CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : Mut = A694A

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	694	A694A		syn	gcC	gcT	2382	2244	0.942065	23642-23644
S	694	A694A		syn	gcC	gcA	2382	136	0.0570949	23642-23644
S	694	A694A		syn	gcC	gcG	2382	2	0.000839631	23642-23644

Details of the mutation A694A 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	694	A694A	gcC	gcT	2244	2382	All	0.000429
S	694	A694A	gcC	gcA	136	2382	All	0.000026
S	694	A694A	gcC	gcG	2	2382	All	0
S	694	A694A	gcC	gcT	1649	1649	B.1.177.54	1
S	694	A694A	gcC	gcT	150	150	B.1.177.4	0.031659
S	694	A694A	gcC	gcT	69	91	B.1.1.7	0.000062
S	694	A694A	gcC	gcA	22	91	B.1.1.7	0.00002
S	694	A694A	gcC	gcT	54	55	AY.75	0.003025
S	694	A694A	gcC	gcA	1	55	AY.75	0.000056
S	694	A694A	gcC	gcT	44	44	V.1	1
S	694	A694A	gcC	gcT	41	43	AY.25	0.000247
S	694	A694A	gcC	gcA	2	43	AY.25	0.000012
S	694	A694A	gcC	gcT	33	35	AY.4	0.000051
S	694	A694A	gcC	gcA	2	35	AY.4	0.000003
S	694	A694A	gcC	gcT	20	32	B.1.617.2	0.000075
S	694	A694A	gcC	gcA	12	32	B.1.617.2	0.000045
S	694	A694A	gcC	gcT	31	31	V.2	1
S	694	A694A	gcC	gcA	16	20	AY.46	0.001665
S	694	A694A	gcC	gcT	4	20	AY.46	0.000416
S	694	A694A	gcC	gcT	17	17	B.1.1.311	0.006089
S	694	A694A	gcC	gcA	8	15	AY.44	0.000049
S	694	A694A	gcC	gcT	7	15	AY.44	0.000043
S	694	A694A	gcC	gcA	13	14	AY.3	0.000129
S	694	A694A	gcC	gcT	1	14	AY.3	0.00001
S	694	A694A	gcC	gcT	7	13	AY.43	0.000031
S	694	A694A	gcC	gcA	6	13	AY.43	0.000027
S	694	A694A	gcC	gcT	9	10	B.1	0.000082
S	694	A694A	gcC	gcA	1	10	B.1	0.000009
S	694	A694A	gcC	gcT	9	10	B.1.1	0.000163
S	694	A694A	gcC	gcA	1	10	B.1.1	0.000018
S	694	A694A	gcC	gcT	8	10	B.1.177	0.000105
S	694	A694A	gcC	gcA	2	10	B.1.177	0.000026
S	694	A694A	gcC	gcA	9	9	AY.46.1	0.00924
S	694	A694A	gcC	gcT	6	6	AY.102	0.000159
S	694	A694A	gcC	gcT	6	6	AY.61	0.000629
S	694	A694A	gcC	gcT	5	6	B.1.2	0.000044
S	694	A694A	gcC	gcA	1	6	B.1.2	0.000009
S	694	A694A	gcC	gcT	5	5	AY.26	0.000142
S	694	A694A	gcC	gcT	3	5	AY.39	0.000074
S	694	A694A	gcC	gcA	2	5	AY.39	0.000049
S	694	A694A	gcC	gcT	4	5	B.1.1.519	0.000159
S	694	A694A	gcC	gcA	1	5	B.1.1.519	0.00004
S	694	A694A	gcC	gcA	3	4	AY.20	0.000117
S	694	A694A	gcC	gcT	1	4	AY.20	0.000039
S	694	A694A	gcC	gcT	4	4	AY.47	0.000124
S	694	A694A	gcC	gcT	4	4	B.1.1.239	0.129032
S	694	A694A	gcC	gcT	3	4	B.1.429	0.000071
S	694	A694A	gcC	gcA	1	4	B.1.429	0.000024
S	694	A694A	gcC	gcT	2	3	AY.103	0.000012
S	694	A694A	gcC	gcA	1	3	AY.103	0.000006
S	694	A694A	gcC	gcT	3	3	AY.120	0.000112
S	694	A694A	gcC	gcT	3	3	AY.13	0.000483
S	694	A694A	gcC	gcA	2	3	AY.42	0.00008
S	694	A694A	gcC	gcT	1	3	AY.42	0.00004
S	694	A694A	gcC	gcA	3	3	AY.46.2	0.001906
S	694	A694A	gcC	gcA	2	3	AY.6	0.000082
S	694	A694A	gcC	gcG	1	3	AY.6	0.000041
S	694	A694A	gcC	gcA	3	3	AY.62	0.001307
S	694	A694A	gcC	gcA	2	3	B.1.160	0.000062
S	694	A694A	gcC	gcT	1	3	B.1.160	0.000031
S	694	A694A	gcC	gcA	3	3	B.1.9	0.018519
S	694	A694A	gcC	gcT	2	2	AY.29	0.000032
S	694	A694A	gcC	gcA	2	2	AY.34	0.000194
S	694	A694A	gcC	gcT	2	2	AY.46.4	0.000329
S	694	A694A	gcC	gcT	1	2	AY.9.1	0.000084
S	694	A694A	gcC	gcA	1	2	AY.9.1	0.000084
S	694	A694A	gcC	gcT	2	2	AY.98	0.000158
S	694	A694A	gcC	gcA	2	2	B	0.000256
S	694	A694A	gcC	gcA	1	2	B.1.1.216	0.00089
S	694	A694A	gcC	gcT	1	2	B.1.1.216	0.00089
S	694	A694A	gcC	gcA	2	2	B.1.1.28	0.000622
S	694	A694A	gcC	gcT	2	2	B.1.426	0.002018
S	694	A694A	gcC	gcT	1	2	P.1	0.000016
S	694	A694A	gcC	gcA	1	2	P.1	0.000016
S	694	A694A	gcC	gcA	1	1	AY.113	0.000142
S	694	A694A	gcC	gcT	1	1	AY.116	0.000287
S	694	A694A	gcC	gcT	1	1	AY.118	0.000063
S	694	A694A	gcC	gcT	1	1	AY.119	0.000035
S	694	A694A	gcC	gcT	1	1	AY.121	0.000135
S	694	A694A	gcC	gcT	1	1	AY.23	0.00007
S	694	A694A	gcC	gcT	1	1	AY.39.1	0.00004
S	694	A694A	gcC	gcT	1	1	AY.4.2	0.000022
S	694	A694A	gcC	gcA	1	1	AY.4.4	0.000409
S	694	A694A	gcC	gcA	1	1	AY.67	0.000464
S	694	A694A	gcC	gcA	1	1	AY.98.1	0.000048
S	694	A694A	gcC	gcT	1	1	B.1.1.153	0.001095
S	694	A694A	gcC	gcT	1	1	B.1.1.164	0.005155
S	694	A694A	gcC	gcT	1	1	B.1.1.214	0.000055
S	694	A694A	gcC	gcT	1	1	B.1.1.222	0.000204
S	694	A694A	gcC	gcT	1	1	B.1.1.306	0.000438
S	694	A694A	gcC	gcT	1	1	B.1.1.318	0.000302
S	694	A694A	gcC	gcA	1	1	B.1.1.369	0.000446
S	694	A694A	gcC	gcT	1	1	B.1.1.434	0.000349
S	694	A694A	gcC	gcT	1	1	B.1.1.514	0.038462
S	694	A694A	gcC	gcT	1	1	B.1.139	0.000733
S	694	A694A	gcC	gcT	1	1	B.1.219	0.009434
S	694	A694A	gcC	gcA	1	1	B.1.221	0.000071
S	694	A694A	gcC	gcT	1	1	B.1.243	0.00007
S	694	A694A	gcC	gcA	1	1	B.1.258.16	0.001637
S	694	A694A	gcC	gcT	1	1	B.1.319	0.003049
S	694	A694A	gcC	gcT	1	1	B.1.36.36	0.000602
S	694	A694A	gcC	gcT	1	1	B.1.509	0.000866
S	694	A694A	gcC	gcT	1	1	B.1.525	0.000113
S	694	A694A	gcC	gcT	1	1	B.1.617.1	0.000129
S	694	A694A	gcC	gcT	1	1	B.1.621	0.000089
S	694	A694A	gcC	gcA	1	1	B.61	0.005747
S	694	A694A	gcC	gcT	1	1	P.1.14	0.000048
S	694	A694A	gcC	gcT	1	1	P.1.17	0.000162
S	694	A694A	gcC	gcT	1	1	P.7	0.004367
S	694	A694A	gcC	gcG	1	1	Q.1	0.000126
S	694	A694A	gcC	gcT	1	1	Q.3	0.000145
S	694	A694A	gcC	gcT	1	1	U.3	0.003861

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.