CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : Mut = S371S

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	371	S371S		syn	tcC	tcT	2763	2444	0.884546	22673-22675
S	371	S371S		syn	tcC	tcA	2763	310	0.112197	22673-22675
S	371	S371S		syn	tcC	tcG	2763	9	0.00325733	22673-22675

Details of the mutation S371S 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	371	S371S	tcC	tcT	2444	2763	All	0.000467
S	371	S371S	tcC	tcA	310	2763	All	0.000059
S	371	S371S	tcC	tcG	9	2763	All	0.000002
S	371	S371S	tcC	tcT	690	697	B.1.1.7	0.000618
S	371	S371S	tcC	tcA	6	697	B.1.1.7	0.000005
S	371	S371S	tcC	tcG	1	697	B.1.1.7	0.000001
S	371	S371S	tcC	tcT	252	434	AY.4	0.000392
S	371	S371S	tcC	tcA	181	434	AY.4	0.000282
S	371	S371S	tcC	tcG	1	434	AY.4	0.000002
S	371	S371S	tcC	tcT	137	137	B.1.1.273	0.925676
S	371	S371S	tcC	tcT	131	131	B.1.1.412	1
S	371	S371S	tcC	tcT	126	126	B.1.160	0.00393
S	371	S371S	tcC	tcT	99	102	AY.103	0.000615
S	371	S371S	tcC	tcA	3	102	AY.103	0.000019
S	371	S371S	tcC	tcT	88	92	AY.25	0.000529
S	371	S371S	tcC	tcA	3	92	AY.25	0.000018
S	371	S371S	tcC	tcG	1	92	AY.25	0.000006
S	371	S371S	tcC	tcT	79	86	AY.44	0.000481
S	371	S371S	tcC	tcA	7	86	AY.44	0.000043
S	371	S371S	tcC	tcT	61	65	B.1.1	0.001107
S	371	S371S	tcC	tcA	3	65	B.1.1	0.000054
S	371	S371S	tcC	tcG	1	65	B.1.1	0.000018
S	371	S371S	tcC	tcT	44	53	B.1.617.2	0.000166
S	371	S371S	tcC	tcA	9	53	B.1.617.2	0.000034
S	371	S371S	tcC	tcT	49	49	AY.46.6	0.003538
S	371	S371S	tcC	tcT	47	47	B.1.126	0.059949
S	371	S371S	tcC	tcT	46	47	B.1.2	0.000405
S	371	S371S	tcC	tcA	1	47	B.1.2	0.000009
S	371	S371S	tcC	tcT	38	46	AY.43	0.000168
S	371	S371S	tcC	tcA	8	46	AY.43	0.000035
S	371	S371S	tcC	tcT	40	43	B.1	0.000366
S	371	S371S	tcC	tcA	3	43	B.1	0.000027
S	371	S371S	tcC	tcT	40	40	AY.118	0.002506
S	371	S371S	tcC	tcT	31	35	P.1	0.000488
S	371	S371S	tcC	tcA	4	35	P.1	0.000063
S	371	S371S	tcC	tcA	26	31	B.1.351	0.000773
S	371	S371S	tcC	tcT	5	31	B.1.351	0.000149
S	371	S371S	tcC	tcT	25	29	AY.3	0.000249
S	371	S371S	tcC	tcA	4	29	AY.3	0.00004
S	371	S371S	tcC	tcT	27	27	AY.34	0.002618
S	371	S371S	tcC	tcT	26	26	B.1.1.56	0.464286
S	371	S371S	tcC	tcT	20	21	AY.26	0.000566
S	371	S371S	tcC	tcG	1	21	AY.26	0.000028
S	371	S371S	tcC	tcT	19	19	B.1.427	0.000959
S	371	S371S	tcC	tcT	15	16	B.1.429	0.000353
S	371	S371S	tcC	tcA	1	16	B.1.429	0.000024
S	371	S371S	tcC	tcT	12	15	AY.20	0.000466
S	371	S371S	tcC	tcA	2	15	AY.20	0.000078
S	371	S371S	tcC	tcG	1	15	AY.20	0.000039
S	371	S371S	tcC	tcT	14	14	P.1.1	0.004447
S	371	S371S	tcC	tcA	8	13	AY.102	0.000212
S	371	S371S	tcC	tcT	5	13	AY.102	0.000133
S	371	S371S	tcC	tcT	13	13	AY.29	0.000205
S	371	S371S	tcC	tcA	13	13	B.1.1.28	0.004046
S	371	S371S	tcC	tcT	12	12	AY.33	0.000801
S	371	S371S	tcC	tcT	7	11	AY.39	0.000173
S	371	S371S	tcC	tcA	4	11	AY.39	0.000099
S	371	S371S	tcC	tcT	10	11	AY.4.2	0.000217
S	371	S371S	tcC	tcA	1	11	AY.4.2	0.000022
S	371	S371S	tcC	tcT	9	9	B.1.1.189	0.013616
S	371	S371S	tcC	tcT	9	9	C.37	0.001045
S	371	S371S	tcC	tcA	7	8	AY.98.1	0.000339
S	371	S371S	tcC	tcT	1	8	AY.98.1	0.000048
S	371	S371S	tcC	tcT	8	8	B.1.1.291	0.005939
S	371	S371S	tcC	tcT	7	7	B.1.177	0.000092
S	371	S371S	tcC	tcT	5	6	AY.113	0.000712
S	371	S371S	tcC	tcA	1	6	AY.113	0.000142
S	371	S371S	tcC	tcT	6	6	AY.75	0.000336
S	371	S371S	tcC	tcT	6	6	P.1.14	0.000287
S	371	S371S	tcC	tcT	5	5	AY.36	0.000741
S	371	S371S	tcC	tcT	5	5	B.1.1.317	0.002058
S	371	S371S	tcC	tcT	5	5	B.1.177.57	0.001405
S	371	S371S	tcC	tcT	5	5	N.5	0.008834
S	371	S371S	tcC	tcT	4	4	A	0.001548
S	371	S371S	tcC	tcA	3	4	AY.119	0.000106
S	371	S371S	tcC	tcT	1	4	AY.119	0.000035
S	371	S371S	tcC	tcT	4	4	AY.39.1	0.000158
S	371	S371S	tcC	tcT	4	4	B.1.1.50	0.002716
S	371	S371S	tcC	tcT	4	4	B.1.1.519	0.000159
S	371	S371S	tcC	tcT	4	4	B.1.177.44	0.002076
S	371	S371S	tcC	tcT	4	4	P.1.10	0.001078
S	371	S371S	tcC	tcT	3	3	AY.100	0.000138
S	371	S371S	tcC	tcT	3	3	AY.106	0.001005
S	371	S371S	tcC	tcT	2	3	AY.120	0.000074
S	371	S371S	tcC	tcG	1	3	AY.120	0.000037
S	371	S371S	tcC	tcT	3	3	AY.42	0.000121
S	371	S371S	tcC	tcT	2	3	AY.47	0.000062
S	371	S371S	tcC	tcA	1	3	AY.47	0.000031
S	371	S371S	tcC	tcT	3	3	AY.6	0.000123
S	371	S371S	tcC	tcT	3	3	AY.9.1	0.000251
S	371	S371S	tcC	tcT	3	3	B.1.258	0.0002
S	371	S371S	tcC	tcT	3	3	B.1.391	0.003382
S	371	S371S	tcC	tcT	3	3	B.1.628	0.001057
S	371	S371S	tcC	tcA	3	3	C.1	0.007177
S	371	S371S	tcC	tcT	2	2	AY.14	0.000176
S	371	S371S	tcC	tcA	2	2	AY.27	0.000129
S	371	S371S	tcC	tcT	2	2	AY.29.1	0.000441
S	371	S371S	tcC	tcT	2	2	AY.34.1	0.00102
S	371	S371S	tcC	tcT	2	2	AY.38	0.000999
S	371	S371S	tcC	tcA	1	2	AY.45	0.000122
S	371	S371S	tcC	tcT	1	2	AY.45	0.000122
S	371	S371S	tcC	tcT	2	2	AY.5	0.000041
S	371	S371S	tcC	tcT	2	2	AY.65	0.001066
S	371	S371S	tcC	tcT	1	2	AY.79	0.001211
S	371	S371S	tcC	tcA	1	2	AY.79	0.001211
S	371	S371S	tcC	tcT	2	2	B.1.1.222	0.000408
S	371	S371S	tcC	tcT	2	2	B.1.1.294	0.002532
S	371	S371S	tcC	tcT	2	2	B.1.210	0.004264
S	371	S371S	tcC	tcT	2	2	B.1.221	0.000142
S	371	S371S	tcC	tcT	2	2	B.1.351.2	0.000605
S	371	S371S	tcC	tcT	2	2	B.1.526	0.000047
S	371	S371S	tcC	tcT	2	2	B.1.617.1	0.000258
S	371	S371S	tcC	tcT	2	2	B.1.637	0.000146
S	371	S371S	tcC	tcT	2	2	D.2	0.00015
S	371	S371S	tcC	tcT	2	2	P.1.15	0.000465
S	371	S371S	tcC	tcT	2	2	Q.8	0.00033
S	371	S371S	tcC	tcT	2	2	R.1	0.00018
S	371	S371S	tcC	tcT	1	1	A.23.1	0.000704
S	371	S371S	tcC	tcT	1	1	AE.8	0.000489
S	371	S371S	tcC	tcA	1	1	AY.110	0.000113
S	371	S371S	tcC	tcT	1	1	AY.116	0.000287
S	371	S371S	tcC	tcT	1	1	AY.116.1	0.000311
S	371	S371S	tcC	tcT	1	1	AY.16	0.00038
S	371	S371S	tcC	tcT	1	1	AY.23	0.00007
S	371	S371S	tcC	tcT	1	1	AY.3.1	0.000085
S	371	S371S	tcC	tcT	1	1	AY.37	0.000316
S	371	S371S	tcC	tcT	1	1	AY.4.2.1	0.000149
S	371	S371S	tcC	tcT	1	1	AY.4.5	0.000107
S	371	S371S	tcC	tcT	1	1	AY.46	0.000104
S	371	S371S	tcC	tcT	1	1	AY.46.5	0.000198
S	371	S371S	tcC	tcT	1	1	AY.5.3	0.000337
S	371	S371S	tcC	tcA	1	1	AY.50	0.000799
S	371	S371S	tcC	tcT	1	1	AY.61	0.000105
S	371	S371S	tcC	tcT	1	1	AY.68	0.000274
S	371	S371S	tcC	tcT	1	1	AY.7	0.000196
S	371	S371S	tcC	tcT	1	1	AY.7.1	0.000113
S	371	S371S	tcC	tcT	1	1	AY.71	0.000475
S	371	S371S	tcC	tcG	1	1	AY.73	0.000665
S	371	S371S	tcC	tcT	1	1	AY.75.1	0.00018
S	371	S371S	tcC	tcT	1	1	AY.9	0.000068
S	371	S371S	tcC	tcT	1	1	AY.9.2	0.000037
S	371	S371S	tcC	tcA	1	1	AY.96	0.002075
S	371	S371S	tcC	tcT	1	1	AY.98	0.000079
S	371	S371S	tcC	tcT	1	1	AY.99	0.001049
S	371	S371S	tcC	tcA	1	1	AY.99.2	0.000092
S	371	S371S	tcC	tcT	1	1	B.1.1.1	0.000327
S	371	S371S	tcC	tcT	1	1	B.1.1.153	0.001095
S	371	S371S	tcC	tcT	1	1	B.1.1.198	0.001468
S	371	S371S	tcC	tcT	1	1	B.1.1.216	0.00089
S	371	S371S	tcC	tcT	1	1	B.1.1.234	0.012048
S	371	S371S	tcC	tcT	1	1	B.1.1.241	0.00207
S	371	S371S	tcC	tcT	1	1	B.1.1.274	0.005051
S	371	S371S	tcC	tcT	1	1	B.1.1.318	0.000302
S	371	S371S	tcC	tcT	1	1	B.1.1.322	0.008772
S	371	S371S	tcC	tcT	1	1	B.1.1.33	0.000421
S	371	S371S	tcC	tcT	1	1	B.1.1.348	0.000796
S	371	S371S	tcC	tcT	1	1	B.1.1.39	0.00051
S	371	S371S	tcC	tcT	1	1	B.1.1.398	0.003226
S	371	S371S	tcC	tcT	1	1	B.1.1.448	0.002033
S	371	S371S	tcC	tcT	1	1	B.1.1.46	0.004367
S	371	S371S	tcC	tcT	1	1	B.1.1.485	0.016667
S	371	S371S	tcC	tcT	1	1	B.1.1.52	0.012195
S	371	S371S	tcC	tcT	1	1	B.1.13	0.002375
S	371	S371S	tcC	tcT	1	1	B.1.143	0.021277
S	371	S371S	tcC	tcT	1	1	B.1.157	0.002985
S	371	S371S	tcC	tcT	1	1	B.1.170	0.00431
S	371	S371S	tcC	tcT	1	1	B.1.177.18	0.00116
S	371	S371S	tcC	tcT	1	1	B.1.177.21	0.000076
S	371	S371S	tcC	tcT	1	1	B.1.177.54	0.000606
S	371	S371S	tcC	tcT	1	1	B.1.177.81	0.000189
S	371	S371S	tcC	tcT	1	1	B.1.182	0.007246
S	371	S371S	tcC	tcT	1	1	B.1.234	0.000132
S	371	S371S	tcC	tcT	1	1	B.1.240	0.000216
S	371	S371S	tcC	tcT	1	1	B.1.243	0.00007
S	371	S371S	tcC	tcT	1	1	B.1.258.11	0.000396
S	371	S371S	tcC	tcT	1	1	B.1.311	0.000275
S	371	S371S	tcC	tcT	1	1	B.1.409	0.000781
S	371	S371S	tcC	tcT	1	1	B.1.422	0.000812
S	371	S371S	tcC	tcT	1	1	B.1.432	0.011236
S	371	S371S	tcC	tcT	1	1	B.1.438.1	0.000107
S	371	S371S	tcC	tcT	1	1	B.1.453	0.003236
S	371	S371S	tcC	tcT	1	1	B.1.524	0.001406
S	371	S371S	tcC	tcT	1	1	B.1.541	0.004425
S	371	S371S	tcC	tcT	1	1	B.1.546	0.003704
S	371	S371S	tcC	tcT	1	1	B.1.560	0.00463
S	371	S371S	tcC	tcT	1	1	B.1.572	0.025
S	371	S371S	tcC	tcG	1	1	B.1.575	0.000303
S	371	S371S	tcC	tcT	1	1	B.1.595	0.000261
S	371	S371S	tcC	tcT	1	1	B.1.596	0.000087
S	371	S371S	tcC	tcT	1	1	B.1.609	0.000479
S	371	S371S	tcC	tcT	1	1	B.1.620	0.000946
S	371	S371S	tcC	tcT	1	1	B.1.621	0.000089
S	371	S371S	tcC	tcT	1	1	B.11	0.005128
S	371	S371S	tcC	tcT	1	1	B.6	0.00091
S	371	S371S	tcC	tcT	1	1	C.9	0.030303
S	371	S371S	tcC	tcT	1	1	N.1	0.016949
S	371	S371S	tcC	tcT	1	1	P.2	0.000187

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.