CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1682

Details of the codons used for the mutation across all lineages (CodonProp is the proportion each codon is used for this AA mutation):

ORF	CodonNum	Mut	ORF1abMut	MutType	RefCodon	MutCodon	AACount	CodonCount	CodonProp	Genome Position
ORF1ab/nsp3	1682	S1682F	S2500F	nonsyn	tCc	tTc	12930	12899	0.997602	7763-7765
ORF1ab/nsp3	1682	S1682F	S2500F	nonsyn	tCC	tTT	12930	31	0.00239753	7763-7765
ORF1ab/nsp3	1682	S1682S	S2500S	syn	tcC	tcT	10510	10217	0.972122	7763-7765
ORF1ab/nsp3	1682	S1682S	S2500S	syn	tcC	tcA	10510	259	0.0246432	7763-7765
ORF1ab/nsp3	1682	S1682S	S2500S	syn	tcC	tcG	10510	34	0.00323501	7763-7765
ORF1ab/nsp3	1682	S1682del	S2500del	del	TCC	---	117	117	1	7763-7765
ORF1ab/nsp3	1682	S1682Y	S2500Y	nonsyn	tCc	tAc	71	71	1	7763-7765
ORF1ab/nsp3	1682	S1682A	S2500A	nonsyn	Tcc	Gcc	30	29	0.966667	7763-7765
ORF1ab/nsp3	1682	S1682A	S2500A	nonsyn	TcC	GcT	30	1	0.0333333	7763-7765
ORF1ab/nsp3	1682	S1682P	S2500P	nonsyn	Tcc	Ccc	9	9	1	7763-7765
ORF1ab/nsp3	1682	S1682T	S2500T	nonsyn	Tcc	Acc	8	8	1	7763-7765
ORF1ab/nsp3	1682	S1682C	S2500C	nonsyn	tCc	tGc	5	5	1	7763-7765
ORF1ab/nsp3	1682	S1682del1	S2500del1	del	tCc	t-c	3	3	1	7763-7765
ORF1ab/nsp3	1682	S1682G	S2500G	nonsyn	TCc	GGc	2	2	1	7763-7765
ORF1ab/nsp3	1682	S1682V	S2500V	nonsyn	TCc	GTc	2	2	1	7763-7765
ORF1ab/nsp3	1682	S1682L	S2500L	nonsyn	TCc	CTc	2	1	0.5	7763-7765
ORF1ab/nsp3	1682	S1682L	S2500L	nonsyn	TCC	CTG	2	1	0.5	7763-7765
ORF1ab/nsp3	1682	S1682X	S2500X	nonsyn	tCC	tAA	1	1	1	7763-7765

Details of the mutation no within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):

ORF	CodonNum	Mut	RefCodon	MutCodon	CodonCount	AACount	Lineage	LineageCodonProp
ORF1ab/nsp3	1682	S1682F	tCc	tTc	12899	12930	All	0.002467
ORF1ab/nsp3	1682	S1682F	tCC	tTT	31	12930	All	0.000006
ORF1ab/nsp3	1682	S1682S	tcC	tcT	10217	10510	All	0.001954
ORF1ab/nsp3	1682	S1682S	tcC	tcA	259	10510	All	0.00005
ORF1ab/nsp3	1682	S1682S	tcC	tcG	34	10510	All	0.000007
ORF1ab/nsp3	1682	S1682F	tCc	tTc	6090	6108	B.1.1.7	0.005452
ORF1ab/nsp3	1682	S1682F	tCC	tTT	18	6108	B.1.1.7	0.000016
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1764	1774	B.1.1.7	0.001579
ORF1ab/nsp3	1682	S1682S	tcC	tcG	8	1774	B.1.1.7	0.000007
ORF1ab/nsp3	1682	S1682S	tcC	tcA	2	1774	B.1.1.7	0.000002
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1279	1284	AY.4	0.001991
ORF1ab/nsp3	1682	S1682F	tCC	tTT	5	1284	AY.4	0.000008
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1187	1187	AY.44	0.007225
ORF1ab/nsp3	1682	S1682S	tcC	tcT	585	594	AY.4	0.000911
ORF1ab/nsp3	1682	S1682S	tcC	tcA	5	594	AY.4	0.000008
ORF1ab/nsp3	1682	S1682S	tcC	tcG	4	594	AY.4	0.000006
ORF1ab/nsp3	1682	S1682S	tcC	tcT	497	499	B.1.617.2	0.001871
ORF1ab/nsp3	1682	S1682S	tcC	tcA	2	499	B.1.617.2	0.000008
ORF1ab/nsp3	1682	S1682F	tCc	tTc	403	403	AY.4.2	0.008741
ORF1ab/nsp3	1682	S1682S	tcC	tcT	237	399	AY.25	0.001426
ORF1ab/nsp3	1682	S1682S	tcC	tcA	162	399	AY.25	0.000974
ORF1ab/nsp3	1682	S1682S	tcC	tcT	352	353	AY.43	0.00156
ORF1ab/nsp3	1682	S1682S	tcC	tcA	1	353	AY.43	0.000004
ORF1ab/nsp3	1682	S1682S	tcC	tcT	294	294	AY.103	0.001825
ORF1ab/nsp3	1682	S1682S	tcC	tcT	294	294	B.1.1.519	0.011675
ORF1ab/nsp3	1682	S1682S	tcC	tcT	282	288	B.1	0.002583
ORF1ab/nsp3	1682	S1682S	tcC	tcA	4	288	B.1	0.000037
ORF1ab/nsp3	1682	S1682S	tcC	tcG	2	288	B.1	0.000018
ORF1ab/nsp3	1682	S1682F	tCc	tTc	279	279	AY.44	0.001698
ORF1ab/nsp3	1682	S1682S	tcC	tcT	272	273	B.1.2	0.002395
ORF1ab/nsp3	1682	S1682S	tcC	tcA	1	273	B.1.2	0.000009
ORF1ab/nsp3	1682	S1682F	tCc	tTc	271	271	B.1.617.2	0.00102
ORF1ab/nsp3	1682	S1682F	tCc	tTc	248	248	AY.103	0.00154
ORF1ab/nsp3	1682	S1682F	tCc	tTc	231	231	AY.29	0.003644
ORF1ab/nsp3	1682	S1682S	tcC	tcT	228	228	B.1.1.50	0.154786
ORF1ab/nsp3	1682	S1682F	tCc	tTc	227	227	AY.3	0.002258
ORF1ab/nsp3	1682	S1682F	tCc	tTc	224	224	B.1.2	0.001972
ORF1ab/nsp3	1682	S1682S	tcC	tcT	202	202	P.7	0.882096
ORF1ab/nsp3	1682	S1682F	tCc	tTc	192	192	AY.25	0.001155
ORF1ab/nsp3	1682	S1682F	tCc	tTc	178	178	B.1.36.18	0.07479
ORF1ab/nsp3	1682	S1682F	tCc	tTc	172	172	B.1.621	0.015225
ORF1ab/nsp3	1682	S1682S	tcC	tcT	162	162	B.1.9.4	0.993865
ORF1ab/nsp3	1682	S1682F	tCc	tTc	157	159	B.1	0.001438
ORF1ab/nsp3	1682	S1682F	tCC	tTT	2	159	B.1	0.000018
ORF1ab/nsp3	1682	S1682S	tcC	tcT	158	158	B.1.9	0.975309
ORF1ab/nsp3	1682	S1682S	tcC	tcT	157	157	B.1.9.5	0.892045
ORF1ab/nsp3	1682	S1682S	tcC	tcT	156	156	B.1.526	0.003667
ORF1ab/nsp3	1682	S1682F	tCc	tTc	152	152	P.1	0.002395
ORF1ab/nsp3	1682	S1682F	tCc	tTc	151	151	AY.34	0.014642
ORF1ab/nsp3	1682	S1682S	tcC	tcT	144	144	B.1.36	0.02101
ORF1ab/nsp3	1682	S1682F	tCc	tTc	143	143	AY.43	0.000634
ORF1ab/nsp3	1682	S1682S	tcC	tcT	128	129	AY.9	0.008652
ORF1ab/nsp3	1682	S1682S	tcC	tcA	1	129	AY.9	0.000068
ORF1ab/nsp3	1682	S1682F	tCc	tTc	124	124	AY.47	0.003857
ORF1ab/nsp3	1682	S1682S	tcC	tcT	120	122	P.1	0.00189
ORF1ab/nsp3	1682	S1682S	tcC	tcG	2	122	P.1	0.000032
ORF1ab/nsp3	1682	S1682del	TCC	---	117	117	All	0.000022
ORF1ab/nsp3	1682	S1682F	tCc	tTc	114	117	B.1.429	0.002682
ORF1ab/nsp3	1682	S1682F	tCC	tTT	3	117	B.1.429	0.000071
ORF1ab/nsp3	1682	S1682S	tcC	tcT	90	112	B.1.177	0.001185
ORF1ab/nsp3	1682	S1682S	tcC	tcA	21	112	B.1.177	0.000277
ORF1ab/nsp3	1682	S1682S	tcC	tcG	1	112	B.1.177	0.000013
ORF1ab/nsp3	1682	S1682S	tcC	tcT	107	107	AY.95	0.081431
ORF1ab/nsp3	1682	S1682S	tcC	tcT	89	93	B.1.1	0.001615
ORF1ab/nsp3	1682	S1682S	tcC	tcA	4	93	B.1.1	0.000073
ORF1ab/nsp3	1682	S1682S	tcC	tcT	92	92	AY.5	0.0019
ORF1ab/nsp3	1682	S1682S	tcC	tcT	87	89	B.1.429	0.002047
ORF1ab/nsp3	1682	S1682S	tcC	tcA	2	89	B.1.429	0.000047
ORF1ab/nsp3	1682	S1682S	tcC	tcT	88	88	AY.75	0.00493
ORF1ab/nsp3	1682	S1682S	tcC	tcT	87	87	B.1.575	0.026396
ORF1ab/nsp3	1682	S1682F	tCc	tTc	82	82	B.1.1	0.001488
ORF1ab/nsp3	1682	S1682F	tCc	tTc	82	82	B.1.177	0.00108
ORF1ab/nsp3	1682	S1682F	tCc	tTc	77	77	AY.75	0.004314
ORF1ab/nsp3	1682	S1682Y	tCc	tAc	71	71	All	0.000014
ORF1ab/nsp3	1682	S1682F	tCc	tTc	68	68	P.1.1	0.021601
ORF1ab/nsp3	1682	S1682F	tCc	tTc	66	66	B.1.258	0.004392
ORF1ab/nsp3	1682	S1682F	tCc	tTc	64	64	AY.3.1	0.005457
ORF1ab/nsp3	1682	S1682F	tCc	tTc	61	61	AY.113	0.008686
ORF1ab/nsp3	1682	S1682F	tCc	tTc	61	61	AY.36	0.009041
ORF1ab/nsp3	1682	S1682S	tcC	tcT	60	61	AY.39	0.001483
ORF1ab/nsp3	1682	S1682S	tcC	tcA	1	61	AY.39	0.000025
ORF1ab/nsp3	1682	S1682F	tCc	tTc	61	61	B.1.526	0.001434
ORF1ab/nsp3	1682	S1682S	tcC	tcT	60	60	C.37	0.006964
ORF1ab/nsp3	1682	S1682S	tcC	tcT	57	58	AY.3	0.000567
ORF1ab/nsp3	1682	S1682S	tcC	tcA	1	58	AY.3	0.00001
ORF1ab/nsp3	1682	S1682S	tcC	tcT	57	57	AY.67	0.026462
ORF1ab/nsp3	1682	S1682F	tCc	tTc	56	56	AY.120	0.002082
ORF1ab/nsp3	1682	S1682S	tcC	tcT	54	54	AY.33	0.003606
ORF1ab/nsp3	1682	S1682F	tCc	tTc	52	53	B.1.36	0.007587
ORF1ab/nsp3	1682	S1682F	tCC	tTT	1	53	B.1.36	0.000146
ORF1ab/nsp3	1682	S1682S	tcC	tcT	52	52	AY.100	0.002392
ORF1ab/nsp3	1682	S1682F	tCc	tTc	52	52	B.1.177.17	0.042693
ORF1ab/nsp3	1682	S1682del	TCC	---	51	51	B.1.1.7	0.000046
ORF1ab/nsp3	1682	S1682S	tcC	tcA	45	49	B.1.596	0.003921
ORF1ab/nsp3	1682	S1682S	tcC	tcT	4	49	B.1.596	0.000349
ORF1ab/nsp3	1682	S1682F	tCc	tTc	48	48	AY.102	0.001273
ORF1ab/nsp3	1682	S1682F	tCc	tTc	46	46	B.1.351	0.001367
ORF1ab/nsp3	1682	S1682F	tCc	tTc	45	45	AY.22	0.094142
ORF1ab/nsp3	1682	S1682S	tcC	tcT	45	45	B.1.428.3	0.576923
ORF1ab/nsp3	1682	S1682S	tcC	tcT	44	44	AY.102	0.001167
ORF1ab/nsp3	1682	S1682S	tcC	tcT	44	44	AY.9.2	0.001616
ORF1ab/nsp3	1682	S1682S	tcC	tcT	43	43	AY.46.6	0.003105
ORF1ab/nsp3	1682	S1682F	tCc	tTc	42	42	B.1.1.318	0.012674
ORF1ab/nsp3	1682	S1682S	tcC	tcT	42	42	B.1.351.2	0.012708
ORF1ab/nsp3	1682	S1682S	tcC	tcT	41	41	C.1.2	0.174468
ORF1ab/nsp3	1682	S1682S	tcC	tcT	38	38	AY.26	0.001076
ORF1ab/nsp3	1682	S1682S	tcC	tcT	38	38	AY.99.2	0.003502
ORF1ab/nsp3	1682	S1682S	tcC	tcT	36	37	AY.29	0.000568
ORF1ab/nsp3	1682	S1682S	tcC	tcG	1	37	AY.29	0.000016
ORF1ab/nsp3	1682	S1682S	tcC	tcT	36	36	AY.120	0.001338
ORF1ab/nsp3	1682	S1682S	tcC	tcT	36	36	AY.45	0.004381
ORF1ab/nsp3	1682	S1682S	tcC	tcT	35	35	B.1.627	0.070707
ORF1ab/nsp3	1682	S1682F	tCc	tTc	33	33	B.1.588	0.030027
ORF1ab/nsp3	1682	S1682S	tcC	tcT	31	31	B.1.351	0.000922
ORF1ab/nsp3	1682	S1682S	tcC	tcT	31	31	B.1.466.2	0.012128
ORF1ab/nsp3	1682	S1682S	tcC	tcT	31	31	B.1.9.1	1
ORF1ab/nsp3	1682	S1682S	tcC	tcT	31	31	N.5	0.05477
ORF1ab/nsp3	1682	S1682A	Tcc	Gcc	29	30	All	0.000006
ORF1ab/nsp3	1682	S1682A	TcC	GcT	1	30	All	0
ORF1ab/nsp3	1682	S1682F	tCc	tTc	30	30	B.1.160	0.000936
ORF1ab/nsp3	1682	S1682F	tCc	tTc	28	28	AY.5	0.000578
ORF1ab/nsp3	1682	S1682F	tCc	tTc	26	26	B.1.525	0.002942
ORF1ab/nsp3	1682	S1682S	tcC	tcT	26	26	B.1.9.3	1
ORF1ab/nsp3	1682	S1682S	tcC	tcT	26	26	Q.2	0.015951
ORF1ab/nsp3	1682	S1682S	tcC	tcT	25	25	AY.46.5	0.00496
ORF1ab/nsp3	1682	S1682S	tcC	tcT	25	25	AY.5.1	0.093985
ORF1ab/nsp3	1682	S1682S	tcC	tcT	25	25	B.1.1.28	0.007781
ORF1ab/nsp3	1682	S1682S	tcC	tcT	25	25	B.1.1.369	0.011156
ORF1ab/nsp3	1682	S1682S	tcC	tcT	24	24	B.1.221.3	0.02
ORF1ab/nsp3	1682	S1682F	tCc	tTc	23	23	AY.39.1	0.000911
ORF1ab/nsp3	1682	S1682S	tcC	tcT	23	23	AY.4.2	0.000499
ORF1ab/nsp3	1682	S1682S	tcC	tcT	23	23	B.1.221	0.001634
ORF1ab/nsp3	1682	S1682F	tCc	tTc	23	23	B.1.575	0.006978
ORF1ab/nsp3	1682	S1682F	tCc	tTc	22	22	AY.20	0.000855
ORF1ab/nsp3	1682	S1682F	tCc	tTc	22	22	AY.39	0.000544
ORF1ab/nsp3	1682	S1682F	tCc	tTc	22	22	B.1.243	0.001531
ORF1ab/nsp3	1682	S1682S	tcC	tcT	22	22	B.1.438.1	0.00236
ORF1ab/nsp3	1682	S1682F	tCc	tTc	22	22	B.1.561	0.008734
ORF1ab/nsp3	1682	S1682F	tCc	tTc	22	22	B.1.596	0.001917
ORF1ab/nsp3	1682	S1682F	tCc	tTc	22	22	P.2	0.004106
ORF1ab/nsp3	1682	S1682S	tcC	tcT	21	21	AY.20	0.000816
ORF1ab/nsp3	1682	S1682A	Tcc	Gcc	21	21	AY.92	0.006033
ORF1ab/nsp3	1682	S1682S	tcC	tcT	21	21	B.1.258.17	0.002183
ORF1ab/nsp3	1682	S1682F	tCc	tTc	20	20	B.1.351.3	0.017528
ORF1ab/nsp3	1682	S1682S	tcC	tcT	20	20	B.1.427	0.00101
ORF1ab/nsp3	1682	S1682F	tCc	tTc	19	19	AY.100	0.000874
ORF1ab/nsp3	1682	S1682S	tcC	tcT	19	19	AY.119	0.000671
ORF1ab/nsp3	1682	S1682S	tcC	tcT	19	19	B.1.232	0.01021
ORF1ab/nsp3	1682	S1682F	tCc	tTc	19	19	B.1.425	0.056886
ORF1ab/nsp3	1682	S1682S	tcC	tcT	19	19	B.1.525	0.00215
ORF1ab/nsp3	1682	S1682F	tCc	tTc	19	19	P.1.14	0.000908
ORF1ab/nsp3	1682	S1682F	tCc	tTc	18	18	AY.4.5	0.001935
ORF1ab/nsp3	1682	S1682S	tcC	tcT	18	18	B.1.1.389	0.109091
ORF1ab/nsp3	1682	S1682S	tcC	tcT	18	18	B.1.177.4	0.003799
ORF1ab/nsp3	1682	S1682S	tcC	tcG	14	18	Q.3	0.00203
ORF1ab/nsp3	1682	S1682S	tcC	tcT	4	18	Q.3	0.00058
ORF1ab/nsp3	1682	S1682S	tcC	tcT	18	18	R.1	0.00162
ORF1ab/nsp3	1682	S1682F	tCc	tTc	17	17	AY.119	0.0006
ORF1ab/nsp3	1682	S1682S	tcC	tcT	17	17	AY.9.1	0.001423
ORF1ab/nsp3	1682	S1682S	tcC	tcT	17	17	B.1.1.434	0.005925
ORF1ab/nsp3	1682	S1682S	tcC	tcT	17	17	B.1.160	0.00053
ORF1ab/nsp3	1682	S1682F	tCc	tTc	17	17	B.1.427	0.000858
ORF1ab/nsp3	1682	S1682S	tcC	tcT	17	17	B.1.637	0.001242
ORF1ab/nsp3	1682	S1682S	tcC	tcT	17	17	P.2	0.003173
ORF1ab/nsp3	1682	S1682F	tCc	tTc	16	16	AY.33	0.001068
ORF1ab/nsp3	1682	S1682S	tcC	tcT	16	16	AY.42	0.000644
ORF1ab/nsp3	1682	S1682F	tCc	tTc	16	16	AY.61	0.001676
ORF1ab/nsp3	1682	S1682S	tcC	tcT	16	16	B.1.1.214	0.000887
ORF1ab/nsp3	1682	S1682F	tCc	tTc	16	16	R.1	0.00144
ORF1ab/nsp3	1682	S1682F	tCc	tTc	15	15	AY.121	0.00203
ORF1ab/nsp3	1682	S1682S	tcC	tcT	15	15	B.1.177.86	0.002752
ORF1ab/nsp3	1682	S1682F	tCc	tTc	15	15	Q.8	0.002474
ORF1ab/nsp3	1682	S1682F	tCc	tTc	14	14	AY.118	0.000877
ORF1ab/nsp3	1682	S1682F	tCc	tTc	14	14	AY.26	0.000396
ORF1ab/nsp3	1682	S1682S	tcC	tcT	14	14	AY.39.1	0.000555
ORF1ab/nsp3	1682	S1682Y	tCc	tAc	14	14	AY.4	0.000022
ORF1ab/nsp3	1682	S1682S	tcC	tcT	14	14	AY.54	0.001335
ORF1ab/nsp3	1682	S1682F	tCc	tTc	14	14	B.1.177.81	0.002651
ORF1ab/nsp3	1682	S1682S	tcC	tcT	14	14	B.1.218	0.072165
ORF1ab/nsp3	1682	S1682S	tcC	tcT	14	14	B.1.565	0.011345
ORF1ab/nsp3	1682	S1682S	tcC	tcT	14	14	P.1.14	0.000669
ORF1ab/nsp3	1682	S1682S	tcC	tcT	13	13	AD.2	0.002847
ORF1ab/nsp3	1682	S1682F	tCc	tTc	13	13	AY.117	0.001099
ORF1ab/nsp3	1682	S1682F	tCc	tTc	13	13	AY.23	0.000907
ORF1ab/nsp3	1682	S1682S	tcC	tcT	13	13	AY.47	0.000404
ORF1ab/nsp3	1682	S1682F	tCc	tTc	13	13	B.1.258.17	0.001352
ORF1ab/nsp3	1682	S1682F	tCc	tTc	13	13	B.1.505	0.057018
ORF1ab/nsp3	1682	S1682S	tcC	tcT	13	13	B.1.597	0.060185
ORF1ab/nsp3	1682	S1682F	tCc	tTc	13	13	C.36.3.1	0.035326
ORF1ab/nsp3	1682	S1682S	tcC	tcT	13	13	C.39	0.245283
ORF1ab/nsp3	1682	S1682F	tCc	tTc	13	13	Q.1	0.001642
ORF1ab/nsp3	1682	S1682Y	tCc	tAc	12	12	AY.103	0.000075
ORF1ab/nsp3	1682	S1682S	tcC	tcT	12	12	AY.106	0.004019
ORF1ab/nsp3	1682	S1682F	tCc	tTc	12	12	AY.29.1	0.002646
ORF1ab/nsp3	1682	S1682F	tCc	tTc	12	12	B.1.1.519	0.000477
ORF1ab/nsp3	1682	S1682S	tcC	tcT	12	12	B.1.177.57	0.003372
ORF1ab/nsp3	1682	S1682S	tcC	tcT	12	12	B.1.214.2	0.007194
ORF1ab/nsp3	1682	S1682F	tCc	tTc	12	12	B.1.436	0.012346
ORF1ab/nsp3	1682	S1682F	tCc	tTc	12	12	B.1.466.2	0.004695
ORF1ab/nsp3	1682	S1682S	tcC	tcT	12	12	B.1.621	0.001062
ORF1ab/nsp3	1682	S1682Y	tCc	tAc	11	11	AY.25	0.000066
ORF1ab/nsp3	1682	S1682S	tcC	tcT	11	11	B.1.1.192	0.025404
ORF1ab/nsp3	1682	S1682S	tcC	tcT	11	11	B.1.177.17	0.009031
ORF1ab/nsp3	1682	S1682F	tCc	tTc	11	11	B.1.208	0.44
ORF1ab/nsp3	1682	S1682F	tCc	tTc	11	11	C.37	0.001277
ORF1ab/nsp3	1682	S1682F	tCc	tTc	10	10	AY.106	0.003349
ORF1ab/nsp3	1682	S1682S	tcC	tcT	10	10	AY.118	0.000626
ORF1ab/nsp3	1682	S1682F	tCc	tTc	10	10	AY.45	0.001217
ORF1ab/nsp3	1682	S1682F	tCc	tTc	10	10	AY.46	0.001041
ORF1ab/nsp3	1682	S1682S	tcC	tcT	10	10	AY.46.4	0.001645
ORF1ab/nsp3	1682	S1682F	tCc	tTc	10	10	B.1.1.28	0.003112
ORF1ab/nsp3	1682	S1682F	tCc	tTc	10	10	B.1.234	0.001319
ORF1ab/nsp3	1682	S1682S	tcC	tcT	10	10	B.1.239	0.01221
ORF1ab/nsp3	1682	S1682S	tcC	tcT	10	10	B.1.311	0.002746
ORF1ab/nsp3	1682	S1682S	tcC	tcT	10	10	B.1.9.2	1
ORF1ab/nsp3	1682	S1682S	tcC	tcT	10	10	P.1.7	0.003193
ORF1ab/nsp3	1682	S1682F	tCc	tTc	10	10	Q.3	0.00145
ORF1ab/nsp3	1682	S1682P	Tcc	Ccc	9	9	All	0.000002
ORF1ab/nsp3	1682	S1682F	tCc	tTc	9	9	AY.109	0.006657
ORF1ab/nsp3	1682	S1682S	tcC	tcT	9	9	AY.120.1	0.002889
ORF1ab/nsp3	1682	S1682S	tcC	tcT	9	9	AY.3.1	0.000767
ORF1ab/nsp3	1682	S1682S	tcC	tcT	9	9	AY.4.3	0.007576
ORF1ab/nsp3	1682	S1682F	tCc	tTc	9	9	AY.42	0.000362
ORF1ab/nsp3	1682	S1682F	tCc	tTc	9	9	AY.75.1	0.001623
ORF1ab/nsp3	1682	S1682F	tCc	tTc	9	9	B.1.1.270	0.092784
ORF1ab/nsp3	1682	S1682F	tCc	tTc	9	9	B.1.1.317	0.003705
ORF1ab/nsp3	1682	S1682F	tCc	tTc	9	9	B.1.177.4	0.0019
ORF1ab/nsp3	1682	S1682F	tCc	tTc	9	9	B.1.240	0.00194
ORF1ab/nsp3	1682	S1682S	tcC	tcT	9	9	B.1.258	0.000599
ORF1ab/nsp3	1682	S1682Y	tCc	tAc	9	9	B.1.258.17	0.000936
ORF1ab/nsp3	1682	S1682S	tcC	tcT	9	9	B.1.527	0.033333
ORF1ab/nsp3	1682	S1682S	tcC	tcT	9	9	Q.1	0.001137
ORF1ab/nsp3	1682	S1682T	Tcc	Acc	8	8	All	0.000002
ORF1ab/nsp3	1682	S1682S	tcC	tcT	8	8	AY.121	0.001083
ORF1ab/nsp3	1682	S1682S	tcC	tcT	8	8	AY.56	0.012841
ORF1ab/nsp3	1682	S1682F	tCc	tTc	8	8	AY.78	0.012327
ORF1ab/nsp3	1682	S1682S	tcC	tcT	8	8	AY.98	0.000632
ORF1ab/nsp3	1682	S1682F	tCc	tTc	8	8	B.1.1.214	0.000444
ORF1ab/nsp3	1682	S1682F	tCc	tTc	8	8	B.1.1.222	0.001632
ORF1ab/nsp3	1682	S1682S	tcC	tcT	8	8	B.1.1.318	0.002414
ORF1ab/nsp3	1682	S1682F	tCc	tTc	8	8	B.1.177.35	0.005529
ORF1ab/nsp3	1682	S1682F	tCc	tTc	8	8	B.1.177.57	0.002248
ORF1ab/nsp3	1682	S1682F	tCc	tTc	8	8	B.1.221	0.000568
ORF1ab/nsp3	1682	S1682S	tcC	tcT	8	8	B.1.243	0.000557
ORF1ab/nsp3	1682	S1682S	tcC	tcT	8	8	B.1.563	0.135593
ORF1ab/nsp3	1682	S1682Y	tCc	tAc	8	8	B.1.628	0.002819
ORF1ab/nsp3	1682	S1682F	tCc	tTc	8	8	B.1.637	0.000585
ORF1ab/nsp3	1682	S1682F	tCc	tTc	8	8	C.18	0.020725
ORF1ab/nsp3	1682	S1682S	tcC	tcT	8	8	C.36	0.007286
ORF1ab/nsp3	1682	S1682S	tcC	tcT	7	7	AY.117	0.000592
ORF1ab/nsp3	1682	S1682F	tCc	tTc	7	7	AY.24	0.003017
ORF1ab/nsp3	1682	S1682F	tCc	tTc	7	7	AY.30	0.00277
ORF1ab/nsp3	1682	S1682S	tcC	tcT	7	7	AY.35	0.001631
ORF1ab/nsp3	1682	S1682F	tCc	tTc	7	7	AY.4.2.1	0.001043
ORF1ab/nsp3	1682	S1682S	tcC	tcT	7	7	B.1.369	0.001997
ORF1ab/nsp3	1682	S1682S	tcC	tcT	7	7	B.1.396	0.00494
ORF1ab/nsp3	1682	S1682S	tcC	tcT	7	7	B.1.409	0.005469
ORF1ab/nsp3	1682	S1682S	tcC	tcT	7	7	B.1.497	0.002203
ORF1ab/nsp3	1682	S1682F	tCc	tTc	7	7	B.1.617.1	0.000903
ORF1ab/nsp3	1682	S1682S	tcC	tcT	6	6	AY.111	0.001099
ORF1ab/nsp3	1682	S1682F	tCc	tTc	6	6	AY.120.1	0.001926
ORF1ab/nsp3	1682	S1682S	tcC	tcT	6	6	AY.13	0.000966
ORF1ab/nsp3	1682	S1682S	tcC	tcT	6	6	AY.61	0.000629
ORF1ab/nsp3	1682	S1682F	tCc	tTc	6	6	AY.85	0.002563
ORF1ab/nsp3	1682	S1682F	tCc	tTc	6	6	AY.98	0.000474
ORF1ab/nsp3	1682	S1682S	tcC	tcT	6	6	B	0.000767
ORF1ab/nsp3	1682	S1682S	tcC	tcT	6	6	B.1.1.163	0.045802
ORF1ab/nsp3	1682	S1682S	tcC	tcT	6	6	B.1.1.174	0.02027
ORF1ab/nsp3	1682	S1682F	tCc	tTc	6	6	B.1.1.306	0.00263
ORF1ab/nsp3	1682	S1682S	tcC	tcT	6	6	B.1.1.433	0.008547
ORF1ab/nsp3	1682	S1682S	tcC	tcT	6	6	B.1.1.526	0.021277
ORF1ab/nsp3	1682	S1682S	tcC	tcT	6	6	B.1.13	0.014252
ORF1ab/nsp3	1682	S1682F	tCc	tTc	6	6	B.1.160.14	0.012712
ORF1ab/nsp3	1682	S1682F	tCc	tTc	6	6	B.1.177.42	0.005367
ORF1ab/nsp3	1682	S1682F	tCc	tTc	6	6	B.1.351.2	0.001815
ORF1ab/nsp3	1682	S1682F	tCc	tTc	6	6	B.1.595	0.001566
ORF1ab/nsp3	1682	S1682del	TCC	---	6	6	B.1.617.2	0.000023
ORF1ab/nsp3	1682	S1682S	tcC	tcT	6	6	C.36.3	0.003403
ORF1ab/nsp3	1682	S1682S	tcC	tcT	6	6	C.36.3.1	0.016304
ORF1ab/nsp3	1682	S1682S	tcC	tcT	6	6	Q.8	0.000989
ORF1ab/nsp3	1682	S1682C	tCc	tGc	5	5	All	0.000001
ORF1ab/nsp3	1682	S1682F	tCc	tTc	5	5	AM.4	0.017857
ORF1ab/nsp3	1682	S1682S	tcC	tcT	5	5	AY.23	0.000349
ORF1ab/nsp3	1682	S1682S	tcC	tcT	5	5	AY.5.4	0.001384
ORF1ab/nsp3	1682	S1682S	tcC	tcT	5	5	AY.71	0.002375
ORF1ab/nsp3	1682	S1682S	tcC	tcT	5	5	AY.78	0.007704
ORF1ab/nsp3	1682	S1682F	tCc	tTc	5	5	AY.81	0.00996
ORF1ab/nsp3	1682	S1682F	tCc	tTc	5	5	AY.9.2	0.000184
ORF1ab/nsp3	1682	S1682F	tCc	tTc	5	5	AY.92	0.001436
ORF1ab/nsp3	1682	S1682F	tCc	tTc	5	5	AY.98.1	0.000242
ORF1ab/nsp3	1682	S1682F	tCc	tTc	5	5	B.1.1.189	0.007564
ORF1ab/nsp3	1682	S1682F	tCc	tTc	5	5	B.1.1.25	0.002843
ORF1ab/nsp3	1682	S1682S	tcC	tcT	5	5	B.1.1.317	0.002058
ORF1ab/nsp3	1682	S1682S	tcC	tcT	5	5	B.1.1.70	0.001705
ORF1ab/nsp3	1682	S1682F	tCc	tTc	5	5	B.1.177.21	0.000382
ORF1ab/nsp3	1682	S1682F	tCc	tTc	5	5	B.1.247	0.074627
ORF1ab/nsp3	1682	S1682S	tcC	tcT	5	5	B.1.265	0.006353
ORF1ab/nsp3	1682	S1682S	tcC	tcT	5	5	B.1.564	0.002129
ORF1ab/nsp3	1682	S1682S	tcC	tcT	5	5	C.30	0.008636
ORF1ab/nsp3	1682	S1682F	tCc	tTc	5	5	D.2	0.000375
ORF1ab/nsp3	1682	S1682S	tcC	tcT	5	5	D.2	0.000375
ORF1ab/nsp3	1682	S1682S	tcC	tcT	5	5	P.1.12	0.00242
ORF1ab/nsp3	1682	S1682del	TCC	---	4	4		0.222222
ORF1ab/nsp3	1682	S1682S	tcC	tcT	4	4	AE.8	0.001956
ORF1ab/nsp3	1682	S1682S	tcC	tcT	4	4	AY.113	0.00057
ORF1ab/nsp3	1682	S1682S	tcC	tcT	4	4	AY.14	0.000352
ORF1ab/nsp3	1682	S1682del	TCC	---	4	4	AY.4	0.000006
ORF1ab/nsp3	1682	S1682S	tcC	tcT	4	4	AY.4.5	0.00043
ORF1ab/nsp3	1682	S1682F	tCc	tTc	4	4	AY.5.4	0.001107
ORF1ab/nsp3	1682	S1682F	tCc	tTc	4	4	AY.54	0.000381
ORF1ab/nsp3	1682	S1682S	tcC	tcT	4	4	AY.6	0.000165
ORF1ab/nsp3	1682	S1682F	tCc	tTc	4	4	AY.65	0.002132
ORF1ab/nsp3	1682	S1682S	tcC	tcT	4	4	AY.65	0.002132
ORF1ab/nsp3	1682	S1682S	tcC	tcT	4	4	AY.75.1	0.000721
ORF1ab/nsp3	1682	S1682F	tCc	tTc	4	4	AY.9.1	0.000335
ORF1ab/nsp3	1682	S1682S	tcC	tcT	4	4	AY.98.1	0.000194
ORF1ab/nsp3	1682	S1682F	tCc	tTc	4	4	B.1.1.263	0.006231
ORF1ab/nsp3	1682	S1682F	tCc	tTc	4	4	B.1.1.37	0.000771
ORF1ab/nsp3	1682	S1682S	tcC	tcT	4	4	B.1.1.420	0.004024
ORF1ab/nsp3	1682	S1682F	tCc	tTc	4	4	B.1.1.523	0.00625
ORF1ab/nsp3	1682	S1682Y	tCc	tAc	4	4	B.1.1.7	0.000004
ORF1ab/nsp3	1682	S1682del	TCC	---	4	4	B.1.177	0.000053
ORF1ab/nsp3	1682	S1682F	tCc	tTc	4	4	B.1.177.75	0.004162
ORF1ab/nsp3	1682	S1682F	tCc	tTc	4	4	B.1.311	0.001098
ORF1ab/nsp3	1682	S1682S	tcC	tcT	4	4	B.1.351.5	0.002398
ORF1ab/nsp3	1682	S1682S	tcC	tcT	4	4	B.1.425	0.011976
ORF1ab/nsp3	1682	S1682F	tCc	tTc	4	4	B.1.438.1	0.000429
ORF1ab/nsp3	1682	S1682S	tcC	tcT	4	4	B.1.443	0.018692
ORF1ab/nsp3	1682	S1682S	tcC	tcT	4	4	B.1.470	0.005618
ORF1ab/nsp3	1682	S1682S	tcC	tcT	4	4	B.1.561	0.001588
ORF1ab/nsp3	1682	S1682F	tCc	tTc	4	4	B.1.564	0.001704
ORF1ab/nsp3	1682	S1682S	tcC	tcT	4	4	B.1.587	0.00759
ORF1ab/nsp3	1682	S1682F	tCc	tTc	4	4	C.36	0.003643
ORF1ab/nsp3	1682	S1682S	tcC	tcT	4	4	P.1.17	0.000647
ORF1ab/nsp3	1682	S1682F	tCc	tTc	4	4	P.1.7	0.001277
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	A	0.001161
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	A.21	0.00831
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	A.3	0.006289
ORF1ab/nsp3	1682	S1682F	tCc	tTc	3	3	A.3	0.006289
ORF1ab/nsp3	1682	S1682del1	tCc	t-c	3	3	All	0.000001
ORF1ab/nsp3	1682	S1682F	tCc	tTc	3	3	AY.104	0.005952
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	AY.105	0.001929
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	AY.110	0.000338
ORF1ab/nsp3	1682	S1682F	tCc	tTc	3	3	AY.111	0.000549
ORF1ab/nsp3	1682	S1682F	tCc	tTc	3	3	AY.114	0.000693
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	AY.114	0.000693
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	AY.12	0.000948
ORF1ab/nsp3	1682	S1682F	tCc	tTc	3	3	AY.12	0.000948
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	AY.2	0.001068
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	AY.24	0.001293
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	AY.27	0.000194
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	AY.30	0.001187
ORF1ab/nsp3	1682	S1682F	tCc	tTc	3	3	AY.39.2	0.004622
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	AY.5.3	0.001012
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	AY.7.1	0.000338
ORF1ab/nsp3	1682	S1682S	tcC	tcA	2	3	AY.70	0.000417
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	3	AY.70	0.000209
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	AY.77	0.003382
ORF1ab/nsp3	1682	S1682F	tCc	tTc	3	3	AY.99.2	0.000276
ORF1ab/nsp3	1682	S1682F	tCc	tTc	3	3	B.1.1.216	0.002671
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	B.1.1.277	0.002276
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	B.1.1.306	0.001315
ORF1ab/nsp3	1682	S1682F	tCc	tTc	3	3	B.1.1.369	0.001339
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	B.1.111	0.003525
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	B.1.177.46	0.002755
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	B.1.177.7	0.000495
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	B.1.281	0.065217
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	B.1.346	0.003932
ORF1ab/nsp3	1682	S1682F	tCc	tTc	3	3	B.1.36.17	0.001482
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	B.1.36.29	0.001552
ORF1ab/nsp3	1682	S1682F	tCc	tTc	3	3	B.1.36.8	0.003
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	B.1.426	0.003027
ORF1ab/nsp3	1682	S1682F	tCc	tTc	3	3	B.1.456	0.009804
ORF1ab/nsp3	1682	S1682F	tCc	tTc	3	3	B.1.558	0.013699
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	B.1.609	0.001438
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	B.1.617.1	0.000387
ORF1ab/nsp3	1682	S1682F	tCc	tTc	3	3	B.1.623	0.001609
ORF1ab/nsp3	1682	S1682S	tcC	tcT	3	3	C.1	0.007177
ORF1ab/nsp3	1682	S1682F	tCc	tTc	3	3	P.1.15	0.000697
ORF1ab/nsp3	1682	S1682C	tCc	tGc	2	2		0.111111
ORF1ab/nsp3	1682	S1682G	TCc	GGc	2	2		0.111111
ORF1ab/nsp3	1682	S1682S	tcC	tcA	1	2	A.2.4	0.003367
ORF1ab/nsp3	1682	S1682S	tcC	tcG	1	2	A.2.4	0.003367
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	A.2.5	0.000998
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	A.2.5	0.000998
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	A.2.5.2	0.003145
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	A.23.1	0.001408
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	A.23.1	0.001408
ORF1ab/nsp3	1682	S1682V	TCc	GTc	2	2	All	0
ORF1ab/nsp3	1682	S1682G	TCc	GGc	2	2	All	0
ORF1ab/nsp3	1682	S1682L	TCC	CTG	1	2	All	0
ORF1ab/nsp3	1682	S1682L	TCc	CTc	1	2	All	0
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	AS.1	0.019048
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	AY.105	0.001286
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	AY.108	0.002205
ORF1ab/nsp3	1682	S1682del	TCC	---	2	2	AY.111	0.000366
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	AY.116	0.000574
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	AY.16	0.000759
ORF1ab/nsp3	1682	S1682del	TCC	---	2	2	AY.19	0.002281
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	2	AY.32	0.000532
ORF1ab/nsp3	1682	S1682S	tcC	tcG	1	2	AY.32	0.000532
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	AY.35	0.000466
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	AY.37	0.000632
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	AY.38	0.000999
ORF1ab/nsp3	1682	S1682A	Tcc	Gcc	2	2	AY.39	0.000049
ORF1ab/nsp3	1682	S1682Y	tCc	tAc	2	2	AY.43	0.000009
ORF1ab/nsp3	1682	S1682del	TCC	---	2	2	AY.46.2	0.001271
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	AY.5.3	0.000675
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	AY.58	0.001815
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	AY.6	0.000082
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	AY.62	0.000871
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	AY.68	0.000547
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	AY.71	0.00095
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	AY.74	0.000231
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	AY.91	0.001461
ORF1ab/nsp3	1682	S1682Y	tCc	tAc	2	2	B.1	0.000018
ORF1ab/nsp3	1682	S1682del	TCC	---	2	2	B.1	0.000018
ORF1ab/nsp3	1682	S1682Y	tCc	tAc	2	2	B.1.1	0.000036
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.1.1	0.000653
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.1.141	0.004024
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.1.207	0.002364
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.1.232	0.00363
ORF1ab/nsp3	1682	S1682del	TCC	---	2	2	B.1.1.236	0.013793
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.1.240	0.00939
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.1.284	0.000215
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.1.304	0.005618
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.1.311	0.000716
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.1.316	0.00185
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.1.33	0.000842
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.1.334	0.032787
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.1.348	0.001592
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.1.348	0.001592
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.1.372	0.001377
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	2	B.1.1.409	0.002833
ORF1ab/nsp3	1682	S1682S	tcC	tcA	1	2	B.1.1.409	0.002833
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.1.420	0.002012
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.1.486	0.003155
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.1.518	0.012658
ORF1ab/nsp3	1682	S1682A	Tcc	Gcc	2	2	B.1.1.7	0.000002
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.126	0.002551
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.127	0.004396
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.177.15	0.001262
ORF1ab/nsp3	1682	S1682del	TCC	---	2	2	B.1.177.21	0.000153
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.177.35	0.001382
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.177.52	0.003515
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.177.52	0.003515
ORF1ab/nsp3	1682	S1682del	TCC	---	2	2	B.1.177.6	0.001953
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.177.69	0.002967
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.177.73	0.001133
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.177.82	0.000955
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.177.9	0.002663
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.179	0.007519
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.192	0.018519
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.214.2	0.001199
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	2	B.1.232	0.000537
ORF1ab/nsp3	1682	S1682F	tCC	tTT	1	2	B.1.232	0.000537
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.234	0.000264
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.240	0.000431
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.241	0.001623
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.241	0.001623
ORF1ab/nsp3	1682	S1682del	TCC	---	2	2	B.1.258	0.000133
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.281	0.043478
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.324	0.00321
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.324	0.00321
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.336	0.004878
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.337	0.011173
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.350	0.005865
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.36.29	0.001035
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.398	0.005952
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.400	0.000858
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.404	0.002604
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.415.1	0.015152
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.422	0.001625
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.517	0.000854
ORF1ab/nsp3	1682	S1682V	TCc	GTc	2	2	B.1.525	0.000226
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.533	0.019231
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.565	0.001621
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	B.1.609	0.000959
ORF1ab/nsp3	1682	S1682A	Tcc	Gcc	2	2	B.1.617.2	0.000008
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.623	0.001073
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.628	0.000705
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.1.8	0.003945
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	B.40	0.000729
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	C.32	0.046512
ORF1ab/nsp3	1682	S1682F	tCc	tTc	2	2	C.35	0.001548
ORF1ab/nsp3	1682	S1682P	Tcc	Ccc	2	2	D.2	0.00015
ORF1ab/nsp3	1682	S1682S	tcC	tcT	2	2	P.1.4	0.001953
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	A	0.000387
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	A	0.000387
ORF1ab/nsp3	1682	S1682Y	tCc	tAc	1	1	A.1	0.000282
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	A.1	0.000282
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	A.11	0.058824
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	A.2.2	0.001689
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	A.21	0.00277
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	A.23	0.010526
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AD.2	0.000219
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AE.5	0.018519
ORF1ab/nsp3	1682	S1682X	tCC	tAA	1	1	All	0
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AN.1	0.02
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AU.1	0.001266
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AV.1	0.005051
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AW.1	0.003049
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.1	0.000396
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.101	0.00049
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.101	0.00049
ORF1ab/nsp3	1682	S1682Y	tCc	tAc	1	1	AY.102	0.000027
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.107	0.000466
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.108	0.001103
ORF1ab/nsp3	1682	S1682T	Tcc	Acc	1	1	AY.114	0.000231
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.116	0.000287
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	AY.120	0.000037
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.120.2	0.001285
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.13	0.000161
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.14	0.000088
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.16.1	0.00047
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.16.1	0.00047
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.23.1	0.000417
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	AY.25	0.000006
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.27	0.000065
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.28	0.00189
ORF1ab/nsp3	1682	S1682P	Tcc	Ccc	1	1	AY.3	0.00001
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.32	0.000532
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	AY.33	0.000067
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.36	0.000148
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.37	0.000316
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.38	0.000499
ORF1ab/nsp3	1682	S1682A	Tcc	Gcc	1	1	AY.4	0.000002
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.4.1	0.000737
ORF1ab/nsp3	1682	S1682Y	tCc	tAc	1	1	AY.4.2	0.000022
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.4.2.1	0.000149
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.4.4	0.000409
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	AY.4.5	0.000107
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.40	0.000964
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.40	0.000964
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.41	0.000294
ORF1ab/nsp3	1682	S1682A	Tcc	Gcc	1	1	AY.43	0.000004
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	AY.43	0.000004
ORF1ab/nsp3	1682	S1682Y	tCc	tAc	1	1	AY.44	0.000006
ORF1ab/nsp3	1682	S1682P	Tcc	Ccc	1	1	AY.44	0.000006
ORF1ab/nsp3	1682	S1682T	Tcc	Acc	1	1	AY.44	0.000006
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	AY.44	0.000006
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.46	0.000104
ORF1ab/nsp3	1682	S1682Y	tCc	tAc	1	1	AY.46	0.000104
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.46.1	0.001027
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.46.4	0.000165
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.46.5	0.000198
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.48	0.000465
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	AY.5	0.000021
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	AY.52	0.000814
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.52	0.000814
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.53	0.000288
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.53	0.000288
ORF1ab/nsp3	1682	S1682T	Tcc	Acc	1	1	AY.54	0.000095
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.56	0.001605
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.57	0.000656
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.58	0.000907
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.59	0.00053
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	AY.6	0.000041
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.60	0.000938
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.62	0.000436
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.63	0.000387
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.67	0.000464
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.68	0.000274
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.69	0.000187
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.69	0.000187
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.73	0.000665
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.74	0.000116
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.79	0.001211
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	AY.81	0.001992
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.82	0.001357
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.84	0.000437
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.84	0.000437
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	AY.84	0.000437
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.86	0.00083
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.88	0.000884
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.9	0.000068
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	AY.9	0.000068
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.93	0.000273
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	AY.93	0.000273
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AY.94	0.000443
ORF1ab/nsp3	1682	S1682del1	tCc	t-c	1	1	AY.98	0.000079
ORF1ab/nsp3	1682	S1682C	tCc	tGc	1	1	AY.98	0.000079
ORF1ab/nsp3	1682	S1682L	TCc	CTc	1	1	AY.99	0.001049
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	AZ.2	0.000821
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B	0.000128
ORF1ab/nsp3	1682	S1682P	Tcc	Ccc	1	1	B	0.000128
ORF1ab/nsp3	1682	S1682del1	tCc	t-c	1	1	B.1	0.000009
ORF1ab/nsp3	1682	S1682L	TCC	CTG	1	1	B.1.1	0.000018
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.1	0.000327
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.121	0.002427
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.129	0.009174
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.1.133	0.008475
ORF1ab/nsp3	1682	S1682T	Tcc	Acc	1	1	B.1.1.135	0.004695
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	B.1.1.170	0.001247
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.1.174	0.003378
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.176	0.000439
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.1.176	0.000439
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.182	0.090909
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.189	0.001513
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.194	0.00495
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.198	0.001468
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.1.207	0.001182
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.222	0.000204
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.232	0.001815
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.1.241	0.00207
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.1.256	0.013699
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.1.294	0.001266
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.302	0.002075
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.1.303	0.002762
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.304	0.002809
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.1.312	0.001912
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.1.33	0.000421
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.336	0.016667
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.354	0.004386
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.362	0.005618
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.37	0.000193
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.376	0.005952
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.388	0.045455
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.39	0.00051
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.1.391	0.008547
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.400	0.05
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.1.402	0.011111
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.448	0.002033
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.1.46	0.004367
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	B.1.1.46	0.004367
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.462	0.008621
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.1.486	0.001577
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.1.50	0.000679
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.1.518	0.006329
ORF1ab/nsp3	1682	S1682T	Tcc	Acc	1	1	B.1.1.53	0.013699
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.1.63	0.000386
ORF1ab/nsp3	1682	S1682X	tCC	tAA	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1682	S1682P	Tcc	Ccc	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1682	S1682T	Tcc	Acc	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.1.70	0.000341
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.1.8	0.003584
ORF1ab/nsp3	1682	S1682S	tcC	tcA	1	1	B.1.1.83	0.00271
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.103	0.019231
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.104	0.00369
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.110.3	0.000718
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.111	0.001175
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.128	0.000635
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.131	0.008772
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.143	0.021277
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.147	0.000756
ORF1ab/nsp3	1682	S1682A	TcC	GcT	1	1	B.1.157	0.002985
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.160.23	0.004831
ORF1ab/nsp3	1682	S1682S	tcC	tcA	1	1	B.1.160.28	0.002924
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.160.29	0.004219
ORF1ab/nsp3	1682	S1682C	tCc	tGc	1	1	B.1.177	0.000013
ORF1ab/nsp3	1682	S1682P	Tcc	Ccc	1	1	B.1.177	0.000013
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.177.10	0.000878
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.177.12	0.000152
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.177.12	0.000152
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.177.15	0.000631
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.177.16	0.000664
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	B.1.177.18	0.00116
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.177.19	0.001431
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.177.2	0.004545
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.177.23	0.003236
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.177.38	0.010417
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	B.1.177.4	0.000211
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.177.44	0.000519
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.177.44	0.000519
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.177.49	0.037037
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	B.1.177.54	0.000606
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	B.1.177.57	0.000281
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.177.58	0.001332
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.177.68	0.015152
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	B.1.177.7	0.000165
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.177.72	0.00339
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.177.73	0.000566
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.177.75	0.001041
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.177.77	0.000726
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	B.1.179	0.003759
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.189	0.004292
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.192	0.009259
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.199	0.004132
ORF1ab/nsp3	1682	S1682T	Tcc	Acc	1	1	B.1.2	0.000009
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.214	0.003663
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.214.1	0.02
ORF1ab/nsp3	1682	S1682Y	tCc	tAc	1	1	B.1.221	0.000071
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.223	0.002778
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.240.2	0.030303
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	B.1.258.10	0.011364
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.258.11	0.000396
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.258.11	0.000396
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.258.22	0.002667
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.258.3	0.001675
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.265	0.001271
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.279	0.000514
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.279	0.000514
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.284	0.013158
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.306	0.005714
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.320	0.001245
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.329	0.000608
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.338	0.008621
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	B.1.36	0.000146
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.36.12	0.009615
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.36.36	0.000602
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.36.36	0.000602
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.36.39	0.002217
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.361	0.001289
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.366	0.004878
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.371	0.001122
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.377	0.004566
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.388	0.090909
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.389	0.001002
ORF1ab/nsp3	1682	S1682P	Tcc	Ccc	1	1	B.1.396	0.000706
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.403	0.003268
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	B.1.409	0.000781
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.416	0.001269
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	B.1.416.1	0.001563
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.420	0.010417
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.422	0.000812
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.428	0.00102
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.436	0.001029
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.441	0.009615
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.453	0.003236
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.462	0.007246
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.465	0.003802
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.468	0.005714
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.469	0.00361
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.497	0.000315
ORF1ab/nsp3	1682	S1682P	Tcc	Ccc	1	1	B.1.497	0.000315
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.499	0.00105
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	B.1.501	0.007353
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.510	0.026316
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.524	0.001406
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.533	0.009615
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.541	0.004425
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.551	0.00129
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	B.1.561	0.000397
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.576	0.000907
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.576	0.000907
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.582	0.000491
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.589	0.007576
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.595	0.000261
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.595.1	0.005848
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	B.1.596	0.000087
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.597	0.00463
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.1.603	0.010638
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	B.1.606	0.006024
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.610	0.003546
ORF1ab/nsp3	1682	S1682del1	tCc	t-c	1	1	B.1.617.1	0.000129
ORF1ab/nsp3	1682	S1682Y	tCc	tAc	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1682	S1682C	tCc	tGc	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.618	0.004032
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.628	0.000352
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.1.81	0.021277
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.10	0.008264
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.3	0.000831
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.3.1	0.001658
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.39	0.002331
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.4	0.002208
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.4.4	0.018868
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	B.4.4	0.018868
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.55	0.00295
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	B.6	0.00091
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	B.6	0.00091
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	C.1	0.002392
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	C.12	0.007194
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	C.14	0.004329
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	C.16	0.00106
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	C.17	0.055556
ORF1ab/nsp3	1682	S1682F	tCC	tTT	1	1	C.30	0.001727
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	C.35	0.000774
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	G.1	0.041667
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	L.3	0.003546
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	M.1	0.023256
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	N.5	0.001767
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	N.9	0.005952
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	P.1	0.000016
ORF1ab/nsp3	1682	S1682T	Tcc	Acc	1	1	P.1	0.000016
ORF1ab/nsp3	1682	S1682del	TCC	---	1	1	P.1.1	0.000318
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	P.1.1	0.000318
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	P.1.11	0.010204
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	P.1.17	0.000162
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	P.5	0.013699
ORF1ab/nsp3	1682	S1682F	tCc	tTc	1	1	Q.2	0.000613
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	Q.6	0.006623
ORF1ab/nsp3	1682	S1682S	tcC	tcA	1	1	W.1	0.008696
ORF1ab/nsp3	1682	S1682S	tcC	tcT	1	1	W.4	0.001351

CoV-GLUE is still in development. CoV-GLUE was originally developed as part of COG-UK by Josh Singer using the GLUE framework at the MRC-University of Glasgow Centre for Virus Research (CVR). In 2021 it was redeveloped by Richard Orton to scale to the millions of genome sequences available. We acknowledge support from the MRC (MC_UU_12014/12), WT (220977/Z/20/Z) and UKRI G2P (MR/W005611/1). Please contact Richard Orton with any queries: Richard.Orton@glasgow.ac.uk

CoV-GLUE uses sequence data from GISAID. GISAID data provided via this web application is subject to GISAID's Terms and Conditions.