CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 718

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	718	Y718H	Y1536H	nonsyn	Tat	Cat	612	612	1	4871-4873
ORF1ab/nsp3	718	Y718C	Y1536C	nonsyn	tAt	tGt	491	491	1	4871-4873
ORF1ab/nsp3	718	Y718Y	Y1536Y	syn	taT	taC	347	347	1	4871-4873
ORF1ab/nsp3	718	Y718del	Y1536del	del	TAT	---	91	91	1	4871-4873
ORF1ab/nsp3	718	Y718X	Y1536X	nonsyn	taT	taA	5	4	0.8	4871-4873
ORF1ab/nsp3	718	Y718X	Y1536X	nonsyn	taT	taG	5	1	0.2	4871-4873
ORF1ab/nsp3	718	Y718N	Y1536N	nonsyn	Tat	Aat	4	3	0.75	4871-4873
ORF1ab/nsp3	718	Y718del1	Y1536del1	del	taT	ta-	4	2	0.5	4871-4873
ORF1ab/nsp3	718	Y718N	Y1536N	nonsyn	TaT	AaC	4	1	0.25	4871-4873
ORF1ab/nsp3	718	Y718del1	Y1536del1	del	tAt	t-t	4	1	0.25	4871-4873
ORF1ab/nsp3	718	Y718del1	Y1536del1	del	tAT	tG-	4	1	0.25	4871-4873
ORF1ab/nsp3	718	Y718S	Y1536S	nonsyn	tAt	tCt	3	3	1	4871-4873
ORF1ab/nsp3	718	Y718F	Y1536F	nonsyn	tAt	tTt	3	3	1	4871-4873
ORF1ab/nsp3	718	Y718del2	Y1536del2	del	TAT	--N	1	1	1	4871-4873
ORF1ab/nsp3	718	Y718D	Y1536D	nonsyn	Tat	Gat	1	1	1	4871-4873
ORF1ab/nsp3	718	Y718K	Y1536K	nonsyn	TaT	AaG	1	1	1	4871-4873

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	718	Y718H	Tat	Cat	612	612	All	0.000117
ORF1ab/nsp3	718	Y718C	tAt	tGt	491	491	All	0.000094
ORF1ab/nsp3	718	Y718Y	taT	taC	347	347	All	0.000066
ORF1ab/nsp3	718	Y718C	tAt	tGt	222	222	AY.4	0.000346
ORF1ab/nsp3	718	Y718H	Tat	Cat	169	169	AY.43	0.000749
ORF1ab/nsp3	718	Y718Y	taT	taC	159	159	AY.44	0.000968
ORF1ab/nsp3	718	Y718H	Tat	Cat	146	146	AY.4	0.000227
ORF1ab/nsp3	718	Y718H	Tat	Cat	139	139	B.1.617.2	0.000523
ORF1ab/nsp3	718	Y718del	TAT	---	91	91	All	0.000017
ORF1ab/nsp3	718	Y718C	tAt	tGt	70	70	B.1.177	0.000922
ORF1ab/nsp3	718	Y718Y	taT	taC	57	57	B.1.1.7	0.000051
ORF1ab/nsp3	718	Y718Y	taT	taC	56	56	AY.99.1	0.086957
ORF1ab/nsp3	718	Y718H	Tat	Cat	42	42	B.1.1.7	0.000038
ORF1ab/nsp3	718	Y718C	tAt	tGt	34	34	B.1.1.7	0.00003
ORF1ab/nsp3	718	Y718del	TAT	---	31	31	B.1.1.7	0.000028
ORF1ab/nsp3	718	Y718C	tAt	tGt	25	25	B.1.617.2	0.000094
ORF1ab/nsp3	718	Y718H	Tat	Cat	19	19	AY.29	0.0003
ORF1ab/nsp3	718	Y718C	tAt	tGt	19	19	B.1.2	0.000167
ORF1ab/nsp3	718	Y718C	tAt	tGt	15	15	B.1.1.318	0.004526
ORF1ab/nsp3	718	Y718Y	taT	taC	15	15	B.1.617.2	0.000056
ORF1ab/nsp3	718	Y718C	tAt	tGt	14	14	AY.44	0.000085
ORF1ab/nsp3	718	Y718Y	taT	taC	13	13	AY.20	0.000505
ORF1ab/nsp3	718	Y718C	tAt	tGt	13	13	AY.25	0.000078
ORF1ab/nsp3	718	Y718H	Tat	Cat	13	13	AY.44	0.000079
ORF1ab/nsp3	718	Y718H	Tat	Cat	10	10	C.5	0.909091
ORF1ab/nsp3	718	Y718C	tAt	tGt	9	9	AY.103	0.000056
ORF1ab/nsp3	718	Y718H	Tat	Cat	9	9	B.1.2	0.000079
ORF1ab/nsp3	718	Y718C	tAt	tGt	8	8	AY.46.6	0.000578
ORF1ab/nsp3	718	Y718Y	taT	taC	7	7	AY.4	0.000011
ORF1ab/nsp3	718	Y718H	Tat	Cat	7	7	B.1.416	0.008883
ORF1ab/nsp3	718	Y718C	tAt	tGt	6	6	AY.39	0.000148
ORF1ab/nsp3	718	Y718del	TAT	---	6	6	AY.4	0.000009
ORF1ab/nsp3	718	Y718X	taT	taA	4	5	All	0.000001
ORF1ab/nsp3	718	Y718X	taT	taG	1	5	All	0
ORF1ab/nsp3	718	Y718Y	taT	taC	5	5	AY.100	0.00023
ORF1ab/nsp3	718	Y718C	tAt	tGt	5	5	AY.29	0.000079
ORF1ab/nsp3	718	Y718H	Tat	Cat	5	5	AY.39.1	0.000198
ORF1ab/nsp3	718	Y718Y	taT	taC	5	5	B	0.000639
ORF1ab/nsp3	718	Y718del	TAT	---	5	5	B.1.177	0.000066
ORF1ab/nsp3	718	Y718N	Tat	Aat	3	4	All	0.000001
ORF1ab/nsp3	718	Y718del1	taT	ta-	2	4	All	0
ORF1ab/nsp3	718	Y718N	TaT	AaC	1	4	All	0
ORF1ab/nsp3	718	Y718del1	tAt	t-t	1	4	All	0
ORF1ab/nsp3	718	Y718del1	tAT	tG-	1	4	All	0
ORF1ab/nsp3	718	Y718H	Tat	Cat	4	4	AY.103	0.000025
ORF1ab/nsp3	718	Y718Y	taT	taC	4	4	AY.120	0.000149
ORF1ab/nsp3	718	Y718C	tAt	tGt	4	4	AY.75.1	0.000721
ORF1ab/nsp3	718	Y718H	Tat	Cat	4	4	AY.9.2	0.000147
ORF1ab/nsp3	718	Y718H	Tat	Cat	4	4	B.1	0.000037
ORF1ab/nsp3	718	Y718C	tAt	tGt	4	4	B.1	0.000037
ORF1ab/nsp3	718	Y718C	tAt	tGt	4	4	P.1	0.000063
ORF1ab/nsp3	718	Y718S	tAt	tCt	3	3	All	0.000001
ORF1ab/nsp3	718	Y718F	tAt	tTt	3	3	All	0.000001
ORF1ab/nsp3	718	Y718C	tAt	tGt	3	3	AY.26	0.000085
ORF1ab/nsp3	718	Y718Y	taT	taC	3	3	AY.3	0.00003
ORF1ab/nsp3	718	Y718Y	taT	taC	3	3	AY.33	0.0002
ORF1ab/nsp3	718	Y718del	TAT	---	3	3	AY.43	0.000013
ORF1ab/nsp3	718	Y718H	Tat	Cat	3	3	AY.45	0.000365
ORF1ab/nsp3	718	Y718H	Tat	Cat	3	3	B.1.1	0.000054
ORF1ab/nsp3	718	Y718C	tAt	tGt	3	3	B.1.1	0.000054
ORF1ab/nsp3	718	Y718C	tAt	tGt	3	3	B.1.36	0.000438
ORF1ab/nsp3	718	Y718del	TAT	---	2	2		0.111111
ORF1ab/nsp3	718	Y718Y	taT	taC	2	2		0.111111
ORF1ab/nsp3	718	Y718H	Tat	Cat	2	2	AY.102	0.000053
ORF1ab/nsp3	718	Y718C	tAt	tGt	2	2	AY.117	0.000169
ORF1ab/nsp3	718	Y718H	Tat	Cat	2	2	AY.119	0.000071
ORF1ab/nsp3	718	Y718del	TAT	---	2	2	AY.3	0.00002
ORF1ab/nsp3	718	Y718C	tAt	tGt	2	2	AY.3	0.00002
ORF1ab/nsp3	718	Y718H	Tat	Cat	2	2	AY.3	0.00002
ORF1ab/nsp3	718	Y718H	Tat	Cat	2	2	AY.34	0.000194
ORF1ab/nsp3	718	Y718H	Tat	Cat	2	2	AY.36	0.000296
ORF1ab/nsp3	718	Y718H	Tat	Cat	2	2	AY.39	0.000049
ORF1ab/nsp3	718	Y718del	TAT	---	2	2	AY.44	0.000012
ORF1ab/nsp3	718	Y718X	taT	taA	2	2	AY.44	0.000012
ORF1ab/nsp3	718	Y718Y	taT	taC	2	2	AY.5.3	0.000675
ORF1ab/nsp3	718	Y718H	Tat	Cat	2	2	AY.5.3	0.000675
ORF1ab/nsp3	718	Y718del1	taT	ta-	2	2	AY.7.1	0.000225
ORF1ab/nsp3	718	Y718C	tAt	tGt	2	2	AZ.2	0.001642
ORF1ab/nsp3	718	Y718del	TAT	---	2	2	B.1	0.000018
ORF1ab/nsp3	718	Y718del	TAT	---	2	2	B.1.1	0.000036
ORF1ab/nsp3	718	Y718Y	taT	taC	2	2	B.1.1.326	0.003521
ORF1ab/nsp3	718	Y718del	TAT	---	2	2	B.1.36	0.000292
ORF1ab/nsp3	718	Y718H	Tat	Cat	2	2	B.1.526	0.000047
ORF1ab/nsp3	718	Y718del	TAT	---	2	2	B.1.617.2	0.000008
ORF1ab/nsp3	718	Y718del	TAT	---	2	2	B.1.619	0.001742
ORF1ab/nsp3	718	Y718del	TAT	---	2	2	P.1	0.000032
ORF1ab/nsp3	718	Y718H	Tat	Cat	2	2	P.1	0.000032
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	A.2.2	0.001689
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	AD.2	0.000219
ORF1ab/nsp3	718	Y718K	TaT	AaG	1	1	All	0
ORF1ab/nsp3	718	Y718D	Tat	Gat	1	1	All	0
ORF1ab/nsp3	718	Y718del2	TAT	--N	1	1	All	0
ORF1ab/nsp3	718	Y718N	Tat	Aat	1	1	AY.1	0.000396
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	AY.1	0.000396
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	AY.100	0.000046
ORF1ab/nsp3	718	Y718Y	taT	taC	1	1	AY.101	0.00049
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	AY.102	0.000027
ORF1ab/nsp3	718	Y718H	Tat	Cat	1	1	AY.114	0.000231
ORF1ab/nsp3	718	Y718H	Tat	Cat	1	1	AY.116	0.000287
ORF1ab/nsp3	718	Y718Y	taT	taC	1	1	AY.116	0.000287
ORF1ab/nsp3	718	Y718Y	taT	taC	1	1	AY.117	0.000085
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	AY.119	0.000035
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	AY.120.1	0.000321
ORF1ab/nsp3	718	Y718H	Tat	Cat	1	1	AY.120.2	0.001285
ORF1ab/nsp3	718	Y718N	Tat	Aat	1	1	AY.14	0.000088
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	AY.25	0.000006
ORF1ab/nsp3	718	Y718H	Tat	Cat	1	1	AY.34.1	0.00051
ORF1ab/nsp3	718	Y718H	Tat	Cat	1	1	AY.4.2	0.000022
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	AY.4.5	0.000107
ORF1ab/nsp3	718	Y718S	tAt	tCt	1	1	AY.4.5	0.000107
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	AY.42	0.00004
ORF1ab/nsp3	718	Y718Y	taT	taC	1	1	AY.43	0.000004
ORF1ab/nsp3	718	Y718F	tAt	tTt	1	1	AY.43	0.000004
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	AY.43	0.000004
ORF1ab/nsp3	718	Y718del1	tAT	tG-	1	1	AY.44	0.000006
ORF1ab/nsp3	718	Y718F	tAt	tTt	1	1	AY.44	0.000006
ORF1ab/nsp3	718	Y718Y	taT	taC	1	1	AY.45	0.000122
ORF1ab/nsp3	718	Y718H	Tat	Cat	1	1	AY.46	0.000104
ORF1ab/nsp3	718	Y718X	taT	taA	1	1	AY.46.6	0.000072
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	AY.5.3	0.000337
ORF1ab/nsp3	718	Y718S	tAt	tCt	1	1	AY.5.4	0.000277
ORF1ab/nsp3	718	Y718Y	taT	taC	1	1	AY.52	0.000814
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	AY.55	0.000917
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	AY.67	0.000464
ORF1ab/nsp3	718	Y718Y	taT	taC	1	1	AY.7	0.000196
ORF1ab/nsp3	718	Y718H	Tat	Cat	1	1	AY.70	0.000209
ORF1ab/nsp3	718	Y718H	Tat	Cat	1	1	AY.75.1	0.00018
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	AY.81	0.001992
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	AY.9	0.000068
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	AY.9.2	0.000037
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	AY.94	0.000443
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	AY.98	0.000079
ORF1ab/nsp3	718	Y718H	Tat	Cat	1	1	AY.98	0.000079
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	AY.98.1	0.000048
ORF1ab/nsp3	718	Y718X	taT	taA	1	1	AY.99	0.001049
ORF1ab/nsp3	718	Y718Y	taT	taC	1	1	B.1	0.000009
ORF1ab/nsp3	718	Y718N	Tat	Aat	1	1	B.1.1	0.000018
ORF1ab/nsp3	718	Y718H	Tat	Cat	1	1	B.1.1.1	0.000327
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	B.1.1.139	0.022727
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	B.1.1.142	0.017544
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	B.1.1.311	0.000358
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	B.1.1.317	0.000412
ORF1ab/nsp3	718	Y718H	Tat	Cat	1	1	B.1.1.326	0.001761
ORF1ab/nsp3	718	Y718S	tAt	tCt	1	1	B.1.1.342	0.0625
ORF1ab/nsp3	718	Y718F	tAt	tTt	1	1	B.1.1.39	0.00051
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	B.1.1.409	0.002833
ORF1ab/nsp3	718	Y718H	Tat	Cat	1	1	B.1.1.466	0.008696
ORF1ab/nsp3	718	Y718Y	taT	taC	1	1	B.1.1.63	0.000386
ORF1ab/nsp3	718	Y718D	Tat	Gat	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	718	Y718N	TaT	AaC	1	1	B.1.149	0.003425
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	B.1.157	0.002985
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	B.1.160	0.000031
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	B.1.160	0.000031
ORF1ab/nsp3	718	Y718H	Tat	Cat	1	1	B.1.160	0.000031
ORF1ab/nsp3	718	Y718H	Tat	Cat	1	1	B.1.177	0.000013
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	B.1.177.16	0.000664
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	B.1.177.18	0.00116
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	B.1.177.50	0.004695
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	B.1.177.63	0.002703
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	B.1.177.7	0.000165
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	B.1.177.86	0.000183
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	B.1.177.87	0.000728
ORF1ab/nsp3	718	Y718Y	taT	taC	1	1	B.1.2	0.000009
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	B.1.2	0.000009
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	B.1.210	0.002132
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	B.1.22	0.001318
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	B.1.221	0.000071
ORF1ab/nsp3	718	Y718del2	TAT	--N	1	1	B.1.258	0.000067
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	B.1.279	0.000514
ORF1ab/nsp3	718	Y718Y	taT	taC	1	1	B.1.281	0.021739
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	B.1.319	0.003049
ORF1ab/nsp3	718	Y718K	TaT	AaG	1	1	B.1.332	0.003497
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	B.1.351	0.00003
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	B.1.351.2	0.000303
ORF1ab/nsp3	718	Y718H	Tat	Cat	1	1	B.1.36	0.000146
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	B.1.36.29	0.000517
ORF1ab/nsp3	718	Y718H	Tat	Cat	1	1	B.1.509	0.000866
ORF1ab/nsp3	718	Y718Y	taT	taC	1	1	B.1.525	0.000113
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	B.1.526	0.000024
ORF1ab/nsp3	718	Y718Y	taT	taC	1	1	B.1.617.1	0.000129
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	B.1.617.1	0.000129
ORF1ab/nsp3	718	Y718del1	tAt	t-t	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	718	Y718X	taT	taG	1	1	B.1.619.1	0.000641
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	B.15	0.017544
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	C.37	0.000116
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	P.1.1	0.000318
ORF1ab/nsp3	718	Y718H	Tat	Cat	1	1	P.3	0.001595
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	Q.1	0.000126
ORF1ab/nsp3	718	Y718C	tAt	tGt	1	1	Q.8	0.000165
ORF1ab/nsp3	718	Y718del	TAT	---	1	1	R.1	0.00009
ORF1ab/nsp3	718	Y718Y	taT	taC	1	1	R.1	0.00009

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.