CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1452

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/nsp3	1452	Y1452Y	Y2270Y	syn	taT	taC	227	227	1	7073-7075
ORF1ab/nsp3	1452	Y1452del	Y2270del	del	TAT	---	119	119	1	7073-7075
ORF1ab/nsp3	1452	Y1452C	Y2270C	nonsyn	tAt	tGt	22	21	0.954545	7073-7075
ORF1ab/nsp3	1452	Y1452C	Y2270C	nonsyn	tAT	tGC	22	1	0.0454545	7073-7075
ORF1ab/nsp3	1452	Y1452H	Y2270H	nonsyn	Tat	Cat	12	12	1	7073-7075
ORF1ab/nsp3	1452	Y1452X	Y2270X	nonsyn	taT	taG	8	7	0.875	7073-7075
ORF1ab/nsp3	1452	Y1452X	Y2270X	nonsyn	taT	taA	8	1	0.125	7073-7075
ORF1ab/nsp3	1452	Y1452del1	Y2270del1	del	taT	ta-	5	3	0.6	7073-7075
ORF1ab/nsp3	1452	Y1452del1	Y2270del1	del	Tat	-at	5	2	0.4	7073-7075
ORF1ab/nsp3	1452	Y1452F	Y2270F	nonsyn	tAt	tTt	4	4	1	7073-7075
ORF1ab/nsp3	1452	Y1452D	Y2270D	nonsyn	Tat	Gat	4	3	0.75	7073-7075
ORF1ab/nsp3	1452	Y1452D	Y2270D	nonsyn	TaT	GaC	4	1	0.25	7073-7075
ORF1ab/nsp3	1452	Y1452S	Y2270S	nonsyn	tAt	tCt	3	2	0.666667	7073-7075
ORF1ab/nsp3	1452	Y1452S	Y2270S	nonsyn	tAT	tCG	3	1	0.333333	7073-7075
ORF1ab/nsp3	1452	Y1452W	Y2270W	nonsyn	tAT	tGG	2	2	1	7073-7075
ORF1ab/nsp3	1452	Y1452N	Y2270N	nonsyn	Tat	Aat	1	1	1	7073-7075
ORF1ab/nsp3	1452	Y1452E	Y2270E	nonsyn	TaT	GaG	1	1	1	7073-7075

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/nsp3	1452	Y1452Y	taT	taC	227	227	All	0.000043
ORF1ab/nsp3	1452	Y1452del	TAT	---	119	119	All	0.000023
ORF1ab/nsp3	1452	Y1452del	TAT	---	45	45	B.1.1.7	0.00004
ORF1ab/nsp3	1452	Y1452Y	taT	taC	37	37	B.1.1.7	0.000033
ORF1ab/nsp3	1452	Y1452C	tAt	tGt	21	22	All	0.000004
ORF1ab/nsp3	1452	Y1452C	tAT	tGC	1	22	All	0
ORF1ab/nsp3	1452	Y1452Y	taT	taC	22	22	AY.103	0.000137
ORF1ab/nsp3	1452	Y1452Y	taT	taC	21	21	AY.44	0.000128
ORF1ab/nsp3	1452	Y1452Y	taT	taC	20	20	B.1.617.2	0.000075
ORF1ab/nsp3	1452	Y1452Y	taT	taC	18	18	Q.2	0.011043
ORF1ab/nsp3	1452	Y1452Y	taT	taC	15	15	B.1.1.330	0.9375
ORF1ab/nsp3	1452	Y1452H	Tat	Cat	12	12	All	0.000002
ORF1ab/nsp3	1452	Y1452C	tAt	tGt	11	11	AY.74	0.001272
ORF1ab/nsp3	1452	Y1452del	TAT	---	10	10	B.1.177	0.000132
ORF1ab/nsp3	1452	Y1452del	TAT	---	9	9	AY.4	0.000014
ORF1ab/nsp3	1452	Y1452Y	taT	taC	9	9	B.1.429	0.000212
ORF1ab/nsp3	1452	Y1452X	taT	taG	7	8	All	0.000001
ORF1ab/nsp3	1452	Y1452X	taT	taA	1	8	All	0
ORF1ab/nsp3	1452	Y1452Y	taT	taC	7	7	AY.26	0.000198
ORF1ab/nsp3	1452	Y1452Y	taT	taC	7	7	B.1.9.5	0.039773
ORF1ab/nsp3	1452	Y1452Y	taT	taC	7	7	C.36.3	0.003971
ORF1ab/nsp3	1452	Y1452del1	taT	ta-	3	5	All	0.000001
ORF1ab/nsp3	1452	Y1452del1	Tat	-at	2	5	All	0
ORF1ab/nsp3	1452	Y1452Y	taT	taC	5	5	AY.4	0.000008
ORF1ab/nsp3	1452	Y1452del	TAT	---	5	5	B.1	0.000046
ORF1ab/nsp3	1452	Y1452Y	taT	taC	5	5	B.1.637	0.000365
ORF1ab/nsp3	1452	Y1452F	tAt	tTt	4	4	All	0.000001
ORF1ab/nsp3	1452	Y1452D	Tat	Gat	3	4	All	0.000001
ORF1ab/nsp3	1452	Y1452D	TaT	GaC	1	4	All	0
ORF1ab/nsp3	1452	Y1452Y	taT	taC	4	4	AY.102	0.000106
ORF1ab/nsp3	1452	Y1452del	TAT	---	4	4	AY.4.5	0.00043
ORF1ab/nsp3	1452	Y1452Y	taT	taC	4	4	AY.43	0.000018
ORF1ab/nsp3	1452	Y1452del	TAT	---	4	4	AY.43	0.000018
ORF1ab/nsp3	1452	Y1452S	tAt	tCt	2	3	All	0
ORF1ab/nsp3	1452	Y1452S	tAT	tCG	1	3	All	0
ORF1ab/nsp3	1452	Y1452Y	taT	taC	3	3	B.1	0.000027
ORF1ab/nsp3	1452	Y1452C	tAt	tGt	3	3	B.1	0.000027
ORF1ab/nsp3	1452	Y1452Y	taT	taC	3	3	P.2	0.00056
ORF1ab/nsp3	1452	Y1452W	tAT	tGG	2	2		0.111111
ORF1ab/nsp3	1452	Y1452del	TAT	---	2	2		0.111111
ORF1ab/nsp3	1452	Y1452W	tAT	tGG	2	2	All	0
ORF1ab/nsp3	1452	Y1452Y	taT	taC	2	2	AY.106	0.00067
ORF1ab/nsp3	1452	Y1452Y	taT	taC	2	2	AY.116	0.000574
ORF1ab/nsp3	1452	Y1452Y	taT	taC	2	2	AY.23	0.000139
ORF1ab/nsp3	1452	Y1452Y	taT	taC	2	2	AY.25	0.000012
ORF1ab/nsp3	1452	Y1452Y	taT	taC	2	2	AY.39	0.000049
ORF1ab/nsp3	1452	Y1452D	Tat	Gat	2	2	AY.4	0.000003
ORF1ab/nsp3	1452	Y1452X	taT	taG	2	2	AY.4	0.000003
ORF1ab/nsp3	1452	Y1452Y	taT	taC	2	2	AY.54	0.000191
ORF1ab/nsp3	1452	Y1452H	Tat	Cat	2	2	B.1	0.000018
ORF1ab/nsp3	1452	Y1452Y	taT	taC	2	2	B.1.160.8	0.002577
ORF1ab/nsp3	1452	Y1452Y	taT	taC	2	2	B.1.177	0.000026
ORF1ab/nsp3	1452	Y1452C	tAt	tGt	2	2	B.1.2	0.000018
ORF1ab/nsp3	1452	Y1452del	TAT	---	2	2	B.1.221	0.000142
ORF1ab/nsp3	1452	Y1452Y	taT	taC	2	2	B.1.400	0.000858
ORF1ab/nsp3	1452	Y1452Y	taT	taC	2	2	B.1.526	0.000047
ORF1ab/nsp3	1452	Y1452H	Tat	Cat	2	2	B.1.621	0.000177
ORF1ab/nsp3	1452	Y1452del	TAT	---	2	2	P.1	0.000032
ORF1ab/nsp3	1452	Y1452del1	taT	ta-	2	2	P.1	0.000032
ORF1ab/nsp3	1452	Y1452Y	taT	taC	2	2	P.1	0.000032
ORF1ab/nsp3	1452	Y1452Y	taT	taC	1	1	A.5	0.001923
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	AD.2	0.000219
ORF1ab/nsp3	1452	Y1452E	TaT	GaG	1	1	All	0
ORF1ab/nsp3	1452	Y1452N	Tat	Aat	1	1	All	0
ORF1ab/nsp3	1452	Y1452X	taT	taG	1	1	AY.102	0.000027
ORF1ab/nsp3	1452	Y1452X	taT	taG	1	1	AY.103	0.000006
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	AY.103	0.000006
ORF1ab/nsp3	1452	Y1452Y	taT	taC	1	1	AY.114	0.000231
ORF1ab/nsp3	1452	Y1452Y	taT	taC	1	1	AY.119	0.000035
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	AY.119	0.000035
ORF1ab/nsp3	1452	Y1452del1	Tat	-at	1	1	AY.19	0.00114
ORF1ab/nsp3	1452	Y1452H	Tat	Cat	1	1	AY.23	0.00007
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	AY.3	0.00001
ORF1ab/nsp3	1452	Y1452F	tAt	tTt	1	1	AY.3	0.00001
ORF1ab/nsp3	1452	Y1452Y	taT	taC	1	1	AY.33	0.000067
ORF1ab/nsp3	1452	Y1452Y	taT	taC	1	1	AY.35	0.000233
ORF1ab/nsp3	1452	Y1452E	TaT	GaG	1	1	AY.4	0.000002
ORF1ab/nsp3	1452	Y1452C	tAt	tGt	1	1	AY.4.2	0.000022
ORF1ab/nsp3	1452	Y1452F	tAt	tTt	1	1	AY.43	0.000004
ORF1ab/nsp3	1452	Y1452X	taT	taA	1	1	AY.43	0.000004
ORF1ab/nsp3	1452	Y1452Y	taT	taC	1	1	AY.5	0.000021
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	AY.5	0.000021
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	AY.60	0.000938
ORF1ab/nsp3	1452	Y1452S	tAt	tCt	1	1	AY.75	0.000056
ORF1ab/nsp3	1452	Y1452Y	taT	taC	1	1	AY.94	0.000443
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B	0.000128
ORF1ab/nsp3	1452	Y1452Y	taT	taC	1	1	B.1.1	0.000018
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.1	0.000018
ORF1ab/nsp3	1452	Y1452H	Tat	Cat	1	1	B.1.1	0.000018
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.1.159	0.004673
ORF1ab/nsp3	1452	Y1452F	tAt	tTt	1	1	B.1.1.222	0.000204
ORF1ab/nsp3	1452	Y1452X	taT	taG	1	1	B.1.1.300	0.010753
ORF1ab/nsp3	1452	Y1452D	Tat	Gat	1	1	B.1.1.326	0.001761
ORF1ab/nsp3	1452	Y1452Y	taT	taC	1	1	B.1.1.34	0.013158
ORF1ab/nsp3	1452	Y1452Y	taT	taC	1	1	B.1.1.39	0.00051
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.1.51	0.001718
ORF1ab/nsp3	1452	Y1452H	Tat	Cat	1	1	B.1.1.519	0.00004
ORF1ab/nsp3	1452	Y1452Y	taT	taC	1	1	B.1.1.519	0.00004
ORF1ab/nsp3	1452	Y1452X	taT	taG	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1452	Y1452H	Tat	Cat	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1452	Y1452del1	Tat	-at	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1452	Y1452S	tAT	tCG	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1452	Y1452C	tAT	tGC	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.1.70	0.000341
ORF1ab/nsp3	1452	Y1452F	tAt	tTt	1	1	B.1.118	0.006711
ORF1ab/nsp3	1452	Y1452H	Tat	Cat	1	1	B.1.160	0.000031
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.160	0.000031
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.160.7	0.002079
ORF1ab/nsp3	1452	Y1452del1	taT	ta-	1	1	B.1.177.10	0.000878
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.177.15	0.000631
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.177.21	0.000076
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.177.4	0.000211
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.177.54	0.000606
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.177.57	0.000281
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.177.6	0.000977
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.177.62	0.001192
ORF1ab/nsp3	1452	Y1452H	Tat	Cat	1	1	B.1.177.63	0.002703
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.177.7	0.000165
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.177.76	0.002494
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.177.9	0.001332
ORF1ab/nsp3	1452	Y1452X	taT	taG	1	1	B.1.2	0.000009
ORF1ab/nsp3	1452	Y1452Y	taT	taC	1	1	B.1.243	0.00007
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.258.3	0.001675
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.265	0.001271
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.311	0.000275
ORF1ab/nsp3	1452	Y1452H	Tat	Cat	1	1	B.1.351.5	0.0006
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.36.17	0.000494
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.36.18	0.00042
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.415	0.014286
ORF1ab/nsp3	1452	Y1452Y	taT	taC	1	1	B.1.416	0.001269
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.416.1	0.001563
ORF1ab/nsp3	1452	Y1452C	tAt	tGt	1	1	B.1.427	0.00005
ORF1ab/nsp3	1452	Y1452C	tAt	tGt	1	1	B.1.525	0.000113
ORF1ab/nsp3	1452	Y1452C	tAt	tGt	1	1	B.1.570	0.002941
ORF1ab/nsp3	1452	Y1452Y	taT	taC	1	1	B.1.582	0.000491
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.596	0.000087
ORF1ab/nsp3	1452	Y1452Y	taT	taC	1	1	B.1.609	0.000479
ORF1ab/nsp3	1452	Y1452H	Tat	Cat	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1452	Y1452N	Tat	Aat	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.1.621	0.000089
ORF1ab/nsp3	1452	Y1452C	tAt	tGt	1	1	B.1.633	0.041667
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	B.34	0.013699
ORF1ab/nsp3	1452	Y1452D	TaT	GaC	1	1	C.35	0.000774
ORF1ab/nsp3	1452	Y1452Y	taT	taC	1	1	P.1.12	0.000484
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	P.1.15	0.000232
ORF1ab/nsp3	1452	Y1452Y	taT	taC	1	1	Q.4	0.000455
ORF1ab/nsp3	1452	Y1452Y	taT	taC	1	1	Q.8	0.000165
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	Q.8	0.000165
ORF1ab/nsp3	1452	Y1452S	tAt	tCt	1	1	U.3	0.003861
ORF1ab/nsp3	1452	Y1452del	TAT	---	1	1	U.3	0.003861

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.