CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF7a : Mut = S83X

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	83	S83X		nonsyn	tCa	tGa	160	82	0.5125	27640-27642
ORF7a	83	S83X		nonsyn	tCa	tAa	160	77	0.48125	27640-27642
ORF7a	83	S83X		nonsyn	tCA	tAG	160	1	0.00625	27640-27642

Details of the mutation S83X 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	83	S83X	tCa	tGa	82	160	All	0.000016
ORF7a	83	S83X	tCa	tAa	77	160	All	0.000015
ORF7a	83	S83X	tCA	tAG	1	160	All	0
ORF7a	83	S83X	tCa	tGa	34	35	B.1.177.21	0.0026
ORF7a	83	S83X	tCa	tAa	1	35	B.1.177.21	0.000076
ORF7a	83	S83X	tCa	tAa	11	21	AY.4	0.000017
ORF7a	83	S83X	tCa	tGa	10	21	AY.4	0.000016
ORF7a	83	S83X	tCa	tAa	12	21	B.1.1.7	0.000011
ORF7a	83	S83X	tCa	tGa	9	21	B.1.1.7	0.000008
ORF7a	83	S83X	tCa	tGa	9	9	AY.99.2	0.000829
ORF7a	83	S83X	tCa	tAa	7	8	AY.43	0.000031
ORF7a	83	S83X	tCa	tGa	1	8	AY.43	0.000004
ORF7a	83	S83X	tCa	tAa	6	7	AY.25	0.000036
ORF7a	83	S83X	tCa	tGa	1	7	AY.25	0.000006
ORF7a	83	S83X	tCa	tGa	7	7	B.1.596	0.00061
ORF7a	83	S83X	tCa	tGa	3	6	B.1	0.000027
ORF7a	83	S83X	tCa	tAa	3	6	B.1	0.000027
ORF7a	83	S83X	tCa	tAa	6	6	B.1.1.519	0.000238
ORF7a	83	S83X	tCa	tAa	2	3	AY.3	0.00002
ORF7a	83	S83X	tCa	tGa	1	3	AY.3	0.00001
ORF7a	83	S83X	tCa	tAa	2	2		0.111111
ORF7a	83	S83X	tCa	tGa	1	2	AY.20	0.000039
ORF7a	83	S83X	tCa	tAa	1	2	AY.20	0.000039
ORF7a	83	S83X	tCa	tAa	2	2	AY.39	0.000049
ORF7a	83	S83X	tCa	tAa	2	2	AY.5	0.000041
ORF7a	83	S83X	tCa	tGa	2	2	AY.9.1	0.000167
ORF7a	83	S83X	tCa	tAa	2	2	B.1.160.28	0.005848
ORF7a	83	S83X	tCa	tAa	2	2	B.1.617.2	0.000008
ORF7a	83	S83X	tCa	tAa	1	1	A	0.000387
ORF7a	83	S83X	tCA	tAG	1	1	A.2.5.1	0.004808
ORF7a	83	S83X	tCa	tAa	1	1	AY.110	0.000113
ORF7a	83	S83X	tCa	tAa	1	1	AY.119	0.000035
ORF7a	83	S83X	tCa	tAa	1	1	AY.3.1	0.000085
ORF7a	83	S83X	tCa	tAa	1	1	AY.38	0.000499
ORF7a	83	S83X	tCa	tAa	1	1	AY.42	0.00004
ORF7a	83	S83X	tCa	tAa	1	1	AY.47	0.000031
ORF7a	83	S83X	tCa	tAa	1	1	AY.58	0.000907
ORF7a	83	S83X	tCa	tAa	1	1	AY.59	0.00053
ORF7a	83	S83X	tCa	tAa	1	1	AY.7.1	0.000113
ORF7a	83	S83X	tCa	tAa	1	1	AY.9.2	0.000037
ORF7a	83	S83X	tCa	tAa	1	1	B	0.000128
ORF7a	83	S83X	tCa	tGa	1	1	B.1.1	0.000018
ORF7a	83	S83X	tCa	tAa	1	1	B.1.1.269	0.001353
ORF7a	83	S83X	tCa	tGa	1	1	B.1.1.398	0.003226
ORF7a	83	S83X	tCa	tAa	1	1	B.1.177	0.000013
ORF7a	83	S83X	tCa	tGa	1	1	B.1.2	0.000009
ORF7a	83	S83X	tCa	tAa	1	1	B.1.243	0.00007
ORF7a	83	S83X	tCa	tAa	1	1	B.1.301	0.005917
ORF7a	83	S83X	tCa	tGa	1	1	B.1.526	0.000024
ORF7a	83	S83X	tCa	tAa	1	1	B.1.623	0.000536
ORF7a	83	S83X	tCa	tAa	1	1	D.2	0.000075

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.