CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF7a : CodonNum = 88

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	88	I88I		syn	atC	atT	3904	3873	0.992059	27655-27657
ORF7a	88	I88I		syn	atC	atA	3904	31	0.00794057	27655-27657
ORF7a	88	I88T		nonsyn	aTc	aCc	2882	2873	0.996877	27655-27657
ORF7a	88	I88T		nonsyn	aTC	aCT	2882	9	0.00312283	27655-27657
ORF7a	88	I88del		del	ATC	---	1980	1980	1	27655-27657
ORF7a	88	I88V		nonsyn	Atc	Gtc	1165	1164	0.999142	27655-27657
ORF7a	88	I88V		nonsyn	AtC	GtA	1165	1	0.000858369	27655-27657
ORF7a	88	I88F		nonsyn	Atc	Ttc	121	120	0.991736	27655-27657
ORF7a	88	I88F		nonsyn	AtC	TtT	121	1	0.00826446	27655-27657
ORF7a	88	I88S		nonsyn	aTc	aGc	89	87	0.977528	27655-27657
ORF7a	88	I88S		nonsyn	ATC	TCT	89	1	0.011236	27655-27657
ORF7a	88	I88S		nonsyn	ATc	TCc	89	1	0.011236	27655-27657
ORF7a	88	I88L		nonsyn	Atc	Ctc	63	63	1	27655-27657
ORF7a	88	I88N		nonsyn	aTc	aAc	24	24	1	27655-27657
ORF7a	88	I88E		nonsyn	ATC	GAA	15	15	1	27655-27657
ORF7a	88	I88M		nonsyn	atC	atG	15	15	1	27655-27657
ORF7a	88	I88del1		del	atC	at-	15	6	0.4	27655-27657
ORF7a	88	I88del1		del	Atc	-tc	15	4	0.266667	27655-27657
ORF7a	88	I88del1		del	ATC	-NN	15	2	0.133333	27655-27657
ORF7a	88	I88del1		del	AtC	-tN	15	1	0.0666667	27655-27657
ORF7a	88	I88del1		del	aTC	a-N	15	1	0.0666667	27655-27657
ORF7a	88	I88del1		del	aTc	a-c	15	1	0.0666667	27655-27657
ORF7a	88	I88del2		del	ATc	--c	10	9	0.9	27655-27657
ORF7a	88	I88del2		del	ATC	G--	10	1	0.1	27655-27657
ORF7a	88	I88Y		nonsyn	ATc	TAc	5	5	1	27655-27657
ORF7a	88	I88K		nonsyn	aTC	aAA	4	4	1	27655-27657
ORF7a	88	I88R		nonsyn	aTC	aGA	1	1	1	27655-27657
ORF7a	88	I88A		nonsyn	ATc	GCc	1	1	1	27655-27657

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	88	I88I	atC	atT	3873	3904	All	0.000741
ORF7a	88	I88I	atC	atA	31	3904	All	0.000006
ORF7a	88	I88T	aTc	aCc	2873	2882	All	0.000549
ORF7a	88	I88T	aTC	aCT	9	2882	All	0.000002
ORF7a	88	I88T	aTc	aCc	2529	2529	AY.4	0.003936
ORF7a	88	I88del	ATC	---	1980	1980	All	0.000379
ORF7a	88	I88I	atC	atT	1440	1440	AY.73	0.958084
ORF7a	88	I88V	Atc	Gtc	1164	1165	All	0.000223
ORF7a	88	I88V	AtC	GtA	1	1165	All	0
ORF7a	88	I88V	Atc	Gtc	688	688	B.1.1	0.012481
ORF7a	88	I88I	atC	atT	634	634	AY.4	0.000987
ORF7a	88	I88del	ATC	---	515	515	B.1.1.7	0.000461
ORF7a	88	I88del	ATC	---	246	246	AY.4	0.000383
ORF7a	88	I88I	atC	atT	224	224	AY.43	0.000992
ORF7a	88	I88del	ATC	---	176	176	B.1.177.21	0.013459
ORF7a	88	I88I	atC	atT	162	167	B.1.1.7	0.000145
ORF7a	88	I88I	atC	atA	5	167	B.1.1.7	0.000004
ORF7a	88	I88I	atC	atT	129	133	B.1.617.2	0.000486
ORF7a	88	I88I	atC	atA	4	133	B.1.617.2	0.000015
ORF7a	88	I88I	atC	atT	127	128	AY.29	0.002003
ORF7a	88	I88I	atC	atA	1	128	AY.29	0.000016
ORF7a	88	I88F	Atc	Ttc	120	121	All	0.000023
ORF7a	88	I88F	AtC	TtT	1	121	All	0
ORF7a	88	I88I	atC	atT	106	106	AY.9.1	0.008875
ORF7a	88	I88I	atC	atT	95	95	AY.102	0.002519
ORF7a	88	I88del	ATC	---	91	91	AY.3	0.000905
ORF7a	88	I88S	aTc	aGc	87	89	All	0.000017
ORF7a	88	I88S	ATc	TCc	1	89	All	0
ORF7a	88	I88S	ATC	TCT	1	89	All	0
ORF7a	88	I88V	Atc	Gtc	82	82	AY.4	0.000128
ORF7a	88	I88del	ATC	---	81	81	AY.29	0.001278
ORF7a	88	I88I	atC	atT	75	75	AY.25	0.000451
ORF7a	88	I88I	atC	atT	74	74	AY.44	0.00045
ORF7a	88	I88del	ATC	---	73	73	AY.25	0.000439
ORF7a	88	I88S	aTc	aGc	63	64	B.1.1.7	0.000056
ORF7a	88	I88S	ATC	TCT	1	64	B.1.1.7	0.000001
ORF7a	88	I88L	Atc	Ctc	63	63	All	0.000012
ORF7a	88	I88I	atC	atT	63	63	AY.90	0.043121
ORF7a	88	I88I	atC	atT	58	58	AY.23	0.004045
ORF7a	88	I88L	Atc	Ctc	58	58	B.1.1.7	0.000052
ORF7a	88	I88I	atC	atT	54	54	AY.47	0.00168
ORF7a	88	I88del	ATC	---	50	50	AY.103	0.00031
ORF7a	88	I88del	ATC	---	50	50	AY.43	0.000222
ORF7a	88	I88V	Atc	Gtc	44	44	AY.69	0.008214
ORF7a	88	I88V	Atc	Gtc	43	43	AY.103	0.000267
ORF7a	88	I88V	Atc	Gtc	43	43	B.1.617.2	0.000162
ORF7a	88	I88I	atC	atT	42	42	AY.20	0.001632
ORF7a	88	I88T	aTc	aCc	42	42	B.1.1.7	0.000038
ORF7a	88	I88del	ATC	---	42	42	B.1.617.2	0.000158
ORF7a	88	I88I	atC	atT	38	40	AY.103	0.000236
ORF7a	88	I88I	atC	atA	2	40	AY.103	0.000012
ORF7a	88	I88I	atC	atT	40	40	AY.26	0.001132
ORF7a	88	I88del	ATC	---	37	37	AY.39	0.000914
ORF7a	88	I88del	ATC	---	37	37	B.1.1.284	0.003974
ORF7a	88	I88T	aTc	aCc	36	36	B.1	0.00033
ORF7a	88	I88T	aTc	aCc	35	35	B.1.617.2	0.000132
ORF7a	88	I88del	ATC	---	34	34	B.1.621	0.00301
ORF7a	88	I88del	ATC	---	31	31	AY.44	0.000189
ORF7a	88	I88V	Atc	Gtc	30	30	AY.9	0.002028
ORF7a	88	I88del	ATC	---	29	29	B.1.2	0.000255
ORF7a	88	I88I	atC	atT	28	28	P.1	0.000441
ORF7a	88	I88del	ATC	---	27	27	B.1	0.000247
ORF7a	88	I88N	aTc	aAc	24	24	All	0.000005
ORF7a	88	I88I	atC	atT	24	24	AY.113	0.003417
ORF7a	88	I88F	Atc	Ttc	24	24	B.1.617.2	0.00009
ORF7a	88	I88I	atC	atT	23	23	AY.27	0.001489
ORF7a	88	I88del	ATC	---	23	23	AY.3.1	0.001961
ORF7a	88	I88V	Atc	Gtc	22	23	AY.44	0.000134
ORF7a	88	I88V	AtC	GtA	1	23	AY.44	0.000006
ORF7a	88	I88del	ATC	---	23	23	B.1.1.214	0.001276
ORF7a	88	I88V	Atc	Gtc	23	23	B.1.1.7	0.000021
ORF7a	88	I88T	aTc	aCc	20	20	AY.5	0.000413
ORF7a	88	I88del	ATC	---	20	20	AY.7.2	0.011186
ORF7a	88	I88I	atC	atT	18	18	AY.5	0.000372
ORF7a	88	I88T	aTc	aCc	18	18	B.1.1	0.000327
ORF7a	88	I88del	ATC	---	18	18	B.1.526	0.000423
ORF7a	88	I88T	aTc	aCc	17	17	AY.103	0.000106
ORF7a	88	I88T	aTc	aCc	17	17	AY.43	0.000075
ORF7a	88	I88del	ATC	---	17	17	P.1	0.000268
ORF7a	88	I88V	Atc	Gtc	16	16	B.1.1.319	0.280702
ORF7a	88	I88M	atC	atG	15	15	All	0.000003
ORF7a	88	I88E	ATC	GAA	15	15	All	0.000003
ORF7a	88	I88del1	atC	at-	6	15	All	0.000001
ORF7a	88	I88del1	Atc	-tc	4	15	All	0.000001
ORF7a	88	I88del1	ATC	-NN	2	15	All	0
ORF7a	88	I88del1	AtC	-tN	1	15	All	0
ORF7a	88	I88del1	aTC	a-N	1	15	All	0
ORF7a	88	I88del1	aTc	a-c	1	15	All	0
ORF7a	88	I88del	ATC	---	15	15	AY.26	0.000425
ORF7a	88	I88I	atC	atT	15	15	AY.46	0.001561
ORF7a	88	I88T	aTc	aCc	15	15	B.1.243	0.001044
ORF7a	88	I88I	atC	atT	14	14	AY.4.2	0.000304
ORF7a	88	I88F	Atc	Ttc	14	14	AY.43	0.000062
ORF7a	88	I88del	ATC	---	14	14	B.1.177	0.000184
ORF7a	88	I88E	ATC	GAA	13	13	B.1.177.21	0.000994
ORF7a	88	I88T	aTc	aCc	13	13	P.1	0.000205
ORF7a	88	I88I	atC	atT	9	12	AY.39	0.000222
ORF7a	88	I88I	atC	atA	3	12	AY.39	0.000074
ORF7a	88	I88F	Atc	Ttc	12	12	AY.4	0.000019
ORF7a	88	I88I	atC	atT	12	12	AY.4.3	0.010101
ORF7a	88	I88I	atC	atT	12	12	AY.61	0.001257
ORF7a	88	I88T	aTc	aCc	12	12	AY.75.1	0.002164
ORF7a	88	I88T	aTc	aCc	12	12	AY.99.2	0.001106
ORF7a	88	I88I	atC	atT	12	12	B.1.2	0.000106
ORF7a	88	I88del	ATC	---	12	12	B.1.324	0.019262
ORF7a	88	I88I	atC	atT	12	12	B.1.429	0.000282
ORF7a	88	I88del	ATC	---	11	11	AY.100	0.000506
ORF7a	88	I88del	ATC	---	11	11	AY.121	0.001488
ORF7a	88	I88I	atC	atT	11	11	AY.3	0.000109
ORF7a	88	I88I	atC	atT	11	11	B.1.1	0.0002
ORF7a	88	I88V	Atc	Gtc	11	11	B.1.1.1	0.003594
ORF7a	88	I88V	Atc	Gtc	11	11	B.1.177.24	0.014249
ORF7a	88	I88del	ATC	---	11	11	B.1.637	0.000804
ORF7a	88	I88del2	ATc	--c	9	10	All	0.000002
ORF7a	88	I88del2	ATC	G--	1	10	All	0
ORF7a	88	I88I	atC	atT	10	10	AY.54	0.000953
ORF7a	88	I88del	ATC	---	10	10	B.1.1.519	0.000397
ORF7a	88	I88I	atC	atT	10	10	B.1.595	0.00261
ORF7a	88	I88T	aTc	aCc	10	10	P.1.14	0.000478
ORF7a	88	I88del	ATC	---	9	9	AY.110	0.001014
ORF7a	88	I88del	ATC	---	9	9	AY.120	0.000335
ORF7a	88	I88I	atC	atT	8	9	B.1	0.000073
ORF7a	88	I88I	atC	atA	1	9	B.1	0.000009
ORF7a	88	I88del	ATC	---	9	9	B.1.1	0.000163
ORF7a	88	I88V	Atc	Gtc	9	9	B.1.1.269	0.012179
ORF7a	88	I88I	atC	atT	9	9	B.1.1.50	0.00611
ORF7a	88	I88del	ATC	---	9	9	B.1.351	0.000268
ORF7a	88	I88F	Atc	Ttc	9	9	B.1.369	0.002567
ORF7a	88	I88del	ATC	---	9	9	R.1	0.00081
ORF7a	88	I88I	atC	atT	8	8	AY.42	0.000322
ORF7a	88	I88I	atC	atA	7	8	AY.69	0.001307
ORF7a	88	I88I	atC	atT	1	8	AY.69	0.000187
ORF7a	88	I88I	atC	atT	8	8	AY.9.2	0.000294
ORF7a	88	I88V	Atc	Gtc	8	8	B.1.1.161	0.028269
ORF7a	88	I88del	ATC	---	8	8	B.1.1.231	0.024768
ORF7a	88	I88M	atC	atG	8	8	B.1.1.7	0.000007
ORF7a	88	I88F	Atc	Ttc	8	8	B.1.1.7	0.000007
ORF7a	88	I88T	aTC	aCT	8	8	B.1.399	0.015474
ORF7a	88	I88F	Atc	Ttc	7	7	AY.105	0.004502
ORF7a	88	I88I	atC	atT	7	7	AY.120	0.00026
ORF7a	88	I88V	Atc	Gtc	7	7	AY.5	0.000145
ORF7a	88	I88V	Atc	Gtc	7	7	AY.54	0.000667
ORF7a	88	I88V	Atc	Gtc	7	7	AY.7.1	0.000789
ORF7a	88	I88I	atC	atT	7	7	B.1.351	0.000208
ORF7a	88	I88del	ATC	---	7	7	B.1.596	0.00061
ORF7a	88	I88del	ATC	---	7	7	C.37	0.000812
ORF7a	88	I88I	atC	atT	6	6	AY.117	0.000507
ORF7a	88	I88I	atC	atT	6	6	AY.119	0.000212
ORF7a	88	I88I	atC	atT	6	6	AY.33	0.000401
ORF7a	88	I88N	aTc	aAc	6	6	AY.39.1	0.000238
ORF7a	88	I88V	Atc	Gtc	6	6	AY.43	0.000027
ORF7a	88	I88F	Atc	Ttc	6	6	AY.61	0.000629
ORF7a	88	I88del	ATC	---	6	6	B.1.160	0.000187
ORF7a	88	I88del	ATC	---	6	6	P.1.15	0.001394
ORF7a	88	I88Y	ATc	TAc	5	5	All	0.000001
ORF7a	88	I88V	Atc	Gtc	5	5	AY.21	0.009488
ORF7a	88	I88del	ATC	---	5	5	AY.23	0.000349
ORF7a	88	I88del	ATC	---	5	5	AY.42	0.000201
ORF7a	88	I88T	aTc	aCc	5	5	AY.44	0.00003
ORF7a	88	I88I	atC	atT	5	5	AY.45	0.000608
ORF7a	88	I88I	atC	atT	5	5	AY.46.5	0.000992
ORF7a	88	I88I	atC	atT	5	5	AY.6	0.000206
ORF7a	88	I88V	Atc	Gtc	5	5	B.1.1.194	0.024752
ORF7a	88	I88T	aTc	aCc	5	5	B.1.1.519	0.000199
ORF7a	88	I88Y	ATc	TAc	5	5	B.1.1.7	0.000004
ORF7a	88	I88I	atC	atT	5	5	B.1.177	0.000066
ORF7a	88	I88V	Atc	Gtc	5	5	B.1.258	0.000333
ORF7a	88	I88del	ATC	---	5	5	B.1.525	0.000566
ORF7a	88	I88V	Atc	Gtc	5	5	B.1.595	0.001305
ORF7a	88	I88T	aTc	aCc	5	5	N.4	0.021277
ORF7a	88	I88I	atC	atT	4	4	A.2.4	0.013468
ORF7a	88	I88K	aTC	aAA	4	4	All	0.000001
ORF7a	88	I88I	atC	atT	4	4	AY.110	0.000451
ORF7a	88	I88del	ATC	---	4	4	AY.118	0.000251
ORF7a	88	I88del	ATC	---	4	4	AY.119	0.000141
ORF7a	88	I88T	aTc	aCc	4	4	AY.119	0.000141
ORF7a	88	I88del	ATC	---	4	4	AY.20	0.000155
ORF7a	88	I88T	aTc	aCc	4	4	AY.26	0.000113
ORF7a	88	I88T	aTc	aCc	4	4	AY.3	0.00004
ORF7a	88	I88S	aTc	aGc	4	4	AY.4	0.000006
ORF7a	88	I88I	atC	atT	4	4	AY.4.2.1	0.000596
ORF7a	88	I88del2	ATc	--c	4	4	AY.43	0.000018
ORF7a	88	I88I	atC	atT	4	4	AY.58	0.00363
ORF7a	88	I88I	atC	atT	4	4	AY.74	0.000463
ORF7a	88	I88I	atC	atT	4	4	AY.75	0.000224
ORF7a	88	I88V	Atc	Gtc	4	4	AY.75.1	0.000721
ORF7a	88	I88I	atC	atT	4	4	AY.77	0.00451
ORF7a	88	I88del	ATC	---	4	4	AY.79	0.004843
ORF7a	88	I88I	atC	atT	4	4	AY.84	0.00175
ORF7a	88	I88I	atC	atT	4	4	AY.85	0.001709
ORF7a	88	I88I	atC	atT	4	4	AY.9	0.00027
ORF7a	88	I88I	atC	atT	4	4	AY.98.1	0.000194
ORF7a	88	I88del	ATC	---	4	4	AY.98.1	0.000194
ORF7a	88	I88I	atC	atT	4	4	B.1.1.157	0.003653
ORF7a	88	I88I	atC	atT	4	4	B.1.1.301	0.004717
ORF7a	88	I88V	Atc	Gtc	4	4	B.1.1.409	0.011331
ORF7a	88	I88I	atC	atT	4	4	B.1.1.519	0.000159
ORF7a	88	I88I	atC	atA	2	4	B.1.160	0.000062
ORF7a	88	I88I	atC	atT	2	4	B.1.160	0.000062
ORF7a	88	I88I	atC	atT	4	4	B.1.36	0.000584
ORF7a	88	I88I	atC	atT	4	4	B.1.617.1	0.000516
ORF7a	88	I88I	atC	atT	4	4	C.37	0.000464
ORF7a	88	I88del	ATC	---	4	4	Q.8	0.00066
ORF7a	88	I88I	atC	atT	3	3	AY.100	0.000138
ORF7a	88	I88I	atC	atT	3	3	AY.118	0.000188
ORF7a	88	I88M	atC	atG	3	3	AY.25	0.000018
ORF7a	88	I88T	aTc	aCc	3	3	AY.25	0.000018
ORF7a	88	I88V	Atc	Gtc	3	3	AY.3	0.00003
ORF7a	88	I88I	atC	atT	2	3	AY.3.1	0.000171
ORF7a	88	I88I	atC	atA	1	3	AY.3.1	0.000085
ORF7a	88	I88I	atC	atT	3	3	AY.34.1	0.00153
ORF7a	88	I88T	aTc	aCc	3	3	AY.39	0.000074
ORF7a	88	I88del	ATC	---	3	3	AY.4.2	0.000065
ORF7a	88	I88V	Atc	Gtc	3	3	AY.4.2	0.000065
ORF7a	88	I88T	aTc	aCc	3	3	AY.4.2	0.000065
ORF7a	88	I88del	ATC	---	3	3	AY.4.5	0.000322
ORF7a	88	I88F	Atc	Ttc	3	3	AY.44	0.000018
ORF7a	88	I88del	ATC	---	3	3	AY.46.4	0.000494
ORF7a	88	I88del	ATC	---	3	3	AY.47	0.000093
ORF7a	88	I88I	atC	atT	3	3	AY.57	0.001969
ORF7a	88	I88V	Atc	Gtc	3	3	AY.61	0.000314
ORF7a	88	I88I	atC	atT	2	3	AY.7.1	0.000225
ORF7a	88	I88I	atC	atA	1	3	AY.7.1	0.000113
ORF7a	88	I88V	Atc	Gtc	3	3	AY.85	0.001282
ORF7a	88	I88I	atC	atT	3	3	AY.92	0.000862
ORF7a	88	I88I	atC	atT	3	3	AY.99.2	0.000276
ORF7a	88	I88V	Atc	Gtc	3	3	B.1	0.000027
ORF7a	88	I88del	ATC	---	3	3	B.1.1.121	0.007282
ORF7a	88	I88del	ATC	---	3	3	B.1.1.25	0.001706
ORF7a	88	I88V	Atc	Gtc	3	3	B.1.1.277	0.002276
ORF7a	88	I88V	Atc	Gtc	3	3	B.1.160	0.000094
ORF7a	88	I88F	Atc	Ttc	3	3	B.1.177	0.00004
ORF7a	88	I88K	aTC	aAA	3	3	B.1.177.21	0.000229
ORF7a	88	I88I	atC	atT	3	3	B.1.177.81	0.000568
ORF7a	88	I88T	aTc	aCc	3	3	B.1.2	0.000026
ORF7a	88	I88I	atC	atT	3	3	B.1.221	0.000213
ORF7a	88	I88del	ATC	---	3	3	B.1.234	0.000396
ORF7a	88	I88S	aTc	aGc	3	3	B.1.258	0.0002
ORF7a	88	I88I	atC	atT	3	3	B.1.258	0.0002
ORF7a	88	I88I	atC	atT	3	3	B.1.526	0.000071
ORF7a	88	I88del	ATC	---	3	3	B.1.575	0.00091
ORF7a	88	I88T	aTc	aCc	3	3	B.1.577	0.002062
ORF7a	88	I88I	atC	atT	3	3	B.1.596	0.000261
ORF7a	88	I88V	Atc	Gtc	3	3	B.1.617.1	0.000387
ORF7a	88	I88N	aTc	aAc	3	3	B.1.617.2	0.000011
ORF7a	88	I88del	ATC	---	3	3	B.1.626	0.017143
ORF7a	88	I88I	atC	atA	2	3	B.1.637	0.000146
ORF7a	88	I88I	atC	atT	1	3	B.1.637	0.000073
ORF7a	88	I88V	Atc	Gtc	3	3	B.1.93	0.002801
ORF7a	88	I88I	atC	atT	3	3	P.1.14	0.000143
ORF7a	88	I88del	ATC	---	3	3	Q.1	0.000379
ORF7a	88	I88del	ATC	---	2	2		0.111111
ORF7a	88	I88del	ATC	---	2	2	A	0.000774
ORF7a	88	I88del	ATC	---	2	2	A.28	0.005291
ORF7a	88	I88T	aTc	aCc	2	2	AY.100	0.000092
ORF7a	88	I88V	Atc	Gtc	2	2	AY.102	0.000053
ORF7a	88	I88F	Atc	Ttc	2	2	AY.103	0.000012
ORF7a	88	I88del1	Atc	-tc	1	2	AY.103	0.000006
ORF7a	88	I88del1	ATC	-NN	1	2	AY.103	0.000006
ORF7a	88	I88del	ATC	---	2	2	AY.106	0.00067
ORF7a	88	I88del	ATC	---	2	2	AY.108	0.002205
ORF7a	88	I88T	aTc	aCc	2	2	AY.110	0.000225
ORF7a	88	I88del	ATC	---	2	2	AY.114	0.000462
ORF7a	88	I88T	aTc	aCc	2	2	AY.118	0.000125
ORF7a	88	I88del	ATC	---	2	2	AY.12	0.000632
ORF7a	88	I88V	Atc	Gtc	2	2	AY.120	0.000074
ORF7a	88	I88I	atC	atT	2	2	AY.121	0.000271
ORF7a	88	I88S	aTc	aGc	2	2	AY.121	0.000271
ORF7a	88	I88I	atC	atT	2	2	AY.14	0.000176
ORF7a	88	I88del	ATC	---	2	2	AY.16	0.000759
ORF7a	88	I88T	aTc	aCc	2	2	AY.20	0.000078
ORF7a	88	I88I	atC	atT	2	2	AY.24	0.000862
ORF7a	88	I88del	ATC	---	2	2	AY.24	0.000862
ORF7a	88	I88V	Atc	Gtc	2	2	AY.25	0.000012
ORF7a	88	I88F	Atc	Ttc	2	2	AY.29	0.000032
ORF7a	88	I88del	ATC	---	2	2	AY.29.1	0.000441
ORF7a	88	I88I	atC	atT	2	2	AY.29.1	0.000441
ORF7a	88	I88del	ATC	---	2	2	AY.33	0.000134
ORF7a	88	I88del	ATC	---	2	2	AY.34	0.000194
ORF7a	88	I88del	ATC	---	2	2	AY.36	0.000296
ORF7a	88	I88I	atC	atT	2	2	AY.39.1	0.000079
ORF7a	88	I88V	Atc	Gtc	2	2	AY.39.1	0.000079
ORF7a	88	I88M	atC	atG	2	2	AY.4	0.000003
ORF7a	88	I88del1	Atc	-tc	1	2	AY.4	0.000002
ORF7a	88	I88del1	aTC	a-N	1	2	AY.4	0.000002
ORF7a	88	I88I	atC	atT	2	2	AY.4.4	0.000818
ORF7a	88	I88I	atC	atT	2	2	AY.40	0.001929
ORF7a	88	I88del1	atC	at-	2	2	AY.44	0.000012
ORF7a	88	I88del	ATC	---	2	2	AY.45	0.000243
ORF7a	88	I88del	ATC	---	2	2	AY.5	0.000041
ORF7a	88	I88del2	ATc	--c	2	2	AY.75	0.000112
ORF7a	88	I88del	ATC	---	2	2	AY.9.1	0.000167
ORF7a	88	I88del	ATC	---	2	2	AY.9.2	0.000073
ORF7a	88	I88S	aTc	aGc	2	2	AY.9.2	0.000073
ORF7a	88	I88del	ATC	---	2	2	AY.99	0.002099
ORF7a	88	I88del	ATC	---	2	2	B	0.000256
ORF7a	88	I88F	Atc	Ttc	2	2	B.1	0.000018
ORF7a	88	I88E	ATC	GAA	2	2	B.1	0.000018
ORF7a	88	I88F	Atc	Ttc	2	2	B.1.1	0.000036
ORF7a	88	I88N	aTc	aAc	2	2	B.1.1	0.000036
ORF7a	88	I88I	atC	atT	2	2	B.1.1.153	0.002191
ORF7a	88	I88I	atC	atT	2	2	B.1.1.189	0.003026
ORF7a	88	I88V	Atc	Gtc	2	2	B.1.1.198	0.002937
ORF7a	88	I88V	Atc	Gtc	2	2	B.1.1.254	0.022472
ORF7a	88	I88I	atC	atT	2	2	B.1.1.284	0.000215
ORF7a	88	I88V	Atc	Gtc	2	2	B.1.1.298	0.001724
ORF7a	88	I88V	Atc	Gtc	2	2	B.1.1.385	0.008929
ORF7a	88	I88V	Atc	Gtc	2	2	B.1.1.419	0.014815
ORF7a	88	I88V	Atc	Gtc	2	2	B.1.1.430	0.083333
ORF7a	88	I88T	aTc	aCc	2	2	B.1.1.434	0.000697
ORF7a	88	I88del1	Atc	-tc	1	2	B.1.1.7	0.000001
ORF7a	88	I88del1	ATC	-NN	1	2	B.1.1.7	0.000001
ORF7a	88	I88T	aTc	aCc	2	2	B.1.160	0.000062
ORF7a	88	I88F	Atc	Ttc	2	2	B.1.160	0.000062
ORF7a	88	I88T	aTc	aCc	2	2	B.1.177	0.000026
ORF7a	88	I88del	ATC	---	2	2	B.1.177.15	0.001262
ORF7a	88	I88del	ATC	---	2	2	B.1.177.86	0.000367
ORF7a	88	I88S	aTc	aGc	2	2	B.1.2	0.000018
ORF7a	88	I88V	Atc	Gtc	2	2	B.1.2	0.000018
ORF7a	88	I88del	ATC	---	2	2	B.1.214.2	0.001199
ORF7a	88	I88F	Atc	Ttc	2	2	B.1.221	0.000142
ORF7a	88	I88del	ATC	---	2	2	B.1.258.11	0.000793
ORF7a	88	I88F	Atc	Ttc	2	2	B.1.351	0.000059
ORF7a	88	I88N	aTc	aAc	2	2	B.1.351	0.000059
ORF7a	88	I88del	ATC	---	2	2	B.1.36	0.000292
ORF7a	88	I88N	aTc	aAc	2	2	B.1.36.1	0.002281
ORF7a	88	I88I	atC	atT	2	2	B.1.427	0.000101
ORF7a	88	I88del	ATC	---	2	2	B.1.427	0.000101
ORF7a	88	I88del	ATC	---	2	2	B.1.429	0.000047
ORF7a	88	I88V	Atc	Gtc	2	2	B.1.526	0.000047
ORF7a	88	I88T	aTc	aCc	2	2	B.1.617.1	0.000258
ORF7a	88	I88S	aTc	aGc	2	2	B.1.9.5	0.011364
ORF7a	88	I88I	atC	atT	2	2	P.1.17.1	0.00175
ORF7a	88	I88I	atC	atT	2	2	Q.1	0.000253
ORF7a	88	I88L	Atc	Ctc	1	1		0.055556
ORF7a	88	I88del	ATC	---	1	1	A.1	0.000282
ORF7a	88	I88del	ATC	---	1	1	A.2.2	0.001689
ORF7a	88	I88T	aTc	aCc	1	1	A.2.4	0.003367
ORF7a	88	I88F	Atc	Ttc	1	1	A.2.5	0.000499
ORF7a	88	I88T	aTc	aCc	1	1	AD.2	0.000219
ORF7a	88	I88R	aTC	aGA	1	1	All	0
ORF7a	88	I88A	ATc	GCc	1	1	All	0
ORF7a	88	I88T	aTc	aCc	1	1	AU.1	0.001266
ORF7a	88	I88I	atC	atT	1	1	AU.3	0.00211
ORF7a	88	I88del	ATC	---	1	1	AY.101	0.00049
ORF7a	88	I88N	aTc	aAc	1	1	AY.102	0.000027
ORF7a	88	I88F	Atc	Ttc	1	1	AY.102	0.000027
ORF7a	88	I88V	Atc	Gtc	1	1	AY.104	0.001984
ORF7a	88	I88T	aTc	aCc	1	1	AY.104	0.001984
ORF7a	88	I88I	atC	atT	1	1	AY.104	0.001984
ORF7a	88	I88I	atC	atT	1	1	AY.105	0.000643
ORF7a	88	I88T	aTc	aCc	1	1	AY.105	0.000643
ORF7a	88	I88I	atC	atT	1	1	AY.106	0.000335
ORF7a	88	I88V	Atc	Gtc	1	1	AY.111	0.000183
ORF7a	88	I88V	Atc	Gtc	1	1	AY.113	0.000142
ORF7a	88	I88del	ATC	---	1	1	AY.113	0.000142
ORF7a	88	I88I	atC	atT	1	1	AY.116	0.000287
ORF7a	88	I88del	ATC	---	1	1	AY.116	0.000287
ORF7a	88	I88del	ATC	---	1	1	AY.116.1	0.000311
ORF7a	88	I88del	ATC	---	1	1	AY.117	0.000085
ORF7a	88	I88V	Atc	Gtc	1	1	AY.118	0.000063
ORF7a	88	I88del2	ATc	--c	1	1	AY.119	0.000035
ORF7a	88	I88V	Atc	Gtc	1	1	AY.119	0.000035
ORF7a	88	I88F	Atc	Ttc	1	1	AY.12	0.000316
ORF7a	88	I88T	aTc	aCc	1	1	AY.120.2.1	0.000498
ORF7a	88	I88I	atC	atT	1	1	AY.120.2.1	0.000498
ORF7a	88	I88F	AtC	TtT	1	1	AY.121	0.000135
ORF7a	88	I88del	ATC	---	1	1	AY.13	0.000161
ORF7a	88	I88del	ATC	---	1	1	AY.14	0.000088
ORF7a	88	I88I	atC	atT	1	1	AY.16	0.00038
ORF7a	88	I88I	atC	atT	1	1	AY.16.1	0.00047
ORF7a	88	I88del	ATC	---	1	1	AY.19	0.00114
ORF7a	88	I88V	Atc	Gtc	1	1	AY.20	0.000039
ORF7a	88	I88F	Atc	Ttc	1	1	AY.25	0.000006
ORF7a	88	I88del1	atC	at-	1	1	AY.25	0.000006
ORF7a	88	I88F	Atc	Ttc	1	1	AY.26	0.000028
ORF7a	88	I88del	ATC	---	1	1	AY.27	0.000065
ORF7a	88	I88I	atC	atT	1	1	AY.28	0.00189
ORF7a	88	I88T	aTc	aCc	1	1	AY.29.1	0.000221
ORF7a	88	I88F	Atc	Ttc	1	1	AY.3	0.00001
ORF7a	88	I88del2	ATc	--c	1	1	AY.3.1	0.000085
ORF7a	88	I88del	ATC	---	1	1	AY.30	0.000396
ORF7a	88	I88F	Atc	Ttc	1	1	AY.32	0.000532
ORF7a	88	I88del1	AtC	-tN	1	1	AY.33	0.000067
ORF7a	88	I88I	atC	atT	1	1	AY.35	0.000233
ORF7a	88	I88I	atC	atT	1	1	AY.36	0.000148
ORF7a	88	I88T	aTc	aCc	1	1	AY.38	0.000499
ORF7a	88	I88del1	atC	at-	1	1	AY.39	0.000025
ORF7a	88	I88F	Atc	Ttc	1	1	AY.39	0.000025
ORF7a	88	I88L	Atc	Ctc	1	1	AY.4	0.000002
ORF7a	88	I88del1	atC	at-	1	1	AY.4.2.1	0.000149
ORF7a	88	I88T	aTc	aCc	1	1	AY.4.2.1	0.000149
ORF7a	88	I88V	Atc	Gtc	1	1	AY.4.5	0.000107
ORF7a	88	I88I	atC	atT	1	1	AY.41	0.000294
ORF7a	88	I88T	aTc	aCc	1	1	AY.42	0.00004
ORF7a	88	I88R	aTC	aGA	1	1	AY.44	0.000006
ORF7a	88	I88T	aTc	aCc	1	1	AY.46	0.000104
ORF7a	88	I88del1	aTc	a-c	1	1	AY.46.2	0.000635
ORF7a	88	I88I	atC	atT	1	1	AY.46.4	0.000165
ORF7a	88	I88V	Atc	Gtc	1	1	AY.47	0.000031
ORF7a	88	I88T	aTc	aCc	1	1	AY.47	0.000031
ORF7a	88	I88del	ATC	---	1	1	AY.5.3	0.000337
ORF7a	88	I88F	Atc	Ttc	1	1	AY.5.3	0.000337
ORF7a	88	I88I	atC	atT	1	1	AY.5.3	0.000337
ORF7a	88	I88I	atC	atT	1	1	AY.5.4	0.000277
ORF7a	88	I88I	atC	atT	1	1	AY.51	0.000909
ORF7a	88	I88del	ATC	---	1	1	AY.53	0.000288
ORF7a	88	I88del	ATC	---	1	1	AY.54	0.000095
ORF7a	88	I88T	aTc	aCc	1	1	AY.6	0.000041
ORF7a	88	I88L	Atc	Ctc	1	1	AY.6	0.000041
ORF7a	88	I88del	ATC	---	1	1	AY.61	0.000105
ORF7a	88	I88I	atC	atT	1	1	AY.62	0.000436
ORF7a	88	I88I	atC	atT	1	1	AY.63	0.000387
ORF7a	88	I88del	ATC	---	1	1	AY.68	0.000274
ORF7a	88	I88del	ATC	---	1	1	AY.69	0.000187
ORF7a	88	I88I	atC	atT	1	1	AY.7	0.000196
ORF7a	88	I88F	Atc	Ttc	1	1	AY.7.1	0.000113
ORF7a	88	I88del	ATC	---	1	1	AY.7.1	0.000113
ORF7a	88	I88del2	ATC	G--	1	1	AY.7.2	0.000559
ORF7a	88	I88del	ATC	---	1	1	AY.71	0.000475
ORF7a	88	I88I	atC	atT	1	1	AY.72	0.001361
ORF7a	88	I88T	aTC	aCT	1	1	AY.73	0.000665
ORF7a	88	I88T	aTc	aCc	1	1	AY.75	0.000056
ORF7a	88	I88del	ATC	---	1	1	AY.75	0.000056
ORF7a	88	I88del	ATC	---	1	1	AY.75.1	0.00018
ORF7a	88	I88S	aTc	aGc	1	1	AY.79	0.001211
ORF7a	88	I88I	atC	atT	1	1	AY.8	0.000606
ORF7a	88	I88I	atC	atT	1	1	AY.81	0.001992
ORF7a	88	I88del1	Atc	-tc	1	1	AY.82	0.001357
ORF7a	88	I88S	aTc	aGc	1	1	AY.85	0.000427
ORF7a	88	I88F	Atc	Ttc	1	1	AY.85	0.000427
ORF7a	88	I88del	ATC	---	1	1	AY.85	0.000427
ORF7a	88	I88T	aTc	aCc	1	1	AY.87	0.000833
ORF7a	88	I88I	atC	atT	1	1	AY.88	0.000884
ORF7a	88	I88I	atC	atT	1	1	AY.89	0.004902
ORF7a	88	I88del	ATC	---	1	1	AY.9	0.000068
ORF7a	88	I88T	aTc	aCc	1	1	AY.9	0.000068
ORF7a	88	I88S	aTc	aGc	1	1	AY.9.1	0.000084
ORF7a	88	I88del	ATC	---	1	1	AY.91	0.00073
ORF7a	88	I88I	atC	atT	1	1	AY.91	0.00073
ORF7a	88	I88I	atC	atT	1	1	AY.93	0.000273
ORF7a	88	I88I	atC	atT	1	1	AY.98	0.000079
ORF7a	88	I88T	aTc	aCc	1	1	AY.98	0.000079
ORF7a	88	I88del	ATC	---	1	1	AY.98	0.000079
ORF7a	88	I88S	aTc	aGc	1	1	AY.98.1	0.000048
ORF7a	88	I88del	ATC	---	1	1	AY.99.2	0.000092
ORF7a	88	I88del	ATC	---	1	1	AZ.2	0.000821
ORF7a	88	I88V	Atc	Gtc	1	1	B	0.000128
ORF7a	88	I88I	atC	atT	1	1	B	0.000128
ORF7a	88	I88F	Atc	Ttc	1	1	B	0.000128
ORF7a	88	I88T	aTc	aCc	1	1	B	0.000128
ORF7a	88	I88S	aTc	aGc	1	1	B.1	0.000009
ORF7a	88	I88I	atC	atT	1	1	B.1.1.1	0.000327
ORF7a	88	I88V	Atc	Gtc	1	1	B.1.1.122	0.045455
ORF7a	88	I88V	Atc	Gtc	1	1	B.1.1.128	0.007092
ORF7a	88	I88V	Atc	Gtc	1	1	B.1.1.137	0.0125
ORF7a	88	I88T	aTc	aCc	1	1	B.1.1.141	0.002012
ORF7a	88	I88V	Atc	Gtc	1	1	B.1.1.145	0.037037
ORF7a	88	I88del	ATC	---	1	1	B.1.1.170	0.001247
ORF7a	88	I88del	ATC	---	1	1	B.1.1.174	0.003378
ORF7a	88	I88N	aTc	aAc	1	1	B.1.1.189	0.001513
ORF7a	88	I88del	ATC	---	1	1	B.1.1.192	0.002309
ORF7a	88	I88I	atC	atA	1	1	B.1.1.207	0.001182
ORF7a	88	I88I	atC	atT	1	1	B.1.1.222	0.000204
ORF7a	88	I88L	Atc	Ctc	1	1	B.1.1.222	0.000204
ORF7a	88	I88del	ATC	---	1	1	B.1.1.222	0.000204
ORF7a	88	I88I	atC	atT	1	1	B.1.1.243	0.004082
ORF7a	88	I88del	ATC	---	1	1	B.1.1.258	0.003257
ORF7a	88	I88F	Atc	Ttc	1	1	B.1.1.265	0.003155
ORF7a	88	I88del	ATC	---	1	1	B.1.1.265	0.003155
ORF7a	88	I88I	atC	atT	1	1	B.1.1.279	0.001121
ORF7a	88	I88N	aTc	aAc	1	1	B.1.1.282	0.011628
ORF7a	88	I88V	Atc	Gtc	1	1	B.1.1.299	0.012195
ORF7a	88	I88N	aTc	aAc	1	1	B.1.1.305	0.003861
ORF7a	88	I88I	atC	atT	1	1	B.1.1.306	0.000438
ORF7a	88	I88T	aTc	aCc	1	1	B.1.1.317	0.000412
ORF7a	88	I88del	ATC	---	1	1	B.1.1.318	0.000302
ORF7a	88	I88I	atC	atT	1	1	B.1.1.318	0.000302
ORF7a	88	I88del	ATC	---	1	1	B.1.1.33	0.000421
ORF7a	88	I88T	aTc	aCc	1	1	B.1.1.33	0.000421
ORF7a	88	I88F	Atc	Ttc	1	1	B.1.1.348	0.000796
ORF7a	88	I88del	ATC	---	1	1	B.1.1.366	0.015873
ORF7a	88	I88F	Atc	Ttc	1	1	B.1.1.372	0.000689
ORF7a	88	I88I	atC	atT	1	1	B.1.1.372	0.000689
ORF7a	88	I88V	Atc	Gtc	1	1	B.1.1.388	0.045455
ORF7a	88	I88I	atC	atT	1	1	B.1.1.39	0.00051
ORF7a	88	I88M	atC	atG	1	1	B.1.1.39	0.00051
ORF7a	88	I88T	aTc	aCc	1	1	B.1.1.39	0.00051
ORF7a	88	I88V	Atc	Gtc	1	1	B.1.1.397	0.002252
ORF7a	88	I88V	Atc	Gtc	1	1	B.1.1.398	0.003226
ORF7a	88	I88V	Atc	Gtc	1	1	B.1.1.407	0.041667
ORF7a	88	I88A	ATc	GCc	1	1	B.1.1.411	0.014706
ORF7a	88	I88V	Atc	Gtc	1	1	B.1.1.416	0.000905
ORF7a	88	I88del	ATC	---	1	1	B.1.1.448	0.002033
ORF7a	88	I88F	Atc	Ttc	1	1	B.1.1.487	0.005587
ORF7a	88	I88T	aTc	aCc	1	1	B.1.1.500	0.02
ORF7a	88	I88I	atC	atT	1	1	B.1.1.61	0.008772
ORF7a	88	I88del2	ATc	--c	1	1	B.1.1.7	0.000001
ORF7a	88	I88N	aTc	aAc	1	1	B.1.1.7	0.000001
ORF7a	88	I88K	aTC	aAA	1	1	B.1.1.7	0.000001
ORF7a	88	I88del	ATC	---	1	1	B.1.1.70	0.000341
ORF7a	88	I88V	Atc	Gtc	1	1	B.1.1.89	0.006061
ORF7a	88	I88I	atC	atT	1	1	B.1.110.1	0.1
ORF7a	88	I88del	ATC	---	1	1	B.1.115	0.021739
ORF7a	88	I88V	Atc	Gtc	1	1	B.1.127	0.002198
ORF7a	88	I88I	atC	atT	1	1	B.1.128	0.000635
ORF7a	88	I88T	aTc	aCc	1	1	B.1.160.32	0.004292
ORF7a	88	I88S	aTc	aGc	1	1	B.1.160.32	0.004292
ORF7a	88	I88V	Atc	Gtc	1	1	B.1.177	0.000013
ORF7a	88	I88N	aTc	aAc	1	1	B.1.177	0.000013
ORF7a	88	I88del	ATC	---	1	1	B.1.177.10	0.000878
ORF7a	88	I88T	aTc	aCc	1	1	B.1.177.21	0.000076
ORF7a	88	I88L	Atc	Ctc	1	1	B.1.177.21	0.000076
ORF7a	88	I88I	atC	atT	1	1	B.1.177.21	0.000076
ORF7a	88	I88I	atC	atT	1	1	B.1.177.23	0.003236
ORF7a	88	I88T	aTc	aCc	1	1	B.1.177.30	0.002513
ORF7a	88	I88I	atC	atT	1	1	B.1.177.44	0.000519
ORF7a	88	I88I	atC	atT	1	1	B.1.177.5	0.001242
ORF7a	88	I88del	ATC	---	1	1	B.1.177.50	0.004695
ORF7a	88	I88del	ATC	---	1	1	B.1.177.57	0.000281
ORF7a	88	I88del	ATC	---	1	1	B.1.177.62	0.001192
ORF7a	88	I88del	ATC	---	1	1	B.1.177.81	0.000189
ORF7a	88	I88I	atC	atT	1	1	B.1.210	0.002132
ORF7a	88	I88T	aTc	aCc	1	1	B.1.221	0.000071
ORF7a	88	I88del	ATC	---	1	1	B.1.221	0.000071
ORF7a	88	I88I	atC	atT	1	1	B.1.232	0.000537
ORF7a	88	I88T	aTc	aCc	1	1	B.1.236	0.002053
ORF7a	88	I88del	ATC	---	1	1	B.1.240	0.000216
ORF7a	88	I88N	aTc	aAc	1	1	B.1.242	0.018868
ORF7a	88	I88del	ATC	---	1	1	B.1.243	0.00007
ORF7a	88	I88I	atC	atT	1	1	B.1.243	0.00007
ORF7a	88	I88del	ATC	---	1	1	B.1.258	0.000067
ORF7a	88	I88T	aTc	aCc	1	1	B.1.258.17	0.000104
ORF7a	88	I88del	ATC	---	1	1	B.1.258.17	0.000104
ORF7a	88	I88del	ATC	---	1	1	B.1.265	0.001271
ORF7a	88	I88del	ATC	---	1	1	B.1.319	0.003049
ORF7a	88	I88I	atC	atT	1	1	B.1.329	0.000608
ORF7a	88	I88T	aTc	aCc	1	1	B.1.351	0.00003
ORF7a	88	I88del	ATC	---	1	1	B.1.351.2	0.000303
ORF7a	88	I88F	Atc	Ttc	1	1	B.1.351.3	0.000876
ORF7a	88	I88N	aTc	aAc	1	1	B.1.36	0.000146
ORF7a	88	I88V	Atc	Gtc	1	1	B.1.36.29	0.000517
ORF7a	88	I88I	atC	atT	1	1	B.1.362	0.001541
ORF7a	88	I88del	ATC	---	1	1	B.1.371	0.001122
ORF7a	88	I88del	ATC	---	1	1	B.1.375	0.00082
ORF7a	88	I88I	atC	atT	1	1	B.1.391	0.001127
ORF7a	88	I88I	atC	atT	1	1	B.1.408	0.00369
ORF7a	88	I88M	atC	atG	1	1	B.1.416	0.001269
ORF7a	88	I88T	aTc	aCc	1	1	B.1.416.1	0.001563
ORF7a	88	I88S	aTc	aGc	1	1	B.1.429	0.000024
ORF7a	88	I88N	aTc	aAc	1	1	B.1.438	0.006536
ORF7a	88	I88V	Atc	Gtc	1	1	B.1.438.1	0.000107
ORF7a	88	I88I	atC	atT	1	1	B.1.438.1	0.000107
ORF7a	88	I88T	aTc	aCc	1	1	B.1.439	0.005917
ORF7a	88	I88del	ATC	---	1	1	B.1.459	0.004082
ORF7a	88	I88I	atC	atT	1	1	B.1.467	0.04
ORF7a	88	I88del	ATC	---	1	1	B.1.468	0.005714
ORF7a	88	I88del	ATC	---	1	1	B.1.470	0.001404
ORF7a	88	I88V	Atc	Gtc	1	1	B.1.497	0.000315
ORF7a	88	I88T	aTc	aCc	1	1	B.1.497	0.000315
ORF7a	88	I88S	ATc	TCc	1	1	B.1.526	0.000024
ORF7a	88	I88del	ATC	---	1	1	B.1.527	0.003704
ORF7a	88	I88T	aTc	aCc	1	1	B.1.551	0.00129
ORF7a	88	I88T	aTc	aCc	1	1	B.1.556	0.007519
ORF7a	88	I88I	atC	atT	1	1	B.1.575	0.000303
ORF7a	88	I88T	aTc	aCc	1	1	B.1.576	0.000907
ORF7a	88	I88del	ATC	---	1	1	B.1.577	0.000687
ORF7a	88	I88I	atC	atT	1	1	B.1.580	0.004065
ORF7a	88	I88del	ATC	---	1	1	B.1.582	0.000491
ORF7a	88	I88del	ATC	---	1	1	B.1.595	0.000261
ORF7a	88	I88I	atC	atT	1	1	B.1.609	0.000479
ORF7a	88	I88del	ATC	---	1	1	B.1.617.1	0.000129
ORF7a	88	I88S	aTc	aGc	1	1	B.1.617.2	0.000004
ORF7a	88	I88del	ATC	---	1	1	B.1.621.1	0.000506
ORF7a	88	I88I	atC	atT	1	1	B.1.621.1	0.000506
ORF7a	88	I88I	atC	atT	1	1	B.1.625	0.002353
ORF7a	88	I88T	aTc	aCc	1	1	B.1.637	0.000073
ORF7a	88	I88del	ATC	---	1	1	B.1.638	0.052632
ORF7a	88	I88I	atC	atA	1	1	B.1.76	0.011364
ORF7a	88	I88del	ATC	---	1	1	B.1.9.1	0.032258
ORF7a	88	I88del	ATC	---	1	1	B.1.93	0.000934
ORF7a	88	I88I	atC	atT	1	1	B.4	0.002208
ORF7a	88	I88I	atC	atT	1	1	B.4.2	0.066667
ORF7a	88	I88I	atC	atT	1	1	B.6.6	0.000889
ORF7a	88	I88F	Atc	Ttc	1	1	C.36	0.000911
ORF7a	88	I88F	Atc	Ttc	1	1	C.36.3	0.000567
ORF7a	88	I88del	ATC	---	1	1	C.36.3	0.000567
ORF7a	88	I88I	atC	atT	1	1	C.36.3	0.000567
ORF7a	88	I88I	atC	atT	1	1	D.2	0.000075
ORF7a	88	I88I	atC	atT	1	1	N.5	0.001767
ORF7a	88	I88del1	atC	at-	1	1	P.1	0.000016
ORF7a	88	I88V	Atc	Gtc	1	1	P.1	0.000016
ORF7a	88	I88S	aTc	aGc	1	1	P.1	0.000016
ORF7a	88	I88del	ATC	---	1	1	P.1.1	0.000318
ORF7a	88	I88del	ATC	---	1	1	P.1.12	0.000484
ORF7a	88	I88I	atC	atT	1	1	P.1.12	0.000484
ORF7a	88	I88del	ATC	---	1	1	P.1.13	0.000898
ORF7a	88	I88del	ATC	---	1	1	P.1.14	0.000048
ORF7a	88	I88I	atC	atT	1	1	P.1.15	0.000232
ORF7a	88	I88V	Atc	Gtc	1	1	P.1.15	0.000232
ORF7a	88	I88del	ATC	---	1	1	P.1.16	0.000374
ORF7a	88	I88del	ATC	---	1	1	P.1.3	0.034483
ORF7a	88	I88del	ATC	---	1	1	P.1.4	0.000977
ORF7a	88	I88I	atC	atT	1	1	P.2	0.000187
ORF7a	88	I88I	atC	atT	1	1	P.3	0.001595
ORF7a	88	I88T	aTc	aCc	1	1	P.6	0.003145
ORF7a	88	I88T	aTc	aCc	1	1	Q.1	0.000126
ORF7a	88	I88F	Atc	Ttc	1	1	Q.3	0.000145
ORF7a	88	I88del	ATC	---	1	1	Q.7	0.001111
ORF7a	88	I88V	Atc	Gtc	1	1	R.1	0.00009
ORF7a	88	I88I	atC	atT	1	1	R.1	0.00009

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.