CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : Mut = A1557T

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
ORF1ab/nsp3	1557	A1557T	A2375T	nonsyn	Gcc	Acc	1006	1006	1	7388-7390

Details of the mutation A1557T 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
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1006	1006	All	0.000192
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	672	672	AY.4	0.001046
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	61	61	AY.103	0.000379
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	30	30	B.1.617.2	0.000113
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	25	25	B.1.1.7	0.000022
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	22	22	B.1.2	0.000194
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	18	18	B.1	0.000165
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	16	16	AY.3	0.000159
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	15	15	AY.43	0.000066
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	13	13	AY.23	0.000907
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	12	12	AY.44	0.000073
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	8	8	AY.102	0.000212
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	7	7	AY.4.2	0.000152
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	6	6	AY.39	0.000148
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	5	5	AY.25	0.00003
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	5	5	AY.46	0.00052
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	5	5	B.1.596	0.000436
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	4	4	AY.100	0.000184
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	4	4	B.1.637	0.000292
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	3	3	AY.26	0.000085
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	3	3	AY.46.4	0.000494
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	3	3	AY.5	0.000062
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	3	3	B.1.1.1	0.00098
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	3	3	B.1.147	0.002268
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	3	3	P.1	0.000047
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	2	2	AY.106	0.00067
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	2	2	AY.110	0.000225
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	2	2	AY.113	0.000285
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	2	2	AY.20	0.000078
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	2	2	AY.42	0.00008
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	2	2	AY.86	0.00166
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	2	2	AY.9.2	0.000073
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	2	2	B.1.1.37	0.000386
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	2	2	B.1.1.409	0.005666
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	2	2	B.1.210	0.004264
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	2	2	B.1.240	0.000431
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	2	2	B.1.36	0.000292
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	2	2	B.6.6	0.001778
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	2	2	Q.1	0.000253
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	AY.1	0.000396
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	AY.12	0.000316
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	AY.120	0.000037
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	AY.39.1	0.00004
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	AY.4.2.1	0.000149
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	AY.46.2	0.000635
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	AY.46.6	0.000072
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	AY.5.4	0.000277
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	AY.75	0.000056
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	AY.84	0.000437
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	AY.9	0.000068
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	AY.9.1	0.000084
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	AY.97	0.001701
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	AY.98	0.000079
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	B.1.1	0.000018
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	B.1.1.222	0.000204
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	B.1.1.47	0.005348
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	B.1.1.519	0.00004
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	B.1.146	0.004237
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	B.1.160	0.000031
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	B.1.160.29	0.004219
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	B.1.177.73	0.000566
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	B.1.243	0.00007
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	B.1.258.14	0.00098
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	B.1.274	0.011905
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	B.1.351	0.00003
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	B.1.416	0.001269
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	B.1.456	0.003268
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	B.1.595	0.000261
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	B.1.596.1	0.009346
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	B.1.605	0.005952
ORF1ab/nsp3	1557	A1557T	Gcc	Acc	1	1	B.6	0.00091

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.