CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : Mut = R190R

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	190	R190R		syn	agG	agA	1038	1027	0.989403	22130-22132
S	190	R190R		syn	Agg	Cgg	1038	9	0.00867052	22130-22132
S	190	R190R		syn	AgG	CgA	1038	1	0.000963391	22130-22132
S	190	R190R		syn	AgG	CgT	1038	1	0.000963391	22130-22132

Details of the mutation R190R 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	190	R190R	agG	agA	1027	1038	All	0.000196
S	190	R190R	Agg	Cgg	9	1038	All	0.000002
S	190	R190R	AgG	CgT	1	1038	All	0
S	190	R190R	AgG	CgA	1	1038	All	0
S	190	R190R	agG	agA	305	306	B.1.1.7	0.000273
S	190	R190R	Agg	Cgg	1	306	B.1.1.7	0.000001
S	190	R190R	agG	agA	139	139	AY.5	0.00287
S	190	R190R	agG	agA	67	68	B.1.617.2	0.000252
S	190	R190R	Agg	Cgg	1	68	B.1.617.2	0.000004
S	190	R190R	agG	agA	42	42	AY.25	0.000253
S	190	R190R	agG	agA	32	32	AY.4	0.00005
S	190	R190R	agG	agA	28	28	C.35	0.021672
S	190	R190R	agG	agA	22	25	AY.43	0.000097
S	190	R190R	Agg	Cgg	1	25	AY.43	0.000004
S	190	R190R	AgG	CgA	1	25	AY.43	0.000004
S	190	R190R	AgG	CgT	1	25	AY.43	0.000004
S	190	R190R	agG	agA	23	23	B.1.429	0.000541
S	190	R190R	agG	agA	21	21	AY.33	0.001402
S	190	R190R	agG	agA	19	19	B.1.2	0.000167
S	190	R190R	agG	agA	18	18	A.23.1	0.012676
S	190	R190R	agG	agA	18	18	B.1.1	0.000327
S	190	R190R	agG	agA	18	18	B.1.177	0.000237
S	190	R190R	agG	agA	13	14	AY.100	0.000598
S	190	R190R	Agg	Cgg	1	14	AY.100	0.000046
S	190	R190R	agG	agA	14	14	B.1.258	0.000932
S	190	R190R	agG	agA	13	13	B.1	0.000119
S	190	R190R	agG	agA	12	12	B.1.110.3	0.008621
S	190	R190R	agG	agA	11	11	AY.32	0.005857
S	190	R190R	agG	agA	10	10	B.1.221	0.00071
S	190	R190R	agG	agA	9	9	AY.34	0.000873
S	190	R190R	agG	agA	9	9	B.1.526	0.000212
S	190	R190R	agG	agA	8	8	AY.3	0.00008
S	190	R190R	agG	agA	4	8	B.1.1.153	0.004381
S	190	R190R	Agg	Cgg	4	8	B.1.1.153	0.004381
S	190	R190R	agG	agA	7	7	AY.103	0.000043
S	190	R190R	agG	agA	7	7	AY.20	0.000272
S	190	R190R	agG	agA	7	7	AY.29	0.00011
S	190	R190R	agG	agA	7	7	AY.44	0.000043
S	190	R190R	agG	agA	7	7	B.1.1.318	0.002112
S	190	R190R	agG	agA	7	7	P.2	0.001306
S	190	R190R	agG	agA	5	6	AY.120	0.000186
S	190	R190R	Agg	Cgg	1	6	AY.120	0.000037
S	190	R190R	agG	agA	6	6	AY.121	0.000812
S	190	R190R	agG	agA	6	6	AY.13	0.000966
S	190	R190R	agG	agA	6	6	AY.74	0.000694
S	190	R190R	agG	agA	6	6	B.1.1.519	0.000238
S	190	R190R	agG	agA	4	4	AY.7.2	0.002237
S	190	R190R	agG	agA	4	4	B.1.160	0.000125
S	190	R190R	agG	agA	3	3	AY.9	0.000203
S	190	R190R	agG	agA	3	3	AY.93	0.000819
S	190	R190R	agG	agA	3	3	AZ.3	0.004559
S	190	R190R	agG	agA	3	3	B.1.177.21	0.000229
S	190	R190R	agG	agA	3	3	B.1.351	0.000089
S	190	R190R	agG	agA	3	3	C.37	0.000348
S	190	R190R	agG	agA	2	2	AU.3	0.004219
S	190	R190R	agG	agA	2	2	AY.102	0.000053
S	190	R190R	agG	agA	2	2	AY.14	0.000176
S	190	R190R	agG	agA	2	2	AY.26	0.000057
S	190	R190R	agG	agA	2	2	AY.69	0.000373
S	190	R190R	agG	agA	2	2	B.1.177.19	0.002861
S	190	R190R	agG	agA	2	2	B.1.177.60	0.000437
S	190	R190R	agG	agA	2	2	B.1.36.36	0.001204
S	190	R190R	agG	agA	2	2	B.1.525	0.000226
S	190	R190R	agG	agA	2	2	B.1.596	0.000174
S	190	R190R	agG	agA	2	2	B.1.602	0.013072
S	190	R190R	agG	agA	2	2	B.1.621	0.000177
S	190	R190R	agG	agA	2	2	B.1.628	0.000705
S	190	R190R	agG	agA	2	2	C.36.3	0.001134
S	190	R190R	agG	agA	2	2	N.5	0.003534
S	190	R190R	agG	agA	1	1		0.055556
S	190	R190R	agG	agA	1	1	A	0.000387
S	190	R190R	agG	agA	1	1	AY.105	0.000643
S	190	R190R	agG	agA	1	1	AY.114	0.000231
S	190	R190R	agG	agA	1	1	AY.116.1	0.000311
S	190	R190R	agG	agA	1	1	AY.117	0.000085
S	190	R190R	agG	agA	1	1	AY.120.2	0.001285
S	190	R190R	agG	agA	1	1	AY.27	0.000065
S	190	R190R	agG	agA	1	1	AY.35	0.000233
S	190	R190R	agG	agA	1	1	AY.39	0.000025
S	190	R190R	agG	agA	1	1	AY.4.1	0.000737
S	190	R190R	agG	agA	1	1	AY.4.2	0.000022
S	190	R190R	agG	agA	1	1	AY.40	0.000964
S	190	R190R	agG	agA	1	1	AY.46	0.000104
S	190	R190R	agG	agA	1	1	AY.46.6	0.000072
S	190	R190R	agG	agA	1	1	AY.5.3	0.000337
S	190	R190R	agG	agA	1	1	AY.59	0.00053
S	190	R190R	agG	agA	1	1	AY.61	0.000105
S	190	R190R	agG	agA	1	1	AY.68	0.000274
S	190	R190R	agG	agA	1	1	AY.71	0.000475
S	190	R190R	agG	agA	1	1	AY.75	0.000056
S	190	R190R	agG	agA	1	1	AY.79	0.001211
S	190	R190R	agG	agA	1	1	B.1.1.1	0.000327
S	190	R190R	agG	agA	1	1	B.1.1.28	0.000311
S	190	R190R	agG	agA	1	1	B.1.1.294	0.001266
S	190	R190R	agG	agA	1	1	B.1.1.304	0.002809
S	190	R190R	agG	agA	1	1	B.1.1.353	0.020833
S	190	R190R	agG	agA	1	1	B.1.1.409	0.002833
S	190	R190R	agG	agA	1	1	B.1.177.57	0.000281
S	190	R190R	agG	agA	1	1	B.1.177.58	0.001332
S	190	R190R	agG	agA	1	1	B.1.234	0.000132
S	190	R190R	agG	agA	1	1	B.1.258.21	0.007752
S	190	R190R	agG	agA	1	1	B.1.36	0.000146
S	190	R190R	agG	agA	1	1	B.1.36.8	0.001
S	190	R190R	agG	agA	1	1	B.1.422	0.000812
S	190	R190R	agG	agA	1	1	B.1.427	0.00005
S	190	R190R	agG	agA	1	1	B.1.438.1	0.000107
S	190	R190R	agG	agA	1	1	B.1.619.1	0.000641
S	190	R190R	agG	agA	1	1	B.1.630	0.005236
S	190	R190R	agG	agA	1	1	D.2	0.000075
S	190	R190R	agG	agA	1	1	P.1	0.000016
S	190	R190R	agG	agA	1	1	Q.3	0.000145
S	190	R190R	agG	agA	1	1	Q.8	0.000165
S	190	R190R	agG	agA	1	1	R.1	0.00009
S	190	R190R	agG	agA	1	1	W.4	0.001351

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.