CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : Mut = T478R

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	478	T478R		nonsyn	aCa	aGa	821	812	0.989038	22994-22996
S	478	T478R		nonsyn	aCA	aGG	821	3	0.00365408	22994-22996
S	478	T478R		nonsyn	ACA	CGG	821	3	0.00365408	22994-22996
S	478	T478R		nonsyn	ACa	CGa	821	2	0.00243605	22994-22996
S	478	T478R		nonsyn	ACA	CGC	821	1	0.00121803	22994-22996

Details of the mutation T478R 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	478	T478R	aCa	aGa	812	821	All	0.000155
S	478	T478R	aCA	aGG	3	821	All	0.000001
S	478	T478R	ACA	CGG	3	821	All	0.000001
S	478	T478R	ACa	CGa	2	821	All	0
S	478	T478R	ACA	CGC	1	821	All	0
S	478	T478R	aCa	aGa	395	395	B.1.609	0.189358
S	478	T478R	aCa	aGa	183	183	B.1.630	0.958115
S	478	T478R	aCa	aGa	60	60	AY.103	0.000373
S	478	T478R	aCa	aGa	31	31	B.1	0.000284
S	478	T478R	aCa	aGa	17	17	C.36.3	0.009643
S	478	T478R	aCa	aGa	13	13	AY.46.6	0.000939
S	478	T478R	aCa	aGa	9	9	B.1.351	0.000268
S	478	T478R	aCA	aGG	2	8		0.111111
S	478	T478R	ACa	CGa	2	8		0.111111
S	478	T478R	aCa	aGa	2	8		0.111111
S	478	T478R	ACA	CGG	2	8		0.111111
S	478	T478R	aCa	aGa	8	8	B.1.617.2	0.00003
S	478	T478R	aCa	aGa	7	7	B.1.1.420	0.007042
S	478	T478R	aCa	aGa	6	6	AY.4	0.000009
S	478	T478R	aCa	aGa	5	6	AY.43	0.000022
S	478	T478R	ACA	CGC	1	6	AY.43	0.000004
S	478	T478R	aCa	aGa	6	6	AY.44	0.000037
S	478	T478R	aCa	aGa	6	6	B.1.2	0.000053
S	478	T478R	aCa	aGa	5	5	A.30	0.714286
S	478	T478R	aCa	aGa	5	5	AY.61	0.000524
S	478	T478R	aCa	aGa	4	4	AY.3	0.00004
S	478	T478R	aCa	aGa	2	4	B.1.1	0.000036
S	478	T478R	ACA	CGG	1	4	B.1.1	0.000018
S	478	T478R	aCA	aGG	1	4	B.1.1	0.000018
S	478	T478R	aCa	aGa	3	3	AY.20	0.000117
S	478	T478R	aCa	aGa	3	3	B	0.000383
S	478	T478R	aCa	aGa	3	3	B.1.258	0.0002
S	478	T478R	aCa	aGa	3	3	B.1.499	0.003151
S	478	T478R	aCa	aGa	3	3	B.1.637	0.000219
S	478	T478R	aCa	aGa	2	2	AY.119	0.000071
S	478	T478R	aCa	aGa	2	2	AY.24	0.000862
S	478	T478R	aCa	aGa	2	2	AY.25	0.000012
S	478	T478R	aCa	aGa	2	2	AY.32	0.001065
S	478	T478R	aCa	aGa	2	2	AY.39	0.000049
S	478	T478R	aCa	aGa	2	2	AY.5	0.000041
S	478	T478R	aCa	aGa	1	1	A.2	0.000662
S	478	T478R	aCa	aGa	1	1	AY.23	0.00007
S	478	T478R	aCa	aGa	1	1	AY.26	0.000028
S	478	T478R	aCa	aGa	1	1	AY.3.1	0.000085
S	478	T478R	aCa	aGa	1	1	AY.47	0.000031
S	478	T478R	aCa	aGa	1	1	AY.52	0.000814
S	478	T478R	aCa	aGa	1	1	AY.55	0.000917
S	478	T478R	aCa	aGa	1	1	AY.6	0.000041
S	478	T478R	aCa	aGa	1	1	AY.62	0.000436
S	478	T478R	aCa	aGa	1	1	AY.67	0.000464
S	478	T478R	aCa	aGa	1	1	AY.68	0.000274
S	478	T478R	aCa	aGa	1	1	AY.75.1	0.00018
S	478	T478R	aCa	aGa	1	1	AY.9.1	0.000084
S	478	T478R	aCa	aGa	1	1	B.1.1.33	0.000421
S	478	T478R	aCa	aGa	1	1	B.1.1.372	0.000689
S	478	T478R	aCa	aGa	1	1	B.1.1.56	0.017857
S	478	T478R	aCa	aGa	1	1	B.1.1.7	0.000001
S	478	T478R	aCa	aGa	1	1	B.1.36	0.000146
S	478	T478R	aCa	aGa	1	1	B.1.429	0.000024
S	478	T478R	aCa	aGa	1	1	B.1.526	0.000024
S	478	T478R	aCa	aGa	1	1	B.1.93	0.000934

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.