CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 833

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	833	F833F		syn	ttC	ttT	363	363	1	24059-24061
S	833	F833del		del	TTC	---	58	58	1	24059-24061
S	833	F833S		nonsyn	tTc	tCc	33	32	0.969697	24059-24061
S	833	F833L		nonsyn	Ttc	Ctc	33	20	0.606061	24059-24061
S	833	F833L		nonsyn	ttC	ttG	33	10	0.30303	24059-24061
S	833	F833L		nonsyn	ttC	ttA	33	3	0.0909091	24059-24061
S	833	F833S		nonsyn	tTC	tCG	33	1	0.030303	24059-24061
S	833	F833V		nonsyn	Ttc	Gtc	17	17	1	24059-24061
S	833	F833Y		nonsyn	tTc	tAc	11	11	1	24059-24061
S	833	F833I		nonsyn	Ttc	Atc	4	3	0.75	24059-24061
S	833	F833I		nonsyn	TtC	AtA	4	1	0.25	24059-24061
S	833	F833del1		del	Ttc	-tc	2	2	1	24059-24061
S	833	F833C		nonsyn	tTc	tGc	2	2	1	24059-24061
S	833	F833A		nonsyn	TTC	GCT	1	1	1	24059-24061

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	833	F833F	ttC	ttT	363	363	All	0.000069
S	833	F833F	ttC	ttT	69	69	B.1.243.2	1
S	833	F833del	TTC	---	58	58	All	0.000011
S	833	F833F	ttC	ttT	46	46	B.1.243	0.003201
S	833	F833F	ttC	ttT	42	42	AY.43	0.000186
S	833	F833S	tTc	tCc	32	33	All	0.000006
S	833	F833L	Ttc	Ctc	20	33	All	0.000004
S	833	F833L	ttC	ttG	10	33	All	0.000002
S	833	F833L	ttC	ttA	3	33	All	0.000001
S	833	F833S	tTC	tCG	1	33	All	0
S	833	F833F	ttC	ttT	28	28	B.1.617.2	0.000105
S	833	F833F	ttC	ttT	24	24	B.1.1.7	0.000021
S	833	F833F	ttC	ttT	24	24	B.1.177	0.000316
S	833	F833V	Ttc	Gtc	17	17	All	0.000003
S	833	F833F	ttC	ttT	14	14	Q.1	0.001769
S	833	F833F	ttC	ttT	13	13	AY.102	0.000345
S	833	F833F	ttC	ttT	13	13	AY.4	0.00002
S	833	F833del	TTC	---	12	12	B.1.1.7	0.000011
S	833	F833Y	tTc	tAc	11	11	All	0.000002
S	833	F833F	ttC	ttT	9	9	AY.44	0.000055
S	833	F833V	Ttc	Gtc	8	8	AY.4	0.000012
S	833	F833S	tTc	tCc	7	7	AY.100	0.000322
S	833	F833F	ttC	ttT	7	7	AY.98.1	0.000339
S	833	F833L	ttC	ttG	6	7	B.1.429	0.000141
S	833	F833L	Ttc	Ctc	1	7	B.1.429	0.000024
S	833	F833L	Ttc	Ctc	5	6	B.1.1.7	0.000004
S	833	F833L	ttC	ttG	1	6	B.1.1.7	0.000001
S	833	F833S	tTc	tCc	6	6	B.1.617.2	0.000023
S	833	F833F	ttC	ttT	5	5	AY.118	0.000313
S	833	F833F	ttC	ttT	5	5	AY.3	0.00005
S	833	F833del	TTC	---	5	5	AY.43	0.000022
S	833	F833F	ttC	ttT	5	5	P.1	0.000079
S	833	F833I	Ttc	Atc	3	4	All	0.000001
S	833	F833I	TtC	AtA	1	4	All	0
S	833	F833F	ttC	ttT	3	3	AY.103	0.000019
S	833	F833F	ttC	ttT	3	3	B.1.1.214	0.000166
S	833	F833F	ttC	ttT	3	3	B.1.351	0.000089
S	833	F833del	TTC	---	3	3	B.1.621	0.000266
S	833	F833F	ttC	ttT	3	3	C.37	0.000348
S	833	F833del	TTC	---	3	3	P.1	0.000047
S	833	F833del	TTC	---	3	3	P.1.15	0.000697
S	833	F833del	TTC	---	2	2		0.111111
S	833	F833del1	Ttc	-tc	2	2	All	0
S	833	F833C	tTc	tGc	2	2	All	0
S	833	F833F	ttC	ttT	2	2	AY.25	0.000012
S	833	F833F	ttC	ttT	2	2	AY.39.1	0.000079
S	833	F833del	TTC	---	2	2	AY.4	0.000003
S	833	F833Y	tTc	tAc	2	2	AY.4	0.000003
S	833	F833L	ttC	ttG	1	2	AY.4	0.000002
S	833	F833L	Ttc	Ctc	1	2	AY.4	0.000002
S	833	F833del	TTC	---	2	2	AY.4.5	0.000215
S	833	F833S	tTc	tCc	2	2	AY.41	0.000588
S	833	F833L	Ttc	Ctc	2	2	AY.44	0.000012
S	833	F833F	ttC	ttT	2	2	AY.75	0.000112
S	833	F833F	ttC	ttT	2	2	AY.9	0.000135
S	833	F833F	ttC	ttT	2	2	AY.99.2	0.000184
S	833	F833L	Ttc	Ctc	2	2	B.1	0.000018
S	833	F833del	TTC	---	2	2	B.1	0.000018
S	833	F833F	ttC	ttT	2	2	B.1	0.000018
S	833	F833del	TTC	---	2	2	B.1.1	0.000036
S	833	F833F	ttC	ttT	2	2	B.1.1	0.000036
S	833	F833del	TTC	---	2	2	B.1.1.236	0.013793
S	833	F833F	ttC	ttT	2	2	B.1.1.273	0.013514
S	833	F833S	tTc	tCc	2	2	B.1.1.7	0.000002
S	833	F833S	tTc	tCc	2	2	B.1.177.12	0.000303
S	833	F833del	TTC	---	2	2	B.1.177.63	0.005405
S	833	F833L	ttC	ttG	1	2	B.1.2	0.000009
S	833	F833L	Ttc	Ctc	1	2	B.1.2	0.000009
S	833	F833F	ttC	ttT	2	2	B.1.221	0.000142
S	833	F833L	ttC	ttA	2	2	B.1.263	0.095238
S	833	F833S	tTC	tCG	1	2	B.1.427	0.00005
S	833	F833S	tTc	tCc	1	2	B.1.427	0.00005
S	833	F833F	ttC	ttT	2	2	B.1.595	0.000522
S	833	F833L	Ttc	Ctc	2	2	B.1.617.2	0.000008
S	833	F833del	TTC	---	2	2	B.1.617.2	0.000008
S	833	F833Y	tTc	tAc	2	2	B.1.617.2	0.000008
S	833	F833F	ttC	ttT	1	1		0.055556
S	833	F833del	TTC	---	1	1	A	0.000387
S	833	F833A	TTC	GCT	1	1	All	0
S	833	F833F	ttC	ttT	1	1	AY.100	0.000046
S	833	F833S	tTc	tCc	1	1	AY.102	0.000027
S	833	F833V	Ttc	Gtc	1	1	AY.103	0.000006
S	833	F833I	Ttc	Atc	1	1	AY.117	0.000085
S	833	F833del	TTC	---	1	1	AY.119	0.000035
S	833	F833S	tTc	tCc	1	1	AY.119	0.000035
S	833	F833del	TTC	---	1	1	AY.120	0.000037
S	833	F833F	ttC	ttT	1	1	AY.120	0.000037
S	833	F833F	ttC	ttT	1	1	AY.16	0.00038
S	833	F833L	Ttc	Ctc	1	1	AY.25	0.000006
S	833	F833C	tTc	tGc	1	1	AY.25	0.000006
S	833	F833del	TTC	---	1	1	AY.25	0.000006
S	833	F833V	Ttc	Gtc	1	1	AY.3	0.00001
S	833	F833S	tTc	tCc	1	1	AY.3.1	0.000085
S	833	F833F	ttC	ttT	1	1	AY.39	0.000025
S	833	F833I	Ttc	Atc	1	1	AY.4	0.000002
S	833	F833S	tTc	tCc	1	1	AY.4	0.000002
S	833	F833del1	Ttc	-tc	1	1	AY.4.5	0.000107
S	833	F833L	Ttc	Ctc	1	1	AY.4.5	0.000107
S	833	F833F	ttC	ttT	1	1	AY.42	0.00004
S	833	F833V	Ttc	Gtc	1	1	AY.43	0.000004
S	833	F833A	TTC	GCT	1	1	AY.43	0.000004
S	833	F833L	Ttc	Ctc	1	1	AY.43	0.000004
S	833	F833Y	tTc	tAc	1	1	AY.43	0.000004
S	833	F833Y	tTc	tAc	1	1	AY.44	0.000006
S	833	F833F	ttC	ttT	1	1	AY.45	0.000122
S	833	F833del	TTC	---	1	1	AY.46.2	0.000635
S	833	F833F	ttC	ttT	1	1	AY.46.4	0.000165
S	833	F833F	ttC	ttT	1	1	AY.5.4	0.000277
S	833	F833Y	tTc	tAc	1	1	AY.55	0.000917
S	833	F833F	ttC	ttT	1	1	AY.67	0.000464
S	833	F833S	tTc	tCc	1	1	AY.68	0.000274
S	833	F833V	Ttc	Gtc	1	1	AY.69	0.000187
S	833	F833F	ttC	ttT	1	1	AY.71	0.000475
S	833	F833F	ttC	ttT	1	1	AY.75.1	0.00018
S	833	F833V	Ttc	Gtc	1	1	AY.85	0.000427
S	833	F833F	ttC	ttT	1	1	AY.9.2	0.000037
S	833	F833del	TTC	---	1	1	AY.9.2	0.000037
S	833	F833del	TTC	---	1	1	AY.98.1	0.000048
S	833	F833S	tTc	tCc	1	1	AY.99.2	0.000092
S	833	F833S	tTc	tCc	1	1	B.1.1	0.000018
S	833	F833F	ttC	ttT	1	1	B.1.1.153	0.001095
S	833	F833F	ttC	ttT	1	1	B.1.1.25	0.000569
S	833	F833F	ttC	ttT	1	1	B.1.1.28	0.000311
S	833	F833F	ttC	ttT	1	1	B.1.1.305	0.003861
S	833	F833V	Ttc	Gtc	1	1	B.1.1.369	0.000446
S	833	F833del	TTC	---	1	1	B.1.1.409	0.002833
S	833	F833C	tTc	tGc	1	1	B.1.1.7	0.000001
S	833	F833del1	Ttc	-tc	1	1	B.1.1.7	0.000001
S	833	F833F	ttC	ttT	1	1	B.1.160	0.000031
S	833	F833del	TTC	---	1	1	B.1.177	0.000013
S	833	F833L	Ttc	Ctc	1	1	B.1.177	0.000013
S	833	F833S	tTc	tCc	1	1	B.1.177	0.000013
S	833	F833del	TTC	---	1	1	B.1.177.17	0.000821
S	833	F833L	Ttc	Ctc	1	1	B.1.177.58	0.001332
S	833	F833Y	tTc	tAc	1	1	B.1.2	0.000009
S	833	F833F	ttC	ttT	1	1	B.1.2	0.000009
S	833	F833del	TTC	---	1	1	B.1.2	0.000009
S	833	F833Y	tTc	tAc	1	1	B.1.234	0.000132
S	833	F833del	TTC	---	1	1	B.1.258	0.000067
S	833	F833V	Ttc	Gtc	1	1	B.1.258.10	0.011364
S	833	F833S	tTc	tCc	1	1	B.1.351	0.00003
S	833	F833F	ttC	ttT	1	1	B.1.351.2	0.000303
S	833	F833V	Ttc	Gtc	1	1	B.1.395	0.007042
S	833	F833F	ttC	ttT	1	1	B.1.402	0.009804
S	833	F833Y	tTc	tAc	1	1	B.1.411	0.003704
S	833	F833L	ttC	ttG	1	1	B.1.427	0.00005
S	833	F833V	Ttc	Gtc	1	1	B.1.429	0.000024
S	833	F833S	tTc	tCc	1	1	B.1.438.1	0.000107
S	833	F833Y	tTc	tAc	1	1	B.1.499	0.00105
S	833	F833F	ttC	ttT	1	1	B.1.526	0.000024
S	833	F833F	ttC	ttT	1	1	B.1.546	0.003704
S	833	F833S	tTc	tCc	1	1	B.1.617.1	0.000129
S	833	F833I	Ttc	Atc	1	1	B.1.617.2	0.000004
S	833	F833del	TTC	---	1	1	B.1.638	0.052632
S	833	F833I	TtC	AtA	1	1	B.6.6	0.000889
S	833	F833L	ttC	ttA	1	1	B.6.6	0.000889
S	833	F833F	ttC	ttT	1	1	C.16	0.00106
S	833	F833del	TTC	---	1	1	C.37	0.000116
S	833	F833S	tTc	tCc	1	1	D.2	0.000075
S	833	F833F	ttC	ttT	1	1	D.2	0.000075
S	833	F833del	TTC	---	1	1	P.1.13	0.000898
S	833	F833F	ttC	ttT	1	1	P.1.15	0.000232
S	833	F833F	ttC	ttT	1	1	P.1.7	0.000319
S	833	F833del	TTC	---	1	1	Q.2	0.000613
S	833	F833L	Ttc	Ctc	1	1	W.1	0.008696

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.