CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 1052 & Codon = ttT

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	1052	F1052F		syn	ttC	ttT	1087	1087	1	24716-24718

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	1052	F1052F	ttC	ttT	1087	1087	All	0.000208
S	1052	F1052F	ttC	ttT	226	226	B.1.637	0.016514
S	1052	F1052F	ttC	ttT	97	97	B.1.617.2	0.000365
S	1052	F1052F	ttC	ttT	95	95	B.1.1.7	0.000085
S	1052	F1052F	ttC	ttT	83	83	AY.4	0.000129
S	1052	F1052F	ttC	ttT	77	77	AY.3	0.000766
S	1052	F1052F	ttC	ttT	58	58	B.1	0.000531
S	1052	F1052F	ttC	ttT	47	47	AY.25	0.000283
S	1052	F1052F	ttC	ttT	46	46	B.1.427	0.002323
S	1052	F1052F	ttC	ttT	39	39	B.1.2	0.000343
S	1052	F1052F	ttC	ttT	22	22	AY.44	0.000134
S	1052	F1052F	ttC	ttT	19	19	AY.61	0.001991
S	1052	F1052F	ttC	ttT	17	17	AY.54	0.001621
S	1052	F1052F	ttC	ttT	15	15	AY.103	0.000093
S	1052	F1052F	ttC	ttT	15	15	AY.20	0.000583
S	1052	F1052F	ttC	ttT	14	14	AY.100	0.000644
S	1052	F1052F	ttC	ttT	14	14	AY.43	0.000062
S	1052	F1052F	ttC	ttT	12	12	B.1.351	0.000357
S	1052	F1052F	ttC	ttT	10	10	AY.102	0.000265
S	1052	F1052F	ttC	ttT	10	10	AY.92	0.002873
S	1052	F1052F	ttC	ttT	9	9	B.1.1.222	0.001836
S	1052	F1052F	ttC	ttT	7	7	AY.9	0.000473
S	1052	F1052F	ttC	ttT	6	6	AY.47	0.000187
S	1052	F1052F	ttC	ttT	6	6	AY.52	0.004886
S	1052	F1052F	ttC	ttT	6	6	B.1.1.33	0.002525
S	1052	F1052F	ttC	ttT	6	6	B.1.177	0.000079
S	1052	F1052F	ttC	ttT	6	6	B.1.235	0.015113
S	1052	F1052F	ttC	ttT	6	6	B.1.416.1	0.009375
S	1052	F1052F	ttC	ttT	5	5	P.1	0.000079
S	1052	F1052F	ttC	ttT	5	5	R.1	0.00045
S	1052	F1052F	ttC	ttT	4	4	AY.3.1	0.000341
S	1052	F1052F	ttC	ttT	4	4	AY.35	0.000932
S	1052	F1052F	ttC	ttT	4	4	AY.98	0.000316
S	1052	F1052F	ttC	ttT	4	4	B.1.1.284	0.00043
S	1052	F1052F	ttC	ttT	4	4	B.1.243	0.000278
S	1052	F1052F	ttC	ttT	3	3		0.166667
S	1052	F1052F	ttC	ttT	3	3	AY.120	0.000112
S	1052	F1052F	ttC	ttT	3	3	AY.30	0.001187
S	1052	F1052F	ttC	ttT	3	3	AY.39	0.000074
S	1052	F1052F	ttC	ttT	3	3	AY.4.2	0.000065
S	1052	F1052F	ttC	ttT	3	3	AY.46.4	0.000494
S	1052	F1052F	ttC	ttT	3	3	AY.5	0.000062
S	1052	F1052F	ttC	ttT	3	3	AY.75.1	0.000541
S	1052	F1052F	ttC	ttT	3	3	B.1.177.72	0.010169
S	1052	F1052F	ttC	ttT	2	2	AY.109	0.001479
S	1052	F1052F	ttC	ttT	2	2	AY.117	0.000169
S	1052	F1052F	ttC	ttT	2	2	AY.23	0.000139
S	1052	F1052F	ttC	ttT	2	2	AY.6	0.000082
S	1052	F1052F	ttC	ttT	2	2	AY.84	0.000875
S	1052	F1052F	ttC	ttT	2	2	B.1.1	0.000036
S	1052	F1052F	ttC	ttT	2	2	B.1.1.316	0.00185
S	1052	F1052F	ttC	ttT	2	2	B.1.221	0.000142
S	1052	F1052F	ttC	ttT	2	2	B.1.36.29	0.001035
S	1052	F1052F	ttC	ttT	2	2	B.1.389	0.002004
S	1052	F1052F	ttC	ttT	2	2	B.1.396	0.001411
S	1052	F1052F	ttC	ttT	2	2	B.1.526	0.000047
S	1052	F1052F	ttC	ttT	2	2	B.1.596	0.000174
S	1052	F1052F	ttC	ttT	2	2	B.1.617.1	0.000258
S	1052	F1052F	ttC	ttT	2	2	P.1.17	0.000324
S	1052	F1052F	ttC	ttT	2	2	S.1	0.009901
S	1052	F1052F	ttC	ttT	1	1	A.2.5	0.000499
S	1052	F1052F	ttC	ttT	1	1	AY.1	0.000396
S	1052	F1052F	ttC	ttT	1	1	AY.105	0.000643
S	1052	F1052F	ttC	ttT	1	1	AY.106	0.000335
S	1052	F1052F	ttC	ttT	1	1	AY.29.1	0.000221
S	1052	F1052F	ttC	ttT	1	1	AY.33	0.000067
S	1052	F1052F	ttC	ttT	1	1	AY.34.1	0.00051
S	1052	F1052F	ttC	ttT	1	1	AY.42	0.00004
S	1052	F1052F	ttC	ttT	1	1	AY.45	0.000122
S	1052	F1052F	ttC	ttT	1	1	AY.46	0.000104
S	1052	F1052F	ttC	ttT	1	1	AY.48	0.000465
S	1052	F1052F	ttC	ttT	1	1	AY.71	0.000475
S	1052	F1052F	ttC	ttT	1	1	AY.87	0.000833
S	1052	F1052F	ttC	ttT	1	1	AY.9.2	0.000037
S	1052	F1052F	ttC	ttT	1	1	B.1.1.139	0.022727
S	1052	F1052F	ttC	ttT	1	1	B.1.1.170	0.001247
S	1052	F1052F	ttC	ttT	1	1	B.1.1.25	0.000569
S	1052	F1052F	ttC	ttT	1	1	B.1.1.317	0.000412
S	1052	F1052F	ttC	ttT	1	1	B.1.1.519	0.00004
S	1052	F1052F	ttC	ttT	1	1	B.1.111	0.001175
S	1052	F1052F	ttC	ttT	1	1	B.1.160	0.000031
S	1052	F1052F	ttC	ttT	1	1	B.1.340	0.004292
S	1052	F1052F	ttC	ttT	1	1	B.1.351.3	0.000876
S	1052	F1052F	ttC	ttT	1	1	B.1.36	0.000146
S	1052	F1052F	ttC	ttT	1	1	B.1.537	0.02
S	1052	F1052F	ttC	ttT	1	1	B.1.633	0.041667
S	1052	F1052F	ttC	ttT	1	1	B.1.9.4	0.006135
S	1052	F1052F	ttC	ttT	1	1	C.35	0.000774
S	1052	F1052F	ttC	ttT	1	1	D.2	0.000075
S	1052	F1052F	ttC	ttT	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.