CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 588

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	588	T588T		syn	acA	acG	388	372	0.958763	23324-23326
S	588	T588T		syn	acA	acT	388	14	0.0360825	23324-23326
S	588	T588T		syn	acA	acC	388	2	0.00515464	23324-23326
S	588	T588I		nonsyn	aCa	aTa	345	344	0.997101	23324-23326
S	588	T588I		nonsyn	aCA	aTT	345	1	0.00289855	23324-23326
S	588	T588A		nonsyn	Aca	Gca	259	259	1	23324-23326
S	588	T588S		nonsyn	Aca	Tca	245	245	1	23324-23326
S	588	T588R		nonsyn	aCa	aGa	46	46	1	23324-23326
S	588	T588K		nonsyn	aCa	aAa	25	25	1	23324-23326
S	588	T588del		del	ACA	---	5	5	1	23324-23326
S	588	T588del1		del	Aca	-ca	1	1	1	23324-23326
S	588	T588del2		del	ACA	--T	1	1	1	23324-23326

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	588	T588T	acA	acG	372	388	All	0.000071
S	588	T588T	acA	acT	14	388	All	0.000003
S	588	T588T	acA	acC	2	388	All	0
S	588	T588I	aCa	aTa	344	345	All	0.000066
S	588	T588I	aCA	aTT	1	345	All	0
S	588	T588T	acA	acG	339	339	AY.27	0.02194
S	588	T588A	Aca	Gca	259	259	All	0.00005
S	588	T588S	Aca	Tca	245	245	All	0.000047
S	588	T588S	Aca	Tca	173	173	B.1.160.32	0.742489
S	588	T588A	Aca	Gca	115	115	B.1.1.519	0.004567
S	588	T588I	aCa	aTa	73	73	B.1.1.7	0.000065
S	588	T588R	aCa	aGa	46	46	All	0.000009
S	588	T588A	Aca	Gca	43	43	AY.4	0.000067
S	588	T588I	aCa	aTa	36	37	AY.4	0.000056
S	588	T588I	aCA	aTT	1	37	AY.4	0.000002
S	588	T588I	aCa	aTa	32	32	AY.7.1	0.003606
S	588	T588R	aCa	aGa	29	29	AY.4	0.000045
S	588	T588I	aCa	aTa	27	27	AY.103	0.000168
S	588	T588K	aCa	aAa	25	25	All	0.000005
S	588	T588I	aCa	aTa	19	19	AY.43	0.000084
S	588	T588A	Aca	Gca	17	17	AY.111	0.003114
S	588	T588A	Aca	Gca	16	16	B.1.617.2	0.00006
S	588	T588A	Aca	Gca	14	14	AY.16	0.005315
S	588	T588I	aCa	aTa	14	14	B.1.617.2	0.000053
S	588	T588I	aCa	aTa	13	13	AY.44	0.000079
S	588	T588I	aCa	aTa	12	12	AY.3	0.000119
S	588	T588A	Aca	Gca	12	12	B.1.1.7	0.000011
S	588	T588I	aCa	aTa	12	12	P.1	0.000189
S	588	T588S	Aca	Tca	11	11	AY.33	0.000735
S	588	T588I	aCa	aTa	7	7	AY.25	0.000042
S	588	T588K	aCa	aAa	7	7	B.1.1.7	0.000006
S	588	T588S	Aca	Tca	7	7	B.1.1.7	0.000006
S	588	T588S	Aca	Tca	7	7	B.1.177	0.000092
S	588	T588I	aCa	aTa	6	6	AY.4.5	0.000645
S	588	T588S	Aca	Tca	6	6	B.1.1.39	0.003058
S	588	T588I	aCa	aTa	6	6	B.1.2	0.000053
S	588	T588del	ACA	---	5	5	All	0.000001
S	588	T588I	aCa	aTa	5	5	AY.3.1	0.000426
S	588	T588T	acA	acT	4	5	AY.4	0.000006
S	588	T588T	acA	acG	1	5	AY.4	0.000002
S	588	T588A	Aca	Gca	5	5	B.1	0.000046
S	588	T588T	acA	acT	3	5	B.1.1.7	0.000003
S	588	T588T	acA	acG	2	5	B.1.1.7	0.000002
S	588	T588S	Aca	Tca	5	5	B.1.160.30	0.014881
S	588	T588T	acA	acG	5	5	B.1.177.56	0.003338
S	588	T588A	Aca	Gca	5	5	P.1	0.000079
S	588	T588R	aCa	aGa	4	4	AY.3	0.00004
S	588	T588A	Aca	Gca	4	4	AY.33	0.000267
S	588	T588I	aCa	aTa	4	4	AY.39	0.000099
S	588	T588I	aCa	aTa	4	4	AY.47	0.000124
S	588	T588I	aCa	aTa	4	4	AY.51	0.003636
S	588	T588I	aCa	aTa	4	4	AY.57	0.002625
S	588	T588S	Aca	Tca	4	4	B.1	0.000037
S	588	T588I	aCa	aTa	4	4	B.1.1	0.000073
S	588	T588R	aCa	aGa	4	4	B.1.1.7	0.000004
S	588	T588I	aCa	aTa	4	4	B.1.177.60	0.000874
S	588	T588I	aCa	aTa	4	4	D.2	0.0003
S	588	T588A	Aca	Gca	3	3	AY.100	0.000138
S	588	T588K	aCa	aAa	3	3	AY.102	0.00008
S	588	T588I	aCa	aTa	3	3	AY.102	0.00008
S	588	T588I	aCa	aTa	3	3	AY.118	0.000188
S	588	T588I	aCa	aTa	3	3	AY.46	0.000312
S	588	T588A	Aca	Gca	3	3	AY.75	0.000168
S	588	T588T	acA	acG	3	3	B.1	0.000027
S	588	T588I	aCa	aTa	3	3	B.1	0.000027
S	588	T588R	aCa	aGa	3	3	B.1.1	0.000054
S	588	T588T	acA	acG	3	3	B.1.160	0.000094
S	588	T588S	Aca	Tca	3	3	B.1.36	0.000438
S	588	T588S	Aca	Tca	2	2	AY.102	0.000053
S	588	T588K	aCa	aAa	2	2	AY.103	0.000012
S	588	T588I	aCa	aTa	2	2	AY.117	0.000169
S	588	T588I	aCa	aTa	2	2	AY.119	0.000071
S	588	T588T	acA	acT	1	2	AY.25	0.000006
S	588	T588T	acA	acG	1	2	AY.25	0.000006
S	588	T588A	Aca	Gca	2	2	AY.27	0.000129
S	588	T588K	aCa	aAa	2	2	AY.29	0.000032
S	588	T588I	aCa	aTa	2	2	AY.34	0.000194
S	588	T588K	aCa	aAa	2	2	AY.4	0.000003
S	588	T588R	aCa	aGa	2	2	AY.4.2	0.000043
S	588	T588S	Aca	Tca	2	2	AY.43	0.000009
S	588	T588T	acA	acG	2	2	AY.45	0.000243
S	588	T588T	acA	acG	1	2	AY.5	0.000021
S	588	T588T	acA	acT	1	2	AY.5	0.000021
S	588	T588K	aCa	aAa	2	2	AY.54	0.000191
S	588	T588I	aCa	aTa	2	2	AY.6	0.000082
S	588	T588I	aCa	aTa	2	2	AY.75	0.000112
S	588	T588A	Aca	Gca	2	2	AY.9.2	0.000073
S	588	T588T	acA	acG	2	2	B.1.1	0.000036
S	588	T588A	Aca	Gca	2	2	B.1.1	0.000036
S	588	T588S	Aca	Tca	2	2	B.1.1.153	0.002191
S	588	T588S	Aca	Tca	2	2	B.1.1.25	0.001137
S	588	T588T	acA	acG	2	2	B.1.110.3	0.001437
S	588	T588I	aCa	aTa	2	2	B.1.160	0.000062
S	588	T588A	Aca	Gca	2	2	B.1.177	0.000026
S	588	T588S	Aca	Tca	2	2	B.1.177.43	0.002954
S	588	T588I	aCa	aTa	2	2	B.1.36.29	0.001035
S	588	T588I	aCa	aTa	2	2	B.1.427	0.000101
S	588	T588I	aCa	aTa	2	2	B.1.526	0.000047
S	588	T588K	aCa	aAa	2	2	B.1.617.2	0.000008
S	588	T588S	Aca	Tca	2	2	B.1.617.2	0.000008
S	588	T588T	acA	acG	2	2	B.1.617.2	0.000008
S	588	T588I	aCa	aTa	1	1	A.21	0.00277
S	588	T588del1	Aca	-ca	1	1	All	0
S	588	T588del2	ACA	--T	1	1	All	0
S	588	T588A	Aca	Gca	1	1	AY.103	0.000006
S	588	T588I	aCa	aTa	1	1	AY.116.1	0.000311
S	588	T588S	Aca	Tca	1	1	AY.119	0.000035
S	588	T588A	Aca	Gca	1	1	AY.20	0.000039
S	588	T588T	acA	acG	1	1	AY.23	0.00007
S	588	T588A	Aca	Gca	1	1	AY.25	0.000006
S	588	T588I	aCa	aTa	1	1	AY.26	0.000028
S	588	T588A	Aca	Gca	1	1	AY.29	0.000016
S	588	T588T	acA	acT	1	1	AY.3	0.00001
S	588	T588A	Aca	Gca	1	1	AY.3	0.00001
S	588	T588S	Aca	Tca	1	1	AY.3.1	0.000085
S	588	T588S	Aca	Tca	1	1	AY.30	0.000396
S	588	T588I	aCa	aTa	1	1	AY.33	0.000067
S	588	T588T	acA	acG	1	1	AY.35	0.000233
S	588	T588T	acA	acG	1	1	AY.38	0.000499
S	588	T588del1	Aca	-ca	1	1	AY.38	0.000499
S	588	T588del	ACA	---	1	1	AY.38	0.000499
S	588	T588A	Aca	Gca	1	1	AY.39	0.000025
S	588	T588R	aCa	aGa	1	1	AY.39	0.000025
S	588	T588S	Aca	Tca	1	1	AY.4	0.000002
S	588	T588I	aCa	aTa	1	1	AY.4.2	0.000022
S	588	T588T	acA	acG	1	1	AY.42	0.00004
S	588	T588del	ACA	---	1	1	AY.43	0.000004
S	588	T588A	Aca	Gca	1	1	AY.43	0.000004
S	588	T588K	aCa	aAa	1	1	AY.43	0.000004
S	588	T588T	acA	acC	1	1	AY.44	0.000006
S	588	T588del2	ACA	--T	1	1	AY.44	0.000006
S	588	T588R	aCa	aGa	1	1	AY.44	0.000006
S	588	T588I	aCa	aTa	1	1	AY.46.5	0.000198
S	588	T588A	Aca	Gca	1	1	AY.5	0.000021
S	588	T588K	aCa	aAa	1	1	AY.5	0.000021
S	588	T588S	Aca	Tca	1	1	AY.5	0.000021
S	588	T588I	aCa	aTa	1	1	AY.5.4	0.000277
S	588	T588T	acA	acT	1	1	AY.58	0.000907
S	588	T588T	acA	acT	1	1	AY.6	0.000041
S	588	T588T	acA	acG	1	1	AY.61	0.000105
S	588	T588I	aCa	aTa	1	1	AY.9.2	0.000037
S	588	T588S	Aca	Tca	1	1	AY.98.1	0.000048
S	588	T588I	aCa	aTa	1	1	AY.99	0.001049
S	588	T588del	ACA	---	1	1	B.1.1.139	0.022727
S	588	T588A	Aca	Gca	1	1	B.1.1.158	0.012195
S	588	T588I	aCa	aTa	1	1	B.1.1.277	0.000759
S	588	T588S	Aca	Tca	1	1	B.1.1.306	0.000438
S	588	T588I	aCa	aTa	1	1	B.1.1.318	0.000302
S	588	T588S	Aca	Tca	1	1	B.1.1.37	0.000193
S	588	T588A	Aca	Gca	1	1	B.1.1.515	0.02
S	588	T588I	aCa	aTa	1	1	B.1.1.519	0.00004
S	588	T588I	aCa	aTa	1	1	B.1.1.523	0.001563
S	588	T588del	ACA	---	1	1	B.1.1.7	0.000001
S	588	T588S	Aca	Tca	1	1	B.1.1.70	0.000341
S	588	T588S	Aca	Tca	1	1	B.1.160	0.000031
S	588	T588S	Aca	Tca	1	1	B.1.160.16	0.000929
S	588	T588S	Aca	Tca	1	1	B.1.160.28	0.002924
S	588	T588T	acA	acG	1	1	B.1.177	0.000013
S	588	T588I	aCa	aTa	1	1	B.1.177	0.000013
S	588	T588I	aCa	aTa	1	1	B.1.177.12	0.000152
S	588	T588S	Aca	Tca	1	1	B.1.177.44	0.000519
S	588	T588A	Aca	Gca	1	1	B.1.177.71	0.010101
S	588	T588S	Aca	Tca	1	1	B.1.177.81	0.000189
S	588	T588I	aCa	aTa	1	1	B.1.177.86	0.000183
S	588	T588A	Aca	Gca	1	1	B.1.2	0.000009
S	588	T588T	acA	acG	1	1	B.1.2	0.000009
S	588	T588I	aCa	aTa	1	1	B.1.221	0.000071
S	588	T588T	acA	acC	1	1	B.1.222	0.001692
S	588	T588R	aCa	aGa	1	1	B.1.243	0.00007
S	588	T588I	aCa	aTa	1	1	B.1.243	0.00007
S	588	T588S	Aca	Tca	1	1	B.1.258	0.000067
S	588	T588I	aCa	aTa	1	1	B.1.258.17	0.000104
S	588	T588K	aCa	aAa	1	1	B.1.311	0.000275
S	588	T588T	acA	acG	1	1	B.1.351.5	0.0006
S	588	T588S	Aca	Tca	1	1	B.1.36.35	0.002604
S	588	T588T	acA	acT	1	1	B.1.36.8	0.001
S	588	T588I	aCa	aTa	1	1	B.1.375	0.00082
S	588	T588S	Aca	Tca	1	1	B.1.429	0.000024
S	588	T588K	aCa	aAa	1	1	B.1.466.2	0.000391
S	588	T588A	Aca	Gca	1	1	B.1.526	0.000024
S	588	T588A	Aca	Gca	1	1	B.1.596	0.000087
S	588	T588K	aCa	aAa	1	1	B.1.602	0.006536
S	588	T588I	aCa	aTa	1	1	B.1.603	0.010638
S	588	T588I	aCa	aTa	1	1	B.1.612	0.002653
S	588	T588R	aCa	aGa	1	1	B.1.617.2	0.000004
S	588	T588del	ACA	---	1	1	B.1.620	0.000946
S	588	T588I	aCa	aTa	1	1	B.1.637	0.000073
S	588	T588I	aCa	aTa	1	1	C.37	0.000116
S	588	T588T	acA	acT	1	1	D.2	0.000075
S	588	T588T	acA	acG	1	1	P.1	0.000016

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.