CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF3a : CodonNum = 156

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
ORF3a	156	Y156C		nonsyn	tAt	tGt	1309	1309	1	25858-25860
ORF3a	156	Y156Y		syn	taT	taC	584	584	1	25858-25860
ORF3a	156	Y156H		nonsyn	Tat	Cat	276	276	1	25858-25860
ORF3a	156	Y156del		del	TAT	---	74	74	1	25858-25860
ORF3a	156	Y156N		nonsyn	Tat	Aat	37	35	0.945946	25858-25860
ORF3a	156	Y156N		nonsyn	TaT	AaC	37	2	0.0540541	25858-25860
ORF3a	156	Y156F		nonsyn	tAt	tTt	24	22	0.916667	25858-25860
ORF3a	156	Y156F		nonsyn	tAT	tTC	24	2	0.0833333	25858-25860
ORF3a	156	Y156S		nonsyn	tAt	tCt	8	8	1	25858-25860
ORF3a	156	Y156X		nonsyn	taT	taG	7	4	0.571429	25858-25860
ORF3a	156	Y156X		nonsyn	taT	taA	7	3	0.428571	25858-25860
ORF3a	156	Y156I		nonsyn	TAT	ATC	4	2	0.5	25858-25860
ORF3a	156	Y156I		nonsyn	TAt	ATt	4	2	0.5	25858-25860
ORF3a	156	Y156del1		del	tAT	tG-	3	2	0.666667	25858-25860
ORF3a	156	Y156del1		del	taT	ta-	3	1	0.333333	25858-25860
ORF3a	156	Y156L		nonsyn	TAt	CTt	1	1	1	25858-25860

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
ORF3a	156	Y156C	tAt	tGt	1309	1309	All	0.00025
ORF3a	156	Y156C	tAt	tGt	663	663	AP.1	0.995495
ORF3a	156	Y156Y	taT	taC	584	584	All	0.000112
ORF3a	156	Y156Y	taT	taC	471	471	B.1.1.7	0.000422
ORF3a	156	Y156H	Tat	Cat	276	276	All	0.000053
ORF3a	156	Y156C	tAt	tGt	179	179	B.1.1.7	0.00016
ORF3a	156	Y156H	Tat	Cat	145	145	AY.4	0.000226
ORF3a	156	Y156C	tAt	tGt	104	104	B.1.1.70	0.035471
ORF3a	156	Y156del	TAT	---	74	74	All	0.000014
ORF3a	156	Y156C	tAt	tGt	46	46	P.1.15	0.010688
ORF3a	156	Y156C	tAt	tGt	45	45	AY.4	0.00007
ORF3a	156	Y156Y	taT	taC	42	42	B.1.1.141	0.084507
ORF3a	156	Y156N	Tat	Aat	35	37	All	0.000007
ORF3a	156	Y156N	TaT	AaC	2	37	All	0
ORF3a	156	Y156C	tAt	tGt	33	33	B.1.1.63	0.012731
ORF3a	156	Y156C	tAt	tGt	33	33	Q.1	0.004169
ORF3a	156	Y156H	Tat	Cat	31	31	B.1.1.7	0.000028
ORF3a	156	Y156C	tAt	tGt	30	30	B.1	0.000275
ORF3a	156	Y156C	tAt	tGt	29	29	B.1.617.2	0.000109
ORF3a	156	Y156N	Tat	Aat	25	25	B.1.1.7	0.000022
ORF3a	156	Y156F	tAt	tTt	22	24	All	0.000004
ORF3a	156	Y156F	tAT	tTC	2	24	All	0
ORF3a	156	Y156H	Tat	Cat	22	22	B.1	0.000202
ORF3a	156	Y156C	tAt	tGt	22	22	B.1.1	0.000399
ORF3a	156	Y156del	TAT	---	19	19	B.1.1.7	0.000017
ORF3a	156	Y156Y	taT	taC	17	17	Q.8	0.002803
ORF3a	156	Y156C	tAt	tGt	14	14	AY.103	0.000087
ORF3a	156	Y156C	tAt	tGt	13	13	AY.3.1	0.001108
ORF3a	156	Y156H	Tat	Cat	12	12	AY.103	0.000075
ORF3a	156	Y156C	tAt	tGt	11	11	AY.61	0.001153
ORF3a	156	Y156C	tAt	tGt	10	10	AY.102	0.000265
ORF3a	156	Y156C	tAt	tGt	10	10	AY.25	0.00006
ORF3a	156	Y156C	tAt	tGt	10	10	B.1.1.519	0.000397
ORF3a	156	Y156S	tAt	tCt	8	8	All	0.000002
ORF3a	156	Y156H	Tat	Cat	8	8	AY.6	0.000329
ORF3a	156	Y156X	taT	taG	4	7	All	0.000001
ORF3a	156	Y156X	taT	taA	3	7	All	0.000001
ORF3a	156	Y156C	tAt	tGt	7	7	AY.119	0.000247
ORF3a	156	Y156F	tAt	tTt	7	7	AY.4	0.000011
ORF3a	156	Y156Y	taT	taC	7	7	AY.4	0.000011
ORF3a	156	Y156H	Tat	Cat	7	7	AY.42	0.000282
ORF3a	156	Y156H	Tat	Cat	7	7	Q.1	0.000884
ORF3a	156	Y156S	tAt	tCt	6	6	AY.4	0.000009
ORF3a	156	Y156del	TAT	---	6	6	B.1	0.000055
ORF3a	156	Y156Y	taT	taC	6	6	B.1.617.2	0.000023
ORF3a	156	Y156Y	taT	taC	5	5	AY.100	0.00023
ORF3a	156	Y156C	tAt	tGt	5	5	B.1.1.397	0.011261
ORF3a	156	Y156C	tAt	tGt	5	5	B.1.351	0.000149
ORF3a	156	Y156H	Tat	Cat	5	5	B.1.617.2	0.000019
ORF3a	156	Y156F	tAT	tTC	2	4		0.111111
ORF3a	156	Y156F	tAt	tTt	2	4		0.111111
ORF3a	156	Y156I	TAt	ATt	2	4		0.111111
ORF3a	156	Y156I	TAT	ATC	2	4		0.111111
ORF3a	156	Y156N	Tat	Aat	2	4		0.111111
ORF3a	156	Y156N	TaT	AaC	2	4		0.111111
ORF3a	156	Y156I	TAt	ATt	2	4	All	0
ORF3a	156	Y156I	TAT	ATC	2	4	All	0
ORF3a	156	Y156H	Tat	Cat	4	4	AY.23	0.000279
ORF3a	156	Y156F	tAt	tTt	4	4	AY.3	0.00004
ORF3a	156	Y156del	TAT	---	4	4	AY.43	0.000018
ORF3a	156	Y156H	Tat	Cat	4	4	B.1.1.50	0.002716
ORF3a	156	Y156F	tAt	tTt	4	4	B.1.234	0.000528
ORF3a	156	Y156Y	taT	taC	4	4	B.1.429	0.000094
ORF3a	156	Y156C	tAt	tGt	4	4	C.23	0.023256
ORF3a	156	Y156Y	taT	taC	3	3	A.5	0.005769
ORF3a	156	Y156del1	tAT	tG-	2	3	All	0
ORF3a	156	Y156del1	taT	ta-	1	3	All	0
ORF3a	156	Y156Y	taT	taC	3	3	AY.103	0.000019
ORF3a	156	Y156H	Tat	Cat	3	3	AY.119	0.000106
ORF3a	156	Y156C	tAt	tGt	3	3	AY.120	0.000112
ORF3a	156	Y156H	Tat	Cat	3	3	AY.25	0.000018
ORF3a	156	Y156N	Tat	Aat	3	3	AY.29	0.000047
ORF3a	156	Y156C	tAt	tGt	3	3	AY.44	0.000018
ORF3a	156	Y156Y	taT	taC	3	3	B.1	0.000027
ORF3a	156	Y156del	TAT	---	3	3	B.1.177	0.00004
ORF3a	156	Y156del	TAT	---	3	3	B.1.177.4	0.000633
ORF3a	156	Y156C	tAt	tGt	3	3	B.1.2	0.000026
ORF3a	156	Y156del1	tAT	tG-	2	2		0.111111
ORF3a	156	Y156Y	taT	taC	2	2		0.111111
ORF3a	156	Y156del	TAT	---	2	2		0.111111
ORF3a	156	Y156C	tAt	tGt	2	2	AY.20	0.000078
ORF3a	156	Y156Y	taT	taC	2	2	AY.26	0.000057
ORF3a	156	Y156C	tAt	tGt	2	2	AY.3	0.00002
ORF3a	156	Y156H	Tat	Cat	2	2	AY.3	0.00002
ORF3a	156	Y156del	TAT	---	2	2	AY.4	0.000003
ORF3a	156	Y156C	tAt	tGt	2	2	AY.43	0.000009
ORF3a	156	Y156H	Tat	Cat	2	2	AY.44	0.000012
ORF3a	156	Y156H	Tat	Cat	2	2	AY.47	0.000062
ORF3a	156	Y156Y	taT	taC	2	2	B.1.1	0.000036
ORF3a	156	Y156del	TAT	---	2	2	B.1.1.315	0.016949
ORF3a	156	Y156X	taT	taG	1	2	B.1.1.7	0.000001
ORF3a	156	Y156X	taT	taA	1	2	B.1.1.7	0.000001
ORF3a	156	Y156H	Tat	Cat	2	2	B.1.160	0.000062
ORF3a	156	Y156C	tAt	tGt	2	2	B.1.177	0.000026
ORF3a	156	Y156del	TAT	---	2	2	B.1.525	0.000226
ORF3a	156	Y156del	TAT	---	2	2	B.1.617.2	0.000008
ORF3a	156	Y156del	TAT	---	2	2	B.1.621	0.000177
ORF3a	156	Y156del	TAT	---	2	2	P.1	0.000032
ORF3a	156	Y156del	TAT	---	2	2	P.1.15	0.000465
ORF3a	156	Y156del	TAT	---	1	1	A	0.000387
ORF3a	156	Y156Y	taT	taC	1	1	A	0.000387
ORF3a	156	Y156del	TAT	---	1	1	AD.2	0.000219
ORF3a	156	Y156L	TAt	CTt	1	1	All	0
ORF3a	156	Y156C	tAt	tGt	1	1	AY.113	0.000142
ORF3a	156	Y156C	tAt	tGt	1	1	AY.117	0.000085
ORF3a	156	Y156H	Tat	Cat	1	1	AY.117	0.000085
ORF3a	156	Y156del	TAT	---	1	1	AY.120	0.000037
ORF3a	156	Y156del	TAT	---	1	1	AY.25	0.000006
ORF3a	156	Y156Y	taT	taC	1	1	AY.25	0.000006
ORF3a	156	Y156del	TAT	---	1	1	AY.29	0.000016
ORF3a	156	Y156Y	taT	taC	1	1	AY.3.1	0.000085
ORF3a	156	Y156H	Tat	Cat	1	1	AY.32	0.000532
ORF3a	156	Y156C	tAt	tGt	1	1	AY.36	0.000148
ORF3a	156	Y156Y	taT	taC	1	1	AY.37	0.000316
ORF3a	156	Y156del	TAT	---	1	1	AY.39	0.000025
ORF3a	156	Y156X	taT	taA	1	1	AY.4	0.000002
ORF3a	156	Y156X	taT	taG	1	1	AY.4.2	0.000022
ORF3a	156	Y156Y	taT	taC	1	1	AY.4.2	0.000022
ORF3a	156	Y156del	TAT	---	1	1	AY.4.5	0.000107
ORF3a	156	Y156H	Tat	Cat	1	1	AY.43	0.000004
ORF3a	156	Y156Y	taT	taC	1	1	AY.43	0.000004
ORF3a	156	Y156F	tAt	tTt	1	1	AY.44	0.000006
ORF3a	156	Y156Y	taT	taC	1	1	AY.44	0.000006
ORF3a	156	Y156H	Tat	Cat	1	1	AY.46.2	0.000635
ORF3a	156	Y156H	Tat	Cat	1	1	AY.46.6	0.000072
ORF3a	156	Y156Y	taT	taC	1	1	AY.5	0.000021
ORF3a	156	Y156C	tAt	tGt	1	1	AY.5.3	0.000337
ORF3a	156	Y156C	tAt	tGt	1	1	AY.51	0.000909
ORF3a	156	Y156H	Tat	Cat	1	1	AY.52	0.000814
ORF3a	156	Y156C	tAt	tGt	1	1	AY.6	0.000041
ORF3a	156	Y156del	TAT	---	1	1	AY.68	0.000274
ORF3a	156	Y156N	Tat	Aat	1	1	AY.7.1	0.000113
ORF3a	156	Y156C	tAt	tGt	1	1	AY.87	0.000833
ORF3a	156	Y156H	Tat	Cat	1	1	AY.9.1	0.000084
ORF3a	156	Y156H	Tat	Cat	1	1	AY.98.1	0.000048
ORF3a	156	Y156Y	taT	taC	1	1	AY.99.2	0.000092
ORF3a	156	Y156del	TAT	---	1	1	B	0.000128
ORF3a	156	Y156S	tAt	tCt	1	1	B.1	0.000009
ORF3a	156	Y156N	Tat	Aat	1	1	B.1	0.000009
ORF3a	156	Y156F	tAt	tTt	1	1	B.1	0.000009
ORF3a	156	Y156L	TAt	CTt	1	1	B.1	0.000009
ORF3a	156	Y156N	Tat	Aat	1	1	B.1.1	0.000018
ORF3a	156	Y156C	tAt	tGt	1	1	B.1.1.161	0.003534
ORF3a	156	Y156del	TAT	---	1	1	B.1.1.170	0.001247
ORF3a	156	Y156Y	taT	taC	1	1	B.1.1.220	0.001859
ORF3a	156	Y156C	tAt	tGt	1	1	B.1.1.221	0.010101
ORF3a	156	Y156Y	taT	taC	1	1	B.1.1.317	0.000412
ORF3a	156	Y156X	taT	taG	1	1	B.1.1.372	0.000689
ORF3a	156	Y156Y	taT	taC	1	1	B.1.1.377	0.001381
ORF3a	156	Y156del	TAT	---	1	1	B.1.1.409	0.002833
ORF3a	156	Y156Y	taT	taC	1	1	B.1.1.524	0.020833
ORF3a	156	Y156N	Tat	Aat	1	1	B.1.1.75	0.010638
ORF3a	156	Y156del	TAT	---	1	1	B.1.140	0.018868
ORF3a	156	Y156C	tAt	tGt	1	1	B.1.142	0.002899
ORF3a	156	Y156X	taT	taG	1	1	B.1.147	0.000756
ORF3a	156	Y156del	TAT	---	1	1	B.1.160	0.000031
ORF3a	156	Y156del	TAT	---	1	1	B.1.160.23	0.004831
ORF3a	156	Y156X	taT	taA	1	1	B.1.177	0.000013
ORF3a	156	Y156C	tAt	tGt	1	1	B.1.177.41	0.0025
ORF3a	156	Y156del	TAT	---	1	1	B.1.177.51	0.004566
ORF3a	156	Y156del	TAT	---	1	1	B.1.177.62	0.001192
ORF3a	156	Y156C	tAt	tGt	1	1	B.1.177.86	0.000183
ORF3a	156	Y156Y	taT	taC	1	1	B.1.2	0.000009
ORF3a	156	Y156N	Tat	Aat	1	1	B.1.2	0.000009
ORF3a	156	Y156del	TAT	---	1	1	B.1.221	0.000071
ORF3a	156	Y156H	Tat	Cat	1	1	B.1.221.1	0.002907
ORF3a	156	Y156Y	taT	taC	1	1	B.1.243	0.00007
ORF3a	156	Y156F	tAt	tTt	1	1	B.1.258.17	0.000104
ORF3a	156	Y156H	Tat	Cat	1	1	B.1.311	0.000275
ORF3a	156	Y156H	Tat	Cat	1	1	B.1.320	0.001245
ORF3a	156	Y156del	TAT	---	1	1	B.1.351.5	0.0006
ORF3a	156	Y156del	TAT	---	1	1	B.1.36.17	0.000494
ORF3a	156	Y156Y	taT	taC	1	1	B.1.36.37	0.002778
ORF3a	156	Y156del	TAT	---	1	1	B.1.416.1	0.001563
ORF3a	156	Y156H	Tat	Cat	1	1	B.1.429	0.000024
ORF3a	156	Y156F	tAt	tTt	1	1	B.1.429	0.000024
ORF3a	156	Y156H	Tat	Cat	1	1	B.1.453	0.003236
ORF3a	156	Y156Y	taT	taC	1	1	B.1.466.2	0.000391
ORF3a	156	Y156C	tAt	tGt	1	1	B.1.466.2	0.000391
ORF3a	156	Y156C	tAt	tGt	1	1	B.1.561	0.000397
ORF3a	156	Y156C	tAt	tGt	1	1	B.1.576	0.000907
ORF3a	156	Y156del	TAT	---	1	1	B.1.596	0.000087
ORF3a	156	Y156H	Tat	Cat	1	1	B.1.612	0.002653
ORF3a	156	Y156del	TAT	---	1	1	B.1.617.1	0.000129
ORF3a	156	Y156del1	taT	ta-	1	1	B.1.617.1	0.000129
ORF3a	156	Y156F	tAt	tTt	1	1	B.1.617.2	0.000004
ORF3a	156	Y156S	tAt	tCt	1	1	B.1.617.2	0.000004
ORF3a	156	Y156C	tAt	tGt	1	1	B.1.621	0.000089
ORF3a	156	Y156del	TAT	---	1	1	B.1.638	0.052632
ORF3a	156	Y156C	tAt	tGt	1	1	C.37	0.000116
ORF3a	156	Y156H	Tat	Cat	1	1	P.1	0.000016
ORF3a	156	Y156C	tAt	tGt	1	1	P.1	0.000016
ORF3a	156	Y156H	Tat	Cat	1	1	P.1.14	0.000048
ORF3a	156	Y156C	tAt	tGt	1	1	P.3	0.001595
ORF3a	156	Y156H	Tat	Cat	1	1	Q.7	0.001111

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.