CoV-GLUE Mutation

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

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	cgT	21185	5323	0.251263	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	cgT	5323	21185	All	0.001018
N	41	R41R	cgG	cgT	2	6457	AY.121	0.000271
N	41	R41R	cgG	cgT	2586	4470	B.1.1.7	0.002315
N	41	R41R	cgG	cgT	111	4407	B.1.617.2	0.000418
N	41	R41R	cgG	cgT	1107	1244	AY.4	0.001723
N	41	R41R	cgG	cgT	4	281	B.1.525	0.000453
N	41	R41R	cgG	cgT	6	212	AY.39	0.000148
N	41	R41R	cgG	cgT	193	193	B.1.623	0.103541
N	41	R41R	cgG	cgT	143	164	B.1.1	0.002594
N	41	R41R	cgG	cgT	15	147	AY.75	0.00084
N	41	R41R	cgG	cgT	3	137	AY.120	0.000112
N	41	R41R	cgG	cgT	132	132	B.1.632	0.885906
N	41	R41R	cgG	cgT	1	128	AY.105	0.000643
N	41	R41R	cgG	cgT	40	121	AY.43	0.000177
N	41	R41R	cgG	cgT	32	121	AY.44	0.000195
N	41	R41R	cgG	cgT	15	101	AY.42	0.000603
N	41	R41R	cgG	cgT	16	94	AY.102	0.000424
N	41	R41R	cgG	cgT	1	89	AY.33	0.000067
N	41	R41R	cgG	cgT	2	84	B.1.1.33	0.000842
N	41	R41R	cgG	cgT	84	84	B.1.438.1	0.00901
N	41	R41R	cgG	cgT	45	77	B.1	0.000412
N	41	R41R	cgG	cgT	43	76	AY.25	0.000259
N	41	R41R	cgG	cgT	40	75	AY.103	0.000248
N	41	R41R	cgG	cgT	9	70	B.1.177	0.000119
N	41	R41R	cgG	cgT	21	70	B.1.2	0.000185
N	41	R41R	cgG	cgT	2	65	AY.46	0.000208
N	41	R41R	cgG	cgT	52	59	AY.119	0.001836
N	41	R41R	cgG	cgT	3	58	B.1.526	0.000071
N	41	R41R	cgG	cgT	11	57	P.1	0.000173
N	41	R41R	cgG	cgT	52	53	B.1.596	0.004531
N	41	R41R	cgG	cgT	49	51	AY.6	0.002015
N	41	R41R	cgG	cgT	1	47	AY.117	0.000085
N	41	R41R	cgG	cgT	25	47	AY.4.2	0.000542
N	41	R41R	cgG	cgT	25	42	AY.3	0.000249
N	41	R41R	cgG	cgT	3	37	AY.45	0.000365
N	41	R41R	cgG	cgT	15	34	AY.20	0.000583
N	41	R41R	cgG	cgT	32	32	B.1.93	0.029879
N	41	R41R	cgG	cgT	10	30	AY.23	0.000697
N	41	R41R	cgG	cgT	4	30	AY.5	0.000083
N	41	R41R	cgG	cgT	27	27	B.1.1.303	0.074586
N	41	R41R	cgG	cgT	25	25	C.16	0.026511
N	41	R41R	cgG	cgT	1	23	AY.118	0.000063
N	41	R41R	cgG	cgT	4	22	AY.84	0.00175
N	41	R41R	cgG	cgT	22	22	B.1.177.73	0.012458
N	41	R41R	cgG	cgT	2	21	AY.29	0.000032
N	41	R41R	cgG	cgT	20	20	B.1.1.354	0.087719
N	41	R41R	cgG	cgT	19	19	B.1.36.8	0.019
N	41	R41R	cgG	cgT	2	17	AY.110	0.000225
N	41	R41R	cgG	cgT	1	15	AY.4.2.1	0.000149
N	41	R41R	cgG	cgT	5	14	B.1.1.519	0.000199
N	41	R41R	cgG	cgT	10	14	B.1.243	0.000696
N	41	R41R	cgG	cgT	14	14	Q.8	0.002309
N	41	R41R	cgG	cgT	1	13	AY.32	0.000532
N	41	R41R	cgG	cgT	1	13	AY.7	0.000196
N	41	R41R	cgG	cgT	2	12	AY.9.2	0.000073
N	41	R41R	cgG	cgT	1	12	AY.98.1	0.000048
N	41	R41R	cgG	cgT	2	11	AY.100	0.000092
N	41	R41R	cgG	cgT	3	11	AY.14	0.000264
N	41	R41R	cgG	cgT	9	11	B.1.429	0.000212
N	41	R41R	cgG	cgT	1	10	AY.95	0.000761
N	41	R41R	cgG	cgT	1	10	B.1.160	0.000031
N	41	R41R	cgG	cgT	8	9	B.1.621	0.000708
N	41	R41R	cgG	cgT	3	8	AY.26	0.000085
N	41	R41R	cgG	cgT	3	8	AY.36	0.000445
N	41	R41R	cgG	cgT	1	8	B	0.000128
N	41	R41R	cgG	cgT	7	7	AY.4.1	0.005162
N	41	R41R	cgG	cgT	7	7	AY.68	0.001916
N	41	R41R	cgG	cgT	1	7	AY.78	0.001541
N	41	R41R	cgG	cgT	1	7	B.1.1.397	0.002252
N	41	R41R	cgG	cgT	5	7	B.1.311	0.001373
N	41	R41R	cgG	cgT	4	7	B.1.351	0.000119
N	41	R41R	cgG	cgT	2	6	AY.27	0.000129
N	41	R41R	cgG	cgT	3	6	AY.47	0.000093
N	41	R41R	cgG	cgT	1	6	AY.93	0.000273
N	41	R41R	cgG	cgT	5	6	B.1.1.28	0.001556
N	41	R41R	cgG	cgT	6	6	B.1.1.372	0.004132
N	41	R41R	cgG	cgT	1	6	B.1.221	0.000071
N	41	R41R	cgG	cgT	3	5	AY.116.1	0.000934
N	41	R41R	cgG	cgT	1	5	AY.4.5	0.000107
N	41	R41R	cgG	cgT	4	5	AY.50	0.003197
N	41	R41R	cgG	cgT	5	5	B.1.1.198	0.007342
N	41	R41R	cgG	cgT	2	5	B.1.36	0.000292
N	41	R41R	cgG	cgT	5	5	B.1.565	0.004052
N	41	R41R	cgG	cgT	1	5	P.1.15	0.000232
N	41	R41R	cgG	cgT	4	5	Q.1	0.000505
N	41	R41R	cgG	cgT	2	4	AY.114	0.000462
N	41	R41R	cgG	cgT	3	4	AY.59	0.001589
N	41	R41R	cgG	cgT	3	4	AY.9	0.000203
N	41	R41R	cgG	cgT	3	4	B.1.1.1	0.00098
N	41	R41R	cgG	cgT	3	4	B.1.1.25	0.001706
N	41	R41R	cgG	cgT	3	4	B.1.1.253	0.007519
N	41	R41R	cgG	cgT	4	4	B.1.1.306	0.001754
N	41	R41R	cgG	cgT	1	4	B.1.595	0.000261
N	41	R41R	cgG	cgT	4	4	B.1.620	0.003784
N	41	R41R	cgG	cgT	2	3	AY.113	0.000285
N	41	R41R	cgG	cgT	3	3	AY.3.1	0.000256
N	41	R41R	cgG	cgT	1	3	AY.35	0.000233
N	41	R41R	cgG	cgT	3	3	AY.61	0.000314
N	41	R41R	cgG	cgT	1	3	AY.7.1	0.000113
N	41	R41R	cgG	cgT	3	3	AY.72	0.004082
N	41	R41R	cgG	cgT	1	3	AY.80	0.001129
N	41	R41R	cgG	cgT	3	3	B.1.1.317	0.001235
N	41	R41R	cgG	cgT	3	3	B.1.1.432	0.003797
N	41	R41R	cgG	cgT	3	3	B.1.1.506	0.111111
N	41	R41R	cgG	cgT	3	3	B.1.36.18	0.001261
N	41	R41R	cgG	cgT	3	3	B.1.36.31	0.005254
N	41	R41R	cgG	cgT	3	3	B.1.411	0.011111
N	41	R41R	cgG	cgT	2	3	B.1.499	0.002101
N	41	R41R	cgG	cgT	3	3	C.36	0.002732
N	41	R41R	cgG	cgT	2	2	AY.13	0.000322
N	41	R41R	cgG	cgT	2	2	AY.24	0.000862
N	41	R41R	cgG	cgT	2	2	AY.46.5	0.000397
N	41	R41R	cgG	cgT	1	2	AY.46.6	0.000072
N	41	R41R	cgG	cgT	1	2	AY.54	0.000095
N	41	R41R	cgG	cgT	2	2	AY.63	0.000774
N	41	R41R	cgG	cgT	2	2	AY.70	0.000417
N	41	R41R	cgG	cgT	1	2	AY.96	0.002075
N	41	R41R	cgG	cgT	2	2	B.1.1.244	0.030769
N	41	R41R	cgG	cgT	2	2	B.1.1.337	0.007194
N	41	R41R	cgG	cgT	2	2	B.1.1.63	0.000772
N	41	R41R	cgG	cgT	2	2	B.1.177.16	0.001329
N	41	R41R	cgG	cgT	2	2	B.1.177.21	0.000153
N	41	R41R	cgG	cgT	1	2	B.1.177.81	0.000189
N	41	R41R	cgG	cgT	1	2	B.1.258.17	0.000104
N	41	R41R	cgG	cgT	2	2	B.1.351.2	0.000605
N	41	R41R	cgG	cgT	1	2	B.1.375	0.00082
N	41	R41R	cgG	cgT	2	2	B.1.617.1	0.000258
N	41	R41R	cgG	cgT	2	2	D.2	0.00015
N	41	R41R	cgG	cgT	2	2	P.1.2	0.002312
N	41	R41R	cgG	cgT	2	2	R.1	0.00018
N	41	R41R	cgG	cgT	1	1	AY.79	0.001211
N	41	R41R	cgG	cgT	1	1	AZ.2	0.000821
N	41	R41R	cgG	cgT	1	1	B.1.1.170	0.001247
N	41	R41R	cgG	cgT	1	1	B.1.1.210	0.005714
N	41	R41R	cgG	cgT	1	1	B.1.1.222	0.000204
N	41	R41R	cgG	cgT	1	1	B.1.1.265	0.003155
N	41	R41R	cgG	cgT	1	1	B.1.1.298	0.000862
N	41	R41R	cgG	cgT	1	1	B.1.1.409	0.002833
N	41	R41R	cgG	cgT	1	1	B.1.1.462	0.008621
N	41	R41R	cgG	cgT	1	1	B.1.1.99	0.02381
N	41	R41R	cgG	cgT	1	1	B.1.177.82	0.000477
N	41	R41R	cgG	cgT	1	1	B.1.206	0.000816
N	41	R41R	cgG	cgT	1	1	B.1.214.2	0.0006
N	41	R41R	cgG	cgT	1	1	B.1.240	0.000216
N	41	R41R	cgG	cgT	1	1	B.1.324	0.001605
N	41	R41R	cgG	cgT	1	1	B.1.36.17	0.000494
N	41	R41R	cgG	cgT	1	1	B.1.387	0.04
N	41	R41R	cgG	cgT	1	1	B.1.416	0.001269
N	41	R41R	cgG	cgT	1	1	B.1.427	0.00005
N	41	R41R	cgG	cgT	1	1	B.1.470	0.001404
N	41	R41R	cgG	cgT	1	1	B.1.509	0.000866
N	41	R41R	cgG	cgT	1	1	B.1.523	0.002451
N	41	R41R	cgG	cgT	1	1	B.1.524	0.001406
N	41	R41R	cgG	cgT	1	1	B.1.576	0.000907
N	41	R41R	cgG	cgT	1	1	B.1.578	0.017857
N	41	R41R	cgG	cgT	1	1	B.1.582	0.000491
N	41	R41R	cgG	cgT	1	1	B.1.609	0.000479
N	41	R41R	cgG	cgT	1	1	B.1.627	0.00202
N	41	R41R	cgG	cgT	1	1	C.14	0.004329
N	41	R41R	cgG	cgT	1	1	C.30	0.001727
N	41	R41R	cgG	cgT	1	1	C.39	0.018868
N	41	R41R	cgG	cgT	1	1	P.1.7	0.000319
N	41	R41R	cgG	cgT	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

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