CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : Mut = S884S

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	884	S884S		syn	tcT	tcC	510	340	0.666667	24212-24214
S	884	S884S		syn	tcT	tcA	510	128	0.25098	24212-24214
S	884	S884S		syn	tcT	tcG	510	41	0.0803922	24212-24214
S	884	S884S		syn	TCt	AGt	510	1	0.00196078	24212-24214

Details of the mutation S884S 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	884	S884S	tcT	tcC	340	510	All	0.000065
S	884	S884S	tcT	tcA	128	510	All	0.000024
S	884	S884S	tcT	tcG	41	510	All	0.000008
S	884	S884S	TCt	AGt	1	510	All	0
S	884	S884S	tcT	tcC	43	73	B.1.1.7	0.000038
S	884	S884S	tcT	tcA	29	73	B.1.1.7	0.000026
S	884	S884S	tcT	tcG	1	73	B.1.1.7	0.000001
S	884	S884S	tcT	tcC	50	51	AY.26	0.001416
S	884	S884S	tcT	tcA	1	51	AY.26	0.000028
S	884	S884S	tcT	tcC	47	49	AY.43	0.000208
S	884	S884S	tcT	tcA	2	49	AY.43	0.000009
S	884	S884S	tcT	tcA	29	33	AY.25	0.000174
S	884	S884S	tcT	tcC	4	33	AY.25	0.000024
S	884	S884S	tcT	tcG	19	31	AY.4	0.00003
S	884	S884S	tcT	tcC	8	31	AY.4	0.000012
S	884	S884S	tcT	tcA	4	31	AY.4	0.000006
S	884	S884S	tcT	tcC	25	26	B.1.160	0.00078
S	884	S884S	tcT	tcA	1	26	B.1.160	0.000031
S	884	S884S	tcT	tcC	19	22	B.1.617.2	0.000072
S	884	S884S	tcT	tcG	2	22	B.1.617.2	0.000008
S	884	S884S	tcT	tcA	1	22	B.1.617.2	0.000004
S	884	S884S	tcT	tcC	17	20	B.1.2	0.00015
S	884	S884S	tcT	tcA	3	20	B.1.2	0.000026
S	884	S884S	tcT	tcC	20	20	B.1.621	0.00177
S	884	S884S	tcT	tcC	17	17	B.1.1.112	1
S	884	S884S	tcT	tcC	13	15	B.1.526	0.000306
S	884	S884S	tcT	tcG	2	15	B.1.526	0.000047
S	884	S884S	tcT	tcC	11	11	AY.39	0.000272
S	884	S884S	tcT	tcA	8	11	B.1	0.000073
S	884	S884S	tcT	tcC	3	11	B.1	0.000027
S	884	S884S	tcT	tcC	6	8	AY.44	0.000037
S	884	S884S	tcT	tcA	1	8	AY.44	0.000006
S	884	S884S	tcT	tcG	1	8	AY.44	0.000006
S	884	S884S	tcT	tcA	7	8	B.1.351	0.000208
S	884	S884S	tcT	tcC	1	8	B.1.351	0.00003
S	884	S884S	tcT	tcC	7	7	B.1.1.70	0.002387
S	884	S884S	tcT	tcC	6	6	AY.29	0.000095
S	884	S884S	tcT	tcA	6	6	AY.47	0.000187
S	884	S884S	tcT	tcG	6	6	AY.74	0.000694
S	884	S884S	tcT	tcC	5	6	B.1.36	0.00073
S	884	S884S	tcT	tcA	1	6	B.1.36	0.000146
S	884	S884S	tcT	tcC	5	5	AY.6	0.000206
S	884	S884S	tcT	tcA	4	5	B.1.177	0.000053
S	884	S884S	tcT	tcC	1	5	B.1.177	0.000013
S	884	S884S	tcT	tcA	5	5	B.1.177.46	0.004591
S	884	S884S	tcT	tcC	2	5	P.1	0.000032
S	884	S884S	tcT	tcA	2	5	P.1	0.000032
S	884	S884S	tcT	tcG	1	5	P.1	0.000016
S	884	S884S	tcT	tcA	4	4	AY.101	0.001962
S	884	S884S	tcT	tcA	2	4	AY.103	0.000012
S	884	S884S	tcT	tcC	2	4	AY.103	0.000012
S	884	S884S	tcT	tcC	3	3	AY.121	0.000406
S	884	S884S	tcT	tcG	3	3	AY.4.2	0.000065
S	884	S884S	tcT	tcC	3	3	B.1.429	0.000071
S	884	S884S	tcT	tcA	3	3	C.36	0.002732
S	884	S884S	tcT	tcG	3	3	R.1	0.00027
S	884	S884S	tcT	tcC	1	2	AY.100	0.000046
S	884	S884S	tcT	tcA	1	2	AY.100	0.000046
S	884	S884S	tcT	tcC	2	2	AY.20	0.000078
S	884	S884S	tcT	tcC	2	2	AY.3	0.00002
S	884	S884S	tcT	tcC	1	2	AY.39.1	0.00004
S	884	S884S	tcT	tcA	1	2	AY.39.1	0.00004
S	884	S884S	tcT	tcA	2	2	P.1.1	0.000635
S	884	S884S	tcT	tcC	1	1	A.2.5.2	0.001572
S	884	S884S	tcT	tcC	1	1	AY.118	0.000063
S	884	S884S	tcT	tcA	1	1	AY.120	0.000037
S	884	S884S	tcT	tcA	1	1	AY.120.1	0.000321
S	884	S884S	tcT	tcA	1	1	AY.2	0.000356
S	884	S884S	tcT	tcC	1	1	AY.33	0.000067
S	884	S884S	tcT	tcC	1	1	AY.34	0.000097
S	884	S884S	tcT	tcG	1	1	AY.42	0.00004
S	884	S884S	tcT	tcA	1	1	AY.85	0.000427
S	884	S884S	tcT	tcC	1	1	AY.99.2	0.000092
S	884	S884S	tcT	tcC	1	1	B	0.000128
S	884	S884S	tcT	tcC	1	1	B.1.1	0.000018
S	884	S884S	tcT	tcA	1	1	B.1.1.214	0.000055
S	884	S884S	tcT	tcA	1	1	B.1.1.294	0.001266
S	884	S884S	tcT	tcC	1	1	B.1.1.322	0.008772
S	884	S884S	tcT	tcC	1	1	B.1.1.416	0.000905
S	884	S884S	tcT	tcA	1	1	B.1.1.523	0.001563
S	884	S884S	tcT	tcG	1	1	B.1.177.19	0.001431
S	884	S884S	tcT	tcA	1	1	B.1.177.7	0.000165
S	884	S884S	tcT	tcA	1	1	B.1.218	0.005155
S	884	S884S	tcT	tcG	1	1	B.1.240	0.000216
S	884	S884S	tcT	tcC	1	1	B.1.243	0.00007
S	884	S884S	tcT	tcC	1	1	B.1.258.17	0.000104
S	884	S884S	tcT	tcC	1	1	B.1.398	0.002976
S	884	S884S	tcT	tcC	1	1	B.1.427	0.00005
S	884	S884S	tcT	tcC	1	1	B.1.438.1	0.000107
S	884	S884S	tcT	tcC	1	1	B.1.596	0.000087
S	884	S884S	tcT	tcA	1	1	B.1.627	0.00202
S	884	S884S	tcT	tcA	1	1	B.1.637	0.000073
S	884	S884S	tcT	tcC	1	1	B.57	0.015152
S	884	S884S	TCt	AGt	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.