CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 42

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	42	Y42Y	Y860Y	syn	taT	taC	1213	1213	1	2843-2845
ORF1ab/nsp3	42	Y42del	Y860del	del	TAT	---	37	37	1	2843-2845
ORF1ab/nsp3	42	Y42H	Y860H	nonsyn	Tat	Cat	33	33	1	2843-2845
ORF1ab/nsp3	42	Y42C	Y860C	nonsyn	tAt	tGt	25	25	1	2843-2845
ORF1ab/nsp3	42	Y42L	Y860L	nonsyn	tAT	tTA	9	4	0.444444	2843-2845
ORF1ab/nsp3	42	Y42L	Y860L	nonsyn	TAt	CTt	9	3	0.333333	2843-2845
ORF1ab/nsp3	42	Y42L	Y860L	nonsyn	TAT	CTA	9	2	0.222222	2843-2845
ORF1ab/nsp3	42	Y42N	Y860N	nonsyn	Tat	Aat	8	7	0.875	2843-2845
ORF1ab/nsp3	42	Y42N	Y860N	nonsyn	TaT	AaC	8	1	0.125	2843-2845
ORF1ab/nsp3	42	Y42X	Y860X	nonsyn	taT	taA	7	7	1	2843-2845
ORF1ab/nsp3	42	Y42F	Y860F	nonsyn	tAt	tTt	6	6	1	2843-2845
ORF1ab/nsp3	42	Y42del1	Y860del1	del	taT	ta-	5	5	1	2843-2845
ORF1ab/nsp3	42	Y42D	Y860D	nonsyn	Tat	Gat	3	3	1	2843-2845
ORF1ab/nsp3	42	Y42S	Y860S	nonsyn	tAt	tCt	3	3	1	2843-2845
ORF1ab/nsp3	42	Y42P	Y860P	nonsyn	TAt	CCt	3	3	1	2843-2845
ORF1ab/nsp3	42	Y42Q	Y860Q	nonsyn	TaT	CaA	2	2	1	2843-2845
ORF1ab/nsp3	42	Y42K	Y860K	nonsyn	TaT	AaA	2	2	1	2843-2845
ORF1ab/nsp3	42	Y42V	Y860V	nonsyn	TAT	GTA	2	1	0.5	2843-2845
ORF1ab/nsp3	42	Y42V	Y860V	nonsyn	TAt	GTt	2	1	0.5	2843-2845
ORF1ab/nsp3	42	Y42I	Y860I	nonsyn	TAT	ATA	2	1	0.5	2843-2845
ORF1ab/nsp3	42	Y42I	Y860I	nonsyn	TAt	ATt	2	1	0.5	2843-2845
ORF1ab/nsp3	42	Y42E	Y860E	nonsyn	TaT	GaA	1	1	1	2843-2845
ORF1ab/nsp3	42	Y42del2	Y860del2	del	TAt	--t	1	1	1	2843-2845

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	42	Y42Y	taT	taC	1213	1213	All	0.000232
ORF1ab/nsp3	42	Y42Y	taT	taC	426	426	AY.103	0.002645
ORF1ab/nsp3	42	Y42Y	taT	taC	163	163	B.1	0.001493
ORF1ab/nsp3	42	Y42Y	taT	taC	108	108	B.1.1.7	0.000097
ORF1ab/nsp3	42	Y42Y	taT	taC	96	96	B.1.401	0.786885
ORF1ab/nsp3	42	Y42Y	taT	taC	84	84	AY.4	0.000131
ORF1ab/nsp3	42	Y42Y	taT	taC	53	53	B.1.617.2	0.0002
ORF1ab/nsp3	42	Y42del	TAT	---	37	37	All	0.000007
ORF1ab/nsp3	42	Y42H	Tat	Cat	33	33	All	0.000006
ORF1ab/nsp3	42	Y42Y	taT	taC	32	32	AY.33	0.002137
ORF1ab/nsp3	42	Y42C	tAt	tGt	25	25	All	0.000005
ORF1ab/nsp3	42	Y42Y	taT	taC	22	22	B.1.36	0.00321
ORF1ab/nsp3	42	Y42Y	taT	taC	20	20	AY.25	0.00012
ORF1ab/nsp3	42	Y42Y	taT	taC	14	14	AY.44	0.000085
ORF1ab/nsp3	42	Y42Y	taT	taC	14	14	AY.73	0.009315
ORF1ab/nsp3	42	Y42Y	taT	taC	12	12	AY.43	0.000053
ORF1ab/nsp3	42	Y42Y	taT	taC	11	11	B.1.1.25	0.006254
ORF1ab/nsp3	42	Y42L	tAT	tTA	4	9	All	0.000001
ORF1ab/nsp3	42	Y42L	TAt	CTt	3	9	All	0.000001
ORF1ab/nsp3	42	Y42L	TAT	CTA	2	9	All	0
ORF1ab/nsp3	42	Y42Y	taT	taC	9	9	B.1.400	0.003861
ORF1ab/nsp3	42	Y42Y	taT	taC	9	9	B.1.621	0.000797
ORF1ab/nsp3	42	Y42N	Tat	Aat	7	8	All	0.000001
ORF1ab/nsp3	42	Y42N	TaT	AaC	1	8	All	0
ORF1ab/nsp3	42	Y42Y	taT	taC	8	8	B.1.1.214	0.000444
ORF1ab/nsp3	42	Y42X	taT	taA	7	7	All	0.000001
ORF1ab/nsp3	42	Y42C	tAt	tGt	7	7	AY.69	0.001307
ORF1ab/nsp3	42	Y42Y	taT	taC	7	7	B.1.221	0.000497
ORF1ab/nsp3	42	Y42Y	taT	taC	7	7	B.1.258.14	0.006863
ORF1ab/nsp3	42	Y42F	tAt	tTt	6	6	All	0.000001
ORF1ab/nsp3	42	Y42Y	taT	taC	6	6	AY.4.2	0.00013
ORF1ab/nsp3	42	Y42del1	taT	ta-	5	5	All	0.000001
ORF1ab/nsp3	42	Y42Y	taT	taC	5	5	AY.118	0.000313
ORF1ab/nsp3	42	Y42Y	taT	taC	5	5	AY.119	0.000177
ORF1ab/nsp3	42	Y42H	Tat	Cat	5	5	AY.99.2	0.000461
ORF1ab/nsp3	42	Y42del	TAT	---	5	5	B.1	0.000046
ORF1ab/nsp3	42	Y42del	TAT	---	5	5	B.1.1.7	0.000004
ORF1ab/nsp3	42	Y42del1	taT	ta-	5	5	B.1.36	0.00073
ORF1ab/nsp3	42	Y42C	tAt	tGt	5	5	B.1.617.2	0.000019
ORF1ab/nsp3	42	Y42Y	taT	taC	5	5	P.1.7	0.001596
ORF1ab/nsp3	42	Y42del	TAT	---	4	4		0.222222
ORF1ab/nsp3	42	Y42L	tAT	tTA	2	4		0.111111
ORF1ab/nsp3	42	Y42L	TAt	CTt	1	4		0.055556
ORF1ab/nsp3	42	Y42L	TAT	CTA	1	4		0.055556
ORF1ab/nsp3	42	Y42Y	taT	taC	4	4	AY.121	0.000541
ORF1ab/nsp3	42	Y42Y	taT	taC	4	4	B.1.1	0.000073
ORF1ab/nsp3	42	Y42H	Tat	Cat	4	4	B.1.1.7	0.000004
ORF1ab/nsp3	42	Y42L	tAT	tTA	2	4	B.1.221	0.000142
ORF1ab/nsp3	42	Y42L	TAt	CTt	1	4	B.1.221	0.000071
ORF1ab/nsp3	42	Y42L	TAT	CTA	1	4	B.1.221	0.000071
ORF1ab/nsp3	42	Y42Y	taT	taC	4	4	B.1.526	0.000094
ORF1ab/nsp3	42	Y42H	Tat	Cat	3	3		0.166667
ORF1ab/nsp3	42	Y42X	taT	taA	3	3		0.166667
ORF1ab/nsp3	42	Y42N	Tat	Aat	3	3		0.166667
ORF1ab/nsp3	42	Y42S	tAt	tCt	3	3	All	0.000001
ORF1ab/nsp3	42	Y42D	Tat	Gat	3	3	All	0.000001
ORF1ab/nsp3	42	Y42P	TAt	CCt	3	3	All	0.000001
ORF1ab/nsp3	42	Y42Y	taT	taC	3	3	AY.6	0.000123
ORF1ab/nsp3	42	Y42Y	taT	taC	3	3	AY.67	0.001393
ORF1ab/nsp3	42	Y42Y	taT	taC	3	3	AY.9.2	0.00011
ORF1ab/nsp3	42	Y42Y	taT	taC	3	3	AY.99.2	0.000276
ORF1ab/nsp3	42	Y42del	TAT	---	3	3	B.1.1.33	0.001263
ORF1ab/nsp3	42	Y42Y	taT	taC	3	3	B.1.1.33	0.001263
ORF1ab/nsp3	42	Y42del	TAT	---	3	3	B.1.1.348	0.002389
ORF1ab/nsp3	42	Y42C	tAt	tGt	3	3	B.1.1.7	0.000003
ORF1ab/nsp3	42	Y42Y	taT	taC	3	3	B.1.466.2	0.001174
ORF1ab/nsp3	42	Y42Y	taT	taC	3	3	B.1.617.1	0.000387
ORF1ab/nsp3	42	Y42Y	taT	taC	3	3	P.1	0.000047
ORF1ab/nsp3	42	Y42P	TAt	CCt	2	2		0.111111
ORF1ab/nsp3	42	Y42S	tAt	tCt	2	2		0.111111
ORF1ab/nsp3	42	Y42F	tAt	tTt	2	2		0.111111
ORF1ab/nsp3	42	Y42K	TaT	AaA	2	2		0.111111
ORF1ab/nsp3	42	Y42I	TAT	ATA	1	2		0.055556
ORF1ab/nsp3	42	Y42I	TAt	ATt	1	2		0.055556
ORF1ab/nsp3	42	Y42K	TaT	AaA	2	2	All	0
ORF1ab/nsp3	42	Y42Q	TaT	CaA	2	2	All	0
ORF1ab/nsp3	42	Y42V	TAt	GTt	1	2	All	0
ORF1ab/nsp3	42	Y42V	TAT	GTA	1	2	All	0
ORF1ab/nsp3	42	Y42I	TAT	ATA	1	2	All	0
ORF1ab/nsp3	42	Y42I	TAt	ATt	1	2	All	0
ORF1ab/nsp3	42	Y42Y	taT	taC	2	2	AY.102	0.000053
ORF1ab/nsp3	42	Y42Y	taT	taC	2	2	AY.113	0.000285
ORF1ab/nsp3	42	Y42C	tAt	tGt	2	2	AY.119	0.000071
ORF1ab/nsp3	42	Y42Y	taT	taC	2	2	AY.120	0.000074
ORF1ab/nsp3	42	Y42Y	taT	taC	2	2	AY.14	0.000176
ORF1ab/nsp3	42	Y42Y	taT	taC	2	2	AY.20	0.000078
ORF1ab/nsp3	42	Y42H	Tat	Cat	2	2	AY.25	0.000012
ORF1ab/nsp3	42	Y42Y	taT	taC	2	2	AY.3.1	0.000171
ORF1ab/nsp3	42	Y42H	Tat	Cat	2	2	AY.4.2	0.000043
ORF1ab/nsp3	42	Y42H	Tat	Cat	2	2	AY.44	0.000012
ORF1ab/nsp3	42	Y42Y	taT	taC	2	2	AY.54	0.000191
ORF1ab/nsp3	42	Y42Y	taT	taC	2	2	AY.98.1	0.000097
ORF1ab/nsp3	42	Y42Y	taT	taC	2	2	B.1.1.222	0.000408
ORF1ab/nsp3	42	Y42Y	taT	taC	2	2	B.1.1.291	0.001485
ORF1ab/nsp3	42	Y42Y	taT	taC	2	2	B.1.1.318	0.000604
ORF1ab/nsp3	42	Y42H	Tat	Cat	2	2	B.1.1.348	0.001592
ORF1ab/nsp3	42	Y42Y	taT	taC	2	2	B.1.160	0.000062
ORF1ab/nsp3	42	Y42Y	taT	taC	2	2	B.1.177	0.000026
ORF1ab/nsp3	42	Y42H	Tat	Cat	2	2	B.1.2	0.000018
ORF1ab/nsp3	42	Y42Y	taT	taC	2	2	B.1.2	0.000018
ORF1ab/nsp3	42	Y42F	tAt	tTt	2	2	B.1.221	0.000142
ORF1ab/nsp3	42	Y42X	taT	taA	2	2	B.1.221	0.000142
ORF1ab/nsp3	42	Y42V	TAt	GTt	1	2	B.1.221	0.000071
ORF1ab/nsp3	42	Y42V	TAT	GTA	1	2	B.1.221	0.000071
ORF1ab/nsp3	42	Y42Y	taT	taC	2	2	B.1.351	0.000059
ORF1ab/nsp3	42	Y42del	TAT	---	2	2	B.1.424	0.016129
ORF1ab/nsp3	42	Y42Y	taT	taC	2	2	B.1.429	0.000047
ORF1ab/nsp3	42	Y42del	TAT	---	2	2	B.1.429	0.000047
ORF1ab/nsp3	42	Y42del	TAT	---	2	2	N.6	0.014184
ORF1ab/nsp3	42	Y42del	TAT	---	2	2	P.1	0.000032
ORF1ab/nsp3	42	Y42Y	taT	taC	2	2	P.2	0.000373
ORF1ab/nsp3	42	Y42Q	TaT	CaA	1	1		0.055556
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	A.2	0.000662
ORF1ab/nsp3	42	Y42N	Tat	Aat	1	1	A.2.4	0.003367
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	A.2.5	0.000499
ORF1ab/nsp3	42	Y42C	tAt	tGt	1	1	A.3	0.002096
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	A.5	0.001923
ORF1ab/nsp3	42	Y42E	TaT	GaA	1	1	All	0
ORF1ab/nsp3	42	Y42del2	TAt	--t	1	1	All	0
ORF1ab/nsp3	42	Y42H	Tat	Cat	1	1	AY.103	0.000006
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	AY.104	0.001984
ORF1ab/nsp3	42	Y42H	Tat	Cat	1	1	AY.12	0.000316
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	AY.120.1	0.000321
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	AY.13	0.000161
ORF1ab/nsp3	42	Y42H	Tat	Cat	1	1	AY.23	0.00007
ORF1ab/nsp3	42	Y42C	tAt	tGt	1	1	AY.25	0.000006
ORF1ab/nsp3	42	Y42H	Tat	Cat	1	1	AY.26	0.000028
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	AY.29	0.000016
ORF1ab/nsp3	42	Y42H	Tat	Cat	1	1	AY.3	0.00001
ORF1ab/nsp3	42	Y42C	tAt	tGt	1	1	AY.4	0.000002
ORF1ab/nsp3	42	Y42C	tAt	tGt	1	1	AY.43	0.000004
ORF1ab/nsp3	42	Y42C	tAt	tGt	1	1	AY.46.6	0.000072
ORF1ab/nsp3	42	Y42H	Tat	Cat	1	1	AY.47	0.000031
ORF1ab/nsp3	42	Y42del	TAT	---	1	1	AY.6	0.000041
ORF1ab/nsp3	42	Y42S	tAt	tCt	1	1	AY.67	0.000464
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	AY.7	0.000196
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	AY.74	0.000116
ORF1ab/nsp3	42	Y42F	tAt	tTt	1	1	AY.75	0.000056
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	AY.77	0.001127
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	AY.9	0.000068
ORF1ab/nsp3	42	Y42del	TAT	---	1	1	AY.9.2	0.000037
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	AY.99	0.001049
ORF1ab/nsp3	42	Y42N	Tat	Aat	1	1	B.1	0.000009
ORF1ab/nsp3	42	Y42del2	TAt	--t	1	1	B.1	0.000009
ORF1ab/nsp3	42	Y42X	taT	taA	1	1	B.1.1	0.000018
ORF1ab/nsp3	42	Y42del	TAT	---	1	1	B.1.1	0.000018
ORF1ab/nsp3	42	Y42N	Tat	Aat	1	1	B.1.1	0.000018
ORF1ab/nsp3	42	Y42H	Tat	Cat	1	1	B.1.1.214	0.000055
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	B.1.1.326	0.001761
ORF1ab/nsp3	42	Y42del	TAT	---	1	1	B.1.1.416	0.000905
ORF1ab/nsp3	42	Y42N	Tat	Aat	1	1	B.1.1.50	0.000679
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	B.1.1.523	0.001563
ORF1ab/nsp3	42	Y42D	Tat	Gat	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	42	Y42del	TAT	---	1	1	B.1.1.70	0.000341
ORF1ab/nsp3	42	Y42F	tAt	tTt	1	1	B.1.160	0.000031
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	B.1.169	0.014925
ORF1ab/nsp3	42	Y42D	Tat	Gat	1	1	B.1.177	0.000013
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	B.1.177.5	0.001242
ORF1ab/nsp3	42	Y42del	TAT	---	1	1	B.1.177.51	0.004566
ORF1ab/nsp3	42	Y42P	TAt	CCt	1	1	B.1.2	0.000009
ORF1ab/nsp3	42	Y42del	TAT	---	1	1	B.1.2	0.000009
ORF1ab/nsp3	42	Y42C	tAt	tGt	1	1	B.1.2	0.000009
ORF1ab/nsp3	42	Y42X	taT	taA	1	1	B.1.2	0.000009
ORF1ab/nsp3	42	Y42Q	TaT	CaA	1	1	B.1.221	0.000071
ORF1ab/nsp3	42	Y42D	Tat	Gat	1	1	B.1.221	0.000071
ORF1ab/nsp3	42	Y42H	Tat	Cat	1	1	B.1.221	0.000071
ORF1ab/nsp3	42	Y42E	TaT	GaA	1	1	B.1.221	0.000071
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	B.1.221.3	0.000833
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	B.1.243	0.00007
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	B.1.258	0.000067
ORF1ab/nsp3	42	Y42H	Tat	Cat	1	1	B.1.311	0.000275
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	B.1.348	0.018182
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	B.1.36.29	0.000517
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	B.1.36.36	0.000602
ORF1ab/nsp3	42	Y42N	TaT	AaC	1	1	B.1.375	0.00082
ORF1ab/nsp3	42	Y42C	tAt	tGt	1	1	B.1.429	0.000024
ORF1ab/nsp3	42	Y42C	tAt	tGt	1	1	B.1.526	0.000024
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	B.1.551	0.00129
ORF1ab/nsp3	42	Y42del	TAT	---	1	1	B.1.561	0.000397
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	B.1.609	0.000479
ORF1ab/nsp3	42	Y42H	Tat	Cat	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	42	Y42L	TAt	CTt	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	42	Y42H	Tat	Cat	1	1	B.1.621	0.000089
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	B.39	0.002331
ORF1ab/nsp3	42	Y42del	TAT	---	1	1	B.57	0.015152
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	C.35	0.000774
ORF1ab/nsp3	42	Y42Y	taT	taC	1	1	N.9	0.005952

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.