CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : CodonNum = 257

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	257	K257K		syn	aaG	aaA	3717	3717	1	29042-29044
N	257	K257R		nonsyn	aAg	aGg	183	183	1	29042-29044
N	257	K257del		del	AAG	---	15	15	1	29042-29044
N	257	K257E		nonsyn	Aag	Gag	8	7	0.875	29042-29044
N	257	K257N		nonsyn	aaG	aaT	8	6	0.75	29042-29044
N	257	K257N		nonsyn	aaG	aaC	8	2	0.25	29042-29044
N	257	K257E		nonsyn	AaG	GaA	8	1	0.125	29042-29044
N	257	K257Q		nonsyn	Aag	Cag	5	5	1	29042-29044
N	257	K257T		nonsyn	aAg	aCg	3	3	1	29042-29044
N	257	K257del1		del	aAG	aG-	3	1	0.333333	29042-29044
N	257	K257del1		del	aaG	aa-	3	1	0.333333	29042-29044
N	257	K257del1		del	Aag	-ag	3	1	0.333333	29042-29044
N	257	K257M		nonsyn	aAg	aTg	2	2	1	29042-29044
N	257	K257G		nonsyn	AAg	GGg	1	1	1	29042-29044
N	257	K257L		nonsyn	AAg	TTg	1	1	1	29042-29044
N	257	K257del2		del	aAG	a--	1	1	1	29042-29044
N	257	K257V		nonsyn	AAg	GTg	1	1	1	29042-29044
N	257	K257S		nonsyn	aAG	aGC	1	1	1	29042-29044

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	257	K257K	aaG	aaA	3717	3717	All	0.000711
N	257	K257K	aaG	aaA	1641	1641	B.1.1.7	0.001469
N	257	K257K	aaG	aaA	988	988	B.1.389	0.98998
N	257	K257R	aAg	aGg	183	183	All	0.000035
N	257	K257K	aaG	aaA	163	163	B.1.1.284	0.017506
N	257	K257K	aaG	aaA	124	124	B.1	0.001136
N	257	K257K	aaG	aaA	116	116	AY.9	0.007841
N	257	K257K	aaG	aaA	97	97	B.1.497	0.030532
N	257	K257K	aaG	aaA	91	91	Q.8	0.015007
N	257	K257K	aaG	aaA	61	61	B.1.617.2	0.00023
N	257	K257K	aaG	aaA	60	60	AY.44	0.000365
N	257	K257R	aAg	aGg	38	38	B.1.1.7	0.000034
N	257	K257R	aAg	aGg	35	35	AY.4	0.000054
N	257	K257K	aaG	aaA	35	35	AY.43	0.000155
N	257	K257K	aaG	aaA	33	33	AY.4	0.000051
N	257	K257K	aaG	aaA	26	26	B.1.177	0.000342
N	257	K257K	aaG	aaA	23	23	AY.103	0.000143
N	257	K257K	aaG	aaA	23	23	B.1.1.519	0.000913
N	257	K257K	aaG	aaA	23	23	C.37	0.002669
N	257	K257K	aaG	aaA	20	20	B.1.2	0.000176
N	257	K257R	aAg	aGg	18	18	AY.120	0.000669
N	257	K257R	aAg	aGg	17	17	B.1.617.2	0.000064
N	257	K257del	AAG	---	15	15	All	0.000003
N	257	K257K	aaG	aaA	13	13	AY.3	0.000129
N	257	K257K	aaG	aaA	12	12	B.1.218	0.061856
N	257	K257R	aAg	aGg	10	10	B.1.526	0.000235
N	257	K257K	aaG	aaA	9	9	AY.50	0.007194
N	257	K257E	Aag	Gag	7	8	All	0.000001
N	257	K257N	aaG	aaT	6	8	All	0.000001
N	257	K257N	aaG	aaC	2	8	All	0
N	257	K257E	AaG	GaA	1	8	All	0
N	257	K257K	aaG	aaA	8	8	AY.25	0.000048
N	257	K257K	aaG	aaA	8	8	B.1.637	0.000585
N	257	K257K	aaG	aaA	8	8	P.1.7	0.002554
N	257	K257K	aaG	aaA	7	7	P.1	0.00011
N	257	K257K	aaG	aaA	6	6	AY.5	0.000124
N	257	K257K	aaG	aaA	6	6	B.1.1	0.000109
N	257	K257R	aAg	aGg	6	6	B.1.2	0.000053
N	257	K257Q	Aag	Cag	5	5	All	0.000001
N	257	K257R	aAg	aGg	5	5	AY.103	0.000031
N	257	K257K	aaG	aaA	5	5	AY.117	0.000423
N	257	K257K	aaG	aaA	5	5	AY.13	0.000805
N	257	K257R	aAg	aGg	5	5	AY.20	0.000194
N	257	K257R	aAg	aGg	5	5	AY.98.1	0.000242
N	257	K257K	aaG	aaA	5	5	B.1.609	0.002397
N	257	K257R	aAg	aGg	4	4	B.1.311	0.001098
N	257	K257K	aaG	aaA	4	4	Q.1	0.000505
N	257	K257T	aAg	aCg	3	3	All	0.000001
N	257	K257del1	aAG	aG-	1	3	All	0
N	257	K257del1	aaG	aa-	1	3	All	0
N	257	K257del1	Aag	-ag	1	3	All	0
N	257	K257K	aaG	aaA	3	3	AU.3	0.006329
N	257	K257K	aaG	aaA	3	3	AY.102	0.00008
N	257	K257K	aaG	aaA	3	3	AY.120	0.000112
N	257	K257R	aAg	aGg	3	3	AY.25	0.000018
N	257	K257K	aaG	aaA	3	3	AY.34	0.000291
N	257	K257R	aAg	aGg	3	3	AY.43	0.000013
N	257	K257K	aaG	aaA	3	3	AY.74	0.000347
N	257	K257K	aaG	aaA	3	3	B.1.1.216	0.002671
N	257	K257K	aaG	aaA	3	3	B.1.258	0.0002
N	257	K257K	aaG	aaA	3	3	B.1.36.39	0.006652
N	257	K257K	aaG	aaA	3	3	B.1.427	0.000151
N	257	K257R	aAg	aGg	3	3	B.1.429	0.000071
N	257	K257K	aaG	aaA	3	3	B.1.509	0.002597
N	257	K257K	aaG	aaA	3	3	P.1.16	0.001122
N	257	K257K	aaG	aaA	2	2		0.111111
N	257	K257M	aAg	aTg	2	2	All	0
N	257	K257R	aAg	aGg	2	2	AY.102	0.000053
N	257	K257K	aaG	aaA	2	2	AY.106	0.00067
N	257	K257K	aaG	aaA	2	2	AY.119	0.000071
N	257	K257del	AAG	---	2	2	AY.25	0.000012
N	257	K257M	aAg	aTg	2	2	AY.25	0.000012
N	257	K257K	aaG	aaA	2	2	AY.26	0.000057
N	257	K257R	aAg	aGg	2	2	AY.3.1	0.000171
N	257	K257K	aaG	aaA	2	2	AY.65	0.001066
N	257	K257K	aaG	aaA	2	2	AY.69	0.000373
N	257	K257K	aaG	aaA	2	2	AY.75	0.000112
N	257	K257K	aaG	aaA	2	2	AY.98	0.000158
N	257	K257R	aAg	aGg	2	2	B.1	0.000018
N	257	K257del	AAG	---	2	2	B.1	0.000018
N	257	K257R	aAg	aGg	2	2	B.1.1	0.000036
N	257	K257E	Aag	Gag	2	2	B.1.1	0.000036
N	257	K257K	aaG	aaA	2	2	B.1.1.326	0.003521
N	257	K257K	aaG	aaA	2	2	B.1.1.33	0.000842
N	257	K257Q	Aag	Cag	2	2	B.1.1.7	0.000002
N	257	K257N	aaG	aaC	2	2	B.1.1.7	0.000002
N	257	K257K	aaG	aaA	2	2	B.1.1.70	0.000682
N	257	K257K	aaG	aaA	2	2	B.1.177.81	0.000379
N	257	K257R	aAg	aGg	2	2	B.1.351	0.000059
N	257	K257K	aaG	aaA	2	2	B.1.400	0.000858
N	257	K257K	aaG	aaA	2	2	B.1.600	0.011696
N	257	K257K	aaG	aaA	2	2	B.1.621	0.000177
N	257	K257R	aAg	aGg	2	2	P.1	0.000032
N	257	K257K	aaG	aaA	2	2	P.1.12	0.000968
N	257	K257R	aAg	aGg	2	2	P.1.14	0.000096
N	257	K257K	aaG	aaA	1	1	AE.8	0.000489
N	257	K257S	aAG	aGC	1	1	All	0
N	257	K257L	AAg	TTg	1	1	All	0
N	257	K257G	AAg	GGg	1	1	All	0
N	257	K257V	AAg	GTg	1	1	All	0
N	257	K257del2	aAG	a--	1	1	All	0
N	257	K257del	AAG	---	1	1	AY.100	0.000046
N	257	K257E	Aag	Gag	1	1	AY.104	0.001984
N	257	K257R	aAg	aGg	1	1	AY.117	0.000085
N	257	K257K	aaG	aaA	1	1	AY.12	0.000316
N	257	K257R	aAg	aGg	1	1	AY.12	0.000316
N	257	K257K	aaG	aaA	1	1	AY.20	0.000039
N	257	K257R	aAg	aGg	1	1	AY.26	0.000028
N	257	K257R	aAg	aGg	1	1	AY.39	0.000025
N	257	K257R	aAg	aGg	1	1	AY.4.2	0.000022
N	257	K257K	aaG	aaA	1	1	AY.4.2	0.000022
N	257	K257R	aAg	aGg	1	1	AY.41	0.000294
N	257	K257R	aAg	aGg	1	1	AY.44	0.000006
N	257	K257del	AAG	---	1	1	AY.44	0.000006
N	257	K257K	aaG	aaA	1	1	AY.45	0.000122
N	257	K257K	aaG	aaA	1	1	AY.46	0.000104
N	257	K257K	aaG	aaA	1	1	AY.46.5	0.000198
N	257	K257K	aaG	aaA	1	1	AY.47	0.000031
N	257	K257del	AAG	---	1	1	AY.67	0.000464
N	257	K257del	AAG	---	1	1	AY.75	0.000056
N	257	K257K	aaG	aaA	1	1	AY.75.1	0.00018
N	257	K257R	aAg	aGg	1	1	AY.75.1	0.00018
N	257	K257del	AAG	---	1	1	AY.9.2	0.000037
N	257	K257R	aAg	aGg	1	1	AY.93	0.000273
N	257	K257R	aAg	aGg	1	1	AY.98	0.000079
N	257	K257K	aaG	aaA	1	1	AY.98.1	0.000048
N	257	K257K	aaG	aaA	1	1	AY.99.2	0.000092
N	257	K257E	Aag	Gag	1	1	B	0.000128
N	257	K257E	Aag	Gag	1	1	B.1	0.000009
N	257	K257L	AAg	TTg	1	1	B.1	0.000009
N	257	K257Q	Aag	Cag	1	1	B.1	0.000009
N	257	K257N	aaG	aaT	1	1	B.1	0.000009
N	257	K257G	AAg	GGg	1	1	B.1.1	0.000018
N	257	K257del	AAG	---	1	1	B.1.1	0.000018
N	257	K257del1	Aag	-ag	1	1	B.1.1	0.000018
N	257	K257E	AaG	GaA	1	1	B.1.1.27	0.00565
N	257	K257K	aaG	aaA	1	1	B.1.1.273	0.006757
N	257	K257R	aAg	aGg	1	1	B.1.1.291	0.000742
N	257	K257K	aaG	aaA	1	1	B.1.1.297	0.002237
N	257	K257V	AAg	GTg	1	1	B.1.1.7	0.000001
N	257	K257del1	aaG	aa-	1	1	B.1.1.7	0.000001
N	257	K257T	aAg	aCg	1	1	B.1.1.7	0.000001
N	257	K257E	Aag	Gag	1	1	B.1.1.7	0.000001
N	257	K257K	aaG	aaA	1	1	B.1.128	0.000635
N	257	K257K	aaG	aaA	1	1	B.1.13	0.002375
N	257	K257S	aAG	aGC	1	1	B.1.177.63	0.002703
N	257	K257K	aaG	aaA	1	1	B.1.177.73	0.000566
N	257	K257T	aAg	aCg	1	1	B.1.177.73	0.000566
N	257	K257del	AAG	---	1	1	B.1.177.83	0.001481
N	257	K257K	aaG	aaA	1	1	B.1.177.84	0.006667
N	257	K257N	aaG	aaT	1	1	B.1.177.86	0.000183
N	257	K257K	aaG	aaA	1	1	B.1.243	0.00007
N	257	K257R	aAg	aGg	1	1	B.1.258	0.000067
N	257	K257R	aAg	aGg	1	1	B.1.258.17	0.000104
N	257	K257K	aaG	aaA	1	1	B.1.258.17	0.000104
N	257	K257R	aAg	aGg	1	1	B.1.265	0.001271
N	257	K257R	aAg	aGg	1	1	B.1.336	0.002439
N	257	K257K	aaG	aaA	1	1	B.1.36	0.000146
N	257	K257del	AAG	---	1	1	B.1.369	0.000285
N	257	K257K	aaG	aaA	1	1	B.1.429	0.000024
N	257	K257del	AAG	---	1	1	B.1.439	0.005917
N	257	K257K	aaG	aaA	1	1	B.1.466.2	0.000391
N	257	K257K	aaG	aaA	1	1	B.1.525	0.000113
N	257	K257K	aaG	aaA	1	1	B.1.526	0.000024
N	257	K257K	aaG	aaA	1	1	B.1.541	0.004425
N	257	K257K	aaG	aaA	1	1	B.1.595	0.000261
N	257	K257N	aaG	aaT	1	1	B.1.595	0.000261
N	257	K257del1	aAG	aG-	1	1	B.1.617.1	0.000129
N	257	K257Q	Aag	Cag	1	1	B.1.617.2	0.000004
N	257	K257del	AAG	---	1	1	B.1.617.2	0.000004
N	257	K257K	aaG	aaA	1	1	B.1.617.3	0.002985
N	257	K257del	AAG	---	1	1	B.1.621	0.000089
N	257	K257K	aaG	aaA	1	1	B.4.6	0.016667
N	257	K257E	Aag	Gag	1	1	B.55	0.00295
N	257	K257N	aaG	aaT	1	1	B.6	0.00091
N	257	K257N	aaG	aaT	1	1	D.2	0.000075
N	257	K257R	aAg	aGg	1	1	D.2	0.000075
N	257	K257K	aaG	aaA	1	1	D.2	0.000075
N	257	K257Q	Aag	Cag	1	1	D.2	0.000075
N	257	K257T	aAg	aCg	1	1	P.1.1	0.000318
N	257	K257K	aaG	aaA	1	1	P.1.14	0.000048
N	257	K257del2	aAG	a--	1	1	P.1.15	0.000232
N	257	K257K	aaG	aaA	1	1	P.1.17.1	0.000875
N	257	K257N	aaG	aaT	1	1	Q.3	0.000145
N	257	K257R	aAg	aGg	1	1	Q.4	0.000455
N	257	K257K	aaG	aaA	1	1	R.1	0.00009

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.