CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF7a : Mut = Y40L

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
ORF7a	40	Y40L		nonsyn	tAC	tTA	40	29	0.725	27511-27513
ORF7a	40	Y40L		nonsyn	tAC	tTG	40	7	0.175	27511-27513
ORF7a	40	Y40L		nonsyn	TAc	CTc	40	4	0.1	27511-27513

Details of the mutation Y40L 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
ORF7a	40	Y40L	tAC	tTA	29	40	All	0.000006
ORF7a	40	Y40L	tAC	tTG	7	40	All	0.000001
ORF7a	40	Y40L	TAc	CTc	4	40	All	0.000001
ORF7a	40	Y40L	tAC	tTA	9	10	B.1	0.000082
ORF7a	40	Y40L	tAC	tTG	1	10	B.1	0.000009
ORF7a	40	Y40L	tAC	tTG	6	9	B.1.617.2	0.000023
ORF7a	40	Y40L	tAC	tTA	3	9	B.1.617.2	0.000011
ORF7a	40	Y40L	tAC	tTA	5	7	B.1.1.7	0.000004
ORF7a	40	Y40L	TAc	CTc	2	7	B.1.1.7	0.000002
ORF7a	40	Y40L	tAC	tTA	6	6	AY.25	0.000036
ORF7a	40	Y40L	tAC	tTA	2	2	B.1.1	0.000036
ORF7a	40	Y40L	tAC	tTA	1	1	AY.103	0.000006
ORF7a	40	Y40L	TAc	CTc	1	1	AY.110	0.000113
ORF7a	40	Y40L	TAc	CTc	1	1	AY.3.1	0.000085
ORF7a	40	Y40L	tAC	tTA	1	1	AY.44	0.000006
ORF7a	40	Y40L	tAC	tTA	1	1	B.1.160	0.000031
ORF7a	40	Y40L	tAC	tTA	1	1	B.1.576	0.000907

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.