CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF7a : CodonNum = 37 & Codon = tcC

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
ORF7a	37	S37S		syn	tcT	tcC	784	465	0.593112	27502-27504

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
ORF7a	37	S37S	tcT	tcC	465	784	All	0.000089
ORF7a	37	S37S	tcT	tcC	49	139	B.1.1.7	0.000044
ORF7a	37	S37S	tcT	tcC	101	111	B.1.351	0.003002
ORF7a	37	S37S	tcT	tcC	59	60	AY.103	0.000366
ORF7a	37	S37S	tcT	tcC	24	46	AY.4	0.000037
ORF7a	37	S37S	tcT	tcC	43	43	B.1.1.500	0.86
ORF7a	37	S37S	tcT	tcC	24	38	B.1.617.2	0.00009
ORF7a	37	S37S	tcT	tcC	4	23	B.1.2	0.000035
ORF7a	37	S37S	tcT	tcC	9	20	B.1	0.000082
ORF7a	37	S37S	tcT	tcC	17	18	B.1.177	0.000224
ORF7a	37	S37S	tcT	tcC	16	17	AY.44	0.000097
ORF7a	37	S37S	tcT	tcC	15	15	P.1.12	0.00726
ORF7a	37	S37S	tcT	tcC	13	13	AY.3	0.000129
ORF7a	37	S37S	tcT	tcC	10	13	B.1.258	0.000665
ORF7a	37	S37S	tcT	tcC	3	10	AY.43	0.000013
ORF7a	37	S37S	tcT	tcC	8	9	B.1.1	0.000145
ORF7a	37	S37S	tcT	tcC	3	9	P.1	0.000047
ORF7a	37	S37S	tcT	tcC	2	8	AY.25	0.000012
ORF7a	37	S37S	tcT	tcC	6	6	B.1.160.30	0.017857
ORF7a	37	S37S	tcT	tcC	4	5	AY.39	0.000099
ORF7a	37	S37S	tcT	tcC	4	4	AY.102	0.000106
ORF7a	37	S37S	tcT	tcC	4	4	AY.119	0.000141
ORF7a	37	S37S	tcT	tcC	4	4	AY.50	0.003197
ORF7a	37	S37S	tcT	tcC	2	3	AY.117	0.000169
ORF7a	37	S37S	tcT	tcC	3	3	AY.26	0.000085
ORF7a	37	S37S	tcT	tcC	2	3	B.1.160	0.000062
ORF7a	37	S37S	tcT	tcC	1	3	B.1.621	0.000089
ORF7a	37	S37S	tcT	tcC	2	2	AY.120	0.000074
ORF7a	37	S37S	tcT	tcC	1	2	AY.23	0.00007
ORF7a	37	S37S	tcT	tcC	2	2	AY.33	0.000134
ORF7a	37	S37S	tcT	tcC	2	2	AY.9.2	0.000073
ORF7a	37	S37S	tcT	tcC	2	2	B.1.1.228	0.006098
ORF7a	37	S37S	tcT	tcC	1	2	B.1.1.519	0.00004
ORF7a	37	S37S	tcT	tcC	2	2	B.1.139	0.001466
ORF7a	37	S37S	tcT	tcC	1	2	P.1.14	0.000048
ORF7a	37	S37S	tcT	tcC	1	1	A.2	0.000662
ORF7a	37	S37S	tcT	tcC	1	1	AD.2	0.000219
ORF7a	37	S37S	tcT	tcC	1	1	AY.109	0.00074
ORF7a	37	S37S	tcT	tcC	1	1	AY.22	0.002092
ORF7a	37	S37S	tcT	tcC	1	1	AY.34	0.000097
ORF7a	37	S37S	tcT	tcC	1	1	AY.4.5	0.000107
ORF7a	37	S37S	tcT	tcC	1	1	AY.75	0.000056
ORF7a	37	S37S	tcT	tcC	1	1	AY.9	0.000068
ORF7a	37	S37S	tcT	tcC	1	1	AY.9.1	0.000084
ORF7a	37	S37S	tcT	tcC	1	1	B.1.1.222	0.000204
ORF7a	37	S37S	tcT	tcC	1	1	B.1.1.33	0.000421
ORF7a	37	S37S	tcT	tcC	1	1	B.1.1.47	0.005348
ORF7a	37	S37S	tcT	tcC	1	1	B.1.1.521	0.005348
ORF7a	37	S37S	tcT	tcC	1	1	B.1.36.1	0.00114
ORF7a	37	S37S	tcT	tcC	1	1	B.1.409	0.000781
ORF7a	37	S37S	tcT	tcC	1	1	B.1.561	0.000397
ORF7a	37	S37S	tcT	tcC	1	1	B.1.573	0.006098
ORF7a	37	S37S	tcT	tcC	1	1	B.1.617.1	0.000129
ORF7a	37	S37S	tcT	tcC	1	1	B.1.67	0.043478
ORF7a	37	S37S	tcT	tcC	1	1	B.40	0.000364
ORF7a	37	S37S	tcT	tcC	1	1	C.14	0.004329
ORF7a	37	S37S	tcT	tcC	1	1	P.1.17	0.000162

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.