CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp8 : CodonNum = 36

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	36	K36Q	K3978Q	nonsyn	Aaa	Caa	450	450	1	12197-12199
ORF1ab/nsp8	36	K36K	K3978K	syn	aaA	aaG	261	261	1	12197-12199
ORF1ab/nsp8	36	K36R	K3978R	nonsyn	aAa	aGa	38	38	1	12197-12199
ORF1ab/nsp8	36	K36del1	K3978del1	del	Aaa	-aa	20	20	1	12197-12199
ORF1ab/nsp8	36	K36del	K3978del	del	AAA	---	18	18	1	12197-12199
ORF1ab/nsp8	36	K36X	K3978X	nonsyn	Aaa	Taa	9	9	1	12197-12199
ORF1ab/nsp8	36	K36N	K3978N	nonsyn	aaA	aaT	9	6	0.666667	12197-12199
ORF1ab/nsp8	36	K36N	K3978N	nonsyn	aaA	aaC	9	3	0.333333	12197-12199
ORF1ab/nsp8	36	K36del2	K3978del2	del	AAa	--a	5	5	1	12197-12199
ORF1ab/nsp8	36	K36E	K3978E	nonsyn	Aaa	Gaa	4	3	0.75	12197-12199
ORF1ab/nsp8	36	K36E	K3978E	nonsyn	AaA	GaG	4	1	0.25	12197-12199
ORF1ab/nsp8	36	K36T	K3978T	nonsyn	aAa	aCa	2	2	1	12197-12199
ORF1ab/nsp8	36	K36G	K3978G	nonsyn	AAa	GGa	2	2	1	12197-12199
ORF1ab/nsp8	36	K36I	K3978I	nonsyn	aAa	aTa	2	2	1	12197-12199

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	36	K36Q	Aaa	Caa	450	450	All	0.000086
ORF1ab/nsp8	36	K36Q	Aaa	Caa	433	433	B.1.574	0.931183
ORF1ab/nsp8	36	K36K	aaA	aaG	261	261	All	0.00005
ORF1ab/nsp8	36	K36K	aaA	aaG	156	156	B.1.1.291	0.115813
ORF1ab/nsp8	36	K36R	aAa	aGa	38	38	All	0.000007
ORF1ab/nsp8	36	K36K	aaA	aaG	38	38	AY.4	0.000059
ORF1ab/nsp8	36	K36del1	Aaa	-aa	20	20	All	0.000004
ORF1ab/nsp8	36	K36del	AAA	---	18	18	All	0.000003
ORF1ab/nsp8	36	K36R	aAa	aGa	15	15	B.1.1.7	0.000013
ORF1ab/nsp8	36	K36K	aaA	aaG	13	13	D.2	0.000976
ORF1ab/nsp8	36	K36K	aaA	aaG	12	12	AY.46.2	0.007624
ORF1ab/nsp8	36	K36Q	Aaa	Caa	10	10	B.1	0.000092
ORF1ab/nsp8	36	K36X	Aaa	Taa	9	9	All	0.000002
ORF1ab/nsp8	36	K36N	aaA	aaT	6	9	All	0.000001
ORF1ab/nsp8	36	K36N	aaA	aaC	3	9	All	0.000001
ORF1ab/nsp8	36	K36del2	AAa	--a	5	5	All	0.000001
ORF1ab/nsp8	36	K36del	AAA	---	5	5	AY.25	0.00003
ORF1ab/nsp8	36	K36K	aaA	aaG	5	5	AY.44	0.00003
ORF1ab/nsp8	36	K36K	aaA	aaG	5	5	B.1.1	0.000091
ORF1ab/nsp8	36	K36K	aaA	aaG	5	5	B.1.1.7	0.000004
ORF1ab/nsp8	36	K36del1	Aaa	-aa	5	5	B.1.2	0.000044
ORF1ab/nsp8	36	K36E	Aaa	Gaa	3	4	All	0.000001
ORF1ab/nsp8	36	K36E	AaA	GaG	1	4	All	0
ORF1ab/nsp8	36	K36K	aaA	aaG	4	4	AY.103	0.000025
ORF1ab/nsp8	36	K36K	aaA	aaG	4	4	AY.34	0.000388
ORF1ab/nsp8	36	K36K	aaA	aaG	4	4	AY.47	0.000124
ORF1ab/nsp8	36	K36Q	Aaa	Caa	4	4	B.1.1.7	0.000004
ORF1ab/nsp8	36	K36del	AAA	---	4	4	B.1.1.7	0.000004
ORF1ab/nsp8	36	K36R	aAa	aGa	4	4	C.35	0.003096
ORF1ab/nsp8	36	K36N	aaA	aaT	3	3	AY.26	0.000085
ORF1ab/nsp8	36	K36R	aAa	aGa	3	3	AY.3	0.00003
ORF1ab/nsp8	36	K36del1	Aaa	-aa	3	3	AY.44	0.000018
ORF1ab/nsp8	36	K36X	Aaa	Taa	3	3	B.1.1.7	0.000003
ORF1ab/nsp8	36	K36del1	Aaa	-aa	3	3	B.1.617.2	0.000011
ORF1ab/nsp8	36	K36I	aAa	aTa	2	2	All	0
ORF1ab/nsp8	36	K36T	aAa	aCa	2	2	All	0
ORF1ab/nsp8	36	K36G	AAa	GGa	2	2	All	0
ORF1ab/nsp8	36	K36R	aAa	aGa	2	2	AY.43	0.000009
ORF1ab/nsp8	36	K36X	Aaa	Taa	2	2	B.1	0.000018
ORF1ab/nsp8	36	K36N	aaA	aaC	2	2	B.1.1.519	0.000079
ORF1ab/nsp8	36	K36del2	AAa	--a	2	2	B.1.1.7	0.000002
ORF1ab/nsp8	36	K36Q	Aaa	Caa	2	2	B.1.2	0.000018
ORF1ab/nsp8	36	K36R	aAa	aGa	2	2	B.1.617.2	0.000008
ORF1ab/nsp8	36	K36del1	Aaa	-aa	2	2	B.1.627	0.00404
ORF1ab/nsp8	36	K36E	Aaa	Gaa	1	1		0.055556
ORF1ab/nsp8	36	K36X	Aaa	Taa	1	1		0.055556
ORF1ab/nsp8	36	K36del2	AAa	--a	1	1	A	0.000387
ORF1ab/nsp8	36	K36K	aaA	aaG	1	1	A.1	0.000282
ORF1ab/nsp8	36	K36N	aaA	aaC	1	1	A.2.2	0.001689
ORF1ab/nsp8	36	K36N	aaA	aaT	1	1	AY.102	0.000027
ORF1ab/nsp8	36	K36K	aaA	aaG	1	1	AY.102	0.000027
ORF1ab/nsp8	36	K36del1	Aaa	-aa	1	1	AY.103	0.000006
ORF1ab/nsp8	36	K36del1	Aaa	-aa	1	1	AY.120.1	0.000321
ORF1ab/nsp8	36	K36E	Aaa	Gaa	1	1	AY.23	0.00007
ORF1ab/nsp8	36	K36E	Aaa	Gaa	1	1	AY.25	0.000006
ORF1ab/nsp8	36	K36K	aaA	aaG	1	1	AY.30	0.000396
ORF1ab/nsp8	36	K36I	aAa	aTa	1	1	AY.33	0.000067
ORF1ab/nsp8	36	K36N	aaA	aaT	1	1	AY.4	0.000002
ORF1ab/nsp8	36	K36R	aAa	aGa	1	1	AY.4	0.000002
ORF1ab/nsp8	36	K36del	AAA	---	1	1	AY.4	0.000002
ORF1ab/nsp8	36	K36K	aaA	aaG	1	1	AY.4.2	0.000022
ORF1ab/nsp8	36	K36del	AAA	---	1	1	AY.43	0.000004
ORF1ab/nsp8	36	K36del1	Aaa	-aa	1	1	AY.43	0.000004
ORF1ab/nsp8	36	K36K	aaA	aaG	1	1	AY.43	0.000004
ORF1ab/nsp8	36	K36R	aAa	aGa	1	1	AY.44	0.000006
ORF1ab/nsp8	36	K36T	aAa	aCa	1	1	AY.46	0.000104
ORF1ab/nsp8	36	K36del1	Aaa	-aa	1	1	AY.46.2	0.000635
ORF1ab/nsp8	36	K36K	aaA	aaG	1	1	AY.46.6	0.000072
ORF1ab/nsp8	36	K36E	AaA	GaG	1	1	AY.55	0.000917
ORF1ab/nsp8	36	K36I	aAa	aTa	1	1	AY.9.2	0.000037
ORF1ab/nsp8	36	K36del	AAA	---	1	1	B	0.000128
ORF1ab/nsp8	36	K36del	AAA	---	1	1	B.1	0.000009
ORF1ab/nsp8	36	K36N	aaA	aaT	1	1	B.1	0.000009
ORF1ab/nsp8	36	K36del1	Aaa	-aa	1	1	B.1	0.000009
ORF1ab/nsp8	36	K36K	aaA	aaG	1	1	B.1	0.000009
ORF1ab/nsp8	36	K36del1	Aaa	-aa	1	1	B.1.1	0.000018
ORF1ab/nsp8	36	K36K	aaA	aaG	1	1	B.1.1.158	0.012195
ORF1ab/nsp8	36	K36R	aAa	aGa	1	1	B.1.1.186	0.003436
ORF1ab/nsp8	36	K36R	aAa	aGa	1	1	B.1.1.216	0.00089
ORF1ab/nsp8	36	K36T	aAa	aCa	1	1	B.1.1.300	0.010753
ORF1ab/nsp8	36	K36K	aaA	aaG	1	1	B.1.1.33	0.000421
ORF1ab/nsp8	36	K36del1	Aaa	-aa	1	1	B.1.1.7	0.000001
ORF1ab/nsp8	36	K36K	aaA	aaG	1	1	B.1.160	0.000031
ORF1ab/nsp8	36	K36K	aaA	aaG	1	1	B.1.177	0.000013
ORF1ab/nsp8	36	K36R	aAa	aGa	1	1	B.1.177	0.000013
ORF1ab/nsp8	36	K36R	aAa	aGa	1	1	B.1.2	0.000009
ORF1ab/nsp8	36	K36del2	AAa	--a	1	1	B.1.2	0.000009
ORF1ab/nsp8	36	K36X	Aaa	Taa	1	1	B.1.2	0.000009
ORF1ab/nsp8	36	K36R	aAa	aGa	1	1	B.1.221	0.000071
ORF1ab/nsp8	36	K36del	AAA	---	1	1	B.1.354	0.043478
ORF1ab/nsp8	36	K36R	aAa	aGa	1	1	B.1.362	0.001541
ORF1ab/nsp8	36	K36del2	AAa	--a	1	1	B.1.429	0.000024
ORF1ab/nsp8	36	K36R	aAa	aGa	1	1	B.1.429	0.000024
ORF1ab/nsp8	36	K36R	aAa	aGa	1	1	B.1.438	0.006536
ORF1ab/nsp8	36	K36K	aaA	aaG	1	1	B.1.438	0.006536
ORF1ab/nsp8	36	K36Q	Aaa	Caa	1	1	B.1.511	0.034483
ORF1ab/nsp8	36	K36K	aaA	aaG	1	1	B.1.526	0.000024
ORF1ab/nsp8	36	K36del	AAA	---	1	1	B.1.595	0.000261
ORF1ab/nsp8	36	K36G	AAa	GGa	1	1	B.1.617.2	0.000004
ORF1ab/nsp8	36	K36K	aaA	aaG	1	1	B.1.617.2	0.000004
ORF1ab/nsp8	36	K36del	AAA	---	1	1	B.1.621	0.000089
ORF1ab/nsp8	36	K36X	Aaa	Taa	1	1	B.3	0.000831
ORF1ab/nsp8	36	K36G	AAa	GGa	1	1	C.17	0.055556
ORF1ab/nsp8	36	K36R	aAa	aGa	1	1	D.2	0.000075
ORF1ab/nsp8	36	K36X	Aaa	Taa	1	1	D.2	0.000075
ORF1ab/nsp8	36	K36del	AAA	---	1	1	N.4	0.004255
ORF1ab/nsp8	36	K36K	aaA	aaG	1	1	P.1	0.000016
ORF1ab/nsp8	36	K36R	aAa	aGa	1	1	P.1	0.000016
ORF1ab/nsp8	36	K36del	AAA	---	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.