CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : Mut = P13S

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
N	13	P13S		nonsyn	Ccc	Tcc	7635	7624	0.998559	28310-28312
N	13	P13S		nonsyn	CcC	TcT	7635	11	0.00144073	28310-28312

Details of the mutation P13S 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
N	13	P13S	Ccc	Tcc	7624	7635	All	0.001458
N	13	P13S	CcC	TcT	11	7635	All	0.000002
N	13	P13S	Ccc	Tcc	1962	1968	B.1.351	0.058323
N	13	P13S	CcC	TcT	6	1968	B.1.351	0.000178
N	13	P13S	Ccc	Tcc	1160	1160	B.1.1.7	0.001038
N	13	P13S	Ccc	Tcc	987	988	B.1.1.420	0.992958
N	13	P13S	CcC	TcT	1	988	B.1.1.420	0.001006
N	13	P13S	Ccc	Tcc	566	566	B.1	0.005184
N	13	P13S	Ccc	Tcc	246	246	AY.91.1	1
N	13	P13S	Ccc	Tcc	240	240	AY.39	0.005931
N	13	P13S	Ccc	Tcc	213	213	B.1.1.240	1
N	13	P13S	Ccc	Tcc	167	167	AY.4	0.00026
N	13	P13S	Ccc	Tcc	132	132	B.1.1	0.002395
N	13	P13S	Ccc	Tcc	123	123	B.1.2	0.001083
N	13	P13S	Ccc	Tcc	120	120	AY.44	0.00073
N	13	P13S	Ccc	Tcc	94	94	B.1.617.2	0.000354
N	13	P13S	Ccc	Tcc	77	77	AY.103	0.000478
N	13	P13S	Ccc	Tcc	76	76	B.1.617.1	0.009801
N	13	P13S	Ccc	Tcc	73	73	AY.43	0.000323
N	13	P13S	Ccc	Tcc	63	63	B.1.160	0.001965
N	13	P13S	Ccc	Tcc	63	63	C.26	0.463235
N	13	P13S	Ccc	Tcc	61	61	AY.29	0.000962
N	13	P13S	Ccc	Tcc	54	54	B.1.562	1
N	13	P13S	Ccc	Tcc	48	48	B.1.177	0.000632
N	13	P13S	Ccc	Tcc	44	44	AY.26	0.001246
N	13	P13S	Ccc	Tcc	42	42	AY.3	0.000418
N	13	P13S	Ccc	Tcc	40	40	AY.4.5	0.0043
N	13	P13S	Ccc	Tcc	37	37	B.1.427	0.001868
N	13	P13S	Ccc	Tcc	36	36	AY.85	0.015378
N	13	P13S	Ccc	Tcc	33	33	AY.25	0.000198
N	13	P13S	Ccc	Tcc	29	32	P.1	0.000457
N	13	P13S	CcC	TcT	3	32	P.1	0.000047
N	13	P13S	Ccc	Tcc	28	28	B.1.36.17	0.013834
N	13	P13S	Ccc	Tcc	26	26	B.1.1.328	0.440678
N	13	P13S	Ccc	Tcc	23	23	B.1.1.242	1
N	13	P13S	Ccc	Tcc	23	23	B.1.36	0.003356
N	13	P13S	Ccc	Tcc	22	22	AJ.1	1
N	13	P13S	Ccc	Tcc	22	22	B.1.1.70	0.007503
N	13	P13S	Ccc	Tcc	21	21	B.1.1.519	0.000834
N	13	P13S	Ccc	Tcc	19	19	B.1.221	0.00135
N	13	P13S	Ccc	Tcc	16	16	AY.4.2	0.000347
N	13	P13S	Ccc	Tcc	16	16	B.1.177.7	0.002638
N	13	P13S	Ccc	Tcc	16	16	B.1.429	0.000376
N	13	P13S	Ccc	Tcc	15	15	B.1.1.526	0.053191
N	13	P13S	Ccc	Tcc	14	14	B.1.234	0.001847
N	13	P13S	Ccc	Tcc	14	14	B.1.397	0.067961
N	13	P13S	Ccc	Tcc	13	13	B.1.403	0.042484
N	13	P13S	Ccc	Tcc	12	12	AY.102	0.000318
N	13	P13S	Ccc	Tcc	12	12	B.1.243	0.000835
N	13	P13S	Ccc	Tcc	11	11	AY.47	0.000342
N	13	P13S	Ccc	Tcc	11	11	B	0.001406
N	13	P13S	Ccc	Tcc	11	11	B.1.258	0.000732
N	13	P13S	Ccc	Tcc	10	10	B.1.1.28	0.003112
N	13	P13S	Ccc	Tcc	10	10	C.16	0.010604
N	13	P13S	Ccc	Tcc	9	9	AY.100	0.000414
N	13	P13S	Ccc	Tcc	9	9	B.1.40	0.176471
N	13	P13S	Ccc	Tcc	9	9	R.1	0.00081
N	13	P13S	Ccc	Tcc	8	8	AY.119	0.000282
N	13	P13S	Ccc	Tcc	8	8	AY.5	0.000165
N	13	P13S	Ccc	Tcc	8	8	B.1.1.214	0.000444
N	13	P13S	Ccc	Tcc	8	8	B.1.1.244	0.123077
N	13	P13S	Ccc	Tcc	8	8	B.1.509	0.006926
N	13	P13S	Ccc	Tcc	8	8	B.1.525	0.000905
N	13	P13S	Ccc	Tcc	8	8	B.1.609	0.003835
N	13	P13S	Ccc	Tcc	8	8	P.1.15	0.001859
N	13	P13S	Ccc	Tcc	7	7	B.1.177.56	0.004673
N	13	P13S	Ccc	Tcc	6	6	A.2.5	0.002994
N	13	P13S	Ccc	Tcc	5	6	AY.23	0.000349
N	13	P13S	CcC	TcT	1	6	AY.23	0.00007
N	13	P13S	Ccc	Tcc	6	6	B.1.258.17	0.000624
N	13	P13S	Ccc	Tcc	6	6	P.1.4	0.005859
N	13	P13S	Ccc	Tcc	5	5	AY.120	0.000186
N	13	P13S	Ccc	Tcc	5	5	AY.13	0.000805
N	13	P13S	Ccc	Tcc	5	5	AY.42	0.000201
N	13	P13S	Ccc	Tcc	5	5	AY.45	0.000608
N	13	P13S	Ccc	Tcc	5	5	AY.46	0.00052
N	13	P13S	Ccc	Tcc	5	5	AY.93	0.001365
N	13	P13S	Ccc	Tcc	5	5	B.1.1.277	0.003794
N	13	P13S	Ccc	Tcc	5	5	B.1.177.35	0.003455
N	13	P13S	Ccc	Tcc	5	5	B.1.177.87	0.003639
N	13	P13S	Ccc	Tcc	5	5	B.1.36.7	0.02
N	13	P13S	Ccc	Tcc	5	5	B.1.526	0.000118
N	13	P13S	Ccc	Tcc	5	5	C.36	0.004554
N	13	P13S	Ccc	Tcc	4	4	AY.117	0.000338
N	13	P13S	Ccc	Tcc	4	4	AY.20	0.000155
N	13	P13S	Ccc	Tcc	4	4	AY.32	0.00213
N	13	P13S	Ccc	Tcc	4	4	AY.33	0.000267
N	13	P13S	Ccc	Tcc	4	4	AY.61	0.000419
N	13	P13S	Ccc	Tcc	4	4	AY.75	0.000224
N	13	P13S	Ccc	Tcc	4	4	B.1.1.409	0.011331
N	13	P13S	Ccc	Tcc	4	4	B.1.417	0.114286
N	13	P13S	Ccc	Tcc	4	4	B.1.527	0.014815
N	13	P13S	Ccc	Tcc	3	3	AY.106	0.001005
N	13	P13S	Ccc	Tcc	3	3	AY.109	0.002219
N	13	P13S	Ccc	Tcc	3	3	AY.118	0.000188
N	13	P13S	Ccc	Tcc	3	3	AY.14	0.000264
N	13	P13S	Ccc	Tcc	3	3	AY.34	0.000291
N	13	P13S	Ccc	Tcc	3	3	AY.36	0.000445
N	13	P13S	Ccc	Tcc	3	3	AY.39.1	0.000119
N	13	P13S	Ccc	Tcc	3	3	AY.98.1	0.000145
N	13	P13S	Ccc	Tcc	3	3	AZ.1	0.002602
N	13	P13S	Ccc	Tcc	3	3	B.1.1.120	0.1
N	13	P13S	Ccc	Tcc	3	3	B.1.1.222	0.000612
N	13	P13S	Ccc	Tcc	3	3	B.1.1.348	0.002389
N	13	P13S	Ccc	Tcc	3	3	B.1.1.464	0.004418
N	13	P13S	Ccc	Tcc	3	3	B.1.177.60	0.000655
N	13	P13S	Ccc	Tcc	3	3	B.1.177.81	0.000568
N	13	P13S	Ccc	Tcc	3	3	B.1.324	0.004815
N	13	P13S	Ccc	Tcc	3	3	B.1.36.18	0.001261
N	13	P13S	Ccc	Tcc	3	3	B.1.393	0.085714
N	13	P13S	Ccc	Tcc	3	3	B.1.408	0.01107
N	13	P13S	Ccc	Tcc	3	3	B.1.478	0.035294
N	13	P13S	Ccc	Tcc	3	3	B.1.540	0.029126
N	13	P13S	Ccc	Tcc	3	3	B.1.596	0.000261
N	13	P13S	Ccc	Tcc	3	3	B.1.621	0.000266
N	13	P13S	Ccc	Tcc	3	3	B.1.637	0.000219
N	13	P13S	Ccc	Tcc	2	2	A.23.1	0.001408
N	13	P13S	Ccc	Tcc	2	2	AT.1	0.010256
N	13	P13S	Ccc	Tcc	2	2	AY.113	0.000285
N	13	P13S	Ccc	Tcc	2	2	AY.3.1	0.000171
N	13	P13S	Ccc	Tcc	2	2	AY.46.5	0.000397
N	13	P13S	Ccc	Tcc	2	2	AY.46.6	0.000144
N	13	P13S	Ccc	Tcc	2	2	AY.5.3	0.000675
N	13	P13S	Ccc	Tcc	2	2	AY.55	0.001835
N	13	P13S	Ccc	Tcc	2	2	AY.59	0.001059
N	13	P13S	Ccc	Tcc	2	2	AY.6	0.000082
N	13	P13S	Ccc	Tcc	2	2	AY.63	0.000774
N	13	P13S	Ccc	Tcc	2	2	AY.9.2	0.000073
N	13	P13S	Ccc	Tcc	2	2	AY.91	0.001461
N	13	P13S	Ccc	Tcc	2	2	AY.98	0.000158
N	13	P13S	Ccc	Tcc	2	2	AY.99	0.002099
N	13	P13S	Ccc	Tcc	2	2	B.1.1.10	0.00223
N	13	P13S	Ccc	Tcc	2	2	B.1.1.189	0.003026
N	13	P13S	Ccc	Tcc	2	2	B.1.1.216	0.001781
N	13	P13S	Ccc	Tcc	2	2	B.1.1.254	0.022472
N	13	P13S	Ccc	Tcc	2	2	B.1.1.306	0.000877
N	13	P13S	Ccc	Tcc	2	2	B.1.1.317	0.000823
N	13	P13S	Ccc	Tcc	2	2	B.1.1.318	0.000604
N	13	P13S	Ccc	Tcc	2	2	B.1.1.33	0.000842
N	13	P13S	Ccc	Tcc	2	2	B.1.1.37	0.000386
N	13	P13S	Ccc	Tcc	2	2	B.1.1.372	0.001377
N	13	P13S	Ccc	Tcc	2	2	B.1.1.434	0.000697
N	13	P13S	Ccc	Tcc	2	2	B.1.1.83	0.00542
N	13	P13S	Ccc	Tcc	2	2	B.1.104	0.00738
N	13	P13S	Ccc	Tcc	2	2	B.1.110	0.00905
N	13	P13S	Ccc	Tcc	2	2	B.1.177.21	0.000153
N	13	P13S	Ccc	Tcc	2	2	B.1.177.42	0.001789
N	13	P13S	Ccc	Tcc	2	2	B.1.36.10	0.009569
N	13	P13S	Ccc	Tcc	2	2	B.1.36.29	0.001035
N	13	P13S	Ccc	Tcc	2	2	B.1.369	0.00057
N	13	P13S	Ccc	Tcc	2	2	B.1.467	0.08
N	13	P13S	Ccc	Tcc	2	2	B.1.568	0.002222
N	13	P13S	Ccc	Tcc	2	2	B.1.575	0.000607
N	13	P13S	Ccc	Tcc	2	2	B.1.620	0.001892
N	13	P13S	Ccc	Tcc	2	2	D.2	0.00015
N	13	P13S	Ccc	Tcc	2	2	N.5	0.003534
N	13	P13S	Ccc	Tcc	2	2	P.1.14	0.000096
N	13	P13S	Ccc	Tcc	2	2	P.1.16	0.000748
N	13	P13S	Ccc	Tcc	2	2	P.1.7	0.000639
N	13	P13S	Ccc	Tcc	2	2	P.2	0.000373
N	13	P13S	Ccc	Tcc	1	1	A	0.000387
N	13	P13S	Ccc	Tcc	1	1	AD.2	0.000219
N	13	P13S	Ccc	Tcc	1	1	AP.1	0.001502
N	13	P13S	Ccc	Tcc	1	1	AY.101	0.00049
N	13	P13S	Ccc	Tcc	1	1	AY.105	0.000643
N	13	P13S	Ccc	Tcc	1	1	AY.107	0.000466
N	13	P13S	Ccc	Tcc	1	1	AY.16.1	0.00047
N	13	P13S	Ccc	Tcc	1	1	AY.19	0.00114
N	13	P13S	Ccc	Tcc	1	1	AY.24	0.000431
N	13	P13S	Ccc	Tcc	1	1	AY.27	0.000065
N	13	P13S	Ccc	Tcc	1	1	AY.30	0.000396
N	13	P13S	Ccc	Tcc	1	1	AY.49	0.003195
N	13	P13S	Ccc	Tcc	1	1	AY.51	0.000909
N	13	P13S	Ccc	Tcc	1	1	AY.52	0.000814
N	13	P13S	Ccc	Tcc	1	1	AY.53	0.000288
N	13	P13S	Ccc	Tcc	1	1	AY.62	0.000436
N	13	P13S	Ccc	Tcc	1	1	AY.68	0.000274
N	13	P13S	Ccc	Tcc	1	1	AY.7	0.000196
N	13	P13S	Ccc	Tcc	1	1	AY.7.1	0.000113
N	13	P13S	Ccc	Tcc	1	1	AY.70	0.000209
N	13	P13S	Ccc	Tcc	1	1	AY.74	0.000116
N	13	P13S	Ccc	Tcc	1	1	AY.84	0.000437
N	13	P13S	Ccc	Tcc	1	1	AY.86	0.00083
N	13	P13S	Ccc	Tcc	1	1	AY.9	0.000068
N	13	P13S	Ccc	Tcc	1	1	AY.99.2	0.000092
N	13	P13S	Ccc	Tcc	1	1	B.1.1.1	0.000327
N	13	P13S	Ccc	Tcc	1	1	B.1.1.174	0.003378
N	13	P13S	Ccc	Tcc	1	1	B.1.1.192	0.002309
N	13	P13S	Ccc	Tcc	1	1	B.1.1.200	0.007463
N	13	P13S	Ccc	Tcc	1	1	B.1.1.203	0.016949
N	13	P13S	Ccc	Tcc	1	1	B.1.1.225	0.007194
N	13	P13S	Ccc	Tcc	1	1	B.1.1.25	0.000569
N	13	P13S	Ccc	Tcc	1	1	B.1.1.282	0.011628
N	13	P13S	Ccc	Tcc	1	1	B.1.1.284	0.000107
N	13	P13S	Ccc	Tcc	1	1	B.1.1.286	0.002899
N	13	P13S	Ccc	Tcc	1	1	B.1.1.309	0.005848
N	13	P13S	Ccc	Tcc	1	1	B.1.1.312	0.001912
N	13	P13S	Ccc	Tcc	1	1	B.1.1.316	0.000925
N	13	P13S	Ccc	Tcc	1	1	B.1.1.370	0.012658
N	13	P13S	Ccc	Tcc	1	1	B.1.1.389	0.006061
N	13	P13S	Ccc	Tcc	1	1	B.1.1.40	0.034483
N	13	P13S	Ccc	Tcc	1	1	B.1.1.412	0.007634
N	13	P13S	Ccc	Tcc	1	1	B.1.1.417	0.002703
N	13	P13S	Ccc	Tcc	1	1	B.1.1.5	0.008333
N	13	P13S	Ccc	Tcc	1	1	B.1.1.523	0.001563
N	13	P13S	Ccc	Tcc	1	1	B.1.1.56	0.017857
N	13	P13S	Ccc	Tcc	1	1	B.1.1.63	0.000386
N	13	P13S	Ccc	Tcc	1	1	B.1.103	0.019231
N	13	P13S	Ccc	Tcc	1	1	B.1.139	0.000733
N	13	P13S	Ccc	Tcc	1	1	B.1.160.17	0.001701
N	13	P13S	Ccc	Tcc	1	1	B.1.170	0.00431
N	13	P13S	Ccc	Tcc	1	1	B.1.177.15	0.000631
N	13	P13S	Ccc	Tcc	1	1	B.1.177.17	0.000821
N	13	P13S	Ccc	Tcc	1	1	B.1.177.31	0.011494
N	13	P13S	Ccc	Tcc	1	1	B.1.177.43	0.001477
N	13	P13S	Ccc	Tcc	1	1	B.1.177.73	0.000566
N	13	P13S	Ccc	Tcc	1	1	B.1.177.82	0.000477
N	13	P13S	Ccc	Tcc	1	1	B.1.189	0.004292
N	13	P13S	Ccc	Tcc	1	1	B.1.22.1	0.03125
N	13	P13S	Ccc	Tcc	1	1	B.1.236	0.002053
N	13	P13S	Ccc	Tcc	1	1	B.1.240	0.000216
N	13	P13S	Ccc	Tcc	1	1	B.1.302	0.013333
N	13	P13S	Ccc	Tcc	1	1	B.1.311	0.000275
N	13	P13S	Ccc	Tcc	1	1	B.1.36.12	0.009615
N	13	P13S	Ccc	Tcc	1	1	B.1.36.22	0.001208
N	13	P13S	Ccc	Tcc	1	1	B.1.36.31	0.001751
N	13	P13S	Ccc	Tcc	1	1	B.1.36.34	0.021277
N	13	P13S	Ccc	Tcc	1	1	B.1.36.36	0.000602
N	13	P13S	Ccc	Tcc	1	1	B.1.367	0.000792
N	13	P13S	Ccc	Tcc	1	1	B.1.420	0.010417
N	13	P13S	Ccc	Tcc	1	1	B.1.422	0.000812
N	13	P13S	Ccc	Tcc	1	1	B.1.433	0.003195
N	13	P13S	Ccc	Tcc	1	1	B.1.434	0.052632
N	13	P13S	Ccc	Tcc	1	1	B.1.456	0.003268
N	13	P13S	Ccc	Tcc	1	1	B.1.459	0.004082
N	13	P13S	Ccc	Tcc	1	1	B.1.517	0.000427
N	13	P13S	Ccc	Tcc	1	1	B.1.520	0.021739
N	13	P13S	Ccc	Tcc	1	1	B.1.524	0.001406
N	13	P13S	Ccc	Tcc	1	1	B.1.533	0.009615
N	13	P13S	Ccc	Tcc	1	1	B.1.551	0.00129
N	13	P13S	Ccc	Tcc	1	1	B.1.554	0.004405
N	13	P13S	Ccc	Tcc	1	1	B.1.564.1	0.001577
N	13	P13S	Ccc	Tcc	1	1	B.1.570	0.002941
N	13	P13S	Ccc	Tcc	1	1	B.1.618	0.004032
N	13	P13S	Ccc	Tcc	1	1	B.1.621.1	0.000506
N	13	P13S	Ccc	Tcc	1	1	B.1.627	0.00202
N	13	P13S	Ccc	Tcc	1	1	B.1.9.4	0.006135
N	13	P13S	Ccc	Tcc	1	1	B.1.9.5	0.005682
N	13	P13S	Ccc	Tcc	1	1	B.39	0.002331
N	13	P13S	Ccc	Tcc	1	1	C.35	0.000774
N	13	P13S	Ccc	Tcc	1	1	P.1.1	0.000318
N	13	P13S	Ccc	Tcc	1	1	P.1.17	0.000162
N	13	P13S	Ccc	Tcc	1	1	Q.1	0.000126
N	13	P13S	Ccc	Tcc	1	1	Q.8	0.000165
N	13	P13S	Ccc	Tcc	1	1	U.3	0.003861
N	13	P13S	Ccc	Tcc	1	1	V.1	0.022727

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.