CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1467

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	1467	S1467F	S2285F	nonsyn	tCt	tTt	4934	4932	0.999595	7118-7120
ORF1ab/nsp3	1467	S1467F	S2285F	nonsyn	tCT	tTC	4934	2	0.000405351	7118-7120
ORF1ab/nsp3	1467	S1467del	S2285del	del	TCT	---	699	699	1	7118-7120
ORF1ab/nsp3	1467	S1467S	S2285S	syn	tcT	tcC	494	452	0.91498	7118-7120
ORF1ab/nsp3	1467	S1467S	S2285S	syn	tcT	tcG	494	29	0.0587045	7118-7120
ORF1ab/nsp3	1467	S1467S	S2285S	syn	tcT	tcA	494	13	0.0263158	7118-7120
ORF1ab/nsp3	1467	S1467T	S2285T	nonsyn	Tct	Act	235	234	0.995745	7118-7120
ORF1ab/nsp3	1467	S1467T	S2285T	nonsyn	TcT	AcG	235	1	0.00425532	7118-7120
ORF1ab/nsp3	1467	S1467Y	S2285Y	nonsyn	tCt	tAt	49	46	0.938776	7118-7120
ORF1ab/nsp3	1467	S1467Y	S2285Y	nonsyn	tCT	tAC	49	3	0.0612245	7118-7120
ORF1ab/nsp3	1467	S1467P	S2285P	nonsyn	Tct	Cct	28	27	0.964286	7118-7120
ORF1ab/nsp3	1467	S1467P	S2285P	nonsyn	TcT	CcC	28	1	0.0357143	7118-7120
ORF1ab/nsp3	1467	S1467A	S2285A	nonsyn	Tct	Gct	23	19	0.826087	7118-7120
ORF1ab/nsp3	1467	S1467A	S2285A	nonsyn	TcT	GcA	23	4	0.173913	7118-7120
ORF1ab/nsp3	1467	S1467del1	S2285del1	del	tcT	tc-	18	9	0.5	7118-7120
ORF1ab/nsp3	1467	S1467del1	S2285del1	del	Tct	-ct	18	3	0.166667	7118-7120
ORF1ab/nsp3	1467	S1467del1	S2285del1	del	tCt	t-t	18	2	0.111111	7118-7120
ORF1ab/nsp3	1467	S1467del1	S2285del1	del	tCT	tS-	18	1	0.0555556	7118-7120
ORF1ab/nsp3	1467	S1467del1	S2285del1	del	tCT	tT-	18	1	0.0555556	7118-7120
ORF1ab/nsp3	1467	S1467del1	S2285del1	del	TCt	-Nt	18	1	0.0555556	7118-7120
ORF1ab/nsp3	1467	S1467del1	S2285del1	del	tCT	t-N	18	1	0.0555556	7118-7120
ORF1ab/nsp3	1467	S1467C	S2285C	nonsyn	tCt	tGt	13	12	0.923077	7118-7120
ORF1ab/nsp3	1467	S1467C	S2285C	nonsyn	tCT	tGC	13	1	0.0769231	7118-7120
ORF1ab/nsp3	1467	S1467del2	S2285del2	del	tCT	t--	8	3	0.375	7118-7120
ORF1ab/nsp3	1467	S1467del2	S2285del2	del	TCT	C--	8	3	0.375	7118-7120
ORF1ab/nsp3	1467	S1467del2	S2285del2	del	TCt	--t	8	2	0.25	7118-7120
ORF1ab/nsp3	1467	S1467H	S2285H	nonsyn	TCT	CAC	5	3	0.6	7118-7120
ORF1ab/nsp3	1467	S1467H	S2285H	nonsyn	TCt	CAt	5	2	0.4	7118-7120
ORF1ab/nsp3	1467	S1467L	S2285L	nonsyn	TCt	CTt	2	1	0.5	7118-7120
ORF1ab/nsp3	1467	S1467L	S2285L	nonsyn	TCT	CTC	2	1	0.5	7118-7120
ORF1ab/nsp3	1467	S1467D	S2285D	nonsyn	TCT	GAC	1	1	1	7118-7120
ORF1ab/nsp3	1467	S1467V	S2285V	nonsyn	TCT	GTG	1	1	1	7118-7120
ORF1ab/nsp3	1467	S1467R	S2285R	nonsyn	TCT	AGA	1	1	1	7118-7120
ORF1ab/nsp3	1467	S1467G	S2285G	nonsyn	TCT	GGA	1	1	1	7118-7120
ORF1ab/nsp3	1467	S1467W	S2285W	nonsyn	tCT	tGG	1	1	1	7118-7120

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	1467	S1467F	tCt	tTt	4932	4934	All	0.000943
ORF1ab/nsp3	1467	S1467F	tCT	tTC	2	4934	All	0
ORF1ab/nsp3	1467	S1467F	tCt	tTt	921	921	B.1.1.7	0.000825
ORF1ab/nsp3	1467	S1467F	tCt	tTt	913	913	AY.4	0.001421
ORF1ab/nsp3	1467	S1467del	TCT	---	699	699	All	0.000134
ORF1ab/nsp3	1467	S1467F	tCt	tTt	605	605	AY.46.6	0.043685
ORF1ab/nsp3	1467	S1467S	tcT	tcC	452	494	All	0.000086
ORF1ab/nsp3	1467	S1467S	tcT	tcG	29	494	All	0.000006
ORF1ab/nsp3	1467	S1467S	tcT	tcA	13	494	All	0.000002
ORF1ab/nsp3	1467	S1467T	Tct	Act	234	235	All	0.000045
ORF1ab/nsp3	1467	S1467T	TcT	AcG	1	235	All	0
ORF1ab/nsp3	1467	S1467F	tCt	tTt	220	221	B.1.617.2	0.000828
ORF1ab/nsp3	1467	S1467F	tCT	tTC	1	221	B.1.617.2	0.000004
ORF1ab/nsp3	1467	S1467F	tCt	tTt	177	177	AY.3	0.001761
ORF1ab/nsp3	1467	S1467F	tCt	tTt	158	158	AY.29	0.002492
ORF1ab/nsp3	1467	S1467S	tcT	tcC	145	145	B.1.1.317	0.059695
ORF1ab/nsp3	1467	S1467del	TCT	---	137	137	AY.4	0.000213
ORF1ab/nsp3	1467	S1467del	TCT	---	112	112	AY.44	0.000682
ORF1ab/nsp3	1467	S1467S	tcT	tcC	105	105	Q.1	0.013264
ORF1ab/nsp3	1467	S1467F	tCt	tTt	104	104	B.1.2	0.000916
ORF1ab/nsp3	1467	S1467F	tCt	tTt	95	95	AY.43	0.000421
ORF1ab/nsp3	1467	S1467F	tCt	tTt	93	93	AY.103	0.000577
ORF1ab/nsp3	1467	S1467F	tCt	tTt	86	86	AY.25	0.000517
ORF1ab/nsp3	1467	S1467F	tCt	tTt	83	83	AY.44	0.000505
ORF1ab/nsp3	1467	S1467F	tCt	tTt	82	82	B.1	0.000751
ORF1ab/nsp3	1467	S1467F	tCt	tTt	80	80	B.1.177.21	0.006118
ORF1ab/nsp3	1467	S1467F	tCt	tTt	79	79	B.1.429	0.001859
ORF1ab/nsp3	1467	S1467S	tcT	tcC	78	78	P.1.14	0.003728
ORF1ab/nsp3	1467	S1467del	TCT	---	76	76	B.1.1.7	0.000068
ORF1ab/nsp3	1467	S1467F	tCt	tTt	60	60	B.1.351	0.001784
ORF1ab/nsp3	1467	S1467T	Tct	Act	56	56	AY.99.2	0.005161
ORF1ab/nsp3	1467	S1467del	TCT	---	52	52	AY.25	0.000313
ORF1ab/nsp3	1467	S1467Y	tCt	tAt	46	49	All	0.000009
ORF1ab/nsp3	1467	S1467Y	tCT	tAC	3	49	All	0.000001
ORF1ab/nsp3	1467	S1467del	TCT	---	49	49	B.1.617.2	0.000185
ORF1ab/nsp3	1467	S1467F	tCt	tTt	48	48	AY.4.2	0.001041
ORF1ab/nsp3	1467	S1467S	tcT	tcC	43	44	B.1.2	0.000379
ORF1ab/nsp3	1467	S1467S	tcT	tcA	1	44	B.1.2	0.000009
ORF1ab/nsp3	1467	S1467T	Tct	Act	43	43	B.1.619.1	0.027582
ORF1ab/nsp3	1467	S1467F	tCt	tTt	42	42	B.1.497	0.01322
ORF1ab/nsp3	1467	S1467F	tCt	tTt	41	41	AY.3.1	0.003496
ORF1ab/nsp3	1467	S1467F	tCt	tTt	37	37	B.1.526	0.00087
ORF1ab/nsp3	1467	S1467F	tCt	tTt	34	34	B.1.517	0.014518
ORF1ab/nsp3	1467	S1467F	tCt	tTt	34	34	P.1	0.000536
ORF1ab/nsp3	1467	S1467F	tCt	tTt	33	33	B.1.243	0.002296
ORF1ab/nsp3	1467	S1467F	tCt	tTt	31	31	B.1.177	0.000408
ORF1ab/nsp3	1467	S1467F	tCt	tTt	29	29	AY.102	0.000769
ORF1ab/nsp3	1467	S1467P	Tct	Cct	27	28	All	0.000005
ORF1ab/nsp3	1467	S1467P	TcT	CcC	1	28	All	0
ORF1ab/nsp3	1467	S1467F	tCt	tTt	28	28	AY.41	0.00823
ORF1ab/nsp3	1467	S1467F	tCt	tTt	28	28	B.1.1.284	0.003007
ORF1ab/nsp3	1467	S1467F	tCt	tTt	25	25	AY.5	0.000516
ORF1ab/nsp3	1467	S1467F	tCt	tTt	24	24	AY.39	0.000593
ORF1ab/nsp3	1467	S1467A	Tct	Gct	19	23	All	0.000004
ORF1ab/nsp3	1467	S1467A	TcT	GcA	4	23	All	0.000001
ORF1ab/nsp3	1467	S1467T	Tct	Act	23	23	AY.69	0.004293
ORF1ab/nsp3	1467	S1467F	tCt	tTt	22	23	B.1.1	0.000399
ORF1ab/nsp3	1467	S1467F	tCT	tTC	1	23	B.1.1	0.000018
ORF1ab/nsp3	1467	S1467del	TCT	---	20	20	AY.43	0.000089
ORF1ab/nsp3	1467	S1467S	tcT	tcC	14	20	B.1.1.7	0.000013
ORF1ab/nsp3	1467	S1467S	tcT	tcG	6	20	B.1.1.7	0.000005
ORF1ab/nsp3	1467	S1467del	TCT	---	20	20	B.1.177	0.000263
ORF1ab/nsp3	1467	S1467del1	tcT	tc-	9	18	All	0.000002
ORF1ab/nsp3	1467	S1467del1	Tct	-ct	3	18	All	0.000001
ORF1ab/nsp3	1467	S1467del1	tCt	t-t	2	18	All	0
ORF1ab/nsp3	1467	S1467del1	tCT	tS-	1	18	All	0
ORF1ab/nsp3	1467	S1467del1	tCT	tT-	1	18	All	0
ORF1ab/nsp3	1467	S1467del1	TCt	-Nt	1	18	All	0
ORF1ab/nsp3	1467	S1467del1	tCT	t-N	1	18	All	0
ORF1ab/nsp3	1467	S1467F	tCt	tTt	18	18	AY.100	0.000828
ORF1ab/nsp3	1467	S1467F	tCt	tTt	18	18	AY.47	0.00056
ORF1ab/nsp3	1467	S1467F	tCt	tTt	18	18	B.1.1.1	0.00588
ORF1ab/nsp3	1467	S1467F	tCt	tTt	18	18	B.1.1.519	0.000715
ORF1ab/nsp3	1467	S1467F	tCt	tTt	18	18	C.37	0.002089
ORF1ab/nsp3	1467	S1467T	Tct	Act	17	17	B.1.1.7	0.000015
ORF1ab/nsp3	1467	S1467F	tCt	tTt	16	16	B.1.637	0.001169
ORF1ab/nsp3	1467	S1467F	tCt	tTt	15	15	B.1.1.401	1
ORF1ab/nsp3	1467	S1467F	tCt	tTt	15	15	B.1.427	0.000757
ORF1ab/nsp3	1467	S1467C	tCt	tGt	12	13	All	0.000002
ORF1ab/nsp3	1467	S1467C	tCT	tGC	1	13	All	0
ORF1ab/nsp3	1467	S1467T	Tct	Act	13	13	B.1.160	0.000405
ORF1ab/nsp3	1467	S1467del	TCT	---	12	12	AY.3	0.000119
ORF1ab/nsp3	1467	S1467F	tCt	tTt	12	12	AY.6	0.000494
ORF1ab/nsp3	1467	S1467del	TCT	---	11	11	AY.103	0.000068
ORF1ab/nsp3	1467	S1467F	tCt	tTt	11	11	AY.20	0.000428
ORF1ab/nsp3	1467	S1467F	tCt	tTt	11	11	AY.23	0.000767
ORF1ab/nsp3	1467	S1467del	TCT	---	11	11	AY.4.2	0.000239
ORF1ab/nsp3	1467	S1467F	tCt	tTt	11	11	AY.9.2	0.000404
ORF1ab/nsp3	1467	S1467F	tCt	tTt	11	11	B.1.221	0.000781
ORF1ab/nsp3	1467	S1467F	tCt	tTt	11	11	B.1.579	0.123596
ORF1ab/nsp3	1467	S1467F	tCt	tTt	11	11	B.1.596	0.000959
ORF1ab/nsp3	1467	S1467Y	tCt	tAt	10	10	AY.4	0.000016
ORF1ab/nsp3	1467	S1467F	tCt	tTt	10	10	B.1.234	0.001319
ORF1ab/nsp3	1467	S1467S	tcT	tcG	9	10	P.1	0.000142
ORF1ab/nsp3	1467	S1467S	tcT	tcC	1	10	P.1	0.000016
ORF1ab/nsp3	1467	S1467S	tcT	tcG	5	9	AY.103	0.000031
ORF1ab/nsp3	1467	S1467S	tcT	tcC	3	9	AY.103	0.000019
ORF1ab/nsp3	1467	S1467S	tcT	tcA	1	9	AY.103	0.000006
ORF1ab/nsp3	1467	S1467F	tCt	tTt	9	9	AY.34	0.000873
ORF1ab/nsp3	1467	S1467F	tCt	tTt	9	9	AY.42	0.000362
ORF1ab/nsp3	1467	S1467F	tCt	tTt	9	9	AY.98.1	0.000436
ORF1ab/nsp3	1467	S1467T	Tct	Act	9	9	B.1	0.000082
ORF1ab/nsp3	1467	S1467T	Tct	Act	9	9	B.1.177	0.000119
ORF1ab/nsp3	1467	S1467F	tCt	tTt	9	9	B.1.22	0.011858
ORF1ab/nsp3	1467	S1467F	tCt	tTt	9	9	D.2	0.000675
ORF1ab/nsp3	1467	S1467del2	TCT	C--	3	8	All	0.000001
ORF1ab/nsp3	1467	S1467del2	tCT	t--	3	8	All	0.000001
ORF1ab/nsp3	1467	S1467del2	TCt	--t	2	8	All	0
ORF1ab/nsp3	1467	S1467del	TCT	---	8	8	AY.102	0.000212
ORF1ab/nsp3	1467	S1467F	tCt	tTt	8	8	AY.117	0.000676
ORF1ab/nsp3	1467	S1467F	tCt	tTt	8	8	AY.119	0.000282
ORF1ab/nsp3	1467	S1467S	tcT	tcC	7	8	AY.44	0.000043
ORF1ab/nsp3	1467	S1467S	tcT	tcA	1	8	AY.44	0.000006
ORF1ab/nsp3	1467	S1467F	tCt	tTt	8	8	B.1.1.301	0.009434
ORF1ab/nsp3	1467	S1467F	tCt	tTt	8	8	B.1.367	0.006339
ORF1ab/nsp3	1467	S1467S	tcT	tcC	8	8	B.1.429	0.000188
ORF1ab/nsp3	1467	S1467del	TCT	---	7	7	AY.4.5	0.000752
ORF1ab/nsp3	1467	S1467del	TCT	---	7	7	AY.5	0.000145
ORF1ab/nsp3	1467	S1467F	tCt	tTt	7	7	AY.74	0.00081
ORF1ab/nsp3	1467	S1467del	TCT	---	7	7	AY.98	0.000553
ORF1ab/nsp3	1467	S1467del	TCT	---	7	7	B.1	0.000064
ORF1ab/nsp3	1467	S1467Y	tCt	tAt	7	7	B.1.1.7	0.000006
ORF1ab/nsp3	1467	S1467C	tCt	tGt	7	7	B.1.1.7	0.000006
ORF1ab/nsp3	1467	S1467F	tCt	tTt	7	7	B.1.525	0.000792
ORF1ab/nsp3	1467	S1467F	tCt	tTt	6	6	AY.113	0.000854
ORF1ab/nsp3	1467	S1467S	tcT	tcC	5	6	AY.3	0.00005
ORF1ab/nsp3	1467	S1467S	tcT	tcA	1	6	AY.3	0.00001
ORF1ab/nsp3	1467	S1467F	tCt	tTt	6	6	AY.32	0.003195
ORF1ab/nsp3	1467	S1467S	tcT	tcC	6	6	AY.4	0.000009
ORF1ab/nsp3	1467	S1467F	tCt	tTt	6	6	AY.46.4	0.000987
ORF1ab/nsp3	1467	S1467F	tCt	tTt	6	6	AY.54	0.000572
ORF1ab/nsp3	1467	S1467F	tCt	tTt	6	6	AY.9	0.000406
ORF1ab/nsp3	1467	S1467F	tCt	tTt	6	6	AY.90	0.004107
ORF1ab/nsp3	1467	S1467del	TCT	---	6	6	AY.98.1	0.000291
ORF1ab/nsp3	1467	S1467F	tCt	tTt	6	6	B.1.1.306	0.00263
ORF1ab/nsp3	1467	S1467F	tCt	tTt	6	6	B.1.1.311	0.002149
ORF1ab/nsp3	1467	S1467P	Tct	Cct	6	6	B.1.1.7	0.000005
ORF1ab/nsp3	1467	S1467F	tCt	tTt	6	6	B.1.177.45	0.002287
ORF1ab/nsp3	1467	S1467F	tCt	tTt	6	6	B.1.177.9	0.007989
ORF1ab/nsp3	1467	S1467del	TCT	---	6	6	B.1.2	0.000053
ORF1ab/nsp3	1467	S1467T	Tct	Act	6	6	B.1.221	0.000426
ORF1ab/nsp3	1467	S1467F	tCt	tTt	6	6	B.1.351.5	0.003597
ORF1ab/nsp3	1467	S1467del	TCT	---	6	6	B.1.526	0.000141
ORF1ab/nsp3	1467	S1467S	tcT	tcC	5	6	B.1.617.2	0.000019
ORF1ab/nsp3	1467	S1467S	tcT	tcG	1	6	B.1.617.2	0.000004
ORF1ab/nsp3	1467	S1467F	tCt	tTt	6	6	R.1	0.00054
ORF1ab/nsp3	1467	S1467H	TCT	CAC	3	5	All	0.000001
ORF1ab/nsp3	1467	S1467H	TCt	CAt	2	5	All	0
ORF1ab/nsp3	1467	S1467F	tCt	tTt	5	5	AY.19	0.005701
ORF1ab/nsp3	1467	S1467P	Tct	Cct	5	5	AY.47	0.000156
ORF1ab/nsp3	1467	S1467F	tCt	tTt	5	5	AY.7.2	0.002796
ORF1ab/nsp3	1467	S1467del	TCT	---	5	5	B.1.1	0.000091
ORF1ab/nsp3	1467	S1467F	tCt	tTt	5	5	B.1.1.207	0.00591
ORF1ab/nsp3	1467	S1467T	Tct	Act	5	5	B.1.1.39	0.002548
ORF1ab/nsp3	1467	S1467Y	tCt	tAt	5	5	B.1.1.416	0.004525
ORF1ab/nsp3	1467	S1467F	tCt	tTt	5	5	B.1.1.46	0.021834
ORF1ab/nsp3	1467	S1467F	tCt	tTt	5	5	B.1.258	0.000333
ORF1ab/nsp3	1467	S1467F	tCt	tTt	5	5	B.1.336	0.012195
ORF1ab/nsp3	1467	S1467T	Tct	Act	5	5	B.1.617.2	0.000019
ORF1ab/nsp3	1467	S1467T	Tct	Act	5	5	B.1.620	0.00473
ORF1ab/nsp3	1467	S1467F	tCt	tTt	5	5	B.4	0.011038
ORF1ab/nsp3	1467	S1467F	tCt	tTt	5	5	P.1.14	0.000239
ORF1ab/nsp3	1467	S1467del	TCT	---	4	4		0.222222
ORF1ab/nsp3	1467	S1467F	tCt	tTt	4	4	AD.2	0.000876
ORF1ab/nsp3	1467	S1467del	TCT	---	4	4	AP.1	0.006006
ORF1ab/nsp3	1467	S1467del	TCT	---	4	4	AY.100	0.000184
ORF1ab/nsp3	1467	S1467F	tCt	tTt	4	4	AY.12	0.001264
ORF1ab/nsp3	1467	S1467F	tCt	tTt	4	4	AY.120	0.000149
ORF1ab/nsp3	1467	S1467del	TCT	---	4	4	AY.39	0.000099
ORF1ab/nsp3	1467	S1467T	Tct	Act	4	4	AY.53	0.00115
ORF1ab/nsp3	1467	S1467F	tCt	tTt	4	4	AY.61	0.000419
ORF1ab/nsp3	1467	S1467del	TCT	---	4	4	AY.88	0.003537
ORF1ab/nsp3	1467	S1467F	tCt	tTt	4	4	AY.9.1	0.000335
ORF1ab/nsp3	1467	S1467F	tCt	tTt	4	4	AY.98	0.000316
ORF1ab/nsp3	1467	S1467F	tCt	tTt	4	4	AY.99.2	0.000369
ORF1ab/nsp3	1467	S1467del	TCT	---	4	4	AY.99.2	0.000369
ORF1ab/nsp3	1467	S1467P	Tct	Cct	3	4	B.1	0.000027
ORF1ab/nsp3	1467	S1467P	TcT	CcC	1	4	B.1	0.000009
ORF1ab/nsp3	1467	S1467del	TCT	---	4	4	B.1.1.214	0.000222
ORF1ab/nsp3	1467	S1467del	TCT	---	4	4	B.1.1.218	0.030769
ORF1ab/nsp3	1467	S1467F	tCt	tTt	4	4	B.1.1.33	0.001684
ORF1ab/nsp3	1467	S1467A	Tct	Gct	4	4	B.1.1.7	0.000004
ORF1ab/nsp3	1467	S1467del2	TCT	C--	2	4	B.1.1.7	0.000002
ORF1ab/nsp3	1467	S1467del1	tcT	tc-	2	4	B.1.1.7	0.000002
ORF1ab/nsp3	1467	S1467del2	TCt	--t	1	4	B.1.1.7	0.000001
ORF1ab/nsp3	1467	S1467del1	Tct	-ct	1	4	B.1.1.7	0.000001
ORF1ab/nsp3	1467	S1467del1	tCT	tS-	1	4	B.1.1.7	0.000001
ORF1ab/nsp3	1467	S1467del2	tCT	t--	1	4	B.1.1.7	0.000001
ORF1ab/nsp3	1467	S1467Y	tCt	tAt	4	4	B.1.177	0.000053
ORF1ab/nsp3	1467	S1467F	tCt	tTt	4	4	B.1.177.57	0.001124
ORF1ab/nsp3	1467	S1467F	tCt	tTt	4	4	B.1.265	0.005083
ORF1ab/nsp3	1467	S1467F	tCt	tTt	4	4	B.1.36	0.000584
ORF1ab/nsp3	1467	S1467F	tCt	tTt	4	4	B.1.561	0.001588
ORF1ab/nsp3	1467	S1467Y	tCt	tAt	3	4	B.1.617.2	0.000011
ORF1ab/nsp3	1467	S1467Y	tCT	tAC	1	4	B.1.617.2	0.000004
ORF1ab/nsp3	1467	S1467F	tCt	tTt	4	4	B.6	0.00364
ORF1ab/nsp3	1467	S1467F	tCt	tTt	4	4	C.36.3	0.002269
ORF1ab/nsp3	1467	S1467F	tCt	tTt	4	4	P.1.7	0.001277
ORF1ab/nsp3	1467	S1467F	tCt	tTt	4	4	Q.8	0.00066
ORF1ab/nsp3	1467	S1467F	tCt	tTt	3	3	AY.104	0.005952
ORF1ab/nsp3	1467	S1467F	tCt	tTt	3	3	AY.109	0.002219
ORF1ab/nsp3	1467	S1467F	tCt	tTt	3	3	AY.110	0.000338
ORF1ab/nsp3	1467	S1467del	TCT	---	3	3	AY.114	0.000693
ORF1ab/nsp3	1467	S1467F	tCt	tTt	3	3	AY.118	0.000188
ORF1ab/nsp3	1467	S1467del	TCT	---	3	3	AY.118	0.000188
ORF1ab/nsp3	1467	S1467del	TCT	---	3	3	AY.119	0.000106
ORF1ab/nsp3	1467	S1467del	TCT	---	3	3	AY.120	0.000112
ORF1ab/nsp3	1467	S1467del	TCT	---	3	3	AY.20	0.000117
ORF1ab/nsp3	1467	S1467S	tcT	tcC	3	3	AY.26	0.000085
ORF1ab/nsp3	1467	S1467F	tCt	tTt	3	3	AY.27	0.000194
ORF1ab/nsp3	1467	S1467F	tCt	tTt	3	3	AY.36	0.000445
ORF1ab/nsp3	1467	S1467F	tCt	tTt	3	3	AY.4.2.1	0.000447
ORF1ab/nsp3	1467	S1467A	Tct	Gct	3	3	AY.44	0.000018
ORF1ab/nsp3	1467	S1467F	tCt	tTt	3	3	AY.46	0.000312
ORF1ab/nsp3	1467	S1467F	tCt	tTt	3	3	AY.63	0.001161
ORF1ab/nsp3	1467	S1467F	tCt	tTt	3	3	AY.85	0.001282
ORF1ab/nsp3	1467	S1467Y	tCt	tAt	2	3	AY.9.2	0.000073
ORF1ab/nsp3	1467	S1467Y	tCT	tAC	1	3	AY.9.2	0.000037
ORF1ab/nsp3	1467	S1467T	Tct	Act	3	3	B	0.000383
ORF1ab/nsp3	1467	S1467del1	tcT	tc-	2	3	B.1	0.000018
ORF1ab/nsp3	1467	S1467S	tcT	tcC	2	3	B.1	0.000018
ORF1ab/nsp3	1467	S1467S	tcT	tcA	1	3	B.1	0.000009
ORF1ab/nsp3	1467	S1467del1	tCt	t-t	1	3	B.1	0.000009
ORF1ab/nsp3	1467	S1467F	tCt	tTt	3	3	B.1.1.222	0.000612
ORF1ab/nsp3	1467	S1467F	tCt	tTt	3	3	B.1.1.50	0.002037
ORF1ab/nsp3	1467	S1467F	tCt	tTt	3	3	B.1.111	0.003525
ORF1ab/nsp3	1467	S1467F	tCt	tTt	3	3	B.1.160	0.000094
ORF1ab/nsp3	1467	S1467T	Tct	Act	3	3	B.1.160.16	0.002788
ORF1ab/nsp3	1467	S1467F	tCt	tTt	3	3	B.1.177.81	0.000568
ORF1ab/nsp3	1467	S1467del1	tcT	tc-	2	3	B.1.2	0.000018
ORF1ab/nsp3	1467	S1467del1	tCt	t-t	1	3	B.1.2	0.000009
ORF1ab/nsp3	1467	S1467S	tcT	tcA	2	3	B.1.351	0.000059
ORF1ab/nsp3	1467	S1467S	tcT	tcC	1	3	B.1.351	0.00003
ORF1ab/nsp3	1467	S1467F	tCt	tTt	3	3	B.1.36.16	0.004274
ORF1ab/nsp3	1467	S1467H	TCT	CAC	2	3	B.1.617.2	0.000008
ORF1ab/nsp3	1467	S1467H	TCt	CAt	1	3	B.1.617.2	0.000004
ORF1ab/nsp3	1467	S1467F	tCt	tTt	3	3	B.1.621	0.000266
ORF1ab/nsp3	1467	S1467del	TCT	---	3	3	B.1.621	0.000266
ORF1ab/nsp3	1467	S1467S	tcT	tcC	3	3	B.1.627	0.006061
ORF1ab/nsp3	1467	S1467S	tcT	tcG	2	3	P.2	0.000373
ORF1ab/nsp3	1467	S1467S	tcT	tcC	1	3	P.2	0.000187
ORF1ab/nsp3	1467	S1467F	tCt	tTt	3	3	Q.4	0.001364
ORF1ab/nsp3	1467	S1467del	TCT	---	2	2	AD.2	0.000438
ORF1ab/nsp3	1467	S1467L	TCt	CTt	1	2	All	0
ORF1ab/nsp3	1467	S1467L	TCT	CTC	1	2	All	0
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	AY.1	0.000791
ORF1ab/nsp3	1467	S1467A	Tct	Gct	1	2	AY.103	0.000006
ORF1ab/nsp3	1467	S1467A	TcT	GcA	1	2	AY.103	0.000006
ORF1ab/nsp3	1467	S1467del	TCT	---	2	2	AY.111	0.000366
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	AY.116.1	0.000623
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	AY.121	0.000271
ORF1ab/nsp3	1467	S1467Y	tCt	tAt	2	2	AY.14	0.000176
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	AY.16	0.000759
ORF1ab/nsp3	1467	S1467del	TCT	---	2	2	AY.2	0.000712
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	AY.22	0.004184
ORF1ab/nsp3	1467	S1467T	Tct	Act	2	2	AY.23	0.000139
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	AY.24	0.000862
ORF1ab/nsp3	1467	S1467A	TcT	GcA	1	2	AY.25	0.000006
ORF1ab/nsp3	1467	S1467A	Tct	Gct	1	2	AY.25	0.000006
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	AY.26	0.000057
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	AY.33	0.000134
ORF1ab/nsp3	1467	S1467S	tcT	tcC	1	2	AY.33	0.000067
ORF1ab/nsp3	1467	S1467S	tcT	tcA	1	2	AY.33	0.000067
ORF1ab/nsp3	1467	S1467del	TCT	---	2	2	AY.34.1	0.00102
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	AY.39.1	0.000079
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	AY.39.2	0.003082
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	AY.4.4	0.000818
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	AY.4.5	0.000215
ORF1ab/nsp3	1467	S1467T	Tct	Act	2	2	AY.43	0.000009
ORF1ab/nsp3	1467	S1467S	tcT	tcC	2	2	AY.45	0.000243
ORF1ab/nsp3	1467	S1467del	TCT	---	2	2	AY.45	0.000243
ORF1ab/nsp3	1467	S1467del	TCT	---	2	2	AY.5.4	0.000553
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	AY.56	0.00321
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	AY.59	0.001059
ORF1ab/nsp3	1467	S1467del	TCT	---	2	2	AY.6	0.000082
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	AY.7	0.000392
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	AY.73	0.001331
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	AY.75.1	0.000361
ORF1ab/nsp3	1467	S1467H	TCT	CAC	1	2	AY.9.2	0.000037
ORF1ab/nsp3	1467	S1467H	TCt	CAt	1	2	AY.9.2	0.000037
ORF1ab/nsp3	1467	S1467del1	tCT	tT-	1	2	AY.9.2	0.000037
ORF1ab/nsp3	1467	S1467del1	tcT	tc-	1	2	AY.9.2	0.000037
ORF1ab/nsp3	1467	S1467del	TCT	---	2	2	AY.92	0.000575
ORF1ab/nsp3	1467	S1467del	TCT	---	2	2	AY.99.1	0.003106
ORF1ab/nsp3	1467	S1467del	TCT	---	2	2	AZ.1	0.001735
ORF1ab/nsp3	1467	S1467Y	tCt	tAt	2	2	B.1	0.000018
ORF1ab/nsp3	1467	S1467T	Tct	Act	2	2	B.1.1	0.000036
ORF1ab/nsp3	1467	S1467S	tcT	tcA	1	2	B.1.1	0.000018
ORF1ab/nsp3	1467	S1467S	tcT	tcC	1	2	B.1.1	0.000018
ORF1ab/nsp3	1467	S1467del1	tcT	tc-	1	2	B.1.1	0.000018
ORF1ab/nsp3	1467	S1467del1	Tct	-ct	1	2	B.1.1	0.000018
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	B.1.1.164	0.010309
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	B.1.1.272	0.010417
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	B.1.1.305	0.007722
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	B.1.1.318	0.000604
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	B.1.1.369	0.000892
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	B.1.1.398	0.006452
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	B.1.1.523	0.003125
ORF1ab/nsp3	1467	S1467T	Tct	Act	2	2	B.1.1.70	0.000682
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	B.1.1.71	0.012121
ORF1ab/nsp3	1467	S1467T	Tct	Act	2	2	B.1.160.9	0.014388
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	B.1.177.4	0.000422
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	B.1.177.41	0.005
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	B.1.177.42	0.001789
ORF1ab/nsp3	1467	S1467T	Tct	Act	2	2	B.1.177.44	0.001038
ORF1ab/nsp3	1467	S1467del	TCT	---	2	2	B.1.177.62	0.002384
ORF1ab/nsp3	1467	S1467T	Tct	Act	2	2	B.1.177.81	0.000379
ORF1ab/nsp3	1467	S1467C	tCt	tGt	2	2	B.1.2	0.000018
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	B.1.240	0.000431
ORF1ab/nsp3	1467	S1467T	Tct	Act	2	2	B.1.258	0.000133
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	B.1.258.22	0.005333
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	B.1.36.17	0.000988
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	B.1.36.18	0.00084
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	B.1.36.36	0.001204
ORF1ab/nsp3	1467	S1467S	tcT	tcC	2	2	B.1.36.8	0.002
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	B.1.369	0.00057
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	B.1.400	0.000858
ORF1ab/nsp3	1467	S1467Y	tCt	tAt	2	2	B.1.466.2	0.000782
ORF1ab/nsp3	1467	S1467S	tcT	tcC	2	2	B.1.551	0.002581
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	B.1.577	0.001375
ORF1ab/nsp3	1467	S1467S	tcT	tcC	2	2	B.1.596	0.000174
ORF1ab/nsp3	1467	S1467del	TCT	---	2	2	B.1.596	0.000174
ORF1ab/nsp3	1467	S1467A	Tct	Gct	2	2	B.1.617.2	0.000008
ORF1ab/nsp3	1467	S1467L	TCT	CTC	1	2	B.1.617.2	0.000004
ORF1ab/nsp3	1467	S1467L	TCt	CTt	1	2	B.1.617.2	0.000004
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	B.1.628	0.000705
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	B.3	0.001661
ORF1ab/nsp3	1467	S1467del	TCT	---	2	2	C.35	0.001548
ORF1ab/nsp3	1467	S1467C	tCt	tGt	2	2	D.2	0.00015
ORF1ab/nsp3	1467	S1467del	TCT	---	2	2	P.1	0.000032
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	P.1.16	0.000748
ORF1ab/nsp3	1467	S1467S	tcT	tcG	2	2	P.1.17	0.000324
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	P.1.17	0.000324
ORF1ab/nsp3	1467	S1467F	tCt	tTt	2	2	Q.3	0.00029
ORF1ab/nsp3	1467	S1467del	TCT	---	2	2	U.3	0.007722
ORF1ab/nsp3	1467	S1467Y	tCt	tAt	1	1		0.055556
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1		0.055556
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	A.2.5	0.000499
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	A.5	0.001923
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AE.3	0.032258
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AE.8	0.000489
ORF1ab/nsp3	1467	S1467G	TCT	GGA	1	1	All	0
ORF1ab/nsp3	1467	S1467V	TCT	GTG	1	1	All	0
ORF1ab/nsp3	1467	S1467W	tCT	tGG	1	1	All	0
ORF1ab/nsp3	1467	S1467D	TCT	GAC	1	1	All	0
ORF1ab/nsp3	1467	S1467R	TCT	AGA	1	1	All	0
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AP.1	0.001502
ORF1ab/nsp3	1467	S1467S	tcT	tcC	1	1	AW.1	0.003049
ORF1ab/nsp3	1467	S1467S	tcT	tcC	1	1	AY.100	0.000046
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.101	0.00049
ORF1ab/nsp3	1467	S1467P	Tct	Cct	1	1	AY.103	0.000006
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.107	0.000466
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.11	0.001339
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.113	0.000142
ORF1ab/nsp3	1467	S1467Y	tCt	tAt	1	1	AY.113	0.000142
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.116.1	0.000311
ORF1ab/nsp3	1467	S1467Y	tCt	tAt	1	1	AY.118	0.000063
ORF1ab/nsp3	1467	S1467A	TcT	GcA	1	1	AY.119	0.000035
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.120.1	0.000321
ORF1ab/nsp3	1467	S1467P	Tct	Cct	1	1	AY.121	0.000135
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.13	0.000161
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.14	0.000088
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.16.1	0.00047
ORF1ab/nsp3	1467	S1467R	TCT	AGA	1	1	AY.23	0.00007
ORF1ab/nsp3	1467	S1467S	tcT	tcA	1	1	AY.25	0.000006
ORF1ab/nsp3	1467	S1467del1	Tct	-ct	1	1	AY.25	0.000006
ORF1ab/nsp3	1467	S1467A	Tct	Gct	1	1	AY.26	0.000028
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.29	0.000016
ORF1ab/nsp3	1467	S1467A	Tct	Gct	1	1	AY.3	0.00001
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.3.1	0.000085
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.30	0.000396
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.33	0.000067
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.34	0.000097
ORF1ab/nsp3	1467	S1467A	Tct	Gct	1	1	AY.34	0.000097
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.34.1	0.00051
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.35	0.000233
ORF1ab/nsp3	1467	S1467P	Tct	Cct	1	1	AY.39	0.000025
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.39.1	0.00004
ORF1ab/nsp3	1467	S1467del1	tCT	t-N	1	1	AY.4	0.000002
ORF1ab/nsp3	1467	S1467del2	tCT	t--	1	1	AY.4	0.000002
ORF1ab/nsp3	1467	S1467P	Tct	Cct	1	1	AY.4	0.000002
ORF1ab/nsp3	1467	S1467P	Tct	Cct	1	1	AY.4.2	0.000022
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.4.3	0.000842
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.42	0.00004
ORF1ab/nsp3	1467	S1467Y	tCT	tAC	1	1	AY.43	0.000004
ORF1ab/nsp3	1467	S1467P	Tct	Cct	1	1	AY.44	0.000006
ORF1ab/nsp3	1467	S1467T	Tct	Act	1	1	AY.44	0.000006
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.45	0.000122
ORF1ab/nsp3	1467	S1467T	Tct	Act	1	1	AY.46	0.000104
ORF1ab/nsp3	1467	S1467A	Tct	Gct	1	1	AY.46	0.000104
ORF1ab/nsp3	1467	S1467S	tcT	tcC	1	1	AY.46	0.000104
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.46.1	0.001027
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.46.4	0.000165
ORF1ab/nsp3	1467	S1467S	tcT	tcG	1	1	AY.46.5	0.000198
ORF1ab/nsp3	1467	S1467Y	tCt	tAt	1	1	AY.5.3	0.000337
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.5.4	0.000277
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.55	0.000917
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.57	0.000656
ORF1ab/nsp3	1467	S1467Y	tCt	tAt	1	1	AY.59	0.00053
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.59	0.00053
ORF1ab/nsp3	1467	S1467P	Tct	Cct	1	1	AY.6	0.000041
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.60	0.000938
ORF1ab/nsp3	1467	S1467A	Tct	Gct	1	1	AY.61	0.000105
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.66	0.00107
ORF1ab/nsp3	1467	S1467S	tcT	tcC	1	1	AY.67	0.000464
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.67	0.000464
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.7	0.000196
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.7.1	0.000113
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.7.1	0.000113
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.73	0.000665
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.75	0.000056
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.78	0.001541
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.83	0.001724
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.84	0.000437
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.84	0.000437
ORF1ab/nsp3	1467	S1467G	TCT	GGA	1	1	AY.85	0.000427
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.88	0.000884
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.9	0.000068
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.9.2	0.000037
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.92	0.000287
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.96	0.002075
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	AY.99	0.001049
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	AY.99	0.001049
ORF1ab/nsp3	1467	S1467del2	tCT	t--	1	1	AZ.2	0.000821
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B	0.000128
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B	0.000128
ORF1ab/nsp3	1467	S1467Y	tCt	tAt	1	1	B.1.1	0.000018
ORF1ab/nsp3	1467	S1467C	tCT	tGC	1	1	B.1.1	0.000018
ORF1ab/nsp3	1467	S1467P	Tct	Cct	1	1	B.1.1	0.000018
ORF1ab/nsp3	1467	S1467S	tcT	tcC	1	1	B.1.1.10	0.001115
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.1.153	0.001095
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.1.159	0.004673
ORF1ab/nsp3	1467	S1467T	Tct	Act	1	1	B.1.1.170	0.001247
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.1.192	0.002309
ORF1ab/nsp3	1467	S1467P	Tct	Cct	1	1	B.1.1.214	0.000055
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.1.214	0.000055
ORF1ab/nsp3	1467	S1467T	Tct	Act	1	1	B.1.1.243	0.004082
ORF1ab/nsp3	1467	S1467D	TCT	GAC	1	1	B.1.1.28	0.000311
ORF1ab/nsp3	1467	S1467S	tcT	tcG	1	1	B.1.1.28	0.000311
ORF1ab/nsp3	1467	S1467S	tcT	tcC	1	1	B.1.1.300	0.010753
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.1.303	0.002762
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.1.305	0.003861
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.1.311	0.000358
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.1.312	0.001912
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.1.312	0.001912
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.1.317	0.000412
ORF1ab/nsp3	1467	S1467Y	tCt	tAt	1	1	B.1.1.318	0.000302
ORF1ab/nsp3	1467	S1467S	tcT	tcG	1	1	B.1.1.33	0.000421
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.1.344	0.010753
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.1.351	0.002793
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.1.354	0.004386
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.1.37	0.000193
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.1.39	0.00051
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.1.392	0.052632
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.1.413	0.006897
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.1.427	0.142857
ORF1ab/nsp3	1467	S1467T	Tct	Act	1	1	B.1.1.445	0.037037
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.1.46	0.004367
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.1.464	0.001473
ORF1ab/nsp3	1467	S1467T	Tct	Act	1	1	B.1.1.47	0.005348
ORF1ab/nsp3	1467	S1467P	Tct	Cct	1	1	B.1.1.521	0.005348
ORF1ab/nsp3	1467	S1467del2	TCT	C--	1	1	B.1.1.525	0.005464
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.1.526	0.003546
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.1.67	0.004566
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.1.70	0.000341
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.1.70	0.000341
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.1.75	0.010638
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.1.98	0.018519
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.139	0.000733
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.140	0.018868
ORF1ab/nsp3	1467	S1467T	Tct	Act	1	1	B.1.146	0.004237
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.160	0.000031
ORF1ab/nsp3	1467	S1467S	tcT	tcC	1	1	B.1.160	0.000031
ORF1ab/nsp3	1467	S1467T	Tct	Act	1	1	B.1.160.12	0.00641
ORF1ab/nsp3	1467	S1467T	Tct	Act	1	1	B.1.160.14	0.002119
ORF1ab/nsp3	1467	S1467T	Tct	Act	1	1	B.1.160.32	0.004292
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.160.7	0.002079
ORF1ab/nsp3	1467	S1467P	Tct	Cct	1	1	B.1.177	0.000013
ORF1ab/nsp3	1467	S1467del2	TCt	--t	1	1	B.1.177	0.000013
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.177.10	0.000878
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.177.10	0.000878
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.177.11	0.001698
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.177.11	0.001698
ORF1ab/nsp3	1467	S1467S	tcT	tcC	1	1	B.1.177.12	0.000152
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.177.12	0.000152
ORF1ab/nsp3	1467	S1467P	Tct	Cct	1	1	B.1.177.15	0.000631
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.177.15	0.000631
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.177.15	0.000631
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.177.16	0.000664
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.177.17	0.000821
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.177.21	0.000076
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.177.33	0.001645
ORF1ab/nsp3	1467	S1467S	tcT	tcC	1	1	B.1.177.4	0.000211
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.177.40	0.005155
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.177.53	0.002392
ORF1ab/nsp3	1467	S1467T	Tct	Act	1	1	B.1.177.53	0.002392
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.177.54	0.000606
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.177.54	0.000606
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.177.57	0.000281
ORF1ab/nsp3	1467	S1467S	tcT	tcC	1	1	B.1.177.57	0.000281
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.177.6	0.000977
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.177.60	0.000218
ORF1ab/nsp3	1467	S1467T	Tct	Act	1	1	B.1.177.62	0.001192
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.177.7	0.000165
ORF1ab/nsp3	1467	S1467T	Tct	Act	1	1	B.1.177.71	0.010101
ORF1ab/nsp3	1467	S1467T	Tct	Act	1	1	B.1.177.75	0.001041
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.177.84	0.006667
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.177.86	0.000183
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.177.9	0.001332
ORF1ab/nsp3	1467	S1467C	tCt	tGt	1	1	B.1.206	0.000816
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.206	0.000816
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.214.2	0.0006
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.221	0.000071
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.229	0.009709
ORF1ab/nsp3	1467	S1467P	Tct	Cct	1	1	B.1.23	0.006061
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.239	0.001221
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.241	0.000812
ORF1ab/nsp3	1467	S1467A	TcT	GcA	1	1	B.1.243	0.00007
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.258	0.000067
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.258.16	0.001637
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.265	0.001271
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.306	0.005714
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.324	0.001605
ORF1ab/nsp3	1467	S1467T	Tct	Act	1	1	B.1.326	0.007576
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.351.3	0.000876
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.355	0.011111
ORF1ab/nsp3	1467	S1467A	Tct	Gct	1	1	B.1.36	0.000146
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.36.17	0.000494
ORF1ab/nsp3	1467	S1467S	tcT	tcA	1	1	B.1.36.31	0.001751
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.36.7	0.004
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.36.8	0.001
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.362.2	0.004717
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.370	0.008
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.396	0.000706
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.411	0.003704
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.415	0.014286
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.416.1	0.001563
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.416.1	0.001563
ORF1ab/nsp3	1467	S1467del1	TCt	-Nt	1	1	B.1.422	0.000812
ORF1ab/nsp3	1467	S1467Y	tCt	tAt	1	1	B.1.429	0.000024
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.438.1	0.000107
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.466.2	0.000391
ORF1ab/nsp3	1467	S1467T	Tct	Act	1	1	B.1.473	0.019231
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.474	0.001901
ORF1ab/nsp3	1467	S1467T	Tct	Act	1	1	B.1.497	0.000315
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.521	0.004975
ORF1ab/nsp3	1467	S1467S	tcT	tcA	1	1	B.1.524	0.001406
ORF1ab/nsp3	1467	S1467del1	tcT	tc-	1	1	B.1.533	0.009615
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.564.1	0.001577
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.573	0.006098
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.1.577	0.000687
ORF1ab/nsp3	1467	S1467S	tcT	tcC	1	1	B.1.595	0.000261
ORF1ab/nsp3	1467	S1467S	tcT	tcA	1	1	B.1.606	0.006024
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.617.1	0.000129
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.618	0.004032
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.619.1	0.000641
ORF1ab/nsp3	1467	S1467A	Tct	Gct	1	1	B.1.619.1	0.000641
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.621.1	0.000506
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.8	0.001972
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	B.1.9	0.006173
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	B.34	0.013699
ORF1ab/nsp3	1467	S1467Y	tCt	tAt	1	1	B.6.6	0.000889
ORF1ab/nsp3	1467	S1467S	tcT	tcC	1	1	C.18	0.002591
ORF1ab/nsp3	1467	S1467V	TCT	GTG	1	1	C.35	0.000774
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	C.36.3	0.000567
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	C.37	0.000116
ORF1ab/nsp3	1467	S1467A	Tct	Gct	1	1	D.2	0.000075
ORF1ab/nsp3	1467	S1467S	tcT	tcG	1	1	D.2	0.000075
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	N.3	0.005814
ORF1ab/nsp3	1467	S1467W	tCT	tGG	1	1	P.1	0.000016
ORF1ab/nsp3	1467	S1467T	TcT	AcG	1	1	P.1	0.000016
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	P.1.1	0.000318
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	P.1.15	0.000232
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	P.1.8	0.004785
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	P.2	0.000187
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	P.5	0.013699
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	Q.1	0.000126
ORF1ab/nsp3	1467	S1467F	tCt	tTt	1	1	Q.7	0.001111
ORF1ab/nsp3	1467	S1467del	TCT	---	1	1	Q.8	0.000165

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.