CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 940 & Codon = tcT

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	940	S940S		syn	tcC	tcT	14292	13449	0.941016	24380-24382

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	940	S940S	tcC	tcT	13449	14292	All	0.002572
S	940	S940S	tcC	tcT	3190	3190	B.1.1.318	0.962583
S	940	S940S	tcC	tcT	1372	1530	B.1.1.7	0.001228
S	940	S940S	tcC	tcT	1201	1201	AZ.2	0.986043
S	940	S940S	tcC	tcT	1150	1150	AZ.1	0.997398
S	940	S940S	tcC	tcT	114	652	AY.3	0.001134
S	940	S940S	tcC	tcT	644	644	AZ.3	0.978723
S	940	S940S	tcC	tcT	552	573	AY.4	0.000859
S	940	S940S	tcC	tcT	452	454	B.1.177.7	0.074514
S	940	S940S	tcC	tcT	284	284	AZ.5	0.996491
S	940	S940S	tcC	tcT	280	280	P.6	0.880503
S	940	S940S	tcC	tcT	270	271	AY.103	0.001676
S	940	S940S	tcC	tcT	222	232	B.1.617.2	0.000836
S	940	S940S	tcC	tcT	215	215	B.1.1.63	0.082948
S	940	S940S	tcC	tcT	193	203	B.1.2	0.001699
S	940	S940S	tcC	tcT	176	176	B.1.637	0.012861
S	940	S940S	tcC	tcT	159	159	B.1.177	0.002094
S	940	S940S	tcC	tcT	150	153	AY.25	0.000902
S	940	S940S	tcC	tcT	128	139	B.1	0.001172
S	940	S940S	tcC	tcT	123	123	AZ.2.1	1
S	940	S940S	tcC	tcT	119	119	AZ.6	1
S	940	S940S	tcC	tcT	102	104	B.1.1	0.00185
S	940	S940S	tcC	tcT	90	91	B.1.427	0.004545
S	940	S940S	tcC	tcT	73	83	AY.43	0.000323
S	940	S940S	tcC	tcT	80	81	AY.44	0.000487
S	940	S940S	tcC	tcT	66	71	P.1	0.00104
S	940	S940S	tcC	tcT	61	63	AY.119	0.002154
S	940	S940S	tcC	tcT	61	61	B.1.240	0.013149
S	940	S940S	tcC	tcT	53	57	AY.102	0.001405
S	940	S940S	tcC	tcT	57	57	B.1.1.432	0.072152
S	940	S940S	tcC	tcT	56	56	AY.75	0.003137
S	940	S940S	tcC	tcT	55	56	B.1.160	0.001715
S	940	S940S	tcC	tcT	53	55	AY.39	0.00131
S	940	S940S	tcC	tcT	55	55	B.1.243	0.003827
S	940	S940S	tcC	tcT	53	54	B.1.429	0.001247
S	940	S940S	tcC	tcT	54	54	B.1.596	0.004705
S	940	S940S	tcC	tcT	52	52	AY.29	0.00082
S	940	S940S	tcC	tcT	52	52	AY.39.1	0.00206
S	940	S940S	tcC	tcT	52	52	AY.47	0.001617
S	940	S940S	tcC	tcT	40	42	AY.26	0.001132
S	940	S940S	tcC	tcT	42	42	AY.42	0.00169
S	940	S940S	tcC	tcT	37	37	AY.4.2	0.000802
S	940	S940S	tcC	tcT	36	36	B.1.526	0.000846
S	940	S940S	tcC	tcT	29	29	B.1.371	0.032548
S	940	S940S	tcC	tcT	27	27	B.1.1.519	0.001072
S	940	S940S	tcC	tcT	26	26	AY.20	0.00101
S	940	S940S	tcC	tcT	25	25	AY.99.2	0.002304
S	940	S940S	tcC	tcT	24	25	B.1.221	0.001705
S	940	S940S	tcC	tcT	24	24	AY.100	0.001104
S	940	S940S	tcC	tcT	23	24	AY.33	0.001536
S	940	S940S	tcC	tcT	22	24	B.1.351	0.000654
S	940	S940S	tcC	tcT	23	23	AY.9.2	0.000845
S	940	S940S	tcC	tcT	23	23	B.1.621	0.002036
S	940	S940S	tcC	tcT	21	21	B.1.311	0.005766
S	940	S940S	tcC	tcT	20	20	AY.9	0.001352
S	940	S940S	tcC	tcT	20	20	B.1.177.57	0.00562
S	940	S940S	tcC	tcT	19	19	B.1.1.37	0.003664
S	940	S940S	tcC	tcT	19	19	B.1.617.1	0.00245
S	940	S940S	tcC	tcT	18	18	B.1.128	0.011436
S	940	S940S	tcC	tcT	14	17	C.37	0.001625
S	940	S940S	tcC	tcT	16	16	AY.109	0.011834
S	940	S940S	tcC	tcT	16	16	B.1.36	0.002334
S	940	S940S	tcC	tcT	16	16	D.2	0.001201
S	940	S940S	tcC	tcT	16	16	K.1	0.380952
S	940	S940S	tcC	tcT	15	15	AY.120	0.000558
S	940	S940S	tcC	tcT	7	15	AY.5	0.000145
S	940	S940S	tcC	tcT	15	15	B.1.1.214	0.000832
S	940	S940S	tcC	tcT	15	15	B.1.1.222	0.00306
S	940	S940S	tcC	tcT	15	15	B.1.36.17	0.007411
S	940	S940S	tcC	tcT	10	14	AY.61	0.001048
S	940	S940S	tcC	tcT	12	14	B.1.234	0.001583
S	940	S940S	tcC	tcT	12	13	AY.46	0.001249
S	940	S940S	tcC	tcT	13	13	AY.5.3	0.004386
S	940	S940S	tcC	tcT	13	13	B.1.346	0.017038
S	940	S940S	tcC	tcT	13	13	B.1.612	0.034483
S	940	S940S	tcC	tcT	12	12	AY.4.3	0.010101
S	940	S940S	tcC	tcT	12	12	B.1.139	0.008798
S	940	S940S	tcC	tcT	12	12	B.1.351.2	0.003631
S	940	S940S	tcC	tcT	12	12	P.1.17	0.001941
S	940	S940S	tcC	tcT	10	11	B	0.001278
S	940	S940S	tcC	tcT	11	11	B.1.1.317	0.004529
S	940	S940S	tcC	tcT	10	10	AY.36	0.001482
S	940	S940S	tcC	tcT	9	9	AY.107	0.004194
S	940	S940S	tcC	tcT	9	9	B.1.1.187	0.079646
S	940	S940S	tcC	tcT	9	9	B.1.1.277	0.006829
S	940	S940S	tcC	tcT	9	9	B.1.385	0.095745
S	940	S940S	tcC	tcT	8	8	AY.121	0.001083
S	940	S940S	tcC	tcT	8	8	AY.23	0.000558
S	940	S940S	tcC	tcT	8	8	AY.45	0.000973
S	940	S940S	tcC	tcT	8	8	AY.6	0.000329
S	940	S940S	tcC	tcT	8	8	B.1.1.153	0.008762
S	940	S940S	tcC	tcT	3	7	AY.75.1	0.000541
S	940	S940S	tcC	tcT	7	7	AY.9.1	0.000586
S	940	S940S	tcC	tcT	6	7	B.1.1.28	0.001867
S	940	S940S	tcC	tcT	7	7	B.1.258	0.000466
S	940	S940S	tcC	tcT	7	7	P.1.14	0.000335
S	940	S940S	tcC	tcT	5	6	AY.113	0.000712
S	940	S940S	tcC	tcT	6	6	AY.35	0.001398
S	940	S940S	tcC	tcT	6	6	AY.4.5	0.000645
S	940	S940S	tcC	tcT	6	6	AY.41	0.001764
S	940	S940S	tcC	tcT	6	6	AY.71	0.00285
S	940	S940S	tcC	tcT	6	6	B.1.1.1	0.00196
S	940	S940S	tcC	tcT	6	6	B.1.1.216	0.005343
S	940	S940S	tcC	tcT	6	6	B.1.1.269	0.008119
S	940	S940S	tcC	tcT	6	6	B.1.1.33	0.002525
S	940	S940S	tcC	tcT	6	6	B.1.1.39	0.003058
S	940	S940S	tcC	tcT	6	6	B.1.126	0.007653
S	940	S940S	tcC	tcT	6	6	B.1.177.21	0.000459
S	940	S940S	tcC	tcT	6	6	B.1.575	0.00182
S	940	S940S	tcC	tcT	5	6	B.1.576	0.004533
S	940	S940S	tcC	tcT	4	5	AY.117	0.000338
S	940	S940S	tcC	tcT	4	5	AY.34	0.000388
S	940	S940S	tcC	tcT	5	5	AY.91	0.003652
S	940	S940S	tcC	tcT	5	5	B.1.1.141	0.01006
S	940	S940S	tcC	tcT	5	5	B.1.1.306	0.002192
S	940	S940S	tcC	tcT	5	5	B.1.177.44	0.002595
S	940	S940S	tcC	tcT	3	5	B.1.609	0.001438
S	940	S940S	tcC	tcT	5	5	Q.8	0.000825
S	940	S940S	tcC	tcT	2	4	AY.16.1	0.00094
S	940	S940S	tcC	tcT	4	4	AY.51	0.003636
S	940	S940S	tcC	tcT	4	4	AY.54	0.000381
S	940	S940S	tcC	tcT	4	4	AY.84	0.00175
S	940	S940S	tcC	tcT	4	4	AY.98	0.000316
S	940	S940S	tcC	tcT	4	4	B.1.367	0.00317
S	940	S940S	tcC	tcT	4	4	P.1.15	0.000929
S	940	S940S	tcC	tcT	3	4	R.1	0.00027
S	940	S940S	tcC	tcT	3	3	A.1	0.000846
S	940	S940S	tcC	tcT	2	3	AY.118	0.000125
S	940	S940S	tcC	tcT	3	3	AY.3.1	0.000256
S	940	S940S	tcC	tcT	3	3	AY.37	0.000948
S	940	S940S	tcC	tcT	3	3	AY.5.4	0.00083
S	940	S940S	tcC	tcT	3	3	AY.55	0.002752
S	940	S940S	tcC	tcT	3	3	AY.62	0.001307
S	940	S940S	tcC	tcT	3	3	AY.92	0.000862
S	940	S940S	tcC	tcT	1	3	AY.95	0.000761
S	940	S940S	tcC	tcT	3	3	AY.98.1	0.000145
S	940	S940S	tcC	tcT	3	3	B.1.1.305	0.011583
S	940	S940S	tcC	tcT	3	3	B.1.177.35	0.002073
S	940	S940S	tcC	tcT	3	3	B.1.177.81	0.000568
S	940	S940S	tcC	tcT	3	3	B.1.258.14	0.002941
S	940	S940S	tcC	tcT	3	3	B.1.258.21	0.023256
S	940	S940S	tcC	tcT	3	3	B.1.284	0.039474
S	940	S940S	tcC	tcT	3	3	B.1.349	0.002144
S	940	S940S	tcC	tcT	3	3	B.1.36.29	0.001552
S	940	S940S	tcC	tcT	3	3	B.1.466.2	0.001174
S	940	S940S	tcC	tcT	2	3	B.1.525	0.000226
S	940	S940S	tcC	tcT	3	3	B.6.6	0.002667
S	940	S940S	tcC	tcT	3	3	Q.1	0.000379
S	940	S940S	tcC	tcT	2	2		0.111111
S	940	S940S	tcC	tcT	2	2	A.2.2	0.003378
S	940	S940S	tcC	tcT	2	2	AT.1	0.010256
S	940	S940S	tcC	tcT	2	2	AY.111	0.000366
S	940	S940S	tcC	tcT	2	2	AY.120.2.1	0.000997
S	940	S940S	tcC	tcT	2	2	AY.19	0.002281
S	940	S940S	tcC	tcT	2	2	AY.23.1	0.000835
S	940	S940S	tcC	tcT	2	2	AY.27	0.000129
S	940	S940S	tcC	tcT	2	2	AY.46.3	0.001867
S	940	S940S	tcC	tcT	2	2	AY.49	0.00639
S	940	S940S	tcC	tcT	2	2	AY.59	0.001059
S	940	S940S	tcC	tcT	1	2	AY.7.1	0.000113
S	940	S940S	tcC	tcT	2	2	AY.74	0.000231
S	940	S940S	tcC	tcT	2	2	AY.88	0.001768
S	940	S940S	tcC	tcT	2	2	B.1.1.316	0.00185
S	940	S940S	tcC	tcT	2	2	B.1.1.348	0.001592
S	940	S940S	tcC	tcT	2	2	B.1.1.369	0.000892
S	940	S940S	tcC	tcT	2	2	B.1.1.397	0.004505
S	940	S940S	tcC	tcT	2	2	B.1.1.46	0.008734
S	940	S940S	tcC	tcT	2	2	B.1.1.54	0.006042
S	940	S940S	tcC	tcT	2	2	B.1.1.70	0.000682
S	940	S940S	tcC	tcT	2	2	B.1.1.89	0.012121
S	940	S940S	tcC	tcT	2	2	B.1.160.16	0.001859
S	940	S940S	tcC	tcT	2	2	B.1.177.12	0.000303
S	940	S940S	tcC	tcT	2	2	B.1.177.4	0.000422
S	940	S940S	tcC	tcT	2	2	B.1.177.82	0.000955
S	940	S940S	tcC	tcT	2	2	B.1.177.87	0.001456
S	940	S940S	tcC	tcT	2	2	B.1.206	0.001631
S	940	S940S	tcC	tcT	2	2	B.1.236	0.004107
S	940	S940S	tcC	tcT	2	2	B.1.258.17	0.000208
S	940	S940S	tcC	tcT	2	2	B.1.298	0.004228
S	940	S940S	tcC	tcT	2	2	B.1.36.36	0.001204
S	940	S940S	tcC	tcT	2	2	B.1.369	0.00057
S	940	S940S	tcC	tcT	2	2	B.1.397	0.009709
S	940	S940S	tcC	tcT	2	2	B.1.438.1	0.000215
S	940	S940S	tcC	tcT	2	2	B.1.550	0.027397
S	940	S940S	tcC	tcT	2	2	B.1.597	0.009259
S	940	S940S	tcC	tcT	2	2	B.1.619.1	0.001283
S	940	S940S	tcC	tcT	2	2	B.1.91	0.004149
S	940	S940S	tcC	tcT	2	2	B.40	0.000729
S	940	S940S	tcC	tcT	2	2	B.6.2	0.125
S	940	S940S	tcC	tcT	2	2	P.1.10	0.000539
S	940	S940S	tcC	tcT	2	2	P.1.2	0.002312
S	940	S940S	tcC	tcT	2	2	P.2	0.000373
S	940	S940S	tcC	tcT	2	2	P.3	0.00319
S	940	S940S	tcC	tcT	2	2	P.5	0.027397
S	940	S940S	tcC	tcT	1	2	Q.3	0.000145
S	940	S940S	tcC	tcT	1	1	A	0.000387
S	940	S940S	tcC	tcT	1	1	A.2	0.000662
S	940	S940S	tcC	tcT	1	1	A.2.5	0.000499
S	940	S940S	tcC	tcT	1	1	A.2.5.2	0.001572
S	940	S940S	tcC	tcT	1	1	AD.2	0.000219
S	940	S940S	tcC	tcT	1	1	AY.101	0.00049
S	940	S940S	tcC	tcT	1	1	AY.105	0.000643
S	940	S940S	tcC	tcT	1	1	AY.106	0.000335
S	940	S940S	tcC	tcT	1	1	AY.110	0.000113
S	940	S940S	tcC	tcT	1	1	AY.115	0.005208
S	940	S940S	tcC	tcT	1	1	AY.116	0.000287
S	940	S940S	tcC	tcT	1	1	AY.120.2	0.001285
S	940	S940S	tcC	tcT	1	1	AY.13	0.000161
S	940	S940S	tcC	tcT	1	1	AY.14	0.000088
S	940	S940S	tcC	tcT	1	1	AY.16	0.00038
S	940	S940S	tcC	tcT	1	1	AY.28	0.00189
S	940	S940S	tcC	tcT	1	1	AY.32	0.000532
S	940	S940S	tcC	tcT	1	1	AY.39.2	0.001541
S	940	S940S	tcC	tcT	1	1	AY.4.4	0.000409
S	940	S940S	tcC	tcT	1	1	AY.46.5	0.000198
S	940	S940S	tcC	tcT	1	1	AY.48	0.000465
S	940	S940S	tcC	tcT	1	1	AY.53	0.000288
S	940	S940S	tcC	tcT	1	1	AY.58	0.000907
S	940	S940S	tcC	tcT	1	1	AY.67	0.000464
S	940	S940S	tcC	tcT	1	1	AY.69	0.000187
S	940	S940S	tcC	tcT	1	1	AY.70	0.000209
S	940	S940S	tcC	tcT	1	1	AY.8	0.000606
S	940	S940S	tcC	tcT	1	1	AY.86	0.00083
S	940	S940S	tcC	tcT	1	1	B.1.1.118	0.010204
S	940	S940S	tcC	tcT	1	1	B.1.1.137	0.0125
S	940	S940S	tcC	tcT	1	1	B.1.1.170	0.001247
S	940	S940S	tcC	tcT	1	1	B.1.1.207	0.001182
S	940	S940S	tcC	tcT	1	1	B.1.1.25	0.000569
S	940	S940S	tcC	tcT	1	1	B.1.1.284	0.000107
S	940	S940S	tcC	tcT	1	1	B.1.1.312	0.001912
S	940	S940S	tcC	tcT	1	1	B.1.1.354	0.004386
S	940	S940S	tcC	tcT	1	1	B.1.1.374	0.002375
S	940	S940S	tcC	tcT	1	1	B.1.1.377	0.001381
S	940	S940S	tcC	tcT	1	1	B.1.1.416	0.000905
S	940	S940S	tcC	tcT	1	1	B.1.1.48	0.002874
S	940	S940S	tcC	tcT	1	1	B.1.1.485	0.016667
S	940	S940S	tcC	tcT	1	1	B.1.1.487	0.005587
S	940	S940S	tcC	tcT	1	1	B.1.1.50	0.000679
S	940	S940S	tcC	tcT	1	1	B.1.1.515	0.02
S	940	S940S	tcC	tcT	1	1	B.1.1.524	0.020833
S	940	S940S	tcC	tcT	1	1	B.1.1.525	0.005464
S	940	S940S	tcC	tcT	1	1	B.1.1.59	0.006494
S	940	S940S	tcC	tcT	1	1	B.1.1.86	0.035714
S	940	S940S	tcC	tcT	1	1	B.1.111	0.001175
S	940	S940S	tcC	tcT	1	1	B.1.13	0.002375
S	940	S940S	tcC	tcT	1	1	B.1.160.10	0.008065
S	940	S940S	tcC	tcT	1	1	B.1.177.23	0.003236
S	940	S940S	tcC	tcT	1	1	B.1.177.52	0.001757
S	940	S940S	tcC	tcT	1	1	B.1.177.54	0.000606
S	940	S940S	tcC	tcT	1	1	B.1.177.56	0.000668
S	940	S940S	tcC	tcT	1	1	B.1.177.6	0.000977
S	940	S940S	tcC	tcT	1	1	B.1.177.60	0.000218
S	940	S940S	tcC	tcT	1	1	B.1.177.63	0.002703
S	940	S940S	tcC	tcT	1	1	B.1.177.65	0.000665
S	940	S940S	tcC	tcT	1	1	B.1.177.72	0.00339
S	940	S940S	tcC	tcT	1	1	B.1.177.86	0.000183
S	940	S940S	tcC	tcT	1	1	B.1.214.2	0.0006
S	940	S940S	tcC	tcT	1	1	B.1.258.2	0.004505
S	940	S940S	tcC	tcT	1	1	B.1.305	0.002151
S	940	S940S	tcC	tcT	1	1	B.1.320	0.001245
S	940	S940S	tcC	tcT	1	1	B.1.333	0.010526
S	940	S940S	tcC	tcT	1	1	B.1.351.5	0.0006
S	940	S940S	tcC	tcT	1	1	B.1.356	0.001727
S	940	S940S	tcC	tcT	1	1	B.1.36.1	0.00114
S	940	S940S	tcC	tcT	1	1	B.1.36.18	0.00042
S	940	S940S	tcC	tcT	1	1	B.1.36.7	0.004
S	940	S940S	tcC	tcT	1	1	B.1.36.8	0.001
S	940	S940S	tcC	tcT	1	1	B.1.389	0.001002
S	940	S940S	tcC	tcT	1	1	B.1.396	0.000706
S	940	S940S	tcC	tcT	1	1	B.1.416.1	0.001563
S	940	S940S	tcC	tcT	1	1	B.1.426	0.001009
S	940	S940S	tcC	tcT	1	1	B.1.428	0.00102
S	940	S940S	tcC	tcT	1	1	B.1.433	0.003195
S	940	S940S	tcC	tcT	1	1	B.1.443	0.004673
S	940	S940S	tcC	tcT	1	1	B.1.446	0.02
S	940	S940S	tcC	tcT	1	1	B.1.468	0.005714
S	940	S940S	tcC	tcT	1	1	B.1.469	0.00361
S	940	S940S	tcC	tcT	1	1	B.1.473	0.019231
S	940	S940S	tcC	tcT	1	1	B.1.497	0.000315
S	940	S940S	tcC	tcT	1	1	B.1.499	0.00105
S	940	S940S	tcC	tcT	1	1	B.1.499.1	0.111111
S	940	S940S	tcC	tcT	1	1	B.1.538	0.008065
S	940	S940S	tcC	tcT	1	1	B.1.554	0.004405
S	940	S940S	tcC	tcT	1	1	B.1.560	0.00463
S	940	S940S	tcC	tcT	1	1	B.1.565	0.00081
S	940	S940S	tcC	tcT	1	1	B.1.567	0.003333
S	940	S940S	tcC	tcT	1	1	B.1.575.1	0.002439
S	940	S940S	tcC	tcT	1	1	B.1.577	0.000687
S	940	S940S	tcC	tcT	1	1	B.1.582	0.000491
S	940	S940S	tcC	tcT	1	1	B.1.603	0.010638
S	940	S940S	tcC	tcT	1	1	B.1.9.5	0.005682
S	940	S940S	tcC	tcT	1	1	B.3	0.000831
S	940	S940S	tcC	tcT	1	1	B.3.1	0.001658
S	940	S940S	tcC	tcT	1	1	C.1.2	0.004255
S	940	S940S	tcC	tcT	1	1	C.11	0.010638
S	940	S940S	tcC	tcT	1	1	C.36	0.000911
S	940	S940S	tcC	tcT	1	1	C.37.1	0.002618
S	940	S940S	tcC	tcT	1	1	L.3	0.003546
S	940	S940S	tcC	tcT	1	1	P.1.12	0.000484
S	940	S940S	tcC	tcT	1	1	P.1.4	0.000977
S	940	S940S	tcC	tcT	1	1	P.1.9	0.004808
S	940	S940S	tcC	tcT	1	1	Q.4	0.000455
S	940	S940S	tcC	tcT	1	1	Z.1	0.00289

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.