CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : Mut = A419A

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	419	A419A		syn	gcC	gcT	3011	2618	0.869479	29528-29530
N	419	A419A		syn	gcC	gcA	3011	353	0.117237	29528-29530
N	419	A419A		syn	gcC	gcG	3011	40	0.0132846	29528-29530

Details of the mutation A419A 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	419	A419A	gcC	gcT	2618	3011	All	0.000501
N	419	A419A	gcC	gcA	353	3011	All	0.000068
N	419	A419A	gcC	gcG	40	3011	All	0.000008
N	419	A419A	gcC	gcT	494	564	B.1.1.7	0.000442
N	419	A419A	gcC	gcA	48	564	B.1.1.7	0.000043
N	419	A419A	gcC	gcG	22	564	B.1.1.7	0.00002
N	419	A419A	gcC	gcT	447	447	AY.81	0.890438
N	419	A419A	gcC	gcT	398	407	AY.4	0.000619
N	419	A419A	gcC	gcA	8	407	AY.4	0.000012
N	419	A419A	gcC	gcG	1	407	AY.4	0.000002
N	419	A419A	gcC	gcA	121	199	B.1.617.2	0.000456
N	419	A419A	gcC	gcT	78	199	B.1.617.2	0.000294
N	419	A419A	gcC	gcT	89	140	AY.43	0.000394
N	419	A419A	gcC	gcA	51	140	AY.43	0.000226
N	419	A419A	gcC	gcT	90	98	AY.39	0.002224
N	419	A419A	gcC	gcA	8	98	AY.39	0.000198
N	419	A419A	gcC	gcT	71	74	AY.103	0.000441
N	419	A419A	gcC	gcA	3	74	AY.103	0.000019
N	419	A419A	gcC	gcT	56	66	AY.44	0.000341
N	419	A419A	gcC	gcA	10	66	AY.44	0.000061
N	419	A419A	gcC	gcT	59	59	B.1.551	0.076129
N	419	A419A	gcC	gcT	35	58	B.1.2	0.000308
N	419	A419A	gcC	gcA	20	58	B.1.2	0.000176
N	419	A419A	gcC	gcG	3	58	B.1.2	0.000026
N	419	A419A	gcC	gcT	46	46	AY.62	0.020044
N	419	A419A	gcC	gcT	45	46	B.1.565	0.036467
N	419	A419A	gcC	gcA	1	46	B.1.565	0.00081
N	419	A419A	gcC	gcT	44	44	AY.76	0.21256
N	419	A419A	gcC	gcT	39	41	B.1.221	0.00277
N	419	A419A	gcC	gcG	2	41	B.1.221	0.000142
N	419	A419A	gcC	gcT	17	31	B.1	0.000156
N	419	A419A	gcC	gcA	14	31	B.1	0.000128
N	419	A419A	gcC	gcT	29	29	AY.9.2	0.001065
N	419	A419A	gcC	gcT	21	21	B.1.1.361	0.954545
N	419	A419A	gcC	gcA	12	20	B.1.427	0.000606
N	419	A419A	gcC	gcT	8	20	B.1.427	0.000404
N	419	A419A	gcC	gcT	14	18	AY.25	0.000084
N	419	A419A	gcC	gcA	3	18	AY.25	0.000018
N	419	A419A	gcC	gcG	1	18	AY.25	0.000006
N	419	A419A	gcC	gcT	16	17	B.1.177	0.000211
N	419	A419A	gcC	gcG	1	17	B.1.177	0.000013
N	419	A419A	gcC	gcT	17	17	B.1.177.12	0.002579
N	419	A419A	gcC	gcT	16	17	P.1	0.000252
N	419	A419A	gcC	gcA	1	17	P.1	0.000016
N	419	A419A	gcC	gcT	16	16	B.1.160	0.000499
N	419	A419A	gcC	gcT	15	15	AY.35	0.003496
N	419	A419A	gcC	gcT	14	14	B.1.1	0.000254
N	419	A419A	gcC	gcT	13	13	AY.121	0.001759
N	419	A419A	gcC	gcT	13	13	AY.4.2	0.000282
N	419	A419A	gcC	gcT	13	13	B.1.526	0.000306
N	419	A419A	gcC	gcT	13	13	C.32	0.302326
N	419	A419A	gcC	gcT	10	11	AY.99.2	0.000922
N	419	A419A	gcC	gcA	1	11	AY.99.2	0.000092
N	419	A419A	gcC	gcT	11	11	B.1.111	0.012926
N	419	A419A	gcC	gcT	10	10	AY.113	0.001424
N	419	A419A	gcC	gcT	10	10	AY.20	0.000389
N	419	A419A	gcC	gcT	10	10	AY.93	0.002731
N	419	A419A	gcC	gcT	6	9	AY.102	0.000159
N	419	A419A	gcC	gcA	3	9	AY.102	0.00008
N	419	A419A	gcC	gcA	5	9	AY.46	0.00052
N	419	A419A	gcC	gcT	4	9	AY.46	0.000416
N	419	A419A	gcC	gcT	9	9	B.1.525	0.001018
N	419	A419A	gcC	gcT	8	8	AY.61	0.000838
N	419	A419A	gcC	gcA	4	8	B.1.596	0.000349
N	419	A419A	gcC	gcT	4	8	B.1.596	0.000349
N	419	A419A	gcC	gcT	8	8	B.1.629	0.106667
N	419	A419A	gcC	gcT	7	8	P.1.1	0.002224
N	419	A419A	gcC	gcA	1	8	P.1.1	0.000318
N	419	A419A	gcC	gcT	8	8	P.1.12	0.003872
N	419	A419A	gcC	gcT	7	7	B.1.1.222	0.001428
N	419	A419A	gcC	gcT	7	7	B.1.36	0.001021
N	419	A419A	gcC	gcT	7	7	Q.2	0.004294
N	419	A419A	gcC	gcT	7	7	Q.3	0.001015
N	419	A419A	gcC	gcT	6	6	AY.120	0.000223
N	419	A419A	gcC	gcT	5	6	AY.29	0.000079
N	419	A419A	gcC	gcA	1	6	AY.29	0.000016
N	419	A419A	gcC	gcT	5	6	AY.3	0.00005
N	419	A419A	gcC	gcA	1	6	AY.3	0.00001
N	419	A419A	gcC	gcT	6	6	AY.47	0.000187
N	419	A419A	gcC	gcA	3	6	AY.5	0.000062
N	419	A419A	gcC	gcT	3	6	AY.5	0.000062
N	419	A419A	gcC	gcT	4	6	AY.64	0.002381
N	419	A419A	gcC	gcG	2	6	AY.64	0.00119
N	419	A419A	gcC	gcT	6	6	AY.90	0.004107
N	419	A419A	gcC	gcT	6	6	B.1.439	0.035503
N	419	A419A	gcC	gcT	5	5	AY.26	0.000142
N	419	A419A	gcC	gcT	5	5	B.1.177.62	0.005959
N	419	A419A	gcC	gcT	4	5	B.1.177.81	0.000757
N	419	A419A	gcC	gcA	1	5	B.1.177.81	0.000189
N	419	A419A	gcC	gcT	5	5	B.1.351.2	0.001513
N	419	A419A	gcC	gcT	5	5	B.1.429	0.000118
N	419	A419A	gcC	gcT	5	5	B.1.528	0.238095
N	419	A419A	gcC	gcT	4	4	AY.100	0.000184
N	419	A419A	gcC	gcT	3	4	AY.117	0.000254
N	419	A419A	gcC	gcA	1	4	AY.117	0.000085
N	419	A419A	gcC	gcA	2	4	AY.27	0.000129
N	419	A419A	gcC	gcT	2	4	AY.27	0.000129
N	419	A419A	gcC	gcT	3	4	AY.45	0.000365
N	419	A419A	gcC	gcA	1	4	AY.45	0.000122
N	419	A419A	gcC	gcT	4	4	AY.88	0.003537
N	419	A419A	gcC	gcT	4	4	AY.98.1	0.000194
N	419	A419A	gcC	gcT	4	4	B.1.1.214	0.000222
N	419	A419A	gcC	gcT	4	4	B.1.1.294	0.005063
N	419	A419A	gcC	gcT	4	4	B.1.1.34	0.052632
N	419	A419A	gcC	gcT	4	4	B.1.243	0.000278
N	419	A419A	gcC	gcT	4	4	B.1.480	0.00995
N	419	A419A	gcC	gcT	4	4	B.1.617.1	0.000516
N	419	A419A	gcC	gcT	4	4	B.1.621	0.000354
N	419	A419A	gcC	gcT	3	3	A.1	0.000846
N	419	A419A	gcC	gcT	2	3	AY.42	0.00008
N	419	A419A	gcC	gcA	1	3	AY.42	0.00004
N	419	A419A	gcC	gcT	3	3	AY.46.6	0.000217
N	419	A419A	gcC	gcT	2	3	AY.51	0.001818
N	419	A419A	gcC	gcA	1	3	AY.51	0.000909
N	419	A419A	gcC	gcT	2	3	AY.69	0.000373
N	419	A419A	gcC	gcA	1	3	AY.69	0.000187
N	419	A419A	gcC	gcT	3	3	AY.75	0.000168
N	419	A419A	gcC	gcT	3	3	B.1.139	0.002199
N	419	A419A	gcC	gcT	3	3	B.1.177.86	0.00055
N	419	A419A	gcC	gcT	3	3	B.1.258.17	0.000312
N	419	A419A	gcC	gcA	2	3	B.1.36.27	0.001527
N	419	A419A	gcC	gcT	1	3	B.1.36.27	0.000763
N	419	A419A	gcC	gcT	2	3	B.1.466.2	0.000782
N	419	A419A	gcC	gcG	1	3	B.1.466.2	0.000391
N	419	A419A	gcC	gcG	3	3	B.1.577	0.002062
N	419	A419A	gcC	gcA	3	3	B.1.595	0.000783
N	419	A419A	gcC	gcT	3	3	B.1.628	0.001057
N	419	A419A	gcC	gcT	3	3	B.1.9.5	0.017045
N	419	A419A	gcC	gcT	3	3	C.16	0.003181
N	419	A419A	gcC	gcT	2	3	C.37	0.000232
N	419	A419A	gcC	gcA	1	3	C.37	0.000116
N	419	A419A	gcC	gcT	2	3	P.1.14	0.000096
N	419	A419A	gcC	gcA	1	3	P.1.14	0.000048
N	419	A419A	gcC	gcT	1	2	A	0.000387
N	419	A419A	gcC	gcA	1	2	A	0.000387
N	419	A419A	gcC	gcT	2	2	AH.3	0.007605
N	419	A419A	gcC	gcT	2	2	AY.104	0.003968
N	419	A419A	gcC	gcT	2	2	AY.105	0.001286
N	419	A419A	gcC	gcT	2	2	AY.108	0.002205
N	419	A419A	gcC	gcT	2	2	AY.16	0.000759
N	419	A419A	gcC	gcT	2	2	AY.2	0.000712
N	419	A419A	gcC	gcT	2	2	AY.23	0.000139
N	419	A419A	gcC	gcT	2	2	AY.33	0.000134
N	419	A419A	gcC	gcA	2	2	AY.36	0.000296
N	419	A419A	gcC	gcA	1	2	AY.38	0.000499
N	419	A419A	gcC	gcT	1	2	AY.38	0.000499
N	419	A419A	gcC	gcA	1	2	AY.5.3	0.000337
N	419	A419A	gcC	gcT	1	2	AY.5.3	0.000337
N	419	A419A	gcC	gcG	2	2	B.1.1.141	0.004024
N	419	A419A	gcC	gcT	2	2	B.1.1.253	0.005013
N	419	A419A	gcC	gcT	2	2	B.1.1.33	0.000842
N	419	A419A	gcC	gcT	2	2	B.1.1.519	0.000079
N	419	A419A	gcC	gcT	2	2	B.1.110.3	0.001437
N	419	A419A	gcC	gcA	2	2	B.1.131	0.017544
N	419	A419A	gcC	gcT	2	2	B.1.160.30	0.005952
N	419	A419A	gcC	gcT	2	2	B.1.177.82	0.000955
N	419	A419A	gcC	gcA	1	2	B.1.234	0.000132
N	419	A419A	gcC	gcT	1	2	B.1.234	0.000132
N	419	A419A	gcC	gcT	2	2	B.1.258	0.000133
N	419	A419A	gcC	gcT	2	2	B.1.36.29	0.001035
N	419	A419A	gcC	gcA	2	2	B.1.605	0.011905
N	419	A419A	gcC	gcT	2	2	C.14	0.008658
N	419	A419A	gcC	gcG	1	2	P.2	0.000187
N	419	A419A	gcC	gcA	1	2	P.2	0.000187
N	419	A419A	gcC	gcT	2	2	Q.1	0.000253
N	419	A419A	gcC	gcT	1	1	A.2.5.1	0.004808
N	419	A419A	gcC	gcT	1	1	AD.2	0.000219
N	419	A419A	gcC	gcT	1	1	AN.1	0.02
N	419	A419A	gcC	gcT	1	1	AY.1	0.000396
N	419	A419A	gcC	gcT	1	1	AY.101	0.00049
N	419	A419A	gcC	gcT	1	1	AY.106	0.000335
N	419	A419A	gcC	gcT	1	1	AY.111	0.000183
N	419	A419A	gcC	gcT	1	1	AY.114	0.000231
N	419	A419A	gcC	gcT	1	1	AY.116	0.000287
N	419	A419A	gcC	gcT	1	1	AY.116.1	0.000311
N	419	A419A	gcC	gcT	1	1	AY.118	0.000063
N	419	A419A	gcC	gcT	1	1	AY.119	0.000035
N	419	A419A	gcC	gcT	1	1	AY.120.1	0.000321
N	419	A419A	gcC	gcT	1	1	AY.24	0.000431
N	419	A419A	gcC	gcA	1	1	AY.29.1	0.000221
N	419	A419A	gcC	gcT	1	1	AY.30	0.000396
N	419	A419A	gcC	gcT	1	1	AY.39.1	0.00004
N	419	A419A	gcC	gcA	1	1	AY.4.2.1	0.000149
N	419	A419A	gcC	gcT	1	1	AY.4.5	0.000107
N	419	A419A	gcC	gcT	1	1	AY.46.2	0.000635
N	419	A419A	gcC	gcT	1	1	AY.48	0.000465
N	419	A419A	gcC	gcA	1	1	AY.7	0.000196
N	419	A419A	gcC	gcT	1	1	AY.74	0.000116
N	419	A419A	gcC	gcA	1	1	AY.91	0.00073
N	419	A419A	gcC	gcT	1	1	B	0.000128
N	419	A419A	gcC	gcT	1	1	B.1.1.144	0.028571
N	419	A419A	gcC	gcT	1	1	B.1.1.164	0.005155
N	419	A419A	gcC	gcA	1	1	B.1.1.202	0.076923
N	419	A419A	gcC	gcT	1	1	B.1.1.216	0.00089
N	419	A419A	gcC	gcT	1	1	B.1.1.273	0.006757
N	419	A419A	gcC	gcT	1	1	B.1.1.277	0.000759
N	419	A419A	gcC	gcT	1	1	B.1.1.306	0.000438
N	419	A419A	gcC	gcT	1	1	B.1.1.318	0.000302
N	419	A419A	gcC	gcT	1	1	B.1.1.326	0.001761
N	419	A419A	gcC	gcT	1	1	B.1.1.37	0.000193
N	419	A419A	gcC	gcT	1	1	B.1.1.413	0.006897
N	419	A419A	gcC	gcT	1	1	B.1.1.433	0.001425
N	419	A419A	gcC	gcT	1	1	B.1.1.485	0.016667
N	419	A419A	gcC	gcA	1	1	B.1.1.50	0.000679
N	419	A419A	gcC	gcT	1	1	B.1.1.523	0.001563
N	419	A419A	gcC	gcT	1	1	B.1.1.63	0.000386
N	419	A419A	gcC	gcG	1	1	B.1.1.70	0.000341
N	419	A419A	gcC	gcT	1	1	B.1.177.50	0.004695
N	419	A419A	gcC	gcT	1	1	B.1.177.56	0.000668
N	419	A419A	gcC	gcT	1	1	B.1.177.63	0.002703
N	419	A419A	gcC	gcT	1	1	B.1.177.73	0.000566
N	419	A419A	gcC	gcT	1	1	B.1.177.9	0.001332
N	419	A419A	gcC	gcT	1	1	B.1.222	0.001692
N	419	A419A	gcC	gcA	1	1	B.1.235	0.002519
N	419	A419A	gcC	gcT	1	1	B.1.349	0.000715
N	419	A419A	gcC	gcT	1	1	B.1.351	0.00003
N	419	A419A	gcC	gcT	1	1	B.1.36.1	0.00114
N	419	A419A	gcC	gcT	1	1	B.1.36.36	0.000602
N	419	A419A	gcC	gcT	1	1	B.1.399	0.001934
N	419	A419A	gcC	gcT	1	1	B.1.426	0.001009
N	419	A419A	gcC	gcT	1	1	B.1.438.1	0.000107
N	419	A419A	gcC	gcT	1	1	B.1.499.1	0.111111
N	419	A419A	gcC	gcA	1	1	B.1.509	0.000866
N	419	A419A	gcC	gcT	1	1	B.1.517	0.000427
N	419	A419A	gcC	gcT	1	1	B.1.527	0.003704
N	419	A419A	gcC	gcT	1	1	B.1.561	0.000397
N	419	A419A	gcC	gcT	1	1	B.1.564	0.000426
N	419	A419A	gcC	gcT	1	1	B.1.595.4	0.007299
N	419	A419A	gcC	gcT	1	1	B.1.609	0.000479
N	419	A419A	gcC	gcT	1	1	B.1.619	0.000871
N	419	A419A	gcC	gcT	1	1	B.23	0.002924
N	419	A419A	gcC	gcT	1	1	B.6	0.00091
N	419	A419A	gcC	gcT	1	1	C.36	0.000911
N	419	A419A	gcC	gcT	1	1	P.1.13	0.000898
N	419	A419A	gcC	gcT	1	1	Q.4	0.000455

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.