CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : Mut = R40C

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	40	R40C		nonsyn	Cgt	Tgt	1936	1936	1	28391-28393

Details of the mutation R40C 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	40	R40C	Cgt	Tgt	1936	1936	All	0.00037
N	40	R40C	Cgt	Tgt	531	531	B.1.1.7	0.000475
N	40	R40C	Cgt	Tgt	201	201	S.1	0.99505
N	40	R40C	Cgt	Tgt	176	176	B.1.1.217	0.64
N	40	R40C	Cgt	Tgt	136	136	AY.3	0.001353
N	40	R40C	Cgt	Tgt	118	118	AY.4	0.000184
N	40	R40C	Cgt	Tgt	52	52	B.1.617.2	0.000196
N	40	R40C	Cgt	Tgt	36	36	B.1	0.00033
N	40	R40C	Cgt	Tgt	30	30	C.36.3	0.017016
N	40	R40C	Cgt	Tgt	28	28	R.1	0.00252
N	40	R40C	Cgt	Tgt	23	23	AY.103	0.000143
N	40	R40C	Cgt	Tgt	23	23	AY.44	0.00014
N	40	R40C	Cgt	Tgt	23	23	B.1.526	0.000541
N	40	R40C	Cgt	Tgt	22	22	AY.43	0.000097
N	40	R40C	Cgt	Tgt	22	22	B.1.1	0.000399
N	40	R40C	Cgt	Tgt	22	22	C.37	0.002553
N	40	R40C	Cgt	Tgt	19	19	AY.26	0.000538
N	40	R40C	Cgt	Tgt	16	16	AY.25	0.000096
N	40	R40C	Cgt	Tgt	16	16	AY.46.6	0.001155
N	40	R40C	Cgt	Tgt	13	13	B.1.160	0.000405
N	40	R40C	Cgt	Tgt	13	13	B.1.2	0.000114
N	40	R40C	Cgt	Tgt	13	13	P.1	0.000205
N	40	R40C	Cgt	Tgt	12	12	AY.34	0.001164
N	40	R40C	Cgt	Tgt	11	11	AY.119	0.000388
N	40	R40C	Cgt	Tgt	11	11	AY.64	0.006548
N	40	R40C	Cgt	Tgt	11	11	B.1.1.311	0.00394
N	40	R40C	Cgt	Tgt	10	10	P.1.14	0.000478
N	40	R40C	Cgt	Tgt	9	9	AY.1	0.003562
N	40	R40C	Cgt	Tgt	9	9	AY.113	0.001282
N	40	R40C	Cgt	Tgt	9	9	AY.61	0.000943
N	40	R40C	Cgt	Tgt	8	8	B.1.1.50	0.005431
N	40	R40C	Cgt	Tgt	8	8	B.1.177.46	0.007346
N	40	R40C	Cgt	Tgt	8	8	B.1.427	0.000404
N	40	R40C	Cgt	Tgt	7	7	AY.47	0.000218
N	40	R40C	Cgt	Tgt	7	7	AY.5	0.000145
N	40	R40C	Cgt	Tgt	7	7	B	0.000895
N	40	R40C	Cgt	Tgt	7	7	B.1.1.519	0.000278
N	40	R40C	Cgt	Tgt	7	7	B.1.177	0.000092
N	40	R40C	Cgt	Tgt	6	6	AY.46	0.000624
N	40	R40C	Cgt	Tgt	6	6	B.1.1.10	0.006689
N	40	R40C	Cgt	Tgt	5	5	AY.3.1	0.000426
N	40	R40C	Cgt	Tgt	5	5	AY.7.1	0.000564
N	40	R40C	Cgt	Tgt	5	5	AY.74	0.000578
N	40	R40C	Cgt	Tgt	5	5	B.1.1.329	0.019231
N	40	R40C	Cgt	Tgt	5	5	B.1.1.70	0.001705
N	40	R40C	Cgt	Tgt	5	5	B.1.147	0.003779
N	40	R40C	Cgt	Tgt	5	5	B.1.177.7	0.000824
N	40	R40C	Cgt	Tgt	5	5	B.1.234	0.00066
N	40	R40C	Cgt	Tgt	5	5	B.1.258	0.000333
N	40	R40C	Cgt	Tgt	5	5	B.1.621	0.000443
N	40	R40C	Cgt	Tgt	5	5	N.5	0.008834
N	40	R40C	Cgt	Tgt	4	4	AY.120	0.000149
N	40	R40C	Cgt	Tgt	4	4	AY.39	0.000099
N	40	R40C	Cgt	Tgt	4	4	AY.54	0.000381
N	40	R40C	Cgt	Tgt	4	4	AY.6	0.000165
N	40	R40C	Cgt	Tgt	4	4	AY.75	0.000224
N	40	R40C	Cgt	Tgt	4	4	B.1.1.1	0.001307
N	40	R40C	Cgt	Tgt	4	4	B.1.1.157	0.003653
N	40	R40C	Cgt	Tgt	4	4	B.1.22	0.00527
N	40	R40C	Cgt	Tgt	3	3	AY.102	0.00008
N	40	R40C	Cgt	Tgt	3	3	AY.33	0.0002
N	40	R40C	Cgt	Tgt	3	3	AY.46.4	0.000494
N	40	R40C	Cgt	Tgt	3	3	AY.98.1	0.000145
N	40	R40C	Cgt	Tgt	3	3	B.1.1.141	0.006036
N	40	R40C	Cgt	Tgt	3	3	B.1.1.433	0.004274
N	40	R40C	Cgt	Tgt	3	3	B.1.36.35	0.007812
N	40	R40C	Cgt	Tgt	3	3	B.1.429	0.000071
N	40	R40C	Cgt	Tgt	3	3	B.1.582	0.001472
N	40	R40C	Cgt	Tgt	3	3	B.1.617.1	0.000387
N	40	R40C	Cgt	Tgt	3	3	B.6	0.00273
N	40	R40C	Cgt	Tgt	2	2	A.1	0.000564
N	40	R40C	Cgt	Tgt	2	2	AY.107	0.000932
N	40	R40C	Cgt	Tgt	2	2	AY.118	0.000125
N	40	R40C	Cgt	Tgt	2	2	AY.16	0.000759
N	40	R40C	Cgt	Tgt	2	2	AY.29	0.000032
N	40	R40C	Cgt	Tgt	2	2	AY.30	0.000791
N	40	R40C	Cgt	Tgt	2	2	AY.4.2	0.000043
N	40	R40C	Cgt	Tgt	2	2	AY.4.5	0.000215
N	40	R40C	Cgt	Tgt	2	2	AY.57	0.001312
N	40	R40C	Cgt	Tgt	2	2	AY.59	0.001059
N	40	R40C	Cgt	Tgt	2	2	AY.91	0.001461
N	40	R40C	Cgt	Tgt	2	2	AY.92	0.000575
N	40	R40C	Cgt	Tgt	2	2	B.1.1.261	0.017241
N	40	R40C	Cgt	Tgt	2	2	B.1.1.28	0.000622
N	40	R40C	Cgt	Tgt	2	2	B.1.1.337	0.007194
N	40	R40C	Cgt	Tgt	2	2	B.1.1.39	0.001019
N	40	R40C	Cgt	Tgt	2	2	B.1.1.449	0.045455
N	40	R40C	Cgt	Tgt	2	2	B.1.221	0.000142
N	40	R40C	Cgt	Tgt	2	2	B.1.243	0.000139
N	40	R40C	Cgt	Tgt	2	2	B.1.306	0.011429
N	40	R40C	Cgt	Tgt	2	2	B.1.344	0.016393
N	40	R40C	Cgt	Tgt	2	2	B.1.36	0.000292
N	40	R40C	Cgt	Tgt	2	2	B.1.369	0.00057
N	40	R40C	Cgt	Tgt	2	2	B.1.595	0.000522
N	40	R40C	Cgt	Tgt	2	2	B.1.596	0.000174
N	40	R40C	Cgt	Tgt	2	2	P.1.15	0.000465
N	40	R40C	Cgt	Tgt	2	2	Q.1	0.000253
N	40	R40C	Cgt	Tgt	1	1	A.5	0.001923
N	40	R40C	Cgt	Tgt	1	1	AD.2	0.000219
N	40	R40C	Cgt	Tgt	1	1	AE.8	0.000489
N	40	R40C	Cgt	Tgt	1	1	AM.4	0.003571
N	40	R40C	Cgt	Tgt	1	1	AU.3	0.00211
N	40	R40C	Cgt	Tgt	1	1	AY.100	0.000046
N	40	R40C	Cgt	Tgt	1	1	AY.105	0.000643
N	40	R40C	Cgt	Tgt	1	1	AY.109	0.00074
N	40	R40C	Cgt	Tgt	1	1	AY.114	0.000231
N	40	R40C	Cgt	Tgt	1	1	AY.116	0.000287
N	40	R40C	Cgt	Tgt	1	1	AY.116.1	0.000311
N	40	R40C	Cgt	Tgt	1	1	AY.12	0.000316
N	40	R40C	Cgt	Tgt	1	1	AY.16.1	0.00047
N	40	R40C	Cgt	Tgt	1	1	AY.2	0.000356
N	40	R40C	Cgt	Tgt	1	1	AY.23	0.00007
N	40	R40C	Cgt	Tgt	1	1	AY.24	0.000431
N	40	R40C	Cgt	Tgt	1	1	AY.27	0.000065
N	40	R40C	Cgt	Tgt	1	1	AY.32	0.000532
N	40	R40C	Cgt	Tgt	1	1	AY.36	0.000148
N	40	R40C	Cgt	Tgt	1	1	AY.39.1	0.00004
N	40	R40C	Cgt	Tgt	1	1	AY.4.4	0.000409
N	40	R40C	Cgt	Tgt	1	1	AY.42	0.00004
N	40	R40C	Cgt	Tgt	1	1	AY.45	0.000122
N	40	R40C	Cgt	Tgt	1	1	AY.46.1	0.001027
N	40	R40C	Cgt	Tgt	1	1	AY.5.4	0.000277
N	40	R40C	Cgt	Tgt	1	1	AY.77	0.001127
N	40	R40C	Cgt	Tgt	1	1	AY.79	0.001211
N	40	R40C	Cgt	Tgt	1	1	AY.82	0.001357
N	40	R40C	Cgt	Tgt	1	1	AY.84	0.000437
N	40	R40C	Cgt	Tgt	1	1	AY.99.2	0.000092
N	40	R40C	Cgt	Tgt	1	1	B.1.1.121	0.002427
N	40	R40C	Cgt	Tgt	1	1	B.1.1.176	0.000439
N	40	R40C	Cgt	Tgt	1	1	B.1.1.214	0.000055
N	40	R40C	Cgt	Tgt	1	1	B.1.1.231	0.003096
N	40	R40C	Cgt	Tgt	1	1	B.1.1.240	0.004695
N	40	R40C	Cgt	Tgt	1	1	B.1.1.263	0.001558
N	40	R40C	Cgt	Tgt	1	1	B.1.1.275	0.011236
N	40	R40C	Cgt	Tgt	1	1	B.1.1.307	0.002532
N	40	R40C	Cgt	Tgt	1	1	B.1.1.315	0.008475
N	40	R40C	Cgt	Tgt	1	1	B.1.1.317	0.000412
N	40	R40C	Cgt	Tgt	1	1	B.1.1.318	0.000302
N	40	R40C	Cgt	Tgt	1	1	B.1.1.33	0.000421
N	40	R40C	Cgt	Tgt	1	1	B.1.1.37	0.000193
N	40	R40C	Cgt	Tgt	1	1	B.1.1.409	0.002833
N	40	R40C	Cgt	Tgt	1	1	B.1.1.434	0.000349
N	40	R40C	Cgt	Tgt	1	1	B.1.1.518	0.006329
N	40	R40C	Cgt	Tgt	1	1	B.1.1.71	0.006061
N	40	R40C	Cgt	Tgt	1	1	B.1.160.23	0.004831
N	40	R40C	Cgt	Tgt	1	1	B.1.160.24	0.004425
N	40	R40C	Cgt	Tgt	1	1	B.1.177.32	0.00135
N	40	R40C	Cgt	Tgt	1	1	B.1.177.82	0.000477
N	40	R40C	Cgt	Tgt	1	1	B.1.240	0.000216
N	40	R40C	Cgt	Tgt	1	1	B.1.268	0.010417
N	40	R40C	Cgt	Tgt	1	1	B.1.346	0.001311
N	40	R40C	Cgt	Tgt	1	1	B.1.351	0.00003
N	40	R40C	Cgt	Tgt	1	1	B.1.36.36	0.000602
N	40	R40C	Cgt	Tgt	1	1	B.1.36.38	0.001642
N	40	R40C	Cgt	Tgt	1	1	B.1.361	0.001289
N	40	R40C	Cgt	Tgt	1	1	B.1.396	0.000706
N	40	R40C	Cgt	Tgt	1	1	B.1.411	0.003704
N	40	R40C	Cgt	Tgt	1	1	B.1.438	0.006536
N	40	R40C	Cgt	Tgt	1	1	B.1.452	0.013699
N	40	R40C	Cgt	Tgt	1	1	B.1.468	0.005714
N	40	R40C	Cgt	Tgt	1	1	B.1.497	0.000315
N	40	R40C	Cgt	Tgt	1	1	B.1.525	0.000113
N	40	R40C	Cgt	Tgt	1	1	B.1.546	0.003704
N	40	R40C	Cgt	Tgt	1	1	B.1.575.1	0.002439
N	40	R40C	Cgt	Tgt	1	1	B.1.628	0.000352
N	40	R40C	Cgt	Tgt	1	1	B.1.637	0.000073
N	40	R40C	Cgt	Tgt	1	1	B.43	0.014286
N	40	R40C	Cgt	Tgt	1	1	C.36	0.000911
N	40	R40C	Cgt	Tgt	1	1	C.36.1	0.004149
N	40	R40C	Cgt	Tgt	1	1	D.2	0.000075
N	40	R40C	Cgt	Tgt	1	1	P.1.17	0.000162
N	40	R40C	Cgt	Tgt	1	1	Q.4	0.000455
N	40	R40C	Cgt	Tgt	1	1	Q.8	0.000165

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.