CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp9 : CodonNum = 42 & Codon = ctC

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
ORF1ab/nsp9	42	L42L	L4182L	syn	ctT	ctC	1739	230	0.13226	12809-12811

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
ORF1ab/nsp9	42	L42L	ctT	ctC	230	1739	All	0.000044
ORF1ab/nsp9	42	L42L	ctT	ctC	59	59	B.1.565	0.047812
ORF1ab/nsp9	42	L42L	ctT	ctC	17	35	B.1.1.7	0.000015
ORF1ab/nsp9	42	L42L	ctT	ctC	2	29	P.1	0.000032
ORF1ab/nsp9	42	L42L	ctT	ctC	28	28	AY.26	0.000793
ORF1ab/nsp9	42	L42L	ctT	ctC	28	28	B.1.427	0.001414
ORF1ab/nsp9	42	L42L	ctT	ctC	19	19	B.1.160	0.000593
ORF1ab/nsp9	42	L42L	ctT	ctC	5	16	B.1.617.2	0.000019
ORF1ab/nsp9	42	L42L	ctT	ctC	2	14	B.1.1	0.000036
ORF1ab/nsp9	42	L42L	ctT	ctC	5	9	AY.13	0.000805
ORF1ab/nsp9	42	L42L	ctT	ctC	9	9	AY.29	0.000142
ORF1ab/nsp9	42	L42L	ctT	ctC	1	9	B.1.429	0.000024
ORF1ab/nsp9	42	L42L	ctT	ctC	4	8	AY.25	0.000024
ORF1ab/nsp9	42	L42L	ctT	ctC	6	8	AY.4	0.000009
ORF1ab/nsp9	42	L42L	ctT	ctC	3	8	AY.44	0.000018
ORF1ab/nsp9	42	L42L	ctT	ctC	4	8	B.1	0.000037
ORF1ab/nsp9	42	L42L	ctT	ctC	6	7	B.1.351	0.000178
ORF1ab/nsp9	42	L42L	ctT	ctC	2	6	B.1.2	0.000018
ORF1ab/nsp9	42	L42L	ctT	ctC	5	5	B.1.170	0.021552
ORF1ab/nsp9	42	L42L	ctT	ctC	4	4	AY.99.2	0.000369
ORF1ab/nsp9	42	L42L	ctT	ctC	1	3	AY.43	0.000004
ORF1ab/nsp9	42	L42L	ctT	ctC	2	3	AY.47	0.000062
ORF1ab/nsp9	42	L42L	ctT	ctC	1	2	AY.23	0.00007
ORF1ab/nsp9	42	L42L	ctT	ctC	1	1	AY.103	0.000006
ORF1ab/nsp9	42	L42L	ctT	ctC	1	1	AY.117	0.000085
ORF1ab/nsp9	42	L42L	ctT	ctC	1	1	AY.118	0.000063
ORF1ab/nsp9	42	L42L	ctT	ctC	1	1	AY.20	0.000039
ORF1ab/nsp9	42	L42L	ctT	ctC	1	1	AY.36	0.000148
ORF1ab/nsp9	42	L42L	ctT	ctC	1	1	AY.69	0.000187
ORF1ab/nsp9	42	L42L	ctT	ctC	1	1	AY.98	0.000079
ORF1ab/nsp9	42	L42L	ctT	ctC	1	1	B.1.1.317	0.000412
ORF1ab/nsp9	42	L42L	ctT	ctC	1	1	B.1.128	0.000635
ORF1ab/nsp9	42	L42L	ctT	ctC	1	1	B.1.139	0.000733
ORF1ab/nsp9	42	L42L	ctT	ctC	1	1	B.1.160.11	0.005714
ORF1ab/nsp9	42	L42L	ctT	ctC	1	1	B.1.177	0.000013
ORF1ab/nsp9	42	L42L	ctT	ctC	1	1	B.1.250	0.014493
ORF1ab/nsp9	42	L42L	ctT	ctC	1	1	B.1.378	0.006849
ORF1ab/nsp9	42	L42L	ctT	ctC	1	1	B.1.524	0.001406
ORF1ab/nsp9	42	L42L	ctT	ctC	1	1	B.1.560	0.00463
ORF1ab/nsp9	42	L42L	ctT	ctC	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.