CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 978

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	978	Y978Y	Y1796Y	syn	taT	taC	5472	5472	1	5651-5653
ORF1ab/nsp3	978	Y978del	Y1796del	del	TAT	---	30	30	1	5651-5653
ORF1ab/nsp3	978	Y978H	Y1796H	nonsyn	Tat	Cat	10	10	1	5651-5653
ORF1ab/nsp3	978	Y978N	Y1796N	nonsyn	Tat	Aat	7	7	1	5651-5653
ORF1ab/nsp3	978	Y978C	Y1796C	nonsyn	tAt	tGt	3	3	1	5651-5653
ORF1ab/nsp3	978	Y978X	Y1796X	nonsyn	taT	taA	2	2	1	5651-5653
ORF1ab/nsp3	978	Y978F	Y1796F	nonsyn	tAt	tTt	2	2	1	5651-5653
ORF1ab/nsp3	978	Y978del1	Y1796del1	del	taT	ta-	1	1	1	5651-5653
ORF1ab/nsp3	978	Y978W	Y1796W	nonsyn	tAT	tGG	1	1	1	5651-5653
ORF1ab/nsp3	978	Y978R	Y1796R	nonsyn	TAt	CGt	1	1	1	5651-5653
ORF1ab/nsp3	978	Y978D	Y1796D	nonsyn	Tat	Gat	1	1	1	5651-5653

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	978	Y978Y	taT	taC	5472	5472	All	0.001047
ORF1ab/nsp3	978	Y978Y	taT	taC	2644	2644	AY.4	0.004115
ORF1ab/nsp3	978	Y978Y	taT	taC	1309	1309	B.1.36.27	0.999237
ORF1ab/nsp3	978	Y978Y	taT	taC	637	637	B.1.36	0.092938
ORF1ab/nsp3	978	Y978Y	taT	taC	246	246	B.1.1.7	0.00022
ORF1ab/nsp3	978	Y978Y	taT	taC	154	154	AY.43	0.000682
ORF1ab/nsp3	978	Y978Y	taT	taC	66	66	AY.103	0.00041
ORF1ab/nsp3	978	Y978Y	taT	taC	64	64	B.1	0.000586
ORF1ab/nsp3	978	Y978Y	taT	taC	43	43	B.1.617.2	0.000162
ORF1ab/nsp3	978	Y978Y	taT	taC	36	36	B.1.36.22	0.043478
ORF1ab/nsp3	978	Y978Y	taT	taC	31	31	AY.9.1	0.002595
ORF1ab/nsp3	978	Y978del	TAT	---	30	30	All	0.000006
ORF1ab/nsp3	978	Y978Y	taT	taC	18	18	B.1.1	0.000327
ORF1ab/nsp3	978	Y978del	TAT	---	12	12	B.1.1.7	0.000011
ORF1ab/nsp3	978	Y978Y	taT	taC	11	11	C.37	0.001277
ORF1ab/nsp3	978	Y978H	Tat	Cat	10	10	All	0.000002
ORF1ab/nsp3	978	Y978Y	taT	taC	9	9	B.1.260	0.0301
ORF1ab/nsp3	978	Y978Y	taT	taC	8	8	B.1.1.526	0.028369
ORF1ab/nsp3	978	Y978Y	taT	taC	8	8	B.1.177.60	0.001747
ORF1ab/nsp3	978	Y978N	Tat	Aat	7	7	All	0.000001
ORF1ab/nsp3	978	Y978Y	taT	taC	7	7	AY.25	0.000042
ORF1ab/nsp3	978	Y978Y	taT	taC	7	7	AY.39	0.000173
ORF1ab/nsp3	978	Y978Y	taT	taC	7	7	AY.61	0.000733
ORF1ab/nsp3	978	Y978Y	taT	taC	7	7	B.1.221	0.000497
ORF1ab/nsp3	978	Y978Y	taT	taC	7	7	B.1.36.38	0.011494
ORF1ab/nsp3	978	Y978Y	taT	taC	6	6	AY.26	0.00017
ORF1ab/nsp3	978	Y978Y	taT	taC	6	6	AY.42	0.000241
ORF1ab/nsp3	978	Y978Y	taT	taC	6	6	AY.44	0.000037
ORF1ab/nsp3	978	Y978Y	taT	taC	6	6	B.1.2	0.000053
ORF1ab/nsp3	978	Y978Y	taT	taC	6	6	B.1.468	0.034286
ORF1ab/nsp3	978	Y978Y	taT	taC	5	5	AY.29	0.000079
ORF1ab/nsp3	978	Y978Y	taT	taC	5	5	B.1.177.53	0.011962
ORF1ab/nsp3	978	Y978Y	taT	taC	5	5	B.1.456	0.01634
ORF1ab/nsp3	978	Y978Y	taT	taC	5	5	P.1	0.000079
ORF1ab/nsp3	978	Y978Y	taT	taC	4	4	AY.102	0.000106
ORF1ab/nsp3	978	Y978Y	taT	taC	4	4	AY.118	0.000251
ORF1ab/nsp3	978	Y978Y	taT	taC	4	4	AY.4.3	0.003367
ORF1ab/nsp3	978	Y978Y	taT	taC	4	4	AY.5	0.000083
ORF1ab/nsp3	978	Y978Y	taT	taC	4	4	B.1.160	0.000125
ORF1ab/nsp3	978	Y978Y	taT	taC	4	4	B.1.177	0.000053
ORF1ab/nsp3	978	Y978Y	taT	taC	4	4	B.1.36.16	0.005698
ORF1ab/nsp3	978	Y978C	tAt	tGt	3	3	All	0.000001
ORF1ab/nsp3	978	Y978Y	taT	taC	3	3	B.1.258	0.0002
ORF1ab/nsp3	978	Y978Y	taT	taC	3	3	B.1.36.17	0.001482
ORF1ab/nsp3	978	Y978Y	taT	taC	3	3	B.1.462	0.021739
ORF1ab/nsp3	978	Y978Y	taT	taC	3	3	B.1.533	0.028846
ORF1ab/nsp3	978	Y978Y	taT	taC	3	3	P.1.15	0.000697
ORF1ab/nsp3	978	Y978F	tAt	tTt	2	2	All	0
ORF1ab/nsp3	978	Y978X	taT	taA	2	2	All	0
ORF1ab/nsp3	978	Y978Y	taT	taC	2	2	AY.14	0.000176
ORF1ab/nsp3	978	Y978Y	taT	taC	2	2	AY.28	0.003781
ORF1ab/nsp3	978	Y978H	Tat	Cat	2	2	AY.4	0.000003
ORF1ab/nsp3	978	Y978Y	taT	taC	2	2	AY.4.2.1	0.000298
ORF1ab/nsp3	978	Y978Y	taT	taC	2	2	AY.74	0.000231
ORF1ab/nsp3	978	Y978Y	taT	taC	2	2	AY.84	0.000875
ORF1ab/nsp3	978	Y978Y	taT	taC	2	2	AY.9	0.000135
ORF1ab/nsp3	978	Y978Y	taT	taC	2	2	B.1.1.273	0.013514
ORF1ab/nsp3	978	Y978H	Tat	Cat	2	2	B.1.1.7	0.000002
ORF1ab/nsp3	978	Y978H	Tat	Cat	2	2	B.1.2	0.000018
ORF1ab/nsp3	978	Y978Y	taT	taC	2	2	B.1.351	0.000059
ORF1ab/nsp3	978	Y978del	TAT	---	2	2	B.1.36	0.000292
ORF1ab/nsp3	978	Y978Y	taT	taC	2	2	B.39	0.004662
ORF1ab/nsp3	978	Y978Y	taT	taC	2	2	C.1	0.004785
ORF1ab/nsp3	978	Y978H	Tat	Cat	2	2	D.2	0.00015
ORF1ab/nsp3	978	Y978del	TAT	---	1	1	A.2.2	0.001689
ORF1ab/nsp3	978	Y978del1	taT	ta-	1	1	All	0
ORF1ab/nsp3	978	Y978W	tAT	tGG	1	1	All	0
ORF1ab/nsp3	978	Y978R	TAt	CGt	1	1	All	0
ORF1ab/nsp3	978	Y978D	Tat	Gat	1	1	All	0
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	AU.2	0.002421
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	AY.10	0.00053
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	AY.100	0.000046
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	AY.116	0.000287
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	AY.119	0.000035
ORF1ab/nsp3	978	Y978H	Tat	Cat	1	1	AY.120.1	0.000321
ORF1ab/nsp3	978	Y978F	tAt	tTt	1	1	AY.20	0.000039
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	AY.23	0.00007
ORF1ab/nsp3	978	Y978X	taT	taA	1	1	AY.24	0.000431
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	AY.27	0.000065
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	AY.30	0.000396
ORF1ab/nsp3	978	Y978del	TAT	---	1	1	AY.35	0.000233
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	AY.38	0.000499
ORF1ab/nsp3	978	Y978N	Tat	Aat	1	1	AY.39.1	0.00004
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	AY.4.2	0.000022
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	AY.4.5	0.000107
ORF1ab/nsp3	978	Y978del	TAT	---	1	1	AY.43	0.000004
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	AY.45	0.000122
ORF1ab/nsp3	978	Y978del	TAT	---	1	1	AY.46	0.000104
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	AY.46	0.000104
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	AY.46.1	0.001027
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	AY.47	0.000031
ORF1ab/nsp3	978	Y978N	Tat	Aat	1	1	AY.69	0.000187
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	AY.71	0.000475
ORF1ab/nsp3	978	Y978del	TAT	---	1	1	AY.71	0.000475
ORF1ab/nsp3	978	Y978del	TAT	---	1	1	AY.75.1	0.00018
ORF1ab/nsp3	978	Y978X	taT	taA	1	1	B	0.000128
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B	0.000128
ORF1ab/nsp3	978	Y978del	TAT	---	1	1	B.1	0.000009
ORF1ab/nsp3	978	Y978N	Tat	Aat	1	1	B.1.1	0.000018
ORF1ab/nsp3	978	Y978C	tAt	tGt	1	1	B.1.1	0.000018
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B.1.1.139	0.022727
ORF1ab/nsp3	978	Y978del	TAT	---	1	1	B.1.1.142	0.017544
ORF1ab/nsp3	978	Y978N	Tat	Aat	1	1	B.1.1.269	0.001353
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B.1.1.291	0.000742
ORF1ab/nsp3	978	Y978del	TAT	---	1	1	B.1.1.315	0.008475
ORF1ab/nsp3	978	Y978del	TAT	---	1	1	B.1.1.385	0.004464
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B.1.1.50	0.000679
ORF1ab/nsp3	978	Y978F	tAt	tTt	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	978	Y978W	tAT	tGG	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B.1.111	0.001175
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B.1.147	0.000756
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B.1.164	0.014925
ORF1ab/nsp3	978	Y978del	TAT	---	1	1	B.1.177	0.000013
ORF1ab/nsp3	978	Y978C	tAt	tGt	1	1	B.1.177	0.000013
ORF1ab/nsp3	978	Y978H	Tat	Cat	1	1	B.1.177	0.000013
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B.1.177.31	0.011494
ORF1ab/nsp3	978	Y978del	TAT	---	1	1	B.1.221	0.000071
ORF1ab/nsp3	978	Y978D	Tat	Gat	1	1	B.1.221.4	0.004167
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B.1.234	0.000132
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B.1.240	0.000216
ORF1ab/nsp3	978	Y978del	TAT	---	1	1	B.1.319	0.003049
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B.1.337	0.005587
ORF1ab/nsp3	978	Y978del1	taT	ta-	1	1	B.1.36	0.000146
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B.1.36.10	0.004785
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B.1.36.18	0.00042
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B.1.36.33	0.007576
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B.1.36.34	0.021277
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B.1.36.7	0.004
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B.1.36.8	0.001
ORF1ab/nsp3	978	Y978N	Tat	Aat	1	1	B.1.369	0.000285
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B.1.408	0.00369
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B.1.429	0.000024
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B.1.517	0.000427
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B.1.523	0.002451
ORF1ab/nsp3	978	Y978N	Tat	Aat	1	1	B.1.612	0.002653
ORF1ab/nsp3	978	Y978del	TAT	---	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	B.1.623	0.000536
ORF1ab/nsp3	978	Y978N	Tat	Aat	1	1	B.1.637	0.000073
ORF1ab/nsp3	978	Y978del	TAT	---	1	1	B.15	0.017544
ORF1ab/nsp3	978	Y978R	TAt	CGt	1	1	C.35	0.000774
ORF1ab/nsp3	978	Y978del	TAT	---	1	1	C.37	0.000116
ORF1ab/nsp3	978	Y978C	tAt	tGt	1	1	D.2	0.000075
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	L.3	0.003546
ORF1ab/nsp3	978	Y978Y	taT	taC	1	1	P.3	0.001595

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.