CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp12 : CodonNum = 45

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
ORF1ab/nsp12	45	F45F	F4437F	syn	ttT	ttC	327	327	1	13573-13575
ORF1ab/nsp12	45	F45del	F4437del	del	TTT	---	43	43	1	13573-13575
ORF1ab/nsp12	45	F45L	F4437L	nonsyn	Ttt	Ctt	11	8	0.727273	13573-13575
ORF1ab/nsp12	45	F45L	F4437L	nonsyn	ttT	ttA	11	3	0.272727	13573-13575
ORF1ab/nsp12	45	F45S	F4437S	nonsyn	tTt	tCt	6	6	1	13573-13575
ORF1ab/nsp12	45	F45C	F4437C	nonsyn	tTt	tGt	6	5	0.833333	13573-13575
ORF1ab/nsp12	45	F45C	F4437C	nonsyn	tTT	tGC	6	1	0.166667	13573-13575
ORF1ab/nsp12	45	F45V	F4437V	nonsyn	Ttt	Gtt	5	5	1	13573-13575
ORF1ab/nsp12	45	F45G	F4437G	nonsyn	TTT	GGC	2	2	1	13573-13575
ORF1ab/nsp12	45	F45del1	F4437del1	del	Ttt	-tt	2	1	0.5	13573-13575
ORF1ab/nsp12	45	F45del2	F4437del2	del	TTt	--t	2	1	0.5	13573-13575
ORF1ab/nsp12	45	F45del1	F4437del1	del	TtT	Ct-	2	1	0.5	13573-13575
ORF1ab/nsp12	45	F45del2	F4437del2	del	tTT	t--	2	1	0.5	13573-13575
ORF1ab/nsp12	45	F45I	F4437I	nonsyn	Ttt	Att	1	1	1	13573-13575
ORF1ab/nsp12	45	F45N	F4437N	nonsyn	TTt	AAt	1	1	1	13573-13575

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
ORF1ab/nsp12	45	F45F	ttT	ttC	327	327	All	0.000063
ORF1ab/nsp12	45	F45F	ttT	ttC	154	154	AY.75	0.008627
ORF1ab/nsp12	45	F45F	ttT	ttC	49	49	B.1.621	0.004337
ORF1ab/nsp12	45	F45del	TTT	---	43	43	All	0.000008
ORF1ab/nsp12	45	F45F	ttT	ttC	21	21	B.1	0.000192
ORF1ab/nsp12	45	F45F	ttT	ttC	15	15	B.1.1.7	0.000013
ORF1ab/nsp12	45	F45F	ttT	ttC	13	13	B.1.1.350	0.52
ORF1ab/nsp12	45	F45L	Ttt	Ctt	8	11	All	0.000002
ORF1ab/nsp12	45	F45L	ttT	ttA	3	11	All	0.000001
ORF1ab/nsp12	45	F45F	ttT	ttC	11	11	AY.44	0.000067
ORF1ab/nsp12	45	F45del	TTT	---	10	10	B.1.1.7	0.000009
ORF1ab/nsp12	45	F45S	tTt	tCt	6	6	All	0.000001
ORF1ab/nsp12	45	F45C	tTt	tGt	5	6	All	0.000001
ORF1ab/nsp12	45	F45C	tTT	tGC	1	6	All	0
ORF1ab/nsp12	45	F45F	ttT	ttC	6	6	AY.42	0.000241
ORF1ab/nsp12	45	F45F	ttT	ttC	6	6	B.1.617.2	0.000023
ORF1ab/nsp12	45	F45V	Ttt	Gtt	5	5	All	0.000001
ORF1ab/nsp12	45	F45F	ttT	ttC	5	5	B.1.1.222	0.00102
ORF1ab/nsp12	45	F45F	ttT	ttC	4	4	AY.4	0.000006
ORF1ab/nsp12	45	F45F	ttT	ttC	4	4	AY.45	0.000487
ORF1ab/nsp12	45	F45F	ttT	ttC	4	4	B.1.2	0.000035
ORF1ab/nsp12	45	F45F	ttT	ttC	3	3	AY.102	0.00008
ORF1ab/nsp12	45	F45del	TTT	---	3	3	AY.43	0.000013
ORF1ab/nsp12	45	F45C	tTt	tGt	3	3	B.1.1.7	0.000003
ORF1ab/nsp12	45	F45F	ttT	ttC	3	3	B.1.637	0.000219
ORF1ab/nsp12	45	F45G	TTT	GGC	2	2	All	0
ORF1ab/nsp12	45	F45del1	TtT	Ct-	1	2	All	0
ORF1ab/nsp12	45	F45del1	Ttt	-tt	1	2	All	0
ORF1ab/nsp12	45	F45del2	TTt	--t	1	2	All	0
ORF1ab/nsp12	45	F45del2	tTT	t--	1	2	All	0
ORF1ab/nsp12	45	F45F	ttT	ttC	2	2	AY.103	0.000012
ORF1ab/nsp12	45	F45F	ttT	ttC	2	2	AY.118	0.000125
ORF1ab/nsp12	45	F45F	ttT	ttC	2	2	AY.25	0.000012
ORF1ab/nsp12	45	F45del	TTT	---	2	2	AY.25	0.000012
ORF1ab/nsp12	45	F45F	ttT	ttC	2	2	AY.33	0.000134
ORF1ab/nsp12	45	F45del	TTT	---	2	2	AY.4	0.000003
ORF1ab/nsp12	45	F45S	tTt	tCt	2	2	B.1	0.000018
ORF1ab/nsp12	45	F45L	ttT	ttA	1	2	B.1.1.7	0.000001
ORF1ab/nsp12	45	F45L	Ttt	Ctt	1	2	B.1.1.7	0.000001
ORF1ab/nsp12	45	F45F	ttT	ttC	2	2	B.1.177	0.000026
ORF1ab/nsp12	45	F45F	ttT	ttC	2	2	B.1.351	0.000059
ORF1ab/nsp12	45	F45G	TTT	GGC	2	2	B.1.351	0.000059
ORF1ab/nsp12	45	F45F	ttT	ttC	2	2	B.1.526	0.000047
ORF1ab/nsp12	45	F45F	ttT	ttC	2	2	B.1.567	0.006667
ORF1ab/nsp12	45	F45del	TTT	---	2	2	P.1	0.000032
ORF1ab/nsp12	45	F45del	TTT	---	2	2	P.1.15	0.000465
ORF1ab/nsp12	45	F45V	Ttt	Gtt	1	1	A.28	0.002646
ORF1ab/nsp12	45	F45I	Ttt	Att	1	1	All	0
ORF1ab/nsp12	45	F45N	TTt	AAt	1	1	All	0
ORF1ab/nsp12	45	F45F	ttT	ttC	1	1	AY.100	0.000046
ORF1ab/nsp12	45	F45V	Ttt	Gtt	1	1	AY.103	0.000006
ORF1ab/nsp12	45	F45F	ttT	ttC	1	1	AY.113	0.000142
ORF1ab/nsp12	45	F45del	TTT	---	1	1	AY.119	0.000035
ORF1ab/nsp12	45	F45del	TTT	---	1	1	AY.120	0.000037
ORF1ab/nsp12	45	F45S	tTt	tCt	1	1	AY.13	0.000161
ORF1ab/nsp12	45	F45C	tTT	tGC	1	1	AY.33	0.000067
ORF1ab/nsp12	45	F45del	TTT	---	1	1	AY.34.1	0.00051
ORF1ab/nsp12	45	F45C	tTt	tGt	1	1	AY.4	0.000002
ORF1ab/nsp12	45	F45F	ttT	ttC	1	1	AY.4.2	0.000022
ORF1ab/nsp12	45	F45V	Ttt	Gtt	1	1	AY.4.2.1	0.000149
ORF1ab/nsp12	45	F45del2	tTT	t--	1	1	AY.4.5	0.000107
ORF1ab/nsp12	45	F45del	TTT	---	1	1	AY.4.5	0.000107
ORF1ab/nsp12	45	F45F	ttT	ttC	1	1	AY.43	0.000004
ORF1ab/nsp12	45	F45del	TTT	---	1	1	AY.6	0.000041
ORF1ab/nsp12	45	F45del	TTT	---	1	1	AY.66	0.00107
ORF1ab/nsp12	45	F45L	Ttt	Ctt	1	1	AY.75	0.000056
ORF1ab/nsp12	45	F45del1	TtT	Ct-	1	1	AY.9.2	0.000037
ORF1ab/nsp12	45	F45del	TTT	---	1	1	AY.98.1	0.000048
ORF1ab/nsp12	45	F45L	ttT	ttA	1	1	AY.98.1	0.000048
ORF1ab/nsp12	45	F45del	TTT	---	1	1	AY.99	0.001049
ORF1ab/nsp12	45	F45del2	TTt	--t	1	1	AY.99	0.001049
ORF1ab/nsp12	45	F45F	ttT	ttC	1	1	AY.99.2	0.000092
ORF1ab/nsp12	45	F45I	Ttt	Att	1	1	B	0.000128
ORF1ab/nsp12	45	F45L	ttT	ttA	1	1	B.1	0.000009
ORF1ab/nsp12	45	F45N	TTt	AAt	1	1	B.1	0.000009
ORF1ab/nsp12	45	F45V	Ttt	Gtt	1	1	B.1	0.000009
ORF1ab/nsp12	45	F45F	ttT	ttC	1	1	B.1.1	0.000018
ORF1ab/nsp12	45	F45del	TTT	---	1	1	B.1.1	0.000018
ORF1ab/nsp12	45	F45L	Ttt	Ctt	1	1	B.1.1	0.000018
ORF1ab/nsp12	45	F45del	TTT	---	1	1	B.1.1.1	0.000327
ORF1ab/nsp12	45	F45del	TTT	---	1	1	B.1.1.139	0.022727
ORF1ab/nsp12	45	F45S	tTt	tCt	1	1	B.1.1.311	0.000358
ORF1ab/nsp12	45	F45del	TTT	---	1	1	B.1.1.348	0.000796
ORF1ab/nsp12	45	F45del	TTT	---	1	1	B.1.1.37	0.000193
ORF1ab/nsp12	45	F45L	Ttt	Ctt	1	1	B.1.1.402	0.011111
ORF1ab/nsp12	45	F45F	ttT	ttC	1	1	B.1.1.409	0.002833
ORF1ab/nsp12	45	F45F	ttT	ttC	1	1	B.1.177.21	0.000076
ORF1ab/nsp12	45	F45S	tTt	tCt	1	1	B.1.177.58	0.001332
ORF1ab/nsp12	45	F45F	ttT	ttC	1	1	B.1.177.65	0.000665
ORF1ab/nsp12	45	F45F	ttT	ttC	1	1	B.1.177.87	0.000728
ORF1ab/nsp12	45	F45L	Ttt	Ctt	1	1	B.1.2	0.000009
ORF1ab/nsp12	45	F45del	TTT	---	1	1	B.1.2	0.000009
ORF1ab/nsp12	45	F45F	ttT	ttC	1	1	B.1.214.1	0.02
ORF1ab/nsp12	45	F45F	ttT	ttC	1	1	B.1.243	0.00007
ORF1ab/nsp12	45	F45del	TTT	---	1	1	B.1.311	0.000275
ORF1ab/nsp12	45	F45C	tTt	tGt	1	1	B.1.351	0.00003
ORF1ab/nsp12	45	F45L	Ttt	Ctt	1	1	B.1.36.17	0.000494
ORF1ab/nsp12	45	F45del	TTT	---	1	1	B.1.36.18	0.00042
ORF1ab/nsp12	45	F45V	Ttt	Gtt	1	1	B.1.369	0.000285
ORF1ab/nsp12	45	F45L	Ttt	Ctt	1	1	B.1.462	0.007246
ORF1ab/nsp12	45	F45L	Ttt	Ctt	1	1	B.1.525	0.000113
ORF1ab/nsp12	45	F45S	tTt	tCt	1	1	B.1.580	0.004065
ORF1ab/nsp12	45	F45del	TTT	---	1	1	B.1.617.2	0.000004
ORF1ab/nsp12	45	F45del1	Ttt	-tt	1	1	B.1.617.2	0.000004
ORF1ab/nsp12	45	F45del	TTT	---	1	1	B.1.621.1	0.000506
ORF1ab/nsp12	45	F45del	TTT	---	1	1	C.17	0.055556
ORF1ab/nsp12	45	F45del	TTT	---	1	1	C.37	0.000116
ORF1ab/nsp12	45	F45F	ttT	ttC	1	1	P.1	0.000016
ORF1ab/nsp12	45	F45del	TTT	---	1	1	P.2	0.000187
ORF1ab/nsp12	45	F45del	TTT	---	1	1	Q.1	0.000126

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.