CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1613

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/nsp3	1613	R1613R	R2431R	syn	agA	agG	124	124	1	7556-7558
ORF1ab/nsp3	1613	R1613K	R2431K	nonsyn	aGa	aAa	104	104	1	7556-7558
ORF1ab/nsp3	1613	R1613del	R2431del	del	AGA	---	91	91	1	7556-7558
ORF1ab/nsp3	1613	R1613I	R2431I	nonsyn	aGa	aTa	11	10	0.909091	7556-7558
ORF1ab/nsp3	1613	R1613I	R2431I	nonsyn	aGA	aTC	11	1	0.0909091	7556-7558
ORF1ab/nsp3	1613	R1613G	R2431G	nonsyn	Aga	Gga	8	8	1	7556-7558
ORF1ab/nsp3	1613	R1613T	R2431T	nonsyn	aGa	aCa	8	6	0.75	7556-7558
ORF1ab/nsp3	1613	R1613del1	R2431del1	del	agA	ag-	8	6	0.75	7556-7558
ORF1ab/nsp3	1613	R1613T	R2431T	nonsyn	aGA	aCC	8	2	0.25	7556-7558
ORF1ab/nsp3	1613	R1613del1	R2431del1	del	aGa	a-a	8	1	0.125	7556-7558
ORF1ab/nsp3	1613	R1613del1	R2431del1	del	Aga	-ga	8	1	0.125	7556-7558
ORF1ab/nsp3	1613	R1613S	R2431S	nonsyn	agA	agT	2	2	1	7556-7558
ORF1ab/nsp3	1613	R1613X	R2431X	nonsyn	Aga	Tga	2	2	1	7556-7558

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/nsp3	1613	R1613R	agA	agG	124	124	All	0.000024
ORF1ab/nsp3	1613	R1613K	aGa	aAa	104	104	All	0.00002
ORF1ab/nsp3	1613	R1613del	AGA	---	91	91	All	0.000017
ORF1ab/nsp3	1613	R1613R	agA	agG	42	42	AY.103	0.000261
ORF1ab/nsp3	1613	R1613del	AGA	---	42	42	B.1.1.7	0.000038
ORF1ab/nsp3	1613	R1613K	aGa	aAa	29	29	B.1.330	0.828571
ORF1ab/nsp3	1613	R1613I	aGa	aTa	10	11	All	0.000002
ORF1ab/nsp3	1613	R1613I	aGA	aTC	1	11	All	0
ORF1ab/nsp3	1613	R1613K	aGa	aAa	11	11	AY.4.2	0.000239
ORF1ab/nsp3	1613	R1613K	aGa	aAa	11	11	B.1.621.1	0.005564
ORF1ab/nsp3	1613	R1613R	agA	agG	10	10	B.1.1.7	0.000009
ORF1ab/nsp3	1613	R1613R	agA	agG	9	9	AY.4.2.1	0.001341
ORF1ab/nsp3	1613	R1613del	AGA	---	9	9	B.1.177	0.000119
ORF1ab/nsp3	1613	R1613K	aGa	aAa	9	9	B.1.617.2	0.000034
ORF1ab/nsp3	1613	R1613G	Aga	Gga	8	8	All	0.000002
ORF1ab/nsp3	1613	R1613T	aGa	aCa	6	8	All	0.000001
ORF1ab/nsp3	1613	R1613del1	agA	ag-	6	8	All	0.000001
ORF1ab/nsp3	1613	R1613T	aGA	aCC	2	8	All	0
ORF1ab/nsp3	1613	R1613del1	Aga	-ga	1	8	All	0
ORF1ab/nsp3	1613	R1613del1	aGa	a-a	1	8	All	0
ORF1ab/nsp3	1613	R1613K	aGa	aAa	8	8	B.1.1.7	0.000007
ORF1ab/nsp3	1613	R1613R	agA	agG	8	8	B.1.617.2	0.00003
ORF1ab/nsp3	1613	R1613R	agA	agG	6	6	A.23.1	0.004225
ORF1ab/nsp3	1613	R1613R	agA	agG	6	6	AY.4	0.000009
ORF1ab/nsp3	1613	R1613del	AGA	---	6	6	AY.4	0.000009
ORF1ab/nsp3	1613	R1613K	aGa	aAa	6	6	B.1	0.000055
ORF1ab/nsp3	1613	R1613R	agA	agG	6	6	B.1.146	0.025424
ORF1ab/nsp3	1613	R1613T	aGA	aCC	2	4		0.111111
ORF1ab/nsp3	1613	R1613T	aGa	aCa	2	4		0.111111
ORF1ab/nsp3	1613	R1613R	agA	agG	4	4	B.1	0.000037
ORF1ab/nsp3	1613	R1613R	agA	agG	4	4	B.1.1.284	0.00043
ORF1ab/nsp3	1613	R1613K	aGa	aAa	3	3	AY.100	0.000138
ORF1ab/nsp3	1613	R1613R	agA	agG	3	3	AY.33	0.0002
ORF1ab/nsp3	1613	R1613K	aGa	aAa	3	3	AY.4	0.000005
ORF1ab/nsp3	1613	R1613R	agA	agG	3	3	AY.43	0.000013
ORF1ab/nsp3	1613	R1613del	AGA	---	3	3	B.1	0.000027
ORF1ab/nsp3	1613	R1613del	AGA	---	3	3	B.1.1	0.000054
ORF1ab/nsp3	1613	R1613K	aGa	aAa	3	3	B.1.177	0.00004
ORF1ab/nsp3	1613	R1613K	aGa	aAa	3	3	B.1.2	0.000026
ORF1ab/nsp3	1613	R1613K	aGa	aAa	3	3	B.1.36.12	0.028846
ORF1ab/nsp3	1613	R1613R	agA	agG	3	3	B.1.427	0.000151
ORF1ab/nsp3	1613	R1613R	agA	agG	3	3	P.1	0.000047
ORF1ab/nsp3	1613	R1613R	agA	agG	2	2	AH.3	0.007605
ORF1ab/nsp3	1613	R1613S	agA	agT	2	2	All	0
ORF1ab/nsp3	1613	R1613X	Aga	Tga	2	2	All	0
ORF1ab/nsp3	1613	R1613del	AGA	---	2	2	AY.25	0.000012
ORF1ab/nsp3	1613	R1613del1	agA	ag-	2	2	B.1.1.7	0.000002
ORF1ab/nsp3	1613	R1613I	aGa	aTa	2	2	B.1.1.7	0.000002
ORF1ab/nsp3	1613	R1613T	aGa	aCa	2	2	B.1.1.7	0.000002
ORF1ab/nsp3	1613	R1613del	AGA	---	2	2	B.1.177.16	0.001329
ORF1ab/nsp3	1613	R1613del	AGA	---	2	2	B.1.177.54	0.001213
ORF1ab/nsp3	1613	R1613del1	aGa	a-a	1	2	B.1.2	0.000009
ORF1ab/nsp3	1613	R1613del1	agA	ag-	1	2	B.1.2	0.000009
ORF1ab/nsp3	1613	R1613G	Aga	Gga	2	2	P.1.1	0.000635
ORF1ab/nsp3	1613	R1613R	agA	agG	1	1	A.2.5	0.000499
ORF1ab/nsp3	1613	R1613K	aGa	aAa	1	1	AB.1	0.008197
ORF1ab/nsp3	1613	R1613K	aGa	aAa	1	1	AT.1	0.005128
ORF1ab/nsp3	1613	R1613K	aGa	aAa	1	1	AY.102	0.000027
ORF1ab/nsp3	1613	R1613I	aGa	aTa	1	1	AY.113	0.000142
ORF1ab/nsp3	1613	R1613R	agA	agG	1	1	AY.118	0.000063
ORF1ab/nsp3	1613	R1613K	aGa	aAa	1	1	AY.120	0.000037
ORF1ab/nsp3	1613	R1613del	AGA	---	1	1	AY.24	0.000431
ORF1ab/nsp3	1613	R1613K	aGa	aAa	1	1	AY.25	0.000006
ORF1ab/nsp3	1613	R1613K	aGa	aAa	1	1	AY.26	0.000028
ORF1ab/nsp3	1613	R1613R	agA	agG	1	1	AY.26	0.000028
ORF1ab/nsp3	1613	R1613R	agA	agG	1	1	AY.3	0.00001
ORF1ab/nsp3	1613	R1613G	Aga	Gga	1	1	AY.36	0.000148
ORF1ab/nsp3	1613	R1613R	agA	agG	1	1	AY.39	0.000025
ORF1ab/nsp3	1613	R1613del1	Aga	-ga	1	1	AY.4	0.000002
ORF1ab/nsp3	1613	R1613I	aGa	aTa	1	1	AY.4	0.000002
ORF1ab/nsp3	1613	R1613T	aGa	aCa	1	1	AY.4	0.000002
ORF1ab/nsp3	1613	R1613R	agA	agG	1	1	AY.4.2	0.000022
ORF1ab/nsp3	1613	R1613G	Aga	Gga	1	1	AY.43	0.000004
ORF1ab/nsp3	1613	R1613del	AGA	---	1	1	AY.43	0.000004
ORF1ab/nsp3	1613	R1613del1	agA	ag-	1	1	AY.44	0.000006
ORF1ab/nsp3	1613	R1613K	aGa	aAa	1	1	AY.44	0.000006
ORF1ab/nsp3	1613	R1613K	aGa	aAa	1	1	AY.45	0.000122
ORF1ab/nsp3	1613	R1613del	AGA	---	1	1	AY.46.2	0.000635
ORF1ab/nsp3	1613	R1613del	AGA	---	1	1	AY.6	0.000041
ORF1ab/nsp3	1613	R1613del	AGA	---	1	1	AY.66	0.00107
ORF1ab/nsp3	1613	R1613K	aGa	aAa	1	1	AY.75	0.000056
ORF1ab/nsp3	1613	R1613K	aGa	aAa	1	1	AY.88	0.000884
ORF1ab/nsp3	1613	R1613R	agA	agG	1	1	B	0.000128
ORF1ab/nsp3	1613	R1613G	Aga	Gga	1	1	B.1	0.000009
ORF1ab/nsp3	1613	R1613S	agA	agT	1	1	B.1	0.000009
ORF1ab/nsp3	1613	R1613R	agA	agG	1	1	B.1.1	0.000018
ORF1ab/nsp3	1613	R1613I	aGa	aTa	1	1	B.1.1	0.000018
ORF1ab/nsp3	1613	R1613K	aGa	aAa	1	1	B.1.1.226	0.005814
ORF1ab/nsp3	1613	R1613del	AGA	---	1	1	B.1.1.232	0.001815
ORF1ab/nsp3	1613	R1613del	AGA	---	1	1	B.1.1.236	0.006897
ORF1ab/nsp3	1613	R1613R	agA	agG	1	1	B.1.1.28	0.000311
ORF1ab/nsp3	1613	R1613del	AGA	---	1	1	B.1.1.306	0.000438
ORF1ab/nsp3	1613	R1613del	AGA	---	1	1	B.1.1.311	0.000358
ORF1ab/nsp3	1613	R1613del	AGA	---	1	1	B.1.1.315	0.008475
ORF1ab/nsp3	1613	R1613K	aGa	aAa	1	1	B.1.1.317	0.000412
ORF1ab/nsp3	1613	R1613del	AGA	---	1	1	B.1.1.37	0.000193
ORF1ab/nsp3	1613	R1613del	AGA	---	1	1	B.1.1.46	0.004367
ORF1ab/nsp3	1613	R1613K	aGa	aAa	1	1	B.1.1.519	0.00004
ORF1ab/nsp3	1613	R1613S	agA	agT	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1613	R1613X	Aga	Tga	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1613	R1613del	AGA	---	1	1	B.1.161	0.017241
ORF1ab/nsp3	1613	R1613R	agA	agG	1	1	B.1.177	0.000013
ORF1ab/nsp3	1613	R1613del1	agA	ag-	1	1	B.1.177.17	0.000821
ORF1ab/nsp3	1613	R1613del	AGA	---	1	1	B.1.177.19	0.001431
ORF1ab/nsp3	1613	R1613del	AGA	---	1	1	B.1.177.21	0.000076
ORF1ab/nsp3	1613	R1613del	AGA	---	1	1	B.1.177.51	0.004566
ORF1ab/nsp3	1613	R1613del	AGA	---	1	1	B.1.177.57	0.000281
ORF1ab/nsp3	1613	R1613R	agA	agG	1	1	B.1.2	0.000009
ORF1ab/nsp3	1613	R1613T	aGa	aCa	1	1	B.1.2	0.000009
ORF1ab/nsp3	1613	R1613G	Aga	Gga	1	1	B.1.2	0.000009
ORF1ab/nsp3	1613	R1613I	aGa	aTa	1	1	B.1.23	0.006061
ORF1ab/nsp3	1613	R1613R	agA	agG	1	1	B.1.240	0.000216
ORF1ab/nsp3	1613	R1613del	AGA	---	1	1	B.1.258	0.000067
ORF1ab/nsp3	1613	R1613R	agA	agG	1	1	B.1.258.3	0.001675
ORF1ab/nsp3	1613	R1613G	Aga	Gga	1	1	B.1.3	0.002618
ORF1ab/nsp3	1613	R1613I	aGa	aTa	1	1	B.1.329	0.000608
ORF1ab/nsp3	1613	R1613R	agA	agG	1	1	B.1.351	0.00003
ORF1ab/nsp3	1613	R1613del1	agA	ag-	1	1	B.1.36	0.000146
ORF1ab/nsp3	1613	R1613R	agA	agG	1	1	B.1.497	0.000315
ORF1ab/nsp3	1613	R1613I	aGa	aTa	1	1	B.1.546	0.003704
ORF1ab/nsp3	1613	R1613del	AGA	---	1	1	B.1.561	0.000397
ORF1ab/nsp3	1613	R1613I	aGa	aTa	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1613	R1613I	aGA	aTC	1	1	B.1.617.3	0.002985
ORF1ab/nsp3	1613	R1613K	aGa	aAa	1	1	B.1.621	0.000089
ORF1ab/nsp3	1613	R1613del	AGA	---	1	1	B.1.621	0.000089
ORF1ab/nsp3	1613	R1613X	Aga	Tga	1	1	D.2	0.000075
ORF1ab/nsp3	1613	R1613G	Aga	Gga	1	1	D.2	0.000075
ORF1ab/nsp3	1613	R1613I	aGa	aTa	1	1	D.2	0.000075
ORF1ab/nsp3	1613	R1613K	aGa	aAa	1	1	Q.1	0.000126
ORF1ab/nsp3	1613	R1613del	AGA	---	1	1	Q.1	0.000126
ORF1ab/nsp3	1613	R1613del	AGA	---	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.