CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 815

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
S	815	R815R		syn	agG	agA	1697	1431	0.843253	24005-24007
S	815	R815R		syn	Agg	Cgg	1697	246	0.144962	24005-24007
S	815	R815R		syn	AgG	CgT	1697	19	0.0111962	24005-24007
S	815	R815R		syn	AgG	CgA	1697	1	0.000589275	24005-24007
S	815	R815K		nonsyn	aGg	aAg	186	186	1	24005-24007
S	815	R815del		del	AGG	---	93	93	1	24005-24007
S	815	R815S		nonsyn	agG	agT	40	31	0.775	24005-24007
S	815	R815S		nonsyn	agG	agC	40	8	0.2	24005-24007
S	815	R815S		nonsyn	AGG	TCA	40	1	0.025	24005-24007
S	815	R815M		nonsyn	aGg	aTg	32	32	1	24005-24007
S	815	R815del1		del	aGg	a-g	11	5	0.454545	24005-24007
S	815	R815del1		del	Agg	-gg	11	3	0.272727	24005-24007
S	815	R815del1		del	AgG	Gg-	11	1	0.0909091	24005-24007
S	815	R815del1		del	agG	ag-	11	1	0.0909091	24005-24007
S	815	R815del1		del	AGG	-TA	11	1	0.0909091	24005-24007
S	815	R815G		nonsyn	Agg	Ggg	10	10	1	24005-24007
S	815	R815T		nonsyn	aGg	aCg	7	5	0.714286	24005-24007
S	815	R815T		nonsyn	aGG	aCA	7	2	0.285714	24005-24007
S	815	R815W		nonsyn	Agg	Tgg	6	6	1	24005-24007
S	815	R815V		nonsyn	AGG	GTT	2	1	0.5	24005-24007
S	815	R815V		nonsyn	AGg	GTg	2	1	0.5	24005-24007
S	815	R815del2		del	aGG	a--	2	1	0.5	24005-24007
S	815	R815del2		del	AGg	--g	2	1	0.5	24005-24007
S	815	R815N		nonsyn	aGG	aAT	1	1	1	24005-24007
S	815	R815E		nonsyn	AGg	GAg	1	1	1	24005-24007
S	815	R815I		nonsyn	aGG	aTA	1	1	1	24005-24007
S	815	R815C		nonsyn	AgG	TgT	1	1	1	24005-24007

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
S	815	R815R	agG	agA	1431	1697	All	0.000274
S	815	R815R	Agg	Cgg	246	1697	All	0.000047
S	815	R815R	AgG	CgT	19	1697	All	0.000004
S	815	R815R	AgG	CgA	1	1697	All	0
S	815	R815R	agG	agA	984	985	B.1.375	0.806557
S	815	R815R	AgG	CgA	1	985	B.1.375	0.00082
S	815	R815K	aGg	aAg	186	186	All	0.000036
S	815	R815R	agG	agA	146	148	AY.39	0.003608
S	815	R815R	Agg	Cgg	2	148	AY.39	0.000049
S	815	R815del	AGG	---	93	93	All	0.000018
S	815	R815R	Agg	Cgg	78	87	AY.4	0.000121
S	815	R815R	agG	agA	8	87	AY.4	0.000012
S	815	R815R	AgG	CgT	1	87	AY.4	0.000002
S	815	R815R	agG	agA	70	79	B.1.617.2	0.000264
S	815	R815R	Agg	Cgg	8	79	B.1.617.2	0.00003
S	815	R815R	AgG	CgT	1	79	B.1.617.2	0.000004
S	815	R815R	agG	agA	77	77	B.1.526	0.00181
S	815	R815K	aGg	aAg	62	62	AY.4	0.000096
S	815	R815R	Agg	Cgg	42	42	B.1.536	1
S	815	R815S	agG	agT	31	40	All	0.000006
S	815	R815S	agG	agC	8	40	All	0.000002
S	815	R815S	AGG	TCA	1	40	All	0
S	815	R815R	Agg	Cgg	24	40	B.1.1.7	0.000021
S	815	R815R	agG	agA	16	40	B.1.1.7	0.000014
S	815	R815R	Agg	Cgg	27	36	AY.25	0.000162
S	815	R815R	agG	agA	9	36	AY.25	0.000054
S	815	R815M	aGg	aTg	32	32	All	0.000006
S	815	R815R	agG	agA	16	31	AY.43	0.000071
S	815	R815R	AgG	CgT	9	31	AY.43	0.00004
S	815	R815R	Agg	Cgg	6	31	AY.43	0.000027
S	815	R815K	aGg	aAg	28	28	B.1.1.7	0.000025
S	815	R815R	Agg	Cgg	12	25	B.1	0.00011
S	815	R815R	agG	agA	12	25	B.1	0.00011
S	815	R815R	AgG	CgT	1	25	B.1	0.000009
S	815	R815K	aGg	aAg	24	24	AY.43	0.000106
S	815	R815R	agG	agA	22	22	AY.120	0.000818
S	815	R815R	Agg	Cgg	19	22	AY.44	0.000116
S	815	R815R	agG	agA	3	22	AY.44	0.000018
S	815	R815del	AGG	---	17	17	B.1.1.7	0.000015
S	815	R815K	aGg	aAg	12	12	AY.103	0.000075
S	815	R815del1	aGg	a-g	5	11	All	0.000001
S	815	R815del1	Agg	-gg	3	11	All	0.000001
S	815	R815del1	AGG	-TA	1	11	All	0
S	815	R815del1	AgG	Gg-	1	11	All	0
S	815	R815del1	agG	ag-	1	11	All	0
S	815	R815R	agG	agA	9	11	AY.102	0.000239
S	815	R815R	AgG	CgT	2	11	AY.102	0.000053
S	815	R815G	Agg	Ggg	10	10	All	0.000002
S	815	R815R	agG	agA	10	10	AY.100	0.00046
S	815	R815S	agG	agT	7	10	B.1	0.000064
S	815	R815S	agG	agC	3	10	B.1	0.000027
S	815	R815K	aGg	aAg	8	8	AY.9.2	0.000294
S	815	R815T	aGg	aCg	5	7	All	0.000001
S	815	R815T	aGG	aCA	2	7	All	0
S	815	R815del	AGG	---	7	7	B.1	0.000064
S	815	R815R	agG	agA	4	7	B.1.177	0.000053
S	815	R815R	Agg	Cgg	3	7	B.1.177	0.00004
S	815	R815del	AGG	---	7	7	B.1.621	0.00062
S	815	R815W	Agg	Tgg	6	6	All	0.000001
S	815	R815del	AGG	---	6	6	AY.43	0.000027
S	815	R815K	aGg	aAg	6	6	B.1.617.2	0.000023
S	815	R815R	Agg	Cgg	3	6	P.1	0.000047
S	815	R815R	agG	agA	3	6	P.1	0.000047
S	815	R815R	agG	agA	3	5	AY.103	0.000019
S	815	R815R	Agg	Cgg	2	5	AY.103	0.000012
S	815	R815R	agG	agA	5	5	AY.113	0.000712
S	815	R815R	agG	agA	5	5	AY.119	0.000177
S	815	R815R	Agg	Cgg	4	5	AY.29	0.000063
S	815	R815R	AgG	CgT	1	5	AY.29	0.000016
S	815	R815R	Agg	Cgg	5	5	AY.4.4	0.002046
S	815	R815M	aGg	aTg	5	5	B.1	0.000046
S	815	R815del	AGG	---	5	5	P.1	0.000079
S	815	R815del	AGG	---	5	5	P.1.15	0.001162
S	815	R815K	aGg	aAg	4	4	AY.39	0.000099
S	815	R815del	AGG	---	4	4	AY.4.5	0.00043
S	815	R815M	aGg	aTg	4	4	B.1.1.7	0.000004
S	815	R815K	aGg	aAg	4	4	B.1.311	0.001098
S	815	R815R	agG	agA	4	4	B.1.367	0.00317
S	815	R815del	AGG	---	4	4	B.1.617.2	0.000015
S	815	R815R	agG	agA	3	3	AE.8	0.001467
S	815	R815K	aGg	aAg	3	3	AY.119	0.000106
S	815	R815K	aGg	aAg	3	3	AY.25	0.000018
S	815	R815M	aGg	aTg	3	3	AY.29	0.000047
S	815	R815R	agG	agA	3	3	AY.3	0.00003
S	815	R815G	Agg	Ggg	3	3	AY.43	0.000013
S	815	R815del1	aGg	a-g	2	3	AY.44	0.000012
S	815	R815del1	AgG	Gg-	1	3	AY.44	0.000006
S	815	R815R	agG	agA	3	3	AY.45	0.000365
S	815	R815R	AgG	CgT	2	3	AY.71	0.00095
S	815	R815R	Agg	Cgg	1	3	AY.71	0.000475
S	815	R815K	aGg	aAg	3	3	B.1	0.000027
S	815	R815K	aGg	aAg	3	3	B.1.1.176	0.001318
S	815	R815S	agG	agT	3	3	D.2	0.000225
S	815	R815T	aGG	aCA	2	2		0.111111
S	815	R815V	AGG	GTT	1	2	All	0
S	815	R815V	AGg	GTg	1	2	All	0
S	815	R815del2	aGG	a--	1	2	All	0
S	815	R815del2	AGg	--g	1	2	All	0
S	815	R815M	aGg	aTg	2	2	AY.103	0.000012
S	815	R815del	AGG	---	2	2	AY.120	0.000074
S	815	R815R	agG	agA	2	2	AY.121	0.000271
S	815	R815del	AGG	---	2	2	AY.25	0.000012
S	815	R815R	Agg	Cgg	2	2	AY.27	0.000129
S	815	R815R	Agg	Cgg	1	2	AY.34	0.000097
S	815	R815R	agG	agA	1	2	AY.34	0.000097
S	815	R815K	aGg	aAg	2	2	AY.36	0.000296
S	815	R815M	aGg	aTg	2	2	AY.4	0.000003
S	815	R815del	AGG	---	2	2	AY.4	0.000003
S	815	R815del	AGG	---	2	2	AY.75	0.000112
S	815	R815del	AGG	---	2	2	B.1.1.236	0.013793
S	815	R815K	aGg	aAg	2	2	B.1.1.269	0.002706
S	815	R815R	Agg	Cgg	2	2	B.1.1.28	0.000622
S	815	R815S	agG	agT	2	2	B.1.1.7	0.000002
S	815	R815W	Agg	Tgg	2	2	B.1.1.7	0.000002
S	815	R815del	AGG	---	2	2	B.1.177.63	0.005405
S	815	R815W	Agg	Tgg	2	2	B.1.235	0.005038
S	815	R815K	aGg	aAg	2	2	B.1.351	0.000059
S	815	R815K	aGg	aAg	2	2	B.1.36.29	0.001035
S	815	R815K	aGg	aAg	2	2	B.1.565	0.001621
S	815	R815G	Agg	Ggg	2	2	B.1.617.2	0.000008
S	815	R815M	aGg	aTg	2	2	D.2	0.00015
S	815	R815S	agG	agT	2	2	P.1.1	0.000635
S	815	R815K	aGg	aAg	1	1	A	0.000387
S	815	R815del	AGG	---	1	1	A	0.000387
S	815	R815G	Agg	Ggg	1	1	A.1	0.000282
S	815	R815I	aGG	aTA	1	1	All	0
S	815	R815C	AgG	TgT	1	1	All	0
S	815	R815E	AGg	GAg	1	1	All	0
S	815	R815N	aGG	aAT	1	1	All	0
S	815	R815del	AGG	---	1	1	AY.10	0.00053
S	815	R815K	aGg	aAg	1	1	AY.100	0.000046
S	815	R815M	aGg	aTg	1	1	AY.113	0.000142
S	815	R815K	aGg	aAg	1	1	AY.117	0.000085
S	815	R815R	Agg	Cgg	1	1	AY.12	0.000316
S	815	R815R	agG	agA	1	1	AY.14	0.000088
S	815	R815del	AGG	---	1	1	AY.24	0.000431
S	815	R815R	agG	agA	1	1	AY.26	0.000028
S	815	R815S	AGG	TCA	1	1	AY.26	0.000028
S	815	R815K	aGg	aAg	1	1	AY.3	0.00001
S	815	R815M	aGg	aTg	1	1	AY.3.1	0.000085
S	815	R815S	agG	agT	1	1	AY.33	0.000067
S	815	R815S	agG	agT	1	1	AY.35	0.000233
S	815	R815M	aGg	aTg	1	1	AY.39	0.000025
S	815	R815G	Agg	Ggg	1	1	AY.39.1	0.00004
S	815	R815R	Agg	Cgg	1	1	AY.39.1	0.00004
S	815	R815T	aGg	aCg	1	1	AY.4	0.000002
S	815	R815del1	aGg	a-g	1	1	AY.4	0.000002
S	815	R815S	agG	agT	1	1	AY.4	0.000002
S	815	R815R	Agg	Cgg	1	1	AY.42	0.00004
S	815	R815del1	AGG	-TA	1	1	AY.43	0.000004
S	815	R815T	aGg	aCg	1	1	AY.43	0.000004
S	815	R815W	Agg	Tgg	1	1	AY.44	0.000006
S	815	R815del	AGG	---	1	1	AY.44	0.000006
S	815	R815K	aGg	aAg	1	1	AY.44	0.000006
S	815	R815del	AGG	---	1	1	AY.46.2	0.000635
S	815	R815S	agG	agC	1	1	AY.47	0.000031
S	815	R815K	aGg	aAg	1	1	AY.47	0.000031
S	815	R815R	agG	agA	1	1	AY.5	0.000021
S	815	R815S	agG	agT	1	1	AY.5	0.000021
S	815	R815M	aGg	aTg	1	1	AY.5	0.000021
S	815	R815K	aGg	aAg	1	1	AY.5.3	0.000337
S	815	R815R	agG	agA	1	1	AY.58	0.000907
S	815	R815del	AGG	---	1	1	AY.68	0.000274
S	815	R815S	agG	agC	1	1	AY.69	0.000187
S	815	R815S	agG	agT	1	1	AY.71	0.000475
S	815	R815R	AgG	CgT	1	1	AY.75	0.000056
S	815	R815I	aGG	aTA	1	1	AY.75	0.000056
S	815	R815R	agG	agA	1	1	AY.75.1	0.00018
S	815	R815R	agG	agA	1	1	AY.79	0.001211
S	815	R815K	aGg	aAg	1	1	AY.85	0.000427
S	815	R815S	agG	agC	1	1	AY.9	0.000068
S	815	R815T	aGg	aCg	1	1	AY.9	0.000068
S	815	R815S	agG	agT	1	1	AY.9.2	0.000037
S	815	R815del1	aGg	a-g	1	1	AY.93	0.000273
S	815	R815R	Agg	Cgg	1	1	AY.98	0.000079
S	815	R815del	AGG	---	1	1	AY.98.1	0.000048
S	815	R815del	AGG	---	1	1	B.1.1	0.000018
S	815	R815R	agG	agA	1	1	B.1.1	0.000018
S	815	R815S	agG	agT	1	1	B.1.1	0.000018
S	815	R815del	AGG	---	1	1	B.1.1.139	0.022727
S	815	R815G	Agg	Ggg	1	1	B.1.1.210	0.005714
S	815	R815V	AGg	GTg	1	1	B.1.1.210	0.005714
S	815	R815M	aGg	aTg	1	1	B.1.1.210	0.005714
S	815	R815M	aGg	aTg	1	1	B.1.1.220	0.001859
S	815	R815R	agG	agA	1	1	B.1.1.222	0.000204
S	815	R815K	aGg	aAg	1	1	B.1.1.244	0.015385
S	815	R815R	agG	agA	1	1	B.1.1.263	0.001558
S	815	R815del	AGG	---	1	1	B.1.1.291	0.000742
S	815	R815del	AGG	---	1	1	B.1.1.315	0.008475
S	815	R815R	agG	agA	1	1	B.1.1.351	0.002793
S	815	R815del	AGG	---	1	1	B.1.1.372	0.000689
S	815	R815G	Agg	Ggg	1	1	B.1.1.406	0.006494
S	815	R815del	AGG	---	1	1	B.1.1.409	0.002833
S	815	R815E	AGg	GAg	1	1	B.1.1.7	0.000001
S	815	R815T	aGg	aCg	1	1	B.1.1.7	0.000001
S	815	R815del1	Agg	-gg	1	1	B.1.1.7	0.000001
S	815	R815C	AgG	TgT	1	1	B.1.1.7	0.000001
S	815	R815del	AGG	---	1	1	B.1.160	0.000031
S	815	R815M	aGg	aTg	1	1	B.1.160	0.000031
S	815	R815G	Agg	Ggg	1	1	B.1.160.16	0.000929
S	815	R815K	aGg	aAg	1	1	B.1.160.8	0.001289
S	815	R815del	AGG	---	1	1	B.1.177	0.000013
S	815	R815M	aGg	aTg	1	1	B.1.177	0.000013
S	815	R815K	aGg	aAg	1	1	B.1.177	0.000013
S	815	R815del	AGG	---	1	1	B.1.177.17	0.000821
S	815	R815del2	aGG	a--	1	1	B.1.177.51	0.004566
S	815	R815K	aGg	aAg	1	1	B.1.177.56	0.000668
S	815	R815S	agG	agT	1	1	B.1.177.73	0.000566
S	815	R815M	aGg	aTg	1	1	B.1.177.86	0.000183
S	815	R815S	agG	agT	1	1	B.1.2	0.000009
S	815	R815del	AGG	---	1	1	B.1.2	0.000009
S	815	R815del	AGG	---	1	1	B.1.258	0.000067
S	815	R815S	agG	agT	1	1	B.1.258.14	0.00098
S	815	R815K	aGg	aAg	1	1	B.1.284	0.013158
S	815	R815R	agG	agA	1	1	B.1.311	0.000275
S	815	R815del	AGG	---	1	1	B.1.351	0.00003
S	815	R815R	agG	agA	1	1	B.1.36	0.000146
S	815	R815V	AGG	GTT	1	1	B.1.36.29	0.000517
S	815	R815W	Agg	Tgg	1	1	B.1.362	0.001541
S	815	R815S	agG	agT	1	1	B.1.369	0.000285
S	815	R815S	agG	agT	1	1	B.1.396	0.000706
S	815	R815R	agG	agA	1	1	B.1.427	0.00005
S	815	R815S	agG	agT	1	1	B.1.427	0.00005
S	815	R815S	agG	agC	1	1	B.1.429	0.000024
S	815	R815M	aGg	aTg	1	1	B.1.511	0.034483
S	815	R815del	AGG	---	1	1	B.1.526	0.000024
S	815	R815S	agG	agT	1	1	B.1.526	0.000024
S	815	R815del	AGG	---	1	1	B.1.561	0.000397
S	815	R815S	agG	agT	1	1	B.1.577	0.000687
S	815	R815S	agG	agC	1	1	B.1.610	0.003546
S	815	R815K	aGg	aAg	1	1	B.1.617.1	0.000129
S	815	R815N	aGG	aAT	1	1	B.1.617.1	0.000129
S	815	R815M	aGg	aTg	1	1	B.1.617.2	0.000004
S	815	R815del2	AGg	--g	1	1	B.1.617.2	0.000004
S	815	R815del1	agG	ag-	1	1	B.1.617.2	0.000004
S	815	R815R	Agg	Cgg	1	1	B.1.621	0.000089
S	815	R815del	AGG	---	1	1	B.1.638	0.052632
S	815	R815M	aGg	aTg	1	1	B.4	0.002208
S	815	R815K	aGg	aAg	1	1	C.37	0.000116
S	815	R815del	AGG	---	1	1	C.37	0.000116
S	815	R815T	aGg	aCg	1	1	D.2	0.000075
S	815	R815del1	aGg	a-g	1	1	D.2	0.000075
S	815	R815K	aGg	aAg	1	1	P.1	0.000016
S	815	R815S	agG	agT	1	1	P.1	0.000016
S	815	R815S	agG	agT	1	1	P.1.10	0.000269
S	815	R815del	AGG	---	1	1	P.1.13	0.000898
S	815	R815M	aGg	aTg	1	1	P.1.14	0.000048
S	815	R815del	AGG	---	1	1	P.1.7	0.000319
S	815	R815del1	Agg	-gg	1	1	Q.1	0.000126
S	815	R815del1	Agg	-gg	1	1	Q.2	0.000613
S	815	R815R	AgG	CgT	1	1	Q.4	0.000455
S	815	R815del	AGG	---	1	1	Q.8	0.000165
S	815	R815M	aGg	aTg	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.