CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp6 : CodonNum = 154

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/nsp6	154	Y154C	Y3723C	nonsyn	tAt	tGt	424	423	0.997642	11432-11434
ORF1ab/nsp6	154	Y154C	Y3723C	nonsyn	tAT	tGC	424	1	0.00235849	11432-11434
ORF1ab/nsp6	154	Y154Y	Y3723Y	syn	taT	taC	201	201	1	11432-11434
ORF1ab/nsp6	154	Y154del	Y3723del	del	TAT	---	35	35	1	11432-11434
ORF1ab/nsp6	154	Y154H	Y3723H	nonsyn	Tat	Cat	25	25	1	11432-11434
ORF1ab/nsp6	154	Y154S	Y3723S	nonsyn	tAt	tCt	14	12	0.857143	11432-11434
ORF1ab/nsp6	154	Y154S	Y3723S	nonsyn	tAT	tCC	14	1	0.0714286	11432-11434
ORF1ab/nsp6	154	Y154S	Y3723S	nonsyn	tAT	tCG	14	1	0.0714286	11432-11434
ORF1ab/nsp6	154	Y154F	Y3723F	nonsyn	tAt	tTt	10	10	1	11432-11434
ORF1ab/nsp6	154	Y154N	Y3723N	nonsyn	Tat	Aat	7	7	1	11432-11434
ORF1ab/nsp6	154	Y154X	Y3723X	nonsyn	taT	taG	3	3	1	11432-11434
ORF1ab/nsp6	154	Y154L	Y3723L	nonsyn	TAt	CTt	3	3	1	11432-11434
ORF1ab/nsp6	154	Y154P	Y3723P	nonsyn	TAt	CCt	3	2	0.666667	11432-11434
ORF1ab/nsp6	154	Y154P	Y3723P	nonsyn	TAT	CCG	3	1	0.333333	11432-11434
ORF1ab/nsp6	154	Y154D	Y3723D	nonsyn	Tat	Gat	2	2	1	11432-11434
ORF1ab/nsp6	154	Y154del1	Y3723del1	del	taT	ta-	2	2	1	11432-11434
ORF1ab/nsp6	154	Y154G	Y3723G	nonsyn	TAt	GGt	1	1	1	11432-11434
ORF1ab/nsp6	154	Y154W	Y3723W	nonsyn	tAT	tGG	1	1	1	11432-11434
ORF1ab/nsp6	154	Y154V	Y3723V	nonsyn	TAt	GTt	1	1	1	11432-11434
ORF1ab/nsp6	154	Y154I	Y3723I	nonsyn	TAt	ATt	1	1	1	11432-11434

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/nsp6	154	Y154C	tAt	tGt	423	424	All	0.000081
ORF1ab/nsp6	154	Y154C	tAT	tGC	1	424	All	0
ORF1ab/nsp6	154	Y154C	tAt	tGt	236	236	C.36.1	0.979253
ORF1ab/nsp6	154	Y154Y	taT	taC	201	201	All	0.000038
ORF1ab/nsp6	154	Y154C	tAt	tGt	54	54	B.1.1.7	0.000048
ORF1ab/nsp6	154	Y154Y	taT	taC	53	53	B.1.1.7	0.000047
ORF1ab/nsp6	154	Y154del	TAT	---	35	35	All	0.000007
ORF1ab/nsp6	154	Y154C	tAt	tGt	26	26	AY.103	0.000161
ORF1ab/nsp6	154	Y154C	tAt	tGt	26	26	P.1.1	0.008259
ORF1ab/nsp6	154	Y154H	Tat	Cat	25	25	All	0.000005
ORF1ab/nsp6	154	Y154Y	taT	taC	23	23	AY.9.1	0.001926
ORF1ab/nsp6	154	Y154Y	taT	taC	20	20	AY.25	0.00012
ORF1ab/nsp6	154	Y154S	tAt	tCt	12	14	All	0.000002
ORF1ab/nsp6	154	Y154S	tAT	tCC	1	14	All	0
ORF1ab/nsp6	154	Y154S	tAT	tCG	1	14	All	0
ORF1ab/nsp6	154	Y154Y	taT	taC	12	12	AY.48	0.005581
ORF1ab/nsp6	154	Y154C	tAt	tGt	11	11	B.1.617.2	0.000041
ORF1ab/nsp6	154	Y154F	tAt	tTt	10	10	All	0.000002
ORF1ab/nsp6	154	Y154Y	taT	taC	10	10	AY.4	0.000016
ORF1ab/nsp6	154	Y154C	tAt	tGt	9	9	C.36	0.008197
ORF1ab/nsp6	154	Y154Y	taT	taC	8	8	AY.44	0.000049
ORF1ab/nsp6	154	Y154Y	taT	taC	8	8	B.1	0.000073
ORF1ab/nsp6	154	Y154N	Tat	Aat	7	7	All	0.000001
ORF1ab/nsp6	154	Y154C	tAt	tGt	7	7	AY.2	0.002493
ORF1ab/nsp6	154	Y154del	TAT	---	7	7	B.1.1.7	0.000006
ORF1ab/nsp6	154	Y154Y	taT	taC	5	5	AY.103	0.000031
ORF1ab/nsp6	154	Y154C	tAt	tGt	5	5	AY.36	0.000741
ORF1ab/nsp6	154	Y154Y	taT	taC	5	5	AY.39	0.000124
ORF1ab/nsp6	154	Y154Y	taT	taC	5	5	AY.43	0.000022
ORF1ab/nsp6	154	Y154H	Tat	Cat	5	5	B.1.1.7	0.000004
ORF1ab/nsp6	154	Y154Y	taT	taC	5	5	B.1.466.2	0.001956
ORF1ab/nsp6	154	Y154S	tAt	tCt	4	4		0.222222
ORF1ab/nsp6	154	Y154F	tAt	tTt	4	4		0.222222
ORF1ab/nsp6	154	Y154H	Tat	Cat	4	4		0.222222
ORF1ab/nsp6	154	Y154Y	taT	taC	4	4	AY.119	0.000141
ORF1ab/nsp6	154	Y154C	tAt	tGt	4	4	AY.44	0.000024
ORF1ab/nsp6	154	Y154C	tAt	tGt	4	4	AY.54	0.000381
ORF1ab/nsp6	154	Y154C	tAt	tGt	4	4	B.1.1.1	0.001307
ORF1ab/nsp6	154	Y154Y	taT	taC	4	4	B.1.1.318	0.001207
ORF1ab/nsp6	154	Y154Y	taT	taC	4	4	B.1.1.70	0.001364
ORF1ab/nsp6	154	Y154del	TAT	---	4	4	B.1.617.2	0.000015
ORF1ab/nsp6	154	Y154Y	taT	taC	4	4	B.1.617.2	0.000015
ORF1ab/nsp6	154	Y154C	tAt	tGt	4	4	C.37	0.000464
ORF1ab/nsp6	154	Y154C	tAt	tGt	3	3	AD.2	0.000657
ORF1ab/nsp6	154	Y154X	taT	taG	3	3	All	0.000001
ORF1ab/nsp6	154	Y154L	TAt	CTt	3	3	All	0.000001
ORF1ab/nsp6	154	Y154P	TAt	CCt	2	3	All	0
ORF1ab/nsp6	154	Y154P	TAT	CCG	1	3	All	0
ORF1ab/nsp6	154	Y154Y	taT	taC	3	3	AY.104	0.005952
ORF1ab/nsp6	154	Y154C	tAt	tGt	3	3	AY.120	0.000112
ORF1ab/nsp6	154	Y154C	tAt	tGt	3	3	AY.4	0.000005
ORF1ab/nsp6	154	Y154Y	taT	taC	3	3	B.1.177	0.00004
ORF1ab/nsp6	154	Y154S	tAt	tCt	3	3	B.1.617.2	0.000011
ORF1ab/nsp6	154	Y154Y	taT	taC	2	2		0.111111
ORF1ab/nsp6	154	Y154L	TAt	CTt	2	2		0.111111
ORF1ab/nsp6	154	Y154P	TAt	CCt	2	2		0.111111
ORF1ab/nsp6	154	Y154del1	taT	ta-	2	2	All	0
ORF1ab/nsp6	154	Y154D	Tat	Gat	2	2	All	0
ORF1ab/nsp6	154	Y154C	tAT	tGC	1	2	AY.113	0.000142
ORF1ab/nsp6	154	Y154C	tAt	tGt	1	2	AY.113	0.000142
ORF1ab/nsp6	154	Y154S	tAT	tCC	1	2	AY.113	0.000142
ORF1ab/nsp6	154	Y154S	tAT	tCG	1	2	AY.113	0.000142
ORF1ab/nsp6	154	Y154C	tAt	tGt	2	2	AY.26	0.000057
ORF1ab/nsp6	154	Y154H	Tat	Cat	2	2	AY.4	0.000003
ORF1ab/nsp6	154	Y154del	TAT	---	2	2	AY.4	0.000003
ORF1ab/nsp6	154	Y154Y	taT	taC	2	2	AY.42	0.00008
ORF1ab/nsp6	154	Y154del	TAT	---	2	2	AY.43	0.000009
ORF1ab/nsp6	154	Y154F	tAt	tTt	2	2	AY.43	0.000009
ORF1ab/nsp6	154	Y154H	Tat	Cat	2	2	AY.9.1	0.000167
ORF1ab/nsp6	154	Y154C	tAt	tGt	2	2	B.1.1.214	0.000111
ORF1ab/nsp6	154	Y154Y	taT	taC	2	2	B.1.429	0.000047
ORF1ab/nsp6	154	Y154H	Tat	Cat	2	2	B.1.617.2	0.000008
ORF1ab/nsp6	154	Y154C	tAt	tGt	2	2	P.3	0.00319
ORF1ab/nsp6	154	Y154del	TAT	---	1	1	A	0.000387
ORF1ab/nsp6	154	Y154I	TAt	ATt	1	1	All	0
ORF1ab/nsp6	154	Y154V	TAt	GTt	1	1	All	0
ORF1ab/nsp6	154	Y154W	tAT	tGG	1	1	All	0
ORF1ab/nsp6	154	Y154G	TAt	GGt	1	1	All	0
ORF1ab/nsp6	154	Y154C	tAt	tGt	1	1	AY.1	0.000396
ORF1ab/nsp6	154	Y154F	tAt	tTt	1	1	AY.102	0.000027
ORF1ab/nsp6	154	Y154W	tAT	tGG	1	1	AY.113	0.000142
ORF1ab/nsp6	154	Y154S	tAt	tCt	1	1	AY.114	0.000231
ORF1ab/nsp6	154	Y154C	tAt	tGt	1	1	AY.117	0.000085
ORF1ab/nsp6	154	Y154S	tAt	tCt	1	1	AY.119	0.000035
ORF1ab/nsp6	154	Y154del	TAT	---	1	1	AY.120	0.000037
ORF1ab/nsp6	154	Y154Y	taT	taC	1	1	AY.120.2	0.001285
ORF1ab/nsp6	154	Y154C	tAt	tGt	1	1	AY.121	0.000135
ORF1ab/nsp6	154	Y154Y	taT	taC	1	1	AY.13	0.000161
ORF1ab/nsp6	154	Y154C	tAt	tGt	1	1	AY.13	0.000161
ORF1ab/nsp6	154	Y154C	tAt	tGt	1	1	AY.25	0.000006
ORF1ab/nsp6	154	Y154H	Tat	Cat	1	1	AY.25	0.000006
ORF1ab/nsp6	154	Y154C	tAt	tGt	1	1	AY.27	0.000065
ORF1ab/nsp6	154	Y154Y	taT	taC	1	1	AY.29	0.000016
ORF1ab/nsp6	154	Y154Y	taT	taC	1	1	AY.29.1	0.000221
ORF1ab/nsp6	154	Y154C	tAt	tGt	1	1	AY.3.1	0.000085
ORF1ab/nsp6	154	Y154Y	taT	taC	1	1	AY.33	0.000067
ORF1ab/nsp6	154	Y154C	tAt	tGt	1	1	AY.37	0.000316
ORF1ab/nsp6	154	Y154X	taT	taG	1	1	AY.4	0.000002
ORF1ab/nsp6	154	Y154N	Tat	Aat	1	1	AY.4	0.000002
ORF1ab/nsp6	154	Y154C	tAt	tGt	1	1	AY.4.2	0.000022
ORF1ab/nsp6	154	Y154del	TAT	---	1	1	AY.42	0.00004
ORF1ab/nsp6	154	Y154C	tAt	tGt	1	1	AY.43	0.000004
ORF1ab/nsp6	154	Y154del	TAT	---	1	1	AY.44	0.000006
ORF1ab/nsp6	154	Y154C	tAt	tGt	1	1	AY.6	0.000041
ORF1ab/nsp6	154	Y154C	tAt	tGt	1	1	AY.62	0.000436
ORF1ab/nsp6	154	Y154Y	taT	taC	1	1	AY.64	0.000595
ORF1ab/nsp6	154	Y154del	TAT	---	1	1	AY.75	0.000056
ORF1ab/nsp6	154	Y154H	Tat	Cat	1	1	AY.75	0.000056
ORF1ab/nsp6	154	Y154del	TAT	---	1	1	AY.78	0.001541
ORF1ab/nsp6	154	Y154C	tAt	tGt	1	1	AY.84	0.000437
ORF1ab/nsp6	154	Y154Y	taT	taC	1	1	AY.9	0.000068
ORF1ab/nsp6	154	Y154N	Tat	Aat	1	1	AY.9.1	0.000084
ORF1ab/nsp6	154	Y154N	Tat	Aat	1	1	AY.9.2	0.000037
ORF1ab/nsp6	154	Y154Y	taT	taC	1	1	AY.9.2	0.000037
ORF1ab/nsp6	154	Y154D	Tat	Gat	1	1	AY.9.2	0.000037
ORF1ab/nsp6	154	Y154C	tAt	tGt	1	1	AY.98.1	0.000048
ORF1ab/nsp6	154	Y154del	TAT	---	1	1	AY.99	0.001049
ORF1ab/nsp6	154	Y154V	TAt	GTt	1	1	B.1	0.000009
ORF1ab/nsp6	154	Y154N	Tat	Aat	1	1	B.1	0.000009
ORF1ab/nsp6	154	Y154G	TAt	GGt	1	1	B.1	0.000009
ORF1ab/nsp6	154	Y154del	TAT	---	1	1	B.1.1	0.000018
ORF1ab/nsp6	154	Y154L	TAt	CTt	1	1	B.1.1	0.000018
ORF1ab/nsp6	154	Y154Y	taT	taC	1	1	B.1.1	0.000018
ORF1ab/nsp6	154	Y154del1	taT	ta-	1	1	B.1.1.139	0.022727
ORF1ab/nsp6	154	Y154C	tAt	tGt	1	1	B.1.1.196	0.005714
ORF1ab/nsp6	154	Y154Y	taT	taC	1	1	B.1.1.214	0.000055
ORF1ab/nsp6	154	Y154X	taT	taG	1	1	B.1.1.220	0.001859
ORF1ab/nsp6	154	Y154Y	taT	taC	1	1	B.1.1.222	0.000204
ORF1ab/nsp6	154	Y154Y	taT	taC	1	1	B.1.1.28	0.000311
ORF1ab/nsp6	154	Y154del	TAT	---	1	1	B.1.1.284	0.000107
ORF1ab/nsp6	154	Y154H	Tat	Cat	1	1	B.1.1.300	0.010753
ORF1ab/nsp6	154	Y154C	tAt	tGt	1	1	B.1.1.33	0.000421
ORF1ab/nsp6	154	Y154del	TAT	---	1	1	B.1.1.409	0.002833
ORF1ab/nsp6	154	Y154N	Tat	Aat	1	1	B.1.1.411	0.014706
ORF1ab/nsp6	154	Y154F	tAt	tTt	1	1	B.1.1.7	0.000001
ORF1ab/nsp6	154	Y154X	taT	taG	1	1	B.1.1.7	0.000001
ORF1ab/nsp6	154	Y154S	tAt	tCt	1	1	B.1.1.7	0.000001
ORF1ab/nsp6	154	Y154del	TAT	---	1	1	B.1.160	0.000031
ORF1ab/nsp6	154	Y154D	Tat	Gat	1	1	B.1.177	0.000013
ORF1ab/nsp6	154	Y154del	TAT	---	1	1	B.1.177.15	0.000631
ORF1ab/nsp6	154	Y154del	TAT	---	1	1	B.1.177.51	0.004566
ORF1ab/nsp6	154	Y154Y	taT	taC	1	1	B.1.177.57	0.000281
ORF1ab/nsp6	154	Y154F	tAt	tTt	1	1	B.1.177.7	0.000165
ORF1ab/nsp6	154	Y154I	TAt	ATt	1	1	B.1.177.7	0.000165
ORF1ab/nsp6	154	Y154N	Tat	Aat	1	1	B.1.177.7	0.000165
ORF1ab/nsp6	154	Y154H	Tat	Cat	1	1	B.1.2	0.000009
ORF1ab/nsp6	154	Y154Y	taT	taC	1	1	B.1.2	0.000009
ORF1ab/nsp6	154	Y154H	Tat	Cat	1	1	B.1.221	0.000071
ORF1ab/nsp6	154	Y154Y	taT	taC	1	1	B.1.243	0.00007
ORF1ab/nsp6	154	Y154del	TAT	---	1	1	B.1.258.3	0.001675
ORF1ab/nsp6	154	Y154Y	taT	taC	1	1	B.1.351	0.00003
ORF1ab/nsp6	154	Y154C	tAt	tGt	1	1	B.1.369	0.000285
ORF1ab/nsp6	154	Y154H	Tat	Cat	1	1	B.1.429	0.000024
ORF1ab/nsp6	154	Y154N	Tat	Aat	1	1	B.1.436	0.001029
ORF1ab/nsp6	154	Y154Y	taT	taC	1	1	B.1.452	0.013699
ORF1ab/nsp6	154	Y154Y	taT	taC	1	1	B.1.538	0.008065
ORF1ab/nsp6	154	Y154del	TAT	---	1	1	B.1.576	0.000907
ORF1ab/nsp6	154	Y154F	tAt	tTt	1	1	B.1.577	0.000687
ORF1ab/nsp6	154	Y154S	tAt	tCt	1	1	B.1.596	0.000087
ORF1ab/nsp6	154	Y154S	tAt	tCt	1	1	B.1.609	0.000479
ORF1ab/nsp6	154	Y154del	TAT	---	1	1	B.1.617.1	0.000129
ORF1ab/nsp6	154	Y154P	TAT	CCG	1	1	B.1.617.2	0.000004
ORF1ab/nsp6	154	Y154del1	taT	ta-	1	1	B.1.617.2	0.000004
ORF1ab/nsp6	154	Y154H	Tat	Cat	1	1	B.1.621	0.000089
ORF1ab/nsp6	154	Y154H	Tat	Cat	1	1	B.1.627	0.00202
ORF1ab/nsp6	154	Y154del	TAT	---	1	1	B.1.630	0.005236
ORF1ab/nsp6	154	Y154del	TAT	---	1	1	C.37	0.000116
ORF1ab/nsp6	154	Y154H	Tat	Cat	1	1	D.2	0.000075
ORF1ab/nsp6	154	Y154del	TAT	---	1	1	N.4	0.004255
ORF1ab/nsp6	154	Y154H	Tat	Cat	1	1	P.1	0.000016
ORF1ab/nsp6	154	Y154del	TAT	---	1	1	Q.2	0.000613
ORF1ab/nsp6	154	Y154Y	taT	taC	1	1	Q.8	0.000165

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.