CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 389

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	389	P389S	P1207S	nonsyn	Cct	Tct	4559	4557	0.999561	3884-3886
ORF1ab/nsp3	389	P389S	P1207S	nonsyn	CcT	TcC	4559	2	0.000438693	3884-3886
ORF1ab/nsp3	389	P389L	P1207L	nonsyn	cCt	cTt	2348	2345	0.998722	3884-3886
ORF1ab/nsp3	389	P389L	P1207L	nonsyn	cCT	cTA	2348	2	0.000851789	3884-3886
ORF1ab/nsp3	389	P389L	P1207L	nonsyn	cCT	cTC	2348	1	0.000425894	3884-3886
ORF1ab/nsp3	389	P389H	P1207H	nonsyn	cCt	cAt	1309	1308	0.999236	3884-3886
ORF1ab/nsp3	389	P389H	P1207H	nonsyn	cCT	cAC	1309	1	0.000763942	3884-3886
ORF1ab/nsp3	389	P389P	P1207P	syn	ccT	ccC	304	193	0.634868	3884-3886
ORF1ab/nsp3	389	P389P	P1207P	syn	ccT	ccA	304	106	0.348684	3884-3886
ORF1ab/nsp3	389	P389P	P1207P	syn	ccT	ccG	304	5	0.0164474	3884-3886
ORF1ab/nsp3	389	P389del	P1207del	del	CCT	---	256	256	1	3884-3886
ORF1ab/nsp3	389	P389T	P1207T	nonsyn	Cct	Act	126	126	1	3884-3886
ORF1ab/nsp3	389	P389R	P1207R	nonsyn	cCt	cGt	22	22	1	3884-3886
ORF1ab/nsp3	389	P389del1	P1207del1	del	Cct	-ct	10	10	1	3884-3886
ORF1ab/nsp3	389	P389F	P1207F	nonsyn	CCt	TTt	2	1	0.5	3884-3886
ORF1ab/nsp3	389	P389F	P1207F	nonsyn	CCT	TTC	2	1	0.5	3884-3886
ORF1ab/nsp3	389	P389Y	P1207Y	nonsyn	CCt	TAt	2	1	0.5	3884-3886
ORF1ab/nsp3	389	P389Y	P1207Y	nonsyn	CCT	TAC	2	1	0.5	3884-3886
ORF1ab/nsp3	389	P389I	P1207I	nonsyn	CCt	ATt	1	1	1	3884-3886
ORF1ab/nsp3	389	P389N	P1207N	nonsyn	CCt	AAt	1	1	1	3884-3886

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	389	P389S	Cct	Tct	4557	4559	All	0.000872
ORF1ab/nsp3	389	P389S	CcT	TcC	2	4559	All	0
ORF1ab/nsp3	389	P389S	Cct	Tct	2787	2787	B.1.628	0.98203
ORF1ab/nsp3	389	P389L	cCt	cTt	2345	2348	All	0.000449
ORF1ab/nsp3	389	P389L	cCT	cTA	2	2348	All	0
ORF1ab/nsp3	389	P389L	cCT	cTC	1	2348	All	0
ORF1ab/nsp3	389	P389H	cCt	cAt	1308	1309	All	0.00025
ORF1ab/nsp3	389	P389H	cCT	cAC	1	1309	All	0
ORF1ab/nsp3	389	P389H	cCt	cAt	767	767	B.1.617.2	0.002888
ORF1ab/nsp3	389	P389S	Cct	Tct	346	346	AY.4	0.000539
ORF1ab/nsp3	389	P389L	cCt	cTt	335	335	B.1.1.7	0.0003
ORF1ab/nsp3	389	P389P	ccT	ccC	193	304	All	0.000037
ORF1ab/nsp3	389	P389P	ccT	ccA	106	304	All	0.00002
ORF1ab/nsp3	389	P389P	ccT	ccG	5	304	All	0.000001
ORF1ab/nsp3	389	P389L	cCt	cTt	297	297	B.1.429	0.006988
ORF1ab/nsp3	389	P389del	CCT	---	256	256	All	0.000049
ORF1ab/nsp3	389	P389S	Cct	Tct	228	228	B.1.1.7	0.000204
ORF1ab/nsp3	389	P389S	Cct	Tct	196	196	B.1.523	0.480392
ORF1ab/nsp3	389	P389L	cCt	cTt	193	193	B.1.612	0.511936
ORF1ab/nsp3	389	P389H	cCt	cAt	190	190	B.1.1.311	0.068052
ORF1ab/nsp3	389	P389S	Cct	Tct	190	190	B.1.2	0.001673
ORF1ab/nsp3	389	P389H	cCt	cAt	171	171	AY.98	0.013508
ORF1ab/nsp3	389	P389L	cCt	cTt	162	162	B.1.1	0.002939
ORF1ab/nsp3	389	P389T	Cct	Act	126	126	All	0.000024
ORF1ab/nsp3	389	P389L	cCt	cTt	112	112	AY.75	0.006275
ORF1ab/nsp3	389	P389L	cCt	cTt	102	102	AY.25	0.000614
ORF1ab/nsp3	389	P389S	Cct	Tct	98	98	B.1	0.000898
ORF1ab/nsp3	389	P389S	Cct	Tct	93	93	B.1.617.2	0.00035
ORF1ab/nsp3	389	P389P	ccT	ccC	89	89	AY.43	0.000394
ORF1ab/nsp3	389	P389L	cCt	cTt	85	85	B.1.427	0.004292
ORF1ab/nsp3	389	P389T	Cct	Act	84	84	B.1.1.7	0.000075
ORF1ab/nsp3	389	P389S	Cct	Tct	76	76	B.1.1.222	0.015504
ORF1ab/nsp3	389	P389P	ccT	ccA	73	73	AY.42	0.002937
ORF1ab/nsp3	389	P389L	cCt	cTt	69	69	B.1.1.265	0.217666
ORF1ab/nsp3	389	P389L	cCt	cTt	68	68	AY.4	0.000106
ORF1ab/nsp3	389	P389L	cCt	cTt	65	65	AY.103	0.000404
ORF1ab/nsp3	389	P389L	cCt	cTt	63	63	B.1.617.2	0.000237
ORF1ab/nsp3	389	P389L	cCt	cTt	61	61	AY.5	0.00126
ORF1ab/nsp3	389	P389L	cCt	cTt	58	58	B.1.256	1
ORF1ab/nsp3	389	P389del	CCT	---	54	54	B.1.1.442	1
ORF1ab/nsp3	389	P389L	cCt	cTt	43	43	B.1	0.000394
ORF1ab/nsp3	389	P389S	Cct	Tct	41	41	B.1.243	0.002853
ORF1ab/nsp3	389	P389S	Cct	Tct	40	40	AY.103	0.000248
ORF1ab/nsp3	389	P389S	Cct	Tct	36	36	P.1	0.000567
ORF1ab/nsp3	389	P389L	cCt	cTt	35	35	B.1.351.3	0.030675
ORF1ab/nsp3	389	P389L	cCt	cTt	35	35	Q.2	0.021472
ORF1ab/nsp3	389	P389S	Cct	Tct	33	33	AY.25	0.000198
ORF1ab/nsp3	389	P389L	cCt	cTt	32	32	AY.43	0.000142
ORF1ab/nsp3	389	P389L	cCt	cTt	31	31	B.1.2	0.000273
ORF1ab/nsp3	389	P389H	cCt	cAt	30	30	C.37	0.003482
ORF1ab/nsp3	389	P389L	cCt	cTt	29	29	B.1.526	0.000682
ORF1ab/nsp3	389	P389H	cCt	cAt	27	27	AY.60	0.025328
ORF1ab/nsp3	389	P389L	cCt	cTt	27	27	B.1.351	0.000803
ORF1ab/nsp3	389	P389L	cCt	cTt	25	25	AY.26	0.000708
ORF1ab/nsp3	389	P389L	cCt	cTt	23	23	B.1.160	0.000717
ORF1ab/nsp3	389	P389R	cCt	cGt	22	22	All	0.000004
ORF1ab/nsp3	389	P389L	cCt	cTt	22	22	AY.44	0.000134
ORF1ab/nsp3	389	P389S	Cct	Tct	22	22	B.1.406	0.133333
ORF1ab/nsp3	389	P389del	CCT	---	20	20	B.1.1.7	0.000018
ORF1ab/nsp3	389	P389P	ccT	ccA	19	20	B.1.429	0.000447
ORF1ab/nsp3	389	P389P	ccT	ccC	1	20	B.1.429	0.000024
ORF1ab/nsp3	389	P389S	Cct	Tct	19	19	AY.100	0.000874
ORF1ab/nsp3	389	P389S	Cct	Tct	19	19	AY.44	0.000116
ORF1ab/nsp3	389	P389L	cCt	cTt	18	18	AY.69	0.00336
ORF1ab/nsp3	389	P389P	ccT	ccC	18	18	B.1.221	0.001279
ORF1ab/nsp3	389	P389S	Cct	Tct	17	17	B.1.324	0.027287
ORF1ab/nsp3	389	P389L	cCt	cTt	16	16	B.1.36	0.002334
ORF1ab/nsp3	389	P389L	cCt	cTt	15	15	AY.3	0.000149
ORF1ab/nsp3	389	P389del	CCT	---	15	15	B.1.2	0.000132
ORF1ab/nsp3	389	P389L	cCt	cTt	14	14	B.1.177.81	0.002651
ORF1ab/nsp3	389	P389S	Cct	Tct	13	13	AY.98	0.001027
ORF1ab/nsp3	389	P389H	cCt	cAt	13	13	B.1.1.7	0.000012
ORF1ab/nsp3	389	P389P	ccT	ccC	10	13	B.1.1.7	0.000009
ORF1ab/nsp3	389	P389P	ccT	ccA	2	13	B.1.1.7	0.000002
ORF1ab/nsp3	389	P389P	ccT	ccG	1	13	B.1.1.7	0.000001
ORF1ab/nsp3	389	P389L	cCt	cTt	13	13	B.1.258	0.000865
ORF1ab/nsp3	389	P389L	cCt	cTt	13	13	P.1	0.000205
ORF1ab/nsp3	389	P389L	cCt	cTt	12	12	AY.121	0.001624
ORF1ab/nsp3	389	P389del	CCT	---	12	12	AY.4	0.000019
ORF1ab/nsp3	389	P389del	CCT	---	12	12	B.1	0.00011
ORF1ab/nsp3	389	P389S	Cct	Tct	12	12	B.1.218	0.061856
ORF1ab/nsp3	389	P389H	cCt	cAt	11	11	AY.4	0.000017
ORF1ab/nsp3	389	P389S	Cct	Tct	11	11	B.1.1	0.0002
ORF1ab/nsp3	389	P389S	Cct	Tct	11	11	B.1.1.519	0.000437
ORF1ab/nsp3	389	P389P	ccT	ccC	10	11	B.1.617.2	0.000038
ORF1ab/nsp3	389	P389P	ccT	ccA	1	11	B.1.617.2	0.000004
ORF1ab/nsp3	389	P389S	Cct	Tct	11	11	P.1.12	0.005324
ORF1ab/nsp3	389	P389del1	Cct	-ct	10	10	All	0.000002
ORF1ab/nsp3	389	P389L	cCt	cTt	10	10	AY.100	0.00046
ORF1ab/nsp3	389	P389S	Cct	Tct	10	10	AY.23	0.000697
ORF1ab/nsp3	389	P389S	Cct	Tct	10	10	AY.39	0.000247
ORF1ab/nsp3	389	P389del	CCT	---	10	10	B.1.1.232	0.018149
ORF1ab/nsp3	389	P389T	Cct	Act	10	10	B.1.210	0.021322
ORF1ab/nsp3	389	P389L	cCt	cTt	10	10	B.1.570	0.029412
ORF1ab/nsp3	389	P389L	cCt	cTt	9	9	AY.33	0.000601
ORF1ab/nsp3	389	P389H	cCt	cAt	9	9	B.1.2	0.000079
ORF1ab/nsp3	389	P389S	Cct	Tct	9	9	B.1.526	0.000212
ORF1ab/nsp3	389	P389del	CCT	---	9	9	B.1.617.2	0.000034
ORF1ab/nsp3	389	P389L	cCt	cTt	9	9	P.2	0.00168
ORF1ab/nsp3	389	P389L	cCt	cTt	8	8	AY.114	0.001849
ORF1ab/nsp3	389	P389S	Cct	Tct	8	8	AY.2	0.002849
ORF1ab/nsp3	389	P389P	ccT	ccC	8	8	AY.4	0.000012
ORF1ab/nsp3	389	P389S	Cct	Tct	8	8	AY.43	0.000035
ORF1ab/nsp3	389	P389H	cCt	cAt	8	8	B	0.001022
ORF1ab/nsp3	389	P389H	cCt	cAt	8	8	B.1	0.000073
ORF1ab/nsp3	389	P389del	CCT	---	8	8	B.1.160	0.00025
ORF1ab/nsp3	389	P389S	Cct	Tct	8	8	B.1.221	0.000568
ORF1ab/nsp3	389	P389L	cCt	cTt	7	7	AU.2	0.016949
ORF1ab/nsp3	389	P389P	ccT	ccC	7	7	AY.27	0.000453
ORF1ab/nsp3	389	P389del	CCT	---	7	7	AY.44	0.000043
ORF1ab/nsp3	389	P389L	cCt	cTt	7	7	B.1.1.222	0.001428
ORF1ab/nsp3	389	P389del	CCT	---	7	7	B.1.390	0.074468
ORF1ab/nsp3	389	P389S	Cct	Tct	7	7	B.1.427	0.000353
ORF1ab/nsp3	389	P389S	Cct	Tct	7	7	B.1.621	0.00062
ORF1ab/nsp3	389	P389S	Cct	Tct	5	6	AY.119	0.000177
ORF1ab/nsp3	389	P389S	CcT	TcC	1	6	AY.119	0.000035
ORF1ab/nsp3	389	P389L	cCt	cTt	6	6	AY.120	0.000223
ORF1ab/nsp3	389	P389S	Cct	Tct	6	6	AY.120	0.000223
ORF1ab/nsp3	389	P389H	cCt	cAt	6	6	AY.25	0.000036
ORF1ab/nsp3	389	P389S	Cct	Tct	6	6	AY.46.6	0.000433
ORF1ab/nsp3	389	P389L	cCt	cTt	6	6	AZ.2	0.004926
ORF1ab/nsp3	389	P389T	Cct	Act	6	6	B.1	0.000055
ORF1ab/nsp3	389	P389S	Cct	Tct	6	6	B.1.177.7	0.000989
ORF1ab/nsp3	389	P389H	cCt	cAt	6	6	B.1.258	0.000399
ORF1ab/nsp3	389	P389S	Cct	Tct	6	6	B.1.36.1	0.006842
ORF1ab/nsp3	389	P389S	Cct	Tct	6	6	B.1.438.1	0.000644
ORF1ab/nsp3	389	P389P	ccT	ccC	6	6	B.1.441	0.057692
ORF1ab/nsp3	389	P389L	cCt	cTt	6	6	B.1.596	0.000523
ORF1ab/nsp3	389	P389S	Cct	Tct	6	6	P.1.2	0.006936
ORF1ab/nsp3	389	P389S	Cct	Tct	5	5	AY.102	0.000133
ORF1ab/nsp3	389	P389L	cCt	cTt	5	5	AY.119	0.000177
ORF1ab/nsp3	389	P389S	Cct	Tct	5	5	AY.42	0.000201
ORF1ab/nsp3	389	P389S	Cct	Tct	5	5	AY.46.4	0.000823
ORF1ab/nsp3	389	P389S	Cct	Tct	5	5	AY.47	0.000156
ORF1ab/nsp3	389	P389L	cCt	cTt	5	5	AY.6	0.000206
ORF1ab/nsp3	389	P389P	ccT	ccC	5	5	AY.92	0.001436
ORF1ab/nsp3	389	P389L	cCt	cTt	5	5	B.1.1.1	0.001633
ORF1ab/nsp3	389	P389R	cCt	cGt	5	5	B.1.1.7	0.000004
ORF1ab/nsp3	389	P389L	cCt	cTt	5	5	B.1.177	0.000066
ORF1ab/nsp3	389	P389P	ccT	ccC	4	5	B.1.2	0.000035
ORF1ab/nsp3	389	P389P	ccT	ccA	1	5	B.1.2	0.000009
ORF1ab/nsp3	389	P389R	cCt	cGt	5	5	B.1.429	0.000118
ORF1ab/nsp3	389	P389S	Cct	Tct	5	5	B.1.429	0.000118
ORF1ab/nsp3	389	P389R	cCt	cGt	5	5	B.1.525	0.000566
ORF1ab/nsp3	389	P389del	CCT	---	5	5	B.1.596	0.000436
ORF1ab/nsp3	389	P389H	cCt	cAt	5	5	B.1.620	0.00473
ORF1ab/nsp3	389	P389L	cCt	cTt	5	5	B.1.637	0.000365
ORF1ab/nsp3	389	P389L	cCt	cTt	4	4	AY.102	0.000106
ORF1ab/nsp3	389	P389L	cCt	cTt	4	4	AY.113	0.00057
ORF1ab/nsp3	389	P389S	Cct	Tct	4	4	AY.113	0.00057
ORF1ab/nsp3	389	P389del	CCT	---	4	4	AY.119	0.000141
ORF1ab/nsp3	389	P389S	Cct	Tct	4	4	AY.16.1	0.00188
ORF1ab/nsp3	389	P389L	cCt	cTt	4	4	AY.35	0.000932
ORF1ab/nsp3	389	P389S	Cct	Tct	4	4	AY.41	0.001176
ORF1ab/nsp3	389	P389L	cCt	cTt	3	4	AY.46.6	0.000217
ORF1ab/nsp3	389	P389L	cCT	cTA	1	4	AY.46.6	0.000072
ORF1ab/nsp3	389	P389L	cCt	cTt	4	4	AY.9.2	0.000147
ORF1ab/nsp3	389	P389P	ccT	ccC	2	4	B.1	0.000018
ORF1ab/nsp3	389	P389P	ccT	ccA	2	4	B.1	0.000018
ORF1ab/nsp3	389	P389H	cCt	cAt	4	4	B.1.1	0.000073
ORF1ab/nsp3	389	P389del	CCT	---	4	4	B.1.1	0.000073
ORF1ab/nsp3	389	P389L	cCt	cTt	4	4	B.1.1.33	0.001684
ORF1ab/nsp3	389	P389S	Cct	Tct	4	4	B.1.177	0.000053
ORF1ab/nsp3	389	P389del	CCT	---	4	4	B.1.177	0.000053
ORF1ab/nsp3	389	P389H	cCt	cAt	4	4	B.1.177	0.000053
ORF1ab/nsp3	389	P389S	Cct	Tct	4	4	B.1.177.86	0.000734
ORF1ab/nsp3	389	P389L	cCt	cTt	4	4	B.1.177.9	0.005326
ORF1ab/nsp3	389	P389L	cCt	cTt	4	4	B.1.466.2	0.001565
ORF1ab/nsp3	389	P389H	cCt	cAt	4	4	B.1.525	0.000453
ORF1ab/nsp3	389	P389L	cCt	cTt	4	4	B.1.544	0.024096
ORF1ab/nsp3	389	P389S	Cct	Tct	4	4	B.1.627	0.008081
ORF1ab/nsp3	389	P389del	CCT	---	3	3	A.1	0.000846
ORF1ab/nsp3	389	P389S	Cct	Tct	3	3	AY.116	0.00086
ORF1ab/nsp3	389	P389del	CCT	---	3	3	AY.16	0.001139
ORF1ab/nsp3	389	P389L	cCt	cTt	3	3	AY.23	0.000209
ORF1ab/nsp3	389	P389del	CCT	---	3	3	AY.23	0.000209
ORF1ab/nsp3	389	P389P	ccT	ccA	2	3	AY.23	0.000139
ORF1ab/nsp3	389	P389P	ccT	ccC	1	3	AY.23	0.00007
ORF1ab/nsp3	389	P389del	CCT	---	3	3	AY.26	0.000085
ORF1ab/nsp3	389	P389L	cCt	cTt	3	3	AY.27	0.000194
ORF1ab/nsp3	389	P389L	cCt	cTt	3	3	AY.29	0.000047
ORF1ab/nsp3	389	P389del	CCT	---	3	3	AY.3	0.00003
ORF1ab/nsp3	389	P389S	Cct	Tct	3	3	AY.33	0.0002
ORF1ab/nsp3	389	P389L	cCt	cTt	3	3	AY.39	0.000074
ORF1ab/nsp3	389	P389T	Cct	Act	3	3	AY.43	0.000013
ORF1ab/nsp3	389	P389P	ccT	ccC	2	3	AY.46.6	0.000144
ORF1ab/nsp3	389	P389P	ccT	ccA	1	3	AY.46.6	0.000072
ORF1ab/nsp3	389	P389H	cCt	cAt	3	3	AY.5	0.000062
ORF1ab/nsp3	389	P389S	Cct	Tct	3	3	AY.6	0.000123
ORF1ab/nsp3	389	P389L	cCt	cTt	3	3	B.1.1.203	0.050847
ORF1ab/nsp3	389	P389P	ccT	ccC	3	3	B.1.177	0.00004
ORF1ab/nsp3	389	P389del	CCT	---	3	3	B.1.221	0.000213
ORF1ab/nsp3	389	P389H	cCt	cAt	3	3	B.1.351	0.000089
ORF1ab/nsp3	389	P389L	cCt	cTt	3	3	B.1.36.35	0.007812
ORF1ab/nsp3	389	P389L	cCt	cTt	3	3	B.1.470	0.004213
ORF1ab/nsp3	389	P389T	Cct	Act	3	3	B.1.617.2	0.000011
ORF1ab/nsp3	389	P389S	Cct	Tct	3	3	C.37	0.000348
ORF1ab/nsp3	389	P389H	cCt	cAt	3	3	D.2	0.000225
ORF1ab/nsp3	389	P389L	cCt	cTt	3	3	D.2	0.000225
ORF1ab/nsp3	389	P389S	Cct	Tct	3	3	P.1.1	0.000953
ORF1ab/nsp3	389	P389S	Cct	Tct	3	3	P.2	0.00056
ORF1ab/nsp3	389	P389del	CCT	---	3	3	R.1	0.00027
ORF1ab/nsp3	389	P389S	Cct	Tct	3	3	R.1	0.00027
ORF1ab/nsp3	389	P389del1	Cct	-ct	2	2		0.111111
ORF1ab/nsp3	389	P389S	CcT	TcC	1	2		0.055556
ORF1ab/nsp3	389	P389H	cCT	cAC	1	2		0.055556
ORF1ab/nsp3	389	P389L	cCT	cTC	1	2		0.055556
ORF1ab/nsp3	389	P389Y	CCt	TAt	1	2		0.055556
ORF1ab/nsp3	389	P389F	CCT	TTC	1	2		0.055556
ORF1ab/nsp3	389	P389F	CCt	TTt	1	2		0.055556
ORF1ab/nsp3	389	P389Y	CCT	TAC	1	2		0.055556
ORF1ab/nsp3	389	P389H	cCt	cAt	1	2		0.055556
ORF1ab/nsp3	389	P389L	cCt	cTt	1	2		0.055556
ORF1ab/nsp3	389	P389S	Cct	Tct	1	2		0.055556
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	A.2.5	0.000998
ORF1ab/nsp3	389	P389Y	CCt	TAt	1	2	All	0
ORF1ab/nsp3	389	P389F	CCT	TTC	1	2	All	0
ORF1ab/nsp3	389	P389F	CCt	TTt	1	2	All	0
ORF1ab/nsp3	389	P389Y	CCT	TAC	1	2	All	0
ORF1ab/nsp3	389	P389P	ccT	ccC	2	2	AY.100	0.000092
ORF1ab/nsp3	389	P389del	CCT	---	2	2	AY.100	0.000092
ORF1ab/nsp3	389	P389S	Cct	Tct	2	2	AY.117	0.000169
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	AY.118	0.000125
ORF1ab/nsp3	389	P389H	cCt	cAt	2	2	AY.121	0.000271
ORF1ab/nsp3	389	P389P	ccT	ccC	2	2	AY.20	0.000078
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	AY.24	0.000862
ORF1ab/nsp3	389	P389S	Cct	Tct	2	2	AY.29	0.000032
ORF1ab/nsp3	389	P389S	Cct	Tct	2	2	AY.30	0.000791
ORF1ab/nsp3	389	P389P	ccT	ccC	2	2	AY.34	0.000194
ORF1ab/nsp3	389	P389S	Cct	Tct	2	2	AY.36	0.000296
ORF1ab/nsp3	389	P389T	Cct	Act	2	2	AY.39	0.000049
ORF1ab/nsp3	389	P389del	CCT	---	2	2	AY.39	0.000049
ORF1ab/nsp3	389	P389S	Cct	Tct	2	2	AY.4.2	0.000043
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	AY.4.2	0.000043
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	AY.42	0.00008
ORF1ab/nsp3	389	P389del	CCT	---	2	2	AY.43	0.000009
ORF1ab/nsp3	389	P389H	cCt	cAt	2	2	AY.44	0.000012
ORF1ab/nsp3	389	P389R	cCt	cGt	2	2	AY.44	0.000012
ORF1ab/nsp3	389	P389del	CCT	---	2	2	AY.47	0.000062
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	AY.47	0.000062
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	AY.54	0.000191
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	AY.67	0.000929
ORF1ab/nsp3	389	P389S	Cct	Tct	2	2	AY.70	0.000417
ORF1ab/nsp3	389	P389H	cCt	cAt	2	2	AY.73	0.001331
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	AY.74	0.000231
ORF1ab/nsp3	389	P389P	ccT	ccC	2	2	AY.75.1	0.000361
ORF1ab/nsp3	389	P389H	cCt	cAt	2	2	AY.99	0.002099
ORF1ab/nsp3	389	P389R	cCt	cGt	2	2	B.1.1.153	0.002191
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	B.1.1.163	0.015267
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	B.1.1.237	0.010811
ORF1ab/nsp3	389	P389del	CCT	---	2	2	B.1.1.269	0.002706
ORF1ab/nsp3	389	P389S	Cct	Tct	2	2	B.1.1.28	0.000622
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	B.1.1.28	0.000622
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	B.1.1.37	0.000386
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	B.1.1.397	0.004505
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	B.1.1.519	0.000079
ORF1ab/nsp3	389	P389S	Cct	Tct	2	2	B.1.177.16	0.001329
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	B.1.214	0.007326
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	B.1.311	0.000549
ORF1ab/nsp3	389	P389P	ccT	ccG	2	2	B.1.351	0.000059
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	B.1.351.2	0.000605
ORF1ab/nsp3	389	P389H	cCt	cAt	2	2	B.1.36.29	0.001035
ORF1ab/nsp3	389	P389S	Cct	Tct	2	2	B.1.36.29	0.001035
ORF1ab/nsp3	389	P389P	ccT	ccA	2	2	B.1.427	0.000101
ORF1ab/nsp3	389	P389del	CCT	---	2	2	B.1.466.2	0.000782
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	B.1.525	0.000226
ORF1ab/nsp3	389	P389del	CCT	---	2	2	B.1.525	0.000226
ORF1ab/nsp3	389	P389del	CCT	---	2	2	B.1.526	0.000047
ORF1ab/nsp3	389	P389del	CCT	---	2	2	B.1.558	0.009132
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	B.1.565	0.001621
ORF1ab/nsp3	389	P389S	Cct	Tct	2	2	B.1.596	0.000174
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	B.1.609	0.000959
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	B.1.617.1	0.000258
ORF1ab/nsp3	389	P389del1	Cct	-ct	2	2	B.1.617.2	0.000008
ORF1ab/nsp3	389	P389del	CCT	---	2	2	B.1.621	0.000177
ORF1ab/nsp3	389	P389S	Cct	Tct	2	2	B.1.637	0.000146
ORF1ab/nsp3	389	P389S	Cct	Tct	2	2	C.2	0.032258
ORF1ab/nsp3	389	P389S	Cct	Tct	2	2	D.2	0.00015
ORF1ab/nsp3	389	P389del	CCT	---	2	2	P.1	0.000032
ORF1ab/nsp3	389	P389H	cCt	cAt	2	2	P.1	0.000032
ORF1ab/nsp3	389	P389del	CCT	---	2	2	P.1.12	0.000968
ORF1ab/nsp3	389	P389L	cCt	cTt	2	2	P.1.15	0.000465
ORF1ab/nsp3	389	P389S	Cct	Tct	2	2	W.3	0.010526
ORF1ab/nsp3	389	P389S	Cct	Tct	2	2	Z.1	0.00578
ORF1ab/nsp3	389	P389P	ccT	ccC	1	1		0.055556
ORF1ab/nsp3	389	P389T	Cct	Act	1	1	A	0.000387
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	A.2	0.000662
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	A.2.4	0.003367
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	A.2.5.2	0.001572
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	A.21	0.00277
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	AD.2	0.000219
ORF1ab/nsp3	389	P389I	CCt	ATt	1	1	All	0
ORF1ab/nsp3	389	P389N	CCt	AAt	1	1	All	0
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.10	0.00053
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	AY.100	0.000046
ORF1ab/nsp3	389	P389N	CCt	AAt	1	1	AY.102	0.000027
ORF1ab/nsp3	389	P389P	ccT	ccC	1	1	AY.102	0.000027
ORF1ab/nsp3	389	P389P	ccT	ccC	1	1	AY.103	0.000006
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	AY.103	0.000006
ORF1ab/nsp3	389	P389del	CCT	---	1	1	AY.103	0.000006
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.104	0.001984
ORF1ab/nsp3	389	P389del	CCT	---	1	1	AY.107	0.000466
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	AY.111	0.000183
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	AY.111	0.000183
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	AY.114	0.000231
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	AY.117	0.000085
ORF1ab/nsp3	389	P389del	CCT	---	1	1	AY.118	0.000063
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	AY.118	0.000063
ORF1ab/nsp3	389	P389P	ccT	ccC	1	1	AY.118	0.000063
ORF1ab/nsp3	389	P389P	ccT	ccC	1	1	AY.119	0.000035
ORF1ab/nsp3	389	P389del	CCT	---	1	1	AY.120	0.000037
ORF1ab/nsp3	389	P389del	CCT	---	1	1	AY.13	0.000161
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.16.1	0.00047
ORF1ab/nsp3	389	P389del	CCT	---	1	1	AY.19	0.00114
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	AY.20	0.000039
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.20	0.000039
ORF1ab/nsp3	389	P389del	CCT	---	1	1	AY.20	0.000039
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.21	0.001898
ORF1ab/nsp3	389	P389del1	Cct	-ct	1	1	AY.23	0.00007
ORF1ab/nsp3	389	P389del	CCT	---	1	1	AY.25	0.000006
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	AY.26	0.000028
ORF1ab/nsp3	389	P389T	Cct	Act	1	1	AY.26	0.000028
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	AY.27	0.000065
ORF1ab/nsp3	389	P389del	CCT	---	1	1	AY.29	0.000016
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	AY.29.1	0.000221
ORF1ab/nsp3	389	P389P	ccT	ccC	1	1	AY.3	0.00001
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	AY.3	0.00001
ORF1ab/nsp3	389	P389del	CCT	---	1	1	AY.3.1	0.000085
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	AY.3.1	0.000085
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.30	0.000396
ORF1ab/nsp3	389	P389T	Cct	Act	1	1	AY.33	0.000067
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	AY.34	0.000097
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.37	0.000316
ORF1ab/nsp3	389	P389P	ccT	ccG	1	1	AY.38	0.000499
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	AY.39	0.000025
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.39.1	0.00004
ORF1ab/nsp3	389	P389P	ccT	ccC	1	1	AY.39.1	0.00004
ORF1ab/nsp3	389	P389T	Cct	Act	1	1	AY.4.2	0.000022
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	AY.4.2.1	0.000149
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.4.4	0.000409
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	AY.4.5	0.000107
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.40	0.000964
ORF1ab/nsp3	389	P389T	Cct	Act	1	1	AY.42	0.00004
ORF1ab/nsp3	389	P389R	cCt	cGt	1	1	AY.43	0.000004
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	AY.43	0.000004
ORF1ab/nsp3	389	P389T	Cct	Act	1	1	AY.44	0.000006
ORF1ab/nsp3	389	P389P	ccT	ccC	1	1	AY.45	0.000122
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	AY.45	0.000122
ORF1ab/nsp3	389	P389del	CCT	---	1	1	AY.45	0.000122
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	AY.46	0.000104
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	AY.46	0.000104
ORF1ab/nsp3	389	P389P	ccT	ccC	1	1	AY.46.2	0.000635
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	AY.47	0.000031
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.48	0.000465
ORF1ab/nsp3	389	P389del	CCT	---	1	1	AY.5	0.000021
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	AY.5	0.000021
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	AY.5.4	0.000277
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.50	0.000799
ORF1ab/nsp3	389	P389T	Cct	Act	1	1	AY.52	0.000814
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.53	0.000288
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	AY.58	0.000907
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.59	0.00053
ORF1ab/nsp3	389	P389del	CCT	---	1	1	AY.6	0.000041
ORF1ab/nsp3	389	P389P	ccT	ccC	1	1	AY.6	0.000041
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.61	0.000105
ORF1ab/nsp3	389	P389P	ccT	ccC	1	1	AY.61	0.000105
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	AY.61	0.000105
ORF1ab/nsp3	389	P389P	ccT	ccC	1	1	AY.62	0.000436
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	AY.62	0.000436
ORF1ab/nsp3	389	P389T	Cct	Act	1	1	AY.62	0.000436
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	AY.63	0.000387
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.65	0.000533
ORF1ab/nsp3	389	P389del	CCT	---	1	1	AY.69	0.000187
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.7.1	0.000113
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	AY.7.2	0.000559
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.73	0.000665
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	AY.75	0.000056
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	AY.77	0.001127
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.8	0.000606
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.81	0.001992
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	AY.82	0.001357
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.84	0.000437
ORF1ab/nsp3	389	P389del1	Cct	-ct	1	1	AY.9.2	0.000037
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	AY.9.2	0.000037
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	AY.90	0.000684
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.98	0.000079
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	AY.98.1	0.000048
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	AY.98.1	0.000048
ORF1ab/nsp3	389	P389del1	Cct	-ct	1	1	B	0.000128
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B	0.000128
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B	0.000128
ORF1ab/nsp3	389	P389T	Cct	Act	1	1	B	0.000128
ORF1ab/nsp3	389	P389P	ccT	ccA	1	1	B.1.1	0.000018
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.1.117	0.009709
ORF1ab/nsp3	389	P389del	CCT	---	1	1	B.1.1.135	0.004695
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.1.141	0.002012
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.1.187	0.00885
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.1.189	0.001513
ORF1ab/nsp3	389	P389del	CCT	---	1	1	B.1.1.192	0.002309
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	B.1.1.214	0.000055
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.1.214	0.000055
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.1.216	0.00089
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.1.216	0.00089
ORF1ab/nsp3	389	P389del	CCT	---	1	1	B.1.1.221	0.010101
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.1.25	0.000569
ORF1ab/nsp3	389	P389del	CCT	---	1	1	B.1.1.25	0.000569
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.1.279	0.001121
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.1.284	0.000107
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.1.29	0.010309
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.1.294	0.001266
ORF1ab/nsp3	389	P389del	CCT	---	1	1	B.1.1.306	0.000438
ORF1ab/nsp3	389	P389del	CCT	---	1	1	B.1.1.315	0.008475
ORF1ab/nsp3	389	P389P	ccT	ccC	1	1	B.1.1.317	0.000412
ORF1ab/nsp3	389	P389del	CCT	---	1	1	B.1.1.318	0.000302
ORF1ab/nsp3	389	P389del	CCT	---	1	1	B.1.1.33	0.000421
ORF1ab/nsp3	389	P389del1	Cct	-ct	1	1	B.1.1.33	0.000421
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.1.369	0.000446
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	B.1.1.397	0.002252
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.1.416	0.000905
ORF1ab/nsp3	389	P389del	CCT	---	1	1	B.1.1.434	0.000349
ORF1ab/nsp3	389	P389T	Cct	Act	1	1	B.1.1.448	0.002033
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.1.482	0.023256
ORF1ab/nsp3	389	P389P	ccT	ccC	1	1	B.1.1.486	0.001577
ORF1ab/nsp3	389	P389del	CCT	---	1	1	B.1.1.519	0.00004
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.1.524	0.020833
ORF1ab/nsp3	389	P389del1	Cct	-ct	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.103	0.019231
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.110.3	0.000718
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.111	0.001175
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	B.1.139	0.000733
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.139	0.000733
ORF1ab/nsp3	389	P389del	CCT	---	1	1	B.1.140	0.018868
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.160	0.000031
ORF1ab/nsp3	389	P389R	cCt	cGt	1	1	B.1.177	0.000013
ORF1ab/nsp3	389	P389P	ccT	ccC	1	1	B.1.177.21	0.000076
ORF1ab/nsp3	389	P389del	CCT	---	1	1	B.1.177.4	0.000211
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	B.1.177.40	0.005155
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.177.56	0.000668
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.177.6	0.000977
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.177.60	0.000218
ORF1ab/nsp3	389	P389P	ccT	ccC	1	1	B.1.177.7	0.000165
ORF1ab/nsp3	389	P389P	ccT	ccA	1	1	B.1.177.73	0.000566
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.177.87	0.000728
ORF1ab/nsp3	389	P389del1	Cct	-ct	1	1	B.1.2	0.000009
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.22	0.001318
ORF1ab/nsp3	389	P389del	CCT	---	1	1	B.1.223	0.002778
ORF1ab/nsp3	389	P389P	ccT	ccC	1	1	B.1.232	0.000537
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.232	0.000537
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.234	0.000132
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.236	0.002053
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.243	0.00007
ORF1ab/nsp3	389	P389del	CCT	---	1	1	B.1.243	0.00007
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.258.17	0.000104
ORF1ab/nsp3	389	P389I	CCt	ATt	1	1	B.1.258.17	0.000104
ORF1ab/nsp3	389	P389T	Cct	Act	1	1	B.1.301	0.005917
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.320	0.001245
ORF1ab/nsp3	389	P389T	Cct	Act	1	1	B.1.332	0.003497
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.349	0.000715
ORF1ab/nsp3	389	P389del	CCT	---	1	1	B.1.351	0.00003
ORF1ab/nsp3	389	P389T	Cct	Act	1	1	B.1.351	0.00003
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.351	0.00003
ORF1ab/nsp3	389	P389del	CCT	---	1	1	B.1.356	0.001727
ORF1ab/nsp3	389	P389T	Cct	Act	1	1	B.1.36	0.000146
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.36	0.000146
ORF1ab/nsp3	389	P389del	CCT	---	1	1	B.1.36	0.000146
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.36.1	0.00114
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.36.16	0.001425
ORF1ab/nsp3	389	P389T	Cct	Act	1	1	B.1.36.22	0.001208
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	B.1.36.35	0.002604
ORF1ab/nsp3	389	P389P	ccT	ccC	1	1	B.1.36.39	0.002217
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.36.8	0.001
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.367	0.000792
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.369	0.000285
ORF1ab/nsp3	389	P389L	cCT	cTA	1	1	B.1.377	0.004566
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	B.1.396	0.000706
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.408	0.00369
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.426	0.001009
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.428	0.00102
ORF1ab/nsp3	389	P389del	CCT	---	1	1	B.1.429	0.000024
ORF1ab/nsp3	389	P389T	Cct	Act	1	1	B.1.459	0.004082
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.497	0.000315
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.544	0.006024
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.561	0.000397
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.576	0.000907
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.580	0.004065
ORF1ab/nsp3	389	P389del	CCT	---	1	1	B.1.595	0.000261
ORF1ab/nsp3	389	P389P	ccT	ccC	1	1	B.1.609	0.000479
ORF1ab/nsp3	389	P389R	cCt	cGt	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.1.621	0.000089
ORF1ab/nsp3	389	P389T	Cct	Act	1	1	B.1.623	0.000536
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	B.1.633	0.041667
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	B.1.636	0.006711
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	B.28	0.003279
ORF1ab/nsp3	389	P389P	ccT	ccG	1	1	B.3.1	0.001658
ORF1ab/nsp3	389	P389del	CCT	---	1	1	B.57	0.015152
ORF1ab/nsp3	389	P389T	Cct	Act	1	1	B.6.6	0.000889
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	C.37	0.000116
ORF1ab/nsp3	389	P389del	CCT	---	1	1	C.37	0.000116
ORF1ab/nsp3	389	P389P	ccT	ccA	1	1	D.2	0.000075
ORF1ab/nsp3	389	P389del	CCT	---	1	1	D.2	0.000075
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	N.4	0.004255
ORF1ab/nsp3	389	P389del	CCT	---	1	1	N.6	0.007092
ORF1ab/nsp3	389	P389del	CCT	---	1	1	P.1.14	0.000048
ORF1ab/nsp3	389	P389H	cCt	cAt	1	1	P.1.14	0.000048
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	P.1.14	0.000048
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	P.1.7	0.000319
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	P.6	0.003145
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	Q.1	0.000126
ORF1ab/nsp3	389	P389del	CCT	---	1	1	Q.2	0.000613
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	Q.4	0.000455
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	Q.8	0.000165
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	R.1	0.00009
ORF1ab/nsp3	389	P389S	Cct	Tct	1	1	U.3	0.003861
ORF1ab/nsp3	389	P389del	CCT	---	1	1	W.4	0.001351
ORF1ab/nsp3	389	P389L	cCt	cTt	1	1	Z.1	0.00289

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.