CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : CodonNum = 354

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	354	N354N		syn	aaT	aaC	782	782	1	29333-29335
N	354	N354T		nonsyn	aAt	aCt	390	390	1	29333-29335
N	354	N354S		nonsyn	aAt	aGt	185	184	0.994595	29333-29335
N	354	N354S		nonsyn	AAt	TCt	185	1	0.00540541	29333-29335
N	354	N354H		nonsyn	Aat	Cat	80	80	1	29333-29335
N	354	N354D		nonsyn	Aat	Gat	37	37	1	29333-29335
N	354	N354del		del	AAT	---	15	15	1	29333-29335
N	354	N354Y		nonsyn	Aat	Tat	13	13	1	29333-29335
N	354	N354I		nonsyn	aAt	aTt	2	2	1	29333-29335
N	354	N354F		nonsyn	AAt	TTt	1	1	1	29333-29335
N	354	N354del1		del	aaT	aa-	1	1	1	29333-29335
N	354	N354K		nonsyn	aaT	aaA	1	1	1	29333-29335
N	354	N354E		nonsyn	AaT	GaG	1	1	1	29333-29335

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	354	N354N	aaT	aaC	782	782	All	0.00015
N	354	N354T	aAt	aCt	390	390	All	0.000075
N	354	N354T	aAt	aCt	350	350	B.1.1.7	0.000313
N	354	N354N	aaT	aaC	225	225	AY.4	0.00035
N	354	N354N	aaT	aaC	208	208	AY.33	0.01389
N	354	N354S	aAt	aGt	184	185	All	0.000035
N	354	N354S	AAt	TCt	1	185	All	0
N	354	N354H	Aat	Cat	80	80	All	0.000015
N	354	N354N	aaT	aaC	60	60	B.1.36.8	0.06
N	354	N354H	Aat	Cat	46	46	AY.4	0.000072
N	354	N354N	aaT	aaC	42	42	AY.43	0.000186
N	354	N354S	aAt	aGt	41	41	AY.3	0.000408
N	354	N354N	aaT	aaC	40	40	B.1.1.7	0.000036
N	354	N354D	Aat	Gat	37	37	All	0.000007
N	354	N354S	aAt	aGt	30	30	AY.4	0.000047
N	354	N354N	aaT	aaC	23	23	AY.5	0.000475
N	354	N354N	aaT	aaC	22	22	B.1.617.2	0.000083
N	354	N354del	AAT	---	15	15	All	0.000003
N	354	N354Y	Aat	Tat	13	13	All	0.000002
N	354	N354N	aaT	aaC	13	13	B.1.184	0.764706
N	354	N354S	aAt	aGt	12	12	AY.44	0.000073
N	354	N354S	aAt	aGt	12	12	B.1.1.7	0.000011
N	354	N354S	aAt	aGt	11	11	AY.100	0.000506
N	354	N354H	Aat	Cat	11	11	B.1.1.7	0.00001
N	354	N354S	aAt	aGt	8	9	B.1.617.2	0.00003
N	354	N354S	AAt	TCt	1	9	B.1.617.2	0.000004
N	354	N354T	aAt	aCt	9	9	Q.8	0.001484
N	354	N354T	aAt	aCt	8	8	AY.3	0.00008
N	354	N354H	Aat	Cat	8	8	AY.3	0.00008
N	354	N354D	Aat	Gat	8	8	AY.3	0.00008
N	354	N354N	aaT	aaC	8	8	AY.3	0.00008
N	354	N354N	aaT	aaC	8	8	B.1.160	0.00025
N	354	N354S	aAt	aGt	7	7	B.1	0.000064
N	354	N354N	aaT	aaC	7	7	B.1.409	0.005469
N	354	N354N	aaT	aaC	6	6	AY.102	0.000159
N	354	N354S	aAt	aGt	6	6	AY.16	0.002278
N	354	N354N	aaT	aaC	6	6	AY.44	0.000037
N	354	N354N	aaT	aaC	5	5	AY.27	0.000324
N	354	N354N	aaT	aaC	5	5	AY.29	0.000079
N	354	N354S	aAt	aGt	5	5	AY.43	0.000022
N	354	N354D	Aat	Gat	5	5	AY.44	0.00003
N	354	N354D	Aat	Gat	5	5	B.1.1.7	0.000004
N	354	N354S	aAt	aGt	5	5	B.1.2	0.000044
N	354	N354N	aaT	aaC	5	5	B.1.561	0.001985
N	354	N354N	aaT	aaC	4	4	AY.10	0.00212
N	354	N354N	aaT	aaC	4	4	AY.103	0.000025
N	354	N354S	aAt	aGt	4	4	AY.45	0.000487
N	354	N354Y	Aat	Tat	4	4	AY.6	0.000165
N	354	N354N	aaT	aaC	4	4	AY.92	0.001149
N	354	N354N	aaT	aaC	4	4	B.1	0.000037
N	354	N354S	aAt	aGt	4	4	B.1.636	0.026846
N	354	N354S	aAt	aGt	3	3	AY.14	0.000264
N	354	N354N	aaT	aaC	3	3	AY.23	0.000209
N	354	N354N	aaT	aaC	3	3	AY.25	0.000018
N	354	N354T	aAt	aCt	3	3	AY.4	0.000005
N	354	N354N	aaT	aaC	3	3	B.1.177	0.00004
N	354	N354N	aaT	aaC	3	3	B.1.177.57	0.000843
N	354	N354N	aaT	aaC	3	3	B.1.36	0.000438
N	354	N354N	aaT	aaC	3	3	D.2	0.000225
N	354	N354N	aaT	aaC	3	3	P.1	0.000047
N	354	N354del	AAT	---	2	2		0.111111
N	354	N354I	aAt	aTt	2	2	All	0
N	354	N354N	aaT	aaC	2	2	AY.1	0.000791
N	354	N354D	Aat	Gat	2	2	AY.103	0.000012
N	354	N354H	Aat	Cat	2	2	AY.118	0.000125
N	354	N354S	aAt	aGt	2	2	AY.25	0.000012
N	354	N354D	Aat	Gat	2	2	AY.25	0.000012
N	354	N354S	aAt	aGt	2	2	AY.26	0.000057
N	354	N354N	aaT	aaC	2	2	AY.26	0.000057
N	354	N354N	aaT	aaC	2	2	AY.29.1	0.000441
N	354	N354S	aAt	aGt	2	2	AY.39	0.000049
N	354	N354T	aAt	aCt	2	2	AY.4.2	0.000043
N	354	N354D	Aat	Gat	2	2	AY.46.4	0.000329
N	354	N354N	aaT	aaC	2	2	AY.46.4	0.000329
N	354	N354S	aAt	aGt	2	2	AY.46.6	0.000144
N	354	N354N	aaT	aaC	2	2	AY.47	0.000062
N	354	N354N	aaT	aaC	2	2	AY.53	0.000575
N	354	N354N	aaT	aaC	2	2	AY.75	0.000112
N	354	N354N	aaT	aaC	2	2	AY.98	0.000158
N	354	N354del	AAT	---	2	2	B.1	0.000018
N	354	N354D	Aat	Gat	2	2	B.1	0.000018
N	354	N354N	aaT	aaC	2	2	B.1.1	0.000036
N	354	N354S	aAt	aGt	2	2	B.1.1	0.000036
N	354	N354T	aAt	aCt	2	2	B.1.1	0.000036
N	354	N354N	aaT	aaC	2	2	B.1.1.519	0.000079
N	354	N354S	aAt	aGt	2	2	B.1.131	0.017544
N	354	N354S	aAt	aGt	2	2	B.1.177	0.000026
N	354	N354S	aAt	aGt	2	2	B.1.177.45	0.000762
N	354	N354H	Aat	Cat	2	2	B.1.177.62	0.002384
N	354	N354N	aaT	aaC	2	2	B.1.258	0.000133
N	354	N354Y	Aat	Tat	2	2	B.1.351	0.000059
N	354	N354N	aaT	aaC	2	2	B.1.456	0.006536
N	354	N354T	aAt	aCt	2	2	B.1.617.2	0.000008
N	354	N354N	aaT	aaC	2	2	L.3	0.007092
N	354	N354D	Aat	Gat	2	2	N.6	0.014184
N	354	N354S	aAt	aGt	2	2	P.1	0.000032
N	354	N354T	aAt	aCt	2	2	P.1	0.000032
N	354	N354N	aaT	aaC	2	2	P.1.14	0.000096
N	354	N354S	aAt	aGt	2	2	P.1.15	0.000465
N	354	N354H	Aat	Cat	1	1	A.2.2	0.001689
N	354	N354Y	Aat	Tat	1	1	A.2.2	0.001689
N	354	N354del1	aaT	aa-	1	1	All	0
N	354	N354K	aaT	aaA	1	1	All	0
N	354	N354F	AAt	TTt	1	1	All	0
N	354	N354E	AaT	GaG	1	1	All	0
N	354	N354T	aAt	aCt	1	1	AU.2	0.002421
N	354	N354H	Aat	Cat	1	1	AY.100	0.000046
N	354	N354del	AAT	---	1	1	AY.103	0.000006
N	354	N354T	aAt	aCt	1	1	AY.103	0.000006
N	354	N354N	aaT	aaC	1	1	AY.106	0.000335
N	354	N354H	Aat	Cat	1	1	AY.117	0.000085
N	354	N354N	aaT	aaC	1	1	AY.119	0.000035
N	354	N354S	aAt	aGt	1	1	AY.12	0.000316
N	354	N354S	aAt	aGt	1	1	AY.23	0.00007
N	354	N354del	AAT	---	1	1	AY.27	0.000065
N	354	N354S	aAt	aGt	1	1	AY.29	0.000016
N	354	N354del	AAT	---	1	1	AY.33	0.000067
N	354	N354N	aaT	aaC	1	1	AY.34.1	0.00051
N	354	N354N	aaT	aaC	1	1	AY.39	0.000025
N	354	N354Y	Aat	Tat	1	1	AY.4	0.000002
N	354	N354D	Aat	Gat	1	1	AY.4	0.000002
N	354	N354H	Aat	Cat	1	1	AY.42	0.00004
N	354	N354D	Aat	Gat	1	1	AY.43	0.000004
N	354	N354H	Aat	Cat	1	1	AY.43	0.000004
N	354	N354Y	Aat	Tat	1	1	AY.44	0.000006
N	354	N354T	aAt	aCt	1	1	AY.44	0.000006
N	354	N354D	Aat	Gat	1	1	AY.45	0.000122
N	354	N354Y	Aat	Tat	1	1	AY.5	0.000021
N	354	N354H	Aat	Cat	1	1	AY.5	0.000021
N	354	N354S	aAt	aGt	1	1	AY.5	0.000021
N	354	N354S	aAt	aGt	1	1	AY.50	0.000799
N	354	N354N	aaT	aaC	1	1	AY.61	0.000105
N	354	N354D	Aat	Gat	1	1	AY.63	0.000387
N	354	N354del	AAT	---	1	1	AY.67	0.000464
N	354	N354D	Aat	Gat	1	1	AY.69	0.000187
N	354	N354S	aAt	aGt	1	1	AY.7.1	0.000113
N	354	N354T	aAt	aCt	1	1	AY.70	0.000209
N	354	N354T	aAt	aCt	1	1	AY.75.1	0.00018
N	354	N354E	AaT	GaG	1	1	AY.85	0.000427
N	354	N354N	aaT	aaC	1	1	AY.88	0.000884
N	354	N354Y	Aat	Tat	1	1	AY.9	0.000068
N	354	N354D	Aat	Gat	1	1	AY.9.2	0.000037
N	354	N354S	aAt	aGt	1	1	AY.9.2	0.000037
N	354	N354N	aaT	aaC	1	1	AY.95	0.000761
N	354	N354N	aaT	aaC	1	1	AY.99.2	0.000092
N	354	N354N	aaT	aaC	1	1	B	0.000128
N	354	N354T	aAt	aCt	1	1	B.1	0.000009
N	354	N354H	Aat	Cat	1	1	B.1	0.000009
N	354	N354del	AAT	---	1	1	B.1.1	0.000018
N	354	N354del	AAT	---	1	1	B.1.1.139	0.022727
N	354	N354H	Aat	Cat	1	1	B.1.1.216	0.00089
N	354	N354S	aAt	aGt	1	1	B.1.1.222	0.000204
N	354	N354N	aaT	aaC	1	1	B.1.1.222	0.000204
N	354	N354S	aAt	aGt	1	1	B.1.1.27	0.00565
N	354	N354N	aaT	aaC	1	1	B.1.1.28	0.000311
N	354	N354N	aaT	aaC	1	1	B.1.1.284	0.000107
N	354	N354K	aaT	aaA	1	1	B.1.1.306	0.000438
N	354	N354N	aaT	aaC	1	1	B.1.1.311	0.000358
N	354	N354T	aAt	aCt	1	1	B.1.1.354	0.004386
N	354	N354N	aaT	aaC	1	1	B.1.1.37	0.000193
N	354	N354S	aAt	aGt	1	1	B.1.1.416	0.000905
N	354	N354I	aAt	aTt	1	1	B.1.1.434	0.000349
N	354	N354F	AAt	TTt	1	1	B.1.1.434	0.000349
N	354	N354Y	Aat	Tat	1	1	B.1.1.434	0.000349
N	354	N354S	aAt	aGt	1	1	B.1.1.485	0.016667
N	354	N354S	aAt	aGt	1	1	B.1.1.519	0.00004
N	354	N354T	aAt	aCt	1	1	B.1.1.528	0.004808
N	354	N354T	aAt	aCt	1	1	B.1.111	0.001175
N	354	N354N	aaT	aaC	1	1	B.1.139	0.000733
N	354	N354D	Aat	Gat	1	1	B.1.160	0.000031
N	354	N354N	aaT	aaC	1	1	B.1.177.4	0.000211
N	354	N354del	AAT	---	1	1	B.1.177.63	0.002703
N	354	N354N	aaT	aaC	1	1	B.1.177.7	0.000165
N	354	N354N	aaT	aaC	1	1	B.1.2	0.000009
N	354	N354T	aAt	aCt	1	1	B.1.2	0.000009
N	354	N354S	aAt	aGt	1	1	B.1.213	0.014925
N	354	N354N	aaT	aaC	1	1	B.1.221	0.000071
N	354	N354N	aaT	aaC	1	1	B.1.240	0.000216
N	354	N354H	Aat	Cat	1	1	B.1.258.12	0.007874
N	354	N354N	aaT	aaC	1	1	B.1.324	0.001605
N	354	N354T	aAt	aCt	1	1	B.1.351	0.00003
N	354	N354N	aaT	aaC	1	1	B.1.351	0.00003
N	354	N354N	aaT	aaC	1	1	B.1.351.3	0.000876
N	354	N354N	aaT	aaC	1	1	B.1.36.16	0.001425
N	354	N354N	aaT	aaC	1	1	B.1.36.17	0.000494
N	354	N354N	aaT	aaC	1	1	B.1.36.19	0.009259
N	354	N354N	aaT	aaC	1	1	B.1.36.29	0.000517
N	354	N354H	Aat	Cat	1	1	B.1.36.8	0.001
N	354	N354del	AAT	---	1	1	B.1.400	0.000429
N	354	N354del	AAT	---	1	1	B.1.415	0.014286
N	354	N354N	aaT	aaC	1	1	B.1.428	0.00102
N	354	N354N	aaT	aaC	1	1	B.1.429	0.000024
N	354	N354N	aaT	aaC	1	1	B.1.438.1	0.000107
N	354	N354S	aAt	aGt	1	1	B.1.465	0.003802
N	354	N354N	aaT	aaC	1	1	B.1.524	0.001406
N	354	N354Y	Aat	Tat	1	1	B.1.526	0.000024
N	354	N354N	aaT	aaC	1	1	B.1.567	0.003333
N	354	N354del	AAT	---	1	1	B.1.617.2	0.000004
N	354	N354N	aaT	aaC	1	1	B.1.619.1	0.000641
N	354	N354D	Aat	Gat	1	1	B.1.621	0.000089
N	354	N354S	aAt	aGt	1	1	B.1.628	0.000352
N	354	N354T	aAt	aCt	1	1	B.1.628	0.000352
N	354	N354del	AAT	---	1	1	B.1.630	0.005236
N	354	N354D	Aat	Gat	1	1	B.1.632	0.006711
N	354	N354S	aAt	aGt	1	1	D.2	0.000075
N	354	N354I	aAt	aTt	1	1	D.2	0.000075
N	354	N354del1	aaT	aa-	1	1	D.2	0.000075
N	354	N354N	aaT	aaC	1	1	N.10	0.029412
N	354	N354H	Aat	Cat	1	1	P.1	0.000016

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.