CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 682

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	682	H682Y	H1500Y	nonsyn	Cat	Tat	2613	2609	0.998469	4763-4765
ORF1ab/nsp3	682	H682Y	H1500Y	nonsyn	CaT	TaC	2613	4	0.00153081	4763-4765
ORF1ab/nsp3	682	H682R	H1500R	nonsyn	cAt	cGt	416	413	0.992788	4763-4765
ORF1ab/nsp3	682	H682R	H1500R	nonsyn	CAT	AGA	416	2	0.00480769	4763-4765
ORF1ab/nsp3	682	H682R	H1500R	nonsyn	cAT	cGC	416	1	0.00240385	4763-4765
ORF1ab/nsp3	682	H682H	H1500H	syn	caT	caC	201	201	1	4763-4765
ORF1ab/nsp3	682	H682del	H1500del	del	CAT	---	80	80	1	4763-4765
ORF1ab/nsp3	682	H682del1	H1500del1	del	caT	ca-	21	18	0.857143	4763-4765
ORF1ab/nsp3	682	H682del1	H1500del1	del	CAt	-Gt	21	1	0.047619	4763-4765
ORF1ab/nsp3	682	H682del1	H1500del1	del	CaT	Ta-	21	1	0.047619	4763-4765
ORF1ab/nsp3	682	H682del1	H1500del1	del	cAt	c-t	21	1	0.047619	4763-4765
ORF1ab/nsp3	682	H682N	H1500N	nonsyn	Cat	Aat	17	15	0.882353	4763-4765
ORF1ab/nsp3	682	H682N	H1500N	nonsyn	CaT	AaC	17	2	0.117647	4763-4765
ORF1ab/nsp3	682	H682Q	H1500Q	nonsyn	caT	caA	16	10	0.625	4763-4765
ORF1ab/nsp3	682	H682Q	H1500Q	nonsyn	caT	caG	16	6	0.375	4763-4765
ORF1ab/nsp3	682	H682L	H1500L	nonsyn	cAt	cTt	6	6	1	4763-4765
ORF1ab/nsp3	682	H682X	H1500X	nonsyn	CAT	TGA	4	2	0.5	4763-4765
ORF1ab/nsp3	682	H682X	H1500X	nonsyn	CaT	TaA	4	2	0.5	4763-4765
ORF1ab/nsp3	682	H682del2	H1500del2	del	cAT	c--	3	3	1	4763-4765
ORF1ab/nsp3	682	H682K	H1500K	nonsyn	CaT	AaA	3	3	1	4763-4765
ORF1ab/nsp3	682	H682S	H1500S	nonsyn	CAT	AGC	2	2	1	4763-4765
ORF1ab/nsp3	682	H682D	H1500D	nonsyn	Cat	Gat	2	2	1	4763-4765
ORF1ab/nsp3	682	H682C	H1500C	nonsyn	CAT	TGC	2	2	1	4763-4765
ORF1ab/nsp3	682	H682P	H1500P	nonsyn	cAt	cCt	1	1	1	4763-4765
ORF1ab/nsp3	682	H682F	H1500F	nonsyn	CAt	TTt	1	1	1	4763-4765
ORF1ab/nsp3	682	H682T	H1500T	nonsyn	CAT	ACA	1	1	1	4763-4765
ORF1ab/nsp3	682	H682A	H1500A	nonsyn	CAt	GCt	1	1	1	4763-4765

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	682	H682Y	Cat	Tat	2609	2613	All	0.000499
ORF1ab/nsp3	682	H682Y	CaT	TaC	4	2613	All	0.000001
ORF1ab/nsp3	682	H682Y	Cat	Tat	596	596	B.1.1.7	0.000534
ORF1ab/nsp3	682	H682R	cAt	cGt	413	416	All	0.000079
ORF1ab/nsp3	682	H682R	CAT	AGA	2	416	All	0
ORF1ab/nsp3	682	H682R	cAT	cGC	1	416	All	0
ORF1ab/nsp3	682	H682H	caT	caC	201	201	All	0.000038
ORF1ab/nsp3	682	H682Y	Cat	Tat	176	176	B.1.617.2	0.000663
ORF1ab/nsp3	682	H682R	cAt	cGt	163	163	AY.34	0.015805
ORF1ab/nsp3	682	H682H	caT	caC	157	157	B.1.1.7	0.000141
ORF1ab/nsp3	682	H682Y	Cat	Tat	123	123	AY.3	0.001223
ORF1ab/nsp3	682	H682Y	Cat	Tat	118	118	AY.121	0.015968
ORF1ab/nsp3	682	H682Y	Cat	Tat	115	115	AY.33	0.007679
ORF1ab/nsp3	682	H682Y	Cat	Tat	113	113	AY.103	0.000702
ORF1ab/nsp3	682	H682Y	Cat	Tat	111	111	C.38	0.895161
ORF1ab/nsp3	682	H682Y	Cat	Tat	99	99	B.1.160	0.003088
ORF1ab/nsp3	682	H682Y	Cat	Tat	97	97	AY.44	0.00059
ORF1ab/nsp3	682	H682Y	Cat	Tat	88	88	AY.25	0.000529
ORF1ab/nsp3	682	H682Y	Cat	Tat	87	87	AY.29	0.001372
ORF1ab/nsp3	682	H682del	CAT	---	80	80	All	0.000015
ORF1ab/nsp3	682	H682Y	Cat	Tat	68	68	B.1.243.2	0.985507
ORF1ab/nsp3	682	H682Y	Cat	Tat	56	56	B.1.1	0.001016
ORF1ab/nsp3	682	H682Y	Cat	Tat	47	47	B.1.637	0.003434
ORF1ab/nsp3	682	H682Y	Cat	Tat	44	44	AY.4	0.000068
ORF1ab/nsp3	682	H682Y	Cat	Tat	39	39	AY.20	0.001516
ORF1ab/nsp3	682	H682R	cAt	cGt	38	38	B.1.634	0.130137
ORF1ab/nsp3	682	H682Y	Cat	Tat	36	36	AY.34	0.003491
ORF1ab/nsp3	682	H682Y	Cat	Tat	34	34	AY.61	0.003562
ORF1ab/nsp3	682	H682Y	Cat	Tat	34	34	AY.98	0.002686
ORF1ab/nsp3	682	H682Y	Cat	Tat	32	32	B.1	0.000293
ORF1ab/nsp3	682	H682Y	Cat	Tat	28	28	B.1.2	0.000247
ORF1ab/nsp3	682	H682Y	Cat	Tat	25	25	AY.120	0.000929
ORF1ab/nsp3	682	H682R	cAt	cGt	25	25	B.1.1.7	0.000022
ORF1ab/nsp3	682	H682del	CAT	---	24	24	B.1.1.7	0.000021
ORF1ab/nsp3	682	H682Y	Cat	Tat	22	22	AY.43	0.000097
ORF1ab/nsp3	682	H682Y	Cat	Tat	22	22	AY.75	0.001232
ORF1ab/nsp3	682	H682R	cAt	cGt	22	22	B.1.617.2	0.000083
ORF1ab/nsp3	682	H682Y	Cat	Tat	22	22	C.39	0.415094
ORF1ab/nsp3	682	H682del1	caT	ca-	18	21	All	0.000003
ORF1ab/nsp3	682	H682del1	CaT	Ta-	1	21	All	0
ORF1ab/nsp3	682	H682del1	cAt	c-t	1	21	All	0
ORF1ab/nsp3	682	H682del1	CAt	-Gt	1	21	All	0
ORF1ab/nsp3	682	H682R	cAt	cGt	20	20	B.1.2	0.000176
ORF1ab/nsp3	682	H682Y	Cat	Tat	19	19	B.1.1.189	0.028744
ORF1ab/nsp3	682	H682Y	Cat	Tat	19	19	P.1	0.000299
ORF1ab/nsp3	682	H682N	Cat	Aat	15	17	All	0.000003
ORF1ab/nsp3	682	H682N	CaT	AaC	2	17	All	0
ORF1ab/nsp3	682	H682R	cAt	cGt	17	17	B.1.1.46	0.074236
ORF1ab/nsp3	682	H682Q	caT	caA	10	16	All	0.000002
ORF1ab/nsp3	682	H682Q	caT	caG	6	16	All	0.000001
ORF1ab/nsp3	682	H682R	cAt	cGt	16	16	AY.4	0.000025
ORF1ab/nsp3	682	H682R	cAt	cGt	13	13	AY.43	0.000058
ORF1ab/nsp3	682	H682R	cAt	cGt	12	12	AY.103	0.000075
ORF1ab/nsp3	682	H682Y	Cat	Tat	12	12	AY.42	0.000483
ORF1ab/nsp3	682	H682Y	Cat	Tat	12	12	B.1.351	0.000357
ORF1ab/nsp3	682	H682Y	Cat	Tat	11	11	B.1.1.329	0.042308
ORF1ab/nsp3	682	H682Y	Cat	Tat	10	10	B.1.258	0.000665
ORF1ab/nsp3	682	H682Y	Cat	Tat	9	9	AY.16	0.003417
ORF1ab/nsp3	682	H682Y	Cat	Tat	8	8	A.2.5	0.003992
ORF1ab/nsp3	682	H682Y	Cat	Tat	8	8	AY.102	0.000212
ORF1ab/nsp3	682	H682Y	Cat	Tat	8	8	AY.99	0.008395
ORF1ab/nsp3	682	H682H	caT	caC	8	8	B.1	0.000073
ORF1ab/nsp3	682	H682Y	Cat	Tat	8	8	B.1.177	0.000105
ORF1ab/nsp3	682	H682Y	Cat	Tat	7	7	AY.39	0.000173
ORF1ab/nsp3	682	H682Y	Cat	Tat	7	7	AY.73	0.004657
ORF1ab/nsp3	682	H682Y	Cat	Tat	7	7	B.1.1.519	0.000278
ORF1ab/nsp3	682	H682L	cAt	cTt	6	6	All	0.000001
ORF1ab/nsp3	682	H682del	CAT	---	6	6	AY.4	0.000009
ORF1ab/nsp3	682	H682R	cAt	cGt	6	6	AY.44	0.000037
ORF1ab/nsp3	682	H682Y	Cat	Tat	6	6	AY.66	0.006417
ORF1ab/nsp3	682	H682R	cAt	cGt	6	6	B.1	0.000055
ORF1ab/nsp3	682	H682Y	Cat	Tat	6	6	B.1.1.214	0.000333
ORF1ab/nsp3	682	H682Y	Cat	Tat	6	6	B.1.160.22	0.040541
ORF1ab/nsp3	682	H682Y	Cat	Tat	6	6	B.1.427	0.000303
ORF1ab/nsp3	682	H682R	cAt	cGt	6	6	B.1.429	0.000141
ORF1ab/nsp3	682	H682Y	Cat	Tat	6	6	B.1.429	0.000141
ORF1ab/nsp3	682	H682Y	Cat	Tat	6	6	B.1.526	0.000141
ORF1ab/nsp3	682	H682Y	Cat	Tat	6	6	Q.8	0.000989
ORF1ab/nsp3	682	H682H	caT	caC	5	5	AY.43	0.000022
ORF1ab/nsp3	682	H682Y	Cat	Tat	5	5	AY.70	0.001043
ORF1ab/nsp3	682	H682Y	Cat	Tat	5	5	B.1.1.1	0.001633
ORF1ab/nsp3	682	H682R	cAt	cGt	5	5	B.1.240	0.001078
ORF1ab/nsp3	682	H682Y	Cat	Tat	5	5	B.1.369	0.001426
ORF1ab/nsp3	682	H682H	caT	caC	5	5	B.1.429	0.000118
ORF1ab/nsp3	682	H682Y	CaT	TaC	4	4		0.222222
ORF1ab/nsp3	682	H682X	CaT	TaA	2	4		0.111111
ORF1ab/nsp3	682	H682X	CAT	TGA	2	4		0.111111
ORF1ab/nsp3	682	H682X	CaT	TaA	2	4	All	0
ORF1ab/nsp3	682	H682X	CAT	TGA	2	4	All	0
ORF1ab/nsp3	682	H682Y	Cat	Tat	4	4	AY.119	0.000141
ORF1ab/nsp3	682	H682H	caT	caC	4	4	AY.25	0.000024
ORF1ab/nsp3	682	H682H	caT	caC	4	4	AY.4	0.000006
ORF1ab/nsp3	682	H682Y	Cat	Tat	4	4	AY.74	0.000463
ORF1ab/nsp3	682	H682Y	Cat	Tat	4	4	AY.75.1	0.000721
ORF1ab/nsp3	682	H682Y	Cat	Tat	4	4	AY.86	0.00332
ORF1ab/nsp3	682	H682R	cAt	cGt	4	4	B.1.1.240	0.018779
ORF1ab/nsp3	682	H682R	cAt	cGt	4	4	B.1.1.448	0.00813
ORF1ab/nsp3	682	H682R	cAt	cGt	4	4	B.1.1.519	0.000159
ORF1ab/nsp3	682	H682H	caT	caC	4	4	B.1.161	0.068966
ORF1ab/nsp3	682	H682H	caT	caC	4	4	B.1.617.2	0.000015
ORF1ab/nsp3	682	H682del1	caT	ca-	4	4	B.1.617.2	0.000015
ORF1ab/nsp3	682	H682Y	Cat	Tat	4	4	P.1.7	0.001277
ORF1ab/nsp3	682	H682K	CaT	AaA	3	3	All	0.000001
ORF1ab/nsp3	682	H682del2	cAT	c--	3	3	All	0.000001
ORF1ab/nsp3	682	H682Y	Cat	Tat	3	3	AY.111	0.000549
ORF1ab/nsp3	682	H682Y	Cat	Tat	3	3	AY.23	0.000209
ORF1ab/nsp3	682	H682Y	Cat	Tat	3	3	AY.26	0.000085
ORF1ab/nsp3	682	H682R	cAt	cGt	3	3	AY.26	0.000085
ORF1ab/nsp3	682	H682R	cAt	cGt	3	3	AY.3	0.00003
ORF1ab/nsp3	682	H682Y	Cat	Tat	3	3	AY.36	0.000445
ORF1ab/nsp3	682	H682del	CAT	---	3	3	AY.43	0.000013
ORF1ab/nsp3	682	H682Y	Cat	Tat	3	3	AY.46.5	0.000595
ORF1ab/nsp3	682	H682Y	Cat	Tat	3	3	AY.5	0.000062
ORF1ab/nsp3	682	H682Y	Cat	Tat	3	3	AY.6	0.000123
ORF1ab/nsp3	682	H682R	cAt	cGt	3	3	AY.91	0.002191
ORF1ab/nsp3	682	H682Y	Cat	Tat	3	3	B.1.1.222	0.000612
ORF1ab/nsp3	682	H682del1	caT	ca-	3	3	B.1.1.7	0.000003
ORF1ab/nsp3	682	H682Y	Cat	Tat	3	3	B.1.177.81	0.000568
ORF1ab/nsp3	682	H682Y	Cat	Tat	3	3	B.1.320	0.003736
ORF1ab/nsp3	682	H682Y	Cat	Tat	3	3	P.2	0.00056
ORF1ab/nsp3	682	H682K	CaT	AaA	2	2		0.111111
ORF1ab/nsp3	682	H682N	CaT	AaC	2	2		0.111111
ORF1ab/nsp3	682	H682C	CAT	TGC	2	2		0.111111
ORF1ab/nsp3	682	H682R	CAT	AGA	2	2		0.111111
ORF1ab/nsp3	682	H682del	CAT	---	2	2		0.111111
ORF1ab/nsp3	682	H682S	CAT	AGC	2	2		0.111111
ORF1ab/nsp3	682	H682C	CAT	TGC	2	2	All	0
ORF1ab/nsp3	682	H682S	CAT	AGC	2	2	All	0
ORF1ab/nsp3	682	H682D	Cat	Gat	2	2	All	0
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	AU.1	0.002532
ORF1ab/nsp3	682	H682L	cAt	cTt	2	2	AY.102	0.000053
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	AY.113	0.000285
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	AY.118	0.000125
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	AY.13	0.000322
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	AY.18	0.020202
ORF1ab/nsp3	682	H682H	caT	caC	2	2	AY.20	0.000078
ORF1ab/nsp3	682	H682R	cAt	cGt	2	2	AY.20	0.000078
ORF1ab/nsp3	682	H682R	cAt	cGt	2	2	AY.25	0.000012
ORF1ab/nsp3	682	H682R	cAt	cGt	2	2	AY.34.1	0.00102
ORF1ab/nsp3	682	H682N	Cat	Aat	2	2	AY.39	0.000049
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	AY.39.1	0.000079
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	AY.4.5	0.000215
ORF1ab/nsp3	682	H682del	CAT	---	2	2	AY.4.5	0.000215
ORF1ab/nsp3	682	H682del	CAT	---	2	2	AY.44	0.000012
ORF1ab/nsp3	682	H682del1	caT	ca-	1	2	AY.44	0.000006
ORF1ab/nsp3	682	H682del1	CaT	Ta-	1	2	AY.44	0.000006
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	AY.47	0.000062
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	AY.54	0.000191
ORF1ab/nsp3	682	H682N	Cat	Aat	2	2	AY.75	0.000112
ORF1ab/nsp3	682	H682R	cAt	cGt	2	2	AY.85	0.000854
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	AY.98.1	0.000097
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	AY.99.1	0.003106
ORF1ab/nsp3	682	H682del1	caT	ca-	2	2	B.1	0.000018
ORF1ab/nsp3	682	H682del	CAT	---	2	2	B.1	0.000018
ORF1ab/nsp3	682	H682R	cAt	cGt	2	2	B.1.1	0.000036
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	B.1.1.176	0.000879
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	B.1.1.229	0.011494
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	B.1.1.244	0.030769
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	B.1.1.348	0.001592
ORF1ab/nsp3	682	H682N	Cat	Aat	2	2	B.1.1.39	0.001019
ORF1ab/nsp3	682	H682Q	caT	caG	2	2	B.1.1.7	0.000002
ORF1ab/nsp3	682	H682R	cAt	cGt	2	2	B.1.160	0.000062
ORF1ab/nsp3	682	H682del	CAT	---	2	2	B.1.177.4	0.000422
ORF1ab/nsp3	682	H682del1	caT	ca-	2	2	B.1.2	0.000018
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	B.1.214.2	0.001199
ORF1ab/nsp3	682	H682R	cAt	cGt	2	2	B.1.232	0.001075
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	B.1.240	0.000431
ORF1ab/nsp3	682	H682del	CAT	---	2	2	B.1.36	0.000292
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	B.1.396	0.001411
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	B.1.474	0.003802
ORF1ab/nsp3	682	H682R	cAt	cGt	2	2	B.1.617.1	0.000258
ORF1ab/nsp3	682	H682del	CAT	---	2	2	B.1.619	0.001742
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	B.1.628	0.000705
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	B.55	0.0059
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	C.37	0.000232
ORF1ab/nsp3	682	H682Q	caT	caA	2	2	D.2	0.00015
ORF1ab/nsp3	682	H682R	cAt	cGt	2	2	P.1	0.000032
ORF1ab/nsp3	682	H682del	CAT	---	2	2	P.1	0.000032
ORF1ab/nsp3	682	H682R	cAt	cGt	2	2	P.1.14	0.000096
ORF1ab/nsp3	682	H682Y	Cat	Tat	2	2	P.1.17	0.000324
ORF1ab/nsp3	682	H682del	CAT	---	1	1	A.2.2	0.001689
ORF1ab/nsp3	682	H682Q	caT	caA	1	1	A.2.5	0.000499
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	A.2.5.2	0.001572
ORF1ab/nsp3	682	H682A	CAt	GCt	1	1	All	0
ORF1ab/nsp3	682	H682F	CAt	TTt	1	1	All	0
ORF1ab/nsp3	682	H682T	CAT	ACA	1	1	All	0
ORF1ab/nsp3	682	H682P	cAt	cCt	1	1	All	0
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AP.1	0.001502
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.100	0.000046
ORF1ab/nsp3	682	H682H	caT	caC	1	1	AY.100	0.000046
ORF1ab/nsp3	682	H682Q	caT	caA	1	1	AY.102	0.000027
ORF1ab/nsp3	682	H682L	cAt	cTt	1	1	AY.106	0.000335
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.106	0.000335
ORF1ab/nsp3	682	H682del	CAT	---	1	1	AY.113	0.000142
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.116.1	0.000311
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.117	0.000085
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	AY.119	0.000035
ORF1ab/nsp3	682	H682del2	cAT	c--	1	1	AY.120	0.000037
ORF1ab/nsp3	682	H682R	cAT	cGC	1	1	AY.120.1	0.000321
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.14	0.000088
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	AY.16	0.00038
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.16.1	0.00047
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	AY.23	0.00007
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.24	0.000431
ORF1ab/nsp3	682	H682Q	caT	caA	1	1	AY.25	0.000006
ORF1ab/nsp3	682	H682del	CAT	---	1	1	AY.25	0.000006
ORF1ab/nsp3	682	H682Q	caT	caG	1	1	AY.26	0.000028
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.27	0.000065
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.29.1	0.000221
ORF1ab/nsp3	682	H682Q	caT	caG	1	1	AY.3	0.00001
ORF1ab/nsp3	682	H682del	CAT	---	1	1	AY.3	0.00001
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.3.1	0.000085
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.32	0.000532
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	AY.33	0.000067
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	AY.35	0.000233
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.35	0.000233
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.38	0.000499
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	AY.39	0.000025
ORF1ab/nsp3	682	H682P	cAt	cCt	1	1	AY.4	0.000002
ORF1ab/nsp3	682	H682N	Cat	Aat	1	1	AY.4	0.000002
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	AY.4.2	0.000022
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.4.2	0.000022
ORF1ab/nsp3	682	H682N	Cat	Aat	1	1	AY.4.5	0.000107
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.40	0.000964
ORF1ab/nsp3	682	H682Q	caT	caG	1	1	AY.43	0.000004
ORF1ab/nsp3	682	H682Q	caT	caG	1	1	AY.44	0.000006
ORF1ab/nsp3	682	H682F	CAt	TTt	1	1	AY.44	0.000006
ORF1ab/nsp3	682	H682H	caT	caC	1	1	AY.44	0.000006
ORF1ab/nsp3	682	H682T	CAT	ACA	1	1	AY.44	0.000006
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.45	0.000122
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.46.2	0.000635
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	AY.46.5	0.000198
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.46.6	0.000072
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.48	0.000465
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.51	0.000909
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.53	0.000288
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	AY.54	0.000095
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.55	0.000917
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.58	0.000907
ORF1ab/nsp3	682	H682H	caT	caC	1	1	AY.6	0.000041
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.62	0.000436
ORF1ab/nsp3	682	H682del	CAT	---	1	1	AY.66	0.00107
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.68	0.000274
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.69	0.000187
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.71	0.000475
ORF1ab/nsp3	682	H682del	CAT	---	1	1	AY.81	0.001992
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.84	0.000437
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AY.85	0.000427
ORF1ab/nsp3	682	H682del1	caT	ca-	1	1	AY.9.2	0.000037
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	AY.90	0.000684
ORF1ab/nsp3	682	H682H	caT	caC	1	1	AY.95	0.000761
ORF1ab/nsp3	682	H682Q	caT	caA	1	1	AY.98.1	0.000048
ORF1ab/nsp3	682	H682del	CAT	---	1	1	AY.99	0.001049
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AZ.2	0.000821
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	AZ.4	0.003356
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	B	0.000128
ORF1ab/nsp3	682	H682D	Cat	Gat	1	1	B	0.000128
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B	0.000128
ORF1ab/nsp3	682	H682N	Cat	Aat	1	1	B.1	0.000009
ORF1ab/nsp3	682	H682L	cAt	cTt	1	1	B.1	0.000009
ORF1ab/nsp3	682	H682K	CaT	AaA	1	1	B.1	0.000009
ORF1ab/nsp3	682	H682A	CAt	GCt	1	1	B.1.1	0.000018
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.1.1	0.000018
ORF1ab/nsp3	682	H682D	Cat	Gat	1	1	B.1.1.1	0.000327
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.1.12	0.007463
ORF1ab/nsp3	682	H682del1	caT	ca-	1	1	B.1.1.139	0.022727
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.1.1.142	0.017544
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	B.1.1.194	0.00495
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.1.198	0.001468
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	B.1.1.220	0.001859
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.1.25	0.000569
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.1.294	0.001266
ORF1ab/nsp3	682	H682H	caT	caC	1	1	B.1.1.306	0.000438
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.1.1.311	0.000358
ORF1ab/nsp3	682	H682L	cAt	cTt	1	1	B.1.1.312	0.001912
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.1.317	0.000412
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.1.351	0.002793
ORF1ab/nsp3	682	H682N	Cat	Aat	1	1	B.1.1.371	0.010417
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.1.409	0.002833
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.1.1.409	0.002833
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.1.41	0.006329
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	B.1.1.63	0.000386
ORF1ab/nsp3	682	H682del2	cAT	c--	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.111	0.001175
ORF1ab/nsp3	682	H682L	cAt	cTt	1	1	B.1.124	0.007812
ORF1ab/nsp3	682	H682del1	cAt	c-t	1	1	B.1.126	0.001276
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.126	0.001276
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.1.149	0.003425
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.1.157	0.002985
ORF1ab/nsp3	682	H682del1	caT	ca-	1	1	B.1.160	0.000031
ORF1ab/nsp3	682	H682N	Cat	Aat	1	1	B.1.160.16	0.000929
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.1.160.7	0.002079
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.1.177	0.000013
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	B.1.177	0.000013
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.1.177.16	0.000664
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.177.19	0.001431
ORF1ab/nsp3	682	H682N	Cat	Aat	1	1	B.1.177.35	0.000691
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.177.5	0.001242
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.1.177.50	0.004695
ORF1ab/nsp3	682	H682N	Cat	Aat	1	1	B.1.177.50	0.004695
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.1.177.57	0.000281
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.177.60	0.000218
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.1.177.63	0.002703
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	B.1.177.73	0.000566
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.1.177.81	0.000189
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.177.87	0.000728
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.189	0.004292
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.206	0.000816
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.1.210	0.002132
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.221	0.000071
ORF1ab/nsp3	682	H682del1	CAt	-Gt	1	1	B.1.243	0.00007
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	B.1.258	0.000067
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.1.258	0.000067
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.265	0.001271
ORF1ab/nsp3	682	H682del1	caT	ca-	1	1	B.1.284	0.013158
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.1.319	0.003049
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.329	0.000608
ORF1ab/nsp3	682	H682Q	caT	caA	1	1	B.1.351	0.00003
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.36	0.000146
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.36.17	0.000494
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.36.18	0.00042
ORF1ab/nsp3	682	H682Q	caT	caA	1	1	B.1.36.36	0.000602
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.36.8	0.001
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	B.1.36.8	0.001
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.362	0.001541
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.381	0.007812
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.470	0.001404
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	B.1.499	0.00105
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	B.1.525	0.000113
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.558	0.004566
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.564	0.000426
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.575	0.000303
ORF1ab/nsp3	682	H682H	caT	caC	1	1	B.1.575	0.000303
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.587	0.001898
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.596	0.000087
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	B.1.599	0.00365
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.609	0.000479
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.1.617.1	0.000129
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.617.1	0.000129
ORF1ab/nsp3	682	H682Q	caT	caA	1	1	B.1.617.1	0.000129
ORF1ab/nsp3	682	H682Q	caT	caA	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	682	H682del2	cAT	c--	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	682	H682N	Cat	Aat	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.1.617.3	0.002985
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	B.1.619	0.000871
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.620	0.000946
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.621	0.000089
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.1.621	0.000089
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.1.623	0.000536
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.1.630	0.005236
ORF1ab/nsp3	682	H682del1	caT	ca-	1	1	B.1.637	0.000073
ORF1ab/nsp3	682	H682N	Cat	Aat	1	1	B.1.91	0.002075
ORF1ab/nsp3	682	H682del	CAT	---	1	1	B.15	0.017544
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	B.3	0.000831
ORF1ab/nsp3	682	H682del1	caT	ca-	1	1	B.52	0.010101
ORF1ab/nsp3	682	H682H	caT	caC	1	1	C.14	0.004329
ORF1ab/nsp3	682	H682R	cAt	cGt	1	1	C.30	0.001727
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	C.30	0.001727
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	C.36.3	0.000567
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	C.36.3.1	0.002717
ORF1ab/nsp3	682	H682H	caT	caC	1	1	P.1	0.000016
ORF1ab/nsp3	682	H682del	CAT	---	1	1	P.1.1	0.000318
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	P.1.14	0.000048
ORF1ab/nsp3	682	H682Y	Cat	Tat	1	1	Q.1	0.000126
ORF1ab/nsp3	682	H682del	CAT	---	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.