CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : Mut = D271del1

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	271	D271del1	D1089del1	del	gaT	ga-	9	5	0.555556	3530-3532
ORF1ab/nsp3	271	D271del1	D1089del1	del	GAT	-NN	9	3	0.333333	3530-3532
ORF1ab/nsp3	271	D271del1	D1089del1	del	GaT	Aa-	9	1	0.111111	3530-3532

Details of the mutation D271del1 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	271	D271del1	gaT	ga-	5	9	All	0.000001
ORF1ab/nsp3	271	D271del1	GAT	-NN	3	9	All	0.000001
ORF1ab/nsp3	271	D271del1	GaT	Aa-	1	9	All	0
ORF1ab/nsp3	271	D271del1	gaT	ga-	2	2		0.111111
ORF1ab/nsp3	271	D271del1	GAT	-NN	1	2	B.1.2	0.000009
ORF1ab/nsp3	271	D271del1	gaT	ga-	1	2	B.1.2	0.000009
ORF1ab/nsp3	271	D271del1	gaT	ga-	2	2	P.1.12	0.000968
ORF1ab/nsp3	271	D271del1	GaT	Aa-	1	1	B	0.000128
ORF1ab/nsp3	271	D271del1	GAT	-NN	1	1	P.1	0.000016
ORF1ab/nsp3	271	D271del1	GAT	-NN	1	1	P.1.15	0.000232

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.