CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp16 : CodonNum = 225

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/nsp16	225	H225H	H7023H	syn	caT	caC	1159	1159	1	21331-21333
ORF1ab/nsp16	225	H225del	H7023del	del	CAT	---	107	107	1	21331-21333
ORF1ab/nsp16	225	H225Y	H7023Y	nonsyn	Cat	Tat	50	47	0.94	21331-21333
ORF1ab/nsp16	225	H225Y	H7023Y	nonsyn	CaT	TaC	50	3	0.06	21331-21333
ORF1ab/nsp16	225	H225Q	H7023Q	nonsyn	caT	caG	20	14	0.7	21331-21333
ORF1ab/nsp16	225	H225Q	H7023Q	nonsyn	caT	caA	20	6	0.3	21331-21333
ORF1ab/nsp16	225	H225P	H7023P	nonsyn	cAt	cCt	9	7	0.777778	21331-21333
ORF1ab/nsp16	225	H225P	H7023P	nonsyn	cAT	cCG	9	1	0.111111	21331-21333
ORF1ab/nsp16	225	H225P	H7023P	nonsyn	cAT	cCA	9	1	0.111111	21331-21333
ORF1ab/nsp16	225	H225N	H7023N	nonsyn	Cat	Aat	6	6	1	21331-21333
ORF1ab/nsp16	225	H225del1	H7023del1	del	caT	ca-	6	3	0.5	21331-21333
ORF1ab/nsp16	225	H225del1	H7023del1	del	cAt	c-t	6	2	0.333333	21331-21333
ORF1ab/nsp16	225	H225del1	H7023del1	del	Cat	-at	6	1	0.166667	21331-21333
ORF1ab/nsp16	225	H225R	H7023R	nonsyn	cAt	cGt	5	4	0.8	21331-21333
ORF1ab/nsp16	225	H225I	H7023I	nonsyn	CAT	ATC	5	4	0.8	21331-21333
ORF1ab/nsp16	225	H225R	H7023R	nonsyn	cAT	cGG	5	1	0.2	21331-21333
ORF1ab/nsp16	225	H225I	H7023I	nonsyn	CAt	ATt	5	1	0.2	21331-21333
ORF1ab/nsp16	225	H225del2	H7023del2	del	CAT	--N	3	2	0.666667	21331-21333
ORF1ab/nsp16	225	H225del2	H7023del2	del	CAt	--t	3	1	0.333333	21331-21333
ORF1ab/nsp16	225	H225C	H7023C	nonsyn	CAt	TGt	2	2	1	21331-21333
ORF1ab/nsp16	225	H225L	H7023L	nonsyn	cAt	cTt	2	2	1	21331-21333
ORF1ab/nsp16	225	H225A	H7023A	nonsyn	CAt	GCt	2	1	0.5	21331-21333
ORF1ab/nsp16	225	H225A	H7023A	nonsyn	CAT	GCA	2	1	0.5	21331-21333
ORF1ab/nsp16	225	H225S	H7023S	nonsyn	CAt	TCt	2	1	0.5	21331-21333
ORF1ab/nsp16	225	H225S	H7023S	nonsyn	CAT	TCC	2	1	0.5	21331-21333
ORF1ab/nsp16	225	H225X	H7023X	nonsyn	CaT	TaA	1	1	1	21331-21333
ORF1ab/nsp16	225	H225E	H7023E	nonsyn	CaT	GaA	1	1	1	21331-21333
ORF1ab/nsp16	225	H225V	H7023V	nonsyn	CAt	GTt	1	1	1	21331-21333
ORF1ab/nsp16	225	H225F	H7023F	nonsyn	CAT	TTC	1	1	1	21331-21333
ORF1ab/nsp16	225	H225D	H7023D	nonsyn	Cat	Gat	1	1	1	21331-21333

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/nsp16	225	H225H	caT	caC	1159	1159	All	0.000222
ORF1ab/nsp16	225	H225H	caT	caC	451	451	B.1.127	0.991209
ORF1ab/nsp16	225	H225H	caT	caC	438	438	B.1	0.004012
ORF1ab/nsp16	225	H225H	caT	caC	124	124	B.1.617.2	0.000467
ORF1ab/nsp16	225	H225del	CAT	---	107	107	All	0.00002
ORF1ab/nsp16	225	H225H	caT	caC	64	64	B.1.2	0.000564
ORF1ab/nsp16	225	H225Y	Cat	Tat	47	50	All	0.000009
ORF1ab/nsp16	225	H225Y	CaT	TaC	3	50	All	0.000001
ORF1ab/nsp16	225	H225H	caT	caC	22	22	B.1.1.7	0.00002
ORF1ab/nsp16	225	H225Q	caT	caG	14	20	All	0.000003
ORF1ab/nsp16	225	H225Q	caT	caA	6	20	All	0.000001
ORF1ab/nsp16	225	H225del	CAT	---	12	12	B.1.2	0.000106
ORF1ab/nsp16	225	H225del	CAT	---	11	11	B.1	0.000101
ORF1ab/nsp16	225	H225del	CAT	---	10	10	AY.43	0.000044
ORF1ab/nsp16	225	H225P	cAt	cCt	7	9	All	0.000001
ORF1ab/nsp16	225	H225P	cAT	cCA	1	9	All	0
ORF1ab/nsp16	225	H225P	cAT	cCG	1	9	All	0
ORF1ab/nsp16	225	H225del	CAT	---	9	9	B.1.1.7	0.000008
ORF1ab/nsp16	225	H225H	caT	caC	7	7	AY.25	0.000042
ORF1ab/nsp16	225	H225Y	Cat	Tat	7	7	B.1	0.000064
ORF1ab/nsp16	225	H225N	Cat	Aat	6	6	All	0.000001
ORF1ab/nsp16	225	H225del1	caT	ca-	3	6	All	0.000001
ORF1ab/nsp16	225	H225del1	cAt	c-t	2	6	All	0
ORF1ab/nsp16	225	H225del1	Cat	-at	1	6	All	0
ORF1ab/nsp16	225	H225del	CAT	---	6	6	P.1	0.000095
ORF1ab/nsp16	225	H225R	cAt	cGt	4	5	All	0.000001
ORF1ab/nsp16	225	H225I	CAT	ATC	4	5	All	0.000001
ORF1ab/nsp16	225	H225R	cAT	cGG	1	5	All	0
ORF1ab/nsp16	225	H225I	CAt	ATt	1	5	All	0
ORF1ab/nsp16	225	H225Q	caT	caG	4	5	B.1	0.000037
ORF1ab/nsp16	225	H225Q	caT	caA	1	5	B.1	0.000009
ORF1ab/nsp16	225	H225del	CAT	---	5	5	B.1.617.2	0.000019
ORF1ab/nsp16	225	H225H	caT	caC	4	4	AY.47	0.000124
ORF1ab/nsp16	225	H225Y	Cat	Tat	4	4	B.1.1.7	0.000004
ORF1ab/nsp16	225	H225Y	Cat	Tat	4	4	B.1.177	0.000053
ORF1ab/nsp16	225	H225del2	CAT	--N	2	3	All	0
ORF1ab/nsp16	225	H225del2	CAt	--t	1	3	All	0
ORF1ab/nsp16	225	H225H	caT	caC	3	3	AY.103	0.000019
ORF1ab/nsp16	225	H225H	caT	caC	3	3	AY.4	0.000005
ORF1ab/nsp16	225	H225del	CAT	---	3	3	AY.4	0.000005
ORF1ab/nsp16	225	H225H	caT	caC	3	3	AY.4.2.1	0.000447
ORF1ab/nsp16	225	H225H	caT	caC	3	3	AY.43	0.000013
ORF1ab/nsp16	225	H225I	CAT	ATC	3	3	B.1.398	0.008929
ORF1ab/nsp16	225	H225del	CAT	---	3	3	B.1.525	0.000339
ORF1ab/nsp16	225	H225Y	CaT	TaC	2	2		0.111111
ORF1ab/nsp16	225	H225del	CAT	---	2	2		0.111111
ORF1ab/nsp16	225	H225del	CAT	---	2	2	A.2.4	0.006734
ORF1ab/nsp16	225	H225Y	Cat	Tat	2	2	A.2.4	0.006734
ORF1ab/nsp16	225	H225L	cAt	cTt	2	2	All	0
ORF1ab/nsp16	225	H225C	CAt	TGt	2	2	All	0
ORF1ab/nsp16	225	H225A	CAT	GCA	1	2	All	0
ORF1ab/nsp16	225	H225S	CAt	TCt	1	2	All	0
ORF1ab/nsp16	225	H225S	CAT	TCC	1	2	All	0
ORF1ab/nsp16	225	H225A	CAt	GCt	1	2	All	0
ORF1ab/nsp16	225	H225H	caT	caC	2	2	AY.102	0.000053
ORF1ab/nsp16	225	H225del	CAT	---	2	2	AY.25	0.000012
ORF1ab/nsp16	225	H225Q	caT	caG	1	2	AY.26	0.000028
ORF1ab/nsp16	225	H225Q	caT	caA	1	2	AY.26	0.000028
ORF1ab/nsp16	225	H225H	caT	caC	2	2	AY.3	0.00002
ORF1ab/nsp16	225	H225del	CAT	---	2	2	AY.33	0.000134
ORF1ab/nsp16	225	H225H	caT	caC	2	2	AY.4.2	0.000043
ORF1ab/nsp16	225	H225S	CAt	TCt	1	2	AY.43	0.000004
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	2	AY.43	0.000004
ORF1ab/nsp16	225	H225Y	CaT	TaC	1	2	AY.43	0.000004
ORF1ab/nsp16	225	H225S	CAT	TCC	1	2	AY.43	0.000004
ORF1ab/nsp16	225	H225A	CAt	GCt	1	2	B.1	0.000009
ORF1ab/nsp16	225	H225P	cAT	cCA	1	2	B.1	0.000009
ORF1ab/nsp16	225	H225A	CAT	GCA	1	2	B.1	0.000009
ORF1ab/nsp16	225	H225P	cAt	cCt	1	2	B.1	0.000009
ORF1ab/nsp16	225	H225del	CAT	---	2	2	B.1.1	0.000036
ORF1ab/nsp16	225	H225del1	cAt	c-t	1	2	B.1.1	0.000018
ORF1ab/nsp16	225	H225del1	Cat	-at	1	2	B.1.1	0.000018
ORF1ab/nsp16	225	H225Q	caT	caG	2	2	B.1.1.7	0.000002
ORF1ab/nsp16	225	H225del	CAT	---	2	2	B.1.177	0.000026
ORF1ab/nsp16	225	H225H	caT	caC	2	2	B.1.177.42	0.001789
ORF1ab/nsp16	225	H225Q	caT	caG	2	2	B.1.2	0.000018
ORF1ab/nsp16	225	H225Y	Cat	Tat	2	2	B.1.2	0.000018
ORF1ab/nsp16	225	H225H	caT	caC	2	2	B.1.222	0.003384
ORF1ab/nsp16	225	H225P	cAt	cCt	2	2	B.1.235	0.005038
ORF1ab/nsp16	225	H225del	CAT	---	2	2	B.1.351	0.000059
ORF1ab/nsp16	225	H225H	caT	caC	2	2	B.1.36.29	0.001035
ORF1ab/nsp16	225	H225Y	Cat	Tat	2	2	B.1.429	0.000047
ORF1ab/nsp16	225	H225del	CAT	---	2	2	B.1.526	0.000047
ORF1ab/nsp16	225	H225del	CAT	---	2	2	B.1.596	0.000174
ORF1ab/nsp16	225	H225del	CAT	---	2	2	B.1.617.1	0.000258
ORF1ab/nsp16	225	H225H	caT	caC	2	2	C.23	0.011628
ORF1ab/nsp16	225	H225del	CAT	---	2	2	C.37	0.000232
ORF1ab/nsp16	225	H225Q	caT	caG	2	2	D.2	0.00015
ORF1ab/nsp16	225	H225Y	Cat	Tat	2	2	D.2	0.00015
ORF1ab/nsp16	225	H225H	caT	caC	2	2	P.2	0.000373
ORF1ab/nsp16	225	H225H	caT	caC	1	1	A.2.4	0.003367
ORF1ab/nsp16	225	H225R	cAt	cGt	1	1	A.2.4	0.003367
ORF1ab/nsp16	225	H225N	Cat	Aat	1	1	A.3	0.002096
ORF1ab/nsp16	225	H225F	CAT	TTC	1	1	All	0
ORF1ab/nsp16	225	H225D	Cat	Gat	1	1	All	0
ORF1ab/nsp16	225	H225E	CaT	GaA	1	1	All	0
ORF1ab/nsp16	225	H225X	CaT	TaA	1	1	All	0
ORF1ab/nsp16	225	H225V	CAt	GTt	1	1	All	0
ORF1ab/nsp16	225	H225del2	CAt	--t	1	1	AV.1	0.005051
ORF1ab/nsp16	225	H225del	CAT	---	1	1	AY.100	0.000046
ORF1ab/nsp16	225	H225del	CAT	---	1	1	AY.102	0.000027
ORF1ab/nsp16	225	H225Q	caT	caG	1	1	AY.103	0.000006
ORF1ab/nsp16	225	H225del	CAT	---	1	1	AY.108	0.001103
ORF1ab/nsp16	225	H225C	CAt	TGt	1	1	AY.110	0.000113
ORF1ab/nsp16	225	H225del	CAT	---	1	1	AY.110	0.000113
ORF1ab/nsp16	225	H225H	caT	caC	1	1	AY.117	0.000085
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	AY.118	0.000063
ORF1ab/nsp16	225	H225del	CAT	---	1	1	AY.119	0.000035
ORF1ab/nsp16	225	H225H	caT	caC	1	1	AY.16.1	0.00047
ORF1ab/nsp16	225	H225H	caT	caC	1	1	AY.19	0.00114
ORF1ab/nsp16	225	H225H	caT	caC	1	1	AY.23	0.00007
ORF1ab/nsp16	225	H225del2	CAT	--N	1	1	AY.26	0.000028
ORF1ab/nsp16	225	H225H	caT	caC	1	1	AY.29	0.000016
ORF1ab/nsp16	225	H225del	CAT	---	1	1	AY.3	0.00001
ORF1ab/nsp16	225	H225X	CaT	TaA	1	1	AY.3	0.00001
ORF1ab/nsp16	225	H225R	cAt	cGt	1	1	AY.30	0.000396
ORF1ab/nsp16	225	H225H	caT	caC	1	1	AY.36	0.000148
ORF1ab/nsp16	225	H225H	caT	caC	1	1	AY.39	0.000025
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	AY.39.1	0.00004
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	AY.4	0.000002
ORF1ab/nsp16	225	H225del	CAT	---	1	1	AY.42	0.00004
ORF1ab/nsp16	225	H225P	cAT	cCG	1	1	AY.43	0.000004
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	AY.44	0.000006
ORF1ab/nsp16	225	H225del	CAT	---	1	1	AY.44	0.000006
ORF1ab/nsp16	225	H225R	cAt	cGt	1	1	AY.46.3	0.000934
ORF1ab/nsp16	225	H225N	Cat	Aat	1	1	AY.46.4	0.000165
ORF1ab/nsp16	225	H225del1	caT	ca-	1	1	AY.46.6	0.000072
ORF1ab/nsp16	225	H225del	CAT	---	1	1	AY.54	0.000095
ORF1ab/nsp16	225	H225V	CAt	GTt	1	1	AY.59	0.00053
ORF1ab/nsp16	225	H225del	CAT	---	1	1	AY.59	0.00053
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	AY.67	0.000464
ORF1ab/nsp16	225	H225del	CAT	---	1	1	AY.68	0.000274
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	AY.74	0.000116
ORF1ab/nsp16	225	H225H	caT	caC	1	1	AY.85	0.000427
ORF1ab/nsp16	225	H225del	CAT	---	1	1	AY.9.2	0.000037
ORF1ab/nsp16	225	H225H	caT	caC	1	1	AY.92	0.000287
ORF1ab/nsp16	225	H225del	CAT	---	1	1	AY.95	0.000761
ORF1ab/nsp16	225	H225del	CAT	---	1	1	AY.99	0.001049
ORF1ab/nsp16	225	H225R	cAT	cGG	1	1	B.1	0.000009
ORF1ab/nsp16	225	H225del2	CAT	--N	1	1	B.1	0.000009
ORF1ab/nsp16	225	H225N	Cat	Aat	1	1	B.1	0.000009
ORF1ab/nsp16	225	H225L	cAt	cTt	1	1	B.1	0.000009
ORF1ab/nsp16	225	H225I	CAT	ATC	1	1	B.1	0.000009
ORF1ab/nsp16	225	H225E	CaT	GaA	1	1	B.1	0.000009
ORF1ab/nsp16	225	H225D	Cat	Gat	1	1	B.1	0.000009
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	B.1.1	0.000018
ORF1ab/nsp16	225	H225P	cAt	cCt	1	1	B.1.1	0.000018
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	B.1.1.234	0.012048
ORF1ab/nsp16	225	H225Q	caT	caA	1	1	B.1.1.274	0.005051
ORF1ab/nsp16	225	H225H	caT	caC	1	1	B.1.1.306	0.000438
ORF1ab/nsp16	225	H225del	CAT	---	1	1	B.1.1.306	0.000438
ORF1ab/nsp16	225	H225F	CAT	TTC	1	1	B.1.1.315	0.008475
ORF1ab/nsp16	225	H225C	CAt	TGt	1	1	B.1.1.46	0.004367
ORF1ab/nsp16	225	H225del	CAT	---	1	1	B.1.1.519	0.00004
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	B.1.1.61	0.008772
ORF1ab/nsp16	225	H225H	caT	caC	1	1	B.1.1.63	0.000386
ORF1ab/nsp16	225	H225del1	caT	ca-	1	1	B.1.1.7	0.000001
ORF1ab/nsp16	225	H225R	cAt	cGt	1	1	B.1.1.7	0.000001
ORF1ab/nsp16	225	H225P	cAt	cCt	1	1	B.1.1.7	0.000001
ORF1ab/nsp16	225	H225H	caT	caC	1	1	B.1.160	0.000031
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	B.1.160	0.000031
ORF1ab/nsp16	225	H225Q	caT	caA	1	1	B.1.160	0.000031
ORF1ab/nsp16	225	H225H	caT	caC	1	1	B.1.177	0.000013
ORF1ab/nsp16	225	H225del	CAT	---	1	1	B.1.177.50	0.004695
ORF1ab/nsp16	225	H225del	CAT	---	1	1	B.1.177.60	0.000218
ORF1ab/nsp16	225	H225del	CAT	---	1	1	B.1.177.68	0.015152
ORF1ab/nsp16	225	H225del1	cAt	c-t	1	1	B.1.2	0.000009
ORF1ab/nsp16	225	H225I	CAt	ATt	1	1	B.1.2	0.000009
ORF1ab/nsp16	225	H225del	CAT	---	1	1	B.1.218	0.005155
ORF1ab/nsp16	225	H225Q	caT	caA	1	1	B.1.221	0.000071
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	B.1.234	0.000132
ORF1ab/nsp16	225	H225H	caT	caC	1	1	B.1.258	0.000067
ORF1ab/nsp16	225	H225del	CAT	---	1	1	B.1.258	0.000067
ORF1ab/nsp16	225	H225N	Cat	Aat	1	1	B.1.258	0.000067
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	B.1.258.17	0.000104
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	B.1.36.16	0.001425
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	B.1.36.29	0.000517
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	B.1.369	0.000285
ORF1ab/nsp16	225	H225del	CAT	---	1	1	B.1.416.1	0.001563
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	B.1.420	0.010417
ORF1ab/nsp16	225	H225del	CAT	---	1	1	B.1.429	0.000024
ORF1ab/nsp16	225	H225H	caT	caC	1	1	B.1.429	0.000024
ORF1ab/nsp16	225	H225Q	caT	caA	1	1	B.1.429	0.000024
ORF1ab/nsp16	225	H225H	caT	caC	1	1	B.1.466.2	0.000391
ORF1ab/nsp16	225	H225H	caT	caC	1	1	B.1.470	0.001404
ORF1ab/nsp16	225	H225L	cAt	cTt	1	1	B.1.479	0.038462
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	B.1.502	0.052632
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	B.1.595	0.000261
ORF1ab/nsp16	225	H225P	cAt	cCt	1	1	B.1.596	0.000087
ORF1ab/nsp16	225	H225Q	caT	caG	1	1	B.1.606	0.006024
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	B.1.609	0.000479
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	B.1.617.1	0.000129
ORF1ab/nsp16	225	H225Q	caT	caG	1	1	B.1.617.2	0.000004
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	B.1.617.2	0.000004
ORF1ab/nsp16	225	H225del1	caT	ca-	1	1	B.1.617.2	0.000004
ORF1ab/nsp16	225	H225N	Cat	Aat	1	1	B.1.617.2	0.000004
ORF1ab/nsp16	225	H225del	CAT	---	1	1	B.1.620	0.000946
ORF1ab/nsp16	225	H225H	caT	caC	1	1	B.1.621	0.000089
ORF1ab/nsp16	225	H225del	CAT	---	1	1	B.1.621	0.000089
ORF1ab/nsp16	225	H225N	Cat	Aat	1	1	B.1.637	0.000073
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	B.3	0.000831
ORF1ab/nsp16	225	H225H	caT	caC	1	1	C.2	0.016129
ORF1ab/nsp16	225	H225Y	Cat	Tat	1	1	C.36.3	0.000567
ORF1ab/nsp16	225	H225P	cAt	cCt	1	1	C.37	0.000116
ORF1ab/nsp16	225	H225del	CAT	---	1	1	P.1.15	0.000232
ORF1ab/nsp16	225	H225H	caT	caC	1	1	Q.2	0.000613

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.