CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 392

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	392	F392F		syn	ttT	ttC	2445	2445	1	22736-22738
S	392	F392del		del	TTT	---	75	75	1	22736-22738
S	392	F392L		nonsyn	Ttt	Ctt	45	40	0.888889	22736-22738
S	392	F392L		nonsyn	ttT	ttA	45	4	0.0888889	22736-22738
S	392	F392L		nonsyn	TtT	CtA	45	1	0.0222222	22736-22738
S	392	F392S		nonsyn	tTt	tCt	16	15	0.9375	22736-22738
S	392	F392S		nonsyn	tTT	tCA	16	1	0.0625	22736-22738
S	392	F392V		nonsyn	Ttt	Gtt	12	10	0.833333	22736-22738
S	392	F392V		nonsyn	TtT	GtC	12	1	0.0833333	22736-22738
S	392	F392V		nonsyn	TtT	GtA	12	1	0.0833333	22736-22738
S	392	F392I		nonsyn	Ttt	Att	9	7	0.777778	22736-22738
S	392	F392I		nonsyn	TtT	AtA	9	2	0.222222	22736-22738
S	392	F392del1		del	Ttt	-tt	4	4	1	22736-22738
S	392	F392A		nonsyn	TTt	GCt	3	3	1	22736-22738
S	392	F392C		nonsyn	tTt	tGt	3	3	1	22736-22738
S	392	F392Y		nonsyn	tTt	tAt	3	3	1	22736-22738
S	392	F392del2		del	TTt	--t	1	1	1	22736-22738
S	392	F392P		nonsyn	TTt	CCt	1	1	1	22736-22738

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	392	F392F	ttT	ttC	2445	2445	All	0.000468
S	392	F392F	ttT	ttC	1498	1498	B.1.619.1	0.960872
S	392	F392F	ttT	ttC	700	700	P.1	0.011028
S	392	F392del	TTT	---	75	75	All	0.000014
S	392	F392F	ttT	ttC	55	55	B.1.1.7	0.000049
S	392	F392L	Ttt	Ctt	40	45	All	0.000008
S	392	F392L	ttT	ttA	4	45	All	0.000001
S	392	F392L	TtT	CtA	1	45	All	0
S	392	F392F	ttT	ttC	23	23	AY.120	0.000855
S	392	F392F	ttT	ttC	20	20	B.1.627	0.040404
S	392	F392del	TTT	---	18	18	B.1.1.7	0.000016
S	392	F392S	tTt	tCt	15	16	All	0.000003
S	392	F392S	tTT	tCA	1	16	All	0
S	392	F392F	ttT	ttC	13	13	B.1.637	0.00095
S	392	F392V	Ttt	Gtt	10	12	All	0.000002
S	392	F392V	TtT	GtC	1	12	All	0
S	392	F392V	TtT	GtA	1	12	All	0
S	392	F392F	ttT	ttC	11	11	B.1.596	0.000959
S	392	F392F	ttT	ttC	10	10	B.1.1.39	0.005097
S	392	F392I	Ttt	Att	7	9	All	0.000001
S	392	F392I	TtT	AtA	2	9	All	0
S	392	F392F	ttT	ttC	9	9	AY.4	0.000014
S	392	F392F	ttT	ttC	8	8	AY.29	0.000126
S	392	F392F	ttT	ttC	8	8	B.1.1.284	0.000859
S	392	F392F	ttT	ttC	8	8	B.1.177	0.000105
S	392	F392F	ttT	ttC	8	8	B.1.619	0.006969
S	392	F392V	Ttt	Gtt	7	7	B.1.1.7	0.000006
S	392	F392del	TTT	---	6	6	AY.25	0.000036
S	392	F392F	ttT	ttC	6	6	AY.43	0.000027
S	392	F392F	ttT	ttC	5	5	AY.103	0.000031
S	392	F392del	TTT	---	5	5	AY.4	0.000008
S	392	F392S	tTt	tCt	4	5	B.1.1.7	0.000004
S	392	F392S	tTT	tCA	1	5	B.1.1.7	0.000001
S	392	F392F	ttT	ttC	5	5	B.1.2	0.000044
S	392	F392F	ttT	ttC	5	5	B.1.617.2	0.000019
S	392	F392F	ttT	ttC	5	5	B.1.621	0.000443
S	392	F392del	TTT	---	4	4		0.222222
S	392	F392del1	Ttt	-tt	4	4	All	0.000001
S	392	F392F	ttT	ttC	4	4	B.1	0.000037
S	392	F392L	Ttt	Ctt	4	4	B.1	0.000037
S	392	F392L	Ttt	Ctt	4	4	B.1.1.7	0.000004
S	392	F392F	ttT	ttC	4	4	B.1.234	0.000528
S	392	F392del	TTT	---	4	4	B.1.258	0.000266
S	392	F392F	ttT	ttC	4	4	B.1.561	0.001588
S	392	F392F	ttT	ttC	4	4	P.1.12	0.001936
S	392	F392V	TtT	GtC	1	3		0.055556
S	392	F392V	Ttt	Gtt	1	3		0.055556
S	392	F392V	TtT	GtA	1	3		0.055556
S	392	F392Y	tTt	tAt	3	3	All	0.000001
S	392	F392A	TTt	GCt	3	3	All	0.000001
S	392	F392C	tTt	tGt	3	3	All	0.000001
S	392	F392L	Ttt	Ctt	3	3	AY.23	0.000209
S	392	F392del	TTT	---	3	3	AY.43	0.000013
S	392	F392del	TTT	---	3	3	B.1	0.000027
S	392	F392F	ttT	ttC	3	3	B.1.1.322	0.026316
S	392	F392F	ttT	ttC	3	3	B.1.36	0.000438
S	392	F392L	Ttt	Ctt	2	3	B.1.617.2	0.000008
S	392	F392L	ttT	ttA	1	3	B.1.617.2	0.000004
S	392	F392A	TTt	GCt	3	3	C.37	0.000348
S	392	F392I	Ttt	Att	2	2		0.111111
S	392	F392F	ttT	ttC	2	2	A.2.5.2	0.003145
S	392	F392F	ttT	ttC	2	2	AY.102	0.000053
S	392	F392del	TTT	---	2	2	AY.4.5	0.000215
S	392	F392L	Ttt	Ctt	2	2	AY.61	0.00021
S	392	F392S	tTt	tCt	2	2	B.1	0.000018
S	392	F392F	ttT	ttC	2	2	B.1.1	0.000036
S	392	F392L	Ttt	Ctt	2	2	B.1.1	0.000036
S	392	F392del	TTT	---	2	2	B.1.2	0.000018
S	392	F392del	TTT	---	2	2	B.1.617.2	0.000008
S	392	F392del	TTT	---	2	2	P.1.1	0.000635
S	392	F392L	ttT	ttA	1	1		0.055556
S	392	F392F	ttT	ttC	1	1		0.055556
S	392	F392F	ttT	ttC	1	1	A	0.000387
S	392	F392S	tTt	tCt	1	1	A.2	0.000662
S	392	F392del	TTT	---	1	1	A.28	0.002646
S	392	F392I	TtT	AtA	1	1	AE.3	0.032258
S	392	F392del2	TTt	--t	1	1	All	0
S	392	F392P	TTt	CCt	1	1	All	0
S	392	F392L	Ttt	Ctt	1	1	AY.100	0.000046
S	392	F392F	ttT	ttC	1	1	AY.100	0.000046
S	392	F392S	tTt	tCt	1	1	AY.103	0.000006
S	392	F392L	Ttt	Ctt	1	1	AY.103	0.000006
S	392	F392del	TTT	---	1	1	AY.107	0.000466
S	392	F392del1	Ttt	-tt	1	1	AY.108	0.001103
S	392	F392S	tTt	tCt	1	1	AY.113	0.000142
S	392	F392del	TTT	---	1	1	AY.118	0.000063
S	392	F392L	Ttt	Ctt	1	1	AY.14	0.000088
S	392	F392F	ttT	ttC	1	1	AY.23	0.00007
S	392	F392I	Ttt	Att	1	1	AY.25	0.000006
S	392	F392F	ttT	ttC	1	1	AY.25	0.000006
S	392	F392S	tTt	tCt	1	1	AY.25	0.000006
S	392	F392S	tTt	tCt	1	1	AY.29	0.000016
S	392	F392F	ttT	ttC	1	1	AY.3	0.00001
S	392	F392del	TTT	---	1	1	AY.33	0.000067
S	392	F392C	tTt	tGt	1	1	AY.39	0.000025
S	392	F392L	Ttt	Ctt	1	1	AY.39	0.000025
S	392	F392S	tTt	tCt	1	1	AY.39.1	0.00004
S	392	F392L	Ttt	Ctt	1	1	AY.4	0.000002
S	392	F392F	ttT	ttC	1	1	AY.4.2	0.000022
S	392	F392F	ttT	ttC	1	1	AY.41	0.000294
S	392	F392S	tTt	tCt	1	1	AY.43	0.000004
S	392	F392L	Ttt	Ctt	1	1	AY.43	0.000004
S	392	F392I	Ttt	Att	1	1	AY.43	0.000004
S	392	F392del1	Ttt	-tt	1	1	AY.43	0.000004
S	392	F392L	Ttt	Ctt	1	1	AY.44	0.000006
S	392	F392F	ttT	ttC	1	1	AY.44	0.000006
S	392	F392Y	tTt	tAt	1	1	AY.45	0.000122
S	392	F392L	Ttt	Ctt	1	1	AY.46.6	0.000072
S	392	F392del	TTT	---	1	1	AY.59	0.00053
S	392	F392del	TTT	---	1	1	AY.67	0.000464
S	392	F392del	TTT	---	1	1	AY.72	0.001361
S	392	F392L	Ttt	Ctt	1	1	AY.75	0.000056
S	392	F392L	Ttt	Ctt	1	1	AY.75.1	0.00018
S	392	F392del	TTT	---	1	1	AY.9	0.000068
S	392	F392C	tTt	tGt	1	1	B.1	0.000009
S	392	F392P	TTt	CCt	1	1	B.1	0.000009
S	392	F392del	TTT	---	1	1	B.1.1	0.000018
S	392	F392F	ttT	ttC	1	1	B.1.1.1	0.000327
S	392	F392L	Ttt	Ctt	1	1	B.1.1.1	0.000327
S	392	F392del	TTT	---	1	1	B.1.1.137	0.0125
S	392	F392I	Ttt	Att	1	1	B.1.1.189	0.001513
S	392	F392I	Ttt	Att	1	1	B.1.1.221	0.010101
S	392	F392L	Ttt	Ctt	1	1	B.1.1.306	0.000438
S	392	F392del	TTT	---	1	1	B.1.1.315	0.008475
S	392	F392L	Ttt	Ctt	1	1	B.1.1.316	0.000925
S	392	F392F	ttT	ttC	1	1	B.1.1.519	0.00004
S	392	F392L	Ttt	Ctt	1	1	B.1.1.519	0.00004
S	392	F392del	TTT	---	1	1	B.1.1.519	0.00004
S	392	F392Y	tTt	tAt	1	1	B.1.1.7	0.000001
S	392	F392del	TTT	---	1	1	B.1.160.29	0.004219
S	392	F392del	TTT	---	1	1	B.1.177	0.000013
S	392	F392V	Ttt	Gtt	1	1	B.1.177	0.000013
S	392	F392L	Ttt	Ctt	1	1	B.1.177.17	0.000821
S	392	F392del	TTT	---	1	1	B.1.177.21	0.000076
S	392	F392del1	Ttt	-tt	1	1	B.1.2	0.000009
S	392	F392L	Ttt	Ctt	1	1	B.1.2	0.000009
S	392	F392F	ttT	ttC	1	1	B.1.240	0.000216
S	392	F392del	TTT	---	1	1	B.1.242	0.018868
S	392	F392S	tTt	tCt	1	1	B.1.243	0.00007
S	392	F392L	Ttt	Ctt	1	1	B.1.243	0.00007
S	392	F392I	Ttt	Att	1	1	B.1.258.4	0.003448
S	392	F392L	Ttt	Ctt	1	1	B.1.332	0.003497
S	392	F392F	ttT	ttC	1	1	B.1.349	0.000715
S	392	F392F	ttT	ttC	1	1	B.1.351	0.00003
S	392	F392del	TTT	---	1	1	B.1.351	0.00003
S	392	F392L	Ttt	Ctt	1	1	B.1.351	0.00003
S	392	F392I	TtT	AtA	1	1	B.1.36	0.000146
S	392	F392F	ttT	ttC	1	1	B.1.36.10	0.004785
S	392	F392F	ttT	ttC	1	1	B.1.36.18	0.00042
S	392	F392del	TTT	---	1	1	B.1.36.29	0.000517
S	392	F392F	ttT	ttC	1	1	B.1.429	0.000024
S	392	F392L	ttT	ttA	1	1	B.1.438.1	0.000107
S	392	F392del	TTT	---	1	1	B.1.446	0.02
S	392	F392V	Ttt	Gtt	1	1	B.1.462	0.007246
S	392	F392C	tTt	tGt	1	1	B.1.466.2	0.000391
S	392	F392L	TtT	CtA	1	1	B.1.525	0.000113
S	392	F392del	TTT	---	1	1	B.1.526	0.000024
S	392	F392L	Ttt	Ctt	1	1	B.1.564.1	0.001577
S	392	F392L	Ttt	Ctt	1	1	B.1.595	0.000261
S	392	F392del1	Ttt	-tt	1	1	B.1.596	0.000087
S	392	F392L	ttT	ttA	1	1	B.1.617.1	0.000129
S	392	F392S	tTt	tCt	1	1	B.1.617.2	0.000004
S	392	F392del2	TTt	--t	1	1	B.1.617.2	0.000004
S	392	F392del	TTT	---	1	1	B.1.620	0.000946
S	392	F392del	TTT	---	1	1	B.1.621	0.000089
S	392	F392F	ttT	ttC	1	1	B.1.630	0.005236
S	392	F392L	Ttt	Ctt	1	1	B.1.9	0.006173
S	392	F392del	TTT	---	1	1	B.34	0.013699
S	392	F392Y	tTt	tAt	1	1	P.1	0.000016
S	392	F392L	Ttt	Ctt	1	1	P.1.1	0.000318
S	392	F392F	ttT	ttC	1	1	P.1.14	0.000048
S	392	F392F	ttT	ttC	1	1	P.2	0.000187
S	392	F392del	TTT	---	1	1	Q.2	0.000613

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.