CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 501

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	501	K501E	K1319E	nonsyn	Aaa	Gaa	530	530	1	4220-4222
ORF1ab/nsp3	501	K501R	K1319R	nonsyn	aAa	aGa	102	95	0.931373	4220-4222
ORF1ab/nsp3	501	K501R	K1319R	nonsyn	AAA	CGT	102	2	0.0196078	4220-4222
ORF1ab/nsp3	501	K501R	K1319R	nonsyn	AAA	CGG	102	2	0.0196078	4220-4222
ORF1ab/nsp3	501	K501R	K1319R	nonsyn	AAa	CGa	102	2	0.0196078	4220-4222
ORF1ab/nsp3	501	K501R	K1319R	nonsyn	aAA	aGG	102	1	0.00980392	4220-4222
ORF1ab/nsp3	501	K501K	K1319K	syn	aaA	aaG	83	83	1	4220-4222
ORF1ab/nsp3	501	K501N	K1319N	nonsyn	aaA	aaC	62	53	0.854839	4220-4222
ORF1ab/nsp3	501	K501N	K1319N	nonsyn	aaA	aaT	62	9	0.145161	4220-4222
ORF1ab/nsp3	501	K501T	K1319T	nonsyn	aAa	aCa	39	39	1	4220-4222
ORF1ab/nsp3	501	K501del	K1319del	del	AAA	---	21	21	1	4220-4222
ORF1ab/nsp3	501	K501I	K1319I	nonsyn	aAa	aTa	13	13	1	4220-4222
ORF1ab/nsp3	501	K501Q	K1319Q	nonsyn	Aaa	Caa	13	13	1	4220-4222
ORF1ab/nsp3	501	K501X	K1319X	nonsyn	Aaa	Taa	4	4	1	4220-4222
ORF1ab/nsp3	501	K501V	K1319V	nonsyn	AAa	GTa	2	2	1	4220-4222
ORF1ab/nsp3	501	K501S	K1319S	nonsyn	aAA	aGT	2	2	1	4220-4222
ORF1ab/nsp3	501	K501del2	K1319del2	del	AAa	--a	1	1	1	4220-4222
ORF1ab/nsp3	501	K501del1	K1319del1	del	AaA	-aT	1	1	1	4220-4222

Details of the mutation no 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	501	K501E	Aaa	Gaa	530	530	All	0.000101
ORF1ab/nsp3	501	K501E	Aaa	Gaa	407	407	B.1.625	0.957647
ORF1ab/nsp3	501	K501R	aAa	aGa	95	102	All	0.000018
ORF1ab/nsp3	501	K501R	AAA	CGG	2	102	All	0
ORF1ab/nsp3	501	K501R	AAa	CGa	2	102	All	0
ORF1ab/nsp3	501	K501R	AAA	CGT	2	102	All	0
ORF1ab/nsp3	501	K501R	aAA	aGG	1	102	All	0
ORF1ab/nsp3	501	K501K	aaA	aaG	83	83	All	0.000016
ORF1ab/nsp3	501	K501N	aaA	aaC	53	62	All	0.00001
ORF1ab/nsp3	501	K501N	aaA	aaT	9	62	All	0.000002
ORF1ab/nsp3	501	K501T	aAa	aCa	39	39	All	0.000007
ORF1ab/nsp3	501	K501R	aAa	aGa	39	39	B.1.429	0.000918
ORF1ab/nsp3	501	K501E	Aaa	Gaa	34	34	B.1	0.000311
ORF1ab/nsp3	501	K501N	aaA	aaC	29	29	B.1.1.7	0.000026
ORF1ab/nsp3	501	K501T	aAa	aCa	26	26	B.1.234	0.003431
ORF1ab/nsp3	501	K501K	aaA	aaG	25	25	B.1.1.7	0.000022
ORF1ab/nsp3	501	K501del	AAA	---	21	21	All	0.000004
ORF1ab/nsp3	501	K501E	Aaa	Gaa	21	21	AY.25	0.000126
ORF1ab/nsp3	501	K501K	aaA	aaG	21	21	B.1.416.1	0.032813
ORF1ab/nsp3	501	K501I	aAa	aTa	13	13	All	0.000002
ORF1ab/nsp3	501	K501Q	Aaa	Caa	13	13	All	0.000002
ORF1ab/nsp3	501	K501R	aAa	aGa	9	9	AY.43	0.00004
ORF1ab/nsp3	501	K501R	aAa	aGa	7	7	AY.4	0.000011
ORF1ab/nsp3	501	K501R	aAa	aGa	7	7	B.1.1.7	0.000006
ORF1ab/nsp3	501	K501T	aAa	aCa	7	7	B.1.1.7	0.000006
ORF1ab/nsp3	501	K501R	AAa	CGa	2	6		0.111111
ORF1ab/nsp3	501	K501R	AAA	CGG	2	6		0.111111
ORF1ab/nsp3	501	K501R	AAA	CGT	2	6		0.111111
ORF1ab/nsp3	501	K501E	Aaa	Gaa	6	6	B.1.1.7	0.000005
ORF1ab/nsp3	501	K501E	Aaa	Gaa	6	6	B.1.128	0.003812
ORF1ab/nsp3	501	K501N	aaA	aaC	5	5	AY.4	0.000008
ORF1ab/nsp3	501	K501N	aaA	aaC	4	5	B.1	0.000037
ORF1ab/nsp3	501	K501N	aaA	aaT	1	5	B.1	0.000009
ORF1ab/nsp3	501	K501N	aaA	aaC	5	5	B.1.177.86	0.000917
ORF1ab/nsp3	501	K501K	aaA	aaG	5	5	B.1.617.2	0.000019
ORF1ab/nsp3	501	K501E	Aaa	Gaa	5	5	P.1	0.000079
ORF1ab/nsp3	501	K501X	Aaa	Taa	4	4	All	0.000001
ORF1ab/nsp3	501	K501R	aAa	aGa	4	4	AY.103	0.000025
ORF1ab/nsp3	501	K501K	aaA	aaG	4	4	AY.25	0.000024
ORF1ab/nsp3	501	K501K	aaA	aaG	4	4	AY.4	0.000006
ORF1ab/nsp3	501	K501E	Aaa	Gaa	4	4	B.1.177	0.000053
ORF1ab/nsp3	501	K501K	aaA	aaG	4	4	B.1.2	0.000035
ORF1ab/nsp3	501	K501R	aAa	aGa	4	4	B.1.320	0.004981
ORF1ab/nsp3	501	K501E	Aaa	Gaa	4	4	B.1.617.2	0.000015
ORF1ab/nsp3	501	K501Q	Aaa	Caa	3	3	AY.25	0.000018
ORF1ab/nsp3	501	K501del	AAA	---	3	3	AY.43	0.000013
ORF1ab/nsp3	501	K501K	aaA	aaG	3	3	AY.81	0.005976
ORF1ab/nsp3	501	K501K	aaA	aaG	3	3	B.1	0.000027
ORF1ab/nsp3	501	K501del	AAA	---	3	3	B.1.1.7	0.000003
ORF1ab/nsp3	501	K501Q	Aaa	Caa	3	3	B.1.2	0.000026
ORF1ab/nsp3	501	K501I	aAa	aTa	3	3	B.1.2	0.000026
ORF1ab/nsp3	501	K501E	Aaa	Gaa	3	3	B.1.36.35	0.007812
ORF1ab/nsp3	501	K501E	Aaa	Gaa	3	3	B.1.36.8	0.003
ORF1ab/nsp3	501	K501E	Aaa	Gaa	3	3	B.1.595	0.000783
ORF1ab/nsp3	501	K501R	aAa	aGa	3	3	B.1.617.2	0.000011
ORF1ab/nsp3	501	K501E	Aaa	Gaa	2	2		0.111111
ORF1ab/nsp3	501	K501S	aAA	aGT	2	2		0.111111
ORF1ab/nsp3	501	K501del	AAA	---	2	2		0.111111
ORF1ab/nsp3	501	K501V	AAa	GTa	2	2	All	0
ORF1ab/nsp3	501	K501S	aAA	aGT	2	2	All	0
ORF1ab/nsp3	501	K501N	aaA	aaC	2	2	AY.102	0.000053
ORF1ab/nsp3	501	K501E	Aaa	Gaa	2	2	AY.103	0.000012
ORF1ab/nsp3	501	K501E	Aaa	Gaa	2	2	AY.43	0.000009
ORF1ab/nsp3	501	K501I	aAa	aTa	2	2	AY.43	0.000009
ORF1ab/nsp3	501	K501E	Aaa	Gaa	2	2	B	0.000256
ORF1ab/nsp3	501	K501R	aAa	aGa	2	2	B.1	0.000018
ORF1ab/nsp3	501	K501I	aAa	aTa	2	2	B.1.1	0.000036
ORF1ab/nsp3	501	K501R	aAa	aGa	2	2	B.1.1	0.000036
ORF1ab/nsp3	501	K501E	Aaa	Gaa	2	2	B.1.1.28	0.000622
ORF1ab/nsp3	501	K501N	aaA	aaC	1	2	B.1.177	0.000013
ORF1ab/nsp3	501	K501N	aaA	aaT	1	2	B.1.177	0.000013
ORF1ab/nsp3	501	K501Q	Aaa	Caa	2	2	B.1.575	0.000607
ORF1ab/nsp3	501	K501R	aAa	aGa	2	2	B.1.576	0.001813
ORF1ab/nsp3	501	K501E	Aaa	Gaa	2	2	D.2	0.00015
ORF1ab/nsp3	501	K501del2	AAa	--a	1	1	All	0
ORF1ab/nsp3	501	K501del1	AaA	-aT	1	1	All	0
ORF1ab/nsp3	501	K501R	aAa	aGa	1	1	AY.100	0.000046
ORF1ab/nsp3	501	K501N	aaA	aaC	1	1	AY.100	0.000046
ORF1ab/nsp3	501	K501Q	Aaa	Caa	1	1	AY.103	0.000006
ORF1ab/nsp3	501	K501N	aaA	aaT	1	1	AY.103	0.000006
ORF1ab/nsp3	501	K501N	aaA	aaC	1	1	AY.117	0.000085
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	AY.120	0.000037
ORF1ab/nsp3	501	K501del	AAA	---	1	1	AY.25	0.000006
ORF1ab/nsp3	501	K501N	aaA	aaC	1	1	AY.26	0.000028
ORF1ab/nsp3	501	K501R	aAa	aGa	1	1	AY.27	0.000065
ORF1ab/nsp3	501	K501Q	Aaa	Caa	1	1	AY.29	0.000016
ORF1ab/nsp3	501	K501N	aaA	aaC	1	1	AY.29	0.000016
ORF1ab/nsp3	501	K501T	aAa	aCa	1	1	AY.29	0.000016
ORF1ab/nsp3	501	K501N	aaA	aaT	1	1	AY.3	0.00001
ORF1ab/nsp3	501	K501T	aAa	aCa	1	1	AY.35	0.000233
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	AY.39	0.000025
ORF1ab/nsp3	501	K501N	aaA	aaT	1	1	AY.39	0.000025
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	AY.4	0.000002
ORF1ab/nsp3	501	K501N	aaA	aaC	1	1	AY.4.3	0.000842
ORF1ab/nsp3	501	K501del	AAA	---	1	1	AY.4.5	0.000107
ORF1ab/nsp3	501	K501N	aaA	aaC	1	1	AY.43	0.000004
ORF1ab/nsp3	501	K501Q	Aaa	Caa	1	1	AY.43	0.000004
ORF1ab/nsp3	501	K501del2	AAa	--a	1	1	AY.43	0.000004
ORF1ab/nsp3	501	K501K	aaA	aaG	1	1	AY.44	0.000006
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	AY.44	0.000006
ORF1ab/nsp3	501	K501R	aAA	aGG	1	1	AY.44	0.000006
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	AY.45	0.000122
ORF1ab/nsp3	501	K501N	aaA	aaT	1	1	AY.46	0.000104
ORF1ab/nsp3	501	K501R	aAa	aGa	1	1	AY.46.2	0.000635
ORF1ab/nsp3	501	K501R	aAa	aGa	1	1	AY.47	0.000031
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	AY.5.3	0.000337
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	AY.53	0.000288
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	AY.54	0.000095
ORF1ab/nsp3	501	K501del	AAA	---	1	1	AY.81	0.001992
ORF1ab/nsp3	501	K501N	aaA	aaT	1	1	AY.98	0.000079
ORF1ab/nsp3	501	K501del	AAA	---	1	1	AY.99	0.001049
ORF1ab/nsp3	501	K501N	aaA	aaC	1	1	B	0.000128
ORF1ab/nsp3	501	K501X	Aaa	Taa	1	1	B.1	0.000009
ORF1ab/nsp3	501	K501del	AAA	---	1	1	B.1	0.000009
ORF1ab/nsp3	501	K501X	Aaa	Taa	1	1	B.1.1	0.000018
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	B.1.1	0.000018
ORF1ab/nsp3	501	K501V	AAa	GTa	1	1	B.1.1.1	0.000327
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	B.1.1.1	0.000327
ORF1ab/nsp3	501	K501I	aAa	aTa	1	1	B.1.1.1	0.000327
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	B.1.1.141	0.002012
ORF1ab/nsp3	501	K501X	Aaa	Taa	1	1	B.1.1.153	0.001095
ORF1ab/nsp3	501	K501del	AAA	---	1	1	B.1.1.216	0.00089
ORF1ab/nsp3	501	K501T	aAa	aCa	1	1	B.1.1.216	0.00089
ORF1ab/nsp3	501	K501V	AAa	GTa	1	1	B.1.1.26	0.005236
ORF1ab/nsp3	501	K501K	aaA	aaG	1	1	B.1.1.291	0.000742
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	B.1.1.294	0.001266
ORF1ab/nsp3	501	K501R	aAa	aGa	1	1	B.1.1.317	0.000412
ORF1ab/nsp3	501	K501K	aaA	aaG	1	1	B.1.1.329	0.003846
ORF1ab/nsp3	501	K501K	aaA	aaG	1	1	B.1.1.519	0.00004
ORF1ab/nsp3	501	K501del	AAA	---	1	1	B.1.1.519	0.00004
ORF1ab/nsp3	501	K501X	Aaa	Taa	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	501	K501del1	AaA	-aT	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	501	K501I	aAa	aTa	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	B.1.1.98	0.018519
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	B.1.157	0.002985
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	B.1.160	0.000031
ORF1ab/nsp3	501	K501R	aAa	aGa	1	1	B.1.160	0.000031
ORF1ab/nsp3	501	K501K	aaA	aaG	1	1	B.1.177.57	0.000281
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	B.1.177.8	0.000752
ORF1ab/nsp3	501	K501del	AAA	---	1	1	B.1.177.86	0.000183
ORF1ab/nsp3	501	K501K	aaA	aaG	1	1	B.1.177.86	0.000183
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	B.1.214.2	0.0006
ORF1ab/nsp3	501	K501Q	Aaa	Caa	1	1	B.1.221	0.000071
ORF1ab/nsp3	501	K501N	aaA	aaT	1	1	B.1.234	0.000132
ORF1ab/nsp3	501	K501I	aAa	aTa	1	1	B.1.234	0.000132
ORF1ab/nsp3	501	K501T	aAa	aCa	1	1	B.1.240	0.000216
ORF1ab/nsp3	501	K501I	aAa	aTa	1	1	B.1.243	0.00007
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	B.1.243	0.00007
ORF1ab/nsp3	501	K501R	aAa	aGa	1	1	B.1.243	0.00007
ORF1ab/nsp3	501	K501Q	Aaa	Caa	1	1	B.1.258	0.000067
ORF1ab/nsp3	501	K501R	aAa	aGa	1	1	B.1.258.7	0.001912
ORF1ab/nsp3	501	K501R	aAa	aGa	1	1	B.1.311	0.000275
ORF1ab/nsp3	501	K501N	aaA	aaT	1	1	B.1.351	0.00003
ORF1ab/nsp3	501	K501del	AAA	---	1	1	B.1.36	0.000146
ORF1ab/nsp3	501	K501T	aAa	aCa	1	1	B.1.36	0.000146
ORF1ab/nsp3	501	K501K	aaA	aaG	1	1	B.1.377	0.004566
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	B.1.396	0.000706
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	B.1.409	0.000781
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	B.1.429	0.000024
ORF1ab/nsp3	501	K501K	aaA	aaG	1	1	B.1.443	0.004673
ORF1ab/nsp3	501	K501R	aAa	aGa	1	1	B.1.446	0.02
ORF1ab/nsp3	501	K501I	aAa	aTa	1	1	B.1.446	0.02
ORF1ab/nsp3	501	K501E	Aaa	Gaa	1	1	B.1.474	0.001901
ORF1ab/nsp3	501	K501R	aAa	aGa	1	1	B.1.567	0.003333
ORF1ab/nsp3	501	K501T	aAa	aCa	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	501	K501R	aAa	aGa	1	1	B.1.621	0.000089
ORF1ab/nsp3	501	K501K	aaA	aaG	1	1	B.1.621	0.000089
ORF1ab/nsp3	501	K501K	aaA	aaG	1	1	B.42	0.033333
ORF1ab/nsp3	501	K501del	AAA	---	1	1	B.57	0.015152
ORF1ab/nsp3	501	K501K	aaA	aaG	1	1	D.2	0.000075
ORF1ab/nsp3	501	K501R	aAa	aGa	1	1	D.2	0.000075
ORF1ab/nsp3	501	K501R	aAa	aGa	1	1	P.1	0.000016
ORF1ab/nsp3	501	K501del	AAA	---	1	1	P.1	0.000016
ORF1ab/nsp3	501	K501K	aaA	aaG	1	1	P.1.17	0.000162
ORF1ab/nsp3	501	K501I	aAa	aTa	1	1	P.1.17	0.000162
ORF1ab/nsp3	501	K501K	aaA	aaG	1	1	Q.3	0.000145
ORF1ab/nsp3	501	K501R	aAa	aGa	1	1	Q.3	0.000145
ORF1ab/nsp3	501	K501K	aaA	aaG	1	1	R.1	0.00009
ORF1ab/nsp3	501	K501R	aAa	aGa	1	1	R.1	0.00009
ORF1ab/nsp3	501	K501del	AAA	---	1	1	R.1	0.00009
ORF1ab/nsp3	501	K501del	AAA	---	1	1	U.3	0.003861

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.