CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : CodonNum = 41 & Codon = cgA

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	41	R41R		syn	cgG	cgA	21185	15597	0.736228	28394-28396

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
N	41	R41R	cgG	cgA	15597	21185	All	0.002983
N	41	R41R	cgG	cgA	6454	6457	AY.121	0.873342
N	41	R41R	cgG	cgA	1862	4470	B.1.1.7	0.001667
N	41	R41R	cgG	cgA	4281	4407	B.1.617.2	0.01612
N	41	R41R	cgG	cgA	130	1244	AY.4	0.000202
N	41	R41R	cgG	cgA	277	281	B.1.525	0.031345
N	41	R41R	cgG	cgA	245	245	B.1.1.305	0.945946
N	41	R41R	cgG	cgA	205	212	AY.39	0.005066
N	41	R41R	cgG	cgA	20	164	B.1.1	0.000363
N	41	R41R	cgG	cgA	127	147	AY.75	0.007115
N	41	R41R	cgG	cgA	134	137	AY.120	0.004982
N	41	R41R	cgG	cgA	127	128	AY.105	0.081672
N	41	R41R	cgG	cgA	79	121	AY.43	0.00035
N	41	R41R	cgG	cgA	86	121	AY.44	0.000523
N	41	R41R	cgG	cgA	86	101	AY.42	0.00346
N	41	R41R	cgG	cgA	77	94	AY.102	0.002042
N	41	R41R	cgG	cgA	87	89	AY.33	0.00581
N	41	R41R	cgG	cgA	82	84	B.1.1.33	0.034512
N	41	R41R	cgG	cgA	27	77	B.1	0.000247
N	41	R41R	cgG	cgA	33	76	AY.25	0.000198
N	41	R41R	cgG	cgA	32	75	AY.103	0.000199
N	41	R41R	cgG	cgA	61	70	B.1.177	0.000803
N	41	R41R	cgG	cgA	27	70	B.1.2	0.000238
N	41	R41R	cgG	cgA	14	65	AY.46	0.001457
N	41	R41R	cgG	cgA	7	59	AY.119	0.000247
N	41	R41R	cgG	cgA	1	58	B.1.526	0.000024
N	41	R41R	cgG	cgA	45	57	P.1	0.000709
N	41	R41R	cgG	cgA	54	54	AY.98	0.004266
N	41	R41R	cgG	cgA	46	47	AY.117	0.003888
N	41	R41R	cgG	cgA	21	47	AY.4.2	0.000455
N	41	R41R	cgG	cgA	44	44	AY.69	0.008214
N	41	R41R	cgG	cgA	43	43	B.1.195	0.21608
N	41	R41R	cgG	cgA	16	42	AY.3	0.000159
N	41	R41R	cgG	cgA	27	37	AY.45	0.003285
N	41	R41R	cgG	cgA	36	36	AY.106	0.012056
N	41	R41R	cgG	cgA	35	35	AY.46.2	0.022236
N	41	R41R	cgG	cgA	10	34	AY.20	0.000389
N	41	R41R	cgG	cgA	19	30	AY.23	0.001325
N	41	R41R	cgG	cgA	26	30	AY.5	0.000537
N	41	R41R	cgG	cgA	22	23	AY.118	0.001378
N	41	R41R	cgG	cgA	22	22	AF.1	0.814815
N	41	R41R	cgG	cgA	18	22	AY.84	0.007874
N	41	R41R	cgG	cgA	19	21	AY.29	0.0003
N	41	R41R	cgG	cgA	21	21	B.1.177.57	0.005901
N	41	R41R	cgG	cgA	13	17	AY.110	0.001465
N	41	R41R	cgG	cgA	17	17	B.1.517	0.007259
N	41	R41R	cgG	cgA	16	16	AY.120.1	0.005136
N	41	R41R	cgG	cgA	15	15	AY.21	0.028463
N	41	R41R	cgG	cgA	14	15	AY.4.2.1	0.002086
N	41	R41R	cgG	cgA	14	14	AY.92	0.004022
N	41	R41R	cgG	cgA	8	14	B.1.1.519	0.000318
N	41	R41R	cgG	cgA	3	14	B.1.243	0.000209
N	41	R41R	cgG	cgA	12	13	AY.32	0.00639
N	41	R41R	cgG	cgA	12	13	AY.7	0.002352
N	41	R41R	cgG	cgA	12	12	AY.77	0.013529
N	41	R41R	cgG	cgA	9	12	AY.9.2	0.000331
N	41	R41R	cgG	cgA	11	12	AY.98.1	0.000533
N	41	R41R	cgG	cgA	12	12	B.1.177.75	0.012487
N	41	R41R	cgG	cgA	9	11	AY.100	0.000414
N	41	R41R	cgG	cgA	8	11	AY.14	0.000704
N	41	R41R	cgG	cgA	2	11	B.1.429	0.000047
N	41	R41R	cgG	cgA	9	10	AY.95	0.006849
N	41	R41R	cgG	cgA	4	10	B.1.160	0.000125
N	41	R41R	cgG	cgA	10	10	B.1.258.4	0.034483
N	41	R41R	cgG	cgA	8	9	AY.116	0.002294
N	41	R41R	cgG	cgA	9	9	AY.5.3	0.003036
N	41	R41R	cgG	cgA	1	9	B.1.621	0.000089
N	41	R41R	cgG	cgA	4	8	AY.26	0.000113
N	41	R41R	cgG	cgA	5	8	AY.36	0.000741
N	41	R41R	cgG	cgA	8	8	AY.46.4	0.001316
N	41	R41R	cgG	cgA	8	8	AY.74	0.000925
N	41	R41R	cgG	cgA	5	8	B	0.000639
N	41	R41R	cgG	cgA	8	8	B.1.637	0.000585
N	41	R41R	cgG	cgA	8	8	N.5	0.014134
N	41	R41R	cgG	cgA	6	8	P.1.17	0.000971
N	41	R41R	cgG	cgA	7	7	AY.108	0.007718
N	41	R41R	cgG	cgA	7	7	AY.41	0.002058
N	41	R41R	cgG	cgA	6	7	AY.78	0.009245
N	41	R41R	cgG	cgA	6	7	B.1.1.397	0.013514
N	41	R41R	cgG	cgA	2	7	B.1.311	0.000549
N	41	R41R	cgG	cgA	2	7	B.1.351	0.000059
N	41	R41R	cgG	cgA	7	7	B.1.466	0.162791
N	41	R41R	cgG	cgA	6	6	AY.111	0.001099
N	41	R41R	cgG	cgA	4	6	AY.27	0.000259
N	41	R41R	cgG	cgA	1	6	AY.47	0.000031
N	41	R41R	cgG	cgA	5	6	AY.93	0.001365
N	41	R41R	cgG	cgA	1	6	B.1.1.28	0.000311
N	41	R41R	cgG	cgA	2	5	AY.116.1	0.000623
N	41	R41R	cgG	cgA	4	5	AY.4.5	0.00043
N	41	R41R	cgG	cgA	5	5	AY.46.1	0.005133
N	41	R41R	cgG	cgA	1	5	AY.50	0.000799
N	41	R41R	cgG	cgA	5	5	AY.82	0.006784
N	41	R41R	cgG	cgA	5	5	AY.88	0.004421
N	41	R41R	cgG	cgA	5	5	AY.99	0.005247
N	41	R41R	cgG	cgA	4	5	P.1.15	0.000929
N	41	R41R	cgG	cgA	1	5	Q.1	0.000126
N	41	R41R	cgG	cgA	4	4	AY.104	0.007937
N	41	R41R	cgG	cgA	4	4	AY.11	0.005355
N	41	R41R	cgG	cgA	2	4	AY.114	0.000462
N	41	R41R	cgG	cgA	4	4	AY.34	0.000388
N	41	R41R	cgG	cgA	4	4	AY.40	0.003857
N	41	R41R	cgG	cgA	4	4	AY.51	0.003636
N	41	R41R	cgG	cgA	2	4	AY.52	0.001629
N	41	R41R	cgG	cgA	4	4	AY.55	0.00367
N	41	R41R	cgG	cgA	1	4	AY.59	0.00053
N	41	R41R	cgG	cgA	3	4	AY.67	0.001393
N	41	R41R	cgG	cgA	4	4	AY.86	0.00332
N	41	R41R	cgG	cgA	1	4	AY.9	0.000068
N	41	R41R	cgG	cgA	4	4	AY.91	0.002922
N	41	R41R	cgG	cgA	1	4	B.1.1.1	0.000327
N	41	R41R	cgG	cgA	1	4	B.1.1.253	0.002506
N	41	R41R	cgG	cgA	4	4	B.1.177.12	0.000607
N	41	R41R	cgG	cgA	3	4	B.1.595	0.000783
N	41	R41R	cgG	cgA	4	4	B.1.76	0.045455
N	41	R41R	cgG	cgA	1	3	AY.113	0.000142
N	41	R41R	cgG	cgA	3	3	AY.17	0.02459
N	41	R41R	cgG	cgA	2	3	AY.35	0.000466
N	41	R41R	cgG	cgA	3	3	AY.62	0.001307
N	41	R41R	cgG	cgA	2	3	AY.64	0.00119
N	41	R41R	cgG	cgA	2	3	AY.7.1	0.000225
N	41	R41R	cgG	cgA	2	3	AY.80	0.002257
N	41	R41R	cgG	cgA	3	3	AY.87	0.002498
N	41	R41R	cgG	cgA	3	3	AY.99.2	0.000276
N	41	R41R	cgG	cgA	3	3	B.1.497	0.000944
N	41	R41R	cgG	cgA	1	3	B.1.499	0.00105
N	41	R41R	cgG	cgA	3	3	P.1.4	0.00293
N	41	R41R	cgG	cgA	2	2	AE.8	0.000978
N	41	R41R	cgG	cgA	2	2	AY.34.1	0.00102
N	41	R41R	cgG	cgA	1	2	AY.46.6	0.000072
N	41	R41R	cgG	cgA	1	2	AY.54	0.000095
N	41	R41R	cgG	cgA	2	2	AY.75.1	0.000361
N	41	R41R	cgG	cgA	2	2	AY.83	0.003448
N	41	R41R	cgG	cgA	1	2	AY.96	0.002075
N	41	R41R	cgG	cgA	2	2	B.1.1.434	0.000697
N	41	R41R	cgG	cgA	1	2	B.1.258.17	0.000104
N	41	R41R	cgG	cgA	1	2	B.1.375	0.00082
N	41	R41R	cgG	cgA	1	2	P.1.14	0.000048
N	41	R41R	cgG	cgA	2	2	P.3	0.00319
N	41	R41R	cgG	cgA	1	1		0.055556
N	41	R41R	cgG	cgA	1	1	A.5	0.001923
N	41	R41R	cgG	cgA	1	1	AA.7	0.009174
N	41	R41R	cgG	cgA	1	1	AY.1	0.000396
N	41	R41R	cgG	cgA	1	1	AY.109	0.00074
N	41	R41R	cgG	cgA	1	1	AY.19	0.00114
N	41	R41R	cgG	cgA	1	1	AY.23.1	0.000417
N	41	R41R	cgG	cgA	1	1	AY.38	0.000499
N	41	R41R	cgG	cgA	1	1	AY.39.1	0.00004
N	41	R41R	cgG	cgA	1	1	AY.53	0.000288
N	41	R41R	cgG	cgA	1	1	AY.57	0.000656
N	41	R41R	cgG	cgA	1	1	AY.58	0.000907
N	41	R41R	cgG	cgA	1	1	AY.66	0.00107
N	41	R41R	cgG	cgA	1	1	AY.73	0.000665
N	41	R41R	cgG	cgA	1	1	AY.9.1	0.000084
N	41	R41R	cgG	cgA	1	1	AY.90	0.000684
N	41	R41R	cgG	cgA	1	1	AY.99.1	0.001553
N	41	R41R	cgG	cgA	1	1	B.1.1.227	0.004348
N	41	R41R	cgG	cgA	1	1	B.1.1.369	0.000446
N	41	R41R	cgG	cgA	1	1	B.1.1.526	0.003546
N	41	R41R	cgG	cgA	1	1	B.1.157	0.002985
N	41	R41R	cgG	cgA	1	1	B.1.177.4	0.000211
N	41	R41R	cgG	cgA	1	1	B.1.203	0.0625
N	41	R41R	cgG	cgA	1	1	B.1.264.1	0.047619
N	41	R41R	cgG	cgA	1	1	B.1.284	0.013158
N	41	R41R	cgG	cgA	1	1	B.1.301	0.005917
N	41	R41R	cgG	cgA	1	1	B.1.36.25	0.002208
N	41	R41R	cgG	cgA	1	1	B.1.362	0.001541
N	41	R41R	cgG	cgA	1	1	B.1.400	0.000429
N	41	R41R	cgG	cgA	1	1	B.1.428	0.00102
N	41	R41R	cgG	cgA	1	1	B.1.438.4	0.021277
N	41	R41R	cgG	cgA	1	1	B.1.466.2	0.000391
N	41	R41R	cgG	cgA	1	1	B.1.533	0.009615
N	41	R41R	cgG	cgA	1	1	B.1.561	0.000397
N	41	R41R	cgG	cgA	1	1	B.1.580	0.004065
N	41	R41R	cgG	cgA	1	1	B.3	0.000831
N	41	R41R	cgG	cgA	1	1	B.40	0.000364
N	41	R41R	cgG	cgA	1	1	C.37	0.000116
N	41	R41R	cgG	cgA	1	1	C.37.1	0.002618
N	41	R41R	cgG	cgA	1	1	N.3	0.005814
N	41	R41R	cgG	cgA	1	1	P.1.1	0.000318
N	41	R41R	cgG	cgA	1	1	P.1.6	0.001946
N	41	R41R	cgG	cgA	1	1	P.1.9	0.004808
N	41	R41R	cgG	cgA	1	1	P.2	0.000187
N	41	R41R	cgG	cgA	1	1	Q.7	0.001111
N	41	R41R	cgG	cgA	1	1	W.3	0.005263

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.