CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : Mut = D53D

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	53	D53D		syn	gaC	gaT	10569	10569	1	21719-21721

Details of the mutation D53D 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	53	D53D	gaC	gaT	10569	10569	All	0.002021
S	53	D53D	gaC	gaT	4187	4187	B.1.1.7	0.003748
S	53	D53D	gaC	gaT	973	973	B.1.617.2	0.003664
S	53	D53D	gaC	gaT	709	709	AY.4	0.001104
S	53	D53D	gaC	gaT	448	448	AY.102	0.011878
S	53	D53D	gaC	gaT	426	426	AY.44	0.002593
S	53	D53D	gaC	gaT	326	326	B.1.1.228	0.993902
S	53	D53D	gaC	gaT	209	209	AY.68	0.057213
S	53	D53D	gaC	gaT	182	182	B.1	0.001667
S	53	D53D	gaC	gaT	170	170	AY.3.1	0.014494
S	53	D53D	gaC	gaT	165	165	B.1.240	0.035568
S	53	D53D	gaC	gaT	139	139	B.1.2	0.001224
S	53	D53D	gaC	gaT	135	135	AY.103	0.000838
S	53	D53D	gaC	gaT	111	111	AY.43	0.000492
S	53	D53D	gaC	gaT	102	102	B.1.234	0.013458
S	53	D53D	gaC	gaT	100	100	AY.39.1	0.003961
S	53	D53D	gaC	gaT	90	90	AY.25	0.000541
S	53	D53D	gaC	gaT	87	87	AY.120	0.003235
S	53	D53D	gaC	gaT	84	84	B.1.1	0.001524
S	53	D53D	gaC	gaT	78	78	B.1.177	0.001027
S	53	D53D	gaC	gaT	74	74	P.1	0.001166
S	53	D53D	gaC	gaT	70	70	Q.8	0.011544
S	53	D53D	gaC	gaT	67	67	B.1.1.433	0.095442
S	53	D53D	gaC	gaT	61	61	AY.3	0.000607
S	53	D53D	gaC	gaT	59	59	B.1.258.17	0.006134
S	53	D53D	gaC	gaT	56	56	P.5	0.767123
S	53	D53D	gaC	gaT	50	50	B.1.427	0.002525
S	53	D53D	gaC	gaT	46	46	AY.39	0.001137
S	53	D53D	gaC	gaT	45	45	AY.5.3	0.015182
S	53	D53D	gaC	gaT	42	42	B.1.36	0.006128
S	53	D53D	gaC	gaT	37	37	B.1.609	0.017737
S	53	D53D	gaC	gaT	28	28	AY.5	0.000578
S	53	D53D	gaC	gaT	28	28	B.1.177.43	0.041359
S	53	D53D	gaC	gaT	27	27	B.1.526	0.000635
S	53	D53D	gaC	gaT	26	26	AY.9.2	0.000955
S	53	D53D	gaC	gaT	25	25	AY.119	0.000883
S	53	D53D	gaC	gaT	25	25	AY.46	0.002602
S	53	D53D	gaC	gaT	25	25	B.1.1.519	0.000993
S	53	D53D	gaC	gaT	22	22	B.1.1.523	0.034375
S	53	D53D	gaC	gaT	22	22	B.1.177.56	0.014686
S	53	D53D	gaC	gaT	21	21	B.1.243	0.001461
S	53	D53D	gaC	gaT	21	21	B.1.429	0.000494
S	53	D53D	gaC	gaT	20	20	AY.121	0.002706
S	53	D53D	gaC	gaT	20	20	AY.29	0.000315
S	53	D53D	gaC	gaT	20	20	AY.4.2	0.000434
S	53	D53D	gaC	gaT	19	19	AY.47	0.000591
S	53	D53D	gaC	gaT	19	19	B.1.1.39	0.009684
S	53	D53D	gaC	gaT	18	18	AY.98	0.001422
S	53	D53D	gaC	gaT	17	17	AY.9.1	0.001423
S	53	D53D	gaC	gaT	17	17	B.1.351	0.000505
S	53	D53D	gaC	gaT	16	16	AY.100	0.000736
S	53	D53D	gaC	gaT	16	16	B.1.258	0.001065
S	53	D53D	gaC	gaT	14	14	AY.117	0.001183
S	53	D53D	gaC	gaT	14	14	B.1.160.11	0.08
S	53	D53D	gaC	gaT	13	13	AY.26	0.000368
S	53	D53D	gaC	gaT	13	13	AY.98.1	0.00063
S	53	D53D	gaC	gaT	13	13	B.1.1.28	0.004046
S	53	D53D	gaC	gaT	13	13	B.1.1.37	0.002507
S	53	D53D	gaC	gaT	13	13	B.1.160	0.000405
S	53	D53D	gaC	gaT	13	13	B.1.177.82	0.006205
S	53	D53D	gaC	gaT	13	13	R.1	0.00117
S	53	D53D	gaC	gaT	12	12	AY.42	0.000483
S	53	D53D	gaC	gaT	12	12	AY.6	0.000494
S	53	D53D	gaC	gaT	12	12	B.1.36.24	0.074074
S	53	D53D	gaC	gaT	12	12	B.1.596	0.001046
S	53	D53D	gaC	gaT	12	12	C.37	0.001393
S	53	D53D	gaC	gaT	11	11	A	0.004257
S	53	D53D	gaC	gaT	11	11	AY.118	0.000689
S	53	D53D	gaC	gaT	11	11	AY.16	0.004176
S	53	D53D	gaC	gaT	11	11	AY.20	0.000428
S	53	D53D	gaC	gaT	10	10	AY.52	0.008143
S	53	D53D	gaC	gaT	10	10	B.1.221	0.00071
S	53	D53D	gaC	gaT	10	10	B.1.450	0.113636
S	53	D53D	gaC	gaT	9	9	AY.33	0.000601
S	53	D53D	gaC	gaT	9	9	B.1.1.214	0.000499
S	53	D53D	gaC	gaT	9	9	B.1.582	0.004416
S	53	D53D	gaC	gaT	8	8	AY.116	0.002294
S	53	D53D	gaC	gaT	8	8	AY.46.2	0.005083
S	53	D53D	gaC	gaT	8	8	AY.7	0.001568
S	53	D53D	gaC	gaT	8	8	B.1.36.18	0.003361
S	53	D53D	gaC	gaT	7	7	AY.120.1	0.002247
S	53	D53D	gaC	gaT	7	7	AY.45	0.000852
S	53	D53D	gaC	gaT	7	7	AY.85	0.00299
S	53	D53D	gaC	gaT	7	7	B.1.400	0.003003
S	53	D53D	gaC	gaT	7	7	P.1.14	0.000335
S	53	D53D	gaC	gaT	6	6	AY.34.1	0.00306
S	53	D53D	gaC	gaT	6	6	AY.36	0.000889
S	53	D53D	gaC	gaT	6	6	AY.74	0.000694
S	53	D53D	gaC	gaT	6	6	AY.97	0.010204
S	53	D53D	gaC	gaT	6	6	B.1.177.17	0.004926
S	53	D53D	gaC	gaT	6	6	B.1.177.7	0.000989
S	53	D53D	gaC	gaT	6	6	B.1.621	0.000531
S	53	D53D	gaC	gaT	6	6	B.1.637	0.000438
S	53	D53D	gaC	gaT	6	6	Q.1	0.000758
S	53	D53D	gaC	gaT	5	5	AY.54	0.000477
S	53	D53D	gaC	gaT	5	5	AY.77	0.005637
S	53	D53D	gaC	gaT	5	5	AY.79	0.006053
S	53	D53D	gaC	gaT	5	5	AY.91	0.003652
S	53	D53D	gaC	gaT	5	5	AY.95	0.003805
S	53	D53D	gaC	gaT	5	5	B.1.1.306	0.002192
S	53	D53D	gaC	gaT	5	5	B.1.1.525	0.027322
S	53	D53D	gaC	gaT	5	5	B.1.139	0.003666
S	53	D53D	gaC	gaT	5	5	B.1.177.60	0.001092
S	53	D53D	gaC	gaT	5	5	B.1.470	0.007022
S	53	D53D	gaC	gaT	5	5	Q.7	0.005556
S	53	D53D	gaC	gaT	4	4	AY.113	0.00057
S	53	D53D	gaC	gaT	4	4	AY.13	0.000644
S	53	D53D	gaC	gaT	4	4	AY.23	0.000279
S	53	D53D	gaC	gaT	4	4	AY.4.5	0.00043
S	53	D53D	gaC	gaT	4	4	AY.46.4	0.000658
S	53	D53D	gaC	gaT	4	4	AY.7.1	0.000451
S	53	D53D	gaC	gaT	4	4	B.1.1.328	0.067797
S	53	D53D	gaC	gaT	4	4	B.1.1.429	0.018433
S	53	D53D	gaC	gaT	4	4	B.1.1.435	0.137931
S	53	D53D	gaC	gaT	4	4	B.1.1.63	0.001543
S	53	D53D	gaC	gaT	4	4	B.1.177.87	0.002911
S	53	D53D	gaC	gaT	4	4	B.1.206	0.003263
S	53	D53D	gaC	gaT	4	4	B.1.36.10	0.019139
S	53	D53D	gaC	gaT	4	4	B.1.36.36	0.002408
S	53	D53D	gaC	gaT	4	4	B.1.438.1	0.000429
S	53	D53D	gaC	gaT	4	4	B.1.575	0.001214
S	53	D53D	gaC	gaT	4	4	B.1.597	0.018519
S	53	D53D	gaC	gaT	4	4	Q.3	0.00058
S	53	D53D	gaC	gaT	3	3	A.1	0.000846
S	53	D53D	gaC	gaT	3	3	AY.106	0.001005
S	53	D53D	gaC	gaT	3	3	AY.110	0.000338
S	53	D53D	gaC	gaT	3	3	AY.37	0.000948
S	53	D53D	gaC	gaT	3	3	AY.5.4	0.00083
S	53	D53D	gaC	gaT	3	3	AY.61	0.000314
S	53	D53D	gaC	gaT	3	3	AY.75	0.000168
S	53	D53D	gaC	gaT	3	3	AY.84	0.001312
S	53	D53D	gaC	gaT	3	3	AY.99.2	0.000276
S	53	D53D	gaC	gaT	3	3	B.1.1.141	0.006036
S	53	D53D	gaC	gaT	3	3	B.1.1.222	0.000612
S	53	D53D	gaC	gaT	3	3	B.1.1.294	0.003797
S	53	D53D	gaC	gaT	3	3	B.1.1.307	0.007595
S	53	D53D	gaC	gaT	3	3	B.1.1.316	0.002775
S	53	D53D	gaC	gaT	3	3	B.1.177.35	0.002073
S	53	D53D	gaC	gaT	3	3	B.1.177.81	0.000568
S	53	D53D	gaC	gaT	3	3	B.1.36.17	0.001482
S	53	D53D	gaC	gaT	3	3	B.1.438	0.019608
S	53	D53D	gaC	gaT	3	3	B.1.466.2	0.001174
S	53	D53D	gaC	gaT	3	3	B.1.589	0.022727
S	53	D53D	gaC	gaT	3	3	B.1.595	0.000783
S	53	D53D	gaC	gaT	3	3	B.1.605	0.017857
S	53	D53D	gaC	gaT	3	3	L.4	0.15
S	53	D53D	gaC	gaT	3	3	P.1.15	0.000697
S	53	D53D	gaC	gaT	3	3	P.1.16	0.001122
S	53	D53D	gaC	gaT	3	3	P.2	0.00056
S	53	D53D	gaC	gaT	2	2	A.2.5.1	0.009615
S	53	D53D	gaC	gaT	2	2	AY.108	0.002205
S	53	D53D	gaC	gaT	2	2	AY.12	0.000632
S	53	D53D	gaC	gaT	2	2	AY.32	0.001065
S	53	D53D	gaC	gaT	2	2	AY.38	0.000999
S	53	D53D	gaC	gaT	2	2	AY.39.2	0.003082
S	53	D53D	gaC	gaT	2	2	AY.46.5	0.000397
S	53	D53D	gaC	gaT	2	2	AY.46.6	0.000144
S	53	D53D	gaC	gaT	2	2	AY.56	0.00321
S	53	D53D	gaC	gaT	2	2	AY.65	0.001066
S	53	D53D	gaC	gaT	2	2	AY.9	0.000135
S	53	D53D	gaC	gaT	2	2	AY.99	0.002099
S	53	D53D	gaC	gaT	2	2	B	0.000256
S	53	D53D	gaC	gaT	2	2	B.1.1.1	0.000653
S	53	D53D	gaC	gaT	2	2	B.1.1.170	0.002494
S	53	D53D	gaC	gaT	2	2	B.1.1.25	0.001137
S	53	D53D	gaC	gaT	2	2	B.1.1.26	0.010471
S	53	D53D	gaC	gaT	2	2	B.1.1.284	0.000215
S	53	D53D	gaC	gaT	2	2	B.1.1.33	0.000842
S	53	D53D	gaC	gaT	2	2	B.1.1.348	0.001592
S	53	D53D	gaC	gaT	2	2	B.1.1.369	0.000892
S	53	D53D	gaC	gaT	2	2	B.1.1.409	0.005666
S	53	D53D	gaC	gaT	2	2	B.1.1.434	0.000697
S	53	D53D	gaC	gaT	2	2	B.1.1.487	0.011173
S	53	D53D	gaC	gaT	2	2	B.1.160.14	0.004237
S	53	D53D	gaC	gaT	2	2	B.1.177.44	0.001038
S	53	D53D	gaC	gaT	2	2	B.1.177.6	0.001953
S	53	D53D	gaC	gaT	2	2	B.1.177.73	0.001133
S	53	D53D	gaC	gaT	2	2	B.1.177.75	0.002081
S	53	D53D	gaC	gaT	2	2	B.1.351.2	0.000605
S	53	D53D	gaC	gaT	2	2	B.1.36.29	0.001035
S	53	D53D	gaC	gaT	2	2	B.1.36.8	0.002
S	53	D53D	gaC	gaT	2	2	B.1.497	0.00063
S	53	D53D	gaC	gaT	2	2	B.1.525	0.000226
S	53	D53D	gaC	gaT	2	2	B.1.527	0.007407
S	53	D53D	gaC	gaT	2	2	B.1.564.1	0.003155
S	53	D53D	gaC	gaT	2	2	B.1.595.4	0.014599
S	53	D53D	gaC	gaT	2	2	B.1.619	0.001742
S	53	D53D	gaC	gaT	2	2	B.39	0.004662
S	53	D53D	gaC	gaT	2	2	D.2	0.00015
S	53	D53D	gaC	gaT	2	2	P.1.1	0.000635
S	53	D53D	gaC	gaT	2	2	P.4	0.007605
S	53	D53D	gaC	gaT	2	2	P.6	0.006289
S	53	D53D	gaC	gaT	1	1		0.055556
S	53	D53D	gaC	gaT	1	1	A.2	0.000662
S	53	D53D	gaC	gaT	1	1	A.23.1	0.000704
S	53	D53D	gaC	gaT	1	1	A.27	0.001656
S	53	D53D	gaC	gaT	1	1	AD.2	0.000219
S	53	D53D	gaC	gaT	1	1	AU.2	0.002421
S	53	D53D	gaC	gaT	1	1	AY.105	0.000643
S	53	D53D	gaC	gaT	1	1	AY.109	0.00074
S	53	D53D	gaC	gaT	1	1	AY.111	0.000183
S	53	D53D	gaC	gaT	1	1	AY.116.1	0.000311
S	53	D53D	gaC	gaT	1	1	AY.120.2.1	0.000498
S	53	D53D	gaC	gaT	1	1	AY.17	0.008197
S	53	D53D	gaC	gaT	1	1	AY.23.1	0.000417
S	53	D53D	gaC	gaT	1	1	AY.24	0.000431
S	53	D53D	gaC	gaT	1	1	AY.27	0.000065
S	53	D53D	gaC	gaT	1	1	AY.4.4	0.000409
S	53	D53D	gaC	gaT	1	1	AY.46.1	0.001027
S	53	D53D	gaC	gaT	1	1	AY.48	0.000465
S	53	D53D	gaC	gaT	1	1	AY.51	0.000909
S	53	D53D	gaC	gaT	1	1	AY.55	0.000917
S	53	D53D	gaC	gaT	1	1	AY.58	0.000907
S	53	D53D	gaC	gaT	1	1	AY.62	0.000436
S	53	D53D	gaC	gaT	1	1	AY.70	0.000209
S	53	D53D	gaC	gaT	1	1	AY.71	0.000475
S	53	D53D	gaC	gaT	1	1	AY.75.1	0.00018
S	53	D53D	gaC	gaT	1	1	AY.86	0.00083
S	53	D53D	gaC	gaT	1	1	AY.88	0.000884
S	53	D53D	gaC	gaT	1	1	B.1.1.123	0.017857
S	53	D53D	gaC	gaT	1	1	B.1.1.153	0.001095
S	53	D53D	gaC	gaT	1	1	B.1.1.157	0.000913
S	53	D53D	gaC	gaT	1	1	B.1.1.176	0.000439
S	53	D53D	gaC	gaT	1	1	B.1.1.216	0.00089
S	53	D53D	gaC	gaT	1	1	B.1.1.258	0.003257
S	53	D53D	gaC	gaT	1	1	B.1.1.318	0.000302
S	53	D53D	gaC	gaT	1	1	B.1.1.326	0.001761
S	53	D53D	gaC	gaT	1	1	B.1.1.383	0.0625
S	53	D53D	gaC	gaT	1	1	B.1.1.389	0.006061
S	53	D53D	gaC	gaT	1	1	B.1.1.398	0.003226
S	53	D53D	gaC	gaT	1	1	B.1.1.432	0.001266
S	53	D53D	gaC	gaT	1	1	B.1.1.485	0.016667
S	53	D53D	gaC	gaT	1	1	B.1.1.517	0.006803
S	53	D53D	gaC	gaT	1	1	B.1.1.52	0.012195
S	53	D53D	gaC	gaT	1	1	B.1.1.70	0.000341
S	53	D53D	gaC	gaT	1	1	B.1.104	0.00369
S	53	D53D	gaC	gaT	1	1	B.1.160.12	0.00641
S	53	D53D	gaC	gaT	1	1	B.1.160.16	0.000929
S	53	D53D	gaC	gaT	1	1	B.1.177.12	0.000152
S	53	D53D	gaC	gaT	1	1	B.1.177.16	0.000664
S	53	D53D	gaC	gaT	1	1	B.1.177.41	0.0025
S	53	D53D	gaC	gaT	1	1	B.1.177.52	0.001757
S	53	D53D	gaC	gaT	1	1	B.1.177.78	0.009709
S	53	D53D	gaC	gaT	1	1	B.1.177.86	0.000183
S	53	D53D	gaC	gaT	1	1	B.1.210	0.002132
S	53	D53D	gaC	gaT	1	1	B.1.22	0.001318
S	53	D53D	gaC	gaT	1	1	B.1.232	0.000537
S	53	D53D	gaC	gaT	1	1	B.1.258.3	0.001675
S	53	D53D	gaC	gaT	1	1	B.1.260	0.003344
S	53	D53D	gaC	gaT	1	1	B.1.264.1	0.047619
S	53	D53D	gaC	gaT	1	1	B.1.311	0.000275
S	53	D53D	gaC	gaT	1	1	B.1.340	0.004292
S	53	D53D	gaC	gaT	1	1	B.1.350	0.002933
S	53	D53D	gaC	gaT	1	1	B.1.351.3	0.000876
S	53	D53D	gaC	gaT	1	1	B.1.36.16	0.001425
S	53	D53D	gaC	gaT	1	1	B.1.36.19	0.009259
S	53	D53D	gaC	gaT	1	1	B.1.36.7	0.004
S	53	D53D	gaC	gaT	1	1	B.1.369	0.000285
S	53	D53D	gaC	gaT	1	1	B.1.396	0.000706
S	53	D53D	gaC	gaT	1	1	B.1.398	0.002976
S	53	D53D	gaC	gaT	1	1	B.1.422	0.000812
S	53	D53D	gaC	gaT	1	1	B.1.426	0.001009
S	53	D53D	gaC	gaT	1	1	B.1.428	0.00102
S	53	D53D	gaC	gaT	1	1	B.1.462	0.007246
S	53	D53D	gaC	gaT	1	1	B.1.517	0.000427
S	53	D53D	gaC	gaT	1	1	B.1.523	0.002451
S	53	D53D	gaC	gaT	1	1	B.1.524	0.001406
S	53	D53D	gaC	gaT	1	1	B.1.561	0.000397
S	53	D53D	gaC	gaT	1	1	B.1.567	0.003333
S	53	D53D	gaC	gaT	1	1	B.1.568	0.001111
S	53	D53D	gaC	gaT	1	1	B.1.571	0.009709
S	53	D53D	gaC	gaT	1	1	B.1.617.1	0.000129
S	53	D53D	gaC	gaT	1	1	B.1.617.3	0.002985
S	53	D53D	gaC	gaT	1	1	B.1.620	0.000946
S	53	D53D	gaC	gaT	1	1	B.1.628	0.000352
S	53	D53D	gaC	gaT	1	1	B.1.634	0.003425
S	53	D53D	gaC	gaT	1	1	B.6.6	0.000889
S	53	D53D	gaC	gaT	1	1	C.1	0.002392
S	53	D53D	gaC	gaT	1	1	C.1.2	0.004255
S	53	D53D	gaC	gaT	1	1	C.35	0.000774
S	53	D53D	gaC	gaT	1	1	C.36.3	0.000567
S	53	D53D	gaC	gaT	1	1	D.5	0.004975
S	53	D53D	gaC	gaT	1	1	N.10	0.029412
S	53	D53D	gaC	gaT	1	1	N.4	0.004255
S	53	D53D	gaC	gaT	1	1	P.1.17	0.000162
S	53	D53D	gaC	gaT	1	1	P.3	0.001595
S	53	D53D	gaC	gaT	1	1	U.3	0.003861
S	53	D53D	gaC	gaT	1	1	W.3	0.005263
S	53	D53D	gaC	gaT	1	1	W.4	0.001351

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.