CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp7 : CodonNum = 72

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/nsp7	72	C72S	C3931S	nonsyn	Tgt	Agt	871	849	0.974742	12056-12058
ORF1ab/nsp7	72	C72S	C3931S	nonsyn	tGt	tCt	871	22	0.0252583	12056-12058
ORF1ab/nsp7	72	C72C	C3931C	syn	tgT	tgC	108	108	1	12056-12058
ORF1ab/nsp7	72	C72del	C3931del	del	TGT	---	11	11	1	12056-12058
ORF1ab/nsp7	72	C72Y	C3931Y	nonsyn	tGt	tAt	11	11	1	12056-12058
ORF1ab/nsp7	72	C72F	C3931F	nonsyn	tGt	tTt	8	8	1	12056-12058
ORF1ab/nsp7	72	C72R	C3931R	nonsyn	Tgt	Cgt	4	4	1	12056-12058
ORF1ab/nsp7	72	C72del1	C3931del1	del	tgT	tg-	4	3	0.75	12056-12058
ORF1ab/nsp7	72	C72del1	C3931del1	del	TGt	-Tt	4	1	0.25	12056-12058
ORF1ab/nsp7	72	C72X	C3931X	nonsyn	tgT	tgA	3	3	1	12056-12058
ORF1ab/nsp7	72	C72W	C3931W	nonsyn	tgT	tgG	3	3	1	12056-12058
ORF1ab/nsp7	72	C72del2	C3931del2	del	TGt	--t	2	1	0.5	12056-12058
ORF1ab/nsp7	72	C72del2	C3931del2	del	TGT	--C	2	1	0.5	12056-12058
ORF1ab/nsp7	72	C72L	C3931L	nonsyn	tGT	tTA	2	1	0.5	12056-12058
ORF1ab/nsp7	72	C72L	C3931L	nonsyn	tGT	tTG	2	1	0.5	12056-12058
ORF1ab/nsp7	72	C72G	C3931G	nonsyn	Tgt	Ggt	1	1	1	12056-12058

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/nsp7	72	C72S	Tgt	Agt	849	871	All	0.000162
ORF1ab/nsp7	72	C72S	tGt	tCt	22	871	All	0.000004
ORF1ab/nsp7	72	C72S	Tgt	Agt	802	802	AY.60	0.752345
ORF1ab/nsp7	72	C72C	tgT	tgC	108	108	All	0.000021
ORF1ab/nsp7	72	C72C	tgT	tgC	25	25	B.1.177	0.000329
ORF1ab/nsp7	72	C72C	tgT	tgC	13	13	B.1.1.7	0.000012
ORF1ab/nsp7	72	C72S	tGt	tCt	12	13	B.1.2	0.000106
ORF1ab/nsp7	72	C72S	Tgt	Agt	1	13	B.1.2	0.000009
ORF1ab/nsp7	72	C72del	TGT	---	11	11	All	0.000002
ORF1ab/nsp7	72	C72Y	tGt	tAt	11	11	All	0.000002
ORF1ab/nsp7	72	C72F	tGt	tTt	8	8	All	0.000002
ORF1ab/nsp7	72	C72S	tGt	tCt	8	8	AY.46.6	0.000578
ORF1ab/nsp7	72	C72S	Tgt	Agt	8	8	B.1.1.7	0.000007
ORF1ab/nsp7	72	C72C	tgT	tgC	8	8	B.1.617.2	0.00003
ORF1ab/nsp7	72	C72C	tgT	tgC	7	7	AY.4	0.000011
ORF1ab/nsp7	72	C72S	Tgt	Agt	7	7	AY.47	0.000218
ORF1ab/nsp7	72	C72C	tgT	tgC	7	7	B.1.2	0.000062
ORF1ab/nsp7	72	C72C	tgT	tgC	5	5	AY.43	0.000022
ORF1ab/nsp7	72	C72C	tgT	tgC	5	5	AY.44	0.00003
ORF1ab/nsp7	72	C72del	TGT	---	4	4		0.222222
ORF1ab/nsp7	72	C72S	Tgt	Agt	4	4		0.222222
ORF1ab/nsp7	72	C72R	Tgt	Cgt	4	4	All	0.000001
ORF1ab/nsp7	72	C72del1	tgT	tg-	3	4	All	0.000001
ORF1ab/nsp7	72	C72del1	TGt	-Tt	1	4	All	0
ORF1ab/nsp7	72	C72C	tgT	tgC	4	4	B.1.1.39	0.002039
ORF1ab/nsp7	72	C72C	tgT	tgC	4	4	B.1.509	0.003463
ORF1ab/nsp7	72	C72W	tgT	tgG	3	3	All	0.000001
ORF1ab/nsp7	72	C72X	tgT	tgA	3	3	All	0.000001
ORF1ab/nsp7	72	C72S	Tgt	Agt	3	3	AY.100	0.000138
ORF1ab/nsp7	72	C72Y	tGt	tAt	3	3	AY.4	0.000005
ORF1ab/nsp7	72	C72S	Tgt	Agt	3	3	AY.43	0.000013
ORF1ab/nsp7	72	C72L	tGT	tTG	1	2		0.055556
ORF1ab/nsp7	72	C72L	tGT	tTA	1	2		0.055556
ORF1ab/nsp7	72	C72del2	TGt	--t	1	2	All	0
ORF1ab/nsp7	72	C72L	tGT	tTA	1	2	All	0
ORF1ab/nsp7	72	C72L	tGT	tTG	1	2	All	0
ORF1ab/nsp7	72	C72del2	TGT	--C	1	2	All	0
ORF1ab/nsp7	72	C72S	Tgt	Agt	2	2	AY.67	0.000929
ORF1ab/nsp7	72	C72S	Tgt	Agt	2	2	AY.75.1	0.000361
ORF1ab/nsp7	72	C72S	Tgt	Agt	1	2	B.1	0.000009
ORF1ab/nsp7	72	C72S	tGt	tCt	1	2	B.1	0.000009
ORF1ab/nsp7	72	C72F	tGt	tTt	2	2	B.1.1	0.000036
ORF1ab/nsp7	72	C72del	TGT	---	2	2	B.1.1.7	0.000002
ORF1ab/nsp7	72	C72S	Tgt	Agt	2	2	B.1.177	0.000026
ORF1ab/nsp7	72	C72S	Tgt	Agt	2	2	B.1.258	0.000133
ORF1ab/nsp7	72	C72del1	tgT	tg-	2	2	B.1.627	0.00404
ORF1ab/nsp7	72	C72C	tgT	tgC	2	2	C.38	0.016129
ORF1ab/nsp7	72	C72C	tgT	tgC	2	2	P.1.17	0.000324
ORF1ab/nsp7	72	C72F	tGt	tTt	1	1		0.055556
ORF1ab/nsp7	72	C72W	tgT	tgG	1	1		0.055556
ORF1ab/nsp7	72	C72X	tgT	tgA	1	1		0.055556
ORF1ab/nsp7	72	C72G	Tgt	Ggt	1	1	All	0
ORF1ab/nsp7	72	C72W	tgT	tgG	1	1	AY.100	0.000046
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	AY.102	0.000027
ORF1ab/nsp7	72	C72Y	tGt	tAt	1	1	AY.103	0.000006
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	AY.103	0.000006
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	AY.104	0.001984
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	AY.118	0.000063
ORF1ab/nsp7	72	C72S	Tgt	Agt	1	1	AY.13	0.000161
ORF1ab/nsp7	72	C72G	Tgt	Ggt	1	1	AY.25	0.000006
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	AY.25	0.000006
ORF1ab/nsp7	72	C72Y	tGt	tAt	1	1	AY.25	0.000006
ORF1ab/nsp7	72	C72S	tGt	tCt	1	1	AY.26	0.000028
ORF1ab/nsp7	72	C72Y	tGt	tAt	1	1	AY.3	0.00001
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	AY.3	0.00001
ORF1ab/nsp7	72	C72del2	TGT	--C	1	1	AY.3	0.00001
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	AY.33	0.000067
ORF1ab/nsp7	72	C72S	Tgt	Agt	1	1	AY.4	0.000002
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	AY.42	0.00004
ORF1ab/nsp7	72	C72Y	tGt	tAt	1	1	AY.43	0.000004
ORF1ab/nsp7	72	C72del	TGT	---	1	1	AY.43	0.000004
ORF1ab/nsp7	72	C72S	Tgt	Agt	1	1	AY.44	0.000006
ORF1ab/nsp7	72	C72Y	tGt	tAt	1	1	AY.5	0.000021
ORF1ab/nsp7	72	C72S	Tgt	Agt	1	1	AY.55	0.000917
ORF1ab/nsp7	72	C72Y	tGt	tAt	1	1	AY.61	0.000105
ORF1ab/nsp7	72	C72S	Tgt	Agt	1	1	AY.75	0.000056
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	AY.75	0.000056
ORF1ab/nsp7	72	C72X	tgT	tgA	1	1	AY.79	0.001211
ORF1ab/nsp7	72	C72S	Tgt	Agt	1	1	AY.88	0.000884
ORF1ab/nsp7	72	C72S	Tgt	Agt	1	1	AY.93	0.000273
ORF1ab/nsp7	72	C72Y	tGt	tAt	1	1	AY.98.1	0.000048
ORF1ab/nsp7	72	C72del2	TGt	--t	1	1	B.1	0.000009
ORF1ab/nsp7	72	C72del	TGT	---	1	1	B.1	0.000009
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	B.1	0.000009
ORF1ab/nsp7	72	C72F	tGt	tTt	1	1	B.1	0.000009
ORF1ab/nsp7	72	C72del1	TGt	-Tt	1	1	B.1	0.000009
ORF1ab/nsp7	72	C72S	Tgt	Agt	1	1	B.1.1	0.000018
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	B.1.1	0.000018
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	B.1.1.207	0.001182
ORF1ab/nsp7	72	C72S	Tgt	Agt	1	1	B.1.1.222	0.000204
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	B.1.1.229	0.005747
ORF1ab/nsp7	72	C72F	tGt	tTt	1	1	B.1.1.279	0.001121
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	B.1.1.284	0.000107
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	B.1.1.317	0.000412
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	B.1.1.464	0.001473
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	B.1.1.63	0.000386
ORF1ab/nsp7	72	C72F	tGt	tTt	1	1	B.1.1.7	0.000001
ORF1ab/nsp7	72	C72X	tgT	tgA	1	1	B.1.1.7	0.000001
ORF1ab/nsp7	72	C72R	Tgt	Cgt	1	1	B.1.1.7	0.000001
ORF1ab/nsp7	72	C72del1	tgT	tg-	1	1	B.1.1.7	0.000001
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	B.1.160	0.000031
ORF1ab/nsp7	72	C72S	Tgt	Agt	1	1	B.1.177.21	0.000076
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	B.1.177.82	0.000477
ORF1ab/nsp7	72	C72F	tGt	tTt	1	1	B.1.2	0.000009
ORF1ab/nsp7	72	C72del	TGT	---	1	1	B.1.2	0.000009
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	B.1.351.3	0.000876
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	B.1.400	0.000429
ORF1ab/nsp7	72	C72W	tgT	tgG	1	1	B.1.409	0.000781
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	B.1.427	0.00005
ORF1ab/nsp7	72	C72R	Tgt	Cgt	1	1	B.1.521	0.004975
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	B.1.564	0.000426
ORF1ab/nsp7	72	C72R	Tgt	Cgt	1	1	B.1.587	0.001898
ORF1ab/nsp7	72	C72F	tGt	tTt	1	1	B.1.596	0.000087
ORF1ab/nsp7	72	C72S	Tgt	Agt	1	1	B.1.617.2	0.000004
ORF1ab/nsp7	72	C72R	Tgt	Cgt	1	1	B.1.617.2	0.000004
ORF1ab/nsp7	72	C72S	Tgt	Agt	1	1	B.1.637	0.000073
ORF1ab/nsp7	72	C72del	TGT	---	1	1	C.17	0.055556
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	C.36.3.1	0.002717
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	D.2	0.000075
ORF1ab/nsp7	72	C72Y	tGt	tAt	1	1	D.2	0.000075
ORF1ab/nsp7	72	C72del	TGT	---	1	1	N.4	0.004255
ORF1ab/nsp7	72	C72C	tgT	tgC	1	1	P.1	0.000016

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.