CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp12 : CodonNum = 524

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/nsp12	524	Q524Q	Q4916Q	syn	caA	caG	2346	2346	1	15010-15012
ORF1ab/nsp12	524	Q524del	Q4916del	del	CAA	---	42	42	1	15010-15012
ORF1ab/nsp12	524	Q524K	Q4916K	nonsyn	Caa	Aaa	39	39	1	15010-15012
ORF1ab/nsp12	524	Q524X	Q4916X	nonsyn	Caa	Taa	31	31	1	15010-15012
ORF1ab/nsp12	524	Q524L	Q4916L	nonsyn	cAa	cTa	16	14	0.875	15010-15012
ORF1ab/nsp12	524	Q524H	Q4916H	nonsyn	caA	caT	16	11	0.6875	15010-15012
ORF1ab/nsp12	524	Q524H	Q4916H	nonsyn	caA	caC	16	5	0.3125	15010-15012
ORF1ab/nsp12	524	Q524L	Q4916L	nonsyn	cAA	cTC	16	1	0.0625	15010-15012
ORF1ab/nsp12	524	Q524L	Q4916L	nonsyn	CAa	TTa	16	1	0.0625	15010-15012
ORF1ab/nsp12	524	Q524del1	Q4916del1	del	cAa	c-a	6	3	0.5	15010-15012
ORF1ab/nsp12	524	Q524del1	Q4916del1	del	Caa	-aa	6	2	0.333333	15010-15012
ORF1ab/nsp12	524	Q524del1	Q4916del1	del	caA	ca-	6	1	0.166667	15010-15012
ORF1ab/nsp12	524	Q524R	Q4916R	nonsyn	cAa	cGa	5	5	1	15010-15012
ORF1ab/nsp12	524	Q524P	Q4916P	nonsyn	cAa	cCa	2	2	1	15010-15012
ORF1ab/nsp12	524	Q524N	Q4916N	nonsyn	CaA	AaT	2	2	1	15010-15012
ORF1ab/nsp12	524	Q524E	Q4916E	nonsyn	Caa	Gaa	2	2	1	15010-15012
ORF1ab/nsp12	524	Q524del2	Q4916del2	del	cAA	c--	1	1	1	15010-15012
ORF1ab/nsp12	524	Q524F	Q4916F	nonsyn	CAA	TTC	1	1	1	15010-15012
ORF1ab/nsp12	524	Q524Y	Q4916Y	nonsyn	CaA	TaC	1	1	1	15010-15012

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/nsp12	524	Q524Q	caA	caG	2346	2346	All	0.000449
ORF1ab/nsp12	524	Q524Q	caA	caG	2118	2118	AY.107	0.986952
ORF1ab/nsp12	524	Q524Q	caA	caG	122	122	B.1.617.2	0.000459
ORF1ab/nsp12	524	Q524del	CAA	---	42	42	All	0.000008
ORF1ab/nsp12	524	Q524K	Caa	Aaa	39	39	All	0.000007
ORF1ab/nsp12	524	Q524X	Caa	Taa	31	31	All	0.000006
ORF1ab/nsp12	524	Q524Q	caA	caG	24	24	B.1.1.7	0.000021
ORF1ab/nsp12	524	Q524K	Caa	Aaa	21	21	AY.4	0.000033
ORF1ab/nsp12	524	Q524L	cAa	cTa	14	16	All	0.000003
ORF1ab/nsp12	524	Q524H	caA	caT	11	16	All	0.000002
ORF1ab/nsp12	524	Q524H	caA	caC	5	16	All	0.000001
ORF1ab/nsp12	524	Q524L	CAa	TTa	1	16	All	0
ORF1ab/nsp12	524	Q524L	cAA	cTC	1	16	All	0
ORF1ab/nsp12	524	Q524del	CAA	---	9	9	B.1.1.7	0.000008
ORF1ab/nsp12	524	Q524Q	caA	caG	7	7	AY.117	0.000592
ORF1ab/nsp12	524	Q524Q	caA	caG	7	7	AY.25	0.000042
ORF1ab/nsp12	524	Q524Q	caA	caG	7	7	AY.5	0.000145
ORF1ab/nsp12	524	Q524del1	cAa	c-a	3	6	All	0.000001
ORF1ab/nsp12	524	Q524del1	Caa	-aa	2	6	All	0
ORF1ab/nsp12	524	Q524del1	caA	ca-	1	6	All	0
ORF1ab/nsp12	524	Q524Q	caA	caG	6	6	AY.92	0.001724
ORF1ab/nsp12	524	Q524X	Caa	Taa	6	6	B.1	0.000055
ORF1ab/nsp12	524	Q524X	Caa	Taa	6	6	B.1.1.7	0.000005
ORF1ab/nsp12	524	Q524R	cAa	cGa	5	5	All	0.000001
ORF1ab/nsp12	524	Q524Q	caA	caG	5	5	AY.43	0.000022
ORF1ab/nsp12	524	Q524del	CAA	---	4	4		0.222222
ORF1ab/nsp12	524	Q524K	Caa	Aaa	4	4	AY.29	0.000063
ORF1ab/nsp12	524	Q524K	Caa	Aaa	3	3		0.166667
ORF1ab/nsp12	524	Q524del	CAA	---	3	3	AY.107	0.001398
ORF1ab/nsp12	524	Q524Q	caA	caG	3	3	AY.23	0.000209
ORF1ab/nsp12	524	Q524Q	caA	caG	3	3	AY.5.3	0.001012
ORF1ab/nsp12	524	Q524L	cAa	cTa	3	3	B.1	0.000027
ORF1ab/nsp12	524	Q524H	caA	caT	3	3	B.1	0.000027
ORF1ab/nsp12	524	Q524del	CAA	---	3	3	B.1.1	0.000054
ORF1ab/nsp12	524	Q524Q	caA	caG	3	3	B.1.2	0.000026
ORF1ab/nsp12	524	Q524X	Caa	Taa	3	3	B.1.258	0.0002
ORF1ab/nsp12	524	Q524E	Caa	Gaa	2	2	All	0
ORF1ab/nsp12	524	Q524N	CaA	AaT	2	2	All	0
ORF1ab/nsp12	524	Q524P	cAa	cCa	2	2	All	0
ORF1ab/nsp12	524	Q524Q	caA	caG	2	2	AY.102	0.000053
ORF1ab/nsp12	524	Q524Q	caA	caG	2	2	AY.103	0.000012
ORF1ab/nsp12	524	Q524Q	caA	caG	2	2	AY.111	0.000366
ORF1ab/nsp12	524	Q524Q	caA	caG	2	2	AY.113	0.000285
ORF1ab/nsp12	524	Q524K	Caa	Aaa	2	2	AY.20	0.000078
ORF1ab/nsp12	524	Q524Q	caA	caG	2	2	AY.36	0.000296
ORF1ab/nsp12	524	Q524Q	caA	caG	2	2	AY.39	0.000049
ORF1ab/nsp12	524	Q524L	cAa	cTa	2	2	AY.4	0.000003
ORF1ab/nsp12	524	Q524Q	caA	caG	2	2	AY.4	0.000003
ORF1ab/nsp12	524	Q524del	CAA	---	2	2	AY.4	0.000003
ORF1ab/nsp12	524	Q524L	cAa	cTa	2	2	AY.44	0.000012
ORF1ab/nsp12	524	Q524Q	caA	caG	2	2	AY.45	0.000243
ORF1ab/nsp12	524	Q524Q	caA	caG	2	2	AY.84	0.000875
ORF1ab/nsp12	524	Q524L	cAa	cTa	2	2	AY.84	0.000875
ORF1ab/nsp12	524	Q524Q	caA	caG	2	2	AY.91	0.001461
ORF1ab/nsp12	524	Q524Q	caA	caG	2	2	AY.95	0.001522
ORF1ab/nsp12	524	Q524X	Caa	Taa	2	2	B.1.1	0.000036
ORF1ab/nsp12	524	Q524L	cAa	cTa	2	2	B.1.1.7	0.000002
ORF1ab/nsp12	524	Q524del1	caA	ca-	1	2	B.1.1.7	0.000001
ORF1ab/nsp12	524	Q524del1	Caa	-aa	1	2	B.1.1.7	0.000001
ORF1ab/nsp12	524	Q524K	Caa	Aaa	2	2	B.1.617.2	0.000008
ORF1ab/nsp12	524	Q524del	CAA	---	2	2	P.1	0.000032
ORF1ab/nsp12	524	Q524X	Caa	Taa	1	1		0.055556
ORF1ab/nsp12	524	Q524F	CAA	TTC	1	1	All	0
ORF1ab/nsp12	524	Q524del2	cAA	c--	1	1	All	0
ORF1ab/nsp12	524	Q524Y	CaA	TaC	1	1	All	0
ORF1ab/nsp12	524	Q524X	Caa	Taa	1	1	AY.102	0.000027
ORF1ab/nsp12	524	Q524N	CaA	AaT	1	1	AY.103	0.000006
ORF1ab/nsp12	524	Q524X	Caa	Taa	1	1	AY.103	0.000006
ORF1ab/nsp12	524	Q524H	caA	caT	1	1	AY.103	0.000006
ORF1ab/nsp12	524	Q524K	Caa	Aaa	1	1	AY.103	0.000006
ORF1ab/nsp12	524	Q524Q	caA	caG	1	1	AY.118	0.000063
ORF1ab/nsp12	524	Q524Q	caA	caG	1	1	AY.119	0.000035
ORF1ab/nsp12	524	Q524Q	caA	caG	1	1	AY.14	0.000088
ORF1ab/nsp12	524	Q524K	Caa	Aaa	1	1	AY.16.1	0.00047
ORF1ab/nsp12	524	Q524del	CAA	---	1	1	AY.25	0.000006
ORF1ab/nsp12	524	Q524del1	cAa	c-a	1	1	AY.25	0.000006
ORF1ab/nsp12	524	Q524H	caA	caT	1	1	AY.26	0.000028
ORF1ab/nsp12	524	Q524Q	caA	caG	1	1	AY.29	0.000016
ORF1ab/nsp12	524	Q524L	cAA	cTC	1	1	AY.3	0.00001
ORF1ab/nsp12	524	Q524Q	caA	caG	1	1	AY.3	0.00001
ORF1ab/nsp12	524	Q524K	Caa	Aaa	1	1	AY.33	0.000067
ORF1ab/nsp12	524	Q524H	caA	caT	1	1	AY.4	0.000002
ORF1ab/nsp12	524	Q524Q	caA	caG	1	1	AY.42	0.00004
ORF1ab/nsp12	524	Q524L	cAa	cTa	1	1	AY.42	0.00004
ORF1ab/nsp12	524	Q524del	CAA	---	1	1	AY.42	0.00004
ORF1ab/nsp12	524	Q524del	CAA	---	1	1	AY.43	0.000004
ORF1ab/nsp12	524	Q524H	caA	caT	1	1	AY.43	0.000004
ORF1ab/nsp12	524	Q524X	Caa	Taa	1	1	AY.43	0.000004
ORF1ab/nsp12	524	Q524del2	cAA	c--	1	1	AY.43	0.000004
ORF1ab/nsp12	524	Q524L	CAa	TTa	1	1	AY.43	0.000004
ORF1ab/nsp12	524	Q524K	Caa	Aaa	1	1	AY.44	0.000006
ORF1ab/nsp12	524	Q524del	CAA	---	1	1	AY.44	0.000006
ORF1ab/nsp12	524	Q524H	caA	caC	1	1	AY.44	0.000006
ORF1ab/nsp12	524	Q524X	Caa	Taa	1	1	AY.44	0.000006
ORF1ab/nsp12	524	Q524X	Caa	Taa	1	1	AY.46	0.000104
ORF1ab/nsp12	524	Q524Q	caA	caG	1	1	AY.46.6	0.000072
ORF1ab/nsp12	524	Q524Q	caA	caG	1	1	AY.55	0.000917
ORF1ab/nsp12	524	Q524Q	caA	caG	1	1	AY.58	0.000907
ORF1ab/nsp12	524	Q524del	CAA	---	1	1	AY.65	0.000533
ORF1ab/nsp12	524	Q524del	CAA	---	1	1	AY.67	0.000464
ORF1ab/nsp12	524	Q524R	cAa	cGa	1	1	AY.68	0.000274
ORF1ab/nsp12	524	Q524X	Caa	Taa	1	1	AY.7	0.000196
ORF1ab/nsp12	524	Q524Q	caA	caG	1	1	AY.75	0.000056
ORF1ab/nsp12	524	Q524Q	caA	caG	1	1	AY.9.1	0.000084
ORF1ab/nsp12	524	Q524H	caA	caT	1	1	AY.9.2	0.000037
ORF1ab/nsp12	524	Q524R	cAa	cGa	1	1	AY.9.2	0.000037
ORF1ab/nsp12	524	Q524Q	caA	caG	1	1	AY.99	0.001049
ORF1ab/nsp12	524	Q524del	CAA	---	1	1	AY.99	0.001049
ORF1ab/nsp12	524	Q524X	Caa	Taa	1	1	B	0.000128
ORF1ab/nsp12	524	Q524K	Caa	Aaa	1	1	B.1	0.000009
ORF1ab/nsp12	524	Q524E	Caa	Gaa	1	1	B.1	0.000009
ORF1ab/nsp12	524	Q524F	CAA	TTC	1	1	B.1.1	0.000018
ORF1ab/nsp12	524	Q524Y	CaA	TaC	1	1	B.1.1	0.000018
ORF1ab/nsp12	524	Q524K	Caa	Aaa	1	1	B.1.1	0.000018
ORF1ab/nsp12	524	Q524H	caA	caC	1	1	B.1.1	0.000018
ORF1ab/nsp12	524	Q524Q	caA	caG	1	1	B.1.1	0.000018
ORF1ab/nsp12	524	Q524L	cAa	cTa	1	1	B.1.1.165	0.015385
ORF1ab/nsp12	524	Q524R	cAa	cGa	1	1	B.1.1.174	0.003378
ORF1ab/nsp12	524	Q524X	Caa	Taa	1	1	B.1.1.222	0.000204
ORF1ab/nsp12	524	Q524del	CAA	---	1	1	B.1.1.306	0.000438
ORF1ab/nsp12	524	Q524del	CAA	---	1	1	B.1.1.311	0.000358
ORF1ab/nsp12	524	Q524Q	caA	caG	1	1	B.1.1.33	0.000421
ORF1ab/nsp12	524	Q524X	Caa	Taa	1	1	B.1.1.39	0.00051
ORF1ab/nsp12	524	Q524Q	caA	caG	1	1	B.1.1.519	0.00004
ORF1ab/nsp12	524	Q524H	caA	caT	1	1	B.1.1.7	0.000001
ORF1ab/nsp12	524	Q524E	Caa	Gaa	1	1	B.1.1.7	0.000001
ORF1ab/nsp12	524	Q524del	CAA	---	1	1	B.1.1.70	0.000341
ORF1ab/nsp12	524	Q524del	CAA	---	1	1	B.1.160.23	0.004831
ORF1ab/nsp12	524	Q524del	CAA	---	1	1	B.1.160.7	0.002079
ORF1ab/nsp12	524	Q524R	cAa	cGa	1	1	B.1.177	0.000013
ORF1ab/nsp12	524	Q524H	caA	caC	1	1	B.1.177	0.000013
ORF1ab/nsp12	524	Q524del	CAA	---	1	1	B.1.177.60	0.000218
ORF1ab/nsp12	524	Q524del	CAA	---	1	1	B.1.177.68	0.015152
ORF1ab/nsp12	524	Q524del	CAA	---	1	1	B.1.177.76	0.002494
ORF1ab/nsp12	524	Q524del	CAA	---	1	1	B.1.177.87	0.000728
ORF1ab/nsp12	524	Q524del	CAA	---	1	1	B.1.177.9	0.001332
ORF1ab/nsp12	524	Q524del1	cAa	c-a	1	1	B.1.2	0.000009
ORF1ab/nsp12	524	Q524X	Caa	Taa	1	1	B.1.2	0.000009
ORF1ab/nsp12	524	Q524X	Caa	Taa	1	1	B.1.220	0.01087
ORF1ab/nsp12	524	Q524Q	caA	caG	1	1	B.1.258	0.000067
ORF1ab/nsp12	524	Q524P	cAa	cCa	1	1	B.1.258	0.000067
ORF1ab/nsp12	524	Q524H	caA	caC	1	1	B.1.258.17	0.000104
ORF1ab/nsp12	524	Q524R	cAa	cGa	1	1	B.1.36	0.000146
ORF1ab/nsp12	524	Q524H	caA	caC	1	1	B.1.416	0.001269
ORF1ab/nsp12	524	Q524Q	caA	caG	1	1	B.1.427	0.00005
ORF1ab/nsp12	524	Q524Q	caA	caG	1	1	B.1.526	0.000024
ORF1ab/nsp12	524	Q524L	cAa	cTa	1	1	B.1.568	0.001111
ORF1ab/nsp12	524	Q524del1	Caa	-aa	1	1	B.1.595	0.000261
ORF1ab/nsp12	524	Q524H	caA	caT	1	1	B.1.617.2	0.000004
ORF1ab/nsp12	524	Q524X	Caa	Taa	1	1	B.1.617.2	0.000004
ORF1ab/nsp12	524	Q524del1	cAa	c-a	1	1	B.1.617.2	0.000004
ORF1ab/nsp12	524	Q524N	CaA	AaT	1	1	B.1.617.2	0.000004
ORF1ab/nsp12	524	Q524P	cAa	cCa	1	1	B.6.6	0.000889
ORF1ab/nsp12	524	Q524X	Caa	Taa	1	1	D.2	0.000075
ORF1ab/nsp12	524	Q524K	Caa	Aaa	1	1	D.2	0.000075
ORF1ab/nsp12	524	Q524H	caA	caT	1	1	P.1	0.000016
ORF1ab/nsp12	524	Q524Q	caA	caG	1	1	P.1	0.000016
ORF1ab/nsp12	524	Q524del	CAA	---	1	1	P.1.4	0.000977
ORF1ab/nsp12	524	Q524del	CAA	---	1	1	Q.8	0.000165

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.