CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : Mut = I458T

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	458	I458T	I1276T	nonsyn	aTc	aCc	2158	2156	0.999073	4091-4093
ORF1ab/nsp3	458	I458T	I1276T	nonsyn	aTC	aCT	2158	1	0.000463392	4091-4093
ORF1ab/nsp3	458	I458T	I1276T	nonsyn	aTC	aCA	2158	1	0.000463392	4091-4093

Details of the mutation I458T 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	458	I458T	aTc	aCc	2156	2158	All	0.000412
ORF1ab/nsp3	458	I458T	aTC	aCA	1	2158	All	0
ORF1ab/nsp3	458	I458T	aTC	aCT	1	2158	All	0
ORF1ab/nsp3	458	I458T	aTc	aCc	1063	1063	B.1.1.7	0.000952
ORF1ab/nsp3	458	I458T	aTc	aCc	288	288	AY.4.2	0.006246
ORF1ab/nsp3	458	I458T	aTc	aCc	246	246	AY.4	0.000383
ORF1ab/nsp3	458	I458T	aTc	aCc	91	91	B.1.617.2	0.000343
ORF1ab/nsp3	458	I458T	aTc	aCc	48	48	AY.43	0.000213
ORF1ab/nsp3	458	I458T	aTc	aCc	38	38	B.1	0.000348
ORF1ab/nsp3	458	I458T	aTc	aCc	37	37	AY.7.1	0.00417
ORF1ab/nsp3	458	I458T	aTc	aCc	32	32	P.1	0.000504
ORF1ab/nsp3	458	I458T	aTc	aCc	28	28	B.1.1.70	0.00955
ORF1ab/nsp3	458	I458T	aTc	aCc	28	28	B.1.2	0.000247
ORF1ab/nsp3	458	I458T	aTc	aCc	18	18	AY.47	0.00056
ORF1ab/nsp3	458	I458T	aTc	aCc	16	16	C.37	0.001857
ORF1ab/nsp3	458	I458T	aTc	aCc	15	15	AY.29	0.000237
ORF1ab/nsp3	458	I458T	aTc	aCc	14	14	AY.44	0.000085
ORF1ab/nsp3	458	I458T	aTc	aCc	13	13	B.1.177	0.000171
ORF1ab/nsp3	458	I458T	aTc	aCc	12	12	B.1.1.153	0.013143
ORF1ab/nsp3	458	I458T	aTc	aCc	10	10	AY.25	0.00006
ORF1ab/nsp3	458	I458T	aTc	aCc	10	10	B.1.1	0.000181
ORF1ab/nsp3	458	I458T	aTc	aCc	10	10	B.1.177.42	0.008945
ORF1ab/nsp3	458	I458T	aTc	aCc	8	8	AY.9	0.000541
ORF1ab/nsp3	458	I458T	aTc	aCc	8	8	B.1.609	0.003835
ORF1ab/nsp3	458	I458T	aTc	aCc	7	7	AY.103	0.000043
ORF1ab/nsp3	458	I458T	aTc	aCc	6	6	AY.35	0.001398
ORF1ab/nsp3	458	I458T	aTc	aCc	6	6	AY.39	0.000148
ORF1ab/nsp3	458	I458T	aTc	aCc	5	5	AY.102	0.000133
ORF1ab/nsp3	458	I458T	aTc	aCc	5	5	AY.3	0.00005
ORF1ab/nsp3	458	I458T	aTc	aCc	4	4	B.1.1.176	0.001757
ORF1ab/nsp3	458	I458T	aTc	aCc	4	4	B.1.1.41	0.025316
ORF1ab/nsp3	458	I458T	aTc	aCc	3	3	AY.106	0.001005
ORF1ab/nsp3	458	I458T	aTc	aCc	3	3	AY.5	0.000062
ORF1ab/nsp3	458	I458T	aTc	aCc	3	3	AY.87	0.002498
ORF1ab/nsp3	458	I458T	aTc	aCc	3	3	B.1.1.432	0.003797
ORF1ab/nsp3	458	I458T	aTc	aCc	3	3	B.1.351	0.000089
ORF1ab/nsp3	458	I458T	aTc	aCc	3	3	B.1.526	0.000071
ORF1ab/nsp3	458	I458T	aTc	aCc	1	2		0.055556
ORF1ab/nsp3	458	I458T	aTC	aCT	1	2		0.055556
ORF1ab/nsp3	458	I458T	aTc	aCc	2	2	AY.100	0.000092
ORF1ab/nsp3	458	I458T	aTc	aCc	2	2	AY.116	0.000574
ORF1ab/nsp3	458	I458T	aTc	aCc	2	2	AY.117	0.000169
ORF1ab/nsp3	458	I458T	aTc	aCc	2	2	AY.120.2.1	0.000997
ORF1ab/nsp3	458	I458T	aTc	aCc	2	2	AY.23.1	0.000835
ORF1ab/nsp3	458	I458T	aTc	aCc	2	2	AY.26	0.000057
ORF1ab/nsp3	458	I458T	aTc	aCc	2	2	AY.61	0.00021
ORF1ab/nsp3	458	I458T	aTc	aCc	2	2	B.1.139	0.001466
ORF1ab/nsp3	458	I458T	aTc	aCc	2	2	B.1.169	0.029851
ORF1ab/nsp3	458	I458T	aTc	aCc	2	2	B.1.367	0.001585
ORF1ab/nsp3	458	I458T	aTc	aCc	1	2	B.1.369	0.000285
ORF1ab/nsp3	458	I458T	aTC	aCA	1	2	B.1.369	0.000285
ORF1ab/nsp3	458	I458T	aTc	aCc	2	2	B.1.617.1	0.000258
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	A.5	0.001923
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	AY.10	0.00053
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	AY.13	0.000161
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	AY.20	0.000039
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	AY.23	0.00007
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	AY.24	0.000431
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	AY.37	0.000316
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	AY.46.4	0.000165
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	AY.5.4	0.000277
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	AY.53	0.000288
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	AY.59	0.00053
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	AY.6	0.000041
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	AY.62	0.000436
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	AY.86	0.00083
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	AY.9.1	0.000084
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	AY.9.2	0.000037
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	AY.99.2	0.000092
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.1.1	0.000327
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.1.222	0.000204
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.1.284	0.000107
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.1.29	0.010309
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.1.333	0.001076
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.1.377	0.001381
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.177.44	0.000519
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.177.7	0.000165
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.177.73	0.000566
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.177.75	0.001041
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.177.77	0.000726
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.237	0.004975
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.239	0.001221
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.36.17	0.000494
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.422	0.000812
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.427	0.00005
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.438.1	0.000107
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.497	0.000315
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.595	0.000261
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.621	0.000089
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.625	0.002353
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	B.1.637	0.000073
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	C.36.3	0.000567
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	D.2	0.000075
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	P.1.10	0.000269
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	Q.8	0.000165
ORF1ab/nsp3	458	I458T	aTc	aCc	1	1	R.1	0.00009

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.