CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 949

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
S	949	Q949Q		syn	caA	caG	114	114	1	24407-24409
S	949	Q949del		del	CAA	---	81	81	1	24407-24409
S	949	Q949R		nonsyn	cAa	cGa	65	65	1	24407-24409
S	949	Q949E		nonsyn	Caa	Gaa	33	33	1	24407-24409
S	949	Q949X		nonsyn	Caa	Taa	18	18	1	24407-24409
S	949	Q949K		nonsyn	Caa	Aaa	18	18	1	24407-24409
S	949	Q949L		nonsyn	cAa	cTa	11	11	1	24407-24409
S	949	Q949H		nonsyn	caA	caT	7	5	0.714286	24407-24409
S	949	Q949H		nonsyn	caA	caC	7	2	0.285714	24407-24409
S	949	Q949del1		del	Caa	-aa	4	2	0.5	24407-24409
S	949	Q949del1		del	caA	ca-	4	2	0.5	24407-24409
S	949	Q949del2		del	CAa	--a	3	2	0.666667	24407-24409
S	949	Q949del2		del	cAA	c--	3	1	0.333333	24407-24409
S	949	Q949P		nonsyn	cAa	cCa	2	2	1	24407-24409
S	949	Q949Y		nonsyn	CaA	TaC	1	1	1	24407-24409
S	949	Q949S		nonsyn	CAa	TCa	1	1	1	24407-24409

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
S	949	Q949Q	caA	caG	114	114	All	0.000022
S	949	Q949del	CAA	---	81	81	All	0.000015
S	949	Q949R	cAa	cGa	65	65	All	0.000012
S	949	Q949Q	caA	caG	52	52	B.1.1.7	0.000047
S	949	Q949R	cAa	cGa	41	41	B.1.616	1
S	949	Q949del	CAA	---	34	34	B.1.1.7	0.00003
S	949	Q949E	Caa	Gaa	33	33	All	0.000006
S	949	Q949E	Caa	Gaa	21	21	AY.4	0.000033
S	949	Q949K	Caa	Aaa	18	18	All	0.000003
S	949	Q949X	Caa	Taa	18	18	All	0.000003
S	949	Q949L	cAa	cTa	11	11	All	0.000002
S	949	Q949R	cAa	cGa	10	10	B.1.1.7	0.000009
S	949	Q949del	CAA	---	10	10	B.1.177	0.000132
S	949	Q949Q	caA	caG	9	9	B.1.36	0.001313
S	949	Q949H	caA	caT	5	7	All	0.000001
S	949	Q949H	caA	caC	2	7	All	0
S	949	Q949Q	caA	caG	7	7	B.1.1.279	0.007848
S	949	Q949X	Caa	Taa	5	5	B.1.1.7	0.000004
S	949	Q949E	Caa	Gaa	5	5	B.1.526	0.000118
S	949	Q949del1	Caa	-aa	2	4	All	0
S	949	Q949del1	caA	ca-	2	4	All	0
S	949	Q949del	CAA	---	4	4	AY.4	0.000006
S	949	Q949Q	caA	caG	4	4	AY.4	0.000006
S	949	Q949del2	CAa	--a	2	3	All	0
S	949	Q949del2	cAA	c--	1	3	All	0
S	949	Q949L	cAa	cTa	3	3	AY.24	0.001293
S	949	Q949del	CAA	---	3	3	AY.43	0.000013
S	949	Q949K	Caa	Aaa	3	3	AY.43	0.000013
S	949	Q949Q	caA	caG	3	3	AY.74	0.000347
S	949	Q949X	Caa	Taa	3	3	B.1	0.000027
S	949	Q949K	Caa	Aaa	3	3	B.1	0.000027
S	949	Q949Q	caA	caG	3	3	B.1.1	0.000054
S	949	Q949H	caA	caT	3	3	B.1.1.7	0.000003
S	949	Q949del2	CAa	--a	2	3	B.1.1.7	0.000002
S	949	Q949del2	cAA	c--	1	3	B.1.1.7	0.000001
S	949	Q949Q	caA	caG	3	3	B.1.2	0.000026
S	949	Q949Q	caA	caG	3	3	B.1.525	0.000339
S	949	Q949del	CAA	---	3	3	B.1.617.2	0.000011
S	949	Q949Q	caA	caG	3	3	P.1	0.000047
S	949	Q949P	cAa	cCa	2	2		0.111111
S	949	Q949X	Caa	Taa	2	2		0.111111
S	949	Q949P	cAa	cCa	2	2	All	0
S	949	Q949Q	caA	caG	2	2	AY.102	0.000053
S	949	Q949Q	caA	caG	2	2	AY.26	0.000057
S	949	Q949K	Caa	Aaa	2	2	AY.3	0.00002
S	949	Q949L	cAa	cTa	2	2	AY.44	0.000012
S	949	Q949del	CAA	---	2	2	B.1	0.000018
S	949	Q949Q	caA	caG	2	2	B.1.1.214	0.000111
S	949	Q949del	CAA	---	2	2	B.1.1.312	0.003824
S	949	Q949L	cAa	cTa	2	2	B.1.1.7	0.000002
S	949	Q949Q	caA	caG	2	2	B.1.177	0.000026
S	949	Q949X	Caa	Taa	2	2	B.1.177	0.000026
S	949	Q949del	CAA	---	2	2	B.1.177.7	0.00033
S	949	Q949R	cAa	cGa	2	2	B.1.2	0.000018
S	949	Q949Q	caA	caG	2	2	B.1.427	0.000101
S	949	Q949R	cAa	cGa	2	2	B.1.617.2	0.000008
S	949	Q949Q	caA	caG	2	2	B.1.621	0.000177
S	949	Q949X	Caa	Taa	2	2	D.2	0.00015
S	949	Q949H	caA	caC	1	1		0.055556
S	949	Q949K	Caa	Aaa	1	1		0.055556
S	949	Q949Y	CaA	TaC	1	1		0.055556
S	949	Q949S	CAa	TCa	1	1		0.055556
S	949	Q949del	CAA	---	1	1	A	0.000387
S	949	Q949Q	caA	caG	1	1	A.27	0.001656
S	949	Q949Y	CaA	TaC	1	1	All	0
S	949	Q949S	CAa	TCa	1	1	All	0
S	949	Q949Q	caA	caG	1	1	AY.100	0.000046
S	949	Q949R	cAa	cGa	1	1	AY.102	0.000027
S	949	Q949R	cAa	cGa	1	1	AY.103	0.000006
S	949	Q949Q	caA	caG	1	1	AY.107	0.000466
S	949	Q949L	cAa	cTa	1	1	AY.117	0.000085
S	949	Q949E	Caa	Gaa	1	1	AY.20	0.000039
S	949	Q949E	Caa	Gaa	1	1	AY.25	0.000006
S	949	Q949del1	caA	ca-	1	1	AY.29	0.000016
S	949	Q949X	Caa	Taa	1	1	AY.39.1	0.00004
S	949	Q949H	caA	caC	1	1	AY.4	0.000002
S	949	Q949K	Caa	Aaa	1	1	AY.4	0.000002
S	949	Q949R	cAa	cGa	1	1	AY.4	0.000002
S	949	Q949L	cAa	cTa	1	1	AY.4	0.000002
S	949	Q949K	Caa	Aaa	1	1	AY.42	0.00004
S	949	Q949R	cAa	cGa	1	1	AY.43	0.000004
S	949	Q949del1	caA	ca-	1	1	AY.44	0.000006
S	949	Q949K	Caa	Aaa	1	1	AY.44	0.000006
S	949	Q949del	CAA	---	1	1	AY.46.2	0.000635
S	949	Q949del	CAA	---	1	1	AY.5	0.000021
S	949	Q949K	Caa	Aaa	1	1	AY.62	0.000436
S	949	Q949del	CAA	---	1	1	AY.81	0.001992
S	949	Q949E	Caa	Gaa	1	1	AY.84	0.000437
S	949	Q949del	CAA	---	1	1	AY.9	0.000068
S	949	Q949K	Caa	Aaa	1	1	B	0.000128
S	949	Q949R	cAa	cGa	1	1	B.1	0.000009
S	949	Q949K	Caa	Aaa	1	1	B.1.1	0.000018
S	949	Q949del	CAA	---	1	1	B.1.1	0.000018
S	949	Q949del	CAA	---	1	1	B.1.1.159	0.004673
S	949	Q949Q	caA	caG	1	1	B.1.1.189	0.001513
S	949	Q949E	Caa	Gaa	1	1	B.1.1.216	0.00089
S	949	Q949del	CAA	---	1	1	B.1.1.236	0.006897
S	949	Q949K	Caa	Aaa	1	1	B.1.1.326	0.001761
S	949	Q949K	Caa	Aaa	1	1	B.1.1.519	0.00004
S	949	Q949del1	Caa	-aa	1	1	B.1.1.7	0.000001
S	949	Q949del	CAA	---	1	1	B.1.1.70	0.000341
S	949	Q949Q	caA	caG	1	1	B.1.1.70	0.000341
S	949	Q949R	cAa	cGa	1	1	B.1.139	0.000733
S	949	Q949Q	caA	caG	1	1	B.1.147	0.000756
S	949	Q949R	cAa	cGa	1	1	B.1.177	0.000013
S	949	Q949L	cAa	cTa	1	1	B.1.177	0.000013
S	949	Q949del	CAA	---	1	1	B.1.177.15	0.000631
S	949	Q949del	CAA	---	1	1	B.1.177.17	0.000821
S	949	Q949del	CAA	---	1	1	B.1.177.21	0.000076
S	949	Q949del	CAA	---	1	1	B.1.177.54	0.000606
S	949	Q949del	CAA	---	1	1	B.1.177.58	0.001332
S	949	Q949del	CAA	---	1	1	B.1.177.6	0.000977
S	949	Q949del	CAA	---	1	1	B.1.177.63	0.002703
S	949	Q949del	CAA	---	1	1	B.1.177.9	0.001332
S	949	Q949R	cAa	cGa	1	1	B.1.199	0.004132
S	949	Q949E	Caa	Gaa	1	1	B.1.2	0.000009
S	949	Q949K	Caa	Aaa	1	1	B.1.2	0.000009
S	949	Q949X	Caa	Taa	1	1	B.1.2	0.000009
S	949	Q949Q	caA	caG	1	1	B.1.221	0.000071
S	949	Q949del1	Caa	-aa	1	1	B.1.222	0.001692
S	949	Q949del	CAA	---	1	1	B.1.23	0.006061
S	949	Q949X	Caa	Taa	1	1	B.1.351	0.00003
S	949	Q949Q	caA	caG	1	1	B.1.351	0.00003
S	949	Q949R	cAa	cGa	1	1	B.1.351	0.00003
S	949	Q949del	CAA	---	1	1	B.1.36.17	0.000494
S	949	Q949Q	caA	caG	1	1	B.1.429	0.000024
S	949	Q949Q	caA	caG	1	1	B.1.526	0.000024
S	949	Q949Q	caA	caG	1	1	B.1.560	0.00463
S	949	Q949E	Caa	Gaa	1	1	B.1.595	0.000261
S	949	Q949X	Caa	Taa	1	1	B.1.609	0.000479
S	949	Q949H	caA	caT	1	1	B.1.617.1	0.000129
S	949	Q949del	CAA	---	1	1	B.1.617.1	0.000129
S	949	Q949Q	caA	caG	1	1	B.1.617.2	0.000004
S	949	Q949E	Caa	Gaa	1	1	B.1.617.2	0.000004
S	949	Q949Q	caA	caG	1	1	B.40	0.000364
S	949	Q949H	caA	caT	1	1	B.40	0.000364
S	949	Q949Q	caA	caG	1	1	B.6	0.00091
S	949	Q949Q	caA	caG	1	1	C.1.2	0.004255
S	949	Q949R	cAa	cGa	1	1	P.1	0.000016
S	949	Q949L	cAa	cTa	1	1	P.1.14	0.000048
S	949	Q949del	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.