CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp6 : CodonNum = 138

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/nsp6	138	R138R	R3707R	syn	agA	agG	696	661	0.949713	11384-11386
ORF1ab/nsp6	138	R138R	R3707R	syn	Aga	Cga	696	35	0.0502874	11384-11386
ORF1ab/nsp6	138	R138del	R3707del	del	AGA	---	39	39	1	11384-11386
ORF1ab/nsp6	138	R138S	R3707S	nonsyn	agA	agC	14	12	0.857143	11384-11386
ORF1ab/nsp6	138	R138S	R3707S	nonsyn	agA	agT	14	2	0.142857	11384-11386
ORF1ab/nsp6	138	R138I	R3707I	nonsyn	aGa	aTa	10	10	1	11384-11386
ORF1ab/nsp6	138	R138G	R3707G	nonsyn	Aga	Gga	7	7	1	11384-11386
ORF1ab/nsp6	138	R138K	R3707K	nonsyn	aGa	aAa	7	7	1	11384-11386
ORF1ab/nsp6	138	R138X	R3707X	nonsyn	Aga	Tga	6	5	0.833333	11384-11386
ORF1ab/nsp6	138	R138del1	R3707del1	del	Aga	-ga	6	3	0.5	11384-11386
ORF1ab/nsp6	138	R138X	R3707X	nonsyn	AGa	TAa	6	1	0.166667	11384-11386
ORF1ab/nsp6	138	R138del1	R3707del1	del	AgA	-gT	6	1	0.166667	11384-11386
ORF1ab/nsp6	138	R138del1	R3707del1	del	agA	ag-	6	1	0.166667	11384-11386
ORF1ab/nsp6	138	R138del1	R3707del1	del	aGa	a-a	6	1	0.166667	11384-11386
ORF1ab/nsp6	138	R138T	R3707T	nonsyn	aGa	aCa	3	2	0.666667	11384-11386
ORF1ab/nsp6	138	R138T	R3707T	nonsyn	aGA	aCC	3	1	0.333333	11384-11386
ORF1ab/nsp6	138	R138del2	R3707del2	del	aGA	a--	2	2	1	11384-11386
ORF1ab/nsp6	138	R138V	R3707V	nonsyn	AGa	GTa	2	1	0.5	11384-11386
ORF1ab/nsp6	138	R138V	R3707V	nonsyn	AGA	GTG	2	1	0.5	11384-11386
ORF1ab/nsp6	138	R138L	R3707L	nonsyn	AGa	TTa	1	1	1	11384-11386

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/nsp6	138	R138R	agA	agG	661	696	All	0.000126
ORF1ab/nsp6	138	R138R	Aga	Cga	35	696	All	0.000007
ORF1ab/nsp6	138	R138R	agA	agG	251	251	U.3	0.969112
ORF1ab/nsp6	138	R138R	agA	agG	237	240	AY.4	0.000369
ORF1ab/nsp6	138	R138R	Aga	Cga	3	240	AY.4	0.000005
ORF1ab/nsp6	138	R138del	AGA	---	39	39	All	0.000007
ORF1ab/nsp6	138	R138R	agA	agG	25	29	AY.25	0.00015
ORF1ab/nsp6	138	R138R	Aga	Cga	4	29	AY.25	0.000024
ORF1ab/nsp6	138	R138R	agA	agG	19	27	B.1.1.7	0.000017
ORF1ab/nsp6	138	R138R	Aga	Cga	8	27	B.1.1.7	0.000007
ORF1ab/nsp6	138	R138R	agA	agG	20	20	B.1.2	0.000176
ORF1ab/nsp6	138	R138R	agA	agG	17	17	AY.103	0.000106
ORF1ab/nsp6	138	R138S	agA	agC	12	14	All	0.000002
ORF1ab/nsp6	138	R138S	agA	agT	2	14	All	0
ORF1ab/nsp6	138	R138del	AGA	---	12	12	B.1.1.7	0.000011
ORF1ab/nsp6	138	R138R	agA	agG	11	11	AY.46.2	0.006989
ORF1ab/nsp6	138	R138I	aGa	aTa	10	10	All	0.000002
ORF1ab/nsp6	138	R138G	Aga	Gga	7	7	All	0.000001
ORF1ab/nsp6	138	R138K	aGa	aAa	7	7	All	0.000001
ORF1ab/nsp6	138	R138R	agA	agG	5	7	B.1.637	0.000365
ORF1ab/nsp6	138	R138R	Aga	Cga	2	7	B.1.637	0.000146
ORF1ab/nsp6	138	R138X	Aga	Tga	5	6	All	0.000001
ORF1ab/nsp6	138	R138del1	Aga	-ga	3	6	All	0.000001
ORF1ab/nsp6	138	R138del1	agA	ag-	1	6	All	0
ORF1ab/nsp6	138	R138X	AGa	TAa	1	6	All	0
ORF1ab/nsp6	138	R138del1	aGa	a-a	1	6	All	0
ORF1ab/nsp6	138	R138del1	AgA	-gT	1	6	All	0
ORF1ab/nsp6	138	R138R	agA	agG	5	6	AY.43	0.000022
ORF1ab/nsp6	138	R138R	Aga	Cga	1	6	AY.43	0.000004
ORF1ab/nsp6	138	R138I	aGa	aTa	6	6	B.1	0.000055
ORF1ab/nsp6	138	R138R	Aga	Cga	4	6	B.1.1	0.000073
ORF1ab/nsp6	138	R138R	agA	agG	2	6	B.1.1	0.000036
ORF1ab/nsp6	138	R138R	Aga	Cga	6	6	B.1.474	0.011407
ORF1ab/nsp6	138	R138R	agA	agG	6	6	P.1	0.000095
ORF1ab/nsp6	138	R138R	agA	agG	5	5	AY.1	0.001979
ORF1ab/nsp6	138	R138R	agA	agG	5	5	AY.3	0.00005
ORF1ab/nsp6	138	R138R	agA	agG	4	5	B.1.617.2	0.000015
ORF1ab/nsp6	138	R138R	Aga	Cga	1	5	B.1.617.2	0.000004
ORF1ab/nsp6	138	R138del	AGA	---	4	4	AY.25	0.000024
ORF1ab/nsp6	138	R138R	agA	agG	4	4	AY.26	0.000113
ORF1ab/nsp6	138	R138X	Aga	Tga	3	4	B.1	0.000027
ORF1ab/nsp6	138	R138X	AGa	TAa	1	4	B.1	0.000009
ORF1ab/nsp6	138	R138R	agA	agG	4	4	B.1.36.21	0.008639
ORF1ab/nsp6	138	R138R	agA	agG	4	4	B.1.526	0.000094
ORF1ab/nsp6	138	R138T	aGa	aCa	2	3	All	0
ORF1ab/nsp6	138	R138T	aGA	aCC	1	3	All	0
ORF1ab/nsp6	138	R138R	agA	agG	3	3	AY.39.1	0.000119
ORF1ab/nsp6	138	R138del	AGA	---	3	3	AY.4	0.000005
ORF1ab/nsp6	138	R138del	AGA	---	3	3	AY.43	0.000013
ORF1ab/nsp6	138	R138G	Aga	Gga	3	3	B.1	0.000027
ORF1ab/nsp6	138	R138R	agA	agG	3	3	B.1.177	0.00004
ORF1ab/nsp6	138	R138del2	aGA	a--	2	2	All	0
ORF1ab/nsp6	138	R138V	AGa	GTa	1	2	All	0
ORF1ab/nsp6	138	R138V	AGA	GTG	1	2	All	0
ORF1ab/nsp6	138	R138R	agA	agG	2	2	AY.102	0.000053
ORF1ab/nsp6	138	R138R	agA	agG	1	2	AY.39	0.000025
ORF1ab/nsp6	138	R138R	Aga	Cga	1	2	AY.39	0.000025
ORF1ab/nsp6	138	R138R	agA	agG	2	2	AY.44	0.000012
ORF1ab/nsp6	138	R138del1	aGa	a-a	1	2	AY.44	0.000006
ORF1ab/nsp6	138	R138del1	AgA	-gT	1	2	AY.44	0.000006
ORF1ab/nsp6	138	R138S	agA	agT	1	2	B.1	0.000009
ORF1ab/nsp6	138	R138V	AGa	GTa	1	2	B.1	0.000009
ORF1ab/nsp6	138	R138S	agA	agC	1	2	B.1	0.000009
ORF1ab/nsp6	138	R138V	AGA	GTG	1	2	B.1	0.000009
ORF1ab/nsp6	138	R138R	agA	agG	2	2	B.1.429	0.000047
ORF1ab/nsp6	138	R138S	agA	agC	2	2	B.1.617.2	0.000008
ORF1ab/nsp6	138	R138R	Aga	Cga	2	2	B.1.621	0.000177
ORF1ab/nsp6	138	R138del	AGA	---	1	1	A	0.000387
ORF1ab/nsp6	138	R138L	AGa	TTa	1	1	All	0
ORF1ab/nsp6	138	R138R	agA	agG	1	1	AY.101	0.00049
ORF1ab/nsp6	138	R138S	agA	agC	1	1	AY.107	0.000466
ORF1ab/nsp6	138	R138S	agA	agC	1	1	AY.113	0.000142
ORF1ab/nsp6	138	R138R	agA	agG	1	1	AY.113	0.000142
ORF1ab/nsp6	138	R138R	Aga	Cga	1	1	AY.118	0.000063
ORF1ab/nsp6	138	R138R	agA	agG	1	1	AY.119	0.000035
ORF1ab/nsp6	138	R138R	agA	agG	1	1	AY.120	0.000037
ORF1ab/nsp6	138	R138del	AGA	---	1	1	AY.120	0.000037
ORF1ab/nsp6	138	R138K	aGa	aAa	1	1	AY.23.1	0.000417
ORF1ab/nsp6	138	R138G	Aga	Gga	1	1	AY.25	0.000006
ORF1ab/nsp6	138	R138R	agA	agG	1	1	AY.29	0.000016
ORF1ab/nsp6	138	R138S	agA	agC	1	1	AY.3	0.00001
ORF1ab/nsp6	138	R138K	aGa	aAa	1	1	AY.3	0.00001
ORF1ab/nsp6	138	R138R	agA	agG	1	1	AY.3.1	0.000085
ORF1ab/nsp6	138	R138I	aGa	aTa	1	1	AY.39	0.000025
ORF1ab/nsp6	138	R138S	agA	agC	1	1	AY.43	0.000004
ORF1ab/nsp6	138	R138K	aGa	aAa	1	1	AY.43	0.000004
ORF1ab/nsp6	138	R138S	agA	agC	1	1	AY.44	0.000006
ORF1ab/nsp6	138	R138del	AGA	---	1	1	AY.44	0.000006
ORF1ab/nsp6	138	R138R	agA	agG	1	1	AY.45	0.000122
ORF1ab/nsp6	138	R138S	agA	agC	1	1	AY.46.6	0.000072
ORF1ab/nsp6	138	R138R	agA	agG	1	1	AY.48	0.000465
ORF1ab/nsp6	138	R138K	aGa	aAa	1	1	AY.5	0.000021
ORF1ab/nsp6	138	R138R	agA	agG	1	1	AY.6	0.000041
ORF1ab/nsp6	138	R138R	agA	agG	1	1	AY.65	0.000533
ORF1ab/nsp6	138	R138del	AGA	---	1	1	AY.75	0.000056
ORF1ab/nsp6	138	R138R	agA	agG	1	1	AY.75	0.000056
ORF1ab/nsp6	138	R138del	AGA	---	1	1	AY.78	0.001541
ORF1ab/nsp6	138	R138S	agA	agC	1	1	AY.84	0.000437
ORF1ab/nsp6	138	R138del1	Aga	-ga	1	1	AY.9	0.000068
ORF1ab/nsp6	138	R138S	agA	agC	1	1	AY.9.2	0.000037
ORF1ab/nsp6	138	R138T	aGA	aCC	1	1	AY.9.2	0.000037
ORF1ab/nsp6	138	R138del	AGA	---	1	1	AY.9.2	0.000037
ORF1ab/nsp6	138	R138S	agA	agC	1	1	AY.99	0.001049
ORF1ab/nsp6	138	R138T	aGa	aCa	1	1	B.1	0.000009
ORF1ab/nsp6	138	R138del1	Aga	-ga	1	1	B.1	0.000009
ORF1ab/nsp6	138	R138K	aGa	aAa	1	1	B.1	0.000009
ORF1ab/nsp6	138	R138L	AGa	TTa	1	1	B.1	0.000009
ORF1ab/nsp6	138	R138G	Aga	Gga	1	1	B.1.1	0.000018
ORF1ab/nsp6	138	R138del	AGA	---	1	1	B.1.1	0.000018
ORF1ab/nsp6	138	R138X	Aga	Tga	1	1	B.1.1	0.000018
ORF1ab/nsp6	138	R138del	AGA	---	1	1	B.1.1.139	0.022727
ORF1ab/nsp6	138	R138R	agA	agG	1	1	B.1.1.25	0.000569
ORF1ab/nsp6	138	R138del	AGA	---	1	1	B.1.1.284	0.000107
ORF1ab/nsp6	138	R138R	agA	agG	1	1	B.1.1.37	0.000193
ORF1ab/nsp6	138	R138R	agA	agG	1	1	B.1.1.398	0.003226
ORF1ab/nsp6	138	R138del2	aGA	a--	1	1	B.1.1.409	0.002833
ORF1ab/nsp6	138	R138del1	agA	ag-	1	1	B.1.1.7	0.000001
ORF1ab/nsp6	138	R138I	aGa	aTa	1	1	B.1.1.7	0.000001
ORF1ab/nsp6	138	R138del2	aGA	a--	1	1	B.1.1.7	0.000001
ORF1ab/nsp6	138	R138K	aGa	aAa	1	1	B.1.1.7	0.000001
ORF1ab/nsp6	138	R138S	agA	agT	1	1	B.1.1.7	0.000001
ORF1ab/nsp6	138	R138T	aGa	aCa	1	1	B.1.1.7	0.000001
ORF1ab/nsp6	138	R138R	agA	agG	1	1	B.1.177.43	0.001477
ORF1ab/nsp6	138	R138del	AGA	---	1	1	B.1.177.51	0.004566
ORF1ab/nsp6	138	R138R	agA	agG	1	1	B.1.177.53	0.002392
ORF1ab/nsp6	138	R138R	agA	agG	1	1	B.1.177.75	0.001041
ORF1ab/nsp6	138	R138R	agA	agG	1	1	B.1.221	0.000071
ORF1ab/nsp6	138	R138R	Aga	Cga	1	1	B.1.223	0.002778
ORF1ab/nsp6	138	R138del	AGA	---	1	1	B.1.258.10	0.011364
ORF1ab/nsp6	138	R138R	agA	agG	1	1	B.1.525	0.000113
ORF1ab/nsp6	138	R138I	aGa	aTa	1	1	B.1.549	0.007194
ORF1ab/nsp6	138	R138del	AGA	---	1	1	B.1.577	0.000687
ORF1ab/nsp6	138	R138R	agA	agG	1	1	B.1.577	0.000687
ORF1ab/nsp6	138	R138del1	Aga	-ga	1	1	B.1.596	0.000087
ORF1ab/nsp6	138	R138R	agA	agG	1	1	B.1.596	0.000087
ORF1ab/nsp6	138	R138del	AGA	---	1	1	B.1.617.1	0.000129
ORF1ab/nsp6	138	R138I	aGa	aTa	1	1	B.1.617.2	0.000004
ORF1ab/nsp6	138	R138K	aGa	aAa	1	1	B.1.617.2	0.000004
ORF1ab/nsp6	138	R138del	AGA	---	1	1	B.1.617.2	0.000004
ORF1ab/nsp6	138	R138del	AGA	---	1	1	B.1.630	0.005236
ORF1ab/nsp6	138	R138G	Aga	Gga	1	1	B.1.9.5	0.005682
ORF1ab/nsp6	138	R138R	agA	agG	1	1	D.2	0.000075
ORF1ab/nsp6	138	R138del	AGA	---	1	1	N.4	0.004255
ORF1ab/nsp6	138	R138G	Aga	Gga	1	1	P.1	0.000016
ORF1ab/nsp6	138	R138R	Aga	Cga	1	1	P.1.10	0.000269
ORF1ab/nsp6	138	R138R	agA	agG	1	1	P.1.12	0.000484
ORF1ab/nsp6	138	R138R	agA	agG	1	1	P.1.14	0.000048
ORF1ab/nsp6	138	R138del	AGA	---	1	1	Q.2	0.000613
ORF1ab/nsp6	138	R138X	Aga	Tga	1	1	Q.3	0.000145

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.