CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = E : Mut = S3S

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
E	3	S3S		syn	tcA	tcT	239	97	0.405858	26251-26253
E	3	S3S		syn	tcA	tcC	239	92	0.384937	26251-26253
E	3	S3S		syn	tcA	tcG	239	50	0.209205	26251-26253

Details of the mutation S3S 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
E	3	S3S	tcA	tcT	97	239	All	0.000019
E	3	S3S	tcA	tcC	92	239	All	0.000018
E	3	S3S	tcA	tcG	50	239	All	0.00001
E	3	S3S	tcA	tcC	51	62	B.1.617.2	0.000192
E	3	S3S	tcA	tcT	10	62	B.1.617.2	0.000038
E	3	S3S	tcA	tcG	1	62	B.1.617.2	0.000004
E	3	S3S	tcA	tcT	11	23	B.1.1.7	0.00001
E	3	S3S	tcA	tcG	6	23	B.1.1.7	0.000005
E	3	S3S	tcA	tcC	6	23	B.1.1.7	0.000005
E	3	S3S	tcA	tcG	13	17	AY.4	0.00002
E	3	S3S	tcA	tcT	3	17	AY.4	0.000005
E	3	S3S	tcA	tcC	1	17	AY.4	0.000002
E	3	S3S	tcA	tcT	15	15	B.1.177	0.000198
E	3	S3S	tcA	tcC	7	11	AY.5	0.000145
E	3	S3S	tcA	tcT	4	11	AY.5	0.000083
E	3	S3S	tcA	tcT	8	10	AY.25	0.000048
E	3	S3S	tcA	tcG	2	10	AY.25	0.000012
E	3	S3S	tcA	tcC	5	9	AY.103	0.000031
E	3	S3S	tcA	tcG	3	9	AY.103	0.000019
E	3	S3S	tcA	tcT	1	9	AY.103	0.000006
E	3	S3S	tcA	tcT	6	7	AY.44	0.000037
E	3	S3S	tcA	tcG	1	7	AY.44	0.000006
E	3	S3S	tcA	tcT	4	7	B.1.1	0.000073
E	3	S3S	tcA	tcG	2	7	B.1.1	0.000036
E	3	S3S	tcA	tcC	1	7	B.1.1	0.000018
E	3	S3S	tcA	tcG	4	7	B.1.2	0.000035
E	3	S3S	tcA	tcT	3	7	B.1.2	0.000026
E	3	S3S	tcA	tcC	7	7	D.2	0.000525
E	3	S3S	tcA	tcT	6	6	AH.1	0.857143
E	3	S3S	tcA	tcT	4	5	AY.43	0.000018
E	3	S3S	tcA	tcG	1	5	AY.43	0.000004
E	3	S3S	tcA	tcC	3	3	AY.16	0.001139
E	3	S3S	tcA	tcC	2	3	AY.39	0.000049
E	3	S3S	tcA	tcT	1	3	AY.39	0.000025
E	3	S3S	tcA	tcC	3	3	B.1.235	0.007557
E	3	S3S	tcA	tcT	2	2	AY.117	0.000169
E	3	S3S	tcA	tcG	2	2	AY.20	0.000078
E	3	S3S	tcA	tcT	2	2	AY.27	0.000129
E	3	S3S	tcA	tcT	2	2	AY.74	0.000231
E	3	S3S	tcA	tcG	1	2	B.1	0.000009
E	3	S3S	tcA	tcT	1	2	B.1	0.000009
E	3	S3S	tcA	tcG	2	2	B.1.1.28	0.000622
E	3	S3S	tcA	tcG	2	2	B.1.427	0.000101
E	3	S3S	tcA	tcT	2	2	P.1	0.000032
E	3	S3S	tcA	tcC	1	1	AY.100	0.000046
E	3	S3S	tcA	tcT	1	1	AY.102	0.000027
E	3	S3S	tcA	tcT	1	1	AY.113	0.000142
E	3	S3S	tcA	tcG	1	1	AY.119	0.000035
E	3	S3S	tcA	tcG	1	1	AY.120	0.000037
E	3	S3S	tcA	tcC	1	1	AY.121	0.000135
E	3	S3S	tcA	tcC	1	1	AY.14	0.000088
E	3	S3S	tcA	tcC	1	1	AY.29	0.000016
E	3	S3S	tcA	tcG	1	1	AY.39.1	0.00004
E	3	S3S	tcA	tcG	1	1	AY.45	0.000122
E	3	S3S	tcA	tcG	1	1	AY.59	0.00053
E	3	S3S	tcA	tcC	1	1	AY.61	0.000105
E	3	S3S	tcA	tcT	1	1	AY.72	0.001361
E	3	S3S	tcA	tcT	1	1	AY.91	0.00073
E	3	S3S	tcA	tcT	1	1	AY.92	0.000287
E	3	S3S	tcA	tcT	1	1	B	0.000128
E	3	S3S	tcA	tcG	1	1	B.1.1.214	0.000055
E	3	S3S	tcA	tcG	1	1	B.1.1.236	0.006897
E	3	S3S	tcA	tcG	1	1	B.1.1.519	0.00004
E	3	S3S	tcA	tcC	1	1	B.1.111	0.001175
E	3	S3S	tcA	tcG	1	1	B.1.177.60	0.000218
E	3	S3S	tcA	tcG	1	1	B.1.243	0.00007
E	3	S3S	tcA	tcT	1	1	B.1.351	0.00003
E	3	S3S	tcA	tcT	1	1	B.1.621.1	0.000506
E	3	S3S	tcA	tcT	1	1	C.37	0.000116
E	3	S3S	tcA	tcT	1	1	P.1.1	0.000318
E	3	S3S	tcA	tcT	1	1	P.1.6	0.001946
E	3	S3S	tcA	tcT	1	1	P.2	0.000187

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.