CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp16 : CodonNum = 30

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/nsp16	30	Y30Y	Y6828Y	syn	taT	taC	4397	4397	1	20746-20748
ORF1ab/nsp16	30	Y30del	Y6828del	del	TAT	---	55	55	1	20746-20748
ORF1ab/nsp16	30	Y30H	Y6828H	nonsyn	Tat	Cat	8	7	0.875	20746-20748
ORF1ab/nsp16	30	Y30H	Y6828H	nonsyn	TaT	CaC	8	1	0.125	20746-20748
ORF1ab/nsp16	30	Y30C	Y6828C	nonsyn	tAt	tGt	7	6	0.857143	20746-20748
ORF1ab/nsp16	30	Y30X	Y6828X	nonsyn	taT	taG	7	5	0.714286	20746-20748
ORF1ab/nsp16	30	Y30X	Y6828X	nonsyn	taT	taA	7	1	0.142857	20746-20748
ORF1ab/nsp16	30	Y30C	Y6828C	nonsyn	tAT	tGC	7	1	0.142857	20746-20748
ORF1ab/nsp16	30	Y30X	Y6828X	nonsyn	tAT	tGA	7	1	0.142857	20746-20748
ORF1ab/nsp16	30	Y30N	Y6828N	nonsyn	Tat	Aat	4	3	0.75	20746-20748
ORF1ab/nsp16	30	Y30N	Y6828N	nonsyn	TaT	AaC	4	1	0.25	20746-20748
ORF1ab/nsp16	30	Y30D	Y6828D	nonsyn	Tat	Gat	3	3	1	20746-20748
ORF1ab/nsp16	30	Y30F	Y6828F	nonsyn	tAt	tTt	3	3	1	20746-20748
ORF1ab/nsp16	30	Y30R	Y6828R	nonsyn	TAt	CGt	3	2	0.666667	20746-20748
ORF1ab/nsp16	30	Y30S	Y6828S	nonsyn	tAt	tCt	3	2	0.666667	20746-20748
ORF1ab/nsp16	30	Y30R	Y6828R	nonsyn	TAT	CGC	3	1	0.333333	20746-20748
ORF1ab/nsp16	30	Y30S	Y6828S	nonsyn	tAT	tCC	3	1	0.333333	20746-20748
ORF1ab/nsp16	30	Y30del2	Y6828del2	del	TAT	C--	2	2	1	20746-20748
ORF1ab/nsp16	30	Y30del1	Y6828del1	del	Tat	-at	2	1	0.5	20746-20748
ORF1ab/nsp16	30	Y30del1	Y6828del1	del	taT	ta-	2	1	0.5	20746-20748
ORF1ab/nsp16	30	Y30I	Y6828I	nonsyn	TAT	ATC	1	1	1	20746-20748
ORF1ab/nsp16	30	Y30A	Y6828A	nonsyn	TAt	GCt	1	1	1	20746-20748
ORF1ab/nsp16	30	Y30T	Y6828T	nonsyn	TAT	ACC	1	1	1	20746-20748

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/nsp16	30	Y30Y	taT	taC	4397	4397	All	0.000841
ORF1ab/nsp16	30	Y30Y	taT	taC	3179	3179	B.1.575	0.964502
ORF1ab/nsp16	30	Y30Y	taT	taC	393	393	B.1.575.1	0.958537
ORF1ab/nsp16	30	Y30Y	taT	taC	208	208	B.1.575.2	1
ORF1ab/nsp16	30	Y30Y	taT	taC	145	145	B.1.576	0.13146
ORF1ab/nsp16	30	Y30Y	taT	taC	123	123	B.1.1.7	0.00011
ORF1ab/nsp16	30	Y30Y	taT	taC	83	83	B.1	0.00076
ORF1ab/nsp16	30	Y30Y	taT	taC	72	72	B.1.363	0.935065
ORF1ab/nsp16	30	Y30del	TAT	---	55	55	All	0.000011
ORF1ab/nsp16	30	Y30Y	taT	taC	28	28	B.1.427	0.001414
ORF1ab/nsp16	30	Y30Y	taT	taC	23	23	B.1.595	0.006002
ORF1ab/nsp16	30	Y30Y	taT	taC	16	16	B.1.1	0.00029
ORF1ab/nsp16	30	Y30del	TAT	---	11	11	B.1.1.7	0.00001
ORF1ab/nsp16	30	Y30Y	taT	taC	10	10	AY.4	0.000016
ORF1ab/nsp16	30	Y30Y	taT	taC	9	9	B.1.177.81	0.001704
ORF1ab/nsp16	30	Y30Y	taT	taC	9	9	B.1.617.2	0.000034
ORF1ab/nsp16	30	Y30H	Tat	Cat	7	8	All	0.000001
ORF1ab/nsp16	30	Y30H	TaT	CaC	1	8	All	0
ORF1ab/nsp16	30	Y30Y	taT	taC	8	8	B.1.177	0.000105
ORF1ab/nsp16	30	Y30C	tAt	tGt	6	7	All	0.000001
ORF1ab/nsp16	30	Y30X	taT	taG	5	7	All	0.000001
ORF1ab/nsp16	30	Y30X	taT	taA	1	7	All	0
ORF1ab/nsp16	30	Y30C	tAT	tGC	1	7	All	0
ORF1ab/nsp16	30	Y30X	tAT	tGA	1	7	All	0
ORF1ab/nsp16	30	Y30Y	taT	taC	7	7	AY.103	0.000043
ORF1ab/nsp16	30	Y30del	TAT	---	6	6		0.333333
ORF1ab/nsp16	30	Y30Y	taT	taC	6	6	AY.44	0.000037
ORF1ab/nsp16	30	Y30Y	taT	taC	5	5	AY.39	0.000124
ORF1ab/nsp16	30	Y30Y	taT	taC	5	5	B.1.258.16	0.008183
ORF1ab/nsp16	30	Y30Y	taT	taC	5	5	B.1.623	0.002682
ORF1ab/nsp16	30	Y30N	Tat	Aat	3	4	All	0.000001
ORF1ab/nsp16	30	Y30N	TaT	AaC	1	4	All	0
ORF1ab/nsp16	30	Y30Y	taT	taC	4	4	B.1.177.83	0.005926
ORF1ab/nsp16	30	Y30Y	taT	taC	4	4	B.1.2	0.000035
ORF1ab/nsp16	30	Y30Y	taT	taC	4	4	B.1.258	0.000266
ORF1ab/nsp16	30	Y30Y	taT	taC	4	4	B.1.517	0.001708
ORF1ab/nsp16	30	Y30del	TAT	---	4	4	B.1.617.2	0.000015
ORF1ab/nsp16	30	Y30F	tAt	tTt	3	3	All	0.000001
ORF1ab/nsp16	30	Y30D	Tat	Gat	3	3	All	0.000001
ORF1ab/nsp16	30	Y30S	tAt	tCt	2	3	All	0
ORF1ab/nsp16	30	Y30R	TAt	CGt	2	3	All	0
ORF1ab/nsp16	30	Y30R	TAT	CGC	1	3	All	0
ORF1ab/nsp16	30	Y30S	tAT	tCC	1	3	All	0
ORF1ab/nsp16	30	Y30Y	taT	taC	3	3	AY.3	0.00003
ORF1ab/nsp16	30	Y30del	TAT	---	3	3	B.1.1	0.000054
ORF1ab/nsp16	30	Y30F	tAt	tTt	3	3	B.1.1.7	0.000003
ORF1ab/nsp16	30	Y30Y	taT	taC	3	3	P.1	0.000047
ORF1ab/nsp16	30	Y30del2	TAT	C--	2	2		0.111111
ORF1ab/nsp16	30	Y30R	TAT	CGC	1	2		0.055556
ORF1ab/nsp16	30	Y30R	TAt	CGt	1	2		0.055556
ORF1ab/nsp16	30	Y30C	tAt	tGt	1	2		0.055556
ORF1ab/nsp16	30	Y30H	TaT	CaC	1	2		0.055556
ORF1ab/nsp16	30	Y30C	tAT	tGC	1	2		0.055556
ORF1ab/nsp16	30	Y30H	Tat	Cat	1	2		0.055556
ORF1ab/nsp16	30	Y30del2	TAT	C--	2	2	All	0
ORF1ab/nsp16	30	Y30del1	taT	ta-	1	2	All	0
ORF1ab/nsp16	30	Y30del1	Tat	-at	1	2	All	0
ORF1ab/nsp16	30	Y30Y	taT	taC	2	2	AY.100	0.000092
ORF1ab/nsp16	30	Y30Y	taT	taC	2	2	AY.113	0.000285
ORF1ab/nsp16	30	Y30Y	taT	taC	2	2	AY.119	0.000071
ORF1ab/nsp16	30	Y30Y	taT	taC	2	2	AY.20	0.000078
ORF1ab/nsp16	30	Y30del	TAT	---	2	2	AY.25	0.000012
ORF1ab/nsp16	30	Y30Y	taT	taC	2	2	AY.26	0.000057
ORF1ab/nsp16	30	Y30del	TAT	---	2	2	AY.4	0.000003
ORF1ab/nsp16	30	Y30N	Tat	Aat	2	2	AY.4	0.000003
ORF1ab/nsp16	30	Y30del	TAT	---	2	2	AY.4.5	0.000215
ORF1ab/nsp16	30	Y30del	TAT	---	2	2	AY.43	0.000009
ORF1ab/nsp16	30	Y30Y	taT	taC	2	2	AY.61	0.00021
ORF1ab/nsp16	30	Y30X	taT	taG	2	2	B.1	0.000018
ORF1ab/nsp16	30	Y30Y	taT	taC	2	2	B.1.429	0.000047
ORF1ab/nsp16	30	Y30Y	taT	taC	2	2	B.1.526	0.000047
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1		0.055556
ORF1ab/nsp16	30	Y30T	TAT	ACC	1	1	All	0
ORF1ab/nsp16	30	Y30I	TAT	ATC	1	1	All	0
ORF1ab/nsp16	30	Y30A	TAt	GCt	1	1	All	0
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	AY.102	0.000027
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	AY.113	0.000142
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	AY.117	0.000085
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	AY.118	0.000063
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	AY.121	0.000135
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	AY.23.1	0.000417
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	AY.25	0.000006
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	AY.29	0.000016
ORF1ab/nsp16	30	Y30H	Tat	Cat	1	1	AY.3	0.00001
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	AY.3	0.00001
ORF1ab/nsp16	30	Y30C	tAt	tGt	1	1	AY.38	0.000499
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	AY.4.2	0.000022
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	AY.42	0.00004
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	AY.43	0.000004
ORF1ab/nsp16	30	Y30A	TAt	GCt	1	1	AY.43	0.000004
ORF1ab/nsp16	30	Y30I	TAT	ATC	1	1	AY.43	0.000004
ORF1ab/nsp16	30	Y30S	tAt	tCt	1	1	AY.43	0.000004
ORF1ab/nsp16	30	Y30D	Tat	Gat	1	1	AY.43	0.000004
ORF1ab/nsp16	30	Y30C	tAt	tGt	1	1	AY.44	0.000006
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	AY.44	0.000006
ORF1ab/nsp16	30	Y30X	tAT	tGA	1	1	AY.44	0.000006
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	AY.45	0.000122
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	AY.46.6	0.000072
ORF1ab/nsp16	30	Y30R	TAt	CGt	1	1	AY.46.6	0.000072
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	AY.67	0.000464
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	AY.70	0.000209
ORF1ab/nsp16	30	Y30del1	taT	ta-	1	1	AY.84	0.000437
ORF1ab/nsp16	30	Y30C	tAt	tGt	1	1	AY.85	0.000427
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	AY.9	0.000068
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	AY.9.2	0.000037
ORF1ab/nsp16	30	Y30N	TaT	AaC	1	1	AY.9.2	0.000037
ORF1ab/nsp16	30	Y30T	TAT	ACC	1	1	AY.9.2	0.000037
ORF1ab/nsp16	30	Y30S	tAT	tCC	1	1	AY.9.2	0.000037
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	AY.98.1	0.000048
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	AY.99	0.001049
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	B.1	0.000009
ORF1ab/nsp16	30	Y30H	Tat	Cat	1	1	B.1	0.000009
ORF1ab/nsp16	30	Y30C	tAt	tGt	1	1	B.1.1	0.000018
ORF1ab/nsp16	30	Y30del1	Tat	-at	1	1	B.1.1.137	0.0125
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	B.1.1.214	0.000055
ORF1ab/nsp16	30	Y30D	Tat	Gat	1	1	B.1.1.7	0.000001
ORF1ab/nsp16	30	Y30H	Tat	Cat	1	1	B.1.1.7	0.000001
ORF1ab/nsp16	30	Y30X	taT	taA	1	1	B.1.1.7	0.000001
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	B.1.160	0.000031
ORF1ab/nsp16	30	Y30H	Tat	Cat	1	1	B.1.177	0.000013
ORF1ab/nsp16	30	Y30X	taT	taG	1	1	B.1.177	0.000013
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	B.1.177.17	0.000821
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	B.1.177.33	0.001645
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	B.1.177.54	0.000606
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	B.1.177.73	0.000566
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	B.1.177.73	0.000566
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	B.1.177.83	0.001481
ORF1ab/nsp16	30	Y30H	Tat	Cat	1	1	B.1.2	0.000009
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	B.1.2	0.000009
ORF1ab/nsp16	30	Y30N	Tat	Aat	1	1	B.1.221	0.000071
ORF1ab/nsp16	30	Y30H	Tat	Cat	1	1	B.1.234	0.000132
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	B.1.258	0.000067
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	B.1.326	0.007576
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	B.1.351	0.00003
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	B.1.351.2	0.000303
ORF1ab/nsp16	30	Y30D	Tat	Gat	1	1	B.1.36.29	0.000517
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	B.1.367	0.000792
ORF1ab/nsp16	30	Y30X	taT	taG	1	1	B.1.399	0.001934
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	B.1.399	0.001934
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	B.1.499	0.00105
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	B.1.525	0.000113
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	B.1.526	0.000024
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	B.1.544	0.006024
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	B.1.617.3	0.002985
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	B.1.620	0.000946
ORF1ab/nsp16	30	Y30S	tAt	tCt	1	1	B.1.637	0.000073
ORF1ab/nsp16	30	Y30C	tAt	tGt	1	1	B.6.8	0.008264
ORF1ab/nsp16	30	Y30Y	taT	taC	1	1	C.6	0.037037
ORF1ab/nsp16	30	Y30X	taT	taG	1	1	D.2	0.000075
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	P.1.1	0.000318
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	P.1.15	0.000232
ORF1ab/nsp16	30	Y30del	TAT	---	1	1	Q.2	0.000613

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.