CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 996

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	996	L996L		syn	ttG	ttA	412	339	0.822816	24548-24550
S	996	L996L		syn	Ttg	Ctg	412	73	0.177184	24548-24550
S	996	L996del		del	TTG	---	35	35	1	24548-24550
S	996	L996F		nonsyn	ttG	ttT	24	19	0.791667	24548-24550
S	996	L996F		nonsyn	ttG	ttC	24	5	0.208333	24548-24550
S	996	L996S		nonsyn	tTg	tCg	8	8	1	24548-24550
S	996	L996K		nonsyn	TTg	AAg	3	3	1	24548-24550
S	996	L996M		nonsyn	Ttg	Atg	2	2	1	24548-24550
S	996	L996P		nonsyn	TTg	CCg	2	2	1	24548-24550
S	996	L996V		nonsyn	Ttg	Gtg	2	2	1	24548-24550
S	996	L996W		nonsyn	tTg	tGg	1	1	1	24548-24550
S	996	L996R		nonsyn	TTG	CGA	1	1	1	24548-24550
S	996	L996X		nonsyn	tTg	tAg	1	1	1	24548-24550

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	996	L996L	ttG	ttA	339	412	All	0.000065
S	996	L996L	Ttg	Ctg	73	412	All	0.000014
S	996	L996L	ttG	ttA	141	141	B.1.617.2	0.000531
S	996	L996L	ttG	ttA	46	46	AY.102	0.00122
S	996	L996del	TTG	---	35	35	All	0.000007
S	996	L996L	ttG	ttA	32	32	B.1.161	0.551724
S	996	L996L	Ttg	Ctg	28	28	B.1.564	0.011925
S	996	L996F	ttG	ttT	19	24	All	0.000004
S	996	L996F	ttG	ttC	5	24	All	0.000001
S	996	L996L	ttG	ttA	21	24	AY.4	0.000033
S	996	L996L	Ttg	Ctg	3	24	AY.4	0.000005
S	996	L996L	ttG	ttA	13	13	AY.29	0.000205
S	996	L996L	Ttg	Ctg	12	12	B.1.369	0.003423
S	996	L996L	ttG	ttA	9	10	B.1.1.7	0.000008
S	996	L996L	Ttg	Ctg	1	10	B.1.1.7	0.000001
S	996	L996L	Ttg	Ctg	8	9	AY.3	0.00008
S	996	L996L	ttG	ttA	1	9	AY.3	0.00001
S	996	L996L	Ttg	Ctg	8	9	B.1	0.000073
S	996	L996L	ttG	ttA	1	9	B.1	0.000009
S	996	L996S	tTg	tCg	8	8	All	0.000002
S	996	L996L	ttG	ttA	8	8	AY.4.2.1	0.001192
S	996	L996L	ttG	ttA	5	8	AY.43	0.000022
S	996	L996L	Ttg	Ctg	3	8	AY.43	0.000013
S	996	L996del	TTG	---	7	7	B.1.1.7	0.000006
S	996	L996L	ttG	ttA	4	5	AY.44	0.000024
S	996	L996L	Ttg	Ctg	1	5	AY.44	0.000006
S	996	L996L	ttG	ttA	5	5	B.1.429	0.000118
S	996	L996F	ttG	ttT	4	4	B.1	0.000037
S	996	L996K	TTg	AAg	3	3	All	0.000001
S	996	L996L	ttG	ttA	3	3	AY.39	0.000074
S	996	L996F	ttG	ttT	3	3	AY.43	0.000013
S	996	L996L	ttG	ttA	3	3	AY.46.3	0.002801
S	996	L996S	tTg	tCg	3	3	B.1	0.000027
S	996	L996del	TTG	---	3	3	B.1	0.000027
S	996	L996L	ttG	ttA	3	3	B.1.1	0.000054
S	996	L996L	ttG	ttA	3	3	B.1.1.192	0.006928
S	996	L996del	TTG	---	3	3	B.1.177	0.00004
S	996	L996M	Ttg	Atg	2	2	All	0
S	996	L996V	Ttg	Gtg	2	2	All	0
S	996	L996P	TTg	CCg	2	2	All	0
S	996	L996L	ttG	ttA	2	2	AY.103	0.000012
S	996	L996L	ttG	ttA	2	2	AY.119	0.000071
S	996	L996F	ttG	ttT	2	2	B	0.000256
S	996	L996F	ttG	ttT	1	2	B.1.1	0.000018
S	996	L996F	ttG	ttC	1	2	B.1.1	0.000018
S	996	L996L	ttG	ttA	2	2	B.1.1.326	0.003521
S	996	L996P	TTg	CCg	2	2	B.1.1.7	0.000002
S	996	L996F	ttG	ttC	1	2	B.1.1.7	0.000001
S	996	L996F	ttG	ttT	1	2	B.1.1.7	0.000001
S	996	L996L	Ttg	Ctg	1	2	B.1.177	0.000013
S	996	L996L	ttG	ttA	1	2	B.1.177	0.000013
S	996	L996L	ttG	ttA	2	2	B.1.234	0.000264
S	996	L996L	ttG	ttA	2	2	B.1.36	0.000292
S	996	L996L	ttG	ttA	2	2	B.1.617.1	0.000258
S	996	L996L	ttG	ttA	2	2	P.1	0.000032
S	996	L996F	ttG	ttT	1	1	A	0.000387
S	996	L996R	TTG	CGA	1	1	All	0
S	996	L996W	tTg	tGg	1	1	All	0
S	996	L996X	tTg	tAg	1	1	All	0
S	996	L996L	ttG	ttA	1	1	AU.1	0.001266
S	996	L996L	ttG	ttA	1	1	AY.106	0.000335
S	996	L996L	ttG	ttA	1	1	AY.117	0.000085
S	996	L996L	ttG	ttA	1	1	AY.118	0.000063
S	996	L996del	TTG	---	1	1	AY.120	0.000037
S	996	L996L	ttG	ttA	1	1	AY.120	0.000037
S	996	L996L	ttG	ttA	1	1	AY.13	0.000161
S	996	L996L	ttG	ttA	1	1	AY.33	0.000067
S	996	L996del	TTG	---	1	1	AY.33	0.000067
S	996	L996S	tTg	tCg	1	1	AY.36	0.000148
S	996	L996F	ttG	ttC	1	1	AY.4	0.000002
S	996	L996L	ttG	ttA	1	1	AY.4.2	0.000022
S	996	L996del	TTG	---	1	1	AY.4.5	0.000107
S	996	L996L	ttG	ttA	1	1	AY.42	0.00004
S	996	L996F	ttG	ttT	1	1	AY.42	0.00004
S	996	L996del	TTG	---	1	1	AY.43	0.000004
S	996	L996M	Ttg	Atg	1	1	AY.43	0.000004
S	996	L996S	tTg	tCg	1	1	AY.43	0.000004
S	996	L996L	ttG	ttA	1	1	AY.45	0.000122
S	996	L996L	ttG	ttA	1	1	AY.46	0.000104
S	996	L996del	TTG	---	1	1	AY.5	0.000021
S	996	L996L	ttG	ttA	1	1	AY.5	0.000021
S	996	L996F	ttG	ttT	1	1	AY.52	0.000814
S	996	L996L	ttG	ttA	1	1	AY.52	0.000814
S	996	L996L	ttG	ttA	1	1	AY.55	0.000917
S	996	L996L	ttG	ttA	1	1	AY.59	0.00053
S	996	L996del	TTG	---	1	1	AY.68	0.000274
S	996	L996del	TTG	---	1	1	AY.81	0.001992
S	996	L996L	ttG	ttA	1	1	AY.88	0.000884
S	996	L996L	Ttg	Ctg	1	1	AY.93	0.000273
S	996	L996L	Ttg	Ctg	1	1	AY.98	0.000079
S	996	L996M	Ttg	Atg	1	1	B.1	0.000009
S	996	L996S	tTg	tCg	1	1	B.1.1	0.000018
S	996	L996W	tTg	tGg	1	1	B.1.1	0.000018
S	996	L996V	Ttg	Gtg	1	1	B.1.1	0.000018
S	996	L996L	ttG	ttA	1	1	B.1.1.222	0.000204
S	996	L996del	TTG	---	1	1	B.1.1.236	0.006897
S	996	L996del	TTG	---	1	1	B.1.1.312	0.001912
S	996	L996del	TTG	---	1	1	B.1.1.315	0.008475
S	996	L996K	TTg	AAg	1	1	B.1.1.315	0.008475
S	996	L996K	TTg	AAg	1	1	B.1.1.326	0.001761
S	996	L996L	Ttg	Ctg	1	1	B.1.1.37	0.000193
S	996	L996L	ttG	ttA	1	1	B.1.1.39	0.00051
S	996	L996K	TTg	AAg	1	1	B.1.1.7	0.000001
S	996	L996S	tTg	tCg	1	1	B.1.1.7	0.000001
S	996	L996V	Ttg	Gtg	1	1	B.1.1.7	0.000001
S	996	L996del	TTG	---	1	1	B.1.140	0.018868
S	996	L996L	ttG	ttA	1	1	B.1.160	0.000031
S	996	L996L	Ttg	Ctg	1	1	B.1.160.14	0.002119
S	996	L996del	TTG	---	1	1	B.1.177.4	0.000211
S	996	L996del	TTG	---	1	1	B.1.177.5	0.001242
S	996	L996del	TTG	---	1	1	B.1.177.62	0.001192
S	996	L996del	TTG	---	1	1	B.1.177.63	0.002703
S	996	L996F	ttG	ttC	1	1	B.1.2	0.000009
S	996	L996del	TTG	---	1	1	B.1.2	0.000009
S	996	L996F	ttG	ttT	1	1	B.1.301	0.005917
S	996	L996L	ttG	ttA	1	1	B.1.311	0.000275
S	996	L996L	Ttg	Ctg	1	1	B.1.351	0.00003
S	996	L996del	TTG	---	1	1	B.1.36.17	0.000494
S	996	L996X	tTg	tAg	1	1	B.1.36.18	0.00042
S	996	L996L	ttG	ttA	1	1	B.1.36.34	0.021277
S	996	L996L	ttG	ttA	1	1	B.1.416	0.001269
S	996	L996L	ttG	ttA	1	1	B.1.526	0.000024
S	996	L996L	Ttg	Ctg	1	1	B.1.533	0.009615
S	996	L996L	ttG	ttA	1	1	B.1.561	0.000397
S	996	L996del	TTG	---	1	1	B.1.585	0.027778
S	996	L996F	ttG	ttT	1	1	B.1.595	0.000261
S	996	L996L	Ttg	Ctg	1	1	B.1.609	0.000479
S	996	L996F	ttG	ttT	1	1	B.1.617.1	0.000129
S	996	L996del	TTG	---	1	1	B.1.617.2	0.000004
S	996	L996F	ttG	ttC	1	1	B.1.617.2	0.000004
S	996	L996F	ttG	ttT	1	1	B.6	0.00091
S	996	L996R	TTG	CGA	1	1	B.6.6	0.000889
S	996	L996del	TTG	---	1	1	C.37	0.000116
S	996	L996S	tTg	tCg	1	1	D.2	0.000075
S	996	L996del	TTG	---	1	1	P.1	0.000016
S	996	L996F	ttG	ttT	1	1	P.1	0.000016
S	996	L996L	ttG	ttA	1	1	P.1.15	0.000232
S	996	L996L	Ttg	Ctg	1	1	P.1.16	0.000374
S	996	L996del	TTG	---	1	1	Q.1	0.000126
S	996	L996L	ttG	ttA	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.