CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : Mut = P162T

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	162	P162T		nonsyn	Cct	Act	195	97	0.497436	28757-28759
N	162	P162T		nonsyn	CcT	AcC	195	46	0.235897	28757-28759
N	162	P162T		nonsyn	CcT	AcA	195	43	0.220513	28757-28759
N	162	P162T		nonsyn	CcT	AcG	195	9	0.0461538	28757-28759

Details of the mutation P162T 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	162	P162T	Cct	Act	97	195	All	0.000019
N	162	P162T	CcT	AcC	46	195	All	0.000009
N	162	P162T	CcT	AcA	43	195	All	0.000008
N	162	P162T	CcT	AcG	9	195	All	0.000002
N	162	P162T	Cct	Act	31	73	B.1	0.000284
N	162	P162T	CcT	AcC	21	73	B.1	0.000192
N	162	P162T	CcT	AcA	16	73	B.1	0.000147
N	162	P162T	CcT	AcG	5	73	B.1	0.000046
N	162	P162T	Cct	Act	9	23	B.1.177	0.000119
N	162	P162T	CcT	AcA	7	23	B.1.177	0.000092
N	162	P162T	CcT	AcC	7	23	B.1.177	0.000092
N	162	P162T	Cct	Act	10	13	B.1.1.7	0.000009
N	162	P162T	CcT	AcG	2	13	B.1.1.7	0.000002
N	162	P162T	CcT	AcA	1	13	B.1.1.7	0.000001
N	162	P162T	Cct	Act	5	12	B.1.1	0.000091
N	162	P162T	CcT	AcC	4	12	B.1.1	0.000073
N	162	P162T	CcT	AcA	2	12	B.1.1	0.000036
N	162	P162T	CcT	AcG	1	12	B.1.1	0.000018
N	162	P162T	CcT	AcA	4	10	B.1.2	0.000035
N	162	P162T	Cct	Act	4	10	B.1.2	0.000035
N	162	P162T	CcT	AcC	2	10	B.1.2	0.000018
N	162	P162T	CcT	AcA	3	9	B.1.258	0.0002
N	162	P162T	CcT	AcC	3	9	B.1.258	0.0002
N	162	P162T	Cct	Act	3	9	B.1.258	0.0002
N	162	P162T	Cct	Act	6	6	AY.4	0.000009
N	162	P162T	Cct	Act	3	6	B.1.160	0.000094
N	162	P162T	CcT	AcA	2	6	B.1.160	0.000062
N	162	P162T	CcT	AcC	1	6	B.1.160	0.000031
N	162	P162T	Cct	Act	4	4	AY.102	0.000106
N	162	P162T	Cct	Act	2	4	B.1.1.39	0.001019
N	162	P162T	CcT	AcA	1	4	B.1.1.39	0.00051
N	162	P162T	CcT	AcC	1	4	B.1.1.39	0.00051
N	162	P162T	Cct	Act	4	4	B.1.617.2	0.000015
N	162	P162T	Cct	Act	1	3	B.1.1.170	0.001247
N	162	P162T	CcT	AcC	1	3	B.1.1.170	0.001247
N	162	P162T	CcT	AcA	1	3	B.1.1.170	0.001247
N	162	P162T	Cct	Act	1	3	B.1.1.515	0.02
N	162	P162T	CcT	AcC	1	3	B.1.1.515	0.02
N	162	P162T	CcT	AcA	1	3	B.1.1.515	0.02
N	162	P162T	CcT	AcC	1	3	B.1.221	0.000071
N	162	P162T	CcT	AcA	1	3	B.1.221	0.000071
N	162	P162T	Cct	Act	1	3	B.1.221	0.000071
N	162	P162T	CcT	AcG	1	3	B.1.609	0.000479
N	162	P162T	Cct	Act	1	3	B.1.609	0.000479
N	162	P162T	CcT	AcA	1	3	B.1.609	0.000479
N	162	P162T	Cct	Act	1	3	B.1.78	0.008547
N	162	P162T	CcT	AcA	1	3	B.1.78	0.008547
N	162	P162T	CcT	AcC	1	3	B.1.78	0.008547
N	162	P162T	CcT	AcC	1	2	B.1.177.44	0.000519
N	162	P162T	Cct	Act	1	2	B.1.177.44	0.000519
N	162	P162T	CcT	AcC	1	2	B.1.177.86	0.000183
N	162	P162T	Cct	Act	1	2	B.1.177.86	0.000183
N	162	P162T	CcT	AcA	1	2	B.1.258.11	0.000396
N	162	P162T	Cct	Act	1	2	B.1.258.11	0.000396
N	162	P162T	Cct	Act	1	2	B.1.389	0.001002
N	162	P162T	CcT	AcA	1	2	B.1.389	0.001002
N	162	P162T	Cct	Act	1	2	B.1.525	0.000113
N	162	P162T	CcT	AcC	1	2	B.1.525	0.000113
N	162	P162T	Cct	Act	1	1		0.055556
N	162	P162T	Cct	Act	1	1	AY.43	0.000004
N	162	P162T	Cct	Act	1	1	AY.44	0.000006
N	162	P162T	Cct	Act	1	1	AY.55	0.000917
N	162	P162T	Cct	Act	1	1	AY.98	0.000079
N	162	P162T	Cct	Act	1	1	B.1.596	0.000087

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.