CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF3a : CodonNum = 42 & Codon = cTt

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
ORF3a	42	P42L		nonsyn	cCt	cTt	64133	64111	0.999657	25516-25518

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
ORF3a	42	P42L	cCt	cTt	64111	64133	All	0.012262
ORF3a	42	P42L	cCt	cTt	41835	41852	B.1.526	0.983312
ORF3a	42	P42L	cCt	cTt	13412	13417	B.1.637	0.980051
ORF3a	42	P42L	cCt	cTt	2121	2121	AY.103	0.013169
ORF3a	42	P42L	cCt	cTt	1214	1214	B.1	0.01112
ORF3a	42	P42L	cCt	cTt	1060	1060	AY.4	0.00165
ORF3a	42	P42L	cCt	cTt	924	924	B.1.1.7	0.000827
ORF3a	42	P42L	cCt	cTt	316	316	AY.25	0.001901
ORF3a	42	P42L	cCt	cTt	224	224	B.1.617.2	0.000843
ORF3a	42	P42L	cCt	cTt	214	214	AY.120	0.007956
ORF3a	42	P42L	cCt	cTt	194	194	AY.9.2	0.007126
ORF3a	42	P42L	cCt	cTt	150	150	B.1.1	0.002721
ORF3a	42	P42L	cCt	cTt	144	144	AY.3	0.001432
ORF3a	42	P42L	cCt	cTt	118	118	AY.26	0.003341
ORF3a	42	P42L	cCt	cTt	107	107	AY.43	0.000474
ORF3a	42	P42L	cCt	cTt	99	99	B.1.177	0.001304
ORF3a	42	P42L	cCt	cTt	95	95	AY.109	0.070266
ORF3a	42	P42L	cCt	cTt	93	93	AY.39	0.002298
ORF3a	42	P42L	cCt	cTt	90	90	AY.6	0.003702
ORF3a	42	P42L	cCt	cTt	89	89	B.1.2	0.000784
ORF3a	42	P42L	cCt	cTt	88	88	AY.29	0.001388
ORF3a	42	P42L	cCt	cTt	73	73	P.1	0.00115
ORF3a	42	P42L	cCt	cTt	71	71	B.1.561	0.028186
ORF3a	42	P42L	cCt	cTt	50	50	AY.119	0.001765
ORF3a	42	P42L	cCt	cTt	46	46	B.1.351	0.001367
ORF3a	42	P42L	cCt	cTt	40	40	A	0.01548
ORF3a	42	P42L	cCt	cTt	40	40	AY.44	0.000243
ORF3a	42	P42L	cCt	cTt	39	39	B.1.623	0.020923
ORF3a	42	P42L	cCt	cTt	38	38	AY.99.2	0.003502
ORF3a	42	P42L	cCt	cTt	36	36	AY.20	0.001399
ORF3a	42	P42L	cCt	cTt	36	36	P.1.7	0.011494
ORF3a	42	P42L	cCt	cTt	33	33	AY.117	0.002789
ORF3a	42	P42L	cCt	cTt	33	33	B.1.346	0.04325
ORF3a	42	P42L	cCt	cTt	27	27	AY.101	0.013242
ORF3a	42	P42L	cCt	cTt	27	27	B.1.160	0.000842
ORF3a	42	P42L	cCt	cTt	26	26	AY.45	0.003164
ORF3a	42	P42L	cCt	cTt	26	26	B.1.177.32	0.035088
ORF3a	42	P42L	cCt	cTt	25	25	AY.4.2	0.000542
ORF3a	42	P42L	cCt	cTt	25	25	B	0.003195
ORF3a	42	P42L	cCt	cTt	25	25	B.1.402	0.245098
ORF3a	42	P42L	cCt	cTt	24	24	B.1.177.73	0.01359
ORF3a	42	P42L	cCt	cTt	22	22	B.1.177.7	0.003627
ORF3a	42	P42L	cCt	cTt	22	22	B.1.429	0.000518
ORF3a	42	P42L	cCt	cTt	21	21	AY.34	0.002036
ORF3a	42	P42L	cCt	cTt	21	21	B.1.1.312	0.040153
ORF3a	42	P42L	cCt	cTt	21	21	B.1.264.1	1
ORF3a	42	P42L	cCt	cTt	19	19	B.1.1.507	0.165217
ORF3a	42	P42L	cCt	cTt	18	18	AY.35	0.004195
ORF3a	42	P42L	cCt	cTt	16	16	AY.116.1	0.004983
ORF3a	42	P42L	cCt	cTt	15	15	B.1.596	0.001307
ORF3a	42	P42L	cCt	cTt	15	15	P.1.17	0.002426
ORF3a	42	P42L	cCt	cTt	14	14	B.1.1.10	0.015608
ORF3a	42	P42L	cCt	cTt	14	14	B.1.240	0.003018
ORF3a	42	P42L	cCt	cTt	14	14	Q.1	0.001769
ORF3a	42	P42L	cCt	cTt	13	13	AY.100	0.000598
ORF3a	42	P42L	cCt	cTt	13	13	AY.47	0.000404
ORF3a	42	P42L	cCt	cTt	12	12	AY.102	0.000318
ORF3a	42	P42L	cCt	cTt	12	12	B.1.1.519	0.000477
ORF3a	42	P42L	cCt	cTt	12	12	B.1.466.2	0.004695
ORF3a	42	P42L	cCt	cTt	11	11	B.1.399	0.021277
ORF3a	42	P42L	cCt	cTt	10	10	AY.14	0.00088
ORF3a	42	P42L	cCt	cTt	10	10	AY.39.1	0.000396
ORF3a	42	P42L	cCt	cTt	10	10	AY.5.4	0.002767
ORF3a	42	P42L	cCt	cTt	10	10	C.37	0.001161
ORF3a	42	P42L	cCt	cTt	10	10	P.1.10	0.002695
ORF3a	42	P42L	cCt	cTt	9	9	AY.46.5	0.001786
ORF3a	42	P42L	cCt	cTt	9	9	AY.5	0.000186
ORF3a	42	P42L	cCt	cTt	8	8	B.1.110.3	0.005747
ORF3a	42	P42L	cCt	cTt	8	8	B.1.214.2	0.004796
ORF3a	42	P42L	cCt	cTt	8	8	B.1.621	0.000708
ORF3a	42	P42L	cCt	cTt	8	8	P.1.14	0.000382
ORF3a	42	P42L	cCt	cTt	7	7	AY.46	0.000729
ORF3a	42	P42L	cCt	cTt	7	7	B.1.1.39	0.003568
ORF3a	42	P42L	cCt	cTt	7	7	B.1.554	0.030837
ORF3a	42	P42L	cCt	cTt	7	7	B.1.617.1	0.000903
ORF3a	42	P42L	cCt	cTt	6	6	AY.62	0.002614
ORF3a	42	P42L	cCt	cTt	6	6	B.1.243	0.000418
ORF3a	42	P42L	cCt	cTt	6	6	B.1.625	0.014118
ORF3a	42	P42L	cCt	cTt	6	6	B.1.636	0.040268
ORF3a	42	P42L	cCt	cTt	5	5	AY.110	0.000563
ORF3a	42	P42L	cCt	cTt	5	5	AY.33	0.000334
ORF3a	42	P42L	cCt	cTt	5	5	B.1.1.220	0.009294
ORF3a	42	P42L	cCt	cTt	5	5	B.1.221	0.000355
ORF3a	42	P42L	cCt	cTt	5	5	B.1.427	0.000252
ORF3a	42	P42L	cCt	cTt	5	5	B.1.544	0.03012
ORF3a	42	P42L	cCt	cTt	5	5	P.2	0.000933
ORF3a	42	P42L	cCt	cTt	5	5	Q.8	0.000825
ORF3a	42	P42L	cCt	cTt	4	4	AD.2	0.000876
ORF3a	42	P42L	cCt	cTt	4	4	AY.118	0.000251
ORF3a	42	P42L	cCt	cTt	4	4	AY.121	0.000541
ORF3a	42	P42L	cCt	cTt	4	4	AY.23	0.000279
ORF3a	42	P42L	cCt	cTt	4	4	AY.55	0.00367
ORF3a	42	P42L	cCt	cTt	4	4	AY.75	0.000224
ORF3a	42	P42L	cCt	cTt	4	4	AY.85	0.001709
ORF3a	42	P42L	cCt	cTt	4	4	AY.98.1	0.000194
ORF3a	42	P42L	cCt	cTt	4	4	B.1.1.416	0.00362
ORF3a	42	P42L	cCt	cTt	4	4	B.1.177.42	0.003578
ORF3a	42	P42L	cCt	cTt	4	4	B.1.258.17	0.000416
ORF3a	42	P42L	cCt	cTt	4	4	B.1.36.7	0.016
ORF3a	42	P42L	cCt	cTt	4	4	B.1.618	0.016129
ORF3a	42	P42L	cCt	cTt	4	4	D.2	0.0003
ORF3a	42	P42L	cCt	cTt	4	4	N.6	0.028369
ORF3a	42	P42L	cCt	cTt	4	4	P.1.1	0.001271
ORF3a	42	P42L	cCt	cTt	3	3	AY.27	0.000194
ORF3a	42	P42L	cCt	cTt	3	3	AY.32	0.001597
ORF3a	42	P42L	cCt	cTt	3	3	AY.42	0.000121
ORF3a	42	P42L	cCt	cTt	3	3	AY.60	0.002814
ORF3a	42	P42L	cCt	cTt	3	3	AY.61	0.000314
ORF3a	42	P42L	cCt	cTt	3	3	B.1.1.316	0.002775
ORF3a	42	P42L	cCt	cTt	3	3	B.1.1.317	0.001235
ORF3a	42	P42L	cCt	cTt	3	3	B.1.1.63	0.001157
ORF3a	42	P42L	cCt	cTt	3	3	B.1.324	0.004815
ORF3a	42	P42L	cCt	cTt	3	3	B.1.533	0.028846
ORF3a	42	P42L	cCt	cTt	3	3	B.1.549	0.021583
ORF3a	42	P42L	cCt	cTt	3	3	B.1.575	0.00091
ORF3a	42	P42L	cCt	cTt	3	3	B.1.628	0.001057
ORF3a	42	P42L	cCt	cTt	3	3	B.40	0.001093
ORF3a	42	P42L	cCt	cTt	2	2	A.23.1	0.001408
ORF3a	42	P42L	cCt	cTt	2	2	AY.113	0.000285
ORF3a	42	P42L	cCt	cTt	2	2	AY.13	0.000322
ORF3a	42	P42L	cCt	cTt	2	2	AY.16.1	0.00094
ORF3a	42	P42L	cCt	cTt	2	2	AY.28	0.003781
ORF3a	42	P42L	cCt	cTt	2	2	AY.30	0.000791
ORF3a	42	P42L	cCt	cTt	2	2	AY.48	0.00093
ORF3a	42	P42L	cCt	cTt	2	2	AY.53	0.000575
ORF3a	42	P42L	cCt	cTt	2	2	AY.69	0.000373
ORF3a	42	P42L	cCt	cTt	2	2	AY.74	0.000231
ORF3a	42	P42L	cCt	cTt	2	2	AY.75.1	0.000361
ORF3a	42	P42L	cCt	cTt	2	2	AY.88	0.001768
ORF3a	42	P42L	cCt	cTt	2	2	AY.90	0.001369
ORF3a	42	P42L	cCt	cTt	2	2	AY.91	0.001461
ORF3a	42	P42L	cCt	cTt	2	2	AY.96	0.004149
ORF3a	42	P42L	cCt	cTt	2	2	AY.98	0.000158
ORF3a	42	P42L	cCt	cTt	2	2	B.1.1.222	0.000408
ORF3a	42	P42L	cCt	cTt	2	2	B.1.1.25	0.001137
ORF3a	42	P42L	cCt	cTt	2	2	B.1.1.273	0.013514
ORF3a	42	P42L	cCt	cTt	2	2	B.1.1.277	0.001517
ORF3a	42	P42L	cCt	cTt	2	2	B.1.1.307	0.005063
ORF3a	42	P42L	cCt	cTt	2	2	B.1.1.318	0.000604
ORF3a	42	P42L	cCt	cTt	2	2	B.1.1.369	0.000892
ORF3a	42	P42L	cCt	cTt	2	2	B.1.1.528	0.009615
ORF3a	42	P42L	cCt	cTt	2	2	B.1.214	0.007326
ORF3a	42	P42L	cCt	cTt	2	2	B.1.234	0.000264
ORF3a	42	P42L	cCt	cTt	2	2	B.1.235	0.005038
ORF3a	42	P42L	cCt	cTt	2	2	B.1.243.1	0.044444
ORF3a	42	P42L	cCt	cTt	2	2	B.1.280	0.014286
ORF3a	42	P42L	cCt	cTt	2	2	B.1.311	0.000549
ORF3a	42	P42L	cCt	cTt	2	2	B.1.336	0.004878
ORF3a	42	P42L	cCt	cTt	2	2	B.1.356	0.003454
ORF3a	42	P42L	cCt	cTt	2	2	B.1.36.18	0.00084
ORF3a	42	P42L	cCt	cTt	2	2	B.1.367	0.001585
ORF3a	42	P42L	cCt	cTt	2	2	B.1.369	0.00057
ORF3a	42	P42L	cCt	cTt	2	2	B.1.375	0.001639
ORF3a	42	P42L	cCt	cTt	2	2	B.1.413	0.008511
ORF3a	42	P42L	cCt	cTt	2	2	B.1.438.1	0.000215
ORF3a	42	P42L	cCt	cTt	2	2	B.1.576	0.001813
ORF3a	42	P42L	cCt	cTt	2	2	B.1.577	0.001375
ORF3a	42	P42L	cCt	cTt	2	2	B.1.635	0.035088
ORF3a	42	P42L	cCt	cTt	2	2	B.3.1	0.003317
ORF3a	42	P42L	cCt	cTt	2	2	P.1.15	0.000465
ORF3a	42	P42L	cCt	cTt	1	1	AP.1	0.001502
ORF3a	42	P42L	cCt	cTt	1	1	AT.1	0.005128
ORF3a	42	P42L	cCt	cTt	1	1	AY.1	0.000396
ORF3a	42	P42L	cCt	cTt	1	1	AY.10	0.00053
ORF3a	42	P42L	cCt	cTt	1	1	AY.104	0.001984
ORF3a	42	P42L	cCt	cTt	1	1	AY.105	0.000643
ORF3a	42	P42L	cCt	cTt	1	1	AY.108	0.001103
ORF3a	42	P42L	cCt	cTt	1	1	AY.114	0.000231
ORF3a	42	P42L	cCt	cTt	1	1	AY.120.2	0.001285
ORF3a	42	P42L	cCt	cTt	1	1	AY.16	0.00038
ORF3a	42	P42L	cCt	cTt	1	1	AY.29.1	0.000221
ORF3a	42	P42L	cCt	cTt	1	1	AY.3.1	0.000085
ORF3a	42	P42L	cCt	cTt	1	1	AY.37	0.000316
ORF3a	42	P42L	cCt	cTt	1	1	AY.4.5	0.000107
ORF3a	42	P42L	cCt	cTt	1	1	AY.46.2	0.000635
ORF3a	42	P42L	cCt	cTt	1	1	AY.46.4	0.000165
ORF3a	42	P42L	cCt	cTt	1	1	AY.46.6	0.000072
ORF3a	42	P42L	cCt	cTt	1	1	AY.50	0.000799
ORF3a	42	P42L	cCt	cTt	1	1	AY.54	0.000095
ORF3a	42	P42L	cCt	cTt	1	1	AY.56	0.001605
ORF3a	42	P42L	cCt	cTt	1	1	AY.67	0.000464
ORF3a	42	P42L	cCt	cTt	1	1	AY.73	0.000665
ORF3a	42	P42L	cCt	cTt	1	1	AY.76	0.004831
ORF3a	42	P42L	cCt	cTt	1	1	AY.78	0.001541
ORF3a	42	P42L	cCt	cTt	1	1	AY.82	0.001357
ORF3a	42	P42L	cCt	cTt	1	1	AY.89	0.004902
ORF3a	42	P42L	cCt	cTt	1	1	AY.9	0.000068
ORF3a	42	P42L	cCt	cTt	1	1	AY.9.1	0.000084
ORF3a	42	P42L	cCt	cTt	1	1	AY.92	0.000287
ORF3a	42	P42L	cCt	cTt	1	1	AY.95	0.000761
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.141	0.002012
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.176	0.000439
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.243	0.004082
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.266	0.012195
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.27	0.00565
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.279	0.001121
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.294	0.001266
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.301	0.001179
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.305	0.003861
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.306	0.000438
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.308	0.011765
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.33	0.000421
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.34	0.013158
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.354	0.004386
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.372	0.000689
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.434	0.000349
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.44	0.00241
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.50	0.000679
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.523	0.001563
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.524	0.020833
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.70	0.000341
ORF3a	42	P42L	cCt	cTt	1	1	B.1.1.89	0.006061
ORF3a	42	P42L	cCt	cTt	1	1	B.1.110	0.004525
ORF3a	42	P42L	cCt	cTt	1	1	B.1.128	0.000635
ORF3a	42	P42L	cCt	cTt	1	1	B.1.157	0.002985
ORF3a	42	P42L	cCt	cTt	1	1	B.1.160.23	0.004831
ORF3a	42	P42L	cCt	cTt	1	1	B.1.177.35	0.000691
ORF3a	42	P42L	cCt	cTt	1	1	B.1.177.57	0.000281
ORF3a	42	P42L	cCt	cTt	1	1	B.1.190	0.01
ORF3a	42	P42L	cCt	cTt	1	1	B.1.195	0.005025
ORF3a	42	P42L	cCt	cTt	1	1	B.1.237	0.004975
ORF3a	42	P42L	cCt	cTt	1	1	B.1.258	0.000067
ORF3a	42	P42L	cCt	cTt	1	1	B.1.293	0.0125
ORF3a	42	P42L	cCt	cTt	1	1	B.1.320	0.001245
ORF3a	42	P42L	cCt	cTt	1	1	B.1.338	0.008621
ORF3a	42	P42L	cCt	cTt	1	1	B.1.350	0.002933
ORF3a	42	P42L	cCt	cTt	1	1	B.1.351.2	0.000303
ORF3a	42	P42L	cCt	cTt	1	1	B.1.36	0.000146
ORF3a	42	P42L	cCt	cTt	1	1	B.1.36.38	0.001642
ORF3a	42	P42L	cCt	cTt	1	1	B.1.428	0.00102
ORF3a	42	P42L	cCt	cTt	1	1	B.1.436	0.001029
ORF3a	42	P42L	cCt	cTt	1	1	B.1.470	0.001404
ORF3a	42	P42L	cCt	cTt	1	1	B.1.497	0.000315
ORF3a	42	P42L	cCt	cTt	1	1	B.1.499	0.00105
ORF3a	42	P42L	cCt	cTt	1	1	B.1.524	0.001406
ORF3a	42	P42L	cCt	cTt	1	1	B.1.525	0.000113
ORF3a	42	P42L	cCt	cTt	1	1	B.1.550	0.013699
ORF3a	42	P42L	cCt	cTt	1	1	B.1.551	0.00129
ORF3a	42	P42L	cCt	cTt	1	1	B.1.558	0.004566
ORF3a	42	P42L	cCt	cTt	1	1	B.1.565	0.00081
ORF3a	42	P42L	cCt	cTt	1	1	B.1.567	0.003333
ORF3a	42	P42L	cCt	cTt	1	1	B.1.568	0.001111
ORF3a	42	P42L	cCt	cTt	1	1	B.1.574	0.002151
ORF3a	42	P42L	cCt	cTt	1	1	B.1.580	0.004065
ORF3a	42	P42L	cCt	cTt	1	1	B.1.595	0.000261
ORF3a	42	P42L	cCt	cTt	1	1	B.1.638	0.052632
ORF3a	42	P42L	cCt	cTt	1	1	B.1.9	0.006173
ORF3a	42	P42L	cCt	cTt	1	1	B.4	0.002208
ORF3a	42	P42L	cCt	cTt	1	1	B.53	0.011765
ORF3a	42	P42L	cCt	cTt	1	1	B.55	0.00295
ORF3a	42	P42L	cCt	cTt	1	1	C.36.3	0.000567
ORF3a	42	P42L	cCt	cTt	1	1	P.1.12	0.000484
ORF3a	42	P42L	cCt	cTt	1	1	P.1.13	0.000898
ORF3a	42	P42L	cCt	cTt	1	1	P.1.4	0.000977
ORF3a	42	P42L	cCt	cTt	1	1	R.1	0.00009

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.