CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : Mut = A217A

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	217	A217A		syn	gcT	gcC	640	438	0.684375	28922-28924
N	217	A217A		syn	gcT	gcA	640	111	0.173438	28922-28924
N	217	A217A		syn	gcT	gcG	640	91	0.142188	28922-28924

Details of the mutation A217A 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	217	A217A	gcT	gcC	438	640	All	0.000084
N	217	A217A	gcT	gcA	111	640	All	0.000021
N	217	A217A	gcT	gcG	91	640	All	0.000017
N	217	A217A	gcT	gcC	161	163	AY.44	0.00098
N	217	A217A	gcT	gcA	2	163	AY.44	0.000012
N	217	A217A	gcT	gcC	59	87	B.1.1.7	0.000053
N	217	A217A	gcT	gcG	15	87	B.1.1.7	0.000013
N	217	A217A	gcT	gcA	13	87	B.1.1.7	0.000012
N	217	A217A	gcT	gcG	58	59	B.1.429	0.001365
N	217	A217A	gcT	gcA	1	59	B.1.429	0.000024
N	217	A217A	gcT	gcC	24	29	B.1.2	0.000211
N	217	A217A	gcT	gcG	3	29	B.1.2	0.000026
N	217	A217A	gcT	gcA	2	29	B.1.2	0.000018
N	217	A217A	gcT	gcC	26	26	AY.117	0.002197
N	217	A217A	gcT	gcA	20	21	B.1.160	0.000624
N	217	A217A	gcT	gcC	1	21	B.1.160	0.000031
N	217	A217A	gcT	gcC	19	19	A.1	0.005355
N	217	A217A	gcT	gcC	14	17	B.1.617.2	0.000053
N	217	A217A	gcT	gcA	3	17	B.1.617.2	0.000011
N	217	A217A	gcT	gcC	13	14	P.1	0.000205
N	217	A217A	gcT	gcG	1	14	P.1	0.000016
N	217	A217A	gcT	gcC	12	13	AY.20	0.000466
N	217	A217A	gcT	gcA	1	13	AY.20	0.000039
N	217	A217A	gcT	gcC	5	13	AY.4	0.000008
N	217	A217A	gcT	gcG	4	13	AY.4	0.000006
N	217	A217A	gcT	gcA	4	13	AY.4	0.000006
N	217	A217A	gcT	gcC	9	13	B.1.177	0.000119
N	217	A217A	gcT	gcA	4	13	B.1.177	0.000053
N	217	A217A	gcT	gcA	12	12	AY.29	0.000189
N	217	A217A	gcT	gcC	11	11	AY.103	0.000068
N	217	A217A	gcT	gcA	10	10	AY.116	0.002868
N	217	A217A	gcT	gcC	6	6	AY.39.1	0.000238
N	217	A217A	gcT	gcC	6	6	AY.9.2	0.00022
N	217	A217A	gcT	gcA	3	6	B.1	0.000027
N	217	A217A	gcT	gcC	2	6	B.1	0.000018
N	217	A217A	gcT	gcG	1	6	B.1	0.000009
N	217	A217A	gcT	gcC	3	5	AY.25	0.000018
N	217	A217A	gcT	gcA	2	5	AY.25	0.000012
N	217	A217A	gcT	gcC	4	5	AY.3	0.00004
N	217	A217A	gcT	gcA	1	5	AY.3	0.00001
N	217	A217A	gcT	gcC	5	5	AY.43	0.000022
N	217	A217A	gcT	gcA	5	5	B.1.177.86	0.000917
N	217	A217A	gcT	gcC	4	4	AY.100	0.000184
N	217	A217A	gcT	gcC	2	4	AY.120	0.000074
N	217	A217A	gcT	gcA	2	4	AY.120	0.000074
N	217	A217A	gcT	gcC	4	4	AY.79	0.004843
N	217	A217A	gcT	gcC	2	4	AY.9	0.000135
N	217	A217A	gcT	gcA	2	4	AY.9	0.000135
N	217	A217A	gcT	gcC	2	4	B.1.1	0.000036
N	217	A217A	gcT	gcG	1	4	B.1.1	0.000018
N	217	A217A	gcT	gcA	1	4	B.1.1	0.000018
N	217	A217A	gcT	gcC	3	3	AY.121	0.000406
N	217	A217A	gcT	gcA	2	3	AY.33	0.000134
N	217	A217A	gcT	gcC	1	3	AY.33	0.000067
N	217	A217A	gcT	gcA	2	3	B.1.351	0.000059
N	217	A217A	gcT	gcC	1	3	B.1.351	0.00003
N	217	A217A	gcT	gcC	2	2	AY.102	0.000053
N	217	A217A	gcT	gcA	2	2	AY.34	0.000194
N	217	A217A	gcT	gcC	2	2	AY.45	0.000243
N	217	A217A	gcT	gcC	2	2	AY.5	0.000041
N	217	A217A	gcT	gcG	2	2	B.1.1.216	0.001781
N	217	A217A	gcT	gcC	2	2	B.1.1.440	0.023529
N	217	A217A	gcT	gcC	2	2	B.1.1.50	0.001358
N	217	A217A	gcT	gcG	1	2	B.1.160.16	0.000929
N	217	A217A	gcT	gcC	1	2	B.1.160.16	0.000929
N	217	A217A	gcT	gcC	2	2	B.1.234	0.000264
N	217	A217A	gcT	gcG	2	2	B.1.241	0.001623
N	217	A217A	gcT	gcC	2	2	B.1.258.17	0.000208
N	217	A217A	gcT	gcC	2	2	B.1.546	0.007407
N	217	A217A	gcT	gcA	2	2	B.1.564	0.000852
N	217	A217A	gcT	gcA	2	2	B.1.564.1	0.003155
N	217	A217A	gcT	gcC	1	1		0.055556
N	217	A217A	gcT	gcC	1	1	A.2.4	0.003367
N	217	A217A	gcT	gcC	1	1	AY.110	0.000113
N	217	A217A	gcT	gcC	1	1	AY.12	0.000316
N	217	A217A	gcT	gcG	1	1	AY.120.1	0.000321
N	217	A217A	gcT	gcC	1	1	AY.19	0.00114
N	217	A217A	gcT	gcA	1	1	AY.26	0.000028
N	217	A217A	gcT	gcC	1	1	AY.39	0.000025
N	217	A217A	gcT	gcC	1	1	AY.4.2	0.000022
N	217	A217A	gcT	gcC	1	1	AY.46	0.000104
N	217	A217A	gcT	gcA	1	1	AY.5.4	0.000277
N	217	A217A	gcT	gcC	1	1	AY.61	0.000105
N	217	A217A	gcT	gcC	1	1	AY.63	0.000387
N	217	A217A	gcT	gcC	1	1	AY.74	0.000116
N	217	A217A	gcT	gcC	1	1	AY.84	0.000437
N	217	A217A	gcT	gcC	1	1	B.1.1.1	0.000327
N	217	A217A	gcT	gcC	1	1	B.1.1.214	0.000055
N	217	A217A	gcT	gcC	1	1	B.1.1.220	0.001859
N	217	A217A	gcT	gcC	1	1	B.1.1.28	0.000311
N	217	A217A	gcT	gcA	1	1	B.1.1.305	0.003861
N	217	A217A	gcT	gcA	1	1	B.1.1.434	0.000349
N	217	A217A	gcT	gcA	1	1	B.1.1.70	0.000341
N	217	A217A	gcT	gcG	1	1	B.1.147	0.000756
N	217	A217A	gcT	gcC	1	1	B.1.160.10	0.008065
N	217	A217A	gcT	gcA	1	1	B.1.160.30	0.002976
N	217	A217A	gcT	gcC	1	1	B.1.162	0.005025
N	217	A217A	gcT	gcC	1	1	B.1.221	0.000071
N	217	A217A	gcT	gcG	1	1	B.1.427	0.00005
N	217	A217A	gcT	gcA	1	1	B.1.526	0.000024
N	217	A217A	gcT	gcC	1	1	B.1.595	0.000261
N	217	A217A	gcT	gcC	1	1	B.1.596	0.000087
N	217	A217A	gcT	gcA	1	1	B.1.609	0.000479
N	217	A217A	gcT	gcA	1	1	B.1.621	0.000089
N	217	A217A	gcT	gcC	1	1	B.1.637	0.000073
N	217	A217A	gcT	gcA	1	1	C.37	0.000116
N	217	A217A	gcT	gcA	1	1	P.1.15	0.000232
N	217	A217A	gcT	gcA	1	1	P.3	0.001595
N	217	A217A	gcT	gcA	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.