CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1539

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	1539	H1539Y	H2357Y	nonsyn	Cat	Tat	1669	1669	1	7334-7336
ORF1ab/nsp3	1539	H1539H	H2357H	syn	caT	caC	330	330	1	7334-7336
ORF1ab/nsp3	1539	H1539del	H2357del	del	CAT	---	79	79	1	7334-7336
ORF1ab/nsp3	1539	H1539R	H2357R	nonsyn	cAt	cGt	57	56	0.982456	7334-7336
ORF1ab/nsp3	1539	H1539R	H2357R	nonsyn	CAT	AGG	57	1	0.0175439	7334-7336
ORF1ab/nsp3	1539	H1539Q	H2357Q	nonsyn	caT	caA	15	8	0.533333	7334-7336
ORF1ab/nsp3	1539	H1539Q	H2357Q	nonsyn	caT	caG	15	7	0.466667	7334-7336
ORF1ab/nsp3	1539	H1539N	H2357N	nonsyn	Cat	Aat	12	12	1	7334-7336
ORF1ab/nsp3	1539	H1539del1	H2357del1	del	caT	ca-	7	6	0.857143	7334-7336
ORF1ab/nsp3	1539	H1539del1	H2357del1	del	Cat	-at	7	1	0.142857	7334-7336
ORF1ab/nsp3	1539	H1539L	H2357L	nonsyn	cAt	cTt	3	3	1	7334-7336
ORF1ab/nsp3	1539	H1539C	H2357C	nonsyn	CAt	TGt	3	3	1	7334-7336
ORF1ab/nsp3	1539	H1539P	H2357P	nonsyn	cAt	cCt	2	2	1	7334-7336
ORF1ab/nsp3	1539	H1539S	H2357S	nonsyn	CAt	TCt	2	2	1	7334-7336
ORF1ab/nsp3	1539	H1539D	H2357D	nonsyn	Cat	Gat	2	1	0.5	7334-7336
ORF1ab/nsp3	1539	H1539D	H2357D	nonsyn	CaT	GaC	2	1	0.5	7334-7336
ORF1ab/nsp3	1539	H1539T	H2357T	nonsyn	CAt	ACt	1	1	1	7334-7336

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	1539	H1539Y	Cat	Tat	1669	1669	All	0.000319
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	661	661	AP.1	0.992492
ORF1ab/nsp3	1539	H1539H	caT	caC	330	330	All	0.000063
ORF1ab/nsp3	1539	H1539H	caT	caC	199	199	B.1.258.17	0.02069
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	172	172	AY.4	0.000268
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	101	101	AY.103	0.000627
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	89	89	B.1.1.7	0.00008
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	88	88	B.1.258.17	0.00915
ORF1ab/nsp3	1539	H1539del	CAT	---	79	79	All	0.000015
ORF1ab/nsp3	1539	H1539H	caT	caC	74	74	B.1.1.7	0.000066
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	60	60	B.1.617.2	0.000226
ORF1ab/nsp3	1539	H1539R	cAt	cGt	56	57	All	0.000011
ORF1ab/nsp3	1539	H1539R	CAT	AGG	1	57	All	0
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	44	44	B.1.2	0.000387
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	43	43	AY.43	0.000191
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	23	23	B.1	0.000211
ORF1ab/nsp3	1539	H1539del	CAT	---	20	20	B.1.1.7	0.000018
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	19	19	B.1.36.24	0.117284
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	16	16	AY.44	0.000097
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	16	16	B.1.160	0.000499
ORF1ab/nsp3	1539	H1539Q	caT	caA	8	15	All	0.000002
ORF1ab/nsp3	1539	H1539Q	caT	caG	7	15	All	0.000001
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	13	13	AY.119	0.000459
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	13	13	AY.35	0.00303
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	13	13	B.1.429	0.000306
ORF1ab/nsp3	1539	H1539N	Cat	Aat	12	12	All	0.000002
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	12	12	AY.25	0.000072
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	11	11	B.1.1	0.0002
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	10	10	AY.33	0.000668
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	10	10	AY.98	0.00079
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	10	10	B.6.4	0.454545
ORF1ab/nsp3	1539	H1539H	caT	caC	9	9	B.1.617.2	0.000034
ORF1ab/nsp3	1539	H1539R	cAt	cGt	8	9	B.1.617.2	0.00003
ORF1ab/nsp3	1539	H1539R	CAT	AGG	1	9	B.1.617.2	0.000004
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	8	8	AY.113	0.001139
ORF1ab/nsp3	1539	H1539del	CAT	---	8	8	AY.43	0.000035
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	8	8	B.1.177	0.000105
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	8	8	B.1.596	0.000697
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	8	8	P.1	0.000126
ORF1ab/nsp3	1539	H1539del1	caT	ca-	6	7	All	0.000001
ORF1ab/nsp3	1539	H1539del1	Cat	-at	1	7	All	0
ORF1ab/nsp3	1539	H1539R	cAt	cGt	7	7	AY.103	0.000043
ORF1ab/nsp3	1539	H1539R	cAt	cGt	7	7	AY.4	0.000011
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	7	7	AY.46.6	0.000505
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	7	7	AY.5	0.000145
ORF1ab/nsp3	1539	H1539R	cAt	cGt	7	7	B.1.637	0.000512
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	7	7	B.35	0.054688
ORF1ab/nsp3	1539	H1539R	cAt	cGt	6	6	AY.36	0.000889
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	6	6	B.1.1.519	0.000238
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	6	6	B.1.551	0.007742
ORF1ab/nsp3	1539	H1539del	CAT	---	6	6	B.1.617.2	0.000023
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	6	6	R.1	0.00054
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	6	6	W.3	0.031579
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	5	5	AY.11	0.006693
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	5	5	AY.120	0.000186
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	5	5	AY.20	0.000194
ORF1ab/nsp3	1539	H1539H	caT	caC	5	5	AY.4	0.000008
ORF1ab/nsp3	1539	H1539H	caT	caC	5	5	B.1.1	0.000091
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	5	5	B.1.1.1	0.001633
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	5	5	B.1.1.189	0.007564
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	5	5	B.1.36	0.00073
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	5	5	B.1.36.17	0.00247
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	4	4	AY.102	0.000106
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	4	4	AY.26	0.000113
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	4	4	AY.46.4	0.000658
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	4	4	AY.70	0.000834
ORF1ab/nsp3	1539	H1539del	CAT	---	4	4	B.1	0.000037
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	3	3		0.166667
ORF1ab/nsp3	1539	H1539C	CAt	TGt	3	3	All	0.000001
ORF1ab/nsp3	1539	H1539L	cAt	cTt	3	3	All	0.000001
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	3	3	AY.100	0.000138
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	3	3	AY.109	0.002219
ORF1ab/nsp3	1539	H1539Q	caT	caG	3	3	AY.118	0.000188
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	3	3	AY.3	0.00003
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	3	3	AY.39	0.000074
ORF1ab/nsp3	1539	H1539del	CAT	---	3	3	AY.42	0.000121
ORF1ab/nsp3	1539	H1539H	caT	caC	3	3	AY.44	0.000018
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	3	3	AY.6	0.000123
ORF1ab/nsp3	1539	H1539del	CAT	---	3	3	B.1.1	0.000054
ORF1ab/nsp3	1539	H1539H	caT	caC	3	3	B.1.1.28	0.000934
ORF1ab/nsp3	1539	H1539R	cAt	cGt	3	3	B.1.1.7	0.000003
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	3	3	B.1.438.1	0.000322
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	3	3	B.1.478	0.035294
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	3	3	B.1.575.1	0.007317
ORF1ab/nsp3	1539	H1539Q	caT	caA	2	3	B.1.617.2	0.000008
ORF1ab/nsp3	1539	H1539Q	caT	caG	1	3	B.1.617.2	0.000004
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	3	3	B.1.621.1	0.001517
ORF1ab/nsp3	1539	H1539C	CAt	TGt	2	2		0.111111
ORF1ab/nsp3	1539	H1539R	cAt	cGt	2	2		0.111111
ORF1ab/nsp3	1539	H1539P	cAt	cCt	2	2		0.111111
ORF1ab/nsp3	1539	H1539S	CAt	TCt	2	2	All	0
ORF1ab/nsp3	1539	H1539P	cAt	cCt	2	2	All	0
ORF1ab/nsp3	1539	H1539D	Cat	Gat	1	2	All	0
ORF1ab/nsp3	1539	H1539D	CaT	GaC	1	2	All	0
ORF1ab/nsp3	1539	H1539H	caT	caC	2	2	AY.103	0.000012
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	2	2	AY.116	0.000574
ORF1ab/nsp3	1539	H1539del	CAT	---	2	2	AY.120.2	0.002571
ORF1ab/nsp3	1539	H1539H	caT	caC	2	2	AY.20	0.000078
ORF1ab/nsp3	1539	H1539del	CAT	---	2	2	AY.25	0.000012
ORF1ab/nsp3	1539	H1539N	Cat	Aat	2	2	AY.25	0.000012
ORF1ab/nsp3	1539	H1539H	caT	caC	2	2	AY.3	0.00002
ORF1ab/nsp3	1539	H1539Q	caT	caA	2	2	AY.3	0.00002
ORF1ab/nsp3	1539	H1539H	caT	caC	2	2	AY.33	0.000134
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	2	2	AY.38	0.000999
ORF1ab/nsp3	1539	H1539N	Cat	Aat	2	2	AY.39.1	0.000079
ORF1ab/nsp3	1539	H1539R	cAt	cGt	2	2	AY.4.4	0.000818
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	2	2	AY.42	0.00008
ORF1ab/nsp3	1539	H1539H	caT	caC	2	2	AY.47	0.000062
ORF1ab/nsp3	1539	H1539R	cAt	cGt	2	2	AY.5	0.000041
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	2	2	AY.71	0.00095
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	2	2	AY.74	0.000231
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	2	2	AY.98.1	0.000097
ORF1ab/nsp3	1539	H1539L	cAt	cTt	2	2	B.1	0.000018
ORF1ab/nsp3	1539	H1539H	caT	caC	2	2	B.1	0.000018
ORF1ab/nsp3	1539	H1539H	caT	caC	2	2	B.1.1.214	0.000111
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	2	2	B.1.1.28	0.000622
ORF1ab/nsp3	1539	H1539Q	caT	caA	2	2	B.1.1.372	0.001377
ORF1ab/nsp3	1539	H1539D	CaT	GaC	1	2	B.1.1.7	0.000001
ORF1ab/nsp3	1539	H1539D	Cat	Gat	1	2	B.1.1.7	0.000001
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	2	2	B.1.177.41	0.005
ORF1ab/nsp3	1539	H1539del	CAT	---	2	2	B.1.2	0.000018
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	2	2	B.1.221	0.000142
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	2	2	B.1.36.10	0.009569
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	2	2	B.1.36.8	0.002
ORF1ab/nsp3	1539	H1539del	CAT	---	2	2	B.1.497	0.00063
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	2	2	B.1.576	0.001813
ORF1ab/nsp3	1539	H1539N	Cat	Aat	2	2	B.1.617.2	0.000008
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	2	2	B.6.6	0.001778
ORF1ab/nsp3	1539	H1539H	caT	caC	2	2	C.36.3	0.001134
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	2	2	C.36.3	0.001134
ORF1ab/nsp3	1539	H1539T	CAt	ACt	1	1		0.055556
ORF1ab/nsp3	1539	H1539S	CAt	TCt	1	1		0.055556
ORF1ab/nsp3	1539	H1539N	Cat	Aat	1	1		0.055556
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	A.3	0.002096
ORF1ab/nsp3	1539	H1539T	CAt	ACt	1	1	All	0
ORF1ab/nsp3	1539	H1539H	caT	caC	1	1	AY.10	0.00053
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	AY.103	0.000006
ORF1ab/nsp3	1539	H1539N	Cat	Aat	1	1	AY.103	0.000006
ORF1ab/nsp3	1539	H1539R	cAt	cGt	1	1	AY.104	0.001984
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.107	0.000466
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.108	0.001103
ORF1ab/nsp3	1539	H1539Q	caT	caA	1	1	AY.109	0.00074
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	AY.113	0.000142
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.117	0.000085
ORF1ab/nsp3	1539	H1539H	caT	caC	1	1	AY.119	0.000035
ORF1ab/nsp3	1539	H1539R	cAt	cGt	1	1	AY.120	0.000037
ORF1ab/nsp3	1539	H1539del1	caT	ca-	1	1	AY.120	0.000037
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.14	0.000088
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.16	0.00038
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.16.1	0.00047
ORF1ab/nsp3	1539	H1539R	cAt	cGt	1	1	AY.20	0.000039
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.23	0.00007
ORF1ab/nsp3	1539	H1539R	cAt	cGt	1	1	AY.29	0.000016
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.29	0.000016
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.30	0.000396
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	AY.33	0.000067
ORF1ab/nsp3	1539	H1539R	cAt	cGt	1	1	AY.33	0.000067
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.34	0.000097
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.34.1	0.00051
ORF1ab/nsp3	1539	H1539H	caT	caC	1	1	AY.39	0.000025
ORF1ab/nsp3	1539	H1539N	Cat	Aat	1	1	AY.4	0.000002
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	AY.4	0.000002
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.4.5	0.000107
ORF1ab/nsp3	1539	H1539del1	caT	ca-	1	1	AY.43	0.000004
ORF1ab/nsp3	1539	H1539H	caT	caC	1	1	AY.43	0.000004
ORF1ab/nsp3	1539	H1539Q	caT	caG	1	1	AY.43	0.000004
ORF1ab/nsp3	1539	H1539R	cAt	cGt	1	1	AY.44	0.000006
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	AY.44	0.000006
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.46.1	0.001027
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.46.5	0.000198
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	AY.46.6	0.000072
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	AY.5	0.000021
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.52	0.000814
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.56	0.001605
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	AY.66	0.00107
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.67	0.000464
ORF1ab/nsp3	1539	H1539R	cAt	cGt	1	1	AY.71	0.000475
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	AY.75	0.000056
ORF1ab/nsp3	1539	H1539H	caT	caC	1	1	AY.75	0.000056
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.75	0.000056
ORF1ab/nsp3	1539	H1539N	Cat	Aat	1	1	AY.75.1	0.00018
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.75.1	0.00018
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.82	0.001357
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.83	0.001724
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.84	0.000437
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	AY.9	0.000068
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	AY.9.2	0.000037
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.9.2.1	0.001976
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	AY.99.2	0.000092
ORF1ab/nsp3	1539	H1539H	caT	caC	1	1	AY.99.2	0.000092
ORF1ab/nsp3	1539	H1539R	cAt	cGt	1	1	AZ.1	0.000867
ORF1ab/nsp3	1539	H1539R	cAt	cGt	1	1	B.1	0.000009
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.1.10	0.001115
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.1.219	0.005
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.1.220	0.001859
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	B.1.1.221	0.010101
ORF1ab/nsp3	1539	H1539H	caT	caC	1	1	B.1.1.279	0.001121
ORF1ab/nsp3	1539	H1539Q	caT	caG	1	1	B.1.1.300	0.010753
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	B.1.1.306	0.000438
ORF1ab/nsp3	1539	H1539del1	Cat	-at	1	1	B.1.1.306	0.000438
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.1.317	0.000412
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.1.33	0.000421
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	B.1.1.354	0.004386
ORF1ab/nsp3	1539	H1539H	caT	caC	1	1	B.1.1.372	0.000689
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	B.1.1.448	0.002033
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	B.1.1.46	0.004367
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	B.1.1.519	0.00004
ORF1ab/nsp3	1539	H1539L	cAt	cTt	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.113	0.015625
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	B.1.115	0.021739
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	B.1.161	0.017241
ORF1ab/nsp3	1539	H1539R	cAt	cGt	1	1	B.1.177	0.000013
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.177.23	0.003236
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.177.60	0.000218
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.177.65	0.000665
ORF1ab/nsp3	1539	H1539H	caT	caC	1	1	B.1.177.7	0.000165
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.177.8	0.000752
ORF1ab/nsp3	1539	H1539H	caT	caC	1	1	B.1.177.81	0.000189
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.192	0.009259
ORF1ab/nsp3	1539	H1539N	Cat	Aat	1	1	B.1.2	0.000009
ORF1ab/nsp3	1539	H1539H	caT	caC	1	1	B.1.2	0.000009
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.234	0.000132
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.240	0.000216
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	B.1.258	0.000067
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.258	0.000067
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.349	0.000715
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	B.1.351	0.00003
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.351	0.00003
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.351.2	0.000303
ORF1ab/nsp3	1539	H1539H	caT	caC	1	1	B.1.356	0.001727
ORF1ab/nsp3	1539	H1539del1	caT	ca-	1	1	B.1.36.10	0.004785
ORF1ab/nsp3	1539	H1539H	caT	caC	1	1	B.1.36.31	0.001751
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.396	0.000706
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.409	0.000781
ORF1ab/nsp3	1539	H1539R	cAt	cGt	1	1	B.1.409	0.000781
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.427	0.00005
ORF1ab/nsp3	1539	H1539N	Cat	Aat	1	1	B.1.466.2	0.000391
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.499	0.00105
ORF1ab/nsp3	1539	H1539H	caT	caC	1	1	B.1.499	0.00105
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	B.1.525	0.000113
ORF1ab/nsp3	1539	H1539Q	caT	caA	1	1	B.1.530	0.007143
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.564	0.000426
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.565	0.00081
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	B.1.575.1	0.002439
ORF1ab/nsp3	1539	H1539del1	caT	ca-	1	1	B.1.576	0.000907
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.577	0.000687
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.582	0.000491
ORF1ab/nsp3	1539	H1539del1	caT	ca-	1	1	B.1.596	0.000087
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	B.1.617.1	0.000129
ORF1ab/nsp3	1539	H1539C	CAt	TGt	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.617.3	0.002985
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.621	0.000089
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	B.1.621	0.000089
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.9.5	0.005682
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	B.1.93	0.000934
ORF1ab/nsp3	1539	H1539S	CAt	TCt	1	1	C.35	0.000774
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	C.37	0.000116
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	D.2	0.000075
ORF1ab/nsp3	1539	H1539H	caT	caC	1	1	D.2	0.000075
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	P.1	0.000016
ORF1ab/nsp3	1539	H1539del1	caT	ca-	1	1	P.1.12	0.000484
ORF1ab/nsp3	1539	H1539Q	caT	caG	1	1	P.1.14	0.000048
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	P.1.15	0.000232
ORF1ab/nsp3	1539	H1539R	cAt	cGt	1	1	P.2	0.000187
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	P.2	0.000187
ORF1ab/nsp3	1539	H1539Y	Cat	Tat	1	1	P.3	0.001595
ORF1ab/nsp3	1539	H1539del	CAT	---	1	1	Q.8	0.000165
ORF1ab/nsp3	1539	H1539H	caT	caC	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.