CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : Mut = S188S

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
N	188	S188S		syn	tcA	tcG	215	154	0.716279	28835-28837
N	188	S188S		syn	tcA	tcT	215	54	0.251163	28835-28837
N	188	S188S		syn	tcA	tcC	215	7	0.0325581	28835-28837

Details of the mutation S188S 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
N	188	S188S	tcA	tcG	154	215	All	0.000029
N	188	S188S	tcA	tcT	54	215	All	0.00001
N	188	S188S	tcA	tcC	7	215	All	0.000001
N	188	S188S	tcA	tcG	29	55	B.1.1.7	0.000026
N	188	S188S	tcA	tcT	24	55	B.1.1.7	0.000021
N	188	S188S	tcA	tcC	2	55	B.1.1.7	0.000002
N	188	S188S	tcA	tcG	28	28	AY.25	0.000168
N	188	S188S	tcA	tcG	11	12	AY.45	0.001339
N	188	S188S	tcA	tcC	1	12	AY.45	0.000122
N	188	S188S	tcA	tcG	12	12	B.1.139	0.008798
N	188	S188S	tcA	tcT	11	11	AY.4	0.000017
N	188	S188S	tcA	tcG	10	10	AY.102	0.000265
N	188	S188S	tcA	tcG	5	8	AY.43	0.000022
N	188	S188S	tcA	tcT	3	8	AY.43	0.000013
N	188	S188S	tcA	tcG	6	6	B.1.1.163	0.045802
N	188	S188S	tcA	tcT	3	5	B.1	0.000027
N	188	S188S	tcA	tcG	2	5	B.1	0.000018
N	188	S188S	tcA	tcG	5	5	B.1.1	0.000091
N	188	S188S	tcA	tcG	5	5	B.1.564	0.002129
N	188	S188S	tcA	tcG	4	5	B.1.617.2	0.000015
N	188	S188S	tcA	tcT	1	5	B.1.617.2	0.000004
N	188	S188S	tcA	tcG	3	3	AY.103	0.000019
N	188	S188S	tcA	tcG	3	3	AY.44	0.000018
N	188	S188S	tcA	tcG	3	3	B.1.1.519	0.000119
N	188	S188S	tcA	tcG	3	3	B.1.375	0.002459
N	188	S188S	tcA	tcG	2	2	AY.23	0.000139
N	188	S188S	tcA	tcG	2	2	AY.99.2	0.000184
N	188	S188S	tcA	tcC	1	2	B.1.177	0.000013
N	188	S188S	tcA	tcG	1	2	B.1.177	0.000013
N	188	S188S	tcA	tcG	2	2	B.1.258.17	0.000208
N	188	S188S	tcA	tcT	2	2	B.1.466.2	0.000782
N	188	S188S	tcA	tcC	2	2	P.1.14	0.000096
N	188	S188S	tcA	tcT	2	2	P.1.15	0.000465
N	188	S188S	tcA	tcG	1	1		0.055556
N	188	S188S	tcA	tcG	1	1	AY.110	0.000113
N	188	S188S	tcA	tcG	1	1	AY.119	0.000035
N	188	S188S	tcA	tcG	1	1	AY.121	0.000135
N	188	S188S	tcA	tcT	1	1	AY.27	0.000065
N	188	S188S	tcA	tcG	1	1	AY.29	0.000016
N	188	S188S	tcA	tcT	1	1	AY.30	0.000396
N	188	S188S	tcA	tcT	1	1	AY.34	0.000097
N	188	S188S	tcA	tcG	1	1	AY.46	0.000104
N	188	S188S	tcA	tcG	1	1	AY.46.3	0.000934
N	188	S188S	tcA	tcT	1	1	AY.5	0.000021
N	188	S188S	tcA	tcG	1	1	AY.55	0.000917
N	188	S188S	tcA	tcG	1	1	AY.95	0.000761
N	188	S188S	tcA	tcG	1	1	AY.98	0.000079
N	188	S188S	tcA	tcG	1	1	B.1.1.192	0.002309
N	188	S188S	tcA	tcG	1	1	B.1.1.413	0.006897
N	188	S188S	tcA	tcT	1	1	B.1.160	0.000031
N	188	S188S	tcA	tcG	1	1	B.1.2	0.000009
N	188	S188S	tcA	tcG	1	1	B.1.221	0.000071
N	188	S188S	tcA	tcT	1	1	B.1.258.11	0.000396
N	188	S188S	tcA	tcG	1	1	B.1.265	0.001271
N	188	S188S	tcA	tcC	1	1	B.1.429	0.000024
N	188	S188S	tcA	tcG	1	1	B.1.623	0.000536
N	188	S188S	tcA	tcT	1	1	B.1.631	0.003367
N	188	S188S	tcA	tcG	1	1	P.1	0.000016
N	188	S188S	tcA	tcT	1	1	Q.8	0.000165
N	188	S188S	tcA	tcG	1	1	R.1	0.00009

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.