CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF7a : CodonNum = 54

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
ORF7a	54	F54del		del	TTT	---	11222	11222	1	27553-27555
ORF7a	54	F54del1		del	ttT	tt-	4050	3468	0.856296	27553-27555
ORF7a	54	F54del1		del	Ttt	-tt	4050	575	0.141975	27553-27555
ORF7a	54	F54del1		del	TTT	CC-	4050	3	0.000740741	27553-27555
ORF7a	54	F54del1		del	TtT	-tN	4050	3	0.000740741	27553-27555
ORF7a	54	F54del1		del	TTT	-NN	4050	1	0.000246914	27553-27555
ORF7a	54	F54L		nonsyn	ttT	ttA	2492	2000	0.802568	27553-27555
ORF7a	54	F54L		nonsyn	Ttt	Ctt	2492	344	0.138042	27553-27555
ORF7a	54	F54L		nonsyn	ttT	ttG	2492	145	0.0581862	27553-27555
ORF7a	54	F54L		nonsyn	TtT	CtG	2492	2	0.000802568	27553-27555
ORF7a	54	F54L		nonsyn	TtT	CtC	2492	1	0.000401284	27553-27555
ORF7a	54	F54del2		del	tTT	t--	2175	1187	0.545747	27553-27555
ORF7a	54	F54del2		del	TTt	--t	2175	985	0.452874	27553-27555
ORF7a	54	F54del2		del	TTT	--N	2175	3	0.00137931	27553-27555
ORF7a	54	F54F		syn	ttT	ttC	471	471	1	27553-27555
ORF7a	54	F54C		nonsyn	tTt	tGt	316	313	0.990506	27553-27555
ORF7a	54	F54C		nonsyn	tTT	tGC	316	3	0.00949367	27553-27555
ORF7a	54	F54S		nonsyn	tTt	tCt	175	160	0.914286	27553-27555
ORF7a	54	F54S		nonsyn	TTt	AGt	175	11	0.0628571	27553-27555
ORF7a	54	F54S		nonsyn	tTT	tCA	175	3	0.0171429	27553-27555
ORF7a	54	F54S		nonsyn	TTT	AGC	175	1	0.00571429	27553-27555
ORF7a	54	F54I		nonsyn	Ttt	Att	77	69	0.896104	27553-27555
ORF7a	54	F54I		nonsyn	TtT	AtA	77	7	0.0909091	27553-27555
ORF7a	54	F54I		nonsyn	TtT	AtC	77	1	0.012987	27553-27555
ORF7a	54	F54V		nonsyn	Ttt	Gtt	60	54	0.9	27553-27555
ORF7a	54	F54V		nonsyn	TtT	GtA	60	4	0.0666667	27553-27555
ORF7a	54	F54V		nonsyn	TtT	GtC	60	1	0.0166667	27553-27555
ORF7a	54	F54V		nonsyn	TtT	GtG	60	1	0.0166667	27553-27555
ORF7a	54	F54G		nonsyn	TTt	GGt	28	21	0.75	27553-27555
ORF7a	54	F54G		nonsyn	TTT	GGA	28	5	0.178571	27553-27555
ORF7a	54	F54G		nonsyn	TTT	GGG	28	2	0.0714286	27553-27555
ORF7a	54	F54Y		nonsyn	tTt	tAt	18	16	0.888889	27553-27555
ORF7a	54	F54Y		nonsyn	tTT	tAC	18	2	0.111111	27553-27555
ORF7a	54	F54X		nonsyn	tTT	tAA	16	6	0.375	27553-27555
ORF7a	54	F54X		nonsyn	tTT	tGA	16	6	0.375	27553-27555
ORF7a	54	F54X		nonsyn	tTT	tAG	16	4	0.25	27553-27555
ORF7a	54	F54N		nonsyn	TTt	AAt	15	14	0.933333	27553-27555
ORF7a	54	F54R		nonsyn	TTT	AGA	15	7	0.466667	27553-27555
ORF7a	54	F54R		nonsyn	TTT	AGG	15	5	0.333333	27553-27555
ORF7a	54	F54R		nonsyn	TTt	CGt	15	3	0.2	27553-27555
ORF7a	54	F54N		nonsyn	TTT	AAC	15	1	0.0666667	27553-27555
ORF7a	54	F54K		nonsyn	TTT	AAA	9	5	0.555556	27553-27555
ORF7a	54	F54K		nonsyn	TTT	AAG	9	4	0.444444	27553-27555
ORF7a	54	F54H		nonsyn	TTt	CAt	7	7	1	27553-27555
ORF7a	54	F54W		nonsyn	tTT	tGG	4	4	1	27553-27555
ORF7a	54	F54D		nonsyn	TTt	GAt	3	3	1	27553-27555
ORF7a	54	F54M		nonsyn	TtT	AtG	3	3	1	27553-27555
ORF7a	54	F54E		nonsyn	TTT	GAA	3	2	0.666667	27553-27555
ORF7a	54	F54T		nonsyn	TTt	ACt	3	2	0.666667	27553-27555
ORF7a	54	F54E		nonsyn	TTT	GAG	3	1	0.333333	27553-27555
ORF7a	54	F54T		nonsyn	TTT	ACA	3	1	0.333333	27553-27555
ORF7a	54	F54P		nonsyn	TTt	CCt	2	2	1	27553-27555
ORF7a	54	F54A		nonsyn	TTt	GCt	2	1	0.5	27553-27555
ORF7a	54	F54A		nonsyn	TTT	GCA	2	1	0.5	27553-27555

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
ORF7a	54	F54del	TTT	---	11222	11222	All	0.002146
ORF7a	54	F54del1	ttT	tt-	3468	4050	All	0.000663
ORF7a	54	F54del1	Ttt	-tt	575	4050	All	0.00011
ORF7a	54	F54del1	TtT	-tN	3	4050	All	0.000001
ORF7a	54	F54del1	TTT	CC-	3	4050	All	0.000001
ORF7a	54	F54del1	TTT	-NN	1	4050	All	0
ORF7a	54	F54L	ttT	ttA	2000	2492	All	0.000383
ORF7a	54	F54L	Ttt	Ctt	344	2492	All	0.000066
ORF7a	54	F54L	ttT	ttG	145	2492	All	0.000028
ORF7a	54	F54L	TtT	CtG	2	2492	All	0
ORF7a	54	F54L	TtT	CtC	1	2492	All	0
ORF7a	54	F54del	TTT	---	2243	2243	B.1.617.2	0.008446
ORF7a	54	F54del2	tTT	t--	1187	2175	All	0.000227
ORF7a	54	F54del2	TTt	--t	985	2175	All	0.000188
ORF7a	54	F54del2	TTT	--N	3	2175	All	0.000001
ORF7a	54	F54del	TTT	---	1623	1623	AY.120.1	0.521027
ORF7a	54	F54del1	ttT	tt-	1248	1409	AY.4	0.001942
ORF7a	54	F54del1	Ttt	-tt	161	1409	AY.4	0.000251
ORF7a	54	F54del	TTT	---	1186	1186	AY.4	0.001846
ORF7a	54	F54del2	tTT	t--	817	966	AY.4	0.001272
ORF7a	54	F54del2	TTt	--t	149	966	AY.4	0.000232
ORF7a	54	F54del	TTT	---	802	802	B.1.1.7	0.000718
ORF7a	54	F54del	TTT	---	694	694	AY.43	0.003075
ORF7a	54	F54del	TTT	---	661	661	AY.25	0.003976
ORF7a	54	F54L	ttT	ttA	497	534	AY.4	0.000774
ORF7a	54	F54L	ttT	ttG	24	534	AY.4	0.000037
ORF7a	54	F54L	Ttt	Ctt	13	534	AY.4	0.00002
ORF7a	54	F54del1	ttT	tt-	324	519	AY.25	0.001949
ORF7a	54	F54del1	Ttt	-tt	195	519	AY.25	0.001173
ORF7a	54	F54F	ttT	ttC	471	471	All	0.00009
ORF7a	54	F54L	ttT	ttA	399	463	B.1.1.7	0.000357
ORF7a	54	F54L	Ttt	Ctt	51	463	B.1.1.7	0.000046
ORF7a	54	F54L	ttT	ttG	12	463	B.1.1.7	0.000011
ORF7a	54	F54L	TtT	CtG	1	463	B.1.1.7	0.000001
ORF7a	54	F54del1	ttT	tt-	386	397	B.1.1.7	0.000346
ORF7a	54	F54del1	Ttt	-tt	11	397	B.1.1.7	0.00001
ORF7a	54	F54del	TTT	---	346	346	AY.103	0.002148
ORF7a	54	F54C	tTt	tGt	313	316	All	0.00006
ORF7a	54	F54C	tTT	tGC	3	316	All	0.000001
ORF7a	54	F54del1	ttT	tt-	276	278	AY.26	0.007814
ORF7a	54	F54del1	Ttt	-tt	2	278	AY.26	0.000057
ORF7a	54	F54del1	ttT	tt-	232	240	AY.43	0.001028
ORF7a	54	F54del1	Ttt	-tt	7	240	AY.43	0.000031
ORF7a	54	F54del1	TTT	-NN	1	240	AY.43	0.000004
ORF7a	54	F54del	TTT	---	237	237	AY.102	0.006284
ORF7a	54	F54del	TTT	---	224	224	AY.3	0.002228
ORF7a	54	F54del	TTT	---	217	217	AY.44	0.001321
ORF7a	54	F54del2	TTt	--t	202	213	AY.44	0.00123
ORF7a	54	F54del2	tTT	t--	11	213	AY.44	0.000067
ORF7a	54	F54del	TTT	---	187	187	AY.100	0.008603
ORF7a	54	F54del	TTT	---	184	184	B.1.351	0.00547
ORF7a	54	F54del	TTT	---	181	181	B.1.177.21	0.013841
ORF7a	54	F54S	tTt	tCt	160	175	All	0.000031
ORF7a	54	F54S	TTt	AGt	11	175	All	0.000002
ORF7a	54	F54S	tTT	tCA	3	175	All	0.000001
ORF7a	54	F54S	TTT	AGC	1	175	All	0
ORF7a	54	F54del2	TTt	--t	167	174	AY.43	0.00074
ORF7a	54	F54del2	tTT	t--	7	174	AY.43	0.000031
ORF7a	54	F54F	ttT	ttC	162	162	AY.26	0.004586
ORF7a	54	F54del	TTT	---	160	160	AY.39	0.003954
ORF7a	54	F54L	ttT	ttA	146	157	B.1.617.2	0.00055
ORF7a	54	F54L	Ttt	Ctt	11	157	B.1.617.2	0.000041
ORF7a	54	F54L	ttT	ttA	122	136	AY.25	0.000734
ORF7a	54	F54L	ttT	ttG	12	136	AY.25	0.000072
ORF7a	54	F54L	Ttt	Ctt	2	136	AY.25	0.000012
ORF7a	54	F54C	tTt	tGt	133	133	AY.4	0.000207
ORF7a	54	F54del	TTT	---	131	131	AY.29	0.002066
ORF7a	54	F54del1	ttT	tt-	108	124	AY.103	0.000671
ORF7a	54	F54del1	Ttt	-tt	16	124	AY.103	0.000099
ORF7a	54	F54del	TTT	---	124	124	AY.120	0.00461
ORF7a	54	F54del1	ttT	tt-	92	123	B.1.617.2	0.000346
ORF7a	54	F54del1	Ttt	-tt	30	123	B.1.617.2	0.000113
ORF7a	54	F54del1	TtT	-tN	1	123	B.1.617.2	0.000004
ORF7a	54	F54C	tTt	tGt	116	116	AY.47	0.003608
ORF7a	54	F54del1	ttT	tt-	110	114	AY.39	0.002718
ORF7a	54	F54del1	Ttt	-tt	3	114	AY.39	0.000074
ORF7a	54	F54del1	TtT	-tN	1	114	AY.39	0.000025
ORF7a	54	F54del2	TTt	--t	56	108	AY.103	0.000348
ORF7a	54	F54del2	tTT	t--	52	108	AY.103	0.000323
ORF7a	54	F54del	TTT	---	108	108	AY.26	0.003057
ORF7a	54	F54del1	ttT	tt-	103	106	AY.29	0.001625
ORF7a	54	F54del1	Ttt	-tt	3	106	AY.29	0.000047
ORF7a	54	F54del	TTT	---	104	104	AY.7.1	0.011721
ORF7a	54	F54L	ttT	ttA	96	101	AY.103	0.000596
ORF7a	54	F54L	Ttt	Ctt	3	101	AY.103	0.000019
ORF7a	54	F54L	ttT	ttG	2	101	AY.103	0.000012
ORF7a	54	F54del2	TTt	--t	71	98	B.1.617.2	0.000267
ORF7a	54	F54del2	tTT	t--	26	98	B.1.617.2	0.000098
ORF7a	54	F54del2	TTT	--N	1	98	B.1.617.2	0.000004
ORF7a	54	F54L	Ttt	Ctt	89	97	AY.47	0.002768
ORF7a	54	F54L	ttT	ttA	8	97	AY.47	0.000249
ORF7a	54	F54del1	ttT	tt-	61	90	AY.44	0.000371
ORF7a	54	F54del1	Ttt	-tt	28	90	AY.44	0.00017
ORF7a	54	F54del1	TtT	-tN	1	90	AY.44	0.000006
ORF7a	54	F54del1	ttT	tt-	71	81	AY.3	0.000706
ORF7a	54	F54del1	Ttt	-tt	10	81	AY.3	0.000099
ORF7a	54	F54I	Ttt	Att	69	77	All	0.000013
ORF7a	54	F54I	TtT	AtA	7	77	All	0.000001
ORF7a	54	F54I	TtT	AtC	1	77	All	0
ORF7a	54	F54del2	TTt	--t	48	74	AY.3	0.000477
ORF7a	54	F54del2	tTT	t--	26	74	AY.3	0.000259
ORF7a	54	F54del2	TTt	--t	56	72	AY.25	0.000337
ORF7a	54	F54del2	tTT	t--	16	72	AY.25	0.000096
ORF7a	54	F54L	ttT	ttA	50	72	AY.43	0.000222
ORF7a	54	F54L	Ttt	Ctt	18	72	AY.43	0.00008
ORF7a	54	F54L	ttT	ttG	3	72	AY.43	0.000013
ORF7a	54	F54L	TtT	CtC	1	72	AY.43	0.000004
ORF7a	54	F54del	TTT	---	71	71	AY.46.4	0.01168
ORF7a	54	F54del	TTT	---	70	70	AY.119	0.002472
ORF7a	54	F54L	ttT	ttA	50	67	AY.44	0.000304
ORF7a	54	F54L	Ttt	Ctt	16	67	AY.44	0.000097
ORF7a	54	F54L	ttT	ttG	1	67	AY.44	0.000006
ORF7a	54	F54L	ttT	ttA	65	65	AY.102	0.001723
ORF7a	54	F54del1	ttT	tt-	61	65	AY.4.2	0.001323
ORF7a	54	F54del1	Ttt	-tt	4	65	AY.4.2	0.000087
ORF7a	54	F54F	ttT	ttC	64	64	AY.4	0.0001
ORF7a	54	F54V	Ttt	Gtt	54	60	All	0.00001
ORF7a	54	F54V	TtT	GtA	4	60	All	0.000001
ORF7a	54	F54V	TtT	GtG	1	60	All	0
ORF7a	54	F54V	TtT	GtC	1	60	All	0
ORF7a	54	F54del2	tTT	t--	56	57	AY.4.2	0.001215
ORF7a	54	F54del2	TTt	--t	1	57	AY.4.2	0.000022
ORF7a	54	F54S	tTt	tCt	55	55	AY.120	0.002045
ORF7a	54	F54L	ttT	ttA	53	54	AY.39.1	0.0021
ORF7a	54	F54L	ttT	ttG	1	54	AY.39.1	0.00004
ORF7a	54	F54del	TTT	---	53	53	B.1.2	0.000467
ORF7a	54	F54L	ttT	ttG	34	51	AY.113	0.004841
ORF7a	54	F54L	Ttt	Ctt	15	51	AY.113	0.002136
ORF7a	54	F54L	ttT	ttA	2	51	AY.113	0.000285
ORF7a	54	F54F	ttT	ttC	51	51	B.1.177	0.000672
ORF7a	54	F54del	TTT	---	49	49	AY.75	0.002745
ORF7a	54	F54del2	tTT	t--	36	49	B.1.177	0.000474
ORF7a	54	F54del2	TTt	--t	13	49	B.1.177	0.000171
ORF7a	54	F54del	TTT	---	48	48	AY.47	0.001493
ORF7a	54	F54del	TTT	---	47	47	B.1.177	0.000619
ORF7a	54	F54del	TTT	---	46	46	B.1	0.000421
ORF7a	54	F54del	TTT	---	44	44	AY.117	0.003719
ORF7a	54	F54del	TTT	---	44	44	B.1.1.284	0.004726
ORF7a	54	F54C	tTt	tGt	43	43	AY.120	0.001599
ORF7a	54	F54del	TTT	---	43	43	AY.3.1	0.003666
ORF7a	54	F54L	ttT	ttA	38	40	AY.13	0.006117
ORF7a	54	F54L	Ttt	Ctt	2	40	AY.13	0.000322
ORF7a	54	F54L	ttT	ttA	37	39	B.1.351	0.0011
ORF7a	54	F54L	ttT	ttG	1	39	B.1.351	0.00003
ORF7a	54	F54L	Ttt	Ctt	1	39	B.1.351	0.00003
ORF7a	54	F54del	TTT	---	38	38	AY.46	0.003955
ORF7a	54	F54del2	TTt	--t	37	37	AY.118	0.002318
ORF7a	54	F54del2	tTT	t--	24	37	B.1.1.7	0.000021
ORF7a	54	F54del2	TTt	--t	12	37	B.1.1.7	0.000011
ORF7a	54	F54del2	TTT	--N	1	37	B.1.1.7	0.000001
ORF7a	54	F54del	TTT	---	37	37	B.1.621	0.003275
ORF7a	54	F54del	TTT	---	36	36	AY.42	0.001448
ORF7a	54	F54F	ttT	ttC	36	36	AY.43	0.000159
ORF7a	54	F54del	TTT	---	36	36	AY.54	0.003432
ORF7a	54	F54del	TTT	---	36	36	B.1.526	0.000846
ORF7a	54	F54del	TTT	---	35	35	AY.118	0.002193
ORF7a	54	F54del2	TTt	--t	33	33	AY.109	0.024408
ORF7a	54	F54L	ttT	ttA	25	32	AY.3	0.000249
ORF7a	54	F54L	ttT	ttG	5	32	AY.3	0.00005
ORF7a	54	F54L	Ttt	Ctt	2	32	AY.3	0.00002
ORF7a	54	F54del1	Ttt	-tt	30	32	AY.7	0.00588
ORF7a	54	F54del1	ttT	tt-	2	32	AY.7	0.000392
ORF7a	54	F54del	TTT	---	31	31	AY.23	0.002162
ORF7a	54	F54L	ttT	ttA	25	31	AY.33	0.001669
ORF7a	54	F54L	ttT	ttG	4	31	AY.33	0.000267
ORF7a	54	F54L	Ttt	Ctt	2	31	AY.33	0.000134
ORF7a	54	F54del	TTT	---	30	30	AY.5	0.000619
ORF7a	54	F54del	TTT	---	30	30	AY.6	0.001234
ORF7a	54	F54L	ttT	ttA	27	29	AY.26	0.000764
ORF7a	54	F54L	ttT	ttG	1	29	AY.26	0.000028
ORF7a	54	F54L	Ttt	Ctt	1	29	AY.26	0.000028
ORF7a	54	F54del	TTT	---	29	29	P.1	0.000457
ORF7a	54	F54G	TTt	GGt	21	28	All	0.000004
ORF7a	54	F54G	TTT	GGA	5	28	All	0.000001
ORF7a	54	F54G	TTT	GGG	2	28	All	0
ORF7a	54	F54del1	Ttt	-tt	18	28	AY.100	0.000828
ORF7a	54	F54del1	ttT	tt-	10	28	AY.100	0.00046
ORF7a	54	F54del2	tTT	t--	28	28	AY.60	0.026266
ORF7a	54	F54F	ttT	ttC	28	28	B.1.617.2	0.000105
ORF7a	54	F54del1	ttT	tt-	27	27	AY.46.6	0.00195
ORF7a	54	F54del	TTT	---	27	27	AY.46.6	0.00195
ORF7a	54	F54del	TTT	---	26	26	AY.33	0.001736
ORF7a	54	F54del1	Ttt	-tt	21	25	AY.39.1	0.000832
ORF7a	54	F54del1	ttT	tt-	4	25	AY.39.1	0.000158
ORF7a	54	F54del	TTT	---	25	25	B.1.1.214	0.001386
ORF7a	54	F54del1	ttT	tt-	24	24	AY.107	0.011184
ORF7a	54	F54del1	ttT	tt-	24	24	AY.120	0.000892
ORF7a	54	F54del	TTT	---	24	24	B.1.234	0.003167
ORF7a	54	F54del	TTT	---	23	23	AY.107	0.010718
ORF7a	54	F54L	Ttt	Ctt	20	23	AY.27	0.001294
ORF7a	54	F54L	ttT	ttA	3	23	AY.27	0.000194
ORF7a	54	F54del	TTT	---	23	23	AY.4.2	0.000499
ORF7a	54	F54del1	ttT	tt-	19	23	AY.47	0.000591
ORF7a	54	F54del1	Ttt	-tt	4	23	AY.47	0.000124
ORF7a	54	F54del2	TTt	--t	17	22	AY.26	0.000481
ORF7a	54	F54del2	tTT	t--	5	22	AY.26	0.000142
ORF7a	54	F54del1	ttT	tt-	15	22	AY.5	0.00031
ORF7a	54	F54del1	Ttt	-tt	7	22	AY.5	0.000145
ORF7a	54	F54L	Ttt	Ctt	22	22	AY.51	0.02
ORF7a	54	F54F	ttT	ttC	22	22	B.1.1.7	0.00002
ORF7a	54	F54S	tTt	tCt	15	22	B.1.617.2	0.000056
ORF7a	54	F54S	TTt	AGt	6	22	B.1.617.2	0.000023
ORF7a	54	F54S	tTT	tCA	1	22	B.1.617.2	0.000004
ORF7a	54	F54del	TTT	---	21	21	AY.7.2	0.011745
ORF7a	54	F54del	TTT	---	20	20	AY.34	0.001939
ORF7a	54	F54del1	ttT	tt-	20	20	AY.6	0.000823
ORF7a	54	F54S	tTt	tCt	19	19	B.1.1.7	0.000017
ORF7a	54	F54Y	tTt	tAt	16	18	All	0.000003
ORF7a	54	F54Y	tTT	tAC	2	18	All	0
ORF7a	54	F54V	Ttt	Gtt	18	18	AY.3	0.000179
ORF7a	54	F54L	ttT	ttG	9	18	AY.5	0.000186
ORF7a	54	F54L	ttT	ttA	7	18	AY.5	0.000145
ORF7a	54	F54L	Ttt	Ctt	2	18	AY.5	0.000041
ORF7a	54	F54del	TTT	---	18	18	AY.9.1	0.001507
ORF7a	54	F54L	ttT	ttA	16	17	AY.39	0.000395
ORF7a	54	F54L	Ttt	Ctt	1	17	AY.39	0.000025
ORF7a	54	F54L	ttT	ttA	17	17	AY.45	0.002069
ORF7a	54	F54del2	tTT	t--	15	17	AY.47	0.000467
ORF7a	54	F54del2	TTt	--t	2	17	AY.47	0.000062
ORF7a	54	F54L	Ttt	Ctt	14	17	B.1.177	0.000184
ORF7a	54	F54L	ttT	ttG	2	17	B.1.177	0.000026
ORF7a	54	F54L	ttT	ttA	1	17	B.1.177	0.000013
ORF7a	54	F54G	TTt	GGt	16	17	B.1.617.2	0.00006
ORF7a	54	F54G	TTT	GGA	1	17	B.1.617.2	0.000004
ORF7a	54	F54X	tTT	tGA	6	16	All	0.000001
ORF7a	54	F54X	tTT	tAA	6	16	All	0.000001
ORF7a	54	F54X	tTT	tAG	4	16	All	0.000001
ORF7a	54	F54del	TTT	---	16	16	AY.20	0.000622
ORF7a	54	F54L	ttT	ttA	16	16	AY.4.2	0.000347
ORF7a	54	F54del	TTT	---	16	16	AY.9	0.001082
ORF7a	54	F54N	TTt	AAt	14	15	All	0.000003
ORF7a	54	F54R	TTT	AGA	7	15	All	0.000001
ORF7a	54	F54R	TTT	AGG	5	15	All	0.000001
ORF7a	54	F54R	TTt	CGt	3	15	All	0.000001
ORF7a	54	F54N	TTT	AAC	1	15	All	0
ORF7a	54	F54del	TTT	---	15	15	AY.1	0.005936
ORF7a	54	F54L	ttT	ttA	14	15	AY.100	0.000644
ORF7a	54	F54L	ttT	ttG	1	15	AY.100	0.000046
ORF7a	54	F54del	TTT	---	15	15	AY.110	0.00169
ORF7a	54	F54del	TTT	---	15	15	AY.121	0.00203
ORF7a	54	F54X	tTT	tGA	6	15	AY.25	0.000036
ORF7a	54	F54X	tTT	tAA	5	15	AY.25	0.00003
ORF7a	54	F54X	tTT	tAG	4	15	AY.25	0.000024
ORF7a	54	F54del2	tTT	t--	8	15	AY.29	0.000126
ORF7a	54	F54del2	TTt	--t	7	15	AY.29	0.00011
ORF7a	54	F54del	TTT	---	15	15	AY.39.1	0.000594
ORF7a	54	F54del	TTT	---	15	15	AY.45	0.001825
ORF7a	54	F54del1	ttT	tt-	15	15	AY.45	0.001825
ORF7a	54	F54del	TTT	---	15	15	AY.9.2	0.000551
ORF7a	54	F54del	TTT	---	15	15	AY.98	0.001185
ORF7a	54	F54del	TTT	---	15	15	AY.98.1	0.000726
ORF7a	54	F54L	ttT	ttA	15	15	B.1.1.222	0.00306
ORF7a	54	F54del	TTT	---	15	15	B.1.596	0.001307
ORF7a	54	F54del	TTT	---	15	15	B.1.637	0.001096
ORF7a	54	F54del	TTT	---	14	14	AY.106	0.004689
ORF7a	54	F54L	ttT	ttA	13	14	AY.110	0.001465
ORF7a	54	F54L	Ttt	Ctt	1	14	AY.110	0.000113
ORF7a	54	F54L	ttT	ttA	13	14	AY.120	0.000483
ORF7a	54	F54L	ttT	ttG	1	14	AY.120	0.000037
ORF7a	54	F54S	tTt	tCt	14	14	AY.43	0.000062
ORF7a	54	F54del	TTT	---	14	14	C.37	0.001625
ORF7a	54	F54del	TTT	---	13	13	AY.111	0.002381
ORF7a	54	F54del1	ttT	tt-	13	13	AY.20	0.000505
ORF7a	54	F54del1	ttT	tt-	13	13	AY.30	0.005144
ORF7a	54	F54del	TTT	---	13	13	AY.68	0.003559
ORF7a	54	F54L	ttT	ttA	8	13	B.1	0.000073
ORF7a	54	F54L	Ttt	Ctt	4	13	B.1	0.000037
ORF7a	54	F54L	ttT	ttG	1	13	B.1	0.000009
ORF7a	54	F54del	TTT	---	13	13	B.1.1	0.000236
ORF7a	54	F54del1	ttT	tt-	13	13	B.1.1.258	0.042345
ORF7a	54	F54del	TTT	---	13	13	R.1	0.00117
ORF7a	54	F54del	TTT	---	12	12	AY.116	0.003441
ORF7a	54	F54L	ttT	ttA	12	12	AY.118	0.000752
ORF7a	54	F54del2	TTt	--t	10	12	AY.119	0.000353
ORF7a	54	F54del2	tTT	t--	2	12	AY.119	0.000071
ORF7a	54	F54L	ttT	ttA	10	12	AY.4.5	0.001075
ORF7a	54	F54L	ttT	ttG	2	12	AY.4.5	0.000215
ORF7a	54	F54L	ttT	ttA	11	12	AY.74	0.001272
ORF7a	54	F54L	Ttt	Ctt	1	12	AY.74	0.000116
ORF7a	54	F54del	TTT	---	12	12	B.1.324	0.019262
ORF7a	54	F54L	ttT	ttA	10	11	AY.119	0.000353
ORF7a	54	F54L	Ttt	Ctt	1	11	AY.119	0.000035
ORF7a	54	F54I	TtT	AtA	6	11	AY.25	0.000036
ORF7a	54	F54I	Ttt	Att	5	11	AY.25	0.00003
ORF7a	54	F54R	TTT	AGA	5	11	AY.25	0.00003
ORF7a	54	F54S	TTt	AGt	5	11	AY.25	0.00003
ORF7a	54	F54G	TTt	GGt	5	11	AY.25	0.00003
ORF7a	54	F54R	TTT	AGG	4	11	AY.25	0.000024
ORF7a	54	F54G	TTT	GGA	4	11	AY.25	0.000024
ORF7a	54	F54S	tTt	tCt	3	11	AY.25	0.000018
ORF7a	54	F54S	tTT	tCA	2	11	AY.25	0.000012
ORF7a	54	F54G	TTT	GGG	2	11	AY.25	0.000012
ORF7a	54	F54R	TTt	CGt	2	11	AY.25	0.000012
ORF7a	54	F54S	TTT	AGC	1	11	AY.25	0.000006
ORF7a	54	F54del	TTT	---	11	11	AY.36	0.00163
ORF7a	54	F54del	TTT	---	11	11	AY.37	0.003477
ORF7a	54	F54del	TTT	---	11	11	AY.46.2	0.006989
ORF7a	54	F54del	TTT	---	11	11	AY.61	0.001153
ORF7a	54	F54del	TTT	---	11	11	AY.99	0.011542
ORF7a	54	F54del	TTT	---	10	10	AY.16	0.003797
ORF7a	54	F54I	Ttt	Att	10	10	AY.4	0.000016
ORF7a	54	F54del	TTT	---	10	10	AY.84	0.004374
ORF7a	54	F54L	ttT	ttA	10	10	AY.9	0.000676
ORF7a	54	F54L	ttT	ttA	5	10	B.1.1	0.000091
ORF7a	54	F54L	ttT	ttG	4	10	B.1.1	0.000073
ORF7a	54	F54L	Ttt	Ctt	1	10	B.1.1	0.000018
ORF7a	54	F54del	TTT	---	10	10	B.1.243	0.000696
ORF7a	54	F54K	TTT	AAA	5	9	All	0.000001
ORF7a	54	F54K	TTT	AAG	4	9	All	0.000001
ORF7a	54	F54del	TTT	---	9	9	AY.113	0.001282
ORF7a	54	F54del	TTT	---	9	9	AY.12	0.002845
ORF7a	54	F54C	tTt	tGt	8	9	AY.25	0.000048
ORF7a	54	F54K	TTT	AAA	5	9	AY.25	0.00003
ORF7a	54	F54K	TTT	AAG	4	9	AY.25	0.000024
ORF7a	54	F54C	tTT	tGC	1	9	AY.25	0.000006
ORF7a	54	F54L	Ttt	Ctt	5	9	AY.29	0.000079
ORF7a	54	F54L	ttT	ttA	4	9	AY.29	0.000063
ORF7a	54	F54del	TTT	---	9	9	AY.30	0.003562
ORF7a	54	F54del1	ttT	tt-	9	9	AY.98	0.000711
ORF7a	54	F54L	ttT	ttA	8	9	AY.98.1	0.000387
ORF7a	54	F54L	ttT	ttG	1	9	AY.98.1	0.000048
ORF7a	54	F54I	Ttt	Att	9	9	B.1.1.7	0.000008
ORF7a	54	F54del	TTT	---	9	9	L.1	0.017143
ORF7a	54	F54del1	ttT	tt-	7	8	AY.102	0.000186
ORF7a	54	F54del1	Ttt	-tt	1	8	AY.102	0.000027
ORF7a	54	F54F	ttT	ttC	8	8	AY.103	0.00005
ORF7a	54	F54del1	ttT	tt-	8	8	AY.113	0.001139
ORF7a	54	F54del1	ttT	tt-	8	8	AY.119	0.000282
ORF7a	54	F54L	ttT	ttA	8	8	AY.20	0.000311
ORF7a	54	F54L	ttT	ttG	4	8	AY.23	0.000279
ORF7a	54	F54L	ttT	ttA	4	8	AY.23	0.000279
ORF7a	54	F54V	Ttt	Gtt	4	8	AY.25	0.000024
ORF7a	54	F54V	TtT	GtA	3	8	AY.25	0.000018
ORF7a	54	F54V	TtT	GtG	1	8	AY.25	0.000006
ORF7a	54	F54S	tTt	tCt	8	8	AY.42	0.000322
ORF7a	54	F54del2	TTt	--t	5	8	AY.45	0.000608
ORF7a	54	F54del2	tTT	t--	3	8	AY.45	0.000365
ORF7a	54	F54del	TTT	---	8	8	AY.7	0.001568
ORF7a	54	F54del2	TTt	--t	7	8	AY.7.1	0.000789
ORF7a	54	F54del2	tTT	t--	1	8	AY.7.1	0.000113
ORF7a	54	F54del	TTT	---	8	8	AY.99.2	0.000737
ORF7a	54	F54del	TTT	---	8	8	B.1.1.231	0.024768
ORF7a	54	F54V	Ttt	Gtt	7	8	B.1.1.7	0.000006
ORF7a	54	F54V	TtT	GtC	1	8	B.1.1.7	0.000001
ORF7a	54	F54F	ttT	ttC	8	8	B.1.2	0.00007
ORF7a	54	F54del	TTT	---	8	8	B.1.429	0.000188
ORF7a	54	F54F	ttT	ttC	8	8	Q.4	0.003638
ORF7a	54	F54H	TTt	CAt	7	7	All	0.000001
ORF7a	54	F54L	ttT	ttA	7	7	AY.34	0.000679
ORF7a	54	F54del	TTT	---	7	7	AY.35	0.001631
ORF7a	54	F54L	ttT	ttA	7	7	AY.46.4	0.001152
ORF7a	54	F54del2	TTt	--t	6	7	AY.5	0.000124
ORF7a	54	F54del2	tTT	t--	1	7	AY.5	0.000021
ORF7a	54	F54L	ttT	ttA	7	7	AY.85	0.00299
ORF7a	54	F54del1	Ttt	-tt	6	7	AY.90	0.004107
ORF7a	54	F54del1	ttT	tt-	1	7	AY.90	0.000684
ORF7a	54	F54L	ttT	ttA	7	7	AY.98	0.000553
ORF7a	54	F54del	TTT	---	7	7	B.1.160	0.000218
ORF7a	54	F54L	ttT	ttA	3	7	B.1.2	0.000026
ORF7a	54	F54L	Ttt	Ctt	3	7	B.1.2	0.000026
ORF7a	54	F54L	ttT	ttG	1	7	B.1.2	0.000009
ORF7a	54	F54L	ttT	ttA	7	7	B.1.221	0.000497
ORF7a	54	F54S	tTt	tCt	7	7	B.1.525	0.000792
ORF7a	54	F54del	TTT	---	7	7	B.1.525	0.000792
ORF7a	54	F54V	Ttt	Gtt	7	7	B.1.617.2	0.000026
ORF7a	54	F54del1	ttT	tt-	7	7	P.1	0.00011
ORF7a	54	F54del	TTT	---	7	7	P.1.15	0.001626
ORF7a	54	F54del	TTT	---	6	6	AY.10	0.00318
ORF7a	54	F54del2	TTt	--t	5	6	AY.102	0.000133
ORF7a	54	F54del2	tTT	t--	1	6	AY.102	0.000027
ORF7a	54	F54del	TTT	---	6	6	AY.14	0.000528
ORF7a	54	F54F	ttT	ttC	6	6	AY.25	0.000036
ORF7a	54	F54Y	tTt	tAt	5	6	AY.25	0.00003
ORF7a	54	F54N	TTt	AAt	5	6	AY.25	0.00003
ORF7a	54	F54N	TTT	AAC	1	6	AY.25	0.000006
ORF7a	54	F54Y	tTT	tAC	1	6	AY.25	0.000006
ORF7a	54	F54del1	ttT	tt-	5	6	AY.33	0.000334
ORF7a	54	F54del1	Ttt	-tt	1	6	AY.33	0.000067
ORF7a	54	F54F	ttT	ttC	6	6	AY.4.2	0.00013
ORF7a	54	F54L	ttT	ttA	6	6	AY.42	0.000241
ORF7a	54	F54F	ttT	ttC	6	6	AY.44	0.000037
ORF7a	54	F54del	TTT	---	6	6	AY.46.1	0.00616
ORF7a	54	F54del	TTT	---	6	6	AY.74	0.000694
ORF7a	54	F54del1	ttT	tt-	6	6	AY.98.1	0.000291
ORF7a	54	F54del2	TTt	--t	5	6	AY.99.2	0.000461
ORF7a	54	F54del2	tTT	t--	1	6	AY.99.2	0.000092
ORF7a	54	F54del2	TTt	--t	6	6	B.1.1.3	0.052174
ORF7a	54	F54del1	ttT	tt-	6	6	B.1.2	0.000053
ORF7a	54	F54del	TTT	---	6	6	B.1.427	0.000303
ORF7a	54	F54del2	TTt	--t	6	6	P.1	0.000095
ORF7a	54	F54del	TTT	---	6	6	P.2	0.00112
ORF7a	54	F54F	ttT	ttC	5	5	AY.102	0.000133
ORF7a	54	F54I	Ttt	Att	5	5	AY.103	0.000031
ORF7a	54	F54del	TTT	---	5	5	AY.109	0.003698
ORF7a	54	F54del1	ttT	tt-	5	5	AY.118	0.000313
ORF7a	54	F54del2	tTT	t--	4	5	AY.120	0.000149
ORF7a	54	F54del2	TTt	--t	1	5	AY.120	0.000037
ORF7a	54	F54del1	ttT	tt-	5	5	AY.13	0.000805
ORF7a	54	F54del2	TTt	--t	3	5	AY.14	0.000264
ORF7a	54	F54del2	tTT	t--	2	5	AY.14	0.000176
ORF7a	54	F54del	TTT	---	5	5	AY.29.1	0.001103
ORF7a	54	F54L	ttT	ttA	4	5	AY.3.1	0.000341
ORF7a	54	F54L	Ttt	Ctt	1	5	AY.3.1	0.000085
ORF7a	54	F54del1	ttT	tt-	5	5	AY.35	0.001165
ORF7a	54	F54del2	TTt	--t	5	5	AY.42	0.000201
ORF7a	54	F54del1	ttT	tt-	5	5	AY.42	0.000201
ORF7a	54	F54L	ttT	ttA	4	5	AY.46	0.000416
ORF7a	54	F54L	Ttt	Ctt	1	5	AY.46	0.000104
ORF7a	54	F54del2	TTt	--t	2	5	AY.54	0.000191
ORF7a	54	F54del2	tTT	t--	2	5	AY.54	0.000191
ORF7a	54	F54del2	TTT	--N	1	5	AY.54	0.000095
ORF7a	54	F54del	TTT	---	5	5	AY.62	0.002179
ORF7a	54	F54del	TTT	---	5	5	AY.90	0.003422
ORF7a	54	F54del	TTT	---	5	5	AY.91	0.003652
ORF7a	54	F54del2	TTt	--t	5	5	AY.98.1	0.000242
ORF7a	54	F54del	TTT	---	5	5	B.1.1.519	0.000199
ORF7a	54	F54del	TTT	---	5	5	B.1.1.56	0.089286
ORF7a	54	F54L	ttT	ttG	2	5	B.1.160	0.000062
ORF7a	54	F54L	ttT	ttA	2	5	B.1.160	0.000062
ORF7a	54	F54L	Ttt	Ctt	1	5	B.1.160	0.000031
ORF7a	54	F54C	tTt	tGt	5	5	B.1.617.2	0.000019
ORF7a	54	F54del	TTT	---	5	5	B.1.70	0.121951
ORF7a	54	F54L	Ttt	Ctt	3	5	P.1	0.000047
ORF7a	54	F54L	ttT	ttA	2	5	P.1	0.000032
ORF7a	54	F54del	TTT	---	4	4	A	0.001548
ORF7a	54	F54W	tTT	tGG	4	4	All	0.000001
ORF7a	54	F54F	ttT	ttC	4	4	AY.100	0.000184
ORF7a	54	F54S	tTt	tCt	4	4	AY.113	0.00057
ORF7a	54	F54del1	ttT	tt-	4	4	AY.114	0.000924
ORF7a	54	F54L	ttT	ttA	3	4	AY.14	0.000264
ORF7a	54	F54L	Ttt	Ctt	1	4	AY.14	0.000088
ORF7a	54	F54del2	TTt	--t	3	4	AY.23	0.000209
ORF7a	54	F54del1	ttT	tt-	3	4	AY.23	0.000209
ORF7a	54	F54del2	tTT	t--	1	4	AY.23	0.00007
ORF7a	54	F54del1	Ttt	-tt	1	4	AY.23	0.00007
ORF7a	54	F54del2	TTt	--t	4	4	AY.24	0.001724
ORF7a	54	F54W	tTT	tGG	4	4	AY.25	0.000024
ORF7a	54	F54H	TTt	CAt	4	4	AY.25	0.000024
ORF7a	54	F54del	TTT	---	4	4	AY.27	0.000259
ORF7a	54	F54del2	tTT	t--	3	4	AY.33	0.0002
ORF7a	54	F54del2	TTt	--t	1	4	AY.33	0.000067
ORF7a	54	F54S	tTt	tCt	4	4	AY.4.2.1	0.000596
ORF7a	54	F54del	TTT	---	4	4	AY.4.2.1	0.000596
ORF7a	54	F54del	TTT	---	4	4	AY.4.5	0.00043
ORF7a	54	F54del2	TTt	--t	3	4	AY.46.6	0.000217
ORF7a	54	F54del2	tTT	t--	1	4	AY.46.6	0.000072
ORF7a	54	F54del	TTT	---	4	4	AY.66	0.004278
ORF7a	54	F54L	Ttt	Ctt	2	4	AY.75.1	0.000361
ORF7a	54	F54L	ttT	ttA	2	4	AY.75.1	0.000361
ORF7a	54	F54del	TTT	---	4	4	AY.85	0.001709
ORF7a	54	F54del2	TTt	--t	4	4	AY.85	0.001709
ORF7a	54	F54del1	ttT	tt-	4	4	AY.87	0.003331
ORF7a	54	F54del1	ttT	tt-	4	4	AY.9	0.00027
ORF7a	54	F54del2	tTT	t--	4	4	AY.9.1	0.000335
ORF7a	54	F54del	TTT	---	4	4	AY.92	0.001149
ORF7a	54	F54del	TTT	---	4	4	AY.95	0.003044
ORF7a	54	F54L	ttT	ttA	4	4	AY.99.2	0.000369
ORF7a	54	F54del1	ttT	tt-	4	4	AY.99.2	0.000369
ORF7a	54	F54V	Ttt	Gtt	4	4	B.1	0.000037
ORF7a	54	F54F	ttT	ttC	4	4	B.1	0.000037
ORF7a	54	F54del2	tTT	t--	4	4	B.1.1	0.000073
ORF7a	54	F54del1	ttT	tt-	4	4	B.1.1	0.000073
ORF7a	54	F54del1	ttT	tt-	4	4	B.1.160	0.000125
ORF7a	54	F54L	ttT	ttA	4	4	B.1.375	0.003279
ORF7a	54	F54L	ttT	ttA	4	4	B.1.427	0.000202
ORF7a	54	F54L	Ttt	Ctt	4	4	B.1.561	0.001588
ORF7a	54	F54I	Ttt	Att	3	4	B.1.617.2	0.000011
ORF7a	54	F54R	TTT	AGA	2	4	B.1.617.2	0.000008
ORF7a	54	F54R	TTT	AGG	1	4	B.1.617.2	0.000004
ORF7a	54	F54R	TTt	CGt	1	4	B.1.617.2	0.000004
ORF7a	54	F54I	TtT	AtA	1	4	B.1.617.2	0.000004
ORF7a	54	F54del2	TTt	--t	3	4	B.1.637	0.000219
ORF7a	54	F54del2	tTT	t--	1	4	B.1.637	0.000073
ORF7a	54	F54F	ttT	ttC	4	4	C.37	0.000464
ORF7a	54	F54del	TTT	---	4	4	D.2	0.0003
ORF7a	54	F54del1	ttT	tt-	4	4	Q.1	0.000505
ORF7a	54	F54M	TtT	AtG	3	3	All	0.000001
ORF7a	54	F54D	TTt	GAt	3	3	All	0.000001
ORF7a	54	F54E	TTT	GAA	2	3	All	0
ORF7a	54	F54T	TTt	ACt	2	3	All	0
ORF7a	54	F54T	TTT	ACA	1	3	All	0
ORF7a	54	F54E	TTT	GAG	1	3	All	0
ORF7a	54	F54N	TTt	AAt	3	3	AY.100	0.000138
ORF7a	54	F54del2	TTt	--t	3	3	AY.100	0.000138
ORF7a	54	F54del	TTT	---	3	3	AY.114	0.000693
ORF7a	54	F54del2	TTt	--t	2	3	AY.117	0.000169
ORF7a	54	F54L	Ttt	Ctt	1	3	AY.117	0.000085
ORF7a	54	F54del2	tTT	t--	1	3	AY.117	0.000085
ORF7a	54	F54L	ttT	ttA	1	3	AY.117	0.000085
ORF7a	54	F54L	ttT	ttG	1	3	AY.117	0.000085
ORF7a	54	F54del2	tTT	t--	3	3	AY.120.1	0.000963
ORF7a	54	F54L	ttT	ttA	2	3	AY.16	0.000759
ORF7a	54	F54L	Ttt	Ctt	1	3	AY.16	0.00038
ORF7a	54	F54F	ttT	ttC	3	3	AY.3	0.00003
ORF7a	54	F54del1	ttT	tt-	3	3	AY.3.1	0.000256
ORF7a	54	F54S	tTt	tCt	3	3	AY.34	0.000291
ORF7a	54	F54del1	ttT	tt-	2	3	AY.34	0.000194
ORF7a	54	F54del1	Ttt	-tt	1	3	AY.34	0.000097
ORF7a	54	F54del	TTT	---	3	3	AY.34.1	0.00153
ORF7a	54	F54L	ttT	ttA	3	3	AY.36	0.000445
ORF7a	54	F54del	TTT	---	3	3	AY.4.3	0.002525
ORF7a	54	F54L	ttT	ttA	3	3	AY.4.4	0.001227
ORF7a	54	F54del	TTT	---	3	3	AY.40	0.002893
ORF7a	54	F54F	ttT	ttC	3	3	AY.45	0.000365
ORF7a	54	F54del1	Ttt	-tt	2	3	AY.46	0.000208
ORF7a	54	F54del1	ttT	tt-	1	3	AY.46	0.000104
ORF7a	54	F54L	ttT	ttG	3	3	AY.46.1	0.00308
ORF7a	54	F54del	TTT	---	3	3	AY.5.3	0.001012
ORF7a	54	F54del	TTT	---	3	3	AY.53	0.000863
ORF7a	54	F54del1	ttT	tt-	3	3	AY.54	0.000286
ORF7a	54	F54L	ttT	ttA	2	3	AY.54	0.000191
ORF7a	54	F54L	ttT	ttG	1	3	AY.54	0.000095
ORF7a	54	F54del1	ttT	tt-	3	3	AY.62	0.001307
ORF7a	54	F54del1	ttT	tt-	3	3	AY.65	0.001599
ORF7a	54	F54del	TTT	---	3	3	AY.65	0.001599
ORF7a	54	F54L	ttT	ttG	2	3	AY.69	0.000373
ORF7a	54	F54L	ttT	ttA	1	3	AY.69	0.000187
ORF7a	54	F54del2	tTT	t--	3	3	AY.7	0.000588
ORF7a	54	F54del2	tTT	t--	2	3	AY.73	0.001331
ORF7a	54	F54del2	TTt	--t	1	3	AY.73	0.000665
ORF7a	54	F54L	ttT	ttA	3	3	AY.84	0.001312
ORF7a	54	F54L	ttT	ttA	3	3	AY.86	0.00249
ORF7a	54	F54L	ttT	ttA	3	3	AY.9.2	0.00011
ORF7a	54	F54I	Ttt	Att	3	3	B.1	0.000027
ORF7a	54	F54del1	ttT	tt-	3	3	B.1	0.000027
ORF7a	54	F54F	ttT	ttC	3	3	B.1.1	0.000054
ORF7a	54	F54I	Ttt	Att	3	3	B.1.1	0.000054
ORF7a	54	F54del	TTT	---	3	3	B.1.1.121	0.007282
ORF7a	54	F54del1	ttT	tt-	3	3	B.1.177	0.00004
ORF7a	54	F54N	TTt	AAt	3	3	B.1.177.21	0.000229
ORF7a	54	F54I	Ttt	Att	2	3	B.1.177.21	0.000153
ORF7a	54	F54I	TtT	AtC	1	3	B.1.177.21	0.000076
ORF7a	54	F54del	TTT	---	3	3	B.1.214.2	0.001799
ORF7a	54	F54del	TTT	---	3	3	B.1.221	0.000213
ORF7a	54	F54del1	ttT	tt-	3	3	B.1.351	0.000089
ORF7a	54	F54L	ttT	ttA	3	3	B.1.429	0.000071
ORF7a	54	F54del	TTT	---	3	3	B.1.582	0.001472
ORF7a	54	F54F	ttT	ttC	3	3	B.1.596	0.000261
ORF7a	54	F54del	TTT	---	3	3	B.1.626	0.017143
ORF7a	54	F54I	Ttt	Att	3	3	D.2	0.000225
ORF7a	54	F54del	TTT	---	3	3	P.1.14	0.000143
ORF7a	54	F54F	ttT	ttC	3	3	P.1.17	0.000485
ORF7a	54	F54del1	ttT	tt-	3	3	Q.8	0.000495
ORF7a	54	F54L	ttT	ttA	3	3	Q.8	0.000495
ORF7a	54	F54V	Ttt	Gtt	2	2		0.111111
ORF7a	54	F54C	tTt	tGt	2	2		0.111111
ORF7a	54	F54F	ttT	ttC	2	2		0.111111
ORF7a	54	F54del	TTT	---	2	2	A.2.4	0.006734
ORF7a	54	F54del	TTT	---	2	2	A.28	0.005291
ORF7a	54	F54P	TTt	CCt	2	2	All	0
ORF7a	54	F54A	TTt	GCt	1	2	All	0
ORF7a	54	F54A	TTT	GCA	1	2	All	0
ORF7a	54	F54V	Ttt	Gtt	2	2	AY.103	0.000012
ORF7a	54	F54del	TTT	---	2	2	AY.108	0.002205
ORF7a	54	F54del1	ttT	tt-	2	2	AY.109	0.001479
ORF7a	54	F54del2	tTT	t--	1	2	AY.110	0.000113
ORF7a	54	F54del2	TTt	--t	1	2	AY.110	0.000113
ORF7a	54	F54F	ttT	ttC	2	2	AY.113	0.000285
ORF7a	54	F54del2	tTT	t--	2	2	AY.114	0.000462
ORF7a	54	F54del1	Ttt	-tt	1	2	AY.117	0.000085
ORF7a	54	F54del1	ttT	tt-	1	2	AY.117	0.000085
ORF7a	54	F54S	tTt	tCt	2	2	AY.119	0.000071
ORF7a	54	F54del2	TTt	--t	2	2	AY.12	0.000632
ORF7a	54	F54del1	ttT	tt-	2	2	AY.120.1	0.000642
ORF7a	54	F54del	TTT	---	2	2	AY.13	0.000322
ORF7a	54	F54del	TTT	---	2	2	AY.19	0.002281
ORF7a	54	F54del1	ttT	tt-	2	2	AY.2	0.000712
ORF7a	54	F54S	tTt	tCt	2	2	AY.20	0.000078
ORF7a	54	F54del2	TTt	--t	2	2	AY.20	0.000078
ORF7a	54	F54F	ttT	ttC	2	2	AY.23	0.000139
ORF7a	54	F54del	TTT	---	2	2	AY.24	0.000862
ORF7a	54	F54M	TtT	AtG	2	2	AY.25	0.000012
ORF7a	54	F54A	TTT	GCA	1	2	AY.25	0.000006
ORF7a	54	F54T	TTt	ACt	1	2	AY.25	0.000006
ORF7a	54	F54T	TTT	ACA	1	2	AY.25	0.000006
ORF7a	54	F54E	TTT	GAG	1	2	AY.25	0.000006
ORF7a	54	F54E	TTT	GAA	1	2	AY.25	0.000006
ORF7a	54	F54A	TTt	GCt	1	2	AY.25	0.000006
ORF7a	54	F54del1	ttT	tt-	2	2	AY.29.1	0.000441
ORF7a	54	F54S	tTt	tCt	2	2	AY.3	0.00002
ORF7a	54	F54L	ttT	ttA	1	2	AY.30	0.000396
ORF7a	54	F54L	Ttt	Ctt	1	2	AY.30	0.000396
ORF7a	54	F54del2	tTT	t--	1	2	AY.34	0.000097
ORF7a	54	F54del2	TTt	--t	1	2	AY.34	0.000097
ORF7a	54	F54del2	TTt	--t	2	2	AY.36	0.000296
ORF7a	54	F54del2	tTT	t--	2	2	AY.39	0.000049
ORF7a	54	F54del2	tTT	t--	2	2	AY.39.1	0.000079
ORF7a	54	F54S	tTt	tCt	2	2	AY.4	0.000003
ORF7a	54	F54V	Ttt	Gtt	2	2	AY.4	0.000003
ORF7a	54	F54del1	Ttt	-tt	2	2	AY.4.2.1	0.000298
ORF7a	54	F54F	ttT	ttC	2	2	AY.46	0.000208
ORF7a	54	F54L	ttT	ttG	1	2	AY.46.2	0.000635
ORF7a	54	F54L	Ttt	Ctt	1	2	AY.46.2	0.000635
ORF7a	54	F54del1	ttT	tt-	2	2	AY.46.4	0.000329
ORF7a	54	F54del1	ttT	tt-	1	2	AY.46.5	0.000198
ORF7a	54	F54del1	Ttt	-tt	1	2	AY.46.5	0.000198
ORF7a	54	F54L	Ttt	Ctt	1	2	AY.46.6	0.000072
ORF7a	54	F54L	ttT	ttA	1	2	AY.46.6	0.000072
ORF7a	54	F54L	ttT	ttA	2	2	AY.48	0.00093
ORF7a	54	F54del	TTT	---	2	2	AY.48	0.00093
ORF7a	54	F54del1	ttT	tt-	2	2	AY.49	0.00639
ORF7a	54	F54F	ttT	ttC	2	2	AY.5	0.000041
ORF7a	54	F54del2	TTt	--t	2	2	AY.5.3	0.000675
ORF7a	54	F54del	TTT	---	2	2	AY.51	0.001818
ORF7a	54	F54L	Ttt	Ctt	1	2	AY.59	0.00053
ORF7a	54	F54L	ttT	ttA	1	2	AY.59	0.00053
ORF7a	54	F54L	ttT	ttA	2	2	AY.6	0.000082
ORF7a	54	F54del2	TTt	--t	1	2	AY.6	0.000041
ORF7a	54	F54del2	tTT	t--	1	2	AY.6	0.000041
ORF7a	54	F54del1	Ttt	-tt	1	2	AY.64	0.000595
ORF7a	54	F54del1	ttT	tt-	1	2	AY.64	0.000595
ORF7a	54	F54L	Ttt	Ctt	2	2	AY.66	0.002139
ORF7a	54	F54del	TTT	---	2	2	AY.69	0.000373
ORF7a	54	F54del1	ttT	tt-	2	2	AY.7.2	0.001119
ORF7a	54	F54L	ttT	ttA	2	2	AY.70	0.000417
ORF7a	54	F54del	TTT	---	2	2	AY.71	0.00095
ORF7a	54	F54del	TTT	---	2	2	AY.73	0.001331
ORF7a	54	F54del1	Ttt	-tt	2	2	AY.73	0.001331
ORF7a	54	F54del2	tTT	t--	1	2	AY.75	0.000056
ORF7a	54	F54del2	TTt	--t	1	2	AY.75	0.000056
ORF7a	54	F54L	ttT	ttA	1	2	AY.87	0.000833
ORF7a	54	F54L	ttT	ttG	1	2	AY.87	0.000833
ORF7a	54	F54del2	TTt	--t	2	2	AY.88	0.001768
ORF7a	54	F54del	TTT	---	2	2	AY.88	0.001768
ORF7a	54	F54L	ttT	ttA	1	2	AY.92	0.000287
ORF7a	54	F54L	ttT	ttG	1	2	AY.92	0.000287
ORF7a	54	F54del	TTT	---	2	2	AY.93	0.000546
ORF7a	54	F54F	ttT	ttC	2	2	AY.99.2	0.000184
ORF7a	54	F54S	tTt	tCt	2	2	B.1.1	0.000036
ORF7a	54	F54del1	ttT	tt-	2	2	B.1.1.220	0.003717
ORF7a	54	F54del	TTT	---	2	2	B.1.1.25	0.001137
ORF7a	54	F54del	TTT	---	2	2	B.1.1.318	0.000604
ORF7a	54	F54del1	ttT	tt-	2	2	B.1.1.372	0.001377
ORF7a	54	F54del1	ttT	tt-	2	2	B.1.1.519	0.000079
ORF7a	54	F54C	tTt	tGt	2	2	B.1.1.7	0.000002
ORF7a	54	F54del	TTT	---	2	2	B.1.160.16	0.001859
ORF7a	54	F54L	ttT	ttA	2	2	B.1.177.16	0.001329
ORF7a	54	F54L	ttT	ttA	1	2	B.1.177.21	0.000076
ORF7a	54	F54L	Ttt	Ctt	1	2	B.1.177.21	0.000076
ORF7a	54	F54del	TTT	---	2	2	B.1.177.43	0.002954
ORF7a	54	F54del	TTT	---	2	2	B.1.177.55	0.004662
ORF7a	54	F54L	ttT	ttA	2	2	B.1.177.60	0.000437
ORF7a	54	F54del	TTT	---	2	2	B.1.177.81	0.000379
ORF7a	54	F54del	TTT	---	2	2	B.1.177.86	0.000367
ORF7a	54	F54del	TTT	---	2	2	B.1.258.11	0.000793
ORF7a	54	F54del2	TTt	--t	2	2	B.1.258.17	0.000208
ORF7a	54	F54del	TTT	---	2	2	B.1.311	0.000549
ORF7a	54	F54I	Ttt	Att	2	2	B.1.351	0.000059
ORF7a	54	F54del	TTT	---	2	2	B.1.351.2	0.000605
ORF7a	54	F54del1	TTT	CC-	2	2	B.1.36	0.000292
ORF7a	54	F54I	Ttt	Att	2	2	B.1.36.1	0.002281
ORF7a	54	F54del	TTT	---	2	2	B.1.375	0.001639
ORF7a	54	F54del1	ttT	tt-	2	2	B.1.525	0.000226
ORF7a	54	F54L	Ttt	Ctt	2	2	B.1.526	0.000047
ORF7a	54	F54del	TTT	---	2	2	B.1.575	0.000607
ORF7a	54	F54V	TtT	GtA	1	2	B.1.588	0.00091
ORF7a	54	F54V	Ttt	Gtt	1	2	B.1.588	0.00091
ORF7a	54	F54del	TTT	---	2	2	B.1.617.1	0.000258
ORF7a	54	F54N	TTt	AAt	2	2	B.1.617.2	0.000008
ORF7a	54	F54Y	tTt	tAt	2	2	B.1.617.2	0.000008
ORF7a	54	F54del	TTT	---	2	2	B.1.621.1	0.001012
ORF7a	54	F54L	ttT	ttA	2	2	B.1.637	0.000146
ORF7a	54	F54L	ttT	ttA	1	2	B.6	0.00091
ORF7a	54	F54L	Ttt	Ctt	1	2	B.6	0.00091
ORF7a	54	F54L	ttT	ttA	2	2	P.1.16	0.000748
ORF7a	54	F54L	ttT	ttA	2	2	P.1.17.1	0.00175
ORF7a	54	F54del	TTT	---	2	2	P.1.2	0.002312
ORF7a	54	F54del	TTT	---	1	1	A.1	0.000282
ORF7a	54	F54L	ttT	ttA	1	1	A.2.5.3	0.010309
ORF7a	54	F54del	TTT	---	1	1	A.23.1	0.000704
ORF7a	54	F54V	Ttt	Gtt	1	1	A.3	0.002096
ORF7a	54	F54del2	TTt	--t	1	1	AY.1	0.000396
ORF7a	54	F54del1	Ttt	-tt	1	1	AY.1	0.000396
ORF7a	54	F54L	ttT	ttA	1	1	AY.1	0.000396
ORF7a	54	F54C	tTT	tGC	1	1	AY.1	0.000396
ORF7a	54	F54del	TTT	---	1	1	AY.101	0.00049
ORF7a	54	F54S	tTt	tCt	1	1	AY.102	0.000027
ORF7a	54	F54Y	tTt	tAt	1	1	AY.103	0.000006
ORF7a	54	F54C	tTt	tGt	1	1	AY.103	0.000006
ORF7a	54	F54del	TTT	---	1	1	AY.105	0.000643
ORF7a	54	F54del2	TTt	--t	1	1	AY.106	0.000335
ORF7a	54	F54L	ttT	ttA	1	1	AY.106	0.000335
ORF7a	54	F54L	ttT	ttA	1	1	AY.109	0.00074
ORF7a	54	F54L	ttT	ttA	1	1	AY.11	0.001339
ORF7a	54	F54del1	ttT	tt-	1	1	AY.110	0.000113
ORF7a	54	F54L	Ttt	Ctt	1	1	AY.111	0.000183
ORF7a	54	F54del1	Ttt	-tt	1	1	AY.111	0.000183
ORF7a	54	F54del2	tTT	t--	1	1	AY.111	0.000183
ORF7a	54	F54del2	tTT	t--	1	1	AY.116	0.000287
ORF7a	54	F54del1	ttT	tt-	1	1	AY.116	0.000287
ORF7a	54	F54del	TTT	---	1	1	AY.116.1	0.000311
ORF7a	54	F54S	tTt	tCt	1	1	AY.117	0.000085
ORF7a	54	F54C	tTt	tGt	1	1	AY.117	0.000085
ORF7a	54	F54I	Ttt	Att	1	1	AY.117	0.000085
ORF7a	54	F54C	tTt	tGt	1	1	AY.119	0.000035
ORF7a	54	F54del1	ttT	tt-	1	1	AY.12	0.000316
ORF7a	54	F54Y	tTt	tAt	1	1	AY.120	0.000037
ORF7a	54	F54Y	tTT	tAC	1	1	AY.120.1	0.000321
ORF7a	54	F54P	TTt	CCt	1	1	AY.120.1	0.000321
ORF7a	54	F54L	ttT	ttG	1	1	AY.120.1	0.000321
ORF7a	54	F54del	TTT	---	1	1	AY.120.2	0.001285
ORF7a	54	F54L	ttT	ttA	1	1	AY.120.2	0.001285
ORF7a	54	F54del	TTT	---	1	1	AY.120.2.1	0.000498
ORF7a	54	F54L	ttT	ttA	1	1	AY.120.2.1	0.000498
ORF7a	54	F54F	ttT	ttC	1	1	AY.120.2.1	0.000498
ORF7a	54	F54L	Ttt	Ctt	1	1	AY.121	0.000135
ORF7a	54	F54del1	ttT	tt-	1	1	AY.121	0.000135
ORF7a	54	F54del1	ttT	tt-	1	1	AY.14	0.000088
ORF7a	54	F54del1	ttT	tt-	1	1	AY.19	0.00114
ORF7a	54	F54Y	tTt	tAt	1	1	AY.20	0.000039
ORF7a	54	F54F	ttT	ttC	1	1	AY.20	0.000039
ORF7a	54	F54del1	ttT	tt-	1	1	AY.22	0.002092
ORF7a	54	F54del	TTT	---	1	1	AY.22	0.002092
ORF7a	54	F54V	Ttt	Gtt	1	1	AY.23.1	0.000417
ORF7a	54	F54L	ttT	ttG	1	1	AY.24	0.000431
ORF7a	54	F54del1	Ttt	-tt	1	1	AY.24	0.000431
ORF7a	54	F54D	TTt	GAt	1	1	AY.25	0.000006
ORF7a	54	F54S	tTt	tCt	1	1	AY.26	0.000028
ORF7a	54	F54C	tTt	tGt	1	1	AY.26	0.000028
ORF7a	54	F54del2	tTT	t--	1	1	AY.29.1	0.000221
ORF7a	54	F54L	ttT	ttA	1	1	AY.29.1	0.000221
ORF7a	54	F54del2	TTt	--t	1	1	AY.3.1	0.000085
ORF7a	54	F54V	Ttt	Gtt	1	1	AY.3.1	0.000085
ORF7a	54	F54I	Ttt	Att	1	1	AY.3.1	0.000085
ORF7a	54	F54del2	tTT	t--	1	1	AY.32	0.000532
ORF7a	54	F54F	ttT	ttC	1	1	AY.34	0.000097
ORF7a	54	F54del2	TTt	--t	1	1	AY.35	0.000233
ORF7a	54	F54del1	Ttt	-tt	1	1	AY.36	0.000148
ORF7a	54	F54S	tTt	tCt	1	1	AY.36	0.000148
ORF7a	54	F54del1	ttT	tt-	1	1	AY.37	0.000316
ORF7a	54	F54del	TTT	---	1	1	AY.38	0.000499
ORF7a	54	F54F	ttT	ttC	1	1	AY.39	0.000025
ORF7a	54	F54F	ttT	ttC	1	1	AY.39.1	0.00004
ORF7a	54	F54L	ttT	ttA	1	1	AY.39.1.1	0.000725
ORF7a	54	F54L	Ttt	Ctt	1	1	AY.4.2.1	0.000149
ORF7a	54	F54del1	ttT	tt-	1	1	AY.4.4	0.000409
ORF7a	54	F54del	TTT	---	1	1	AY.4.4	0.000409
ORF7a	54	F54del2	TTt	--t	1	1	AY.4.5	0.000107
ORF7a	54	F54del2	tTT	t--	1	1	AY.41	0.000294
ORF7a	54	F54L	ttT	ttA	1	1	AY.41	0.000294
ORF7a	54	F54F	ttT	ttC	1	1	AY.42	0.00004
ORF7a	54	F54H	TTt	CAt	1	1	AY.44	0.000006
ORF7a	54	F54V	Ttt	Gtt	1	1	AY.44	0.000006
ORF7a	54	F54del	TTT	---	1	1	AY.46.5	0.000198
ORF7a	54	F54L	ttT	ttA	1	1	AY.46.5	0.000198
ORF7a	54	F54del2	tTT	t--	1	1	AY.46.5	0.000198
ORF7a	54	F54V	Ttt	Gtt	1	1	AY.46.6	0.000072
ORF7a	54	F54F	ttT	ttC	1	1	AY.46.6	0.000072
ORF7a	54	F54del1	ttT	tt-	1	1	AY.48	0.000465
ORF7a	54	F54I	Ttt	Att	1	1	AY.5	0.000021
ORF7a	54	F54S	tTt	tCt	1	1	AY.5	0.000021
ORF7a	54	F54L	Ttt	Ctt	1	1	AY.5.3	0.000337
ORF7a	54	F54del	TTT	---	1	1	AY.5.4	0.000277
ORF7a	54	F54del2	tTT	t--	1	1	AY.52	0.000814
ORF7a	54	F54del1	ttT	tt-	1	1	AY.52	0.000814
ORF7a	54	F54F	ttT	ttC	1	1	AY.53	0.000288
ORF7a	54	F54L	ttT	ttA	1	1	AY.53	0.000288
ORF7a	54	F54I	Ttt	Att	1	1	AY.54	0.000095
ORF7a	54	F54del	TTT	---	1	1	AY.57	0.000656
ORF7a	54	F54del1	ttT	tt-	1	1	AY.57	0.000656
ORF7a	54	F54L	ttT	ttA	1	1	AY.57	0.000656
ORF7a	54	F54del	TTT	---	1	1	AY.59	0.00053
ORF7a	54	F54L	Ttt	Ctt	1	1	AY.61	0.000105
ORF7a	54	F54del1	ttT	tt-	1	1	AY.61	0.000105
ORF7a	54	F54S	tTt	tCt	1	1	AY.61	0.000105
ORF7a	54	F54F	ttT	ttC	1	1	AY.62	0.000436
ORF7a	54	F54del1	ttT	tt-	1	1	AY.66	0.00107
ORF7a	54	F54del2	TTt	--t	1	1	AY.69	0.000187
ORF7a	54	F54del1	ttT	tt-	1	1	AY.7.1	0.000113
ORF7a	54	F54del	TTT	---	1	1	AY.70	0.000209
ORF7a	54	F54L	ttT	ttA	1	1	AY.72	0.001361
ORF7a	54	F54L	ttT	ttA	1	1	AY.75	0.000056
ORF7a	54	F54F	ttT	ttC	1	1	AY.75	0.000056
ORF7a	54	F54del1	ttT	tt-	1	1	AY.75	0.000056
ORF7a	54	F54del	TTT	---	1	1	AY.75.1	0.00018
ORF7a	54	F54L	ttT	ttA	1	1	AY.77	0.001127
ORF7a	54	F54del	TTT	---	1	1	AY.79	0.001211
ORF7a	54	F54del1	ttT	tt-	1	1	AY.79	0.001211
ORF7a	54	F54del	TTT	---	1	1	AY.8	0.000606
ORF7a	54	F54L	ttT	ttA	1	1	AY.8	0.000606
ORF7a	54	F54del	TTT	---	1	1	AY.81	0.001992
ORF7a	54	F54del1	ttT	tt-	1	1	AY.88	0.000884
ORF7a	54	F54del	TTT	---	1	1	AY.89	0.004902
ORF7a	54	F54F	ttT	ttC	1	1	AY.9	0.000068
ORF7a	54	F54L	ttT	ttA	1	1	AY.9.1	0.000084
ORF7a	54	F54del1	Ttt	-tt	1	1	AY.9.1	0.000084
ORF7a	54	F54I	Ttt	Att	1	1	AY.9.1	0.000084
ORF7a	54	F54L	ttT	ttA	1	1	AY.91	0.00073
ORF7a	54	F54L	ttT	ttA	1	1	AY.93	0.000273
ORF7a	54	F54del	TTT	---	1	1	AY.94	0.000443
ORF7a	54	F54del1	ttT	tt-	1	1	AY.96	0.002075
ORF7a	54	F54del2	TTt	--t	1	1	AY.98	0.000079
ORF7a	54	F54F	ttT	ttC	1	1	AY.98.1	0.000048
ORF7a	54	F54del	TTT	---	1	1	AZ.2	0.000821
ORF7a	54	F54S	tTt	tCt	1	1	B	0.000128
ORF7a	54	F54del	TTT	---	1	1	B	0.000128
ORF7a	54	F54L	ttT	ttA	1	1	B	0.000128
ORF7a	54	F54Y	tTt	tAt	1	1	B.1	0.000009
ORF7a	54	F54del	TTT	---	1	1	B.1.1.1	0.000327
ORF7a	54	F54S	tTt	tCt	1	1	B.1.1.139	0.022727
ORF7a	54	F54del	TTT	---	1	1	B.1.1.157	0.000913
ORF7a	54	F54del	TTT	---	1	1	B.1.1.174	0.003378
ORF7a	54	F54I	Ttt	Att	1	1	B.1.1.189	0.001513
ORF7a	54	F54del	TTT	---	1	1	B.1.1.192	0.002309
ORF7a	54	F54del1	ttT	tt-	1	1	B.1.1.194	0.00495
ORF7a	54	F54del1	ttT	tt-	1	1	B.1.1.205	0.003717
ORF7a	54	F54L	ttT	ttA	1	1	B.1.1.205	0.003717
ORF7a	54	F54del	TTT	---	1	1	B.1.1.207	0.001182
ORF7a	54	F54del1	ttT	tt-	1	1	B.1.1.209	0.008929
ORF7a	54	F54I	Ttt	Att	1	1	B.1.1.214	0.000055
ORF7a	54	F54S	tTt	tCt	1	1	B.1.1.214	0.000055
ORF7a	54	F54L	ttT	ttA	1	1	B.1.1.240	0.004695
ORF7a	54	F54del1	ttT	tt-	1	1	B.1.1.241	0.00207
ORF7a	54	F54F	ttT	ttC	1	1	B.1.1.25	0.000569
ORF7a	54	F54L	ttT	ttG	1	1	B.1.1.25	0.000569
ORF7a	54	F54del	TTT	---	1	1	B.1.1.258	0.003257
ORF7a	54	F54I	Ttt	Att	1	1	B.1.1.28	0.000311
ORF7a	54	F54I	Ttt	Att	1	1	B.1.1.282	0.011628
ORF7a	54	F54del1	ttT	tt-	1	1	B.1.1.284	0.000107
ORF7a	54	F54L	Ttt	Ctt	1	1	B.1.1.284	0.000107
ORF7a	54	F54del	TTT	---	1	1	B.1.1.303	0.002762
ORF7a	54	F54I	Ttt	Att	1	1	B.1.1.305	0.003861
ORF7a	54	F54Y	tTt	tAt	1	1	B.1.1.316	0.000925
ORF7a	54	F54L	ttT	ttA	1	1	B.1.1.318	0.000302
ORF7a	54	F54L	Ttt	Ctt	1	1	B.1.1.33	0.000421
ORF7a	54	F54del	TTT	---	1	1	B.1.1.33	0.000421
ORF7a	54	F54del	TTT	---	1	1	B.1.1.348	0.000796
ORF7a	54	F54del	TTT	---	1	1	B.1.1.366	0.015873
ORF7a	54	F54L	ttT	ttA	1	1	B.1.1.37	0.000193
ORF7a	54	F54S	tTt	tCt	1	1	B.1.1.372	0.000689
ORF7a	54	F54I	Ttt	Att	1	1	B.1.1.411	0.014706
ORF7a	54	F54I	Ttt	Att	1	1	B.1.1.420	0.001006
ORF7a	54	F54del1	ttT	tt-	1	1	B.1.1.432	0.001266
ORF7a	54	F54L	ttT	ttG	1	1	B.1.1.50	0.000679
ORF7a	54	F54L	ttT	ttA	1	1	B.1.1.519	0.00004
ORF7a	54	F54del	TTT	---	1	1	B.1.1.525	0.005464
ORF7a	54	F54H	TTt	CAt	1	1	B.1.1.7	0.000001
ORF7a	54	F54Y	tTt	tAt	1	1	B.1.1.7	0.000001
ORF7a	54	F54L	ttT	ttA	1	1	B.1.1.70	0.000341
ORF7a	54	F54del	TTT	---	1	1	B.1.115	0.021739
ORF7a	54	F54del	TTT	---	1	1	B.1.140	0.018868
ORF7a	54	F54del1	ttT	tt-	1	1	B.1.160.16	0.000929
ORF7a	54	F54L	Ttt	Ctt	1	1	B.1.160.8	0.001289
ORF7a	54	F54del	TTT	---	1	1	B.1.165	0.011905
ORF7a	54	F54I	Ttt	Att	1	1	B.1.177	0.000013
ORF7a	54	F54S	tTt	tCt	1	1	B.1.177	0.000013
ORF7a	54	F54del	TTT	---	1	1	B.1.177.10	0.000878
ORF7a	54	F54F	ttT	ttC	1	1	B.1.177.12	0.000152
ORF7a	54	F54L	Ttt	Ctt	1	1	B.1.177.20	0.001517
ORF7a	54	F54S	tTt	tCt	1	1	B.1.177.21	0.000076
ORF7a	54	F54F	ttT	ttC	1	1	B.1.177.21	0.000076
ORF7a	54	F54del1	ttT	tt-	1	1	B.1.177.21	0.000076
ORF7a	54	F54Y	tTt	tAt	1	1	B.1.177.21	0.000076
ORF7a	54	F54del	TTT	---	1	1	B.1.177.5	0.001242
ORF7a	54	F54del	TTT	---	1	1	B.1.177.50	0.004695
ORF7a	54	F54del	TTT	---	1	1	B.1.177.53	0.002392
ORF7a	54	F54del	TTT	---	1	1	B.1.177.57	0.000281
ORF7a	54	F54del	TTT	---	1	1	B.1.177.62	0.001192
ORF7a	54	F54del	TTT	---	1	1	B.1.177.63	0.002703
ORF7a	54	F54del	TTT	---	1	1	B.1.177.83	0.001481
ORF7a	54	F54L	Ttt	Ctt	1	1	B.1.177.9	0.001332
ORF7a	54	F54C	tTT	tGC	1	1	B.1.2	0.000009
ORF7a	54	F54del1	ttT	tt-	1	1	B.1.214.2	0.0006
ORF7a	54	F54del1	ttT	tt-	1	1	B.1.236	0.002053
ORF7a	54	F54del	TTT	---	1	1	B.1.240	0.000216
ORF7a	54	F54I	Ttt	Att	1	1	B.1.242	0.018868
ORF7a	54	F54L	ttT	ttG	1	1	B.1.258	0.000067
ORF7a	54	F54del1	ttT	tt-	1	1	B.1.258	0.000067
ORF7a	54	F54del	TTT	---	1	1	B.1.258	0.000067
ORF7a	54	F54del	TTT	---	1	1	B.1.258.17	0.000104
ORF7a	54	F54del1	ttT	tt-	1	1	B.1.258.9	0.005
ORF7a	54	F54S	tTt	tCt	1	1	B.1.311	0.000275
ORF7a	54	F54L	ttT	ttA	1	1	B.1.319	0.003049
ORF7a	54	F54V	Ttt	Gtt	1	1	B.1.332	0.003497
ORF7a	54	F54L	Ttt	Ctt	1	1	B.1.350	0.002933
ORF7a	54	F54N	TTt	AAt	1	1	B.1.351	0.00003
ORF7a	54	F54F	ttT	ttC	1	1	B.1.351	0.00003
ORF7a	54	F54del	TTT	---	1	1	B.1.351.3	0.000876
ORF7a	54	F54del	TTT	---	1	1	B.1.356	0.001727
ORF7a	54	F54I	Ttt	Att	1	1	B.1.36	0.000146
ORF7a	54	F54L	Ttt	Ctt	1	1	B.1.36	0.000146
ORF7a	54	F54del1	ttT	tt-	1	1	B.1.36.35	0.002604
ORF7a	54	F54del	TTT	---	1	1	B.1.371	0.001122
ORF7a	54	F54L	Ttt	Ctt	1	1	B.1.371	0.001122
ORF7a	54	F54V	Ttt	Gtt	1	1	B.1.382	0.008929
ORF7a	54	F54del	TTT	---	1	1	B.1.401	0.008197
ORF7a	54	F54del	TTT	---	1	1	B.1.406	0.006061
ORF7a	54	F54F	ttT	ttC	1	1	B.1.416	0.001269
ORF7a	54	F54P	TTt	CCt	1	1	B.1.416	0.001269
ORF7a	54	F54del1	ttT	tt-	1	1	B.1.416.1	0.001563
ORF7a	54	F54del	TTT	---	1	1	B.1.416.1	0.001563
ORF7a	54	F54S	tTt	tCt	1	1	B.1.429	0.000024
ORF7a	54	F54I	Ttt	Att	1	1	B.1.438	0.006536
ORF7a	54	F54del	TTT	---	1	1	B.1.438.1	0.000107
ORF7a	54	F54del	TTT	---	1	1	B.1.459	0.004082
ORF7a	54	F54del	TTT	---	1	1	B.1.466.2	0.000391
ORF7a	54	F54del1	TTT	CC-	1	1	B.1.468	0.005714
ORF7a	54	F54F	ttT	ttC	1	1	B.1.469	0.00361
ORF7a	54	F54I	Ttt	Att	1	1	B.1.469	0.00361
ORF7a	54	F54del	TTT	---	1	1	B.1.470	0.001404
ORF7a	54	F54del2	tTT	t--	1	1	B.1.470	0.001404
ORF7a	54	F54I	Ttt	Att	1	1	B.1.497	0.000315
ORF7a	54	F54L	ttT	ttA	1	1	B.1.525	0.000113
ORF7a	54	F54I	Ttt	Att	1	1	B.1.525	0.000113
ORF7a	54	F54H	TTt	CAt	1	1	B.1.525	0.000113
ORF7a	54	F54Y	tTt	tAt	1	1	B.1.525	0.000113
ORF7a	54	F54I	Ttt	Att	1	1	B.1.526	0.000024
ORF7a	54	F54F	ttT	ttC	1	1	B.1.527	0.003704
ORF7a	54	F54del	TTT	---	1	1	B.1.535	0.028571
ORF7a	54	F54L	ttT	ttA	1	1	B.1.558	0.004566
ORF7a	54	F54I	Ttt	Att	1	1	B.1.558	0.004566
ORF7a	54	F54L	ttT	ttA	1	1	B.1.565	0.00081
ORF7a	54	F54del	TTT	---	1	1	B.1.568	0.001111
ORF7a	54	F54del1	ttT	tt-	1	1	B.1.575	0.000303
ORF7a	54	F54D	TTt	GAt	1	1	B.1.588	0.00091
ORF7a	54	F54L	ttT	ttA	1	1	B.1.588	0.00091
ORF7a	54	F54Y	tTt	tAt	1	1	B.1.588	0.00091
ORF7a	54	F54X	tTT	tAA	1	1	B.1.588	0.00091
ORF7a	54	F54E	TTT	GAA	1	1	B.1.588	0.00091
ORF7a	54	F54del	TTT	---	1	1	B.1.595	0.000261
ORF7a	54	F54I	Ttt	Att	1	1	B.1.596	0.000087
ORF7a	54	F54del2	tTT	t--	1	1	B.1.617.1	0.000129
ORF7a	54	F54F	ttT	ttC	1	1	B.1.617.1	0.000129
ORF7a	54	F54M	TtT	AtG	1	1	B.1.617.2	0.000004
ORF7a	54	F54D	TTt	GAt	1	1	B.1.617.2	0.000004
ORF7a	54	F54T	TTt	ACt	1	1	B.1.617.2	0.000004
ORF7a	54	F54del	TTT	---	1	1	B.1.617.3	0.002985
ORF7a	54	F54del2	tTT	t--	1	1	B.1.617.3	0.002985
ORF7a	54	F54L	Ttt	Ctt	1	1	B.1.617.3	0.002985
ORF7a	54	F54del1	ttT	tt-	1	1	B.1.621	0.000089
ORF7a	54	F54L	Ttt	Ctt	1	1	B.1.621.1	0.000506
ORF7a	54	F54L	Ttt	Ctt	1	1	B.1.627	0.00202
ORF7a	54	F54del1	Ttt	-tt	1	1	B.1.630	0.005236
ORF7a	54	F54S	tTt	tCt	1	1	B.1.636	0.006711
ORF7a	54	F54S	tTt	tCt	1	1	B.1.637	0.000073
ORF7a	54	F54del	TTT	---	1	1	B.1.638	0.052632
ORF7a	54	F54del	TTT	---	1	1	B.1.9.1	0.032258
ORF7a	54	F54del1	ttT	tt-	1	1	B.11	0.005128
ORF7a	54	F54del	TTT	---	1	1	B.39	0.002331
ORF7a	54	F54del	TTT	---	1	1	C.36.3	0.000567
ORF7a	54	F54del1	ttT	tt-	1	1	C.36.3	0.000567
ORF7a	54	F54del2	TTt	--t	1	1	C.37	0.000116
ORF7a	54	F54L	Ttt	Ctt	1	1	D.2	0.000075
ORF7a	54	F54S	tTt	tCt	1	1	D.2	0.000075
ORF7a	54	F54del	TTT	---	1	1	K.3	0.006173
ORF7a	54	F54L	Ttt	Ctt	1	1	L.3	0.003546
ORF7a	54	F54F	ttT	ttC	1	1	P.1	0.000016
ORF7a	54	F54del	TTT	---	1	1	P.1.1	0.000318
ORF7a	54	F54del	TTT	---	1	1	P.1.13	0.000898
ORF7a	54	F54L	ttT	ttG	1	1	P.1.14	0.000048
ORF7a	54	F54del	TTT	---	1	1	P.1.16	0.000374
ORF7a	54	F54del	TTT	---	1	1	P.1.17	0.000162
ORF7a	54	F54del	TTT	---	1	1	P.1.3	0.034483
ORF7a	54	F54del	TTT	---	1	1	P.1.4	0.000977
ORF7a	54	F54L	ttT	ttG	1	1	P.1.7	0.000319
ORF7a	54	F54del	TTT	---	1	1	Q.1	0.000126
ORF7a	54	F54del	TTT	---	1	1	Q.4	0.000455
ORF7a	54	F54L	TtT	CtG	1	1	Q.4	0.000455
ORF7a	54	F54del	TTT	---	1	1	Q.7	0.001111
ORF7a	54	F54F	ttT	ttC	1	1	Q.8	0.000165
ORF7a	54	F54S	tTt	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.