CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 55 & 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	55	F55F		syn	ttC	ttT	7891	7891	1	21725-21727

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	55	F55F	ttC	ttT	7891	7891	All	0.001509
S	55	F55F	ttC	ttT	2187	2187	B.1.1.7	0.001958
S	55	F55F	ttC	ttT	1062	1062	AY.4	0.001653
S	55	F55F	ttC	ttT	634	634	B.1.2	0.005583
S	55	F55F	ttC	ttT	451	451	C.37	0.052344
S	55	F55F	ttC	ttT	327	327	B.1.617.2	0.001231
S	55	F55F	ttC	ttT	250	250	AY.43	0.001108
S	55	F55F	ttC	ttT	184	184	B.1.177	0.002423
S	55	F55F	ttC	ttT	147	147	B.1.1	0.002667
S	55	F55F	ttC	ttT	142	142	B.1.1.219	0.71
S	55	F55F	ttC	ttT	115	115	C.38	0.927419
S	55	F55F	ttC	ttT	113	113	AY.39	0.002792
S	55	F55F	ttC	ttT	102	102	B.1.526	0.002397
S	55	F55F	ttC	ttT	91	91	B.1	0.000834
S	55	F55F	ttC	ttT	80	80	AY.3	0.000796
S	55	F55F	ttC	ttT	78	78	AY.5	0.001611
S	55	F55F	ttC	ttT	76	76	B.1.398	0.22619
S	55	F55F	ttC	ttT	75	75	B.1.429	0.001765
S	55	F55F	ttC	ttT	70	70	B.1.1.157	0.063927
S	55	F55F	ttC	ttT	68	68	AY.10	0.036036
S	55	F55F	ttC	ttT	67	67	AY.44	0.000408
S	55	F55F	ttC	ttT	67	67	P.1	0.001056
S	55	F55F	ttC	ttT	63	63	AY.25	0.000379
S	55	F55F	ttC	ttT	59	59	B.1.258.17	0.006134
S	55	F55F	ttC	ttT	59	59	B.1.258.9	0.295
S	55	F55F	ttC	ttT	58	58	AY.117	0.004902
S	55	F55F	ttC	ttT	57	57	B.1.351	0.001694
S	55	F55F	ttC	ttT	56	56	AY.103	0.000348
S	55	F55F	ttC	ttT	38	38	AY.42	0.001529
S	55	F55F	ttC	ttT	35	35	B.1.221	0.002486
S	55	F55F	ttC	ttT	33	33	P.1.14	0.001577
S	55	F55F	ttC	ttT	32	32	B.1.427	0.001616
S	55	F55F	ttC	ttT	32	32	P.2	0.005972
S	55	F55F	ttC	ttT	30	30	B.1.1.519	0.001191
S	55	F55F	ttC	ttT	26	26	B.1.1.214	0.001442
S	55	F55F	ttC	ttT	25	25	B.1.177.60	0.005461
S	55	F55F	ttC	ttT	23	23	AY.47	0.000715
S	55	F55F	ttC	ttT	20	20	AY.119	0.000706
S	55	F55F	ttC	ttT	19	19	C.36.3	0.010777
S	55	F55F	ttC	ttT	18	18	AY.20	0.0007
S	55	F55F	ttC	ttT	18	18	AY.26	0.00051
S	55	F55F	ttC	ttT	18	18	B.1.243	0.001253
S	55	F55F	ttC	ttT	18	18	B.1.595	0.004697
S	55	F55F	ttC	ttT	16	16	AY.100	0.000736
S	55	F55F	ttC	ttT	16	16	B.1.1.330	1
S	55	F55F	ttC	ttT	14	14	AY.102	0.000371
S	55	F55F	ttC	ttT	14	14	AY.70	0.002919
S	55	F55F	ttC	ttT	14	14	B.1.1.51	0.024055
S	55	F55F	ttC	ttT	14	14	B.1.160	0.000437
S	55	F55F	ttC	ttT	14	14	P.1.12	0.006776
S	55	F55F	ttC	ttT	13	13	AY.29	0.000205
S	55	F55F	ttC	ttT	13	13	AY.5.3	0.004386
S	55	F55F	ttC	ttT	13	13	AY.95	0.009893
S	55	F55F	ttC	ttT	12	12	AY.88	0.01061
S	55	F55F	ttC	ttT	12	12	B.1.1.418	0.272727
S	55	F55F	ttC	ttT	12	12	B.1.499	0.012605
S	55	F55F	ttC	ttT	11	11	P.1.15	0.002556
S	55	F55F	ttC	ttT	10	10	AY.120	0.000372
S	55	F55F	ttC	ttT	10	10	AY.71	0.004751
S	55	F55F	ttC	ttT	10	10	B.1.1.284	0.001074
S	55	F55F	ttC	ttT	10	10	B.1.258	0.000665
S	55	F55F	ttC	ttT	10	10	B.1.596	0.000871
S	55	F55F	ttC	ttT	10	10	R.1	0.0009
S	55	F55F	ttC	ttT	9	9	AY.113	0.001282
S	55	F55F	ttC	ttT	9	9	AY.19	0.010262
S	55	F55F	ttC	ttT	9	9	B.1.637	0.000658
S	55	F55F	ttC	ttT	8	8	AP.1	0.012012
S	55	F55F	ttC	ttT	8	8	AY.118	0.000501
S	55	F55F	ttC	ttT	8	8	AY.23	0.000558
S	55	F55F	ttC	ttT	8	8	AY.46.6	0.000578
S	55	F55F	ttC	ttT	8	8	B.1.1.70	0.002729
S	55	F55F	ttC	ttT	8	8	B.1.177.81	0.001515
S	55	F55F	ttC	ttT	7	7	B.1.1.222	0.001428
S	55	F55F	ttC	ttT	7	7	B.1.1.486	0.011041
S	55	F55F	ttC	ttT	7	7	B.1.36	0.001021
S	55	F55F	ttC	ttT	6	6	AY.106	0.002009
S	55	F55F	ttC	ttT	6	6	AY.110	0.000676
S	55	F55F	ttC	ttT	6	6	AY.33	0.000401
S	55	F55F	ttC	ttT	6	6	AY.39.1	0.000238
S	55	F55F	ttC	ttT	6	6	AY.4.2	0.00013
S	55	F55F	ttC	ttT	6	6	AY.6	0.000247
S	55	F55F	ttC	ttT	6	6	AY.9.1	0.000502
S	55	F55F	ttC	ttT	6	6	B.1.1.280	0.018519
S	55	F55F	ttC	ttT	6	6	B.1.466.2	0.002347
S	55	F55F	ttC	ttT	6	6	C.37.1	0.015707
S	55	F55F	ttC	ttT	5	5	A.23.1	0.003521
S	55	F55F	ttC	ttT	5	5	AU.1	0.006329
S	55	F55F	ttC	ttT	5	5	AY.121	0.000677
S	55	F55F	ttC	ttT	5	5	AY.27	0.000324
S	55	F55F	ttC	ttT	5	5	AY.7	0.00098
S	55	F55F	ttC	ttT	5	5	B.1.1.1	0.001633
S	55	F55F	ttC	ttT	5	5	B.1.177.59	0.080645
S	55	F55F	ttC	ttT	5	5	B.1.311	0.001373
S	55	F55F	ttC	ttT	5	5	B.1.621	0.000443
S	55	F55F	ttC	ttT	5	5	B.1.621.1	0.002529
S	55	F55F	ttC	ttT	5	5	P.1.2	0.00578
S	55	F55F	ttC	ttT	4	4	AD.2	0.000876
S	55	F55F	ttC	ttT	4	4	AY.114	0.000924
S	55	F55F	ttC	ttT	4	4	AY.45	0.000487
S	55	F55F	ttC	ttT	4	4	AY.63	0.001547
S	55	F55F	ttC	ttT	4	4	AY.75	0.000224
S	55	F55F	ttC	ttT	4	4	AY.98.1	0.000194
S	55	F55F	ttC	ttT	4	4	B.1.1.216	0.003562
S	55	F55F	ttC	ttT	4	4	B.1.1.226	0.023256
S	55	F55F	ttC	ttT	4	4	B.1.1.277	0.003035
S	55	F55F	ttC	ttT	4	4	B.1.1.291	0.00297
S	55	F55F	ttC	ttT	4	4	B.1.240	0.000862
S	55	F55F	ttC	ttT	4	4	B.1.628	0.001409
S	55	F55F	ttC	ttT	3	3	A.28	0.007937
S	55	F55F	ttC	ttT	3	3	AY.29.1	0.000662
S	55	F55F	ttC	ttT	3	3	AY.36	0.000445
S	55	F55F	ttC	ttT	3	3	AY.46.1	0.00308
S	55	F55F	ttC	ttT	3	3	AY.9	0.000203
S	55	F55F	ttC	ttT	3	3	AY.98	0.000237
S	55	F55F	ttC	ttT	3	3	B	0.000383
S	55	F55F	ttC	ttT	3	3	B.1.1.25	0.001706
S	55	F55F	ttC	ttT	3	3	B.1.1.317	0.001235
S	55	F55F	ttC	ttT	3	3	B.1.1.396	0.136364
S	55	F55F	ttC	ttT	3	3	B.1.1.63	0.001157
S	55	F55F	ttC	ttT	3	3	B.1.189	0.012876
S	55	F55F	ttC	ttT	3	3	B.1.234	0.000396
S	55	F55F	ttC	ttT	3	3	B.1.3	0.007853
S	55	F55F	ttC	ttT	3	3	B.1.36.29	0.001552
S	55	F55F	ttC	ttT	3	3	B.1.369	0.000856
S	55	F55F	ttC	ttT	3	3	B.1.438.1	0.000322
S	55	F55F	ttC	ttT	3	3	B.1.517	0.001281
S	55	F55F	ttC	ttT	3	3	B.1.525	0.000339
S	55	F55F	ttC	ttT	3	3	B.1.587	0.005693
S	55	F55F	ttC	ttT	3	3	C.36.3.1	0.008152
S	55	F55F	ttC	ttT	3	3	P.1.1	0.000953
S	55	F55F	ttC	ttT	2	2		0.111111
S	55	F55F	ttC	ttT	2	2	A.1	0.000564
S	55	F55F	ttC	ttT	2	2	A.19	0.018868
S	55	F55F	ttC	ttT	2	2	AY.14	0.000176
S	55	F55F	ttC	ttT	2	2	AY.16.1	0.00094
S	55	F55F	ttC	ttT	2	2	AY.4.5	0.000215
S	55	F55F	ttC	ttT	2	2	AY.46	0.000208
S	55	F55F	ttC	ttT	2	2	AY.46.4	0.000329
S	55	F55F	ttC	ttT	2	2	AY.55	0.001835
S	55	F55F	ttC	ttT	2	2	AY.59	0.001059
S	55	F55F	ttC	ttT	2	2	AY.75.1	0.000361
S	55	F55F	ttC	ttT	2	2	AY.82	0.002714
S	55	F55F	ttC	ttT	2	2	AY.91	0.001461
S	55	F55F	ttC	ttT	2	2	AY.94	0.000885
S	55	F55F	ttC	ttT	2	2	B.1.1.117	0.019417
S	55	F55F	ttC	ttT	2	2	B.1.1.141	0.004024
S	55	F55F	ttC	ttT	2	2	B.1.1.159	0.009346
S	55	F55F	ttC	ttT	2	2	B.1.1.255	0.006061
S	55	F55F	ttC	ttT	2	2	B.1.1.28	0.000622
S	55	F55F	ttC	ttT	2	2	B.1.1.309	0.011696
S	55	F55F	ttC	ttT	2	2	B.1.1.315	0.016949
S	55	F55F	ttC	ttT	2	2	B.1.1.318	0.000604
S	55	F55F	ttC	ttT	2	2	B.1.1.362	0.011236
S	55	F55F	ttC	ttT	2	2	B.1.1.409	0.005666
S	55	F55F	ttC	ttT	2	2	B.1.1.50	0.001358
S	55	F55F	ttC	ttT	2	2	B.1.160.8	0.002577
S	55	F55F	ttC	ttT	2	2	B.1.177.73	0.001133
S	55	F55F	ttC	ttT	2	2	B.1.214.2	0.001199
S	55	F55F	ttC	ttT	2	2	B.1.258.11	0.000793
S	55	F55F	ttC	ttT	2	2	B.1.324	0.00321
S	55	F55F	ttC	ttT	2	2	B.1.351.3	0.001753
S	55	F55F	ttC	ttT	2	2	B.1.36.27	0.001527
S	55	F55F	ttC	ttT	2	2	B.1.36.34	0.042553
S	55	F55F	ttC	ttT	2	2	B.1.396	0.001411
S	55	F55F	ttC	ttT	2	2	B.1.606	0.012048
S	55	F55F	ttC	ttT	2	2	B.1.623	0.001073
S	55	F55F	ttC	ttT	2	2	B.4	0.004415
S	55	F55F	ttC	ttT	2	2	B.6.6	0.001778
S	55	F55F	ttC	ttT	2	2	D.2	0.00015
S	55	F55F	ttC	ttT	2	2	P.1.11	0.020408
S	55	F55F	ttC	ttT	2	2	P.1.16	0.000748
S	55	F55F	ttC	ttT	2	2	Q.1	0.000253
S	55	F55F	ttC	ttT	2	2	Q.7	0.002222
S	55	F55F	ttC	ttT	1	1	A.21	0.00277
S	55	F55F	ttC	ttT	1	1	AA.1	0.007246
S	55	F55F	ttC	ttT	1	1	AV.1	0.005051
S	55	F55F	ttC	ttT	1	1	AY.104	0.001984
S	55	F55F	ttC	ttT	1	1	AY.109	0.00074
S	55	F55F	ttC	ttT	1	1	AY.111	0.000183
S	55	F55F	ttC	ttT	1	1	AY.115	0.005208
S	55	F55F	ttC	ttT	1	1	AY.116.1	0.000311
S	55	F55F	ttC	ttT	1	1	AY.13	0.000161
S	55	F55F	ttC	ttT	1	1	AY.2	0.000356
S	55	F55F	ttC	ttT	1	1	AY.34	0.000097
S	55	F55F	ttC	ttT	1	1	AY.39.2	0.001541
S	55	F55F	ttC	ttT	1	1	AY.4.1	0.000737
S	55	F55F	ttC	ttT	1	1	AY.46.5	0.000198
S	55	F55F	ttC	ttT	1	1	AY.53	0.000288
S	55	F55F	ttC	ttT	1	1	AY.54	0.000095
S	55	F55F	ttC	ttT	1	1	AY.61	0.000105
S	55	F55F	ttC	ttT	1	1	AY.64	0.000595
S	55	F55F	ttC	ttT	1	1	AY.73	0.000665
S	55	F55F	ttC	ttT	1	1	AY.84	0.000437
S	55	F55F	ttC	ttT	1	1	AY.86	0.00083
S	55	F55F	ttC	ttT	1	1	AY.9.2	0.000037
S	55	F55F	ttC	ttT	1	1	AY.92	0.000287
S	55	F55F	ttC	ttT	1	1	AY.99	0.001049
S	55	F55F	ttC	ttT	1	1	AY.99.2	0.000092
S	55	F55F	ttC	ttT	1	1	AZ.1	0.000867
S	55	F55F	ttC	ttT	1	1	AZ.2	0.000821
S	55	F55F	ttC	ttT	1	1	B.1.1.153	0.001095
S	55	F55F	ttC	ttT	1	1	B.1.1.198	0.001468
S	55	F55F	ttC	ttT	1	1	B.1.1.203	0.016949
S	55	F55F	ttC	ttT	1	1	B.1.1.27	0.00565
S	55	F55F	ttC	ttT	1	1	B.1.1.298	0.000862
S	55	F55F	ttC	ttT	1	1	B.1.1.303	0.002762
S	55	F55F	ttC	ttT	1	1	B.1.1.305	0.003861
S	55	F55F	ttC	ttT	1	1	B.1.1.326	0.001761
S	55	F55F	ttC	ttT	1	1	B.1.1.348	0.000796
S	55	F55F	ttC	ttT	1	1	B.1.1.372	0.000689
S	55	F55F	ttC	ttT	1	1	B.1.1.397	0.002252
S	55	F55F	ttC	ttT	1	1	B.1.1.406	0.006494
S	55	F55F	ttC	ttT	1	1	B.1.1.416	0.000905
S	55	F55F	ttC	ttT	1	1	B.1.1.448	0.002033
S	55	F55F	ttC	ttT	1	1	B.1.1.525	0.005464
S	55	F55F	ttC	ttT	1	1	B.1.1.54	0.003021
S	55	F55F	ttC	ttT	1	1	B.1.104	0.00369
S	55	F55F	ttC	ttT	1	1	B.1.110.3	0.000718
S	55	F55F	ttC	ttT	1	1	B.1.111	0.001175
S	55	F55F	ttC	ttT	1	1	B.1.134	0.005464
S	55	F55F	ttC	ttT	1	1	B.1.160.14	0.002119
S	55	F55F	ttC	ttT	1	1	B.1.160.16	0.000929
S	55	F55F	ttC	ttT	1	1	B.1.177.40	0.005155
S	55	F55F	ttC	ttT	1	1	B.1.177.44	0.000519
S	55	F55F	ttC	ttT	1	1	B.1.177.56	0.000668
S	55	F55F	ttC	ttT	1	1	B.1.177.7	0.000165
S	55	F55F	ttC	ttT	1	1	B.1.177.72	0.00339
S	55	F55F	ttC	ttT	1	1	B.1.177.75	0.001041
S	55	F55F	ttC	ttT	1	1	B.1.177.83	0.001481
S	55	F55F	ttC	ttT	1	1	B.1.218	0.005155
S	55	F55F	ttC	ttT	1	1	B.1.258.14	0.00098
S	55	F55F	ttC	ttT	1	1	B.1.264	0.012346
S	55	F55F	ttC	ttT	1	1	B.1.336	0.002439
S	55	F55F	ttC	ttT	1	1	B.1.340	0.004292
S	55	F55F	ttC	ttT	1	1	B.1.349	0.000715
S	55	F55F	ttC	ttT	1	1	B.1.351.2	0.000303
S	55	F55F	ttC	ttT	1	1	B.1.36.1	0.00114
S	55	F55F	ttC	ttT	1	1	B.1.36.18	0.00042
S	55	F55F	ttC	ttT	1	1	B.1.36.31	0.001751
S	55	F55F	ttC	ttT	1	1	B.1.36.37	0.002778
S	55	F55F	ttC	ttT	1	1	B.1.375	0.00082
S	55	F55F	ttC	ttT	1	1	B.1.389	0.001002
S	55	F55F	ttC	ttT	1	1	B.1.400	0.000429
S	55	F55F	ttC	ttT	1	1	B.1.409	0.000781
S	55	F55F	ttC	ttT	1	1	B.1.416.1	0.001563
S	55	F55F	ttC	ttT	1	1	B.1.424	0.008065
S	55	F55F	ttC	ttT	1	1	B.1.428.2	0.033333
S	55	F55F	ttC	ttT	1	1	B.1.438	0.006536
S	55	F55F	ttC	ttT	1	1	B.1.438.2	0.019231
S	55	F55F	ttC	ttT	1	1	B.1.459	0.004082
S	55	F55F	ttC	ttT	1	1	B.1.470	0.001404
S	55	F55F	ttC	ttT	1	1	B.1.503	0.002488
S	55	F55F	ttC	ttT	1	1	B.1.527	0.003704
S	55	F55F	ttC	ttT	1	1	B.1.560	0.00463
S	55	F55F	ttC	ttT	1	1	B.1.561	0.000397
S	55	F55F	ttC	ttT	1	1	B.1.564	0.000426
S	55	F55F	ttC	ttT	1	1	B.1.577	0.000687
S	55	F55F	ttC	ttT	1	1	B.1.580	0.004065
S	55	F55F	ttC	ttT	1	1	B.1.589	0.007576
S	55	F55F	ttC	ttT	1	1	B.1.596.1	0.009346
S	55	F55F	ttC	ttT	1	1	B.1.612	0.002653
S	55	F55F	ttC	ttT	1	1	B.1.617.1	0.000129
S	55	F55F	ttC	ttT	1	1	B.1.618	0.004032
S	55	F55F	ttC	ttT	1	1	B.1.619.1	0.000641
S	55	F55F	ttC	ttT	1	1	B.1.625	0.002353
S	55	F55F	ttC	ttT	1	1	B.1.629	0.013333
S	55	F55F	ttC	ttT	1	1	B.1.634	0.003425
S	55	F55F	ttC	ttT	1	1	B.28	0.003279
S	55	F55F	ttC	ttT	1	1	B.3	0.000831
S	55	F55F	ttC	ttT	1	1	B.31	0.003731
S	55	F55F	ttC	ttT	1	1	B.40	0.000364
S	55	F55F	ttC	ttT	1	1	C.18	0.002591
S	55	F55F	ttC	ttT	1	1	C.35	0.000774
S	55	F55F	ttC	ttT	1	1	C.36	0.000911
S	55	F55F	ttC	ttT	1	1	K.2	0.04
S	55	F55F	ttC	ttT	1	1	L.3	0.003546
S	55	F55F	ttC	ttT	1	1	N.4	0.004255
S	55	F55F	ttC	ttT	1	1	N.5	0.001767
S	55	F55F	ttC	ttT	1	1	P.1.10	0.000269
S	55	F55F	ttC	ttT	1	1	P.1.17	0.000162
S	55	F55F	ttC	ttT	1	1	P.1.4	0.000977
S	55	F55F	ttC	ttT	1	1	P.1.7	0.000319

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.