CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 355

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
S	355	R355S		nonsyn	agG	agC	156	87	0.557692	22625-22627
S	355	R355S		nonsyn	agG	agT	156	69	0.442308	22625-22627
S	355	R355del		del	AGG	---	32	32	1	22625-22627
S	355	R355del1		del	agG	ag-	13	7	0.538462	22625-22627
S	355	R355del1		del	aGg	a-g	13	4	0.307692	22625-22627
S	355	R355del1		del	Agg	-gg	13	2	0.153846	22625-22627
S	355	R355M		nonsyn	aGg	aTg	7	7	1	22625-22627
S	355	R355G		nonsyn	Agg	Ggg	6	6	1	22625-22627
S	355	R355T		nonsyn	aGg	aCg	4	3	0.75	22625-22627
S	355	R355T		nonsyn	aGG	aCA	4	1	0.25	22625-22627
S	355	R355K		nonsyn	aGg	aAg	3	3	1	22625-22627
S	355	R355Q		nonsyn	AGg	CAg	3	3	1	22625-22627
S	355	R355W		nonsyn	Agg	Tgg	2	2	1	22625-22627
S	355	R355del2		del	AGg	--g	2	2	1	22625-22627
S	355	R355C		nonsyn	AgG	TgT	1	1	1	22625-22627

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
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	R355S	agG	agC	87	156	All	0.000017
S	355	R355S	agG	agT	69	156	All	0.000013
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	R355S	agG	agT	30	52	B.1	0.000275
S	355	R355S	agG	agC	22	52	B.1	0.000202
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	R355del	AGG	---	32	32	All	0.000006
S	355	R355S	agG	agC	26	26	AY.29	0.00041
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	R355S	agG	agC	11	15	B.1.258	0.000732
S	355	R355S	agG	agT	4	15	B.1.258	0.000266
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	R355del1	agG	ag-	7	13	All	0.000001
S	355	R355del1	aGg	a-g	4	13	All	0.000001
S	355	R355del1	Agg	-gg	2	13	All	0
S	355	R355R	agG	agA	12	12	AY.119	0.000424
S	355	R355del	AGG	---	12	12	B.1.1.7	0.000011
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	R355S	agG	agC	8	9	B.1.1.7	0.000007
S	355	R355S	agG	agT	1	9	B.1.1.7	0.000001
S	355	R355M	aGg	aTg	7	7	All	0.000001
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	R355G	Agg	Ggg	6	6	All	0.000001
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	R355S	agG	agC	4	6	B.1.258.11	0.001585
S	355	R355S	agG	agT	2	6	B.1.258.11	0.000793
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	R355T	aGg	aCg	3	4	All	0.000001
S	355	R355T	aGG	aCA	1	4	All	0
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	R355S	agG	agC	2	4	B.1.617.2	0.000008
S	355	R355S	agG	agT	2	4	B.1.617.2	0.000008
S	355	R355R	agG	agA	4	4	Q.8	0.00066
S	355	R355S	agG	agT	3	3		0.166667
S	355	R355Q	AGg	CAg	3	3	All	0.000001
S	355	R355K	aGg	aAg	3	3	All	0.000001
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	R355del	AGG	---	3	3	B.1	0.000027
S	355	R355T	aGg	aCg	3	3	B.1	0.000027
S	355	R355S	agG	agT	2	3	B.1.1	0.000036
S	355	R355S	agG	agC	1	3	B.1.1	0.000018
S	355	R355R	agG	agA	3	3	B.1.160	0.000094
S	355	R355S	agG	agT	3	3	B.1.177	0.00004
S	355	R355S	agG	agT	2	3	B.1.221	0.000142
S	355	R355S	agG	agC	1	3	B.1.221	0.000071
S	355	R355del1	agG	ag-	3	3	B.1.258	0.0002
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	R355W	Agg	Tgg	2	2	All	0
S	355	R355del2	AGg	--g	2	2	All	0
S	355	R355R	agG	agA	2	2	AY.101	0.000981
S	355	R355S	agG	agT	1	2	AY.23	0.00007
S	355	R355S	agG	agC	1	2	AY.23	0.00007
S	355	R355R	agG	agA	2	2	AY.39	0.000049
S	355	R355S	agG	agC	1	2	AY.4	0.000002
S	355	R355S	agG	agT	1	2	AY.4	0.000002
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	R355Q	AGg	CAg	2	2	B.1.1.7	0.000002
S	355	R355R	agG	agA	2	2	B.1.177.54	0.001213
S	355	R355del	AGG	---	2	2	B.1.2	0.000018
S	355	R355S	agG	agT	1	2	B.1.2	0.000009
S	355	R355S	agG	agC	1	2	B.1.2	0.000009
S	355	R355R	agG	agA	2	2	B.1.243	0.000139
S	355	R355S	agG	agT	1	2	B.1.437	0.020833
S	355	R355S	agG	agC	1	2	B.1.437	0.020833
S	355	R355R	agG	agA	2	2	B.1.525	0.000226
S	355	R355S	agG	agT	2	2	B.1.617.1	0.000258
S	355	R355R	agG	agA	2	2	B.1.621	0.000177
S	355	R355S	agG	agC	1	2	B.1.78	0.008547
S	355	R355S	agG	agT	1	2	B.1.78	0.008547
S	355	R355M	aGg	aTg	2	2	B.6	0.00182
S	355	R355W	Agg	Tgg	1	1		0.055556
S	355	R355C	AgG	TgT	1	1		0.055556
S	355	R355R	agG	agA	1	1		0.055556
S	355	R355S	agG	agT	1	1	A	0.000387
S	355	R355S	agG	agT	1	1	AD.2	0.000219
S	355	R355C	AgG	TgT	1	1	All	0
S	355	R355R	agG	agA	1	1	AY.10	0.00053
S	355	R355del1	aGg	a-g	1	1	AY.103	0.000006
S	355	R355del	AGG	---	1	1	AY.107	0.000466
S	355	R355del	AGG	---	1	1	AY.120	0.000037
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	R355G	Agg	Ggg	1	1	AY.23.1	0.000417
S	355	R355S	agG	agC	1	1	AY.29.1	0.000221
S	355	R355M	aGg	aTg	1	1	AY.3	0.00001
S	355	R355G	Agg	Ggg	1	1	AY.3	0.00001
S	355	R355R	agG	agA	1	1	AY.3.1	0.000085
S	355	R355del	AGG	---	1	1	AY.33	0.000067
S	355	R355S	agG	agC	1	1	AY.33	0.000067
S	355	R355R	agG	agA	1	1	AY.35	0.000233
S	355	R355S	agG	agC	1	1	AY.35	0.000233
S	355	R355R	Agg	Cgg	1	1	AY.39.1.1	0.000725
S	355	R355del1	aGg	a-g	1	1	AY.4	0.000002
S	355	R355del	AGG	---	1	1	AY.4	0.000002
S	355	R355S	agG	agT	1	1	AY.42	0.00004
S	355	R355del	AGG	---	1	1	AY.43	0.000004
S	355	R355T	aGG	aCA	1	1	AY.44	0.000006
S	355	R355G	Agg	Ggg	1	1	AY.44	0.000006
S	355	R355del1	aGg	a-g	1	1	AY.44	0.000006
S	355	R355S	agG	agC	1	1	AY.46	0.000104
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	R355del	AGG	---	1	1	AY.72	0.001361
S	355	R355R	agG	agA	1	1	AY.74	0.000116
S	355	R355S	agG	agC	1	1	AY.75.1	0.00018
S	355	R355M	aGg	aTg	1	1	AY.9	0.000068
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	R355M	aGg	aTg	1	1	B.1	0.000009
S	355	R355Q	AGg	CAg	1	1	B.1	0.000009
S	355	R355G	Agg	Ggg	1	1	B.1.1	0.000018
S	355	R355del	AGG	---	1	1	B.1.1	0.000018
S	355	R355R	agG	agA	1	1	B.1.1.1	0.000327
S	355	R355S	agG	agT	1	1	B.1.1.1	0.000327
S	355	R355del1	Agg	-gg	1	1	B.1.1.279	0.001121
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	R355S	agG	agC	1	1	B.1.1.311	0.000358
S	355	R355M	aGg	aTg	1	1	B.1.1.326	0.001761
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	R355K	aGg	aAg	1	1	B.1.1.7	0.000001
S	355	R355del1	agG	ag-	1	1	B.1.1.7	0.000001
S	355	R355S	agG	agT	1	1	B.1.160	0.000031
S	355	R355S	agG	agC	1	1	B.1.166	0.008475
S	355	R355del1	agG	ag-	1	1	B.1.177	0.000013
S	355	R355del	AGG	---	1	1	B.1.177.18	0.00116
S	355	R355del1	agG	ag-	1	1	B.1.177.50	0.004695
S	355	R355S	agG	agT	1	1	B.1.177.6	0.000977
S	355	R355del	AGG	---	1	1	B.1.177.62	0.001192
S	355	R355del2	AGg	--g	1	1	B.1.177.7	0.000165
S	355	R355R	agG	agA	1	1	B.1.177.86	0.000183
S	355	R355del2	AGg	--g	1	1	B.1.2	0.000009
S	355	R355R	agG	agA	1	1	B.1.241	0.000812
S	355	R355del1	agG	ag-	1	1	B.1.242	0.018868
S	355	R355del	AGG	---	1	1	B.1.258	0.000067
S	355	R355R	agG	agA	1	1	B.1.258.11	0.000396
S	355	R355M	aGg	aTg	1	1	B.1.260	0.003344
S	355	R355R	agG	agA	1	1	B.1.36	0.000146
S	355	R355del1	aGg	a-g	1	1	B.1.369	0.000285
S	355	R355del	AGG	---	1	1	B.1.369	0.000285
S	355	R355R	agG	agA	1	1	B.1.402	0.009804
S	355	R355del	AGG	---	1	1	B.1.409	0.000781
S	355	R355S	agG	agT	1	1	B.1.417	0.028571
S	355	R355R	agG	agA	1	1	B.1.417	0.028571
S	355	R355W	Agg	Tgg	1	1	B.1.427	0.00005
S	355	R355K	aGg	aAg	1	1	B.1.446	0.02
S	355	R355R	agG	agA	1	1	B.1.471	0.002732
S	355	R355S	agG	agT	1	1	B.1.525	0.000113
S	355	R355S	agG	agT	1	1	B.1.596	0.000087
S	355	R355S	agG	agT	1	1	B.1.609	0.000479
S	355	R355R	agG	agA	1	1	B.1.617.1	0.000129
S	355	R355del	AGG	---	1	1	B.1.617.2	0.000004
S	355	R355S	agG	agT	1	1	B.1.619	0.000871
S	355	R355del	AGG	---	1	1	B.1.620	0.000946
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	R355G	Agg	Ggg	1	1	D.2	0.000075
S	355	R355R	agG	agA	1	1	L.3	0.003546
S	355	R355R	agG	agA	1	1	N.1	0.016949
S	355	R355K	aGg	aAg	1	1	N.6	0.007092
S	355	R355S	agG	agT	1	1	P.1.1	0.000318
S	355	R355S	agG	agT	1	1	P.1.12	0.000484
S	355	R355G	Agg	Ggg	1	1	P.1.15	0.000232
S	355	R355del	AGG	---	1	1	Q.1	0.000126
S	355	R355del1	Agg	-gg	1	1	Q.3	0.000145

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.