CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp2 : CodonNum = 99

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/nsp2	99	S99S	S279S	syn	tcC	tcT	6121	6076	0.992648	1100-1102
ORF1ab/nsp2	99	S99S	S279S	syn	tcC	tcA	6121	42	0.00686162	1100-1102
ORF1ab/nsp2	99	S99S	S279S	syn	tcC	tcG	6121	3	0.000490116	1100-1102
ORF1ab/nsp2	99	S99F	S279F	nonsyn	tCc	tTc	5033	5027	0.998808	1100-1102
ORF1ab/nsp2	99	S99F	S279F	nonsyn	tCC	tTT	5033	6	0.00119213	1100-1102
ORF1ab/nsp2	99	S99del	S279del	del	TCC	---	82	82	1	1100-1102
ORF1ab/nsp2	99	S99A	S279A	nonsyn	Tcc	Gcc	42	42	1	1100-1102
ORF1ab/nsp2	99	S99Y	S279Y	nonsyn	tCc	tAc	31	31	1	1100-1102
ORF1ab/nsp2	99	S99T	S279T	nonsyn	Tcc	Acc	27	27	1	1100-1102
ORF1ab/nsp2	99	S99P	S279P	nonsyn	Tcc	Ccc	19	18	0.947368	1100-1102
ORF1ab/nsp2	99	S99P	S279P	nonsyn	TcC	CcT	19	1	0.0526316	1100-1102
ORF1ab/nsp2	99	S99C	S279C	nonsyn	tCc	tGc	17	17	1	1100-1102
ORF1ab/nsp2	99	S99L	S279L	nonsyn	tCC	tTA	9	6	0.666667	1100-1102
ORF1ab/nsp2	99	S99L	S279L	nonsyn	TCc	CTc	9	1	0.111111	1100-1102
ORF1ab/nsp2	99	S99L	S279L	nonsyn	tCC	tTG	9	1	0.111111	1100-1102
ORF1ab/nsp2	99	S99L	S279L	nonsyn	TCC	CTT	9	1	0.111111	1100-1102
ORF1ab/nsp2	99	S99V	S279V	nonsyn	TCc	GTc	2	2	1	1100-1102
ORF1ab/nsp2	99	S99W	S279W	nonsyn	tCC	tGG	2	2	1	1100-1102
ORF1ab/nsp2	99	S99del1	S279del1	del	tcC	tc-	2	1	0.5	1100-1102
ORF1ab/nsp2	99	S99del1	S279del1	del	tCc	t-c	2	1	0.5	1100-1102
ORF1ab/nsp2	99	S99I	S279I	nonsyn	TCc	ATc	1	1	1	1100-1102
ORF1ab/nsp2	99	S99X	S279X	nonsyn	tCC	tAA	1	1	1	1100-1102
ORF1ab/nsp2	99	S99H	S279H	nonsyn	TCc	CAc	1	1	1	1100-1102
ORF1ab/nsp2	99	S99D	S279D	nonsyn	TCc	GAc	1	1	1	1100-1102
ORF1ab/nsp2	99	S99R	S279R	nonsyn	TCC	CGG	1	1	1	1100-1102

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/nsp2	99	S99S	tcC	tcT	6076	6121	All	0.001162
ORF1ab/nsp2	99	S99S	tcC	tcA	42	6121	All	0.000008
ORF1ab/nsp2	99	S99S	tcC	tcG	3	6121	All	0.000001
ORF1ab/nsp2	99	S99F	tCc	tTc	5027	5033	All	0.000961
ORF1ab/nsp2	99	S99F	tCC	tTT	6	5033	All	0.000001
ORF1ab/nsp2	99	S99F	tCc	tTc	3069	3069	AY.93	0.838067
ORF1ab/nsp2	99	S99S	tcC	tcT	986	987	B.1.1.7	0.000883
ORF1ab/nsp2	99	S99S	tcC	tcA	1	987	B.1.1.7	0.000001
ORF1ab/nsp2	99	S99F	tCc	tTc	655	660	B.1.1.7	0.000586
ORF1ab/nsp2	99	S99F	tCC	tTT	5	660	B.1.1.7	0.000004
ORF1ab/nsp2	99	S99S	tcC	tcT	425	426	B.1.2	0.003742
ORF1ab/nsp2	99	S99S	tcC	tcA	1	426	B.1.2	0.000009
ORF1ab/nsp2	99	S99S	tcC	tcT	377	377	B.1.526	0.008861
ORF1ab/nsp2	99	S99S	tcC	tcT	365	367	AY.4	0.000568
ORF1ab/nsp2	99	S99S	tcC	tcA	2	367	AY.4	0.000003
ORF1ab/nsp2	99	S99F	tCc	tTc	317	317	AY.4	0.000493
ORF1ab/nsp2	99	S99S	tcC	tcT	309	310	AY.43	0.001369
ORF1ab/nsp2	99	S99S	tcC	tcA	1	310	AY.43	0.000004
ORF1ab/nsp2	99	S99S	tcC	tcT	298	298	B.1.617.2	0.001122
ORF1ab/nsp2	99	S99S	tcC	tcT	268	269	P.1	0.004222
ORF1ab/nsp2	99	S99S	tcC	tcA	1	269	P.1	0.000016
ORF1ab/nsp2	99	S99S	tcC	tcT	180	180	B.1.1.519	0.007148
ORF1ab/nsp2	99	S99S	tcC	tcT	180	180	B.1.596	0.015685
ORF1ab/nsp2	99	S99S	tcC	tcT	147	147	AY.25	0.000884
ORF1ab/nsp2	99	S99S	tcC	tcT	144	144	AY.39	0.003558
ORF1ab/nsp2	99	S99S	tcC	tcT	116	117	B.1.351	0.003448
ORF1ab/nsp2	99	S99S	tcC	tcG	1	117	B.1.351	0.00003
ORF1ab/nsp2	99	S99S	tcC	tcT	113	113	B.1.177	0.001488
ORF1ab/nsp2	99	S99S	tcC	tcT	109	109	AY.3.1	0.009293
ORF1ab/nsp2	99	S99S	tcC	tcT	102	102	AY.39.1	0.004041
ORF1ab/nsp2	99	S99S	tcC	tcT	98	101	B.1	0.000898
ORF1ab/nsp2	99	S99S	tcC	tcA	2	101	B.1	0.000018
ORF1ab/nsp2	99	S99S	tcC	tcG	1	101	B.1	0.000009
ORF1ab/nsp2	99	S99S	tcC	tcT	93	94	AY.44	0.000566
ORF1ab/nsp2	99	S99S	tcC	tcA	1	94	AY.44	0.000006
ORF1ab/nsp2	99	S99del	TCC	---	82	82	All	0.000016
ORF1ab/nsp2	99	S99S	tcC	tcT	80	80	B.1.177.21	0.006118
ORF1ab/nsp2	99	S99F	tCc	tTc	77	77	B.1	0.000705
ORF1ab/nsp2	99	S99S	tcC	tcT	72	72	AY.119	0.002542
ORF1ab/nsp2	99	S99F	tCc	tTc	70	71	AY.43	0.00031
ORF1ab/nsp2	99	S99F	tCC	tTT	1	71	AY.43	0.000004
ORF1ab/nsp2	99	S99F	tCc	tTc	65	65	B.1.1.274	0.328283
ORF1ab/nsp2	99	S99F	tCc	tTc	58	58	B.1.1.14	1
ORF1ab/nsp2	99	S99S	tcC	tcT	55	55	AY.5	0.001136
ORF1ab/nsp2	99	S99S	tcC	tcT	46	54	AY.3	0.000458
ORF1ab/nsp2	99	S99S	tcC	tcA	8	54	AY.3	0.00008
ORF1ab/nsp2	99	S99S	tcC	tcT	53	54	B.1.429	0.001247
ORF1ab/nsp2	99	S99S	tcC	tcA	1	54	B.1.429	0.000024
ORF1ab/nsp2	99	S99S	tcC	tcT	52	52	AY.103	0.000323
ORF1ab/nsp2	99	S99S	tcC	tcT	52	52	AY.20	0.002021
ORF1ab/nsp2	99	S99S	tcC	tcT	52	52	B.1.1	0.000943
ORF1ab/nsp2	99	S99F	tCc	tTc	51	51	AY.103	0.000317
ORF1ab/nsp2	99	S99S	tcC	tcT	50	50	B.1.1.316	0.046253
ORF1ab/nsp2	99	S99S	tcC	tcT	46	46	AY.26	0.001302
ORF1ab/nsp2	99	S99F	tCc	tTc	46	46	B.1.617.2	0.000173
ORF1ab/nsp2	99	S99S	tcC	tcT	45	45	B.1.456	0.147059
ORF1ab/nsp2	99	S99S	tcC	tcT	44	44	AY.29	0.000694
ORF1ab/nsp2	99	S99F	tCc	tTc	43	43	AY.25	0.000259
ORF1ab/nsp2	99	S99S	tcC	tcT	43	43	B.1.160	0.001341
ORF1ab/nsp2	99	S99A	Tcc	Gcc	42	42	All	0.000008
ORF1ab/nsp2	99	S99S	tcC	tcT	41	41	AY.100	0.001886
ORF1ab/nsp2	99	S99S	tcC	tcT	37	37	AY.23	0.002581
ORF1ab/nsp2	99	S99S	tcC	tcT	35	35	AY.29.1	0.007718
ORF1ab/nsp2	99	S99S	tcC	tcT	32	32	AY.4.2	0.000694
ORF1ab/nsp2	99	S99S	tcC	tcT	32	32	C.37	0.003714
ORF1ab/nsp2	99	S99F	tCc	tTc	32	32	P.1	0.000504
ORF1ab/nsp2	99	S99Y	tCc	tAc	31	31	All	0.000006
ORF1ab/nsp2	99	S99F	tCc	tTc	29	29	B.1.1	0.000526
ORF1ab/nsp2	99	S99S	tcC	tcT	28	28	AD.2	0.006131
ORF1ab/nsp2	99	S99S	tcC	tcT	28	28	B.1.243	0.001948
ORF1ab/nsp2	99	S99T	Tcc	Acc	27	27	All	0.000005
ORF1ab/nsp2	99	S99S	tcC	tcT	27	27	AY.102	0.000716
ORF1ab/nsp2	99	S99S	tcC	tcT	27	27	AY.98.1	0.001308
ORF1ab/nsp2	99	S99F	tCc	tTc	27	27	B.1.1.416	0.024434
ORF1ab/nsp2	99	S99F	tCc	tTc	26	26	B.1.2	0.000229
ORF1ab/nsp2	99	S99S	tcC	tcT	26	26	Q.1	0.003284
ORF1ab/nsp2	99	S99F	tCc	tTc	25	25	AY.26	0.000708
ORF1ab/nsp2	99	S99S	tcC	tcT	23	23	B.1.177.54	0.013948
ORF1ab/nsp2	99	S99S	tcC	tcT	21	21	B.1.258.17	0.002183
ORF1ab/nsp2	99	S99S	tcC	tcT	20	20	B.1.234	0.002639
ORF1ab/nsp2	99	S99P	Tcc	Ccc	18	19	All	0.000003
ORF1ab/nsp2	99	S99P	TcC	CcT	1	19	All	0
ORF1ab/nsp2	99	S99F	tCc	tTc	19	19	AY.44	0.000116
ORF1ab/nsp2	99	S99S	tcC	tcT	18	18	AY.120	0.000669
ORF1ab/nsp2	99	S99S	tcC	tcT	18	18	AY.34	0.001745
ORF1ab/nsp2	99	S99F	tCc	tTc	18	18	AY.42	0.000724
ORF1ab/nsp2	99	S99S	tcC	tcA	18	18	P.1.13	0.016173
ORF1ab/nsp2	99	S99C	tCc	tGc	17	17	All	0.000003
ORF1ab/nsp2	99	S99del	TCC	---	17	17	B.1.1.7	0.000015
ORF1ab/nsp2	99	S99S	tcC	tcT	16	16	B.1.1.39	0.008155
ORF1ab/nsp2	99	S99F	tCc	tTc	16	16	B.1.258.17	0.001664
ORF1ab/nsp2	99	S99S	tcC	tcT	16	16	B.1.36.29	0.008277
ORF1ab/nsp2	99	S99S	tcC	tcT	14	14	AY.92	0.004022
ORF1ab/nsp2	99	S99Y	tCc	tAc	14	14	B.1.1.214	0.000776
ORF1ab/nsp2	99	S99S	tcC	tcT	13	13	B	0.001662
ORF1ab/nsp2	99	S99S	tcC	tcT	13	13	B.1.427	0.000656
ORF1ab/nsp2	99	S99S	tcC	tcT	13	13	B.1.637	0.00095
ORF1ab/nsp2	99	S99S	tcC	tcT	13	13	P.1.7	0.004151
ORF1ab/nsp2	99	S99F	tCc	tTc	12	12	AE.7	1
ORF1ab/nsp2	99	S99S	tcC	tcT	11	11	A.2.5	0.005489
ORF1ab/nsp2	99	S99F	tCc	tTc	11	11	AY.119	0.000388
ORF1ab/nsp2	99	S99F	tCc	tTc	11	11	AY.23	0.000767
ORF1ab/nsp2	99	S99F	tCc	tTc	11	11	AY.4.2	0.000239
ORF1ab/nsp2	99	S99S	tcC	tcT	11	11	AY.42	0.000443
ORF1ab/nsp2	99	S99T	Tcc	Acc	11	11	B.1	0.000101
ORF1ab/nsp2	99	S99F	tCc	tTc	11	11	B.1.195	0.055276
ORF1ab/nsp2	99	S99S	tcC	tcT	11	11	B.1.617.1	0.001419
ORF1ab/nsp2	99	S99S	tcC	tcT	10	10	AY.45	0.001217
ORF1ab/nsp2	99	S99S	tcC	tcT	10	10	AY.84	0.004374
ORF1ab/nsp2	99	S99F	tCc	tTc	10	10	B.1.177	0.000132
ORF1ab/nsp2	99	S99S	tcC	tcT	10	10	B.1.36	0.001459
ORF1ab/nsp2	99	S99S	tcC	tcT	10	10	B.1.36.8	0.01
ORF1ab/nsp2	99	S99F	tCc	tTc	10	10	P.1.1	0.003177
ORF1ab/nsp2	99	S99S	tcC	tcT	10	10	P.1.16	0.003741
ORF1ab/nsp2	99	S99S	tcC	tcT	10	10	Q.7	0.011111
ORF1ab/nsp2	99	S99L	tCC	tTA	6	9	All	0.000001
ORF1ab/nsp2	99	S99L	TCC	CTT	1	9	All	0
ORF1ab/nsp2	99	S99L	tCC	tTG	1	9	All	0
ORF1ab/nsp2	99	S99L	TCc	CTc	1	9	All	0
ORF1ab/nsp2	99	S99S	tcC	tcA	5	9	AY.36	0.000741
ORF1ab/nsp2	99	S99S	tcC	tcT	4	9	AY.36	0.000593
ORF1ab/nsp2	99	S99A	Tcc	Gcc	9	9	AY.44	0.000055
ORF1ab/nsp2	99	S99S	tcC	tcT	9	9	AY.46.6	0.00065
ORF1ab/nsp2	99	S99S	tcC	tcT	9	9	AY.61	0.000943
ORF1ab/nsp2	99	S99F	tCc	tTc	9	9	B.1.1.214	0.000499
ORF1ab/nsp2	99	S99A	Tcc	Gcc	9	9	B.1.1.7	0.000008
ORF1ab/nsp2	99	S99S	tcC	tcT	9	9	B.1.258	0.000599
ORF1ab/nsp2	99	S99F	tCc	tTc	8	8	A	0.003096
ORF1ab/nsp2	99	S99S	tcC	tcT	8	8	A.1	0.002255
ORF1ab/nsp2	99	S99F	tCc	tTc	8	8	AY.102	0.000212
ORF1ab/nsp2	99	S99S	tcC	tcT	8	8	AY.9.1	0.00067
ORF1ab/nsp2	99	S99S	tcC	tcT	8	8	B.1.1.317	0.003294
ORF1ab/nsp2	99	S99S	tcC	tcT	8	8	B.1.628	0.002819
ORF1ab/nsp2	99	S99S	tcC	tcT	8	8	P.1.14	0.000382
ORF1ab/nsp2	99	S99L	tCC	tTA	6	7		0.333333
ORF1ab/nsp2	99	S99L	TCc	CTc	1	7		0.055556
ORF1ab/nsp2	99	S99F	tCc	tTc	7	7	AY.117	0.000592
ORF1ab/nsp2	99	S99S	tcC	tcT	7	7	AY.27	0.000453
ORF1ab/nsp2	99	S99S	tcC	tcT	7	7	AY.46	0.000729
ORF1ab/nsp2	99	S99S	tcC	tcT	7	7	AY.47	0.000218
ORF1ab/nsp2	99	S99S	tcC	tcT	7	7	AY.5.1	0.026316
ORF1ab/nsp2	99	S99S	tcC	tcT	7	7	AY.65	0.003731
ORF1ab/nsp2	99	S99S	tcC	tcT	7	7	AY.68	0.001916
ORF1ab/nsp2	99	S99S	tcC	tcT	7	7	B.1.1.214	0.000388
ORF1ab/nsp2	99	S99F	tCc	tTc	7	7	B.1.160	0.000218
ORF1ab/nsp2	99	S99S	tcC	tcT	7	7	B.1.177.86	0.001284
ORF1ab/nsp2	99	S99F	tCc	tTc	7	7	B.1.36.29	0.003621
ORF1ab/nsp2	99	S99S	tcC	tcT	7	7	B.1.36.7	0.028
ORF1ab/nsp2	99	S99S	tcC	tcT	7	7	B.1.361	0.009021
ORF1ab/nsp2	99	S99S	tcC	tcT	7	7	C.37.1	0.018325
ORF1ab/nsp2	99	S99S	tcC	tcT	7	7	C.38	0.056452
ORF1ab/nsp2	99	S99S	tcC	tcT	7	7	P.2	0.001306
ORF1ab/nsp2	99	S99F	tCc	tTc	7	7	Q.1	0.000884
ORF1ab/nsp2	99	S99del	TCC	---	6	6	AY.25	0.000036
ORF1ab/nsp2	99	S99C	tCc	tGc	6	6	AY.4	0.000009
ORF1ab/nsp2	99	S99S	tcC	tcT	6	6	AY.4.5	0.000645
ORF1ab/nsp2	99	S99P	Tcc	Ccc	6	6	B.1.1.7	0.000005
ORF1ab/nsp2	99	S99F	tCc	tTc	6	6	B.1.221	0.000426
ORF1ab/nsp2	99	S99S	tcC	tcT	6	6	B.1.349	0.004289
ORF1ab/nsp2	99	S99del	TCC	---	6	6	B.1.617.2	0.000023
ORF1ab/nsp2	99	S99S	tcC	tcT	5	5	AY.101	0.002452
ORF1ab/nsp2	99	S99S	tcC	tcT	5	5	AY.113	0.000712
ORF1ab/nsp2	99	S99S	tcC	tcT	5	5	AY.118	0.000313
ORF1ab/nsp2	99	S99F	tCc	tTc	5	5	AY.3	0.00005
ORF1ab/nsp2	99	S99S	tcC	tcT	5	5	AY.33	0.000334
ORF1ab/nsp2	99	S99F	tCc	tTc	5	5	AY.33	0.000334
ORF1ab/nsp2	99	S99A	Tcc	Gcc	5	5	AY.43	0.000022
ORF1ab/nsp2	99	S99S	tcC	tcT	5	5	AY.56	0.008026
ORF1ab/nsp2	99	S99F	tCc	tTc	5	5	AY.61	0.000524
ORF1ab/nsp2	99	S99F	tCc	tTc	5	5	B.1.1.170	0.006234
ORF1ab/nsp2	99	S99F	tCc	tTc	5	5	B.1.1.222	0.00102
ORF1ab/nsp2	99	S99S	tcC	tcT	5	5	B.1.1.222	0.00102
ORF1ab/nsp2	99	S99F	tCc	tTc	5	5	B.1.1.306	0.002192
ORF1ab/nsp2	99	S99del	TCC	---	5	5	B.1.1.33	0.002104
ORF1ab/nsp2	99	S99S	tcC	tcT	5	5	B.1.1.434	0.001743
ORF1ab/nsp2	99	S99S	tcC	tcT	5	5	B.1.160.16	0.004647
ORF1ab/nsp2	99	S99F	tCc	tTc	5	5	B.1.234	0.00066
ORF1ab/nsp2	99	S99S	tcC	tcT	5	5	B.1.311	0.001373
ORF1ab/nsp2	99	S99F	tCc	tTc	5	5	B.1.617.1	0.000645
ORF1ab/nsp2	99	S99S	tcC	tcT	4	4	AY.117	0.000338
ORF1ab/nsp2	99	S99S	tcC	tcT	4	4	AY.120.1	0.001284
ORF1ab/nsp2	99	S99F	tCc	tTc	4	4	AY.121	0.000541
ORF1ab/nsp2	99	S99S	tcC	tcT	4	4	AY.13	0.000644
ORF1ab/nsp2	99	S99S	tcC	tcT	4	4	AY.14	0.000352
ORF1ab/nsp2	99	S99del	TCC	---	4	4	AY.4	0.000006
ORF1ab/nsp2	99	S99T	Tcc	Acc	4	4	AY.4	0.000006
ORF1ab/nsp2	99	S99del	TCC	---	4	4	AY.43	0.000018
ORF1ab/nsp2	99	S99F	tCc	tTc	4	4	AY.47	0.000124
ORF1ab/nsp2	99	S99S	tcC	tcT	4	4	AY.75	0.000224
ORF1ab/nsp2	99	S99F	tCc	tTc	4	4	B	0.000511
ORF1ab/nsp2	99	S99S	tcC	tcT	4	4	B.1.1.28	0.001245
ORF1ab/nsp2	99	S99S	tcC	tcT	4	4	B.1.1.303	0.01105
ORF1ab/nsp2	99	S99F	tCc	tTc	4	4	B.1.1.33	0.001684
ORF1ab/nsp2	99	S99F	tCc	tTc	4	4	B.1.1.348	0.003185
ORF1ab/nsp2	99	S99del	TCC	---	4	4	B.1.1.348	0.003185
ORF1ab/nsp2	99	S99S	tcC	tcT	4	4	B.1.1.372	0.002755
ORF1ab/nsp2	99	S99F	tCc	tTc	4	4	B.1.1.372	0.002755
ORF1ab/nsp2	99	S99F	tCc	tTc	4	4	B.1.1.519	0.000159
ORF1ab/nsp2	99	S99S	tcC	tcT	4	4	B.1.110.3	0.002874
ORF1ab/nsp2	99	S99F	tCc	tTc	4	4	B.1.258.3	0.0067
ORF1ab/nsp2	99	S99S	tcC	tcT	4	4	B.1.265	0.005083
ORF1ab/nsp2	99	S99F	tCc	tTc	4	4	B.1.36	0.000584
ORF1ab/nsp2	99	S99S	tcC	tcT	4	4	B.1.428	0.004082
ORF1ab/nsp2	99	S99S	tcC	tcT	4	4	B.1.588	0.00364
ORF1ab/nsp2	99	S99F	tCc	tTc	4	4	B.1.596	0.000349
ORF1ab/nsp2	99	S99S	tcC	tcT	4	4	C.14	0.017316
ORF1ab/nsp2	99	S99F	tCc	tTc	4	4	C.37	0.000464
ORF1ab/nsp2	99	S99S	tcC	tcT	4	4	P.1.15	0.000929
ORF1ab/nsp2	99	S99F	tCc	tTc	4	4	Q.8	0.00066
ORF1ab/nsp2	99	S99Y	tCc	tAc	3	3		0.166667
ORF1ab/nsp2	99	S99S	tcC	tcT	3	3	A.2.5.3	0.030928
ORF1ab/nsp2	99	S99F	tCc	tTc	3	3	AY.111	0.000549
ORF1ab/nsp2	99	S99S	tcC	tcT	3	3	AY.121	0.000406
ORF1ab/nsp2	99	S99F	tCc	tTc	3	3	AY.29	0.000047
ORF1ab/nsp2	99	S99T	Tcc	Acc	3	3	AY.39.1	0.000119
ORF1ab/nsp2	99	S99A	Tcc	Gcc	3	3	AY.4	0.000005
ORF1ab/nsp2	99	S99S	tcC	tcT	3	3	AY.6	0.000123
ORF1ab/nsp2	99	S99S	tcC	tcT	3	3	AY.9	0.000203
ORF1ab/nsp2	99	S99S	tcC	tcT	3	3	AY.98	0.000237
ORF1ab/nsp2	99	S99S	tcC	tcT	3	3	AY.99.2	0.000276
ORF1ab/nsp2	99	S99S	tcC	tcT	3	3	AZ.2	0.002463
ORF1ab/nsp2	99	S99S	tcC	tcT	3	3	B.1.1.170	0.003741
ORF1ab/nsp2	99	S99F	tCc	tTc	3	3	B.1.1.232	0.005445
ORF1ab/nsp2	99	S99F	tCc	tTc	3	3	B.1.1.434	0.001046
ORF1ab/nsp2	99	S99F	tCc	tTc	3	3	B.1.1.70	0.001023
ORF1ab/nsp2	99	S99S	tcC	tcT	3	3	B.1.1.70	0.001023
ORF1ab/nsp2	99	S99F	tCc	tTc	3	3	B.1.162	0.015075
ORF1ab/nsp2	99	S99S	tcC	tcT	3	3	B.1.177.12	0.000455
ORF1ab/nsp2	99	S99S	tcC	tcT	3	3	B.1.177.62	0.003576
ORF1ab/nsp2	99	S99F	tCc	tTc	3	3	B.1.218	0.015464
ORF1ab/nsp2	99	S99S	tcC	tcT	3	3	B.1.351.3	0.002629
ORF1ab/nsp2	99	S99S	tcC	tcT	3	3	B.1.367	0.002377
ORF1ab/nsp2	99	S99S	tcC	tcT	3	3	B.1.466.2	0.001174
ORF1ab/nsp2	99	S99F	tCc	tTc	3	3	B.1.526	0.000071
ORF1ab/nsp2	99	S99S	tcC	tcT	3	3	B.1.595	0.000783
ORF1ab/nsp2	99	S99S	tcC	tcT	3	3	B.1.621	0.000266
ORF1ab/nsp2	99	S99P	Tcc	Ccc	3	3	D.2	0.000225
ORF1ab/nsp2	99	S99S	tcC	tcT	3	3	P.1.12	0.001452
ORF1ab/nsp2	99	S99F	tCc	tTc	3	3	P.1.15	0.000697
ORF1ab/nsp2	99	S99S	tcC	tcT	3	3	P.3	0.004785
ORF1ab/nsp2	99	S99S	tcC	tcT	3	3	P.6	0.009434
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	A.29	0.010638
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	AL.1	0.025974
ORF1ab/nsp2	99	S99W	tCC	tGG	2	2	All	0
ORF1ab/nsp2	99	S99V	TCc	GTc	2	2	All	0
ORF1ab/nsp2	99	S99del1	tcC	tc-	1	2	All	0
ORF1ab/nsp2	99	S99del1	tCc	t-c	1	2	All	0
ORF1ab/nsp2	99	S99del	TCC	---	2	2	AY.103	0.000012
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	AY.110	0.000225
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	AY.12	0.000632
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	AY.120.2.1	0.000997
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	AY.3.1	0.000171
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	AY.39.2	0.003082
ORF1ab/nsp2	99	S99del	TCC	---	2	2	AY.4.5	0.000215
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	AY.5	0.000041
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	AY.60	0.001876
ORF1ab/nsp2	99	S99C	tCc	tGc	2	2	AY.7.1	0.000225
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	AY.70	0.000417
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	AY.75	0.000112
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	AZ.1	0.001735
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	AZ.3	0.00304
ORF1ab/nsp2	99	S99Y	tCc	tAc	2	2	B.1	0.000018
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	B.1.1.1	0.000653
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	B.1.1.189	0.003026
ORF1ab/nsp2	99	S99C	tCc	tGc	2	2	B.1.1.28	0.000622
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	B.1.1.306	0.000877
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	B.1.1.337	0.007194
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	B.1.1.397	0.004505
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	B.1.1.448	0.004065
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	B.1.1.449	0.045455
ORF1ab/nsp2	99	S99Y	tCc	tAc	2	2	B.1.1.7	0.000002
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	B.1.1.8	0.007168
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	B.1.111	0.00235
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	B.1.164	0.029851
ORF1ab/nsp2	99	S99A	Tcc	Gcc	2	2	B.1.177	0.000026
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	B.1.177.4	0.000422
ORF1ab/nsp2	99	S99A	Tcc	Gcc	2	2	B.1.2	0.000018
ORF1ab/nsp2	99	S99Y	tCc	tAc	2	2	B.1.2	0.000018
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	B.1.221	0.000142
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	B.1.232	0.001075
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	B.1.235	0.005038
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	B.1.240	0.000431
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	B.1.240	0.000431
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	B.1.245	0.0625
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	B.1.258	0.000133
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	B.1.258.21	0.015504
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	B.1.351.2	0.000605
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	B.1.351.5	0.001199
ORF1ab/nsp2	99	S99del	TCC	---	2	2	B.1.429	0.000047
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	B.1.438.1	0.000215
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	B.1.462	0.014493
ORF1ab/nsp2	99	S99Y	tCc	tAc	2	2	B.1.462	0.014493
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	B.1.466.2	0.000782
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	B.1.497	0.00063
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	B.1.517	0.000854
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	B.1.582	0.000981
ORF1ab/nsp2	99	S99C	tCc	tGc	2	2	B.1.617.2	0.000008
ORF1ab/nsp2	99	S99P	Tcc	Ccc	2	2	B.1.617.2	0.000008
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	B.1.621	0.000177
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	B.1.623	0.001073
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	B.1.630	0.010471
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	D.2	0.00015
ORF1ab/nsp2	99	S99del	TCC	---	2	2	N.6	0.014184
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	P.1.14	0.000096
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	P.1.17	0.000324
ORF1ab/nsp2	99	S99T	Tcc	Acc	2	2	P.1.7	0.000639
ORF1ab/nsp2	99	S99del	TCC	---	2	2	P.2	0.000373
ORF1ab/nsp2	99	S99F	tCc	tTc	2	2	R.1	0.00018
ORF1ab/nsp2	99	S99S	tcC	tcT	2	2	R.1	0.00018
ORF1ab/nsp2	99	S99P	Tcc	Ccc	1	1		0.055556
ORF1ab/nsp2	99	S99V	TCc	GTc	1	1		0.055556
ORF1ab/nsp2	99	S99T	Tcc	Acc	1	1		0.055556
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1		0.055556
ORF1ab/nsp2	99	S99H	TCc	CAc	1	1		0.055556
ORF1ab/nsp2	99	S99A	Tcc	Gcc	1	1		0.055556
ORF1ab/nsp2	99	S99D	TCc	GAc	1	1		0.055556
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	A.1	0.000282
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	A.2	0.000662
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	A.2.4	0.003367
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	A.2.5.2	0.001572
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	A.23.1	0.000704
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	A.24	0.071429
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AE.2	0.058824
ORF1ab/nsp2	99	S99D	TCc	GAc	1	1	All	0
ORF1ab/nsp2	99	S99I	TCc	ATc	1	1	All	0
ORF1ab/nsp2	99	S99R	TCC	CGG	1	1	All	0
ORF1ab/nsp2	99	S99X	tCC	tAA	1	1	All	0
ORF1ab/nsp2	99	S99H	TCc	CAc	1	1	All	0
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AW.1	0.003049
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.100	0.000046
ORF1ab/nsp2	99	S99A	Tcc	Gcc	1	1	AY.102	0.000027
ORF1ab/nsp2	99	S99A	Tcc	Gcc	1	1	AY.103	0.000006
ORF1ab/nsp2	99	S99A	Tcc	Gcc	1	1	AY.107	0.000466
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.109	0.00074
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.110	0.000113
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.114	0.000231
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.116	0.000287
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.120	0.000037
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.16	0.00038
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.20	0.000039
ORF1ab/nsp2	99	S99del	TCC	---	1	1	AY.26	0.000028
ORF1ab/nsp2	99	S99Y	tCc	tAc	1	1	AY.26	0.000028
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.30	0.000396
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.32	0.000532
ORF1ab/nsp2	99	S99P	Tcc	Ccc	1	1	AY.33	0.000067
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.34	0.000097
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.34.1	0.00051
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.34.1	0.00051
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.36	0.000148
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.37	0.000316
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.39	0.000025
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.39.1	0.00004
ORF1ab/nsp2	99	S99P	Tcc	Ccc	1	1	AY.4	0.000002
ORF1ab/nsp2	99	S99Y	tCc	tAc	1	1	AY.4	0.000002
ORF1ab/nsp2	99	S99Y	tCc	tAc	1	1	AY.4.2	0.000022
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.4.2.1	0.000149
ORF1ab/nsp2	99	S99A	Tcc	Gcc	1	1	AY.4.2.1	0.000149
ORF1ab/nsp2	99	S99C	tCc	tGc	1	1	AY.4.2.1	0.000149
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.4.2.1	0.000149
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.4.5	0.000107
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.40	0.000964
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.41	0.000294
ORF1ab/nsp2	99	S99Y	tCc	tAc	1	1	AY.43	0.000004
ORF1ab/nsp2	99	S99L	TCC	CTT	1	1	AY.43	0.000004
ORF1ab/nsp2	99	S99X	tCC	tAA	1	1	AY.43	0.000004
ORF1ab/nsp2	99	S99P	TcC	CcT	1	1	AY.43	0.000004
ORF1ab/nsp2	99	S99del	TCC	---	1	1	AY.44	0.000006
ORF1ab/nsp2	99	S99P	Tcc	Ccc	1	1	AY.44	0.000006
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.46.1	0.001027
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.46.4	0.000165
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.46.6	0.000072
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.48	0.000465
ORF1ab/nsp2	99	S99P	Tcc	Ccc	1	1	AY.5	0.000021
ORF1ab/nsp2	99	S99del	TCC	---	1	1	AY.5.3	0.000337
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.52	0.000814
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.53	0.000288
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.54	0.000095
ORF1ab/nsp2	99	S99P	Tcc	Ccc	1	1	AY.55	0.000917
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.57	0.000656
ORF1ab/nsp2	99	S99A	Tcc	Gcc	1	1	AY.58	0.000907
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.59	0.00053
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.62	0.000436
ORF1ab/nsp2	99	S99del	TCC	---	1	1	AY.62	0.000436
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.64	0.000595
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.67	0.000464
ORF1ab/nsp2	99	S99A	Tcc	Gcc	1	1	AY.69	0.000187
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.7.2	0.000559
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.71	0.000475
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.73	0.000665
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.74	0.000116
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.75.1	0.00018
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.8	0.000606
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.82	0.001357
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.83	0.001724
ORF1ab/nsp2	99	S99del	TCC	---	1	1	AY.84	0.000437
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.89	0.004902
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.9.1	0.000084
ORF1ab/nsp2	99	S99A	Tcc	Gcc	1	1	AY.9.1	0.000084
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	AY.9.2	0.000037
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.9.2	0.000037
ORF1ab/nsp2	99	S99A	Tcc	Gcc	1	1	AY.9.2	0.000037
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.98	0.000079
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.98.1	0.000048
ORF1ab/nsp2	99	S99del	TCC	---	1	1	AY.99	0.001049
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	AY.99.2	0.000092
ORF1ab/nsp2	99	S99C	tCc	tGc	1	1	B.1	0.000009
ORF1ab/nsp2	99	S99P	Tcc	Ccc	1	1	B.1	0.000009
ORF1ab/nsp2	99	S99del	TCC	---	1	1	B.1	0.000009
ORF1ab/nsp2	99	S99del	TCC	---	1	1	B.1.1	0.000018
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.1.10	0.001115
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.1.101	0.01
ORF1ab/nsp2	99	S99R	TCC	CGG	1	1	B.1.1.137	0.0125
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.1.141	0.002012
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.1.171	0.003676
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.1.174	0.003378
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.1.192	0.002309
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.1.198	0.001468
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.1.216	0.00089
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.1.217	0.003636
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.1.220	0.001859
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.1.231	0.003096
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.1.243	0.004082
ORF1ab/nsp2	99	S99C	tCc	tGc	1	1	B.1.1.25	0.000569
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.1.251	0.007937
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.1.263	0.001558
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.1.27	0.00565
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.1.279	0.001121
ORF1ab/nsp2	99	S99Y	tCc	tAc	1	1	B.1.1.28	0.000311
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.1.29	0.010309
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.1.307	0.002532
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.1.312	0.001912
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.1.318	0.000302
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.1.318	0.000302
ORF1ab/nsp2	99	S99I	TCc	ATc	1	1	B.1.1.318	0.000302
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.1.334	0.016393
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.1.358	0.034483
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.1.368	0.003086
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.1.369	0.000446
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.1.37	0.000193
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.1.39	0.00051
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.1.409	0.002833
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.1.413	0.006897
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.1.416	0.000905
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.1.421	0.030303
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.1.464	0.001473
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.1.528	0.004808
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.1.58	0.005376
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.1.63	0.000386
ORF1ab/nsp2	99	S99C	tCc	tGc	1	1	B.1.1.7	0.000001
ORF1ab/nsp2	99	S99T	Tcc	Acc	1	1	B.1.1.7	0.000001
ORF1ab/nsp2	99	S99W	tCC	tGG	1	1	B.1.1.7	0.000001
ORF1ab/nsp2	99	S99del	TCC	---	1	1	B.1.1.70	0.000341
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.1.71	0.006061
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.1.74	0.00431
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.104	0.00369
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.111	0.001175
ORF1ab/nsp2	99	S99del	TCC	---	1	1	B.1.177	0.000013
ORF1ab/nsp2	99	S99T	Tcc	Acc	1	1	B.1.177	0.000013
ORF1ab/nsp2	99	S99del1	tcC	tc-	1	1	B.1.177.15	0.000631
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.177.35	0.000691
ORF1ab/nsp2	99	S99del	TCC	---	1	1	B.1.177.4	0.000211
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.177.42	0.000894
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.177.43	0.001477
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.177.48	0.003125
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.177.52	0.001757
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.177.52	0.001757
ORF1ab/nsp2	99	S99del	TCC	---	1	1	B.1.177.54	0.000606
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.177.57	0.000281
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.177.58	0.001332
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.177.6	0.000977
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.177.62	0.001192
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.177.69	0.001484
ORF1ab/nsp2	99	S99del	TCC	---	1	1	B.1.177.7	0.000165
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.177.79	0.002342
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.177.81	0.000189
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.177.82	0.000477
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.177.83	0.001481
ORF1ab/nsp2	99	S99del	TCC	---	1	1	B.1.177.87	0.000728
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.177.87	0.000728
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.177.87	0.000728
ORF1ab/nsp2	99	S99del	TCC	---	1	1	B.1.177.9	0.001332
ORF1ab/nsp2	99	S99del	TCC	---	1	1	B.1.2	0.000009
ORF1ab/nsp2	99	S99C	tCc	tGc	1	1	B.1.2	0.000009
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.206	0.000816
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.206	0.000816
ORF1ab/nsp2	99	S99T	Tcc	Acc	1	1	B.1.210	0.002132
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.214.2	0.0006
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.221.3	0.000833
ORF1ab/nsp2	99	S99del	TCC	---	1	1	B.1.23	0.006061
ORF1ab/nsp2	99	S99T	Tcc	Acc	1	1	B.1.234	0.000132
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.247	0.014925
ORF1ab/nsp2	99	S99del	TCC	---	1	1	B.1.258.10	0.011364
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.258.14	0.00098
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.3	0.002618
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.305	0.002151
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.306	0.005714
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.329	0.000608
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.336	0.002439
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.346	0.001311
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.351.3	0.000876
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.36.18	0.00042
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.36.26	0.002857
ORF1ab/nsp2	99	S99S	tcC	tcA	1	1	B.1.362	0.001541
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.375	0.00082
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.375	0.00082
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.380	0.006623
ORF1ab/nsp2	99	S99T	Tcc	Acc	1	1	B.1.382	0.008929
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.389	0.001002
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.396	0.000706
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.404	0.001302
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.427	0.00005
ORF1ab/nsp2	99	S99A	Tcc	Gcc	1	1	B.1.497	0.000315
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.499	0.00105
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.525	0.000113
ORF1ab/nsp2	99	S99A	Tcc	Gcc	1	1	B.1.526	0.000024
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.549	0.007194
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.560	0.00463
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.561	0.000397
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.570	0.002941
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.575	0.000303
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.576	0.000907
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.577	0.000687
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.578	0.017857
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.595	0.000261
ORF1ab/nsp2	99	S99del1	tCc	t-c	1	1	B.1.596	0.000087
ORF1ab/nsp2	99	S99del	TCC	---	1	1	B.1.596	0.000087
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.600	0.005848
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.609	0.000479
ORF1ab/nsp2	99	S99T	Tcc	Acc	1	1	B.1.617.2	0.000004
ORF1ab/nsp2	99	S99W	tCC	tGG	1	1	B.1.617.2	0.000004
ORF1ab/nsp2	99	S99A	Tcc	Gcc	1	1	B.1.617.2	0.000004
ORF1ab/nsp2	99	S99del	TCC	---	1	1	B.1.617.3	0.002985
ORF1ab/nsp2	99	S99del	TCC	---	1	1	B.1.621	0.000089
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.621.1	0.000506
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.627	0.00202
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.1.631	0.003367
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.9	0.006173
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.1.94	0.027027
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.12	0.00641
ORF1ab/nsp2	99	S99Y	tCc	tAc	1	1	B.3	0.000831
ORF1ab/nsp2	99	S99del	TCC	---	1	1	B.34	0.013699
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.4	0.002208
ORF1ab/nsp2	99	S99V	TCc	GTc	1	1	B.4	0.002208
ORF1ab/nsp2	99	S99L	tCC	tTG	1	1	B.4	0.002208
ORF1ab/nsp2	99	S99S	tcC	tcG	1	1	B.4	0.002208
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.40	0.000364
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	B.6	0.00091
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	B.6.6	0.000889
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	C.1	0.002392
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	C.1	0.002392
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	C.14	0.004329
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	C.16	0.00106
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	C.36	0.000911
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	C.36.3	0.000567
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	D.2	0.000075
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	K.3	0.006173
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	L.3	0.003546
ORF1ab/nsp2	99	S99del	TCC	---	1	1	N.4	0.004255
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	P.1.1	0.000318
ORF1ab/nsp2	99	S99del	TCC	---	1	1	P.1.1	0.000318
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	P.1.12	0.000484
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	P.1.7	0.000319
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	P.2	0.000187
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	P.7	0.004367
ORF1ab/nsp2	99	S99del	TCC	---	1	1	Q.1	0.000126
ORF1ab/nsp2	99	S99del	TCC	---	1	1	Q.2	0.000613
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	Q.3	0.000145
ORF1ab/nsp2	99	S99S	tcC	tcT	1	1	Q.8	0.000165
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	U.1	0.012821
ORF1ab/nsp2	99	S99F	tCc	tTc	1	1	W.4	0.001351
ORF1ab/nsp2	99	S99S	tcC	tcT	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.