GGA>CGA	Missense	GU280_gp10	0
CAMB-779EB	MN908947.3	2975	A	G	0.023	0.0075	6.5e-11	0.00027	0.0182303245887061	TAC	ORF1ab:nsp3	T86A	A256G	ACA>GCA	Missense	ORF1ab:nsp3	0.981769675411294
CAMB-779EB	MN908947.3	3037	C	T	1	1	0	0	0.999524036173251	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000317309217832778
CAMB-779EB	MN908947.3	4359	AAG	-	0.0064	0.0126666666666667	9.6e-05;0.0028;0.003	4.3e-07;4.3e-05;5e-05	0.00729859741600162	CAA	ORF1ab:nsp3	.	1640-1642-delinframe	.	no-SNV	ORF1ab:nsp3	0.992873327973101
CAMB-779EB	MN908947.3	6286	C	T	1	1	0	0	0.99994334491615	CCT	ORF1ab:nsp3	T1189T	C3567T	ACC>ACT	Synonymous	ORF1ab:nsp3	3.77700558996827e-05
CAMB-779EB	MN908947.3	8848	A	G	0.023	0.0087	6.6e-12	0.00016	0.021906764808973	AAG	ORF1ab:nsp4	E98E	A294G	GAA>GAG	Synonymous	ORF1ab:nsp4	0.977917981072555
CAMB-779EB	MN908947.3	9799	T	C	0.0023	0.0068	0.0062	4.2e-05	0.00281896818041396	CTG	ORF1ab:nsp4	A415A	T1245C	GCT>GCC	Synonymous	ORF1ab:nsp4	0.997181031819586
CAMB-77A15	MN908947.3	11083	G	T	0.84	1	0	1.1e-06	0.844416747644598	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-77A15	MN908947.3	1321	A	G	0.0079	0.087	3.4e-05	8.4e-06	0.00804644530454268	AAG	ORF1ab:nsp2	E172E	A516G	GAA>GAG	Synonymous	ORF1ab:nsp2	0.991953554695457
CAMB-77A15	MN908947.3	14805	C	T	1	1	0	7.8e-21	0.999020807833537	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000244798041615667
CAMB-77A15	MN908947.3	15405	A	G	1	1	0	8.1e-48	0.999568742452993	TAG	ORF1ab:RNA-dependent-RNA-polymerase	L646L	A1938G	TTA>TTG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000215628773503536
CAMB-77A15	MN908947.3	2480	A	G	1	1	0	2.4e-14	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-77A15	MN908947.3	2558	C	T	1	1	0	2e-25	0.999482996323529	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000287224264705882
CAMB-77A15	MN908947.3	27331	C	T	1	1	0	5.2e-09	0.999509747846976	ACT	ORF6	L44L	C130T	CTA>TTA	Synonymous	GU280_gp06	0.0004248851992875
CAMB-77A15	MN908947.3	28657	C	T	0.064	0.11	7.9e-28	3.7e-05	0.0636393768644349	ACG	N	D128D	C384T	GAC>GAT	Synonymous	GU280_gp10	0.936360623135565
CAMB-77A15	MN908947.3	583	C	T	1	1	0	5.3e-23	0.999706182537964	TCC	ORF1ab:leader-protein	V106V	C318T	GTC>GTT	Synonymous	ORF1ab:leader-protein	9.27844616954814e-05
CAMB-77A15	MN908947.3	700	A	G	1	1	0	2.1e-16	0.999497024707694	TAG	ORF1ab:leader-protein	L145L	A435G	TTA>TTG	Synonymous	ORF1ab:leader-protein	0.000170237791242039
CAMB-77A24	MN908947.3	10523	G	C	1	1	0	0	0.999959681483721	TGT	ORF1ab:3C-like-proteinase	V157L	G469C	GTC>CTC	Missense	ORF1ab:3C-like-proteinase	2.01592581393005e-05
CAMB-77A24	MN908947.3	11074	C	INS	0.022	0.019	6.1e-06	0.002	0.0216185201816095	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.978216833807314
CAMB-77A24	MN908947.3	11075	T	-	0.052	0.026	6.3e-13	4e-07	0.0481587016580576	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.941206830000304
CAMB-77A24	MN908947.3	13778	AT	-	0.049	0.056	6e-14;1e-13	7.3e-17;2.8e-16	0.0497496415234678	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.952310959880649
CAMB-77A24	MN908947.3	13780	A	T	0.037	0.022	9.2e-10	4.1e-07	0.0352136593800173	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I105L	A313T	ATA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.963759725824379
CAMB-77A24	MN908947.3	14408	C	T	1	1	0	0	0.999139039819408	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000335984460718692
CAMB-77A24	MN908947.3	1486	A	-	0.004	0.0096	0.00075	1.4e-05	0.0049035115469788	GAG	ORF1ab:nsp2	.	681-681-delfrshift	.	no-SNV	ORF1ab:nsp2	0.991774754824423
CAMB-77A24	MN908947.3	1547	A	-	0.0052	0.0081	0.00024	3.1e-05	0.00568844807467911	TAG	ORF1ab:nsp2	.	742-742-delfrshift	.	no-SNV	ORF1ab:nsp2	0.959597432905484
CAMB-77A24	MN908947.3	1547	A	G	0.013	0.013	3.8e-07	4.9e-06	0.0131271878646441	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.959597432905484
CAMB-77A24	MN908947.3	1547	A	T	0.019	0.033	8.6e-10	8.2e-13	0.0215869311551925	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.959597432905484
CAMB-77A24	MN908947.3	20667	A	G	0.014	0.017	1.6e-05	9.7e-07	0.0144366504642431	AAG	ORF1ab:2'-O-ribose-methyltransferase	Q3Q	A9G	CAA>CAG	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.98535960648485
CAMB-77A24	MN908947.3	23403	A	G	1	1	0	0	0.999907964974099	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.56001998474848e-05
CAMB-77A24	MN908947.3	23415	C	T	0.0086	0.0085	5.3e-05	8.8e-06	0.00855519566018855	ACA	S	T618I	C1853T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0.991421762258387
CAMB-77A24	MN908947.3	241	C	T	0.99	1	0	0	0.994859443278395	TCG	NA	NA	NA	NA	NA	NA	0.000123868836665176
CAMB-77A24	MN908947.3	25556	TT	-	0.012	0.0033	1.3e-05;0.00027	0.0015;NA	0.0103548075892379	GTT	ORF3a	.	164-165-delfrshift	.	no-SNV	GU280_gp03	0.988111674012628
CAMB-77A24	MN908947.3	25906	G	T	0.0044	0.012	0.00073	3.3e-07	0.0053196453569762	AGG	ORF3a	G172C	G514T	GGT>TGT	Missense	GU280_gp03	0.994680354643024
CAMB-77A24	MN908947.3	27288	T	C	0.02	0.017	2.2e-09	3.9e-09	0.0194051295602054	TTG	ORF6	L29L	T87C	CTT>CTC	Synonymous	GU280_gp06	0.980558537431256
CAMB-77A24	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999616825613079	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	2.37614351906855e-05
CAMB-77A24	MN908947.3	28957	C	T	1	1	0	0	0.999627220368679	ACC	N	N228N	C684T	AAC>AAT	Synonymous	GU280_gp10	0.000354140649754897
CAMB-77A24	MN908947.3	29242	A	T	0.025	0.018	5.5e-12	1.2e-09	0.0238542785535267	AAG	N	E323D	A969T	GAA>GAT	Missense	GU280_gp10	0.97124507697816
CAMB-77A24	MN908947.3	29414	G	T	1	0.99	0	0	0.997808085728203	AGC	N	A381S	G1141T	GCC>TCC	Missense	GU280_gp10	0.00219191427179737
CAMB-77A24	MN908947.3	3037	C	T	0.99	1	0	0	0.995086606337656	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000155487141213422
CAMB-77A24	MN908947.3	6081	A	C	0.0052	0.0097	4e-04	6.6e-06	0.00591613015486341	GAT	ORF1ab:nsp3	D1121A	A3362C	GAT>GCT	Missense	ORF1ab:nsp3	0.993996867931094
CAMB-77A24	MN908947.3	6133	A	G	0.013	0.0086	3.6e-07	3e-05	0.0125613978581206	AAG	ORF1ab:nsp3	K1138K	A3414G	AAA>AAG	Synonymous	ORF1ab:nsp3	0.987358080360738
CAMB-77A24	MN908947.3	934	C	T	0.0062	0.012	0.00025	1.9e-07	0.00712471783295711	ACA	ORF1ab:nsp2	D43D	C129T	GAC>GAT	Synonymous	ORF1ab:nsp2	0.992853577009898
CAMB-77A33	MN908947.3	11074	C	INS	0.026	0.028	9.5e-06	1.3e-06	0.0270384074395936	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.972235909656958
CAMB-77A33	MN908947.3	11075	T	-	0.033	0.033	3e-08	3.2e-08	0.0331148169446042	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962123825953613
CAMB-77A33	MN908947.3	11345	C	T	0.0083	0.0098	1.4e-05	3.9e-06	0.00905474376769145	CCT	ORF1ab:nsp6	L125F	C373T	CTT>TTT	Missense	ORF1ab:nsp6	0.99090153990754
CAMB-77A33	MN908947.3	14408	C	T	1	1	0	0	0.996689771462927	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000421553112236788
CAMB-77A33	MN908947.3	21137	A	G	0.016	0.013	2.2e-07	5.3e-06	0.014374826523308	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.985522913531912
CAMB-77A33	MN908947.3	23403	A	G	1	1	0	0	0.999535808638544	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000120345908525648
CAMB-77A33	MN908947.3	241	C	T	1	1	0	0	0.99795873544953	TCG	NA	NA	NA	NA	NA	NA	0.000258387917780965
CAMB-77A33	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998472164085391	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000255451568704861
CAMB-77A33	MN908947.3	3037	C	T	1	1	0	0	0.999485914044828	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	2.05634382068682e-05
CAMB-77A33	MN908947.3	5159	T	C	0.0078	0.0095	3.4e-05	7.6e-06	0.00856841550224097	TTT	ORF1ab:nsp3	F814L	T2440C	TTT>CTT	Missense	ORF1ab:nsp3	0.990508832059056
CAMB-77A42	MN908947.3	11075	T	-	0.042	0.038	4.1e-10	5.5e-10	0.0414658822288391	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953753650081273
CAMB-77A42	MN908947.3	11224	C	T	0.017	0.016	2.9e-08	3.8e-09	0.0165975637193456	TCT	ORF1ab:nsp6	V84V	C252T	GTC>GTT	Synonymous	ORF1ab:nsp6	0.982881753607817
CAMB-77A42	MN908947.3	14408	C	T	1	1	0	0	0.998741734019104	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000560249816311536
CAMB-77A42	MN908947.3	20268	A	G	1	1	0	0	0.999302325581395	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0.000232558139534884
CAMB-77A42	MN908947.3	23403	A	G	1	1	0	0	0.999090536493719	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.5733000661156e-05
CAMB-77A42	MN908947.3	23971	A	G	0.017	0.014	4.8e-08	5.2e-08	0.0163592783887834	CAC	S	S803S	A2409G	TCA>TCG	Synonymous	GU280_gp02, spike glycoprotein	0.98348163624601
CAMB-77A42	MN908947.3	241	C	T	1	1	0	0	0.998646153846154	TCG	NA	NA	NA	NA	NA	NA	0.000135384615384615
CAMB-77A42	MN908947.3	28854	C	T	1	1	0	0	0.999246936400356	TCA	N	S194L	C581T	TCA>TTA	Missense	GU280_gp10	9.78004674862346e-05
CAMB-77A42	MN908947.3	3037	C	T	1	1	0	0	0.999101977539986	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00015124588800242
CAMB-77A42	MN908947.3	3722	A	G	0.028	0.023	8.8e-13	5.9e-11	0.02698417446974	TAT	ORF1ab:nsp3	I335V	A1003G	ATT>GTT	Missense	ORF1ab:nsp3	0.972043557603135
CAMB-77A42	MN908947.3	7798	G	T	1	1	0	0	0.999912324283251	AGA	ORF1ab:nsp3	K1693N	G5079T	AAG>AAT	Missense	ORF1ab:nsp3	2.92252389163281e-05
CAMB-77A51	MN908947.3	106	C	T	0.012	0.0049	5.2e-07	0.00098	0.00922219407144667	GCA	NA	NA	NA	NA	NA	NA	0.990760915463221
CAMB-77A51	MN908947.3	11074	C	INS	0.02	0.027	5e-04	7.4e-06	0.023504728312099	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.976353371646345
CAMB-77A51	MN908947.3	11075	T	-	0.036	0.039	7.5e-09	1.5e-09	0.0370219834593907	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955944723262883
CAMB-77A51	MN908947.3	11438	A	G	0.0079	0.0035	2.5e-05	0.0016	0.00597352276396513	TAA	ORF1ab:nsp6	N156D	A466G	AAT>GAT	Missense	ORF1ab:nsp6	0.994026477236035
CAMB-77A51	MN908947.3	13038	C	T	0.026	0.021	6.3e-13	6.2e-11	0.0238180035439008	ACA	ORF1ab:nsp10	T5I	C14T	ACA>ATA	Missense	ORF1ab:nsp10	0.97614242436234
CAMB-77A51	MN908947.3	14408	C	T	1	1	0	0	0.997890141279386	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000535579521386664
CAMB-77A51	MN908947.3	1962	C	T	0.0043	0.0072	0.00034	1.6e-05	0.00555542854530075	GCT	ORF1ab:nsp2	A386V	C1157T	GCT>GTT	Missense	ORF1ab:nsp2	0.994421709608834
CAMB-77A51	MN908947.3	20031	C	A	1	1	0	0	1	CCC	ORF1ab:endoRNAse	A137A	C411A	GCC>GCA	Synonymous	ORF1ab:endoRNAse	0
CAMB-77A51	MN908947.3	20549	A	G	0.0063	0.0065	3.6e-05	3.6e-05	0.00642465807417918	GAT	ORF1ab:endoRNAse	D310G	A929G	GAT>GGT	Missense	ORF1ab:endoRNAse	0.993457096685192
CAMB-77A51	MN908947.3	2144	G	A	0.014	0.015	2.3e-08	1.3e-08	0.0143891570738953	CGT	ORF1ab:nsp2	V447I	G1339A	GTC>ATC	Missense	ORF1ab:nsp2	0.985332343111771
CAMB-77A51	MN908947.3	23403	A	G	1	1	0	0	0.999861906561619	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.4484984155595e-05
CAMB-77A51	MN908947.3	241	C	T	1	1	0	0	0.997335553705246	TCG	NA	NA	NA	NA	NA	NA	0.00118419835322416
CAMB-77A51	MN908947.3	25296	A	G	0.016	0.013	3.3e-08	1.1e-06	0.0147164393395549	AAG	S	K1245R	A3734G	AAG>AGG	Missense	GU280_gp02, spike glycoprotein	0.985211773151472
CAMB-77A51	MN908947.3	25587	C	T	0.0039	0.0072	0.0013	4.8e-05	0.00554166996527974	TCA	ORF3a	L65L	C195T	CTC>CTT	Synonymous	GU280_gp03	0.994198210832268
CAMB-77A51	MN908947.3	25663	T	A	1	1	0	0	0.999126374453984	TTA	ORF3a	Y91N	T271A	TAC>AAC	Missense	GU280_gp03	0.000572375357734599
CAMB-77A51	MN908947.3	26147	C	T	0.025	0.033	3e-12	1.5e-15	0.0294258246135869	TCA	ORF3a	S252L	C755T	TCA>TTA	Missense	GU280_gp03	0.970521060179529
CAMB-77A51	MN908947.3	27046	C	T	1	1	0	0	0.999839101830664	ACG	M	T175M	C524T	ACG>ATG	Missense	GU280_gp05	7.15102974828375e-05
CAMB-77A51	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999518008938743	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	7.26023087534184e-05
CAMB-77A51	MN908947.3	3037	C	T	1	1	0	0	0.998768814060143	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.07796484964142e-05
CAMB-77A51	MN908947.3	6223	A	G	0.035	0.032	1e-16	1.2e-15	0.0332900727190326	TAC	ORF1ab:nsp3	L1168L	A3504G	TTA>TTG	Synonymous	ORF1ab:nsp3	0.966627526110871
CAMB-77A60	MN908947.3	11075	T	-	0.044	0.045	1.3e-10	1.8e-11	0.0440354173463992	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951509287490296
CAMB-77A60	MN908947.3	14408	C	T	1	1	0	0	0.998546485053478	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000383947344364201
CAMB-77A60	MN908947.3	15652	G	T	0.038	0.04	8.2e-18	5.7e-19	0.0383709233375688	TGA	ORF1ab:RNA-dependent-RNA-polymerase	D729Y	G2185T	GAC>TAC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.96156289707751
CAMB-77A60	MN908947.3	1684	C	T	0.017	0.014	1.3e-08	1.6e-07	0.0155071694105151	TCG	ORF1ab:nsp2	I293I	C879T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.984250056900083
CAMB-77A60	MN908947.3	20268	A	G	1	1	0	9.8e-252	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-77A60	MN908947.3	23403	A	G	1	1	0	0	0.999487282663015	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.49009287322902e-05
CAMB-77A60	MN908947.3	241	C	T	1	1	0	0	0.998603535211532	TCG	NA	NA	NA	NA	NA	NA	0.000159328197342031
CAMB-77A60	MN908947.3	25355	C	T	0.0066	0.008	0.00012	2.2e-05	0.00706977561146972	GCT	S	L1265F	C3793T	CTC>TTC	Missense	GU280_gp02, spike glycoprotein	0.992578931190445
CAMB-77A60	MN908947.3	26137	A	C	0.024	0.013	6.1e-06	0.0094	0.0200697338209031	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.979845224934093
CAMB-77A60	MN908947.3	28227	C	T	0.039	0.037	2.7e-18	4.6e-18	0.0385749034196595	TCA	ORF8	H112Y	C334T	CAT>TAT	Missense	GU280_gp09	0.961282014594363
CAMB-77A60	MN908947.3	2937	C	T	1	1	0	0	0.999826832330404	ACA	ORF1ab:nsp3	T73I	C218T	ACA>ATA	Missense	ORF1ab:nsp3	0.000129875752197065
CAMB-77A60	MN908947.3	3037	C	T	1	1	0	0	0.999120956399437	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000158227848101266
CAMB-77A7F	MN908947.3	10047	TTT	-	0.00306666666666667	0.0122666666666667	0.00017;NA;NA	1.3e-08;1.5e-06;0.00065	0.00670171800947867	GTT	ORF1ab:nsp4	.	1493-1495-delinframe	.	no-SNV	ORF1ab:nsp4	0.98541172985782
CAMB-77A7F	MN908947.3	10083	C	T	0.0028	0.0091	0.0028	4.9e-06	0.00599682168450721	TCT	ORF1ab:3C-like-proteinase	S10F	C29T	TCT>TTT	Missense	ORF1ab:3C-like-proteinase	0.99397319420707
CAMB-77A7F	MN908947.3	10438	TGCTATGAGGCCCAATTTCACTATTAAGGGTTCATTCCTTAATGGTTC	-	0.00971875	0.000254291666666667	4.4e-06;4.4e-06;4e-06;1.8e-06;1.8e-06;2.6e-06;3.8e-06;3.5e-06;4e-06;3.3e-06;9e-06;4.4e-06;3.5e-06;3.8e-06;3.3e-06;3.3e-06;2.2e-06;8e-06;9.2e-06;1.6e-05;7.5e-06;1e-05;2.4e-05;3.1e-06;6.5e-06;6e-06;5.5e-06;8.8e-06;6.8e-06;7.5e-06;8e-06;9.1e-06;2.6e-05;9e-06;6.9e-06;7.6e-06;7.1e-06;5e-06;5.8e-06;2e-05;1.2e-05;1.8e-05;6.4e-06;6.1e-06;5.9e-06;3.6e-06;4.7e-06;5.5e-06	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00029;0.00013;NA;NA;NA;0.47;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.46;NA;NA;NA;NA;NA;NA;NA	0.00492506004317028	GTG	ORF1ab:3C-like-proteinase	.	384-431-delinframe	.	no-SNV	ORF1ab:3C-like-proteinase	0.995103389280552
CAMB-77A7F	MN908947.3	11075	T	-	0.034	0.054	2e-08	5e-13	0.0436199078867507	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955469670463065
CAMB-77A7F	MN908947.3	11335	G	-	0.0072	0.0056	3.7e-05	0.00017	0.00639530393141268	TGT	ORF1ab:nsp6	.	363-363-delfrshift	.	no-SNV	ORF1ab:nsp6	0.990762338765737
CAMB-77A7F	MN908947.3	11416	C	T	0.014	0.014	5.5e-08	7.7e-08	0.0139551526717557	TCG	ORF1ab:nsp6	L148L	C444T	CTC>CTT	Synonymous	ORF1ab:nsp6	0.986044847328244
CAMB-77A7F	MN908947.3	12392	G	A	0.0059	0.0074	9.2e-05	2.2e-05	0.00664866412994558	TGA	ORF1ab:nsp8	D101N	G301A	GAT>AAT	Missense	ORF1ab:nsp8	0.993351335870054
CAMB-77A7F	MN908947.3	13458	C	T	0.013	0.0067	5.9e-07	0.00029	0.0105823499230375	TCG	ORF1ab:nsp11	S6L	C17T	TCG>TTG	Missense	ORF1ab:nsp11	0.989417650076963
CAMB-77A7F	MN908947.3	13883	C	T	0.009	0.0053	2.5e-06	9.1e-05	0.00737028301886792	ACA	ORF1ab:RNA-dependent-RNA-polymerase	T139I	C416T	ACA>ATA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.992600235849057
CAMB-77A7F	MN908947.3	14408	C	T	1	1	0	0	0.999634678613317	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000221115576150282
CAMB-77A7F	MN908947.3	14681	ATTTTAACAAAGACTTCTATGACTTTGCT	-	0.00597241379310345	0.00017548275862069	9.1e-05;0.00031;0.00011;0.00011;0.00015;1e-04;0.00012;0.00017;0.00037;0.00014;1e-04;3.4e-05;1e-04;0.00014;0.00014;0.00012;3.5e-05;0.00019;0.00014;0.00015;0.00013;0.00013;3.9e-05;0.00014;6.7e-05;0.00017;0.00029;6.9e-05;0.00073	NA;0.0024;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.48;0.48;0.48;0.48;0.45;0.46;0.46;0.45;0.47;0.47	0.00298605481616779	AAT	ORF1ab:RNA-dependent-RNA-polymerase	.	1214-1242-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.996855677717517
CAMB-77A7F	MN908947.3	14790	C	T	0.013	0.014	2.2e-07	8e-08	0.0133514697228412	TCA	ORF1ab:RNA-dependent-RNA-polymerase	I441I	C1323T	ATC>ATT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.986552060120202
CAMB-77A7F	MN908947.3	15392	G	T	0.017	0.0063	1.3e-09	4.7e-05	0.0127111128628579	CGT	ORF1ab:RNA-dependent-RNA-polymerase	R642L	G1925T	CGT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.987249472833691
CAMB-77A7F	MN908947.3	16393	C	T	0.026	0.028	6.6e-13	1.8e-13	0.0270190023752969	TCC	ORF1ab:helicase	P53S	C157T	CCA>TCA	Missense	ORF1ab:helicase	0.972980997624703
CAMB-77A7F	MN908947.3	17012	C	T	0.0028	0.011	0.0037	9.8e-07	0.00665600970151311	TCA	ORF1ab:helicase	S259L	C776T	TCA>TTA	Missense	ORF1ab:helicase	0.993330209740099
CAMB-77A7F	MN908947.3	17167	C	T	0.027	0.015	3.1e-13	3.3e-08	0.0216320658622898	TCA	ORF1ab:helicase	H311Y	C931T	CAT>TAT	Missense	ORF1ab:helicase	0.978357433134864
CAMB-77A7F	MN908947.3	17499	TT	-	0.0055	0.00755	0.00048;0.00029	1.1e-05;0.00019	0.00647748693748972	ATT	ORF1ab:helicase	.	1263-1264-delfrshift	.	no-SNV	ORF1ab:helicase	0.992760768357069
CAMB-77A7F	MN908947.3	17769	T	A	0.081	0.064	6.3e-37	2.3e-29	0.0725885232901587	TTA	ORF1ab:helicase	F511L	T1533A	TTT>TTA	Missense	ORF1ab:helicase	0.927388491110319
CAMB-77A7F	MN908947.3	203	C	T	0.021	0.024	2.7e-10	1.8e-11	0.0220405826601361	TCG	NA	NA	NA	NA	NA	NA	0.977911710450989
CAMB-77A7F	MN908947.3	20762	C	T	0.0074	0.012	7.2e-05	6.6e-07	0.0103403410258166	ACA	ORF1ab:2'-O-ribose-methyltransferase	T35I	C104T	ACA>ATA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.989591179894542
CAMB-77A7F	MN908947.3	2094	C	T	0.016	0.0078	5.4e-09	2.8e-05	0.0122378736694499	TCG	ORF1ab:nsp2	S430L	C1289T	TCG>TTG	Missense	ORF1ab:nsp2	0.98776212633055
CAMB-77A7F	MN908947.3	21604	GT	-	0.018	0.004	3.2e-08;2.8e-08	0.0032;0.0026	0.0100155797907857	AGT	S	.	42-43-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.990002221728505
CAMB-77A7F	MN908947.3	21742	C	T	0.03	0.018	4.1e-14	1.4e-09	0.0238036809815951	CCA	S	S60S	C180T	TCC>TCT	Synonymous	GU280_gp02, spike glycoprotein	0.972822085889571
CAMB-77A7F	MN908947.3	22103	G	T	0.01	0.0085	1.4e-06	8e-06	0.00942612589837119	AGG	S	G181*	G541T	GGA>TGA	Nonsense	GU280_gp02, spike glycoprotein	0.985228791216729
CAMB-77A7F	MN908947.3	22103	GG	TC	0.0125	0.0042855	1.4e-06;4.3e-06	8e-06;NA	0.00852395338800173	AGG	S	.	541-542-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.985228791216729
CAMB-77A7F	MN908947.3	22760	T	-	0.011	0.0078	1.3e-06	2.1e-05	0.00936011520141786	ATT	S	.	1198-1198-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.990621423032899
CAMB-77A7F	MN908947.3	22760	TT	-	0.0055	0.00575	1.3e-06;NA	2.1e-05;0.00052	0.00548363897878461	ATT	S	.	1198-1199-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.990621423032899
CAMB-77A7F	MN908947.3	23126	G	A	0.077	0.056	9.9e-35	2.4e-25	0.0655212706106375	AGC	S	A522T	G1564A	GCA>ACA	Missense	GU280_gp02, spike glycoprotein	0.934478729389362
CAMB-77A7F	MN908947.3	23403	A	G	1	0.99	0	0	0.995071232759968	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.5223641038024e-05
CAMB-77A7F	MN908947.3	23435	C	T	0.01	0.019	1.9e-06	3.4e-10	0.0147448899984397	TCA	S	H625Y	C1873T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.985240925403197
CAMB-77A7F	MN908947.3	23516	G	-	0.016	0.0059	3e-08	0.00043	0.010924981791697	AGG	S	.	1954-1954-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.988856518572469
CAMB-77A7F	MN908947.3	241	C	T	1	1	0	0	0.99985964036743	TCG	NA	NA	NA	NA	NA	NA	9.3573088379782e-05
CAMB-77A7F	MN908947.3	24202	T	C	0.023	0.0078	9.9e-12	2.7e-05	0.0152627393405518	GTA	S	G880G	T2640C	GGT>GGC	Synonymous	GU280_gp02, spike glycoprotein	0.984706674007463
CAMB-77A7F	MN908947.3	24213	C	T	0.033	0.013	6.3e-14	2e-06	0.0223462029260765	TCT	S	S884F	C2651T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.977653797073924
CAMB-77A7F	MN908947.3	2439	A	-	0.016	0.0042	3.2e-08	0.0016	0.00999733404425487	GAA	ORF1ab:nsp2	.	1634-1634-delfrshift	.	no-SNV	ORF1ab:nsp2	0.989736070381232
CAMB-77A7F	MN908947.3	2499	A	-	0.0084	0.0036	1e-05	0.00074	0.00602990834539315	GAA	ORF1ab:nsp2	.	1694-1694-delfrshift	.	no-SNV	ORF1ab:nsp2	0.993849493487699
CAMB-77A7F	MN908947.3	25521	C	T	0.012	0.017	1.2e-06	1.4e-08	0.0141879502620162	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.985741911565785
CAMB-77A7F	MN908947.3	25549	C	T	0.019	0.026	9.1e-10	6.3e-13	0.0220921696984323	TCT	ORF3a	L53F	C157T	CTT>TTT	Missense	GU280_gp03	0.977887719086549
CAMB-77A7F	MN908947.3	25831	C	T	0.0065	0.011	0.00026	4.7e-06	0.00849783128264141	TCT	ORF3a	L147F	C439T	CTT>TTT	Missense	GU280_gp03	0.990971054262193
CAMB-77A7F	MN908947.3	26160	TAATCCAG	-	0.013375	0.0019625	6.5e-05;0.00043;3.5e-05;0.00063;0.00071;0.00099;1.7e-06;2.3e-05	0.0022;0.0084;NA;NA;NA;NA;NA;NA	0.0068714632174616	TTA	ORF3a	.	768-775-delfrshift	.	no-SNV	GU280_gp03	0.989759747932257
CAMB-77A7F	MN908947.3	26768	C	T	0.029	0.02	5.5e-14	2.4e-10	0.0246644668545158	TCG	M	I82I	C246T	ATC>ATT	Synonymous	GU280_gp05	0.973926664689307
CAMB-77A7F	MN908947.3	26894	C	T	0.015	0.012	2.7e-08	3.9e-07	0.0136252080453609	TCC	M	L124L	C372T	CTC>CTT	Synonymous	GU280_gp05	0.986374791954639
CAMB-77A7F	MN908947.3	28253	C	T	0.062	0.057	4.2e-27	2.5e-25	0.0595291774696577	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.940217187089017
CAMB-77A7F	MN908947.3	28603	C	T	0.0093	0.02	0.00046	7.1e-07	0.0146470212889379	TCT	N	F110F	C330T	TTC>TTT	Synonymous	GU280_gp10	0.98236556644817
CAMB-77A7F	MN908947.3	28828	T	C	0.0073	0.01	3.8e-05	2.7e-06	0.00857109764101772	GTT	N	R185R	T555C	CGT>CGC	Synonymous	GU280_gp10	0.988263001428516
CAMB-77A7F	MN908947.3	29253	C	T	0.06	0.036	3.4e-27	3.1e-17	0.0472560975609756	TCG	N	S327L	C980T	TCG>TTG	Missense	GU280_gp10	0.952722730352303
CAMB-77A7F	MN908947.3	3037	C	T	1	1	0	0	0.999644597887896	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77A7F	MN908947.3	3833	T	C	0.011	0.0053	3.9e-06	0.0013	0.00803256249549744	CTT	ORF1ab:nsp3	F372L	T1114C	TTT>CTT	Missense	ORF1ab:nsp3	0.991643253367913
CAMB-77A7F	MN908947.3	4158	C	T	0.0076	0.0048	3.5e-05	6e-04	0.00615384615384615	GCT	ORF1ab:nsp3	A480V	C1439T	GCT>GTT	Missense	ORF1ab:nsp3	0.993785584494246
CAMB-77A7F	MN908947.3	5599	ATTT	-	0.01225	0.0016	2.9e-07;1.1e-07;2.8e-07;1.4e-06	NA;6.7e-05;NA;NA	0.00636374690932674	AAT	ORF1ab:nsp3	.	2880-2883-delfrshift	.	no-SNV	ORF1ab:nsp3	0.993649772919095
CAMB-77A7F	MN908947.3	6108	AGAAACCTGCTTCAAGAGAGCTTAAAGTTACA	-	0.006696875	0.0001125	5.8e-05;6.9e-05;6.5e-05;4.2e-05;6.3e-05;5.8e-05;7.5e-05;7e-05;1e-04;6e-05;5.6e-05;8.7e-05;5.7e-05;5.6e-05;7.5e-05;0.00011;5.8e-05;0.00014;6.4e-05;0.00021;7.4e-06;7.2e-05;9.5e-05;0.00018;7.7e-05;0.00035;0.00013;6.5e-05;1.4e-05;0.00015;1e-04;0.00013	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00086;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00366784037558685	AAG	ORF1ab:nsp3	.	3389-3420-delfrshift	.	no-SNV	ORF1ab:nsp3	0.991129509166174
CAMB-77A7F	MN908947.3	635	C	T	0.064	0.097	9.4e-29	3.5e-44	0.0757889735094967	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.924197827435556
CAMB-77A7F	MN908947.3	7432	AT	-	0.0105	0.00835	2.6e-05;0.00031	0.00022;0.0019	0.00962752525252525	CAT	ORF1ab:nsp3	.	4713-4714-delfrshift	.	no-SNV	ORF1ab:nsp3	0.99078045653996
CAMB-77A7F	MN908947.3	7528	C	T	0.017	0.0075	5.1e-09	5.5e-05	0.0129135592371991	TCG	ORF1ab:nsp3	V1603V	C4809T	GTC>GTT	Synonymous	ORF1ab:nsp3	0.987086440762801
CAMB-77A7F	MN908947.3	7735	C	T	0.024	0.0084	3.6e-08	0.00062	0.0156481390068121	TCG	ORF1ab:nsp3	I1672I	C5016T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.984302497778655
CAMB-77A7F	MN908947.3	8104	T	C	0.014	0.0099	4.3e-08	1.9e-06	0.0125030347171644	TTG	ORF1ab:nsp3	V1795V	T5385C	GTT>GTC	Synonymous	ORF1ab:nsp3	0.987448409808206
CAMB-77A7F	MN908947.3	815	C	T	0.023	0.017	1.3e-11	5.8e-09	0.0199116222115743	TCG	ORF1ab:nsp2	R4C	C10T	CGC>TGC	Missense	ORF1ab:nsp2	0.98007506788053
CAMB-77A7F	MN908947.3	815	CG	TC	0.01485	0.0085	1.3e-11;3.8e-05	5.8e-09;NA	0.0118378298210843	TCG	ORF1ab:nsp2	.	10-11-mnv	.	no-SNV	ORF1ab:nsp2	0.98007506788053
CAMB-77A7F	MN908947.3	8950	C	T	0.046	0.022	1.5e-21	1.5e-11	0.0346635526268753	TCT	ORF1ab:nsp4	I132I	C396T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.965336447373125
CAMB-77A7F	MN908947.3	9521	C	T	1	1	0	0	0.999927881668241	CCT	ORF1ab:nsp4	L323F	C967T	CTT>TTT	Missense	ORF1ab:nsp4	5.76946654069998e-05
CAMB-77A8E	MN908947.3	11075	T	-	0.041	0.042	3.9e-10	1.8e-10	0.0412700785047905	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954899076506773
CAMB-77A8E	MN908947.3	14408	C	T	1	1	0	0	0.99815079270884	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00053217352685562
CAMB-77A8E	MN908947.3	21621	C	T	0.011	0.01	1.4e-05	4.1e-06	0.0104496327700484	ACC	S	T20I	C59T	ACC>ATC	Missense	GU280_gp02, spike glycoprotein	0.989520511136323
CAMB-77A8E	MN908947.3	22215	A	G	0.012	0.0097	6.8e-06	4.9e-06	0.0112917543003831	CAG	S	Q218R	A653G	CAG>CGG	Missense	GU280_gp02, spike glycoprotein	0.988620278775181
CAMB-77A8E	MN908947.3	23403	A	G	1	1	0	0	0.999297394956686	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.49302799610865e-05
CAMB-77A8E	MN908947.3	241	C	T	1	1	0	0	0.999266411481685	TCG	NA	NA	NA	NA	NA	NA	0.000122947796365663
CAMB-77A8E	MN908947.3	25650	G	T	1	1	0	0	0.997617256082267	TGT	ORF3a	L86F	G258T	TTG>TTT	Missense	GU280_gp03	0.000259175654209514
CAMB-77A8E	MN908947.3	26918	G	A	0.015	0.016	2.6e-07	1.1e-08	0.0151413587792279	CGC	M	P132P	G396A	CCG>CCA	Synonymous	GU280_gp05	0.984766636436523
CAMB-77A8E	MN908947.3	29200	C	T	1	1	0	0	0.99895536394058	CCA	N	P309P	C927T	CCC>CCT	Synonymous	GU280_gp10	0.00017115506058299
CAMB-77A8E	MN908947.3	3037	C	T	1	1	0	0	0.998663988822913	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000130981487949703
CAMB-77A8E	MN908947.3	4353	A	C	0.066	0.068	4.6e-33	3.8e-31	0.0666534104424358	GAG	ORF1ab:nsp3	E545A	A1634C	GAG>GCG	Missense	ORF1ab:nsp3	0.933105004162702
CAMB-77A8E	MN908947.3	6990	C	T	1	1	0	0	0.997237569060773	TCT	ORF1ab:nsp3	S1424F	C4271T	TCT>TTT	Missense	ORF1ab:nsp3	0.000134752728742757
CAMB-77A9D	MN908947.3	1059	C	T	1	1	0	0	0.99969704510782	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.000205576533979637
CAMB-77A9D	MN908947.3	11075	T	-	0.04	0.043	7.1e-10	2.2e-10	0.0413986313469723	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954434739161856
CAMB-77A9D	MN908947.3	14408	C	T	1	1	0	0	0.998311107211792	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000548341814353395
CAMB-77A9D	MN908947.3	14805	C	T	0.034	0.039	3e-16	7.2e-18	0.0369522998749634	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.962908031604991
CAMB-77A9D	MN908947.3	16329	C	T	1	1	0	0	0.999752392069472	ACG	ORF1ab:helicase	Y31Y	C93T	TAC>TAT	Synonymous	ORF1ab:helicase	7.07451230080826e-05
CAMB-77A9D	MN908947.3	23403	A	G	1	1	0	0	0.99943043672642	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.57407078507867e-05
CAMB-77A9D	MN908947.3	23536	C	T	0.99	1	0	0	0.995061979272506	ACT	S	N658N	C1974T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.000162568583621215
CAMB-77A9D	MN908947.3	23868	G	T	0.053	0.053	2.1e-24	6.1e-24	0.0528667028395732	GGA	S	G769V	G2306T	GGA>GTA	Missense	GU280_gp02, spike glycoprotein	0.946545487429915
CAMB-77A9D	MN908947.3	241	C	T	1	1	0	0	0.998784466764762	TCG	NA	NA	NA	NA	NA	NA	0.000127950866867123
CAMB-77A9D	MN908947.3	24865	C	T	0.06	0.06	3.2e-27	5.9e-27	0.0595485851605708	ACT	S	H1101H	C3303T	CAC>CAT	Synonymous	GU280_gp02, spike glycoprotein	0.940416920582723
CAMB-77A9D	MN908947.3	25563	G	T	1	1	0	0	0.999755470133122	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	4.89059733755881e-05
CAMB-77A9D	MN908947.3	25731	C	T	1	1	0	0	0.999473272844666	ACT	ORF3a	Y113Y	C339T	TAC>TAT	Synonymous	GU280_gp03	8.49559927957318e-05
CAMB-77A9D	MN908947.3	29625	C	T	1	1	0	0	0.999718578170325	TCT	ORF10	S23F	C68T	TCT>TTT	Missense	GU280_gp11	0.000173182664415292
CAMB-77A9D	MN908947.3	3037	C	T	1	1	0	0	0.999280954891904	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000127830241439369
CAMB-77A9D	MN908947.3	6894	G	T	0.098	0.087	1.2e-36	1.1e-33	0.0910616869492237	TGT	ORF1ab:nsp3	C1392F	G4175T	TGT>TTT	Missense	ORF1ab:nsp3	0.908798433347321
CAMB-77A9D	MN908947.3	9170	C	T	0.039	0.039	2.9e-18	4.1e-18	0.0388104764836067	CCT	ORF1ab:nsp4	L206F	C616T	CTT>TTT	Missense	ORF1ab:nsp4	0.96116021046769
CAMB-77A9D	MN908947.3	9474	C	T	0.018	0.018	1.8e-09	2.2e-09	0.018262576589796	GCT	ORF1ab:nsp4	A307V	C920T	GCT>GTT	Missense	ORF1ab:nsp4	0.981697765263429
CAMB-77AAC	MN908947.3	11521	G	T	0.99	1	4.29999999999291e-313	3.1e-149	0.995249406175772	TGT	ORF1ab:nsp6	M183I	G549T	ATG>ATT	Missense	ORF1ab:nsp6	0
CAMB-77AAC	MN908947.3	13914	T	G	0.011	0.0012	1.9e-07	0.0076	0.00781153130812151	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.992188468691878
CAMB-77AAC	MN908947.3	14408	C	T	1	1	0	0	0.999531835205993	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000351123595505618
CAMB-77AAC	MN908947.3	15016	G	T	1	1	9.7e-146	0	1	TGC	ORF1ab:RNA-dependent-RNA-polymerase	A517S	G1549T	GCA>TCA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-77AAC	MN908947.3	17502	C	T	0.77	0.49	0	1.8e-244	0.730505494505495	TCA	ORF1ab:helicase	F422F	C1266T	TTC>TTT	Synonymous	ORF1ab:helicase	0.269494505494505
CAMB-77AAC	MN908947.3	23403	A	G	1	1	0	0	0.999919297891657	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.07021083425804e-05
CAMB-77AAC	MN908947.3	241	C	T	1	1	0	0	0.999954349364315	TCG	NA	NA	NA	NA	NA	NA	2.2825317842551e-05
CAMB-77AAC	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999798061389338	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-77AAC	MN908947.3	29284	C	T	1	1	0	0	1	TCA	N	I337I	C1011T	ATC>ATT	Synonymous	GU280_gp10	0
CAMB-77AAC	MN908947.3	3037	C	T	1	1	0	1.1e-204	0.999507995079951	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77AAC	MN908947.3	6408	C	A	0.83	1	0	0	0.845186162118292	TCT	ORF1ab:nsp3	S1230Y	C3689A	TCT>TAT	Missense	ORF1ab:nsp3	0.154780020966487
CAMB-77ABB	MN908947.3	11195	C	T	1	1	0	0	0.999708150927663	TCT	ORF1ab:nsp6	L75F	C223T	CTT>TTT	Missense	ORF1ab:nsp6	6.25390869293308e-05
CAMB-77ABB	MN908947.3	14408	C	T	1	1	0	0	0.999575046744858	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000339962604113548
CAMB-77ABB	MN908947.3	23403	A	G	1	1	0	0	0.999935164573923	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.32236173845389e-05
CAMB-77ABB	MN908947.3	241	C	T	1	0.82	0	0	0.892458364875095	TCG	NA	NA	NA	NA	NA	NA	0.000141937925813777
CAMB-77ABB	MN908947.3	26078	C	T	1	1	3.5e-144	1.4e-205	1	ACC	ORF3a	T229I	C686T	ACC>ATC	Missense	GU280_gp03	0
CAMB-77ABB	MN908947.3	26305	C	T	0.18	0.13	7.4e-83	5.8e-58	0.162976489385985	TCT	E	L21F	C61T	CTT>TTT	Missense	GU280_gp04	0.83565396028304
CAMB-77ABB	MN908947.3	28253	C	T	0.029	0.038	1.9e-13	3.3e-17	0.0340452322146351	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.965870017918543
CAMB-77ABB	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999528301886792	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000541125541125541
CAMB-77ABB	MN908947.3	3037	C	T	1	1	0	0	0.999629355077835	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77ABB	MN908947.3	3373	C	A	1	1	0	0	1	ACA	ORF1ab:nsp3	D218E	C654A	GAC>GAA	Missense	ORF1ab:nsp3	0
CAMB-77ABB	MN908947.3	683	C	T	0.067	0.18	2.6e-31	7.9e-84	0.126243853331785	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.873736787083285
CAMB-77ACA	MN908947.3	11074	C	INS	0.017	0.03	0.00063	3.1e-06	0.0184865773296183	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.981314404493388
CAMB-77ACA	MN908947.3	11075	T	-	0.032	0.032	7.2e-08	1.2e-08	0.0319236798837609	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.966370970825527
CAMB-77ACA	MN908947.3	1440	G	A	1	1	0	0	0.999851829900726	GGC	ORF1ab:nsp2	G212D	G635A	GGC>GAC	Missense	ORF1ab:nsp2	0.000148170099273967
CAMB-77ACA	MN908947.3	18698	C	T	1	1	0	0	0.999915129911856	GCT	ORF1ab:3'-to-5'-exonuclease	A220V	C659T	GCT>GTT	Missense	ORF1ab:3'-to-5'-exonuclease	3.63728949187066e-05
CAMB-77ACA	MN908947.3	19962	G	A	0.41	0.38	1.7e-184	1.9e-79	0.404340567612688	CGA	ORF1ab:endoRNAse	T114T	G342A	ACG>ACA	Synonymous	ORF1ab:endoRNAse	0.595325542570952
CAMB-77ACA	MN908947.3	20407	TTTGAATTAGAAGA	-	0.00462857142857143	0.0384285714285714	0.046;0.036;0.046;0.052;0.081;0.084;0.019;0.019;0.017;0.012;0.012;0.011;0.0099;0.01	6.3e-05;2.9e-06;3.2e-06;3.2e-06;7.4e-06;7.7e-06;4.5e-06;5.2e-06;5.1e-06;3.1e-06;2e-06;1.8e-06;1.5e-06;2.2e-06	0.00833796553640912	TTT	ORF1ab:endoRNAse	.	787-800-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.993345432546884
CAMB-77ACA	MN908947.3	28362	G	T	1	1	0	0	0.999473220744095	GGA	N	G30V	G89T	GGA>GTA	Missense	GU280_gp10	5.50366386766047e-05
CAMB-77ACA	MN908947.3	28708	C	T	1	1	0	0	0.999165931316257	ACA	N	H145H	C435T	CAC>CAT	Synonymous	GU280_gp10	0.000175275303105395
CAMB-77ACA	MN908947.3	2891	G	A	1	1	0	0	0.999858499060948	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	0.000141500939051686
CAMB-77ACA	MN908947.3	4668	C	T	1	1	0	0	0.999476435170614	TCT	ORF1ab:nsp3	S650F	C1949T	TCT>TTT	Missense	ORF1ab:nsp3	0.000505916576709601
CAMB-77AD9	MN908947.3	14408	C	T	1	1	0	1.1e-161	0.999470563320627	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000317662007623888
CAMB-77AD9	MN908947.3	3037	C	T	1	1	0	3.4e-14	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77AE8	MN908947.3	10047	T	-	0.012	0.015	1.4e-05	7e-07	0.0127515024823622	GTT	ORF1ab:nsp4	.	1493-1493-delfrshift	.	no-SNV	ORF1ab:nsp4	0.987056876578695
CAMB-77AE8	MN908947.3	10170	C	T	0.012	0.014	2.5e-06	4.9e-08	0.0121923924183345	CCA	ORF1ab:3C-like-proteinase	P39L	C116T	CCA>CTA	Missense	ORF1ab:3C-like-proteinase	0.987784047403079
CAMB-77AE8	MN908947.3	11075	T	-	0.075	0.058	3.8e-19	3.9e-14	0.0718010665566719	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.919120153880473
CAMB-77AE8	MN908947.3	12270	AA	-	0.017	0.02	1.3e-10;2.9e-06	4.6e-10;1e-10	0.0176355323318093	GAA	ORF1ab:nsp8	.	179-180-delfrshift	.	no-SNV	ORF1ab:nsp8	0.972973297906873
CAMB-77AE8	MN908947.3	14362	CTGCAT	TCTGCA	0.0009055	0.00763333333333333	0.41;0.42;0.00074;0.44;0.42;0.41	3.7e-05;3.7e-05;2.9e-05;1.3e-05;1.4e-05;5.2e-06	0.00156071285700602	TCT	ORF1ab:RNA-dependent-RNA-polymerase	.	895-900-mnv	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.998495897655881
CAMB-77AE8	MN908947.3	14408	C	T	1	0.99	0	0	0.997471024455967	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00189949254835699
CAMB-77AE8	MN908947.3	15548	A	G	0.0082	0.0079	8.3e-05	1.4e-05	0.00816661855807447	AAT	ORF1ab:RNA-dependent-RNA-polymerase	N694S	A2081G	AAT>AGT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.991820059062549
CAMB-77AE8	MN908947.3	18799	C	T	0.012	0.02	9.4e-05	7e-08	0.0131143599115129	ACA	ORF1ab:3'-to-5'-exonuclease	Q254*	C760T	CAA>TAA	Nonsense	ORF1ab:3'-to-5'-exonuclease	0.986832740213523
CAMB-77AE8	MN908947.3	23025	G	T	0.0068	0.0079	5.3e-05	1.4e-05	0.00708768355827179	TGT	S	C488F	G1463T	TGT>TTT	Missense	GU280_gp02, spike glycoprotein	0.992869875222816
CAMB-77AE8	MN908947.3	23254	A	G	0.013	0.0032	1.5e-06	0.00096	0.0109716239545447	AAT	S	Q564Q	A1692G	CAA>CAG	Synonymous	GU280_gp02, spike glycoprotein	0.988971389303253
CAMB-77AE8	MN908947.3	23403	A	G	1	1	0	0	0.99988652221251	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.20090168836546e-05
CAMB-77AE8	MN908947.3	23865	C	T	0.0065	0.0096	0.00011	1.4e-06	0.00701073985680191	ACT	S	T768I	C2303T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.992964399363564
CAMB-77AE8	MN908947.3	241	C	T	1	1	0	0	0.999812108069176	TCG	NA	NA	NA	NA	NA	NA	6.26306436081514e-05
CAMB-77AE8	MN908947.3	24404	C	T	0.0076	0.013	8.5e-05	1e-07	0.00832067728697451	ACT	S	L948F	C2842T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.991663166058099
CAMB-77AE8	MN908947.3	27106	C	T	0.0044	0.0073	0.0013	3e-05	0.00476595115823697	GCA	M	A195V	C584T	GCA>GTA	Missense	GU280_gp05	0.995197103483947
CAMB-77AE8	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999736915665028	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	7.22386765874449e-05
CAMB-77AE8	MN908947.3	3037	C	T	1	1	0	0	0.999491137308116	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77AE8	MN908947.3	5628	C	T	0.017	0.0053	2.3e-08	0.00037	0.0152008804524305	ACG	ORF1ab:nsp3	T970M	C2909T	ACG>ATG	Missense	ORF1ab:nsp3	0.984788222859073
CAMB-77AE8	MN908947.3	567	G	T	0.0059	0.0078	0.00048	5.9e-06	0.00613530599701466	GGT	ORF1ab:leader-protein	G101V	G302T	GGT>GTT	Missense	ORF1ab:leader-protein	0.993804328738256
CAMB-77AE8	MN908947.3	5736	C	T	0.0086	0.0099	4e-05	3.5e-06	0.00884478084325969	GCT	ORF1ab:nsp3	A1006V	C3017T	GCT>GTT	Missense	ORF1ab:nsp3	0.991081614877878
CAMB-77AE8	MN908947.3	7504	C	T	0.053	0.06	4.1e-24	9.9e-27	0.0543971800693034	ACA	ORF1ab:nsp3	Y1595Y	C4785T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.945304098458597
CAMB-77AE8	MN908947.3	7528	C	T	0.066	0.052	6.4e-29	2.6e-23	0.063269207790656	TCG	ORF1ab:nsp3	V1603V	C4809T	GTC>GTT	Synonymous	ORF1ab:nsp3	0.936700920062134
CAMB-77AE8	MN908947.3	8869	T	-	0.0082	0.013	3.3e-05	3.5e-07	0.00915651925094586	GTT	ORF1ab:nsp4	.	315-315-delfrshift	.	no-SNV	ORF1ab:nsp4	0.990779893809811
CAMB-77AE8	MN908947.3	913	C	T	1	1	0	0	0.999768391540196	CCG	ORF1ab:nsp2	S36S	C108T	TCC>TCT	Synonymous	ORF1ab:nsp2	0.000207228621929664
CAMB-77AF7	MN908947.3	11074	C	INS	0.037	0.045	3.2e-09	1.6e-10	0.0397055273956071	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.960053101617186
CAMB-77AF7	MN908947.3	1136	A	-	0.014	0.018	4.9e-07	8.7e-09	0.0153418951752864	GAA	ORF1ab:nsp2	.	331-331-delfrshift	.	no-SNV	ORF1ab:nsp2	0.984426703690848
CAMB-77AF7	MN908947.3	12263	AAGTTGG	-	0.0221428571428571	0.00514285714285714	4.6e-08;6.1e-15;9.6e-13;7.8e-14;7.1e-14;3.3e-07;1.1e-07	NA;NA;NA;NA;NA;7.3e-17;NA	0.022148070907195	TAA	ORF1ab:nsp8	.	172-178-delfrshift	.	no-SNV	ORF1ab:nsp8	0.988696087428047
CAMB-77AF7	MN908947.3	14408	C	T	1	1	0	0	0.999298586381785	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000521563972518974
CAMB-77AF7	MN908947.3	1547	A	T	0.013	0.028	5.2e-07	2.6e-10	0.0180099054479964	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.981990094552004
CAMB-77AF7	MN908947.3	1547	AG	TT	0.012	0.014	5.2e-07;4.3e-06	2.6e-10;NA	0.0125	TAG	ORF1ab:nsp2	.	742-743-mnv	.	no-SNV	ORF1ab:nsp2	0.981990094552004
CAMB-77AF7	MN908947.3	17165	C	T	0.0041	0.011	0.0012	6.2e-07	0.00629446490741208	TCT	ORF1ab:helicase	S310F	C929T	TCT>TTT	Missense	ORF1ab:helicase	0.993680306776326
CAMB-77AF7	MN908947.3	17644	C	T	0.0062	0.021	9.9e-05	4.2e-11	0.0120388683463754	TCA	ORF1ab:helicase	Q470*	C1408T	CAA>TAA	Nonsense	ORF1ab:helicase	0.987896637716055
CAMB-77AF7	MN908947.3	23403	A	G	1	1	0	0	0.999897028234858	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.23774121135985e-05
CAMB-77AF7	MN908947.3	241	C	T	1	1	0	0	0.999787647130203	TCG	NA	NA	NA	NA	NA	NA	0.00012134449702706
CAMB-77AF7	MN908947.3	25350	C	T	1	1	0	0	0.99978265594436	CCA	S	P1263L	C3788T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	0.000186294904834353
CAMB-77AF7	MN908947.3	26782	TTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGT	-	0.0288134583333333	0.0427083333333333	8.9e-05;1e-04;0.00024;2.3e-05;1e-04;1.7e-06;1.8e-06;4.9e-07;8.5e-07;7.9e-07;1.6e-06;8.4e-07;1.3e-06;2.6e-06;6.8e-07;2.1e-06;1.2e-06;1.2e-06;8.3e-07;2.4e-06;1e-06;1.5e-06;1.2e-06;5.5e-07;2.1e-06;9.1e-07;1.2e-07;1.4e-06;1.9e-06;2e-06;6.2e-07;2e-06;4e-07;9e-07;5.2e-07;0.037;0.049;0.037;0.037;NA;NA;NA;NA;NA;NA;NA;NA;0.5	3.2e-05;3.3e-05;9.5e-05;7e-06;2.9e-05;1e-08;1.1e-08;1.5e-09;3.8e-09;3.3e-09;1e-08;3.5e-09;6.8e-09;1.6e-08;2.5e-09;1.2e-08;7.2e-09;6.6e-09;3.5e-09;1.4e-08;5.5e-09;8.8e-09;5.4e-09;2.6e-09;9.9e-09;4e-09;1.5e-09;4.6e-09;1.1e-08;8.8e-09;3.8e-09;1e-08;1.4e-09;4.1e-09;2.9e-09;4.7e-06;3.3e-05;9.7e-06;1.7e-05;0.00092;6e-04;6e-04;0.00079;8e-04;8e-04;0.00073;6e-04;5.7e-05	0.0434238960544735	CTT	M	.	260-307-delinframe	.	no-SNV	GU280_gp05	0.971390025369173
CAMB-77AF7	MN908947.3	27132	TATAAAT	-	0.0215714285714286	0.0494285714285714	2e-05;4.3e-05;0.00028;0.00016;0.00048;0.00018;0.00043	4.1e-07;1.1e-06;6.3e-10;7.1e-11;1.8e-09;1.7e-10;1e-09	0.0298766080336046	CTA	M	.	610-616-delfrshift	.	no-SNV	GU280_gp05	0.977550704443412
CAMB-77AF7	MN908947.3	3037	C	T	1	1	0	0	0.999611449294133	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77AF7	MN908947.3	3043	T	C	0.025	0.0087	8.4e-12	2e-05	0.0164614071454701	CTC	ORF1ab:nsp3	P108P	T324C	CCT>CCC	Synonymous	ORF1ab:nsp3	0.978295329837825
CAMB-77AF7	MN908947.3	4335	C	T	0.0047	0.015	0.00022	6.8e-09	0.00816046042176695	CCA	ORF1ab:nsp3	P539L	C1616T	CCA>CTA	Missense	ORF1ab:nsp3	0.991825222981002
CAMB-77AF7	MN908947.3	4493	AAAATACAAGAGGGTGTGGTTGATTATGGTGCTAGATTTTACTTTTACACCAGTAAAACAACTGTAGCGTCACTTATCAACACACTTAACGATC	-	0.0323085106382979	0.00122542553191489	6.7e-15;4.7e-16;8.7e-13;9.9e-15;2.4e-14;1.6e-14;1.8e-15;7.8e-15;5.1e-15;1.2e-14;2.4e-14;4.1e-13;3.7e-14;2.7e-13;1.4e-13;3e-13;6.9e-14;1.8e-13;5.6e-14;3.3e-15;2.6e-15;4.8e-14;3.3e-14;6.8e-16;6.6e-10;1.9e-14;6.6e-14;8.1e-14;3.3e-13;1e-13;8e-14;3.1e-14;5.4e-11;9e-10;2.3e-07;3e-07;2.1e-11;4.4e-09;7.9e-09;5.3e-09;1e-08;7.3e-09;3.8e-05;2.6e-05;6.8e-05;5.3e-05;6.4e-05;8.3e-05;8.4e-05;6.7e-05;3.7e-05;8.5e-05;7.4e-05;8.4e-05;1.8e-05;0.00028;0.00028;0.00034;0.00033;0.00032;0.00027;3e-04;6.7e-09;1.7e-10;2e-08;2.5e-08;8.9e-11;4.6e-10;1.2e-09;1.2e-10;1.4e-10;1.1e-11;4.3e-11;8e-13;5.8e-13;3.7e-13;5.8e-13;6.3e-13;9.1e-13;1.4e-10;1.3e-10;7.8e-13;7.8e-13;8.3e-13;3.7e-13;8.5e-13;1e-08;1.1e-07;2.9e-07;3.3e-07;5.1e-07;4.9e-07;5.2e-07;2e-07	5.1e-10;4.5e-11;NA;NA;NA;NA;NA;NA;NA;NA;6.5e-14;1.9e-21;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0189670572164136	TAA	ORF1ab:nsp3	.	1774-1867-delfrshift	.	no-SNV	ORF1ab:nsp3	0.972669098738114
CAMB-77AF7	MN908947.3	5837	G	-	0.036	0.026	2.7e-17	9.5e-13	0.0323817825234256	AGA	ORF1ab:nsp3	.	3118-3118-delfrshift	.	no-SNV	ORF1ab:nsp3	0.967531052516888
CAMB-77AF7	MN908947.3	9270	GTAGATGGGTACTTAACAATGATTATTACAGATCTTTACCAGGAGTTTTCTGTGGT	-	0.0144642857142857	0.00135714285714286	4e-08;3e-08;2.7e-08;2.5e-08;2e-08;6.9e-09;1.4e-07;2.6e-08;2.4e-08;1.8e-08;6.7e-09;2.7e-08;3.4e-08;2.2e-08;2.6e-08;3.1e-08;3.7e-08;2.8e-08;2.5e-08;2.5e-08;3.5e-08;2.6e-08;1.5e-08;2.5e-08;2.1e-08;2.5e-08;2.6e-08;2.5e-08;2.3e-08;2.3e-08;1.1e-08;2.1e-08;2e-08;1.9e-08;3.3e-08;2e-08;1.8e-08;2.4e-08;1.6e-08;1.1e-08;1.6e-08;4e-08;2.9e-08;1.7e-08;2e-08;3.9e-08;5.6e-09;5.1e-09;1.7e-08;2.7e-08;4.6e-08;5.3e-05;2e-09;2.4e-08;2.3e-08;1.4e-08	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;1.1e-11;2.7e-11;1.6e-11;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0106528270964217	GGT	ORF1ab:nsp4	.	716-771-delfrshift	.	no-SNV	ORF1ab:nsp4	0.98943991444994
CAMB-77B03	MN908947.3	11075	T	-	0.0057	0.25	0.0064	2.5e-67	0.0827890895121014	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.91692278140607
CAMB-77B03	MN908947.3	11474	A	G	1	1	0	3.8e-210	1	TAT	ORF1ab:nsp6	I168V	A502G	ATA>GTA	Missense	ORF1ab:nsp6	0
CAMB-77B03	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999254621347645	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000447293872073953
CAMB-77B03	MN908947.3	17066	A	G	0.31	0.2	3e-139	1.4e-85	0.255883675610853	TAT	ORF1ab:helicase	Y277C	A830G	TAT>TGT	Missense	ORF1ab:helicase	0.744116324389147
CAMB-77B03	MN908947.3	1998	T	C	0.0063	0.083	0.0052	9.1e-18	0.0411663807890223	CTG	ORF1ab:nsp2	L398P	T1193C	CTG>CCG	Missense	ORF1ab:nsp2	0.958833619210978
CAMB-77B03	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0638108108108108	0.0610589459459459	8e-12;6.4e-16;1.4e-12;1.6e-12;1.7e-11;1.5e-14;7.1e-13;3.5e-11;3.9e-11;4.2e-12;1.1e-11;6.4e-12;2.9e-11;1.5e-11;2.5e-11;6.7e-11;9.4e-12;4.9e-11;2.1e-11;1.9e-11;1.7e-11;5.5e-11;1.7e-11;3.1e-11;1.7e-11;7e-12;4.3e-11;1.2e-11;1.5e-12;2.4e-11;4.3e-11;4e-11;8.5e-12;4.5e-11;2.1e-12;1.3e-11;3.4e-12	NA;NA;NA;NA;NA;2.3e-16;1e-14;1.1e-12;1.2e-12;1e-13;3.3e-13;1.2e-13;1.1e-12;3.8e-13;7.4e-13;2.1e-12;2.9e-13;1.7e-12;6.2e-13;5.8e-13;3.8e-13;1.7e-12;5.1e-13;9.8e-13;4.5e-13;2.7e-13;1.1e-12;3.4e-13;1.9e-13;5e-13;1.3e-12;9.6e-13;3.3e-13;1.3e-12;5.1e-14;3.1e-13;1.5e-13	0.0646952521767702	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.961123463248758
CAMB-77B03	MN908947.3	29683	A	T	0.95	0.98	5.1e-206	4.4e-150	0.962962962962963	TAA	NA	NA	NA	NA	NA	NA	0.00673400673400673
CAMB-77B03	MN908947.3	431	G	A	0.75	1	0	0	0.779875661984803	AGT	ORF1ab:leader-protein	V56I	G166A	GTT>ATT	Missense	ORF1ab:leader-protein	0.000115127791848952
CAMB-77B12	MN908947.3	10755	C	T	0.011	0.016	3.3e-06	1.7e-08	0.0130095667540065	GCT	ORF1ab:3C-like-proteinase	A234V	C701T	GCT>GTT	Missense	ORF1ab:3C-like-proteinase	0.986959965876546
CAMB-77B12	MN908947.3	10933	TT	-	0.00835	0.00445	5.9e-05;2.4e-05	0.0027;0.0011	0.00660991810150255	CTT	ORF1ab:3C-like-proteinase	.	879-880-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.993232084453224
CAMB-77B12	MN908947.3	11074	C	INS	0.04	0.044	1.9e-11	2.4e-11	0.0412991740165197	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.958440831183376
CAMB-77B12	MN908947.3	11075	T	-	0.027	0.035	8.1e-07	5e-09	0.0301717777565599	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964507365003863
CAMB-77B12	MN908947.3	11083	G	-	0.032	0.024	3.3e-13	2.8e-10	0.0287391556298343	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.85101326099554
CAMB-77B12	MN908947.3	11083	G	T	0.13	0.11	8.9e-28	1e-22	0.120205591621805	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.85101326099554
CAMB-77B12	MN908947.3	12493	C	T	0.011	0.011	1.5e-06	1.1e-06	0.0107803333366422	ACT	ORF1ab:nsp8	D134D	C402T	GAC>GAT	Synonymous	ORF1ab:nsp8	0.989189886737013
CAMB-77B12	MN908947.3	14408	C	T	1	1	0	0	0.998218180946521	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000263677259034941
CAMB-77B12	MN908947.3	23403	A	G	1	1	0	0	0.997332584585147	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00162852730591043
CAMB-77B12	MN908947.3	241	C	T	0.99	1	0	0	0.994849431104411	TCG	NA	NA	NA	NA	NA	NA	0.000107677398514052
CAMB-77B12	MN908947.3	26781	CTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0287777777777778	0.0373333333333333	6e-05;0.00054;0.00056;0.0027;0.00013;0.00036;0.00013;0.00014;6.3e-05;9.4e-05;7.3e-05;0.00013;1e-04;0.00013;0.00018;9e-05;0.00016;0.00011;0.00011;8.7e-05;0.00018;8.8e-05;0.00012;1e-04;7e-05;0.00016;9.1e-05;2.8e-05;0.00012;0.00015;0.00015;9.3e-05;0.00015;5.7e-05;9e-05;4.7e-05	0.00015;0.00028;0.00029;6e-04;5.2e-05;0.00014;2e-06;2e-06;5.9e-07;1.1e-06;8.5e-07;1.9e-06;1.2e-06;7.7e-07;1.3e-06;1e-06;2.2e-06;1.5e-06;1.4e-06;9.6e-07;2.5e-06;1.1e-06;1.6e-06;1.3e-06;8.6e-07;2e-06;1.1e-06;6.3e-07;1.2e-06;2e-06;1.9e-06;1.3e-06;2e-06;5.2e-07;1.1e-06;6.2e-07	0.0332849600148208	TCT	M	.	259-294-delinframe	.	no-SNV	GU280_gp05	0.973986646046137
CAMB-77B12	MN908947.3	28881	GGG	AAC	0.996666666666667	0.996666666666667	0;0;0	0;0;0	0.996499073284105	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00944169425958103
CAMB-77B12	MN908947.3	29750	C	T	1	0.99	0	0	0.992638512204572	ACG	NA	NA	NA	NA	NA	NA	0.000232468035645099
CAMB-77B12	MN908947.3	3037	C	T	1	1	0	0	0.998190659278525	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000113083795092163
CAMB-77B12	MN908947.3	8831	G	C	0.0069	0.004	3.3e-05	0.00036	0.00605077662029817	TGC	ORF1ab:nsp4	A93P	G277C	GCA>CCA	Missense	ORF1ab:nsp4	0.991765953465161
CAMB-77B21	MN908947.3	14408	C	T	1	1	0	0	0.9995787995788	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000280800280800281
CAMB-77B21	MN908947.3	23403	A	G	1	1	0	0	0.99991037338448	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.58506462078979e-05
CAMB-77B21	MN908947.3	241	C	T	1	1	0	0	1	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-77B21	MN908947.3	28077	G	T	0.036	0.03	1.4e-11	7.3e-10	0.0329479768786127	CGT	ORF8	V62L	G184T	GTG>TTG	Missense	GU280_gp09	0.966473988439306
CAMB-77B21	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998891966759003	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-77B21	MN908947.3	3037	C	T	1	1	0	0	0.999541073887104	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77B21	MN908947.3	313	C	T	1	1	0	0	1	TCA	ORF1ab:leader-protein	L16L	C48T	CTC>CTT	Synonymous	ORF1ab:leader-protein	0
CAMB-77B21	MN908947.3	669	GTT	-	1	1	0;0;0	0;0;0	0.999562453349806	AGT	ORF1ab:leader-protein	.	404-406-delinframe	.	no-SNV	ORF1ab:leader-protein	0.000154428229480349
CAMB-77B30	MN908947.3	11074	C	INS	0.032	0.024	9.2e-08	6.9e-05	0.0283785745391203	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.970968210190158
CAMB-77B30	MN908947.3	11075	T	-	0.031	0.039	8.4e-08	1.1e-09	0.0344098064837285	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959990044178956
CAMB-77B30	MN908947.3	11782	A	G	0.012	0.0048	4e-05	0.0044	0.0082089552238806	AAC	ORF1ab:nsp6	K270K	A810G	AAA>AAG	Synonymous	ORF1ab:nsp6	0.991791044776119
CAMB-77B30	MN908947.3	12153	C	T	0.0071	0.0072	4.4e-05	3.5e-05	0.00711879526274399	GCT	ORF1ab:nsp8	A21V	C62T	GCT>GTT	Missense	ORF1ab:nsp8	0.991414016925479
CAMB-77B30	MN908947.3	12820	A	G	0.011	0.011	1.6e-06	1.3e-06	0.0108010692211861	TAT	ORF1ab:nsp9	L45L	A135G	TTA>TTG	Synonymous	ORF1ab:nsp9	0.989053787631385
CAMB-77B30	MN908947.3	13095	C	T	0.0081	0.0069	1.4e-05	3.3e-05	0.00756973243197182	GCT	ORF1ab:nsp10	A24V	C71T	GCT>GTT	Missense	ORF1ab:nsp10	0.99241606544339
CAMB-77B30	MN908947.3	14408	C	T	1	1	0	0	0.996235155394593	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000286364019203234
CAMB-77B30	MN908947.3	1572	C	T	0.012	0.015	1.2e-06	4.5e-08	0.0132897448653258	ACA	ORF1ab:nsp2	T256I	C767T	ACA>ATA	Missense	ORF1ab:nsp2	0.986568118825954
CAMB-77B30	MN908947.3	16376	C	T	0.87	0.87	0	0	0.867335363305272	CCG	ORF1ab:helicase	P47L	C140T	CCG>CTG	Missense	ORF1ab:helicase	0.13260493163771
CAMB-77B30	MN908947.3	18698	C	T	1	1	0	0	0.999755848021206	GCT	ORF1ab:3'-to-5'-exonuclease	A220V	C659T	GCT>GTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.000232525694089197
CAMB-77B30	MN908947.3	22526	C	T	0.025	0.019	3.9e-09	1.7e-07	0.0217142857142857	ACC	S	P322S	C964T	CCA>TCA	Missense	GU280_gp02, spike glycoprotein	0.978285714285714
CAMB-77B30	MN908947.3	23403	A	G	1	1	0	0	0.99899145202697	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.05278302818292e-05
CAMB-77B30	MN908947.3	241	C	T	1	1	0	0	0.998321474725569	TCG	NA	NA	NA	NA	NA	NA	0.000237667295494719
CAMB-77B30	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0304054054054054	0.0261351351351351	0.00045;3.6e-05;0.00015;2e-04;0.00036;3.3e-05;0.00012;5.9e-05;6.1e-05;2.3e-05;3.4e-05;2.9e-05;5.3e-05;4.1e-05;5.3e-05;7.8e-05;3.9e-05;6.8e-05;4.4e-05;4.3e-05;4.7e-05;7.7e-05;4.2e-05;5.5e-05;4.1e-05;2.8e-05;6.5e-05;3.7e-05;2.6e-05;4.4e-05;6.3e-05;5.9e-05;2.6e-05;6.3e-05;2.7e-05;4.2e-05;2.4e-05	0.003;0.00041;0.0013;0.0012;0.0018;0.00027;0.00071;0.00026;0.00026;9.7e-05;0.00017;0.00015;0.00026;0.00019;0.00018;0.00026;0.00018;0.00029;0.00022;2e-04;0.00019;0.00032;2e-04;0.00024;2e-04;0.00015;0.00026;0.00018;0.00017;0.00017;0.00027;0.00023;0.00015;0.00027;0.00012;0.00017;0.00013	0.0290698183027005	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.978405663173679
CAMB-77B30	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998894230769231	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000107014821552785
CAMB-77B30	MN908947.3	29743	C	T	0.012	0.0061	2.2e-06	0.00048	0.00945428960907612	GCG	NA	NA	NA	NA	NA	NA	0.990105975990502
CAMB-77B30	MN908947.3	3037	C	T	1	1	0	0	0.998761086864705	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000394199633957483
CAMB-77B30	MN908947.3	3620	G	A	0.0085	0.0066	2.6e-05	0.00015	0.00766830138207758	CGG	ORF1ab:nsp3	G301S	G901A	GGC>AGC	Missense	ORF1ab:nsp3	0.991707534551939
CAMB-77B30	MN908947.3	522	TT	-	0.0365	0.039	2.3e-05;0.00038	5e-06;0.00017	0.0373967126603248	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.954694828515907
CAMB-77B30	MN908947.3	8172	C	T	0.0099	0.0075	3.1e-06	2.3e-05	0.00893321245089151	GCA	ORF1ab:nsp3	A1818V	C5453T	GCA>GTA	Missense	ORF1ab:nsp3	0.991066787549108
CAMB-77B4F	MN908947.3	10626	C	T	0.075	0.08	7.4e-33	2.7e-34	0.0768051771117166	GCA	ORF1ab:3C-like-proteinase	A191V	C572T	GCA>GTA	Missense	ORF1ab:3C-like-proteinase	0.923194822888283
CAMB-77B4F	MN908947.3	11075	T	-	0.06	0.066	6.3e-15	1.3e-16	0.06261943520419	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.93722131785689
CAMB-77B4F	MN908947.3	14408	C	T	1	1	0	0	0.999174082715616	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000412958642191984
CAMB-77B4F	MN908947.3	22105	A	C	0.048	0.16	3.2e-21	1.5e-61	0.0775271273557967	GAA	S	G181G	A543C	GGA>GGC	Synonymous	GU280_gp02, spike glycoprotein	0.922472872644203
CAMB-77B4F	MN908947.3	23403	A	G	1	1	0	0	0.999892469264131	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.97392977048162e-05
CAMB-77B4F	MN908947.3	23569	TA	-	0.0555	0.032	1.6e-05;2.8e-06	0.0015;7e-04	0.0429166221842639	GTA	S	.	2007-2008-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.96269477543538
CAMB-77B4F	MN908947.3	241	C	T	1	1	0	0	0.999861816423118	TCG	NA	NA	NA	NA	NA	NA	3.45458942204719e-05
CAMB-77B4F	MN908947.3	25429	G	T	1	1	0	0	0.999717973749864	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0.000108471634667534
CAMB-77B4F	MN908947.3	26773	TGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGAC	-	0.130722222222222	0.0246296296296296	3.6e-43;3.3e-31;6.2e-19;4e-19;9.1e-22;3.3e-18;1e-15;1.8e-20;1.7e-27;7e-22;8.2e-22;5.8e-20;5.1e-25;2.6e-22;2e-27;2.2e-27;7.6e-29;1.2e-28;3.2e-29;1.4e-27;2.4e-28;1.1e-27;6.4e-27;1e-28;4.1e-27;4.7e-28;6.1e-28;6.8e-28;4.4e-27;8e-28;1.7e-27;4.3e-28;1.7e-29;2.6e-27;2.5e-28;7.6e-28;6.5e-28;2.5e-27;1.8e-27;9.4e-29;2.7e-27;9.1e-31;2.5e-28;2.6e-29;3.7e-19;8.1e-16;8.4e-18;1.1e-16;3.5e-15;2.8e-16;5.9e-16;4.8e-15;6.3e-15;5.6e-15	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;3.4e-08;3.9e-07;3.6e-06;3.6e-06;8.8e-07;1.7e-06;1.4e-06;3.4e-06;2.1e-06;2.6e-06;4.9e-06;1.7e-06;4.1e-06;2.6e-06;2.5e-06;2.5e-06;4.5e-06;2.7e-06;3.4e-06;2.3e-06;1.5e-06;3.6e-06;2e-06;1.6e-06;2.1e-06;3.7e-06;3e-06;1.6e-06;3.9e-06;9.4e-07;1.7e-06;1.4e-06;4.1e-05;0.00018;7e-05;0.00011;NA;NA;NA;NA;NA;NA	0.10617557362765	ATG	M	.	251-304-delinframe	.	no-SNV	GU280_gp05	0.917574866566525
CAMB-77B4F	MN908947.3	3037	C	T	1	1	0	0	0.999538106235566	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00023094688221709
CAMB-77B4F	MN908947.3	9429	T	C	0.068	0.024	6.2e-29	2.4e-10	0.0560190703218117	ATC	ORF1ab:nsp4	I292T	T875C	ATC>ACC	Missense	ORF1ab:nsp4	0.943980929678188
CAMB-77B5E	MN908947.3	10046	G	A	0.042	0.045	5.6e-20	3.8e-21	0.0434829250849276	TGT	ORF1ab:nsp4	V498I	G1492A	GTT>ATT	Missense	ORF1ab:nsp4	0.956517074915072
CAMB-77B5E	MN908947.3	1005	A	C	0.05	0.025	9.8e-23	5.8e-12	0.0396988364134155	AAG	ORF1ab:nsp2	K67T	A200C	AAG>ACG	Missense	ORF1ab:nsp2	0.960270051645822
CAMB-77B5E	MN908947.3	11074	C	INS	0.051	0.05	1.8e-15	3.6e-13	0.0505313719603723	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.944521164815371
CAMB-77B5E	MN908947.3	11075	T	-	0.029	0.031	1.7e-07	3.4e-08	0.0298918470092387	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961563120776095
CAMB-77B5E	MN908947.3	11083	G	-	0.045	0.081	6.7e-19	1.8e-34	0.0602128937395158	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.653995899517469
CAMB-77B5E	MN908947.3	11083	G	T	0.31	0.25	5.1e-76	1.7e-57	0.285729078219811	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.653995899517469
CAMB-77B5E	MN908947.3	12047	A	G	0.0083	0.0059	1.3e-05	9.9e-05	0.00727410136507487	AAA	ORF1ab:nsp7	N69D	A205G	AAC>GAC	Missense	ORF1ab:nsp7	0.992659770440697
CAMB-77B5E	MN908947.3	14408	C	T	1	0.99	0	0	0.995208978243511	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000404721015959134
CAMB-77B5E	MN908947.3	16376	CG	TT	0.00875	0.0055	4.1e-05;2.1e-06	NA;1.1e-06	0.00746993351759169	CCG	ORF1ab:helicase	.	140-141-mnv	.	no-SNV	ORF1ab:helicase	0.995568241568392
CAMB-77B5E	MN908947.3	16377	G	T	0.01	0.011	2.1e-06	1.1e-06	0.0106248606880155	CGT	ORF1ab:helicase	P47P	G141T	CCG>CCT	Synonymous	ORF1ab:helicase	0.988780741511256
CAMB-77B5E	MN908947.3	1660	T	A	0.013	0.01	2.3e-07	1.4e-06	0.0121761153321644	GTG	ORF1ab:nsp2	G285G	T855A	GGT>GGA	Synonymous	ORF1ab:nsp2	0.98774595752971
CAMB-77B5E	MN908947.3	21137	A	G	0.48	0.37	7.8e-240	1e-167	0.431908355375759	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.568033297028162
CAMB-77B5E	MN908947.3	22021	G	T	0.31	0.32	1.7e-96	2.1e-100	0.312230815542074	TGG	S	M153I	G459T	ATG>ATT	Missense	GU280_gp02, spike glycoprotein	0.687630250544158
CAMB-77B5E	MN908947.3	23403	A	G	1	1	0	0	0.999900770176095	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.8697570395927e-05
CAMB-77B5E	MN908947.3	23709	C	T	0.38	0.34	1e-191	4.6e-169	0.363130276066621	ACA	S	T716I	C2147T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0.636869723933379
CAMB-77B5E	MN908947.3	241	C	T	1	1	0	0	0.99984836231298	TCG	NA	NA	NA	NA	NA	NA	0.000101091791346543
CAMB-77B5E	MN908947.3	25816	G	A	0.01	0.013	1.2e-06	9.6e-08	0.0109917355371901	TGA	ORF3a	D142N	G424A	GAT>AAT	Missense	GU280_gp03	0.98900826446281
CAMB-77B5E	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0273939393939394	0.0341212121212121	0.0062;0.015;0.00017;0.00016;6.7e-05;0.00012;9.3e-05;0.00015;0.00012;0.00015;0.00022;0.00011;0.00019;0.00012;0.00013;0.00011;0.00022;0.00013;0.00015;0.00013;8.7e-05;0.00019;0.00011;3.6e-05;0.00015;0.00018;0.00018;1e-04;0.00019;6.5e-05;0.00011;7.6e-05;0.0067	2.9e-06;1.6e-05;1.4e-05;1.4e-05;4.3e-06;8.7e-06;6.7e-06;1.4e-05;8.9e-06;1.2e-05;1.9e-05;8.2e-06;1.7e-05;1e-05;1e-05;8.1e-06;1.8e-05;1.1e-05;1.3e-05;9.9e-06;7.1e-06;1.5e-05;8.3e-06;4.8e-06;8.9e-06;1.5e-05;1.3e-05;1e-05;1.5e-05;4.4e-06;8e-06;6.5e-06;0.00028	0.0305928869540907	GTA	M	.	263-295-delinframe	.	no-SNV	GU280_gp05	0.972996991202123
CAMB-77B5E	MN908947.3	27434	C	T	0.0081	0.01	5.1e-05	4e-06	0.00906887655382691	ACT	ORF7a	T14I	C41T	ACT>ATT	Missense	GU280_gp07	0.990913750119442
CAMB-77B5E	MN908947.3	27625	C	T	0.02	0.031	9.3e-05	4.8e-06	0.0246575342465753	ACG	ORF7a	R78C	C232T	CGT>TGT	Missense	GU280_gp07	0.975342465753425
CAMB-77B5E	MN908947.3	27750	G	C	1	1	1.1e-258	4.6e-215	1	AGA	ORF7a	K119N	G357C	AAG>AAC	Missense	GU280_gp07	0
CAMB-77B5E	MN908947.3	2842	C	T	0.0077	0.015	2.4e-05	6e-08	0.0114480198019802	CCT	ORF1ab:nsp3	A41A	C123T	GCC>GCT	Synonymous	ORF1ab:nsp3	0.98855198019802
CAMB-77B5E	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999271276799755	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000212811236433284
CAMB-77B5E	MN908947.3	3037	C	T	0.99	1	0	0	0.996716101694915	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.29661016949153e-05
CAMB-77B5E	MN908947.3	337	C	T	0.014	0.014	1.8e-07	2.4e-07	0.0140487448875644	GCG	ORF1ab:leader-protein	R24R	C72T	CGC>CGT	Synonymous	ORF1ab:leader-protein	0.985936050843077
CAMB-77B5E	MN908947.3	4231	A	G	0.015	0.029	9.7e-09	1.5e-14	0.0212038878462788	CAG	ORF1ab:nsp3	T504T	A1512G	ACA>ACG	Synonymous	ORF1ab:nsp3	0.978726086104031
CAMB-77B5E	MN908947.3	522	TT	-	0.0365	0.027	4e-05;9.9e-05	0.00051;0.0012	0.0335539792446122	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.962944733511461
CAMB-77B5E	MN908947.3	6655	TAATAGTGTCCCTTGGGATACTATAGC	-	0.0172111111111111	0.0226666666666667	0.00024;3.6e-08;6.4e-06;0.0037;2.7e-05;5.4e-06;3.1e-05;4.7e-06;2.9e-05;6.7e-06;2.3e-06;3.8e-06;1.9e-07;4.2e-09;1.9e-08;2.6e-09;9.9e-09;1.4e-08;7.2e-09;1.8e-08;1.3e-08;1.2e-08;8.7e-09;1.7e-09;1.8e-08;2.7e-09;4.5e-09	1e-07;7.6e-10;4.4e-07;7.4e-05;3e-06;5e-07;3.2e-06;2.9e-07;2.9e-06;6.7e-07;1.4e-07;3.4e-07;4.7e-09;5.5e-11;4e-10;5.5e-11;2.3e-10;2e-10;1.3e-10;3.2e-10;3.4e-10;2.1e-10;1.8e-10;3.6e-11;4.1e-10;5.8e-11;1.2e-10	0.0213895394223263	TTA	ORF1ab:nsp3	.	3936-3962-delinframe	.	no-SNV	ORF1ab:nsp3	0.990135635018496
CAMB-77B5E	MN908947.3	9180	C	T	1	1	0	0	0.999850790808714	TCT	ORF1ab:nsp4	S209F	C626T	TCT>TTT	Missense	ORF1ab:nsp4	0.000127893592531014
CAMB-77B6D	MN908947.3	10097	G	A	1	1	0	0	1	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0
CAMB-77B6D	MN908947.3	11075	T	-	0.019	0.04	2e-05	3.6e-10	0.0273759007428692	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962678338735006
CAMB-77B6D	MN908947.3	14408	C	T	1	0.99	0	0	0.994465795541891	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000217781193953369
CAMB-77B6D	MN908947.3	23403	A	G	1	1	0	0	0.999945783785738	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.51801785520656e-05
CAMB-77B6D	MN908947.3	23731	C	T	1	1	0	0	0.999809069212411	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-77B6D	MN908947.3	241	C	T	1	1	0	0	0.999576783555018	TCG	NA	NA	NA	NA	NA	NA	0.00030229746070133
CAMB-77B6D	MN908947.3	26730	G	T	0.1	0.062	1.6e-46	2e-28	0.0863911799360377	TGT	M	V70F	G208T	GTT>TTT	Missense	GU280_gp05	0.913566739606127
CAMB-77B6D	MN908947.3	28580	G	T	1	1	0	0	0.999788978656698	AGA	N	D103Y	G307T	GAT>TAT	Missense	GU280_gp10	0.00018087543711564
CAMB-77B6D	MN908947.3	28792	A	T	0.0064	0.027	4.1e-05	2.1e-13	0.0134879513117855	CAG	N	A173A	A519T	GCA>GCT	Synonymous	GU280_gp10	0.985854099843737
CAMB-77B6D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999752618124845	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-77B6D	MN908947.3	2904	T	INS	0.014	0.0093	7.6e-07	6.4e-05	0.0120551090700344	ATA	ORF1ab:nsp3	.	184-185-insfrshift	.	no-SNV	ORF1ab:nsp3	0.987873134328358
CAMB-77B6D	MN908947.3	3037	C	T	1	1	0	0	0.999637516991391	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77B6D	MN908947.3	522	T	-	0.057	0.027	3e-07	0.0011	0.0488877392653906	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.950971170577999
CAMB-77B7C	MN908947.3	10097	G	A	1	1	0	0	0.999738778353433	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	8.70738821890374e-05
CAMB-77B7C	MN908947.3	11075	T	-	0.037	0.036	1.7e-09	2.3e-09	0.036436105966664	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958759427758542
CAMB-77B7C	MN908947.3	13313	G	A	0.017	0.017	4.1e-09	3.6e-09	0.016932116421485	TGT	ORF1ab:nsp10	V97I	G289A	GTA>ATA	Missense	ORF1ab:nsp10	0.982894157209955
CAMB-77B7C	MN908947.3	13536	C	T	1	1	0	0	0.999670132174625	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	3.41242577973929e-05
CAMB-77B7C	MN908947.3	14184	C	T	1	1	0	0	0.999782933569323	CCA	ORF1ab:RNA-dependent-RNA-polymerase	T239T	C717T	ACC>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00014192805082694
CAMB-77B7C	MN908947.3	14408	C	T	1	1	0	0	0.998145834959794	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000361074244671715
CAMB-77B7C	MN908947.3	1684	C	T	1	1	0	0	0.999800616554961	TCG	ORF1ab:nsp2	I293I	C879T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.000138034692719437
CAMB-77B7C	MN908947.3	21058	C	T	1	1	0	0	0.99971540666355	CCC	ORF1ab:2'-O-ribose-methyltransferase	P134S	C400T	CCT>TCT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.000101640477303681
CAMB-77B7C	MN908947.3	21786	G	T	0.024	0.026	2.3e-11	2.5e-12	0.0249898650605201	GGT	S	G75V	G224T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.974546823420397
CAMB-77B7C	MN908947.3	23403	A	G	1	1	0	0	0.999399186591077	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.8513680059157e-05
CAMB-77B7C	MN908947.3	23731	C	T	1	1	0	0	0.999851160944632	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	2.48065092280214e-05
CAMB-77B7C	MN908947.3	241	C	T	1	1	0	0	0.998763386027537	TCG	NA	NA	NA	NA	NA	NA	0.000101988781234064
CAMB-77B7C	MN908947.3	26769	G	T	0.022	0.02	2e-11	1.2e-10	0.0209858467545144	CGC	M	A83S	G247T	GCA>TCA	Missense	GU280_gp05	0.978713819123775
CAMB-77B7C	MN908947.3	27145	C	T	0.012	0.013	5.8e-07	1.8e-07	0.0127416073245168	ACA	M	T208I	C623T	ACA>ATA	Missense	GU280_gp05	0.987245676500509
CAMB-77B7C	MN908947.3	28357	G	T	0.02	0.02	8.8e-11	1.7e-10	0.0202020202020202	AGA	N	Q28H	G84T	CAG>CAT	Missense	GU280_gp10	0.97970823735878
CAMB-77B7C	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999601024038302	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	7.45489786789921e-05
CAMB-77B7C	MN908947.3	3037	C	T	1	1	0	0	0.999183468375102	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000146556958315014
CAMB-77B7C	MN908947.3	4002	C	T	1	1	0	0	0.999703140770647	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	2.96859229353441e-05
CAMB-77B7C	MN908947.3	4963	G	T	0.015	0.015	1.3e-08	2e-08	0.0149772433147693	GGA	ORF1ab:nsp3	R748S	G2244T	AGG>AGT	Missense	ORF1ab:nsp3	0.984964592633523
CAMB-77B8B	MN908947.3	14408	C	T	1	1	0	9.4e-51	0.998567754955893	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.0004394388203509
CAMB-77B8B	MN908947.3	1594	C	T	0.015	0.065	5.9e-08	5.8e-05	0.0157728706624606	CCG	ORF1ab:nsp2	S263S	C789T	TCC>TCT	Synonymous	ORF1ab:nsp2	0.984227129337539
CAMB-77B8B	MN908947.3	24240	C	T	1	1	0	7.7e-136	0.999476302697041	GCA	S	A893V	C2678T	GCA>GTA	Missense	GU280_gp02, spike glycoprotein	0.000104739460591778
CAMB-77B8B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	1e-22;1.7e-27;6.8e-26	0.999605332397825	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000147037200411704
CAMB-77B8B	MN908947.3	3037	C	T	1	1	0	1e-07	0.999931801132101	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77B9A	MN908947.3	10156	C	T	0.16	0.077	1.8e-72	1e-34	0.14258899090868	ACG	ORF1ab:3C-like-proteinase	D34D	C102T	GAC>GAT	Synonymous	ORF1ab:3C-like-proteinase	0.857343163417613
CAMB-77B9A	MN908947.3	13914	T	G	0.0057	0.0028	3.9e-05	0.00084	0.00513229927007299	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994791666666667
CAMB-77B9A	MN908947.3	14408	C	T	1	1	0	0	0.99946116818737	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000377182268841152
CAMB-77B9A	MN908947.3	18859	G	T	1	1	0	0	0.999865025982498	TGC	ORF1ab:3'-to-5'-exonuclease	A274S	G820T	GCA>TCA	Missense	ORF1ab:3'-to-5'-exonuclease	5.62391739590129e-05
CAMB-77B9A	MN908947.3	1914	G	A	0.13	0.021	1.5e-58	2e-09	0.118769458401406	CGC	ORF1ab:nsp2	R370H	G1109A	CGC>CAC	Missense	ORF1ab:nsp2	0.881199716408249
CAMB-77B9A	MN908947.3	21624	G	T	1	1	0	0	1	AGA	S	R21I	G62T	AGA>ATA	Missense	GU280_gp02, spike glycoprotein	0
CAMB-77B9A	MN908947.3	23403	A	G	1	1	0	0	0.99988445851483	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.93248911021502e-05
CAMB-77B9A	MN908947.3	241	C	T	1	1	0	0	0.999647868248551	TCG	NA	NA	NA	NA	NA	NA	0.000135435289018907
CAMB-77B9A	MN908947.3	26681	C	T	0.23	0.21	1.5e-105	4.5e-96	0.225620901665538	TCC	M	F53F	C159T	TTC>TTT	Synonymous	GU280_gp05	0.774353533675048
CAMB-77B9A	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999786762197202	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.64792005577504e-05
CAMB-77B9A	MN908947.3	3037	C	T	1	1	0	0	0.99968671679198	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77B9A	MN908947.3	4080	G	A	0.25	0.11	8e-121	4.6e-49	0.234035951430404	AGT	ORF1ab:nsp3	S454N	G1361A	AGT>AAT	Missense	ORF1ab:nsp3	0.765922677533459
CAMB-77BA9	MN908947.3	11075	T	-	0.036	0.043	8.3e-09	9.2e-11	0.0369026080457601	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959878495924582
CAMB-77BA9	MN908947.3	13778	AT	-	0.027	0.0115	2.9e-08;3.9e-08	9.9e-05;0.00012	0.0246740916352555	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.97629055383827
CAMB-77BA9	MN908947.3	13780	A	T	0.021	0.019	3.2e-06	2.5e-06	0.0208365139409566	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I105L	A313T	ATA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.978083493070516
CAMB-77BA9	MN908947.3	14408	C	T	1	1	0	0	0.999273818168831	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00053173970151149
CAMB-77BA9	MN908947.3	1461	A	G	0.0033	0.019	0.0034	2.5e-08	0.00544928825622776	AAG	ORF1ab:nsp2	K219R	A656G	AAG>AGG	Missense	ORF1ab:nsp2	0.993772241992883
CAMB-77BA9	MN908947.3	15002	A	G	1	1	0	0	0.999919385177621	TAT	ORF1ab:RNA-dependent-RNA-polymerase	Y512C	A1535G	TAT>TGT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	5.37432149191165e-05
CAMB-77BA9	MN908947.3	1547	A	-	0.013	0.015	3.7e-07	9.3e-08	0.013466587617515	TAG	ORF1ab:nsp2	.	742-742-delfrshift	.	no-SNV	ORF1ab:nsp2	0.919623951892945
CAMB-77BA9	MN908947.3	1547	A	G	0.027	0.026	1.5e-12	6.3e-11	0.0269331752350301	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.919623951892945
CAMB-77BA9	MN908947.3	1547	A	T	0.038	0.05	2.9e-17	1.9e-19	0.03997628525451	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.919623951892945
CAMB-77BA9	MN908947.3	170	A	G	0.0093	0.0056	2.7e-05	0.00023	0.0085960058110446	AAC	NA	NA	NA	NA	NA	NA	0.99086146927802
CAMB-77BA9	MN908947.3	1938	C	T	0.0062	0.0081	0.00026	1.3e-05	0.00645730164950657	TCT	ORF1ab:nsp2	S378F	C1133T	TCT>TTT	Missense	ORF1ab:nsp2	0.993520431793081
CAMB-77BA9	MN908947.3	2164	G	A	1	1	0	0	0.999694277901388	AGA	ORF1ab:nsp2	E453E	G1359A	GAG>GAA	Synonymous	ORF1ab:nsp2	0.000271752976544321
CAMB-77BA9	MN908947.3	23403	A	G	1	1	0	0	0.999887909341075	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.24747936130743e-05
CAMB-77BA9	MN908947.3	23679	C	T	1	1	0	0	0.999875682193961	GCT	S	A706V	C2117T	GCT>GTT	Missense	GU280_gp02, spike glycoprotein	2.48635612078718e-05
CAMB-77BA9	MN908947.3	241	C	T	1	1	0	0	0.999726975939028	TCG	NA	NA	NA	NA	NA	NA	9.87533837556493e-05
CAMB-77BA9	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999769309816916	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.78835472131776e-05
CAMB-77BA9	MN908947.3	3037	C	T	1	1	0	0	0.999661260956091	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77BA9	MN908947.3	3605	TG	CT	0.012	0.0019	8.3e-07;2.6e-06	NA;0.0017	0.0100977461830519	CTG	ORF1ab:nsp3	.	886-887-mnv	.	no-SNV	ORF1ab:nsp3	0.989397829868301
CAMB-77BA9	MN908947.3	4276	C	T	0.011	0.0031	5.5e-06	0.0062	0.00996701735801815	ACA	ORF1ab:nsp3	Y519Y	C1557T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.990028167657751
CAMB-77BA9	MN908947.3	4518	A	T	0.0023	0.013	0.0056	8.7e-08	0.00397807361002349	TAT	ORF1ab:nsp3	Y600F	A1799T	TAT>TTT	Missense	ORF1ab:nsp3	0.995259723309841
CAMB-77BA9	MN908947.3	6041	G	C	0.0027	0.0085	0.0079	1.6e-05	0.00359968502756009	CGA	ORF1ab:nsp3	D1108H	G3322C	GAT>CAT	Missense	ORF1ab:nsp3	0.996287824815329
CAMB-77BA9	MN908947.3	7113	C	T	1	1	0	1.6e-239	0.998678996036988	ACT	ORF1ab:nsp3	T1465I	C4394T	ACT>ATT	Missense	ORF1ab:nsp3	0.00132100396301189
CAMB-77BB8	MN908947.3	241	C	T	1	1	0	0	0.999745773484174	TCG	NA	NA	NA	NA	NA	NA	0.0001271132579128
CAMB-77BB8	MN908947.3	25563	G	T	1	1	0	0	0.999855376382963	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	8.67741702219973e-05
CAMB-77BB8	MN908947.3	29742	G	T	1	1	0	4.3e-115	0.998861047835991	CGC	NA	NA	NA	NA	NA	NA	0.00113895216400911
CAMB-77BB8	MN908947.3	29750	C	T	1	0.99	0	1.5e-109	0.998857142857143	ACG	NA	NA	NA	NA	NA	NA	0
CAMB-77BB8	MN908947.3	3037	C	T	1	1	0	3.7e-176	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77BC7	MN908947.3	1440	G	A	1	1	0	1.9e-261	0.999501743896363	GGC	ORF1ab:nsp2	G212D	G635A	GGC>GAC	Missense	ORF1ab:nsp2	0
CAMB-77BC7	MN908947.3	14411	C	T	0.093	0.18	2.7e-42	1.9e-83	0.107472151529058	ACA	ORF1ab:RNA-dependent-RNA-polymerase	T315I	C944T	ACA>ATA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.780695898869373
CAMB-77BC7	MN908947.3	16466	C	T	0.032	0.21	6.4e-09	3.1e-29	0.0515832482124617	CCA	ORF1ab:helicase	P77L	C230T	CCA>CTA	Missense	ORF1ab:helicase	0.948416751787538
CAMB-77BC7	MN908947.3	17252	G	T	0.12	0.062	6.3e-56	5.8e-29	0.112979677823584	CGT	ORF1ab:helicase	R339L	G1016T	CGT>CTT	Missense	ORF1ab:helicase	0.886893195067468
CAMB-77BC7	MN908947.3	18756	G	T	0.22	0.33	1e-103	7.1e-169	0.240529197080292	CGT	ORF1ab:3'-to-5'-exonuclease	P239P	G717T	CCG>CCT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.759324817518248
CAMB-77BC7	MN908947.3	23554	ACCCATTGGTGCAGGTATATGCGCTAGTTATC	-	0.0946959375	0.1234375	0.5;5e-09;2.5e-09;5.8e-09;7.8e-09;1.7e-10;1.4e-09;1.7e-10;1.3e-09;1.5e-09;1.7e-09;1.2e-09;9.6e-10;2.3e-10;1.9e-10;5.6e-12;4e-13;6.6e-12;3.7e-13;5.8e-12;3.9e-13;6.9e-12;1.2e-10;1.4e-11;1.4e-11;5.6e-18;7.5e-17;5.2e-11;3.3e-11;0.5;NA;NA	1.3e-12;1.8e-10;1.1e-10;2e-10;3.3e-10;6.2e-12;6.4e-11;2.5e-12;2.5e-11;3.6e-11;2.8e-11;2.6e-11;2.9e-11;3.4e-12;2.9e-12;1.1e-13;8.1e-15;2.5e-13;1.9e-14;2.5e-13;6.9e-15;1.7e-13;2.5e-12;2.6e-13;2.4e-13;1.3e-19;4.5e-19;2e-12;1.4e-12;4.6e-18;2.7e-34;2.2e-34	0.105238837867498	TAC	S	.	1992-2023-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.987128374530129
CAMB-77BC7	MN908947.3	25587	C	T	1	1	0	0	0.999755451395965	TCA	ORF3a	L65L	C195T	CTC>CTT	Synonymous	GU280_gp03	0.000101895251681272
CAMB-77BC7	MN908947.3	2891	G	A	1	1	0	0	1	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	0
CAMB-77BD6	MN908947.3	1059	C	T	1	1	0	0	0.999538721365385	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.00020087940539696
CAMB-77BD6	MN908947.3	11075	T	-	0.038	0.04	6.4e-09	2.5e-10	0.0380373405098878	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957421246125381
CAMB-77BD6	MN908947.3	14408	C	T	1	1	0	0	0.999032689269656	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00039372949325556
CAMB-77BD6	MN908947.3	20762	C	T	1	1	0	0	0.999140249721961	ACA	ORF1ab:2'-O-ribose-methyltransferase	T35I	C104T	ACA>ATA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.000157752344594222
CAMB-77BD6	MN908947.3	23403	A	G	1	1	0	0	0.999621238783808	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.38523367555918e-05
CAMB-77BD6	MN908947.3	241	C	T	1	1	0	0	0.999101433648121	TCG	NA	NA	NA	NA	NA	NA	9.8552438593135e-05
CAMB-77BD6	MN908947.3	25563	G	T	1	1	0	0	0.999698929317385	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000156807647195338
CAMB-77BD6	MN908947.3	26137	A	C	0.026	0.015	4.7e-06	0.0025	0.0237913543116219	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.975849530906316
CAMB-77BD6	MN908947.3	26801	C	T	0.99	0.99	0	0	0.992301154472696	TCA	M	L93L	C279T	CTC>CTT	Synonymous	GU280_gp05	0.000169983709894468
CAMB-77BD6	MN908947.3	27890	G	T	1	1	0	0	0.999878591049125	CGA	NA	NA	NA	NA	NA	NA	0
CAMB-77BD6	MN908947.3	28780	A	G	0.0098	0.0094	2.3e-05	9.8e-06	0.00975359342915811	AAG	N	K169K	A507G	AAA>AAG	Synonymous	GU280_gp10	0.990048965408308
CAMB-77BD6	MN908947.3	3037	C	T	1	1	0	0	0.999215980068471	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000130669988588154
CAMB-77BE5	MN908947.3	14408	C	T	1	1	0	0	0.99954752335578	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000346011551462564
CAMB-77BE5	MN908947.3	23403	A	G	1	1	0	0	0.99991575755023	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.58182047933954e-05
CAMB-77BE5	MN908947.3	241	C	T	1	1	0	0	0.999848759830611	TCG	NA	NA	NA	NA	NA	NA	5.04133897963299e-05
CAMB-77BE5	MN908947.3	25429	G	T	1	1	0	0	0.99980092074157	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0
CAMB-77BE5	MN908947.3	3037	C	T	1	1	0	1.1e-196	0.999557913351017	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77C00	MN908947.3	1060	C	T	0.35	0.11	2.1e-180	2.8e-48	0.279634429136543	CCT	ORF1ab:nsp2	T85T	C255T	ACC>ACT	Synonymous	ORF1ab:nsp2	0.720320101850589
CAMB-77C00	MN908947.3	1440	G	A	1	1	0	2.1e-79	1	GGC	ORF1ab:nsp2	G212D	G635A	GGC>GAC	Missense	ORF1ab:nsp2	0
CAMB-77C00	MN908947.3	20611	C	T	1	1	0	8.4e-190	1	GCT	ORF1ab:endoRNAse	L331F	C991T	CTT>TTT	Missense	ORF1ab:endoRNAse	0
CAMB-77C00	MN908947.3	27897	AAATTT	-	0.471666666666667	0.328333333333333	5.6e-157;1.2e-68;2.2e-57;2.6e-171;1.1e-67;1e-54	1.5e-64;6e-36;4.3e-30;2.1e-68;8.6e-35;1.7e-29	0.438783894823336	GAA	ORF8	.	4-9-delinframe	.	no-SNV	GU280_gp09	0.56609894566099
CAMB-77C00	MN908947.3	2891	G	A	1	1	0	0	0.999518304431599	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	0
CAMB-77C00	MN908947.3	4665	G	A	1	1	0	0	0.999973759479388	AGA	ORF1ab:nsp3	R649K	G1946A	AGA>AAA	Missense	ORF1ab:nsp3	2.62405206119289e-05
CAMB-77C1F	MN908947.3	10376	C	T	0.0078	0.0081	0.00015	1.7e-05	0.00780309601782255	ACC	ORF1ab:3C-like-proteinase	P108S	C322T	CCA>TCA	Missense	ORF1ab:3C-like-proteinase	0.992082264961348
CAMB-77C1F	MN908947.3	10459	T	C	0.014	0.016	3.7e-07	7.6e-09	0.0146314491089277	CTA	ORF1ab:3C-like-proteinase	T135T	T405C	ACT>ACC	Synonymous	ORF1ab:3C-like-proteinase	0.985166517800179
CAMB-77C1F	MN908947.3	1059	C	T	1	1	0	0	0.9997854635288	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.000136523208945521
CAMB-77C1F	MN908947.3	11074	C	T	0.0079	0.008	1.5e-07	0.00011	0.00793262995336941	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.971219332693897
CAMB-77C1F	MN908947.3	11075	T	-	0.037	0.037	8.7e-09	1.3e-09	0.0368031751758975	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95857838715497
CAMB-77C1F	MN908947.3	11736	A	G	0.013	0.015	2.5e-06	6.3e-07	0.0134772842547641	AAT	ORF1ab:nsp6	N255S	A764G	AAT>AGT	Missense	ORF1ab:nsp6	0.986087964640244
CAMB-77C1F	MN908947.3	14408	C	T	1	1	0	0	0.998879501197307	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000659648488682058
CAMB-77C1F	MN908947.3	19875	C	A	0.0077	0.0073	0.00023	2.9e-05	0.00763985228316302	TCT	ORF1ab:endoRNAse	I85I	C255A	ATC>ATA	Synonymous	ORF1ab:endoRNAse	0.992164755075324
CAMB-77C1F	MN908947.3	20762	C	T	1	1	0	0	0.999034104113409	ACA	ORF1ab:2'-O-ribose-methyltransferase	T35I	C104T	ACA>ATA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.000137985126655822
CAMB-77C1F	MN908947.3	21575	C	T	0.025	0.026	6.8e-07	8.6e-08	0.0251388032078964	TCT	S	L5F	C13T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.974151758173967
CAMB-77C1F	MN908947.3	22894	G	T	0.043	0.043	3.9e-19	4.3e-20	0.043159748427673	AGG	S	K444N	G1332T	AAG>AAT	Missense	GU280_gp02, spike glycoprotein	0.956769811320755
CAMB-77C1F	MN908947.3	23403	A	G	1	1	0	0	0.999515463245092	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000102498159692133
CAMB-77C1F	MN908947.3	241	C	T	1	1	0	0	0.998906846899794	TCG	NA	NA	NA	NA	NA	NA	0.000164560681751396
CAMB-77C1F	MN908947.3	25150	T	G	0.01	0.011	2.6e-05	7.5e-07	0.0102210322656296	CTC	S	S1196S	T3588G	TCT>TCG	Synonymous	GU280_gp02, spike glycoprotein	0.989651937696652
CAMB-77C1F	MN908947.3	25563	G	T	1	1	0	0	0.999624423221376	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000119230723372799
CAMB-77C1F	MN908947.3	26333	C	T	0.01	0.011	4e-05	4e-06	0.0103292894280763	ACA	E	T30I	C89T	ACA>ATA	Missense	GU280_gp04	0.989428076256499
CAMB-77C1F	MN908947.3	26801	C	T	0.99	0.99	0	0	0.994789479711417	TCA	M	L93L	C279T	CTC>CTT	Synonymous	GU280_gp05	0.000101792826150577
CAMB-77C1F	MN908947.3	27527	C	T	0.015	0.014	1.2e-06	2.3e-06	0.0149789835689721	CCA	ORF7a	P45L	C134T	CCA>CTA	Missense	GU280_gp07	0.984868169659916
CAMB-77C1F	MN908947.3	27551	AATTTGCACTGACTTGCTTTAGCACTC	-	0.0488148148148148	0.0447037037037037	3.6e-22;1e-21;1.4e-20;4.7e-20;3.6e-19;8.6e-19;1.5e-19;5.3e-19;1.9e-18;1.6e-18;1.9e-18;8.5e-19;4.7e-19;9.3e-19;1.1e-18;3.9e-18;2.1e-18;4.2e-18;1e-17;4.1e-17;2.1e-17;1.1e-17;3.9e-18;4.7e-18;1.3e-17;1.2e-17;5.2e-17	1.6e-16;2.6e-16;1.8e-16;5.1e-16;8.4e-16;7.8e-16;4.1e-16;1.2e-15;2.2e-15;1.2e-15;1.3e-15;1.2e-15;1.3e-15;1.3e-15;1.6e-15;2e-15;1.6e-15;5.9e-16;1e-15;1.9e-15;2e-15;8.2e-16;7.3e-16;1.2e-15;9.5e-16;1.3e-15;2.6e-15	0.0482867270578968	AAA	ORF7a	.	158-184-delinframe	.	no-SNV	GU280_gp07	0.950333279141603
CAMB-77C1F	MN908947.3	27890	G	T	1	1	0	0	0.999726106188631	CGA	NA	NA	NA	NA	NA	NA	1.36946905684666e-05
CAMB-77C1F	MN908947.3	3037	C	T	1	1	0	0	0.99915596451741	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000115848007414272
CAMB-77C1F	MN908947.3	3613	T	C	0.0084	0.0084	0.00022	2.4e-05	0.00841182863871026	ATG	ORF1ab:nsp3	H298H	T894C	CAT>CAC	Synonymous	ORF1ab:nsp3	0.991395706910606
CAMB-77C1F	MN908947.3	4784	C	T	0.037	0.036	1.4e-16	1.3e-17	0.0371258657399476	ACT	ORF1ab:nsp3	L689F	C2065T	CTT>TTT	Missense	ORF1ab:nsp3	0.962751768189716
CAMB-77C1F	MN908947.3	6029	A	C	0.034	0.03	7.7e-16	6.6e-14	0.0333749678556996	AAA	ORF1ab:nsp3	N1104H	A3310C	AAC>CAC	Missense	ORF1ab:nsp3	0.966312773226553
CAMB-77C1F	MN908947.3	8053	T	C	0.0064	0.0069	0.00046	3.3e-05	0.00645545001476028	ATA	ORF1ab:nsp3	N1778N	T5334C	AAT>AAC	Synonymous	ORF1ab:nsp3	0.993496796151909
CAMB-77C1F	MN908947.3	9165	C	T	0.018	0.019	5.3e-09	3.5e-10	0.0186065372790886	ACC	ORF1ab:nsp4	T204I	C611T	ACC>ATC	Missense	ORF1ab:nsp4	0.981327448650484
CAMB-77C1F	MN908947.3	9180	C	T	0.0098	0.011	1.4e-05	1.7e-06	0.00992819785480011	TCT	ORF1ab:nsp4	S209F	C626T	TCT>TTT	Missense	ORF1ab:nsp4	0.98999300692413
CAMB-77C1F	MN908947.3	9438	C	T	0.57	0.58	0	0	0.570025722094207	ACA	ORF1ab:nsp4	T295I	C884T	ACA>ATA	Missense	ORF1ab:nsp4	0.429786720968866
CAMB-77C1F	MN908947.3	9474	C	T	0.015	0.015	1.3e-07	2.6e-08	0.0151984348073958	GCT	ORF1ab:nsp4	A307V	C920T	GCT>GTT	Missense	ORF1ab:nsp4	0.984659039375996
CAMB-77C1F	MN908947.3	9491	C	T	0.012	0.013	3e-06	3.9e-07	0.0120963444527337	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.987797079825216
CAMB-77C1F	MN908947.3	9642	T	C	0.024	0.021	3.8e-11	2.9e-11	0.0231586940015186	ATT	ORF1ab:nsp4	I363T	T1088C	ATT>ACT	Missense	ORF1ab:nsp4	0.97635619674344
CAMB-77C2E	MN908947.3	11075	T	-	0.12	0.0057	1.5e-29	0.0059	0.10978032582165	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.890106147471193
CAMB-77C2E	MN908947.3	14408	C	T	1	1	0	0	0.999528991794541	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000322268772155978
CAMB-77C2E	MN908947.3	23403	A	G	1	1	0	0	0.999908136784328	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.42079476992092e-05
CAMB-77C2E	MN908947.3	241	C	T	1	1	0	0	0.999884486542682	TCG	NA	NA	NA	NA	NA	NA	5.77567286588888e-05
CAMB-77C2E	MN908947.3	27281	G	T	1	1	0	0	0.999873041667725	TGG	ORF6	W27L	G80T	TGG>TTG	Missense	GU280_gp06	1.26958332275347e-05
CAMB-77C2E	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999778122919902	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-77C2E	MN908947.3	3037	C	T	1	1	0	1.2e-262	0.999673149207387	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77C3D	MN908947.3	11075	T	-	0.045	0.044	2.7e-11	2.1e-11	0.0449068741356015	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.949353718856742
CAMB-77C3D	MN908947.3	12410	A	G	1	1	0	0	0.99981989380939	TAT	ORF1ab:nsp8	I107V	A319G	ATC>GTC	Missense	ORF1ab:nsp8	2.88169904975974e-05
CAMB-77C3D	MN908947.3	13438	T	C	0.029	0.038	4.3e-13	2.5e-18	0.0299937185929648	TTC	ORF1ab:nsp10	L138L	T414C	CTT>CTC	Synonymous	ORF1ab:nsp10	0.96967912479062
CAMB-77C3D	MN908947.3	14408	C	T	1	1	0	0	0.998505921863634	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000845047109198381
CAMB-77C3D	MN908947.3	14928	C	T	0.022	0.019	2.1e-10	2.9e-10	0.0216525354944245	ACA	ORF1ab:RNA-dependent-RNA-polymerase	N487N	C1461T	AAC>AAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.978310003371502
CAMB-77C3D	MN908947.3	18788	C	T	1	1	0	0	0.999503933651126	ACA	ORF1ab:3'-to-5'-exonuclease	T250I	C749T	ACA>ATA	Missense	ORF1ab:3'-to-5'-exonuclease	3.10041468046351e-05
CAMB-77C3D	MN908947.3	19839	T	C	1	1	0	0	0.999572125725652	ATA	ORF1ab:endoRNAse	N73N	T219C	AAT>AAC	Synonymous	ORF1ab:endoRNAse	0.000265975900270602
CAMB-77C3D	MN908947.3	21093	T	C	1	1	0	0	0.999683999567578	CTA	ORF1ab:2'-O-ribose-methyltransferase	S145S	T435C	TCT>TCC	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	4.15790042660058e-05
CAMB-77C3D	MN908947.3	23403	A	G	1	1	0	0	0.999341868801181	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000352136619294172
CAMB-77C3D	MN908947.3	241	C	T	1	1	0	0	0.998760508980507	TCG	NA	NA	NA	NA	NA	NA	0.000218187557738463
CAMB-77C3D	MN908947.3	2453	C	T	0.017	0.013	4.4e-08	4.2e-07	0.0161331708255821	ACT	ORF1ab:nsp2	L550F	C1648T	CTC>TTC	Missense	ORF1ab:nsp2	0.983866829174418
CAMB-77C3D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999285451197053	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000148522204069508
CAMB-77C3D	MN908947.3	3037	C	T	1	1	0	0	0.99902613757206	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000190294957183635
CAMB-77C4C	MN908947.3	12196	T	INS	0.025	0.0094	1.1e-11	6.7e-06	0.0226478433721173	TTA	ORF1ab:nsp8	.	104-105-insfrshift	.	no-SNV	ORF1ab:nsp8	0.977241833104149
CAMB-77C4C	MN908947.3	14408	C	T	1	1	0	0	0.999436774997603	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000347521809989455
CAMB-77C4C	MN908947.3	22550	C	T	0.028	0.021	1.5e-13	2.3e-11	0.026569442189322	TCC	S	P330S	C988T	CCT>TCT	Missense	GU280_gp02, spike glycoprotein	0.973401036208245
CAMB-77C4C	MN908947.3	23403	A	G	1	1	0	0	0.999942104613104	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.24566170567529e-05
CAMB-77C4C	MN908947.3	241	C	T	1	1	0	0	0.999808786808539	TCG	NA	NA	NA	NA	NA	NA	6.74870087508155e-05
CAMB-77C4C	MN908947.3	28881	GGGG	-	0.0092	0.0215	3.5e-06;7.7e-06;1.6e-05;5.5e-05	3.2e-11;7.5e-11;5.8e-10;1.6e-08	0.0112269446672013	AGG	N	.	608-611-delfrshift	.	no-SNV	GU280_gp10	6.96621386276559e-05
CAMB-77C4C	MN908947.3	28888	TTCTCCTGCTA	-	0.00896363636363636	0.0205454545454545	6.1e-05;9.3e-05;0.0048;0.0057;0.0059;0.0079;0.0071;0.0074;0.01;0.0099;0.0014	2.8e-08;3.6e-08;0.00012;0.00019;2e-04;0.00046;0.00028;0.00034;0.00085;0.00086;4.8e-06	0.0107655502392345	CTT	N	.	615-625-delfrshift	.	no-SNV	GU280_gp10	0.9850430468408
CAMB-77C4C	MN908947.3	28902	TGGCTGGCAATGGCGGTGATGCTGCT	-	0.00903076923076923	0.0207692307692308	0.00015;0.00017;4.4e-05;4.6e-05;3.8e-05;3.3e-05;1.9e-05;4.7e-05;1.6e-05;3.3e-05;4.4e-05;3.2e-05;2.8e-05;2.7e-05;1.6e-05;2.9e-05;2.1e-05;2.7e-05;1.4e-05;1.8e-05;1.6e-05;1.9e-05;1.5e-05;1.6e-05;1.6e-05;1.3e-05	1e-08;2e-08;3.8e-09;3.4e-09;3.5e-09;2.8e-09;1.4e-09;6.1e-09;1.1e-09;4.5e-09;6.6e-09;2.6e-09;2.1e-09;1.9e-09;1.1e-09;2e-09;1.5e-09;2e-09;6.6e-10;1.1e-09;9e-10;1.2e-09;6.4e-10;1e-09;7.7e-10;5.7e-10	0.0108205590622182	ATG	N	.	629-654-delfrshift	.	no-SNV	GU280_gp10	0.985678751790156
CAMB-77C4C	MN908947.3	29635	C	T	0.023	0.02	1.8e-11	6.1e-10	0.0219348294662102	ACA	ORF10	Y26Y	C78T	TAC>TAT	Synonymous	GU280_gp11	0.97806517053379
CAMB-77C4C	MN908947.3	29675	C	T	0.0061	0.013	0.00019	1.5e-06	0.00849720806020879	GCA	NA	NA	NA	NA	NA	NA	0.991502791939791
CAMB-77C4C	MN908947.3	29781	G	T	0.03	0.031	6.6e-13	5.2e-12	0.0304796055580457	AGA	NA	NA	NA	NA	NA	NA	0.969520394441954
CAMB-77C4C	MN908947.3	3037	C	T	1	1	0	0	0.999628321873258	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77C4C	MN908947.3	3205	A	G	0.043	0.17	2.7e-19	2.1e-78	0.0628285075677938	TAG	ORF1ab:nsp3	L162L	A486G	TTA>TTG	Synonymous	ORF1ab:nsp3	0.937100050009696
CAMB-77C4C	MN908947.3	3476	G	A	0.02	0.021	1e-09	4.2e-11	0.0201214845528613	TGT	ORF1ab:nsp3	V253I	G757A	GTT>ATT	Missense	ORF1ab:nsp3	0.979859139920367
CAMB-77C4C	MN908947.3	6361	C	T	0.11	0.22	3.1e-49	1.4e-102	0.125403378024574	ACG	ORF1ab:nsp3	D1214D	C3642T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.874547912176232
CAMB-77C4C	MN908947.3	6875	A	T	0.024	0.011	3.3e-08	0.0023	0.0210656753407683	TAA	ORF1ab:nsp3	K1386*	A4156T	AAG>TAG	Nonsense	ORF1ab:nsp3	0.978934324659232
CAMB-77C4C	MN908947.3	7709	A	T	1	1	0	0	0.999874775639688	AAA	ORF1ab:nsp3	N1664Y	A4990T	AAT>TAT	Missense	ORF1ab:nsp3	4.17414534374087e-05
CAMB-77C5B	MN908947.3	11075	T	-	0.043	0.036	6.7e-11	5.6e-09	0.0416279061900622	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956308626982704
CAMB-77C5B	MN908947.3	14408	C	T	1	1	0	0	0.998089545110243	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000679107011593327
CAMB-77C5B	MN908947.3	18464	C	T	0.0094	0.013	3e-05	1.2e-07	0.00995132354901429	CCT	ORF1ab:3'-to-5'-exonuclease	P142L	C425T	CCT>CTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.989556855841404
CAMB-77C5B	MN908947.3	18730	A	G	0.049	0.051	3.1e-22	1.8e-23	0.0494591499109188	TAT	ORF1ab:3'-to-5'-exonuclease	I231V	A691G	ATT>GTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.950318147111224
CAMB-77C5B	MN908947.3	23403	A	G	1	1	0	0	0.999477787122933	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000140595774594846
CAMB-77C5B	MN908947.3	241	C	T	1	0.99	0	0	0.997244541181374	TCG	NA	NA	NA	NA	NA	NA	7.8727394817885e-05
CAMB-77C5B	MN908947.3	24138	C	T	0.014	0.0064	8.3e-07	0.00018	0.0126803996546195	ACT	S	T859I	C2576T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.980574107032723
CAMB-77C5B	MN908947.3	2440	A	G	1	1	0	0	0.999748590309952	AAG	ORF1ab:nsp2	E545E	A1635G	GAA>GAG	Synonymous	ORF1ab:nsp2	0.00017957835003412
CAMB-77C5B	MN908947.3	24400	A	C	0.27	0.29	7.7e-145	9.1e-147	0.270325729860816	GAA	S	G946G	A2838C	GGA>GGC	Synonymous	GU280_gp02, spike glycoprotein	0.728896995574717
CAMB-77C5B	MN908947.3	25500	G	T	0.19	0.21	2.9e-92	3.7e-98	0.193017111116739	CGA	ORF3a	P36P	G108T	CCG>CCT	Synonymous	GU280_gp03	0.804425085049088
CAMB-77C5B	MN908947.3	2566	A	G	0.014	0.01	1.3e-07	1.3e-06	0.013561976352674	AAC	ORF1ab:nsp2	E587E	A1761G	GAA>GAG	Synonymous	ORF1ab:nsp2	0.986093493070237
CAMB-77C5B	MN908947.3	25974	A	G	0.067	0.065	1.9e-29	5.4e-27	0.0665652835107539	AAT	ORF3a	E194E	A582G	GAA>GAG	Synonymous	GU280_gp03	0.933434716489246
CAMB-77C5B	MN908947.3	26137	A	C	0.021	0.016	3.5e-05	0.0055	0.0206211180124224	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.979130434782609
CAMB-77C5B	MN908947.3	26159	TTAATCCAGTAATGGAACCAATTT	-	0.00607916666666667	0.0162083333333333	0.001;0.002;0.0053;0.0019;0.011;0.012;0.014;7.5e-05;0.0016;0.012;0.01;0.0044;0.02;0.018;0.02;0.018;0.021;0.019;0.021;0.017;0.0043;0.0012;0.0095;0.00064	1.2e-07;3.7e-07;4.5e-06;2.2e-06;0.00013;0.00013;0.00023;8.5e-09;9.2e-07;0.00014;0.00011;8.5e-06;0.00066;0.00042;0.00067;0.00036;0.00072;5e-04;0.00068;0.00066;7.7e-06;2.1e-07;0.00011;1.7e-08	0.00691813539779279	GTT	ORF3a	.	767-790-delinframe	.	no-SNV	GU280_gp03	0.99135446685879
CAMB-77C5B	MN908947.3	26895	C	T	0.015	0.011	2.9e-07	1.9e-06	0.0146078801827488	CCA	M	H125Y	C373T	CAT>TAT	Missense	GU280_gp05	0.985366356360139
CAMB-77C5B	MN908947.3	27476	C	T	0.0064	0.0081	0.00067	4.1e-05	0.00667300092259815	ACA	ORF7a	T28I	C83T	ACA>ATA	Missense	GU280_gp07	0.993321491028766
CAMB-77C5B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999357712191886	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000153366995422585
CAMB-77C5B	MN908947.3	29035	T	C	0.016	0.013	1.3e-05	1.9e-05	0.0151516529075899	CTT	N	A254A	T762C	GCT>GCC	Synonymous	GU280_gp10	0.984752882132596
CAMB-77C5B	MN908947.3	3037	C	T	1	1	0	0	0.99892076518934	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.92986159703033e-05
CAMB-77C5B	MN908947.3	3045	C	T	0.0057	0.008	0.00073	2.6e-05	0.00614475003959246	CCA	ORF1ab:nsp3	P109L	C326T	CCA>CTA	Missense	ORF1ab:nsp3	0.993401256400781
CAMB-77C5B	MN908947.3	4651	T	C	0.016	0.011	2.6e-08	4.6e-07	0.0156436421823898	CTG	ORF1ab:nsp3	A644A	T1932C	GCT>GCC	Synonymous	ORF1ab:nsp3	0.984314248417388
CAMB-77C5B	MN908947.3	6016	C	T	0.14	0.14	2.3e-64	6.6e-60	0.139332681230301	ACC	ORF1ab:nsp3	N1099N	C3297T	AAC>AAT	Synonymous	ORF1ab:nsp3	0.860640147810021
CAMB-77C5B	MN908947.3	6582	C	T	0.0052	0.0083	0.00091	1.9e-05	0.00577829350889241	ACT	ORF1ab:nsp3	T1288I	C3863T	ACT>ATT	Missense	ORF1ab:nsp3	0.994150661898785
CAMB-77C5B	MN908947.3	7065	G	T	0.0085	0.018	0.002	3.2e-05	0.0101676581936182	AGA	ORF1ab:nsp3	R1449I	G4346T	AGA>ATA	Missense	ORF1ab:nsp3	0.989291508923743
CAMB-77C5B	MN908947.3	8782	C	T	0.33	0.35	5.6e-164	7e-179	0.333159457507423	GCC	ORF1ab:nsp4	S76S	C228T	AGC>AGT	Synonymous	ORF1ab:nsp4	0.665887569215954
CAMB-77C6A	MN908947.3	11075	T	-	0.011	0.038	0.0036	9.1e-10	0.0161499422139591	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.975880609014622
CAMB-77C6A	MN908947.3	11152	C	T	0.033	0.031	1.1e-14	2.5e-15	0.0324076950156344	TCA	ORF1ab:nsp6	V60V	C180T	GTC>GTT	Synonymous	ORF1ab:nsp6	0.967550889399681
CAMB-77C6A	MN908947.3	14408	C	T	1	0.99	0	0	0.99706357100738	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00147119261902067
CAMB-77C6A	MN908947.3	17167	C	T	0.0074	0.012	2e-04	8.1e-07	0.00821823992694898	TCA	ORF1ab:helicase	H311Y	C931T	CAT>TAT	Missense	ORF1ab:helicase	0.991757301025649
CAMB-77C6A	MN908947.3	1848	C	T	0.0085	0.012	3.8e-05	1.9e-07	0.00893811240106497	TCA	ORF1ab:nsp2	S348L	C1043T	TCA>TTA	Missense	ORF1ab:nsp2	0.991043775922337
CAMB-77C6A	MN908947.3	19694	C	T	0.012	0.013	1.4e-06	1.1e-07	0.0119453924914676	TCT	ORF1ab:endoRNAse	S25F	C74T	TCT>TTT	Missense	ORF1ab:endoRNAse	0.988054607508532
CAMB-77C6A	MN908947.3	20133	C	T	0.027	0.031	5e-11	7.3e-10	0.0278745644599303	CCG	ORF1ab:endoRNAse	A171A	C513T	GCC>GCT	Synonymous	ORF1ab:endoRNAse	0.97212543554007
CAMB-77C6A	MN908947.3	20406	T	G	0.02	0.03	7.1e-07	1.2e-05	0.0212539851222104	CTT	ORF1ab:endoRNAse	P262P	T786G	CCT>CCG	Synonymous	ORF1ab:endoRNAse	0.977683315621679
CAMB-77C6A	MN908947.3	20847	TAATATGAGAGTT	-	0.00586971538461538	0.0101769230769231	0.00049;0.00059;0.00099;0.0016;0.00041;0.00046;0.0016;0.0011;0.00056;9e-04;0.001;0.00056;NA	5.5e-06;6.7e-06;1.7e-05;3e-05;3.8e-06;3.3e-06;3.2e-05;1.8e-05;5.9e-06;1.5e-05;1.9e-05;5.3e-06;4.1e-06	0.00695188563364085	ATA	ORF1ab:2'-O-ribose-methyltransferase	.	189-201-delfrshift	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.993137330555341
CAMB-77C6A	MN908947.3	23403	A	G	1	1	0	0	0.999889629673062	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.89814543360018e-05
CAMB-77C6A	MN908947.3	241	C	T	1	0.98	0	0	0.993623408645645	TCG	NA	NA	NA	NA	NA	NA	5.21450227575778e-05
CAMB-77C6A	MN908947.3	24213	C	T	0.013	0.0074	4.9e-06	0.00019	0.0117599044696706	TCT	S	S884F	C2651T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.988224979971885
CAMB-77C6A	MN908947.3	25384	AACG	-	0.00127825	0.006525	NA;NA;0.37;0.00086	4.8e-05;3.1e-05;6.2e-05;6.3e-05	0.00128135120376728	AAA	S	.	3822-3822-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.998629503649153
CAMB-77C6A	MN908947.3	25494	G	T	0.09	0.13	1.9e-40	6.5e-59	0.0972432563529063	CGA	ORF3a	T34T	G102T	ACG>ACT	Synonymous	GU280_gp03	0.902659732140451
CAMB-77C6A	MN908947.3	28253	C	T	0.03	0.03	1.2e-12	6.2e-14	0.0299350953826411	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.969872411835838
CAMB-77C6A	MN908947.3	29191	ATTTG	-	0.00752	0.00088	0.00041;1.6e-05;7.5e-06;3.3e-05;2.8e-05	NA;0.00061;NA;NA;NA	0.00602165087956698	AAT	N	.	918-922-delfrshift	.	no-SNV	GU280_gp10	0.99434758531136
CAMB-77C6A	MN908947.3	29218	C	T	0.0085	0.0041	1.8e-05	0.00098	0.00747915247087835	TCG	N	F315F	C945T	TTC>TTT	Synonymous	GU280_gp10	0.986664070865375
CAMB-77C6A	MN908947.3	3037	C	T	0.99	1	0	0	0.99546056991385	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.62690523525514e-05
CAMB-77C6A	MN908947.3	3096	C	T	0.029	0.031	3.6e-11	4.2e-12	0.02934128399465	TCA	ORF1ab:nsp3	S126L	C377T	TCA>TTA	Missense	ORF1ab:nsp3	0.970602987070887
CAMB-77C6A	MN908947.3	3247	T	G	0.01	0.0066	1e-05	3.7e-05	0.00948160163755564	GTG	ORF1ab:nsp3	S176R	T528G	AGT>AGG	Missense	ORF1ab:nsp3	0.990441155171914
CAMB-77C6A	MN908947.3	478	C	T	0.026	0.032	2.6e-12	4.7e-16	0.0265226955719173	TCA	ORF1ab:leader-protein	I71I	C213T	ATC>ATT	Synonymous	ORF1ab:leader-protein	0.973435667543354
CAMB-77C6A	MN908947.3	5338	T	C	0.04	0.031	5.9e-18	3.1e-13	0.0384180790960452	ATC	ORF1ab:nsp3	N873N	T2619C	AAT>AAC	Synonymous	ORF1ab:nsp3	0.961581920903955
CAMB-77C6A	MN908947.3	635	C	T	0.043	0.029	7.2e-19	6.1e-14	0.0412775996270607	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.958722400372939
CAMB-77C6A	MN908947.3	7735	C	T	0.0079	0.022	0.0015	1.4e-07	0.0108455732076192	TCG	ORF1ab:nsp3	I1672I	C5016T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.989154426792381
CAMB-77C6A	MN908947.3	9078	T	C	0.0067	0.0074	2e-04	2.6e-05	0.00682742196908645	GTA	ORF1ab:nsp4	V175A	T524C	GTA>GCA	Missense	ORF1ab:nsp4	0.993082028667928
CAMB-77C79	MN908947.3	103	C	T	0.042	0.0043	1.1e-18	0.00049	0.0358336059062661	GCT	NA	NA	NA	NA	NA	NA	0.9641430306995
CAMB-77C79	MN908947.3	11059	T	G	0.03	0.0027	5.3e-14	0.0015	0.0252717464650788	CTC	ORF1ab:nsp6	T29T	T87G	ACT>ACG	Synonymous	ORF1ab:nsp6	0.974624143502184
CAMB-77C79	MN908947.3	11075	T	-	0.049	0.039	3.6e-12	8e-10	0.0474796328718586	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.948727652301205
CAMB-77C79	MN908947.3	12071	GACAACAGGGCAACCTTA	-	0.000486677777777778	0.00653333333333333	NA;NA;NA;NA;NA;NA;0.37;0.38;NA;NA;NA;NA;NA;NA;NA;0.38;0.0026;0.0019	7.1e-05;8.2e-05;9e-05;7.4e-05;4.5e-05;7.2e-05;5.1e-05;8.2e-06;7.1e-05;8.1e-05;6.4e-05;3.9e-05;2.6e-05;6.9e-05;6.1e-05;5.6e-05;5.9e-05;6.3e-05	0.00123536297394397	GGA	ORF1ab:nsp7	.	229-246-delinframe	.	no-SNV	ORF1ab:nsp7	0.99868605571606
CAMB-77C79	MN908947.3	14408	C	T	1	1	0	0	0.999455600636845	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000400595757793642
CAMB-77C79	MN908947.3	17550	C	T	0.032	0.049	2.7e-14	7e-23	0.0350997150997151	TCG	ORF1ab:helicase	L438L	C1314T	CTC>CTT	Synonymous	ORF1ab:helicase	0.964873470755824
CAMB-77C79	MN908947.3	21889	T	C	0.012	0.024	1.8e-06	2.2e-11	0.014004542013626	CTT	S	T109T	T327C	ACT>ACC	Synonymous	GU280_gp02, spike glycoprotein	0.985957607872824
CAMB-77C79	MN908947.3	22142	T	-	0.0049	0.012	0.00077	3.2e-07	0.00578688431886298	GTT	S	.	580-580-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.994175416109027
CAMB-77C79	MN908947.3	23403	A	G	1	1	0	0	0.998464272115751	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.39408554385074e-05
CAMB-77C79	MN908947.3	23841	G	A	0.0075	0.0066	7e-05	2.3e-05	0.00743136912047561	TGT	S	C760Y	G2279A	TGT>TAT	Missense	GU280_gp02, spike glycoprotein	0.992551145305123
CAMB-77C79	MN908947.3	24010	A	G	0.0043	0.0068	0.0013	1.7e-05	0.00458311299136259	CAT	S	S816S	A2448G	TCA>TCG	Synonymous	GU280_gp02, spike glycoprotein	0.99540709403216
CAMB-77C79	MN908947.3	24076	T	A	1	1	0	0	0.999780081083148	GTG	S	G838G	T2514A	GGT>GGA	Synonymous	GU280_gp02, spike glycoprotein	8.60552283332058e-05
CAMB-77C79	MN908947.3	241	C	T	1	1	0	0	0.998056496305419	TCG	NA	NA	NA	NA	NA	NA	6.41420361247947e-05
CAMB-77C79	MN908947.3	27087	G	A	0.036	0.028	3.5e-16	7.4e-14	0.0343227617411706	AGG	M	G189S	G565A	GGT>AGT	Missense	GU280_gp05	0.965656290586116
CAMB-77C79	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999166724533019	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	5.89263616900081e-05
CAMB-77C79	MN908947.3	29750	C	T	0.052	0.034	1.6e-22	2.5e-14	0.047774251651085	ACG	NA	NA	NA	NA	NA	NA	0.951453812505361
CAMB-77C79	MN908947.3	29831	C	T	0.38	0.39	1.5e-188	3.7e-178	0.380750353547958	GCT	NA	NA	NA	NA	NA	NA	0.619249646452042
CAMB-77C79	MN908947.3	3037	C	T	1	1	0	0	0.999316917672316	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.5055459779462e-05
CAMB-77C79	MN908947.3	3230	G	A	1	1	0	0	0.99981562606015	TGG	ORF1ab:nsp3	G171S	G511A	GGT>AGT	Missense	ORF1ab:nsp3	0.000169624024661858
CAMB-77C79	MN908947.3	5324	G	T	0.0048	0.0098	0.00048	1e-05	0.00589825509953306	AGA	ORF1ab:nsp3	E869*	G2605T	GAG>TAG	Nonsense	ORF1ab:nsp3	0.994101744900467
CAMB-77C79	MN908947.3	8106	C	T	0.0058	0.009	0.00029	4.9e-06	0.00624558735675881	GCA	ORF1ab:nsp3	A1796V	C5387T	GCA>GTA	Missense	ORF1ab:nsp3	0.993678379405855
CAMB-77C79	MN908947.3	8538	TAGCACTTAAGGGTGG	-	0.000449875	0.00663125	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00014;NA;NA;NA;NA;NA	2.2e-05;3.3e-05;2.6e-05;3.6e-05;2.9e-05;3.1e-05;4.5e-05;3.3e-05;4.6e-05;3.7e-05;0.00023;4.4e-05;5.7e-05;7.2e-05;3.5e-05;3.6e-05	0.00139659386274586	ATA	ORF1ab:nsp3	.	5819-5834-delfrshift	.	no-SNV	ORF1ab:nsp3	0.998258143180631
CAMB-77C79	MN908947.3	9474	C	T	0.012	0.0058	6.9e-07	0.00012	0.0114816055111706	GCT	ORF1ab:nsp4	A307V	C920T	GCT>GTT	Missense	ORF1ab:nsp4	0.988446634454385
CAMB-77C79	MN908947.3	9491	C	T	0.58	0.61	0	0	0.583205747261807	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.416723589683194
CAMB-77C79	MN908947.3	9737	A	G	0.02	0.059	5.6e-10	1.2e-27	0.0271183691126372	TAG	ORF1ab:nsp4	S395G	A1183G	AGT>GGT	Missense	ORF1ab:nsp4	0.972841075001352
CAMB-77C79	MN908947.3	9848	A	G	0.012	0.012	1.4e-06	3e-07	0.0120008941294811	TAG	ORF1ab:nsp4	S432G	A1294G	AGT>GGT	Missense	ORF1ab:nsp4	0.987971164324234
CAMB-77C88	MN908947.3	11071	G	INS	0.026	0.024	3.3e-07	8.5e-08	0.0258228202481146	TGT	ORF1ab:nsp6	.	98-99-insfrshift	.	no-SNV	ORF1ab:nsp6	0.974082693216217
CAMB-77C88	MN908947.3	11074	C	-	0.0057	0.011	1.1e-09	5.4e-11	0.00638443291922969	TCT	ORF1ab:nsp6	.	102-102-delfrshift	.	no-SNV	ORF1ab:nsp6	0.812350741768182
CAMB-77C88	MN908947.3	11074	C	INS	0.12	0.089	7e-88	2.3e-31	0.11838539782093	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.812350741768182
CAMB-77C88	MN908947.3	11074	C	T	0.06	0.076	2.3e-76	1.9e-59	0.062863345796647	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.812350741768182
CAMB-77C88	MN908947.3	11083	G	-	0.12	0.15	7.7e-46	7.4e-64	0.121250720397623	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.67081591225282e-05
CAMB-77C88	MN908947.3	11083	G	T	0.88	0.85	0	0	0.876080596434169	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.67081591225282e-05
CAMB-77C88	MN908947.3	12400	C	T	0.0069	0.01	0.00025	2.5e-06	0.00739367120845537	TCA	ORF1ab:nsp8	L103L	C309T	CTC>CTT	Synonymous	ORF1ab:nsp8	0.992582452565898
CAMB-77C88	MN908947.3	14805	C	T	1	0.99	0	0	0.995528988857897	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	2.9831600614531e-05
CAMB-77C88	MN908947.3	16887	C	T	0.021	0.016	1.5e-08	1.8e-07	0.0204461160193366	ACA	ORF1ab:helicase	Y217Y	C651T	TAC>TAT	Synonymous	ORF1ab:helicase	0.97927258709785
CAMB-77C88	MN908947.3	17247	T	C	0.99	1	0	0	0.994947316314263	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000979421540202249
CAMB-77C88	MN908947.3	18312	C	T	0.0031	0.009	0.0065	5.4e-06	0.00397525492654917	TCG	ORF1ab:3'-to-5'-exonuclease	V91V	C273T	GTC>GTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.99600189878077
CAMB-77C88	MN908947.3	2485	C	T	0.038	0.027	6.6e-17	1.7e-12	0.0360952874158467	TCT	ORF1ab:nsp2	I560I	C1680T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.963904712584153
CAMB-77C88	MN908947.3	26144	G	T	1	1	0	0	0.996629986244842	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.00330123796423659
CAMB-77C88	MN908947.3	26340	C	T	0.022	0.017	6.3e-10	3.8e-09	0.0211085694723247	CCA	E	A32A	C96T	GCC>GCT	Synonymous	GU280_gp04	0.978829186312497
CAMB-77C88	MN908947.3	28253	C	T	0.0047	0.017	0.0068	2.3e-08	0.00652996528514182	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.99319469714728
CAMB-77C88	MN908947.3	29614	C	T	1	1	0	0	0.999945259470112	GCA	ORF10	C19C	C57T	TGC>TGT	Synonymous	GU280_gp11	5.47405298883293e-05
CAMB-77C88	MN908947.3	6717	G	T	1	1	0	0	0.999960825792298	AGT	ORF1ab:nsp3	S1333I	G3998T	AGT>ATT	Missense	ORF1ab:nsp3	0
CAMB-77C88	MN908947.3	7393	G	T	0.021	0.017	1e-09	4.1e-09	0.0202627477176575	CGA	ORF1ab:nsp3	P1558P	G4674T	CCG>CCT	Synonymous	ORF1ab:nsp3	0.97961936945787
CAMB-77C97	MN908947.3	10028	A	G	0.0047	0.0073	0.0017	2.2e-05	0.005132328942078	AAC	ORF1ab:nsp4	T492A	A1474G	ACC>GCC	Missense	ORF1ab:nsp4	0.994536553061659
CAMB-77C97	MN908947.3	11074	C	INS	0.11	0.13	8.8e-78	1.9e-52	0.116072800355448	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.879326310194624
CAMB-77C97	MN908947.3	11083	G	-	0.15	0.16	5.1e-59	9.7e-73	0.149387214309374	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.31094540776632e-05
CAMB-77C97	MN908947.3	11083	G	T	0.85	0.83	0	0	0.847878166958103	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.31094540776632e-05
CAMB-77C97	MN908947.3	11595	A	G	0.013	0.0086	1e-06	2.6e-05	0.0120736677596298	CAG	ORF1ab:nsp6	Q208R	A623G	CAG>CGG	Missense	ORF1ab:nsp6	0.987865044586768
CAMB-77C97	MN908947.3	14805	C	T	1	1	0	0	0.999363467827277	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	4.37615868747066e-05
CAMB-77C97	MN908947.3	19097	C	T	0.01	0.021	9.7e-06	3.3e-11	0.0119757868193676	GCA	ORF1ab:3'-to-5'-exonuclease	A353V	C1058T	GCA>GTA	Missense	ORF1ab:3'-to-5'-exonuclease	0.987951544571292
CAMB-77C97	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-77C97	MN908947.3	2558	C	T	1	1	0	0	0.999868355230247	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-77C97	MN908947.3	26144	G	T	1	1	0	0	0.999949919871795	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	5.00801282051282e-05
CAMB-77C97	MN908947.3	26211	G	T	0.016	0.013	3.2e-08	3.6e-07	0.0158169274777049	TGC	ORF3a	V273V	G819T	GTG>GTT	Synonymous	GU280_gp03	0.984141006225812
CAMB-77C97	MN908947.3	26333	C	T	0.01	0.0051	2.4e-05	0.0014	0.00931283351393347	ACA	E	T30I	C89T	ACA>ATA	Missense	GU280_gp04	0.990666721187463
CAMB-77C97	MN908947.3	3016	T	A	0.0037	0.0094	0.0032	3.1e-06	0.00476886776777109	CTT	ORF1ab:nsp3	A99A	T297A	GCT>GCA	Synonymous	ORF1ab:nsp3	0.994932039480243
CAMB-77C97	MN908947.3	522	T	-	0.027	0.039	0.005	3.7e-05	0.0281861492717443	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.971599729428539
CAMB-77C97	MN908947.3	6539	C	T	0.015	0.023	6.8e-08	6.7e-11	0.016893477240732	CCA	ORF1ab:nsp3	H1274Y	C3820T	CAC>TAC	Missense	ORF1ab:nsp3	0.983106522759268
CAMB-77C97	MN908947.3	9165	C	T	0.0091	0.0086	3.3e-05	1.2e-05	0.00903388843072127	ACC	ORF1ab:nsp4	T204I	C611T	ACC>ATC	Missense	ORF1ab:nsp4	0.990920715145004
CAMB-77C97	MN908947.3	9438	C	T	0.12	0.12	1e-53	8.3e-53	0.122772434623639	ACA	ORF1ab:nsp4	T295I	C884T	ACA>ATA	Missense	ORF1ab:nsp4	0.877179874413799
CAMB-77C97	MN908947.3	9491	C	T	0.013	0.0038	1.2e-06	0.0022	0.0114091593757011	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.988574816524052
CAMB-77C97	MN908947.3	9629	T	C	0.017	0.027	4.6e-08	1.5e-13	0.0186418428163508	TTT	ORF1ab:nsp4	F359L	T1075C	TTT>CTT	Missense	ORF1ab:nsp4	0.981017995055672
CAMB-77C97	MN908947.3	9642	T	C	0.0024	0.007	0.0097	2.7e-05	0.00318823635218995	ATT	ORF1ab:nsp4	I363T	T1088C	ATT>ACT	Missense	ORF1ab:nsp4	0.995584135263963
CAMB-77C97	MN908947.3	9924	C	T	0.0083	0.0082	7e-05	1.2e-05	0.00829458057592559	GCA	ORF1ab:nsp4	A457V	C1370T	GCA>GTA	Missense	ORF1ab:nsp4	0.99151538186371
CAMB-77CA6	MN908947.3	110	C	T	1	1	0	0	0.999833461013223	GCT	NA	NA	NA	NA	NA	NA	5.82886453718816e-05
CAMB-77CA6	MN908947.3	11074	C	INS	0.039	0.051	7.3e-15	2.6e-13	0.0410412202326108	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.958727116689745
CAMB-77CA6	MN908947.3	11075	T	-	0.013	0.038	0.0015	9.4e-10	0.0170410679443568	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.982804523697004
CAMB-77CA6	MN908947.3	14408	C	T	1	1	0	0	0.999468328799045	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000418549668836715
CAMB-77CA6	MN908947.3	21372	G	T	1	1	2.3e-248	8.5e-73	1	AGT	ORF1ab:2'-O-ribose-methyltransferase	Q238H	G714T	CAG>CAT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0
CAMB-77CA6	MN908947.3	23403	A	G	1	1	0	0	0.999902729282176	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.7145741722765e-05
CAMB-77CA6	MN908947.3	241	C	T	1	1	0	0	0.999712387036224	TCG	NA	NA	NA	NA	NA	NA	0.000128668957478694
CAMB-77CA6	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999438053682401	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-77CA6	MN908947.3	29614	C	T	1	1	0	0	1	GCA	ORF10	C19C	C57T	TGC>TGT	Synonymous	GU280_gp11	0
CAMB-77CA6	MN908947.3	3037	C	T	1	1	0	0	0.999643910875979	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.08698748601078e-05
CAMB-77CA6	MN908947.3	313	C	T	1	1	0	0	0.999802201647812	TCA	ORF1ab:leader-protein	L16L	C48T	CTC>CTT	Synonymous	ORF1ab:leader-protein	0.000152152578605826
CAMB-77CA6	MN908947.3	9695	T	C	0.007	0.0076	0.00013	1.5e-05	0.00712070335529183	TTA	ORF1ab:nsp4	Y381H	T1141C	TAT>CAT	Missense	ORF1ab:nsp4	0.992828031681747
CAMB-77CB5	MN908947.3	11074	C	INS	0.022	0.021	8.7e-06	0.00062	0.0218503247365726	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.977395100654863
CAMB-77CB5	MN908947.3	11075	T	-	0.036	0.04	1.1e-08	2.7e-10	0.036660837122537	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958666200303136
CAMB-77CB5	MN908947.3	14408	C	T	1	1	0	0	0.997654683175045	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000455803623224438
CAMB-77CB5	MN908947.3	17010	C	T	0.08	0.077	1.9e-35	3.5e-35	0.0796917537066563	TCT	ORF1ab:helicase	I258I	C774T	ATC>ATT	Synonymous	ORF1ab:helicase	0.920248592717925
CAMB-77CB5	MN908947.3	17835	T	C	0.92	0.92	0	0	0.9188475618322	TTG	ORF1ab:helicase	V533V	T1599C	GTT>GTC	Synonymous	ORF1ab:helicase	0.0810904613553916
CAMB-77CB5	MN908947.3	17894	C	T	0.011	0.01	5.7e-06	1.3e-06	0.0111971567054503	GCT	ORF1ab:helicase	A553V	C1658T	GCT>GTT	Missense	ORF1ab:helicase	0.988701778322406
CAMB-77CB5	MN908947.3	19961	C	T	0.077	0.063	5.8e-34	2e-23	0.0759065605327506	ACG	ORF1ab:endoRNAse	T114M	C341T	ACG>ATG	Missense	ORF1ab:endoRNAse	0.923729254461266
CAMB-77CB5	MN908947.3	20102	G	T	0.92	0.91	0	0	0.917956026058632	AGT	ORF1ab:endoRNAse	S161I	G482T	AGT>ATT	Missense	ORF1ab:endoRNAse	0.0806188925081433
CAMB-77CB5	MN908947.3	23403	A	G	1	1	0	0	0.999508177229146	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000116199885421508
CAMB-77CB5	MN908947.3	241	C	T	1	1	0	0	0.998665081615646	TCG	NA	NA	NA	NA	NA	NA	0.000122433342943693
CAMB-77CB5	MN908947.3	28881	GGG	AAC	0.0933333333333333	0.0943333333333333	3e-37;6.2e-45;6.2e-55	8.7e-39;1.4e-41;2.5e-45	0.0948167837478641	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.913422678053988
CAMB-77CB5	MN908947.3	29281	C	T	0.1	0.1	2.5e-45	1.3e-46	0.102276457736674	CCA	N	A336A	C1008T	GCC>GCT	Synonymous	GU280_gp10	0.897610341978062
CAMB-77CB5	MN908947.3	3037	C	T	1	1	0	0	0.99932666820084	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.40927493245374e-05
CAMB-77CC4	MN908947.3	10073	G	A	0.01	0.0098	1.8e-05	5.7e-06	0.010060102902059	GGC	ORF1ab:3C-like-proteinase	A7T	G19A	GCA>ACA	Missense	ORF1ab:3C-like-proteinase	0.989792631181717
CAMB-77CC4	MN908947.3	11075	T	-	0.037	0.037	9.7e-09	6.2e-10	0.0369350374638582	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958161352132796
CAMB-77CC4	MN908947.3	11605	G	T	0.011	0.0086	3.5e-06	8.8e-06	0.0107451336942596	TGC	ORF1ab:nsp6	M211I	G633T	ATG>ATT	Missense	ORF1ab:nsp6	0.988903583088813
CAMB-77CC4	MN908947.3	14408	C	T	1	1	0	0	0.997429208725568	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000491474802464935
CAMB-77CC4	MN908947.3	23403	A	G	1	1	0	0	0.999578164183814	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.63954627738196e-05
CAMB-77CC4	MN908947.3	241	C	T	1	1	0	0	0.998682814604666	TCG	NA	NA	NA	NA	NA	NA	0.000125162413131325
CAMB-77CC4	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.02553125	0.02771875	0.001;0.0021;8e-04;0.00077;0.00021;0.00054;0.00046;0.00075;0.00059;0.00064;0.00094;0.00053;0.00085;0.00054;0.00067;0.00061;0.001;0.00061;7e-04;0.00064;4e-04;8e-04;0.00057;0.00036;7e-04;0.00087;0.00072;0.00047;0.00079;0.00033;0.00058;0.00056	0.00029;0.00067;0.00017;0.00017;7.1e-05;1e-04;8.7e-05;0.00016;1e-04;0.00012;2e-04;1e-04;0.00018;0.00013;0.00012;0.00011;0.00019;0.00012;0.00014;0.00011;9.8e-05;0.00016;1e-04;3.4e-05;0.00011;0.00016;0.00016;8.4e-05;0.00015;6.5e-05;9.6e-05;7.1e-05	0.0257471627186249	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.974949820059597
CAMB-77CC4	MN908947.3	28001	G	T	0.086	0.077	4.9e-37	3.3e-33	0.0847301607689508	CGT	ORF8	P36P	G108T	CCG>CCT	Synonymous	GU280_gp09	0.914991544109777
CAMB-77CC4	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998981701484247	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000230762403479187
CAMB-77CC4	MN908947.3	3037	C	T	1	1	0	0	0.999042183820888	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000119727022388953
CAMB-77CC4	MN908947.3	3429	C	T	1	1	0	0	0.999585759598542	ACA	ORF1ab:nsp3	T237I	C710T	ACA>ATA	Missense	ORF1ab:nsp3	0.000236708800833215
CAMB-77CC4	MN908947.3	4406	C	T	0.051	0.054	1.5e-22	1.2e-24	0.0516930779548928	ACA	ORF1ab:nsp3	H563Y	C1687T	CAT>TAT	Missense	ORF1ab:nsp3	0.948273777958012
CAMB-77CC4	MN908947.3	6123	G	A	1	1	0	0	0.999279439071031	AGA	ORF1ab:nsp3	R1135K	G3404A	AGA>AAA	Missense	ORF1ab:nsp3	2.77138818834354e-05
CAMB-77CC4	MN908947.3	655	A	G	0.13	0.13	1.1e-60	6.8e-59	0.132973789765293	GAG	ORF1ab:leader-protein	G130G	A390G	GGA>GGG	Synonymous	ORF1ab:leader-protein	0.866626944882954
CAMB-77CC4	MN908947.3	662	G	T	0.0076	0.0089	0.00012	5.4e-06	0.00784006561713731	TGG	ORF1ab:leader-protein	G133C	G397T	GGC>TGC	Missense	ORF1ab:leader-protein	0.992015842696214
CAMB-77CC4	MN908947.3	7675	G	T	0.0091	0.0052	2.3e-05	0.00033	0.00838242720080794	CGA	ORF1ab:nsp3	A1652A	G4956T	GCG>GCT	Synonymous	ORF1ab:nsp3	0.991449250967851
CAMB-77CD3	MN908947.3	13914	T	G	0.011	0.0092	2.4e-07	4.8e-06	0.0103813559322034	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.989512711864407
CAMB-77CD3	MN908947.3	14408	C	T	1	1	0	0	0.999677661974858	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000322338025142366
CAMB-77CD3	MN908947.3	19782	A	G	1	1	0	0	1	CAT	ORF1ab:endoRNAse	A54A	A162G	GCA>GCG	Synonymous	ORF1ab:endoRNAse	0
CAMB-77CD3	MN908947.3	23403	A	G	1	1	0	0	0.999867199834738	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.90222956721902e-05
CAMB-77CD3	MN908947.3	241	C	T	1	1	0	0	1	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-77CD3	MN908947.3	3037	C	T	1	1	0	1.9e-202	0.99974025974026	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77CE2	MN908947.3	10871	C	A	0.02	0.15	5.2e-10	2e-66	0.0385553498486585	GCA	ORF1ab:3C-like-proteinase	Q273K	C817A	CAA>AAA	Missense	ORF1ab:3C-like-proteinase	0.961356490052602
CAMB-77CE2	MN908947.3	11075	T	-	0.053	0.066	1.2e-12	5.9e-16	0.0555332228682361	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.944216759973724
CAMB-77CE2	MN908947.3	11233	T	A	0.062	0.043	2.7e-28	1.8e-20	0.0580506040850052	CTG	ORF1ab:nsp6	P87P	T261A	CCT>CCA	Synonymous	ORF1ab:nsp6	0.941732751584527
CAMB-77CE2	MN908947.3	13043	G	T	0.0044	0.0083	0.0019	1.4e-05	0.00521676918032135	AGT	ORF1ab:nsp10	V7L	G19T	GTG>TTG	Missense	ORF1ab:nsp10	0.994745471347516
CAMB-77CE2	MN908947.3	13778	AT	-	0.0155	0.023	1.3e-05;1.5e-05	6.6e-08;7.4e-08	0.0168703925398526	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.983808772127636
CAMB-77CE2	MN908947.3	13780	A	T	0.014	0.026	6.1e-05	4.7e-08	0.0161975339887218	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I105L	A313T	ATA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.983731285441992
CAMB-77CE2	MN908947.3	13980	A	G	0.0069	0.016	0.00014	7.4e-09	0.00862290711813675	AAC	ORF1ab:RNA-dependent-RNA-polymerase	E171E	A513G	GAA>GAG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.991371246843139
CAMB-77CE2	MN908947.3	14408	C	T	1	1	0	0	0.996194736228443	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000328588236541132
CAMB-77CE2	MN908947.3	14694	C	T	0.0065	0.0082	0.00019	6.4e-06	0.00685370895313708	ACT	ORF1ab:RNA-dependent-RNA-polymerase	D409D	C1227T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.993129842145375
CAMB-77CE2	MN908947.3	14849	TATTTG	-	0.0338333333333333	0.0208333333333333	3.7e-05;1.6e-05;2.9e-05;3.1e-05;0.00011;0.00041	0.0082;0.0067;0.00024;0.00022;0.00062;0.0054	0.0313206470446215	CTA	ORF1ab:RNA-dependent-RNA-polymerase	.	1382-1387-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.974328088123879
CAMB-77CE2	MN908947.3	15195	TACTGT	-	0.0040065	0.00645	0.43;3.6e-07;6.5e-07;NA;NA;NA	4.2e-05;4.4e-05;5.4e-05;4.6e-05;0.00028;0.00064	0.00135499897837379	CTA	ORF1ab:RNA-dependent-RNA-polymerase	.	1728-1733-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.998578675989999
CAMB-77CE2	MN908947.3	1546	TA	-	0.017	0.00315	1.9e-06;1.4e-08	NA;0.00025	0.0149802890932983	CTA	ORF1ab:nsp2	.	741-742-delfrshift	.	no-SNV	ORF1ab:nsp2	0.984555984555985
CAMB-77CE2	MN908947.3	1547	A	G	0.036	0.0095	9.4e-16	0.00017	0.0318855134320864	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.918654280692945
CAMB-77CE2	MN908947.3	1547	A	T	0.034	0.04	4.6e-15	3.5e-13	0.0346472508159679	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.918654280692945
CAMB-77CE2	MN908947.3	20104	C	T	0.031	0.015	1.7e-08	0.00029	0.0283831728332489	TCT	ORF1ab:endoRNAse	L162F	C484T	CTT>TTT	Missense	ORF1ab:endoRNAse	0.971616827166751
CAMB-77CE2	MN908947.3	20134	G	T	1	1	0	1.3e-302	0.999545867393279	CGT	ORF1ab:endoRNAse	V172L	G514T	GTA>TTA	Missense	ORF1ab:endoRNAse	0
CAMB-77CE2	MN908947.3	21930	CTA	-	0.0146666666666667	0.00316666666666667	2.7e-08;6.1e-08;9.2e-08	NA;3.9e-06;NA	0.0114129100875399	GCT	S	.	368-370-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.987977247263639
CAMB-77CE2	MN908947.3	23133	TTTGTGGACCTA	-	0.008425	0.0017175	5.2e-06;1.4e-05;1.7e-05;2e-05;1.7e-05;1.8e-05;1.6e-05;1.6e-05;1.3e-05;1.3e-05;1.4e-05;0.00025	2.1e-06;3.6e-06;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.48	0.00621868019078669	GTT	S	.	1571-1582-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.989564765300059
CAMB-77CE2	MN908947.3	23403	A	G	1	1	0	0	0.999902106730669	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.0761339585e-05
CAMB-77CE2	MN908947.3	23761	G	A	0.014	0.06	2e-07	4.5e-27	0.0223731920149819	AGA	S	K733K	G2199A	AAG>AAA	Synonymous	GU280_gp02, spike glycoprotein	0.977606885285094
CAMB-77CE2	MN908947.3	241	C	T	1	1	0	0	0.999797185220597	TCG	NA	NA	NA	NA	NA	NA	0.000101407389701355
CAMB-77CE2	MN908947.3	24863	C	T	0.014	0.0086	3.8e-07	1.1e-05	0.0130645995822394	ACA	S	H1101Y	C3301T	CAC>TAC	Missense	GU280_gp02, spike glycoprotein	0.986901864591917
CAMB-77CE2	MN908947.3	25521	C	G	0.0073	0.019	0.001	5.5e-08	0.00955664878201032	TCG	ORF3a	F43L	C129G	TTC>TTG	Missense	GU280_gp03	0.99034426724928
CAMB-77CE2	MN908947.3	25918	A	G	0.011	0.015	7.1e-07	3.2e-08	0.0121105232216343	AAC	ORF3a	T176A	A526G	ACA>GCA	Missense	GU280_gp03	0.987830687830688
CAMB-77CE2	MN908947.3	2657	A	G	0.0098	0.012	1.1e-05	5.2e-05	0.0104022191400832	AAA	ORF1ab:nsp2	K618E	A1852G	AAG>GAG	Missense	ORF1ab:nsp2	0.989597780859917
CAMB-77CE2	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.0286829268292683	0.0524878048780488	2.3e-05;3.8e-06;9.9e-05;1e-04;0.00023;2.9e-05;0.00011;0.00047;0.00044;0.00012;0.00035;0.00027;0.00047;0.00039;0.00045;6e-04;0.00037;0.00053;0.00031;0.00041;0.00042;0.00064;0.00045;0.00047;4e-04;3e-04;5e-04;0.00035;0.00026;4e-04;0.00054;5e-04;4e-04;0.00054;0.00017;0.00034;0.00027;0.029;0.038;0.0089;0.0098	3.5e-05;1.1e-06;1.2e-06;1.7e-06;3e-06;4.5e-07;7.1e-07;9.7e-10;9.4e-10;2.8e-10;4.3e-10;3.7e-10;8.5e-10;4e-10;6.4e-10;1.3e-09;3.2e-10;1.2e-09;6e-10;6.1e-10;3.7e-10;1.2e-09;2.2e-10;7.1e-10;5.4e-10;2.2e-10;8e-10;4.2e-10;3e-10;5.1e-10;8.6e-10;6.6e-10;3.1e-10;7.8e-10;9.2e-11;3.8e-10;2.6e-10;1.8e-05;9.1e-05;5.1e-06;1e-05	0.033877287231894	GTC	M	.	258-298-delfrshift	.	no-SNV	GU280_gp05	0.96701526297393
CAMB-77CE2	MN908947.3	28860	A	T	0.015	0.013	7.9e-08	1.6e-07	0.0144212742637939	AAT	N	N196I	A587T	AAT>ATT	Missense	GU280_gp10	0.985319142799458
CAMB-77CE2	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999467025723022	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	6.20713199466187e-05
CAMB-77CE2	MN908947.3	28909	C	T	0.016	0.0026	3.9e-08	0.0067	0.0136227505234423	GCA	N	G212G	C636T	GGC>GGT	Synonymous	GU280_gp10	0.986271235853807
CAMB-77CE2	MN908947.3	29242	A	G	0.015	0.015	7.7e-08	3.3e-08	0.0149756900801886	AAG	N	E323E	A969G	GAA>GAG	Synonymous	GU280_gp10	0.954722165385402
CAMB-77CE2	MN908947.3	29242	A	T	0.018	0.0079	6.2e-09	2.6e-05	0.0156479884637495	AAG	N	E323D	A969T	GAA>GAT	Missense	GU280_gp10	0.954722165385402
CAMB-77CE2	MN908947.3	3037	C	T	1	1	0	0	0.999542086420781	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.32570144034635e-05
CAMB-77CE2	MN908947.3	3900	A	T	0.011	0.013	2.6e-06	9e-08	0.0111725168035848	AAG	ORF1ab:nsp3	K394M	A1181T	AAG>ATG	Missense	ORF1ab:nsp3	0.98873786407767
CAMB-77CE2	MN908947.3	4535	T	C	0.01	0.0079	1.1e-05	6.1e-05	0.00960255249957816	CTT	ORF1ab:nsp3	F606L	T1816C	TTT>CTT	Missense	ORF1ab:nsp3	0.990305410256017
CAMB-77CE2	MN908947.3	522	TTG	-	0.0586666666666667	0.0233333333333333	1.2e-11;1.1e-07;0.00061	8.5e-05;5.5e-05;NA	0.0559620728136071	GTT	ORF1ab:leader-protein	.	257-259-delinframe	.	no-SNV	ORF1ab:leader-protein	0.905409906266356
CAMB-77CE2	MN908947.3	5830	G	T	0.012	0.014	2.3e-06	3.2e-08	0.0123363221902219	AGT	ORF1ab:nsp3	K1037N	G3111T	AAG>AAT	Missense	ORF1ab:nsp3	0.987628697690146
CAMB-77CE2	MN908947.3	8300	A	-	0.0095	0.012	3.5e-05	2.9e-06	0.00990615815811272	CAA	ORF1ab:nsp3	.	5581-5581-delfrshift	.	no-SNV	ORF1ab:nsp3	0.989969021979643
CAMB-77CE2	MN908947.3	8477	T	-	0.014	0.014	1.2e-07	6.7e-08	0.0138639132200244	CTT	ORF1ab:nsp3	.	5758-5758-delfrshift	.	no-SNV	ORF1ab:nsp3	0.985788038749347
CAMB-77CE2	MN908947.3	9041	T	C	0.011	0.0019	2.6e-06	0.0079	0.00928924759177298	TTC	ORF1ab:nsp4	S163P	T487C	TCT>CCT	Missense	ORF1ab:nsp4	0.990648268680031
CAMB-77CF1	MN908947.3	11074	C	INS	0.023	0.017	1e-06	0.0055	0.0219773724505761	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.97663535154756
CAMB-77CF1	MN908947.3	11075	T	-	0.043	0.047	2.4e-11	1.9e-11	0.0437347418200802	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951600669440649
CAMB-77CF1	MN908947.3	13255	C	T	0.012	0.027	5e-06	1.6e-13	0.0142512544517392	GCC	ORF1ab:nsp10	C77C	C231T	TGC>TGT	Synonymous	ORF1ab:nsp10	0.985725989054126
CAMB-77CF1	MN908947.3	14408	C	T	1	1	0	0	0.999156909894335	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00030836758728607
CAMB-77CF1	MN908947.3	16466	C	T	0.021	0.01	2.8e-06	0.00026	0.0198140289565652	CCA	ORF1ab:helicase	P77L	C230T	CCA>CTA	Missense	ORF1ab:helicase	0.980107963055417
CAMB-77CF1	MN908947.3	17491	C	T	0.012	0.012	2.3e-06	4.1e-07	0.0123234551211356	ACC	ORF1ab:helicase	P419S	C1255T	CCA>TCA	Missense	ORF1ab:helicase	0.987676544878864
CAMB-77CF1	MN908947.3	2137	C	T	0.011	0.0089	4.3e-06	2.7e-06	0.0108106736369289	TCA	ORF1ab:nsp2	L444L	C1332T	CTC>CTT	Synonymous	ORF1ab:nsp2	0.98917663777899
CAMB-77CF1	MN908947.3	23403	A	G	1	1	0	0	0.998817969669804	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00061559203334964
CAMB-77CF1	MN908947.3	241	C	T	1	1	0	0	0.998734126667199	TCG	NA	NA	NA	NA	NA	NA	7.18792428719751e-05
CAMB-77CF1	MN908947.3	25429	G	T	1	1	0	0	0.997483310590523	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	8.98817646241717e-05
CAMB-77CF1	MN908947.3	29582	TTTCCG	-	0.0428333333333333	0.0476666666666667	5.1e-18;8.8e-21;3e-18;5.5e-18;7.6e-19;8.1e-18	6e-21;1.6e-23;9.5e-21;1.1e-20;3.3e-21;1.4e-20	0.0421489535835379	TTT	ORF10	.	25-30-delinframe	.	no-SNV	GU280_gp11	0.957155648991669
CAMB-77CF1	MN908947.3	3037	C	T	1	1	0	0	0.998398137691013	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000103717703459562
CAMB-77CF1	MN908947.3	7299	C	T	0.0052	0.014	0.0014	3e-05	0.00754716981132075	GCA	ORF1ab:nsp3	A1527V	C4580T	GCA>GTA	Missense	ORF1ab:nsp3	0.991194968553459
CAMB-77CF1	MN908947.3	7765	C	T	0.026	0.038	1.2e-11	3.5e-17	0.0282914394366786	CCA	ORF1ab:nsp3	S1682S	C5046T	TCC>TCT	Synonymous	ORF1ab:nsp3	0.9713115610439
CAMB-77D0D	MN908947.3	10604	C	T	0.052	0.049	4.8e-23	1.9e-22	0.051118452303839	ACC	ORF1ab:3C-like-proteinase	P184S	C550T	CCT>TCT	Missense	ORF1ab:3C-like-proteinase	0.948773588979574
CAMB-77D0D	MN908947.3	11074	C	INS	0.021	0.019	1.5e-05	0.0025	0.0209423246140309	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.978353731701464
CAMB-77D0D	MN908947.3	11075	T	-	0.037	0.04	7.7e-09	4.4e-10	0.0372842443402471	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957763037913749
CAMB-77D0D	MN908947.3	13778	AT	-	0.0325	0.027	8e-09;1.1e-08	1.3e-08;2.4e-08	0.0313202317619653	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.969865472026827
CAMB-77D0D	MN908947.3	13780	A	T	0.026	0.023	1.4e-06	5.6e-07	0.0255878457732577	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I105L	A313T	ATA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.965766261026013
CAMB-77D0D	MN908947.3	14408	C	T	1	1	0	0	0.998410182040912	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000441365892324737
CAMB-77D0D	MN908947.3	1547	A	-	0.014	0.014	7.2e-07	2.2e-07	0.0139943366027825	TAG	ORF1ab:nsp2	.	742-742-delfrshift	.	no-SNV	ORF1ab:nsp2	0.899413140723109
CAMB-77D0D	MN908947.3	1547	A	G	0.035	0.033	6.7e-15	7.1e-15	0.0348422046210038	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.899413140723109
CAMB-77D0D	MN908947.3	1547	A	T	0.051	0.044	1.8e-22	2.1e-19	0.0494931669881397	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.899413140723109
CAMB-77D0D	MN908947.3	21997	C	T	0.016	0.015	1.6e-07	3e-08	0.0153958882534763	ACC	S	Y145Y	C435T	TAC>TAT	Synonymous	GU280_gp02, spike glycoprotein	0.984102987375035
CAMB-77D0D	MN908947.3	23403	A	G	1	1	0	0	0.999393889220689	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.27858625399885e-05
CAMB-77D0D	MN908947.3	241	C	T	1	1	0	0	0.998777831187294	TCG	NA	NA	NA	NA	NA	NA	0.000178978696421449
CAMB-77D0D	MN908947.3	26456	C	T	1	1	0	0	0.999177510434569	CCT	E	P71L	C212T	CCT>CTT	Missense	GU280_gp04	0.000104345691136754
CAMB-77D0D	MN908947.3	26530	A	G	1	1	0	0	0.999199368644989	GAT	M	D3G	A8G	GAT>GGT	Missense	GU280_gp05	0.000571879539293843
CAMB-77D0D	MN908947.3	27267	TAAAGTTTCCATTTGGAATCTTG	-	0.0354347826086957	0.035695652173913	1.5e-08;2.6e-09;4.1e-09;5.4e-09;7.2e-09;1.8e-09;1.1e-08;1.3e-08;6.5e-09;2.6e-09;4.9e-09;2.1e-09;9.8e-09;1.1e-08;7.9e-09;2.2e-08;4.6e-09;6.3e-09;6.2e-09;8.6e-09;1.4e-09;7.6e-09;1e-09	1.2e-09;2.3e-10;4e-10;5.3e-10;6.7e-10;1.4e-10;9.6e-10;1.1e-09;7e-10;4e-10;5.2e-10;3.5e-10;1.3e-09;1e-09;7.2e-10;2.7e-09;5.9e-10;1.1e-09;7.1e-10;8.6e-10;1.2e-10;8.3e-10;7.1e-11	0.0350520822646723	TTA	ORF6	.	66-88-delfrshift	.	no-SNV	GU280_gp06	0.966275223234005
CAMB-77D0D	MN908947.3	3037	C	T	1	1	0	0	0.999020706409665	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000122411698791891
CAMB-77D0D	MN908947.3	5079	C	T	0.064	0.065	1.6e-29	1.1e-27	0.06405707527374	ACT	ORF1ab:nsp3	T787I	C2360T	ACT>ATT	Missense	ORF1ab:nsp3	0.935542329556293
CAMB-77D0D	MN908947.3	5365	C	T	0.02	0.018	9.2e-09	5e-09	0.0194473644691395	ACA	ORF1ab:nsp3	Y882Y	C2646T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.980440006006908
CAMB-77D0D	MN908947.3	5767	T	C	0.0072	0.0089	0.00014	5.6e-06	0.00753948981243785	GTC	ORF1ab:nsp3	G1016G	T3048C	GGT>GGC	Synonymous	ORF1ab:nsp3	0.992287055667337
CAMB-77D1C	MN908947.3	10347	CACCTAA	-	0.00243238571428571	0.00457142857142857	0.00045;0.00036;0.00035;NA;NA;0.4;NA	0.00087;0.00053;0.00056;0.00037;0.00072;0.00075;3.1e-05	0.000855087072890959	ACA	ORF1ab:3C-like-proteinase	.	293-299-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.994663813477257
CAMB-77D1C	MN908947.3	11075	T	-	0.05	0.039	2.2e-12	7.7e-10	0.0479853450162518	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.947001321218114
CAMB-77D1C	MN908947.3	13980	A	G	0.0046	0.0097	0.0015	3.8e-06	0.00547966387529174	AAC	ORF1ab:RNA-dependent-RNA-polymerase	E171E	A513G	GAA>GAG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.993819673636245
CAMB-77D1C	MN908947.3	14408	C	T	1	1	0	0	0.999500228156711	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000336802763955586
CAMB-77D1C	MN908947.3	15017	C	T	0.028	0.012	5.2e-13	3.3e-06	0.0240231199951833	GCA	ORF1ab:RNA-dependent-RNA-polymerase	A517V	C1550T	GCA>GTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.975976880004817
CAMB-77D1C	MN908947.3	1547	A	T	0.014	0.013	1.9e-07	4.2e-07	0.0141968325791855	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.973981900452489
CAMB-77D1C	MN908947.3	16150	T	C	0.0042	0.0073	0.0015	2e-05	0.00464061686678959	TTC	ORF1ab:RNA-dependent-RNA-polymerase	S895P	T2683C	TCT>CCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.995346149434921
CAMB-77D1C	MN908947.3	1912	C	T	0.0061	0.008	0.00044	3.4e-05	0.00638746692610542	CCC	ORF1ab:nsp2	S369S	C1107T	TCC>TCT	Synonymous	ORF1ab:nsp2	0.993548885716624
CAMB-77D1C	MN908947.3	22166	AA	-	0.00355	0.0096	9.8e-05;NA	8.3e-06;7.8e-07	0.00462361917777019	TAA	S	.	604-605-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.992550488739612
CAMB-77D1C	MN908947.3	23403	A	G	1	1	0	0	0.999923448172673	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.87147992080366e-05
CAMB-77D1C	MN908947.3	241	C	T	1	1	0	0	0.99976201679945	TCG	NA	NA	NA	NA	NA	NA	0.000124400309378161
CAMB-77D1C	MN908947.3	28621	G	C	0.0069	0.0079	0.00038	2.3e-05	0.00706165079951936	GGC	N	G116G	G348C	GGG>GGC	Synonymous	GU280_gp10	0.992624087253905
CAMB-77D1C	MN908947.3	28762	A	G	0.0024	0.0078	0.0072	1.9e-05	0.00321106293214579	AAG	N	Q163Q	A489G	CAA>CAG	Synonymous	GU280_gp10	0.996695183405602
CAMB-77D1C	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999533763307172	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	5.6663644605621e-05
CAMB-77D1C	MN908947.3	3037	C	T	1	1	0	0	0.99970820668693	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77D2B	MN908947.3	11074	C	INS	0.11	0.11	3e-43	1.5e-41	0.110316992061789	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.886156404205106
CAMB-77D2B	MN908947.3	11083	G	-	0.17	0.17	5.2e-76	5.1e-77	0.172232756577388	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.37022991230149e-05
CAMB-77D2B	MN908947.3	11083	G	T	0.83	0.83	0	0	0.827411708935767	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.37022991230149e-05
CAMB-77D2B	MN908947.3	12396	C	T	0.15	0.15	1.3e-67	5.7e-68	0.148535924667842	GCA	ORF1ab:nsp8	A102V	C305T	GCA>GTA	Missense	ORF1ab:nsp8	0.851421077525046
CAMB-77D2B	MN908947.3	14805	C	T	1	1	0	0	0.998440362662658	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000497956499271856
CAMB-77D2B	MN908947.3	16375	C	T	0.47	0.48	9.1e-204	2.9e-212	0.473454188685977	TCC	ORF1ab:helicase	P47S	C139T	CCG>TCG	Missense	ORF1ab:helicase	0.526501215242937
CAMB-77D2B	MN908947.3	16949	C	T	0.28	0.28	3.4e-136	1.4e-136	0.278316604927835	CCT	ORF1ab:helicase	P238L	C713T	CCT>CTT	Missense	ORF1ab:helicase	0.721468205782444
CAMB-77D2B	MN908947.3	17247	T	C	1	1	0	0	0.99887658285812	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000659397018060152
CAMB-77D2B	MN908947.3	2091	C	T	1	1	0	0	0.999620390997273	ACT	ORF1ab:nsp2	T429I	C1286T	ACT>ATT	Missense	ORF1ab:nsp2	0.000119876527177008
CAMB-77D2B	MN908947.3	24107	C	T	0.034	0.033	3.6e-16	5.5e-16	0.0333804809052334	CCT	S	L849F	C2545T	CTC>TTC	Missense	GU280_gp02, spike glycoprotein	0.966453115899825
CAMB-77D2B	MN908947.3	25658	C	T	0.13	0.13	5.8e-57	3.4e-56	0.126609850487449	ACA	ORF3a	T89I	C266T	ACA>ATA	Missense	GU280_gp03	0.872734578213885
CAMB-77D2B	MN908947.3	26144	G	T	1	1	0	0	0.999738276990185	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000218102508178844
CAMB-77D2B	MN908947.3	26204	C	T	0.021	0.021	2.8e-10	1.5e-10	0.021151100758885	ACT	ORF3a	T271I	C812T	ACT>ATT	Missense	GU280_gp03	0.978811330678488
CAMB-77D2B	MN908947.3	26959	G	A	1	1	0	0	0.999228958688418	CGT	M	R146H	G437A	CGT>CAT	Missense	GU280_gp05	0.000101452804155507
CAMB-77D2B	MN908947.3	27247	C	T	0.02	0.019	1.4e-10	5.7e-10	0.0195762158419425	ACT	ORF6	L16L	C46T	CTA>TTA	Synonymous	GU280_gp06	0.980392311142234
CAMB-77D2B	MN908947.3	27873	A	INS	0.12	0.12	3.9e-53	1e-51	0.118262785786429	AAC	NA	NA	NA	NA	NA	NA	0.881645395280507
CAMB-77D2B	MN908947.3	27876	TG	GT	0.13	0.13	3.2e-57;5.5e-57	5.8e-57;7.3e-56	0.129447787984373	TTG	NA	NA	NA	NA	NA	NA	0.870509256831174
CAMB-77D2B	MN908947.3	27880	ACG	-	0.133333333333333	0.133333333333333	2e-58;4.8e-59;1e-61	1.2e-56;2.7e-57;2.2e-59	0.132469402447804	CAC	NA	NA	NA	NA	NA	NA	0.868510876763972
CAMB-77D2B	MN908947.3	27883	C	T	0.13	0.13	4.8e-58	1.5e-56	0.130995063652897	GCC	NA	NA	NA	NA	NA	NA	0.86858924395947
CAMB-77D2B	MN908947.3	4987	A	G	0.011	0.012	5.5e-07	4.9e-07	0.0114545589782278	TAG	ORF1ab:nsp3	V756V	A2268G	GTA>GTG	Synonymous	ORF1ab:nsp3	0.988343551763343
CAMB-77D2B	MN908947.3	5097	A	G	0.0072	0.01	5.2e-05	5.3e-06	0.00869970483144322	AAT	ORF1ab:nsp3	N793S	A2378G	AAT>AGT	Missense	ORF1ab:nsp3	0.989436072704676
CAMB-77D2B	MN908947.3	9510	C	T	0.0067	0.0072	3.8e-05	2.7e-05	0.00698935794920038	ACT	ORF1ab:nsp4	T319I	C956T	ACT>ATT	Missense	ORF1ab:nsp4	0.992959195672625
CAMB-77D2B	MN908947.3	9848	A	G	0.0094	0.011	3.9e-06	1.2e-06	0.0102412651534999	TAG	ORF1ab:nsp4	S432G	A1294G	AGT>GGT	Missense	ORF1ab:nsp4	0.989401481410913
CAMB-77D3A	MN908947.3	11074	C	INS	0.12	0.13	3.1e-51	2.5e-52	0.125256076279117	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.870102936341334
CAMB-77D3A	MN908947.3	11083	G	-	0.17	0.15	1.1e-73	3.6e-64	0.156827257653955	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-77D3A	MN908947.3	11083	G	T	0.83	0.85	0	0	0.842962565096565	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-77D3A	MN908947.3	14805	C	T	1	1	0	0	0.997091644149254	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000928198675769889
CAMB-77D3A	MN908947.3	1515	A	G	1	1	0	0	0.998892988929889	CAT	ORF1ab:nsp2	H237R	A710G	CAT>CGT	Missense	ORF1ab:nsp2	0.000553505535055351
CAMB-77D3A	MN908947.3	17247	T	C	1	1	0	0	0.999260181748684	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000308257604715108
CAMB-77D3A	MN908947.3	24023	C	T	0.039	0.032	2.3e-18	1.8e-15	0.0360580845162343	TCT	S	L821L	C2461T	CTA>TTA	Synonymous	GU280_gp02, spike glycoprotein	0.953046536502239
CAMB-77D3A	MN908947.3	25763	T	C	0.014	0.012	7.7e-08	2.6e-07	0.0129913953096001	ATA	ORF3a	I124T	T371C	ATA>ACA	Missense	GU280_gp03	0.986772397502953
CAMB-77D3A	MN908947.3	25910	A	G	0.02	0.017	1.8e-10	3e-09	0.0187095534055232	GAT	ORF3a	D173G	A518G	GAT>GGT	Missense	GU280_gp03	0.981290446594477
CAMB-77D3A	MN908947.3	26144	G	T	1	1	0	0	0.999398935256741	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.00034346556757685
CAMB-77D3A	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0403947368421053	0.0368421052631579	6.9e-05;1.2e-06;2e-05;2e-05;7.2e-05;1.9e-07;4.6e-06;5.1e-07;4.8e-07;7.6e-08;1.7e-07;9e-08;4.1e-07;2.2e-07;2.8e-07;5.7e-07;1.8e-07;5.4e-07;2.7e-07;3.2e-07;2.8e-07;6e-07;2.4e-07;4e-07;2.7e-07;1.6e-07;4.1e-07;2.1e-07;5.8e-08;2.4e-07;4.4e-07;4.1e-07;2.6e-07;6.9e-07;1.4e-07;3.1e-07;1.7e-07;0.00027	0.00014;1.6e-05;3.7e-05;4.6e-05;7.9e-05;1.9e-06;4.8e-06;2.2e-06;2.1e-06;1.6e-06;1.4e-06;1.1e-06;1.7e-06;1.5e-06;1.6e-06;2.4e-06;1.2e-06;2.4e-06;1.3e-06;1.8e-06;1.5e-06;3e-06;1.6e-06;2e-06;1.5e-06;8.2e-07;1.8e-06;1.5e-06;1.1e-07;1.7e-06;2.4e-06;2.2e-06;9.8e-07;2.6e-06;4.1e-07;1.5e-06;7.7e-07;0.00047	0.0400544605809129	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.973331953802977
CAMB-77D3A	MN908947.3	5170	C	T	1	1	0	0	0.999012183075403	ACC	ORF1ab:nsp3	Y817Y	C2451T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.00016463615409944
CAMB-77D3A	MN908947.3	522	TT	-	0.031	0.036	0.00011;0.0012	1.3e-05;0.00044	0.0327973925731975	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.96016653538877
CAMB-77D3A	MN908947.3	5302	A	T	0.0054	0.008	0.00025	1.8e-05	0.00644857929737355	CAT	ORF1ab:nsp3	A861A	A2583T	GCA>GCT	Synonymous	ORF1ab:nsp3	0.993551420702626
CAMB-77D3A	MN908947.3	9223	C	T	1	1	0	0	0.996170833061375	ACG	ORF1ab:nsp4	H223H	C669T	CAC>CAT	Synonymous	ORF1ab:nsp4	0.000195809672997846
CAMB-77D58	MN908947.3	11075	T	-	0.029	0.036	2.7e-07	3.7e-09	0.0303195893914962	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962757594145275
CAMB-77D58	MN908947.3	14408	C	T	1	1	0	0	0.999528758153724	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000359631935315856
CAMB-77D58	MN908947.3	15652	G	T	0.007	0.0077	0.00028	2e-05	0.00715711805555556	TGA	ORF1ab:RNA-dependent-RNA-polymerase	D729Y	G2185T	GAC>TAC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.992821180555556
CAMB-77D58	MN908947.3	17339	C	T	0.01	0.0045	2.2e-05	0.0013	0.00939276042262654	GCA	ORF1ab:helicase	A368V	C1103T	GCA>GTA	Missense	ORF1ab:helicase	0.990581810784351
CAMB-77D58	MN908947.3	2164	G	A	1	1	0	0	0.999185854217021	AGA	ORF1ab:nsp2	E453E	G1359A	GAG>GAA	Synonymous	ORF1ab:nsp2	0.000763261671543061
CAMB-77D58	MN908947.3	23403	A	G	1	1	0	0	0.9998814698766	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.79161888957888e-05
CAMB-77D58	MN908947.3	241	C	T	1	1	0	0	0.99979580376742	TCG	NA	NA	NA	NA	NA	NA	0.000114860380825974
CAMB-77D58	MN908947.3	264	A	G	1	0.99	0	0	0.998822001389434	AAG	NA	NA	NA	NA	NA	NA	0.00111758842540852
CAMB-77D58	MN908947.3	28881	GGG	AAC	1	0.996666666666667	0;0;0	0;0;0	0.998709199192291	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000950584033068802
CAMB-77D58	MN908947.3	3037	C	T	1	1	0	0	0.998399318859089	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000255427841634738
CAMB-77D58	MN908947.3	5826	C	T	1	1	0	0	0.999914095989142	ACA	ORF1ab:nsp3	T1036I	C3107T	ACA>ATA	Missense	ORF1ab:nsp3	3.43616043433068e-05
CAMB-77D67	MN908947.3	14408	C	T	1	1	0	0	0.999374413512668	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000547388176415389
CAMB-77D67	MN908947.3	17014	G	T	1	1	0	0	0.999846492350202	AGA	ORF1ab:helicase	D260Y	G778T	GAT>TAT	Missense	ORF1ab:helicase	5.11692165992939e-05
CAMB-77D67	MN908947.3	18189	C	T	1	1	0	0	0.999935379644588	CCT	ORF1ab:3'-to-5'-exonuclease	T50T	C150T	ACC>ACT	Synonymous	ORF1ab:3'-to-5'-exonuclease	6.46203554119548e-05
CAMB-77D67	MN908947.3	19053	T	C	1	1	0	0	0.99978265594436	TTA	ORF1ab:3'-to-5'-exonuclease	I338I	T1014C	ATT>ATC	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.000217344055640078
CAMB-77D67	MN908947.3	241	C	T	1	1	0	0	0.999929824561404	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-77D67	MN908947.3	28881	G	A	1	1	0	1.4e-280	0.999512195121951	AGG	N	R203K	G608A	AGG>AAG	Missense	GU280_gp10	0
CAMB-77D67	MN908947.3	28881	GGG	AAC	1	1	0;0;0	1.4e-280;9.6e-303;3.60000000046285e-315	0.999570446735395	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-77D67	MN908947.3	28883	G	C	1	1	0	3.60000000046285e-315	0.999214145383104	GGG	N	G204R	G610C	GGA>CGA	Missense	GU280_gp10	0
CAMB-77D67	MN908947.3	3037	C	T	1	1	0	1.4e-163	0.999227202472952	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77D76	MN908947.3	10341	C	T	0.033	0.049	7.2e-16	2.1e-23	0.0358738173847904	CCT	ORF1ab:3C-like-proteinase	P96L	C287T	CCT>CTT	Missense	ORF1ab:3C-like-proteinase	0.96412618261521
CAMB-77D76	MN908947.3	10369	C	T	0.26	0.31	1.6e-123	1.4e-155	0.267288989466311	GCA	ORF1ab:3C-like-proteinase	R105R	C315T	CGC>CGT	Synonymous	ORF1ab:3C-like-proteinase	0.732670599962283
CAMB-77D76	MN908947.3	14408	C	T	1	1	0	0	0.999569312373202	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000306014892724779
CAMB-77D76	MN908947.3	17012	C	T	1	1	0	0	0.999700017646021	TCA	ORF1ab:helicase	S259L	C776T	TCA>TTA	Missense	ORF1ab:helicase	7.05840832892183e-05
CAMB-77D76	MN908947.3	17479	G	A	0.32	0.43	2.8e-162	1.8e-229	0.333874297102997	GGG	ORF1ab:helicase	G415S	G1243A	GGC>AGC	Missense	ORF1ab:helicase	0.666111467008328
CAMB-77D76	MN908947.3	17944	G	T	1	1	0	0	0.999938591284056	AGT	ORF1ab:helicase	V570L	G1708T	GTA>TTA	Missense	ORF1ab:helicase	2.04695719812499e-05
CAMB-77D76	MN908947.3	23403	A	G	1	1	0	0	0.999883088110645	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.35295114836703e-05
CAMB-77D76	MN908947.3	241	C	T	1	1	0	0	0.999734004233766	TCG	NA	NA	NA	NA	NA	NA	6.64989415585135e-05
CAMB-77D76	MN908947.3	24126	TTAACGGCCTTACTG	-	0.0138	0.0366	2.9e-05;8.1e-05;0.0013;0.0038;0.0044;0.0043;0.0041;0.0041;0.0041;0.0073;0.01;0.011;0.015;0.019;0.013	1.1e-11;1.5e-10;1e-07;8.4e-07;1.2e-06;1e-06;1e-06;1.1e-06;1e-06;2.1e-06;1e-05;8e-06;2e-05;4.2e-05;9.1e-06	0.0162443237977911	TTT	S	.	2564-2578-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.983702597533133
CAMB-77D76	MN908947.3	25413	C	T	0.2	0.16	8.5e-92	4e-73	0.192754791330826	TCT	ORF3a	I7I	C21T	ATC>ATT	Synonymous	GU280_gp03	0.807227297152069
CAMB-77D76	MN908947.3	25587	C	T	0.22	0.18	1.1e-101	1e-86	0.210861953622534	TCA	ORF3a	L65L	C195T	CTC>CTT	Synonymous	GU280_gp03	0.789068540995143
CAMB-77D76	MN908947.3	28253	C	T	0.046	0.061	4.5e-19	2e-27	0.048072556939034	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.951742226895777
CAMB-77D76	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999620081411126	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-77D76	MN908947.3	29274	C	T	0.042	0.02	1.9e-19	2.5e-10	0.0379129050501665	ACA	N	T334I	C1001T	ACA>ATA	Missense	GU280_gp10	0.962087094949833
CAMB-77D76	MN908947.3	29520	C	T	0.026	0.0058	4.7e-12	0.0016	0.0215343203230148	TCA	N	S416L	C1247T	TCA>TTA	Missense	GU280_gp10	0.978465679676985
CAMB-77D76	MN908947.3	29730	C	T	0.013	0.016	1.5e-06	3.1e-06	0.0139056831922612	TCA	NA	NA	NA	NA	NA	NA	0.986094316807739
CAMB-77D76	MN908947.3	29736	G	T	0.0055	0.023	0.0014	1.4e-07	0.0107391029690461	AGG	NA	NA	NA	NA	NA	NA	0.989260897030954
CAMB-77D76	MN908947.3	3037	C	T	1	1	0	0	0.999568965517241	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77D76	MN908947.3	635	C	T	0.03	0.063	4.8e-14	8.8e-28	0.0322240976168724	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.967760417473172
CAMB-77D76	MN908947.3	6978	T	C	0.21	0.38	1.7e-57	2.5e-38	0.232484076433121	GTT	ORF1ab:nsp3	V1420A	T4259C	GTT>GCT	Missense	ORF1ab:nsp3	0.767515923566879
CAMB-77D85	MN908947.3	11074	C	INS	0.024	0.023	3.5e-07	0.00018	0.024119658340771	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.975121482190517
CAMB-77D85	MN908947.3	11075	T	-	0.033	0.036	4.8e-08	3.6e-09	0.0332699121341733	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.963703847968899
CAMB-77D85	MN908947.3	11652	T	C	0.3	0.32	8.2e-149	1.8e-154	0.306695327811848	CTC	ORF1ab:nsp6	L227P	T680C	CTC>CCC	Missense	ORF1ab:nsp6	0.693178225959411
CAMB-77D85	MN908947.3	14211	T	A	0.031	0.027	1.4e-14	4.7e-13	0.0302926002693012	TTG	ORF1ab:RNA-dependent-RNA-polymerase	V248V	T744A	GTT>GTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.969563671573596
CAMB-77D85	MN908947.3	14408	C	T	1	1	0	0	0.996785726243578	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000405504443807873
CAMB-77D85	MN908947.3	15905	A	G	0.078	0.084	1.1e-33	4.2e-38	0.0790962867381284	CAG	ORF1ab:RNA-dependent-RNA-polymerase	Q813R	A2438G	CAG>CGG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.920740475875846
CAMB-77D85	MN908947.3	16332	C	T	0.084	0.086	3.3e-37	3.3e-38	0.0843838285435947	ACC	ORF1ab:helicase	D32D	C96T	GAC>GAT	Synonymous	ORF1ab:helicase	0.91520701412567
CAMB-77D85	MN908947.3	21077	C	T	0.01	0.0065	1.4e-05	0.00012	0.00963821346968242	ACA	ORF1ab:2'-O-ribose-methyltransferase	T140I	C419T	ACA>ATA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.989505883403666
CAMB-77D85	MN908947.3	23403	A	G	1	1	0	0	0.999799044023713	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000180860378658475
CAMB-77D85	MN908947.3	241	C	T	1	1	0	0	0.997179795373926	TCG	NA	NA	NA	NA	NA	NA	0.000633226818328399
CAMB-77D85	MN908947.3	25169	C	T	0.63	0.62	0	0	0.626131332737225	ACT	S	L1203F	C3607T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.373159880487645
CAMB-77D85	MN908947.3	25429	G	T	1	1	0	0	0.998114825908071	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	5.50415793263828e-05
CAMB-77D85	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0283513513513514	0.036	0.013;0.0026;0.0055;0.0056;0.0088;0.00073;0.0014;0.00038;0.00038;0.00012;0.00022;0.00017;0.00036;0.00027;0.00031;0.00044;0.00025;0.00038;0.00026;3e-04;0.00029;0.00046;0.00027;0.00034;0.00029;2e-04;0.00037;0.00026;0.00031;0.00022;0.00034;0.00031;3e-04;4e-04;0.00017;0.00029;0.00022	2.5e-05;1e-06;1.7e-05;1.7e-05;3.5e-05;3.9e-06;1.1e-05;6.6e-06;6.3e-06;2.2e-06;4.1e-06;3.5e-06;5.8e-06;2.7e-06;3.7e-06;5.8e-06;2.4e-06;5e-06;3.4e-06;3.3e-06;2.8e-06;5.6e-06;3.3e-06;4e-06;2.9e-06;1.8e-06;4.5e-06;2.5e-06;7.8e-07;3.1e-06;4.2e-06;4e-06;2.4e-06;4.7e-06;1.7e-06;5.2e-06;3.6e-06	0.031108985091286	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.981319622964867
CAMB-77D85	MN908947.3	3037	C	T	1	1	0	0	0.999603154062495	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.6270855979433e-05
CAMB-77D85	MN908947.3	6121	A	G	0.087	0.072	3.9e-38	1.6e-29	0.0845277056765602	CAA	ORF1ab:nsp3	S1134S	A3402G	TCA>TCG	Synonymous	ORF1ab:nsp3	0.915303013203927
CAMB-77D85	MN908947.3	7765	C	T	0.0061	0.0083	0.00044	2.6e-05	0.00659762819442125	CCA	ORF1ab:nsp3	S1682S	C5046T	TCC>TCT	Synonymous	ORF1ab:nsp3	0.993291019430989
CAMB-77DA3	MN908947.3	11074	C	INS	0.02	0.017	2.2e-05	0.0058	0.0199172908068817	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.979165605203716
CAMB-77DA3	MN908947.3	11075	T	-	0.036	0.035	6.4e-09	4.2e-09	0.035774173443343	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959050572802279
CAMB-77DA3	MN908947.3	14408	C	T	1	1	0	0	0.996618968186884	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000658253981314563
CAMB-77DA3	MN908947.3	16206	G	T	1	1	0	0	0.999618705231909	AGG	ORF1ab:RNA-dependent-RNA-polymerase	E913D	G2739T	GAG>GAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00013617670288967
CAMB-77DA3	MN908947.3	23403	A	G	1	1	0	0	0.999691683356172	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.85148097396437e-05
CAMB-77DA3	MN908947.3	241	C	T	1	1	0	0	0.999023873407663	TCG	NA	NA	NA	NA	NA	NA	9.81031751092624e-05
CAMB-77DA3	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998989492510619	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	9.86835612923599e-05
CAMB-77DA3	MN908947.3	3037	C	T	1	1	0	0	0.9990214053519	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000123730357805698
CAMB-77DB2	MN908947.3	11074	C	INS	0.021	0.022	3.7e-05	0.00036	0.0209565506102948	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.978666411556491
CAMB-77DB2	MN908947.3	11075	T	-	0.029	0.041	6.8e-07	3e-10	0.0310241792615405	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.963535607570923
CAMB-77DB2	MN908947.3	12081	C	T	0.049	0.039	1.1e-21	1.6e-18	0.0465882255458425	GCA	ORF1ab:nsp7	A80V	C239T	GCA>GTA	Missense	ORF1ab:nsp7	0.953261590089904
CAMB-77DB2	MN908947.3	14408	C	T	1	1	0	0	0.99810897815697	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.0006418611999842
CAMB-77DB2	MN908947.3	16877	C	T	0.063	0.06	3.4e-27	1.5e-27	0.0621620552317147	ACA	ORF1ab:helicase	T214I	C641T	ACA>ATA	Missense	ORF1ab:helicase	0.937818162635508
CAMB-77DB2	MN908947.3	17074	C	T	0.79	0.81	0	0	0.793258189503346	ACT	ORF1ab:helicase	L280F	C838T	CTC>TTC	Missense	ORF1ab:helicase	0.206460021134202
CAMB-77DB2	MN908947.3	17645	A	T	0.01	0.012	1.5e-05	2.6e-07	0.0106635545849779	CAA	ORF1ab:helicase	Q470L	A1409T	CAA>CTA	Missense	ORF1ab:helicase	0.989216236251077
CAMB-77DB2	MN908947.3	1960	C	T	0.012	0.013	1.1e-06	6.5e-08	0.0125979913341849	CCG	ORF1ab:nsp2	A385A	C1155T	GCC>GCT	Synonymous	ORF1ab:nsp2	0.987095198737696
CAMB-77DB2	MN908947.3	20628	C	T	0.018	0.02	3.6e-08	1.3e-09	0.0182179464478939	GCC	ORF1ab:endoRNAse	G336G	C1008T	GGC>GGT	Synonymous	ORF1ab:endoRNAse	0.981398414291054
CAMB-77DB2	MN908947.3	21141	A	G	1	1	0	0	0.999659516513449	TAG	ORF1ab:2'-O-ribose-methyltransferase	L161L	A483G	CTA>CTG	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	5.52135383596058e-05
CAMB-77DB2	MN908947.3	23403	A	G	1	1	0	0	0.999442688709941	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.67554471338515e-05
CAMB-77DB2	MN908947.3	241	C	T	1	1	0	0	0.997777015689493	TCG	NA	NA	NA	NA	NA	NA	0.000128602398128529
CAMB-77DB2	MN908947.3	24983	T	C	0.016	0.013	5.1e-08	9.4e-08	0.0149503679022629	TTT	S	L1141L	T3421C	TTG>CTG	Synonymous	GU280_gp02, spike glycoprotein	0.985032278217409
CAMB-77DB2	MN908947.3	26062	G	C	0.0097	0.013	2e-05	1.8e-07	0.0103571018486623	TGG	ORF3a	G224R	G670C	GGT>CGT	Missense	GU280_gp03	0.988770237685153
CAMB-77DB2	MN908947.3	27600	C	A	0.078	0.081	5.5e-31	2.1e-21	0.0784869976359338	ACG	ORF7a	D69E	C207A	GAC>GAA	Missense	GU280_gp07	0.920567375886525
CAMB-77DB2	MN908947.3	28514	G	T	1	1	0	0	0.999071415060272	AGA	N	D81Y	G241T	GAT>TAT	Missense	GU280_gp10	6.87840696094784e-05
CAMB-77DB2	MN908947.3	3037	C	T	1	1	0	0	0.999457365791591	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.35576221394757e-05
CAMB-77DB2	MN908947.3	3602	C	T	1	1	0	0	1	ACA	ORF1ab:nsp3	H295Y	C883T	CAC>TAC	Missense	ORF1ab:nsp3	0
CAMB-77DB2	MN908947.3	4888	T	C	0.034	0.035	2.7e-15	9e-17	0.0341614741012457	CTA	ORF1ab:nsp3	P723P	T2169C	CCT>CCC	Synonymous	ORF1ab:nsp3	0.965811828904302
CAMB-77DB2	MN908947.3	5622	C	T	0.062	0.067	6.1e-27	2.1e-30	0.0633595386753511	CCT	ORF1ab:nsp3	P968L	C2903T	CCT>CTT	Missense	ORF1ab:nsp3	0.93655748926549
CAMB-77DB2	MN908947.3	6027	C	T	0.0067	0.0088	0.00019	1.3e-05	0.00723582805274876	CCA	ORF1ab:nsp3	P1103L	C3308T	CCA>CTA	Missense	ORF1ab:nsp3	0.992250385339955
CAMB-77DB2	MN908947.3	64	C	T	0.0083	0.0078	5.6e-05	1.6e-05	0.00819165552346814	TCT	NA	NA	NA	NA	NA	NA	0.991673502410302
CAMB-77DC1	MN908947.3	12116	C	T	0.37	0.1	9.1e-193	4.1e-46	0.343564365046922	CCT	ORF1ab:nsp8	L9F	C25T	CTT>TTT	Missense	ORF1ab:nsp8	0.65636605581986
CAMB-77DC1	MN908947.3	14184	C	A	0.082	0.17	5.4e-38	6e-80	0.100057047895429	CCA	ORF1ab:RNA-dependent-RNA-polymerase	T239T	C717A	ACC>ACA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.899818934940596
CAMB-77DC1	MN908947.3	14408	C	T	1	1	0	0	0.999588229704476	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000316746381172595
CAMB-77DC1	MN908947.3	23403	A	G	1	1	0	0	0.99979537167944	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000204628320559565
CAMB-77DC1	MN908947.3	241	C	T	1	1	0	0	0.99977306767122	TCG	NA	NA	NA	NA	NA	NA	0.000181545863023646
CAMB-77DC1	MN908947.3	25429	G	T	1	1	0	0	0.999878515458908	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	2.02474235153577e-05
CAMB-77DC1	MN908947.3	28006	CTATTCACTT	-	0.122	0.29	1.1e-46;4.6e-46;5.4e-48;6.5e-52;1.4e-45;4.3e-45;1.6e-46;4.4e-50;2.5e-53;3.2e-45	2.1e-63;1.8e-61;1.4e-62;1.9e-65;4.1e-61;2.4e-61;5.9e-62;6.4e-64;2.4e-68;5.1e-61	0.137828825490923	CCT	ORF8	.	113-122-delfrshift	.	no-SNV	GU280_gp09	0.861256544502618
CAMB-77DC1	MN908947.3	28824	C	T	0.68	0.71	0	5.4e-238	0.684444444444444	TCT	N	S184F	C551T	TCT>TTT	Missense	GU280_gp10	0.315555555555556
CAMB-77DD0	MN908947.3	11074	C	INS	0.025	0.026	1.4e-07	2.7e-05	0.025276515038761	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.974310998090654
CAMB-77DD0	MN908947.3	11075	T	-	0.035	0.032	1.1e-08	2.7e-08	0.0346464377606246	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960928489042676
CAMB-77DD0	MN908947.3	14408	C	T	1	1	0	0	0.997594684171574	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000418315796248029
CAMB-77DD0	MN908947.3	23403	A	G	1	1	0	0	0.999638566483405	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.85420484626349e-05
CAMB-77DD0	MN908947.3	23564	G	T	0.069	0.064	1.8e-31	6e-28	0.0681125746987189	TGC	S	A668S	G2002T	GCA>TCA	Missense	GU280_gp02, spike glycoprotein	0.928054171827395
CAMB-77DD0	MN908947.3	241	C	T	1	1	0	0	0.9990108930223	TCG	NA	NA	NA	NA	NA	NA	7.70732709896208e-05
CAMB-77DD0	MN908947.3	25785	G	T	0.15	0.14	1.3e-68	7.6e-61	0.148608589510827	GGA	ORF3a	W131C	G393T	TGG>TGT	Missense	GU280_gp03	0.851196520704475
CAMB-77DD0	MN908947.3	28008	ATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAAT	-	0.00485869565217391	0.00522173913043478	0.0027;0.0024;0.014;0.0074;0.0048;0.0052;0.0014;0.0051;0.0025;0.0052;0.0097;0.0043;0.011;0.0094;0.0098;0.0024;0.0025;0.0033;0.0034;0.0026;0.0041;0.0031;0.0032;0.0061;0.0044;0.0046;0.0083;0.01;0.013;0.013;0.014;0.0048;0.0055;0.0052;0.012;0.0063;0.0068;0.0095;0.0068;0.0039;0.004;0.004;0.0058;9.5e-05;8.3e-05;0.013	0.00024;0.00019;0.00084;0.00039;3e-04;0.00034;1e-04;0.00032;0.00018;0.00033;0.00059;3e-04;5e-04;0.00042;0.00046;0.00012;0.00014;0.00033;0.00022;0.00025;0.00028;0.00055;0.00054;0.00035;0.00027;0.00028;6e-04;0.00049;6e-04;0.00063;0.00052;0.00028;0.00024;0.00032;0.00057;0.00035;4e-04;0.00063;0.00036;0.00041;0.00089;0.00054;0.00032;5.1e-05;4.8e-05;0.00064	0.00475723465608853	TAT	ORF8	.	115-160-delfrshift	.	no-SNV	GU280_gp09	0.994637565266475
CAMB-77DD0	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998856313983654	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	9.29732856759158e-05
CAMB-77DD0	MN908947.3	29745	G	T	0.13	0.13	4.8e-63	1.6e-56	0.126508797565907	GGA	NA	NA	NA	NA	NA	NA	0.872790599915928
CAMB-77DD0	MN908947.3	3037	C	T	1	1	0	0	0.999249639741808	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000144955958968937
CAMB-77DD0	MN908947.3	3874	C	T	0.078	0.086	8.3e-34	3.8e-38	0.0800080293281777	TCG	ORF1ab:nsp3	I385I	C1155T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.919918016333344
CAMB-77DD0	MN908947.3	7173	C	T	0.011	0.037	6.5e-05	4.8e-08	0.0158251695553881	TCT	ORF1ab:nsp3	S1485F	C4454T	TCT>TTT	Missense	ORF1ab:nsp3	0.984174830444612
CAMB-77DEF	MN908947.3	10097	G	A	1	1	0	0	0.999622580008749	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000325953628807439
CAMB-77DEF	MN908947.3	11074	C	INS	0.022	0.017	1.8e-05	0.0067	0.0207470942880229	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.978768102430232
CAMB-77DEF	MN908947.3	11075	T	-	0.039	0.038	3e-09	8.2e-10	0.0387863790413686	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956312873204583
CAMB-77DEF	MN908947.3	13536	C	T	1	1	0	0	0.999573668984419	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000233466984723139
CAMB-77DEF	MN908947.3	14184	C	T	1	1	0	0	0.999702686538269	CCA	ORF1ab:RNA-dependent-RNA-polymerase	T239T	C717T	ACC>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000255827862419924
CAMB-77DEF	MN908947.3	14408	C	T	1	1	0	0	0.998607530896914	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000477004986870317
CAMB-77DEF	MN908947.3	1684	C	T	1	1	0	0	0.999730559896535	TCG	ORF1ab:nsp2	I293I	C879T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.000177060639419857
CAMB-77DEF	MN908947.3	21058	C	T	1	1	0	0	0.999408019875005	CCC	ORF1ab:2'-O-ribose-methyltransferase	P134S	C400T	CCT>TCT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.000359069911882303
CAMB-77DEF	MN908947.3	22243	A	C	1	1	0	0	0.999373896404477	TAG	S	V227V	A681C	GTA>GTC	Synonymous	GU280_gp02, spike glycoprotein	0.000204011283934463
CAMB-77DEF	MN908947.3	23403	A	G	1	1	0	0	0.999661009139589	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.91146414431137e-05
CAMB-77DEF	MN908947.3	23731	C	T	1	1	0	0	0.999615880253767	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000334555908009516
CAMB-77DEF	MN908947.3	241	C	T	1	1	0	0	0.998891572391	TCG	NA	NA	NA	NA	NA	NA	0.0001271132579128
CAMB-77DEF	MN908947.3	26137	A	C	0.024	0.013	1.5e-05	0.0074	0.0221042936713302	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.977544844524363
CAMB-77DEF	MN908947.3	28812	G	T	0.02	0.02	2e-09	2.6e-10	0.0201384788792872	AGT	N	S180I	G539T	AGT>ATT	Missense	GU280_gp10	0.979399924856422
CAMB-77DEF	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999221623793203	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000167058790772786
CAMB-77DEF	MN908947.3	3037	C	T	1	1	0	0	0.999181548352743	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000108469495419629
CAMB-77DEF	MN908947.3	4002	C	T	1	1	0	0	0.999486838090483	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0.00033286177914621
CAMB-77E0A	MN908947.3	11074	C	INS	0.022	0.03	4.8e-06	1.2e-06	0.0232401038369539	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.976619690783408
CAMB-77E0A	MN908947.3	11075	T	-	0.034	0.033	2.6e-08	1.2e-08	0.0335694714366318	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961193941785381
CAMB-77E0A	MN908947.3	14408	C	T	1	1	0	0	0.999269218973044	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000401361600296856
CAMB-77E0A	MN908947.3	19170	C	T	1	1	0	0	0.999836257309942	TCA	ORF1ab:3'-to-5'-exonuclease	F377F	C1131T	TTC>TTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	9.82456140350877e-05
CAMB-77E0A	MN908947.3	23403	A	G	1	1	0	0	0.999206059398929	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.85229938476519e-05
CAMB-77E0A	MN908947.3	241	C	T	1	1	0	0	0.999710232417748	TCG	NA	NA	NA	NA	NA	NA	0.00012073649260489
CAMB-77E0A	MN908947.3	25996	G	T	0.055	0.055	2.9e-17	4.5e-18	0.0547745399248984	TGT	ORF3a	V202L	G604T	GTA>TTA	Missense	GU280_gp03	0.945194426341433
CAMB-77E0A	MN908947.3	28077	G	T	1	1	0	0	0.999887201931103	CGT	ORF8	V62L	G184T	GTG>TTG	Missense	GU280_gp09	0
CAMB-77E0A	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999441486833349	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	5.38343516998197e-05
CAMB-77E0A	MN908947.3	3037	C	T	1	1	0	0	0.999331457267681	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000171022559430339
CAMB-77E0A	MN908947.3	3241	C	T	1	1	0	0	0.999835460915112	ACG	ORF1ab:nsp3	D174D	C522T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.000137115904073714
CAMB-77E0A	MN908947.3	7001	T	G	0.0076	0.0057	9e-06	1e-04	0.00743052459503641	CTC	ORF1ab:nsp3	S1428A	T4282G	TCA>GCA	Missense	ORF1ab:nsp3	0.992123643929261
CAMB-77E19	MN908947.3	14408	C	T	1	1	0	0	0.999311382590732	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000510086969828356
CAMB-77E19	MN908947.3	17366	CA	TC	0.019	0.00175	8.6e-10;6.3e-10	NA;0.00025	0.0159064628035462	TCA	ORF1ab:helicase	.	1130-1131-mnv	.	no-SNV	ORF1ab:helicase	0.984635147729276
CAMB-77E19	MN908947.3	23403	A	G	1	1	0	0	0.99988827283773	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.07783193441616e-05
CAMB-77E19	MN908947.3	241	C	T	1	1	0	0	0.999874580628978	TCG	NA	NA	NA	NA	NA	NA	3.13548427554636e-05
CAMB-77E19	MN908947.3	28087	C	T	1	1	0	0	0.998609421171563	GCT	ORF8	A65V	C194T	GCT>GTT	Missense	GU280_gp09	0.00139057882843734
CAMB-77E19	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999608150470219	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-77E19	MN908947.3	29633	T	C	1	1	0	0	1	CTA	ORF10	Y26H	T76C	TAC>CAC	Missense	GU280_gp11	0
CAMB-77E19	MN908947.3	3037	C	T	1	0.99	0	2.79999999999768e-313	0.999074074074074	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000154320987654321
CAMB-77E28	MN908947.3	11074	C	INS	0.12	0.12	4.2e-77	9.5e-49	0.120427815840568	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.876492445714031
CAMB-77E28	MN908947.3	11083	G	-	0.14	0.17	3e-58	9.3e-75	0.148079175327347	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.0526499045126982
CAMB-77E28	MN908947.3	11083	G	T	0.8	0.78	1.20057951939423e-321	6.00000000000067e-312	0.799096827289321	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.0526499045126982
CAMB-77E28	MN908947.3	11893	G	T	0.044	0.046	4.8e-19	3.4e-21	0.0446978989951716	TGC	ORF1ab:nsp7	L17F	G51T	TTG>TTT	Missense	ORF1ab:nsp7	0.95489494975858
CAMB-77E28	MN908947.3	12048	A	G	0.011	0.0094	2.4e-06	3.2e-06	0.0106928794054184	AAC	ORF1ab:nsp7	N69S	A206G	AAC>AGC	Missense	ORF1ab:nsp7	0.989122170085968
CAMB-77E28	MN908947.3	14408	C	T	0.052	0.051	1.3e-23	6e-22	0.0517880058396588	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.948004177122461
CAMB-77E28	MN908947.3	14805	C	T	0.94	0.95	0	0	0.944645898690847	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.054927248540205
CAMB-77E28	MN908947.3	16887	C	T	0.02	0.019	1.5e-08	1.5e-08	0.0200457797636997	ACA	ORF1ab:helicase	Y217Y	C651T	TAC>TAT	Synonymous	ORF1ab:helicase	0.979919953946106
CAMB-77E28	MN908947.3	19017	C	T	0.046	0.052	4e-20	5.6e-24	0.0475393654027861	TCC	ORF1ab:3'-to-5'-exonuclease	F326F	C978T	TTC>TTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.952397291005738
CAMB-77E28	MN908947.3	2061	C	T	0.039	0.04	4.7e-17	1.2e-18	0.0396427162959296	GCC	ORF1ab:nsp2	A419V	C1256T	GCC>GTC	Missense	ORF1ab:nsp2	0.960231420492209
CAMB-77E28	MN908947.3	23403	A	G	0.051	0.048	1.2e-16	1.7e-16	0.0500262884118443	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.949936423060717
CAMB-77E28	MN908947.3	241	C	T	0.042	0.041	1.1e-17	1.4e-17	0.0417914947336687	TCG	NA	NA	NA	NA	NA	NA	0.958007524227636
CAMB-77E28	MN908947.3	26028	C	T	0.0085	0.0082	7.9e-05	2.7e-05	0.00841063496211131	ACC	ORF3a	Y212Y	C636T	TAC>TAT	Synonymous	GU280_gp03	0.991589365037889
CAMB-77E28	MN908947.3	26144	G	T	0.94	0.94	0	0	0.942819813242132	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.0570649041232756
CAMB-77E28	MN908947.3	27879	C	T	0.055	0.056	2e-23	1.7e-24	0.0553209761683246	TCA	NA	NA	NA	NA	NA	NA	0.944559746177151
CAMB-77E28	MN908947.3	28842	G	T	0.93	0.93	0	0	0.930737217598097	AGT	N	S190I	G569T	AGT>ATT	Missense	GU280_gp10	0.0687974978028227
CAMB-77E28	MN908947.3	28881	GGG	AAC	0.0593333333333333	0.0573333333333333	2.8e-23;6.8e-27;7.4e-31	7.3e-23;1.5e-25;1.3e-27	0.0597952154455353	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.944945531217055
CAMB-77E28	MN908947.3	2918	C	T	0.0091	0.0075	2.8e-05	3.3e-05	0.00872554996951555	ACC	ORF1ab:nsp3	P67S	C199T	CCA>TCA	Missense	ORF1ab:nsp3	0.991244465322685
CAMB-77E28	MN908947.3	3037	C	T	0.041	0.042	2.1e-07	5.1e-08	0.0411812243248704	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.958190226053382
CAMB-77E37	MN908947.3	11075	T	-	0.04	0.044	1.8e-09	1.6e-11	0.0406747964312152	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954291502707757
CAMB-77E37	MN908947.3	14408	C	T	1	1	0	0	0.998636131769002	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000445673477058555
CAMB-77E37	MN908947.3	21408	T	C	0.007	0.009	0.0011	4.7e-05	0.00735073507350735	TTC	ORF1ab:2'-O-ribose-methyltransferase	F250F	T750C	TTT>TTC	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.992529252925292
CAMB-77E37	MN908947.3	23403	A	G	1	1	0	0	0.999459585371535	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.83282863576365e-05
CAMB-77E37	MN908947.3	241	C	T	1	1	0	0	0.999073396233176	TCG	NA	NA	NA	NA	NA	NA	8.70290830718195e-05
CAMB-77E37	MN908947.3	25521	C	T	1	1	0	0	0.997670468029828	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	8.1190122284815e-05
CAMB-77E37	MN908947.3	26137	A	C	0.029	0.016	5.4e-07	0.0014	0.0258403149288382	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.973806399515494
CAMB-77E37	MN908947.3	28514	G	T	1	1	0	0	0.998150219392584	AGA	N	D81Y	G241T	GAT>TAT	Missense	GU280_gp10	0.000666781381743096
CAMB-77E37	MN908947.3	28544	A	C	0.017	0.0077	2.4e-06	0.0069	0.0153776571687019	TAC	N	T91P	A271C	ACC>CCC	Missense	GU280_gp10	0.983183257267382
CAMB-77E37	MN908947.3	3037	C	T	1	1	0	0	0.99913609023782	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.52007367683255e-05
CAMB-77E37	MN908947.3	4084	C	T	0.01	0.011	1.7e-05	1.6e-06	0.0104921303529091	ACA	ORF1ab:nsp3	D455D	C1365T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.989455134332228
CAMB-77E37	MN908947.3	521	G	A	0.0098	0.01	3.8e-05	1.2e-05	0.00991366971509499	GGT	ORF1ab:leader-protein	V86I	G256A	GTT>ATT	Missense	ORF1ab:leader-protein	0.983088002651681
CAMB-77E37	MN908947.3	5672	C	T	0.015	0.016	2.9e-07	1.2e-08	0.0147005653431501	ACC	ORF1ab:nsp3	P985S	C2953T	CCT>TCT	Missense	ORF1ab:nsp3	0.985176176702603
CAMB-77E37	MN908947.3	9646	G	A	0.0071	0.0072	7.6e-05	1.7e-05	0.00714381992182235	AGT	ORF1ab:nsp4	Q364Q	G1092A	CAG>CAA	Synonymous	ORF1ab:nsp4	0.992671731897475
CAMB-77E46	MN908947.3	10097	G	A	1	1	0	0	0.999580536912752	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000299616490891659
CAMB-77E46	MN908947.3	11003	C	T	0.015	0.015	3e-08	3e-08	0.0153823985013869	ACA	ORF1ab:nsp6	H11Y	C31T	CAC>TAC	Missense	ORF1ab:nsp6	0.984617601498613
CAMB-77E46	MN908947.3	11075	T	-	0.039	0.04	1.2e-10	2e-10	0.0397776146019092	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955816636945348
CAMB-77E46	MN908947.3	13536	C	T	1	1	0	0	0.999486966506242	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000109935748662448
CAMB-77E46	MN908947.3	14408	C	T	1	1	0	0	0.998348136915078	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000595753899480069
CAMB-77E46	MN908947.3	23403	A	G	1	1	0	0	0.999031970235189	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000143100052189431
CAMB-77E46	MN908947.3	23731	C	T	1	1	0	0	0.999633867276888	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000183066361556064
CAMB-77E46	MN908947.3	241	C	T	1	1	0	0	0.998732328824275	TCG	NA	NA	NA	NA	NA	NA	0.000144418235209166
CAMB-77E46	MN908947.3	27681	T	A	0.046	0.049	5.1e-17	1.6e-18	0.0472955974842767	TTT	ORF7a	L96L	T288A	CTT>CTA	Synonymous	GU280_gp07	0.952452830188679
CAMB-77E46	MN908947.3	28663	C	T	0.014	0.0087	9.2e-08	5e-06	0.0108695652173913	TCA	N	I130I	C390T	ATC>ATT	Synonymous	GU280_gp10	0.988917306052856
CAMB-77E46	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999214042441708	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.0002324905550712
CAMB-77E46	MN908947.3	29519	T	C	0.012	0.012	6.7e-07	7.3e-07	0.0116945912515462	CTC	N	S416P	T1246C	TCA>CCA	Missense	GU280_gp10	0.988192960755651
CAMB-77E46	MN908947.3	3037	C	T	1	1	0	0	0.999191182002859	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000131668046046197
CAMB-77E46	MN908947.3	4002	C	T	1	1	0	0	0.999907058878201	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	4.64705608996701e-05
CAMB-77E46	MN908947.3	643	C	T	0.045	0.046	4.3e-21	2.8e-21	0.0455330890668114	ACG	ORF1ab:leader-protein	N126N	C378T	AAC>AAT	Synonymous	ORF1ab:leader-protein	0.954412629483874
CAMB-77E64	MN908947.3	11074	C	INS	0.036	0.038	9.3e-14	1.9e-09	0.0366202727159929	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.961903620953009
CAMB-77E64	MN908947.3	11075	T	-	0.034	0.034	2.1e-08	9.6e-09	0.0341480908673189	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960988019590044
CAMB-77E64	MN908947.3	11083	G	-	0.023	0.025	1.2e-08	1.6e-10	0.0231989653727755	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.848671196196652
CAMB-77E64	MN908947.3	11083	G	T	0.13	0.13	7.1e-25	1e-27	0.128049691251207	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.848671196196652
CAMB-77E64	MN908947.3	12846	C	T	0.0094	0.016	2.6e-05	4.6e-09	0.0107124532917343	GCT	ORF1ab:nsp9	A54V	C161T	GCT>GTT	Missense	ORF1ab:nsp9	0.989230538006665
CAMB-77E64	MN908947.3	14408	C	T	1	1	0	0	0.998871106979215	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000335933563278555
CAMB-77E64	MN908947.3	22987	C	T	0.0075	0.01	2e-04	8.8e-06	0.00803929020375947	CCG	S	A475A	C1425T	GCC>GCT	Synonymous	GU280_gp02, spike glycoprotein	0.991770690209606
CAMB-77E64	MN908947.3	23403	A	G	1	1	0	0	0.999664852825528	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.12517615018816e-05
CAMB-77E64	MN908947.3	241	C	T	1	1	0	0	0.998849205548041	TCG	NA	NA	NA	NA	NA	NA	0.000429024247440997
CAMB-77E64	MN908947.3	24834	G	T	0.0068	0.0075	0.00021	2.4e-05	0.00695376513146962	CGT	S	R1091L	G3272T	CGT>CTT	Missense	GU280_gp02, spike glycoprotein	0.992905625647122
CAMB-77E64	MN908947.3	26137	A	C	0.024	0.015	8.3e-06	0.0042	0.0222431922351038	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.977284982475061
CAMB-77E64	MN908947.3	28881	GGG	AAC	0.99	1	0;0;0	0;0;0	0.994291543670776	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	6.01279522824571e-05
CAMB-77E64	MN908947.3	3037	C	T	1	1	0	0	0.999274931010227	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.49315513229804e-05
CAMB-77E64	MN908947.3	7549	T	C	0.34	0.35	3.9e-185	3.2e-178	0.344354263461279	ATG	ORF1ab:nsp3	N1610N	T4830C	AAT>AAC	Synonymous	ORF1ab:nsp3	0.655626457943745
CAMB-77E73	MN908947.3	14408	C	T	1	1	0	0	0.999701652843248	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000238677725401277
CAMB-77E73	MN908947.3	17233	A	T	0.036	0.00038	4.8e-17	0.0093	0.0304104998603742	AAT	ORF1ab:helicase	I333F	A997T	ATT>TTT	Missense	ORF1ab:helicase	0.969394024015638
CAMB-77E73	MN908947.3	17747	C	T	0.94	1	0	0	0.94916929054733	CCT	ORF1ab:helicase	P504L	C1511T	CCT>CTT	Missense	ORF1ab:helicase	0.0508139612782207
CAMB-77E73	MN908947.3	23403	A	G	1	1	0	0	0.999888975241479	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.40165056807668e-05
CAMB-77E73	MN908947.3	241	C	T	1	1	0	0	0.999644043663977	TCG	NA	NA	NA	NA	NA	NA	0.000118652112007594
CAMB-77E73	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999688182101653	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00017343045438779
CAMB-77E73	MN908947.3	3037	C	T	1	1	0	6.89999999999998e-310	0.999210360075805	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77E82	MN908947.3	11074	C	INS	0.023	0.034	0.00021	3e-07	0.0278434649645289	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.971374215457924
CAMB-77E82	MN908947.3	11075	T	-	0.04	0.031	4.1e-10	2.9e-08	0.0354905450178683	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959734942199459
CAMB-77E82	MN908947.3	14408	C	T	1	1	0	0	0.996217631655514	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.001062605153635
CAMB-77E82	MN908947.3	14786	C	T	1	1	0	0	0.999461571066891	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A440V	C1319T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	4.58237389879827e-05
CAMB-77E82	MN908947.3	15569	C	T	0.0081	0.0083	9.9e-06	8.3e-06	0.00818891072598416	ACT	ORF1ab:RNA-dependent-RNA-polymerase	T701I	C2102T	ACT>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.99178131141683
CAMB-77E82	MN908947.3	18109	C	T	0.0095	0.011	4.9e-06	8e-07	0.0104424821346936	ACC	ORF1ab:3'-to-5'-exonuclease	P24S	C70T	CCT>TCT	Missense	ORF1ab:3'-to-5'-exonuclease	0.989485334809076
CAMB-77E82	MN908947.3	20578	G	T	1	1	0	0	0.999885662016922	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	2.28675966155957e-05
CAMB-77E82	MN908947.3	23403	A	G	1	1	0	0	0.999495126024312	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.8254689502505e-05
CAMB-77E82	MN908947.3	241	C	T	1	1	0	0	0.999742316744258	TCG	NA	NA	NA	NA	NA	NA	0.000120252186012953
CAMB-77E82	MN908947.3	2416	C	T	1	1	0	0	0.997156667614444	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0.000142166619277794
CAMB-77E82	MN908947.3	25563	G	T	1	1	0	0	0.998735890040238	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000160239290674073
CAMB-77E82	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.0408048780487805	0.0494390243902439	6.2e-05;1.2e-06;1.2e-05;1.7e-05;5.3e-05;1.4e-07;1.6e-06;2e-07;2e-07;2.5e-08;8.2e-08;5.4e-08;1.9e-07;9.8e-08;8.8e-08;2.1e-07;8e-08;2.5e-07;1.3e-07;1.4e-07;1.4e-07;2.4e-07;1.1e-07;1.8e-07;1.1e-07;7.3e-08;2e-07;9.2e-08;4.4e-08;1e-07;2.1e-07;1.9e-07;6.8e-08;1.9e-07;3.5e-08;8.1e-08;5.4e-08;0.00024;0.0016;0.00091;0.0016	5.7e-06;4.1e-07;4e-06;4.2e-06;1.8e-05;9.8e-09;4e-08;2.9e-09;2.6e-09;2.5e-09;1.4e-09;7.2e-10;1.8e-09;1.3e-09;2e-09;3.5e-09;1.1e-09;3.3e-09;1.7e-09;2.2e-09;1.4e-09;4.1e-09;1.5e-09;2.2e-09;1.8e-09;7.8e-10;2.7e-09;1.8e-09;1.5e-10;1.8e-09;3e-09;2.8e-09;9.7e-10;2.4e-09;1.7e-10;1.2e-09;2.9e-10;4.3e-05;0.00028;9.4e-05;0.00016	0.0484854939069845	GTC	M	.	258-298-delfrshift	.	no-SNV	GU280_gp05	0.969632854359474
CAMB-77E82	MN908947.3	3037	C	T	1	1	0	0	0.998465980869879	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000135354629128316
CAMB-77E82	MN908947.3	3309	A	G	0.068	0.086	3.6e-31	4.7e-39	0.0771830820327426	GAA	ORF1ab:nsp3	E197G	A590G	GAA>GGA	Missense	ORF1ab:nsp3	0.922816917967257
CAMB-77E82	MN908947.3	4053	T	C	0.89	0.86	0	0	0.876852431642663	CTT	ORF1ab:nsp3	L445P	T1334C	CTT>CCT	Missense	ORF1ab:nsp3	0.123147568357337
CAMB-77E82	MN908947.3	522	TT	-	0.036	0.0385	1.8e-05;0.00023	1.6e-05;4.6e-05	0.0371120343539434	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.957459771350751
CAMB-77E82	MN908947.3	5812	C	T	0.078	0.075	6.3e-35	1.6e-33	0.076486330102705	ACG	ORF1ab:nsp3	D1031D	C3093T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.922030956169536
CAMB-77E91	MN908947.3	11075	T	-	0.038	0.039	2.1e-10	1.3e-10	0.0383227245882276	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95741190366822
CAMB-77E91	MN908947.3	14408	C	T	1	1	0	0	0.997500287795813	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000740046376239578
CAMB-77E91	MN908947.3	14634	A	G	0.016	0.013	5.8e-09	4.4e-08	0.0145820745216516	TAG	ORF1ab:RNA-dependent-RNA-polymerase	V389V	A1167G	GTA>GTG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.985377643504532
CAMB-77E91	MN908947.3	17977	C	T	0.034	0.036	2.7e-16	6e-17	0.0351364964238944	CCT	ORF1ab:helicase	L581F	C1741T	CTT>TTT	Missense	ORF1ab:helicase	0.964782915281555
CAMB-77E91	MN908947.3	23086	C	T	1	1	0	0	0.999438139116755	ACA	S	Y508Y	C1524T	TAC>TAT	Synonymous	GU280_gp02, spike glycoprotein	0.000112372176649062
CAMB-77E91	MN908947.3	23403	A	G	1	1	0	0	0.99950646424548	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.65613432755753e-05
CAMB-77E91	MN908947.3	241	C	T	1	1	0	0	0.998785607716596	TCG	NA	NA	NA	NA	NA	NA	0.000156136150723431
CAMB-77E91	MN908947.3	25521	C	T	0.023	0.023	1.6e-11	1.4e-11	0.0232194644269519	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.97612142668826
CAMB-77E91	MN908947.3	25556	T	G	0.06	0.055	7.5e-28	9.4e-26	0.0576364860785361	GTT	ORF3a	V55G	T164G	GTT>GGT	Missense	GU280_gp03	0.941388198685647
CAMB-77E91	MN908947.3	27237	A	G	1	1	0	0	0.99972633801165	CAG	ORF6	A12A	A36G	GCA>GCG	Synonymous	GU280_gp06	0.000143346755802286
CAMB-77E91	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999341498748848	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	7.47160789001793e-05
CAMB-77E91	MN908947.3	3037	C	T	1	1	0	0	0.999102651257648	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.15771583956492e-05
CAMB-77E91	MN908947.3	7279	C	T	0.015	0.0091	4e-07	3.8e-05	0.012095092450994	TCT	ORF1ab:nsp3	F1520F	C4560T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.987765883497845
CAMB-77EA0	MN908947.3	11074	C	INS	0.17	0.14	3e-65	5.3e-41	0.159064493267186	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.840085046066619
CAMB-77EA0	MN908947.3	11083	G	-	0.14	0.13	2.8e-63	5.2e-58	0.139301496033647	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.66198157908747e-05
CAMB-77EA0	MN908947.3	11083	G	T	0.86	0.87	0	0	0.860485545440026	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.66198157908747e-05
CAMB-77EA0	MN908947.3	1368	T	C	1	1	0	0	1	ATT	ORF1ab:nsp2	I188T	T563C	ATT>ACT	Missense	ORF1ab:nsp2	0
CAMB-77EA0	MN908947.3	14805	C	T	1	1	0	0	0.999883720930233	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	7.75193798449612e-05
CAMB-77EA0	MN908947.3	1612	C	A	0.034	0.0028	1.2e-16	0.00058	0.0193361905711153	ACC	ORF1ab:nsp2	N269K	C807A	AAC>AAA	Missense	ORF1ab:nsp2	0.980663809428885
CAMB-77EA0	MN908947.3	17167	C	T	0.035	0.036	1.6e-16	4.8e-17	0.035161307027083	TCA	ORF1ab:helicase	H311Y	C931T	CAT>TAT	Missense	ORF1ab:helicase	0.964838692972917
CAMB-77EA0	MN908947.3	22075	C	T	1	1	0	0	0.999773550724638	TCT	S	V171V	C513T	GTC>GTT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-77EA0	MN908947.3	22301	A	G	0.0039	0.15	0.00057	9.8e-58	0.0510577705451587	AAG	S	S247G	A739G	AGT>GGT	Missense	GU280_gp02, spike glycoprotein	0.948942229454841
CAMB-77EA0	MN908947.3	22858	C	T	0.1	0.029	1e-45	2e-13	0.0742043902951371	GCG	S	C432C	C1296T	TGC>TGT	Synonymous	GU280_gp02, spike glycoprotein	0.925795609704863
CAMB-77EA0	MN908947.3	23707	C	T	1	1	0	0	0.999835607430544	CCA	S	P715P	C2145T	CCC>CCT	Synonymous	GU280_gp02, spike glycoprotein	0.000164392569455861
CAMB-77EA0	MN908947.3	28253	C	T	0.044	0.046	5.2e-20	9.8e-21	0.0448493204648414	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.954796139452433
CAMB-77EA0	MN908947.3	29253	C	T	0.15	0.039	1.3e-60	6.8e-13	0.124824191279887	TCG	N	S327L	C980T	TCG>TTG	Missense	GU280_gp10	0.875175808720112
CAMB-77EA0	MN908947.3	29469	A	T	0.0091	0.028	0.00012	8.4e-09	0.0180072028811525	GAT	N	D399V	A1196T	GAT>GTT	Missense	GU280_gp10	0.981992797118848
CAMB-77EA0	MN908947.3	5619	T	C	0.088	0.015	2.1e-38	2.4e-08	0.0611425171080036	ATA	ORF1ab:nsp3	I967T	T2900C	ATA>ACA	Missense	ORF1ab:nsp3	0.938857482891996
CAMB-77EA0	MN908947.3	635	C	T	0.12	0.095	2.4e-53	3.4e-41	0.109698202780604	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.890217022719566
CAMB-77EA0	MN908947.3	6990	C	T	1	1	2.3e-222	2.1e-112	1	TCT	ORF1ab:nsp3	S1424F	C4271T	TCT>TTT	Missense	ORF1ab:nsp3	0
CAMB-77EA0	MN908947.3	9430	C	T	0.061	0.069	2.6e-21	2.3e-23	0.0650087260034904	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.93499127399651
CAMB-77EA0	MN908947.3	9479	G	T	0.16	0.024	8.4e-59	3.9e-10	0.0988654781199352	TGG	ORF1ab:nsp4	G309C	G925T	GGT>TGT	Missense	ORF1ab:nsp4	0.901134521880065
CAMB-77EBF	MN908947.3	10702	C	T	0.34	0.36	1.9e-172	3.8e-184	0.34585321287179	ACA	ORF1ab:3C-like-proteinase	D216D	C648T	GAC>GAT	Synonymous	ORF1ab:3C-like-proteinase	0.653987267427527
CAMB-77EBF	MN908947.3	11074	C	INS	0.029	0.025	2.3e-06	5.3e-05	0.0273963354532075	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.972414631182404
CAMB-77EBF	MN908947.3	11075	T	-	0.032	0.033	2.9e-08	1.4e-08	0.0323845315146032	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964019764771383
CAMB-77EBF	MN908947.3	11824	C	T	0.012	0.022	1e-05	3.6e-09	0.0173410404624277	TCA	ORF1ab:nsp6	I284I	C852T	ATC>ATT	Synonymous	ORF1ab:nsp6	0.982658959537572
CAMB-77EBF	MN908947.3	14408	C	T	1	1	0	0	0.998505231689088	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-77EBF	MN908947.3	14580	G	T	1	1	0	0	0.999454132219101	TGC	ORF1ab:RNA-dependent-RNA-polymerase	M371I	G1113T	ATG>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-77EBF	MN908947.3	18267	C	T	0.0096	0.012	2.7e-06	1.8e-07	0.0107267851461297	GCG	ORF1ab:3'-to-5'-exonuclease	R76R	C228T	CGC>CGT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.989227762374438
CAMB-77EBF	MN908947.3	21557	C	T	0.013	0.016	4.9e-07	3e-08	0.015106303618053	ACG	NA	NA	NA	NA	NA	NA	0.983961208504289
CAMB-77EBF	MN908947.3	22432	C	T	0.013	0.021	1.5e-05	8.3e-08	0.0172955974842767	ACT	S	D290D	C870T	GAC>GAT	Synonymous	GU280_gp02, spike glycoprotein	0.982704402515723
CAMB-77EBF	MN908947.3	23403	A	G	1	1	0	0	0.999421657133046	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	1.80732145923135e-05
CAMB-77EBF	MN908947.3	241	C	T	1	1	0	0	0.999252972216924	TCG	NA	NA	NA	NA	NA	NA	6.35768326021998e-05
CAMB-77EBF	MN908947.3	28742	A	G	0.064	0.072	2.1e-29	8.3e-33	0.067588863596568	AAT	N	I157V	A469G	ATC>GTC	Missense	GU280_gp10	0.932376116266853
CAMB-77EBF	MN908947.3	29520	C	T	0.029	0.038	5.9e-14	2.4e-17	0.0331067263582601	TCA	N	S416L	C1247T	TCA>TTA	Missense	GU280_gp10	0.966782733653899
CAMB-77EBF	MN908947.3	29523	C	T	0.0046	0.0098	0.00064	4e-06	0.0069221678203613	ACT	N	T417I	C1250T	ACT>ATT	Missense	GU280_gp10	0.993021554392481
CAMB-77EBF	MN908947.3	29706	G	T	0.013	0.013	3.9e-07	2.3e-07	0.0127881541309103	GGA	NA	NA	NA	NA	NA	NA	0.987127713276123
CAMB-77EBF	MN908947.3	29769	C	T	0.037	0.039	1.3e-16	2.7e-17	0.0381373271135117	ACA	NA	NA	NA	NA	NA	NA	0.961862672886488
CAMB-77EBF	MN908947.3	3037	C	T	1	1	0	0	0.999509547475804	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.26968349463772e-05
CAMB-77EBF	MN908947.3	4276	C	T	0.037	0.032	1.6e-17	1.2e-15	0.0351924458102269	ACA	ORF1ab:nsp3	Y519Y	C1557T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.964501430539366
CAMB-77EBF	MN908947.3	9400	A	G	0.0077	0.0054	2e-05	0.00015	0.00661257347303859	CAT	ORF1ab:nsp4	A282A	A846G	GCA>GCG	Synonymous	ORF1ab:nsp4	0.993227702530028
CAMB-77EBF	MN908947.3	9693	C	T	0.076	0.068	1.2e-34	2.1e-31	0.0726426932680973	GCT	ORF1ab:nsp4	A380V	C1139T	GCT>GTT	Missense	ORF1ab:nsp4	0.92640665204771
CAMB-77ECE	MN908947.3	11074	C	INS	0.11	0.034	6.3e-36	2.7e-07	0.0855611988614165	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.913992297817715
CAMB-77ECE	MN908947.3	11083	G	-	0.26	0.19	1.9e-125	1.7e-86	0.240379931807112	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-77ECE	MN908947.3	11083	G	T	0.74	0.81	6.9e-274	0	0.759498295177789	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-77ECE	MN908947.3	12100	C	A	0.019	0.03	2.6e-10	6.8e-15	0.0238990753800345	CCT	ORF1ab:nsp8	A3A	C9A	GCC>GCA	Synonymous	ORF1ab:nsp8	0.976022566995769
CAMB-77ECE	MN908947.3	12254	ATGCA	CATGC	0.0466	0.007	1.9e-20;2.2e-19;1.6e-18;1.2e-19;1.5e-21	NA;NA;6.9e-15;NA;NA	0.028438769587928	CAT	ORF1ab:nsp8	.	163-167-mnv	.	no-SNV	ORF1ab:nsp8	0.970887794941436
CAMB-77ECE	MN908947.3	12328	GAG	AGA	0.0196666666666667	0.0100666666666667	1.2e-07;5.5e-09;2.2e-10	NA;2e-13;NA	0.0111653872993719	AGA	ORF1ab:nsp8	.	237-239-mnv	.	no-SNV	ORF1ab:nsp8	0.988324624428478
CAMB-77ECE	MN908947.3	14805	C	T	1	1	0	0	0.999825986078886	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	8.70069605568445e-05
CAMB-77ECE	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-77ECE	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-77ECE	MN908947.3	26110	C	T	1	1	1.7e-180	6.7e-142	1	GCC	ORF3a	P240S	C718T	CCT>TCT	Missense	GU280_gp03	0
CAMB-77ECE	MN908947.3	26144	G	T	1	1	5.8e-176	6.2e-140	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-77ECE	MN908947.3	27271	G	T	0.37	0.24	4.4e-192	9e-117	0.315577745052261	AGT	ORF6	V24F	G70T	GTT>TTT	Missense	GU280_gp06	0.684296541072519
CAMB-77ECE	MN908947.3	29627	C	T	0.13	0.13	1.3e-35	1.4e-29	0.12649945474373	TCG	ORF10	R24C	C70T	CGT>TGT	Missense	GU280_gp11	0.87350054525627
CAMB-77EDD	MN908947.3	10228	C	T	0.014	0.011	7.2e-08	6.6e-07	0.0128433753225072	TCA	ORF1ab:3C-like-proteinase	L58L	C174T	CTC>CTT	Synonymous	ORF1ab:3C-like-proteinase	0.9871376536652
CAMB-77EDD	MN908947.3	10236	A	G	0.0056	0.0068	0.00015	3.9e-05	0.00603468354966439	AAG	ORF1ab:3C-like-proteinase	K61R	A182G	AAG>AGG	Missense	ORF1ab:3C-like-proteinase	0.993859444809113
CAMB-77EDD	MN908947.3	1025	C	T	0.0041	0.009	0.00043	3.5e-06	0.00623018033889618	ACC	ORF1ab:nsp2	P74S	C220T	CCT>TCT	Missense	ORF1ab:nsp2	0.993769819661104
CAMB-77EDD	MN908947.3	11075	T	-	0.058	0.035	6.7e-14	3.7e-09	0.0485159266409266	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.945137548262548
CAMB-77EDD	MN908947.3	11075	TT	-	0.0290305	0.0217	6.7e-14;0.49	3.7e-09;0.00028	0.0261380644690249	CTT	ORF1ab:nsp6	.	103-104-delfrshift	.	no-SNV	ORF1ab:nsp6	0.945137548262548
CAMB-77EDD	MN908947.3	11134	T	C	0.012	0.009	2e-06	4.8e-05	0.0110715806535804	CTT	ORF1ab:nsp6	A54A	T162C	GCT>GCC	Synonymous	ORF1ab:nsp6	0.988818527727029
CAMB-77EDD	MN908947.3	11235	C	T	0.0063	0.011	1e-04	9e-07	0.00814444592354144	GCT	ORF1ab:nsp6	A88V	C263T	GCT>GTT	Missense	ORF1ab:nsp6	0.991831350671039
CAMB-77EDD	MN908947.3	14408	C	T	1	0.99	0	0	0.994714930658809	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000689356870590144
CAMB-77EDD	MN908947.3	14730	G	A	0.037	0.016	1e-17	5.7e-09	0.0271346469622332	AGG	ORF1ab:RNA-dependent-RNA-polymerase	K421K	G1263A	AAG>AAA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.972824302134647
CAMB-77EDD	MN908947.3	15578	AC	-	0.0013115	0.00735	NA;0.006	3e-05;3.6e-05	0.00388041614562519	AAC	ORF1ab:RNA-dependent-RNA-polymerase	.	2111-2112-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.99676534520236
CAMB-77EDD	MN908947.3	16877	C	T	0.0086	0.0062	1.5e-05	0.00014	0.00762475579917683	ACA	ORF1ab:helicase	T214I	C641T	ACA>ATA	Missense	ORF1ab:helicase	0.992356277146596
CAMB-77EDD	MN908947.3	17529	TA	-	0.0054	0.0064	0.00012;1e-04	3.5e-05;3.4e-05	0.00581554029938485	CTA	ORF1ab:helicase	.	1293-1294-delfrshift	.	no-SNV	ORF1ab:helicase	0.994178364987614
CAMB-77EDD	MN908947.3	19763	C	T	0.0086	0.011	1.3e-05	8.9e-07	0.00977157360406091	ACA	ORF1ab:endoRNAse	T48I	C143T	ACA>ATA	Missense	ORF1ab:endoRNAse	0.990228426395939
CAMB-77EDD	MN908947.3	23403	A	G	1	1	0	0	0.999878593175069	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.33898653318142e-05
CAMB-77EDD	MN908947.3	241	C	T	1	1	0	0	0.999660241455073	TCG	NA	NA	NA	NA	NA	NA	0.000135903417970962
CAMB-77EDD	MN908947.3	26058	C	T	0.0056	0.013	0.001	9.3e-06	0.00896191187453323	ACA	ORF3a	D222D	C666T	GAC>GAT	Synonymous	GU280_gp03	0.991038088125467
CAMB-77EDD	MN908947.3	26735	C	T	0.022	0.027	4.4e-11	2.5e-13	0.0241097238452549	ACA	M	Y71Y	C213T	TAC>TAT	Synonymous	GU280_gp05	0.975828771757181
CAMB-77EDD	MN908947.3	28512	C	T	0.0072	0.006	4.4e-05	0.00013	0.00663114268798105	CCA	N	P80L	C239T	CCA>CTA	Missense	GU280_gp10	0.993368857312019
CAMB-77EDD	MN908947.3	28609	C	T	0.0082	0.0059	1.3e-05	9.2e-05	0.00720408902483197	ACC	N	Y112Y	C336T	TAC>TAT	Synonymous	GU280_gp10	0.992795910975168
CAMB-77EDD	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999725425590335	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-77EDD	MN908947.3	3037	C	T	1	0.99	0	0	0.996958725561188	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.24112961622013e-05
CAMB-77EDD	MN908947.3	346	C	T	0.013	0.0046	9e-08	0.00074	0.00990222462360117	TCG	ORF1ab:leader-protein	L27L	C81T	CTC>CTT	Synonymous	ORF1ab:leader-protein	0.990087384794422
CAMB-77EDD	MN908947.3	4512	TTGATTATGGTGC	-	0.00430769230769231	0.00587692307692308	NA;NA;NA;NA;NA;0.0027;5.5e-05;7.9e-05;8.8e-05;9.9e-05;5.2e-05;8e-05;6e-05	0.00077;0.00062;6.8e-05;6.8e-05;4.8e-05;0.00074;0.00017;0.00022;0.00025;0.00025;0.00021;2e-04;0.00026	0.00765505389782846	GTT	ORF1ab:nsp3	.	1793-1805-delfrshift	.	no-SNV	ORF1ab:nsp3	0.998169645007466
CAMB-77EDD	MN908947.3	4531	TTACTTTTACACCAGTAAAACAACTGTAGCGTCACTTATCAACACACTTAACGATCTA	-	0.0217413793103448	0.00531541379310345	0.00023;0.00059;0.00079;0.00078;0.00021;0.00013;0.00039;0.00032;0.00035;5e-04;0.00043;0.00044;0.00027;5e-04;0.00044;0.00046;0.00017;0.00072;7e-04;0.00076;0.00081;0.00071;0.00062;7e-04;0.00059;1.7e-05;4.6e-06;6.5e-06;1.8e-07;4.5e-07;9.6e-07;1.8e-07;2.7e-07;4.9e-08;1.1e-07;7.8e-09;7.5e-09;7.2e-09;5.5e-09;8e-09;9.8e-09;2.4e-07;2.5e-07;7.4e-09;9.5e-09;7.6e-09;5.8e-09;7.2e-09;4.1e-06;2.2e-05;4e-05;4.4e-05;6.5e-05;5.7e-05;5.6e-05;3.3e-05;2.4e-06;1.7e-07	0.18;0.24;0.25;0.26;0.21;0.17;0.013;0.013;0.012;0.015;0.015;0.014;0.011;0.015;0.014;0.014;0.0097;0.037;0.037;0.037;0.038;0.037;0.033;0.034;0.032;0.027;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00919608424799763	TTT	ORF1ab:nsp3	.	1812-1869-delfrshift	.	no-SNV	ORF1ab:nsp3	0.979733616531705
CAMB-77EDD	MN908947.3	522	TT	-	0.018	0.0545	0.0046;0.035	3e-08;6.5e-07	0.0324685744851565	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.961736530261919
CAMB-77EDD	MN908947.3	5296	C	T	0.011	0.011	1.3e-06	1.8e-06	0.0111265646731572	CCA	ORF1ab:nsp3	A859A	C2577T	GCC>GCT	Synonymous	ORF1ab:nsp3	0.988873435326843
CAMB-77EDD	MN908947.3	5670	C	T	0.0048	0.012	5e-04	5.1e-07	0.00782877706925942	TCA	ORF1ab:nsp3	S984L	C2951T	TCA>TTA	Missense	ORF1ab:nsp3	0.992171222930741
CAMB-77EDD	MN908947.3	7420	C	T	0.018	0.024	3.2e-09	1.6e-11	0.0199118942731278	TCT	ORF1ab:nsp3	I1567I	C4701T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.979823788546256
CAMB-77EEC	MN908947.3	11075	T	-	0.038	0.042	5.1e-10	1.2e-10	0.0402162586646934	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955238080855369
CAMB-77EEC	MN908947.3	11305	A	C	0.032	0.025	1.9e-15	2.8e-12	0.0276808048599467	AAG	ORF1ab:nsp6	K111N	A333C	AAA>AAC	Missense	ORF1ab:nsp6	0.97226421836774
CAMB-77EEC	MN908947.3	14408	C	T	1	1	0	0	0.998133532423208	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000533276450511945
CAMB-77EEC	MN908947.3	17731	T	C	0.022	0.02	1.3e-11	7.4e-11	0.0208916246968849	ATT	ORF1ab:helicase	F499L	T1495C	TTC>CTC	Missense	ORF1ab:helicase	0.979092155097605
CAMB-77EEC	MN908947.3	19737	T	C	0.0092	0.0067	3.7e-06	4.7e-05	0.0076571108413484	ATG	ORF1ab:endoRNAse	D39D	T117C	GAT>GAC	Synonymous	ORF1ab:endoRNAse	0.9922961994584
CAMB-77EEC	MN908947.3	23403	A	G	1	1	0	0	0.999240840576521	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000220046209704038
CAMB-77EEC	MN908947.3	241	C	T	1	1	0	0	0.998165367135054	TCG	NA	NA	NA	NA	NA	NA	0.000166784805904182
CAMB-77EEC	MN908947.3	24381	C	T	0.017	0.02	2.9e-09	2.7e-10	0.0184014943762172	TCC	S	S940F	C2819T	TCC>TTC	Missense	GU280_gp02, spike glycoprotein	0.981519017527125
CAMB-77EEC	MN908947.3	26533	C	T	0.0072	0.0096	4.1e-05	4.5e-06	0.00857555515435999	TCC	M	S4F	C11T	TCC>TTC	Missense	GU280_gp05	0.991289041343203
CAMB-77EEC	MN908947.3	26858	C	T	0.008	0.011	9.3e-06	5e-07	0.0098037329228401	TCA	M	F112F	C336T	TTC>TTT	Synonymous	GU280_gp05	0.990032711179527
CAMB-77EEC	MN908947.3	28758	C	T	1	1	0	0	0.999464629880791	CCT	N	P162L	C485T	CCT>CTT	Missense	GU280_gp10	0.000428296095367264
CAMB-77EEC	MN908947.3	28819	C	T	0.013	0.013	8.6e-08	1.3e-07	0.0131180993331633	CCT	N	A182A	C546T	GCC>GCT	Synonymous	GU280_gp10	0.986663265677951
CAMB-77EEC	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99903637677668	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000134024303073624
CAMB-77EEC	MN908947.3	3037	C	T	1	1	0	0	0.998964760445567	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000165638328709263
CAMB-77EEC	MN908947.3	3039	A	G	0.046	0.054	2.2e-21	1.9e-24	0.05068735428893	TAC	ORF1ab:nsp3	Y107C	A320G	TAC>TGC	Missense	ORF1ab:nsp3	0.948669507195112
CAMB-77EEC	MN908947.3	3377	G	A	0.0091	0.0067	3e-06	3.6e-05	0.00768600412557574	TGT	ORF1ab:nsp3	V220I	G658A	GTA>ATA	Missense	ORF1ab:nsp3	0.992229223770098
CAMB-77EEC	MN908947.3	857	C	T	0.017	0.019	1.9e-09	2.6e-10	0.0180747359870024	TCT	ORF1ab:nsp2	L18F	C52T	CTT>TTT	Missense	ORF1ab:nsp2	0.981815909516966
CAMB-77EEC	MN908947.3	9430	C	T	0.011	0.0061	1.2e-05	0.00088	0.00791472775722865	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.991210277214334
CAMB-77EFB	MN908947.3	1059	C	T	1	1	0	0	0.999871231321225	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	9.95030699623644e-05
CAMB-77EFB	MN908947.3	11075	T	-	0.029	0.041	5.2e-07	2e-10	0.0308026824347584	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.965271271890646
CAMB-77EFB	MN908947.3	14408	C	T	1	1	0	0	0.9986235028879	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00104266226431488
CAMB-77EFB	MN908947.3	23403	A	G	1	1	0	0	0.999896507115136	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.82147477360931e-05
CAMB-77EFB	MN908947.3	23426	G	C	1	1	0	0	0.997473256431486	TGT	S	V622L	G1864C	GTT>CTT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-77EFB	MN908947.3	241	C	T	1	1	0	0	0.999175155451473	TCG	NA	NA	NA	NA	NA	NA	6.92177243519491e-05
CAMB-77EFB	MN908947.3	25273	G	T	0.0033	0.0071	0.0034	3e-05	0.00398022136154188	TGA	S	M1237I	G3711T	ATG>ATT	Missense	GU280_gp02, spike glycoprotein	0.995927927376269
CAMB-77EFB	MN908947.3	25413	C	T	0.21	0.24	2.7e-94	8.8e-114	0.212013194568747	TCT	ORF3a	I7I	C21T	ATC>ATT	Synonymous	GU280_gp03	0.787951006213721
CAMB-77EFB	MN908947.3	25563	G	T	1	1	0	0	0.999805080167742	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	7.23987948385228e-05
CAMB-77EFB	MN908947.3	25855	G	T	0.021	0.018	2.4e-10	4e-09	0.0208086874753541	CGA	ORF3a	D155Y	G463T	GAC>TAC	Missense	GU280_gp03	0.977098310431644
CAMB-77EFB	MN908947.3	29266	G	T	0.019	0.027	2e-09	8.4e-14	0.0208662849844431	TGA	N	L331F	G993T	TTG>TTT	Missense	GU280_gp10	0.9771807495526
CAMB-77EFB	MN908947.3	3037	C	T	1	1	0	0	0.998146333712894	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000105923787834653
CAMB-77EFB	MN908947.3	3564	G	T	0.012	0.0039	6.3e-06	0.0088	0.0104618525133963	GGT	ORF1ab:nsp3	G282V	G845T	GGT>GTT	Missense	ORF1ab:nsp3	0.987922088968274
CAMB-77EFB	MN908947.3	8024	G	A	0.005	0.0079	0.00062	1.3e-05	0.00548371558783208	TGC	ORF1ab:nsp3	A1769T	G5305A	GCA>ACA	Missense	ORF1ab:nsp3	0.994247656452629
CAMB-77EFB	MN908947.3	8092	C	T	0.039	0.019	7.6e-18	3.7e-10	0.0353869111063739	TCA	ORF1ab:nsp3	L1791L	C5373T	CTC>CTT	Synonymous	ORF1ab:nsp3	0.964603399158931
CAMB-77F07	MN908947.3	11074	C	INS	0.026	0.04	2.4e-05	4.9e-09	0.0315732705790067	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.968116226242421
CAMB-77F07	MN908947.3	11075	T	-	0.029	0.026	9.8e-08	2.8e-07	0.0280520252292649	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.970340757148067
CAMB-77F07	MN908947.3	14408	C	T	1	1	0	0	0.997593640335172	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00224880040105994
CAMB-77F07	MN908947.3	16293	C	T	0.01	0.011	5.5e-06	6.4e-06	0.0103457307490833	GCA	ORF1ab:helicase	C19C	C57T	TGC>TGT	Synonymous	ORF1ab:helicase	0.989654269250917
CAMB-77F07	MN908947.3	20538	A	-	0.0055	0.0098	0.00015	2.2e-06	0.00693284752795911	TAA	ORF1ab:endoRNAse	.	918-918-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.992965943019078
CAMB-77F07	MN908947.3	21707	C	T	0.0075	0.0037	3.8e-05	0.0021	0.00601282736504543	ACA	S	H49Y	C145T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.993853554249065
CAMB-77F07	MN908947.3	23403	A	G	1	1	0	0	0.995775359324057	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00100105616016899
CAMB-77F07	MN908947.3	241	C	T	1	0.99	0	0	0.994665466932322	TCG	NA	NA	NA	NA	NA	NA	8.56953103241425e-05
CAMB-77F07	MN908947.3	24958	TG	-	0.0039	0.0077	0.0055;0.0018	0.00015;3.1e-05	0.00553080350284222	TTG	S	.	3396-3397-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.994200678411205
CAMB-77F07	MN908947.3	27264	TTTTAAAGTTTCCATTTGGAATCTTGA	-	1	1	0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0	0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0	0.999990823583391	CTT	ORF6	.	63-89-delinframe	.	no-SNV	GU280_gp06	0.000834670947030498
CAMB-77F07	MN908947.3	28254	A	G	0.012	0.0028	4.2e-07	0.0027	0.00801002694019852	CAT	ORF8	I121V	A361G	ATC>GTC	Missense	GU280_gp09	0.987048535576909
CAMB-77F07	MN908947.3	29730	CACCGAGGCCACGCGGAGTACGATCGAGTG	-	0.00697666666666667	0.0162666666666667	0.0024;0.0014;0.0019;0.002;0.0027;0.0026;0.0036;0.0038;0.0011;0.0012;0.00078;0.0013;0.0014;0.0011;0.0015;0.0016;0.0016;0.00091;0.002;0.002;0.0046;0.0049;0.0017;0.0019;0.00096;0.001;0.00054;0.0033;0.0023;0.0044	1.9e-07;2.2e-08;1.4e-07;1.5e-07;2.1e-07;1.5e-07;2.5e-07;3.4e-07;4.6e-07;4.9e-07;2.4e-07;5.8e-07;6.2e-07;1.4e-07;3e-07;6.4e-07;7.5e-07;2.1e-06;7.4e-06;5.3e-06;3.5e-05;3.3e-05;8.1e-06;6e-06;5.5e-06;5.3e-06;6.5e-06;1.9e-05;8e-06;1.5e-05	0.0101341841043446	TCA	NA	NA	NA	NA	NA	NA	0.989952553725928
CAMB-77F07	MN908947.3	3037	C	T	1	1	0	0	0.999492231136387	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000101553772722657
CAMB-77F07	MN908947.3	4135	TG	-	0.00315	0.017	0.0086;0.015	2.8e-08;2e-07	0.0082161870139225	TTG	ORF1ab:nsp3	.	1416-1417-delfrshift	.	no-SNV	ORF1ab:nsp3	0.991560894272978
CAMB-77F07	MN908947.3	4535	T	C	0.005	0.0089	0.0012	2.3e-05	0.00669063900023579	CTT	ORF1ab:nsp3	F606L	T1816C	TTT>CTT	Missense	ORF1ab:nsp3	0.993279886819146
CAMB-77F07	MN908947.3	5570	A	G	0.0075	0.0099	3.7e-05	1.2e-05	0.00825346112886049	TAT	ORF1ab:nsp3	M951V	A2851G	ATG>GTG	Missense	ORF1ab:nsp3	0.99174653887114
CAMB-77F07	MN908947.3	5917	G	A	0.025	0.017	2e-12	1.4e-09	0.0215702955624468	TGG	ORF1ab:nsp3	L1066L	G3198A	TTG>TTA	Synonymous	ORF1ab:nsp3	0.978347375065177
CAMB-77F07	MN908947.3	6483	GA	-	0.0011	0.0058	NA;0.0032	5.3e-05;4.7e-05	0.0026056710217426	GGA	ORF1ab:nsp3	.	3764-3765-delfrshift	.	no-SNV	ORF1ab:nsp3	0.998088211865341
CAMB-77F07	MN908947.3	6588	AG	-	0.0098	0.019	2.6e-05;3.8e-05	4.1e-06;3.9e-10	0.013443072702332	AAG	ORF1ab:nsp3	.	3869-3870-delfrshift	.	no-SNV	ORF1ab:nsp3	0.988639591025277
CAMB-77F07	MN908947.3	6701	C	T	0.011	0.0049	4.3e-06	0.0012	0.00843044879742127	TCT	ORF1ab:nsp3	L1328F	C3982T	CTT>TTT	Missense	ORF1ab:nsp3	0.991569551202579
CAMB-77F07	MN908947.3	7550	G	-	0.009	0.0056	8.5e-06	0.00027	0.00745650372825186	TGG	ORF1ab:nsp3	.	4831-4831-delfrshift	.	no-SNV	ORF1ab:nsp3	0.992439933719967
CAMB-77F16	MN908947.3	11075	T	-	0.038	0.045	9.3e-10	3.1e-11	0.0390037532099822	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956755777967999
CAMB-77F16	MN908947.3	1170	C	T	1	1	0	0	0.999099599066754	TCT	ORF1ab:nsp2	S122F	C365T	TCT>TTT	Missense	ORF1ab:nsp2	0.000124583776927085
CAMB-77F16	MN908947.3	14408	C	T	1	1	0	0	0.998812167365618	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000395944211460605
CAMB-77F16	MN908947.3	23403	A	G	1	1	0	0	0.999649136092285	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.32018224729595e-05
CAMB-77F16	MN908947.3	241	C	T	1	1	0	0	0.998293553877199	TCG	NA	NA	NA	NA	NA	NA	7.2230523716441e-05
CAMB-77F16	MN908947.3	25216	A	G	0.014	0.023	1.3e-06	3.5e-11	0.014964203278432	TAG	S	L1218L	A3654G	CTA>CTG	Synonymous	GU280_gp02, spike glycoprotein	0.984409843120379
CAMB-77F16	MN908947.3	25418	C	A	0.018	0.023	2.1e-08	1.3e-11	0.0186141962457193	ACA	ORF3a	T9K	C26A	ACA>AAA	Missense	GU280_gp03	0.981347564136337
CAMB-77F16	MN908947.3	25442	A	T	0.0068	0.0084	0.00033	1.1e-05	0.00702937304769808	CAA	ORF3a	Q17L	A50T	CAA>CTA	Missense	GU280_gp03	0.992523145231713
CAMB-77F16	MN908947.3	26895	C	T	0.011	0.0067	2e-05	0.00022	0.0105187429829629	CCA	M	H125Y	C373T	CAT>TAT	Missense	GU280_gp05	0.989263251981121
CAMB-77F16	MN908947.3	2704	C	T	0.0086	0.0073	3.4e-05	3.3e-05	0.00844551244663229	TCA	ORF1ab:nsp2	F633F	C1899T	TTC>TTT	Synonymous	ORF1ab:nsp2	0.991531157408488
CAMB-77F16	MN908947.3	2825	A	G	0.0061	0.0065	3e-04	4.2e-05	0.00614023504555658	TAA	ORF1ab:nsp3	N36D	A106G	AAT>GAT	Missense	ORF1ab:nsp3	0.99355165280162
CAMB-77F16	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999281589345417	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	6.16123964141585e-05
CAMB-77F16	MN908947.3	3037	C	T	1	1	0	0	0.999664639925346	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.37426184331394e-05
CAMB-77F25	MN908947.3	14408	C	T	1	1	0	0	0.999455693446549	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000326583932070542
CAMB-77F25	MN908947.3	203	C	T	0.62	0.31	0	2.1e-120	0.528460278460278	TCG	NA	NA	NA	NA	NA	NA	0.471334971334971
CAMB-77F25	MN908947.3	23403	A	G	1	1	0	0	0.999910281715414	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.97182845863987e-05
CAMB-77F25	MN908947.3	241	C	T	1	1	0	0	1	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-77F25	MN908947.3	28881	GGG	AAC	1	1	2.7e-272;5e-287;9.3e-306	1.3e-223;1.6e-240;2.2e-246	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-77F34	MN908947.3	11074	C	INS	0.052	0.031	8.1e-24	1.4e-06	0.0487629630307635	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.951072281768006
CAMB-77F34	MN908947.3	11075	T	-	0.014	0.021	0.001	3.8e-06	0.0150876198955846	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.984754542879113
CAMB-77F34	MN908947.3	14408	C	T	1	1	0	0	0.999564820737603	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000372261778677265
CAMB-77F34	MN908947.3	16289	C	T	1	1	0	0	1	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0
CAMB-77F34	MN908947.3	18266	G	-	0.0054	0.0075	0.00053	1.7e-05	0.00574633609681348	CGC	ORF1ab:3'-to-5'-exonuclease	.	227-227-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.994047385171506
CAMB-77F34	MN908947.3	18883	G	C	0.0049	0.0074	0.0027	2.1e-05	0.00521614029729589	TGT	ORF1ab:3'-to-5'-exonuclease	V282L	G844C	GTC>CTC	Missense	ORF1ab:3'-to-5'-exonuclease	0.994643208770188
CAMB-77F34	MN908947.3	19983	C	INS	0.036	0.035	2.3e-08	0.00045	0.0358945597307908	TCT	ORF1ab:endoRNAse	.	362-363-insfrshift	.	no-SNV	ORF1ab:endoRNAse	0.964105440269209
CAMB-77F34	MN908947.3	20635	G	-	0.01	0.017	0.00025	1.2e-05	0.0112291959093643	AGA	ORF1ab:endoRNAse	.	1015-1015-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.988770804090636
CAMB-77F34	MN908947.3	23403	A	G	1	1	0	0	0.999299285500953	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.89227376111379e-05
CAMB-77F34	MN908947.3	241	C	T	1	1	0	0	0.999817934650677	TCG	NA	NA	NA	NA	NA	NA	0.00010923920959363
CAMB-77F34	MN908947.3	25429	G	T	1	1	0	0	0.999920135370547	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	1.99661573632693e-05
CAMB-77F34	MN908947.3	26349	TG	-	0.004114	0.00665	0.3;8.2e-05	1.6e-05;0.00023	0.00441728631377457	CTG	E	.	105-106-delfrshift	.	no-SNV	GU280_gp04	0.999156484525212
CAMB-77F34	MN908947.3	27845	C	T	0.091	0.14	9.9e-40	9e-55	0.0980392156862745	TCT	NA	NA	NA	NA	NA	NA	0.901960784313726
CAMB-77F34	MN908947.3	28195	G	T	0.0027	0.0091	0.0093	3.6e-06	0.00351359256180536	CGT	ORF8	R101L	G302T	CGT>CTT	Missense	GU280_gp09	0.996074628244204
CAMB-77F34	MN908947.3	28357	G	A	0.051	0.086	4.2e-23	1.9e-39	0.0556258090026373	AGA	N	Q28Q	G84A	CAG>CAA	Synonymous	GU280_gp10	0.944348079096677
CAMB-77F34	MN908947.3	29269	C	T	0.21	0.22	1.6e-99	1e-100	0.210572363964778	CCT	N	T332T	C996T	ACC>ACT	Synonymous	GU280_gp10	0.789399412960036
CAMB-77F34	MN908947.3	29545	C	T	0.032	0.03	1.1e-13	6.4e-12	0.0316855815370554	ACC	NA	NA	NA	NA	NA	NA	0.968314418462945
CAMB-77F34	MN908947.3	3037	C	T	1	1	0	0	0.999529331222455	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.55761413717855e-05
CAMB-77F34	MN908947.3	3544	T	C	0.012	0.019	1.1e-06	5.3e-07	0.0127576054955839	CTA	ORF1ab:nsp3	T275T	T825C	ACT>ACC	Synonymous	ORF1ab:nsp3	0.987242394504416
CAMB-77F34	MN908947.3	6109	G	A	0.0073	0.0089	6.3e-05	1.8e-05	0.00755261371350984	AGA	ORF1ab:nsp3	K1130K	G3390A	AAG>AAA	Synonymous	ORF1ab:nsp3	0.99244738628649
CAMB-77F43	MN908947.3	10718	C	T	0.0049	0.0098	0.00094	7.4e-06	0.00706648070664807	TCG	ORF1ab:3C-like-proteinase	R222*	C664T	CGA>TGA	Nonsense	ORF1ab:3C-like-proteinase	0.992933519293352
CAMB-77F43	MN908947.3	11075	T	-	0.023	0.073	9.2e-07	1.2e-18	0.0430654538634659	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956606339084771
CAMB-77F43	MN908947.3	11094	CCTTTTTA	-	0.022625	0.0215	5e-09;5.4e-09;1.3e-10;1.3e-06;2.6e-05;4e-05;4.7e-05;3.7e-05	1.2e-08;1.4e-08;7e-10;2.5e-06;3.5e-05;5e-05;5.4e-05;4.8e-05	0.022263902759847	GCC	ORF1ab:nsp6	.	122-129-delfrshift	.	no-SNV	ORF1ab:nsp6	0.976577815117493
CAMB-77F43	MN908947.3	14032	A	C	1	1	0	0	0.99993721156563	AAA	ORF1ab:RNA-dependent-RNA-polymerase	N189H	A565C	AAT>CAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	3.13942171851945e-05
CAMB-77F43	MN908947.3	14408	C	T	1	1	0	0	0.998976982097187	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000831202046035806
CAMB-77F43	MN908947.3	14809	C	T	0.021	0.024	1.6e-11	8e-13	0.0226067224507162	TCG	ORF1ab:RNA-dependent-RNA-polymerase	R448C	C1342T	CGT>TGT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.977393277549284
CAMB-77F43	MN908947.3	14903	TT	-	0.0115	0.0385	NA;2.1e-07	7.1e-09;1.7e-11	0.0232558139534884	ATT	ORF1ab:RNA-dependent-RNA-polymerase	.	1436-1437-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.983083929733247
CAMB-77F43	MN908947.3	14904	TAATGC	-	0.0231666666666667	0.00633333333333333	2.1e-07;1.2e-06;1.5e-06;8.3e-07;8.8e-07;7.6e-07	1.7e-11;NA;NA;NA;NA;NA	0.0129032258064516	TTA	ORF1ab:RNA-dependent-RNA-polymerase	.	1437-1442-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.970474967907574
CAMB-77F43	MN908947.3	15951	C	T	0.13	0.27	3.7e-59	6.9e-133	0.190194420963652	TCC	ORF1ab:RNA-dependent-RNA-polymerase	I828I	C2484T	ATC>ATT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.809805579036348
CAMB-77F43	MN908947.3	17167	C	T	0.014	0.014	1.2e-07	7.2e-08	0.0138497387905438	TCA	ORF1ab:helicase	H311Y	C931T	CAT>TAT	Missense	ORF1ab:helicase	0.986150261209456
CAMB-77F43	MN908947.3	21614	C	T	0.19	0.56	3.6e-59	3.7e-187	0.351333333333333	TCT	S	L18F	C52T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.648666666666667
CAMB-77F43	MN908947.3	23403	A	G	1	1	0	0	0.999763621321357	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000185726104648218
CAMB-77F43	MN908947.3	241	C	T	1	1	0	0	0.999712017114411	TCG	NA	NA	NA	NA	NA	NA	0.000164561648907722
CAMB-77F43	MN908947.3	24174	C	T	0.029	0.017	3.3e-14	3.4e-09	0.024378765060241	GCT	S	A871V	C2612T	GCT>GTT	Missense	GU280_gp02, spike glycoprotein	0.975621234939759
CAMB-77F43	MN908947.3	28197	TG	-	0.01	0.014	NA;1.3e-08	4.6e-06;3.3e-06	0.0118418978562421	TTG	ORF8	.	304-305-delfrshift	.	no-SNV	GU280_gp09	0.993881754300945
CAMB-77F43	MN908947.3	28198	G	-	0.02	0.014	1.3e-08	3.3e-06	0.0174108774697474	TGT	ORF8	.	305-305-delfrshift	.	no-SNV	GU280_gp09	0.971969449200639
CAMB-77F43	MN908947.3	28253	C	T	0.04	0.026	4.8e-18	2.3e-12	0.0339291790940209	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.966010769261565
CAMB-77F43	MN908947.3	28378	G	T	0.12	0.14	3.6e-56	8.6e-64	0.129081471283187	CGC	N	A35A	G105T	GCG>GCT	Synonymous	GU280_gp10	0.870732478743791
CAMB-77F43	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999559082892416	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00049480455220188
CAMB-77F43	MN908947.3	29070	AAGCATACAATGTAACACAAGCTT	-	0.0127916666666667	0.0289166666666667	0.0022;0.0018;0.0017;0.002;0.0019;0.0039;0.0028;0.0026;0.0027;0.0013;0.0025;0.0025;0.00027;0.00022;1.5e-05;2.3e-05;2.5e-05;1.3e-05;8.3e-06;6.4e-06;8.4e-06;9.3e-06;9.2e-06;5.4e-06	8.6e-07;8.3e-07;6.8e-07;8.4e-07;7.4e-07;3.6e-06;1.3e-06;6.4e-07;1.1e-06;1.5e-07;1.1e-06;5.3e-07;1.3e-08;1.2e-08;1.7e-11;3e-11;1.4e-10;1.8e-11;1.3e-11;1.3e-11;5.4e-10;1.4e-11;1.4e-11;5.8e-12	0.0206364804595963	AAA	N	.	797-820-delinframe	.	no-SNV	GU280_gp10	0.979863784424045
CAMB-77F43	MN908947.3	3037	C	T	1	1	0	0	0.999655291278869	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-77F43	MN908947.3	522	T	-	0.026	0.064	0.0015	1.4e-08	0.0432117920868891	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.956477889837083
CAMB-77F43	MN908947.3	635	C	T	0.42	0.28	2.3e-219	1.4e-131	0.359334203655352	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.640535248041775
CAMB-77F43	MN908947.3	8748	C	T	0.069	0.031	6.2e-27	1e-12	0.051697766901193	GCT	ORF1ab:nsp4	A65V	C194T	GCT>GTT	Missense	ORF1ab:nsp4	0.948302233098807
CAMB-77F43	MN908947.3	9130	G	A	0.11	0.063	2.6e-49	4e-29	0.0889201919267509	TGC	ORF1ab:nsp4	V192V	G576A	GTG>GTA	Synonymous	ORF1ab:nsp4	0.910991768279262
CAMB-77F43	MN908947.3	9489	G	T	0.034	0.033	8.2e-15	2.5e-13	0.0333843797856049	AGT	ORF1ab:nsp4	S312I	G935T	AGT>ATT	Missense	ORF1ab:nsp4	0.966615620214395
CAMB-77F52	MN908947.3	11075	T	-	0.036	0.038	6.8e-09	2.1e-09	0.0366895443925234	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958838346962617
CAMB-77F52	MN908947.3	12485	A	G	0.032	0.027	1.5e-15	2.5e-13	0.0295921732439266	CAT	ORF1ab:nsp8	I132V	A394G	ATA>GTA	Missense	ORF1ab:nsp8	0.970319885676597
CAMB-77F52	MN908947.3	13417	T	C	0.011	0.012	1e-06	5.1e-07	0.0112897449912358	ATC	ORF1ab:nsp10	D131D	T393C	GAT>GAC	Synonymous	ORF1ab:nsp10	0.988691407354355
CAMB-77F52	MN908947.3	14408	C	T	1	1	0	0	0.9990227091531	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000480072696722647
CAMB-77F52	MN908947.3	14597	A	G	0.057	0.049	4.2e-26	8.4e-23	0.0528994310773972	AAT	ORF1ab:RNA-dependent-RNA-polymerase	N377S	A1130G	AAT>AGT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.946796847220576
CAMB-77F52	MN908947.3	17858	A	G	0.015	0.013	2.1e-08	1.3e-07	0.0141212128170097	TAT	ORF1ab:helicase	Y541C	A1622G	TAT>TGT	Missense	ORF1ab:helicase	0.985821383878856
CAMB-77F52	MN908947.3	18445	G	T	0.011	0.013	6.1e-07	1.9e-07	0.0120440287799922	AGT	ORF1ab:3'-to-5'-exonuclease	V136F	G406T	GTT>TTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.987746509849921
CAMB-77F52	MN908947.3	22936	G	T	0.0093	0.0087	5.7e-06	8e-06	0.0090251854651987	AGT	S	K458N	G1374T	AAG>AAT	Missense	GU280_gp02, spike glycoprotein	0.990927562254879
CAMB-77F52	MN908947.3	23403	A	G	1	1	0	0	0.999404559373937	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000117779464496035
CAMB-77F52	MN908947.3	241	C	T	1	1	0	0	0.999141893242115	TCG	NA	NA	NA	NA	NA	NA	0.000164568419320332
CAMB-77F52	MN908947.3	26137	A	C	0.022	0.014	3.5e-05	0.0059	0.0185036202735318	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.981094127111826
CAMB-77F52	MN908947.3	26204	C	T	0.0091	0.011	1.1e-05	1.9e-06	0.0100437805820242	ACT	ORF3a	T271I	C812T	ACT>ATT	Missense	GU280_gp03	0.989956219417976
CAMB-77F52	MN908947.3	26822	C	T	0.015	0.013	2.3e-08	1.1e-07	0.0140656068486576	TCA	M	F100F	C300T	TTC>TTT	Synonymous	GU280_gp05	0.984954894067174
CAMB-77F52	MN908947.3	28253	C	T	0.036	0.04	2.8e-16	5.3e-18	0.0380886634450881	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.961631199287651
CAMB-77F52	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999389813090115	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	3.66824401159165e-05
CAMB-77F52	MN908947.3	3037	C	T	1	1	0	0	0.999583766909469	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.91928051137208e-05
CAMB-77F52	MN908947.3	7420	C	T	0.011	0.011	2.4e-06	1.7e-06	0.011147023642888	TCT	ORF1ab:nsp3	I1567I	C4701T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.988852976357112
CAMB-77F52	MN908947.3	9042	C	A	0.0089	0.012	6.8e-06	7.1e-07	0.0102812915150465	TCT	ORF1ab:nsp4	S163Y	C488A	TCT>TAT	Missense	ORF1ab:nsp4	0.989680201775159
CAMB-77F52	MN908947.3	9496	A	G	0.014	0.017	4.8e-08	6e-09	0.0157839433030025	TAG	ORF1ab:nsp4	V314V	A942G	GTA>GTG	Synonymous	ORF1ab:nsp4	0.983433566589908
CAMB-77F61	MN908947.3	10324	G	T	0.0052	0.017	0.00027	2e-09	0.00947421257372318	AGG	ORF1ab:3C-like-proteinase	K90N	G270T	AAG>AAT	Missense	ORF1ab:3C-like-proteinase	0.990525787426277
CAMB-77F61	MN908947.3	1076	C	T	0.022	0.026	2.1e-11	2.8e-13	0.0239383208320553	TCC	ORF1ab:nsp2	P91S	C271T	CCA>TCA	Missense	ORF1ab:nsp2	0.976061679167945
CAMB-77F61	MN908947.3	11074	C	INS	0.034	0.047	1.5e-08	8.9e-12	0.0387512132791095	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.960978486564854
CAMB-77F61	MN908947.3	11075	T	-	0.032	0.037	3.9e-08	1.1e-09	0.0340989792565426	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956350762642697
CAMB-77F61	MN908947.3	11083	G	-	0.02	0.018	1.3e-08	5.2e-08	0.0194568215573944	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.885062592828347
CAMB-77F61	MN908947.3	11083	G	T	0.091	0.1	2.3e-19	1.9e-22	0.0953851050286442	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.885062592828347
CAMB-77F61	MN908947.3	12473	C	T	0.0043	0.0085	0.001	1.1e-05	0.00592411138329251	ACT	ORF1ab:nsp8	L128L	C382T	CTA>TTA	Synonymous	ORF1ab:nsp8	0.994075888616707
CAMB-77F61	MN908947.3	1289	G	A	0.0084	0.0068	2.6e-05	1e-04	0.00775287704421563	CGA	ORF1ab:nsp2	E162K	G484A	GAA>AAA	Missense	ORF1ab:nsp2	0.992222895215021
CAMB-77F61	MN908947.3	13704	T	G	0.005	0.0062	0.00016	2.9e-05	0.005449116406604	ATT	ORF1ab:RNA-dependent-RNA-polymerase	N79K	T237G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994469553497775
CAMB-77F61	MN908947.3	14408	C	T	0.99	1	0	0	0.994912940981844	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00183010050043426
CAMB-77F61	MN908947.3	14853	T	C	0.017	0.012	2.6e-09	2e-07	0.0155498928592112	TTG	ORF1ab:RNA-dependent-RNA-polymerase	F462F	T1386C	TTT>TTC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.978456014362657
CAMB-77F61	MN908947.3	17066	A	T	0.015	0.0098	2.4e-08	1.8e-06	0.0131314326274695	TAT	ORF1ab:helicase	Y277F	A830T	TAT>TTT	Missense	ORF1ab:helicase	0.986380574943807
CAMB-77F61	MN908947.3	22299	G	A	1	1	0	0	0.998987512656092	AGA	S	R246K	G737A	AGA>AAA	Missense	GU280_gp02, spike glycoprotein	5.19224278927283e-05
CAMB-77F61	MN908947.3	23403	A	G	1	1	0	0	0.999282555116648	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.53215841183024e-05
CAMB-77F61	MN908947.3	23519	G	T	0.019	0.0083	5.7e-10	1.7e-05	0.0153204662475914	GGC	S	A653S	G1957T	GCT>TCT	Missense	GU280_gp02, spike glycoprotein	0.984553179391604
CAMB-77F61	MN908947.3	241	C	T	1	1	0	0	0.997866553751445	TCG	NA	NA	NA	NA	NA	NA	0.000195430190707294
CAMB-77F61	MN908947.3	2509	C	T	0.039	0.051	1.2e-17	3.2e-22	0.0436217008797654	CCA	ORF1ab:nsp2	P568P	C1704T	CCC>CCT	Synonymous	ORF1ab:nsp2	0.956378299120235
CAMB-77F61	MN908947.3	25528	C	T	1	1	0	0	0.99606998654105	GCT	ORF3a	L46F	C136T	CTT>TTT	Missense	GU280_gp03	9.42126514131898e-05
CAMB-77F61	MN908947.3	26781	CTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCT	-	0.0238205128205128	0.0394615384615385	0.00049;0.0033;0.0035;0.0063;0.00066;0.0025;0.00057;0.00058;0.00021;0.00022;0.00025;0.00048;0.00022;0.00032;0.00075;0.00036;0.00066;0.00048;0.00047;0.00041;0.00073;0.00043;0.00055;0.00024;0.00026;0.00043;0.00041;0.00018;0.00038;0.00061;0.00058;4e-04;0.00061;0.00028;0.00038;0.00029;0.021;0.047;0.032	0.00024;0.00039;4e-04;0.00081;1e-05;2.8e-05;3.4e-07;3.2e-07;2.7e-07;1.9e-07;9.8e-08;2e-07;1.5e-07;2.7e-07;4.8e-07;1.7e-07;3.9e-07;2.4e-07;2.8e-07;2.3e-07;4.7e-07;2.3e-07;3.1e-07;2.3e-07;1.5e-07;3.4e-07;2.3e-07;9e-08;2e-07;3.7e-07;3.2e-07;8.7e-08;2.5e-07;3.5e-08;1.4e-07;5.2e-08;0.00016;0.00077;0.00047	0.0318472062556199	TCT	M	.	259-297-delinframe	.	no-SNV	GU280_gp05	0.977609719140646
CAMB-77F61	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99837339598771	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000150496638908398
CAMB-77F61	MN908947.3	3037	C	T	1	1	0	0	0.999754891948201	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.08513419665836e-05
CAMB-77F61	MN908947.3	522	T	-	0.062	0.043	8.9e-08	1.2e-05	0.0552881488226877	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.944581761415377
CAMB-77F61	MN908947.3	522	TT	-	0.0455	0.032	8.9e-08;0.00031	1.2e-05;0.0036	0.0406539143774869	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.944581761415377
CAMB-77F61	MN908947.3	6573	C	T	1	1	0	0	0.999743194658449	TCT	ORF1ab:nsp3	S1285F	C3854T	TCT>TTT	Missense	ORF1ab:nsp3	0.000192604006163328
CAMB-77F61	MN908947.3	9936	C	T	0.033	0.026	1.1e-15	6e-13	0.0300462679079101	ACT	ORF1ab:nsp4	T461I	C1382T	ACT>ATT	Missense	ORF1ab:nsp4	0.969897987624728
CAMB-77F70	MN908947.3	11075	T	-	0.04	0.037	7.3e-10	3.2e-09	0.0385712333135906	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958066426716479
CAMB-77F70	MN908947.3	14408	C	T	1	1	0	0	0.997988650855465	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000590566344565506
CAMB-77F70	MN908947.3	14786	C	T	1	1	0	0	0.999380377577512	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A440V	C1319T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000180396401483956
CAMB-77F70	MN908947.3	20578	G	T	1	1	0	0	0.999329904018605	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	7.88348213405861e-05
CAMB-77F70	MN908947.3	23403	A	G	1	1	0	0	0.999482574551838	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.20465813897131e-05
CAMB-77F70	MN908947.3	241	C	T	1	1	0	0	0.998255714408013	TCG	NA	NA	NA	NA	NA	NA	0.000107011386011472
CAMB-77F70	MN908947.3	2416	C	T	1	1	0	0	0.999219436042541	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0
CAMB-77F70	MN908947.3	25563	G	T	1	1	0	0	0.999807481740846	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	8.42267383797182e-05
CAMB-77F70	MN908947.3	3037	C	T	1	1	0	0	0.999262913193854	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.66989850881669e-05
CAMB-77F8F	MN908947.3	11025	T	C	0.24	0.089	1e-116	1.6e-41	0.184009332750036	ATT	ORF1ab:nsp6	I18T	T53C	ATT>ACT	Missense	ORF1ab:nsp6	0.815949003187301
CAMB-77F8F	MN908947.3	11074	C	INS	0.17	0.039	2.5e-67	1.7e-08	0.125962300826108	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.873577329343461
CAMB-77F8F	MN908947.3	11083	G	-	0.03	0.17	5.8e-13	5.7e-77	0.0837617525820944	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.31577972303275e-05
CAMB-77F8F	MN908947.3	11083	G	T	0.97	0.83	0	0	0.916029827242833	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.31577972303275e-05
CAMB-77F8F	MN908947.3	14189	C	T	1	1	0	0	0.999764157896288	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A241V	C722T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000117921051855783
CAMB-77F8F	MN908947.3	14805	C	T	1	1	0	0	0.999965139789444	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-77F8F	MN908947.3	15197	CTGTAGTAATT	-	0.0484545454545455	0.00409090909090909	1e-22;3.9e-23;2.2e-21;1.5e-22;9.8e-22;1.1e-21;1e-22;4.7e-22;5.1e-23;3.5e-22;9e-22	NA;NA;1.7e-07;1.5e-07;2.1e-07;NA;NA;NA;NA;NA;NA	0.0339996430483669	ACT	ORF1ab:RNA-dependent-RNA-polymerase	.	1730-1740-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.966044444444444
CAMB-77F8F	MN908947.3	16325	G	T	0.11	0.074	5.2e-41	7.2e-27	0.0931452935388652	TGT	ORF1ab:helicase	C30F	G89T	TGT>TTT	Missense	ORF1ab:helicase	0.906854706461135
CAMB-77F8F	MN908947.3	1887	C	T	1	1	0	0	1	GCT	ORF1ab:nsp2	A361V	C1082T	GCT>GTT	Missense	ORF1ab:nsp2	0
CAMB-77F8F	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-77F8F	MN908947.3	2558	C	T	1	1	0	0	0.999664091367148	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-77F8F	MN908947.3	26144	G	T	1	1	1.6e-161	2.3e-148	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-77F8F	MN908947.3	26787	GGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.0965882352941176	0.0441470588235294	1.1e-17;1e-17;4.2e-19;1.2e-18;3.1e-19;1.2e-17;1.6e-18;4.4e-18;2.7e-17;1.2e-18;1.8e-17;5.2e-18;6e-18;1.7e-18;2.1e-17;4.1e-18;9.8e-18;3.6e-18;4.7e-19;9.6e-18;2.5e-18;3.4e-18;2.2e-18;1.3e-17;8.7e-18;1.8e-18;1.1e-17;1.1e-19;2.4e-18;7.9e-19;5.2e-13;1.1e-10;4.8e-12;2.9e-11	2.5e-07;2.4e-07;1.7e-07;1.1e-07;8.7e-08;2.2e-07;1.6e-07;2e-07;3.5e-07;1.3e-07;2.8e-07;1.5e-07;2e-07;1.6e-07;3.4e-07;1.2e-07;2.2e-07;1.7e-07;8.6e-08;2e-07;1.8e-07;1.1e-07;1.2e-07;2.8e-07;1.9e-07;6.6e-08;2.4e-07;3.7e-08;1.4e-07;2e-16;6.7e-06;4.3e-05;1.4e-05;2.3e-05	0.0733060747663551	AGG	M	.	265-298-delfrshift	.	no-SNV	GU280_gp05	0.928433085219505
CAMB-77F8F	MN908947.3	29581	TTTTCCG	-	0.0277142857142857	0.014	6.8e-10;1.9e-11;3e-12;1.7e-11;2.4e-11;9.5e-12;2.4e-11	4.1e-05;2e-06;6e-07;1.2e-06;1.8e-06;9.5e-07;1.4e-06	0.0214626391096979	CTT	ORF10	.	24-30-delfrshift	.	no-SNV	GU280_gp11	0.97792937399679
CAMB-77F8F	MN908947.3	944	G	A	1	1	0	0	0.999595141700405	GGG	ORF1ab:nsp2	G47S	G139A	GGT>AGT	Missense	ORF1ab:nsp2	0.000347021399652979
CAMB-77F9E	MN908947.3	1030	T	C	0.025	0.021	2e-11	6.1e-11	0.024236557325364	TTG	ORF1ab:nsp2	F75F	T225C	TTT>TTC	Synonymous	ORF1ab:nsp2	0.975750121005164
CAMB-77F9E	MN908947.3	11074	C	INS	0.031	0.03	4.5e-11	1.2e-06	0.0311272169434748	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.967933566050436
CAMB-77F9E	MN908947.3	11075	T	-	0.035	0.041	6.9e-09	3.6e-10	0.0363041526336249	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959529797064156
CAMB-77F9E	MN908947.3	14408	C	T	1	1	0	0	0.997427340486052	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000663093931059972
CAMB-77F9E	MN908947.3	14786	C	T	1	1	0	0	0.999905098501211	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A440V	C1319T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	4.254205118136e-05
CAMB-77F9E	MN908947.3	1513	C	T	0.017	0.014	7.6e-08	3e-07	0.0168588937354492	GCC	ORF1ab:nsp2	C236C	C708T	TGC>TGT	Synonymous	ORF1ab:nsp2	0.982900264925473
CAMB-77F9E	MN908947.3	18231	T	C	0.009	0.0052	3.4e-05	0.00016	0.00833859664952329	ATC	ORF1ab:3'-to-5'-exonuclease	Y64Y	T192C	TAT>TAC	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.991653884327348
CAMB-77F9E	MN908947.3	20578	G	T	1	1	0	0	0.999957119272743	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	2.14403636285671e-05
CAMB-77F9E	MN908947.3	21587	C	T	0.032	0.039	7.8e-14	2.5e-16	0.0326656394453005	GCC	S	P9S	C25T	CCA>TCA	Missense	GU280_gp02, spike glycoprotein	0.967231638418079
CAMB-77F9E	MN908947.3	22012	A	G	0.011	0.015	5e-06	1.4e-08	0.0118231244647729	AAA	S	K150K	A450G	AAA>AAG	Synonymous	GU280_gp02, spike glycoprotein	0.988170237059952
CAMB-77F9E	MN908947.3	22300	A	C	0.0076	0.012	0.00038	3.2e-07	0.00820317479360842	GAA	S	R246S	A738C	AGA>AGC	Missense	GU280_gp02, spike glycoprotein	0.991699346895316
CAMB-77F9E	MN908947.3	23403	A	G	1	1	0	0	0.999626726390444	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.39897616381379e-05
CAMB-77F9E	MN908947.3	23557	C	T	0.0098	0.0069	3.9e-05	7.1e-05	0.00929091175465156	CCA	S	P665P	C1995T	CCC>CCT	Synonymous	GU280_gp02, spike glycoprotein	0.980783317868828
CAMB-77F9E	MN908947.3	23868	G	T	0.0085	0.0072	7.3e-05	2.3e-05	0.00836337213444085	GGA	S	G769V	G2306T	GGA>GTA	Missense	GU280_gp02, spike glycoprotein	0.991323179506176
CAMB-77F9E	MN908947.3	241	C	T	1	1	0	0	0.998394579548152	TCG	NA	NA	NA	NA	NA	NA	0.00018125714778931
CAMB-77F9E	MN908947.3	2416	C	T	1	1	0	0	0.997960440237051	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0.000269375817748018
CAMB-77F9E	MN908947.3	25563	G	T	1	1	0	0	0.999477385952916	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000112337598905929
CAMB-77F9E	MN908947.3	3037	C	T	1	1	0	0	0.998454079992085	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000408122882089589
CAMB-77F9E	MN908947.3	7273	G	T	0.01	0.013	2.1e-05	1.6e-05	0.0109409190371991	GGT	ORF1ab:nsp3	R1518S	G4554T	AGG>AGT	Missense	ORF1ab:nsp3	0.989059080962801
CAMB-77FAD	MN908947.3	10992	T	C	1	1	0	0	0.999723060732781	ATC	ORF1ab:nsp6	I7T	T20C	ATC>ACC	Missense	ORF1ab:nsp6	5.53878534437398e-05
CAMB-77FAD	MN908947.3	11074	C	INS	0.11	0.12	7.5e-44	2.7e-47	0.118570975279084	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.868635878501168
CAMB-77FAD	MN908947.3	11074	C	T	0.011	0.01	4.5e-07	1.1e-06	0.010716243113047	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.868635878501168
CAMB-77FAD	MN908947.3	11083	G	-	0.17	0.16	1.8e-73	5e-70	0.161987069361205	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.62284762566719e-05
CAMB-77FAD	MN908947.3	11083	G	T	0.83	0.84	0	0	0.837789988590613	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.62284762566719e-05
CAMB-77FAD	MN908947.3	14805	C	T	1	1	0	0	0.998212957507027	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000666518551433015
CAMB-77FAD	MN908947.3	23707	C	T	1	1	0	0	0.999624377875857	CCA	S	P715P	C2145T	CCC>CCT	Synonymous	GU280_gp02, spike glycoprotein	0.000344320280464519
CAMB-77FAD	MN908947.3	26144	G	T	1	1	0	0	0.999805891202019	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000194108797981269
CAMB-77FAD	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0331081081081081	0.0324054054054054	0.00048;4e-05;0.00018;0.00017;0.00046;5.1e-06;3.2e-05;1.4e-05;1.5e-05;4.6e-06;5.1e-06;3.7e-06;1.3e-05;6.3e-06;7.9e-06;1.8e-05;5.4e-06;1.5e-05;1.1e-05;9.9e-06;6.3e-06;1.7e-05;6.2e-06;1.2e-05;9.4e-06;5.4e-06;1.4e-05;8.2e-06;5.8e-06;6.6e-06;1.4e-05;1.1e-05;5e-06;1e-05;4.7e-06;8.6e-06;4.3e-06	7e-04;1e-04;0.00027;0.00032;0.00056;4.2e-05;7.3e-05;1.7e-05;1.5e-05;9.1e-06;1.1e-05;8.5e-06;9.9e-06;9.6e-06;1.3e-05;1.7e-05;8.8e-06;1.6e-05;8.6e-06;1.2e-05;9.9e-06;1.9e-05;1.1e-05;1.2e-05;1e-05;5.7e-06;1.3e-05;9.9e-06;2.1e-06;1.1e-05;1.3e-05;1.2e-05;6.6e-06;1.6e-05;3.3e-06;1.1e-05;6e-06	0.0337910334243301	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.977390189687854
CAMB-77FAD	MN908947.3	29686	C	T	0.028	0.028	8e-13	4.6e-13	0.0278430736807976	TCA	NA	NA	NA	NA	NA	NA	0.971792169895436
CAMB-77FBC	MN908947.3	11074	C	INS	0.066	0.026	1.7e-33	5.3e-05	0.0597858885220628	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.939975759051053
CAMB-77FBC	MN908947.3	11650	C	T	0.013	0.032	1.8e-07	4.4e-13	0.0152657715652014	GCC	ORF1ab:nsp6	G226G	C678T	GGC>GGT	Synonymous	ORF1ab:nsp6	0.984734228434799
CAMB-77FBC	MN908947.3	11668	C	T	0.0085	0.0023	9.2e-06	0.0057	0.00775688994342033	ACC	ORF1ab:nsp6	N232N	C696T	AAC>AAT	Synonymous	ORF1ab:nsp6	0.992151852527834
CAMB-77FBC	MN908947.3	12473	C	T	0.031	0.01	2.8e-14	1.8e-06	0.0277792447847901	ACT	ORF1ab:nsp8	L128L	C382T	CTA>TTA	Synonymous	ORF1ab:nsp8	0.972207552152099
CAMB-77FBC	MN908947.3	12688	T	C	0.023	0.013	7.7e-11	8.1e-08	0.0207244739443581	ATA	ORF1ab:nsp9	N1N	T3C	AAT>AAC	Synonymous	ORF1ab:nsp9	0.97920491456009
CAMB-77FBC	MN908947.3	13627	G	T	0.0018	0.011	0.0067	3e-07	0.00287825671261254	TGA	ORF1ab:RNA-dependent-RNA-polymerase	D54Y	G160T	GAC>TAC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.997086885507131
CAMB-77FBC	MN908947.3	14408	C	T	1	1	0	0	0.999540001568176	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000324089804239304
CAMB-77FBC	MN908947.3	15279	C	T	0.044	0.0084	6e-20	4.1e-06	0.0403365431378271	ACC	ORF1ab:RNA-dependent-RNA-polymerase	H604H	C1812T	CAC>CAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.959624550141037
CAMB-77FBC	MN908947.3	15540	C	T	0.012	0.0087	2.5e-06	1.5e-05	0.0116274633243671	TCA	ORF1ab:RNA-dependent-RNA-polymerase	V691V	C2073T	GTC>GTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.988348690360366
CAMB-77FBC	MN908947.3	23403	A	G	1	0.99	0	0	0.998155091946228	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00182163894318348
CAMB-77FBC	MN908947.3	241	C	T	0.98	0.98	0	0	0.984026954927284	TCG	NA	NA	NA	NA	NA	NA	0.0158671318024453
CAMB-77FBC	MN908947.3	27281	G	T	0.98	0.99	0	0	0.983707468203066	TGG	ORF6	W27L	G80T	TGG>TTG	Missense	GU280_gp06	0.0118253342754647
CAMB-77FBC	MN908947.3	28253	C	T	0.011	0.005	4.2e-05	0.0028	0.00973822322087862	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.989904483632004
CAMB-77FBC	MN908947.3	28338	A	G	0.01	0.01	1.6e-05	1.5e-06	0.0102215689086476	GAT	N	D22G	A65G	GAT>GGT	Missense	GU280_gp10	0.989742578517138
CAMB-77FBC	MN908947.3	28881	GGG	AAC	0.876666666666667	1	0;0;0	0;0;0	0.895056790913454	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.117953076308944
CAMB-77FBC	MN908947.3	28930	T	A	0.0029	0.0081	0.0066	7.7e-06	0.00358810306069514	TTG	N	L219L	T657A	CTT>CTA	Synonymous	GU280_gp10	0.996347051703268
CAMB-77FBC	MN908947.3	29144	C	T	0.41	0.41	1.7e-219	5.8e-220	0.410823166408594	ACT	N	L291L	C871T	CTA>TTA	Synonymous	GU280_gp10	0.589137130119621
CAMB-77FBC	MN908947.3	3037	C	T	1	1	0	0	0.999725425590335	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.49148819330038e-05
CAMB-77FBC	MN908947.3	5779	T	C	0.014	0.018	3.8e-06	5.5e-08	0.0147424444971952	ATA	ORF1ab:nsp3	H1020H	T3060C	CAT>CAC	Synonymous	ORF1ab:nsp3	0.985120125935458
CAMB-77FBC	MN908947.3	635	C	T	0.0071	0.01	0.00026	3.9e-06	0.00738540628958664	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.992608444329656
CAMB-77FBC	MN908947.3	7290	G	A	0.014	0.042	1.3e-05	1.3e-08	0.0214521452145215	GGA	ORF1ab:nsp3	G1524E	G4571A	GGA>GAA	Missense	ORF1ab:nsp3	0.978547854785479
CAMB-77FBC	MN908947.3	8958	C	T	0.0099	0.022	1.3e-05	1.3e-11	0.0119352750809061	ACA	ORF1ab:nsp4	T135I	C404T	ACA>ATA	Missense	ORF1ab:nsp4	0.988047464940669
CAMB-77FCB	MN908947.3	11074	C	INS	0.039	0.034	3.4e-09	1.8e-07	0.0366895147823598	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.963103738927146
CAMB-77FCB	MN908947.3	11075	T	-	0.07	0.029	6.4e-17	8.5e-08	0.051189081133246	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.94348934996898
CAMB-77FCB	MN908947.3	11083	GTATGAAAATGCCTT	-	0.0127333333333333	0.0017742	1.1e-05;2.8e-06;3e-06;2.7e-05;2.3e-05;8.5e-07;6.8e-07;5.4e-07;2.7e-07;5.9e-07;4.1e-07;7.2e-06;8.7e-06;4.1e-06;0.00027	0.5;NA;NA;1.2e-05;1.1e-05;0.48;NA;NA;NA;NA;NA;NA;NA;0.5;NA	0.00681394154070789	TGT	ORF1ab:nsp6	.	111-125-delinframe	.	no-SNV	ORF1ab:nsp6	0.986304518292188
CAMB-77FCB	MN908947.3	11134	T	C	0.0069	0.013	4e-04	1.1e-06	0.00955105430720251	CTT	ORF1ab:nsp6	A54A	T162C	GCT>GCC	Synonymous	ORF1ab:nsp6	0.990402805333826
CAMB-77FCB	MN908947.3	14408	C	T	1	1	0	0	0.999417688566144	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000376789751318764
CAMB-77FCB	MN908947.3	14741	C	T	1	1	0	0	0.999571842827394	TCT	ORF1ab:RNA-dependent-RNA-polymerase	S425F	C1274T	TCT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	9.73084483194831e-05
CAMB-77FCB	MN908947.3	14801	ACTACTATCGTTATAATCTACCAACAATGTGTGATATCAGACA	-	0.00712093023255814	0.00158520930232558	0.00016;0.00013;0.00017;6e-05;3.6e-05;2.5e-05;2.4e-05;2.6e-05;2.4e-05;2.5e-05;3e-05;2.8e-05;3.3e-05;2.4e-05;3.5e-05;2.2e-05;1.9e-05;1.4e-05;2.6e-05;3.1e-05;3e-05;2.9e-05;3.2e-05;3.6e-05;3.5e-05;3.6e-05;2.2e-05;6e-05;9.5e-05;3.1e-05;6.4e-05;3.5e-05;3.9e-05;6.7e-05;5.2e-05;3.1e-05;2.9e-05;3.8e-05;0.00012;0.00023;3.4e-05;3.3e-05;4e-05	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;4e-08;3.8e-08;7.8e-08;4.6e-08;2.7e-08;NA;NA;NA;NA;NA;NA;NA	0.00423522293742962	GAC	ORF1ab:RNA-dependent-RNA-polymerase	.	1334-1376-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.995446920680566
CAMB-77FCB	MN908947.3	15352	C	T	0.022	0.015	2e-11	9.2e-09	0.0190798439776305	TCT	ORF1ab:RNA-dependent-RNA-polymerase	L629F	C1885T	CTT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.980779171953569
CAMB-77FCB	MN908947.3	1863	TTTATGCAT	-	0.00977777777777778	0.00491111111111111	4.2e-06;4.6e-06;6.5e-06;6.4e-06;3.7e-05;3.9e-05;3.8e-05;3.2e-05;2.8e-05	0.00075;0.00076;0.00099;0.0011;0.0034;0.0036;0.0037;0.0036;0.0013	0.00763306985107033	CTT	ORF1ab:nsp2	.	1058-1066-delinframe	.	no-SNV	ORF1ab:nsp2	0.992191295897827
CAMB-77FCB	MN908947.3	187	A	G	1	1	0	0	0.999705188679245	CAG	NA	NA	NA	NA	NA	NA	0.000265330188679245
CAMB-77FCB	MN908947.3	21892	A	-	0.016	0.024	0.00027	2e-05	0.0186941964285714	TAG	S	.	330-330-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.981305803571429
CAMB-77FCB	MN908947.3	23403	A	G	1	1	0	0	0.99983716007165	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000130271942680345
CAMB-77FCB	MN908947.3	23817	T	-	0.011	0.009	4.9e-06	3.6e-05	0.0101800217073992	CTT	S	.	2255-2255-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.989595418990232
CAMB-77FCB	MN908947.3	2384	G	A	0.0038	0.02	0.0044	7.2e-09	0.0106145251396648	TGA	ORF1ab:nsp2	E527K	G1579A	GAA>AAA	Missense	ORF1ab:nsp2	0.989106145251397
CAMB-77FCB	MN908947.3	241	C	T	1	1	0	0	0.999638923993501	TCG	NA	NA	NA	NA	NA	NA	0.000270807004874526
CAMB-77FCB	MN908947.3	26335	C	T	0.0068	0.011	2.2e-05	3.1e-07	0.00842393966108336	ACT	E	L31L	C91T	CTA>TTA	Synonymous	GU280_gp04	0.991576060338917
CAMB-77FCB	MN908947.3	26681	C	T	0.0066	0.014	0.00038	2.2e-07	0.0099256700953525	TCC	M	F53F	C159T	TTC>TTT	Synonymous	GU280_gp05	0.990059313762295
CAMB-77FCB	MN908947.3	27390	G	T	0.02	0.015	1.7e-10	1.2e-08	0.0176233139706606	CGA	NA	NA	NA	NA	NA	NA	0.982229004627351
CAMB-77FCB	MN908947.3	28726	T	A	0.0013	0.0063	0.0059	3.8e-05	0.00377279396352966	CTG	N	P151P	T453A	CCT>CCA	Synonymous	GU280_gp10	0.995886606581429
CAMB-77FCB	MN908947.3	28854	C	T	0.051	0.048	2.5e-22	9.5e-21	0.0494424449820048	TCA	N	S194L	C581T	TCA>TTA	Missense	GU280_gp10	0.950380553424981
CAMB-77FCB	MN908947.3	29033	G	T	0.095	0.17	8.5e-16	6e-28	0.132848155914642	GGC	N	A254S	G760T	GCT>TCT	Missense	GU280_gp10	0.86712100653756
CAMB-77FCB	MN908947.3	3037	C	T	1	1	0	0	0.999597099113618	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000100725221595488
CAMB-77FCB	MN908947.3	5412	C	T	0.11	0.066	1.6e-41	1.9e-23	0.0928748670684155	GCC	ORF1ab:nsp3	A898V	C2693T	GCC>GTC	Missense	ORF1ab:nsp3	0.907125132931585
CAMB-77FCB	MN908947.3	5650	A	G	1	1	0	0	0.999825266468635	AAT	ORF1ab:nsp3	K977K	A2931G	AAA>AAG	Synonymous	ORF1ab:nsp3	0.000116489020909779
CAMB-77FDA	MN908947.3	11074	C	INS	0.025	0.023	2.1e-07	0.00018	0.024556658040409	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.974810460746193
CAMB-77FDA	MN908947.3	11075	T	-	0.041	0.037	3.4e-10	1.9e-09	0.0405138339920949	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954036063363667
CAMB-77FDA	MN908947.3	11991	A	G	0.027	0.027	8.4e-12	7.9e-13	0.0272915799082148	GAA	ORF1ab:nsp7	E50G	A149G	GAA>GGA	Missense	ORF1ab:nsp7	0.971429653092387
CAMB-77FDA	MN908947.3	1207	A	C	0.017	0.014	2.1e-08	4.1e-08	0.0166557310856508	AAA	ORF1ab:nsp2	Q134H	A402C	CAA>CAC	Missense	ORF1ab:nsp2	0.983136773274562
CAMB-77FDA	MN908947.3	14408	C	T	1	1	0	0	0.998071524750668	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000627610288244289
CAMB-77FDA	MN908947.3	17573	C	T	0.01	0.011	1.7e-05	1.5e-06	0.0101105679090224	GCT	ORF1ab:helicase	A446V	C1337T	GCT>GTT	Missense	ORF1ab:helicase	0.989863148118944
CAMB-77FDA	MN908947.3	18032	C	T	0.021	0.022	7.7e-10	1.1e-11	0.0212069904820912	ACT	ORF1ab:helicase	T599I	C1796T	ACT>ATT	Missense	ORF1ab:helicase	0.978760962686806
CAMB-77FDA	MN908947.3	2098	G	A	0.01	0.01	1.6e-05	1.1e-06	0.0100444598526125	AGT	ORF1ab:nsp2	Q431Q	G1293A	CAG>CAA	Synonymous	ORF1ab:nsp2	0.989918060819579
CAMB-77FDA	MN908947.3	21090	C	T	0.046	0.044	2.1e-20	9.5e-21	0.0457130229817325	ACT	ORF1ab:2'-O-ribose-methyltransferase	D144D	C432T	GAC>GAT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.954117560400707
CAMB-77FDA	MN908947.3	21618	C	T	0.019	0.014	7.9e-09	3.2e-07	0.0180405913304936	ACA	S	T19I	C56T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0.981887819021369
CAMB-77FDA	MN908947.3	23403	A	G	1	1	0	0	0.999359017048482	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.54963594388208e-05
CAMB-77FDA	MN908947.3	241	C	T	1	1	0	0	0.998871186599289	TCG	NA	NA	NA	NA	NA	NA	0.00016376567471458
CAMB-77FDA	MN908947.3	24502	C	T	0.017	0.017	2.6e-08	6.8e-09	0.0172671112538492	TCC	S	I980I	C2940T	ATC>ATT	Synonymous	GU280_gp02, spike glycoprotein	0.98267621332628
CAMB-77FDA	MN908947.3	26155	GTT	-	0.01	0.013	3.3e-05;3.4e-05;3.2e-05	6e-07;7.5e-07;6.8e-07	0.0106711915535445	AGT	ORF3a	.	763-765-delinframe	.	no-SNV	GU280_gp03	0.98934766214178
CAMB-77FDA	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999193022750551	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	6.71539055592241e-05
CAMB-77FDA	MN908947.3	3037	C	T	1	1	0	0	0.999224715141548	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.87337013978621e-05
CAMB-77FDA	MN908947.3	394	T	C	0.013	0.01	1.9e-06	2.2e-06	0.0123905088389796	GTC	ORF1ab:leader-protein	R43R	T129C	CGT>CGC	Synonymous	ORF1ab:leader-protein	0.987565741571173
CAMB-77FDA	MN908947.3	4886	C	T	0.0078	0.0099	1e-04	2.4e-06	0.00819124191864618	TCC	ORF1ab:nsp3	P723S	C2167T	CCT>TCT	Missense	ORF1ab:nsp3	0.991785864727752
CAMB-77FDA	MN908947.3	7444	A	G	0.011	0.013	6.2e-06	1.8e-07	0.0115817503291395	TAT	ORF1ab:nsp3	V1575V	A4725G	GTA>GTG	Synonymous	ORF1ab:nsp3	0.988368755011334
CAMB-77FDA	MN908947.3	8950	C	T	0.019	0.017	8.8e-09	3e-09	0.0183516241411123	TCT	ORF1ab:nsp4	I132I	C396T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.981638048552112
CAMB-77FE9	MN908947.3	11075	T	-	0.045	0.063	2.7e-11	1.4e-15	0.0541245516791653	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.945634453721949
CAMB-77FE9	MN908947.3	11595	A	G	0.089	0.013	8.5e-33	1.9e-05	0.066951566951567	CAG	ORF1ab:nsp6	Q208R	A623G	CAG>CGG	Missense	ORF1ab:nsp6	0.933048433048433
CAMB-77FE9	MN908947.3	12459	C	T	0.0052	0.018	0.00093	2e-09	0.0105887563243998	ACA	ORF1ab:nsp8	T123I	C368T	ACA>ATA	Missense	ORF1ab:nsp8	0.989397823198636
CAMB-77FE9	MN908947.3	14408	C	T	1	1	0	0	0.999431208762635	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000406279455260506
CAMB-77FE9	MN908947.3	15872	A	-	0.019	0.032	1.7e-10	4.2e-16	0.0252299605781866	GAA	ORF1ab:RNA-dependent-RNA-polymerase	.	2405-2405-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.974628525219852
CAMB-77FE9	MN908947.3	16311	ATGTTGTAAATGCTGTTACGACCATG	-	0.0224230769230769	0.00193961538461538	1.5e-05;7.5e-06;3.2e-05;4.9e-05;2.9e-05;3.7e-05;1.8e-05;4.9e-06;8.9e-10;4.3e-10;1.5e-09;2.3e-09;1.8e-09;2.8e-09;6.9e-09;1.2e-09;7.6e-10;7.5e-10;3.8e-10;4e-10;4e-10;4.8e-10;4.5e-10;2.4e-10;2.9e-10;4.4e-10	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;5.9e-11;1.6e-10;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00978286805058459	TAT	ORF1ab:helicase	.	75-100-delfrshift	.	no-SNV	ORF1ab:helicase	0.989755122438781
CAMB-77FE9	MN908947.3	1912	C	T	0.0086	0.011	1.7e-05	1.1e-06	0.00965891070553297	CCC	ORF1ab:nsp2	S369S	C1107T	TCC>TCT	Synonymous	ORF1ab:nsp2	0.990254591586656
CAMB-77FE9	MN908947.3	23403	A	G	1	1	0	0	0.999947098903889	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.23208768885691e-05
CAMB-77FE9	MN908947.3	241	C	T	1	1	0	0	0.999764277295618	TCG	NA	NA	NA	NA	NA	NA	0.000171434694096218
CAMB-77FE9	MN908947.3	24133	C	T	0.059	0.039	6.7e-28	4.4e-19	0.0485575549842902	GCC	S	G857G	C2571T	GGC>GGT	Synonymous	GU280_gp02, spike glycoprotein	0.95144244501571
CAMB-77FE9	MN908947.3	26767	TCGCAATGGCT	-	0.0226363636363636	0.00307090909090909	1e-10;1.9e-10;1.6e-10;1.4e-10;9.8e-11;5.6e-12;3.6e-13;1.6e-09;0.00051;0.00051;3e-04	0.46;0.46;0.46;0.47;0.46;0.47;0.46;0.48;0.5;0.5;3.6e-05	0.0103129988201818	ATC	M	.	245-255-delfrshift	.	no-SNV	GU280_gp05	0.989501714859326
CAMB-77FE9	MN908947.3	26777	TTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGT	-	0.0313962264150943	0.0462075471698113	3e-04;0.0011;0.0032;0.0021;0.00018;0.0014;0.0019;0.003;0.00077;0.0016;3.5e-06;3.3e-06;5.7e-07;1.8e-06;1.4e-06;3.5e-06;1.9e-06;2.5e-06;4.9e-06;1.6e-06;4.1e-06;2.3e-06;2.4e-06;2.2e-06;4.4e-06;2.2e-06;3.2e-06;2.1e-06;1.5e-06;3.6e-06;1.9e-06;5.5e-07;1.9e-06;3.6e-06;3.4e-06;1.4e-06;3.7e-06;8.9e-07;1.8e-06;1.4e-06;3.5e-05;0.00017;7.5e-05;0.00013;0.0018;0.0012;0.0015;0.0016;0.0016;0.0016;0.0015;0.0013;0.00014	3.6e-05;0.00013;0.00068;0.00029;1.9e-05;0.00018;0.00021;0.00044;5.7e-05;0.00017;6.2e-10;5.8e-10;1.3e-10;2.1e-10;1.6e-10;5.7e-10;2.4e-10;3.6e-10;9e-10;1.9e-10;7.4e-10;4.2e-10;3.7e-10;2.8e-10;7.9e-10;2e-10;5e-10;3.4e-10;1.3e-10;4.9e-10;2.4e-10;7.6e-11;3.3e-10;5.7e-10;5.1e-10;2.1e-10;6.1e-10;5.4e-11;2.5e-10;1.3e-10;9.8e-08;1.4e-06;3e-07;6.9e-07;4e-04;0.00023;0.00024;0.00034;0.00034;0.00034;0.00031;0.00024;2e-05	0.0467146205447345	CTT	M	.	255-307-delfrshift	.	no-SNV	GU280_gp05	0.969698081367622
CAMB-77FE9	MN908947.3	26862	C	T	0.014	0.018	3.1e-08	7.3e-10	0.0158211794546607	TCC	M	P114S	C340T	CCA>TCA	Missense	GU280_gp05	0.984115409004439
CAMB-77FE9	MN908947.3	27937	C	T	0.0088	0.0077	1.5e-05	3.5e-05	0.00821454457598454	GCA	ORF8	A15V	C44T	GCA>GTA	Missense	GU280_gp09	0.991785455424015
CAMB-77FE9	MN908947.3	3037	C	T	1	1	0	0	0.999295278365046	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000201349038558341
CAMB-77FE9	MN908947.3	4117	AT	-	0.023	0.051	4.1e-06;3.6e-06	4.7e-13;3.3e-12	0.0341586156146889	CAT	ORF1ab:nsp3	.	1398-1399-delfrshift	.	no-SNV	ORF1ab:nsp3	0.967177991019534
CAMB-77FE9	MN908947.3	4455	C	T	0.064	0.035	8.9e-29	8.5e-17	0.0468181818181818	GCC	ORF1ab:nsp3	A579V	C1736T	GCC>GTC	Missense	ORF1ab:nsp3	0.953181818181818
CAMB-77FE9	MN908947.3	4576	A	T	0.033	0.061	2.2e-16	5.3e-28	0.0492851497952439	CAC	ORF1ab:nsp3	T619T	A1857T	ACA>ACT	Synonymous	ORF1ab:nsp3	0.950714850204756
CAMB-77FE9	MN908947.3	4579	T	A	0.033	0.061	1.9e-16	2e-28	0.0495993069092484	TTA	ORF1ab:nsp3	L620L	T1860A	CTT>CTA	Synonymous	ORF1ab:nsp3	0.950328496137463
CAMB-77FE9	MN908947.3	4927	C	T	0.038	0.023	1.8e-18	6.6e-12	0.0309259961203148	ACA	ORF1ab:nsp3	D736D	C2208T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.969051706838503
CAMB-77FF8	MN908947.3	11074	C	INS	0.028	0.052	3.6e-06	7.1e-14	0.0386049956237797	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.961193024978119
CAMB-77FF8	MN908947.3	11075	T	-	0.039	0.026	1.2e-09	4.6e-07	0.0331121249827181	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.966807226139453
CAMB-77FF8	MN908947.3	11083	G	T	0.019	0.031	0.00022	9.3e-07	0.0239874346033469	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.975030893783131
CAMB-77FF8	MN908947.3	1440	G	A	1	0.98	0	0	0.994472084024323	GGC	ORF1ab:nsp2	G212D	G635A	GGC>GAC	Missense	ORF1ab:nsp2	0.00552791597567717
CAMB-77FF8	MN908947.3	1707	C	A	1	0.99	0	0	0.997407388941517	TCT	ORF1ab:nsp2	S301Y	C902A	TCT>TAT	Missense	ORF1ab:nsp2	0.00251782420102707
CAMB-77FF8	MN908947.3	17224	T	C	0.0054	0.0069	0.00018	3.2e-05	0.00602270822859058	ATG	ORF1ab:helicase	C330R	T988C	TGT>CGT	Missense	ORF1ab:helicase	0.993914446120328
CAMB-77FF8	MN908947.3	17644	C	T	0.013	0.011	1.5e-07	4.8e-07	0.0121403109986052	TCA	ORF1ab:helicase	Q470*	C1408T	CAA>TAA	Nonsense	ORF1ab:helicase	0.987825248402817
CAMB-77FF8	MN908947.3	1807	A	-	0.0074	0.0086	0.00016	4.8e-05	0.00781914391004441	GAA	ORF1ab:nsp2	.	1002-1002-delfrshift	.	no-SNV	ORF1ab:nsp2	0.987361806671076
CAMB-77FF8	MN908947.3	18373	TCTACAGGTG	-	0.0021	0.0292	NA;NA;NA;4.5e-05;NA;NA;NA;NA;NA;NA	1.2e-06;1.5e-06;1.4e-06;1.7e-06;1.4e-06;1.2e-06;9.5e-07;2.8e-06;4.9e-07;2.7e-06	0.0115288307713709	TTC	ORF1ab:3'-to-5'-exonuclease	.	334-343-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.988371077857904
CAMB-77FF8	MN908947.3	22739	ACTAATGTCTATGCAGATTCATTTGTA	-	0.00145662962962963	0.0127777777777778	NA;NA;NA;0.49;4.6e-05;2.8e-05;1.1e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00015;0.00018;2.6e-05;3.7e-05;1.5e-05;7.2e-06;2.7e-06;1e-07;4.1e-08;4.6e-08;4.3e-09;1.9e-08;6.9e-08;1.8e-07;2e-07;1.5e-07;1.6e-07;7.9e-08;1.5e-07;1.4e-07;7.1e-08;1.1e-07;1.3e-07;2.1e-07;2e-07;2.6e-07;1.8e-07	0.00536109573879358	TAC	S	.	1177-1203-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.994381423135735
CAMB-77FF8	MN908947.3	2891	G	A	1	0.99	0	0	0.995843187844908	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	0.0040851429800043
CAMB-77FF8	MN908947.3	29726	TTTTCACCGAGGCCACGCGGAGTA	-	0.0224166666666667	0.0180166666666667	2.7e-14;5.2e-15;NA;NA;NA;NA;NA;NA;NA;NA;3.3e-14;1e-13;9.3e-14;1.4e-13;1.7e-14;1.4e-13;2e-13;8.9e-14;1.6e-13;2.5e-13;1.3e-13;2.8e-12;2.8e-11;1.9e-11	1.4e-16;4e-17;1.5e-05;3e-05;4.7e-05;1.7e-05;3.9e-05;4.1e-05;5.7e-05;5.6e-06;1.9e-08;2.7e-08;3.6e-08;4.1e-08;1.3e-10;5.5e-10;6.6e-10;3.4e-08;4.9e-08;5.3e-08;5.1e-08;2.2e-07;9.1e-07;4.4e-06	0.0253411306042885	ATT	NA	NA	NA	NA	NA	NA	0.962028749660971
CAMB-77FF8	MN908947.3	29779	GA	-	0.00765	0.00265	0.00063;1.1e-05	NA;0.00089	0.00496219281663516	GGA	NA	NA	NA	NA	NA	NA	0.994326911712563
CAMB-77FF8	MN908947.3	522	T	-	0.045	0.047	7.9e-06	3.6e-06	0.0456577062081649	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.954192596394431
CAMB-77FF8	MN908947.3	8456	A	C	1	1	0	0	0.99911777679753	TAG	ORF1ab:nsp3	S1913R	A5737C	AGT>CGT	Missense	ORF1ab:nsp3	0.000220555800617556
CAMB-78003	MN908947.3	10587	A	G	0.0057	0.0075	0.00016	2.7e-05	0.00654110747716251	GAA	ORF1ab:3C-like-proteinase	E178G	A533G	GAA>GGA	Missense	ORF1ab:3C-like-proteinase	0.993120559377467
CAMB-78003	MN908947.3	11074	C	INS	0.024	0.031	9e-05	3.2e-06	0.0268313752591569	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.972494816862474
CAMB-78003	MN908947.3	11075	T	-	0.04	0.036	3.6e-10	1.4e-09	0.0384179126463873	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95764896516167
CAMB-78003	MN908947.3	12364	T	C	0.24	0.26	1.1e-116	5e-124	0.250146325148416	TTT	ORF1ab:nsp8	L91L	T273C	CTT>CTC	Synonymous	ORF1ab:nsp8	0.749853674851584
CAMB-78003	MN908947.3	14408	C	T	1	1	0	0	0.996010655085784	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000694348007221219
CAMB-78003	MN908947.3	14786	C	T	1	1	0	0	0.999535764025283	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A440V	C1319T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	5.9517432656025e-05
CAMB-78003	MN908947.3	18032	C	T	1	1	0	0	0.999084599792634	ACT	ORF1ab:helicase	T599I	C1796T	ACT>ATT	Missense	ORF1ab:helicase	4.67040922125597e-05
CAMB-78003	MN908947.3	18654	C	T	0.014	0.013	3e-08	1.5e-07	0.0136076462011988	GCA	ORF1ab:3'-to-5'-exonuclease	R205R	C615T	CGC>CGT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.984306658026891
CAMB-78003	MN908947.3	20578	G	T	1	1	0	0	0.999625617730744	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	2.49588179503819e-05
CAMB-78003	MN908947.3	23403	A	G	1	1	0	0	0.999416478237764	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.29402202794652e-05
CAMB-78003	MN908947.3	23559	TTGGTGCAGGTATATGCGCTAGT	-	0.039304347826087	0.0358695652173913	0.00019;0.00037;0.00013;0.00026;0.00029;0.00026;0.00024;0.00024;0.00016;0.00015;7.1e-05;1.5e-05;0.00014;6.4e-05;0.00014;6.9e-05;0.00016;0.00031;0.00019;0.00024;6.3e-06;1.4e-05;0.0012	0.00059;0.00089;4e-04;0.00071;0.00071;0.00073;0.00066;0.00066;0.00044;0.00042;9e-05;3.9e-05;0.00035;0.00016;0.00029;8.7e-05;0.00018;0.00041;0.00023;0.00024;6.6e-06;1.5e-05;0.00099	0.0362088974854932	ATT	S	.	1997-2019-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.953218146913206
CAMB-78003	MN908947.3	241	C	T	1	1	0	0	0.997460501423142	TCG	NA	NA	NA	NA	NA	NA	8.52180730489322e-05
CAMB-78003	MN908947.3	2416	C	T	0.99	0.99	0	0	0.994448941829536	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0
CAMB-78003	MN908947.3	25563	G	T	1	1	0	0	0.999823168467401	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	3.53663065197786e-05
CAMB-78003	MN908947.3	26158	GTTA	-	0.0067	0.01225	0.0032;0.00083;0.0014;0.0039	1.1e-05;7.6e-06;3.4e-06;6.4e-05	0.00908928889680984	TGT	ORF3a	.	766-769-delfrshift	.	no-SNV	GU280_gp03	0.991734554320033
CAMB-78003	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0450789473684211	0.042	4.8e-05;9.1e-07;1.3e-05;1.5e-05;4.1e-05;2e-08;3.1e-07;5.6e-08;5.2e-08;5.7e-09;1.7e-08;8.3e-09;4.4e-08;1.8e-08;2.7e-08;6.2e-08;1.5e-08;5.1e-08;2.5e-08;2.6e-08;2.7e-08;5.7e-08;2e-08;3.8e-08;2.1e-08;9.1e-09;3.8e-08;1.6e-08;7.4e-09;2e-08;4.2e-08;3.7e-08;2e-08;5e-08;7.9e-09;2e-08;1.1e-08;0.00057	0.00011;8.8e-06;2.4e-05;2.8e-05;6.6e-05;4.8e-07;1.1e-06;1.4e-07;1.3e-07;7.9e-08;7.1e-08;5.8e-08;8.2e-08;8e-08;1.2e-07;1.8e-07;7.3e-08;1.4e-07;6.8e-08;9.7e-08;7.7e-08;1.8e-07;7.3e-08;1.1e-07;8e-08;4e-08;1.2e-07;8.5e-08;9.4e-09;8.9e-08;1.4e-07;1.3e-07;5.5e-08;1.4e-07;1.5e-08;8.1e-08;3.3e-08;0.00034	0.0461083623106264	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.97256681949918
CAMB-78003	MN908947.3	27925	C	T	0.0083	0.01	4.4e-05	8.3e-06	0.00916475734222037	ACA	ORF8	T11I	C32T	ACA>ATA	Missense	GU280_gp09	0.99083524265778
CAMB-78003	MN908947.3	3037	C	T	1	1	0	0	0.998992274101444	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.73231814279849e-05
CAMB-78003	MN908947.3	522	T	-	0.038	0.039	6.2e-05	4.7e-05	0.0384800012387928	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.961411604391521
CAMB-78012	MN908947.3	14408	C	T	1	1	0	0	0.999635043156147	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000328461159467893
CAMB-78012	MN908947.3	15566	C	A	0.016	0.0082	7.6e-09	8.2e-06	0.0123019546289961	TCT	ORF1ab:RNA-dependent-RNA-polymerase	S700Y	C2099A	TCT>TAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.987671214499403
CAMB-78012	MN908947.3	18255	G	T	0.16	0.12	2.5e-71	6.8e-57	0.140174424432786	TGT	ORF1ab:3'-to-5'-exonuclease	M72I	G216T	ATG>ATT	Missense	ORF1ab:3'-to-5'-exonuclease	0.859825575567214
CAMB-78012	MN908947.3	18351	TTTACCTTTACAGCTAGG	-	0.0435	0.0102371111111111	8e-15;3.8e-09;1.5e-10;1.1e-10;7.7e-10;7.5e-10;4.3e-09;1.7e-08;5.5e-07;1.5e-07;1.6e-07;1.7e-08;3.2e-08;4.9e-07;4.7e-07;4.1e-10;1.5e-07;4.4e-07	0.5;1.4e-05;3.2e-06;3e-06;7.1e-06;7.2e-06;0.5;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0148744055475248	ATT	ORF1ab:3'-to-5'-exonuclease	.	312-329-delinframe	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.960526938177002
CAMB-78012	MN908947.3	22289	GCTTTA	-	0.0341666666666667	0.00753833333333333	6.6e-11;7.4e-13;4.3e-07;4e-12;2.2e-10;1.3e-09	NA;NA;NA;NA;NA;1.8e-12	0.0212656491167896	TGC	S	.	727-732-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.978175469227412
CAMB-78012	MN908947.3	22294	A	-	0.033	0.045	1.3e-09	1.8e-12	0.0372884196413608	TAC	S	.	732-732-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.962627786157198
CAMB-78012	MN908947.3	22587	TTA	-	0.00866666666666667	0.0226666666666667	NA;0.00037;0.00044	6.4e-07;3.4e-06;4.3e-06	0.0177446864340068	TTT	S	.	1025-1027-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.989101533007255
CAMB-78012	MN908947.3	23403	A	G	0.98	1	0	0	0.989872893365601	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000163516253515599
CAMB-78012	MN908947.3	241	C	T	1	1	0	0	0.999971531059614	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-78012	MN908947.3	28885	A	G	0.063	0.0071	7.4e-26	0.00018	0.0289133942980097	GAA	N	G204G	A612G	GGA>GGG	Synonymous	GU280_gp10	0.97108660570199
CAMB-78012	MN908947.3	3037	C	T	1	1	0	0	0.999658080692956	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78030	MN908947.3	11075	T	-	0.018	0.029	1.9e-05	4e-08	0.0228216110734426	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.977095701929914
CAMB-78030	MN908947.3	14408	C	T	1	1	0	0	0.999183721065827	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000660797232425709
CAMB-78030	MN908947.3	1876	A	T	0.0058	0.015	3.3e-05	7.9e-09	0.0103848150925979	CAT	ORF1ab:nsp2	A357A	A1071T	GCA>GCT	Synonymous	ORF1ab:nsp2	0.989615184907402
CAMB-78030	MN908947.3	21714	C	T	0.035	0.11	2.1e-16	3.6e-46	0.06125805125394	ACT	S	T51I	C152T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.93874194874606
CAMB-78030	MN908947.3	22295	C	A	0.38	0.31	5.2e-176	2.5e-128	0.352488262910798	ACA	S	H245N	C733A	CAT>AAT	Missense	GU280_gp02, spike glycoprotein	0.647511737089202
CAMB-78030	MN908947.3	23403	A	G	1	1	0	0	0.999850508949078	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.51306687686014e-05
CAMB-78030	MN908947.3	241	C	T	1	0.98	0	0	0.991346547389347	TCG	NA	NA	NA	NA	NA	NA	8.77039115944571e-05
CAMB-78030	MN908947.3	28691	AATAC	-	0.00186	0.011	NA;NA;NA;0.0015;0.00098	2.6e-06;2e-06;5e-06;3.5e-06;1.9e-06	0.00541850848424355	GAA	N	.	418-422-delfrshift	.	no-SNV	GU280_gp10	0.994652035004862
CAMB-78030	MN908947.3	28695	C	T	0.99	0.99	0	0	0.991866344251484	ACA	N	T141I	C422T	ACA>ATA	Missense	GU280_gp10	0.00014655235582912
CAMB-78030	MN908947.3	28883	G	C	0.99	1	5.5e-145	5.2e-113	0.994047619047619	GGG	N	G204R	G610C	GGA>CGA	Missense	GU280_gp10	0
CAMB-78030	MN908947.3	3037	C	T	1	1	0	0	0.999285075960679	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000178731009830206
CAMB-78030	MN908947.3	686	AAGTCATTTGAC	-	0.04225	0.0220833333333333	4.8e-07;3.6e-07;2.9e-06;4.5e-07;3.5e-06;9.6e-07;1.4e-07;1.8e-08;2.8e-07;4.7e-06;1.5e-07;1.4e-07	0.00028;0.00023;0.00073;0.00026;8e-04;0.00035;0.00014;0.00041;0.0011;0.04;0.01;0.0098	0.038039770363591	AAA	ORF1ab:leader-protein	.	421-432-delinframe	.	no-SNV	ORF1ab:leader-protein	0.961093657128301
CAMB-7804F	MN908947.3	11074	C	INS	0.07	0.021	1.7e-20	0.00094	0.0478765913948518	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.952030480438621
CAMB-7804F	MN908947.3	11075	T	-	0.023	0.028	1.2e-06	8e-08	0.0256116936765173	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.974165872259295
CAMB-7804F	MN908947.3	14408	C	T	1	1	0	0	0.999342782658225	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00052577387341994
CAMB-7804F	MN908947.3	17333	C	T	0.036	0.018	3.2e-17	1.4e-09	0.0266201146123363	ACG	ORF1ab:helicase	T366M	C1097T	ACG>ATG	Missense	ORF1ab:helicase	0.973365153724901
CAMB-7804F	MN908947.3	17409	ACGTGCTAAGCACTA	-	0.00443333333333333	0.00756666666666667	0.002;0.0019;0.0018;0.0016;0.0019;0.0017;0.0018;0.0021;0.0014;0.0014;0.0017;0.0017;0.0014;0.0015;0.0013	0.00012;0.00012;0.00012;1e-04;1.7e-06;1.4e-06;0.00012;0.00014;9.2e-05;9e-05;0.00011;0.00012;8.6e-05;9.7e-05;7.9e-05	0.00571859322606639	TAC	ORF1ab:helicase	.	1173-1187-delinframe	.	no-SNV	ORF1ab:helicase	0.994011237736248
CAMB-7804F	MN908947.3	2106	C	T	0.0061	0.014	1e-04	7.3e-08	0.00974025974025974	ACT	ORF1ab:nsp2	T434I	C1301T	ACT>ATT	Missense	ORF1ab:nsp2	0.99025974025974
CAMB-7804F	MN908947.3	23403	A	G	0.99	1	0	0	0.993898224545337	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000140394833470128
CAMB-7804F	MN908947.3	241	C	T	1	1	0	0	0.999533582089552	TCG	NA	NA	NA	NA	NA	NA	0.000192054433713784
CAMB-7804F	MN908947.3	26801	C	T	0.0097	0.0068	9.6e-06	0.00013	0.00837947252485563	TCA	M	L93L	C279T	CTC>CTT	Synonymous	GU280_gp05	0.983657796035006
CAMB-7804F	MN908947.3	27143	C	T	0.015	0.056	1.3e-08	1.1e-25	0.0357142857142857	ACA	M	N207N	C621T	AAC>AAT	Synonymous	GU280_gp05	0.964285714285714
CAMB-7804F	MN908947.3	28072	T	A	0.015	0.0093	3.7e-08	5.6e-06	0.0132631578947368	TTG	ORF8	L60*	T179A	TTG>TAG	Nonsense	GU280_gp09	0.986315789473684
CAMB-7804F	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7804F	MN908947.3	3037	C	T	1	1	0	0	0.9991801358632	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000351370344342937
CAMB-7804F	MN908947.3	4048	C	T	1	1	0	0	0.999821141119657	GCA	ORF1ab:nsp3	G443G	C1329T	GGC>GGT	Synonymous	ORF1ab:nsp3	0.000178858880343409
CAMB-7804F	MN908947.3	9154	A	T	0.02	0.018	1.3e-10	9.7e-10	0.0193046632442901	AAT	ORF1ab:nsp4	Q200H	A600T	CAA>CAT	Missense	ORF1ab:nsp4	0.980480157388337
CAMB-7806D	MN908947.3	11074	C	INS	0.11	0.11	1.9e-36	1.7e-39	0.108748253416488	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.888099376341887
CAMB-7806D	MN908947.3	11083	G	-	0.16	0.15	2.1e-73	1.3e-66	0.15774377102811	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	4.65137913391321e-05
CAMB-7806D	MN908947.3	11083	G	T	0.83	0.85	0	0	0.841992650820968	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	4.65137913391321e-05
CAMB-7806D	MN908947.3	14805	C	T	1	1	0	0	0.998386242408564	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000726806854158197
CAMB-7806D	MN908947.3	21538	G	T	1	0.99	0	0	0.995095463303556	TGT	ORF1ab:2'-O-ribose-methyltransferase	V294F	G880T	GTT>TTT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.0045542126466982
CAMB-7806D	MN908947.3	2480	A	G	1	1	0	0	0.999929755549312	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-7806D	MN908947.3	2558	C	T	1	1	0	0	0.999025083781862	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000142175281811719
CAMB-7806D	MN908947.3	26144	G	T	1	1	0	0	0.999397989284209	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000602010715790741
CAMB-7806D	MN908947.3	26748	A	G	0.45	0.43	3.3e-251	5.6e-236	0.441041942604857	GAT	M	I76V	A226G	ATC>GTC	Missense	GU280_gp05	0.558728476821192
CAMB-7806D	MN908947.3	27384	T	C	1	1	0	0	0.99883351316672	ATT	ORF6	D61D	T183C	GAT>GAC	Synonymous	GU280_gp06	0.000218716281239975
CAMB-7809A	MN908947.3	10097	G	A	1	1	0	0	0.999740273232559	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000121205824805638
CAMB-7809A	MN908947.3	11075	T	-	0.045	0.041	4e-11	2.5e-10	0.0431332451626527	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953232492748147
CAMB-7809A	MN908947.3	13536	C	T	1	1	0	0	0.999831121833534	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000120627261761158
CAMB-7809A	MN908947.3	14408	C	T	1	1	0	0	0.997474925304065	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000623723630071527
CAMB-7809A	MN908947.3	23403	A	G	1	1	0	0	0.999519660781131	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.79719746910922e-05
CAMB-7809A	MN908947.3	23731	C	T	1	1	0	0	0.99990985847781	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-7809A	MN908947.3	241	C	T	1	1	0	0	0.998141415237682	TCG	NA	NA	NA	NA	NA	NA	0.000162795745604515
CAMB-7809A	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999321625084797	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	2.74763016897926e-05
CAMB-7809A	MN908947.3	3037	C	T	1	1	0	0	0.9993251419529	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.98129014241832e-05
CAMB-7809A	MN908947.3	4002	C	T	1	1	0	0	0.999891777819864	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	5.41110900679094e-05
CAMB-7809A	MN908947.3	7000	C	T	0.96	0.96	0	0	0.961029923451635	ACT	ORF1ab:nsp3	Y1427Y	C4281T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.0389700765483647
CAMB-780A9	MN908947.3	11075	T	-	0.099	0.12	9.5e-25	5e-31	0.110090785766461	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.88977877491391
CAMB-780A9	MN908947.3	1170	C	T	1	1	0	0	0.999527757372232	TCT	ORF1ab:nsp2	S122F	C365T	TCT>TTT	Missense	ORF1ab:nsp2	0
CAMB-780A9	MN908947.3	12908	T	-	0.019	0.027	5.6e-10	2.9e-13	0.0216336006753905	GTT	ORF1ab:nsp9	.	223-223-delfrshift	.	no-SNV	ORF1ab:nsp9	0.978155339805825
CAMB-780A9	MN908947.3	14408	C	T	1	1	0	0	0.999417837460219	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000388108359854071
CAMB-780A9	MN908947.3	17678	C	T	0.033	0.056	9.3e-16	2e-25	0.041180086047941	ACG	ORF1ab:helicase	T481M	C1442T	ACG>ATG	Missense	ORF1ab:helicase	0.958819913952059
CAMB-780A9	MN908947.3	23403	A	G	1	1	0	0	0.99985266432021	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.54825243513137e-05
CAMB-780A9	MN908947.3	241	C	T	1	1	0	0	0.999900234449045	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-780A9	MN908947.3	24213	C	T	0.17	0.044	1.3e-61	2e-17	0.0994991652754591	TCT	S	S884F	C2651T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.900500834724541
CAMB-780A9	MN908947.3	28705	T	C	0.021	0.019	2.9e-11	2.1e-10	0.0202375096620055	ATC	N	D144D	T432C	GAT>GAC	Synonymous	GU280_gp10	0.979762490337995
CAMB-780A9	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999758103531688	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-780A9	MN908947.3	28895	G	C	0.0034	0.015	0.0018	7.5e-08	0.00864815657715066	TGC	N	A208P	G622C	GCT>CCT	Missense	GU280_gp10	0.99112426035503
CAMB-780A9	MN908947.3	29640	C	T	0.19	0.34	2e-71	2.2e-101	0.230734966592428	GCA	ORF10	A28V	C83T	GCA>GTA	Missense	GU280_gp11	0.769265033407572
CAMB-780A9	MN908947.3	3037	C	T	1	0.95	0	0	0.976489028213166	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000223914017017465
CAMB-780A9	MN908947.3	4668	C	T	0.028	0.055	2.4e-14	3.9e-26	0.0417776343044683	TCT	ORF1ab:nsp3	S650F	C1949T	TCT>TTT	Missense	ORF1ab:nsp3	0.958114760713421
CAMB-780A9	MN908947.3	9006	T	-	0.051	0.08	1.4e-22	8.9e-35	0.0618543553118225	GTT	ORF1ab:nsp4	.	452-452-delfrshift	.	no-SNV	ORF1ab:nsp4	0.938060621519364
CAMB-780B8	MN908947.3	11074	C	INS	0.26	0.075	5.7e-100	2.1e-19	0.168963188112124	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.830361364403918
CAMB-780B8	MN908947.3	11083	G	-	0.031	0.12	2.2e-13	2.1e-54	0.0811961826603252	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-780B8	MN908947.3	11083	G	T	0.97	0.88	0	0	0.918679474027791	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-780B8	MN908947.3	14805	C	T	1	1	0	0	0.99990574929312	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	4.71253534401508e-05
CAMB-780B8	MN908947.3	19910	C	T	0.0058	0.0085	9.1e-05	1.6e-05	0.00675	TCT	ORF1ab:endoRNAse	S97F	C290T	TCT>TTT	Missense	ORF1ab:endoRNAse	0.99325
CAMB-780B8	MN908947.3	23707	C	T	1	1	0	0	0.999582898852972	CCA	S	P715P	C2145T	CCC>CCT	Synonymous	GU280_gp02, spike glycoprotein	0.000417101147028154
CAMB-780B8	MN908947.3	28460	G	T	0.41	0.61	9.79999999999999e-198	0	0.50752688172043	AGA	N	D63Y	G187T	GAC>TAC	Missense	GU280_gp10	0.492329749103943
CAMB-780B8	MN908947.3	29421	C	T	1	1	0	1.1e-279	1	CCG	N	P383L	C1148T	CCG>CTG	Missense	GU280_gp10	0
CAMB-780B8	MN908947.3	6644	T	C	1	1	0	0	1	TTT	ORF1ab:nsp3	L1309L	T3925C	TTA>CTA	Synonymous	ORF1ab:nsp3	0
CAMB-780D6	MN908947.3	10029	C	T	0.019	0.015	4.5e-10	4e-08	0.0173274319615783	ACC	ORF1ab:nsp4	T492I	C1475T	ACC>ATC	Missense	ORF1ab:nsp4	0.982625482625483
CAMB-780D6	MN908947.3	11074	C	INS	0.038	0.024	1.7e-09	0.00011	0.032728660326406	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.967065868263473
CAMB-780D6	MN908947.3	11075	T	-	0.028	0.049	2.7e-07	2.3e-12	0.0362466038646116	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958890892009243
CAMB-780D6	MN908947.3	11083	G	-	0.016	0.0075	3.7e-07	0.0012	0.0127492031748016	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.943603524779701
CAMB-780D6	MN908947.3	11083	G	T	0.056	0.025	4.2e-12	1.2e-05	0.0436472720454972	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.943603524779701
CAMB-780D6	MN908947.3	13847	A	-	0.01	0.0033	5.3e-07	0.00082	0.00744939677443628	GAA	ORF1ab:RNA-dependent-RNA-polymerase	.	380-380-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.992450274649477
CAMB-780D6	MN908947.3	14099	G	T	0.0036	0.0082	0.0038	3e-05	0.0056825832862029	GGT	ORF1ab:RNA-dependent-RNA-polymerase	G211V	G632T	GGT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994250087527942
CAMB-780D6	MN908947.3	14408	C	T	1	1	0	0	0.999339479049999	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000502570288044571
CAMB-780D6	MN908947.3	14653	G	T	0.0048	0.0079	0.00046	1.7e-05	0.00613578587305179	TGT	ORF1ab:RNA-dependent-RNA-polymerase	V396F	G1186T	GTT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993810975203972
CAMB-780D6	MN908947.3	14951	TTCCATTTAATAAATGGGGTA	-	0.000223809523809524	0.00737619047619048	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.002;NA;NA;NA;NA;NA	2e-05;2.3e-05;2.8e-05;2.2e-05;1.9e-05;3.3e-05;1.4e-05;0.00012;0.00025;0.00018;2.6e-05;4.3e-05;8.9e-06;8e-06;7.5e-06;0.00023;3.4e-05;1.6e-05;1.6e-05;1.8e-05;2.6e-05	0.00251742835011619	TTT	ORF1ab:RNA-dependent-RNA-polymerase	.	1484-1504-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.997518610421836
CAMB-780D6	MN908947.3	16081	T	C	0.0087	0.0057	1e-05	0.00021	0.00749488081747878	CTT	ORF1ab:RNA-dependent-RNA-polymerase	F872L	T2614C	TTT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.992326196298284
CAMB-780D6	MN908947.3	1627	C	T	1	1	0	0	0.999844660194175	TCC	ORF1ab:nsp2	L274L	C822T	CTC>CTT	Synonymous	ORF1ab:nsp2	0.000129449838187702
CAMB-780D6	MN908947.3	16375	C	T	0.0088	0.012	0.00011	7.4e-06	0.0103418245155672	TCC	ORF1ab:helicase	P47S	C139T	CCG>TCG	Missense	ORF1ab:helicase	0.989549314173743
CAMB-780D6	MN908947.3	186	C	T	0.06	0.021	3.5e-27	9.9e-11	0.0436904634485711	GCA	NA	NA	NA	NA	NA	NA	0.953441078882586
CAMB-780D6	MN908947.3	19215	T	C	0.0077	0.0072	1.6e-05	2.3e-05	0.00754536048653696	ATC	ORF1ab:3'-to-5'-exonuclease	Y392Y	T1176C	TAT>TAC	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.99242940419411
CAMB-780D6	MN908947.3	2040	C	T	0.0056	0.0094	0.00016	4.5e-06	0.00703743524582152	ACT	ORF1ab:nsp2	T412I	C1235T	ACT>ATT	Missense	ORF1ab:nsp2	0.984752223634053
CAMB-780D6	MN908947.3	22444	C	T	0.02	0.012	2.1e-06	3e-04	0.01669449081803	ACC	S	D294D	C882T	GAC>GAT	Synonymous	GU280_gp02, spike glycoprotein	0.979966611018364
CAMB-780D6	MN908947.3	22708	G	C	1	1	0	0	0.999975715187722	TGT	S	V382V	G1146C	GTG>GTC	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-780D6	MN908947.3	23403	A	G	1	1	0	0	0.999885789041978	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.19140718283098e-05
CAMB-780D6	MN908947.3	241	C	T	0.99	1	0	0	0.99474453191443	TCG	NA	NA	NA	NA	NA	NA	0.000719628410057352
CAMB-780D6	MN908947.3	24826	C	T	0.0087	0.0066	7.3e-06	4.7e-05	0.00777967485710044	ACT	S	H1088H	C3264T	CAC>CAT	Synonymous	GU280_gp02, spike glycoprotein	0.992190631727414
CAMB-780D6	MN908947.3	2536	C	T	0.0095	0.011	8.8e-06	2.2e-06	0.0102320938357874	TCT	ORF1ab:nsp2	V577V	C1731T	GTC>GTT	Synonymous	ORF1ab:nsp2	0.989643124532069
CAMB-780D6	MN908947.3	26948	T	C	0.0041	0.0096	0.0012	5.3e-06	0.00608288770053476	CTG	M	A142A	T426C	GCT>GCC	Synonymous	GU280_gp05	0.993917112299465
CAMB-780D6	MN908947.3	27874	C	T	0.069	0.083	4.8e-29	3.1e-33	0.0739893211289092	ACT	NA	NA	NA	NA	NA	NA	0.926010678871091
CAMB-780D6	MN908947.3	28077	G	T	1	1	0	0	0.999855177407676	CGT	ORF8	V62L	G184T	GTG>TTG	Missense	GU280_gp09	0.000144822592324403
CAMB-780D6	MN908947.3	28591	A	T	0.016	0.0073	1.4e-08	2.3e-05	0.0121363168445576	CAA	N	P106P	A318T	CCA>CCT	Synonymous	GU280_gp10	0.98748442325405
CAMB-780D6	MN908947.3	3037	C	T	1	1	0	0	0.999709238932907	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-780D6	MN908947.3	5784	C	T	0.019	0.025	3.8e-09	3.1e-11	0.0217604224332496	ACT	ORF1ab:nsp3	T1022I	C3065T	ACT>ATT	Missense	ORF1ab:nsp3	0.97823957756675
CAMB-780D6	MN908947.3	7083	C	T	0.013	0.0068	3.9e-05	0.0018	0.00981079187105816	TCT	ORF1ab:nsp3	S1455F	C4364T	TCT>TTT	Missense	ORF1ab:nsp3	0.990189208128942
CAMB-780D6	MN908947.3	9073	C	T	1	1	0	0	0.99969904446618	CCA	ORF1ab:nsp4	T173T	C519T	ACC>ACT	Synonymous	ORF1ab:nsp4	0.000100318511273293
CAMB-780D6	MN908947.3	9534	C	T	1	1	0	0	0.999772070202378	ACT	ORF1ab:nsp4	T327I	C980T	ACT>ATT	Missense	ORF1ab:nsp4	0.000119963051380175
CAMB-780E5	MN908947.3	11195	C	T	1	1	0	0	0.999700726806327	TCT	ORF1ab:nsp6	L75F	C223T	CTT>TTT	Missense	ORF1ab:nsp6	8.55066267635742e-05
CAMB-780E5	MN908947.3	12459	C	T	0.016	0.0084	1.9e-08	3.1e-05	0.0103597011476546	ACA	ORF1ab:nsp8	T123I	C368T	ACA>ATA	Missense	ORF1ab:nsp8	0.989601786952168
CAMB-780E5	MN908947.3	14408	C	T	1	1	0	0	0.999459329568665	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000300372461852697
CAMB-780E5	MN908947.3	15216	C	T	1	1	0	0	0.99983119513842	GCA	ORF1ab:RNA-dependent-RNA-polymerase	S583S	C1749T	AGC>AGT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000168804861580014
CAMB-780E5	MN908947.3	23403	A	G	1	1	0	0	0.999970586505089	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.94134949114654e-05
CAMB-780E5	MN908947.3	241	C	T	1	1	0	0	0.999939598936941	TCG	NA	NA	NA	NA	NA	NA	6.04010630587098e-05
CAMB-780E5	MN908947.3	24453	AACAACTTAGCTCCAATT	-	0.0464444444444444	0.0982777777777778	8.4e-11;6e-11;1.3e-10;9.3e-11;9.5e-11;8.1e-11;1.9e-10;2.1e-10;2.9e-10;4.3e-10;3.9e-10;3.8e-10;4.1e-10;3.3e-10;4.5e-10;2.6e-10;1.5e-08;9.8e-11	2.3e-28;9.3e-30;3.7e-28;4.3e-28;3.2e-28;2.4e-28;2e-28;6.3e-28;1.4e-27;4.5e-28;1.5e-27;1.8e-27;1.9e-27;9.4e-28;9e-28;1.1e-27;6.4e-25;8.1e-29	0.0807174887892377	AAA	S	.	2891-2908-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.919372900335946
CAMB-780E5	MN908947.3	26298	T	C	0.034	0.034	2.4e-14	2.1e-16	0.0340185292414592	TTC	E	L18L	T54C	CTT>CTC	Synonymous	GU280_gp04	0.965981470758541
CAMB-780E5	MN908947.3	26873	C	T	0.059	0.054	9.5e-27	1.6e-25	0.0551612804970912	ACA	M	N117N	C351T	AAC>AAT	Synonymous	GU280_gp05	0.944838719502909
CAMB-780E5	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-780E5	MN908947.3	3037	C	T	1	1	1.5e-270	0	0.999693721286371	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-780E5	MN908947.3	3373	C	A	1	1	0	0	0.999885753455958	ACA	ORF1ab:nsp3	D218E	C654A	GAC>GAA	Missense	ORF1ab:nsp3	0
CAMB-780E5	MN908947.3	5158	T	-	0.039	0.032	8.5e-05	3.5e-06	0.0343511450381679	CTT	ORF1ab:nsp3	.	2439-2439-delfrshift	.	no-SNV	ORF1ab:nsp3	0.961832061068702
CAMB-780E5	MN908947.3	6870	C	T	0.097	0.039	1.2e-09	2.5e-07	0.0552995391705069	ACT	ORF1ab:nsp3	T1384I	C4151T	ACT>ATT	Missense	ORF1ab:nsp3	0.944700460829493
CAMB-78100	MN908947.3	11074	C	INS	0.027	0.024	3.4e-05	0.00011	0.0249274618874337	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.974864141325083
CAMB-78100	MN908947.3	11075	T	-	0.038	0.04	4.8e-10	3.5e-10	0.0395720757600568	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956197805796627
CAMB-78100	MN908947.3	14408	C	T	1	1	0	0	0.998885157065846	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000395134204510175
CAMB-78100	MN908947.3	23403	A	G	1	1	0	0	0.999345743109198	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000327128445401207
CAMB-78100	MN908947.3	241	C	T	1	1	0	0	0.998754392161966	TCG	NA	NA	NA	NA	NA	NA	0.000111546970570191
CAMB-78100	MN908947.3	26270	C	T	0.0089	0.009	2.6e-05	2.6e-05	0.00895231521893587	ACA	E	T9I	C26T	ACA>ATA	Missense	GU280_gp04	0.991047684781064
CAMB-78100	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99871644026099	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-78100	MN908947.3	3037	C	T	1	1	0	0	0.997516002675074	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000334384255278494
CAMB-7811F	MN908947.3	11075	T	-	0.045	0.035	4.1e-11	4.8e-09	0.0405939930276213	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95558460713328
CAMB-7811F	MN908947.3	12142	T	A	0.01	0.0094	2.2e-06	3.2e-06	0.00989799446749654	CTG	ORF1ab:nsp8	T17T	T51A	ACT>ACA	Synonymous	ORF1ab:nsp8	0.98916551406178
CAMB-7811F	MN908947.3	12493	C	T	0.039	0.036	1.2e-18	3.1e-17	0.0376975138311162	ACT	ORF1ab:nsp8	D134D	C402T	GAC>GAT	Synonymous	ORF1ab:nsp8	0.962302486168884
CAMB-7811F	MN908947.3	14408	C	T	1	1	0	0	0.997879262294172	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000732820359081976
CAMB-7811F	MN908947.3	15418	G	T	0.21	0.2	1.8e-97	2e-95	0.20450186167212	TGC	ORF1ab:RNA-dependent-RNA-polymerase	A651S	G1951T	GCT>TCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.79511734175787
CAMB-7811F	MN908947.3	16289	C	T	1	1	0	0	0.999081796617951	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0.000382584742520468
CAMB-7811F	MN908947.3	17708	C	T	0.0073	0.0072	2.8e-05	2.8e-05	0.00723000197233101	CCA	ORF1ab:helicase	P491L	C1472T	CCA>CTA	Missense	ORF1ab:helicase	0.992595305852188
CAMB-7811F	MN908947.3	19656	G	T	0.013	0.016	2.7e-07	1e-08	0.0142588183177363	AGG	ORF1ab:endoRNAse	K12N	G36T	AAG>AAT	Missense	ORF1ab:endoRNAse	0.985685807630544
CAMB-7811F	MN908947.3	23403	A	G	1	1	0	0	0.999497149160158	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000348751388922683
CAMB-7811F	MN908947.3	241	C	T	1	1	0	0	0.998307251183197	TCG	NA	NA	NA	NA	NA	NA	0.000449096624866135
CAMB-7811F	MN908947.3	25273	G	A	0.0081	0.006	1.4e-05	7.6e-05	0.00716510903426791	TGA	S	M1237I	G3711A	ATG>ATA	Missense	GU280_gp02, spike glycoprotein	0.992710280373832
CAMB-7811F	MN908947.3	25429	G	T	1	1	0	0	0.998620187715122	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0.000348743764309866
CAMB-7811F	MN908947.3	26137	A	C	0.023	0.016	2.4e-05	0.0029	0.0200721695985566	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.979927830401443
CAMB-7811F	MN908947.3	26155	GTT	-	0.00623333333333333	0.00866666666666667	0.00035;0.00041;0.00043	3.6e-05;4.5e-05;4.6e-05	0.00727190943848864	AGT	ORF3a	.	763-765-delinframe	.	no-SNV	GU280_gp03	0.992438987872436
CAMB-7811F	MN908947.3	27400	A	T	0.0092	0.0079	5.9e-06	1.3e-05	0.00859061950474214	AAT	ORF7a	I3F	A7T	ATT>TTT	Missense	GU280_gp07	0.99134211613672
CAMB-7811F	MN908947.3	27403	A	C	0.0085	0.007	9.4e-06	2.7e-05	0.00785603275084341	TAT	ORF7a	I4L	A10C	ATT>CTT	Missense	GU280_gp07	0.992068155111633
CAMB-7811F	MN908947.3	28311	C	T	0.0081	0.0093	3.4e-05	9.9e-06	0.00863518839270025	CCC	N	P13L	C38T	CCC>CTC	Missense	GU280_gp10	0.991276953585862
CAMB-7811F	MN908947.3	29749	ACGATC	-	0.011	0.0138333333333333	0.00011;0.00065;0.00078;0.00022;0.00024;3e-04	1.9e-05;0.00014;0.00015;3.7e-05;4.1e-05;4.5e-05	0.0116848024538085	TAC	NA	NA	NA	NA	NA	NA	0.987150470906038
CAMB-7811F	MN908947.3	3037	C	T	1	1	0	0	0.998845265588915	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000561762686474003
CAMB-7811F	MN908947.3	344	C	T	0.014	0.014	6.7e-08	5.8e-08	0.014287766589612	GCT	ORF1ab:leader-protein	L27F	C79T	CTC>TTC	Missense	ORF1ab:leader-protein	0.985601222426831
CAMB-7811F	MN908947.3	3736	C	T	0.011	0.018	2.6e-06	3.1e-09	0.0139235987147447	ACC	ORF1ab:nsp3	D339D	C1017T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.986076401285255
CAMB-7811F	MN908947.3	3818	A	G	0.29	0.29	2e-144	3.3e-143	0.292092343048156	CAA	ORF1ab:nsp3	K367E	A1099G	AAA>GAA	Missense	ORF1ab:nsp3	0.707636059751384
CAMB-7811F	MN908947.3	5128	A	G	0.041	0.046	3.6e-18	6e-20	0.0434498529892192	TAC	ORF1ab:nsp3	L803L	A2409G	TTA>TTG	Synonymous	ORF1ab:nsp3	0.956223456386802
CAMB-7811F	MN908947.3	6531	A	G	0.0039	0.0071	0.00097	4.1e-05	0.00526731630234396	GAG	ORF1ab:nsp3	E1271G	A3812G	GAG>GGG	Missense	ORF1ab:nsp3	0.994680010534633
CAMB-7811F	MN908947.3	7303	C	T	0.017	0.0071	4.8e-06	0.0017	0.0125852123754588	TCA	ORF1ab:nsp3	I1528I	C4584T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.987414787624541
CAMB-7812E	MN908947.3	11652	T	C	0.3	0.24	2.1e-69	2.8e-64	0.26491646778043	CTC	ORF1ab:nsp6	L227P	T680C	CTC>CCC	Missense	ORF1ab:nsp6	0.73508353221957
CAMB-7812E	MN908947.3	14408	C	T	1	1	0	0	0.999340438087965	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000416565418127538
CAMB-7812E	MN908947.3	15905	A	G	0.046	0.13	4.9e-22	1.3e-58	0.0908807287929367	CAG	ORF1ab:RNA-dependent-RNA-polymerase	Q813R	A2438G	CAG>CGG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.909119271207063
CAMB-7812E	MN908947.3	16332	C	T	0.064	0.095	1.4e-24	3.5e-35	0.0794747753973739	ACC	ORF1ab:helicase	D32D	C96T	GAC>GAT	Synonymous	ORF1ab:helicase	0.920525224602626
CAMB-7812E	MN908947.3	23403	A	G	1	1	0	0	0.999917643958361	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.94136249835288e-05
CAMB-7812E	MN908947.3	24014	ATTGAAGATCTA	-	0.1125	0.0490833333333333	NA;5.3e-15;2.7e-14;6.1e-14;2.1e-14;3.2e-13;3.8e-13;2e-13;6e-13;1.6e-13;2e-14;5.4e-14	2.8e-08;1.6e-06;2.4e-06;2.8e-06;2.7e-06;6.5e-06;6.4e-06;5.9e-06;8.8e-06;5.5e-06;2.7e-06;3.9e-06	0.0763732129420617	TAT	S	.	2452-2463-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.968310556545851
CAMB-7812E	MN908947.3	241	C	T	1	1	0	0	0.999843878068772	TCG	NA	NA	NA	NA	NA	NA	0.000117091448421217
CAMB-7812E	MN908947.3	25169	C	T	0.33	0.66	4.8e-151	0	0.527121814355857	ACT	S	L1203F	C3607T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.472644376899696
CAMB-7812E	MN908947.3	25429	G	T	0.93	1	0	0	0.968139913232104	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	3.38937093275488e-05
CAMB-7812E	MN908947.3	3037	C	T	1	1	0	0	0.999074645280691	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7812E	MN908947.3	522	TT	-	0.096	0.042	2.8e-13;9.8e-14	1.4e-07;0.00052	0.0622619639013082	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.926862494678587
CAMB-7813D	MN908947.3	11075	T	-	0.039	0.037	8.6e-10	1.4e-09	0.0380781330986849	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955533322886658
CAMB-7813D	MN908947.3	11273	G	T	0.0071	0.0048	3e-05	0.00026	0.00599880699148012	GGT	ORF1ab:nsp6	V101F	G301T	GTT>TTT	Missense	ORF1ab:nsp6	0.993674803885156
CAMB-7813D	MN908947.3	12385	G	T	0.05	0.051	4e-23	1e-23	0.0504297269969666	TGG	ORF1ab:nsp8	L98F	G294T	TTG>TTT	Missense	ORF1ab:nsp8	0.949544994944388
CAMB-7813D	MN908947.3	14408	C	T	1	1	0	0	0.998232627531991	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000516440006885867
CAMB-7813D	MN908947.3	16289	C	T	1	1	0	0	0.99978789292835	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	4.24214143299538e-05
CAMB-7813D	MN908947.3	2003	C	T	0.17	0.17	2.1e-79	5.3e-77	0.168249563407574	ACT	ORF1ab:nsp2	L400F	C1198T	CTC>TTC	Missense	ORF1ab:nsp2	0.831415516375206
CAMB-7813D	MN908947.3	20356	G	T	0.014	0.016	7.7e-05	1.5e-05	0.0152403282532239	AGG	ORF1ab:endoRNAse	G246C	G736T	GGT>TGT	Missense	ORF1ab:endoRNAse	0.984759671746776
CAMB-7813D	MN908947.3	23119	T	C	0.07	0.065	1.5e-31	2.5e-29	0.0671633104411593	ATG	S	H519H	T1557C	CAT>CAC	Synonymous	GU280_gp02, spike glycoprotein	0.932759088969076
CAMB-7813D	MN908947.3	23403	A	G	1	1	0	0	0.999564668123464	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.38951106255121e-05
CAMB-7813D	MN908947.3	241	C	T	1	1	0	0	0.999082825519214	TCG	NA	NA	NA	NA	NA	NA	0.000264270613107822
CAMB-7813D	MN908947.3	25373	C	T	0.0053	0.0067	0.00017	4.1e-05	0.0060246634660642	ACA	S	H1271Y	C3811T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.993948440714891
CAMB-7813D	MN908947.3	25429	G	T	1	1	0	0	0.997912790961477	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0.000105872922243901
CAMB-7813D	MN908947.3	27915	G	A	1	1	0	0	0.997287951725541	AGG	ORF8	G8R	G22A	GGA>AGA	Missense	GU280_gp09	0.00155942775781409
CAMB-7813D	MN908947.3	3037	C	T	1	1	0	0	0.999053528236408	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000140218039050724
CAMB-7814C	MN908947.3	11075	T	-	0.035	0.039	3e-09	2.5e-10	0.0370344635908838	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95850125069483
CAMB-7814C	MN908947.3	14408	C	T	1	1	0	0	0.997970220016298	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000859322912808356
CAMB-7814C	MN908947.3	23403	A	G	1	1	0	0	0.999549119734924	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000115341463158888
CAMB-7814C	MN908947.3	241	C	T	1	1	0	0	0.998201663461298	TCG	NA	NA	NA	NA	NA	NA	0.000149861378225142
CAMB-7814C	MN908947.3	25350	C	T	1	1	0	0	0.999104383253723	CCA	S	P1263L	C3788T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	0.000491711154818769
CAMB-7814C	MN908947.3	26137	A	C	0.027	0.014	7.7e-07	0.0068	0.0208831500079707	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.97895743663319
CAMB-7814C	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.029625	0.02871875	3.8e-05;0.00029;8.6e-05;8.7e-05;2.3e-05;3.6e-05;2.4e-05;7.8e-05;4.7e-05;5.5e-05;1e-04;3.8e-05;9.3e-05;4.9e-05;5.7e-05;5.9e-05;9.8e-05;4.9e-05;7.5e-05;5.2e-05;3.5e-05;7.2e-05;5.1e-05;3.7e-05;3.5e-05;8e-05;3.1e-05;1.7e-05;6.2e-05;3.9e-05;5.1e-05;2.3e-05	8.8e-05;0.00032;0.00011;0.00011;4e-05;5.6e-05;4.7e-05;0.00011;6.9e-05;8.6e-05;0.00014;6.1e-05;0.00013;7.7e-05;8.1e-05;8.8e-05;0.00014;7.5e-05;0.00011;8.1e-05;5.9e-05;9.9e-05;7.1e-05;6.2e-05;5.3e-05;0.00011;4.6e-05;2.7e-05;8.1e-05;5.3e-05;7.4e-05;3.7e-05	0.0289620234303701	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.970197555909772
CAMB-7814C	MN908947.3	3037	C	T	1	1	0	0	0.998840933353668	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000152508769254232
CAMB-7814C	MN908947.3	635	C	T	1	1	0	0	0.999715840472841	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	9.94558345054914e-05
CAMB-7815B	MN908947.3	10986	G	T	0.01	0.017	0.00074	1.7e-05	0.0140568521576152	AGA	ORF1ab:nsp6	R5I	G14T	AGA>ATA	Missense	ORF1ab:nsp6	0.98460440001785
CAMB-7815B	MN908947.3	11074	C	INS	0.11	0.12	2.7e-36	4.6e-37	0.113035654032167	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.879586098301653
CAMB-7815B	MN908947.3	11083	G	-	0.17	0.15	9.8e-75	3.4e-67	0.159445263354579	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-7815B	MN908947.3	11083	G	T	0.83	0.85	0	0	0.840430170033425	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-7815B	MN908947.3	1155	T	C	1	1	0	0	0.999366350686876	ATG	ORF1ab:nsp2	M117T	T350C	ATG>ACG	Missense	ORF1ab:nsp2	0.000405535560399453
CAMB-7815B	MN908947.3	12140	AC	-	0.018	0.0195	9e-04;1.7e-05	0.00053;9e-06	0.0187664758277107	TAC	ORF1ab:nsp8	.	49-50-delfrshift	.	no-SNV	ORF1ab:nsp8	0.986413865301849
CAMB-7815B	MN908947.3	12164	G	T	0.024	0.024	5.6e-09	5.3e-09	0.0237418452935694	GGC	ORF1ab:nsp8	A25S	G73T	GCT>TCT	Missense	ORF1ab:nsp8	0.974871854613234
CAMB-7815B	MN908947.3	12538	T	-	0.0076	0.0094	6.2e-05	1.2e-05	0.00847146200413902	ATG	ORF1ab:nsp8	.	447-447-delfrshift	.	no-SNV	ORF1ab:nsp8	0.990909618397385
CAMB-7815B	MN908947.3	12578	G	T	0.024	0.022	7.2e-09	2.2e-08	0.0228484993233023	AGA	ORF1ab:nsp8	D163Y	G487T	GAT>TAT	Missense	ORF1ab:nsp8	0.974146166706472
CAMB-7815B	MN908947.3	12789	C	T	0.023	0.025	5.4e-12	7.1e-13	0.0241395853849456	ACA	ORF1ab:nsp9	T35I	C104T	ACA>ATA	Missense	ORF1ab:nsp9	0.975052395020579
CAMB-7815B	MN908947.3	13548	C	-	0.011	0.016	0.00018	1.6e-05	0.0137735067190244	ACA	ORF1ab:RNA-dependent-RNA-polymerase	.	81-81-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.985338516486769
CAMB-7815B	MN908947.3	13570	GG	-	0.0125	0.013	5.3e-06;8.1e-06	4.3e-06;4.9e-06	0.0127245218605734	TGG	ORF1ab:RNA-dependent-RNA-polymerase	.	103-104-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.98555661534269
CAMB-7815B	MN908947.3	13571	G	T	0.063	0.061	2.1e-13	4.8e-13	0.0620868287779797	GGT	ORF1ab:RNA-dependent-RNA-polymerase	G35V	G104T	GGT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.925948119225268
CAMB-7815B	MN908947.3	13627	G	T	1	1	0	0	0.999756349821986	TGA	ORF1ab:RNA-dependent-RNA-polymerase	D54Y	G160T	GAC>TAC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	1.98898104501064e-05
CAMB-7815B	MN908947.3	14277	G	T	0.012	0.011	3e-06	4.9e-06	0.0116115411681914	GGT	ORF1ab:RNA-dependent-RNA-polymerase	R270S	G810T	AGG>AGT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.9882765018233
CAMB-7815B	MN908947.3	14805	C	T	1	1	0	0	0.999100367675819	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000312915591019323
CAMB-7815B	MN908947.3	15540	C	T	1	1	0	0	0.999667006597432	TCA	ORF1ab:RNA-dependent-RNA-polymerase	V691V	C2073T	GTC>GTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000124872525963079
CAMB-7815B	MN908947.3	15960	C	T	1	1	0	0	0.999212245717552	CCG	ORF1ab:RNA-dependent-RNA-polymerase	A831A	C2493T	GCC>GCT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000432492547226642
CAMB-7815B	MN908947.3	16508	G	T	0.022	0.019	1.5e-06	5.4e-06	0.0205902539464653	GGT	ORF1ab:helicase	G91V	G272T	GGT>GTT	Missense	ORF1ab:helicase	0.979409746053535
CAMB-7815B	MN908947.3	19679	G	T	0.013	0.017	1e-06	4.9e-08	0.0152873937084708	GGT	ORF1ab:endoRNAse	G20V	G59T	GGT>GTT	Missense	ORF1ab:endoRNAse	0.984573207564704
CAMB-7815B	MN908947.3	20578	G	T	0.013	0.013	2.2e-06	2.1e-06	0.0125915913779612	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	0.987123852884684
CAMB-7815B	MN908947.3	20627	G	T	0.01	0.0096	3.3e-05	4.5e-05	0.00979412352588447	GGC	ORF1ab:endoRNAse	G336V	G1007T	GGC>GTC	Missense	ORF1ab:endoRNAse	0.989920333514177
CAMB-7815B	MN908947.3	20922	G	T	0.017	0.017	4.6e-08	5e-08	0.0165936657681941	GGT	ORF1ab:2'-O-ribose-methyltransferase	W88C	G264T	TGG>TGT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.982648247978437
CAMB-7815B	MN908947.3	20925	G	T	0.011	0.01	1.6e-06	1.9e-06	0.0104206379463718	TGC	ORF1ab:2'-O-ribose-methyltransferase	L89F	G267T	TTG>TTT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.98877451603338
CAMB-7815B	MN908947.3	22879	C	-	0.0073	0.009	1e-04	2.1e-05	0.00814321926489227	ACA	S	.	1317-1317-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.991476552598226
CAMB-7815B	MN908947.3	22899	G	T	0.019	0.022	1.2e-06	1.2e-07	0.0202879164277979	GGT	S	G446V	G1337T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.977928530479648
CAMB-7815B	MN908947.3	24443	A	G	0.0099	0.0097	1.6e-06	1.9e-06	0.00977810153535806	CAC	S	T961A	A2881G	ACG>GCG	Missense	GU280_gp02, spike glycoprotein	0.990193880981733
CAMB-7815B	MN908947.3	24933	G	T	0.035	0.036	1.6e-06	1.3e-06	0.0354260840448686	GGT	S	G1124V	G3371T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.963100619454211
CAMB-7815B	MN908947.3	25489	G	T	0.0083	0.0072	1.2e-05	3.8e-05	0.00775095028774076	TGC	ORF3a	A33S	G97T	GCA>TCA	Missense	GU280_gp03	0.992100401350577
CAMB-7815B	MN908947.3	26144	G	T	1	1	0	0	0.999427683754395	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000408797318289592
CAMB-7815B	MN908947.3	26314	G	C	1	1	0	0	0.999346115223839	CGT	E	V24L	G70C	GTG>CTG	Missense	GU280_gp04	0.000140118166320263
CAMB-7815B	MN908947.3	27879	C	T	1	1	0	0	0.999568733153639	TCA	NA	NA	NA	NA	NA	NA	0.000323450134770889
CAMB-7815B	MN908947.3	28079	G	T	0.019	0.017	2.4e-08	1.3e-07	0.0177361287590004	TGG	ORF8	V62V	G186T	GTG>GTT	Synonymous	GU280_gp09	0.981787378229564
CAMB-7815B	MN908947.3	28086	G	T	0.006	0.0085	0.00025	2.1e-05	0.00709858558033586	GGC	ORF8	A65S	G193T	GCT>TCT	Missense	GU280_gp09	0.992318694707846
CAMB-7815B	MN908947.3	28338	A	G	1	1	0	0	0.999601225325817	GAT	N	D22G	A65G	GAT>GGT	Missense	GU280_gp10	0.000145008972430169
CAMB-7815B	MN908947.3	29009	G	A	0.086	0.086	8.4e-40	7e-40	0.0863971145394478	TGT	N	V246I	G736A	GTC>ATC	Missense	GU280_gp10	0.913345255054102
CAMB-7815B	MN908947.3	29543	G	T	0.014	0.017	1.5e-07	1.1e-08	0.015333968639002	AGA	NA	NA	NA	NA	NA	NA	0.983972970631552
CAMB-7815B	MN908947.3	29779	G	T	0.012	0.014	2.6e-05	3.3e-06	0.0127066231867761	GGA	NA	NA	NA	NA	NA	NA	0.985887776903182
CAMB-7815B	MN908947.3	29781	G	T	0.018	0.014	1.5e-08	6.6e-07	0.0159746187242569	AGA	NA	NA	NA	NA	NA	NA	0.983413113659134
CAMB-7815B	MN908947.3	3211	T	-	0.0075	0.0095	2.9e-05	3.8e-06	0.00849690178472042	ATG	ORF1ab:nsp3	.	492-492-delfrshift	.	no-SNV	ORF1ab:nsp3	0.990761010723164
CAMB-7815B	MN908947.3	3259	G	T	0.014	0.015	7.4e-06	3.7e-06	0.0142955876468662	AGA	ORF1ab:nsp3	Q180H	G540T	CAG>CAT	Missense	ORF1ab:nsp3	0.984940525990324
CAMB-7815B	MN908947.3	3564	G	T	0.018	0.019	6.6e-08	1.9e-08	0.0185485820869745	GGT	ORF1ab:nsp3	G282V	G845T	GGT>GTT	Missense	ORF1ab:nsp3	0.980207937549653
CAMB-7815B	MN908947.3	4505	G	T	0.017	0.019	7.1e-09	8.3e-10	0.0175299961295317	GGG	ORF1ab:nsp3	G596C	G1786T	GGT>TGT	Missense	ORF1ab:nsp3	0.981324990323829
CAMB-7815B	MN908947.3	481	AC	-	0.01375	0.01525	0.001;3.8e-07	0.00033;1.4e-07	0.0147212901685654	AAC	ORF1ab:leader-protein	.	216-217-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.9958389594643
CAMB-7815B	MN908947.3	558	G	T	0.037	0.034	1.2e-09	4e-09	0.0355063550635506	GGT	ORF1ab:leader-protein	G98V	G293T	GGT>GTT	Missense	ORF1ab:leader-protein	0.9640016400164
CAMB-7815B	MN908947.3	6513	G	T	0.012	0.014	8.1e-07	8.8e-08	0.0125922709509336	AGT	ORF1ab:nsp3	S1265I	G3794T	AGT>ATT	Missense	ORF1ab:nsp3	0.986671449338292
CAMB-7815B	MN908947.3	7029	C	T	0.013	0.012	9.6e-07	2.9e-06	0.012779552715655	TCT	ORF1ab:nsp3	S1437F	C4310T	TCT>TTT	Missense	ORF1ab:nsp3	0.987042953496628
CAMB-7815B	MN908947.3	7214	G	T	0.013	0.012	2e-06	4e-06	0.0125944584382872	GGA	ORF1ab:nsp3	D1499Y	G4495T	GAT>TAT	Missense	ORF1ab:nsp3	0.987272968314994
CAMB-7815B	MN908947.3	8790	G	T	0.0097	0.012	6.4e-06	1e-06	0.0106068772232403	GGT	ORF1ab:nsp4	G79V	G236T	GGT>GTT	Missense	ORF1ab:nsp4	0.988422981567317
CAMB-7816A	MN908947.3	103	C	T	0.017	0.021	2.3e-09	4.6e-11	0.018557372305021	GCT	NA	NA	NA	NA	NA	NA	0.981171321082333
CAMB-7816A	MN908947.3	11075	T	-	0.044	0.046	5.3e-11	5e-12	0.0447213383321256	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.950993982546234
CAMB-7816A	MN908947.3	12153	C	T	0.0098	0.0093	2e-06	2.4e-06	0.00964710478340134	GCT	ORF1ab:nsp8	A21V	C62T	GCT>GTT	Missense	ORF1ab:nsp8	0.989235176664641
CAMB-7816A	MN908947.3	13536	C	T	0.0066	0.0096	9.3e-05	4.7e-06	0.00792290618941927	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.991964712162504
CAMB-7816A	MN908947.3	14408	C	T	1	1	0	0	0.998721995534683	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000631303410578182
CAMB-7816A	MN908947.3	21022	A	G	0.021	0.022	4.6e-11	2.2e-11	0.0216561393766919	TAA	ORF1ab:2'-O-ribose-methyltransferase	N122D	A364G	AAT>GAT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.977996807107656
CAMB-7816A	MN908947.3	21036	C	T	0.007	0.0073	2.7e-05	1.5e-05	0.00711459581110022	TCA	ORF1ab:2'-O-ribose-methyltransferase	L126L	C378T	CTC>CTT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.9928854041889
CAMB-7816A	MN908947.3	23403	A	G	1	1	0	0	0.999569445319556	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.35093356856321e-05
CAMB-7816A	MN908947.3	241	C	T	1	1	0	0	0.998678005564215	TCG	NA	NA	NA	NA	NA	NA	7.8925040942365e-05
CAMB-7816A	MN908947.3	26137	A	C	0.031	0.024	8.1e-08	4.8e-05	0.0285175583313693	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.971246759368371
CAMB-7816A	MN908947.3	27476	C	T	0.013	0.012	3.7e-07	4.3e-07	0.012568056395758	ACA	ORF7a	T28I	C83T	ACA>ATA	Missense	GU280_gp07	0.987407251941382
CAMB-7816A	MN908947.3	280	C	T	0.0058	0.0073	0.00011	2.1e-05	0.00644568944518353	TCC	ORF1ab:leader-protein	V5V	C15T	GTC>GTT	Synonymous	ORF1ab:leader-protein	0.993498098146864
CAMB-7816A	MN908947.3	3037	C	T	1	1	0	0	0.999613631094969	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.86368905030523e-05
CAMB-7816A	MN908947.3	3429	C	T	0.014	0.015	2.7e-08	9.1e-09	0.0145634102131383	ACA	ORF1ab:nsp3	T237I	C710T	ACA>ATA	Missense	ORF1ab:nsp3	0.985405337833615
CAMB-7816A	MN908947.3	3792	C	T	1	1	0	0	0.999598167644459	GCT	ORF1ab:nsp3	A358V	C1073T	GCT>GTT	Missense	ORF1ab:nsp3	0.000241099413324761
CAMB-7816A	MN908947.3	559	T	C	0.0068	0.004	3.3e-05	0.00045	0.00557156865658337	GTC	ORF1ab:leader-protein	G98G	T294C	GGT>GGC	Synonymous	ORF1ab:leader-protein	0.994383858794164
CAMB-7816A	MN908947.3	813	C	T	0.0067	0.0087	3.7e-05	4e-06	0.00756737278319734	ACT	ORF1ab:nsp2	T3I	C8T	ACT>ATT	Missense	ORF1ab:nsp2	0.99239401817199
CAMB-78179	MN908947.3	10069	A	C	0.0029	0.014	0.0052	4.9e-08	0.00869406392694064	AAA	ORF1ab:3C-like-proteinase	K5N	A15C	AAA>AAC	Missense	ORF1ab:3C-like-proteinase	0.988164383561644
CAMB-78179	MN908947.3	11001	C	T	0.0092	0.0037	2.5e-05	0.0061	0.00650785854616896	ACA	ORF1ab:nsp6	T10I	C29T	ACA>ATA	Missense	ORF1ab:nsp6	0.993430746561886
CAMB-78179	MN908947.3	11075	T	-	0.055	0.029	1.9e-13	1.2e-07	0.0426366029901296	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954127376271501
CAMB-78179	MN908947.3	14408	C	T	1	1	0	0	0.99777285701486	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000691182305732973
CAMB-78179	MN908947.3	23403	A	G	1	1	0	0	0.999921532385328	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.10303669668779e-05
CAMB-78179	MN908947.3	241	C	T	1	1	0	0	0.997996695580339	TCG	NA	NA	NA	NA	NA	NA	0.000454357703428335
CAMB-78179	MN908947.3	25418	C	T	0.0049	0.0085	0.00034	9.7e-06	0.00670406732117812	ACA	ORF3a	T9I	C26T	ACA>ATA	Missense	GU280_gp03	0.98796633941094
CAMB-78179	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99906073888541	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	5.87440521647183e-05
CAMB-78179	MN908947.3	3037	C	T	1	0.99	0	0	0.996725672771923	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.11613629387087e-05
CAMB-78179	MN908947.3	3867	A	-	0.0087	0.01	6.3e-05	1.7e-05	0.00930099449094942	CAA	ORF1ab:nsp3	.	1148-1148-delfrshift	.	no-SNV	ORF1ab:nsp3	0.990627459397582
CAMB-78179	MN908947.3	3867	AA	-	0.00875	0.005	6.3e-05;1e-05	1.7e-05;NA	0.00725731120212689	CAA	ORF1ab:nsp3	.	1148-1149-delfrshift	.	no-SNV	ORF1ab:nsp3	0.990627459397582
CAMB-78179	MN908947.3	5625	G	T	0.0034	0.0064	0.00097	4.6e-05	0.00490885885394509	TGT	ORF1ab:nsp3	C969F	G2906T	TGT>TTT	Missense	ORF1ab:nsp3	0.99492751251759
CAMB-78179	MN908947.3	8016	C	-	0.0037	0.0085	0.0012	7.4e-06	0.00615336068160303	GCG	ORF1ab:nsp3	.	5297-5297-delfrshift	.	no-SNV	ORF1ab:nsp3	0.993720416535185
CAMB-78179	MN908947.3	8829	C	T	0.0097	0.006	2.7e-06	0.00011	0.00794414015135677	GCT	ORF1ab:nsp4	A92V	C275T	GCT>GTT	Missense	ORF1ab:nsp4	0.992055859848643
CAMB-78188	MN908947.3	11074	C	INS	0.12	0.11	8.2e-49	7.1e-44	0.115446178471389	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.879051620648259
CAMB-78188	MN908947.3	11083	G	-	0.18	0.18	1.3e-78	4e-80	0.17828678662104	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-78188	MN908947.3	11083	G	T	0.82	0.82	0	0	0.821558670934982	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-78188	MN908947.3	11651	C	INS	0.015	0.013	1.9e-07	6.3e-07	0.0138817480719794	CCT	ORF1ab:nsp6	.	678-679-insfrshift	.	no-SNV	ORF1ab:nsp6	0.981491002570694
CAMB-78188	MN908947.3	11653	C	T	0.99	1	0	0	0.995563400438889	TCT	ORF1ab:nsp6	L227L	C681T	CTC>CTT	Synonymous	ORF1ab:nsp6	0.000238526858124225
CAMB-78188	MN908947.3	12885	C	T	0.01	0.011	3e-06	1e-06	0.010484402673458	ACA	ORF1ab:nsp9	T67I	C200T	ACA>ATA	Missense	ORF1ab:nsp9	0.989489741832896
CAMB-78188	MN908947.3	14805	C	T	1	1	0	0	0.998085321515393	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000720693586902739
CAMB-78188	MN908947.3	21137	A	G	1	1	0	0	0.999894069666849	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0
CAMB-78188	MN908947.3	21637	C	T	0.074	0.066	6.9e-31	2.5e-27	0.0700778642936596	CCC	S	P25P	C75T	CCC>CCT	Synonymous	GU280_gp02, spike glycoprotein	0.929226918798665
CAMB-78188	MN908947.3	21987	G	A	1	1	0	0	0.996812431517083	GGT	S	G142D	G425A	GGT>GAT	Missense	GU280_gp02, spike glycoprotein	0.000149417272636717
CAMB-78188	MN908947.3	22259	A	G	0.036	0.0036	3.1e-12	0.0041	0.0203389830508475	TAT	S	I233V	A697G	ATT>GTT	Missense	GU280_gp02, spike glycoprotein	0.979661016949153
CAMB-78188	MN908947.3	23917	C	T	0.01	0.014	1.1e-06	5.3e-08	0.0121276209044495	TCA	S	V785V	C2355T	GTC>GTT	Synonymous	GU280_gp02, spike glycoprotein	0.98787237909555
CAMB-78188	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-78188	MN908947.3	25207	C	T	0.0037	0.0086	0.003	2.3e-05	0.00623626003858405	ACA	S	Y1215Y	C3645T	TAC>TAT	Synonymous	GU280_gp02, spike glycoprotein	0.993718874781282
CAMB-78188	MN908947.3	2558	C	T	1	1	0	0	0.998879986215215	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000143591510869877
CAMB-78188	MN908947.3	26144	G	T	1	1	0	0	0.999488141955298	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000511858044702269
CAMB-78188	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0321315789473684	0.0387105263157895	0.00026;9.6e-06;0.00013;0.00014;0.00026;5.9e-06;2.9e-05;2.3e-05;2.3e-05;5.5e-06;1.1e-05;9e-06;2.1e-05;1.3e-05;1.7e-05;3.1e-05;1.2e-05;2.6e-05;1.7e-05;1.6e-05;1.1e-05;2.9e-05;1.5e-05;2e-05;1.5e-05;9.5e-06;2.3e-05;1.3e-05;1.8e-05;1.2e-05;2.3e-05;1.8e-05;7.9e-06;1.9e-05;9.8e-06;1.6e-05;1.5e-05;0.0035	0.00013;9.2e-06;7.2e-05;7.1e-05;6.5e-05;2e-06;5.6e-06;1.4e-06;1.3e-06;3.5e-07;6.3e-07;5.5e-07;8.3e-07;5.5e-07;6.9e-07;1.2e-06;4.8e-07;1.1e-06;7e-07;6.4e-07;4.1e-07;1.2e-06;6.2e-07;8.4e-07;5e-07;3.2e-07;8e-07;5.1e-07;1.1e-06;5e-07;9.5e-07;7.2e-07;2.7e-07;6.1e-07;1.7e-07;5e-07;4.2e-07;0.00065	0.0369297842556875	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.97460544886874
CAMB-78188	MN908947.3	2689	A	G	0.0066	0.0093	8.6e-05	6.6e-06	0.00798863838096929	TAA	ORF1ab:nsp2	V628V	A1884G	GTA>GTG	Synonymous	ORF1ab:nsp2	0.991774661222558
CAMB-78188	MN908947.3	27487	A	G	0.0058	0.0089	9.5e-05	3.1e-06	0.00702490377860669	AAA	ORF7a	K32E	A94G	AAA>GAA	Missense	GU280_gp07	0.992955307760045
CAMB-78188	MN908947.3	27739	C	A	0.0059	0.017	0.0013	1.2e-05	0.00965250965250965	ACT	ORF7a	L116I	C346A	CTC>ATC	Missense	GU280_gp07	0.99034749034749
CAMB-78188	MN908947.3	6026	C	T	0.014	0.0078	3.1e-07	6.6e-05	0.01085776330076	TCC	ORF1ab:nsp3	P1103S	C3307T	CCA>TCA	Missense	ORF1ab:nsp3	0.98687197709999
CAMB-78188	MN908947.3	9724	C	T	1	1	0	0	0.999830483334393	TCT	ORF1ab:nsp4	F390F	C1170T	TTC>TTT	Synonymous	ORF1ab:nsp4	3.17843748013477e-05
CAMB-78188	MN908947.3	9858	TAT	-	0.0106666666666667	0.015	0.00016;7e-05;0.00023	8.8e-06;2.5e-06;1.1e-05	0.012990461406483	CTA	ORF1ab:nsp4	.	1304-1306-delinframe	.	no-SNV	ORF1ab:nsp4	0.986785814241734
CAMB-78AD8	MN908947.3	10448	C	A	0.012	0.0088	4.3e-07	5.1e-06	0.0101949915866574	GCC	ORF1ab:3C-like-proteinase	P132T	C394A	CCC>ACC	Missense	ORF1ab:3C-like-proteinase	0.989739021412782
CAMB-78AD8	MN908947.3	11074	C	INS	0.11	0.12	1e-43	2.1e-43	0.112948296778942	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.881462902632189
CAMB-78AD8	MN908947.3	11083	G	-	0.17	0.15	4.8e-77	4.5e-68	0.164634296857644	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.70269803263311e-05
CAMB-78AD8	MN908947.3	11083	G	T	0.83	0.85	0	0	0.835118856606847	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.70269803263311e-05
CAMB-78AD8	MN908947.3	12049	C	T	0.025	0.024	1.1e-12	4e-12	0.0242901384276706	ACA	ORF1ab:nsp7	N69N	C207T	AAC>AAT	Synonymous	ORF1ab:nsp7	0.975635237491138
CAMB-78AD8	MN908947.3	14805	C	T	1	1	0	0	0.999858523933035	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	8.25277057297807e-05
CAMB-78AD8	MN908947.3	17247	T	C	1	1	0	0	0.998783423829526	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000153672779428337
CAMB-78AD8	MN908947.3	1778	T	C	0.015	0.025	1.2e-08	6.8e-13	0.0197375012523795	ATC	ORF1ab:nsp2	S325P	T973C	TCC>CCC	Missense	ORF1ab:nsp2	0.980237451157199
CAMB-78AD8	MN908947.3	25157	G	A	0.0052	0.0074	0.00025	2.8e-05	0.00635037114391352	CGA	S	D1199N	G3595A	GAT>AAT	Missense	GU280_gp02, spike glycoprotein	0.993282718523327
CAMB-78AD8	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-78AD8	MN908947.3	4129	T	C	1	1	0	0	0.999501997308666	GTG	ORF1ab:nsp3	G470G	T1410C	GGT>GGC	Synonymous	ORF1ab:nsp3	0.000275490850525022
CAMB-78AF6	MN908947.3	10279	C	A	0.0087	0.0041	8.1e-06	3e-04	0.00693223979691467	TCA	ORF1ab:3C-like-proteinase	L75L	C225A	CTC>CTA	Synonymous	ORF1ab:3C-like-proteinase	0.993011967528663
CAMB-78AF6	MN908947.3	11074	C	INS	0.1	0.13	1.6e-41	4.3e-49	0.111762545899633	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.882301101591187
CAMB-78AF6	MN908947.3	11083	G	-	0.15	0.15	2.6e-63	1.7e-65	0.147058823529412	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-78AF6	MN908947.3	11083	G	T	0.85	0.85	0	0	0.85284199854539	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-78AF6	MN908947.3	14805	C	T	1	1	0	0	0.997702451081808	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00101266374119364
CAMB-78AF6	MN908947.3	1515	A	G	1	1	0	0	0.998581336696091	CAT	ORF1ab:nsp2	H237R	A710G	CAT>CGT	Missense	ORF1ab:nsp2	0.000157629255989912
CAMB-78AF6	MN908947.3	15315	C	T	0.0084	0.012	6.5e-06	1.6e-07	0.00980495797875152	CCA	ORF1ab:RNA-dependent-RNA-polymerase	A616A	C1848T	GCC>GCT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.990195042021249
CAMB-78AF6	MN908947.3	17247	T	C	1	1	0	0	0.999777096684313	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000122596823627751
CAMB-78AF6	MN908947.3	18807	C	T	0.018	0.012	1.4e-09	4.5e-07	0.0150320008982708	ACC	ORF1ab:3'-to-5'-exonuclease	N256N	C768T	AAC>AAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.984939928138334
CAMB-78AF6	MN908947.3	2047	T	C	1	1	0	0	1	ATC	ORF1ab:nsp2	N414N	T1242C	AAT>AAC	Synonymous	ORF1ab:nsp2	0
CAMB-78AF6	MN908947.3	21569	G	INS	0.046	0.06	3.3e-19	1.3e-24	0.052732379979571	TGT	S	.	6-7-insfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.945224719101124
CAMB-78AF6	MN908947.3	21575	C	-	0.012	0.02	9.1e-07	1.8e-09	0.0157627571466738	TCT	S	.	13-13-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.000267165375367352
CAMB-78AF6	MN908947.3	21575	C	T	0.99	0.98	0	0	0.983970077477959	TCT	S	L5F	C13T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.000267165375367352
CAMB-78AF6	MN908947.3	25532	TT	-	0.043	0.03	5.8e-11;5.2e-10	3.3e-08;1.6e-07	0.0371894977707532	ATT	ORF3a	.	140-141-delfrshift	.	no-SNV	GU280_gp03	0.962526031806134
CAMB-78AF6	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-78AF6	MN908947.3	26735	C	T	1	1	0	0	0.999176845849686	ACA	M	Y71Y	C213T	TAC>TAT	Synonymous	GU280_gp05	2.93983625112081e-05
CAMB-78AF6	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0355263157894737	0.0380263157894737	0.0015;0.00042;0.00086;0.00095;0.0019;2e-04;0.00087;8.2e-06;8.3e-06;7.6e-07;1.8e-06;1.2e-06;3.5e-06;9.9e-07;1.4e-06;2.6e-06;9.9e-07;2.2e-06;1.2e-06;1.3e-06;9.9e-07;2.4e-06;1.2e-06;1.7e-06;1.2e-06;7e-07;1.8e-06;9.6e-07;1.1e-06;8.8e-07;1.9e-06;1.4e-06;6.4e-07;1.8e-06;9.4e-07;1.9e-06;1.3e-06;0.0026	0.00013;1.2e-05;9.7e-05;1e-04;0.00018;1.9e-05;4.1e-05;9.5e-07;8.8e-07;6.4e-07;5.1e-07;4.6e-07;7.5e-07;6.3e-07;8.2e-07;1.3e-06;5.6e-07;1.1e-06;5.9e-07;7.7e-07;7.1e-07;1.3e-06;7.7e-07;8.6e-07;6.6e-07;4e-07;9.7e-07;7e-07;5.3e-07;5.4e-07;1e-06;9e-07;3.9e-07;1e-06;1.8e-07;3e-07;1.5e-07;0.00059	0.039710554182845	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.977108380772359
CAMB-78AF6	MN908947.3	27684	CTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAGACAGA	-	0.000463888888888889	0.0166111111111111	0.0035;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00059;0.00024;0.00019;0.00016;0.00012;2e-04;0.00011;3e-04;0.00031;0.00027;0.00028;0.00033;0.00038;0.00042;0.00032;0.00026;0.00029;9.2e-05;0.00014;0.00018;0.00011;9.4e-05;0.00012;0.00014;1e-04;0.00011;9.7e-05;9.9e-05;0.00011;6.4e-05;8.7e-05;0.00015;0.00016;0.00012;0.00027;0.00014;2e-04;0.00023;0.00013;0.00013;0.00011;0.00012;9.2e-05;9.6e-05;0.00012;7.7e-05;0.00011;8.6e-05;1e-04;0.00011;0.00011;1e-04;0.00011;0.00013;0.00012;1e-04;9.6e-05;0.00011;0.00037;0.00012;9e-05;0.00011;0.00014;9.7e-05;8e-05;3.9e-05;0.00011;5.6e-05;8.3e-05;0.00011;0.00028;7.6e-05	0.00711743772241993	ACT	ORF7a	.	291-362-delinframe	.	no-SNV	GU280_gp07	0.987522281639929
CAMB-78AF6	MN908947.3	27997	A	G	0.0057	0.011	0.00021	2e-06	0.0073181887482848	GAC	ORF8	D35G	A104G	GAC>GGC	Missense	GU280_gp09	0.992681811251715
CAMB-78AF6	MN908947.3	3549	GACCACTTAAAGTGGGTGGTAGTTGTGTTT	-	0.00968	0.00093	0.00024;0.00029;0.00073;0.00025;0.00029;0.00018;0.00017;8.8e-05;7.2e-05;2.8e-05;1.6e-05;3.1e-05;2.7e-05;4.8e-05;3.3e-05;3.4e-05;1.7e-05;4e-05;3.1e-05;3.1e-05;1.7e-05;2.9e-05;2.4e-05;3.8e-05;3.4e-05;2.1e-05;2.8e-05;5.2e-05;1.8e-05;1.8e-05	0.089;0.095;0.13;0.09;0.095;0.094;0.095;0.064;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0087;0.0095;NA;NA;NA;NA;NA	0.0060568411243982	GGA	ORF1ab:nsp3	.	830-859-delinframe	.	no-SNV	ORF1ab:nsp3	0.993022173980462
CAMB-78AF6	MN908947.3	522	T	-	0.045	0.083	7.3e-06	6.9e-11	0.0611362413566347	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.93860470677321
CAMB-78AF6	MN908947.3	9223	C	T	1	1	0	0	0.999880399465784	ACG	ORF1ab:nsp4	H223H	C669T	CAC>CAT	Synonymous	ORF1ab:nsp4	9.96671118464329e-05
CAMB-78B02	MN908947.3	11075	T	-	0.038	0.038	1.1e-10	9.6e-11	0.0382712693666757	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.9564555585757
CAMB-78B02	MN908947.3	14183	C	T	0.022	0.02	1.2e-11	6.7e-11	0.0215197222942841	ACC	ORF1ab:RNA-dependent-RNA-polymerase	T239I	C716T	ACC>ATC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.978344389677451
CAMB-78B02	MN908947.3	14408	C	T	1	1	0	0	0.998004864330775	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000475032302196549
CAMB-78B02	MN908947.3	23403	A	G	1	1	0	0	0.999550975505714	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.49024494286163e-05
CAMB-78B02	MN908947.3	241	C	T	1	1	0	0	0.998534550783452	TCG	NA	NA	NA	NA	NA	NA	0.000225453725622816
CAMB-78B02	MN908947.3	26589	G	C	1	1	0	0	0.996585614908418	AGT	M	V23L	G67C	GTA>CTA	Missense	GU280_gp05	0.000989214372327526
CAMB-78B02	MN908947.3	27128	C	T	1	1	0	0	0.999807713438084	GCA	M	G202G	C606T	GGC>GGT	Synonymous	GU280_gp05	0.000109878035380727
CAMB-78B02	MN908947.3	28554	T	G	0.011	0.0046	2.3e-05	0.006	0.00761421319796954	ATT	N	I94S	T281G	ATT>AGT	Missense	GU280_gp10	0.992204496011603
CAMB-78B02	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999274486094317	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-78B02	MN908947.3	3037	C	T	1	1	0	0	0.998905271003657	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.31684252206927e-05
CAMB-78B02	MN908947.3	313	C	T	1	1	0	0	0.998182802350758	TCA	ORF1ab:leader-protein	L16L	C48T	CTC>CTT	Synonymous	ORF1ab:leader-protein	9.66594494277761e-05
CAMB-78B02	MN908947.3	960	G	T	0.17	0.17	1.3e-80	5.1e-82	0.172877929099604	CGT	ORF1ab:nsp2	R52L	G155T	CGT>CTT	Missense	ORF1ab:nsp2	0.826633650995582
CAMB-78B11	MN908947.3	11074	C	INS	0.045	0.19	1.6e-10	2.4e-62	0.127048606247374	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.872601204650511
CAMB-78B11	MN908947.3	11083	G	-	0.077	0.11	2.7e-32	1.7e-45	0.0922598260206997	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-78B11	MN908947.3	11083	G	T	0.92	0.89	0	0	0.90761318178932	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-78B11	MN908947.3	1312	G	C	1	1	0	0	0.999267015706806	TGA	ORF1ab:nsp2	L169F	G507C	TTG>TTC	Missense	ORF1ab:nsp2	0.000209424083769634
CAMB-78B11	MN908947.3	14805	C	T	1	1	0	0	0.999905033238367	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-78B11	MN908947.3	2480	A	G	1	1	8e-282	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-78B11	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-78B20	MN908947.3	13914	T	G	0.0015	0.012	0.0044	1.3e-07	0.00618832580699114	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993811674193009
CAMB-78B20	MN908947.3	14408	C	T	1	1	0	0	0.999590633699034	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000409366300966104
CAMB-78B20	MN908947.3	1594	C	T	0.027	0.065	1.5e-05	6.5e-16	0.054	CCG	ORF1ab:nsp2	S263S	C789T	TCC>TCT	Synonymous	ORF1ab:nsp2	0.946
CAMB-78B20	MN908947.3	18814	C	T	0.25	0.46	8.7e-122	1.5e-254	0.33999933228725	TCT	ORF1ab:3'-to-5'-exonuclease	L259L	C775T	CTG>TTG	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.659900510800254
CAMB-78B20	MN908947.3	23403	A	G	1	1	0	0	0.999875067671678	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.32882188814392e-05
CAMB-78B20	MN908947.3	241	C	T	1	1	0	0	0.99984962406015	TCG	NA	NA	NA	NA	NA	NA	0.000150375939849624
CAMB-78B20	MN908947.3	27297	C	T	0.11	0.059	5.6e-49	8.3e-28	0.0753184868229116	TCA	ORF6	I32I	C96T	ATC>ATT	Synonymous	GU280_gp06	0.92458426529223
CAMB-78B20	MN908947.3	28253	C	T	0.41	0.16	2.1e-220	2.5e-73	0.299859043558978	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.700072197201499
CAMB-78B20	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-78B20	MN908947.3	29733	C	T	0.025	0.014	1.2e-05	0.00029	0.0188284518828452	CCG	NA	NA	NA	NA	NA	NA	0.981171548117155
CAMB-78B20	MN908947.3	29754	C	T	0.03	0.047	6.1e-07	4.5e-11	0.039832285115304	TCG	NA	NA	NA	NA	NA	NA	0.960167714884696
CAMB-78B20	MN908947.3	3037	C	T	1	1	0	1.6e-267	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78B20	MN908947.3	440	G	T	0.2	0.2	1.8e-83	2e-76	0.198469846984698	AGG	ORF1ab:leader-protein	G59C	G175T	GGC>TGC	Missense	ORF1ab:leader-protein	0.801530153015302
CAMB-78B20	MN908947.3	635	C	T	0.5	0.6	2.8e-241	8.69999999999999e-262	0.531281281281281	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.468718718718719
CAMB-78B3F	MN908947.3	11074	C	INS	0.077	0.089	9.4e-27	7.7e-29	0.0818109392599104	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.914521579077498
CAMB-78B3F	MN908947.3	11083	G	-	0.17	0.16	1.3e-73	9.3e-69	0.162314177684883	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.17423263897043e-05
CAMB-78B3F	MN908947.3	11083	G	T	0.83	0.84	0	0	0.837368779502595	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.17423263897043e-05
CAMB-78B3F	MN908947.3	11651	C	INS	0.0053	0.015	0.00012	4.7e-08	0.010051993067591	CCT	ORF1ab:nsp6	.	678-679-insfrshift	.	no-SNV	ORF1ab:nsp6	0.985961871750433
CAMB-78B3F	MN908947.3	11653	C	T	1	1	0	0	0.998581057112451	TCT	ORF1ab:nsp6	L227L	C681T	CTC>CTT	Synonymous	ORF1ab:nsp6	0
CAMB-78B3F	MN908947.3	12473	C	T	0.0035	0.014	0.002	7.3e-08	0.00793930094736694	ACT	ORF1ab:nsp8	L128L	C382T	CTA>TTA	Synonymous	ORF1ab:nsp8	0.992046622277904
CAMB-78B3F	MN908947.3	12809	C	T	0.0062	0.01	0.00012	2.3e-06	0.00791489361702128	ACT	ORF1ab:nsp9	L42F	C124T	CTT>TTT	Missense	ORF1ab:nsp9	0.992085106382979
CAMB-78B3F	MN908947.3	12885	C	T	0.011	0.015	1e-06	9.9e-09	0.0128940077712533	ACA	ORF1ab:nsp9	T67I	C200T	ACA>ATA	Missense	ORF1ab:nsp9	0.987088567893921
CAMB-78B3F	MN908947.3	13042	A	G	0.007	0.0082	3.6e-05	9.8e-06	0.00752570772847291	AAG	ORF1ab:nsp10	E6E	A18G	GAA>GAG	Synonymous	ORF1ab:nsp10	0.992468721799485
CAMB-78B3F	MN908947.3	13517	C	T	0.0029	0.032	0.0064	1.6e-14	0.0148982558139535	ACT	ORF1ab:RNA-dependent-RNA-polymerase	T17I	C50T	ACT>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.985101744186046
CAMB-78B3F	MN908947.3	14805	C	T	1	1	0	0	0.998385016812698	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	6.02605666903692e-05
CAMB-78B3F	MN908947.3	16375	C	T	0.014	0.011	2.6e-06	3.1e-05	0.0125883212864452	TCC	ORF1ab:helicase	P47S	C139T	CCG>TCG	Missense	ORF1ab:helicase	0.987411678713555
CAMB-78B3F	MN908947.3	16549	G	C	0.21	0.28	8.8e-29	9e-35	0.240343347639485	TGA	ORF1ab:helicase	D105H	G313C	GAC>CAC	Missense	ORF1ab:helicase	0.759656652360515
CAMB-78B3F	MN908947.3	19836	C	T	0.008	0.0053	1e-05	0.00011	0.00675675675675676	TCA	ORF1ab:endoRNAse	L72L	C216T	CTC>CTT	Synonymous	ORF1ab:endoRNAse	0.993183448935661
CAMB-78B3F	MN908947.3	20549	A	G	0.005	0.016	0.00012	2.4e-09	0.00947980562415359	GAT	ORF1ab:endoRNAse	D310G	A929G	GAT>GGT	Missense	ORF1ab:endoRNAse	0.990520194375846
CAMB-78B3F	MN908947.3	21137	A	G	1	1	0	0	0.999908395548024	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	6.87033389822745e-05
CAMB-78B3F	MN908947.3	21637	C	T	0.13	0.16	1.3e-49	7.6e-63	0.141862845445241	CCC	S	P25P	C75T	CCC>CCT	Synonymous	GU280_gp02, spike glycoprotein	0.857932446264074
CAMB-78B3F	MN908947.3	21987	G	A	1	1	0	0	0.999749968746093	GGT	S	G142D	G425A	GGT>GAT	Missense	GU280_gp02, spike glycoprotein	0.000250031253906738
CAMB-78B3F	MN908947.3	22482	C	T	0.022	0.016	4.5e-07	2.1e-05	0.0196353436185133	ACT	S	T307I	C920T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.980364656381487
CAMB-78B3F	MN908947.3	23561	GGTGCAGGTATATGCGCTAGTTA	-	0.0408695652173913	0.0236434782608696	0.00012;0.00024;0.00025;0.00026;0.00023;0.00022;0.00014;0.00013;5.5e-05;7.3e-06;5.7e-05;2.1e-05;5.8e-05;1.9e-05;5.2e-05;0.00011;6.2e-05;6.2e-05;5.3e-07;1.5e-06;7.9e-05;0.00018;0.00063	0.004;0.0057;0.0057;0.0059;0.0056;0.0056;0.0045;0.0042;0.0029;0.0012;0.0024;0.0016;0.0024;0.0018;0.0028;0.0041;0.0031;0.0031;0.00048;0.00064;0.0033;0.0026;0.052	0.0345023117857454	TGG	S	.	1999-2021-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.965934962842046
CAMB-78B3F	MN908947.3	24169	G	T	0.0048	0.013	4e-04	8.1e-08	0.00831826401446655	TGA	S	M869I	G2607T	ATG>ATT	Missense	GU280_gp02, spike glycoprotein	0.991520996584288
CAMB-78B3F	MN908947.3	24378	C	T	0.013	0.0063	1.2e-07	0.00012	0.0104949937673409	TCT	S	S939F	C2816T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.98660983553822
CAMB-78B3F	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-78B3F	MN908947.3	2558	C	T	1	1	0	0	0.998952660242983	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.00104733975701718
CAMB-78B3F	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-78B3F	MN908947.3	2689	A	G	0.017	0.0058	1.2e-07	0.00068	0.0115163147792706	TAA	ORF1ab:nsp2	V628V	A1884G	GTA>GTG	Synonymous	ORF1ab:nsp2	0.988003838771593
CAMB-78B3F	MN908947.3	27487	A	G	0.035	0.02	1.2e-16	1.4e-10	0.0286111571541706	AAA	ORF7a	K32E	A94G	AAA>GAA	Missense	GU280_gp07	0.971379634233936
CAMB-78B3F	MN908947.3	28057	C	T	0.014	0.0083	7.5e-08	1.9e-05	0.0123982235381199	GCA	ORF8	A55V	C164T	GCA>GTA	Missense	GU280_gp09	0.98760177646188
CAMB-78B3F	MN908947.3	29728	TTCACCGAGGCCACGCG	-	0.0123529411764706	0.0339411764705882	8.6e-07;2.7e-06;4.7e-06;7.3e-07;3.7e-06;3.6e-06;4.8e-06;3.6e-06;6.3e-06;8.6e-06;1.1e-05;1.4e-05;6.7e-06;1.4e-05;1.6e-05;1e-05;1.6e-05	1.4e-14;9.5e-14;2.1e-13;3.9e-15;1.5e-13;1.4e-13;2.9e-13;9.6e-14;2.3e-13;4e-13;5.2e-13;6.6e-13;5.3e-14;7.1e-13;9.2e-13;4.8e-13;6.5e-13	0.0193403298350825	TTT	NA	NA	NA	NA	NA	NA	0.978367748279253
CAMB-78B3F	MN908947.3	3365	C	T	0.0035	0.0067	0.0013	4.7e-05	0.00497875557177489	ACT	ORF1ab:nsp3	L216F	C646T	CTT>TTT	Missense	ORF1ab:nsp3	0.994890910512734
CAMB-78B3F	MN908947.3	4284	A	G	0.0057	0.0071	7.7e-05	1.7e-05	0.00631066235289935	GAG	ORF1ab:nsp3	E522G	A1565G	GAG>GGG	Missense	ORF1ab:nsp3	0.99367156113343
CAMB-78B3F	MN908947.3	522	TT	-	0.0285	0.0375	0.00024;0.0014	3.4e-06;0.00045	0.0316419905408184	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.961507047819787
CAMB-78B3F	MN908947.3	7682	T	C	0.0079	0.011	2.1e-05	1.6e-06	0.00908711963318049	CTT	ORF1ab:nsp3	L1655L	T4963C	TTG>CTG	Synonymous	ORF1ab:nsp3	0.990912880366819
CAMB-78B3F	MN908947.3	8140	C	T	0.096	0.054	1.4e-43	7.2e-25	0.0793252792341008	CCT	ORF1ab:nsp3	S1807S	C5421T	TCC>TCT	Synonymous	ORF1ab:nsp3	0.920537953043082
CAMB-78B3F	MN908947.3	9138	A	G	0.01	0.0083	1.8e-06	8.9e-06	0.00932003150433184	GAT	ORF1ab:nsp4	D195G	A584G	GAT>GGT	Missense	ORF1ab:nsp4	0.990636212479216
CAMB-78B3F	MN908947.3	9724	C	T	1	1	0	0	0.999802743032188	TCT	ORF1ab:nsp4	F390F	C1170T	TTC>TTT	Synonymous	ORF1ab:nsp4	5.8016755238913e-05
CAMB-78B4E	MN908947.3	11195	C	T	1	1	0	0	0.999355745578072	TCT	ORF1ab:nsp6	L75F	C223T	CTT>TTT	Missense	ORF1ab:nsp6	0.000351411502869861
CAMB-78B4E	MN908947.3	13914	T	G	0.0021	0.013	0.0024	5.7e-06	0.00382741823242867	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.996172581767571
CAMB-78B4E	MN908947.3	14408	C	T	1	1	0	0	0.999620853080569	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000252764612954186
CAMB-78B4E	MN908947.3	23403	A	G	1	1	0	0	0.999943155979991	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.84220100045475e-05
CAMB-78B4E	MN908947.3	241	C	T	1	1	0	2.9e-08	0.999520958083832	TCG	NA	NA	NA	NA	NA	NA	0.000479041916167665
CAMB-78B4E	MN908947.3	26951	G	T	1	1	0	0	0.999757516973812	TGA	M	V143V	G429T	GTG>GTT	Synonymous	GU280_gp05	0
CAMB-78B4E	MN908947.3	28881	GGG	AAC	1	1	0;0;0	3.3e-270;1.1e-287;2.8e-301	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-78B4E	MN908947.3	29051	C	INS	0.075	0.097	2.6e-19	2.5e-25	0.0850495804729214	GCA	N	.	777-778-insfrshift	.	no-SNV	GU280_gp10	0.914950419527079
CAMB-78B4E	MN908947.3	3037	C	T	1	1	0	4.9e-145	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78B4E	MN908947.3	3373	C	A	0.84	1	0	0	0.904731457800512	ACA	ORF1ab:nsp3	D218E	C654A	GAC>GAA	Missense	ORF1ab:nsp3	0.000639386189258312
CAMB-78B4E	MN908947.3	9358	T	A	1	1	0	3.9999999999988e-312	1	TTA	ORF1ab:nsp4	F268L	T804A	TTT>TTA	Missense	ORF1ab:nsp4	0
CAMB-78B5D	MN908947.3	14408	C	T	0.85	1	0	0	0.90575637910085	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000607533414337789
CAMB-78B5D	MN908947.3	23403	A	G	1	1	0	0	0.999957877887997	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-78B5D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998963730569948	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-78B5D	MN908947.3	3037	C	T	1	1	7.99999986927772e-317	4.9e-251	0.999146029035013	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78B8A	MN908947.3	11074	C	INS	0.042	0.04	2.9e-09	1.7e-09	0.0413823145055902	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.958472484390881
CAMB-78B8A	MN908947.3	11083	G	-	0.051	0.025	9.6e-22	4.3e-10	0.0459001268596471	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-78B8A	MN908947.3	11083	G	T	0.95	0.97	0	0	0.953869219236536	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-78B8A	MN908947.3	13968	C	T	1	1	0	0	0.999616564417178	CCA	ORF1ab:RNA-dependent-RNA-polymerase	A167A	C501T	GCC>GCT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000383435582822086
CAMB-78B8A	MN908947.3	14805	C	T	1	1	0	0	0.9996824052509	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000211729832733432
CAMB-78B8A	MN908947.3	2480	A	G	1	1	5.6e-258	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-78B8A	MN908947.3	2558	C	T	1	1	7.1e-301	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-78B8A	MN908947.3	27294	C	T	0.51	0.49	1.5e-288	1.2e-248	0.50525994816283	ACA	ORF6	Y31Y	C93T	TAC>TAT	Synonymous	GU280_gp06	0.494663820704376
CAMB-78B99	MN908947.3	11075	T	-	0.038	0.041	1.8e-09	3.2e-10	0.0392068309999685	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955856868284793
CAMB-78B99	MN908947.3	13133	C	T	0.057	0.066	2.6e-26	1e-30	0.0612084285351612	ACC	ORF1ab:nsp10	P37S	C109T	CCA>TCA	Missense	ORF1ab:nsp10	0.938757721926039
CAMB-78B99	MN908947.3	13279	T	C	0.011	0.0064	1.1e-06	6e-05	0.00858125663263439	ATC	ORF1ab:nsp10	N85N	T255C	AAT>AAC	Synonymous	ORF1ab:nsp10	0.991400446444908
CAMB-78B99	MN908947.3	13716	T	C	0.011	0.013	5.9e-07	9.9e-08	0.0118506864262694	ATT	ORF1ab:RNA-dependent-RNA-polymerase	D83D	T249C	GAT>GAC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.98809010243527
CAMB-78B99	MN908947.3	14408	C	T	1	1	0	0	0.997278599625184	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000867259460106065
CAMB-78B99	MN908947.3	1481	T	G	0.013	0.0081	2.2e-07	1.7e-05	0.0104995766299746	CTT	ORF1ab:nsp2	F226V	T676G	TTT>GTT	Missense	ORF1ab:nsp2	0.988653683319221
CAMB-78B99	MN908947.3	17550	C	T	0.017	0.025	5.6e-09	2.3e-12	0.0206369036394494	TCG	ORF1ab:helicase	L438L	C1314T	CTC>CTT	Synonymous	ORF1ab:helicase	0.978479162738073
CAMB-78B99	MN908947.3	21952	C	T	0.0082	0.011	1.6e-05	9.9e-07	0.00948640483383686	TCT	S	V130V	C390T	GTC>GTT	Synonymous	GU280_gp02, spike glycoprotein	0.990513595166163
CAMB-78B99	MN908947.3	23029	C	T	0.0065	0.009	0.00014	1.1e-05	0.00761704049375282	ACT	S	Y489Y	C1467T	TAC>TAT	Synonymous	GU280_gp02, spike glycoprotein	0.991901249435496
CAMB-78B99	MN908947.3	23403	A	G	1	1	0	0	0.999419393879921	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.45326529610912e-05
CAMB-78B99	MN908947.3	23589	C	T	0.0051	0.0073	0.00021	2.3e-05	0.00608766233766234	ACT	S	T676I	C2027T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.993871753246753
CAMB-78B99	MN908947.3	241	C	T	1	1	0	0	0.998417292857856	TCG	NA	NA	NA	NA	NA	NA	0.000199620720630801
CAMB-78B99	MN908947.3	2834	T	G	0.011	0.011	8.6e-07	7.1e-07	0.0113413838120104	GTG	ORF1ab:nsp3	C39G	T115G	TGC>GGC	Missense	ORF1ab:nsp3	0.9884954308094
CAMB-78B99	MN908947.3	28937	C	T	0.011	0.0076	1.7e-06	4.4e-05	0.00941356948608884	GCT	N	L222L	C664T	CTG>TTG	Synonymous	GU280_gp10	0.990551565441741
CAMB-78B99	MN908947.3	2940	C	T	1	1	0	0	0.999764289923394	CCA	ORF1ab:nsp3	P74L	C221T	CCA>CTA	Missense	ORF1ab:nsp3	0.000235710076605775
CAMB-78B99	MN908947.3	29482	C	A	0.028	0.037	5.8e-12	4.3e-15	0.0329387545033453	TCT	N	F403L	C1209A	TTC>TTA	Missense	GU280_gp10	0.966803911477097
CAMB-78B99	MN908947.3	3037	C	T	1	1	0	0	0.999158417825512	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78B99	MN908947.3	3241	C	T	0.13	0.12	1.4e-58	7.1e-56	0.126563136160065	ACG	ORF1ab:nsp3	D174D	C522T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.873242986486748
CAMB-78B99	MN908947.3	3777	C	T	0.0083	0.0064	1.8e-05	0.00011	0.00753295668549906	ACA	ORF1ab:nsp3	T353I	C1058T	ACA>ATA	Missense	ORF1ab:nsp3	0.992467043314501
CAMB-78B99	MN908947.3	8443	A	C	0.012	0.018	9.9e-07	4.4e-09	0.0145905526171804	GAA	ORF1ab:nsp3	R1908R	A5724C	CGA>CGC	Synonymous	ORF1ab:nsp3	0.98401118609034
CAMB-78B99	MN908947.3	8933	A	G	0.011	0.013	6.3e-07	6.7e-08	0.0120511586791841	TAG	ORF1ab:nsp4	S127G	A379G	AGT>GGT	Missense	ORF1ab:nsp4	0.987904083071311
CAMB-78B99	MN908947.3	9052	A	G	0.0071	0.0087	7.7e-05	1.5e-05	0.00787308771185442	CAG	ORF1ab:nsp4	P166P	A498G	CCA>CCG	Synonymous	ORF1ab:nsp4	0.99207976805035
CAMB-78B99	MN908947.3	9169	C	T	0.007	0.0094	3.7e-05	3.4e-06	0.00813162234395436	ACC	ORF1ab:nsp4	Y205Y	C615T	TAC>TAT	Synonymous	ORF1ab:nsp4	0.99181151316413
CAMB-78B99	MN908947.3	9286	C	T	0.015	0.012	2.4e-08	4.9e-07	0.0135260922683111	ACA	ORF1ab:nsp4	N244N	C732T	AAC>AAT	Synonymous	ORF1ab:nsp4	0.986444819361219
CAMB-78BA8	MN908947.3	11075	T	-	0.11	0.047	2.2e-25	7.1e-12	0.0811781878064299	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.909976670783587
CAMB-78BA8	MN908947.3	11758	C	T	0.027	0.058	6.4e-06	1.2e-07	0.0359712230215827	CCA	ORF1ab:nsp6	P262P	C786T	CCC>CCT	Synonymous	ORF1ab:nsp6	0.964028776978417
CAMB-78BA8	MN908947.3	13459	G	INS	0.016	0.022	1.1e-07	1.3e-09	0.0186853520186854	CGT	ORF1ab:nsp11	.	17-18-insfrshift	.	no-SNV	ORF1ab:nsp11	0.981147814481148
CAMB-78BA8	MN908947.3	14408	C	T	1	0.99	0	0	0.995407289883512	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000278346067665929
CAMB-78BA8	MN908947.3	18280	AGACATGTACGTGCATGGATT	-	0.000434285714285714	0.00926190476190476	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;5.3e-06;NA;NA;NA;NA;NA;NA;NA;NA	3.2e-06;2.2e-06;3.9e-06;4.1e-06;1.8e-06;4.3e-06;4.9e-06;4.5e-06;8.6e-06;7.2e-06;8.8e-06;4.2e-06;4.6e-06;3.7e-06;2.6e-06;2.5e-06;5.4e-06;2.9e-06;2.3e-06;1.8e-06;2.9e-06	0.0036889426612578	AAG	ORF1ab:3'-to-5'-exonuclease	.	241-261-delinframe	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.996058854440357
CAMB-78BA8	MN908947.3	1871	T	-	0.0088	0.011	0.00012	1.5e-05	0.00945773827267554	ATT	ORF1ab:nsp2	.	1066-1066-delfrshift	.	no-SNV	ORF1ab:nsp2	0.990515162190727
CAMB-78BA8	MN908947.3	18740	ATT	-	0.013	0.0326666666666667	0.0044;0.0017;0.0045	6.8e-06;6e-07;7.6e-06	0.0205237171141517	GAT	ORF1ab:3'-to-5'-exonuclease	.	701-703-delinframe	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.979439183462913
CAMB-78BA8	MN908947.3	23403	A	G	1	1	0	0	0.999970875482982	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.70817233947537e-06
CAMB-78BA8	MN908947.3	241	C	T	1	1	0	0	0.999861733857428	TCG	NA	NA	NA	NA	NA	NA	0.00011851383649041
CAMB-78BA8	MN908947.3	27877	GTCACGC	TGTCACG	0.000235714285714286	0.00871428571428571	NA;0.0052;NA;NA;NA;NA;NA	2.2e-05;7.6e-06;2.5e-05;6.1e-06;1e-05;6.5e-06;1.3e-05	0.00272536687631027	TGT	NA	NA	NA	NA	NA	NA	0.997195253505933
CAMB-78BA8	MN908947.3	27928	CTGTAGCTGCAT	ACTGTAGCTGCA	0.000379166666666667	0.00904166666666667	NA;NA;NA;NA;NA;0.11;NA;0.0018;NA;NA;NA;NA	9.1e-06;9.3e-06;5.7e-06;6.7e-06;4.1e-06;1e-05;5.1e-06;2.6e-05;1.7e-05;4.3e-06;9.2e-06;3.6e-06	0.00292233337079915	ACT	ORF8	.	35-46-mnv	.	no-SNV	GU280_gp09	0.997237263786054
CAMB-78BA8	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999778724345854	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-78BA8	MN908947.3	29726	T	-	0.012	0.017	1.8e-05	6.3e-07	0.0135065823217644	ATT	NA	NA	NA	NA	NA	NA	0.986322448281758
CAMB-78BA8	MN908947.3	3037	C	T	1	1	0	0	0.999660470248706	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000169764875647229
CAMB-78BA8	MN908947.3	7432	ATTTT	-	0.0164	0.0186	NA;6.5e-14;6.5e-09;NA;NA	9.4e-08;1.7e-06;7.2e-05;0.00042;0.00091	0.00682325154179242	CAT	ORF1ab:nsp3	.	4713-4717-delfrshift	.	no-SNV	ORF1ab:nsp3	0.993528313627878
CAMB-78BB7	MN908947.3	14120	C	T	1	1	0	0	0.999421095287716	CCA	ORF1ab:RNA-dependent-RNA-polymerase	P218L	C653T	CCA>CTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-78BB7	MN908947.3	14408	C	T	1	1	0	0	0.998986682107701	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000723798494499131
CAMB-78BB7	MN908947.3	23403	A	G	1	1	0	0	0.999871624802088	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000106979331593136
CAMB-78BB7	MN908947.3	241	C	T	1	1	0	0	0.999853744149766	TCG	NA	NA	NA	NA	NA	NA	9.75039001560062e-05
CAMB-78BB7	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99963768115942	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-78BB7	MN908947.3	3037	C	T	1	1	0	0	0.99909338168631	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78BD5	MN908947.3	11075	T	-	0.04	0.044	4.4e-10	2.2e-11	0.0417033897119514	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.949175305325891
CAMB-78BD5	MN908947.3	12789	C	T	0.064	0.09	1.7e-29	3.4e-41	0.0747404114763603	ACA	ORF1ab:nsp9	T35I	C104T	ACA>ATA	Missense	ORF1ab:nsp9	0.923186394223167
CAMB-78BD5	MN908947.3	14408	C	T	1	1	0	0	0.99926963779997	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000491876583693546
CAMB-78BD5	MN908947.3	14704	T	C	0.0035	0.0084	0.0065	3.9e-05	0.00558978710843818	CTT	ORF1ab:RNA-dependent-RNA-polymerase	F413L	T1237C	TTT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994244179611113
CAMB-78BD5	MN908947.3	18928	C	T	0.011	0.0038	1.6e-06	0.0015	0.0077872375260939	TCC	ORF1ab:3'-to-5'-exonuclease	P297S	C889T	CCT>TCT	Missense	ORF1ab:3'-to-5'-exonuclease	0.992130899267324
CAMB-78BD5	MN908947.3	2086	G	T	0.0026	0.011	0.0065	7.8e-07	0.00615250761295134	AGT	ORF1ab:nsp2	Q427H	G1281T	CAG>CAT	Missense	ORF1ab:nsp2	0.993847492387049
CAMB-78BD5	MN908947.3	21982	TTTGGGTGT	-	0.0528888888888889	0.100555555555556	8.1e-11;1.1e-08;7.5e-09;7.4e-10;9.5e-09;2e-08;1.5e-08;5.1e-09;8.3e-10	2.3e-20;5.7e-16;3.3e-16;1.5e-18;3.3e-16;1.3e-15;1e-15;6.2e-17;1.3e-17	0.0717987612185564	TTT	S	.	420-428-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.916432763460066
CAMB-78BD5	MN908947.3	21991	TTA	-	0.296666666666667	0.36	2.4e-16;3.4e-31;5.4e-31	7.8e-20;1e-38;1.6e-38	0.323273518216422	TTT	S	.	429-431-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.670248163038957
CAMB-78BD5	MN908947.3	23403	A	G	1	1	0	0	0.999947756125594	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.13463246434356e-05
CAMB-78BD5	MN908947.3	23416	AGAAGTCCCTGTTGCT	-	0.01005	0.0033875	4.8e-07;7.1e-06;3.1e-06;2.5e-06;4.6e-06;3.9e-06;1.7e-05;3.6e-06;4.3e-06;5.7e-06;2.4e-05;0.00012;0.00011;6.5e-06;3.9e-06;2.2e-05	0.0044;0.0047;0.0027;0.0023;0.0029;0.0027;0.0064;0.0026;0.0029;0.0047;0.0085;0.016;0.014;0.0046;0.0037;0.009	0.00712999336499879	CAG	S	.	1854-1869-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.99132769807851
CAMB-78BD5	MN908947.3	23987	C	A	0.026	0.025	3.1e-13	6.1e-13	0.0253822764729212	TCC	S	P809T	C2425A	CCA>ACA	Missense	GU280_gp02, spike glycoprotein	0.974573657074869
CAMB-78BD5	MN908947.3	241	C	T	1	1	0	0	0.997417250050975	TCG	NA	NA	NA	NA	NA	NA	6.79671039217019e-05
CAMB-78BD5	MN908947.3	26161	A	-	0.0073	0.02	0.0095	6e-06	0.0125687352710134	TAA	ORF3a	.	769-769-delfrshift	.	no-SNV	GU280_gp03	0.987431264728987
CAMB-78BD5	MN908947.3	28045	C	T	0.036	0.039	2e-15	5.1e-16	0.0372903795233892	GCT	ORF8	A51V	C152T	GCT>GTT	Missense	GU280_gp09	0.962709620476611
CAMB-78BD5	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999628903143721	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000117102874875578
CAMB-78BD5	MN908947.3	29077	C	T	0.01	0.0095	1.8e-06	3.8e-06	0.0100275417975872	ACA	N	Y268Y	C804T	TAC>TAT	Synonymous	GU280_gp10	0.989972458202413
CAMB-78BD5	MN908947.3	3037	C	T	0.99	1	0	0	0.993756328045899	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78BD5	MN908947.3	3892	G	T	0.077	0.055	9.9e-35	1.1e-24	0.0699810551696423	AGG	ORF1ab:nsp3	E391D	G1173T	GAG>GAT	Missense	ORF1ab:nsp3	0.930018944830358
CAMB-78BD5	MN908947.3	643	C	T	0.013	0.0042	1.3e-07	0.00097	0.00954589371980676	ACG	ORF1ab:leader-protein	N126N	C378T	AAC>AAT	Synonymous	ORF1ab:leader-protein	0.990454106280193
CAMB-78BD5	MN908947.3	657	C	T	0.0083	0.0043	2.6e-05	0.0016	0.00670013658680645	GCT	ORF1ab:leader-protein	A131V	C392T	GCT>GTT	Missense	ORF1ab:leader-protein	0.993281405736646
CAMB-78BF3	MN908947.3	11075	T	-	0.14	0.0058	1.9e-34	0.0059	0.0745440126883426	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.925455987311657
CAMB-78BF3	MN908947.3	14408	C	T	1	1	0	0	0.999421445101568	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000449987143224479
CAMB-78BF3	MN908947.3	23403	A	G	1	1	0	0	0.999917467915652	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.06330210869476e-05
CAMB-78BF3	MN908947.3	241	C	T	1	1	0	0	0.999786522450722	TCG	NA	NA	NA	NA	NA	NA	0.000142318366185156
CAMB-78BF3	MN908947.3	28437	CT	-	0.00395	0.0505	0.00048;0.00054	1.5e-24;4.4e-24	0.0253324369968355	GCT	N	.	164-165-delfrshift	.	no-SNV	GU280_gp10	0.97430200941707
CAMB-78BF3	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-78BF3	MN908947.3	3037	C	T	1	1	0	8.79999985620549e-317	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78BF3	MN908947.3	3800	GATA	-	0.14	0.00275	5.9e-50;1.6e-50;4.6e-50;3.4e-48	NA;NA;NA;0.00067	0.0963081861958267	TGA	ORF1ab:nsp3	.	1081-1084-delfrshift	.	no-SNV	ORF1ab:nsp3	0.904051172707889
CAMB-78BF3	MN908947.3	514	TGTT	-	0.175	0.09125	2.7e-05;0.00032;1.9e-05;5.2e-05	6.1e-05;0.0084;0.003;0.0045	0.153855768028996	ATG	ORF1ab:leader-protein	.	249-252-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.871574509485974
CAMB-78C0F	MN908947.3	11075	T	-	0.037	0.038	1.8e-09	5e-10	0.0374318294496777	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958660211729709
CAMB-78C0F	MN908947.3	14408	C	T	1	1	0	0	0.998459069838521	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000674952880647955
CAMB-78C0F	MN908947.3	15699	C	T	0.033	0.032	4.6e-16	7.5e-16	0.0325458052073288	TCT	ORF1ab:RNA-dependent-RNA-polymerase	F744F	C2232T	TTC>TTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.967368094778895
CAMB-78C0F	MN908947.3	21098	A	G	0.018	0.016	8.2e-10	5.1e-09	0.017134984644528	GAG	ORF1ab:2'-O-ribose-methyltransferase	E147G	A440G	GAG>GGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.982549295370397
CAMB-78C0F	MN908947.3	2130	A	C	0.066	0.064	4.4e-30	3.5e-29	0.0649642762635618	GAA	ORF1ab:nsp2	E442A	A1325C	GAA>GCA	Missense	ORF1ab:nsp2	0.934352121372497
CAMB-78C0F	MN908947.3	23403	A	G	1	1	0	0	0.999564059553256	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.52926961021238e-05
CAMB-78C0F	MN908947.3	241	C	T	1	1	0	0	0.998799423723387	TCG	NA	NA	NA	NA	NA	NA	0.000208099887946214
CAMB-78C0F	MN908947.3	25613	C	T	0.017	0.019	1.7e-09	3.8e-10	0.017813655632723	TCC	ORF3a	S74F	C221T	TCC>TTC	Missense	GU280_gp03	0.982036018159406
CAMB-78C0F	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999278882647639	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.26985482493595e-05
CAMB-78C0F	MN908947.3	29274	C	T	0.0078	0.0085	6.8e-05	2.9e-05	0.00809426058512325	ACA	N	T334I	C1001T	ACA>ATA	Missense	GU280_gp10	0.991855671823629
CAMB-78C0F	MN908947.3	3037	C	T	1	1	0	0	0.999549319472403	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.00453685064447e-05
CAMB-78C0F	MN908947.3	4294	G	A	0.013	0.012	1.7e-07	2.4e-07	0.0123743037878979	AGA	ORF1ab:nsp3	K525K	G1575A	AAG>AAA	Synonymous	ORF1ab:nsp3	0.987600493964062
CAMB-78C0F	MN908947.3	745	C	T	0.022	0.021	3.9e-11	5.1e-11	0.0213749343802068	ACT	ORF1ab:leader-protein	N160N	C480T	AAC>AAT	Synonymous	ORF1ab:leader-protein	0.978533768516194
CAMB-78C1E	MN908947.3	10369	C	T	0.0048	0.0084	0.0014	3.2e-05	0.00627626682465332	GCA	ORF1ab:3C-like-proteinase	R105R	C315T	CGC>CGT	Synonymous	ORF1ab:3C-like-proteinase	0.993723733175347
CAMB-78C1E	MN908947.3	10594	C	T	0.0076	0.0047	2.6e-05	0.00049	0.00633155080213904	ACT	ORF1ab:3C-like-proteinase	N180N	C540T	AAC>AAT	Synonymous	ORF1ab:3C-like-proteinase	0.993668449197861
CAMB-78C1E	MN908947.3	11075	T	-	0.034	0.044	1.2e-08	2.1e-11	0.038023269761305	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956339210747271
CAMB-78C1E	MN908947.3	11083	G	-	0.013	0.0072	1.1e-05	0.0016	0.0105086952478378	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.945131591183856
CAMB-78C1E	MN908947.3	11083	G	T	0.03	0.067	1.5e-06	1.7e-14	0.044319857581273	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.945131591183856
CAMB-78C1E	MN908947.3	11916	C	T	0.043	0.034	4.1e-20	1.9e-16	0.0393886724602937	TCA	ORF1ab:nsp7	S25L	C74T	TCA>TTA	Missense	ORF1ab:nsp7	0.960587353910698
CAMB-78C1E	MN908947.3	12924	C	T	0.032	0.027	1.6e-15	1.7e-13	0.0296774447483912	CCT	ORF1ab:nsp9	P80L	C239T	CCT>CTT	Missense	ORF1ab:nsp9	0.970322555251609
CAMB-78C1E	MN908947.3	14408	C	T	1	1	0	0	0.99716682560084	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000511353428141023
CAMB-78C1E	MN908947.3	15763	C	T	0.0091	0.015	5.5e-06	2.4e-08	0.0114955920618276	TCT	ORF1ab:RNA-dependent-RNA-polymerase	L766L	C2296T	CTA>TTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.988387898559167
CAMB-78C1E	MN908947.3	18138	C	T	0.0084	0.0095	7.2e-06	2e-06	0.00889613547298264	TCA	ORF1ab:3'-to-5'-exonuclease	F33F	C99T	TTC>TTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.991075259589805
CAMB-78C1E	MN908947.3	203	C	T	0.029	0.0077	9.9e-14	9.4e-05	0.0199849428512764	TCG	NA	NA	NA	NA	NA	NA	0.979992243287021
CAMB-78C1E	MN908947.3	20956	C	T	0.019	0.023	7e-10	1.5e-11	0.0203862392884803	TCT	ORF1ab:2'-O-ribose-methyltransferase	L100F	C298T	CTT>TTT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.979463861893222
CAMB-78C1E	MN908947.3	2127	A	G	0.005	0.011	9.6e-05	2.3e-07	0.00717318948697349	TAT	ORF1ab:nsp2	Y441C	A1322G	TAT>TGT	Missense	ORF1ab:nsp2	0.992769424997131
CAMB-78C1E	MN908947.3	23403	A	G	1	1	0	0	0.999904134977951	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.26066764662023e-05
CAMB-78C1E	MN908947.3	241	C	-	0.0099	0.011	1.3e-05	2.1e-06	0.0105232322321871	TCG	NA	NA	NA	NA	NA	NA	0.000563342196583893
CAMB-78C1E	MN908947.3	241	C	T	0.99	0.99	0	0	0.988800757131912	TCG	NA	NA	NA	NA	NA	NA	0.000563342196583893
CAMB-78C1E	MN908947.3	25499	C	T	0.0026	0.0078	0.0055	1.9e-05	0.0046667097274254	CCG	ORF3a	P36L	C107T	CCG>CTG	Missense	GU280_gp03	0.995317142488051
CAMB-78C1E	MN908947.3	25521	C	T	0.004	0.0096	0.0034	1e-05	0.00623024417059874	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.991998411898545
CAMB-78C1E	MN908947.3	26122	G	A	0.0098	0.0085	1.2e-05	6.3e-05	0.00924321201617562	TGT	ORF3a	V244I	G730A	GTC>ATC	Missense	GU280_gp03	0.990179087232813
CAMB-78C1E	MN908947.3	26628	CAATTTGCCTATGCCAACAGGAATAGGTT	-	0.0491724137931034	0.0363793103448276	1.1e-21;2.1e-23;1.9e-23;3.9e-26;4.2e-21;2.5e-20;8e-21;2.2e-21;1.2e-20;7e-21;2.2e-21;1.4e-20;1.2e-20;1.4e-20;8.8e-21;8.8e-23;2.7e-23;7.5e-21;2.3e-23;3.2e-21;8.3e-21;6.4e-23;5.6e-31;1.3e-29;4e-24;6.3e-21;5.7e-21;2.6e-29;2e-29	1.5e-16;4.7e-18;4.7e-18;4.1e-19;3.1e-16;7.5e-16;4.2e-16;1.2e-16;4.6e-16;3.4e-16;1.7e-16;6.3e-16;5.2e-16;4.6e-16;3.8e-16;2e-17;4.7e-18;4e-16;1.7e-18;5.9e-16;3.3e-16;1.4e-17;2.9e-24;1.1e-21;5.1e-19;3.1e-16;3.7e-16;1.7e-21;4.2e-22	0.0404480485713884	ACA	M	.	106-134-delfrshift	.	no-SNV	GU280_gp05	0.958953097395566
CAMB-78C1E	MN908947.3	26958	C	T	0.03	0.021	1.4e-14	9.8e-11	0.0264936963274255	TCG	M	R146C	C436T	CGT>TGT	Missense	GU280_gp05	0.97241001279006
CAMB-78C1E	MN908947.3	28253	C	T	0.033	0.046	3.9e-15	6.8e-21	0.0386364282263336	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.960624662517407
CAMB-78C1E	MN908947.3	28377	C	T	1	1	0	0	0.998724884080371	GCG	N	A35V	C104T	GCG>GTG	Missense	GU280_gp10	0.000553838227717671
CAMB-78C1E	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999430880427978	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000373831775700935
CAMB-78C1E	MN908947.3	29085	C	T	0.0031	0.0095	0.0037	4.5e-06	0.00562998708912735	ACA	N	T271I	C812T	ACA>ATA	Missense	GU280_gp10	0.992486295426165
CAMB-78C1E	MN908947.3	29445	C	T	0.083	0.062	5.7e-30	1.6e-24	0.0703928288953335	ACT	N	T391I	C1172T	ACT>ATT	Missense	GU280_gp10	0.929343527550751
CAMB-78C1E	MN908947.3	29754	C	T	0.0092	0.0041	1.3e-05	0.0019	0.00705671028996664	TCG	NA	NA	NA	NA	NA	NA	0.992943289710033
CAMB-78C1E	MN908947.3	29814	A	G	0.01	0.0086	2.4e-06	9e-06	0.00946450809464508	AAA	NA	NA	NA	NA	NA	NA	0.990535491905355
CAMB-78C1E	MN908947.3	3037	C	T	1	1	0	0	0.999614767255217	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000128410914927769
CAMB-78C1E	MN908947.3	3096	C	T	0.026	0.029	1.3e-10	1.4e-11	0.0275843307943417	TCA	ORF1ab:nsp3	S126L	C377T	TCA>TTA	Missense	ORF1ab:nsp3	0.972143634385201
CAMB-78C1E	MN908947.3	597	T	A	0.0097	0.0037	2.4e-06	0.00025	0.00744766923220546	GTG	ORF1ab:leader-protein	V111E	T332A	GTG>GAG	Missense	ORF1ab:leader-protein	0.992386365993818
CAMB-78C1E	MN908947.3	635	C	T	0.039	0.034	2.7e-18	2.8e-16	0.0370508541134891	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.962949145886511
CAMB-78C1E	MN908947.3	683	C	T	0.015	0.0086	3.1e-08	1.9e-05	0.0126385439889561	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.985925438144125
CAMB-78C1E	MN908947.3	8394	C	T	0.054	0.052	1.8e-24	6e-23	0.0534538821476723	GCT	ORF1ab:nsp3	A1892V	C5675T	GCT>GTT	Missense	ORF1ab:nsp3	0.946308192560869
CAMB-78C1E	MN908947.3	8950	C	T	0.0066	0.017	7.2e-05	1.7e-09	0.0108405987826945	TCT	ORF1ab:nsp4	I132I	C396T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.989126501069255
CAMB-78C1E	MN908947.3	9430	C	T	0.015	0.012	1.6e-07	2.4e-06	0.0141291108404385	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.985870889159562
CAMB-78C2D	MN908947.3	10986	G	C	0.0071	0.0067	1.8e-05	2.9e-05	0.00694306685181512	AGA	ORF1ab:nsp6	R5T	G14C	AGA>ACA	Missense	ORF1ab:nsp6	0.993056933148185
CAMB-78C2D	MN908947.3	11075	T	-	0.068	0.056	2.2e-16	4.9e-14	0.0625969855213267	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.933381910429233
CAMB-78C2D	MN908947.3	11506	AGTTACAACTGTCATGTT	-	0.00055	0.0100777777777778	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0096;0.0027	0.00035;0.00029;0.00026;0.00026;5.7e-05;9e-05;8.5e-05;5.8e-05;6.8e-05;5.4e-05;7.1e-05;5.3e-05;4.8e-05;5.3e-05;2.7e-05;6.6e-05;0.00037;2e-05	0.00451612903225806	TAG	ORF1ab:nsp6	.	534-551-delinframe	.	no-SNV	ORF1ab:nsp6	0.994774657086871
CAMB-78C2D	MN908947.3	14408	C	T	1	1	0	0	0.999348681788576	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000523886387449381
CAMB-78C2D	MN908947.3	17835	T	C	1	1	0	0	0.999921365101832	TTG	ORF1ab:helicase	V533V	T1599C	GTT>GTC	Synonymous	ORF1ab:helicase	5.89761736258552e-05
CAMB-78C2D	MN908947.3	18121	AGT	-	0.0031	0.0103333333333333	0.00096;0.0042;0.0034	1e-06;2e-06;8.7e-07	0.00652036103480545	CAG	ORF1ab:3'-to-5'-exonuclease	.	82-84-delinframe	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.993507464919367
CAMB-78C2D	MN908947.3	18154	TG	-	0.00305	0.016	0.0012;0.0011	4.4e-09;3.2e-09	0.00936775295984377	ATG	ORF1ab:3'-to-5'-exonuclease	.	115-116-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.990680138742271
CAMB-78C2D	MN908947.3	19007	C	T	0.0072	0.019	5.7e-05	2.6e-10	0.0125436441225915	GCA	ORF1ab:3'-to-5'-exonuclease	A323V	C968T	GCA>GTA	Missense	ORF1ab:3'-to-5'-exonuclease	0.987391697918014
CAMB-78C2D	MN908947.3	20055	A	G	0.55	0.45	1.8e-139	2.2e-106	0.504283965728274	AAG	ORF1ab:endoRNAse	E145E	A435G	GAA>GAG	Synonymous	ORF1ab:endoRNAse	0.495716034271726
CAMB-78C2D	MN908947.3	20680	G	T	0.0084	0.012	9.8e-06	3.7e-07	0.00980564852328107	GGG	ORF1ab:2'-O-ribose-methyltransferase	G8C	G22T	GGT>TGT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.990018202102049
CAMB-78C2D	MN908947.3	20860	ATACATTTTGGTGCTGGTTCTGATA	-	0.00021532	0.01652	NA;NA;NA;NA;NA;0.0015;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	7.4e-07;3.6e-07;5.5e-07;3.8e-07;3.3e-07;3.2e-10;2.9e-07;2.7e-07;9.9e-09;8.9e-09;7.2e-09;7.2e-09;9.8e-09;5.7e-09;6e-12;5.7e-15;2.3e-15;4.5e-09;6.4e-09;8.7e-09;8.7e-09;9.2e-09;8.1e-09;5.7e-09;1.8e-08	0.00733838340363261	TAT	ORF1ab:2'-O-ribose-methyltransferase	.	202-226-delfrshift	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.994839979717839
CAMB-78C2D	MN908947.3	20973	T	C	0.017	0.022	2.3e-09	1.6e-11	0.0197118863332383	CTG	ORF1ab:2'-O-ribose-methyltransferase	S105S	T315C	TCT>TCC	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.980244260749446
CAMB-78C2D	MN908947.3	21002	G	T	0.0056	0.0083	0.00017	1.2e-05	0.00684776713071777	TGT	ORF1ab:2'-O-ribose-methyltransferase	C115F	G344T	TGT>TTT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.99303923341168
CAMB-78C2D	MN908947.3	23403	A	G	1	1	0	0	0.999886803325924	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.23248538733844e-05
CAMB-78C2D	MN908947.3	241	C	T	1	1	0	0	0.999729102167183	TCG	NA	NA	NA	NA	NA	NA	3.86996904024768e-05
CAMB-78C2D	MN908947.3	25204	G	T	0.01	0.0024	1.9e-06	0.0036	0.00584418572546132	GGT	S	W1214C	G3642T	TGG>TGT	Missense	GU280_gp02, spike glycoprotein	0.994109797064102
CAMB-78C2D	MN908947.3	2531	G	T	0.0091	0.0046	7.8e-06	0.00068	0.00714951818464408	AGT	ORF1ab:nsp2	V576F	G1726T	GTT>TTT	Missense	ORF1ab:nsp2	0.992850481815356
CAMB-78C2D	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0402972972972973	0.0343783783783784	8.6e-05;2.1e-06;4.6e-05;5.5e-05;6.1e-05;1.8e-06;1.7e-05;4.9e-07;4.5e-07;7.2e-08;2.3e-07;1.5e-07;4.4e-07;2.5e-07;3.7e-07;7.1e-07;2.1e-07;5.8e-07;3.1e-07;3.4e-07;2.6e-07;6.6e-07;3.4e-07;4.4e-07;2.9e-07;2e-07;5e-07;2.5e-07;2.6e-07;2.7e-07;5.2e-07;4.3e-07;1.9e-07;5.1e-07;9e-08;2.4e-07;1.6e-07	6.2e-05;5.4e-06;4.3e-05;4.5e-05;9.8e-05;1.2e-05;3.7e-05;7.3e-06;7e-06;5e-06;4.4e-06;3.3e-06;6.1e-06;5.2e-06;6.6e-06;9.5e-06;4.5e-06;8.1e-06;4.8e-06;6e-06;5.8e-06;9.7e-06;6e-06;7e-06;5.3e-06;3.9e-06;7.4e-06;5.3e-06;5.1e-07;5.5e-06;7.9e-06;7.2e-06;3.4e-06;8.3e-06;1.3e-06;4.6e-06;2.5e-06	0.0389172224401726	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.972494471414925
CAMB-78C2D	MN908947.3	2871	A	C	0.028	0.015	5e-14	1.1e-08	0.021875	AAT	ORF1ab:nsp3	N51T	A152C	AAT>ACT	Missense	ORF1ab:nsp3	0.978053977272727
CAMB-78C2D	MN908947.3	3037	C	T	1	1	0	0	0.999731855559528	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78C2D	MN908947.3	3838	G	T	0.0082	0.0091	8.7e-06	5.4e-06	0.00846200820029661	TGG	ORF1ab:nsp3	L373F	G1119T	TTG>TTT	Missense	ORF1ab:nsp3	0.991537991799703
CAMB-78C2D	MN908947.3	5158	T	C	0.0077	0.016	0.0041	1.5e-05	0.0124113475177305	CTT	ORF1ab:nsp3	A813A	T2439C	GCT>GCC	Synonymous	ORF1ab:nsp3	0.987588652482269
CAMB-78C2D	MN908947.3	522	T	-	0.042	0.025	1.6e-05	0.0017	0.0344364012409514	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.965425715270596
CAMB-78C2D	MN908947.3	5387	G	T	0.0083	0.011	2.1e-05	3.4e-06	0.00947867298578199	TGC	ORF1ab:nsp3	A890S	G2668T	GCT>TCT	Missense	ORF1ab:nsp3	0.989963758015054
CAMB-78C2D	MN908947.3	5825	A	-	0.0039	0.01	0.0073	3.7e-05	0.0068673233135816	TAC	ORF1ab:nsp3	.	3106-3106-delfrshift	.	no-SNV	ORF1ab:nsp3	0.992975709296394
CAMB-78C2D	MN908947.3	6308	A	C	0.019	0.0066	3.4e-10	1.2e-05	0.0148501545491197	GAG	ORF1ab:nsp3	S1197R	A3589C	AGC>CGC	Missense	ORF1ab:nsp3	0.984881064373068
CAMB-78C2D	MN908947.3	6308	AG	CA	0.0144	0.0033335	3.4e-10;2.7e-06	1.2e-05;NA	0.0106871597248673	GAG	ORF1ab:nsp3	.	3589-3590-mnv	.	no-SNV	ORF1ab:nsp3	0.984881064373068
CAMB-78C2D	MN908947.3	7432	ATTT	-	0.00355	0.01775	NA;NA;NA;0.0018	1.1e-07;1.8e-06;1e-04;0.00053	0.00779407240283048	CAT	ORF1ab:nsp3	.	4713-4716-delfrshift	.	no-SNV	ORF1ab:nsp3	0.992654073650067
CAMB-78C4B	MN908947.3	11075	T	-	0.038	0.035	1e-09	1.7e-09	0.0369968851157393	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959445428449276
CAMB-78C4B	MN908947.3	14408	C	T	1	1	0	0	0.998388096714197	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000551078046428325
CAMB-78C4B	MN908947.3	18570	C	A	0.89	0.88	0	0	0.883367188624622	TCT	ORF1ab:3'-to-5'-exonuclease	L177L	C531A	CTC>CTA	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.116568832872155
CAMB-78C4B	MN908947.3	19596	C	A	0.027	0.031	4e-13	5e-15	0.0287226001511716	TCT	ORF1ab:3'-to-5'-exonuclease	L519L	C1557A	CTC>CTA	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.971201814058957
CAMB-78C4B	MN908947.3	23403	A	G	1	1	0	0	0.999469970172831	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.27491919643321e-05
CAMB-78C4B	MN908947.3	241	C	T	1	1	0	0	0.998660075687617	TCG	NA	NA	NA	NA	NA	NA	9.05354265123943e-05
CAMB-78C4B	MN908947.3	27213	C	T	0.01	0.0088	6.4e-06	2.6e-05	0.00967380959851076	TCG	ORF6	L4L	C12T	CTC>CTT	Synonymous	GU280_gp06	0.989259456802518
CAMB-78C4B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99899481945411	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	8.56567733093494e-05
CAMB-78C4B	MN908947.3	29148	T	C	1	1	0	0	0.999665522401197	ATC	N	I292T	T875C	ATC>ACC	Missense	GU280_gp10	8.80204207376111e-05
CAMB-78C4B	MN908947.3	3037	C	T	1	1	0	0	0.999686598972045	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78C5A	MN908947.3	10066	A	-	0.0062	0.0099	0.00062	1.8e-05	0.00778779716594449	GAA	ORF1ab:3C-like-proteinase	.	12-12-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.992095093102237
CAMB-78C5A	MN908947.3	10636	TGG	-	0.00670333333333333	0.01	NA;1.5e-08;NA	7.6e-06;4.1e-05;2.9e-06	0.00411604594038372	CTG	ORF1ab:3C-like-proteinase	.	582-584-delinframe	.	no-SNV	ORF1ab:3C-like-proteinase	0.995656531907785
CAMB-78C5A	MN908947.3	11075	T	-	0.087	0.049	6.7e-21	1.6e-12	0.0718169460806525	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.923395257513971
CAMB-78C5A	MN908947.3	11562	G	T	0.0079	0.013	9.2e-05	5.5e-06	0.00992829564258136	TGC	ORF1ab:nsp6	C197F	G590T	TGC>TTC	Missense	ORF1ab:nsp6	0.985107556536128
CAMB-78C5A	MN908947.3	11903	AGAGTAGA	GAGAGTAG	0.00098875	0.0085	NA;0.44;0.45;0.45;0.44;0.44;4.4e-05;0.45	9.6e-06;9.3e-06;1.6e-05;1.2e-05;9.6e-06;6.7e-06;9.3e-06;1.4e-05	0.00319869691461486	CAG	ORF1ab:nsp7	.	61-68-mnv	.	no-SNV	ORF1ab:nsp7	0.993716931216931
CAMB-78C5A	MN908947.3	12733	C	T	0.091	0.079	1.1e-41	1.2e-36	0.0864676110204633	CCG	ORF1ab:nsp9	A16A	C48T	GCC>GCT	Synonymous	ORF1ab:nsp9	0.913511603496118
CAMB-78C5A	MN908947.3	14118	G	-	0.0059	0.0065	6.1e-05	2.7e-05	0.00615279094631942	CGC	ORF1ab:RNA-dependent-RNA-polymerase	.	651-651-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.988481168425087
CAMB-78C5A	MN908947.3	14408	C	T	0.99	1	0	0	0.995332108968473	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000248699112335476
CAMB-78C5A	MN908947.3	15858	T	A	0.0077	0.0072	1.3e-05	1e-05	0.00748953540664891	CTA	ORF1ab:RNA-dependent-RNA-polymerase	T797T	T2391A	ACT>ACA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.992475870896323
CAMB-78C5A	MN908947.3	16975	G	T	0.014	0.0067	6e-08	6.5e-05	0.0108850665036817	TGT	ORF1ab:helicase	V247F	G739T	GTT>TTT	Missense	ORF1ab:helicase	0.989027620128642
CAMB-78C5A	MN908947.3	17060	AA	-	0.012	0.0035	1.3e-06;1.4e-07	0.00021;NA	0.00868013952126102	CAA	ORF1ab:helicase	.	824-825-delfrshift	.	no-SNV	ORF1ab:helicase	0.989757641863311
CAMB-78C5A	MN908947.3	17081	G	T	0.0062	0.0066	7.2e-05	4.2e-05	0.0063758389261745	GGA	ORF1ab:helicase	G282V	G845T	GGA>GTA	Missense	ORF1ab:helicase	0.993572534847703
CAMB-78C5A	MN908947.3	18984	G	T	0.12	0.074	7.1e-57	4.7e-33	0.110515764534354	TGG	ORF1ab:3'-to-5'-exonuclease	M315I	G945T	ATG>ATT	Missense	ORF1ab:3'-to-5'-exonuclease	0.889374886094405
CAMB-78C5A	MN908947.3	19738	G	T	0.11	0.031	4.4e-49	3.5e-14	0.0818417080008626	TGT	ORF1ab:endoRNAse	V40L	G118T	GTA>TTA	Missense	ORF1ab:endoRNAse	0.918158291999137
CAMB-78C5A	MN908947.3	23066	G	-	0.0084	0.017	6.1e-06	3.2e-09	0.011150234741784	TGG	S	.	1504-1504-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.985426447574335
CAMB-78C5A	MN908947.3	23066	GG	-	0.0083	0.0085	6.1e-06;7.9e-06	3.2e-09;NA	0.00833010461061604	TGG	S	.	1504-1505-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.985426447574335
CAMB-78C5A	MN908947.3	23335	T	C	0.01	0.008	4.1e-05	0.00036	0.00940788008228619	CTT	S	S591S	T1773C	TCT>TCC	Synonymous	GU280_gp02, spike glycoprotein	0.990461090947208
CAMB-78C5A	MN908947.3	23403	A	G	1	1	0	0	0.99990548315828	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.54438156449002e-05
CAMB-78C5A	MN908947.3	23468	TATTCTACAGGTTC	-	0.000621428571428571	0.00935	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00012	2.1e-05;2.1e-06;3.6e-06;4.4e-06;3.5e-06;4.7e-06;4.4e-06;5e-06;5.6e-06;7.1e-06;6.5e-06;6.8e-06;2.8e-05;5.3e-05	0.00344294402638903	TTA	S	.	1906-1919-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.996569158540989
CAMB-78C5A	MN908947.3	241	C	T	1	0.98	0	0	0.991325031481741	TCG	NA	NA	NA	NA	NA	NA	0.000186558462758267
CAMB-78C5A	MN908947.3	2418	G	-	0.013	0.019	6.4e-06	2.5e-07	0.0154189490768919	AGA	ORF1ab:nsp2	.	1613-1613-delfrshift	.	no-SNV	ORF1ab:nsp2	0.984378170014202
CAMB-78C5A	MN908947.3	24381	C	T	0.018	0.02	1.3e-09	1.1e-10	0.0186577554998608	TCC	S	S940F	C2819T	TCC>TTC	Missense	GU280_gp02, spike glycoprotein	0.981342244500139
CAMB-78C5A	MN908947.3	25429	G	T	1	1	0	0	0.999864595624504	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	7.73739288546724e-05
CAMB-78C5A	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.026459375	0.02615625	0.049;0.093;0.0059;0.006;0.0023;0.0041;0.0034;0.006;6.3e-05;8.2e-05;0.00015;5.6e-05;0.00013;8.5e-05;8.8e-05;8.8e-05;0.00014;8.6e-05;0.00011;7.9e-05;5.9e-05;0.00012;6.9e-05;5.5e-05;6.4e-05;0.00012;1.3e-06;5.7e-07;1.5e-06;3.7e-05;0.0043;0.0039	2.8e-05;9.5e-05;0.00035;0.00033;0.00021;0.00024;2e-04;0.00029;0.00027;0.00032;0.00043;0.00024;0.00037;0.00022;3e-04;0.00033;0.00043;0.00031;0.00033;0.00026;0.00022;0.00035;0.00027;3e-05;0.00029;0.00036;0.00034;0.00021;4e-04;0.00011;0.00023;0.00016	0.0273319561417448	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.979502701824239
CAMB-78C5A	MN908947.3	29091	C	T	0.0068	0.0036	3.7e-05	0.00099	0.00570916825254674	GCT	N	A273V	C818T	GCT>GTT	Missense	GU280_gp10	0.994290831747453
CAMB-78C5A	MN908947.3	29736	G	C	0.011	0.0042	1.1e-06	0.00082	0.00880626223091976	AGG	NA	NA	NA	NA	NA	NA	0.989481409001957
CAMB-78C5A	MN908947.3	3037	C	T	1	1	0	0	0.999738857938719	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.70473537604457e-05
CAMB-78C5A	MN908947.3	3334	TGAAGTGAA	-	0.0427777777777778	0.0234444444444444	8.4e-09;7.6e-09;1.6e-08;2e-08;4.7e-08;5.6e-08;8.5e-08;7.4e-08;7.2e-09	5.1e-06;6e-06;1.1e-05;8.3e-06;1.4e-05;1.4e-05;1.8e-05;1.9e-05;5.1e-06	0.0354733474804421	TTG	ORF1ab:nsp3	.	615-623-delinframe	.	no-SNV	ORF1ab:nsp3	0.964202152550304
CAMB-78C5A	MN908947.3	4320	C	T	0.044	0.12	6.5e-21	6.7e-57	0.0744124688522988	GCC	ORF1ab:nsp3	A534V	C1601T	GCC>GTC	Missense	ORF1ab:nsp3	0.925587531147701
CAMB-78C5A	MN908947.3	7620	GTGTTA	-	0.003995	0.011	NA;NA;NA;0.00018;0.00029;0.001	3.3e-06;2e-06;5.2e-06;1.5e-05;2.8e-05;0.00013	0.00652476200663173	TGT	ORF1ab:nsp3	.	4901-4906-delinframe	.	no-SNV	ORF1ab:nsp3	0.996016365202412
CAMB-78C5A	MN908947.3	837	G	-	0.0073	0.012	0.00013	1.2e-06	0.00910611410518491	TGT	ORF1ab:nsp2	.	32-32-delfrshift	.	no-SNV	ORF1ab:nsp2	0.990811290755539
CAMB-78C5A	MN908947.3	9332	G	T	0.013	0.0071	3.7e-07	0.00013	0.0107658429165647	TGC	ORF1ab:nsp4	A260S	G778T	GCT>TCT	Missense	ORF1ab:nsp4	0.989111817959383
CAMB-78C69	MN908947.3	14408	C	T	1	1	0	0	0.999253048045877	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000602380608163462
CAMB-78C69	MN908947.3	17354	TTGATGAAA	-	0.0244444444444444	0.00422222222222222	1.4e-08;6.1e-08;2.7e-08;3.7e-08;5.4e-09;1.3e-08;4.1e-08;3.1e-09;2.1e-08	NA;NA;NA;NA;NA;NA;0.00012;3e-05;8.1e-05	0.015553927193795	TTT	ORF1ab:helicase	.	1118-1126-delinframe	.	no-SNV	ORF1ab:helicase	0.984404595667022
CAMB-78C69	MN908947.3	23403	A	G	1	1	0	0	0.999881602159577	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.55193521270172e-05
CAMB-78C69	MN908947.3	241	C	T	1	1	0	0	0.999707495429616	TCG	NA	NA	NA	NA	NA	NA	0.000182815356489945
CAMB-78C69	MN908947.3	29734	G	C	1	1	0	0	1	CGA	NA	NA	NA	NA	NA	NA	0
CAMB-78C69	MN908947.3	3037	C	T	1	1	0	0	0.999708921554359	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.0002910784456411
CAMB-78C69	MN908947.3	522	TT	-	0.02	0.06	0.0066;0.0065	2.9e-08;1.6e-08	0.0338463352792028	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.964617909903338
CAMB-78C69	MN908947.3	6504	C	T	0.97	1	0	0	0.979463856953193	GCA	ORF1ab:nsp3	A1262V	C3785T	GCA>GTA	Missense	ORF1ab:nsp3	0
CAMB-78C69	MN908947.3	6847	G	A	0.045	0.04	3.2e-10	3.9e-07	0.0432432432432432	TGC	ORF1ab:nsp3	M1376I	G4128A	ATG>ATA	Missense	ORF1ab:nsp3	0.956756756756757
CAMB-78C78	MN908947.3	14408	C	T	1	1	0	0	0.999363723128664	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000318138435667863
CAMB-78C78	MN908947.3	14786	C	T	1	1	0	0	0.999764871855161	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A440V	C1319T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000141076886903362
CAMB-78C78	MN908947.3	20578	G	T	1	1	2.40000000001213e-313	6.8e-169	1	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	0
CAMB-78C78	MN908947.3	23403	A	G	1	1	0	0	0.999883371043363	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.33031653098831e-05
CAMB-78C78	MN908947.3	241	C	T	1	1	0	0	1	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-78C78	MN908947.3	2416	C	T	1	1	0	6.3e-128	1	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0
CAMB-78C78	MN908947.3	25563	G	T	1	1	0	0	0.999801718440185	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000132187706543291
CAMB-78C78	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78C87	MN908947.3	11074	C	INS	0.11	0.11	3.2e-34	2.3e-34	0.108376441114384	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.886937762416201
CAMB-78C87	MN908947.3	11083	G	-	0.18	0.17	4e-82	6.7e-75	0.174463059708961	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.00164134590364e-05
CAMB-78C87	MN908947.3	11083	G	T	0.82	0.83	0	0	0.825396825396825	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.00164134590364e-05
CAMB-78C87	MN908947.3	14805	C	T	1	1	0	0	0.998845846189007	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000365672494572049
CAMB-78C87	MN908947.3	21709	T	C	1	1	0	0	0.999808607861432	ATT	S	H49H	T147C	CAT>CAC	Synonymous	GU280_gp02, spike glycoprotein	0.00016746812124692
CAMB-78C87	MN908947.3	23942	A	G	0.048	0.051	1.8e-22	1.5e-23	0.0495547361210302	AAT	S	I794V	A2380G	ATT>GTT	Missense	GU280_gp02, spike glycoprotein	0.95034323942225
CAMB-78C87	MN908947.3	2480	A	G	1	1	0	0	0.999790958975699	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000156780768225764
CAMB-78C87	MN908947.3	2558	C	T	1	1	0	0	0.999174031551995	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000123895267200793
CAMB-78C87	MN908947.3	26144	G	T	1	1	0	0	0.99929940449382	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000350297753090127
CAMB-78C87	MN908947.3	26151	C	A	0.011	0.014	1.7e-06	1.6e-07	0.0123354123354123	CCG	ORF3a	S253S	C759A	TCC>TCA	Synonymous	GU280_gp03	0.987525987525988
CAMB-78C87	MN908947.3	26301	T	A	0.027	0.027	4e-13	7.1e-13	0.0270307516635823	TTT	E	L19L	T57A	CTT>CTA	Synonymous	GU280_gp04	0.972418002126235
CAMB-78C87	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.02840625	0.026125	0.00036;7e-04;0.00012;0.00012;3.4e-05;6.8e-05;5.1e-05;0.00011;6.9e-05;7.9e-05;0.00015;5e-05;0.00014;9.6e-05;9.1e-05;6.4e-05;0.00015;7.3e-05;1e-04;8.4e-05;5.6e-05;0.00012;7.5e-05;5.7e-05;7.1e-05;0.00013;8.7e-05;4e-05;0.00011;5.2e-05;7.8e-05;6.2e-05	0.00045;0.00098;0.00031;3e-04;0.00023;2e-04;0.00017;0.00025;0.00022;0.00026;0.00035;0.00019;3e-04;0.00022;0.00025;2e-04;0.00037;0.00022;0.00027;0.00023;0.00016;0.00029;0.00024;0.00011;0.00021;0.00031;0.00027;0.00016;0.00032;0.00012;0.00022;0.00013	0.0270393331231831	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.974820219743141
CAMB-78C87	MN908947.3	313	C	T	0.013	0.014	2.2e-07	7.2e-08	0.0134692391700036	TCA	ORF1ab:leader-protein	L16L	C48T	CTC>CTT	Synonymous	ORF1ab:leader-protein	0.986435795571453
CAMB-78C87	MN908947.3	6546	A	G	0.01	0.0091	3.3e-06	7.7e-06	0.009560071183214	GAT	ORF1ab:nsp3	D1276G	A3827G	GAT>GGT	Missense	ORF1ab:nsp3	0.990398543227248
CAMB-78C87	MN908947.3	8735	G	A	0.012	0.011	3.6e-07	9.8e-07	0.0116028450319707	AGA	ORF1ab:nsp4	D61N	G181A	GAT>AAT	Missense	ORF1ab:nsp4	0.988199583303398
CAMB-78C96	MN908947.3	11075	T	-	0.052	0.032	8.7e-13	2.1e-08	0.0433537584177638	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955724079354486
CAMB-78C96	MN908947.3	11515	T	A	0.013	0.011	1.5e-07	5.6e-07	0.0122373300370828	CTG	ORF1ab:nsp6	T181T	T543A	ACT>ACA	Synonymous	ORF1ab:nsp6	0.987515451174289
CAMB-78C96	MN908947.3	11824	C	T	0.069	0.068	1e-21	1.3e-21	0.0680722891566265	TCA	ORF1ab:nsp6	I284I	C852T	ATC>ATT	Synonymous	ORF1ab:nsp6	0.931927710843373
CAMB-78C96	MN908947.3	127	G	T	0.0034	0.0093	0.00093	2.7e-06	0.00599739647904786	AGT	NA	NA	NA	NA	NA	NA	0.993878626332755
CAMB-78C96	MN908947.3	1419	C	T	0.021	0.027	1e-09	5.5e-12	0.0241207594148771	GCC	ORF1ab:nsp2	A205V	C614T	GCC>GTC	Missense	ORF1ab:nsp2	0.975879240585123
CAMB-78C96	MN908947.3	14408	C	T	1	1	0	0	0.997080400331548	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00164536760976334
CAMB-78C96	MN908947.3	1583	G	A	0.069	0.11	2.6e-28	4.4e-47	0.0935028248587571	TGG	ORF1ab:nsp2	G260R	G778A	GGA>AGA	Missense	ORF1ab:nsp2	0.90635593220339
CAMB-78C96	MN908947.3	16968	G	A	0.023	0.027	1e-11	8.9e-14	0.0248733881685284	AGC	ORF1ab:helicase	E244E	G732A	GAG>GAA	Synonymous	ORF1ab:helicase	0.975036816206314
CAMB-78C96	MN908947.3	17072	C	T	0.027	0.017	1.8e-13	2.9e-09	0.0226011982121913	ACA	ORF1ab:helicase	T279I	C836T	ACA>ATA	Missense	ORF1ab:helicase	0.977398801787809
CAMB-78C96	MN908947.3	17795	C	T	0.017	0.031	4.1e-09	5.1e-15	0.0233692742983865	GCT	ORF1ab:helicase	A520V	C1559T	GCT>GTT	Missense	ORF1ab:helicase	0.976584843618567
CAMB-78C96	MN908947.3	188	G	T	0.01	0.0045	1.8e-06	0.00068	0.00773704434520719	AGG	NA	NA	NA	NA	NA	NA	0.992245646830754
CAMB-78C96	MN908947.3	19269	C	T	0.019	0.0094	3e-10	4.9e-06	0.0154067674586033	ACT	ORF1ab:3'-to-5'-exonuclease	N410N	C1230T	AAC>AAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.984569234461243
CAMB-78C96	MN908947.3	23403	A	G	1	1	0	0	0.999961259079903	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.90556900726392e-05
CAMB-78C96	MN908947.3	241	C	T	1	1	0	0	0.998539067065415	TCG	NA	NA	NA	NA	NA	NA	8.59372314461517e-05
CAMB-78C96	MN908947.3	25459	G	T	0.021	0.018	8.9e-11	1.6e-09	0.0196778730797871	TGC	ORF3a	A23S	G67T	GCT>TCT	Missense	GU280_gp03	0.980253178521195
CAMB-78C96	MN908947.3	26213	C	T	0.032	0.024	8.8e-14	1.1e-10	0.0286633518572682	CCT	ORF3a	P274L	C821T	CCT>CTT	Missense	GU280_gp03	0.971336648142732
CAMB-78C96	MN908947.3	28812	G	T	0.015	0.014	3.4e-08	5.6e-08	0.0144332186077495	AGT	N	S180I	G539T	AGT>ATT	Missense	GU280_gp10	0.985307723622368
CAMB-78C96	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999191970740835	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.74045982460299e-05
CAMB-78C96	MN908947.3	29421	C	T	0.027	0.025	6.1e-12	5.6e-11	0.0258667388949079	CCG	N	P383L	C1148T	CCG>CTG	Missense	GU280_gp10	0.974133261105092
CAMB-78C96	MN908947.3	29700	A	G	0.011	0.021	2.9e-06	3e-10	0.0154808444096951	TAG	NA	NA	NA	NA	NA	NA	0.984440969507428
CAMB-78C96	MN908947.3	3037	C	T	1	1	0	0	0.999637894355678	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78C96	MN908947.3	4331	C	T	0.0066	0.0069	5.3e-05	3.6e-05	0.0067289190050644	TCT	ORF1ab:nsp3	L538L	C1612T	CTA>TTA	Synonymous	ORF1ab:nsp3	0.99322386051069
CAMB-78C96	MN908947.3	843	C	T	0.029	0.025	2.2e-14	1.2e-12	0.0274697374240364	CCT	ORF1ab:nsp2	P13L	C38T	CCT>CTT	Missense	ORF1ab:nsp2	0.972448361152517
CAMB-78C96	MN908947.3	8606	C	INS	0.021	0.028	9e-11	1.7e-13	0.0238684228120612	CCT	ORF1ab:nsp4	.	51-52-insfrshift	.	no-SNV	ORF1ab:nsp4	0.975195560607074
CAMB-78C96	MN908947.3	8612	G	-	0.031	0.044	9.1e-15	4.6e-20	0.0364137931034483	TGT	ORF1ab:nsp4	.	58-58-delfrshift	.	no-SNV	ORF1ab:nsp4	0.000206896551724138
CAMB-78C96	MN908947.3	8612	G	T	0.97	0.96	0	0	0.963379310344828	TGT	ORF1ab:nsp4	V20F	G58T	GTT>TTT	Missense	ORF1ab:nsp4	0.000206896551724138
CAMB-78CA5	MN908947.3	11075	T	-	0.043	0.038	9e-11	7.1e-10	0.0411981761482936	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955571568785797
CAMB-78CA5	MN908947.3	11455	C	T	1	1	0	0	0.999692906131641	CCA	ORF1ab:nsp6	A161A	C483T	GCC>GCT	Synonymous	ORF1ab:nsp6	0.000307093868359095
CAMB-78CA5	MN908947.3	14408	C	T	1	1	0	0	0.998040925543225	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000621169949709125
CAMB-78CA5	MN908947.3	23403	A	G	1	1	0	0	0.99948462621596	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.28279295778537e-05
CAMB-78CA5	MN908947.3	241	C	T	1	1	0	0	0.997779736280126	TCG	NA	NA	NA	NA	NA	NA	6.77943120572184e-05
CAMB-78CA5	MN908947.3	27634	T	C	0.93	0.87	7.3e-297	5.3e-177	0.906896551724138	ATC	ORF7a	S81P	T241C	TCA>CCA	Missense	GU280_gp07	0.0931034482758621
CAMB-78CA5	MN908947.3	27760	TTGAAC	-	0.0768333333333333	0.034	3.7e-19;4e-19;2.1e-19;4.3e-19;2e-19;1.1e-19	2.4e-07;2.3e-07;1.3e-07;1.3e-07;1.1e-07;9.7e-08	0.0630914826498423	ATT	NA	NA	NA	NA	NA	NA	0.936305732484076
CAMB-78CA5	MN908947.3	28378	G	C	0.0066	0.0095	8.4e-05	4.1e-06	0.00789540708039732	CGC	N	A35A	G105C	GCG>GCC	Synonymous	GU280_gp10	0.990455168398967
CAMB-78CA5	MN908947.3	28516	T	C	0.028	0.028	1.1e-13	9.7e-14	0.0283048319400604	ATG	N	D81D	T243C	GAT>GAC	Synonymous	GU280_gp10	0.971591106177807
CAMB-78CA5	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999202097344124	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000126002772060985
CAMB-78CA5	MN908947.3	3037	C	T	1	1	0	0	0.998029427220179	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000558328954282712
CAMB-78CA5	MN908947.3	4534	C	T	0.0058	0.008	9.8e-05	9.6e-06	0.00673050750995967	ACT	ORF1ab:nsp3	Y605Y	C1815T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.991388909509316
CAMB-78CA5	MN908947.3	5830	G	T	0.0048	0.01	0.00023	1.2e-06	0.00712921705919796	AGT	ORF1ab:nsp3	K1037N	G3111T	AAG>AAT	Missense	ORF1ab:nsp3	0.992870782940802
CAMB-78CA5	MN908947.3	7851	C	T	0.012	0.011	5.7e-07	2.7e-06	0.0114578879863189	GCT	ORF1ab:nsp3	A1711V	C5132T	GCT>GTT	Missense	ORF1ab:nsp3	0.988542112013681
CAMB-78CA5	MN908947.3	851	T	C	0.013	0.014	1.4e-07	5.3e-08	0.0136745722005404	CTA	ORF1ab:nsp2	Y16H	T46C	TAC>CAC	Missense	ORF1ab:nsp2	0.985920144100871
CAMB-78CB4	MN908947.3	10030	C	T	0.006	0.0066	8.3e-05	3.9e-05	0.00623941527765398	CCT	ORF1ab:nsp4	T492T	C1476T	ACC>ACT	Synonymous	ORF1ab:nsp4	0.993716017470363
CAMB-78CB4	MN908947.3	11075	T	-	0.053	0.029	5e-13	7.7e-08	0.0423882946956947	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.940319778489603
CAMB-78CB4	MN908947.3	11195	C	T	1	1	0	0	0.999588340537374	TCT	ORF1ab:nsp6	L75F	C223T	CTT>TTT	Missense	ORF1ab:nsp6	6.33322250193955e-05
CAMB-78CB4	MN908947.3	14408	C	T	1	1	0	0	0.999335029489997	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000534867584133225
CAMB-78CB4	MN908947.3	14709	T	C	0.0096	0.0088	5.3e-06	1.1e-05	0.00924805806698077	CTG	ORF1ab:RNA-dependent-RNA-polymerase	A414A	T1242C	GCT>GCC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.988109639628168
CAMB-78CB4	MN908947.3	15017	C	T	0.01	0.016	1.4e-05	5.6e-08	0.0129333768068688	GCA	ORF1ab:RNA-dependent-RNA-polymerase	A517V	C1550T	GCA>GTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.987066623193131
CAMB-78CB4	MN908947.3	16343	C	T	0.0071	0.01	3.1e-05	1.6e-06	0.00865521250484434	TCA	ORF1ab:helicase	S36L	C107T	TCA>TTA	Missense	ORF1ab:helicase	0.991344787495156
CAMB-78CB4	MN908947.3	16343	CA	TG	0.01005	0.005135	3.1e-05;2.6e-07	1.6e-06;NA	0.00767130412170069	TCA	ORF1ab:helicase	.	107-108-mnv	.	no-SNV	ORF1ab:helicase	0.991344787495156
CAMB-78CB4	MN908947.3	16465	C	T	0.058	0.053	1.9e-25	2.3e-23	0.0552740672501152	ACC	ORF1ab:helicase	P77S	C229T	CCA>TCA	Missense	ORF1ab:helicase	0.944725932749885
CAMB-78CB4	MN908947.3	1782	G	-	0.0079	0.0037	3.9e-05	0.003	0.00606221123569053	TGT	ORF1ab:nsp2	.	977-977-delfrshift	.	no-SNV	ORF1ab:nsp2	0.993937788764309
CAMB-78CB4	MN908947.3	18162	CATACCTGG	-	0.00796666666666667	0.00344444444444444	0.00022;3.1e-06;2.7e-06;3.5e-06;0.00022;8.5e-05;2.9e-06;3.5e-06;2.9e-06	0.00065;0.00069;0.00073;0.00078;0.00085;0.00052;0.00072;0.00087;0.00065	0.00697796287613426	ACA	ORF1ab:3'-to-5'-exonuclease	.	123-131-delinframe	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.995787744721435
CAMB-78CB4	MN908947.3	18807	C	T	0.061	0.12	7.7e-28	8e-55	0.0873810006076565	ACC	ORF1ab:3'-to-5'-exonuclease	N256N	C768T	AAC>AAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.912551482006617
CAMB-78CB4	MN908947.3	21883	TACTACTT	-	0.021125	0.0046125	3e-04;0.00043;8.8e-06;1.4e-07;7e-07;7.9e-05;8.5e-05;6e-05	NA;NA;NA;0.0033;0.0056;0.038;0.051;0.035	0.0154643415316279	GTA	S	.	321-328-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.992673088005269
CAMB-78CB4	MN908947.3	23403	A	G	1	1	0	0	0.999954043695255	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.75737828472688e-05
CAMB-78CB4	MN908947.3	241	C	T	1	1	0	0	0.999670797375785	TCG	NA	NA	NA	NA	NA	NA	0.000141086838949373
CAMB-78CB4	MN908947.3	26078	C	T	1	1	0	0	1	ACC	ORF3a	T229I	C686T	ACC>ATC	Missense	GU280_gp03	0
CAMB-78CB4	MN908947.3	26305	C	T	0.079	0.051	7.7e-36	1.1e-23	0.0678602921443086	TCT	E	L21F	C61T	CTT>TTT	Missense	GU280_gp04	0.931526281486025
CAMB-78CB4	MN908947.3	27920	C	T	0.039	0.034	2.4e-17	1.6e-14	0.0372719037142487	TCA	ORF8	I9I	C27T	ATC>ATT	Synonymous	GU280_gp09	0.962728096285751
CAMB-78CB4	MN908947.3	28253	C	T	0.0098	0.0094	2.4e-05	3.3e-05	0.0096476950540796	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.990102908747243
CAMB-78CB4	MN908947.3	28278	C	T	0.057	0.031	1.6e-26	1.9e-15	0.0451733510435499	TCT	N	S2F	C5T	TCT>TTT	Missense	GU280_gp10	0.954789752671906
CAMB-78CB4	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999331606650514	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	9.25840199981483e-05
CAMB-78CB4	MN908947.3	3037	C	T	1	1	0	0	0.998936382370538	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.6476101841388e-05
CAMB-78CB4	MN908947.3	3373	C	A	1	1	0	0	0.999902990323285	ACA	ORF1ab:nsp3	D218E	C654A	GAC>GAA	Missense	ORF1ab:nsp3	0
CAMB-78CB4	MN908947.3	9803	C	T	0.019	0.0054	7.5e-10	0.00058	0.0131250349963604	GCT	ORF1ab:nsp4	L417L	C1249T	CTG>TTG	Synonymous	ORF1ab:nsp4	0.986796573156392
CAMB-78CC3	MN908947.3	11074	C	INS	0.24	0.02	3.2e-107	0.00031	0.215223922308391	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.784147278697687
CAMB-78CC3	MN908947.3	11083	G	-	0.3	0.53	9e-146	4.4e-281	0.334559844487642	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-78CC3	MN908947.3	11083	G	T	0.7	0.47	5.2e-248	3.5e-125	0.665093029713968	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-78CC3	MN908947.3	14805	C	T	0.96	1	0	0	0.97027447494166	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000111123458162018
CAMB-78CC3	MN908947.3	19007	C	T	0.096	0.055	5e-39	2.5e-22	0.0774663429706467	GCA	ORF1ab:3'-to-5'-exonuclease	A323V	C968T	GCA>GTA	Missense	ORF1ab:3'-to-5'-exonuclease	0.922533657029353
CAMB-78CC3	MN908947.3	21709	T	C	1	1	0	0	1	ATT	S	H49H	T147C	CAT>CAC	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-78CC3	MN908947.3	2480	A	G	1	1	0	3.8043054729776e-322	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-78CC3	MN908947.3	24909	C	T	0.074	0.25	8.9e-34	6.9e-119	0.135709644481574	ACT	S	T1116I	C3347T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.864290355518426
CAMB-78CC3	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-78CC3	MN908947.3	29769	C	T	0.021	0.022	1.6e-09	2.3e-06	0.0214341387373344	ACA	NA	NA	NA	NA	NA	NA	0.97817614964926
CAMB-78CE1	MN908947.3	11074	C	INS	0.11	0.16	6.2e-44	7.7e-55	0.128851001597167	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.86112340523794
CAMB-78CE1	MN908947.3	11083	G	-	0.11	0.15	1.7e-45	3.1e-65	0.117739484771048	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.72663858001243e-05
CAMB-78CE1	MN908947.3	11083	G	T	0.89	0.85	0	0	0.882036052213551	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.72663858001243e-05
CAMB-78CE1	MN908947.3	1136	A	-	0.006	0.024	0.0011	2.7e-11	0.0121839314845024	GAA	ORF1ab:nsp2	.	331-331-delfrshift	.	no-SNV	ORF1ab:nsp2	0.987586663947798
CAMB-78CE1	MN908947.3	13459	G	INS	0.013	0.013	3.3e-06	3.3e-06	0.0129418582190458	CGT	ORF1ab:nsp11	.	17-18-insfrshift	.	no-SNV	ORF1ab:nsp11	0.987058141780954
CAMB-78CE1	MN908947.3	14805	C	T	1	1	0	0	0.999905228990452	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	7.10782571611344e-05
CAMB-78CE1	MN908947.3	15941	C	T	0.024	0.013	1.3e-12	2.5e-08	0.0210891617725574	CCA	ORF1ab:RNA-dependent-RNA-polymerase	P825L	C2474T	CCA>CTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.965994496693909
CAMB-78CE1	MN908947.3	16156	A	G	0.0013	0.034	0.0078	2.6e-17	0.010546011226399	TAT	ORF1ab:RNA-dependent-RNA-polymerase	M897V	A2689G	ATG>GTG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.989378390126817
CAMB-78CE1	MN908947.3	17074	C	T	0.0078	0.017	1.7e-05	1.6e-09	0.0105843301809983	ACT	ORF1ab:helicase	L280F	C838T	CTC>TTC	Missense	ORF1ab:helicase	0.989415669819002
CAMB-78CE1	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-78CE1	MN908947.3	2558	C	T	1	1	0	0	0.99966078697422	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-78CE1	MN908947.3	26144	G	T	1	1	6.9e-231	2.9e-170	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-78CE1	MN908947.3	28727	G	T	0.054	0.075	2.4e-24	7e-33	0.0602737066873726	TGC	N	A152S	G454T	GCT>TCT	Missense	GU280_gp10	0.939386586431137
CAMB-78CF0	MN908947.3	11075	T	-	0.11	0.059	2.7e-27	1.2e-15	0.100717088350697	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.899201731836017
CAMB-78CF0	MN908947.3	12753	G	T	0.011	0.015	4.4e-07	3e-09	0.0117717586789471	TGC	ORF1ab:nsp9	C23F	G68T	TGC>TTC	Missense	ORF1ab:nsp9	0.979544752665904
CAMB-78CF0	MN908947.3	14408	C	T	1	1	0	0	0.999250104985302	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000449937008818765
CAMB-78CF0	MN908947.3	15673	T	-	0.012	0.014	7.2e-07	9.7e-08	0.0122345903005933	GTT	ORF1ab:RNA-dependent-RNA-polymerase	.	2206-2206-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.987716373265336
CAMB-78CF0	MN908947.3	15673	TT	-	0.012	0.007	7.2e-07;2e-07	9.7e-08;NA	0.0105803062589821	GTT	ORF1ab:RNA-dependent-RNA-polymerase	.	2206-2207-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.987716373265336
CAMB-78CF0	MN908947.3	22058	T	C	0.025	0.056	3.6e-12	4.1e-18	0.0298716920609463	TTG	S	C166R	T496C	TGC>CGC	Missense	GU280_gp02, spike glycoprotein	0.970128307939054
CAMB-78CF0	MN908947.3	22845	ATTTTACAGGCTGCGTTATAGCTTGGA	-	0.000280407407407407	0.0129259259259259	NA;NA;NA;NA;NA;0.0073;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00036;0.00092;0.00014;3e-04;0.00042;0.00038;0.00026;0.00028;0.00027;0.00047;0.00044;0.00044;0.00032;0.00046;0.00033;0.00014;0.00018;0.00097;1.9e-05;2.2e-05;2e-05;3.1e-05;2.1e-05;1.3e-05;1.1e-05;1.5e-05;9.8e-06	0.00276617670987688	GAT	S	.	1283-1309-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.998062678062678
CAMB-78CF0	MN908947.3	23403	A	G	1	1	0	0	0.999942724044446	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.8183970369239e-05
CAMB-78CF0	MN908947.3	24026	CTTT	-	0.03708	0.041	4.3e-05;1.8e-07;1.8e-06;NA	0.00031;1.2e-05;3.3e-05;1.3e-06	0.0481308411214953	ACT	S	.	2464-2467-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.95457552370452
CAMB-78CF0	MN908947.3	241	C	T	1	1	0	0	0.999711333063911	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-78CF0	MN908947.3	26787	GGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.0510588235294118	0.112558823529412	8.4e-10;8.1e-10;1.1e-10;2.2e-10;1.2e-10;8.2e-10;3.1e-10;5.1e-10;1.4e-09;2.2e-10;1.1e-09;5.6e-10;5.7e-10;2.6e-10;1.3e-09;3.3e-10;6.3e-10;4.5e-10;1.1e-10;7.9e-10;3.4e-10;2.3e-10;2.7e-10;9.1e-10;6.4e-10;2.3e-10;7.9e-10;7.2e-05;1e-04;7.7e-05;0.00057;0.0017;0.00086;0.0011	3e-22;2.5e-22;7.7e-23;7.8e-23;2.4e-23;1.8e-22;5.8e-23;1.6e-22;7.3e-22;2e-23;4.7e-22;1.1e-22;1.5e-22;2.9e-22;6e-22;1.5e-22;2.7e-22;8e-23;1.9e-23;2.6e-22;7.4e-23;6.1e-25;1e-22;3.2e-22;2.9e-22;3.9e-23;5e-22;2.4e-25;6.2e-23;5.4e-24;5.3e-14;1.8e-11;9.7e-13;7.2e-12	0.0701848566893847	AGG	M	.	265-298-delfrshift	.	no-SNV	GU280_gp05	0.931493447397161
CAMB-78CF0	MN908947.3	28745	G	C	0.0092	0.01	1.2e-05	6.2e-06	0.00952380952380952	CGT	N	V158L	G472C	GTG>CTG	Missense	GU280_gp10	0.990408645727795
CAMB-78CF0	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99971181556196	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-78CF0	MN908947.3	29416	C	T	0.0099	0.034	0.00038	2e-07	0.0187110187110187	CCT	N	A381A	C1143T	GCC>GCT	Synonymous	GU280_gp10	0.981288981288981
CAMB-78CF0	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78CF0	MN908947.3	3847	GAGTGA	AGAGTG	0.015	0.00105	1.1e-08;1.9e-07;2.7e-08;2e-08;2.5e-08;1.1e-08	NA;NA;NA;NA;NA;0.0029	0.0135329686150302	AGA	ORF1ab:nsp3	.	1128-1133-mnv	.	no-SNV	ORF1ab:nsp3	0.985884567126725
CAMB-78CF0	MN908947.3	3894	A	G	0.016	0.053	1.5e-08	4.9e-13	0.0193528878137285	GAA	ORF1ab:nsp3	E392G	A1175G	GAA>GGA	Missense	ORF1ab:nsp3	0.980647112186272
CAMB-78CF0	MN908947.3	3960	TCA	ATC	0.0146666666666667	0.00213333333333333	3.8e-08;9.2e-08;7.8e-09	0.00042;NA;NA	0.0130324221233312	ATC	ORF1ab:nsp3	.	1241-1243-mnv	.	no-SNV	ORF1ab:nsp3	0.986703772418058
CAMB-78CF0	MN908947.3	508	T	-	0.065	0.079	2.5e-07	1.5e-08	0.0686640242480765	ATG	ORF1ab:leader-protein	.	243-243-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.929470739100023
CAMB-78CF0	MN908947.3	513	AT	-	0.18	0.145	0.00078;1.3e-07	0.0014;1.9e-06	0.167232237539767	CAT	ORF1ab:leader-protein	.	248-249-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.853787108110608
CAMB-78CF0	MN908947.3	514	T	-	0.21	0.16	1.3e-07	1.9e-06	0.195998011434253	ATG	ORF1ab:leader-protein	.	249-249-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.799279144916729
CAMB-78CF0	MN908947.3	516	TTATGGT	-	0.129285714285714	0.17	2e-04;0.00036;0.00043;0.0041;0.0073;0.0015;6.8e-16	8.2e-05;0.00019;9.4e-05;0.00048;0.00087;0.00022;3.1e-22	0.131526954558284	GTT	ORF1ab:leader-protein	.	251-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.836083074534162
CAMB-78CF0	MN908947.3	522	T	-	0.12	0.16	6.8e-16	3.1e-22	0.127763900453326	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.872143584050328
CAMB-78CF0	MN908947.3	523	TG	-	0.017	0.035	4.9e-05;NA	3.2e-05;3.8e-07	0.0203258722843976	TTG	ORF1ab:leader-protein	.	258-259-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.964981569246972
CAMB-78D0C	MN908947.3	14805	C	T	0.85	1	0	0	0.899512046355596	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.100487953644404
CAMB-78D0C	MN908947.3	17247	T	C	1	1	0	0	0.999874689857397	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000125310142602942
CAMB-78D0C	MN908947.3	29625	C	T	1	1	0	1.8e-297	1	TCT	ORF10	S23F	C68T	TCT>TTT	Missense	GU280_gp11	0
CAMB-78D1B	MN908947.3	11074	C	INS	0.028	0.022	3.3e-06	0.00058	0.0259630351664626	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.973855616508743
CAMB-78D1B	MN908947.3	11075	T	-	0.041	0.048	3.9e-10	2.3e-12	0.0435564177174264	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.950391205948917
CAMB-78D1B	MN908947.3	11077	TTTTT	-	0.00114	0.00916	0.0056;0.0059;NA;NA;NA	5.5e-06;7.2e-06;9.1e-06;1.2e-05;4.3e-05	0.00341392882962487	TTT	ORF1ab:nsp6	.	105-109-delfrshift	.	no-SNV	ORF1ab:nsp6	0.994754353484129
CAMB-78D1B	MN908947.3	12067	G	T	1	1	0	0	0.999177108248667	TGC	ORF1ab:nsp7	M75I	G225T	ATG>ATT	Missense	ORF1ab:nsp7	4.38875600710978e-05
CAMB-78D1B	MN908947.3	14408	C	T	1	1	0	0	0.998136668219443	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000561388421065205
CAMB-78D1B	MN908947.3	23403	A	G	1	1	0	0	0.999879687875975	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.73435083015366e-05
CAMB-78D1B	MN908947.3	23713	T	C	0.057	0.059	4.8e-26	7.4e-27	0.0581235480965249	ATT	S	N717N	T2151C	AAT>AAC	Synonymous	GU280_gp02, spike glycoprotein	0.940975679135258
CAMB-78D1B	MN908947.3	241	C	T	1	1	0	0	0.998299292441478	TCG	NA	NA	NA	NA	NA	NA	9.62664655767164e-05
CAMB-78D1B	MN908947.3	25658	C	T	1	1	0	0	0.999846696305381	ACA	ORF3a	T89I	C266T	ACA>ATA	Missense	GU280_gp03	0.00015330369461904
CAMB-78D1B	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0381052631578947	0.0363421052631579	0.00056;1.7e-05;4e-05;4.8e-05;0.00015;2.7e-08;5.9e-07;2.2e-06;2.2e-06;5e-07;5.6e-07;3.2e-07;1.5e-06;7.1e-07;1e-06;2.3e-06;5.6e-07;1.9e-06;1.1e-06;1.1e-06;8.2e-07;2.1e-06;7.1e-07;1.3e-06;9.8e-07;4.5e-07;1.5e-06;7.8e-07;2.1e-07;7.9e-07;1.7e-06;1.4e-06;8.7e-07;2.2e-06;5.6e-07;1.8e-06;1e-06;0.00039	4e-05;3e-06;2.8e-05;2.8e-05;3.5e-05;6.1e-08;2.8e-07;4.8e-06;4.5e-06;2e-06;1.6e-06;1.2e-06;2.2e-06;1.8e-06;2.4e-06;3.6e-06;1.6e-06;3e-06;1.9e-06;2.3e-06;1.9e-06;3.7e-06;2e-06;2.5e-06;1.9e-06;1.3e-06;2.7e-06;3.5e-06;1.1e-06;3.5e-06;5.2e-06;4.9e-06;2.4e-06;5.2e-06;1.1e-06;3.2e-06;1.5e-06;0.00057	0.0387105731487208	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.974737267582862
CAMB-78D1B	MN908947.3	27813	C	T	1	1	0	0	1	CCT	NA	NA	NA	NA	NA	NA	0
CAMB-78D1B	MN908947.3	3037	C	T	1	1	0	0	0.998378119355671	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78D2A	MN908947.3	11071	G	INS	0.19	0.23	2.9e-50	2.4e-61	0.205947649719063	TGT	ORF1ab:nsp6	.	98-99-insfrshift	.	no-SNV	ORF1ab:nsp6	0.79338540952903
CAMB-78D2A	MN908947.3	11072	TT	-	0.0162	0.0305	0.038;8.8e-15	1.1e-07;1.2e-18	0.0228244244872348	GTT	ORF1ab:nsp6	.	100-101-delfrshift	.	no-SNV	ORF1ab:nsp6	0.987988859997624
CAMB-78D2A	MN908947.3	11073	T	-	0.03	0.039	8.8e-15	1.2e-18	0.0340795794434877	TTC	ORF1ab:nsp6	.	101-101-delfrshift	.	no-SNV	ORF1ab:nsp6	0.965765042534733
CAMB-78D2A	MN908947.3	11074	C	-	0.18	0.19	3.1e-170	6.2e-173	0.186090961974523	TCT	ORF1ab:nsp6	.	102-102-delfrshift	.	no-SNV	ORF1ab:nsp6	0.000142461980458965
CAMB-78D2A	MN908947.3	11074	C	T	0.82	0.81	0	0	0.813683473223084	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.000142461980458965
CAMB-78D2A	MN908947.3	11083	G	T	1	1	0	0	0.999431656720659	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-78D2A	MN908947.3	11147	T	-	0.018	0.019	5.5e-08	3.8e-08	0.0185443780372005	GTT	ORF1ab:nsp6	.	175-175-delfrshift	.	no-SNV	ORF1ab:nsp6	0.981306671135192
CAMB-78D2A	MN908947.3	1314	C	T	1	1	0	0	1	ACT	ORF1ab:nsp2	T170I	C509T	ACT>ATT	Missense	ORF1ab:nsp2	0
CAMB-78D2A	MN908947.3	14805	C	T	1	1	0	0	0.999888833305542	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	2.77916736145851e-05
CAMB-78D2A	MN908947.3	17247	T	C	1	1	0	0	0.999762489114084	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000217718312089304
CAMB-78D2A	MN908947.3	26144	G	T	1	1	0	2.8e-249	0.998075072184793	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000962463907603465
CAMB-78D2A	MN908947.3	5298	C	T	0.029	0.0096	1.1e-13	1.1e-05	0.0228202084157763	ACT	ORF1ab:nsp3	T860I	C2579T	ACT>ATT	Missense	ORF1ab:nsp3	0.977179791584224
CAMB-78D2A	MN908947.3	5498	AA	-	0.00255	0.0125	0.0052;NA	2.1e-05;1.2e-06	0.0059291395516992	CAA	ORF1ab:nsp3	.	2779-2780-delfrshift	.	no-SNV	ORF1ab:nsp3	0.99258326336412
CAMB-78D2A	MN908947.3	9571	T	-	0.0085	0.014	0.0018	3.7e-05	0.010715620216241	CTG	ORF1ab:nsp4	.	1017-1017-delfrshift	.	no-SNV	ORF1ab:nsp4	0.989091522726999
CAMB-78D39	MN908947.3	10626	C	T	0.23	0.3	5.2e-103	6.2e-139	0.267387171019714	GCA	ORF1ab:3C-like-proteinase	A191V	C572T	GCA>GTA	Missense	ORF1ab:3C-like-proteinase	0.732612828980286
CAMB-78D39	MN908947.3	11071	G	C	0.088	0.031	1.1e-40	9.8e-16	0.0598860078670627	TGT	ORF1ab:nsp6	L33F	G99C	TTG>TTC	Missense	ORF1ab:nsp6	0.940033715982981
CAMB-78D39	MN908947.3	11074	C	INS	0.1	0.092	8.9e-32	9.6e-28	0.0971800335494401	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.902411932719771
CAMB-78D39	MN908947.3	11082	TG	-	0.12645	0.125	0.15;5.1e-119	2.9e-16;5.1e-63	0.128815665524222	TTG	ORF1ab:nsp6	.	110-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.941258318209316
CAMB-78D39	MN908947.3	11083	G	-	0.25	0.14	5.1e-119	5.1e-63	0.19817109614695	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.99226999242937e-05
CAMB-78D39	MN908947.3	11083	G	T	0.75	0.86	2.4e-283	0	0.80168944495358	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.99226999242937e-05
CAMB-78D39	MN908947.3	12052	GCT	AGC	0.0126666666666667	0.029	NA;NA;4e-17	4.5e-15;3.4e-13;7.4e-14	0.0141845145486444	AGC	ORF1ab:nsp7	.	210-212-mnv	.	no-SNV	ORF1ab:nsp7	0.985234055922086
CAMB-78D39	MN908947.3	12054	T	C	0.038	0.03	4e-17	7.4e-14	0.0341582666354107	CTT	ORF1ab:nsp7	L71P	T212C	CTT>CCT	Missense	ORF1ab:nsp7	0.965691035129433
CAMB-78D39	MN908947.3	1356	C	T	0.0042	0.018	0.0058	3.2e-06	0.0103329506314581	GCT	ORF1ab:nsp2	A184V	C551T	GCT>GTT	Missense	ORF1ab:nsp2	0.989667049368542
CAMB-78D39	MN908947.3	14805	C	T	1	1	0	0	0.999881852551985	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	9.45179584120983e-05
CAMB-78D39	MN908947.3	21742	C	T	0.04	0.13	8.7e-18	1.6e-50	0.0723981900452489	CCA	S	S60S	C180T	TCC>TCT	Synonymous	GU280_gp02, spike glycoprotein	0.927601809954751
CAMB-78D39	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-78D39	MN908947.3	25519	T	A	1	1	0	0	0.999220472616317	TTT	ORF3a	F43I	T127A	TTC>ATC	Missense	GU280_gp03	2.22722109623822e-05
CAMB-78D39	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-78D39	MN908947.3	522	T	-	0.038	0.073	4.2e-05	8.5e-10	0.0510440835266821	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.948893208753998
CAMB-78D39	MN908947.3	522	TT	-	0.037	0.0365	4.2e-05;2.7e-05	8.5e-10;NA	0.0363680593565651	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.948893208753998
CAMB-78D39	MN908947.3	8208	C	T	0.024	0.037	3.3e-12	6.3e-17	0.0291852955787382	ACT	ORF1ab:nsp3	T1830I	C5489T	ACT>ATT	Missense	ORF1ab:nsp3	0.970814704421262
CAMB-78D39	MN908947.3	9165	C	T	0.064	0.04	3.1e-29	5.7e-19	0.0521283860687457	ACC	ORF1ab:nsp4	T204I	C611T	ACC>ATC	Missense	ORF1ab:nsp4	0.947814705212839
CAMB-78D39	MN908947.3	9852	ATGTGCTA	-	0.031	0.003475	8e-15;5.2e-15;6.5e-15;5.3e-13;3.9e-14;5.5e-12;1.8e-10;8.2e-12	NA;NA;NA;6.5e-05;4.1e-05;0.00013;NA;NA	0.0186347782760339	GAT	ORF1ab:nsp4	.	1298-1305-delfrshift	.	no-SNV	ORF1ab:nsp4	0.981648675171737
CAMB-78D48	MN908947.3	13914	T	G	0.018	0.0019	2.6e-10	0.0046	0.0149112872782182	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.985088712721782
CAMB-78D48	MN908947.3	23403	A	G	1	1	0	0	0.999874460178769	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000125539821231295
CAMB-78D48	MN908947.3	29730	CACCGAGGCCACGCGGAGTACGATCGAGTG	-	1	1	1.6e-263;2.6e-263;1.1e-263;1.2e-263;1.8e-263;4.2e-263;5.6e-263;4e-263;7.2e-263;9.49999999999999e-263;1.9e-262;1.1e-262;1.3e-262;9.7e-263;1.7e-262;1.6e-262;2.9e-262;3.4e-252;6.4e-242;6.6e-242;7.7e-222;8.7e-222;1.2e-231;5.7e-242;5e-242;3.6e-242;1.9e-231;6.2e-232;1.6e-238;1.8e-231	3.3e-167;4.5e-167;2.4e-167;2.6e-167;3.8e-167;7.8e-167;1e-166;7.8e-167;1.3e-166;1.7e-166;3.1e-166;2e-166;2.3e-166;1.7e-166;3e-166;2.9e-166;4.7e-166;7.9e-161;2.5e-155;2.5e-155;1.5e-144;1.7e-144;8e-150;2.1e-155;1.9e-155;1.4e-155;1.1e-149;4.9e-150;2.5e-155;3.8e-150	1	TCA	NA	NA	NA	NA	NA	NA	0
CAMB-78D48	MN908947.3	3037	C	T	1	1	0	0	0.998046875	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00146484375
CAMB-78D75	MN908947.3	10870	G	T	0.0079	0.0027	3e-05	0.0068	0.00526944424927984	TGC	ORF1ab:3C-like-proteinase	L272L	G816T	CTG>CTT	Synonymous	ORF1ab:3C-like-proteinase	0.994590037237406
CAMB-78D75	MN908947.3	11074	C	INS	0.13	0.09	1.8e-57	5.3e-30	0.113929648241206	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.882331658291457
CAMB-78D75	MN908947.3	11083	G	-	0.16	0.15	2.1e-70	1.7e-66	0.156126012686798	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-78D75	MN908947.3	11083	G	T	0.84	0.85	0	0	0.843767076097028	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-78D75	MN908947.3	12948	TATACTTTATTAAAGGATTAAACAACCTAAA	-	0.00623548387096774	0.000592612903225806	0.00037;5e-04;0.00014;0.00015;0.00016;0.00018;0.00014;0.00017;0.00016;6.9e-05;0.00013;0.00017;5.4e-05;6.5e-05;5.4e-05;0.00013;0.00014;0.00012;0.00015;0.00024;0.00017;0.00013;0.00017;8.9e-05;0.00036;0.00013;0.00034;9.7e-05;0.00027;7.4e-05;2.1e-05	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.46;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00077;0.0023;0.00076;0.00027	0.00361407919547454	TTA	ORF1ab:nsp9	.	263-293-delfrshift	.	no-SNV	ORF1ab:nsp9	0.996456726286344
CAMB-78D75	MN908947.3	1404	C	T	0.013	0.0047	8.3e-07	0.00086	0.0089535534415221	CCT	ORF1ab:nsp2	P200L	C599T	CCT>CTT	Missense	ORF1ab:nsp2	0.991046446558478
CAMB-78D75	MN908947.3	14805	C	T	0.99	0.99	0	0	0.993439400454573	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00390687388660237
CAMB-78D75	MN908947.3	14958	TAA	-	0.0083	0.0055	3e-05;7.2e-05;5e-05	0.00044;0.00089;0.00074	0.00701446733888645	TTA	ORF1ab:RNA-dependent-RNA-polymerase	.	1491-1493-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.9929165160824
CAMB-78D75	MN908947.3	1515	A	G	1	1	0	0	0.99803536345776	CAT	ORF1ab:nsp2	H237R	A710G	CAT>CGT	Missense	ORF1ab:nsp2	0.00112264945270839
CAMB-78D75	MN908947.3	16887	C	T	0.014	0.01	8.1e-07	2.4e-05	0.0124604193410355	ACA	ORF1ab:helicase	Y217Y	C651T	TAC>TAT	Synonymous	ORF1ab:helicase	0.9866324347454
CAMB-78D75	MN908947.3	17247	T	C	1	0.99	0	0	0.995311867608041	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.00336151459279579
CAMB-78D75	MN908947.3	18357	TTTACAGCTAGGTTTTTCTA	-	0.011395	0.015	0.00086;0.00083;0.0023;0.0017;0.0017;5.8e-05;8.2e-05;0.0023;0.0023;0.00028;0.0018;0.0023;0.00082;0.0012;0.00071;0.0021;0.00037;0.00043;0.00041;0.00046	2.8e-06;4.9e-06;3e-04;0.00018;0.00017;6e-05;7.7e-05;0.00028;0.00028;1.4e-05;0.00018;0.00027;5.3e-05;0.00012;4.7e-05;0.00024;0.00053;6e-04;6e-04;0.00068	0.0117371225577265	CTT	ORF1ab:3'-to-5'-exonuclease	.	318-337-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.984934773034459
CAMB-78D75	MN908947.3	20315	T	A	0.017	0.018	3.1e-05	2.4e-05	0.0174418604651163	TTC	ORF1ab:endoRNAse	F232Y	T695A	TTC>TAC	Missense	ORF1ab:endoRNAse	0.976744186046512
CAMB-78D75	MN908947.3	21642	C	T	0.013	0.013	6.1e-07	4.3e-07	0.0131549609810479	GCA	S	A27V	C80T	GCA>GTA	Missense	GU280_gp02, spike glycoprotein	0.986845039018952
CAMB-78D75	MN908947.3	219	G	T	0.0026	0.0085	0.0064	1.3e-05	0.00537141141341518	CGA	NA	NA	NA	NA	NA	NA	0.994461774567535
CAMB-78D75	MN908947.3	23436	A	G	0.02	0.021	1.5e-10	2.8e-11	0.0204245138065762	CAT	S	H625R	A1874G	CAT>CGT	Missense	GU280_gp02, spike glycoprotein	0.976173229729136
CAMB-78D75	MN908947.3	23448	TTACTCCTACTTGGCGTGTTT	-	0.00288095238095238	0.0109380952380952	0.009;0.016;0.044;0.046;0.046;0.048;0.046;0.06;0.034;0.0062;0.0059;0.0066;0.0047;0.0041;0.0047;0.0056;0.0062;0.0057;0.0087;0.009;0.0085	0.00023;8e-05;1.4e-05;1.6e-05;1.9e-05;1.6e-05;3.2e-05;0.00036;3.3e-05;4.8e-06;4.6e-06;7.5e-06;3.4e-06;3.2e-06;3.3e-06;4.5e-06;5.1e-06;4.6e-06;6.4e-06;0.00083;0.00062	0.0058637247808151	CTT	S	.	1886-1906-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.995289641280241
CAMB-78D75	MN908947.3	23555	CCCATTGGTGCAGGTATATGCGCTAGTT	-	0.0493571428571429	0.034225	0.00076;0.00065;8e-04;0.00082;6.9e-06;2.1e-05;8.4e-06;2.1e-05;2.4e-05;2.5e-05;2.2e-05;1.9e-05;1e-05;9.4e-06;1.2e-06;1.3e-07;9e-06;3.2e-06;8e-06;3e-06;9.7e-06;2.5e-05;1.2e-05;1.2e-05;4.5e-08;1.3e-07;0.00018;0.00014	0.49;0.49;0.49;0.46;0.00031;0.00048;0.00011;0.00021;0.00022;0.00023;0.00021;0.00021;0.00012;0.00011;1.6e-05;3.5e-06;4.5e-05;2e-05;4.6e-05;1.9e-05;4.4e-05;1e-04;5.3e-05;0.00017;4.5e-06;9.2e-07;0.085;0.074	0.0441563505214933	ACC	S	.	1993-2020-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.979428240293606
CAMB-78D75	MN908947.3	26144	G	T	1	1	0	0	0.998327759197324	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.00167224080267559
CAMB-78D75	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0489473684210526	0.0505	1.5e-07;5.7e-10;5.6e-08;6.3e-08;3.9e-07;1.7e-11;6.8e-10;2.3e-08;2.4e-08;3.9e-09;6.8e-09;3.2e-09;2.4e-08;9.2e-09;1.5e-08;4e-08;8.2e-09;3.2e-08;1.7e-08;1.7e-08;8.7e-09;3.4e-08;8.2e-09;2e-08;1.4e-08;4.6e-09;2.1e-08;1.1e-08;1.6e-08;9e-09;2.7e-08;1.9e-08;7.6e-09;2.1e-08;3.8e-09;1.1e-08;4.9e-09;0.00095	5.8e-07;1.4e-08;3.1e-07;3.2e-07;1e-05;7.1e-08;3e-07;3.3e-09;3.1e-09;2.4e-09;1.7e-09;9.4e-10;2.6e-09;2e-09;2.9e-09;5e-09;1.6e-09;4e-09;1.8e-09;2.6e-09;2.5e-09;5e-09;2.7e-09;3e-09;2.1e-09;9.2e-10;3.1e-09;2.1e-09;1.6e-09;1.8e-09;3.5e-09;2.5e-09;7.7e-10;3.4e-09;2.9e-10;1.8e-09;5.1e-10;0.00015	0.0511314213677907	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.959907206616572
CAMB-78D75	MN908947.3	27267	TA	-	0.00915	0.028	0.0015;0.0014	3.5e-08;1.1e-08	0.0179590255242892	TTA	ORF6	.	66-67-delfrshift	.	no-SNV	GU280_gp06	0.981961254398515
CAMB-78D75	MN908947.3	27907	T	G	0.011	0.007	1.4e-06	3.3e-05	0.00910688608403898	GTT	ORF8	V5G	T14G	GTT>GGT	Missense	GU280_gp09	0.990733343984662
CAMB-78D75	MN908947.3	28919	G	T	0.022	0.022	3.1e-11	4.4e-11	0.0218142548596112	TGA	N	D216Y	G646T	GAT>TAT	Missense	GU280_gp10	0.977825773938085
CAMB-78D75	MN908947.3	29466	C	T	0.019	0.029	3.2e-07	1.6e-09	0.0235109717868339	GCA	N	A398V	C1193T	GCA>GTA	Missense	GU280_gp10	0.976489028213166
CAMB-78D75	MN908947.3	29742	G	A	0.012	0.018	1.3e-06	2.2e-08	0.0146978769733261	CGC	NA	NA	NA	NA	NA	NA	0.985302123026674
CAMB-78D75	MN908947.3	522	T	-	0.046	0.06	4.6e-06	7.8e-08	0.0520867719877387	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.947701013911813
CAMB-78D75	MN908947.3	522	TTG	-	0.0346666666666667	0.029	4.6e-06;6.4e-06;0.00031	7.8e-08;0.0027;0.073	0.0328370886981402	GTT	ORF1ab:leader-protein	.	257-259-delinframe	.	no-SNV	ORF1ab:leader-protein	0.947701013911813
CAMB-78D75	MN908947.3	6040	C	T	0.0042	0.015	0.0037	3.9e-07	0.00906790383804302	TCG	ORF1ab:nsp3	F1107F	C3321T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.990932096161957
CAMB-78D75	MN908947.3	686	AAGTCATTT	-	0.0805555555555556	0.0974444444444444	3.7e-11;1.9e-11;7.9e-10;3.3e-11;1.2e-09;1e-10;5.7e-12;1.5e-10;1.2e-08	2.3e-13;1.2e-13;8.5e-12;1.6e-13;1.3e-11;7.9e-13;6.6e-15;7.2e-13;8e-11	0.0859576645521518	AAA	ORF1ab:leader-protein	.	421-429-delinframe	.	no-SNV	ORF1ab:leader-protein	0.914238778204513
CAMB-78D75	MN908947.3	8303	G	A	1	1	0	0	0.997753877863806	AGT	ORF1ab:nsp3	V1862I	G5584A	GTT>ATT	Missense	ORF1ab:nsp3	0.00219327220357794
CAMB-78D75	MN908947.3	9223	C	T	1	0.99	0	0	0.995104880538255	ACG	ORF1ab:nsp4	H223H	C669T	CAC>CAT	Synonymous	ORF1ab:nsp4	0.00241631428749974
CAMB-78D75	MN908947.3	9805	G	A	0.0034	0.0082	0.0021	1.5e-05	0.00558599434979882	TGT	ORF1ab:nsp4	L417L	G1251A	CTG>CTA	Synonymous	ORF1ab:nsp4	0.994392603372999
CAMB-78D84	MN908947.3	11075	T	-	0.021	0.026	1e-05	5.1e-07	0.0233759027734274	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.971800356187186
CAMB-78D84	MN908947.3	11124	C	T	1	1	0	0	0.99990613765851	GCT	ORF1ab:nsp6	A51V	C152T	GCT>GTT	Missense	ORF1ab:nsp6	3.75449365959883e-05
CAMB-78D84	MN908947.3	14408	C	T	1	1	0	0	0.998620232904686	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000358739444781721
CAMB-78D84	MN908947.3	20030	C	T	1	1	0	0	1	GCC	ORF1ab:endoRNAse	A137V	C410T	GCC>GTC	Missense	ORF1ab:endoRNAse	0
CAMB-78D84	MN908947.3	21123	G	T	0.45	0.42	3.1e-244	1.1e-228	0.436679257413807	GGT	ORF1ab:2'-O-ribose-methyltransferase	G155G	G465T	GGG>GGT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.563256449409306
CAMB-78D84	MN908947.3	23403	A	G	1	1	0	0	0.999922020657437	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.67122491369105e-05
CAMB-78D84	MN908947.3	241	C	T	1	1	0	0	0.999798479963151	TCG	NA	NA	NA	NA	NA	NA	0.000115154306771073
CAMB-78D84	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999586776859504	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	3.88500388500389e-05
CAMB-78D84	MN908947.3	3037	C	T	1	1	0	0	0.999416861046318	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000124958347217594
CAMB-78D84	MN908947.3	5438	T	C	0.023	0.036	3.8e-11	1.5e-15	0.0272127928180671	GTT	ORF1ab:nsp3	L907L	T2719C	TTA>CTA	Synonymous	ORF1ab:nsp3	0.972646935054005
CAMB-78D93	MN908947.3	10757	A	G	0.0043	0.0081	0.00058	1.3e-05	0.00582971800433839	TAT	ORF1ab:3C-like-proteinase	M235V	A703G	ATG>GTG	Missense	ORF1ab:3C-like-proteinase	0.994170281995662
CAMB-78D93	MN908947.3	11075	T	-	0.041	0.043	3e-10	5.2e-11	0.0418828530349441	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951578420953929
CAMB-78D93	MN908947.3	11083	G	T	0.018	0.023	0.00045	2.6e-05	0.0198563372216067	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.978898751353841
CAMB-78D93	MN908947.3	14371	G	T	1	1	0	0	0.999788174487735	TGC	ORF1ab:RNA-dependent-RNA-polymerase	A302S	G904T	GCA>TCA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-78D93	MN908947.3	14554	C	T	0.0061	0.008	0.00026	3.6e-05	0.00688191139539078	ACT	ORF1ab:RNA-dependent-RNA-polymerase	L363F	C1087T	CTT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993090338961886
CAMB-78D93	MN908947.3	14657	C	T	0.013	0.013	1.3e-07	1e-07	0.013208981564443	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A397V	C1190T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.986763867394315
CAMB-78D93	MN908947.3	1565	A	G	1	1	0	0	1	TAA	ORF1ab:nsp2	N254D	A760G	AAC>GAC	Missense	ORF1ab:nsp2	0
CAMB-78D93	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999156173993613	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000612268537671063
CAMB-78D93	MN908947.3	16141	G	T	0.025	0.041	1.4e-12	1e-19	0.0303682994322882	AGA	ORF1ab:RNA-dependent-RNA-polymerase	D892Y	G2674T	GAC>TAC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.969617436453371
CAMB-78D93	MN908947.3	16247	C	T	0.014	0.014	3e-06	9.2e-06	0.0140552311194695	GCT	ORF1ab:helicase	A4V	C11T	GCT>GTT	Missense	ORF1ab:helicase	0.985944768880531
CAMB-78D93	MN908947.3	16474	A	G	0.02	0.0061	3.4e-10	0.00023	0.014795008912656	TAG	ORF1ab:helicase	S80G	A238G	AGT>GGT	Missense	ORF1ab:helicase	0.985204991087344
CAMB-78D93	MN908947.3	17072	C	T	0.0088	0.0098	1.2e-05	3.4e-06	0.00918160148318178	ACA	ORF1ab:helicase	T279I	C836T	ACA>ATA	Missense	ORF1ab:helicase	0.990800741590889
CAMB-78D93	MN908947.3	1740	A	G	1	1	0	0	0.999403912886126	AAA	ORF1ab:nsp2	K312R	A935G	AAA>AGA	Missense	ORF1ab:nsp2	0.00057479828837843
CAMB-78D93	MN908947.3	17425	G	T	0.012	0.0077	1.6e-07	1.1e-05	0.010668420506075	TGT	ORF1ab:helicase	V397L	G1189T	GTG>TTG	Missense	ORF1ab:helicase	0.989269272041261
CAMB-78D93	MN908947.3	20132	C	T	0.018	0.022	2.2e-05	2.1e-05	0.019790454016298	GCC	ORF1ab:endoRNAse	A171V	C512T	GCC>GTC	Missense	ORF1ab:endoRNAse	0.980209545983702
CAMB-78D93	MN908947.3	24246	A	-	0.0059	0.0079	0.00023	3.1e-05	0.00675239561094285	CAA	S	.	2684-2684-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.992949704582692
CAMB-78D93	MN908947.3	25231	CTTGATTGCCATAGTAATGGTGACAATTAT	-	0.0122566666666667	0.000196666666666667	1.3e-11;4.3e-05;1.2e-06;1.2e-07;8.2e-09;5.5e-06;1.6e-06;2e-04;9.5e-05;2.9e-07;4.7e-07;0.00057;4.8e-05;4.5e-05;2.8e-05;9.8e-06;2.8e-06;1.5e-07;0.00028;0.00032;8.4e-07;1.1e-06;0.00027;2.3e-07;5.7e-05;6.1e-10;1.5e-05;0.00029;5.3e-08;4.2e-06	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0048;NA;NA;0.02;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00509799005474071	GCT	S	.	3669-3698-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.988174901457512
CAMB-78D93	MN908947.3	25693	C	T	0.01	0.0068	1.8e-06	8.5e-05	0.00936385255648038	CCT	ORF3a	L101F	C301T	CTT>TTT	Missense	GU280_gp03	0.990487514863258
CAMB-78D93	MN908947.3	26211	G	T	0.017	0.0058	3.8e-08	0.00072	0.0127016821146584	TGC	ORF3a	V273V	G819T	GTG>GTT	Synonymous	GU280_gp03	0.986611740473738
CAMB-78D93	MN908947.3	26325	G	T	1	1	0	0	0.999908237237329	TGC	E	L27F	G81T	TTG>TTT	Missense	GU280_gp04	0
CAMB-78D93	MN908947.3	26495	T	C	1	1	0	0	0.998654516543331	TTT	NA	NA	NA	NA	NA	NA	0.00122316677879029
CAMB-78D93	MN908947.3	26681	C	T	0.5	0.49	1.5e-284	8.09999999999999e-280	0.495048829723389	TCC	M	F53F	C159T	TTC>TTT	Synonymous	GU280_gp05	0.504910251513994
CAMB-78D93	MN908947.3	27046	C	T	0.009	0.011	1e-05	1.1e-06	0.00990427447635295	ACG	M	T175M	C524T	ACG>ATG	Missense	GU280_gp05	0.990095725523647
CAMB-78D93	MN908947.3	27870	GA	AG	0.115	0.125	9.5e-52;7.2e-47	1e-55;7.6e-51	0.117886770484646	TGA	NA	NA	NA	NA	NA	NA	0.875835512932287
CAMB-78D93	MN908947.3	27873	A	T	0.12	0.13	7.3e-53	4.2e-54	0.12247117685447	AAC	NA	NA	NA	NA	NA	NA	0.875426002465376
CAMB-78D93	MN908947.3	27876	TG	GT	0.12	0.13	1.2e-53;1.3e-53	6e-57;2.4e-56	0.126549059629684	TTG	NA	NA	NA	NA	NA	NA	0.872593021572318
CAMB-78D93	MN908947.3	27880	ACG	-	0.126666666666667	0.143333333333333	1.5e-54;4.9e-55;1.4e-57	2.4e-60;2.4e-61;1.2e-63	0.132382310984308	CAC	NA	NA	NA	NA	NA	NA	0.869016566795911
CAMB-78D93	MN908947.3	27883	C	T	0.12	0.14	4.5e-54	8.4e-60	0.130094838195902	GCC	NA	NA	NA	NA	NA	NA	0.869325997248968
CAMB-78D93	MN908947.3	27896	G	T	0.044	0.031	1.2e-19	3e-14	0.0387326556355272	TGA	ORF8	M1I	G3T	ATG>ATT	Missense	GU280_gp09	0.956741114491356
CAMB-78D93	MN908947.3	27917	AATCATCACAACTGTAGCTGCATT	-	0.0310625	0.0261741666666667	0.00062;6.8e-05;5.1e-15;5e-15;7.2e-15;4.6e-15;3.3e-15;3.8e-15;8.3e-15;1.8e-15;3.9e-15;3.4e-15;1.1e-15;3e-15;2.2e-11;1.6e-15;2.8e-16;1.1e-15;2.7e-15;4.6e-15;1.6e-15;2.5e-15;4.5e-16;6.1e-11	0.017;0.017;5.6e-13;2.1e-13;6.4e-13;6.1e-13;1.9e-13;5.4e-13;4.3e-13;3.5e-13;3.2e-13;2.7e-13;6.3e-14;2.7e-13;1.4e-10;7.7e-14;8.6e-14;1e-13;2.5e-13;3.3e-13;1.2e-13;3.2e-13;1.5e-13;1.5e-09	0.0312784004847016	GAA	ORF8	.	24-47-delinframe	.	no-SNV	GU280_gp09	0.995893524968835
CAMB-78D93	MN908947.3	27919	TCATCACAACTGTAGCTGCATT	-	0.0333181818181818	0.0284545454545455	5.1e-15;5e-15;7.2e-15;4.6e-15;3.3e-15;3.8e-15;8.3e-15;1.8e-15;3.9e-15;3.4e-15;1.1e-15;3e-15;2.2e-11;1.6e-15;2.8e-16;1.1e-15;2.7e-15;4.6e-15;1.6e-15;2.5e-15;4.5e-16;6.1e-11	5.6e-13;2.1e-13;6.4e-13;6.1e-13;1.9e-13;5.4e-13;4.3e-13;3.5e-13;3.2e-13;2.7e-13;6.3e-14;2.7e-13;1.4e-10;7.7e-14;8.6e-14;1e-13;2.5e-13;3.3e-13;1.2e-13;3.2e-13;1.5e-13;1.5e-09	0.0312784004847016	ATC	ORF8	.	26-47-delfrshift	.	no-SNV	GU280_gp09	0.969104851791771
CAMB-78D93	MN908947.3	28146	C	T	0.004	0.0068	0.00092	4.6e-05	0.00516891033782068	ACC	ORF8	P85S	C253T	CCT>TCT	Missense	GU280_gp09	0.994831089662179
CAMB-78D93	MN908947.3	28242	G	T	0.0082	0.0093	2.5e-05	7.5e-06	0.00868248086337941	TGT	ORF8	V117F	G349T	GTT>TTT	Missense	GU280_gp09	0.988693841118715
CAMB-78D93	MN908947.3	311	C	T	0.002	0.011	0.0066	3.7e-07	0.005590221049938	ACT	ORF1ab:leader-protein	L16F	C46T	CTC>TTC	Missense	ORF1ab:leader-protein	0.994390095073126
CAMB-78D93	MN908947.3	6701	C	T	0.017	0.02	1.2e-08	7.7e-10	0.0183928840645259	TCT	ORF1ab:nsp3	L1328F	C3982T	CTT>TTT	Missense	ORF1ab:nsp3	0.981305593245892
CAMB-78D93	MN908947.3	6705	AC	-	0.00915	0.00255	1.4e-05;4.6e-05	NA;0.00097	0.00618705035971223	AAC	ORF1ab:nsp3	.	3986-3987-delfrshift	.	no-SNV	ORF1ab:nsp3	0.994400235779546
CAMB-78DA2	MN908947.3	10097	G	A	1	1	0	0	1	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0
CAMB-78DA2	MN908947.3	10123	T	C	1	1	0	0	1	GTA	ORF1ab:3C-like-proteinase	G23G	T69C	GGT>GGC	Synonymous	ORF1ab:3C-like-proteinase	0
CAMB-78DA2	MN908947.3	13536	C	T	1	1	0	0	0.999123575810692	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-78DA2	MN908947.3	14408	C	T	1	1	0	0	0.999392220421394	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000445705024311183
CAMB-78DA2	MN908947.3	23403	A	G	1	1	0	0	0.999827864443249	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000107584722969338
CAMB-78DA2	MN908947.3	23731	C	T	1	1	0	0	0.999727446170619	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000272553829381303
CAMB-78DA2	MN908947.3	241	C	T	1	1	0	0	0.999279474016032	TCG	NA	NA	NA	NA	NA	NA	0.000540394487976223
CAMB-78DA2	MN908947.3	27970	C	T	1	1	7.7e-173	3.3e-205	1	ACT	ORF8	T26I	C77T	ACT>ATT	Missense	GU280_gp09	0
CAMB-78DA2	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-78DA2	MN908947.3	3037	C	T	1	1	3.2e-134	1.80000000023142e-315	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78DA2	MN908947.3	4002	C	T	1	1	0	0	0.999196787148594	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-78DB1	MN908947.3	11074	C	INS	0.11	0.1	1.5e-35	3.7e-31	0.104883366034445	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.890037061260083
CAMB-78DB1	MN908947.3	11083	G	-	0.16	0.16	1.1e-70	8.1e-72	0.159660045459037	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	5.92943966795138e-05
CAMB-78DB1	MN908947.3	11083	G	T	0.84	0.84	0	0	0.840063247356458	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	5.92943966795138e-05
CAMB-78DB1	MN908947.3	11590	A	G	0.84	0.83	0	0	0.839334799340297	CAC	ORF1ab:nsp6	T206T	A618G	ACA>ACG	Synonymous	ORF1ab:nsp6	0.160252886201209
CAMB-78DB1	MN908947.3	12528	C	T	0.0092	0.0096	5e-06	2.8e-06	0.00936425627291204	ACA	ORF1ab:nsp8	T146I	C437T	ACA>ATA	Missense	ORF1ab:nsp8	0.990578760423196
CAMB-78DB1	MN908947.3	14805	C	T	1	1	0	0	0.99930221011527	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000322056869875606
CAMB-78DB1	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-78DB1	MN908947.3	2558	C	T	1	1	0	0	0.999570894378716	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	6.13008030405198e-05
CAMB-78DB1	MN908947.3	26106	T	C	0.041	0.038	2.1e-18	2.3e-17	0.0395674761386976	ATG	ORF3a	D238D	T714C	GAT>GAC	Synonymous	GU280_gp03	0.960372115500785
CAMB-78DB1	MN908947.3	26144	G	T	1	1	0	0	0.999763830666588	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	5.90423333530141e-05
CAMB-78DB1	MN908947.3	29013	C	T	1	1	0	0	0.999713494413141	ACT	N	T247I	C740T	ACT>ATT	Missense	GU280_gp10	9.55018622863146e-05
CAMB-78DB1	MN908947.3	29470	T	C	0.0085	0.0034	3.2e-05	0.002	0.00609169605642834	ATT	N	D399D	T1197C	GAT>GAC	Synonymous	GU280_gp10	0.993267072779737
CAMB-78DB1	MN908947.3	4185	G	A	1	1	0	0	0.999754540991654	GGT	ORF1ab:nsp3	G489D	G1466A	GGT>GAT	Missense	ORF1ab:nsp3	6.81830578737795e-05
CAMB-78DB1	MN908947.3	6872	G	A	0.067	0.058	2.6e-25	1.3e-21	0.0625938908362544	TGT	ORF1ab:nsp3	V1385I	G4153A	GTT>ATT	Missense	ORF1ab:nsp3	0.936404606910366
CAMB-78DB1	MN908947.3	9438	C	T	0.82	0.82	0	0	0.822278962056885	ACA	ORF1ab:nsp4	T295I	C884T	ACA>ATA	Missense	ORF1ab:nsp4	0.177364764562674
CAMB-78DB1	MN908947.3	9803	C	T	0.017	0.018	7e-09	1.3e-09	0.0173809561091712	GCT	ORF1ab:nsp4	L417L	C1249T	CTG>TTG	Synonymous	ORF1ab:nsp4	0.982540751295742
CAMB-78DC0	MN908947.3	1059	C	T	1	1	0	0	0.999878386184671	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0
CAMB-78DC0	MN908947.3	10833	C	T	1	1	0	7.5e-309	1	GCC	ORF1ab:3C-like-proteinase	A260V	C779T	GCC>GTC	Missense	ORF1ab:3C-like-proteinase	0
CAMB-78DC0	MN908947.3	12786	C	T	1	1	0	0	0.999877383360922	ACA	ORF1ab:nsp9	T34I	C101T	ACA>ATA	Missense	ORF1ab:nsp9	0.000122616639077923
CAMB-78DC0	MN908947.3	14408	C	T	1	1	0	0	0.999438667771511	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000294031167303734
CAMB-78DC0	MN908947.3	16061	A	G	0.6	0.78	0	0	0.6670580796676	AAT	ORF1ab:RNA-dependent-RNA-polymerase	N865S	A2594G	AAT>AGT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.3329419203324
CAMB-78DC0	MN908947.3	20755	A	C	1	1	0	0	0.999461061708434	TAG	ORF1ab:2'-O-ribose-methyltransferase	S33R	A97C	AGT>CGT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0
CAMB-78DC0	MN908947.3	23403	A	G	1	1	0	0	0.999871445767644	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000105180735563944
CAMB-78DC0	MN908947.3	241	C	T	1	1	0	0	0.999851946898287	TCG	NA	NA	NA	NA	NA	NA	4.93510339041603e-05
CAMB-78DC0	MN908947.3	25487	C	T	0.14	0.12	4.4e-64	2.9e-53	0.133371317332574	ACT	ORF3a	T32I	C95T	ACT>ATT	Missense	GU280_gp03	0.86646250267075
CAMB-78DC0	MN908947.3	25563	G	T	1	1	0	0	0.999741842213961	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000206526228831062
CAMB-78DC0	MN908947.3	29698	T	C	0.017	0.05	1.5e-06	4.9e-12	0.0294117647058824	ATT	NA	NA	NA	NA	NA	NA	0.970588235294118
CAMB-78DC0	MN908947.3	3037	C	T	1	1	0	0	0.999259990133202	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000246669955599408
CAMB-78DC0	MN908947.3	4454	G	T	1	1	0	0	0.999900960681391	AGC	ORF1ab:nsp3	A579S	G1735T	GCC>TCC	Missense	ORF1ab:nsp3	0
CAMB-78DDF	MN908947.3	10376	C	T	0.01	0.01	2.6e-06	2.2e-06	0.0102798457527484	ACC	ORF1ab:3C-like-proteinase	P108S	C322T	CCA>TCA	Missense	ORF1ab:3C-like-proteinase	0.989611110560385
CAMB-78DDF	MN908947.3	11075	T	-	0.038	0.042	2.3e-09	2.2e-10	0.0398197840058305	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955409792619095
CAMB-78DDF	MN908947.3	14408	C	T	1	1	0	0	0.999169222339081	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000441903011127118
CAMB-78DDF	MN908947.3	16289	C	T	1	1	0	0	0.999579407806191	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	5.60789591745177e-05
CAMB-78DDF	MN908947.3	18086	C	T	1	1	0	0	0.999430459050006	ACT	ORF1ab:3'-to-5'-exonuclease	T16I	C47T	ACT>ATT	Missense	ORF1ab:3'-to-5'-exonuclease	0.000113908189998861
CAMB-78DDF	MN908947.3	20739	T	A	0.0073	0.0062	3.6e-05	8.4e-05	0.00682460155460712	TTC	ORF1ab:2'-O-ribose-methyltransferase	L27L	T81A	CTT>CTA	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.992969217129544
CAMB-78DDF	MN908947.3	21494	G	T	0.011	0.013	2.8e-06	5.9e-07	0.0118515030217408	AGA	ORF1ab:2'-O-ribose-methyltransferase	R279I	G836T	AGA>ATA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.987991523428302
CAMB-78DDF	MN908947.3	23403	A	G	1	1	0	0	0.999275947534044	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.35445153025704e-05
CAMB-78DDF	MN908947.3	241	C	T	1	1	0	0	0.999168995996072	TCG	NA	NA	NA	NA	NA	NA	4.53274911233663e-05
CAMB-78DDF	MN908947.3	25429	G	T	1	1	0	0	0.9990310657081	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	9.5697214014857e-05
CAMB-78DDF	MN908947.3	29810	G	T	1	1	0	0	0.999705757347893	TGT	NA	NA	NA	NA	NA	NA	0
CAMB-78DDF	MN908947.3	3037	C	T	1	1	0	0	0.998995071062832	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.78537589127626e-05
CAMB-78DDF	MN908947.3	635	C	T	0.0075	0.01	9.6e-05	5.6e-06	0.00880867159139949	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.99107286404522
CAMB-78DDF	MN908947.3	733	T	G	0.0093	0.012	7.5e-06	5.8e-07	0.0104919388176933	ATT	ORF1ab:leader-protein	D156E	T468G	GAT>GAG	Missense	ORF1ab:leader-protein	0.989028524183547
CAMB-78DDF	MN908947.3	9524	A	G	0.065	0.066	7.1e-30	3e-30	0.0654180861767665	TAT	ORF1ab:nsp4	M324V	A970G	ATG>GTG	Missense	ORF1ab:nsp4	0.934540725965414
CAMB-78DEE	MN908947.3	1059	C	T	1	1	0	0	0.999761075841354	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	8.53300566591576e-05
CAMB-78DEE	MN908947.3	11075	T	-	0.04	0.045	3.5e-10	2.8e-11	0.0421203154422279	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953688890147386
CAMB-78DEE	MN908947.3	14408	C	T	1	1	0	0	0.99747403261982	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000511726150295059
CAMB-78DEE	MN908947.3	23403	A	G	1	1	0	0	0.999488700276102	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.65276455827637e-05
CAMB-78DEE	MN908947.3	241	C	T	1	1	0	0	0.998188629533572	TCG	NA	NA	NA	NA	NA	NA	0.000137225035335447
CAMB-78DEE	MN908947.3	24368	G	T	1	1	0	0	0.99986044044994	AGA	S	D936Y	G2806T	GAC>TAC	Missense	GU280_gp02, spike glycoprotein	0
CAMB-78DEE	MN908947.3	25463	C	A	1	1	0	0	0.999282276450224	ACT	ORF3a	T24N	C71A	ACT>AAT	Missense	GU280_gp03	0.00033775225871823
CAMB-78DEE	MN908947.3	25563	G	T	1	1	0	0	0.999687881281389	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000127684930340777
CAMB-78DEE	MN908947.3	26446	T	C	0.15	0.15	7.1e-68	2.8e-67	0.148340280524538	TTC	E	S68P	T202C	TCT>CCT	Missense	GU280_gp04	0.849484285149238
CAMB-78DEE	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.02896875	0.024875	5.4e-05;0.00031;0.00012;0.00012;4.1e-05;5.5e-05;3.9e-05;0.00012;6.7e-05;8.5e-05;0.00016;6.2e-05;0.00014;8.8e-05;8.5e-05;6.6e-05;0.00014;8.4e-05;1e-04;8.4e-05;5.8e-05;0.00012;8e-05;3.4e-05;7.1e-05;0.00012;0.00011;5.7e-05;0.00012;5.3e-05;8.8e-05;6.6e-05	0.0011;0.0021;0.00053;0.00053;0.00022;0.00035;0.00029;0.00049;0.00033;0.00036;0.00056;0.00029;0.00052;4e-04;0.00037;4e-04;0.00057;4e-04;0.00046;0.00034;0.00031;0.00049;0.00033;0.00031;0.00032;0.00048;0.00045;0.00029;5e-04;0.00026;0.00036;0.00034	0.026817081739402	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.973203047366678
CAMB-78DEE	MN908947.3	27998	C	T	0.025	0.023	6.3e-12	2.7e-11	0.0243653579299649	ACC	ORF8	D35D	C105T	GAC>GAT	Synonymous	GU280_gp09	0.97538976410089
CAMB-78DEE	MN908947.3	3037	C	T	1	1	0	0	0.999273391213623	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.58929835674628e-05
CAMB-78DEE	MN908947.3	5554	G	T	1	1	0	0	0.999556816167346	AGG	ORF1ab:nsp3	K945N	G2835T	AAG>AAT	Missense	ORF1ab:nsp3	0.000177273533061514
CAMB-78DFD	MN908947.3	10665	TTTTAGCTTG	-	0.013	0.00454	0.00011;0.00051;0.00049;0.00016;1e-04;1e-04;0.00013;3.7e-05;1.3e-05;6.5e-08	0.0094;0.013;0.011;0.0069;0.038;0.036;0.038;0.0053;0.0082;0.03	0.00898210745084924	GTT	ORF1ab:3C-like-proteinase	.	611-620-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.98901068172921
CAMB-78DFD	MN908947.3	11074	C	INS	0.03	0.018	5.3e-07	0.0037	0.0241942988306089	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.975598912290497
CAMB-78DFD	MN908947.3	11075	T	-	0.03	0.034	1.1e-07	1.2e-08	0.0320508368636711	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.96076116396972
CAMB-78DFD	MN908947.3	12401	A	T	0.0042	0.009	0.00064	5.6e-06	0.00635362357714037	CAA	ORF1ab:nsp8	N104Y	A310T	AAC>TAC	Missense	ORF1ab:nsp8	0.993311092856784
CAMB-78DFD	MN908947.3	14408	C	T	1	1	0	0	0.995793357297404	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000310326101011146
CAMB-78DFD	MN908947.3	15324	C	T	1	1	0	0	0.997127413652434	ACA	ORF1ab:RNA-dependent-RNA-polymerase	N619N	C1857T	AAC>AAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	3.39951047049225e-05
CAMB-78DFD	MN908947.3	18060	C	T	0.0098	0.012	1.7e-05	2.2e-06	0.0107364995361711	TCT	ORF1ab:3'-to-5'-exonuclease	L7L	C21T	CTC>CTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.989263500463829
CAMB-78DFD	MN908947.3	22162	TTTTA	-	0.0010082	0.00776	0.07;0.0093;NA;NA;NA	0.00087;0.00047;7.8e-06;6e-06;1.2e-05	0.00361757105943152	ATT	S	.	600-604-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.991391791928818
CAMB-78DFD	MN908947.3	23403	A	G	1	1	0	0	0.99884332625388	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.92092795294886e-05
CAMB-78DFD	MN908947.3	241	C	T	1	0.99	0	0	0.995396850999417	TCG	NA	NA	NA	NA	NA	NA	0.000186111145576138
CAMB-78DFD	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0410526315789474	0.0559210526315789	1.6e-05;3.9e-07;7.8e-06;1e-05;9.7e-06;1.1e-07;8.5e-07;6.3e-07;6.3e-07;1.4e-07;3e-07;2.1e-07;6.9e-07;3.4e-07;2.6e-07;5.3e-07;2.9e-07;8.1e-07;4.9e-07;4.7e-07;2.5e-07;8.2e-07;2.9e-07;5.5e-07;4.1e-07;2e-07;6.5e-07;3.7e-07;2.4e-07;3.4e-07;7.6e-07;6.2e-07;2.5e-07;6.8e-07;1.7e-07;3.7e-07;2e-07;0.011	6e-07;9.7e-09;6.5e-08;3.3e-08;1.8e-07;1.3e-09;6.1e-09;6e-10;5.8e-10;1.9e-10;2.2e-10;1.6e-10;6e-10;2.8e-10;4.4e-10;8.8e-10;2.3e-10;7.1e-10;4.4e-10;3.8e-10;2.7e-10;8.2e-10;3.3e-10;5.1e-10;3.1e-10;1.2e-10;4.4e-10;2.6e-10;2.1e-09;2.3e-10;5.7e-10;1.4e-10;8e-11;2.8e-10;1.1e-10;1.9e-10;6.2e-11;0.00014	0.049856574602872	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.965262603318276
CAMB-78DFD	MN908947.3	29247	C	T	0.017	0.011	5.4e-09	1.3e-06	0.0140359287816441	ACA	N	T325I	C974T	ACA>ATA	Missense	GU280_gp10	0.985924120756928
CAMB-78DFD	MN908947.3	3037	C	T	1	1	0	0	0.998453100829701	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78DFD	MN908947.3	522	TT	-	0.0445	0.038	1.9e-06;1.9e-05	5.5e-06;0.00023	0.0418958131822578	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.950542342521644
CAMB-78DFD	MN908947.3	7062	ACAGAGA	TACAGAG	0.0167142857142857	0.00401428571428571	1e-06;5.2e-08;1.8e-06;4.4e-08;5e-07;4.8e-08;2.8e-06	0.054;0.038;0.039;0.053;5.7e-07;0.054;0.044	0.0100961538461538	TAC	ORF1ab:nsp3	.	4343-4349-mnv	.	no-SNV	ORF1ab:nsp3	0.990559186637618
CAMB-78DFD	MN908947.3	7078	GA	TG	0.0175	0.00345	3.8e-07;6.7e-08	0.054;0.0014	0.0105083088954057	TGA	ORF1ab:nsp3	.	4359-4360-mnv	.	no-SNV	ORF1ab:nsp3	0.989768574908648
CAMB-78DFD	MN908947.3	7090	TGTCACTAT	ATGTCACTA	0.0412222222222222	0.00412222222222222	2.1e-06;7.6e-08;7.9e-08;2e-16;1.5e-16;3e-16;2.1e-16;1.1e-16;3.4e-16	0.061;0.042;0.036;0.0069;0.005;0.02;0.0056;0.0066;0.017	0.0338563170933113	ATG	ORF1ab:nsp3	.	4371-4379-mnv	.	no-SNV	ORF1ab:nsp3	0.990930292821975
CAMB-78DFD	MN908947.3	7100	GCA	TGC	0.0533333333333333	0.0053	1.2e-16;3.4e-16;1.3e-16	0.0064;0.016;0.0051	0.0339531123686338	TGC	ORF1ab:nsp3	.	4381-4383-mnv	.	no-SNV	ORF1ab:nsp3	0.965058236272879
CAMB-78DFD	MN908947.3	7106	TACTGTACTG	CTACTGTACT	0.0526	0.00586	4.6e-15;1.7e-16;4.9e-16;9.4e-17;5.7e-16;5.1e-17;7.1e-16;7.8e-16;2.9e-16;4.5e-16	0.0066;0.026;0.0051;0.0065;0.0067;0.0052;0.0073;0.0048;0.0066;0.007	0.033112582781457	CTA	ORF1ab:nsp3	.	4387-4396-mnv	.	no-SNV	ORF1ab:nsp3	0.968620974401321
CAMB-78DFD	MN908947.3	7117	T	G	0.057	0.0061	3.3e-17	0.0051	0.0357751277683135	GTT	ORF1ab:nsp3	G1466G	T4398G	GGT>GGG	Synonymous	ORF1ab:nsp3	0.964224872231687
CAMB-78DFD	MN908947.3	7119	CTATAC	TCTATA	0.0531666666666667	0.00653333333333333	3.1e-16;4.9e-14;2.2e-15;8.9e-17;2.7e-17;1.1e-16	0.012;0.0017;0.0052;0.0052;0.0054;0.0044	0.0333611342785655	TCT	ORF1ab:nsp3	.	4400-4405-mnv	.	no-SNV	ORF1ab:nsp3	0.964676198486123
CAMB-78DFD	MN908947.3	7126	T	C	0.066	0.0078	6.4e-18	0.0047	0.0417558886509636	CTT	ORF1ab:nsp3	P1469P	T4407C	CCT>CCC	Synonymous	ORF1ab:nsp3	0.958244111349036
CAMB-78DFD	MN908947.3	7128	GTAGTGT	TGTAGTG	0.056	0.00661428571428571	2.3e-15;2.4e-17;4.9e-16;2.5e-15;2.4e-18;9.6e-15;3.9e-18	0.0043;0.0067;0.004;0.0052;0.0065;0.0067;0.0077	0.0349586016559338	TGT	ORF1ab:nsp3	.	4409-4415-mnv	.	no-SNV	ORF1ab:nsp3	0.96849087893864
CAMB-78DFD	MN908947.3	7137	GTCT	TGTC	0.05825	0.006875	1.8e-17;5.2e-17;1.4e-17;1.7e-16	0.0048;0.0051;0.0035;0.0044	0.0375586854460094	TGT	ORF1ab:nsp3	.	4418-4421-mnv	.	no-SNV	ORF1ab:nsp3	0.963247863247863
CAMB-78DFD	MN908947.3	7142	AGTG	TAGT	0.055	0.006475	1.8e-16;1.6e-15;3e-17;2.2e-16	0.0045;0.0038;0.0052;0.0045	0.0347284060552093	TAG	ORF1ab:nsp3	.	4423-4426-mnv	.	no-SNV	ORF1ab:nsp3	0.964154411764706
CAMB-78DFD	MN908947.3	7147	T	G	0.065	0.0074	1.1e-17	0.0071	0.0407523510971787	GTT	ORF1ab:nsp3	G1476G	T4428G	GGT>GGG	Synonymous	ORF1ab:nsp3	0.959247648902821
CAMB-78DFD	MN908947.3	7150	AGAT	TAGA	0.05825	0.00615	1.4e-16;2.8e-16;2.3e-17;9.6e-18	0.0055;0.0045;0.0041;0.014	0.0355191256830601	TAG	ORF1ab:nsp3	.	4431-4434-mnv	.	no-SNV	ORF1ab:nsp3	0.962488563586459
CAMB-78DFD	MN908947.3	7155	CT	TC	0.055	0.0065	3.6e-17;3.7e-15	0.0052;0.006	0.034703196347032	TCT	ORF1ab:nsp3	.	4436-4437-mnv	.	no-SNV	ORF1ab:nsp3	0.963523131672598
CAMB-78DFD	MN908947.3	7159	AGACAC	TAGACA	0.0555	0.00616666666666667	1.9e-16;1e-16;7.6e-17;1.6e-15;2.7e-16;2.2e-16	0.0055;0.0045;0.0044;0.019;0.005;0.0046	0.033717834960071	TAG	ORF1ab:nsp3	.	4440-4445-mnv	.	no-SNV	ORF1ab:nsp3	0.965397923875433
CAMB-78DFD	MN908947.3	7166	TATC	CTAT	0.05075	0.006575	6.9e-15;6.8e-15;1.5e-14;1.2e-15	0.0072;0.004;0.0045;0.0064	0.0313364055299539	CTA	ORF1ab:nsp3	.	4447-4450-mnv	.	no-SNV	ORF1ab:nsp3	0.967562557924004
CAMB-78DFD	MN908947.3	7171	T	C	0.046	0.009	1.4e-13	0.0015	0.0305343511450382	CTT	ORF1ab:nsp3	P1484P	T4452C	CCT>CCC	Synonymous	ORF1ab:nsp3	0.968511450381679
CAMB-78DFD	MN908947.3	7173	CT	TC	0.0495	0.00685	1.3e-14;4.8e-14	0.0056;0.0063	0.0316091954022989	TCT	ORF1ab:nsp3	.	4454-4455-mnv	.	no-SNV	ORF1ab:nsp3	0.968015051740358
CAMB-78DFD	MN908947.3	7177	AGA	TAG	0.0543333333333333	0.00593333333333333	2e-15;5e-17;1.9e-15	0.0047;0.0042;0.019	0.0340699815837937	TAG	ORF1ab:nsp3	.	4458-4460-mnv	.	no-SNV	ORF1ab:nsp3	0.967600700525394
CAMB-78DFD	MN908947.3	7182	CTATACA	ACTATAC	0.0504285714285714	0.0065	1.8e-14;1.1e-14;7e-16;3.3e-15;2.3e-14;9.2e-16;1.7e-14	0.0038;0.0056;0.0049;0.0041;0.0049;0.0045;0.004	0.03125	ACT	ORF1ab:nsp3	.	4463-4469-mnv	.	no-SNV	ORF1ab:nsp3	0.967954759660697
CAMB-78DFD	MN908947.3	7191	T	A	0.057	0.0069	2.2e-16	0.0038	0.0357497517378352	ATT	ORF1ab:nsp3	I1491N	T4472A	ATT>AAT	Missense	ORF1ab:nsp3	0.964250248262165
CAMB-78DFD	MN908947.3	7193	AC	TA	0.0575	0.006	5.5e-16;8.2e-17	0.016;0.0038	0.0346878097125867	TAC	ORF1ab:nsp3	.	4474-4475-mnv	.	no-SNV	ORF1ab:nsp3	0.96697247706422
CAMB-78DFD	MN908947.3	7196	AT	CA	0.0495	0.00595	1.5e-13;2.3e-15	0.0049;0.015	0.0310981535471331	CAT	ORF1ab:nsp3	.	4477-4478-mnv	.	no-SNV	ORF1ab:nsp3	0.970506912442396
CAMB-78DFD	MN908947.3	7200	CATCT	TCATC	0.0502	0.00648	1.8e-16;6e-16;1.1e-14;3.4e-13;7.8e-13	0.0062;0.0044;0.0041;0.007;0.045	0.0310834813499112	TCA	ORF1ab:nsp3	.	4481-4485-mnv	.	no-SNV	ORF1ab:nsp3	0.963531669865643
CAMB-78DFD	MN908947.3	7208	A	T	0.05	0.0064	3.1e-15	0.0049	0.0323144104803493	TAA	ORF1ab:nsp3	K1497*	A4489T	AAA>TAA	Nonsense	ORF1ab:nsp3	0.967685589519651
CAMB-78DFD	MN908947.3	7211	TG	AT	0.047	0.00575	2.7e-13;8.7e-15	0.0037;0.018	0.0296367112810707	ATG	ORF1ab:nsp3	.	4492-4493-mnv	.	no-SNV	ORF1ab:nsp3	0.971126082771896
CAMB-78DFD	MN908947.3	7215	AT	GA	0.0445	0.0053	3.7e-14;3e-13	0.0049;0.017	0.0274207369323051	GAT	ORF1ab:nsp3	.	4496-4497-mnv	.	no-SNV	ORF1ab:nsp3	0.9698314108252
CAMB-78DFD	MN908947.3	7219	A	T	0.046	0.0062	2.1e-14	0.0055	0.030176026823135	TAA	ORF1ab:nsp3	L1500F	A4500T	TTA>TTT	Missense	ORF1ab:nsp3	0.969823973176865
CAMB-78DFD	MN908947.3	7221	CTGCT	ACTGC	0.046	0.00492	3e-12;7.8e-11;5.7e-15;1.8e-15;9e-14	0.018;0.021;0.0049;0.014;NA	0.0322916666666667	ACT	ORF1ab:nsp3	.	4502-4506-mnv	.	no-SNV	ORF1ab:nsp3	0.97239263803681
CAMB-78DFD	MN908947.3	7234	AGT	TAG	0.0406666666666667	0.00513333333333333	9.2e-12;1.2e-13;3.4e-12	0.018;0.016;0.0052	0.0259391771019678	TAG	ORF1ab:nsp3	.	4515-4517-mnv	.	no-SNV	ORF1ab:nsp3	0.97554347826087
CAMB-78DFD	MN908947.3	7238	GCAGAGTG	TGCAGAGT	0.02925	0.004625	5.5e-13;2.1e-07;2.5e-07;1.7e-07;2.2e-10;1.8e-08;2.2e-08;9.7e-09	0.005;0.0017;NA;0.01;0.0087;0.0077;0.01;NA	0.0190389845874887	TGC	ORF1ab:nsp3	.	4519-4526-mnv	.	no-SNV	ORF1ab:nsp3	0.969724770642202
CAMB-78DFD	MN908947.3	7247	T	G	0.035	0.0054	7.6e-11	0.0085	0.0236139630390144	GTT	ORF1ab:nsp3	F1510V	T4528G	TTT>GTT	Missense	ORF1ab:nsp3	0.971252566735113
CAMB-78E09	MN908947.3	10171	A	T	0.02	0.014	3.7e-10	8.7e-08	0.016912963449908	CAA	ORF1ab:3C-like-proteinase	P39P	A117T	CCA>CCT	Synonymous	ORF1ab:3C-like-proteinase	0.982382329739679
CAMB-78E09	MN908947.3	11075	T	-	0.036	0.045	5.7e-09	7.9e-11	0.0407571217957864	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954027361646138
CAMB-78E09	MN908947.3	11660	T	A	0.0038	0.011	0.0012	2e-06	0.00662874335950355	TTT	ORF1ab:nsp6	L230I	T688A	TTA>ATA	Missense	ORF1ab:nsp6	0.993371256640496
CAMB-78E09	MN908947.3	12820	A	G	0.0077	0.008	3.1e-05	2.3e-05	0.00784204193881059	TAT	ORF1ab:nsp9	L45L	A135G	TTA>TTG	Synonymous	ORF1ab:nsp9	0.991932365073909
CAMB-78E09	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999169152109075	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000511296456076439
CAMB-78E09	MN908947.3	16466	C	T	0.012	0.015	0.00011	1.7e-05	0.0137340030078602	CCA	ORF1ab:helicase	P77L	C230T	CCA>CTA	Missense	ORF1ab:helicase	0.985982236599415
CAMB-78E09	MN908947.3	18326	C	T	0.074	0.09	2.9e-33	2.4e-40	0.0814696033580154	GCT	ORF1ab:3'-to-5'-exonuclease	A96V	C287T	GCT>GTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.918077630523983
CAMB-78E09	MN908947.3	20759	C	T	0.032	0.026	4.2e-15	1.7e-12	0.0290632729593872	GCA	ORF1ab:2'-O-ribose-methyltransferase	A34V	C101T	GCA>GTA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.970318359530839
CAMB-78E09	MN908947.3	23525	C	T	0.013	0.013	3.8e-07	2.8e-07	0.0131983598154792	ACA	S	H655Y	C1963T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.985725269092773
CAMB-78E09	MN908947.3	25464	T	C	0.015	0.0083	3.8e-08	2.5e-05	0.0116943273165362	CTC	ORF3a	T24T	T72C	ACT>ACC	Synonymous	GU280_gp03	0.988222586876597
CAMB-78E09	MN908947.3	26509	C	T	1	1	0	0	0.999901093621952	ACT	NA	NA	NA	NA	NA	NA	7.06474128917399e-05
CAMB-78E09	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.034972972972973	0.0361621621621622	0.00037;3.3e-05;0.00021;0.00028;4e-04;8.7e-06;4.9e-05;1e-05;1e-05;2.2e-06;3.3e-06;2.8e-06;5.2e-06;3.1e-06;4.7e-06;9.3e-06;3e-06;8e-06;4.5e-06;4.6e-06;4.2e-06;7.3e-06;4e-06;6e-06;4.4e-06;2.4e-06;6.4e-06;3.8e-06;1.8e-06;3.9e-06;7e-06;6.3e-06;3.4e-06;8.7e-06;2.2e-06;4.7e-06;3.3e-06	0.00034;1.4e-05;8.6e-05;9.5e-05;0.00017;1e-05;2.5e-05;4.4e-06;4.4e-06;1.9e-06;2.5e-06;1.9e-06;4.4e-06;2.4e-06;3.1e-06;4.9e-06;2.2e-06;4.2e-06;3.2e-06;2.9e-06;1.8e-06;4.8e-06;2.6e-06;3.5e-06;2.5e-06;2.3e-06;3.8e-06;2.2e-06;1.4e-06;2.5e-06;3.6e-06;3.7e-06;2.6e-06;4e-06;1.2e-06;4.1e-06;2.9e-06	0.0370965800649942	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.975550728603681
CAMB-78E09	MN908947.3	27683	ACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTG	-	0.0168625	0.017325	4e-05;8.7e-05;1.3e-05;1.2e-05;7.4e-06;2.4e-06;1.4e-05;2.4e-06;2.3e-05;9.3e-06;8e-06;5.6e-06;7.3e-06;1e-05;1e-05;8.6e-06;6.6e-06;5.8e-06;2e-06;4.4e-06;5.3e-06;2.1e-06;2.5e-06;4.6e-06;4.4e-06;6.1e-07;2.3e-06;1.9e-06;3.5e-06;3.4e-06;2e-07;2.9e-06;6.3e-06;6.5e-06;4.2e-06;6.4e-06;4.8e-06;2.6e-06;2.8e-06;4.4e-06;4.2e-06;3.5e-06;5.7e-06;4.1e-06;2.6e-06;5.1e-06;1.9e-06;4.8e-06;3e-06;2.8e-06;4e-06;3.4e-06;4.3e-06;5e-06;4.6e-06;5.2e-06;4.1e-06;3.8e-06;4.1e-06;1.6e-05;4.5e-06;3.4e-06;4.3e-06;5.7e-06;3.8e-06;3.9e-06;1.2e-06;4.6e-06;2.3e-06;3.9e-06;4.6e-06;1.2e-05;4e-06;2.1e-06;4.8e-06;5.7e-06;5.6e-06;5.7e-06;5.2e-06;3e-06	0.00011;0.00021;4.6e-05;4.5e-05;2.6e-05;1.5e-05;4.8e-05;1.4e-05;6.6e-05;3.9e-05;3.3e-05;3.2e-05;1.2e-05;1.5e-05;1.3e-05;9.7e-06;9.1e-06;1.1e-05;3.6e-06;5.3e-06;7.3e-06;1.4e-05;1.4e-05;1.6e-05;1.7e-05;1.4e-05;1e-05;1.1e-05;1.6e-05;1.4e-05;5.9e-06;1.4e-05;2.1e-05;2e-05;1.5e-05;3e-05;1.7e-05;2.5e-05;3.2e-05;1.6e-05;1.7e-05;1.3e-05;1.6e-05;1.3e-05;1.1e-05;1.6e-05;9e-06;1.4e-05;1.2e-05;1e-05;1.5e-05;1.5e-05;1.4e-05;1.5e-05;1.7e-05;1.5e-05;1.3e-05;1.3e-05;1.3e-05;5e-05;1.6e-05;1.1e-05;1.4e-05;1.7e-05;1.4e-05;1.1e-05;4.7e-06;1.3e-05;9.2e-06;1.1e-05;1.3e-05;3.6e-05;1.2e-05;7.6e-06;1.7e-05;1.7e-05;5e-06;5.6e-06;4.7e-06;9.5e-06	0.0164533820840951	TAC	ORF7a	.	290-366-delfrshift	.	no-SNV	GU280_gp07	0.983208955223881
CAMB-78E09	MN908947.3	28253	C	T	0.009	0.011	6e-05	1.2e-05	0.00983025957759254	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.989383665183778
CAMB-78E09	MN908947.3	8655	C	T	0.0095	0.0033	7.8e-06	0.0039	0.00648799932151641	TCT	ORF1ab:nsp4	S34F	C101T	TCT>TTT	Missense	ORF1ab:nsp4	0.993512000678484
CAMB-78E09	MN908947.3	9532	C	T	0.0051	0.007	0.00031	4.7e-05	0.00607156409741289	TCA	ORF1ab:nsp4	F326F	C978T	TTC>TTT	Synonymous	ORF1ab:nsp4	0.993827987231858
CAMB-78E27	MN908947.3	11074	C	INS	0.072	0.041	2.7e-23	2.6e-09	0.059780708723979	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.939917368504688
CAMB-78E27	MN908947.3	11075	T	-	0.073	0.053	1.3e-17	2.1e-13	0.0652635591374428	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.934518623393596
CAMB-78E27	MN908947.3	11075	TT	-	0.0565	0.026555	1.3e-17;5.2e-15	2.1e-13;0.48	0.0450906199446135	CTT	ORF1ab:nsp6	.	103-104-delfrshift	.	no-SNV	ORF1ab:nsp6	0.934518623393596
CAMB-78E27	MN908947.3	12459	C	T	0.0052	0.013	0.00093	4.5e-07	0.00809894090772745	ACA	ORF1ab:nsp8	T123I	C368T	ACA>ATA	Missense	ORF1ab:nsp8	0.991877985186553
CAMB-78E27	MN908947.3	14408	C	T	1	0.96	0	0	0.986654047897852	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.0132336664474423
CAMB-78E27	MN908947.3	21066	T	A	0.025	0.03	1.3e-12	1.4e-14	0.0269849620763734	CTA	ORF1ab:2'-O-ribose-methyltransferase	T136T	T408A	ACT>ACA	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.972839668551887
CAMB-78E27	MN908947.3	21991	TTA	-	0.13	0.0343333333333333	8.5e-08;3.5e-13;3.6e-13	0.0012;0.00021;0.00024	0.101849905402565	TTT	S	.	429-431-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.89659036337442
CAMB-78E27	MN908947.3	23403	A	G	1	1	0	0	0.999971550228072	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.48325730922057e-06
CAMB-78E27	MN908947.3	241	C	T	1	1	0	0	0.99964146997311	TCG	NA	NA	NA	NA	NA	NA	0.000179265013444876
CAMB-78E27	MN908947.3	28411	C	T	0.028	0.021	8.3e-14	1e-10	0.0251218282641573	CCA	N	P46P	C138T	CCC>CCT	Synonymous	GU280_gp10	0.97477314737019
CAMB-78E27	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99977588525325	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000250689395838556
CAMB-78E27	MN908947.3	28899	GAATGGCTGGCAATGGCGGTGATG	-	0.0105416666666667	0.00146916666666667	0.00021;8.2e-05;6.6e-05;2.1e-07;4e-07;8.3e-08;6.5e-08;7e-08;5.9e-08;4.1e-05;7.6e-05;3.1e-05;5.9e-05;5.1e-05;6.2e-05;5.4e-05;4.9e-05;5.1e-05;5.2e-05;3.7e-05;5.8e-05;2.6e-05;3.3e-05;4e-05	NA;NA;NA;NA;1.1e-10;NA;NA;NA;NA;NA;NA;1.1e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00492347211816333	AGA	N	.	626-649-delinframe	.	no-SNV	GU280_gp10	0.99508779264214
CAMB-78E27	MN908947.3	28910	A	-	0.0089	0.01	3.1e-05	1.1e-05	0.0094136327549053	CAA	N	.	637-637-delfrshift	.	no-SNV	GU280_gp10	0.990586367245095
CAMB-78E27	MN908947.3	29642	C	T	0.016	0.011	2e-07	2.2e-05	0.0134608572440666	ACA	ORF10	Q29*	C85T	CAA>TAA	Nonsense	GU280_gp11	0.986539142755933
CAMB-78E27	MN908947.3	3037	C	T	1	1	0	0	0.999408371542671	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78E27	MN908947.3	9491	C	T	0.029	0.041	3e-13	2.3e-16	0.03280032800328	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.96719967199672
CAMB-78E36	MN908947.3	10843	T	G	0.0094	0.015	0.00015	8.2e-07	0.0119146577999446	ATA	ORF1ab:3C-like-proteinase	D263E	T789G	GAT>GAG	Missense	ORF1ab:3C-like-proteinase	0.988085342200055
CAMB-78E36	MN908947.3	11075	T	-	0.015	0.018	0.00014	2.4e-05	0.0165904554718934	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.979459938960641
CAMB-78E36	MN908947.3	12269	G	A	0.012	0.015	7.3e-07	2.2e-08	0.0134115674769489	GGA	ORF1ab:nsp8	E60K	G178A	GAA>AAA	Missense	ORF1ab:nsp8	0.986588432523051
CAMB-78E36	MN908947.3	12521	G	T	0.0066	0.014	5.4e-05	2.9e-08	0.0104431348029108	TGG	ORF1ab:nsp8	G144C	G430T	GGT>TGT	Missense	ORF1ab:nsp8	0.989490348414905
CAMB-78E36	MN908947.3	13004	G	C	0.0066	0.0082	0.00012	2.4e-05	0.00742889982198674	AGC	ORF1ab:nsp9	A107P	G319C	GCT>CCT	Missense	ORF1ab:nsp9	0.984455377542296
CAMB-78E36	MN908947.3	13004	G	T	0.0067	0.0094	9.6e-05	6.7e-06	0.00808768905148368	AGC	ORF1ab:nsp9	A107S	G319T	GCT>TCT	Missense	ORF1ab:nsp9	0.984455377542296
CAMB-78E36	MN908947.3	14408	C	T	1	1	0	0	0.999501619735858	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000328477901366015
CAMB-78E36	MN908947.3	16289	C	T	1	1	0	0	1	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0
CAMB-78E36	MN908947.3	16368	TG	-	0.0076	0.0042	2.5e-05;4.8e-05	NA;3e-05	0.00618695359784802	CTG	ORF1ab:helicase	.	132-133-delfrshift	.	no-SNV	ORF1ab:helicase	0.995295698924731
CAMB-78E36	MN908947.3	16369	G	-	0.0076	0.0084	4.8e-05	3e-05	0.00794184950868219	TGT	ORF1ab:helicase	.	133-133-delfrshift	.	no-SNV	ORF1ab:helicase	0.991923542872527
CAMB-78E36	MN908947.3	1938	CTGTGCGTGT	TCTGTGCGTG	0.0002048	0.01486	NA;NA;NA;NA;0.0054;NA;NA;NA;NA;NA	1.9e-05;2.4e-05;1.6e-05;9.4e-06;1.7e-05;4.9e-12;7.4e-12;3.7e-12;4e-11;4.4e-12	0.0054013550220113	TCT	ORF1ab:nsp2	.	1133-1142-mnv	.	no-SNV	ORF1ab:nsp2	0.996405375597402
CAMB-78E36	MN908947.3	22644	G	-	0.016	0.0084	1.3e-05	0.0016	0.0122063991122619	TGT	S	.	1082-1082-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.987793600887738
CAMB-78E36	MN908947.3	22986	C	T	0.0064	0.0074	0.00013	4.5e-05	0.00680551749337718	GCC	S	A475V	C1424T	GCC>GTC	Missense	GU280_gp02, spike glycoprotein	0.993057458664474
CAMB-78E36	MN908947.3	23403	A	G	0.99	1	0	0	0.997133868246355	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.2103843858447e-05
CAMB-78E36	MN908947.3	241	C	T	1	1	0	0	0.999748316869062	TCG	NA	NA	NA	NA	NA	NA	0.00011011136978544
CAMB-78E36	MN908947.3	24659	G	C	0.0059	0.01	8.6e-05	1.7e-06	0.00792141951837769	TGT	S	V1033L	G3097C	GTA>CTA	Missense	GU280_gp02, spike glycoprotein	0.987536966624419
CAMB-78E36	MN908947.3	25429	G	T	1	1	0	0	0.999796079630904	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	6.37251153424588e-05
CAMB-78E36	MN908947.3	25511	C	T	1	1	0	0	0.999725338863178	TCA	ORF3a	S40L	C119T	TCA>TTA	Missense	GU280_gp03	4.11991705233668e-05
CAMB-78E36	MN908947.3	25626	C	T	1	0.99	0	0	0.994533343377059	ACT	ORF3a	H78H	C234T	CAC>CAT	Synonymous	GU280_gp03	9.68502157607584e-05
CAMB-78E36	MN908947.3	26550	G	A	0.035	0.02	5e-17	1.8e-10	0.0276038476780632	CGT	M	V10I	G28A	GTT>ATT	Missense	GU280_gp05	0.972381741542674
CAMB-78E36	MN908947.3	26776	CTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0380714285714286	0.0206453333333333	2e-04;4.6e-06;3.1e-05;0.00014;9.3e-07;4.7e-09;3.8e-07;5.3e-07;1.8e-06;4.2e-08;3.5e-07;3.6e-06;3.5e-06;6.3e-07;1.7e-06;1.3e-06;3.3e-06;2e-06;2.7e-06;5e-06;1.6e-06;4.2e-06;2.3e-06;2.3e-06;2.3e-06;4.5e-06;2.4e-06;3.2e-06;2.2e-06;1.3e-06;3.4e-06;2e-06;1.3e-06;2e-06;3.6e-06;3.5e-06;1.4e-06;3.6e-06;8.6e-07;1.8e-06;1.2e-06;0.00038	NA;0.5;0.5;0.11;2.8e-05;1.1e-06;1.7e-05;2.1e-05;4.9e-05;0.00036;0.00064;0.002;0.002;0.0011;0.0015;0.0013;0.002;0.0015;0.0017;0.0024;0.0015;0.0022;0.0018;0.0017;0.0013;0.0024;0.0015;0.0019;0.0016;0.0014;0.0021;0.0015;0.0011;0.0015;0.002;0.0019;0.0013;0.002;0.0011;0.0015;0.0013;NA	0.0297652208515718	GCT	M	.	254-295-delinframe	.	no-SNV	GU280_gp05	0.983800829397535
CAMB-78E36	MN908947.3	28557	G	T	0.0085	0.0034	2.2e-05	0.0037	0.0059142434696895	CGT	N	R95L	G284T	CGT>CTT	Missense	GU280_gp10	0.993944941209604
CAMB-78E36	MN908947.3	2887	TG	-	0.01	0.00545	2.4e-06;4.2e-06	0.00033;0.00048	0.0080466472303207	TTG	ORF1ab:nsp3	.	168-169-delfrshift	.	no-SNV	ORF1ab:nsp3	0.991553149723395
CAMB-78E36	MN908947.3	3037	C	-	0.009	0.0085	1.7e-05	2.2e-05	0.00874972883071806	TCT	ORF1ab:nsp3	.	318-318-delfrshift	.	no-SNV	ORF1ab:nsp3	0
CAMB-78E36	MN908947.3	3037	C	T	0.99	0.99	0	0	0.990961023935209	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78E36	MN908947.3	3954	AG	-	0.026	0.0145	4.2e-06;2.7e-06	0.00065;0.00069	0.0199284619315278	AAG	ORF1ab:nsp3	.	1235-1236-delfrshift	.	no-SNV	ORF1ab:nsp3	0.980246737502674
CAMB-78E36	MN908947.3	5344	T	C	0.0069	0.0091	0.00015	2.7e-05	0.00786802030456853	CTG	ORF1ab:nsp3	P875P	T2625C	CCT>CCC	Synonymous	ORF1ab:nsp3	0.985532994923858
CAMB-78E36	MN908947.3	5491	T	A	0.26	0.29	5.1e-103	6.5e-112	0.275738585496867	ATT	ORF1ab:nsp3	D924E	T2772A	GAT>GAA	Missense	ORF1ab:nsp3	0.724261414503133
CAMB-78E36	MN908947.3	6308	A	G	0.014	0.0066	5.6e-08	8.9e-05	0.010462649074458	GAG	ORF1ab:nsp3	S1197G	A3589G	AGC>GGC	Missense	ORF1ab:nsp3	0.988330122186182
CAMB-78E36	MN908947.3	7936	G	T	1	1	0	0	0.999915945196268	CGT	ORF1ab:nsp3	A1739A	G5217T	GCG>GCT	Synonymous	ORF1ab:nsp3	0
CAMB-78E36	MN908947.3	820	T	C	0.012	0.0059	3.6e-07	7.7e-05	0.00873237891503483	ATG	ORF1ab:nsp2	Y5Y	T15C	TAT>TAC	Synonymous	ORF1ab:nsp2	0.991212769458614
CAMB-78E36	MN908947.3	8889	G	A	0.02	0.017	9.6e-11	3.9e-09	0.0185385742498567	CGC	ORF1ab:nsp4	R112H	G335A	CGC>CAC	Missense	ORF1ab:nsp4	0.981461425750143
CAMB-78E36	MN908947.3	9558	ACTCATTCTTACCTGG	-	0.0134375	0.0018746875	8.9e-05;0.00015;0.00013;0.00011;5.5e-05;3e-05;7.8e-05;9.8e-05;1.2e-05;3.2e-05;5.2e-05;3.1e-05;3.8e-05;1.2e-05;8e-06;4.1e-05	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.5;0.00034;0.00012;0.00037	0.00694699079350293	TAC	ORF1ab:nsp4	.	1004-1019-delfrshift	.	no-SNV	ORF1ab:nsp4	0.993134701228782
CAMB-78E45	MN908947.3	11074	C	INS	0.029	0.027	2.4e-06	2.8e-05	0.0279596656719795	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.971828197259189
CAMB-78E45	MN908947.3	11075	T	-	0.019	0.025	2.1e-05	4.8e-07	0.0212969724540002	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.978547400428573
CAMB-78E45	MN908947.3	11632	TTGTACTTGTTACTTTG	-	0.0157058823529412	0.00515647058823529	7.8e-07;7.8e-07;8.5e-07;1.5e-06;1.2e-06;1.6e-06;4.6e-07;2.4e-06;1e-06;4.9e-08;8.2e-08;8.8e-08;6e-08;4.2e-08;1.5e-08;1.4e-08;1.3e-08	0.00069;0.00074;0.00068;0.00081;0.00082;0.00082;0.00048;0.00099;0.00079;NA;NA;NA;NA;NA;NA;NA;NA	0.0135615829257448	TTT	ORF1ab:nsp6	.	660-676-delfrshift	.	no-SNV	ORF1ab:nsp6	0.986474501108647
CAMB-78E45	MN908947.3	11660	T	A	0.052	0.075	1.1e-21	2.9e-27	0.0588669950738916	TTT	ORF1ab:nsp6	L230I	T688A	TTA>ATA	Missense	ORF1ab:nsp6	0.941133004926108
CAMB-78E45	MN908947.3	1481	T	-	0.012	0.0087	8.1e-06	0.00016	0.0106167846309403	CTT	ORF1ab:nsp2	.	676-676-delfrshift	.	no-SNV	ORF1ab:nsp2	0.98938321536906
CAMB-78E45	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999478985758944	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000322540627713683
CAMB-78E45	MN908947.3	17043	T	C	0.0024	0.0082	0.0032	7.7e-06	0.00473616473616474	ATC	ORF1ab:helicase	Y269Y	T807C	TAT>TAC	Synonymous	ORF1ab:helicase	0.995212355212355
CAMB-78E45	MN908947.3	20889	A	T	0.009	0.011	9.5e-06	7.9e-07	0.00999884850113231	GAG	ORF1ab:2'-O-ribose-methyltransferase	G77G	A231T	GGA>GGT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.989790043373124
CAMB-78E45	MN908947.3	2114	T	C	0.011	0.012	2.4e-06	7.5e-07	0.0111682468262896	CTT	ORF1ab:nsp2	F437L	T1309C	TTT>CTT	Missense	ORF1ab:nsp2	0.988751406074241
CAMB-78E45	MN908947.3	22580	G	T	0.0065	0.0095	4e-05	1.8e-06	0.00766120451159821	TGA	S	E340*	G1018T	GAA>TAA	Nonsense	GU280_gp02, spike glycoprotein	0.992312194083848
CAMB-78E45	MN908947.3	23567	GGTATATGCGCTAG	-	0.0405714285714286	0.0281428571428571	0.00088;0.00081;6.2e-05;8.6e-06;6.5e-05;2.8e-05;6.3e-05;2.7e-05;6.9e-05;0.00014;8.3e-05;8e-05;8.5e-07;2.2e-06	0.0012;0.0011;0.00053;0.00021;0.00059;0.00036;0.00063;0.00033;0.00063;0.0011;7e-04;0.028;0.014;0.015	0.0360004514163187	AGG	S	.	2005-2018-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.9698280523413
CAMB-78E45	MN908947.3	24098	G	T	0.0059	0.015	7.3e-05	5e-09	0.00931371311744365	TGC	S	A846S	G2536T	GCT>TCT	Missense	GU280_gp02, spike glycoprotein	0.990661046467604
CAMB-78E45	MN908947.3	26509	C	T	1	1	0	0	0.999846799644575	ACT	NA	NA	NA	NA	NA	NA	9.19202132548948e-05
CAMB-78E45	MN908947.3	26787	GGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0324333333333333	0.022	3.7e-05;3.7e-05;1.3e-05;1.8e-05;1.3e-05;4e-05;2.3e-05;2.7e-05;5.2e-05;1.8e-05;4.4e-05;2.9e-05;2.8e-05;2.7e-05;4.8e-05;2.9e-05;3.5e-05;2.7e-05;1.6e-05;4e-05;2.4e-05;2.5e-05;1.9e-05;4.1e-05;3.1e-05;1.3e-05;3.6e-05;1.5e-05;2.3e-05;1.5e-05	0.0018;0.0018;0.00089;0.0013;0.0011;0.0017;0.0013;0.0016;0.0021;0.0014;0.0019;0.0015;0.0014;0.0014;0.0021;0.0014;0.0017;0.0014;0.0013;0.0018;0.0013;0.0012;0.0012;0.0018;0.0015;0.00097;0.0018;0.00098;0.0012;0.00098	0.0273950012883277	AGG	M	.	265-294-delinframe	.	no-SNV	GU280_gp05	0.97009396458258
CAMB-78E45	MN908947.3	28001	G	-	0.0028	0.0099	0.0023	4.4e-06	0.00558971492453885	CGT	ORF8	.	108-108-delfrshift	.	no-SNV	GU280_gp09	0.993851313583007
CAMB-78E45	MN908947.3	28704	A	C	0.008	0.0046	3.7e-05	0.00054	0.00640839805306764	GAT	N	D144A	A431C	GAT>GCT	Missense	GU280_gp10	0.993179633500664
CAMB-78E45	MN908947.3	29296	C	T	0.0096	0.0033	5.8e-06	0.0024	0.00673357351175159	ACA	N	D341D	C1023T	GAC>GAT	Synonymous	GU280_gp10	0.993223537484989
CAMB-78E45	MN908947.3	29738	CCACGCGGAGTACGATCGAGT	-	0.0221428571428571	0.0146190476190476	2.4e-09;3.1e-09;9.8e-10;3.5e-09;4e-09;2.1e-09;3.4e-09;4.7e-09;4.1e-09;2.2e-08;9.6e-08;7e-08;1.1e-06;1.1e-06;6.3e-08;6.9e-08;6.9e-08;9e-08;3.1e-08;3.7e-07;1.1e-07	2.3e-06;2.7e-06;1.9e-06;2.9e-06;3.1e-06;2.3e-06;3.3e-06;3.6e-06;4.8e-07;1.6e-06;5e-06;2.3e-05;1e-04;1e-04;2.2e-05;2e-05;2e-05;2e-05;1.4e-05;5.1e-05;2.4e-05	0.0181293778327153	GCC	NA	NA	NA	NA	NA	NA	0.982048143614851
CAMB-78E45	MN908947.3	4665	G	T	0.0057	0.0066	9.6e-05	3.2e-05	0.00604701725777959	AGA	ORF1ab:nsp3	R649I	G1946T	AGA>ATA	Missense	ORF1ab:nsp3	0.993885038728088
CAMB-78E45	MN908947.3	6472	C	T	0.02	0.015	7.5e-11	4.7e-09	0.0182830383719627	CCG	ORF1ab:nsp3	T1251T	C3753T	ACC>ACT	Synonymous	ORF1ab:nsp3	0.981704507242225
CAMB-78E45	MN908947.3	909	TG	-	0.00365	0.00805	NA;2.8e-05	6.2e-06;1.5e-05	0.00560863098989186	TTG	ORF1ab:nsp2	.	104-105-delfrshift	.	no-SNV	ORF1ab:nsp2	0.996215229071275
CAMB-78E45	MN908947.3	910	G	-	0.0073	0.0077	2.8e-05	1.5e-05	0.00748360705047224	TGT	ORF1ab:nsp2	.	105-105-delfrshift	.	no-SNV	ORF1ab:nsp2	0.986801419719666
CAMB-78E45	MN908947.3	9332	G	C	0.011	0.0062	1.2e-06	0.00015	0.00836497389653536	TGC	ORF1ab:nsp4	A260P	G778C	GCT>CCT	Missense	ORF1ab:nsp4	0.991575700047461
CAMB-78E45	MN908947.3	9333	C	T	0.0065	0.016	7.4e-05	5.2e-09	0.0119441816461684	GCT	ORF1ab:nsp4	A260V	C779T	GCT>GTT	Missense	ORF1ab:nsp4	0.988055818353832
CAMB-78E54	MN908947.3	11075	T	-	0.022	0.072	5.3e-06	2.6e-18	0.035901066196654	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.94738362853593
CAMB-78E54	MN908947.3	12911	G	A	0.023	0.04	9.8e-12	7.1e-19	0.032557240846295	TGT	ORF1ab:nsp9	V76I	G226A	GTT>ATT	Missense	ORF1ab:nsp9	0.967367618802263
CAMB-78E54	MN908947.3	17249	C	T	0.011	0.0084	1.6e-06	2.4e-05	0.00966067358825019	GCT	ORF1ab:helicase	A338V	C1013T	GCT>GTT	Missense	ORF1ab:helicase	0.990263357812104
CAMB-78E54	MN908947.3	17333	C	T	0.0044	0.018	0.0011	2e-09	0.0113261084683525	ACG	ORF1ab:helicase	T366M	C1097T	ACG>ATG	Missense	ORF1ab:helicase	0.988626202653886
CAMB-78E54	MN908947.3	17718	C	-	0.0025	0.016	0.0017	7.8e-10	0.00475588406924723	GCG	ORF1ab:helicase	.	1482-1482-delfrshift	.	no-SNV	ORF1ab:helicase	0.995010698307722
CAMB-78E54	MN908947.3	22736	T	C	0.0032	0.012	0.003	8e-07	0.0041917329710848	CTT	S	F392L	T1174C	TTT>CTT	Missense	GU280_gp02, spike glycoprotein	0.99576945468659
CAMB-78E54	MN908947.3	23403	A	G	1	1	0	0	0.999916424452348	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.78585158839971e-05
CAMB-78E54	MN908947.3	240	TC	-	0.0084	0.009	2e-05;6.2e-05	NA;3e-09	0.0086733190181466	TTC	NA	NA	NA	NA	NA	NA	0.994370176696327
CAMB-78E54	MN908947.3	241	C	-	0.0084	0.018	6.2e-05	3e-09	0.0120021019442985	TCG	NA	NA	NA	NA	NA	NA	6.30583289542827e-05
CAMB-78E54	MN908947.3	241	C	T	0.99	0.98	0	0	0.987892800840778	TCG	NA	NA	NA	NA	NA	NA	6.30583289542827e-05
CAMB-78E54	MN908947.3	25672	C	T	0.036	0.06	4.3e-17	2.8e-18	0.0382913806254767	CCT	ORF3a	L94F	C280T	CTT>TTT	Missense	GU280_gp03	0.961708619374523
CAMB-78E54	MN908947.3	26333	C	T	0.0082	0.014	6.2e-05	1e-06	0.00906653045588048	ACA	E	T30I	C89T	ACA>ATA	Missense	GU280_gp04	0.990869620738092
CAMB-78E54	MN908947.3	28975	G	T	1	1	0	0	0.998058072868504	TGT	N	M234I	G702T	ATG>ATT	Missense	GU280_gp10	9.24727205474385e-05
CAMB-78E54	MN908947.3	29520	C	T	0.014	0.024	1.2e-07	1.8e-07	0.0143506551386042	TCA	N	S416L	C1247T	TCA>TTA	Missense	GU280_gp10	0.985114537837597
CAMB-78E54	MN908947.3	3230	G	-	0.0078	0.012	0.00035	8.9e-06	0.00873077598534835	TGG	ORF1ab:nsp3	.	511-511-delfrshift	.	no-SNV	ORF1ab:nsp3	0.991219047141173
CAMB-78E54	MN908947.3	6310	C	T	0.042	0.044	9.7e-20	4.6e-21	0.0425078489201789	GCA	ORF1ab:nsp3	S1197S	C3591T	AGC>AGT	Synonymous	ORF1ab:nsp3	0.957473123394539
CAMB-78E54	MN908947.3	8841	C	T	0.0062	0.022	5.6e-05	1e-10	0.0102295976358263	ACA	ORF1ab:nsp4	T96I	C287T	ACA>ATA	Missense	ORF1ab:nsp4	0.989770402364174
CAMB-78E54	MN908947.3	9314	G	INS	0.011	0.019	4.4e-06	2.3e-09	0.0136169455322179	AGT	ORF1ab:nsp4	.	759-760-insfrshift	.	no-SNV	ORF1ab:nsp4	0.978996084015664
CAMB-78E72	MN908947.3	14408	C	T	1	1	0	0	0.999698386367064	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000251344694113507
CAMB-78E72	MN908947.3	23403	A	G	1	1	0	0	0.999974089236669	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.59107633310877e-05
CAMB-78E72	MN908947.3	241	C	T	1	1	0	0	1	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-78E72	MN908947.3	25487	C	T	0.18	0.36	5.8e-84	1.3e-183	0.289527639776043	ACT	ORF3a	T32I	C95T	ACT>ATT	Missense	GU280_gp03	0.710432931156849
CAMB-78E72	MN908947.3	28881	G	A	0.99	1	0	0	0.99843321582452	AGG	N	R203K	G608A	AGG>AAG	Missense	GU280_gp10	0
CAMB-78E72	MN908947.3	28881	GGG	AAC	0.996666666666667	1	0;0;0	0;0;0	0.998977156495056	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-78E72	MN908947.3	28883	G	C	1	1	0	0	1	GGG	N	G204R	G610C	GGA>CGA	Missense	GU280_gp10	0
CAMB-78E72	MN908947.3	3037	C	T	1	1	4.3e-281	0	0.999416228838295	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78E72	MN908947.3	6636	C	T	1	1	8.1e-261	0	1	ACT	ORF1ab:nsp3	T1306I	C3917T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-78E90	MN908947.3	14408	C	T	1	1	0	0	0.999501992031873	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-78E90	MN908947.3	16206	G	T	1	1	0	0	1	AGG	ORF1ab:RNA-dependent-RNA-polymerase	E913D	G2739T	GAG>GAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-78E90	MN908947.3	23403	A	G	1	1	0	0	0.99985892443993	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000112860448055979
CAMB-78E90	MN908947.3	241	C	T	1	1	0	0	0.999852005327808	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-78E90	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-78E90	MN908947.3	3037	C	T	1	1	0	0	0.999466239658393	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78EAF	MN908947.3	11979	CTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTT	-	0.0009905	0.0508863636363636	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.5;NA;NA;NA;NA;NA;NA;NA;NA;0.44;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;1.1e-19;NA;NA;NA;0.085;NA;NA;NA	3.6e-23;5.2e-23;6.8e-23;4.3e-23;3.7e-23;3e-27;7.3e-23;1.7e-23;1.1e-23;4e-25;2.1e-23;5.1e-23;9.1e-21;2.2e-23;1.8e-23;1.3e-23;2.8e-24;4.7e-25;1.5e-24;1.3e-23;2.3e-23;4.1e-23;2.5e-23;6e-23;1.9e-23;4.3e-24;2.2e-24;2.1e-23;6.5e-25;4.8e-24;2.5e-24;4.7e-26;6.3e-23;3.9e-23;7e-23;3.7e-23;6.8e-25;1e-25;4.2e-23;1.1e-22;6.2e-24;1.1e-25;1.4e-23;5.3e-24	0.0213920637248818	ACT	ORF1ab:nsp7	.	137-180-delfrshift	.	no-SNV	ORF1ab:nsp7	0.979199145289827
CAMB-78EAF	MN908947.3	12540	C	T	0.26	0.15	1.3e-125	3e-71	0.216104009614334	GCA	ORF1ab:nsp8	A150V	C449T	GCA>GTA	Missense	ORF1ab:nsp8	0.783895990385666
CAMB-78EAF	MN908947.3	12970	C	T	0.45	0.63	1.5e-246	0	0.510237347433706	ACA	ORF1ab:nsp9	N95N	C285T	AAC>AAT	Synonymous	ORF1ab:nsp9	0.489762652566294
CAMB-78EAF	MN908947.3	14408	C	T	1	1	0	0	0.999423561178362	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000364066624192227
CAMB-78EAF	MN908947.3	14571	C	T	0.18	0.12	2e-86	8.8e-57	0.1578437789778	ACC	ORF1ab:RNA-dependent-RNA-polymerase	D368D	C1104T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.841719849451808
CAMB-78EAF	MN908947.3	16790	ATCGTGTAACTA	-	0.0185833333333333	0.0222783333333333	4.5e-10;5.5e-10;5.5e-10;1.3e-09;1.5e-09;2.5e-09;3.5e-10;7.2e-10;2.5e-10;4.8e-10;1.4e-10;1.4e-09	NA;4.9e-25;6.5e-25;1e-24;2e-24;2.9e-24;NA;NA;NA;NA;NA;0.49	0.0129107600480099	TAT	ORF1ab:helicase	.	554-565-delinframe	.	no-SNV	ORF1ab:helicase	0.986927039186282
CAMB-78EAF	MN908947.3	17167	C	T	0.026	0.057	8.4e-13	3.6e-26	0.0368256931333659	TCA	ORF1ab:helicase	H311Y	C931T	CAT>TAT	Missense	ORF1ab:helicase	0.963163700388197
CAMB-78EAF	MN908947.3	21000	T	C	0.84	0.61	0	0	0.756863232976694	ATT	ORF1ab:2'-O-ribose-methyltransferase	D114D	T342C	GAT>GAC	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.243053827651986
CAMB-78EAF	MN908947.3	23403	A	G	1	1	0	0	0.999961307796479	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	1.28974011736635e-05
CAMB-78EAF	MN908947.3	241	C	T	1	1	0	0	0.999821524183473	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-78EAF	MN908947.3	27046	C	T	1	1	0	0	0.999879951980792	ACG	M	T175M	C524T	ACG>ATG	Missense	GU280_gp05	0.000120048019207683
CAMB-78EAF	MN908947.3	27297	C	T	0.39	0.59	7.6e-206	0	0.458744844498941	TCA	ORF6	I32I	C96T	ATC>ATT	Synonymous	GU280_gp06	0.541255155501059
CAMB-78EAF	MN908947.3	28311	C	T	0.048	0.13	2.4e-22	3.5e-60	0.0801012337867763	CCC	N	P13L	C38T	CCC>CTC	Missense	GU280_gp10	0.919898766213224
CAMB-78EAF	MN908947.3	28744	C	T	0.38	0.46	2.8e-197	1.6e-238	0.405165947871742	TCG	N	I157I	C471T	ATC>ATT	Synonymous	GU280_gp10	0.594834052128258
CAMB-78EAF	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-78EAF	MN908947.3	3037	C	T	1	1	0	0	0.999711482977496	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78EAF	MN908947.3	5148	G	A	1	1	5e-170	1.6e-136	1	CGT	ORF1ab:nsp3	R810H	G2429A	CGT>CAT	Missense	ORF1ab:nsp3	0
CAMB-78EAF	MN908947.3	6762	C	T	1	1	0	0	1	ACT	ORF1ab:nsp3	T1348I	C4043T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-78EAF	MN908947.3	7735	C	T	0.48	0.7	5.8e-165	6.6e-270	0.54395002192021	TCG	ORF1ab:nsp3	I1672I	C5016T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.45604997807979
CAMB-78EEB	MN908947.3	10582	C	T	0.0065	0.013	0.00011	2.4e-07	0.00906396322866103	ACT	ORF1ab:3C-like-proteinase	D176D	C528T	GAC>GAT	Synonymous	ORF1ab:3C-like-proteinase	0.99080716525624
CAMB-78EEB	MN908947.3	11075	T	-	0.026	0.054	7.7e-07	4e-13	0.0380580906577801	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961856704661643
CAMB-78EEB	MN908947.3	12596	C	T	0.0042	0.0067	0.00054	3.9e-05	0.00530645376237264	ACT	ORF1ab:nsp8	L169F	C505T	CTT>TTT	Missense	ORF1ab:nsp8	0.994681431046389
CAMB-78EEB	MN908947.3	12966	TAAACAACCTAAA	-	0.000790692307692308	0.00960769230769231	NA;6e-04;0.00045;NA;NA;0.44;0.44;NA;NA;NA;0.44;NA;NA	9.6e-06;1.3e-05;1.4e-05;6.9e-06;9.4e-06;1.9e-06;2e-05;7.8e-06;3.8e-05;4.3e-06;1.1e-05;2.4e-06;2.7e-07	0.00438511483670898	TTA	ORF1ab:nsp9	.	281-293-delfrshift	.	no-SNV	ORF1ab:nsp9	0.995724012920918
CAMB-78EEB	MN908947.3	13317	A	-	0.0054	0.0096	0.00039	5.8e-06	0.00740179647147237	CAA	ORF1ab:nsp10	.	293-293-delfrshift	.	no-SNV	ORF1ab:nsp10	0.992496809056316
CAMB-78EEB	MN908947.3	13499	CACCGTGCGGCACAGGCACTA	-	0.0067	0.000571428571428571	0.00073;0.00085;7e-04;0.00081;0.00074;0.00061;0.00058;0.00023;0.00069;0.00078;0.00016;8.9e-05;1e-04;6.6e-05;7.4e-05;6.3e-05;1e-04;4.1e-05;6.9e-05;5.2e-05;5.4e-05	NA;NA;NA;NA;3.2e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00299691494050242	ACA	ORF1ab:RNA-dependent-RNA-polymerase	.	32-52-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.996909492273731
CAMB-78EEB	MN908947.3	14408	C	T	1	0.99	0	0	0.994614117348879	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000506906602458497
CAMB-78EEB	MN908947.3	14420	G	T	0.0044	0.018	0.00046	8.2e-10	0.010282610795668	GGA	ORF1ab:RNA-dependent-RNA-polymerase	G318V	G953T	GGA>GTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.989685188961757
CAMB-78EEB	MN908947.3	14576	CTATGCACGCTGCTTCTGGTAAT	-	0.00969565217391304	0.000164695652173913	0.00063;0.00057;6e-04;0.00021;2.2e-06;2.3e-06;2.1e-06;2.4e-06;3.5e-06;3e-06;3.2e-06;2.1e-06;1.8e-06;1.1e-06;1.5e-06;2.1e-06;1.3e-06;2.5e-06;8.2e-08;1.1e-07;5.4e-08;1.7e-06;2.8e-06	0.46;0.46;0.0026;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.45;NA;NA;NA;NA;NA	0.00553012610929472	GCT	ORF1ab:RNA-dependent-RNA-polymerase	.	1109-1131-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.996952891415165
CAMB-78EEB	MN908947.3	14786	C	T	1	1	0	0	0.999866446131561	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A440V	C1319T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	4.10934979812819e-05
CAMB-78EEB	MN908947.3	1486	A	C	0.0013	0.008	0.0023	3e-05	0.00400320256204964	GAG	ORF1ab:nsp2	G227G	A681C	GGA>GGC	Synonymous	ORF1ab:nsp2	0.99599679743795
CAMB-78EEB	MN908947.3	18390	AGTTGCTGTACCTACAGGTTATGTTGATACACCTAATAATACAGATTTTTCCAG	-	0.0104111111111111	0.000502537037037037	0.00028;0.00016;6.2e-05;7.3e-05;0.00015;0.00021;0.00014;0.00014;3.5e-05;2.3e-05;3.3e-06;2.1e-05;7.2e-06;6e-06;9.1e-06;6.8e-06;2.4e-05;1.6e-05;2.9e-07;1.2e-05;0.00013;0.00072;0.00081;0.00028;3.4e-05;2.5e-05;3.1e-05;2.3e-05;2.6e-05;3e-05;3.8e-05;6.5e-05;4.7e-05;2.2e-05;1.3e-05;2e-05;3.2e-05;2e-05;2.9e-05;1e-08;2.5e-05;2.3e-05;2.7e-05;1.7e-05;5.4e-05;4.9e-05;2.3e-05;5.4e-05;0.00011;9.5e-05;1.6e-05;1.6e-05;1.6e-05;2.5e-05	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.46;4.3e-05;1.1e-06;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.45;NA;NA;NA;NA;NA;NA;NA;NA	0.0039956590370955	TAG	ORF1ab:3'-to-5'-exonuclease	.	351-404-delinframe	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.9955728772514
CAMB-78EEB	MN908947.3	1909	C	T	0.0032	0.012	0.0017	1.3e-07	0.00672316104200737	TCT	ORF1ab:nsp2	F368F	C1104T	TTC>TTT	Synonymous	ORF1ab:nsp2	0.993276838957993
CAMB-78EEB	MN908947.3	20578	G	T	1	1	0	0	1	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	0
CAMB-78EEB	MN908947.3	2189	C	G	0.023	0.046	3.1e-12	1.6e-21	0.0327362569487338	TCT	ORF1ab:nsp2	L462V	C1384G	CTT>GTT	Missense	ORF1ab:nsp2	0.967201976528721
CAMB-78EEB	MN908947.3	22136	T	A	0.008	0.016	0.00038	4.1e-07	0.0114487926727727	ATT	S	F192I	T574A	TTT>ATT	Missense	GU280_gp02, spike glycoprotein	0.988481820704968
CAMB-78EEB	MN908947.3	22246	T	-	0.0038	0.013	0.0011	1.1e-07	0.00752289576973397	ATT	S	.	684-684-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.992477104230266
CAMB-78EEB	MN908947.3	22765	A	-	0.0044	0.0082	0.00026	6.3e-06	0.00614663202585387	TAA	S	.	1203-1203-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.993747755740025
CAMB-78EEB	MN908947.3	23182	TTTCAA	-	0.00935	0.00477433333333333	5.5e-06;2.8e-05;0.00084;0.00055;0.00073;0.00097	0.45;NA;0.002;0.0015;0.0019;0.0023	0.00850692262404826	ATT	S	.	1620-1625-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.994324608444557
CAMB-78EEB	MN908947.3	23193	ATGGTTTA	-	0.0064945	0.008325	4.2e-05;3.9e-05;6.8e-05;3.8e-06;0.00028;0.44;NA;NA	0.00034;0.00029;0.00046;5.1e-05;2e-05;8.9e-06;1.2e-05;1.2e-05	0.00847009822205645	AAT	S	.	1631-1638-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.989416433926209
CAMB-78EEB	MN908947.3	23403	A	G	1	1	0	0	0.999924279137388	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.30046038284468e-05
CAMB-78EEB	MN908947.3	241	C	T	1	1	0	0	0.99973841163545	TCG	NA	NA	NA	NA	NA	NA	8.71961215165149e-05
CAMB-78EEB	MN908947.3	2416	C	T	1	1	0	0	1	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0
CAMB-78EEB	MN908947.3	24756	TGACTTA	-	0.00214785714285714	0.022	NA;NA;NA;NA;0.44;NA;3.4e-08	1.6e-08;2.7e-07;3.6e-07;9.7e-07;2.4e-10;3.3e-10;8e-19	0.00798201008893661	GTG	S	.	3194-3200-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.991918332624415
CAMB-78EEB	MN908947.3	24762	A	-	0.015	0.04	3.4e-08	8e-19	0.025138984701538	TAT	S	.	3200-3200-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.974749421742483
CAMB-78EEB	MN908947.3	25166	G	C	1	1	0	0	0.999878846619821	AGA	S	E1202Q	G3604C	GAA>CAA	Missense	GU280_gp02, spike glycoprotein	0
CAMB-78EEB	MN908947.3	25563	G	T	1	1	0	0	0.999836069708204	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.00011349020201256
CAMB-78EEB	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.0185555555555556	0.0385555555555556	0.00048;0.002;0.0055;0.0054;0.0023;0.0034;0.003;0.0054;0.0041;0.0047;0.0066;0.0037;0.006;0.0043;0.0045;0.0047;0.0062;0.0039;0.0052;0.0043;0.0038;0.0056;0.0041;0.0034;0.0039;0.0056;0.0049;0.0027;0.0054;0.0036;0.0039;0.0033;0.066;0.079;0.065;0.065	1.7e-05;3e-05;1.5e-06;1.5e-06;5.6e-07;9.1e-07;7.2e-07;1.4e-06;9.1e-07;1.2e-06;1.9e-06;7.8e-07;1.7e-06;1.2e-06;1.1e-06;9.1e-07;1.9e-06;8.7e-07;1.3e-06;9.9e-07;6.6e-07;1.5e-06;8.3e-07;6.9e-07;9.6e-07;1.4e-06;1.4e-06;7.8e-07;1.5e-06;3.4e-07;8.1e-07;5.4e-07;2.1e-05;8e-04;0.00042;0.00061	0.028156783678847	GTA	M	.	263-298-delinframe	.	no-SNV	GU280_gp05	0.970675255608404
CAMB-78EEB	MN908947.3	27264	TTTTAAAGTTTCCATTTGGAATCTTGA	-	0.00641548148148148	0.0129259259259259	NA;NA;0.0041;0.0074;0.0074;0.0052;0.0053;0.006;0.0056;0.0064;0.0066;0.0061;0.0052;0.0057;0.0056;0.0062;0.0066;0.0067;0.007;0.0058;0.0058;0.0059;0.0063;0.005;0.0063;0.0047;0.0044	1.2e-06;2.2e-05;8.7e-05;0.00023;0.00018;0.00015;0.00017;0.00018;0.00012;2e-04;2e-04;0.00019;0.00016;0.00017;0.00018;0.00022;0.00021;2e-04;0.00028;0.00018;0.00021;0.00019;2e-04;0.00011;2e-04;9.5e-05;9.5e-05	0.00950059936002219	CTT	ORF6	.	63-89-delinframe	.	no-SNV	GU280_gp06	0.991754385964912
CAMB-78EEB	MN908947.3	27389	C	T	0.0059	0.022	0.00025	2.5e-11	0.0132912544759362	ACG	NA	NA	NA	NA	NA	NA	0.986658169974308
CAMB-78EEB	MN908947.3	29729	TCACCGAGGCCACGCGGAGTACGATCGAGTG	-	0.0184838709677419	0.0130645161290323	2.2e-08;4.6e-08;5.2e-09;3.4e-08;3.4e-08;6.5e-08;4.2e-08;7.5e-08;1.1e-07;1.2e-07;1.4e-07;8.5e-08;1.6e-07;1.9e-07;1.2e-07;1.8e-07;1.9e-07;1.7e-07;6.8e-07;2.2e-06;1.9e-06;1.3e-05;1.2e-05;2e-06;1.6e-06;1.6e-06;1.9e-06;8.5e-07;6e-06;2.2e-06;4.5e-06	7.1e-06;1.1e-05;4.6e-06;8.6e-06;9.2e-06;1.3e-05;1.4e-05;1.8e-05;2e-05;2.5e-05;3e-05;2.3e-05;3.4e-05;4.8e-07;3.1e-07;4.8e-07;4.3e-05;3.8e-05;7.8e-05;0.00018;0.00015;0.00035;0.00037;0.00013;1.5e-06;9.4e-05;9.7e-05;9.1e-05;0.00021;0.00013;0.00017	0.0154121063211972	TTC	NA	NA	NA	NA	NA	NA	0.984087292566492
CAMB-78EEB	MN908947.3	3037	C	T	1	1	0	0	0.997811534500515	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000193099897013388
CAMB-78EEB	MN908947.3	3177	C	A	0.0081	0.01	1.4e-05	1.4e-06	0.00899464727762873	CCT	ORF1ab:nsp3	P153H	C458A	CCT>CAT	Missense	ORF1ab:nsp3	0.990473968661301
CAMB-78EEB	MN908947.3	4105	G	A	0.0068	0.0076	5e-05	1.9e-05	0.00714086341644957	AGA	ORF1ab:nsp3	K462K	G1386A	AAG>AAA	Synonymous	ORF1ab:nsp3	0.99284750651284
CAMB-78EEB	MN908947.3	4493	AAAATACAAGAGGGTGTGGTTGATTATGGTGCTAGATTTTACT	-	0.0137441860465116	0.00247325581395349	1.4e-05;3.6e-06;2.3e-05;8.8e-06;1.2e-05;1.2e-05;8.5e-06;1.2e-05;1.1e-05;1.4e-05;1.4e-05;9.1e-05;2.1e-05;6.2e-05;8e-05;4.7e-05;4.1e-05;9.1e-05;2.2e-05;1.1e-05;7.9e-06;1.6e-05;1.3e-05;7.9e-06;0.00029;3.1e-05;4.5e-05;5.8e-05;3.9e-08;7.8e-09;1.8e-08;7.7e-09;7.4e-07;3.7e-06;0.00012;0.00011;1.1e-06;2.3e-05;5.3e-05;2e-04;0.00026;0.00026;0.00041	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.48;2.2e-06;2.7e-05;NA;0.027;0.03;NA;NA	0.00448320834691881	TAA	ORF1ab:nsp3	.	1774-1816-delfrshift	.	no-SNV	ORF1ab:nsp3	0.995141493351517
CAMB-78EEB	MN908947.3	522	TT	-	0.037	0.0225	6.1e-06;0.00031	0.0032;0.0028	0.0314084468440815	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.962929602837279
CAMB-78EEB	MN908947.3	5301	C	T	0.038	0.027	7.3e-17	1.2e-11	0.0348041080258653	GCA	ORF1ab:nsp3	A861V	C2582T	GCA>GTA	Missense	ORF1ab:nsp3	0.965195891974135
CAMB-78EEB	MN908947.3	5302	A	G	0.23	0.097	1.8e-98	1.3e-36	0.18580375782881	CAT	ORF1ab:nsp3	A861A	A2583G	GCA>GCG	Synonymous	ORF1ab:nsp3	0.81419624217119
CAMB-78EEB	MN908947.3	7263	T	-	0.043	0.077	1.9e-07	6.7e-09	0.0552995391705069	CTT	ORF1ab:nsp3	.	4544-4544-delfrshift	.	no-SNV	ORF1ab:nsp3	0.944700460829493
CAMB-78EEB	MN908947.3	8284	T	C	0.5	0.44	4.8e-291	2.5e-244	0.476597508735219	ATA	ORF1ab:nsp3	Y1855Y	T5565C	TAT>TAC	Synonymous	ORF1ab:nsp3	0.523402491264781
CAMB-78EEB	MN908947.3	8467	A	C	0.0095	0.017	3.4e-06	2.4e-09	0.0126384453353265	AAA	ORF1ab:nsp3	K1916N	A5748C	AAA>AAC	Missense	ORF1ab:nsp3	0.987293606033838
CAMB-78EEB	MN908947.3	8689	A	C	0.0045	0.0099	0.00028	2.4e-06	0.0067971405133013	GAT	ORF1ab:nsp4	G45G	A135C	GGA>GGC	Synonymous	ORF1ab:nsp4	0.993085667408883
CAMB-78EEB	MN908947.3	9336	TAAATTTACTTACTA	-	0.0197333333333333	0.00058	2.3e-09;7e-10;2.5e-09;4.1e-09;1.2e-09;6.8e-09;9.7e-09;4.4e-08;3.6e-08;1.8e-09;8.7e-09;7.8e-09;5.4e-09;6.9e-10;6.1e-11	NA;4.1e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00902151283830673	GTA	ORF1ab:nsp4	.	782-796-delinframe	.	no-SNV	ORF1ab:nsp4	0.990446371226718
CAMB-78EEB	MN908947.3	9485	T	C	0.23	0.28	1.1e-106	3e-130	0.257213583971532	ATA	ORF1ab:nsp4	Y311H	T931C	TAC>CAC	Missense	ORF1ab:nsp4	0.74263170109074
CAMB-78EEB	MN908947.3	9491	C	T	0.04	0.063	2.1e-18	6.5e-28	0.0522388059701493	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.947761194029851
CAMB-78EEB	MN908947.3	9744	A	G	0.026	0.021	4e-13	5.4e-11	0.0239255810563335	TAC	ORF1ab:nsp4	Y397C	A1190G	TAC>TGC	Missense	ORF1ab:nsp4	0.976065307907468
CAMB-78EEB	MN908947.3	9793	AG	-	0.0061	0.00875	6.4e-05;0.00012	4.2e-06;8.3e-06	0.00728319473636114	AAG	ORF1ab:nsp4	.	1239-1240-delfrshift	.	no-SNV	ORF1ab:nsp4	0.992300768007967
CAMB-78F24	MN908947.3	10078	C	T	0.012	0.021	3.2e-07	4.8e-11	0.0167531308859003	TCC	ORF1ab:3C-like-proteinase	F8F	C24T	TTC>TTT	Synonymous	ORF1ab:3C-like-proteinase	0.983147738162112
CAMB-78F24	MN908947.3	11075	T	-	0.029	0.033	1.5e-07	2.8e-08	0.0310469703368888	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964172425258126
CAMB-78F24	MN908947.3	14408	C	T	1	1	0	0	0.997773946045561	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00050177445694319
CAMB-78F24	MN908947.3	16431	A	G	0.0066	0.015	5.1e-05	2.2e-08	0.00974739154310818	TAG	ORF1ab:helicase	L65L	A195G	TTA>TTG	Synonymous	ORF1ab:helicase	0.990252608456892
CAMB-78F24	MN908947.3	23403	A	G	1	1	0	0	0.999913034025438	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.34829872812262e-05
CAMB-78F24	MN908947.3	23770	A	G	0.022	0.0071	4.3e-11	2.5e-05	0.0150630416186261	TAG	S	V736V	A2208G	GTA>GTG	Synonymous	GU280_gp02, spike glycoprotein	0.984936958381374
CAMB-78F24	MN908947.3	24014	A	G	0.18	0.2	2.3e-84	1.5e-94	0.189571701508041	TAT	S	I818V	A2452G	ATT>GTT	Missense	GU280_gp02, spike glycoprotein	0.809074214909759
CAMB-78F24	MN908947.3	241	C	T	1	1	0	0	0.997999538355005	TCG	NA	NA	NA	NA	NA	NA	0.000169269831499577
CAMB-78F24	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999878670225673	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000133695797495432
CAMB-78F24	MN908947.3	3037	C	T	1	1	0	0	0.999500748876685	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78F24	MN908947.3	835	C	T	0.013	0.0089	1.7e-07	1e-05	0.0109903058218628	TCT	ORF1ab:nsp2	F10F	C30T	TTC>TTT	Synonymous	ORF1ab:nsp2	0.987970649670612
CAMB-78F33	MN908947.3	11074	C	INS	0.15	0.13	7.4e-50	1.9e-40	0.139951931965243	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.859801565292414
CAMB-78F33	MN908947.3	14408	C	T	1	1	0	0	0.999483821014937	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000354873052230861
CAMB-78F33	MN908947.3	23403	A	G	1	1	0	0	0.999905796223774	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.7288411589756e-05
CAMB-78F33	MN908947.3	241	C	T	1	1	0	0	0.999933439829606	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-78F33	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999416796267496	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-78F33	MN908947.3	3037	C	T	1	1	0	0	0.999701759618252	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78F33	MN908947.3	686	AAGTCATTT	-	0.0288888888888889	0.142222222222222	0.00028;2e-04;0.00081;0.00027;0.00094;0.00032;9.6e-05;0.00037;0.0012	3.4e-20;1.6e-20;5.6e-18;2.6e-20;1e-17;8.1e-19;1.3e-20;9.1e-19;2.8e-16	0.0588329400471943	AAA	ORF1ab:leader-protein	.	421-429-delinframe	.	no-SNV	ORF1ab:leader-protein	0.941310155097484
CAMB-78F42	MN908947.3	16289	C	T	1	1	9.4e-210	9.4e-210	1	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0
CAMB-78F42	MN908947.3	23403	A	G	1	1	0	0	0.999900264299606	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.4933925098489e-05
CAMB-78F42	MN908947.3	241	C	T	1	1	0	0	0.999472481097239	TCG	NA	NA	NA	NA	NA	NA	0.000351679268507122
CAMB-78F42	MN908947.3	25429	G	T	1	1	0	0	1	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0
CAMB-78F42	MN908947.3	3037	C	T	1	1	2.2e-273	5.2e-140	0.998522895125554	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-78F60	MN908947.3	1059	C	T	1	1	0	0	0.999896399129753	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	7.40006216052215e-05
CAMB-78F60	MN908947.3	11075	T	-	0.032	0.031	2.8e-08	3.4e-08	0.0316914455097031	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.96820434440276
CAMB-78F60	MN908947.3	13006	T	C	1	1	0	0	0.999841857228706	CTG	ORF1ab:nsp9	A107A	T321C	GCT>GCC	Synonymous	ORF1ab:nsp9	0.000158142771293924
CAMB-78F60	MN908947.3	13240	G	A	0.0083	0.0083	2e-05	1.8e-05	0.00825601344490739	CGT	ORF1ab:nsp10	S72S	G216A	TCG>TCA	Synonymous	ORF1ab:nsp10	0.991729981443227
CAMB-78F60	MN908947.3	1437	C	T	1	1	0	0	1	TCT	ORF1ab:nsp2	S211F	C632T	TCT>TTT	Missense	ORF1ab:nsp2	0
CAMB-78F60	MN908947.3	14408	C	T	0.99	1	0	0	0.995428160476704	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00047516309652232
CAMB-78F60	MN908947.3	18645	ACCTGAGCGC	-	0.01115	0.00968	6.5e-05;3.2e-05;6e-05;7.6e-05;4.8e-05;0.00069;2.5e-05;3.4e-05;3.5e-05;4.1e-05	0.00013;7.4e-05;0.00012;0.00016;0.00012;0.0011;6.8e-05;9.2e-05;8e-05;9.7e-05	0.00796389216246097	GAC	ORF1ab:3'-to-5'-exonuclease	.	606-615-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.987065066634505
CAMB-78F60	MN908947.3	18698	C	T	0.11	0.053	7.7e-50	3.6e-24	0.0854201874327854	GCT	ORF1ab:3'-to-5'-exonuclease	A220V	C659T	GCT>GTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.914520722786201
CAMB-78F60	MN908947.3	23403	A	G	1	1	0	0	0.999914346161423	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.85230708614206e-05
CAMB-78F60	MN908947.3	241	C	T	1	1	0	0	0.999796804754769	TCG	NA	NA	NA	NA	NA	NA	5.07988113078154e-05
CAMB-78F60	MN908947.3	25563	G	T	1	1	0	0	0.999805662690226	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	7.47451191437199e-05
CAMB-78F60	MN908947.3	25688	C	T	1	1	0	0	1	GCT	ORF3a	A99V	C296T	GCT>GTT	Missense	GU280_gp03	0
CAMB-78F60	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.014775	0.0383333333333333	0.13;0.21;0.017;0.017;0.0086;0.013;0.011;0.017;0.014;0.015;0.021;0.012;0.019;0.015;0.015;0.014;0.02;0.013;0.017;0.015;0.012;0.018;0.014;0.0084;0.013;0.018;0.017;0.012;0.017;0.013;0.014;0.011;0.14;0.15;0.14;0.13	0.00027;0.00036;1.5e-06;1.5e-06;6.1e-07;7.9e-07;7e-07;1.5e-06;8.3e-07;1.1e-06;2e-06;7.7e-07;1.7e-06;1.2e-06;1.1e-06;7.7e-07;1.9e-06;9.8e-07;1.2e-06;1e-06;6.1e-07;1.6e-06;8.7e-07;2.6e-06;7e-07;1.5e-06;3.9e-07;3.2e-07;8e-07;4.4e-07;8.9e-07;4.8e-07;1e-04;0.00042;0.00015;0.00024	0.0263700809867656	GTA	M	.	263-298-delinframe	.	no-SNV	GU280_gp05	0.981931708902764
CAMB-78F60	MN908947.3	29067	C	T	0.0031	0.011	0.002	7e-07	0.00629679710993158	ACT	N	T265I	C794T	ACT>ATT	Missense	GU280_gp10	0.993683020848049
CAMB-78F60	MN908947.3	3037	C	T	1	1	0	0	0.999558069648223	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000265158211065936
CAMB-78F60	MN908947.3	3176	C	T	0.011	0.0024	4.2e-07	0.004	0.00770964298422488	ACC	ORF1ab:nsp3	P153S	C457T	CCT>TCT	Missense	ORF1ab:nsp3	0.99217174712371
CAMB-78F60	MN908947.3	4579	T	A	0.007	0.011	1.8e-05	3.4e-07	0.00808149150503684	TTA	ORF1ab:nsp3	L620L	T1860A	CTT>CTA	Synonymous	ORF1ab:nsp3	0.991880920162382
CAMB-78F60	MN908947.3	5691	CAC	-	0.00443333333333333	0.0097	0.00074;0.001;0.00074	3.3e-06;7.6e-06;3.4e-06	0.00642953106007293	GCA	ORF1ab:nsp3	.	2972-2974-delinframe	.	no-SNV	ORF1ab:nsp3	0.993314567206193
CAMB-78F60	MN908947.3	5906	ACTTA	-	0.00306	0.0132	0.1;0.097;0.075;0.22;0.0014	2e-06;2.1e-06;3.8e-07;2.7e-05;0.00022	0.00577208823865585	TAC	ORF1ab:nsp3	.	3187-3191-delfrshift	.	no-SNV	ORF1ab:nsp3	0.994271685761047
CAMB-78F60	MN908947.3	9624	TTTCT	-	0.01006	0.001806	2.5e-05;8.9e-06;6.1e-06;2.3e-06;0.00022	NA;NA;NA;NA;0.00051	0.00530653858909949	GTT	ORF1ab:nsp4	.	1070-1074-delfrshift	.	no-SNV	ORF1ab:nsp4	0.994595192177769
CAMB-78F60	MN908947.3	9741	A	T	0.0085	0.0014	7.2e-06	0.0047	0.00526290834953298	AAT	ORF1ab:nsp4	N396I	A1187T	AAT>ATT	Missense	ORF1ab:nsp4	0.994689678061732
CAMB-78F7F	MN908947.3	10030	C	T	0.0079	0.0094	1.2e-05	2.6e-06	0.00858787937933054	CCT	ORF1ab:nsp4	T492T	C1476T	ACC>ACT	Synonymous	ORF1ab:nsp4	0.991363325851469
CAMB-78F7F	MN908947.3	10609	TG	-	0.006	0.017	NA;2.1e-06	7.1e-09;1.9e-08	0.0106142959696441	TTG	ORF1ab:3C-like-proteinase	.	555-556-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.992496765847348
CAMB-78F7F	MN908947.3	10610	G	-	0.012	0.017	2.1e-06	1.9e-08	0.0137724246582304	TGT	ORF1ab:3C-like-proteinase	.	556-556-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.98622757534177
CAMB-78F7F	MN908947.3	11074	C	INS	0.11	0.094	2.9e-43	8e-34	0.101982675649663	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.892730189284568
CAMB-78F7F	MN908947.3	11083	G	-	0.18	0.22	1.8e-81	1.2e-99	0.199230638683034	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.13141370141992e-05
CAMB-78F7F	MN908947.3	11083	G	T	0.82	0.78	0	2.59999999999996e-312	0.800622277535781	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.13141370141992e-05
CAMB-78F7F	MN908947.3	13627	G	T	1	1	0	0	0.999925533182414	TGA	ORF1ab:RNA-dependent-RNA-polymerase	D54Y	G160T	GAC>TAC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	1.48933635172167e-05
CAMB-78F7F	MN908947.3	14408	C	T	0.012	0.0081	1.5e-06	6.4e-05	0.0103885915296916	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.989586101304584
CAMB-78F7F	MN908947.3	14536	C	T	0.0063	0.0092	9.9e-05	5e-06	0.00765332990064714	ACT	ORF1ab:RNA-dependent-RNA-polymerase	L357F	C1069T	CTT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.992323265420758
CAMB-78F7F	MN908947.3	14805	C	T	0.99	1	0	0	0.995841149355087	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-78F7F	MN908947.3	15540	C	T	1	1	0	0	0.99996489832214	TCA	ORF1ab:RNA-dependent-RNA-polymerase	V691V	C2073T	GTC>GTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	3.51016778602017e-05
CAMB-78F7F	MN908947.3	15806	A	-	0.0041	0.0099	0.0023	6.9e-06	0.00707575502751015	CAA	ORF1ab:RNA-dependent-RNA-polymerase	.	2339-2339-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.992864179140338
CAMB-78F7F	MN908947.3	1616	C	T	0.0081	0.015	1e-05	9e-09	0.0110042669606582	TCT	ORF1ab:nsp2	L271F	C811T	CTT>TTT	Missense	ORF1ab:nsp2	0.988995733039342
CAMB-78F7F	MN908947.3	1714	C	T	0.0088	0.024	6.1e-06	2.8e-12	0.0151511530648823	CCA	ORF1ab:nsp2	S303S	C909T	TCC>TCT	Synonymous	ORF1ab:nsp2	0.984801051499582
CAMB-78F7F	MN908947.3	18525	G	T	1	1	0	0	0.999900155757019	TGC	ORF1ab:3'-to-5'-exonuclease	V162V	G486T	GTG>GTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	1.99688485961899e-05
CAMB-78F7F	MN908947.3	21614	C	T	0.031	0.014	3.5e-13	6.2e-07	0.0226465364120782	TCT	S	L18F	C52T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.977353463587922
CAMB-78F7F	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-78F7F	MN908947.3	27132	TA	-	0.019	0.016	3.8e-05;7.6e-05	0.00026;0.00045	0.0174551957392217	CTA	M	.	610-611-delfrshift	.	no-SNV	GU280_gp05	0.982594936708861
CAMB-78F7F	MN908947.3	28122	G	A	0.025	0.017	6.9e-13	1.9e-09	0.0212049268480753	CGG	ORF8	G77S	G229A	GGT>AGT	Missense	GU280_gp09	0.978764635457884
CAMB-78F7F	MN908947.3	28338	A	G	1	1	0	0	0.999930788663183	GAT	N	D22G	A65G	GAT>GGT	Missense	GU280_gp10	4.61408912113137e-05
CAMB-78F7F	MN908947.3	29545	C	T	0.49	0.43	1.4e-213	9.49999999999999e-184	0.453598484848485	ACC	NA	NA	NA	NA	NA	NA	0.545612373737374
CAMB-78F7F	MN908947.3	3833	T	-	0.0052	0.011	0.0071	3e-05	0.00757474192250972	CTT	ORF1ab:nsp3	.	1114-1114-delfrshift	.	no-SNV	ORF1ab:nsp3	0.992358224963132
CAMB-78F7F	MN908947.3	5778	AT	-	0.016	0.0135	1.3e-07;1.6e-08	8.9e-07;3.2e-07	0.014815644125989	CAT	ORF1ab:nsp3	.	3059-3060-delfrshift	.	no-SNV	ORF1ab:nsp3	0.985997414907367
CAMB-78F7F	MN908947.3	5974	C	T	0.0049	0.01	0.00048	3.6e-06	0.00741239892183288	ACA	ORF1ab:nsp3	D1085D	C3255T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.988376010781671
CAMB-78F7F	MN908947.3	934	C	T	0.0029	0.014	0.0023	3.6e-08	0.00759493670886076	ACA	ORF1ab:nsp2	D43D	C129T	GAC>GAT	Synonymous	ORF1ab:nsp2	0.992385884158036
CAMB-78F7F	MN908947.3	9858	TAT	-	0.00403333333333333	0.0126666666666667	0.0039;0.0028;NA	3.6e-05;1.6e-05;6.2e-05	0.00910536204653852	CTA	ORF1ab:nsp4	.	1304-1306-delinframe	.	no-SNV	ORF1ab:nsp4	0.991014424213762
CAMB-78F9D	MN908947.3	11074	C	INS	0.1	0.097	5.6e-34	6.9e-34	0.0993797039120007	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.895707551071045
CAMB-78F9D	MN908947.3	11083	G	-	0.18	0.18	2.8e-79	1.7e-78	0.176164905595011	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	4.33050407067383e-05
CAMB-78F9D	MN908947.3	11083	G	T	0.82	0.82	0	0	0.823633004215024	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	4.33050407067383e-05
CAMB-78F9D	MN908947.3	11651	C	INS	0.022	0.022	2.7e-10	3.2e-10	0.0217774803820184	CCT	ORF1ab:nsp6	.	678-679-insfrshift	.	no-SNV	ORF1ab:nsp6	0.971500699555934
CAMB-78F9D	MN908947.3	11651	C	T	0.0055	0.0077	0.00022	3.1e-05	0.00663057363586593	CCT	ORF1ab:nsp6	L227F	C679T	CTC>TTC	Missense	ORF1ab:nsp6	0.971500699555934
CAMB-78F9D	MN908947.3	11653	C	T	1	1	0	0	0.996811005158668	TCT	ORF1ab:nsp6	L227L	C681T	CTC>CTT	Synonymous	ORF1ab:nsp6	9.37939659215257e-05
CAMB-78F9D	MN908947.3	1376	C	T	0.0072	0.0083	8.2e-05	3e-05	0.00775310879524745	TCC	ORF1ab:nsp2	P191S	C571T	CCA>TCA	Missense	ORF1ab:nsp2	0.992246891204753
CAMB-78F9D	MN908947.3	14134	C	T	0.011	0.011	5.9e-07	6.4e-07	0.0111705408671111	TCC	ORF1ab:RNA-dependent-RNA-polymerase	P223S	C667T	CCT>TCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.988787210491183
CAMB-78F9D	MN908947.3	14805	C	T	1	1	0	0	0.999497468378435	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00020859803159312
CAMB-78F9D	MN908947.3	21137	A	G	1	1	0	0	0.999899779514933	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	2.50551212667869e-05
CAMB-78F9D	MN908947.3	21987	G	A	1	1	0	0	0.999273705447209	GGT	S	G142D	G425A	GGT>GAT	Missense	GU280_gp02, spike glycoprotein	0.000295897780766644
CAMB-78F9D	MN908947.3	22215	A	C	0.011	0.003	4.3e-06	0.0031	0.00652472527472527	CAG	S	Q218P	A653C	CAG>CCG	Missense	GU280_gp02, spike glycoprotein	0.993131868131868
CAMB-78F9D	MN908947.3	2480	A	G	1	1	0	0	0.999807840122982	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000144119907763259
CAMB-78F9D	MN908947.3	2558	C	T	1	1	0	0	0.99964127228762	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	6.64310578481652e-05
CAMB-78F9D	MN908947.3	26144	G	T	1	1	0	0	0.999844048500916	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	7.79757495418925e-05
CAMB-78F9D	MN908947.3	3775	C	T	0.03	0.024	7e-14	3.5e-11	0.0270701098455207	GCA	ORF1ab:nsp3	R352R	C1056T	CGC>CGT	Synonymous	ORF1ab:nsp3	0.972929890154479
CAMB-78F9D	MN908947.3	6312	C	T	1	1	0	0	0.999220413903958	ACA	ORF1ab:nsp3	T1198I	C3593T	ACA>ATA	Missense	ORF1ab:nsp3	0.000192887281494876
CAMB-78F9D	MN908947.3	8251	C	T	0.027	0.027	1.7e-13	1.6e-13	0.0273700438615538	ACA	ORF1ab:nsp3	D1844D	C5532T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.972608242497937
CAMB-78F9D	MN908947.3	9724	C	T	1	1	0	0	0.999408087887111	TCT	ORF1ab:nsp4	F390F	C1170T	TTC>TTT	Synonymous	ORF1ab:nsp4	7.10294535467374e-05
CAMB-78FAC	MN908947.3	11075	T	-	0.041	0.036	3e-10	2.9e-09	0.0389484562717995	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956056495715454
CAMB-78FAC	MN908947.3	14408	C	T	1	1	0	0	0.998775002008193	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000522130291589686
CAMB-78FAC	MN908947.3	1887	C	T	1	1	0	0	0.999428195671441	GCT	ORF1ab:nsp2	A361V	C1082T	GCT>GTT	Missense	ORF1ab:nsp2	0.000571804328558767
CAMB-78FAC	MN908947.3	21575	C	T	0.018	0.017	1.8e-05	3.8e-05	0.0176937156802929	TCT	S	L5F	C13T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.981899532235103
CAMB-78FAC	MN908947.3	23403	A	G	1	1	0	0	0.999301958482394	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.5187479673507e-05
CAMB-78FAC	MN908947.3	241	C	T	1	1	0	0	0.997670665052639	TCG	NA	NA	NA	NA	NA	NA	9.17061002897913e-05
CAMB-78FAC	MN908947.3	2449	C	T	0.01	0.013	4.7e-06	4.3e-07	0.0113532459615971	GCC	ORF1ab:nsp2	G548G	C1644T	GGC>GGT	Synonymous	ORF1ab:nsp2	0.988646754038403
CAMB-78FAC	MN908947.3	25252	G	T	0.01	0.0092	2e-06	3.5e-06	0.00966728429871908	TGA	S	V1230V	G3690T	GTG>GTT	Synonymous	GU280_gp02, spike glycoprotein	0.990211874647547
CAMB-78FAC	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999194613575594	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	7.33621891277236e-05
CAMB-78FAC	MN908947.3	3037	C	T	1	1	0	0	0.998940178991993	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000117757889778615
CAMB-78FAC	MN908947.3	3704	C	T	1	1	0	0	0.999626377732113	ACC	ORF1ab:nsp3	P329S	C985T	CCA>TCA	Missense	ORF1ab:nsp3	0.000186811133943583
CAMB-78FAC	MN908947.3	8043	C	T	0.21	0.2	5.3e-100	3.1e-95	0.207302902295315	GCT	ORF1ab:nsp3	A1775V	C5324T	GCT>GTT	Missense	ORF1ab:nsp3	0.792656085524067
CAMB-78FD9	MN908947.3	10066	A	C	0.024	0.022	8.8e-12	6.3e-11	0.0227239097807935	GAA	ORF1ab:3C-like-proteinase	R4S	A12C	AGA>AGC	Missense	ORF1ab:3C-like-proteinase	0.976472826431606
CAMB-78FD9	MN908947.3	11003	C	G	0.012	0.011	3.7e-07	5.2e-07	0.0116339698885485	ACA	ORF1ab:nsp6	H11D	C31G	CAC>GAC	Missense	ORF1ab:nsp6	0.988170501205762
CAMB-78FD9	MN908947.3	11074	C	INS	0.093	0.087	3e-32	2.2e-30	0.0895676471802778	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.904017949317953
CAMB-78FD9	MN908947.3	11083	G	-	0.11	0.11	7.8e-47	8.4e-48	0.110036188178528	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.309915560916767
CAMB-78FD9	MN908947.3	11083	G	T	0.58	0.58	1.8e-176	3.6e-178	0.579686369119421	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.309915560916767
CAMB-78FD9	MN908947.3	11714	A	G	0.02	0.022	3.9e-08	5.3e-09	0.0213036565977742	TAC	ORF1ab:nsp6	T248A	A742G	ACA>GCA	Missense	ORF1ab:nsp6	0.978696343402226
CAMB-78FD9	MN908947.3	11747	C	G	0.041	0.037	2.7e-05	6.9e-05	0.039135959339263	ACT	ORF1ab:nsp6	L259V	C775G	CTA>GTA	Missense	ORF1ab:nsp6	0.960609911054638
CAMB-78FD9	MN908947.3	11817	C	A	0.021	0.014	3.4e-09	6.4e-07	0.0173464603844351	CCT	ORF1ab:nsp6	P282H	C845A	CCT>CAT	Missense	ORF1ab:nsp6	0.982184716361931
CAMB-78FD9	MN908947.3	14691	A	T	0.0064	0.0087	6.5e-05	6.5e-06	0.00752800417553298	AAG	ORF1ab:RNA-dependent-RNA-polymerase	K408N	A1224T	AAA>AAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.992251174368651
CAMB-78FD9	MN908947.3	14760	C	T	0.28	0.28	9.6e-138	2.3e-139	0.278437841557706	TCT	ORF1ab:RNA-dependent-RNA-polymerase	F431F	C1293T	TTC>TTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.721410355017609
CAMB-78FD9	MN908947.3	14805	C	T	0.71	0.71	0	0	0.711956310490924	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.287800754071598
CAMB-78FD9	MN908947.3	15240	C	T	0.0094	0.01	1e-05	3.3e-06	0.00991615020051039	ACA	ORF1ab:RNA-dependent-RNA-polymerase	N591N	C1773T	AAC>AAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.989923441487423
CAMB-78FD9	MN908947.3	1605	ATG	-	0.27	0.273333333333333	5.7e-134;2.5e-130;2.9e-130	3.3e-136;7.1e-134;2.2e-133	0.27058935542226	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.723820882275444
CAMB-78FD9	MN908947.3	16056	T	C	0.012	0.013	4.9e-07	1.8e-07	0.0122826120139617	ATC	ORF1ab:RNA-dependent-RNA-polymerase	H863H	T2589C	CAT>CAC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.987676683389472
CAMB-78FD9	MN908947.3	16466	C	T	0.024	0.022	1.9e-07	5.6e-07	0.0231975525738925	CCA	ORF1ab:helicase	P77L	C230T	CCA>CTA	Missense	ORF1ab:helicase	0.970804326355599
CAMB-78FD9	MN908947.3	16915	C	T	0.017	0.018	2e-08	6.3e-09	0.0176420981615787	GCT	ORF1ab:helicase	L227L	C679T	CTG>TTG	Synonymous	ORF1ab:helicase	0.980114690504301
CAMB-78FD9	MN908947.3	17093	C	G	0.016	0.015	1.7e-08	3.6e-08	0.0152125488522229	ACT	ORF1ab:helicase	T286S	C857G	ACT>AGT	Missense	ORF1ab:helicase	0.984634058502621
CAMB-78FD9	MN908947.3	17491	C	T	0.28	0.27	3.6e-137	1.4e-134	0.275707506602046	ACC	ORF1ab:helicase	P419S	C1255T	CCA>TCA	Missense	ORF1ab:helicase	0.724221666852165
CAMB-78FD9	MN908947.3	19893	T	C	0.0094	0.0074	6.3e-06	4.3e-05	0.00841014600013456	ATG	ORF1ab:endoRNAse	D91D	T273C	GAT>GAC	Synonymous	ORF1ab:endoRNAse	0.991455291663863
CAMB-78FD9	MN908947.3	20270	C	T	0.22	0.24	4.5e-48	1.1e-66	0.233155080213904	GCT	ORF1ab:endoRNAse	A217V	C650T	GCT>GTT	Missense	ORF1ab:endoRNAse	0.765775401069519
CAMB-78FD9	MN908947.3	21618	C	G	0.01	0.011	4.4e-06	1.9e-06	0.0107905982905983	ACA	S	T19R	C56G	ACA>AGA	Missense	GU280_gp02, spike glycoprotein	0.988888888888889
CAMB-78FD9	MN908947.3	21639	C	G	0.015	0.014	1.5e-07	2.7e-07	0.0146079484425349	CCT	S	P26R	C77G	CCT>CGT	Missense	GU280_gp02, spike glycoprotein	0.984425349087003
CAMB-78FD9	MN908947.3	21846	C	A	0.0081	0.011	0.00013	1.7e-05	0.00947618855599016	ACT	S	T95N	C284A	ACT>AAT	Missense	GU280_gp02, spike glycoprotein	0.987822089600387
CAMB-78FD9	MN908947.3	22191	T	C	0.028	0.023	1.2e-13	1.9e-11	0.0252696130260097	ATT	S	I210T	T629C	ATT>ACT	Missense	GU280_gp02, spike glycoprotein	0.97473038697399
CAMB-78FD9	MN908947.3	22743	A	C	0.12	0.13	5.8e-53	4.8e-56	0.12438265200249	AAT	S	N394T	A1181C	AAT>ACT	Missense	GU280_gp02, spike glycoprotein	0.874621290724217
CAMB-78FD9	MN908947.3	23525	C	T	0.043	0.038	1.2e-19	1.3e-17	0.0409658899020601	ACA	S	H655Y	C1963T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.958899020601148
CAMB-78FD9	MN908947.3	2480	A	G	0.73	0.72	0	0	0.722036563790053	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.277897909704475
CAMB-78FD9	MN908947.3	2558	C	T	0.73	0.72	0	0	0.725016795431643	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.274542324487739
CAMB-78FD9	MN908947.3	25757	G	T	0.036	0.042	9.8e-17	1.9e-19	0.0383954000752324	AGA	ORF3a	R122I	G365T	AGA>ATA	Missense	GU280_gp03	0.961604599924768
CAMB-78FD9	MN908947.3	26144	G	T	0.71	0.72	0	0	0.717340828546988	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.282659171453012
CAMB-78FD9	MN908947.3	26224	C	G	0.013	0.011	5.4e-07	2.8e-06	0.0121639401236254	ACA	NA	NA	NA	NA	NA	NA	0.981418960851972
CAMB-78FD9	MN908947.3	26748	A	G	0.011	0.007	5.9e-07	3.1e-05	0.00891535635306204	GAT	M	I76V	A226G	ATC>GTC	Missense	GU280_gp05	0.990840864371659
CAMB-78FD9	MN908947.3	27689	C	T	0.74	0.74	4.8e-286	0	0.743225806451613	CCA	ORF7a	P99L	C296T	CCA>CTA	Missense	GU280_gp07	0.256774193548387
CAMB-78FD9	MN908947.3	27922	T	G	0.25	0.26	9.6e-121	1.6e-123	0.255085508550855	ATC	ORF8	I10S	T29G	ATC>AGC	Missense	GU280_gp09	0.744284428442844
CAMB-78FD9	MN908947.3	28253	C	T	0.011	0.012	8.7e-06	3.9e-06	0.0112372288115178	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.987459082600008
CAMB-78FD9	MN908947.3	29414	G	A	0.95	0.94	0	0	0.948866631523458	AGC	N	A381T	G1141A	GCC>ACC	Missense	GU280_gp10	0.0511333684765419
CAMB-78FD9	MN908947.3	29683	A	T	0.24	0.25	1.9e-112	5.5e-114	0.245102239532619	TAA	NA	NA	NA	NA	NA	NA	0.754352482960078
CAMB-78FD9	MN908947.3	29784	C	T	0.0096	0.011	1.8e-05	6.8e-06	0.0102885565359588	GCT	NA	NA	NA	NA	NA	NA	0.989234490512043
CAMB-78FD9	MN908947.3	3236	C	G	0.013	0.011	1.9e-07	1e-06	0.0116894472824336	ACA	ORF1ab:nsp3	Q173E	C517G	CAA>GAA	Missense	ORF1ab:nsp3	0.988264531271573
CAMB-78FD9	MN908947.3	3874	C	A	0.26	0.26	2e-127	3.1e-126	0.263480392156863	TCG	ORF1ab:nsp3	I385I	C1155A	ATC>ATA	Synonymous	ORF1ab:nsp3	0.735814022578728
CAMB-78FD9	MN908947.3	3987	C	T	0.0041	0.0069	0.00064	4.3e-05	0.00546277508974559	ACA	ORF1ab:nsp3	T423I	C1268T	ACA>ATA	Missense	ORF1ab:nsp3	0.994381145621976
CAMB-78FD9	MN908947.3	7006	C	G	0.015	0.02	1.1e-06	2.2e-08	0.0170517051705171	CCG	ORF1ab:nsp3	T1429T	C4287G	ACC>ACG	Synonymous	ORF1ab:nsp3	0.982123212321232
CAMB-78FD9	MN908947.3	8921	C	A	0.0064	0.007	6.4e-05	3.1e-05	0.00666354683812159	ACC	ORF1ab:nsp4	P123T	C367A	CCT>ACT	Missense	ORF1ab:nsp4	0.993102466020998
CAMB-78FD9	MN908947.3	9116	G	A	0.01	0.0069	1.2e-06	3e-05	0.0085293678818322	TGA	ORF1ab:nsp4	D188N	G562A	GAC>AAC	Missense	ORF1ab:nsp4	0.991197095538867
CAMB-78FD9	MN908947.3	9438	C	T	0.0085	0.0088	2.3e-05	1.9e-05	0.00865475070555033	ACA	ORF1ab:nsp4	T295I	C884T	ACA>ATA	Missense	ORF1ab:nsp4	0.99134524929445
CAMB-78FD9	MN908947.3	9458	A	G	0.043	0.05	6.8e-20	1.1e-22	0.0466681137399609	TAT	ORF1ab:nsp4	M302V	A904G	ATG>GTG	Missense	ORF1ab:nsp4	0.953259532595326
CAMB-78FD9	MN908947.3	9531	T	C	0.026	0.026	3.7e-13	2.9e-13	0.0261542759088551	TTC	ORF1ab:nsp4	F326S	T977C	TTC>TCC	Missense	ORF1ab:nsp4	0.973773893611078
CAMB-78FD9	MN908947.3	959	C	T	0.73	0.72	0	0	0.721626727652381	CCG	ORF1ab:nsp2	R52C	C154T	CGT>TGT	Missense	ORF1ab:nsp2	0.278065029332803
CAMB-78FD9	MN908947.3	9615	C	T	0.7	0.7	0	0	0.702242529910419	ACT	ORF1ab:nsp4	T354I	C1061T	ACT>ATT	Missense	ORF1ab:nsp4	0.297396741417664
CAMB-78FD9	MN908947.3	9618	A	G	0.016	0.018	3.6e-09	1.2e-09	0.0170336796224246	AAT	ORF1ab:nsp4	N355S	A1064G	AAT>AGT	Missense	ORF1ab:nsp4	0.98244488120546
CAMB-78FD9	MN908947.3	9627	C	G	0.013	0.012	2.5e-07	1.1e-06	0.0125688061567814	TCT	ORF1ab:nsp4	S358C	C1073G	TCT>TGT	Missense	ORF1ab:nsp4	0.986038956853544
CAMB-78FF7	MN908947.3	10097	G	A	1	1	0	0	0.999930417840866	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	6.95821591343979e-05
CAMB-78FF7	MN908947.3	11075	T	-	0.058	0.043	8.3e-14	1.3e-10	0.0508087609318164	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.946811392307097
CAMB-78FF7	MN908947.3	12792	AGGGAGGTAGGTTTGT	-	0.00844375	0.0002208125	2.4e-05;5.3e-05;2.4e-05;3.4e-05;4.3e-05;3.8e-05;3.1e-05;2.1e-05;5.7e-06;3e-05;2.5e-05;1.2e-05;5.2e-06;1.8e-05;2.9e-05;2e-05	NA;NA;NA;NA;NA;0.0032;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00423202723449703	AAG	ORF1ab:nsp9	.	107-122-delfrshift	.	no-SNV	ORF1ab:nsp9	0.994965396608107
CAMB-78FF7	MN908947.3	13499	C	T	0.0078	0.019	2.1e-05	1.4e-09	0.0112326337570204	ACA	ORF1ab:RNA-dependent-RNA-polymerase	T11I	C32T	ACA>ATA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.988570302492856
CAMB-78FF7	MN908947.3	13536	C	T	1	1	0	0	0.999553471757089	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000223264121455682
CAMB-78FF7	MN908947.3	14184	C	T	1	1	0	0	0.999852817493692	CCA	ORF1ab:RNA-dependent-RNA-polymerase	T239T	C717T	ACC>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000136669470142977
CAMB-78FF7	MN908947.3	14408	C	T	1	1	0	0	0.996863720963712	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000483295458050983
CAMB-78FF7	MN908947.3	15763	C	T	0.0086	0.0022	1.1e-05	0.0065	0.00557644554806669	TCT	ORF1ab:RNA-dependent-RNA-polymerase	L766L	C2296T	CTA>TTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.991159985810571
CAMB-78FF7	MN908947.3	16949	C	T	0.063	0.036	8.3e-29	1.8e-17	0.0509046763786337	CCT	ORF1ab:helicase	P238L	C713T	CCT>CTT	Missense	ORF1ab:helicase	0.949012173218918
CAMB-78FF7	MN908947.3	17721	G	T	0.0023	0.019	0.0082	4.3e-10	0.0092563528435209	TGG	ORF1ab:helicase	V495V	G1485T	GTG>GTT	Synonymous	ORF1ab:helicase	0.98918813345331
CAMB-78FF7	MN908947.3	17750	C	T	0.019	0.032	4.7e-10	6.2e-16	0.0242910389591984	GCT	ORF1ab:helicase	A505V	C1514T	GCT>GTT	Missense	ORF1ab:helicase	0.975694788906053
CAMB-78FF7	MN908947.3	18029	C	T	0.036	0.031	3.1e-17	3.2e-15	0.0338865235902337	GCA	ORF1ab:helicase	A598V	C1793T	GCA>GTA	Missense	ORF1ab:helicase	0.966050284757384
CAMB-78FF7	MN908947.3	18695	C	T	0.0035	0.0073	0.0018	3.9e-05	0.00525415954297152	ACT	ORF1ab:3'-to-5'-exonuclease	T219I	C656T	ACT>ATT	Missense	ORF1ab:3'-to-5'-exonuclease	0.994714565697844
CAMB-78FF7	MN908947.3	18910	G	T	0.071	0.043	7.5e-32	6.5e-20	0.0579441587374295	TGA	ORF1ab:3'-to-5'-exonuclease	D291Y	G871T	GAC>TAC	Missense	ORF1ab:3'-to-5'-exonuclease	0.942045430885507
CAMB-78FF7	MN908947.3	21058	C	T	1	1	0	0	0.999835844906267	CCC	ORF1ab:2'-O-ribose-methyltransferase	P134S	C400T	CCT>TCT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.000114908565612791
CAMB-78FF7	MN908947.3	21510	A	T	0.0036	0.012	0.00099	1.3e-06	0.0071296540797465	AAA	ORF1ab:2'-O-ribose-methyltransferase	E284D	A852T	GAA>GAT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.991021917084764
CAMB-78FF7	MN908947.3	23403	A	G	1	1	0	0	0.999806934898448	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000185342497490154
CAMB-78FF7	MN908947.3	23731	C	T	1	1	0	0	0.999923430321593	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	3.82848392036753e-05
CAMB-78FF7	MN908947.3	241	C	T	1	1	0	0	0.999625592811382	TCG	NA	NA	NA	NA	NA	NA	0.000228804393044346
CAMB-78FF7	MN908947.3	25413	C	T	0.0096	0.0086	1e-05	2.5e-05	0.00915387560474749	TCT	ORF3a	I7I	C21T	ATC>ATT	Synonymous	GU280_gp03	0.99082292065481
CAMB-78FF7	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998699709346795	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00026628794603231
CAMB-78FF7	MN908947.3	3037	C	T	1	1	0	0	0.999338561844468	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000236227912690163
CAMB-78FF7	MN908947.3	4002	C	T	1	1	0	0	0.999594752038904	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0.000202623980548098
CAMB-78FF7	MN908947.3	4074	TTG	-	0.00303333333333333	0.0102666666666667	0.002;0.0045;0.0051	8.5e-07;5.5e-06;7e-06	0.00619195046439629	CTT	ORF1ab:nsp3	.	1355-1357-delinframe	.	no-SNV	ORF1ab:nsp3	0.99333973020263
CAMB-78FF7	MN908947.3	583	C	T	1	1	0	0	0.999860271771405	TCC	ORF1ab:leader-protein	V106V	C318T	GTC>GTT	Synonymous	ORF1ab:leader-protein	0.000139728228595382
CAMB-79002	MN908947.3	11074	C	INS	0.099	0.1	4.6e-35	1.8e-36	0.100906653814874	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.895523961565107
CAMB-79002	MN908947.3	11083	G	-	0.18	0.18	5.4e-82	4.3e-82	0.182820220448499	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	4.07232448281479e-05
CAMB-79002	MN908947.3	11083	G	T	0.82	0.82	0	0	0.817003312157246	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	4.07232448281479e-05
CAMB-79002	MN908947.3	14805	C	T	1	1	0	0	0.999276646901807	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000173197220694011
CAMB-79002	MN908947.3	15831	A	T	1	1	0	0	0.999718301506346	CAA	ORF1ab:RNA-dependent-RNA-polymerase	A788A	A2364T	GCA>GCT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	5.93049460324991e-05
CAMB-79002	MN908947.3	20649	A	T	0.022	0.024	3.7e-11	7.7e-12	0.0231319992656508	CAA	ORF1ab:endoRNAse	P343P	A1029T	CCA>CCT	Synonymous	ORF1ab:endoRNAse	0.976454929318891
CAMB-79002	MN908947.3	23707	C	T	1	1	0	0	0.999571550985433	CCA	S	P715P	C2145T	CCC>CCT	Synonymous	GU280_gp02, spike glycoprotein	0.000296618548546569
CAMB-79002	MN908947.3	26144	G	T	1	1	0	0	0.999846563011457	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000102291325695581
CAMB-79002	MN908947.3	27147	G	C	0.052	0.055	5e-24	2.9e-25	0.0535974636088033	AGA	M	D209H	G625C	GAC>CAC	Missense	GU280_gp05	0.946171113836755
CAMB-79002	MN908947.3	27384	T	C	0.049	0.047	1e-22	6.9e-22	0.0482631327089661	ATT	ORF6	D61D	T183C	GAT>GAC	Synonymous	GU280_gp06	0.951522017246599
CAMB-79002	MN908947.3	29020	A	G	1	1	0	0	0.999478003048462	AAT	N	K249K	A747G	AAA>AAG	Synonymous	GU280_gp10	2.08798780615121e-05
CAMB-79002	MN908947.3	7963	T	C	1	1	0	0	0.999526776559666	GTC	ORF1ab:nsp3	C1748C	T5244C	TGT>TGC	Synonymous	ORF1ab:nsp3	0.000315482293556274
CAMB-79011	MN908947.3	11074	C	INS	0.025	0.025	4.7e-05	4.4e-05	0.024794789220078	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.974963074166445
CAMB-79011	MN908947.3	11075	T	-	0.046	0.039	2.8e-11	1.1e-09	0.042121556929196	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95420856782606
CAMB-79011	MN908947.3	1141	G	T	0.0098	0.0088	3.6e-06	1.1e-05	0.00926332546522479	AGC	ORF1ab:nsp2	K112N	G336T	AAG>AAT	Missense	ORF1ab:nsp2	0.990681780754241
CAMB-79011	MN908947.3	14408	C	T	1	1	0	0	0.997958191541079	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000729217306757414
CAMB-79011	MN908947.3	14681	A	G	1	1	0	0	0.999453239130992	AAT	ORF1ab:RNA-dependent-RNA-polymerase	N405S	A1214G	AAT>AGT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000162319632986767
CAMB-79011	MN908947.3	18651	G	T	1	1	0	0	0.99873357370601	AGC	ORF1ab:3'-to-5'-exonuclease	E204D	G612T	GAG>GAT	Missense	ORF1ab:3'-to-5'-exonuclease	1.48991328704669e-05
CAMB-79011	MN908947.3	20932	G	A	0.0095	0.007	4.6e-06	5.4e-05	0.00815660685154975	GGG	ORF1ab:2'-O-ribose-methyltransferase	G92S	G274A	GGT>AGT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.991555512906631
CAMB-79011	MN908947.3	21077	C	T	0.0063	0.0087	0.00014	1.4e-05	0.00756591072225348	ACA	ORF1ab:2'-O-ribose-methyltransferase	T140I	C419T	ACA>ATA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.992104293169341
CAMB-79011	MN908947.3	21575	C	T	0.022	0.02	1e-06	7.1e-06	0.021347918136909	TCT	S	L5F	C13T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.978299223712068
CAMB-79011	MN908947.3	23403	A	G	1	1	0	0	0.999019141824547	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.79055659928925e-05
CAMB-79011	MN908947.3	241	C	T	1	1	0	0	0.998742483112193	TCG	NA	NA	NA	NA	NA	NA	0.000403050284553501
CAMB-79011	MN908947.3	25247	A	G	0.016	0.011	9.6e-09	8.3e-07	0.0137032310069188	AAT	S	M1229V	A3685G	ATG>GTG	Missense	GU280_gp02, spike glycoprotein	0.984550278766709
CAMB-79011	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99940321743643	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	5.81006884931586e-05
CAMB-79011	MN908947.3	3037	C	T	1	1	0	0	0.999152406478363	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000137447598103223
CAMB-79011	MN908947.3	7688	C	T	1	1	0	0	0.999665756782352	ACT	ORF1ab:nsp3	L1657L	C4969T	CTA>TTA	Synonymous	ORF1ab:nsp3	0.000222828811765361
CAMB-79011	MN908947.3	8111	G	A	0.011	0.0097	1.7e-06	7.8e-06	0.0104849279161206	TGC	ORF1ab:nsp3	A1798T	G5392A	GCA>ACA	Missense	ORF1ab:nsp3	0.98920363858142
CAMB-7903F	MN908947.3	11075	T	-	0.038	0.035	1.1e-09	2.3e-09	0.0366218901046763	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.963229843133766
CAMB-7903F	MN908947.3	11075	TTTT	-	0.00950675	0.0325	1.1e-09;NA;NA;NA	2.3e-09;4.2e-12;9.2e-16;1.2e-15	0.01387387112986	CTT	ORF1ab:nsp6	.	103-106-delfrshift	.	no-SNV	ORF1ab:nsp6	0.963229843133766
CAMB-7903F	MN908947.3	13122	G	A	0.082	0.015	1.3e-37	8.8e-09	0.0493838082683818	AGT	ORF1ab:nsp10	S33N	G98A	AGT>AAT	Missense	ORF1ab:nsp10	0.950616191731618
CAMB-7903F	MN908947.3	14408	C	T	1	1	0	0	0.999310600837885	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000424245638224532
CAMB-7903F	MN908947.3	16838	AA	-	0.00385	0.0205	0.0021;NA	1.5e-08;4.9e-10	0.0107648725212465	GAA	ORF1ab:helicase	.	602-603-delfrshift	.	no-SNV	ORF1ab:helicase	0.986676572560674
CAMB-7903F	MN908947.3	1723	T	C	0.0091	0.008	4.4e-05	0.00014	0.00860737995985796	CTT	ORF1ab:nsp2	A306A	T918C	GCT>GCC	Synonymous	ORF1ab:nsp2	0.99135402192373
CAMB-7903F	MN908947.3	18570	C	T	1	1	0	0	0.999920195361754	TCT	ORF1ab:3'-to-5'-exonuclease	L177L	C531T	CTC>CTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	6.38437105964599e-05
CAMB-7903F	MN908947.3	23403	A	G	1	1	0	0	0.999920563995631	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.95770032767352e-05
CAMB-7903F	MN908947.3	23540	T	C	0.019	0.015	1.7e-08	1.6e-06	0.0169264774313634	ATA	S	Y660H	T1978C	TAT>CAT	Missense	GU280_gp02, spike glycoprotein	0.983073522568637
CAMB-7903F	MN908947.3	241	C	T	1	1	0	0	0.99988792588165	TCG	NA	NA	NA	NA	NA	NA	0.000112074118350269
CAMB-7903F	MN908947.3	2623	C	T	0.13	0.047	8e-28	5.6e-08	0.104018912529551	ACG	ORF1ab:nsp2	N606N	C1818T	AAC>AAT	Synonymous	ORF1ab:nsp2	0.895981087470449
CAMB-7903F	MN908947.3	26333	C	T	0.012	0.012	9.3e-07	9.6e-07	0.012427930813581	ACA	E	T30I	C89T	ACA>ATA	Missense	GU280_gp04	0.987572069186419
CAMB-7903F	MN908947.3	27046	C	T	1	1	0	0	0.999939298288212	ACG	M	T175M	C524T	ACG>ATG	Missense	GU280_gp05	0
CAMB-7903F	MN908947.3	28744	C	T	0.17	0.17	1.9e-75	4.9e-79	0.168846065611379	TCG	N	I157I	C471T	ATC>ATT	Synonymous	GU280_gp10	0.831153934388621
CAMB-7903F	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999884379697075	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7903F	MN908947.3	29408	A	G	0.0091	0.035	0.00012	1.6e-10	0.0204081632653061	AAC	N	T379A	A1135G	ACT>GCT	Missense	GU280_gp10	0.979591836734694
CAMB-7903F	MN908947.3	29741	C	T	0.0094	0.016	5.5e-05	3.7e-07	0.0125600295530107	ACG	NA	NA	NA	NA	NA	NA	0.987439970446989
CAMB-7903F	MN908947.3	3037	C	T	1	1	0	0	0.999523809523809	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7903F	MN908947.3	3828	C	T	0.13	0.084	2.1e-57	6e-36	0.111904108335621	TCA	ORF1ab:nsp3	S370L	C1109T	TCA>TTA	Missense	ORF1ab:nsp3	0.888095891664379
CAMB-7903F	MN908947.3	6787	T	-	0.0023	0.011	0.0075	3.1e-06	0.00576718773713765	CTT	ORF1ab:nsp3	.	4068-4068-delfrshift	.	no-SNV	ORF1ab:nsp3	0.994081044164517
CAMB-7903F	MN908947.3	8326	C	T	1	1	0	0	0.999891716296697	ACC	ORF1ab:nsp3	D1869D	C5607T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.000108283703302653
CAMB-7903F	MN908947.3	9290	G	T	0.011	0.022	1.4e-06	6.8e-09	0.0132850241545894	TGA	ORF1ab:nsp4	D246Y	G736T	GAT>TAT	Missense	ORF1ab:nsp4	0.986714975845411
CAMB-7904E	MN908947.3	10186	C	T	1	1	0	0	0.999884712935209	GCA	ORF1ab:3C-like-proteinase	C44C	C132T	TGC>TGT	Synonymous	ORF1ab:3C-like-proteinase	0.000103758358312197
CAMB-7904E	MN908947.3	11074	C	INS	0.11	0.12	1.8e-48	2.4e-52	0.116058242329693	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.880894435777431
CAMB-7904E	MN908947.3	11083	G	-	0.16	0.15	1.9e-68	5.3e-67	0.155162767763164	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	9.48253790644528e-06
CAMB-7904E	MN908947.3	11083	G	T	0.84	0.85	0	0	0.844685511630333	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	9.48253790644528e-06
CAMB-7904E	MN908947.3	1150	C	T	0.0082	0.0093	1.2e-05	4.6e-06	0.00878375375864674	GCT	ORF1ab:nsp2	G115G	C345T	GGC>GGT	Synonymous	ORF1ab:nsp2	0.991171809038527
CAMB-7904E	MN908947.3	13778	AT	-	0.0135	0.02	2.9e-05;3.1e-05	5.1e-07;7.5e-07	0.0164971774440074	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.984119857498414
CAMB-7904E	MN908947.3	13780	A	T	0.02	0.019	1.8e-06	2.6e-06	0.0195524481209732	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I105L	A313T	ATA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.977358183776753
CAMB-7904E	MN908947.3	14805	C	T	1	1	0	0	0.999963824149189	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	9.04396270269781e-06
CAMB-7904E	MN908947.3	1547	A	-	0.0092	0.014	6.2e-06	1.8e-07	0.0112197467542875	TAG	ORF1ab:nsp2	.	742-742-delfrshift	.	no-SNV	ORF1ab:nsp2	0.938451674947908
CAMB-7904E	MN908947.3	1547	A	G	0.018	0.026	6.1e-09	9e-12	0.0217983651226158	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.938451674947908
CAMB-7904E	MN908947.3	1547	A	T	0.029	0.024	2.3e-13	2.1e-11	0.0269273922102901	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.938451674947908
CAMB-7904E	MN908947.3	1884	C	T	0.11	0.12	1.3e-50	2.9e-53	0.116999970107315	GCT	ORF1ab:nsp2	A360V	C1079T	GCT>GTT	Missense	ORF1ab:nsp2	0.882596478641676
CAMB-7904E	MN908947.3	18840	A	C	0.0094	0.0042	1.8e-05	0.0014	0.00680710620632751	CAC	ORF1ab:3'-to-5'-exonuclease	A267A	A801C	GCA>GCC	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.992806126395586
CAMB-7904E	MN908947.3	21457	A	G	0.028	0.017	6.2e-13	1.2e-08	0.0231229597388466	AAT	ORF1ab:2'-O-ribose-methyltransferase	I267V	A799G	ATC>GTC	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.976877040261153
CAMB-7904E	MN908947.3	21652	TTCTT	-	0.0318	0.0434	4.9e-15;4.9e-14;1.6e-13;6e-14;3.7e-14	1.6e-19;2.4e-18;9.2e-18;2.5e-18;1.5e-18	0.036863028550777	ATT	S	.	90-94-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.959700708847466
CAMB-7904E	MN908947.3	21859	C	T	0.02	0.025	3e-10	2.9e-12	0.0220685261864677	ACA	S	N99N	C297T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.977885971697684
CAMB-7904E	MN908947.3	25446	T	A	0.26	0.23	4.5e-127	2.9e-109	0.241641718054843	GTG	ORF3a	G18G	T54A	GGT>GGA	Synonymous	GU280_gp03	0.757380216844189
CAMB-7904E	MN908947.3	26030	A	G	0.011	0.018	8.9e-07	3.2e-09	0.013687915526007	CAG	ORF3a	Q213R	A638G	CAG>CGG	Missense	GU280_gp03	0.986181723373745
CAMB-7904E	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7904E	MN908947.3	27694	TTTCTTA	-	0.0451428571428571	0.0358571428571429	8.4e-11;1.4e-10;2.1e-10;1.8e-10;1.5e-10;8e-11;1.2e-10	3e-08;7.5e-08;8.7e-08;9.9e-08;6.3e-08;5.5e-08;3.9e-08	0.040625	TTT	ORF7a	.	301-307-delfrshift	.	no-SNV	GU280_gp07	0.954924874791319
CAMB-7904E	MN908947.3	28089	G	A	0.064	0.06	3.3e-28	1.7e-26	0.0624397631832576	TGG	ORF8	G66S	G196A	GGT>AGT	Missense	GU280_gp09	0.937422552664188
CAMB-7904E	MN908947.3	28857	G	T	1	1	0	0	0.999039269845082	AGA	N	R195I	G584T	AGA>ATA	Missense	GU280_gp10	0.000240182538729434
CAMB-7904E	MN908947.3	29197	C	T	0.021	0.019	1e-10	5e-10	0.0196567319958251	CCC	N	A308A	C924T	GCC>GCT	Synonymous	GU280_gp10	0.978937144845181
CAMB-7904E	MN908947.3	29666	C	T	0.021	0.016	2.9e-10	2.5e-08	0.0183965640658554	TCT	ORF10	L37F	C109T	CTC>TTC	Missense	GU280_gp11	0.981460272011453
CAMB-7904E	MN908947.3	3931	T	C	1	1	0	0	0.999151052089018	TTG	ORF1ab:nsp3	V404V	T1212C	GTT>GTC	Synonymous	ORF1ab:nsp3	0.000394154387241526
CAMB-7904E	MN908947.3	9491	C	T	0.027	0.02	5.3e-13	2.8e-10	0.0235985758052496	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.97640142419475
CAMB-7905D	MN908947.3	10332	C	T	0.086	0.094	1.2e-38	2.1e-42	0.0892542759893727	ACA	ORF1ab:3C-like-proteinase	T93I	C278T	ACA>ATA	Missense	ORF1ab:3C-like-proteinase	0.910510984731277
CAMB-7905D	MN908947.3	11074	C	INS	0.094	0.092	5.9e-34	5.3e-32	0.0928741352437724	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.902873861803068
CAMB-7905D	MN908947.3	11083	G	-	0.17	0.18	1.3e-73	1.7e-79	0.172085560207024	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-7905D	MN908947.3	11083	G	T	0.83	0.82	0	0	0.827685217580137	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-7905D	MN908947.3	11956	C	T	0.027	0.026	2.4e-13	4.6e-13	0.0263855617833802	ACA	ORF1ab:nsp7	D38D	C114T	GAC>GAT	Synonymous	ORF1ab:nsp7	0.973428378724097
CAMB-7905D	MN908947.3	14189	C	T	1	1	0	0	0.999285216332366	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A241V	C722T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	8.82448972388172e-05
CAMB-7905D	MN908947.3	14805	C	T	1	1	0	0	0.998628929585741	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000852022328861032
CAMB-7905D	MN908947.3	19955	C	T	1	1	0	0	1	ACT	ORF1ab:endoRNAse	T112I	C335T	ACT>ATT	Missense	ORF1ab:endoRNAse	0
CAMB-7905D	MN908947.3	21294	TGG	AAA	1	1	1.4e-285;8.3e-251;1.3e-296	0;0;0	1	TTG	ORF1ab:2'-O-ribose-methyltransferase	.	636-638-mnv	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.00141043723554302
CAMB-7905D	MN908947.3	2480	A	G	1	1	0	0	0.999874213836478	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	6.28930817610063e-05
CAMB-7905D	MN908947.3	2558	C	T	1	1	0	0	0.999181144185017	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000309837335398916
CAMB-7905D	MN908947.3	26144	G	T	1	1	0	0	0.999936057292666	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7905D	MN908947.3	28001	G	T	0.014	0.014	1.7e-07	2e-07	0.0136576612501246	CGT	ORF8	P36P	G108T	CCG>CCT	Synonymous	GU280_gp09	0.98569434752268
CAMB-7906C	MN908947.3	11075	T	-	0.08	0.048	1.2e-19	3.8e-12	0.064376169012357	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.935363198724435
CAMB-7906C	MN908947.3	14408	C	T	1	1	0	0	0.999102539285903	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000492723529308251
CAMB-7906C	MN908947.3	17835	T	C	1	1	0	0	0.999783532213113	TTG	ORF1ab:helicase	V533V	T1599C	GTT>GTC	Synonymous	ORF1ab:helicase	0.000189409313526531
CAMB-7906C	MN908947.3	20102	G	T	1	1	1.3e-181	1.9e-161	1	AGT	ORF1ab:endoRNAse	S161I	G482T	AGT>ATT	Missense	ORF1ab:endoRNAse	0
CAMB-7906C	MN908947.3	21908	T	C	0.0089	0.056	3.2e-05	6.5e-23	0.0321334146837503	GTC	S	S116P	T346C	TCC>CCC	Missense	GU280_gp02, spike glycoprotein	0.96786658531625
CAMB-7906C	MN908947.3	23403	A	G	1	1	0	0	0.999897515315767	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.10974970962673e-05
CAMB-7906C	MN908947.3	241	C	T	1	1	0	0	0.999795918367347	TCG	NA	NA	NA	NA	NA	NA	0.000158730158730159
CAMB-7906C	MN908947.3	3037	C	T	1	1	0	0	0.999127856270713	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7906C	MN908947.3	3877	T	G	0.0091	0.0019	5.4e-06	0.0065	0.00575113279888463	CTG	ORF1ab:nsp3	A386A	T1158G	GCT>GCG	Synonymous	ORF1ab:nsp3	0.99355176019519
CAMB-7906C	MN908947.3	522	TTG	-	0.0566666666666667	0.01	4e-11;1.1e-08;3.7e-06	0.00043;NA;NA	0.0362752132663637	GTT	ORF1ab:leader-protein	.	257-259-delinframe	.	no-SNV	ORF1ab:leader-protein	0.93701971266288
CAMB-7907B	MN908947.3	10317	A	G	0.006	0.013	0.00012	1.1e-07	0.00915535698144394	AAG	ORF1ab:3C-like-proteinase	K88R	A263G	AAG>AGG	Missense	ORF1ab:3C-like-proteinase	0.990844643018556
CAMB-7907B	MN908947.3	11075	T	-	0.046	0.052	2.7e-11	1.2e-12	0.0488715684079855	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.947740084250799
CAMB-7907B	MN908947.3	14408	C	T	1	1	0	0	0.999115418999671	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000517573989554416
CAMB-7907B	MN908947.3	16289	C	T	1	1	0	0	0.999710915818686	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0.000289084181313599
CAMB-7907B	MN908947.3	17427	G	T	0.0057	0.01	0.00014	1.1e-06	0.0078040257280728	TGT	ORF1ab:helicase	V397V	G1191T	GTG>GTT	Synonymous	ORF1ab:helicase	0.992143204751602
CAMB-7907B	MN908947.3	17906	A	G	0.0044	0.0089	0.00047	5.1e-06	0.0064688085290304	AAT	ORF1ab:helicase	N557S	A1670G	AAT>AGT	Missense	ORF1ab:helicase	0.993430341449359
CAMB-7907B	MN908947.3	19604	C	T	0.0091	0.008	6.8e-06	1.9e-05	0.00858225056336002	ACT	ORF1ab:3'-to-5'-exonuclease	T522I	C1565T	ACT>ATT	Missense	ORF1ab:3'-to-5'-exonuclease	0.99141774943664
CAMB-7907B	MN908947.3	21812	C	T	0.0054	0.0092	0.00042	9.7e-06	0.00731204299731267	CCT	S	L84L	C250T	CTA>TTA	Synonymous	GU280_gp02, spike glycoprotein	0.992687957002687
CAMB-7907B	MN908947.3	22207	T	C	0.008	0.0032	2.2e-05	0.0029	0.00576625386996904	ATC	S	D215D	T645C	GAT>GAC	Synonymous	GU280_gp02, spike glycoprotein	0.994233746130031
CAMB-7907B	MN908947.3	22227	C	T	0.019	0.012	7.2e-10	5.5e-07	0.0155280909049753	GCT	S	A222V	C665T	GCT>GTT	Missense	GU280_gp02, spike glycoprotein	0.984426637692969
CAMB-7907B	MN908947.3	2306	C	T	0.076	0.065	2.7e-32	4.4e-28	0.0695034231735852	GCT	ORF1ab:nsp2	L501F	C1501T	CTT>TTT	Missense	ORF1ab:nsp2	0.930496576826415
CAMB-7907B	MN908947.3	23403	A	G	1	1	0	0	0.999349140700951	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000107103428957472
CAMB-7907B	MN908947.3	241	C	T	1	1	0	0	0.999221227123547	TCG	NA	NA	NA	NA	NA	NA	5.56266340323747e-05
CAMB-7907B	MN908947.3	25429	G	T	0.99	0.99	0	0	0.986812725904543	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	7.40165056807668e-05
CAMB-7907B	MN908947.3	27214	G	T	0.015	0.02	2.6e-08	2.5e-10	0.0172167911743625	CGT	ORF6	V5F	G13T	GTT>TTT	Missense	GU280_gp06	0.981674831711408
CAMB-7907B	MN908947.3	27680	TTTACTCTCCAA	-	0.02525	0.0121666666666667	1.4e-05;3.2e-05;6.6e-06;5.1e-05;8.6e-05;2.4e-05;2e-05;1.5e-05;8.7e-06;2.4e-05;8.1e-06;2.4e-05	0.00023;0.00044;0.00014;7e-04;0.001;0.00045;0.00037;0.00028;2e-04;0.00041;2e-04;0.00051	0.0163132137030995	CTT	ORF7a	.	287-298-delinframe	.	no-SNV	GU280_gp07	0.98371335504886
CAMB-7907B	MN908947.3	27769	C	T	0.05	0.021	4.7e-10	7.1e-07	0.0302066772655008	TCA	NA	NA	NA	NA	NA	NA	0.969793322734499
CAMB-7907B	MN908947.3	28835	T	C	0.0031	0.0083	0.0039	2.2e-05	0.00575874532867733	ATC	N	S188P	T562C	TCA>CCA	Missense	GU280_gp10	0.99359799056546
CAMB-7907B	MN908947.3	3037	C	T	1	1	0	0	0.999507024895243	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000154054720236628
CAMB-7907B	MN908947.3	3410	G	T	0.02	0.014	1.9e-10	4.9e-08	0.017348493728754	AGC	ORF1ab:nsp3	A231S	G691T	GCT>TCT	Missense	ORF1ab:nsp3	0.982417067166803
CAMB-7907B	MN908947.3	4070	A	G	0.012	0.01	2.9e-07	1.2e-06	0.0111643515157382	CAC	ORF1ab:nsp3	T451A	A1351G	ACT>GCT	Missense	ORF1ab:nsp3	0.988787248116419
CAMB-7907B	MN908947.3	4523	G	A	0.0021	0.0093	0.0044	2.1e-06	0.00489054494643689	TGC	ORF1ab:nsp3	A602T	G1804A	GCT>ACT	Missense	ORF1ab:nsp3	0.994776764921152
CAMB-7907B	MN908947.3	7453	T	C	0.022	0.012	1.7e-11	2.4e-07	0.0177991100444978	GTT	ORF1ab:nsp3	S1578S	T4734C	AGT>AGC	Synonymous	ORF1ab:nsp3	0.982150892455377
CAMB-7907B	MN908947.3	8400	T	C	0.039	0.032	5.6e-18	5e-15	0.0352447167343567	ATA	ORF1ab:nsp3	I1894T	T5681C	ATA>ACA	Missense	ORF1ab:nsp3	0.964548771253528
CAMB-7907B	MN908947.3	9296	T	C	0.008	0.006	1.9e-05	0.00013	0.00710342588082481	TTA	ORF1ab:nsp4	Y248H	T742C	TAC>CAC	Missense	ORF1ab:nsp4	0.992855983114142
CAMB-7908A	MN908947.3	10995	A	G	0.31	0.3	6.1e-152	3.3e-144	0.302530645531232	AAG	ORF1ab:nsp6	K8R	A23G	AAG>AGG	Missense	ORF1ab:nsp6	0.697418384770254
CAMB-7908A	MN908947.3	11074	C	INS	0.017	0.025	0.0055	2.6e-05	0.0206841932033243	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.978616391014564
CAMB-7908A	MN908947.3	11075	T	-	0.03	0.035	1.5e-07	1.1e-08	0.032112286217089	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962334910898871
CAMB-7908A	MN908947.3	11587	T	C	0.008	0.0065	2.1e-05	7.7e-05	0.00742047320722584	ATA	ORF1ab:nsp6	N205N	T615C	AAT>AAC	Synonymous	ORF1ab:nsp6	0.992579526792774
CAMB-7908A	MN908947.3	11980	T	C	0.0093	0.0085	1.7e-05	3.5e-05	0.00893539716073029	CTG	ORF1ab:nsp7	T46T	T138C	ACT>ACC	Synonymous	ORF1ab:nsp7	0.991031721892956
CAMB-7908A	MN908947.3	14408	C	T	1	1	0	0	0.997069274707758	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000199256110520723
CAMB-7908A	MN908947.3	17835	T	C	1	1	0	0	0.999318730298027	TTG	ORF1ab:helicase	V533V	T1599C	GTT>GTC	Synonymous	ORF1ab:helicase	0.000150110273316167
CAMB-7908A	MN908947.3	23403	A	G	1	1	0	0	0.999387906989685	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000132156445408955
CAMB-7908A	MN908947.3	241	C	T	1	1	0	0	0.998188968229328	TCG	NA	NA	NA	NA	NA	NA	0.0010736831211839
CAMB-7908A	MN908947.3	25613	C	T	0.048	0.041	4.9e-22	3e-19	0.0445191096178076	TCC	ORF3a	S74F	C221T	TCC>TTC	Missense	GU280_gp03	0.955440891182176
CAMB-7908A	MN908947.3	25886	C	T	0.024	0.05	7.5e-12	9.4e-23	0.0337731699654414	TCT	ORF3a	S165F	C494T	TCT>TTT	Missense	GU280_gp03	0.966109016650958
CAMB-7908A	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0359210526315789	0.0177	0.00054;3.9e-05;0.00016;0.00015;4e-04;3.2e-06;1.7e-05;4.1e-06;4.2e-06;1.1e-06;1.9e-06;1.5e-06;4.3e-06;2.4e-06;3.2e-06;6.3e-06;2e-06;5.1e-06;3.3e-06;3.3e-06;2.1e-06;5.6e-06;2.4e-06;3.5e-06;3e-06;1.4e-06;4.3e-06;2.6e-06;1.6e-06;2.1e-06;4.6e-06;3.9e-06;1.7e-06;4.2e-06;1.3e-06;1.5e-06;9.1e-07;0.00071	0.3;0.19;0.3;0.21;0.23;0.06;0.074;0.0039;0.0039;0.0022;0.0031;0.0029;0.0038;0.0031;0.0035;0.0045;0.003;0.0042;0.0034;0.0033;0.0027;0.0045;0.0028;0.0036;0.0031;0.0027;0.0041;0.003;0.0016;0.0031;0.004;0.0038;0.0029;0.0039;0.0024;0.0029;0.0024;0.026	0.0293024558782333	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.984815497124993
CAMB-7908A	MN908947.3	3037	C	T	1	1	0	0	0.999689501261401	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.88123423248593e-05
CAMB-7908A	MN908947.3	6696	C	T	0.006	0.0089	0.00065	4e-05	0.00753397013318983	CCT	ORF1ab:nsp3	P1326L	C3977T	CCT>CTT	Missense	ORF1ab:nsp3	0.989842593838289
CAMB-7908A	MN908947.3	9955	T	G	0.062	0.066	9.2e-28	8.2e-30	0.0638851392808934	CTT	ORF1ab:nsp4	A467A	T1401G	GCT>GCG	Synonymous	ORF1ab:nsp4	0.936041232053013
CAMB-79099	MN908947.3	11074	CTT	-	0.0126833333333333	0.068	0.11;1.7e-09;NA	7.4e-63;3e-20;3.3e-14	0.0274702405727129	TCT	ORF1ab:nsp6	.	102-104-delinframe	.	no-SNV	ORF1ab:nsp6	0.943343628732082
CAMB-79099	MN908947.3	11083	G	T	0.038	0.078	2.9e-08	5.7e-17	0.0522175412763985	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.945846455887766
CAMB-79099	MN908947.3	12880	C	T	0.013	0.041	1.4e-07	1.2e-19	0.0234646144560133	TCT	ORF1ab:nsp9	I65I	C195T	ATC>ATT	Synonymous	ORF1ab:nsp9	0.976516523313717
CAMB-79099	MN908947.3	13329	C	T	0.025	0.059	1.6e-12	2.8e-27	0.0402010050251256	ACT	ORF1ab:nsp10	T102I	C305T	ACT>ATT	Missense	ORF1ab:nsp10	0.959777209748163
CAMB-79099	MN908947.3	14408	C	T	0.99	1	0	0	0.994048858868688	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000416579879191835
CAMB-79099	MN908947.3	17002	C	T	1	1	0	0	0.999896109293024	ACT	ORF1ab:helicase	L256F	C766T	CTC>TTC	Missense	ORF1ab:helicase	7.79180302321957e-05
CAMB-79099	MN908947.3	20703	C	T	0.02	0.058	2.2e-10	4.4e-26	0.0372258738251735	ACA	ORF1ab:2'-O-ribose-methyltransferase	Y15Y	C45T	TAC>TAT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.962774126174826
CAMB-79099	MN908947.3	23403	A	G	1	1	0	0	0.999946643901398	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.20136591612421e-05
CAMB-79099	MN908947.3	23539	ATATGAGTGTGACATACCCATTGGTGCAGGTA	-	0.01525	0.05959375	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.002;0.0013;0.0038;0.0032;0.0038;0.0039;0.0019;0.003;0.0023;0.0033;0.0036;0.0036;0.0034;0.0033;0.0026;0.0025;0.0015;0.00044	3.8e-10;1.5e-08;4.1e-08;7.4e-09;1.6e-08;2.3e-08;2e-08;2.1e-08;2.3e-08;1.2e-07;1.1e-07;1.9e-06;6.4e-07;7e-07;2.8e-05;1e-05;7.6e-05;6e-05;8e-05;9e-05;1.8e-05;4.5e-05;5.6e-09;3.1e-08;3.4e-08;3.7e-08;3.5e-08;3.1e-08;7.7e-09;6e-09;8.9e-10;7.6e-10	0.0342335186656076	CAT	S	.	1977-2008-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.981481481481482
CAMB-79099	MN908947.3	23571	TATGCGCTAGTT	-	0.0248333333333333	0.160833333333333	0.0015;9e-04;0.0015;0.00086;0.0016;0.0024;0.0017;0.0017;0.00016;0.00025;0.0019;NA	3.2e-17;7.8e-19;8.2e-17;6e-21;1e-18;6.9e-17;2.1e-18;2.2e-18;1.9e-28;2e-27;7.4e-17;3.5e-17	0.081102870041922	ATA	S	.	2009-2020-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.913506092328814
CAMB-79099	MN908947.3	241	C	T	1	1	0	0	0.999564684000158	TCG	NA	NA	NA	NA	NA	NA	0.000237445090822747
CAMB-79099	MN908947.3	24707	C	A	0.024	0.031	4.8e-11	1.9e-12	0.0269396551724138	TCT	S	L1049I	C3145A	CTT>ATT	Missense	GU280_gp02, spike glycoprotein	0.973060344827586
CAMB-79099	MN908947.3	27134	TAAATT	-	0.0168333333333333	0.0263333333333333	0.00058;0.00036;0.001;0.00048;0.00074;NA	4.7e-05;2.2e-05;9.3e-05;4.3e-05;8e-05;3.1e-06	0.0228868660598179	ATA	M	.	612-617-delinframe	.	no-SNV	GU280_gp05	0.978095663835494
CAMB-79099	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999093107617896	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79099	MN908947.3	29640	C	T	0.014	0.016	9.1e-07	1.9e-07	0.0147110332749562	GCA	ORF10	A28V	C83T	GCA>GTA	Missense	GU280_gp11	0.985288966725044
CAMB-79099	MN908947.3	3037	C	T	1	1	0	0	0.999249699879952	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000450180072028812
CAMB-79099	MN908947.3	3345	GTTTTAGTG	-	0.0311111111111111	0.0292222222222222	1e-14;1.3e-14;3.2e-15;2.7e-15;2.8e-15;8.7e-15;6.7e-15;7.1e-15;5.4e-15	5.9e-14;1.4e-13;9.6e-15;2.2e-14;2.5e-14;5.9e-14;4.7e-14;2.9e-14;3.4e-14	0.0300054112554113	AGT	ORF1ab:nsp3	.	626-634-delinframe	.	no-SNV	ORF1ab:nsp3	0.970460492594891
CAMB-790B7	MN908947.3	14408	C	T	1	1	0	0	0.999285339939969	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000619372052027252
CAMB-790B7	MN908947.3	23403	A	G	1	1	0	0	0.999929480624802	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.05193751983357e-05
CAMB-790B7	MN908947.3	241	C	T	1	1	0	0	0.99978427354115	TCG	NA	NA	NA	NA	NA	NA	0.000215726458850178
CAMB-790B7	MN908947.3	28253	C	T	0.092	0.14	3.5e-41	6.7e-65	0.111246582428139	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.888642577403384
CAMB-790B7	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999423298731257	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000319693094629156
CAMB-790B7	MN908947.3	28932	C	T	0.062	0.21	3.9e-22	2e-87	0.16587279349958	GCT	N	A220V	C659T	GCT>GTT	Missense	GU280_gp10	0.83412720650042
CAMB-790B7	MN908947.3	29754	C	T	0.058	0.074	2.9e-11	1.5e-10	0.063758389261745	TCG	NA	NA	NA	NA	NA	NA	0.936241610738255
CAMB-790B7	MN908947.3	3037	C	T	1	1	1.1e-170	7.6e-230	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-790B7	MN908947.3	635	C	T	0.093	0.19	1.5e-41	7.4e-80	0.120513598220605	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.879486401779395
CAMB-790C6	MN908947.3	11074	C	INS	0.1	0.11	4.3e-38	2.5e-39	0.104958245609077	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.893346144607254
CAMB-790C6	MN908947.3	11083	G	-	0.2	0.19	9.5e-91	7.4e-87	0.196644423260248	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.81315538608198e-05
CAMB-790C6	MN908947.3	11083	G	T	0.8	0.81	0	0	0.803228471560216	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.81315538608198e-05
CAMB-790C6	MN908947.3	11208	C	T	0.014	0.0098	2.9e-08	1.9e-06	0.0119566318775965	GCT	ORF1ab:nsp6	A79V	C236T	GCT>GTT	Missense	ORF1ab:nsp6	0.987970991416123
CAMB-790C6	MN908947.3	14805	C	T	1	1	0	0	0.999924656244114	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	1.25572926477052e-05
CAMB-790C6	MN908947.3	1564	T	C	0.024	0.04	3.3e-11	2.3e-17	0.0322685260256202	GTA	ORF1ab:nsp2	C253C	T759C	TGT>TGC	Synonymous	ORF1ab:nsp2	0.96773147397438
CAMB-790C6	MN908947.3	17247	T	C	1	1	0	0	0.999099750385334	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000204602185151337
CAMB-790C6	MN908947.3	19263	C	T	1	1	0	0	0.999936476679001	ACC	ORF1ab:3'-to-5'-exonuclease	N408N	C1224T	AAC>AAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	4.76424907494164e-05
CAMB-790C6	MN908947.3	25000	C	T	0.012	0.011	2.3e-07	1.3e-06	0.0113106915154487	ACT	S	D1146D	C3438T	GAC>GAT	Synonymous	GU280_gp02, spike glycoprotein	0.988689308484551
CAMB-790C6	MN908947.3	26144	G	T	1	1	0	0	0.999235474006116	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000764525993883792
CAMB-790C6	MN908947.3	26208	C	T	1	1	0	0	0.999816681943171	GCG	ORF3a	S272S	C816T	AGC>AGT	Synonymous	GU280_gp03	0.000183318056828598
CAMB-790D5	MN908947.3	11075	T	-	0.041	0.044	8.2e-11	4.3e-11	0.0424850042844901	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952904884318766
CAMB-790D5	MN908947.3	11455	C	T	1	1	0	0	0.999792315680166	CCA	ORF1ab:nsp6	A161A	C483T	GCC>GCT	Synonymous	ORF1ab:nsp6	0.000124610591900312
CAMB-790D5	MN908947.3	13279	T	C	0.087	0.085	5e-40	7.8e-39	0.0862635595679763	ATC	ORF1ab:nsp10	N85N	T255C	AAT>AAC	Synonymous	ORF1ab:nsp10	0.913712909728377
CAMB-790D5	MN908947.3	14408	C	T	1	1	0	0	0.998613105538986	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000527756299323735
CAMB-790D5	MN908947.3	23403	A	G	1	1	0	0	0.999559265560129	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.93321991767081e-05
CAMB-790D5	MN908947.3	241	C	T	1	1	0	0	0.99881526734991	TCG	NA	NA	NA	NA	NA	NA	0.000171286648205772
CAMB-790D5	MN908947.3	28725	C	T	0.75	0.76	0	0	0.753899270848423	CCT	N	P151L	C452T	CCT>CTT	Missense	GU280_gp10	0.24588343232411
CAMB-790D5	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99931567506642	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.45275625612254e-05
CAMB-790D5	MN908947.3	3037	C	T	1	1	0	0	0.999315420160876	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.77971198748197e-05
CAMB-790E4	MN908947.3	11074	C	INS	0.11	0.048	1.1e-32	6.3e-11	0.0816924066924067	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.918275418275418
CAMB-790E4	MN908947.3	11083	G	-	0.034	0.057	1.8e-14	1.7e-24	0.0444822212778014	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.83326250177079e-05
CAMB-790E4	MN908947.3	11083	G	T	0.97	0.94	0	0	0.955234452472022	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.83326250177079e-05
CAMB-790E4	MN908947.3	14805	C	T	1	1	0	0	1	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-790E4	MN908947.3	23280	C	T	0.042	0.046	6.5e-20	4.2e-22	0.0437118834744508	ACT	S	T573I	C1718T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.955947658239091
CAMB-790E4	MN908947.3	24011	TTTATTGAAGATCTACT	-	0.0147058823529412	0.0875294117647059	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;3.8e-12;7.8e-19	4.5e-21;2e-17;1.9e-14;3.4e-13;1.9e-10;3.1e-10;4e-10;2.9e-10;1.7e-09;1.7e-09;1.6e-09;2.6e-09;1.7e-09;3.6e-10;6.9e-10;2.7e-08;4.6e-12	0.0242208370436331	ATT	S	.	2449-2465-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.975389069851611
CAMB-790E4	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-790E4	MN908947.3	2558	C	T	1	1	0	0	0.999601116872756	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000398883127243718
CAMB-790E4	MN908947.3	26782	TTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCA	-	0.0811904761904762	0.256667928571429	1.1e-16;1.7e-16;6.5e-15;1.7e-19;4.1e-17;1.6e-14;1.6e-14;4.9e-16;2.8e-15;9.4e-16;1.6e-14;3.5e-15;7.9e-15;3.4e-14;2.8e-15;2.5e-14;8.4e-15;8.3e-15;3.4e-15;2.7e-14;4.7e-15;1.1e-14;5.8e-15;1.3e-15;1.6e-14;3.7e-15;8.9e-16;4.2e-15;1.9e-14;1.4e-14;4.1e-15;1.5e-14;4.7e-16;3.6e-15;9e-16;6.8e-11;4.8e-09;5.6e-10;1.9e-09;6e-12;1.3e-12;2.4e-12	1.2e-35;2.3e-35;6.6e-33;3.2e-81;1.8e-78;4.1e-68;4e-68;4.7e-70;5.5e-70;4.4e-71;2.4e-68;4.7e-70;6.2e-69;2.1e-67;1.8e-70;1.3e-67;4.7e-69;4.2e-69;2.8e-70;9.3e-68;1.6e-70;1.6e-68;8.7e-70;5.7e-72;1e-68;3e-70;3.7e-66;1.6e-69;1.5e-68;1.5e-68;1.9e-69;3.6e-68;1.3e-76;1.6e-70;6.4e-72;5.5e-20;2.3e-16;3.1e-18;6.1e-17;NA;NA;NA	0.171382289416847	CTT	M	.	260-301-delinframe	.	no-SNV	GU280_gp05	0.879377521613833
CAMB-790E4	MN908947.3	26817	TCTT	-	0.0795	0.14	6.8e-11;4.8e-09;5.6e-10;1.9e-09	5.5e-20;2.3e-16;3.1e-18;6.1e-17	0.104889539010906	TTC	M	.	295-298-delfrshift	.	no-SNV	GU280_gp05	0.894645941278066
CAMB-790E4	MN908947.3	27384	T	C	1	1	0	0	0.999949327320175	ATT	ORF6	D61D	T183C	GAT>GAC	Synonymous	GU280_gp06	2.53363399123363e-05
CAMB-790F3	MN908947.3	11075	T	-	0.017	0.046	7.2e-05	4.1e-11	0.0309936189608022	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962821956494539
CAMB-790F3	MN908947.3	13647	C	T	0.12	0.13	7e-54	5e-62	0.123701696100717	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y60Y	C180T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.876280818324882
CAMB-790F3	MN908947.3	13711	A	G	0.0037	0.0078	0.00075	1.1e-05	0.00573246297094006	TAA	ORF1ab:RNA-dependent-RNA-polymerase	K82E	A244G	AAG>GAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994223356196914
CAMB-790F3	MN908947.3	14408	C	T	1	1	0	0	0.998521354185566	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00105228781886135
CAMB-790F3	MN908947.3	17906	A	G	0.033	0.041	6.6e-16	2.3e-19	0.0363589031586255	AAT	ORF1ab:helicase	N557S	A1670G	AAT>AGT	Missense	ORF1ab:helicase	0.963583246557908
CAMB-790F3	MN908947.3	21707	C	T	0.023	0.032	1.8e-11	1.7e-15	0.0269854047810717	ACA	S	H49Y	C145T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.972909593643905
CAMB-790F3	MN908947.3	22205	G	T	0.026	0.026	5.2e-13	5.4e-13	0.0259067357512953	TGA	S	D215Y	G643T	GAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.974059399234651
CAMB-790F3	MN908947.3	23311	G	T	0.016	0.013	7.4e-09	8.1e-08	0.0147430790294011	AGA	S	E583D	G1749T	GAG>GAT	Missense	GU280_gp02, spike glycoprotein	0.984939782334604
CAMB-790F3	MN908947.3	23403	A	G	1	1	0	0	0.999392748705126	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.00089301661011e-05
CAMB-790F3	MN908947.3	241	C	T	1	1	0	0	0.999425159471888	TCG	NA	NA	NA	NA	NA	NA	0.000185432428423083
CAMB-790F3	MN908947.3	25463	C	T	0.0078	0.0055	2.2e-05	2e-04	0.00668117352461974	ACT	ORF3a	T24I	C71T	ACT>ATT	Missense	GU280_gp03	0.993242282752512
CAMB-790F3	MN908947.3	25469	C	T	1	1	0	0	0.999858962397205	TCA	ORF3a	S26L	C77T	TCA>TTA	Missense	GU280_gp03	6.50942782129451e-05
CAMB-790F3	MN908947.3	27207	T	G	0.095	0.077	1.7e-43	2.5e-35	0.0860920441033402	TTC	ORF6	F2L	T6G	TTT>TTG	Missense	GU280_gp06	0.912874283861204
CAMB-790F3	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999184829243178	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.73574540632696e-05
CAMB-790F3	MN908947.3	3037	C	T	1	1	0	0	0.999666580224503	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-790F3	MN908947.3	3261	C	T	1	1	0	0	0.999874543259052	ACA	ORF1ab:nsp3	T181I	C542T	ACA>ATA	Missense	ORF1ab:nsp3	3.1364185236878e-05
CAMB-790F3	MN908947.3	7104	C	T	0.0077	0.029	0.0015	3.5e-09	0.0213333333333333	ACC	ORF1ab:nsp3	T1462I	C4385T	ACC>ATC	Missense	ORF1ab:nsp3	0.978666666666667
CAMB-790F3	MN908947.3	8170	A	G	0.16	0.15	2.8e-74	2.1e-69	0.156917201874675	CAG	ORF1ab:nsp3	S1817S	A5451G	TCA>TCG	Synonymous	ORF1ab:nsp3	0.8429092171498
CAMB-790F3	MN908947.3	9052	A	G	0.018	0.022	3e-09	5.5e-11	0.0199441329869318	CAG	ORF1ab:nsp4	P166P	A498G	CCA>CCG	Synonymous	ORF1ab:nsp4	0.979997265251109
CAMB-790F3	MN908947.3	9409	A	G	0.0085	0.0034	9.2e-06	0.0012	0.00678685047720042	TAG	ORF1ab:nsp4	V285V	A855G	GTA>GTG	Synonymous	ORF1ab:nsp4	0.993160127253446
CAMB-790F3	MN908947.3	9857	C	T	0.023	0.02	2.4e-11	4.4e-10	0.0213380984916172	GCT	ORF1ab:nsp4	L435L	C1303T	CTA>TTA	Synonymous	ORF1ab:nsp4	0.978609344615546
CAMB-7911E	MN908947.3	11075	T	-	0.04	0.037	3.9e-10	2.7e-09	0.0380915966687776	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956603300156524
CAMB-7911E	MN908947.3	14408	C	T	1	1	0	0	0.997860784863495	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00074768684382691
CAMB-7911E	MN908947.3	15390	C	A	0.032	0.032	3.2e-15	3e-15	0.0317846232179226	ACC	ORF1ab:RNA-dependent-RNA-polymerase	H641Q	C1923A	CAC>CAA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.968164460285132
CAMB-7911E	MN908947.3	17484	A	G	0.98	0.99	0	0	0.985011572319416	CAC	ORF1ab:helicase	T416T	A1248G	ACA>ACG	Synonymous	ORF1ab:helicase	0.0148267184136321
CAMB-7911E	MN908947.3	20569	G	A	0.35	0.35	1.9e-180	4.4e-177	0.34816452228457	GGT	ORF1ab:endoRNAse	V317I	G949A	GTT>ATT	Missense	ORF1ab:endoRNAse	0.651665438606435
CAMB-7911E	MN908947.3	22326	C	T	0.99	0.98	0	0	0.984714873603763	TCT	S	S255F	C764T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.0149911816578483
CAMB-7911E	MN908947.3	23403	A	G	1	1	0	0	0.999231689958592	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000121312111801242
CAMB-7911E	MN908947.3	241	C	T	1	1	0	0	0.998835162887277	TCG	NA	NA	NA	NA	NA	NA	0.000151935275572606
CAMB-7911E	MN908947.3	25429	G	T	1	1	0	0	0.999277536956763	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	2.77870401244859e-05
CAMB-7911E	MN908947.3	26137	A	C	0.026	0.018	1.3e-06	0.00045	0.0219517743403094	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.978048225659691
CAMB-7911E	MN908947.3	26458	G	C	1	1	0	0	0.999393790448104	TGA	E	D72H	G214C	GAT>CAT	Missense	GU280_gp04	0
CAMB-7911E	MN908947.3	28045	C	T	1	1	0	0	0.999706529713866	GCT	ORF8	A51V	C152T	GCT>GTT	Missense	GU280_gp09	0.000244558571777941
CAMB-7911E	MN908947.3	29463	C	T	0.008	0.011	5.8e-05	3.2e-06	0.00963912072410956	GCT	N	A397V	C1190T	GCT>GTT	Missense	GU280_gp10	0.99036087927589
CAMB-7911E	MN908947.3	3037	C	T	1	1	0	0	0.999129596085535	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.40977204827213e-05
CAMB-7911E	MN908947.3	7471	C	T	0.012	0.012	5.9e-07	6.2e-07	0.0119634608397779	ACG	ORF1ab:nsp3	D1584D	C4752T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.988036539160222
CAMB-7912D	MN908947.3	10165	C	T	1	1	0	0	0.999798234552333	ACT	ORF1ab:3C-like-proteinase	Y37Y	C111T	TAC>TAT	Synonymous	ORF1ab:3C-like-proteinase	0.000201765447667087
CAMB-7912D	MN908947.3	11074	C	INS	0.045	0.053	2e-10	1.6e-12	0.0461197884639036	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.95203541999754
CAMB-7912D	MN908947.3	11083	G	-	0.28	0.034	7.6e-132	4.7e-12	0.237042444467619	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-7912D	MN908947.3	11083	G	T	0.72	0.97	4.1e-255	0	0.762644697048702	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-7912D	MN908947.3	11653	C	T	0.99	1	4.6999999973105e-316	6.1e-114	0.990049751243781	TCT	ORF1ab:nsp6	L227L	C681T	CTC>CTT	Synonymous	ORF1ab:nsp6	0
CAMB-7912D	MN908947.3	14805	C	T	1	1	0	4.4e-218	1	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-7912D	MN908947.3	21137	A	G	1	1	0	0	1	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0
CAMB-7912D	MN908947.3	21987	G	A	1	1	0	0	1	GGT	S	G142D	G425A	GGT>GAT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7912D	MN908947.3	2480	A	G	1	1	0	1.1e-234	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-7912D	MN908947.3	24902	A	G	1	1	0	0	0.999651000465333	AAT	S	I1114V	A3340G	ATC>GTC	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7912D	MN908947.3	2558	C	T	1	1	0	1.5e-265	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-7912D	MN908947.3	27434	C	T	0.18	0.036	8.2e-84	1.4e-16	0.11765180878553	ACT	ORF7a	T14I	C41T	ACT>ATT	Missense	GU280_gp07	0.88234819121447
CAMB-7912D	MN908947.3	4084	C	T	0.042	0.18	3.3e-20	3.6e-81	0.0870505010807624	ACA	ORF1ab:nsp3	D455D	C1365T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.912883998165979
CAMB-7912D	MN908947.3	9724	C	T	1	1	0	0	0.999821988037596	TCT	ORF1ab:nsp4	F390F	C1170T	TTC>TTT	Synonymous	ORF1ab:nsp4	3.56023924807747e-05
CAMB-7913C	MN908947.3	11075	T	-	0.038	0.038	1e-09	7e-10	0.0381616958408632	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957049954490892
CAMB-7913C	MN908947.3	14408	C	T	1	1	0	0	0.997701227908459	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000569002992955743
CAMB-7913C	MN908947.3	17835	T	C	1	1	0	0	0.999562177437544	TTG	ORF1ab:helicase	V533V	T1599C	GTT>GTC	Synonymous	ORF1ab:helicase	0.00041128786170114
CAMB-7913C	MN908947.3	18697	G	T	0.0071	0.0074	3.2e-05	2.2e-05	0.0072511792912557	TGC	ORF1ab:3'-to-5'-exonuclease	A220S	G658T	GCT>TCT	Missense	ORF1ab:3'-to-5'-exonuclease	0.992397957194651
CAMB-7913C	MN908947.3	20055	A	G	0.99	0.99	0	0	0.988212180746562	AAG	ORF1ab:endoRNAse	E145E	A435G	GAA>GAG	Synonymous	ORF1ab:endoRNAse	0.0117878192534381
CAMB-7913C	MN908947.3	23403	A	G	1	1	0	0	0.99965762804711	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.99150917556834e-05
CAMB-7913C	MN908947.3	241	C	T	1	1	0	0	0.999021018437486	TCG	NA	NA	NA	NA	NA	NA	0.000192829701707285
CAMB-7913C	MN908947.3	26137	A	C	0.021	0.013	3.9e-05	0.0089	0.0175438596491228	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.982194291699398
CAMB-7913C	MN908947.3	3037	C	T	1	1	0	0	0.998882129672958	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.19939686996308e-05
CAMB-7915A	MN908947.3	11075	T	-	0.041	0.046	3.5e-10	2.8e-11	0.0431216902211453	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951944477945772
CAMB-7915A	MN908947.3	13019	C	T	0.012	0.013	2.6e-07	1.7e-07	0.0124547753978164	TCT	ORF1ab:nsp9	L112L	C334T	CTA>TTA	Synonymous	ORF1ab:nsp9	0.987289085262383
CAMB-7915A	MN908947.3	14408	C	T	1	1	0	0	0.997129944248342	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000505833580751933
CAMB-7915A	MN908947.3	16182	G	A	0.011	0.011	9.7e-07	3.4e-07	0.0110071361249495	GGT	ORF1ab:RNA-dependent-RNA-polymerase	R905R	G2715A	AGG>AGA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.988959202908308
CAMB-7915A	MN908947.3	23403	A	G	1	1	0	0	0.999299545482847	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	1.55656559367412e-05
CAMB-7915A	MN908947.3	241	C	T	1	1	0	0	0.998673027177747	TCG	NA	NA	NA	NA	NA	NA	0.00085665334094803
CAMB-7915A	MN908947.3	25429	G	T	1	1	0	0	0.997549872621219	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	8.35270697311821e-05
CAMB-7915A	MN908947.3	26137	A	C	0.024	0.017	3.8e-05	0.0032	0.0210030004286327	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.978996999571367
CAMB-7915A	MN908947.3	26781	CTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0307777777777778	0.0272222222222222	0.00013;0.00088;0.00064;0.00078;4.1e-05;0.00013;4.6e-05;4.7e-05;9.2e-06;2.4e-05;1.8e-05;3.5e-05;2.3e-05;2.8e-05;4.9e-05;2e-05;4.3e-05;2.8e-05;2.9e-05;1.9e-05;4.9e-05;2.3e-05;3.2e-05;2.6e-05;1.4e-05;2.9e-05;2.3e-05;9e-06;2.2e-05;4e-05;3.4e-05;1.7e-05;3.2e-05;1.2e-05;1.9e-05;1.1e-05	0.00033;0.0011;0.0013;0.0019;0.00015;3e-04;0.00018;0.00017;9.3e-05;1e-04;9.6e-05;0.00017;0.00012;0.00014;0.00022;0.00011;0.00019;0.00014;0.00014;6.7e-05;0.00017;9e-05;0.00013;0.00013;9.5e-05;0.00018;0.00012;0.00013;1e-04;0.00017;0.00015;9.8e-05;0.00017;7.6e-05;0.00012;9.8e-05	0.0296644943277818	TCT	M	.	259-294-delinframe	.	no-SNV	GU280_gp05	0.976379421683289
CAMB-7915A	MN908947.3	27920	C	T	0.012	0.017	1.1e-06	1.1e-08	0.0146106133700896	TCA	ORF8	I9I	C27T	ATC>ATT	Synonymous	GU280_gp09	0.985320468642316
CAMB-7915A	MN908947.3	3037	C	T	1	1	0	0	0.999094570545443	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00012488682131818
CAMB-7915A	MN908947.3	6568	C	T	0.011	0.018	9.2e-07	2.2e-09	0.014401274666013	ACA	ORF1ab:nsp3	D1283D	C3849T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.985598725333987
CAMB-7915A	MN908947.3	6601	A	G	0.014	0.0094	5.8e-08	4.8e-06	0.0118768125949454	AAT	ORF1ab:nsp3	E1294E	A3882G	GAA>GAG	Synonymous	ORF1ab:nsp3	0.988123187405055
CAMB-79178	MN908947.3	1059	C	T	1	1	0	0	0.999872409921404	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	5.10360314381954e-05
CAMB-79178	MN908947.3	12073	C	T	0.011	0.045	7.2e-07	2.5e-21	0.0304442063828197	ACA	ORF1ab:nsp7	D77D	C231T	GAC>GAT	Synonymous	ORF1ab:nsp7	0.969518423478413
CAMB-79178	MN908947.3	14408	C	T	1	1	0	0	0.9994038120956	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000473443335846675
CAMB-79178	MN908947.3	1481	T	-	0.02	0.039	2.9e-07	1.1e-11	0.0285204991087344	CTT	ORF1ab:nsp2	.	676-676-delfrshift	.	no-SNV	ORF1ab:nsp2	0.971479500891266
CAMB-79178	MN908947.3	17667	G	A	1	1	0	0	0.999789458909397	AGG	ORF1ab:helicase	K477K	G1431A	AAG>AAA	Synonymous	ORF1ab:helicase	0.000105270545301425
CAMB-79178	MN908947.3	1929	C	T	0.038	0.026	6.7e-19	1.2e-13	0.0334064619066613	GCT	ORF1ab:nsp2	A375V	C1124T	GCT>GTT	Missense	ORF1ab:nsp2	0.966593538093339
CAMB-79178	MN908947.3	23403	A	G	1	1	0	0	0.999909709603512	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.51451982438518e-05
CAMB-79178	MN908947.3	241	C	T	1	1	0	0	0.999701724035077	TCG	NA	NA	NA	NA	NA	NA	0.000119310385969099
CAMB-79178	MN908947.3	25563	G	T	1	1	0	0	0.999897519983603	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	8.19840131174421e-05
CAMB-79178	MN908947.3	3037	C	T	1	1	0	0	0.999529854254819	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79178	MN908947.3	4206	C	T	0.044	0.032	5.3e-21	7.7e-16	0.0383917985912546	GCG	ORF1ab:nsp3	A496V	C1487T	GCG>GTG	Missense	ORF1ab:nsp3	0.96150359160332
CAMB-79196	MN908947.3	1059	C	T	1	1	0	0	0.999628203030889	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.000133846908879999
CAMB-79196	MN908947.3	11075	T	-	0.04	0.042	2.4e-10	8.9e-11	0.0413450309055174	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953784145611986
CAMB-79196	MN908947.3	14408	C	T	1	1	0	0	0.998594287094897	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000472231679058172
CAMB-79196	MN908947.3	21974	G	C	0.11	0.1	4.5e-23	2.9e-22	0.106414702926972	TGA	S	D138H	G412C	GAT>CAT	Missense	GU280_gp02, spike glycoprotein	0.893455641632362
CAMB-79196	MN908947.3	23403	A	G	1	1	0	0	0.999530759921958	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.5858256567303e-05
CAMB-79196	MN908947.3	241	C	T	1	1	0	0	0.999000775517509	TCG	NA	NA	NA	NA	NA	NA	0.000119310385969099
CAMB-79196	MN908947.3	24368	G	T	1	1	0	0	0.999784859486352	AGA	S	D936Y	G2806T	GAC>TAC	Missense	GU280_gp02, spike glycoprotein	5.37851284119941e-05
CAMB-79196	MN908947.3	25449	A	T	1	1	0	0	0.999488595683748	AAA	ORF3a	E19D	A57T	GAA>GAT	Missense	GU280_gp03	0.000219173278393898
CAMB-79196	MN908947.3	25549	C	T	1	1	0	0	0.998599311835815	TCT	ORF3a	L53F	C157T	CTT>TTT	Missense	GU280_gp03	0.000167473584848208
CAMB-79196	MN908947.3	25563	G	T	1	1	0	0	0.999649053206586	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000106809893647863
CAMB-79196	MN908947.3	3037	C	T	1	1	0	0	0.999263927864931	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.9006762662741e-05
CAMB-791A5	MN908947.3	11074	C	INS	0.028	0.023	5.5e-06	0.00018	0.0253456221198157	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.973985431841831
CAMB-791A5	MN908947.3	11075	T	-	0.044	0.038	8.7e-11	1.3e-09	0.0409906773231342	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954633796522444
CAMB-791A5	MN908947.3	11747	C	T	0.024	0.02	1.3e-09	5e-08	0.0221583914649159	ACT	ORF1ab:nsp6	L259L	C775T	CTA>TTA	Synonymous	ORF1ab:nsp6	0.977020927369717
CAMB-791A5	MN908947.3	14408	C	T	0.99	1	0	0	0.995898243711834	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000470525658991643
CAMB-791A5	MN908947.3	14786	C	T	1	1	0	0	0.99964144140555	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A440V	C1319T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000288838867751638
CAMB-791A5	MN908947.3	17607	T	C	0.0085	0.015	7.3e-06	1.6e-08	0.011634266394869	ATG	ORF1ab:helicase	Y457Y	T1371C	TAT>TAC	Synonymous	ORF1ab:helicase	0.988328444289763
CAMB-791A5	MN908947.3	17731	T	C	0.039	0.051	7.6e-19	4.9e-24	0.0448663629702781	ATT	ORF1ab:helicase	F499L	T1495C	TTC>CTC	Missense	ORF1ab:helicase	0.955006211971584
CAMB-791A5	MN908947.3	20578	G	T	1	1	0	0	0.999705066949802	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	0
CAMB-791A5	MN908947.3	2150	G	T	0.11	0.12	5.2e-49	4e-54	0.110888510467795	TGA	ORF1ab:nsp2	D449Y	G1345T	GAT>TAT	Missense	ORF1ab:nsp2	0.889061404387459
CAMB-791A5	MN908947.3	23403	A	G	1	1	0	0	0.999720289204011	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.23804236347147e-05
CAMB-791A5	MN908947.3	241	C	T	1	1	0	0	0.997927807486631	TCG	NA	NA	NA	NA	NA	NA	0.000116978609625668
CAMB-791A5	MN908947.3	2416	C	T	1	1	0	0	0.996656566711942	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0
CAMB-791A5	MN908947.3	2508	C	T	0.0098	0.0061	4.7e-06	0.00014	0.00788855320577375	CCC	ORF1ab:nsp2	P568L	C1703T	CCC>CTC	Missense	ORF1ab:nsp2	0.992111446794226
CAMB-791A5	MN908947.3	25080	A	G	0.021	0.011	5.5e-11	7.5e-07	0.0164321300585613	AAT	S	N1173S	A3518G	AAT>AGT	Missense	GU280_gp02, spike glycoprotein	0.982781225417359
CAMB-791A5	MN908947.3	25460	C	T	1	1	0	0	0.999781037880447	GCT	ORF3a	A23V	C68T	GCT>GTT	Missense	GU280_gp03	0.000103040997436855
CAMB-791A5	MN908947.3	25563	G	T	1	1	0	0	0.999750256315886	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000105155235416283
CAMB-791A5	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0308648648648649	0.0318108108108108	0.0024;0.00023;0.00092;0.00082;0.0016;7.9e-05;0.00032;4e-05;4e-05;1.2e-05;1.9e-05;1.4e-05;3.8e-05;1.7e-05;2.2e-05;4.1e-05;1.5e-05;3.5e-05;2.3e-05;2.2e-05;1.4e-05;3.9e-05;1.7e-05;2.5e-05;2.1e-05;1.3e-05;3.2e-05;1.8e-05;7.7e-06;1.8e-05;3.2e-05;2.7e-05;1.1e-05;2e-05;6.4e-06;1.2e-05;4.8e-06	0.00028;1.8e-05;0.00013;0.00015;0.00031;1.7e-05;5.5e-05;4.2e-05;4.3e-05;1.7e-05;1.4e-05;1.1e-05;2.1e-05;1.4e-05;1.6e-05;2.3e-05;1.3e-05;2.5e-05;1.7e-05;1.7e-05;1.6e-05;2.7e-05;1.4e-05;2e-05;1.5e-05;1.1e-05;2.3e-05;1.3e-05;1.8e-05;1.5e-05;2.1e-05;1.7e-05;1.8e-05;4.2e-05;1.5e-05;1.8e-05;1.3e-05	0.0326488483268144	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.97814680586358
CAMB-791A5	MN908947.3	28214	C	INS	0.52	0.51	1.6e-301	5e-293	0.518004280207829	ACT	ORF8	.	320-321-insfrshift	.	no-SNV	GU280_gp09	0.481610850968295
CAMB-791A5	MN908947.3	29717	G	A	0.0088	0.011	9.4e-06	1.5e-06	0.00997220859898643	AGC	NA	NA	NA	NA	NA	NA	0.989537354912539
CAMB-791A5	MN908947.3	3037	C	T	1	1	0	0	0.999516300667505	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-791A5	MN908947.3	4549	A	G	0.0092	0.014	3e-06	1.8e-08	0.011240656030347	AAA	ORF1ab:nsp3	K610K	A1830G	AAA>AAG	Synonymous	ORF1ab:nsp3	0.984101305366507
CAMB-791A5	MN908947.3	9967	C	T	0.024	0.02	3.5e-12	2.2e-10	0.0222406028857642	TCG	ORF1ab:nsp4	L471L	C1413T	CTC>CTT	Synonymous	ORF1ab:nsp4	0.977690469625954
CAMB-791B4	MN908947.3	10097	G	A	1	1	0	0	0.99980311730927	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	6.56275635767022e-05
CAMB-791B4	MN908947.3	11075	T	-	0.032	0.036	1.4e-08	1.2e-09	0.0334571052835151	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962442948866713
CAMB-791B4	MN908947.3	13536	C	T	1	1	0	0	0.999577574485499	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	7.92047839689517e-05
CAMB-791B4	MN908947.3	14408	C	T	1	1	0	0	0.998168018843235	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000701862910708763
CAMB-791B4	MN908947.3	18322	C	T	0.012	0.012	3.6e-07	2.4e-07	0.0122687081083792	TCA	ORF1ab:3'-to-5'-exonuclease	H95Y	C283T	CAT>TAT	Missense	ORF1ab:3'-to-5'-exonuclease	0.987689504738663
CAMB-791B4	MN908947.3	20956	C	T	0.0096	0.011	3.8e-06	1.2e-06	0.010225991733319	TCT	ORF1ab:2'-O-ribose-methyltransferase	L100F	C298T	CTT>TTT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.98958612915347
CAMB-791B4	MN908947.3	2106	C	T	0.026	0.027	1e-12	2.8e-13	0.0267808086957813	ACT	ORF1ab:nsp2	T434I	C1301T	ACT>ATT	Missense	ORF1ab:nsp2	0.973018725034525
CAMB-791B4	MN908947.3	22344	G	T	1	1	0	0	0.997606019151847	GGT	S	G261V	G782T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.00119699042407661
CAMB-791B4	MN908947.3	23403	A	G	1	1	0	0	0.999608241180975	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.1228876186406e-05
CAMB-791B4	MN908947.3	2358	C	T	0.0089	0.009	1.2e-05	1.1e-05	0.00897750897750898	GCT	ORF1ab:nsp2	A518V	C1553T	GCT>GTT	Missense	ORF1ab:nsp2	0.990927990927991
CAMB-791B4	MN908947.3	23731	C	T	1	1	0	0	0.999716472923164	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000180426321622806
CAMB-791B4	MN908947.3	241	C	T	1	1	0	0	0.998882855365122	TCG	NA	NA	NA	NA	NA	NA	0.000141410713275638
CAMB-791B4	MN908947.3	26625	C	T	0.035	0.032	3.4e-17	5.9e-16	0.0338560442201394	TCT	M	L35L	C103T	CTA>TTA	Synonymous	GU280_gp05	0.966023792357606
CAMB-791B4	MN908947.3	27578	AATT	-	1	1	0;0;0;0	0;0;0;0	0.998921251348436	CAA	ORF7a	.	185-188-delfrshift	.	no-SNV	GU280_gp07	0.000808625336927224
CAMB-791B4	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999322554421461	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000149730485126772
CAMB-791B4	MN908947.3	3037	C	T	1	1	0	0	0.99926943308007	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000146113383985973
CAMB-791B4	MN908947.3	3622	C	T	0.047	0.047	1.2e-20	1.3e-20	0.0471413957717663	GCC	ORF1ab:nsp3	G301G	C903T	GGC>GGT	Synonymous	ORF1ab:nsp3	0.952546033189361
CAMB-791B4	MN908947.3	4002	C	T	1	1	0	0	0.999670415688213	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0.000164792155893379
CAMB-791B4	MN908947.3	6802	G	C	0.061	0.063	1.8e-27	2.7e-28	0.0622615803814714	TGT	ORF1ab:nsp3	L1361F	G4083C	TTG>TTC	Missense	ORF1ab:nsp3	0.937302452316076
CAMB-791C3	MN908947.3	11074	C	INS	0.11	0.1	5.3e-45	3e-43	0.105058723717431	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.893704449509869
CAMB-791C3	MN908947.3	11083	G	-	0.18	0.18	6.3e-78	2.8e-77	0.175799946716153	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.83737402504341e-05
CAMB-791C3	MN908947.3	11083	G	T	0.82	0.82	0	0	0.823961194660591	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.83737402504341e-05
CAMB-791C3	MN908947.3	14805	C	T	1	1	0	0	0.999332461082481	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000489528539513854
CAMB-791C3	MN908947.3	16323	C	T	0.03	0.03	3.9e-14	3.6e-14	0.0300870676034558	GCT	ORF1ab:helicase	C29C	C87T	TGC>TGT	Synonymous	ORF1ab:helicase	0.969341446196255
CAMB-791C3	MN908947.3	21724	G	T	1	1	0	0	0.999544865735392	TGT	S	L54F	G162T	TTG>TTT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-791C3	MN908947.3	222	C	T	0.071	0.072	4e-32	1.2e-32	0.0714563218556197	TCA	NA	NA	NA	NA	NA	NA	0.927910557290243
CAMB-791C3	MN908947.3	2480	A	G	1	1	0	0	0.999869118513186	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-791C3	MN908947.3	2558	C	T	1	1	0	0	0.999757081086333	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	2.42918913666618e-05
CAMB-791C3	MN908947.3	26144	G	T	1	1	0	0	0.999735257131511	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.00013237143424449
CAMB-791C3	MN908947.3	26882	C	T	0.0079	0.011	2.1e-05	1.1e-06	0.00956010593630902	TCA	M	L120L	C360T	CTC>CTT	Synonymous	GU280_gp05	0.990426975001615
CAMB-791C3	MN908947.3	27092	C	T	0.0086	0.0075	6.9e-06	2.2e-05	0.00801940389826064	ACT	M	D190D	C570T	GAC>GAT	Synonymous	GU280_gp05	0.991936893628179
CAMB-791C3	MN908947.3	27297	C	T	1	1	0	0	0.998714811223469	TCA	ORF6	I32I	C96T	ATC>ATT	Synonymous	GU280_gp06	0.00030782964707331
CAMB-791C3	MN908947.3	27309	A	G	0.0098	0.01	2.6e-06	2.3e-06	0.0099543464959759	TAA	ORF6	I36M	A108G	ATA>ATG	Missense	GU280_gp06	0.990014276525313
CAMB-791C3	MN908947.3	6681	C	T	0.012	0.0075	4.2e-07	3.7e-05	0.00943444078113112	GCT	ORF1ab:nsp3	A1321V	C3962T	GCT>GTT	Missense	ORF1ab:nsp3	0.99051483641897
CAMB-791C3	MN908947.3	6720	C	T	0.0097	0.011	4.5e-06	1e-06	0.0107097476856054	ACA	ORF1ab:nsp3	T1334I	C4001T	ACA>ATA	Missense	ORF1ab:nsp3	0.989063350880378
CAMB-791C3	MN908947.3	7859	A	G	0.014	0.013	9.8e-08	3.4e-07	0.0134224450013924	CAC	ORF1ab:nsp3	T1714A	A5140G	ACT>GCT	Missense	ORF1ab:nsp3	0.986466165413534
CAMB-791D2	MN908947.3	11075	T	-	0.03	0.04	7.5e-08	4.1e-10	0.0348696488152463	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.96284567098343
CAMB-791D2	MN908947.3	11325	C	T	0.036	0.029	3.1e-17	1.8e-14	0.0327036903597715	TCA	ORF1ab:nsp6	S118L	C353T	TCA>TTA	Missense	ORF1ab:nsp6	0.967255134077925
CAMB-791D2	MN908947.3	14408	C	T	0.99	1	0	0	0.995348512918584	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000707185402099643
CAMB-791D2	MN908947.3	16206	G	T	1	1	0	0	0.99967099250594	AGG	ORF1ab:RNA-dependent-RNA-polymerase	E913D	G2739T	GAG>GAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	7.3112776457686e-05
CAMB-791D2	MN908947.3	23403	A	G	1	1	0	0	0.999665783194335	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.7724838526648e-05
CAMB-791D2	MN908947.3	241	C	T	1	1	0	0	0.999229305273754	TCG	NA	NA	NA	NA	NA	NA	9.43707828056434e-05
CAMB-791D2	MN908947.3	25493	C	T	0.0075	0.0052	4.2e-05	0.00039	0.00632496039828015	ACG	ORF3a	T34M	C101T	ACG>ATG	Missense	GU280_gp03	0.993629780493324
CAMB-791D2	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0352432432432432	0.0284594594594595	0.00026;1.7e-05;9.8e-05;8.1e-05;0.00017;5.9e-07;6.4e-06;7e-06;7.2e-06;1.8e-06;2.8e-06;1.9e-06;6.7e-06;3.5e-06;4.4e-06;9.3e-06;2.8e-06;7.8e-06;5e-06;4.9e-06;4.4e-06;8.8e-06;4e-06;6.1e-06;4.4e-06;2.4e-06;6.7e-06;3.9e-06;2.4e-06;3.4e-06;7e-06;5.8e-06;3.1e-06;6.8e-06;2.2e-06;3.6e-06;2.6e-06	0.0029;0.00047;0.0015;0.0015;0.0026;6.6e-05;0.00016;9.4e-05;9.4e-05;4e-05;6.3e-05;5.3e-05;8.9e-05;6.5e-05;8.1e-05;0.00012;6.2e-05;0.00011;7.7e-05;7.4e-05;6e-05;0.00012;7.4e-05;8.5e-05;5.6e-05;4.7e-05;8.2e-05;6e-05;3e-05;6.8e-05;9.4e-05;8.9e-05;5.5e-05;9.7e-05;3.7e-05;4.9e-05;3.4e-05	0.0327794265151437	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.978326956881398
CAMB-791D2	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998700838549663	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000194250194250194
CAMB-791D2	MN908947.3	3037	C	T	1	1	0	0	0.999461329099569	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000113404400090724
CAMB-791F0	MN908947.3	11074	C	INS	0.037	0.068	3.3e-08	3e-20	0.0538104249096852	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.946086358162739
CAMB-791F0	MN908947.3	12454	T	C	0.016	0.012	7.3e-09	2.5e-07	0.0143367697594502	CTC	ORF1ab:nsp8	P121P	T363C	CCT>CCC	Synonymous	ORF1ab:nsp8	0.985635738831615
CAMB-791F0	MN908947.3	13517	C	T	0.14	0.074	1.4e-59	9.9e-31	0.111688747274862	ACT	ORF1ab:RNA-dependent-RNA-polymerase	T17I	C50T	ACT>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.888143551903404
CAMB-791F0	MN908947.3	13571	G	T	0.024	0.09	6.5e-06	2.4e-18	0.0530152418820411	GGT	ORF1ab:RNA-dependent-RNA-polymerase	G35V	G104T	GGT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.938369781312127
CAMB-791F0	MN908947.3	14408	C	T	1	1	0	0	0.999421920162487	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000421842043590345
CAMB-791F0	MN908947.3	15255	T	C	0.025	0.012	7.6e-13	1.3e-07	0.0189903846153846	TTT	ORF1ab:RNA-dependent-RNA-polymerase	V596V	T1788C	GTT>GTC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.981009615384615
CAMB-791F0	MN908947.3	15543	G	T	0.011	0.02	9.2e-07	1.5e-10	0.015246995613095	CGG	ORF1ab:RNA-dependent-RNA-polymerase	T692T	G2076T	ACG>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.984710135608237
CAMB-791F0	MN908947.3	15939	T	G	0.13	0.14	4.5e-61	5.2e-64	0.134196575685937	ATC	ORF1ab:RNA-dependent-RNA-polymerase	D824E	T2472G	GAT>GAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.865767605129307
CAMB-791F0	MN908947.3	18318	G	T	0.016	0.015	7.1e-09	1.6e-08	0.0156355232750083	GGT	ORF1ab:3'-to-5'-exonuclease	G93G	G279T	GGG>GGT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.979333113238693
CAMB-791F0	MN908947.3	2110	C	T	0.045	0.051	2.2e-20	2.7e-22	0.0472758720092246	ACA	ORF1ab:nsp2	N435N	C1305T	AAC>AAT	Synonymous	ORF1ab:nsp2	0.941337561256846
CAMB-791F0	MN908947.3	22899	G	T	0.016	0.044	7.1e-06	1.2e-13	0.0284414796846574	GGT	S	G446V	G1337T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.971558520315343
CAMB-791F0	MN908947.3	23403	A	G	1	1	0	0	0.999885600539965	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.86396760207292e-05
CAMB-791F0	MN908947.3	23553	TACCCATTGGTGCAGGTATATGCGC	-	0.0234	0.05348	0.0042;0.0029;0.0075;0.0064;0.0074;0.0075;0.0043;0.0063;0.0052;0.0072;0.0073;0.0075;0.0072;0.0069;0.0057;0.0054;0.0041;0.0012;0.0041;0.0028;0.0039;0.0024;0.004;0.0054;0.0041	0.00091;0.00056;2.1e-05;1.6e-05;2.1e-05;2.8e-05;5.1e-06;1.3e-05;4.3e-06;1.1e-05;1.3e-05;1.3e-05;1.2e-05;1.2e-05;5.2e-06;4.6e-06;2.5e-06;7.6e-07;3.4e-06;1.2e-06;4.3e-06;5.6e-07;2.1e-06;6.6e-06;2.6e-06	0.0368064952638701	ATA	S	.	1991-2015-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.97485835694051
CAMB-791F0	MN908947.3	24015	TTGAAGATCTACTTT	-	0.0480666666666667	0.0440666666666667	2.3e-06;3.1e-06;4.1e-06;3.5e-06;8.6e-06;1e-05;8.4e-06;1.1e-05;7e-06;2.6e-06;5.3e-06;5.1e-05;8.2e-08;1.4e-06;3.7e-08	3.3e-06;5.3e-06;6.5e-06;4.4e-06;1.1e-05;1.5e-05;8.7e-06;1.8e-05;1.4e-05;6e-06;8.8e-06;7.6e-05;4.5e-07;5.5e-06;1e-04	0.0460628509977297	ATT	S	.	2453-2467-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.952469021638617
CAMB-791F0	MN908947.3	241	C	T	1	1	0	0	0.999876971531212	TCG	NA	NA	NA	NA	NA	NA	4.9211387515071e-05
CAMB-791F0	MN908947.3	2412	T	C	0.016	0.0099	1.6e-07	8.1e-06	0.0119820269595607	TTG	ORF1ab:nsp2	L536S	T1607C	TTG>TCG	Missense	ORF1ab:nsp2	0.988017973040439
CAMB-791F0	MN908947.3	24459	TTAGCTCCAA	-	0.0025	0.0181	NA;NA;NA;NA;NA;NA;NA;NA;1e-10;NA	1.5e-17;1.4e-07;1.8e-07;1.9e-07;2.1e-07;2.3e-07;2.4e-07;1.9e-07;2.2e-07;1.6e-07	0.00727829917640299	CTT	S	.	2897-2906-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.980207916833267
CAMB-791F0	MN908947.3	24933	G	T	0.035	0.043	1.8e-06	1.4e-07	0.0394736842105263	GGT	S	G1124V	G3371T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.96042147200671
CAMB-791F0	MN908947.3	25350	C	T	1	1	0	0	0.999905440928948	CCA	S	P1263L	C3788T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	9.4559071051686e-05
CAMB-791F0	MN908947.3	25588	A	-	0.021	0.027	5.7e-09	5.6e-11	0.0239461509441455	CAA	ORF3a	.	196-196-delfrshift	.	no-SNV	GU280_gp03	0.975954569823084
CAMB-791F0	MN908947.3	25588	AA	-	0.0105	0.028	5.7e-09;NA	5.6e-11;1.3e-14	0.0187563919001841	CAA	ORF3a	.	196-197-delfrshift	.	no-SNV	GU280_gp03	0.975954569823084
CAMB-791F0	MN908947.3	25904	C	T	0.028	0.018	1e-12	9.3e-09	0.023853550295858	TCA	ORF3a	S171L	C512T	TCA>TTA	Missense	GU280_gp03	0.976146449704142
CAMB-791F0	MN908947.3	26574	GAACAATGGAACCTAGTAATAGGTTTCCTATTCCTT	-	0.029	0.0287563888888889	1.2e-05;0.00048;0.00088;0.00092;1e-06;1.1e-06;1.6e-06;4.9e-07;1.6e-06;1.8e-06;9.3e-07;1.2e-06;2e-06;1.4e-06;4.8e-07;1.4e-06;7.3e-07;3.8e-07;7.9e-07;1.1e-06;4.6e-07;9.2e-07;1e-06;8.3e-07;6.1e-07;1.2e-06;1.2e-06;1.1e-06;9.7e-07;3.2e-07;8.5e-09;1.1e-08;3.2e-09;8.2e-10;1.3e-09;1.7e-09	NA;1.3e-07;5.8e-07;6.4e-07;3.7e-07;4e-07;7e-07;1.5e-07;5.3e-07;6.3e-07;4.2e-07;4.3e-07;7.6e-07;5.8e-07;2e-07;4.9e-07;4e-07;1.6e-07;4.6e-07;5e-07;1.7e-07;3.5e-07;3.9e-07;3.3e-07;2.7e-07;4.3e-07;4.3e-07;3.9e-07;3.6e-07;1.1e-07;NA;NA;NA;NA;0.46;NA	0.0335355968317199	TGA	M	.	52-87-delinframe	.	no-SNV	GU280_gp05	0.986067489319897
CAMB-791F0	MN908947.3	26789	CTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0287931034482759	0.0203103448275862	3.8e-05;6.2e-05;4.8e-05;0.00012;7.6e-05;9.6e-05;0.00017;6.5e-05;0.00015;9.6e-05;9.8e-05;7.1e-05;0.00016;8.5e-05;0.00012;9.2e-05;5.9e-05;0.00013;8.2e-05;3.2e-05;8.2e-05;0.00013;0.00012;6e-05;0.00013;4.9e-05;8e-05;6.3e-05;0.00047	1.4e-05;2.8e-05;2.3e-05;0.015;0.012;0.013;0.017;0.011;0.015;0.013;6.9e-09;5.8e-09;0.017;0.013;0.014;0.012;0.011;0.015;0.012;0.0098;0.011;0.015;0.014;0.0094;0.014;0.011;0.011;0.011;0.016	0.0223226639608892	GCT	M	.	267-295-delfrshift	.	no-SNV	GU280_gp05	0.965146291717055
CAMB-791F0	MN908947.3	28825	T	C	0.0087	0.01	1e-04	3.5e-05	0.00924195223260644	CTC	N	S184S	T552C	TCT>TCC	Synonymous	GU280_gp10	0.990758047767394
CAMB-791F0	MN908947.3	29114	C	-	0.0058	0.017	0.004	5.3e-06	0.0111335459400298	ACA	N	.	841-841-delfrshift	.	no-SNV	GU280_gp10	0.988809842809428
CAMB-791F0	MN908947.3	29755	G	C	0.012	0.03	7.8e-07	2.5e-13	0.0238713025428127	CGA	NA	NA	NA	NA	NA	NA	0.974052932018682
CAMB-791F0	MN908947.3	3037	C	T	1	1	0	0	0.999754088282307	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-791F0	MN908947.3	4768	T	C	0.016	0.0021	8.4e-09	0.0084	0.0092998300992578	TTA	ORF1ab:nsp3	F683F	T2049C	TTT>TTC	Synonymous	ORF1ab:nsp3	0.990700169900742
CAMB-791F0	MN908947.3	522	TT	-	0.043	0.094	7.3e-08;0.00079	8.6e-14;4.1e-13	0.0666482491884799	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.920236753100338
CAMB-791F0	MN908947.3	6121	A	G	0.0032	0.027	0.0025	5.6e-11	0.015511892450879	CAA	ORF1ab:nsp3	S1134S	A3402G	TCA>TCG	Synonymous	ORF1ab:nsp3	0.984488107549121
CAMB-791F0	MN908947.3	6373	G	T	0.98	1	0	0	0.987992377287276	TGG	ORF1ab:nsp3	M1218I	G3654T	ATG>ATT	Missense	ORF1ab:nsp3	9.25086495587337e-05
CAMB-791F0	MN908947.3	8765	TTTGACACATGGTT	-	0.027	0.0272142857142857	5.7e-09;1.1e-07;2e-07;2.5e-07;4.7e-07;1e-06;1.7e-07;2.2e-07;3.2e-07;2.3e-07;5.2e-07;4.2e-07;NA;NA	1.6e-05;6.6e-05;8.8e-05;0.00011;1.7e-07;4.3e-07;6.6e-08;1e-07;9.4e-08;1.3e-07;1.6e-07;1.8e-07;2e-06;2.1e-07	0.0326033261979252	TTT	ORF1ab:nsp4	.	211-224-delfrshift	.	no-SNV	ORF1ab:nsp4	0.973609958506224
CAMB-791F0	MN908947.3	9245	G	T	0.0052	0.016	0.00012	1.7e-09	0.011226275407188	AGC	ORF1ab:nsp4	A231S	G691T	GCT>TCT	Missense	ORF1ab:nsp4	0.988612195450262
CAMB-7920C	MN908947.3	11075	T	-	0.038	0.045	1.7e-09	4.9e-11	0.0413671043026988	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953813233073685
CAMB-7920C	MN908947.3	11875	A	G	0.99	0.98	0	0	0.98429003021148	TAG	ORF1ab:nsp7	V11V	A33G	GTA>GTG	Synonymous	ORF1ab:nsp7	0.0157099697885196
CAMB-7920C	MN908947.3	14178	C	A	0.025	0.024	1.6e-12	1.9e-12	0.0243258366301157	CCT	ORF1ab:RNA-dependent-RNA-polymerase	T237T	C711A	ACC>ACA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.975320761384943
CAMB-7920C	MN908947.3	14408	C	T	1	1	0	0	0.996912876629051	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000436946692503515
CAMB-7920C	MN908947.3	14773	G	A	1	1	0	0	0.999560952625717	GGA	ORF1ab:RNA-dependent-RNA-polymerase	D436N	G1306A	GAT>AAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000406921956652103
CAMB-7920C	MN908947.3	23403	A	G	1	1	0	0	0.998026616217627	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.96992628351491e-05
CAMB-7920C	MN908947.3	241	C	T	1	1	0	0	0.999447267814098	TCG	NA	NA	NA	NA	NA	NA	0.000460610154918549
CAMB-7920C	MN908947.3	25437	G	A	0.0074	0.006	3.5e-05	0.00014	0.00672315459478515	TGA	ORF3a	L15L	G45A	TTG>TTA	Synonymous	GU280_gp03	0.991275007239352
CAMB-7920C	MN908947.3	26137	A	C	0.032	0.016	5.9e-07	0.0038	0.022894838960031	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.977105161039969
CAMB-7920C	MN908947.3	27970	C	T	0.022	0.019	1.2e-10	2.1e-09	0.0200920887400586	ACT	ORF8	T26I	C77T	ACT>ATT	Missense	GU280_gp09	0.979740477187108
CAMB-7920C	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999353143319183	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000223503643109383
CAMB-7920C	MN908947.3	3037	C	T	1	1	0	0	0.999055575735561	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000108972030512169
CAMB-7920C	MN908947.3	3784	C	T	0.04	0.037	1.6e-16	2.5e-16	0.038502221281997	TCT	ORF1ab:nsp3	V355V	C1065T	GTC>GTT	Synonymous	ORF1ab:nsp3	0.961497778718003
CAMB-7920C	MN908947.3	8160	C	T	1	1	0	0	0.999789495842543	ACT	ORF1ab:nsp3	T1814I	C5441T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-7922A	MN908947.3	11075	T	-	0.048	0.038	1.3e-11	1.5e-09	0.0430074441687345	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954034739454094
CAMB-7922A	MN908947.3	14408	C	T	1	1	0	0	0.998318080633193	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00031659658669305
CAMB-7922A	MN908947.3	20679	G	T	0.0079	0.004	2.4e-05	0.0012	0.00588204401029358	CGG	ORF1ab:2'-O-ribose-methyltransferase	P7P	G21T	CCG>CCT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.993960401239431
CAMB-7922A	MN908947.3	22264	C	T	0.0082	0.0047	1.9e-05	0.00062	0.00667217175887696	ACA	S	N234N	C702T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.993294797687861
CAMB-7922A	MN908947.3	23403	A	G	1	1	0	0	0.999404270191269	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.94306411641355e-05
CAMB-7922A	MN908947.3	241	C	T	1	1	0	0	0.999513732202599	TCG	NA	NA	NA	NA	NA	NA	5.83521356881662e-05
CAMB-7922A	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999299835255354	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.51365380275333e-05
CAMB-7922A	MN908947.3	3037	C	T	1	1	0	0	0.999632892804699	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000203948441833904
CAMB-7922A	MN908947.3	6004	T	C	0.012	0.017	4.5e-07	9.3e-09	0.0147719215315528	ATC	ORF1ab:nsp3	D1095D	T3285C	GAT>GAC	Synonymous	ORF1ab:nsp3	0.985109903096195
CAMB-7922A	MN908947.3	8137	G	T	1	1	0	0	0.997908244805866	TGT	ORF1ab:nsp3	V1806V	G5418T	GTG>GTT	Synonymous	ORF1ab:nsp3	0.0002820344081978
CAMB-79239	MN908947.3	11075	T	-	0.039	0.034	7.1e-10	1.6e-08	0.0364403567224627	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959140514334737
CAMB-79239	MN908947.3	14408	C	T	0.99	1	0	0	0.995727251570863	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000893646730276937
CAMB-79239	MN908947.3	14741	C	T	1	1	0	0	0.998992823870074	TCT	ORF1ab:RNA-dependent-RNA-polymerase	S425F	C1274T	TCT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000154950173834726
CAMB-79239	MN908947.3	18049	G	T	0.01	0.01	1.4e-06	1.9e-06	0.0102008047301509	TGT	ORF1ab:3'-to-5'-exonuclease	V4L	G10T	GTA>TTA	Missense	ORF1ab:3'-to-5'-exonuclease	0.989723633753329
CAMB-79239	MN908947.3	187	A	G	1	1	0	0	0.999455015046324	CAG	NA	NA	NA	NA	NA	NA	1.18474989929626e-05
CAMB-79239	MN908947.3	22259	A	G	0.18	0.17	3.8e-83	1.6e-78	0.175021240441801	TAT	S	I233V	A697G	ATT>GTT	Missense	GU280_gp02, spike glycoprotein	0.824913404352657
CAMB-79239	MN908947.3	23403	A	G	1	1	0	0	0.999575103922499	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.37344116251567e-05
CAMB-79239	MN908947.3	241	C	T	1	1	0	0	0.998433063537506	TCG	NA	NA	NA	NA	NA	NA	0.000106033294454459
CAMB-79239	MN908947.3	26137	A	C	0.031	0.019	8.7e-08	0.00018	0.0247397797556192	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.974807663297632
CAMB-79239	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0337567567567568	0.033027027027027	0.00071;5.1e-05;4e-04;0.00038;0.00089;1.3e-05;7.3e-05;1.1e-05;1.2e-05;2.2e-06;3.9e-06;2.3e-06;8.8e-06;4.3e-06;6e-06;1.3e-05;3.8e-06;1e-05;6.9e-06;6.7e-06;4.7e-06;1.2e-05;4.7e-06;7.7e-06;6.1e-06;3.1e-06;8.7e-06;5.1e-06;2.4e-06;4.6e-06;9.7e-06;8.5e-06;4.6e-06;9e-06;3e-06;5.1e-06;2.7e-06	9e-04;8.5e-05;0.00032;0.00037;7e-04;6.2e-05;0.00011;1.3e-05;1.2e-05;4.4e-06;7.4e-06;6.5e-06;1.2e-05;7.6e-06;9.4e-06;1.6e-05;7.1e-06;1.3e-05;9.7e-06;9.4e-06;6e-06;1.3e-05;7.2e-06;1.1e-05;8.2e-06;6.3e-06;1.2e-05;7.4e-06;9.2e-06;7.4e-06;1.2e-05;9.6e-06;5e-06;1.1e-05;3.8e-06;6.5e-06;6e-06	0.0349310931752045	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.977991310343318
CAMB-79239	MN908947.3	28253	C	T	0.013	0.014	1.2e-06	4.4e-07	0.0134695413493891	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.986054542234815
CAMB-79239	MN908947.3	29445	C	T	0.005	0.013	0.00079	1.3e-06	0.00868137024870953	ACT	N	T391I	C1172T	ACT>ATT	Missense	GU280_gp10	0.99131862975129
CAMB-79239	MN908947.3	3037	C	T	1	1	0	0	0.999133254149144	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000160508490899169
CAMB-79239	MN908947.3	635	C	T	0.007	0.0089	0.00016	2.4e-05	0.00790224822045246	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.99205370357319
CAMB-79248	MN908947.3	1018	G	T	0.0037	0.0088	0.00098	7.2e-06	0.0063081532881249	TGC	ORF1ab:nsp2	L71F	G213T	TTG>TTT	Missense	ORF1ab:nsp2	0.993442148977553
CAMB-79248	MN908947.3	10550	G	T	0.003	0.0095	0.0021	3e-06	0.00586770230908861	GGA	ORF1ab:3C-like-proteinase	E166*	G496T	GAA>TAA	Nonsense	ORF1ab:3C-like-proteinase	0.994132297690911
CAMB-79248	MN908947.3	11068	TTTG	-	0.003175	0.006175	0.0017;0.001;0.0021;0.0023	5e-07;0.00025;0.00065;0.00078	0.00379497409200379	CTT	ORF1ab:nsp6	.	96-99-delfrshift	.	no-SNV	ORF1ab:nsp6	0.991953611568473
CAMB-79248	MN908947.3	11074	C	INS	0.02	0.027	0.00094	1.3e-05	0.0234383733495634	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.974089853308326
CAMB-79248	MN908947.3	11075	T	-	0.034	0.055	1.2e-08	2.6e-13	0.0443663449433487	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952633235417541
CAMB-79248	MN908947.3	11075	TT	-	0.017055	0.0318	1.2e-08;0.47	2.6e-13;0.00026	0.0246031324661534	CTT	ORF1ab:nsp6	.	103-104-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952633235417541
CAMB-79248	MN908947.3	11575	C	T	0.012	0.011	6.5e-07	1.8e-06	0.011417466294182	TCA	ORF1ab:nsp6	F201F	C603T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.988582533705818
CAMB-79248	MN908947.3	12578	G	T	0.0097	0.024	0.00015	6.4e-09	0.0169378235394505	AGA	ORF1ab:nsp8	D163Y	G487T	GAT>TAT	Missense	ORF1ab:nsp8	0.983019511917629
CAMB-79248	MN908947.3	13548	C	-	0.0055	0.026	0.0038	8.5e-08	0.0132668506811504	ACA	ORF1ab:RNA-dependent-RNA-polymerase	.	81-81-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.9864660315199
CAMB-79248	MN908947.3	13571	G	T	0.047	0.018	1.9e-10	9e-05	0.03611014894354	GGT	ORF1ab:RNA-dependent-RNA-polymerase	G35V	G104T	GGT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.962331139591271
CAMB-79248	MN908947.3	14408	C	T	1	1	0	0	0.998626041460573	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000395700059355009
CAMB-79248	MN908947.3	14652	T	C	0.0097	0.0099	2.4e-06	1.6e-06	0.00976882629846715	ATG	ORF1ab:RNA-dependent-RNA-polymerase	N395N	T1185C	AAT>AAC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.990218061183011
CAMB-79248	MN908947.3	18780	G	T	0.0058	0.0078	0.00017	2.8e-05	0.00684599011687972	GGG	ORF1ab:3'-to-5'-exonuclease	W247C	G741T	TGG>TGT	Missense	ORF1ab:3'-to-5'-exonuclease	0.993066879099815
CAMB-79248	MN908947.3	19186	C	T	0.0064	0.0067	6.7e-05	4.4e-05	0.00654439815479896	CCT	ORF1ab:3'-to-5'-exonuclease	L383L	C1147T	CTA>TTA	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.993439639898482
CAMB-79248	MN908947.3	20627	G	T	0.019	0.006	9.2e-09	0.0011	0.0128290348311619	GGC	ORF1ab:endoRNAse	G336V	G1007T	GGC>GTC	Missense	ORF1ab:endoRNAse	0.987038021802712
CAMB-79248	MN908947.3	20759	C	T	0.15	0.16	2.7e-68	8e-72	0.155824005319738	GCA	ORF1ab:2'-O-ribose-methyltransferase	A34V	C101T	GCA>GTA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.844175994680261
CAMB-79248	MN908947.3	20922	G	T	0.012	0.0079	3.2e-06	0.00012	0.00996677740863787	GGT	ORF1ab:2'-O-ribose-methyltransferase	W88C	G264T	TGG>TGT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.98999169435216
CAMB-79248	MN908947.3	21569	G	INS	0.0072	0.049	0.00068	9.8e-18	0.0258562793821357	TGT	S	.	6-7-insfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.96507723304231
CAMB-79248	MN908947.3	21575	C	T	0.096	0.095	1.1e-24	3.6e-23	0.0958135520069055	TCT	S	L5F	C13T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.899870522227018
CAMB-79248	MN908947.3	22899	G	T	0.025	0.02	1.6e-08	3.9e-07	0.0228174603174603	GGT	S	G446V	G1337T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.975351037851038
CAMB-79248	MN908947.3	23009	G	T	0.011	0.013	6.8e-07	2.1e-07	0.011938202247191	TGT	S	V483F	G1447T	GTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.988061797752809
CAMB-79248	MN908947.3	23301	A	T	0.0038	0.0087	0.00068	6.2e-06	0.00630431078548305	CAG	S	Q580L	A1739T	CAG>CTG	Missense	GU280_gp02, spike glycoprotein	0.993089869559456
CAMB-79248	MN908947.3	23403	A	G	1	1	0	0	0.998965221341679	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.88898423434792e-05
CAMB-79248	MN908947.3	241	C	T	1	1	0	0	0.999712643678161	TCG	NA	NA	NA	NA	NA	NA	4.42086648983201e-05
CAMB-79248	MN908947.3	24557	G	T	0.0033	0.0091	0.003	1.7e-05	0.00541923829595062	AGG	S	G999C	G2995T	GGC>TGC	Missense	GU280_gp02, spike glycoprotein	0.994580761704049
CAMB-79248	MN908947.3	24933	G	T	0.033	0.023	5e-06	0.00012	0.0273844626748022	GGT	S	G1124V	G3371T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.972600940063644
CAMB-79248	MN908947.3	26526	G	T	0.014	0.021	4.3e-06	4.4e-08	0.0173853009477186	GGC	M	A2S	G4T	GCA>TCA	Missense	GU280_gp05	0.981579112533735
CAMB-79248	MN908947.3	27389	C	T	0.0087	0.01	1.5e-05	3.1e-06	0.00953241389483	ACG	NA	NA	NA	NA	NA	NA	0.990458367136219
CAMB-79248	MN908947.3	28079	G	T	0.011	0.0041	2.6e-05	0.006	0.00677430281133567	TGG	ORF8	V62V	G186T	GTG>GTT	Synonymous	GU280_gp09	0.993112792141809
CAMB-79248	MN908947.3	28327	TG	-	0.00505	0.01135	0.00028;0.002	0.00095;5.5e-08	0.00818522745801402	GTG	N	.	54-55-delfrshift	.	no-SNV	GU280_gp10	0.994814493382512
CAMB-79248	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998824566558919	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	6.56297171359191e-05
CAMB-79248	MN908947.3	29113	AC	-	0.0123	0.0055	0.00021;5.5e-06	0.035;5e-04	0.00901293792702428	AAC	N	.	840-841-delfrshift	.	no-SNV	GU280_gp10	0.995280565561613
CAMB-79248	MN908947.3	29543	G	T	0.004	0.0093	0.0028	1.3e-05	0.00718711276332094	AGA	NA	NA	NA	NA	NA	NA	0.992482445270549
CAMB-79248	MN908947.3	3037	C	T	1	1	0	0	0.999747933051018	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79248	MN908947.3	3770	G	T	0.0062	0.01	0.00051	1.6e-05	0.00827667750517292	TGT	ORF1ab:nsp3	V351F	G1051T	GTT>TTT	Missense	ORF1ab:nsp3	0.991132131244458
CAMB-79248	MN908947.3	4048	C	T	1	1	0	0	0.999801734820322	GCA	ORF1ab:nsp3	G443G	C1329T	GGC>GGT	Synonymous	ORF1ab:nsp3	0.000198265179677819
CAMB-79248	MN908947.3	4136	G	T	0.0097	0.007	3.8e-06	5.8e-05	0.00847739540074472	TGT	ORF1ab:nsp3	V473F	G1417T	GTT>TTT	Missense	ORF1ab:nsp3	0.989397890308942
CAMB-79248	MN908947.3	482	C	-	0.0094	0.015	0.00061	3.2e-05	0.0117223867964452	ACG	ORF1ab:leader-protein	.	217-217-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.988150655945832
CAMB-79248	MN908947.3	558	G	T	0.017	0.0091	3e-05	0.0014	0.0133224417050349	GGT	ORF1ab:leader-protein	G98V	G293T	GGT>GTT	Missense	ORF1ab:leader-protein	0.986618149413337
CAMB-79248	MN908947.3	6013	A	T	0.0053	0.0076	0.00017	2.4e-05	0.00650557620817844	CAA	ORF1ab:nsp3	P1098P	A3294T	CCA>CCT	Synonymous	ORF1ab:nsp3	0.991171003717472
CAMB-79248	MN908947.3	663	G	T	0.0031	0.015	0.0046	2.5e-08	0.00814507030626565	GGC	ORF1ab:leader-protein	G133V	G398T	GGC>GTC	Missense	ORF1ab:leader-protein	0.99167606835255
CAMB-79248	MN908947.3	664	C	T	0.0099	0.0028	2.7e-06	0.0041	0.00684687156970362	GCC	ORF1ab:leader-protein	G133G	C399T	GGC>GGT	Synonymous	ORF1ab:leader-protein	0.993070801317234
CAMB-79248	MN908947.3	6683	AATTATGCTAAGCCTTTTCTTAACAAAGTTGT	-	0.0001590625	0.00723125	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0022;NA;NA;NA;NA;NA;NA;NA	0.00015;6.6e-05;0.00058;0.00029;2.6e-05;0.00011;0.00023;5.8e-05;4.6e-05;3e-05;9.3e-05;0.00011;2.4e-05;0.00011;1e-04;3.1e-05;3.4e-05;3.6e-05;2.8e-05;3e-05;9.5e-05;2.1e-05;8.5e-05;0.00023;0.00017;6.3e-06;2.5e-05;3.4e-05;3.5e-05;4.8e-05;4.4e-05;3e-05	0.00442350225983268	TAA	ORF1ab:nsp3	.	3964-3995-delfrshift	.	no-SNV	ORF1ab:nsp3	0.995536986041212
CAMB-79248	MN908947.3	719	G	T	0.0075	0.0021	2.1e-05	0.0064	0.00491475353372104	TGA	ORF1ab:leader-protein	D152Y	G454T	GAT>TAT	Missense	ORF1ab:leader-protein	0.994979267953422
CAMB-79248	MN908947.3	8018	GA	TT	0.003073	0.00935	6.7e-05;NA	9e-08;3.8e-05	0.00548838245946398	GGA	ORF1ab:nsp3	.	5299-5300-mnv	.	no-SNV	ORF1ab:nsp3	0.991293880521807
CAMB-79257	MN908947.3	14408	C	T	1	1	0	0	0.999214564788335	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000563902203246466
CAMB-79257	MN908947.3	23403	A	G	1	1	0	0	0.999882008684161	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.89956579195771e-05
CAMB-79257	MN908947.3	241	C	T	1	1	0	0	0.999853747714808	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-79257	MN908947.3	26532	T	G	1	1	0	0	0.999714013346044	TTC	M	S4A	T10G	TCC>GCC	Missense	GU280_gp05	0
CAMB-79257	MN908947.3	28090	G	A	0.0092	0.016	1e-05	9.7e-08	0.0120174799708667	GGT	ORF8	G66D	G197A	GGT>GAT	Missense	GU280_gp09	0.987982520029133
CAMB-79257	MN908947.3	28717	C	A	1	1	0	0	0.999929115718589	CCC	N	T148T	C444A	ACC>ACA	Synonymous	GU280_gp10	3.54421407052986e-05
CAMB-79257	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999663865546218	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79257	MN908947.3	29421	C	A	1	1	0	6.7e-190	1	CCG	N	P383Q	C1148A	CCG>CAG	Missense	GU280_gp10	0
CAMB-79257	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79266	MN908947.3	11074	C	INS	0.061	0.12	3.2e-16	3.1e-36	0.0817499876622415	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.918101959236046
CAMB-79266	MN908947.3	11075	T	-	0.05	0.0056	1.3e-12	0.0071	0.0344414096329358	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.965447560677725
CAMB-79266	MN908947.3	14408	C	T	1	1	0	0	0.999448145374276	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000413890969293232
CAMB-79266	MN908947.3	15094	A	G	0.037	0.11	7e-16	2.2e-45	0.0813877372899847	GAA	ORF1ab:RNA-dependent-RNA-polymerase	N543D	A1627G	AAT>GAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.918612262710015
CAMB-79266	MN908947.3	23403	A	G	1	1	0	0	0.99997577313968	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	1.21134301600184e-05
CAMB-79266	MN908947.3	241	C	T	1	1	0	0	0.999831635659567	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-79266	MN908947.3	28725	C	T	1	1	0	0	0.999927304448968	CCT	N	P151L	C452T	CCT>CTT	Missense	GU280_gp10	7.26955510322768e-05
CAMB-79266	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79266	MN908947.3	29113	AC	-	0.047	0.0135	6.4e-19;7.6e-13	NA;1.6e-08	0.0313263026650735	AAC	N	.	840-841-delfrshift	.	no-SNV	GU280_gp10	0.973585736297601
CAMB-79266	MN908947.3	29114	C	-	0.044	0.027	7.6e-13	1.6e-08	0.0360657350915174	ACA	N	.	841-841-delfrshift	.	no-SNV	GU280_gp10	0.963737453257233
CAMB-79266	MN908947.3	3037	C	T	1	1	0	0	0.999697565401482	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79266	MN908947.3	6172	T	C	0.062	0.0058	4.8e-22	0.0018	0.0411105178857448	CTA	ORF1ab:nsp3	A1151A	T3453C	GCT>GCC	Synonymous	ORF1ab:nsp3	0.958889482114255
CAMB-79275	MN908947.3	10097	G	A	1	1	0	0	0.999788270167267	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000211729832733432
CAMB-79275	MN908947.3	11074	C	INS	0.053	0.021	4.7e-14	0.00071	0.0425111550158723	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.957200257508824
CAMB-79275	MN908947.3	14408	C	T	1	1	0	0	0.999423714162224	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000576285837775537
CAMB-79275	MN908947.3	17749	G	T	1	1	0	0	0.999948971781395	TGC	ORF1ab:helicase	A505S	G1513T	GCT>TCT	Missense	ORF1ab:helicase	5.10282186048885e-05
CAMB-79275	MN908947.3	23403	A	G	1	1	0	0	0.999851414043024	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000115566855425864
CAMB-79275	MN908947.3	23731	C	T	1	1	0	0	1	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-79275	MN908947.3	241	C	T	1	1	0	0	0.999833656778486	TCG	NA	NA	NA	NA	NA	NA	0.000110895481009149
CAMB-79275	MN908947.3	28580	G	T	1	1	0	0	0.99945139346061	AGA	N	D103Y	G307T	GAT>TAT	Missense	GU280_gp10	0.00043888523151196
CAMB-79275	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998989898989899	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79275	MN908947.3	3037	C	T	1	1	0	0	0.999208860759494	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000197784810126582
CAMB-79275	MN908947.3	3096	C	T	0.058	0.038	5.7e-20	8.7e-14	0.047419072615923	TCA	ORF1ab:nsp3	S126L	C377T	TCA>TTA	Missense	ORF1ab:nsp3	0.952580927384077
CAMB-79284	MN908947.3	11075	T	-	0.041	0.041	2.2e-11	4.3e-11	0.0409006984025046	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954443284900056
CAMB-79284	MN908947.3	14408	C	T	1	1	0	0	0.999306518723994	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000297206261145235
CAMB-79284	MN908947.3	17135	C	T	0.011	0.011	1.5e-06	8.9e-07	0.0109533691574014	CCT	ORF1ab:helicase	P300L	C899T	CCT>CTT	Missense	ORF1ab:helicase	0.988964171350824
CAMB-79284	MN908947.3	20544	C	T	1	1	0	0	0.999776707390985	CCC	ORF1ab:endoRNAse	S308S	C924T	TCC>TCT	Synonymous	ORF1ab:endoRNAse	9.56968324348464e-05
CAMB-79284	MN908947.3	23403	A	G	1	1	0	0	0.999635365495447	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.11586261382167e-05
CAMB-79284	MN908947.3	241	C	T	1	1	0	0	0.999161626444697	TCG	NA	NA	NA	NA	NA	NA	0.000194622432480987
CAMB-79284	MN908947.3	26228	C	T	0.012	0.012	4.4e-07	5.5e-07	0.0119975588781936	GCT	NA	NA	NA	NA	NA	NA	0.987960831091015
CAMB-79284	MN908947.3	28544	A	C	0.016	0.0088	1.7e-05	0.003	0.0113979215554811	TAC	N	T91P	A271C	ACC>CCC	Missense	GU280_gp10	0.98809922896413
CAMB-79284	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999105845534816	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000129382843834907
CAMB-79284	MN908947.3	3037	C	T	1	1	0	0	0.99943313228425	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000136048251779965
CAMB-79284	MN908947.3	313	C	T	1	1	0	0	0.999433297595344	TCA	ORF1ab:leader-protein	L16L	C48T	CTC>CTT	Synonymous	ORF1ab:leader-protein	0.000199111655689998
CAMB-79284	MN908947.3	4228	A	G	1	1	0	0	0.999717896637328	CAA	ORF1ab:nsp3	P503P	A1509G	CCA>CCG	Synonymous	ORF1ab:nsp3	8.86610568397975e-05
CAMB-79284	MN908947.3	8602	G	T	0.013	0.015	1.4e-07	5.5e-08	0.0140103402055275	TGT	ORF1ab:nsp4	V16V	G48T	GTG>GTT	Synonymous	ORF1ab:nsp4	0.985798174506925
CAMB-792A2	MN908947.3	11074	C	INS	0.049	0.028	2.2e-12	1.5e-05	0.0402079192783978	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.959677419354839
CAMB-792A2	MN908947.3	14408	C	T	1	1	0	0	0.999220257704829	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000623793836137157
CAMB-792A2	MN908947.3	186	CAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGAT	-	0.693055555555556	0.7175	3.5e-234;2e-248;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0	6.6e-228;2.7e-240;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0	0.712249134948097	GCA	NA	NA	NA	NA	NA	NA	0.566488685481821
CAMB-792A2	MN908947.3	23403	A	G	1	0.97	0	0	0.987763215845921	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.5710459593615e-05
CAMB-792A2	MN908947.3	241	C	T	1	1	0	0	1	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-792A2	MN908947.3	28014	T	C	0.22	0.21	3.8e-83	7.2e-78	0.219106957424714	CTT	ORF8	F41L	T121C	TTC>CTC	Missense	GU280_gp09	0.780893042575286
CAMB-792A2	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999276934201012	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-792A2	MN908947.3	3037	C	T	1	1	0	0	0.999840383080607	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-792A2	MN908947.3	358	T	C	0.074	0.074	1.3e-34	2e-34	0.073810994441013	TTG	ORF1ab:leader-protein	F31F	T93C	TTT>TTC	Synonymous	ORF1ab:leader-protein	0.926189005558987
CAMB-792A2	MN908947.3	8994	C	T	0.053	0.095	1.2e-24	4.6e-43	0.0733957148173747	ACA	ORF1ab:nsp4	T147I	C440T	ACA>ATA	Missense	ORF1ab:nsp4	0.92655111914509
CAMB-792C0	MN908947.3	11075	T	-	0.04	0.035	7.5e-10	7.9e-09	0.0374123076350509	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958624090511547
CAMB-792C0	MN908947.3	14408	C	T	1	1	0	0	0.997821270310192	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000877031019202363
CAMB-792C0	MN908947.3	18395	C	T	0.026	0.017	2e-11	1.4e-08	0.0211507846258813	GCT	ORF1ab:3'-to-5'-exonuclease	A119V	C356T	GCT>GTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.976347509665681
CAMB-792C0	MN908947.3	18651	G	T	1	1	0	0	0.995269210341037	AGC	ORF1ab:3'-to-5'-exonuclease	E204D	G612T	GAG>GAT	Missense	ORF1ab:3'-to-5'-exonuclease	3.70557936733408e-05
CAMB-792C0	MN908947.3	20136	A	G	0.017	0.015	7.9e-07	4.8e-06	0.0157924421883813	TAA	ORF1ab:endoRNAse	V172V	A516G	GTA>GTG	Synonymous	ORF1ab:endoRNAse	0.983079526226734
CAMB-792C0	MN908947.3	20339	TTA	-	0.0216666666666667	0.049	0.00041;3.1e-05;2.4e-05	8.1e-08;3.1e-10;7.1e-10	0.0339425587467363	TTT	ORF1ab:endoRNAse	.	719-721-delinframe	.	no-SNV	ORF1ab:endoRNAse	0.966057441253264
CAMB-792C0	MN908947.3	21807	C	A	0.81	0.8	0	0	0.80155659942894	CCT	S	P82H	C245A	CCT>CAT	Missense	GU280_gp02, spike glycoprotein	0.198351294095975
CAMB-792C0	MN908947.3	23403	A	G	1	1	0	0	0.998892884794894	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.68325651063337e-05
CAMB-792C0	MN908947.3	241	C	T	1	1	0	0	0.998397462649195	TCG	NA	NA	NA	NA	NA	NA	1.66930974042234e-05
CAMB-792C0	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0381351351351351	0.0332972972972973	0.00046;2.4e-05;1e-04;8.2e-05;0.00019;2.7e-07;2.8e-06;2e-06;2e-06;3.8e-07;8.7e-07;5.9e-07;1.9e-06;1.1e-06;1.5e-06;3e-06;1e-06;2.5e-06;1.2e-06;1.2e-06;7.2e-07;2.2e-06;7.9e-07;1.4e-06;1e-06;5.2e-07;1.6e-06;8.2e-07;2.4e-07;9e-07;1.7e-06;1.2e-06;6e-07;1.6e-06;3.7e-07;8.2e-07;4.1e-07	0.00054;6e-05;0.00019;0.00016;0.00033;8.7e-06;1.7e-05;2.2e-05;2.2e-05;8.9e-06;6.9e-06;4.9e-06;1.8e-05;7.5e-06;8.5e-06;1.7e-05;6.5e-06;1.5e-05;1.1e-05;7.8e-06;5.3e-06;1.7e-05;9.3e-06;1.2e-05;9e-06;6.5e-06;1.3e-05;8.1e-06;3e-06;8.7e-06;1.3e-05;1.3e-05;5.8e-06;1.4e-05;5.8e-06;1.1e-05;8e-06	0.0370385188593376	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.976978660721395
CAMB-792C0	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998448489863467	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000113947128532361
CAMB-792C0	MN908947.3	3037	C	T	1	1	0	0	0.997932632329353	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.5644270183568e-05
CAMB-792C0	MN908947.3	522	TT	-	0.0375	0.0295	8.4e-06;0.00033	0.00023;0.0014	0.0333787809927789	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.959728318744968
CAMB-792C0	MN908947.3	7688	C	T	1	1	0	0	0.999839914621131	ACT	ORF1ab:nsp3	L1657L	C4969T	CTA>TTA	Synonymous	ORF1ab:nsp3	0.00016008537886873
CAMB-792EE	MN908947.3	10252	C	T	0.054	0.014	3.9e-25	8.8e-08	0.0340359331423476	TCT	ORF1ab:3C-like-proteinase	F66F	C198T	TTC>TTT	Synonymous	ORF1ab:3C-like-proteinase	0.965850234305337
CAMB-792EE	MN908947.3	10410	A	G	0.016	0.011	4.7e-09	4.5e-07	0.0133248379411602	AAT	ORF1ab:3C-like-proteinase	N119S	A356G	AAT>AGT	Missense	ORF1ab:3C-like-proteinase	0.98667516205884
CAMB-792EE	MN908947.3	11075	T	-	0.022	0.064	3e-06	9.6e-16	0.0417428946893762	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953953979746966
CAMB-792EE	MN908947.3	12838	GAAATGGGCTA	-	0.0113636363636364	0.00137636363636364	5.1e-07;5.2e-07;1.8e-07;1.5e-07;3.4e-07;6.9e-07;3.6e-07;4.4e-07;5e-07;5.1e-07;2.7e-07	NA;0.47;NA;NA;NA;NA;NA;NA;NA;7.6e-09;NA	0.00628496009050343	TGA	ORF1ab:nsp9	.	153-163-delfrshift	.	no-SNV	ORF1ab:nsp9	0.993639340159746
CAMB-792EE	MN908947.3	13729	GCTA	-	0.008625	0.0135	0.00017;0.00023;0.00022;0.00012	1.9e-06;4.1e-06;4e-06;1.5e-06	0.010832298136646	TGC	ORF1ab:RNA-dependent-RNA-polymerase	.	262-265-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.989168611076999
CAMB-792EE	MN908947.3	14216	C	T	0.0093	0.011	2.8e-06	6.2e-07	0.00989905666045785	ACT	ORF1ab:RNA-dependent-RNA-polymerase	T250I	C749T	ACT>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.990085922009253
CAMB-792EE	MN908947.3	14408	C	T	1	1	0	0	0.999313401160976	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000483740091130391
CAMB-792EE	MN908947.3	168	T	C	0.023	0.0029	4.1e-12	0.0012	0.0167538283280619	GTA	NA	NA	NA	NA	NA	NA	0.983246171671938
CAMB-792EE	MN908947.3	1811	G	INS	0.0051	0.0075	0.00012	9.4e-06	0.00606159895150721	AGC	ORF1ab:nsp2	.	1005-1006-insfrshift	.	no-SNV	ORF1ab:nsp2	0.993840104849279
CAMB-792EE	MN908947.3	1909	C	T	0.0046	0.007	0.00035	2.8e-05	0.00550929536363865	TCT	ORF1ab:nsp2	F368F	C1104T	TTC>TTT	Synonymous	ORF1ab:nsp2	0.994440391436693
CAMB-792EE	MN908947.3	21462	T	C	0.0066	0.095	9e-05	1.7e-31	0.0407422347720855	ATG	ORF1ab:2'-O-ribose-methyltransferase	N268N	T804C	AAT>AAC	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.959257765227915
CAMB-792EE	MN908947.3	23403	A	G	1	1	0	0	0.999882061563864	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.8282030113614e-05
CAMB-792EE	MN908947.3	23554	ACCCATTGGTGCAGGTATATGCGCTAGTTATCAG	-	0.0558529411764706	0.0353529411764706	6.2e-06;5.4e-05;4.3e-05;5.8e-05;5.9e-05;6.6e-08;6e-06;2.2e-06;6.6e-06;7.2e-06;7.4e-06;6.8e-06;5.9e-06;2.7e-06;2.5e-06;4.8e-07;4.3e-08;5.4e-07;1.5e-07;5.7e-07;1.2e-07;6.1e-07;2.1e-06;8.1e-07;7.7e-07;4.7e-10;2.2e-09;9.3e-06;6.9e-06;1e-08;2e-16;2.2e-16;1.9e-07;9.9e-08	NA;0.00024;0.00019;0.00024;0.00029;9.3e-05;0.00018;8.1e-05;0.00016;0.00018;0.00018;0.00017;0.00016;9.2e-05;8.6e-05;4e-05;7.8e-06;5.2e-05;2.1e-05;6.2e-05;1.4e-05;3.8e-05;8.6e-05;4.4e-05;4.3e-05;5.2e-07;9.1e-07;5.4e-05;4.9e-05;NA;NA;NA;NA;NA	0.0500404017084151	TAC	S	.	1992-2025-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.974692944872893
CAMB-792EE	MN908947.3	241	C	T	1	1	0	0	0.999746152625734	TCG	NA	NA	NA	NA	NA	NA	6.34618435665556e-05
CAMB-792EE	MN908947.3	25429	G	T	1	1	0	0	0.999770631680352	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	4.5873663929538e-05
CAMB-792EE	MN908947.3	26270	C	T	0.18	0.11	2.3e-84	2.4e-50	0.152383997726142	ACA	E	T9I	C26T	ACA>ATA	Missense	GU280_gp04	0.847580473246643
CAMB-792EE	MN908947.3	26458	G	C	1	1	0	0	0.999680893498205	TGA	E	D72H	G214C	GAT>CAT	Missense	GU280_gp04	0
CAMB-792EE	MN908947.3	26709	G	A	0.025	0.0056	7.6e-13	0.00013	0.0152336957932162	AGC	M	A63T	G187A	GCT>ACT	Missense	GU280_gp05	0.984727376534399
CAMB-792EE	MN908947.3	28045	C	T	1	1	0	0	0.999869774710249	GCT	ORF8	A51V	C152T	GCT>GTT	Missense	GU280_gp09	0.00013022528975127
CAMB-792EE	MN908947.3	28757	C	T	0.0076	0.012	0.00021	6.2e-06	0.00927967658948916	TCC	N	P162S	C484T	CCT>TCT	Missense	GU280_gp10	0.990720323410511
CAMB-792EE	MN908947.3	28759	TCA	CTC	0.0100333333333333	0.0116666666666667	0.00028;7.4e-07;1e-04	6.6e-06;1.7e-05;5.5e-06	0.00945250350959289	CTC	N	.	486-488-mnv	.	no-SNV	GU280_gp10	0.990547496490407
CAMB-792EE	MN908947.3	28763	G	A	0.0072	0.011	0.00028	1.1e-05	0.00880809595202399	AGG	N	G164R	G490A	GGA>AGA	Missense	GU280_gp10	0.991191904047976
CAMB-792EE	MN908947.3	28765	A	G	0.0078	0.011	0.00024	1.2e-05	0.00926354793886058	GAA	N	G164G	A492G	GGA>GGG	Synonymous	GU280_gp10	0.990736452061139
CAMB-792EE	MN908947.3	28768	A	C	0.008	0.012	0.00014	4.9e-06	0.00959007145543437	CAA	N	T165T	A495C	ACA>ACC	Synonymous	GU280_gp10	0.990221887927792
CAMB-792EE	MN908947.3	28770	CAT	ACA	0.00766666666666667	0.0113333333333333	0.00021;2e-04;0.00017	9.5e-06;6.1e-06;3.4e-06	0.00926792735442801	ACA	N	.	497-499-mnv	.	no-SNV	GU280_gp10	0.991047531149054
CAMB-792EE	MN908947.3	28774	GC	TG	0.0079	0.011	0.00019;0.00015	1.1e-05;7.6e-06	0.00927591102697586	TGC	N	.	501-502-mnv	.	no-SNV	GU280_gp10	0.990501519756839
CAMB-792EE	MN908947.3	28777	A	C	0.0084	0.013	0.00017	4.1e-06	0.0101898101898102	CAA	N	P168P	A504C	CCA>CCC	Synonymous	GU280_gp10	0.988711288711289
CAMB-792EE	MN908947.3	28781	G	A	0.0079	0.01	0.00014	1.6e-05	0.00895920701486847	AGG	N	G170S	G508A	GGC>AGC	Missense	GU280_gp10	0.991040792985131
CAMB-792EE	MN908947.3	28783	CT	GC	0.00805	0.0115	0.00016;0.00013	5.4e-06;6e-06	0.00949605114704776	GCT	N	.	510-511-mnv	.	no-SNV	GU280_gp10	0.990661187896899
CAMB-792EE	MN908947.3	28786	CTACGCAGA	TCTACGCAG	0.00774444444444444	0.0115555555555556	0.00015;0.00033;0.00017;0.00026;0.00014;0.00022;7.9e-05;0.00019;0.00019	1.2e-05;6.3e-06;5e-06;6.5e-06;5e-06;4.1e-06;2.1e-06;1.7e-05;9.8e-06	0.00937350549976088	TCT	N	.	513-521-mnv	.	no-SNV	GU280_gp10	0.990826555702667
CAMB-792EE	MN908947.3	28796	G	A	0.0068	0.012	0.00041	4.4e-06	0.00895608628659476	AGG	N	G175R	G523A	GGG>AGG	Missense	GU280_gp10	0.991043913713405
CAMB-792EE	MN908947.3	28799	AGCAGAG	GAGCAGA	0.00751428571428571	0.0114571428571429	0.00015;0.00076;2e-04;0.00021;0.00021;3e-04;0.00024	4.1e-06;3.5e-05;5.1e-06;3e-06;1.5e-05;1.1e-05;5.1e-06	0.00915750915750916	GAG	N	.	526-532-mnv	.	no-SNV	GU280_gp10	0.989259342134706
CAMB-792EE	MN908947.3	28807	CGGCAGTCA	GCTGCAGTC	0.00695888888888889	0.0115555555555556	0.00016;0.00016;0.042;0.00019;0.00013;0.00024;2e-04;0.00046;0.00018	5.5e-06;4.4e-06;6.5e-07;7e-06;3.2e-06;1.1e-05;4.1e-06;1.2e-05;6.6e-06	0.009375	GCG	N	.	534-542-mnv	.	no-SNV	GU280_gp10	0.990488623647893
CAMB-792EE	MN908947.3	28817	GC	AG	0.00755	0.0115	0.00011;0.00052	2.4e-06;1.7e-05	0.00911300121506683	AGC	N	.	544-545-mnv	.	no-SNV	GU280_gp10	0.98928258967629
CAMB-792EE	MN908947.3	28820	TCT	CTC	0.00796666666666667	0.0116666666666667	0.00023;0.00035;0.00016	9.8e-06;1.1e-05;4.7e-06	0.00950209045990118	CTC	N	.	547-549-mnv	.	no-SNV	GU280_gp10	0.990592930444698
CAMB-792EE	MN908947.3	28824	CTCGT	TCTCG	0.00784	0.0118	0.00037;0.00021;0.00063;0.00012;0.00011	6.8e-06;5.1e-06;2.2e-05;3.6e-06;5.3e-06	0.00959581273626054	TCT	N	.	551-555-mnv	.	no-SNV	GU280_gp10	0.990960451977401
CAMB-792EE	MN908947.3	28830	C	T	0.0068	0.011	0.00045	8.6e-06	0.00869154463863958	TCC	N	S186F	C557T	TCC>TTC	Missense	GU280_gp10	0.99130845536136
CAMB-792EE	MN908947.3	28832	TCATCACGTAGTCGCA	CTCATCACGTAGTCGC	0.00759375	0.0116875	0.00026;0.00022;0.00017;9.8e-05;0.00069;0.00016;0.00027;0.00014;0.00012;0.00032;0.00015;0.00013;0.00069;0.00013;0.00066;0.00035	5.8e-06;7.9e-06;4.8e-06;2.2e-06;7e-06;3.2e-06;6.1e-06;3.4e-06;2.6e-06;4.1e-06;9.4e-06;5.4e-06;7.8e-06;5.4e-06;5.8e-06;5.4e-06	0.00957414979555201	CTC	N	.	559-574-mnv	.	no-SNV	GU280_gp10	0.990277102576568
CAMB-792EE	MN908947.3	28850	AGT	CAG	0.00773333333333333	0.012	0.00022;0.00025;0.00019	5e-06;6e-06;5.7e-06	0.00952568005499362	CAG	N	.	577-579-mnv	.	no-SNV	GU280_gp10	0.99039780521262
CAMB-792EE	MN908947.3	28854	CA	TC	0.0079	0.0115	0.00041;0.00013	1.9e-05;4.9e-06	0.00941176470588235	TCA	N	.	581-582-mnv	.	no-SNV	GU280_gp10	0.991079901309546
CAMB-792EE	MN908947.3	28857	GA	AG	0.00725	0.0105	0.00027;0.00044	2.1e-05;1.6e-05	0.00868621064060804	AGA	N	.	584-585-mnv	.	no-SNV	GU280_gp10	0.991420118343195
CAMB-792EE	MN908947.3	28861	T	A	0.0077	0.01	0.00019	2.1e-05	0.00880300590445518	ATT	N	N196K	T588A	AAT>AAA	Missense	GU280_gp10	0.990767579173376
CAMB-792EE	MN908947.3	28863	C	T	0.0066	0.012	0.00058	5.3e-06	0.00881868398100591	TCA	N	S197L	C590T	TCA>TTA	Missense	GU280_gp10	0.991181316018994
CAMB-792EE	MN908947.3	28866	CTC	ACT	0.00763333333333333	0.0116666666666667	0.00021;0.00015;0.00048	7.1e-06;4e-06;1.4e-05	0.00913900913900914	ACT	N	.	593-595-mnv	.	no-SNV	GU280_gp10	0.990668590668591
CAMB-792EE	MN908947.3	28871	G	A	0.0081	0.011	0.00013	1e-05	0.00935223469186848	AGG	N	G200S	G598A	GGC>AGC	Missense	GU280_gp10	0.990647765308131
CAMB-792EE	MN908947.3	28873	CAGC	GCAG	0.007575	0.0115	0.00016;0.00041;0.00031;0.00029	7.8e-06;7.9e-06;9.5e-06;9.4e-06	0.00906671922735784	GCA	N	.	600-603-mnv	.	no-SNV	GU280_gp10	0.990602975724354
CAMB-792EE	MN908947.3	28878	G	A	0.0061	0.011	0.00081	1.3e-05	0.00801015922633584	AGT	N	S202N	G605A	AGT>AAT	Missense	GU280_gp10	0.99189215590505
CAMB-792EE	MN908947.3	3037	C	T	1	1	0	0	0.99970934457201	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.26638569975294e-05
CAMB-792EE	MN908947.3	444	T	-	0.041	0.022	5.9e-07	0.00087	0.0330518766988607	GTT	ORF1ab:leader-protein	.	179-179-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.966803539413568
CAMB-792EE	MN908947.3	4527	GATT	-	0.0165	0.02775	NA;4.8e-05;1.3e-05;0.0078	1.8e-05;1.7e-05;4.3e-06;3.7e-05	0.0204433497536946	AGA	ORF1ab:nsp3	.	1808-1811-delfrshift	.	no-SNV	ORF1ab:nsp3	0.993134038157735
CAMB-792EE	MN908947.3	4531	TTAC	-	0.0435	0.019	5.5e-06;2.5e-05;3.1e-05;3.2e-05	0.0062;0.011;0.013;0.012	0.0347391516333496	TTT	ORF1ab:nsp3	.	1812-1815-delfrshift	.	no-SNV	ORF1ab:nsp3	0.964734269628163
CAMB-792EE	MN908947.3	4540	CACCAGTAAAACAACTG	-	0.0416470588235294	0.0187058823529412	2.1e-05;1.3e-05;1.7e-05;7.9e-06;1.7e-05;1.2e-05;1.6e-05;3.3e-06;2.7e-06;2.2e-06;3.3e-06;3.2e-06;2.7e-06;2.1e-06;3.2e-06;1.9e-06;8.6e-05	0.0079;0.0069;0.0076;0.0057;0.0077;0.0072;0.0076;0.0047;0.0029;0.0028;0.0028;0.0027;0.0027;0.0024;0.0025;0.0021;0.0012	0.0340463458110517	ACA	ORF1ab:nsp3	.	1821-1837-delfrshift	.	no-SNV	ORF1ab:nsp3	0.966465380782084
CAMB-792EE	MN908947.3	522	T	-	0.05	0.037	1.3e-06	5.7e-05	0.044908051305826	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.954875598825529
CAMB-792FD	MN908947.3	10097	G	A	1	1	0	0	1	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0
CAMB-792FD	MN908947.3	13536	C	T	1	1	0	2.3e-219	1	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-792FD	MN908947.3	14408	C	T	1	1	0	0	0.99945079086116	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00054920913884007
CAMB-792FD	MN908947.3	23403	A	G	1	1	0	0	0.999952885747939	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-792FD	MN908947.3	23731	C	T	1	1	0	0	0.999334774654914	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000498919008814236
CAMB-792FD	MN908947.3	241	C	T	1	1	0	0	1	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-792FD	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999643366619116	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000396982929734021
CAMB-792FD	MN908947.3	29616	G	-	0.029	0.038	2e-08	2e-12	0.0347705146036161	AGA	ORF10	.	59-59-delfrshift	.	no-SNV	GU280_gp11	0.965229485396384
CAMB-792FD	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-792FD	MN908947.3	4002	C	T	1	1	0	0	1	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-79327	MN908947.3	1059	C	T	1	1	0	0	0.999951489279131	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	4.85107208693121e-05
CAMB-79327	MN908947.3	1099	T	C	0.018	0.012	4.9e-10	3.5e-07	0.0144179509547349	ATT	ORF1ab:nsp2	N98N	T294C	AAT>AAC	Synonymous	ORF1ab:nsp2	0.985557817194921
CAMB-79327	MN908947.3	11075	T	-	0.026	0.063	4.4e-07	3.3e-16	0.0389708039906103	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.947421508215962
CAMB-79327	MN908947.3	13059	C	T	0.022	0.013	1.2e-11	7.4e-08	0.0183569140163411	ACT	ORF1ab:nsp10	T12I	C35T	ACT>ATT	Missense	ORF1ab:nsp10	0.981630447832873
CAMB-79327	MN908947.3	13346	G	-	0.015	0.055	3.8e-05	4.2e-15	0.0328217880805982	TGT	ORF1ab:nsp10	.	322-322-delfrshift	.	no-SNV	ORF1ab:nsp10	0.966990853502751
CAMB-79327	MN908947.3	14120	C	T	1	1	0	0	0.999245240824085	CCA	ORF1ab:RNA-dependent-RNA-polymerase	P218L	C653T	CCA>CTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	8.38621306571996e-05
CAMB-79327	MN908947.3	14408	C	T	1	1	0	0	0.9993503028053	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000464069424785948
CAMB-79327	MN908947.3	174	G	-	0.029	0.06	4.5e-14	3.8e-27	0.0371708828084667	CGT	NA	NA	NA	NA	NA	NA	0.962700051626226
CAMB-79327	MN908947.3	19868	C	T	0.029	0.0049	9.6e-14	0.00051	0.0187474527917403	ACT	ORF1ab:endoRNAse	T83I	C248T	ACT>ATT	Missense	ORF1ab:endoRNAse	0.98125254720826
CAMB-79327	MN908947.3	22281	C	T	0.036	0.059	5.2e-17	3e-24	0.0430019172829362	ACT	S	T240I	C719T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.956998082717064
CAMB-79327	MN908947.3	23403	A	G	1	1	0	0	0.999929034394663	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.73104035577423e-05
CAMB-79327	MN908947.3	241	C	T	1	1	0	0	0.999688293182527	TCG	NA	NA	NA	NA	NA	NA	0.000133588636060026
CAMB-79327	MN908947.3	25563	G	T	1	1	0	0	0.999852743184113	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	8.41467519353753e-05
CAMB-79327	MN908947.3	2882	T	C	0.026	0.019	1.7e-11	8.6e-09	0.0214946760871729	CTG	ORF1ab:nsp3	C55R	T163C	TGT>CGT	Missense	ORF1ab:nsp3	0.978505323912827
CAMB-79327	MN908947.3	29596	A	G	0.023	0.024	4.6e-11	6.6e-11	0.0234848484848485	TAT	ORF10	I13M	A39G	ATA>ATG	Missense	GU280_gp11	0.976515151515152
CAMB-79327	MN908947.3	3037	C	T	1	1	0	0	0.999358151476252	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000513478818998716
CAMB-79336	MN908947.3	11075	T	-	0.026	0.057	5.3e-07	4.5e-14	0.0396260922576712	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960224886540676
CAMB-79336	MN908947.3	11083	G	T	0.11	0.031	4.4e-24	6.3e-07	0.0750239984857294	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.910238903235401
CAMB-79336	MN908947.3	14408	C	T	1	1	0	0	0.99966333115122	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00028055737398298
CAMB-79336	MN908947.3	1616	C	A	0.019	0.019	2.7e-10	1.5e-10	0.0188630740062341	TCT	ORF1ab:nsp2	L271I	C811A	CTT>ATT	Missense	ORF1ab:nsp2	0.981104791285067
CAMB-79336	MN908947.3	16289	C	T	1	1	0	0	0.999101123595506	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0.000674157303370786
CAMB-79336	MN908947.3	16792	C	T	0.12	0.073	7.9e-55	1.6e-33	0.100981996726678	TCG	ORF1ab:helicase	R186C	C556T	CGT>TGT	Missense	ORF1ab:helicase	0.898994622398878
CAMB-79336	MN908947.3	16880	C	T	0.007	0.01	2e-05	8.2e-07	0.00824236477370293	ACA	ORF1ab:helicase	T215I	C644T	ACA>ATA	Missense	ORF1ab:helicase	0.991708573531216
CAMB-79336	MN908947.3	16883	C	T	0.12	0.14	3.8e-55	8.3e-63	0.126736455645962	ACT	ORF1ab:helicase	T216I	C647T	ACT>ATT	Missense	ORF1ab:helicase	0.873164318317126
CAMB-79336	MN908947.3	16887	C	T	0.058	0.017	1.1e-23	9e-08	0.0409935130602077	ACA	ORF1ab:helicase	Y217Y	C651T	TAC>TAT	Synonymous	ORF1ab:helicase	0.958981821769479
CAMB-79336	MN908947.3	17159	C	T	0.044	0.038	6.2e-21	7.5e-19	0.0415041659280269	GCT	ORF1ab:helicase	A308V	C923T	GCT>GTT	Missense	ORF1ab:helicase	0.958429356497075
CAMB-79336	MN908947.3	17249	C	T	0.22	0.27	2.1e-105	1e-130	0.23971276621817	GCT	ORF1ab:helicase	A338V	C1013T	GCT>GTT	Missense	ORF1ab:helicase	0.760238217778105
CAMB-79336	MN908947.3	17321	C	T	0.31	0.21	3.4e-153	3.2e-97	0.267414281437815	GCA	ORF1ab:helicase	A362V	C1085T	GCA>GTA	Missense	ORF1ab:helicase	0.732585718562185
CAMB-79336	MN908947.3	17792	A	T	0.046	0.11	1.9e-21	3.4e-49	0.0692347600518807	AAT	ORF1ab:helicase	N519I	A1556T	AAT>ATT	Missense	ORF1ab:helicase	0.930687418936446
CAMB-79336	MN908947.3	18404	C	T	0.026	0.011	2.2e-13	3.6e-07	0.0205479452054795	ACA	ORF1ab:3'-to-5'-exonuclease	T122I	C365T	ACA>ATA	Missense	ORF1ab:3'-to-5'-exonuclease	0.979416194506204
CAMB-79336	MN908947.3	21975	ATCCATTTTTGGGTGTTTATT	-	0.0985714285714286	0.0143619047619048	1.7e-47;3.6e-47;4.8e-47;5.9e-47;7.2e-48;1.8e-32;6.4e-21;1.5e-20;2e-18;7.2e-19;1.3e-21;1.6e-18;7.3e-18;2.1e-18;1.7e-19;4.6e-20;0.00015;3.9e-06;4.1e-06;1.7e-13;3.5e-12	2e-07;2.3e-07;2.7e-07;2.4e-07;5.5e-07;0.00024;0.002;0.0031;0.0048;0.0047;0.0035;0.0051;0.0061;0.0057;0.0049;0.005;0.034;0.073;0.08;8.1e-07;2.5e-06	0.0609866371948156	GAT	S	.	413-433-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.939748290555941
CAMB-79336	MN908947.3	22095	A	G	1	1	0	0	0.999769903359411	GAC	S	D178G	A533G	GAC>GGC	Missense	GU280_gp02, spike glycoprotein	0.000230096640589047
CAMB-79336	MN908947.3	23403	A	G	1	1	0	0	0.999939432115515	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.42271537939723e-05
CAMB-79336	MN908947.3	23540	TATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATC	-	0.00969891304347826	0.0733260869565217	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.012;0.015;0.016;0.016;0.016;0.015;0.013;0.013;0.0097;0.0033;0.0089;0.0068;0.0087;0.0067;0.0097;0.013;0.011;0.01;0.0026;0.0037;0.0095;0.008;0.00043;NA;NA	4e-06;6.9e-06;2.4e-06;4.1e-06;5.1e-06;4.4e-06;4.8e-06;5.1e-06;1.5e-05;1.4e-05;9.8e-05;4.9e-05;6e-05;0.00063;5e-07;9.1e-09;6.4e-09;9.6e-09;1.9e-08;6.9e-10;3e-09;2.9e-10;2e-09;2.6e-09;2.6e-09;2.4e-09;2.2e-09;3.9e-10;3.7e-10;2.6e-11;2.9e-12;5.4e-11;6.9e-12;5.5e-11;2.3e-12;3.4e-11;3e-10;4.5e-11;3.9e-13;6.4e-20;3.2e-19;2e-10;2.2e-07;1.5e-05;2.8e-10;2.6e-10	0.0491239048811014	ATA	S	.	1978-2023-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.985434217778128
CAMB-79336	MN908947.3	241	C	T	1	0.97	0	0	0.987027815661772	TCG	NA	NA	NA	NA	NA	NA	0.00012686732849123
CAMB-79336	MN908947.3	25429	G	T	1	1	0	0	0.999930800636634	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	1.72998408414643e-05
CAMB-79336	MN908947.3	28261	C	T	0.016	0.0076	1.5e-08	3.6e-05	0.0118619645742064	ACG	NA	NA	NA	NA	NA	NA	0.988050708079235
CAMB-79336	MN908947.3	28888	T	C	0.004	0.019	0.0045	2.6e-09	0.0116493656286044	CTT	N	T205T	T615C	ACT>ACC	Synonymous	GU280_gp10	0.98719723183391
CAMB-79336	MN908947.3	2919	C	T	1	1	0	0	1	CCA	ORF1ab:nsp3	P67L	C200T	CCA>CTA	Missense	ORF1ab:nsp3	0
CAMB-79336	MN908947.3	29508	G	A	1	1	0	0	0.99927797833935	AGC	N	S412N	G1235A	AGC>AAC	Missense	GU280_gp10	0.000722021660649819
CAMB-79336	MN908947.3	3037	C	T	1	1	0	0	0.999713330148113	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000191113234591495
CAMB-79336	MN908947.3	3619	C	T	0.016	0.074	1.1e-05	9.6e-20	0.0424528301886792	TCG	ORF1ab:nsp3	V300V	C900T	GTC>GTT	Synonymous	ORF1ab:nsp3	0.957547169811321
CAMB-79336	MN908947.3	9969	C	T	0.024	0.053	2.6e-12	4.1e-24	0.0380379010740918	GCA	ORF1ab:nsp4	A472V	C1415T	GCA>GTA	Missense	ORF1ab:nsp4	0.961962098925908
CAMB-79363	MN908947.3	11003	C	T	0.092	0.094	4.6e-41	1.4e-41	0.0933756502648785	ACA	ORF1ab:nsp6	H11Y	C31T	CAC>TAC	Missense	ORF1ab:nsp6	0.906600486803799
CAMB-79363	MN908947.3	11074	C	INS	0.029	0.024	6.3e-06	0.00015	0.0260043489109899	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.973354008483941
CAMB-79363	MN908947.3	11075	T	-	0.037	0.036	9.5e-10	2.8e-09	0.0363588188535932	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959769776547826
CAMB-79363	MN908947.3	14408	C	T	1	1	0	0	0.996738308672643	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00088562479749433
CAMB-79363	MN908947.3	16289	C	T	1	1	0	0	0.999655320982335	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	2.87232514720666e-05
CAMB-79363	MN908947.3	23248	C	T	0.024	0.023	1.7e-10	2.5e-10	0.0234663889648843	TCC	S	F562F	C1686T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.976339455127922
CAMB-79363	MN908947.3	23403	A	G	1	1	0	0	0.999570294100634	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000123953624817168
CAMB-79363	MN908947.3	241	C	T	1	1	0	0	0.998466257668712	TCG	NA	NA	NA	NA	NA	NA	0.000238251235928286
CAMB-79363	MN908947.3	25429	G	T	1	1	0	0	0.998166720586649	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0.00016946280291476
CAMB-79363	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.03090625	0.0319375	2.3e-05;0.00018;5.4e-05;5.5e-05;1.8e-05;1.7e-05;1.1e-05;5.7e-05;2.4e-05;2.9e-05;7e-05;2.3e-05;6e-05;4e-05;3.9e-05;2e-05;6.7e-05;2.9e-05;4.4e-05;3.6e-05;1.9e-05;5.2e-05;3.2e-05;2.2e-05;2.7e-05;5.4e-05;4.4e-05;2.3e-05;4.5e-05;2e-05;2.9e-05;2.4e-05	3.8e-05;1e-04;3.7e-05;3.8e-05;1.6e-05;1.9e-05;1.5e-05;3.4e-05;2.1e-05;2.5e-05;4.1e-05;1.9e-05;3.9e-05;2.8e-05;2.6e-05;1.8e-05;4.1e-05;1.9e-05;2.9e-05;2.3e-05;1.8e-05;3.5e-05;2.2e-05;1.3e-05;2.3e-05;3.4e-05;3.3e-05;2.1e-05;3.5e-05;1.2e-05;2.3e-05;2.1e-05	0.0312879591862829	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.968084933949267
CAMB-79363	MN908947.3	3037	C	T	1	1	0	0	0.99888232476449	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.56193973677608e-05
CAMB-79363	MN908947.3	9854	G	T	0.0097	0.012	2.1e-06	5.1e-07	0.0107901046844845	TGT	ORF1ab:nsp4	V434L	G1300T	GTG>TTG	Missense	ORF1ab:nsp4	0.988449616936663
CAMB-79372	MN908947.3	11074	C	INS	0.017	0.026	0.0063	3.5e-05	0.0210558353162526	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.978833490122295
CAMB-79372	MN908947.3	11075	T	-	0.034	0.033	1.2e-08	1.6e-08	0.0330951440506541	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951440506541228
CAMB-79372	MN908947.3	11088	A	-	0.015	0.005	6.6e-08	0.0015	0.0102260559906642	GAA	ORF1ab:nsp6	.	116-116-delfrshift	.	no-SNV	ORF1ab:nsp6	0.989725821392909
CAMB-79372	MN908947.3	12801	GGTTTGTACTTGCACTGTTATCCGATTT	-	0.0111785714285714	0.00138482142857143	2.5e-06;2.1e-06;5.5e-07;2.1e-07;1.2e-06;2.5e-06;1.6e-06;1.4e-06;1.3e-06;1e-06;1.2e-06;1.6e-06;1.2e-06;9.3e-07;1.1e-06;3.4e-07;1.7e-06;1.6e-06;1.7e-06;9.8e-07;1.6e-06;2e-06;1.5e-06;2.3e-06;1.9e-06;1.3e-11;1.1e-06;2e-06	NA;NA;NA;NA;0.00017;0.00024;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0021;0.0024;0.0021;0.0028;0.0025;0.0069;0.0019;0.0028	0.0059302458922399	AGG	ORF1ab:nsp9	.	116-143-delfrshift	.	no-SNV	ORF1ab:nsp9	0.989905036157443
CAMB-79372	MN908947.3	14408	C	T	0.99	1	0	0	0.995899104525775	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000430257885820314
CAMB-79372	MN908947.3	15014	ATGCACTTTTCGCATATACAAAACGTA	-	0.00623333333333333	0.014962962962963	NA;NA;NA;NA;NA;NA;NA;NA;0.0025;0.0099;0.014;0.015;0.017;0.019;0.018;0.017;0.01;0.011;0.0082;0.0095;0.0095;0.009;0.0095;0.0076;5.8e-05;0.00011;0.0081	1.4e-08;1.9e-08;2e-08;1.8e-08;1.8e-08;2.4e-08;9.7e-08;4.7e-09;1.6e-05;0.00021;4e-04;0.00057;0.00069;0.00086;0.00067;0.00071;0.00022;0.00025;0.00012;9e-05;0.00016;0.00017;0.00022;0.00016;0.00019;0.00018;2e-04	0.0118610907312301	GAT	ORF1ab:RNA-dependent-RNA-polymerase	.	1547-1573-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.99119373776908
CAMB-79372	MN908947.3	15103	C	T	0.0094	0.0077	7.3e-06	2.8e-05	0.00841930511087395	TCG	ORF1ab:RNA-dependent-RNA-polymerase	R546C	C1636T	CGC>TGC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.991580694889126
CAMB-79372	MN908947.3	1642	CAA	-	0.00966666666666667	0.00406666666666667	2.4e-06;1.1e-06;2e-06	0.00024;0.00029;0.00023	0.00718294704394102	TCA	ORF1ab:nsp2	.	837-839-delinframe	.	no-SNV	ORF1ab:nsp2	0.99291103202847
CAMB-79372	MN908947.3	17603	T	-	0.014	0.017	7.9e-08	5.5e-09	0.0153666498580111	GTT	ORF1ab:helicase	.	1367-1367-delfrshift	.	no-SNV	ORF1ab:helicase	0.984500650229571
CAMB-79372	MN908947.3	18737	TTGATTACGTCTATA	-	0.0024096	0.0287333333333333	NA;0.46;0.48;0.0061;0.0026;0.0063;NA;NA;NA;NA;NA;NA;NA;NA;NA	1.4e-09;2.3e-18;9.5e-14;1.5e-07;1.9e-05;0.00011;0.00016;4.2e-05;8e-05;3.9e-05;4.4e-05;1.4e-05;1.1e-05;4.4e-09;3.8e-11	0.0125540668846925	TTT	ORF1ab:3'-to-5'-exonuclease	.	698-712-delinframe	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.989027900146843
CAMB-79372	MN908947.3	18877	C	T	0.011	0.013	2.2e-06	3.3e-07	0.011765689576913	TCT	ORF1ab:3'-to-5'-exonuclease	L280L	C838T	CTA>TTA	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.988222365560572
CAMB-79372	MN908947.3	1929	C	T	0.0024	0.013	0.0049	7.5e-08	0.0070313043881837	GCT	ORF1ab:nsp2	A375V	C1124T	GCT>GTT	Missense	ORF1ab:nsp2	0.992968695611816
CAMB-79372	MN908947.3	23403	A	G	1	1	0	0	0.999901864573111	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.88812561334642e-05
CAMB-79372	MN908947.3	24014	ATTGAAGATCTACT	-	0.00744214285714286	0.0531428571428571	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.5;0.0095;1.7e-05;1.2e-05	7.1e-07;1.8e-07;2.7e-07;2.9e-07;2.5e-07;8.6e-07;1e-06;8.9e-07;1.2e-06;7.3e-07;3.3e-07;4.5e-07;3e-04;5.5e-06	0.0237420072282458	TAT	S	.	2452-2465-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.983094775284208
CAMB-79372	MN908947.3	24029	TTC	-	0.00666666666666667	0.02	0.00038;NA;NA	0.00034;1e-10;6.6e-10	0.00839063046265004	TTT	S	.	2467-2469-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.980191097646236
CAMB-79372	MN908947.3	241	C	T	1	1	0	0	0.99992464488904	TCG	NA	NA	NA	NA	NA	NA	3.76775554802004e-05
CAMB-79372	MN908947.3	25511	C	T	0.011	0.0068	1.3e-06	7e-05	0.00896717373899119	TCA	ORF3a	S40L	C119T	TCA>TTA	Missense	GU280_gp03	0.990984787830264
CAMB-79372	MN908947.3	26775	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTT	-	0.0358074210526316	0.0425614035087719	NA;NA;0.27;0.32;0.49;0.00015;4.7e-06;8.2e-05;9.3e-05;0.00025;1.5e-10;6.7e-09;1.3e-07;1.3e-07;1.8e-08;3.8e-08;2e-08;1.2e-07;3.1e-10;5.4e-10;1.6e-09;2.4e-10;1.2e-09;5.2e-10;1.8e-13;1.6e-13;1.4e-09;3.3e-10;8.4e-10;4.7e-10;2.2e-10;9.3e-10;3.6e-10;1.1e-09;3.5e-10;9.7e-10;5.8e-10;1.7e-10;8e-10;2.5e-08;5.6e-08;3.2e-08;0.0019;0.0044;0.0026;0.003;0.28;0.26;0.24;0.23;0.23;0.23;0.22;0.25;NA;NA;NA	4.8e-06;5.2e-06;1.7e-06;1.1e-05;6.2e-05;1.4e-06;2.1e-11;3.4e-09;4.5e-09;1.9e-08;3.5e-10;2.1e-09;4e-08;3.9e-08;8.7e-09;2e-08;1.7e-08;3.4e-08;2.1e-08;3e-08;5.4e-08;1.9e-08;4.5e-08;2.6e-08;2.5e-08;2.3e-08;5.1e-08;2.2e-08;3.3e-08;2.1e-08;1.6e-08;3.8e-08;1.7e-08;4.2e-09;2.3e-08;3.6e-08;3.4e-08;2e-08;4e-08;5.3e-09;2.1e-06;1.7e-06;2e-04;0.00063;0.00032;0.00047;4.2e-05;1.9e-05;2.5e-05;3.6e-05;3.5e-05;3.4e-05;3.3e-05;1.9e-05;7.6e-07;4.3e-07;2.4e-08	0.0464227003073404	GGC	M	.	253-309-delinframe	.	no-SNV	GU280_gp05	0.984489040266784
CAMB-79372	MN908947.3	28255	TCTAAACGAACAAACTA	-	0.00574117647058824	0.000404941176470588	0.00019;0.00019;0.00016;0.00015;8.7e-05;5e-05;0.00014;1e-04;0.00015;0.00013;0.00015;8.3e-06;0.00018;0.00022;0.00019;0.00015;4e-04	NA;NA;NA;NA;0.16;0.15;0.21;0.29;NA;NA;NA;NA;NA;NA;NA;0.13;0.00019	0.00304142772924594	ATC	ORF8	.	362-366-delfrshift	.	no-SNV	GU280_gp09	0.997064491838011
CAMB-79372	MN908947.3	28881	GGG	AAC	1	0.993333333333333	0;0;0	0;0;0	0.996335318369217	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79372	MN908947.3	3037	C	T	1	1	0	0	0.998966651009864	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000469704086425552
CAMB-79372	MN908947.3	3546	ATGGACCACTT	-	0.0102709090909091	0.0730909090909091	4.6e-05;3.1e-05;1.7e-05;NA;NA;NA;NA;NA;NA;NA;NA	1.7e-11;8.2e-12;3.7e-13;3.3e-18;7e-18;2.4e-16;4.1e-18;8.4e-18;6e-19;6.9e-19;1.3e-19	0.0258760107816712	AAT	ORF1ab:nsp3	.	827-837-delfrshift	.	no-SNV	ORF1ab:nsp3	0.942872989462008
CAMB-79372	MN908947.3	4557	TAGCGTCACTTATCAACACACTTAA	-	0.012	0.002926	8.9e-10;1.6e-09;2.4e-05;3.9e-05;6.8e-05;2.2e-05;3.1e-05;1.1e-05;1.6e-05;3.5e-06;3e-06;2.8e-06;2.5e-06;2.9e-06;3.3e-06;2.7e-05;2.8e-05;2.7e-06;3.2e-06;2.7e-06;2.4e-06;2.6e-06;0.00021;0.00068;0.00097	1.4e-10;2e-10;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00671573631332939	GTA	ORF1ab:nsp3	.	1838-1862-delfrshift	.	no-SNV	ORF1ab:nsp3	0.9650897608327
CAMB-79372	MN908947.3	522	TT	-	0.04	0.081	1.7e-06;0.00015	2e-11;3.2e-11	0.0587246755671739	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.933514117084064
CAMB-79372	MN908947.3	5663	C	T	0.007	0.014	2.7e-05	3.4e-08	0.0101674641148325	ACA	ORF1ab:nsp3	Q982*	C2944T	CAG>TAG	Nonsense	ORF1ab:nsp3	0.989795155502392
CAMB-79372	MN908947.3	6506	AAT	-	0.00466666666666667	0.00953333333333333	NA;NA;2.6e-08	1.6e-06;1.6e-06;3e-06	0.00466014343369821	AAA	ORF1ab:nsp3	.	3787-3789-delinframe	.	no-SNV	ORF1ab:nsp3	0.995229715382714
CAMB-79372	MN908947.3	6508	T	-	0.014	0.0093	2.6e-08	3e-06	0.0116808187913755	ATA	ORF1ab:nsp3	.	3789-3789-delfrshift	.	no-SNV	ORF1ab:nsp3	0.988276653955743
CAMB-79372	MN908947.3	6812	ACTA	-	0.02375	0.005225	1.5e-10;2.6e-10;1.5e-10;7.6e-11	0.0013;0.0013;0.001;0.0012	0.0122513922036595	TAC	ORF1ab:nsp3	.	4093-4096-delfrshift	.	no-SNV	ORF1ab:nsp3	0.987685910762834
CAMB-79372	MN908947.3	7768	C	T	0.46	0.55	6.7e-233	3.9e-306	0.505243728500713	TCC	ORF1ab:nsp3	I1683I	C5049T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.494756271499287
CAMB-79390	MN908947.3	10819	T	C	0.0091	0.0072	5.2e-06	3.5e-05	0.00832665145253809	CTC	ORF1ab:3C-like-proteinase	A255A	T765C	GCT>GCC	Synonymous	ORF1ab:3C-like-proteinase	0.991549990748165
CAMB-79390	MN908947.3	11074	C	INS	0.054	0.016	8.6e-16	0.0077	0.0375844312178158	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.962281816357922
CAMB-79390	MN908947.3	11075	T	-	0.022	0.045	5.4e-06	2.1e-11	0.0319780721790772	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964926907263591
CAMB-79390	MN908947.3	11418	T	C	0.0058	0.0079	0.00017	3.4e-05	0.00661864901693596	GTT	ORF1ab:nsp6	V149A	T446C	GTT>GCT	Missense	ORF1ab:nsp6	0.993381350983064
CAMB-79390	MN908947.3	11919	C	T	0.023	0.011	1.1e-11	9.9e-07	0.0180549856380796	TCT	ORF1ab:nsp7	S26F	C77T	TCT>TTT	Missense	ORF1ab:nsp7	0.981909332572122
CAMB-79390	MN908947.3	13862	C	T	0.11	0.048	1.1e-52	3.2e-23	0.0829813198160143	ACA	ORF1ab:RNA-dependent-RNA-polymerase	T132I	C395T	ACA>ATA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.916987390093557
CAMB-79390	MN908947.3	14224	A	G	0.0051	0.0087	0.00014	3.3e-06	0.00658722322165262	AAC	ORF1ab:RNA-dependent-RNA-polymerase	T253A	A757G	ACA>GCA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993412776778347
CAMB-79390	MN908947.3	14408	C	T	1	1	0	0	0.997678169070467	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000468941222220951
CAMB-79390	MN908947.3	15919	G	T	0.0067	0.004	4.2e-05	5e-04	0.00562277486567086	TGT	ORF1ab:RNA-dependent-RNA-polymerase	V818L	G2452T	GTG>TTG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994350950485424
CAMB-79390	MN908947.3	17550	C	T	0.013	0.013	2e-07	3.3e-07	0.0129542827789906	TCG	ORF1ab:helicase	L438L	C1314T	CTC>CTT	Synonymous	ORF1ab:helicase	0.987013612430975
CAMB-79390	MN908947.3	21137	A	G	0.091	0.14	7.3e-36	1.7e-57	0.111789368496513	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.888210631503487
CAMB-79390	MN908947.3	22746	TCTATGCAGATTCATTTGTAATTAGAGGTGA	-	0.00579032258064516	0.000132258064516129	9.2e-05;5.2e-05;6.8e-05;1.9e-05;3.5e-05;7.3e-05;0.00011;0.00013;0.00011;1e-04;7.1e-05;9.4e-05;9.2e-05;6.4e-05;0.00015;8.8e-05;0.00012;0.00013;0.00015;0.00011;1e-04;8.1e-05;0.00011;0.00019;2e-04;9.6e-05;3.2e-08;0.00013;0.00014;0.00022;0.00021	NA;0.00044;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00312222363244066	GTC	S	.	1184-1214-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.996150509650835
CAMB-79390	MN908947.3	23403	A	G	1	1	0	0	0.999907100086988	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.44544663744542e-05
CAMB-79390	MN908947.3	24064	C	T	0.018	0.019	4.4e-10	1.4e-10	0.0184645286686103	TCA	S	I834I	C2502T	ATC>ATT	Synonymous	GU280_gp02, spike glycoprotein	0.98153547133139
CAMB-79390	MN908947.3	24076	T	A	1	1	0	0	0.999721225215179	GTG	S	G838G	T2514A	GGT>GGA	Synonymous	GU280_gp02, spike glycoprotein	6.96936962051782e-05
CAMB-79390	MN908947.3	241	C	T	1	1	0	0	0.999702574588716	TCG	NA	NA	NA	NA	NA	NA	0.000130123617436565
CAMB-79390	MN908947.3	25000	C	T	0.0098	0.012	3e-06	2.3e-07	0.0109579694323144	ACT	S	D1146D	C3438T	GAC>GAT	Synonymous	GU280_gp02, spike glycoprotein	0.989028384279476
CAMB-79390	MN908947.3	25035	A	G	0.013	0.03	9.2e-08	5.3e-15	0.0207726236776161	AAT	S	N1158S	A3473G	AAT>AGT	Missense	GU280_gp02, spike glycoprotein	0.979227376322384
CAMB-79390	MN908947.3	25057	T	-	0.012	0.0095	4.2e-07	6e-06	0.0110858160942294	ATT	S	.	3495-3495-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.988815203404929
CAMB-79390	MN908947.3	25416	C	T	0.01	0.031	3e-06	4.4e-15	0.0189856854996991	TCA	ORF3a	F8F	C24T	TTC>TTT	Synonymous	GU280_gp03	0.980975060843169
CAMB-79390	MN908947.3	25539	C	T	0.087	0.078	2.2e-39	1.8e-35	0.083436478859293	GCG	ORF3a	G49G	C147T	GGC>GGT	Synonymous	GU280_gp03	0.916514011288246
CAMB-79390	MN908947.3	25602	A	C	0.0052	0.016	0.00067	2.6e-08	0.00955314009661836	AAC	ORF3a	Q70H	A210C	CAA>CAC	Missense	GU280_gp03	0.990398550724638
CAMB-79390	MN908947.3	2570	C	T	0.012	0.01	7.7e-07	8.9e-06	0.0115295926210607	ACC	ORF1ab:nsp2	P589S	C1765T	CCT>TCT	Missense	ORF1ab:nsp2	0.988470407378939
CAMB-79390	MN908947.3	27012	C	T	0.0071	0.003	3.4e-05	0.0024	0.00533751962323391	CCT	M	L164L	C490T	CTG>TTG	Synonymous	GU280_gp05	0.994592708878423
CAMB-79390	MN908947.3	27393	C	T	0.0093	0.0038	6.4e-06	0.0016	0.00700974688614645	ACA	NA	NA	NA	NA	NA	NA	0.992961641902073
CAMB-79390	MN908947.3	28603	C	T	0.014	0.01	3.1e-05	0.00022	0.0121795689325341	TCT	N	F110F	C330T	TTC>TTT	Synonymous	GU280_gp10	0.987724780002551
CAMB-79390	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999613665213312	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79390	MN908947.3	28901	A	C	0.0027	0.0078	0.004	2.3e-05	0.00515587529976019	AAT	N	M210L	A628C	ATG>CTG	Missense	GU280_gp10	0.994664268585132
CAMB-79390	MN908947.3	29831	C	T	0.46	0.42	3.8e-229	6.5e-209	0.43646080760095	GCT	NA	NA	NA	NA	NA	NA	0.563242280285036
CAMB-79390	MN908947.3	3037	C	T	1	1	0	0	0.999660993965693	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000135602413722964
CAMB-79390	MN908947.3	319	G	-	0.0064	0.009	0.00032	2.8e-05	0.00750860360830118	TGC	ORF1ab:leader-protein	.	54-54-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.992387110230472
CAMB-79390	MN908947.3	3230	G	A	1	1	0	0	0.999935721631814	TGG	ORF1ab:nsp3	G171S	G511A	GGT>AGT	Missense	ORF1ab:nsp3	6.4278368186493e-05
CAMB-79390	MN908947.3	324	T	-	0.0064	0.0096	0.00054	2.3e-05	0.00771645077944823	GTT	ORF1ab:leader-protein	.	59-59-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.992266208881722
CAMB-79390	MN908947.3	3469	A	-	0.0079	0.0042	3.4e-05	0.0013	0.00626787817600538	GAG	ORF1ab:nsp3	.	750-750-delfrshift	.	no-SNV	ORF1ab:nsp3	0.993584889786303
CAMB-79390	MN908947.3	414	C	T	0.012	0.018	1.2e-07	2.3e-10	0.0146986187045458	ACT	ORF1ab:leader-protein	T50I	C149T	ACT>ATT	Missense	ORF1ab:leader-protein	0.985301381295454
CAMB-79390	MN908947.3	4175	A	-	0.015	0.009	1.1e-06	0.00023	0.0123606160688009	TAA	ORF1ab:nsp3	.	1456-1456-delfrshift	.	no-SNV	ORF1ab:nsp3	0.987541283803669
CAMB-79390	MN908947.3	4175	AA	-	0.0075	0.0088	1.1e-06;NA	0.00023;9e-06	0.00793573356750252	TAA	ORF1ab:nsp3	.	1456-1457-delfrshift	.	no-SNV	ORF1ab:nsp3	0.987541283803669
CAMB-79390	MN908947.3	5730	C	T	0.0078	0.0069	2.5e-05	5.6e-05	0.00744409601125407	ACT	ORF1ab:nsp3	T1004I	C3011T	ACT>ATT	Missense	ORF1ab:nsp3	0.992555903988746
CAMB-79390	MN908947.3	6401	C	T	0.025	0.051	9.3e-13	4.7e-24	0.0359594124941057	ACC	ORF1ab:nsp3	P1228S	C3682T	CCA>TCA	Missense	ORF1ab:nsp3	0.963970729492307
CAMB-79390	MN908947.3	7936	G	C	0.067	0.065	4.2e-29	2.4e-28	0.0659261626977785	CGT	ORF1ab:nsp3	A1739A	G5217C	GCG>GCC	Synonymous	ORF1ab:nsp3	0.934073837302221
CAMB-79390	MN908947.3	8191	T	C	0.008	0.0032	1.5e-05	0.0023	0.00604967497087889	TTG	ORF1ab:nsp3	V1824V	T5472C	GTT>GTC	Synonymous	ORF1ab:nsp3	0.993950325029121
CAMB-79390	MN908947.3	9158	C	T	0.0061	0.0074	7.7e-05	2.1e-05	0.00671488632514396	TCC	ORF1ab:nsp4	P202S	C604T	CCT>TCT	Missense	ORF1ab:nsp4	0.993265188196146
CAMB-79390	MN908947.3	9438	C	T	0.013	0.019	3.8e-07	1.8e-09	0.0148660582867236	ACA	ORF1ab:nsp4	T295I	C884T	ACA>ATA	Missense	ORF1ab:nsp4	0.985133941713276
CAMB-79390	MN908947.3	9491	C	T	0.27	0.36	1.8e-126	1.3e-174	0.303710723919224	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.696216373842677
CAMB-79390	MN908947.3	9737	A	G	0.042	0.008	6e-20	1.2e-05	0.0274392640930891	TAG	ORF1ab:nsp4	S395G	A1183G	AGT>GGT	Missense	ORF1ab:nsp4	0.972534528395838
CAMB-79390	MN908947.3	9848	A	G	0.011	0.031	5.6e-07	2.2e-15	0.0202753441802253	TAG	ORF1ab:nsp4	S432G	A1294G	AGT>GGT	Missense	ORF1ab:nsp4	0.979724655819775
CAMB-79390	MN908947.3	9924	C	T	0.13	0.13	6.4e-58	7.9e-57	0.128048489476447	GCA	ORF1ab:nsp4	A457V	C1370T	GCA>GTA	Missense	ORF1ab:nsp4	0.871856058798263
CAMB-793AF	MN908947.3	14408	C	T	1	1	0	0	0.999427606536733	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000515154116939985
CAMB-793AF	MN908947.3	14599	C	T	0.24	0.21	1.5e-114	8.1e-98	0.22644943620705	TCT	ORF1ab:RNA-dependent-RNA-polymerase	L378L	C1132T	CTA>TTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.77355056379295
CAMB-793AF	MN908947.3	23403	A	G	1	1	0	0	0.999905587341151	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.55301270794388e-05
CAMB-793AF	MN908947.3	241	C	T	1	1	0	0	0.99978877701894	TCG	NA	NA	NA	NA	NA	NA	0.000140815320706893
CAMB-793AF	MN908947.3	26530	A	G	1	1	0	0	0.999725425590335	GAT	M	D3G	A8G	GAT>GGT	Missense	GU280_gp05	0.00013728720483251
CAMB-793AF	MN908947.3	28739	G	T	1	1	0	0	1	TGC	N	A156S	G466T	GCA>TCA	Missense	GU280_gp10	0
CAMB-793AF	MN908947.3	29039	A	T	0.011	0.02	4.2e-05	1.2e-07	0.0128919306063982	TAA	N	K256*	A766T	AAG>TAG	Nonsense	GU280_gp10	0.987108069393602
CAMB-793AF	MN908947.3	29404	TG	-	0.057	0.062	2.7e-08;2.8e-08	2.9e-06;1.9e-06	0.0588235294117647	ATG	N	.	1131-1132-delfrshift	.	no-SNV	GU280_gp10	0.942408376963351
CAMB-793AF	MN908947.3	3037	C	T	1	1	0	0	0.999231754161332	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-793BE	MN908947.3	11075	T	-	0.039	0.039	8.8e-10	8.7e-10	0.0392109500805153	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956270128824477
CAMB-793BE	MN908947.3	14408	C	T	1	1	0	0	0.998824979222194	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000850218286380267
CAMB-793BE	MN908947.3	23403	A	G	1	1	0	0	0.999117897779919	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.89514843778956e-05
CAMB-793BE	MN908947.3	241	C	T	1	1	0	0	0.997898444552975	TCG	NA	NA	NA	NA	NA	NA	0.000429190901152896
CAMB-793BE	MN908947.3	25429	G	T	1	1	0	0	0.999398732109013	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	6.53552055421214e-05
CAMB-793BE	MN908947.3	29421	C	T	0.022	0.023	4.3e-10	1.6e-10	0.0228001425008906	CCG	N	P383L	C1148T	CCG>CTG	Missense	GU280_gp10	0.976962356014725
CAMB-793BE	MN908947.3	3037	C	T	1	1	0	0	0.999177389975909	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000117515717727246
CAMB-793BE	MN908947.3	936	C	T	1	1	0	0	0.999961908631504	ACT	ORF1ab:nsp2	T44I	C131T	ACT>ATT	Missense	ORF1ab:nsp2	3.80913684958988e-05
CAMB-793CD	MN908947.3	11075	T	-	0.084	0.0067	1.2e-20	0.0038	0.0559171781042713	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.944020829458806
CAMB-793CD	MN908947.3	14408	C	T	1	1	0	0	0.999354446722868	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000531632110579479
CAMB-793CD	MN908947.3	23403	A	G	1	1	0	0	0.999916075699719	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.79747667603821e-05
CAMB-793CD	MN908947.3	23540	TATGAGTGTGACATACCCATTGGTGCAGG	-	0.0492413793103448	0.0238620689655172	8.3e-09;2e-08;2.7e-09;9e-09;1.3e-08;1.1e-08;1.1e-08;1.4e-08;7.4e-08;6.8e-08;1.2e-06;4e-07;4.7e-07;2e-05;7.1e-06;5.2e-05;4.2e-05;5.8e-05;6e-05;1.4e-05;3.3e-05;1.5e-05;3.5e-05;4.1e-05;3.8e-05;3.5e-05;3.3e-05;1.8e-05;1.6e-05	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;6.4e-05;3e-05;0.00018;0.00015;0.00018;0.00023;7.2e-05;0.00014;5.7e-05;0.00012;0.00013;0.00012;0.00012;0.00012;6.8e-05;6.1e-05	0.0455591348366314	ATA	S	.	1978-2006-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.973302107728337
CAMB-793CD	MN908947.3	23683	C	T	0.091	0.077	4.3e-39	1.6e-33	0.0841489481381483	ACT	S	Y707Y	C2121T	TAC>TAT	Synonymous	GU280_gp02, spike glycoprotein	0.915738553268084
CAMB-793CD	MN908947.3	241	C	T	1	0.95	0	0	0.985301746498357	TCG	NA	NA	NA	NA	NA	NA	8.64603147155456e-05
CAMB-793CD	MN908947.3	25429	G	T	1	1	0	0	0.999816201810412	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0.000114873868492395
CAMB-793CD	MN908947.3	25916	C	T	1	1	0	0	1	ACA	ORF3a	T175I	C524T	ACA>ATA	Missense	GU280_gp03	0
CAMB-793CD	MN908947.3	29445	C	T	0.96	0.91	2.7e-215	1e-199	0.931372549019608	ACT	N	T391I	C1172T	ACT>ATT	Missense	GU280_gp10	0.0686274509803922
CAMB-793CD	MN908947.3	3037	C	T	1	1	0	0	0.999838527369611	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000161472630389149
CAMB-793CD	MN908947.3	6500	C	T	0.0038	0.028	0.00067	1.9e-14	0.0164432240348894	ACC	ORF1ab:nsp3	P1261S	C3781T	CCA>TCA	Missense	ORF1ab:nsp3	0.983556775965111
CAMB-793DC	MN908947.3	10074	C	T	1	1	0	0	0.999502499348511	GCA	ORF1ab:3C-like-proteinase	A7V	C20T	GCA>GTA	Missense	ORF1ab:3C-like-proteinase	0.000189524057710076
CAMB-793DC	MN908947.3	11075	T	-	0.039	0.038	5.5e-10	1.3e-09	0.0384942732777278	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956447729980789
CAMB-793DC	MN908947.3	11674	C	T	0.03	0.033	1.1e-10	3.5e-12	0.0316509837467921	ACT	ORF1ab:nsp6	Y234Y	C702T	TAC>TAT	Synonymous	ORF1ab:nsp6	0.968349016253208
CAMB-793DC	MN908947.3	14352	C	T	1	1	0	0	0.999818575454469	ACA	ORF1ab:RNA-dependent-RNA-polymerase	D295D	C885T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	7.25698182126054e-05
CAMB-793DC	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999399549662247	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000312746287701565
CAMB-793DC	MN908947.3	18680	C	T	0.013	0.012	1.1e-07	2.7e-07	0.0126795352666728	GCC	ORF1ab:3'-to-5'-exonuclease	A214V	C641T	GCC>GTC	Missense	ORF1ab:3'-to-5'-exonuclease	0.987247278382582
CAMB-793DC	MN908947.3	19018	C	T	0.014	0.011	5.5e-08	1.1e-06	0.0122106524833321	CCC	ORF1ab:3'-to-5'-exonuclease	P327S	C979T	CCA>TCA	Missense	ORF1ab:3'-to-5'-exonuclease	0.987751891527455
CAMB-793DC	MN908947.3	20756	G	T	0.018	0.018	1.8e-09	1.4e-09	0.0179074682949742	AGT	ORF1ab:2'-O-ribose-methyltransferase	S33I	G98T	AGT>ATT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.981955534679818
CAMB-793DC	MN908947.3	23009	G	A	1	1	0	0	0.999765282703943	TGT	S	V483I	G1447A	GTT>ATT	Missense	GU280_gp02, spike glycoprotein	7.82390986855831e-05
CAMB-793DC	MN908947.3	25817	A	G	0.016	0.013	1.4e-08	2.3e-07	0.0143375776070715	GAT	ORF3a	D142G	A425G	GAT>GGT	Missense	GU280_gp03	0.985583499947385
CAMB-793DC	MN908947.3	26137	A	C	0.023	0.014	1.2e-05	0.0046	0.0185389538733171	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.98135069521077
CAMB-793DC	MN908947.3	28399	C	T	1	1	0	0	0.999365461042648	CCC	N	P42P	C126T	CCC>CCT	Synonymous	GU280_gp10	0.000601142170123234
CAMB-793DC	MN908947.3	28460	G	A	0.0067	0.0053	3.5e-05	0.00014	0.00608143839238498	AGA	N	D63N	G187A	GAC>AAC	Missense	GU280_gp10	0.993786356425172
CAMB-793DC	MN908947.3	29508	G	T	0.0089	0.008	1.6e-05	3.4e-05	0.00840941854877463	AGC	N	S412I	G1235T	AGC>ATC	Missense	GU280_gp10	0.991590581451225
CAMB-793FA	MN908947.3	11075	T	-	0.036	0.038	3.2e-09	1e-09	0.0370090265918517	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95895340326909
CAMB-793FA	MN908947.3	14408	C	T	1	1	0	0	0.998076505750755	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000611572530529306
CAMB-793FA	MN908947.3	15030	T	C	0.014	0.015	1.2e-07	2.1e-08	0.0145371855521491	ATA	ORF1ab:RNA-dependent-RNA-polymerase	Y521Y	T1563C	TAT>TAC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.98446795119079
CAMB-793FA	MN908947.3	15327	G	T	0.27	0.27	1.2e-130	2.9e-131	0.267729282111948	TGC	ORF1ab:RNA-dependent-RNA-polymerase	M620I	G1860T	ATG>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.732059024967312
CAMB-793FA	MN908947.3	20268	A	G	1	1	0	0	0.999024390243902	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0.000975609756097561
CAMB-793FA	MN908947.3	23403	A	G	1	1	0	0	0.999489457682138	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.62003459495706e-05
CAMB-793FA	MN908947.3	241	C	T	1	1	0	0	0.999029247044182	TCG	NA	NA	NA	NA	NA	NA	0.000112009956440572
CAMB-793FA	MN908947.3	2937	C	T	1	1	0	0	0.999769975533761	ACA	ORF1ab:nsp3	T73I	C218T	ACA>ATA	Missense	ORF1ab:nsp3	8.36452604504297e-05
CAMB-793FA	MN908947.3	3037	C	T	1	1	0	0	0.999340159827953	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000171069674234463
CAMB-793FA	MN908947.3	6696	C	INS	0.14	0.14	1.4e-28	5.2e-30	0.140321437893873	CCT	ORF1ab:nsp3	.	3976-3977-insfrshift	.	no-SNV	ORF1ab:nsp3	0.85744117537383
CAMB-793FA	MN908947.3	6701	C	T	1	0.99	0	0	0.994432682506077	TCT	ORF1ab:nsp3	L1328F	C3982T	CTT>TTT	Missense	ORF1ab:nsp3	0.000313651689798479
CAMB-79406	MN908947.3	11075	T	-	0.036	0.039	3.6e-09	1.1e-09	0.0376850201293889	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957948604963246
CAMB-79406	MN908947.3	14408	C	T	1	1	0	0	0.999059407426679	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000460289982689094
CAMB-79406	MN908947.3	23403	A	G	1	1	0	0	0.999774189906289	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.5270031237063e-05
CAMB-79406	MN908947.3	241	C	T	1	1	0	0	0.998871421743056	TCG	NA	NA	NA	NA	NA	NA	0.000172606086356153
CAMB-79406	MN908947.3	26137	A	C	0.033	0.015	2.1e-08	0.0025	0.0233276687780009	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.976363355476595
CAMB-79406	MN908947.3	27442	C	T	0.11	0.1	5.9e-49	1.3e-47	0.105616872472954	GCT	ORF7a	L17F	C49T	CTT>TTT	Missense	GU280_gp07	0.894301169271118
CAMB-79406	MN908947.3	27527	CATTT	-	1	1	0;0;0;0;0	0;0;0;0;0	0.996550237171195	CCA	ORF7a	.	134-138-delfrshift	.	no-SNV	GU280_gp07	0.00301984469370147
CAMB-79406	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999491429084273	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	3.28925728570489e-05
CAMB-79406	MN908947.3	3037	C	T	1	1	0	0	0.998885653689924	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000107839965491211
CAMB-79415	MN908947.3	10802	C	T	0.0081	0.01	1.4e-05	1.5e-06	0.00928479750948961	ACT	ORF1ab:3C-like-proteinase	L250L	C748T	CTA>TTA	Synonymous	ORF1ab:3C-like-proteinase	0.990687894262541
CAMB-79415	MN908947.3	11075	T	-	0.04	0.03	8.2e-10	8.4e-08	0.0350125779693827	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961602124694902
CAMB-79415	MN908947.3	14408	C	T	0.99	1	0	0	0.994965039941644	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00098742149554326
CAMB-79415	MN908947.3	20268	A	G	1	1	5.5e-288	0	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-79415	MN908947.3	23403	A	G	1	1	0	0	0.999650110178072	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.46667857780954e-05
CAMB-79415	MN908947.3	23876	G	A	0.011	0.0098	7e-07	2e-06	0.0104714355145142	TGT	S	V772I	G2314A	GTT>ATT	Missense	GU280_gp02, spike glycoprotein	0.989322375881824
CAMB-79415	MN908947.3	241	C	T	1	1	0	0	0.998111079046095	TCG	NA	NA	NA	NA	NA	NA	0.000104940052994727
CAMB-79415	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.02015625	0.02959375	0.0014;0.0049;0.0039;0.0039;0.0016;0.0025;0.0023;0.0039;0.0025;0.0032;0.0049;0.0023;0.0042;0.0034;0.0033;0.0026;0.0041;0.0026;0.0032;0.0031;0.0023;0.0041;0.0029;0.0011;0.0028;0.0041;0.0033;0.002;0.0035;0.0025;0.0035;0.003	0.00049;0.00065;9.4e-05;9.1e-05;4.6e-05;6.7e-05;5.9e-05;8.7e-05;6.4e-05;7.9e-05;0.00011;5.9e-05;1e-04;7.8e-05;5.9e-05;4.4e-05;0.00011;5.1e-05;8.3e-05;6.9e-05;5.4e-05;9.4e-05;6.1e-05;3.6e-05;6.8e-05;9.2e-05;8.2e-05;5.5e-05;8.9e-05;5.2e-05;6.5e-05;4.6e-05	0.0248562765789888	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.976052758954501
CAMB-79415	MN908947.3	27264	TTTTAAAGTTTCCATTTGGAATCTTGA	-	0.00484074074074074	0.0128888888888889	0.0059;0.0094;0.016;0.025;0.028;0.02;0.02;0.021;0.014;0.022;0.023;0.022;0.019;0.021;0.016;0.022;0.023;0.023;0.024;0.021;0.021;0.021;0.022;0.02;0.022;0.019;0.018	2.2e-06;3.7e-05;9.8e-05;0.00025;0.00019;0.00017;0.00018;2e-04;0.00014;0.00022;0.00023;0.00021;0.00016;0.00018;0.00013;0.00022;0.00023;0.00022;0.00032;2e-04;0.00022;2e-04;0.00022;0.00012;0.00022;7.3e-05;7.3e-05	0.00877287988736055	CTT	ORF6	.	63-89-delinframe	.	no-SNV	GU280_gp06	0.991826670623958
CAMB-79415	MN908947.3	2937	C	T	1	1	0	0	0.999813803376365	ACA	ORF1ab:nsp3	T73I	C218T	ACA>ATA	Missense	ORF1ab:nsp3	9.30983118172791e-05
CAMB-79415	MN908947.3	3037	C	T	1	1	0	0	0.999290674232808	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000111998805346076
CAMB-79415	MN908947.3	484	T	C	0.0092	0.012	4.9e-06	2.3e-07	0.0106562037984761	GTT	ORF1ab:leader-protein	R73R	T219C	CGT>CGC	Synonymous	ORF1ab:leader-protein	0.989195951324918
CAMB-79415	MN908947.3	6696	C	INS	0.14	0.15	5.1e-30	8.6e-32	0.146466370775009	CCT	ORF1ab:nsp3	.	3976-3977-insfrshift	.	no-SNV	ORF1ab:nsp3	0.85051781040173
CAMB-79415	MN908947.3	6701	C	-	0.007	0.0033	3.7e-05	0.0012	0.00490077444336883	TCT	ORF1ab:nsp3	.	3982-3982-delfrshift	.	no-SNV	ORF1ab:nsp3	0.0026621490803485
CAMB-79415	MN908947.3	6701	C	T	0.99	0.99	0	0	0.992437076476283	TCT	ORF1ab:nsp3	L1328F	C3982T	CTT>TTT	Missense	ORF1ab:nsp3	0.0026621490803485
CAMB-79415	MN908947.3	9810	C	T	0.013	0.018	1.1e-07	1.6e-09	0.0154152911978025	ACC	ORF1ab:nsp4	T419I	C1256T	ACC>ATC	Missense	ORF1ab:nsp4	0.984572660899737
CAMB-79424	MN908947.3	10097	G	A	1	1	0	0	0.999843014128728	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	9.8116169544741e-05
CAMB-79424	MN908947.3	10626	C	T	0.051	0.049	7.4e-23	6.4e-22	0.049753815854259	GCA	ORF1ab:3C-like-proteinase	A191V	C572T	GCA>GTA	Missense	ORF1ab:3C-like-proteinase	0.950246184145741
CAMB-79424	MN908947.3	11075	T	-	0.036	0.046	5e-09	3.1e-11	0.0410682692022575	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955590918525694
CAMB-79424	MN908947.3	13536	C	T	1	1	0	0	0.99959250203749	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00023285597857725
CAMB-79424	MN908947.3	14408	C	T	1	1	0	0	0.997947837767247	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000774224842356628
CAMB-79424	MN908947.3	23403	A	G	1	1	0	0	0.999235033986347	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.28539060621735e-05
CAMB-79424	MN908947.3	23731	C	T	1	1	0	0	0.999869613403742	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000130386596257905
CAMB-79424	MN908947.3	241	C	T	1	1	0	0	0.99825048180091	TCG	NA	NA	NA	NA	NA	NA	0.000150349220234271
CAMB-79424	MN908947.3	27644	C	T	0.017	0.0099	2.4e-05	0.00031	0.0118595825426945	CCT	ORF7a	P84L	C251T	CCT>CTT	Missense	GU280_gp07	0.988140417457306
CAMB-79424	MN908947.3	28269	C	T	0.012	0.01	4.8e-07	1.6e-06	0.0109920140892114	ACT	NA	NA	NA	NA	NA	NA	0.98890677031144
CAMB-79424	MN908947.3	28321	G	A	0.56	0.56	0	0	0.558228807306519	CGT	N	T16T	G48A	ACG>ACA	Synonymous	GU280_gp10	0.441402277304724
CAMB-79424	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999109947643979	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	5.77567286588888e-05
CAMB-79424	MN908947.3	29614	C	T	0.046	0.047	3.3e-20	1.2e-20	0.0465328764888236	GCA	ORF10	C19C	C57T	TGC>TGT	Synonymous	GU280_gp11	0.95340186000979
CAMB-79424	MN908947.3	3037	C	T	1	1	0	0	0.999529817412429	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	2.61212548650837e-05
CAMB-79424	MN908947.3	4002	C	T	1	1	0	0	0.999443400820984	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0.00010436234606554
CAMB-79424	MN908947.3	816	G	T	0.041	0.045	2.3e-19	5.5e-21	0.0426343877642289	CGC	ORF1ab:nsp2	R4L	G11T	CGC>CTC	Missense	ORF1ab:nsp2	0.95670969857786
CAMB-79424	MN908947.3	9724	C	T	0.013	0.011	1e-07	9.7e-07	0.0122683123382958	TCT	ORF1ab:nsp4	F390F	C1170T	TTC>TTT	Synonymous	ORF1ab:nsp4	0.987710480553081
CAMB-79433	MN908947.3	10965	C	T	0.76	0.76	0	0	0.76266270992109	ACT	ORF1ab:3C-like-proteinase	T304I	C911T	ACT>ATT	Missense	ORF1ab:3C-like-proteinase	0.236550437265349
CAMB-79433	MN908947.3	11074	C	INS	0.033	0.03	3.1e-08	1.4e-06	0.031762790902292	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.967357353394043
CAMB-79433	MN908947.3	11075	T	-	0.042	0.038	3.7e-10	1.3e-09	0.0401613127520512	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955333055207899
CAMB-79433	MN908947.3	11083	G	-	0.013	0.013	1.1e-05	1e-05	0.0128090395480226	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.939308474576271
CAMB-79433	MN908947.3	11083	G	T	0.047	0.049	6.7e-10	1.6e-10	0.0476203389830508	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.939308474576271
CAMB-79433	MN908947.3	13730	C	T	1	1	0	0	0.997678905687545	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A88V	C263T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	7.48740100791937e-05
CAMB-79433	MN908947.3	14408	C	T	1	1	0	0	0.996707588308436	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000936936305844031
CAMB-79433	MN908947.3	23403	A	G	1	1	0	0	0.999681371053577	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000135586785711865
CAMB-79433	MN908947.3	241	C	T	1	1	0	0	0.997603182371469	TCG	NA	NA	NA	NA	NA	NA	0.000476853769027093
CAMB-79433	MN908947.3	25429	G	T	1	1	0	0	0.998008207146457	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0.000131986273427564
CAMB-79433	MN908947.3	25536	T	C	0.059	0.063	6.7e-27	9.9e-29	0.0607996912914685	TTG	ORF3a	V48V	T144C	GTT>GTC	Synonymous	GU280_gp03	0.939007365876358
CAMB-79433	MN908947.3	25889	C	T	0.044	0.054	4.4e-20	9.5e-25	0.0478927677708679	TCA	ORF3a	S166L	C497T	TCA>TTA	Missense	GU280_gp03	0.951958573870816
CAMB-79433	MN908947.3	29540	G	T	0.095	0.099	1.1e-41	1.8e-43	0.0964751158925916	TGC	NA	NA	NA	NA	NA	NA	0.903349951893641
CAMB-79433	MN908947.3	3037	C	T	1	1	0	0	0.999125067984582	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.45872449100239e-05
CAMB-79433	MN908947.3	6865	G	T	0.019	0.034	2.1e-08	2.5e-13	0.025	AGA	ORF1ab:nsp3	K1382N	G4146T	AAG>AAT	Missense	ORF1ab:nsp3	0.973058252427184
CAMB-79442	MN908947.3	11075	T	-	0.11	0.093	5.4e-28	2.4e-23	0.105302864857353	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.894538307292184
CAMB-79442	MN908947.3	11606	C	T	0.021	0.021	1.5e-08	6e-07	0.0214446952595937	GCT	ORF1ab:nsp6	L212L	C634T	CTA>TTA	Synonymous	ORF1ab:nsp6	0.978555304740406
CAMB-79442	MN908947.3	14408	C	T	1	1	0	0	0.999437652302501	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000374898464999063
CAMB-79442	MN908947.3	18781	G	A	0.045	0.042	3e-21	6.9e-20	0.0437415772297001	GGG	ORF1ab:3'-to-5'-exonuclease	G248S	G742A	GGT>AGT	Missense	ORF1ab:3'-to-5'-exonuclease	0.956225949439023
CAMB-79442	MN908947.3	23403	A	G	1	1	0	0	0.999889207588049	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.69308039836027e-05
CAMB-79442	MN908947.3	241	C	T	1	1	0	0	0.999774510688193	TCG	NA	NA	NA	NA	NA	NA	9.01957247226481e-05
CAMB-79442	MN908947.3	26532	TC	CT	0.0265	0.0595	NA;3.5e-24	7.2e-22;9.5e-32	0.0421135234109338	TTC	M	.	10-11-mnv	.	no-SNV	GU280_gp05	0.977414871438499
CAMB-79442	MN908947.3	26533	C	T	0.053	0.071	3.5e-24	9.5e-32	0.0617943107221007	TCC	M	S4F	C11T	TCC>TTC	Missense	GU280_gp05	0.938205689277899
CAMB-79442	MN908947.3	26768	C	T	0.021	0.033	9.7e-11	4.9e-16	0.0257561359242389	TCG	M	I82I	C246T	ATC>ATT	Synonymous	GU280_gp05	0.974227479765377
CAMB-79442	MN908947.3	28253	C	T	0.081	0.028	4.3e-36	3e-13	0.0568231109568838	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.942858795292213
CAMB-79442	MN908947.3	29598	A	G	0.15	0.11	2.8e-49	4.9e-34	0.132343846629561	TAT	ORF10	Y14C	A41G	TAT>TGT	Missense	GU280_gp11	0.867656153370439
CAMB-79442	MN908947.3	29730	C	T	0.027	0.034	3e-09	3.4e-11	0.0303030303030303	TCA	NA	NA	NA	NA	NA	NA	0.96969696969697
CAMB-79442	MN908947.3	3037	C	T	1	1	0	0	0.999463950683463	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79442	MN908947.3	346	C	T	0.067	0.028	1.3e-31	3.6e-14	0.0547933477451253	TCG	ORF1ab:leader-protein	L27L	C81T	CTC>CTT	Synonymous	ORF1ab:leader-protein	0.945142441300486
CAMB-79451	MN908947.3	10097	G	A	1	1	0	0	0.999883249175447	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	8.75631184145238e-05
CAMB-79451	MN908947.3	10456	C	T	0.026	0.0085	9.1e-13	9.7e-06	0.0184527025105911	TCA	ORF1ab:3C-like-proteinase	F134F	C402T	TTC>TTT	Synonymous	ORF1ab:3C-like-proteinase	0.981547297489409
CAMB-79451	MN908947.3	11075	T	-	0.038	0.052	1.5e-09	1.2e-12	0.0446856302303854	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954479495895203
CAMB-79451	MN908947.3	13536	C	T	1	1	0	0	0.998875702685821	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000687070580886946
CAMB-79451	MN908947.3	1404	C	T	0.0054	0.0089	0.00032	1.7e-05	0.00673124281727138	CCT	ORF1ab:nsp2	P200L	C599T	CCT>CTT	Missense	ORF1ab:nsp2	0.993268757182729
CAMB-79451	MN908947.3	14408	C	T	1	1	0	0	0.998952859275922	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00052357036203921
CAMB-79451	MN908947.3	18781	G	A	0.01	0.0042	2.3e-06	0.00046	0.00722822023114563	GGG	ORF1ab:3'-to-5'-exonuclease	G248S	G742A	GGT>AGT	Missense	ORF1ab:3'-to-5'-exonuclease	0.991013918587414
CAMB-79451	MN908947.3	18844	G	T	0.032	0.035	1.4e-15	1e-16	0.0335715860888064	TGT	ORF1ab:3'-to-5'-exonuclease	V269L	G805T	GTA>TTA	Missense	ORF1ab:3'-to-5'-exonuclease	0.966337609775714
CAMB-79451	MN908947.3	18928	C	T	0.0047	0.0091	0.00076	8.2e-06	0.0067003389299926	TCC	ORF1ab:3'-to-5'-exonuclease	P297S	C889T	CCT>TCT	Missense	ORF1ab:3'-to-5'-exonuclease	0.993281600857258
CAMB-79451	MN908947.3	19186	C	T	0.0027	0.0085	0.0035	8.9e-06	0.0053101840094198	CCT	ORF1ab:3'-to-5'-exonuclease	L383L	C1147T	CTA>TTA	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.994470482303235
CAMB-79451	MN908947.3	22289	GCTTTA	-	0.0371666666666667	0.0441666666666667	5e-12;7.5e-14;1.9e-07;5.6e-13;3.3e-11;1.7e-10	3e-14;1.5e-16;1.7e-08;5.3e-15;5.3e-13;2.8e-12	0.0395685388422638	TGC	S	.	727-732-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.957614413825061
CAMB-79451	MN908947.3	23403	A	G	1	1	0	0	0.999324859151651	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.0001086433549068
CAMB-79451	MN908947.3	23731	C	T	1	1	0	0	0.999967572475517	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	3.2427524482781e-05
CAMB-79451	MN908947.3	241	C	T	1	1	0	0	0.996424801661616	TCG	NA	NA	NA	NA	NA	NA	0.000136198031938438
CAMB-79451	MN908947.3	24374	C	T	0.0033	0.0077	0.0026	3.1e-05	0.00523617027049025	ACT	S	L938F	C2812T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.9947366993136
CAMB-79451	MN908947.3	2450	C	T	0.016	0.018	2.1e-08	1.9e-09	0.0169416941694169	CCT	ORF1ab:nsp2	L549L	C1645T	CTA>TTA	Synonymous	ORF1ab:nsp2	0.983058305830583
CAMB-79451	MN908947.3	25583	C	T	0.0039	0.013	0.00078	6.6e-08	0.00825315763075099	ACC	ORF3a	T64I	C191T	ACC>ATC	Missense	GU280_gp03	0.991724043591264
CAMB-79451	MN908947.3	25654	G	T	0.3	0.29	2.6e-150	8.4e-141	0.300305410122164	TGT	ORF3a	V88L	G262T	GTA>TTA	Missense	GU280_gp03	0.699258289703316
CAMB-79451	MN908947.3	27970	C	T	1	1	0	0	0.999820143884892	ACT	ORF8	T26I	C77T	ACT>ATT	Missense	GU280_gp09	0
CAMB-79451	MN908947.3	28551	G	A	0.032	0.032	7.3e-15	2.6e-15	0.0319632010379194	CGA	N	R93Q	G278A	CGA>CAA	Missense	GU280_gp10	0.96771244913605
CAMB-79451	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99878433138226	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79451	MN908947.3	3037	C	T	1	1	0	0	0.999348986589124	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000130202682175253
CAMB-79451	MN908947.3	4002	C	T	1	1	0	0	0.999345415865483	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0.000531849609295095
CAMB-79451	MN908947.3	6016	C	T	0.0076	0.0047	2.9e-05	0.00038	0.00614422765980382	ACC	ORF1ab:nsp3	N1099N	C3297T	AAC>AAT	Synonymous	ORF1ab:nsp3	0.993855772340196
CAMB-79451	MN908947.3	7809	G	A	0.27	0.28	6.6e-126	3.3e-133	0.276222640774177	AGA	ORF1ab:nsp3	R1697K	G5090A	AGA>AAA	Missense	ORF1ab:nsp3	0.723647463791648
CAMB-79451	MN908947.3	8018	G	T	0.0024	0.0067	0.0038	3.5e-05	0.0040038015893879	GGA	ORF1ab:nsp3	E1767*	G5299T	GAA>TAA	Nonsense	ORF1ab:nsp3	0.995975977190464
CAMB-79451	MN908947.3	8612	G	A	0.0083	0.0024	1.2e-05	0.0019	0.00556245115616237	TGT	ORF1ab:nsp4	V20I	G58A	GTT>ATT	Missense	ORF1ab:nsp4	0.99361007677102
CAMB-79451	MN908947.3	9078	T	C	0.016	0.038	7.1e-09	3.5e-18	0.0268574297188755	GTA	ORF1ab:nsp4	V175A	T524C	GTA>GCA	Missense	ORF1ab:nsp4	0.973052925989673
CAMB-79460	MN908947.3	11075	T	-	0.055	0.048	2.4e-13	1.4e-11	0.0512679904563996	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.945903563457246
CAMB-79460	MN908947.3	14408	C	T	1	1	0	0	0.998132359768708	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000453720508166969
CAMB-79460	MN908947.3	14786	C	T	1	1	0	0	0.999934421929307	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A440V	C1319T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	3.27890353465801e-05
CAMB-79460	MN908947.3	15284	T	C	0.0032	0.0075	0.0012	1.5e-05	0.00518256772673734	ATG	ORF1ab:RNA-dependent-RNA-polymerase	M606T	T1817C	ATG>ACG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994581861012956
CAMB-79460	MN908947.3	16796	TAAC	-	0.00405	0.007075	0.0012;0.0015;0.00086;0.00098	5.1e-05;6.8e-05;3.8e-05;4.5e-05	0.00549203727050095	GTA	ORF1ab:helicase	.	560-563-delfrshift	.	no-SNV	ORF1ab:helicase	0.994341813265141
CAMB-79460	MN908947.3	1970	A	G	0.022	0.016	7e-12	3e-09	0.0198250728862974	AAT	ORF1ab:nsp2	I389V	A1165G	ATA>GTA	Missense	ORF1ab:nsp2	0.980174927113703
CAMB-79460	MN908947.3	19906	A	G	0.038	0.084	6.1e-18	8.9e-38	0.0599220959393842	TAT	ORF1ab:endoRNAse	I96V	A286G	ATA>GTA	Missense	ORF1ab:endoRNAse	0.940077904060616
CAMB-79460	MN908947.3	20578	G	T	1	1	0	0	1	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	0
CAMB-79460	MN908947.3	20850	TATGAGAGT	ATATGAGAG	0.000612222222222222	0.016	NA;NA;NA;NA;0.46;NA;NA;NA;8.5e-05	1.2e-09;6.1e-09;1.3e-09;2.4e-08;3.6e-09;2.3e-09;6.3e-09;2.2e-09;3.2e-09	0.00813761284580313	ATA	ORF1ab:2'-O-ribose-methyltransferase	.	192-200-mnv	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.99134613543681
CAMB-79460	MN908947.3	23403	A	G	1	1	0	0	0.999876582825266	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.40503048404216e-05
CAMB-79460	MN908947.3	23538	CATATGAGTG	-	0.0121	0.0173	NA;NA;0.0015;0.0015;0.0011;0.0015;0.0017;0.0017;0.0016;0.0017	6.5e-07;0.00013;6e-04;0.00071;0.00051;0.00061;0.00071;0.00068;0.00069;0.00071	0.0163579243852237	TCA	S	.	1976-1985-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.990060176230389
CAMB-79460	MN908947.3	23550	ACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACT	-	0.0538780487804878	0.0143239756097561	0.00024;0.00014;0.00016;0.00024;0.00011;0.00055;0.00043;6.7e-05;7e-05;5.3e-08;2e-07;4.8e-08;1.9e-07;2.3e-07;2.5e-07;2.1e-07;1.8e-07;6.4e-08;5.4e-08;3.2e-07;3e-08;4.4e-07;6.6e-08;5.4e-09;5.9e-10;5.2e-09;3.2e-08;7.6e-09;8e-09;2.8e-13;1.5e-12;8.2e-06;4.1e-05;4.8e-05;3.1e-05;3.1e-05;2.8e-06;1.7e-06;1.9e-06;2.1e-06;1.7e-06	0.0036;NA;NA;NA;NA;0.047;0.043;0.045;0.044;0.037;0.045;0.0031;0.0044;0.0046;0.0046;0.0046;0.0044;0.0034;0.0032;1.7e-06;4.8e-07;0.037;0.034;0.038;0.034;0.042;0.048;0.043;0.042;0.025;0.027;0.039;0.033;NA;NA;NA;NA;NA;NA;NA;NA	0.0330456630980992	GAC	S	.	1988-2028-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.978111955474687
CAMB-79460	MN908947.3	24043	A	C	0.0093	0.0092	2.5e-06	2.8e-06	0.009204550022107	CAC	S	T827T	A2481C	ACA>ACC	Synonymous	GU280_gp02, spike glycoprotein	0.990634671811568
CAMB-79460	MN908947.3	2407	G	A	0.018	0.043	5.4e-09	7.7e-19	0.0329772410589875	AGG	ORF1ab:nsp2	K534K	G1602A	AAG>AAA	Synonymous	ORF1ab:nsp2	0.967022758941013
CAMB-79460	MN908947.3	241	C	T	1	1	0	0	0.99979744784282	TCG	NA	NA	NA	NA	NA	NA	0.000121531294308284
CAMB-79460	MN908947.3	2416	C	T	1	1	0	0	0.999653379549393	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0.000173310225303293
CAMB-79460	MN908947.3	25563	G	T	1	1	0	0	0.999845767726196	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	7.0105579001977e-05
CAMB-79460	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0300810810810811	0.0373513513513513	2.9e-05;6.3e-07;1.8e-05;1.9e-05;6e-05;1.9e-06;1.6e-05;9.7e-05;9.6e-05;2.8e-05;5.2e-05;3.6e-05;9.9e-05;6.1e-05;7.9e-05;0.00013;5.5e-05;0.00012;8e-05;8e-05;5.5e-05;0.00013;6.6e-05;8.9e-05;7.1e-05;4.5e-05;1e-04;6.4e-05;2.8e-05;5.8e-05;0.00011;9.9e-05;6.2e-05;1e-04;4.2e-05;6.3e-05;4.3e-05	0.0013;0.00012;0.00097;0.0011;0.0018;7.1e-07;2.2e-06;1.5e-06;1.5e-06;4.5e-07;9e-07;6.8e-07;1.4e-06;9.2e-07;1.3e-06;2e-06;8.3e-07;1.8e-06;1.1e-06;1.1e-06;8.5e-07;2e-06;9.9e-07;1.4e-06;9.5e-07;7.3e-07;1.5e-06;8.2e-07;3e-07;1e-06;1.5e-06;1.4e-06;8.1e-07;1.6e-06;3.4e-07;7.8e-07;6.3e-07	0.0343997056232647	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.974923228717448
CAMB-79460	MN908947.3	29268	C	T	0.0074	0.0026	2.1e-05	0.0033	0.00497081808289643	ACC	N	T332I	C995T	ACC>ATC	Missense	GU280_gp10	0.995029181917104
CAMB-79460	MN908947.3	3037	C	T	1	1	0	0	0.999532792150908	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000175202943409449
CAMB-79460	MN908947.3	522	TT	-	0.044	0.0375	5.9e-06;3.3e-06	1.2e-05;0.00011	0.0409200137315482	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.95565190753352
CAMB-79460	MN908947.3	6516	TAAAAATTACA	-	0.000472727272727273	0.00854545454545455	0.00037;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	1.3e-05;4.1e-05;2e-05;1.1e-05;2.2e-05;2.1e-05;7.8e-06;6.7e-06;6.2e-06;3.9e-06;3.9e-06	0.00459086868257991	TTA	ORF1ab:nsp3	.	3797-3807-delfrshift	.	no-SNV	ORF1ab:nsp3	0.992979615670453
CAMB-79460	MN908947.3	722	C	T	0.0091	0.0073	3.1e-06	1.7e-05	0.00825835907076675	TCC	ORF1ab:leader-protein	P153S	C457T	CCT>TCT	Missense	ORF1ab:leader-protein	0.991741640929233
CAMB-79460	MN908947.3	7564	C	A	0.039	0.035	2.3e-18	1.7e-16	0.0371602884082085	CCT	ORF1ab:nsp3	S1615S	C4845A	TCC>TCA	Synonymous	ORF1ab:nsp3	0.962760478567467
CAMB-79460	MN908947.3	8139	C	T	0.041	0.035	1.2e-19	4.9e-17	0.0386489252814739	TCC	ORF1ab:nsp3	S1807F	C5420T	TCC>TTC	Missense	ORF1ab:nsp3	0.961351074718526
CAMB-7949D	MN908947.3	10032	C	T	0.0082	0.0082	1.1e-05	1e-05	0.00821544679729374	TCT	ORF1ab:nsp4	S493F	C1478T	TCT>TTT	Missense	ORF1ab:nsp4	0.991784553202706
CAMB-7949D	MN908947.3	10032	CT	TC	0.0096	0.0041	1.1e-05;1.3e-06	1e-05;NA	0.00678733031674208	TCT	ORF1ab:nsp4	.	1478-1479-mnv	.	no-SNV	ORF1ab:nsp4	0.991784553202706
CAMB-7949D	MN908947.3	10369	C	T	0.0096	0.018	1.1e-05	2.5e-09	0.0135014759051927	GCA	ORF1ab:3C-like-proteinase	R105R	C315T	CGC>CGT	Synonymous	ORF1ab:3C-like-proteinase	0.986463591427523
CAMB-7949D	MN908947.3	11074	C	INS	0.025	0.042	4.8e-05	2.9e-10	0.0327817537669138	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.966947910590043
CAMB-7949D	MN908947.3	11075	T	-	0.06	0.051	1.5e-14	1.1e-12	0.0560125248389233	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.939892816282291
CAMB-7949D	MN908947.3	12062	G	A	0.0044	0.008	0.0014	3.4e-05	0.00622497885537074	AGA	ORF1ab:nsp7	E74K	G220A	GAA>AAA	Missense	ORF1ab:nsp7	0.991903016633775
CAMB-7949D	MN908947.3	12089	C	T	0.0043	0.0068	5e-04	4.5e-05	0.00558991558714627	ACA	ORF1ab:nsp7	Q83*	C247T	CAA>TAA	Nonsense	ORF1ab:nsp7	0.99437931423531
CAMB-7949D	MN908947.3	13351	TT	-	0.0043	0.00685	0.0011;0.00033	7.1e-05;2.8e-05	0.00558010930997185	GTT	ORF1ab:nsp10	.	327-328-delfrshift	.	no-SNV	ORF1ab:nsp10	0.994160135238973
CAMB-7949D	MN908947.3	1350	AA	-	0.011	0.00985	2.8e-05;4.4e-06	7.3e-05;8.9e-06	0.0104529616724739	CAA	ORF1ab:nsp2	.	545-546-delfrshift	.	no-SNV	ORF1ab:nsp2	0.98872910998834
CAMB-7949D	MN908947.3	13684	C	T	0.0032	0.0063	0.0011	3.7e-05	0.00464315298426124	ACA	ORF1ab:RNA-dependent-RNA-polymerase	H73Y	C217T	CAT>TAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.995356847015739
CAMB-7949D	MN908947.3	14148	TTA	-	0.00746666666666667	0.000966666666666667	1.4e-05;2.2e-05;1.6e-05	0.0016;NA;NA	0.00373329659732746	CTT	ORF1ab:RNA-dependent-RNA-polymerase	.	681-683-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.994710088027441
CAMB-7949D	MN908947.3	14408	C	T	1	1	0	0	0.999466428420752	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000397076524091377
CAMB-7949D	MN908947.3	18060	C	T	0.0066	0.015	0.00036	8.6e-08	0.011115279992496	TCT	ORF1ab:3'-to-5'-exonuclease	L7L	C21T	CTC>CTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.988837820091924
CAMB-7949D	MN908947.3	18568	C	T	0.014	0.011	4.5e-08	7e-07	0.0126711744985511	TCT	ORF1ab:3'-to-5'-exonuclease	L177F	C529T	CTC>TTC	Missense	ORF1ab:3'-to-5'-exonuclease	0.987314620148872
CAMB-7949D	MN908947.3	186	CAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGAT	-	0.000149444444444444	0.004525	NA;NA;NA;NA;NA;NA;NA;NA;0.15;0.16;0.34;NA;NA;NA;0.00037;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00043;0.00027;0.00028;0.00048;0.00047;0.00047;0.00035;0.00027;0.00026;0.00031;4e-04;0.00032;0.00053;3e-04;0.00054;0.00027;0.00046;0.00054;0.00054;3e-04;0.00025;0.00024;0.00036;9.4e-05;2.1e-08;0.00015;0.00027;0.00025;0.00039;0.00022;0.00024;0.00027;0.00028;0.00033;2e-04;0.00033	0.00189774819430676	GCA	NA	NA	NA	NA	NA	NA	0.997847899605914
CAMB-7949D	MN908947.3	19177	G	T	0.007	0.0064	3.5e-05	6.3e-05	0.00673575129533679	TGG	ORF1ab:3'-to-5'-exonuclease	G380C	G1138T	GGT>TGT	Missense	ORF1ab:3'-to-5'-exonuclease	0.993249009448339
CAMB-7949D	MN908947.3	19904	AT	-	0.014	0.00895	1.2e-07;1.3e-07	2e-05;2.2e-05	0.0118654169149916	CAT	ORF1ab:endoRNAse	.	284-285-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.988039578123301
CAMB-7949D	MN908947.3	20875	GG	-	0.0049	0.00775	0.0015;0.00086	8.3e-05;4.5e-05	0.00622311001843884	TGG	ORF1ab:2'-O-ribose-methyltransferase	.	217-218-delfrshift	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.993722608179748
CAMB-7949D	MN908947.3	21077	C	T	1	1	0	0	0.999882103277529	ACA	ORF1ab:2'-O-ribose-methyltransferase	T140I	C419T	ACA>ATA	Missense	ORF1ab:2'-O-ribose-methyltransferase	1.96494537451859e-05
CAMB-7949D	MN908947.3	22105	A	-	0.0066	0.0094	0.00026	1.7e-05	0.00780937124549459	GAA	S	.	543-543-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.989854492057135
CAMB-7949D	MN908947.3	22105	AA	-	0.0074	0.0047	0.00026;3.3e-05	1.7e-05;NA	0.00635134125382949	GAA	S	.	543-544-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.989854492057135
CAMB-7949D	MN908947.3	23067	GT	-	0.00535	0.0069	0.00014;0.00017	2.8e-05;3.6e-05	0.00613873542050338	GGT	S	.	1505-1506-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.993810651791854
CAMB-7949D	MN908947.3	23403	A	G	1	1	0	0	0.999719429083438	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000271520241834029
CAMB-7949D	MN908947.3	241	C	T	1	1	0	0	0.999858533272974	TCG	NA	NA	NA	NA	NA	NA	0.000141466727025804
CAMB-7949D	MN908947.3	24537	A	-	0.0091	0.0055	1.2e-05	0.00042	0.00744985673352436	CAA	S	.	2975-2975-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.98945558739255
CAMB-7949D	MN908947.3	25079	A	T	0.0067	0.0056	4.1e-05	0.00011	0.0062133571246495	TAA	S	N1173Y	A3517T	AAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.993627326026
CAMB-7949D	MN908947.3	25448	AAATCAAGGATGCTACTCCTTCAGATT	-	0.118148148148148	0.0438888888888889	3.8e-27;5.7e-18;7.8e-18;7.3e-18;2.6e-31;5.7e-50;1.7e-50;3.5e-60;3.5e-53;1e-50;3.8e-50;9.3e-52;1.6e-53;9.1e-55;3e-62;3.4e-52;4.2e-54;3e-50;1.8e-51;4.2e-54;4.4e-52;1.2e-53;1.2e-50;1.5e-52;1.7e-46;7.7e-51;3.8e-50	8.6e-11;1.3e-07;1.3e-07;1.2e-07;2.6e-12;7.1e-19;3.7e-19;5.1e-22;9e-20;6.5e-19;6.3e-19;1.6e-19;5.9e-20;2.6e-20;5.3e-23;2.3e-19;8e-20;6.8e-19;2e-19;3e-20;3.5e-19;3.9e-20;1.4e-22;2.7e-23;2.2e-17;5.1e-19;3.3e-19	0.0753389529608248	GAA	ORF3a	.	56-82-delinframe	.	no-SNV	GU280_gp03	0.923737816375853
CAMB-7949D	MN908947.3	25474	T	G	0.051	0.021	1.3e-23	7.2e-11	0.0350906476298084	TTT	ORF3a	F28V	T82G	TTT>GTT	Missense	GU280_gp03	0.891338400698475
CAMB-7949D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999607403252945	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7949D	MN908947.3	29754	C	T	0.15	0.16	8.6e-62	3.4e-67	0.152904464714354	TCG	NA	NA	NA	NA	NA	NA	0.844815170427268
CAMB-7949D	MN908947.3	3037	C	T	1	1	0	0	0.999705903977649	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000147048011175649
CAMB-7949D	MN908947.3	3093	CAT	-	0.0061	0.0095	5.6e-05;6e-05;5.2e-05	2.1e-06;2.4e-06;2.2e-06	0.00777285282970386	CCA	ORF1ab:nsp3	.	374-376-delinframe	.	no-SNV	ORF1ab:nsp3	0.992162908717158
CAMB-7949D	MN908947.3	4336	ATCTATT	-	0.0108571428571429	0.00242685714285714	3e-07;5.9e-07;2.9e-07;3.8e-07;4.3e-07;3.4e-07;4.4e-07	NA;0.19;0.089;5.2e-06;5.8e-06;NA;NA	0.00595792217464159	CAT	ORF1ab:nsp3	.	1617-1623-delfrshift	.	no-SNV	ORF1ab:nsp3	0.993933138656731
CAMB-7949D	MN908947.3	4375	TG	-	0.0099	0.00195	1.1e-06;2.4e-06	0.0049;0.011	0.00630256995736154	CTG	ORF1ab:nsp3	.	1656-1657-delfrshift	.	no-SNV	ORF1ab:nsp3	0.993474772266012
CAMB-7949D	MN908947.3	4625	AC	-	0.013	0.00255	1.1e-07;1.3e-07	NA;0.00056	0.00827003620359196	AAC	ORF1ab:nsp3	.	1906-1907-delfrshift	.	no-SNV	ORF1ab:nsp3	0.992789656887121
CAMB-7949D	MN908947.3	4815	C	T	0.021	0.0083	2.3e-10	4.3e-05	0.0145423154819217	TCT	ORF1ab:nsp3	S699F	C2096T	TCT>TTT	Missense	ORF1ab:nsp3	0.985424482884558
CAMB-7949D	MN908947.3	71	C	T	0.006	0.015	0.00025	3.4e-08	0.0099714733622883	ACG	NA	NA	NA	NA	NA	NA	0.990002826964098
CAMB-7949D	MN908947.3	8873	C	T	0.012	0.017	1.4e-06	1.7e-08	0.0139116786758936	GCC	ORF1ab:nsp4	P107S	C319T	CCT>TCT	Missense	ORF1ab:nsp4	0.986088321324106
CAMB-7949D	MN908947.3	9644	C	T	0.0057	0.0067	0.00011	4.1e-05	0.00622721378061611	TCA	ORF1ab:nsp4	Q364*	C1090T	CAG>TAG	Nonsense	ORF1ab:nsp4	0.993699380948885
CAMB-794AC	MN908947.3	14408	C	T	1	1	0	0	0.999535363964894	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000361383582860093
CAMB-794AC	MN908947.3	17484	A	G	1	1	0	0	0.999854925286523	CAC	ORF1ab:helicase	T416T	A1248G	ACA>ACG	Synonymous	ORF1ab:helicase	0.000145074713477441
CAMB-794AC	MN908947.3	241	C	T	1	1	0	8.6e-271	0.999717593900028	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-794AC	MN908947.3	25429	G	T	1	1	0	0	1	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0
CAMB-794AC	MN908947.3	28045	C	T	1	1	9.99999999999999e-290	0	1	GCT	ORF8	A51V	C152T	GCT>GTT	Missense	GU280_gp09	0
CAMB-794AC	MN908947.3	3037	C	T	1	1	0	0	0.998831775700935	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-794CA	MN908947.3	14408	C	T	1	1	0	0	0.999473666896937	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000394749827296951
CAMB-794CA	MN908947.3	23403	A	G	1	1	0	0	0.99989127395856	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.21291665372309e-05
CAMB-794CA	MN908947.3	241	C	T	1	1	0	0	0.999946065476512	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-794CA	MN908947.3	28881	GGG	AAC	1	0.996666666666667	0;0;0	0;0;0	0.999810498389236	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-794CA	MN908947.3	3037	C	T	1	1	0	0	0.999183228968146	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-794D9	MN908947.3	10323	A	G	0.03	0.0093	1.2e-08	0.0013	0.0213957402731922	AAG	ORF1ab:3C-like-proteinase	K90R	A269G	AAG>AGG	Missense	ORF1ab:3C-like-proteinase	0.978523337864958
CAMB-794D9	MN908947.3	1059	C	T	1	1	0	0	0.999900640161247	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	7.09713133951257e-05
CAMB-794D9	MN908947.3	10765	C	T	0.0043	0.0082	0.00062	1.3e-05	0.0056359753203607	ACA	ORF1ab:3C-like-proteinase	Y237Y	C711T	TAC>TAT	Synonymous	ORF1ab:3C-like-proteinase	0.994304698623635
CAMB-794D9	MN908947.3	10886	G	T	0.0051	0.011	0.00079	2.8e-06	0.00728372156943586	TGG	ORF1ab:3C-like-proteinase	G278*	G832T	GGA>TGA	Nonsense	ORF1ab:3C-like-proteinase	0.992716278430564
CAMB-794D9	MN908947.3	11075	T	-	0.019	0.03	2e-05	4.8e-08	0.0236230720839931	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.976235927026617
CAMB-794D9	MN908947.3	12437	C	-	0.0042	0.011	0.0067	2e-05	0.0065198983911939	TCC	ORF1ab:nsp8	.	346-346-delfrshift	.	no-SNV	ORF1ab:nsp8	0.993282528930285
CAMB-794D9	MN908947.3	12781	C	T	0.0042	0.0092	0.0013	7.3e-06	0.0060822844033928	ACA	ORF1ab:nsp9	Y32Y	C96T	TAC>TAT	Synonymous	ORF1ab:nsp9	0.993887530562347
CAMB-794D9	MN908947.3	14091	TGATTTCGG	-	0.0082	0.0114444444444444	0.00016;0.00045;9.1e-05;7.3e-05;7.7e-05;0.00011;0.00011;7.7e-06;0.00013	1.9e-06;1.4e-05;1.2e-06;6.9e-07;9e-07;1.5e-06;1.5e-06;6.3e-05;1.9e-06	0.00884955752212389	ATG	ORF1ab:RNA-dependent-RNA-polymerase	.	624-632-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.99070424726443
CAMB-794D9	MN908947.3	14408	C	T	1	1	0	0	0.999295152079899	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000501756146512795
CAMB-794D9	MN908947.3	14825	C	T	0.0048	0.012	0.00022	1e-07	0.00759052210483126	ACA	ORF1ab:RNA-dependent-RNA-polymerase	T453I	C1358T	ACA>ATA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.989691250384655
CAMB-794D9	MN908947.3	15814	G	INS	0.0029	0.0074	0.0043	3.6e-05	0.004779123574481	TGT	ORF1ab:RNA-dependent-RNA-polymerase	.	2346-2347-insfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.99351404657749
CAMB-794D9	MN908947.3	16824	A	T	1	1	0	0	0.999881357943086	GAG	ORF1ab:helicase	G196G	A588T	GGA>GGT	Synonymous	ORF1ab:helicase	1.69488652734699e-05
CAMB-794D9	MN908947.3	19984	T	-	0.028	0.03	4.4e-06	1.8e-05	0.0289855072463768	CTT	ORF1ab:endoRNAse	.	364-364-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.971014492753623
CAMB-794D9	MN908947.3	20849	AT	-	0.00645	0.0093	0.00063;0.00072	4.6e-05;6.6e-05	0.00761446748822763	AAT	ORF1ab:2'-O-ribose-methyltransferase	.	191-192-delfrshift	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.992595479345284
CAMB-794D9	MN908947.3	23403	A	G	1	1	0	0	0.999835256782652	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00013006043474868
CAMB-794D9	MN908947.3	241	C	T	1	1	0	0	0.999289078467964	TCG	NA	NA	NA	NA	NA	NA	0.000159957344708078
CAMB-794D9	MN908947.3	25563	G	T	1	1	0	0	0.99980901732066	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	8.81458520031145e-05
CAMB-794D9	MN908947.3	25603	C	T	0.015	0.0068	3.3e-08	7.6e-05	0.0116474200405236	ACT	ORF3a	L71L	C211T	CTA>TTA	Synonymous	GU280_gp03	0.988327718870809
CAMB-794D9	MN908947.3	2992	T	C	0.0032	0.0081	0.0018	1.5e-05	0.00566011037215226	ATG	ORF1ab:nsp3	D91D	T273C	GAT>GAC	Synonymous	ORF1ab:nsp3	0.994151219282109
CAMB-794D9	MN908947.3	3037	C	T	1	1	0	0	0.999573342435361	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.26657564638621e-05
CAMB-794D9	MN908947.3	6990	C	T	0.0048	0.037	0.0068	6.8e-09	0.0174165457184325	TCT	ORF1ab:nsp3	S1424F	C4271T	TCT>TTT	Missense	ORF1ab:nsp3	0.979680696661829
CAMB-794D9	MN908947.3	8003	G	C	0.0056	0.0071	5.5e-05	9.6e-06	0.00617971836693344	TGT	ORF1ab:nsp3	V1762L	G5284C	GTT>CTT	Missense	ORF1ab:nsp3	0.993752743727417
CAMB-794D9	MN908947.3	8912	C	T	0.0057	0.01	0.00025	3.9e-06	0.00716768027801911	GCA	ORF1ab:nsp4	H120Y	C358T	CAT>TAT	Missense	ORF1ab:nsp4	0.992832319721981
CAMB-794D9	MN908947.3	9942	A	G	0.0058	0.007	9e-05	2.6e-05	0.00630202699524996	TAC	ORF1ab:nsp4	Y463C	A1388G	TAC>TGC	Missense	ORF1ab:nsp4	0.993650942952547
CAMB-794F7	MN908947.3	11074	C	-	0.004	0.0038	1.1e-05	2.6e-05	0.00387147940602532	TCT	ORF1ab:nsp6	.	102-102-delfrshift	.	no-SNV	ORF1ab:nsp6	0.867315739494308
CAMB-794F7	MN908947.3	11074	C	INS	0.11	0.1	2.2e-45	9.6e-41	0.1041229690386	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.867315739494308
CAMB-794F7	MN908947.3	11074	C	T	0.022	0.028	3e-17	1.8e-21	0.0246898120610671	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.867315739494308
CAMB-794F7	MN908947.3	11083	G	-	0.2	0.17	4.1e-87	3.2e-74	0.182768345960294	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	9.2167597559402e-06
CAMB-794F7	MN908947.3	11083	G	T	0.8	0.83	0	0	0.817102619403123	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	9.2167597559402e-06
CAMB-794F7	MN908947.3	14805	C	T	1	1	0	0	0.999034024834002	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000328243988445812
CAMB-794F7	MN908947.3	16320	A	T	0.014	0.01	9.8e-08	3.5e-06	0.0116359182423639	AAT	ORF1ab:helicase	K28N	A84T	AAA>AAT	Missense	ORF1ab:helicase	0.987522008726939
CAMB-794F7	MN908947.3	16375	C	T	0.031	0.023	6.2e-12	2.5e-09	0.0264462224739786	TCC	ORF1ab:helicase	P47S	C139T	CCG>TCG	Missense	ORF1ab:helicase	0.973482971040147
CAMB-794F7	MN908947.3	17761	G	T	0.0083	0.0057	1.4e-05	0.00016	0.00712731292242858	AGC	ORF1ab:helicase	A509S	G1525T	GCT>TCT	Missense	ORF1ab:helicase	0.992078204700112
CAMB-794F7	MN908947.3	20518	G	T	0.0084	0.0044	1e-05	0.00051	0.00655906372580541	TGA	ORF1ab:endoRNAse	D300Y	G898T	GAT>TAT	Missense	ORF1ab:endoRNAse	0.993344479454697
CAMB-794F7	MN908947.3	2480	A	G	1	1	0	0	0.999858986110132	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	7.0506944934076e-05
CAMB-794F7	MN908947.3	25416	CACAATTGGAACTGTAACTTTGAAGCA	-	0.246666666666667	0.231481481481481	2.1e-114;1.4e-112;1.3e-114;2e-115;5.1e-120;1.6e-92;5.8e-89;8.1e-59;1.1e-51;3.7e-56;9.7e-63;1.1e-51;7.9e-53;1.1e-56;2.8e-50;2.6e-64;3.1e-52;1.1e-53;1.4e-54;4.4e-64;5.9e-46;1.3e-61;8.1e-70;1.9e-46;2.4e-61;1.2e-37;3.7e-47	2.2e-108;1.7e-106;5e-108;5.3e-109;9.1e-114;1.4e-85;7.2e-84;1.6e-55;5.9e-49;4e-53;3.1e-60;1e-48;1.5e-49;8.9e-54;5.5e-48;4.4e-60;1.8e-49;4e-49;2.2e-49;1.6e-57;2.3e-43;5.5e-58;1.2e-58;1.6e-43;4.5e-57;1.8e-35;6.4e-44	0.233721249256939	TCA	ORF3a	.	24-50-delinframe	.	no-SNV	GU280_gp03	0.766393583107668
CAMB-794F7	MN908947.3	25439	AGCA	-	0.2425	0.2275	1.9e-46;2.4e-61;1.2e-37;3.7e-47	1.6e-43;4.5e-57;1.8e-35;6.4e-44	0.233512747551624	AAG	ORF3a	.	47-50-delfrshift	.	no-SNV	GU280_gp03	0.769354856904351
CAMB-794F7	MN908947.3	2558	C	T	1	1	0	0	0.999052711993888	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000183346065699007
CAMB-794F7	MN908947.3	26144	G	T	1	1	0	0	0.999655231856576	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000258576107567661
CAMB-794F7	MN908947.3	26211	G	T	0.0088	0.0057	1.3e-05	0.00023	0.0072976054732041	TGC	ORF3a	V273V	G819T	GTG>GTT	Synonymous	GU280_gp03	0.992702394526796
CAMB-794F7	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.027625	0.029125	0.00021;0.00071;0.00021;2e-04;5.7e-05;0.00013;9.8e-05;0.00019;0.00014;0.00016;0.00027;0.00012;0.00024;0.00016;0.00016;0.00014;0.00026;0.00015;2e-04;0.00015;0.00011;0.00021;0.00014;4.8e-05;0.00014;0.00022;0.00019;0.00014;0.00026;0.00013;0.00024;2e-04	0.00012;0.00032;0.00011;0.00011;5.2e-05;6.3e-05;5.5e-05;0.00011;7.3e-05;7.4e-05;0.00011;6.6e-05;0.00012;9.3e-05;8.6e-05;6e-05;0.00013;8.2e-05;9.8e-05;8e-05;6.5e-05;0.00011;7.6e-05;6.9e-05;6.4e-05;9.5e-05;1e-04;6.6e-05;0.00011;4.3e-05;7e-05;6e-05	0.0282618935468676	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.971406667385393
CAMB-794F7	MN908947.3	27211	C	T	0.0085	0.0051	1e-05	0.00019	0.00698061184296906	TCT	ORF6	L4F	C10T	CTC>TTC	Missense	GU280_gp06	0.98980991144762
CAMB-794F7	MN908947.3	373	G	T	0.0088	0.013	6.7e-06	7.4e-08	0.0106589934918906	AGG	ORF1ab:leader-protein	E36D	G108T	GAG>GAT	Missense	ORF1ab:leader-protein	0.98903212870992
CAMB-794F7	MN908947.3	4084	C	T	0.0095	0.0075	6e-06	3.8e-05	0.00859529878221467	ACA	ORF1ab:nsp3	D455D	C1365T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.991333899745115
CAMB-794F7	MN908947.3	8016	C	T	0.0079	0.015	6.5e-05	3.4e-08	0.0109634055265123	GCG	ORF1ab:nsp3	A1766V	C5297T	GCG>GTG	Missense	ORF1ab:nsp3	0.988991784914115
CAMB-79503	MN908947.3	10029	C	T	0.0073	0.0075	5.9e-05	4.7e-05	0.00741015190811412	ACC	ORF1ab:nsp4	T492I	C1475T	ACC>ATC	Missense	ORF1ab:nsp4	0.992437286140836
CAMB-79503	MN908947.3	11075	T	-	0.041	0.044	3.6e-10	8e-11	0.0424871385488735	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953698775944651
CAMB-79503	MN908947.3	12899	C	T	0.006	0.0078	0.00012	2e-05	0.00688715953307393	ACC	ORF1ab:nsp9	P72S	C214T	CCT>TCT	Missense	ORF1ab:nsp9	0.993112840466926
CAMB-79503	MN908947.3	13482	A	G	0.035	0.038	1.6e-16	5.2e-18	0.0358803525574294	TAA	ORF1ab:RNA-dependent-RNA-polymerase	V5V	A15G	GTA>GTG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.96400397899461
CAMB-79503	MN908947.3	13968	C	T	0.006	0.0084	0.00015	1.1e-05	0.00702481016770212	CCA	ORF1ab:RNA-dependent-RNA-polymerase	A167A	C501T	GCC>GCT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.992853372314939
CAMB-79503	MN908947.3	14408	C	T	1	1	0	0	0.999000429721802	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00070997515086972
CAMB-79503	MN908947.3	15173	C	T	0.016	0.014	1.3e-08	6.1e-08	0.01515909903468	TCA	ORF1ab:RNA-dependent-RNA-polymerase	S569L	C1706T	TCA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.984650220474318
CAMB-79503	MN908947.3	15546	C	A	0.012	0.013	4.9e-07	1.2e-07	0.012286747864803	CCA	ORF1ab:RNA-dependent-RNA-polymerase	A693A	C2079A	GCC>GCA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.987659738424984
CAMB-79503	MN908947.3	1670	C	T	0.0088	0.0086	3.1e-05	3.6e-05	0.00870868438107583	ACT	ORF1ab:nsp2	L289F	C865T	CTT>TTT	Missense	ORF1ab:nsp2	0.991291315618924
CAMB-79503	MN908947.3	17061	A	T	0.017	0.013	1e-08	1.8e-07	0.0150689119302983	AAA	ORF1ab:helicase	Q275H	A825T	CAA>CAT	Missense	ORF1ab:helicase	0.984854660790258
CAMB-79503	MN908947.3	19118	C	T	0.023	0.021	1.3e-11	8.7e-11	0.0217290167209436	GCT	ORF1ab:3'-to-5'-exonuclease	A360V	C1079T	GCT>GTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.978147833939958
CAMB-79503	MN908947.3	19259	C	T	0.027	0.025	2e-13	9.6e-13	0.0261837947720795	TCT	ORF1ab:3'-to-5'-exonuclease	S407F	C1220T	TCT>TTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.973772013169233
CAMB-79503	MN908947.3	20268	A	G	1	1	2.4e-308	2.3e-271	0.998242530755712	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-79503	MN908947.3	22381	G	T	0.0063	0.02	0.0021	1e-05	0.014475271411339	GGA	S	R273S	G819T	AGG>AGT	Missense	GU280_gp02, spike glycoprotein	0.985524728588661
CAMB-79503	MN908947.3	23403	A	G	1	1	0	0	0.999872990257606	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.9653935807782e-05
CAMB-79503	MN908947.3	23415	C	T	0.016	0.02	1.4e-08	1.9e-10	0.0174174399819664	ACA	S	T618I	C1853T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0.982334598189127
CAMB-79503	MN908947.3	23481	C	T	0.0082	0.0096	3.2e-05	6.4e-06	0.00880823847697889	TCT	S	S640F	C1919T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.991048386091336
CAMB-79503	MN908947.3	241	C	T	1	1	0	0	0.99936214918205	TCG	NA	NA	NA	NA	NA	NA	0.000187603181749962
CAMB-79503	MN908947.3	26259	T	C	0.0077	0.005	3e-05	0.00042	0.00648560380817402	TTT	E	V5V	T15C	GTT>GTC	Synonymous	GU280_gp04	0.993483585722428
CAMB-79503	MN908947.3	27970	C	A	0.016	0.02	2.2e-08	5.5e-10	0.017879847425302	ACT	ORF8	T26N	C77A	ACT>AAT	Missense	GU280_gp09	0.981881754609027
CAMB-79503	MN908947.3	28048	G	T	0.0096	0.01	1.2e-05	6.9e-06	0.00997876857749469	AGA	ORF8	R52I	G155T	AGA>ATA	Missense	GU280_gp09	0.989879688605803
CAMB-79503	MN908947.3	28253	C	T	0.035	0.04	9.5e-16	5.3e-18	0.0371818845206604	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.962419045881602
CAMB-79503	MN908947.3	2937	C	T	1	1	0	0	0.999976265071679	ACA	ORF1ab:nsp3	T73I	C218T	ACA>ATA	Missense	ORF1ab:nsp3	2.37349283205165e-05
CAMB-79503	MN908947.3	29738	CCACGCGGAGTACGATCGAGT	-	0.0669047619047619	0.0695714285714286	4.4e-27;5e-27;8.8e-29;5e-27;9.3e-27;1.3e-27;4e-27;4.9e-27;1.2e-27;2.9e-24;4.9e-22;1.6e-22;2.3e-18;2.4e-18;9.3e-23;5.7e-22;2.2e-22;1e-21;6.7e-25;8.6e-20;7.9e-22	1.4e-28;1.9e-28;1e-29;2.3e-28;3.6e-28;9.1e-29;1.8e-28;3e-28;5.8e-29;1.5e-25;4.9e-23;2.1e-23;3.9e-19;3.6e-19;2.3e-23;2e-23;3.2e-23;8.3e-23;8.9e-25;1.1e-20;6.2e-23	0.0671063778288757	GCC	NA	NA	NA	NA	NA	NA	0.932622190080154
CAMB-79503	MN908947.3	3037	C	T	1	1	0	0	0.999441886423887	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.58113576112739e-05
CAMB-79503	MN908947.3	3096	C	T	0.034	0.035	4.3e-13	3.1e-13	0.0344416607885584	TCA	ORF1ab:nsp3	S126L	C377T	TCA>TTA	Missense	ORF1ab:nsp3	0.965388076764041
CAMB-79503	MN908947.3	635	C	T	0.023	0.025	1.9e-11	2.8e-12	0.024215338874501	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.975747262918743
CAMB-79503	MN908947.3	6481	A	G	0.063	0.069	7.2e-29	1.3e-31	0.0660028229742351	TAG	ORF1ab:nsp3	V1254V	A3762G	GTA>GTG	Synonymous	ORF1ab:nsp3	0.933407301812462
CAMB-79512	MN908947.3	11075	T	-	0.035	0.04	9.1e-09	6e-10	0.0373087961182283	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957247255835971
CAMB-79512	MN908947.3	14408	C	T	1	1	0	0	0.998865114734132	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00074736346776649
CAMB-79512	MN908947.3	23403	A	G	1	1	0	0	0.999443785769698	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.85488663475753e-05
CAMB-79512	MN908947.3	241	C	T	1	1	0	0	0.999158714213963	TCG	NA	NA	NA	NA	NA	NA	6.27825213460573e-05
CAMB-79512	MN908947.3	25496	T	C	0.29	0.26	1.3e-146	1e-128	0.279565749824566	ATA	ORF3a	I35T	T104C	ATA>ACA	Missense	GU280_gp03	0.720062743371355
CAMB-79512	MN908947.3	26137	A	C	0.028	0.018	1.3e-06	0.00091	0.0227333511634127	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.976731746456272
CAMB-79512	MN908947.3	28359	A	G	0.0089	0.0081	5.7e-06	1.1e-05	0.00848479719007215	AAT	N	N29S	A86G	AAT>AGT	Missense	GU280_gp10	0.991335350500413
CAMB-79512	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999099369558691	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79512	MN908947.3	3037	C	T	1	1	0	0	0.999411126607779	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.29800092980009e-05
CAMB-79512	MN908947.3	3429	C	T	1	1	0	0	0.999554310454603	ACA	ORF1ab:nsp3	T237I	C710T	ACA>ATA	Missense	ORF1ab:nsp3	0.00027590305191222
CAMB-79512	MN908947.3	6123	G	A	1	1	0	0	0.999088942033937	AGA	ORF1ab:nsp3	R1135K	G3404A	AGA>AAA	Missense	ORF1ab:nsp3	0
CAMB-79530	MN908947.3	11083	G	T	0.065	0.11	3.3e-14	1.9e-23	0.0800347222222222	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.917643229166667
CAMB-79530	MN908947.3	12855	C	T	0.06	0.032	4e-28	6.4e-16	0.0493739664540515	CCT	ORF1ab:nsp9	P57L	C170T	CCT>CTT	Missense	ORF1ab:nsp9	0.950592285106814
CAMB-79530	MN908947.3	14408	C	T	1	1	0	0	0.999109150299071	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000636321214949306
CAMB-79530	MN908947.3	16985	C	T	0.045	0.044	6.8e-21	1.1e-20	0.0445900086812406	ACT	ORF1ab:helicase	T250I	C749T	ACT>ATT	Missense	ORF1ab:helicase	0.955331070949412
CAMB-79530	MN908947.3	2164	G	A	1	1	0	0	0.998454404945904	AGA	ORF1ab:nsp2	E453E	G1359A	GAG>GAA	Synonymous	ORF1ab:nsp2	0.000515198351365276
CAMB-79530	MN908947.3	23403	A	G	1	1	0	0	0.999851101846337	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000148898153662895
CAMB-79530	MN908947.3	241	C	T	1	1	0	0	0.999610500895848	TCG	NA	NA	NA	NA	NA	NA	0.000311599283321648
CAMB-79530	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999164578111946	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79530	MN908947.3	3037	C	T	1	1	0	0	0.999388753056235	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79530	MN908947.3	5932	T	C	0.0022	0.1	0.0074	9e-44	0.0413402233705618	GTA	ORF1ab:nsp3	C1071C	T3213C	TGT>TGC	Synonymous	ORF1ab:nsp3	0.958576429404901
CAMB-79530	MN908947.3	9838	A	-	0.029	0.06	3.9e-13	1.7e-23	0.0414214083278832	TAA	ORF1ab:nsp4	.	1284-1284-delfrshift	.	no-SNV	ORF1ab:nsp4	0.958578591672117
CAMB-7954F	MN908947.3	10721	T	C	0.0097	0.0097	3.2e-06	3.5e-06	0.00968868945964348	ATT	ORF1ab:3C-like-proteinase	F223L	T667C	TTT>CTT	Missense	ORF1ab:3C-like-proteinase	0.990099230932369
CAMB-7954F	MN908947.3	11075	T	-	0.04	0.038	5.7e-10	1.8e-09	0.0391597927892947	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956180807439887
CAMB-7954F	MN908947.3	11866	C	T	0.064	0.057	5.3e-24	4.8e-22	0.0602261553588987	GCA	ORF1ab:nsp7	C8C	C24T	TGC>TGT	Synonymous	ORF1ab:nsp7	0.939036381514258
CAMB-7954F	MN908947.3	13730	C	T	1	1	0	0	0.998043243393628	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A88V	C263T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	4.17317759652792e-05
CAMB-7954F	MN908947.3	14408	C	T	1	1	0	0	0.997906309504321	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000585888698379328
CAMB-7954F	MN908947.3	23403	A	G	1	1	0	0	0.999353078877692	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.66928992070214e-05
CAMB-7954F	MN908947.3	241	C	T	1	1	0	0	0.997791108127423	TCG	NA	NA	NA	NA	NA	NA	0.000205730125387097
CAMB-7954F	MN908947.3	25350	C	T	0.016	0.015	1.4e-08	2.8e-08	0.0158771093793799	CCA	S	P1263L	C3788T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	0.984010764141952
CAMB-7954F	MN908947.3	25429	G	T	1	1	0	0	0.99894167895075	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	7.55943606606947e-05
CAMB-7954F	MN908947.3	25844	C	T	0.0075	0.0093	3.4e-05	5.6e-06	0.00839601652717449	ACT	ORF3a	T151I	C452T	ACT>ATT	Missense	GU280_gp03	0.991603983472826
CAMB-7954F	MN908947.3	27625	C	T	0.0082	0.015	0.0028	6.3e-06	0.012987012987013	ACG	ORF7a	R78C	C232T	CGT>TGT	Missense	GU280_gp07	0.987012987012987
CAMB-7954F	MN908947.3	3037	C	T	1	1	0	0	0.998733308703225	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000184725814113052
CAMB-7954F	MN908947.3	7843	C	T	0.053	0.052	3.5e-23	7e-23	0.0522605029800843	ACC	ORF1ab:nsp3	N1708N	C5124T	AAC>AAT	Synonymous	ORF1ab:nsp3	0.947739497019916
CAMB-7955E	MN908947.3	11075	T	-	0.073	0.12	1e-18	1.1e-30	0.0913844325609031	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.874113685878392
CAMB-7955E	MN908947.3	11195	C	T	1	1	0	0	0.999725576289791	TCT	ORF1ab:nsp6	L75F	C223T	CTT>TTT	Missense	ORF1ab:nsp6	0
CAMB-7955E	MN908947.3	1230	A	G	0.075	0.077	4.5e-34	2e-34	0.0757187391756148	AAG	ORF1ab:nsp2	K142R	A425G	AAG>AGG	Missense	ORF1ab:nsp2	0.924281260824385
CAMB-7955E	MN908947.3	14408	C	T	1	1	0	0	0.999020328190056	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000816393174953057
CAMB-7955E	MN908947.3	15216	C	T	1	1	0	0	0.999827124211254	GCA	ORF1ab:RNA-dependent-RNA-polymerase	S583S	C1749T	AGC>AGT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	8.64378943728931e-05
CAMB-7955E	MN908947.3	15678	C	T	0.075	0.046	2.4e-34	8.2e-22	0.0618680658031371	ACG	ORF1ab:RNA-dependent-RNA-polymerase	Y737Y	C2211T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.938131934196863
CAMB-7955E	MN908947.3	23403	A	G	1	1	0	0	0.999878831939901	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.07787067329052e-05
CAMB-7955E	MN908947.3	241	C	T	1	1	0	0	0.99975301323849	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-7955E	MN908947.3	26533	C	T	0.21	0.16	2.8e-87	6.7e-63	0.191494002181025	TCC	M	S4F	C11T	TCC>TTC	Missense	GU280_gp05	0.808287895310796
CAMB-7955E	MN908947.3	28041	G	A	0.045	0.019	2.2e-15	9.5e-08	0.0330769230769231	AGG	ORF8	G50R	G148A	GGA>AGA	Missense	GU280_gp09	0.966923076923077
CAMB-7955E	MN908947.3	2842	C	T	0.048	0.018	4.3e-08	0.00013	0.0324074074074074	CCT	ORF1ab:nsp3	A41A	C123T	GCC>GCT	Synonymous	ORF1ab:nsp3	0.967592592592593
CAMB-7955E	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999536393138618	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7955E	MN908947.3	29730	C	T	0.016	0.0087	9.3e-08	2.1e-05	0.0117860380779692	TCA	NA	NA	NA	NA	NA	NA	0.988213961922031
CAMB-7955E	MN908947.3	3037	C	T	1	1	0	0	0.996287894411219	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00226850897092184
CAMB-7955E	MN908947.3	3373	C	A	1	1	0	0	0.999785131070047	ACA	ORF1ab:nsp3	D218E	C654A	GAC>GAA	Missense	ORF1ab:nsp3	0.000214868929952729
CAMB-7955E	MN908947.3	5654	C	T	0.88	1	0	7.00091020157046e-321	0.902335456475584	TCT	ORF1ab:nsp3	L979L	C2935T	CTA>TTA	Synonymous	ORF1ab:nsp3	0.0976645435244161
CAMB-7955E	MN908947.3	5886	C	T	0.12	0.22	1.1e-45	1.6e-49	0.138354700854701	ACA	ORF1ab:nsp3	T1056I	C3167T	ACA>ATA	Missense	ORF1ab:nsp3	0.861645299145299
CAMB-7956D	MN908947.3	1059	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0
CAMB-7956D	MN908947.3	13006	T	C	1	1	0	0	0.999697725383511	CTG	ORF1ab:nsp9	A107A	T321C	GCT>GCC	Synonymous	ORF1ab:nsp9	0.00022670596236681
CAMB-7956D	MN908947.3	14408	C	T	1	1	0	0	0.998982517805938	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000739987050226621
CAMB-7956D	MN908947.3	19005	A	G	0.004	0.016	0.0013	3.9e-08	0.0100172711571675	TAG	ORF1ab:3'-to-5'-exonuclease	L322L	A966G	TTA>TTG	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.989982728842832
CAMB-7956D	MN908947.3	23403	A	G	1	1	0	0	0.999958954151788	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.10458482124533e-05
CAMB-7956D	MN908947.3	24070	A	T	1	1	0	1.3e-294	1	AAT	S	Q836H	A2508T	CAA>CAT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7956D	MN908947.3	241	C	T	1	1	0	0	0.999843859786088	TCG	NA	NA	NA	NA	NA	NA	7.80701069560465e-05
CAMB-7956D	MN908947.3	25563	G	T	1	1	0	0	0.999869876382563	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	6.50618087182824e-05
CAMB-7956D	MN908947.3	27945	C	T	1	1	1.699999999988e-313	1.5e-137	1	CCA	ORF8	Q18*	C52T	CAA>TAA	Nonsense	GU280_gp09	0
CAMB-7956D	MN908947.3	3037	C	T	1	1	0	1e-297	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7956D	MN908947.3	516	TTATG	-	0.17	0.286	3.9e-07;1.7e-06;2.1e-06;NA;NA	4.7e-07;2.4e-06;5.8e-07;2.5e-05;6.9e-05	0.281861231212683	GTT	ORF1ab:leader-protein	.	251-255-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.710509621484458
CAMB-7957C	MN908947.3	11075	T	-	0.045	0.045	5.3e-11	4.5e-11	0.044813082677528	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951799584514465
CAMB-7957C	MN908947.3	14408	C	T	1	1	0	0	0.998089229023815	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000756346844739906
CAMB-7957C	MN908947.3	23403	A	G	1	1	0	0	0.999580061940864	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.24878330446259e-05
CAMB-7957C	MN908947.3	241	C	T	1	1	0	0	0.997749313209546	TCG	NA	NA	NA	NA	NA	NA	0.000148942508191838
CAMB-7957C	MN908947.3	26137	A	C	0.029	0.016	2.2e-06	0.0029	0.0220170454545455	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.977627840909091
CAMB-7957C	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999488996388908	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	3.78558449424591e-05
CAMB-7957C	MN908947.3	3037	C	T	1	1	0	0	0.998233133398428	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000185985958060166
CAMB-7958B	MN908947.3	11074	C	INS	0.11	0.083	5.5e-42	2.4e-24	0.0992945209995385	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.886216786444254
CAMB-7958B	MN908947.3	11074	C	T	0.012	0.014	3.1e-08	5.5e-08	0.0130381749851652	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.886216786444254
CAMB-7958B	MN908947.3	11076	T	C	0.012	0.0073	6.2e-06	0.00056	0.0104445756323509	TTT	ORF1ab:nsp6	F35S	T104C	TTT>TCT	Missense	ORF1ab:nsp6	0.989525150235381
CAMB-7958B	MN908947.3	11083	G	-	0.12	0.2	2.2e-53	2.8e-91	0.153763048397693	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-7958B	MN908947.3	11083	G	T	0.88	0.8	0	0	0.846163953573253	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-7958B	MN908947.3	11960	C	T	0.009	0.0078	1.1e-05	3.2e-05	0.00848919712532706	TCT	ORF1ab:nsp7	L40F	C118T	CTC>TTC	Missense	ORF1ab:nsp7	0.991499377306537
CAMB-7958B	MN908947.3	11960	CT	TC	0.004575	0.0079	1.1e-05;0.46	3.2e-05;3.1e-05	0.00610173423815324	TCT	ORF1ab:nsp7	.	118-119-mnv	.	no-SNV	ORF1ab:nsp7	0.991499377306537
CAMB-7958B	MN908947.3	14333	GTGT	TGTG	0.00180675	0.0107	NA;NA;5.3e-05;NA	7.7e-09;1.2e-06;2.3e-05;1.5e-06	0.00423127083031445	TGT	ORF1ab:RNA-dependent-RNA-polymerase	.	866-869-mnv	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.987892610268756
CAMB-7958B	MN908947.3	14409	TAC	CTT	0.00470366666666667	0.0188666666666667	0.45;0.45;5.8e-08	5.6e-06;2.7e-06;4.6e-18	0.00413950119010659	CTA	ORF1ab:RNA-dependent-RNA-polymerase	.	942-944-mnv	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.995773232442658
CAMB-7958B	MN908947.3	14411	C	T	0.014	0.038	5.8e-08	4.6e-18	0.0248671998132041	ACA	ORF1ab:RNA-dependent-RNA-polymerase	T315I	C944T	ACA>ATA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.969543517599673
CAMB-7958B	MN908947.3	14805	C	T	1	1	0	0	0.99992163500721	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	1.56729985580841e-05
CAMB-7958B	MN908947.3	14852	T	C	0.0055	0.0087	0.00011	3.7e-06	0.00683810817485799	TTT	ORF1ab:RNA-dependent-RNA-polymerase	F462S	T1385C	TTT>TCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993146455915041
CAMB-7958B	MN908947.3	14999	G	T	0.0027	0.0061	0.00078	3.3e-05	0.00396982929734021	AGT	ORF1ab:RNA-dependent-RNA-polymerase	S511I	G1532T	AGT>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.99603017070266
CAMB-7958B	MN908947.3	15054	TA	-	0.0065	0.00955	NA;2.4e-07	6e-06;3e-06	0.00723000451875282	CTA	ORF1ab:RNA-dependent-RNA-polymerase	.	1587-1588-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.996184284906727
CAMB-7958B	MN908947.3	15055	A	-	0.013	0.01	2.4e-07	3e-06	0.0117760929182126	TAT	ORF1ab:RNA-dependent-RNA-polymerase	.	1588-1588-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.987901274399097
CAMB-7958B	MN908947.3	15952	C	T	0.03	0.027	6.9e-13	8.8e-12	0.0290211120268814	CCT	ORF1ab:RNA-dependent-RNA-polymerase	L829L	C2485T	CTA>TTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.970963038103088
CAMB-7958B	MN908947.3	16246	GC	CT	0.01865	0.036	2e-05;5.1e-12	NA;9.4e-27	0.0243745991019885	GGC	ORF1ab:helicase	.	10-11-mnv	.	no-SNV	ORF1ab:helicase	0.995022554051952
CAMB-7958B	MN908947.3	16247	C	T	0.03	0.072	5.1e-12	9.4e-27	0.0458533355404734	GCT	ORF1ab:helicase	A4V	C11T	GCT>GTT	Missense	ORF1ab:helicase	0.954146664459527
CAMB-7958B	MN908947.3	16318	A	G	0.038	0.0049	2.1e-17	0.00043	0.0253326919993587	TAA	ORF1ab:helicase	K28E	A82G	AAA>GAA	Missense	ORF1ab:helicase	0.974667308000641
CAMB-7958B	MN908947.3	17547	C	A	0.018	0.005	4.2e-10	0.00011	0.0119396984924623	TCC	ORF1ab:helicase	F437L	C1311A	TTC>TTA	Missense	ORF1ab:helicase	0.988
CAMB-7958B	MN908947.3	17934	C	T	0.071	0.12	8.7e-33	2.5e-55	0.0914535679973835	CCA	ORF1ab:helicase	T566T	C1698T	ACC>ACT	Synonymous	ORF1ab:helicase	0.908485108644549
CAMB-7958B	MN908947.3	18290	G	T	0.0089	0.0026	6.9e-06	0.0049	0.00626944129632755	CGT	ORF1ab:3'-to-5'-exonuclease	R84L	G251T	CGT>CTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.993622049142775
CAMB-7958B	MN908947.3	2229	G	T	0.0075	0.012	1.8e-05	1.7e-07	0.00976591995972816	TGT	ORF1ab:nsp2	C475F	G1424T	TGT>TTT	Missense	ORF1ab:nsp2	0.989680342310597
CAMB-7958B	MN908947.3	23766	C	T	0.017	0.035	2.9e-09	2.6e-16	0.024	TCA	S	S735L	C2204T	TCA>TTA	Missense	GU280_gp02, spike glycoprotein	0.976
CAMB-7958B	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-7958B	MN908947.3	25135	G	C	0.0035	0.0083	0.00068	6.5e-06	0.00563421505140307	AGA	S	K1191N	G3573C	AAG>AAC	Missense	GU280_gp02, spike glycoprotein	0.994292613324553
CAMB-7958B	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-7958B	MN908947.3	26069	A	G	0.012	0.013	3.1e-06	4.4e-06	0.0120525931336742	GAA	ORF3a	E226G	A677G	GAA>GGA	Missense	GU280_gp03	0.987947406866326
CAMB-7958B	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7958B	MN908947.3	26227	G	T	0.0081	0.0048	9.1e-06	0.00026	0.00661778529798834	AGC	NA	NA	NA	NA	NA	NA	0.993344613649182
CAMB-7958B	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0351351351351351	0.0145405405405405	4.6e-05;3.7e-05;1.7e-05;2.2e-05;6.1e-05;5.5e-08;8.4e-07;8.6e-06;8e-06;1.8e-06;4.4e-06;3e-06;7.7e-06;4.9e-06;6.5e-06;1.1e-05;4.2e-06;9.8e-06;5.4e-06;6.1e-06;5.3e-06;1.1e-05;5.9e-06;7.8e-06;5.1e-06;2.4e-06;7.2e-06;4.8e-06;5.7e-06;4.9e-06;8.7e-06;6.1e-06;2.6e-06;7.6e-06;2.6e-06;4.6e-06;2.7e-06	0.017;0.0033;0.014;0.015;0.022;0.0069;0.014;0.028;0.028;0.016;0.023;0.022;0.027;0.025;0.027;0.032;0.023;0.03;0.024;0.024;0.025;0.032;0.025;0.027;0.024;0.021;0.028;0.023;0.018;0.024;0.029;0.026;0.019;0.028;0.021;0.022;0.019	0.0263521953447141	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.977570567882763
CAMB-7958B	MN908947.3	28881	G	T	0.092	0.089	2.2e-40	9.1e-39	0.090790939472707	AGG	N	R203M	G608T	AGG>ATG	Missense	GU280_gp10	0.909147171679663
CAMB-7958B	MN908947.3	28887	C	T	0.036	0.043	9.1e-17	1.9e-19	0.039265357821406	ACT	N	T205I	C614T	ACT>ATT	Missense	GU280_gp10	0.960671310956301
CAMB-7958B	MN908947.3	3351	G	T	0.0072	0.014	7.9e-05	1.3e-07	0.00938064664949445	AGT	ORF1ab:nsp3	S211I	G632T	AGT>ATT	Missense	ORF1ab:nsp3	0.990542462804198
CAMB-7958B	MN908947.3	5393	T	C	0.012	0.013	4e-05	4e-05	0.0122123062470643	CTT	ORF1ab:nsp3	F892L	T2674C	TTT>CTT	Missense	ORF1ab:nsp3	0.987787693752936
CAMB-7958B	MN908947.3	5918	G	C	0.0087	0.012	4.3e-06	2e-07	0.00979928363857539	GGA	ORF1ab:nsp3	D1067H	G3199C	GAT>CAT	Missense	ORF1ab:nsp3	0.989930391295533
CAMB-7958B	MN908947.3	5924	G	C	0.008	0.00061	1.1e-05	0.0067	0.00518440740254627	TGT	ORF1ab:nsp3	V1069L	G3205C	GTT>CTT	Missense	ORF1ab:nsp3	0.989663997899987
CAMB-7958B	MN908947.3	6231	C	T	0.054	0.054	1.9e-25	8.3e-26	0.0537851631326326	CCT	ORF1ab:nsp3	P1171L	C3512T	CCT>CTT	Missense	ORF1ab:nsp3	0.946154079834741
CAMB-7958B	MN908947.3	6573	C	-	0.0089	0.0062	9.6e-06	0.00011	0.00766703176341731	TCT	ORF1ab:nsp3	.	3854-3854-delfrshift	.	no-SNV	ORF1ab:nsp3	0.991894852135816
CAMB-7958B	MN908947.3	7749	C	T	0.024	0.012	4.5e-11	8.2e-06	0.0200113271663206	ACA	ORF1ab:nsp3	T1677I	C5030T	ACA>ATA	Missense	ORF1ab:nsp3	0.979988672833679
CAMB-7958B	MN908947.3	7800	C	T	0.015	0.018	3.3e-08	1.3e-08	0.0160030481996571	ACT	ORF1ab:nsp3	T1694I	C5081T	ACT>ATT	Missense	ORF1ab:nsp3	0.983806439321776
CAMB-7958B	MN908947.3	789	G	T	0.011	0.0038	4.7e-07	0.0011	0.00800585875734425	CGT	ORF1ab:leader-protein	R175L	G524T	CGT>CTT	Missense	ORF1ab:leader-protein	0.991844343469649
CAMB-7958B	MN908947.3	8482	TT	-	0.0195	0.00435	1.8e-08;4.5e-09	0.0088;0.0032	0.0135915732246007	CTT	ORF1ab:nsp3	.	5763-5764-delfrshift	.	no-SNV	ORF1ab:nsp3	0.975749410575952
CAMB-7958B	MN908947.3	8934	G	T	0.0097	0.0091	1.5e-06	2.3e-06	0.00943928478430692	AGT	ORF1ab:nsp4	S127I	G380T	AGT>ATT	Missense	ORF1ab:nsp4	0.990495616699939
CAMB-7958B	MN908947.3	9866	C	T	0.082	0.12	7.1e-37	2.4e-53	0.10085514720282	TCT	ORF1ab:nsp4	L438F	C1312T	CTT>TTT	Missense	ORF1ab:nsp4	0.89914485279718
CAMB-7958B	MN908947.3	9989	AG	-	0.0185	0.00835	6.9e-10;3.6e-10	6.1e-06;5e-06	0.0132767588283603	CAG	ORF1ab:nsp4	.	1435-1436-delfrshift	.	no-SNV	ORF1ab:nsp4	0.986760752688172
CAMB-7959A	MN908947.3	12974	C	T	0.25	0.26	1.8e-122	4.1e-122	0.256830025793546	CCT	ORF1ab:nsp9	L97L	C289T	CTA>TTA	Synonymous	ORF1ab:nsp9	0.743117334315945
CAMB-7959A	MN908947.3	14408	C	T	1	1	0	0	0.999551703526599	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-7959A	MN908947.3	23403	A	G	1	1	0	0	0.999929027679205	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.097232079489e-05
CAMB-7959A	MN908947.3	241	C	T	1	1	0	0	0.998231913953146	TCG	NA	NA	NA	NA	NA	NA	0.00162074554294976
CAMB-7959A	MN908947.3	28881	GGG	AAC	1	0.98	0;0;0	0;0;0	0.9917914051183	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00942872989462008
CAMB-7959A	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-795A9	MN908947.3	11075	T	-	0.0063	0.046	0.007	9.2e-12	0.0235051546391753	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.968583428789614
CAMB-795A9	MN908947.3	14408	C	T	1	1	0	0	0.999153876426604	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000629673356946084
CAMB-795A9	MN908947.3	15104	G	T	0.013	0.011	3.4e-07	5.9e-06	0.0121951219512195	CGC	ORF1ab:RNA-dependent-RNA-polymerase	R546L	G1637T	CGC>CTC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.98780487804878
CAMB-795A9	MN908947.3	15530	G	T	0.0067	0.01	2.8e-05	8.4e-07	0.00813102567080962	TGT	ORF1ab:RNA-dependent-RNA-polymerase	C688F	G2063T	TGT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.991843161549283
CAMB-795A9	MN908947.3	20965	T	C	0.025	0.026	2.6e-12	1.3e-12	0.0255127703571229	CTT	ORF1ab:2'-O-ribose-methyltransferase	F103L	T307C	TTT>CTT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.974235734644833
CAMB-795A9	MN908947.3	23143	T	INS	0.013	0.01	3e-07	7.2e-06	0.0118663375735713	CTA	S	.	1580-1581-insfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.988133662426429
CAMB-795A9	MN908947.3	23403	A	G	1	1	0	0	0.999742409872727	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00014050370578524
CAMB-795A9	MN908947.3	241	C	T	1	1	0	0	0.999766518795237	TCG	NA	NA	NA	NA	NA	NA	5.83703011907541e-05
CAMB-795A9	MN908947.3	26882	C	T	0.0027	0.0086	0.0043	9e-06	0.00555006462404014	TCA	M	L120L	C360T	CTC>CTT	Synonymous	GU280_gp05	0.994441487789013
CAMB-795A9	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999714611872146	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.0001267186213014
CAMB-795A9	MN908947.3	3037	C	T	1	1	0	0	0.99956797235023	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000144009216589862
CAMB-795A9	MN908947.3	829	C	T	0.026	0.057	1.7e-13	7.6e-27	0.0402198289671489	ACA	ORF1ab:nsp2	N8N	C24T	AAC>AAT	Synonymous	ORF1ab:nsp2	0.95970623752372
CAMB-795B8	MN908947.3	11074	C	INS	0.036	0.044	9.1e-08	6.8e-10	0.0405687451082703	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.959257326724063
CAMB-795B8	MN908947.3	11083	G	-	0.2	0.12	1.3e-88	3.2e-52	0.153413859796373	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-795B8	MN908947.3	11083	G	T	0.8	0.88	0	0	0.846549647848776	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-795B8	MN908947.3	1168	A	G	1	1	0	0	0.999702380952381	GAT	ORF1ab:nsp2	R121R	A363G	CGA>CGG	Synonymous	ORF1ab:nsp2	0.000238095238095238
CAMB-795B8	MN908947.3	14805	C	T	1	1	0	0	0.999966648879402	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-795B8	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-795B8	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-795B8	MN908947.3	26144	G	T	1	1	1.6e-157	9.8e-56	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-795B8	MN908947.3	569	G	A	1	1	0	0	0.999914478747969	TGA	ORF1ab:leader-protein	E102K	G304A	GAG>AAG	Missense	ORF1ab:leader-protein	8.55212520311297e-05
CAMB-795B8	MN908947.3	5850	C	T	0.25	0.37	1.3e-116	3.5e-158	0.286453616250485	CCT	ORF1ab:nsp3	P1044L	C3131T	CCT>CTT	Missense	ORF1ab:nsp3	0.71341700090568
CAMB-795B8	MN908947.3	6813	C	T	0.41	0.013	4.5e-189	4.7e-06	0.311215991116047	ACT	ORF1ab:nsp3	T1365I	C4094T	ACT>ATT	Missense	ORF1ab:nsp3	0.688784008883953
CAMB-795C7	MN908947.3	11074	C	INS	0.025	0.024	3.7e-05	0.00011	0.0246305418719212	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.97490094238595
CAMB-795C7	MN908947.3	11075	T	-	0.036	0.037	3.7e-09	1.5e-09	0.03660783609331	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959313038137508
CAMB-795C7	MN908947.3	13117	A	G	0.011	0.0063	4.4e-07	3.6e-05	0.00968269378161566	TAG	ORF1ab:nsp10	L31L	A93G	CTA>CTG	Synonymous	ORF1ab:nsp10	0.990202340197231
CAMB-795C7	MN908947.3	14408	C	T	1	1	0	0	0.997719234456087	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.0002864729668683
CAMB-795C7	MN908947.3	17208	T	C	0.0066	0.0036	4.3e-05	0.00086	0.00496797814089618	ATT	ORF1ab:helicase	Y324Y	T972C	TAT>TAC	Synonymous	ORF1ab:helicase	0.993476828701954
CAMB-795C7	MN908947.3	19728	T	C	1	1	0	0	0.999073567187434	ATG	ORF1ab:endoRNAse	D36D	T108C	GAT>GAC	Synonymous	ORF1ab:endoRNAse	0.000463216406282899
CAMB-795C7	MN908947.3	22624	C	T	0.027	0.027	9.6e-14	1.6e-13	0.0273133867982727	ACA	S	N354N	C1062T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.97242442936459
CAMB-795C7	MN908947.3	23403	A	G	1	1	0	0	0.999616380550494	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.9960359323551e-05
CAMB-795C7	MN908947.3	241	C	T	1	1	0	0	0.998318896740369	TCG	NA	NA	NA	NA	NA	NA	0.000128219740141327
CAMB-795C7	MN908947.3	26137	A	C	0.029	0.021	5.1e-07	7.9e-05	0.0245548266166823	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.974882849109653
CAMB-795C7	MN908947.3	26592	A	C	0.0048	0.0088	4e-04	8.3e-06	0.0069305875005712	AAT	M	I24L	A70C	ATA>CTA	Missense	GU280_gp05	0.991515742334466
CAMB-795C7	MN908947.3	28253	C	T	0.0055	0.0097	0.0017	2.6e-05	0.00770023177955189	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.991823332474891
CAMB-795C7	MN908947.3	28913	G	T	0.0083	0.0098	1.3e-05	3.7e-06	0.00908549299970212	TGG	N	G214C	G640T	GGC>TGC	Missense	GU280_gp10	0.990825141495383
CAMB-795C7	MN908947.3	3037	C	T	1	1	0	0	0.998773234200743	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000148698884758364
CAMB-795D6	MN908947.3	11075	T	-	0.043	0.043	1.2e-10	7.6e-11	0.0429806773419108	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952672307297858
CAMB-795D6	MN908947.3	13694	C	T	0.024	0.017	2.7e-12	1.3e-09	0.0205075532884791	ACA	ORF1ab:RNA-dependent-RNA-polymerase	T76I	C227T	ACA>ATA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.97941166287752
CAMB-795D6	MN908947.3	14408	C	T	0.99	0.99	0	0	0.993846995282696	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00118502313073996
CAMB-795D6	MN908947.3	14502	A	G	0.13	0.13	7e-60	9.6e-60	0.130680781164446	TAC	ORF1ab:RNA-dependent-RNA-polymerase	V345V	A1035G	GTA>GTG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.869308482655701
CAMB-795D6	MN908947.3	23403	A	G	1	1	0	0	0.999424645480083	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.92276711679697e-05
CAMB-795D6	MN908947.3	241	C	T	1	1	0	0	0.999887961458742	TCG	NA	NA	NA	NA	NA	NA	5.60192706290964e-05
CAMB-795D6	MN908947.3	26461	C	INS	0.01	0.011	2.7e-05	1.1e-05	0.0108865506823627	TCT	E	.	216-217-insfrshift	.	no-SNV	GU280_gp04	0.987316387123659
CAMB-795D6	MN908947.3	26464	C	T	0.98	0.97	0	0	0.972155907429963	TCT	E	L74L	C220T	CTG>TTG	Synonymous	GU280_gp04	0.0273812423873325
CAMB-795D6	MN908947.3	27509	C	T	0.0097	0.0082	4.4e-06	1.7e-05	0.00912765680010432	ACA	ORF7a	T39I	C116T	ACA>ATA	Missense	GU280_gp07	0.990862312807808
CAMB-795D6	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.997439709283119	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000273510507361991
CAMB-795D6	MN908947.3	29738	C	T	0.16	0.19	6.5e-68	6e-81	0.17340532395781	GCC	NA	NA	NA	NA	NA	NA	0.825715720743345
CAMB-795D6	MN908947.3	3037	C	T	1	1	0	0	0.999652133580705	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-795D6	MN908947.3	522	TT	-	0.0425	0.05	5.8e-07;0.00015	1.8e-07;4.6e-06	0.0458695394413673	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.943952287946429
CAMB-795D6	MN908947.3	8884	A	G	0.0071	0.011	1.8e-05	3.5e-07	0.00940945158345622	TAT	ORF1ab:nsp4	I110M	A330G	ATA>ATG	Missense	ORF1ab:nsp4	0.990590548416544
CAMB-795E5	MN908947.3	11075	T	-	0.066	0.0066	1.2e-16	0.0039	0.043462067384827	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956308732523493
CAMB-795E5	MN908947.3	14408	C	T	1	1	0	0	0.999339061467284	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000540767890404374
CAMB-795E5	MN908947.3	23403	A	G	1	1	0	0	0.999889424565439	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.63452607368747e-05
CAMB-795E5	MN908947.3	241	C	T	1	1	0	0	0.99992953280248	TCG	NA	NA	NA	NA	NA	NA	7.04671975195546e-05
CAMB-795E5	MN908947.3	26768	C	T	0.13	0.047	2e-58	2.5e-22	0.0829713901420685	TCG	M	I82I	C246T	ATC>ATT	Synonymous	GU280_gp05	0.917000588449575
CAMB-795E5	MN908947.3	27191	AGTGACAACAGATGTTTCATCTCGTTGACTT	-	0.0938064516129032	0.0419677419354839	2.4e-07;2.8e-07;9.2e-07;3.1e-07;3e-06;1e-06;7.3e-08;1.2e-05;6.5e-06;4.4e-09;1.3e-07;7.3e-08;2.8e-15;5e-18;3e-16;5.5e-15;8.3e-15;8.2e-15;5.3e-15;7.3e-15;5.8e-15;7.8e-15;7.2e-15;3.7e-15;1.2e-15;4.4e-15;3e-15;2.8e-15;3.8e-15;1.8e-16;1.1e-15	0.00029;0.00031;0.00049;0.00032;0.00079;0.00053;2e-04;0.0013;0.0011;6.5e-05;0.00024;0.00019;1.7e-07;1.4e-08;7.4e-08;2.3e-07;2.7e-07;2.6e-07;2.4e-07;2.6e-07;2.4e-07;2.5e-07;2.7e-07;1.9e-07;1.2e-07;2.1e-07;1.7e-07;1.8e-07;2.2e-07;5.7e-08;1.2e-07	0.0720855800005767	AAG	M	.	669-669-delfrshift	.	no-SNV	GU280_gp05	0.935058187863674
CAMB-795E5	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-795E5	MN908947.3	3037	C	T	1	1	0	0	0.999582114500627	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-795F4	MN908947.3	11075	T	-	0.036	0.038	1e-09	4.2e-10	0.0370739485748455	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958241977277257
CAMB-795F4	MN908947.3	14408	C	T	1	1	0	0	0.998107719254348	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00064118603778306
CAMB-795F4	MN908947.3	23403	A	G	1	1	0	0	0.999621044653572	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.42122992062991e-05
CAMB-795F4	MN908947.3	241	C	T	1	1	0	0	0.998925493735628	TCG	NA	NA	NA	NA	NA	NA	4.29802505748609e-05
CAMB-795F4	MN908947.3	25425	A	C	0.073	0.071	2.7e-33	2.9e-32	0.071809449127622	GAA	ORF3a	G11G	A33C	GGA>GGC	Synonymous	GU280_gp03	0.927622034895119
CAMB-795F4	MN908947.3	26137	A	C	0.027	0.017	1.3e-06	0.0011	0.0218878248974008	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.978112175102599
CAMB-795F4	MN908947.3	26217	G	T	0.086	0.08	7.5e-38	3.7e-35	0.0831115351780244	TGT	ORF3a	L275F	G825T	TTG>TTT	Missense	GU280_gp03	0.916536935670165
CAMB-795F4	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999212288302481	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-795F4	MN908947.3	29402	G	T	0.016	0.011	4.6e-08	5e-06	0.0135322692574601	TGA	N	D377Y	G1129T	GAT>TAT	Missense	GU280_gp10	0.985773768216516
CAMB-795F4	MN908947.3	3037	C	T	1	1	0	0	0.999301739579222	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.03591487294696e-05
CAMB-795F4	MN908947.3	5927	G	A	0.018	0.018	5.1e-10	8.4e-10	0.0182205985795648	TGT	ORF1ab:nsp3	V1070I	G3208A	GTT>ATT	Missense	ORF1ab:nsp3	0.981597876154387
CAMB-795F4	MN908947.3	8290	C	T	0.045	0.046	3.5e-21	1.3e-21	0.0454198315719947	TCA	ORF1ab:nsp3	L1857L	C5571T	CTC>CTT	Synonymous	ORF1ab:nsp3	0.954538887054161
CAMB-7961F	MN908947.3	11074	C	INS	0.031	0.04	2.1e-06	6.7e-09	0.0354407537192857	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.964370396793755
CAMB-7961F	MN908947.3	11075	T	-	0.043	0.034	3e-11	5e-09	0.0385919586630066	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95765828803129
CAMB-7961F	MN908947.3	11537	A	INS	0.01	0.0042	2.8e-06	0.00033	0.00689348454525239	TAT	ORF1ab:nsp6	.	564-565-insfrshift	.	no-SNV	ORF1ab:nsp6	0.992884144985546
CAMB-7961F	MN908947.3	11540	G	T	0.034	0.041	4.7e-15	9.8e-18	0.0377462714048978	TGT	ORF1ab:nsp6	V190F	G568T	GTT>TTT	Missense	ORF1ab:nsp6	0.961333087829129
CAMB-7961F	MN908947.3	14408	C	T	1	1	0	0	0.998456958210798	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000490142685981919
CAMB-7961F	MN908947.3	20629	C	T	0.01	0.016	2.9e-06	7.6e-09	0.0133912543979321	CCA	ORF1ab:endoRNAse	H337Y	C1009T	CAT>TAT	Missense	ORF1ab:endoRNAse	0.986501041143103
CAMB-7961F	MN908947.3	23384	G	T	0.053	0.032	6.1e-25	9.4e-16	0.0424440821000485	GGT	S	V608F	G1822T	GTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.955464831157192
CAMB-7961F	MN908947.3	23403	A	G	1	1	0	0	0.998039745049476	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.34761071919054e-05
CAMB-7961F	MN908947.3	241	C	T	1	1	0	0	0.998696352342732	TCG	NA	NA	NA	NA	NA	NA	5.11234375399402e-05
CAMB-7961F	MN908947.3	24235	T	C	0.023	0.0046	2e-11	0.00039	0.0113813149922214	GTG	S	G891G	T2673C	GGT>GGC	Synonymous	GU280_gp02, spike glycoprotein	0.988536805043806
CAMB-7961F	MN908947.3	24571	T	-	0.0089	0.0023	2e-05	0.0078	0.00433839479392625	GTT	S	.	3009-3009-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.995661605206074
CAMB-7961F	MN908947.3	25906	G	T	1	1	0	0	0.99992432841468	AGG	ORF3a	G172C	G514T	GGT>TGT	Missense	GU280_gp03	7.56715853197124e-05
CAMB-7961F	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0359210526315789	0.0413947368421053	0.0015;0.00011;0.00033;0.00016;4e-04;1e-05;8e-05;1.9e-06;1.8e-06;3.1e-07;8.8e-07;5.5e-07;1.7e-06;8.9e-07;1.4e-06;2.7e-06;8.4e-07;2.3e-06;1.3e-06;1.4e-06;1e-06;2.5e-06;1.3e-06;1.6e-06;1.1e-06;7.2e-07;2e-06;9.9e-07;1.7e-07;1.1e-06;2e-06;1.8e-06;8.7e-07;2.1e-06;4.3e-07;9.5e-07;4.8e-07;0.00028	6.9e-05;2e-06;1.1e-05;5.4e-06;1.6e-05;3.3e-07;2.3e-06;5e-07;4.8e-07;1.1e-07;1e-07;6.7e-08;1.7e-07;1.1e-07;1.6e-07;2.6e-07;9.5e-08;2.2e-07;1.3e-07;1.3e-07;1.1e-07;2.5e-07;1.3e-07;1.6e-07;1.2e-07;7.8e-08;1.8e-07;9e-08;2.5e-08;1.1e-07;1.8e-07;1.7e-07;2.9e-07;5.4e-07;9.4e-08;2.3e-07;6.9e-08;0.00084	0.0415877703465648	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.975363496481734
CAMB-7961F	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999059376837155	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	6.48887158523133e-05
CAMB-7961F	MN908947.3	29543	G	T	1	1	0	0	0.999639119451462	AGA	NA	NA	NA	NA	NA	NA	0.000270660411403825
CAMB-7961F	MN908947.3	3037	C	T	0.99	1	0	0	0.996920289855072	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.05797101449275e-05
CAMB-7961F	MN908947.3	4158	C	T	0.017	0.0095	3.4e-09	4.6e-06	0.0127047936893204	GCT	ORF1ab:nsp3	A480V	C1439T	GCT>GTT	Missense	ORF1ab:nsp3	0.98729520631068
CAMB-7961F	MN908947.3	514	T	-	0.15	0.16	9.8e-06	8.4e-06	0.154455283889138	ATG	ORF1ab:leader-protein	.	249-249-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.842034368749745
CAMB-7961F	MN908947.3	522	TT	-	0.0575	0.04	1.2e-10;6.1e-05	3e-07;0.00092	0.0478639240506329	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.932582647610798
CAMB-7961F	MN908947.3	9634	A	T	0.0065	0.0058	3e-05	7.7e-05	0.00606872234747673	TAG	ORF1ab:nsp4	L360F	A1080T	TTA>TTT	Missense	ORF1ab:nsp4	0.993066738994084
CAMB-7962E	MN908947.3	11074	C	INS	0.098	0.13	8.3e-38	3.9e-45	0.109434414204018	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.890146411569209
CAMB-7962E	MN908947.3	11083	G	-	0.22	0.18	2e-100	4.7e-82	0.206807182714939	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-7962E	MN908947.3	11083	G	T	0.78	0.82	4.9e-309	0	0.793087033559887	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-7962E	MN908947.3	13461	TTTTAAACGGGTTTGCGGTGTA	-	0.00664090909090909	0.00254545454545455	0.00066;3e-04;0.00036;0.00055;0.00043;1.9e-05;6.8e-06;2.9e-05;0.00029;4.8e-05;4.7e-05;7.4e-05;1.5e-05;2.8e-05;4.6e-05;3.9e-05;3.9e-05;8.9e-05;5.7e-05;3.8e-05;4.2e-05;4.9e-05	NA;2.7e-07;5.1e-07;1e-06;7.1e-07;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00428281068524971	TTT	ORF1ab:nsp11	.	20-39-delfrshift	.	no-SNV	ORF1ab:nsp11	0.994538943598926
CAMB-7962E	MN908947.3	14805	C	T	1	1	0	0	0.999901685393258	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	2.80898876404494e-05
CAMB-7962E	MN908947.3	1508	G	A	1	1	0	0	1	TGG	ORF1ab:nsp2	G235S	G703A	GGT>AGT	Missense	ORF1ab:nsp2	0
CAMB-7962E	MN908947.3	20928	T	C	1	1	0	0	0.999858477214832	CTA	ORF1ab:2'-O-ribose-methyltransferase	P90P	T270C	CCT>CCC	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	2.83045570336824e-05
CAMB-7962E	MN908947.3	23555	CCCATTGGTGCAGGTATATGCGCTAGTT	-	0.0609285714285714	0.00160714285714286	1.1e-05;1e-05;1.3e-05;1.4e-05;1e-06;2.2e-06;2.2e-06;6.2e-06;7.2e-06;7.4e-06;6e-06;6.3e-06;2.8e-06;2.4e-06;4.3e-07;3.4e-08;3.1e-07;1.1e-07;3.4e-07;1.3e-07;5.8e-07;2.1e-06;8.1e-07;8.1e-07;6.3e-10;2.2e-09;1.2e-06;9.7e-07	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.012;0.0054;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0358310131945285	ACC	S	.	1993-2020-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.96435429668747
CAMB-7962E	MN908947.3	23707	C	T	1	1	0	0	0.999641191245066	CCA	S	P715P	C2145T	CCC>CCT	Synonymous	GU280_gp02, spike glycoprotein	0.000239205836622414
CAMB-7962E	MN908947.3	23898	AAG	-	0.0150666666666667	0.027	0.49;3.8e-10;1.5e-10	5.4e-13;8.5e-12;3.7e-12	0.0235941801022414	CAA	S	.	2336-2338-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.990467660418399
CAMB-7962E	MN908947.3	26144	G	T	1	1	0	3.50000001691885e-316	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7962E	MN908947.3	26575	AACAATGGAACCTAGTAATAGGTTTCCTATT	-	0.00578064516129032	0.0166451612903226	0.051;0.06;0.061;0.055;0.054;0.054;0.053;0.055;0.056;0.053;0.054;0.055;0.058;0.054;0.058;0.052;0.056;0.048;0.048;0.046;0.049;0.049;0.052;0.046;0.049;0.05;0.049;0.053;0.048;0.00046;0.00045	0.00035;0.00067;0.00071;0.00051;0.00053;0.00061;0.00037;0.00061;0.00067;0.00052;0.00055;0.00066;0.00063;4e-04;0.00061;0.00044;0.00039;0.00046;0.00047;0.00035;0.00047;0.00049;0.00048;0.00038;0.00051;0.00051;0.00049;0.00051;0.00032;2.1e-05;2.1e-05	0.0098839441643856	GAA	M	.	53-83-delfrshift	.	no-SNV	GU280_gp05	0.9902175623812
CAMB-7962E	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCT	-	0.05065	0.035505	5.8e-05;1.7e-06;2e-06;2.1e-06;9.8e-06;2e-07;2.3e-06;2.3e-09;2.4e-09;2.1e-10;8.4e-10;4.3e-10;2.7e-09;7.9e-10;1.3e-09;4.2e-09;5.7e-10;3.2e-09;1.7e-09;1.7e-09;1.1e-09;3.7e-09;1.4e-09;2.4e-09;1.4e-09;4e-10;2.5e-09;1.1e-09;1.5e-09;8.2e-10;2.7e-09;2e-09;7.9e-10;2.4e-09;3.2e-10;1e-09;6.3e-10;4e-06;0.00054;0.00023	0.00022;1.1e-05;0.00014;0.00014;0.00036;3.5e-05;0.00014;3e-05;3.1e-05;8.4e-06;1.3e-07;8.8e-08;2.6e-07;1.3e-07;1.8e-07;3.8e-07;9.9e-08;3.1e-07;1.9e-07;1.7e-07;1.5e-07;3.4e-07;1.7e-07;2.4e-07;1.6e-07;8.6e-08;2.6e-07;1.3e-07;1.8e-07;1.2e-07;2.7e-07;2.1e-07;1.7e-05;3e-05;1e-05;1.7e-05;1.5e-05;0.2;0.21;0.19	0.0502932950523476	GTC	M	.	258-297-delfrshift	.	no-SNV	GU280_gp05	0.973283109237409
CAMB-7962E	MN908947.3	27374	TGGAGAT	-	0.00612857142857143	0.00241428571428571	5.6e-05;4.2e-05;1e-04;0.00011;8.4e-05;7.7e-05;7.7e-05	0.00086;0.0016;0.0032;0.0032;0.0024;0.002;0.0027	0.0048798606485988	ATG	ORF6	.	173-179-delfrshift	.	no-SNV	GU280_gp06	0.99464016449623
CAMB-7962E	MN908947.3	29275	A	-	0.0024	0.0081	0.0027	5e-06	0.00350549783113084	CAG	N	.	1002-1002-delfrshift	.	no-SNV	GU280_gp10	0.996191869262585
CAMB-7962E	MN908947.3	29412	A	C	1	1	0	0	1	CAA	N	Q380P	A1139C	CAA>CCA	Missense	GU280_gp10	0
CAMB-7962E	MN908947.3	335	C	T	1	1	0	0	0.999882068518191	TCG	ORF1ab:leader-protein	R24C	C70T	CGC>TGC	Missense	ORF1ab:leader-protein	0.000103190046582935
CAMB-7962E	MN908947.3	3987	C	T	0.0094	0.0089	3.7e-06	5.6e-06	0.00928046989720998	ACA	ORF1ab:nsp3	T423I	C1268T	ACA>ATA	Missense	ORF1ab:nsp3	0.99071953010279
CAMB-7962E	MN908947.3	4525	TAGAT	-	0.0138	0.0036	1.5e-05;5e-05;0.00083;0.00074;0.00029	NA;NA;NA;NA;0.0028	0.00753598122181728	CTA	ORF1ab:nsp3	.	1806-1810-delfrshift	.	no-SNV	ORF1ab:nsp3	0.99226575377203
CAMB-7962E	MN908947.3	4557	TAGCGTCACTTATCAACACACTTAACGATCTA	-	0.00252996875	0.01309375	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0011;0.0013;0.0017;0.0015;0.0015;0.001;0.00017;4.4e-05	6.1e-05;7.5e-05;3.8e-06;7.4e-06;1.3e-05;3.8e-06;4.7e-06;1.7e-06;2.4e-06;4.4e-07;3.7e-07;3.5e-07;2.9e-07;3.5e-07;3.9e-07;4.1e-06;4.6e-06;3.4e-07;3.6e-07;3.1e-07;2.8e-07;3.4e-07;4.3e-05;0.00017;0.00028;0.00031;4e-04;0.00036;0.00036;0.00025;2.9e-05;4.8e-06	0.00416964498451275	GTA	ORF1ab:nsp3	.	1838-1869-delfrshift	.	no-SNV	ORF1ab:nsp3	0.995143370367906
CAMB-7962E	MN908947.3	6199	T	C	0.0058	0.011	0.00094	6.9e-06	0.00726226639039208	CTT	ORF1ab:nsp3	S1160S	T3480C	TCT>TCC	Synonymous	ORF1ab:nsp3	0.992737733609608
CAMB-7962E	MN908947.3	6341	GATGTACTGA	TGATGTACTG	0.0009514	0.01079	NA;NA;NA;0.47;NA;NA;0.22;0.48;NA;3.1e-06	2.5e-07;1.1e-07;5.1e-07;5.9e-07;2.5e-07;1.1e-07;1.7e-07;1.3e-06;7.1e-07;1.4e-07	0.00329573103295731	TGA	ORF1ab:nsp3	.	3622-3631-mnv	.	no-SNV	ORF1ab:nsp3	0.996626875479137
CAMB-7962E	MN908947.3	6350	A	G	0.0091	0.012	3.1e-06	1.4e-07	0.0100034336728854	GAA	ORF1ab:nsp3	K1211E	A3631G	AAG>GAG	Missense	ORF1ab:nsp3	0.989950784021976
CAMB-7963D	MN908947.3	10302	AA	-	0.00805	0.00245	0.00014;2.3e-05	0.0035;NA	0.00575774035850081	CAA	ORF1ab:3C-like-proteinase	.	248-249-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.992997832291066
CAMB-7963D	MN908947.3	11074	C	INS	0.029	0.024	1e-06	0.00011	0.0267317138370034	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.972332676178702
CAMB-7963D	MN908947.3	11075	T	-	0.044	0.076	1.3e-10	2.7e-18	0.0575137898560474	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.94125617420384
CAMB-7963D	MN908947.3	11916	C	T	0.0064	0.0076	0.00018	4.6e-05	0.00693873524285573	TCA	ORF1ab:nsp7	S25L	C74T	TCA>TTA	Missense	ORF1ab:nsp7	0.993053043506857
CAMB-7963D	MN908947.3	1223	C	T	0.016	0.0055	1.2e-08	0.00013	0.0112958577633695	TCT	ORF1ab:nsp2	L140F	C418T	CTC>TTC	Missense	ORF1ab:nsp2	0.988678815201287
CAMB-7963D	MN908947.3	12231	C	T	0.019	0.01	7.9e-10	4.5e-06	0.0156636998696751	TCT	ORF1ab:nsp8	S47F	C140T	TCT>TTT	Missense	ORF1ab:nsp8	0.984330123592521
CAMB-7963D	MN908947.3	14408	C	T	1	1	0	0	0.999426372273965	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000458902180828318
CAMB-7963D	MN908947.3	14790	C	T	0.0094	0.015	7e-06	2.6e-08	0.0114271685395766	TCA	ORF1ab:RNA-dependent-RNA-polymerase	I441I	C1323T	ATC>ATT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.988561672116146
CAMB-7963D	MN908947.3	15738	C	T	0.014	0.0058	1.5e-07	0.00028	0.0100940681242215	TCA	ORF1ab:RNA-dependent-RNA-polymerase	F757F	C2271T	TTC>TTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.989873716764744
CAMB-7963D	MN908947.3	15944	C	T	0.0042	0.0089	0.0017	1.2e-05	0.00579987407371531	TCA	ORF1ab:RNA-dependent-RNA-polymerase	S826L	C2477T	TCA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994200125926285
CAMB-7963D	MN908947.3	16193	C	T	0.007	0.018	2.9e-05	7.8e-10	0.0130327868852459	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P909L	C2726T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.986967213114754
CAMB-7963D	MN908947.3	16239	T	-	0.005	0.0065	0.00016	3.8e-05	0.00572809451355947	CTG	ORF1ab:helicase	.	3-3-delfrshift	.	no-SNV	ORF1ab:helicase	0.994271905486441
CAMB-7963D	MN908947.3	16245	G	A	1	1	0	0	0.999920710434507	GGG	ORF1ab:helicase	G3G	G9A	GGG>GGA	Synonymous	ORF1ab:helicase	7.92895654931811e-05
CAMB-7963D	MN908947.3	17167	C	T	0.027	0.0036	3.2e-13	0.0038	0.017846008502598	TCA	ORF1ab:helicase	H311Y	C931T	CAT>TAT	Missense	ORF1ab:helicase	0.982135096835144
CAMB-7963D	MN908947.3	17892	A	G	0.0069	0.0042	4.1e-05	0.00046	0.00588127182503216	CAG	ORF1ab:helicase	T552T	A1656G	ACA>ACG	Synonymous	ORF1ab:helicase	0.993951646589029
CAMB-7963D	MN908947.3	19661	A	G	0.067	0.072	5.6e-30	2.7e-32	0.0688533861162166	CAC	ORF1ab:endoRNAse	H14R	A41G	CAC>CGC	Missense	ORF1ab:endoRNAse	0.931146613883783
CAMB-7963D	MN908947.3	203	C	T	0.014	0.023	2.6e-07	2.7e-11	0.0166358201969919	TCG	NA	NA	NA	NA	NA	NA	0.983342906375646
CAMB-7963D	MN908947.3	2168	T	-	0.0049	0.01	0.00088	4.2e-06	0.00678098715524548	GTT	ORF1ab:nsp2	.	1363-1363-delfrshift	.	no-SNV	ORF1ab:nsp2	0.993219012844755
CAMB-7963D	MN908947.3	21962	C	T	0.007	0.0085	6.5e-05	1.5e-05	0.00761224172751282	TCA	S	Q134*	C400T	CAA>TAA	Nonsense	GU280_gp02, spike glycoprotein	0.992387758272487
CAMB-7963D	MN908947.3	23403	A	G	1	1	0	0	0.999924005805956	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.79970970217875e-05
CAMB-7963D	MN908947.3	23435	C	T	0.016	0.0037	1.1e-08	0.0014	0.0110490961551569	TCA	S	H625Y	C1873T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.988935757722629
CAMB-7963D	MN908947.3	23896	C	T	0.01	0.0058	1.7e-06	0.00013	0.00881496445155705	CCC	S	T778T	C2334T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.991080095495448
CAMB-7963D	MN908947.3	241	C	T	1	1	0	0	0.999736586156589	TCG	NA	NA	NA	NA	NA	NA	8.10504133571081e-05
CAMB-7963D	MN908947.3	24213	C	T	0.0044	0.01	0.0029	1.6e-05	0.00719743107075628	TCT	S	S884F	C2651T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.992774886502048
CAMB-7963D	MN908947.3	2550	A	G	1	1	0	0	0.9991961414791	GAT	ORF1ab:nsp2	D582G	A1745G	GAT>GGT	Missense	ORF1ab:nsp2	0
CAMB-7963D	MN908947.3	25521	C	T	0.071	0.068	1.8e-31	8e-31	0.0697882207779775	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.930158595087913
CAMB-7963D	MN908947.3	25673	TT	-	0.00535	0.0079	0.0016;0.00034	0.00029;1.9e-05	0.00605676456088457	CTT	ORF3a	.	281-282-delfrshift	.	no-SNV	GU280_gp03	0.992983933207044
CAMB-7963D	MN908947.3	25710	C	T	0.0044	0.013	0.00069	1.5e-07	0.00703993683794986	TCT	ORF3a	L106L	C318T	CTC>CTT	Synonymous	GU280_gp03	0.99296006316205
CAMB-7963D	MN908947.3	26761	T	C	0.0099	0.023	4.2e-06	1.3e-11	0.0163022525747646	ATT	M	I80T	T239C	ATT>ACT	Missense	GU280_gp05	0.977676194672395
CAMB-7963D	MN908947.3	26768	C	T	0.021	0.021	1.9e-10	1.5e-10	0.0206097615733465	TCG	M	I82I	C246T	ATC>ATT	Synonymous	GU280_gp05	0.979345336985317
CAMB-7963D	MN908947.3	2720	G	A	0.11	0.047	3.4e-39	7.3e-16	0.0855855855855856	TGC	ORF1ab:nsp3	A1T	G1A	GCA>ACA	Missense	ORF1ab:nsp3	0.914414414414414
CAMB-7963D	MN908947.3	27223	C	T	0.012	0.0029	5.5e-07	0.0024	0.00841103456467514	TCA	ORF6	Q8*	C22T	CAG>TAG	Nonsense	GU280_gp06	0.99152957595914
CAMB-7963D	MN908947.3	28253	C	T	0.052	0.026	1e-22	3.3e-12	0.040436527297892	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.959075565822621
CAMB-7963D	MN908947.3	28872	G	A	0.13	0.15	4.9e-58	6.2e-68	0.137592250922509	GGC	N	G200D	G599A	GGC>GAC	Missense	GU280_gp10	0.862407749077491
CAMB-7963D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999508212845481	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	5.4421768707483e-05
CAMB-7963D	MN908947.3	29743	C	T	0.0046	0.011	0.0022	5.8e-06	0.00826239359038558	GCG	NA	NA	NA	NA	NA	NA	0.989984977466199
CAMB-7963D	MN908947.3	3037	C	T	1	1	0	0	0.999589790337283	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.11577028258888e-05
CAMB-7963D	MN908947.3	3722	A	T	0.0052	0.0078	0.00024	2.3e-05	0.00669642857142857	TAT	ORF1ab:nsp3	I335F	A1003T	ATT>TTT	Missense	ORF1ab:nsp3	0.993303571428571
CAMB-7963D	MN908947.3	4815	C	T	0.01	0.0049	9.3e-06	0.0013	0.00797488867055416	TCT	ORF1ab:nsp3	S699F	C2096T	TCT>TTT	Missense	ORF1ab:nsp3	0.991935792576336
CAMB-7963D	MN908947.3	635	C	T	0.091	0.091	3.4e-41	1.2e-41	0.0913062337340439	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.908662783492378
CAMB-7963D	MN908947.3	683	C	T	0.02	0.015	4.1e-10	3e-08	0.0179808515606756	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.981980228847202
CAMB-7963D	MN908947.3	815	C	T	0.0079	0.0027	3.7e-05	0.0085	0.00583852505268492	TCG	ORF1ab:nsp2	R4C	C10T	CGC>TGC	Missense	ORF1ab:nsp2	0.994161474947315
CAMB-7963D	MN908947.3	9430	C	T	0.0046	0.019	0.0043	1e-08	0.00822147651006711	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.991778523489933
CAMB-7964C	MN908947.3	11074	C	INS	0.23	0.2	1.7e-122	2.6e-85	0.220002359116511	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.775367874730913
CAMB-7964C	MN908947.3	11083	G	-	0.19	0.2	4.2e-84	1.3e-89	0.191289418993404	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	6.02391494232101e-05
CAMB-7964C	MN908947.3	11083	G	T	0.81	0.8	0	0	0.808514803770971	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	6.02391494232101e-05
CAMB-7964C	MN908947.3	11983	A	G	0.011	0.014	1.1e-06	3.1e-08	0.0125461667599328	AAG	ORF1ab:nsp7	E47E	A141G	GAA>GAG	Synonymous	ORF1ab:nsp7	0.98740906547286
CAMB-7964C	MN908947.3	14805	C	T	1	1	0	0	0.999927973609531	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	5.76211123755744e-05
CAMB-7964C	MN908947.3	1515	A	G	1	1	0	0	0.998316498316498	CAT	ORF1ab:nsp2	H237R	A710G	CAT>CGT	Missense	ORF1ab:nsp2	0.00168350168350168
CAMB-7964C	MN908947.3	17247	T	C	1	1	0	0	0.999855649268967	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000134039964530963
CAMB-7964C	MN908947.3	20849	ATATG	-	0.00886	0.003877	6e-05;9.7e-05;1.4e-05;1.5e-05;0.00011	NA;NA;0.0032;0.0041;3e-06	0.00640432518732198	AAT	ORF1ab:2'-O-ribose-methyltransferase	.	191-195-delfrshift	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.99499122077442
CAMB-7964C	MN908947.3	20853	GA	-	0.0042165	0.0125	0.00011;NA	3e-06;1.8e-06	0.00788492274906766	TGA	ORF1ab:2'-O-ribose-methyltransferase	.	195-196-delfrshift	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.989875008728441
CAMB-7964C	MN908947.3	22214	C	G	0.023	0.027	5.7e-12	1.7e-13	0.0251882845188285	TCA	S	Q218E	C652G	CAG>GAG	Missense	GU280_gp02, spike glycoprotein	0.974811715481172
CAMB-7964C	MN908947.3	25000	C	T	0.52	0.44	9.99999999999999e-303	1.1e-242	0.480299479371471	ACT	S	D1146D	C3438T	GAC>GAT	Synonymous	GU280_gp02, spike glycoprotein	0.519700520628529
CAMB-7964C	MN908947.3	25556	T	-	0.011	0.012	2.4e-05	8.5e-06	0.0114771727441588	GTT	ORF3a	.	164-164-delfrshift	.	no-SNV	GU280_gp03	0.988405513735458
CAMB-7964C	MN908947.3	25556	TT	-	0.0055	0.011	2.4e-05;NA	8.5e-06;8.8e-05	0.00784952070898897	GTT	ORF3a	.	164-165-delfrshift	.	no-SNV	GU280_gp03	0.988405513735458
CAMB-7964C	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7964C	MN908947.3	26840	G	T	0.29	0.37	7.4e-143	1.9e-196	0.326629113406033	CGC	M	T106T	G318T	ACG>ACT	Synonymous	GU280_gp05	0.673250523579115
CAMB-7964C	MN908947.3	26950	TGATCCTTCGTGGACATCTTCGTATT	-	0.00731923076923077	0.000161538461538462	0.00023;0.00024;0.00026;0.00025;0.00028;2e-04;0.00019;0.00025;0.00043;3e-04;0.00016;0.00021;0.00015;0.00016;0.00018;0.00014;0.00014;0.00016;7.1e-05;5.1e-05;1.4e-07;0.00012;9.7e-05;9.2e-05;9.1e-05;9.8e-05	NA;0.0033;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00367875787822229	GTG	M	.	428-453-delfrshift	.	no-SNV	GU280_gp05	0.99622083036021
CAMB-7964C	MN908947.3	28841	A	G	0.012	0.023	3.9e-07	1e-11	0.0177302734988997	TAG	N	S190G	A568G	AGT>GGT	Missense	GU280_gp10	0.982081106570261
CAMB-7964C	MN908947.3	28904	G	A	0.014	0.014	2.2e-07	1.1e-07	0.0138805432039418	GGC	N	A211T	G631A	GCT>ACT	Missense	GU280_gp10	0.986119456796058
CAMB-7964C	MN908947.3	2904	T	INS	0.015	0.01	4.7e-07	3.5e-05	0.0122937560659981	ATA	ORF1ab:nsp3	.	184-185-insfrshift	.	no-SNV	ORF1ab:nsp3	0.987598403968511
CAMB-7964C	MN908947.3	29104	T	C	0.0086	0.025	1e-05	6.1e-13	0.0147965863738899	GTG	N	R277R	T831C	CGT>CGC	Synonymous	GU280_gp10	0.98520341362611
CAMB-7964C	MN908947.3	3302	G	T	0.0073	0.0091	3.2e-05	5e-06	0.00806273121067442	AGA	ORF1ab:nsp3	E195*	G583T	GAG>TAG	Nonsense	ORF1ab:nsp3	0.991842413128024
CAMB-7964C	MN908947.3	3425	C	T	0.043	0.064	1.8e-20	1.2e-29	0.0521525657146279	ACC	ORF1ab:nsp3	P236S	C706T	CCA>TCA	Missense	ORF1ab:nsp3	0.947847434285372
CAMB-7964C	MN908947.3	4486	G	T	0.014	0.089	6.2e-08	1.5e-40	0.0526785407872611	AGG	ORF1ab:nsp3	K589N	G1767T	AAG>AAT	Missense	ORF1ab:nsp3	0.947287140945125
CAMB-7964C	MN908947.3	522	T	-	0.043	0.026	1e-05	0.0016	0.0351710105609922	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.964635209766496
CAMB-7964C	MN908947.3	9223	C	T	1	1	0	0	0.99988864142539	ACG	ORF1ab:nsp4	H223H	C669T	CAC>CAT	Synonymous	ORF1ab:nsp4	8.35189309576837e-05
CAMB-7964C	MN908947.3	9803	C	T	0.0099	0.024	6.3e-06	3.2e-12	0.0167220928197326	GCT	ORF1ab:nsp4	L417L	C1249T	CTG>TTG	Synonymous	ORF1ab:nsp4	0.983250979494567
CAMB-7965B	MN908947.3	11075	T	-	0.028	0.075	8.7e-08	3.5e-19	0.0426641384214269	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957292766489259
CAMB-7965B	MN908947.3	11075	TTT	-	0.0253333333333333	0.025	8.7e-08;1.5e-09;2.7e-12	3.5e-19;NA;NA	0.0163938043334363	CTT	ORF1ab:nsp6	.	103-105-delinframe	.	no-SNV	ORF1ab:nsp6	0.957292766489259
CAMB-7965B	MN908947.3	12578	G	T	0.025	0.03	1.7e-09	7e-11	0.0277295434509657	AGA	ORF1ab:nsp8	D163Y	G487T	GAT>TAT	Missense	ORF1ab:nsp8	0.972270456549034
CAMB-7965B	MN908947.3	14408	C	T	1	1	0	0	0.999424832842045	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000407410070218324
CAMB-7965B	MN908947.3	15815	T	-	0.018	0.036	8.7e-09	2.5e-16	0.0266399556711138	GTT	ORF1ab:RNA-dependent-RNA-polymerase	.	2348-2348-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.973253484506202
CAMB-7965B	MN908947.3	20698	C	T	0.046	0.0074	1.2e-14	0.00074	0.0301204819277108	TCT	ORF1ab:2'-O-ribose-methyltransferase	L14F	C40T	CTT>TTT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.969879518072289
CAMB-7965B	MN908947.3	2146	C	T	0.023	0.0021	5.7e-11	0.0033	0.015063731170336	TCC	ORF1ab:nsp2	V447V	C1341T	GTC>GTT	Synonymous	ORF1ab:nsp2	0.984936268829664
CAMB-7965B	MN908947.3	23270	GCTGACACTACTGATGCTGTC	TGCTGACACTACTGATGCTGT	0.0261904761904762	0.00180571428571429	6.2e-12;6.6e-12;1.5e-11;6.4e-12;2.4e-12;1.2e-11;2e-12;2.2e-11;4.2e-14;1.2e-10;3.4e-11;2.6e-12;5.9e-11;2.1e-12;7.6e-12;6.5e-12;4.6e-12;1.3e-11;6.1e-12;6.8e-12;8e-12	0.49;0.49;0.48;0.48;0.48;0.48;0.48;0.48;2.5e-12;0.48;0.48;0.48;0.5;0.48;0.48;0.49;0.48;0.48;0.48;0.48;0.49	0.0169087708692637	TGC	S	.	1708-1728-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.982773502121844
CAMB-7965B	MN908947.3	23403	A	G	1	1	0	0	0.999902644815836	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.73551841635567e-05
CAMB-7965B	MN908947.3	241	C	T	1	1	0	0	0.999741174034579	TCG	NA	NA	NA	NA	NA	NA	0.00010353038616834
CAMB-7965B	MN908947.3	26510	T	C	0.062	0.044	9.3e-26	2.8e-19	0.0513775130305287	CTT	NA	NA	NA	NA	NA	NA	0.948324646314222
CAMB-7965B	MN908947.3	27476	C	T	0.011	0.027	1.1e-06	3.1e-13	0.0178901798268334	ACA	ORF7a	T28I	C83T	ACA>ATA	Missense	GU280_gp07	0.98209131947014
CAMB-7965B	MN908947.3	27841	G	T	0.017	0.028	3.5e-08	7.3e-11	0.0214814814814815	TGG	NA	NA	NA	NA	NA	NA	0.978518518518519
CAMB-7965B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000176740897843761
CAMB-7965B	MN908947.3	3037	C	T	1	1	0	0	0.999640158330335	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000179920834832674
CAMB-7966A	MN908947.3	1059	C	T	1	1	0	0	0.999833163407174	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.000129761794420243
CAMB-7966A	MN908947.3	11075	T	-	0.04	0.038	3.8e-10	5.3e-10	0.039164677463158	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955975472048713
CAMB-7966A	MN908947.3	11514	C	T	0.0091	0.0073	2.1e-05	0.00012	0.00814046288906624	ACT	ORF1ab:nsp6	T181I	C542T	ACT>ATT	Missense	ORF1ab:nsp6	0.991316839584996
CAMB-7966A	MN908947.3	14335	G	T	0.017	0.02	4.5e-09	1.8e-10	0.0182637481591501	TGT	ORF1ab:RNA-dependent-RNA-polymerase	V290F	G868T	GTT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.981308293579367
CAMB-7966A	MN908947.3	14408	C	T	1	1	0	0	0.997783048051145	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000554237987213859
CAMB-7966A	MN908947.3	16329	C	T	1	1	0	0	0.999751484877855	ACG	ORF1ab:helicase	Y31Y	C93T	TAC>TAT	Synonymous	ORF1ab:helicase	0
CAMB-7966A	MN908947.3	186	C	T	0.38	0.38	6.6e-200	5.6e-198	0.381090441787209	GCA	NA	NA	NA	NA	NA	NA	0.618815527590152
CAMB-7966A	MN908947.3	1973	C	T	0.077	0.082	8.9e-35	2.1e-37	0.0791792869393862	ACT	ORF1ab:nsp2	L390L	C1168T	CTA>TTA	Synonymous	ORF1ab:nsp2	0.920610882020217
CAMB-7966A	MN908947.3	23403	A	G	1	1	0	0	0.999443631039531	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.92825768667643e-05
CAMB-7966A	MN908947.3	23536	C	-	0.008	0.0074	3.4e-05	6.3e-05	0.00768876448286858	ACT	S	.	1974-1974-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.000141728377564398
CAMB-7966A	MN908947.3	23536	C	T	0.99	0.99	0	0	0.992134075045176	ACT	S	N658N	C1974T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.000141728377564398
CAMB-7966A	MN908947.3	23555	CCCATTGGTGCAGGTATATGCGCTAGT	-	0.0452962962962963	0.0472962962962963	0.00055;0.00045;6e-04;0.00061;6.1e-05;0.00012;2.5e-05;5.6e-05;6.5e-05;6.5e-05;5.9e-05;4.8e-05;2.9e-05;2.5e-05;5.4e-06;1.2e-06;2.8e-05;9.5e-06;3.2e-05;1.2e-05;3.4e-05;7.8e-05;4.2e-05;6.5e-05;6.6e-07;2.4e-06;0.00067	0.00049;0.00043;0.00058;0.00068;3.4e-05;7.4e-05;1.8e-05;3.9e-05;4.2e-05;4.3e-05;3.9e-05;3.7e-05;1.9e-05;1.8e-05;3.7e-06;1.6e-06;1.8e-05;5.5e-06;1.8e-05;5.3e-06;1.8e-05;4.3e-05;2e-05;3.5e-05;3.1e-07;6e-07;0.00045	0.0446489323785763	ACC	S	.	1993-2019-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.96222150468195
CAMB-7966A	MN908947.3	241	C	T	1	1	0	0	0.999085980837116	TCG	NA	NA	NA	NA	NA	NA	0.000141830559757943
CAMB-7966A	MN908947.3	25563	G	T	1	1	0	0	0.999749530369443	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000107344127381698
CAMB-7966A	MN908947.3	25731	C	T	1	1	0	0	0.999783115545193	ACT	ORF3a	Y113Y	C339T	TAC>TAT	Synonymous	GU280_gp03	5.42211137016754e-05
CAMB-7966A	MN908947.3	26166	AG	-	0.00905	0.0101	3.3e-05;0.00035	1.3e-05;0.00024	0.00947352839591454	CAG	ORF3a	.	774-775-delfrshift	.	no-SNV	GU280_gp03	0.989588288145447
CAMB-7966A	MN908947.3	29625	C	T	1	1	0	0	0.999599423169364	TCT	ORF10	S23F	C68T	TCT>TTT	Missense	GU280_gp11	0.000160230732254446
CAMB-7966A	MN908947.3	3037	C	T	1	1	0	0	0.999071215201948	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000125511459196225
CAMB-79679	MN908947.3	11075	T	-	0.36	0.0067	7.1e-104	0.0033	0.183470964304742	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.816462440063932
CAMB-79679	MN908947.3	14408	C	T	1	1	0	0	0.999611222704594	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000259184863603966
CAMB-79679	MN908947.3	23403	A	G	1	1	0	0	0.999893358927191	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.99808046068943e-05
CAMB-79679	MN908947.3	241	C	T	1	1	0	0	0.999882999883	TCG	NA	NA	NA	NA	NA	NA	0.000117000117000117
CAMB-79679	MN908947.3	25528	C	T	1	1	0	0	0.999836253479614	GCT	ORF3a	L46F	C136T	CTT>TTT	Missense	GU280_gp03	0
CAMB-79679	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999076979878161	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79679	MN908947.3	3037	C	T	1	1	8.1e-282	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79679	MN908947.3	6573	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	S1285F	C3854T	TCT>TTT	Missense	ORF1ab:nsp3	0
CAMB-79688	MN908947.3	11455	C	T	1	1	4.5e-186	3.7e-185	1	CCA	ORF1ab:nsp6	A161A	C483T	GCC>GCT	Synonymous	ORF1ab:nsp6	0
CAMB-79688	MN908947.3	14408	C	T	1	1	0	0	0.999553099861867	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000243763711708784
CAMB-79688	MN908947.3	23403	A	G	1	1	0	0	0.999898528665652	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.07356671740233e-05
CAMB-79688	MN908947.3	241	C	T	0.95	1	0	0	0.958702064896755	TCG	NA	NA	NA	NA	NA	NA	6.41272284211876e-05
CAMB-79688	MN908947.3	28881	GGG	AAC	1	1	0;0;0	3.3000000201869e-316;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79688	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79697	MN908947.3	10096	G	A	0.072	0.034	3.5e-32	6e-16	0.0553716521215769	AGG	ORF1ab:3C-like-proteinase	E14E	G42A	GAG>GAA	Synonymous	ORF1ab:3C-like-proteinase	0.944528036914435
CAMB-79697	MN908947.3	11254	T	C	0.077	0.0097	1.5e-35	1.5e-06	0.0534807731359265	TTA	ORF1ab:nsp6	I94I	T282C	ATT>ATC	Synonymous	ORF1ab:nsp6	0.946482305377614
CAMB-79697	MN908947.3	14408	C	T	1	1	0	0	0.999206959530905	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000576756704796693
CAMB-79697	MN908947.3	20679	G	T	1	1	0	0	0.999635833940277	CGG	ORF1ab:2'-O-ribose-methyltransferase	P7P	G21T	CCG>CCT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	7.28332119446468e-05
CAMB-79697	MN908947.3	23403	A	G	1	1	0	0	0.999950714637753	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.92853622474125e-05
CAMB-79697	MN908947.3	241	C	T	1	1	0	0	0.999885452462772	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-79697	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999760536398467	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79697	MN908947.3	29051	C	INS	0.02	0.032	0.00025	1.7e-08	0.0262605042016807	GCA	N	.	777-778-insfrshift	.	no-SNV	GU280_gp10	0.973613445378151
CAMB-79697	MN908947.3	3037	C	T	1	1	0	0	0.999468179400815	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000177273533061514
CAMB-796A6	MN908947.3	10341	C	T	0.0056	0.0087	0.00014	6.5e-06	0.00708918692569919	CCT	ORF1ab:3C-like-proteinase	P96L	C287T	CCT>CTT	Missense	ORF1ab:3C-like-proteinase	0.99281644785732
CAMB-796A6	MN908947.3	10755	C	T	0.0081	0.01	4.4e-05	5.7e-06	0.00891577317814345	GCT	ORF1ab:3C-like-proteinase	A234V	C701T	GCT>GTT	Missense	ORF1ab:3C-like-proteinase	0.990711541769394
CAMB-796A6	MN908947.3	11074	C	INS	0.034	0.024	6e-08	0.00016	0.0298038427872405	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.969550431201481
CAMB-796A6	MN908947.3	11075	T	-	0.034	0.035	9.9e-09	2.8e-09	0.0346928976818053	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960567299050808
CAMB-796A6	MN908947.3	11083	G	T	0.035	0.035	1.1e-07	1.3e-07	0.0350745546088304	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.958777110766847
CAMB-796A6	MN908947.3	11653	C	T	0.018	0.014	3.2e-09	1.3e-07	0.0159536856991338	TCT	ORF1ab:nsp6	L227L	C681T	CTC>CTT	Synonymous	ORF1ab:nsp6	0.983957928230511
CAMB-796A6	MN908947.3	1218	C	T	0.015	0.014	3.2e-08	3.4e-08	0.0145649406069425	TCA	ORF1ab:nsp2	S138L	C413T	TCA>TTA	Missense	ORF1ab:nsp2	0.985407076798231
CAMB-796A6	MN908947.3	1226	A	G	0.0058	0.0075	0.00014	2.3e-05	0.00654138915318744	CAT	ORF1ab:nsp2	M141V	A421G	ATG>GTG	Missense	ORF1ab:nsp2	0.993062163019347
CAMB-796A6	MN908947.3	12877	TATCTA	-	0.00931666666666667	0.00586666666666667	4.9e-06;2e-06;4.7e-06;7.9e-06;5.4e-06;1.8e-06	0.00011;7.4e-05;8.2e-05;9.4e-05;9.7e-05;5.9e-05	0.00760504669625953	CTA	ORF1ab:nsp9	.	192-197-delinframe	.	no-SNV	ORF1ab:nsp9	0.991851792445264
CAMB-796A6	MN908947.3	13730	C	T	1	1	0	0	0.996561822476782	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A88V	C263T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000129437271462318
CAMB-796A6	MN908947.3	14408	C	T	1	1	0	0	0.996419213973799	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000731441048034935
CAMB-796A6	MN908947.3	20629	C	T	0.038	0.044	1.1e-17	2.4e-20	0.0404239658471956	CCA	ORF1ab:endoRNAse	H337Y	C1009T	CAT>TAT	Missense	ORF1ab:endoRNAse	0.959193287207419
CAMB-796A6	MN908947.3	20841	A	G	0.0073	0.0068	2.2e-05	3.1e-05	0.00706697133165296	TAC	ORF1ab:2'-O-ribose-methyltransferase	V61V	A183G	GTA>GTG	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.992909472097242
CAMB-796A6	MN908947.3	21864	T	C	0.017	0.011	3.1e-09	1.2e-06	0.0134127232842369	ATA	S	I101T	T302C	ATA>ACA	Missense	GU280_gp02, spike glycoprotein	0.986524600438734
CAMB-796A6	MN908947.3	2218	T	C	0.0072	0.0059	4.2e-05	0.00013	0.00661429383710271	TTA	ORF1ab:nsp2	F471F	T1413C	TTT>TTC	Synonymous	ORF1ab:nsp2	0.993374102138622
CAMB-796A6	MN908947.3	23403	A	G	1	1	0	0	0.999422371122111	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.99793830923584e-05
CAMB-796A6	MN908947.3	24058	C	T	0.0028	0.0081	0.0017	8.4e-06	0.00509262972170984	GCT	S	G832G	C2496T	GGC>GGT	Synonymous	GU280_gp02, spike glycoprotein	0.994867270831662
CAMB-796A6	MN908947.3	241	C	T	1	1	0	0	0.99894425277605	TCG	NA	NA	NA	NA	NA	NA	1.88526289991139e-05
CAMB-796A6	MN908947.3	25429	G	T	1	1	0	0	0.997348288579353	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	7.6198604041574e-05
CAMB-796A6	MN908947.3	25433	C	T	0.028	0.025	6.8e-14	6.9e-13	0.0268175868633984	ACT	ORF3a	T14I	C41T	ACT>ATT	Missense	GU280_gp03	0.971650404569253
CAMB-796A6	MN908947.3	26109	G	T	0.012	0.0073	7.9e-07	6e-05	0.0102871037127092	AGC	ORF3a	E239D	G717T	GAG>GAT	Missense	GU280_gp03	0.98961937716263
CAMB-796A6	MN908947.3	26137	A	C	0.032	0.02	3.2e-08	0.00033	0.0277719774483191	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.972019210691167
CAMB-796A6	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0319375	0.03159375	1.6e-05;0.00014;4.5e-05;4.5e-05;8.9e-06;1.7e-05;1.1e-05;3.5e-05;1.9e-05;2.6e-05;4.6e-05;1.5e-05;4.3e-05;2.6e-05;2.7e-05;2.7e-05;4.6e-05;2.3e-05;3.3e-05;2.4e-05;1.4e-05;3.4e-05;2.2e-05;1.5e-05;2.2e-05;3.9e-05;3.3e-05;1.8e-05;4.2e-05;1.8e-05;2.8e-05;1.9e-05	5.3e-05;0.00025;4.2e-05;4.2e-05;1.1e-05;2.2e-05;1.3e-05;3.4e-05;2.1e-05;2.6e-05;4.4e-05;2e-05;4.5e-05;2.9e-05;2.9e-05;3.1e-05;4.8e-05;2.7e-05;3.7e-05;2.7e-05;1.8e-05;3.9e-05;2.3e-05;1.8e-05;2.4e-05;4e-05;3.3e-05;1.8e-05;3.8e-05;1.3e-05;2.3e-05;1.7e-05	0.0315233050126479	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.967948239020964
CAMB-796A6	MN908947.3	2695	C	T	1	1	0	0	0.999522569444444	ACA	ORF1ab:nsp2	N630N	C1890T	AAC>AAT	Synonymous	ORF1ab:nsp2	4.34027777777778e-05
CAMB-796A6	MN908947.3	27089	T	A	0.0078	0.0097	2.2e-05	2.8e-06	0.0085830594928638	GTG	M	G189G	T567A	GGT>GGA	Synonymous	GU280_gp05	0.991343371425769
CAMB-796A6	MN908947.3	27877	G	INS	0.0062	0.0073	8.5e-05	2.8e-05	0.00665445076670846	TGT	NA	NA	NA	NA	NA	NA	0.993249107917832
CAMB-796A6	MN908947.3	27880	ACG	-	0.0069	0.0073	1e-04;5.1e-05;4.6e-05	5.3e-05;3.9e-05;3.9e-05	0.00714554343738247	CAC	NA	NA	NA	NA	NA	NA	0.993277938567827
CAMB-796A6	MN908947.3	27883	C	T	0.0059	0.0074	0.00019	4.7e-05	0.0065309985802177	GCC	NA	NA	NA	NA	NA	NA	0.993374349266446
CAMB-796A6	MN908947.3	28854	C	T	0.0092	0.012	6.3e-05	2.8e-06	0.0105606460630533	TCA	N	S194L	C581T	TCA>TTA	Missense	GU280_gp10	0.989439353936947
CAMB-796A6	MN908947.3	28869	C	T	0.58	0.59	0	0	0.587304752409438	CCA	N	P199L	C596T	CCA>CTA	Missense	GU280_gp10	0.41036889332004
CAMB-796A6	MN908947.3	29743	C	T	0.026	0.019	3e-12	2.6e-09	0.0231914337947245	GCG	NA	NA	NA	NA	NA	NA	0.974510316009402
CAMB-796A6	MN908947.3	3037	C	T	1	1	0	0	0.999200894997603	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000159821000479463
CAMB-796A6	MN908947.3	4802	G	T	0.023	0.019	9.2e-12	5e-10	0.0209782781879016	AGA	ORF1ab:nsp3	D695Y	G2083T	GAT>TAT	Missense	ORF1ab:nsp3	0.978888947899517
CAMB-796A6	MN908947.3	5392	C	T	0.013	0.018	3.6e-07	3.9e-09	0.0152091254752852	ACT	ORF1ab:nsp3	N891N	C2673T	AAC>AAT	Synonymous	ORF1ab:nsp3	0.984402886629937
CAMB-796A6	MN908947.3	5812	C	T	0.076	0.064	1.2e-33	7.7e-29	0.0703880462757053	ACG	ORF1ab:nsp3	D1031D	C3093T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.927762924464656
CAMB-796A6	MN908947.3	7148	T	C	0.99	1	0	0	0.996832101372756	TTT	ORF1ab:nsp3	L1477L	T4429C	TTA>CTA	Synonymous	ORF1ab:nsp3	0
CAMB-796A6	MN908947.3	8031	A	G	0.021	0.019	9e-11	3.6e-10	0.0198652466855032	AAA	ORF1ab:nsp3	K1771R	A5312G	AAA>AGA	Missense	ORF1ab:nsp3	0.980134753314497
CAMB-796A6	MN908947.3	8326	C	T	0.063	0.061	2.4e-28	3.7e-27	0.0620498044865199	ACC	ORF1ab:nsp3	D1869D	C5607T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.93795019551348
CAMB-796A6	MN908947.3	9866	C	T	0.0097	0.0064	4.2e-06	7e-05	0.00815007520019511	TCT	ORF1ab:nsp4	L438F	C1312T	CTT>TTT	Missense	ORF1ab:nsp4	0.991849924799805
CAMB-796B5	MN908947.3	1059	C	T	1	1	0	0	0.999835961849413	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.000128887118318375
CAMB-796B5	MN908947.3	11074	C	INS	0.026	0.02	9.9e-06	0.00075	0.0236038311521397	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.976172647719526
CAMB-796B5	MN908947.3	11075	T	-	0.035	0.042	1e-08	2.4e-10	0.0380067567567568	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959431306306306
CAMB-796B5	MN908947.3	14408	C	T	1	1	0	0	0.998294057330563	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000353892362276889
CAMB-796B5	MN908947.3	20790	C	T	1	1	0	0	0.999567438968342	TCG	ORF1ab:2'-O-ribose-methyltransferase	V44V	C132T	GTC>GTT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.000405525967179432
CAMB-796B5	MN908947.3	21957	AATT	-	0.04725	0.04875	1.3e-20;3.4e-21;1e-21;1.3e-21	2.3e-21;3.3e-22;3.8e-22;5.9e-22	0.0483123759099934	GAA	S	.	395-398-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.953643083421331
CAMB-796B5	MN908947.3	22159	TTATT	-	0.031	0.0248	5e-11;1.5e-11;3.8e-17;4.2e-15;2.1e-16	1.4e-08;6.2e-09;1.4e-14;7.5e-13;5.5e-14	0.033768315018315	GTT	S	.	597-601-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.977517246309468
CAMB-796B5	MN908947.3	23403	A	G	1	1	0	0	0.999857286589934	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000128442069059019
CAMB-796B5	MN908947.3	23741	C	T	0.94	0.93	0	0	0.938946384936036	TCT	S	L727L	C2179T	CTA>TTA	Synonymous	GU280_gp02, spike glycoprotein	0.0596880839442288
CAMB-796B5	MN908947.3	241	C	T	1	1	0	0	0.998494361383381	TCG	NA	NA	NA	NA	NA	NA	0.000286071337157655
CAMB-796B5	MN908947.3	25563	G	T	1	1	0	0	0.999891310911177	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	3.62296962743796e-05
CAMB-796B5	MN908947.3	25855	G	C	0.21	0.21	4.8e-100	6.3e-96	0.21201650830214	CGA	ORF3a	D155H	G463C	GAC>CAC	Missense	GU280_gp03	0.787119685190517
CAMB-796B5	MN908947.3	26137	A	C	0.025	0.016	3e-05	0.0051	0.0210622710622711	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.978937728937729
CAMB-796B5	MN908947.3	3037	C	T	1	1	0	0	0.999407933688573	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.55435624174523e-05
CAMB-796C4	MN908947.3	14408	C	T	1	1	0	0	0.999303971230811	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000502687444414369
CAMB-796C4	MN908947.3	23403	A	G	1	1	0	0	0.999890964033708	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.23062664527485e-05
CAMB-796C4	MN908947.3	241	C	T	1	1	0	0	0.999693204479215	TCG	NA	NA	NA	NA	NA	NA	0.000153397760392698
CAMB-796C4	MN908947.3	2554	A	G	0.034	0.006	6.1e-13	0.0031	0.026840490797546	TAC	ORF1ab:nsp2	L583L	A1749G	TTA>TTG	Synonymous	ORF1ab:nsp2	0.973159509202454
CAMB-796C4	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999486784706184	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-796C4	MN908947.3	3037	C	T	1	1	0	0	0.99944118468846	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-796C4	MN908947.3	4118	T	C	0.015	0.0085	1.8e-07	0.00011	0.0124813401890861	ATA	ORF1ab:nsp3	Y467H	T1399C	TAT>CAT	Missense	ORF1ab:nsp3	0.987435727317963
CAMB-796E2	MN908947.3	14408	C	T	1	1	0	0	0.999307778835338	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000692221164662109
CAMB-796E2	MN908947.3	17167	C	T	0.043	0.043	3.6e-20	1.5e-19	0.0430416068866571	TCA	ORF1ab:helicase	H311Y	C931T	CAT>TAT	Missense	ORF1ab:helicase	0.956958393113343
CAMB-796E2	MN908947.3	17333	C	T	0.12	0.19	4.5e-54	4e-83	0.143248701673399	ACG	ORF1ab:helicase	T366M	C1097T	ACG>ATG	Missense	ORF1ab:helicase	0.856751298326601
CAMB-796E2	MN908947.3	23403	A	G	1	1	0	0	0.999966393332437	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-796E2	MN908947.3	241	C	T	1	1	0	0	0.999813970793415	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-796E2	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999314128943759	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-796E2	MN908947.3	3037	C	T	1	1	0	3.4e-275	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-796F1	MN908947.3	10078	C	T	0.0095	0.012	5.2e-06	4.6e-07	0.0114316686787061	TCC	ORF1ab:3C-like-proteinase	F8F	C24T	TTC>TTT	Synonymous	ORF1ab:3C-like-proteinase	0.988543694104314
CAMB-796F1	MN908947.3	11075	T	-	0.045	0.039	1.2e-11	4.1e-10	0.04149377593361	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95492571275599
CAMB-796F1	MN908947.3	14408	C	T	1	1	0	0	0.99837807421138	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000695111052265731
CAMB-796F1	MN908947.3	2037	C	T	0.0099	0.0095	2.7e-06	5.2e-06	0.00966954335581502	GCT	ORF1ab:nsp2	A411V	C1232T	GCT>GTT	Missense	ORF1ab:nsp2	0.990124978847874
CAMB-796F1	MN908947.3	23369	A	G	0.011	0.01	1.7e-06	3e-06	0.0103165964696418	AAA	S	N603D	A1807G	AAT>GAT	Missense	GU280_gp02, spike glycoprotein	0.989505939141546
CAMB-796F1	MN908947.3	23403	A	G	1	1	0	0	0.999639773160013	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000113214149710275
CAMB-796F1	MN908947.3	241	C	T	1	1	0	0	0.998504978268241	TCG	NA	NA	NA	NA	NA	NA	7.7062975863876e-05
CAMB-796F1	MN908947.3	25613	C	T	0.0071	0.0089	2e-05	4.3e-06	0.00818086225026288	TCC	ORF3a	S74F	C221T	TCC>TTC	Missense	GU280_gp03	0.991819137749737
CAMB-796F1	MN908947.3	25702	C	T	0.0063	0.007	5.3e-05	3.9e-05	0.00676751592356688	CCC	ORF3a	P104S	C310T	CCT>TCT	Missense	GU280_gp03	0.993232484076433
CAMB-796F1	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999529000134571	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000266595574513463
CAMB-796F1	MN908947.3	3037	C	T	1	1	0	0	0.999403864361609	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000105200406774906
CAMB-796F1	MN908947.3	8705	G	A	0.0086	0.01	5.2e-06	2.4e-06	0.00960189407225535	TGG	ORF1ab:nsp4	G51S	G151A	GGT>AGT	Missense	ORF1ab:nsp4	0.989762364082778
CAMB-7970D	MN908947.3	11074	C	INS	0.6	0.6	0	0	0.596575575235392	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.398086880035184
CAMB-7970D	MN908947.3	11083	G	T	1	1	0	0	0.998008002935575	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.74736584598717e-05
CAMB-7970D	MN908947.3	11173	C	T	0.0072	0.0046	3.9e-05	0.00053	0.00590392700599338	TCT	ORF1ab:nsp6	L67L	C201T	CTC>CTT	Synonymous	ORF1ab:nsp6	0.993917166115037
CAMB-7970D	MN908947.3	14805	C	T	1	1	0	0	0.999131319123692	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000370778422814526
CAMB-7970D	MN908947.3	14874	G	T	0.046	0.046	2e-21	9.4e-22	0.0459378368143552	AGT	ORF1ab:RNA-dependent-RNA-polymerase	K469N	G1407T	AAG>AAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.953984483478497
CAMB-7970D	MN908947.3	17013	A	C	0.013	0.0099	9.4e-08	1.8e-06	0.0111023776773433	CAG	ORF1ab:helicase	S259S	A777C	TCA>TCC	Synonymous	ORF1ab:helicase	0.988570118556363
CAMB-7970D	MN908947.3	23707	C	T	1	1	0	0	0.999592527582748	CCA	S	P715P	C2145T	CCC>CCT	Synonymous	GU280_gp02, spike glycoprotein	0.000376128385155466
CAMB-7970D	MN908947.3	24751	G	A	0.038	0.037	2.2e-18	1e-17	0.0370891939123501	TGC	S	L1063L	G3189A	TTG>TTA	Synonymous	GU280_gp02, spike glycoprotein	0.962724172449482
CAMB-7970D	MN908947.3	25455	G	T	1	1	0	0	0.99952335557674	AGG	ORF3a	K21N	G63T	AAG>AAT	Missense	GU280_gp03	7.06139886311478e-05
CAMB-7970D	MN908947.3	258	A	G	0.012	0.011	2.3e-07	4.2e-07	0.0115716834100085	AAA	NA	NA	NA	NA	NA	NA	0.988381372641067
CAMB-7970D	MN908947.3	26144	G	T	1	1	0	0	0.999861188228762	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	4.62705904127337e-05
CAMB-7970D	MN908947.3	28918	T	C	0.0093	0.0092	5.4e-06	6.2e-06	0.00924688057040998	GTG	N	G215G	T645C	GGT>GGC	Synonymous	GU280_gp10	0.99075311942959
CAMB-7971C	MN908947.3	11075	T	-	0.056	0.036	8.6e-14	2.9e-09	0.0457364893768715	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.948429107847331
CAMB-7971C	MN908947.3	14408	C	T	1	1	0	0	0.99548524621575	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00155681164974133
CAMB-7971C	MN908947.3	15668	A	G	0.73	0.7	0	0	0.714666525204567	AAT	ORF1ab:RNA-dependent-RNA-polymerase	N734S	A2201G	AAT>AGT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.284776467779797
CAMB-7971C	MN908947.3	20580	G	T	0.0059	0.029	0.00013	2.6e-14	0.0190463766225295	TGA	ORF1ab:endoRNAse	V320V	G960T	GTG>GTT	Synonymous	ORF1ab:endoRNAse	0.98088839606027
CAMB-7971C	MN908947.3	21621	C	A	0.0018	0.0094	0.0041	7.2e-06	0.00574382538770821	ACC	S	T20N	C59A	ACC>AAC	Missense	GU280_gp02, spike glycoprotein	0.994256174612292
CAMB-7971C	MN908947.3	23403	A	G	1	1	0	0	0.999925762175003	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.12432361092781e-05
CAMB-7971C	MN908947.3	241	C	T	1	1	0	0	0.996256723360954	TCG	NA	NA	NA	NA	NA	NA	7.26849832824538e-05
CAMB-7971C	MN908947.3	25801	A	C	1	1	5e-255	7.3e-271	0.99864446165763	AAA	ORF3a	N137H	A409C	AAC>CAC	Missense	GU280_gp03	0.00122643945262071
CAMB-7971C	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0366486486486486	0.0385675675675676	0.0024;0.00022;0.00019;0.00023;0.00022;5.9e-08;1.3e-06;2.2e-06;2.2e-06;4.3e-07;9.7e-07;6.4e-07;2e-06;1e-06;1.5e-06;3.2e-06;8.6e-07;2.7e-06;1.3e-06;1.6e-06;1.1e-06;3e-06;1.2e-06;2e-06;1.4e-06;5.5e-07;2.2e-06;1.2e-06;3.8e-07;1.4e-06;2.4e-06;2e-06;7.1e-07;2.2e-06;5.1e-07;1.1e-06;6.8e-07	0.00073;5.6e-05;6.9e-05;8e-05;0.00022;1.3e-05;6.2e-05;1.9e-06;1.9e-06;5.2e-07;4.8e-07;2.1e-07;4.7e-07;3.1e-07;7.4e-07;1.2e-06;4.3e-07;1.1e-06;6.1e-07;6.5e-07;4.7e-07;1.2e-06;5.4e-07;8.3e-07;6e-07;2.6e-07;9e-07;5e-07;2.5e-07;6e-07;9.1e-07;7.8e-07;4.2e-07;9.9e-07;2.1e-07;5.2e-07;6.7e-07	0.039636311976133	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.978984983745291
CAMB-7971C	MN908947.3	27197	A	T	0.0092	0.006	5.4e-06	0.00013	0.00745080116886174	CAA	NA	NA	NA	NA	NA	NA	0.987168834046561
CAMB-7971C	MN908947.3	27297	C	T	0.038	0.041	4e-18	2.9e-19	0.0394673962950122	TCA	ORF6	I32I	C96T	ATC>ATT	Synonymous	GU280_gp06	0.960513863250907
CAMB-7971C	MN908947.3	28027	G	T	0.049	0.037	1.1e-20	3e-16	0.0425219941348974	TGG	ORF8	W45L	G134T	TGG>TTG	Missense	GU280_gp09	0.95584881068752
CAMB-7971C	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.997805381205285	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.93583415597236e-05
CAMB-7971C	MN908947.3	3037	C	T	1	1	0	0	0.999595360129485	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7971C	MN908947.3	4076	G	A	0.015	0.0092	5.8e-09	2.5e-06	0.0114484567278596	TGT	ORF1ab:nsp3	V453I	G1357A	GTT>ATT	Missense	ORF1ab:nsp3	0.98552551946742
CAMB-7971C	MN908947.3	4161	TGGTTA	-	0.00788333333333333	0.000854	1.5e-05;1.8e-05;1.1e-05;5.6e-06;4.8e-06;7.8e-06	0.0027;0.0035;NA;NA;NA;NA	0.00321340146446821	GTG	ORF1ab:nsp3	.	1442-1447-delinframe	.	no-SNV	ORF1ab:nsp3	0.995329362655264
CAMB-7971C	MN908947.3	522	TT	-	0.0475	0.03	2.6e-07;1.1e-05	0.00029;0.00043	0.0379459846465932	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.956522635016793
CAMB-7971C	MN908947.3	6870	C	T	0.025	0.015	3.1e-07	6.1e-05	0.0200573065902579	ACT	ORF1ab:nsp3	T1384I	C4151T	ACT>ATT	Missense	ORF1ab:nsp3	0.979942693409742
CAMB-7971C	MN908947.3	7010	G	T	0.02	0.0071	1.1e-06	0.00081	0.0132530120481928	TGC	ORF1ab:nsp3	A1431S	G4291T	GCT>TCT	Missense	ORF1ab:nsp3	0.986746987951807
CAMB-7971C	MN908947.3	7360	G	C	0.011	0.022	3.3e-07	3.1e-11	0.0173609215482885	TGT	ORF1ab:nsp3	M1547I	G4641C	ATG>ATC	Missense	ORF1ab:nsp3	0.982639078451712
CAMB-7971C	MN908947.3	8522	G	T	0.0097	0.0031	1e-05	0.0063	0.00585828528919472	TGT	ORF1ab:nsp3	V1935F	G5803T	GTT>TTT	Missense	ORF1ab:nsp3	0.994141714710805
CAMB-7973A	MN908947.3	11075	T	-	0.038	0.036	7.1e-10	1.1e-09	0.0374837451235371	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957867360208062
CAMB-7973A	MN908947.3	12085	C	T	0.0076	0.0074	2.6e-05	2.8e-05	0.00753379786790543	CCT	ORF1ab:nsp7	T81T	C243T	ACC>ACT	Synonymous	ORF1ab:nsp7	0.992361979631946
CAMB-7973A	MN908947.3	1440	G	A	1	1	0	0	0.999820014398848	GGC	ORF1ab:nsp2	G212D	G635A	GGC>GAC	Missense	ORF1ab:nsp2	8.99928005759539e-05
CAMB-7973A	MN908947.3	26137	A	C	0.024	0.017	7.5e-06	0.00097	0.0209003215434084	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.978563772775991
CAMB-7973A	MN908947.3	28362	G	T	1	1	0	0	0.999656612274051	GGA	N	G30V	G89T	GGA>GTA	Missense	GU280_gp10	8.24130542277897e-05
CAMB-7973A	MN908947.3	28708	C	T	1	1	0	0	0.998916847192135	ACA	N	H145H	C435T	CAC>CAT	Synonymous	GU280_gp10	0.000541576403932678
CAMB-7973A	MN908947.3	2891	G	A	1	1	0	0	0.999475275480373	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	0.000449763873966168
CAMB-7973A	MN908947.3	4668	C	T	1	1	0	0	0.999407714036527	TCT	ORF1ab:nsp3	S650F	C1949T	TCT>TTT	Missense	ORF1ab:nsp3	0.000331940485023626
CAMB-7973A	MN908947.3	539	C	T	0.023	0.025	6.2e-12	1.1e-12	0.0240801913657592	ACT	ORF1ab:leader-protein	L92F	C274T	CTC>TTC	Missense	ORF1ab:leader-protein	0.975885636177241
CAMB-7973A	MN908947.3	854	C	T	0.0072	0.0071	3.7e-05	4e-05	0.00715371254884933	CCC	ORF1ab:nsp2	P17S	C49T	CCT>TCT	Missense	ORF1ab:nsp2	0.992813721233174
CAMB-79749	MN908947.3	11075	T	-	0.044	0.045	9.9e-11	3.3e-11	0.0439827368040492	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952311550976139
CAMB-79749	MN908947.3	14408	C	T	1	1	0	0	0.997328823928568	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000818586215438967
CAMB-79749	MN908947.3	16289	C	T	1	1	0	0	0.999595108915702	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	8.09782168596648e-05
CAMB-79749	MN908947.3	16466	C	T	0.021	0.02	7.4e-07	1.5e-06	0.0207054697511297	CCA	ORF1ab:helicase	P77L	C230T	CCA>CTA	Missense	ORF1ab:helicase	0.97929453024887
CAMB-79749	MN908947.3	16472	T	C	0.04	0.044	1.5e-18	2.3e-20	0.0416580596295531	ATT	ORF1ab:helicase	I79T	T236C	ATT>ACT	Missense	ORF1ab:helicase	0.958066515182813
CAMB-79749	MN908947.3	17321	C	T	0.019	0.019	1.3e-09	1.3e-09	0.0186032293634071	GCA	ORF1ab:helicase	A362V	C1085T	GCA>GTA	Missense	ORF1ab:helicase	0.981320348919724
CAMB-79749	MN908947.3	17372	C	T	0.0081	0.0087	1.2e-05	6.7e-06	0.0083870417004567	GCC	ORF1ab:helicase	A379V	C1136T	GCC>GTC	Missense	ORF1ab:helicase	0.991495582397883
CAMB-79749	MN908947.3	23403	A	G	1	1	0	0	0.999376863493666	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.46536465317326e-05
CAMB-79749	MN908947.3	241	C	T	1	1	0	0	0.998894202461477	TCG	NA	NA	NA	NA	NA	NA	0.000172332083925725
CAMB-79749	MN908947.3	24910	T	C	0.0075	0.0064	1.9e-05	5e-05	0.00697732369798156	CTA	S	T1116T	T3348C	ACT>ACC	Synonymous	GU280_gp02, spike glycoprotein	0.992965170886925
CAMB-79749	MN908947.3	25429	G	T	1	1	0	0	0.998382937808662	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	5.827251139956e-05
CAMB-79749	MN908947.3	27382	GATTA	-	0.012	0.0128	6.8e-07;7.1e-06;5.6e-07;6.9e-06;2.5e-08	1.7e-07;2.4e-06;1.8e-07;2.5e-06;2e-08	0.0116342397836538	TGA	ORF6	.	181-185-delfrshift	.	no-SNV	GU280_gp06	0.988078983794574
CAMB-79749	MN908947.3	27925	C	A	0.0091	0.01	8.3e-05	4.2e-05	0.00947668567594767	ACA	ORF8	T11K	C32A	ACA>AAA	Missense	GU280_gp09	0.990187856424019
CAMB-79749	MN908947.3	29810	G	T	1	1	0	0	0.999663846714102	TGT	NA	NA	NA	NA	NA	NA	0.000112051095299457
CAMB-79749	MN908947.3	3037	C	T	1	1	0	0	0.998828839122486	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000114259597806216
CAMB-79749	MN908947.3	8873	C	A	0.0097	0.0072	4.6e-06	3.3e-05	0.00853570569848521	GCC	ORF1ab:nsp4	P107T	C319A	CCT>ACT	Missense	ORF1ab:nsp4	0.990966235015285
CAMB-79758	MN908947.3	10646	A	G	0.037	0.039	3.2e-17	2.1e-18	0.0376231050127255	CAC	ORF1ab:3C-like-proteinase	T198A	A592G	ACA>GCA	Missense	ORF1ab:3C-like-proteinase	0.962127918557043
CAMB-79758	MN908947.3	11075	T	-	0.037	0.041	2.7e-09	1.7e-10	0.0386488357146388	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956815148069412
CAMB-79758	MN908947.3	14408	C	T	1	1	0	0	0.997221914775872	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000376314333148866
CAMB-79758	MN908947.3	22470	T	G	0.016	0.01	1.5e-06	4.3e-05	0.0127423822714681	TTG	S	L303W	T908G	TTG>TGG	Missense	GU280_gp02, spike glycoprotein	0.986703601108033
CAMB-79758	MN908947.3	23403	A	G	1	1	0	0	0.999575102755762	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.53850956452368e-05
CAMB-79758	MN908947.3	241	C	T	1	1	0	0	0.998760801678701	TCG	NA	NA	NA	NA	NA	NA	0.000148703798555921
CAMB-79758	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999168127395347	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	6.55651717807501e-05
CAMB-79758	MN908947.3	3037	C	T	1	1	0	0	0.999136570696996	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000178640545449132
CAMB-79767	MN908947.3	11075	T	-	0.044	0.043	1.9e-11	2.6e-11	0.0433334774899451	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952493188600095
CAMB-79767	MN908947.3	14408	C	T	1	1	0	0	0.997232333563972	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000526458289461809
CAMB-79767	MN908947.3	15324	C	T	1	1	0	0	0.998415955646758	ACA	ORF1ab:RNA-dependent-RNA-polymerase	N619N	C1857T	AAC>AAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000126003528098787
CAMB-79767	MN908947.3	23403	A	G	1	1	0	0	0.999427023648297	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.20887592457548e-05
CAMB-79767	MN908947.3	241	C	T	1	1	0	0	0.998635141102324	TCG	NA	NA	NA	NA	NA	NA	0.000321143270041347
CAMB-79767	MN908947.3	25186	G	T	0.04	0.043	1.4e-18	7.8e-20	0.0416037939211037	AGT	S	Q1208H	G3624T	CAG>CAT	Missense	GU280_gp02, spike glycoprotein	0.958126751455055
CAMB-79767	MN908947.3	25433	C	T	1	1	0	0	0.99784587442715	ACT	ORF3a	T14I	C41T	ACT>ATT	Missense	GU280_gp03	0.000253426537982302
CAMB-79767	MN908947.3	26137	A	C	0.026	0.018	2.4e-06	0.00045	0.0219244823386114	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.977923264311815
CAMB-79767	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0285	0.03046875	6.2e-05;0.00037;0.00012;0.00012;3.5e-05;5.3e-05;4.2e-05;0.00012;6.5e-05;7.4e-05;0.00014;5.5e-05;0.00012;8.5e-05;8.7e-05;5.9e-05;0.00014;7.6e-05;1e-04;7.9e-05;4.3e-05;0.00011;7.3e-05;5e-05;5.7e-05;0.00012;9.4e-05;5.2e-05;0.00012;6.1e-05;8.1e-05;5.8e-05	4.7e-05;0.00019;5.8e-05;5.8e-05;2e-05;2.6e-05;2e-05;5.1e-05;3.2e-05;3.9e-05;6.5e-05;2.9e-05;5.9e-05;4e-05;3.9e-05;2.9e-05;6e-05;3.5e-05;4.3e-05;3.7e-05;2.4e-05;5.2e-05;3.3e-05;2.9e-05;2.9e-05;5.4e-05;4.5e-05;2.5e-05;5e-05;2e-05;3e-05;2e-05	0.0293113482056256	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.969980054030853
CAMB-79767	MN908947.3	29546	C	T	1	1	0	0	0.999941680760483	CCA	NA	NA	NA	NA	NA	NA	0
CAMB-79767	MN908947.3	3037	C	T	1	1	0	0	0.999334043686734	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00013319126265317
CAMB-79767	MN908947.3	584	C	T	0.044	0.045	8.5e-21	4.6e-21	0.0448062276130501	CCT	ORF1ab:leader-protein	L107F	C319T	CTT>TTT	Missense	ORF1ab:leader-protein	0.954973943853206
CAMB-79776	MN908947.3	11074	C	INS	0.044	0.048	1.2e-10	6.2e-11	0.0452244897959184	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.954775510204082
CAMB-79776	MN908947.3	11083	G	-	0.029	0.032	3.6e-12	2e-11	0.0299360457205062	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.00013607293509321
CAMB-79776	MN908947.3	11083	G	T	0.97	0.97	0	0	0.969927881344401	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.00013607293509321
CAMB-79776	MN908947.3	13458	C	T	0.43	0.69	2.9e-30	5.1e-99	0.620481927710843	TCG	ORF1ab:nsp11	S6L	C17T	TCG>TTG	Missense	ORF1ab:nsp11	0.379518072289157
CAMB-79776	MN908947.3	14805	C	T	1	0.59	0	0	0.762941332625431	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.237058667374569
CAMB-79776	MN908947.3	1605	ATG	-	0.00996666666666667	0.02	9.3e-06;9.3e-06;9.4e-06	4.6e-09;5.2e-09;5e-09	0.0142898804316127	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.985446985446986
CAMB-79776	MN908947.3	17247	T	C	0.9	1	0	0	0.962238267148014	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.0377617328519856
CAMB-79776	MN908947.3	8293	C	T	1	1	0	0	1	CCT	ORF1ab:nsp3	T1858T	C5574T	ACC>ACT	Synonymous	ORF1ab:nsp3	0
CAMB-79785	MN908947.3	14408	C	T	1	1	0	0	0.999384438608011	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00041037426132633
CAMB-79785	MN908947.3	23403	A	G	1	1	0	0	0.999865098208504	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.44312540470537e-05
CAMB-79785	MN908947.3	241	C	T	1	1	0	0	0.999855353371713	TCG	NA	NA	NA	NA	NA	NA	5.78586513148379e-05
CAMB-79785	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999614197530864	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79785	MN908947.3	29051	C	INS	0.02	0.031	0.00022	3e-08	0.023857138833338	GCA	N	.	777-778-insfrshift	.	no-SNV	GU280_gp10	0.975973861363828
CAMB-79785	MN908947.3	3037	C	T	1	1	0	0	0.998839009287926	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000386996904024768
CAMB-79785	MN908947.3	6636	C	T	1	1	0	0	1	ACT	ORF1ab:nsp3	T1306I	C3917T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-79794	MN908947.3	10504	TAACATAGATTA	-	0.0105416666666667	0.00281666666666667	0.00025;0.00021;2e-04;3e-04;0.00026;0.00018;0.00024;0.00016;6.5e-05;2.8e-05;5.4e-05;5.6e-05	NA;NA;NA;NA;NA;NA;NA;0.0024;0.0012;0.00081;0.0011;0.0011	0.00615747412550766	TTA	ORF1ab:3C-like-proteinase	.	450-461-delinframe	.	no-SNV	ORF1ab:3C-like-proteinase	0.99412300306266
CAMB-79794	MN908947.3	11074	C	INS	0.035	0.033	1.9e-08	3.6e-07	0.0345753263899076	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.9651312894235
CAMB-79794	MN908947.3	11075	T	-	0.051	0.038	2.3e-12	6.9e-10	0.0456902059069242	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.950992677772864
CAMB-79794	MN908947.3	13721	C	T	0.025	0.0063	6.1e-13	9.8e-05	0.0171757550255341	CCA	ORF1ab:RNA-dependent-RNA-polymerase	P85L	C254T	CCA>CTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.982785991622516
CAMB-79794	MN908947.3	1385	C	T	1	1	0	0	1	TCA	ORF1ab:nsp2	H194Y	C580T	CAC>TAC	Missense	ORF1ab:nsp2	0
CAMB-79794	MN908947.3	14408	C	T	1	1	0	0	0.999531420836154	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00031238610923101
CAMB-79794	MN908947.3	18086	C	T	0.01	0.007	3.9e-06	7.7e-05	0.00870986630233239	ACT	ORF1ab:3'-to-5'-exonuclease	T16I	C47T	ACT>ATT	Missense	ORF1ab:3'-to-5'-exonuclease	0.991290133697668
CAMB-79794	MN908947.3	2059	G	A	0.02	0.027	2.9e-11	8.5e-14	0.0230912898296451	TGG	ORF1ab:nsp2	M418I	G1254A	ATG>ATA	Missense	ORF1ab:nsp2	0.976908710170355
CAMB-79794	MN908947.3	2147	C	T	0.036	0.045	1.3e-17	3.3e-21	0.0396925668561803	CCT	ORF1ab:nsp2	L448F	C1342T	CTT>TTT	Missense	ORF1ab:nsp2	0.96030743314382
CAMB-79794	MN908947.3	21569	G	INS	0.039	0.087	5.2e-15	1.6e-31	0.0611944689614593	TGT	S	.	6-7-insfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.937334510150044
CAMB-79794	MN908947.3	21575	C	-	0.021	0.01	1.9e-09	1.4e-05	0.0160752198968759	TCT	S	.	13-13-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0
CAMB-79794	MN908947.3	21575	C	T	0.98	0.99	0	0	0.983924780103124	TCT	S	L5F	C13T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-79794	MN908947.3	21614	C	T	0.025	0.01	7.1e-11	1.5e-05	0.0185561032183242	TCT	S	L18F	C52T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.981443896781676
CAMB-79794	MN908947.3	2306	C	T	0.008	0.0051	2.8e-05	0.00048	0.00683267537200121	GCT	ORF1ab:nsp2	L501F	C1501T	CTT>TTT	Missense	ORF1ab:nsp2	0.993167324627999
CAMB-79794	MN908947.3	23403	A	G	1	1	0	0	0.997584306810668	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.69803835133348e-05
CAMB-79794	MN908947.3	23444	C	T	0.0029	0.0068	0.0027	4.3e-05	0.00458574807272202	TCA	S	Q628*	C1882T	CAA>TAA	Nonsense	GU280_gp02, spike glycoprotein	0.995387170737872
CAMB-79794	MN908947.3	23982	CAG	-	0.00743333333333333	0.004396	1.1e-05;2.4e-05;1.3e-05	NA;3.9e-05;2.6e-05	0.00719398965199518	CCA	S	.	2420-2422-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.995327102803738
CAMB-79794	MN908947.3	241	C	T	0.99	1	0	0	0.994818875631517	TCG	NA	NA	NA	NA	NA	NA	0.00509513060303128
CAMB-79794	MN908947.3	26110	C	T	0.0089	0.0084	4.2e-05	0.00013	0.00874271440466278	GCC	ORF3a	P240S	C718T	CCT>TCT	Missense	GU280_gp03	0.991257285595337
CAMB-79794	MN908947.3	2635	G	C	0.0041	0.0073	3e-04	2.5e-05	0.00538647993536224	TGC	ORF1ab:nsp2	L610F	G1830C	TTG>TTC	Missense	ORF1ab:nsp2	0.994613520064638
CAMB-79794	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998401583193789	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.20609884332282e-05
CAMB-79794	MN908947.3	29427	G	T	0.017	0.0093	2e-08	1.3e-05	0.013533325814819	AGA	N	R385I	G1154T	AGA>ATA	Missense	GU280_gp10	0.986241118754934
CAMB-79794	MN908947.3	300	C	-	0.0053	0.0074	0.00027	2.9e-05	0.00621067751006453	ACA	ORF1ab:leader-protein	.	35-35-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.993627480730715
CAMB-79794	MN908947.3	3037	C	T	1	1	0	0	0.999332354119375	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000133529176124983
CAMB-79794	MN908947.3	3586	AC	-	0.014	0.01	5.5e-06;5.5e-06	0.00026;0.00025	0.0123772940674349	GAC	ORF1ab:nsp3	.	867-868-delfrshift	.	no-SNV	ORF1ab:nsp3	0.987601539119282
CAMB-79794	MN908947.3	4579	T	A	0.031	0.034	1.5e-15	1.1e-16	0.0321740747628789	TTA	ORF1ab:nsp3	L620L	T1860A	CTT>CTA	Synonymous	ORF1ab:nsp3	0.967732936581737
CAMB-79794	MN908947.3	4788	C	T	0.0062	0.011	8.6e-05	4.8e-07	0.00865469838897482	GCT	ORF1ab:nsp3	A690V	C2069T	GCT>GTT	Missense	ORF1ab:nsp3	0.991258407048887
CAMB-79794	MN908947.3	4806	G	-	0.0061	0.01	0.00074	2e-05	0.00799703063841274	TGG	ORF1ab:nsp3	.	2087-2087-delfrshift	.	no-SNV	ORF1ab:nsp3	0.991834255635038
CAMB-79794	MN908947.3	6080	G	A	0.023	0.017	8.2e-11	1.3e-08	0.0203361693297365	TGA	ORF1ab:nsp3	D1121N	G3361A	GAT>AAT	Missense	ORF1ab:nsp3	0.979663830670264
CAMB-79794	MN908947.3	6375	A	G	0.012	0.006	1.2e-07	5.6e-05	0.00980465758772391	GAT	ORF1ab:nsp3	D1219G	A3656G	GAT>GGT	Missense	ORF1ab:nsp3	0.990180327622708
CAMB-79794	MN908947.3	8015	GCG	-	0.00203333333333333	0.009	NA;8.9e-05;NA	3.4e-06;4.7e-06;2.7e-06	0.00358477382507519	TGC	ORF1ab:nsp3	.	5296-5298-delinframe	.	no-SNV	ORF1ab:nsp3	0.996384846735729
CAMB-79794	MN908947.3	8139	CC	TT	0.0034	0.00905	NA;1e-04	1.7e-05;3.2e-06	0.00565656565656566	TCC	ORF1ab:nsp3	.	5420-5421-mnv	.	no-SNV	ORF1ab:nsp3	0.996659748346089
CAMB-797A3	MN908947.3	11074	C	INS	0.1	0.15	3.9e-32	6.2e-48	0.121302903208236	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.878125170216243
CAMB-797A3	MN908947.3	11082	TG	-	0.077	0.06575	4e-09;1.4e-40	0.46;8.4e-55	0.0716851205072948	TTG	ORF1ab:nsp6	.	110-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962753277711561
CAMB-797A3	MN908947.3	11083	G	-	0.094	0.13	1.4e-40	8.4e-55	0.106004447739066	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-797A3	MN908947.3	11083	G	T	0.91	0.87	0	0	0.893847294292068	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-797A3	MN908947.3	14805	C	T	1	1	0	0	0.999902840301843	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	3.23865660524015e-05
CAMB-797A3	MN908947.3	1515	A	G	1	1	2.40017090749678e-320	0	1	CAT	ORF1ab:nsp2	H237R	A710G	CAT>CGT	Missense	ORF1ab:nsp2	0
CAMB-797A3	MN908947.3	17247	T	C	1	1	0	0	0.999886096134862	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	7.59359100918825e-05
CAMB-797A3	MN908947.3	9223	C	T	1	1	0	0	0.999729863581108	ACG	ORF1ab:nsp4	H223H	C669T	CAC>CAT	Synonymous	ORF1ab:nsp4	0.000180090945927693
CAMB-797B2	MN908947.3	11075	T	-	0.028	0.032	2.9e-07	2e-08	0.0296500640788931	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.965820970089276
CAMB-797B2	MN908947.3	14408	C	T	1	1	0	0	0.998284170185659	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000503447071273721
CAMB-797B2	MN908947.3	17835	T	C	1	1	0	0	0.999851411589896	TTG	ORF1ab:helicase	V533V	T1599C	GTT>GTC	Synonymous	ORF1ab:helicase	9.90589400693413e-05
CAMB-797B2	MN908947.3	23403	A	G	1	1	0	0	0.999862884427704	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000104853084697096
CAMB-797B2	MN908947.3	241	C	T	1	1	0	0	0.998626321692775	TCG	NA	NA	NA	NA	NA	NA	0.000138628086050234
CAMB-797B2	MN908947.3	26137	A	C	0.027	0.017	6.1e-06	0.0025	0.0220897615708275	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.977910238429172
CAMB-797B2	MN908947.3	27892	A	C	1	1	0	0	0.999688206407358	AAC	NA	NA	NA	NA	NA	NA	0.000155896796320836
CAMB-797B2	MN908947.3	28057	C	T	0.01	0.016	2.6e-06	1.9e-08	0.0125204137180185	GCA	ORF8	A55V	C164T	GCA>GTA	Missense	GU280_gp09	0.987479586281982
CAMB-797B2	MN908947.3	3037	C	T	1	1	0	0	0.99962634014544	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.74861314707827e-05
CAMB-797B2	MN908947.3	6532	G	T	1	1	0	0	0.999953314659197	AGG	ORF1ab:nsp3	E1271D	G3813T	GAG>GAT	Missense	ORF1ab:nsp3	4.66853408029879e-05
CAMB-797C1	MN908947.3	11074	CT	-	0.030012	0.0228	NA;2.1e-14	0.00011;1.1e-10	0.0291468763788315	TCT	ORF1ab:nsp6	.	102-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.977626100994081
CAMB-797C1	MN908947.3	11075	T	-	0.06	0.042	2.1e-14	1.1e-10	0.0525641332726532	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.942729167165681
CAMB-797C1	MN908947.3	14408	C	T	0.99	1	0	0	0.993948150692232	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000521098570531876
CAMB-797C1	MN908947.3	20234	C	T	0.15	0.2	1.3e-30	2.7e-40	0.17595818815331	CCC	ORF1ab:endoRNAse	P205L	C614T	CCC>CTC	Missense	ORF1ab:endoRNAse	0.82404181184669
CAMB-797C1	MN908947.3	23403	A	G	1	1	0	0	0.999964039448725	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.5960551275251e-05
CAMB-797C1	MN908947.3	241	C	T	0.99	1	0	0	0.997201441349161	TCG	NA	NA	NA	NA	NA	NA	9.14561650600867e-05
CAMB-797C1	MN908947.3	25064	G	T	0.0096	0.028	2.8e-06	5.7e-14	0.0185428788262079	TGA	S	D1168Y	G3502T	GAC>TAC	Missense	GU280_gp02, spike glycoprotein	0.981305337718189
CAMB-797C1	MN908947.3	26137	A	C	0.034	0.021	1.4e-05	0.0055	0.0287581699346405	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.971241830065359
CAMB-797C1	MN908947.3	26781	CTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0344324324324324	0.0333513513513514	0.00022;6.2e-05;6.8e-05;0.00019;2.3e-06;1.9e-05;9.5e-06;9.2e-06;2.3e-06;4.2e-06;2.7e-06;9.1e-06;4.8e-06;6.3e-06;1.3e-05;4e-06;1.1e-05;6.9e-06;7e-06;6.4e-06;1.2e-05;6.5e-06;8.8e-06;6.3e-06;2.5e-06;8.6e-06;5.5e-06;4.8e-06;4.6e-06;9.9e-06;5.2e-06;2.3e-06;6.7e-06;3.3e-06;5.6e-06;3.3e-06;0.00068	0.00026;0.00074;0.00077;0.0014;5.6e-06;2.4e-05;9.9e-06;1e-05;3.2e-06;5.4e-06;4.2e-06;1e-05;6e-06;7.8e-06;1.4e-05;5.2e-06;1.2e-05;7.8e-06;7.6e-06;7.3e-06;1.3e-05;7.5e-06;9.8e-06;6.7e-06;3.3e-06;9.7e-06;5.8e-06;6.6e-06;5.6e-06;1.1e-05;5.6e-06;1.8e-06;7.5e-06;3.3e-06;1.1e-05;7.3e-06;9e-04	0.035014404299655	TCT	M	.	259-295-delfrshift	.	no-SNV	GU280_gp05	0.976659493461348
CAMB-797C1	MN908947.3	27720	TA	-	0.022	0.019	2.6e-05;2.4e-05	0.0012;0.0013	0.0209580838323353	TTA	ORF7a	.	327-328-delfrshift	.	no-SNV	GU280_gp07	0.979591836734694
CAMB-797C1	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99967173138248	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	5.13584304863643e-05
CAMB-797C1	MN908947.3	3037	C	T	1	1	0	0	0.999300780794779	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000291341335508682
CAMB-797C1	MN908947.3	324	TTTT	-	0.007425	0.002875	4.3e-06;9.4e-07;0.00076;0.00073	0.004;0.01;0.0039;0.0034	0.00516333165278768	GTT	ORF1ab:leader-protein	.	59-62-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.991842552679936
CAMB-797C1	MN908947.3	4900	C	T	0.0077	0.0028	1.6e-05	0.0018	0.00536026936026936	ACC	ORF1ab:nsp3	H727H	C2181T	CAC>CAT	Synonymous	ORF1ab:nsp3	0.994626262626263
CAMB-797C1	MN908947.3	522	TT	-	0.048	0.053	2.2e-07;1.4e-05	2.7e-09;4e-05	0.0498109758630717	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.936471644087354
CAMB-797C1	MN908947.3	6665	CCTTGGGATACTATAGC	-	0.00811764705882353	0.00548235294117647	0.00077;0.00093;0.00027;5.2e-05;0.00013;3.7e-05;8.4e-05;8.7e-05;8.1e-05;9.7e-05;9.4e-05;7.2e-05;7e-05;3.7e-05;1e-04;4.3e-05;6.3e-05	0.0033;0.004;0.0017;0.00062;0.0011;0.00064;0.00087;0.00091;0.00088;0.00096;0.00096;0.00082;0.00081;6e-04;0.001;0.00064;0.00079	0.00645161290322581	CCC	ORF1ab:nsp3	.	3946-3962-delfrshift	.	no-SNV	ORF1ab:nsp3	0.990292668791655
CAMB-797C1	MN908947.3	835	C	T	0.0073	0.0093	5.2e-05	6.6e-06	0.00823330588898037	TCT	ORF1ab:nsp2	F10F	C30T	TTC>TTT	Synonymous	ORF1ab:nsp2	0.99172336092213
CAMB-797D0	MN908947.3	10396	G	T	0.15	0.16	4.4e-70	1.7e-75	0.156522712016111	TGT	ORF1ab:3C-like-proteinase	V114V	G342T	GTG>GTT	Synonymous	ORF1ab:3C-like-proteinase	0.843277498961097
CAMB-797D0	MN908947.3	11075	T	-	0.043	0.044	1.1e-10	5.6e-11	0.0432465981216479	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952584490713633
CAMB-797D0	MN908947.3	12823	C	T	0.013	0.0095	1.7e-07	3.3e-06	0.0111283529150964	CCG	ORF1ab:nsp9	S46S	C138T	TCC>TCT	Synonymous	ORF1ab:nsp9	0.988709081504471
CAMB-797D0	MN908947.3	14408	C	T	1	1	0	0	0.997790804497135	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000546830570016186
CAMB-797D0	MN908947.3	1843	G	T	0.01	0.0098	1.6e-06	2.2e-06	0.0100273020600645	AGA	ORF1ab:nsp2	Q346H	G1038T	CAG>CAT	Missense	ORF1ab:nsp2	0.989923057830727
CAMB-797D0	MN908947.3	20426	T	C	0.2	0.24	1.4e-47	2.2e-60	0.220524017467249	ATT	ORF1ab:endoRNAse	I269T	T806C	ATT>ACT	Missense	ORF1ab:endoRNAse	0.779475982532751
CAMB-797D0	MN908947.3	23191	C	T	0.046	0.053	7.9e-09	5.7e-10	0.049084355101826	TCA	S	F543F	C1629T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.95042230174183
CAMB-797D0	MN908947.3	23403	A	G	1	1	0	0	0.999641101401374	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.3464790378179e-05
CAMB-797D0	MN908947.3	23873	G	T	1	1	0	0	0.99992653001249	AGC	S	A771S	G2311T	GCT>TCT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-797D0	MN908947.3	241	C	T	1	1	0	0	0.999265437294361	TCG	NA	NA	NA	NA	NA	NA	9.18203382049124e-05
CAMB-797D0	MN908947.3	26195	C	T	0.0091	0.011	9.8e-06	1.2e-06	0.010226216299969	ACG	ORF3a	T268M	C803T	ACG>ATG	Missense	GU280_gp03	0.989773783700031
CAMB-797D0	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999558603829961	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000186414137648199
CAMB-797D0	MN908947.3	3037	C	T	1	1	0	0	0.998984083982391	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.07853338669458e-05
CAMB-797D0	MN908947.3	6474	A	T	0.005	0.0073	0.00019	1.9e-05	0.00609422135672494	GAA	ORF1ab:nsp3	E1252V	A3755T	GAA>GTA	Missense	ORF1ab:nsp3	0.993862310587949
CAMB-797D0	MN908947.3	7231	C	T	0.85	0.84	0	0	0.840768702814001	GCT	ORF1ab:nsp3	G1504G	C4512T	GGC>GGT	Synonymous	ORF1ab:nsp3	0.159231297185999
CAMB-797D0	MN908947.3	745	C	T	0.065	0.06	5.1e-30	7.5e-28	0.063005980122116	ACT	ORF1ab:leader-protein	N160N	C480T	AAC>AAT	Synonymous	ORF1ab:leader-protein	0.936952127603867
CAMB-797D0	MN908947.3	850	C	T	0.0086	0.0043	8e-06	0.00059	0.00650120799472875	GCT	ORF1ab:nsp2	G15G	C45T	GGC>GGT	Synonymous	ORF1ab:nsp2	0.99348781023501
CAMB-797EF	MN908947.3	10202	C	T	0.0075	0.0046	3.8e-05	0.00075	0.00615685597560274	GCT	ORF1ab:3C-like-proteinase	L50F	C148T	CTT>TTT	Missense	ORF1ab:3C-like-proteinase	0.993804783551029
CAMB-797EF	MN908947.3	10517	G	T	0.0073	0.0051	3.8e-05	0.00032	0.00639362490733877	TGA	ORF1ab:3C-like-proteinase	D155Y	G463T	GAC>TAC	Missense	ORF1ab:3C-like-proteinase	0.993606375092661
CAMB-797EF	MN908947.3	11075	T	-	0.032	0.045	2.8e-08	1.3e-11	0.0372284871960974	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95758913816581
CAMB-797EF	MN908947.3	11452	A	G	1	1	0	0	0.998480243161094	AAG	ORF1ab:nsp6	Q160Q	A480G	CAA>CAG	Synonymous	ORF1ab:nsp6	0
CAMB-797EF	MN908947.3	12028	G	T	0.008	0.0028	2.8e-05	0.0062	0.00572634116937914	TGC	ORF1ab:nsp7	M62I	G186T	ATG>ATT	Missense	ORF1ab:nsp7	0.992678822583886
CAMB-797EF	MN908947.3	12056	TG	-	0.0031	0.00715	0.004;0.0075	4.8e-05;0.00012	0.00482900973446817	TTG	ORF1ab:nsp7	.	214-215-delfrshift	.	no-SNV	ORF1ab:nsp7	0.994493362414842
CAMB-797EF	MN908947.3	12067	G	T	0.0069	0.0078	0.00012	4.8e-05	0.00730902610538484	TGC	ORF1ab:nsp7	M75I	G225T	ATG>ATT	Missense	ORF1ab:nsp7	0.992654850207109
CAMB-797EF	MN908947.3	14408	C	T	1	1	0	0	0.999354392437169	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000476519867804166
CAMB-797EF	MN908947.3	15726	TGT	-	0.00124366666666667	0.00793333333333333	NA;0.0028;NA	2.5e-06;1.3e-05;0.00053	0.00383553237189322	CTG	ORF1ab:RNA-dependent-RNA-polymerase	.	2259-2261-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.995627427951938
CAMB-797EF	MN908947.3	18357	TTTACAGCTAGGTTTTTCTACAGGTGTTAACCTAGTT	-	0.0153783783783784	0.00093927027027027	3.7e-05;4.9e-05;0.00026;0.00014;0.00015;4.8e-05;6.6e-05;0.00025;0.00022;8.8e-06;0.00015;0.00024;3.5e-05;9.1e-05;3.6e-05;0.00018;0.00043;0.00053;5e-04;0.00056;0.00049;0.00041;0.00036;6e-04;0.00025;0.00057;1.4e-05;3e-05;5.4e-08;1.1e-07;5.7e-08;8.1e-08;8.4e-07;2.4e-07;0.00013;5e-05;5.8e-05	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.5;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00052;0.00033;0.0067;0.004;0.0044	0.00795929389692714	CTT	ORF1ab:3'-to-5'-exonuclease	.	318-354-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.991386049308479
CAMB-797EF	MN908947.3	1969	A	G	0.011	0.0023	6.8e-07	0.0063	0.00675559626724681	CAA	ORF1ab:nsp2	T388T	A1164G	ACA>ACG	Synonymous	ORF1ab:nsp2	0.993244403732753
CAMB-797EF	MN908947.3	23403	A	G	1	1	0	0	0.999925856588106	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.56075589208426e-05
CAMB-797EF	MN908947.3	241	C	T	0.99	1	0	0	0.992920726151258	TCG	NA	NA	NA	NA	NA	NA	0.000116819700474288
CAMB-797EF	MN908947.3	26131	C	T	0.011	0.0033	8.5e-06	0.0051	0.0080296479308215	TCA	ORF3a	H247Y	C739T	CAC>TAC	Missense	GU280_gp03	0.991970352069178
CAMB-797EF	MN908947.3	26333	C	T	0.0042	0.0092	0.0037	2.2e-05	0.00652335471085299	ACA	E	T30I	C89T	ACA>ATA	Missense	GU280_gp04	0.991907737194132
CAMB-797EF	MN908947.3	26336	T	C	0.015	0.003	2.1e-08	0.0043	0.00949171581016568	CTA	E	L31P	T92C	CTA>CCA	Missense	GU280_gp04	0.990480202190396
CAMB-797EF	MN908947.3	26768	C	A	0.0084	0.005	9.6e-06	0.00017	0.00688336068573857	TCG	M	I82I	C246A	ATC>ATA	Synonymous	GU280_gp05	0.993069412139745
CAMB-797EF	MN908947.3	27476	C	T	0.011	0.0028	3.4e-06	0.0097	0.00781985139037607	ACA	ORF7a	T28I	C83T	ACA>ATA	Missense	GU280_gp07	0.992136885254767
CAMB-797EF	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999458288190683	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-797EF	MN908947.3	3037	C	T	1	1	0	0	0.999650593990217	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000174703004891684
CAMB-797EF	MN908947.3	4921	C	T	0.0058	0.008	0.00022	2.2e-05	0.00676783895305675	CCT	ORF1ab:nsp3	T734T	C2202T	ACC>ACT	Synonymous	ORF1ab:nsp3	0.993214896151655
CAMB-797EF	MN908947.3	5371	A	G	0.015	0.0053	1.8e-07	0.00059	0.0103558151885289	CAA	ORF1ab:nsp3	A884A	A2652G	GCA>GCG	Synonymous	ORF1ab:nsp3	0.989644184811471
CAMB-797EF	MN908947.3	6681	C	T	1	1	0	0	1	GCT	ORF1ab:nsp3	A1321V	C3962T	GCT>GTT	Missense	ORF1ab:nsp3	0
CAMB-797EF	MN908947.3	7448	A	-	0.011	0.02	6.1e-06	2.4e-09	0.0145342269749228	GAA	ORF1ab:nsp3	.	4729-4729-delfrshift	.	no-SNV	ORF1ab:nsp3	0.985239852398524
CAMB-797EF	MN908947.3	7448	AA	-	0.01	0.01	6.1e-06;6e-06	2.4e-09;NA	0.0103614261238476	GAA	ORF1ab:nsp3	.	4729-4730-delfrshift	.	no-SNV	ORF1ab:nsp3	0.985239852398524
CAMB-797EF	MN908947.3	7515	G	T	0.011	0.0046	4e-06	0.0016	0.00833333333333333	AGA	ORF1ab:nsp3	R1599I	G4796T	AGA>ATA	Missense	ORF1ab:nsp3	0.991666666666667
CAMB-797EF	MN908947.3	9738	G	T	0.02	0.0032	1.3e-10	0.00087	0.0126003335765662	AGT	ORF1ab:nsp4	S395I	G1184T	AGT>ATT	Missense	ORF1ab:nsp4	0.987360575419577
CAMB-797EF	MN908947.3	9753	G	T	0.0072	0.006	2.6e-05	6.7e-05	0.00668659827066457	AGA	ORF1ab:nsp4	R400I	G1199T	AGA>ATA	Missense	ORF1ab:nsp4	0.99323896835341
CAMB-797FE	MN908947.3	10033	T	C	0.024	0.058	6.1e-12	3.9e-26	0.0398094067015063	CTA	ORF1ab:nsp4	S493S	T1479C	TCT>TCC	Synonymous	ORF1ab:nsp4	0.959985654267855
CAMB-797FE	MN908947.3	11075	T	-	0.055	0.033	2e-13	7.4e-09	0.0457495755052856	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951114640959632
CAMB-797FE	MN908947.3	11075	TT	-	0.0314	0.0165335	2e-13;0.00048	7.4e-09;0.49	0.0253651782623745	CTT	ORF1ab:nsp6	.	103-104-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951114640959632
CAMB-797FE	MN908947.3	11651	C	INS	0.024	0.023	2.9e-11	2.4e-10	0.0238696350700023	CCT	ORF1ab:nsp6	.	678-679-insfrshift	.	no-SNV	ORF1ab:nsp6	0.971310534771632
CAMB-797FE	MN908947.3	11653	C	T	1	0.99	0	0	0.99593398708443	TCT	ORF1ab:nsp6	L227L	C681T	CTC>CTT	Synonymous	ORF1ab:nsp6	0
CAMB-797FE	MN908947.3	14408	C	T	1	1	0	0	0.999341860531662	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00048645091138009
CAMB-797FE	MN908947.3	14854	GTA	-	0.049	0.0153333333333333	8.3e-07;1.2e-10;2.4e-10	0.0017;0.0026;0.0028	0.031617105944561	TGT	ORF1ab:RNA-dependent-RNA-polymerase	.	1387-1389-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.963599443975033
CAMB-797FE	MN908947.3	16301	GACCATT	-	0.008	0.0152857142857143	0.00081;0.0011;0.0013;0.0011;0.00088;0.00072;0.00087	1.3e-05;2.4e-05;3.1e-05;2.1e-05;1.6e-05;6.7e-06;8.3e-06	0.0107714240456201	AGA	ORF1ab:helicase	.	65-71-delfrshift	.	no-SNV	ORF1ab:helicase	0.987567851514621
CAMB-797FE	MN908947.3	18396	TGTACCTACAGGTTA	-	0.000654933333333333	0.0125333333333333	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00038;NA;0.46;NA;NA	0.00043;0.00048;0.00013;9e-05;1.8e-05;7.5e-05;3e-05;3.3e-05;3.8e-05;3.2e-05;9e-05;6.3e-05;2.1e-06;3.9e-05;9.9e-07	0.00570957590289225	CTG	ORF1ab:3'-to-5'-exonuclease	.	357-371-delinframe	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.99423622734881
CAMB-797FE	MN908947.3	18651	GCGCACCTGTTGTCTATG	-	0.0052	0.016	NA;NA;NA;NA;NA;NA;NA;0.00097;0.0061;0.00034;0.0086;0.0075;0.008;0.0067;0.0068;0.0083;0.003;0.0044	2.9e-05;4.1e-05;3.7e-05;4.5e-05;2e-06;7.3e-08;2.1e-07;9.9e-06;2e-04;0.00059;0.00039;0.00017;0.00025;0.00015;0.00017;0.00024;8.9e-08;2.6e-07	0.0105268906759875	AGC	ORF1ab:3'-to-5'-exonuclease	.	612-629-delinframe	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.993228982222537
CAMB-797FE	MN908947.3	21980	TTTTTGGGTGT	-	0.00206272727272727	0.0380909090909091	0.5;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00062	9.5e-09;1.8e-08;3.4e-08;9e-07;6.7e-07;1.3e-07;8.7e-07;1.5e-06;1e-06;5.1e-07;5.8e-05	0.0179792352494302	ATT	S	.	418-428-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.98398444732457
CAMB-797FE	MN908947.3	23403	A	G	1	0.99	0	0	0.996773372690722	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.12504453152832e-05
CAMB-797FE	MN908947.3	241	C	T	1	1	0	0	0.999782939005861	TCG	NA	NA	NA	NA	NA	NA	0.000151942695897547
CAMB-797FE	MN908947.3	24469	T	-	0.017	0.018	2.9e-05	2.6e-05	0.0172980074447121	ATT	S	.	2907-2907-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.982483030435735
CAMB-797FE	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.0349804878048781	0.0635609756097561	0.088;0.034;0.082;0.085;0.11;1.5e-05;8.6e-05;1.1e-06;1e-06;2.2e-07;4.3e-07;2.7e-07;1.1e-06;4.9e-07;7.1e-07;1.6e-06;3.8e-07;1.3e-06;7.1e-07;7.4e-07;5.1e-07;1.5e-06;6.3e-07;9.6e-07;6.4e-07;3.8e-07;1.1e-06;5.5e-07;1.8e-07;5.3e-07;1.1e-06;1e-06;5e-07;1.2e-06;2.3e-07;5.4e-07;4.2e-07;0.00026;0.00091;0.0031;0.0035	3.7e-08;1e-10;1.6e-08;1.9e-08;7.5e-08;3.2e-12;4.9e-11;2.7e-12;2.5e-12;3.3e-13;6.9e-13;4.2e-13;2.6e-12;9.2e-13;1.6e-12;4.6e-12;7.4e-13;3.7e-12;1.6e-12;1.5e-12;8.6e-13;3.7e-12;1.3e-12;2.4e-12;1.2e-12;5.9e-13;2.7e-12;8.2e-13;3.5e-13;1.1e-12;2.8e-12;2.3e-12;1.6e-12;3.1e-12;1.2e-13;7.6e-13;5.1e-13;1.2e-05;7.1e-05;2.4e-05;4.2e-05	0.0530345107104793	GTC	M	.	258-298-delfrshift	.	no-SNV	GU280_gp05	0.974588200059898
CAMB-797FE	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999909362820629	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-797FE	MN908947.3	2904	T	INS	0.013	0.018	1.1e-06	2.5e-08	0.0151426481346013	ATA	ORF1ab:nsp3	.	184-185-insfrshift	.	no-SNV	ORF1ab:nsp3	0.984857351865399
CAMB-797FE	MN908947.3	29180	CAAATTGCACA	-	0.000889909090909091	0.00593636363636364	NA;NA;NA;NA;NA;NA;NA;0.00027;0.00029;NA;NA	0.00016;0.00022;1.5e-05;0.00011;0.00013;0.00012;0.00013;3.8e-06;4.5e-06;2e-04;0.00021	0.00211704218962649	GCA	N	.	907-917-delfrshift	.	no-SNV	GU280_gp10	0.998131558740722
CAMB-797FE	MN908947.3	3037	C	T	1	1	0	0	0.99955003599712	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000179985601151908
CAMB-797FE	MN908947.3	5230	G	T	0.0092	0.017	0.00016	3.7e-06	0.0123784261715296	AGT	ORF1ab:nsp3	K837N	G2511T	AAG>AAT	Missense	ORF1ab:nsp3	0.986737400530504
CAMB-797FE	MN908947.3	596	G	T	0.0088	0.003	5.3e-06	0.0022	0.00628816421982591	TGT	ORF1ab:leader-protein	V111L	G331T	GTG>TTG	Missense	ORF1ab:leader-protein	0.993685851630505
CAMB-797FE	MN908947.3	6696	C	INS	0.027	0.024	3.1e-05	0.00015	0.0257890685142417	CCT	ORF1ab:nsp3	.	3976-3977-insfrshift	.	no-SNV	ORF1ab:nsp3	0.974018475750577
CAMB-797FE	MN908947.3	8482	T	-	0.0093	0.013	3.2e-05	1.5e-06	0.0109963345551483	CTT	ORF1ab:nsp3	.	5763-5763-delfrshift	.	no-SNV	ORF1ab:nsp3	0.98878151727202
CAMB-797FE	MN908947.3	8482	TT	-	0.00935	0.0065	3.2e-05;1e-05	1.5e-06;NA	0.00785105428443248	CTT	ORF1ab:nsp3	.	5763-5764-delfrshift	.	no-SNV	ORF1ab:nsp3	0.98878151727202
CAMB-797FE	MN908947.3	9188	GTG	-	0.0083	0.00833333333333333	2e-05;9.8e-05;3e-05	1.7e-05;9e-05;2.6e-05	0.00836307112989032	AGT	ORF1ab:nsp4	.	634-636-delinframe	.	no-SNV	ORF1ab:nsp4	0.991773524926434
CAMB-7980A	MN908947.3	11075	T	-	0.036	0.043	5.6e-09	6.4e-11	0.0383909397382218	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955502501409667
CAMB-7980A	MN908947.3	14408	C	T	1	1	0	0	0.998723324509827	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000491930005387805
CAMB-7980A	MN908947.3	14932	C	T	0.021	0.013	5.6e-11	9.8e-08	0.0174697242978614	CCT	ORF1ab:RNA-dependent-RNA-polymerase	L489L	C1465T	CTA>TTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.982530275702139
CAMB-7980A	MN908947.3	21481	CTTAGTAAAG	-	0.0119	0.0168	0.004;0.0044;0.0046;0.0055;0.0045;0.0049;0.0054;0.0036;0.0017;0.0041	0.00015;0.00015;0.00013;0.00015;0.00012;0.00015;0.00017;9.7e-05;2.6e-05;9.4e-05	0.0143594345972627	TCT	ORF1ab:2'-O-ribose-methyltransferase	.	823-832-delfrshift	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.985845877330937
CAMB-7980A	MN908947.3	21496	CTTATAATTAGAGAAAACAACAGAGTTGTTATT	-	0.0138787878787879	0.0175454545454545	0.0011;0.0015;0.0019;0.0023;0.0021;0.0023;0.0021;0.0021;0.0023;0.0027;0.0016;0.002;0.0018;0.0017;0.002;0.002;0.0015;0.0021;0.0021;0.0021;0.0016;0.0027;0.0017;0.002;0.0023;0.0011;0.0013;0.0021;0.002;0.0024;0.0029;0.0027;0.003	5.8e-05;8.7e-05;0.00013;0.00016;0.00015;0.00017;0.00019;0.00018;0.00019;0.00023;0.00011;0.00017;0.00011;9.3e-06;0.00017;0.00017;0.00012;0.00015;0.00019;0.00018;0.00013;0.00026;0.00015;0.00019;2e-04;7e-05;8.9e-05;0.00017;0.00016;0.00023;3e-04;0.00031;3e-04	0.0155560715114929	ACT	ORF1ab:2'-O-ribose-methyltransferase	.	838-870-delinframe	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.981461286804798
CAMB-7980A	MN908947.3	21543	TGTTAACAA	-	0.016	0.0211111111111111	0.0017;0.0019;0.0011;0.0011;0.0011;3e-04;7e-04;0.002;0.0013	3.5e-05;5.8e-05;2.9e-05;3e-05;4.3e-05;1.1e-05;1.9e-05;9.8e-05;4.6e-05	0.0183950333409979	TTG	ORF1ab:2'-O-ribose-methyltransferase	.	885-893-delinframe	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.979691705407389
CAMB-7980A	MN908947.3	23403	A	G	1	1	0	0	0.999020480854853	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.01424755120214e-05
CAMB-7980A	MN908947.3	241	C	T	1	1	0	0	0.997904662126768	TCG	NA	NA	NA	NA	NA	NA	0.00196437925615506
CAMB-7980A	MN908947.3	2416	C	T	1	1	0	0	0.998211963589077	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0
CAMB-7980A	MN908947.3	24789	C	T	0.016	0.017	1e-08	1.9e-09	0.0163819951678002	ACA	S	T1076I	C3227T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0.983604038936916
CAMB-7980A	MN908947.3	25563	G	T	1	1	0	0	0.99992516426444	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	2.99342942241779e-05
CAMB-7980A	MN908947.3	26137	A	C	0.024	0.018	2.3e-05	0.0028	0.0222036028487641	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.977796397151236
CAMB-7980A	MN908947.3	27697	C	T	0.025	0.042	9.4e-08	2.7e-10	0.0321285140562249	TCT	ORF7a	L102F	C304T	CTT>TTT	Missense	GU280_gp07	0.967871485943775
CAMB-7980A	MN908947.3	29774	C	T	0.012	0.0051	4.4e-06	0.0026	0.00906560636182903	GCT	NA	NA	NA	NA	NA	NA	0.990059642147117
CAMB-7980A	MN908947.3	3037	C	T	1	1	0	0	0.999604273842501	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.59543595831684e-05
CAMB-7980A	MN908947.3	3177	C	T	0.027	0.02	2.5e-13	3e-10	0.0240367356706952	CCT	ORF1ab:nsp3	P153L	C458T	CCT>CTT	Missense	ORF1ab:nsp3	0.975843604164174
CAMB-7980A	MN908947.3	3718	T	C	0.0057	0.022	4e-04	1.1e-09	0.0121137206427688	CTG	ORF1ab:nsp3	A333A	T999C	GCT>GCC	Synonymous	ORF1ab:nsp3	0.987639060568603
CAMB-7980A	MN908947.3	5387	GCTA	-	0.006175	0.000925	1.8e-05;0.00063;0.00048;0.00043	0.0056;NA;NA;NA	0.00277291301809691	TGC	ORF1ab:nsp3	.	2668-2671-delfrshift	.	no-SNV	ORF1ab:nsp3	0.992633251480572
CAMB-7980A	MN908947.3	5773	T	C	0.033	0.03	7.4e-16	1.5e-14	0.0315019688730546	ATA	ORF1ab:nsp3	Y1018Y	T3054C	TAT>TAC	Synonymous	ORF1ab:nsp3	0.96844445634995
CAMB-79819	MN908947.3	11075	T	-	0.04	0.04	4.2e-10	3.5e-10	0.0400827703730753	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955291826425659
CAMB-79819	MN908947.3	12410	A	G	0.012	0.0093	5.5e-07	5.3e-06	0.0107104528868856	TAT	ORF1ab:nsp8	I107V	A319G	ATC>GTC	Missense	ORF1ab:nsp8	0.989289547113114
CAMB-79819	MN908947.3	1439	G	T	0.012	0.019	6e-07	2.3e-09	0.0149055720305915	TGG	ORF1ab:nsp2	G212C	G634T	GGC>TGC	Missense	ORF1ab:nsp2	0.98493834868113
CAMB-79819	MN908947.3	14408	C	T	1	1	0	0	0.999472384373597	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000404131118096093
CAMB-79819	MN908947.3	23403	A	G	1	1	0	0	0.998969808076056	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.86704845957916e-05
CAMB-79819	MN908947.3	241	C	T	1	1	0	0	0.999412536471694	TCG	NA	NA	NA	NA	NA	NA	0.00011749270566119
CAMB-79819	MN908947.3	25047	C	T	0.031	0.039	6.5e-15	1.7e-18	0.0341022362287176	CCA	S	P1162L	C3485T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	0.96586755807046
CAMB-79819	MN908947.3	26137	A	C	0.022	0.016	4.3e-05	0.0028	0.0193482688391039	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.980448065173116
CAMB-79819	MN908947.3	26728	C	T	0.016	0.017	1.3e-08	3.3e-09	0.0165272773205334	GCT	M	A69V	C206T	GCT>GTT	Missense	GU280_gp05	0.983459426398436
CAMB-79819	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.9996782967274	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	3.29489291598023e-05
CAMB-79819	MN908947.3	3037	C	T	1	1	0	0	0.999292619665173	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.84225418533365e-05
CAMB-79819	MN908947.3	392	C	T	1	1	0	0	0.999765776958563	ACG	ORF1ab:leader-protein	R43C	C127T	CGT>TGT	Missense	ORF1ab:leader-protein	0.000234223041437111
CAMB-79828	MN908947.3	12924	C	T	0.12	0.18	2e-54	8.2e-83	0.148442172801914	CCT	ORF1ab:nsp9	P80L	C239T	CCT>CTT	Missense	ORF1ab:nsp9	0.851557827198086
CAMB-79828	MN908947.3	14408	C	T	1	1	0	0	0.999472330321219	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000461710968933448
CAMB-79828	MN908947.3	23403	A	G	1	1	0	0	0.999975776954194	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.42230458057796e-05
CAMB-79828	MN908947.3	241	C	T	1	1	0	0	0.9997943938044	TCG	NA	NA	NA	NA	NA	NA	0.000137070797066685
CAMB-79828	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99974632166413	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79828	MN908947.3	3037	C	T	1	1	2.5e-306	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79828	MN908947.3	505	TCAT	-	0.09625	0.0118175	5.3e-36;2.8e-33;4.2e-26;1.1e-13	NA;NA;NA;2.1e-05	0.0440721649484536	CTC	ORF1ab:leader-protein	.	240-243-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.957727384767069
CAMB-79828	MN908947.3	508	T	-	0.13	0.047	1.1e-13	2.1e-05	0.087423862414905	ATG	ORF1ab:leader-protein	.	243-243-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.911501254030813
CAMB-79837	MN908947.3	10078	C	T	0.0098	0.017	4.1e-06	6.3e-09	0.0132680195941218	TCC	ORF1ab:3C-like-proteinase	F8F	C24T	TTC>TTT	Synonymous	ORF1ab:3C-like-proteinase	0.986620013995801
CAMB-79837	MN908947.3	10183	C	T	0.025	0.015	7.1e-13	1.4e-08	0.0204136771636997	TCT	ORF1ab:3C-like-proteinase	I43I	C129T	ATC>ATT	Synonymous	ORF1ab:3C-like-proteinase	0.9795863228363
CAMB-79837	MN908947.3	10191	C	T	0.011	0.0021	6.8e-07	0.0056	0.00663680354761869	TCT	ORF1ab:3C-like-proteinase	S46F	C137T	TCT>TTT	Missense	ORF1ab:3C-like-proteinase	0.993348214954531
CAMB-79837	MN908947.3	10416	C	T	0.0073	0.0066	2e-05	3.7e-05	0.00697149456664392	TCA	ORF1ab:3C-like-proteinase	S121L	C362T	TCA>TTA	Missense	ORF1ab:3C-like-proteinase	0.992335555672214
CAMB-79837	MN908947.3	10442	A	-	0.0087	0.005	9.9e-06	0.00037	0.00699650174912544	TAT	ORF1ab:3C-like-proteinase	.	388-388-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.992772844347057
CAMB-79837	MN908947.3	10718	C	T	0.0047	0.011	0.001	1.8e-06	0.00735644981708287	TCG	ORF1ab:3C-like-proteinase	R222*	C664T	CGA>TGA	Nonsense	ORF1ab:3C-like-proteinase	0.992623667886114
CAMB-79837	MN908947.3	11075	T	-	0.047	0.034	1.2e-11	8.5e-09	0.0411482915690729	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95712150280717
CAMB-79837	MN908947.3	11152	C	T	0.0035	0.014	0.0017	3.6e-08	0.00845105023952831	TCA	ORF1ab:nsp6	V60V	C180T	GTC>GTT	Synonymous	ORF1ab:nsp6	0.991512099250706
CAMB-79837	MN908947.3	11719	G	T	0.0053	0.015	0.0015	2.2e-05	0.00984528832630099	AGG	ORF1ab:nsp6	Q249H	G747T	CAG>CAT	Missense	ORF1ab:nsp6	0.990154711673699
CAMB-79837	MN908947.3	11782	A	G	0.084	0.054	4.3e-19	3.4e-12	0.0706455542021924	AAC	ORF1ab:nsp6	K270K	A810G	AAA>AAG	Synonymous	ORF1ab:nsp6	0.929354445797808
CAMB-79837	MN908947.3	11824	C	T	0.1	0.061	4.1e-28	2.8e-16	0.083743842364532	TCA	ORF1ab:nsp6	I284I	C852T	ATC>ATT	Synonymous	ORF1ab:nsp6	0.915270935960591
CAMB-79837	MN908947.3	1238	C	T	0.26	0.29	4.9e-126	7.9e-145	0.272725917533765	TCA	ORF1ab:nsp2	H145Y	C433T	CAT>TAT	Missense	ORF1ab:nsp2	0.726245490593602
CAMB-79837	MN908947.3	12498	A	G	0.07	0.054	3.6e-32	2e-25	0.0633734411230181	AAC	ORF1ab:nsp8	N136S	A407G	AAC>AGC	Missense	ORF1ab:nsp8	0.936610891771636
CAMB-79837	MN908947.3	12853	C	T	0.0063	0.0077	6.1e-05	1.5e-05	0.00693775293890923	TCC	ORF1ab:nsp9	F56F	C168T	TTC>TTT	Synonymous	ORF1ab:nsp9	0.993047422802674
CAMB-79837	MN908947.3	13458	C	T	0.035	0.02	2.2e-16	7.9e-10	0.0266425107902169	TCG	ORF1ab:nsp11	S6L	C17T	TCG>TTG	Missense	ORF1ab:nsp11	0.973357489209783
CAMB-79837	MN908947.3	13778	AT	-	0.00605	0.016	0.0031;0.0031	5.6e-06;7.1e-06	0.0108851588838677	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.988763660032202
CAMB-79837	MN908947.3	13821	C	T	0.016	0.02	3.1e-09	3.9e-11	0.0179854132603384	TCG	ORF1ab:RNA-dependent-RNA-polymerase	L118L	C354T	CTC>CTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.981959473113736
CAMB-79837	MN908947.3	1392	C	T	0.0085	0.0028	3.3e-05	0.0052	0.00558387958242292	TCA	ORF1ab:nsp2	S196L	C587T	TCA>TTA	Missense	ORF1ab:nsp2	0.994416120417577
CAMB-79837	MN908947.3	14408	C	T	1	1	0	0	0.997985938639088	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000494248186726965
CAMB-79837	MN908947.3	14790	C	T	0.0084	0.014	1.7e-05	6.9e-08	0.0109935271755882	TCA	ORF1ab:RNA-dependent-RNA-polymerase	I441I	C1323T	ATC>ATT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.988983640992271
CAMB-79837	MN908947.3	1547	A	-	0.0019	0.01	0.0042	3.1e-06	0.00613775858149579	TAG	ORF1ab:nsp2	.	742-742-delfrshift	.	no-SNV	ORF1ab:nsp2	0.983632643782678
CAMB-79837	MN908947.3	15738	C	T	0.0093	0.011	7.8e-06	1.1e-06	0.0102284946236559	TCA	ORF1ab:RNA-dependent-RNA-polymerase	F757F	C2271T	TTC>TTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.989758064516129
CAMB-79837	MN908947.3	16474	A	G	0.015	0.0044	4.3e-08	0.0012	0.0102527075812274	TAG	ORF1ab:helicase	S80G	A238G	AGT>GGT	Missense	ORF1ab:helicase	0.989747292418773
CAMB-79837	MN908947.3	17010	C	T	0.0088	0.01	6e-06	1.8e-06	0.00942900374293223	TCT	ORF1ab:helicase	I258I	C774T	ATC>ATT	Synonymous	ORF1ab:helicase	0.990507286772318
CAMB-79837	MN908947.3	17167	C	T	0.017	0.02	4.3e-09	4.4e-10	0.0185526212679257	TCA	ORF1ab:helicase	H311Y	C931T	CAT>TAT	Missense	ORF1ab:helicase	0.981398401379202
CAMB-79837	MN908947.3	18512	C	T	0.017	0.025	2.7e-09	8.2e-13	0.0211949399588136	CCT	ORF1ab:3'-to-5'-exonuclease	P158L	C473T	CCT>CTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.978751571233719
CAMB-79837	MN908947.3	20238	G	T	0.11	0.053	2.1e-20	2.7e-12	0.0756172839506173	GGA	ORF1ab:endoRNAse	R206S	G618T	AGG>AGT	Missense	ORF1ab:endoRNAse	0.924382716049383
CAMB-79837	MN908947.3	20268	A	G	1	1	6.1e-268	0	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-79837	MN908947.3	203	C	T	0.026	0.033	1.1e-12	2.9e-15	0.0295959210111109	TCG	NA	NA	NA	NA	NA	NA	0.969191675939612
CAMB-79837	MN908947.3	20480	C	T	0.052	0.041	4e-10	1e-09	0.0450281425891182	TCA	ORF1ab:endoRNAse	S287L	C860T	TCA>TTA	Missense	ORF1ab:endoRNAse	0.954971857410882
CAMB-79837	MN908947.3	21110	C	T	0.0082	0.0028	1.5e-05	0.0029	0.0056369785794814	ACT	ORF1ab:2'-O-ribose-methyltransferase	T151I	C452T	ACT>ATT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.994269071777527
CAMB-79837	MN908947.3	21306	C	T	0.035	0.026	1.7e-05	0.00075	0.031413612565445	GCG	ORF1ab:2'-O-ribose-methyltransferase	R216R	C648T	CGC>CGT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.963350785340314
CAMB-79837	MN908947.3	21658	C	T	0.0042	0.0094	0.0013	1.1e-05	0.00692546017860397	TCA	S	F32F	C96T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.993074539821396
CAMB-79837	MN908947.3	21741	C	T	0.0086	0.0025	1.1e-05	0.0045	0.00557247084506233	TCC	S	S60F	C179T	TCC>TTC	Missense	GU280_gp02, spike glycoprotein	0.994427529154938
CAMB-79837	MN908947.3	22295	C	T	0.02	0.032	2.4e-10	2.7e-15	0.0254916241806264	ACA	S	H245Y	C733T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.9714957293253
CAMB-79837	MN908947.3	22452	C	T	0.014	0.036	0.0013	5.4e-06	0.0254433307632999	TCA	S	S297L	C890T	TCA>TTA	Missense	GU280_gp02, spike glycoprotein	0.9745566692367
CAMB-79837	MN908947.3	22837	A	G	0.01	0.005	7.4e-07	0.00012	0.00780234070221066	TAC	S	L425L	A1275G	TTA>TTG	Synonymous	GU280_gp02, spike glycoprotein	0.992197659297789
CAMB-79837	MN908947.3	23062	T	C	0.012	0.023	1.9e-07	1e-11	0.0170280963589923	CTA	S	T500T	T1500C	ACT>ACC	Synonymous	GU280_gp02, spike glycoprotein	0.981419341914158
CAMB-79837	MN908947.3	23185	C	T	0.37	0.38	2e-98	2.1e-102	0.37590355968419	TCA	S	F541F	C1623T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.623505432723636
CAMB-79837	MN908947.3	23320	C	T	0.26	0.26	5.6e-131	1.7e-126	0.260919432366772	ACA	S	D586D	C1758T	GAC>GAT	Synonymous	GU280_gp02, spike glycoprotein	0.738308986830993
CAMB-79837	MN908947.3	23403	A	G	1	1	0	0	0.999926101776329	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.61863897946553e-05
CAMB-79837	MN908947.3	23444	C	T	0.002	0.0098	0.0068	2.1e-06	0.00580609166816389	TCA	S	Q628*	C1882T	CAA>TAA	Nonsense	GU280_gp02, spike glycoprotein	0.99325774697166
CAMB-79837	MN908947.3	23900	G	C	0.012	0.0062	1.4e-07	4.4e-05	0.00916836912651353	AGA	S	E780Q	G2338C	GAA>CAA	Missense	GU280_gp02, spike glycoprotein	0.990756888733868
CAMB-79837	MN908947.3	23917	C	T	0.0099	0.0049	1.7e-06	0.00025	0.00736927781077454	TCA	S	V785V	C2355T	GTC>GTT	Synonymous	GU280_gp02, spike glycoprotein	0.992630722189225
CAMB-79837	MN908947.3	241	C	T	1	1	0	0	0.999682156251987	TCG	NA	NA	NA	NA	NA	NA	4.76765622020215e-05
CAMB-79837	MN908947.3	2455	C	T	0.3	0.3	3e-136	9.5e-133	0.302971665514858	TCA	ORF1ab:nsp2	L550L	C1650T	CTC>CTT	Synonymous	ORF1ab:nsp2	0.697028334485142
CAMB-79837	MN908947.3	24904	C	T	0.012	0.0035	6.9e-07	0.0019	0.00744058265485713	TCA	S	I1114I	C3342T	ATC>ATT	Synonymous	GU280_gp02, spike glycoprotein	0.992530799719547
CAMB-79837	MN908947.3	25521	C	T	0.06	0.037	5.7e-27	2.2e-17	0.0491149581793425	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.95009308917109
CAMB-79837	MN908947.3	25524	A	C	0.033	0.041	5.1e-16	2.3e-19	0.0369633657698912	GAT	ORF3a	G44G	A132C	GGA>GGC	Synonymous	GU280_gp03	0.962206639954207
CAMB-79837	MN908947.3	25916	C	T	1	1	0	0	0.99993609406953	ACA	ORF3a	T175I	C524T	ACA>ATA	Missense	GU280_gp03	6.39059304703477e-05
CAMB-79837	MN908947.3	26530	A	G	0.075	0.11	3.5e-34	7.5e-52	0.0932236584410497	GAT	M	D3G	A8G	GAT>GGT	Missense	GU280_gp05	0.90677634155895
CAMB-79837	MN908947.3	27059	C	T	0.017	0.021	2.4e-09	8.8e-11	0.0189424602532137	ACA	M	Y179Y	C537T	TAC>TAT	Synonymous	GU280_gp05	0.979568047145679
CAMB-79837	MN908947.3	28253	C	T	0.62	0.61	0	0	0.612339288495872	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.386977725056017
CAMB-79837	MN908947.3	28409	C	T	0.015	0.017	1.5e-08	3.4e-09	0.0160882904565215	ACC	N	P46S	C136T	CCC>TCC	Missense	GU280_gp10	0.982762545939441
CAMB-79837	MN908947.3	28556	C	T	0.35	0.35	2.8e-177	5.4e-176	0.353159433325838	TCG	N	R95C	C283T	CGT>TGT	Missense	GU280_gp10	0.646503260625141
CAMB-79837	MN908947.3	28603	C	T	0.011	0.025	0.00014	3.1e-08	0.0174700484833914	TCT	N	F110F	C330T	TTC>TTT	Synonymous	GU280_gp10	0.982529951516609
CAMB-79837	MN908947.3	28886	ACT	-	0.0493333333333333	0.0376666666666667	1.2e-25;2.3e-19;4e-15	3.4e-20;2.3e-15;5.6e-12	0.0367203483187326	AAC	N	.	613-615-delinframe	.	no-SNV	GU280_gp10	0.942520372526193
CAMB-79837	MN908947.3	29468	G	C	0.0019	0.012	0.004	2.4e-06	0.00723938223938224	AGA	N	D399H	G1195C	GAT>CAT	Missense	GU280_gp10	0.992277992277992
CAMB-79837	MN908947.3	29743	C	T	0.0099	0.0066	1.6e-05	0.00047	0.00857661223816593	GCG	NA	NA	NA	NA	NA	NA	0.990103908955962
CAMB-79837	MN908947.3	3037	C	T	1	1	0	0	0.999349920217481	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.90981620471603e-05
CAMB-79837	MN908947.3	3096	C	T	0.0093	0.047	7.6e-05	1.2e-17	0.0270570614098662	TCA	ORF1ab:nsp3	S126L	C377T	TCA>TTA	Missense	ORF1ab:nsp3	0.972894622409045
CAMB-79837	MN908947.3	346	C	T	0.055	0.044	1e-25	9e-21	0.0494601370040461	TCG	ORF1ab:leader-protein	L27L	C81T	CTC>CTT	Synonymous	ORF1ab:leader-protein	0.950196971890549
CAMB-79837	MN908947.3	3545	A	G	0.0036	0.012	0.00098	1.2e-06	0.00697799248523886	TAA	ORF1ab:nsp3	N276D	A826G	AAT>GAT	Missense	ORF1ab:nsp3	0.993022007514761
CAMB-79837	MN908947.3	3828	C	T	0.05	0.051	4.6e-23	2.3e-23	0.0507434611250448	TCA	ORF1ab:nsp3	S370L	C1109T	TCA>TTA	Missense	ORF1ab:nsp3	0.949256538874955
CAMB-79837	MN908947.3	4673	A	G	0.0072	0.0072	2.1e-05	2.1e-05	0.00718369740507257	CAA	ORF1ab:nsp3	K652E	A1954G	AAA>GAA	Missense	ORF1ab:nsp3	0.992800013031651
CAMB-79837	MN908947.3	5051	C	T	0.06	0.064	1.9e-19	2.1e-21	0.0623896409652737	TCC	ORF1ab:nsp3	P778S	C2332T	CCA>TCA	Missense	ORF1ab:nsp3	0.937610359034726
CAMB-79837	MN908947.3	516	TTATG	-	0.332	0.35	5.9e-07;2.2e-06;6.5e-07;5.1e-05;0.00012	2.7e-07;1.3e-06;2.8e-07;2.9e-05;6.8e-05	0.337425534611694	GTT	ORF1ab:leader-protein	.	251-255-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.659941631772618
CAMB-79837	MN908947.3	5183	C	T	0.014	0.0039	1.2e-06	0.0027	0.00819061801935964	TCC	ORF1ab:nsp3	P822S	C2464T	CCT>TCT	Missense	ORF1ab:nsp3	0.991437081161579
CAMB-79837	MN908947.3	5654	C	T	0.013	0.008	1.1e-07	2.1e-05	0.0107142857142857	TCT	ORF1ab:nsp3	L979L	C2935T	CTA>TTA	Synonymous	ORF1ab:nsp3	0.989188532555879
CAMB-79837	MN908947.3	635	C	T	0.12	0.1	1.3e-55	1.4e-47	0.113451420554192	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.88653104173974
CAMB-79837	MN908947.3	6573	C	T	0.011	0.006	2.6e-06	2e-04	0.00834088848594742	TCT	ORF1ab:nsp3	S1285F	C3854T	TCT>TTT	Missense	ORF1ab:nsp3	0.988848594741614
CAMB-79837	MN908947.3	683	C	T	0.023	0.018	1e-11	2.5e-09	0.0205228306324258	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.979084063628908
CAMB-79837	MN908947.3	686	AAGTCATTT	-	0.438888888888889	0.484444444444444	2e-74;2.3e-76;1.2e-64;6.6e-75;3e-63;3.9e-69;1.1e-76;3e-68;9.9e-58	3.1e-85;1.1e-87;1.7e-74;7.1e-86;5.1e-73;9.6e-79;6.8e-87;5.8e-78;3.2e-66	0.457792120838801	AAA	ORF1ab:leader-protein	.	421-429-delinframe	.	no-SNV	ORF1ab:leader-protein	0.543803582746773
CAMB-79837	MN908947.3	7528	C	T	0.013	0.031	3.4e-07	7.4e-15	0.0212451115104112	TCG	ORF1ab:nsp3	V1603V	C4809T	GTC>GTT	Synonymous	ORF1ab:nsp3	0.978754888489589
CAMB-79837	MN908947.3	7735	C	T	0.018	0.013	1.5e-06	2.3e-05	0.0163910958413857	TCG	ORF1ab:nsp3	I1672I	C5016T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.983465750483144
CAMB-79837	MN908947.3	815	C	T	0.017	0.018	5.1e-09	1e-09	0.0176490553230003	TCG	ORF1ab:nsp2	R4C	C10T	CGC>TGC	Missense	ORF1ab:nsp2	0.982339631179998
CAMB-79837	MN908947.3	9430	C	T	0.05	0.059	8.4e-22	8.7e-26	0.0541819852941176	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.945818014705882
CAMB-79846	MN908947.3	11075	T	-	0.041	0.041	9e-11	8.2e-11	0.0407274311227268	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954568223891974
CAMB-79846	MN908947.3	13730	C	T	1	1	0	0	0.997339746604146	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A88V	C263T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000107484985691061
CAMB-79846	MN908947.3	14408	C	T	1	1	0	0	0.997180389855923	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000537844709563857
CAMB-79846	MN908947.3	23403	A	G	1	1	0	0	0.999507968766713	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.55706492673013e-05
CAMB-79846	MN908947.3	241	C	T	1	1	0	0	0.998614253889737	TCG	NA	NA	NA	NA	NA	NA	0.000245575260046659
CAMB-79846	MN908947.3	25429	G	T	1	1	0	0	0.998490174869299	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	4.50694068866054e-05
CAMB-79846	MN908947.3	25515	C	T	0.023	0.024	3.2e-12	1.6e-12	0.0236462237818008	TCC	ORF3a	L41L	C123T	CTC>CTT	Synonymous	GU280_gp03	0.975935082542468
CAMB-79846	MN908947.3	26137	A	C	0.025	0.016	4e-06	0.0019	0.0209134245732739	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.979086575426726
CAMB-79846	MN908947.3	3037	C	T	1	1	0	0	0.999163004812722	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000119570741039668
CAMB-79855	MN908947.3	10097	G	A	1	1	0	0	0.999832205380614	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	5.59315397952906e-05
CAMB-79855	MN908947.3	11075	T	-	0.07	0.018	5.3e-17	1.2e-05	0.0482359912239963	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951619877328123
CAMB-79855	MN908947.3	13090	T	C	0.011	0.029	4.1e-07	4.2e-15	0.0169096800324018	ATG	ORF1ab:nsp10	D22D	T66C	GAT>GAC	Synonymous	ORF1ab:nsp10	0.983077663021466
CAMB-79855	MN908947.3	13335	C	T	0.008	0.0052	2.1e-05	0.00033	0.00718532250847024	GCT	ORF1ab:nsp10	A104V	C311T	GCT>GTT	Missense	ORF1ab:nsp10	0.99276353640606
CAMB-79855	MN908947.3	13536	C	T	1	1	0	0	0.999552672780139	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-79855	MN908947.3	14408	C	T	1	0.99	0	0	0.996811767476405	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00070648334329656
CAMB-79855	MN908947.3	17609	ATA	-	0.0113333333333333	0.00453333333333333	4.1e-07;4.4e-07;2.3e-07	4.7e-05;4.9e-05;NA	0.00910960152000208	GAT	ORF1ab:helicase	.	1373-1375-delinframe	.	no-SNV	ORF1ab:helicase	0.99089110972309
CAMB-79855	MN908947.3	20753	A	C	0.41	0.31	3.6e-216	3.4e-153	0.358610941320293	GAT	ORF1ab:2'-O-ribose-methyltransferase	D32A	A95C	GAT>GCT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.641274449877751
CAMB-79855	MN908947.3	23403	A	G	1	1	0	0	0.999933505480257	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.64945197433312e-05
CAMB-79855	MN908947.3	23731	C	T	1	1	0	0	0.999802078179119	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000148441365660564
CAMB-79855	MN908947.3	241	C	T	1	0.99	0	0	0.996056531217087	TCG	NA	NA	NA	NA	NA	NA	0.00382100080828863
CAMB-79855	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0355135135135135	0.0131621621621622	3e-06;1.9e-08;1.7e-06;2e-06;6.2e-06;2.3e-07;1.3e-06;1.1e-05;1.1e-05;2.4e-06;4.6e-06;3.4e-06;1e-05;5.3e-06;7.3e-06;1.6e-05;4.6e-06;1.4e-05;7.6e-06;7.6e-06;4.4e-06;1.4e-05;6.8e-06;9.6e-06;6.7e-06;3.1e-06;1.1e-05;5.9e-06;3.7e-06;5.7e-06;1.2e-05;8.6e-06;4.3e-06;9.5e-06;3.6e-06;6e-06;4e-06	0.028;0.0067;0.028;0.028;0.036;0.017;0.027;0.046;0.046;0.027;0.036;0.035;0.045;0.038;0.041;0.052;0.036;0.049;0.041;0.04;0.035;0.052;0.039;0.044;0.04;0.033;0.048;0.038;0.023;0.037;0.048;0.044;0.034;0.046;0.037;0.037;0.034	0.0247481126810211	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.975190895526755
CAMB-79855	MN908947.3	27434	C	T	0.029	0.016	6.8e-14	2e-08	0.0234170839598815	ACT	ORF7a	T14I	C41T	ACT>ATT	Missense	GU280_gp07	0.976553717681066
CAMB-79855	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99947418235356	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79855	MN908947.3	29666	C	T	0.085	0.057	8.2e-29	1e-17	0.0737656157049375	TCT	ORF10	L37F	C109T	CTC>TTC	Missense	GU280_gp11	0.926234384295062
CAMB-79855	MN908947.3	3037	C	T	1	1	0	0	0.999294283697953	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00040326645831233
CAMB-79855	MN908947.3	4002	C	T	1	1	0	0	0.999886698391117	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0.000113301608882846
CAMB-79855	MN908947.3	683	C	T	0.0071	0.0094	9.1e-05	8.5e-06	0.00819094592214198	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.991799268001487
CAMB-79855	MN908947.3	9219	G	-	0.019	0.013	1.9e-08	2.1e-06	0.0169580323167705	AGG	ORF1ab:nsp4	.	665-665-delfrshift	.	no-SNV	ORF1ab:nsp4	0.982986819610655
CAMB-79855	MN908947.3	9219	GGCACGGCACTT	-	0.01825	0.00108333333333333	1.9e-08;1.7e-08;3.1e-09;2.3e-09;3.6e-10;3.7e-10;2.8e-10;2.1e-09;2.9e-08;4.5e-08;3e-09;1.7e-09	2.1e-06;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0116503249972458	AGG	ORF1ab:nsp4	.	665-676-delinframe	.	no-SNV	ORF1ab:nsp4	0.982986819610655
CAMB-79864	MN908947.3	11075	T	-	0.042	0.044	1e-10	2.3e-11	0.0429734129137276	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953150918533447
CAMB-79864	MN908947.3	14408	C	T	1	1	0	0	0.996996653049797	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000687206505554919
CAMB-79864	MN908947.3	14786	C	T	1	1	0	0	0.999357932127212	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A440V	C1319T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000124271201184719
CAMB-79864	MN908947.3	16393	C	T	0.013	0.01	2.6e-07	3.2e-06	0.0116951902764596	TCC	ORF1ab:helicase	P53S	C157T	CCA>TCA	Missense	ORF1ab:helicase	0.987906805865965
CAMB-79864	MN908947.3	20578	G	T	1	1	0	0	0.999785494673118	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	4.76678504182854e-05
CAMB-79864	MN908947.3	23403	A	G	1	1	0	0	0.999433504181279	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.39519827353655e-05
CAMB-79864	MN908947.3	241	C	T	1	1	0	0	0.99818747966724	TCG	NA	NA	NA	NA	NA	NA	0.000216882774860188
CAMB-79864	MN908947.3	2416	C	T	1	1	0	0	0.99720132936855	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	8.74584572328144e-05
CAMB-79864	MN908947.3	25563	G	T	1	1	0	0	0.999759578231526	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000103037900774502
CAMB-79864	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0336756756756757	0.0350540540540541	0.00064;3e-05;0.00024;0.00028;0.00055;9.2e-06;4.9e-05;9.8e-06;9.3e-06;1.8e-06;4.8e-06;3.2e-06;7.3e-06;4.3e-06;6.3e-06;1.1e-05;3.9e-06;9.7e-06;5.2e-06;5.9e-06;5e-06;1.1e-05;6.9e-06;7.7e-06;4.9e-06;4.6e-06;8.1e-06;4.3e-06;1.5e-06;4.8e-06;8.4e-06;7.2e-06;3.4e-06;9e-06;2.1e-06;4.6e-06;3.6e-06	0.00063;3.5e-05;0.00024;0.00025;0.00039;6.6e-06;2.2e-05;4.4e-06;4.3e-06;9.3e-07;2.5e-06;1.9e-06;3.7e-06;2.5e-06;3.3e-06;5.3e-06;2.2e-06;4.5e-06;2.6e-06;2.6e-06;2.6e-06;4.7e-06;3.4e-06;3.8e-06;2.5e-06;2.6e-06;4e-06;2.1e-06;8e-07;2.5e-06;4e-06;3.5e-06;2.1e-06;4.1e-06;8.9e-07;2.1e-06;1.7e-06	0.0357104176014606	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.97763230514503
CAMB-79864	MN908947.3	3037	C	T	1	1	0	0	0.999014334394097	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000112647497817455
CAMB-79864	MN908947.3	9935	A	G	0.032	0.028	1.6e-15	1.1e-13	0.0297539149888143	AAC	ORF1ab:nsp4	T461A	A1381G	ACT>GCT	Missense	ORF1ab:nsp4	0.970171513795675
CAMB-79873	MN908947.3	10262	G	A	1	1	0	0	0.999751261828018	GGC	ORF1ab:3C-like-proteinase	A70T	G208A	GCT>ACT	Missense	ORF1ab:3C-like-proteinase	0.000124369085990859
CAMB-79873	MN908947.3	11075	T	-	0.039	0.044	9.8e-10	4.6e-11	0.041340782122905	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954759557454267
CAMB-79873	MN908947.3	14408	C	T	1	1	0	0	0.997844203481451	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000589894569752352
CAMB-79873	MN908947.3	16075	G	A	0.012	0.011	3.4e-07	7.8e-07	0.0114273236771235	TGA	ORF1ab:RNA-dependent-RNA-polymerase	D870N	G2608A	GAT>AAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.987653759371133
CAMB-79873	MN908947.3	19839	T	C	1	1	0	0	0.99910662545876	ATA	ORF1ab:endoRNAse	N73N	T219C	AAT>AAC	Synonymous	ORF1ab:endoRNAse	0.000338033610198957
CAMB-79873	MN908947.3	21721	C	T	0.012	0.016	6.7e-07	1.4e-08	0.0139977603583427	ACT	S	D53D	C159T	GAC>GAT	Synonymous	GU280_gp02, spike glycoprotein	0.985967245240762
CAMB-79873	MN908947.3	22995	C	T	1	1	0	0	0.999619727373779	ACA	S	T478I	C1433T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0.000146258702392792
CAMB-79873	MN908947.3	23403	A	G	1	1	0	0	0.99956714199376	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000155175511670832
CAMB-79873	MN908947.3	241	C	T	1	1	0	0	0.998949579831933	TCG	NA	NA	NA	NA	NA	NA	5.52852720035383e-05
CAMB-79873	MN908947.3	27669	A	G	1	1	0	0	0.99746192893401	AAG	ORF7a	E92E	A276G	GAA>GAG	Synonymous	GU280_gp07	0.000423011844331641
CAMB-79873	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998768409709037	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000230063555057085
CAMB-79873	MN908947.3	3037	C	T	1	1	0	0	0.99921393615133	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	2.53568983441945e-05
CAMB-79873	MN908947.3	6655	T	-	0.2	0.21	6.4e-88	1e-92	0.201106529568349	TTA	ORF1ab:nsp3	.	3936-3936-delfrshift	.	no-SNV	ORF1ab:nsp3	0.798841275640691
CAMB-79873	MN908947.3	6656	AA	-	0.32	0.335	1.8e-152;7.4e-90	1.3e-161;3.5e-95	0.328218663326474	TAA	ORF1ab:nsp3	.	3937-3938-delfrshift	.	no-SNV	ORF1ab:nsp3	0.673422222222222
CAMB-79873	MN908947.3	6658	T	-	0.21	0.21	1.2e-39	4e-41	0.211436678125171	ATA	ORF1ab:nsp3	.	3939-3939-delfrshift	.	no-SNV	ORF1ab:nsp3	0.788399628962733
CAMB-79873	MN908947.3	6659	AGTGTCCCTTGGGATACTATAGC	-	0.39695652173913	0.421739130434783	9.4e-90;5e-108;8.9e-88;8.8e-111;2.7e-86;5.1e-102;1e-105;4.4e-106;9.4e-152;3.8e-203;4.9e-190;7.9e-211;5.9e-191;3.9e-192;2e-195;1.1e-187;7.1e-192;2.4e-194;1.8e-197;6.5e-211;4.3e-187;3.8e-207;2.7e-198	2.7e-97;6.1e-117;3.9e-95;1.1e-121;5.3e-94;2.4e-110;5.6e-115;2e-115;2.2e-166;7.1e-221;1.1e-207;2.4e-224;2.4e-208;4.7e-212;1.9e-213;6.1e-207;9.3e-209;2e-212;1.2e-215;1.6e-228;2e-204;4.4e-221;2e-216	0.407821539830886	TAG	ORF1ab:nsp3	.	3940-3962-delfrshift	.	no-SNV	ORF1ab:nsp3	0.601922241529105
CAMB-79873	MN908947.3	9438	C	T	1	1	0	0	0.99962391044644	ACA	ORF1ab:nsp4	T295I	C884T	ACA>ATA	Missense	ORF1ab:nsp4	8.84916596610769e-05
CAMB-79882	MN908947.3	11074	C	INS	0.027	0.028	2.1e-05	1.3e-05	0.0275636363636364	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.971836363636364
CAMB-79882	MN908947.3	11075	T	-	0.041	0.041	1.9e-10	1.2e-10	0.040997053194398	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954704256159431
CAMB-79882	MN908947.3	14408	C	T	1	1	0	0	0.998737451122198	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000502567999901938
CAMB-79882	MN908947.3	14786	C	T	1	1	0	0	0.997763753453818	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A440V	C1319T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00202122283981809
CAMB-79882	MN908947.3	20578	G	T	1	1	0	0	0.997561368858076	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	0.00225724535450844
CAMB-79882	MN908947.3	23403	A	G	1	1	0	0	0.999452192159848	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.28487864663609e-05
CAMB-79882	MN908947.3	241	C	T	1	1	0	0	0.999220305473177	TCG	NA	NA	NA	NA	NA	NA	8.35386993024519e-05
CAMB-79882	MN908947.3	2416	C	T	1	1	0	0	0.996430224102598	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0.002313743637205
CAMB-79882	MN908947.3	25563	G	T	1	1	0	0	0.997742548713422	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.0020537714712472
CAMB-79882	MN908947.3	3037	C	T	1	1	0	0	0.999342087949683	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000131582410063423
CAMB-79891	MN908947.3	10356	A	G	0.005	0.0075	0.00017	1.3e-05	0.00611654981873932	TAT	ORF1ab:3C-like-proteinase	Y101C	A302G	TAT>TGT	Missense	ORF1ab:3C-like-proteinase	0.99385150997333
CAMB-79891	MN908947.3	11075	T	-	0.04	0.048	6e-10	3e-12	0.0428954083251876	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955505058839958
CAMB-79891	MN908947.3	11671	C	T	0.013	0.0043	9.5e-06	0.0028	0.00962309542902967	GCT	ORF1ab:nsp6	R233R	C699T	CGC>CGT	Synonymous	ORF1ab:nsp6	0.99037690457097
CAMB-79891	MN908947.3	12786	C	T	0.16	0.16	1.8e-71	2e-72	0.155609816026291	ACA	ORF1ab:nsp9	T34I	C101T	ACA>ATA	Missense	ORF1ab:nsp9	0.844021622285697
CAMB-79891	MN908947.3	14408	C	T	1	1	0	0	0.998137802607076	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000532056397978186
CAMB-79891	MN908947.3	18687	C	T	0.015	0.029	3.7e-08	3.6e-14	0.0199299131387952	GCT	ORF1ab:3'-to-5'-exonuclease	C216C	C648T	TGC>TGT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.980036870339307
CAMB-79891	MN908947.3	18956	A	G	0.0081	0.0096	9.2e-06	1.2e-06	0.00865464737519885	AAT	ORF1ab:3'-to-5'-exonuclease	N306S	A917G	AAT>AGT	Missense	ORF1ab:3'-to-5'-exonuclease	0.991326414665556
CAMB-79891	MN908947.3	23403	A	G	1	1	0	0	0.998027689317773	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.77261663090851e-05
CAMB-79891	MN908947.3	241	C	T	1	1	0	0	0.99916825095057	TCG	NA	NA	NA	NA	NA	NA	9.90177439797212e-05
CAMB-79891	MN908947.3	26137	A	C	0.031	0.022	4.8e-06	0.0028	0.0275526742301459	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.971636952998379
CAMB-79891	MN908947.3	26753	C	T	0.0051	0.0084	3e-04	9.1e-06	0.00638037119862538	CCG	M	T77T	C231T	ACC>ACT	Synonymous	GU280_gp05	0.993569091207722
CAMB-79891	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0315675675675676	0.0365135135135135	0.00085;5.8e-05;0.00038;0.00043;0.00063;3.3e-05;0.00018;2.7e-05;2.6e-05;6.9e-06;1.4e-05;9.6e-06;2.6e-05;1.6e-05;2e-05;3.7e-05;1.4e-05;3.1e-05;2.1e-05;2e-05;1.7e-05;3.5e-05;1.6e-05;2.5e-05;1.9e-05;1.2e-05;2.5e-05;1.7e-05;1.6e-05;1.5e-05;2.9e-05;2.3e-05;1e-05;2.7e-05;9.3e-06;1.5e-05;1e-05	2.1e-05;1.8e-06;3.6e-05;4.2e-05;6e-05;2.1e-06;1e-05;2.9e-06;2.9e-06;7.2e-07;1.6e-06;1.2e-06;2.7e-06;1.8e-06;2.3e-06;3.9e-06;1.6e-06;3.4e-06;2.2e-06;2e-06;1.7e-06;3.7e-06;1.7e-06;2.7e-06;1.8e-06;1.3e-06;2.6e-06;1.6e-06;1.8e-06;1.6e-06;2.9e-06;2.3e-06;1.2e-06;2.9e-06;7.2e-07;1.4e-06;8.8e-07	0.0345639046255369	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.97498386856604
CAMB-79891	MN908947.3	27224	A	C	0.023	0.026	1.2e-11	1.9e-13	0.0237502853229856	CAG	ORF6	Q8P	A23C	CAG>CCG	Missense	GU280_gp06	0.975348094042456
CAMB-79891	MN908947.3	27346	T	C	0.0048	0.0066	0.00035	4e-05	0.005449660026996	ATA	ORF6	Y49H	T145C	TAT>CAT	Missense	GU280_gp06	0.994499880157939
CAMB-79891	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.997877641413675	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000266595574513463
CAMB-79891	MN908947.3	3037	C	T	1	1	0	0	0.99942709825265	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79891	MN908947.3	522	TT	-	0.049	0.0445	1.3e-07;1.5e-05	1.3e-06;1.1e-05	0.0469246974265769	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.94431770173215
CAMB-798A0	MN908947.3	11075	T	-	0.039	0.045	9.5e-10	2.7e-11	0.0415956656617294	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952975488268449
CAMB-798A0	MN908947.3	13730	C	T	1	1	0	0	0.997681765815941	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A88V	C263T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	2.12033614395669e-05
CAMB-798A0	MN908947.3	14408	C	T	1	1	0	0	0.997814060460394	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000486915442471458
CAMB-798A0	MN908947.3	23403	A	G	1	1	0	0	0.999443166686842	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000137190816285357
CAMB-798A0	MN908947.3	241	C	T	1	1	0	0	0.998913906178203	TCG	NA	NA	NA	NA	NA	NA	0.000111394238133033
CAMB-798A0	MN908947.3	25429	G	T	1	1	0	0	0.999007617583339	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0.000181703822768887
CAMB-798A0	MN908947.3	3037	C	T	1	1	0	0	0.99954787663491	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.68835782334894e-05
CAMB-798CE	MN908947.3	10029	C	T	0.04	0.022	1.8e-18	2.4e-11	0.0294001734058485	ACC	ORF1ab:nsp4	T492I	C1475T	ACC>ATC	Missense	ORF1ab:nsp4	0.970599826594151
CAMB-798CE	MN908947.3	11074	C	INS	0.14	0.17	9.8e-47	1.4e-62	0.153498871331828	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.846059475905388
CAMB-798CE	MN908947.3	11083	G	-	0.14	0.15	9.5e-64	2.9e-68	0.148305373317291	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-798CE	MN908947.3	11083	G	T	0.86	0.85	0	0	0.851490318040453	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-798CE	MN908947.3	14411	C	T	0.009	0.0091	9.1e-06	9.3e-06	0.00906171563561199	ACA	ORF1ab:RNA-dependent-RNA-polymerase	T315I	C944T	ACA>ATA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.990938284364388
CAMB-798CE	MN908947.3	14805	C	T	1	1	0	0	1	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-798CE	MN908947.3	15535	G	T	0.011	0.0069	7e-07	3.7e-05	0.00841451973731688	AGC	ORF1ab:RNA-dependent-RNA-polymerase	A690S	G2068T	GCT>TCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.991426715739337
CAMB-798CE	MN908947.3	15848	C	T	0.082	0.11	7.4e-38	1.2e-48	0.0966614565954233	ACT	ORF1ab:RNA-dependent-RNA-polymerase	T794I	C2381T	ACT>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.903338543404577
CAMB-798CE	MN908947.3	16799	C	T	0.015	0.026	6.7e-09	1.7e-13	0.0215165113335635	ACT	ORF1ab:helicase	T188I	C563T	ACT>ATT	Missense	ORF1ab:helicase	0.978454723276953
CAMB-798CE	MN908947.3	17009	T	C	0.13	0.15	2.6e-59	5.3e-68	0.139708652517895	ATC	ORF1ab:helicase	I258T	T773C	ATC>ACC	Missense	ORF1ab:helicase	0.860259952279292
CAMB-798CE	MN908947.3	17441	C	T	0.013	0.028	1.8e-07	7.4e-14	0.0209941758092916	CCT	ORF1ab:helicase	P402L	C1205T	CCT>CTT	Missense	ORF1ab:helicase	0.978951645672491
CAMB-798CE	MN908947.3	17871	A	G	0.027	0.0092	4.6e-14	2.7e-06	0.0167665082971838	TAT	ORF1ab:helicase	I545M	A1635G	ATA>ATG	Missense	ORF1ab:helicase	0.983130207257454
CAMB-798CE	MN908947.3	20937	G	A	0.029	0.025	5.2e-14	3.5e-12	0.0265413205072147	CGC	ORF1ab:2'-O-ribose-methyltransferase	T93T	G279A	ACG>ACA	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.973371228683865
CAMB-798CE	MN908947.3	21600	G	T	0.029	0.0035	3.3e-09	0.0034	0.00962052378407269	AGT	S	S13I	G38T	AGT>ATT	Missense	GU280_gp02, spike glycoprotein	0.989845002672368
CAMB-798CE	MN908947.3	21639	C	T	0.1	0.088	9.9e-27	4.9e-32	0.0921052631578947	CCT	S	P26L	C77T	CCT>CTT	Missense	GU280_gp02, spike glycoprotein	0.907894736842105
CAMB-798CE	MN908947.3	21980	TTT	-	0.356666666666667	0.296666666666667	1.7e-109;1.1e-68;3.1e-68	5.5e-91;7.7e-57;2.1e-55	0.315844838921762	ATT	S	.	418-420-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.66504110352515
CAMB-798CE	MN908947.3	21991	TTA	-	0.136666666666667	0.113333333333333	3e-08;8.3e-14;7.6e-14	3.2e-07;8.9e-12;7.6e-12	0.123499142367067	TTT	S	.	429-431-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.874950659193179
CAMB-798CE	MN908947.3	22003	A	C	0.072	0.069	4.6e-32	1.9e-31	0.0704196237855716	AAA	S	K147N	A441C	AAA>AAC	Missense	GU280_gp02, spike glycoprotein	0.926066285399297
CAMB-798CE	MN908947.3	22799	G	-	0.013	0.0085	3e-07	2.8e-05	0.0109535400571489	AGG	S	.	1237-1237-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.989046459942851
CAMB-798CE	MN908947.3	23608	G	C	0.029	0.036	5.2e-14	3.6e-17	0.0334459459459459	GGC	S	R682R	G2046C	CGG>CGC	Synonymous	GU280_gp02, spike glycoprotein	0.966469594594595
CAMB-798CE	MN908947.3	23701	C	T	0.11	0.12	2.1e-45	9.4e-54	0.115283483976993	CCA	S	A713A	C2139T	GCC>GCT	Synonymous	GU280_gp02, spike glycoprotein	0.884716516023007
CAMB-798CE	MN908947.3	2480	A	G	1	1	0	0	0.999658236500342	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000341763499658237
CAMB-798CE	MN908947.3	24899	C	A	0.064	0.042	2e-29	1.2e-19	0.0497778636275835	ACA	S	Q1113K	C3337A	CAA>AAA	Missense	GU280_gp02, spike glycoprotein	0.950222136372416
CAMB-798CE	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-798CE	MN908947.3	25642	C	T	0.0081	0.011	2.7e-05	1.5e-06	0.00968101406881181	GCT	ORF3a	L84L	C250T	CTG>TTG	Synonymous	GU280_gp03	0.990266750243767
CAMB-798CE	MN908947.3	25720	G	T	1	1	0	0	0.999453153481589	TGC	ORF3a	A110S	G328T	GCT>TCT	Missense	GU280_gp03	0
CAMB-798CE	MN908947.3	26144	G	T	1	1	4.29999999999291e-313	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-798CE	MN908947.3	26927	A	G	0.013	0.013	2.1e-07	1.8e-07	0.0129743893162032	AAA	M	E135E	A405G	GAA>GAG	Synonymous	GU280_gp05	0.987025610683797
CAMB-798CE	MN908947.3	27235	G	A	0.026	0.022	2.1e-13	1.1e-11	0.0236767216846898	AGC	ORF6	A12T	G34A	GCA>ACA	Missense	GU280_gp06	0.976309049516221
CAMB-798CE	MN908947.3	27478	G	T	0.013	0.0062	9.4e-08	6.1e-05	0.00896702580057878	AGT	ORF7a	V29L	G85T	GTA>TTA	Missense	GU280_gp07	0.990937869380324
CAMB-798CE	MN908947.3	27920	C	T	0.014	0.0079	1.9e-06	0.00012	0.0102359965880011	TCA	ORF8	I9I	C27T	ATC>ATT	Synonymous	GU280_gp09	0.988058003980665
CAMB-798CE	MN908947.3	6762	C	T	0.016	0.019	2.9e-08	1.2e-09	0.0176573426573427	ACT	ORF1ab:nsp3	T1348I	C4043T	ACT>ATT	Missense	ORF1ab:nsp3	0.982342657342657
CAMB-798CE	MN908947.3	7814	TC	-	0.011	0.015	6e-05;5.5e-05	1.4e-06;1.5e-06	0.0130333379064344	TTC	ORF1ab:nsp3	.	5095-5096-delfrshift	.	no-SNV	ORF1ab:nsp3	0.986672162682055
CAMB-798CE	MN908947.3	8498	G	A	0.023	0.014	4.9e-11	1.1e-07	0.0188335358444714	TGC	ORF1ab:nsp3	A1927T	G5779A	GCA>ACA	Missense	ORF1ab:nsp3	0.981166464155529
CAMB-798DD	MN908947.3	14408	C	T	1	1	0	0	0.999382716049383	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000493827160493827
CAMB-798DD	MN908947.3	23403	A	G	1	1	0	0	1	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-798DD	MN908947.3	241	C	T	1	1	0	0	0.99949924887331	TCG	NA	NA	NA	NA	NA	NA	0.000250375563345017
CAMB-798DD	MN908947.3	28881	GGG	AAC	1	1	0;0;0	2.7e-304;7.69999999999856e-312;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-798DD	MN908947.3	3037	C	T	1	1	1.6e-266	6.1e-241	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-798DD	MN908947.3	7420	C	T	1	1	1.1e-138	3e-149	1	TCT	ORF1ab:nsp3	I1567I	C4701T	ATC>ATT	Synonymous	ORF1ab:nsp3	0
CAMB-798EC	MN908947.3	11075	T	-	0.048	0.042	9.2e-12	1.5e-10	0.0452260183674837	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95013742095502
CAMB-798EC	MN908947.3	14408	C	T	1	1	0	0	0.997313735981742	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000502309531869356
CAMB-798EC	MN908947.3	15639	A	G	0.072	0.059	4.7e-33	3.8e-27	0.0659296193807759	GAA	ORF1ab:RNA-dependent-RNA-polymerase	R724R	A2172G	AGA>AGG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.933770166553543
CAMB-798EC	MN908947.3	23282	G	T	1	1	0	0	0.999271199519849	TGA	S	D574Y	G1720T	GAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.00017148246591786
CAMB-798EC	MN908947.3	23403	A	G	1	1	0	0	0.999905927427286	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.69684685840367e-05
CAMB-798EC	MN908947.3	241	C	T	1	1	0	0	0.999201660546064	TCG	NA	NA	NA	NA	NA	NA	0.000175634679865879
CAMB-798EC	MN908947.3	26159	TTA	-	0.0123333333333333	0.00903333333333333	1.1e-05;3.1e-05;0.00013	0.00034;0.00059;8e-04	0.0100531380152233	GTT	ORF3a	.	767-769-delinframe	.	no-SNV	GU280_gp03	0.988758782201405
CAMB-798EC	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.997977243994943	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00035880875493362
CAMB-798EC	MN908947.3	3037	C	T	1	1	0	0	0.999408265595316	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.11439160360024e-05
CAMB-798EC	MN908947.3	8318	C	T	0.0083	0.0059	7.9e-06	7.3e-05	0.00719487694625816	ACC	ORF1ab:nsp3	P1867S	C5599T	CCC>TCC	Missense	ORF1ab:nsp3	0.992742340532396
CAMB-798EC	MN908947.3	8715	C	T	0.0083	0.0045	1.1e-05	0.00047	0.00645161290322581	ACT	ORF1ab:nsp4	T54I	C161T	ACT>ATT	Missense	ORF1ab:nsp4	0.993548387096774
CAMB-798FB	MN908947.3	10604	C	T	0.0045	0.0076	0.00037	1.7e-05	0.0059627738428595	ACC	ORF1ab:3C-like-proteinase	P184S	C550T	CCT>TCT	Missense	ORF1ab:3C-like-proteinase	0.993872508647669
CAMB-798FB	MN908947.3	11075	T	-	0.039	0.038	8e-10	7.9e-10	0.0383101790713644	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957345095346257
CAMB-798FB	MN908947.3	14408	C	T	1	1	0	0	0.998671045401689	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000932823900737314
CAMB-798FB	MN908947.3	17745	C	T	0.0049	0.0071	0.00025	2.6e-05	0.00592594792888862	ACC	ORF1ab:helicase	N503N	C1509T	AAC>AAT	Synonymous	ORF1ab:helicase	0.994074052071111
CAMB-798FB	MN908947.3	18760	A	G	0.014	0.011	5.1e-08	3.9e-07	0.0124490805954239	TAT	ORF1ab:3'-to-5'-exonuclease	M241V	A721G	ATG>GTG	Missense	ORF1ab:3'-to-5'-exonuclease	0.987132142993109
CAMB-798FB	MN908947.3	23403	A	G	1	1	0	0	0.999268071319131	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.90361963130313e-05
CAMB-798FB	MN908947.3	241	C	T	1	1	0	0	0.999696028833836	TCG	NA	NA	NA	NA	NA	NA	0.000130273356927286
CAMB-798FB	MN908947.3	24962	A	T	0.0071	0.006	2.6e-05	8e-05	0.00651238088229883	CAA	S	N1134Y	A3400T	AAC>TAC	Missense	GU280_gp02, spike glycoprotein	0.993322050112219
CAMB-798FB	MN908947.3	28877	AG	TC	0.0093	0.00765	4e-06;4.7e-06	1.7e-05;1.8e-05	0.00852861781620437	CAG	N	.	604-605-mnv	.	no-SNV	GU280_gp10	0.990610881948537
CAMB-798FB	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999251901417231	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000360490266762797
CAMB-798FB	MN908947.3	29729	TCACCGAGGCCACGCGGAGTACGATCGAGTG	-	0.0116451612903226	0.00860967741935484	1.3e-05;1.5e-05;3.4e-06;1.2e-05;1.2e-05;1.6e-05;1.2e-05;2.7e-05;2.4e-05;1.4e-05;1.7e-05;9.1e-06;1.3e-05;1.3e-05;1.2e-05;1.7e-05;1.8e-05;1.7e-05;2.8e-05;7.4e-05;8.3e-05;0.00044;0.00043;0.00012;0.00014;0.00012;0.00013;0.00012;3e-04;0.00017;3e-04	7.4e-05;0.00012;7.2e-05;0.00015;0.00015;0.00021;0.00024;0.00019;0.00028;2e-04;0.00015;9.8e-05;0.00023;0.00025;0.00021;0.00025;0.00031;0.00035;0.00057;0.0011;0.0015;0.0034;0.0023;0.0012;0.0011;0.001;0.00099;0.00096;0.0021;0.0014;0.001	0.00979843225083987	TTC	NA	NA	NA	NA	NA	NA	0.989974463255462
CAMB-798FB	MN908947.3	3037	C	T	1	1	0	0	0.999075851283145	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-798FB	MN908947.3	4084	C	T	0.0097	0.011	3.8e-06	1.5e-06	0.0101460813537983	ACA	ORF1ab:nsp3	D455D	C1365T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.989372535224306
CAMB-79907	MN908947.3	11075	T	-	0.046	0.042	3.6e-12	3.4e-11	0.044007561436673	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951909262759924
CAMB-79907	MN908947.3	14408	C	T	1	1	0	0	0.997453580901857	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000363774156877605
CAMB-79907	MN908947.3	21137	A	G	0.052	0.048	5e-21	1.8e-19	0.0500992766983407	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.949865267337966
CAMB-79907	MN908947.3	21762	C	T	0.0095	0.012	5.7e-06	7.3e-07	0.0104715578975814	GCT	S	A67V	C200T	GCT>GTT	Missense	GU280_gp02, spike glycoprotein	0.988886636940954
CAMB-79907	MN908947.3	22588	T	C	1	1	0	0	0.999306396115818	TTA	S	F342F	T1026C	TTT>TTC	Synonymous	GU280_gp02, spike glycoprotein	0.000530402970256633
CAMB-79907	MN908947.3	23403	A	G	1	1	0	0	0.999343407169629	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000155028862726502
CAMB-79907	MN908947.3	241	C	T	1	1	0	0	0.998499834727555	TCG	NA	NA	NA	NA	NA	NA	0.000127132650207226
CAMB-79907	MN908947.3	25951	G	T	0.007	0.0076	4e-05	2e-05	0.00729118754365343	TGG	ORF3a	G187C	G559T	GGT>TGT	Missense	GU280_gp03	0.992674741486516
CAMB-79907	MN908947.3	27112	G	C	1	1	0	0	0.999655922050705	AGT	M	S197T	G590C	AGT>ACT	Missense	GU280_gp05	0.000265878415364644
CAMB-79907	MN908947.3	28090	GTTCTA	-	0.0445	0.0456666666666667	3.1e-19;3.5e-19;1.9e-19;5.6e-20;2.6e-19;7.9e-19	8.1e-20;1.1e-19;7.3e-20;1.9e-20;8e-20;2.2e-19	0.0446829368969609	GGT	ORF8	.	197-202-delinframe	.	no-SNV	GU280_gp09	0.955237703231118
CAMB-79907	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99922570654278	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79907	MN908947.3	3037	C	T	1	1	0	0	0.999331039755352	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.16743119266055e-05
CAMB-79907	MN908947.3	5979	C	T	0.007	0.0084	0.00011	3.1e-05	0.00767536541413602	TCT	ORF1ab:nsp3	S1087F	C3260T	TCT>TTT	Missense	ORF1ab:nsp3	0.992124407662017
CAMB-79907	MN908947.3	6121	A	T	0.011	0.011	2.8e-06	2.6e-06	0.0106863335340157	CAA	ORF1ab:nsp3	S1134S	A3402T	TCA>TCT	Synonymous	ORF1ab:nsp3	0.989238410596026
CAMB-79907	MN908947.3	6337	G	A	0.018	0.017	6.5e-10	1.9e-09	0.0177284715990973	CGT	ORF1ab:nsp3	S1206S	G3618A	TCG>TCA	Synonymous	ORF1ab:nsp3	0.981936173876789
CAMB-79916	MN908947.3	11074	C	INS	0.02	0.029	0.001	7.1e-06	0.0240225655203333	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.975771953748155
CAMB-79916	MN908947.3	11075	T	-	0.036	0.04	3.1e-09	1.3e-10	0.0374521163769905	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958558900813626
CAMB-79916	MN908947.3	11224	C	T	0.21	0.18	6.5e-101	5.1e-86	0.199692544196772	TCT	ORF1ab:nsp6	V84V	C252T	GTC>GTT	Synonymous	ORF1ab:nsp6	0.800096079938509
CAMB-79916	MN908947.3	11452	A	G	1	1	0	0	0.999893932965634	AAG	ORF1ab:nsp6	Q160Q	A480G	CAA>CAG	Synonymous	ORF1ab:nsp6	0.000106067034365719
CAMB-79916	MN908947.3	14408	C	T	1	1	0	0	0.997517271157167	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00040093757710338
CAMB-79916	MN908947.3	16883	C	T	0.0071	0.0084	2.3e-05	5.5e-06	0.00765497776604601	ACT	ORF1ab:helicase	T216I	C647T	ACT>ATT	Missense	ORF1ab:helicase	0.992284107291519
CAMB-79916	MN908947.3	17440	C	T	0.047	0.038	6.1e-22	2.9e-18	0.0433820493765998	CCC	ORF1ab:helicase	P402S	C1204T	CCT>TCT	Missense	ORF1ab:helicase	0.956601436710429
CAMB-79916	MN908947.3	17761	G	T	0.05	0.046	2e-23	4.8e-22	0.048503186994199	AGC	ORF1ab:helicase	A509S	G1525T	GCT>TCT	Missense	ORF1ab:helicase	0.951067105922796
CAMB-79916	MN908947.3	17906	A	G	0.0085	0.0081	6.8e-06	8.7e-06	0.00831605058761335	AAT	ORF1ab:helicase	N557S	A1670G	AAT>AGT	Missense	ORF1ab:helicase	0.99164328412834
CAMB-79916	MN908947.3	22664	C	A	0.014	0.018	3.2e-08	5e-10	0.0155839518453337	CCT	S	L368I	C1102A	CTA>ATA	Missense	GU280_gp02, spike glycoprotein	0.984365036855664
CAMB-79916	MN908947.3	23403	A	G	1	1	0	0	0.999423576881904	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.41098968320256e-05
CAMB-79916	MN908947.3	241	C	T	1	1	0	0	0.999157222382399	TCG	NA	NA	NA	NA	NA	NA	0.000133070150147486
CAMB-79916	MN908947.3	24814	T	A	0.0023	0.0061	0.0022	4.8e-05	0.00400949735686766	ATG	S	D1084E	T3252A	GAT>GAA	Missense	GU280_gp02, spike glycoprotein	0.995878505510259
CAMB-79916	MN908947.3	24865	C	T	0.0048	0.0082	0.00041	1.2e-05	0.00631654935932142	ACT	S	H1101H	C3303T	CAC>CAT	Synonymous	GU280_gp02, spike glycoprotein	0.993615773326114
CAMB-79916	MN908947.3	25443	A	C	0.011	0.0071	5.9e-07	4.3e-05	0.00960502487220044	AAG	ORF3a	Q17H	A51C	CAA>CAC	Missense	GU280_gp03	0.99028035669257
CAMB-79916	MN908947.3	26152	G	T	0.0084	0.016	2.3e-05	3.8e-08	0.0116229923922232	CGG	ORF3a	G254*	G760T	GGA>TGA	Nonsense	GU280_gp03	0.988165680473373
CAMB-79916	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999397841493353	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000311801694122538
CAMB-79916	MN908947.3	29032	G	A	0.0076	0.012	9.7e-05	1.3e-06	0.00947080935040526	AGG	N	E253E	G759A	GAG>GAA	Synonymous	GU280_gp10	0.970691883002467
CAMB-79916	MN908947.3	29357	A	G	0.0091	0.01	1.7e-05	7.1e-06	0.00969997744191293	AAC	N	T362A	A1084G	ACA>GCA	Missense	GU280_gp10	0.990300022558087
CAMB-79916	MN908947.3	3037	C	T	1	1	0	0	0.998125180271128	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.80723007403134e-05
CAMB-79916	MN908947.3	4058	C	T	0.05	0.053	8e-23	6.3e-24	0.0509064836628086	TCC	ORF1ab:nsp3	P447S	C1339T	CCA>TCA	Missense	ORF1ab:nsp3	0.948735019973369
CAMB-79916	MN908947.3	5012	G	T	0.0038	0.019	0.0067	3e-06	0.0100671140939597	AGT	ORF1ab:nsp3	V765F	G2293T	GTT>TTT	Missense	ORF1ab:nsp3	0.98993288590604
CAMB-79916	MN908947.3	6681	C	T	1	1	0	0	0.99934836439463	GCT	ORF1ab:nsp3	A1321V	C3962T	GCT>GTT	Missense	ORF1ab:nsp3	0.000130327121073895
CAMB-79916	MN908947.3	7909	A	G	0.036	0.04	1.3e-16	8.1e-18	0.0379299909210128	AAT	ORF1ab:nsp3	K1730K	A5190G	AAA>AAG	Synonymous	ORF1ab:nsp3	0.961565620901846
CAMB-79916	MN908947.3	7981	A	G	0.0038	0.0074	0.00057	1.3e-05	0.00523517214477817	TAG	ORF1ab:nsp3	L1754L	A5262G	CTA>CTG	Synonymous	ORF1ab:nsp3	0.994600587160484
CAMB-79925	MN908947.3	11074	C	INS	0.11	0.11	1.1e-42	1.3e-44	0.106543965034427	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.887833430337905
CAMB-79925	MN908947.3	11083	G	-	0.2	0.19	1.2e-91	1.7e-83	0.195346821378617	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.97001635113571e-05
CAMB-79925	MN908947.3	11083	G	T	0.8	0.81	0	0	0.804337976005201	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.97001635113571e-05
CAMB-79925	MN908947.3	14805	C	T	1	1	0	0	0.999441629089432	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000169203306232604
CAMB-79925	MN908947.3	17440	C	T	0.0059	0.0087	0.00026	1.5e-05	0.00721883039588373	CCC	ORF1ab:helicase	P402S	C1204T	CCT>TCT	Missense	ORF1ab:helicase	0.992675575010559
CAMB-79925	MN908947.3	20331	T	C	0.0082	0.025	0.0012	7.6e-06	0.0141592920353982	ATG	ORF1ab:endoRNAse	Y237Y	T711C	TAT>TAC	Synonymous	ORF1ab:endoRNAse	0.982300884955752
CAMB-79925	MN908947.3	21569	G	INS	0.014	0.019	8.8e-07	4.9e-09	0.0165759732105483	TGT	S	.	6-7-insfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.983089158643784
CAMB-79925	MN908947.3	21575	C	T	0.24	0.27	2.4e-73	3.8e-83	0.25184262431226	TCT	S	L5F	C13T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.744212602512198
CAMB-79925	MN908947.3	241	C	T	1	1	0	0	0.999154657434989	TCG	NA	NA	NA	NA	NA	NA	0.000241526447145962
CAMB-79925	MN908947.3	2480	A	G	1	1	0	0	0.999826147426982	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	5.79508576726936e-05
CAMB-79925	MN908947.3	25000	C	T	1	1	0	0	0.999928155758316	ACT	S	D1146D	C3438T	GAC>GAT	Synonymous	GU280_gp02, spike glycoprotein	7.1844241684029e-05
CAMB-79925	MN908947.3	25141	A	T	0.0065	0.013	0.00011	3.8e-07	0.00918257111991358	TAA	S	L1193F	A3579T	TTA>TTT	Missense	GU280_gp02, spike glycoprotein	0.990817428880086
CAMB-79925	MN908947.3	25513	C	T	0.086	0.093	3.9e-39	2e-42	0.0893014686802636	ACT	ORF3a	L41F	C121T	CTC>TTC	Missense	GU280_gp03	0.909894130468628
CAMB-79925	MN908947.3	2558	C	T	1	1	0	0	0.99967220503575	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	2.04871852656164e-05
CAMB-79925	MN908947.3	26144	G	T	1	1	0	0	0.999531678597712	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000401418344818358
CAMB-79925	MN908947.3	27689	C	T	0.22	0.22	3.2e-70	5.9e-60	0.220394736842105	CCA	ORF7a	P99L	C296T	CCA>CTA	Missense	GU280_gp07	0.779605263157895
CAMB-79925	MN908947.3	3737	C	T	0.37	0.36	1.7e-185	6.4e-177	0.369092747030579	CCC	ORF1ab:nsp3	P340S	C1018T	CCT>TCT	Missense	ORF1ab:nsp3	0.630907252969421
CAMB-79925	MN908947.3	9328	A	G	0.025	0.021	2.1e-12	1.1e-10	0.0228674892703863	TAG	ORF1ab:nsp4	V258V	A774G	GTA>GTG	Synonymous	ORF1ab:nsp4	0.976886623748212
CAMB-79B3E	MN908947.3	1284	C	T	1	1	0	0	1	ACT	ORF1ab:nsp2	T160I	C479T	ACT>ATT	Missense	ORF1ab:nsp2	0
CAMB-79B3E	MN908947.3	14408	C	T	1	1	0	0	0.999479505530254	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000292778139232271
CAMB-79B3E	MN908947.3	23403	A	G	0.94	1	0	0	0.954992007201279	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.65599925504012e-05
CAMB-79B3E	MN908947.3	241	C	T	1	1	0	0	0.99976320151551	TCG	NA	NA	NA	NA	NA	NA	0.000189438787591759
CAMB-79B3E	MN908947.3	25555	G	T	1	1	0	0	0.998045056786446	TGT	ORF3a	V55F	G163T	GTT>TTT	Missense	GU280_gp03	0
CAMB-79B3E	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999408284023669	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79B3E	MN908947.3	29095	C	T	0.091	0.21	1.1e-39	1.7e-94	0.144828177221699	TCG	N	F274F	C822T	TTC>TTT	Synonymous	GU280_gp10	0.855000428485731
CAMB-79B3E	MN908947.3	3037	C	T	1	1	0	3.99995546873073e-320	0.999731182795699	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79B3E	MN908947.3	6439	G	T	1	1	0	0	1	AGA	ORF1ab:nsp3	Q1240H	G3720T	CAG>CAT	Missense	ORF1ab:nsp3	0
CAMB-79B3E	MN908947.3	7747	T	C	0.075	0.23	2.1e-32	3.1e-90	0.11064862989941	TTA	ORF1ab:nsp3	V1676V	T5028C	GTT>GTC	Synonymous	ORF1ab:nsp3	0.889235749797665
CAMB-79B4D	MN908947.3	11074	CT	-	0.01245	0.02735	0.0014;4.3e-06	0.00013;3.4e-12	0.0220051233909847	TCT	ORF1ab:nsp6	.	102-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.977909445256491
CAMB-79B4D	MN908947.3	11075	T	-	0.023	0.052	4.3e-06	3.4e-12	0.0385683611927392	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955202661605317
CAMB-79B4D	MN908947.3	1170	C	T	1	1	0	0	0.999532393444156	TCT	ORF1ab:nsp2	S122F	C365T	TCT>TTT	Missense	ORF1ab:nsp2	5.84508194804891e-05
CAMB-79B4D	MN908947.3	12410	A	G	0.0074	0.0099	4.5e-05	4.7e-06	0.00877571960900794	TAT	ORF1ab:nsp8	I107V	A319G	ATC>GTC	Missense	ORF1ab:nsp8	0.99119727817681
CAMB-79B4D	MN908947.3	14408	C	T	1	1	0	0	0.998382439643834	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000362817276149299
CAMB-79B4D	MN908947.3	1602	T	C	0.012	0.0061	4.6e-07	0.00012	0.00899331924855821	CTT	ORF1ab:nsp2	L266P	T797C	CTT>CCT	Missense	ORF1ab:nsp2	0.990978130531605
CAMB-79B4D	MN908947.3	22094	G	A	0.068	0.063	7.2e-31	1.2e-28	0.0653583650010398	GGA	S	D178N	G532A	GAC>AAC	Missense	GU280_gp02, spike glycoprotein	0.934584916718658
CAMB-79B4D	MN908947.3	22987	C	T	0.011	0.0086	4.5e-06	3.5e-05	0.00963128709018387	CCG	S	A475A	C1425T	GCC>GCT	Synonymous	GU280_gp02, spike glycoprotein	0.990336284333755
CAMB-79B4D	MN908947.3	23403	A	G	1	1	0	0	0.998606097865321	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.86952710804872e-05
CAMB-79B4D	MN908947.3	241	C	T	1	1	0	0	0.999434460223702	TCG	NA	NA	NA	NA	NA	NA	8.79728540907377e-05
CAMB-79B4D	MN908947.3	26155	GTT	-	0.014	0.013	2.3e-07;2.9e-07;2.7e-07	1.1e-06;1.4e-06;1.3e-06	0.0134648868253047	AGT	ORF3a	.	763-765-delinframe	.	no-SNV	GU280_gp03	0.986419036564132
CAMB-79B4D	MN908947.3	26873	C	T	0.0097	0.0091	7.9e-06	1.4e-05	0.00940787939641102	ACA	M	N117N	C351T	AAC>AAT	Synonymous	GU280_gp05	0.990577844610575
CAMB-79B4D	MN908947.3	27494	C	T	0.034	0.042	7.4e-16	5.7e-19	0.0384215271516749	CCT	ORF7a	P34L	C101T	CCT>CTT	Missense	GU280_gp07	0.961538016968352
CAMB-79B4D	MN908947.3	27925	C	T	0.059	0.056	2e-25	2e-24	0.0580920564216778	ACA	ORF8	T11I	C32T	ACA>ATA	Missense	GU280_gp09	0.941753278891364
CAMB-79B4D	MN908947.3	28253	C	T	0.006	0.0093	0.0011	4.7e-05	0.00767199600701992	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.991780579304127
CAMB-79B4D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999381379523662	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	5.26981450252951e-05
CAMB-79B4D	MN908947.3	3037	C	T	1	1	0	0	0.998934192588921	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	2.47862188623126e-05
CAMB-79B4D	MN908947.3	7375	T	C	0.023	0.0052	9.5e-12	0.00025	0.0136913142690683	ATC	ORF1ab:nsp3	N1552N	T4656C	AAT>AAC	Synonymous	ORF1ab:nsp3	0.986284410351022
CAMB-79B5C	MN908947.3	14408	C	T	1	1	0	0	0.999211480838984	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000578247384744783
CAMB-79B5C	MN908947.3	15210	A	C	0.00048	0.013	0.0013	4.2e-08	0.00466708151835719	GAA	ORF1ab:RNA-dependent-RNA-polymerase	G581G	A1743C	GGA>GGC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.995332918481643
CAMB-79B5C	MN908947.3	17301	T	C	1	1	0	0	1	ATG	ORF1ab:helicase	Y355Y	T1065C	TAT>TAC	Synonymous	ORF1ab:helicase	0
CAMB-79B5C	MN908947.3	21691	C	T	0.073	0.055	1.5e-31	8.5e-21	0.0683679899180844	TCA	S	F43F	C129T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.931632010081916
CAMB-79B5C	MN908947.3	23403	A	G	1	1	0	0	0.999791107132199	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00017905102954342
CAMB-79B5C	MN908947.3	241	C	T	1	1	0	0	0.999909465393147	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-79B5C	MN908947.3	24337	C	T	1	1	0	0	1	ACC	S	N925N	C2775T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-79B5C	MN908947.3	28881	G	A	1	1	0	0	0.999194847020934	AGG	N	R203K	G608A	AGG>AAG	Missense	GU280_gp10	0.000268384326355341
CAMB-79B5C	MN908947.3	28881	GGG	AAC	1	0.993333333333333	0;0;0	0;0;0	0.999504827927705	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000268384326355341
CAMB-79B5C	MN908947.3	28883	G	C	1	0.98	0	0	0.989862581662537	GGG	N	G204R	G610C	GGA>CGA	Missense	GU280_gp10	0
CAMB-79B5C	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79B6B	MN908947.3	11074	C	INS	0.026	0.023	2.4e-05	9.3e-05	0.0244948587459282	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.975041443028877
CAMB-79B6B	MN908947.3	11075	T	-	0.032	0.038	2.4e-08	2e-09	0.0354949596384844	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960208180448805
CAMB-79B6B	MN908947.3	12774	C	T	0.012	0.012	3.2e-07	4.6e-07	0.0118960365337994	GCT	ORF1ab:nsp9	A30V	C89T	GCT>GTT	Missense	ORF1ab:nsp9	0.987263911597226
CAMB-79B6B	MN908947.3	14408	C	T	1	1	0	0	0.99576751170081	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000526865763384586
CAMB-79B6B	MN908947.3	17443	G	T	0.091	0.09	3.3e-41	1.7e-40	0.0904198830223969	TGC	ORF1ab:helicase	A403S	G1207T	GCT>TCT	Missense	ORF1ab:helicase	0.908961942652443
CAMB-79B6B	MN908947.3	2142	C	T	0.023	0.025	1.5e-11	3.6e-12	0.02414041089234	CCC	ORF1ab:nsp2	P446L	C1337T	CCC>CTC	Missense	ORF1ab:nsp2	0.975788321120592
CAMB-79B6B	MN908947.3	23403	A	G	1	1	0	0	0.9995837976451	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.7129412080609e-05
CAMB-79B6B	MN908947.3	241	C	T	1	1	0	0	0.99828356546691	TCG	NA	NA	NA	NA	NA	NA	0.000117922983189424
CAMB-79B6B	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0345135135135135	0.0322972972972973	0.00047;3.7e-05;0.00014;0.00015;0.00035;3.6e-06;2.9e-05;8.4e-06;8.5e-06;2.5e-06;2.9e-06;2.3e-06;8.6e-06;4.4e-06;5.2e-06;1.1e-05;3.6e-06;9.3e-06;5.5e-06;6.1e-06;3.7e-06;1e-05;4.2e-06;7.1e-06;5.6e-06;2.6e-06;6.8e-06;5.2e-06;5e-06;3.2e-06;8.6e-06;5.6e-06;1.7e-06;6.3e-06;2.5e-06;4.7e-06;2.4e-06	0.0011;0.00014;0.00059;0.00058;0.00087;2.8e-05;7.2e-05;2.1e-05;2e-05;7.9e-06;1.2e-05;9.4e-06;1.8e-05;1.2e-05;1.6e-05;2.3e-05;1.1e-05;2.1e-05;1.5e-05;1.4e-05;1.1e-05;2.3e-05;1.2e-05;1.6e-05;1.3e-05;9.4e-06;1.8e-05;1.1e-05;5.2e-06;1.3e-05;1.8e-05;1.8e-05;1.1e-05;1.9e-05;6.9e-06;1.2e-05;7.5e-06	0.0345701660946069	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.977818012723477
CAMB-79B6B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999094366962507	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000201953904021407
CAMB-79B6B	MN908947.3	3037	C	T	1	1	0	0	0.999132049924488	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000138872012081865
CAMB-79B6B	MN908947.3	8137	G	T	1	1	0	0	0.99951700821086	TGT	ORF1ab:nsp3	V1806V	G5418T	GTG>GTT	Synonymous	ORF1ab:nsp3	0.000183996872053175
CAMB-79B6B	MN908947.3	843	C	T	1	1	0	0	0.999367418640634	CCT	ORF1ab:nsp2	P13L	C38T	CCT>CTT	Missense	ORF1ab:nsp2	0.000299193886186646
CAMB-79B7A	MN908947.3	11074	C	INS	0.15	0.32	4.9e-49	7.2e-121	0.208704453441296	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.790890688259109
CAMB-79B7A	MN908947.3	14408	C	T	1	1	0	0	0.999253960591565	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000307192697590732
CAMB-79B7A	MN908947.3	23403	A	G	1	1	0	0	0.99996487222271	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	1.7563888644946e-05
CAMB-79B7A	MN908947.3	241	C	T	1	1	0	0	0.999818148754319	TCG	NA	NA	NA	NA	NA	NA	0.000121234163787355
CAMB-79B7A	MN908947.3	25034	A	G	0.016	0.35	3.7e-09	8.9e-182	0.135061927958234	GAA	S	N1158D	A3472G	AAT>GAT	Missense	GU280_gp02, spike glycoprotein	0.864916227964787
CAMB-79B7A	MN908947.3	26681	C	T	1	1	0	0	0.999847708005483	TCC	M	F53F	C159T	TTC>TTT	Synonymous	GU280_gp05	0.000152291994517488
CAMB-79B7A	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79B7A	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79B89	MN908947.3	11075	T	-	0.038	0.049	1.9e-09	9.9e-12	0.043351694324362	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952569376655975
CAMB-79B89	MN908947.3	14408	C	T	1	1	0	0	0.997952504427017	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000395269415633696
CAMB-79B89	MN908947.3	23403	A	G	1	1	0	0	0.999590866583541	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.74127182044888e-05
CAMB-79B89	MN908947.3	241	C	T	1	1	0	0	0.99843137254902	TCG	NA	NA	NA	NA	NA	NA	0.000168067226890756
CAMB-79B89	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999033052039381	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00017500194446605
CAMB-79B89	MN908947.3	3037	C	T	1	1	0	0	0.999304095472179	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000133258313838136
CAMB-79B98	MN908947.3	11074	C	INS	0.029	0.027	1.2e-06	1.6e-05	0.0280420924346114	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.970750914033936
CAMB-79B98	MN908947.3	11075	T	-	0.031	0.041	6.2e-08	2.4e-10	0.0357225074818084	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960143730795023
CAMB-79B98	MN908947.3	12295	C	T	0.11	0.11	1.8e-51	9.4e-51	0.112691882832438	CCC	ORF1ab:nsp8	T68T	C204T	ACC>ACT	Synonymous	ORF1ab:nsp8	0.887022435531177
CAMB-79B98	MN908947.3	1469	C	T	0.017	0.022	1.2e-08	2e-10	0.0191617742987606	TCG	ORF1ab:nsp2	R222C	C664T	CGC>TGC	Missense	ORF1ab:nsp2	0.980104370515329
CAMB-79B98	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999440078389025	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000179971204607263
CAMB-79B98	MN908947.3	16260	C	T	0.018	0.015	1.1e-08	9e-08	0.0169097253288002	GCA	ORF1ab:helicase	C8C	C24T	TGC>TGT	Synonymous	ORF1ab:helicase	0.982598192717187
CAMB-79B98	MN908947.3	17347	G	A	0.011	0.011	6.8e-07	8.7e-07	0.0110498387264593	AGT	ORF1ab:helicase	V371I	G1111A	GTT>ATT	Missense	ORF1ab:helicase	0.98797211528457
CAMB-79B98	MN908947.3	17999	C	T	0.07	0.068	9.9e-32	3.2e-31	0.0693597655235528	ACA	ORF1ab:helicase	T588I	C1763T	ACA>ATA	Missense	ORF1ab:helicase	0.930263043989068
CAMB-79B98	MN908947.3	18486	C	T	1	1	0	0	0.999675400555714	TCA	ORF1ab:3'-to-5'-exonuclease	L149L	C447T	CTC>CTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	9.08878444000104e-05
CAMB-79B98	MN908947.3	18795	C	T	1	1	0	0	0.999553616426916	ACC	ORF1ab:3'-to-5'-exonuclease	N252N	C756T	AAC>AAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.000345587282388008
CAMB-79B98	MN908947.3	18877	C	T	0.026	0.024	1.3e-12	3.6e-12	0.0250100847115773	TCT	ORF1ab:3'-to-5'-exonuclease	L280L	C838T	CTA>TTA	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.974615340286982
CAMB-79B98	MN908947.3	2059	G	A	1	1	0	0	0.999678237129485	TGG	ORF1ab:nsp2	M418I	G1254A	ATG>ATA	Missense	ORF1ab:nsp2	7.8003120124805e-05
CAMB-79B98	MN908947.3	24142	T	C	0.055	0.056	4.3e-25	1.1e-25	0.0551565194035541	TTT	S	V860V	T2580C	GTT>GTC	Synonymous	GU280_gp02, spike glycoprotein	0.942434823292929
CAMB-79B98	MN908947.3	26781	CTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.03275	0.0333888888888889	0.00014;0.00069;8e-04;0.0014;8.7e-05;2e-04;1.9e-05;1.8e-05;4.9e-06;1.1e-05;8.3e-06;1.8e-05;1.1e-05;1.4e-05;2.4e-05;8e-06;2.1e-05;1.3e-05;1.2e-05;9.4e-06;2.2e-05;1.1e-05;1.6e-05;1.2e-05;7.1e-06;1.7e-05;1.1e-05;1.1e-05;1e-05;1.9e-05;1.2e-05;3.9e-06;1.6e-05;7.1e-06;1.3e-05;8.4e-06	0.00011;0.00048;0.00061;0.00063;5.7e-05;8.4e-05;1.4e-05;1.3e-05;4.8e-06;7.9e-06;6.9e-06;1.1e-05;6.7e-06;8e-06;1.2e-05;5.7e-06;1.2e-05;8.2e-06;7.6e-06;4.9e-06;1.3e-05;6.8e-06;9.1e-06;7.2e-06;4.6e-06;9.8e-06;6.3e-06;9e-06;6.3e-06;1e-05;8.4e-06;3.9e-06;1e-05;3.7e-06;7e-06;5.2e-06	0.034239607436368	TCT	M	.	259-294-delinframe	.	no-SNV	GU280_gp05	0.975113122171946
CAMB-79B98	MN908947.3	28377	C	T	0.015	0.016	2.7e-08	8.1e-09	0.0157492809679659	GCG	N	A35V	C104T	GCG>GTG	Missense	GU280_gp10	0.982991173261926
CAMB-79B98	MN908947.3	28811	A	T	0.52	0.52	4.70000004671707e-317	3.00000000038571e-315	0.518682170542636	CAG	N	S180C	A538T	AGT>TGT	Missense	GU280_gp10	0.480723514211886
CAMB-79B98	MN908947.3	28836	C	T	0.065	0.064	7.5e-27	8.4e-27	0.0644812162310704	TCA	N	S188L	C563T	TCA>TTA	Missense	GU280_gp10	0.935493417436817
CAMB-79B98	MN908947.3	28887	C	T	0.12	0.12	1.7e-52	2.7e-53	0.122490536483488	ACT	N	T205I	C614T	ACT>ATT	Missense	GU280_gp10	0.877344123917678
CAMB-79B98	MN908947.3	28932	C	T	0.02	0.018	3.5e-09	1.1e-08	0.0189582552126481	GCT	N	A220V	C659T	GCT>GTT	Missense	GU280_gp10	0.980753969984216
CAMB-79B98	MN908947.3	29032	G	A	1	1	0	0	0.999833411229009	AGG	N	E253E	G759A	GAG>GAA	Synonymous	GU280_gp10	6.94119879130592e-05
CAMB-79B98	MN908947.3	29095	C	T	0.0098	0.0094	2.3e-05	3.5e-05	0.0096222453264836	TCG	N	F274F	C822T	TTC>TTT	Synonymous	GU280_gp10	0.990286017165107
CAMB-79B98	MN908947.3	29518	C	T	0.14	0.15	2.4e-64	4e-66	0.145506296360186	ACT	N	D415D	C1245T	GAC>GAT	Synonymous	GU280_gp10	0.854493703639814
CAMB-79B98	MN908947.3	29767	AACAAT	-	0.0251666666666667	0.0226666666666667	5.4e-11;7.1e-11;8.6e-11;8e-12;6.8e-13;2.7e-11	3.8e-10;5.5e-10;5.9e-10;1e-10;1.5e-11;2.3e-10	0.0231677708736266	GAA	NA	NA	NA	NA	NA	NA	0.976982097186701
CAMB-79B98	MN908947.3	4704	C	T	0.0078	0.0066	2.8e-05	7.9e-05	0.00729960225359292	CCT	ORF1ab:nsp3	P662L	C1985T	CCT>CTT	Missense	ORF1ab:nsp3	0.992582075016611
CAMB-79B98	MN908947.3	6317	C	T	0.8	0.8	0	0	0.800036604709806	ACC	ORF1ab:nsp3	P1200S	C3598T	CCA>TCA	Missense	ORF1ab:nsp3	0.199943059340302
CAMB-79B98	MN908947.3	8832	C	T	0.013	0.015	5.9e-07	4.9e-08	0.013628742946765	GCA	ORF1ab:nsp4	A93V	C278T	GCA>GTA	Missense	ORF1ab:nsp4	0.986281119864434
CAMB-79B98	MN908947.3	929	A	G	0.084	0.093	3.1e-38	2.1e-42	0.0880704486680318	TAT	ORF1ab:nsp2	I42V	A124G	ATT>GTT	Missense	ORF1ab:nsp2	0.911621915227026
CAMB-79B98	MN908947.3	9936	C	T	0.069	0.062	3.5e-31	5.1e-28	0.0655853172606709	ACT	ORF1ab:nsp4	T461I	C1382T	ACT>ATT	Missense	ORF1ab:nsp4	0.934394558370731
CAMB-79BA7	MN908947.3	10097	G	A	1	1	0	0	1	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0
CAMB-79BA7	MN908947.3	13914	T	G	0.0058	0.0038	3.4e-05	0.0016	0.00562851782363977	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.99437148217636
CAMB-79BA7	MN908947.3	14408	C	T	1	1	0	0	0.998572593800979	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00101957585644372
CAMB-79BA7	MN908947.3	23403	A	G	1	1	0	0	0.999855559166576	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000108330625067707
CAMB-79BA7	MN908947.3	23731	C	T	1	1	0	0	0.999754480726737	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000245519273262951
CAMB-79BA7	MN908947.3	241	C	T	1	1	0	0	0.999919820397691	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-79BA7	MN908947.3	28580	G	T	1	1	0	0	0.999718309859155	AGA	N	D103Y	G307T	GAT>TAT	Missense	GU280_gp10	0.00028169014084507
CAMB-79BA7	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79BA7	MN908947.3	3037	C	T	1	1	0	2.9e-175	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79BB6	MN908947.3	11036	C	T	0.045	0.024	5.5e-21	2.4e-12	0.034679809688138	ACT	ORF1ab:nsp6	L22F	C64T	CTT>TTT	Missense	ORF1ab:nsp6	0.965286023011677
CAMB-79BB6	MN908947.3	11074	C	INS	0.017	0.03	0.0047	5.9e-07	0.0238981758720127	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.97583665712802
CAMB-79BB6	MN908947.3	11075	T	-	0.026	0.028	8.3e-07	2.4e-07	0.0270475484976156	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.972711699615723
CAMB-79BB6	MN908947.3	11152	C	T	0.009	0.006	8e-06	0.00015	0.00748141528984543	TCA	ORF1ab:nsp6	V60V	C180T	GTC>GTT	Synonymous	ORF1ab:nsp6	0.992490065973344
CAMB-79BB6	MN908947.3	11298	A	G	0.0076	0.012	3.3e-05	6.1e-07	0.00963210702341137	AAG	ORF1ab:nsp6	K109R	A326G	AAG>AGG	Missense	ORF1ab:nsp6	0.990359531772575
CAMB-79BB6	MN908947.3	12119	C	T	0.0076	0.0093	2.6e-05	4.7e-06	0.00839542717158314	TCC	ORF1ab:nsp8	P10S	C28T	CCA>TCA	Missense	ORF1ab:nsp8	0.991570548807458
CAMB-79BB6	MN908947.3	13072	C	T	0.013	0.0089	9.2e-08	5.9e-06	0.0111717115127947	TCT	ORF1ab:nsp10	F16F	C48T	TTC>TTT	Synonymous	ORF1ab:nsp10	0.98879945294864
CAMB-79BB6	MN908947.3	13458	C	T	0.0092	0.0042	2.1e-05	0.0033	0.00690925840626439	TCG	ORF1ab:nsp11	S6L	C17T	TCG>TTG	Missense	ORF1ab:nsp11	0.993024939132724
CAMB-79BB6	MN908947.3	14120	C	T	1	1	0	0	0.999106680476437	CCA	ORF1ab:RNA-dependent-RNA-polymerase	P218L	C653T	CCA>CTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000129466597617815
CAMB-79BB6	MN908947.3	14408	C	T	1	1	0	0	0.998259860788863	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000256741850823476
CAMB-79BB6	MN908947.3	17167	C	T	0.015	0.013	3.5e-08	3.1e-07	0.0142922352867104	TCA	ORF1ab:helicase	H311Y	C931T	CAT>TAT	Missense	ORF1ab:helicase	0.985699894539674
CAMB-79BB6	MN908947.3	203	C	T	0.016	0.009	4.8e-08	2.8e-05	0.0124339588267444	TCG	NA	NA	NA	NA	NA	NA	0.987535677415437
CAMB-79BB6	MN908947.3	203	CG	TT	0.008	0.00835	4.8e-08;NA	2.8e-05;2e-05	0.00789755161247784	TCG	NA	NA	NA	NA	NA	NA	0.987535677415437
CAMB-79BB6	MN908947.3	21597	C	T	0.0059	0.022	0.00042	7e-10	0.0136195752539243	TCT	S	S12F	C35T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.986149584487535
CAMB-79BB6	MN908947.3	21658	C	T	0.012	0.0054	1.9e-06	0.00042	0.00861205687963148	TCA	S	F32F	C96T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.991387943120368
CAMB-79BB6	MN908947.3	21691	C	T	0.017	0.025	5.1e-09	2.6e-12	0.0208161501904874	TCA	S	F43F	C129T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.979066022544283
CAMB-79BB6	MN908947.3	22281	CTTTACTTG	-	0.00515555555555556	0.0103333333333333	0.0055;0.012;0.011;0.017;0.024;0.03;0.00055;0.00032;0.0013	2.5e-06;8.6e-06;4.6e-06;2e-05;4.9e-05;6.9e-05;0.00029;0.00015;0.00061	0.00638876142741167	ACT	S	.	719-727-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.993456886185188
CAMB-79BB6	MN908947.3	22452	C	T	0.047	0.02	4.2e-07	0.00027	0.0327380952380952	TCA	S	S297L	C890T	TCA>TTA	Missense	GU280_gp02, spike glycoprotein	0.967261904761905
CAMB-79BB6	MN908947.3	23403	A	G	1	1	0	0	0.999896341598857	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.92333720818309e-05
CAMB-79BB6	MN908947.3	23435	C	T	0.0077	0.011	2.7e-05	8.6e-07	0.00945105492408836	TCA	S	H625Y	C1873T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.990497178734387
CAMB-79BB6	MN908947.3	23638	C	T	0.046	0.053	1.1e-18	2.8e-21	0.0492713393476752	TCA	S	I692I	C2076T	ATC>ATT	Synonymous	GU280_gp02, spike glycoprotein	0.950728660652325
CAMB-79BB6	MN908947.3	241	C	T	0.99	1	0	0	0.996571245148677	TCG	NA	NA	NA	NA	NA	NA	0.000116723569406752
CAMB-79BB6	MN908947.3	24213	C	T	0.022	0.0042	8.8e-10	0.0036	0.0133715633206496	TCT	S	S884F	C2651T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.986601639959269
CAMB-79BB6	MN908947.3	25521	C	T	0.031	0.014	1.4e-14	2.4e-07	0.0224503215995726	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.977518854160245
CAMB-79BB6	MN908947.3	25758	A	G	0.0027	0.01	0.0043	2.7e-06	0.00623728813559322	GAA	ORF3a	R122R	A366G	AGA>AGG	Synonymous	GU280_gp03	0.993762711864407
CAMB-79BB6	MN908947.3	26958	C	T	0.012	0.0085	5.6e-07	1.7e-05	0.0101007290333352	TCG	M	R146C	C436T	CGT>TGT	Missense	GU280_gp05	0.989871445266848
CAMB-79BB6	MN908947.3	27208	C	T	0.0098	0.0033	6.2e-06	0.0043	0.00675941540191119	TCA	ORF6	H3Y	C7T	CAT>TAT	Missense	GU280_gp06	0.993226531759415
CAMB-79BB6	MN908947.3	28253	C	T	0.069	0.064	3.6e-30	5e-28	0.0661790351672662	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.933362564649374
CAMB-79BB6	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.997114344114464	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79BB6	MN908947.3	29735	AGGCCACGCGGAGT	-	0.110714285714286	0.131428571428571	2.7e-43;1.7e-42;1.2e-40;5.9e-41;1.4e-40;1.5e-42;7.8e-41;2.9e-40;2.5e-41;2.9e-41;1.9e-40;2.5e-41;6.9e-37;7.4e-34	1.9e-51;1.5e-50;2.3e-49;3e-49;3.8e-49;3.7e-52;4e-49;6.3e-49;8.8e-50;2.6e-49;8.5e-49;1.1e-49;6.8e-45;1.7e-40	0.119096509240246	GAG	NA	NA	NA	NA	NA	NA	0.87463976945245
CAMB-79BB6	MN908947.3	3037	C	T	1	1	0	0	0.999409681227863	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000118063754427391
CAMB-79BB6	MN908947.3	3096	C	T	0.016	0.011	3.7e-07	1.9e-05	0.0138360251002983	TCA	ORF1ab:nsp3	S126L	C377T	TCA>TTA	Missense	ORF1ab:nsp3	0.986163974899702
CAMB-79BB6	MN908947.3	3728	G	T	0.0084	0.0059	3.3e-05	4e-04	0.00739176346356917	TGG	ORF1ab:nsp3	G337C	G1009T	GGT>TGT	Missense	ORF1ab:nsp3	0.992608236536431
CAMB-79BB6	MN908947.3	4058	C	T	0.0044	0.019	7e-04	6.9e-10	0.0120125130344108	TCC	ORF1ab:nsp3	P447S	C1339T	CCA>TCA	Missense	ORF1ab:nsp3	0.987987486965589
CAMB-79BB6	MN908947.3	4570	C	T	0.0037	0.0061	0.00057	4.7e-05	0.00475943428146076	TCA	ORF1ab:nsp3	I617I	C1851T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.995150339476237
CAMB-79BB6	MN908947.3	4815	C	T	0.0031	0.022	0.0095	7.5e-11	0.0111679443728818	TCT	ORF1ab:nsp3	S699F	C2096T	TCT>TTT	Missense	ORF1ab:nsp3	0.988769525143507
CAMB-79BB6	MN908947.3	5365	C	T	0.0041	0.009	0.0027	4.2e-05	0.00599672905687807	ACA	ORF1ab:nsp3	Y882Y	C2646T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.994003270943122
CAMB-79BB6	MN908947.3	635	C	T	0.049	0.062	1.3e-22	2.7e-28	0.0545426870518198	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.945406575564876
CAMB-79BB6	MN908947.3	683	C	T	0.016	0.014	1.9e-08	9.2e-08	0.0150146836125979	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.984979185442685
CAMB-79BB6	MN908947.3	7823	C	T	0.0079	0.0024	2.4e-05	0.0036	0.00494806976288458	TCA	ORF1ab:nsp3	H1702Y	C5104T	CAT>TAT	Missense	ORF1ab:nsp3	0.995002939447384
CAMB-79BB6	MN908947.3	9430	C	T	0.0062	0.046	0.00085	3.2e-20	0.0285398230088496	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.97146017699115
CAMB-79BB6	MN908947.3	9700	C	T	0.0036	0.0082	0.00095	1.1e-05	0.00576380698425722	TCA	ORF1ab:nsp4	I382I	C1146T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.994236193015743
CAMB-79BD4	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.9990234375	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000266335227272727
CAMB-79BD4	MN908947.3	21008	C	T	0.094	0.1	1.3e-41	4.1e-46	0.0989106462607766	ACT	ORF1ab:2'-O-ribose-methyltransferase	T117I	C350T	ACT>ATT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.901089353739223
CAMB-79BD4	MN908947.3	26029	C	A	0.34	0.093	7.9e-43	6.9e-08	0.269736842105263	CCA	ORF3a	Q213K	C637A	CAG>AAG	Missense	GU280_gp03	0.730263157894737
CAMB-79BD4	MN908947.3	26256	C	T	1	1	0	0	0.999851433665132	TCG	E	F4F	C12T	TTC>TTT	Synonymous	GU280_gp04	0.000148566334868519
CAMB-79BD4	MN908947.3	27944	C	T	1	1	0	0	1	ACC	ORF8	H17H	C51T	CAC>CAT	Synonymous	GU280_gp09	0
CAMB-79BD4	MN908947.3	28622	C	T	0.023	0.032	1.8e-11	2.1e-14	0.026001705029838	GCC	N	P117S	C349T	CCA>TCA	Missense	GU280_gp10	0.973913043478261
CAMB-79BD4	MN908947.3	28854	C	T	0.011	0.021	4.3e-05	2.4e-08	0.0157456004939796	TCA	N	S194L	C581T	TCA>TTA	Missense	GU280_gp10	0.98425439950602
CAMB-79BD4	MN908947.3	29771	A	G	1	1	0	0	1	AAT	NA	NA	NA	NA	NA	NA	0
CAMB-79BD4	MN908947.3	3406	A	G	1	1	0	0	0.999869366427172	AAG	ORF1ab:nsp3	E229E	A687G	GAA>GAG	Synonymous	ORF1ab:nsp3	0
CAMB-79BD4	MN908947.3	6548	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	L1277L	C3829T	CTA>TTA	Synonymous	ORF1ab:nsp3	0
CAMB-79BE3	MN908947.3	10507	C	T	1	1	0	0	1	ACA	ORF1ab:3C-like-proteinase	N151N	C453T	AAC>AAT	Synonymous	ORF1ab:3C-like-proteinase	0
CAMB-79BE3	MN908947.3	2891	G	A	1	1	0	0	1	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	0
CAMB-79BE3	MN908947.3	994	A	G	1	1	0	0	1	AAC	ORF1ab:nsp2	E63E	A189G	GAA>GAG	Synonymous	ORF1ab:nsp2	0
CAMB-79BF2	MN908947.3	14408	C	T	1	1	0	0	0.999533612093921	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000305564490189772
CAMB-79BF2	MN908947.3	23403	A	G	1	1	0	0	0.999943928377848	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.67263517933574e-05
CAMB-79BF2	MN908947.3	241	C	T	1	1	0	0	0.999726429406352	TCG	NA	NA	NA	NA	NA	NA	0.000198960431744137
CAMB-79BF2	MN908947.3	28167	G	A	0.01	0.027	2.1e-06	1.4e-13	0.0180104756998111	GGA	ORF8	E92K	G274A	GAA>AAA	Missense	GU280_gp09	0.981989524300189
CAMB-79BF2	MN908947.3	28624	A	T	1	1	0	0	0.999737509843381	CAG	N	P117P	A351T	CCA>CCT	Synonymous	GU280_gp10	4.37483594365211e-05
CAMB-79BF2	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999909494071862	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	9.96611520829181e-05
CAMB-79BF2	MN908947.3	3037	C	T	1	1	0	0	0.999416143628667	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79C0E	MN908947.3	10812	TTTCTGCTCAAACTGGAA	-	0.000183333333333333	0.00594444444444444	NA;NA;NA;NA;NA;0.0021;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00015;7.9e-05;0.00011;0.00012;0.00011;0.00017;9.9e-05;0.00012;0.00013;0.00034;7.7e-05;7.1e-05;9.6e-05;7.8e-05;0.00011;7e-05;0.00011;8.6e-06	0.0022766078542971	CTT	ORF1ab:3C-like-proteinase	.	758-775-delinframe	.	no-SNV	ORF1ab:3C-like-proteinase	0.997567864428056
CAMB-79C0E	MN908947.3	11074	C	INS	0.027	0.017	7.8e-06	0.0043	0.0221614434126461	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.977687210144536
CAMB-79C0E	MN908947.3	11075	T	-	0.027	0.029	6.4e-07	1.4e-07	0.0277995444191344	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.972027334851936
CAMB-79C0E	MN908947.3	14408	C	T	1	1	0	0	0.998431498364659	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000267358233296794
CAMB-79C0E	MN908947.3	21058	C	T	0.0078	0.0065	2.6e-05	8.1e-05	0.00720104492489602	CCC	ORF1ab:2'-O-ribose-methyltransferase	P134S	C400T	CCT>TCT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.992764582545629
CAMB-79C0E	MN908947.3	23403	A	G	1	1	0	0	0.999964430279791	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.84557761668647e-05
CAMB-79C0E	MN908947.3	241	C	T	1	1	0	0	0.999350613463026	TCG	NA	NA	NA	NA	NA	NA	0.000110533878633801
CAMB-79C0E	MN908947.3	26849	G	T	0.0029	0.012	0.0054	7.4e-07	0.00705071508435826	TGT	M	M109I	G327T	ATG>ATT	Missense	GU280_gp05	0.992949284915642
CAMB-79C0E	MN908947.3	28086	G	T	1	0.99	0	0	0.99604442415944	GGC	ORF8	A65S	G193T	GCT>TCT	Missense	GU280_gp09	0.00182565038795071
CAMB-79C0E	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998508086172943	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000598802395209581
CAMB-79C0E	MN908947.3	29726	T	-	0.31	0.3	1.8e-115	1.1e-115	0.304950495049505	ATT	NA	NA	NA	NA	NA	NA	0.695049504950495
CAMB-79C0E	MN908947.3	3037	C	T	1	1	0	0	0.999510230735742	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79C0E	MN908947.3	3903	C	T	1	1	0	0	0.999953637164449	CCA	ORF1ab:nsp3	P395L	C1184T	CCA>CTA	Missense	ORF1ab:nsp3	4.63628355510223e-05
CAMB-79C1D	MN908947.3	11001	C	T	1	1	0	9.99999999999999e-264	0.999074930619796	ACA	ORF1ab:nsp6	T10I	C29T	ACA>ATA	Missense	ORF1ab:nsp6	0.000925069380203515
CAMB-79C1D	MN908947.3	11596	G	T	0.097	0.032	2e-21	8.5e-06	0.0810810810810811	AGT	ORF1ab:nsp6	Q208H	G624T	CAG>CAT	Missense	ORF1ab:nsp6	0.918918918918919
CAMB-79C1D	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999238095238095	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000380952380952381
CAMB-79C1D	MN908947.3	19791	T	C	0.37	1	7.8e-90	0	0.694555112881806	TTT	ORF1ab:endoRNAse	L57L	T171C	CTT>CTC	Synonymous	ORF1ab:endoRNAse	0.305444887118194
CAMB-79C1D	MN908947.3	29625	C	T	1	1	1.9e-100	6.6e-177	1	TCT	ORF10	S23F	C68T	TCT>TTT	Missense	GU280_gp11	0
CAMB-79C1D	MN908947.3	6548	C	T	1	1	6.6e-205	1.7e-263	1	TCT	ORF1ab:nsp3	L1277L	C3829T	CTA>TTA	Synonymous	ORF1ab:nsp3	0
CAMB-79C1D	MN908947.3	6696	C	T	1	1	2.7e-174	2.2e-243	1	CCT	ORF1ab:nsp3	P1326L	C3977T	CCT>CTT	Missense	ORF1ab:nsp3	0
CAMB-79C2C	MN908947.3	13914	T	G	0.0099	0.0012	4.9e-07	0.0061	0.00564269814153336	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994357301858467
CAMB-79C2C	MN908947.3	14408	C	T	1	1	0	0	0.999446800663839	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000316113906377598
CAMB-79C2C	MN908947.3	16394	C	T	0.026	0.058	4.7e-10	2.2e-17	0.0381270903010033	CCA	ORF1ab:helicase	P53L	C158T	CCA>CTA	Missense	ORF1ab:helicase	0.961872909698997
CAMB-79C2C	MN908947.3	1643	A	G	0.74	0.32	0	8.2e-149	0.551295896328294	CAA	ORF1ab:nsp2	N280D	A838G	AAC>GAC	Missense	ORF1ab:nsp2	0.448704103671706
CAMB-79C2C	MN908947.3	21707	C	T	1	1	0	0	1	ACA	S	H49Y	C145T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-79C2C	MN908947.3	23403	A	G	1	1	0	0	0.999930177349532	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.49113252339059e-05
CAMB-79C2C	MN908947.3	241	C	T	1	1	0	0	0.999824098504837	TCG	NA	NA	NA	NA	NA	NA	3.51802990325418e-05
CAMB-79C2C	MN908947.3	25640	TGC	-	0.042	0.0016	1.4e-20;1.7e-20;1.2e-20	0.0056;0.0095;0.0057	0.0275226872545036	TTG	ORF3a	.	248-250-delinframe	.	no-SNV	GU280_gp03	0.97239604496817
CAMB-79C2C	MN908947.3	25642	C	T	0.29	0.31	2.5e-145	3.2e-156	0.299516514558887	GCT	ORF3a	L84L	C250T	CTG>TTG	Synonymous	GU280_gp03	0.67288678835289
CAMB-79C2C	MN908947.3	2940	C	T	1	1	0	0	0.999728260869565	CCA	ORF1ab:nsp3	P74L	C221T	CCA>CTA	Missense	ORF1ab:nsp3	0.000271739130434783
CAMB-79C2C	MN908947.3	3037	C	T	1	1	0	0	0.99972972972973	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79C2C	MN908947.3	3951	A	G	1	1	0	0	1	GAT	ORF1ab:nsp3	D411G	A1232G	GAT>GGT	Missense	ORF1ab:nsp3	0
CAMB-79C2C	MN908947.3	9848	A	G	0.36	0.29	5.7e-157	8.7e-125	0.318484288354898	TAG	ORF1ab:nsp4	S432G	A1294G	AGT>GGT	Missense	ORF1ab:nsp4	0.681515711645102
CAMB-79C3B	MN908947.3	11074	C	INS	0.039	0.028	3.4e-11	1.8e-06	0.0343048887143699	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.963321255823085
CAMB-79C3B	MN908947.3	11074	CT	-	0.019549	0.02445	0.13;2.3e-09	1.4e-06;1e-10	0.0232089546101274	TCT	ORF1ab:nsp6	.	102-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.963321255823085
CAMB-79C3B	MN908947.3	11075	T	-	0.039	0.044	2.3e-09	1e-10	0.0411051881000862	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956423924897237
CAMB-79C3B	MN908947.3	14408	C	T	1	0.99	0	0	0.994785085804866	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000352255584399672
CAMB-79C3B	MN908947.3	23403	A	G	1	1	0	0	0.999262467732963	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.37541017419512e-05
CAMB-79C3B	MN908947.3	241	C	T	1	1	0	0	0.999749920113369	TCG	NA	NA	NA	NA	NA	NA	0.000111146616280201
CAMB-79C3B	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0335757575757576	0.038030303030303	0.00012;0.00051;2.3e-05;2.3e-05;6.7e-06;1.1e-05;8.1e-06;2.4e-05;1.4e-05;1.8e-05;3.2e-05;1.2e-05;2.8e-05;1.7e-05;1.7e-05;1.7e-05;3e-05;1.6e-05;2.3e-05;1.6e-05;1.2e-05;2.3e-05;1.5e-05;1.3e-05;1.2e-05;2.5e-05;2.3e-05;9.8e-06;2.5e-05;8e-06;1.3e-05;1e-05;0.00062	1.3e-05;1.5e-05;3.1e-06;2.9e-06;1.3e-06;1.8e-06;1.7e-06;2.7e-06;1.9e-06;2.5e-06;3.8e-06;1.8e-06;3.3e-06;2.3e-06;2.2e-06;1.4e-06;3.8e-06;1.6e-06;2.4e-06;1.9e-06;1.4e-06;3e-06;1.7e-06;8.1e-07;2.1e-06;2.9e-06;2.5e-06;1.5e-06;2.8e-06;7.3e-07;1.7e-06;1.4e-06;0.00053	0.0356664590470258	GTA	M	.	263-295-delinframe	.	no-SNV	GU280_gp05	0.968062692458029
CAMB-79C3B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998685601622996	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	9.56968324348464e-05
CAMB-79C3B	MN908947.3	28898	AGAATGGCTGGCAATGGCGGTG	-	0.0265909090909091	0.00187727272727273	8.8e-06;3.5e-09;2e-10;7.5e-11;8.3e-10;2.7e-09;1.3e-27;4.9e-28;8.7e-27;1.9e-09;7.5e-10;4.8e-09;3.1e-10;2.1e-09;4.8e-09;3.9e-09;2e-09;1.6e-09;1.5e-09;3.9e-09;1.5e-09;1.3e-09	0.1;0.061;0.056;0.051;0.091;0.043;0.00092;0.00083;0.00062;0.077;0.059;0.06;0.065;0.06;0.058;0.07;NA;NA;NA;NA;NA;NA	0.0112495530434304	TAG	N	.	625-646-delfrshift	.	no-SNV	GU280_gp10	0.986390220916373
CAMB-79C3B	MN908947.3	3037	C	T	1	1	0	0	0.997210867997115	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.80884828083674e-05
CAMB-79C3B	MN908947.3	522	TT	-	0.027	0.0325	0.00046;0.0029	4.3e-05;0.00073	0.0290388029419224	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.965292475491787
CAMB-79C3B	MN908947.3	5824	T	C	0.0054	0.013	0.00028	1.2e-07	0.00891307315741228	TTA	ORF1ab:nsp3	L1035L	T3105C	CTT>CTC	Synonymous	ORF1ab:nsp3	0.98728375558286
CAMB-79C3B	MN908947.3	6343	T	-	9e-04	0.008	0.0082	1.6e-05	0.00403494886478266	ATG	ORF1ab:nsp3	.	3624-3624-delfrshift	.	no-SNV	ORF1ab:nsp3	0.995840898862455
CAMB-79C59	MN908947.3	14408	C	T	1	1	0	0	0.999538777298619	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000161427945483477
CAMB-79C59	MN908947.3	17274	C	T	0.024	0.02	4.1e-12	8.5e-11	0.0219891335121945	TCA	ORF1ab:helicase	F346F	C1038T	TTC>TTT	Synonymous	ORF1ab:helicase	0.97799738449301
CAMB-79C59	MN908947.3	23403	A	G	1	1	0	0	0.999888506403913	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000111493596086575
CAMB-79C59	MN908947.3	241	C	T	1	1	0	0	0.999962451186542	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-79C59	MN908947.3	25528	C	T	1	1	0	0	0.999882708266135	GCT	ORF3a	L46F	C136T	CTT>TTT	Missense	GU280_gp03	2.9322933466264e-05
CAMB-79C59	MN908947.3	28834	A	C	0.0085	0.019	0.00016	1.4e-08	0.0133971291866029	CAT	N	S187S	A561C	TCA>TCC	Synonymous	GU280_gp10	0.986602870813397
CAMB-79C59	MN908947.3	28868	C	T	0.0073	0.012	0.00038	8.1e-06	0.0092485549132948	TCC	N	P199S	C595T	CCA>TCA	Missense	GU280_gp10	0.990751445086705
CAMB-79C59	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.9997187456054	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79C59	MN908947.3	29836	C	T	0.015	0.0032	2.4e-07	0.0056	0.0102766798418972	CCC	NA	NA	NA	NA	NA	NA	0.989723320158103
CAMB-79C59	MN908947.3	3037	C	T	1	1	0	0	0.999471319058948	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79C59	MN908947.3	5183	C	T	0.057	0.087	3.1e-09	3.6e-13	0.0725806451612903	TCC	ORF1ab:nsp3	P822S	C2464T	CCT>TCT	Missense	ORF1ab:nsp3	0.92741935483871
CAMB-79C59	MN908947.3	6573	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	S1285F	C3854T	TCT>TTT	Missense	ORF1ab:nsp3	0
CAMB-79C68	MN908947.3	14805	C	T	1	1	0	0	1	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-79C68	MN908947.3	28144	T	C	1	1	0	0	0.999833272199807	TTA	ORF8	L84S	T251C	TTA>TCA	Missense	GU280_gp09	0.000166727800193404
CAMB-79C68	MN908947.3	28657	C	T	1	1	0	0	0.999758337361044	ACG	N	D128D	C384T	GAC>GAT	Synonymous	GU280_gp10	0
CAMB-79C68	MN908947.3	28863	C	T	1	1	0	0	1	TCA	N	S197L	C590T	TCA>TTA	Missense	GU280_gp10	0
CAMB-79C68	MN908947.3	4340	A	G	1	1	0	0	1	TAT	ORF1ab:nsp3	I541V	A1621G	ATT>GTT	Missense	ORF1ab:nsp3	0
CAMB-79C68	MN908947.3	8782	C	T	1	1	2e-111	1.8e-296	1	GCC	ORF1ab:nsp4	S76S	C228T	AGC>AGT	Synonymous	ORF1ab:nsp4	0
CAMB-79C68	MN908947.3	9477	T	A	1	1	3.1e-176	2.6e-300	1	TTT	ORF1ab:nsp4	F308Y	T923A	TTT>TAT	Missense	ORF1ab:nsp4	0
CAMB-79C77	MN908947.3	11074	C	INS	0.025	0.02	2.1e-05	0.00085	0.0225239029173817	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.976842771921222
CAMB-79C77	MN908947.3	11075	T	-	0.033	0.037	2.2e-08	3.7e-09	0.0351733278253985	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959809287755172
CAMB-79C77	MN908947.3	14408	C	T	1	1	0	0	0.99752348211449	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000448054222707388
CAMB-79C77	MN908947.3	15750	T	C	0.0098	0.0096	4.8e-06	5.9e-06	0.00972259483822504	ATG	ORF1ab:RNA-dependent-RNA-polymerase	Y761Y	T2283C	TAT>TAC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.990245211139132
CAMB-79C77	MN908947.3	18267	C	T	0.056	0.053	2.1e-25	4e-24	0.0540784978035545	GCG	ORF1ab:3'-to-5'-exonuclease	R76R	C228T	CGC>CGT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.945821011226277
CAMB-79C77	MN908947.3	18627	G	A	1	1	0	0	0.998931509202981	AGT	ORF1ab:3'-to-5'-exonuclease	K196K	G588A	AAG>AAA	Synonymous	ORF1ab:3'-to-5'-exonuclease	5.36930048753248e-05
CAMB-79C77	MN908947.3	20268	A	G	1	1	0	0	0.998461538461539	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-79C77	MN908947.3	23403	A	G	1	1	0	0	0.999449645670752	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.94700520672298e-05
CAMB-79C77	MN908947.3	241	C	T	1	1	0	0	0.998414382768	TCG	NA	NA	NA	NA	NA	NA	0.000121970556307707
CAMB-79C77	MN908947.3	29300	G	C	0.013	0.013	2.8e-07	3.1e-07	0.0129056928445103	AGA	N	D343H	G1027C	GAT>CAT	Missense	GU280_gp10	0.986482481716935
CAMB-79C77	MN908947.3	3037	C	T	1	1	0	0	0.999083708334182	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000101810185090917
CAMB-79CA4	MN908947.3	10702	C	T	0.37	0.39	3.9e-190	8.2e-201	0.374764775300609	ACA	ORF1ab:3C-like-proteinase	D216D	C648T	GAC>GAT	Synonymous	ORF1ab:3C-like-proteinase	0.625235224699391
CAMB-79CA4	MN908947.3	10755	C	T	0.017	0.017	1e-08	2.2e-08	0.0168989355865247	GCT	ORF1ab:3C-like-proteinase	A234V	C701T	GCT>GTT	Missense	ORF1ab:3C-like-proteinase	0.983101064413475
CAMB-79CA4	MN908947.3	11074	C	INS	0.11	0.094	3.6e-45	4.9e-34	0.104768862911796	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.883475026567481
CAMB-79CA4	MN908947.3	11082	T	-	0.038	0.021	3.4e-06	0.00039	0.0294949934697431	TTG	ORF1ab:nsp6	.	110-110-delfrshift	.	no-SNV	ORF1ab:nsp6	0.970468727325497
CAMB-79CA4	MN908947.3	11083	G	-	0.12	0.26	5.5e-52	2e-121	0.188078738455256	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.20101365552526e-05
CAMB-79CA4	MN908947.3	11083	G	T	0.88	0.74	0	3.7e-277	0.811801160179191	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.20101365552526e-05
CAMB-79CA4	MN908947.3	12758	G	T	0.0056	0.0075	0.00015	2.1e-05	0.00652679443623192	TGA	ORF1ab:nsp9	D25Y	G73T	GAT>TAT	Missense	ORF1ab:nsp9	0.993395402716184
CAMB-79CA4	MN908947.3	14805	C	T	0.99	1	0	0	0.995435192906992	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00444776075728979
CAMB-79CA4	MN908947.3	15405	A	G	1	1	0	0	0.999784417712241	TAG	ORF1ab:RNA-dependent-RNA-polymerase	L646L	A1938G	TTA>TTG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000215582287759238
CAMB-79CA4	MN908947.3	16247	C	T	0.0099	0.016	0.00021	3.5e-06	0.0119361067228366	GCT	ORF1ab:helicase	A4V	C11T	GCT>GTT	Missense	ORF1ab:helicase	0.988063893277163
CAMB-79CA4	MN908947.3	16375	C	T	0.026	0.025	2.9e-10	1.8e-09	0.0257365391127667	TCC	ORF1ab:helicase	P47S	C139T	CCG>TCG	Missense	ORF1ab:helicase	0.974263460887233
CAMB-79CA4	MN908947.3	16466	C	T	0.019	0.019	2.2e-06	4.3e-06	0.0189649630343941	CCA	ORF1ab:helicase	P77L	C230T	CCA>CTA	Missense	ORF1ab:helicase	0.981035036965606
CAMB-79CA4	MN908947.3	16948	CC	TT	0.012	0.0175	2e-07;2.7e-07	4.7e-11;6.4e-08	0.0142397495543284	ACC	ORF1ab:helicase	.	712-713-mnv	.	no-SNV	ORF1ab:helicase	0.984385924027033
CAMB-79CA4	MN908947.3	17252	G	T	0.028	0.018	4e-14	6.3e-10	0.0233118971061093	CGT	ORF1ab:helicase	R339L	G1016T	CGT>CTT	Missense	ORF1ab:helicase	0.976475316814829
CAMB-79CA4	MN908947.3	17252	GT	TC	0.014	0.0132	4e-14;NA	6.3e-10;1.1e-05	0.0148060486522025	CGT	ORF1ab:helicase	.	1016-1017-mnv	.	no-SNV	ORF1ab:helicase	0.976475316814829
CAMB-79CA4	MN908947.3	17412	T	-	0.0036	0.01	0.0046	5.3e-06	0.00642692035968805	GTG	ORF1ab:helicase	.	1176-1176-delfrshift	.	no-SNV	ORF1ab:helicase	0.993422180763137
CAMB-79CA4	MN908947.3	21665	G	-	0.019	0.0053	2e-08	0.0015	0.0117276887871854	TGG	S	.	103-103-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.987700228832952
CAMB-79CA4	MN908947.3	21998	CA	-	0.005	0.00775	0.00025;0.00029	1.4e-05;1.8e-05	0.00607648364443474	CCA	S	.	436-437-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.993822647854375
CAMB-79CA4	MN908947.3	22195	T	C	0.013	0.013	5.9e-08	6.1e-08	0.0129828804174887	ATT	S	N211N	T633C	AAT>AAC	Synonymous	GU280_gp02, spike glycoprotein	0.987017119582511
CAMB-79CA4	MN908947.3	22332	G	T	0.011	0.05	0.00045	1.2e-10	0.0291079812206573	GGT	S	G257V	G770T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.970892018779343
CAMB-79CA4	MN908947.3	22801	G	T	0.66	0.7	0	0	0.682334086490463	GGC	S	G413G	G1239T	GGG>GGT	Synonymous	GU280_gp02, spike glycoprotein	0.31724554673953
CAMB-79CA4	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-79CA4	MN908947.3	2558	C	T	1	1	0	0	0.999492256917999	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000507743082000508
CAMB-79CA4	MN908947.3	26144	G	T	1	1	0	6.4e-227	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-79CA4	MN908947.3	27331	C	T	0.99	1	0	0	0.996079658216587	ACT	ORF6	L44L	C130T	CTA>TTA	Synonymous	GU280_gp06	0.00391056536998837
CAMB-79CA4	MN908947.3	28242	G	T	0.024	0.043	6.8e-12	5.3e-20	0.0327540106951872	TGT	ORF8	V117F	G349T	GTT>TTT	Missense	GU280_gp09	0.966833778966132
CAMB-79CA4	MN908947.3	2964	G	-	0.017	0.017	8.9e-09	1.3e-08	0.0171536936470994	TGG	ORF1ab:nsp3	.	245-245-delfrshift	.	no-SNV	ORF1ab:nsp3	0.982760106887337
CAMB-79CA4	MN908947.3	2964	GG	-	0.017	0.0085	8.9e-09;1.5e-09	1.3e-08;NA	0.0134563961010955	TGG	ORF1ab:nsp3	.	245-246-delfrshift	.	no-SNV	ORF1ab:nsp3	0.982760106887337
CAMB-79CA4	MN908947.3	398	C	T	0.049	0.026	4e-23	2.8e-13	0.0406475161167994	ACA	ORF1ab:leader-protein	H45Y	C133T	CAT>TAT	Missense	ORF1ab:leader-protein	0.959328782707622
CAMB-79CA4	MN908947.3	583	C	T	1	1	0	0	0.99986371194156	TCC	ORF1ab:leader-protein	V106V	C318T	GTC>GTT	Synonymous	ORF1ab:leader-protein	0.000109030446752256
CAMB-79CA4	MN908947.3	700	A	G	1	1	0	0	0.999875463419775	TAG	ORF1ab:leader-protein	L145L	A435G	TTA>TTG	Synonymous	ORF1ab:leader-protein	8.62176324638125e-05
CAMB-79CA4	MN908947.3	7279	C	T	1	0.98	1.1e-212	1.3e-141	0.992673992673993	TCT	ORF1ab:nsp3	F1520F	C4560T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79CA4	MN908947.3	9464	T	-	0.0093	0.019	7.9e-06	8.5e-10	0.0147584973166369	GTT	ORF1ab:nsp4	.	910-910-delfrshift	.	no-SNV	ORF1ab:nsp4	0.985241502683363
CAMB-79CB3	MN908947.3	11074	C	INS	0.025	0.021	1.7e-05	0.00023	0.022647335656137	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.976915074555392
CAMB-79CB3	MN908947.3	11075	T	-	0.036	0.043	6.1e-09	3.6e-10	0.0399374903642658	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954932795133779
CAMB-79CB3	MN908947.3	1128	T	C	0.013	0.013	1.4e-07	2e-07	0.0133602450744342	GTT	ORF1ab:nsp2	V108A	T323C	GTT>GCT	Missense	ORF1ab:nsp2	0.986363124084301
CAMB-79CB3	MN908947.3	14408	C	T	1	1	0	0	0.99902744973503	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000482967138386625
CAMB-79CB3	MN908947.3	17010	C	T	1	1	0	0	0.999668925940572	TCT	ORF1ab:helicase	I258I	C774T	ATC>ATT	Synonymous	ORF1ab:helicase	3.67860066030882e-05
CAMB-79CB3	MN908947.3	23403	A	G	1	1	0	0	0.999841123934679	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.10673067102441e-05
CAMB-79CB3	MN908947.3	241	C	T	1	1	0	0	0.999306191136961	TCG	NA	NA	NA	NA	NA	NA	0.000132857016326651
CAMB-79CB3	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999621492635563	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	5.50842789467886e-05
CAMB-79CB3	MN908947.3	29281	C	T	1	1	0	0	0.999560447137304	CCA	N	A336A	C1008T	GCC>GCT	Synonymous	GU280_gp10	0.000301653925379438
CAMB-79CB3	MN908947.3	3037	C	T	1	1	0	0	0.998979123066714	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.0002211900022119
CAMB-79CC2	MN908947.3	11074	C	INS	0.051	0.3	6.2e-12	1.4e-113	0.174353800326703	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.825454021331796
CAMB-79CC2	MN908947.3	11083	G	-	0.22	0.025	6.2e-100	1.2e-10	0.138109544719205	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-79CC2	MN908947.3	11083	G	T	0.78	0.98	9.99999999999997e-311	0	0.861798012479778	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-79CC2	MN908947.3	13914	T	G	0.019	0.0039	2e-09	0.00039	0.00984936268829664	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.990150637311703
CAMB-79CC2	MN908947.3	14805	C	T	1	1	0	0	1	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-79CC2	MN908947.3	1547	A	T	0.21	0.19	2e-44	5.7e-39	0.197898423817863	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.70753064798599
CAMB-79CC2	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-79CC2	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-79CD1	MN908947.3	11075	T	-	0.006	0.082	0.007	5.4e-20	0.0478891094393755	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952010808827209
CAMB-79CD1	MN908947.3	14408	C	T	1	1	0	0	0.99925970100146	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000431841082481647
CAMB-79CD1	MN908947.3	186	C	T	0.036	0.066	3.3e-17	4.2e-30	0.054742000576535	GCA	NA	NA	NA	NA	NA	NA	0.94522917267224
CAMB-79CD1	MN908947.3	2306	CTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGC	-	0.0528461538461538	0.000907692307692308	1.9e-17;4.5e-18;7.2e-17;2.6e-16;4.6e-17;6.5e-17;2.1e-17;2e-17;7.7e-17;2.2e-17;1e-17;9.1e-18;1.2e-17;4.9e-18;9.9e-18;1.9e-17;3.2e-17;4.1e-18;9.8e-19;2.8e-17;9.7e-17;1.5e-17;5.3e-17;2.7e-17;3.2e-17;2e-17;4e-17;3e-17;1.1e-17;2.1e-17;4.5e-17;1.1e-17;5.9e-19;7e-18;6.9e-18;1.6e-18;5.1e-20;1.2e-18;8.3e-18;5.8e-18;3.6e-21;9.1e-18;9.7e-19;7.9e-19;7.6e-18;4.7e-18;1.4e-18;1.3e-17;8.8e-18;1e-18;8.3e-18;1.4e-18;4.5e-18;2.4e-18;1.7e-20;2.7e-18;1.2e-19;1.8e-18;6.7e-18;2.2e-18;4.3e-18;1.4e-18;4.2e-21;3.4e-20;5e-19	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;6.5e-22;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0213160333642261	GCT	ORF1ab:nsp2	.	1501-1565-delfrshift	.	no-SNV	ORF1ab:nsp2	0.979232505643341
CAMB-79CD1	MN908947.3	23148	A	G	0.015	0.0026	8.8e-09	0.0036	0.00852647160208447	AAG	S	K529R	A1586G	AAG>AGG	Missense	GU280_gp02, spike glycoprotein	0.991463389906118
CAMB-79CD1	MN908947.3	23403	A	G	1	1	0	0	0.999887059016797	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.16041726559612e-05
CAMB-79CD1	MN908947.3	241	C	T	1	1	0	0	0.999854142357059	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-79CD1	MN908947.3	28086	G	T	0.97	0.98	0	0	0.977277338202475	GGC	ORF8	A65S	G193T	GCT>TCT	Missense	GU280_gp09	0.00223168999797119
CAMB-79CD1	MN908947.3	28086	GCTGGT	-	0.0278333333333333	0.014	1.9e-12;1.4e-12;2.6e-12;9e-13;6.7e-12;8.3e-12	2.8e-07;2.9e-07;3.4e-07;1.6e-07;1.1e-06;1.3e-06	0.0206713057715923	GGC	ORF8	.	193-198-delinframe	.	no-SNV	GU280_gp09	0.00223168999797119
CAMB-79CD1	MN908947.3	28095	A	G	0.027	0.014	5e-12	2.7e-07	0.0200532023736444	TAA	ORF8	K68E	A202G	AAA>GAA	Missense	GU280_gp09	0.979946797626356
CAMB-79CD1	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999780509218613	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79CD1	MN908947.3	28928	C	T	0.0025	0.0093	0.0055	6.3e-06	0.00584608843537415	TCT	N	L219F	C655T	CTT>TTT	Missense	GU280_gp10	0.994153911564626
CAMB-79CD1	MN908947.3	29051	C	INS	0.033	0.019	1.8e-08	5e-04	0.0249956301345919	GCA	N	.	777-778-insfrshift	.	no-SNV	GU280_gp10	0.974771310376974
CAMB-79CD1	MN908947.3	29242	A	T	0.06	0.059	3.6e-27	3.4e-27	0.0595830446557914	AAG	N	E323D	A969T	GAA>GAT	Missense	GU280_gp10	0.92278138187315
CAMB-79CD1	MN908947.3	29413	A	G	0.011	0.018	0.0011	3e-07	0.0167785234899329	AAG	N	Q380Q	A1140G	CAA>CAG	Synonymous	GU280_gp10	0.983221476510067
CAMB-79CD1	MN908947.3	3037	C	T	1	1	0	0	0.999484978540773	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000171673819742489
CAMB-79CD1	MN908947.3	313	C	T	1	1	0	0	0.999761670688474	TCA	ORF1ab:leader-protein	L16L	C48T	CTC>CTT	Synonymous	ORF1ab:leader-protein	0.000208538147585426
CAMB-79CE0	MN908947.3	10147	G	C	0.0088	0.0037	6.6e-06	0.00083	0.00660078999514455	GGC	ORF1ab:3C-like-proteinase	W31C	G93C	TGG>TGC	Missense	ORF1ab:3C-like-proteinase	0.993294227261394
CAMB-79CE0	MN908947.3	11075	T	-	0.055	0.079	3.4e-13	6.2e-19	0.066240086517664	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.929684370744212
CAMB-79CE0	MN908947.3	11176	T	-	0.0037	0.0097	0.0053	3.7e-05	0.00658448711400687	GTT	ORF1ab:nsp6	.	204-204-delfrshift	.	no-SNV	ORF1ab:nsp6	0.989909308007675
CAMB-79CE0	MN908947.3	1136	A	-	0.0052	0.011	0.0025	5.6e-06	0.00820683979517191	GAA	ORF1ab:nsp2	.	331-331-delfrshift	.	no-SNV	ORF1ab:nsp2	0.991724579370885
CAMB-79CE0	MN908947.3	11527	G	A	0.008	0.0018	1.4e-05	0.0073	0.00620235172502907	TGG	ORF1ab:nsp6	L185L	G555A	TTG>TTA	Synonymous	ORF1ab:nsp6	0.993797648274971
CAMB-79CE0	MN908947.3	13394	A	G	0.005	0.01	0.00068	4.3e-06	0.00710258475507066	GAA	ORF1ab:nsp10	K124E	A370G	AAA>GAA	Missense	ORF1ab:nsp10	0.992824192721681
CAMB-79CE0	MN908947.3	1391	T	INS	0.0018	0.0048	0.00044	4.5e-05	0.0029673590504451	TTC	ORF1ab:nsp2	.	585-586-insfrshift	.	no-SNV	ORF1ab:nsp2	0.997032640949555
CAMB-79CE0	MN908947.3	14408	C	T	1	1	0	0	0.998278607393381	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00026896759478418
CAMB-79CE0	MN908947.3	16466	C	T	0.0083	0.021	0.00093	8.1e-07	0.0133047527533447	CCA	ORF1ab:helicase	P77L	C230T	CCA>CTA	Missense	ORF1ab:helicase	0.986695247246655
CAMB-79CE0	MN908947.3	17491	C	T	0.0034	0.015	0.0016	1.7e-08	0.00799900717541405	ACC	ORF1ab:helicase	P419S	C1255T	CCA>TCA	Missense	ORF1ab:helicase	0.991989710727018
CAMB-79CE0	MN908947.3	18374	C	T	0.015	0.0046	7.5e-09	0.00042	0.00967246068345749	TCT	ORF1ab:3'-to-5'-exonuclease	S112F	C335T	TCT>TTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.990280241220291
CAMB-79CE0	MN908947.3	21658	CA	-	0.00375	0.019	0.0048;0.0035	8.9e-08;3.1e-08	0.00973053892215569	TCA	S	.	96-97-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.990657563780093
CAMB-79CE0	MN908947.3	23403	A	G	1	1	0	0	0.999905012190102	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.74939049488649e-05
CAMB-79CE0	MN908947.3	23945	A	-	0.0058	0.011	0.00012	4.6e-07	0.0082010782899233	TAA	S	.	2383-2383-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.991571113979801
CAMB-79CE0	MN908947.3	23992	A	-	0.0064	0.0084	0.00031	4.2e-05	0.00732248520710059	CAA	S	.	2430-2430-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.992418639053254
CAMB-79CE0	MN908947.3	241	C	T	1	1	0	0	0.999789922756213	TCG	NA	NA	NA	NA	NA	NA	0.000113118515885072
CAMB-79CE0	MN908947.3	25429	G	T	0.99	1	0	0	0.996447042004793	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	6.30702602699407e-05
CAMB-79CE0	MN908947.3	25708	C	T	0.072	0.022	1.3e-31	2e-10	0.0558052845082776	TCT	ORF3a	L106F	C316T	CTC>TTC	Missense	GU280_gp03	0.944085078390527
CAMB-79CE0	MN908947.3	26378	AT	-	0.0101	0.011	1.9e-06;6.7e-06	8.1e-07;2.6e-06	0.010306373042393	AAT	E	.	134-135-delfrshift	.	no-SNV	GU280_gp04	0.988546140830405
CAMB-79CE0	MN908947.3	27925	C	T	0.0073	0.011	0.00011	6.6e-06	0.00836999678077047	ACA	ORF8	T11I	C32T	ACA>ATA	Missense	GU280_gp09	0.99163000321923
CAMB-79CE0	MN908947.3	28502	A	-	0.0016	0.0097	0.0086	3.6e-06	0.00513242761081378	CAA	N	.	229-229-delfrshift	.	no-SNV	GU280_gp10	0.994757787841361
CAMB-79CE0	MN908947.3	29582	TTTCCG	-	0.0216666666666667	0.0273333333333333	1.4e-10;2e-11;1.1e-10;2e-10;6.2e-11;2e-10	2e-12;1.5e-13;1.6e-12;2.1e-12;9e-13;2.1e-12	0.0236136906341205	TTT	ORF10	.	25-30-delinframe	.	no-SNV	GU280_gp11	0.973698336017177
CAMB-79CE0	MN908947.3	3037	C	T	1	1	0	0	0.998480718530765	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.46847490951338e-05
CAMB-79CE0	MN908947.3	4625	AC	-	0.014	0.0061	5.5e-08;6.8e-08	0.00016;2e-04	0.0105501493400135	AAC	ORF1ab:nsp3	.	1906-1907-delfrshift	.	no-SNV	ORF1ab:nsp3	0.989383264163691
CAMB-79CE0	MN908947.3	7927	AA	-	0.0145	0.006	2.2e-06;3.6e-08	0.0014;0.00012	0.0103354487760653	CAA	ORF1ab:nsp3	.	5208-5209-delfrshift	.	no-SNV	ORF1ab:nsp3	0.989832712655908
CAMB-79CE0	MN908947.3	879	T	C	0.0093	0.0035	2.9e-06	0.0012	0.00647018970189702	CTA	ORF1ab:nsp2	L25P	T74C	CTA>CCA	Missense	ORF1ab:nsp2	0.993157181571816
CAMB-79CFF	MN908947.3	11075	T	-	0.17	0.005	1e-43	0.0095	0.120348543525846	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.879609361845428
CAMB-79CFF	MN908947.3	14408	C	T	0.94	1	0	0	0.947330237957052	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000362739408009286
CAMB-79CFF	MN908947.3	23403	A	G	1	1	0	0	0.999912612238656	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.36938806720119e-05
CAMB-79CFF	MN908947.3	241	C	T	1	1	0	0	0.99952862305557	TCG	NA	NA	NA	NA	NA	NA	0.000261876080238831
CAMB-79CFF	MN908947.3	28600	TTTC	-	0.06375	0.02225	1.1e-27;9e-29;7.1e-27;3.7e-26	NA;NA;NA;3.2e-34	0.0338252891902673	ATT	N	.	327-330-delfrshift	.	no-SNV	GU280_gp10	0.965755627009646
CAMB-79CFF	MN908947.3	28603	CTA	-	0.02243	0.085	3.7e-26;NA;NA	3.2e-34;1.8e-35;4.9e-36	0.0373534208278326	TCT	N	.	330-332-delinframe	.	no-SNV	GU280_gp10	0.923168959917956
CAMB-79CFF	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999341238471673	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79CFF	MN908947.3	3037	C	T	1	1	1.4e-243	1e-236	0.99875	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79D0B	MN908947.3	11074	C	INS	0.027	0.021	1.1e-05	0.00055	0.0239200500288628	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.97522609197614
CAMB-79D0B	MN908947.3	11075	T	-	0.032	0.041	3.7e-08	3.6e-10	0.036136331608721	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959323978821493
CAMB-79D0B	MN908947.3	14184	C	T	0.0092	0.0085	9.2e-06	1.5e-05	0.00888700510012646	CCA	ORF1ab:RNA-dependent-RNA-polymerase	T239T	C717T	ACC>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.990821162050612
CAMB-79D0B	MN908947.3	14408	C	T	1	1	0	0	0.998176113783727	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000485254130934951
CAMB-79D0B	MN908947.3	1461	A	C	0.012	0.011	3.2e-06	4.9e-06	0.0114078299196267	AAG	ORF1ab:nsp2	K219T	A656C	AAG>ACG	Missense	ORF1ab:nsp2	0.988008815141302
CAMB-79D0B	MN908947.3	16206	G	T	1	1	0	0	0.999802470909352	AGG	ORF1ab:RNA-dependent-RNA-polymerase	E913D	G2739T	GAG>GAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	7.18287602355983e-05
CAMB-79D0B	MN908947.3	18814	C	T	0.059	0.058	3.1e-27	1.3e-26	0.0586040586040586	TCT	ORF1ab:3'-to-5'-exonuclease	L259L	C775T	CTG>TTG	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.941259441259441
CAMB-79D0B	MN908947.3	23403	A	G	1	1	0	0	0.999534628501573	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.25125893409089e-05
CAMB-79D0B	MN908947.3	241	C	T	1	1	0	0	0.999024737252742	TCG	NA	NA	NA	NA	NA	NA	0.000195052549451558
CAMB-79D0B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999049035624589	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	5.30898279889573e-05
CAMB-79D0B	MN908947.3	3037	C	T	1	1	0	0	0.999152063312606	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000158988128886376
CAMB-79D0B	MN908947.3	478	C	T	0.012	0.012	7.2e-07	5e-07	0.011589854464962	TCA	ORF1ab:leader-protein	I71I	C213T	ATC>ATT	Synonymous	ORF1ab:leader-protein	0.988204234415102
CAMB-79D0B	MN908947.3	936	C	T	0.011	0.012	1e-06	6e-07	0.0114291883888083	ACT	ORF1ab:nsp2	T44I	C131T	ACT>ATT	Missense	ORF1ab:nsp2	0.9885091155875
CAMB-79D1A	MN908947.3	12862	T	C	1	1	0	0	0.999782372143634	GTG	ORF1ab:nsp9	S59S	T177C	AGT>AGC	Synonymous	ORF1ab:nsp9	0.000108813928182807
CAMB-79D1A	MN908947.3	16349	C	T	1	1	0	1.2e-82	1	TCA	ORF1ab:helicase	S38L	C113T	TCA>TTA	Missense	ORF1ab:helicase	0
CAMB-79D1A	MN908947.3	21707	C	T	1	1	0	0	1	ACA	S	H49Y	C145T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-79D1A	MN908947.3	23403	A	G	1	1	0	0	0.999789501381397	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000184186291277463
CAMB-79D1A	MN908947.3	241	C	T	1	1	0	0	1	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-79D1A	MN908947.3	2940	C	T	1	1	0	0	1	CCA	ORF1ab:nsp3	P74L	C221T	CCA>CTA	Missense	ORF1ab:nsp3	0
CAMB-79D1A	MN908947.3	3037	C	T	1	1	6e-227	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79D1A	MN908947.3	3951	A	G	1	1	1.3e-231	0	1	GAT	ORF1ab:nsp3	D411G	A1232G	GAT>GGT	Missense	ORF1ab:nsp3	0
CAMB-79D29	MN908947.3	10171	A	-	0.015	0.0073	4.2e-08	8.6e-05	0.0114008905416646	CAA	ORF1ab:3C-like-proteinase	.	117-117-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.988452316876254
CAMB-79D29	MN908947.3	1059	C	T	1	1	0	0	0.999984255191851	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	1.57448081495127e-05
CAMB-79D29	MN908947.3	1149	G	T	0.0078	0.021	2.1e-05	6.5e-11	0.0138747495977144	GGC	ORF1ab:nsp2	G115V	G344T	GGC>GTC	Missense	ORF1ab:nsp2	0.986010311648222
CAMB-79D29	MN908947.3	13836	G	A	0.012	0.0071	4.1e-07	6.4e-05	0.00998691941947138	GGC	ORF1ab:RNA-dependent-RNA-polymerase	R123R	G369A	AGG>AGA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.989930029275585
CAMB-79D29	MN908947.3	14408	C	T	1	0.99	0	0	0.996328739608324	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00024549461585672
CAMB-79D29	MN908947.3	17094	T	C	0.0061	0.011	7.3e-05	7.3e-07	0.00808274389039653	CTG	ORF1ab:helicase	T286T	T858C	ACT>ACC	Synonymous	ORF1ab:helicase	0.991895312008544
CAMB-79D29	MN908947.3	18079	G	T	0.0067	0.013	3.8e-05	7.6e-08	0.00980597675447791	GGT	ORF1ab:3'-to-5'-exonuclease	V14L	G40T	GTA>TTA	Missense	ORF1ab:3'-to-5'-exonuclease	0.990194023245522
CAMB-79D29	MN908947.3	20115	C	T	0.028	0.06	1e-08	1e-16	0.0452793834296724	TCA	ORF1ab:endoRNAse	V165V	C495T	GTC>GTT	Synonymous	ORF1ab:endoRNAse	0.954720616570328
CAMB-79D29	MN908947.3	21843	C	T	0.02	0.0068	1.7e-10	3.5e-05	0.0136401874774667	TCC	S	S94F	C281T	TCC>TTC	Missense	GU280_gp02, spike glycoprotein	0.986359812522533
CAMB-79D29	MN908947.3	22104	G	T	0.027	0.048	1.1e-13	2e-22	0.0364610333506134	GGA	S	G181V	G542T	GGA>GTA	Missense	GU280_gp02, spike glycoprotein	0.963481366280744
CAMB-79D29	MN908947.3	23403	A	G	1	1	0	0	0.999840604026846	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000100671140939597
CAMB-79D29	MN908947.3	23426	G	C	1	1	0	0	0.999940062848385	TGT	S	V622L	G1864C	GTT>CTT	Missense	GU280_gp02, spike glycoprotein	8.56245023075803e-06
CAMB-79D29	MN908947.3	241	C	T	1	0.99	0	0	0.992515380696736	TCG	NA	NA	NA	NA	NA	NA	9.79662212469141e-05
CAMB-79D29	MN908947.3	24673	A	-	0.022	0.0077	2.8e-08	0.0041	0.0156726768377254	CAA	S	.	3111-3111-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.984327323162275
CAMB-79D29	MN908947.3	25498	CCGATACAAGCCTCACTCCCTTTCGGATGGCTTATTGTTGGCGTTGCACTTCTTGCTGTTTT	-	0.0144903225806452	0.00129611290322581	0.00095;4.2e-05;2.4e-05;3.1e-08;1.2e-08;2.1e-08;1.7e-07;7.3e-08;4.9e-08;1.5e-07;1.4e-07;2.4e-06;2.4e-06;9.6e-07;1.6e-06;1.6e-07;7.1e-08;1.9e-07;9.8e-08;5.3e-07;1.2e-07;5.4e-05;0.00025;0.00018;0.00011;7e-05;6e-05;6.7e-05;0.00015;6.5e-05;5.7e-05;3.4e-05;7.1e-10;8.3e-11;0.00015;0.00032;3.1e-05;1.6e-05;3.4e-05;0.00011;9.8e-05;3.6e-05;8.8e-05;2.1e-05;7.7e-05;3.4e-05;4.4e-05;3.5e-05;9e-05;9e-05;0.00017;0.00011;6.4e-05;0.00011;5e-05;0.00016;0.00016;0.00033;8.6e-08;7.2e-06;2.2e-06;5.5e-08	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.45;1.3e-08;1.4e-08;2.9e-09;9.3e-09;NA;NA;0.45;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.48;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.5;NA;NA;NA	0.00779439415803052	ACC	ORF3a	.	106-167-delfrshift	.	no-SNV	GU280_gp03	0.99225657701552
CAMB-79D29	MN908947.3	25563	G	T	1	1	0	0	0.999749307611498	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.00017906599178684
CAMB-79D29	MN908947.3	27900	T	-	0.0085	0.041	3.5e-05	8.3e-18	0.01998001998002	ATT	ORF8	.	7-7-delfrshift	.	no-SNV	GU280_gp09	0.97992007992008
CAMB-79D29	MN908947.3	3037	C	T	1	1	0	0	0.999756616975966	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79D29	MN908947.3	3421	AA	-	0.01	0.0031	4.3e-06;1.2e-06	0.00022;NA	0.00680894762691432	TAA	ORF1ab:nsp3	.	702-703-delfrshift	.	no-SNV	ORF1ab:nsp3	0.991416496967308
CAMB-79D29	MN908947.3	4918	C	T	0.2	0.16	8.4e-96	3.2e-73	0.184680464469239	TCA	ORF1ab:nsp3	I733I	C2199T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.815248559180081
CAMB-79D29	MN908947.3	516	TTA	-	0.253333333333333	0.283333333333333	1.2e-05;3.2e-05;4.8e-05	2.3e-06;8.8e-06;8.8e-06	0.263775510204082	GTT	ORF1ab:leader-protein	.	251-253-delinframe	.	no-SNV	ORF1ab:leader-protein	0.729673863114378
CAMB-79D29	MN908947.3	6406	C	T	0.032	0.023	3.5e-16	2.9e-12	0.0280595661047698	TCT	ORF1ab:nsp3	V1229V	C3687T	GTC>GTT	Synonymous	ORF1ab:nsp3	0.971925315594527
CAMB-79D29	MN908947.3	881	GCACGTGCTGGTAAAGCTTCATGCACTTT	-	0.0157931034482759	0.0118275862068966	1.4e-08;2.5e-08;4.3e-08;2.2e-08;2.5e-07;1.4e-08;2.4e-08;1.1e-08;3.1e-10;2.7e-08;2.4e-08;5.2e-09;3.2e-08;1.9e-09;1.4e-09;9.9e-09;4.3e-09;7.9e-10;6.5e-09;9.7e-09;6.2e-09;6.1e-09;1.1e-08;1.2e-08;1.1e-08;7.4e-09;2.2e-08;7e-09;4.6e-09	5.3e-07;9.9e-07;2.1e-06;9.5e-07;5.7e-06;7.4e-07;9.1e-07;4.9e-07;1.7e-08;1e-06;9.3e-07;2.5e-07;1.2e-06;1.1e-07;8.4e-08;2.8e-07;1.7e-07;8e-08;2.3e-07;2.9e-07;2.2e-07;2.5e-07;3e-07;3.2e-07;3.3e-07;2.3e-07;7.5e-07;2.3e-07;1.9e-07	0.0134083844408973	AGC	ORF1ab:nsp2	.	76-104-delfrshift	.	no-SNV	ORF1ab:nsp2	0.986464218455744
CAMB-79D29	MN908947.3	8998	A	G	0.017	0.011	4.1e-09	5.2e-07	0.0143438994156189	CAG	ORF1ab:nsp4	S148S	A444G	TCA>TCG	Synonymous	ORF1ab:nsp4	0.985636424453495
CAMB-79D29	MN908947.3	9328	A	G	0.0073	0.0088	2.7e-05	6e-06	0.0081480353335364	TAG	ORF1ab:nsp4	V258V	A774G	GTA>GTG	Synonymous	ORF1ab:nsp4	0.991851964666464
CAMB-79D38	MN908947.3	1547	A	T	0.051	0.074	3.7e-13	4.2e-15	0.0597826086956522	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.91304347826087
CAMB-79D38	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999438412579558	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	6.24063904143784e-05
CAMB-79D38	MN908947.3	17410	C	T	1	0.97	0	0	0.991378316697019	ACG	ORF1ab:helicase	R392C	C1174T	CGT>TGT	Missense	ORF1ab:helicase	4.61052583047097e-05
CAMB-79D38	MN908947.3	29242	A	G	0.024	0.017	7.9e-10	1.8e-06	0.0212053571428571	AAG	N	E323E	A969G	GAA>GAG	Synonymous	GU280_gp10	0.955915178571429
CAMB-79D38	MN908947.3	514	T	C	1	0.94	0	0	0.983950828068977	ATG	ORF1ab:leader-protein	H83H	T249C	CAT>CAC	Synonymous	ORF1ab:leader-protein	8.53679358033123e-05
CAMB-79D47	MN908947.3	10097	G	A	1	1	0	0	0.999777017987216	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000148654675189535
CAMB-79D47	MN908947.3	11075	T	-	0.034	0.04	1.2e-08	3.7e-10	0.0370577970493364	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957812913119349
CAMB-79D47	MN908947.3	11355	C	T	1	1	0	0	0.999836585731211	GCA	ORF1ab:nsp6	A128V	C383T	GCA>GTA	Missense	ORF1ab:nsp6	2.04267835986546e-05
CAMB-79D47	MN908947.3	13536	C	T	1	1	0	0	0.999713880241714	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	9.1558322651529e-05
CAMB-79D47	MN908947.3	14408	C	T	1	1	0	0	0.999084287906665	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000347631442840064
CAMB-79D47	MN908947.3	15432	T	C	0.0077	0.0075	3.5e-05	3.7e-05	0.00763855992420654	GTG	ORF1ab:RNA-dependent-RNA-polymerase	S655S	T1965C	AGT>AGC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.992341702194852
CAMB-79D47	MN908947.3	20623	G	T	0.021	0.023	1.4e-10	2.1e-11	0.021913021513072	AGA	ORF1ab:endoRNAse	D335Y	G1003T	GAT>TAT	Missense	ORF1ab:endoRNAse	0.977918578705848
CAMB-79D47	MN908947.3	21853	G	A	0.025	0.026	8.3e-12	1.4e-12	0.0253948933580459	AGT	S	K97K	G291A	AAG>AAA	Synonymous	GU280_gp02, spike glycoprotein	0.974577443359429
CAMB-79D47	MN908947.3	23403	A	G	1	1	0	0	0.999729083557404	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.41832885192385e-05
CAMB-79D47	MN908947.3	23731	C	T	1	1	0	0	0.999871009351822	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	8.59937654520047e-05
CAMB-79D47	MN908947.3	241	C	T	1	1	0	0	0.999033083240518	TCG	NA	NA	NA	NA	NA	NA	0.000220310147730194
CAMB-79D47	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999389785955689	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	5.25942093775475e-05
CAMB-79D47	MN908947.3	29212	G	A	0.0059	0.0077	0.00024	3.9e-05	0.00673135978381034	CGT	N	A313A	G939A	GCG>GCA	Synonymous	GU280_gp10	0.992912418621791
CAMB-79D47	MN908947.3	29825	G	A	0.056	0.059	6.1e-25	3.6e-26	0.0575224292615597	AGT	NA	NA	NA	NA	NA	NA	0.942339544513458
CAMB-79D47	MN908947.3	3037	C	T	1	1	0	0	0.999474837471252	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000162981474439072
CAMB-79D47	MN908947.3	4002	C	T	1	1	0	0	0.999883378524155	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-79D47	MN908947.3	990	C	T	1	1	0	0	0.999840841946105	ACG	ORF1ab:nsp2	T62M	C185T	ACG>ATG	Missense	ORF1ab:nsp2	6.9631648579017e-05
CAMB-79D65	MN908947.3	106	C	T	0.035	0.055	2e-16	3.1e-25	0.0435967734267286	GCA	NA	NA	NA	NA	NA	NA	0.956371531354495
CAMB-79D65	MN908947.3	11074	C	INS	0.12	0.13	1.8e-52	3e-59	0.127418256511013	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.872135210261334
CAMB-79D65	MN908947.3	11083	G	-	0.18	0.12	2e-78	6.2e-50	0.148079606819975	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-79D65	MN908947.3	11083	G	T	0.82	0.88	0	0	0.85170802742552	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-79D65	MN908947.3	1314	C	T	1	1	0	0	1	ACT	ORF1ab:nsp2	T170I	C509T	ACT>ATT	Missense	ORF1ab:nsp2	0
CAMB-79D65	MN908947.3	13860	C	T	0.25	0.21	7.5e-123	1e-99	0.233544464149987	ACA	ORF1ab:RNA-dependent-RNA-polymerase	D131D	C393T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.76643864538468
CAMB-79D65	MN908947.3	14805	C	T	1	1	0	0	0.99995917978583	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-79D65	MN908947.3	17247	T	C	1	1	0	0	0.997820870354757	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.00214021661586354
CAMB-79D65	MN908947.3	19638	T	-	0.014	0.011	1.5e-06	2.5e-05	0.0124493341053851	CTT	ORF1ab:endoRNAse	.	18-18-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.987550665894615
CAMB-79D65	MN908947.3	26144	G	T	1	1	0	4.94065645841247e-324	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-79D65	MN908947.3	26217	G	T	0.0034	0.035	0.0029	3.1e-10	0.0127388535031847	TGT	ORF3a	L275F	G825T	TTG>TTT	Missense	GU280_gp03	0.987261146496815
CAMB-79D65	MN908947.3	26456	C	T	0.011	0.013	6.1e-06	1.2e-06	0.0116739376312813	CCT	E	P71L	C212T	CCT>CTT	Missense	GU280_gp04	0.987598965907255
CAMB-79D65	MN908947.3	6863	AAG	-	0.036	0.0163333333333333	2.8e-07;7.1e-07;8.1e-07	0.00056;8e-04;0.00083	0.0256410256410256	AAA	ORF1ab:nsp3	.	4144-4146-delinframe	.	no-SNV	ORF1ab:nsp3	0.974736842105263
CAMB-79D74	MN908947.3	11074	C	INS	0.11	0.11	8.6e-53	2.2e-46	0.111544454500499	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.882325498941004
CAMB-79D74	MN908947.3	11083	G	-	0.15	0.16	5.4e-65	8e-71	0.155790872472073	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	8.30530293592459e-06
CAMB-79D74	MN908947.3	11083	G	T	0.85	0.84	0	0	0.844076242680952	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	8.30530293592459e-06
CAMB-79D74	MN908947.3	14805	C	T	1	1	0	0	0.998871884969254	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	2.77405335429285e-05
CAMB-79D74	MN908947.3	23707	C	T	1	1	0	0	0.999525511656597	CCA	S	P715P	C2145T	CCC>CCT	Synonymous	GU280_gp02, spike glycoprotein	0.000379590674722424
CAMB-79D74	MN908947.3	25455	G	T	1	1	0	0	0.999902767874506	AGG	ORF3a	K21N	G63T	AAG>AAT	Missense	GU280_gp03	1.08035694993626e-05
CAMB-79D74	MN908947.3	26144	G	T	1	1	0	0	0.999433106575964	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000377928949357521
CAMB-79D74	MN908947.3	6311	A	T	0.0079	0.0028	1.6e-05	0.0018	0.00561467343145942	CAC	ORF1ab:nsp3	T1198S	A3592T	ACA>TCA	Missense	ORF1ab:nsp3	0.994275542451166
CAMB-79D83	MN908947.3	10754	G	T	0.0079	0.0067	1.9e-05	4.9e-05	0.00744909112991377	GGC	ORF1ab:3C-like-proteinase	A234S	G700T	GCT>TCT	Missense	ORF1ab:3C-like-proteinase	0.992510424679163
CAMB-79D83	MN908947.3	11074	C	INS	0.026	0.036	1.1e-05	4.2e-09	0.0310135284054533	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.968682108710026
CAMB-79D83	MN908947.3	11075	T	-	0.046	0.055	5e-11	2.4e-13	0.050132740630981	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.945298512070136
CAMB-79D83	MN908947.3	11536	TA	-	0.00215	0.0102	0.0081;0.0084	7.4e-06;3.6e-06	0.00503947589450697	GTA	ORF1ab:nsp6	.	564-565-delfrshift	.	no-SNV	ORF1ab:nsp6	0.995414947271894
CAMB-79D83	MN908947.3	12114	C	T	0.007	0.0072	5.3e-05	4e-05	0.0070979879963927	TCC	ORF1ab:nsp8	S8F	C23T	TCC>TTC	Missense	ORF1ab:nsp8	0.992894237646547
CAMB-79D83	MN908947.3	12164	G	T	0.012	0.012	3.7e-05	3.2e-05	0.0118859710714787	GGC	ORF1ab:nsp8	A25S	G73T	GCT>TCT	Missense	ORF1ab:nsp8	0.987984833590788
CAMB-79D83	MN908947.3	14408	C	T	1	1	0	0	0.997103889855287	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000471890151374958
CAMB-79D83	MN908947.3	18508	C	T	0.0032	0.0099	0.0046	4.7e-06	0.00631321265219352	ACT	ORF1ab:3'-to-5'-exonuclease	L157F	C469T	CTT>TTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.993643840322962
CAMB-79D83	MN908947.3	20627	G	T	0.014	0.013	8.7e-07	2.7e-06	0.013527513838321	GGC	ORF1ab:endoRNAse	G336V	G1007T	GGC>GTC	Missense	ORF1ab:endoRNAse	0.986354083414735
CAMB-79D83	MN908947.3	21811	C	T	1	1	0	0	1	TCC	S	V83V	C249T	GTC>GTT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-79D83	MN908947.3	22878	AC	-	0.0016	0.0079	NA;0.0046	0.00038;5e-06	0.00403269754768392	AAC	S	.	1316-1317-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.998061093835742
CAMB-79D83	MN908947.3	22899	G	T	0.015	0.015	1.1e-05	9.1e-06	0.0150779453105034	GGT	S	G446V	G1337T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.984483954583622
CAMB-79D83	MN908947.3	23386	TGC	-	0.00256666666666667	0.00736666666666667	0.0034;0.0035;0.0033	2.1e-05;2.8e-05;2.5e-05	0.00472886184404085	TTG	S	.	1824-1826-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.994970876118417
CAMB-79D83	MN908947.3	23403	A	G	1	1	0	0	0.999930138326114	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.89031717199944e-05
CAMB-79D83	MN908947.3	23855	C	T	0.0064	0.013	3e-04	2.5e-07	0.00918216156430643	CCG	S	R765C	C2293T	CGT>TGT	Missense	GU280_gp02, spike glycoprotein	0.990817838435694
CAMB-79D83	MN908947.3	241	C	T	1	0.99	0	0	0.996387294787154	TCG	NA	NA	NA	NA	NA	NA	6.3941685183113e-05
CAMB-79D83	MN908947.3	25831	C	T	0.003	0.0084	0.009	4.5e-05	0.00521355524363345	TCT	ORF3a	L147F	C439T	CTT>TTT	Missense	GU280_gp03	0.994786444756367
CAMB-79D83	MN908947.3	26428	G	T	0.037	0.029	2.2e-17	2.5e-14	0.0334045445717615	TGT	E	V62F	G184T	GTT>TTT	Missense	GU280_gp04	0.966456732236495
CAMB-79D83	MN908947.3	26961	G	T	0.002	0.0075	0.0042	1.7e-05	0.00464563811534908	TGG	M	G147*	G439T	GGA>TGA	Nonsense	GU280_gp05	0.995248779200211
CAMB-79D83	MN908947.3	27889	C	T	0.0079	0.013	3.6e-05	4.3e-07	0.00975224037954665	ACG	NA	NA	NA	NA	NA	NA	0.990247759620453
CAMB-79D83	MN908947.3	28328	G	-	0.01	0.0071	3.8e-05	0.00048	0.00892373340558114	TGG	N	.	55-55-delfrshift	.	no-SNV	GU280_gp10	0.988722568409645
CAMB-79D83	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999531136780188	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79D83	MN908947.3	3037	C	T	1	1	0	0	0.999311075781664	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000158982511923688
CAMB-79D83	MN908947.3	558	G	T	0.02	0.013	6.4e-06	0.00016	0.0170776322528719	GGT	ORF1ab:leader-protein	G98V	G293T	GGT>GTT	Missense	ORF1ab:leader-protein	0.982922367747128
CAMB-79D83	MN908947.3	660	G	T	0.0056	0.0074	0.00016	2.2e-05	0.00626997289753651	GGT	ORF1ab:leader-protein	G132V	G395T	GGT>GTT	Missense	ORF1ab:leader-protein	0.993716543289781
CAMB-79D83	MN908947.3	8751	AC	-	0.0105	0.00445	7.1e-07;1.8e-06	0.00071;9e-04	0.00798251872993222	AAC	ORF1ab:nsp4	.	197-198-delfrshift	.	no-SNV	ORF1ab:nsp4	0.991584272246493
CAMB-79DA1	MN908947.3	11074	C	INS	0.032	0.038	1.7e-07	1.8e-09	0.035031436968001	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.964804645880411
CAMB-79DA1	MN908947.3	11075	T	-	0.045	0.022	4.5e-11	3.6e-06	0.0341115658417199	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.96470026708371
CAMB-79DA1	MN908947.3	12623	C	T	0.0097	0.0039	2.8e-06	0.00078	0.00694843229585391	ACC	ORF1ab:nsp8	P178S	C532T	CCT>TCT	Missense	ORF1ab:nsp8	0.993037211439072
CAMB-79DA1	MN908947.3	14408	C	T	1	1	0	0	0.998698681890689	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000251868021156914
CAMB-79DA1	MN908947.3	21127	A	G	0.46	0.49	2e-260	1.8e-281	0.476672179022554	TAT	ORF1ab:2'-O-ribose-methyltransferase	I157V	A469G	ATA>GTA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.522377819218184
CAMB-79DA1	MN908947.3	23403	A	G	1	1	0	0	0.999824300797035	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000175699202964525
CAMB-79DA1	MN908947.3	23415	C	T	0.058	0.047	1.1e-26	5.9e-22	0.0525275096253547	ACA	S	T618I	C1853T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0.946451680317657
CAMB-79DA1	MN908947.3	241	C	T	1	0.98	0	0	0.990566739850407	TCG	NA	NA	NA	NA	NA	NA	0.000111636214788077
CAMB-79DA1	MN908947.3	28009	T	C	0.013	0.024	2.2e-07	2e-11	0.017932228543161	ATT	ORF8	I39T	T116C	ATT>ACT	Missense	GU280_gp09	0.981449418748454
CAMB-79DA1	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998259478784458	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000512583935619458
CAMB-79DA1	MN908947.3	3037	C	T	0.99	1	0	0	0.994312364918667	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79DA1	MN908947.3	8683	C	T	1	1	0	0	1	TCA	ORF1ab:nsp4	I43I	C129T	ATC>ATT	Synonymous	ORF1ab:nsp4	0
CAMB-79DA1	MN908947.3	992	G	A	0.0091	0.005	3.6e-06	0.00017	0.00722049634748551	GGA	ORF1ab:nsp2	E63K	G187A	GAA>AAA	Missense	ORF1ab:nsp2	0.992758370492473
CAMB-79DB0	MN908947.3	11074	C	INS	0.13	0.082	3.4e-60	1.8e-26	0.110611407089647	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.88581378721834
CAMB-79DB0	MN908947.3	11083	G	-	0.13	0.13	2.3e-55	4.7e-56	0.129063127346862	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.04016060079676e-05
CAMB-79DB0	MN908947.3	11083	G	T	0.87	0.87	0	0	0.870739242138986	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.04016060079676e-05
CAMB-79DB0	MN908947.3	13011	C	T	0.0072	0.011	7.9e-05	1.4e-06	0.00896061664458629	ACA	ORF1ab:nsp9	T109I	C326T	ACA>ATA	Missense	ORF1ab:nsp9	0.991003251836686
CAMB-79DB0	MN908947.3	14805	C	T	1	1	0	0	0.999905571293673	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	4.72143531633617e-05
CAMB-79DB0	MN908947.3	22224	C	T	0.013	0.0081	4.4e-07	7.1e-05	0.0110164432626038	TCG	S	S221L	C662T	TCG>TTG	Missense	GU280_gp02, spike glycoprotein	0.988929288543984
CAMB-79DB0	MN908947.3	22643	TG	-	0.0125	0.00355	6.2e-07;0.00033	NA;0.0038	0.00904427245500104	CTG	S	.	1081-1082-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.990894264745855
CAMB-79DB0	MN908947.3	23559	TTGGTGCAGGTATATGCGCTAGTT	-	0.04225	0.0232916666666667	0.00014;0.00027;0.00017;0.00031;0.00016;0.00034;0.00032;0.00029;0.00019;0.00017;6.4e-05;1.1e-05;6.7e-05;2.8e-05;6e-05;2.8e-05;6.9e-05;0.00014;8.3e-05;1.6e-05;5.3e-08;1.7e-07;0.00012;0.00046	0.01;0.015;0.014;0.017;0.018;0.018;0.018;0.018;0.015;0.015;0.0015;0.00066;0.0015;0.0011;0.0016;0.00096;0.0017;0.0025;0.0018;0.0017;2e-04;0.00026;0.0019;0.051	0.0345037935109993	ATT	S	.	1997-2020-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.958245402472113
CAMB-79DB0	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-79DB0	MN908947.3	24949	A	-	0.004	0.011	0.001	1.4e-06	0.006812528889965	TAA	S	.	3387-3387-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.993044396997645
CAMB-79DB0	MN908947.3	25394	T	C	0.083	0.044	1e-37	9.2e-21	0.0672293761659917	ATG	ORF3a	M1T	T2C	ATG>ACG	Missense	GU280_gp03	0.93272512171816
CAMB-79DB0	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-79DB0	MN908947.3	25630	G	C	0.014	0.0077	2.7e-06	9.4e-05	0.0113651787572503	TGT	ORF3a	V80L	G238C	GTT>CTT	Missense	GU280_gp03	0.988453847058717
CAMB-79DB0	MN908947.3	26144	G	T	1	1	0	0	0.999254287844892	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-79DB0	MN908947.3	26378	AT	-	0.00255	0.015	0.00051;NA	8.2e-09;4.4e-08	0.00777934936350778	AAT	E	.	134-135-delfrshift	.	no-SNV	GU280_gp04	0.989611908081126
CAMB-79DB0	MN908947.3	27267	TA	-	0.21	0.24	4.6e-55;4.4e-62	1.8e-65;5.1e-73	0.22150429709554	TTA	ORF6	.	66-67-delfrshift	.	no-SNV	GU280_gp06	0.779383154550485
CAMB-79DB0	MN908947.3	27643	C	T	1	1	3.7e-154	9.8e-141	1	ACC	ORF7a	P84S	C250T	CCT>TCT	Missense	GU280_gp07	0
CAMB-79DB0	MN908947.3	28948	C	G	0.048	0.079	1.5e-21	5.6e-35	0.0640648952478283	ACA	N	D225E	C675G	GAC>GAG	Missense	GU280_gp10	0.935807358201329
CAMB-79DB0	MN908947.3	29726	TT	-	0.00475	0.0115	0.013;0.0034	4e-05;1.4e-05	0.00808547502165752	ATT	NA	NA	NA	NA	NA	NA	0.991611223604281
CAMB-79DB0	MN908947.3	3230	G	T	0.0057	0.009	0.00037	1.3e-05	0.00716028963875835	TGG	ORF1ab:nsp3	G171C	G511T	GGT>TGT	Missense	ORF1ab:nsp3	0.984852457693782
CAMB-79DB0	MN908947.3	3877	T	G	0.0022	0.01	0.0039	1.5e-06	0.00532558702493343	CTG	ORF1ab:nsp3	A386A	T1158G	GCT>GCG	Synonymous	ORF1ab:nsp3	0.994270959412572
CAMB-79DB0	MN908947.3	5425	G	T	0.01	0.0064	8e-06	0.00033	0.00870285951098218	AGA	ORF1ab:nsp3	K902N	G2706T	AAG>AAT	Missense	ORF1ab:nsp3	0.991297140489018
CAMB-79DB0	MN908947.3	6680	GCTAATT	-	0.00998571428571429	0.00394285714285714	2.8e-06;3.6e-06;7.3e-06;6e-04;3.1e-06;6.3e-05;3.1e-05	0.00014;2e-04;0.00026;0.00031;NA;NA;NA	0.00868580060422961	AGC	ORF1ab:nsp3	.	3961-3967-delfrshift	.	no-SNV	ORF1ab:nsp3	0.990087793826112
CAMB-79DB0	MN908947.3	7020	T	-	0.02	0.0068	7.1e-06	0.0056	0.0129716981132075	GTT	ORF1ab:nsp3	.	4301-4301-delfrshift	.	no-SNV	ORF1ab:nsp3	0.987028301886792
CAMB-79DB0	MN908947.3	8653	G	T	0.0083	0.011	9e-06	9e-07	0.0093661147349055	TGT	ORF1ab:nsp4	M33I	G99T	ATG>ATT	Missense	ORF1ab:nsp4	0.990466633216257
CAMB-79DCF	MN908947.3	1059	C	T	1	1	0	0	0.999937189875008	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	3.14050624960744e-05
CAMB-79DCF	MN908947.3	11074	C	INS	0.017	0.027	0.0026	1.2e-05	0.0260704692684468	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.97365866871318
CAMB-79DCF	MN908947.3	11075	T	-	0.039	0.06	8.3e-11	2.1e-14	0.0584694588526748	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.936169389177054
CAMB-79DCF	MN908947.3	11916	C	T	1	1	0	0	0.999727238012111	TCA	ORF1ab:nsp7	S25L	C74T	TCA>TTA	Missense	ORF1ab:nsp7	0.000218209590311494
CAMB-79DCF	MN908947.3	14408	C	T	0.99	1	0	0	0.999414809813189	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000247580463650686
CAMB-79DCF	MN908947.3	15977	ATA	-	0.00353333333333333	0.00973333333333333	0.037;0.025;0.0027	0.00066;0.00015;1.5e-06	0.0093741533459767	GAT	ORF1ab:RNA-dependent-RNA-polymerase	.	2510-2512-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.990749355378931
CAMB-79DCF	MN908947.3	17000	C	T	0.013	0.022	4.1e-07	2.3e-11	0.0211044112980006	ACA	ORF1ab:helicase	T255I	C764T	ACA>ATA	Missense	ORF1ab:helicase	0.97886385274516
CAMB-79DCF	MN908947.3	1731	A	C	0.0056	0.0035	3.4e-05	0.00062	0.00362435197504244	GAA	ORF1ab:nsp2	E309A	A926C	GAA>GCA	Missense	ORF1ab:nsp2	0.996329770151856
CAMB-79DCF	MN908947.3	18929	C	T	0.0028	0.0082	0.004	1.5e-05	0.00783913627440851	CCT	ORF1ab:3'-to-5'-exonuclease	P297L	C890T	CCT>CTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.992135034611013
CAMB-79DCF	MN908947.3	2228	TG	-	0.00355	0.00665	0.0038;0.0043	3.6e-05;4.3e-05	0.00636893799877225	CTG	ORF1ab:nsp2	.	1423-1424-delfrshift	.	no-SNV	ORF1ab:nsp2	0.992996767738956
CAMB-79DCF	MN908947.3	23403	A	G	1	1	0	0	0.995808469451421	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000111987457404771
CAMB-79DCF	MN908947.3	241	C	T	1	1	0	0	0.999341489619797	TCG	NA	NA	NA	NA	NA	NA	0.000173292205316605
CAMB-79DCF	MN908947.3	24304	T	C	0.0057	0.0085	0.00044	7.8e-06	0.00832675957577351	ATG	S	N914N	T2742C	AAT>AAC	Synonymous	GU280_gp02, spike glycoprotein	0.991585590323429
CAMB-79DCF	MN908947.3	24781	G	C	0.047	0.038	1.6e-20	4.4e-18	0.0387817143506549	AGA	S	K1073N	G3219C	AAG>AAC	Missense	GU280_gp02, spike glycoprotein	0.961189874137
CAMB-79DCF	MN908947.3	25563	G	T	1	1	0	0	0.999861315285829	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0
CAMB-79DCF	MN908947.3	25747	AACTTTGTAAGAATAATAATGA	-	0.00858636363636364	0.00191727272727273	0.00024;0.00018;0.00023;0.00051;0.00017;0.00021;3e-04;0.00021;0.00044;0.00031;0.00038;0.00082;0.00085;0.00088;0.00034;2e-04;0.00015;0.00012;4.9e-05;4.3e-05;0.00011;9.8e-05	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;8.9e-07;1.3e-06;1.1e-06;5.9e-07	0.000521648408972353	AAA	ORF3a	.	355-376-delfrshift	.	no-SNV	GU280_gp03	0.999489882673015
CAMB-79DCF	MN908947.3	27382	GATTA	-	0.00206	0.00808	0.0053;0.01;0.01;0.013;0.022	1.1e-05;6.8e-05;1.4e-05;7.5e-05;2.9e-05	0.00770346202646366	TGA	ORF6	.	181-185-delfrshift	.	no-SNV	GU280_gp06	0.99218282397751
CAMB-79DCF	MN908947.3	27987	G	A	0.059	0.068	4.3e-12	3.4e-28	0.0673748103186646	TGT	ORF8	V32I	G94A	GTA>ATA	Missense	GU280_gp09	0.932625189681335
CAMB-79DCF	MN908947.3	28969	C	T	0.015	0.013	3e-06	8.1e-08	0.0135791456041233	GCA	N	S232S	C696T	AGC>AGT	Synonymous	GU280_gp10	0.986420854395877
CAMB-79DCF	MN908947.3	3037	C	T	1	1	1.1e-263	0	0.999877959482548	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79DCF	MN908947.3	376	G	T	0.0083	0.013	9.1e-06	4.4e-08	0.0130890052356021	AGG	ORF1ab:leader-protein	E37D	G111T	GAG>GAT	Missense	ORF1ab:leader-protein	0.986717734284409
CAMB-79DCF	MN908947.3	829	C	T	0.0044	0.007	0.0013	4.2e-05	0.00689094932631166	ACA	ORF1ab:nsp2	N8N	C24T	AAC>AAT	Synonymous	ORF1ab:nsp2	0.993081038684557
CAMB-79DDE	MN908947.3	10507	C	T	0.039	0.014	2.7e-18	4.7e-08	0.0260913834796996	ACA	ORF1ab:3C-like-proteinase	N151N	C453T	AAC>AAT	Synonymous	ORF1ab:3C-like-proteinase	0.9739086165203
CAMB-79DDE	MN908947.3	11075	T	-	0.067	0.038	3.5e-16	9.6e-10	0.0531691781885972	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.946688415928745
CAMB-79DDE	MN908947.3	12194	C	T	0.011	0.0042	3.9e-06	0.0031	0.00771512887326155	TCT	ORF1ab:nsp8	L35F	C103T	CTT>TTT	Missense	ORF1ab:nsp8	0.992269174018146
CAMB-79DDE	MN908947.3	12239	G	T	0.011	0.018	1.9e-05	5.3e-08	0.0145530145530146	TGA	ORF1ab:nsp8	D50Y	G148T	GAC>TAC	Missense	ORF1ab:nsp8	0.985446985446986
CAMB-79DDE	MN908947.3	12239	GAC	TGA	0.00366666666666667	0.0173333333333333	1.9e-05;NA;NA	5.3e-08;5.3e-08;1.5e-07	0.00857588357588358	TGA	ORF1ab:nsp8	.	148-150-mnv	.	no-SNV	ORF1ab:nsp8	0.985446985446986
CAMB-79DDE	MN908947.3	13143	ATTGTGTT	-	0.01350875	0.02225	NA;0.5;0.5;6.4e-07;3.1e-08;8.5e-08;2.9e-10;5.8e-11	8.5e-06;8e-06;7.4e-06;3.3e-07;2.1e-08;3.9e-08;1.4e-10;2.6e-11	0.0220082530949106	AAT	ORF1ab:nsp10	.	119-126-delfrshift	.	no-SNV	ORF1ab:nsp10	0.989109105896256
CAMB-79DDE	MN908947.3	13729	GCTA	-	0.02025	0.01125	6.9e-09;2e-08;2.5e-08;2.6e-09	1.7e-05;2.9e-05;2.5e-05;1.3e-05	0.0162207094875424	TGC	ORF1ab:RNA-dependent-RNA-polymerase	.	262-265-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.978515625
CAMB-79DDE	MN908947.3	14408	C	T	1	1	0	0	0.999625555211239	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000206590228282202
CAMB-79DDE	MN908947.3	18739	GATTACGTCTA	-	0.0288181818181818	0.00428372727272727	4.3e-09;3.2e-05;3.8e-06;3.6e-05;4.6e-05;1e-05;2.2e-05;9e-06;1.2e-05;3e-06;1.7e-06	0.47;0.0019;0.00062;0.002;NA;NA;NA;NA;NA;NA;NA	0.0152407581417734	TGA	ORF1ab:3'-to-5'-exonuclease	.	700-710-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.984747541582058
CAMB-79DDE	MN908947.3	2309	G	A	1	1	0	0	1	TGT	ORF1ab:nsp2	V502I	G1504A	GTA>ATA	Missense	ORF1ab:nsp2	0
CAMB-79DDE	MN908947.3	23403	A	G	1	1	0	0	0.999962875307439	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.71246925611397e-05
CAMB-79DDE	MN908947.3	241	C	T	1	1	0	0	0.999888150683399	TCG	NA	NA	NA	NA	NA	NA	6.71095899604053e-05
CAMB-79DDE	MN908947.3	24912	C	T	0.012	0.015	5.6e-07	1.8e-08	0.0134001554418031	ACA	S	T1117I	C3350T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0.986573044247313
CAMB-79DDE	MN908947.3	24950	ATAGGAATT	-	0.00182244444444444	0.0192222222222222	0.44;0.46;0.44;5.6e-05;0.5;0.45;0.45;0.45;0.46	2.8e-10;4e-10;5.7e-10;9.8e-06;1.4e-06;7.6e-09;1.3e-08;2.5e-08;1e-08	0.00882499562118538	AAT	S	.	3388-3396-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.991004682494044
CAMB-79DDE	MN908947.3	25647	GTTGTTTGTAACAGTTTACTCACACC	-	0.0101923076923077	0.00124615384615385	0.00023;0.00089;0.00053;0.00043;0.00014;0.00021;4.3e-05;4.5e-05;2.5e-05;2.8e-05;2.3e-05;2.3e-05;2.2e-05;1.8e-05;2.5e-05;6.1e-05;3.1e-05;2.9e-05;2.3e-05;2.7e-05;1.3e-05;1.3e-05;2.3e-05;2e-05;3.9e-05;3.2e-05	7.4e-06;6e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0064661231374754	TGT	ORF3a	.	255-280-delfrshift	.	no-SNV	GU280_gp03	0.987908269631689
CAMB-79DDE	MN908947.3	25726	G	T	0.028	0.008	2.1e-13	2e-05	0.0203197370386971	AGT	ORF3a	V112F	G334T	GTC>TTC	Missense	GU280_gp03	0.979680262961303
CAMB-79DDE	MN908947.3	28881	GGG	AAC	0.986666666666667	1	0;0;0	0;0;0	0.993366979091565	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000158679784195493
CAMB-79DDE	MN908947.3	29728	TTC	-	0.293333333333333	0.133333333333333	6.9e-84;1.3e-78;8.3e-77	5.1e-39;2.6e-37;6.1e-37	0.201906412478336	TTT	NA	NA	NA	NA	NA	NA	0.783636363636364
CAMB-79DDE	MN908947.3	3037	C	T	1	1	0	0	0.999547852298417	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79DDE	MN908947.3	3259	G	T	0.021	0.015	6e-08	3e-06	0.0178858586853073	AGA	ORF1ab:nsp3	Q180H	G540T	CAG>CAT	Missense	ORF1ab:nsp3	0.9820156870467
CAMB-79DDE	MN908947.3	9800	GC	-	0.013	0.02	1.8e-07;1.6e-07	8.2e-11;6.9e-11	0.0157826913507789	TGC	ORF1ab:nsp4	.	1246-1247-delfrshift	.	no-SNV	ORF1ab:nsp4	0.984196462654282
CAMB-79DED	MN908947.3	10108	A	G	0.0028	0.014	0.0023	2.8e-08	0.00766794465744291	TAC	ORF1ab:3C-like-proteinase	V18V	A54G	GTA>GTG	Synonymous	ORF1ab:3C-like-proteinase	0.991298549758293
CAMB-79DED	MN908947.3	11023	A	G	0.65	0.71	0	0	0.680138163493467	CAA	ORF1ab:nsp6	T17T	A51G	ACA>ACG	Synonymous	ORF1ab:nsp6	0.319845150094278
CAMB-79DED	MN908947.3	11074	C	INS	0.033	0.023	6.6e-08	0.00018	0.0282979309683835	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.96740107105632
CAMB-79DED	MN908947.3	11075	T	-	0.043	0.012	1.4e-10	0.00044	0.0283526701058255	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.963797076035316
CAMB-79DED	MN908947.3	11620	C	T	0.005	0.0091	0.00062	2.5e-05	0.00647365581729905	TCT	ORF1ab:nsp6	F216F	C648T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.993526344182701
CAMB-79DED	MN908947.3	13518	T	C	0.032	0.078	5.5e-15	7.6e-32	0.0492784771261897	CTA	ORF1ab:RNA-dependent-RNA-polymerase	T17T	T51C	ACT>ACC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.950568007368744
CAMB-79DED	MN908947.3	14408	C	T	1	1	0	0	0.99942799108133	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000396904147648343
CAMB-79DED	MN908947.3	19719	A	-	0.0062	0.012	0.00064	3.4e-06	0.00864693703568384	CAA	ORF1ab:endoRNAse	.	99-99-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.988125685056631
CAMB-79DED	MN908947.3	23403	A	G	1	1	0	0	0.998764015898148	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.46266197046564e-05
CAMB-79DED	MN908947.3	241	C	T	1	1	0	0	0.99970168111466	TCG	NA	NA	NA	NA	NA	NA	0.000140385357807181
CAMB-79DED	MN908947.3	26378	AT	-	0.00705	0.015	4.2e-05;1e-04	1.5e-08;7.5e-08	0.0101351351351351	AAT	E	.	134-135-delfrshift	.	no-SNV	GU280_gp04	0.988619983309309
CAMB-79DED	MN908947.3	26494	TT	-	0.00215	0.028	0.0033;NA	1.3e-13;1.9e-13	0.0123207177607885	GTT	NA	NA	NA	NA	NA	NA	0.985789055253743
CAMB-79DED	MN908947.3	26615	G	T	1	1	0	0	0.999861272134526	GGA	M	W31C	G93T	TGG>TGT	Missense	GU280_gp05	1.98182664962296e-05
CAMB-79DED	MN908947.3	28230	G	C	0.0058	0.008	0.00014	1.8e-05	0.00684916494980932	TGA	ORF8	D113H	G337C	GAC>CAC	Missense	GU280_gp09	0.992624819182045
CAMB-79DED	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999374706893857	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	8.6333419666753e-05
CAMB-79DED	MN908947.3	3037	C	T	1	1	0	0	0.999648580264268	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.02839471464717e-05
CAMB-79DED	MN908947.3	4582	C	T	0.0087	0.011	2.3e-05	3.9e-06	0.00957942728343835	ACG	ORF1ab:nsp3	N621N	C1863T	AAC>AAT	Synonymous	ORF1ab:nsp3	0.990420572716562
CAMB-79DED	MN908947.3	6456	G	A	0.0038	0.011	7e-04	3.7e-07	0.00697231534381541	TGT	ORF1ab:nsp3	C1246Y	G3737A	TGT>TAT	Missense	ORF1ab:nsp3	0.992996206934542
CAMB-79DED	MN908947.3	646	TAA	-	0.001243	0.0084	NA;NA;0.00087	5.7e-06;7.3e-06;4.1e-06	0.00304146283369061	GTA	ORF1ab:leader-protein	.	381-383-delinframe	.	no-SNV	ORF1ab:leader-protein	0.996949614162506
CAMB-79DFC	MN908947.3	1048	G	A	0.018	0.035	5.2e-10	3.6e-17	0.0240448262060897	AGA	ORF1ab:nsp2	K81K	G243A	AAG>AAA	Synonymous	ORF1ab:nsp2	0.975924386564453
CAMB-79DFC	MN908947.3	11075	T	-	0.023	0.069	1.8e-06	1.9e-17	0.0393899891630413	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951265097139985
CAMB-79DFC	MN908947.3	11083	G	T	0.015	0.052	0.0015	1.9e-11	0.0278100715902833	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.97075200391605
CAMB-79DFC	MN908947.3	14408	C	T	1	1	0	0	0.99946526447128	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000378770999509826
CAMB-79DFC	MN908947.3	15324	C	T	1	1	0	0	0.999919852528653	ACA	ORF1ab:RNA-dependent-RNA-polymerase	N619N	C1857T	AAC>AAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-79DFC	MN908947.3	23403	A	G	1	1	0	0	0.999837792119014	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000127449049345955
CAMB-79DFC	MN908947.3	241	C	T	1	1	0	0	0.999927293878144	TCG	NA	NA	NA	NA	NA	NA	3.63530609277301e-05
CAMB-79DFC	MN908947.3	25433	C	T	1	1	0	0	0.999782143705934	ACT	ORF3a	T14I	C41T	ACT>ATT	Missense	GU280_gp03	1.98051176423988e-05
CAMB-79DFC	MN908947.3	2559	C	T	0.016	0.0032	1.3e-08	0.0026	0.0116775847336941	CCA	ORF1ab:nsp2	P585L	C1754T	CCA>CTA	Missense	ORF1ab:nsp2	0.988322415266306
CAMB-79DFC	MN908947.3	27925	C	T	0.091	0.057	1.6e-36	3.1e-20	0.0807814149947202	ACA	ORF8	T11I	C32T	ACA>ATA	Missense	GU280_gp09	0.918954593453009
CAMB-79DFC	MN908947.3	28079	G	T	0.0097	0.045	6.7e-05	4.6e-15	0.0204451345755694	TGG	ORF8	V62V	G186T	GTG>GTT	Synonymous	GU280_gp09	0.979296066252588
CAMB-79DFC	MN908947.3	29546	C	T	1	1	0	0	1	CCA	NA	NA	NA	NA	NA	NA	0
CAMB-79DFC	MN908947.3	3037	C	T	1	1	0	0	0.999520981030849	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.58037938302357e-05
CAMB-79DFC	MN908947.3	676	C	T	0.025	0.015	3.6e-13	1.1e-08	0.0206610791976646	GCG	ORF1ab:leader-protein	G137G	C411T	GGC>GGT	Synonymous	ORF1ab:leader-protein	0.979301252471984
CAMB-79E08	MN908947.3	11074	C	INS	0.026	0.021	1.1e-05	0.00036	0.0238097762135459	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.975002915266455
CAMB-79E08	MN908947.3	11075	T	-	0.033	0.038	2.7e-08	1.7e-09	0.0355680586290619	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959817948878755
CAMB-79E08	MN908947.3	12784	C	T	1	1	0	0	0.99945990755627	ACA	ORF1ab:nsp9	N33N	C99T	AAC>AAT	Synonymous	ORF1ab:nsp9	0.000138163183279743
CAMB-79E08	MN908947.3	14408	C	T	1	1	0	0	0.998723411310244	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000522240827627369
CAMB-79E08	MN908947.3	18448	A	C	0.032	0.029	1.9e-15	2.8e-14	0.0306163984202246	TAG	ORF1ab:3'-to-5'-exonuclease	S137R	A409C	AGT>CGT	Missense	ORF1ab:3'-to-5'-exonuclease	0.969339596695233
CAMB-79E08	MN908947.3	2062	C	T	0.0077	0.0085	3.8e-05	1.4e-05	0.0080795269235204	CCT	ORF1ab:nsp2	A419A	C1257T	GCC>GCT	Synonymous	ORF1ab:nsp2	0.991755752853778
CAMB-79E08	MN908947.3	23403	A	G	1	1	0	0	0.99944631153346	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.65735697454321e-05
CAMB-79E08	MN908947.3	241	C	T	1	1	0	0	0.998927089790663	TCG	NA	NA	NA	NA	NA	NA	0.000131133470030041
CAMB-79E08	MN908947.3	28086	G	T	1	1	0	0	0.996681605145223	GGC	ORF8	A65S	G193T	GCT>TCT	Missense	GU280_gp09	0.000307892306113373
CAMB-79E08	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999235663062293	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.89883897516289e-05
CAMB-79E08	MN908947.3	3037	C	T	1	1	0	0	0.999126748776539	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.45782014663343e-05
CAMB-79E08	MN908947.3	3903	C	T	1	1	0	0	0.999610407680534	CCA	ORF1ab:nsp3	P395L	C1184T	CCA>CTA	Missense	ORF1ab:nsp3	0.000139140114094894
CAMB-79E17	MN908947.3	11074	C	INS	0.018	0.029	0.003	6.1e-06	0.022614813162005	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.975298271404008
CAMB-79E17	MN908947.3	11075	T	-	0.051	0.03	1.9e-12	5.4e-08	0.0422461964038728	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954998616874136
CAMB-79E17	MN908947.3	13778	AT	-	0.017	0.0155	4.4e-06;4.7e-06	6.4e-06;9.2e-06	0.0162130988781406	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.984427929665107
CAMB-79E17	MN908947.3	13780	A	T	0.021	0.019	8.8e-07	2.3e-06	0.0203674860858484	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I105L	A313T	ATA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.976669970483483
CAMB-79E17	MN908947.3	14408	C	T	1	1	0	0	0.996189473684211	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000252631578947368
CAMB-79E17	MN908947.3	1547	A	-	0.012	0.016	7.6e-07	1.7e-08	0.0138443017656501	TAG	ORF1ab:nsp2	.	742-742-delfrshift	.	no-SNV	ORF1ab:nsp2	0.927668539325843
CAMB-79E17	MN908947.3	1547	A	G	0.02	0.014	7.8e-10	2e-07	0.0172552166934189	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.927668539325843
CAMB-79E17	MN908947.3	1547	A	T	0.041	0.041	2.9e-18	4.2e-18	0.0410313001605136	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.927668539325843
CAMB-79E17	MN908947.3	15842	C	T	0.0047	0.0077	9e-04	4.2e-05	0.00603741216060176	ACT	ORF1ab:RNA-dependent-RNA-polymerase	T792I	C2375T	ACT>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.992049091089044
CAMB-79E17	MN908947.3	21077	C	T	1	1	0	0	0.998807924053925	ACA	ORF1ab:2'-O-ribose-methyltransferase	T140I	C419T	ACA>ATA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.00034678572976722
CAMB-79E17	MN908947.3	22203	G	A	0.016	0.012	1.4e-08	1.3e-06	0.0145266965106282	CGT	S	R214H	G641A	CGT>CAT	Missense	GU280_gp02, spike glycoprotein	0.985414010850553
CAMB-79E17	MN908947.3	23403	A	G	1	1	0	0	0.999961174396844	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.8825603155745e-05
CAMB-79E17	MN908947.3	241	C	T	1	1	0	0	0.998942880909469	TCG	NA	NA	NA	NA	NA	NA	0.000294606959656176
CAMB-79E17	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0291081081081081	0.0361891891891892	0.0022;1e-04;0.00046;0.00039;0.00061;2.4e-05;0.00013;9.3e-05;8.9e-05;2.8e-05;4.8e-05;4e-05;8.4e-05;5.8e-05;7.2e-05;0.00012;5.4e-05;1e-04;6.2e-05;6.8e-05;5.5e-05;0.00011;6.3e-05;8.1e-05;6.4e-05;4.4e-05;9.2e-05;5.8e-05;1.7e-05;5.6e-05;9.5e-05;8.8e-05;4.4e-05;9.3e-05;3.1e-05;7.8e-05;6.1e-05	0.00034;6.3e-05;0.00019;0.00021;3e-04;3.4e-06;6.3e-06;3.3e-06;3.3e-06;1.7e-06;1.7e-06;1.3e-06;2.3e-06;1.4e-06;1.6e-06;3.1e-06;1.2e-06;2.7e-06;1.9e-06;1.8e-06;1.7e-06;3e-06;2e-06;2.2e-06;1.6e-06;1.4e-06;2.4e-06;1.5e-06;1.3e-06;1.4e-06;2.3e-06;2.3e-06;2.7e-06;3.8e-06;8.3e-07;2e-06;1.6e-06	0.0335642849148938	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.978558199173671
CAMB-79E17	MN908947.3	28677	C	T	0.012	0.011	5.5e-07	2.1e-06	0.0117400209821652	ACT	N	T135I	C404T	ACT>ATT	Missense	GU280_gp10	0.98803517010541
CAMB-79E17	MN908947.3	28795	A	G	0.005	0.008	0.00086	4.2e-05	0.0063661196017789	AAG	N	E174E	A522G	GAA>GAG	Synonymous	GU280_gp10	0.990021897645439
CAMB-79E17	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998723661004363	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000102040816326531
CAMB-79E17	MN908947.3	29241	AA	-	0.0064	0.0069	6e-05;0.00088	2.9e-05;0.00073	0.00661757219940951	GAA	N	.	968-969-delfrshift	.	no-SNV	GU280_gp10	0.991824872104288
CAMB-79E17	MN908947.3	29242	A	G	0.0088	0.0069	1.2e-05	7.2e-05	0.00789429103845502	AAG	N	E323E	A969G	GAA>GAG	Synonymous	GU280_gp10	0.976351007962053
CAMB-79E17	MN908947.3	29242	A	T	0.0084	0.011	1.8e-05	1.9e-06	0.00945282059969507	AAG	N	E323D	A969T	GAA>GAT	Missense	GU280_gp10	0.976351007962053
CAMB-79E17	MN908947.3	3037	C	T	1	1	0	0	0.999666790077749	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.70233246945576e-05
CAMB-79E17	MN908947.3	4554	C	T	0.0075	0.0046	3.1e-05	0.00062	0.0061750538075228	ACT	ORF1ab:nsp3	T612I	C1835T	ACT>ATT	Missense	ORF1ab:nsp3	0.976017218407297
CAMB-79E17	MN908947.3	517	T	C	0.01	0.0047	3.8e-05	0.0035	0.00789789961655125	TTA	ORF1ab:leader-protein	V84V	T252C	GTT>GTC	Synonymous	ORF1ab:leader-protein	0.937474961368969
CAMB-79E17	MN908947.3	522	TT	-	0.0405	0.0345	7.6e-06;4.9e-05	2.5e-05;0.00047	0.0380711678100052	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.955756331279945
CAMB-79E26	MN908947.3	10628	C	T	0.0023	0.008	0.005	1.4e-05	0.00454088152921663	ACA	ORF1ab:3C-like-proteinase	Q192*	C574T	CAA>TAA	Nonsense	ORF1ab:3C-like-proteinase	0.995404736656062
CAMB-79E26	MN908947.3	11074	C	INS	0.1	0.097	6.1e-44	3.4e-37	0.0995952914107279	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.893645869712595
CAMB-79E26	MN908947.3	11083	G	-	0.16	0.16	1.6e-71	2.3e-70	0.162272555053459	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	9.24103388687126e-06
CAMB-79E26	MN908947.3	11083	G	T	0.84	0.84	0	0	0.837579588404351	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	9.24103388687126e-06
CAMB-79E26	MN908947.3	11747	C	T	0.006	0.044	0.0013	1.3e-13	0.021021021021021	ACT	ORF1ab:nsp6	L259L	C775T	CTA>TTA	Synonymous	ORF1ab:nsp6	0.978978978978979
CAMB-79E26	MN908947.3	14805	C	T	1	1	0	0	0.998694656860358	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	1.94827334274999e-05
CAMB-79E26	MN908947.3	16996	C	T	0.013	0.012	1.6e-07	1.9e-07	0.0126744458374089	CCC	ORF1ab:helicase	P254S	C760T	CCA>TCA	Missense	ORF1ab:helicase	0.987256671304779
CAMB-79E26	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-79E26	MN908947.3	25538	G	C	0.00092	0.008	0.0085	1.6e-05	0.00379684687142	GGC	ORF3a	G49A	G146C	GGC>GCC	Missense	GU280_gp03	0.996170421690033
CAMB-79E26	MN908947.3	2558	C	T	1	1	0	0	0.999269495343033	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-79E26	MN908947.3	25906	G	T	1	0.99	0	0	0.998102996150198	AGG	ORF3a	G172C	G514T	GGT>TGT	Missense	GU280_gp03	5.57942308765274e-05
CAMB-79E26	MN908947.3	26144	G	T	1	1	0	0	0.999131944444444	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-79E26	MN908947.3	29013	C	T	1	1	0	0	0.999774984248897	ACT	N	T247I	C740T	ACT>ATT	Missense	GU280_gp10	0.000195013650955567
CAMB-79E26	MN908947.3	29474	G	T	0.018	0.028	2.3e-08	4e-12	0.0229781482315837	GGA	N	D401Y	G1201T	GAT>TAT	Missense	GU280_gp10	0.975444920027033
CAMB-79E26	MN908947.3	29687	A	T	0.015	0.011	6.2e-08	2e-06	0.0132170235263019	CAG	NA	NA	NA	NA	NA	NA	0.986386465767909
CAMB-79E26	MN908947.3	29774	C	T	0.0083	0.017	0.00013	4.2e-08	0.012223580397822	GCT	NA	NA	NA	NA	NA	NA	0.987776419602178
CAMB-79E26	MN908947.3	3270	T	C	0.081	0.075	9.4e-37	6.8e-34	0.0782428776062391	ATT	ORF1ab:nsp3	I184T	T551C	ATT>ACT	Missense	ORF1ab:nsp3	0.921725290466338
CAMB-79E26	MN908947.3	4185	G	A	1	1	0	0	0.999874559532905	GGT	ORF1ab:nsp3	G489D	G1466A	GGT>GAT	Missense	ORF1ab:nsp3	0.000102633109441106
CAMB-79E26	MN908947.3	683	C	T	0.17	0.14	1.9e-78	2.4e-67	0.15924194461332	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.839290580910253
CAMB-79E35	MN908947.3	11075	T	-	0.051	0.037	2.4e-12	2e-09	0.044785455572707	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955103564474308
CAMB-79E35	MN908947.3	11083	G	T	0.024	0.013	2.6e-05	0.0031	0.019041769041769	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.980182865428767
CAMB-79E35	MN908947.3	11615	TG	-	0.021	0.0335	1.5e-08;3.6e-08	6.5e-11;1.9e-10	0.0248496993987976	TTG	ORF1ab:nsp6	.	643-644-delfrshift	.	no-SNV	ORF1ab:nsp6	0.974627466774064
CAMB-79E35	MN908947.3	14408	C	T	0.99	1	0	0	0.992483957182976	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000203502964359848
CAMB-79E35	MN908947.3	17354	TTGATGAAA	-	0.00220377777777778	0.0174444444444444	NA;NA;NA;NA;0.00041;0.00055;NA;NA;NA	1.9e-06;5.4e-06;2.9e-06;4.1e-06;1.4e-06;2.3e-06;4.8e-06;8e-07;3.2e-06	0.00809576074822465	TTT	ORF1ab:helicase	.	1118-1126-delinframe	.	no-SNV	ORF1ab:helicase	0.991838649155722
CAMB-79E35	MN908947.3	2185	G	INS	0.01	0.032	9.4e-07	4.2e-15	0.0188095238095238	AGT	ORF1ab:nsp2	.	1379-1380-insfrshift	.	no-SNV	ORF1ab:nsp2	0.981071428571429
CAMB-79E35	MN908947.3	23403	A	G	1	1	0	0	0.999883087427222	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.79417151853844e-05
CAMB-79E35	MN908947.3	23433	TTCATGCAGATCAACTT	-	0.0147058823529412	0.0107077647058824	3e-08;2.1e-08;3.1e-08;2.4e-09;1.9e-08;3.3e-08;3.6e-08;4.4e-08;3.9e-08;2.8e-08;3.3e-08;2.5e-08;3.8e-08;7.4e-07;1.1e-06;2.8e-08;1.1e-06	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;4.3e-17;8.8e-17;7.3e-22;5.8e-17	0.00745799968597896	ATT	S	.	1871-1887-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.992398864216437
CAMB-79E35	MN908947.3	241	C	T	1	1	0	0	0.999632845233467	TCG	NA	NA	NA	NA	NA	NA	0.000280765409701525
CAMB-79E35	MN908947.3	25797	C	INS	0.0062	0.021	0.0017	1.2e-08	0.0102441929720071	CCA	ORF3a	.	404-405-insfrshift	.	no-SNV	GU280_gp03	0.989041095890411
CAMB-79E35	MN908947.3	26700	G	T	1	1	0	0	0.99966731673741	AGT	M	V60L	G178T	GTA>TTA	Missense	GU280_gp05	0.000263852242744063
CAMB-79E35	MN908947.3	26834	G	T	0.014	0.027	1e-07	3.1e-13	0.0196777712511538	CGC	M	A104A	G312T	GCG>GCT	Synonymous	GU280_gp05	0.980263489133171
CAMB-79E35	MN908947.3	27461	G	-	0.01	0.016	1.9e-06	4.2e-09	0.0126713350532652	TGT	ORF7a	.	68-68-delfrshift	.	no-SNV	GU280_gp07	0.987311114621176
CAMB-79E35	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998885974053976	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79E35	MN908947.3	29026	T	A	0.033	0.01	9.5e-16	1.9e-06	0.0221651220516147	CTG	N	A251A	T753A	GCT>GCA	Synonymous	GU280_gp10	0.97772261790423
CAMB-79E35	MN908947.3	3037	C	T	1	1	0	0	0.999854524294443	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79E35	MN908947.3	522	T	-	0.046	0.056	4.3e-06	1.9e-07	0.049982689977497	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.949757659684958
CAMB-79E35	MN908947.3	6996	T	C	1	1	0	0	1	ATC	ORF1ab:nsp3	I1426T	T4277C	ATC>ACC	Missense	ORF1ab:nsp3	0
CAMB-79E35	MN908947.3	9553	AGT	-	0.0156666666666667	0.033	0.0015;0.0014;0.00017	2e-05;1.5e-05;1.4e-07	0.0235295350689641	CAG	ORF1ab:nsp4	.	999-1001-delinframe	.	no-SNV	ORF1ab:nsp4	0.97631457273759
CAMB-79E44	MN908947.3	11074	C	INS	0.11	0.062	1.7e-43	4e-16	0.0924387137854187	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.897755491881566
CAMB-79E44	MN908947.3	11083	G	-	0.19	0.24	8.4e-87	9.5e-115	0.212888819354563	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	4.26687906242444e-05
CAMB-79E44	MN908947.3	11083	G	T	0.81	0.75	0	8.8e-290	0.786912059622523	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	4.26687906242444e-05
CAMB-79E44	MN908947.3	13726	G	-	0.0052	0.014	0.0051	9.1e-06	0.00859546077809385	TGT	ORF1ab:RNA-dependent-RNA-polymerase	.	259-259-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.991363608456296
CAMB-79E44	MN908947.3	13971	C	T	0.003	0.0062	0.00095	3e-05	0.00416141406747726	ACT	ORF1ab:RNA-dependent-RNA-polymerase	N168N	C504T	AAC>AAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.995797920648476
CAMB-79E44	MN908947.3	14805	C	T	1	1	0	0	0.999900550288404	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-79E44	MN908947.3	15928	C	-	0.0066	0.0017	3e-05	0.0052	0.00446096654275093	TCC	ORF1ab:RNA-dependent-RNA-polymerase	.	2461-2461-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.995487161753264
CAMB-79E44	MN908947.3	21736	C	T	0.038	0.1	3.8e-17	4.6e-44	0.0674459380479252	TCT	S	F58F	C174T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.927995324371712
CAMB-79E44	MN908947.3	23608	GC	-	0.011	0.00315	2.2e-05;4.5e-06	0.0013;NA	0.00755241375143496	GGC	S	.	2046-2047-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.99080781639983
CAMB-79E44	MN908947.3	2480	A	G	1	0.99	0	0	0.997059544229355	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-79E44	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-79E44	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-79E44	MN908947.3	26776	CTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0505714285714286	0.0117380952380952	0.00011;6.7e-05;0.00028;0.00093;2.8e-08;4.6e-11;7.7e-09;1.3e-08;6.6e-08;4.5e-10;6.7e-09;4.4e-09;4.2e-09;4.9e-10;1.3e-09;8.6e-10;4.6e-09;1.6e-09;2.6e-09;7.3e-09;1.2e-09;5.6e-09;2.6e-09;2.7e-09;2.4e-09;5.7e-09;2.5e-09;3.8e-09;2.1e-09;5.1e-10;3.5e-09;1.9e-09;2.4e-09;1.4e-09;4.7e-09;1.7e-09;4.4e-10;2.6e-09;7.1e-10;1.9e-09;8.2e-10;2e-04	0.17;0.0094;0.017;0.042;0.051;0.015;0.044;0.043;0.063;0.022;0.05;0.079;0.079;0.047;0.065;0.061;0.078;0.066;0.07;0.089;0.061;0.083;0.072;0.07;0.075;0.088;0.065;0.078;0.07;0.065;0.084;0.066;0.031;0.069;0.081;0.079;0.064;0.083;0.064;0.065;0.064;0.062	0.036759012585467	GCT	M	.	254-295-delinframe	.	no-SNV	GU280_gp05	0.976225594845321
CAMB-79E44	MN908947.3	27382	G	-	0.06	0.04	4e-28	1.7e-19	0.0515260255817152	TGA	ORF6	.	181-181-delfrshift	.	no-SNV	GU280_gp06	0.948398954725616
CAMB-79E44	MN908947.3	27414	G	A	0.012	0.0057	1.6e-07	6.7e-05	0.00943607912607027	TGG	ORF7a	L7L	G21A	TTG>TTA	Synonymous	GU280_gp07	0.990528491290227
CAMB-79E44	MN908947.3	28266	A	G	0.073	0.096	1.5e-33	7.2e-44	0.0824028554111388	CAA	NA	NA	NA	NA	NA	NA	0.917139201293016
CAMB-79E44	MN908947.3	28347	G	A	0.071	0.093	3.3e-32	1.8e-42	0.0800901269971323	GGC	N	G25D	G74A	GGC>GAC	Missense	GU280_gp10	0.919885774875292
CAMB-79E44	MN908947.3	28575	TG	-	0.0125	0.0041	1.2e-06;1.1e-06	0.0039;0.0035	0.00955577308534937	ATG	N	.	302-303-delfrshift	.	no-SNV	GU280_gp10	0.990057159325616
CAMB-79E44	MN908947.3	29041	G	C	0.019	0.026	0.00032	4.5e-05	0.0218441299968447	AGA	N	K256N	G768C	AAG>AAC	Missense	GU280_gp10	0.973301618892745
CAMB-79E44	MN908947.3	29171	C	T	0.0031	0.0081	0.0034	1.8e-05	0.00518270928005408	ACA	N	H300Y	C898T	CAT>TAT	Missense	GU280_gp10	0.994817290719946
CAMB-79E44	MN908947.3	3230	G	-	0.012	0.0057	4.8e-06	0.0027	0.00995221879042264	TGG	ORF1ab:nsp3	.	511-511-delfrshift	.	no-SNV	ORF1ab:nsp3	0.989994984292917
CAMB-79E44	MN908947.3	5812	C	T	0.057	0.026	7.4e-26	1.1e-12	0.0450684479630546	ACG	ORF1ab:nsp3	D1031D	C3093T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.954931552036945
CAMB-79E44	MN908947.3	9427	TATCG	-	0.00952	0.0092	2.2e-05;1.7e-05;4.2e-05;3.6e-05;3.5e-05	6e-05;5.1e-05;9.2e-05;9e-05;0.00011	0.00942089221390967	CTA	ORF1ab:nsp4	.	873-877-delfrshift	.	no-SNV	ORF1ab:nsp4	0.990477504830251
CAMB-79E44	MN908947.3	9438	C	T	0.11	0.066	7.7e-46	2.2e-26	0.0941545169641641	ACA	ORF1ab:nsp4	T295I	C884T	ACA>ATA	Missense	ORF1ab:nsp4	0.905845483035836
CAMB-79E44	MN908947.3	9603	C	T	0.031	0.066	4.1e-15	1.2e-30	0.046166541200996	ACA	ORF1ab:nsp4	T350I	C1049T	ACA>ATA	Missense	ORF1ab:nsp4	0.953818981990851
CAMB-79E44	MN908947.3	9860	T	G	0.0069	0.0024	3.5e-05	0.00084	0.00521617012739492	ATT	ORF1ab:nsp4	L436V	T1306G	TTA>GTA	Missense	ORF1ab:nsp4	0.989868592637175
CAMB-79E53	MN908947.3	13914	T	G	0.0095	0.0015	6.8e-07	0.0036	0.00572883513685551	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994271164863144
CAMB-79E53	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999261640027797	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	8.68658790826963e-05
CAMB-79E53	MN908947.3	17898	C	T	1	1	0	0	0.999767374236697	ACT	ORF1ab:helicase	H554H	C1662T	CAC>CAT	Synonymous	ORF1ab:helicase	0.000174469322477464
CAMB-79E62	MN908947.3	11075	T	-	0.041	0.04	2.4e-10	2.5e-10	0.0406924931851541	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954904067938771
CAMB-79E62	MN908947.3	14408	C	T	1	1	0	0	0.996140267229734	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000658425001986627
CAMB-79E62	MN908947.3	23403	A	G	1	1	0	0	0.999502231376588	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.58221764503948e-06
CAMB-79E62	MN908947.3	241	C	T	1	1	0	0	0.998348953527898	TCG	NA	NA	NA	NA	NA	NA	0.000194240761423785
CAMB-79E62	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0292702702702703	0.0324324324324324	0.0018;2e-04;0.00088;0.00098;0.0016;6.1e-05;0.00019;7.1e-05;7.1e-05;1.8e-05;4.3e-05;3.5e-05;6.7e-05;3.7e-05;4.2e-05;7.6e-05;3e-05;6.8e-05;4.6e-05;4.6e-05;3.8e-05;7.5e-05;4.4e-05;5.5e-05;4.3e-05;2.6e-05;6.3e-05;3.9e-05;3.7e-05;3e-05;6.5e-05;4.9e-05;2e-05;5.3e-05;2.4e-05;3.7e-05;3e-05	0.00045;2.1e-05;0.00024;0.00023;0.00051;1.4e-05;6.5e-05;1.6e-05;1.6e-05;4e-06;7.4e-06;5.4e-06;1.2e-05;8.2e-06;1e-05;1.6e-05;7.9e-06;1.6e-05;1e-05;1e-05;9e-06;1.7e-05;7.8e-06;1.3e-05;9.2e-06;6.6e-06;1.4e-05;7.1e-06;8.1e-06;8e-06;1.3e-05;1.1e-05;8.1e-06;1.6e-05;4.8e-06;9.5e-06;7.3e-06	0.0317308712724186	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.978743129594067
CAMB-79E62	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998897186249488	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000104116054695634
CAMB-79E62	MN908947.3	29281	C	T	1	1	0	0	0.999127786647744	CCA	N	A336A	C1008T	GCC>GCT	Synonymous	GU280_gp10	0.000340015374608243
CAMB-79E62	MN908947.3	3037	C	T	1	1	0	0	0.999326448136507	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	2.80646609788954e-05
CAMB-79E62	MN908947.3	522	TT	-	0.03	0.035	0.00012;0.0016	1.6e-05;0.00055	0.0322243122501763	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.960453073648722
CAMB-79E62	MN908947.3	7528	C	T	0.0083	0.0082	2.9e-05	2.8e-05	0.00826530960756857	TCG	ORF1ab:nsp3	V1603V	C4809T	GTC>GTT	Synonymous	ORF1ab:nsp3	0.991632227876635
CAMB-79E71	MN908947.3	10097	G	A	0.37	0.43	8.2e-191	5.9e-231	0.393872101194659	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.606127898805341
CAMB-79E71	MN908947.3	11075	T	-	0.019	0.084	2.3e-05	2.4e-20	0.0469835259253162	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951164298282622
CAMB-79E71	MN908947.3	13536	C	T	0.36	0.45	5.6e-176	2.7e-219	0.396142938173568	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.603857061826432
CAMB-79E71	MN908947.3	14408	C	T	1	0.99	0	0	0.996568784796396	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00322091491693139
CAMB-79E71	MN908947.3	15324	C	T	0.53	0.57	1.20000000000112e-312	0	0.545321200597582	ACA	ORF1ab:RNA-dependent-RNA-polymerase	N619N	C1857T	AAC>AAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.454597310878718
CAMB-79E71	MN908947.3	18176	C	T	0.0033	0.0073	0.0019	2.8e-05	0.00499043977055449	CCT	ORF1ab:3'-to-5'-exonuclease	P46L	C137T	CCT>CTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.99491395793499
CAMB-79E71	MN908947.3	21077	C	T	0.0037	0.0095	0.0023	6.4e-06	0.00626799066614433	ACA	ORF1ab:2'-O-ribose-methyltransferase	T140I	C419T	ACA>ATA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.993732009333856
CAMB-79E71	MN908947.3	2180	G	A	0.0061	0.003	4.1e-05	0.0011	0.00515776699029126	TGT	ORF1ab:nsp2	V459I	G1375A	GTA>ATA	Missense	ORF1ab:nsp2	0.994842233009709
CAMB-79E71	MN908947.3	23349	G	T	0.0027	0.018	0.0028	1.2e-09	0.00939348444947618	AGT	S	S596I	G1787T	AGT>ATT	Missense	GU280_gp02, spike glycoprotein	0.990549088134675
CAMB-79E71	MN908947.3	23403	A	G	1	1	0	0	0.999944463838025	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.76024245501571e-05
CAMB-79E71	MN908947.3	23731	C	T	0.39	0.42	2.5e-208	9.4e-223	0.403710038928866	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.596260469505721
CAMB-79E71	MN908947.3	241	C	T	1	1	0	0	0.999792957090357	TCG	NA	NA	NA	NA	NA	NA	8.62678790179265e-05
CAMB-79E71	MN908947.3	25169	C	T	0.38	0.38	1.9e-194	1.7e-196	0.380142067876874	ACT	S	L1203F	C3607T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.619542225730071
CAMB-79E71	MN908947.3	26408	C	T	0.0031	0.012	0.0031	5.1e-07	0.00644187216909914	TCT	E	S55F	C164T	TCT>TTT	Missense	GU280_gp04	0.993423922160711
CAMB-79E71	MN908947.3	26750	C	T	0.0046	0.012	4e-04	5e-07	0.00767850204451681	TCA	M	I76I	C228T	ATC>ATT	Synonymous	GU280_gp05	0.99227524191907
CAMB-79E71	MN908947.3	28881	GGG	AAC	0.456666666666667	0.403333333333333	8.4e-226;1.1e-245;2.7e-263	5.1e-194;4e-201;1.7e-213	0.440538857757401	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.58288146463763
CAMB-79E71	MN908947.3	29315	G	T	0.0076	0.0045	1.8e-05	0.00043	0.00616694980335575	AGA	N	D348Y	G1042T	GAT>TAT	Missense	GU280_gp10	0.993833050196644
CAMB-79E71	MN908947.3	29730	CACCGAGGCCACGCGGAGTACGATCGAGTG	-	0.632333333333333	0.561666666666667	0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;1.9e-304;4.1e-307;2.4e-248;1.3e-247;2.8e-299;2.5e-306;1.3e-306;3.3e-301;6.2e-304;5.5e-272;5.1e-302;3.6e-274	1.1e-282;1.6e-304;2.5e-283;1.8e-283;1.7e-280;1.4e-288;2.5e-284;3.5e-280;2.2e-281;6.2e-282;1.8e-292;2e-281;7.1e-281;1.5e-282;2.3e-282;7.3e-281;2.7e-284;1.4e-256;8.7e-231;3.7e-234;3.6e-192;9.2e-193;3.9e-224;2.7e-233;2.2e-232;1.4e-230;5.9e-236;3e-209;1.8e-232;3.6e-211	0.610583768391077	TCA	NA	NA	NA	NA	NA	NA	0.391294061982494
CAMB-79E71	MN908947.3	3037	C	T	1	1	0	0	0.99963405150725	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.57435615937057e-05
CAMB-79E71	MN908947.3	4002	C	T	0.34	0.3	2.4e-173	1.9e-148	0.324743947016033	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0.675219861749484
CAMB-79E71	MN908947.3	4455	C	T	0.046	0.057	1.2e-21	2.4e-26	0.0504067722075638	GCC	ORF1ab:nsp3	A579V	C1736T	GCC>GTC	Missense	ORF1ab:nsp3	0.949565743183817
CAMB-79E71	MN908947.3	4891	C	T	0.0051	0.0094	0.00038	3.9e-06	0.00662535268037082	CCA	ORF1ab:nsp3	T724T	C2172T	ACC>ACT	Synonymous	ORF1ab:nsp3	0.993349455864571
CAMB-79E71	MN908947.3	7410	G	-	0.005	0.0097	0.00082	8.2e-06	0.00686831330075287	AGA	ORF1ab:nsp3	.	4691-4691-delfrshift	.	no-SNV	ORF1ab:nsp3	0.992999603751156
CAMB-79E71	MN908947.3	827	AACA	-	0.0018975	0.008775	0.00068;0.00067;0.22;NA	2e-05;2e-05;2.9e-05;4.2e-08	0.00429855412270418	TAA	ORF1ab:nsp2	.	22-25-delfrshift	.	no-SNV	ORF1ab:nsp2	0.994235931989261
CAMB-79E71	MN908947.3	8871	TG	-	9e-04	0.0097	NA;0.0093	8.7e-07;3.1e-06	0.00433306530867507	TTG	ORF1ab:nsp4	.	317-318-delfrshift	.	no-SNV	ORF1ab:nsp4	0.995596143148526
CAMB-79E80	MN908947.3	11074	C	INS	0.058	0.045	4.1e-14	1.2e-10	0.0504734826233052	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.94945602368588
CAMB-79E80	MN908947.3	14408	C	T	1	1	0	0	0.999663450751627	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000196320394884451
CAMB-79E80	MN908947.3	18877	C	T	1	1	0	0	0.99989183927316	TCT	ORF1ab:3'-to-5'-exonuclease	L280L	C838T	CTA>TTA	Synonymous	ORF1ab:3'-to-5'-exonuclease	1.80267878066807e-05
CAMB-79E80	MN908947.3	23403	A	G	1	0.98	0	0	0.990964548024509	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00902192584977885
CAMB-79E80	MN908947.3	241	C	T	1	1	0	0	0.999840694571668	TCG	NA	NA	NA	NA	NA	NA	0.000119479071249353
CAMB-79E80	MN908947.3	24197	G	T	1	1	0	0	1	AGC	S	A879S	G2635T	GCG>TCG	Missense	GU280_gp02, spike glycoprotein	0
CAMB-79E80	MN908947.3	249	T	C	0.0072	0.079	4e-05	5.1e-36	0.0426280306519827	GTG	NA	NA	NA	NA	NA	NA	0.957330095054646
CAMB-79E80	MN908947.3	25563	G	T	1	1	0	0	0.999756815252547	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000194547797962112
CAMB-79E80	MN908947.3	26735	C	T	1	1	0	0	0.999034213004322	ACA	M	Y71Y	C213T	TAC>TAT	Synonymous	GU280_gp05	0
CAMB-79E80	MN908947.3	26775	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATT	-	0.0347948717948718	0.0182620512820513	2.3e-06;2.1e-06;4.3e-07;6.3e-06;3.5e-05;5.1e-06;5.6e-08;2.1e-06;2.6e-06;9.6e-06;2.1e-07;2.3e-06;1.6e-05;1.6e-05;3.6e-06;7.6e-06;5.8e-06;1.6e-05;9.3e-06;1.2e-05;2.3e-05;8.1e-06;1.9e-05;1.1e-05;1.1e-05;9.1e-06;2.1e-05;1.1e-05;1.4e-05;1e-05;6.9e-06;1.7e-05;9.8e-06;2.3e-06;9.4e-06;1.7e-05;1.5e-05;7.5e-06;1.7e-05	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.5;0.5;0.00028;0.00028;9.9e-05;0.00019;0.00016;0.00027;2e-04;0.00025;0.00035;0.00019;0.00031;0.00023;0.00022;0.00024;0.00035;0.00021;0.00027;0.00021;0.00016;3e-04;0.00018;9.6e-05;2e-04;0.00029;0.00028;2e-04;0.00031	0.0292800614113648	GGC	M	.	253-291-delinframe	.	no-SNV	GU280_gp05	0.984921887757879
CAMB-79E80	MN908947.3	27384	T	C	0.11	0.012	3.2e-48	5.1e-07	0.0435931070421017	ATT	ORF6	D61D	T183C	GAT>GAC	Synonymous	GU280_gp06	0.956352985570789
CAMB-79E80	MN908947.3	28531	CTACCGAAGAGCTACCAGACGAATTCGTGGTGGTGACGGTAAAATG	-	0.00850869565217391	0.000743478260869565	9.4e-05;6.7e-05;2.3e-05;6.5e-05;7.5e-05;9e-05;7.8e-05;3.5e-05;5.8e-05;6.8e-05;1e-04;4.4e-05;4.4e-05;5.2e-05;0.00017;0.00017;0.00031;0.00013;6.9e-06;8.9e-05;8.2e-05;2.6e-05;5.2e-06;7.4e-06;2.1e-05;7.2e-05;9.9e-05;2.3e-05;6.8e-05;3.2e-05;1.9e-05;4.3e-05;3e-05;2.1e-05;3e-05;2.5e-05;3e-05;3e-05;2.6e-05;1.3e-05;8.5e-06;1.3e-05;7.7e-06;1.5e-05;7e-05;6.6e-05	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00085;0.0016;0.0016;0.0024;0.0015;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00361723117395594	ACT	N	.	258-303-delfrshift	.	no-SNV	GU280_gp10	0.996490309062336
CAMB-79E80	MN908947.3	3037	C	T	1	1	0	0	0.999629423753937	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79E80	MN908947.3	3464	C	T	0.091	0.018	6.4e-41	3.9e-10	0.0541176470588235	ACA	ORF1ab:nsp3	H249Y	C745T	CAT>TAT	Missense	ORF1ab:nsp3	0.945882352941177
CAMB-79E80	MN908947.3	3959	A	G	0.033	0.039	2.3e-15	9.1e-17	0.0351038412056607	AAT	ORF1ab:nsp3	I414V	A1240G	ATC>GTC	Missense	ORF1ab:nsp3	0.964712369049807
CAMB-79E9F	MN908947.3	10081	A	C	0.045	0.031	1.1e-20	5.8e-15	0.038275930455477	CAT	ORF1ab:3C-like-proteinase	P9P	A27C	CCA>CCC	Synonymous	ORF1ab:3C-like-proteinase	0.961641435843194
CAMB-79E9F	MN908947.3	11074	C	INS	0.027	0.02	4.1e-06	0.0011	0.023754201070495	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.975654537156135
CAMB-79E9F	MN908947.3	11075	T	-	0.032	0.041	5.2e-08	3.9e-10	0.0360203289949701	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960597316781882
CAMB-79E9F	MN908947.3	11245	G	T	1	1	0	0	0.999880788160561	TGA	ORF1ab:nsp6	V91V	G273T	GTG>GTT	Synonymous	ORF1ab:nsp6	1.70302627769547e-05
CAMB-79E9F	MN908947.3	13458	C	T	0.0087	0.011	3.3e-05	4.7e-06	0.00976471682321213	TCG	ORF1ab:nsp11	S6L	C17T	TCG>TTG	Missense	ORF1ab:nsp11	0.990049288570631
CAMB-79E9F	MN908947.3	14554	C	T	0.032	0.031	4.9e-15	1e-14	0.0316141570719545	ACT	ORF1ab:RNA-dependent-RNA-polymerase	L363F	C1087T	CTT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.968223242561033
CAMB-79E9F	MN908947.3	16020	G	A	0.0093	0.0077	7.2e-06	2.9e-05	0.00860739873527302	TGT	ORF1ab:RNA-dependent-RNA-polymerase	V851V	G2553A	GTG>GTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.991285421012276
CAMB-79E9F	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999518554181172	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	9.25857343900452e-05
CAMB-79E9F	MN908947.3	16742	T	C	0.12	0.072	3.6e-31	7.7e-20	0.0954128440366973	GTT	ORF1ab:helicase	V169A	T506C	GTT>GCT	Missense	ORF1ab:helicase	0.902752293577982
CAMB-79E9F	MN908947.3	16767	C	T	0.92	0.89	0	0	0.902687673772011	ACC	ORF1ab:helicase	N177N	C531T	AAC>AAT	Synonymous	ORF1ab:helicase	0.0973123262279889
CAMB-79E9F	MN908947.3	17004	C	A	0.044	0.043	1.3e-20	1.9e-20	0.0432705347270034	TCA	ORF1ab:helicase	L256L	C768A	CTC>CTA	Synonymous	ORF1ab:helicase	0.954663996161148
CAMB-79E9F	MN908947.3	17012	C	T	0.014	0.0081	3.8e-08	1.2e-05	0.0116443332257023	TCA	ORF1ab:helicase	S259L	C776T	TCA>TTA	Missense	ORF1ab:helicase	0.988315305134001
CAMB-79E9F	MN908947.3	17111	C	T	0.022	0.021	1.8e-11	3e-11	0.0220087304341473	GCT	ORF1ab:helicase	A292V	C875T	GCT>GTT	Missense	ORF1ab:helicase	0.977960828721545
CAMB-79E9F	MN908947.3	17395	G	T	0.01	0.0083	2.3e-06	1e-05	0.00947786942920845	TGT	ORF1ab:helicase	V387F	G1159T	GTC>TTC	Missense	ORF1ab:helicase	0.990454310395985
CAMB-79E9F	MN908947.3	17456	C	T	0.032	0.036	5.7e-15	2.4e-17	0.0335124398380402	GCA	ORF1ab:helicase	A407V	C1220T	GCA>GTA	Missense	ORF1ab:helicase	0.966445117862266
CAMB-79E9F	MN908947.3	17522	T	C	0.012	0.0079	4.6e-07	1.4e-05	0.0103961686030317	ATG	ORF1ab:helicase	M429T	T1286C	ATG>ACG	Missense	ORF1ab:helicase	0.989073689696382
CAMB-79E9F	MN908947.3	17545	T	C	0.011	0.011	1.3e-06	9.4e-07	0.0111405787688533	GTT	ORF1ab:helicase	F437L	T1309C	TTC>CTC	Missense	ORF1ab:helicase	0.98702821678574
CAMB-79E9F	MN908947.3	17627	A	G	0.13	0.13	1.5e-58	4.9e-58	0.126616845150963	CAT	ORF1ab:helicase	H464R	A1391G	CAT>CGT	Missense	ORF1ab:helicase	0.873383154849037
CAMB-79E9F	MN908947.3	17671	G	T	0.077	0.08	4.6e-35	9.8e-37	0.0786038663969311	TGT	ORF1ab:helicase	V479F	G1435T	GTT>TTT	Missense	ORF1ab:helicase	0.92124503689278
CAMB-79E9F	MN908947.3	19029	C	T	0.032	0.038	4e-15	1.3e-17	0.0345280432511191	ACG	ORF1ab:3'-to-5'-exonuclease	H330H	C990T	CAC>CAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.965462370951199
CAMB-79E9F	MN908947.3	20274	G	T	0.17	0.15	9.5e-51	2.4e-43	0.157260273972603	TGG	ORF1ab:endoRNAse	M218I	G654T	ATG>ATT	Missense	ORF1ab:endoRNAse	0.841643835616438
CAMB-79E9F	MN908947.3	23426	G	T	0.0085	0.0076	2.4e-05	5.1e-05	0.00809604127393591	TGT	S	V622F	G1864T	GTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.991381420114429
CAMB-79E9F	MN908947.3	26074	G	T	0.057	0.062	2e-25	1.7e-27	0.0594757071055484	TGT	ORF3a	V228F	G682T	GTT>TTT	Missense	GU280_gp03	0.940327190302553
CAMB-79E9F	MN908947.3	26801	C	T	0.011	0.012	6.6e-06	3.2e-06	0.0112955242664989	TCA	M	L93L	C279T	CTC>CTT	Synonymous	GU280_gp05	0.984920947062062
CAMB-79E9F	MN908947.3	2854	A	G	0.0076	0.0057	3.8e-05	0.00022	0.00679514453760481	AAC	ORF1ab:nsp3	E45E	A135G	GAA>GAG	Synonymous	ORF1ab:nsp3	0.993204855462395
CAMB-79E9F	MN908947.3	28826	C	T	0.016	0.0068	1.2e-07	0.00096	0.0115980522355024	TCG	N	R185C	C553T	CGT>TGT	Missense	GU280_gp10	0.988357680389553
CAMB-79E9F	MN908947.3	5184	C	T	0.2	0.2	2.8e-88	1.2e-86	0.201389578163772	CCT	ORF1ab:nsp3	P822L	C2465T	CCT>CTT	Missense	ORF1ab:nsp3	0.798610421836228
CAMB-79E9F	MN908947.3	6539	C	T	1	1	0	0	0.999352424809325	CCA	ORF1ab:nsp3	H1274Y	C3820T	CAC>TAC	Missense	ORF1ab:nsp3	0.000575622391711038
CAMB-79E9F	MN908947.3	8078	C	T	0.13	0.12	8.5e-60	2.2e-55	0.127438173888016	ACC	ORF1ab:nsp3	P1787S	C5359T	CCA>TCA	Missense	ORF1ab:nsp3	0.872351495560918
CAMB-79EAE	MN908947.3	10029	C	T	0.055	0.0031	5.3e-24	0.0054	0.031294051310967	ACC	ORF1ab:nsp4	T492I	C1475T	ACC>ATC	Missense	ORF1ab:nsp4	0.968705948689033
CAMB-79EAE	MN908947.3	11075	T	-	0.0071	0.061	0.0043	1.9e-15	0.0284643775863997	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.971293293069381
CAMB-79EAE	MN908947.3	15517	G	INS	0.005	0.019	0.00024	1.2e-10	0.011934491369914	TGT	ORF1ab:RNA-dependent-RNA-polymerase	.	2049-2050-insfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.987968928931139
CAMB-79EAE	MN908947.3	1605	ATG	-	1	1	0;0;0	0;0;0	0.999491934459545	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.000254032770227359
CAMB-79EAE	MN908947.3	16289	C	T	1	1	0	0	1	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0
CAMB-79EAE	MN908947.3	16369	G	A	1	1	0	0	1	TGT	ORF1ab:helicase	V45I	G133A	GTT>ATT	Missense	ORF1ab:helicase	0
CAMB-79EAE	MN908947.3	16474	A	G	0.028	0.013	7.3e-12	9.1e-07	0.0197846959557754	TAG	ORF1ab:helicase	S80G	A238G	AGT>GGT	Missense	ORF1ab:helicase	0.980215304044225
CAMB-79EAE	MN908947.3	17074	C	T	0.072	0.11	2.6e-33	9.5e-49	0.0901168682023914	ACT	ORF1ab:helicase	L280F	C838T	CTC>TTC	Missense	ORF1ab:helicase	0.909849354860501
CAMB-79EAE	MN908947.3	1989	A	G	0.21	0.12	3e-89	4.7e-51	0.167990919409762	CAG	ORF1ab:nsp2	Q395R	A1184G	CAG>CGG	Missense	ORF1ab:nsp2	0.832009080590238
CAMB-79EAE	MN908947.3	21727	C	T	0.029	0.11	5.1e-13	2.6e-42	0.0628662759722962	TCT	S	F55F	C165T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.937133724027704
CAMB-79EAE	MN908947.3	23561	GGTGCAGGTATATGCGCTAGTTA	-	0.0455217391304348	0.0405652173913044	4.9e-05;0.00011;0.00012;0.00012;0.00011;9.7e-05;6.1e-05;5.2e-05;1.7e-05;2e-06;1.8e-05;6.7e-06;1.5e-05;6.5e-06;2.2e-05;4.6e-05;2.4e-05;2.3e-05;1.6e-07;4e-07;3e-05;2.3e-05;8.7e-08	0.00012;0.00026;0.00026;0.00027;0.00024;0.00024;0.00015;0.00014;5.1e-05;1.3e-05;5.8e-05;2.7e-05;4.3e-05;2.7e-05;6.8e-05;0.00014;7.6e-05;7.5e-05;1.6e-06;2.5e-06;1e-04;8.3e-05;4.8e-07	0.041596130592503	TGG	S	.	1999-2021-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.958904109589041
CAMB-79EAE	MN908947.3	25022	AA	-	0.0145	0.0043	7e-08;1.9e-08	0.00082;0.00025	0.0100813218019879	TAA	S	.	3460-3461-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.990002249493864
CAMB-79EAE	MN908947.3	25717	TATGCTTTAGTCTACTTCTTGCAGAGTATAAACTTTGTAAGAATAATAATGAGGCTTTGGCTTTGCTG	-	0.0445735294117647	3.08823529411765e-05	9e-19;3.6e-19;4.4e-19;4.5e-18;1.7e-18;1.4e-18;1.1e-18;5.6e-18;3e-18;1.8e-18;2.6e-18;1e-17;2.4e-20;7.4e-19;2.4e-18;2.9e-18;1.8e-18;2.3e-18;1.1e-18;3e-18;3.2e-18;7.1e-19;1.2e-18;2.7e-18;1.6e-18;2.9e-18;8.9e-19;1.7e-20;1.2e-19;9.5e-19;5.9e-19;1.2e-20;2.1e-19;6.2e-20;2.9e-22;3.6e-19;1.1e-18;1.1e-18;1.5e-19;1.5e-19;7e-19;5.3e-19;1.7e-19;2.2e-18;6.8e-19;1.1e-18;4.4e-19;2.7e-20;1.2e-19;3.7e-19;3.8e-19;3.5e-20;6.6e-19;4e-19;1.8e-18;8e-19;1.9e-19;1.1e-18;5.8e-19;4.7e-20;2e-19;1.1e-20;5.7e-21;3.1e-18;6.6e-18;4.7e-19;1.3e-19;6.1e-18	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0071;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0317365269461078	TTA	ORF3a	.	325-392-delfrshift	.	no-SNV	GU280_gp03	0.968414779499404
CAMB-79EAE	MN908947.3	274	C	T	0.089	0.031	1.3e-40	1.3e-15	0.0644507378148755	GCC	ORF1ab:leader-protein	S3S	C9T	AGC>AGT	Synonymous	ORF1ab:leader-protein	0.935459830078998
CAMB-79EAE	MN908947.3	28077	G	T	0.015	0.013	3e-05	2.7e-05	0.0137636449928809	CGT	ORF8	V62L	G184T	GTG>TTG	Missense	GU280_gp09	0.986236355007119
CAMB-79EAE	MN908947.3	29160	C	T	1	1	0	0	0.999394673123487	ACT	N	T296I	C887T	ACT>ATT	Missense	GU280_gp10	7.56658595641647e-05
CAMB-79EAE	MN908947.3	422	T	G	1	1	0	0	0.99988597058041	CTT	ORF1ab:leader-protein	L53V	T157G	TTA>GTA	Missense	ORF1ab:leader-protein	0
CAMB-79EBD	MN908947.3	11075	T	-	0.037	0.043	7e-10	4.7e-11	0.0401531071750225	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955081056739718
CAMB-79EBD	MN908947.3	13339	T	C	0.086	0.087	4.4e-39	1.2e-39	0.0866752156679879	ATG	ORF1ab:nsp10	N105N	T315C	AAT>AAC	Synonymous	ORF1ab:nsp10	0.913261638299526
CAMB-79EBD	MN908947.3	14097	C	T	1	1	0	0	0.999071245052427	TCG	ORF1ab:RNA-dependent-RNA-polymerase	F210F	C630T	TTC>TTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000156239150059024
CAMB-79EBD	MN908947.3	14408	C	T	1	1	0	0	0.998455717705196	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000319887046780723
CAMB-79EBD	MN908947.3	23403	A	G	1	1	0	0	0.999683836346857	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.27248179922754e-05
CAMB-79EBD	MN908947.3	241	C	T	1	1	0	0	0.998758843241901	TCG	NA	NA	NA	NA	NA	NA	0.00017065905423855
CAMB-79EBD	MN908947.3	2416	C	T	1	1	0	0	0.999174035565057	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	9.71722864639005e-05
CAMB-79EBD	MN908947.3	2483	A	G	0.012	0.012	8.6e-07	6.5e-07	0.0121710808262621	TAT	ORF1ab:nsp2	I560V	A1678G	ATC>GTC	Missense	ORF1ab:nsp2	0.987657495500129
CAMB-79EBD	MN908947.3	25563	G	T	1	1	0	0	0.999774449657163	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	9.02201371346084e-05
CAMB-79EBD	MN908947.3	26028	C	T	0.15	0.15	2.1e-65	7.2e-65	0.14643188137164	ACC	ORF3a	Y212Y	C636T	TAC>TAT	Synonymous	GU280_gp03	0.85356811862836
CAMB-79EBD	MN908947.3	28001	G	T	0.033	0.034	3.9e-15	1.8e-15	0.0332880732337611	CGT	ORF8	P36P	G108T	CCG>CCT	Synonymous	GU280_gp09	0.966580526477158
CAMB-79EBD	MN908947.3	3037	C	T	1	1	0	0	0.999255712906341	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00028162214354683
CAMB-79EBD	MN908947.3	4987	A	G	0.0099	0.0097	1.8e-06	2e-06	0.00978991923965826	TAG	ORF1ab:nsp3	V756V	A2268G	GTA>GTG	Synonymous	ORF1ab:nsp3	0.990080240982627
CAMB-79EBD	MN908947.3	5052	C	T	0.0075	0.0088	5.7e-05	2.1e-05	0.00823858955346845	CCA	ORF1ab:nsp3	P778L	C2333T	CCA>CTA	Missense	ORF1ab:nsp3	0.991596638655462
CAMB-79EBD	MN908947.3	5536	A	G	0.014	0.012	1.3e-07	9.7e-07	0.0133498686898162	AAC	ORF1ab:nsp3	Q939Q	A2817G	CAA>CAG	Synonymous	ORF1ab:nsp3	0.986504231105924
CAMB-79EBD	MN908947.3	860	G	A	1	1	0	0	0.99947487035862	TGA	ORF1ab:nsp2	E19K	G55A	GAG>AAG	Missense	ORF1ab:nsp2	6.5641205172527e-05
CAMB-79ECC	MN908947.3	10323	A	G	1	1	0	0	0.999719455744144	AAG	ORF1ab:3C-like-proteinase	K90R	A269G	AAG>AGG	Missense	ORF1ab:3C-like-proteinase	0.000280544255856361
CAMB-79ECC	MN908947.3	11075	T	-	0.0069	0.37	0.0033	1.6e-104	0.123931825692838	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.875879325810868
CAMB-79ECC	MN908947.3	14408	C	T	1	1	0	0	0.999733418639369	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000213265088505012
CAMB-79ECC	MN908947.3	21778	G	A	1	1	2.4e-189	0	1	GGA	S	G72G	G216A	GGG>GGA	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-79ECC	MN908947.3	23403	A	G	1	1	0	0	0.999917408271562	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.12958642191984e-05
CAMB-79ECC	MN908947.3	241	C	T	1	1	0	0	0.999626656710846	TCG	NA	NA	NA	NA	NA	NA	0.000373343289154377
CAMB-79ECC	MN908947.3	3037	C	T	1	1	2.7e-148	0	0.999079189686924	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79ECC	MN908947.3	7798	G	A	0.15	0.24	8.4e-35	3e-76	0.213913043478261	AGA	ORF1ab:nsp3	K1693K	G5079A	AAG>AAA	Synonymous	ORF1ab:nsp3	0.786086956521739
CAMB-79EDB	MN908947.3	10702	C	T	0.02	0.023	2.5e-10	1.1e-11	0.0208787475582482	ACA	ORF1ab:3C-like-proteinase	D216D	C648T	GAC>GAT	Synonymous	ORF1ab:3C-like-proteinase	0.979121252441752
CAMB-79EDB	MN908947.3	11074	C	INS	0.091	0.11	2.4e-37	1.1e-42	0.0972109477566319	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.889891063608029
CAMB-79EDB	MN908947.3	11074	C	T	0.012	0.011	6.3e-09	1.9e-07	0.0112143351071826	TCT	ORF1ab:nsp6	F34F	C102T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.889891063608029
CAMB-79EDB	MN908947.3	11083	G	-	0.16	0.16	3.2e-68	8.2e-71	0.158980679369752	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.54669669536535e-05
CAMB-79EDB	MN908947.3	11083	G	T	0.84	0.84	0	0	0.840824252312003	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.54669669536535e-05
CAMB-79EDB	MN908947.3	13505	G	T	0.0014	0.006	0.0073	4.7e-05	0.00306790761806274	TGC	ORF1ab:RNA-dependent-RNA-polymerase	C13F	G38T	TGC>TTC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.996897621509824
CAMB-79EDB	MN908947.3	1431	ATG	-	0.00656666666666667	0.0091	0.00012;0.00015;0.00014	7.8e-05;6.1e-06;1.7e-05	0.00753567420234087	AAT	ORF1ab:nsp2	.	626-628-delinframe	.	no-SNV	ORF1ab:nsp2	0.992911153119093
CAMB-79EDB	MN908947.3	14805	C	T	1	1	0	0	0.997607078595411	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000788365579031331
CAMB-79EDB	MN908947.3	15714	C	T	0.0061	0.009	0.00011	6.4e-06	0.00744221732041815	TCT	ORF1ab:RNA-dependent-RNA-polymerase	L749L	C2247T	CTC>CTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.992212525175026
CAMB-79EDB	MN908947.3	16550	A	G	0.4	0.59	8.6e-49	2.1e-48	0.461077844311377	GAC	ORF1ab:helicase	D105G	A314G	GAC>GGC	Missense	ORF1ab:helicase	0.538922155688623
CAMB-79EDB	MN908947.3	18580	G	A	0.023	0.025	1.2e-11	1e-12	0.0237514836700573	AGT	ORF1ab:3'-to-5'-exonuclease	V181I	G541A	GTC>ATC	Missense	ORF1ab:3'-to-5'-exonuclease	0.976235753576762
CAMB-79EDB	MN908947.3	20284	AT	TC	1	1	5.1e-248;6.1e-246	6.7e-185;1.4e-183	0.994505494505495	CAT	ORF1ab:endoRNAse	.	664-665-mnv	.	no-SNV	ORF1ab:endoRNAse	0
CAMB-79EDB	MN908947.3	24745	C	T	0.014	0.007	9.9e-08	4.2e-05	0.0107378372595172	TCT	S	V1061V	C3183T	GTC>GTT	Synonymous	GU280_gp02, spike glycoprotein	0.989252436438617
CAMB-79EDB	MN908947.3	2480	A	G	1	1	0	0	0.999888913574761	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000111086425238836
CAMB-79EDB	MN908947.3	2558	C	T	1	1	0	0	0.998040466642362	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-79EDB	MN908947.3	26144	G	T	1	1	0	0	0.999732548809842	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000133725595078898
CAMB-79EDB	MN908947.3	27378	GATT	-	0.005	0.0074	0.00029;0.00027;0.00024;0.00028	2.2e-05;2e-05;2e-05;2.3e-05	0.00598141976203127	AGA	ORF6	.	177-180-delfrshift	.	no-SNV	GU280_gp06	0.993918017771922
CAMB-79EDB	MN908947.3	27386	A	-	0.014	0.0067	1.3e-07	0.00012	0.0107765451664025	TAA	ORF6	.	185-185-delfrshift	.	no-SNV	GU280_gp06	0.989136291600634
CAMB-79EDB	MN908947.3	29281	C	T	0.01	0.0073	1.4e-06	2.4e-05	0.00916260974935692	CCA	N	A336A	C1008T	GCC>GCT	Synonymous	GU280_gp10	0.990773613384638
CAMB-79EDB	MN908947.3	29730	C	T	0.014	0.018	9.9e-08	2.4e-09	0.0158220796006596	TCA	NA	NA	NA	NA	NA	NA	0.982573427820119
CAMB-79EDB	MN908947.3	4815	C	T	0.0049	0.0092	0.0015	1.7e-05	0.00658227848101266	TCT	ORF1ab:nsp3	S699F	C2096T	TCT>TTT	Missense	ORF1ab:nsp3	0.993381555153707
CAMB-79EDB	MN908947.3	5770	C	T	0.0044	0.015	0.00047	2.7e-08	0.00850024655411276	ACT	ORF1ab:nsp3	H1017H	C3051T	CAC>CAT	Synonymous	ORF1ab:nsp3	0.991452790757743
CAMB-79EDB	MN908947.3	6374	GATAATCTTGCCTGCGAAGATCTA	-	0.0017875	0.013125	0.041;0.041;0.052;0.05;0.011;0.0082;0.0091;0.0077;0.0083;0.0088;0.0071;0.009;0.0064;0.0092;0.0094;0.0065;0.0079;0.0066;0.0067;0.0058;0.0061;0.0053;0.0038;0.021	1.4e-06;4.9e-07;1.6e-06;1.1e-06;1.8e-07;1.1e-07;1.1e-07;1.1e-08;7.5e-08;8.3e-08;8.3e-08;9.6e-07;4.3e-08;4.4e-07;2.4e-06;1e-07;9.9e-08;1.1e-07;7.5e-08;9.2e-08;6e-08;2.2e-08;1.1e-07;2.4e-07	0.00601346239646176	GGA	ORF1ab:nsp3	.	3655-3678-delinframe	.	no-SNV	ORF1ab:nsp3	0.99334455179716
CAMB-79EDB	MN908947.3	6508	TAATAGTTTAAAAAT	-	0.0112333333333333	0.00362	2.6e-06;1.8e-06;2.8e-05;3e-05;2.3e-05;5e-05;3.2e-05;3.3e-05;1.2e-06;4.3e-06;2e-06;1.2e-06;2.8e-06;3e-06;4.1e-06	0.0012;0.00042;0.0037;0.0044;0.0039;0.0094;0.018;0.012;0.0026;0.008;0.0041;0.0022;0.0027;0.0028;0.0017	0.00838138314401132	ATA	ORF1ab:nsp3	.	3789-3803-delinframe	.	no-SNV	ORF1ab:nsp3	0.992440291488296
CAMB-79EDB	MN908947.3	7435	TTA	-	0.0087	0.0253333333333333	0.0062;0.012;0.097	1.4e-05;4.1e-05;0.00013	0.016188408533132	TTT	ORF1ab:nsp3	.	4716-4718-delinframe	.	no-SNV	ORF1ab:nsp3	0.982833258695328
CAMB-79EDB	MN908947.3	8320	C	T	0.0045	0.012	0.00058	2.8e-07	0.00749635133342179	CCC	ORF1ab:nsp3	P1867P	C5601T	CCC>CCT	Synonymous	ORF1ab:nsp3	0.992437309274247
CAMB-79EDB	MN908947.3	8639	C	T	0.0064	0.0089	5.8e-05	4e-06	0.0073693281431076	ACC	ORF1ab:nsp4	P29S	C85T	CCT>TCT	Missense	ORF1ab:nsp4	0.992184946364366
CAMB-79EDB	MN908947.3	9055	A	-	9e-04	0.012	0.0078	3.9e-07	0.00542427045664788	TAC	ORF1ab:nsp4	.	501-501-delfrshift	.	no-SNV	ORF1ab:nsp4	0.994344462198301
CAMB-79EEA	MN908947.3	10252	C	T	1	1	0	0	0.999589111453518	TCT	ORF1ab:3C-like-proteinase	F66F	C198T	TTC>TTT	Synonymous	ORF1ab:3C-like-proteinase	0
CAMB-79EEA	MN908947.3	10790	C	T	0.12	0.22	1.1e-30	8.9e-40	0.158249158249158	CCA	ORF1ab:3C-like-proteinase	H246Y	C736T	CAT>TAT	Missense	ORF1ab:3C-like-proteinase	0.841750841750842
CAMB-79EEA	MN908947.3	11075	T	-	0.13	0.014	2.3e-32	5.8e-05	0.0706112329550873	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.929245732812053
CAMB-79EEA	MN908947.3	2891	G	A	1	1	0	0	0.999245852187029	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	0.000754147812971342
CAMB-79EEA	MN908947.3	29567	A	G	0.17	0.023	2e-30	2.6e-05	0.11178247734139	TAT	ORF10	I4V	A10G	ATA>GTA	Missense	GU280_gp11	0.88821752265861
CAMB-79EEA	MN908947.3	8254	A	T	1	1	3.3e-252	0	1	TAG	ORF1ab:nsp3	I1845I	A5535T	ATA>ATT	Synonymous	ORF1ab:nsp3	0
CAMB-79EF9	MN908947.3	10252	C	T	1	0.99	0	0	0.995349430730621	TCT	ORF1ab:3C-like-proteinase	F66F	C198T	TTC>TTT	Synonymous	ORF1ab:3C-like-proteinase	0.000113428518765331
CAMB-79EF9	MN908947.3	11074	C	INS	0.029	0.025	8e-07	3.3e-05	0.0272411068815858	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.972635769471492
CAMB-79EF9	MN908947.3	11075	T	-	0.039	0.03	1.6e-09	1.2e-07	0.0346757398376771	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960396294169574
CAMB-79EF9	MN908947.3	1298	G	T	0.0018	0.0072	0.0095	3.4e-05	0.00414530910220565	TGG	ORF1ab:nsp2	G165C	G493T	GGC>TGC	Missense	ORF1ab:nsp2	0.995738195091643
CAMB-79EF9	MN908947.3	1440	G	A	0.99	1	0	0	0.996736596736597	GGC	ORF1ab:nsp2	G212D	G635A	GGC>GAC	Missense	ORF1ab:nsp2	0
CAMB-79EF9	MN908947.3	176	C	T	0.017	0.018	3.8e-09	6e-10	0.0176002289460676	TCT	NA	NA	NA	NA	NA	NA	0.982399771053932
CAMB-79EF9	MN908947.3	22155	ATGGTTA	-	0.000342857142857143	0.00637142857142857	NA;NA;0.0063;NA;NA;NA;NA	2.3e-05;3e-06;2e-04;0.00083;0.00062;0.00071;0.00057	0.00246047295757962	GAT	S	.	593-599-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.995985401459854
CAMB-79EF9	MN908947.3	23386	T	C	0.0099	0.0027	2.7e-06	0.0023	0.00664279487308803	TTG	S	V608V	T1824C	GTT>GTC	Synonymous	GU280_gp02, spike glycoprotein	0.991505580091789
CAMB-79EF9	MN908947.3	2891	G	A	1	1	0	0	0.999889073765946	GGC	ORF1ab:nsp3	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp3	0.000110926234054354
CAMB-79EF9	MN908947.3	6131	A	G	0.0072	0.0094	3.8e-05	8.4e-06	0.00802833530106257	TAA	ORF1ab:nsp3	K1138E	A3412G	AAA>GAA	Missense	ORF1ab:nsp3	0.991971664698937
CAMB-79EF9	MN908947.3	7011	C	T	1	1	4.2e-270	1e-268	1	GCT	ORF1ab:nsp3	A1431V	C4292T	GCT>GTT	Missense	ORF1ab:nsp3	0
CAMB-79EF9	MN908947.3	8254	A	T	1	1	0	0	0.999945610790819	TAG	ORF1ab:nsp3	I1845I	A5535T	ATA>ATT	Synonymous	ORF1ab:nsp3	1.35973022952246e-05
CAMB-79F14	MN908947.3	10232	C	T	1	1	0	0	0.999801103873502	TCG	ORF1ab:3C-like-proteinase	R60C	C178T	CGT>TGT	Missense	ORF1ab:3C-like-proteinase	3.97792252995873e-05
CAMB-79F14	MN908947.3	11075	T	-	0.032	0.039	3.2e-08	7.9e-10	0.0356486884164595	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959673245725303
CAMB-79F14	MN908947.3	13778	AT	-	0.0275	0.029	1e-08;1.4e-08	3e-09;6.6e-09	0.0282734646581692	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.972594330910553
CAMB-79F14	MN908947.3	13780	A	T	0.023	0.022	6.6e-07	9.3e-07	0.0227591175452828	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I105L	A313T	ATA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.970961135913683
CAMB-79F14	MN908947.3	14408	C	T	1	1	0	0	0.997983906780113	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000532888075741158
CAMB-79F14	MN908947.3	1547	A	-	0.018	0.016	6.1e-09	3.1e-08	0.016580865146754	TAG	ORF1ab:nsp2	.	742-742-delfrshift	.	no-SNV	ORF1ab:nsp2	0.900113659156248
CAMB-79F14	MN908947.3	1547	A	G	0.032	0.032	1.7e-14	2.3e-14	0.0316908470950057	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.900113659156248
CAMB-79F14	MN908947.3	1547	A	T	0.05	0.05	5e-22	7.4e-22	0.049943170421876	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.900113659156248
CAMB-79F14	MN908947.3	21304	C	A	0.24	0.18	1.8e-56	5.8e-28	0.22061191626409	ACG	ORF1ab:2'-O-ribose-methyltransferase	R216S	C646A	CGC>AGC	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.77938808373591
CAMB-79F14	MN908947.3	21974	G	T	0.0052	0.0073	3e-04	3.7e-05	0.00610896761370279	TGA	S	D138Y	G412T	GAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.99374488483573
CAMB-79F14	MN908947.3	23403	A	G	1	1	0	0	0.999582616336543	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.39351224691539e-05
CAMB-79F14	MN908947.3	241	C	T	1	1	0	0	0.998844606738368	TCG	NA	NA	NA	NA	NA	NA	9.98488003879839e-05
CAMB-79F14	MN908947.3	27528	A	G	0.0085	0.011	0.00011	4.5e-05	0.00931532370749884	CAT	ORF7a	P45P	A135G	CCA>CCG	Synonymous	GU280_gp07	0.989753143921751
CAMB-79F14	MN908947.3	28795	A	G	0.0064	0.0094	0.00021	1e-05	0.00779742765273312	AAG	N	E174E	A522G	GAA>GAG	Synonymous	GU280_gp10	0.987647374062165
CAMB-79F14	MN908947.3	29242	A	T	0.0084	0.0069	2.2e-05	9.2e-05	0.00770349798320439	AAG	N	E323D	A969T	GAA>GAT	Missense	GU280_gp10	0.981892922480108
CAMB-79F14	MN908947.3	3037	C	T	1	1	0	0	0.999121756487026	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.98003992015968e-05
CAMB-79F14	MN908947.3	4554	C	T	0.0058	0.0077	0.00024	3.3e-05	0.00665722703085391	ACT	ORF1ab:nsp3	T612I	C1835T	ACT>ATT	Missense	ORF1ab:nsp3	0.987838856281545
CAMB-79F23	MN908947.3	10029	C	T	0.013	0.0035	2.5e-07	0.0028	0.00821963533191472	ACC	ORF1ab:nsp4	T492I	C1475T	ACC>ATC	Missense	ORF1ab:nsp4	0.991655192556432
CAMB-79F23	MN908947.3	11074	C	INS	0.091	0.08	8.1e-33	4.6e-27	0.0858442446232318	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.908502918441395
CAMB-79F23	MN908947.3	11083	G	-	0.15	0.16	2.2e-66	8.8e-73	0.158082713041156	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.11263170777841e-05
CAMB-79F23	MN908947.3	11083	G	T	0.85	0.84	0	0	0.841806023788066	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.11263170777841e-05
CAMB-79F23	MN908947.3	14805	C	T	1	1	0	0	0.999912554653342	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	3.74765771392879e-05
CAMB-79F23	MN908947.3	15933	C	T	0.0078	0.0082	1.7e-05	1.1e-05	0.00796043750867322	ACC	ORF1ab:RNA-dependent-RNA-polymerase	Y822Y	C2466T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.99202694690098
CAMB-79F23	MN908947.3	17212	C	T	0.0099	0.018	2.8e-06	9.4e-10	0.0140369306186342	GCC	ORF1ab:helicase	P326S	C976T	CCT>TCT	Missense	ORF1ab:helicase	0.98594247227114
CAMB-79F23	MN908947.3	18512	C	A	1	0.99	0	0	0.996422212237698	CCT	ORF1ab:3'-to-5'-exonuclease	P158H	C473A	CCT>CAT	Missense	ORF1ab:3'-to-5'-exonuclease	0.000166408733130315
CAMB-79F23	MN908947.3	24581	T	C	0.015	0.012	1.2e-05	0.00012	0.013722799451088	ATA	S	Y1007H	T3019C	TAT>CAT	Missense	GU280_gp02, spike glycoprotein	0.98529700058812
CAMB-79F23	MN908947.3	2480	A	G	0.99	1	0	0	0.997407311381903	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-79F23	MN908947.3	2558	C	T	1	1	0	0	0.998772360575237	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.00122763942476324
CAMB-79F23	MN908947.3	25769	G	-	0.009	0.003	1.5e-05	0.0073	0.00658281415305043	AGG	ORF3a	.	377-377-delfrshift	.	no-SNV	GU280_gp03	0.99341718584695
CAMB-79F23	MN908947.3	25771	C	T	0.008	0.0028	3.2e-05	0.0073	0.00596108424249241	GCT	ORF3a	L127F	C379T	CTT>TTT	Missense	GU280_gp03	0.994038915757508
CAMB-79F23	MN908947.3	25806	A	T	0.0028	0.015	0.00079	1.1e-08	0.00785308686722242	CAT	ORF3a	P138P	A414T	CCA>CCT	Synonymous	GU280_gp03	0.991905279690709
CAMB-79F23	MN908947.3	26144	G	T	1	1	0	0	0.999384993849939	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000615006150061501
CAMB-79F23	MN908947.3	28009	T	C	0.016	0.0034	9.4e-08	0.0024	0.00875211744776962	ATT	ORF8	I39T	T116C	ATT>ACT	Missense	GU280_gp09	0.990683229813665
CAMB-79F23	MN908947.3	3902	C	T	0.018	0.014	9.1e-10	7.1e-08	0.0164813000633896	GCC	ORF1ab:nsp3	P395S	C1183T	CCA>TCA	Missense	ORF1ab:nsp3	0.98351869993661
CAMB-79F32	MN908947.3	11075	T	-	0.036	0.042	4.3e-09	3.4e-10	0.0393926924198001	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953868971074876
CAMB-79F32	MN908947.3	14408	C	T	1	1	0	0	0.998825021132713	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000371935756551141
CAMB-79F32	MN908947.3	22112	G	A	1	1	0	0	0.999725175993066	GGG	S	G184S	G550A	GGT>AGT	Missense	GU280_gp02, spike glycoprotein	0.000274824006934021
CAMB-79F32	MN908947.3	23403	A	G	1	1	0	0	0.999731101243829	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000227529716759977
CAMB-79F32	MN908947.3	241	C	T	1	1	0	0	0.998874919637117	TCG	NA	NA	NA	NA	NA	NA	7.14336738338453e-05
CAMB-79F32	MN908947.3	25528	C	T	1	1	0	0	0.999431178257358	GCT	ORF3a	L46F	C136T	CTT>TTT	Missense	GU280_gp03	0.000329916610732529
CAMB-79F32	MN908947.3	28651	C	T	0.012	0.015	5e-07	3.4e-08	0.0140148585624224	ACA	N	N126N	C378T	AAC>AAT	Synonymous	GU280_gp10	0.985797651690923
CAMB-79F32	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999385908972815	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	2.61089788778361e-05
CAMB-79F32	MN908947.3	3037	C	T	1	1	0	0	0.999198917156985	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000110494185243502
CAMB-79F32	MN908947.3	4039	C	T	0.0097	0.008	5.2e-06	2.9e-05	0.00877671561069336	ACA	ORF1ab:nsp3	D440D	C1320T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.991199563536305
CAMB-79F32	MN908947.3	5605	G	A	1	1	0	0	0.998892210571043	AGA	ORF1ab:nsp3	K962K	G2886A	AAG>AAA	Synonymous	ORF1ab:nsp3	3.0350395313899e-05
CAMB-79F32	MN908947.3	6573	C	T	1	1	0	0	0.999846484494934	TCT	ORF1ab:nsp3	S1285F	C3854T	TCT>TTT	Missense	ORF1ab:nsp3	0.000153515505066012
CAMB-79F32	MN908947.3	6813	C	T	0.015	0.01	3e-08	2.8e-06	0.0129667831431819	ACT	ORF1ab:nsp3	T1365I	C4094T	ACT>ATT	Missense	ORF1ab:nsp3	0.986696417294658
CAMB-79F41	MN908947.3	14408	C	T	1	1	0	0	0.997816259681419	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00205108319642438
CAMB-79F41	MN908947.3	15720	C	T	1	1	0	0	0.999913082108435	ACG	ORF1ab:RNA-dependent-RNA-polymerase	D751D	C2253T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-79F41	MN908947.3	16289	C	T	1	1	0	0	0.998641304347826	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0
CAMB-79F41	MN908947.3	16397	G	T	0.0089	0.002	7e-06	0.0086	0.00679686827841349	GGT	ORF1ab:helicase	G54V	G161T	GGT>GTT	Missense	ORF1ab:helicase	0.993203131721586
CAMB-79F41	MN908947.3	16439	T	C	0.011	0.017	1e-05	1.2e-07	0.0124110541121959	ATG	ORF1ab:helicase	M68T	T203C	ATG>ACG	Missense	ORF1ab:helicase	0.987588945887804
CAMB-79F41	MN908947.3	20578	G	T	1	1	0	0	1	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	0
CAMB-79F41	MN908947.3	21439	T	C	0.0076	0.014	2e-04	1.4e-06	0.0105401844532279	GTC	ORF1ab:2'-O-ribose-methyltransferase	S261P	T781C	TCT>CCT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.989459815546772
CAMB-79F41	MN908947.3	21953	TG	-	0.0077	0.00835	3.8e-05;0.00067	2.5e-05;0.00047	0.00792985131528784	CTG	S	.	391-392-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.991116947319635
CAMB-79F41	MN908947.3	23403	A	G	1	1	0	0	0.999925266662137	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.39696990284666e-05
CAMB-79F41	MN908947.3	23898	AAG	-	0.00863333333333333	0.002588	1.5e-05;6e-05;4.1e-05	NA;NA;0.00014	0.00555338825527228	CAA	S	.	2336-2338-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.991929698708752
CAMB-79F41	MN908947.3	241	C	T	0.99	1	0	0	0.993835880313343	TCG	NA	NA	NA	NA	NA	NA	0.000149822353495141
CAMB-79F41	MN908947.3	24413	G	-	0.009	0.0052	3.2e-05	0.00076	0.00766072194643623	TGT	S	.	2851-2851-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.992339278053564
CAMB-79F41	MN908947.3	24518	A	-	0.004	0.013	0.0079	3e-06	0.00730575575081449	CAA	S	.	2956-2956-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.992694244249186
CAMB-79F41	MN908947.3	25429	G	T	1	1	0	0	0.999863763592678	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	6.1925639691858e-05
CAMB-79F41	MN908947.3	26486	TA	-	0.0115	0.013	5.5e-07;6.6e-07	1.2e-07;1.1e-07	0.0122960979721355	TTA	NA	NA	NA	NA	NA	NA	0.987555599980009
CAMB-79F41	MN908947.3	28514	G	C	0.029	0.021	8.5e-14	1.1e-10	0.0256528986849417	AGA	N	D81H	G241C	GAT>CAT	Missense	GU280_gp10	0.974069272087424
CAMB-79F41	MN908947.3	3037	C	T	1	1	0	0	0.999564080209241	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000108979947689625
CAMB-79F41	MN908947.3	377	G	T	0.0082	0.0027	1.1e-05	0.0026	0.00641042413459274	GGT	ORF1ab:leader-protein	V38F	G112T	GTC>TTC	Missense	ORF1ab:leader-protein	0.993511080876004
CAMB-79F50	MN908947.3	11075	T	-	0.037	0.042	2.2e-09	2.1e-10	0.0397611685246969	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955417446496867
CAMB-79F50	MN908947.3	13064	T	C	0.0096	0.0094	3.8e-06	4e-06	0.00951466081149078	ATT	ORF1ab:nsp10	L14L	T40C	TTA>CTA	Synonymous	ORF1ab:nsp10	0.99038622813839
CAMB-79F50	MN908947.3	14408	C	T	1	1	0	0	0.998759497596527	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000474309742504538
CAMB-79F50	MN908947.3	14932	C	T	0.016	0.016	1.6e-08	1.8e-08	0.0159746444327647	CCT	ORF1ab:RNA-dependent-RNA-polymerase	L489L	C1465T	CTA>TTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.983818306337299
CAMB-79F50	MN908947.3	23403	A	G	1	1	0	0	0.999630022269813	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.96093888963991e-05
CAMB-79F50	MN908947.3	24062	A	G	0.01	0.011	2.8e-06	1.5e-06	0.0103428421879089	CAT	S	I834V	A2500G	ATC>GTC	Missense	GU280_gp02, spike glycoprotein	0.989552473174562
CAMB-79F50	MN908947.3	241	C	T	1	1	0	0	0.998827916888652	TCG	NA	NA	NA	NA	NA	NA	0.000173148641449121
CAMB-79F50	MN908947.3	2416	C	T	1	1	0	0	0.998497531659154	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	5.36595836016313e-05
CAMB-79F50	MN908947.3	25563	G	T	1	1	0	0	0.999771164291994	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	8.43078924231293e-05
CAMB-79F50	MN908947.3	27697	C	T	0.02	0.023	1.4e-08	2e-09	0.0215195432586737	TCT	ORF7a	L102F	C304T	CTT>TTT	Missense	GU280_gp07	0.976943346508564
CAMB-79F50	MN908947.3	28316	A	G	0.0067	0.0068	4.3e-05	4.3e-05	0.00675945924326054	CAT	N	I15V	A43G	ATT>GTT	Missense	GU280_gp10	0.993170546356292
CAMB-79F50	MN908947.3	3037	C	T	1	1	0	0	0.999256616116563	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000130092179601546
CAMB-79F50	MN908947.3	3177	C	T	0.018	0.018	3e-09	2.6e-09	0.0180804556210645	CCT	ORF1ab:nsp3	P153L	C458T	CCT>CTT	Missense	ORF1ab:nsp3	0.981831307905186
CAMB-79F50	MN908947.3	5773	T	C	0.02	0.022	2e-10	5.3e-11	0.0208139239434234	ATA	ORF1ab:nsp3	Y1018Y	T3054C	TAT>TAC	Synonymous	ORF1ab:nsp3	0.979186076056577
CAMB-79F6F	MN908947.3	10076	T	C	0.03	0.026	3.3e-14	6.5e-13	0.0282237236306535	ATT	ORF1ab:3C-like-proteinase	F8L	T22C	TTC>CTC	Missense	ORF1ab:3C-like-proteinase	0.971342383107089
CAMB-79F6F	MN908947.3	11075	T	-	0.034	0.04	1.6e-08	4.6e-10	0.0368824887725231	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959262895689013
CAMB-79F6F	MN908947.3	14408	C	T	1	1	0	0	0.99919157170501	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00035261234143195
CAMB-79F6F	MN908947.3	15720	C	T	1	1	0	0	0.999813927524771	ACG	ORF1ab:RNA-dependent-RNA-polymerase	D751D	C2253T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	3.48885891054566e-05
CAMB-79F6F	MN908947.3	16289	C	T	1	1	0	0	0.999514865895072	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	9.24064961766812e-05
CAMB-79F6F	MN908947.3	17615	A	G	0.0073	0.0067	4.2e-05	4.8e-05	0.00707637605884198	AAG	ORF1ab:helicase	K460R	A1379G	AAG>AGG	Missense	ORF1ab:helicase	0.992775473210862
CAMB-79F6F	MN908947.3	20578	G	T	1	1	0	0	0.999638472783288	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	3.14371492793034e-05
CAMB-79F6F	MN908947.3	23403	A	G	1	1	0	0	0.999564465509511	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.32639467110741e-05
CAMB-79F6F	MN908947.3	241	C	T	1	1	0	0	0.998460259292335	TCG	NA	NA	NA	NA	NA	NA	0.000297683203481867
CAMB-79F6F	MN908947.3	25429	G	T	1	1	0	0	0.999300991014352	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	6.76460308691388e-05
CAMB-79F6F	MN908947.3	27925	C	T	0.0074	0.01	0.00013	7.9e-06	0.00842654735272185	ACA	ORF8	T11I	C32T	ACA>ATA	Missense	GU280_gp09	0.991424310216257
CAMB-79F6F	MN908947.3	3037	C	T	1	1	0	0	0.999348655438727	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.58295338233926e-05
CAMB-79F6F	MN908947.3	745	C	A	0.051	0.057	2e-23	2.9e-26	0.0531865333250512	ACT	ORF1ab:leader-protein	N160K	C480A	AAC>AAA	Missense	ORF1ab:leader-protein	0.946580532952357
CAMB-79F6F	MN908947.3	9438	C	T	0.26	0.27	2.7e-125	1.1e-129	0.267366307001654	ACA	ORF1ab:nsp4	T295I	C884T	ACA>ATA	Missense	ORF1ab:nsp4	0.732358037331653
CAMB-79F6F	MN908947.3	9474	C	T	0.02	0.026	4.3e-10	1.7e-12	0.0226737051249586	GCT	ORF1ab:nsp4	A307V	C920T	GCT>GTT	Missense	ORF1ab:nsp4	0.977209420106356
CAMB-79F6F	MN908947.3	9479	G	T	0.064	0.064	3.3e-28	1.2e-28	0.063983155338885	TGG	ORF1ab:nsp4	G309C	G925T	GGT>TGT	Missense	ORF1ab:nsp4	0.935959937022213
CAMB-79F6F	MN908947.3	9491	C	T	0.0081	0.0084	3.9e-05	2.6e-05	0.00826740506329114	TCA	ORF1ab:nsp4	H313Y	C937T	CAT>TAT	Missense	ORF1ab:nsp4	0.991653481012658
CAMB-79F6F	MN908947.3	9737	A	G	0.018	0.017	2.2e-09	1.6e-09	0.0175932200482077	TAG	ORF1ab:nsp4	S395G	A1183G	AGT>GGT	Missense	ORF1ab:nsp4	0.982372468454867
CAMB-79F6F	MN908947.3	9866	C	T	0.052	0.056	1.2e-23	1.7e-25	0.053846784104875	TCT	ORF1ab:nsp4	L438F	C1312T	CTT>TTT	Missense	ORF1ab:nsp4	0.94608766898812
CAMB-79F7E	MN908947.3	1059	C	T	1	1	0	0	0.999985121040337	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	1.48789596631404e-05
CAMB-79F7E	MN908947.3	10963	TAC	-	0.00386666666666667	0.012	0.00074;0.001;0.00087	2.7e-07;3.3e-07;2.7e-07	0.00678654579679992	TTA	ORF1ab:3C-like-proteinase	.	909-911-delinframe	.	no-SNV	ORF1ab:3C-like-proteinase	0.993185940487279
CAMB-79F7E	MN908947.3	11075	T	-	0.029	0.012	2e-07	0.00045	0.0217916380716406	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.972637902298594
CAMB-79F7E	MN908947.3	13665	C	T	0.016	0.003	3e-09	0.0025	0.0105352321456933	ACA	ORF1ab:RNA-dependent-RNA-polymerase	H66H	C198T	CAC>CAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.989411826989253
CAMB-79F7E	MN908947.3	13778	AT	-	0.0175	0.0185	1.7e-06;2.5e-06	1.1e-06;1.3e-06	0.0180093459579607	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.982577401072936
CAMB-79F7E	MN908947.3	14408	C	T	0.99	1	0	0	0.99675792134075	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000403965072558342
CAMB-79F7E	MN908947.3	1547	A	-	0.0022	0.023	0.0029	1.4e-10	0.0121059844677935	TAG	ORF1ab:nsp2	.	742-742-delfrshift	.	no-SNV	ORF1ab:nsp2	0.941297396071265
CAMB-79F7E	MN908947.3	1547	A	G	0.013	0.0094	1.1e-06	2.2e-05	0.011192325262677	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.941297396071265
CAMB-79F7E	MN908947.3	1547	A	T	0.042	0.025	8.9e-18	1.4e-11	0.0342622201918684	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.941297396071265
CAMB-79F7E	MN908947.3	18954	T	C	0.0055	0.0072	0.00015	2.6e-05	0.0062992125984252	TTA	ORF1ab:3'-to-5'-exonuclease	I305I	T915C	ATT>ATC	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.993688811712224
CAMB-79F7E	MN908947.3	19254	GC	-	0.009	0.0027	4e-06;3.5e-06	NA;0.00011	0.00592349310147647	TGC	ORF1ab:3'-to-5'-exonuclease	.	1215-1216-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.995324720721246
CAMB-79F7E	MN908947.3	19979	C	A	0.0045	0.019	0.0016	6.8e-07	0.010989010989011	ACT	ORF1ab:endoRNAse	T120N	C359A	ACT>AAT	Missense	ORF1ab:endoRNAse	0.988165680473373
CAMB-79F7E	MN908947.3	21741	CCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGA	-	0.0234615384615385	0.0162564102564103	4.1e-05;6.2e-05;8e-05;6.8e-05;0.00015;0.00016;9.2e-05;1e-04;8.9e-05;0.00014;0.00011;6.6e-05;7.5e-05;7.5e-05;8.2e-05;8.9e-05;7.8e-05;7e-05;7.2e-05;5.5e-05;7.3e-05;6.7e-05;4.4e-05;2.1e-05;1e-04;4.6e-05;8.5e-05;9.1e-05;7.5e-05;4.8e-05;3.5e-05;3.4e-05;6e-05;8.2e-05;6e-05;4.1e-05;6.4e-05;7.6e-05;7.1e-05	0.00078;0.001;0.0012;0.0011;0.0018;0.002;0.0014;0.0016;0.0014;0.0019;0.0015;0.0011;0.0012;0.0012;0.0012;0.0013;0.0012;0.0011;0.0012;0.00097;0.0012;0.0011;0.00094;0.00069;0.0015;0.00093;0.0014;0.0014;0.0013;0.001;0.00081;0.00079;0.0011;0.0013;0.0011;0.00084;0.0012;0.0012;0.0012	0.0201827875095202	TCC	S	.	179-217-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.979938368656059
CAMB-79F7E	MN908947.3	21789	C	T	0.0057	0.0097	0.00018	4.1e-06	0.00740979381443299	ACT	S	T76I	C227T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.992590206185567
CAMB-79F7E	MN908947.3	22304	TAT	-	0.00723333333333333	0.00343333333333333	2.9e-05;5.4e-05;0.00026	0.00052;0.00096;NA	0.00745955032569868	TTA	S	.	742-744-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.993405776910932
CAMB-79F7E	MN908947.3	23403	A	G	1	1	0	0	0.998087484934433	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	1.44340759665418e-05
CAMB-79F7E	MN908947.3	241	C	T	1	1	0	0	0.999865956234711	TCG	NA	NA	NA	NA	NA	NA	5.02664119835126e-05
CAMB-79F7E	MN908947.3	24368	G	T	1	1	0	0	0.999785829020168	AGA	S	D936Y	G2806T	GAC>TAC	Missense	GU280_gp02, spike glycoprotein	0.000107085489916116
CAMB-79F7E	MN908947.3	25563	G	T	1	1	0	0	0.999729733049962	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000122848613653395
CAMB-79F7E	MN908947.3	29241	AA	-	0.00535	0.00655	0.00041;0.00059	3.7e-05;0.00067	0.00595185479831462	GAA	N	.	968-969-delfrshift	.	no-SNV	GU280_gp10	0.993097114416069
CAMB-79F7E	MN908947.3	29242	A	G	0.015	0.0055	2e-08	0.00029	0.0102866186038333	AAG	N	E323E	A969G	GAA>GAG	Synonymous	GU280_gp10	0.977697673055507
CAMB-79F7E	MN908947.3	29242	A	T	0.0048	0.0088	6e-04	1e-05	0.00679913252447102	AAG	N	E323D	A969T	GAA>GAT	Missense	GU280_gp10	0.977697673055507
CAMB-79F7E	MN908947.3	29491	A	T	0.0024	0.012	0.0083	3.6e-05	0.00730207532667179	AAT	N	Q406H	A1218T	CAA>CAT	Missense	GU280_gp10	0.992697924673328
CAMB-79F7E	MN908947.3	3037	C	T	1	1	0	0	0.999612665827443	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.84167715696717e-05
CAMB-79F7E	MN908947.3	462	A	G	0.009	0.0056	6.7e-06	0.00021	0.00764322398796452	CAG	ORF1ab:leader-protein	Q66R	A197G	CAG>CGG	Missense	ORF1ab:leader-protein	0.988604333465908
CAMB-79F7E	MN908947.3	723	C	T	0.0024	0.012	0.0023	1.5e-07	0.00701141705842848	CCT	ORF1ab:leader-protein	P153L	C458T	CCT>CTT	Missense	ORF1ab:leader-protein	0.992948287441236
CAMB-79F7E	MN908947.3	729	A	-	0.0066	0.0066	3.4e-05	3e-05	0.00659259842933312	GAA	ORF1ab:leader-protein	.	464-464-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.993302340241116
CAMB-79F7E	MN908947.3	7623	TTA	-	0.0017	0.00996666666666667	NA;NA;0.0077	2.2e-05;4.4e-05;0.00022	0.00426603618421053	GTT	ORF1ab:nsp3	.	4904-4906-delinframe	.	no-SNV	ORF1ab:nsp3	0.995733963815789
CAMB-79F7E	MN908947.3	7927	AA	-	0.00225	0.00775	0.036;0.0052	0.00039;2.3e-05	0.00457905770716098	CAA	ORF1ab:nsp3	.	5208-5209-delfrshift	.	no-SNV	ORF1ab:nsp3	0.995380566149218
CAMB-79F7E	MN908947.3	8140	C	T	0.0036	0.018	0.0032	2.2e-09	0.00949670461354104	CCT	ORF1ab:nsp3	S1807S	C5421T	TCC>TCT	Synonymous	ORF1ab:nsp3	0.990413421210306
CAMB-79F7E	MN908947.3	9052	A	G	0.0066	0.02	0.00013	2.2e-10	0.0126124662347422	CAG	ORF1ab:nsp4	P166P	A498G	CCA>CCG	Synonymous	ORF1ab:nsp4	0.987346913906209
CAMB-79F8D	MN908947.3	10834	C	T	0.021	0.02	1.1e-10	3e-10	0.0205741626794258	CCG	ORF1ab:3C-like-proteinase	A260A	C780T	GCC>GCT	Synonymous	ORF1ab:3C-like-proteinase	0.979369546861807
CAMB-79F8D	MN908947.3	11074	C	INS	0.14	0.11	2e-71	6.7e-49	0.127862334369899	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.8668666842974
CAMB-79F8D	MN908947.3	11083	G	-	0.14	0.19	7.1e-58	1e-84	0.159843926750496	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.45913733462301e-05
CAMB-79F8D	MN908947.3	11083	G	T	0.86	0.81	0	0	0.83998393363608	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.45913733462301e-05
CAMB-79F8D	MN908947.3	1302	C	T	0.03	0.0046	3.9e-15	0.00048	0.017447298366789	ACT	ORF1ab:nsp2	T166I	C497T	ACT>ATT	Missense	ORF1ab:nsp2	0.982552701633211
CAMB-79F8D	MN908947.3	13119	C	T	0.0073	0.012	3.6e-05	2.9e-07	0.00933310022996544	GCT	ORF1ab:nsp10	A32V	C95T	GCT>GTT	Missense	ORF1ab:nsp10	0.99065345149881
CAMB-79F8D	MN908947.3	14805	C	T	1	1	0	0	0.998108237547893	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000311302681992337
CAMB-79F8D	MN908947.3	2480	A	G	1	1	0	0	0.999924064089908	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	7.59359100918825e-05
CAMB-79F8D	MN908947.3	25096	C	T	0.07	0.088	4.2e-31	2.2e-39	0.077790964950498	ACA	S	N1178N	C3534T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.922103871520214
CAMB-79F8D	MN908947.3	25502	T	G	0.065	0.07	3.5e-29	9.6e-32	0.0669762813070161	ATA	ORF3a	I37R	T110G	ATA>AGA	Missense	GU280_gp03	0.932415547078012
CAMB-79F8D	MN908947.3	2558	C	T	1	1	0	0	0.99961527700056	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000384722999440403
CAMB-79F8D	MN908947.3	26144	G	T	1	1	0	0	0.999326825984517	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000168293503870751
CAMB-79F8D	MN908947.3	26681	C	T	0.086	0.077	1.2e-37	2.7e-34	0.0818830457925931	TCC	M	F53F	C159T	TTC>TTT	Synonymous	GU280_gp05	0.918088640567783
CAMB-79F8D	MN908947.3	27689	C	T	1	0.99	0	0	0.996900826446281	CCA	ORF7a	P99L	C296T	CCA>CTA	Missense	GU280_gp07	0
CAMB-79F8D	MN908947.3	29414	G	A	1	1	0	0	0.999148090302428	AGC	N	A381T	G1141A	GCC>ACC	Missense	GU280_gp10	0
CAMB-79F8D	MN908947.3	7618	T	C	0.0096	0.016	4.2e-06	6.1e-09	0.0125980687990344	ATT	ORF1ab:nsp3	N1633N	T4899C	AAT>AAC	Synonymous	ORF1ab:nsp3	0.987351639509153
CAMB-79F8D	MN908947.3	7990	A	G	0.0084	0.016	1.1e-05	5.5e-09	0.0116299910385343	CAT	ORF1ab:nsp3	A1757A	A5271G	GCA>GCG	Synonymous	ORF1ab:nsp3	0.988270437120382
CAMB-79F8D	MN908947.3	8425	A	T	0.0059	0.0077	9.9e-05	1.6e-05	0.00668967348022299	CAT	ORF1ab:nsp3	S1902S	A5706T	TCA>TCT	Synonymous	ORF1ab:nsp3	0.993151048579772
CAMB-79F8D	MN908947.3	959	C	T	1	1	0	0	0.999181268780175	CCG	ORF1ab:nsp2	R52C	C154T	CGT>TGT	Missense	ORF1ab:nsp2	0.000801850163746244
CAMB-79F8D	MN908947.3	9615	C	T	1	1	0	0	0.99996467554488	ACT	ORF1ab:nsp4	T354I	C1061T	ACT>ATT	Missense	ORF1ab:nsp4	3.53244551202798e-05
CAMB-79F9C	MN908947.3	1059	C	T	1	1	0	0	0.999863882612365	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	8.16704325810579e-05
CAMB-79F9C	MN908947.3	11075	T	-	0.038	0.046	1.5e-09	1.3e-11	0.0410863418162688	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.94238179785625
CAMB-79F9C	MN908947.3	14408	C	T	1	1	0	0	0.999457197137429	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000342822860571086
CAMB-79F9C	MN908947.3	23403	A	G	1	1	0	0	0.999946100361128	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.69498194362098e-05
CAMB-79F9C	MN908947.3	241	C	T	1	1	0	0	0.999803459119497	TCG	NA	NA	NA	NA	NA	NA	0.000122838050314465
CAMB-79F9C	MN908947.3	25550	T	-	0.023	0.016	1.3e-06	3.2e-05	0.0202528181180616	CTT	ORF3a	.	158-158-delfrshift	.	no-SNV	GU280_gp03	0.979610338516276
CAMB-79F9C	MN908947.3	25550	TTGCTGT	-	0.0214285714285714	0.00232714285714286	1.3e-06;2.9e-06;7e-07;5.1e-06;4.5e-06;1.1e-05;1.8e-11	3.2e-05;NA;NA;NA;NA;NA;0.5	0.0126211956438495	CTT	ORF3a	.	158-164-delfrshift	.	no-SNV	GU280_gp03	0.979610338516276
CAMB-79F9C	MN908947.3	25563	G	T	1	1	0	0	0.999863364645602	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	5.12382578992314e-05
CAMB-79F9C	MN908947.3	26776	CTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0458095238095238	0.0317160476190476	2.8e-05;1.5e-05;5.2e-05;0.00025;1.4e-08;3.8e-11;4.4e-09;6.7e-09;3.8e-08;3.6e-10;3.6e-09;7.8e-08;7.8e-08;1.8e-08;2.9e-08;1.9e-08;8.8e-08;3.8e-08;5.1e-08;1.3e-07;3e-08;1e-07;6.1e-08;5.6e-08;2.2e-08;1.1e-07;3.5e-08;6.1e-08;4.9e-08;2e-08;8.3e-08;4.2e-08;1.8e-08;3.6e-08;9.1e-08;7.3e-08;2.8e-08;7.3e-08;1.6e-08;4.2e-08;2.1e-08;0.00066	NA;NA;NA;NA;NA;NA;NA;NA;NA;7.4e-08;1e-07;9.3e-07;8.9e-07;3.4e-07;5e-07;4.5e-07;8.3e-07;5.5e-07;6.9e-07;1.2e-06;4.4e-07;1.1e-06;7e-07;6.5e-07;3.8e-07;1.1e-06;4.5e-07;7.6e-07;6e-07;3.2e-07;8.4e-07;5.3e-07;6.5e-07;4.4e-07;8.9e-07;6.3e-07;2.7e-07;7.9e-07;2.2e-07;4.9e-07;3.4e-07;1.5e-05	0.0440727314246568	GCT	M	.	254-295-delinframe	.	no-SNV	GU280_gp05	0.975706767837474
CAMB-79F9C	MN908947.3	3037	C	T	1	1	0	0	0.999278499278499	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79FAB	MN908947.3	11074	C	INS	0.026	0.021	2.2e-05	0.00039	0.0236262498072658	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.975519789356327
CAMB-79FAB	MN908947.3	11075	T	-	0.034	0.034	1.1e-08	1e-08	0.0342881037006063	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960395448164631
CAMB-79FAB	MN908947.3	14028	G	T	0.017	0.015	2.2e-09	1.9e-08	0.016218094468323	TGC	ORF1ab:RNA-dependent-RNA-polymerase	M187I	G561T	ATG>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.983698813291737
CAMB-79FAB	MN908947.3	14408	C	T	1	1	0	0	0.998078464316406	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000511765785077682
CAMB-79FAB	MN908947.3	14430	G	T	0.011	0.011	9.8e-07	5.3e-07	0.0110854417408801	TGA	ORF1ab:RNA-dependent-RNA-polymerase	V321V	G963T	GTG>GTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.988905242761859
CAMB-79FAB	MN908947.3	23403	A	G	1	1	0	0	0.999296361182113	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.58999396881013e-05
CAMB-79FAB	MN908947.3	241	C	T	1	1	0	0	0.998701986087307	TCG	NA	NA	NA	NA	NA	NA	0.000176429075511644
CAMB-79FAB	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999395023409964	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	5.85223116313094e-05
CAMB-79FAB	MN908947.3	29766	G	C	0.022	0.02	1.9e-10	2.8e-09	0.0211595027991271	TGA	NA	NA	NA	NA	NA	NA	0.978698168706708
CAMB-79FAB	MN908947.3	3037	C	T	1	1	0	0	0.999177441328432	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	2.5704958486492e-05
CAMB-79FAB	MN908947.3	815	C	T	0.01	0.0099	4.8e-06	4.8e-06	0.0100058017583791	TCG	ORF1ab:nsp2	R4C	C10T	CGC>TGC	Missense	ORF1ab:nsp2	0.989940643548891
CAMB-79FBA	MN908947.3	11075	T	-	0.068	0.013	2.4e-16	0.00029	0.0414907679843077	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955268432049806
CAMB-79FBA	MN908947.3	14408	C	T	1	1	0	0	0.99946270469783	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000327049314364473
CAMB-79FBA	MN908947.3	14741	C	T	0.65	0.64	0	0	0.647647502082149	TCT	ORF1ab:RNA-dependent-RNA-polymerase	S425F	C1274T	TCT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.352127758021231
CAMB-79FBA	MN908947.3	17010	C	T	0.32	0.35	1.2e-164	6.4e-180	0.33651316831997	TCT	ORF1ab:helicase	I258I	C774T	ATC>ATT	Synonymous	ORF1ab:helicase	0.663423446265014
CAMB-79FBA	MN908947.3	187	A	G	0.56	0.6	0	0	0.574784325953643	CAG	NA	NA	NA	NA	NA	NA	0.425181027613207
CAMB-79FBA	MN908947.3	1995	CACTGAGACTCAT	TCACTGAGACTCA	0.0105	0.000353846153846154	1.2e-06;3.3e-07;7.8e-07;1.4e-06;8.4e-07;5.2e-07;1.2e-06;1e-06;5.8e-07;2.2e-06;2.5e-06;2.6e-07;2.2e-07	NA;NA;NA;NA;0.00077;NA;NA;NA;0.067;NA;NA;NA;NA	0.00509060056966244	TCA	ORF1ab:nsp2	.	1190-1202-mnv	.	no-SNV	ORF1ab:nsp2	0.994948894699311
CAMB-79FBA	MN908947.3	19961	C	T	0.29	0.34	2e-82	1.5e-104	0.314720812182741	ACG	ORF1ab:endoRNAse	T114M	C341T	ACG>ATG	Missense	ORF1ab:endoRNAse	0.685279187817259
CAMB-79FBA	MN908947.3	23323	TACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGATGTTA	-	0.00654302325581395	6.31627906976744e-05	0.00054;6.9e-05;6.8e-05;4.9e-05;8.1e-05;6.7e-05;2.1e-05;6e-05;0.00017;3.5e-05;5.1e-05;7.5e-05;0.00027;2.8e-05;2.7e-05;2.6e-05;7.9e-05;5.9e-05;5.9e-05;5.9e-05;4.5e-05;6e-05;6e-05;4.8e-05;4.7e-05;4.5e-05;8.4e-05;5.9e-05;6.4e-05;5.1e-05;6.5e-05;7.6e-05;3.6e-05;3.4e-05;3.4e-05;6.6e-05;6e-05;5.7e-05;7.7e-05;4e-05;5.3e-05;6.8e-05;2e-05;3.2e-05;6.3e-05;7.8e-05;2.9e-05;1.7e-05;2.6e-05;2.7e-05;6.3e-05;2.5e-05;4.5e-05;6.8e-05;1.7e-05;3.4e-05;1.7e-05;7.8e-05;6.5e-05;2.3e-05;7e-05;6e-05;1.7e-05;7e-05;9e-05;8.3e-05;1e-04;0.00017;5.3e-05;6.4e-05;5.9e-05;8.9e-05;7e-05;3e-05;4.7e-05;7.5e-05;8.8e-05;4.5e-05;7.9e-05;6.7e-05;0.00055;0.00011;1e-04;8e-05;8.2e-05;8.6e-05	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.46;NA;NA;NA;0.45;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.001;NA;NA;NA;NA;NA	0.00333851218880627	TTA	S	.	1761-1846-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.99625639413597
CAMB-79FBA	MN908947.3	23888	A	-	0.016	0.0072	8.6e-07	0.0022	0.0120235004782074	CAA	S	.	2326-2326-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.987566607460036
CAMB-79FBA	MN908947.3	241	C	T	1	1	0	0	0.997711353075803	TCG	NA	NA	NA	NA	NA	NA	0.00220195575282613
CAMB-79FBA	MN908947.3	24867	G	-	0.0021	0.0075	0.0082	2.9e-05	0.00451933940719729	TGG	S	.	3305-3305-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.995348445876103
CAMB-79FBA	MN908947.3	28881	GGG	AAC	0.31	0.376666666666667	2.5e-133;2.4e-150;6.6e-162	1.8e-168;7.9e-182;1.7e-191	0.340934460213682	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.685709554562014
CAMB-79FBA	MN908947.3	29281	C	T	0.46	0.46	6.8e-254	5e-251	0.457911832946636	CCA	N	A336A	C1008T	GCC>GCT	Synonymous	GU280_gp10	0.54199535962877
CAMB-79FBA	MN908947.3	3037	C	T	1	0.99	0	0	0.995529241179314	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000120831319478009
CAMB-79FBA	MN908947.3	6433	C	T	0.0064	0.0065	3.6e-05	3.1e-05	0.00645695978625237	CCA	ORF1ab:nsp3	T1238T	C3714T	ACC>ACT	Synonymous	ORF1ab:nsp3	0.993530670558985
CAMB-79FBA	MN908947.3	7623	TTA	-	0.01	0.0084	1.5e-05;3.1e-05;0.00016	0.00015;0.00023;0.00082	0.0097182523478971	GTT	ORF1ab:nsp3	.	4904-4906-delinframe	.	no-SNV	ORF1ab:nsp3	0.990281747652103
CAMB-79FBA	MN908947.3	8947	C	T	0.36	0.32	7.9e-188	8e-162	0.340799522163915	ACA	ORF1ab:nsp4	N131N	C393T	AAC>AAT	Synonymous	ORF1ab:nsp4	0.659186256524027
CAMB-79FC9	MN908947.3	14408	C	T	1	1	0	0	0.999224004138645	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000387997930677703
CAMB-79FC9	MN908947.3	18636	G	A	1	1	0	0	0.999581064097193	TGA	ORF1ab:3'-to-5'-exonuclease	V199V	G597A	GTG>GTA	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.000174556626169529
CAMB-79FC9	MN908947.3	21123	G	T	0.35	0.78	3.4e-152	0	0.566136413161909	GGT	ORF1ab:2'-O-ribose-methyltransferase	G155G	G465T	GGG>GGT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.433863586838091
CAMB-79FC9	MN908947.3	23403	A	G	1	1	0	0	0.999934961464668	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.25192676660922e-05
CAMB-79FC9	MN908947.3	241	C	T	1	1	0	0	0.99962116428842	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-79FC9	MN908947.3	28253	C	T	0.6	0.63	0	0	0.613015263687049	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.386954269871736
CAMB-79FC9	MN908947.3	28881	GGG	AAC	1	1	0;0;0	9e-278;9.6e-303;1.79997996092883e-319	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-79FC9	MN908947.3	3037	C	T	1	1	2e-129	4.2e-236	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79FD8	MN908947.3	10582	C	T	0.59	0.42	2.4e-215	8.8e-157	0.490415335463259	ACT	ORF1ab:3C-like-proteinase	D176D	C528T	GAC>GAT	Synonymous	ORF1ab:3C-like-proteinase	0.509052183173589
CAMB-79FD8	MN908947.3	14408	C	T	1	1	0	0	0.999358563181527	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00042762454564892
CAMB-79FD8	MN908947.3	17010	C	T	1	1	0	0	1	TCT	ORF1ab:helicase	I258I	C774T	ATC>ATT	Synonymous	ORF1ab:helicase	0
CAMB-79FD8	MN908947.3	23403	A	G	1	1	0	0	0.999851161999532	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000106312857476983
CAMB-79FD8	MN908947.3	241	C	T	1	1	0	0	1	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-79FD8	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999471737982039	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000286779466590192
CAMB-79FD8	MN908947.3	29281	C	T	1	1	0	0	0.999637155297533	CCA	N	A336A	C1008T	GCC>GCT	Synonymous	GU280_gp10	0.000362844702467344
CAMB-79FD8	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-79FE7	MN908947.3	11074	C	INS	0.098	0.13	9.5e-35	5.8e-45	0.110346432608551	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.889171487465922
CAMB-79FE7	MN908947.3	11083	G	-	0.16	0.18	6.6e-70	4.9e-80	0.166587268504734	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.97743107247067e-05
CAMB-79FE7	MN908947.3	11083	G	T	0.84	0.82	0	0	0.833263859941642	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.97743107247067e-05
CAMB-79FE7	MN908947.3	13038	C	T	0.0066	0.0093	9.6e-05	5.4e-06	0.00779194031900043	ACA	ORF1ab:nsp10	T5I	C14T	ACA>ATA	Missense	ORF1ab:nsp10	0.992190896816861
CAMB-79FE7	MN908947.3	14805	C	T	1	1	0	0	0.999923286410188	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-79FE7	MN908947.3	15444	G	-	0.0081	0.012	0.00014	2.5e-06	0.00980030560092734	TGT	ORF1ab:RNA-dependent-RNA-polymerase	.	1977-1977-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.990094314768955
CAMB-79FE7	MN908947.3	16391	C	T	0.019	0.0052	8.7e-10	0.00042	0.0134753314496849	GCT	ORF1ab:helicase	A52V	C155T	GCT>GTT	Missense	ORF1ab:helicase	0.986524668550315
CAMB-79FE7	MN908947.3	18512	C	A	1	1	0	0	0.999818988143723	CCT	ORF1ab:3'-to-5'-exonuclease	P158H	C473A	CCT>CAT	Missense	ORF1ab:3'-to-5'-exonuclease	0.00013575889220744
CAMB-79FE7	MN908947.3	20844	C	T	0.0065	0.0071	8.8e-05	3.9e-05	0.00670793713092966	CCT	ORF1ab:2'-O-ribose-methyltransferase	P62P	C186T	CCC>CCT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.993202861577436
CAMB-79FE7	MN908947.3	22008	ACAA	-	0.0035	0.00885	NA;NA;3.3e-07;NA	9.3e-07;9.6e-07;0.00021;2.3e-05	0.00296456003234066	AAC	S	.	446-449-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.996258123810149
CAMB-79FE7	MN908947.3	22313	C	A	0.029	0.025	1.9e-14	1.7e-12	0.0277747161908961	TCC	S	P251T	C751A	CCT>ACT	Missense	GU280_gp02, spike glycoprotein	0.972115066681362
CAMB-79FE7	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-79FE7	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-79FE7	MN908947.3	26144	G	T	1	1	6.4e-305	4e-268	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-79FE7	MN908947.3	27882	G	A	0.018	0.017	2.3e-08	6.9e-08	0.0179288199090179	CGC	NA	NA	NA	NA	NA	NA	0.982071180090982
CAMB-79FE7	MN908947.3	28242	G	T	0.0088	0.0056	1.3e-05	0.00034	0.00734521028037383	TGT	ORF8	V117F	G349T	GTT>TTT	Missense	GU280_gp09	0.99253796728972
CAMB-79FE7	MN908947.3	28826	C	T	0.042	0.3	2.5e-17	1.7e-134	0.179242853463817	TCG	N	R185C	C553T	CGT>TGT	Missense	GU280_gp10	0.820757146536183
CAMB-79FE7	MN908947.3	29518	C	T	0.0025	0.014	0.0072	5.7e-06	0.0061624649859944	ACT	N	D415D	C1245T	GAC>GAT	Synonymous	GU280_gp10	0.993837535014006
CAMB-79FE7	MN908947.3	4135	TG	-	0.0145	0.0365	2.1e-07;1.3e-06	3.5e-16;2.1e-14	0.0234018691588785	TTG	ORF1ab:nsp3	.	1416-1417-delfrshift	.	no-SNV	ORF1ab:nsp3	0.96219645757015
CAMB-79FE7	MN908947.3	4667	T	C	0.006	0.022	7.6e-05	4.5e-12	0.013175212119515	ATC	ORF1ab:nsp3	S650P	T1948C	TCT>CCT	Missense	ORF1ab:nsp3	0.986810786592367
CAMB-79FF6	MN908947.3	1059	C	T	1	1	0	0	0.999520221764162	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.000177695642902836
CAMB-79FF6	MN908947.3	10874	A	G	1	1	0	0	0.999529868990159	AAA	ORF1ab:3C-like-proteinase	N274D	A820G	AAT>GAT	Missense	ORF1ab:3C-like-proteinase	0.000188052403936564
CAMB-79FF6	MN908947.3	11075	T	-	0.041	0.046	3.1e-10	4.7e-12	0.0425930392588073	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953788964401754
CAMB-79FF6	MN908947.3	14408	C	T	1	1	0	0	0.996550940470302	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000668422389476358
CAMB-79FF6	MN908947.3	23403	A	G	1	1	0	0	0.999455280435011	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.82259343851836e-05
CAMB-79FF6	MN908947.3	241	C	T	1	1	0	0	0.997885338345865	TCG	NA	NA	NA	NA	NA	NA	0.00028531149301826
CAMB-79FF6	MN908947.3	24368	G	T	1	1	0	0	0.999927643717666	AGA	S	D936Y	G2806T	GAC>TAC	Missense	GU280_gp02, spike glycoprotein	7.23562823342137e-05
CAMB-79FF6	MN908947.3	25563	G	T	1	1	0	0	0.999553395976991	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000107184965522169
CAMB-79FF6	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.02803125	0.0325	0.00021;0.00083;2e-04;2e-04;5.2e-05;0.00011;9.1e-05;0.00019;0.00012;0.00014;0.00022;1e-04;2e-04;0.00013;0.00013;0.00011;0.00021;0.00013;0.00017;0.00013;9.1e-05;0.00018;0.00012;4.1e-05;0.00012;0.00019;0.00017;8.3e-05;0.00017;7e-05;0.00011;9.7e-05	2.2e-05;9.4e-05;2.1e-05;2.1e-05;5.5e-06;9.8e-06;8.3e-06;2.1e-05;1.2e-05;1.4e-05;2.5e-05;1.1e-05;2.3e-05;1.5e-05;1.5e-05;9.3e-06;2.7e-05;1.2e-05;1.7e-05;1.4e-05;9.1e-06;2.1e-05;1.2e-05;9.3e-06;1.2e-05;2.1e-05;1.8e-05;1.1e-05;2e-05;6.7e-06;1.2e-05;1e-05	0.029096183160917	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.971259158546718
CAMB-79FF6	MN908947.3	3037	C	T	1	1	0	0	0.999158249158249	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.23519142037661e-05
CAMB-79FF6	MN908947.3	3696	T	A	0.011	0.013	1.9e-05	2.7e-06	0.0115363629277418	CTA	ORF1ab:nsp3	L326Q	T977A	CTA>CAA	Missense	ORF1ab:nsp3	0.988385688674098
CAMB-79FF6	MN908947.3	5554	G	T	1	1	0	0	0.999398677089597	AGG	ORF1ab:nsp3	K945N	G2835T	AAG>AAT	Missense	ORF1ab:nsp3	0.000225496091401082
CAMB-7A001	MN908947.3	11075	T	-	0.044	0.047	1.3e-11	2.2e-12	0.0452164535510707	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.950752323730293
CAMB-7A001	MN908947.3	14408	C	T	1	1	0	0	0.997034059122025	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00236150742890879
CAMB-7A001	MN908947.3	18570	C	T	0.0064	0.0067	4.8e-05	2.9e-05	0.00652495627606619	TCT	ORF1ab:3'-to-5'-exonuclease	L177L	C531T	CTC>CTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.99339095923584
CAMB-7A001	MN908947.3	20759	C	T	0.0086	0.0081	2.4e-05	3.6e-05	0.00837091108398316	GCA	ORF1ab:2'-O-ribose-methyltransferase	A34V	C101T	GCA>GTA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.991504521786791
CAMB-7A001	MN908947.3	23403	A	G	1	1	0	0	0.998067088148834	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.0015704908790722
CAMB-7A001	MN908947.3	241	C	T	1	1	0	0	0.997110236499663	TCG	NA	NA	NA	NA	NA	NA	0.00179058965358295
CAMB-7A001	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.997739137583755	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.0018491124260355
CAMB-7A001	MN908947.3	3037	C	T	1	1	0	0	0.996992983628466	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.0021478688368097
CAMB-7A010	MN908947.3	13914	T	G	0.0029	0.0069	0.00067	1e-05	0.00520973681846762	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994790263181532
CAMB-7A010	MN908947.3	14408	C	T	0.98	1	0	0	0.989798087141339	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000361317747077577
CAMB-7A010	MN908947.3	1813	T	INS	0.024	0.027	7.9e-09	4.3e-10	0.0256710254645561	CTA	ORF1ab:nsp2	.	1007-1008-insfrshift	.	no-SNV	ORF1ab:nsp2	0.974122505161734
CAMB-7A010	MN908947.3	21123	G	T	1	1	0	0	0.999905879400138	GGT	ORF1ab:2'-O-ribose-methyltransferase	G155G	G465T	GGG>GGT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	6.27470665746376e-05
CAMB-7A010	MN908947.3	23403	A	G	1	1	0	0	0.999814827674004	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000162025785246395
CAMB-7A010	MN908947.3	241	C	T	1	1	0	0	0.999850372199155	TCG	NA	NA	NA	NA	NA	NA	0.000112220850634048
CAMB-7A010	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999745676500509	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A010	MN908947.3	3037	C	T	1	1	0	0	0.999068901303538	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00074487895716946
CAMB-7A010	MN908947.3	5933	ACAGA	TACAG	0.0396	0.00119	7.8e-13;5.8e-14;1.6e-13;8.3e-16;9.9e-12	NA;NA;NA;NA;0.004	0.0152963671128107	TAC	ORF1ab:nsp3	.	3214-3218-mnv	.	no-SNV	ORF1ab:nsp3	0.986164122137405
CAMB-7A010	MN908947.3	6336	C	T	1	1	0	0	0.999786387546394	TCG	ORF1ab:nsp3	S1206L	C3617T	TCG>TTG	Missense	ORF1ab:nsp3	0.00018691089690529
CAMB-7A010	MN908947.3	8917	C	T	1	1	0	0	0.999608926895401	TCT	ORF1ab:nsp4	F121F	C363T	TTC>TTT	Synonymous	ORF1ab:nsp4	2.60715403066013e-05
CAMB-7A02F	MN908947.3	11075	T	-	0.044	0.037	7.1e-11	3.1e-09	0.0405223142477496	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954622201352742
CAMB-7A02F	MN908947.3	14408	C	T	1	1	0	0	0.995756950844504	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000675237930121999
CAMB-7A02F	MN908947.3	14786	C	T	1	1	0	0	0.999325905814062	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A440V	C1319T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	2.80872577474019e-05
CAMB-7A02F	MN908947.3	20578	G	T	1	1	0	0	0.999385371850031	AGT	ORF1ab:endoRNAse	V320L	G958T	GTG>TTG	Missense	ORF1ab:endoRNAse	0.000153657037492317
CAMB-7A02F	MN908947.3	22675	C	T	1	1	0	0	0.999387643059251	CCG	S	S371S	C1113T	TCC>TCT	Synonymous	GU280_gp02, spike glycoprotein	0.000295620592085814
CAMB-7A02F	MN908947.3	23403	A	G	1	1	0	0	0.999413762124465	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000327379592831148
CAMB-7A02F	MN908947.3	241	C	T	1	1	0	0	0.999290605986194	TCG	NA	NA	NA	NA	NA	NA	6.82109628659518e-05
CAMB-7A02F	MN908947.3	2416	C	T	1	0.99	0	0	0.995359281437126	ACA	ORF1ab:nsp2	Y537Y	C1611T	TAC>TAT	Synonymous	ORF1ab:nsp2	0
CAMB-7A02F	MN908947.3	25460	C	T	1	1	0	0	0.999635013529671	GCT	ORF3a	A23V	C68T	GCT>GTT	Missense	GU280_gp03	0.000100685922849412
CAMB-7A02F	MN908947.3	25563	G	T	1	1	0	0	0.999847291329965	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	6.36286125144755e-05
CAMB-7A02F	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0364864864864865	0.0356756756756757	1e-04;7.2e-06;5.1e-05;7.1e-05;0.00016;1.3e-05;3.6e-05;4e-06;4e-06;1.1e-06;1.6e-06;1.3e-06;3.8e-06;2e-06;2.5e-06;5.5e-06;1.7e-06;4.5e-06;2.7e-06;2.7e-06;1.9e-06;4.7e-06;2.6e-06;3.1e-06;2.4e-06;1.2e-06;4e-06;2.2e-06;5.1e-06;1.6e-06;4.1e-06;1.2e-06;6.3e-07;2.1e-06;1.5e-06;2.6e-06;1.3e-06	0.00045;3.7e-05;0.00012;0.00013;0.00019;5.6e-06;2.1e-05;4.8e-06;4.7e-06;1.3e-06;2.5e-06;1.6e-06;4.7e-06;2.4e-06;3.3e-06;5.3e-06;2.1e-06;4.5e-06;2.7e-06;2.7e-06;2.3e-06;4.9e-06;3.2e-06;3.6e-06;2.5e-06;1.6e-06;4e-06;1.7e-06;3.7e-06;1.9e-06;3.2e-06;2.2e-06;1.5e-06;2.6e-06;1.4e-06;2.6e-06;2.4e-06	0.0375634207469894	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.97465369879163
CAMB-7A02F	MN908947.3	28214	C	INS	0.52	0.52	2e-297	3.3e-297	0.518512843004116	ACT	ORF8	.	320-321-insfrshift	.	no-SNV	GU280_gp09	0.479653574429185
CAMB-7A02F	MN908947.3	3037	C	T	1	1	0	0	0.999119154388213	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00012011531069827
CAMB-7A03E	MN908947.3	11075	T	-	0.036	0.031	5e-09	2.4e-08	0.0344453336549108	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961882105309317
CAMB-7A03E	MN908947.3	14408	C	T	1	1	0	0	0.998009672989272	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000567243198057441
CAMB-7A03E	MN908947.3	21123	G	T	1	1	0	0	0.999738082765846	GGT	ORF1ab:2'-O-ribose-methyltransferase	G155G	G465T	GGG>GGT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.000221622275053391
CAMB-7A03E	MN908947.3	23403	A	G	1	1	0	0	0.999543410268703	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.84884596945415e-05
CAMB-7A03E	MN908947.3	241	C	T	1	1	0	0	0.998781301313629	TCG	NA	NA	NA	NA	NA	NA	0.000115455665024631
CAMB-7A03E	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999151242124506	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000107534590293211
CAMB-7A03E	MN908947.3	3037	C	T	1	1	0	0	0.999040767386091	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00010658140154543
CAMB-7A03E	MN908947.3	6286	C	T	0.029	0.026	6.1e-14	5e-13	0.0278692045982109	CCT	ORF1ab:nsp3	T1189T	C3567T	ACC>ACT	Synonymous	ORF1ab:nsp3	0.972019928352169
CAMB-7A03E	MN908947.3	6336	C	T	1	1	0	0	0.999448154075382	TCG	ORF1ab:nsp3	S1206L	C3617T	TCG>TTG	Missense	ORF1ab:nsp3	0.000151757629269908
CAMB-7A03E	MN908947.3	8917	C	T	1	1	0	0	0.998404076858208	TCT	ORF1ab:nsp4	F121F	C363T	TTC>TTT	Synonymous	ORF1ab:nsp4	9.06774512382006e-05
CAMB-7A04D	MN908947.3	11074	CT	-	0.01965	0.017555	0.00081;2.2e-09	0.11;7.3e-09	0.020218388248128	TCT	ORF1ab:nsp6	.	102-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.983510366900134
CAMB-7A04D	MN908947.3	11075	T	-	0.037	0.035	2.2e-09	7.3e-09	0.0362764495472754	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960273291683317
CAMB-7A04D	MN908947.3	14408	C	T	1	0.99	0	0	0.995664283174653	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00185675344684549
CAMB-7A04D	MN908947.3	23403	A	G	1	1	0	0	0.999946976124106	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.54490364804266e-05
CAMB-7A04D	MN908947.3	241	C	T	1	1	0	0	0.999396707747996	TCG	NA	NA	NA	NA	NA	NA	0.000143641012381855
CAMB-7A04D	MN908947.3	25429	G	T	1	1	0	0	0.999939154984424	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	2.43380062305296e-05
CAMB-7A04D	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0308918918918919	0.017972972972973	0.00052;3.3e-05;0.00032;0.00024;0.00055;2.4e-05;0.00011;4.1e-05;4e-05;1.1e-05;2.1e-05;1.6e-05;4e-05;2.4e-05;3.1e-05;5.7e-05;2.1e-05;4.8e-05;3e-05;3.1e-05;2.4e-05;5.1e-05;2.7e-05;3.6e-05;2.9e-05;1.6e-05;4.1e-05;2.6e-05;6.8e-06;2.5e-05;4.4e-05;4.1e-05;1.8e-05;4.2e-05;1.5e-05;2.5e-05;1.5e-05	0.084;0.036;0.036;0.037;0.053;0.0026;0.0068;0.0064;0.0064;0.0035;0.0046;0.0041;0.0062;0.0051;0.0057;0.0075;0.0046;0.0069;0.0057;0.0054;0.0022;0.0074;0.0034;0.0038;0.0053;0.0045;0.0065;0.005;0.0041;0.0048;0.0065;0.0059;0.0042;0.0065;0.0041;0.0047;0.0023	0.024792812176269	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.983882221602009
CAMB-7A04D	MN908947.3	28312	C	A	0.11	0.099	3.5e-50	2.5e-45	0.104110676765209	CCC	N	P13P	C39A	CCC>CCA	Synonymous	GU280_gp10	0.895838423324375
CAMB-7A04D	MN908947.3	29358	C	T	0.028	0.013	4.3e-11	0.00011	0.0244798041615667	ACA	N	T362I	C1085T	ACA>ATA	Missense	GU280_gp10	0.975520195838433
CAMB-7A04D	MN908947.3	29642	C	T	0.054	0.059	8.4e-24	3e-25	0.056441717791411	ACA	ORF10	Q29*	C85T	CAA>TAA	Nonsense	GU280_gp11	0.943558282208589
CAMB-7A04D	MN908947.3	3037	C	T	1	1	0	0	0.997814040974023	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000152508769254232
CAMB-7A07A	MN908947.3	11074	C	INS	0.08	0.044	4.5e-23	4.2e-10	0.0626330811398541	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.937027137226476
CAMB-7A07A	MN908947.3	11075	T	-	0.085	0.071	5.5e-21	1.1e-17	0.0777490634453192	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.922050604002644
CAMB-7A07A	MN908947.3	13627	G	T	0.015	0.0031	2.3e-09	0.00064	0.00974381876497097	TGA	ORF1ab:RNA-dependent-RNA-polymerase	D54Y	G160T	GAC>TAC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.990256181235029
CAMB-7A07A	MN908947.3	14408	C	T	1	1	0	0	0.999287863821185	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000505386965610714
CAMB-7A07A	MN908947.3	14805	C	T	0.029	0.035	1.3e-14	4.5e-17	0.0312313316925136	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.968673086573156
CAMB-7A07A	MN908947.3	17617	C	T	0.024	0.025	1.8e-12	4.5e-13	0.0239965893172544	GCT	ORF1ab:helicase	L461F	C1381T	CTT>TTT	Missense	ORF1ab:helicase	0.976003410682746
CAMB-7A07A	MN908947.3	23403	A	G	1	1	0	0	0.999914262442663	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.85791857789972e-05
CAMB-7A07A	MN908947.3	241	C	T	1	1	0	0	0.999693721286371	TCG	NA	NA	NA	NA	NA	NA	0.000153139356814701
CAMB-7A07A	MN908947.3	28881	GGG	AAC	0.923333333333333	1	0;0;0	0;0;0	0.947908007758382	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.0572033898305085
CAMB-7A07A	MN908947.3	3037	C	T	0.95	1	0	0	0.976484420928865	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.0235155790711346
CAMB-7A089	MN908947.3	1059	C	T	1	1	0	0	0.999486125385406	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	0.000342583076396026
CAMB-7A089	MN908947.3	14408	C	T	1	1	0	0	0.999203782035332	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000597163473500871
CAMB-7A089	MN908947.3	14464	G	T	0.069	0.19	8.3e-32	3.4e-89	0.112455684235405	AGT	ORF1ab:RNA-dependent-RNA-polymerase	V333F	G997T	GTT>TTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.887449775466793
CAMB-7A089	MN908947.3	23403	A	G	1	1	0	0	0.999767463491768	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.65073016463585e-05
CAMB-7A089	MN908947.3	25459	G	T	1	1	0	0	0.999843578914438	TGC	ORF3a	A23S	G67T	GCT>TCT	Missense	GU280_gp03	0.000156421085562334
CAMB-7A089	MN908947.3	25563	G	T	1	1	0	0	0.999840281105255	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000159718894745248
CAMB-7A089	MN908947.3	3037	C	T	1	1	7.8e-169	2.7e-289	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A089	MN908947.3	3116	A	G	1	1	6.9e-265	0	1	TAC	ORF1ab:nsp3	T133A	A397G	ACT>GCT	Missense	ORF1ab:nsp3	0
CAMB-7A089	MN908947.3	9767	A	G	1	1	0	0	0.999740946064971	TAA	ORF1ab:nsp4	N405D	A1213G	AAT>GAT	Missense	ORF1ab:nsp4	0.000103621574011709
CAMB-7A098	MN908947.3	11075	T	-	0.035	0.038	5.5e-09	3.3e-10	0.0358293204069267	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959434894919795
CAMB-7A098	MN908947.3	14408	C	T	1	1	0	0	0.995524567124671	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000641296783964851
CAMB-7A098	MN908947.3	23403	A	G	1	1	0	0	0.999333743337433	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.15006150061501e-05
CAMB-7A098	MN908947.3	241	C	T	1	1	0	0	0.99795101405832	TCG	NA	NA	NA	NA	NA	NA	0.000246637196683678
CAMB-7A098	MN908947.3	25482	C	T	0.41	0.43	1.4e-223	3.7e-236	0.420561555075594	GCG	ORF3a	R30R	C90T	CGC>CGT	Synonymous	GU280_gp03	0.579041036717063
CAMB-7A098	MN908947.3	26137	A	C	0.033	0.016	1.1e-08	0.0021	0.027798424260443	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.972052921064367
CAMB-7A098	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0371052631578947	0.0365263157894737	0.00018;1.4e-05;6.4e-05;8.9e-05;0.00018;2.1e-06;1e-05;2.3e-06;2.2e-06;6e-07;8.2e-07;6.6e-07;2.2e-06;1.2e-06;1.5e-06;3.2e-06;8.5e-07;2.7e-06;1.6e-06;1.5e-06;7.4e-07;2.9e-06;1.1e-06;1.8e-06;1.4e-06;6.9e-07;2.3e-06;1.3e-06;4.3e-07;1.1e-06;2.4e-06;1.8e-06;5e-07;1.8e-06;5.6e-07;1.2e-06;5.8e-07;0.00096	0.00044;2.9e-05;0.00022;0.00024;0.00035;1.1e-05;2.1e-05;1.8e-06;1.8e-06;4.2e-07;7.9e-07;6e-07;1.4e-06;8.4e-07;9.5e-07;1.6e-06;7.2e-07;1.6e-06;8.6e-07;9.2e-07;6.2e-07;1.7e-06;7.1e-07;1.1e-06;8e-07;5.1e-07;1.4e-06;7.3e-07;2.3e-07;8.2e-07;1.4e-06;1e-06;6.7e-07;1.3e-06;3.6e-07;7.5e-07;6.2e-07;0.00052	0.0387441445111156	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.975219370795721
CAMB-7A098	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998587360594796	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000123839009287926
CAMB-7A098	MN908947.3	3037	C	T	1	1	0	0	0.998768768768769	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00012012012012012
CAMB-7A098	MN908947.3	522	TT	-	0.04	0.0395	3.5e-06;0.00021	4.2e-06;0.00011	0.039543663369065	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.951331274636763
CAMB-7A0A7	MN908947.3	11075	T	-	0.037	0.036	2.9e-09	2.3e-09	0.0368653256561729	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957472946555426
CAMB-7A0A7	MN908947.3	12896	C	T	0.0046	0.0086	4e-04	5.8e-06	0.00617879899594516	ACC	ORF1ab:nsp9	P71S	C211T	CCA>TCA	Missense	ORF1ab:nsp9	0.99380740904201
CAMB-7A0A7	MN908947.3	14408	C	T	1	1	0	0	0.99837205254482	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000460739845805732
CAMB-7A0A7	MN908947.3	23403	A	G	1	1	0	0	0.999884901549718	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.22131787725572e-05
CAMB-7A0A7	MN908947.3	241	C	T	1	1	0	0	0.998126140342226	TCG	NA	NA	NA	NA	NA	NA	6.57494616762825e-05
CAMB-7A0A7	MN908947.3	26137	A	C	0.022	0.014	2.7e-05	0.0075	0.0191188694929343	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.980673316708229
CAMB-7A0A7	MN908947.3	27923	C	T	1	1	0	0	0.999912242211496	TCA	ORF8	I10I	C30T	ATC>ATT	Synonymous	GU280_gp09	8.77577885037297e-05
CAMB-7A0A7	MN908947.3	28045	C	T	0.0049	0.0094	0.00088	1.3e-05	0.00666730164777598	GCT	ORF8	A51V	C152T	GCT>GTT	Missense	GU280_gp09	0.993332698352224
CAMB-7A0A7	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999100209951011	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000218786464410735
CAMB-7A0A7	MN908947.3	3037	C	T	1	1	0	0	0.999503031507802	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000149090547659278
CAMB-7A0B6	MN908947.3	13626	T	C	0.73	0.84	0	0	0.785612738129087	ATG	ORF1ab:RNA-dependent-RNA-polymerase	D53D	T159C	GAT>GAC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.214387261870913
CAMB-7A0B6	MN908947.3	14408	C	T	1	1	0	0	0.999432087079981	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000473260766682442
CAMB-7A0B6	MN908947.3	23403	A	G	1	1	0	0	0.999970621933664	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7A0B6	MN908947.3	241	C	T	1	1	0	0	0.99956347127641	TCG	NA	NA	NA	NA	NA	NA	0.00034922297887201
CAMB-7A0B6	MN908947.3	28280	GAT	CTA	1	1	0;0;0	0;0;0	0.999853954901273	TGA	N	.	7-9-mnv	.	no-SNV	GU280_gp10	2.93599530240752e-05
CAMB-7A0B6	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99937343358396	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A0B6	MN908947.3	29555	C	T	0.61	0.72	4.9e-112	1.8e-115	0.653731343283582	GCA	NA	NA	NA	NA	NA	NA	0.346268656716418
CAMB-7A0B6	MN908947.3	3037	C	T	1	1	6e-280	0	0.998958333333333	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A0C5	MN908947.3	11075	T	-	0.035	0.034	7.2e-09	7.4e-09	0.0343787122832027	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961107151342362
CAMB-7A0C5	MN908947.3	14408	C	T	1	1	0	0	0.995723193207923	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000412860061611425
CAMB-7A0C5	MN908947.3	17853	A	G	0.86	0.86	0	0	0.859258631166886	CAG	ORF1ab:helicase	S539S	A1617G	TCA>TCG	Synonymous	ORF1ab:helicase	0.140388066872995
CAMB-7A0C5	MN908947.3	19145	C	T	0.0097	0.0084	4.2e-06	1.4e-05	0.00911438761427146	TCT	ORF1ab:3'-to-5'-exonuclease	S369F	C1106T	TCT>TTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.990858282887635
CAMB-7A0C5	MN908947.3	23403	A	G	1	1	0	0	0.999453062848051	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.28692654468311e-05
CAMB-7A0C5	MN908947.3	24014	A	G	0.012	0.015	2.7e-07	2.5e-08	0.0133300571288163	TAT	S	I818V	A2452G	ATT>GTT	Missense	GU280_gp02, spike glycoprotein	0.985011364334419
CAMB-7A0C5	MN908947.3	241	C	T	1	1	0	0	0.998094061590047	TCG	NA	NA	NA	NA	NA	NA	5.29427336098121e-05
CAMB-7A0C5	MN908947.3	26137	A	C	0.023	0.017	2.1e-05	0.00078	0.0204755614266843	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.979194187582563
CAMB-7A0C5	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.03053125	0.03275	3.7e-05;0.00022;6.4e-05;6.3e-05;2e-05;2.6e-05;2.3e-05;6.2e-05;3.7e-05;4.4e-05;8.4e-05;3.4e-05;7.2e-05;4.6e-05;4.8e-05;3.4e-05;7.9e-05;4.6e-05;5.7e-05;4.1e-05;2.3e-05;5.7e-05;4.3e-05;3.1e-05;3.4e-05;6.3e-05;5.6e-05;2.5e-05;6.7e-05;2.7e-05;4.7e-05;3.4e-05	1.7e-05;5.8e-05;2.5e-05;2.5e-05;8.3e-06;1.2e-05;8.8e-06;2.2e-05;1.4e-05;1.7e-05;3e-05;1.2e-05;2.6e-05;1.8e-05;1.7e-05;1.2e-05;2.8e-05;1.3e-05;2e-05;1.6e-05;1e-05;2.3e-05;1.3e-05;6.3e-06;1.4e-05;2.3e-05;2.1e-05;1.6e-05;2.4e-05;8.3e-06;2.1e-05;1.4e-05	0.0313370558252132	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.967906751457008
CAMB-7A0C5	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998937163837805	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	3.63834818992178e-05
CAMB-7A0C5	MN908947.3	3037	C	T	1	1	0	0	0.999151883525337	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00021202911866563
CAMB-7A0C5	MN908947.3	4540	C	T	0.98	0.98	0	0	0.980883218842002	ACA	ORF1ab:nsp3	Y607Y	C1821T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.000117762512266928
CAMB-7A0D4	MN908947.3	10097	G	A	1	1	0	0	0.99971671388102	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000106232294617564
CAMB-7A0D4	MN908947.3	11075	T	-	0.038	0.039	5.1e-10	1.8e-10	0.0384216414115733	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957530763754704
CAMB-7A0D4	MN908947.3	13536	C	T	1	1	0	0	0.999482585299509	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	8.86996629412808e-05
CAMB-7A0D4	MN908947.3	14408	C	T	1	1	0	0	0.997843080864859	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000392167115480143
CAMB-7A0D4	MN908947.3	23403	A	G	1	1	0	0	0.999248210741565	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.0143140674806e-05
CAMB-7A0D4	MN908947.3	23731	C	T	1	1	0	0	0.99988926211657	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	3.69126278099738e-05
CAMB-7A0D4	MN908947.3	241	C	T	1	1	0	0	0.998670465337132	TCG	NA	NA	NA	NA	NA	NA	0.000303893637226971
CAMB-7A0D4	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999323623573973	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000196511913534758
CAMB-7A0D4	MN908947.3	3037	C	T	1	1	0	0	0.999167087329632	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.04795557799091e-05
CAMB-7A0D4	MN908947.3	4002	C	T	1	1	0	0	0.999851661392405	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	4.94462025316456e-05
CAMB-7A0E3	MN908947.3	11075	T	-	0.035	0.036	8.9e-09	4e-09	0.0353656473585225	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959738489248007
CAMB-7A0E3	MN908947.3	11514	C	T	0.0053	0.0085	0.00078	3.2e-05	0.00675977653631285	ACT	ORF1ab:nsp6	T181I	C542T	ACT>ATT	Missense	ORF1ab:nsp6	0.993072625698324
CAMB-7A0E3	MN908947.3	14408	C	T	1	1	0	0	0.997867564534231	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000392817059483726
CAMB-7A0E3	MN908947.3	23403	A	G	1	1	0	0	0.999643893531743	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.57673336717608e-05
CAMB-7A0E3	MN908947.3	241	C	T	1	1	0	0	0.999336606076688	TCG	NA	NA	NA	NA	NA	NA	0.000103194610292925
CAMB-7A0E3	MN908947.3	24703	T	C	0.0078	0.0022	2.6e-05	0.0057	0.00610360875867857	ATC	S	Y1047Y	T3141C	TAT>TAC	Synonymous	GU280_gp02, spike glycoprotein	0.993362325474937
CAMB-7A0E3	MN908947.3	27281	G	T	1	1	0	0	0.998665879316755	TGG	ORF6	W27L	G80T	TGG>TTG	Missense	GU280_gp06	7.29027695762162e-06
CAMB-7A0E3	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999254065343876	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.12014338098966e-05
CAMB-7A0E3	MN908947.3	3037	C	T	1	1	0	0	0.998841880496544	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.61912344830082e-05
CAMB-7A0E3	MN908947.3	4111	T	C	0.069	0.072	1.1e-31	4.1e-33	0.0703087985284691	ATG	ORF1ab:nsp3	D464D	T1392C	GAT>GAC	Synonymous	ORF1ab:nsp3	0.929670299044062
CAMB-7A0E3	MN908947.3	5055	C	T	0.0087	0.013	4.3e-05	3.5e-06	0.010412147505423	ACT	ORF1ab:nsp3	T779I	C2336T	ACT>ATT	Missense	ORF1ab:nsp3	0.989587852494577
CAMB-7A0E3	MN908947.3	6740	C	T	0.015	0.011	2.8e-08	2.6e-06	0.0132854804180834	ACG	ORF1ab:nsp3	R1341W	C4021T	CGG>TGG	Missense	ORF1ab:nsp3	0.986714519581917
CAMB-7A0E3	MN908947.3	9073	C	T	0.015	0.0094	4.2e-08	4e-06	0.0123859704309531	CCA	ORF1ab:nsp4	T173T	C519T	ACC>ACT	Synonymous	ORF1ab:nsp4	0.987299465240642
CAMB-7A0F2	MN908947.3	11074	C	INS	0.1	0.1	1.2e-42	5.4e-34	0.103993240716373	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.891893014945219
CAMB-7A0F2	MN908947.3	11083	G	-	0.16	0.19	7.8e-71	1.1e-87	0.172808513705047	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	4.80457395440459e-05
CAMB-7A0F2	MN908947.3	11083	G	T	0.84	0.81	0	0	0.826891200422803	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	4.80457395440459e-05
CAMB-7A0F2	MN908947.3	13627	G	T	1	1	0	0	0.99987171572204	TGA	ORF1ab:RNA-dependent-RNA-polymerase	D54Y	G160T	GAC>TAC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	4.81066042349847e-05
CAMB-7A0F2	MN908947.3	14805	C	T	1	1	0	0	0.999628065460479	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	2.39957767432932e-05
CAMB-7A0F2	MN908947.3	15540	C	T	1	1	0	0	0.999838183673977	TCA	ORF1ab:RNA-dependent-RNA-polymerase	V691V	C2073T	GTC>GTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000112026687246384
CAMB-7A0F2	MN908947.3	18467	G	A	0.0038	0.0061	0.00061	4e-05	0.00464466019417476	GGA	ORF1ab:3'-to-5'-exonuclease	G143E	G428A	GGA>GAA	Missense	ORF1ab:3'-to-5'-exonuclease	0.995339805825243
CAMB-7A0F2	MN908947.3	18525	G	T	1	1	0	0	0.999259091252741	TGC	ORF1ab:3'-to-5'-exonuclease	V162V	G486T	GTG>GTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.000120964693430105
CAMB-7A0F2	MN908947.3	26144	G	T	1	1	0	0	0.999840357598978	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7A0F2	MN908947.3	28338	A	G	1	1	0	0	0.999861551628656	GAT	N	D22G	A65G	GAT>GGT	Missense	GU280_gp10	8.81035090369028e-05
CAMB-7A0F2	MN908947.3	29218	C	T	1	1	0	0	0.999280873411929	TCG	N	F315F	C945T	TTC>TTT	Synonymous	GU280_gp10	0.000196125433110331
CAMB-7A0F2	MN908947.3	29306	A	C	0.018	0.014	1e-08	8.4e-08	0.0164127658814495	AAA	N	N345H	A1033C	AAT>CAT	Missense	GU280_gp10	0.983569374743271
CAMB-7A10E	MN908947.3	12490	A	G	0.036	0.037	1.6e-17	7.6e-18	0.0364022414849838	CAG	ORF1ab:nsp8	P133P	A399G	CCA>CCG	Synonymous	ORF1ab:nsp8	0.963510200507836
CAMB-7A10E	MN908947.3	14408	C	T	1	1	0	0	0.99959767702211	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000192415337251609
CAMB-7A10E	MN908947.3	1651	TA	AG	0.0255	0.0055	6.2e-13;2.9e-13	NA;4.6e-07	0.01508373480156	ATA	ORF1ab:nsp2	.	846-847-mnv	.	no-SNV	ORF1ab:nsp2	0.987479973891889
CAMB-7A10E	MN908947.3	1652	A	G	0.026	0.011	2.9e-13	4.6e-07	0.0178720097685519	TAT	ORF1ab:nsp2	I283V	A847G	ATT>GTT	Missense	ORF1ab:nsp2	0.982072487095521
CAMB-7A10E	MN908947.3	21624	G	T	1	1	0	4.2e-220	1	AGA	S	R21I	G62T	AGA>ATA	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7A10E	MN908947.3	22951	T	C	0.04	0.033	1.3e-16	3.2e-14	0.0362821470494077	CTT	S	P463P	T1389C	CCT>CCC	Synonymous	GU280_gp02, spike glycoprotein	0.963291004161776
CAMB-7A10E	MN908947.3	2296	A	G	0.036	0.043	5e-13	2e-16	0.0401404917210236	CAT	ORF1ab:nsp2	T497T	A1491G	ACA>ACG	Synonymous	ORF1ab:nsp2	0.959859508278976
CAMB-7A10E	MN908947.3	23403	A	G	1	1	0	0	0.999909012328829	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.54938355852782e-05
CAMB-7A10E	MN908947.3	241	C	T	1	0.92	0	0	0.962775772162054	TCG	NA	NA	NA	NA	NA	NA	8.02246289610911e-05
CAMB-7A10E	MN908947.3	25517	C	T	0.61	0.57	0	0	0.583859634447279	CCT	ORF3a	P42L	C125T	CCT>CTT	Missense	GU280_gp03	0.416056715044544
CAMB-7A10E	MN908947.3	25792	C	T	0.088	0.15	3.9e-26	1e-42	0.117790414297319	CCG	ORF3a	R134C	C400T	CGT>TGT	Missense	GU280_gp03	0.882209585702681
CAMB-7A10E	MN908947.3	26333	C	T	0.076	0.042	4.7e-32	3.7e-18	0.0584008361640972	ACA	E	T30I	C89T	ACA>ATA	Missense	GU280_gp04	0.941468513195715
CAMB-7A10E	MN908947.3	26794	TG	-	0.0225	0.0485	0.00086;0.0013	9.9e-09;2.2e-08	0.03601661420831	ATG	M	.	272-273-delfrshift	.	no-SNV	GU280_gp05	0.96315265745727
CAMB-7A10E	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999781611705613	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A10E	MN908947.3	29166	ACAAACATTGGCCGCAAATTGCACAATTTGCCCCC	-	0.000785428571428571	0.0148628571428571	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.074;NA;NA;2.2e-13;NA;NA;NA;NA;NA;NA;NA;NA	2e-05;6.8e-08;1.9e-08;3.1e-08;6.2e-08;3.1e-08;1.1e-08;3.9e-09;6.8e-09;1.4e-08;1.5e-08;3.2e-08;2.2e-07;2.5e-06;3e-08;1.2e-08;1.5e-11;1.1e-08;1.3e-08;1.5e-08;1.4e-08;2.2e-08;2.7e-08;2.7e-08;1.3e-08;2e-09;5.2e-09;4.4e-10;1.3e-08;7.4e-09;7.9e-06;1.6e-05;2.1e-06;2.7e-08;2.7e-08	0.0114509887080528	TAC	N	.	893-927-delfrshift	.	no-SNV	GU280_gp10	0.993860743698528
CAMB-7A10E	MN908947.3	3037	C	T	1	1	0	0	0.999504214179474	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A11D	MN908947.3	11075	T	-	0.036	0.037	5.3e-09	7.2e-10	0.0359684554722062	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959909872777732
CAMB-7A11D	MN908947.3	14408	C	T	1	1	0	0	0.997996410748089	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000528554219829388
CAMB-7A11D	MN908947.3	23403	A	G	1	1	0	0	0.999505220429348	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.05852535492861e-05
CAMB-7A11D	MN908947.3	241	C	T	1	1	0	0	0.998906377321268	TCG	NA	NA	NA	NA	NA	NA	0.000278766565167045
CAMB-7A11D	MN908947.3	25563	G	T	1	1	0	0	0.999626060204307	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000203967161287033
CAMB-7A11D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99931498569529	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.45851353158857e-05
CAMB-7A11D	MN908947.3	3037	C	T	1	1	0	0	0.99904629154134	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.66810945638618e-05
CAMB-7A11D	MN908947.3	8644	T	A	1	1	0	0	0.999579909155355	TTC	ORF1ab:nsp4	V30V	T90A	GTT>GTA	Synonymous	ORF1ab:nsp4	0.000131278388951611
CAMB-7A12C	MN908947.3	10029	C	T	0.034	0.007	2.9e-16	6.8e-05	0.0224314694975642	ACC	ORF1ab:nsp4	T492I	C1475T	ACC>ATC	Missense	ORF1ab:nsp4	0.977532174798226
CAMB-7A12C	MN908947.3	10497	TTGGTTTTAACATAGATTATGACTGTGTCTCTTT	-	0.0101176470588235	0.0131941176470588	NA;NA;NA;NA;3e-04;0.00021;4e-04;0.00056;0.00046;0.00046;0.00064;7e-04;0.00034;0.00054;0.00045;0.00017;9.5e-07;2.4e-06;2.2e-06;2.6e-06;1.8e-06;9.8e-07;1.2e-06;1e-06;5.5e-06;2.4e-06;6.1e-07;5.7e-06;6.3e-06;2.2e-06;1e-06;0.012;0.0087;0.0024	0.00042;0.00054;0.00049;0.00057;4e-06;5e-06;1.7e-05;2.6e-05;2e-05;2.3e-05;3.6e-05;3.5e-06;1.3e-05;2.3e-05;2.2e-05;4.6e-06;1.5e-06;3.7e-06;3.7e-06;3.3e-06;2.7e-06;1.8e-06;1.8e-06;1.5e-06;8.5e-06;3.3e-06;9.8e-07;7e-06;8.6e-06;3.3e-06;1.6e-06;4.1e-05;4.6e-05;0.00064	0.0107425090549885	GTT	ORF1ab:3C-like-proteinase	.	443-476-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.997223935842073
CAMB-7A12C	MN908947.3	11074	C	INS	0.11	0.18	1.7e-49	1.9e-87	0.143190327776267	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.846737925408413
CAMB-7A12C	MN908947.3	11083	G	-	0.17	0.1	5.5e-76	2.4e-44	0.140496814921638	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.9100919709284e-05
CAMB-7A12C	MN908947.3	11083	G	T	0.83	0.9	0	0	0.859302625421414	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.9100919709284e-05
CAMB-7A12C	MN908947.3	11595	A	G	0.026	0.0033	3.5e-12	0.0052	0.01519661601128	CAG	ORF1ab:nsp6	Q208R	A623G	CAG>CGG	Missense	ORF1ab:nsp6	0.98480338398872
CAMB-7A12C	MN908947.3	13146	GTGTTAAGA	-	0.00805555555555556	0.00235555555555556	0.00019;2.3e-05;4.4e-05;1.4e-06;2.5e-05;0.00082;0.00046;0.00057;0.00062	0.025;0.007;0.0097;0.0024;0.0012;NA;NA;NA;NA	0.006186132638365	TGT	ORF1ab:nsp10	.	122-130-delinframe	.	no-SNV	ORF1ab:nsp10	0.992124855882909
CAMB-7A12C	MN908947.3	14657	C	T	0.01	0.0046	3.4e-06	7e-04	0.00761890514302811	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A397V	C1190T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.992359723454046
CAMB-7A12C	MN908947.3	14790	C	T	0.0064	0.011	0.00012	1e-06	0.00852464001042504	TCA	ORF1ab:RNA-dependent-RNA-polymerase	I441I	C1323T	ATC>ATT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.991388484677367
CAMB-7A12C	MN908947.3	14805	C	T	1	1	0	0	0.999897352843896	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	2.28104791341142e-05
CAMB-7A12C	MN908947.3	16375	C	T	0.015	0.0053	8.9e-07	0.0018	0.0104685521317011	TCC	ORF1ab:helicase	P47S	C139T	CCG>TCG	Missense	ORF1ab:helicase	0.989531447868299
CAMB-7A12C	MN908947.3	17019	G	T	0.038	0.045	3.4e-18	5.4e-21	0.0414857975236708	AGT	ORF1ab:helicase	E261D	G783T	GAG>GAT	Missense	ORF1ab:helicase	0.957203204661326
CAMB-7A12C	MN908947.3	19719	A	-	0.013	0.006	7.7e-07	0.001	0.0110265569187762	CAA	ORF1ab:endoRNAse	.	99-99-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.984857897189005
CAMB-7A12C	MN908947.3	19816	G	T	1	1	0	0	0.999838043566281	AGT	ORF1ab:endoRNAse	V66L	G196T	GTA>TTA	Missense	ORF1ab:endoRNAse	8.09782168596648e-05
CAMB-7A12C	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-7A12C	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-7A12C	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7A12C	MN908947.3	26617	T	-	0.0048	0.0091	0.00051	6.8e-06	0.00683494827744979	ATT	M	.	95-95-delfrshift	.	no-SNV	GU280_gp05	0.993124123888554
CAMB-7A12C	MN908947.3	2668	C	T	0.33	0.37	2.4e-123	1.5e-101	0.340571428571429	CCC	ORF1ab:nsp2	A621A	C1863T	GCC>GCT	Synonymous	ORF1ab:nsp2	0.659428571428571
CAMB-7A12C	MN908947.3	28887	C	T	0.038	0.037	2.1e-17	1.3e-16	0.0373002978608178	ACT	N	T205I	C614T	ACT>ATT	Missense	GU280_gp10	0.961751963173572
CAMB-7A12C	MN908947.3	28892	C	A	0.026	0.018	8.8e-13	1.1e-09	0.0227974508902175	TCC	N	P207T	C619A	CCT>ACT	Missense	GU280_gp10	0.976151369818015
CAMB-7A12C	MN908947.3	29272	C	T	0.18	0.17	8.7e-82	4.6e-79	0.17381932196747	ACA	N	Y333Y	C999T	TAC>TAT	Synonymous	GU280_gp10	0.826150529854234
CAMB-7A12C	MN908947.3	3833	TT	-	0.00735	0.00585	0.00098;3.6e-05	0.0045;0.00016	0.00673861028370526	CTT	ORF1ab:nsp3	.	1114-1115-delfrshift	.	no-SNV	ORF1ab:nsp3	0.993184488836663
CAMB-7A12C	MN908947.3	4300	G	A	0.012	0.0061	2.7e-07	7.6e-05	0.0091637496947355	TGC	ORF1ab:nsp3	V527V	G1581A	GTG>GTA	Synonymous	ORF1ab:nsp3	0.990812992057308
CAMB-7A12C	MN908947.3	5826	C	T	0.017	0.016	2.8e-07	5e-07	0.0162656634820969	ACA	ORF1ab:nsp3	T1036I	C3107T	ACA>ATA	Missense	ORF1ab:nsp3	0.982029283607134
CAMB-7A12C	MN908947.3	669	GTT	-	0.018	0.0283333333333333	4.7e-10;1.2e-09;3.2e-09	7.1e-14;1.4e-14;7.5e-14	0.0220033741288965	AGT	ORF1ab:leader-protein	.	404-406-delinframe	.	no-SNV	ORF1ab:leader-protein	0.977022640326863
CAMB-7A12C	MN908947.3	7067	G	A	0.078	0.0072	6.8e-27	0.0028	0.0592734225621415	AGA	ORF1ab:nsp3	E1450K	G4348A	GAA>AAA	Missense	ORF1ab:nsp3	0.940726577437858
CAMB-7A12C	MN908947.3	9091	T	C	0.0098	0.0053	3.2e-06	0.00022	0.00781784080351978	CTG	ORF1ab:nsp4	S179S	T537C	TCT>TCC	Synonymous	ORF1ab:nsp4	0.99218215919648
CAMB-7A13B	MN908947.3	11075	T	-	0.038	0.04	1.7e-09	1.2e-10	0.038671225916313	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95746989109985
CAMB-7A13B	MN908947.3	14408	C	T	1	1	0	0	0.996543222428386	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000444805937523829
CAMB-7A13B	MN908947.3	16289	C	T	1	1	0	0	0.99922113325112	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	3.24527812033491e-05
CAMB-7A13B	MN908947.3	23403	A	G	1	1	0	0	0.999360741921018	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.58704882214314e-05
CAMB-7A13B	MN908947.3	241	C	T	1	1	0	0	0.998608988339544	TCG	NA	NA	NA	NA	NA	NA	0.000309113702323505
CAMB-7A13B	MN908947.3	25429	G	T	1	1	0	0	0.998383143849139	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0.000102117230580707
CAMB-7A13B	MN908947.3	26137	A	C	0.024	0.017	7.9e-06	0.0011	0.0216756982075865	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.97804640822565
CAMB-7A13B	MN908947.3	27915	G	A	1	1	0	0	0.998745779064158	AGG	ORF8	G8R	G22A	GGA>AGA	Missense	GU280_gp09	0
CAMB-7A13B	MN908947.3	29451	C	T	0.011	0.0072	4.7e-06	0.00013	0.0098026734563972	ACT	N	T393I	C1178T	ACT>ATT	Missense	GU280_gp10	0.990197326543603
CAMB-7A13B	MN908947.3	3037	C	T	1	1	0	0	0.998870269252495	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.76576915835059e-05
CAMB-7A14A	MN908947.3	11075	T	-	0.059	0.044	3.4e-14	7.7e-11	0.0522679015961341	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.944867476936594
CAMB-7A14A	MN908947.3	14408	C	T	0.99	1	0	0	0.995292820874216	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000325256139209628
CAMB-7A14A	MN908947.3	17805	A	T	0.01	0.0089	2.9e-06	8.7e-06	0.00956214109926169	CAA	ORF1ab:helicase	S523S	A1569T	TCA>TCT	Synonymous	ORF1ab:helicase	0.989732875307629
CAMB-7A14A	MN908947.3	20937	G	T	1	1	0	0	0.999354973675953	CGC	ORF1ab:2'-O-ribose-methyltransferase	T93T	G279T	ACG>ACT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	1.74331438931697e-05
CAMB-7A14A	MN908947.3	23403	A	G	1	1	0	0	0.999574820581616	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.06374759003907e-05
CAMB-7A14A	MN908947.3	241	C	T	1	1	0	0	0.99817333374267	TCG	NA	NA	NA	NA	NA	NA	0.000291652595708102
CAMB-7A14A	MN908947.3	25599	G	T	1	1	0	0	0.9992404481356	GGC	ORF3a	W69C	G207T	TGG>TGT	Missense	GU280_gp03	9.99410347894742e-06
CAMB-7A14A	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0273684210526316	0.0400263157894737	0.0076;0.0012;0.0043;0.0032;0.0055;0.00011;4e-04;0.00032;0.00032;0.00011;0.00012;6.5e-05;0.00015;7.5e-05;9.2e-05;0.00016;6.5e-05;0.00013;9e-05;9.1e-05;7.1e-05;0.00015;7.9e-05;1e-04;8.2e-05;5.3e-05;0.00012;7.8e-05;4.2e-05;6.9e-05;0.00012;0.00011;1e-04;0.00019;0.00011;0.00015;0.00011;0.0021	3e-04;1.5e-05;0.00013;0.00014;0.00023;8.9e-06;3e-05;4.5e-07;4.4e-07;9.7e-08;2.3e-07;1.7e-07;4.3e-07;2.6e-07;3.7e-07;6.3e-07;2.3e-07;5.4e-07;3.1e-07;3e-07;2.1e-07;5.8e-07;2.8e-07;3.9e-07;2.7e-07;1.8e-07;4.5e-07;2.2e-07;8.8e-08;2.7e-07;4.6e-07;4.1e-07;2.1e-07;3.9e-07;6.6e-08;1.7e-07;1.3e-07;0.00047	0.0353648243816025	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.979721482467821
CAMB-7A14A	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999323501555946	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000219603250128102
CAMB-7A14A	MN908947.3	3037	C	T	1	1	0	0	0.999756846296465	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A14A	MN908947.3	3712	ATC	-	0.0126666666666667	0.00433333333333333	3.3e-07;1.3e-06;1.2e-06	0.00098;0.0013;0.0012	0.00761140326598395	TAT	ORF1ab:nsp3	.	993-995-delinframe	.	no-SNV	ORF1ab:nsp3	0.991194364393212
CAMB-7A14A	MN908947.3	4149	T	C	1	1	0	0	0.999236098585721	GTT	ORF1ab:nsp3	V477A	T1430C	GTT>GCT	Missense	ORF1ab:nsp3	0.000689633221223728
CAMB-7A14A	MN908947.3	522	TT	-	0.0435	0.0485	1e-06;6.5e-05	2.2e-07;1.3e-05	0.0457263957146943	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.944420595100749
CAMB-7A159	MN908947.3	10369	C	T	0.0081	0.011	4.9e-05	2e-06	0.00993869455463397	GCA	ORF1ab:3C-like-proteinase	R105R	C315T	CGC>CGT	Synonymous	ORF1ab:3C-like-proteinase	0.990032455824017
CAMB-7A159	MN908947.3	11075	T	-	0.058	0.011	2.6e-14	9e-04	0.0302284710017575	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.966703946317303
CAMB-7A159	MN908947.3	13916	A	T	0.0054	0.011	5.1e-05	3.4e-07	0.00868419476552674	AAA	ORF1ab:RNA-dependent-RNA-polymerase	K150I	A449T	AAA>ATA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.991235950569963
CAMB-7A159	MN908947.3	14408	C	T	1	1	0	0	0.99963530269876	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000262126185266229
CAMB-7A159	MN908947.3	17503	A	-	0.0073	0.008	1.5e-05	1.2e-05	0.0077117500071804	CAA	ORF1ab:helicase	.	1267-1267-delfrshift	.	no-SNV	ORF1ab:helicase	0.992187724387512
CAMB-7A159	MN908947.3	17972	G	C	0.011	0.0053	5.7e-07	0.00017	0.00747367994269728	AGA	ORF1ab:helicase	R579T	G1736C	AGA>ACA	Missense	ORF1ab:helicase	0.992499290473423
CAMB-7A159	MN908947.3	18654	C	T	0.026	0.0063	6.2e-13	0.00011	0.0153586307848215	GCA	ORF1ab:3'-to-5'-exonuclease	R205R	C615T	CGC>CGT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.980734151559509
CAMB-7A159	MN908947.3	20655	A	G	0.029	0.037	1.6e-14	7e-18	0.0333834997947736	TAC	ORF1ab:endoRNAse	L345L	A1035G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0.966616500205226
CAMB-7A159	MN908947.3	21662	C	T	0.016	0.012	1.6e-07	3.9e-06	0.0141743444365698	ACG	S	R34C	C100T	CGT>TGT	Missense	GU280_gp02, spike glycoprotein	0.98582565556343
CAMB-7A159	MN908947.3	22159	TTAT	-	0.00765	0.0029725	0.00039;0.00029;0.00022;2.1e-05	0.47;0.00065;0.00058;NA	0.0046634114226148	GTT	S	.	597-600-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.993472179048803
CAMB-7A159	MN908947.3	22601	T	-	0.0071	0.006	2.9e-05	8.8e-05	0.00649234006518002	ATT	S	.	1039-1039-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.99350765993482
CAMB-7A159	MN908947.3	23403	A	G	1	1	0	0	0.999912600608618	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.35631937326691e-05
CAMB-7A159	MN908947.3	241	C	T	1	1	0	0	0.999855308374028	TCG	NA	NA	NA	NA	NA	NA	7.23458129860734e-05
CAMB-7A159	MN908947.3	24313	T	A	0.0044	0.0096	0.00033	2.6e-06	0.00700770847932726	ATG	S	Y917*	T2751A	TAT>TAA	Nonsense	GU280_gp02, spike glycoprotein	0.988130693763139
CAMB-7A159	MN908947.3	24313	TG	CA	0.00195	0.0088	NA;0.00051	2.3e-06;1.2e-05	0.00534826390339698	ATG	S	.	2751-2752-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.988130693763139
CAMB-7A159	MN908947.3	25429	G	T	1	1	0	0	0.999865564293876	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0.000107548564898837
CAMB-7A159	MN908947.3	25772	TTTGGCTTTGCTGGAAATGCCG	-	0.00940909090909091	0.000263636363636364	4.1e-05;2.1e-05;2.6e-05;8.2e-06;6.6e-06;7.4e-06;4.8e-11;6.9e-06;3.4e-05;8.4e-05;2e-05;1.6e-05;4.9e-05;6.9e-06;1.3e-05;2.3e-06;2.9e-06;5.6e-06;7.6e-06;6e-06;4.4e-06;6.6e-06	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;5.7e-05	0.00399815469783177	CTT	ORF3a	.	380-401-delfrshift	.	no-SNV	GU280_gp03	0.995692405871091
CAMB-7A159	MN908947.3	25916	C	T	1	1	0	0	1	ACA	ORF3a	T175I	C524T	ACA>ATA	Missense	GU280_gp03	0
CAMB-7A159	MN908947.3	27364	G	T	0.046	0.074	6.2e-22	5e-34	0.0623419134057432	AGA	ORF6	E55*	G163T	GAG>TAG	Nonsense	GU280_gp06	0.937638248276546
CAMB-7A159	MN908947.3	29041	G	C	0.026	0.032	4.2e-05	9.9e-06	0.0298956377803347	AGA	N	K256N	G768C	AAG>AAC	Missense	GU280_gp10	0.965845091745897
CAMB-7A159	MN908947.3	29445	C	T	0.98	0.97	0	0	0.973413897280967	ACT	N	T391I	C1172T	ACT>ATT	Missense	GU280_gp10	0.0241691842900302
CAMB-7A159	MN908947.3	3037	C	T	1	1	0	0	0.99965015393227	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A159	MN908947.3	3184	A	C	0.0071	0.0051	3.5e-05	0.00026	0.00597631445960495	AAG	ORF1ab:nsp3	E155D	A465C	GAA>GAC	Missense	ORF1ab:nsp3	0.993957770307385
CAMB-7A159	MN908947.3	354	G	C	0.003	0.0097	0.00075	1.3e-06	0.00673313354848625	GGC	ORF1ab:leader-protein	G30A	G89C	GGC>GCC	Missense	ORF1ab:leader-protein	0.992949900107576
CAMB-7A159	MN908947.3	3892	G	T	0.0073	0.0077	1.9e-05	1.2e-05	0.00747468252692493	AGG	ORF1ab:nsp3	E391D	G1173T	GAG>GAT	Missense	ORF1ab:nsp3	0.992525317473075
CAMB-7A159	MN908947.3	4213	T	-	0.033	0.012	6.5e-16	8.8e-07	0.0192831770255793	CTT	ORF1ab:nsp3	.	1494-1494-delfrshift	.	no-SNV	ORF1ab:nsp3	0.980547672298758
CAMB-7A159	MN908947.3	4525	TAGA	-	0.007925	0.015	0.00026;0.00055;0.0044;0.0042	7.9e-07;3.4e-06;0.00011;0.00011	0.0120810246162231	CTA	ORF1ab:nsp3	.	1806-1809-delfrshift	.	no-SNV	ORF1ab:nsp3	0.987435169177575
CAMB-7A159	MN908947.3	4581	ACGATCTAAAT	-	0.00342727272727273	0.0151818181818182	0.0045;0.005;0.0062;0.0055;0.0056;NA;NA;NA;NA;NA;NA	0.00011;0.00011;0.00015;0.00013;0.00014;8.7e-05;8.3e-06;6.7e-07;7.7e-07;1.2e-07;3.4e-06	0.00872970791354002	AAC	ORF1ab:nsp3	.	1862-1872-delfrshift	.	no-SNV	ORF1ab:nsp3	0.988010817307692
CAMB-7A159	MN908947.3	4733	C	T	0.0075	0.0022	2.5e-05	0.0078	0.00430907266395136	TCT	ORF1ab:nsp3	L672F	C2014T	CTT>TTT	Missense	ORF1ab:nsp3	0.995676170237884
CAMB-7A159	MN908947.3	4744	T	C	0.0075	0.0023	2.8e-05	0.0076	0.00437798583070802	CTT	ORF1ab:nsp3	S675S	T2025C	TCT>TCC	Synonymous	ORF1ab:nsp3	0.995577642691278
CAMB-7A159	MN908947.3	5239	C	T	0.0031	0.0095	0.0068	3.3e-05	0.00696643445218493	ACC	ORF1ab:nsp3	Y840Y	C2520T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.991133628879037
CAMB-7A159	MN908947.3	5894	ATAAAACCAGTTACTT	-	0.007603125	0.0090875	NA;0.47;0.48;3.2e-06;1.2e-06;3e-07;1.3e-05;1.1e-05;2.6e-06;4.1e-06;8e-06;2.1e-05;8.9e-05;9.7e-05;3.1e-05;0.00066	3.1e-06;4.8e-05;1.3e-05;4.4e-06;1.5e-06;3.1e-07;1.9e-05;1.7e-05;1.9e-06;5e-06;9.2e-06;2.6e-05;0.00016;0.00016;5.4e-05;9e-04	0.00885841254892728	CAT	ORF1ab:nsp3	.	3175-3190-delfrshift	.	no-SNV	ORF1ab:nsp3	0.994009502168973
CAMB-7A159	MN908947.3	6236	G	INS	0.0072	0.0079	2.8e-05	1.5e-05	0.00759010786635096	TGT	ORF1ab:nsp3	.	3516-3517-insfrshift	.	no-SNV	ORF1ab:nsp3	0.987937384898711
CAMB-7A159	MN908947.3	6813	C	T	0.0045	0.0081	0.00094	2.5e-05	0.00654843110504775	ACT	ORF1ab:nsp3	T1365I	C4094T	ACT>ATT	Missense	ORF1ab:nsp3	0.993360618462938
CAMB-7A159	MN908947.3	6968	C	T	0.0071	0.022	0.00086	1.2e-07	0.015353121801433	ACT	ORF1ab:nsp3	L1417L	C4249T	CTA>TTA	Synonymous	ORF1ab:nsp3	0.984646878198567
CAMB-7A159	MN908947.3	9231	G	C	0.0073	0.007	1.4e-05	2.2e-05	0.00716109970454204	TGT	ORF1ab:nsp4	C226S	G677C	TGT>TCT	Missense	ORF1ab:nsp4	0.99188742550954
CAMB-7A159	MN908947.3	9502	C	T	0.015	0.0069	9.6e-07	0.0019	0.0107218235542423	CCT	ORF1ab:nsp4	A316A	C948T	GCC>GCT	Synonymous	ORF1ab:nsp4	0.989278176445758
CAMB-7A168	MN908947.3	11416	C	T	0.047	0.068	1e-15	1.9e-22	0.0580688723835246	TCG	ORF1ab:nsp6	L148L	C444T	CTC>CTT	Synonymous	ORF1ab:nsp6	0.941931127616475
CAMB-7A168	MN908947.3	12442	G	-	0.015	0.005	1.1e-08	7.6e-05	0.0105004395532836	TGA	ORF1ab:nsp8	.	351-351-delfrshift	.	no-SNV	ORF1ab:nsp8	0.979552632435776
CAMB-7A168	MN908947.3	12561	A	T	0.047	0.042	3.8e-22	6.3e-20	0.0442883895131086	CAA	ORF1ab:nsp8	Q157L	A470T	CAA>CTA	Missense	ORF1ab:nsp8	0.955594569288389
CAMB-7A168	MN908947.3	12759	A	G	0.94	0.97	0	0	0.956795846467643	GAT	ORF1ab:nsp9	D25G	A74G	GAT>GGT	Missense	ORF1ab:nsp9	0.0431925644353792
CAMB-7A168	MN908947.3	13914	T	G	0.0037	0.0062	0.00029	2e-05	0.00496545768566494	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.99496257915947
CAMB-7A168	MN908947.3	1396	AGT	-	0.009	0.0376666666666667	NA;NA;6.8e-10	1.5e-08;1.4e-08;1.8e-08	0.00864197530864197	AAG	ORF1ab:nsp2	.	591-593-delinframe	.	no-SNV	ORF1ab:nsp2	0.987569060773481
CAMB-7A168	MN908947.3	1398	TA	-	0.027	0.0185	6.8e-10;5.8e-10	1.8e-08;NA	0.0246305418719212	GTA	ORF1ab:nsp2	.	593-594-delfrshift	.	no-SNV	ORF1ab:nsp2	0.97037037037037
CAMB-7A168	MN908947.3	14408	C	T	1	1	0	0	0.99938645397071	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000346786886120522
CAMB-7A168	MN908947.3	14599	C	T	0.35	0.23	3.2e-183	3.7e-108	0.284247465557577	TCT	ORF1ab:RNA-dependent-RNA-polymerase	L378L	C1132T	CTA>TTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.715726540161165
CAMB-7A168	MN908947.3	16402	G	T	0.014	0.022	1.6e-07	2.4e-10	0.0176329147742453	TGA	ORF1ab:helicase	D56Y	G166T	GAT>TAT	Missense	ORF1ab:helicase	0.982367085225755
CAMB-7A168	MN908947.3	17338	G	T	0.003	0.011	0.0021	6.3e-07	0.0070541388676459	AGC	ORF1ab:helicase	A368S	G1102T	GCA>TCA	Missense	ORF1ab:helicase	0.992761266844229
CAMB-7A168	MN908947.3	1738	G	T	0.018	0.006	5.4e-10	3.2e-05	0.0123313168915775	TGA	ORF1ab:nsp2	V311V	G933T	GTG>GTT	Synonymous	ORF1ab:nsp2	0.987668683108422
CAMB-7A168	MN908947.3	17410	C	T	0.018	0.0084	4.5e-09	6.1e-05	0.0134098997088321	ACG	ORF1ab:helicase	R392C	C1174T	CGT>TGT	Missense	ORF1ab:helicase	0.986565836298932
CAMB-7A168	MN908947.3	18017	G	T	0.018	0.011	7.4e-10	4e-07	0.0145241494756536	CGT	ORF1ab:helicase	R594L	G1781T	CGT>CTT	Missense	ORF1ab:helicase	0.985360970246008
CAMB-7A168	MN908947.3	18636	G	A	1	0.98	0	0	0.987568251226209	TGA	ORF1ab:3'-to-5'-exonuclease	V199V	G597A	GTG>GTA	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.0122466607027177
CAMB-7A168	MN908947.3	203	C	T	0.012	0.12	9e-07	4e-53	0.0595501965304253	TCG	NA	NA	NA	NA	NA	NA	0.940390696574755
CAMB-7A168	MN908947.3	22452	C	T	0.022	0.053	0.00028	2.6e-06	0.0318352059925094	TCA	S	S297L	C890T	TCA>TTA	Missense	GU280_gp02, spike glycoprotein	0.968164794007491
CAMB-7A168	MN908947.3	23403	A	G	1	1	0	0	0.999933552168193	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.31582654457985e-05
CAMB-7A168	MN908947.3	23553	TACCCATTGGTGCAGGTATATGCGCTAGT	-	0.00152172413793103	0.0488965517241379	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0011;0.0016;NA	2.7e-05;1.1e-05;8.1e-05;6.4e-05;8.1e-05;1e-04;2.2e-05;4.5e-05;2.1e-05;4.8e-05;5.5e-05;5.4e-05;5.2e-05;5.1e-05;2.6e-05;2.3e-05;8.4e-06;1.2e-06;1.1e-05;3.5e-06;8.1e-06;2.7e-06;9.4e-06;2.4e-05;1.1e-05;1.1e-05;6.6e-08;1.3e-07;1.7e-05	0.0166222222222222	ATA	S	.	1991-2019-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.984460241362209
CAMB-7A168	MN908947.3	24034	C	T	0.049	0.04	5.9e-22	3e-18	0.0442745889818287	ACA	S	N824N	C2472T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.955725411018171
CAMB-7A168	MN908947.3	241	C	T	0.99	1	0	0	0.992437022042285	TCG	NA	NA	NA	NA	NA	NA	8.43454790823212e-05
CAMB-7A168	MN908947.3	27364	G	C	0.022	0.089	1.4e-11	3.5e-41	0.0570729103819557	AGA	ORF6	E55Q	G163C	GAG>CAG	Missense	GU280_gp06	0.942869076901657
CAMB-7A168	MN908947.3	28253	C	T	0.14	0.037	2e-65	8.1e-17	0.0914488002424309	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.908275710074658
CAMB-7A168	MN908947.3	28428	G	C	0.011	0.003	9.3e-07	0.0013	0.00691667667076065	TGG	N	W52S	G155C	TGG>TCG	Missense	GU280_gp10	0.985381710053653
CAMB-7A168	MN908947.3	28793	G	C	0.0039	0.007	0.001	4.4e-05	0.00540223135642983	AGA	N	E174Q	G520C	GAA>CAA	Missense	GU280_gp10	0.919788608338227
CAMB-7A168	MN908947.3	28881	GGG	AAC	0.976666666666667	0.98	0;0;0	0;0;0	0.977595698374088	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.0251921434671221
CAMB-7A168	MN908947.3	29080	TG	-	0.021	0.0105	4.8e-05;3.7e-05	0.0078;0.0072	0.0154090188080671	ATG	N	.	807-808-delfrshift	.	no-SNV	GU280_gp10	0.983978325584507
CAMB-7A168	MN908947.3	29139	AGG	-	0.0116666666666667	0.00833333333333333	9.8e-08;3.2e-07;2.3e-07	4.7e-08;1.7e-07;NA	0.0118742497485644	CAG	N	.	866-868-delinframe	.	no-SNV	GU280_gp10	0.986501806844753
CAMB-7A168	MN908947.3	29525	C	T	0.14	0.24	1.8e-54	2.1e-86	0.16967706622879	TCA	N	Q418*	C1252T	CAG>TAG	Nonsense	GU280_gp10	0.83032293377121
CAMB-7A168	MN908947.3	29760	TA	-	0.0335	0.0225	2.1e-12;2.5e-12	4.1e-08;4.9e-08	0.0290037831021438	GTA	NA	NA	NA	NA	NA	NA	0.97083685545224
CAMB-7A168	MN908947.3	3037	C	T	1	1	0	0	0.997950399672064	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000204960032793605
CAMB-7A168	MN908947.3	4531	TTACT	-	0.043	0.0054	6.3e-06;2.6e-05;4.4e-05;4e-05;1.2e-05	NA;NA;NA;NA;9e-04	0.0201471498315341	TTT	ORF1ab:nsp3	.	1812-1816-delfrshift	.	no-SNV	ORF1ab:nsp3	0.979558011049724
CAMB-7A168	MN908947.3	522	TTGAG	-	0.0322	0.0106	2.2e-06;1.7e-06;5.1e-05;2.3e-11;3.5e-13	0.00098;0.00081;NA;NA;NA	0.0149091541337043	GTT	ORF1ab:leader-protein	.	257-261-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.961402848949274
CAMB-7A168	MN908947.3	635	C	T	0.067	0.037	1.5e-30	1.5e-17	0.0534266619211453	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.94653379206707
CAMB-7A168	MN908947.3	683	C	T	0.017	0.023	3.2e-09	6.3e-12	0.0199975192601883	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.980002480739812
CAMB-7A168	MN908947.3	739	AG	-	0.0195	0.0225	NA;6.6e-10	2.4e-06;2.9e-06	0.0209764754061064	AAG	ORF1ab:leader-protein	.	474-475-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.989102015317337
CAMB-7A168	MN908947.3	740	G	-	0.039	0.022	6.6e-10	2.9e-06	0.0308129517330887	AGA	ORF1ab:leader-protein	.	475-475-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.969075163910582
CAMB-7A168	MN908947.3	9286	C	T	0.11	0.19	4.4e-44	4.3e-69	0.147127981189117	ACA	ORF1ab:nsp4	N244N	C732T	AAC>AAT	Synonymous	ORF1ab:nsp4	0.852872018810883
CAMB-7A168	MN908947.3	9430	C	T	0.15	0.06	5.7e-54	2.5e-20	0.112098956320062	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.887901043679938
CAMB-7A177	MN908947.3	10323	A	G	0.024	0.022	3.2e-07	9.1e-07	0.0234287594603488	AAG	ORF1ab:3C-like-proteinase	K90R	A269G	AAG>AGG	Missense	ORF1ab:3C-like-proteinase	0.976516397937918
CAMB-7A177	MN908947.3	11074	C	INS	0.12	0.11	3e-43	2.8e-39	0.112908805031447	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.882311320754717
CAMB-7A177	MN908947.3	11083	G	-	0.16	0.16	5.1e-69	5.9e-72	0.15919123278515	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.3925055352095e-05
CAMB-7A177	MN908947.3	11083	G	T	0.84	0.84	0	0	0.840627741495272	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.3925055352095e-05
CAMB-7A177	MN908947.3	14805	C	T	1	1	0	0	0.998496363654962	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000767161400529853
CAMB-7A177	MN908947.3	1607	G	A	0.0083	0.007	1e-05	3.1e-05	0.00766532591178104	TGA	ORF1ab:nsp2	D268N	G802A	GAC>AAC	Missense	ORF1ab:nsp2	0.991996099622151
CAMB-7A177	MN908947.3	16131	A	G	0.0064	0.0069	6.4e-05	4.3e-05	0.00665669122160835	GAC	ORF1ab:RNA-dependent-RNA-polymerase	G888G	A2664G	GGA>GGG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.993237799263352
CAMB-7A177	MN908947.3	16933	A	C	0.018	0.02	1.3e-06	4.8e-07	0.0188303791870877	AAT	ORF1ab:helicase	M233L	A697C	ATG>CTG	Missense	ORF1ab:helicase	0.981003795555883
CAMB-7A177	MN908947.3	23053	C	T	0.0082	0.0077	1.3e-05	1.9e-05	0.00796425285845709	TCC	S	F497F	C1491T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.992009462478644
CAMB-7A177	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-7A177	MN908947.3	2558	C	T	1	1	0	0	0.999185820755308	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.000109601052170101
CAMB-7A177	MN908947.3	25907	G	A	0.012	0.015	3.4e-07	2.6e-08	0.0135338711245019	GGT	ORF3a	G172D	G515A	GGT>GAT	Missense	GU280_gp03	0.986466128875498
CAMB-7A177	MN908947.3	26144	G	T	1	1	0	0	0.999758360719118	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.0001933114247052
CAMB-7A177	MN908947.3	26159	TTA	-	0.703333333333333	0.716666666666667	0;0;0	0;0;0	0.705717083138223	GTT	ORF3a	.	767-769-delinframe	.	no-SNV	GU280_gp03	0.274966099470714
CAMB-7A177	MN908947.3	26519	A	T	0.13	0.13	3.5e-61	9.7e-62	0.133792641669016	TAG	NA	NA	NA	NA	NA	NA	0.866066394135889
CAMB-7A177	MN908947.3	27907	T	C	0.67	0.67	0	0	0.670643581163005	GTT	ORF8	V5A	T14C	GTT>GCT	Missense	GU280_gp09	0.329065425093361
CAMB-7A177	MN908947.3	5753	A	G	1	1	0	0	0.999724019502622	TAA	ORF1ab:nsp3	N1012D	A3034G	AAT>GAT	Missense	ORF1ab:nsp3	6.13289994173745e-05
CAMB-7A177	MN908947.3	6666	C	T	0.12	0.11	8.2e-54	1.8e-48	0.117427337457686	CCT	ORF1ab:nsp3	P1316L	C3947T	CCT>CTT	Missense	ORF1ab:nsp3	0.882164118127699
CAMB-7A195	MN908947.3	10789	C	T	0.059	0.06	4.4e-26	8.3e-25	0.0596507494977592	ACC	ORF1ab:3C-like-proteinase	D245D	C735T	GAC>GAT	Synonymous	ORF1ab:3C-like-proteinase	0.940349250502241
CAMB-7A195	MN908947.3	1376	C	T	0.033	0.019	6.3e-12	6.3e-07	0.0273264401772526	TCC	ORF1ab:nsp2	P191S	C571T	CCA>TCA	Missense	ORF1ab:nsp2	0.972673559822747
CAMB-7A195	MN908947.3	14408	C	T	1	1	0	0	0.999512172458651	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000371678126742241
CAMB-7A195	MN908947.3	15536	C	T	0.014	0.0073	8.5e-08	5.9e-05	0.0110964447861215	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A690V	C2069T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.988874544900712
CAMB-7A195	MN908947.3	1659	G	T	0.0092	0.006	5.1e-06	0.00012	0.0078890218499313	GGT	ORF1ab:nsp2	G285V	G854T	GGT>GTT	Missense	ORF1ab:nsp2	0.991933696760183
CAMB-7A195	MN908947.3	19934	C	T	0.027	0.012	4.6e-07	0.002	0.0216919739696312	ACT	ORF1ab:endoRNAse	T105I	C314T	ACT>ATT	Missense	ORF1ab:endoRNAse	0.978308026030369
CAMB-7A195	MN908947.3	23403	A	G	1	1	0	0	0.999900148351021	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.55871276959945e-05
CAMB-7A195	MN908947.3	241	C	T	1	1	0	0	0.99988520261738	TCG	NA	NA	NA	NA	NA	NA	7.65315884131175e-05
CAMB-7A195	MN908947.3	24726	C	T	0.017	0.014	1.8e-09	2e-08	0.0159454154593887	TCA	S	S1055L	C3164T	TCA>TTA	Missense	GU280_gp02, spike glycoprotein	0.98401719786896
CAMB-7A195	MN908947.3	24734	C	T	0.017	0.0085	2.5e-09	6.9e-06	0.0135801320807367	TCA	S	H1058Y	C3172T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.986401264998605
CAMB-7A195	MN908947.3	27923	C	T	1	1	0	0	0.999123268455199	TCA	ORF8	I10I	C30T	ATC>ATT	Synonymous	GU280_gp09	0.000876731544800982
CAMB-7A195	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999314285714286	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A195	MN908947.3	2949	T	C	0.049	0.024	1.2e-20	2.2e-11	0.0365342383709323	ATT	ORF1ab:nsp3	I77T	T230C	ATT>ACT	Missense	ORF1ab:nsp3	0.961469355160711
CAMB-7A195	MN908947.3	3037	C	T	1	1	0	0	0.999576510446076	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A195	MN908947.3	4335	C	T	0.0032	0.01	0.001	6.4e-07	0.00684464640727066	CCA	ORF1ab:nsp3	P539L	C1616T	CCA>CTA	Missense	ORF1ab:nsp3	0.993155353592729
CAMB-7A1A4	MN908947.3	14408	C	T	1	1	0	0	0.999670619235837	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000219587176108915
CAMB-7A1A4	MN908947.3	23403	A	G	1	1	0	0	0.999855803893295	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000115356885364095
CAMB-7A1A4	MN908947.3	241	C	T	1	1	0	0	0.999874356074884	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-7A1A4	MN908947.3	28881	GGG	AAC	1	1	0;0;0	6e-294;3.3e-307;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A1A4	MN908947.3	3037	C	T	1	0.87	2.9e-142	6.7e-266	0.876796714579055	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000513347022587269
CAMB-7A1B3	MN908947.3	11075	T	-	0.038	0.035	1.6e-09	2.6e-09	0.0369482247777834	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957552854918897
CAMB-7A1B3	MN908947.3	14408	C	T	1	1	0	0	0.998676051237949	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000282895034626352
CAMB-7A1B3	MN908947.3	17835	T	C	1	1	0	0	0.999544070910383	TTG	ORF1ab:helicase	V533V	T1599C	GTT>GTC	Synonymous	ORF1ab:helicase	0.00040229037319137
CAMB-7A1B3	MN908947.3	18512	C	A	0.0058	0.0065	1e-04	3.6e-05	0.00605498658349841	CCT	ORF1ab:3'-to-5'-exonuclease	P158H	C473A	CCT>CAT	Missense	ORF1ab:3'-to-5'-exonuclease	0.993832623874348
CAMB-7A1B3	MN908947.3	22180	G	A	0.037	0.044	1.2e-11	1.2e-13	0.039843994510918	AGC	S	K206K	G618A	AAG>AAA	Synonymous	GU280_gp02, spike glycoprotein	0.960107855646773
CAMB-7A1B3	MN908947.3	23403	A	G	1	1	0	0	0.999736717870502	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.72360823619131e-05
CAMB-7A1B3	MN908947.3	241	C	T	1	1	0	0	0.998460171750074	TCG	NA	NA	NA	NA	NA	NA	0.000207284572105419
CAMB-7A1B3	MN908947.3	29835	C	T	0.99	0.99	0	0	0.992622742304757	TCC	NA	NA	NA	NA	NA	NA	0.00737725769524294
CAMB-7A1B3	MN908947.3	3037	C	T	1	1	0	0	0.999420508214296	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	2.89745892851969e-05
CAMB-7A1B3	MN908947.3	709	G	A	0.0063	0.0072	8.8e-05	2.8e-05	0.00665273983609192	AGC	ORF1ab:leader-protein	E148E	G444A	GAG>GAA	Synonymous	ORF1ab:leader-protein	0.993293695430928
CAMB-7A1C2	MN908947.3	14408	C	T	1	1	0	0	0.999642516682555	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000357483317445186
CAMB-7A1C2	MN908947.3	23403	A	G	1	1	0	0	0.999872179970601	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.58650220489551e-05
CAMB-7A1C2	MN908947.3	241	C	T	1	1	0	0	0.999437886453064	TCG	NA	NA	NA	NA	NA	NA	0.000421585160202361
CAMB-7A1C2	MN908947.3	28881	GGG	AAC	1	1	9.98012604599318e-322;0;0	0;0;0	0.998930481283422	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A1C2	MN908947.3	28902	T	A	1	1	0	0	0.998997995991984	ATG	N	M210K	T629A	ATG>AAG	Missense	GU280_gp10	0
CAMB-7A1C2	MN908947.3	3037	C	T	1	1	1.2e-300	9.5e-209	0.99895178197065	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A1D1	MN908947.3	11075	T	-	0.027	0.024	4.1e-07	1.1e-06	0.0256700470843897	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.968908457080768
CAMB-7A1D1	MN908947.3	14408	C	T	1	1	0	0	0.999353945546839	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000380710659898477
CAMB-7A1D1	MN908947.3	16111	C	T	0.014	0.018	6e-08	5e-10	0.0159028282357457	GCT	ORF1ab:RNA-dependent-RNA-polymerase	L882L	C2644T	CTA>TTA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.984069753094882
CAMB-7A1D1	MN908947.3	21137	A	G	0.0059	0.016	0.0017	1.7e-07	0.00994286228460881	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.990012147388312
CAMB-7A1D1	MN908947.3	23403	A	G	1	1	0	0	0.999848166611838	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.06111293873523e-05
CAMB-7A1D1	MN908947.3	241	C	T	1	0.99	0	0	0.996695144675316	TCG	NA	NA	NA	NA	NA	NA	5.27370530534754e-05
CAMB-7A1D1	MN908947.3	25563	G	T	1	1	0	0	0.999855985127191	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	7.85535669865542e-05
CAMB-7A1D1	MN908947.3	26137	A	C	0.03	0.017	1.6e-06	0.0061	0.0256839754327191	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.974316024567281
CAMB-7A1D1	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998656687775859	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.2450227108715e-05
CAMB-7A1D1	MN908947.3	29742	G	A	0.86	0.85	0	0	0.856453052012806	CGC	NA	NA	NA	NA	NA	NA	0.142707185220175
CAMB-7A1D1	MN908947.3	3037	C	T	1	1	0	0	0.998844447757856	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A1D1	MN908947.3	362	G	A	0.01	0.0075	1.6e-06	1.2e-05	0.00898956456141821	AGA	ORF1ab:leader-protein	D33N	G97A	GAC>AAC	Missense	ORF1ab:leader-protein	0.990996465641284
CAMB-7A1D1	MN908947.3	8644	T	A	1	1	0	0	0.998836689038031	TTC	ORF1ab:nsp4	V30V	T90A	GTT>GTA	Synonymous	ORF1ab:nsp4	0.000313199105145414
CAMB-7A1E0	MN908947.3	11075	T	-	0.022	0.13	1.7e-06	4e-31	0.0822660351225184	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.917545869598673
CAMB-7A1E0	MN908947.3	12903	G	-	0.023	0.023	1.5e-08	1.6e-08	0.0228970045137464	TGT	ORF1ab:nsp9	.	218-218-delfrshift	.	no-SNV	ORF1ab:nsp9	0.968403775133361
CAMB-7A1E0	MN908947.3	13914	T	G	0.0011	0.016	0.0063	2e-09	0.0098611742490471	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.990103857047942
CAMB-7A1E0	MN908947.3	14408	C	T	1	1	0	0	0.999439950217797	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000404480398257623
CAMB-7A1E0	MN908947.3	21965	T	C	0.062	0.031	4.1e-25	3.1e-14	0.0437371663244353	ATT	S	F135L	T403C	TTT>CTT	Missense	GU280_gp02, spike glycoprotein	0.956262833675565
CAMB-7A1E0	MN908947.3	23045	TATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAG	-	0.0391020408163265	0.00208163265306122	9.6e-17;2.8e-17;3.4e-17;1.7e-16;2.3e-16;5.7e-17;4.1e-17;1.8e-16;6.7e-17;1.8e-16;1.6e-16;8.7e-18;3.3e-16;9.2e-17;3.1e-16;2.6e-16;1.6e-16;6.2e-17;2.1e-18;6.4e-22;2.7e-19;1.5e-16;2.3e-16;1.8e-16;4.6e-16;2.6e-16;4.2e-16;4.4e-16;4.7e-16;1.1e-16;1e-16;3.1e-16;3.8e-16;5.6e-16;7.7e-16;3.5e-16;4.3e-16;7.1e-16;1.2e-16;9.9e-17;1.1e-15;7.9e-16;4e-16;2.4e-15;1.2e-15;6.7e-16;8.7e-16;5.6e-16;7.7e-16	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;2.3e-15;1.5e-15;2.2e-15;NA;NA	0.014453288646837	ATA	S	.	1483-1531-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.984642007354532
CAMB-7A1E0	MN908947.3	23403	A	G	1	1	0	0	0.999892172954581	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.18846969460985e-05
CAMB-7A1E0	MN908947.3	23855	C	T	0.055	0.02	1.7e-21	8.5e-10	0.0315643426985779	CCG	S	R765C	C2293T	CGT>TGT	Missense	GU280_gp02, spike glycoprotein	0.968435657301422
CAMB-7A1E0	MN908947.3	241	C	T	1	1	0	0	0.999808036856923	TCG	NA	NA	NA	NA	NA	NA	6.39877143588431e-05
CAMB-7A1E0	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999729802756012	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A1E0	MN908947.3	3037	C	T	1	1	0	0	0.999738322648175	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A1E0	MN908947.3	7472	G	-	0.076	0.055	5.1e-24	5.7e-20	0.0617511520737327	CGG	ORF1ab:nsp3	.	4753-4753-delfrshift	.	no-SNV	ORF1ab:nsp3	0.938248847926267
CAMB-7A1FF	MN908947.3	11074	C	INS	0.029	0.017	1.6e-06	0.0061	0.0244868563197695	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.975230207315191
CAMB-7A1FF	MN908947.3	11075	T	-	0.047	0.021	2.7e-11	3.8e-06	0.0376480864770432	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961980673691107
CAMB-7A1FF	MN908947.3	14408	C	T	1	1	0	0	0.999467120181406	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000226757369614512
CAMB-7A1FF	MN908947.3	180	C	T	0.023	0.0059	7.9e-12	4.9e-05	0.0170592480808346	TCT	NA	NA	NA	NA	NA	NA	0.982940751919165
CAMB-7A1FF	MN908947.3	23403	A	G	1	1	0	0	0.999884214269764	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.92449116306766e-05
CAMB-7A1FF	MN908947.3	241	C	T	1	1	0	0	0.998526512400124	TCG	NA	NA	NA	NA	NA	NA	0.000124520078862717
CAMB-7A1FF	MN908947.3	25563	G	T	0.0069	0.0079	8.4e-05	2.2e-05	0.00721286333900458	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.99272722915818
CAMB-7A1FF	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999397203022022	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A1FF	MN908947.3	3037	C	T	1	1	0	0	0.998795059744954	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A1FF	MN908947.3	515	G	-	0.56	0.53	1.3e-10	1.6e-10	0.548076779890697	TGT	ORF1ab:leader-protein	.	250-250-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.451923220109303
CAMB-7A1FF	MN908947.3	516	TT	-	0.71	0.7	3.5e-17;2.3e-15	2e-17;1.3e-15	0.705156592646213	GTT	ORF1ab:leader-protein	.	251-252-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.292312951331026
CAMB-7A1FF	MN908947.3	518	A	G	0.022	0.012	6.7e-10	1.7e-06	0.0181886678722122	TAT	ORF1ab:leader-protein	M85V	A253G	ATG>GTG	Missense	ORF1ab:leader-protein	0.000195901145268234
CAMB-7A1FF	MN908947.3	518	ATG	-	0.993333333333333	0.996666666666667	4.4e-47;4.4e-69;4.2e-52	4.9e-55;2.4e-56;2.8e-57	0.999471554535572	TAT	ORF1ab:leader-protein	.	253-255-delinframe	.	no-SNV	ORF1ab:leader-protein	0.000195901145268234
CAMB-7A1FF	MN908947.3	9492	A	C	0.0086	0.0043	1e-05	0.00021	0.00713089255802824	CAT	ORF1ab:nsp4	H313P	A938C	CAT>CCT	Missense	ORF1ab:nsp4	0.992725532424025
CAMB-7A1FF	MN908947.3	9518	T	C	0.0074	0.0021	2.6e-05	0.0039	0.00545557943844159	ATT	ORF1ab:nsp4	F322L	T964C	TTC>CTC	Missense	ORF1ab:nsp4	0.994496226396908
CAMB-7A20B	MN908947.3	11075	T	-	0.034	0.038	9.3e-09	5.5e-10	0.0357017212399182	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961027792617301
CAMB-7A20B	MN908947.3	14408	C	T	1	1	0	0	0.997281519342554	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00093956704750451
CAMB-7A20B	MN908947.3	17304	C	T	0.0083	0.0079	1.5e-05	1.9e-05	0.00815718437006771	TCT	ORF1ab:helicase	V356V	C1068T	GTC>GTT	Synonymous	ORF1ab:helicase	0.991710058560618
CAMB-7A20B	MN908947.3	21481	CTTAGTAAAG	-	0.00989	0.0193	0.0065;0.01;0.012;0.013;0.012;0.012;0.013;0.0088;0.004;0.01	3.8e-05;4.1e-05;5e-05;5.6e-05;5.2e-05;5.2e-05;6.5e-05;3.4e-05;1e-05;4.4e-05	0.0124301927580616	TCT	ORF1ab:2'-O-ribose-methyltransferase	.	823-832-delfrshift	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.98697247706422
CAMB-7A20B	MN908947.3	21496	CTTATAATTAGAGAAAACAACAGAGTTGTTATT	-	0.0120909090909091	0.0216666666666667	0.002;0.0032;0.001;0.0017;0.0035;0.0019;0.0044;0.005;0.0056;0.0061;0.0042;0.0047;0.0035;0.0035;0.0043;0.0041;0.003;0.0047;0.0049;0.0043;0.0037;0.0058;0.0045;0.0045;0.0051;0.0028;0.0024;0.0048;0.0054;0.0032;0.0034;0.0062;0.0058	3.4e-06;6.9e-06;1.2e-05;1.8e-05;1.7e-05;2e-05;2.1e-05;2.2e-05;2.5e-05;2.9e-05;1.2e-05;2.1e-05;1.6e-05;1.5e-05;1.9e-05;1.6e-05;1.4e-05;1.9e-05;2.3e-05;2.1e-05;1.5e-05;2.9e-05;1.7e-05;2.1e-05;2.3e-05;8.6e-06;1.1e-05;2.3e-05;3.3e-05;4.2e-05;3.6e-05;1.2e-05;4e-05	0.0149225176965755	ACT	ORF1ab:2'-O-ribose-methyltransferase	.	838-870-delinframe	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.98179335457442
CAMB-7A20B	MN908947.3	21531	TAGTGA	-	0.0121666666666667	0.0215	0.0059;0.0044;0.0053;0.006;0.0054;0.0028	2.7e-05;3.1e-05;3.9e-05;4.4e-05;4.5e-05;3e-05	0.0145821648906338	CTA	ORF1ab:2'-O-ribose-methyltransferase	.	873-878-delinframe	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.985398727068514
CAMB-7A20B	MN908947.3	21543	TGTTAACAA	-	0.0133333333333333	0.0234444444444444	0.0049;0.0062;0.0033;0.0036;0.0044;0.0013;0.0025;0.0052;0.0038	2.2e-05;3.3e-05;1.6e-05;1.7e-05;1.6e-05;4.4e-06;4.7e-06;5e-05;2.2e-05	0.0160837853001683	TTG	ORF1ab:2'-O-ribose-methyltransferase	.	885-893-delinframe	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.982307843522705
CAMB-7A20B	MN908947.3	21587	C	T	0.006	0.0087	0.00041	4.6e-05	0.00689206762028609	GCC	S	P9S	C25T	CCA>TCA	Missense	GU280_gp02, spike glycoprotein	0.99297789336801
CAMB-7A20B	MN908947.3	21921	T	C	0.002	0.0098	0.0068	3.7e-06	0.00501946322474903	GTT	S	V120A	T359C	GTT>GCT	Missense	GU280_gp02, spike glycoprotein	0.994878098750256
CAMB-7A20B	MN908947.3	21985	G	T	0.019	0.019	7e-10	7.8e-10	0.0190433682957673	TGG	S	L141F	G423T	TTG>TTT	Missense	GU280_gp02, spike glycoprotein	0.964219296288031
CAMB-7A20B	MN908947.3	22002	A	C	0.011	0.0098	1.2e-06	1.4e-06	0.0105018378216188	AAA	S	K147T	A440C	AAA>ACA	Missense	GU280_gp02, spike glycoprotein	0.988954317005476
CAMB-7A20B	MN908947.3	22025	A	G	0.52	0.51	3.7e-303	3.3e-291	0.516520705779018	AAG	S	S155G	A463G	AGT>GGT	Missense	GU280_gp02, spike glycoprotein	0.483427626650133
CAMB-7A20B	MN908947.3	22243	A	T	0.028	0.019	1.4e-13	5e-10	0.0245734493172608	TAG	S	V227V	A681T	GTA>GTT	Synonymous	GU280_gp02, spike glycoprotein	0.975323300895692
CAMB-7A20B	MN908947.3	22285	ACTTGCTTTACATAG	-	0.0141333333333333	0.00998666666666667	3.9e-06;8.8e-06;2.7e-05;1.1e-05;3.9e-05;4.2e-06;0.00073;4e-06;1.7e-05;6.5e-05;6e-06;1.9e-06;8.2e-06;1.1e-06;2e-07	4.9e-05;0.00011;0.00029;0.00013;0.00024;6.3e-05;0.0023;7.6e-05;0.00053;0.0012;0.00028;0.00015;0.00026;9.6e-05;8.4e-06	0.0122824974411464	TAC	S	.	723-737-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.987178830996008
CAMB-7A20B	MN908947.3	23403	A	G	1	1	0	0	0.999908890468121	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.28876255033802e-05
CAMB-7A20B	MN908947.3	241	C	T	1	1	0	0	0.996669316887638	TCG	NA	NA	NA	NA	NA	NA	4.29765562885446e-05
CAMB-7A20B	MN908947.3	26137	A	C	0.024	0.022	2e-05	0.00011	0.0230966638152267	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.976903336184773
CAMB-7A20B	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.023125	0.02921875	0.00099;0.0035;0.0012;0.0012;0.00046;7e-04;0.00057;0.0011;0.00079;0.00079;0.0013;0.00071;0.0013;0.00087;0.00088;0.00083;0.0013;0.00078;0.0011;0.00084;0.00071;0.0011;0.00081;0.00081;0.00071;0.0012;0.001;0.00047;0.0011;7e-04;0.00069;0.00054	2.7e-05;0.00013;8.2e-05;8.5e-05;2.6e-05;4.7e-05;3.7e-05;8.2e-05;5.4e-05;7.1e-05;0.00011;5.8e-05;9.7e-05;6.4e-05;6.2e-05;5.8e-05;1e-04;6.3e-05;8e-05;5.9e-05;4.8e-05;8.7e-05;5.2e-05;5.1e-05;4.6e-05;8.7e-05;7.9e-05;4.3e-05;8.9e-05;3.3e-05;5.2e-05;3.5e-05	0.0253164556962025	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.973379730317529
CAMB-7A20B	MN908947.3	27493	C	T	0.01	0.011	2.4e-06	7.2e-07	0.0107413750917543	ACC	ORF7a	P34S	C100T	CCT>TCT	Missense	GU280_gp07	0.989124051871789
CAMB-7A20B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999317690762291	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	8.38820618210796e-05
CAMB-7A20B	MN908947.3	3037	C	T	1	1	0	0	0.998523779125439	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.0001595914458985
CAMB-7A20B	MN908947.3	3237	A	T	0.011	0.008	5e-07	6.4e-06	0.0102401592331666	CAA	ORF1ab:nsp3	Q173L	A518T	CAA>CTA	Missense	ORF1ab:nsp3	0.98955032344237
CAMB-7A20B	MN908947.3	4423	C	T	0.0098	0.012	2.8e-06	3.3e-07	0.010586964350018	GCA	ORF1ab:nsp3	R568R	C1704T	CGC>CGT	Synonymous	ORF1ab:nsp3	0.989250990277278
CAMB-7A20B	MN908947.3	6448	T	C	0.019	0.023	3.9e-10	2.9e-12	0.0206162658634142	TTC	ORF1ab:nsp3	V1243V	T3729C	GTT>GTC	Synonymous	ORF1ab:nsp3	0.979001036985828
CAMB-7A21A	MN908947.3	11074	C	INS	0.12	0.12	7.7e-53	1.7e-50	0.121692634968091	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.874144770884839
CAMB-7A21A	MN908947.3	11083	G	-	0.19	0.17	1.2e-82	4.2e-74	0.177769547242715	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-7A21A	MN908947.3	11083	G	T	0.81	0.83	0	0	0.822130351655172	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-7A21A	MN908947.3	13356	C	T	0.077	0.073	2.1e-35	8.5e-34	0.0754816033598597	ACA	ORF1ab:nsp10	T111I	C332T	ACA>ATA	Missense	ORF1ab:nsp10	0.924492787953674
CAMB-7A21A	MN908947.3	13914	TA	CG	0.0073	0.0013155	1.1e-05;2.9e-05	0.0032;NA	0.00441416086505703	ATA	ORF1ab:RNA-dependent-RNA-polymerase	.	447-448-mnv	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.994637871692985
CAMB-7A21A	MN908947.3	14805	C	T	1	1	0	0	0.999888479982157	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	2.23040035686406e-05
CAMB-7A21A	MN908947.3	17440	C	T	0.013	0.041	2.6e-07	1.7e-19	0.0261861986066771	CCC	ORF1ab:helicase	P402S	C1204T	CCT>TCT	Missense	ORF1ab:helicase	0.973775026173273
CAMB-7A21A	MN908947.3	18859	G	T	0.0043	0.01	0.0017	4.3e-06	0.0069768750351657	TGC	ORF1ab:3'-to-5'-exonuclease	A274S	G820T	GCA>TCA	Missense	ORF1ab:3'-to-5'-exonuclease	0.99285432960108
CAMB-7A21A	MN908947.3	18910	G	T	0.0079	0.012	3.1e-05	6e-07	0.00967212580284078	TGA	ORF1ab:3'-to-5'-exonuclease	D291Y	G871T	GAC>TAC	Missense	ORF1ab:3'-to-5'-exonuclease	0.99027353641175
CAMB-7A21A	MN908947.3	23904	TT	-	0.0053	0.00655	0.00069;0.00014	0.00025;3e-05	0.00587025736269567	GTT	S	.	2342-2343-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.99399665387265
CAMB-7A21A	MN908947.3	2480	A	G	1	1	0	0	0.999857407671467	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.000142592328532725
CAMB-7A21A	MN908947.3	25070	TCTGGCATT	ATCTCTGGC	0.000431111111111111	0.01	NA;0.0025;0.46;0.48;NA;0.46;0.21;NA;0.45	2.3e-06;2.9e-06;1.5e-06;2.5e-06;1.4e-06;3.6e-06;1.3e-06;6.4e-07;4e-06	0.00387689656822859	CTC	S	.	3508-3516-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.996310689163264
CAMB-7A21A	MN908947.3	25570	T	C	0.0085	0.0071	2.9e-05	0.00011	0.0078827302705877	TTC	ORF3a	S60P	T178C	TCC>CCC	Missense	GU280_gp03	0.992083389799883
CAMB-7A21A	MN908947.3	2558	C	T	1	1	0	0	0.999628494473855	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-7A21A	MN908947.3	2568	A	G	0.0061	0.011	5.3e-05	6.2e-07	0.0084128934681917	CAA	ORF1ab:nsp2	Q588R	A1763G	CAA>CGA	Missense	ORF1ab:nsp2	0.991303525853105
CAMB-7A21A	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7A21A	MN908947.3	27847	C	G	0.017	0.00097	7.3e-09	0.0047	0.00865176640230714	TCA	NA	NA	NA	NA	NA	NA	0.991039241940468
CAMB-7A21A	MN908947.3	2937	C	T	0.043	0.033	7.1e-20	6.7e-16	0.0378685641843537	ACA	ORF1ab:nsp3	T73I	C218T	ACA>ATA	Missense	ORF1ab:nsp3	0.962090541037909
CAMB-7A21A	MN908947.3	6347	C	T	0.0073	0.006	2.9e-05	9.8e-05	0.00668195871147901	ACT	ORF1ab:nsp3	L1210L	C3628T	CTG>TTG	Synonymous	ORF1ab:nsp3	0.993305574947641
CAMB-7A229	MN908947.3	11075	T	-	0.02	0.022	1.3e-05	2.3e-06	0.0205550101283756	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.97627598891471
CAMB-7A229	MN908947.3	11782	A	G	0.38	0.39	3.3e-95	6.1e-65	0.380246913580247	AAC	ORF1ab:nsp6	K270K	A810G	AAA>AAG	Synonymous	ORF1ab:nsp6	0.618518518518518
CAMB-7A229	MN908947.3	12809	C	T	0.11	0.061	6.7e-49	2e-28	0.0913277735298825	ACT	ORF1ab:nsp9	L42F	C124T	CTT>TTT	Missense	ORF1ab:nsp9	0.907249675480555
CAMB-7A229	MN908947.3	13579	AA	-	0.0015	0.0088	0.0019;NA	5.5e-06;2.1e-06	0.00526064084170253	TAA	ORF1ab:RNA-dependent-RNA-polymerase	.	112-113-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.99406739439962
CAMB-7A229	MN908947.3	14408	C	T	1	1	0	0	0.999374132629459	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000326539497673406
CAMB-7A229	MN908947.3	17809	A	C	0.04	0.034	5.9e-19	2.2e-16	0.0379347462974648	GAT	ORF1ab:helicase	I525L	A1573C	ATT>CTT	Missense	ORF1ab:helicase	0.961991017408411
CAMB-7A229	MN908947.3	18636	G	A	0.99	1	0	0	0.996729140593208	TGA	ORF1ab:3'-to-5'-exonuclease	V199V	G597A	GTG>GTA	Synonymous	ORF1ab:3'-to-5'-exonuclease	8.4458810973503e-05
CAMB-7A229	MN908947.3	23403	A	G	1	1	0	0	0.999902045294256	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.81592351696575e-05
CAMB-7A229	MN908947.3	241	C	T	1	0.99	0	0	0.997055199348384	TCG	NA	NA	NA	NA	NA	NA	8.354044401746e-05
CAMB-7A229	MN908947.3	24691	T	C	0.0061	0.0086	0.00012	1.8e-05	0.00690387679235263	GTG	S	C1043C	T3129C	TGT>TGC	Synonymous	GU280_gp02, spike glycoprotein	0.992963356346256
CAMB-7A229	MN908947.3	26528	AGATTCCAACGGTAC	-	0.000614866666666667	0.00446666666666667	0.00034;0.00037;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00051;9.6e-06;0.00018;3.9e-05;0.00022;0.00036;2e-04;0.00018;0.00014;0.00019;0.00021;0.00022;0.00028;0.00033;0.00029	0.0014366021236727	CAG	M	.	6-20-delinframe	.	no-SNV	GU280_gp05	0.995475113122172
CAMB-7A229	MN908947.3	26681	C	T	0.018	0.033	6.1e-09	2.4e-15	0.0236287271918113	TCC	M	F53F	C159T	TTC>TTT	Synonymous	GU280_gp05	0.976329550511793
CAMB-7A229	MN908947.3	26783	TGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0184411764705882	0.0324411764705882	0.052;0.48;0.47;0.48;0.004;0.0039;0.0018;0.0026;0.0024;0.004;0.0029;0.0034;0.0049;0.0027;0.0044;0.0033;0.0033;0.0026;0.0047;0.0031;0.0038;0.0032;0.0026;0.0042;0.0031;0.0024;0.0027;0.0042;0.0034;0.002;0.0037;0.0026;0.003;0.0022	0.00037;0.00069;3.6e-06;1.3e-05;2.2e-05;2.2e-05;5.9e-06;1.5e-05;1.2e-05;2.2e-05;1.1e-06;1.5e-06;2.9e-05;1.3e-05;2.5e-05;1.7e-05;1.6e-05;1.8e-05;2.7e-05;1.6e-05;2.1e-05;1.5e-05;1.2e-05;2.3e-05;1.2e-05;7e-06;1.5e-05;2.3e-05;2.1e-05;1.4e-05;2.4e-05;6.8e-06;1.2e-05;9.8e-06	0.0244038842849153	TTG	M	.	261-294-delfrshift	.	no-SNV	GU280_gp05	0.983449063064777
CAMB-7A229	MN908947.3	27806	G	T	0.056	0.073	1.1e-11	1.2e-08	0.0606060606060606	TGC	NA	NA	NA	NA	NA	NA	0.939393939393939
CAMB-7A229	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999399714864561	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00024877684716809
CAMB-7A229	MN908947.3	28907	G	T	0.0089	0.0019	5e-06	0.0051	0.00659612477669369	TGG	N	G212C	G634T	GGC>TGC	Missense	GU280_gp10	0.99257935962622
CAMB-7A229	MN908947.3	3037	C	T	1	1	0	0	0.999667928538221	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.64142923557149e-05
CAMB-7A229	MN908947.3	3618	T	C	0.0088	0.0034	2.4e-05	0.0043	0.00688816855753647	GTC	ORF1ab:nsp3	V300A	T899C	GTC>GCC	Missense	ORF1ab:nsp3	0.993111831442464
CAMB-7A229	MN908947.3	430	A	C	0.17	0.2	4.1e-81	4.8e-94	0.182095956312573	AAG	ORF1ab:leader-protein	E55D	A165C	GAA>GAC	Missense	ORF1ab:leader-protein	0.817817362284922
CAMB-7A229	MN908947.3	4313	A	-	0.0047	0.0092	0.0025	2.5e-05	0.00647328888810709	TAA	ORF1ab:nsp3	.	1594-1594-delfrshift	.	no-SNV	ORF1ab:nsp3	0.993421168358282
CAMB-7A229	MN908947.3	4668	C	T	0.0073	0.033	3.6e-05	2.9e-16	0.0170957446808511	TCT	ORF1ab:nsp3	S650F	C1949T	TCT>TTT	Missense	ORF1ab:nsp3	0.982872340425532
CAMB-7A229	MN908947.3	5810	GACGGTGCTT	-	0.0062	0.0171	0.0035;0.0031;0.0037;0.0031;0.0031;0.0025;0.0029;0.028;0.03;0.077	2.3e-06;1.8e-06;2.3e-06;1.5e-06;2e-06;1.4e-06;1.6e-06;0.00018;9.7e-05;0.00054	0.0103803577584556	AGA	ORF1ab:nsp3	.	3091-3100-delfrshift	.	no-SNV	ORF1ab:nsp3	0.99002649786545
CAMB-7A229	MN908947.3	5821	ACTT	-	0.006225	0.0185	0.099;0.047;0.0082;0.0088	0.00077;0.00016;9.6e-06;2.3e-05	0.0110251894954445	TAC	ORF1ab:nsp3	.	3102-3105-delfrshift	.	no-SNV	ORF1ab:nsp3	0.988535792972105
CAMB-7A229	MN908947.3	7333	A	G	0.015	0.05	8.9e-09	9.2e-23	0.0255474452554745	TAC	ORF1ab:nsp3	V1538V	A4614G	GTA>GTG	Synonymous	ORF1ab:nsp3	0.974452554744526
CAMB-7A229	MN908947.3	7441	TGTATG	-	0.00658333333333333	0.00188333333333333	0.00024;0.00032;0.00012;0.00014;2.8e-05;8.4e-05	0.00079;0.00098;NA;NA;NA;NA	0.00461842973389048	ATG	ORF1ab:nsp3	.	4722-4727-delinframe	.	no-SNV	ORF1ab:nsp3	0.993711611582334
CAMB-7A229	MN908947.3	7647	G	A	0.0022	0.009	0.0033	3.7e-06	0.00415773403495095	GGT	ORF1ab:nsp3	G1643D	G4928A	GGT>GAT	Missense	ORF1ab:nsp3	0.995842265965049
CAMB-7A247	MN908947.3	11075	T	-	0.037	0.037	1.5e-09	6.3e-10	0.0369722666754657	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958358767921073
CAMB-7A247	MN908947.3	14408	C	T	1	1	0	0	0.9971769432267	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000705764193325099
CAMB-7A247	MN908947.3	18457	C	T	0.0089	0.0091	6.3e-06	4.2e-06	0.00897484101943732	ACC	ORF1ab:3'-to-5'-exonuclease	P140S	C418T	CCA>TCA	Missense	ORF1ab:3'-to-5'-exonuclease	0.99084533520786
CAMB-7A247	MN908947.3	21219	C	T	0.033	0.058	7.7e-06	1.9e-08	0.0441595441595442	TCG	ORF1ab:2'-O-ribose-methyltransferase	F187F	C561T	TTC>TTT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.955840455840456
CAMB-7A247	MN908947.3	23403	A	G	1	1	0	0	0.999514904317352	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	1.97998237815683e-05
CAMB-7A247	MN908947.3	241	C	T	1	1	0	0	0.998545402518123	TCG	NA	NA	NA	NA	NA	NA	0.000333842045020984
CAMB-7A247	MN908947.3	26137	A	C	0.023	0.018	9.1e-06	0.00078	0.0216173980987108	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.977861700742284
CAMB-7A247	MN908947.3	26439	G	T	0.019	0.019	8.1e-10	2.2e-10	0.0189408660434863	TGA	E	L65L	G195T	CTG>CTT	Synonymous	GU280_gp04	0.980793225469942
CAMB-7A247	MN908947.3	28817	G	T	0.08	0.078	1.4e-35	6.3e-35	0.0793241023233983	AGC	N	A182S	G544T	GCC>TCC	Missense	GU280_gp10	0.919932723147931
CAMB-7A247	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998902528249736	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000405862457722661
CAMB-7A247	MN908947.3	3037	C	T	1	1	0	0	0.998911600743297	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000212370586673746
CAMB-7A256	MN908947.3	11379	C	T	1	1	1.6e-163	1.5e-160	1	GCT	ORF1ab:nsp6	A136V	C407T	GCT>GTT	Missense	ORF1ab:nsp6	0
CAMB-7A256	MN908947.3	1170	C	T	1	1	0	0	0.999720943211944	TCT	ORF1ab:nsp2	S122F	C365T	TCT>TTT	Missense	ORF1ab:nsp2	0
CAMB-7A256	MN908947.3	14408	C	T	1	1	0	0	0.999187652315191	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000487408610885459
CAMB-7A256	MN908947.3	23403	A	G	1	1	0	0	0.999943840732317	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7A256	MN908947.3	241	C	T	1	1	0	0	0.999906655465323	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-7A256	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999042604116802	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A256	MN908947.3	3037	C	T	1	1	0	0	0.999545040946315	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A265	MN908947.3	1427	C	T	1	1	6.59997592997029e-319	4.9e-170	1	CCA	ORF1ab:nsp2	H208Y	C622T	CAT>TAT	Missense	ORF1ab:nsp2	0
CAMB-7A265	MN908947.3	14408	C	T	1	1	0	0	0.99964585472961	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000283316216311931
CAMB-7A265	MN908947.3	23403	A	G	1	1	0	0	0.999908752879987	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.12471200127746e-05
CAMB-7A265	MN908947.3	26952	A	G	0.055	0.18	1.2e-22	5.9e-73	0.125356125356125	GAT	M	I144V	A430G	ATC>GTC	Missense	GU280_gp05	0.874643874643875
CAMB-7A265	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999609679937549	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A265	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A265	MN908947.3	522	TTG	-	0.07	0.07	4.4e-10;2.6e-10;4.4e-13	4.2e-15;3.4e-15;NA	0.0854667701060253	GTT	ORF1ab:leader-protein	.	257-259-delinframe	.	no-SNV	ORF1ab:leader-protein	0.907158836689038
CAMB-7A274	MN908947.3	11075	T	-	0.055	0.025	1.1e-13	9.2e-07	0.0385584415584416	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961298701298701
CAMB-7A274	MN908947.3	14408	C	T	1	1	0	0	0.999474343315657	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000309209814319506
CAMB-7A274	MN908947.3	14575	G	C	0.0071	0.012	0.00046	8.2e-06	0.00967044635746521	TGC	ORF1ab:RNA-dependent-RNA-polymerase	A370P	G1108C	GCT>CCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.990132352383481
CAMB-7A274	MN908947.3	23403	A	G	1	1	0	0	0.999905662355087	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.43376449131045e-05
CAMB-7A274	MN908947.3	241	C	T	1	1	0	0	0.999762074708542	TCG	NA	NA	NA	NA	NA	NA	0.000118962645729241
CAMB-7A274	MN908947.3	28881	GGG	AAC	0.996666666666667	1	0;0;0	0;0;0	0.999661284859433	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A274	MN908947.3	3037	C	T	1	1	0	0	0.999424626006905	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000143843498273878
CAMB-7A283	MN908947.3	10252	C	T	0.0064	0.011	0.00017	2.4e-06	0.00876093534379075	TCT	ORF1ab:3C-like-proteinase	F66F	C198T	TTC>TTT	Synonymous	ORF1ab:3C-like-proteinase	0.991163102789067
CAMB-7A283	MN908947.3	10507	C	T	0.023	0.013	1.8e-11	1.3e-07	0.0180956611876203	ACA	ORF1ab:3C-like-proteinase	N151N	C453T	AAC>AAT	Synonymous	ORF1ab:3C-like-proteinase	0.981874722345624
CAMB-7A283	MN908947.3	11074	C	INS	0.025	0.02	3.3e-05	0.00087	0.022509292827314	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.975907484741407
CAMB-7A283	MN908947.3	11075	T	-	0.049	0.039	5.9e-12	9.9e-10	0.0441329982601972	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953489271215929
CAMB-7A283	MN908947.3	14408	C	T	1	1	0	0	0.99845031905196	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000364630811303555
CAMB-7A283	MN908947.3	18788	C	T	1	1	0	0	0.999535816962147	ACA	ORF1ab:3'-to-5'-exonuclease	T250I	C749T	ACA>ATA	Missense	ORF1ab:3'-to-5'-exonuclease	7.48682319118352e-05
CAMB-7A283	MN908947.3	19839	T	C	1	1	0	0	0.999896365897471	ATA	ORF1ab:endoRNAse	N73N	T219C	AAT>AAC	Synonymous	ORF1ab:endoRNAse	6.90894016857814e-05
CAMB-7A283	MN908947.3	23403	A	G	1	1	0	0	0.999472601264271	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.94252096595678e-05
CAMB-7A283	MN908947.3	241	C	T	1	1	0	0	0.999462646888301	TCG	NA	NA	NA	NA	NA	NA	4.24226140814797e-05
CAMB-7A283	MN908947.3	28877	AG	TC	0.019	0.014	6.7e-10;5.4e-10	9.4e-08;8.1e-08	0.0161975402561177	CAG	N	.	604-605-mnv	.	no-SNV	GU280_gp10	0.983452735687567
CAMB-7A283	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999598581655182	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	3.65590611633093e-05
CAMB-7A283	MN908947.3	3037	C	T	1	1	0	0	0.999620017479196	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.79982520804043e-05
CAMB-7A292	MN908947.3	11075	T	-	0.036	0.033	2.5e-09	4.7e-09	0.0345291238638197	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960988902633608
CAMB-7A292	MN908947.3	14408	C	T	1	1	0	0	0.995722247326405	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000707937942461214
CAMB-7A292	MN908947.3	15126	C	T	0.017	0.015	3.9e-09	2.2e-08	0.0161285898455715	TCT	ORF1ab:RNA-dependent-RNA-polymerase	I553I	C1659T	ATC>ATT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.983843980579861
CAMB-7A292	MN908947.3	2015	A	G	0.99	0.99	0	0	0.992623104701114	TAT	ORF1ab:nsp2	M404V	A1210G	ATG>GTG	Missense	ORF1ab:nsp2	0.00712290040087021
CAMB-7A292	MN908947.3	21123	G	T	1	1	0	0	0.999563626598637	GGT	ORF1ab:2'-O-ribose-methyltransferase	G155G	G465T	GGG>GGT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.00026853747776174
CAMB-7A292	MN908947.3	23403	A	G	1	1	0	0	0.999365241987572	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.45444219247645e-05
CAMB-7A292	MN908947.3	241	C	T	1	1	0	0	0.997848422579475	TCG	NA	NA	NA	NA	NA	NA	0.000193400217575245
CAMB-7A292	MN908947.3	26137	A	C	0.023	0.014	1.9e-05	0.0071	0.0194158645867906	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.980584135413209
CAMB-7A292	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0301081081081081	0.0348648648648649	0.0013;0.00012;0.00048;0.00055;0.0011;1.4e-05;7.2e-05;4.7e-05;4.7e-05;1.3e-05;2.3e-05;1.8e-05;4.4e-05;2.7e-05;3.2e-05;6.1e-05;2.3e-05;5.2e-05;3.3e-05;3.2e-05;2.3e-05;5.5e-05;3.1e-05;4.1e-05;3e-05;2e-05;4.3e-05;2.7e-05;1.7e-05;2.4e-05;4.6e-05;3.6e-05;1.4e-05;3.7e-05;1.5e-05;2.4e-05;1.4e-05	0.00037;2.2e-05;0.00015;0.00013;3e-04;1.9e-06;1.6e-05;5e-06;4.7e-06;1.2e-06;2.1e-06;1.5e-06;3.7e-06;2.2e-06;3.1e-06;4.7e-06;2e-06;4.5e-06;2.8e-06;2.7e-06;2.7e-06;4.9e-06;2.9e-06;3.7e-06;2.6e-06;1.8e-06;4.1e-06;2.2e-06;1.7e-06;2.6e-06;4.1e-06;3.7e-06;2.2e-06;4.9e-06;1.1e-06;2.3e-06;2.1e-06	0.0330948443230028	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.97826399109739
CAMB-7A292	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998624484181568	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000190803281816447
CAMB-7A292	MN908947.3	3037	C	T	1	1	0	0	0.999215661667817	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000125494133149275
CAMB-7A292	MN908947.3	522	TT	-	0.035	0.0365	2.2e-05;0.00043	1.5e-05;0.00024	0.0355069000970213	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.957338592484949
CAMB-7A292	MN908947.3	6336	C	T	0.0073	0.0087	3.9e-05	8.3e-06	0.00784671339349147	TCG	ORF1ab:nsp3	S1206L	C3617T	TCG>TTG	Missense	ORF1ab:nsp3	0.992026042605533
CAMB-7A292	MN908947.3	8917	C	T	0.0055	0.007	0.00023	3.8e-05	0.00605597148389802	TCT	ORF1ab:nsp4	F121F	C363T	TTC>TTT	Synonymous	ORF1ab:nsp4	0.993783687112251
CAMB-7A2A1	MN908947.3	11020	C	T	0.37	0.095	4.2e-100	4.8e-37	0.147952979327118	TCA	ORF1ab:nsp6	L16L	C48T	CTC>CTT	Synonymous	ORF1ab:nsp6	0.852047020672882
CAMB-7A2A1	MN908947.3	11375	GGTGCTA	-	0.000885714285714286	0.0345714285714286	0.0015;NA;NA;NA;NA;NA;NA	1.6e-12;9.5e-13;1.1e-12;5.7e-12;1.3e-12;7.8e-13;2.3e-12	0.0241635687732342	TGG	ORF1ab:nsp6	.	403-409-delfrshift	.	no-SNV	ORF1ab:nsp6	0.973977695167286
CAMB-7A2A1	MN908947.3	13914	T	G	0.0066	0.0096	1.6e-05	6.3e-07	0.00888252148997135	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.991060171919771
CAMB-7A2A1	MN908947.3	14408	C	T	1	1	0	0	0.999466544734034	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000381039475689681
CAMB-7A2A1	MN908947.3	16480	C	INS	0.0019	0.0036	1e-04	4.2e-05	0.00248911014312383	TCC	ORF1ab:helicase	.	243-244-insfrshift	.	no-SNV	ORF1ab:helicase	0.997510889856876
CAMB-7A2A1	MN908947.3	23403	A	G	1	1	0	0	0.999846523763237	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000140686550365785
CAMB-7A2A1	MN908947.3	241	C	T	1	1	0	0	0.999852890697788	TCG	NA	NA	NA	NA	NA	NA	9.80728681410288e-05
CAMB-7A2A1	MN908947.3	25350	C	T	1	1	0	0	0.999900378561466	CCA	S	P1263L	C3788T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	6.64142923557149e-05
CAMB-7A2A1	MN908947.3	26151	C	T	0.15	0.27	1.1e-21	4.3e-55	0.231738035264484	CCG	ORF3a	S253S	C759T	TCC>TCT	Synonymous	GU280_gp03	0.768261964735516
CAMB-7A2A1	MN908947.3	29051	C	INS	0.016	0.035	0.0039	2.4e-09	0.0265550671403625	GCA	N	.	777-778-insfrshift	.	no-SNV	GU280_gp10	0.973264286144397
CAMB-7A2A1	MN908947.3	3037	C	T	1	1	0	0	0.999727297518407	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A2B0	MN908947.3	11075	T	-	0.038	0.036	7.9e-10	1.7e-09	0.0370981912927561	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958145241918381
CAMB-7A2B0	MN908947.3	14408	C	T	1	1	0	0	0.998781270044901	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00059012187299551
CAMB-7A2B0	MN908947.3	20268	A	G	1	1	0	0	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-7A2B0	MN908947.3	219	G	T	0.072	0.072	1.1e-32	1.7e-32	0.0717409240924092	CGA	NA	NA	NA	NA	NA	NA	0.92787403740374
CAMB-7A2B0	MN908947.3	23403	A	G	1	1	0	0	0.999567656798106	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.84338367511374e-05
CAMB-7A2B0	MN908947.3	241	C	T	1	1	0	0	0.998641932501156	TCG	NA	NA	NA	NA	NA	NA	0.000115580212667591
CAMB-7A2B0	MN908947.3	26137	A	C	0.026	0.018	1.4e-06	0.00043	0.021724372029871	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.977823036886173
CAMB-7A2B0	MN908947.3	26158	GTTA	-	0.009925	0.01225	4.7e-05;4.2e-05;0.00011;0.00093	4.8e-06;5.9e-06;1.5e-05;0.00016	0.0108825337141618	TGT	ORF3a	.	766-769-delfrshift	.	no-SNV	GU280_gp03	0.988994334788727
CAMB-7A2B0	MN908947.3	28391	C	T	0.025	0.028	3e-12	1.6e-13	0.0261154112390661	ACG	N	R40C	C118T	CGT>TGT	Missense	GU280_gp10	0.973720974136304
CAMB-7A2B0	MN908947.3	2937	C	T	1	1	0	0	0.999870035350385	ACA	ORF1ab:nsp3	T73I	C218T	ACA>ATA	Missense	ORF1ab:nsp3	7.79787897691828e-05
CAMB-7A2B0	MN908947.3	3037	C	T	1	1	0	0	0.999331895897233	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000212578578152996
CAMB-7A2CF	MN908947.3	11075	T	-	0.052	0.034	1.7e-12	9.2e-09	0.0442080929759077	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951592721411605
CAMB-7A2CF	MN908947.3	14408	C	T	1	1	0	0	0.998551214039063	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000577335758869729
CAMB-7A2CF	MN908947.3	2164	G	A	1	1	0	0	0.999822411649796	AGA	ORF1ab:nsp2	E453E	G1359A	GAG>GAA	Synonymous	ORF1ab:nsp2	0.000118392233469484
CAMB-7A2CF	MN908947.3	22093	G	A	0.0045	0.012	0.00043	2e-07	0.00806712792580598	TGG	S	M177I	G531A	ATG>ATA	Missense	GU280_gp02, spike glycoprotein	0.99063742087443
CAMB-7A2CF	MN908947.3	23403	A	G	1	1	0	0	0.999922707106309	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.8646446845677e-05
CAMB-7A2CF	MN908947.3	241	C	T	1	1	0	0	0.999831233123312	TCG	NA	NA	NA	NA	NA	NA	5.62556255625563e-05
CAMB-7A2CF	MN908947.3	25291	T	C	0.0084	0.022	2.9e-05	6e-11	0.01398891966759	GTC	S	C1243C	T3729C	TGT>TGC	Synonymous	GU280_gp02, spike glycoprotein	0.985918744228994
CAMB-7A2CF	MN908947.3	26137	A	C	0.032	0.019	7.7e-07	0.0021	0.0268052516411379	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.973194748358862
CAMB-7A2CF	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999622546552592	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000280085893007189
CAMB-7A2CF	MN908947.3	3037	C	T	1	1	0	0	0.999491470574638	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A2CF	MN908947.3	7528	C	T	0.013	0.0031	1.8e-07	0.0052	0.00902596569277495	TCG	ORF1ab:nsp3	V1603V	C4809T	GTC>GTT	Synonymous	ORF1ab:nsp3	0.99080292595286
CAMB-7A2CF	MN908947.3	7761	G	A	1	1	0	0	0.999841055392196	GGT	ORF1ab:nsp3	G1681D	G5042A	GGT>GAT	Missense	ORF1ab:nsp3	0.00015894460780418
CAMB-7A2DE	MN908947.3	11075	T	-	0.054	0.031	3.5e-13	3.1e-08	0.0436985433818873	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.950830716990285
CAMB-7A2DE	MN908947.3	11698	T	C	0.016	0.032	3e-05	3.7e-08	0.0236087689713322	ATG	ORF1ab:nsp6	Y242Y	T726C	TAT>TAC	Synonymous	ORF1ab:nsp6	0.974704890387858
CAMB-7A2DE	MN908947.3	14408	C	T	0.99	0.99	0	0	0.993590797041906	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000397151465351958
CAMB-7A2DE	MN908947.3	1471	C	T	0.15	0.18	2.8e-61	5.8e-71	0.163902815271886	GCA	ORF1ab:nsp2	R222R	C666T	CGC>CGT	Synonymous	ORF1ab:nsp2	0.835904357886618
CAMB-7A2DE	MN908947.3	19072	G	A	1	1	0	0	0.999566630552546	TGA	ORF1ab:3'-to-5'-exonuclease	D345N	G1033A	GAT>AAT	Missense	ORF1ab:3'-to-5'-exonuclease	7.22282412423257e-05
CAMB-7A2DE	MN908947.3	22743	ATG	-	0.0186666666666667	0.0196666666666667	1.2e-06;7.7e-07;2.4e-07	7.5e-07;4.3e-07;1e-07	0.0184078576825331	AAT	S	.	1181-1183-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.976495987616604
CAMB-7A2DE	MN908947.3	23403	A	G	1	1	0	0	0.999923482215081	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.3724448525393e-05
CAMB-7A2DE	MN908947.3	241	C	T	1	1	0	0	0.999781394701802	TCG	NA	NA	NA	NA	NA	NA	0.000119239253562273
CAMB-7A2DE	MN908947.3	26159	TTA	-	0.0113333333333333	0.0233333333333333	0.00042;2e-04;0.001	1.3e-07;1.5e-07;2.3e-06	0.0167025862068966	GTT	ORF3a	.	767-769-delinframe	.	no-SNV	GU280_gp03	0.983548766157462
CAMB-7A2DE	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0223783783783784	0.0397837837837838	0.05;0.016;0.044;0.016;0.026;0.0031;0.0088;8e-04;0.00081;0.00029;0.00049;0.00039;8e-04;0.00055;0.00017;0.00029;0.00049;0.00091;0.00066;0.00068;0.00054;0.001;0.00064;0.00077;0.00061;0.00044;0.00083;0.00057;0.00038;0.00051;0.00086;0.00071;4e-04;8e-04;0.00043;0.00054;0.00038	2e-04;1.1e-05;4.9e-05;5.2e-05;0.00013;3.3e-08;1.8e-07;5.3e-07;5.5e-07;1.4e-07;2.7e-07;1.9e-07;5.2e-07;3e-07;4.3e-07;7.7e-07;2.5e-07;6.4e-07;4.1e-07;3.8e-07;2.8e-07;7e-07;3.8e-07;5.1e-07;3.3e-07;2.2e-07;5.2e-07;3e-07;3.4e-07;2.8e-07;5.7e-07;4.5e-07;2.3e-07;5.4e-07;3.7e-07;7.6e-07;4.5e-07	0.0322625796066905	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.982165140701897
CAMB-7A2DE	MN908947.3	28341	C	T	1	1	0	0	0.999258956792644	TCA	N	S23L	C68T	TCA>TTA	Missense	GU280_gp10	0.00010586331533657
CAMB-7A2DE	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998783796426233	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A2DE	MN908947.3	28894	T	C	0.024	0.012	2.5e-11	2.1e-06	0.0183319720482802	CTG	N	P207P	T621C	CCT>CCC	Synonymous	GU280_gp10	0.977674925129322
CAMB-7A2DE	MN908947.3	29460	C	A	0.012	0.0089	5.1e-06	7.7e-05	0.010752688172043	CCT	N	P396H	C1187A	CCT>CAT	Missense	GU280_gp10	0.989247311827957
CAMB-7A2DE	MN908947.3	3037	C	T	1	1	0	0	0.999523298772494	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000178762960314623
CAMB-7A2DE	MN908947.3	4903	A	G	0.03	0.039	1.2e-14	6.9e-19	0.033976833976834	TAG	ORF1ab:nsp3	L728L	A2184G	CTA>CTG	Synonymous	ORF1ab:nsp3	0.966023166023166
CAMB-7A2DE	MN908947.3	522	TT	-	0.0285	0.0425	0.00024;0.0017	3.6e-06;1.5e-05	0.0346345443614189	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.960623858861832
CAMB-7A2DE	MN908947.3	7424	T	G	0.0077	0.013	2e-05	9.6e-08	0.00985586509428588	CTT	ORF1ab:nsp3	F1569V	T4705G	TTT>GTT	Missense	ORF1ab:nsp3	0.99008716458725
CAMB-7A2DE	MN908947.3	8644	T	A	1	1	0	0	0.999820989035578	TTC	ORF1ab:nsp4	V30V	T90A	GTT>GTA	Synonymous	ORF1ab:nsp4	0.000179010964421571
CAMB-7A2DE	MN908947.3	9724	C	T	0.0076	0.0034	2.9e-05	0.0023	0.00562274707380551	TCT	ORF1ab:nsp4	F390F	C1170T	TTC>TTT	Synonymous	ORF1ab:nsp4	0.994349417544641
CAMB-7A2DE	MN908947.3	9922	A	G	0.024	0.011	2.2e-12	7.7e-07	0.0180904917003493	GAG	ORF1ab:nsp4	G456G	A1368G	GGA>GGG	Synonymous	ORF1ab:nsp4	0.980693011026959
CAMB-7A2ED	MN908947.3	11075	T	-	0.37	0.006	5.4e-106	0.005	0.253764675855028	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.746043899948954
CAMB-7A2ED	MN908947.3	12138	C	T	1	1	0	0	1	GCT	ORF1ab:nsp8	A16V	C47T	GCT>GTT	Missense	ORF1ab:nsp8	0
CAMB-7A2ED	MN908947.3	13521	T	C	1	1	7.4e-202	3.9e-113	1	GTA	ORF1ab:RNA-dependent-RNA-polymerase	S18S	T54C	AGT>AGC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-7A2ED	MN908947.3	14408	C	T	1	1	0	0	0.99930657215502	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000462285229986902
CAMB-7A2ED	MN908947.3	18768	T	C	1	1	0	0	0.999882005899705	ATG	ORF1ab:3'-to-5'-exonuclease	D243D	T729C	GAT>GAC	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.000117994100294985
CAMB-7A2ED	MN908947.3	23403	A	G	1	1	0	0	0.99983280387895	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.17990302624979e-05
CAMB-7A2ED	MN908947.3	241	C	T	1	1	0	0	0.999901263823065	TCG	NA	NA	NA	NA	NA	NA	9.87361769352291e-05
CAMB-7A2ED	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999406528189911	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A2ED	MN908947.3	3037	C	T	1	1	0	1.2e-254	0.99927060539752	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000729394602479942
CAMB-7A2ED	MN908947.3	6487	C	T	1	1	0	0	0.999367288832648	ACA	ORF1ab:nsp3	D1256D	C3768T	GAC>GAT	Synonymous	ORF1ab:nsp3	0.000632711167352104
CAMB-7A2FC	MN908947.3	11075	T	-	0.037	0.033	1.7e-09	7.8e-09	0.0349929373389058	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.961206331639265
CAMB-7A2FC	MN908947.3	11083	G	T	0.044	0.045	1.5e-09	9.9e-10	0.0442147251327284	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.946487260878115
CAMB-7A2FC	MN908947.3	14041	A	G	0.01	0.011	1.3e-06	7.8e-07	0.0105610117045607	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I192V	A574G	ATT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.988990537692273
CAMB-7A2FC	MN908947.3	14139	T	G	0.0075	0.005	4.1e-05	0.00051	0.00616973582217753	TTG	ORF1ab:RNA-dependent-RNA-polymerase	V224V	T672G	GTT>GTG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.993746464709949
CAMB-7A2FC	MN908947.3	14336	T	C	0.026	0.027	2.9e-13	1.3e-13	0.0263860575956818	GTT	ORF1ab:RNA-dependent-RNA-polymerase	V290A	T869C	GTT>GCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.973585230698556
CAMB-7A2FC	MN908947.3	14408	C	T	0.95	0.95	0	0	0.946624630105921	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.0524212505876822
CAMB-7A2FC	MN908947.3	1454	C	T	0.045	0.041	5.5e-19	6.4e-18	0.0419793621013133	TCT	ORF1ab:nsp2	L217F	C649T	CTT>TTT	Missense	ORF1ab:nsp2	0.957903377110694
CAMB-7A2FC	MN908947.3	1479	C	T	0.019	0.014	1.3e-09	1.9e-07	0.015710750026902	GCC	ORF1ab:nsp2	A225V	C674T	GCC>GTC	Missense	ORF1ab:nsp2	0.984289249973098
CAMB-7A2FC	MN908947.3	14805	C	T	0.051	0.049	1.3e-23	4.8e-23	0.0502177781940802	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.949735387785688
CAMB-7A2FC	MN908947.3	18202	A	C	0.0087	0.0077	4e-06	1.2e-05	0.00811645346272607	CAT	ORF1ab:3'-to-5'-exonuclease	I55L	A163C	ATC>CTC	Missense	ORF1ab:3'-to-5'-exonuclease	0.99170710189678
CAMB-7A2FC	MN908947.3	18807	C	T	0.051	0.05	3.8e-24	1.7e-23	0.0507740750459197	ACC	ORF1ab:3'-to-5'-exonuclease	N256N	C768T	AAC>AAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.949182191900638
CAMB-7A2FC	MN908947.3	20930	C	T	0.0092	0.0085	1.3e-05	2.8e-05	0.00878334417696812	ACG	ORF1ab:2'-O-ribose-methyltransferase	T91M	C272T	ACG>ATG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.991054001301236
CAMB-7A2FC	MN908947.3	21786	G	T	0.02	0.021	6e-10	1.8e-10	0.020688349192823	GGT	S	G75V	G224T	GGT>GTT	Missense	GU280_gp02, spike glycoprotein	0.978932916725844
CAMB-7A2FC	MN908947.3	21855	C	T	0.051	0.057	6.5e-23	9.5e-26	0.0546121450889825	TCT	S	S98F	C293T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.945387854911018
CAMB-7A2FC	MN908947.3	23403	A	G	0.95	0.94	0	0	0.943880597014925	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.05564756860857
CAMB-7A2FC	MN908947.3	241	C	T	0.94	0.94	0	0	0.941612707728621	TCG	NA	NA	NA	NA	NA	NA	0.0571273643583937
CAMB-7A2FC	MN908947.3	2480	A	G	0.059	0.054	4.3e-25	1.5e-23	0.05612968591692	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.94387031408308
CAMB-7A2FC	MN908947.3	25429	G	T	0.94	0.94	0	0	0.940915833111475	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0.0580192446658807
CAMB-7A2FC	MN908947.3	2558	C	T	0.056	0.053	1.2e-25	1.9e-24	0.0544245806207158	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.945127622196962
CAMB-7A2FC	MN908947.3	26137	A	C	0.024	0.017	2.9e-05	0.0012	0.0199948731094591	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.979748782363496
CAMB-7A2FC	MN908947.3	26144	G	T	0.049	0.052	1.4e-21	1.1e-22	0.0506049633489358	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.948600194294798
CAMB-7A2FC	MN908947.3	26176	C	T	0.01	0.01	1.9e-06	2.5e-06	0.0103255891414772	ACC	ORF3a	P262S	C784T	CCA>TCA	Missense	GU280_gp03	0.98909151469731
CAMB-7A2FC	MN908947.3	3037	C	T	0.95	0.94	0	0	0.945574023965984	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.0539234634712022
CAMB-7A2FC	MN908947.3	4331	C	T	0.024	0.024	1.4e-12	1.8e-12	0.0243536117389966	TCT	ORF1ab:nsp3	L538L	C1612T	CTA>TTA	Synonymous	ORF1ab:nsp3	0.975556273138935
CAMB-7A2FC	MN908947.3	4524	C	T	0.056	0.058	7.3e-26	1.3e-26	0.0568751951701884	GCT	ORF1ab:nsp3	A602V	C1805T	GCT>GTT	Missense	ORF1ab:nsp3	0.942895805142084
CAMB-7A2FC	MN908947.3	7039	C	T	0.012	0.0097	5e-06	2.3e-05	0.0106272680145153	GCA	ORF1ab:nsp3	G1440G	C4320T	GGC>GGT	Synonymous	ORF1ab:nsp3	0.989372731985485
CAMB-7A2FC	MN908947.3	7732	C	T	0.074	0.076	6.3e-31	1.9e-31	0.0746139592340951	ACA	ORF1ab:nsp3	Y1671Y	C5013T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.924891908585547
CAMB-7A2FC	MN908947.3	8316	C	T	0.072	0.076	2.1e-33	7.3e-35	0.0742778541953232	ACA	ORF1ab:nsp3	T1866I	C5597T	ACA>ATA	Missense	ORF1ab:nsp3	0.925667561843628
CAMB-7A2FC	MN908947.3	9333	C	T	0.045	0.046	6.1e-21	5.2e-21	0.0454335864252559	GCT	ORF1ab:nsp4	A260V	C779T	GCT>GTT	Missense	ORF1ab:nsp4	0.954504933755495
CAMB-7A308	MN908947.3	10236	A	G	1	1	0	0	0.999849147684417	AAG	ORF1ab:3C-like-proteinase	K61R	A182G	AAG>AGG	Missense	ORF1ab:3C-like-proteinase	0
CAMB-7A308	MN908947.3	11074	C	INS	0.04	0.064	7e-09	8.1e-16	0.043647321862545	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.955866627782638
CAMB-7A308	MN908947.3	11083	G	-	0.26	0.036	2.4e-119	5.4e-13	0.221235365361324	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-7A308	MN908947.3	11083	G	T	0.74	0.96	2.4e-277	0	0.778764634638676	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-7A308	MN908947.3	13914	T	G	0.0082	0.017	5.2e-06	2.7e-05	0.00873044743543107	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.991269552564569
CAMB-7A308	MN908947.3	14805	C	T	1	1	0	0	0.999926900584795	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-7A308	MN908947.3	17247	T	C	1	1	0	0	0.999793191876577	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000206808123423088
CAMB-7A308	MN908947.3	17750	C	T	1	1	0	0	0.999801014824396	GCT	ORF1ab:helicase	A505V	C1514T	GCT>GTT	Missense	ORF1ab:helicase	0.000198985175604417
CAMB-7A308	MN908947.3	24130	C	T	1	1	0	0	1	ACG	S	N856N	C2568T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-7A308	MN908947.3	25563	G	T	1	1	0	0	0.999747027573994	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000252972426005565
CAMB-7A308	MN908947.3	6027	C	T	1	1	5e-144	2.3e-156	1	CCA	ORF1ab:nsp3	P1103L	C3308T	CCA>CTA	Missense	ORF1ab:nsp3	0
CAMB-7A308	MN908947.3	8313	T	INS	0.0015	0.0075	0.0048	1.9e-05	0.00407925407925408	ATG	ORF1ab:nsp3	.	5593-5594-insfrshift	.	no-SNV	ORF1ab:nsp3	0.995920745920746
CAMB-7A308	MN908947.3	8315	ACACC	-	0.00152	0.00754	0.0077;0.008;0.0084;0.017;0.0068	2.9e-05;3.1e-05;3e-05;6.5e-05;2.5e-05	0.00408639813193228	GAC	ORF1ab:nsp3	.	5596-5600-delfrshift	.	no-SNV	ORF1ab:nsp3	0.995911214953271
CAMB-7A326	MN908947.3	11075	T	-	0.026	0.0056	5e-07	0.0079	0.0183205078552545	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.981511105124017
CAMB-7A326	MN908947.3	1223	C	T	0.021	0.0051	4.9e-11	9.3e-05	0.0138496847547946	TCT	ORF1ab:nsp2	L140F	C418T	CTC>TTC	Missense	ORF1ab:nsp2	0.986123934893292
CAMB-7A326	MN908947.3	14408	C	T	1	1	0	0	0.999486148346738	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000402144772117962
CAMB-7A326	MN908947.3	15738	C	T	0.029	0.03	2.8e-14	1.2e-14	0.0292852876766872	TCA	ORF1ab:RNA-dependent-RNA-polymerase	F757F	C2271T	TTC>TTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.970694803902051
CAMB-7A326	MN908947.3	16332	C	T	0.082	0.14	4e-29	5.2e-43	0.104461371055495	ACC	ORF1ab:helicase	D32D	C96T	GAC>GAT	Synonymous	ORF1ab:helicase	0.895538628944505
CAMB-7A326	MN908947.3	17010	C	T	0.013	0.021	5.2e-08	2.9e-11	0.0164943836996679	TCT	ORF1ab:helicase	I258I	C774T	ATC>ATT	Synonymous	ORF1ab:helicase	0.983505616300332
CAMB-7A326	MN908947.3	17167	C	T	0.015	0.026	4.5e-08	8.2e-13	0.0197841516317248	TCA	ORF1ab:helicase	H311Y	C931T	CAT>TAT	Missense	ORF1ab:helicase	0.980192462846252
CAMB-7A326	MN908947.3	17410	C	T	0.56	0.65	0	0	0.599645688626956	ACG	ORF1ab:helicase	R392C	C1174T	CGT>TGT	Missense	ORF1ab:helicase	0.400310460955588
CAMB-7A326	MN908947.3	17835	T	C	1	1	0	0	0.99983113812901	TTG	ORF1ab:helicase	V533V	T1599C	GTT>GTC	Synonymous	ORF1ab:helicase	0.000140718225824609
CAMB-7A326	MN908947.3	20016	C	T	0.6	0.49	4.2e-93	8.9e-33	0.577540106951872	ACT	ORF1ab:endoRNAse	D132D	C396T	GAC>GAT	Synonymous	ORF1ab:endoRNAse	0.422459893048128
CAMB-7A326	MN908947.3	203	C	T	0.022	0.071	5.9e-11	4e-32	0.0470631054370345	TCG	NA	NA	NA	NA	NA	NA	0.952936894562965
CAMB-7A326	MN908947.3	21128	T	C	0.022	0.014	2e-11	2.1e-08	0.0189592726735162	ATA	ORF1ab:2'-O-ribose-methyltransferase	I157T	T470C	ATA>ACA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.981003769679947
CAMB-7A326	MN908947.3	23309	GAGAT	TGAGA	0.004254	0.0188	0.48;2.3e-09;0.5;0.48;0.48	9.6e-08;1.1e-08;9.3e-09;9.6e-09;1.1e-09	0.0084960158015071	TGA	S	.	1747-1751-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.992694322908227
CAMB-7A326	MN908947.3	23403	A	G	1	1	0	0	0.999888132053895	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.45786307363397e-05
CAMB-7A326	MN908947.3	23435	C	T	0.05	0.02	1.2e-23	6.1e-11	0.037231207783355	TCA	S	H625Y	C1873T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.962744004461796
CAMB-7A326	MN908947.3	23538	C	T	0.021	0.046	2e-10	4.1e-20	0.0303471211806277	TCA	S	S659L	C1976T	TCA>TTA	Missense	GU280_gp02, spike glycoprotein	0.969652878819372
CAMB-7A326	MN908947.3	241	C	T	1	1	0	0	0.999791384166058	TCG	NA	NA	NA	NA	NA	NA	7.82309377281736e-05
CAMB-7A326	MN908947.3	25521	C	T	0.16	0.13	7.7e-75	2.7e-58	0.147879243078592	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.852120756921408
CAMB-7A326	MN908947.3	25690	G	T	0.016	0.035	2.3e-08	4e-13	0.0210468014400443	TGG	ORF3a	G100C	G298T	GGC>TGC	Missense	GU280_gp03	0.978953198559956
CAMB-7A326	MN908947.3	28253	C	T	0.078	0.079	1.3e-34	2e-35	0.0784752999237001	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.92111884933197
CAMB-7A326	MN908947.3	28485	G	T	0.016	0.0082	1e-08	1.1e-05	0.0130734122379516	GGC	N	G71V	G212T	GGC>GTC	Missense	GU280_gp10	0.986849230293185
CAMB-7A326	MN908947.3	28536	GAA	-	0.0113333333333333	0.018	7.4e-06;5.2e-06;1.3e-06	3.9e-08;3.2e-08;3.9e-09	0.013141268637857	CGA	N	.	263-265-delinframe	.	no-SNV	GU280_gp10	0.98761561373256
CAMB-7A326	MN908947.3	28603	C	T	0.01	0.018	2e-04	2.6e-06	0.0129049724754084	TCT	N	F110F	C330T	TTC>TTT	Synonymous	GU280_gp10	0.987004782961827
CAMB-7A326	MN908947.3	29520	C	T	0.0051	0.019	0.003	8.7e-07	0.010752688172043	TCA	N	S416L	C1247T	TCA>TTA	Missense	GU280_gp10	0.989247311827957
CAMB-7A326	MN908947.3	3037	C	T	1	1	0	0	0.999011075949367	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000197784810126582
CAMB-7A326	MN908947.3	3096	C	T	0.015	0.022	1.2e-06	1.5e-08	0.0177910868416417	TCA	ORF1ab:nsp3	S126L	C377T	TCA>TTA	Missense	ORF1ab:nsp3	0.982208913158358
CAMB-7A326	MN908947.3	635	C	T	0.81	0.67	0	0	0.748117766041128	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.251826047870547
CAMB-7A326	MN908947.3	683	C	T	0.0079	0.014	4e-05	7.4e-08	0.0108405668848662	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.974531825457763
CAMB-7A326	MN908947.3	686	AAGTCATTT	-	0.558888888888889	0.653333333333333	5.9e-106;1.6e-107;3.6e-94;1.9e-107;5.9e-93;4.2e-98;4.8e-106;2.6e-98;5.3e-84	7.3e-139;2e-140;2.7e-122;1.3e-139;6.4e-121;7.1e-127;5.5e-137;9.9e-127;4e-109	0.598913719369044	AAA	ORF1ab:leader-protein	.	421-429-delinframe	.	no-SNV	ORF1ab:leader-protein	0.402272065249053
CAMB-7A326	MN908947.3	7417	C	T	0.039	0.012	3.3e-17	1.7e-06	0.0295424836601307	ACA	ORF1ab:nsp3	Y1566Y	C4698T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.970457516339869
CAMB-7A326	MN908947.3	9430	C	T	0.18	0.14	3.7e-69	2.6e-51	0.161508159819921	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.838491840180079
CAMB-7A335	MN908947.3	11075	T	-	0.037	0.034	1.6e-09	3.4e-09	0.0359078590785908	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.96064438422162
CAMB-7A335	MN908947.3	14408	C	T	1	1	0	0	0.99815396700707	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000497512437810945
CAMB-7A335	MN908947.3	19017	C	T	0.45	0.45	4.8e-251	1.1e-251	0.452976416167438	TCC	ORF1ab:3'-to-5'-exonuclease	F326F	C978T	TTC>TTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.546887085766285
CAMB-7A335	MN908947.3	21638	C	T	0.5	0.52	1.7e-268	4.5e-248	0.508274767626389	CCC	S	P26S	C76T	CCT>TCT	Missense	GU280_gp02, spike glycoprotein	0.491725232373611
CAMB-7A335	MN908947.3	21952	C	T	0.0061	0.008	0.00014	1.8e-05	0.00683521009507953	TCT	S	V130V	C390T	GTC>GTT	Synonymous	GU280_gp02, spike glycoprotein	0.993120974455593
CAMB-7A335	MN908947.3	23403	A	G	1	1	0	0	0.999209640435186	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.78177294238181e-05
CAMB-7A335	MN908947.3	241	C	T	1	1	0	0	0.998565750820805	TCG	NA	NA	NA	NA	NA	NA	0.000103680663556247
CAMB-7A335	MN908947.3	25665	C	T	0.017	0.014	6.8e-09	9.8e-08	0.0156531666866963	ACT	ORF3a	Y91Y	C273T	TAC>TAT	Synonymous	GU280_gp03	0.983926210791972
CAMB-7A335	MN908947.3	26029	C	A	0.019	0.019	1.1e-09	1.2e-09	0.0191819171548551	CCA	ORF3a	Q213K	C637A	CAG>AAG	Missense	GU280_gp03	0.980610710767795
CAMB-7A335	MN908947.3	27813	C	T	1	1	0	0	0.999031789575601	CCT	NA	NA	NA	NA	NA	NA	0.000968210424398903
CAMB-7A335	MN908947.3	28851	GTT	-	0.032	0.0286666666666667	6.5e-15;1.6e-15;4.2e-15	1.3e-13;5e-14;1.3e-13	0.0309281998655296	AGT	N	.	578-580-delinframe	.	no-SNV	GU280_gp10	0.969580455272381
CAMB-7A335	MN908947.3	29530	C	T	0.012	0.012	7.7e-07	2.7e-07	0.0119206476292145	CCT	N	A419A	C1257T	GCC>GCT	Synonymous	GU280_gp10	0.987856952228449
CAMB-7A335	MN908947.3	29682	TA	-	0.027	0.025	3.1e-11;4.1e-13	6.9e-11;1.5e-12	0.0261163650028183	TTA	NA	NA	NA	NA	NA	NA	0.97468734968735
CAMB-7A335	MN908947.3	3037	C	T	1	1	0	0	0.999105303112461	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	2.71120268951307e-05
CAMB-7A335	MN908947.3	411	G	A	0.0083	0.0073	1.7e-05	3.7e-05	0.00792964548579623	GGC	ORF1ab:leader-protein	G49D	G146A	GGC>GAC	Missense	ORF1ab:leader-protein	0.992038720290191
CAMB-7A335	MN908947.3	6526	A	G	0.0055	0.0066	0.00016	4e-05	0.00590486122841678	CAG	ORF1ab:nsp3	T1269T	A3807G	ACA>ACG	Synonymous	ORF1ab:nsp3	0.993992317804919
CAMB-7A344	MN908947.3	14408	C	T	1	1	0	0	0.999138054877173	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000766173442513049
CAMB-7A344	MN908947.3	23403	A	G	1	1	0	0	0.999870613808094	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.0001293861919056
CAMB-7A344	MN908947.3	241	C	T	1	1	0	0	0.999896351575456	TCG	NA	NA	NA	NA	NA	NA	0.000103648424543947
CAMB-7A344	MN908947.3	3037	C	T	1	1	2.7e-194	0	0.998146431881372	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A353	MN908947.3	11075	T	-	0.039	0.0058	3.7e-10	0.0056	0.030363001926983	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.969506796521015
CAMB-7A353	MN908947.3	12741	C	T	0.056	0.023	7.3e-26	1.2e-11	0.0492188701632572	ACA	ORF1ab:nsp9	T19I	C56T	ACA>ATA	Missense	ORF1ab:nsp9	0.950759157126848
CAMB-7A353	MN908947.3	12820	A	G	0.011	0.021	9.5e-07	2.3e-11	0.013988107115776	TAT	ORF1ab:nsp9	L45L	A135G	TTA>TTG	Synonymous	ORF1ab:nsp9	0.985991938380492
CAMB-7A353	MN908947.3	14408	C	T	1	1	0	0	0.999345721015441	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000490709238419262
CAMB-7A353	MN908947.3	14870	A	C	0.0027	0.073	0.0014	3e-32	0.0140461709062805	GAT	ORF1ab:RNA-dependent-RNA-polymerase	D468A	A1403C	GAT>GCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.985886622534359
CAMB-7A353	MN908947.3	23403	A	G	1	1	0	0	0.999849168162416	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.54159187921386e-05
CAMB-7A353	MN908947.3	24011	TTTATTGAAGATCTAC	-	0.0391875	0.260625	NA;NA;NA;NA;6.9e-07;8.9e-07;1.3e-06;1.2e-06;3.6e-06;3.8e-06;2.8e-06;4.5e-06;1.5e-06;1.1e-06;2e-06;1.9e-05	2.7e-41;4.9e-37;9.8e-32;1.3e-29;1.6e-24;2.5e-24;1.2e-23;3.2e-24;8.3e-23;1.4e-22;7.1e-23;3.7e-22;9.9e-22;4.7e-24;8.7e-24;2.9e-20	0.0687303252885624	ATT	S	.	2449-2464-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.978550095031225
CAMB-7A353	MN908947.3	241	C	T	1	1	0	0	0.999742168364058	TCG	NA	NA	NA	NA	NA	NA	6.44579089854325e-05
CAMB-7A353	MN908947.3	25429	G	T	1	1	0	0	0.999906283679303	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	4.68581603486247e-05
CAMB-7A353	MN908947.3	25614	C	T	1	1	0	0	0.999979879275654	CCA	ORF3a	S74S	C222T	TCC>TCT	Synonymous	GU280_gp03	2.01207243460765e-05
CAMB-7A353	MN908947.3	3037	C	T	1	1	0	0	0.996473492418009	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A353	MN908947.3	519	TGGTT	-	0.019	0.264	0.097;0.09;0.063;0.0025;0.074	5.3e-05;0.00012;1.4e-06;1.2e-37;1.7e-39	0.0333109983727386	ATG	ORF1ab:leader-protein	.	254-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.96957554170377
CAMB-7A362	MN908947.3	11074	C	INS	0.12	0.12	2.4e-52	4.2e-44	0.117933204259439	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.877819457889642
CAMB-7A362	MN908947.3	11083	G	-	0.16	0.14	4.1e-70	4.8e-63	0.153225009063643	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.000109862342484866
CAMB-7A362	MN908947.3	11083	G	T	0.84	0.86	0	0	0.84595102336772	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.000109862342484866
CAMB-7A362	MN908947.3	14805	C	T	1	1	0	0	0.997909941026975	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000991060827584853
CAMB-7A362	MN908947.3	1515	A	G	1	1	0	0	0.99901768172888	CAT	ORF1ab:nsp2	H237R	A710G	CAT>CGT	Missense	ORF1ab:nsp2	0.000368369351669941
CAMB-7A362	MN908947.3	17247	T	C	1	1	0	0	0.998918791867434	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000458338230109296
CAMB-7A362	MN908947.3	2047	T	C	1	1	0	0	0.999392475373555	ATC	ORF1ab:nsp2	N414N	T1242C	AAT>AAC	Synonymous	ORF1ab:nsp2	2.89297441164133e-05
CAMB-7A362	MN908947.3	21569	G	INS	0.056	0.06	1.8e-23	5.1e-24	0.0574497898178421	TGT	S	.	6-7-insfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.940331620737973
CAMB-7A362	MN908947.3	21575	C	-	0.015	0.012	1.3e-07	1.2e-06	0.0137999014292755	TCT	S	.	13-13-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.000369640216855594
CAMB-7A362	MN908947.3	21575	C	T	0.98	0.99	0	0	0.985830458353869	TCT	S	L5F	C13T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.000369640216855594
CAMB-7A362	MN908947.3	26144	G	T	1	1	0	0	0.999796195652174	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000135869565217391
CAMB-7A362	MN908947.3	26735	C	T	1	1	0	0	0.999131149830109	ACA	M	Y71Y	C213T	TAC>TAT	Synonymous	GU280_gp05	3.10303632104014e-05
CAMB-7A362	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0359210526315789	0.0415	4e-04;2.2e-05;0.00012;0.00015;0.00028;7e-06;2.8e-05;4e-06;3.9e-06;1.1e-06;1.8e-06;1.5e-06;3.7e-06;2.1e-06;2.6e-06;4.9e-06;1.8e-06;4.5e-06;2.7e-06;2.8e-06;1.9e-06;4.1e-06;1.4e-06;2.8e-06;2.2e-06;1.1e-06;3.2e-06;2.3e-06;7.8e-07;2.1e-06;4.1e-06;3.4e-06;1.4e-06;3.6e-06;1.2e-06;1.9e-06;1.2e-06;0.00088	6.3e-05;2.4e-06;2.2e-05;2.2e-05;4.6e-05;6.5e-07;2.2e-06;2.5e-07;2.4e-07;5.1e-08;1.2e-07;9.1e-08;2.2e-07;1.2e-07;1.7e-07;3.2e-07;1e-07;2.3e-07;1.6e-07;1.6e-07;9.8e-08;2.9e-07;1.4e-07;2e-07;1.3e-07;9.3e-08;2.3e-07;1.1e-07;3.2e-07;9.4e-08;2.2e-07;1.4e-07;9.2e-08;2.1e-07;4.4e-08;1.1e-07;9e-08;0.00017	0.0401153521523024	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.974511291357881
CAMB-7A362	MN908947.3	522	TT	-	0.043	0.043	1.7e-06;8.7e-05	6.5e-07;0.00014	0.0425799949609473	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.946927547366204
CAMB-7A362	MN908947.3	9223	C	T	1	1	0	0	0.998098369748232	ACG	ORF1ab:nsp4	H223H	C669T	CAC>CAT	Synonymous	ORF1ab:nsp4	3.96172969118317e-05
CAMB-7A371	MN908947.3	11074	C	INS	0.031	0.02	2.9e-07	0.0016	0.0266924768564242	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.973109996181145
CAMB-7A371	MN908947.3	11075	T	-	0.044	0.036	1.1e-10	2.4e-09	0.0407553563864179	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.951073506788844
CAMB-7A371	MN908947.3	11476	A	G	0.086	0.082	1.7e-37	8.1e-35	0.0844527854602924	TAA	ORF1ab:nsp6	I168M	A504G	ATA>ATG	Missense	ORF1ab:nsp6	0.915547214539708
CAMB-7A371	MN908947.3	14408	C	T	0.99	1	0	0	0.995711924548365	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000254279406835493
CAMB-7A371	MN908947.3	16853	G	A	0.11	0.11	5.9e-48	9.4e-53	0.108566568490022	GGT	ORF1ab:helicase	G206D	G617A	GGT>GAT	Missense	ORF1ab:helicase	0.891401930982344
CAMB-7A371	MN908947.3	187	A	G	1	1	0	0	0.999294816904246	CAG	NA	NA	NA	NA	NA	NA	3.35801474168472e-05
CAMB-7A371	MN908947.3	19572	C	T	0.0023	0.0093	0.0072	5.1e-06	0.00434954527481218	ACA	ORF1ab:3'-to-5'-exonuclease	Y511Y	C1533T	TAC>TAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.995650454725188
CAMB-7A371	MN908947.3	20295	TAAATTAGAAGGCTATGCCTTCGAACATATCG	-	0.022725	0.04953125	0.12;0.13;0.00029;0.00032;0.00044;0.00052;0.0027;0.00083;0.0013;0.0023;0.00077;0.0024;0.0025;0.0033;0.0021;0.0025;0.0024;0.0016;0.00031;1e-04;0.0011;0.0022;0.0024;0.0011;0.001;0.0024;0.0012;0.0013;0.0019;0.00091;0.0016;0.0014	4e-05;6.6e-05;6.2e-05;7.1e-05;9.9e-05;0.00012;0.00011;2.1e-05;7.8e-05;0.00011;2.7e-05;1e-04;0.00012;0.00013;0.00011;9.6e-05;9.5e-05;5.1e-05;1.1e-05;6e-06;2.9e-05;8e-05;0.00011;5.4e-05;6.2e-05;1e-04;3.9e-05;4.9e-05;8.3e-05;2.6e-05;7.8e-05;6.5e-05	0.0298165137614679	ATA	ORF1ab:endoRNAse	.	675-706-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.982142857142857
CAMB-7A371	MN908947.3	20329	T	-	0.028	0.055	0.00028	1.6e-05	0.0365168539325843	TTA	ORF1ab:endoRNAse	.	709-709-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.963483146067416
CAMB-7A371	MN908947.3	20331	TGGAGATTT	-	0.0234	0.0527777777777778	0.00043;0.001;0.00047;0.00035;0.001;0.00067;0.00026;0.00022;0.088	1.4e-05;5.2e-05;1.9e-05;1.6e-05;3.7e-05;3.4e-05;1.2e-05;8.9e-06;2.4e-05	0.0327455919395466	ATG	ORF1ab:endoRNAse	.	711-719-delinframe	.	no-SNV	ORF1ab:endoRNAse	0.966145833333333
CAMB-7A371	MN908947.3	2317	A	G	0.021	0.018	2.1e-10	2.3e-09	0.0200201884253028	AAT	ORF1ab:nsp2	K504K	A1512G	AAA>AAG	Synonymous	ORF1ab:nsp2	0.979475100942127
CAMB-7A371	MN908947.3	23403	A	G	1	1	0	0	0.999648512486819	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.50625016898438e-05
CAMB-7A371	MN908947.3	23554	ACCCATTGGTGCAGGTATATGCGCTAGT	-	0.0419285714285714	0.0331785714285714	0.00089;6e-04;0.00045;6e-04;0.00065;0.00012;0.00017;7.2e-05;0.00015;0.00017;0.00017;0.00016;0.00014;8.6e-05;7.8e-05;4.1e-06;1e-06;0.00012;3.6e-05;9.3e-05;3.3e-05;8.8e-05;0.00018;0.00011;1e-04;1.1e-06;3.1e-06;0.00037	0.0094;0.0016;0.0013;0.0016;0.0017;0.00068;0.0012;0.00049;0.00084;0.00088;0.00087;0.00084;0.00089;0.00055;0.00052;0.00046;0.00013;0.00041;2e-04;0.00039;0.00014;0.00032;0.00057;0.00035;0.00035;1.5e-05;2.3e-05;0.00041	0.0364722020495441	TAC	S	.	1992-2019-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.975905530595205
CAMB-7A371	MN908947.3	241	C	T	1	1	0	0	0.998383143849139	TCG	NA	NA	NA	NA	NA	NA	0.0007658792293553
CAMB-7A371	MN908947.3	25091	G	C	0.065	0.06	9.8e-30	1.1e-27	0.0638124154823565	TGT	S	V1177L	G3529C	GTA>CTA	Missense	GU280_gp02, spike glycoprotein	0.936111040236777
CAMB-7A371	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0393513513513514	0.0406756756756757	0.00077;0.00022;0.0013;0.0015;0.0031;8.1e-06;5.5e-05;5.3e-07;5.4e-07;1.2e-07;1.7e-07;1.3e-07;6.1e-07;2.6e-07;3.5e-07;8.4e-07;2.3e-07;6.9e-07;3.9e-07;3.8e-07;2.6e-07;7.4e-07;2.5e-07;5.2e-07;3.7e-07;1.4e-07;5.1e-07;3.1e-07;2.9e-07;2.3e-07;5.8e-07;4.9e-07;1.7e-07;5.4e-07;1.3e-07;2.9e-07;2e-07	3.7e-06;4.3e-08;2e-06;2e-06;1.3e-05;1.7e-07;1.3e-06;5.8e-07;5.9e-07;1.7e-07;2.9e-07;1.8e-07;5.9e-07;3.1e-07;2.5e-07;4.4e-07;2.7e-07;6.8e-07;4.5e-07;4e-07;3.6e-07;7.7e-07;1.2e-07;2e-07;3.5e-07;2.2e-07;5.5e-07;3e-07;1.6e-07;3.2e-07;6e-07;5.2e-07;3.2e-07;6.2e-07;1.3e-07;2.7e-07;1.5e-07	0.041989144637652	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.973684210526316
CAMB-7A371	MN908947.3	2902	C	T	1	1	0	0	0.999354937797573	TCA	ORF1ab:nsp3	V61V	C183T	GTC>GTT	Synonymous	ORF1ab:nsp3	0.00061434495469206
CAMB-7A371	MN908947.3	3037	C	T	1	1	0	0	0.998460241228874	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.33218462440884e-05
CAMB-7A371	MN908947.3	5305	G	A	0.012	0.015	3.5e-07	4.7e-08	0.0132205696510158	TGT	ORF1ab:nsp3	L862L	G2586A	TTG>TTA	Synonymous	ORF1ab:nsp3	0.986779430348984
CAMB-7A380	MN908947.3	11074	C	INS	0.034	0.027	9.8e-08	1.5e-05	0.0305492497646863	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.965893361386413
CAMB-7A380	MN908947.3	11075	T	-	0.023	0.053	1.9e-06	5.1e-13	0.0374061068347248	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957396339620009
CAMB-7A380	MN908947.3	11083	G	-	0.044	0.035	1.6e-18	7.9e-15	0.0397194393356104	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.819440477958396
CAMB-7A380	MN908947.3	11083	G	T	0.12	0.16	2.7e-26	2.4e-36	0.140794388786712	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.819440477958396
CAMB-7A380	MN908947.3	11083	GTATGAAAATGCC	-	0.00338807692307692	0.0127692307692308	1.6e-18;NA;NA;NA;NA;0.48;NA;NA;NA;NA;NA;NA;NA	7.9e-15;1.1e-05;1.1e-05;7.4e-05;6e-05;4.9e-06;3.1e-06;2.4e-06;1.2e-06;2.6e-06;1.7e-06;2.1e-05;2.2e-05	0.00502305098740797	TGT	ORF1ab:nsp6	.	111-123-delfrshift	.	no-SNV	ORF1ab:nsp6	0.819440477958396
CAMB-7A380	MN908947.3	13542	T	-	0.0051	0.011	0.0014	5e-06	0.00817783920755586	CTT	ORF1ab:RNA-dependent-RNA-polymerase	.	75-75-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.991706979958535
CAMB-7A380	MN908947.3	14408	C	T	1	1	0	0	0.997329999088292	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000286536683207648
CAMB-7A380	MN908947.3	1997	C	T	0.032	0.022	6.4e-16	7.9e-12	0.0269399032926548	ACT	ORF1ab:nsp2	L398L	C1192T	CTG>TTG	Synonymous	ORF1ab:nsp2	0.973060096707345
CAMB-7A380	MN908947.3	20518	G	T	0.083	0.019	2.6e-36	9e-10	0.0577636459989401	TGA	ORF1ab:endoRNAse	D300Y	G898T	GAT>TAT	Missense	ORF1ab:endoRNAse	0.94223635400106
CAMB-7A380	MN908947.3	20679	G	T	1	1	0	0	1	CGG	ORF1ab:2'-O-ribose-methyltransferase	P7P	G21T	CCG>CCT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0
CAMB-7A380	MN908947.3	22281	CTTTAC	-	0.0037465	0.00793333333333333	NA;0.47;NA;0.0066;0.00013;0.00019	3.7e-05;0.00012;7.7e-05;0.00021;0.00042;0.00056	0.00409175449473032	ACT	S	.	719-724-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.997131275335204
CAMB-7A380	MN908947.3	23403	A	G	1	1	0	0	0.999328836538139	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.1947716366321e-05
CAMB-7A380	MN908947.3	23936	C	A	1	1	0	0	0.999781193588972	ACC	S	P792T	C2374A	CCA>ACA	Missense	GU280_gp02, spike glycoprotein	0.000164104808270882
CAMB-7A380	MN908947.3	241	C	T	0.99	1	0	0	0.991645149778533	TCG	NA	NA	NA	NA	NA	NA	6.29762579507526e-05
CAMB-7A380	MN908947.3	25910	A	T	0.0052	0.01	8.9e-05	8.3e-07	0.00664355863662623	GAT	ORF3a	D173V	A518T	GAT>GTT	Missense	GU280_gp03	0.993356441363374
CAMB-7A380	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999566442662042	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A380	MN908947.3	3037	C	T	1	1	0	0	0.998437316873071	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00011720123451967
CAMB-7A380	MN908947.3	3638	G	T	0.012	0.0042	7e-06	0.0032	0.00809061488673139	AGG	ORF1ab:nsp3	G307C	G919T	GGT>TGT	Missense	ORF1ab:nsp3	0.987864077669903
CAMB-7A380	MN908947.3	522	T	-	0.04	0.046	3.2e-05	4.7e-06	0.0427546190258055	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.957054512139258
CAMB-7A380	MN908947.3	522	TT	-	0.0325	0.0415	3.2e-05;0.0012	4.7e-06;2.2e-05	0.0361323996985904	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.957054512139258
CAMB-7A380	MN908947.3	6539	CA	-	0.0068	0.015	0.00016;0.00011	3.4e-07;1e-07	0.0101165603694744	CCA	ORF1ab:nsp3	.	3820-3821-delfrshift	.	no-SNV	ORF1ab:nsp3	0.990244914902449
CAMB-7A380	MN908947.3	8205	A	-	0.0037	0.0081	0.00051	5e-06	0.00543706916081427	GAA	ORF1ab:nsp3	.	5486-5486-delfrshift	.	no-SNV	ORF1ab:nsp3	0.994498203825366
CAMB-7A39F	MN908947.3	11075	T	-	0.033	0.034	2e-08	5.9e-09	0.0334967892586106	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.963292469352014
CAMB-7A39F	MN908947.3	14408	C	T	1	1	0	0	0.998578734607812	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00119992078192896
CAMB-7A39F	MN908947.3	23403	A	G	1	1	0	0	0.999911078704239	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.00291661850096e-05
CAMB-7A39F	MN908947.3	241	C	T	1	1	0	0	0.998482492459299	TCG	NA	NA	NA	NA	NA	NA	9.36733049815464e-05
CAMB-7A39F	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999207946932445	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000148975791433892
CAMB-7A39F	MN908947.3	3037	C	T	1	1	0	0	0.998727072846149	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.78603251750275e-05
CAMB-7A39F	MN908947.3	8898	A	C	0.023	0.015	5.7e-12	1.4e-08	0.0186437059702555	AAT	ORF1ab:nsp4	N115T	A344C	AAT>ACT	Missense	ORF1ab:nsp4	0.981356294029745
CAMB-7A39F	MN908947.3	8991	C	T	0.018	0.03	7.3e-09	6e-14	0.0238736385193521	GCA	ORF1ab:nsp4	A146V	C437T	GCA>GTA	Missense	ORF1ab:nsp4	0.976126361480648
CAMB-7A3AE	MN908947.3	10369	C	T	0.0046	0.0086	0.0017	3e-05	0.00641333974667308	GCA	ORF1ab:3C-like-proteinase	R105R	C315T	CGC>CGT	Synonymous	ORF1ab:3C-like-proteinase	0.993586660253327
CAMB-7A3AE	MN908947.3	11075	T	-	0.055	0.024	2.1e-13	1.1e-06	0.0405626275038475	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956896243184882
CAMB-7A3AE	MN908947.3	12396	C	T	0.037	0.011	1e-17	5.8e-07	0.0259430157142396	GCA	ORF1ab:nsp8	A102V	C305T	GCA>GTA	Missense	ORF1ab:nsp8	0.97402471685328
CAMB-7A3AE	MN908947.3	14408	C	T	1	1	0	0	0.997326093777711	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000313774709758393
CAMB-7A3AE	MN908947.3	16448	A	G	0.028	0.027	8.2e-14	5.6e-13	0.0275678987134981	TAT	ORF1ab:helicase	Y71C	A212G	TAT>TGT	Missense	ORF1ab:helicase	0.972432101286502
CAMB-7A3AE	MN908947.3	17445	T	C	0.022	0.018	2.7e-11	7.6e-10	0.020011134014414	CTC	ORF1ab:helicase	A403A	T1209C	GCT>GCC	Synonymous	ORF1ab:helicase	0.979973820020162
CAMB-7A3AE	MN908947.3	17518	C	T	0.02	0.007	1.2e-09	0.00012	0.0138826061863389	ACT	ORF1ab:helicase	L428F	C1282T	CTT>TTT	Missense	ORF1ab:helicase	0.986101795379744
CAMB-7A3AE	MN908947.3	17761	G	T	0.16	0.19	9.3e-75	6.8e-87	0.172051290635776	AGC	ORF1ab:helicase	A509S	G1525T	GCT>TCT	Missense	ORF1ab:helicase	0.82789849007332
CAMB-7A3AE	MN908947.3	19032	C	T	1	0.99	0	0	0.993175962676694	ACA	ORF1ab:3'-to-5'-exonuclease	D331D	C993T	GAC>GAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	2.32110113037625e-05
CAMB-7A3AE	MN908947.3	19969	G	T	0.013	0.0067	1.4e-05	0.001	0.0100066711140761	TGC	ORF1ab:endoRNAse	A117S	G349T	GCA>TCA	Missense	ORF1ab:endoRNAse	0.989993328885924
CAMB-7A3AE	MN908947.3	23403	A	G	1	1	0	0	0.998044895003621	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.52570601013758e-05
CAMB-7A3AE	MN908947.3	241	C	T	1	1	0	0	0.999898154560639	TCG	NA	NA	NA	NA	NA	NA	8.14763514889803e-05
CAMB-7A3AE	MN908947.3	25181	GAGC	-	0.0056	0.0092	NA;0.00022;0.00023;2.3e-05	5.6e-05;5.7e-08;4.1e-05;0.00034	0.00661337900846893	TGA	S	.	3619-3622-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.997535571468427
CAMB-7A3AE	MN908947.3	25947	G	T	0.02	0.025	1.2e-10	2.3e-12	0.0218740461898464	AGA	ORF3a	Q185H	G555T	CAG>CAT	Missense	GU280_gp03	0.978125953810154
CAMB-7A3AE	MN908947.3	26043	T	C	1	1	0	0	0.999246420497362	CTC	ORF3a	T217T	T651C	ACT>ACC	Synonymous	GU280_gp03	0
CAMB-7A3AE	MN908947.3	28253	C	T	0.047	0.021	8.6e-21	4.9e-10	0.0345422526831822	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.965100782941862
CAMB-7A3AE	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999770466717674	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A3AE	MN908947.3	3037	C	T	1	1	0	0	0.997975708502024	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.74763832658569e-05
CAMB-7A3AE	MN908947.3	3168	C	T	0.02	0.011	9.4e-11	8.3e-07	0.0161742753563754	GCT	ORF1ab:nsp3	A150V	C449T	GCT>GTT	Missense	ORF1ab:nsp3	0.983809320713243
CAMB-7A3AE	MN908947.3	3177	C	T	0.016	0.011	1.8e-08	2.5e-06	0.0135546933542038	CCT	ORF1ab:nsp3	P153L	C458T	CCT>CTT	Missense	ORF1ab:nsp3	0.986445306645796
CAMB-7A3AE	MN908947.3	5457	C	T	0.005	0.0099	0.00023	3.6e-06	0.0071760236386661	ACA	ORF1ab:nsp3	T913I	C2738T	ACA>ATA	Missense	ORF1ab:nsp3	0.992823976361334
CAMB-7A3AE	MN908947.3	9226	C	T	1	1	0	0	0.999870561332355	GCA	ORF1ab:nsp4	G224G	C672T	GGC>GGT	Synonymous	ORF1ab:nsp4	8.62924450964318e-05
CAMB-7A3BD	MN908947.3	1059	C	T	1	1	0	0	0.99990348421967	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	6.43438535533893e-05
CAMB-7A3BD	MN908947.3	13006	T	C	1	1	0	0	0.999783247435095	CTG	ORF1ab:nsp9	A107A	T321C	GCT>GCC	Synonymous	ORF1ab:nsp9	0.000168585328259718
CAMB-7A3BD	MN908947.3	1437	C	T	1	1	1.1e-305	0	1	TCT	ORF1ab:nsp2	S211F	C632T	TCT>TTT	Missense	ORF1ab:nsp2	0
CAMB-7A3BD	MN908947.3	14408	C	T	1	1	0	0	0.999339965112442	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000471453491113102
CAMB-7A3BD	MN908947.3	18202	A	G	1	0.97	0	0	0.983835973096116	CAT	ORF1ab:3'-to-5'-exonuclease	I55V	A163G	ATC>GTC	Missense	ORF1ab:3'-to-5'-exonuclease	0.0161640269038837
CAMB-7A3BD	MN908947.3	20762	C	T	0.96	0.95	0	0	0.957248734634852	ACA	ORF1ab:2'-O-ribose-methyltransferase	T35I	C104T	ACA>ATA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.0427512653651482
CAMB-7A3BD	MN908947.3	23403	A	G	1	1	0	0	0.999938340115921	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.0829942039709e-05
CAMB-7A3BD	MN908947.3	241	C	T	1	1	0	0	0.999772675608093	TCG	NA	NA	NA	NA	NA	NA	9.74247393888221e-05
CAMB-7A3BD	MN908947.3	25563	G	T	1	1	0	0	0.999853501318488	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	2.92997363023733e-05
CAMB-7A3BD	MN908947.3	25688	C	T	1	1	0	0	0.998935415188077	GCT	ORF3a	A99V	C296T	GCT>GTT	Missense	GU280_gp03	0
CAMB-7A3BD	MN908947.3	26775	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	-	0.0170378571428571	0.097	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.00016;0.00016;3.9e-05;8.8e-05;6.3e-05;0.00015;1e-04;0.00013;0.00021;8.5e-05;0.00018;0.00011;0.00012;9.6e-05;2e-04;0.00011;0.00014;0.00011;6.9e-05;0.00016;9.6e-05;3.1e-05;1e-04;0.00016;0.00015;7.7e-05;0.00016;5.9e-05;9.3e-05;7e-05;0.00054;0.0016;0.00084;0.0011;NA;NA;NA;NA;NA;NA;NA;NA;0.5;NA	1.4e-10;9.6e-11;8.1e-12;3e-10;9e-09;6.5e-11;1.2e-14;1.8e-11;2.1e-11;1.6e-10;6.2e-13;7.5e-12;1.7e-17;1.6e-17;7.2e-19;3.5e-27;1.5e-27;3.4e-26;7.1e-27;2.5e-26;1e-25;3.8e-27;6.8e-26;1.1e-26;1.2e-26;4.2e-27;7.1e-26;9.5e-27;2.9e-26;8.6e-27;8.5e-28;3.3e-26;4.1e-27;1.4e-27;7.6e-27;3.8e-26;2.3e-26;6.1e-18;1.6e-17;1.3e-19;2.6e-18;1.3e-18;7.4e-13;1.1e-10;9e-12;4.9e-11;8.3e-09;2e-09;3.7e-09;9.3e-09;9.3e-09;9.4e-09;7.8e-09;2.4e-09;4.9e-12;1.6e-12	0.0583170254403131	GGC	M	.	253-308-delfrshift	.	no-SNV	GU280_gp05	0.973138374337701
CAMB-7A3BD	MN908947.3	29051	C	INS	0.056	0.018	1.9e-17	0.0012	0.0480364454183726	GCA	N	.	777-778-insfrshift	.	no-SNV	GU280_gp10	0.951905887780405
CAMB-7A3BD	MN908947.3	3037	C	T	1	1	0	0	0.999755501222494	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A3BD	MN908947.3	4531	TTACTTTTACACCAGTAAAACAACTGTAGCGTCACTTATCAACACACTTA	-	0.04678	0.0187	0.00016;1.3e-07;2.7e-07;2.3e-07;1.7e-08;1e-08;1.5e-07;7.4e-08;8.6e-08;1.7e-07;1.6e-07;1.3e-07;3.5e-08;1.6e-07;1.3e-07;1.4e-07;8.3e-09;9.4e-09;8.9e-09;1.4e-08;1.3e-08;1.1e-08;8.9e-09;1.2e-08;1e-08;4.1e-10;9.4e-10;1.5e-09;2.2e-12;1.2e-11;4.6e-11;1.9e-12;3.8e-12;1.1e-13;8.4e-13;8e-15;4.5e-15;4.1e-15;4.2e-15;6.5e-15;9.2e-15;3.3e-12;3.2e-12;5.6e-15;9.6e-15;5e-15;4.8e-15;6.5e-15;4.3e-10;7e-09	NA;NA;0.00021;0.00021;5.7e-05;3.5e-05;0.00012;9.3e-05;9.2e-05;0.00013;0.00013;1e-04;5.9e-05;0.00012;0.00011;0.00012;2.9e-05;2.1e-05;2.2e-05;2.4e-05;2.4e-05;2.3e-05;1.9e-05;2.1e-05;1.9e-05;3.8e-06;8.8e-11;1.4e-10;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0413754542913056	TTT	ORF1ab:nsp3	.	1812-1861-delfrshift	.	no-SNV	ORF1ab:nsp3	0.98203487348089
CAMB-7A3BD	MN908947.3	6431	A	G	1	1	0	0	0.999861706541281	TAC	ORF1ab:nsp3	T1238A	A3712G	ACC>GCC	Missense	ORF1ab:nsp3	5.5317383487761e-05
CAMB-7A3BD	MN908947.3	8039	G	A	0.97	1	0	0	0.979764392931788	TGA	ORF1ab:nsp3	D1774N	G5320A	GAT>AAT	Missense	ORF1ab:nsp3	0
CAMB-7A3CC	MN908947.3	10531	T	C	0.0096	0.0023	3.8e-06	0.0065	0.00519837932879749	TTT	ORF1ab:3C-like-proteinase	F159F	T477C	TTT>TTC	Synonymous	ORF1ab:3C-like-proteinase	0.99113217643911
CAMB-7A3CC	MN908947.3	11074	C	INS	0.058	0.027	1.1e-16	4.5e-06	0.0400503922579167	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.959606024165378
CAMB-7A3CC	MN908947.3	11075	T	-	0.046	0.016	2.3e-11	8.6e-05	0.0287500719231286	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.971048543316903
CAMB-7A3CC	MN908947.3	11083	G	T	0.042	0.014	4.2e-09	0.0029	0.0254950910073216	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.96991262551931
CAMB-7A3CC	MN908947.3	13721	C	T	0.0049	0.0073	0.00043	3.4e-05	0.00644001307616868	CCA	ORF1ab:RNA-dependent-RNA-polymerase	P85L	C254T	CCA>CTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.990715920235371
CAMB-7A3CC	MN908947.3	13730	C	T	1	1	0	0	0.999921898186476	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A88V	C263T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	3.1240725409644e-05
CAMB-7A3CC	MN908947.3	13914	T	G	0.011	0.015	1.9e-07	9.1e-09	0.0134459654507057	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.983880034640453
CAMB-7A3CC	MN908947.3	14408	C	T	0.99	0.99	0	0	0.9936626894824	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00326950023353573
CAMB-7A3CC	MN908947.3	16838	AA	-	0.0068	0.01005	0.0028;3e-04	4.4e-05;4.5e-05	0.00864100549882168	GAA	ORF1ab:helicase	.	602-603-delfrshift	.	no-SNV	ORF1ab:helicase	0.989903675185924
CAMB-7A3CC	MN908947.3	17917	T	-	0.0058	0.012	0.0017	1.2e-05	0.00927351182215044	ATT	ORF1ab:helicase	.	1681-1681-delfrshift	.	no-SNV	ORF1ab:helicase	0.990713871154962
CAMB-7A3CC	MN908947.3	18289	C	T	0.016	0.0064	2.3e-08	0.00035	0.0106199900366831	ACG	ORF1ab:3'-to-5'-exonuclease	R84C	C250T	CGT>TGT	Missense	ORF1ab:3'-to-5'-exonuclease	0.989372461995984
CAMB-7A3CC	MN908947.3	18688	T	-	0.0077	0.01	0.00021	1.6e-05	0.00910993742340603	CTT	ORF1ab:3'-to-5'-exonuclease	.	649-649-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.990684004468207
CAMB-7A3CC	MN908947.3	20951	C	T	0.013	0.0054	2.3e-07	0.00059	0.00894969108561341	TCA	ORF1ab:2'-O-ribose-methyltransferase	S98L	C293T	TCA>TTA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.991032656663725
CAMB-7A3CC	MN908947.3	22040	TATTCTAGTGCGAATAATTGCACTTTTGAA	-	0.000280333333333333	0.00789666666666667	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;2.1e-05	2.4e-05;2.2e-05;2.1e-05;2e-05;1.6e-05;2.2e-05;1.8e-05;1.5e-05;1.8e-05;1.8e-05;1.4e-05;1.8e-05;1.2e-05;3.6e-06;1.2e-05;1e-05;7.5e-06;8.7e-06;1.7e-05;1.6e-05;1.1e-05;1.3e-05;1e-05;1.2e-05;2.2e-06;6.3e-06;1.4e-05;3.2e-05;1.1e-05;2.2e-05	0.00497362471740769	TTA	S	.	478-507-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.995335624605457
CAMB-7A3CC	MN908947.3	22069	AT	-	0.0081	0.0041	2.1e-05;4.3e-05	2.2e-05;NA	0.00544905719549963	AAT	S	.	507-508-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.991637182373754
CAMB-7A3CC	MN908947.3	2306	C	T	0.0082	0.0054	2.5e-05	0.00034	0.00684386439598918	GCT	ORF1ab:nsp2	L501F	C1501T	CTT>TTT	Missense	ORF1ab:nsp2	0.993156135604011
CAMB-7A3CC	MN908947.3	23403	A	G	1	1	0	0	0.999865513384957	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.90954005577655e-05
CAMB-7A3CC	MN908947.3	24070	AT	-	0.0125	0.0092	6e-07;9.5e-06	1.1e-05;0.00011	0.0105279103234113	AAT	S	.	2508-2509-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.987936107608239
CAMB-7A3CC	MN908947.3	241	C	T	1	0.98	0	0	0.989880249620509	TCG	NA	NA	NA	NA	NA	NA	8.4331253162422e-05
CAMB-7A3CC	MN908947.3	25429	G	T	1	1	0	0	0.999869567485783	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	6.5216257108572e-05
CAMB-7A3CC	MN908947.3	25573	A	-	0.0084	0.018	3.7e-05	3.9e-09	0.0135299910894339	CAA	ORF3a	.	181-181-delfrshift	.	no-SNV	GU280_gp03	0.986106551610937
CAMB-7A3CC	MN908947.3	26111	C	T	0.021	0.0062	2.2e-06	0.0014	0.0112589559877175	CCT	ORF3a	P240L	C719T	CCT>CTT	Missense	GU280_gp03	0.988741044012282
CAMB-7A3CC	MN908947.3	26378	AT	-	0.0175	0.012	8.5e-10;7.7e-09	2.3e-07;8.7e-07	0.0138585244747471	AAT	E	.	134-135-delfrshift	.	no-SNV	GU280_gp04	0.984748327492832
CAMB-7A3CC	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0323783783783784	0.0415135135135135	3e-04;1.5e-05;0.00017;0.00022;5e-04;4.1e-07;3.2e-06;2.4e-05;2.4e-05;5.8e-06;1.1e-05;9.4e-06;2.4e-05;1.4e-05;1.9e-05;3.4e-05;1.5e-05;2.9e-05;1.7e-05;1.7e-05;1.3e-05;3.1e-05;1.6e-05;2.1e-05;1.7e-05;1.1e-05;2.4e-05;1.6e-05;1.4e-05;1.2e-05;2.6e-05;2.1e-05;8.4e-06;2.4e-05;8.8e-06;1.5e-05;1e-05	4.4e-06;7.1e-08;2.3e-06;2.6e-06;8.9e-06;8.4e-09;4.4e-08;6.1e-07;6.1e-07;1.7e-07;2.7e-07;2.1e-07;6.3e-07;3.5e-07;4.7e-07;8.9e-07;3e-07;7.2e-07;4.7e-07;4.4e-07;2.3e-07;8.1e-07;3.4e-07;5.4e-07;4.1e-07;2.3e-07;6.1e-07;3.3e-07;3.4e-07;3.4e-07;6.4e-07;5.2e-07;3.4e-07;6.4e-07;1.3e-07;3.1e-07;2.5e-07	0.0375285940038236	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.970572959832035
CAMB-7A3CC	MN908947.3	27016	C	T	0.0093	0.0056	2.6e-06	9.9e-05	0.00721955954619911	CCT	M	P165L	C494T	CCT>CTT	Missense	GU280_gp05	0.992780440453801
CAMB-7A3CC	MN908947.3	27298	A	T	0.0074	0.0076	1.7e-05	1.9e-05	0.00751850218105181	CAT	ORF6	I33L	A97T	ATA>TTA	Missense	GU280_gp06	0.992334460618536
CAMB-7A3CC	MN908947.3	28308	CA	-	0.01	0.0031	1.6e-06;1.8e-06	0.0017;0.0028	0.0061986491623052	GCA	N	.	35-36-delfrshift	.	no-SNV	GU280_gp10	0.993500644123943
CAMB-7A3CC	MN908947.3	28691	AATACACCAAAAGATCACATT	-	0.000690285714285714	0.0102904761904762	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0011;0.0012;NA;NA;0.0011;8e-04;NA;NA;NA;NA	8e-07;5.2e-07;1.2e-06;9.2e-07;7.2e-07;5.4e-07;4.5e-09;4e-09;5.6e-06;1.5e-05;8.3e-06;1.2e-05;1.4e-05;1e-05;1.2e-05;2e-05;1.6e-05;1.1e-05;8.4e-06;8.6e-06;7.7e-06	0.00432631208933834	GAA	N	.	418-438-delinframe	.	no-SNV	GU280_gp10	0.993166951377026
CAMB-7A3CC	MN908947.3	2882	T	-	0.0077	0.0044	2e-05	0.00057	0.0059546117010202	CTG	ORF1ab:nsp3	.	163-163-delfrshift	.	no-SNV	ORF1ab:nsp3	0.993545700603789
CAMB-7A3CC	MN908947.3	29688	GTG	-	0.00936666666666667	0.00933333333333333	2.7e-05;1.5e-05;0.00097	8.4e-06;2.5e-06;NA	0.0113821138211382	AGT	NA	NA	NA	NA	NA	NA	0.988323061952644
CAMB-7A3CC	MN908947.3	29779	GA	-	0.012	0.0052	0.00056;2.5e-08	0.0016;0.0023	0.00905401186387761	GGA	NA	NA	NA	NA	NA	NA	0.99437148217636
CAMB-7A3CC	MN908947.3	3037	C	T	1	1	0	0	0.999774011299435	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A3CC	MN908947.3	3545	A	-	0.012	0.0068	1.5e-05	0.0012	0.00956937799043062	TAA	ORF1ab:nsp3	.	826-826-delfrshift	.	no-SNV	ORF1ab:nsp3	0.990131578947368
CAMB-7A3CC	MN908947.3	3670	TGAAAATTT	-	0.0105444444444444	0.00748888888888889	0.00054;2.9e-05;2.4e-05;1.3e-05;1.3e-05;1.2e-05;2.3e-05;1.2e-05;5e-06	0.00036;0.00058;0.00056;0.00032;0.00033;3e-04;0.00051;0.00032;0.00012	0.00941105039465695	ATG	ORF1ab:nsp3	.	951-959-delinframe	.	no-SNV	ORF1ab:nsp3	0.992825112107623
CAMB-7A3CC	MN908947.3	4212	C	T	0.017	0.011	1.3e-09	5.3e-07	0.0140059460491504	GCT	ORF1ab:nsp3	A498V	C1493T	GCT>GTT	Missense	ORF1ab:nsp3	0.985966778496031
CAMB-7A3CC	MN908947.3	4403	G	T	0.044	0.075	3e-21	1.2e-34	0.0619142077857674	TGC	ORF1ab:nsp3	A562S	G1684T	GCA>TCA	Missense	ORF1ab:nsp3	0.937937019588396
CAMB-7A3CC	MN908947.3	8358	AT	-	0.0205	0.00635	4.6e-10;2e-10	0.00023;0.00021	0.0131252929752896	CAT	ORF1ab:nsp3	.	5639-5640-delfrshift	.	no-SNV	ORF1ab:nsp3	0.986968986187125
CAMB-7A3DB	MN908947.3	1101	C	T	0.0038	0.016	0.002	8.8e-09	0.00908024503627753	TCC	ORF1ab:nsp2	S99F	C296T	TCC>TTC	Missense	ORF1ab:nsp2	0.990253580686739
CAMB-7A3DB	MN908947.3	11074	C	INS	0.13	0.12	2.1e-57	1.6e-45	0.126138110059279	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.872596246981183
CAMB-7A3DB	MN908947.3	11083	G	-	0.17	0.15	2.2e-73	3e-65	0.159283120534145	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.34274335246574e-05
CAMB-7A3DB	MN908947.3	11083	G	T	0.83	0.85	0	0	0.840107766194213	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.34274335246574e-05
CAMB-7A3DB	MN908947.3	13297	C	T	0.0047	0.0067	0.00028	1.9e-05	0.0052046395644117	ACT	ORF1ab:nsp10	D91D	C273T	GAC>GAT	Synonymous	ORF1ab:nsp10	0.994761044130768
CAMB-7A3DB	MN908947.3	14805	C	T	1	1	0	0	0.998783237304513	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	3.57871381025659e-05
CAMB-7A3DB	MN908947.3	1627	C	T	0.0069	0.0047	4e-05	0.00031	0.0060604864181933	TCC	ORF1ab:nsp2	L274L	C822T	CTC>CTT	Synonymous	ORF1ab:nsp2	0.993900031585597
CAMB-7A3DB	MN908947.3	1835	G	A	1	1	0	0	0.998439444104684	TGG	ORF1ab:nsp2	G344S	G1030A	GGT>AGT	Missense	ORF1ab:nsp2	0.000189797338619541
CAMB-7A3DB	MN908947.3	18779	G	-	0.0053	0.0098	0.0016	1.7e-05	0.00721204943670098	TGG	ORF1ab:3'-to-5'-exonuclease	.	740-740-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.991299990890043
CAMB-7A3DB	MN908947.3	1973	C	T	0.0076	0.0099	1e-05	9.8e-07	0.00861337683523654	ACT	ORF1ab:nsp2	L390L	C1168T	CTA>TTA	Synonymous	ORF1ab:nsp2	0.989820554649266
CAMB-7A3DB	MN908947.3	21094	AAA	-	0.0064	0.0038	2.6e-05;0.00086;0.00097	0.0058;0.0028;0.0033	0.0045786497561869	TAA	ORF1ab:2'-O-ribose-methyltransferase	.	436-438-delinframe	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.993281051733822
CAMB-7A3DB	MN908947.3	2480	A	G	1	1	0	0	0.999695307739183	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-7A3DB	MN908947.3	2512	AG	-	0.00655	0.00375	4.3e-05;5e-05	0.00052;0.00053	0.00508187464709204	CAG	ORF1ab:nsp2	.	1707-1708-delfrshift	.	no-SNV	ORF1ab:nsp2	0.992543733868655
CAMB-7A3DB	MN908947.3	25261	G	T	0.41	0.42	1.5e-215	2e-219	0.411017548825361	TGC	S	M1233I	G3699T	ATG>ATT	Missense	GU280_gp02, spike glycoprotein	0.588805547693179
CAMB-7A3DB	MN908947.3	25568	C	T	1	1	0	0	0.999908202740804	GCT	ORF3a	A59V	C176T	GCT>GTT	Missense	GU280_gp03	6.55694708543702e-05
CAMB-7A3DB	MN908947.3	2558	C	T	1	1	0	0	0.999702070609266	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	7.4482347683599e-05
CAMB-7A3DB	MN908947.3	26144	G	T	1	1	0	0	0.999597504528074	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.00020124773596297
CAMB-7A3DB	MN908947.3	28845	G	A	1	1	0	0	0.999295188056641	CGC	N	R191H	G572A	CGC>CAC	Missense	GU280_gp10	9.61107195489204e-05
CAMB-7A3DB	MN908947.3	6440	A	G	0.0097	0.0018	2.1e-06	0.0061	0.00648404237006094	GAA	ORF1ab:nsp3	K1241E	A3721G	AAA>GAA	Missense	ORF1ab:nsp3	0.993504481448753
CAMB-7A3EA	MN908947.3	11074	C	INS	0.026	0.027	2.8e-05	1.3e-05	0.0262230279225521	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.973361532844877
CAMB-7A3EA	MN908947.3	11075	T	-	0.038	0.029	1.6e-09	1.8e-07	0.0328653848182173	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.965109533703895
CAMB-7A3EA	MN908947.3	14408	C	T	1	1	0	0	0.999354105615693	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000394713234854375
CAMB-7A3EA	MN908947.3	17019	G	T	0.014	0.019	7e-08	4.1e-10	0.0159740710730409	AGT	ORF1ab:helicase	E261D	G783T	GAG>GAT	Missense	ORF1ab:helicase	0.984009392621501
CAMB-7A3EA	MN908947.3	23403	A	G	1	1	0	0	0.999385121538314	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000127766953077586
CAMB-7A3EA	MN908947.3	241	C	T	1	1	0	0	0.999423778731033	TCG	NA	NA	NA	NA	NA	NA	8.5366113921079e-05
CAMB-7A3EA	MN908947.3	25273	G	T	0.031	0.024	1e-14	3.4e-12	0.0285822021116139	TGA	S	M1237I	G3711T	ATG>ATT	Missense	GU280_gp02, spike glycoprotein	0.971380090497738
CAMB-7A3EA	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99953805882051	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A3EA	MN908947.3	29024	GCTGCTGAG	-	0.00537777777777778	0.0613333333333333	0.00092;0.0017;0.0035;0.0066;0.0087;0.0082;0.0047;0.011;0.022	2.7e-28;3.2e-21;5.5e-16;2e-14;4.6e-12;2.9e-12;4.4e-13;5.1e-12;1.4e-08	0.0173901321110812	TGC	N	.	751-759-delinframe	.	no-SNV	GU280_gp10	0.982283346345565
CAMB-7A3EA	MN908947.3	3037	C	T	1	1	0	0	0.999749232023071	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.13459971161683e-05
CAMB-7A405	MN908947.3	11074	C	INS	0.1	0.1	1.1e-39	3.8e-36	0.100883064723753	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.892989547397147
CAMB-7A405	MN908947.3	11083	G	-	0.18	0.18	5.3e-81	2e-81	0.18195779534725	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	3.41277515499687e-05
CAMB-7A405	MN908947.3	11083	G	T	0.82	0.82	0	0	0.817882941812184	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	3.41277515499687e-05
CAMB-7A405	MN908947.3	14189	C	T	1	1	0	0	0.999389526396348	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A241V	C722T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	3.53897741247666e-05
CAMB-7A405	MN908947.3	14805	C	T	1	1	0	0	0.998255982947389	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000827967691643692
CAMB-7A405	MN908947.3	1887	C	T	1	1	0	0	0.998186623183109	GCT	ORF1ab:nsp2	A361V	C1082T	GCT>GTT	Missense	ORF1ab:nsp2	0.000590401754336641
CAMB-7A405	MN908947.3	21543	T	C	0.015	0.008	1.7e-07	0.00019	0.0130718954248366	TTG	ORF1ab:2'-O-ribose-methyltransferase	L295L	T885C	CTT>CTC	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.984044598231449
CAMB-7A405	MN908947.3	23559	TTGGTGCAGGTATATGCGCTAGT	-	0.0370869565217391	0.0391304347826087	0.00026;0.00044;0.00015;0.00028;0.00032;0.00033;3e-04;0.00026;0.00018;0.00015;9e-05;7.7e-05;0.00048;0.00027;0.00063;0.00015;3e-04;0.00054;0.00036;0.00052;2.2e-05;5.3e-05;0.002	2e-04;0.00037;0.00011;2e-04;0.00022;0.00022;0.00021;0.00021;0.00012;0.00011;2.8e-05;1.3e-05;0.00021;1e-04;0.00021;9.4e-05;0.00022;0.00041;0.00023;0.00026;9.5e-06;1.5e-05;0.00089	0.0368791094329796	ATT	S	.	1997-2019-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.950914712702912
CAMB-7A405	MN908947.3	2480	A	G	1	1	0	0	0.999753921870194	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.00018455859735466
CAMB-7A405	MN908947.3	2558	C	T	1	1	0	0	0.998851858259543	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	7.86398452367846e-05
CAMB-7A405	MN908947.3	26144	G	T	1	1	0	0	0.999852311327721	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7A405	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0406842105263158	0.0407894736842105	4.6e-05;1.2e-06;1.4e-05;1.7e-05;4.1e-05;5.9e-07;3e-06;5.5e-07;5.3e-07;7.8e-08;2.2e-07;1.8e-07;5e-07;2.4e-07;3.1e-07;6.7e-07;1.9e-07;5.7e-07;2.9e-07;3.1e-07;3.2e-07;6.3e-07;2.9e-07;4.6e-07;2.8e-07;1.7e-07;4.8e-07;2.4e-07;4.8e-08;2.6e-07;5.1e-07;4.8e-07;2e-07;5.1e-07;9.1e-08;2.4e-07;2e-07;0.0015	7.7e-05;2.9e-06;2.1e-05;1.9e-05;4.2e-05;4e-07;1.7e-06;3.6e-07;3.8e-07;1.1e-07;1.6e-07;1.1e-07;3.2e-07;1.8e-07;2.4e-07;4.3e-07;1.5e-07;3.5e-07;2.4e-07;2.2e-07;1.6e-07;3.7e-07;2.2e-07;2.8e-07;2e-07;1.2e-07;3.1e-07;1.6e-07;1.3e-07;1.6e-07;3.1e-07;2.9e-07;1.9e-07;3e-07;6.7e-08;1.6e-07;8.8e-08;0.00079	0.0425675908188899	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.97187496412623
CAMB-7A405	MN908947.3	944	G	A	1	1	0	0	0.999342659353752	GGG	ORF1ab:nsp2	G47S	G139A	GGT>AGT	Missense	ORF1ab:nsp2	0.000503276432283642
CAMB-7A441	MN908947.3	10097	G	A	1	1	0	0	1	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0
CAMB-7A441	MN908947.3	13536	C	T	1	1	4.8e-233	0	1	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-7A441	MN908947.3	14184	C	T	1	1	0	0	0.999823984980052	CCA	ORF1ab:RNA-dependent-RNA-polymerase	T239T	C717T	ACC>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	5.8671673316123e-05
CAMB-7A441	MN908947.3	14408	C	T	1	1	0	0	0.99951837071694	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000275216733177377
CAMB-7A441	MN908947.3	1684	C	T	1	1	0	0	0.999720410065238	TCG	ORF1ab:nsp2	I293I	C879T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.000279589934762349
CAMB-7A441	MN908947.3	21058	C	T	1	1	0	0	1	CCC	ORF1ab:2'-O-ribose-methyltransferase	P134S	C400T	CCT>TCT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0
CAMB-7A441	MN908947.3	23403	A	G	1	1	0	0	1	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7A441	MN908947.3	23731	C	T	1	1	0	0	0.999795291709314	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000204708290685773
CAMB-7A441	MN908947.3	241	C	T	1	1	0	0	0.999432881528951	TCG	NA	NA	NA	NA	NA	NA	0.000340271082629161
CAMB-7A441	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999503722084367	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A441	MN908947.3	3037	C	T	1	1	0	0	0.999625327838142	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A441	MN908947.3	4002	C	T	1	1	0	0	1	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-7A450	MN908947.3	10097	G	A	1	1	0	0	1	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0
CAMB-7A450	MN908947.3	11075	T	-	0.11	0.14	1.1e-27	1.9e-36	0.125028137762485	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.874875389908994
CAMB-7A450	MN908947.3	14408	C	T	1	1	0	0	0.999373106258489	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000452756591091143
CAMB-7A450	MN908947.3	1926	C	-	0.016	0.018	1.3e-09	2.9e-10	0.0166246454459502	ACT	ORF1ab:nsp2	.	1121-1121-delfrshift	.	no-SNV	ORF1ab:nsp2	0.98337535455405
CAMB-7A450	MN908947.3	1926	CTG	-	0.016	0.006	1.3e-09;1e-09;1.9e-09	2.9e-10;NA;NA	0.0110619469026549	ACT	ORF1ab:nsp2	.	1121-1123-delinframe	.	no-SNV	ORF1ab:nsp2	0.98337535455405
CAMB-7A450	MN908947.3	19889	G	A	1	1	0	0	0.997660271408517	AGA	ORF1ab:endoRNAse	R90K	G269A	AGA>AAA	Missense	ORF1ab:endoRNAse	0.000467945718296678
CAMB-7A450	MN908947.3	21569	G	INS	0.11	0.051	2.2e-18	4.1e-14	0.0663780663780664	TGT	S	.	6-7-insfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.932178932178932
CAMB-7A450	MN908947.3	21575	C	T	0.99	1	8.9e-177	0	0.997076023391813	TCT	S	L5F	C13T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7A450	MN908947.3	23403	A	G	1	1	0	0	0.99996409593566	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	1.79520321700416e-05
CAMB-7A450	MN908947.3	23731	C	T	1	1	0	0	0.999804916113929	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000195083886071011
CAMB-7A450	MN908947.3	241	C	T	1	1	0	0	0.999746989171137	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-7A450	MN908947.3	28376	GC	-	0.0135	0.0185	5.3e-06;2.8e-06	6.3e-08;2e-08	0.0158582443878908	GGC	N	.	103-104-delfrshift	.	no-SNV	GU280_gp10	0.984255375181054
CAMB-7A450	MN908947.3	28580	G	T	1	1	0	0	0.999878802569386	AGA	N	D103Y	G307T	GAT>TAT	Missense	GU280_gp10	0
CAMB-7A450	MN908947.3	28777	A	-	0.022	0.023	1.4e-08	3.2e-09	0.0225352112676056	CAA	N	.	504-504-delfrshift	.	no-SNV	GU280_gp10	0.976901408450704
CAMB-7A450	MN908947.3	28777	AA	-	0.011	0.0225	1.4e-08;NA	3.2e-09;1.3e-10	0.0167130919220056	CAA	N	.	504-505-delfrshift	.	no-SNV	GU280_gp10	0.976901408450704
CAMB-7A450	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A450	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A46F	MN908947.3	10097	G	A	1	1	0	0	0.999536607970343	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.000202734012974977
CAMB-7A46F	MN908947.3	11074	C	INS	0.027	0.025	2.3e-05	7.1e-05	0.0262857367882177	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.973005434354572
CAMB-7A46F	MN908947.3	11075	T	-	0.034	0.033	6.7e-09	7.3e-09	0.0332291440319588	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962408277199258
CAMB-7A46F	MN908947.3	11083	G	T	0.025	0.026	1.6e-05	6.6e-06	0.0252481622141448	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.969454450620202
CAMB-7A46F	MN908947.3	13536	C	T	1	1	0	0	0.999706400469759	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000108168247983435
CAMB-7A46F	MN908947.3	14184	C	T	1	1	0	0	0.999798856354702	CCA	ORF1ab:RNA-dependent-RNA-polymerase	T239T	C717T	ACC>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	6.70478817658496e-05
CAMB-7A46F	MN908947.3	14408	C	T	1	1	0	0	0.997187905262439	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000450481195822811
CAMB-7A46F	MN908947.3	1684	C	T	1	1	0	0	0.999802358521642	TCG	ORF1ab:nsp2	I293I	C879T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.000175681314096229
CAMB-7A46F	MN908947.3	21058	C	T	1	1	0	0	0.999767765908035	CCC	ORF1ab:2'-O-ribose-methyltransferase	P134S	C400T	CCT>TCT	Missense	ORF1ab:2'-O-ribose-methyltransferase	6.63525977042001e-05
CAMB-7A46F	MN908947.3	23403	A	G	1	1	0	0	0.999411742381115	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000104368287221526
CAMB-7A46F	MN908947.3	23731	C	T	1	1	0	0	0.999874651374134	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.000125348625865689
CAMB-7A46F	MN908947.3	241	C	T	1	1	0	0	0.998599762491359	TCG	NA	NA	NA	NA	NA	NA	0.000194969779684149
CAMB-7A46F	MN908947.3	26936	C	T	0.0066	0.0074	8.7e-05	3.2e-05	0.00691162570888469	TCG	M	L138L	C414T	CTC>CTT	Synonymous	GU280_gp05	0.992911153119093
CAMB-7A46F	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999137187230371	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	9.13909705721075e-05
CAMB-7A46F	MN908947.3	3037	C	T	1	1	0	0	0.999151143598208	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	2.35793444942231e-05
CAMB-7A46F	MN908947.3	3523	A	G	1	1	0	0	0.999108109829904	AAT	ORF1ab:nsp3	E268E	A804G	GAA>GAG	Synonymous	ORF1ab:nsp3	0.00082818372937504
CAMB-7A46F	MN908947.3	4002	C	T	1	1	0	0	0.999721572558191	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-7A46F	MN908947.3	508	T	-	0.076	0.078	3.5e-08	1.5e-08	0.076638610465019	ATG	ORF1ab:leader-protein	.	243-243-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.921303191044327
CAMB-7A46F	MN908947.3	514	T	-	0.16	0.17	1.8e-05	6.5e-06	0.165869717144223	ATG	ORF1ab:leader-protein	.	249-249-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.829569279435024
CAMB-7A46F	MN908947.3	522	T	-	0.12	0.12	2.2e-15	3.9e-16	0.122458812350272	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.877313668544815
CAMB-7A46F	MN908947.3	8157	C	T	0.017	0.018	3.7e-09	1.5e-09	0.0172324821342007	TCT	ORF1ab:nsp3	S1813F	C5438T	TCT>TTT	Missense	ORF1ab:nsp3	0.982658055638087
CAMB-7A46F	MN908947.3	8240	C	T	0.0094	0.01	4.8e-06	1.9e-06	0.00967027063326842	ACA	ORF1ab:nsp3	H1841Y	C5521T	CAT>TAT	Missense	ORF1ab:nsp3	0.990222281915251
CAMB-7A47E	MN908947.3	10367	CG	-	0.0285	0.0265	2.9e-14;1.8e-14	1.4e-13;1.1e-13	0.0276782909205152	TCG	ORF1ab:3C-like-proteinase	.	313-314-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.972454012470143
CAMB-7A47E	MN908947.3	11075	T	-	0.05	0.038	9.3e-13	3.7e-10	0.0444180051556613	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.942712671029149
CAMB-7A47E	MN908947.3	11146	G	T	0.045	0.03	6.6e-21	1.1e-14	0.038127820943509	TGT	ORF1ab:nsp6	M58I	G174T	ATG>ATT	Missense	ORF1ab:nsp6	0.961789740524721
CAMB-7A47E	MN908947.3	11979	C	T	0.021	0.014	5.8e-11	4.7e-08	0.0171467248251485	ACT	ORF1ab:nsp7	T46I	C137T	ACT>ATT	Missense	ORF1ab:nsp7	0.98281567270813
CAMB-7A47E	MN908947.3	12554	G	A	0.019	0.016	3.5e-10	8.6e-09	0.0175376583827288	GGA	ORF1ab:nsp8	E155K	G463A	GAA>AAA	Missense	ORF1ab:nsp8	0.982462341617271
CAMB-7A47E	MN908947.3	12554	GA	AT	0.0095	0.013	3.5e-10;NA	8.6e-09;6.4e-07	0.011044012839345	GGA	ORF1ab:nsp8	.	463-464-mnv	.	no-SNV	ORF1ab:nsp8	0.982462341617271
CAMB-7A47E	MN908947.3	12758	G	T	0.0056	0.011	0.00013	7e-07	0.00796473955900495	TGA	ORF1ab:nsp9	D25Y	G73T	GAT>TAT	Missense	ORF1ab:nsp9	0.989220653228414
CAMB-7A47E	MN908947.3	12773	G	C	0.012	0.007	1.4e-07	1.5e-05	0.00978593272171254	AGC	ORF1ab:nsp9	A30P	G88C	GCT>CCT	Missense	ORF1ab:nsp9	0.989998201115309
CAMB-7A47E	MN908947.3	12988	G	T	0.071	0.015	8e-33	1.2e-08	0.044128924823068	TGG	ORF1ab:nsp9	M101I	G303T	ATG>ATT	Missense	ORF1ab:nsp9	0.955827253007296
CAMB-7A47E	MN908947.3	14408	C	T	1	1	0	0	0.999395810955961	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000492302184031507
CAMB-7A47E	MN908947.3	15001	TA	-	0.012	0.027	2.1e-06;1.3e-06	2.4e-11;5.8e-12	0.0191953720746779	TTA	ORF1ab:RNA-dependent-RNA-polymerase	.	1534-1535-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.980572328695196
CAMB-7A47E	MN908947.3	15004	G	C	0.0096	0.025	9.2e-05	1e-08	0.0168787327966762	TGA	ORF1ab:RNA-dependent-RNA-polymerase	E513Q	G1537C	GAG>CAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.965203843157621
CAMB-7A47E	MN908947.3	16068	G	T	0.033	0.045	1.7e-16	1.1e-21	0.0380838035778605	AGT	ORF1ab:RNA-dependent-RNA-polymerase	E867D	G2601T	GAG>GAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.961868171449154
CAMB-7A47E	MN908947.3	16324	TG	-	0.0215	0.013	1e-09;3.2e-08	NA;9.8e-10	0.0176933158584535	CTG	ORF1ab:helicase	.	88-89-delfrshift	.	no-SNV	ORF1ab:helicase	0.986450760079313
CAMB-7A47E	MN908947.3	16325	G	-	0.02	0.026	3.2e-08	9.8e-10	0.0224171539961014	TGT	ORF1ab:helicase	.	89-89-delfrshift	.	no-SNV	ORF1ab:helicase	0.977582846003899
CAMB-7A47E	MN908947.3	1684	C	T	0.023	0.017	1.9e-11	1.2e-08	0.0201723462593028	TCG	ORF1ab:nsp2	I293I	C879T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.979827653740697
CAMB-7A47E	MN908947.3	17257	G	T	0.0078	0.0069	1.6e-05	3.8e-05	0.00734998843958772	AGA	ORF1ab:helicase	E341*	G1021T	GAG>TAG	Nonsense	ORF1ab:helicase	0.992613504995315
CAMB-7A47E	MN908947.3	1772	G	T	0.017	0.026	4.7e-09	9.7e-13	0.0209406110538963	TGT	ORF1ab:nsp2	V323F	G967T	GTT>TTT	Missense	ORF1ab:nsp2	0.975145897699966
CAMB-7A47E	MN908947.3	18515	G	-	0.041	0.035	2e-19	7e-17	0.0381484605651624	TGG	ORF1ab:3'-to-5'-exonuclease	.	476-476-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.961746098692535
CAMB-7A47E	MN908947.3	1883	G	T	0.017	0.016	1.6e-09	4.1e-09	0.0163631733095632	GGC	ORF1ab:nsp2	A360S	G1078T	GCT>TCT	Missense	ORF1ab:nsp2	0.981026359353113
CAMB-7A47E	MN908947.3	23403	A	G	1	1	0	0	0.999850616208141	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.46918959292917e-05
CAMB-7A47E	MN908947.3	241	C	T	1	1	0	0	0.999800949754031	TCG	NA	NA	NA	NA	NA	NA	0.00014217874712088
CAMB-7A47E	MN908947.3	25647	G	-	0.03	0.023	4e-10	1.3e-07	0.0276398186136903	TGT	ORF3a	.	255-255-delfrshift	.	no-SNV	GU280_gp03	0.97236018138631
CAMB-7A47E	MN908947.3	25647	GTTGTTTGTAACAGTTTACTCACACC	-	0.0663461538461538	0.111269230769231	4e-10;3.8e-16;5.8e-19;2.1e-20;2.4e-24;1e-20;1.5e-25;4.9e-25;2.3e-27;2.9e-27;2.4e-27;2.5e-27;7e-28;2.1e-27;3.1e-28;1.2e-23;4.3e-25;5.1e-25;1.8e-25;1.9e-25;1.1e-27;7.5e-28;1.9e-25;1.2e-26;4.7e-24;2.2e-14	1.3e-07;1.1e-29;7.6e-35;6.8e-38;1.7e-36;2.9e-31;2.6e-38;7.5e-38;4.1e-41;6.5e-41;3.4e-41;2.4e-41;1.2e-41;1.1e-41;1.6e-42;8.6e-36;4.7e-38;6.3e-38;2.8e-38;4.8e-38;1.8e-41;1.2e-41;2.7e-38;2.1e-39;3.8e-36;2.3e-36	0.0841283607979185	TGT	ORF3a	.	255-280-delfrshift	.	no-SNV	GU280_gp03	0.97236018138631
CAMB-7A47E	MN908947.3	26647	G	T	0.015	0.0098	8.4e-09	1.9e-06	0.0124468832602804	AGG	M	R42M	G125T	AGG>ATG	Missense	GU280_gp05	0.987519657376117
CAMB-7A47E	MN908947.3	28198	G	T	0.01	0.007	2.5e-06	7.4e-05	0.00864864864864865	TGT	ORF8	C102F	G305T	TGT>TTT	Missense	GU280_gp09	0.985328185328185
CAMB-7A47E	MN908947.3	28253	C	T	0.011	0.0075	9.9e-06	0.00023	0.00903634500472445	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.990231697741579
CAMB-7A47E	MN908947.3	28436	G	T	0.0078	0.011	2.4e-05	1.1e-06	0.00937913980393889	CGC	N	A55S	G163T	GCT>TCT	Missense	GU280_gp10	0.988951691247902
CAMB-7A47E	MN908947.3	28575	TG	-	0.011	0.0079	5e-06;5.1e-06	8.9e-05;7.6e-05	0.00946595083356881	ATG	N	.	302-303-delfrshift	.	no-SNV	GU280_gp10	0.990164882846399
CAMB-7A47E	MN908947.3	28793	G	C	0.012	0.012	2.4e-07	3.2e-07	0.0122619878377031	AGA	N	E174Q	G520C	GAA>CAA	Missense	GU280_gp10	0.971388695045359
CAMB-7A47E	MN908947.3	28793	G	T	0.004	0.015	0.00099	2.5e-08	0.00976971388695045	AGA	N	E174*	G520T	GAA>TAA	Nonsense	GU280_gp10	0.971388695045359
CAMB-7A47E	MN908947.3	28851	G	T	0.0094	0.0073	6e-06	4.4e-05	0.00828460038986355	AGT	N	S193I	G578T	AGT>ATT	Missense	GU280_gp10	0.991423001949318
CAMB-7A47E	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.9996825060853	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000116918040453642
CAMB-7A47E	MN908947.3	29219	G	T	0.0068	0.0055	4.3e-05	0.00011	0.00634225527577485	CGG	N	G316*	G946T	GGA>TGA	Nonsense	GU280_gp10	0.993619993204726
CAMB-7A47E	MN908947.3	29254	G	T	0.0075	0.0049	3.4e-05	0.00037	0.00654971656197334	CGG	N	S327S	G981T	TCG>TCT	Synonymous	GU280_gp10	0.993411981001992
CAMB-7A47E	MN908947.3	29404	TG	-	0.023	0.0073	1.6e-08;1.3e-08	0.00091;0.00083	0.0132300742174895	ATG	N	.	1131-1132-delfrshift	.	no-SNV	GU280_gp10	0.986921850079745
CAMB-7A47E	MN908947.3	29670	C	T	0.016	0.0047	3.7e-08	0.00072	0.0110725141120278	ACA	ORF10	T38I	C113T	ACA>ATA	Missense	GU280_gp11	0.988927485887972
CAMB-7A47E	MN908947.3	29686	C	T	0.11	0.083	3.7e-45	2.5e-31	0.101115594588179	TCA	NA	NA	NA	NA	NA	NA	0.898172323759791
CAMB-7A47E	MN908947.3	29777	G	C	0.01	0.0079	2.1e-06	1.5e-05	0.00923142979819665	AGG	NA	NA	NA	NA	NA	NA	0.990768570201803
CAMB-7A47E	MN908947.3	3037	C	T	1	1	0	0	0.999723298284449	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A47E	MN908947.3	3096	C	T	0.03	0.072	1e-10	5.9e-24	0.0524802300503235	TCA	ORF1ab:nsp3	S126L	C377T	TCA>TTA	Missense	ORF1ab:nsp3	0.947519769949676
CAMB-7A47E	MN908947.3	370	GG	CC	0.01965	0.007	4.3e-06;5.7e-16	NA;1.1e-08	0.0132919506106201	TGG	ORF1ab:leader-protein	.	105-106-mnv	.	no-SNV	ORF1ab:leader-protein	0.995986599323164
CAMB-7A47E	MN908947.3	371	G	C	0.031	0.014	5.7e-16	1.1e-08	0.0224218998376922	GGA	ORF1ab:leader-protein	E36Q	G106C	GAG>CAG	Missense	ORF1ab:leader-protein	0.977494436356943
CAMB-7A47E	MN908947.3	5610	G	T	0.0016	0.022	0.0058	1.3e-11	0.0112194789251125	GGT	ORF1ab:nsp3	G964V	G2891T	GGT>GTT	Missense	ORF1ab:nsp3	0.988780521074887
CAMB-7A47E	MN908947.3	662	GG	-	0.00036	0.022	0.0069;NA	7.2e-12;9.2e-12	0.0106608802301995	TGG	ORF1ab:leader-protein	.	397-398-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.989135524960195
CAMB-7A47E	MN908947.3	686	AAGTCATTT	-	0.0737777777777778	0.0831111111111111	2.6e-10;1.5e-10;3.2e-09;1.9e-10;4.8e-09;6.4e-10;9.2e-11;9.4e-10;1.8e-08	1.2e-11;7.2e-12;2e-10;9.4e-12;2.9e-10;4.5e-11;5e-12;5.4e-11;1.6e-09	0.0773768821313168	AAA	ORF1ab:leader-protein	.	421-429-delinframe	.	no-SNV	ORF1ab:leader-protein	0.923098419119604
CAMB-7A47E	MN908947.3	8462	G	-	0.036	0.041	2.8e-15	1.1e-16	0.0380296069423175	TGC	ORF1ab:nsp3	.	5743-5743-delfrshift	.	no-SNV	ORF1ab:nsp3	0.961970393057683
CAMB-7A47E	MN908947.3	8792	G	-	0.075	0.037	2.9e-32	9.3e-17	0.0569503171247357	TGG	ORF1ab:nsp4	.	238-238-delfrshift	.	no-SNV	ORF1ab:nsp4	0.943049682875264
CAMB-7A47E	MN908947.3	9758	G	T	0.02	0.019	2.4e-10	1.1e-09	0.0195098932569643	TGT	ORF1ab:nsp4	V402L	G1204T	GTA>TTA	Missense	ORF1ab:nsp4	0.968709320489456
CAMB-7A47E	MN908947.3	991	GG	CC	0.0145	0.0070105	6.3e-09;3e-08	NA;2.1e-08	0.0107553296022557	CGG	ORF1ab:nsp2	.	186-187-mnv	.	no-SNV	ORF1ab:nsp2	0.983812930436175
CAMB-7A47E	MN908947.3	992	G	C	0.014	0.014	3e-08	2.1e-08	0.0139635260307048	GGA	ORF1ab:nsp2	E63Q	G187C	GAA>CAA	Missense	ORF1ab:nsp2	0.9859616884435
CAMB-7A48D	MN908947.3	11074	C	INS	0.046	0.021	9.6e-13	0.00047	0.0323576315654097	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.967477750913113
CAMB-7A48D	MN908947.3	11075	T	-	0.035	0.022	1e-08	6.3e-06	0.0277414153323335	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.969068321904448
CAMB-7A48D	MN908947.3	11075	TT	-	0.02155	0.011	1e-08;0.00039	6.3e-06;NA	0.0158124890676928	CTT	ORF1ab:nsp6	.	103-104-delfrshift	.	no-SNV	ORF1ab:nsp6	0.969068321904448
CAMB-7A48D	MN908947.3	11782	A	G	0.012	0.024	0.00028	2.1e-05	0.0161030595813204	AAC	ORF1ab:nsp6	K270K	A810G	AAA>AAG	Synonymous	ORF1ab:nsp6	0.98389694041868
CAMB-7A48D	MN908947.3	11824	C	T	0.014	0.0078	1.6e-05	0.0023	0.011968085106383	TCA	ORF1ab:nsp6	I284I	C852T	ATC>ATT	Synonymous	ORF1ab:nsp6	0.988031914893617
CAMB-7A48D	MN908947.3	14220	C	T	0.032	0.014	1.1e-15	4.8e-08	0.0224809728656519	ACT	ORF1ab:RNA-dependent-RNA-polymerase	D251D	C753T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.977508686300463
CAMB-7A48D	MN908947.3	14408	C	T	1	1	0	0	0.999539269259616	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000342869388192435
CAMB-7A48D	MN908947.3	15575	G	C	0.0075	0.0016	3.2e-05	0.006	0.00420387911592242	GGT	ORF1ab:RNA-dependent-RNA-polymerase	G703A	G2108C	GGT>GCT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.995778078484438
CAMB-7A48D	MN908947.3	15639	A	-	0.0099	0.0059	3.9e-06	0.00023	0.007660226402247	GAA	ORF1ab:RNA-dependent-RNA-polymerase	.	2172-2172-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.992283031179959
CAMB-7A48D	MN908947.3	16466	C	T	0.018	0.031	4.1e-06	2.3e-09	0.0259436171209141	CCA	ORF1ab:helicase	P77L	C230T	CCA>CTA	Missense	ORF1ab:helicase	0.974056382879086
CAMB-7A48D	MN908947.3	16877	C	T	0.0089	0.0045	9.7e-06	0.00098	0.00628349962892719	ACA	ORF1ab:helicase	T214I	C641T	ACA>ATA	Missense	ORF1ab:helicase	0.993716500371073
CAMB-7A48D	MN908947.3	17691	A	G	0.022	0.0078	1.9e-11	1.3e-05	0.013899572932969	CAT	ORF1ab:helicase	S485S	A1455G	TCA>TCG	Synonymous	ORF1ab:helicase	0.986087164115759
CAMB-7A48D	MN908947.3	18377	C	T	0.21	0.12	9.9e-99	3.6e-53	0.158816222717325	ACA	ORF1ab:3'-to-5'-exonuclease	T113I	C338T	ACA>ATA	Missense	ORF1ab:3'-to-5'-exonuclease	0.841154202567085
CAMB-7A48D	MN908947.3	1937	T	C	0.01	0.012	1.6e-06	1.9e-07	0.0111276093982007	TTC	ORF1ab:nsp2	S378P	T1132C	TCT>CCT	Missense	ORF1ab:nsp2	0.988872390601799
CAMB-7A48D	MN908947.3	19984	T	-	0.025	0.014	1.2e-05	0.0028	0.0185295875672445	CTT	ORF1ab:endoRNAse	.	364-364-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.980872683801554
CAMB-7A48D	MN908947.3	22713	C	T	1	1	0	0	0.9997611655123	CCT	S	P384L	C1151T	CCT>CTT	Missense	GU280_gp02, spike glycoprotein	1.9902873975002e-05
CAMB-7A48D	MN908947.3	23403	A	G	1	1	0	0	0.999901108246913	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.93350518522425e-05
CAMB-7A48D	MN908947.3	241	C	T	1	1	0	0	0.999784507766009	TCG	NA	NA	NA	NA	NA	NA	0.00011603427984153
CAMB-7A48D	MN908947.3	24213	C	T	0.013	0.046	1.6e-06	6.5e-19	0.028891864747238	TCT	S	S884F	C2651T	TCT>TTT	Missense	GU280_gp02, spike glycoprotein	0.971041178439906
CAMB-7A48D	MN908947.3	25572	C	T	0.1	0.068	3e-47	7.7e-31	0.0838031266242853	CCA	ORF3a	S60S	C180T	TCC>TCT	Synonymous	GU280_gp03	0.916166886569909
CAMB-7A48D	MN908947.3	25617	G	T	1	1	0	0	0.999934373872051	AGG	ORF3a	K75N	G225T	AAG>AAT	Missense	GU280_gp03	2.18753759830247e-05
CAMB-7A48D	MN908947.3	26464	C	T	0.0081	0.0082	1.7e-05	1.6e-05	0.0081462762003865	TCT	E	L74L	C220T	CTG>TTG	Synonymous	GU280_gp04	0.991734800059462
CAMB-7A48D	MN908947.3	28087	C	T	0.01	0.014	8.3e-06	3.9e-07	0.0122393794919234	GCT	ORF8	A65V	C194T	GCT>GTT	Missense	GU280_gp09	0.987689461324984
CAMB-7A48D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999682287529785	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	5.77333872178281e-05
CAMB-7A48D	MN908947.3	29635	C	T	0.0032	0.0083	0.0018	1.4e-05	0.00562312017784752	ACA	ORF10	Y26Y	C78T	TAC>TAT	Synonymous	GU280_gp11	0.994376879822153
CAMB-7A48D	MN908947.3	29679	C	T	0.013	0.052	4.5e-07	1.4e-21	0.0352615810094492	TCT	NA	NA	NA	NA	NA	NA	0.964738418990551
CAMB-7A48D	MN908947.3	3037	C	T	1	0.99	0	0	0.994797290664572	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A48D	MN908947.3	3497	G	A	0.93	0.94	0	0	0.934365614194493	GGC	ORF1ab:nsp3	A260T	G778A	GCT>ACT	Missense	ORF1ab:nsp3	0.0656217662350774
CAMB-7A48D	MN908947.3	6154	A	-	0.027	0.016	3.4e-12	3e-08	0.0201837873318018	TAA	ORF1ab:nsp3	.	3435-3435-delfrshift	.	no-SNV	ORF1ab:nsp3	0.979816212668198
CAMB-7A48D	MN908947.3	6525	C	T	0.026	0.022	2.3e-13	2.1e-11	0.0236837953467653	ACA	ORF1ab:nsp3	T1269I	C3806T	ACA>ATA	Missense	ORF1ab:nsp3	0.976306924169165
CAMB-7A48D	MN908947.3	6890	T	A	0.017	0.01	9.4e-06	0.0015	0.0143712574850299	ATT	ORF1ab:nsp3	F1391I	T4171A	TTT>ATT	Missense	ORF1ab:nsp3	0.983233532934132
CAMB-7A48D	MN908947.3	8715	C	T	0.0097	0.008	2.3e-06	1.2e-05	0.00876442924326635	ACT	ORF1ab:nsp4	T54I	C161T	ACT>ATT	Missense	ORF1ab:nsp4	0.991235570756734
CAMB-7A48D	MN908947.3	8726	G	A	0.013	0.028	2.2e-07	1.2e-13	0.0208821233411397	AGC	ORF1ab:nsp4	A58T	G172A	GCA>ACA	Missense	ORF1ab:nsp4	0.978987769971376
CAMB-7A48D	MN908947.3	8917	C	T	0.0061	0.0084	0.00011	1.1e-05	0.0072234762979684	TCT	ORF1ab:nsp4	F121F	C363T	TTC>TTT	Synonymous	ORF1ab:nsp4	0.992764947618221
CAMB-7A49C	MN908947.3	10934	TTT	-	0.00903333333333333	0.00263333333333333	3.7e-05;7.9e-05;1.7e-05	NA;0.0034;0.0098	0.00656471465870944	TTT	ORF1ab:3C-like-proteinase	.	880-882-delinframe	.	no-SNV	ORF1ab:3C-like-proteinase	0.994693175872636
CAMB-7A49C	MN908947.3	11074	C	INS	0.033	0.028	1.5e-07	1.5e-05	0.0314086891104006	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.968420332723511
CAMB-7A49C	MN908947.3	11075	T	-	0.043	0.044	9.7e-11	2.3e-11	0.0433088224836081	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.952267846221679
CAMB-7A49C	MN908947.3	14408	C	-	0.012	0.005	4.1e-06	0.0011	0.00912173312929457	CCT	ORF1ab:RNA-dependent-RNA-polymerase	.	941-941-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.00036006841299847
CAMB-7A49C	MN908947.3	14408	C	T	0.99	0.99	0	0	0.990413178503916	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00036006841299847
CAMB-7A49C	MN908947.3	15259	A	G	0.0063	0.0067	4.6e-05	2.8e-05	0.0064783532444011	TAG	ORF1ab:RNA-dependent-RNA-polymerase	S598G	A1792G	AGT>GGT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993486816899446
CAMB-7A49C	MN908947.3	17013	A	C	0.0089	0.0057	4.8e-06	0.00011	0.00761547587157017	CAG	ORF1ab:helicase	S259S	A777C	TCA>TCC	Synonymous	ORF1ab:helicase	0.992193180513566
CAMB-7A49C	MN908947.3	18175	C	T	0.0074	0.0025	2.5e-05	0.0039	0.00553643573245548	ACC	ORF1ab:3'-to-5'-exonuclease	P46S	C136T	CCT>TCT	Missense	ORF1ab:3'-to-5'-exonuclease	0.994463564267545
CAMB-7A49C	MN908947.3	18570	C	T	0.01	0.0036	1.5e-06	7e-04	0.00721525782310777	TCT	ORF1ab:3'-to-5'-exonuclease	L177L	C531T	CTC>CTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.992768953866557
CAMB-7A49C	MN908947.3	186	C	T	0.03	0.046	1.6e-14	3.6e-21	0.0371744130628484	GCA	NA	NA	NA	NA	NA	NA	0.962784143890259
CAMB-7A49C	MN908947.3	20736	C	T	0.013	0.014	1.4e-07	4.8e-08	0.0130411544628541	ACC	ORF1ab:2'-O-ribose-methyltransferase	D26D	C78T	GAC>GAT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.986887582398005
CAMB-7A49C	MN908947.3	23403	A	G	1	1	0	0	0.998293804815262	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.98442473284575e-05
CAMB-7A49C	MN908947.3	241	C	T	1	0.99	0	0	0.995760853676363	TCG	NA	NA	NA	NA	NA	NA	2.08824942051079e-05
CAMB-7A49C	MN908947.3	26775	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	-	0.0463392857142857	0.0476785714285714	7.8e-05;5.7e-05;2.2e-05;8.7e-05;0.00051;4.9e-07;2.4e-09;1.5e-08;1.7e-08;8.5e-08;8.4e-12;3.1e-10;3.1e-09;3.2e-09;3.4e-10;1.1e-09;5.1e-10;3.4e-09;1.2e-09;1.9e-09;5.6e-09;8.7e-10;4.2e-09;2.1e-09;2.1e-09;1.4e-09;4.8e-09;2e-09;2.8e-09;1.7e-09;7.3e-10;3.1e-09;1.3e-09;4.9e-10;1.3e-09;3.4e-09;3.1e-09;1.7e-09;3.9e-09;2.9e-10;1.2e-09;8.4e-10;6.4e-06;4.5e-05;8.3e-06;1.4e-05;5.2e-05;3e-05;3.4e-05;5.3e-05;5.2e-05;5.3e-05;4.9e-05;3.2e-05;1.7e-05;9.7e-06	0.00085;0.00033;0.00056;0.0015;0.0025;5.8e-08;1.4e-10;2.9e-08;3.3e-08;1.2e-07;1.2e-12;1.6e-11;2.7e-10;3.1e-10;3.5e-11;3e-11;1.8e-11;9.2e-11;3.7e-11;5.5e-11;1.5e-10;2.5e-11;1.1e-10;5.6e-11;5.5e-11;4e-11;1.3e-10;5.6e-11;7.9e-11;4.2e-11;1.9e-11;8.9e-11;3e-11;1.5e-11;3.9e-11;8.8e-11;7.8e-11;5.8e-11;1.1e-10;6e-12;2.8e-11;2e-11;3e-05;7.3e-05;0.00011;0.00016;0.00064;0.00039;0.00046;0.00055;0.00055;0.00056;0.00053;4e-04;0.00012;7e-05	0.055333582454224	GGC	M	.	253-308-delfrshift	.	no-SNV	GU280_gp05	0.977012662639405
CAMB-7A49C	MN908947.3	27461	G	T	0.0048	0.022	0.00022	8.6e-12	0.0123012613212158	TGT	ORF7a	C23F	G68T	TGT>TTT	Missense	GU280_gp07	0.987688340317566
CAMB-7A49C	MN908947.3	285	G	A	1	1	0	0	0.998011770319707	GGT	ORF1ab:leader-protein	G7D	G20A	GGT>GAT	Missense	ORF1ab:leader-protein	0.00198822968029267
CAMB-7A49C	MN908947.3	29635	C	T	0.021	0.014	9.3e-11	4.1e-07	0.0190661478599222	ACA	ORF10	Y26Y	C78T	TAC>TAT	Synonymous	GU280_gp11	0.980933852140078
CAMB-7A49C	MN908947.3	3037	C	T	1	1	0	0	0.99798747763864	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A49C	MN908947.3	4197	AAATGCTAGCGAAAGCTTT	-	0.00426636842105263	0.00826315789473684	0.46;NA;NA;0.00036;0.00044;0.00034;0.00033;5e-05;0.00051;0.00051;0.00043;0.00061;0.00023;0.00026;0.00032;0.00033;0.00054;0.00015;0.00023	3e-08;1.3e-05;1.1e-05;2.1e-05;2.5e-05;1.9e-05;1.9e-05;1.4e-06;2.8e-05;2.9e-05;2.3e-05;3.3e-05;1.2e-05;1.4e-05;1.8e-05;1.9e-05;2.4e-05;5.8e-06;1.2e-05	0.00598866622571015	GAA	ORF1ab:nsp3	.	1478-1496-delfrshift	.	no-SNV	ORF1ab:nsp3	0.993471949218257
CAMB-7A49C	MN908947.3	4489	TAT	-	0.00553333333333333	0.00156666666666667	0.00021;3.4e-05;9.5e-05	0.0052;0.0039;0.0088	0.00391351518908865	GTA	ORF1ab:nsp3	.	1770-1772-delinframe	.	no-SNV	ORF1ab:nsp3	0.996643866266061
CAMB-7A49C	MN908947.3	522	TT	-	0.0715	0.0675	3e-10;2.6e-09	1.1e-10;6.1e-08	0.0694314887180134	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.920292123109025
CAMB-7A49C	MN908947.3	7433	T	-	0.014	0.011	3.9e-05	0.00078	0.0130787129904517	ATT	ORF1ab:nsp3	.	4714-4714-delfrshift	.	no-SNV	ORF1ab:nsp3	0.986841049506539
CAMB-7A49C	MN908947.3	9693	C	T	0.017	0.009	2.2e-09	5.8e-06	0.013718434244229	GCT	ORF1ab:nsp4	A380V	C1139T	GCT>GTT	Missense	ORF1ab:nsp4	0.982824457469711
CAMB-7A49C	MN908947.3	9855	TGCTATT	-	0.0100857142857143	0.00364285714285714	0.00016;1e-04;3e-04;8e-05;3.4e-05;0.00012;8.9e-05	0.002;0.0016;0.003;0.0078;0.0064;NA;NA	0.00883087791849746	GTG	ORF1ab:nsp4	.	1301-1307-delfrshift	.	no-SNV	ORF1ab:nsp4	0.993035676137577
CAMB-7A4AB	MN908947.3	10661	A	-	0.047	0.036	2e-09	1.9e-07	0.0427189682966147	TAA	ORF1ab:3C-like-proteinase	.	607-607-delfrshift	.	no-SNV	ORF1ab:3C-like-proteinase	0.95710191653233
CAMB-7A4AB	MN908947.3	11074	C	INS	0.15	0.034	1.3e-60	3.5e-07	0.103960755813953	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.895675872093023
CAMB-7A4AB	MN908947.3	11083	G	-	0.089	0.19	6.2e-38	2.7e-88	0.131463670126655	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.58715043011777e-05
CAMB-7A4AB	MN908947.3	11083	G	T	0.91	0.81	0	0	0.868282385804527	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.58715043011777e-05
CAMB-7A4AB	MN908947.3	12103	AG	-	0.0145	0.018	1.3e-08;3.4e-08	3.3e-10;1.9e-09	0.0162235294117647	CAG	ORF1ab:nsp8	.	12-13-delfrshift	.	no-SNV	ORF1ab:nsp8	0.982878098438669
CAMB-7A4AB	MN908947.3	14805	C	T	1	1	0	0	0.999885788251418	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	3.80705828606236e-05
CAMB-7A4AB	MN908947.3	15358	C	T	0.0097	0.028	2.8e-06	1e-13	0.0173435784851811	TCG	ORF1ab:RNA-dependent-RNA-polymerase	R631C	C1891T	CGC>TGC	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.982656421514819
CAMB-7A4AB	MN908947.3	15971	TAGATGA	-	0.00314857142857143	0.0247142857142857	NA;NA;NA;NA;NA;NA;3.5e-07	2.2e-12;8.6e-13;7e-11;2.9e-12;1.4e-10;4.2e-12;1.8e-07	0.0110315023314	GTA	ORF1ab:RNA-dependent-RNA-polymerase	.	2504-2510-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.989163915172735
CAMB-7A4AB	MN908947.3	15977	AT	-	0.022	0.012	3.5e-07;1.6e-08	1.8e-07;NA	0.017529845116052	GAT	ORF1ab:RNA-dependent-RNA-polymerase	.	2510-2511-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.976969373931197
CAMB-7A4AB	MN908947.3	1658	G	T	0.013	0.019	1e-07	1.8e-10	0.0159055255359944	TGG	ORF1ab:nsp2	G285C	G853T	GGT>TGT	Missense	ORF1ab:nsp2	0.984007320899425
CAMB-7A4AB	MN908947.3	16888	A	-	0.011	0.024	7.3e-07	2.9e-12	0.0162339452069897	CAA	ORF1ab:helicase	.	652-652-delfrshift	.	no-SNV	ORF1ab:helicase	0.98365580728736
CAMB-7A4AB	MN908947.3	16893	A	T	0.011	0.012	4.7e-07	1.3e-07	0.0114797382619676	TAA	ORF1ab:helicase	L219F	A657T	TTA>TTT	Missense	ORF1ab:helicase	0.983469176902767
CAMB-7A4AB	MN908947.3	19050	TAT	-	0.0176666666666667	0.0266666666666667	1.5e-12;2.7e-14;NA	3.2e-13;7.8e-15;2.8e-13	0.0248659916617034	CTA	ORF1ab:3'-to-5'-exonuclease	.	1011-1013-delinframe	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.975103997297126
CAMB-7A4AB	MN908947.3	24615	TCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATG	-	0.001	0.0301428571428571	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;1.7e-08;4.1e-09;NA;NA;NA;NA	7.4e-12;2.3e-11;4.8e-11;6.2e-11;9.1e-12;1.5e-11;1.3e-11;5.6e-12;1.3e-11;1.7e-11;1.6e-11;1.9e-11;4.5e-12;1.4e-11;2.1e-11;1e-11;1.4e-11;2.2e-11;2.6e-12;1.7e-11;4.3e-11;4.4e-11;3.9e-12;2.1e-11;1.4e-20;4.5e-20;1.7e-19;1.5e-11;2.1e-11;1.1e-10;2.2e-11;1.1e-11;5.5e-12;2.1e-11;5.8e-11	0.00762300762300762	ATC	S	.	3053-3087-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.992097701149425
CAMB-7A4AB	MN908947.3	2464	A	-	0.028	0.018	1.4e-11	6e-08	0.0228599221789883	TAA	ORF1ab:nsp2	.	1659-1659-delfrshift	.	no-SNV	ORF1ab:nsp2	0.976410505836576
CAMB-7A4AB	MN908947.3	2464	AA	-	0.014	0.0185	1.4e-11;NA	6e-08;7e-09	0.0163771712158809	TAA	ORF1ab:nsp2	.	1659-1660-delfrshift	.	no-SNV	ORF1ab:nsp2	0.976410505836576
CAMB-7A4AB	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-7A4AB	MN908947.3	2558	C	T	0.95	1	0	0	0.974927476170742	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-7A4AB	MN908947.3	26144	G	T	1	1	7e-113	1.6e-157	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7A4AB	MN908947.3	29068	TAAAGCATACAATG	-	0.0171428571428571	0.0152857142857143	6.3e-07;1.3e-06;0.00023;0.00023;2e-04;0.00025;0.00023;0.00056;0.00031;0.00026;0.00029;1e-04;0.00025;0.00024	2.9e-06;6.9e-06;0.00054;0.00051;0.00046;0.00058;0.00056;0.0013;0.00091;0.00066;0.00079;0.00034;0.00071;0.00062	0.0160342404497253	CTA	N	.	795-808-delfrshift	.	no-SNV	GU280_gp10	0.983987240829346
CAMB-7A4AB	MN908947.3	3386	AA	-	0.0105	0.003978	2.6e-05;1.6e-06	0.00023;NA	0.0078292128884282	TAA	ORF1ab:nsp3	.	667-668-delfrshift	.	no-SNV	ORF1ab:nsp3	0.990789924605894
CAMB-7A4AB	MN908947.3	5359	TTA	-	0.0045	0.034	0.0025;0.0026;0.0023	1e-11;1.9e-11;2.2e-11	0.0136744596382885	CTT	ORF1ab:nsp3	.	2640-2642-delinframe	.	no-SNV	ORF1ab:nsp3	0.986179224253232
CAMB-7A4AB	MN908947.3	5382	AAGCTGCTAACTTTTGTGCACTT	-	0.0224782608695652	0.00114347826086957	5.8e-10;1.5e-10;9.7e-10;3.9e-09;3.6e-09;3.6e-09;1.2e-09;9.3e-10;3.9e-10;2.6e-09;2.4e-09;6.7e-09;1.5e-09;5.9e-10;8.3e-10;2.1e-09;1.6e-09;2e-09;8.3e-10;5.3e-10;6.5e-10;1.8e-10;1.6e-10	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;9.3e-05;2.6e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0151853506029477	GAA	ORF1ab:nsp3	.	2663-2685-delfrshift	.	no-SNV	ORF1ab:nsp3	0.98479427549195
CAMB-7A4AB	MN908947.3	9628	TT	CC	0.009514	0.0135	NA;5.4e-10	1.9e-06;1.5e-08	0.0112434870044791	CTT	ORF1ab:nsp4	.	1074-1075-mnv	.	no-SNV	ORF1ab:nsp4	0.993849991398589
CAMB-7A4AB	MN908947.3	9629	T	C	0.019	0.015	5.4e-10	1.5e-08	0.0172469846223869	TTT	ORF1ab:nsp4	F359L	T1075C	TTT>CTT	Missense	ORF1ab:nsp4	0.982671738353002
CAMB-7A4AB	MN908947.3	9874	AT	-	0.018	0.0215	1e-08;1.1e-08	6.5e-10;3e-10	0.0192268496501121	AAT	ORF1ab:nsp4	.	1320-1321-delfrshift	.	no-SNV	ORF1ab:nsp4	0.979897712743287
CAMB-7A4BA	MN908947.3	11074	C	INS	0.027	0.028	7.4e-06	2.9e-06	0.0277306295875814	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.971988354709261
CAMB-7A4BA	MN908947.3	11075	T	-	0.03	0.046	1.3e-07	2.4e-11	0.0378865166663575	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960091632505426
CAMB-7A4BA	MN908947.3	14805	C	T	1	1	0	0	0.99887529874877	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	5.40721755399107e-05
CAMB-7A4BA	MN908947.3	23561	GGTGCAGGTATATGC	-	0.027	0.0376666666666667	0.0023;0.0033;0.0035;0.0036;0.0034;0.0031;0.0025;0.0023;0.0018;0.00056;0.0024;0.0016;0.0022;0.0016;0.0027	0.00017;0.00032;0.00035;0.00035;0.00033;0.00032;2e-04;0.00017;0.00017;6.1e-05;0.00011;4.8e-05;0.00069;0.00045;0.00085	0.032027507340442	TGG	S	.	1999-2013-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.968261868300153
CAMB-7A4BA	MN908947.3	25979	G	T	1	1	0	0	0.999091239549255	GGA	ORF3a	G196V	G587T	GGA>GTA	Missense	GU280_gp03	0
CAMB-7A4BA	MN908947.3	26176	C	A	0.0074	0.014	2.6e-05	1.1e-07	0.0103523790563408	ACC	ORF3a	P262T	C784A	CCA>ACA	Missense	GU280_gp03	0.989647620943659
CAMB-7A4BA	MN908947.3	26256	C	T	0.0059	0.0088	0.00017	8e-06	0.00722451234541668	TCG	E	F4F	C12T	TTC>TTT	Synonymous	GU280_gp04	0.992754239088862
CAMB-7A4BA	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.025	0.0368157894736842	0.021;0.0049;0.016;0.01;0.016;0.00029;0.0012;0.00049;0.00048;0.00017;0.00025;0.00021;5e-04;0.00014;0.00016;0.00029;0.00012;0.00025;0.00016;0.00016;0.00014;0.00027;0.00016;2e-04;0.00016;0.00011;0.00022;0.00015;5.6e-05;0.00013;0.00023;0.00021;0.00025;0.00049;6e-04;0.00077;0.00063;0.017	5.5e-05;1.4e-06;3.3e-05;3.4e-05;9.6e-05;8.6e-07;5.1e-06;3.2e-06;3.2e-06;7.2e-07;1.5e-06;1.2e-06;3.1e-06;2e-06;2.7e-06;4.4e-06;9.9e-07;3.8e-06;2.3e-06;2.3e-06;1.9e-06;4e-06;1.9e-06;2.9e-06;2.1e-06;1.4e-06;3.2e-06;1.6e-06;7e-07;2e-06;3.3e-06;3e-06;2.2e-06;3.5e-06;8.2e-07;1.6e-06;1.2e-06;7e-04	0.0317236857330196	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.979578837653689
CAMB-7A4BA	MN908947.3	28144	T	C	1	1	0	0	0.999853301450849	TTA	ORF8	L84S	T251C	TTA>TCA	Missense	GU280_gp09	7.33492745756744e-05
CAMB-7A4BA	MN908947.3	28657	C	T	1	1	0	0	0.999784926414109	ACG	N	D128D	C384T	GAC>GAT	Synonymous	GU280_gp10	3.07247979844533e-05
CAMB-7A4BA	MN908947.3	28863	C	T	1	1	0	0	0.997976293726511	TCA	N	S197L	C590T	TCA>TTA	Missense	GU280_gp10	0.000289100896212778
CAMB-7A4BA	MN908947.3	29353	C	T	0.0092	0.0041	5.2e-06	0.00075	0.00684481676615245	ACA	N	Y360Y	C1080T	TAC>TAT	Synonymous	GU280_gp10	0.991841678950364
CAMB-7A4BA	MN908947.3	3177	C	T	0.01	0.0083	4.3e-06	2.7e-05	0.00941779837402114	CCT	ORF1ab:nsp3	P153L	C458T	CCT>CTT	Missense	ORF1ab:nsp3	0.990547704196037
CAMB-7A4BA	MN908947.3	3354	G	A	0.01	0.016	1.6e-06	1.1e-08	0.0128571428571429	GGT	ORF1ab:nsp3	G212D	G635A	GGT>GAT	Missense	ORF1ab:nsp3	0.986712328767123
CAMB-7A4BA	MN908947.3	5099	TCACATGAAGGTAAAACATTTTATGTTTTACCTAATG	-	0.0183054054054054	0.0115405405405405	1e-05;4e-08;9.5e-08;1.2e-07;5.3e-08;7.3e-08;1.1e-07;1e-07;1.1e-07;6e-08;8e-08;1.2e-07;2.7e-07;1.9e-07;3.4e-08;8.4e-08;1.5e-07;1e-07;2e-07;1.7e-07;9.2e-08;2.2e-07;2.9e-07;1.7e-07;1.8e-07;5.7e-08;9.2e-08;1.7e-07;1.5e-07;1.5e-07;1e-07;1e-07;1.5e-06;8.2e-07;8.2e-07;0.00041;0.00051	NA;NA;NA;NA;NA;6.5e-06;1.2e-05;1.1e-05;1.3e-05;8.4e-06;9.4e-06;1.1e-05;2.9e-05;1.7e-05;1.1e-05;1.3e-05;1.3e-05;9.8e-06;5.5e-05;2.9e-05;1.3e-05;2.4e-05;2.4e-05;1.7e-05;1.8e-05;3.3e-05;1.3e-05;1.5e-05;1.3e-05;1.7e-05;1.4e-05;1.2e-05;1.1e-05;1.4e-05;8.4e-06;1.2e-05;1.4e-05	0.0163455925277291	TTC	ORF1ab:nsp3	.	2380-2416-delfrshift	.	no-SNV	ORF1ab:nsp3	0.991859737006888
CAMB-7A4BA	MN908947.3	5104	TGAAGGTAAAACATTTTATGTTTTACCTAATG	-	0.018259375	0.01334375	7.3e-08;1.1e-07;1e-07;1.1e-07;6e-08;8e-08;1.2e-07;2.7e-07;1.9e-07;3.4e-08;8.4e-08;1.5e-07;1e-07;2e-07;1.7e-07;9.2e-08;2.2e-07;2.9e-07;1.7e-07;1.8e-07;5.7e-08;9.2e-08;1.7e-07;1.5e-07;1.5e-07;1e-07;1e-07;1.5e-06;8.2e-07;8.2e-07;0.00041;0.00051	6.5e-06;1.2e-05;1.1e-05;1.3e-05;8.4e-06;9.4e-06;1.1e-05;2.9e-05;1.7e-05;1.1e-05;1.3e-05;1.3e-05;9.8e-06;5.5e-05;2.9e-05;1.3e-05;2.4e-05;2.4e-05;1.7e-05;1.8e-05;3.3e-05;1.3e-05;1.5e-05;1.3e-05;1.7e-05;1.4e-05;1.2e-05;1.1e-05;1.4e-05;8.4e-06;1.2e-05;1.4e-05	0.0161756210283073	ATG	ORF1ab:nsp3	.	2385-2416-delfrshift	.	no-SNV	ORF1ab:nsp3	0.981157469717362
CAMB-7A4BA	MN908947.3	8782	C	T	1	1	0	0	0.999862593322035	GCC	ORF1ab:nsp4	S76S	C228T	AGC>AGT	Synonymous	ORF1ab:nsp4	9.16044519763661e-05
CAMB-7A4BA	MN908947.3	9477	T	A	1	1	0	0	0.999954590863682	TTT	ORF1ab:nsp4	F308Y	T923A	TTT>TAT	Missense	ORF1ab:nsp4	0
CAMB-7A4C9	MN908947.3	10097	G	A	0.99	0.99	0	0	0.990139741413086	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.00953375995820818
CAMB-7A4C9	MN908947.3	11075	T	-	0.039	0.035	2.5e-10	1.4e-09	0.0375365160670695	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958121573492337
CAMB-7A4C9	MN908947.3	13536	C	T	0.99	0.99	0	0	0.990828653387742	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00896933457234051
CAMB-7A4C9	MN908947.3	14184	C	T	0.99	0.99	0	0	0.991454981038011	CCA	ORF1ab:RNA-dependent-RNA-polymerase	T239T	C717T	ACC>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.0085159212810739
CAMB-7A4C9	MN908947.3	14408	C	T	1	1	0	0	0.998820527941949	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000448712195997487
CAMB-7A4C9	MN908947.3	16206	G	T	0.0082	0.011	2.6e-05	1.9e-06	0.0092752459345513	AGG	ORF1ab:RNA-dependent-RNA-polymerase	E913D	G2739T	GAG>GAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.990644448905842
CAMB-7A4C9	MN908947.3	1684	C	T	0.99	0.99	0	0	0.992283140958377	TCG	ORF1ab:nsp2	I293I	C879T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.00767313746065058
CAMB-7A4C9	MN908947.3	21058	C	T	0.99	0.99	0	0	0.992131681287872	CCC	ORF1ab:2'-O-ribose-methyltransferase	P134S	C400T	CCT>TCT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.00777787826716107
CAMB-7A4C9	MN908947.3	23403	A	G	1	1	0	0	0.999631485849057	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.52771226415094e-05
CAMB-7A4C9	MN908947.3	23731	C	T	0.99	0.99	0	0	0.99104094120829	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.00882382771560905
CAMB-7A4C9	MN908947.3	241	C	T	1	1	0	0	0.999294924814579	TCG	NA	NA	NA	NA	NA	NA	0.000149150519992949
CAMB-7A4C9	MN908947.3	27505	G	T	0.0075	0.0069	2e-05	3.1e-05	0.00720299613988372	TGG	ORF7a	G38*	G112T	GGA>TGA	Nonsense	GU280_gp07	0.992682062432352
CAMB-7A4C9	MN908947.3	28881	GGG	AAC	0.99	0.99	0;0;0	0;0;0	0.990079008798707	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.0103702954269527
CAMB-7A4C9	MN908947.3	29736	G	T	0.99	0.99	0	0	0.989952446694278	AGG	NA	NA	NA	NA	NA	NA	0.00974075778493634
CAMB-7A4C9	MN908947.3	3037	C	T	1	1	0	0	0.999432919049194	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.08851188507159e-05
CAMB-7A4C9	MN908947.3	4002	C	T	0.99	0.99	0	0	0.992080109239873	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0.00782885753299955
CAMB-7A4D8	MN908947.3	14408	C	T	1	1	0	0	0.999588488656004	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000192038627198156
CAMB-7A4D8	MN908947.3	20611	C	T	1	1	0	0	0.999756829050823	GCT	ORF1ab:endoRNAse	L331F	C991T	CTT>TTT	Missense	ORF1ab:endoRNAse	8.10569830590905e-05
CAMB-7A4D8	MN908947.3	23403	A	G	1	1	0	0	0.999863465695756	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.10228694959609e-05
CAMB-7A4D8	MN908947.3	241	C	T	1	1	0	0	0.999773512258649	TCG	NA	NA	NA	NA	NA	NA	0.00016986580601325
CAMB-7A4D8	MN908947.3	28881	GGG	AAC	1	0.99	0;0;0	0;0;0	0.99717633771001	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A4D8	MN908947.3	28902	TGGCTGGCAATGGCGGTGATGCTGCT	-	0.000169230769230769	0.00895	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0013;NA;NA;NA	0.00043;0.00052;0.00014;0.00014;0.00012;0.00011;7.3e-05;0.00011;6.6e-05;1e-04;1e-04;9.5e-05;8.2e-05;8e-05;8.5e-05;7.5e-05;6.7e-05;8.1e-05;4.5e-05;5.2e-05;3.5e-05;5e-05;3.9e-05;5e-05;4.2e-05;3.4e-05	0.00227607444102289	ATG	N	.	629-654-delfrshift	.	no-SNV	GU280_gp10	0.997130801687764
CAMB-7A4D8	MN908947.3	29338	G	A	0.012	0.017	2.6e-07	1.5e-09	0.0142633404183913	AGC	N	K355K	G1065A	AAG>AAA	Synonymous	GU280_gp10	0.985680724913301
CAMB-7A4D8	MN908947.3	29730	CACCGAGGCCACGCGGAGTACGATCGAGTGTACAGTG	-	0.484324324324324	0.388378378378378	1.5e-153;1.6e-163;3e-154;8.7e-155;6.4e-153;5e-157;1e-155;3.3e-152;2e-154;5.7e-153;1.4e-157;4.2e-153;2.8e-152;6.9e-155;1.2e-154;1.7e-153;8.3e-156;8.7e-143;6.6e-132;4e-133;4.2e-116;9.5e-115;1.4e-130;5.9e-132;3.9e-134;2.5e-132;5.3e-130;1e-122;3.4e-134;1.7e-123;1.4e-153;2.3e-154;3e-154;2.1e-153;6.3e-152;2.3e-154;7e-154	5.6e-121;6.8e-129;1.9e-120;6.1e-121;1.4e-119;1.7e-124;5.8e-122;3.4e-120;1.5e-119;2e-119;1.6e-126;8.8e-120;1.4e-119;6.6e-121;7.4e-120;2.4e-119;7.3e-121;1.5e-111;1.6e-103;2.2e-108;8.6e-94;1.4e-94;9e-103;2.6e-103;3.1e-104;1.3e-103;1.1e-106;1.5e-95;9.4e-104;7e-96;1.8e-121;8.5e-121;9.6e-121;2.9e-122;8.4e-121;1.4e-121;1.5e-121	0.430971512052593	TCA	NA	NA	NA	NA	NA	NA	0.570284049526584
CAMB-7A4D8	MN908947.3	3037	C	T	1	1	0	0	0.999799438427597	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A4D8	MN908947.3	522	T	-	0.045	0.079	5.5e-06	1.5e-10	0.0593569661995054	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.940452787113958
CAMB-7A4D8	MN908947.3	522	TT	-	0.0225	0.077	5.5e-06;NA	1.5e-10;4.7e-11	0.0452022693635915	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.940452787113958
CAMB-7A4D8	MN908947.3	683	C	T	0.0085	0.013	2.1e-05	2.7e-07	0.0107852504412884	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.989214749558712
CAMB-7A4E7	MN908947.3	11083	G	-	0.98	0.031	0	6.5e-13	0.490461941275482	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-7A4E7	MN908947.3	11083	G	T	0.015	0.97	0.0013	0	0.509444548344866	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-7A4E7	MN908947.3	13914	T	G	0.0041	0.012	0.00025	4e-07	0.00690846286701209	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.993091537132988
CAMB-7A4E7	MN908947.3	14805	C	T	1	1	0	0	1	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-7A4E7	MN908947.3	2480	A	G	1	1	0	2.7999999542472e-317	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-7A4E7	MN908947.3	2558	C	T	1	1	0	0	0.998998998998999	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.001001001001001
CAMB-7A4E7	MN908947.3	25906	G	T	1	1	0	1.9e-239	0.998760842627014	AGG	ORF3a	G172C	G514T	GGT>TGT	Missense	GU280_gp03	0
CAMB-7A4E7	MN908947.3	29013	C	T	1	1	0	0	1	ACT	N	T247I	C740T	ACT>ATT	Missense	GU280_gp10	0
CAMB-7A4E7	MN908947.3	4185	G	A	1	1	0	0	0.999750561237216	GGT	ORF1ab:nsp3	G489D	G1466A	GGT>GAT	Missense	ORF1ab:nsp3	0.000249438762783737
CAMB-7A4F6	MN908947.3	11074	C	INS	0.26	0.2	9.3e-98	2.9e-71	0.232473957285927	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.767043397820054
CAMB-7A4F6	MN908947.3	11083	G	-	0.12	0.17	5.7e-50	7.4e-74	0.143272578332992	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-7A4F6	MN908947.3	11083	G	T	0.88	0.83	0	0	0.856522629531026	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-7A4F6	MN908947.3	13458	C	T	1	1	3.8e-136	0	0.997361477572559	TCG	ORF1ab:nsp11	S6L	C17T	TCG>TTG	Missense	ORF1ab:nsp11	0.00263852242744063
CAMB-7A4F6	MN908947.3	14805	C	T	1	1	0	0	0.999912168986869	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	4.39155065653682e-05
CAMB-7A4F6	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-7A4F6	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-7A502	MN908947.3	14408	C	T	1	1	0	0	0.999570815450644	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000297127764938924
CAMB-7A502	MN908947.3	23403	A	G	1	1	0	0	0.99996070109251	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.92989074903718e-05
CAMB-7A502	MN908947.3	241	C	T	1	1	0	0	0.999870834409713	TCG	NA	NA	NA	NA	NA	NA	3.22913975716869e-05
CAMB-7A502	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0502227297297297	0.042972972972973	NA;NA;NA;0.5;0.5;3.8e-13;1.2e-11;4.7e-10;4.4e-10;3.6e-11;1.6e-10;9.9e-11;4.3e-10;2.1e-10;3.4e-10;8e-10;1.6e-10;6.4e-10;2.4e-10;2.7e-10;1.5e-10;6.5e-10;2.1e-10;4.1e-10;2.3e-10;8.2e-11;4.5e-10;1.8e-10;2.5e-11;1.7e-10;5.3e-10;3.9e-10;1.2e-10;4.6e-10;4.5e-11;1.9e-10;8.7e-11	9.1e-08;3e-10;3.6e-08;3.4e-08;2.1e-07;1.7e-09;2.5e-08;3.6e-07;3.5e-07;8.1e-08;1.4e-07;8.7e-08;3.5e-07;2e-07;2.7e-07;5.1e-07;1.7e-07;4.3e-07;2.6e-07;2.5e-07;1.7e-07;4.7e-07;2.5e-07;3.1e-07;2.2e-07;1.7e-07;3.7e-07;1.8e-07;3.1e-07;1.2e-07;3.7e-07;8.2e-08;6.7e-08;2.3e-07;8.3e-08;1.8e-07;9.4e-08	0.0493223064553182	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.978501524145676
CAMB-7A502	MN908947.3	28086	G	T	0.23	0.18	1.9e-70	4.2e-54	0.20565371024735	GGC	ORF8	A65S	G193T	GCT>TCT	Missense	GU280_gp09	0.79434628975265
CAMB-7A502	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A502	MN908947.3	29779	G	T	0.1	0.018	1.7e-26	6.8e-06	0.0599600266489007	GGA	NA	NA	NA	NA	NA	NA	0.940039973351099
CAMB-7A502	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A511	MN908947.3	11075	T	-	0.042	0.041	2.7e-10	3e-10	0.041368280583088	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955229354059918
CAMB-7A511	MN908947.3	14408	C	T	1	1	0	0	0.996358325406205	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000518866564815082
CAMB-7A511	MN908947.3	18828	C	T	0.1	0.11	1.2e-46	6.6e-48	0.104101140918902	TCC	ORF1ab:3'-to-5'-exonuclease	V263V	C789T	GTC>GTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.895775516497071
CAMB-7A511	MN908947.3	23130	C	T	0.5	0.48	1.4e-282	8.5e-271	0.491269504298907	ACT	S	T523I	C1568T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.508703959239996
CAMB-7A511	MN908947.3	23403	A	G	1	1	0	0	0.998580440157562	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000103411644151131
CAMB-7A511	MN908947.3	241	C	T	1	1	0	0	0.997522644576914	TCG	NA	NA	NA	NA	NA	NA	0.000154834713942866
CAMB-7A511	MN908947.3	25002	C	T	0.0092	0.0073	7.6e-06	4.1e-05	0.00846749974363106	TCA	S	S1147L	C3440T	TCA>TTA	Missense	GU280_gp02, spike glycoprotein	0.991517850602833
CAMB-7A511	MN908947.3	26137	A	C	0.02	0.028	2e-04	2.9e-06	0.0227737973387922	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.977226202661208
CAMB-7A511	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999109163576829	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00010873110796999
CAMB-7A511	MN908947.3	3037	C	T	1	1	0	0	0.998959769068733	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000104023093126674
CAMB-7A511	MN908947.3	686	AAGTCA	-	0.451666666666667	0.438333333333333	7.3e-79;1.2e-79;1.8e-67;3.5e-78;3e-66;5.6e-73	1.7e-77;6.4e-79;2.5e-64;2.6e-74;3.8e-63;1.4e-67	0.445223525869208	AAA	ORF1ab:leader-protein	.	421-426-delinframe	.	no-SNV	ORF1ab:leader-protein	0.547635568911351
CAMB-7A511	MN908947.3	692	T	-	0.52	0.49	1.6e-83	9.8e-78	0.50561050872678	ATT	ORF1ab:leader-protein	.	427-427-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.494212638280745
CAMB-7A511	MN908947.3	693	TT	-	0.45	0.43	6e-72;2.2e-60	7.2e-67;5.3e-57	0.439550609658698	TTT	ORF1ab:leader-protein	.	428-429-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.549647225476041
CAMB-7A520	MN908947.3	10190	T	G	0.01	0.014	2.3e-06	6.2e-08	0.0123172403289674	CTC	ORF1ab:3C-like-proteinase	S46A	T136G	TCT>GCT	Missense	ORF1ab:3C-like-proteinase	0.987549497410905
CAMB-7A520	MN908947.3	11074	C	INS	0.065	0.031	3.4e-20	2.1e-06	0.0502126146415184	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.949416976575349
CAMB-7A520	MN908947.3	11083	G	-	0.027	0.052	1.4e-11	5.8e-22	0.0382721771920374	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.763276248700249
CAMB-7A520	MN908947.3	11083	G	T	0.18	0.22	2.2e-40	4e-51	0.198326296931962	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.763276248700249
CAMB-7A520	MN908947.3	11562	G	C	0.016	0.0049	1.2e-06	0.0043	0.0103004291845494	TGC	ORF1ab:nsp6	C197S	G590C	TGC>TCC	Missense	ORF1ab:nsp6	0.972532188841202
CAMB-7A520	MN908947.3	12242	C	T	0.048	0.09	4.1e-22	2e-40	0.0665774243080436	CCG	ORF1ab:nsp8	R51C	C151T	CGT>TGT	Missense	ORF1ab:nsp8	0.933383204063152
CAMB-7A520	MN908947.3	13147	TGTT	-	0.00505	0.0083	0.0041;0.005;0.0011;0.00051	0.00034;0.00047;4.8e-05;1.9e-05	0.00662308471028294	GTG	ORF1ab:nsp10	.	123-126-delfrshift	.	no-SNV	ORF1ab:nsp10	0.993207339512648
CAMB-7A520	MN908947.3	14175	AACCTTG	-	0.0114285714285714	0.00545714285714286	8.2e-07;3.1e-05;1.9e-05;1.8e-05;1.1e-06;5e-06;1.4e-06	5.9e-06;0.00011;7.6e-05;7.2e-05;NA;NA;NA	0.0104000997910625	TAA	ORF1ab:RNA-dependent-RNA-polymerase	.	708-714-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.988935834415638
CAMB-7A520	MN908947.3	14408	C	T	0.99	1	0	0	0.995321777724465	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00440832483656211
CAMB-7A520	MN908947.3	1701	C	T	0.01	0.0085	7.4e-07	3.8e-06	0.00952317305443245	TCT	ORF1ab:nsp2	S299F	C896T	TCT>TTT	Missense	ORF1ab:nsp2	0.990443412303271
CAMB-7A520	MN908947.3	17461	CG	TT	0.00775	0.00325	4.3e-05;6.4e-06	8.8e-05;NA	0.00575633383010432	ACG	ORF1ab:helicase	.	1225-1226-mnv	.	no-SNV	ORF1ab:helicase	0.993125
CAMB-7A520	MN908947.3	17878	C	T	0.0053	0.0079	0.00019	1.3e-05	0.00642074020231389	TCA	ORF1ab:helicase	Q548*	C1642T	CAA>TAA	Nonsense	ORF1ab:helicase	0.993559068790761
CAMB-7A520	MN908947.3	22584	TTT	-	0.016	0.00633333333333333	6.1e-06;0.00056;0.00043	0.012;0.0055;NA	0.0115440115440115	GTT	S	.	1022-1024-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.982176489503422
CAMB-7A520	MN908947.3	23403	A	G	1	1	0	0	0.999884336234566	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.71091769559225e-05
CAMB-7A520	MN908947.3	23432	A	G	0.0065	0.006	3.9e-05	6.4e-05	0.00625548941153508	TAT	S	I624V	A1870G	ATT>GTT	Missense	GU280_gp02, spike glycoprotein	0.993695715819264
CAMB-7A520	MN908947.3	241	C	T	1	0.98	0	0	0.992721480210758	TCG	NA	NA	NA	NA	NA	NA	4.90136012743536e-05
CAMB-7A520	MN908947.3	26776	CTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0323095238095238	0.0135714285714286	9.9e-05;4.7e-05;2e-04;0.00081;0.00034;1.6e-05;0.00019;0.00025;0.00055;5.1e-05;0.00023;1.6e-05;1.6e-05;3.8e-06;7.8e-06;6.2e-06;1.6e-05;9.5e-06;1.2e-05;2.3e-05;8e-06;1.9e-05;1.1e-05;1.1e-05;9.2e-06;2e-05;1.2e-05;1.5e-05;1e-05;5.7e-06;1.6e-05;9.4e-06;1.2e-05;8.4e-06;1.7e-05;1.1e-05;4.1e-06;1.4e-05;5.8e-06;9.2e-06;6.6e-06;0.00011	0.013;0.0071;0.012;0.024;0.026;0.0069;0.025;0.025;0.035;0.014;0.024;0.044;0.044;0.027;0.035;0.033;0.044;0.038;0.041;0.051;0.037;0.047;0.04;0.04;0.035;0.051;0.036;0.042;0.038;0.036;0.047;0.037;0.021;0.037;0.046;0.045;0.037;0.046;0.036;0.036;0.032;0.038	0.0244561860975777	GCT	M	.	254-295-delinframe	.	no-SNV	GU280_gp05	0.973367064401108
CAMB-7A520	MN908947.3	27128	C	T	0.052	0.014	7.1e-24	4.7e-08	0.0322967874699897	GCA	M	G202G	C606T	GGC>GGT	Synonymous	GU280_gp05	0.96770321253001
CAMB-7A520	MN908947.3	28029	TA	-	0.00865	0.00725	3.2e-05;3.3e-05	1e-04;9.5e-05	0.00790413054563998	GTA	ORF8	.	136-137-delfrshift	.	no-SNV	GU280_gp09	0.991566572961922
CAMB-7A520	MN908947.3	29734	G	C	1	1	2.8e-130	1.3e-152	1	CGA	NA	NA	NA	NA	NA	NA	0
CAMB-7A520	MN908947.3	3037	C	T	1	1	0	0	0.999216546537136	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000156690692572861
CAMB-7A520	MN908947.3	3405	A	G	0.005	0.008	0.00026	1.1e-05	0.00620802937339968	GAA	ORF1ab:nsp3	E229G	A686G	GAA>GGA	Missense	ORF1ab:nsp3	0.993767814870284
CAMB-7A520	MN908947.3	5826	C	T	0.011	0.012	2.8e-05	6.8e-06	0.011398924486859	ACA	ORF1ab:nsp3	T1036I	C3107T	ACA>ATA	Missense	ORF1ab:nsp3	0.988601075513141
CAMB-7A520	MN908947.3	6038	TTCGATAA	-	0.045125	0.034625	3.2e-16;1.4e-15;1.5e-14;1.1e-14;6.4e-15;1.6e-15;5.8e-14;7.5e-08	1.9e-13;1.5e-12;5e-12;6.8e-12;2.7e-12;3.1e-12;4.5e-11;2.1e-06	0.0390342052313883	CTT	ORF1ab:nsp3	.	3319-3326-delfrshift	.	no-SNV	ORF1ab:nsp3	0.952634122764621
CAMB-7A53F	MN908947.3	11075	T	-	0.22	0.0088	6.7e-58	0.0011	0.178106229331174	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.821826280623608
CAMB-7A53F	MN908947.3	14408	C	T	1	1	0	0	0.998984513835999	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000761614623000762
CAMB-7A53F	MN908947.3	21992	TA	-	0.365	0.56	2.8e-32;7.9e-33	5.5e-55;1.4e-54	0.456599286563615	TTA	S	.	430-431-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.545023696682464
CAMB-7A53F	MN908947.3	23403	A	G	1	1	0	0	0.99991789819376	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.10509031198686e-05
CAMB-7A53F	MN908947.3	28881	GGG	AAC	0.996666666666667	1	6.5e-223;1.4e-243;7.5e-262	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A53F	MN908947.3	29286	A	G	1	1	0	0	0.999261447562777	AAA	N	K338R	A1013G	AAA>AGA	Missense	GU280_gp10	0.000738552437223043
CAMB-7A53F	MN908947.3	3037	C	T	1	1	7.69999999999999e-291	1.2e-300	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A53F	MN908947.3	4108	A	G	1	1	0	0	1	AAG	ORF1ab:nsp3	K463K	A1389G	AAA>AAG	Synonymous	ORF1ab:nsp3	0
CAMB-7A55D	MN908947.3	10323	A	G	0.069	0.056	3.2e-18	5.2e-15	0.0626235900292438	AAG	ORF1ab:3C-like-proteinase	K90R	A269G	AAG>AGG	Missense	ORF1ab:3C-like-proteinase	0.93734855869656
CAMB-7A55D	MN908947.3	11074	C	INS	0.028	0.018	5.1e-06	0.0038	0.0235876101710735	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.976132378628478
CAMB-7A55D	MN908947.3	11075	T	-	0.04	0.035	7.2e-10	3.3e-09	0.0379549257183924	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959170381682818
CAMB-7A55D	MN908947.3	13694	C	T	0.013	0.0048	1.2e-07	3e-04	0.00920340110203306	ACA	ORF1ab:RNA-dependent-RNA-polymerase	T76I	C227T	ACA>ATA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.990784723541706
CAMB-7A55D	MN908947.3	14408	C	T	1	1	0	0	0.999208642582223	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000563542403568303
CAMB-7A55D	MN908947.3	16323	C	T	0.049	0.054	8.8e-22	6.6e-24	0.0515268746398881	GCT	ORF1ab:helicase	C29C	C87T	TGC>TGT	Synonymous	ORF1ab:helicase	0.94839081405877
CAMB-7A55D	MN908947.3	16929	A	G	0.33	0.32	1.2e-166	1.5e-160	0.322706174691734	CAG	ORF1ab:helicase	T231T	A693G	ACA>ACG	Synonymous	ORF1ab:helicase	0.677215684435901
CAMB-7A55D	MN908947.3	23403	A	G	1	1	0	0	0.999911729539308	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.22212860203664e-05
CAMB-7A55D	MN908947.3	241	C	T	1	1	0	0	0.99972436182105	TCG	NA	NA	NA	NA	NA	NA	0.000153132321639128
CAMB-7A55D	MN908947.3	25355	C	T	0.32	0.32	1.1e-158	6.5e-164	0.319558367835846	GCT	S	L1265F	C3793T	CTC>TTC	Missense	GU280_gp02, spike glycoprotein	0.679347967606697
CAMB-7A55D	MN908947.3	26137	A	C	0.034	0.026	8.2e-07	1e-04	0.0306834030683403	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.96931659693166
CAMB-7A55D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999311561464653	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A55D	MN908947.3	3037	C	T	1	1	0	0	0.998859129678927	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A55D	MN908947.3	6401	C	T	0.014	0.018	3.3e-08	5e-10	0.0161256345979651	ACC	ORF1ab:nsp3	P1228S	C3682T	CCA>TCA	Missense	ORF1ab:nsp3	0.983832234416802
CAMB-7A55D	MN908947.3	7504	C	T	0.14	0.098	6.4e-62	1.1e-43	0.119338904021052	ACA	ORF1ab:nsp3	Y1595Y	C4785T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.880568764138313
CAMB-7A55D	MN908947.3	7528	C	T	0.13	0.11	1.4e-56	6.1e-51	0.121406784360847	TCG	ORF1ab:nsp3	V1603V	C4809T	GTC>GTT	Synonymous	ORF1ab:nsp3	0.878084850725575
CAMB-7A55D	MN908947.3	823	C	T	0.0049	0.011	8e-04	1.9e-06	0.00787080113172436	TCG	ORF1ab:nsp2	V6V	C18T	GTC>GTT	Synonymous	ORF1ab:nsp2	0.992110210204508
CAMB-7A55D	MN908947.3	8368	G	A	0.011	0.0042	1.1e-06	0.0013	0.00753295668549906	CGC	ORF1ab:nsp3	A1883A	G5649A	GCG>GCA	Synonymous	ORF1ab:nsp3	0.992467043314501
CAMB-7A55D	MN908947.3	913	C	T	1	1	0	0	0.999833624490475	CCG	ORF1ab:nsp2	S36S	C108T	TCC>TCT	Synonymous	ORF1ab:nsp2	0.000135180101489061
CAMB-7A56C	MN908947.3	11074	C	INS	0.026	0.038	3e-05	2.5e-08	0.0303044772318515	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.969377198427478
CAMB-7A56C	MN908947.3	11075	T	-	0.068	0.018	3e-16	1.6e-05	0.0490069952560907	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.947120152233926
CAMB-7A56C	MN908947.3	14408	C	T	1	0.99	0	0	0.997590636271617	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000384927932937
CAMB-7A56C	MN908947.3	18785	T	C	0.0033	0.0072	0.0015	2.1e-05	0.00459821145430329	TTT	ORF1ab:3'-to-5'-exonuclease	F249S	T746C	TTT>TCT	Missense	ORF1ab:3'-to-5'-exonuclease	0.995148094120632
CAMB-7A56C	MN908947.3	1983	T	C	0.012	0.003	8.3e-08	0.0013	0.00905612244897959	ATT	ORF1ab:nsp2	I393T	T1178C	ATT>ACT	Missense	ORF1ab:nsp2	0.990752551020408
CAMB-7A56C	MN908947.3	22858	C	T	0.0055	0.011	0.0011	4.4e-06	0.00740846274398062	GCG	S	C432C	C1296T	TGC>TGT	Synonymous	GU280_gp02, spike glycoprotein	0.992573728451346
CAMB-7A56C	MN908947.3	23403	A	G	1	1	0	0	0.999843145456447	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000115026665272404
CAMB-7A56C	MN908947.3	23873	G	T	1	1	0	0	0.999926122931442	AGC	S	A771S	G2311T	GCT>TCT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7A56C	MN908947.3	241	C	T	1	1	0	0	0.999862610941665	TCG	NA	NA	NA	NA	NA	NA	2.74778116670788e-05
CAMB-7A56C	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999220055710306	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A56C	MN908947.3	3037	C	T	0.99	1	0	0	0.996209983065882	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000161277316345456
CAMB-7A56C	MN908947.3	3122	G	T	0.24	0.23	2.9e-111	1.8e-103	0.235727696265906	AGA	ORF1ab:nsp3	D135Y	G403T	GAT>TAT	Missense	ORF1ab:nsp3	0.762672971281552
CAMB-7A56C	MN908947.3	6573	C	T	0.4	0.34	9.6e-199	1.8e-145	0.386354621182071	TCT	ORF1ab:nsp3	S1285F	C3854T	TCT>TTT	Missense	ORF1ab:nsp3	0.613513156154965
CAMB-7A56C	MN908947.3	8977	G	T	0.0056	0.014	0.00014	1.6e-08	0.00840855106888361	AGT	ORF1ab:nsp4	E141D	G423T	GAG>GAT	Missense	ORF1ab:nsp4	0.991496437054632
CAMB-7A57B	MN908947.3	10097	G	A	0.14	0.15	7.1e-66	3.1e-68	0.147465255843335	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0.852455780164245
CAMB-7A57B	MN908947.3	11074	C	INS	0.093	0.094	2.7e-25	4.6e-26	0.0935512438612028	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.902705096208035
CAMB-7A57B	MN908947.3	11083	G	-	0.14	0.13	7.2e-61	6.1e-58	0.134668168062496	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.162150749524949
CAMB-7A57B	MN908947.3	11083	G	T	0.7	0.7	1.1e-248	3.4e-250	0.702969948624111	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.162150749524949
CAMB-7A57B	MN908947.3	13536	C	T	0.14	0.14	9.6e-61	8.9e-62	0.136545227556464	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.863386675746226
CAMB-7A57B	MN908947.3	14184	C	T	0.15	0.15	5.5e-69	4e-69	0.149170798427082	CCA	ORF1ab:RNA-dependent-RNA-polymerase	T239T	C717T	ACC>ACT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.850786459223799
CAMB-7A57B	MN908947.3	14408	C	T	0.16	0.15	1.8e-69	2.2e-69	0.15497784236683	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.844591563952132
CAMB-7A57B	MN908947.3	14805	C	T	0.84	0.84	0	0	0.837005355737746	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.162677361220397
CAMB-7A57B	MN908947.3	1684	C	T	0.17	0.18	1.4e-77	1.3e-80	0.172464840858623	TCG	ORF1ab:nsp2	I293I	C879T	ATC>ATT	Synonymous	ORF1ab:nsp2	0.827535159141377
CAMB-7A57B	MN908947.3	18999	ATT	-	0.0873333333333333	0.0843333333333333	1.5e-39;4.3e-42;1.1e-38	7.1e-38;4.7e-40;2.5e-37	0.0841852517455735	CAT	ORF1ab:3'-to-5'-exonuclease	.	960-962-delinframe	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.915726364788027
CAMB-7A57B	MN908947.3	21058	C	T	0.15	0.16	9.3e-70	1.7e-71	0.154628954658113	CCC	ORF1ab:2'-O-ribose-methyltransferase	P134S	C400T	CCT>TCT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.845166933955387
CAMB-7A57B	MN908947.3	21703	T	G	0.058	0.06	3.2e-26	5.3e-27	0.0589120292109	TTT	S	V47V	T141G	GTT>GTG	Synonymous	GU280_gp02, spike glycoprotein	0.940918926228954
CAMB-7A57B	MN908947.3	22243	A	C	0.14	0.14	5.9e-64	1.8e-64	0.137541785766193	TAG	S	V227V	A681C	GTA>GTC	Synonymous	GU280_gp02, spike glycoprotein	0.862248276084815
CAMB-7A57B	MN908947.3	23403	A	G	0.16	0.15	1.1e-54	5.6e-54	0.154901191799028	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.844924504869599
CAMB-7A57B	MN908947.3	23731	C	T	0.14	0.14	2.6e-61	1.1e-64	0.139496860020066	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0.860465980454089
CAMB-7A57B	MN908947.3	241	C	T	0.15	0.15	5.8e-65	2.6e-64	0.147635399066151	TCG	NA	NA	NA	NA	NA	NA	0.852073908540906
CAMB-7A57B	MN908947.3	2480	A	G	0.85	0.85	0	0	0.85259880239521	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.147305389221557
CAMB-7A57B	MN908947.3	2558	C	T	0.84	0.84	0	0	0.841731384193696	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.157846048423938
CAMB-7A57B	MN908947.3	25906	G	T	0.86	0.86	0	0	0.85775481920121	AGG	ORF3a	G172C	G514T	GGT>TGT	Missense	GU280_gp03	0.142194783923397
CAMB-7A57B	MN908947.3	26144	G	T	0.8	0.8	0	0	0.798286913608259	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.201599636961824
CAMB-7A57B	MN908947.3	28881	GGG	AAC	0.183333333333333	0.193333333333333	4.8e-72;1.2e-76;1.9e-89	9.4e-78;6.2e-85;6.4e-96	0.190802159660625	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.825279905715969
CAMB-7A57B	MN908947.3	29013	C	T	0.76	0.76	0	0	0.758599088838269	ACT	N	T247I	C740T	ACT>ATT	Missense	GU280_gp10	0.240774487471526
CAMB-7A57B	MN908947.3	29736	G	T	0.023	0.023	6.5e-11	4.1e-11	0.0227682790617751	AGG	NA	NA	NA	NA	NA	NA	0.976630294698857
CAMB-7A57B	MN908947.3	3037	C	T	0.14	0.14	2.7e-24	1e-24	0.138026010603048	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.861870444002651
CAMB-7A57B	MN908947.3	3099	C	T	0.0074	0.0077	3.3e-05	2.9e-05	0.00756748616392455	ACT	ORF1ab:nsp3	T127I	C380T	ACT>ATT	Missense	ORF1ab:nsp3	0.992432513836075
CAMB-7A57B	MN908947.3	4002	C	T	0.14	0.14	2.4e-60	6e-61	0.135524688421653	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0.864475311578346
CAMB-7A57B	MN908947.3	4185	G	A	0.84	0.84	0	0	0.836083776542246	GGT	ORF1ab:nsp3	G489D	G1466A	GGT>GAT	Missense	ORF1ab:nsp3	0.163634608112131
CAMB-7A58A	MN908947.3	14408	C	T	1	1	0	0	0.999268417587241	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000438949447655278
CAMB-7A58A	MN908947.3	17410	C	T	0.13	0.09	1e-57	5.3e-41	0.105276205429079	ACG	ORF1ab:helicase	R392C	C1174T	CGT>TGT	Missense	ORF1ab:helicase	0.894641160186754
CAMB-7A58A	MN908947.3	19027	C	T	0.25	0.25	1.1e-57	8.7e-80	0.248041775456919	TCA	ORF1ab:3'-to-5'-exonuclease	H330Y	C988T	CAC>TAC	Missense	ORF1ab:3'-to-5'-exonuclease	0.751958224543081
CAMB-7A58A	MN908947.3	23403	A	G	1	1	0	0	0.999935228965607	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.23855171967096e-05
CAMB-7A58A	MN908947.3	241	C	T	1	1	0	0	0.999499374217772	TCG	NA	NA	NA	NA	NA	NA	0.000500625782227785
CAMB-7A58A	MN908947.3	26530	A	G	1	1	0	0	1	GAT	M	D3G	A8G	GAT>GGT	Missense	GU280_gp05	0
CAMB-7A58A	MN908947.3	27509	C	T	0.1	0.17	1.1e-47	4.7e-76	0.132804695304695	ACA	ORF7a	T39I	C116T	ACA>ATA	Missense	GU280_gp07	0.866633366633367
CAMB-7A58A	MN908947.3	27945	C	T	0.036	0.082	3e-08	1.8e-19	0.0634920634920635	CCA	ORF8	Q18*	C52T	CAA>TAA	Nonsense	GU280_gp09	0.936507936507937
CAMB-7A58A	MN908947.3	28253	C	T	0.15	0.27	2e-68	3.3e-128	0.199982976550198	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.799846788951781
CAMB-7A58A	MN908947.3	683	C	T	0.39	0.59	3.1e-194	0	0.49564767732483	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.50435232267517
CAMB-7A599	MN908947.3	1063	C	T	0.33	0.38	1.2e-167	2.6e-199	0.350801627183537	TCA	ORF1ab:nsp2	F86F	C258T	TTC>TTT	Synonymous	ORF1ab:nsp2	0.649092020951317
CAMB-7A599	MN908947.3	11074	C	INS	0.11	0.018	4.1e-34	0.0032	0.0715545904865305	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.927834701771052
CAMB-7A599	MN908947.3	11083	G	-	0.018	0.14	5.1e-08	6.4e-63	0.0750466818815021	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.480245413319897
CAMB-7A599	MN908947.3	11083	G	T	0.6	0.27	2.4e-187	5.1e-64	0.444559708349388	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.480245413319897
CAMB-7A599	MN908947.3	14408	C	T	0.5	0.77	2.5e-279	0	0.590085852052217	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.409825943784547
CAMB-7A599	MN908947.3	14805	C	T	0.42	0.46	8.5e-227	4.5e-256	0.44068458022076	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.559259672204259
CAMB-7A599	MN908947.3	16206	G	T	0.65	0.69	1.5e-265	5.9e-244	0.664009809932557	AGG	ORF1ab:RNA-dependent-RNA-polymerase	E913D	G2739T	GAG>GAT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.335990190067443
CAMB-7A599	MN908947.3	203	C	T	0.079	0.029	1.6e-35	1e-13	0.0522463580522934	TCG	NA	NA	NA	NA	NA	NA	0.947565366783554
CAMB-7A599	MN908947.3	21709	T	C	0.55	0.46	1.6e-260	9.4e-161	0.525314183123878	ATT	S	H49H	T147C	CAT>CAC	Synonymous	GU280_gp02, spike glycoprotein	0.474685816876122
CAMB-7A599	MN908947.3	23403	A	G	0.5	0.58	3.5e-222	1.1e-282	0.535690073698253	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.464266188466333
CAMB-7A599	MN908947.3	241	C	T	0.52	0.54	1.4e-292	3.80000000015919e-314	0.529257502508438	TCG	NA	NA	NA	NA	NA	NA	0.470605673629481
CAMB-7A599	MN908947.3	2480	A	G	0.55	0.24	1e-223	2.6e-75	0.431946584488957	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0.56753980482794
CAMB-7A599	MN908947.3	2558	C	T	0.55	0.32	5.7e-246	5.6e-115	0.4513839602555	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0.5486160397445
CAMB-7A599	MN908947.3	26144	G	T	0.46	0.46	4.5e-130	1.2e-97	0.458115183246073	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.541884816753927
CAMB-7A599	MN908947.3	27813	C	T	0.36	0.3	8e-117	9.5e-85	0.335883703136955	CCT	NA	NA	NA	NA	NA	NA	0.664116296863045
CAMB-7A599	MN908947.3	3037	C	T	0.47	0.56	9.7e-103	4.6e-129	0.508986819331647	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.491013180668353
CAMB-7A599	MN908947.3	8899	T	C	0.022	0.002	4.3e-11	0.0061	0.0152705061082024	ATG	ORF1ab:nsp4	N115N	T345C	AAT>AAC	Synonymous	ORF1ab:nsp4	0.984729493891798
CAMB-7A5A8	MN908947.3	11075	T	-	0.0052	0.11	0.0088	8e-28	0.0533534767224586	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.922076889436648
CAMB-7A5A8	MN908947.3	14408	C	T	1	1	0	0	0.998975465084929	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000754920463736856
CAMB-7A5A8	MN908947.3	23403	A	G	1	1	0	0	0.99992899408284	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.10059171597633e-05
CAMB-7A5A8	MN908947.3	241	C	T	1	1	0	0	0.999915139171758	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-7A5A8	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00060313630880579
CAMB-7A5A8	MN908947.3	3037	C	T	1	1	6.4e-246	4.1e-187	0.998496240601504	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00150375939849624
CAMB-7A5B7	MN908947.3	11075	T	-	0.038	0.042	1.3e-09	8.2e-11	0.0397945586504004	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956194936414091
CAMB-7A5B7	MN908947.3	14408	C	T	1	1	0	0	0.998373616980863	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000557956218243981
CAMB-7A5B7	MN908947.3	17677	A	G	0.019	0.017	5e-10	2.8e-09	0.0178352819614318	CAC	ORF1ab:helicase	T481A	A1441G	ACG>GCG	Missense	ORF1ab:helicase	0.982142255466828
CAMB-7A5B7	MN908947.3	23403	A	G	1	1	0	0	0.999408008036739	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000161452353616533
CAMB-7A5B7	MN908947.3	241	C	T	1	1	0	0	0.999114356462487	TCG	NA	NA	NA	NA	NA	NA	0.000253041010718094
CAMB-7A5B7	MN908947.3	26137	A	C	0.025	0.016	4.2e-06	0.0017	0.0204391497313712	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.979327259985985
CAMB-7A5B7	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999072114129962	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	3.18106629342155e-05
CAMB-7A5B7	MN908947.3	3037	C	T	1	1	0	0	0.999575641841714	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.0622594040799e-05
CAMB-7A5B7	MN908947.3	5497	C	T	0.044	0.042	8.4e-20	8.6e-19	0.0431137724550898	GCA	ORF1ab:nsp3	C926C	C2778T	TGC>TGT	Synonymous	ORF1ab:nsp3	0.956646706586826
CAMB-7A5B7	MN908947.3	7948	C	T	1	1	0	0	0.998340005858803	ACA	ORF1ab:nsp3	Y1743Y	C5229T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.000585880285128405
CAMB-7A5C6	MN908947.3	11008	C	A	0.017	0.018	3.3e-09	1e-09	0.0176988155668359	ACT	ORF1ab:nsp6	H12Q	C36A	CAC>CAA	Missense	ORF1ab:nsp6	0.982098138747885
CAMB-7A5C6	MN908947.3	11075	T	-	0.039	0.039	4.1e-10	2.5e-10	0.0388513513513514	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956799884991374
CAMB-7A5C6	MN908947.3	13568	C	T	1	1	0	0	0.999772998986062	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A34V	C101T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	6.05336037167633e-05
CAMB-7A5C6	MN908947.3	14408	C	T	1	1	0	0	0.999157759333558	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000444090533214909
CAMB-7A5C6	MN908947.3	17193	G	T	0.053	0.057	8.3e-25	1.2e-26	0.0548220675117189	AGA	ORF1ab:helicase	E319D	G957T	GAG>GAT	Missense	ORF1ab:helicase	0.945122458602613
CAMB-7A5C6	MN908947.3	20355	A	G	1	1	0	0	0.998767714109673	TAG	ORF1ab:endoRNAse	L245L	A735G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-7A5C6	MN908947.3	23403	A	G	1	1	0	0	0.999663135017658	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.346644933442e-05
CAMB-7A5C6	MN908947.3	241	C	T	1	1	0	0	0.999332025809386	TCG	NA	NA	NA	NA	NA	NA	8.5273300929479e-05
CAMB-7A5C6	MN908947.3	26137	A	C	0.03	0.014	2.4e-07	0.0084	0.0220958214832641	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.977466637497265
CAMB-7A5C6	MN908947.3	26530	A	G	1	1	0	0	0.999350860110354	GAT	M	D3G	A8G	GAT>GGT	Missense	GU280_gp05	0.000324569944823109
CAMB-7A5C6	MN908947.3	2775	A	G	1	1	0	0	0.999681559866745	AAG	ORF1ab:nsp3	K19R	A56G	AAG>AGG	Missense	ORF1ab:nsp3	0.000171467764060357
CAMB-7A5C6	MN908947.3	3037	C	T	1	1	0	0	0.998943196829591	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.80669308674593e-05
CAMB-7A5C6	MN908947.3	4255	G	T	1	1	0	0	0.998907324969648	CGG	ORF1ab:nsp3	P512P	G1536T	CCG>CCT	Synonymous	ORF1ab:nsp3	0.000809388911371914
CAMB-7A5D5	MN908947.3	10519	C	T	0.093	0.053	2.3e-39	8.9e-22	0.0781746773891902	ACT	ORF1ab:3C-like-proteinase	D155D	C465T	GAC>GAT	Synonymous	ORF1ab:3C-like-proteinase	0.92182532261081
CAMB-7A5D5	MN908947.3	11138	G	T	1	1	0	0	0.999358403136696	TGC	ORF1ab:nsp6	A56S	G166T	GCA>TCA	Missense	ORF1ab:nsp6	0
CAMB-7A5D5	MN908947.3	11514	C	T	1	1	2e-264	3.8e-160	1	ACT	ORF1ab:nsp6	T181I	C542T	ACT>ATT	Missense	ORF1ab:nsp6	0
CAMB-7A5D5	MN908947.3	14408	C	T	1	1	0	0	0.999607130579974	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000196434710013259
CAMB-7A5D5	MN908947.3	15720	C	T	0.053	0.025	1.3e-24	2.4e-12	0.0396946100498844	ACG	ORF1ab:RNA-dependent-RNA-polymerase	D751D	C2253T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.960305389950116
CAMB-7A5D5	MN908947.3	18501	C	T	1	1	0	0	0.999750530123488	ACA	ORF1ab:3'-to-5'-exonuclease	Y154Y	C462T	TAC>TAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0
CAMB-7A5D5	MN908947.3	21811	C	T	1	1	0	0	0.999768946395564	TCC	S	V83V	C249T	GTC>GTT	Synonymous	GU280_gp02, spike glycoprotein	0.000231053604436229
CAMB-7A5D5	MN908947.3	23403	A	G	1	1	0	0	0.999926211514693	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.37884853068679e-05
CAMB-7A5D5	MN908947.3	241	C	T	0.92	1	0	0	0.951525397075012	TCG	NA	NA	NA	NA	NA	NA	3.93143576033968e-05
CAMB-7A5D5	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A5D5	MN908947.3	3037	C	T	1	1	0	0	0.999012833168806	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A5E4	MN908947.3	11074	C	INS	0.019	0.039	0.0019	1.6e-08	0.0276897378790475	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.972010450573925
CAMB-7A5E4	MN908947.3	11083	G	-	0.094	0.071	1.6e-40	2.9e-30	0.0843096714909258	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.60930569545318
CAMB-7A5E4	MN908947.3	11083	G	T	0.3	0.32	2e-72	2.2e-79	0.306331619219283	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.60930569545318
CAMB-7A5E4	MN908947.3	14408	C	T	0.99	1	0	0	0.993132094094423	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000555189998354993
CAMB-7A5E4	MN908947.3	16887	C	T	0.011	0.011	1e-05	1.6e-05	0.0110041739970334	ACA	ORF1ab:helicase	Y217Y	C651T	TAC>TAT	Synonymous	ORF1ab:helicase	0.988995826002967
CAMB-7A5E4	MN908947.3	18906	T	C	0.029	0.011	2e-14	6.7e-07	0.0207547507105955	GTG	ORF1ab:3'-to-5'-exonuclease	R289R	T867C	CGT>CGC	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.979245249289404
CAMB-7A5E4	MN908947.3	20268	A	G	1	1	3.7e-69	6.9e-190	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-7A5E4	MN908947.3	22643	TG	-	0.0335	0.0165	6.2e-16;7.2e-09	7e-09;4.4e-05	0.0226280269948392	CTG	S	.	1081-1082-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.973285532554643
CAMB-7A5E4	MN908947.3	23403	A	G	1	1	0	0	0.99991769450552	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.35158555656151e-05
CAMB-7A5E4	MN908947.3	241	C	T	1	1	0	0	0.999897695593238	TCG	NA	NA	NA	NA	NA	NA	5.11522033811606e-05
CAMB-7A5E4	MN908947.3	24814	T	C	0.037	0.054	1.1e-17	5.8e-25	0.0441786806465706	ATG	S	D1084D	T3252C	GAT>GAC	Synonymous	GU280_gp02, spike glycoprotein	0.955821319353429
CAMB-7A5E4	MN908947.3	2937	C	T	1	1	0	0	1	ACA	ORF1ab:nsp3	T73I	C218T	ACA>ATA	Missense	ORF1ab:nsp3	0
CAMB-7A5E4	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A5E4	MN908947.3	3411	C	T	0.047	0.097	4.7e-22	1.3e-43	0.0702970773749338	GCT	ORF1ab:nsp3	A231V	C692T	GCT>GTT	Missense	ORF1ab:nsp3	0.929702922625066
CAMB-7A5F3	MN908947.3	10097	G	A	1	1	0	0	0.999921883137173	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	5.20779085511926e-05
CAMB-7A5F3	MN908947.3	11075	T	-	0.036	0.046	3.9e-09	1.4e-11	0.0401073294732382	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954996940168526
CAMB-7A5F3	MN908947.3	11674	C	T	0.014	0.022	8.5e-06	1.1e-07	0.0182876142975894	ACT	ORF1ab:nsp6	Y234Y	C702T	TAC>TAT	Synonymous	ORF1ab:nsp6	0.981712385702411
CAMB-7A5F3	MN908947.3	13536	C	T	1	1	0	0	0.999805985351894	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	4.8503662026483e-05
CAMB-7A5F3	MN908947.3	14408	C	T	1	1	0	0	0.998597363499521	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000832459061259864
CAMB-7A5F3	MN908947.3	16080	C	T	0.036	0.022	3.5e-17	1.7e-11	0.029650664517697	TCT	ORF1ab:RNA-dependent-RNA-polymerase	V871V	C2613T	GTC>GTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.970310961024342
CAMB-7A5F3	MN908947.3	21967	T	C	0.0076	0.0032	3.5e-05	0.0028	0.0053581772542962	TTT	S	F135F	T405C	TTT>TTC	Synonymous	GU280_gp02, spike glycoprotein	0.994641822745704
CAMB-7A5F3	MN908947.3	23403	A	G	1	1	0	0	0.998606046697436	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000518482630831867
CAMB-7A5F3	MN908947.3	23644	C	T	0.035	0.019	1.6e-16	3.5e-10	0.0273406847561227	CCT	S	A694A	C2082T	GCC>GCT	Synonymous	GU280_gp02, spike glycoprotein	0.972618015115847
CAMB-7A5F3	MN908947.3	23731	C	T	1	1	0	0	0.999959758551308	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	4.02414486921529e-05
CAMB-7A5F3	MN908947.3	24010	A	C	0.013	0.012	9.3e-08	2.3e-07	0.0124899274778405	CAT	S	S816S	A2448C	TCA>TCC	Synonymous	GU280_gp02, spike glycoprotein	0.987510072522159
CAMB-7A5F3	MN908947.3	241	C	T	1	1	0	0	0.998144592697762	TCG	NA	NA	NA	NA	NA	NA	6.45359061647924e-05
CAMB-7A5F3	MN908947.3	26533	C	T	0.0084	0.0076	1.6e-05	3e-05	0.00804520846364558	TCC	M	S4F	C11T	TCC>TTC	Missense	GU280_gp05	0.991911653689364
CAMB-7A5F3	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998910230213867	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A5F3	MN908947.3	3037	C	T	1	1	0	0	0.999489622320517	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.50629465804695e-05
CAMB-7A5F3	MN908947.3	4002	C	T	1	1	0	0	0.999859773768346	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	9.34841544358231e-05
CAMB-7A5F3	MN908947.3	8946	A	G	0.012	0.0081	1.7e-07	8.1e-06	0.0104035708930693	AAC	ORF1ab:nsp4	N131S	A392G	AAC>AGC	Missense	ORF1ab:nsp4	0.98955029353756
CAMB-7A5F3	MN908947.3	988	C	T	0.043	0.052	2.5e-20	2.2e-24	0.0471071651318927	ACA	ORF1ab:nsp2	Y61Y	C183T	TAC>TAT	Synonymous	ORF1ab:nsp2	0.952697166477113
CAMB-7A60F	MN908947.3	11074	C	INS	0.02	0.027	0.00086	2.4e-05	0.0230208093373263	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.975489518544114
CAMB-7A60F	MN908947.3	11075	T	-	0.041	0.035	3.2e-10	2.6e-09	0.0386388583973655	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.958765416155485
CAMB-7A60F	MN908947.3	11322	C	T	0.016	0.015	6e-09	1.6e-08	0.0154881994670727	GCA	ORF1ab:nsp6	A117V	C350T	GCA>GTA	Missense	ORF1ab:nsp6	0.984476113437381
CAMB-7A60F	MN908947.3	14408	C	T	1	1	0	0	0.996603194701471	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000365247881562287
CAMB-7A60F	MN908947.3	1547	A	G	0.0088	0.01	2.3e-05	6.4e-06	0.00951955972036293	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.974564926372155
CAMB-7A60F	MN908947.3	1547	A	T	0.011	0.014	1.1e-06	1.3e-07	0.0124944221329764	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.974564926372155
CAMB-7A60F	MN908947.3	23403	A	G	1	1	0	0	0.999220598998185	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.80195610641675e-05
CAMB-7A60F	MN908947.3	241	C	T	1	1	0	0	0.998649419821191	TCG	NA	NA	NA	NA	NA	NA	0.00015217804831653
CAMB-7A60F	MN908947.3	25521	C	T	0.99	1	0	0	0.993323573416561	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	6.43510995994144e-05
CAMB-7A60F	MN908947.3	26137	A	C	0.026	0.023	6.3e-06	0.00022	0.0252167060677699	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.97478329393223
CAMB-7A60F	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.02275	0.027875	0.0027;0.009;0.0012;0.0013;0.00049;0.00081;0.00061;0.0013;0.00091;0.0011;0.0017;0.00077;0.0014;9e-04;0.001;0.00094;0.0016;0.00091;0.0012;0.00095;0.00076;0.0014;0.00092;0.00036;0.00088;0.0013;0.0012;0.00079;0.0013;0.00063;0.00084;0.00058	6.6e-05;0.00023;0.00026;0.00026;8.6e-05;0.00011;8.4e-05;0.00018;9.7e-05;0.00012;0.00018;8.4e-05;0.00016;1e-04;1e-04;1e-04;0.00017;1e-04;0.00013;1e-04;8.4e-05;0.00015;9e-05;4.2e-05;9.7e-05;0.00014;0.00014;0.00013;2e-04;7.5e-05;0.00016;0.00014	0.0249938606783268	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.975394902092583
CAMB-7A60F	MN908947.3	28102	C	T	0.024	0.024	1.4e-11	2.4e-11	0.0237142857142857	CCC	ORF8	P70L	C209T	CCC>CTC	Missense	GU280_gp09	0.976
CAMB-7A60F	MN908947.3	28514	G	T	1	1	0	0	0.99810973245444	AGA	N	D81Y	G241T	GAT>TAT	Missense	GU280_gp10	4.84683986041101e-05
CAMB-7A60F	MN908947.3	28674	C	T	0.0064	0.0084	0.00025	3.4e-05	0.00713052956671814	GCA	N	A134V	C401T	GCA>GTA	Missense	GU280_gp10	0.992869470433282
CAMB-7A60F	MN908947.3	3037	C	T	1	1	0	0	0.998776384215356	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A60F	MN908947.3	3546	ATGGACCACTTAAAGTGGGTGGTAGTTGTGTTT	-	0.0175151515151515	0.00264454545454545	0.00064;0.00051;0.00044;1.1e-06;1.5e-06;6.1e-06;1.1e-06;1.6e-06;5.6e-07;5.7e-07;2.5e-07;1.6e-07;6.7e-08;2.1e-08;7.5e-08;5.7e-08;1.2e-07;6.1e-08;6.8e-08;2.6e-08;1e-07;5.2e-08;5.1e-08;1.8e-08;6.7e-08;4.8e-08;1e-07;7.9e-08;4e-08;6.8e-08;9.4e-08;2.3e-08;2.8e-08	2e-04;0.00016;6.1e-05;NA;NA;NA;0.48;0.48;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00909090909090909	AAT	ORF1ab:nsp3	.	827-859-delinframe	.	no-SNV	ORF1ab:nsp3	0.973661259375545
CAMB-7A60F	MN908947.3	9457	T	C	0.009	0.0078	8.5e-06	2.4e-05	0.00848610713262675	TTA	ORF1ab:nsp4	F301F	T903C	TTT>TTC	Synonymous	ORF1ab:nsp4	0.991513892867373
CAMB-7A61E	MN908947.3	10702	C	T	1	1	0	0	1	ACA	ORF1ab:3C-like-proteinase	D216D	C648T	GAC>GAT	Synonymous	ORF1ab:3C-like-proteinase	0
CAMB-7A61E	MN908947.3	11074	C	INS	0.043	0.18	5.9e-10	5.6e-55	0.0985707627776915	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.901118533478328
CAMB-7A61E	MN908947.3	11083	G	-	0.29	0.041	4e-138	6e-17	0.196653556429571	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-7A61E	MN908947.3	11083	G	T	0.71	0.96	7.2e-251	0	0.803146456902873	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-7A61E	MN908947.3	12672	C	T	1	1	0	0	0.999880103111324	GCT	ORF1ab:nsp8	A194V	C581T	GCT>GTT	Missense	ORF1ab:nsp8	5.99484443378694e-05
CAMB-7A61E	MN908947.3	1314	C	T	1	1	1.2e-213	3.9e-211	1	ACT	ORF1ab:nsp2	T170I	C509T	ACT>ATT	Missense	ORF1ab:nsp2	0
CAMB-7A61E	MN908947.3	14805	C	T	1	1	0	0	0.999877563513927	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00012243648607285
CAMB-7A61E	MN908947.3	17247	T	C	1	1	0	0	0.999858202958832	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000141797041168408
CAMB-7A61E	MN908947.3	23555	CCCATTGGTGCAGGTATATGCGCTAGTT	-	0.13	0.208571428571429	4.3e-11;2.2e-11;4.5e-11;9.6e-11;1.7e-12;9.3e-12;3.6e-13;5e-12;7.3e-12;6.3e-12;5.9e-12;4.1e-12;5.7e-13;5.4e-13;1.4e-14;1.1e-16;2.1e-14;1e-15;1.7e-14;3.8e-16;1.8e-14;3.3e-13;2.7e-14;3.2e-14;4.9e-22;1.4e-20;2.3e-13;1.5e-13	2.2e-17;1.1e-17;3.2e-17;1.1e-16;9e-19;2e-18;1.4e-20;7.5e-19;1.1e-18;9.2e-19;9.7e-19;8.5e-19;1.5e-20;1.9e-20;3.7e-23;1.5e-24;2.6e-22;2.3e-24;3.3e-22;2.6e-25;1.1e-22;1.1e-20;2.2e-22;2e-22;3.3e-33;2.6e-32;5.7e-21;6.7e-21	0.15022245485475	ACC	S	.	1993-2020-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.851487710219922
CAMB-7A61E	MN908947.3	27132	TA	-	0.0245	0.095	3e-06;7.4e-06	4.3e-22;1.6e-20	0.0481452249408051	CTA	M	.	610-611-delfrshift	.	no-SNV	GU280_gp05	0.952262945089344
CAMB-7A61E	MN908947.3	29572	CGTTTTCGCTTTTC	-	0.000785714285714286	0.0380714285714286	NA;NA;NA;NA;NA;NA;NA;NA;NA;0.0058;NA;NA;NA;NA	1e-07;1.3e-07;6.8e-07;5.6e-07;4.3e-07;4.4e-07;9.9e-07;1.1e-06;5.4e-07;1.5e-05;9.3e-07;3.8e-07;5.5e-07;7e-07	0.0124688279301746	ACG	ORF10	.	15-28-delfrshift	.	no-SNV	GU280_gp11	0.987468671679198
CAMB-7A61E	MN908947.3	4538	TA	-	0.16	0.043	1.3e-17;1e-17	NA;7.9e-10	0.0934244791666667	TTA	ORF1ab:nsp3	.	1819-1820-delfrshift	.	no-SNV	ORF1ab:nsp3	0.930465717981889
CAMB-7A61E	MN908947.3	4539	A	-	0.16	0.086	1e-17	7.9e-10	0.117666338905277	TAC	ORF1ab:nsp3	.	1820-1820-delfrshift	.	no-SNV	ORF1ab:nsp3	0.882005899705015
CAMB-7A62D	MN908947.3	10097	G	A	1	1	0	0	1	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0
CAMB-7A62D	MN908947.3	10623	C	T	0.41	0.3	9.19999999999999e-198	4.6e-133	0.35527027027027	ACA	ORF1ab:3C-like-proteinase	T190I	C569T	ACA>ATA	Missense	ORF1ab:3C-like-proteinase	0.64472972972973
CAMB-7A62D	MN908947.3	13536	C	T	1	1	0	0	1	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-7A62D	MN908947.3	14408	C	T	1	1	0	0	0.999361958550937	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00047262329560224
CAMB-7A62D	MN908947.3	17012	C	T	0.017	0.019	1.6e-09	3.2e-10	0.0177653393362334	TCA	ORF1ab:helicase	S259L	C776T	TCA>TTA	Missense	ORF1ab:helicase	0.982234660663767
CAMB-7A62D	MN908947.3	1931	C	INS	0.022	0.0089	5.2e-12	3e-06	0.0163670512476523	TCA	ORF1ab:nsp2	.	1125-1126-insfrshift	.	no-SNV	ORF1ab:nsp2	0.983632948752348
CAMB-7A62D	MN908947.3	23403	A	G	1	1	0	0	0.999926893103095	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.84855175237232e-05
CAMB-7A62D	MN908947.3	23476	AGGTTCT	-	0.0268571428571429	0.0351428571428571	9.5e-14;1.9e-13;2.5e-13;2e-13;7.7e-12;2.8e-11;1.5e-13	1.7e-17;3.6e-17;5.1e-17;4.8e-17;4.1e-15;2.1e-14;3.1e-17	0.0301652613827993	CAG	S	.	1914-1920-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.969237939874155
CAMB-7A62D	MN908947.3	23731	C	T	1	1	0	0	1	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-7A62D	MN908947.3	241	C	T	1	1	0	0	0.999653643668606	TCG	NA	NA	NA	NA	NA	NA	0.000173178165696869
CAMB-7A62D	MN908947.3	2636	C	T	0.028	0.014	7.7e-06	8e-04	0.0206896551724138	GCT	ORF1ab:nsp2	L611F	C1831T	CTC>TTC	Missense	ORF1ab:nsp2	0.979310344827586
CAMB-7A62D	MN908947.3	28210	A	T	1	1	0	0	0.999473911654736	GAA	ORF8	E106V	A317T	GAA>GTA	Missense	GU280_gp09	3.75777389474475e-05
CAMB-7A62D	MN908947.3	28312	C	T	0.016	0.023	8.3e-09	8.9e-12	0.0189247545951046	CCC	N	P13P	C39T	CCC>CCT	Synonymous	GU280_gp10	0.981038956326094
CAMB-7A62D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A62D	MN908947.3	3037	C	T	1	1	0	0	0.999104210212004	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A62D	MN908947.3	4002	C	T	1	1	0	0	1	ACT	ORF1ab:nsp3	T428I	C1283T	ACT>ATT	Missense	ORF1ab:nsp3	0
CAMB-7A62D	MN908947.3	5548	C	T	1	1	0	0	1	CCC	ORF1ab:nsp3	T943T	C2829T	ACC>ACT	Synonymous	ORF1ab:nsp3	0
CAMB-7A62D	MN908947.3	635	C	T	0.15	0.032	1.7e-68	5.1e-15	0.0965164190285928	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.903483580971407
CAMB-7A62D	MN908947.3	680	GATCTA	CGATCT	0.00237033333333333	0.0216666666666667	NA;NA;NA;1.1e-07;0.25;NA	1e-10;1.6e-10;9.7e-11;2.5e-18;1.4e-10;1.3e-10	0.00823370376222328	CGA	ORF1ab:leader-protein	.	415-420-mnv	.	no-SNV	ORF1ab:leader-protein	0.991535292788487
CAMB-7A62D	MN908947.3	7692	A	T	0.00067	0.033	0.0093	3.8e-14	0.0128529287821323	CAG	ORF1ab:nsp3	Q1658L	A4973T	CAG>CTG	Missense	ORF1ab:nsp3	0.987147071217868
CAMB-7A63C	MN908947.3	14408	C	T	1	1	0	0	0.999187707303865	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00040614634806742
CAMB-7A63C	MN908947.3	19201	A	G	0.0048	0.096	0.0026	4.6e-33	0.061050061050061	CAA	ORF1ab:3'-to-5'-exonuclease	N388D	A1162G	AAT>GAT	Missense	ORF1ab:3'-to-5'-exonuclease	0.938949938949939
CAMB-7A63C	MN908947.3	23403	A	G	0.91	1	0	0	0.96523381294964	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.0347122302158273
CAMB-7A63C	MN908947.3	241	C	T	1	1	0	0	0.999788494077834	TCG	NA	NA	NA	NA	NA	NA	0.000211505922165821
CAMB-7A63C	MN908947.3	28651	C	T	0.0069	0.021	5.1e-05	6.1e-11	0.0137101287073307	ACA	N	N126N	C378T	AAC>AAT	Synonymous	GU280_gp10	0.986289871292669
CAMB-7A63C	MN908947.3	28877	AG	TC	0.0275	0.019	8.9e-12;3.1e-12	5.1e-09;2.8e-09	0.0227572559366755	CAG	N	.	604-605-mnv	.	no-SNV	GU280_gp10	0.97634691195795
CAMB-7A63C	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.99930483142162	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A63C	MN908947.3	29541	C	T	0.039	0.035	2.4e-15	6.6e-13	0.0373611578593066	GCA	NA	NA	NA	NA	NA	NA	0.962638842140693
CAMB-7A63C	MN908947.3	29642	C	T	0.012	0.016	3.2e-06	3.9e-07	0.0140449438202247	ACA	ORF10	Q29*	C85T	CAA>TAA	Nonsense	GU280_gp11	0.98560393258427
CAMB-7A63C	MN908947.3	3037	C	T	0.96	1	0	0	0.974897540983607	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.0245901639344262
CAMB-7A63C	MN908947.3	9321	G	-	0.11	0.12	1.1e-20	4e-15	0.117533718689788	TGT	ORF1ab:nsp4	.	767-767-delfrshift	.	no-SNV	ORF1ab:nsp4	0.882466281310212
CAMB-7A64B	MN908947.3	11075	T	-	0.043	0.046	1.6e-10	2.3e-11	0.0442691013160812	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.948455166575972
CAMB-7A64B	MN908947.3	14408	C	T	1	1	0	0	0.996575925351168	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000350416996225508
CAMB-7A64B	MN908947.3	22346	G	T	1	1	0	0	0.99934036939314	TGC	S	A262S	G784T	GCT>TCT	Missense	GU280_gp02, spike glycoprotein	0.000659630606860158
CAMB-7A64B	MN908947.3	23403	A	G	1	1	0	0	0.998886195888337	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.13747637088108e-05
CAMB-7A64B	MN908947.3	241	C	T	1	1	0	0	0.998815783908759	TCG	NA	NA	NA	NA	NA	NA	7.04890530500613e-05
CAMB-7A64B	MN908947.3	271	G	T	1	1	0	0	0.999779958632223	AGA	ORF1ab:leader-protein	E2D	G6T	GAG>GAT	Missense	ORF1ab:leader-protein	0.000110020683888571
CAMB-7A64B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999553813302738	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	6.99325151229064e-05
CAMB-7A64B	MN908947.3	29035	T	C	0.05	0.052	1.6e-16	2.7e-17	0.0510799489306026	CTT	N	A254A	T762C	GCT>GCC	Synonymous	GU280_gp10	0.948497989933842
CAMB-7A64B	MN908947.3	3037	C	T	1	1	0	0	0.999242953645469	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A64B	MN908947.3	703	C	T	0.0085	0.01	1.3e-05	2e-06	0.0092367052851353	GCG	ORF1ab:leader-protein	G146G	C438T	GGC>GGT	Synonymous	ORF1ab:leader-protein	0.990707004544152
CAMB-7A65A	MN908947.3	11075	T	-	0.026	0.039	5.5e-07	9.3e-10	0.0323088384977807	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.965214745170463
CAMB-7A65A	MN908947.3	14408	C	T	1	1	0	0	0.998028451299479	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000250528287911465
CAMB-7A65A	MN908947.3	173	CG	TC	0.0015	0.00815	0.0016;NA	1.6e-05;7.6e-06	0.00470984598459846	TCG	NA	NA	NA	NA	NA	NA	0.994736386460047
CAMB-7A65A	MN908947.3	19869	T	-	0.012	0.0074	4.7e-07	3.1e-05	0.0105802277781522	CTG	ORF1ab:endoRNAse	.	249-249-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.989150212278455
CAMB-7A65A	MN908947.3	19869	TG	-	0.0115	0.0037	4.7e-07;8e-07	3.1e-05;NA	0.00957546538100978	CTG	ORF1ab:endoRNAse	.	249-250-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.989150212278455
CAMB-7A65A	MN908947.3	20268	A	G	1	1	6.2e-207	2.9e-66	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-7A65A	MN908947.3	20857	G	T	0.0032	0.0078	0.0017	1.3e-05	0.0050942361532023	AGT	ORF1ab:2'-O-ribose-methyltransferase	V67F	G199T	GTT>TTT	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.994891332582908
CAMB-7A65A	MN908947.3	22948	ACCTTT	-	0.00865	0.00193333333333333	0.00021;0.00088;0.00044;5.7e-08;1.7e-07;0.00065	NA;NA;NA;0.0023;0.00041;NA	0.00265076209410205	AAC	S	.	1386-1391-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.99657743552133
CAMB-7A65A	MN908947.3	23403	A	G	1	1	0	0	0.999920827197441	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.3338242047092e-05
CAMB-7A65A	MN908947.3	241	C	T	1	1	0	0	0.999699322591486	TCG	NA	NA	NA	NA	NA	NA	0.000123808344682432
CAMB-7A65A	MN908947.3	25872	C	-	0.011	0.00051	9.5e-07	0.0055	0.00678516819571865	ACA	ORF3a	.	480-480-delfrshift	.	no-SNV	GU280_gp03	0.993214831804281
CAMB-7A65A	MN908947.3	28854	C	T	1	1	0	0	0.999348806921252	TCA	N	S194L	C581T	TCA>TTA	Missense	GU280_gp10	0
CAMB-7A65A	MN908947.3	29201	AGCGCTTCAGCG	-	0.00236425	0.00609166666666667	NA;NA;NA;NA;NA;0.0057;0.00077;0.0015;0.0012;0.0016;0.00093;0.0017	0.00022;0.00036;0.00097;0.00029;0.00015;3.5e-05;6.4e-06;0.00022;0.00016;0.00021;0.00013;0.00017	0.00492576540824674	CAG	N	.	928-939-delinframe	.	no-SNV	GU280_gp10	0.996743137325078
CAMB-7A65A	MN908947.3	3037	C	T	1	1	0	0	0.999197382231277	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A65A	MN908947.3	3770	G	T	0.011	0.004	9.9e-06	0.0037	0.00771971496437055	TGT	ORF1ab:nsp3	V351F	G1051T	GTT>TTT	Missense	ORF1ab:nsp3	0.989608076009501
CAMB-7A65A	MN908947.3	7798	G	T	1	1	0	0	0.999921911603936	AGA	ORF1ab:nsp3	K1693N	G5079T	AAG>AAT	Missense	ORF1ab:nsp3	7.80883960643448e-05
CAMB-7A65A	MN908947.3	8965	A	-	0.0064	0.015	0.00031	4.2e-08	0.01041040288635	CAA	ORF1ab:nsp4	.	411-411-delfrshift	.	no-SNV	ORF1ab:nsp4	0.989420475045099
CAMB-7A65A	MN908947.3	9180	C	T	0.03	0.009	2e-14	8.9e-06	0.0205717712914834	TCT	ORF1ab:nsp4	S209F	C626T	TCT>TTT	Missense	ORF1ab:nsp4	0.97936825269892
CAMB-7A669	MN908947.3	11075	T	-	0.041	0.039	1.6e-10	2.9e-10	0.040396881644224	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954888608141004
CAMB-7A669	MN908947.3	13730	C	T	1	1	0	0	0.996387450291316	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A88V	C263T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000115601590677888
CAMB-7A669	MN908947.3	14358	C	T	0.068	0.068	4.9e-31	2.8e-31	0.067880226882997	GCA	ORF1ab:RNA-dependent-RNA-polymerase	C297C	C891T	TGC>TGT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.931921910038254
CAMB-7A669	MN908947.3	14408	C	T	1	1	0	0	0.9970187172707	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000388862964691243
CAMB-7A669	MN908947.3	18392	T	C	0.0087	0.008	5.9e-06	8.1e-06	0.00839150341514674	GTT	ORF1ab:3'-to-5'-exonuclease	V118A	T353C	GTT>GCT	Missense	ORF1ab:3'-to-5'-exonuclease	0.990902949786084
CAMB-7A669	MN908947.3	21890	T	C	0.066	0.062	3.6e-29	1.7e-27	0.0642001691821379	TTT	S	L110L	T328C	TTA>CTA	Synonymous	GU280_gp02, spike glycoprotein	0.933573750055652
CAMB-7A669	MN908947.3	23403	A	G	1	1	0	0	0.999402103847088	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000130789783449487
CAMB-7A669	MN908947.3	241	C	T	1	1	0	0	0.998435304173971	TCG	NA	NA	NA	NA	NA	NA	0.000173855091781001
CAMB-7A669	MN908947.3	25096	C	T	0.0086	0.0089	1.3e-05	7.6e-06	0.00870091330778761	ACA	S	N1178N	C3534T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.991299086692212
CAMB-7A669	MN908947.3	25429	G	T	1	1	0	0	0.99774332980367	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0.000104154009061399
CAMB-7A669	MN908947.3	26785	TAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0298125	0.02896875	5.5e-05;0.00026;9.1e-05;9.3e-05;2.3e-05;4.3e-05;3.6e-05;8.4e-05;5e-05;6.2e-05;0.00011;4.9e-05;9e-05;5.4e-05;5.6e-05;4.5e-05;9.6e-05;5.4e-05;7.1e-05;5.6e-05;3.8e-05;8.1e-05;4.9e-05;2e-05;5e-05;8.3e-05;8e-05;3.8e-05;8.6e-05;3.4e-05;5.7e-05;3.8e-05	0.00011;0.00038;1e-04;1e-04;3.4e-05;5.8e-05;4.7e-05;8.6e-05;6.1e-05;7.1e-05;0.00011;6.2e-05;9.8e-05;7.1e-05;6.3e-05;5.9e-05;0.00011;6.3e-05;8.6e-05;6.4e-05;4.9e-05;9.5e-05;5.7e-05;5.3e-05;5.7e-05;9.4e-05;7.7e-05;4.7e-05;9.6e-05;3.7e-05;5.4e-05;4.2e-05	0.0292797218653163	GTA	M	.	263-294-delfrshift	.	no-SNV	GU280_gp05	0.970352995462586
CAMB-7A669	MN908947.3	28900	A	G	0.0081	0.0066	2.1e-05	7.7e-05	0.00744228432563791	GAA	N	R209R	A627G	AGA>AGG	Synonymous	GU280_gp10	0.991190765492102
CAMB-7A669	MN908947.3	29400	C	T	0.025	0.032	1.7e-11	7.7e-13	0.0265594172105024	GCT	N	A376V	C1127T	GCT>GTT	Missense	GU280_gp10	0.973288814691152
CAMB-7A669	MN908947.3	3037	C	T	1	1	0	0	0.999097258516653	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	2.37563548249157e-05
CAMB-7A669	MN908947.3	4160	G	T	0.053	0.055	1.6e-24	2.4e-25	0.0539486448496367	TGT	ORF1ab:nsp3	V481L	G1441T	GTG>TTG	Missense	ORF1ab:nsp3	0.943636039674526
CAMB-7A669	MN908947.3	7488	C	T	0.006	0.0079	0.00016	1.9e-05	0.00668864210964253	ACT	ORF1ab:nsp3	T1590I	C4769T	ACT>ATT	Missense	ORF1ab:nsp3	0.993183345601178
CAMB-7A669	MN908947.3	7764	C	T	0.039	0.036	4.1e-11	1.9e-10	0.0383561643835616	TCC	ORF1ab:nsp3	S1682F	C5045T	TCC>TTC	Missense	ORF1ab:nsp3	0.961095890410959
CAMB-7A678	MN908947.3	10046	G	-	0.011	0.0048	6.7e-06	0.0025	0.00840234296101798	TGT	ORF1ab:nsp4	.	1492-1492-delfrshift	.	no-SNV	ORF1ab:nsp4	0.991436073520501
CAMB-7A678	MN908947.3	104	TG	-	0.01	0.00355	6.7e-05;3.5e-06	NA;0.00038	0.00746220546046482	CTG	NA	NA	NA	NA	NA	NA	0.995666482030563
CAMB-7A678	MN908947.3	11074	C	INS	0.033	0.027	7.4e-08	1.7e-05	0.0304969879518072	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.969282301620274
CAMB-7A678	MN908947.3	11075	T	-	0.036	0.027	4.8e-09	2.7e-07	0.0319609257195306	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.96779868441181
CAMB-7A678	MN908947.3	1134	AG	-	0.0042	0.00535	0.0016;0.00015	5e-04;3.6e-05	0.00478186116483989	AAG	ORF1ab:nsp2	.	329-330-delfrshift	.	no-SNV	ORF1ab:nsp2	0.996526772793054
CAMB-7A678	MN908947.3	119	C	T	0.0086	0.022	7.2e-06	1.1e-11	0.0140459224069675	ACT	NA	NA	NA	NA	NA	NA	0.985954077593032
CAMB-7A678	MN908947.3	12543	CAG	-	0.00346666666666667	0.00583333333333333	0.00096;0.00088;0.00088	0.00071;2.5e-05;2.4e-05	0.00497783743725268	TCA	ORF1ab:nsp8	.	452-454-delinframe	.	no-SNV	ORF1ab:nsp8	0.996518279035066
CAMB-7A678	MN908947.3	13004	G	C	0.0077	0.003	4.4e-05	0.005	0.00571905003843097	AGC	ORF1ab:nsp9	A107P	G319C	GCT>CCT	Missense	ORF1ab:nsp9	0.991362801422597
CAMB-7A678	MN908947.3	13730	C	T	0.99	1	0	0	0.992908748349578	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A88V	C263T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	7.41762724939546e-05
CAMB-7A678	MN908947.3	13891	TG	-	0.00785	0.00465	1.5e-05;2.4e-05	0.00048;0.00067	0.00640592885968465	TTG	ORF1ab:RNA-dependent-RNA-polymerase	.	424-425-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.991140473725872
CAMB-7A678	MN908947.3	14265	C	T	0.48	0.52	5.3e-281	1.5e-307	0.497368287317686	TCA	ORF1ab:RNA-dependent-RNA-polymerase	F266F	C798T	TTC>TTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.502602673094096
CAMB-7A678	MN908947.3	14342	G	-	0.007	0.0054	2.9e-05	0.00013	0.0063484137881841	TGT	ORF1ab:RNA-dependent-RNA-polymerase	.	875-875-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.993508925227812
CAMB-7A678	MN908947.3	14408	C	T	1	1	0	0	0.997198156682028	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000313364055299539
CAMB-7A678	MN908947.3	14452	GT	-	0.002034	0.00975	0.001;0.053	3.1e-08;6.3e-05	0.00545215960966234	TGT	ORF1ab:RNA-dependent-RNA-polymerase	.	985-986-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.991606459838504
CAMB-7A678	MN908947.3	14463	AG	-	0.00815	0.00515	2e-05;2.4e-05	0.00045;0.00045	0.00688905639209774	TAG	ORF1ab:RNA-dependent-RNA-polymerase	.	996-997-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.992854349603612
CAMB-7A678	MN908947.3	15101	C	-	0.0067	0.0096	3.7e-05	2.4e-06	0.00788265815206546	GCT	ORF1ab:RNA-dependent-RNA-polymerase	.	1634-1634-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.992117341847935
CAMB-7A678	MN908947.3	15400	AG	-	0.011	0.00265	7.5e-07;1.3e-06	0.006;0.0071	0.00756422674230893	TAG	ORF1ab:RNA-dependent-RNA-polymerase	.	1933-1934-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.992133749735835
CAMB-7A678	MN908947.3	15973	GAT	-	0.00953333333333333	0.0036	3.5e-05;1.3e-05;6.6e-05	0.006;0.004;0.0067	0.00682949415441602	AGA	ORF1ab:RNA-dependent-RNA-polymerase	.	2506-2508-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.993127098043755
CAMB-7A678	MN908947.3	16319	AATGCTG	-	0.00848571428571429	0.0101857142857143	0.00036;0.00034;1.1e-05;1.5e-05;1.1e-05;6.4e-05;0.00016	0.00075;0.00075;9e-04;7.4e-05;0.0011;1.2e-09;4.1e-09	0.00726032190342897	AAA	ORF1ab:helicase	.	83-89-delfrshift	.	no-SNV	ORF1ab:helicase	0.993759044862518
CAMB-7A678	MN908947.3	1709	G	T	0.0044	0.0075	0.00079	2.9e-05	0.00566306703899705	TGC	ORF1ab:nsp2	A302S	G904T	GCT>TCT	Missense	ORF1ab:nsp2	0.992130289597532
CAMB-7A678	MN908947.3	172	TCG	-	0.00913333333333333	0.014	2.5e-06;7.9e-06;2e-05	7.3e-09;7e-08;2.3e-07	0.0106304857152848	CTC	NA	NA	NA	NA	NA	NA	0.987601219684578
CAMB-7A678	MN908947.3	1781	TGTG	-	0.00935	0.008	0.00065;7.4e-07;1.8e-05;3e-07	NA;4.2e-06;1.3e-06;8.8e-07	0.0099959855479727	CTG	ORF1ab:nsp2	.	976-979-delfrshift	.	no-SNV	ORF1ab:nsp2	0.994820898433268
CAMB-7A678	MN908947.3	18077	AG	-	0.0062	0.01085	0.0016;0.00015	0.00097;1.2e-07	0.00813161875945537	AAG	ORF1ab:3'-to-5'-exonuclease	.	38-39-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.995487169639214
CAMB-7A678	MN908947.3	18122	G	-	0.0043	0.008	0.001	2.2e-05	0.00586744273375892	AGT	ORF1ab:3'-to-5'-exonuclease	.	83-83-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.994062147953436
CAMB-7A678	MN908947.3	18461	CG	-	0.0032	0.00655	NA;4.2e-05	3.3e-05;3.8e-05	0.00481701903791142	CCG	ORF1ab:3'-to-5'-exonuclease	.	422-423-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.996539620517236
CAMB-7A678	MN908947.3	18462	G	-	0.0064	0.0065	4.2e-05	3.8e-05	0.00646520056815399	CGC	ORF1ab:3'-to-5'-exonuclease	.	423-423-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.990089957714976
CAMB-7A678	MN908947.3	18546	G	-	0.0074	0.0072	3.2e-05	4e-05	0.00731603706792114	TGT	ORF1ab:3'-to-5'-exonuclease	.	507-507-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.99265249610598
CAMB-7A678	MN908947.3	18895	TTTG	-	0.0185	0.0107	8.5e-07;7.8e-11;5.7e-08;7.9e-08	0.00023;0.00024;8.2e-05;3.9e-08	0.015564790328674	CTT	ORF1ab:3'-to-5'-exonuclease	.	856-859-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.990332027332415
CAMB-7A678	MN908947.3	19230	TG	-	0.0047	0.016	0.0073;0.013	3.8e-06;1.4e-05	0.0104305043050431	TTG	ORF1ab:3'-to-5'-exonuclease	.	1191-1192-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.989320077761646
CAMB-7A678	MN908947.3	19645	G	-	0.012	0.0034	1.1e-06	0.0097	0.0102915951972556	TGT	ORF1ab:endoRNAse	.	25-25-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.985334476843911
CAMB-7A678	MN908947.3	2162	G	-	0.0089	0.0044	2.9e-05	0.0028	0.00653890442506991	AGA	ORF1ab:nsp2	.	1357-1357-delfrshift	.	no-SNV	ORF1ab:nsp2	0.99346109557493
CAMB-7A678	MN908947.3	21722	TTG	-	0.00426666666666667	0.0181333333333333	NA;0.0024;0.0039	1.4e-05;1.4e-08;8e-08	0.0127641317172584	CTT	S	.	160-162-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.996602766318855
CAMB-7A678	MN908947.3	22103	GG	-	0.01	0.019	0.0011;0.00051	1.4e-05;4.7e-06	0.0126624737945493	AGG	S	.	541-542-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.98476430976431
CAMB-7A678	MN908947.3	22643	T	-	0.011	0.0072	8.1e-06	4e-04	0.00985655196691015	CTG	S	.	1081-1081-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.989879433248262
CAMB-7A678	MN908947.3	23331	G	T	0.0051	0.0093	0.0021	3.2e-05	0.00711156144745607	TGT	S	C590F	G1769T	TGT>TTT	Missense	GU280_gp02, spike glycoprotein	0.989360803850376
CAMB-7A678	MN908947.3	23403	A	G	1	1	0	0	0.999930755714817	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.19332138869414e-05
CAMB-7A678	MN908947.3	23559	TTGGTGCAGGTATATGCGCTAGTT	-	0.0392083333333333	0.00750416666666667	0.00057;0.00096;0.00019;0.00035;0.00039;4e-04;0.00036;0.00033;0.00023;2e-04;1.5e-05;2.1e-06;8.8e-05;4e-05;8.2e-05;3.5e-05;8.9e-05;0.00018;0.00011;1e-04;1.5e-06;2.8e-05;0.00047;0.00037	NA;NA;0.17;0.18;0.18;0.18;0.18;0.17;0.18;0.17;0.18;0.12;0.16;0.17;0.16;0.16;0.18;0.18;0.18;0.17;0.0084;0.0096;0.15;0.13	0.02559990496555	ATT	S	.	1997-2020-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.974555703436937
CAMB-7A678	MN908947.3	23666	G	-	0.021	0.0094	8.3e-07	6e-04	0.0162408759124088	AGA	S	.	2104-2104-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.983637469586375
CAMB-7A678	MN908947.3	23868	G	A	0.007	0.0072	4.7e-05	3.7e-05	0.00704268479392492	GGA	S	G769E	G2306A	GGA>GAA	Missense	GU280_gp02, spike glycoprotein	0.992957315206075
CAMB-7A678	MN908947.3	241	C	T	1	0.99	0	0	0.997774834437086	TCG	NA	NA	NA	NA	NA	NA	7.06401766004415e-05
CAMB-7A678	MN908947.3	24350	G	C	0.012	0.0073	3.9e-07	3.4e-05	0.0103562702840681	TGC	S	A930P	G2788C	GCT>CCT	Missense	GU280_gp02, spike glycoprotein	0.987565182511031
CAMB-7A678	MN908947.3	24382	CACAG	-	0.0042718	0.0088	NA;NA;4.7e-05;2.5e-05;3.9e-05	6.7e-06;3.9e-06;7e-06;2.8e-06;5.5e-06	0.00762452796259666	CCA	S	.	2820-2824-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.996701159802764
CAMB-7A678	MN908947.3	25264	TTGCTGTATGACCAG	-	0.00111333333333333	0.0109866666666667	NA;NA;NA;NA;0.00012;1.4e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA	5.3e-05;8.4e-07;0.00025;3.5e-08;2.8e-05;1.2e-06;9.9e-05;5.7e-08;6.6e-07;0.00011;3.2e-07;9.8e-06;0.00043;1e-06;5.9e-05	0.00331568533076635	TTT	S	.	3702-3716-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.996823282266742
CAMB-7A678	MN908947.3	25301	T	-	0.017	0.008	1.1e-07	0.00017	0.0142160659771267	CTG	S	.	3739-3739-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.985328290882581
CAMB-7A678	MN908947.3	25318	CTG	-	0.0053	0.00613333333333333	0.00013;0.00014;0.00021	4.1e-05;4.5e-05;7.5e-05	0.00569274475524476	CCT	S	.	3756-3758-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.994205053630589
CAMB-7A678	MN908947.3	25429	G	T	1	1	0	0	0.999837998963193	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	8.10005184033178e-05
CAMB-7A678	MN908947.3	25927	A	G	0.0086	0.0019	3.6e-06	0.0039	0.00666594989786044	TAT	ORF3a	I179V	A535G	ATT>GTT	Missense	GU280_gp03	0.99268895817654
CAMB-7A678	MN908947.3	25946	AG	-	0.0087	0.00965	2.6e-05;5.3e-05	2e-05;3.9e-05	0.00896906177567268	CAG	ORF3a	.	554-555-delfrshift	.	no-SNV	GU280_gp03	0.990177439797212
CAMB-7A678	MN908947.3	26192	CGA	-	0.011	0.0079	4.7e-06;6.1e-06;4.4e-06	0.00012;0.00013;1e-04	0.00969162995594714	CCG	ORF3a	.	800-802-delinframe	.	no-SNV	GU280_gp03	0.989867841409692
CAMB-7A678	MN908947.3	26239	G	-	0.0069	0.00091	1.4e-05	0.0068	0.00497449517305341	CGA	NA	NA	NA	NA	NA	NA	0.994266683529362
CAMB-7A678	MN908947.3	26620	G	T	0.0086	0.0034	1.6e-05	0.0032	0.00635193784717389	TGT	M	C33F	G98T	TGT>TTT	Missense	GU280_gp05	0.993610102364895
CAMB-7A678	MN908947.3	26787	GGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0300645161290323	0.0215806451612903	9.6e-05;9.3e-05;2.5e-05;5.7e-05;5.2e-05;9e-05;6.7e-05;8e-05;0.00013;5.8e-05;0.00011;6.7e-05;1.3e-05;1e-05;0.00012;6.6e-05;8.7e-05;6.5e-05;4.3e-05;9.3e-05;5.9e-05;1.4e-05;6.3e-05;1e-04;9e-05;4.6e-05;1e-04;3.4e-05;5.7e-05;3.9e-05;0.00039	0.0017;0.0017;0.00087;0.0011;0.00093;0.0017;0.0013;0.0015;0.0021;0.0012;0.0019;0.0015;0.0014;0.0012;0.0021;0.0014;0.0016;0.0014;0.0011;0.0018;0.0013;0.00086;0.0013;0.0018;0.0017;0.0011;0.0018;0.00096;0.0012;0.00098;0.086	0.0259772824151852	AGG	M	.	265-295-delfrshift	.	no-SNV	GU280_gp05	0.974653759875158
CAMB-7A678	MN908947.3	26849	G	-	0.0045	0.0094	0.0015	1e-05	0.00657396001137117	TGT	M	.	327-327-delfrshift	.	no-SNV	GU280_gp05	0.993366815123662
CAMB-7A678	MN908947.3	28116	G	-	0.0078	0.0051	9.8e-06	0.00013	0.00650561651559179	CGA	ORF8	.	223-223-delfrshift	.	no-SNV	GU280_gp09	0.991802923190354
CAMB-7A678	MN908947.3	29121	AA	-	0.00985	0.003418	7.8e-06;1.5e-06	NA;4e-05	0.00686531585220501	CAA	N	.	848-849-delfrshift	.	no-SNV	GU280_gp10	0.994819326025173
CAMB-7A678	MN908947.3	29122	AGG	-	0.00633333333333333	0.0066	1.5e-06;0.0019;0.0016	4e-05;0.00013;0.00012	0.00525107164727495	AAG	N	.	849-851-delinframe	.	no-SNV	GU280_gp10	0.990835965335366
CAMB-7A678	MN908947.3	29395	G	INS	0.0019	0.02	0.0044	4.2e-06	0.00430570505920344	AGA	N	.	1121-1122-insfrshift	.	no-SNV	GU280_gp10	0.995694294940797
CAMB-7A678	MN908947.3	3037	C	T	1	1	0	0	0.999783783783784	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000144144144144144
CAMB-7A678	MN908947.3	3997	AG	-	0.007	0.0048	0.00029;1.2e-05	0.00057;3e-04	0.00622441306708998	AAG	ORF1ab:nsp3	.	1278-1279-delfrshift	.	no-SNV	ORF1ab:nsp3	0.994651959555444
CAMB-7A678	MN908947.3	4508	GTG	-	0.00313333333333333	0.00786666666666667	0.0022;NA;4e-04	2.3e-05;2.1e-05;5.2e-05	0.00531812955155232	TGT	ORF1ab:nsp3	.	1789-1791-delinframe	.	no-SNV	ORF1ab:nsp3	0.994780523358334
CAMB-7A678	MN908947.3	4903	AG	-	0.0033	0.00725	0.0017;0.0016	2.7e-05;2.6e-05	0.00497770924814802	TAG	ORF1ab:nsp3	.	2184-2185-delfrshift	.	no-SNV	ORF1ab:nsp3	0.994904931419027
CAMB-7A678	MN908947.3	5225	AA	-	0.017	0.0145	6.4e-06;7.8e-05	0.0028;0.00045	0.01620029455081	TAA	ORF1ab:nsp3	.	2506-2507-delfrshift	.	no-SNV	ORF1ab:nsp3	0.980113636363636
CAMB-7A678	MN908947.3	5226	AAA	-	0.00433333333333333	0.0156666666666667	7.8e-05;NA;NA	0.00045;3.7e-05;1.8e-05	0.0046583850931677	AAA	ORF1ab:nsp3	.	2507-2509-delinframe	.	no-SNV	ORF1ab:nsp3	0.986238532110092
CAMB-7A678	MN908947.3	5373	G	-	0.0032	0.0086	0.0023	1.8e-05	0.00556153570147112	AGG	ORF1ab:nsp3	.	2654-2654-delfrshift	.	no-SNV	ORF1ab:nsp3	0.994079655543595
CAMB-7A678	MN908947.3	5655	TAG	-	0.00373333333333333	0.00863333333333333	0.00093;0.0015;0.0015	5.7e-06;1e-05;1e-05	0.00570215497025499	CTA	ORF1ab:nsp3	.	2936-2938-delinframe	.	no-SNV	ORF1ab:nsp3	0.994004098464341
CAMB-7A678	MN908947.3	578	G	T	0.14	0.12	6.3e-67	1.3e-56	0.135386645369631	TGG	ORF1ab:leader-protein	G105C	G313T	GGT>TGT	Missense	ORF1ab:leader-protein	0.86232160838918
CAMB-7A678	MN908947.3	594	ATG	-	0.00293333333333333	0.00563333333333333	0.47;0.0013;0.00028	0.00033;0.00038;2e-05	0.0036015756893641	CAT	ORF1ab:leader-protein	.	329-331-delinframe	.	no-SNV	ORF1ab:leader-protein	0.997952260786828
CAMB-7A678	MN908947.3	6011	C	T	0.068	0.053	7.3e-28	4.9e-21	0.0620847176079734	ACC	ORF1ab:nsp3	P1098S	C3292T	CCA>TCA	Missense	ORF1ab:nsp3	0.937915282392027
CAMB-7A678	MN908947.3	7093	C	T	0.027	0.028	1e-05	2.8e-05	0.0276073619631902	TCA	ORF1ab:nsp3	V1458V	C4374T	GTC>GTT	Synonymous	ORF1ab:nsp3	0.97239263803681
CAMB-7A678	MN908947.3	7093	CACT	TCAC	0.02825	0.02725	1e-05;5.9e-06;7.5e-06;7.3e-06	2.8e-05;0.00017;2e-05;2.1e-05	0.0286624203821656	TCA	ORF1ab:nsp3	.	4374-4377-mnv	.	no-SNV	ORF1ab:nsp3	0.97239263803681
CAMB-7A678	MN908947.3	7100	G	T	0.028	0.03	8.2e-06	2.2e-05	0.029126213592233	TGC	ORF1ab:nsp3	A1461S	G4381T	GCA>TCA	Missense	ORF1ab:nsp3	0.970873786407767
CAMB-7A678	MN908947.3	7102	A	C	0.021	0.028	5.4e-05	1.9e-05	0.0243161094224924	CAA	ORF1ab:nsp3	A1461A	A4383C	GCA>GCC	Synonymous	ORF1ab:nsp3	0.972644376899696
CAMB-7A678	MN908947.3	7104	C	A	0.028	0.023	6.9e-06	0.00016	0.0258899676375405	ACC	ORF1ab:nsp3	T1462N	C4385A	ACC>AAC	Missense	ORF1ab:nsp3	0.97411003236246
CAMB-7A678	MN908947.3	7106	TACT	CTAC	0.0235	0.0305	6.9e-05;7.5e-05;6.7e-06;6.4e-05	2.2e-05;2.5e-05;1.5e-05;1.7e-05	0.0255591054313099	CTA	ORF1ab:nsp3	.	4387-4390-mnv	.	no-SNV	ORF1ab:nsp3	0.974603174603175
CAMB-7A678	MN908947.3	7111	TA	GT	0.022	0.029	5.4e-05;7.5e-05	1.9e-05;2.7e-05	0.0248447204968944	GTA	ORF1ab:nsp3	.	4392-4393-mnv	.	no-SNV	ORF1ab:nsp3	0.975384615384615
CAMB-7A678	MN908947.3	7114	TG	CT	0.025	0.029	6.2e-05;9.9e-06	2.5e-05;2.5e-05	0.0252365930599369	CTG	ORF1ab:nsp3	.	4395-4396-mnv	.	no-SNV	ORF1ab:nsp3	0.974522292993631
CAMB-7A678	MN908947.3	7115	G	T	0.027	0.029	9.9e-06	2.5e-05	0.0282131661442006	TGG	ORF1ab:nsp3	G1466C	G4396T	GGT>TGT	Missense	ORF1ab:nsp3	0.971786833855799
CAMB-7A678	MN908947.3	7117	T	G	0.024	0.015	4.2e-05	0.0017	0.0198675496688742	GTT	ORF1ab:nsp3	G1466G	T4398G	GGT>GGG	Synonymous	ORF1ab:nsp3	0.980132450331126
CAMB-7A678	MN908947.3	7119	C	T	0.029	0.029	1.8e-05	5.3e-05	0.0289389067524116	TCT	ORF1ab:nsp3	S1467F	C4400T	TCT>TTT	Missense	ORF1ab:nsp3	0.971061093247588
CAMB-7A678	MN908947.3	7120	T	C	0.023	0.031	5.5e-05	1.7e-05	0.0260586319218241	CTA	ORF1ab:nsp3	S1467S	T4401C	TCT>TCC	Synonymous	ORF1ab:nsp3	0.973941368078176
CAMB-7A678	MN908947.3	7121	ATA	TAT	0.028	0.0273333333333333	6.8e-06;6.5e-06;6.8e-06	0.00016;1.8e-05;1.9e-05	0.0287539936102236	TAT	ORF1ab:nsp3	.	4402-4404-mnv	.	no-SNV	ORF1ab:nsp3	0.97444089456869
CAMB-7A678	MN908947.3	7126	T	C	0.028	0.038	3.8e-05	1.1e-05	0.032258064516129	CTT	ORF1ab:nsp3	P1469P	T4407C	CCT>CCC	Synonymous	ORF1ab:nsp3	0.967741935483871
CAMB-7A678	MN908947.3	7128	G	T	0.023	0.023	3.6e-05	0.00013	0.0228013029315961	TGT	ORF1ab:nsp3	C1470F	G4409T	TGT>TTT	Missense	ORF1ab:nsp3	0.977198697068404
CAMB-7A678	MN908947.3	7129	T	G	0.026	0.033	5e-05	2.2e-05	0.0290909090909091	GTA	ORF1ab:nsp3	C1470W	T4410G	TGT>TGG	Missense	ORF1ab:nsp3	0.970909090909091
CAMB-7A678	MN908947.3	7130	A	T	0.025	0.026	3.8e-05	0.00012	0.0251798561151079	TAG	ORF1ab:nsp3	S1471C	A4411T	AGT>TGT	Missense	ORF1ab:nsp3	0.974820143884892
CAMB-7A678	MN908947.3	7132	T	G	0.03	0.033	8.9e-06	2.1e-05	0.0316901408450704	GTG	ORF1ab:nsp3	S1471R	T4413G	AGT>AGG	Missense	ORF1ab:nsp3	0.96830985915493
CAMB-7A678	MN908947.3	7134	T	G	0.025	0.034	7.5e-05	2.5e-05	0.0291970802919708	GTT	ORF1ab:nsp3	V1472G	T4415G	GTT>GGT	Missense	ORF1ab:nsp3	0.970802919708029
CAMB-7A678	MN908947.3	7137	GTC	TGT	0.0223333333333333	0.0323333333333333	5e-05;0.00034;2.9e-05	1.6e-05;1.5e-05;1.1e-05	0.0282685512367491	TGT	ORF1ab:nsp3	.	4418-4420-mnv	.	no-SNV	ORF1ab:nsp3	0.97427652733119
CAMB-7A678	MN908947.3	7139	CT	TC	0.0265	0.026	2.9e-05;3.3e-05	1.1e-05;0.0016	0.026615969581749	TCT	ORF1ab:nsp3	.	4420-4421-mnv	.	no-SNV	ORF1ab:nsp3	0.970149253731343
CAMB-7A678	MN908947.3	7142	A	T	0.025	0.018	3.7e-05	0.0014	0.021978021978022	TAG	ORF1ab:nsp3	S1475C	A4423T	AGT>TGT	Missense	ORF1ab:nsp3	0.978021978021978
CAMB-7A678	MN908947.3	7144	T	G	0.018	0.032	0.00038	1.6e-05	0.0238907849829352	GTG	ORF1ab:nsp3	S1475R	T4425G	AGT>AGG	Missense	ORF1ab:nsp3	0.976109215017065
CAMB-7A678	MN908947.3	7145	GGT	TTG	0.0256666666666667	0.0193333333333333	4.2e-05;5.3e-06;1e-05	0.00016;NA;1.9e-05	0.0226537216828479	TGG	ORF1ab:nsp3	.	4426-4428-mnv	.	no-SNV	ORF1ab:nsp3	0.97741935483871
CAMB-7A678	MN908947.3	7147	T	G	0.031	0.036	1e-05	1.9e-05	0.033210332103321	GTT	ORF1ab:nsp3	G1476G	T4428G	GGT>GGG	Synonymous	ORF1ab:nsp3	0.966789667896679
CAMB-7A678	MN908947.3	7151	G	A	0.03	0.032	4.9e-06	1.3e-05	0.0307167235494881	AGA	ORF1ab:nsp3	D1478N	G4432A	GAT>AAT	Missense	ORF1ab:nsp3	0.969283276450512
CAMB-7A678	MN908947.3	7151	GAT	AGA	0.0306666666666667	0.0296666666666667	4.9e-06;5.3e-06;3.7e-06	1.3e-05;0.00015;1.1e-05	0.0307167235494881	AGA	ORF1ab:nsp3	.	4432-4434-mnv	.	no-SNV	ORF1ab:nsp3	0.969283276450512
CAMB-7A678	MN908947.3	7153	T	A	0.033	0.034	3.7e-06	1.1e-05	0.033457249070632	ATT	ORF1ab:nsp3	D1478E	T4434A	GAT>GAA	Missense	ORF1ab:nsp3	0.966542750929368
CAMB-7A678	MN908947.3	7155	CT	TC	0.0215	0.0315	0.00035;4.9e-05	1.5e-05;2.1e-05	0.0241379310344828	TCT	ORF1ab:nsp3	.	4436-4437-mnv	.	no-SNV	ORF1ab:nsp3	0.975945017182131
CAMB-7A678	MN908947.3	7159	AGA	TAG	0.0313333333333333	0.03	6.7e-06;3.6e-06;4.2e-06	1.9e-05;1.2e-05;0.00013	0.033210332103321	TAG	ORF1ab:nsp3	.	4440-4442-mnv	.	no-SNV	ORF1ab:nsp3	0.970684039087948
CAMB-7A678	MN908947.3	7163	AC	CA	0.03	0.03	5.9e-06;4.2e-06	2e-05;1.6e-05	0.0301003344481605	CAC	ORF1ab:nsp3	.	4444-4445-mnv	.	no-SNV	ORF1ab:nsp3	0.970588235294118
CAMB-7A678	MN908947.3	7166	T	C	0.026	0.035	5.4e-05	1.6e-05	0.0296296296296296	CTA	ORF1ab:nsp3	Y1483H	T4447C	TAT>CAT	Missense	ORF1ab:nsp3	0.97037037037037
CAMB-7A678	MN908947.3	7168	T	A	0.031	0.032	4e-06	1.3e-05	0.0314685314685315	ATC	ORF1ab:nsp3	Y1483*	T4449A	TAT>TAA	Nonsense	ORF1ab:nsp3	0.968531468531469
CAMB-7A678	MN908947.3	7168	TC	AT	0.028	0.0325	4e-06;5.5e-05	1.3e-05;1.9e-05	0.0280701754385965	ATC	ORF1ab:nsp3	.	4449-4450-mnv	.	no-SNV	ORF1ab:nsp3	0.968531468531469
CAMB-7A678	MN908947.3	7171	T	C	0.027	0.024	3.5e-05	0.00018	0.025830258302583	CTT	ORF1ab:nsp3	P1484P	T4452C	CCT>CCC	Synonymous	ORF1ab:nsp3	0.974169741697417
CAMB-7A678	MN908947.3	7173	C	T	0.031	0.032	5.9e-06	2e-05	0.0315789473684211	TCT	ORF1ab:nsp3	S1485F	C4454T	TCT>TTT	Missense	ORF1ab:nsp3	0.968421052631579
CAMB-7A678	MN908947.3	7173	CT	TC	0.0295	0.0285	5.9e-06;4e-05	2e-05;0.00022	0.0253623188405797	TCT	ORF1ab:nsp3	.	4454-4455-mnv	.	no-SNV	ORF1ab:nsp3	0.968421052631579
CAMB-7A678	MN908947.3	7177	A	T	0.03	0.03	5e-06	1.7e-05	0.0299003322259136	TAG	ORF1ab:nsp3	L1486F	A4458T	TTA>TTT	Missense	ORF1ab:nsp3	0.970099667774086
CAMB-7A678	MN908947.3	7177	AGA	TAG	0.0266666666666667	0.027	5e-06;3.9e-05;4.2e-05	1.7e-05;0.00012;0.00016	0.024390243902439	TAG	ORF1ab:nsp3	.	4458-4460-mnv	.	no-SNV	ORF1ab:nsp3	0.970099667774086
CAMB-7A678	MN908947.3	7184	A	T	0.031	0.034	4.7e-06	1.1e-05	0.0320284697508897	TAT	ORF1ab:nsp3	I1489L	A4465T	ATA>TTA	Missense	ORF1ab:nsp3	0.9644128113879
CAMB-7A678	MN908947.3	7184	ATACA	TATAC	0.0266	0.0286	4.7e-06;3.4e-05;5.4e-06;3.8e-05;3.1e-05	1.1e-05;0.00012;0.00017;1.4e-05;1.3e-05	0.0277777777777778	TAT	ORF1ab:nsp3	.	4465-4469-mnv	.	no-SNV	ORF1ab:nsp3	0.9644128113879
CAMB-7A678	MN908947.3	7191	T	A	0.026	0.019	2.8e-05	0.0011	0.0231660231660232	ATT	ORF1ab:nsp3	I1491N	T4472A	ATT>AAT	Missense	ORF1ab:nsp3	0.976833976833977
CAMB-7A678	MN908947.3	7193	AC	TA	0.0295	0.0345	5.5e-06;2.2e-05	1.4e-05;8.7e-06	0.0298507462686567	TAC	ORF1ab:nsp3	.	4474-4475-mnv	.	no-SNV	ORF1ab:nsp3	0.97
CAMB-7A678	MN908947.3	7196	A	C	0.019	0.033	0.00033	1.4e-05	0.0252707581227437	CAT	ORF1ab:nsp3	I1493L	A4477C	ATT>CTT	Missense	ORF1ab:nsp3	0.974729241877256
CAMB-7A678	MN908947.3	7200	C	T	0.031	0.032	7.3e-06	2.2e-05	0.0314685314685315	TCA	ORF1ab:nsp3	S1494L	C4481T	TCA>TTA	Missense	ORF1ab:nsp3	0.968531468531469
CAMB-7A678	MN908947.3	7200	CATC	TCAT	0.0255	0.03125	7.3e-06;0.00031;3.3e-05;9.1e-06	2.2e-05;1.4e-05;1.4e-05;2.3e-05	0.0273037542662116	TCA	ORF1ab:nsp3	.	4481-4484-mnv	.	no-SNV	ORF1ab:nsp3	0.968531468531469
CAMB-7A678	MN908947.3	7208	A	T	0.029	0.029	6.3e-06	1.9e-05	0.029126213592233	TAA	ORF1ab:nsp3	K1497*	A4489T	AAA>TAA	Nonsense	ORF1ab:nsp3	0.970873786407767
CAMB-7A678	MN908947.3	7211	TG	AT	0.03	0.034	3e-06;3.1e-05	1e-05;1.2e-05	0.0297397769516729	ATG	ORF1ab:nsp3	.	4492-4493-mnv	.	no-SNV	ORF1ab:nsp3	0.966542750929368
CAMB-7A678	MN908947.3	7216	T	A	0.027	0.015	7.1e-06	0.0017	0.0219435736677116	ATT	ORF1ab:nsp3	D1499E	T4497A	GAT>GAA	Missense	ORF1ab:nsp3	0.974921630094044
CAMB-7A678	MN908947.3	7219	A	T	0.027	0.03	8.3e-06	1.8e-05	0.0286624203821656	TAA	ORF1ab:nsp3	L1500F	A4500T	TTA>TTT	Missense	ORF1ab:nsp3	0.955414012738854
CAMB-7A678	MN908947.3	7229	G	T	0.026	0.023	3.1e-05	0.00017	0.025	TGG	ORF1ab:nsp3	G1504C	G4510T	GGC>TGC	Missense	ORF1ab:nsp3	0.975
CAMB-7A678	MN908947.3	7231	C	G	0.027	0.028	2.5e-05	8.8e-05	0.0274509803921569	GCT	ORF1ab:nsp3	G1504G	C4512G	GGC>GGG	Synonymous	ORF1ab:nsp3	0.972549019607843
CAMB-7A678	MN908947.3	7235	G	A	0.025	0.018	3.6e-05	0.0013	0.0216606498194946	AGT	ORF1ab:nsp3	V1506I	G4516A	GTT>ATT	Missense	ORF1ab:nsp3	0.978339350180505
CAMB-7A678	MN908947.3	7463	GTTGTAGACG	-	0.00236	0.0147	NA;NA;NA;NA;NA;2e-06;8.1e-08;NA;NA;NA	3.8e-07;9e-08;8e-10;7.3e-10;1.3e-07;9.1e-09;8.7e-09;6.8e-08;1.3e-07;2.6e-06	0.00408807953172907	TGT	ORF1ab:nsp3	.	4744-4753-delfrshift	.	no-SNV	ORF1ab:nsp3	0.995928338762215
CAMB-7A678	MN908947.3	7802	TATG	-	0.0024	0.0079	NA;NA;0.00047;0.00045	1e-05;4.1e-05;1e-04;9.5e-05	0.00436456996148909	TTA	ORF1ab:nsp3	.	5083-5086-delfrshift	.	no-SNV	ORF1ab:nsp3	0.99604641168887
CAMB-7A678	MN908947.3	7926	C	INS	0.0049	0.0099	0.00029	2.7e-06	0.00673107380424454	GCA	ORF1ab:nsp3	.	5206-5207-insfrshift	.	no-SNV	ORF1ab:nsp3	0.993110547988597
CAMB-7A678	MN908947.3	8872	G	T	0.0078	0.0023	2.4e-05	0.0091	0.00587723117109273	TGC	ORF1ab:nsp4	L106F	G318T	TTG>TTT	Missense	ORF1ab:nsp4	0.992308808590916
CAMB-7A678	MN908947.3	9241	AG	-	0.0065	0.0098	4.2e-05;4.3e-05	1e-06;1.3e-06	0.00777166119257991	CAG	ORF1ab:nsp4	.	687-688-delfrshift	.	no-SNV	ORF1ab:nsp4	0.991970361643751
CAMB-7A678	MN908947.3	9496	A	-	0.0073	0.0037	3.8e-05	0.0015	0.00614192009540847	TAG	ORF1ab:nsp4	.	942-942-delfrshift	.	no-SNV	ORF1ab:nsp4	0.993798449612403
CAMB-7A678	MN908947.3	9917	AG	TT	0.01205	0.0021	4.3e-06;5.3e-07	NA;0.0052	0.00791431889543636	TAG	ORF1ab:nsp4	.	1363-1364-mnv	.	no-SNV	ORF1ab:nsp4	0.991578947368421
CAMB-7A687	MN908947.3	11075	T	-	0.04	0.049	8.5e-10	5.2e-12	0.0437843093564527	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95451414912796
CAMB-7A687	MN908947.3	14408	C	T	1	1	0	0	0.998509836193187	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000389221889839085
CAMB-7A687	MN908947.3	18877	C	T	1	1	0	0	0.995923099940156	TCT	ORF1ab:3'-to-5'-exonuclease	L280L	C838T	CTA>TTA	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.0040394973070018
CAMB-7A687	MN908947.3	23403	A	G	1	1	0	0	0.999951961569255	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.80384307445957e-05
CAMB-7A687	MN908947.3	241	C	T	1	1	0	0	0.99981725702799	TCG	NA	NA	NA	NA	NA	NA	0.000106600067005756
CAMB-7A687	MN908947.3	25563	G	T	1	1	0	0	0.999709517270519	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000198056406464561
CAMB-7A687	MN908947.3	25721	C	T	0.0043	0.0076	0.00064	2.8e-05	0.00538095609451766	GCT	ORF3a	A110V	C329T	GCT>GTT	Missense	GU280_gp03	0.994541059034547
CAMB-7A687	MN908947.3	25728	C	T	0.005	0.0077	0.00026	2e-05	0.00587142326272761	TCT	ORF3a	V112V	C336T	GTC>GTT	Synonymous	GU280_gp03	0.994128576737272
CAMB-7A687	MN908947.3	26333	C	T	0.0082	0.018	6e-05	2.8e-09	0.0122831959056014	ACA	E	T30I	C89T	ACA>ATA	Missense	GU280_gp04	0.987574637475121
CAMB-7A687	MN908947.3	2662	C	T	0.026	0.0035	8.9e-12	0.004	0.0181259600614439	ACT	ORF1ab:nsp2	Y619Y	C1857T	TAC>TAT	Synonymous	ORF1ab:nsp2	0.981874039938556
CAMB-7A687	MN908947.3	29625	C	T	1	1	0	0	0.99775089660203	TCT	ORF10	S23F	C68T	TCT>TTT	Missense	GU280_gp11	0.00206674366299921
CAMB-7A687	MN908947.3	3037	C	T	1	1	0	0	0.999273540094999	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A687	MN908947.3	3983	AC	-	0.0039	0.0105	0.00095;0.00071	1.4e-06;9.5e-07	0.00614124872057318	TAC	ORF1ab:nsp3	.	1264-1265-delfrshift	.	no-SNV	ORF1ab:nsp3	0.994019933554817
CAMB-7A687	MN908947.3	514	T	C	0.0035	0.0094	0.0041	1.7e-05	0.00595592614651578	ATG	ORF1ab:leader-protein	H83H	T249C	CAT>CAC	Synonymous	ORF1ab:leader-protein	0.97866224719683
CAMB-7A687	MN908947.3	681	A	G	0.018	0.024	9.4e-10	1e-12	0.0204754108552836	GAT	ORF1ab:leader-protein	D139G	A416G	GAT>GGT	Missense	ORF1ab:leader-protein	0.97950386504466
CAMB-7A687	MN908947.3	9931	T	C	0.027	0.017	1.6e-13	2.5e-09	0.0228967360720315	ATA	ORF1ab:nsp4	D459D	T1377C	GAT>GAC	Synonymous	ORF1ab:nsp4	0.977068092290377
CAMB-7A696	MN908947.3	11074	C	INS	0.036	0.086	9.2e-08	8.1e-27	0.0639798994974874	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.907155778894472
CAMB-7A696	MN908947.3	11083	G	-	0.21	0.2	1.2e-96	1.1e-92	0.206794707934644	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.72717537738782e-05
CAMB-7A696	MN908947.3	11083	G	T	0.79	0.8	2.0997789948253e-320	0	0.792963487512522	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.72717537738782e-05
CAMB-7A696	MN908947.3	11094	C	T	0.034	0.11	1.1e-16	9.2e-52	0.076740048444835	GCC	ORF1ab:nsp6	A41V	C122T	GCC>GTC	Missense	ORF1ab:nsp6	0.923217080019721
CAMB-7A696	MN908947.3	12664	C	T	0.039	0.027	4.1e-19	1.2e-13	0.0313269187737749	CCA	ORF1ab:nsp8	A191A	C573T	GCC>GCT	Synonymous	ORF1ab:nsp8	0.968645110763034
CAMB-7A696	MN908947.3	13914	T	G	0.0056	0.0035	3.5e-05	0.00035	0.00437345502947328	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.995626544970527
CAMB-7A696	MN908947.3	14712	G	T	1	1	0	0	0.999888388704937	TGT	ORF1ab:RNA-dependent-RNA-polymerase	V415V	G1245T	GTG>GTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	3.72037650210201e-05
CAMB-7A696	MN908947.3	14805	C	T	1	1	0	0	0.999818419523533	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-7A696	MN908947.3	1758	C	T	0.019	0.026	6.4e-10	7.7e-13	0.0224233202530632	GCA	ORF1ab:nsp2	A318V	C953T	GCA>GTA	Missense	ORF1ab:nsp2	0.977536638103628
CAMB-7A696	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-7A696	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-7A696	MN908947.3	26144	G	T	1	1	7.6e-97	1.7e-153	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7A696	MN908947.3	26681	C	T	0.023	0.03	2.6e-11	7.1e-14	0.0269997722910771	TCC	M	F53F	C159T	TTC>TTT	Synonymous	GU280_gp05	0.973000227708923
CAMB-7A696	MN908947.3	28705	T	C	0.1	0.07	2.2e-46	2.3e-32	0.0851035344519814	ATC	N	D144D	T432C	GAT>GAC	Synonymous	GU280_gp10	0.914851838629061
CAMB-7A696	MN908947.3	6427	T	C	1	1	0	0	0.999931003553317	ATC	ORF1ab:nsp3	N1236N	T3708C	AAT>AAC	Synonymous	ORF1ab:nsp3	0
CAMB-7A696	MN908947.3	9901	T	C	0.03	0.052	7.5e-15	3.8e-23	0.0394320155276331	ATA	ORF1ab:nsp4	N449N	T1347C	AAT>AAC	Synonymous	ORF1ab:nsp4	0.960567984472367
CAMB-7A6A5	MN908947.3	12498	A	G	0.032	0.05	5.4e-16	1.7e-23	0.0411853133172711	AAC	ORF1ab:nsp8	N136S	A407G	AAC>AGC	Missense	ORF1ab:nsp8	0.958814686682729
CAMB-7A6A5	MN908947.3	14408	C	T	1	1	0	0	0.999391648198844	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000369356450701777
CAMB-7A6A5	MN908947.3	16887	C	T	0.021	0.017	1.4e-09	9e-08	0.0189704310651942	ACA	ORF1ab:helicase	Y217Y	C651T	TAC>TAT	Synonymous	ORF1ab:helicase	0.980940505878162
CAMB-7A6A5	MN908947.3	203	C	T	0.049	0.057	2.5e-22	7.7e-26	0.0532850241545894	TCG	NA	NA	NA	NA	NA	NA	0.946690821256039
CAMB-7A6A5	MN908947.3	22452	C	T	0.083	0.037	8.5e-09	3.6e-05	0.0592991913746631	TCA	S	S297L	C890T	TCA>TTA	Missense	GU280_gp02, spike glycoprotein	0.940700808625337
CAMB-7A6A5	MN908947.3	23062	T	C	0.12	0.031	6.9e-52	2.2e-14	0.0854503464203233	CTA	S	T500T	T1500C	ACT>ACC	Synonymous	GU280_gp02, spike glycoprotein	0.914549653579677
CAMB-7A6A5	MN908947.3	23403	A	G	1	1	0	0	0.99990822507291	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.1774927089919e-05
CAMB-7A6A5	MN908947.3	241	C	T	1	1	0	0	0.999744779582367	TCG	NA	NA	NA	NA	NA	NA	0.000139211136890951
CAMB-7A6A5	MN908947.3	24904	C	T	0.027	0.058	2.3e-13	1.8e-26	0.0400681172066316	TCA	S	I1114I	C3342T	ATC>ATT	Synonymous	GU280_gp02, spike glycoprotein	0.959861513778253
CAMB-7A6A5	MN908947.3	25708	C	T	0.035	0.037	4.1e-14	2.1e-14	0.0362292051756007	TCT	ORF3a	L106F	C316T	CTC>TTC	Missense	GU280_gp03	0.963770794824399
CAMB-7A6A5	MN908947.3	25916	C	T	1	1	0	0	0.999655528763348	ACA	ORF3a	T175I	C524T	ACA>ATA	Missense	GU280_gp03	0
CAMB-7A6A5	MN908947.3	26530	A	G	0.23	0.36	4.6e-105	5.7e-181	0.28902378592666	GAT	M	D3G	A8G	GAT>GGT	Missense	GU280_gp05	0.710914271555996
CAMB-7A6A5	MN908947.3	26775	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0306303953488372	0.0293720930232558	NA;NA;NA;NA;NA;NA;NA;NA;0.5;0.5;3.2e-08;1.8e-07;1.5e-06;1.4e-06;2e-07;8.4e-07;6.2e-07;1.6e-06;6.7e-07;9.7e-07;2.3e-06;5e-07;1.6e-06;1e-06;1e-06;9.6e-07;2e-06;8.1e-07;1.4e-06;9.7e-07;6e-07;1.6e-06;8.7e-07;2.1e-07;7.2e-07;1.6e-06;1.6e-06;8.3e-07;1.7e-06;3.4e-07;7.9e-07;6.5e-07;1.8e-05	1.9e-05;1.7e-05;3.4e-06;2.2e-05;2e-04;5.4e-05;1.4e-06;2.8e-05;3.3e-05;9e-05;1.1e-05;3.3e-05;0.00014;0.00014;4.8e-05;9.2e-05;7.5e-05;0.00014;9.4e-05;0.00012;0.00018;8.2e-05;0.00016;0.00011;0.00011;1e-04;0.00017;8.8e-05;0.00013;0.00011;7.6e-05;0.00015;8.9e-05;2.8e-05;1e-04;0.00015;0.00013;8.3e-05;0.00015;5.5e-05;8.7e-05;7.9e-05;0.00054	0.0337455432290217	GGC	M	.	253-295-delfrshift	.	no-SNV	GU280_gp05	0.986082975980637
CAMB-7A6A5	MN908947.3	28253	C	T	0.17	0.1	3.2e-78	1.8e-46	0.13909343806251	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.860696168501765
CAMB-7A6A5	MN908947.3	28326	GT	-	0.0019	0.011	NA;8e-04	9.7e-07;8.5e-07	0.00618664119651811	GGT	N	.	53-54-delfrshift	.	no-SNV	GU280_gp10	0.994761638413217
CAMB-7A6A5	MN908947.3	28603	C	T	0.029	0.014	2.5e-09	2e-05	0.0219330464896631	TCT	N	F110F	C330T	TTC>TTT	Synonymous	GU280_gp10	0.977962010704166
CAMB-7A6A5	MN908947.3	28886	A	-	0.17	0.23	3.2e-69	5.3e-97	0.195692102187343	AAC	N	.	613-613-delfrshift	.	no-SNV	GU280_gp10	0.798630823175822
CAMB-7A6A5	MN908947.3	28886	ACT	-	0.143333333333333	0.196666666666667	3.2e-69;1.6e-53;2.7e-39	5.3e-97;3.2e-72;2e-54	0.145937188434696	AAC	N	.	613-615-delinframe	.	no-SNV	GU280_gp10	0.798630823175822
CAMB-7A6A5	MN908947.3	29051	C	INS	0.028	0.038	8.3e-07	1.5e-10	0.0334026426990408	GCA	N	.	777-778-insfrshift	.	no-SNV	GU280_gp10	0.966329062982091
CAMB-7A6A5	MN908947.3	29241	A	-	0.014	0.011	1.7e-07	2.1e-06	0.0126195028680688	GAA	N	.	968-968-delfrshift	.	no-SNV	GU280_gp10	0.987380497131931
CAMB-7A6A5	MN908947.3	29241	AA	-	0.007	0.011	1.7e-07;NA	2.1e-06;6.6e-06	0.0092401680030546	GAA	N	.	968-969-delfrshift	.	no-SNV	GU280_gp10	0.987380497131931
CAMB-7A6A5	MN908947.3	29754	C	T	0.027	0.024	2.7e-11	5.8e-10	0.0255009107468124	TCG	NA	NA	NA	NA	NA	NA	0.971584699453552
CAMB-7A6A5	MN908947.3	3037	C	T	1	1	0	0	0.999692717402438	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A6A5	MN908947.3	3096	C	T	0.039	0.028	7.1e-15	4.5e-11	0.0339810054892393	TCA	ORF1ab:nsp3	S126L	C377T	TCA>TTA	Missense	ORF1ab:nsp3	0.965931863727455
CAMB-7A6A5	MN908947.3	346	C	T	0.27	0.25	2.9e-135	7.9e-123	0.261628844912885	TCG	ORF1ab:leader-protein	L27L	C81T	CTC>CTT	Synonymous	ORF1ab:leader-protein	0.738357711335771
CAMB-7A6A5	MN908947.3	3828	C	T	0.22	0.17	1.5e-100	7.9e-73	0.203741566141893	TCA	ORF1ab:nsp3	S370L	C1109T	TCA>TTA	Missense	ORF1ab:nsp3	0.796258433858107
CAMB-7A6A5	MN908947.3	4543	C	T	0.028	0.021	1.5e-13	1.2e-10	0.0236617853892612	CCA	ORF1ab:nsp3	T608T	C1824T	ACC>ACT	Synonymous	ORF1ab:nsp3	0.962935385124514
CAMB-7A6A5	MN908947.3	635	C	T	0.11	0.16	2.8e-52	1.2e-74	0.132661130881771	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.867338869118229
CAMB-7A6A5	MN908947.3	683	C	T	0.018	0.027	1.4e-09	1.3e-13	0.0225493009716699	TCT	ORF1ab:leader-protein	L140L	C418T	CTA>TTA	Synonymous	ORF1ab:leader-protein	0.977437032785317
CAMB-7A6A5	MN908947.3	686	AAGTCATTT	-	0.0187777777777778	0.0621111111111111	0.0054;0.0047;0.0093;0.0051;0.01;0.0057;0.0033;0.0066;0.011	1.3e-07;9.1e-08;2.7e-08;2.4e-09;3.7e-08;9e-09;1.2e-09;6.3e-09;2.1e-06	0.0412298895678009	AAA	ORF1ab:leader-protein	.	421-429-delinframe	.	no-SNV	ORF1ab:leader-protein	0.964685231879414
CAMB-7A6A5	MN908947.3	9430	C	T	0.042	0.1	6e-16	4.5e-38	0.0740396530359356	TCG	ORF1ab:nsp4	I292I	C876T	ATC>ATT	Synonymous	ORF1ab:nsp4	0.925960346964064
CAMB-7A6B4	MN908947.3	10369	C	T	0.01	0.011	7.1e-06	3.4e-06	0.0105135084544831	GCA	ORF1ab:3C-like-proteinase	R105R	C315T	CGC>CGT	Synonymous	ORF1ab:3C-like-proteinase	0.989392899482124
CAMB-7A6B4	MN908947.3	11075	T	-	0.041	0.038	3.6e-10	9e-10	0.0393390833416909	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956874937318223
CAMB-7A6B4	MN908947.3	11139	C	T	0.015	0.015	2e-08	2.2e-08	0.0153218557698956	GCA	ORF1ab:nsp6	A56V	C167T	GCA>GTA	Missense	ORF1ab:nsp6	0.984581345502316
CAMB-7A6B4	MN908947.3	12747	C	T	0.093	0.095	1.8e-42	1.2e-43	0.0936323112657952	ACT	ORF1ab:nsp9	T21I	C62T	ACT>ATT	Missense	ORF1ab:nsp9	0.906262450105614
CAMB-7A6B4	MN908947.3	14408	C	T	1	1	0	0	0.999132165420842	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000462845108884312
CAMB-7A6B4	MN908947.3	16289	C	T	0.026	0.025	3e-12	4.3e-12	0.0255915814991323	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0.974243133797967
CAMB-7A6B4	MN908947.3	20268	A	G	1	1	0	1.6e-148	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-7A6B4	MN908947.3	21057	C	T	0.013	0.014	2.5e-07	6.5e-08	0.0130281132971148	ACC	ORF1ab:2'-O-ribose-methyltransferase	D133D	C399T	GAC>GAT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.986919141304921
CAMB-7A6B4	MN908947.3	23403	A	G	1	1	0	0	0.999288274319412	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.32021724579108e-05
CAMB-7A6B4	MN908947.3	241	C	T	1	1	0	0	0.99899423619976	TCG	NA	NA	NA	NA	NA	NA	0.000135391280801516
CAMB-7A6B4	MN908947.3	27338	A	G	0.029	0.029	2.7e-14	1.6e-14	0.0290109930579852	GAG	ORF6	E46G	A137G	GAG>GGG	Missense	GU280_gp06	0.970850903198483
CAMB-7A6B4	MN908947.3	28011	C	G	0.0078	0.008	7.6e-05	3e-05	0.00785835074107232	TCA	ORF8	H40D	C118G	CAC>GAC	Missense	GU280_gp09	0.992091912861832
CAMB-7A6B4	MN908947.3	28693	T	C	0.016	0.017	8.5e-09	2.9e-09	0.0167329517896983	ATA	N	N140N	T420C	AAT>AAC	Synonymous	GU280_gp10	0.983267048210302
CAMB-7A6B4	MN908947.3	28854	C	T	1	1	0	0	0.999504907242916	TCA	N	S194L	C581T	TCA>TTA	Missense	GU280_gp10	0.000116492413431575
CAMB-7A6B4	MN908947.3	3037	C	T	1	1	0	0	0.999136383264017	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000159087293470603
CAMB-7A6B4	MN908947.3	3722	A	G	0.005	0.0074	0.00048	4.1e-05	0.00596777402029043	TAT	ORF1ab:nsp3	I335V	A1003G	ATT>GTT	Missense	ORF1ab:nsp3	0.993634374378357
CAMB-7A6B4	MN908947.3	6723	C	T	0.01	0.0093	2.5e-06	4.9e-06	0.00993016849253636	ACT	ORF1ab:nsp3	T1335I	C4004T	ACT>ATT	Missense	ORF1ab:nsp3	0.990069831507464
CAMB-7A6B4	MN908947.3	7798	G	T	1	1	0	0	0.999858717151738	AGA	ORF1ab:nsp3	K1693N	G5079T	AAG>AAT	Missense	ORF1ab:nsp3	0
CAMB-7A6B4	MN908947.3	7851	C	T	0.0091	0.0074	1.2e-05	5.4e-05	0.0084106272598648	GCT	ORF1ab:nsp3	A1711V	C5132T	GCT>GTT	Missense	ORF1ab:nsp3	0.991510768747052
CAMB-7A6C3	MN908947.3	11074	C	INS	0.14	0.11	3.9e-55	2.3e-36	0.128350383162835	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.864921350786492
CAMB-7A6C3	MN908947.3	11083	G	-	0.21	0.18	6e-96	7.1e-82	0.199378125822585	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-7A6C3	MN908947.3	11083	G	T	0.79	0.82	6.2000297896618e-320	0	0.800457357199263	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-7A6C3	MN908947.3	11566	TATTTTCTTCATAACTGGTAATACACTTCAGTGTATAATGCTAGTTTATTGTT	-	0.000113207547169811	0.0137924528301887	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;8e-04;NA;NA;NA;NA;NA;NA;NA;NA	8.7e-07;8.3e-07;2.6e-06;6.1e-07;6.8e-07;3.8e-07;3.6e-07;4.8e-07;3.6e-07;5.1e-07;5.2e-07;4.2e-07;4.1e-07;3.1e-07;4.6e-07;3.9e-07;6.4e-07;3.1e-07;5.3e-07;3.9e-06;1.6e-06;9.6e-07;1.8e-06;1.4e-06;1.2e-06;1.1e-06;2.4e-06;1.3e-06;2.1e-06;2.1e-06;4.1e-06;3.6e-06;1.4e-06;2.7e-06;3.4e-06;2e-06;2.4e-06;1.2e-06;1.6e-06;2.1e-06;1.4e-06;1.2e-06;1.4e-06;1.5e-06;9.3e-06;3.2e-06;3.8e-06;4.3e-06;9.4e-06;1.1e-08;2.5e-08;2.6e-05;1.6e-05	0.00449775112443778	CTA	ORF1ab:nsp6	.	594-646-delfrshift	.	no-SNV	ORF1ab:nsp6	0.994887089902003
CAMB-7A6C3	MN908947.3	12743	C	A	0.034	0.039	1.3e-16	4.9e-19	0.0358201709520259	ACA	ORF1ab:nsp9	Q20K	C58A	CAA>AAA	Missense	ORF1ab:nsp9	0.964075801445984
CAMB-7A6C3	MN908947.3	14778	T	C	0.0072	0.02	3.3e-05	1e-10	0.0123339126534731	GTA	ORF1ab:RNA-dependent-RNA-polymerase	G437G	T1311C	GGT>GGC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.987666087346527
CAMB-7A6C3	MN908947.3	14805	C	T	0.99	1	0	0	0.995605228262929	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.0043568857738208
CAMB-7A6C3	MN908947.3	17544	G	C	0.0059	0.018	5.6e-05	3.1e-10	0.0110386106068783	TGT	ORF1ab:helicase	M436I	G1308C	ATG>ATC	Missense	ORF1ab:helicase	0.985159201295197
CAMB-7A6C3	MN908947.3	18786	T	C	0.059	0.044	5.7e-27	6.5e-21	0.0535415778950474	TTA	ORF1ab:3'-to-5'-exonuclease	F249F	T747C	TTT>TTC	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.946278147431905
CAMB-7A6C3	MN908947.3	20865	T	-	0.011	0.021	3.1e-06	2.1e-10	0.0146119806361557	ATT	ORF1ab:2'-O-ribose-methyltransferase	.	207-207-delfrshift	.	no-SNV	ORF1ab:2'-O-ribose-methyltransferase	0.985388019363844
CAMB-7A6C3	MN908947.3	22690	T	-	0.012	0.0081	6.9e-06	2e-04	0.0100627569790089	CTT	S	.	1128-1128-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.9862223184015
CAMB-7A6C3	MN908947.3	22777	TG	-	0.00665	0.00745	4e-05;6e-05	1.7e-05;2.4e-05	0.00698109519421407	ATG	S	.	1215-1216-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.992756735091185
CAMB-7A6C3	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-7A6C3	MN908947.3	25547	TTCTTGCTGTT	-	0.0114545454545455	0.00348090909090909	0.00026;0.00044;0.00029;0.00025;0.00035;0.00019;0.00044;0.00048;0.00092;1.1e-06;3.7e-05	NA;NA;NA;NA;NA;4e-04;0.00079;0.00096;0.0017;0.5;NA	0.00687473959319723	CTT	ORF3a	.	155-165-delfrshift	.	no-SNV	GU280_gp03	0.99308620461046
CAMB-7A6C3	MN908947.3	2558	C	T	1	0.98	0	0	0.995050730017322	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-7A6C3	MN908947.3	26144	G	T	1	1	1.3e-294	4.4e-174	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7A6C3	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0293783783783784	0.0425957027027027	4e-05;8.7e-07;2e-05;2.4e-05;7.7e-05;2.2e-06;2.1e-05;0.00013;0.00012;3.3e-05;5.6e-05;4.3e-05;0.00012;7.7e-05;9.4e-05;0.00017;6.8e-05;0.00014;9.5e-05;9.6e-05;7.2e-05;0.00016;8.4e-05;0.00011;8.7e-05;5.6e-05;0.00013;7.8e-05;6.9e-05;7.4e-05;0.00013;1e-04;5.4e-05;0.00012;5.2e-05;7.8e-05;5.8e-05	NA;NA;NA;NA;NA;0.048;0.079;6.1e-09;6.2e-09;8.6e-10;1.8e-09;1.2e-09;6.1e-09;3e-09;4.7e-09;9.5e-09;2.2e-09;7.8e-09;4e-09;3.7e-09;2.6e-09;8.2e-09;3.3e-09;5.4e-09;3.1e-09;1.6e-09;6.7e-09;2.6e-09;6.9e-09;2.7e-09;6.4e-09;4.2e-09;2.1e-09;5.9e-09;8.1e-10;2.5e-09;1.6e-09	0.0375291492609928	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.982628107218987
CAMB-7A6C3	MN908947.3	27264	T	-	0.0085	0.011	6.7e-05	6.3e-06	0.00943724510390713	CTT	ORF6	.	63-63-delfrshift	.	no-SNV	GU280_gp06	0.990423562490431
CAMB-7A6C3	MN908947.3	29659	C	T	0.0032	0.0096	0.0016	7.5e-06	0.00519390581717452	ACT	ORF10	N34N	C102T	AAC>AAT	Synonymous	GU280_gp11	0.994806094182826
CAMB-7A6C3	MN908947.3	3960	TC	-	0.0105	0.00825	1.2e-06;9.6e-07	8.4e-06;7.1e-06	0.00974953773743486	ATC	ORF1ab:nsp3	.	1241-1242-delfrshift	.	no-SNV	ORF1ab:nsp3	0.990293678446989
CAMB-7A6C3	MN908947.3	3995	GAA	-	0.00286666666666667	0.013	NA;NA;1.3e-05	1.1e-07;2.7e-07;5e-07	0.00335543660621555	GGA	ORF1ab:nsp3	.	1276-1278-delinframe	.	no-SNV	ORF1ab:nsp3	0.996535796766744
CAMB-7A6C3	MN908947.3	3997	AG	-	0.0086	0.0065	1.3e-05;7.3e-06	5e-07;NA	0.00801078680203046	AAG	ORF1ab:nsp3	.	1278-1279-delfrshift	.	no-SNV	ORF1ab:nsp3	0.990249702734839
CAMB-7A6C3	MN908947.3	7393	G	A	0.017	0.0058	3.8e-09	4e-04	0.0137203928365107	CGA	ORF1ab:nsp3	P1558P	G4674A	CCG>CCA	Synonymous	ORF1ab:nsp3	0.986279607163489
CAMB-7A6C3	MN908947.3	7890	T	-	0.016	0.011	2.4e-06	0.00022	0.0142039850069047	GTT	ORF1ab:nsp3	.	5171-5171-delfrshift	.	no-SNV	ORF1ab:nsp3	0.985598737423555
CAMB-7A6C3	MN908947.3	9320	TG	-	0.0072	0.011	5.4e-05;0.0048	1.5e-06;0.00042	0.00883854101829951	CTG	ORF1ab:nsp4	.	766-767-delfrshift	.	no-SNV	ORF1ab:nsp4	0.990927419354839
CAMB-7A6E1	MN908947.3	13780	A	T	0.012	0.024	7.8e-05	1.5e-07	0.0173043291504311	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I105L	A313T	ATA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.982634307980241
CAMB-7A6E1	MN908947.3	13940	A	-	0.014	0.013	2.9e-08	6.1e-08	0.0137153645399522	GAA	ORF1ab:RNA-dependent-RNA-polymerase	.	473-473-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.986145815980898
CAMB-7A6E1	MN908947.3	14408	C	T	1	1	0	0	0.999239440904558	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00054084202342522
CAMB-7A6E1	MN908947.3	16297	CGTAGACCATTC	-	0.00954166666666667	0.0123083333333333	1.9e-05;1.6e-05;5.8e-05;4.5e-05;3e-04;0.00046;0.00054;0.00041;0.00034;0.00023;0.00029;0.00083	NA;NA;NA;NA;3.1e-06;8.5e-06;1.1e-05;6.4e-06;5.2e-06;2.3e-06;2.8e-06;1.7e-05	0.0122184954480115	ACG	ORF1ab:helicase	.	61-72-delinframe	.	no-SNV	ORF1ab:helicase	0.994323342415986
CAMB-7A6E1	MN908947.3	16948	CCTACACTAGTGCCACAAGA	-	0.00181	0.00792	0.007;0.0044;0.0018;0.0022;0.0026;0.0023;0.0021;0.0012;0.002;0.0025;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00046;0.00014;1.8e-05;2.4e-05;3.1e-05;2.8e-05;2.5e-05;7.1e-06;1.4e-05;2.2e-05;6.6e-06;1.1e-05;6.8e-06;1.8e-05;1.4e-05;1.3e-05;1e-05;7.3e-06;5.2e-06;7.4e-06	0.00404148951081624	ACC	ORF1ab:helicase	.	712-731-delfrshift	.	no-SNV	ORF1ab:helicase	0.995019469347098
CAMB-7A6E1	MN908947.3	17504	A	T	0.011	0.013	1.1e-05	1e-06	0.0118608503589177	AAT	ORF1ab:helicase	N423I	A1268T	AAT>ATT	Missense	ORF1ab:helicase	0.988117062396466
CAMB-7A6E1	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0130567027027027	0.0433783783783784	NA;NA;NA;NA;NA;NA;NA;0.023;0.023;0.012;0.016;0.014;0.023;0.018;0.02;0.027;0.017;0.025;0.02;0.02;0.016;3.6e-08;0.018;0.022;0.02;0.016;0.023;0.019;0.011;0.018;0.025;0.023;0.015;0.024;0.017;0.018;0.016	0.00055;4.2e-05;0.00037;0.00037;0.00089;3.3e-10;4.9e-09;9.8e-08;9.7e-08;2.3e-08;3.6e-08;2.4e-08;9.6e-08;4.8e-08;7e-08;1.4e-07;4.5e-08;1.2e-07;6.6e-08;6.5e-08;4.7e-08;1.3e-07;4.3e-08;8.7e-08;5.9e-08;2.6e-08;8.5e-08;5e-08;6.1e-08;4.4e-08;9.9e-08;8.4e-08;4.4e-08;9.5e-08;1.6e-08;4.3e-08;3.1e-08	0.0309002467002105	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.988174354964816
CAMB-7A6E1	MN908947.3	3037	C	T	1	1	0	0	0.999452294884434	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000109541023113156
CAMB-7A6E1	MN908947.3	442	C	T	1	0.97	0	0	0.987440735972872	GCG	ORF1ab:leader-protein	G59G	C177T	GGC>GGT	Synonymous	ORF1ab:leader-protein	9.41944802034601e-05
CAMB-7A6E1	MN908947.3	8298	AC	-	0.00385	0.014	NA;1.1e-05	2.5e-08;2.5e-08	0.00676575568696393	AAC	ORF1ab:nsp3	.	5579-5580-delfrshift	.	no-SNV	ORF1ab:nsp3	0.995985503206022
CAMB-7A6E1	MN908947.3	8299	C	-	0.0077	0.014	1.1e-05	2.5e-08	0.00933435348125478	ACA	ORF1ab:nsp3	.	5580-5580-delfrshift	.	no-SNV	ORF1ab:nsp3	0.990665646518745
CAMB-7A6F0	MN908947.3	11075	T	-	0.034	0.036	9.4e-09	1.2e-09	0.0349689869055824	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.96078566505858
CAMB-7A6F0	MN908947.3	14408	C	T	1	1	0	0	0.998462856566878	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000478782380808386
CAMB-7A6F0	MN908947.3	23403	A	G	1	1	0	0	0.999497701748567	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.5818603989954e-05
CAMB-7A6F0	MN908947.3	241	C	T	1	1	0	0	0.998778377277817	TCG	NA	NA	NA	NA	NA	NA	5.09009467576097e-05
CAMB-7A6F0	MN908947.3	25671	C	T	0.079	0.076	1.4e-35	5.9e-34	0.0780483171326346	ACC	ORF3a	H93H	C279T	CAC>CAT	Synonymous	GU280_gp03	0.921666719437672
CAMB-7A6F0	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999394349638391	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	3.84970742223591e-05
CAMB-7A6F0	MN908947.3	3037	C	T	1	1	0	0	0.999168323992045	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	3.61598264328331e-05
CAMB-7A6F0	MN908947.3	6541	C	T	0.023	0.028	3.2e-11	3e-13	0.0244864729458918	ACA	ORF1ab:nsp3	H1274H	C3822T	CAC>CAT	Synonymous	ORF1ab:nsp3	0.975513527054108
CAMB-7A6F0	MN908947.3	6872	G	A	0.99	1	0	6.3e-283	0.995383194829178	TGT	ORF1ab:nsp3	V1385I	G4153A	GTT>ATT	Missense	ORF1ab:nsp3	0.00461680517082179
CAMB-7A70C	MN908947.3	11075	T	-	0.056	0.021	8.8e-14	4.1e-06	0.0406444289657663	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956143745324149
CAMB-7A70C	MN908947.3	11922	AATTG	-	0.0018234	0.00684	NA;NA;NA;0.0015;0.00096	0.00092;0.00088;0.00077;4.5e-07;1.7e-05	0.00195469492144684	AAA	ORF1ab:nsp7	.	80-84-delfrshift	.	no-SNV	ORF1ab:nsp7	0.998036089114709
CAMB-7A70C	MN908947.3	12488	C	T	0.03	0.043	6.6e-15	2.6e-20	0.0354688137283041	ACC	ORF1ab:nsp8	P133S	C397T	CCA>TCA	Missense	ORF1ab:nsp8	0.96450097433496
CAMB-7A70C	MN908947.3	13859	AC	-	0.00625	0.0077	1e-04;9.1e-05	2.1e-05;1.8e-05	0.00688544939679584	GAC	ORF1ab:RNA-dependent-RNA-polymerase	.	392-393-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.993061828525302
CAMB-7A70C	MN908947.3	14082	T	C	0.0042	0.0072	0.00041	2e-05	0.00569953758468653	GTA	ORF1ab:RNA-dependent-RNA-polymerase	G205G	T615C	GGT>GGC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.994300462415313
CAMB-7A70C	MN908947.3	14408	C	T	0.99	1	0	0	0.996451077943615	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000563847429519071
CAMB-7A70C	MN908947.3	16775	A	G	0.0043	0.0072	0.00035	1.7e-05	0.00556742409529358	TAT	ORF1ab:helicase	Y180C	A539G	TAT>TGT	Missense	ORF1ab:helicase	0.994416391532336
CAMB-7A70C	MN908947.3	17164	T	C	0.0039	0.0075	0.00093	2e-05	0.00561236718063434	CTC	ORF1ab:helicase	S310P	T928C	TCT>CCT	Missense	ORF1ab:helicase	0.993149316928977
CAMB-7A70C	MN908947.3	18555	C	T	0.049	0.036	3.9e-23	8.6e-18	0.0431181924565667	ACA	ORF1ab:3'-to-5'-exonuclease	D172D	C516T	GAC>GAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.956791790440184
CAMB-7A70C	MN908947.3	18788	C	T	1	1	0	0	0.999444930363991	ACA	ORF1ab:3'-to-5'-exonuclease	T250I	C749T	ACA>ATA	Missense	ORF1ab:3'-to-5'-exonuclease	6.72811680010765e-05
CAMB-7A70C	MN908947.3	18973	G	T	0.011	0.0082	2.7e-06	4.8e-05	0.00970366824768287	GGT	ORF1ab:3'-to-5'-exonuclease	V312F	G934T	GTT>TTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.990252817544928
CAMB-7A70C	MN908947.3	1913	C	T	0.017	0.015	8.2e-10	4.3e-09	0.0162035001319145	CCG	ORF1ab:nsp2	R370C	C1108T	CGC>TGC	Missense	ORF1ab:nsp2	0.979531263741096
CAMB-7A70C	MN908947.3	19839	T	C	1	1	0	0	0.999761777142517	ATA	ORF1ab:endoRNAse	N73N	T219C	AAT>AAC	Synonymous	ORF1ab:endoRNAse	0.000178667143112382
CAMB-7A70C	MN908947.3	20339	TTA	-	0.09	0.03	3.7e-09;3.1e-11;5.8e-11	0.00089;0.00018;0.00014	0.05859375	TTT	ORF1ab:endoRNAse	.	719-721-delinframe	.	no-SNV	ORF1ab:endoRNAse	0.941860465116279
CAMB-7A70C	MN908947.3	22011	A	T	0.055	0.028	3.2e-25	7.1e-14	0.0412917988454938	AAA	S	K150I	A449T	AAA>ATA	Missense	GU280_gp02, spike glycoprotein	0.958656196370066
CAMB-7A70C	MN908947.3	23403	A	G	1	1	0	0	0.999970942339916	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	1.93717733889949e-05
CAMB-7A70C	MN908947.3	23559	TTGGTGCAGGTATATGCGCTAGTT	-	0.0460416666666667	0.0345	6.4e-05;0.00013;7.1e-05;0.00014;0.00016;0.00016;0.00015;0.00014;8.7e-05;7.8e-05;7e-08;4.5e-09;2.8e-05;1.1e-05;2.8e-05;1.1e-05;3.2e-05;7.1e-05;3.7e-05;3.9e-05;3.4e-07;8.1e-07;5e-05;0.00047	0.00039;0.00076;0.00049;0.00085;0.00089;0.00089;0.00086;0.00086;0.00057;0.00053;0.00027;7.5e-05;0.00029;0.00016;0.00027;0.00014;3e-04;0.00053;0.00033;0.00033;1.6e-05;2.2e-05;4e-04;0.00033	0.0380497446878603	ATT	S	.	1997-2020-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.94949494949495
CAMB-7A70C	MN908947.3	241	C	T	1	1	0	0	0.999841111312875	TCG	NA	NA	NA	NA	NA	NA	2.26983838750681e-05
CAMB-7A70C	MN908947.3	24588	C	T	0.046	0.032	1.3e-16	1.4e-12	0.0379492334757477	ACT	S	T1009I	C3026T	ACT>ATT	Missense	GU280_gp02, spike glycoprotein	0.961799447097261
CAMB-7A70C	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0424736842105263	0.0661578947368421	0.0015;0.00012;0.0011;0.0012;0.0023;0.00027;0.0011;5.6e-08;5.8e-08;9.8e-09;2.1e-08;1.2e-08;6.2e-08;2.6e-08;4e-08;9.3e-08;2.1e-08;7.4e-08;4.1e-08;4.1e-08;2.5e-08;8.6e-08;3.2e-08;5e-08;3.3e-08;1.5e-08;5.8e-08;2.7e-08;1.9e-08;2.6e-08;6.6e-08;5.3e-08;2.8e-08;5.7e-08;1e-08;2.8e-08;1.3e-08;0.00017	3.3e-10;1.6e-13;2.6e-09;2.8e-09;2.8e-07;5.5e-09;3.5e-08;1.9e-12;2e-12;2.5e-13;7e-13;3e-13;2.1e-12;7.6e-13;1.3e-12;3.3e-12;5.6e-13;2.6e-12;1.3e-12;1.2e-12;6.1e-13;3e-12;9e-13;1.6e-12;9.5e-13;3.6e-13;1.8e-12;6.6e-13;1.3e-12;7.7e-13;2.2e-12;1.8e-12;1.3e-12;2.1e-12;9.9e-14;6.1e-13;2.6e-13;4.6e-06	0.0578209953994145	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.963312327944995
CAMB-7A70C	MN908947.3	26952	ATCCTTC	-	0.00884285714285714	0.00342857142857143	4.7e-05;4.8e-05;5.1e-05;3.3e-05;3.5e-05;4.7e-05;8.3e-05	NA;NA;NA;NA;2.3e-06;3.3e-06;NA	0.00459715919137149	GAT	M	.	430-436-delfrshift	.	no-SNV	GU280_gp05	0.995167089055225
CAMB-7A70C	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999671959060491	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	7.06863646002686e-05
CAMB-7A70C	MN908947.3	28896	CTA	-	0.056	0.0313333333333333	3.8e-06;1.7e-06;3.5e-14	0.00019;0.00013;9.9e-09	0.0440358568343912	GCT	N	.	623-625-delinframe	.	no-SNV	GU280_gp10	0.954979090433874
CAMB-7A70C	MN908947.3	3037	C	T	1	1	0	0	0.999385308882287	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000102448519618892
CAMB-7A70C	MN908947.3	4529	T	-	0.039	0.035	9.1e-07	4.4e-06	0.0374414976599064	ATT	ORF1ab:nsp3	.	1810-1810-delfrshift	.	no-SNV	ORF1ab:nsp3	0.962476393792594
CAMB-7A70C	MN908947.3	519	T	G	0.0038	0.011	0.0097	1.4e-05	0.00671058679332005	ATG	ORF1ab:leader-protein	M85R	T254G	ATG>AGG	Missense	ORF1ab:leader-protein	0.910862570859507
CAMB-7A70C	MN908947.3	522	TT	-	0.0345	0.089	1.1e-05;0.00069	5.1e-13;5e-12	0.0571470415934388	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.93415823699422
CAMB-7A70C	MN908947.3	5810	GACGGTGCT	-	0.000955555555555556	0.0176666666666667	NA;NA;0.00058;NA;NA;NA;NA;NA;NA	1.4e-06;8.6e-07;1.4e-06;9.5e-07;1.1e-06;7.7e-07;8.9e-07;0.00013;5.2e-05	0.00793814432989691	AGA	ORF1ab:nsp3	.	3091-3099-delinframe	.	no-SNV	ORF1ab:nsp3	0.992281598741458
CAMB-7A70C	MN908947.3	5906	ACTTA	-	0.0044	0.0276	NA;NA;NA;0.00014;0.00089	9.6e-12;1e-11;4.3e-13;9.9e-10;4.9e-08	0.0116879817057678	TAC	ORF1ab:nsp3	.	3187-3191-delfrshift	.	no-SNV	ORF1ab:nsp3	0.988375996642887
CAMB-7A70C	MN908947.3	9286	C	T	0.015	0.014	1.6e-08	5.4e-08	0.0149239633512799	ACA	ORF1ab:nsp4	N244N	C732T	AAC>AAT	Synonymous	ORF1ab:nsp4	0.98507603664872
CAMB-7A71B	MN908947.3	11075	T	-	0.03	0.033	8.8e-08	1.1e-08	0.0311102831594635	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.965039741679086
CAMB-7A71B	MN908947.3	13778	AT	-	0.015	0.0135	1.2e-05;1.3e-05	3.6e-05;3.8e-05	0.0142532261476624	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.98624429656993
CAMB-7A71B	MN908947.3	14408	C	T	1	1	0	0	0.998624163421402	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000594641233122683
CAMB-7A71B	MN908947.3	1547	A	-	0.0097	0.0074	5e-06	3.3e-05	0.00910139725676195	TAG	ORF1ab:nsp2	.	742-742-delfrshift	.	no-SNV	ORF1ab:nsp2	0.95359569285989
CAMB-7A71B	MN908947.3	1547	A	G	0.014	0.014	1.5e-07	5.7e-07	0.0141007563132932	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.95359569285989
CAMB-7A71B	MN908947.3	1547	A	T	0.022	0.024	6.5e-11	4.9e-11	0.0228175874887835	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.95359569285989
CAMB-7A71B	MN908947.3	23403	A	G	1	1	0	0	0.999235721478924	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000242770824341821
CAMB-7A71B	MN908947.3	241	C	T	1	1	0	0	0.998850680397205	TCG	NA	NA	NA	NA	NA	NA	6.12970454824077e-05
CAMB-7A71B	MN908947.3	28086	G	T	1	1	0	0	0.999234345091605	GGC	ORF8	A65S	G193T	GCT>TCT	Missense	GU280_gp09	5.46896363139185e-05
CAMB-7A71B	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999191902007486	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000141643059490085
CAMB-7A71B	MN908947.3	29767	A	G	0.71	0.71	0	0	0.706758385930076	GAA	NA	NA	NA	NA	NA	NA	0.293099780157436
CAMB-7A71B	MN908947.3	3037	C	T	1	1	0	0	0.999127834537752	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	9.34462995265387e-05
CAMB-7A71B	MN908947.3	313	C	T	1	1	0	0	0.998974358974359	TCA	ORF1ab:leader-protein	L16L	C48T	CTC>CTT	Synonymous	ORF1ab:leader-protein	9.32400932400932e-05
CAMB-7A71B	MN908947.3	3903	C	T	0.075	0.069	2.8e-33	7.2e-31	0.0724182596067041	CCA	ORF1ab:nsp3	P395L	C1184T	CCA>CTA	Missense	ORF1ab:nsp3	0.927542489304078
CAMB-7A71B	MN908947.3	4950	T	C	0.048	0.056	1.7e-22	8.3e-26	0.0516387499539159	TTG	ORF1ab:nsp3	L744S	T2231C	TTG>TCG	Missense	ORF1ab:nsp3	0.948164624629791
CAMB-7A71B	MN908947.3	8389	C	T	0.019	0.018	7.7e-10	1e-09	0.0187243295482	ACA	ORF1ab:nsp3	N1890N	C5670T	AAC>AAT	Synonymous	ORF1ab:nsp3	0.98111460095031
CAMB-7A72A	MN908947.3	13730	C	T	1	1	0	0	0.999862239977958	GCT	ORF1ab:RNA-dependent-RNA-polymerase	A88V	C263T	GCT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-7A72A	MN908947.3	14408	C	T	1	1	0	0	0.999698976520169	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-7A72A	MN908947.3	17350	GT	TC	0.016	0.012	3.7e-09;1.5e-09	NA;2.7e-12	0.0142565176212552	TGT	ORF1ab:helicase	.	1114-1115-mnv	.	no-SNV	ORF1ab:helicase	0.990618685653805
CAMB-7A72A	MN908947.3	17351	T	C	0.017	0.024	1.5e-09	2.7e-12	0.0196017584690975	GTC	ORF1ab:helicase	V372A	T1115C	GTC>GCC	Missense	ORF1ab:helicase	0.980398241530902
CAMB-7A72A	MN908947.3	23403	A	G	1	1	0	0	0.999951606658924	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.4196670538134e-05
CAMB-7A72A	MN908947.3	241	C	T	1	1	0	0	0.999896120085182	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-7A72A	MN908947.3	25429	G	T	1	1	0	0	0.999851895734597	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	7.40521327014218e-05
CAMB-7A72A	MN908947.3	29364	C	T	0.028	0.047	1.6e-06	1e-08	0.0368098159509202	CCA	N	P364L	C1091T	CCA>CTA	Missense	GU280_gp10	0.96319018404908
CAMB-7A72A	MN908947.3	3037	C	T	1	1	0	7.1e-302	0.999547715965626	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A739	MN908947.3	11074	C	INS	0.15	0.037	7.8e-67	7.1e-08	0.116124419020379	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.883518055058992
CAMB-7A739	MN908947.3	11083	G	-	0.18	0.15	1.2e-79	2.5e-68	0.169920062517298	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.62805463751364e-05
CAMB-7A739	MN908947.3	11083	G	T	0.82	0.85	0	0	0.8298845709262	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.62805463751364e-05
CAMB-7A739	MN908947.3	12125	T	C	0.018	0.032	1.4e-08	1.7e-14	0.0224728013007786	ATA	ORF1ab:nsp8	Y12H	T34C	TAT>CAT	Missense	ORF1ab:nsp8	0.977447882929925
CAMB-7A739	MN908947.3	14805	C	T	1	1	0	0	0.999931126314339	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	4.59157904403324e-05
CAMB-7A739	MN908947.3	15971	TAGATGA	-	0.0358571428571429	0.00358428571428571	6.9e-17;1.7e-17;2.8e-15;6.3e-17;4.1e-14;1.4e-16;4.2e-10	NA;NA;NA;NA;NA;NA;6.8e-08	0.0231052431128602	GTA	ORF1ab:RNA-dependent-RNA-polymerase	.	2504-2510-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.977468440383963
CAMB-7A739	MN908947.3	15977	AT	-	0.017047	0.025	4.2e-10;0.48	6.8e-08;2.4e-09	0.0198415155079552	GAT	ORF1ab:RNA-dependent-RNA-polymerase	.	2510-2511-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.968816771436534
CAMB-7A739	MN908947.3	17247	T	C	1	1	0	0	0.999831174782336	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.00012058944118853
CAMB-7A739	MN908947.3	17641	G	T	0.25	0.17	7.6e-121	6.3e-77	0.216110545766161	AGC	ORF1ab:helicase	A469S	G1405T	GCT>TCT	Missense	ORF1ab:helicase	0.783782336243372
CAMB-7A739	MN908947.3	17847	G	A	1	1	0	0	0.999769638332182	AGG	ORF1ab:helicase	Q537Q	G1611A	CAG>CAA	Synonymous	ORF1ab:helicase	8.63856254319281e-05
CAMB-7A739	MN908947.3	18028	G	T	0.014	0.0084	2.2e-07	6.5e-05	0.0116654832118481	GGC	ORF1ab:helicase	A598S	G1792T	GCA>TCA	Missense	ORF1ab:helicase	0.98788528699987
CAMB-7A739	MN908947.3	1813	T	INS	0.02	0.012	2.8e-07	0.00023	0.0167727996361155	CTA	ORF1ab:nsp2	.	1007-1008-insfrshift	.	no-SNV	ORF1ab:nsp2	0.983113486468046
CAMB-7A739	MN908947.3	26144	G	T	1	1	1.8e-152	9e-127	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7A739	MN908947.3	26270	C	T	0.032	0.15	4.2e-15	2.8e-62	0.0655344936931858	ACA	E	T9I	C26T	ACA>ATA	Missense	GU280_gp04	0.934395039109295
CAMB-7A739	MN908947.3	26927	A	G	1	1	0	0	0.999881079795457	AAA	M	E135E	A405G	GAA>GAG	Synonymous	GU280_gp05	0
CAMB-7A739	MN908947.3	28820	T	C	0.02	0.011	5.6e-09	4.6e-05	0.0166432725085222	CTC	N	S183P	T547C	TCT>CCT	Missense	GU280_gp10	0.983356727491478
CAMB-7A739	MN908947.3	28820	TCT	CTC	0.0206666666666667	0.00366666666666667	5.6e-09;9.7e-09;1.9e-09	4.6e-05;NA;NA	0.0124323240425105	CTC	N	.	547-549-mnv	.	no-SNV	GU280_gp10	0.983356727491478
CAMB-7A739	MN908947.3	29465	G	T	0.15	0.21	5.5e-34	3.3e-50	0.183195592286501	TGC	N	A398S	G1192T	GCA>TCA	Missense	GU280_gp10	0.816804407713499
CAMB-7A739	MN908947.3	9438	C	T	0.24	0.18	9.6e-98	7.4e-61	0.221288515406162	ACA	ORF1ab:nsp4	T295I	C884T	ACA>ATA	Missense	ORF1ab:nsp4	0.778711484593838
CAMB-7A739	MN908947.3	9479	G	T	0.38	0.35	4.5e-164	1.3e-130	0.36849710982659	TGG	ORF1ab:nsp4	G309C	G925T	GGT>TGT	Missense	ORF1ab:nsp4	0.63150289017341
CAMB-7A739	MN908947.3	9519	T	C	0.1	0.02	2.3e-48	4e-11	0.0684568553608907	TTC	ORF1ab:nsp4	F322S	T965C	TTC>TCC	Missense	ORF1ab:nsp4	0.931513374317143
CAMB-7A739	MN908947.3	9603	C	T	0.021	0.038	5.4e-11	1.6e-18	0.0282486887094753	ACA	ORF1ab:nsp4	T350I	C1049T	ACA>ATA	Missense	ORF1ab:nsp4	0.971715508136267
CAMB-7A748	MN908947.3	14408	C	T	1	1	0	0	0.998918825411928	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000908186653980885
CAMB-7A748	MN908947.3	16289	C	T	1	1	0	1.3e-242	1	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0
CAMB-7A748	MN908947.3	23403	A	G	1	1	0	0	0.999881703470032	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000118296529968454
CAMB-7A748	MN908947.3	241	C	T	1	1	0	0	0.999742500321875	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-7A748	MN908947.3	25429	G	T	1	1	0	0	1	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0
CAMB-7A748	MN908947.3	29810	G	T	1	1	4.3e-256	5.4e-128	1	TGT	NA	NA	NA	NA	NA	NA	0
CAMB-7A748	MN908947.3	3037	C	T	1	1	1.2e-219	5e-263	0.998778998778999	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A757	MN908947.3	11075	T	-	0.036	0.048	5.1e-09	2.1e-12	0.0395046001415428	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956801132342534
CAMB-7A757	MN908947.3	14408	C	T	1	1	0	0	0.995562051554611	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000863672601647622
CAMB-7A757	MN908947.3	1577	G	A	0.0081	0.0043	1.7e-05	4e-04	0.00648760866744518	TGT	ORF1ab:nsp2	V258I	G772A	GTT>ATT	Missense	ORF1ab:nsp2	0.992993382639159
CAMB-7A757	MN908947.3	17999	C	T	0.007	0.0074	7.6e-05	3.9e-05	0.00710278501302344	ACA	ORF1ab:helicase	T588I	C1763T	ACA>ATA	Missense	ORF1ab:helicase	0.992416349428972
CAMB-7A757	MN908947.3	20268	A	G	1	1	2e-294	2.6e-269	1	TAG	ORF1ab:endoRNAse	L216L	A648G	TTA>TTG	Synonymous	ORF1ab:endoRNAse	0
CAMB-7A757	MN908947.3	20739	T	A	0.0091	0.01	5.2e-06	1.2e-06	0.00938092895790879	TTC	ORF1ab:2'-O-ribose-methyltransferase	L27L	T81A	CTT>CTA	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.990232590822852
CAMB-7A757	MN908947.3	21982	TTTGGGTGT	-	0.0425555555555556	0.0368888888888889	1.2e-07;6e-07;5e-07;1.8e-08;1.5e-07;3e-07;1.6e-07;7.5e-08;6.8e-08	5.3e-06;5.9e-06;5.2e-06;2.1e-07;1.3e-06;1.9e-06;1.6e-06;5.4e-07;9.4e-08	0.0419854690413425	TTT	S	.	420-428-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.962736554594524
CAMB-7A757	MN908947.3	21991	TTA	-	0.216666666666667	0.22	1.4e-11;8.7e-22;7.8e-22	4.3e-12;2.1e-22;3.2e-22	0.217063876119042	TTT	S	.	429-431-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.780051861455825
CAMB-7A757	MN908947.3	22005	A	C	0.023	0.027	1.7e-11	2.2e-13	0.0243537255819394	AAC	S	N148T	A443C	AAC>ACC	Missense	GU280_gp02, spike glycoprotein	0.97541232892736
CAMB-7A757	MN908947.3	22012	A	C	0.0088	0.0091	1e-05	2.9e-06	0.00889476805181773	AAA	S	K150N	A450C	AAA>AAC	Missense	GU280_gp02, spike glycoprotein	0.991082424850613
CAMB-7A757	MN908947.3	23403	A	G	1	1	0	0	0.999228250213796	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.34324093194001e-05
CAMB-7A757	MN908947.3	241	C	T	1	1	0	0	0.998320985581464	TCG	NA	NA	NA	NA	NA	NA	0.000503704325560896
CAMB-7A757	MN908947.3	26526	G	T	1	1	0	0	0.999603279555673	GGC	M	A2S	G4T	GCA>TCA	Missense	GU280_gp05	0.000132240148108966
CAMB-7A757	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0313513513513514	0.0301621621621622	0.0015;0.00013;0.00067;0.00066;0.0015;6.4e-06;5.8e-05;3.4e-05;3.2e-05;7.2e-06;1.4e-05;1.1e-05;3.1e-05;1.3e-05;1.8e-05;3.2e-05;1.2e-05;2.7e-05;1.7e-05;1.8e-05;1.2e-05;3e-05;1.3e-05;2.1e-05;1.5e-05;1.1e-05;2.3e-05;1.3e-05;1.3e-05;1.3e-05;2.5e-05;2.1e-05;9.9e-06;2.4e-05;9.8e-06;1.6e-05;1e-05	0.00071;0.00011;0.00015;0.00013;0.00036;1.4e-05;4.9e-05;4.1e-05;3.8e-05;2.5e-05;2.2e-05;1.9e-05;3.4e-05;3e-05;3.8e-05;5.1e-05;2.5e-05;4.6e-05;2.4e-05;3.1e-05;3.4e-05;5e-05;3.1e-05;4.1e-05;2.7e-05;2.2e-05;4e-05;3.1e-05;5e-06;3.2e-05;4.5e-05;4.3e-05;2.1e-05;4.7e-05;1e-05;2.7e-05;1.7e-05	0.0319665631401573	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.979218551566031
CAMB-7A757	MN908947.3	28854	C	T	1	1	0	0	0.999417376738766	TCA	N	S194L	C581T	TCA>TTA	Missense	GU280_gp10	0
CAMB-7A757	MN908947.3	3037	C	T	1	1	0	0	0.998784576697402	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.19111483654652e-05
CAMB-7A757	MN908947.3	5025	C	T	0.0096	0.016	0.00018	5.3e-06	0.0124269005847953	TCA	ORF1ab:nsp3	S769L	C2306T	TCA>TTA	Missense	ORF1ab:nsp3	0.985380116959064
CAMB-7A757	MN908947.3	5164	G	A	0.015	0.013	1.2e-07	7.7e-07	0.0142480211081794	AGT	ORF1ab:nsp3	E815E	G2445A	GAG>GAA	Synonymous	ORF1ab:nsp3	0.985751978891821
CAMB-7A757	MN908947.3	5790	A	G	0.0056	0.0088	0.00014	4.8e-06	0.00671721750597544	AAA	ORF1ab:nsp3	K1024R	A3071G	AAA>AGA	Missense	ORF1ab:nsp3	0.992870683260529
CAMB-7A757	MN908947.3	5817	C	T	0.0078	0.0073	2.1e-05	2.9e-05	0.00763014601324871	GCT	ORF1ab:nsp3	A1033V	C3098T	GCT>GTT	Missense	ORF1ab:nsp3	0.987375576596261
CAMB-7A757	MN908947.3	7798	G	T	1	1	0	0	0.998789956640113	AGA	ORF1ab:nsp3	K1693N	G5079T	AAG>AAT	Missense	ORF1ab:nsp3	0.000100836946657255
CAMB-7A766	MN908947.3	11074	C	INS	0.034	0.02	2.8e-07	0.001	0.0264956584083486	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.971958894288218
CAMB-7A766	MN908947.3	11075	T	-	0.025	0.035	7.2e-07	5.6e-09	0.0298597597799101	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.965188217137489
CAMB-7A766	MN908947.3	14408	C	T	0.012	0.013	1.2e-06	9.2e-07	0.0127044733480751	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.987268057520362
CAMB-7A766	MN908947.3	15183	C	T	0.0065	0.0047	2.8e-05	0.00018	0.00560386473429952	CCA	ORF1ab:RNA-dependent-RNA-polymerase	A572A	C1716T	GCC>GCT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.9943961352657
CAMB-7A766	MN908947.3	1605	ATG	-	0.98	0.98	0;0;0	0;0;0	0.981935080823594	AAT	ORF1ab:nsp2	.	800-802-delinframe	.	no-SNV	ORF1ab:nsp2	0.016193277967249
CAMB-7A766	MN908947.3	16466	C	T	0.019	0.023	2.3e-06	1.8e-07	0.0211762887394698	CCA	ORF1ab:helicase	P77L	C230T	CCA>CTA	Missense	ORF1ab:helicase	0.97882371126053
CAMB-7A766	MN908947.3	18083	T	C	0.98	0.99	0	0	0.985442329227324	ATC	ORF1ab:3'-to-5'-exonuclease	I15T	T44C	ATC>ACC	Missense	ORF1ab:3'-to-5'-exonuclease	0.0144971399170727
CAMB-7A766	MN908947.3	1912	C	T	0.98	0.98	0	0	0.983952236333517	CCC	ORF1ab:nsp2	S369S	C1107T	TCC>TCT	Synonymous	ORF1ab:nsp2	0.0160477636664826
CAMB-7A766	MN908947.3	20275	GATGAATTCATTGAACGGTATAAATTAGAAGGCTATGCCTTCGAACATATCGTTTATGGAGATT	-	0.024734375	0.406875	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.013;0.0073;0.01;0.012;0.0067;0.012;0.012;0.012;0.012;0.012;0.013;0.0084;0.0052;0.0051;0.0083;0.012;0.011;0.0099;0.0077;0.012;0.0089;0.0087;0.011;0.0095;0.011;0.0098;0.0051;0.0031;0.0064;0.0053;0.0076;0.0082;0.0073;0.0057;0.0066;0.0062;0.0056;0.0047	4.4e-61;1.8e-63;1e-61;3.2e-61;7.5e-66;1.7e-57;9.4e-55;1.1e-56;1e-54;4.6e-53;3.8e-53;3.6e-51;1.2e-50;3.9e-50;4e-53;2.3e-52;2.5e-54;3.8e-53;1.4e-62;1.9e-63;9.2e-51;4.7e-50;2.4e-50;4.2e-51;2.5e-50;2.8e-50;3.2e-47;8.1e-58;2e-50;1.3e-47;1.7e-54;5.2e-48;3.7e-48;2.1e-44;8.4e-48;1.8e-47;1.6e-48;1.3e-51;3.9e-62;6.9e-67;1.3e-54;1.2e-48;5.5e-48;1.4e-51;1.3e-51;1.1e-48;4e-52;1.5e-51;1.7e-48;1e-54;3.9e-52;5.3e-51;4.6e-74;3.2e-77;8.8e-62;1.1e-61;1.4e-58;3.2e-51;3.2e-58;3e-58;8.5e-53;8.1e-55;3.3e-63;1.2e-62	0.320689655172414	GGA	ORF1ab:endoRNAse	.	655-718-delfrshift	.	no-SNV	ORF1ab:endoRNAse	0.714285714285714
CAMB-7A766	MN908947.3	21601	TCAGTGTGT	-	0.077	0.111111111111111	1.5e-25;8.5e-25;2.2e-25;3e-24;2e-24;9.3e-25;1.5e-25;8.1e-25;1e-25	1e-39;3.5e-39;2.7e-39;1e-38;1.1e-38;2.3e-39;2.6e-40;1.5e-39;1.7e-40	0.0969503868912153	GTC	S	.	39-47-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.901022304832714
CAMB-7A766	MN908947.3	21762	C	A	0.013	0.011	1e-07	7.9e-07	0.0118681318681319	GCT	S	A67D	C200A	GCT>GAT	Missense	GU280_gp02, spike glycoprotein	0.988131868131868
CAMB-7A766	MN908947.3	21981	TTTTGGGTGT	-	0.0373	0.0738	0.00013;2.4e-08;5.6e-07;4.3e-07;8.3e-08;5.8e-07;1.1e-06;6.5e-07;3.2e-07;0.00019	3.4e-07;4.8e-14;1.3e-12;5.2e-13;9e-15;8.7e-13;2.8e-12;1.3e-12;2.4e-13;4.2e-13	0.0603789592760181	TTT	S	.	419-428-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.970473295701259
CAMB-7A766	MN908947.3	22293	T	C	0.019	0.036	2.7e-10	2.7e-17	0.0284137519576404	TTA	S	L244S	T731C	TTA>TCA	Missense	GU280_gp02, spike glycoprotein	0.967633678872399
CAMB-7A766	MN908947.3	22313	C	T	0.006	0.0077	2.8e-05	6.4e-06	0.00689853406151193	TCC	S	P251S	C751T	CCT>TCT	Missense	GU280_gp02, spike glycoprotein	0.992957746478873
CAMB-7A766	MN908947.3	23403	A	G	0.025	0.017	1.4e-09	9.1e-07	0.0208524751809605	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.97914752481904
CAMB-7A766	MN908947.3	2398	G	A	0.026	0.014	5.8e-11	1.2e-06	0.020049504950495	CGC	ORF1ab:nsp2	T531T	G1593A	ACG>ACA	Synonymous	ORF1ab:nsp2	0.979950495049505
CAMB-7A766	MN908947.3	241	C	T	0.0081	0.028	6.6e-05	1.5e-12	0.0190008997043828	TCG	NA	NA	NA	NA	NA	NA	0.980934835696842
CAMB-7A766	MN908947.3	25047	C	T	0.98	0.99	0	0	0.98253488037058	CCA	S	P1162L	C3485T	CCA>CTA	Missense	GU280_gp02, spike glycoprotein	0.0174651196294203
CAMB-7A766	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0476486486486487	0.0264594594594595	6.8e-06;8.4e-08;3.6e-06;4e-06;1.4e-05;2.4e-09;4.8e-08;1.7e-08;1.7e-08;2.9e-09;5.4e-09;2.8e-09;1.7e-08;7.7e-09;1.1e-08;2.8e-08;6.1e-09;2.2e-08;1.2e-08;1.2e-08;6.5e-09;2.5e-08;1.1e-08;1.5e-08;9.5e-09;4.6e-09;1.8e-08;8.3e-09;3.8e-09;7.1e-09;1.9e-08;1.6e-08;6.6e-09;1.6e-08;2.8e-09;7.8e-09;3.3e-09	0.009;0.0027;0.0079;0.0083;0.012;0.00019;0.00042;0.00037;0.00036;9.2e-05;8.7e-05;7.3e-05;0.00011;9.8e-05;0.00012;0.00016;9.2e-05;0.00014;9.9e-05;0.00011;0.00011;0.00017;0.00013;0.00012;9.8e-05;7.2e-05;0.00013;1e-04;6.1e-05;9.4e-05;0.00014;0.00013;6.6e-05;0.00014;4.5e-05;9.2e-05;5e-05	0.0379975691279246	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.97627262916293
CAMB-7A766	MN908947.3	26858	C	T	0.028	0.024	3.1e-14	2.1e-12	0.0257956108685015	TCA	M	F112F	C336T	TTC>TTT	Synonymous	GU280_gp05	0.974176691625197
CAMB-7A766	MN908947.3	27882	G	A	0.0093	0.016	6.4e-05	4.2e-07	0.0123497997329773	CGC	NA	NA	NA	NA	NA	NA	0.9869826435247
CAMB-7A766	MN908947.3	28311	C	T	0.0057	0.01	0.00037	3.6e-06	0.00834515968608614	CCC	N	P13L	C38T	CCC>CTC	Missense	GU280_gp10	0.991606321943646
CAMB-7A766	MN908947.3	28881	GGG	AAC	0.02	0.021	2.3e-09;2.6e-10;8.2e-11	6.7e-10;1.1e-10;9.1e-11	0.0210192128742679	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.980291251505529
CAMB-7A766	MN908947.3	29726	TT	-	0.0042	0.0098	0.0087;0.0087	3.5e-05;7.1e-05	0.00726177825008856	ATT	NA	NA	NA	NA	NA	NA	0.991722437477985
CAMB-7A766	MN908947.3	3037	C	T	0.017	0.02	8.1e-05	2.6e-05	0.018866117601992	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.981038115303582
CAMB-7A766	MN908947.3	550	T	C	0.043	0.022	1.7e-20	1.2e-11	0.032247228753779	TTC	ORF1ab:leader-protein	I95I	T285C	ATT>ATC	Synonymous	ORF1ab:leader-protein	0.967730377337364
CAMB-7A766	MN908947.3	5777	C	T	0.012	0.008	2.7e-07	1.1e-05	0.00967979635584137	ACA	ORF1ab:nsp3	H1020Y	C3058T	CAT>TAT	Missense	ORF1ab:nsp3	0.990253215434084
CAMB-7A775	MN908947.3	11074	C	INS	0.036	0.037	1.1e-07	3.9e-08	0.0366881095663001	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.962938368956215
CAMB-7A775	MN908947.3	11083	G	-	0.1	0.23	2.9e-45	7.5e-106	0.154546095788954	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-7A775	MN908947.3	11083	G	T	0.9	0.77	0	3.4e-299	0.845348099033646	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-7A775	MN908947.3	14805	C	T	1	1	0	0	0.999944149678861	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	5.58503211393465e-05
CAMB-7A775	MN908947.3	1547	A	T	0.18	0.31	2.6e-28	8.9e-58	0.256	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.744
CAMB-7A775	MN908947.3	2480	A	G	1	1	0	7.19999999999999e-288	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-7A775	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-7A775	MN908947.3	4744	T	C	1	1	0	0	1	CTT	ORF1ab:nsp3	S675S	T2025C	TCT>TCC	Synonymous	ORF1ab:nsp3	0
CAMB-7A784	MN908947.3	11139	C	T	0.33	0.3	1.3e-169	2.4e-149	0.317557438737113	GCA	ORF1ab:nsp6	A56V	C167T	GCA>GTA	Missense	ORF1ab:nsp6	0.682411968060697
CAMB-7A784	MN908947.3	14408	C	T	1	1	0	0	0.999220551459842	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000584586405118379
CAMB-7A784	MN908947.3	1814	AA	-	0.00475	0.0175	0.0019;NA	1.4e-06;2e-09	0.0089984206853491	TAA	ORF1ab:nsp2	.	1009-1010-delfrshift	.	no-SNV	ORF1ab:nsp2	0.987445276601903
CAMB-7A784	MN908947.3	2189	C	T	1	1	0	0	0.999204708127883	TCT	ORF1ab:nsp2	L462F	C1384T	CTT>TTT	Missense	ORF1ab:nsp2	0.00047717512327024
CAMB-7A784	MN908947.3	22584	T	-	0.022	0.026	1.2e-05	1e-06	0.0238849181217769	GTT	S	.	1022-1022-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.962679815434724
CAMB-7A784	MN908947.3	23403	A	G	1	1	0	0	0.99977168475892	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00015566948255464
CAMB-7A784	MN908947.3	241	C	T	1	1	0	0	0.99985990473522	TCG	NA	NA	NA	NA	NA	NA	0.000100068046271465
CAMB-7A784	MN908947.3	25690	G	A	1	1	0	0	1	TGG	ORF3a	G100S	G298A	GGC>AGC	Missense	GU280_gp03	0
CAMB-7A784	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0559189189189189	0.0955675675675676	4.8e-10;1.3e-13;1.2e-10;1.9e-10;1.2e-09;1.9e-12;7.9e-11;2.7e-09;2.5e-09;2.6e-10;8.4e-10;5.5e-10;2.4e-09;1.1e-09;1.8e-09;4.3e-09;8.5e-10;3.3e-09;1.3e-09;1.5e-09;1.8e-09;3.6e-09;1.5e-09;2.5e-09;1.4e-09;5.7e-10;2.5e-09;1.1e-09;6.1e-10;1.1e-09;2.8e-09;2.5e-09;5.9e-10;2.9e-09;2.7e-10;1e-09;4.7e-10	1.9e-18;1e-23;2.1e-19;3.6e-19;9.7e-18;3e-21;4.1e-20;2.5e-17;2.7e-17;2.5e-18;6.3e-18;3.6e-18;2.5e-17;6.3e-18;1.5e-17;4.9e-17;4.3e-18;3.8e-17;1.8e-17;1.4e-17;4.3e-18;4.2e-17;5e-18;1.5e-17;9e-18;2.1e-18;2.3e-17;6e-18;3.2e-18;9.4e-18;2.2e-17;1.9e-17;5.4e-18;2.4e-17;2.9e-19;5.3e-18;1.4e-18	0.0695637667862207	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.930508568576341
CAMB-7A784	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A784	MN908947.3	29164	T	C	0.0088	0.016	6e-06	5.3e-09	0.0117084154235857	ATT	N	D297D	T891C	GAT>GAC	Synonymous	GU280_gp10	0.987053194483535
CAMB-7A784	MN908947.3	29635	C	T	0.0048	0.0082	4e-04	1.5e-05	0.0065164268259571	ACA	ORF10	Y26Y	C78T	TAC>TAT	Synonymous	GU280_gp11	0.993483573174043
CAMB-7A784	MN908947.3	3037	C	T	1	1	0	0	0.99931693989071	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A793	MN908947.3	1059	C	T	1	1	0	0	0.999797476557912	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	8.10093768353687e-05
CAMB-7A793	MN908947.3	11075	T	-	0.043	0.039	3.7e-11	3.7e-10	0.0406489178598894	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.954974914856996
CAMB-7A793	MN908947.3	11572	C	T	0.024	0.024	9.1e-12	1.6e-11	0.0239788660841292	TCT	ORF1ab:nsp6	F200F	C600T	TTC>TTT	Synonymous	ORF1ab:nsp6	0.975817923186344
CAMB-7A793	MN908947.3	14408	C	T	1	1	0	0	0.998014501492801	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000397099701439854
CAMB-7A793	MN908947.3	16329	C	T	1	1	0	0	0.999753116899148	ACG	ORF1ab:helicase	Y31Y	C93T	TAC>TAT	Synonymous	ORF1ab:helicase	3.08603876064683e-05
CAMB-7A793	MN908947.3	18555	C	T	0.17	0.17	8.1e-78	1.5e-78	0.167973620316294	ACA	ORF1ab:3'-to-5'-exonuclease	D172D	C516T	GAC>GAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.831796705820592
CAMB-7A793	MN908947.3	23403	A	G	1	1	0	0	0.999593765791116	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.95407571809328e-05
CAMB-7A793	MN908947.3	23535	ACTC	-	0.007075	0.009025	0.0043;2.3e-05;0.00081;0.00031	0.00074;2.8e-06;0.00022;0.00011	0.00900939186604904	AAC	S	.	1973-1976-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.995186468127221
CAMB-7A793	MN908947.3	23536	CTC	-	0.00816666666666667	0.0101666666666667	2.3e-05;0.00081;0.00031	2.8e-06;0.00022;0.00011	0.00862911103874959	ACT	S	.	1974-1976-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	8.89125989152663e-05
CAMB-7A793	MN908947.3	23555	CCCATTGGTGCAGGTATATGCGCTAGT	-	0.0424814814814815	0.0473703703703704	0.00079;0.00064;0.00086;0.00098;8.9e-05;0.00018;4.1e-05;9.2e-05;1e-04;1e-04;9.4e-05;8.5e-05;4.9e-05;4.2e-05;1e-05;1.8e-06;6.7e-05;2.8e-05;8.3e-05;2.5e-05;6.6e-05;0.00013;7.8e-05;9.9e-05;1.3e-06;3.1e-06;0.00073	0.00033;0.00027;0.00034;5e-04;2.8e-05;6.1e-05;1.3e-05;3.1e-05;3.4e-05;3.4e-05;3.3e-05;3.2e-05;1.5e-05;1.4e-05;3e-06;1.1e-06;1.8e-05;7.6e-06;2.4e-05;6.9e-06;2.1e-05;4.7e-05;2.2e-05;3.2e-05;4.3e-07;8.3e-07;0.00048	0.0426708484648399	ACC	S	.	1993-2019-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.962186416479706
CAMB-7A793	MN908947.3	241	C	T	1	1	0	0	0.998859639260532	TCG	NA	NA	NA	NA	NA	NA	0.000160614188657426
CAMB-7A793	MN908947.3	25563	G	T	1	1	0	0	0.999047421826465	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000144957548146614
CAMB-7A793	MN908947.3	25731	C	T	1	1	0	0	0.999712064497553	ACT	ORF3a	Y113Y	C339T	TAC>TAT	Synonymous	GU280_gp03	6.39856672105448e-05
CAMB-7A793	MN908947.3	28087	C	T	0.0088	0.0088	3.5e-05	3.5e-05	0.00881595881595882	GCT	ORF8	A65V	C194T	GCT>GTT	Missense	GU280_gp09	0.990926640926641
CAMB-7A793	MN908947.3	28311	C	T	0.0098	0.0089	5.4e-06	1.4e-05	0.00933666442458602	CCC	N	P13L	C38T	CCC>CTC	Missense	GU280_gp10	0.990583261266455
CAMB-7A793	MN908947.3	29625	C	T	1	1	0	0	0.999676763945327	TCT	ORF10	S23F	C68T	TCT>TTT	Missense	GU280_gp11	9.23531584780199e-05
CAMB-7A793	MN908947.3	3037	C	T	1	1	0	0	0.99908043158411	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000183913683178028
CAMB-7A793	MN908947.3	3333	TTG	-	0.25	0.25	1.4e-52;2.2e-45;9.7e-44	3.4e-51;1.6e-44;1.8e-42	0.250596569724087	ATT	ORF1ab:nsp3	.	614-616-delinframe	.	no-SNV	ORF1ab:nsp3	0.740675768438716
CAMB-7A793	MN908947.3	3903	C	T	0.0061	0.0078	0.00012	2.3e-05	0.00700142216387704	CCA	ORF1ab:nsp3	P395L	C1184T	CCA>CTA	Missense	ORF1ab:nsp3	0.992998577836123
CAMB-7A7A2	MN908947.3	11075	T	-	0.041	0.039	4.4e-11	2.2e-10	0.039597888112634	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955869020318916
CAMB-7A7A2	MN908947.3	14408	C	T	1	1	0	0	0.997888901654412	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000287224264705882
CAMB-7A7A2	MN908947.3	23403	A	G	1	1	0	0	0.999639189320004	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.92023443893939e-05
CAMB-7A7A2	MN908947.3	241	C	T	1	1	0	0	0.998641094005332	TCG	NA	NA	NA	NA	NA	NA	0.000103208050227918
CAMB-7A7A2	MN908947.3	24237	C	G	0.013	0.01	1.9e-07	1.6e-06	0.0114105547631559	GCT	S	A892G	C2675G	GCT>GGT	Missense	GU280_gp02, spike glycoprotein	0.988063959162225
CAMB-7A7A2	MN908947.3	26137	A	C	0.022	0.02	3.9e-05	9.7e-05	0.0209144670416847	AAT	ORF3a	I249L	A745C	ATC>CTC	Missense	GU280_gp03	0.97894129525458
CAMB-7A7A2	MN908947.3	26164	C	T	0.065	0.064	1.5e-28	3.1e-28	0.0641598119858989	TCC	ORF3a	P258S	C772T	CCA>TCA	Missense	GU280_gp03	0.935323149236193
CAMB-7A7A2	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999413871703028	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000215455328928469
CAMB-7A7A2	MN908947.3	3037	C	T	1	1	0	0	0.998861807763256	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000215864044899721
CAMB-7A7A2	MN908947.3	313	C	T	1	1	0	0	0.9978669464114	TCA	ORF1ab:leader-protein	L16L	C48T	CTC>CTT	Synonymous	ORF1ab:leader-protein	5.24521374246001e-05
CAMB-7A7A2	MN908947.3	6384	C	T	0.0085	0.0068	2e-05	0.00011	0.00760828938078824	GCC	ORF1ab:nsp3	A1222V	C3665T	GCC>GTC	Missense	ORF1ab:nsp3	0.992275426720379
CAMB-7A7B1	MN908947.3	11074	C	INS	0.11	0.11	1.1e-46	4.4e-48	0.11377178063368	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.881351159568836
CAMB-7A7B1	MN908947.3	11083	G	-	0.15	0.15	3.2e-66	1.9e-67	0.153069145434358	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	9.82598186123748e-06
CAMB-7A7B1	MN908947.3	11083	G	T	0.85	0.85	0	0	0.846714682964695	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	9.82598186123748e-06
CAMB-7A7B1	MN908947.3	14376	C	T	0.0073	0.0088	4.2e-05	9.7e-06	0.00807741194800935	ACT	ORF1ab:RNA-dependent-RNA-polymerase	N303N	C909T	AAC>AAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.991891836483661
CAMB-7A7B1	MN908947.3	14805	C	T	1	1	0	0	0.99943419808134	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	3.37792190244562e-05
CAMB-7A7B1	MN908947.3	1547	A	G	0.011	0.011	2.1e-06	2.6e-06	0.0112348477382478	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.970828816398936
CAMB-7A7B1	MN908947.3	1547	A	T	0.016	0.012	2.8e-08	7.8e-07	0.0136986301369863	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.970828816398936
CAMB-7A7B1	MN908947.3	16608	C	T	0.99	0.99	9.7e-281	2.2e-259	0.988636363636364	ACA	ORF1ab:helicase	N124N	C372T	AAC>AAT	Synonymous	ORF1ab:helicase	0.0113636363636364
CAMB-7A7B1	MN908947.3	2480	A	G	1	1	0	0	0.999793757734085	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-7A7B1	MN908947.3	2558	C	T	1	1	0	0	0.999763624425476	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-7A7B1	MN908947.3	26144	G	T	1	1	0	0	0.99984160925002	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000158390749980201
CAMB-7A7B1	MN908947.3	4127	G	A	0.012	0.012	3.2e-07	3e-07	0.0119189595933782	GGG	ORF1ab:nsp3	G470S	G1408A	GGT>AGT	Missense	ORF1ab:nsp3	0.988024249652157
CAMB-7A7B1	MN908947.3	7170	C	T	0.01	0.012	3e-05	4.9e-06	0.0114942528735632	CCT	ORF1ab:nsp3	P1484L	C4451T	CCT>CTT	Missense	ORF1ab:nsp3	0.988505747126437
CAMB-7A7C0	MN908947.3	1076	C	T	0.017	0.015	2.8e-09	1.3e-08	0.0162218162981543	TCC	ORF1ab:nsp2	P91S	C271T	CCA>TCA	Missense	ORF1ab:nsp2	0.98373728836664
CAMB-7A7C0	MN908947.3	11075	T	-	0.041	0.037	1.9e-10	1.4e-09	0.0392761722833873	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956671012042284
CAMB-7A7C0	MN908947.3	12815	C	T	0.012	0.012	3.6e-07	1.9e-07	0.0118922814834229	ACT	ORF1ab:nsp9	L44L	C130T	CTG>TTG	Synonymous	ORF1ab:nsp9	0.988042196304547
CAMB-7A7C0	MN908947.3	14408	C	T	1	1	0	0	0.999109164081496	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000324893099689779
CAMB-7A7C0	MN908947.3	20031	C	A	1	1	0	0	0.999151823579305	CCC	ORF1ab:endoRNAse	A137A	C411A	GCC>GCA	Synonymous	ORF1ab:endoRNAse	0
CAMB-7A7C0	MN908947.3	23403	A	G	1	1	0	0	0.999616846253695	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.69167852618739e-05
CAMB-7A7C0	MN908947.3	241	C	T	1	1	0	0	0.999215037338764	TCG	NA	NA	NA	NA	NA	NA	0.000169721656483367
CAMB-7A7C0	MN908947.3	25663	T	A	1	1	0	0	0.999365625063949	TTA	ORF3a	Y91N	T271A	TAC>AAC	Missense	GU280_gp03	0.000491128982749095
CAMB-7A7C0	MN908947.3	27046	C	T	1	1	0	0	0.999782666844991	ACG	M	T175M	C524T	ACG>ATG	Missense	GU280_gp05	0.000117025545004681
CAMB-7A7C0	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999462433594738	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000143497757847534
CAMB-7A7C0	MN908947.3	3037	C	T	1	1	0	0	0.999357426159403	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.86308745651548e-05
CAMB-7A7C0	MN908947.3	5227	A	G	0.018	0.018	6e-09	5.4e-09	0.0178073894609328	AAA	ORF1ab:nsp3	K836K	A2508G	AAA>AAG	Synonymous	ORF1ab:nsp3	0.982192610539067
CAMB-7A7DF	MN908947.3	11075	T	-	0.022	0.044	5.5e-06	7e-11	0.0329128165403272	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960456666482229
CAMB-7A7DF	MN908947.3	11109	C	T	1	1	0	0	0.999958989080843	GCT	ORF1ab:nsp6	A46V	C137T	GCT>GTT	Missense	ORF1ab:nsp6	1.02527297893064e-05
CAMB-7A7DF	MN908947.3	12416	A	-	0.0085	0.0044	8.6e-06	0.00035	0.00669456066945607	CAA	ORF1ab:nsp8	.	325-325-delfrshift	.	no-SNV	ORF1ab:nsp8	0.992983585452205
CAMB-7A7DF	MN908947.3	12493	C	T	0.0033	0.0071	0.0013	2.6e-05	0.00488324822765356	ACT	ORF1ab:nsp8	D134D	C402T	GAC>GAT	Synonymous	ORF1ab:nsp8	0.995116751772346
CAMB-7A7DF	MN908947.3	14408	C	T	0.99	1	0	0	0.994602415572955	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000369416424664703
CAMB-7A7DF	MN908947.3	15720	C	T	0.016	0.0095	2.5e-08	9.7e-06	0.0128169691758034	ACG	ORF1ab:RNA-dependent-RNA-polymerase	D751D	C2253T	GAC>GAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.987172793628369
CAMB-7A7DF	MN908947.3	1594	C	T	0.98	1	0	0	0.989112683723462	CCG	ORF1ab:nsp2	S263S	C789T	TCC>TCT	Synonymous	ORF1ab:nsp2	0.00163309744148067
CAMB-7A7DF	MN908947.3	16274	C	T	0.01	0.033	1.8e-06	1.7e-15	0.0227951153324288	TCA	ORF1ab:helicase	S13L	C38T	TCA>TTA	Missense	ORF1ab:helicase	0.977204884667571
CAMB-7A7DF	MN908947.3	16866	T	G	0.0041	0.011	0.00067	9.8e-07	0.00681841409820268	TTT	ORF1ab:helicase	V210V	T630G	GTT>GTG	Synonymous	ORF1ab:helicase	0.993137784526434
CAMB-7A7DF	MN908947.3	18502	A	-	0.011	0.01	1.9e-06	6.5e-06	0.0106666666666667	CAA	ORF1ab:3'-to-5'-exonuclease	.	463-463-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.989127147766323
CAMB-7A7DF	MN908947.3	22992	G	T	0.023	0.032	7.1e-12	2e-15	0.0271419890621835	AGC	S	S477I	G1430T	AGC>ATC	Missense	GU280_gp02, spike glycoprotein	0.972807372898521
CAMB-7A7DF	MN908947.3	23403	A	G	1	1	0	0	0.999899415893726	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.46612111763311e-05
CAMB-7A7DF	MN908947.3	23561	GGTGCAGGTATATGCGCTAGTTA	-	0.0334347826086957	0.0421304347826087	0.00042;0.00028;0.00031;0.00031;0.00028;0.00025;0.00017;0.00015;5.6e-05;7.6e-06;0.00017;6e-05;0.00064;0.00035;0.00071;0.0012;8e-04;0.0079;0.0015;0.00013;0.001;0.0041;0.023	8.4e-05;0.00017;0.00019;0.00019;0.00018;0.00018;1e-04;9.2e-05;3.7e-05;1.1e-05;4.5e-05;2e-05;4.1e-05;1.4e-05;4e-05;8.8e-05;4.4e-05;4.4e-05;5.9e-07;1e-06;6.5e-05;4.6e-05;6.7e-06	0.037547044498561	TGG	S	.	1999-2021-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.96280487804878
CAMB-7A7DF	MN908947.3	241	C	T	1	0.99	0	0	0.993103448275862	TCG	NA	NA	NA	NA	NA	NA	0.000167465935906219
CAMB-7A7DF	MN908947.3	24665	G	T	0.0022	0.01	0.0061	2.5e-06	0.00553125803961924	TGG	S	G1035*	G3103T	GGA>TGA	Nonsense	GU280_gp02, spike glycoprotein	0.994468741960381
CAMB-7A7DF	MN908947.3	25563	G	T	1	1	0	0	0.999796148566924	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000135900955383716
CAMB-7A7DF	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0278378378378378	0.0641081081081081	0.00057;3.3e-05;7.5e-05;0.00011;6.1e-06;5.7e-07;1.5e-06;0.00032;0.00031;0.00012;0.00019;0.00017;3e-04;0.00022;0.00026;0.00041;2e-04;0.00036;0.00024;0.00024;0.00019;0.00039;2e-04;0.00028;0.00023;0.00015;0.00032;0.00022;7.3e-05;0.00021;0.00034;0.00028;0.00015;0.00031;0.00014;0.00021;0.00018	1.2e-11;2.9e-15;3.1e-12;4.4e-12;2.6e-11;1.1e-13;1e-12;6.3e-11;5.8e-11;1.3e-11;2.1e-11;1.3e-11;5.8e-11;2.3e-11;3.6e-11;8e-11;1.7e-11;6.5e-11;3.6e-11;3.3e-11;2.9e-11;6.9e-11;2.7e-11;4.8e-11;2.6e-11;1.7e-11;4.1e-11;2.1e-11;6.2e-11;2e-11;4.7e-11;4.6e-11;1.8e-11;5.5e-11;3.5e-12;1.7e-11;1e-11	0.0416772502362253	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.960721782657839
CAMB-7A7DF	MN908947.3	2707	A	T	0.0018	0.0095	0.0026	1.5e-05	0.00465657741559953	CAC	ORF1ab:nsp2	T634T	A1902T	ACA>ACT	Synonymous	ORF1ab:nsp2	0.994761350407451
CAMB-7A7DF	MN908947.3	28329	G	A	0.0087	0.053	8.1e-06	1.2e-24	0.0286944700418784	GGA	N	G19E	G56A	GGA>GAA	Missense	GU280_gp10	0.971278158444568
CAMB-7A7DF	MN908947.3	28377	C	T	0.029	0.023	6.3e-14	1.8e-11	0.0260346124905944	GCG	N	A35V	C104T	GCG>GTG	Missense	GU280_gp10	0.973231753197893
CAMB-7A7DF	MN908947.3	28405	T	-	0.0074	0.019	0.00029	2.6e-09	0.0128087057850618	GTT	N	.	132-132-delfrshift	.	no-SNV	GU280_gp10	0.987181896778559
CAMB-7A7DF	MN908947.3	29715	G	A	0.0039	0.0085	0.00092	1.2e-05	0.0066744535291173	AGA	NA	NA	NA	NA	NA	NA	0.993325546470883
CAMB-7A7DF	MN908947.3	29728	TTCACCGAGGCCACGCGGAGTACGATCGAGTGTACAGTG	-	0.0429487179487179	0.022051282051282	1.8e-18;2.7e-17;1.1e-16;5.4e-19;8.5e-17;5.8e-17;1.9e-16;2.3e-17;8.2e-17;2.6e-16;3.4e-16;4.1e-16;8.5e-18;4.6e-16;4.8e-16;2.1e-16;4.1e-16;6.6e-16;4.4e-16;1.2e-14;1.8e-13;1.2e-13;1.4e-11;1.4e-11;8.1e-14;9.2e-14;9.5e-14;1.9e-13;2.2e-15;2.2e-12;1.2e-13;1.5e-12;8.9e-17;1.1e-16;2.3e-16;1.1e-16;1.3e-16;1.2e-16;8.3e-17	1.1e-10;5.3e-10;1.2e-09;6.6e-11;9e-10;8.9e-10;1.5e-09;9.5e-10;1.5e-09;2.3e-09;3e-09;3.4e-09;1.2e-09;3.8e-09;4.6e-09;2.9e-09;4.8e-09;4.9e-09;4.3e-09;2.4e-08;1.2e-07;9.7e-08;2.1e-07;1.3e-06;1.1e-07;8.9e-08;8.6e-08;1e-07;4.1e-08;4.2e-07;1.1e-07;3e-07;1.4e-09;1.8e-09;1.9e-09;8.9e-10;1.2e-09;1.3e-09;8.3e-10	0.0295443164747121	TTT	NA	NA	NA	NA	NA	NA	0.96736938588451
CAMB-7A7DF	MN908947.3	3022	T	C	0.017	0.011	2.4e-07	7.9e-05	0.0138552708455054	ATA	ORF1ab:nsp3	H101H	T303C	CAT>CAC	Synonymous	ORF1ab:nsp3	0.984058091978967
CAMB-7A7DF	MN908947.3	3037	C	T	1	1	0	0	0.999884473197782	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	5.77634011090573e-05
CAMB-7A7DF	MN908947.3	3670	TGAAAATT	-	0.0085625	0.009675	NA;NA;0.0016;0.0011;4.5e-06;4.8e-06;1.1e-05;6.1e-06	4.5e-05;8.6e-05;6.8e-05;4e-05;3.7e-05;3.7e-05;6.1e-05;4.3e-05	0.00967634300967634	ATG	ORF1ab:nsp3	.	951-958-delfrshift	.	no-SNV	ORF1ab:nsp3	0.993664554851617
CAMB-7A7DF	MN908947.3	3874	C	T	0.0063	0.0085	0.00012	1.4e-05	0.00739983646770237	TCG	ORF1ab:nsp3	I385I	C1155T	ATC>ATT	Synonymous	ORF1ab:nsp3	0.992600163532298
CAMB-7A7DF	MN908947.3	522	TT	-	0.066	0.044	1e-09;4.4e-08	2.5e-06;7.3e-06	0.0572956455309396	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.934943665729472
CAMB-7A7DF	MN908947.3	5699	G	C	0.0063	0.0077	7.2e-05	1.4e-05	0.00692867139284649	TGC	ORF1ab:nsp3	A994P	G2980C	GCT>CCT	Missense	ORF1ab:nsp3	0.992750131920068
CAMB-7A7DF	MN908947.3	6646	A	G	0.11	0.056	1e-47	1.4e-24	0.0827571973996492	TAG	ORF1ab:nsp3	L1309L	A3927G	TTA>TTG	Synonymous	ORF1ab:nsp3	0.917242802600351
CAMB-7A7DF	MN908947.3	7432	ATTTTATTA	-	0.00322222222222222	0.0201111111111111	NA;2.6e-05;6e-04;NA;NA;NA;NA;NA;NA	1.4e-06;8.7e-11;8.7e-09;6.8e-05;0.00018;0.00096;4e-04;0.00096;5e-04	0.00849987023098884	CAT	ORF1ab:nsp3	.	4713-4721-delinframe	.	no-SNV	ORF1ab:nsp3	0.994008922880816
CAMB-7A7DF	MN908947.3	8559	TTGTTAATAATTGGTTGAAGCAGTTAATTAAAGTT	-	0.00154285714285714	0.01174	NA;NA;NA;NA;NA;NA;0.00039;0.00017;0.00017;6.7e-05;1e-04;0.00011;0.00027;1e-04;6.2e-05;0.00013;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00027;0.00028;0.00024;0.00019;0.00037;0.00049;1e-06;3.2e-07;2.8e-07;1.1e-10;4.3e-10;4e-10;5.7e-10;5.6e-10;1.4e-10;1.3e-09;9.6e-07;9e-07;1.2e-06;1e-06;9.7e-07;7.6e-07;6.9e-07;3.7e-05;3.7e-05;4e-05;3e-07;3.4e-07;4.2e-07;6.3e-07;4.2e-07;4.4e-07;5.3e-07;6.1e-07;5.3e-07	0.00589499965323531	ATT	ORF1ab:nsp4	.	5-39-delfrshift	.	no-SNV	ORF1ab:nsp4	0.997715043856416
CAMB-7A7EE	MN908947.3	11003	C	T	0.0065	0.0085	0.00017	2.4e-05	0.00722773490138429	ACA	ORF1ab:nsp6	H11Y	C31T	CAC>TAC	Missense	ORF1ab:nsp6	0.990077177508269
CAMB-7A7EE	MN908947.3	11074	C	INS	0.039	0.03	5.5e-10	1.7e-06	0.0344036430127063	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.965433306546475
CAMB-7A7EE	MN908947.3	11075	T	-	0.024	0.046	1.9e-06	3e-11	0.0343745048328316	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.960119236254159
CAMB-7A7EE	MN908947.3	11108	G	T	0.077	0.049	8.5e-35	9.9e-23	0.0632490683855373	TGC	ORF1ab:nsp6	A46S	G136T	GCT>TCT	Missense	ORF1ab:nsp6	0.93668043106053
CAMB-7A7EE	MN908947.3	11342	A	C	0.28	0.33	1.7e-141	1.4e-170	0.301867034454576	AAT	ORF1ab:nsp6	I124L	A370C	ATC>CTC	Missense	ORF1ab:nsp6	0.698115938327416
CAMB-7A7EE	MN908947.3	13503	G	A	0.01	0.0065	3.5e-06	0.00016	0.00832389302073585	CGT	ORF1ab:RNA-dependent-RNA-polymerase	P12P	G36A	CCG>CCA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.991626853174408
CAMB-7A7EE	MN908947.3	14408	C	T	1	1	0	0	0.99843190417417	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000263035428848917
CAMB-7A7EE	MN908947.3	14889	C	T	0.044	0.018	1.4e-20	8.7e-10	0.0309722426509214	ACG	ORF1ab:RNA-dependent-RNA-polymerase	Y474Y	C1422T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.968996238784644
CAMB-7A7EE	MN908947.3	16393	C	T	0.069	0.1	1.2e-30	7.4e-45	0.0866146806728105	TCC	ORF1ab:helicase	P53S	C157T	CCA>TCA	Missense	ORF1ab:helicase	0.91332087388026
CAMB-7A7EE	MN908947.3	18555	C	T	0.0081	0.0081	1.8e-05	1.7e-05	0.00813850055097516	ACA	ORF1ab:3'-to-5'-exonuclease	D172D	C516T	GAC>GAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.987865269977828
CAMB-7A7EE	MN908947.3	19697	T	C	0.1	0.064	3.7e-44	1.7e-28	0.0834060842119401	ATC	ORF1ab:endoRNAse	I26T	T77C	ATC>ACC	Missense	ORF1ab:endoRNAse	0.91659391578806
CAMB-7A7EE	MN908947.3	19868	C	A	0.007	0.007	2.2e-05	2e-05	0.00699650174912544	ACT	ORF1ab:endoRNAse	T83N	C248A	ACT>AAT	Missense	ORF1ab:endoRNAse	0.992941029485257
CAMB-7A7EE	MN908947.3	21575	C	T	0.045	0.096	3.9e-11	1.5e-24	0.0738137082601054	TCT	S	L5F	C13T	CTT>TTT	Missense	GU280_gp02, spike glycoprotein	0.92530755711775
CAMB-7A7EE	MN908947.3	23337	TTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGG	-	0.000184393939393939	0.00545606060606061	NA;NA;NA;NA;NA;NA;NA;NA;5.7e-05;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.48;NA;NA;NA;NA;NA;NA;NA;0.00015;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	8.5e-05;1e-04;0.00027;0.00019;0.00016;0.00017;0.00015;2e-04;0.00017;0.00017;0.00016;0.00015;0.00025;0.00021;2e-04;0.00018;0.00024;0.00026;0.00013;9.4e-05;0.00011;0.00018;0.00016;0.00017;2e-04;0.00012;0.00015;0.00018;7.6e-05;1e-04;0.00016;0.00023;9.7e-05;5.2e-05;8.6e-05;7.4e-05;0.00016;7.2e-05;0.00013;2e-04;6.4e-05;9.2e-05;5.5e-05;0.00021;0.00018;0.00011;0.00021;0.00016;6.2e-05;0.00021;0.00023;0.00021;0.00026;0.00044;0.00017;0.00018;0.00017;0.00029;0.00019;0.00013;0.00018;0.00018;0.00021;2.7e-07;0.00018;0.00017	0.00258148075865373	TTT	S	.	1775-1840-delinframe	.	no-SNV	GU280_gp02, spike glycoprotein	0.996794490095669
CAMB-7A7EE	MN908947.3	23403	A	G	1	0.99	0	0	0.997537413954103	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.95822693804695e-05
CAMB-7A7EE	MN908947.3	24034	C	T	0.0074	0.0093	1.8e-05	2.5e-06	0.00821337357789645	ACA	S	N824N	C2472T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.991757603900627
CAMB-7A7EE	MN908947.3	241	C	T	1	1	0	0	0.999816463246765	TCG	NA	NA	NA	NA	NA	NA	7.64736471811814e-05
CAMB-7A7EE	MN908947.3	24959	G	T	0.038	0.0078	5.1e-18	2.5e-05	0.0252148189885899	TGT	S	V1133F	G3397T	GTC>TTC	Missense	GU280_gp02, spike glycoprotein	0.974759569209492
CAMB-7A7EE	MN908947.3	25429	G	T	1	1	0	0	0.999850952548711	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	8.12986097937725e-05
CAMB-7A7EE	MN908947.3	25459	G	T	0.0058	0.0091	3e-04	9.4e-06	0.00722592447406246	TGC	ORF3a	A23S	G67T	GCT>TCT	Missense	GU280_gp03	0.992695674898733
CAMB-7A7EE	MN908947.3	26927	A	G	0.045	0.022	5e-21	3.6e-11	0.0345753608593488	AAA	M	E135E	A405G	GAA>GAG	Synonymous	GU280_gp05	0.96536360584699
CAMB-7A7EE	MN908947.3	27098	T	-	0.011	0.0056	1.1e-05	0.0014	0.0082818372937504	GTT	M	.	576-576-delfrshift	.	no-SNV	GU280_gp05	0.991654456265528
CAMB-7A7EE	MN908947.3	3037	C	T	1	1	0	0	0.999524771296186	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000118807175953428
CAMB-7A7EE	MN908947.3	5144	C	T	0.018	0.0093	4.8e-06	0.0013	0.0142302716688228	TCT	ORF1ab:nsp3	L809L	C2425T	CTA>TTA	Synonymous	ORF1ab:nsp3	0.985769728331177
CAMB-7A7EE	MN908947.3	6175	T	C	0.0067	0.023	0.00013	1.7e-10	0.0141649048625793	TTG	ORF1ab:nsp3	I1152I	T3456C	ATT>ATC	Synonymous	ORF1ab:nsp3	0.985835095137421
CAMB-7A7EE	MN908947.3	6507	A	G	0.042	0.086	7.3e-20	1.1e-39	0.0624420302988305	AAT	ORF1ab:nsp3	N1263S	A3788G	AAT>AGT	Missense	ORF1ab:nsp3	0.93755796970117
CAMB-7A7EE	MN908947.3	664	C	A	0.0055	0.0062	1e-04	3.1e-05	0.00577721080954266	GCC	ORF1ab:leader-protein	G133G	C399A	GGC>GGA	Synonymous	ORF1ab:leader-protein	0.994017507588088
CAMB-7A7EE	MN908947.3	832	C	T	0.011	0.0039	1.1e-06	0.00097	0.00735440799010546	ACT	ORF1ab:nsp2	N9N	C27T	AAC>AAT	Synonymous	ORF1ab:nsp2	0.992605694679026
CAMB-7A7FD	MN908947.3	14408	C	T	1	1	0	0	0.999267911217597	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000499151442547669
CAMB-7A7FD	MN908947.3	18743	ACGTCTA	-	0.0928571428571429	0.0343091428571429	6e-14;8.7e-16;1.1e-14;8.8e-16;1.4e-15;6.3e-18;1.9e-18	NA;NA;NA;0.5;0.5;4.3e-22;7.9e-23	0.0479496765770577	TAC	ORF1ab:3'-to-5'-exonuclease	.	704-710-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.952738301222855
CAMB-7A7FD	MN908947.3	20075	A	T	1	1	1.5e-152	2.6e-131	1	CAA	ORF1ab:endoRNAse	Q152L	A455T	CAA>CTA	Missense	ORF1ab:endoRNAse	0
CAMB-7A7FD	MN908947.3	23403	A	G	1	1	0	0	0.999913811678518	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.30941607412196e-05
CAMB-7A7FD	MN908947.3	241	C	T	1	0.87	0	0	0.934106701213049	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-7A7FD	MN908947.3	25782	C	T	1	1	0	0	1	GCT	ORF3a	C130C	C390T	TGC>TGT	Synonymous	GU280_gp03	0
CAMB-7A7FD	MN908947.3	25973	A	C	0.21	0.07	8.5e-39	1.4e-08	0.181481481481481	GAA	ORF3a	E194A	A581C	GAA>GCA	Missense	GU280_gp03	0.818518518518519
CAMB-7A7FD	MN908947.3	26530	A	G	1	1	0	0	0.999717912552891	GAT	M	D3G	A8G	GAT>GGT	Missense	GU280_gp05	0.000282087447108604
CAMB-7A7FD	MN908947.3	28739	G	T	1	1	0	0	0.999375520399667	TGC	N	A156S	G466T	GCA>TCA	Missense	GU280_gp10	0.000312239800166528
CAMB-7A7FD	MN908947.3	3037	C	T	1	1	0	1.09999999999999e-310	0.999588815789474	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A7FD	MN908947.3	686	AAGTCATTT	-	1	1	0;0;0;0;0;0;0;0;0	0;0;0;0;0;0;0;0;0	0.999849823542663	AAA	ORF1ab:leader-protein	.	421-429-delinframe	.	no-SNV	ORF1ab:leader-protein	0.000150180216259511
CAMB-7A809	MN908947.3	11074	C	INS	0.1	0.12	4.5e-42	8.1e-53	0.110043132484089	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.886830013774243
CAMB-7A809	MN908947.3	11083	G	-	0.17	0.15	2.4e-76	2.5e-67	0.164497934893636	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	8.88217791002354e-06
CAMB-7A809	MN908947.3	11083	G	T	0.83	0.85	0	0	0.835368832437714	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	8.88217791002354e-06
CAMB-7A809	MN908947.3	14568	T	C	0.022	0.018	4.6e-11	1.2e-09	0.0198891685864992	CTG	ORF1ab:RNA-dependent-RNA-polymerase	A367A	T1101C	GCT>GCC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.980110831413501
CAMB-7A809	MN908947.3	14805	C	T	1	1	0	0	0.999962992089559	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-7A809	MN908947.3	15741	T	C	0.0042	0.0091	0.00081	6.5e-06	0.00663799318797703	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N758N	T2274C	AAT>AAC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.993324714715461
CAMB-7A809	MN908947.3	22564	C	T	0.013	0.013	1.4e-07	1e-07	0.0128515523883483	ACT	S	N334N	C1002T	AAC>AAT	Synonymous	GU280_gp02, spike glycoprotein	0.986326191890122
CAMB-7A809	MN908947.3	23525	C	T	0.015	0.0073	3.6e-08	8.6e-05	0.0116038408034472	ACA	S	H655Y	C1963T	CAT>TAT	Missense	GU280_gp02, spike glycoprotein	0.988396159196553
CAMB-7A809	MN908947.3	24554	A	G	0.0097	0.0065	3.5e-06	6.1e-05	0.00809838032393521	CAC	S	T998A	A2992G	ACA>GCA	Missense	GU280_gp02, spike glycoprotein	0.991376724655069
CAMB-7A809	MN908947.3	2480	A	G	1	1	0	0	0.99889012208657	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-7A809	MN908947.3	2558	C	T	1	1	0	0	0.999672866623049	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-7A809	MN908947.3	26144	G	T	1	1	0	0	0.999827049463853	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000172950536146662
CAMB-7A809	MN908947.3	26534	C	T	0.028	0.036	9.3e-14	2.6e-17	0.0316172993045946	CCA	M	S4S	C12T	TCC>TCT	Synonymous	GU280_gp05	0.968330151167475
CAMB-7A809	MN908947.3	2866	A	G	0.014	0.016	4.3e-08	5.1e-09	0.014723806737848	AAG	ORF1ab:nsp3	E49E	A147G	GAA>GAG	Synonymous	ORF1ab:nsp3	0.985203061771732
CAMB-7A809	MN908947.3	29686	C	T	0.99	1	0	0	0.996203097081596	TCA	NA	NA	NA	NA	NA	NA	0.00290351399642644
CAMB-7A809	MN908947.3	29722	CACATTTTCA	-	0.0094	0.00923	2e-05;1.6e-05;1.5e-05;1.1e-05;9.5e-05;2.4e-05;3.8e-05;1.8e-05;2.9e-05;1.2e-05	1.8e-05;1.5e-05;1.3e-05;1.1e-05;6.9e-05;1.4e-05;2.2e-05;5.3e-05;8.7e-05;1.8e-05	0.00903323679492484	CCA	NA	NA	NA	NA	NA	NA	0.99140194276713
CAMB-7A809	MN908947.3	674	G	A	0.026	0.026	3e-13	3.1e-13	0.0261663544619127	CGG	ORF1ab:leader-protein	G137S	G409A	GGC>AGC	Missense	ORF1ab:leader-protein	0.973784608142169
CAMB-7A809	MN908947.3	9048	A	G	1	1	0	0	0.999980942579993	AAG	ORF1ab:nsp4	K165R	A494G	AAG>AGG	Missense	ORF1ab:nsp4	0
CAMB-7A818	MN908947.3	11075	T	-	0.033	0.053	3.2e-08	1.1e-12	0.0418967912445363	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95440992105174
CAMB-7A818	MN908947.3	11195	C	T	1	1	0	0	0.99966966966967	TCT	ORF1ab:nsp6	L75F	C223T	CTT>TTT	Missense	ORF1ab:nsp6	4.004004004004e-05
CAMB-7A818	MN908947.3	14408	C	T	1	1	0	0	0.997513513513513	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000498960498960499
CAMB-7A818	MN908947.3	1547	A	T	0.0091	0.0055	8.4e-06	2e-04	0.00759723324639982	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.987526930490985
CAMB-7A818	MN908947.3	15705	G	T	0.013	0.0075	2.4e-07	2.5e-05	0.0102369295421846	TGA	ORF1ab:RNA-dependent-RNA-polymerase	M746I	G2238T	ATG>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.989752719669603
CAMB-7A818	MN908947.3	22126	T	C	0.011	0.013	8.5e-07	1.1e-07	0.0122765957446809	ATC	S	N188N	T564C	AAT>AAC	Synonymous	GU280_gp02, spike glycoprotein	0.987042553191489
CAMB-7A818	MN908947.3	22484	G	T	0.48	0.51	8.4e-164	2e-198	0.499749624436655	TGT	S	V308L	G922T	GTA>TTA	Missense	GU280_gp02, spike glycoprotein	0.499248873309965
CAMB-7A818	MN908947.3	23403	A	G	1	1	0	0	0.999396184641705	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.03179465246023e-05
CAMB-7A818	MN908947.3	241	C	T	1	1	0	0	0.999591790452432	TCG	NA	NA	NA	NA	NA	NA	0.000124730695090146
CAMB-7A818	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999586935355383	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A818	MN908947.3	29465	G	T	0.12	0.11	2.6e-47	2.3e-44	0.117345971563981	TGC	N	A398S	G1192T	GCA>TCA	Missense	GU280_gp10	0.881706161137441
CAMB-7A818	MN908947.3	3037	C	T	1	1	0	0	0.998577103219304	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000148218414655837
CAMB-7A818	MN908947.3	3373	C	A	1	1	0	0	0.999577081494557	ACA	ORF1ab:nsp3	D218E	C654A	GAC>GAA	Missense	ORF1ab:nsp3	5.51632833186231e-05
CAMB-7A827	MN908947.3	11075	T	-	0.043	0.043	2.3e-10	1.9e-10	0.0425450805865352	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953642795085019
CAMB-7A827	MN908947.3	14408	C	T	1	1	0	0	0.997369529524022	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000971382888187812
CAMB-7A827	MN908947.3	20132	C	T	1	1	1.5e-283	2.1e-267	1	GCC	ORF1ab:endoRNAse	A171V	C512T	GCC>GTC	Missense	ORF1ab:endoRNAse	0
CAMB-7A827	MN908947.3	20944	G	A	1	1	0	0	0.99974206860975	TGT	ORF1ab:2'-O-ribose-methyltransferase	V96I	G286A	GTC>ATC	Missense	ORF1ab:2'-O-ribose-methyltransferase	5.95226285192754e-05
CAMB-7A827	MN908947.3	21742	C	T	0.0085	0.0059	1.7e-05	0.00021	0.00726552179656539	CCA	S	S60S	C180T	TCC>TCT	Synonymous	GU280_gp02, spike glycoprotein	0.991743725231176
CAMB-7A827	MN908947.3	23403	A	G	1	1	0	0	0.998428913254976	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.86037706081881e-05
CAMB-7A827	MN908947.3	241	C	T	1	1	0	0	0.995823216556827	TCG	NA	NA	NA	NA	NA	NA	0.000419123598103827
CAMB-7A827	MN908947.3	27281	G	T	1	1	0	0	0.997511649703642	TGG	ORF6	W27L	G80T	TGG>TTG	Missense	GU280_gp06	2.64015946563172e-05
CAMB-7A827	MN908947.3	28881	GGG	AAC	0.996666666666667	1	0;0;0	0;0;0	0.99778822822049	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00168258406995758
CAMB-7A827	MN908947.3	3037	C	T	1	1	0	0	0.999127055643163	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	8.44784861455283e-05
CAMB-7A827	MN908947.3	8302	A	G	0.019	0.026	7e-10	4e-13	0.0218061400746276	AAG	ORF1ab:nsp3	K1861K	A5583G	AAA>AAG	Synonymous	ORF1ab:nsp3	0.978012539723439
CAMB-7A836	MN908947.3	11074	C	INS	0.026	0.025	5.8e-06	4.8e-05	0.0256088044833142	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.972617732602329
CAMB-7A836	MN908947.3	11075	T	-	0.032	0.037	6.1e-08	3.2e-09	0.0338596323164413	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.959382375225339
CAMB-7A836	MN908947.3	13603	CG	-	0.0064	0.00375	0.00023;2.5e-05	0.0014;0.00045	0.00528627801355074	TCG	ORF1ab:RNA-dependent-RNA-polymerase	.	136-137-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.995394884033112
CAMB-7A836	MN908947.3	14408	C	T	1	1	0	0	0.997491733134292	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000746404672840417
CAMB-7A836	MN908947.3	16038	T	C	0.059	0.064	6.4e-27	2.3e-29	0.0610851366584739	CTT	ORF1ab:RNA-dependent-RNA-polymerase	A857A	T2571C	GCT>GCC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.938702345092676
CAMB-7A836	MN908947.3	20031	C	A	1	1	7.7e-89	1.9e-217	1	CCC	ORF1ab:endoRNAse	A137A	C411A	GCC>GCA	Synonymous	ORF1ab:endoRNAse	0
CAMB-7A836	MN908947.3	23403	A	G	1	1	0	0	0.999664401375954	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.58853211558976e-05
CAMB-7A836	MN908947.3	241	C	T	1	1	0	0	0.998676402789965	TCG	NA	NA	NA	NA	NA	NA	0.000639490786871105
CAMB-7A836	MN908947.3	25663	T	A	1	1	0	0	0.999799021906612	TTA	ORF3a	Y91N	T271A	TAC>AAC	Missense	GU280_gp03	0.00010048904669391
CAMB-7A836	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0237567567567568	0.0300810810810811	0.0033;0.00052;0.0025;0.00066;0.0014;2e-04;0.00089;0.00093;0.00091;0.00033;0.00059;0.00051;0.00092;0.00065;0.00079;0.0012;0.00057;0.001;0.00072;0.00048;0.00043;0.0011;0.00078;0.00088;0.00071;0.00052;0.00094;0.00066;0.00043;0.00064;0.00097;0.00089;0.00043;0.0012;0.00055;0.00075;0.00068	0.00045;2.4e-05;0.00017;6.8e-05;0.00015;1.4e-05;4.6e-05;5.3e-05;5.4e-05;3e-05;4.3e-05;3.4e-05;6.8e-05;4.6e-05;5.2e-05;5.6e-05;3.4e-05;7.7e-05;5.8e-05;5.5e-05;5.1e-05;8.7e-05;4.7e-05;6.4e-05;5e-05;3.7e-05;7e-05;4.5e-05;2.1e-05;5.1e-05;6.8e-05;4.8e-05;2.6e-05;7e-05;2.4e-05;4.1e-05;3.4e-05	0.0266731956095939	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.979291954022989
CAMB-7A836	MN908947.3	27046	C	T	1	1	0	0	0.999073391597347	ACG	M	T175M	C524T	ACG>ATG	Missense	GU280_gp05	8.42371275139518e-05
CAMB-7A836	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998775519815386	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000155130956382346
CAMB-7A836	MN908947.3	3037	C	T	1	1	0	0	0.997650894098471	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A854	MN908947.3	1059	C	T	1	1	0	0	0.999927769150204	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	3.61154248979739e-05
CAMB-7A854	MN908947.3	14110	C	G	0.11	0.083	1e-50	2e-38	0.0991105239982387	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Q215E	C643G	CAA>GAA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.90078379568472
CAMB-7A854	MN908947.3	14408	C	T	1	1	0	0	0.999287503734859	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000551610011721713
CAMB-7A854	MN908947.3	15727	G	-	0.0027	0.0079	0.0095	3.8e-05	0.00485664854176965	TGT	ORF1ab:RNA-dependent-RNA-polymerase	.	2260-2260-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.99510627780524
CAMB-7A854	MN908947.3	21137	A	G	1	1	0	0	1	AAG	ORF1ab:2'-O-ribose-methyltransferase	K160R	A479G	AAG>AGG	Missense	ORF1ab:2'-O-ribose-methyltransferase	0
CAMB-7A854	MN908947.3	23403	A	G	1	1	0	0	0.999884175169262	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.42362405365849e-05
CAMB-7A854	MN908947.3	23559	TTGGTGCAGGTATATGCGCTAG	-	0.0220454545454545	0.0398181818181818	0.0071;0.011;0.01;0.013;0.014;0.014;0.013;0.011;0.011;0.011;0.00025;5.5e-05;0.009;0.0059;0.009;0.0055;0.008;0.01;0.0088;0.0087;0.0019;0.0028	0.00023;3e-04;0.00017;0.00031;0.00031;0.00034;0.00032;0.00031;0.00019;0.00018;8.6e-05;2.3e-05;8.9e-05;3.8e-05;8.9e-05;3.5e-05;7.5e-05;0.00018;8.8e-05;9.6e-05;2e-06;3.6e-06	0.0284434490481523	ATT	S	.	1997-2018-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.963322131541047
CAMB-7A854	MN908947.3	241	C	T	1	1	0	0	0.999782990392393	TCG	NA	NA	NA	NA	NA	NA	5.918443843832e-05
CAMB-7A854	MN908947.3	24368	G	T	1	1	0	0	0.999934119507214	AGA	S	D936Y	G2806T	GAC>TAC	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7A854	MN908947.3	25563	G	T	1	1	0	0	0.999867058597616	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	0.000103398868520953
CAMB-7A854	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0545263157894737	0.0365	2.3e-05;5e-07;1.2e-05;1.2e-05;4.8e-05;2.8e-08;3.6e-07;4.8e-10;4.9e-10;6.8e-11;7.7e-11;3.5e-11;5.5e-10;1.4e-10;2.1e-10;9e-10;1e-10;6.8e-10;3.6e-10;3.4e-10;1.2e-10;7.7e-10;9.3e-11;4.2e-10;2.7e-10;4.6e-11;3.3e-10;2.2e-10;2.1e-10;1.3e-10;5.6e-10;3.7e-10;1.2e-10;3.9e-10;6.2e-11;2.1e-10;1.1e-10;5.1e-05	0.02;0.0067;0.018;0.019;0.025;0.01;0.018;5.4e-07;4.8e-07;3.2e-07;2.9e-07;2.3e-07;4.2e-07;3.5e-07;4.8e-07;7.3e-07;3e-07;6e-07;3e-07;4.2e-07;4.2e-07;7.2e-07;4e-07;4.9e-07;3.6e-07;2e-07;5e-07;3.5e-07;1.2e-07;3.4e-07;5.6e-07;5.2e-07;2.3e-07;6.2e-07;7.2e-08;2.9e-07;1.2e-07;0.00064	0.0512259506765916	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.97696430063378
CAMB-7A854	MN908947.3	27476	C	T	0.84	0.93	0	0	0.873573751871547	ACA	ORF7a	T28I	C83T	ACA>ATA	Missense	GU280_gp07	0.126374619236925
CAMB-7A854	MN908947.3	28079	G	T	0.014	0.012	1.4e-06	7.6e-06	0.0133288341488105	TGG	ORF8	V62V	G186T	GTG>GTT	Synonymous	GU280_gp09	0.986333727011979
CAMB-7A854	MN908947.3	28674	C	T	0.061	0.17	8.8e-27	4.8e-73	0.105131860299359	GCA	N	A134V	C401T	GCA>GTA	Missense	GU280_gp10	0.894868139700641
CAMB-7A854	MN908947.3	3037	C	T	1	1	0	0	0.999689376682543	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A854	MN908947.3	9993	A	G	0.043	0.023	2.4e-20	9.9e-12	0.0353221957040573	AAC	ORF1ab:nsp4	N480S	A1439G	AAC>AGC	Missense	ORF1ab:nsp4	0.964598249801114
CAMB-7A863	MN908947.3	11074	C	INS	0.046	0.082	7.2e-11	1e-21	0.0593984759955842	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.940251487654487
CAMB-7A863	MN908947.3	11083	G	-	0.075	0.02	4.3e-32	6.8e-09	0.0554597440319506	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.579763093401107
CAMB-7A863	MN908947.3	11083	G	T	0.33	0.43	1.7e-81	1.3e-117	0.364754470363983	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0.579763093401107
CAMB-7A863	MN908947.3	13914	T	G	0.0018	0.01	0.0025	3.4e-07	0.00551343900758098	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.994417643004824
CAMB-7A863	MN908947.3	1440	GCTTGAAAACCATTCTTCGTAAGGGTGGTCGCACTA	-	0.00855	0.0011	4.4e-05;2.5e-05;2.3e-05;3.6e-05;5.6e-05;0.00013;4.6e-05;4.5e-05;4.1e-05;4.5e-05;4.4e-05;3e-05;3.8e-05;7.9e-05;9e-05;2.5e-05;3.9e-05;9.5e-05;0.00023;3.8e-05;3.1e-05;1.9e-05;7.3e-05;9.9e-05;0.00015;9.6e-05;7.3e-05;5.9e-05;5.7e-05;0.00012;0.00011;5.6e-05;5.3e-05;8.5e-05;0.00014;8.1e-05	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;2.2e-07;4.4e-07;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.00513149454778704	GGC	ORF1ab:nsp2	.	635-670-delinframe	.	no-SNV	ORF1ab:nsp2	0.994498777506112
CAMB-7A863	MN908947.3	14408	C	T	0.99	1	0	0	0.99477996564028	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000572661997268843
CAMB-7A863	MN908947.3	15739	AA	-	0.00295	0.00795	0.00036;NA	7.2e-05;1.6e-05	0.00545971141525377	CAA	ORF1ab:RNA-dependent-RNA-polymerase	.	2272-2273-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.993340252551462
CAMB-7A863	MN908947.3	17268	T	C	0.12	0.15	3.8e-55	5.5e-69	0.131424607428896	ATA	ORF1ab:helicase	D344D	T1032C	GAT>GAC	Synonymous	ORF1ab:helicase	0.868543860755502
CAMB-7A863	MN908947.3	20132	C	T	1	1	2.6e-185	5.4e-144	1	GCC	ORF1ab:endoRNAse	A171V	C512T	GCC>GTC	Missense	ORF1ab:endoRNAse	0
CAMB-7A863	MN908947.3	20944	G	A	1	1	0	0	0.999794597925439	TGT	ORF1ab:2'-O-ribose-methyltransferase	V96I	G286A	GTC>ATC	Missense	ORF1ab:2'-O-ribose-methyltransferase	0
CAMB-7A863	MN908947.3	23403	A	G	1	1	0	0	0.999927818680525	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	4.3308791684712e-05
CAMB-7A863	MN908947.3	241	C	T	1	1	0	0	0.999788141203888	TCG	NA	NA	NA	NA	NA	NA	5.29646990280978e-05
CAMB-7A863	MN908947.3	25554	T	C	0.076	0.021	7.9e-35	4.4e-11	0.0488016770854974	CTG	ORF3a	A54A	T162C	GCT>GCC	Synonymous	GU280_gp03	0.926230901433455
CAMB-7A863	MN908947.3	26787	GGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.0292941176470588	0.0357941176470588	9.8e-05;9.9e-05;2.4e-05;5.2e-05;4.1e-05;9.2e-05;6.1e-05;7.9e-05;0.00013;5.7e-05;0.00011;7.2e-05;7.6e-05;6.5e-05;0.00012;6.8e-05;8.8e-05;6.8e-05;4.9e-05;1e-04;6e-05;1.6e-05;6.2e-05;1e-04;9.6e-05;5.4e-05;0.00011;3.5e-05;5.7e-05;4.3e-05;4e-04;0.0012;0.00063;0.00082	5.5e-06;5e-06;3.4e-06;3.3e-06;2.7e-06;4e-06;3.5e-06;4.6e-06;7.2e-06;3.3e-06;6.1e-06;3.3e-06;4.4e-06;4.1e-06;7.2e-06;3.7e-06;4.7e-06;3.6e-06;1.8e-06;5.4e-06;4.1e-06;2.7e-06;3.5e-06;5.8e-06;3e-06;1.2e-06;4.6e-06;1.4e-06;3.6e-06;1.9e-06;5.6e-05;0.00024;8.6e-05;0.00014	0.0315258741513315	AGG	M	.	265-298-delfrshift	.	no-SNV	GU280_gp05	0.969255290888161
CAMB-7A863	MN908947.3	27281	G	T	1	1	0	0	0.99989965716197	TGG	ORF6	W27L	G80T	TGG>TTG	Missense	GU280_gp06	0
CAMB-7A863	MN908947.3	2861	ACAGA	-	0.00154	0.0128	NA;NA;NA;NA;4.6e-05	1.2e-07;4.3e-07;6e-07;1.1e-06;6.1e-07	0.00507895465878659	TAC	ORF1ab:nsp3	.	142-146-delfrshift	.	no-SNV	ORF1ab:nsp3	0.994450610432852
CAMB-7A863	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999556776881482	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	9.86777185711466e-05
CAMB-7A863	MN908947.3	29774	C	T	0.13	0.15	1.1e-48	1.7e-51	0.13776493256262	GCT	NA	NA	NA	NA	NA	NA	0.860950545921644
CAMB-7A863	MN908947.3	3037	C	T	1	1	0	0	0.999429679479868	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000228128208052926
CAMB-7A863	MN908947.3	3411	C	T	0.015	0.0075	2.1e-08	2.6e-05	0.0118122073794081	GCT	ORF1ab:nsp3	A231V	C692T	GCT>GTT	Missense	ORF1ab:nsp3	0.988101885657833
CAMB-7A863	MN908947.3	7404	T	A	0.041	0.0029	1.3e-17	0.00049	0.0294868159909271	ATG	ORF1ab:nsp3	M1562K	T4685A	ATG>AAG	Missense	ORF1ab:nsp3	0.970513184009073
CAMB-7A863	MN908947.3	7926	C	T	0.026	0.026	8.8e-12	8.3e-12	0.0256208119826567	GCA	ORF1ab:nsp3	A1736V	C5207T	GCA>GTA	Missense	ORF1ab:nsp3	0.974379188017343
CAMB-7A872	MN908947.3	11075	T	-	0.043	0.044	4.4e-11	1.9e-11	0.0435098410898719	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.95223838290786
CAMB-7A872	MN908947.3	14408	C	T	1	1	0	0	0.997508753961773	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000636651765324623
CAMB-7A872	MN908947.3	23403	A	G	1	1	0	0	0.99953078939584	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.14016136764691e-05
CAMB-7A872	MN908947.3	241	C	T	1	1	0	0	0.999070372780515	TCG	NA	NA	NA	NA	NA	NA	0.000130147810727898
CAMB-7A872	MN908947.3	26501	G	T	1	1	0	0	0.99852745752972	TGT	NA	NA	NA	NA	NA	NA	3.5915670006824e-05
CAMB-7A872	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998870804454482	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.37120251781265e-05
CAMB-7A872	MN908947.3	3037	C	T	1	1	0	0	0.999002677024828	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000104981365807569
CAMB-7A881	MN908947.3	14408	C	T	1	1	0	0	0.999290243209993	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00047317119333775
CAMB-7A881	MN908947.3	23403	A	G	1	1	0	0	0.99983850129199	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000113049095607235
CAMB-7A881	MN908947.3	241	C	T	1	1	0	0	0.999759942386173	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-7A881	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998226321390564	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000388500388500389
CAMB-7A881	MN908947.3	29567	A	G	0.045	0.11	2.1e-15	2.2e-26	0.0664172123479888	TAT	ORF10	I4V	A10G	ATA>GTA	Missense	GU280_gp11	0.933582787652011
CAMB-7A881	MN908947.3	3037	C	T	1	1	0	0	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A890	MN908947.3	11074	C	INS	0.12	0.12	3.8e-51	2.1e-38	0.11932291745594	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.876252102623164
CAMB-7A890	MN908947.3	11083	G	-	0.18	0.17	9.4e-81	1e-78	0.179486825769072	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-7A890	MN908947.3	11083	G	T	0.82	0.82	0	0	0.820347634156435	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-7A890	MN908947.3	14805	C	T	1	1	0	0	0.997679417655968	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000403048512384582
CAMB-7A890	MN908947.3	1547	A	G	0.53	0.54	1.3e-280	1.1e-260	0.533223729277983	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.466228250445267
CAMB-7A890	MN908947.3	1601	C	T	0.49	0.49	1.1e-280	1.9e-280	0.488781046863528	TCT	ORF1ab:nsp2	L266F	C796T	CTT>TTT	Missense	ORF1ab:nsp2	0.509016349408162
CAMB-7A890	MN908947.3	16438	A	G	0.023	0.02	2.9e-11	2.8e-10	0.0217988403016959	TAT	ORF1ab:helicase	M68V	A202G	ATG>GTG	Missense	ORF1ab:helicase	0.978113964337097
CAMB-7A890	MN908947.3	17247	T	C	1	1	0	0	0.99723570340354	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.00144497322087672
CAMB-7A890	MN908947.3	224	T	C	0.025	0.025	2.1e-12	5.3e-13	0.0248481178332129	ATC	NA	NA	NA	NA	NA	NA	0.975015139379969
CAMB-7A890	MN908947.3	23559	TTGGTGCAGGTATATGCGCTAGT	-	0.0302608695652174	0.0367826086956522	0.0017;0.003;0.0013;0.0021;0.0022;0.0023;0.0022;0.0018;0.0013;0.0012;0.00019;5.4e-05;0.00089;0.00064;0.00082;0.00051;0.00096;0.0015;0.001;0.0015;0.00011;0.00019;0.0049	0.00027;0.00042;0.00015;0.00041;0.00044;0.00043;0.00043;0.00043;0.00027;0.00025;8.2e-05;4.3e-05;0.00023;9.7e-05;0.00022;9.2e-05;0.00019;0.00032;0.00023;0.00032;1.2e-05;1.9e-05;0.00091	0.031184928111056	ATT	S	.	1997-2019-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.960654664484452
CAMB-7A890	MN908947.3	26144	G	T	1	1	0	0	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7A890	MN908947.3	26152	G	A	0.044	0.045	2.5e-19	5.8e-19	0.0442090395480226	CGG	ORF3a	G254R	G760A	GGA>AGA	Missense	GU280_gp03	0.955790960451977
CAMB-7A890	MN908947.3	26204	C	T	0.0042	0.0098	0.0015	9.7e-06	0.00621446515932831	ACT	ORF3a	T271I	C812T	ACT>ATT	Missense	GU280_gp03	0.993785534840672
CAMB-7A890	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0356578947368421	0.0389210526315789	0.00049;2.6e-05;0.00028;0.00031;0.00051;3.4e-06;2.7e-05;4e-06;3.9e-06;8.5e-07;1.8e-06;1.2e-06;3.9e-06;1.6e-06;1.7e-06;3.1e-06;1.4e-06;3.3e-06;2e-06;2.3e-06;2.1e-06;3.5e-06;1.5e-06;2.4e-06;1.9e-06;1.1e-06;3.1e-06;1.6e-06;9.7e-07;1.7e-06;3.2e-06;2.8e-06;1.5e-06;3.3e-06;9.5e-07;2e-06;1.4e-06;0.0026	2.3e-05;1.2e-06;1.3e-05;1.2e-05;1.9e-05;3.5e-07;1.7e-06;1.2e-06;1.1e-06;7e-07;5.8e-07;5.6e-07;8.1e-07;4e-07;5.1e-07;8.3e-07;3.7e-07;6.1e-07;3.1e-07;4.8e-07;5.3e-07;8.4e-07;4.4e-07;5.7e-07;4e-07;2.7e-07;5.7e-07;4.2e-07;1.2e-07;4.8e-07;6.9e-07;6.2e-07;2.3e-07;6.8e-07;1e-07;3.9e-07;1.1e-07;0.00051	0.0386165526291124	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.97470189385083
CAMB-7A890	MN908947.3	3871	G	A	0.025	0.026	1.9e-12	4.5e-13	0.0255246502331779	AGA	ORF1ab:nsp3	K384K	G1152A	AAG>AAA	Synonymous	ORF1ab:nsp3	0.974433710859427
CAMB-7A890	MN908947.3	522	TT	-	0.04	0.0405	5.1e-06;8.9e-05	1.2e-06;0.00021	0.0400358058061572	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.951434041323508
CAMB-7A890	MN908947.3	7312	G	A	0.44	0.46	5.3e-149	1.4e-135	0.449233016800584	TGT	ORF1ab:nsp3	L1531L	G4593A	TTG>TTA	Synonymous	ORF1ab:nsp3	0.550036523009496
CAMB-7A890	MN908947.3	8293	C	T	0.019	0.024	3.8e-10	2e-12	0.0204340687390482	CCT	ORF1ab:nsp3	T1858T	C5574T	ACC>ACT	Synonymous	ORF1ab:nsp3	0.979565931260952
CAMB-7A8EB	MN908947.3	11074	C	INS	0.042	0.042	1.7e-09	2.1e-09	0.0419612260058952	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.957703275899255
CAMB-7A8EB	MN908947.3	11082	TG	-	0.0585	0.08575	1e-06;2.2e-32	0.46;3.1e-75	0.06976790756353	TTG	ORF1ab:nsp6	.	110-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0.975621540010065
CAMB-7A8EB	MN908947.3	11083	G	-	0.076	0.17	2.2e-32	3.1e-75	0.114727971791143	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	0
CAMB-7A8EB	MN908947.3	11083	G	T	0.92	0.83	0	0	0.88523218519035	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	0
CAMB-7A8EB	MN908947.3	14805	C	T	1	1	0	0	0.999894553698529	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	7.90847261032319e-05
CAMB-7A8EB	MN908947.3	2480	A	G	1	1	0	0	1	AAT	ORF1ab:nsp2	I559V	A1675G	ATT>GTT	Missense	ORF1ab:nsp2	0
CAMB-7A8EB	MN908947.3	2558	C	T	1	1	0	0	1	ACC	ORF1ab:nsp2	P585S	C1753T	CCA>TCA	Missense	ORF1ab:nsp2	0
CAMB-7A8EB	MN908947.3	26144	G	T	1	1	1.7e-154	4.9e-68	1	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0
CAMB-7A8EB	MN908947.3	28739	G	T	0.014	0.0048	1.8e-07	0.0016	0.0103712433706541	TGC	N	A156S	G466T	GCA>TCA	Missense	GU280_gp10	0.989451974071892
CAMB-7A924	MN908947.3	13487	C	T	0.0061	0.064	0.0015	3.7e-18	0.0285929270127916	GCA	ORF1ab:RNA-dependent-RNA-polymerase	A7V	C20T	GCA>GTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.971407072987208
CAMB-7A924	MN908947.3	14408	C	T	1	1	0	0	0.999177225604739	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000452525917393451
CAMB-7A924	MN908947.3	14942	C	T	0.019	0.015	2.4e-08	1.3e-05	0.0180921052631579	TCA	ORF1ab:RNA-dependent-RNA-polymerase	S492L	C1475T	TCA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.981907894736842
CAMB-7A924	MN908947.3	16289	C	T	1	1	0	0	1	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0
CAMB-7A924	MN908947.3	17045	A	-	0.018	0.025	2.7e-09	2.4e-12	0.0210132017724179	CAA	ORF1ab:helicase	.	809-809-delfrshift	.	no-SNV	ORF1ab:helicase	0.978712712987072
CAMB-7A924	MN908947.3	17045	AA	-	0.019	0.0125	2.7e-09;7.6e-11	2.4e-12;NA	0.0161165798108473	CAA	ORF1ab:helicase	.	809-810-delfrshift	.	no-SNV	ORF1ab:helicase	0.978712712987072
CAMB-7A924	MN908947.3	17910	A	-	0.04	0.021	3.8e-19	2e-11	0.0301163271874569	TAA	ORF1ab:helicase	.	1674-1674-delfrshift	.	no-SNV	ORF1ab:helicase	0.969745735436112
CAMB-7A924	MN908947.3	17910	AA	-	0.042	0.0105	3.8e-19;5.7e-21	2e-11;NA	0.0257624824786118	TAA	ORF1ab:helicase	.	1674-1675-delfrshift	.	no-SNV	ORF1ab:helicase	0.969745735436112
CAMB-7A924	MN908947.3	1928	G	C	0.013	0.016	1.8e-08	1.1e-09	0.0146230007616146	TGC	ORF1ab:nsp2	A375P	G1123C	GCT>CCT	Missense	ORF1ab:nsp2	0.985173902005585
CAMB-7A924	MN908947.3	21633	T	C	0.18	0.074	1.2e-37	1.4e-16	0.126297577854671	TTA	S	L24S	T71C	TTA>TCA	Missense	GU280_gp02, spike glycoprotein	0.873702422145329
CAMB-7A924	MN908947.3	23403	A	G	1	1	0	0	0.999885809366895	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.78776855189964e-05
CAMB-7A924	MN908947.3	241	C	T	1	1	0	0	0.999749718433237	TCG	NA	NA	NA	NA	NA	NA	0.000187711175071956
CAMB-7A924	MN908947.3	24851	T	G	0.032	0.034	1.3e-15	3e-16	0.0329817227299242	TTC	S	S1097A	T3289G	TCA>GCA	Missense	GU280_gp02, spike glycoprotein	0.966945362628816
CAMB-7A924	MN908947.3	25429	G	T	1	1	0	0	0.999885541617068	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0
CAMB-7A924	MN908947.3	28799	A	G	0.011	0.0075	3.2e-05	0.00067	0.00914014895057549	GAG	N	S176G	A526G	AGC>GGC	Missense	GU280_gp10	0.990859851049425
CAMB-7A924	MN908947.3	28835	T	A	0.01	0.0068	3.2e-05	0.00059	0.0083088954056696	ATC	N	S188T	T562A	TCA>ACA	Missense	GU280_gp10	0.991528185076572
CAMB-7A924	MN908947.3	28885	A	G	0.011	0.0039	5.4e-06	0.0047	0.00695074040495618	GAA	N	G204G	A612G	GGA>GGG	Synonymous	GU280_gp10	0.993049259595044
CAMB-7A924	MN908947.3	29051	C	INS	0.018	0.028	0.0011	4e-06	0.0215924426450742	GCA	N	.	777-778-insfrshift	.	no-SNV	GU280_gp10	0.97795771479982
CAMB-7A924	MN908947.3	3037	C	T	1	1	0	0	0.99976241387503	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A924	MN908947.3	4029	T	C	0.037	0.016	9.5e-17	5.1e-08	0.028273546562997	CTT	ORF1ab:nsp3	L437P	T1310C	CTT>CCT	Missense	ORF1ab:nsp3	0.971726453437003
CAMB-7A942	MN908947.3	13914	T	G	0.0015	0.022	0.0039	8.3e-12	0.0118577075098814	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N149K	T447G	AAT>AAG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.988142292490119
CAMB-7A942	MN908947.3	14408	C	T	1	1	0	0	0.999323480432972	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000572439633638635
CAMB-7A942	MN908947.3	16852	G	T	1	1	0	0	0.999909730998375	TGG	ORF1ab:helicase	G206C	G616T	GGT>TGT	Missense	ORF1ab:helicase	0
CAMB-7A942	MN908947.3	23403	A	G	1	1	0	0	0.999960391333624	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7A942	MN908947.3	241	C	T	1	1	0	0	0.999703681754204	TCG	NA	NA	NA	NA	NA	NA	0.000296318245795985
CAMB-7A942	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999134199134199	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A942	MN908947.3	3037	C	T	1	1	0	0	0.999301432064268	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A942	MN908947.3	635	C	T	1	1	0	0	0.999528153507392	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.000471846492607738
CAMB-7A960	MN908947.3	11074	C	INS	0.025	0.042	5.8e-05	2e-09	0.0319351853600499	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.967724877717135
CAMB-7A960	MN908947.3	14408	C	T	1	0.97	0	0	0.987083084402876	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.0128139098906079
CAMB-7A960	MN908947.3	16852	G	T	1	1	0	0	0.999965052072412	TGG	ORF1ab:helicase	G206C	G616T	GGT>TGT	Missense	ORF1ab:helicase	0
CAMB-7A960	MN908947.3	2340	C	T	0.92	0.83	0	0	0.878140703517588	TCT	ORF1ab:nsp2	S512F	C1535T	TCT>TTT	Missense	ORF1ab:nsp2	0.121859296482412
CAMB-7A960	MN908947.3	23403	A	G	1	1	0	0	0.999925716832566	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.42831674342594e-05
CAMB-7A960	MN908947.3	23674	A	T	0.079	0.025	1.3e-34	1.1e-12	0.0507206208425721	CAG	S	S704S	A2112T	TCA>TCT	Synonymous	GU280_gp02, spike glycoprotein	0.949094604582409
CAMB-7A960	MN908947.3	241	C	T	1	1	0	0	0.999956829563115	TCG	NA	NA	NA	NA	NA	NA	0
CAMB-7A960	MN908947.3	26781	CTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0435277777777778	0.00353319444444444	0.00016;2.1e-08;2.8e-08;1.5e-07;6.6e-10;2e-08;3e-07;2.9e-07;3.6e-08;1.3e-07;8.9e-08;2.4e-07;1.4e-07;2.2e-07;4.4e-07;1.2e-07;3.7e-07;1.8e-07;1.9e-07;1.8e-07;3.9e-07;1.9e-07;2.6e-07;1.7e-07;9.3e-08;2.8e-07;1.4e-07;8e-08;1.5e-07;3.1e-07;2.6e-07;1.3e-07;3.3e-07;5.1e-08;1.3e-07;9.8e-08	0.00031;0.0012;0.0014;0.0024;0.00052;0.0013;NA;NA;NA;0.5;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	0.0235997252787398	TCT	M	.	259-294-delinframe	.	no-SNV	GU280_gp05	0.976712257346935
CAMB-7A960	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999817618092285	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7A960	MN908947.3	3037	C	T	1	1	0	0	0.999512432959532	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A960	MN908947.3	4421	C	T	0.028	0.069	2e-11	5.4e-25	0.0410917590288773	ACG	ORF1ab:nsp3	R568C	C1702T	CGC>TGC	Missense	ORF1ab:nsp3	0.958908240971123
CAMB-7A960	MN908947.3	8318	C	A	0.1	0.039	2.2e-46	4.2e-19	0.0764313312258518	ACC	ORF1ab:nsp3	P1867T	C5599A	CCC>ACC	Missense	ORF1ab:nsp3	0.923217421847559
CAMB-7A98E	MN908947.3	11074	C	INS	0.054	0.031	7.5e-15	3.2e-06	0.0446399885767322	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.955110127440831
CAMB-7A98E	MN908947.3	14408	C	T	1	0.98	0	0	0.993020520597976	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000417840230276394
CAMB-7A98E	MN908947.3	16289	C	T	1	1	0	0	1	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0
CAMB-7A98E	MN908947.3	18366	AGGTTTT	-	0.0188571428571429	0.00379	7.6e-05;0.00072;0.001;1.5e-10;7.2e-09;0.00025;0.00089	0.47;0.47;0.46;0.5;0.47;0.47;3e-06	0.00704910478076089	TAG	ORF1ab:3'-to-5'-exonuclease	.	327-333-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.992132135483511
CAMB-7A98E	MN908947.3	18372	TTCTACAGGTGTTAACCTAGTTGCTGTACCTACAGGTTA	-	0.00318182051282051	0.0251282051282051	0.00089;0.0018;0.0021;0.002;0.0022;0.002;0.0017;0.0015;0.0022;0.0011;0.0021;NA;NA;0.45;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	3e-06;8.1e-06;9.7e-06;9.5e-06;1.1e-05;8.8e-06;7.9e-06;6.5e-06;1.5e-05;3.6e-06;1.5e-05;5.7e-08;1.7e-07;8.8e-12;3e-11;7.2e-12;1.1e-11;5.3e-10;7.4e-11;1.5e-06;3.1e-07;3.8e-07;9.1e-07;1.8e-06;8.1e-07;8.7e-07;1.1e-07;4.7e-08;2.1e-09;5.2e-08;7.8e-09;7.9e-09;1.3e-08;1.1e-08;7.5e-08;4.1e-08;2.9e-11;1.6e-08;1.2e-11	0.0104065148086358	TTT	ORF1ab:3'-to-5'-exonuclease	.	333-371-delinframe	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.982077316228176
CAMB-7A98E	MN908947.3	21077	C	T	0.026	0.015	4.8e-13	1.8e-08	0.0218017276840806	ACA	ORF1ab:2'-O-ribose-methyltransferase	T140I	C419T	ACA>ATA	Missense	ORF1ab:2'-O-ribose-methyltransferase	0.978198272315919
CAMB-7A98E	MN908947.3	23403	A	G	0.99	1	0	0	0.993648879509597	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	8.03939302582655e-05
CAMB-7A98E	MN908947.3	241	C	T	1	1	0	0	0.999750896771622	TCG	NA	NA	NA	NA	NA	NA	0.000174372259864488
CAMB-7A98E	MN908947.3	25429	G	T	1	1	0	0	0.999855606093423	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	3.60984766442856e-05
CAMB-7A98E	MN908947.3	26146	T	C	1	1	8.49999999999999e-224	2.5e-170	1	TTC	ORF3a	S252P	T754C	TCA>CCA	Missense	GU280_gp03	0
CAMB-7A98E	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCT	-	0.040975	0.0174225	6.3e-05;1.4e-06;4.1e-05;6e-05;0.00011;2.1e-05;3.8e-05;2.1e-07;2e-07;3.9e-08;1e-07;6.6e-08;2e-07;9.2e-08;1.4e-07;3.2e-07;7.6e-08;2.5e-07;1.5e-07;1.6e-07;5.5e-08;3e-07;8.2e-08;1.6e-07;1.3e-07;4.4e-08;2.2e-07;1.1e-07;1.4e-07;8.8e-08;2.3e-07;1.2e-07;5.4e-08;1.6e-07;4.7e-08;1.1e-07;6e-08;0.00029;0.00098;0.00047	0.17;0.1;0.0032;0.0033;0.0049;0.0018;0.003;0.0068;0.0067;0.005;0.0055;0.0053;0.0061;0.0057;0.0062;0.0081;0.0052;0.0072;0.0055;0.006;0.0059;0.0081;0.0061;0.0065;0.0058;0.005;0.0071;0.0059;0.0032;0.0057;0.0071;0.0069;0.0046;0.0073;0.0039;0.0055;0.005;0.0094;0.1;0.084	0.0324535416105575	GTC	M	.	258-297-delfrshift	.	no-SNV	GU280_gp05	0.980997784193917
CAMB-7A98E	MN908947.3	28300	G	T	0.0054	0.0075	0.00023	2.4e-05	0.00629890971162053	AGC	N	Q9H	G27T	CAG>CAT	Missense	GU280_gp10	0.993580882087776
CAMB-7A98E	MN908947.3	28691	AATACACCAAAAGATCACA	-	0.00274210526315789	0.00738421052631579	NA;0.0016;0.0019;0.0023;0.002;0.0016;0.0019;0.0016;0.01;0.0033;0.002;0.0026;0.0027;0.0018;0.0019;0.0045;NA;NA;NA	1.6e-05;1.3e-05;2.1e-05;2.1e-05;1.7e-05;1.2e-05;1.6e-05;1.3e-05;0.00013;9.2e-05;4.6e-05;6.6e-05;7.7e-05;5.5e-05;6.3e-05;0.00014;1e-04;5.1e-05;4.1e-05	0.00397110677484509	GAA	N	.	418-436-delfrshift	.	no-SNV	GU280_gp10	0.995959913951414
CAMB-7A98E	MN908947.3	28826	C	T	0.0095	0.011	8.9e-05	2.9e-05	0.010125835627212	TCG	N	R185C	C553T	CGT>TGT	Missense	GU280_gp10	0.989677546205269
CAMB-7A98E	MN908947.3	28849	C	T	0.088	0.15	1.8e-38	1.1e-62	0.111383468967546	ACA	N	N192N	C576T	AAC>AAT	Synonymous	GU280_gp10	0.883812138444946
CAMB-7A98E	MN908947.3	3037	C	T	1	1	0	0	0.999635479951397	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000121506682867558
CAMB-7A98E	MN908947.3	4531	TTACTTTTACACCAGTAAAACAACTGTA	-	0.00125	0.0361428571428571	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;7e-06;9.5e-06	5.7e-05;0.00018;0.00023;0.00021;6.9e-05;4.8e-05;0.00014;0.00011;1.1e-06;0.00014;0.00014;0.00012;5.9e-05;0.00014;0.00012;0.00013;3.3e-05;2.4e-05;2.3e-05;2.6e-05;2.8e-05;2.6e-05;2.1e-05;2.3e-05;2.1e-05;3.9e-06;1.5e-10;2.1e-10	0.0142774353300669	TTT	ORF1ab:nsp3	.	1812-1839-delfrshift	.	no-SNV	ORF1ab:nsp3	0.985360544217687
CAMB-7A99D	MN908947.3	11916	C	T	0.041	0.039	2.7e-19	1.4e-18	0.0404718942454792	TCA	ORF1ab:nsp7	S25L	C74T	TCA>TTA	Missense	ORF1ab:nsp7	0.95950849252736
CAMB-7A99D	MN908947.3	14408	C	T	1	1	0	0	0.999276718856365	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000468005445881552
CAMB-7A99D	MN908947.3	15738	C	T	0.98	0.98	0	0	0.981307162370828	TCA	ORF1ab:RNA-dependent-RNA-polymerase	F757F	C2271T	TTC>TTT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.0185740586768025
CAMB-7A99D	MN908947.3	20030	C	T	1	1	4.3e-251	6.79999999999999e-310	1	GCC	ORF1ab:endoRNAse	A137V	C410T	GCC>GTC	Missense	ORF1ab:endoRNAse	0
CAMB-7A99D	MN908947.3	23403	A	G	1	1	0	0	0.999889593243106	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.36045045956813e-05
CAMB-7A99D	MN908947.3	241	C	T	1	1	0	0	0.999758377785625	TCG	NA	NA	NA	NA	NA	NA	9.2931620913332e-05
CAMB-7A99D	MN908947.3	25044	C	T	0.023	0.0071	9.4e-12	2.5e-05	0.0158062723018164	TCA	S	S1161L	C3482T	TCA>TTA	Missense	GU280_gp02, spike glycoprotein	0.984166831035163
CAMB-7A99D	MN908947.3	25521	C	T	0.032	0.034	5.8e-15	4.4e-16	0.0325536332179931	TCG	ORF3a	F43F	C129T	TTC>TTT	Synonymous	GU280_gp03	0.967418685121107
CAMB-7A99D	MN908947.3	25549	CTTGCTG	-	0.0302857142857143	0.00486228571428571	2.7e-08;4.4e-09;2e-08;2e-09;4.7e-08;4.2e-08;1.1e-07	NA;NA;NA;NA;NA;4.4e-09;NA	0.018588283999172	TCT	ORF3a	.	157-163-delfrshift	.	no-SNV	GU280_gp03	0.981370830860944
CAMB-7A99D	MN908947.3	27164	T	C	0.2	0.19	1.3e-93	1e-87	0.194928498866922	GTG	M	S214S	T642C	AGT>AGC	Synonymous	GU280_gp05	0.805071501133078
CAMB-7A99D	MN908947.3	28253	C	T	0.039	0.052	1.7e-17	2.7e-23	0.044909099653713	TCA	ORF8	F120F	C360T	TTC>TTT	Synonymous	GU280_gp09	0.954994709503655
CAMB-7A99D	MN908947.3	28556	C	T	0.019	0.0095	9.6e-10	6.4e-06	0.014274899967557	TCG	N	R95C	C283T	CGT>TGT	Missense	GU280_gp10	0.985725100032443
CAMB-7A99D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999315381104518	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000124968757810547
CAMB-7A99D	MN908947.3	3037	C	T	1	1	0	0	0.999510523739599	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000122369065100343
CAMB-7A99D	MN908947.3	635	C	T	0.017	0.086	3.5e-09	5.2e-39	0.0447111653176627	TCG	ORF1ab:leader-protein	R124C	C370T	CGT>TGT	Missense	ORF1ab:leader-protein	0.955288834682337
CAMB-7A9AC	MN908947.3	12578	G	T	0.012	0.013	3.2e-05	1.2e-05	0.0124940349659451	AGA	ORF1ab:nsp8	D163Y	G487T	GAT>TAT	Missense	ORF1ab:nsp8	0.987491504345437
CAMB-7A9AC	MN908947.3	13033	T	C	0.011	0.056	1.1e-06	2.4e-26	0.0296220542857016	ATG	ORF1ab:nsp10	N3N	T9C	AAT>AAC	Synonymous	ORF1ab:nsp10	0.970364664267152
CAMB-7A9AC	MN908947.3	13571	G	T	0.017	0.02	0.00019	4.3e-05	0.0187002406961674	GGT	ORF1ab:RNA-dependent-RNA-polymerase	G35V	G104T	GGT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.975745232364377
CAMB-7A9AC	MN908947.3	14408	C	T	1	1	0	0	0.999531760047092	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000254187403007438
CAMB-7A9AC	MN908947.3	16289	C	T	1	1	0	0	0.999725576289791	GCT	ORF1ab:helicase	A18V	C53T	GCT>GTT	Missense	ORF1ab:helicase	0.000274423710208562
CAMB-7A9AC	MN908947.3	16995	C	T	0.009	0.0099	5.1e-06	1.6e-06	0.0093160187126956	ACC	ORF1ab:helicase	Y253Y	C759T	TAC>TAT	Synonymous	ORF1ab:helicase	0.9906234876593
CAMB-7A9AC	MN908947.3	17624	C	T	0.017	0.053	1.5e-09	4.5e-25	0.030547218681906	GCA	ORF1ab:helicase	A463V	C1388T	GCA>GTA	Missense	ORF1ab:helicase	0.969432224643342
CAMB-7A9AC	MN908947.3	23403	A	G	1	1	0	0	0.999932065794278	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	3.39671028608792e-05
CAMB-7A9AC	MN908947.3	241	C	T	1	1	0	0	0.99982698629347	TCG	NA	NA	NA	NA	NA	NA	5.76712355101021e-05
CAMB-7A9AC	MN908947.3	25429	G	T	1	1	0	0	0.999957976130442	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	2.80159130386059e-05
CAMB-7A9AC	MN908947.3	26146	T	C	1	1	7.8e-274	1.5e-134	1	TTC	ORF3a	S252P	T754C	TCA>CCA	Missense	GU280_gp03	0
CAMB-7A9AC	MN908947.3	28045	C	T	0.033	0.04	2.1e-14	1.8e-15	0.0349432450478522	GCT	ORF8	A51V	C152T	GCT>GTT	Missense	GU280_gp09	0.964834186512353
CAMB-7A9AC	MN908947.3	29659	C	T	0.032	0.016	2.7e-14	3.9e-08	0.0250716332378223	ACT	ORF10	N34N	C102T	AAC>AAT	Synonymous	GU280_gp11	0.974928366762178
CAMB-7A9AC	MN908947.3	3037	C	T	1	1	0	0	0.999094920239846	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000339404910057699
CAMB-7A9AC	MN908947.3	5107	A	C	0.061	0.08	5.6e-19	1.6e-20	0.0685328185328185	AAG	ORF1ab:nsp3	E796D	A2388C	GAA>GAC	Missense	ORF1ab:nsp3	0.931467181467181
CAMB-7A9CA	MN908947.3	11195	C	T	1	1	0	0	0.999712505989459	TCT	ORF1ab:nsp6	L75F	C223T	CTT>TTT	Missense	ORF1ab:nsp6	0
CAMB-7A9CA	MN908947.3	14408	C	T	1	1	0	0	0.999023556694739	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000854387892103015
CAMB-7A9CA	MN908947.3	15216	C	T	1	1	0	0	1	GCA	ORF1ab:RNA-dependent-RNA-polymerase	S583S	C1749T	AGC>AGT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-7A9CA	MN908947.3	23403	A	G	1	1	0	0	0.99995129791068	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7A9CA	MN908947.3	241	C	T	1	1	0	0	0.99927832571566	TCG	NA	NA	NA	NA	NA	NA	0.000240558094779889
CAMB-7A9CA	MN908947.3	28775	C	T	1	1	0	0	1	GCC	N	P168S	C502T	CCA>TCA	Missense	GU280_gp10	0
CAMB-7A9CA	MN908947.3	28881	GGG	AAC	0.996666666666667	1	0;0;0	1.4e-305;9.88131291682493e-324;0	0.998714652956298	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.00144717800289436
CAMB-7A9CA	MN908947.3	3373	C	A	1	1	0	0	0.999896608767576	ACA	ORF1ab:nsp3	D218E	C654A	GAC>GAA	Missense	ORF1ab:nsp3	0.00010339123242349
CAMB-7A9D9	MN908947.3	12758	G	C	0.01	0.015	1.1e-06	9.1e-09	0.0120772444758559	TGA	ORF1ab:nsp9	D25H	G73C	GAT>CAT	Missense	ORF1ab:nsp9	0.987766853056728
CAMB-7A9D9	MN908947.3	14408	C	T	1	1	0	0	0.99934428758775	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000366427524492787
CAMB-7A9D9	MN908947.3	19170	C	T	1	1	0	0	0.999943824958571	TCA	ORF1ab:3'-to-5'-exonuclease	F377F	C1131T	TTC>TTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	5.61750414290931e-05
CAMB-7A9D9	MN908947.3	19983	C	INS	0.044	0.04	1.9e-08	5.5e-06	0.0428134556574924	TCT	ORF1ab:endoRNAse	.	362-363-insfrshift	.	no-SNV	ORF1ab:endoRNAse	0.957186544342508
CAMB-7A9D9	MN908947.3	23403	A	G	1	1	0	0	0.999885947722583	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000114052277416612
CAMB-7A9D9	MN908947.3	241	C	T	1	1	0	0	0.99971839528637	TCG	NA	NA	NA	NA	NA	NA	0.000194957109435924
CAMB-7A9D9	MN908947.3	26542	C	T	0.12	0.036	9.2e-55	2.5e-17	0.078921568627451	ACT	M	T7I	C20T	ACT>ATT	Missense	GU280_gp05	0.921023965141612
CAMB-7A9D9	MN908947.3	26885	C	T	0.099	0.021	2e-45	3.6e-11	0.0638546231538545	ACG	M	N121N	C363T	AAC>AAT	Synonymous	GU280_gp05	0.936135484573
CAMB-7A9D9	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999172967863894	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000387847446670976
CAMB-7A9D9	MN908947.3	3037	C	T	1	1	0	0	0.999750374438342	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7A9D9	MN908947.3	4525	TAGATTTTACTTTTACACCAGTAAAACAACTG	-	0.05284375	0.0586615625	7.9e-20;1.7e-17;4.4e-13;7.5e-13;2.7e-09;9.2e-08;4.1e-07;2.4e-06;3.8e-06;3.4e-06;3e-07;2.1e-07;1.4e-06;1e-06;7.1e-07;2.4e-06;1.4e-06;1.9e-06;6.8e-07;1.7e-06;1.1e-06;1.6e-06;2.3e-07;2.3e-07;2e-07;2.9e-07;3.2e-07;2.5e-07;1.8e-07;2.6e-07;1.7e-07;1.5e-08	NA;NA;NA;NA;NA;NA;1.5e-11;2.3e-10;4e-10;2.9e-10;8.1e-12;5.9e-12;2.1e-10;7.6e-11;4.2e-11;2.2e-10;8.5e-11;1.6e-10;2.2e-11;9.9e-11;5.9e-11;1.4e-10;2.4e-12;1e-05;9.5e-06;1.1e-05;1.1e-05;9.6e-06;7.9e-06;9.7e-06;6.6e-06;1.3e-06	0.0676338809473011	CTA	ORF1ab:nsp3	.	1806-1837-delfrshift	.	no-SNV	ORF1ab:nsp3	0.969586463423528
CAMB-7A9D9	MN908947.3	558	G	T	0.025	0.016	2.8e-07	3.1e-05	0.0220080650673228	GGT	ORF1ab:leader-protein	G98V	G293T	GGT>GTT	Missense	ORF1ab:leader-protein	0.977889412890438
CAMB-7A9D9	MN908947.3	6198	C	A	0.0079	0.018	5.6e-06	3.5e-10	0.0119493455851125	TCT	ORF1ab:nsp3	S1160Y	C3479A	TCT>TAT	Missense	ORF1ab:nsp3	0.987992741592989
CAMB-7A9D9	MN908947.3	8917	C	T	1	1	0	0	0.999516176532458	TCT	ORF1ab:nsp4	F121F	C363T	TTC>TTT	Synonymous	ORF1ab:nsp4	2.10358029365981e-05
CAMB-7A9D9	MN908947.3	9321	G	-	0.025	0.045	1.3e-07	5.3e-13	0.03464499572284	TGT	ORF1ab:nsp4	.	767-767-delfrshift	.	no-SNV	ORF1ab:nsp4	0.965069860279441
CAMB-7A9E8	MN908947.3	1059	C	T	1	1	0	0	0.999940747061054	ACC	ORF1ab:nsp2	T85I	C254T	ACC>ATC	Missense	ORF1ab:nsp2	4.74023511566174e-05
CAMB-7A9E8	MN908947.3	11074	C	INS	0.026	0.016	1.7e-05	0.0083	0.0205732802103182	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.977898244291144
CAMB-7A9E8	MN908947.3	11075	T	-	0.049	0.056	7.1e-12	2.2e-13	0.0527681514664863	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.943673400388809
CAMB-7A9E8	MN908947.3	14408	C	T	1	0.99	0	0	0.995307138531925	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00120265087801924
CAMB-7A9E8	MN908947.3	16887	C	T	0.01	0.0083	3.7e-05	0.00016	0.00912652684950449	ACA	ORF1ab:helicase	Y217Y	C651T	TAC>TAT	Synonymous	ORF1ab:helicase	0.990850426365522
CAMB-7A9E8	MN908947.3	20055	A	G	0.014	0.016	2.1e-05	2.2e-06	0.015185601799775	AAG	ORF1ab:endoRNAse	E145E	A435G	GAA>GAG	Synonymous	ORF1ab:endoRNAse	0.984814398200225
CAMB-7A9E8	MN908947.3	23403	A	G	1	1	0	0	0.99849714066373	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.10823840163428e-05
CAMB-7A9E8	MN908947.3	23426	G	C	1	1	0	0	0.997928231825546	TGT	S	V622L	G1864C	GTT>CTT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7A9E8	MN908947.3	241	C	T	1	1	0	0	0.99701138903099	TCG	NA	NA	NA	NA	NA	NA	0.000148084327293288
CAMB-7A9E8	MN908947.3	25563	G	T	1	1	0	0	0.998624238018008	AGA	ORF3a	Q57H	G171T	CAG>CAT	Missense	GU280_gp03	2.23701135283262e-05
CAMB-7A9E8	MN908947.3	25618	G	A	0.0054	0.011	0.00023	1.1e-06	0.00827865212886674	GGG	ORF3a	G76S	G226A	GGT>AGT	Missense	GU280_gp03	0.991672011446051
CAMB-7A9E8	MN908947.3	25649	TGTTTGTAACAGTTTACTCACACC	-	0.0096125	0.00326666666666667	0.00093;0.00072;1.6e-05;3.8e-05;4.5e-06;5e-06;2e-06;2.1e-06;1.8e-06;1.8e-06;1.6e-06;1.5e-06;1.5e-06;0.00082;0.00048;0.00046;0.00039;0.00043;0.00026;0.00025;0.00038;0.00032;0.00054;0.00047	0.051;0.097;0.017;0.014;0.0079;0.0081;0.0071;0.0082;0.0052;0.0052;0.0069;0.021;0.029;0.028;0.021;0.02;0.017;0.019;0.017;0.017;0.017;0.017;0.021;0.021	0.00638523005071697	TTG	ORF3a	.	257-280-delinframe	.	no-SNV	GU280_gp03	0.993284916608883
CAMB-7A9E8	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0328918918918919	0.0285945945945946	0.00051;4.4e-05;2e-04;0.00024;0.00031;2.4e-06;1.6e-05;2e-05;2e-05;4.7e-06;1.1e-05;8.6e-06;2e-05;1.2e-05;1.2e-05;1.5e-05;7.2e-06;1.7e-05;1.5e-05;1.5e-05;1.2e-05;1.3e-05;6.8e-06;1.7e-05;1.3e-05;8.2e-06;2e-05;1.2e-05;3.4e-06;1.2e-05;2.1e-05;1.9e-05;9.1e-06;2.1e-05;8.1e-06;1.5e-05;1e-05	0.0036;0.00098;0.0027;0.003;0.0046;0.00019;0.00036;0.00013;0.00013;4e-05;5.5e-05;4.7e-05;7.6e-05;5.5e-05;6.7e-05;9.7e-05;5e-05;8.5e-05;6.7e-05;6.3e-05;4.4e-05;9.5e-05;5e-05;6.6e-05;5.6e-05;4.4e-05;8e-05;5.2e-05;3e-05;5.4e-05;7.8e-05;7.7e-05;5.6e-05;7.6e-05;3.1e-05;4.9e-05;3.2e-05	0.0318216053367764	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.979433849127863
CAMB-7A9E8	MN908947.3	28374	G	A	1	1	0	0	0.99931376034527	GGG	N	G34E	G101A	GGG>GAG	Missense	GU280_gp10	0.000140555110005043
CAMB-7A9E8	MN908947.3	28754	C	T	0.013	0.013	1.6e-07	3e-07	0.0128312859296013	ACT	N	L161F	C481T	CTT>TTT	Missense	GU280_gp10	0.986728555613354
CAMB-7A9E8	MN908947.3	29625	C	T	0.12	0.11	2.2e-52	1.5e-47	0.113624002900653	TCT	ORF10	S23F	C68T	TCT>TTT	Missense	GU280_gp11	0.88633067440174
CAMB-7A9E8	MN908947.3	3037	C	T	1	1	0	0	0.999292900073924	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000385690868768682
CAMB-7A9E8	MN908947.3	5348	C	T	0.02	0.017	4.3e-10	8.5e-09	0.0184162062615101	TCT	ORF1ab:nsp3	L877L	C2629T	CTA>TTA	Synonymous	ORF1ab:nsp3	0.98158379373849
CAMB-7A9E8	MN908947.3	6692	A	G	0.014	0.021	9.2e-08	1.7e-10	0.0176227515799708	TAA	ORF1ab:nsp3	K1325E	A3973G	AAG>GAG	Missense	ORF1ab:nsp3	0.982377248420029
CAMB-7A9E8	MN908947.3	9344	C	T	1	1	0	0	0.999143331370134	ACT	ORF1ab:nsp4	L264F	C790T	CTT>TTT	Missense	ORF1ab:nsp4	0
CAMB-7AA21	MN908947.3	11075	T	-	0.04	0.036	2.3e-10	2.8e-09	0.0380173849750143	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.957671365182458
CAMB-7AA21	MN908947.3	14408	C	T	1	1	0	0	0.998663101604278	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000411353352529823
CAMB-7AA21	MN908947.3	23403	A	G	1	1	0	0	0.999632399828953	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.00163544565894e-05
CAMB-7AA21	MN908947.3	241	C	T	1	1	0	0	0.999108079115793	TCG	NA	NA	NA	NA	NA	NA	0.000132582834138874
CAMB-7AA21	MN908947.3	28086	G	T	0.99	1	0	0	0.996014863482148	GGC	ORF8	A65S	G193T	GCT>TCT	Missense	GU280_gp09	0.000807797942807906
CAMB-7AA21	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999305724303121	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000115167568812622
CAMB-7AA21	MN908947.3	3037	C	T	1	1	0	0	0.999199757764513	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000108140842633446
CAMB-7AA21	MN908947.3	337	C	T	0.024	0.023	2.3e-11	2.9e-11	0.0235167640932608	GCG	ORF1ab:leader-protein	R24R	C72T	CGC>CGT	Synonymous	ORF1ab:leader-protein	0.976449640529463
CAMB-7B589	MN908947.3	11074	C	INS	0.12	0.12	8.5e-46	3.5e-48	0.119839790069747	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.87605828326773
CAMB-7B589	MN908947.3	11083	G	-	0.17	0.17	2.2e-73	1.5e-76	0.169080259222333	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	2.49252243270189e-05
CAMB-7B589	MN908947.3	11083	G	T	0.83	0.83	0	0	0.830807577268195	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	2.49252243270189e-05
CAMB-7B589	MN908947.3	14805	C	T	1	1	0	0	0.997134166022751	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.00104656735687947
CAMB-7B589	MN908947.3	17247	T	C	1	1	0	0	0.999332792590073	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000484052434652921
CAMB-7B589	MN908947.3	18138	C	T	0.018	0.017	9.7e-10	2.4e-09	0.0174648862726427	TCA	ORF1ab:3'-to-5'-exonuclease	F33F	C99T	TTC>TTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.982232129331054
CAMB-7B589	MN908947.3	23559	TTGGTGCAGGTATATGCGCTAG	-	0.0395454545454545	0.0344090909090909	0.00024;0.00043;0.00012;0.00024;0.00027;0.00028;0.00026;0.00023;0.00015;0.00014;4.2e-05;9.2e-06;0.00014;6.8e-05;0.00016;7.9e-05;0.00019;0.00033;0.00021;0.00028;7.3e-06;1.7e-05	0.00037;0.00086;0.00035;0.00061;0.00065;0.00063;0.00061;0.00057;0.00037;0.00035;0.00011;3.9e-05;0.00045;3e-04;0.00064;0.00043;0.00079;0.0013;0.00088;0.0011;1e-04;0.00015	0.0352512908138628	ATT	S	.	1997-2018-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.952821869488536
CAMB-7B589	MN908947.3	26144	G	T	1	1	0	0	0.999670013670862	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000141422712487626
CAMB-7B589	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	-	0.0518536585365854	0.0496341463414634	1e-06;6.8e-09;1.3e-07;1.7e-07;6.6e-07;2e-10;4.3e-09;1.6e-09;1.6e-09;1.5e-10;3.9e-10;2.7e-10;1.3e-09;4.9e-10;7.9e-10;2.1e-09;3.5e-10;1.6e-09;6.7e-10;7.5e-10;5.4e-10;1.6e-09;4.4e-10;1.1e-09;6e-10;2.7e-10;1.2e-09;4.6e-10;1e-10;4.8e-10;1.3e-09;1.1e-09;2.7e-10;1.2e-09;1.4e-10;5.8e-10;2.2e-10;3.5e-05;0.00049;0.00027;0.00054	1.3e-06;2.7e-08;2.7e-07;2.7e-07;9.2e-07;1.3e-09;8.5e-09;4.7e-09;4.9e-09;1.7e-09;1.4e-09;9.5e-10;4.3e-09;1.6e-09;2.4e-09;5.4e-09;1.4e-09;4.5e-09;2.7e-09;2.3e-09;9.9e-10;4.9e-09;2e-09;2.9e-09;2e-09;1.2e-09;3.7e-09;1.7e-09;2.1e-09;1.8e-09;3.5e-09;3.3e-09;1.7e-09;3.5e-09;6e-10;2.2e-09;1.6e-09;9.8e-05;0.00091;0.00044;0.00082	0.0543520490869874	GTC	M	.	258-298-delfrshift	.	no-SNV	GU280_gp05	0.963105211037658
CAMB-7B589	MN908947.3	27384	T	C	0.027	0.026	4.1e-13	1.6e-12	0.0260470568840613	ATT	ORF6	D61D	T183C	GAT>GAC	Synonymous	GU280_gp06	0.973339316951652
CAMB-7B589	MN908947.3	28093	C	T	0.015	0.014	1.3e-07	2.5e-07	0.0146106736657918	TCT	ORF8	S67F	C200T	TCT>TTT	Missense	GU280_gp09	0.983989501312336
CAMB-7B589	MN908947.3	29736	G	T	0.017	0.015	1.8e-08	9.7e-08	0.0157117702830828	AGG	NA	NA	NA	NA	NA	NA	0.982324258431532
CAMB-7B589	MN908947.3	4794	C	T	0.0075	0.0071	3.4e-05	5.5e-05	0.00726449084016947	TCC	ORF1ab:nsp3	S692F	C2075T	TCC>TTC	Missense	ORF1ab:nsp3	0.99253599971834
CAMB-7B589	MN908947.3	522	TT	-	0.0485	0.0465	2.3e-07;1.6e-05	5.6e-07;3.3e-05	0.0470392853052342	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.942765486463771
CAMB-7B598	MN908947.3	11075	T	-	0.054	0.055	3.1e-13	5.3e-14	0.0545420726559929	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.944971455552217
CAMB-7B598	MN908947.3	11638	T	C	1	1	0	0	1	CTT	ORF1ab:nsp6	T222T	T666C	ACT>ACC	Synonymous	ORF1ab:nsp6	0
CAMB-7B598	MN908947.3	12235	ATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCT	-	0.000425272727272727	0.00944727272727273	NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;0.48;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;6.6e-12;NA;NA;NA;NA	5.3e-05;5e-06;2.8e-06;5.6e-06;5.2e-06;1.2e-06;3.3e-06;2.3e-06;6.2e-06;3.2e-06;3e-06;2e-06;1.7e-06;8.4e-06;3.1e-06;3.5e-06;2.7e-06;2.6e-06;5e-06;2.6e-06;3.3e-06;7.9e-06;2.8e-06;1.1e-06;2.6e-07;2.2e-06;2.7e-06;1.2e-06;4.3e-06;2.4e-06;7.6e-06;4.4e-06;5.7e-06;1.1e-05;2.9e-06;2.1e-05;4.8e-06;4.1e-07;2.4e-06;5.6e-06;2.5e-06;1.8e-06;2.4e-06;2.3e-06;2.9e-06;3.2e-06;3.1e-06;1.6e-06;2.5e-06;2.9e-06;3.2e-06;2.3e-06;1.7e-06;1.8e-06;3.5e-06	0.00481729526495124	AAT	ORF1ab:nsp8	.	144-198-delfrshift	.	no-SNV	ORF1ab:nsp8	0.994977297384177
CAMB-7B598	MN908947.3	12733	C	T	0.013	0.014	1e-07	2.7e-08	0.0137411216153474	CCG	ORF1ab:nsp9	A16A	C48T	GCC>GCT	Synonymous	ORF1ab:nsp9	0.986239121200447
CAMB-7B598	MN908947.3	12741	C	A	1	1	0	0	0.999873147217533	ACA	ORF1ab:nsp9	T19K	C56A	ACA>AAA	Missense	ORF1ab:nsp9	0
CAMB-7B598	MN908947.3	13778	AT	-	0.0385	0.04	6e-12;4.4e-12	1.5e-12;4.6e-12	0.0392818908012847	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.962352012628256
CAMB-7B598	MN908947.3	14408	C	T	1	0.99	0	0	0.993459568969643	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00626924242665943
CAMB-7B598	MN908947.3	1547	A	T	0.035	0.027	6.1e-11	1.6e-07	0.0322128851540616	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.967787114845938
CAMB-7B598	MN908947.3	17342	A	-	0.017	0.017	9.7e-09	4.8e-09	0.0172229504890592	GAT	ORF1ab:helicase	.	1106-1106-delfrshift	.	no-SNV	ORF1ab:helicase	0.982756882121609
CAMB-7B598	MN908947.3	17342	AT	-	0.0085	0.0175	9.7e-09;NA	4.8e-09;2.5e-09	0.0125943804926352	GAT	ORF1ab:helicase	.	1106-1107-delfrshift	.	no-SNV	ORF1ab:helicase	0.982756882121609
CAMB-7B598	MN908947.3	23403	A	G	1	1	0	0	0.999945103808698	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.48961913022475e-05
CAMB-7B598	MN908947.3	241	C	T	0.97	1	0	0	0.981298388784264	TCG	NA	NA	NA	NA	NA	NA	7.84682988072819e-05
CAMB-7B598	MN908947.3	24569	A	G	0.048	0.002	1.4e-17	0.0079	0.0211576846307385	AAG	S	S1003G	A3007G	AGT>GGT	Missense	GU280_gp02, spike glycoprotein	0.978842315369261
CAMB-7B598	MN908947.3	27837	TTT	-	0.0143333333333333	0.00286666666666667	2e-06;2e-07;2.6e-07	1e-04;NA;NA	0.00651340996168582	CTT	NA	NA	NA	NA	NA	NA	0.988888888888889
CAMB-7B598	MN908947.3	28313	C	T	0.035	0.038	1.6e-16	4e-18	0.0361751664268248	CCG	N	R14C	C40T	CGC>TGC	Missense	GU280_gp10	0.963766335567957
CAMB-7B598	MN908947.3	28716	C	T	0.025	0.0066	7.3e-13	6.2e-05	0.0151992991677617	ACC	N	T148I	C443T	ACC>ATC	Missense	GU280_gp10	0.984756898817346
CAMB-7B598	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7B598	MN908947.3	29708	C	T	1	1	0	0	1	ACT	NA	NA	NA	NA	NA	NA	0
CAMB-7B598	MN908947.3	3037	C	T	1	1	0	0	0.999333111037012	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000166722240746916
CAMB-7B598	MN908947.3	508	T	-	0.077	0.04	1.7e-08	8.6e-05	0.0644299439963007	ATG	ORF1ab:leader-protein	.	243-243-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.933412115295689
CAMB-7B598	MN908947.3	514	T	-	0.14	0.078	1.7e-05	0.0011	0.122534718170148	ATG	ORF1ab:leader-protein	.	249-249-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.87238884350566
CAMB-7B598	MN908947.3	522	T	-	0.1	0.054	1.8e-13	3.1e-07	0.0857715758890207	GTT	ORF1ab:leader-protein	.	257-257-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.913941973237304
CAMB-7B5A7	MN908947.3	10280	A	C	0.0083	0.004	7.6e-06	0.00052	0.00616254621909664	CAG	ORF1ab:3C-like-proteinase	R76R	A226C	AGG>CGG	Synonymous	ORF1ab:3C-like-proteinase	0.993764953237149
CAMB-7B5A7	MN908947.3	11075	T	-	0.046	0.031	2.5e-11	4.1e-08	0.0389097172965853	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.956186037085824
CAMB-7B5A7	MN908947.3	1371	A	G	0.014	0.0023	5.8e-07	0.0063	0.00857449088960343	TAT	ORF1ab:nsp2	Y189C	A566G	TAT>TGT	Missense	ORF1ab:nsp2	0.991425509110397
CAMB-7B5A7	MN908947.3	14408	C	T	1	1	0	0	0.997237275528637	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000202857391253948
CAMB-7B5A7	MN908947.3	1554	A	C	0.013	0.0026	1.1e-06	0.0022	0.00835322195704057	AAC	ORF1ab:nsp2	N250T	A749C	AAC>ACC	Missense	ORF1ab:nsp2	0.991646778042959
CAMB-7B5A7	MN908947.3	17206	T	C	0.052	0.039	5.3e-24	1.6e-18	0.0455840455840456	ATA	ORF1ab:helicase	Y324H	T970C	TAT>CAT	Missense	ORF1ab:helicase	0.951392896730517
CAMB-7B5A7	MN908947.3	17676	C	T	0.01	0.013	3.8e-06	1.6e-07	0.0115355277826674	TCA	ORF1ab:helicase	I480I	C1440T	ATC>ATT	Synonymous	ORF1ab:helicase	0.988464472217333
CAMB-7B5A7	MN908947.3	18487	A	G	0.0077	0.0083	1.8e-05	1e-05	0.00800138606687773	CAT	ORF1ab:3'-to-5'-exonuclease	I150V	A448G	ATA>GTA	Missense	ORF1ab:3'-to-5'-exonuclease	0.99176235253351
CAMB-7B5A7	MN908947.3	19017	C	T	0.58	0.54	0	2.96439387504748e-323	0.559254310455585	TCC	ORF1ab:3'-to-5'-exonuclease	F326F	C978T	TTC>TTT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.440694298121644
CAMB-7B5A7	MN908947.3	19263	C	T	0.0047	0.0086	0.00034	6.2e-06	0.0065212835463948	ACC	ORF1ab:3'-to-5'-exonuclease	N408N	C1224T	AAC>AAT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.993429406181043
CAMB-7B5A7	MN908947.3	2180	G	A	0.54	0.54	3.59976229559932e-320	8.59674223763769e-322	0.536876556678537	TGT	ORF1ab:nsp2	V459I	G1375A	GTA>ATA	Missense	ORF1ab:nsp2	0.463102859142463
CAMB-7B5A7	MN908947.3	2276	A	C	0.0083	0.013	1.7e-05	3e-07	0.0107807337854286	AAT	ORF1ab:nsp2	I491L	A1471C	ATT>CTT	Missense	ORF1ab:nsp2	0.989219266214571
CAMB-7B5A7	MN908947.3	23403	A	G	1	1	0	0	0.999816573757287	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.38004322479285e-05
CAMB-7B5A7	MN908947.3	241	C	T	1	1	0	0	0.999180095235092	TCG	NA	NA	NA	NA	NA	NA	7.88369966257766e-05
CAMB-7B5A7	MN908947.3	25387	G	A	0.014	0.022	7e-08	2.3e-11	0.0177667163609034	CGA	NA	NA	NA	NA	NA	NA	0.981025836896123
CAMB-7B5A7	MN908947.3	25467	T	A	0.0018	0.0077	0.0042	1.6e-05	0.00472094853080826	CTT	ORF3a	P25P	T75A	CCT>CCA	Synonymous	GU280_gp03	0.993881759231625
CAMB-7B5A7	MN908947.3	25520	TCGGAT	-	0.0134166666666667	0.00605	3e-05;6.1e-06;0.00011;0.00068;0.00063;0.00063	0.015;0.0011;0.0039;0.0099;0.01;0.011	0.00849213971591771	TTC	ORF3a	.	128-133-delinframe	.	no-SNV	GU280_gp03	0.987983124659771
CAMB-7B5A7	MN908947.3	26550	G	A	0.42	0.39	2.7e-228	4.7e-208	0.40482603483743	CGT	M	V10I	G28A	GTT>ATT	Missense	GU280_gp05	0.594648591851534
CAMB-7B5A7	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0385675675675676	0.0308918918918919	4.9e-05;1.8e-06;1.1e-05;1.6e-05;4e-05;6e-07;2.7e-06;1.5e-06;1.4e-06;4.8e-07;6.7e-07;5.2e-07;1.5e-06;8.5e-07;1.1e-06;2.2e-06;6.3e-07;1.8e-06;1.1e-06;1.1e-06;6.2e-07;2e-06;9.3e-07;1.3e-06;1e-06;5.6e-07;1.5e-06;9.4e-07;8.4e-07;7.3e-07;1.6e-06;1.2e-06;3.5e-07;1.3e-06;8.6e-07;3.2e-06;2.2e-06	0.00058;4.5e-05;0.00048;0.00054;0.00079;1.8e-05;3.6e-05;4.4e-05;4.2e-05;1.8e-05;3.2e-05;2.8e-05;4e-05;2.8e-05;3.5e-05;5.4e-05;2.8e-05;4.8e-05;3.4e-05;3.4e-05;2.8e-05;5.4e-05;3.5e-05;2.2e-05;1.7e-05;1.3e-05;2.5e-05;1.5e-05;9.7e-06;1.7e-05;2.4e-05;2.3e-05;1.7e-05;2.6e-05;1.8e-05;3.2e-05;3.1e-05	0.0354473113093803	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.974392529235021
CAMB-7B5A7	MN908947.3	27264	TT	-	0.00385	0.0145	0.016;0.0094	5.1e-07;6e-06	0.00892444388726523	CTT	ORF6	.	63-64-delfrshift	.	no-SNV	GU280_gp06	0.990449842133233
CAMB-7B5A7	MN908947.3	27266	TTAAAGTTTCCATTTGGAATCTTGATTACATCATA	-	0.340571428571429	0.300285714285714	3e-103;2.5e-92;6.2e-104;2.2e-99;7.1e-99;3.5e-95;3.3e-104;1.7e-93;1.8e-92;2.6e-95;2.9e-98;1e-98;3.2e-103;6e-94;2.5e-93;1.6e-95;2.8e-88;5.7e-99;1e-95;2.8e-97;1.2e-93;2.1e-106;6.2e-94;4.7e-108;1.2e-109;4.4e-175;8.7e-124;2.5e-173;8.2e-168;8.7e-158;1.7e-164;4.6e-151;1.9e-178;4.1e-181;5.6e-170	1.3e-92;2e-82;4.6e-92;3.2e-86;5.4e-85;2.4e-84;3e-92;2e-82;4.6e-82;4.6e-84;4.4e-86;3.8e-85;2.1e-85;4.3e-80;6.8e-82;4.2e-84;7.6e-77;3.3e-84;1.1e-80;1.2e-83;1.6e-82;3.1e-92;1.3e-82;2e-94;5.3e-94;8.4e-141;2.1e-102;4.8e-143;1.2e-136;8e-128;1.9e-132;6.7e-126;6.6e-145;2.1e-146;2.1e-139	0.321403125445305	TTT	ORF6	.	65-99-delfrshift	.	no-SNV	GU280_gp06	0.689917531258313
CAMB-7B5A7	MN908947.3	28333	C	T	0.016	0.012	1.5e-08	4.6e-07	0.0142823362497044	CCT	N	P20P	C60T	CCC>CCT	Synonymous	GU280_gp10	0.985547410735398
CAMB-7B5A7	MN908947.3	28514	G	T	1	1	0	0	0.9988771554605	AGA	N	D81Y	G241T	GAT>TAT	Missense	GU280_gp10	8.02031813928619e-05
CAMB-7B5A7	MN908947.3	28581	A	G	0.38	0.36	4e-194	9e-184	0.367451300840868	GAT	N	D103G	A308G	GAT>GGT	Missense	GU280_gp10	0.632126947307378
CAMB-7B5A7	MN908947.3	3037	C	T	1	1	0	0	0.999786416061512	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.11946461626086e-05
CAMB-7B5A7	MN908947.3	3987	C	T	0.021	0.027	9.7e-11	4.1e-13	0.0235211220346945	ACA	ORF1ab:nsp3	T423I	C1268T	ACA>ATA	Missense	ORF1ab:nsp3	0.976478877965306
CAMB-7B5A7	MN908947.3	522	TT	-	0.042	0.0525	1.8e-06;8.6e-05	9.9e-08;1.8e-06	0.0465161433484966	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.944112828549042
CAMB-7B5A7	MN908947.3	5533	A	G	0.0094	0.0085	7.6e-06	2e-05	0.00896309314586995	GAC	ORF1ab:nsp3	G938G	A2814G	GGA>GGG	Synonymous	ORF1ab:nsp3	0.99103690685413
CAMB-7B5A7	MN908947.3	7644	C	T	0.39	0.3	5.2e-199	1e-146	0.349384288747346	GCT	ORF1ab:nsp3	A1642V	C4925T	GCT>GTT	Missense	ORF1ab:nsp3	0.650530785562633
CAMB-7B5A7	MN908947.3	84	C	T	0.025	0.024	1.3e-12	3.4e-12	0.0242692622891895	TCT	NA	NA	NA	NA	NA	NA	0.97573073771081
CAMB-7B5C5	MN908947.3	11075	T	-	0.023	0.051	2.3e-06	1.5e-12	0.0358158321842166	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.964159761797259
CAMB-7B5C5	MN908947.3	1233	G	T	0.021	0.011	3.7e-11	6e-07	0.0165686798503474	TGT	ORF1ab:nsp2	C143F	G428T	TGT>TTT	Missense	ORF1ab:nsp2	0.983431320149653
CAMB-7B5C5	MN908947.3	14408	C	T	0.99	1	0	0	0.995554280797361	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000273783294004146
CAMB-7B5C5	MN908947.3	17178	T	C	0.0024	0.0093	0.0094	7.6e-06	0.00564688038042141	TTG	ORF1ab:helicase	V314V	T942C	GTT>GTC	Synonymous	ORF1ab:helicase	0.994260883823891
CAMB-7B5C5	MN908947.3	23403	A	G	1	1	0	0	0.999933944192279	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.60558077209803e-05
CAMB-7B5C5	MN908947.3	23873	G	T	1	1	0	0	1	AGC	S	A771S	G2311T	GCT>TCT	Missense	GU280_gp02, spike glycoprotein	0
CAMB-7B5C5	MN908947.3	241	C	T	1	1	0	0	0.999806938625789	TCG	NA	NA	NA	NA	NA	NA	9.65306871054308e-05
CAMB-7B5C5	MN908947.3	27849	C	T	0.0072	0.02	0.00048	1.6e-08	0.0135338345864662	ACT	NA	NA	NA	NA	NA	NA	0.986466165413534
CAMB-7B5C5	MN908947.3	28881	GGG	AAC	0.996666666666667	1	0;0;0	0;0;0	0.999417022930431	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7B5C5	MN908947.3	29203	C	T	0.014	0.0073	1.2e-07	6.6e-05	0.0104532397063517	GCG	N	S310S	C930T	AGC>AGT	Synonymous	GU280_gp10	0.989413767422066
CAMB-7B5C5	MN908947.3	29274	C	T	0.07	0.02	1.1e-31	2.8e-10	0.0451537865081416	ACA	N	T334I	C1001T	ACA>ATA	Missense	GU280_gp10	0.954820367019902
CAMB-7B5C5	MN908947.3	29327	TTGCTGAATAAGCATA	-	0.00719375	0.0135	0.00014;0.00059;0.00046;0.00051;0.0011;0.00034;0.0013;0.0013;0.0012;0.0012;0.0011;0.001;0.0015;0.00034;0.00051;0.00049	3e-07;3.2e-06;2.1e-06;1.8e-06;7.9e-06;6.3e-07;8.5e-06;8.6e-06;8.1e-06;8.4e-06;7e-06;6.7e-06;1.6e-05;7e-07;1.2e-06;1.8e-06	0.00999729137425821	TTT	N	.	1054-1069-delfrshift	.	no-SNV	GU280_gp10	0.986902485659656
CAMB-7B5C5	MN908947.3	3037	C	T	1	1	0	0	0.999558654779769	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000176538088092506
CAMB-7B5C5	MN908947.3	7979	C	T	0.27	0.17	4.9e-132	3.2e-77	0.215313074510652	ACT	ORF1ab:nsp3	L1754L	C5260T	CTA>TTA	Synonymous	ORF1ab:nsp3	0.784659889693955
CAMB-7B5C5	MN908947.3	9496	A	T	0.021	0.021	1.5e-10	1.9e-10	0.0209761163032191	TAG	ORF1ab:nsp4	V314V	A942T	GTA>GTT	Synonymous	ORF1ab:nsp4	0.979023883696781
CAMB-7B5D4	MN908947.3	10369	C	T	0.011	0.014	3.4e-06	1.2e-07	0.012291611217305	GCA	ORF1ab:3C-like-proteinase	R105R	C315T	CGC>CGT	Synonymous	ORF1ab:3C-like-proteinase	0.987696290740158
CAMB-7B5D4	MN908947.3	11074	C	INS	0.026	0.029	1.5e-05	4.1e-06	0.0272927441241231	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.972169593937222
CAMB-7B5D4	MN908947.3	11075	T	-	0.038	0.026	1.8e-09	3.4e-07	0.0334889061353802	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.962779472895249
CAMB-7B5D4	MN908947.3	13778	ATA	-	0.0267333333333333	0.0226333333333333	1.3e-11;1.4e-11;0.00037	1.3e-10;4.2e-10;0.0024	0.0360276255295228	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-313-delinframe	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.964307745691483
CAMB-7B5D4	MN908947.3	13780	A	T	0.031	0.032	6.6e-09	3.8e-09	0.0316190858461693	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I105L	A313T	ATA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.958255983141839
CAMB-7B5D4	MN908947.3	14198	C	T	0.071	0.068	3e-32	1.9e-31	0.0697148268967694	GCA	ORF1ab:RNA-dependent-RNA-polymerase	A244V	C731T	GCA>GTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.929978252481672
CAMB-7B5D4	MN908947.3	14408	C	T	0.99	1	0	0	0.994718647006057	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000624892911497022
CAMB-7B5D4	MN908947.3	1547	A	-	0.019	0.019	1.2e-09	2.1e-09	0.0189111747851003	TAG	ORF1ab:nsp2	.	742-742-delfrshift	.	no-SNV	ORF1ab:nsp2	0.894441260744986
CAMB-7B5D4	MN908947.3	1547	A	G	0.033	0.032	1.1e-14	1.5e-14	0.0325501432664756	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.894441260744986
CAMB-7B5D4	MN908947.3	1547	A	T	0.054	0.051	1.9e-23	5.9e-22	0.052836676217765	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.894441260744986
CAMB-7B5D4	MN908947.3	15842	C	T	0.01	0.0095	4.3e-06	6.4e-06	0.00987306064880113	ACT	ORF1ab:RNA-dependent-RNA-polymerase	T792I	C2375T	ACT>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.986285504603988
CAMB-7B5D4	MN908947.3	16887	C	T	0.05	0.057	2.7e-20	5.3e-23	0.052875027697762	ACA	ORF1ab:helicase	Y217Y	C651T	TAC>TAT	Synonymous	ORF1ab:helicase	0.946460226013738
CAMB-7B5D4	MN908947.3	18756	G	T	0.015	0.015	3e-08	1.8e-08	0.0151961307843706	CGT	ORF1ab:3'-to-5'-exonuclease	P239P	G717T	CCG>CCT	Synonymous	ORF1ab:3'-to-5'-exonuclease	0.98436141159239
CAMB-7B5D4	MN908947.3	19220	C	T	0.015	0.015	2.5e-08	9.2e-09	0.015167965600645	GCT	ORF1ab:3'-to-5'-exonuclease	A394V	C1181T	GCT>GTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.984799785004031
CAMB-7B5D4	MN908947.3	1999	G	A	0.0083	0.008	7.9e-06	9.4e-06	0.0081909962537304	TGA	ORF1ab:nsp2	L398L	G1194A	CTG>CTA	Synonymous	ORF1ab:nsp2	0.99180900374627
CAMB-7B5D4	MN908947.3	23148	A	G	0.004	0.0083	0.00093	8.8e-06	0.00566451585425584	AAG	S	K529R	A1586G	AAG>AGG	Missense	GU280_gp02, spike glycoprotein	0.988692263463873
CAMB-7B5D4	MN908947.3	23403	A	G	1	1	0	0	0.999383021732248	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.00012989016163207
CAMB-7B5D4	MN908947.3	241	C	T	1	1	0	0	0.997624415560835	TCG	NA	NA	NA	NA	NA	NA	0.000226966666162296
CAMB-7B5D4	MN908947.3	26532	T	G	1	1	0	0	0.999180556848869	TTC	M	S4A	T10G	TCC>GCC	Missense	GU280_gp05	0.000111742247881553
CAMB-7B5D4	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	-	0.0356486486486486	0.0413513513513514	0.0014;0.00012;0.00092;0.001;0.0015;1.4e-06;1.3e-05;2.5e-06;2.6e-06;4.7e-07;1e-06;6.3e-07;2.6e-06;1.2e-06;1.8e-06;3.9e-06;1.1e-06;3.2e-06;1.9e-06;1.8e-06;1.2e-06;3.5e-06;1.4e-06;2.2e-06;1.4e-06;9.2e-07;2.6e-06;1.3e-06;4.1e-07;1.4e-06;2.9e-06;2.4e-06;1.1e-06;2.7e-06;6.7e-07;1.4e-06;8e-07	4.1e-05;3.1e-06;2.6e-05;2.6e-05;6.4e-05;1e-07;3.4e-07;5e-07;5.1e-07;3.1e-07;3.1e-07;2.1e-07;4.2e-07;7.8e-08;1.2e-07;2.1e-07;6.2e-08;1.7e-07;8.5e-08;1.1e-07;8.5e-08;2e-07;1e-07;1.3e-07;9.2e-08;3.9e-08;1.4e-07;9e-08;4.6e-08;8.9e-08;1.5e-07;1.2e-07;4.9e-08;1.4e-07;8.6e-08;3.1e-07;1.4e-07	0.0404165633523432	GTC	M	.	258-294-delfrshift	.	no-SNV	GU280_gp05	0.975921589755279
CAMB-7B5D4	MN908947.3	26895	C	T	0.014	0.017	2.2e-07	9.7e-09	0.0149483543978957	CCA	M	H125Y	C373T	CAT>TAT	Missense	GU280_gp05	0.985051645602104
CAMB-7B5D4	MN908947.3	28717	C	A	1	1	0	0	0.997149616070736	CCC	N	T148T	C444A	ACC>ACA	Synonymous	GU280_gp10	0.000310245869851858
CAMB-7B5D4	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.997249472815623	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000455373406193078
CAMB-7B5D4	MN908947.3	29421	C	A	1	1	0	0	1	CCG	N	P383Q	C1148A	CCG>CAG	Missense	GU280_gp10	0
CAMB-7B5D4	MN908947.3	3037	C	T	1	1	0	0	0.998996366153314	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.00024225644575186
CAMB-7B5D4	MN908947.3	522	TT	-	0.0525	0.066	6.2e-08;5.4e-06	2.1e-10;1.4e-07	0.0575990875392073	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.929916884644554
CAMB-7B5D4	MN908947.3	9052	A	T	0.011	0.0073	8.8e-06	0.00013	0.00933926450380791	CAG	ORF1ab:nsp4	P166P	A498T	CCA>CCT	Synonymous	ORF1ab:nsp4	0.984721801709481
CAMB-7B61D	MN908947.3	11075	T	-	0.031	0.033	5.1e-08	6.1e-09	0.0317567112965081	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.963641256812218
CAMB-7B61D	MN908947.3	13778	AT	-	0.069	0.067	2e-19;4e-19	1.3e-19;1.2e-18	0.0682999307521127	CAT	ORF1ab:RNA-dependent-RNA-polymerase	.	311-312-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.933998266516604
CAMB-7B61D	MN908947.3	13780	A	G	0.011	0.0099	1.4e-06	2e-06	0.0103622384059344	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I105V	A313G	ATA>GTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.9339145030728
CAMB-7B61D	MN908947.3	13780	A	T	0.052	0.054	3.6e-13	9.7e-14	0.0530430191948453	TAT	ORF1ab:RNA-dependent-RNA-polymerase	I105L	A313T	ATA>TTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.9339145030728
CAMB-7B61D	MN908947.3	13980	A	G	0.015	0.017	4.8e-08	2.9e-09	0.0154981484119071	AAC	ORF1ab:RNA-dependent-RNA-polymerase	E171E	A513G	GAA>GAG	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.978083606323885
CAMB-7B61D	MN908947.3	14408	C	T	1	1	0	0	0.998202968695715	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000886535443447425
CAMB-7B61D	MN908947.3	1547	A	-	0.03	0.027	9.8e-14	1.5e-12	0.0284183274128485	TAG	ORF1ab:nsp2	.	742-742-delfrshift	.	no-SNV	ORF1ab:nsp2	0.817026913119393
CAMB-7B61D	MN908947.3	1547	A	G	0.053	0.059	3.6e-23	1.7e-25	0.0559937383346378	TAG	ORF1ab:nsp2	S248G	A742G	AGC>GGC	Missense	ORF1ab:nsp2	0.817026913119393
CAMB-7B61D	MN908947.3	1547	A	T	0.09	0.099	4e-39	1.8e-42	0.0941056053946655	TAG	ORF1ab:nsp2	S248C	A742T	AGC>TGC	Missense	ORF1ab:nsp2	0.817026913119393
CAMB-7B61D	MN908947.3	15842	C	T	0.013	0.018	1.7e-07	1.2e-09	0.015266393442623	ACT	ORF1ab:RNA-dependent-RNA-polymerase	T792I	C2375T	ACT>ATT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.979025175644028
CAMB-7B61D	MN908947.3	16012	C	G	0.012	0.015	1.4e-06	8.8e-08	0.0130145343236937	ACG	ORF1ab:RNA-dependent-RNA-polymerase	R849G	C2545G	CGG>GGG	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.981184579489265
CAMB-7B61D	MN908947.3	170	A	G	0.01	0.012	1.9e-06	5.1e-07	0.0108192341941229	AAC	NA	NA	NA	NA	NA	NA	0.983860195903829
CAMB-7B61D	MN908947.3	17504	A	T	0.015	0.014	6.9e-07	7.7e-07	0.0145053986258043	AAT	ORF1ab:helicase	N423I	A1268T	AAT>ATT	Missense	ORF1ab:helicase	0.985287381393827
CAMB-7B61D	MN908947.3	18010	A	T	0.0073	0.0076	7.1e-05	4.4e-05	0.00738759793272737	AAT	ORF1ab:helicase	I592F	A1774T	ATT>TTT	Missense	ORF1ab:helicase	0.992502607618166
CAMB-7B61D	MN908947.3	19943	C	G	0.016	0.0059	5.3e-06	0.0013	0.0116959064327485	GCC	ORF1ab:endoRNAse	A108G	C323G	GCC>GGC	Missense	ORF1ab:endoRNAse	0.966165413533835
CAMB-7B61D	MN908947.3	19943	C	T	0.014	0.011	1.2e-06	2.5e-05	0.0129490392648287	GCC	ORF1ab:endoRNAse	A108V	C323T	GCC>GTC	Missense	ORF1ab:endoRNAse	0.966165413533835
CAMB-7B61D	MN908947.3	20667	A	G	0.017	0.019	1.5e-06	4.4e-07	0.0181724795773614	AAG	ORF1ab:2'-O-ribose-methyltransferase	Q3Q	A9G	CAA>CAG	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.968130900552756
CAMB-7B61D	MN908947.3	23148	A	G	0.0081	0.0081	1.4e-05	1.1e-05	0.00810645239418159	AAG	S	K529R	A1586G	AAG>AGG	Missense	GU280_gp02, spike glycoprotein	0.978857688307618
CAMB-7B61D	MN908947.3	23148	A	T	0.012	0.011	3.1e-05	2.6e-05	0.0114188428715932	AAG	S	K529M	A1586T	AAG>ATG	Missense	GU280_gp02, spike glycoprotein	0.978857688307618
CAMB-7B61D	MN908947.3	23403	A	G	1	1	0	0	0.999378277558523	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	9.01047016633328e-05
CAMB-7B61D	MN908947.3	241	C	T	1	1	0	0	0.998592633315008	TCG	NA	NA	NA	NA	NA	NA	0.000263881253435954
CAMB-7B61D	MN908947.3	26449	A	T	0.0054	0.0079	0.00029	2e-05	0.00637149234085576	TAG	E	R69*	A205T	AGA>TGA	Nonsense	GU280_gp04	0.985711833044009
CAMB-7B61D	MN908947.3	28794	AA	-	0.0083	0.0079	2e-05;1.3e-05	2.5e-05;1.4e-05	0.00813109832374281	GAA	N	.	521-522-delfrshift	.	no-SNV	GU280_gp10	0.991053261520048
CAMB-7B61D	MN908947.3	28795	A	G	0.019	0.017	1.8e-09	8.5e-09	0.0178191228012709	AAG	N	E174E	A522G	GAA>GAG	Synonymous	GU280_gp10	0.972059353401684
CAMB-7B61D	MN908947.3	28860	A	T	0.01	0.0082	3.2e-06	1.4e-05	0.00927276515940821	AAT	N	N196I	A587T	AAT>ATT	Missense	GU280_gp10	0.990102104605126
CAMB-7B61D	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998996319839411	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	3.77230374589762e-05
CAMB-7B61D	MN908947.3	29241	AA	-	0.0135	0.013	3.6e-08;1.8e-05	5.1e-08;1.8e-05	0.013386793224777	GAA	N	.	968-969-delfrshift	.	no-SNV	GU280_gp10	0.983024741930198
CAMB-7B61D	MN908947.3	29242	A	G	0.015	0.016	4.2e-08	8.4e-09	0.0152669260191572	AAG	N	E323E	A969G	GAA>GAG	Synonymous	GU280_gp10	0.954182876197326
CAMB-7B61D	MN908947.3	29242	A	T	0.018	0.02	1.6e-09	2e-10	0.0188956814541175	AAG	N	E323D	A969T	GAA>GAT	Missense	GU280_gp10	0.954182876197326
CAMB-7B61D	MN908947.3	29491	A	T	0.013	0.012	3.5e-05	3.6e-05	0.0124718871396442	AAT	N	Q406H	A1218T	CAA>CAT	Missense	GU280_gp10	0.987425884277244
CAMB-7B61D	MN908947.3	3037	C	T	1	1	0	0	0.998970386350265	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	4.90292214159639e-05
CAMB-7B61D	MN908947.3	4554	C	T	0.016	0.018	9.3e-09	1.3e-09	0.0168854754411989	ACT	ORF1ab:nsp3	T612I	C1835T	ACT>ATT	Missense	ORF1ab:nsp3	0.973063646319992
CAMB-7B61D	MN908947.3	462	A	G	0.0077	0.0084	3.2e-05	1.3e-05	0.00798733466115112	CAG	ORF1ab:leader-protein	Q66R	A197G	CAG>CGG	Missense	ORF1ab:leader-protein	0.979633318012359
CAMB-7B61D	MN908947.3	5416	C	T	0.034	0.032	2.2e-15	7.1e-15	0.0329648540127894	ACT	ORF1ab:nsp3	Y899Y	C2697T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.967035145987211
CAMB-7B61D	MN908947.3	8415	A	T	0.016	0.016	2.3e-05	1.3e-05	0.0160608917286408	GAT	ORF1ab:nsp3	D1899V	A5696T	GAT>GTT	Missense	ORF1ab:nsp3	0.983729618379247
CAMB-7B61D	MN908947.3	8663	AC	-	0.00885	0.0105	9.6e-05;2e-04	2.2e-05;6.8e-05	0.00946516716706529	TAC	ORF1ab:nsp4	.	109-110-delfrshift	.	no-SNV	ORF1ab:nsp4	0.990565089154042
CAMB-7B61D	MN908947.3	9052	A	G	0.011	0.0097	1.2e-06	4.9e-06	0.0106425473636156	CAG	ORF1ab:nsp4	P166P	A498G	CCA>CCG	Synonymous	ORF1ab:nsp4	0.971125313855284
CAMB-7B61D	MN908947.3	9052	A	T	0.015	0.016	2.7e-07	1.1e-07	0.0157212965076467	CAG	ORF1ab:nsp4	P166P	A498T	CCA>CCT	Synonymous	ORF1ab:nsp4	0.971125313855284
CAMB-7B62C	MN908947.3	10731	C	A	0.0024	0.007	0.0011	1.2e-05	0.00441248570027782	ACT	ORF1ab:3C-like-proteinase	T226N	C677A	ACT>AAT	Missense	ORF1ab:3C-like-proteinase	0.995554829220461
CAMB-7B62C	MN908947.3	10802	CTAGGACCT	TACTAGGAC	0.0111555555555556	0.00197	9.5e-07;9.7e-08;1.3e-07;2.8e-06;1.1e-06;7.7e-06;1.9e-07;1.7e-07;1.7e-06	NA;NA;NA;NA;NA;NA;NA;2.1e-09;0.17	0.0051267839822641	ACT	ORF1ab:3C-like-proteinase	.	748-756-mnv	.	no-SNV	ORF1ab:3C-like-proteinase	0.995281110961305
CAMB-7B62C	MN908947.3	10817	GCT	CTG	0.0113333333333333	0.00198666666666667	6.8e-07;1e-06;5.8e-07	7.8e-05;NA;NA	0.0053206002728513	TGC	ORF1ab:3C-like-proteinase	.	763-765-mnv	.	no-SNV	ORF1ab:3C-like-proteinase	0.991806581598388
CAMB-7B62C	MN908947.3	10883	AATG	TGAA	0.006875	0.0025	3.8e-05;2.4e-05;2e-05;4.4e-05	NA;NA;9.3e-07;NA	0.0028220685762664	GAA	ORF1ab:3C-like-proteinase	.	829-832-mnv	.	no-SNV	ORF1ab:3C-like-proteinase	0.997106242248863
CAMB-7B62C	MN908947.3	11074	C	INS	0.047	0.02	1.7e-12	0.0014	0.0362206522980535	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.963583560392227
CAMB-7B62C	MN908947.3	11075	T	-	0.022	0.018	2.8e-06	1.7e-05	0.0205722912234955	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.972936251972826
CAMB-7B62C	MN908947.3	13115	C	T	0.028	0.028	8.6e-14	5.3e-14	0.0279889009530703	TCT	ORF1ab:nsp10	L31L	C91T	CTA>TTA	Synonymous	ORF1ab:nsp10	0.971985247229547
CAMB-7B62C	MN908947.3	13345	TG	-	0.0115	0.01	3.4e-07;0.00029	1e-06;0.00044	0.0110634710931358	CTG	ORF1ab:nsp10	.	321-322-delfrshift	.	no-SNV	ORF1ab:nsp10	0.988399900357054
CAMB-7B62C	MN908947.3	13571	G	T	0.02	0.022	4.8e-05	2.6e-05	0.021034180543383	GGT	ORF1ab:RNA-dependent-RNA-polymerase	G35V	G104T	GGT>GTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.978965819456617
CAMB-7B62C	MN908947.3	14408	C	T	1	0.99	0	0	0.995897468017475	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000595023722656311
CAMB-7B62C	MN908947.3	1483	TG	-	0.0036	0.011	NA;2e-04	1.8e-06;1.5e-05	0.00737415838409747	TTG	ORF1ab:nsp2	.	678-679-delfrshift	.	no-SNV	ORF1ab:nsp2	0.993182633656261
CAMB-7B62C	MN908947.3	15957	G	A	0.007	0.011	2.1e-05	4.2e-07	0.00841614906832298	GGG	ORF1ab:RNA-dependent-RNA-polymerase	G830G	G2490A	GGG>GGA	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.991506211180124
CAMB-7B62C	MN908947.3	1717	A	G	0.3	0.38	2.1e-148	6.9e-196	0.336487183898159	CAA	ORF1ab:nsp2	T304T	A912G	ACA>ACG	Synonymous	ORF1ab:nsp2	0.663340787889214
CAMB-7B62C	MN908947.3	18355	CCTTTACAGCTAGGTTTTTCTACAGGTG	-	0.00128871428571429	0.0175714285714286	0.0017;0.0017;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA;NA	8.2e-05;8.1e-05;1e-08;3.6e-08;9.2e-07;0.00015;0.00014;4.8e-05;6e-05;0.00024;0.00025;8.7e-06;0.00015;0.00022;2e-05;8.6e-05;4.3e-05;0.00022;0.00045;5e-04;5e-04;0.00057;0.00047;0.00042;0.00035;0.00059;0.00025;0.00055	0.00603970310091072	ACC	ORF1ab:3'-to-5'-exonuclease	.	316-343-delfrshift	.	no-SNV	ORF1ab:3'-to-5'-exonuclease	0.977520944946982
CAMB-7B62C	MN908947.3	2092	T	A	0.047	0.033	1.2e-21	6.3e-16	0.0398890045091918	CTT	ORF1ab:nsp2	T429T	T1287A	ACT>ACA	Synonymous	ORF1ab:nsp2	0.955139322465025
CAMB-7B62C	MN908947.3	23403	A	G	1	0.99	0	0	0.997276509143148	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	5.98569419088379e-05
CAMB-7B62C	MN908947.3	23555	CCCATTGGTGCAGGTATATGCGCTAG	-	0.0513076923076923	0.0317307692307692	0.00061;0.00049;0.00065;7e-04;4.6e-06;9e-06;2.8e-06;7.9e-06;9.4e-06;9.4e-06;8.4e-06;7e-06;3.5e-06;3.2e-06;5.2e-05;1.4e-05;5.9e-06;2.3e-06;7.1e-06;1.6e-06;5.6e-06;1.6e-05;7.3e-06;7e-06;2e-08;5.9e-08	0.0028;0.0023;0.0028;0.0031;0.002;0.0026;0.0016;0.0024;0.0024;0.0026;0.0024;0.00022;0.00012;0.00011;9.7e-05;2.7e-05;0.00092;6e-04;0.0011;0.00059;0.00099;0.00011;0.0011;0.0011;9.8e-05;0.00014	0.0388139606712653	ACC	S	.	1993-2018-delfrshift	.	no-SNV	GU280_gp02, spike glycoprotein	0.967733674775928
CAMB-7B62C	MN908947.3	241	C	T	1	1	0	0	0.999750005208225	TCG	NA	NA	NA	NA	NA	NA	4.16657986291952e-05
CAMB-7B62C	MN908947.3	25339	CGACTCTGAGC	ACGACTCTGAG	0.00848181818181818	0.000436818181818182	1.7e-05;1.5e-05;2.2e-05;1.5e-05;2.4e-05;1.7e-05;2.4e-05;2.4e-05;2.1e-05;1.2e-06;1.1e-06	NA;NA;0.46;NA;0.0011;NA;NA;NA;0.46;NA;NA	0.00449081380170281	ACG	S	.	3777-3787-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.995467085189554
CAMB-7B62C	MN908947.3	25405	ATGAGA	TATGAG	0.011	0.00149083333333333	8e-07;9.2e-07;6.9e-07;1.1e-06;4.8e-07;3.3e-06	NA;NA;8.1e-06;NA;NA;0.47	0.00643659068325745	TAT	ORF3a	.	13-18-mnv	.	no-SNV	GU280_gp03	0.993512104392144
CAMB-7B62C	MN908947.3	25429	G	T	1	1	0	0	0.999857102029151	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	6.35102092661395e-05
CAMB-7B62C	MN908947.3	25550	TTGCTGT	-	0.00477857142857143	0.0214285714285714	0.0069;0.0077;0.0071;0.0089;0.01;0.018;0.48	1.9e-06;4.3e-06;3e-09;6.8e-06;7.1e-06;1.5e-05;1.9e-10	0.0112196409714889	CTT	ORF3a	.	158-164-delfrshift	.	no-SNV	GU280_gp03	0.987263885672698
CAMB-7B62C	MN908947.3	26780	TCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	-	0.0531052631578947	0.0317368421052632	1.6e-06;1.4e-08;7.7e-07;8e-07;3.5e-06;1.1e-12;4.5e-11;2.2e-09;2.1e-09;2.9e-10;7.2e-10;3.1e-10;2.3e-09;8.8e-10;1.4e-09;3.7e-09;6.4e-10;2.9e-09;1.5e-09;1.5e-09;8.3e-10;3.4e-09;9.8e-10;1.8e-09;1.2e-09;4.8e-10;2.3e-09;9.4e-10;5.5e-10;8e-10;2.4e-09;2.1e-09;1.3e-09;2.1e-09;2.7e-10;9.2e-10;4e-10;0.00042	0.00066;1e-04;0.00051;0.00054;0.00099;0.00023;0.00048;1.3e-05;1.3e-05;9.1e-06;8.8e-06;6.9e-06;1.1e-05;8.9e-06;1.1e-05;1.8e-05;8e-06;1.5e-05;8.7e-06;1.1e-05;8.5e-06;1.7e-05;1e-05;1.2e-05;9.6e-06;6.1e-06;1.3e-05;9.8e-06;1.2e-06;1e-05;1.4e-05;1.3e-05;6.4e-06;1.4e-05;3e-06;8.3e-06;4.3e-06;0.0084	0.0461339591621591	GTC	M	.	258-295-delfrshift	.	no-SNV	GU280_gp05	0.969571924895584
CAMB-7B62C	MN908947.3	28474	T	C	0.011	0.0024	2.7e-06	0.0093	0.00679035632223327	CTC	N	P67P	T201C	CCT>CCC	Synonymous	GU280_gp10	0.993209643677767
CAMB-7B62C	MN908947.3	28550	CG	-	0.00915	0.0036	2.8e-05;2.4e-05	0.0075;0.0052	0.0065666372462489	ACG	N	.	277-278-delfrshift	.	no-SNV	GU280_gp10	0.993466129829766
CAMB-7B62C	MN908947.3	29250	C	T	0.018	0.016	1.3e-09	5e-09	0.0169775048061319	CCT	N	P326L	C977T	CCT>CTT	Missense	GU280_gp10	0.983022495193868
CAMB-7B62C	MN908947.3	3037	C	T	1	1	0	0	0.999421463696847	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	7.23170378941279e-05
CAMB-7B62C	MN908947.3	522	TTG	-	0.047	0.0313603333333333	8.8e-11;1.1e-05;8.9e-05	3.2e-07;6.7e-06;NA	0.0394482090997096	GTT	ORF1ab:leader-protein	.	257-259-delinframe	.	no-SNV	ORF1ab:leader-protein	0.928836388518745
CAMB-7B62C	MN908947.3	6317	C	T	0.034	0.011	4.9e-17	3.9e-07	0.0262837186459792	ACC	ORF1ab:nsp3	P1200S	C3598T	CCA>TCA	Missense	ORF1ab:nsp3	0.973679902504684
CAMB-7B62C	MN908947.3	7434	TTTA	-	0.01975	0.0085	3e-05;0.00018;0.00042;0.00089	NA;0.0056;0.011;0.013	0.0163434565190877	TTT	ORF1ab:nsp3	.	4715-4718-delfrshift	.	no-SNV	ORF1ab:nsp3	0.986937590711176
CAMB-7B64A	MN908947.3	11075	T	-	0.045	0.038	4.8e-11	9e-10	0.0419188068804498	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.953792824129223
CAMB-7B64A	MN908947.3	12213	C	T	0.014	0.01	1.1e-06	1.9e-05	0.0121167239151672	TCT	ORF1ab:nsp8	S41F	C122T	TCT>TTT	Missense	ORF1ab:nsp8	0.987843884914757
CAMB-7B64A	MN908947.3	14408	C	T	1	1	0	0	0.996719595184087	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000488570930029663
CAMB-7B64A	MN908947.3	17553	A	T	0.0082	0.0071	1.3e-05	2.1e-05	0.00772896253050066	GAA	ORF1ab:helicase	G439G	A1317T	GGA>GGT	Synonymous	ORF1ab:helicase	0.992117735733357
CAMB-7B64A	MN908947.3	22131	G	A	0.2	0.22	7.3e-54	3.5e-58	0.209991411394217	AGG	S	R190K	G569A	AGG>AAG	Missense	GU280_gp02, spike glycoprotein	0.78989407386201
CAMB-7B64A	MN908947.3	23403	A	G	1	1	0	0	0.999346044026895	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.44745325596389e-05
CAMB-7B64A	MN908947.3	241	C	T	1	1	0	0	0.998638020333781	TCG	NA	NA	NA	NA	NA	NA	1.91828122002686e-05
CAMB-7B64A	MN908947.3	27494	C	T	0.0087	0.0075	3.3e-05	1e-04	0.0082449317919279	CCT	ORF7a	P34L	C101T	CCT>CTT	Missense	GU280_gp07	0.99171097766373
CAMB-7B64A	MN908947.3	28073	G	T	0.02	0.02	5.4e-10	2.7e-10	0.0199403060900489	TGT	ORF8	L60F	G180T	TTG>TTT	Missense	GU280_gp09	0.979805677271861
CAMB-7B64A	MN908947.3	28603	C	T	0.27	0.25	9e-81	1.7e-74	0.258210958471498	TCT	N	F110F	C330T	TTC>TTT	Synonymous	GU280_gp10	0.740288962576978
CAMB-7B64A	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.998930154363442	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000100003333444448
CAMB-7B64A	MN908947.3	29738	C	T	0.16	0.14	2.6e-70	4.3e-63	0.152473498233216	GCC	NA	NA	NA	NA	NA	NA	0.846348645465253
CAMB-7B64A	MN908947.3	3037	C	T	1	1	0	0	0.999222867955129	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000168941748884984
CAMB-7B64A	MN908947.3	7948	C	T	1	1	0	0	0.998342724560822	ACA	ORF1ab:nsp3	Y1743Y	C5229T	TAC>TAT	Synonymous	ORF1ab:nsp3	0.000580046403712297
CAMB-7B64A	MN908947.3	8318	C	A	0.11	0.13	1.3e-52	8e-60	0.120538418986908	ACC	ORF1ab:nsp3	P1867T	C5599A	CCC>ACC	Missense	ORF1ab:nsp3	0.879013776571925
CAMB-7B659	MN908947.3	10097	G	A	1	1	0	0	1	GGG	ORF1ab:3C-like-proteinase	G15S	G43A	GGT>AGT	Missense	ORF1ab:3C-like-proteinase	0
CAMB-7B659	MN908947.3	11075	T	-	0.005	0.16	0.0097	5.2e-41	0.0875992566311877	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.912105085318466
CAMB-7B659	MN908947.3	13536	C	T	1	1	8.99999861777332e-318	4.4e-205	1	ACA	ORF1ab:RNA-dependent-RNA-polymerase	Y23Y	C69T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0
CAMB-7B659	MN908947.3	14408	C	T	1	1	0	0	0.99974206860975	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000128965695125097
CAMB-7B659	MN908947.3	23202	C	T	0.15	0.33	2.1e-67	3.3e-164	0.202123081336967	ACA	S	T547I	C1640T	ACA>ATA	Missense	GU280_gp02, spike glycoprotein	0.797267250035863
CAMB-7B659	MN908947.3	23403	A	G	1	1	0	0	0.999788895925691	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.03680247695447e-05
CAMB-7B659	MN908947.3	23731	C	T	1	1	0	0	1	CCA	S	T723T	C2169T	ACC>ACT	Synonymous	GU280_gp02, spike glycoprotein	0
CAMB-7B659	MN908947.3	241	C	T	1	1	0	0	0.999370990061643	TCG	NA	NA	NA	NA	NA	NA	0.000377405963014216
CAMB-7B659	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	1	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0
CAMB-7B659	MN908947.3	29118	C	T	1	1	0	0	0.999823943661972	ACC	N	T282I	C845T	ACC>ATC	Missense	GU280_gp10	0.000176056338028169
CAMB-7B659	MN908947.3	29745	GAGTACG	-	0.121428571428571	0.337142857142857	1.5e-14;1.4e-14;3.5e-14;1.2e-13;1.9e-13;1.5e-12;9.9e-13	2e-37;9.2e-38;9.4e-36;4.8e-34;1.1e-34;5.3e-32;4e-32	0.225	GGA	NA	NA	NA	NA	NA	NA	0.777227722772277
CAMB-7B659	MN908947.3	29753	TC	-	0.12	0.33	9.6e-14;1.3e-13	2e-34;1.9e-34	0.221674876847291	ATC	NA	NA	NA	NA	NA	NA	0.776119402985075
CAMB-7B659	MN908947.3	3037	C	T	1	1	3.6e-263	8e-203	1	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7B668	MN908947.3	11074	C	INS	0.026	0.043	4.1e-05	7.4e-10	0.0336047046586522	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.966015242133899
CAMB-7B668	MN908947.3	11075	T	-	0.037	0.1	1.5e-09	5e-25	0.0648384965870018	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.934941309981538
CAMB-7B668	MN908947.3	12820	ATC	TAT	0.001547	0.016	NA;NA;0.00042	2.3e-09;1.6e-08;5.6e-09	0.00729177803913183	TAT	ORF1ab:nsp9	.	135-137-mnv	.	no-SNV	ORF1ab:nsp9	0.992124051762606
CAMB-7B668	MN908947.3	12919	C	T	0.0082	0.014	1.2e-05	4.5e-08	0.0107113078057854	ACA	ORF1ab:nsp9	D78D	C234T	GAC>GAT	Synonymous	ORF1ab:nsp9	0.986338272080046
CAMB-7B668	MN908947.3	12919	CACAC	TCACA	0.0016644	0.00874	1.2e-05;0.047;NA;NA;NA	4.5e-08;1.2e-05;1.7e-05;1.2e-05;1.4e-05	0.00335749877034281	ACA	ORF1ab:nsp9	.	234-238-mnv	.	no-SNV	ORF1ab:nsp9	0.986338272080046
CAMB-7B668	MN908947.3	14408	C	T	1	0.98	0	0	0.990739400954999	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.00103096512805672
CAMB-7B668	MN908947.3	14408	CTACAAG	-	0.00926571428571429	0.026	0.026;0.47;0.47;0.0054;0.0036;0.0027;0.0044	5.5e-08;0.00064;4e-04;0.00018;9e-05;5e-05;9.2e-05	0.0211097595209133	CCT	ORF1ab:RNA-dependent-RNA-polymerase	.	941-947-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.00103096512805672
CAMB-7B668	MN908947.3	15315	C	T	0.018	0.016	4.6e-10	4e-09	0.0171814911301327	CCA	ORF1ab:RNA-dependent-RNA-polymerase	A616A	C1848T	GCC>GCT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.982818508869867
CAMB-7B668	MN908947.3	15443	TG	-	0.0076	0.0275	0.48;1.2e-07	6.2e-10;5.5e-16	0.0152380952380952	ATG	ORF1ab:RNA-dependent-RNA-polymerase	.	1976-1977-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.992667686814588
CAMB-7B668	MN908947.3	15444	G	-	0.015	0.036	1.2e-07	5.5e-16	0.0227097539282538	TGT	ORF1ab:RNA-dependent-RNA-polymerase	.	1977-1977-delfrshift	.	no-SNV	ORF1ab:RNA-dependent-RNA-polymerase	0.977112362881708
CAMB-7B668	MN908947.3	1658	GG	TT	0.0029	0.01065	0.00013;NA	4e-06;4.4e-07	0.00619279454722493	TGG	ORF1ab:nsp2	.	853-854-mnv	.	no-SNV	ORF1ab:nsp2	0.992641046606705
CAMB-7B668	MN908947.3	23149	G	A	0.015	0.023	2.8e-05	1.9e-07	0.0185056784219964	AGT	S	K529K	G1587A	AAG>AAA	Synonymous	GU280_gp02, spike glycoprotein	0.98148236700538
CAMB-7B668	MN908947.3	23149	GTCTACTA	AGTCTACT	0.0155	0.0235	2.8e-05;0.00022;5.4e-05;9.2e-07;5.5e-05;9.8e-05;3.3e-06;7.8e-05	1.9e-07;1.2e-05;8.8e-07;1.5e-09;7.4e-07;1.7e-06;1e-08;1.8e-06	0.0190185572863073	AGT	S	.	1587-1594-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.98148236700538
CAMB-7B668	MN908947.3	23155	T	C	0.016	0.024	3.3e-06	1e-08	0.0192357436801881	CTA	S	T531T	T1593C	ACT>ACC	Synonymous	GU280_gp02, spike glycoprotein	0.98071722516167
CAMB-7B668	MN908947.3	23158	T	A	0.017	0.025	1e-04	3.5e-06	0.0203829371701215	ATT	S	N532K	T1596A	AAT>AAA	Missense	GU280_gp02, spike glycoprotein	0.979542898110036
CAMB-7B668	MN908947.3	23161	G	T	0.015	0.023	1.4e-05	9e-08	0.0189502630320421	TGG	S	L533F	G1599T	TTG>TTT	Missense	GU280_gp02, spike glycoprotein	0.981037780966045
CAMB-7B668	MN908947.3	23163	T	G	0.016	0.023	0.00014	5.9e-06	0.0190297022538982	GTT	S	V534G	T1601G	GTT>GGT	Missense	GU280_gp02, spike glycoprotein	0.980958238365713
CAMB-7B668	MN908947.3	23165	A	T	0.016	0.023	3.2e-06	1.3e-08	0.0191110535792038	TAA	S	K535*	A1603T	AAA>TAA	Nonsense	GU280_gp02, spike glycoprotein	0.980771267519446
CAMB-7B668	MN908947.3	23170	C	A	0.012	0.019	2.7e-05	1.3e-07	0.0152611296309431	ACA	S	N536K	C1608A	AAC>AAA	Missense	GU280_gp02, spike glycoprotein	0.984727049199707
CAMB-7B668	MN908947.3	23170	CA	AC	0.0135	0.021	2.7e-05;0.00027	1.3e-07;1.6e-05	0.0169499489034804	ACA	S	.	1608-1609-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.984727049199707
CAMB-7B668	MN908947.3	23174	TGTGTCA	ATGTGTC	0.0154285714285714	0.0232857142857143	0.00014;2.8e-05;0.00016;4.5e-05;0.00025;1.5e-05;0.00017	2.7e-06;2.6e-07;5.5e-06;7.1e-07;1.3e-05;6.7e-08;8.9e-06	0.019064601833457	ATG	S	.	1612-1618-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.981988596040428
CAMB-7B668	MN908947.3	23179	C	T	0.015	0.023	1.5e-05	6.7e-08	0.0184690961479417	TCA	S	V539V	C1617T	GTC>GTT	Synonymous	GU280_gp02, spike glycoprotein	0.981495477197043
CAMB-7B668	MN908947.3	23182	T	A	0.015	0.023	0.00012	2.8e-06	0.0183550068309467	ATT	S	N540K	T1620A	AAT>AAA	Missense	GU280_gp02, spike glycoprotein	0.981543793958407
CAMB-7B668	MN908947.3	23185	CA	TC	0.0155	0.024	5.1e-05;0.00019	7.6e-07;1.1e-05	0.0195017583552615	TCA	S	.	1623-1624-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.980853509591206
CAMB-7B668	MN908947.3	23188	CT	AC	0.015	0.023	4.7e-05;1.7e-06	8.4e-07;2.2e-09	0.018795910450376	ACT	S	.	1626-1627-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.981260880378015
CAMB-7B668	MN908947.3	23189	T	C	0.015	0.023	1.7e-06	2.2e-09	0.0189038059494723	CTT	S	F543L	T1627C	TTC>CTC	Missense	GU280_gp02, spike glycoprotein	0.981045817485706
CAMB-7B668	MN908947.3	23191	CA	TC	0.016	0.0235	0.00045;0.00014	1.8e-05;1.1e-05	0.0194868221298624	TCA	S	.	1629-1630-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.981311356199249
CAMB-7B668	MN908947.3	23194	TG	AT	0.016	0.025	5.2e-08;1.8e-07	1.3e-11;1.8e-11	0.0202729503018907	ATG	S	.	1632-1633-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.978918563588278
CAMB-7B668	MN908947.3	23197	T	G	0.018	0.026	1.4e-08	6e-12	0.022028340724263	GTT	S	G545G	T1635G	GGT>GGG	Synonymous	GU280_gp02, spike glycoprotein	0.977899435207789
CAMB-7B668	MN908947.3	23200	A	T	0.018	0.026	1.9e-08	8.6e-12	0.021493088065209	TAA	S	L546F	A1638T	TTA>TTT	Missense	GU280_gp02, spike glycoprotein	0.978396761579556
CAMB-7B668	MN908947.3	23202	CAG	ACA	0.0173333333333333	0.026	5.1e-08;1.2e-08;3.6e-08	9.8e-12;6.7e-12;8.6e-12	0.0212330016700114	ACA	S	.	1640-1642-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.978919833820588
CAMB-7B668	MN908947.3	23206	CACAG	GCACA	0.0176	0.0258	2.5e-08;7.1e-09;1e-07;7.5e-09;3.3e-08	1.2e-11;4.5e-12;2e-11;3e-12;8.1e-12	0.0215187921438885	GCA	S	.	1644-1648-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.978922846525043
CAMB-7B668	MN908947.3	23212	TGT	GTG	0.0186666666666667	0.026	2.3e-08;2.6e-08;2.9e-09	9e-12;1.4e-11;3.2e-12	0.0214844297446534	GTG	S	.	1650-1652-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.978641701936822
CAMB-7B668	MN908947.3	23216	CT	TC	0.018	0.026	5e-08;7.7e-09	1.1e-11;7.9e-12	0.0218167048652412	TCT	S	.	1654-1655-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.978646668193268
CAMB-7B668	MN908947.3	23219	ACTGAGTCTA	TACTGAGTCT	0.0178	0.0259	2.4e-08;4.9e-08;2.9e-08;2.3e-08;2.5e-08;1.4e-08;9.5e-09;6.6e-08;1.5e-08;1e-08	7.1e-12;1.1e-11;1.1e-11;3.7e-12;1.2e-11;3.5e-12;6.1e-12;1.1e-11;1.1e-11;6.6e-12	0.0217388229636649	TAC	S	.	1657-1666-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.978136122612043
CAMB-7B668	MN908947.3	23230	CA	AC	0.017	0.025	6.5e-08;1.4e-08	1.6e-11;9.2e-12	0.0209129213483146	ACA	S	.	1668-1669-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.979654450853976
CAMB-7B668	MN908947.3	23236	GT	AG	0.0175	0.0255	2.7e-08;1e-08	1.2e-11;4.6e-12	0.0215728027021073	AGT	S	.	1674-1675-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.978866333952903
CAMB-7B668	MN908947.3	23240	CTGC	TCTG	0.018	0.02575	1.8e-08;2.5e-08;1.9e-08;1.5e-08	5.4e-12;2.2e-11;6.2e-12;4.4e-12	0.0217829770068576	TCT	S	.	1678-1681-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.977932350942141
CAMB-7B668	MN908947.3	23245	T	C	0.018	0.026	2.1e-08	1.2e-11	0.0219367015098722	CTT	S	P561P	T1683C	CCT>CCC	Synonymous	GU280_gp02, spike glycoprotein	0.97797619047619
CAMB-7B668	MN908947.3	23248	C	T	0.018	0.027	2.6e-08	7.2e-12	0.0222658808120498	TCC	S	F562F	C1686T	TTC>TTT	Synonymous	GU280_gp02, spike glycoprotein	0.977705013461398
CAMB-7B668	MN908947.3	23250	A	C	0.018	0.026	9.1e-09	7.4e-12	0.0219445244847511	CAA	S	Q563P	A1688C	CAA>CCA	Missense	GU280_gp02, spike glycoprotein	0.977403357648736
CAMB-7B668	MN908947.3	23252	CA	AC	0.0185	0.0265	7.3e-08;9.5e-10	1.2e-11;1.3e-12	0.0224964059463815	ACA	S	.	1690-1691-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.979351818935893
CAMB-7B668	MN908947.3	23255	T	A	0.022	0.029	8.7e-10	5.3e-13	0.0254560032070555	ATT	S	F565I	T1693A	TTT>ATT	Missense	GU280_gp02, spike glycoprotein	0.974307112010058
CAMB-7B668	MN908947.3	23258	G	T	0.018	0.026	2.1e-08	7.5e-12	0.0220501497232389	TGG	S	G566C	G1696T	GGC>TGC	Missense	GU280_gp02, spike glycoprotein	0.977813738241432
CAMB-7B668	MN908947.3	23260	CAGAGACAT	GCAGAGACA	0.0186666666666667	0.0262222222222222	1.5e-08;3.2e-09;7.3e-08;3.7e-09;5.8e-08;3e-08;4.7e-09;4.9e-10;2.2e-08	1e-11;2.5e-12;2.9e-11;4.6e-12;1.8e-11;2.1e-11;3.4e-12;4.3e-13;7.8e-12	0.0220355623431875	GCA	S	.	1698-1706-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.978290203604306
CAMB-7B668	MN908947.3	23270	GCTGACACTACTGATGCTGTC	TGCTGACACTACTGATGCTGT	0.018047619047619	0.0257619047619048	4.2e-08;1.2e-08;1.7e-08;4.3e-08;5.7e-09;3.8e-08;3.8e-09;3.2e-08;1.2e-09;2e-08;4.8e-08;2.9e-09;9.3e-08;5.4e-09;3.3e-08;3.4e-08;2.3e-08;4.3e-08;1.5e-08;2.2e-08;3.5e-08	1.2e-11;1.2e-11;2.5e-11;9.5e-12;3.9e-12;1.1e-11;4.2e-12;9e-12;6.7e-13;2.2e-11;1.7e-11;8.2e-12;3.9e-11;6.3e-12;3.1e-11;1.2e-11;6.7e-12;3.5e-11;1e-11;7.3e-12;1e-11	0.0217408076038822	TGC	S	.	1708-1728-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.978508022953493
CAMB-7B668	MN908947.3	23292	GTGATC	CGTGAT	0.0178333333333333	0.0256666666666667	4.2e-08;6.5e-09;8.3e-08;6.5e-09;4.5e-08;4.1e-08	1.7e-11;4.9e-12;2.1e-11;4.5e-12;1.5e-11;1.1e-11	0.0214457611112804	CGT	S	.	1730-1735-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.978970334232296
CAMB-7B668	MN908947.3	23299	ACAGACACT	CACAGACAC	0.0173333333333333	0.0255555555555556	1.2e-08;4.9e-08;4.1e-09;1.3e-07;3.6e-07;1e-07;1.7e-07;9.2e-07;4.6e-09	1.4e-11;9.5e-12;3.2e-12;1.6e-11;1.3e-10;1.6e-11;1.1e-09;1.5e-10;8.2e-13	0.0202616206353644	CAC	S	.	1737-1745-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.978373525288642
CAMB-7B668	MN908947.3	23309	GAGAT	TGAGA	0.0158	0.0248	1.5e-06;1.2e-07;2.1e-07;8.3e-08;5.7e-09	1.9e-10;6e-11;2e-11;1.6e-11;1.4e-12	0.0202675851106107	TGA	S	.	1747-1751-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.982586412742786
CAMB-7B668	MN908947.3	23315	CT	TC	0.0165	0.025	1.5e-07;6.6e-08	3.6e-11;2.8e-11	0.0202358875454343	TCT	S	.	1753-1754-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.979853587115666
CAMB-7B668	MN908947.3	23318	GACAT	TGACA	0.0162	0.0248	9.3e-08;1.3e-07;2.3e-07;5.1e-08;6.1e-08	1.9e-11;3.3e-11;3.6e-11;1e-11;1.8e-11	0.0201150740961189	TGA	S	.	1756-1760-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.97948376554604
CAMB-7B668	MN908947.3	23324	ACAC	TACA	0.0131	0.0205	0.00028;1.8e-05;8.3e-08;7.9e-05	9.9e-06;5.9e-08;5.4e-11;1.7e-06	0.0179649345223517	TAC	S	.	1762-1765-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.981129877693652
CAMB-7B668	MN908947.3	23329	A	C	0.012	0.013	6.2e-06	2.4e-06	0.0123890014662515	CAT	S	P589P	A1767C	CCA>CCC	Synonymous	GU280_gp02, spike glycoprotein	0.987446251173825
CAMB-7B668	MN908947.3	23329	ATGT	CATG	0.009675	0.01275	6.2e-06;0.00036;9e-05;1.8e-05	2.4e-06;2.4e-05;1.9e-06;7.6e-07	0.0108708966193043	CAT	S	.	1767-1770-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.987446251173825
CAMB-7B668	MN908947.3	23332	T	G	0.01	0.013	1.8e-05	7.6e-07	0.0116425278256415	GTT	S	C590W	T1770G	TGT>TGG	Missense	GU280_gp02, spike glycoprotein	0.988341948803924
CAMB-7B668	MN908947.3	23334	CT	TC	0.0079	0.0125	0.00015;0.00025	7.8e-07;5.5e-06	0.0101611199547733	TCT	S	.	1772-1773-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.989877600060074
CAMB-7B668	MN908947.3	23339	G	T	0.008	0.012	9.4e-05	9.9e-07	0.0100904317799069	TGG	S	G593C	G1777T	GGT>TGT	Missense	GU280_gp02, spike glycoprotein	0.98983880782893
CAMB-7B668	MN908947.3	23341	TG	GT	0.0081	0.012	6.3e-05;5.2e-05	1.5e-06;8e-07	0.00993006397798363	GTG	S	.	1779-1780-mnv	.	no-SNV	GU280_gp02, spike glycoprotein	0.990379956104096
CAMB-7B668	MN908947.3	23403	A	G	1	1	0	0	0.999863260952798	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	0.000109391237761855
CAMB-7B668	MN908947.3	241	C	T	1	1	0	0	0.999754977029096	TCG	NA	NA	NA	NA	NA	NA	0.000183767228177642
CAMB-7B668	MN908947.3	25186	G	T	0.0093	0.11	8.6e-06	8.2e-48	0.0507359100155558	AGT	S	Q1208H	G3624T	CAG>CAT	Missense	GU280_gp02, spike glycoprotein	0.949264089984444
CAMB-7B668	MN908947.3	25429	G	T	1	1	0	0	0.999731168342384	TGT	ORF3a	V13L	G37T	GTA>TTA	Missense	GU280_gp03	0.000188182160331201
CAMB-7B668	MN908947.3	26458	G	C	1	1	0	0	1	TGA	E	D72H	G214C	GAT>CAT	Missense	GU280_gp04	0
CAMB-7B668	MN908947.3	26775	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	-	0.0243444642857143	0.0581785714285714	NA;NA;0.5;0.5;0.5;0.021;0.0062;0.015;0.015;0.033;1e-07;4.5e-06;3.5e-05;3.8e-05;1e-05;1e-05;5.7e-06;3.9e-05;1.4e-05;1.9e-05;5.2e-05;1.3e-05;4.4e-05;2.8e-05;2.7e-05;2.1e-05;4.9e-05;2.3e-05;3.5e-05;2.4e-05;1.4e-05;3.6e-05;2.2e-05;5.5e-06;1.7e-05;4.1e-05;3.4e-05;1.5e-05;3.5e-05;1.4e-05;2e-05;1.5e-05;0.00017;0.00069;0.00023;0.00027;0.012;0.01;0.0084;0.011;0.011;0.011;0.0096;0.011;0.0021;0.00093	4.8e-05;0.00016;4.7e-05;0.00018;0.00049;9.7e-10;3.1e-12;3.6e-10;5.4e-10;1.9e-09;8.2e-11;1.9e-10;1.2e-13;1.1e-13;6.5e-14;5.3e-14;3.2e-14;7e-14;5.1e-14;1.1e-13;2.1e-13;4.3e-14;1.5e-13;4.7e-14;8.5e-14;5.1e-14;1.9e-13;5.9e-14;9e-14;5.7e-14;2e-14;1.1e-13;5.2e-14;6.2e-15;6.8e-14;1.2e-13;1.1e-13;3.6e-14;1.4e-13;1.9e-15;4.8e-14;1.8e-14;1.3e-06;1.2e-05;3.4e-06;7.3e-06;3e-04;0.00017;0.00021;0.00025;0.00025;0.00026;0.00025;0.00017;1.2e-05;7.1e-06	0.0550298466965134	GGC	M	.	253-308-delfrshift	.	no-SNV	GU280_gp05	0.986383571889981
CAMB-7B668	MN908947.3	27210	TC	-	0.018	0.033	0.0012;0.0013	8.1e-06;7.9e-06	0.0246392294517644	ATC	ORF6	.	9-10-delfrshift	.	no-SNV	GU280_gp06	0.975261235239147
CAMB-7B668	MN908947.3	28045	C	T	1	1	0	0	1	GCT	ORF8	A51V	C152T	GCT>GTT	Missense	GU280_gp09	0
CAMB-7B668	MN908947.3	28407	TACCCAATA	-	0.00718888888888889	0.0263333333333333	0.0019;0.012;0.006;0.0091;0.0092;0.0084;0.0075;0.0079;0.0095	7.5e-09;1.9e-06;3.3e-08;4.2e-07;4.2e-07;1.6e-07;1.4e-07;1.6e-07;5.3e-07	0.0151292669647424	TTA	N	.	134-142-delinframe	.	no-SNV	GU280_gp10	0.984256419920169
CAMB-7B668	MN908947.3	2885	G	T	1	1	0	0	0.999670836076366	TGT	ORF1ab:nsp3	V56F	G166T	GTT>TTT	Missense	ORF1ab:nsp3	0
CAMB-7B668	MN908947.3	28974	TG	-	0.00265	0.0105	NA;0.00015	1.8e-06;3.9e-06	0.00533807829181495	ATG	N	.	701-702-delfrshift	.	no-SNV	GU280_gp10	0.996166950596252
CAMB-7B668	MN908947.3	2905	A	-	0.022	0.026	8.3e-10	2.1e-11	0.0242872228088701	TAA	ORF1ab:nsp3	.	186-186-delfrshift	.	no-SNV	ORF1ab:nsp3	0.975580781414995
CAMB-7B668	MN908947.3	2905	AA	-	0.0225	0.013	8.3e-10;2.1e-11	2.1e-11;NA	0.0175508575987236	TAA	ORF1ab:nsp3	.	186-187-delfrshift	.	no-SNV	ORF1ab:nsp3	0.975580781414995
CAMB-7B668	MN908947.3	3037	C	T	1	1	0	0	0.99949554397175	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7B668	MN908947.3	522	TT	-	0.06	0.059	2.7e-08;1.6e-08	3.8e-08;2.2e-08	0.0597377590317257	GTT	ORF1ab:leader-protein	.	257-258-delfrshift	.	no-SNV	ORF1ab:leader-protein	0.937770382695507
CAMB-7B677	MN908947.3	11075	T	-	0.039	0.04	8e-10	1.5e-10	0.0396827481156604	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.955681907713318
CAMB-7B677	MN908947.3	13115	C	T	0.021	0.022	5.6e-11	1e-11	0.0216721639477412	TCT	ORF1ab:nsp10	L31L	C91T	CTA>TTA	Synonymous	ORF1ab:nsp10	0.978278310997534
CAMB-7B677	MN908947.3	14408	C	T	1	1	0	0	0.99825589419928	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000589733616070868
CAMB-7B677	MN908947.3	14790	C	T	0.01	0.014	2.4e-06	8e-08	0.0116903207051568	TCA	ORF1ab:RNA-dependent-RNA-polymerase	I441I	C1323T	ATC>ATT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.98814356461342
CAMB-7B677	MN908947.3	17946	A	G	0.02	0.018	1.1e-10	5.2e-10	0.0196651260137787	TAG	ORF1ab:helicase	V570V	A1710G	GTA>GTG	Synonymous	ORF1ab:helicase	0.980276736141391
CAMB-7B677	MN908947.3	20148	C	T	0.042	0.05	7.5e-11	3.1e-11	0.0452488687782805	TCA	ORF1ab:endoRNAse	F176F	C528T	TTC>TTT	Synonymous	ORF1ab:endoRNAse	0.951734539969834
CAMB-7B677	MN908947.3	20679	G	T	1	1	0	0	0.999443384223919	CGG	ORF1ab:2'-O-ribose-methyltransferase	P7P	G21T	CCG>CCT	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	7.95165394402036e-05
CAMB-7B677	MN908947.3	2189	C	T	0.014	0.012	7.5e-08	3.7e-07	0.0132587735357099	TCT	ORF1ab:nsp2	L462F	C1384T	CTT>TTT	Missense	ORF1ab:nsp2	0.986641369592473
CAMB-7B677	MN908947.3	23311	G	C	0.0084	0.0071	9.5e-06	1.7e-05	0.00791170733649138	AGA	S	E583D	G1749C	GAG>GAC	Missense	GU280_gp02, spike glycoprotein	0.991093109350742
CAMB-7B677	MN908947.3	23403	A	G	1	1	0	0	0.999643356835203	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	2.74340895997366e-05
CAMB-7B677	MN908947.3	241	C	T	1	1	0	0	0.998963976603138	TCG	NA	NA	NA	NA	NA	NA	0.000151086745375666
CAMB-7B677	MN908947.3	25300	C	T	0.047	0.03	2.7e-21	4.6e-14	0.0386148373548194	GCT	S	G1246G	C3738T	GGC>GGT	Synonymous	GU280_gp02, spike glycoprotein	0.961256589379848
CAMB-7B677	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999586496145553	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	9.95850622406639e-05
CAMB-7B677	MN908947.3	3037	C	T	1	1	0	0	0.999319466224813	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0
CAMB-7B677	MN908947.3	6831	G	A	0.08	0.077	2.1e-35	4e-34	0.0788007133303611	AGA	ORF1ab:nsp3	R1371K	G4112A	AGA>AAA	Missense	ORF1ab:nsp3	0.921143557735176
CAMB-7B686	MN908947.3	10702	C	T	1	1	0	0	0.999763760926057	ACA	ORF1ab:3C-like-proteinase	D216D	C648T	GAC>GAT	Synonymous	ORF1ab:3C-like-proteinase	0.000181722364571408
CAMB-7B686	MN908947.3	11020	C	T	0.036	0.038	6.4e-17	8.4e-18	0.0370160402841231	TCA	ORF1ab:nsp6	L16L	C48T	CTC>CTT	Synonymous	ORF1ab:nsp6	0.962750525227599
CAMB-7B686	MN908947.3	11074	C	INS	0.11	0.11	1.4e-35	2.5e-35	0.107895590142672	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.886207036316472
CAMB-7B686	MN908947.3	11083	G	-	0.16	0.15	6.2e-71	7.1e-68	0.156047240650288	TGT	ORF1ab:nsp6	.	111-111-delfrshift	.	no-SNV	ORF1ab:nsp6	1.82255595246774e-05
CAMB-7B686	MN908947.3	11083	G	T	0.84	0.85	0	0	0.843460669242546	TGT	ORF1ab:nsp6	L37F	G111T	TTG>TTT	Missense	ORF1ab:nsp6	1.82255595246774e-05
CAMB-7B686	MN908947.3	12115	C	T	0.11	0.11	4.1e-50	2.8e-49	0.108170495166953	CCC	ORF1ab:nsp8	S8S	C24T	TCC>TCT	Synonymous	ORF1ab:nsp8	0.89168523475947
CAMB-7B686	MN908947.3	12672	C	T	1	1	0	0	0.999477348664439	GCT	ORF1ab:nsp8	A194V	C581T	GCT>GTT	Missense	ORF1ab:nsp8	0.000298657906034756
CAMB-7B686	MN908947.3	1314	C	T	1	1	0	0	0.999092205939567	ACT	ORF1ab:nsp2	T170I	C509T	ACT>ATT	Missense	ORF1ab:nsp2	0.000259369731552328
CAMB-7B686	MN908947.3	14805	C	T	1	1	0	0	0.999120828272312	ACT	ORF1ab:RNA-dependent-RNA-polymerase	Y446Y	C1338T	TAC>TAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.000300769275261727
CAMB-7B686	MN908947.3	14961	T	C	0.0095	0.009	4.2e-06	7.3e-06	0.00928430608408601	ATA	ORF1ab:RNA-dependent-RNA-polymerase	N498N	T1494C	AAT>AAC	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.990371830727614
CAMB-7B686	MN908947.3	15911	A	G	0.011	0.0088	1.1e-06	5.8e-06	0.00975296317969548	GAT	ORF1ab:RNA-dependent-RNA-polymerase	D815G	A2444G	GAT>GGT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.990189666448659
CAMB-7B686	MN908947.3	17247	T	C	1	1	0	0	0.999475624238498	GTG	ORF1ab:helicase	R337R	T1011C	CGT>CGC	Synonymous	ORF1ab:helicase	0.000246765064236031
CAMB-7B686	MN908947.3	19901	C	T	0.23	0.24	4.8e-109	8.1e-115	0.236278388278388	GCA	ORF1ab:endoRNAse	A94V	C281T	GCA>GTA	Missense	ORF1ab:endoRNAse	0.763663003663004
CAMB-7B686	MN908947.3	21772	C	T	0.0072	0.0077	4.5e-05	3e-05	0.00743583593187815	TCT	S	V70V	C210T	GTC>GTT	Synonymous	GU280_gp02, spike glycoprotein	0.989617242915396
CAMB-7B686	MN908947.3	24803	A	G	0.0099	0.0068	1.4e-06	3.2e-05	0.00822979717532123	CAT	S	I1081V	A3241G	ATT>GTT	Missense	GU280_gp02, spike glycoprotein	0.991531273229266
CAMB-7B686	MN908947.3	25423	GGAACTGTA	-	0.035	0.0355555555555556	2.3e-09;1.8e-08;4.9e-09;3.8e-10;1.7e-08;1.1e-08;3.9e-09;2.2e-08;6.2e-10	2.5e-09;1.5e-08;4.4e-09;1.5e-10;1.7e-08;1.1e-08;3.5e-09;1.6e-08;5.4e-10	0.0345817190414694	TGG	ORF3a	.	31-39-delinframe	.	no-SNV	GU280_gp03	0.96406509102174
CAMB-7B686	MN908947.3	26144	G	T	1	1	0	0	0.999699579411176	GGT	ORF3a	G251V	G752T	GGT>GTT	Missense	GU280_gp03	0.000250350490686962
CAMB-7B686	MN908947.3	29421	C	T	0.065	0.065	6.7e-25	3.5e-26	0.0649025567673878	CCG	N	P383L	C1148T	CCG>CTG	Missense	GU280_gp10	0.934382263543715
CAMB-7B686	MN908947.3	9693	C	T	0.0085	0.0097	1e-05	3.3e-06	0.00913788154243613	GCT	ORF1ab:nsp4	A380V	C1139T	GCT>GTT	Missense	ORF1ab:nsp4	0.990303958153925
CAMB-7B686	MN908947.3	9802	G	A	0.006	0.0072	7.3e-05	2.2e-05	0.00661243768039885	CGC	ORF1ab:nsp4	A416A	G1248A	GCG>GCA	Synonymous	ORF1ab:nsp4	0.993256363159276
CAMB-7B695	MN908947.3	11074	C	INS	0.019	0.026	0.0011	2.1e-05	0.0201932868368974	TCT	ORF1ab:nsp6	.	101-102-insfrshift	.	no-SNV	ORF1ab:nsp6	0.979287951274809
CAMB-7B695	MN908947.3	11075	T	-	0.025	0.034	1.4e-06	7.1e-10	0.0258501674151419	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.968786200549058
CAMB-7B695	MN908947.3	14120	C	T	1	1	0	0	0.998551511859497	CCA	ORF1ab:RNA-dependent-RNA-polymerase	P218L	C653T	CCA>CTA	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000181061017562919
CAMB-7B695	MN908947.3	14408	C	T	1	1	0	0	0.997827916001305	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000755507477806968
CAMB-7B695	MN908947.3	17285	C	T	0.23	0.23	3.3e-107	5.3e-109	0.226071373601003	TCA	ORF1ab:helicase	S350L	C1049T	TCA>TTA	Missense	ORF1ab:helicase	0.77384067371754
CAMB-7B695	MN908947.3	17734	CT	TC	0.00435	0.00785	0.00045;0.00045	6.4e-06;8.8e-06	0.00544835268960395	CCT	ORF1ab:helicase	.	1498-1499-mnv	.	no-SNV	ORF1ab:helicase	0.994531560524663
CAMB-7B695	MN908947.3	18110	C	T	0.0066	0.011	8e-05	9.1e-07	0.00928109419215739	CCT	ORF1ab:3'-to-5'-exonuclease	P24L	C71T	CCT>CTT	Missense	ORF1ab:3'-to-5'-exonuclease	0.990651529443471
CAMB-7B695	MN908947.3	1912	C	T	0.029	0.037	2.8e-14	1.6e-17	0.0325720765836982	CCC	ORF1ab:nsp2	S369S	C1107T	TCC>TCT	Synonymous	ORF1ab:nsp2	0.967427923416302
CAMB-7B695	MN908947.3	20555	C	T	0.007	0.0093	4.9e-05	4.5e-06	0.00800204978615212	TCT	ORF1ab:endoRNAse	S312F	C935T	TCT>TTT	Missense	ORF1ab:endoRNAse	0.99191911228492
CAMB-7B695	MN908947.3	23403	A	G	1	1	0	0	0.999828847717256	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	6.41821060288392e-05
CAMB-7B695	MN908947.3	241	C	T	1	1	0	0	0.999669667189694	TCG	NA	NA	NA	NA	NA	NA	8.25832025765959e-05
CAMB-7B695	MN908947.3	26140	G	T	1	1	0	0	0.999706572769953	CGA	ORF3a	D250Y	G748T	GAC>TAC	Missense	GU280_gp03	0.000293427230046948
CAMB-7B695	MN908947.3	26873	C	G	0.0023	0.0075	0.0023	2e-05	0.00485784170113032	ACA	M	N117K	C351G	AAC>AAG	Missense	GU280_gp05	0.995026333181171
CAMB-7B695	MN908947.3	27261	G	T	0.012	0.0055	2.7e-07	0.00018	0.00939456467390156	GGA	ORF6	R20S	G60T	AGG>AGT	Missense	GU280_gp06	0.990570223314577
CAMB-7B695	MN908947.3	27382	GAT	CTC	0.00606666666666667	0.00876666666666667	0.00017;0.00016;0.00022	1.1e-05;9.7e-06;1.4e-05	0.00730367291173093	TGA	ORF6	.	181-183-mnv	.	no-SNV	GU280_gp06	0.992338806306143
CAMB-7B695	MN908947.3	27393	C	T	0.033	0.044	1.6e-15	2.3e-20	0.0374896482194937	ACA	NA	NA	NA	NA	NA	NA	0.962474345587441
CAMB-7B695	MN908947.3	28520	C	A	0.019	0.02	6.3e-10	2.3e-10	0.0196114880565108	CCA	N	Q83K	C247A	CAA>AAA	Missense	GU280_gp10	0.980326548316138
CAMB-7B695	MN908947.3	28881	GGG	AAC	1	0.993333333333333	0;0;0	8.1e-208;1.7e-228;7.7e-237	0.999039385206532	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	0.000302938503483793
CAMB-7B695	MN908947.3	3037	C	T	1	1	0	0	0.999632982627844	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	6.11695620259359e-05
CAMB-7B695	MN908947.3	4165	T	C	0.0075	0.0027	2.6e-05	0.0031	0.00532377568878968	TTA	ORF1ab:nsp3	V482V	T1446C	GTT>GTC	Synonymous	ORF1ab:nsp3	0.99467622431121
CAMB-7B695	MN908947.3	8655	C	T	0.018	0.016	3.1e-09	0.00027	0.0176264949402024	TCT	ORF1ab:nsp4	S34F	C101T	TCT>TTT	Missense	ORF1ab:nsp4	0.982373505059798
CAMB-7B6A4	MN908947.3	10030	C	T	0.032	0.041	1.9e-15	1.7e-19	0.0355499505777293	CCT	ORF1ab:nsp4	T492T	C1476T	ACC>ACT	Synonymous	ORF1ab:nsp4	0.964450049422271
CAMB-7B6A4	MN908947.3	11075	T	-	0.046	0.074	2.1e-11	2.7e-18	0.057053055430831	CTT	ORF1ab:nsp6	.	103-103-delfrshift	.	no-SNV	ORF1ab:nsp6	0.94281658724526
CAMB-7B6A4	MN908947.3	12410	A	G	1	1	0	0	0.998933010352683	TAT	ORF1ab:nsp8	I107V	A319G	ATC>GTC	Missense	ORF1ab:nsp8	2.88375580355855e-05
CAMB-7B6A4	MN908947.3	13105	C	T	0.0098	0.012	2.2e-06	3.4e-07	0.0105819218514171	ACA	ORF1ab:nsp10	Y27Y	C81T	TAC>TAT	Synonymous	ORF1ab:nsp10	0.989384537984236
CAMB-7B6A4	MN908947.3	13438	T	C	0.038	0.0072	3.7e-18	3.7e-05	0.0280080663231011	TTC	ORF1ab:nsp10	L138L	T414C	CTT>CTC	Synonymous	ORF1ab:nsp10	0.971917245500037
CAMB-7B6A4	MN908947.3	14408	C	T	1	1	0	0	0.999177236887213	CCT	ORF1ab:RNA-dependent-RNA-polymerase	P314L	C941T	CCT>CTT	Missense	ORF1ab:RNA-dependent-RNA-polymerase	0.000589646897497429
CAMB-7B6A4	MN908947.3	14928	C	T	0.048	0.044	3.6e-22	4.6e-20	0.0468014128728414	ACA	ORF1ab:RNA-dependent-RNA-polymerase	N487N	C1461T	AAC>AAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.953198587127159
CAMB-7B6A4	MN908947.3	14931	C	T	0.0059	0.011	7.4e-05	1.1e-06	0.0076297560485895	ACC	ORF1ab:RNA-dependent-RNA-polymerase	N488N	C1464T	AAC>AAT	Synonymous	ORF1ab:RNA-dependent-RNA-polymerase	0.99237024395141
CAMB-7B6A4	MN908947.3	18788	C	T	1	1	0	0	0.99923977228528	ACA	ORF1ab:3'-to-5'-exonuclease	T250I	C749T	ACA>ATA	Missense	ORF1ab:3'-to-5'-exonuclease	5.30391428874509e-05
CAMB-7B6A4	MN908947.3	19839	T	C	1	1	0	0	0.999874419188748	ATA	ORF1ab:endoRNAse	N73N	T219C	AAT>AAC	Synonymous	ORF1ab:endoRNAse	6.27904056260203e-05
CAMB-7B6A4	MN908947.3	21093	T	C	1	1	0	0	0.999632632711433	CTA	ORF1ab:2'-O-ribose-methyltransferase	S145S	T435C	TCT>TCC	Synonymous	ORF1ab:2'-O-ribose-methyltransferase	0.00023616468550736
CAMB-7B6A4	MN908947.3	23403	A	G	1	1	0	0	0.998824499535063	GAT	S	D614G	A1841G	GAT>GGT	Missense	GU280_gp02, spike glycoprotein	7.89515237644087e-05
CAMB-7B6A4	MN908947.3	241	C	T	1	1	0	0	0.999770062083237	TCG	NA	NA	NA	NA	NA	NA	8.3613787913627e-05
CAMB-7B6A4	MN908947.3	2453	C	T	0.012	0.01	7.2e-07	6.5e-06	0.0113330772185939	ACT	ORF1ab:nsp2	L550F	C1648T	CTC>TTC	Missense	ORF1ab:nsp2	0.988474836726854
CAMB-7B6A4	MN908947.3	28531	C	T	0.0084	0.0028	2.8e-05	0.0081	0.00592553576719228	ACT	N	Y86Y	C258T	TAC>TAT	Synonymous	GU280_gp10	0.993416071369786
CAMB-7B6A4	MN908947.3	28881	GGG	AAC	1	1	0;0;0	0;0;0	0.999262568863055	AGG	N	.	608-610-mnv	.	no-SNV	GU280_gp10	4.89356496207487e-05
CAMB-7B6A4	MN908947.3	3037	C	T	1	1	0	0	0.999539994888832	TCT	ORF1ab:nsp3	F106F	C318T	TTC>TTT	Synonymous	ORF1ab:nsp3	0.000102223358037312
CAMB-7B6A4	MN908947.3	6178	T	C	0.011	0.013	1.6e-06	7.2e-07	0.0120084058841189	ATT	ORF1ab:nsp3	D1153D	T3459C	GAT>GAC	Synonymous	ORF1ab:nsp3	0.987991594115881
CAMB-7B6A4	MN908947.3	6407	T	A	0.0045	0.015	2e-04	5.3e-09	0.00821917808219178	CTC	ORF1ab:nsp3	S1230T	T3688A	TCT>ACT	Missense	ORF1ab:nsp3	0.989993199261634
CAMB-7B6A4	MN908947.3	6423	AA	-	0.0022	0.00645	0.0035;NA	0.00037;2.3e-05	0.0036207540126913	GAA	ORF1ab:nsp3	.	3704-3705-delfrshift	.	no-SNV	ORF1ab:nsp3	0.994712962615771
CAMB-7B6A4	MN908947.3	6554	GCT	-	0.00193333333333333	0.0123333333333333	NA;NA;0.00021	7.9e-07;1.2e-06;1.5e-06	0.0050125313283208	GGC	ORF1ab:nsp3	.	3835-3837-delinframe	.	no-SNV	ORF1ab:nsp3	0.994794377928162
CAMB-7B6A4	MN908947.3	9866	C	T	0.0019	0.012	0.0034	2.5e-07	0.00600561394346889	TCT	ORF1ab:nsp4	L438F	C1312T	CTT>TTT	Missense	ORF1ab:nsp4	0.993733272406815