CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : Mut = A575A

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	575	A575A		syn	gcT	gcC	8083	7935	0.98169	23285-23287
S	575	A575A		syn	gcT	gcA	8083	115	0.0142274	23285-23287
S	575	A575A		syn	gcT	gcG	8083	33	0.00408264	23285-23287

Details of the mutation A575A 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	575	A575A	gcT	gcC	7935	8083	All	0.001518
S	575	A575A	gcT	gcA	115	8083	All	0.000022
S	575	A575A	gcT	gcG	33	8083	All	0.000006
S	575	A575A	gcT	gcC	3282	3282	B.1.1.318	0.990344
S	575	A575A	gcT	gcC	1205	1205	AZ.2	0.989327
S	575	A575A	gcT	gcC	1139	1139	AZ.1	0.987858
S	575	A575A	gcT	gcC	655	655	AZ.3	0.995441
S	575	A575A	gcT	gcC	294	298	AY.43	0.001303
S	575	A575A	gcT	gcA	3	298	AY.43	0.000013
S	575	A575A	gcT	gcG	1	298	AY.43	0.000004
S	575	A575A	gcT	gcC	298	298	AZ.4	1
S	575	A575A	gcT	gcC	284	284	AZ.5	0.996491
S	575	A575A	gcT	gcC	123	123	AZ.2.1	1
S	575	A575A	gcT	gcC	119	119	AZ.6	1
S	575	A575A	gcT	gcC	48	86	B.1.1.7	0.000043
S	575	A575A	gcT	gcA	34	86	B.1.1.7	0.00003
S	575	A575A	gcT	gcG	4	86	B.1.1.7	0.000004
S	575	A575A	gcT	gcC	68	68	B.1.221	0.00483
S	575	A575A	gcT	gcC	53	53	B.1.1	0.000961
S	575	A575A	gcT	gcC	41	48	B.1.617.2	0.000154
S	575	A575A	gcT	gcA	6	48	B.1.617.2	0.000023
S	575	A575A	gcT	gcG	1	48	B.1.617.2	0.000004
S	575	A575A	gcT	gcA	34	39	B.1.177	0.000448
S	575	A575A	gcT	gcC	4	39	B.1.177	0.000053
S	575	A575A	gcT	gcG	1	39	B.1.177	0.000013
S	575	A575A	gcT	gcC	19	29	P.1	0.000299
S	575	A575A	gcT	gcG	5	29	P.1	0.000079
S	575	A575A	gcT	gcA	5	29	P.1	0.000079
S	575	A575A	gcT	gcC	28	28	A.1	0.007892
S	575	A575A	gcT	gcC	23	23	AY.39	0.000568
S	575	A575A	gcT	gcC	14	22	AY.4	0.000022
S	575	A575A	gcT	gcA	8	22	AY.4	0.000012
S	575	A575A	gcT	gcC	17	20	AY.102	0.000451
S	575	A575A	gcT	gcA	3	20	AY.102	0.00008
S	575	A575A	gcT	gcC	18	18	AY.4.5	0.001935
S	575	A575A	gcT	gcC	10	15	AY.44	0.000061
S	575	A575A	gcT	gcA	5	15	AY.44	0.00003
S	575	A575A	gcT	gcC	13	13	AY.46.4	0.002139
S	575	A575A	gcT	gcC	11	11	AY.99	0.011542
S	575	A575A	gcT	gcC	11	11	B.1	0.000101
S	575	A575A	gcT	gcC	8	10	AY.103	0.00005
S	575	A575A	gcT	gcA	2	10	AY.103	0.000012
S	575	A575A	gcT	gcC	9	10	AY.23	0.000628
S	575	A575A	gcT	gcA	1	10	AY.23	0.00007
S	575	A575A	gcT	gcC	10	10	AY.5	0.000206
S	575	A575A	gcT	gcG	10	10	B.1.1.139	0.227273
S	575	A575A	gcT	gcC	9	10	B.1.617.1	0.001161
S	575	A575A	gcT	gcA	1	10	B.1.617.1	0.000129
S	575	A575A	gcT	gcC	8	9	B.1.2	0.00007
S	575	A575A	gcT	gcA	1	9	B.1.2	0.000009
S	575	A575A	gcT	gcC	7	7	AT.1	0.035897
S	575	A575A	gcT	gcC	5	5	AY.25	0.00003
S	575	A575A	gcT	gcC	5	5	B.1.1.28	0.001556
S	575	A575A	gcT	gcC	5	5	B.1.1.409	0.014164
S	575	A575A	gcT	gcG	5	5	B.1.291	0.096154
S	575	A575A	gcT	gcA	3	4	AY.4.2	0.000065
S	575	A575A	gcT	gcC	1	4	AY.4.2	0.000022
S	575	A575A	gcT	gcC	4	4	AY.72	0.005442
S	575	A575A	gcT	gcC	4	4	B.1.1.411	0.058824
S	575	A575A	gcT	gcC	4	4	B.1.1.448	0.00813
S	575	A575A	gcT	gcC	4	4	B.1.110.3	0.002874
S	575	A575A	gcT	gcC	4	4	B.1.234	0.000528
S	575	A575A	gcT	gcC	3	3	A	0.001161
S	575	A575A	gcT	gcC	3	3	AY.114	0.000693
S	575	A575A	gcT	gcC	2	3	AY.20	0.000078
S	575	A575A	gcT	gcG	1	3	AY.20	0.000039
S	575	A575A	gcT	gcC	3	3	AY.3	0.00003
S	575	A575A	gcT	gcC	3	3	AY.30	0.001187
S	575	A575A	gcT	gcC	2	3	B.1.351	0.000059
S	575	A575A	gcT	gcG	1	3	B.1.351	0.00003
S	575	A575A	gcT	gcC	3	3	B.1.525	0.000339
S	575	A575A	gcT	gcC	3	3	B.1.576	0.00272
S	575	A575A	gcT	gcC	3	3	B.1.596	0.000261
S	575	A575A	gcT	gcC	3	3	B.1.621	0.000266
S	575	A575A	gcT	gcA	1	2	A.2.5	0.000499
S	575	A575A	gcT	gcC	1	2	A.2.5	0.000499
S	575	A575A	gcT	gcC	1	2	AY.34	0.000097
S	575	A575A	gcT	gcA	1	2	AY.34	0.000097
S	575	A575A	gcT	gcC	2	2	AY.39.1	0.000079
S	575	A575A	gcT	gcC	2	2	AY.46.6	0.000144
S	575	A575A	gcT	gcC	2	2	AY.47	0.000062
S	575	A575A	gcT	gcC	1	2	B	0.000128
S	575	A575A	gcT	gcG	1	2	B	0.000128
S	575	A575A	gcT	gcC	2	2	B.1.1.484	0.2
S	575	A575A	gcT	gcA	2	2	B.1.396	0.001411
S	575	A575A	gcT	gcA	1	2	B.1.526	0.000024
S	575	A575A	gcT	gcG	1	2	B.1.526	0.000024
S	575	A575A	gcT	gcA	2	2	B.1.561	0.000794
S	575	A575A	gcT	gcC	2	2	B.1.575	0.000607
S	575	A575A	gcT	gcG	2	2	B.23	0.005848
S	575	A575A	gcT	gcC	2	2	N.5	0.003534
S	575	A575A	gcT	gcC	1	1	AY.110	0.000113
S	575	A575A	gcT	gcC	1	1	AY.119	0.000035
S	575	A575A	gcT	gcA	1	1	AY.13	0.000161
S	575	A575A	gcT	gcC	1	1	AY.14	0.000088
S	575	A575A	gcT	gcC	1	1	AY.26	0.000028
S	575	A575A	gcT	gcC	1	1	AY.27	0.000065
S	575	A575A	gcT	gcC	1	1	AY.29	0.000016
S	575	A575A	gcT	gcC	1	1	AY.36	0.000148
S	575	A575A	gcT	gcC	1	1	AY.42	0.00004
S	575	A575A	gcT	gcC	1	1	AY.59	0.00053
S	575	A575A	gcT	gcC	1	1	AY.67	0.000464
S	575	A575A	gcT	gcC	1	1	AY.71	0.000475
S	575	A575A	gcT	gcC	1	1	AY.75	0.000056
S	575	A575A	gcT	gcC	1	1	AY.75.1	0.00018
S	575	A575A	gcT	gcC	1	1	AY.9.2	0.000037
S	575	A575A	gcT	gcC	1	1	B.1.1.142	0.017544
S	575	A575A	gcT	gcC	1	1	B.1.1.222	0.000204
S	575	A575A	gcT	gcC	1	1	B.1.1.307	0.002532
S	575	A575A	gcT	gcA	1	1	B.1.160	0.000031
S	575	A575A	gcT	gcC	1	1	B.1.177.16	0.000664
S	575	A575A	gcT	gcC	1	1	B.1.177.57	0.000281
S	575	A575A	gcT	gcC	1	1	B.1.177.7	0.000165
S	575	A575A	gcT	gcC	1	1	B.1.218	0.005155
S	575	A575A	gcT	gcC	1	1	B.1.369	0.000285
S	575	A575A	gcT	gcC	1	1	B.1.429	0.000024
S	575	A575A	gcT	gcC	1	1	B.1.470	0.001404
S	575	A575A	gcT	gcC	1	1	B.1.620	0.000946
S	575	A575A	gcT	gcC	1	1	B.58	0.010204
S	575	A575A	gcT	gcC	1	1	D.2	0.000075
S	575	A575A	gcT	gcC	1	1	P.1.7	0.000319

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.