CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : Mut = R355R

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	355	R355R		syn	agG	agA	1159	1052	0.907679	22625-22627
S	355	R355R		syn	Agg	Cgg	1159	107	0.092321	22625-22627

Details of the mutation R355R 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	355	R355R	agG	agA	1052	1159	All	0.000201
S	355	R355R	Agg	Cgg	107	1159	All	0.00002
S	355	R355R	agG	agA	409	409	B.1.1.7	0.000366
S	355	R355R	agG	agA	95	95	AD.2	0.020801
S	355	R355R	agG	agA	68	68	B.1.243.2	0.985507
S	355	R355R	Agg	Cgg	54	60	B.1.177	0.000711
S	355	R355R	agG	agA	6	60	B.1.177	0.000079
S	355	R355R	agG	agA	57	57	B.1.1.49	1
S	355	R355R	agG	agA	41	41	B.1.429	0.000965
S	355	R355R	agG	agA	38	38	AY.4	0.000059
S	355	R355R	agG	agA	24	24	B.1.1.214	0.001331
S	355	R355R	agG	agA	22	24	B.1.617.2	0.000083
S	355	R355R	Agg	Cgg	2	24	B.1.617.2	0.000008
S	355	R355R	agG	agA	22	22	B.1.2	0.000194
S	355	R355R	agG	agA	19	21	AY.3	0.000189
S	355	R355R	Agg	Cgg	2	21	AY.3	0.00002
S	355	R355R	agG	agA	18	21	B.1	0.000165
S	355	R355R	Agg	Cgg	3	21	B.1	0.000027
S	355	R355R	agG	agA	19	19	AY.87	0.01582
S	355	R355R	agG	agA	19	19	B.1.36.29	0.009829
S	355	R355R	agG	agA	9	17	AY.44	0.000055
S	355	R355R	Agg	Cgg	8	17	AY.44	0.000049
S	355	R355R	Agg	Cgg	16	16	B.1.427	0.000808
S	355	R355R	agG	agA	15	15	P.1	0.000236
S	355	R355R	agG	agA	10	14	AY.43	0.000044
S	355	R355R	Agg	Cgg	4	14	AY.43	0.000018
S	355	R355R	agG	agA	12	12	AY.119	0.000424
S	355	R355R	agG	agA	10	10	B.1.438.1	0.001073
S	355	R355R	agG	agA	9	9	AY.27	0.000582
S	355	R355R	agG	agA	7	7	AY.46.6	0.000505
S	355	R355R	agG	agA	7	7	B.1.258	0.000466
S	355	R355R	agG	agA	6	6	AY.103	0.000037
S	355	R355R	Agg	Cgg	5	6	AY.42	0.000201
S	355	R355R	agG	agA	1	6	AY.42	0.00004
S	355	R355R	agG	agA	6	6	B.1.1.519	0.000238
S	355	R355R	agG	agA	4	5	B.1.1	0.000073
S	355	R355R	Agg	Cgg	1	5	B.1.1	0.000018
S	355	R355R	agG	agA	3	5	B.1.351	0.000089
S	355	R355R	Agg	Cgg	2	5	B.1.351	0.000059
S	355	R355R	agG	agA	5	5	B.1.367	0.003962
S	355	R355R	Agg	Cgg	3	4	AY.7.1	0.000338
S	355	R355R	agG	agA	1	4	AY.7.1	0.000113
S	355	R355R	agG	agA	4	4	AY.75	0.000224
S	355	R355R	agG	agA	4	4	B.1.575	0.001214
S	355	R355R	agG	agA	4	4	Q.8	0.00066
S	355	R355R	Agg	Cgg	2	3	AY.102	0.000053
S	355	R355R	agG	agA	1	3	AY.102	0.000027
S	355	R355R	agG	agA	3	3	AY.25	0.000018
S	355	R355R	agG	agA	2	3	AY.26	0.000057
S	355	R355R	Agg	Cgg	1	3	AY.26	0.000028
S	355	R355R	agG	agA	3	3	AY.29	0.000047
S	355	R355R	agG	agA	3	3	B.1.160	0.000094
S	355	R355R	agG	agA	3	3	B.1.398	0.008929
S	355	R355R	agG	agA	3	3	B.1.561	0.001191
S	355	R355R	agG	agA	3	3	B.1.609	0.001438
S	355	R355R	agG	agA	2	2	AY.101	0.000981
S	355	R355R	agG	agA	2	2	AY.39	0.000049
S	355	R355R	agG	agA	2	2	AY.4.2	0.000043
S	355	R355R	agG	agA	2	2	AY.46.4	0.000329
S	355	R355R	agG	agA	2	2	AY.77	0.002255
S	355	R355R	agG	agA	2	2	AY.9.2	0.000073
S	355	R355R	agG	agA	2	2	B.1.1.222	0.000408
S	355	R355R	agG	agA	2	2	B.1.1.28	0.000622
S	355	R355R	agG	agA	2	2	B.1.1.33	0.000842
S	355	R355R	Agg	Cgg	2	2	B.1.1.335	0.025974
S	355	R355R	agG	agA	2	2	B.1.177.54	0.001213
S	355	R355R	agG	agA	2	2	B.1.243	0.000139
S	355	R355R	agG	agA	2	2	B.1.525	0.000226
S	355	R355R	agG	agA	2	2	B.1.621	0.000177
S	355	R355R	agG	agA	1	1		0.055556
S	355	R355R	agG	agA	1	1	AY.10	0.00053
S	355	R355R	agG	agA	1	1	AY.120.1	0.000321
S	355	R355R	agG	agA	1	1	AY.14	0.000088
S	355	R355R	agG	agA	1	1	AY.20	0.000039
S	355	R355R	agG	agA	1	1	AY.23	0.00007
S	355	R355R	agG	agA	1	1	AY.3.1	0.000085
S	355	R355R	agG	agA	1	1	AY.35	0.000233
S	355	R355R	Agg	Cgg	1	1	AY.39.1.1	0.000725
S	355	R355R	agG	agA	1	1	AY.46	0.000104
S	355	R355R	agG	agA	1	1	AY.5.3	0.000337
S	355	R355R	agG	agA	1	1	AY.74	0.000116
S	355	R355R	agG	agA	1	1	AY.93	0.000273
S	355	R355R	agG	agA	1	1	AY.98	0.000079
S	355	R355R	agG	agA	1	1	B	0.000128
S	355	R355R	agG	agA	1	1	B.1.1.1	0.000327
S	355	R355R	agG	agA	1	1	B.1.1.284	0.000107
S	355	R355R	agG	agA	1	1	B.1.1.306	0.000438
S	355	R355R	agG	agA	1	1	B.1.1.416	0.000905
S	355	R355R	agG	agA	1	1	B.1.1.432	0.001266
S	355	R355R	agG	agA	1	1	B.1.177.86	0.000183
S	355	R355R	agG	agA	1	1	B.1.241	0.000812
S	355	R355R	agG	agA	1	1	B.1.258.11	0.000396
S	355	R355R	agG	agA	1	1	B.1.36	0.000146
S	355	R355R	agG	agA	1	1	B.1.402	0.009804
S	355	R355R	agG	agA	1	1	B.1.417	0.028571
S	355	R355R	agG	agA	1	1	B.1.471	0.002732
S	355	R355R	agG	agA	1	1	B.1.617.1	0.000129
S	355	R355R	Agg	Cgg	1	1	B.6	0.00091
S	355	R355R	agG	agA	1	1	C.30	0.001727
S	355	R355R	agG	agA	1	1	C.35	0.000774
S	355	R355R	agG	agA	1	1	L.3	0.003546
S	355	R355R	agG	agA	1	1	N.1	0.016949

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.