CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : Mut = M1L

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
N	1	M1L		nonsyn	Atg	Ttg	593	392	0.661046	28274-28276
N	1	M1L		nonsyn	Atg	Ctg	593	113	0.190556	28274-28276
N	1	M1L		nonsyn	AtG	TtA	593	88	0.148398	28274-28276

Details of the mutation M1L 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
N	1	M1L	Atg	Ttg	392	593	All	0.000075
N	1	M1L	Atg	Ctg	113	593	All	0.000022
N	1	M1L	AtG	TtA	88	593	All	0.000017
N	1	M1L	Atg	Ttg	239	239	B.1.1.7	0.000214
N	1	M1L	Atg	Ttg	87	163	P.1	0.001371
N	1	M1L	AtG	TtA	76	163	P.1	0.001197
N	1	M1L	Atg	Ctg	30	30	AY.25	0.00018
N	1	M1L	Atg	Ctg	21	21	AY.103	0.00013
N	1	M1L	Atg	Ctg	16	16	AY.44	0.000097
N	1	M1L	Atg	Ttg	16	16	AY.99.2	0.001475
N	1	M1L	Atg	Ttg	6	12	P.1.4	0.005859
N	1	M1L	AtG	TtA	6	12	P.1.4	0.005859
N	1	M1L	Atg	Ctg	9	9	AY.3	0.00009
N	1	M1L	Atg	Ctg	7	7	AY.47	0.000218
N	1	M1L	Atg	Ttg	7	7	B.1.1.515	0.14
N	1	M1L	Atg	Ctg	6	6	AY.119	0.000212
N	1	M1L	Atg	Ttg	3	6	P.1.2	0.003468
N	1	M1L	AtG	TtA	3	6	P.1.2	0.003468
N	1	M1L	Atg	Ttg	5	5	B.1.1	0.000091
N	1	M1L	Atg	Ctg	4	4	AY.100	0.000184
N	1	M1L	Atg	Ttg	4	4	B.1	0.000037
N	1	M1L	AtG	TtA	2	4	P.1.15	0.000465
N	1	M1L	Atg	Ttg	2	4	P.1.15	0.000465
N	1	M1L	Atg	Ctg	3	3	AY.39	0.000074
N	1	M1L	Atg	Ttg	2	3	B.1.617.1	0.000258
N	1	M1L	Atg	Ctg	1	3	B.1.617.1	0.000129
N	1	M1L	Atg	Ttg	3	3	B.1.617.2	0.000011
N	1	M1L	Atg	Ttg	3	3	B.1.617.3	0.008955
N	1	M1L	Atg	Ctg	2	2	AY.113	0.000285
N	1	M1L	Atg	Ctg	2	2	AY.3.1	0.000171
N	1	M1L	Atg	Ctg	1	2	AY.43	0.000004
N	1	M1L	Atg	Ttg	1	2	AY.43	0.000004
N	1	M1L	Atg	Ctg	2	2	AY.75	0.000112
N	1	M1L	Atg	Ttg	2	2	AY.99.1	0.003106
N	1	M1L	Atg	Ttg	2	2	B.1.526	0.000047
N	1	M1L	Atg	Ttg	1	2	P.1.12	0.000484
N	1	M1L	AtG	TtA	1	2	P.1.12	0.000484
N	1	M1L	Atg	Ttg	1	1	AY.101	0.00049
N	1	M1L	Atg	Ctg	1	1	AY.105	0.000643
N	1	M1L	Atg	Ctg	1	1	AY.117	0.000085
N	1	M1L	Atg	Ctg	1	1	AY.20	0.000039
N	1	M1L	Atg	Ctg	1	1	AY.23	0.00007
N	1	M1L	Atg	Ctg	1	1	AY.26	0.000028
N	1	M1L	Atg	Ctg	1	1	AY.46	0.000104
N	1	M1L	Atg	Ctg	1	1	AY.84	0.000437
N	1	M1L	Atg	Ctg	1	1	AY.92	0.000287
N	1	M1L	Atg	Ttg	1	1	B.1.160	0.000031
N	1	M1L	Atg	Ttg	1	1	B.1.177.73	0.000566
N	1	M1L	Atg	Ttg	1	1	B.1.351	0.00003
N	1	M1L	Atg	Ttg	1	1	B.1.417	0.028571
N	1	M1L	Atg	Ttg	1	1	B.1.575	0.000303
N	1	M1L	Atg	Ctg	1	1	B.1.595	0.000261
N	1	M1L	Atg	Ttg	1	1	P.1.1	0.000318
N	1	M1L	Atg	Ttg	1	1	P.1.10	0.000269
N	1	M1L	Atg	Ttg	1	1	Q.4	0.000455

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.