CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = M : Mut = L90F

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
M	90	L90F		nonsyn	ttG	ttT	328	319	0.972561	26790-26792
M	90	L90F		nonsyn	ttG	ttC	328	9	0.027439	26790-26792

Details of the mutation L90F 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
M	90	L90F	ttG	ttT	319	328	All	0.000061
M	90	L90F	ttG	ttC	9	328	All	0.000002
M	90	L90F	ttG	ttT	97	99	B.1.1.7	0.000087
M	90	L90F	ttG	ttC	2	99	B.1.1.7	0.000002
M	90	L90F	ttG	ttT	43	43	AY.103	0.000267
M	90	L90F	ttG	ttT	14	14	AY.43	0.000062
M	90	L90F	ttG	ttT	13	13	B.1	0.000119
M	90	L90F	ttG	ttT	13	13	B.1.516	0.02544
M	90	L90F	ttG	ttT	12	12	B.1.1.88	0.857143
M	90	L90F	ttG	ttT	11	12	B.1.617.2	0.000041
M	90	L90F	ttG	ttC	1	12	B.1.617.2	0.000004
M	90	L90F	ttG	ttT	7	7	AY.102	0.000186
M	90	L90F	ttG	ttT	7	7	AY.4	0.000011
M	90	L90F	ttG	ttT	7	7	B.1.1.402	0.077778
M	90	L90F	ttG	ttT	7	7	P.1.14	0.000335
M	90	L90F	ttG	ttT	6	6	AY.3	0.00006
M	90	L90F	ttG	ttT	5	6	B.1.1	0.000091
M	90	L90F	ttG	ttC	1	6	B.1.1	0.000018
M	90	L90F	ttG	ttT	4	6	B.1.2	0.000035
M	90	L90F	ttG	ttC	2	6	B.1.2	0.000018
M	90	L90F	ttG	ttT	5	5	AY.25	0.00003
M	90	L90F	ttG	ttT	5	5	B.1.1.153	0.005476
M	90	L90F	ttG	ttT	4	4	AY.20	0.000155
M	90	L90F	ttG	ttT	4	4	AY.4.2	0.000087
M	90	L90F	ttG	ttT	4	4	B.1.427	0.000202
M	90	L90F	ttG	ttT	3	3	AY.16.1	0.00141
M	90	L90F	ttG	ttT	3	3	AY.39	0.000074
M	90	L90F	ttG	ttT	3	3	B.1.351	0.000089
M	90	L90F	ttG	ttT	3	3	B.1.526	0.000071
M	90	L90F	ttG	ttT	3	3	C.37	0.000348
M	90	L90F	ttG	ttC	2	2		0.111111
M	90	L90F	ttG	ttC	1	2	AY.32	0.000532
M	90	L90F	ttG	ttT	1	2	AY.32	0.000532
M	90	L90F	ttG	ttT	2	2	AY.36	0.000296
M	90	L90F	ttG	ttT	2	2	AY.4.5	0.000215
M	90	L90F	ttG	ttT	2	2	AY.67	0.000929
M	90	L90F	ttG	ttT	2	2	B	0.000256
M	90	L90F	ttG	ttT	2	2	P.1	0.000032
M	90	L90F	ttG	ttT	1	1	AD.2	0.000219
M	90	L90F	ttG	ttT	1	1	AY.117	0.000085
M	90	L90F	ttG	ttT	1	1	AY.118	0.000063
M	90	L90F	ttG	ttT	1	1	AY.23	0.00007
M	90	L90F	ttG	ttT	1	1	AY.29	0.000016
M	90	L90F	ttG	ttT	1	1	AY.39.1	0.00004
M	90	L90F	ttG	ttT	1	1	AY.44	0.000006
M	90	L90F	ttG	ttT	1	1	AY.5	0.000021
M	90	L90F	ttG	ttT	1	1	AY.59	0.00053
M	90	L90F	ttG	ttT	1	1	AY.61	0.000105
M	90	L90F	ttG	ttT	1	1	AY.75	0.000056
M	90	L90F	ttG	ttT	1	1	B.1.1.311	0.000358
M	90	L90F	ttG	ttT	1	1	B.1.1.432	0.001266
M	90	L90F	ttG	ttT	1	1	B.1.1.71	0.006061
M	90	L90F	ttG	ttT	1	1	B.1.214.2	0.0006
M	90	L90F	ttG	ttT	1	1	B.1.221	0.000071
M	90	L90F	ttG	ttT	1	1	B.1.258	0.000067
M	90	L90F	ttG	ttT	1	1	B.1.391	0.001127
M	90	L90F	ttG	ttT	1	1	B.1.429	0.000024
M	90	L90F	ttG	ttT	1	1	B.1.524	0.001406
M	90	L90F	ttG	ttT	1	1	B.1.577	0.000687
M	90	L90F	ttG	ttT	1	1	B.1.621	0.000089
M	90	L90F	ttG	ttT	1	1	P.1.17	0.000162
M	90	L90F	ttG	ttT	1	1	P.7	0.004367
M	90	L90F	ttG	ttT	1	1	Q.6	0.006623

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.