CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 674

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	674	S674S	S1492S	syn	tcT	tcC	134	80	0.597015	4739-4741
ORF1ab/nsp3	674	S674S	S1492S	syn	tcT	tcG	134	42	0.313433	4739-4741
ORF1ab/nsp3	674	S674S	S1492S	syn	tcT	tcA	134	12	0.0895522	4739-4741
ORF1ab/nsp3	674	S674del	S1492del	del	TCT	---	64	64	1	4739-4741
ORF1ab/nsp3	674	S674F	S1492F	nonsyn	tCt	tTt	24	24	1	4739-4741
ORF1ab/nsp3	674	S674P	S1492P	nonsyn	Tct	Cct	13	10	0.769231	4739-4741
ORF1ab/nsp3	674	S674P	S1492P	nonsyn	TcT	CcA	13	2	0.153846	4739-4741
ORF1ab/nsp3	674	S674P	S1492P	nonsyn	TcT	CcG	13	1	0.0769231	4739-4741
ORF1ab/nsp3	674	S674A	S1492A	nonsyn	Tct	Gct	11	11	1	4739-4741
ORF1ab/nsp3	674	S674T	S1492T	nonsyn	Tct	Act	10	10	1	4739-4741
ORF1ab/nsp3	674	S674Y	S1492Y	nonsyn	tCt	tAt	5	5	1	4739-4741
ORF1ab/nsp3	674	S674C	S1492C	nonsyn	tCt	tGt	5	4	0.8	4739-4741
ORF1ab/nsp3	674	S674C	S1492C	nonsyn	tCT	tGC	5	1	0.2	4739-4741
ORF1ab/nsp3	674	S674X	S1492X	nonsyn	tCT	tAA	4	4	1	4739-4741
ORF1ab/nsp3	674	S674del1	S1492del1	del	tcT	tc-	3	2	0.666667	4739-4741
ORF1ab/nsp3	674	S674L	S1492L	nonsyn	tCT	tTA	3	1	0.333333	4739-4741
ORF1ab/nsp3	674	S674L	S1492L	nonsyn	TCt	CTt	3	1	0.333333	4739-4741
ORF1ab/nsp3	674	S674L	S1492L	nonsyn	TCT	CTA	3	1	0.333333	4739-4741
ORF1ab/nsp3	674	S674del1	S1492del1	del	Tct	-ct	3	1	0.333333	4739-4741
ORF1ab/nsp3	674	S674H	S1492H	nonsyn	TCt	CAt	1	1	1	4739-4741
ORF1ab/nsp3	674	S674Q	S1492Q	nonsyn	TCT	CAA	1	1	1	4739-4741
ORF1ab/nsp3	674	S674del2	S1492del2	del	TCt	--t	1	1	1	4739-4741

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	674	S674S	tcT	tcC	80	134	All	0.000015
ORF1ab/nsp3	674	S674S	tcT	tcG	42	134	All	0.000008
ORF1ab/nsp3	674	S674S	tcT	tcA	12	134	All	0.000002
ORF1ab/nsp3	674	S674del	TCT	---	64	64	All	0.000012
ORF1ab/nsp3	674	S674S	tcT	tcC	38	38	B.1.1	0.000689
ORF1ab/nsp3	674	S674F	tCt	tTt	24	24	All	0.000005
ORF1ab/nsp3	674	S674del	TCT	---	19	19	B.1.1.7	0.000017
ORF1ab/nsp3	674	S674S	tcT	tcG	16	16	B.1.1.424	0.727273
ORF1ab/nsp3	674	S674S	tcT	tcA	7	15	B.1.1.7	0.000006
ORF1ab/nsp3	674	S674S	tcT	tcC	6	15	B.1.1.7	0.000005
ORF1ab/nsp3	674	S674S	tcT	tcG	2	15	B.1.1.7	0.000002
ORF1ab/nsp3	674	S674P	Tct	Cct	10	13	All	0.000002
ORF1ab/nsp3	674	S674P	TcT	CcA	2	13	All	0
ORF1ab/nsp3	674	S674P	TcT	CcG	1	13	All	0
ORF1ab/nsp3	674	S674A	Tct	Gct	11	11	All	0.000002
ORF1ab/nsp3	674	S674T	Tct	Act	10	10	All	0.000002
ORF1ab/nsp3	674	S674F	tCt	tTt	10	10	B.1.1.7	0.000009
ORF1ab/nsp3	674	S674S	tcT	tcC	5	7	B.1.617.2	0.000019
ORF1ab/nsp3	674	S674S	tcT	tcG	2	7	B.1.617.2	0.000008
ORF1ab/nsp3	674	S674Y	tCt	tAt	5	5	All	0.000001
ORF1ab/nsp3	674	S674C	tCt	tGt	4	5	All	0.000001
ORF1ab/nsp3	674	S674C	tCT	tGC	1	5	All	0
ORF1ab/nsp3	674	S674S	tcT	tcC	5	5	AY.103	0.000031
ORF1ab/nsp3	674	S674A	Tct	Gct	5	5	B.1.1.7	0.000004
ORF1ab/nsp3	674	S674del	TCT	---	4	4		0.222222
ORF1ab/nsp3	674	S674X	tCT	tAA	4	4	All	0.000001
ORF1ab/nsp3	674	S674S	tcT	tcC	4	4	AY.4	0.000006
ORF1ab/nsp3	674	S674S	tcT	tcG	4	4	AY.44	0.000024
ORF1ab/nsp3	674	S674del1	tcT	tc-	2	3	All	0
ORF1ab/nsp3	674	S674L	TCT	CTA	1	3	All	0
ORF1ab/nsp3	674	S674L	tCT	tTA	1	3	All	0
ORF1ab/nsp3	674	S674del1	Tct	-ct	1	3	All	0
ORF1ab/nsp3	674	S674L	TCt	CTt	1	3	All	0
ORF1ab/nsp3	674	S674S	tcT	tcG	2	3	AY.29	0.000032
ORF1ab/nsp3	674	S674S	tcT	tcC	1	3	AY.29	0.000016
ORF1ab/nsp3	674	S674S	tcT	tcG	2	3	AY.39	0.000049
ORF1ab/nsp3	674	S674S	tcT	tcA	1	3	AY.39	0.000025
ORF1ab/nsp3	674	S674F	tCt	tTt	3	3	AY.4	0.000005
ORF1ab/nsp3	674	S674del	TCT	---	3	3	AY.4.5	0.000322
ORF1ab/nsp3	674	S674P	Tct	Cct	3	3	B.1	0.000027
ORF1ab/nsp3	674	S674L	TCt	CTt	1	3	B.1.1	0.000018
ORF1ab/nsp3	674	S674L	tCT	tTA	1	3	B.1.1	0.000018
ORF1ab/nsp3	674	S674L	TCT	CTA	1	3	B.1.1	0.000018
ORF1ab/nsp3	674	S674S	tcT	tcC	2	3	B.1.2	0.000018
ORF1ab/nsp3	674	S674S	tcT	tcA	1	3	B.1.2	0.000009
ORF1ab/nsp3	674	S674F	tCt	tTt	3	3	B.1.396	0.002117
ORF1ab/nsp3	674	S674S	tcT	tcG	3	3	B.1.429	0.000071
ORF1ab/nsp3	674	S674T	Tct	Act	3	3	P.1.14	0.000143
ORF1ab/nsp3	674	S674T	Tct	Act	2	2		0.111111
ORF1ab/nsp3	674	S674X	tCT	tAA	2	2		0.111111
ORF1ab/nsp3	674	S674A	Tct	Gct	2	2	AY.103	0.000012
ORF1ab/nsp3	674	S674C	tCt	tGt	1	2	AY.43	0.000004
ORF1ab/nsp3	674	S674C	tCT	tGC	1	2	AY.43	0.000004
ORF1ab/nsp3	674	S674del	TCT	---	2	2	AY.44	0.000012
ORF1ab/nsp3	674	S674S	tcT	tcC	2	2	AY.73	0.001331
ORF1ab/nsp3	674	S674Y	tCt	tAt	2	2	B.1	0.000018
ORF1ab/nsp3	674	S674del	TCT	---	2	2	B.1	0.000018
ORF1ab/nsp3	674	S674S	tcT	tcC	2	2	B.1	0.000018
ORF1ab/nsp3	674	S674F	tCt	tTt	2	2	B.1.1	0.000036
ORF1ab/nsp3	674	S674S	tcT	tcG	2	2	B.1.1.220	0.003717
ORF1ab/nsp3	674	S674T	Tct	Act	2	2	B.1.1.7	0.000002
ORF1ab/nsp3	674	S674S	tcT	tcC	2	2	B.1.177	0.000026
ORF1ab/nsp3	674	S674S	tcT	tcA	2	2	B.1.427	0.000101
ORF1ab/nsp3	674	S674P	Tct	Cct	1	2	B.1.596	0.000087
ORF1ab/nsp3	674	S674P	TcT	CcA	1	2	B.1.596	0.000087
ORF1ab/nsp3	674	S674del	TCT	---	2	2	B.1.619	0.001742
ORF1ab/nsp3	674	S674S	tcT	tcG	1	2	B.1.619.1	0.000641
ORF1ab/nsp3	674	S674S	tcT	tcC	1	2	B.1.619.1	0.000641
ORF1ab/nsp3	674	S674del	TCT	---	2	2	P.1	0.000032
ORF1ab/nsp3	674	S674del	TCT	---	1	1	A.2.2	0.001689
ORF1ab/nsp3	674	S674Q	TCT	CAA	1	1	All	0
ORF1ab/nsp3	674	S674del2	TCt	--t	1	1	All	0
ORF1ab/nsp3	674	S674H	TCt	CAt	1	1	All	0
ORF1ab/nsp3	674	S674S	tcT	tcG	1	1	AM.4	0.003571
ORF1ab/nsp3	674	S674S	tcT	tcG	1	1	AY.104	0.001984
ORF1ab/nsp3	674	S674del	TCT	---	1	1	AY.113	0.000142
ORF1ab/nsp3	674	S674S	tcT	tcC	1	1	AY.120	0.000037
ORF1ab/nsp3	674	S674del	TCT	---	1	1	AY.120	0.000037
ORF1ab/nsp3	674	S674F	tCt	tTt	1	1	AY.20	0.000039
ORF1ab/nsp3	674	S674S	tcT	tcC	1	1	AY.23	0.00007
ORF1ab/nsp3	674	S674del	TCT	---	1	1	AY.25	0.000006
ORF1ab/nsp3	674	S674S	tcT	tcC	1	1	AY.25	0.000006
ORF1ab/nsp3	674	S674F	tCt	tTt	1	1	AY.3	0.00001
ORF1ab/nsp3	674	S674del	TCT	---	1	1	AY.3	0.00001
ORF1ab/nsp3	674	S674S	tcT	tcC	1	1	AY.3	0.00001
ORF1ab/nsp3	674	S674del2	TCt	--t	1	1	AY.39	0.000025
ORF1ab/nsp3	674	S674A	Tct	Gct	1	1	AY.4	0.000002
ORF1ab/nsp3	674	S674P	Tct	Cct	1	1	AY.4	0.000002
ORF1ab/nsp3	674	S674del	TCT	---	1	1	AY.43	0.000004
ORF1ab/nsp3	674	S674S	tcT	tcC	1	1	AY.43	0.000004
ORF1ab/nsp3	674	S674F	tCt	tTt	1	1	AY.44	0.000006
ORF1ab/nsp3	674	S674A	Tct	Gct	1	1	AY.62	0.000436
ORF1ab/nsp3	674	S674del	TCT	---	1	1	AY.67	0.000464
ORF1ab/nsp3	674	S674T	Tct	Act	1	1	AY.7	0.000196
ORF1ab/nsp3	674	S674S	tcT	tcC	1	1	AY.82	0.001357
ORF1ab/nsp3	674	S674del	TCT	---	1	1	AY.84	0.000437
ORF1ab/nsp3	674	S674del	TCT	---	1	1	AY.99	0.001049
ORF1ab/nsp3	674	S674Y	tCt	tAt	1	1	B	0.000128
ORF1ab/nsp3	674	S674P	Tct	Cct	1	1	B	0.000128
ORF1ab/nsp3	674	S674del1	tcT	tc-	1	1	B.1	0.000009
ORF1ab/nsp3	674	S674T	Tct	Act	1	1	B.1	0.000009
ORF1ab/nsp3	674	S674Y	tCt	tAt	1	1	B.1.1	0.000018
ORF1ab/nsp3	674	S674H	TCt	CAt	1	1	B.1.1	0.000018
ORF1ab/nsp3	674	S674X	tCT	tAA	1	1	B.1.1	0.000018
ORF1ab/nsp3	674	S674del	TCT	---	1	1	B.1.1	0.000018
ORF1ab/nsp3	674	S674Q	TCT	CAA	1	1	B.1.1	0.000018
ORF1ab/nsp3	674	S674del	TCT	---	1	1	B.1.1.142	0.017544
ORF1ab/nsp3	674	S674A	Tct	Gct	1	1	B.1.1.194	0.00495
ORF1ab/nsp3	674	S674S	tcT	tcG	1	1	B.1.1.214	0.000055
ORF1ab/nsp3	674	S674T	Tct	Act	1	1	B.1.1.371	0.010417
ORF1ab/nsp3	674	S674S	tcT	tcC	1	1	B.1.1.39	0.00051
ORF1ab/nsp3	674	S674del	TCT	---	1	1	B.1.1.409	0.002833
ORF1ab/nsp3	674	S674P	Tct	Cct	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	674	S674X	tCT	tAA	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	674	S674C	tCt	tGt	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	674	S674del	TCT	---	1	1	B.1.149	0.003425
ORF1ab/nsp3	674	S674S	tcT	tcG	1	1	B.1.149	0.003425
ORF1ab/nsp3	674	S674del	TCT	---	1	1	B.1.157	0.002985
ORF1ab/nsp3	674	S674S	tcT	tcC	1	1	B.1.160.28	0.002924
ORF1ab/nsp3	674	S674del	TCT	---	1	1	B.1.160.7	0.002079
ORF1ab/nsp3	674	S674del	TCT	---	1	1	B.1.177	0.000013
ORF1ab/nsp3	674	S674del	TCT	---	1	1	B.1.177.50	0.004695
ORF1ab/nsp3	674	S674del	TCT	---	1	1	B.1.177.63	0.002703
ORF1ab/nsp3	674	S674del	TCT	---	1	1	B.1.177.69	0.001484
ORF1ab/nsp3	674	S674P	Tct	Cct	1	1	B.1.177.73	0.000566
ORF1ab/nsp3	674	S674C	tCt	tGt	1	1	B.1.177.73	0.000566
ORF1ab/nsp3	674	S674del	TCT	---	1	1	B.1.177.81	0.000189
ORF1ab/nsp3	674	S674P	Tct	Cct	1	1	B.1.2	0.000009
ORF1ab/nsp3	674	S674F	tCt	tTt	1	1	B.1.2	0.000009
ORF1ab/nsp3	674	S674C	tCt	tGt	1	1	B.1.2	0.000009
ORF1ab/nsp3	674	S674del	TCT	---	1	1	B.1.210	0.002132
ORF1ab/nsp3	674	S674S	tcT	tcC	1	1	B.1.241	0.000812
ORF1ab/nsp3	674	S674del	TCT	---	1	1	B.1.243	0.00007
ORF1ab/nsp3	674	S674S	tcT	tcC	1	1	B.1.258	0.000067
ORF1ab/nsp3	674	S674del	TCT	---	1	1	B.1.258	0.000067
ORF1ab/nsp3	674	S674del	TCT	---	1	1	B.1.319	0.003049
ORF1ab/nsp3	674	S674S	tcT	tcA	1	1	B.1.351.2	0.000303
ORF1ab/nsp3	674	S674P	TcT	CcG	1	1	B.1.36	0.000146
ORF1ab/nsp3	674	S674del	TCT	---	1	1	B.1.36	0.000146
ORF1ab/nsp3	674	S674Y	tCt	tAt	1	1	B.1.36.8	0.001
ORF1ab/nsp3	674	S674P	TcT	CcA	1	1	B.1.366	0.004878
ORF1ab/nsp3	674	S674F	tCt	tTt	1	1	B.1.429	0.000024
ORF1ab/nsp3	674	S674S	tcT	tcG	1	1	B.1.497	0.000315
ORF1ab/nsp3	674	S674S	tcT	tcG	1	1	B.1.546	0.003704
ORF1ab/nsp3	674	S674P	Tct	Cct	1	1	B.1.564	0.000426
ORF1ab/nsp3	674	S674S	tcT	tcG	1	1	B.1.565	0.00081
ORF1ab/nsp3	674	S674F	tCt	tTt	1	1	B.1.596	0.000087
ORF1ab/nsp3	674	S674del	TCT	---	1	1	B.1.617.1	0.000129
ORF1ab/nsp3	674	S674del	TCT	---	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	674	S674A	Tct	Gct	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	674	S674del1	tcT	tc-	1	1	B.1.621	0.000089
ORF1ab/nsp3	674	S674del	TCT	---	1	1	B.1.621	0.000089
ORF1ab/nsp3	674	S674S	tcT	tcG	1	1	B.1.628	0.000352
ORF1ab/nsp3	674	S674del	TCT	---	1	1	B.15	0.017544
ORF1ab/nsp3	674	S674del	TCT	---	1	1	P.1.1	0.000318
ORF1ab/nsp3	674	S674S	tcT	tcC	1	1	P.1.14	0.000048
ORF1ab/nsp3	674	S674S	tcT	tcC	1	1	P.6	0.003145
ORF1ab/nsp3	674	S674del1	Tct	-ct	1	1	U.3	0.003861

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.