CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : Mut = S172S

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	172	S172S		syn	tcT	tcC	962	737	0.766112	22076-22078
S	172	S172S		syn	tcT	tcG	962	210	0.218295	22076-22078
S	172	S172S		syn	tcT	tcA	962	14	0.014553	22076-22078
S	172	S172S		syn	TCT	AGC	962	1	0.0010395	22076-22078

Details of the mutation S172S 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	172	S172S	tcT	tcC	737	962	All	0.000141
S	172	S172S	tcT	tcG	210	962	All	0.00004
S	172	S172S	tcT	tcA	14	962	All	0.000003
S	172	S172S	TCT	AGC	1	962	All	0
S	172	S172S	tcT	tcC	514	520	B.1.1.7	0.00046
S	172	S172S	tcT	tcG	5	520	B.1.1.7	0.000004
S	172	S172S	tcT	tcA	1	520	B.1.1.7	0.000001
S	172	S172S	tcT	tcG	93	93	B.1.591	0.989362
S	172	S172S	tcT	tcC	54	54	P.1.10	0.014551
S	172	S172S	tcT	tcG	30	31	B.1.525	0.003395
S	172	S172S	TCT	AGC	1	31	B.1.525	0.000113
S	172	S172S	tcT	tcC	29	30	AY.4	0.000045
S	172	S172S	tcT	tcG	1	30	AY.4	0.000002
S	172	S172S	tcT	tcC	26	26	B.1.361	0.033505
S	172	S172S	tcT	tcG	17	20	B.1.429	0.0004
S	172	S172S	tcT	tcC	2	20	B.1.429	0.000047
S	172	S172S	tcT	tcA	1	20	B.1.429	0.000024
S	172	S172S	tcT	tcG	17	18	B.1.1.519	0.000675
S	172	S172S	tcT	tcA	1	18	B.1.1.519	0.00004
S	172	S172S	tcT	tcC	10	13	B.1.2	0.000088
S	172	S172S	tcT	tcG	3	13	B.1.2	0.000026
S	172	S172S	tcT	tcC	6	12	B.1	0.000055
S	172	S172S	tcT	tcG	6	12	B.1	0.000055
S	172	S172S	tcT	tcC	10	10	AY.44	0.000061
S	172	S172S	tcT	tcC	7	7	AY.25	0.000042
S	172	S172S	tcT	tcG	4	7	AY.5	0.000083
S	172	S172S	tcT	tcC	3	7	AY.5	0.000062
S	172	S172S	tcT	tcC	7	7	P.1.12	0.003388
S	172	S172S	tcT	tcC	5	6	AY.103	0.000031
S	172	S172S	tcT	tcG	1	6	AY.103	0.000006
S	172	S172S	tcT	tcG	6	6	B.1.177.4	0.001266
S	172	S172S	tcT	tcC	6	6	B.1.617.2	0.000023
S	172	S172S	tcT	tcC	4	5	AY.3	0.00004
S	172	S172S	tcT	tcG	1	5	AY.3	0.00001
S	172	S172S	tcT	tcC	4	4	AY.43	0.000018
S	172	S172S	tcT	tcG	4	4	B.1.160	0.000125
S	172	S172S	tcT	tcC	2	3	AY.29	0.000032
S	172	S172S	tcT	tcG	1	3	AY.29	0.000016
S	172	S172S	tcT	tcC	3	3	B.1.1.214	0.000166
S	172	S172S	tcT	tcG	3	3	B.1.265	0.003812
S	172	S172S	tcT	tcG	2	2		0.111111
S	172	S172S	tcT	tcC	1	2	AY.102	0.000027
S	172	S172S	tcT	tcG	1	2	AY.102	0.000027
S	172	S172S	tcT	tcA	2	2	AY.120	0.000074
S	172	S172S	tcT	tcC	2	2	AY.20	0.000078
S	172	S172S	tcT	tcG	1	2	AY.39	0.000025
S	172	S172S	tcT	tcA	1	2	AY.39	0.000025
S	172	S172S	tcT	tcC	2	2	AY.61	0.00021
S	172	S172S	tcT	tcA	2	2	AY.69	0.000373
S	172	S172S	tcT	tcC	2	2	AY.86	0.00166
S	172	S172S	tcT	tcC	2	2	B	0.000256
S	172	S172S	tcT	tcC	2	2	B.1.234	0.000264
S	172	S172S	tcT	tcC	2	2	B.1.36.2	0.021505
S	172	S172S	tcT	tcC	2	2	P.1	0.000032
S	172	S172S	tcT	tcC	2	2	Q.1	0.000253
S	172	S172S	tcT	tcA	1	1	A	0.000387
S	172	S172S	tcT	tcG	1	1	AT.1	0.005128
S	172	S172S	tcT	tcG	1	1	AY.100	0.000046
S	172	S172S	tcT	tcG	1	1	AY.106	0.000335
S	172	S172S	tcT	tcC	1	1	AY.117	0.000085
S	172	S172S	tcT	tcC	1	1	AY.16	0.00038
S	172	S172S	tcT	tcC	1	1	AY.23	0.00007
S	172	S172S	tcT	tcC	1	1	AY.23.1	0.000417
S	172	S172S	tcT	tcC	1	1	AY.30	0.000396
S	172	S172S	tcT	tcC	1	1	AY.33	0.000067
S	172	S172S	tcT	tcC	1	1	AY.39.1	0.00004
S	172	S172S	tcT	tcG	1	1	AY.4.2	0.000022
S	172	S172S	tcT	tcC	1	1	AY.45	0.000122
S	172	S172S	tcT	tcC	1	1	AY.46.3	0.000934
S	172	S172S	tcT	tcG	1	1	AY.58	0.000907
S	172	S172S	tcT	tcC	1	1	AY.59	0.00053
S	172	S172S	tcT	tcA	1	1	AY.75	0.000056
S	172	S172S	tcT	tcG	1	1	AY.85	0.000427
S	172	S172S	tcT	tcC	1	1	AY.9.2	0.000037
S	172	S172S	tcT	tcC	1	1	AY.90	0.000684
S	172	S172S	tcT	tcC	1	1	B.1.1	0.000018
S	172	S172S	tcT	tcC	1	1	B.1.1.216	0.00089
S	172	S172S	tcT	tcC	1	1	B.1.1.25	0.000569
S	172	S172S	tcT	tcA	1	1	B.1.1.28	0.000311
S	172	S172S	tcT	tcC	1	1	B.1.177	0.000013
S	172	S172S	tcT	tcC	1	1	B.1.177.10	0.000878
S	172	S172S	tcT	tcC	1	1	B.1.177.23	0.003236
S	172	S172S	tcT	tcA	1	1	B.1.177.56	0.000668
S	172	S172S	tcT	tcA	1	1	B.1.177.7	0.000165
S	172	S172S	tcT	tcC	1	1	B.1.22	0.001318
S	172	S172S	tcT	tcA	1	1	B.1.258.17	0.000104
S	172	S172S	tcT	tcC	1	1	B.1.346	0.001311
S	172	S172S	tcT	tcG	1	1	B.1.351	0.00003
S	172	S172S	tcT	tcG	1	1	B.1.36	0.000146
S	172	S172S	tcT	tcG	1	1	B.1.427	0.00005
S	172	S172S	tcT	tcC	1	1	B.1.526	0.000024
S	172	S172S	tcT	tcG	1	1	B.1.561	0.000397
S	172	S172S	tcT	tcC	1	1	B.1.576	0.000907
S	172	S172S	tcT	tcG	1	1	B.1.595	0.000261
S	172	S172S	tcT	tcC	1	1	B.1.609	0.000479
S	172	S172S	tcT	tcC	1	1	B.1.617.1	0.000129
S	172	S172S	tcT	tcC	1	1	B.1.621	0.000089
S	172	S172S	tcT	tcC	1	1	B.1.637	0.000073
S	172	S172S	tcT	tcG	1	1	C.37	0.000116
S	172	S172S	tcT	tcG	1	1	C.38	0.008065
S	172	S172S	tcT	tcC	1	1	P.1.1	0.000318
S	172	S172S	tcT	tcG	1	1	P.3	0.001595
S	172	S172S	tcT	tcC	1	1	Q.4	0.000455

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.