CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp4 : CodonNum = 389

Details of the codons used for the mutation across all lineages (CodonProp is the proportion each codon is used for this AA mutation):

ORF	CodonNum	Mut	ORF1abMut	MutType	RefCodon	MutCodon	AACount	CodonCount	CodonProp	Genome Position
ORF1ab/nsp4	389	H389H	H3152H	syn	caT	caC	754	754	1	9719-9721
ORF1ab/nsp4	389	H389del	H3152del	del	CAT	---	110	110	1	9719-9721
ORF1ab/nsp4	389	H389Q	H3152Q	nonsyn	caT	caG	110	62	0.563636	9719-9721
ORF1ab/nsp4	389	H389Q	H3152Q	nonsyn	caT	caA	110	48	0.436364	9719-9721
ORF1ab/nsp4	389	H389N	H3152N	nonsyn	Cat	Aat	16	16	1	9719-9721
ORF1ab/nsp4	389	H389Y	H3152Y	nonsyn	Cat	Tat	15	12	0.8	9719-9721
ORF1ab/nsp4	389	H389Y	H3152Y	nonsyn	CaT	TaC	15	3	0.2	9719-9721
ORF1ab/nsp4	389	H389L	H3152L	nonsyn	cAt	cTt	5	5	1	9719-9721
ORF1ab/nsp4	389	H389P	H3152P	nonsyn	cAt	cCt	5	4	0.8	9719-9721
ORF1ab/nsp4	389	H389del1	H3152del1	del	caT	ca-	5	3	0.6	9719-9721
ORF1ab/nsp4	389	H389P	H3152P	nonsyn	cAT	cCA	5	1	0.2	9719-9721
ORF1ab/nsp4	389	H389del1	H3152del1	del	CAt	T-t	5	1	0.2	9719-9721
ORF1ab/nsp4	389	H389del1	H3152del1	del	Cat	-at	5	1	0.2	9719-9721
ORF1ab/nsp4	389	H389D	H3152D	nonsyn	Cat	Gat	4	4	1	9719-9721
ORF1ab/nsp4	389	H389S	H3152S	nonsyn	CAt	TCt	2	2	1	9719-9721
ORF1ab/nsp4	389	H389R	H3152R	nonsyn	cAt	cGt	2	2	1	9719-9721
ORF1ab/nsp4	389	H389V	H3152V	nonsyn	CAt	GTt	2	2	1	9719-9721
ORF1ab/nsp4	389	H389A	H3152A	nonsyn	CAt	GCt	2	1	0.5	9719-9721
ORF1ab/nsp4	389	H389A	H3152A	nonsyn	CAT	GCA	2	1	0.5	9719-9721
ORF1ab/nsp4	389	H389T	H3152T	nonsyn	CAt	ACt	2	1	0.5	9719-9721
ORF1ab/nsp4	389	H389T	H3152T	nonsyn	CAT	ACA	2	1	0.5	9719-9721
ORF1ab/nsp4	389	H389del2	H3152del2	del	CAt	--t	2	1	0.5	9719-9721
ORF1ab/nsp4	389	H389del2	H3152del2	del	cAT	c--	2	1	0.5	9719-9721
ORF1ab/nsp4	389	H389I	H3152I	nonsyn	CAt	ATt	1	1	1	9719-9721
ORF1ab/nsp4	389	H389F	H3152F	nonsyn	CAt	TTt	1	1	1	9719-9721
ORF1ab/nsp4	389	H389E	H3152E	nonsyn	CaT	GaA	1	1	1	9719-9721
ORF1ab/nsp4	389	H389K	H3152K	nonsyn	CaT	AaA	1	1	1	9719-9721

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/nsp4	389	H389H	caT	caC	754	754	All	0.000144
ORF1ab/nsp4	389	H389H	caT	caC	328	328	AW.1	1
ORF1ab/nsp4	389	H389del	CAT	---	110	110	All	0.000021
ORF1ab/nsp4	389	H389Q	caT	caG	62	110	All	0.000012
ORF1ab/nsp4	389	H389Q	caT	caA	48	110	All	0.000009
ORF1ab/nsp4	389	H389H	caT	caC	98	98	B.1.1.7	0.000088
ORF1ab/nsp4	389	H389H	caT	caC	61	61	P.1.14	0.002916
ORF1ab/nsp4	389	H389del	CAT	---	48	48	B.1.1.7	0.000043
ORF1ab/nsp4	389	H389Q	caT	caA	35	37	AY.103	0.000217
ORF1ab/nsp4	389	H389Q	caT	caG	2	37	AY.103	0.000012
ORF1ab/nsp4	389	H389H	caT	caC	31	31	AY.4	0.000048
ORF1ab/nsp4	389	H389Q	caT	caG	31	31	B.1.517	0.013237
ORF1ab/nsp4	389	H389H	caT	caC	20	20	B.1.1.464	0.029455
ORF1ab/nsp4	389	H389H	caT	caC	19	19	AY.9	0.001284
ORF1ab/nsp4	389	H389H	caT	caC	18	18	AY.103	0.000112
ORF1ab/nsp4	389	H389N	Cat	Aat	16	16	All	0.000003
ORF1ab/nsp4	389	H389H	caT	caC	16	16	B.1.177	0.000211
ORF1ab/nsp4	389	H389Y	Cat	Tat	12	15	All	0.000002
ORF1ab/nsp4	389	H389Y	CaT	TaC	3	15	All	0.000001
ORF1ab/nsp4	389	H389H	caT	caC	14	14	AY.43	0.000062
ORF1ab/nsp4	389	H389H	caT	caC	14	14	B.1.2	0.000123
ORF1ab/nsp4	389	H389H	caT	caC	14	14	B.1.617.2	0.000053
ORF1ab/nsp4	389	H389H	caT	caC	13	13	AY.20	0.000505
ORF1ab/nsp4	389	H389H	caT	caC	13	13	AY.33	0.000868
ORF1ab/nsp4	389	H389H	caT	caC	10	10	B.1	0.000092
ORF1ab/nsp4	389	H389H	caT	caC	9	9	AY.23	0.000628
ORF1ab/nsp4	389	H389H	caT	caC	9	9	B.1.1.192	0.020785
ORF1ab/nsp4	389	H389del	CAT	---	9	9	B.1.177	0.000119
ORF1ab/nsp4	389	H389del	CAT	---	8	8	AY.4.5	0.00086
ORF1ab/nsp4	389	H389del	CAT	---	7	7	AY.4	0.000011
ORF1ab/nsp4	389	H389Q	caT	caA	6	6	AY.4.2	0.00013
ORF1ab/nsp4	389	H389L	cAt	cTt	5	5	All	0.000001
ORF1ab/nsp4	389	H389P	cAt	cCt	4	5	All	0.000001
ORF1ab/nsp4	389	H389del1	caT	ca-	3	5	All	0.000001
ORF1ab/nsp4	389	H389del1	CAt	T-t	1	5	All	0
ORF1ab/nsp4	389	H389P	cAT	cCA	1	5	All	0
ORF1ab/nsp4	389	H389del1	Cat	-at	1	5	All	0
ORF1ab/nsp4	389	H389Q	caT	caG	4	5	AY.4	0.000006
ORF1ab/nsp4	389	H389Q	caT	caA	1	5	AY.4	0.000002
ORF1ab/nsp4	389	H389H	caT	caC	5	5	AY.47	0.000156
ORF1ab/nsp4	389	H389D	Cat	Gat	4	4	All	0.000001
ORF1ab/nsp4	389	H389H	caT	caC	4	4	AY.102	0.000106
ORF1ab/nsp4	389	H389del	CAT	---	4	4	AY.43	0.000018
ORF1ab/nsp4	389	H389H	caT	caC	4	4	AY.44	0.000024
ORF1ab/nsp4	389	H389N	Cat	Aat	4	4	B.1	0.000037
ORF1ab/nsp4	389	H389Q	caT	caG	3	4	B.1.1	0.000054
ORF1ab/nsp4	389	H389Q	caT	caA	1	4	B.1.1	0.000018
ORF1ab/nsp4	389	H389Y	Cat	Tat	4	4	B.1.1.7	0.000004
ORF1ab/nsp4	389	H389Q	caT	caG	4	4	B.1.177.81	0.000757
ORF1ab/nsp4	389	H389H	caT	caC	4	4	B.1.526	0.000094
ORF1ab/nsp4	389	H389Y	CaT	TaC	2	3		0.111111
ORF1ab/nsp4	389	H389Y	Cat	Tat	1	3		0.055556
ORF1ab/nsp4	389	H389H	caT	caC	3	3	AY.25	0.000018
ORF1ab/nsp4	389	H389H	caT	caC	3	3	AY.42	0.000121
ORF1ab/nsp4	389	H389N	Cat	Aat	3	3	AY.44	0.000018
ORF1ab/nsp4	389	H389H	caT	caC	3	3	AY.79	0.003632
ORF1ab/nsp4	389	H389H	caT	caC	3	3	B.1.1	0.000054
ORF1ab/nsp4	389	H389H	caT	caC	3	3	B.1.36.29	0.001552
ORF1ab/nsp4	389	H389H	caT	caC	3	3	P.1	0.000047
ORF1ab/nsp4	389	H389V	CAt	GTt	2	2		0.111111
ORF1ab/nsp4	389	H389del	CAT	---	2	2		0.111111
ORF1ab/nsp4	389	H389H	caT	caC	2	2		0.111111
ORF1ab/nsp4	389	H389S	CAt	TCt	2	2		0.111111
ORF1ab/nsp4	389	H389T	CAt	ACt	1	2		0.055556
ORF1ab/nsp4	389	H389P	cAt	cCt	1	2		0.055556
ORF1ab/nsp4	389	H389A	CAT	GCA	1	2		0.055556
ORF1ab/nsp4	389	H389A	CAt	GCt	1	2		0.055556
ORF1ab/nsp4	389	H389P	cAT	cCA	1	2		0.055556
ORF1ab/nsp4	389	H389T	CAT	ACA	1	2		0.055556
ORF1ab/nsp4	389	H389S	CAt	TCt	2	2	All	0
ORF1ab/nsp4	389	H389V	CAt	GTt	2	2	All	0
ORF1ab/nsp4	389	H389R	cAt	cGt	2	2	All	0
ORF1ab/nsp4	389	H389del2	cAT	c--	1	2	All	0
ORF1ab/nsp4	389	H389A	CAT	GCA	1	2	All	0
ORF1ab/nsp4	389	H389del2	CAt	--t	1	2	All	0
ORF1ab/nsp4	389	H389T	CAT	ACA	1	2	All	0
ORF1ab/nsp4	389	H389A	CAt	GCt	1	2	All	0
ORF1ab/nsp4	389	H389T	CAt	ACt	1	2	All	0
ORF1ab/nsp4	389	H389Q	caT	caA	2	2	AY.114	0.000462
ORF1ab/nsp4	389	H389Q	caT	caG	2	2	AY.121	0.000271
ORF1ab/nsp4	389	H389Q	caT	caG	2	2	AY.25	0.000012
ORF1ab/nsp4	389	H389Q	caT	caG	2	2	AY.39	0.000049
ORF1ab/nsp4	389	H389H	caT	caC	2	2	AY.39.1	0.000079
ORF1ab/nsp4	389	H389Q	caT	caG	2	2	AY.44	0.000012
ORF1ab/nsp4	389	H389del1	caT	ca-	1	2	AY.44	0.000006
ORF1ab/nsp4	389	H389del1	CAt	T-t	1	2	AY.44	0.000006
ORF1ab/nsp4	389	H389N	Cat	Aat	2	2	AY.45	0.000243
ORF1ab/nsp4	389	H389N	Cat	Aat	2	2	AY.5	0.000041
ORF1ab/nsp4	389	H389H	caT	caC	2	2	AY.5	0.000041
ORF1ab/nsp4	389	H389L	cAt	cTt	2	2	B	0.000256
ORF1ab/nsp4	389	H389Q	caT	caG	2	2	B.1.177	0.000026
ORF1ab/nsp4	389	H389del	CAT	---	2	2	B.1.177.69	0.002967
ORF1ab/nsp4	389	H389del	CAT	---	2	2	B.1.2	0.000018
ORF1ab/nsp4	389	H389H	caT	caC	2	2	B.1.258	0.000133
ORF1ab/nsp4	389	H389Q	caT	caG	2	2	B.1.617.2	0.000008
ORF1ab/nsp4	389	H389H	caT	caC	2	2	B.1.619.1	0.001283
ORF1ab/nsp4	389	H389E	CaT	GaA	1	1		0.055556
ORF1ab/nsp4	389	H389Q	caT	caA	1	1		0.055556
ORF1ab/nsp4	389	H389N	Cat	Aat	1	1		0.055556
ORF1ab/nsp4	389	H389K	CaT	AaA	1	1		0.055556
ORF1ab/nsp4	389	H389D	Cat	Gat	1	1		0.055556
ORF1ab/nsp4	389	H389del	CAT	---	1	1	AD.2	0.000219
ORF1ab/nsp4	389	H389H	caT	caC	1	1	AL.1	0.012987
ORF1ab/nsp4	389	H389I	CAt	ATt	1	1	All	0
ORF1ab/nsp4	389	H389K	CaT	AaA	1	1	All	0
ORF1ab/nsp4	389	H389E	CaT	GaA	1	1	All	0
ORF1ab/nsp4	389	H389F	CAt	TTt	1	1	All	0
ORF1ab/nsp4	389	H389Q	caT	caG	1	1	AU.1	0.001266
ORF1ab/nsp4	389	H389del1	caT	ca-	1	1	AY.103	0.000006
ORF1ab/nsp4	389	H389H	caT	caC	1	1	AY.104	0.001984
ORF1ab/nsp4	389	H389del	CAT	---	1	1	AY.106	0.000335
ORF1ab/nsp4	389	H389H	caT	caC	1	1	AY.110	0.000113
ORF1ab/nsp4	389	H389Y	Cat	Tat	1	1	AY.119	0.000035
ORF1ab/nsp4	389	H389del	CAT	---	1	1	AY.19	0.00114
ORF1ab/nsp4	389	H389Q	caT	caG	1	1	AY.20	0.000039
ORF1ab/nsp4	389	H389N	Cat	Aat	1	1	AY.25	0.000006
ORF1ab/nsp4	389	H389H	caT	caC	1	1	AY.29	0.000016
ORF1ab/nsp4	389	H389H	caT	caC	1	1	AY.3	0.00001
ORF1ab/nsp4	389	H389H	caT	caC	1	1	AY.3.1	0.000085
ORF1ab/nsp4	389	H389H	caT	caC	1	1	AY.4.2.1	0.000149
ORF1ab/nsp4	389	H389del	CAT	---	1	1	AY.4.3	0.000842
ORF1ab/nsp4	389	H389I	CAt	ATt	1	1	AY.44	0.000006
ORF1ab/nsp4	389	H389H	caT	caC	1	1	AY.45	0.000122
ORF1ab/nsp4	389	H389del	CAT	---	1	1	AY.46.2	0.000635
ORF1ab/nsp4	389	H389H	caT	caC	1	1	AY.54	0.000095
ORF1ab/nsp4	389	H389Q	caT	caG	1	1	AY.58	0.000907
ORF1ab/nsp4	389	H389del	CAT	---	1	1	AY.6	0.000041
ORF1ab/nsp4	389	H389H	caT	caC	1	1	AY.61	0.000105
ORF1ab/nsp4	389	H389del	CAT	---	1	1	AY.68	0.000274
ORF1ab/nsp4	389	H389H	caT	caC	1	1	AY.75.1	0.00018
ORF1ab/nsp4	389	H389del	CAT	---	1	1	AY.9	0.000068
ORF1ab/nsp4	389	H389R	cAt	cGt	1	1	AY.9.2	0.000037
ORF1ab/nsp4	389	H389H	caT	caC	1	1	AY.9.2	0.000037
ORF1ab/nsp4	389	H389del	CAT	---	1	1	AY.99	0.001049
ORF1ab/nsp4	389	H389del	CAT	---	1	1	AY.99.1	0.001553
ORF1ab/nsp4	389	H389L	cAt	cTt	1	1	B.1	0.000009
ORF1ab/nsp4	389	H389Q	caT	caA	1	1	B.1	0.000009
ORF1ab/nsp4	389	H389del	CAT	---	1	1	B.1.1	0.000018
ORF1ab/nsp4	389	H389Y	CaT	TaC	1	1	B.1.1	0.000018
ORF1ab/nsp4	389	H389P	cAt	cCt	1	1	B.1.1	0.000018
ORF1ab/nsp4	389	H389del	CAT	---	1	1	B.1.1.139	0.022727
ORF1ab/nsp4	389	H389Y	Cat	Tat	1	1	B.1.1.174	0.003378
ORF1ab/nsp4	389	H389del	CAT	---	1	1	B.1.1.236	0.006897
ORF1ab/nsp4	389	H389H	caT	caC	1	1	B.1.1.28	0.000311
ORF1ab/nsp4	389	H389Y	Cat	Tat	1	1	B.1.1.331	0.011628
ORF1ab/nsp4	389	H389Q	caT	caG	1	1	B.1.1.369	0.000446
ORF1ab/nsp4	389	H389del	CAT	---	1	1	B.1.1.37	0.000193
ORF1ab/nsp4	389	H389Q	caT	caG	1	1	B.1.1.377	0.001381
ORF1ab/nsp4	389	H389D	Cat	Gat	1	1	B.1.1.7	0.000001
ORF1ab/nsp4	389	H389del1	Cat	-at	1	1	B.1.1.7	0.000001
ORF1ab/nsp4	389	H389del2	CAt	--t	1	1	B.1.1.7	0.000001
ORF1ab/nsp4	389	H389L	cAt	cTt	1	1	B.1.1.7	0.000001
ORF1ab/nsp4	389	H389del	CAT	---	1	1	B.1.1.70	0.000341
ORF1ab/nsp4	389	H389Q	caT	caG	1	1	B.1.160	0.000031
ORF1ab/nsp4	389	H389P	cAt	cCt	1	1	B.1.160.7	0.002079
ORF1ab/nsp4	389	H389H	caT	caC	1	1	B.1.167	0.007812
ORF1ab/nsp4	389	H389D	Cat	Gat	1	1	B.1.177	0.000013
ORF1ab/nsp4	389	H389L	cAt	cTt	1	1	B.1.177	0.000013
ORF1ab/nsp4	389	H389del	CAT	---	1	1	B.1.177.11	0.001698
ORF1ab/nsp4	389	H389del	CAT	---	1	1	B.1.177.17	0.000821
ORF1ab/nsp4	389	H389H	caT	caC	1	1	B.1.177.21	0.000076
ORF1ab/nsp4	389	H389del2	cAT	c--	1	1	B.1.177.4	0.000211
ORF1ab/nsp4	389	H389del	CAT	---	1	1	B.1.177.4	0.000211
ORF1ab/nsp4	389	H389del	CAT	---	1	1	B.1.177.55	0.002331
ORF1ab/nsp4	389	H389del	CAT	---	1	1	B.1.177.56	0.000668
ORF1ab/nsp4	389	H389del	CAT	---	1	1	B.1.177.58	0.001332
ORF1ab/nsp4	389	H389H	caT	caC	1	1	B.1.177.60	0.000218
ORF1ab/nsp4	389	H389del	CAT	---	1	1	B.1.177.76	0.002494
ORF1ab/nsp4	389	H389H	caT	caC	1	1	B.1.189	0.004292
ORF1ab/nsp4	389	H389Y	Cat	Tat	1	1	B.1.2	0.000009
ORF1ab/nsp4	389	H389del1	caT	ca-	1	1	B.1.2	0.000009
ORF1ab/nsp4	389	H389del	CAT	---	1	1	B.1.258.3	0.001675
ORF1ab/nsp4	389	H389H	caT	caC	1	1	B.1.320	0.001245
ORF1ab/nsp4	389	H389H	caT	caC	1	1	B.1.351	0.00003
ORF1ab/nsp4	389	H389N	Cat	Aat	1	1	B.1.351.3	0.000876
ORF1ab/nsp4	389	H389del	CAT	---	1	1	B.1.36.17	0.000494
ORF1ab/nsp4	389	H389del	CAT	---	1	1	B.1.36.38	0.001642
ORF1ab/nsp4	389	H389H	caT	caC	1	1	B.1.427	0.00005
ORF1ab/nsp4	389	H389Q	caT	caA	1	1	B.1.576	0.000907
ORF1ab/nsp4	389	H389Y	Cat	Tat	1	1	B.1.596	0.000087
ORF1ab/nsp4	389	H389H	caT	caC	1	1	B.1.596	0.000087
ORF1ab/nsp4	389	H389D	Cat	Gat	1	1	B.1.596	0.000087
ORF1ab/nsp4	389	H389Y	Cat	Tat	1	1	B.1.617.1	0.000129
ORF1ab/nsp4	389	H389del	CAT	---	1	1	B.1.617.2	0.000004
ORF1ab/nsp4	389	H389N	Cat	Aat	1	1	B.1.617.2	0.000004
ORF1ab/nsp4	389	H389Y	Cat	Tat	1	1	B.1.617.2	0.000004
ORF1ab/nsp4	389	H389F	CAt	TTt	1	1	C.35	0.000774
ORF1ab/nsp4	389	H389R	cAt	cGt	1	1	D.3	0.005917
ORF1ab/nsp4	389	H389P	cAt	cCt	1	1	P.1.1	0.000318
ORF1ab/nsp4	389	H389H	caT	caC	1	1	P.1.17	0.000162
ORF1ab/nsp4	389	H389del	CAT	---	1	1	Q.1	0.000126
ORF1ab/nsp4	389	H389del	CAT	---	1	1	U.3	0.003861
ORF1ab/nsp4	389	H389N	Cat	Aat	1	1	W.1	0.008696

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.