CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp8 : CodonNum = 43

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/nsp8	43	N43H	N3985H	nonsyn	Aat	Cat	543	542	0.998158	12218-12220
ORF1ab/nsp8	43	N43H	N3985H	nonsyn	AaT	CaC	543	1	0.00184162	12218-12220
ORF1ab/nsp8	43	N43N	N3985N	syn	aaT	aaC	245	245	1	12218-12220
ORF1ab/nsp8	43	N43S	N3985S	nonsyn	aAt	aGt	12	12	1	12218-12220
ORF1ab/nsp8	43	N43del	N3985del	del	AAT	---	6	6	1	12218-12220
ORF1ab/nsp8	43	N43Y	N3985Y	nonsyn	Aat	Tat	5	5	1	12218-12220
ORF1ab/nsp8	43	N43del1	N3985del1	del	aaT	aa-	3	3	1	12218-12220
ORF1ab/nsp8	43	N43K	N3985K	nonsyn	aaT	aaA	3	2	0.666667	12218-12220
ORF1ab/nsp8	43	N43K	N3985K	nonsyn	aaT	aaG	3	1	0.333333	12218-12220
ORF1ab/nsp8	43	N43I	N3985I	nonsyn	aAt	aTt	2	2	1	12218-12220
ORF1ab/nsp8	43	N43A	N3985A	nonsyn	AAt	GCt	2	2	1	12218-12220
ORF1ab/nsp8	43	N43D	N3985D	nonsyn	Aat	Gat	2	2	1	12218-12220
ORF1ab/nsp8	43	N43T	N3985T	nonsyn	aAt	aCt	1	1	1	12218-12220

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/nsp8	43	N43H	Aat	Cat	542	543	All	0.000104
ORF1ab/nsp8	43	N43H	AaT	CaC	1	543	All	0
ORF1ab/nsp8	43	N43H	Aat	Cat	524	524	L.1	0.998095
ORF1ab/nsp8	43	N43N	aaT	aaC	245	245	All	0.000047
ORF1ab/nsp8	43	N43N	aaT	aaC	79	79	AY.4	0.000123
ORF1ab/nsp8	43	N43N	aaT	aaC	25	25	B.1.617.2	0.000094
ORF1ab/nsp8	43	N43N	aaT	aaC	23	23	B.1.1.7	0.000021
ORF1ab/nsp8	43	N43N	aaT	aaC	18	18	B.1.427	0.000909
ORF1ab/nsp8	43	N43N	aaT	aaC	13	13	AY.102	0.000345
ORF1ab/nsp8	43	N43S	aAt	aGt	12	12	All	0.000002
ORF1ab/nsp8	43	N43N	aaT	aaC	10	10	AY.25	0.00006
ORF1ab/nsp8	43	N43N	aaT	aaC	9	9	AY.9.1	0.000754
ORF1ab/nsp8	43	N43N	aaT	aaC	9	9	B.1.351	0.000268
ORF1ab/nsp8	43	N43N	aaT	aaC	8	8	AY.44	0.000049
ORF1ab/nsp8	43	N43N	aaT	aaC	7	7	AY.43	0.000031
ORF1ab/nsp8	43	N43N	aaT	aaC	7	7	B.1.243	0.000487
ORF1ab/nsp8	43	N43del	AAT	---	6	6	All	0.000001
ORF1ab/nsp8	43	N43Y	Aat	Tat	5	5	All	0.000001
ORF1ab/nsp8	43	N43N	aaT	aaC	4	4	AY.118	0.000251
ORF1ab/nsp8	43	N43H	Aat	Cat	4	4	AY.25	0.000024
ORF1ab/nsp8	43	N43H	Aat	Cat	4	4	B.1.1.10	0.004459
ORF1ab/nsp8	43	N43N	aaT	aaC	4	4	B.1.160	0.000125
ORF1ab/nsp8	43	N43del1	aaT	aa-	3	3	All	0.000001
ORF1ab/nsp8	43	N43K	aaT	aaA	2	3	All	0
ORF1ab/nsp8	43	N43K	aaT	aaG	1	3	All	0
ORF1ab/nsp8	43	N43N	aaT	aaC	3	3	AY.121	0.000406
ORF1ab/nsp8	43	N43H	Aat	Cat	3	3	AY.4	0.000005
ORF1ab/nsp8	43	N43N	aaT	aaC	3	3	AY.46.3	0.002801
ORF1ab/nsp8	43	N43N	aaT	aaC	3	3	AY.9.2	0.00011
ORF1ab/nsp8	43	N43Y	Aat	Tat	3	3	B.1.1.7	0.000003
ORF1ab/nsp8	43	N43I	aAt	aTt	2	2	All	0
ORF1ab/nsp8	43	N43D	Aat	Gat	2	2	All	0
ORF1ab/nsp8	43	N43A	AAt	GCt	2	2	All	0
ORF1ab/nsp8	43	N43H	Aat	Cat	2	2	AY.113	0.000285
ORF1ab/nsp8	43	N43S	aAt	aGt	2	2	AY.119	0.000071
ORF1ab/nsp8	43	N43N	aaT	aaC	2	2	AY.39	0.000049
ORF1ab/nsp8	43	N43N	aaT	aaC	2	2	B.1	0.000018
ORF1ab/nsp8	43	N43del	AAT	---	2	2	B.1	0.000018
ORF1ab/nsp8	43	N43S	aAt	aGt	2	2	B.1.1.7	0.000002
ORF1ab/nsp8	43	N43N	aaT	aaC	2	2	B.1.2	0.000018
ORF1ab/nsp8	43	N43N	aaT	aaC	2	2	B.1.258.17	0.000208
ORF1ab/nsp8	43	N43N	aaT	aaC	2	2	B.1.526	0.000047
ORF1ab/nsp8	43	N43Y	Aat	Tat	1	1		0.055556
ORF1ab/nsp8	43	N43T	aAt	aCt	1	1	All	0
ORF1ab/nsp8	43	N43N	aaT	aaC	1	1	AY.113	0.000142
ORF1ab/nsp8	43	N43N	aaT	aaC	1	1	AY.12	0.000316
ORF1ab/nsp8	43	N43H	Aat	Cat	1	1	AY.120.2.1	0.000498
ORF1ab/nsp8	43	N43del	AAT	---	1	1	AY.25	0.000006
ORF1ab/nsp8	43	N43S	aAt	aGt	1	1	AY.29	0.000016
ORF1ab/nsp8	43	N43T	aAt	aCt	1	1	AY.3	0.00001
ORF1ab/nsp8	43	N43N	aaT	aaC	1	1	AY.3	0.00001
ORF1ab/nsp8	43	N43S	aAt	aGt	1	1	AY.4	0.000002
ORF1ab/nsp8	43	N43H	AaT	CaC	1	1	AY.44	0.000006
ORF1ab/nsp8	43	N43K	aaT	aaA	1	1	AY.44	0.000006
ORF1ab/nsp8	43	N43N	aaT	aaC	1	1	AY.47	0.000031
ORF1ab/nsp8	43	N43S	aAt	aGt	1	1	AY.61	0.000105
ORF1ab/nsp8	43	N43S	aAt	aGt	1	1	AY.78	0.001541
ORF1ab/nsp8	43	N43del1	aaT	aa-	1	1	AY.79	0.001211
ORF1ab/nsp8	43	N43N	aaT	aaC	1	1	AY.98	0.000079
ORF1ab/nsp8	43	N43H	Aat	Cat	1	1	B.1	0.000009
ORF1ab/nsp8	43	N43I	aAt	aTt	1	1	B.1	0.000009
ORF1ab/nsp8	43	N43D	Aat	Gat	1	1	B.1	0.000009
ORF1ab/nsp8	43	N43N	aaT	aaC	1	1	B.1.1	0.000018
ORF1ab/nsp8	43	N43H	Aat	Cat	1	1	B.1.1	0.000018
ORF1ab/nsp8	43	N43H	Aat	Cat	1	1	B.1.1.230	0.009174
ORF1ab/nsp8	43	N43S	aAt	aGt	1	1	B.1.1.398	0.003226
ORF1ab/nsp8	43	N43del	AAT	---	1	1	B.1.1.7	0.000001
ORF1ab/nsp8	43	N43K	aaT	aaG	1	1	B.1.1.7	0.000001
ORF1ab/nsp8	43	N43I	aAt	aTt	1	1	B.1.1.7	0.000001
ORF1ab/nsp8	43	N43S	aAt	aGt	1	1	B.1.177	0.000013
ORF1ab/nsp8	43	N43del	AAT	---	1	1	B.1.2	0.000009
ORF1ab/nsp8	43	N43Y	Aat	Tat	1	1	B.1.2	0.000009
ORF1ab/nsp8	43	N43del1	aaT	aa-	1	1	B.1.2	0.000009
ORF1ab/nsp8	43	N43D	Aat	Gat	1	1	B.1.336	0.002439
ORF1ab/nsp8	43	N43N	aaT	aaC	1	1	B.1.416	0.001269
ORF1ab/nsp8	43	N43S	aAt	aGt	1	1	B.1.552	0.015152
ORF1ab/nsp8	43	N43del1	aaT	aa-	1	1	B.1.595	0.000261
ORF1ab/nsp8	43	N43N	aaT	aaC	1	1	B.1.596	0.000087
ORF1ab/nsp8	43	N43A	AAt	GCt	1	1	B.1.617.2	0.000004
ORF1ab/nsp8	43	N43S	aAt	aGt	1	1	B.1.617.2	0.000004
ORF1ab/nsp8	43	N43N	aaT	aaC	1	1	B.1.628	0.000352
ORF1ab/nsp8	43	N43K	aaT	aaA	1	1	B.1.637	0.000073
ORF1ab/nsp8	43	N43A	AAt	GCt	1	1	C.17	0.055556
ORF1ab/nsp8	43	N43del	AAT	---	1	1	N.4	0.004255
ORF1ab/nsp8	43	N43H	Aat	Cat	1	1	P.1.7	0.000319
ORF1ab/nsp8	43	N43N	aaT	aaC	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.