CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF7a : Mut = Y40X

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	Y40X		nonsyn	taC	taA	232	163	0.702586	27511-27513
ORF7a	40	Y40X		nonsyn	taC	taG	232	64	0.275862	27511-27513
ORF7a	40	Y40X		nonsyn	tAC	tGA	232	5	0.0215517	27511-27513

Details of the mutation Y40X 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	Y40X	taC	taA	163	232	All	0.000031
ORF7a	40	Y40X	taC	taG	64	232	All	0.000012
ORF7a	40	Y40X	tAC	tGA	5	232	All	0.000001
ORF7a	40	Y40X	taC	taA	47	63	B.1.1.7	0.000042
ORF7a	40	Y40X	taC	taG	16	63	B.1.1.7	0.000014
ORF7a	40	Y40X	taC	taA	36	37	AY.4	0.000056
ORF7a	40	Y40X	taC	taG	1	37	AY.4	0.000002
ORF7a	40	Y40X	taC	taG	21	24	B.1.160	0.000655
ORF7a	40	Y40X	taC	taA	2	24	B.1.160	0.000062
ORF7a	40	Y40X	tAC	tGA	1	24	B.1.160	0.000031
ORF7a	40	Y40X	taC	taG	13	21	B.1.617.2	0.000049
ORF7a	40	Y40X	taC	taA	6	21	B.1.617.2	0.000023
ORF7a	40	Y40X	tAC	tGA	2	21	B.1.617.2	0.000008
ORF7a	40	Y40X	taC	taA	11	12	B.1	0.000101
ORF7a	40	Y40X	taC	taG	1	12	B.1	0.000009
ORF7a	40	Y40X	taC	taA	9	9	AY.5	0.000186
ORF7a	40	Y40X	taC	taA	6	6	AY.103	0.000037
ORF7a	40	Y40X	taC	taA	5	6	AY.25	0.00003
ORF7a	40	Y40X	tAC	tGA	1	6	AY.25	0.000006
ORF7a	40	Y40X	taC	taG	5	6	AY.3	0.00005
ORF7a	40	Y40X	taC	taA	1	6	AY.3	0.00001
ORF7a	40	Y40X	taC	taA	6	6	AY.46.4	0.000987
ORF7a	40	Y40X	taC	taG	3	4	AY.43	0.000013
ORF7a	40	Y40X	taC	taA	1	4	AY.43	0.000004
ORF7a	40	Y40X	taC	taA	4	4	B.1.1	0.000073
ORF7a	40	Y40X	taC	taA	3	3	AY.102	0.00008
ORF7a	40	Y40X	taC	taA	3	3	AY.29	0.000047
ORF7a	40	Y40X	taC	taA	2	2	AY.120	0.000074
ORF7a	40	Y40X	taC	taA	1	2	AY.44	0.000006
ORF7a	40	Y40X	taC	taG	1	2	AY.44	0.000006
ORF7a	40	Y40X	taC	taA	2	2	AY.47	0.000062
ORF7a	40	Y40X	taC	taA	2	2	B.1.1.385	0.008929
ORF7a	40	Y40X	taC	taA	2	2	B.1.177	0.000026
ORF7a	40	Y40X	taC	taA	2	2	B.1.177.76	0.004988
ORF7a	40	Y40X	taC	taA	2	2	B.1.575	0.000607
ORF7a	40	Y40X	taC	taA	2	2	P.1	0.000032
ORF7a	40	Y40X	taC	taG	1	1	AY.119	0.000035
ORF7a	40	Y40X	taC	taA	1	1	AY.121	0.000135
ORF7a	40	Y40X	taC	taA	1	1	AY.26	0.000028
ORF7a	40	Y40X	taC	taA	1	1	AY.39	0.000025
ORF7a	40	Y40X	taC	taA	1	1	AY.70	0.000209
ORF7a	40	Y40X	taC	taA	1	1	B.1.221	0.000071
ORF7a	40	Y40X	taC	taA	1	1	B.1.351	0.00003
ORF7a	40	Y40X	taC	taG	1	1	B.1.427	0.00005
ORF7a	40	Y40X	taC	taG	1	1	B.1.429	0.000024
ORF7a	40	Y40X	tAC	tGA	1	1	B.1.538	0.008065
ORF7a	40	Y40X	taC	taA	1	1	B.1.576	0.000907
ORF7a	40	Y40X	taC	taA	1	1	C.37	0.000116

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.