CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : CodonNum = 6 & Codon = ccT

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	6	P6P		syn	ccC	ccT	13407	12992	0.969046	28289-28291

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	6	P6P	ccC	ccT	12992	13407	All	0.002485
N	6	P6P	ccC	ccT	6326	6378	AY.4	0.009846
N	6	P6P	ccC	ccT	1490	1491	B.1.232	0.800645
N	6	P6P	ccC	ccT	880	889	B.1.1.7	0.000788
N	6	P6P	ccC	ccT	532	532	AY.34	0.051585
N	6	P6P	ccC	ccT	225	446	AY.44	0.00137
N	6	P6P	ccC	ccT	314	330	B.1.617.2	0.001182
N	6	P6P	ccC	ccT	313	320	B.1.2	0.002756
N	6	P6P	ccC	ccT	235	235	B.1.596	0.020478
N	6	P6P	ccC	ccT	204	204	B.1.526	0.004795
N	6	P6P	ccC	ccT	163	173	AY.43	0.000722
N	6	P6P	ccC	ccT	161	161	AY.25	0.000968
N	6	P6P	ccC	ccT	136	145	P.1	0.002143
N	6	P6P	ccC	ccT	129	136	AY.103	0.000801
N	6	P6P	ccC	ccT	136	136	B.1.1.413	0.937931
N	6	P6P	ccC	ccT	113	122	B.1	0.001035
N	6	P6P	ccC	ccT	81	81	B.1.1	0.001469
N	6	P6P	ccC	ccT	74	77	AY.39	0.001829
N	6	P6P	ccC	ccT	73	73	P.2	0.013624
N	6	P6P	ccC	ccT	59	59	AY.29	0.000931
N	6	P6P	ccC	ccT	57	58	AY.5	0.001177
N	6	P6P	ccC	ccT	39	48	AY.3	0.000388
N	6	P6P	ccC	ccT	46	46	B.1.234	0.006069
N	6	P6P	ccC	ccT	40	42	B.1.177	0.000527
N	6	P6P	ccC	ccT	40	41	B.1.351	0.001189
N	6	P6P	ccC	ccT	38	38	B.1.1.353	0.791667
N	6	P6P	ccC	ccT	38	38	B.1.243	0.002644
N	6	P6P	ccC	ccT	35	35	B.1.1.37	0.00675
N	6	P6P	ccC	ccT	32	32	AY.42	0.001287
N	6	P6P	ccC	ccT	29	30	B.1.160	0.000904
N	6	P6P	ccC	ccT	29	29	AY.121	0.003924
N	6	P6P	ccC	ccT	12	29	B.1.429	0.000282
N	6	P6P	ccC	ccT	26	27	AY.102	0.000689
N	6	P6P	ccC	ccT	27	27	AY.23	0.001883
N	6	P6P	ccC	ccT	27	27	AY.79	0.032688
N	6	P6P	ccC	ccT	26	26	B.1.1.432	0.032911
N	6	P6P	ccC	ccT	24	24	P.1.14	0.001147
N	6	P6P	ccC	ccT	23	23	AY.61	0.00241
N	6	P6P	ccC	ccT	19	19	AY.100	0.000874
N	6	P6P	ccC	ccT	18	19	AY.33	0.001202
N	6	P6P	ccC	ccT	19	19	AY.6	0.000781
N	6	P6P	ccC	ccT	1	17	B.1.1.222	0.000204
N	6	P6P	ccC	ccT	17	17	B.1.1.318	0.00513
N	6	P6P	ccC	ccT	17	17	B.1.146	0.072034
N	6	P6P	ccC	ccT	16	16	AY.119	0.000565
N	6	P6P	ccC	ccT	16	16	B.1.1.176	0.00703
N	6	P6P	ccC	ccT	16	16	B.1.36.38	0.026273
N	6	P6P	ccC	ccT	16	16	C.36.3	0.009075
N	6	P6P	ccC	ccT	16	16	P.1.16	0.005986
N	6	P6P	ccC	ccT	14	15	AY.26	0.000396
N	6	P6P	ccC	ccT	15	15	AY.62	0.006536
N	6	P6P	ccC	ccT	10	14	AY.4.2	0.000217
N	6	P6P	ccC	ccT	14	14	AY.9.1	0.001172
N	6	P6P	ccC	ccT	14	14	B.1.438.1	0.001502
N	6	P6P	ccC	ccT	13	13	A.2.5	0.006487
N	6	P6P	ccC	ccT	13	13	B.1.1.301	0.01533
N	6	P6P	ccC	ccT	13	13	B.1.1.306	0.005699
N	6	P6P	ccC	ccT	12	13	B.1.177.82	0.005728
N	6	P6P	ccC	ccT	13	13	P.1.15	0.00302
N	6	P6P	ccC	ccT	12	12	AY.113	0.001709
N	6	P6P	ccC	ccT	12	12	AY.9.2	0.000441
N	6	P6P	ccC	ccT	11	12	B.1.258.17	0.001144
N	6	P6P	ccC	ccT	12	12	Q.4	0.005457
N	6	P6P	ccC	ccT	11	11	AY.59	0.005826
N	6	P6P	ccC	ccT	9	11	AY.75	0.000504
N	6	P6P	ccC	ccT	10	11	B.1.1.519	0.000397
N	6	P6P	ccC	ccT	11	11	B.1.336	0.026829
N	6	P6P	ccC	ccT	10	10	AY.14	0.00088
N	6	P6P	ccC	ccT	9	10	AY.46	0.000937
N	6	P6P	ccC	ccT	9	10	B.1.258	0.000599
N	6	P6P	ccC	ccT	9	9	B.1.621	0.000797
N	6	P6P	ccC	ccT	8	8	AY.70	0.001668
N	6	P6P	ccC	ccT	8	8	B.1.1.316	0.007401
N	6	P6P	ccC	ccT	7	7	AY.120.1	0.002247
N	6	P6P	ccC	ccT	4	7	AY.20	0.000155
N	6	P6P	ccC	ccT	7	7	AY.4.5	0.000752
N	6	P6P	ccC	ccT	7	7	AY.46.4	0.001152
N	6	P6P	ccC	ccT	7	7	AY.88	0.006189
N	6	P6P	ccC	ccT	6	6	A.21	0.01662
N	6	P6P	ccC	ccT	6	6	AY.120	0.000223
N	6	P6P	ccC	ccT	6	6	AY.39.1	0.000238
N	6	P6P	ccC	ccT	6	6	AY.4.4	0.002455
N	6	P6P	ccC	ccT	5	6	AY.47	0.000156
N	6	P6P	ccC	ccT	6	6	D.2	0.00045
N	6	P6P	ccC	ccT	5	5	AY.110	0.000563
N	6	P6P	ccC	ccT	5	5	AY.41	0.00147
N	6	P6P	ccC	ccT	5	5	B.1.1.286	0.014493
N	6	P6P	ccC	ccT	5	5	B.1.36	0.00073
N	6	P6P	ccC	ccT	5	5	B.1.398	0.014881
N	6	P6P	ccC	ccT	5	5	B.1.404	0.00651
N	6	P6P	ccC	ccT	4	5	B.1.427	0.000202
N	6	P6P	ccC	ccT	5	5	B.1.466	0.116279
N	6	P6P	ccC	ccT	5	5	Q.8	0.000825
N	6	P6P	ccC	ccT	5	5	R.1	0.00045
N	6	P6P	ccC	ccT	4	4	AY.117	0.000338
N	6	P6P	ccC	ccT	4	4	AY.120.2.1	0.001993
N	6	P6P	ccC	ccT	3	4	AY.27	0.000194
N	6	P6P	ccC	ccT	4	4	AY.3.1	0.000341
N	6	P6P	ccC	ccT	4	4	AY.45	0.000487
N	6	P6P	ccC	ccT	4	4	AY.5.4	0.001107
N	6	P6P	ccC	ccT	4	4	AY.92	0.001149
N	6	P6P	ccC	ccT	4	4	AY.93	0.001092
N	6	P6P	ccC	ccT	4	4	B.1.1.214	0.000222
N	6	P6P	ccC	ccT	4	4	B.1.400	0.001716
N	6	P6P	ccC	ccT	4	4	B.1.637	0.000292
N	6	P6P	ccC	ccT	3	3	A.2	0.001985
N	6	P6P	ccC	ccT	2	3	AY.105	0.001286
N	6	P6P	ccC	ccT	3	3	AY.106	0.001005
N	6	P6P	ccC	ccT	3	3	AY.16.1	0.00141
N	6	P6P	ccC	ccT	3	3	AY.69	0.00056
N	6	P6P	ccC	ccT	3	3	AY.84	0.001312
N	6	P6P	ccC	ccT	3	3	AY.9	0.000203
N	6	P6P	ccC	ccT	3	3	B.1.1.28	0.000934
N	6	P6P	ccC	ccT	3	3	B.1.221	0.000213
N	6	P6P	ccC	ccT	3	3	B.1.420	0.03125
N	6	P6P	ccC	ccT	2	2	AY.116	0.000574
N	6	P6P	ccC	ccT	2	2	AY.46.2	0.001271
N	6	P6P	ccC	ccT	2	2	AY.54	0.000191
N	6	P6P	ccC	ccT	2	2	AY.63	0.000774
N	6	P6P	ccC	ccT	2	2	AY.75.1	0.000361
N	6	P6P	ccC	ccT	2	2	AY.87	0.001665
N	6	P6P	ccC	ccT	2	2	AY.97	0.003401
N	6	P6P	ccC	ccT	2	2	AY.98.1	0.000097
N	6	P6P	ccC	ccT	2	2	B	0.000256
N	6	P6P	ccC	ccT	2	2	B.1.1.216	0.001781
N	6	P6P	ccC	ccT	2	2	B.1.1.348	0.001592
N	6	P6P	ccC	ccT	2	2	B.1.1.372	0.001377
N	6	P6P	ccC	ccT	2	2	B.1.1.50	0.001358
N	6	P6P	ccC	ccT	2	2	B.1.170	0.008621
N	6	P6P	ccC	ccT	2	2	B.1.177.81	0.000379
N	6	P6P	ccC	ccT	2	2	B.1.214.2	0.001199
N	6	P6P	ccC	ccT	2	2	B.1.240	0.000431
N	6	P6P	ccC	ccT	2	2	B.1.36.29	0.001035
N	6	P6P	ccC	ccT	2	2	B.1.466.2	0.000782
N	6	P6P	ccC	ccT	2	2	B.1.518	0.023529
N	6	P6P	ccC	ccT	2	2	B.1.524	0.002813
N	6	P6P	ccC	ccT	2	2	B.1.564.1	0.003155
N	6	P6P	ccC	ccT	2	2	Q.3	0.00029
N	6	P6P	ccC	ccT	1	1	A.23.1	0.000704
N	6	P6P	ccC	ccT	1	1	AY.104	0.001984
N	6	P6P	ccC	ccT	1	1	AY.109	0.00074
N	6	P6P	ccC	ccT	1	1	AY.111	0.000183
N	6	P6P	ccC	ccT	1	1	AY.114	0.000231
N	6	P6P	ccC	ccT	1	1	AY.13	0.000161
N	6	P6P	ccC	ccT	1	1	AY.19	0.00114
N	6	P6P	ccC	ccT	1	1	AY.29.1	0.000221
N	6	P6P	ccC	ccT	1	1	AY.30	0.000396
N	6	P6P	ccC	ccT	1	1	AY.32	0.000532
N	6	P6P	ccC	ccT	1	1	AY.34.1	0.00051
N	6	P6P	ccC	ccT	1	1	AY.39.2	0.001541
N	6	P6P	ccC	ccT	1	1	AY.4.3	0.000842
N	6	P6P	ccC	ccT	1	1	AY.46.1	0.001027
N	6	P6P	ccC	ccT	1	1	AY.53	0.000288
N	6	P6P	ccC	ccT	1	1	AY.55	0.000917
N	6	P6P	ccC	ccT	1	1	AY.68	0.000274
N	6	P6P	ccC	ccT	1	1	AY.71	0.000475
N	6	P6P	ccC	ccT	1	1	AY.72	0.001361
N	6	P6P	ccC	ccT	1	1	AY.74	0.000116
N	6	P6P	ccC	ccT	1	1	AY.8	0.000606
N	6	P6P	ccC	ccT	1	1	AY.98	0.000079
N	6	P6P	ccC	ccT	1	1	AY.99.2	0.000092
N	6	P6P	ccC	ccT	1	1	AZ.1	0.000867
N	6	P6P	ccC	ccT	1	1	AZ.2	0.000821
N	6	P6P	ccC	ccT	1	1	B.1.1.16	0.055556
N	6	P6P	ccC	ccT	1	1	B.1.1.174	0.003378
N	6	P6P	ccC	ccT	1	1	B.1.1.244	0.015385
N	6	P6P	ccC	ccT	1	1	B.1.1.326	0.001761
N	6	P6P	ccC	ccT	1	1	B.1.1.33	0.000421
N	6	P6P	ccC	ccT	1	1	B.1.1.39	0.00051
N	6	P6P	ccC	ccT	1	1	B.1.1.409	0.002833
N	6	P6P	ccC	ccT	1	1	B.1.1.417	0.002703
N	6	P6P	ccC	ccT	1	1	B.1.1.434	0.000349
N	6	P6P	ccC	ccT	1	1	B.1.1.466	0.008696
N	6	P6P	ccC	ccT	1	1	B.1.1.99	0.02381
N	6	P6P	ccC	ccT	1	1	B.1.110.3	0.000718
N	6	P6P	ccC	ccT	1	1	B.1.157	0.002985
N	6	P6P	ccC	ccT	1	1	B.1.177.54	0.000606
N	6	P6P	ccC	ccT	1	1	B.1.177.55	0.002331
N	6	P6P	ccC	ccT	1	1	B.1.177.60	0.000218
N	6	P6P	ccC	ccT	1	1	B.1.177.63	0.002703
N	6	P6P	ccC	ccT	1	1	B.1.177.7	0.000165
N	6	P6P	ccC	ccT	1	1	B.1.177.77	0.000726
N	6	P6P	ccC	ccT	1	1	B.1.214	0.003663
N	6	P6P	ccC	ccT	1	1	B.1.237	0.004975
N	6	P6P	ccC	ccT	1	1	B.1.241	0.000812
N	6	P6P	ccC	ccT	1	1	B.1.260	0.003344
N	6	P6P	ccC	ccT	1	1	B.1.265	0.001271
N	6	P6P	ccC	ccT	1	1	B.1.284	0.013158
N	6	P6P	ccC	ccT	1	1	B.1.311	0.000275
N	6	P6P	ccC	ccT	1	1	B.1.349	0.000715
N	6	P6P	ccC	ccT	1	1	B.1.36.10	0.004785
N	6	P6P	ccC	ccT	1	1	B.1.36.18	0.00042
N	6	P6P	ccC	ccT	1	1	B.1.36.22	0.001208
N	6	P6P	ccC	ccT	1	1	B.1.36.7	0.004
N	6	P6P	ccC	ccT	1	1	B.1.36.8	0.001
N	6	P6P	ccC	ccT	1	1	B.1.361	0.001289
N	6	P6P	ccC	ccT	1	1	B.1.362	0.001541
N	6	P6P	ccC	ccT	1	1	B.1.369	0.000285
N	6	P6P	ccC	ccT	1	1	B.1.417	0.028571
N	6	P6P	ccC	ccT	1	1	B.1.422	0.000812
N	6	P6P	ccC	ccT	1	1	B.1.428	0.00102
N	6	P6P	ccC	ccT	1	1	B.1.438	0.006536
N	6	P6P	ccC	ccT	1	1	B.1.443	0.004673
N	6	P6P	ccC	ccT	1	1	B.1.460	0.017857
N	6	P6P	ccC	ccT	1	1	B.1.538	0.008065
N	6	P6P	ccC	ccT	1	1	B.1.564	0.000426
N	6	P6P	ccC	ccT	1	1	B.1.595	0.000261
N	6	P6P	ccC	ccT	1	1	B.1.605	0.005952
N	6	P6P	ccC	ccT	1	1	B.1.607	0.052632
N	6	P6P	ccC	ccT	1	1	B.1.617.1	0.000129
N	6	P6P	ccC	ccT	1	1	B.1.620	0.000946
N	6	P6P	ccC	ccT	1	1	B.1.621.1	0.000506
N	6	P6P	ccC	ccT	1	1	B.1.623	0.000536
N	6	P6P	ccC	ccT	1	1	B.1.626	0.005714
N	6	P6P	ccC	ccT	1	1	B.1.93	0.000934
N	6	P6P	ccC	ccT	1	1	C.11	0.010638
N	6	P6P	ccC	ccT	1	1	N.4	0.004255
N	6	P6P	ccC	ccT	1	1	P.1.12	0.000484
N	6	P6P	ccC	ccT	1	1	P.1.17	0.000162
N	6	P6P	ccC	ccT	1	1	P.1.7	0.000319
N	6	P6P	ccC	ccT	1	1	Q.1	0.000126

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.