CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : Mut = A846A

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
S	846	A846A		syn	gcT	gcC	286	226	0.79021	24098-24100
S	846	A846A		syn	gcT	gcA	286	54	0.188811	24098-24100
S	846	A846A		syn	gcT	gcG	286	6	0.020979	24098-24100

Details of the mutation A846A 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
S	846	A846A	gcT	gcC	226	286	All	0.000043
S	846	A846A	gcT	gcA	54	286	All	0.00001
S	846	A846A	gcT	gcG	6	286	All	0.000001
S	846	A846A	gcT	gcC	61	61	B.1.617.2	0.00023
S	846	A846A	gcT	gcC	38	38	AY.102	0.001008
S	846	A846A	gcT	gcA	35	35	B.1.637	0.002558
S	846	A846A	gcT	gcC	13	19	B.1.1.7	0.000012
S	846	A846A	gcT	gcA	4	19	B.1.1.7	0.000004
S	846	A846A	gcT	gcG	2	19	B.1.1.7	0.000002
S	846	A846A	gcT	gcC	12	12	AY.105	0.007717
S	846	A846A	gcT	gcC	12	12	AY.36	0.001779
S	846	A846A	gcT	gcC	8	9	AY.39	0.000198
S	846	A846A	gcT	gcG	1	9	AY.39	0.000025
S	846	A846A	gcT	gcA	6	6	B.1.1.63	0.002315
S	846	A846A	gcT	gcC	6	6	B.6	0.00546
S	846	A846A	gcT	gcC	5	5	AY.4	0.000008
S	846	A846A	gcT	gcC	5	5	B.1.2	0.000044
S	846	A846A	gcT	gcC	4	4	AY.103	0.000025
S	846	A846A	gcT	gcA	2	4	B.1	0.000018
S	846	A846A	gcT	gcC	2	4	B.1	0.000018
S	846	A846A	gcT	gcC	4	4	B.1.1.174	0.013514
S	846	A846A	gcT	gcC	1	3		0.055556
S	846	A846A	gcT	gcG	1	3		0.055556
S	846	A846A	gcT	gcA	1	3		0.055556
S	846	A846A	gcT	gcC	3	3	AY.26	0.000085
S	846	A846A	gcT	gcC	3	3	AY.33	0.0002
S	846	A846A	gcT	gcC	3	3	AY.44	0.000018
S	846	A846A	gcT	gcC	3	3	AY.93	0.000819
S	846	A846A	gcT	gcC	2	3	B.1.1	0.000036
S	846	A846A	gcT	gcA	1	3	B.1.1	0.000018
S	846	A846A	gcT	gcC	2	3	B.1.351	0.000059
S	846	A846A	gcT	gcG	1	3	B.1.351	0.00003
S	846	A846A	gcT	gcC	2	2	AU.1	0.002532
S	846	A846A	gcT	gcC	2	2	AY.25	0.000012
S	846	A846A	gcT	gcG	1	2	AY.43	0.000004
S	846	A846A	gcT	gcC	1	2	AY.43	0.000004
S	846	A846A	gcT	gcC	2	2	AY.45	0.000243
S	846	A846A	gcT	gcC	2	2	AY.6	0.000082
S	846	A846A	gcT	gcC	2	2	B.1.1.222	0.000408
S	846	A846A	gcT	gcC	2	2	B.1.157	0.00597
S	846	A846A	gcT	gcC	2	2	B.1.526	0.000047
S	846	A846A	gcT	gcC	1	1	AY.121	0.000135
S	846	A846A	gcT	gcC	1	1	AY.20	0.000039
S	846	A846A	gcT	gcC	1	1	AY.29.1	0.000221
S	846	A846A	gcT	gcC	1	1	AY.32	0.000532
S	846	A846A	gcT	gcC	1	1	AY.4.5	0.000107
S	846	A846A	gcT	gcC	1	1	AY.46	0.000104
S	846	A846A	gcT	gcC	1	1	AY.47	0.000031
S	846	A846A	gcT	gcC	1	1	AY.5.3	0.000337
S	846	A846A	gcT	gcC	1	1	AY.51	0.000909
S	846	A846A	gcT	gcC	1	1	AY.75.1	0.00018
S	846	A846A	gcT	gcC	1	1	AY.86	0.00083
S	846	A846A	gcT	gcC	1	1	AY.9	0.000068
S	846	A846A	gcT	gcC	1	1	AY.98.1	0.000048
S	846	A846A	gcT	gcA	1	1	B	0.000128
S	846	A846A	gcT	gcC	1	1	B.1.1.277	0.000759
S	846	A846A	gcT	gcC	1	1	B.1.1.370	0.012658
S	846	A846A	gcT	gcC	1	1	B.1.1.432	0.001266
S	846	A846A	gcT	gcC	1	1	B.1.1.448	0.002033
S	846	A846A	gcT	gcA	1	1	B.1.177	0.000013
S	846	A846A	gcT	gcC	1	1	B.1.177.44	0.000519
S	846	A846A	gcT	gcC	1	1	B.1.221	0.000071
S	846	A846A	gcT	gcC	1	1	B.1.243	0.00007
S	846	A846A	gcT	gcC	1	1	B.1.350	0.002933
S	846	A846A	gcT	gcC	1	1	B.1.36.37	0.002778
S	846	A846A	gcT	gcA	1	1	B.1.621	0.000089
S	846	A846A	gcT	gcA	1	1	D.2	0.000075
S	846	A846A	gcT	gcC	1	1	P.1	0.000016
S	846	A846A	gcT	gcA	1	1	P.1.17	0.000162
S	846	A846A	gcT	gcC	1	1	Q.1	0.000126

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.