CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 494 & Codon = Cca

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	494	S494P		nonsyn	Tca	Cca	13139	13139	1	23042-23044

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	494	S494P	Tca	Cca	13139	13139	All	0.002513
S	494	S494P	Tca	Cca	3735	3735	B.1.1.7	0.003344
S	494	S494P	Tca	Cca	3198	3198	B.1.575	0.970267
S	494	S494P	Tca	Cca	1684	1684	B.1.623	0.903433
S	494	S494P	Tca	Cca	1258	1258	B.1.2	0.011077
S	494	S494P	Tca	Cca	604	604	B.1.1.523	0.94375
S	494	S494P	Tca	Cca	390	390	B.1.575.1	0.95122
S	494	S494P	Tca	Cca	206	206	B.1.575.2	0.990385
S	494	S494P	Tca	Cca	203	203	B.1	0.001859
S	494	S494P	Tca	Cca	147	147	AY.4	0.000229
S	494	S494P	Tca	Cca	106	106	B.1.177	0.001396
S	494	S494P	Tca	Cca	100	100	B.1.617.2	0.000377
S	494	S494P	Tca	Cca	93	93	B.1.1	0.001687
S	494	S494P	Tca	Cca	64	64	AY.98.1	0.0031
S	494	S494P	Tca	Cca	62	62	B.1.427	0.003131
S	494	S494P	Tca	Cca	56	56	B.1.1.519	0.002224
S	494	S494P	Tca	Cca	49	49	AY.25	0.000295
S	494	S494P	Tca	Cca	48	48	AY.103	0.000298
S	494	S494P	Tca	Cca	48	48	AY.44	0.000292
S	494	S494P	Tca	Cca	46	46	B.1.177.75	0.047867
S	494	S494P	Tca	Cca	42	42	Q.8	0.006926
S	494	S494P	Tca	Cca	37	37	B.1.1.174	0.125
S	494	S494P	Tca	Cca	37	37	B.1.160	0.001154
S	494	S494P	Tca	Cca	36	36	AY.43	0.000159
S	494	S494P	Tca	Cca	32	32	AY.3	0.000318
S	494	S494P	Tca	Cca	31	31	B.1.324	0.049759
S	494	S494P	Tca	Cca	28	28	AY.75	0.001569
S	494	S494P	Tca	Cca	28	28	B.1.221.3	0.023333
S	494	S494P	Tca	Cca	25	25	AY.4.2	0.000542
S	494	S494P	Tca	Cca	25	25	B.1.1.253	0.062657
S	494	S494P	Tca	Cca	25	25	B.1.429	0.000588
S	494	S494P	Tca	Cca	24	24	B.1.595	0.006263
S	494	S494P	Tca	Cca	19	19	B.1.596	0.001656
S	494	S494P	Tca	Cca	17	17	AY.39	0.00042
S	494	S494P	Tca	Cca	16	16	AY.69	0.002987
S	494	S494P	Tca	Cca	16	16	B.1.177.60	0.003495
S	494	S494P	Tca	Cca	15	15	AY.100	0.00069
S	494	S494P	Tca	Cca	15	15	AY.26	0.000425
S	494	S494P	Tca	Cca	15	15	B.1.243	0.001044
S	494	S494P	Tca	Cca	13	13	B.1.1.214	0.000721
S	494	S494P	Tca	Cca	13	13	B.1.526	0.000306
S	494	S494P	Tca	Cca	12	12	AY.5	0.000248
S	494	S494P	Tca	Cca	11	11	B.1.574	0.023656
S	494	S494P	Tca	Cca	10	10	B.1.1.222	0.00204
S	494	S494P	Tca	Cca	10	10	B.1.258	0.000665
S	494	S494P	Tca	Cca	10	10	B.1.258.17	0.00104
S	494	S494P	Tca	Cca	10	10	B.1.36	0.001459
S	494	S494P	Tca	Cca	10	10	B.1.637	0.000731
S	494	S494P	Tca	Cca	9	9	AY.119	0.000318
S	494	S494P	Tca	Cca	9	9	B.1.1.33	0.003788
S	494	S494P	Tca	Cca	8	8	AY.29	0.000126
S	494	S494P	Tca	Cca	8	8	AY.34.1	0.00408
S	494	S494P	Tca	Cca	8	8	AY.45	0.000973
S	494	S494P	Tca	Cca	8	8	B.1.177.44	0.004152
S	494	S494P	Tca	Cca	8	8	B.1.177.81	0.001515
S	494	S494P	Tca	Cca	8	8	B.1.400	0.003432
S	494	S494P	Tca	Cca	7	7	AY.113	0.000997
S	494	S494P	Tca	Cca	7	7	B.1.486	0.777778
S	494	S494P	Tca	Cca	7	7	B.1.620	0.006623
S	494	S494P	Tca	Cca	6	6	AY.14	0.000528
S	494	S494P	Tca	Cca	6	6	AY.54	0.000572
S	494	S494P	Tca	Cca	6	6	AY.6	0.000247
S	494	S494P	Tca	Cca	6	6	B.1.1.306	0.00263
S	494	S494P	Tca	Cca	6	6	B.1.131	0.052632
S	494	S494P	Tca	Cca	6	6	B.1.367	0.004754
S	494	S494P	Tca	Cca	5	5	AY.102	0.000133
S	494	S494P	Tca	Cca	5	5	AY.118	0.000313
S	494	S494P	Tca	Cca	5	5	AY.20	0.000194
S	494	S494P	Tca	Cca	5	5	AY.33	0.000334
S	494	S494P	Tca	Cca	5	5	B.1.241	0.004058
S	494	S494P	Tca	Cca	5	5	B.1.621	0.000443
S	494	S494P	Tca	Cca	5	5	B.1.635	0.087719
S	494	S494P	Tca	Cca	5	5	P.1	0.000079
S	494	S494P	Tca	Cca	4	4	A.2.5	0.001996
S	494	S494P	Tca	Cca	4	4	AY.108	0.00441
S	494	S494P	Tca	Cca	4	4	AY.4.2.1	0.000596
S	494	S494P	Tca	Cca	4	4	AY.46.6	0.000289
S	494	S494P	Tca	Cca	4	4	AY.74	0.000463
S	494	S494P	Tca	Cca	4	4	AY.9.1	0.000335
S	494	S494P	Tca	Cca	4	4	B.1.1.216	0.003562
S	494	S494P	Tca	Cca	4	4	B.1.1.294	0.005063
S	494	S494P	Tca	Cca	4	4	B.1.1.297	0.008949
S	494	S494P	Tca	Cca	4	4	B.1.1.355	0.061538
S	494	S494P	Tca	Cca	4	4	B.1.177.73	0.002265
S	494	S494P	Tca	Cca	4	4	B.1.351	0.000119
S	494	S494P	Tca	Cca	4	4	B.1.36.29	0.002069
S	494	S494P	Tca	Cca	4	4	B.1.619.1	0.002566
S	494	S494P	Tca	Cca	4	4	P.1.14	0.000191
S	494	S494P	Tca	Cca	4	4	Q.1	0.000505
S	494	S494P	Tca	Cca	4	4	Q.3	0.00058
S	494	S494P	Tca	Cca	3	3	AD.2	0.000657
S	494	S494P	Tca	Cca	3	3	AY.30	0.001187
S	494	S494P	Tca	Cca	3	3	AY.39.1	0.000119
S	494	S494P	Tca	Cca	3	3	AY.47	0.000093
S	494	S494P	Tca	Cca	3	3	AY.61	0.000314
S	494	S494P	Tca	Cca	3	3	AY.71	0.001425
S	494	S494P	Tca	Cca	3	3	AY.9.2	0.00011
S	494	S494P	Tca	Cca	3	3	B.1.1.157	0.00274
S	494	S494P	Tca	Cca	3	3	B.1.1.269	0.00406
S	494	S494P	Tca	Cca	3	3	B.1.1.37	0.000579
S	494	S494P	Tca	Cca	3	3	B.1.234	0.000396
S	494	S494P	Tca	Cca	3	3	B.1.36.8	0.003
S	494	S494P	Tca	Cca	3	3	B.1.470	0.004213
S	494	S494P	Tca	Cca	3	3	B.1.517	0.001281
S	494	S494P	Tca	Cca	3	3	B.1.595.3	0.078947
S	494	S494P	Tca	Cca	3	3	B.1.617.1	0.000387
S	494	S494P	Tca	Cca	2	2	A.29	0.010638
S	494	S494P	Tca	Cca	2	2	AY.110	0.000225
S	494	S494P	Tca	Cca	2	2	AY.17	0.016393
S	494	S494P	Tca	Cca	2	2	AY.23	0.000139
S	494	S494P	Tca	Cca	2	2	AY.27	0.000129
S	494	S494P	Tca	Cca	2	2	AY.3.1	0.000171
S	494	S494P	Tca	Cca	2	2	AY.32	0.001065
S	494	S494P	Tca	Cca	2	2	AY.34	0.000194
S	494	S494P	Tca	Cca	2	2	AY.35	0.000466
S	494	S494P	Tca	Cca	2	2	AY.37	0.000632
S	494	S494P	Tca	Cca	2	2	AY.4.4	0.000818
S	494	S494P	Tca	Cca	2	2	AY.42	0.00008
S	494	S494P	Tca	Cca	2	2	AY.55	0.001835
S	494	S494P	Tca	Cca	2	2	AY.57	0.001312
S	494	S494P	Tca	Cca	2	2	AY.73	0.001331
S	494	S494P	Tca	Cca	2	2	AY.9	0.000135
S	494	S494P	Tca	Cca	2	2	AY.98	0.000158
S	494	S494P	Tca	Cca	2	2	B.1.1.141	0.004024
S	494	S494P	Tca	Cca	2	2	B.1.1.28	0.000622
S	494	S494P	Tca	Cca	2	2	B.1.1.284	0.000215
S	494	S494P	Tca	Cca	2	2	B.1.1.317	0.000823
S	494	S494P	Tca	Cca	2	2	B.1.1.348	0.001592
S	494	S494P	Tca	Cca	2	2	B.1.1.50	0.001358
S	494	S494P	Tca	Cca	2	2	B.1.1.525	0.010929
S	494	S494P	Tca	Cca	2	2	B.1.1.70	0.000682
S	494	S494P	Tca	Cca	2	2	B.1.110.3	0.001437
S	494	S494P	Tca	Cca	2	2	B.1.111	0.00235
S	494	S494P	Tca	Cca	2	2	B.1.177.43	0.002954
S	494	S494P	Tca	Cca	2	2	B.1.177.7	0.00033
S	494	S494P	Tca	Cca	2	2	B.1.177.83	0.002963
S	494	S494P	Tca	Cca	2	2	B.1.221	0.000142
S	494	S494P	Tca	Cca	2	2	B.1.459	0.008163
S	494	S494P	Tca	Cca	2	2	B.1.525	0.000226
S	494	S494P	Tca	Cca	2	2	B.1.561	0.000794
S	494	S494P	Tca	Cca	2	2	B.1.609	0.000959
S	494	S494P	Tca	Cca	2	2	B.1.628	0.000705
S	494	S494P	Tca	Cca	2	2	Q.4	0.00091
S	494	S494P	Tca	Cca	2	2	W.1	0.017391
S	494	S494P	Tca	Cca	1	1	A.19	0.009434
S	494	S494P	Tca	Cca	1	1	A.2.4	0.003367
S	494	S494P	Tca	Cca	1	1	A.23.1	0.000704
S	494	S494P	Tca	Cca	1	1	AE.8	0.000489
S	494	S494P	Tca	Cca	1	1	AT.1	0.005128
S	494	S494P	Tca	Cca	1	1	AY.10	0.00053
S	494	S494P	Tca	Cca	1	1	AY.104	0.001984
S	494	S494P	Tca	Cca	1	1	AY.12	0.000316
S	494	S494P	Tca	Cca	1	1	AY.120	0.000037
S	494	S494P	Tca	Cca	1	1	AY.120.1	0.000321
S	494	S494P	Tca	Cca	1	1	AY.13	0.000161
S	494	S494P	Tca	Cca	1	1	AY.16.1	0.00047
S	494	S494P	Tca	Cca	1	1	AY.2	0.000356
S	494	S494P	Tca	Cca	1	1	AY.24	0.000431
S	494	S494P	Tca	Cca	1	1	AY.29.1	0.000221
S	494	S494P	Tca	Cca	1	1	AY.46	0.000104
S	494	S494P	Tca	Cca	1	1	AY.48	0.000465
S	494	S494P	Tca	Cca	1	1	AY.59	0.00053
S	494	S494P	Tca	Cca	1	1	AY.68	0.000274
S	494	S494P	Tca	Cca	1	1	AY.91	0.00073
S	494	S494P	Tca	Cca	1	1	AY.99	0.001049
S	494	S494P	Tca	Cca	1	1	B.1.1.148	0.008772
S	494	S494P	Tca	Cca	1	1	B.1.1.161	0.003534
S	494	S494P	Tca	Cca	1	1	B.1.1.163	0.007634
S	494	S494P	Tca	Cca	1	1	B.1.1.186	0.003436
S	494	S494P	Tca	Cca	1	1	B.1.1.189	0.001513
S	494	S494P	Tca	Cca	1	1	B.1.1.196	0.005714
S	494	S494P	Tca	Cca	1	1	B.1.1.218	0.007692
S	494	S494P	Tca	Cca	1	1	B.1.1.265	0.003155
S	494	S494P	Tca	Cca	1	1	B.1.1.289	0.002083
S	494	S494P	Tca	Cca	1	1	B.1.1.301	0.001179
S	494	S494P	Tca	Cca	1	1	B.1.1.303	0.002762
S	494	S494P	Tca	Cca	1	1	B.1.1.318	0.000302
S	494	S494P	Tca	Cca	1	1	B.1.1.332	0.03125
S	494	S494P	Tca	Cca	1	1	B.1.1.337	0.003597
S	494	S494P	Tca	Cca	1	1	B.1.1.369	0.000446
S	494	S494P	Tca	Cca	1	1	B.1.1.377	0.001381
S	494	S494P	Tca	Cca	1	1	B.1.1.416	0.000905
S	494	S494P	Tca	Cca	1	1	B.1.1.429	0.004608
S	494	S494P	Tca	Cca	1	1	B.1.1.434	0.000349
S	494	S494P	Tca	Cca	1	1	B.1.1.459	0.015385
S	494	S494P	Tca	Cca	1	1	B.1.1.507	0.008696
S	494	S494P	Tca	Cca	1	1	B.1.1.513	0.012346
S	494	S494P	Tca	Cca	1	1	B.1.1.67	0.004566
S	494	S494P	Tca	Cca	1	1	B.1.1.89	0.006061
S	494	S494P	Tca	Cca	1	1	B.1.160.14	0.002119
S	494	S494P	Tca	Cca	1	1	B.1.160.16	0.000929
S	494	S494P	Tca	Cca	1	1	B.1.177.10	0.000878
S	494	S494P	Tca	Cca	1	1	B.1.177.20	0.001517
S	494	S494P	Tca	Cca	1	1	B.1.177.23	0.003236
S	494	S494P	Tca	Cca	1	1	B.1.177.4	0.000211
S	494	S494P	Tca	Cca	1	1	B.1.177.45	0.000381
S	494	S494P	Tca	Cca	1	1	B.1.177.5	0.001242
S	494	S494P	Tca	Cca	1	1	B.1.177.57	0.000281
S	494	S494P	Tca	Cca	1	1	B.1.177.86	0.000183
S	494	S494P	Tca	Cca	1	1	B.1.206	0.000816
S	494	S494P	Tca	Cca	1	1	B.1.232	0.000537
S	494	S494P	Tca	Cca	1	1	B.1.236	0.002053
S	494	S494P	Tca	Cca	1	1	B.1.240	0.000216
S	494	S494P	Tca	Cca	1	1	B.1.258.16	0.001637
S	494	S494P	Tca	Cca	1	1	B.1.305	0.002151
S	494	S494P	Tca	Cca	1	1	B.1.311	0.000275
S	494	S494P	Tca	Cca	1	1	B.1.330	0.028571
S	494	S494P	Tca	Cca	1	1	B.1.349	0.000715
S	494	S494P	Tca	Cca	1	1	B.1.356	0.001727
S	494	S494P	Tca	Cca	1	1	B.1.36.17	0.000494
S	494	S494P	Tca	Cca	1	1	B.1.36.38	0.001642
S	494	S494P	Tca	Cca	1	1	B.1.375	0.00082
S	494	S494P	Tca	Cca	1	1	B.1.393	0.028571
S	494	S494P	Tca	Cca	1	1	B.1.396	0.000706
S	494	S494P	Tca	Cca	1	1	B.1.399	0.001934
S	494	S494P	Tca	Cca	1	1	B.1.416	0.001269
S	494	S494P	Tca	Cca	1	1	B.1.438.1	0.000107
S	494	S494P	Tca	Cca	1	1	B.1.456	0.003268
S	494	S494P	Tca	Cca	1	1	B.1.466.2	0.000391
S	494	S494P	Tca	Cca	1	1	B.1.476	0.1
S	494	S494P	Tca	Cca	1	1	B.1.501	0.007353
S	494	S494P	Tca	Cca	1	1	B.1.506	0.02381
S	494	S494P	Tca	Cca	1	1	B.1.551	0.00129
S	494	S494P	Tca	Cca	1	1	B.1.554	0.004405
S	494	S494P	Tca	Cca	1	1	B.1.565	0.00081
S	494	S494P	Tca	Cca	1	1	B.1.568	0.001111
S	494	S494P	Tca	Cca	1	1	B.1.576	0.000907
S	494	S494P	Tca	Cca	1	1	B.1.577	0.000687
S	494	S494P	Tca	Cca	1	1	B.1.587	0.001898
S	494	S494P	Tca	Cca	1	1	B.1.588	0.00091
S	494	S494P	Tca	Cca	1	1	B.1.634	0.003425
S	494	S494P	Tca	Cca	1	1	B.3.1	0.001658
S	494	S494P	Tca	Cca	1	1	B.40	0.000364
S	494	S494P	Tca	Cca	1	1	B.6	0.00091
S	494	S494P	Tca	Cca	1	1	B.6.6	0.000889
S	494	S494P	Tca	Cca	1	1	C.2	0.016129
S	494	S494P	Tca	Cca	1	1	C.27	0.018519
S	494	S494P	Tca	Cca	1	1	C.33	0.058824
S	494	S494P	Tca	Cca	1	1	C.37	0.000116
S	494	S494P	Tca	Cca	1	1	C.4	0.01
S	494	S494P	Tca	Cca	1	1	C.40	0.027778
S	494	S494P	Tca	Cca	1	1	D.2	0.000075
S	494	S494P	Tca	Cca	1	1	P.1.12	0.000484
S	494	S494P	Tca	Cca	1	1	P.1.13	0.000898
S	494	S494P	Tca	Cca	1	1	P.1.16	0.000374
S	494	S494P	Tca	Cca	1	1	P.1.4	0.000977
S	494	S494P	Tca	Cca	1	1	P.1.7	0.000319
S	494	S494P	Tca	Cca	1	1	P.2	0.000187
S	494	S494P	Tca	Cca	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.