CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : Mut = A1557A

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
ORF1ab/nsp3	1557	A1557A	A2375A	syn	gcC	gcT	3611	3491	0.966768	7388-7390
ORF1ab/nsp3	1557	A1557A	A2375A	syn	gcC	gcA	3611	108	0.0299086	7388-7390
ORF1ab/nsp3	1557	A1557A	A2375A	syn	gcC	gcG	3611	12	0.00332318	7388-7390

Details of the mutation A1557A 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
ORF1ab/nsp3	1557	A1557A	gcC	gcT	3491	3611	All	0.000668
ORF1ab/nsp3	1557	A1557A	gcC	gcA	108	3611	All	0.000021
ORF1ab/nsp3	1557	A1557A	gcC	gcG	12	3611	All	0.000002
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1181	1195	B.1.1.7	0.001057
ORF1ab/nsp3	1557	A1557A	gcC	gcA	9	1195	B.1.1.7	0.000008
ORF1ab/nsp3	1557	A1557A	gcC	gcG	5	1195	B.1.1.7	0.000004
ORF1ab/nsp3	1557	A1557A	gcC	gcT	316	345	AY.4	0.000492
ORF1ab/nsp3	1557	A1557A	gcC	gcA	29	345	AY.4	0.000045
ORF1ab/nsp3	1557	A1557A	gcC	gcT	262	262	AY.6	0.010776
ORF1ab/nsp3	1557	A1557A	gcC	gcT	237	237	B.1.221.4	0.9875
ORF1ab/nsp3	1557	A1557A	gcC	gcT	217	223	B.1.617.2	0.000817
ORF1ab/nsp3	1557	A1557A	gcC	gcA	6	223	B.1.617.2	0.000023
ORF1ab/nsp3	1557	A1557A	gcC	gcT	144	144	AY.38	0.071892
ORF1ab/nsp3	1557	A1557A	gcC	gcT	138	138	B.1.221	0.009803
ORF1ab/nsp3	1557	A1557A	gcC	gcT	65	65	AY.29	0.001025
ORF1ab/nsp3	1557	A1557A	gcC	gcT	63	63	B.1.1.333	0.067815
ORF1ab/nsp3	1557	A1557A	gcC	gcT	58	58	AY.43	0.000257
ORF1ab/nsp3	1557	A1557A	gcC	gcT	51	51	AY.103	0.000317
ORF1ab/nsp3	1557	A1557A	gcC	gcT	49	49	B.1.429	0.001153
ORF1ab/nsp3	1557	A1557A	gcC	gcT	46	46	AY.9.2	0.00169
ORF1ab/nsp3	1557	A1557A	gcC	gcT	37	40	B.1.2	0.000326
ORF1ab/nsp3	1557	A1557A	gcC	gcA	3	40	B.1.2	0.000026
ORF1ab/nsp3	1557	A1557A	gcC	gcT	31	39	AY.44	0.000189
ORF1ab/nsp3	1557	A1557A	gcC	gcA	8	39	AY.44	0.000049
ORF1ab/nsp3	1557	A1557A	gcC	gcT	38	38	B.1.177	0.0005
ORF1ab/nsp3	1557	A1557A	gcC	gcT	34	35	B.1	0.000311
ORF1ab/nsp3	1557	A1557A	gcC	gcA	1	35	B.1	0.000009
ORF1ab/nsp3	1557	A1557A	gcC	gcT	29	29	B.1.160	0.000904
ORF1ab/nsp3	1557	A1557A	gcC	gcT	22	25	AY.25	0.000132
ORF1ab/nsp3	1557	A1557A	gcC	gcA	3	25	AY.25	0.000018
ORF1ab/nsp3	1557	A1557A	gcC	gcT	21	21	B.1.177.21	0.001606
ORF1ab/nsp3	1557	A1557A	gcC	gcT	18	18	B.1.1.205	0.066914
ORF1ab/nsp3	1557	A1557A	gcC	gcT	17	17	AY.39	0.00042
ORF1ab/nsp3	1557	A1557A	gcC	gcT	17	17	B.1.1.326	0.02993
ORF1ab/nsp3	1557	A1557A	gcC	gcT	16	16	D.2	0.001201
ORF1ab/nsp3	1557	A1557A	gcC	gcT	13	16	P.1	0.000205
ORF1ab/nsp3	1557	A1557A	gcC	gcA	3	16	P.1	0.000047
ORF1ab/nsp3	1557	A1557A	gcC	gcA	14	14	B.1.421	0.104478
ORF1ab/nsp3	1557	A1557A	gcC	gcT	13	13	AY.26	0.000368
ORF1ab/nsp3	1557	A1557A	gcC	gcT	10	12	AY.3	0.000099
ORF1ab/nsp3	1557	A1557A	gcC	gcA	2	12	AY.3	0.00002
ORF1ab/nsp3	1557	A1557A	gcC	gcT	12	12	B.1.466.2	0.004695
ORF1ab/nsp3	1557	A1557A	gcC	gcT	10	10	AY.102	0.000265
ORF1ab/nsp3	1557	A1557A	gcC	gcT	9	10	AY.47	0.00028
ORF1ab/nsp3	1557	A1557A	gcC	gcA	1	10	AY.47	0.000031
ORF1ab/nsp3	1557	A1557A	gcC	gcT	10	10	B.1.263	0.47619
ORF1ab/nsp3	1557	A1557A	gcC	gcT	9	9	AY.98.1	0.000436
ORF1ab/nsp3	1557	A1557A	gcC	gcT	9	9	B.1.36.36	0.005418
ORF1ab/nsp3	1557	A1557A	gcC	gcT	8	8	AY.23	0.000558
ORF1ab/nsp3	1557	A1557A	gcC	gcT	7	8	B.1.1	0.000127
ORF1ab/nsp3	1557	A1557A	gcC	gcA	1	8	B.1.1	0.000018
ORF1ab/nsp3	1557	A1557A	gcC	gcT	7	8	B.1.621	0.00062
ORF1ab/nsp3	1557	A1557A	gcC	gcA	1	8	B.1.621	0.000089
ORF1ab/nsp3	1557	A1557A	gcC	gcT	7	8	B.40	0.00255
ORF1ab/nsp3	1557	A1557A	gcC	gcG	1	8	B.40	0.000364
ORF1ab/nsp3	1557	A1557A	gcC	gcA	6	7	AY.91	0.004383
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	7	AY.91	0.00073
ORF1ab/nsp3	1557	A1557A	gcC	gcT	7	7	B	0.000895
ORF1ab/nsp3	1557	A1557A	gcC	gcG	4	7	B.1.525	0.000453
ORF1ab/nsp3	1557	A1557A	gcC	gcA	2	7	B.1.525	0.000226
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	7	B.1.525	0.000113
ORF1ab/nsp3	1557	A1557A	gcC	gcT	7	7	B.1.596	0.00061
ORF1ab/nsp3	1557	A1557A	gcC	gcT	7	7	R.1	0.00063
ORF1ab/nsp3	1557	A1557A	gcC	gcT	6	6	AY.100	0.000276
ORF1ab/nsp3	1557	A1557A	gcC	gcT	6	6	AY.20	0.000233
ORF1ab/nsp3	1557	A1557A	gcC	gcT	5	6	AY.46	0.00052
ORF1ab/nsp3	1557	A1557A	gcC	gcA	1	6	AY.46	0.000104
ORF1ab/nsp3	1557	A1557A	gcC	gcT	6	6	AY.5	0.000124
ORF1ab/nsp3	1557	A1557A	gcC	gcT	6	6	AY.54	0.000572
ORF1ab/nsp3	1557	A1557A	gcC	gcT	6	6	AY.9	0.000406
ORF1ab/nsp3	1557	A1557A	gcC	gcT	6	6	B.1.1.28	0.001867
ORF1ab/nsp3	1557	A1557A	gcC	gcT	6	6	B.1.351	0.000178
ORF1ab/nsp3	1557	A1557A	gcC	gcT	6	6	B.1.509	0.005195
ORF1ab/nsp3	1557	A1557A	gcC	gcT	6	6	B.1.639	0.130435
ORF1ab/nsp3	1557	A1557A	gcC	gcT	5	5	AY.119	0.000177
ORF1ab/nsp3	1557	A1557A	gcC	gcT	5	5	AY.34	0.000485
ORF1ab/nsp3	1557	A1557A	gcC	gcT	5	5	AY.75	0.00028
ORF1ab/nsp3	1557	A1557A	gcC	gcA	5	5	B.1.177.73	0.002831
ORF1ab/nsp3	1557	A1557A	gcC	gcT	5	5	B.1.526	0.000118
ORF1ab/nsp3	1557	A1557A	gcC	gcT	5	5	Q.8	0.000825
ORF1ab/nsp3	1557	A1557A	gcC	gcT	4	4		0.222222
ORF1ab/nsp3	1557	A1557A	gcC	gcT	4	4	AY.3.1	0.000341
ORF1ab/nsp3	1557	A1557A	gcC	gcT	4	4	AY.30	0.001583
ORF1ab/nsp3	1557	A1557A	gcC	gcT	4	4	AY.33	0.000267
ORF1ab/nsp3	1557	A1557A	gcC	gcT	4	4	AY.93	0.001092
ORF1ab/nsp3	1557	A1557A	gcC	gcT	4	4	AY.99.2	0.000369
ORF1ab/nsp3	1557	A1557A	gcC	gcT	4	4	B.1.540	0.038835
ORF1ab/nsp3	1557	A1557A	gcC	gcT	3	3	AY.120	0.000112
ORF1ab/nsp3	1557	A1557A	gcC	gcT	3	3	AY.4.2	0.000065
ORF1ab/nsp3	1557	A1557A	gcC	gcT	3	3	AY.45	0.000365
ORF1ab/nsp3	1557	A1557A	gcC	gcT	3	3	AY.7.2	0.001678
ORF1ab/nsp3	1557	A1557A	gcC	gcT	2	3	AY.75.1	0.000361
ORF1ab/nsp3	1557	A1557A	gcC	gcA	1	3	AY.75.1	0.00018
ORF1ab/nsp3	1557	A1557A	gcC	gcT	3	3	B.1.258	0.0002
ORF1ab/nsp3	1557	A1557A	gcC	gcT	3	3	B.1.36.29	0.001552
ORF1ab/nsp3	1557	A1557A	gcC	gcT	3	3	B.1.478	0.035294
ORF1ab/nsp3	1557	A1557A	gcC	gcT	3	3	B.1.543	0.03
ORF1ab/nsp3	1557	A1557A	gcC	gcT	3	3	B.1.568	0.003333
ORF1ab/nsp3	1557	A1557A	gcC	gcT	3	3	B.1.575	0.00091
ORF1ab/nsp3	1557	A1557A	gcC	gcA	1	2	AY.35	0.000233
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	2	AY.35	0.000233
ORF1ab/nsp3	1557	A1557A	gcC	gcT	2	2	AY.36	0.000296
ORF1ab/nsp3	1557	A1557A	gcC	gcT	2	2	AY.39.1	0.000079
ORF1ab/nsp3	1557	A1557A	gcC	gcT	2	2	AY.5.3	0.000675
ORF1ab/nsp3	1557	A1557A	gcC	gcT	2	2	AY.92	0.000575
ORF1ab/nsp3	1557	A1557A	gcC	gcT	2	2	AY.99	0.002099
ORF1ab/nsp3	1557	A1557A	gcC	gcG	1	2	B.1.1.519	0.00004
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	2	B.1.1.519	0.00004
ORF1ab/nsp3	1557	A1557A	gcC	gcA	2	2	B.1.111	0.00235
ORF1ab/nsp3	1557	A1557A	gcC	gcT	2	2	B.1.177.46	0.001837
ORF1ab/nsp3	1557	A1557A	gcC	gcT	2	2	B.1.177.82	0.000955
ORF1ab/nsp3	1557	A1557A	gcC	gcA	2	2	B.1.243	0.000139
ORF1ab/nsp3	1557	A1557A	gcC	gcT	2	2	B.1.36.38	0.003284
ORF1ab/nsp3	1557	A1557A	gcC	gcT	2	2	B.1.396	0.001411
ORF1ab/nsp3	1557	A1557A	gcC	gcT	2	2	B.1.560	0.009259
ORF1ab/nsp3	1557	A1557A	gcC	gcT	2	2	B.1.582	0.000981
ORF1ab/nsp3	1557	A1557A	gcC	gcT	2	2	B.1.614	0.25
ORF1ab/nsp3	1557	A1557A	gcC	gcT	2	2	B.6.6	0.001778
ORF1ab/nsp3	1557	A1557A	gcC	gcT	2	2	P.1.16	0.000748
ORF1ab/nsp3	1557	A1557A	gcC	gcT	2	2	Q.1	0.000253
ORF1ab/nsp3	1557	A1557A	gcC	gcA	1	1	A.3	0.002096
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AP.1	0.001502
ORF1ab/nsp3	1557	A1557A	gcC	gcA	1	1	AY.1	0.000396
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.101	0.00049
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.105	0.000643
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.107	0.000466
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.108	0.001103
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.110	0.000113
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.114	0.000231
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.116	0.000287
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.117	0.000085
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.118	0.000063
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.12	0.000316
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.121	0.000135
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.27	0.000065
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.28	0.00189
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.29.1	0.000221
ORF1ab/nsp3	1557	A1557A	gcC	gcA	1	1	AY.4.5	0.000107
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.42	0.00004
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.46.4	0.000165
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.51	0.000909
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.55	0.000917
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.58	0.000907
ORF1ab/nsp3	1557	A1557A	gcC	gcA	1	1	AY.59	0.00053
ORF1ab/nsp3	1557	A1557A	gcC	gcA	1	1	AY.61	0.000105
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.69	0.000187
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.74	0.000116
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.77	0.001127
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.85	0.000427
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.87	0.000833
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.94	0.000443
ORF1ab/nsp3	1557	A1557A	gcC	gcA	1	1	AY.98	0.000079
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	AY.99.1	0.001553
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.1.1	0.000327
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.1.170	0.001247
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.1.186	0.003436
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.1.231	0.003096
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.1.25	0.000569
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.1.263	0.001558
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.1.294	0.001266
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.1.346	0.029412
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.1.397	0.002252
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.1.485	0.016667
ORF1ab/nsp3	1557	A1557A	gcC	gcA	1	1	B.1.1.51	0.001718
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.139	0.000733
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.177.26	0.006993
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.177.4	0.000211
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.177.43	0.001477
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.177.81	0.000189
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.234	0.000132
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.258.3	0.001675
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.311	0.000275
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.349	0.000715
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.36	0.000146
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.362	0.001541
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.390	0.010638
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.416	0.001269
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.416.1	0.001563
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.427	0.00005
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.468	0.005714
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.537	0.02
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.595	0.000261
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.610	0.003546
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.623	0.000536
ORF1ab/nsp3	1557	A1557A	gcC	gcG	1	1	B.1.636	0.006711
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	B.1.637	0.000073
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	C.36.3	0.000567
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	C.4	0.01
ORF1ab/nsp3	1557	A1557A	gcC	gcT	1	1	P.1.15	0.000232

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.