CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = M : CodonNum = 48

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
M	48	I48V		nonsyn	Ata	Gta	1558	1558	1	26664-26666
M	48	I48T		nonsyn	aTa	aCa	153	150	0.980392	26664-26666
M	48	I48T		nonsyn	aTA	aCT	153	3	0.0196078	26664-26666
M	48	I48L		nonsyn	Ata	Cta	91	61	0.67033	26664-26666
M	48	I48L		nonsyn	Ata	Tta	91	28	0.307692	26664-26666
M	48	I48L		nonsyn	AtA	CtT	91	2	0.021978	26664-26666
M	48	I48del		del	ATA	---	39	39	1	26664-26666
M	48	I48M		nonsyn	atA	atG	24	24	1	26664-26666
M	48	I48I		syn	atA	atT	14	10	0.714286	26664-26666
M	48	I48I		syn	atA	atC	14	4	0.285714	26664-26666
M	48	I48K		nonsyn	aTa	aAa	5	4	0.8	26664-26666
M	48	I48F		nonsyn	AtA	TtT	5	3	0.6	26664-26666
M	48	I48F		nonsyn	AtA	TtC	5	2	0.4	26664-26666
M	48	I48K		nonsyn	aTA	aAG	5	1	0.2	26664-26666
M	48	I48del1		del	atA	at-	4	2	0.5	26664-26666
M	48	I48del1		del	aTa	a-a	4	2	0.5	26664-26666
M	48	I48E		nonsyn	ATa	GAa	1	1	1	26664-26666

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
M	48	I48V	Ata	Gta	1558	1558	All	0.000298
M	48	I48V	Ata	Gta	974	974	B.1.375	0.798361
M	48	I48V	Ata	Gta	212	212	B.1.1.7	0.00019
M	48	I48T	aTa	aCa	150	153	All	0.000029
M	48	I48T	aTA	aCT	3	153	All	0.000001
M	48	I48L	Ata	Cta	61	91	All	0.000012
M	48	I48L	Ata	Tta	28	91	All	0.000005
M	48	I48L	AtA	CtT	2	91	All	0
M	48	I48V	Ata	Gta	86	86	B.1.258.3	0.144054
M	48	I48T	aTa	aCa	70	70	AY.3	0.000696
M	48	I48V	Ata	Gta	69	69	AY.44	0.00042
M	48	I48del	ATA	---	39	39	All	0.000007
M	48	I48V	Ata	Gta	34	34	AY.103	0.000211
M	48	I48V	Ata	Gta	31	31	B.1	0.000284
M	48	I48V	Ata	Gta	26	26	B.1.258	0.00173
M	48	I48T	aTa	aCa	25	25	AY.46	0.002602
M	48	I48M	atA	atG	24	24	All	0.000005
M	48	I48del	ATA	---	17	17	B.1.177.21	0.0013
M	48	I48V	Ata	Gta	15	15	AY.20	0.000583
M	48	I48V	Ata	Gta	15	15	AY.4	0.000023
M	48	I48L	Ata	Tta	15	15	AY.5	0.00031
M	48	I48I	atA	atT	10	14	All	0.000002
M	48	I48I	atA	atC	4	14	All	0.000001
M	48	I48V	Ata	Gta	10	10	B.1.617.2	0.000038
M	48	I48T	aTa	aCa	9	9	AY.44	0.000055
M	48	I48L	Ata	Cta	8	9	B.1.1	0.000145
M	48	I48L	Ata	Tta	1	9	B.1.1	0.000018
M	48	I48V	Ata	Gta	8	8	AY.25	0.000048
M	48	I48V	Ata	Gta	8	8	B.1.427	0.000404
M	48	I48L	Ata	Tta	3	7		0.166667
M	48	I48L	AtA	CtT	2	7		0.111111
M	48	I48L	Ata	Cta	2	7		0.111111
M	48	I48T	aTa	aCa	7	7	AY.4	0.000011
M	48	I48T	aTa	aCa	7	7	AZ.2	0.005747
M	48	I48del	ATA	---	7	7	B.1.1.7	0.000006
M	48	I48T	aTa	aCa	7	7	B.1.1.7	0.000006
M	48	I48M	atA	atG	6	6	AY.57	0.003937
M	48	I48L	Ata	Tta	5	6	B.1.177	0.000066
M	48	I48L	Ata	Cta	1	6	B.1.177	0.000013
M	48	I48L	Ata	Cta	6	6	B.1.2	0.000053
M	48	I48V	Ata	Gta	6	6	B.1.2	0.000053
M	48	I48I	atA	atT	4	5		0.222222
M	48	I48I	atA	atC	1	5		0.055556
M	48	I48K	aTa	aAa	4	5	All	0.000001
M	48	I48F	AtA	TtT	3	5	All	0.000001
M	48	I48F	AtA	TtC	2	5	All	0
M	48	I48K	aTA	aAG	1	5	All	0
M	48	I48V	Ata	Gta	5	5	AY.43	0.000022
M	48	I48L	Ata	Cta	5	5	B.1.1.161	0.017668
M	48	I48L	Ata	Cta	5	5	B.1.1.267	0.050505
M	48	I48L	Ata	Cta	5	5	B.1.1.301	0.005896
M	48	I48F	AtA	TtT	3	4		0.166667
M	48	I48F	AtA	TtC	1	4		0.055556
M	48	I48del1	atA	at-	2	4	All	0
M	48	I48del1	aTa	a-a	2	4	All	0
M	48	I48V	Ata	Gta	4	4	AY.3	0.00004
M	48	I48L	Ata	Cta	4	4	AY.3	0.00004
M	48	I48V	Ata	Gta	4	4	AY.5	0.000083
M	48	I48L	Ata	Cta	3	4	B.1.1.7	0.000003
M	48	I48L	Ata	Tta	1	4	B.1.1.7	0.000001
M	48	I48I	atA	atT	4	4	B.1.241	0.003247
M	48	I48V	Ata	Gta	4	4	B.1.367	0.00317
M	48	I48L	Ata	Tta	2	4	B.1.596	0.000174
M	48	I48L	Ata	Cta	2	4	B.1.596	0.000174
M	48	I48T	aTa	aCa	4	4	B.1.617.2	0.000015
M	48	I48M	atA	atG	4	4	C.37	0.000464
M	48	I48T	aTa	aCa	3	3	AY.105	0.001929
M	48	I48T	aTa	aCa	3	3	AY.25	0.000018
M	48	I48V	Ata	Gta	3	3	AY.34	0.000291
M	48	I48L	Ata	Cta	3	3	B.1	0.000027
M	48	I48V	Ata	Gta	3	3	B.1.1	0.000054
M	48	I48V	Ata	Gta	3	3	B.1.1.222	0.000612
M	48	I48T	aTA	aCT	3	3	B.1.177.21	0.000229
M	48	I48T	aTa	aCa	3	3	B.40	0.001093
M	48	I48del	ATA	---	2	2		0.111111
M	48	I48T	aTa	aCa	2	2	AY.117	0.000169
M	48	I48V	Ata	Gta	2	2	AY.119	0.000071
M	48	I48V	Ata	Gta	2	2	AY.121	0.000271
M	48	I48V	Ata	Gta	2	2	AY.29	0.000032
M	48	I48T	aTa	aCa	2	2	AY.39.1	0.000079
M	48	I48M	atA	atG	2	2	AY.4	0.000003
M	48	I48del	ATA	---	2	2	AY.43	0.000009
M	48	I48M	atA	atG	2	2	AY.47	0.000062
M	48	I48V	Ata	Gta	2	2	AY.69	0.000373
M	48	I48L	Ata	Cta	2	2	B.1.1.318	0.000604
M	48	I48V	Ata	Gta	2	2	B.1.1.519	0.000079
M	48	I48M	atA	atG	2	2	B.1.1.7	0.000002
M	48	I48I	atA	atT	1	2	B.1.1.7	0.000001
M	48	I48I	atA	atC	1	2	B.1.1.7	0.000001
M	48	I48V	Ata	Gta	2	2	B.1.240	0.000431
M	48	I48M	atA	atG	2	2	B.1.429	0.000047
M	48	I48V	Ata	Gta	2	2	C.37	0.000232
M	48	I48L	Ata	Cta	2	2	P.1	0.000032
M	48	I48V	Ata	Gta	1	1	A	0.000387
M	48	I48E	ATa	GAa	1	1	All	0
M	48	I48T	aTa	aCa	1	1	AY.100	0.000046
M	48	I48V	Ata	Gta	1	1	AY.113	0.000142
M	48	I48K	aTA	aAG	1	1	AY.117	0.000085
M	48	I48V	Ata	Gta	1	1	AY.117	0.000085
M	48	I48V	Ata	Gta	1	1	AY.118	0.000063
M	48	I48del	ATA	---	1	1	AY.120	0.000037
M	48	I48T	aTa	aCa	1	1	AY.16	0.00038
M	48	I48T	aTa	aCa	1	1	AY.20	0.000039
M	48	I48V	Ata	Gta	1	1	AY.27	0.000065
M	48	I48I	atA	atC	1	1	AY.3.1	0.000085
M	48	I48E	ATa	GAa	1	1	AY.30	0.000396
M	48	I48V	Ata	Gta	1	1	AY.33	0.000067
M	48	I48T	aTa	aCa	1	1	AY.4.2	0.000022
M	48	I48V	Ata	Gta	1	1	AY.4.2.1	0.000149
M	48	I48L	Ata	Cta	1	1	AY.44	0.000006
M	48	I48M	atA	atG	1	1	AY.44	0.000006
M	48	I48V	Ata	Gta	1	1	AY.46	0.000104
M	48	I48V	Ata	Gta	1	1	AY.47	0.000031
M	48	I48V	Ata	Gta	1	1	AY.59	0.00053
M	48	I48del	ATA	---	1	1	AY.68	0.000274
M	48	I48T	aTa	aCa	1	1	AY.69	0.000187
M	48	I48V	Ata	Gta	1	1	AY.71	0.000475
M	48	I48del	ATA	---	1	1	AY.84	0.000437
M	48	I48V	Ata	Gta	1	1	AY.9.2	0.000037
M	48	I48L	Ata	Tta	1	1	AY.93	0.000273
M	48	I48I	atA	atT	1	1	B.1	0.000009
M	48	I48T	aTa	aCa	1	1	B.1	0.000009
M	48	I48del	ATA	---	1	1	B.1	0.000009
M	48	I48del1	atA	at-	1	1	B.1	0.000009
M	48	I48del1	atA	at-	1	1	B.1.1	0.000018
M	48	I48K	aTa	aAa	1	1	B.1.1	0.000018
M	48	I48M	atA	atG	1	1	B.1.1.318	0.000302
M	48	I48V	Ata	Gta	1	1	B.1.1.332	0.03125
M	48	I48L	Ata	Cta	1	1	B.1.1.348	0.000796
M	48	I48K	aTa	aAa	1	1	B.1.1.372	0.000689
M	48	I48L	Ata	Cta	1	1	B.1.1.519	0.00004
M	48	I48F	AtA	TtC	1	1	B.1.1.7	0.000001
M	48	I48I	atA	atC	1	1	B.1.160	0.000031
M	48	I48del	ATA	---	1	1	B.1.161	0.017241
M	48	I48M	atA	atG	1	1	B.1.177	0.000013
M	48	I48V	Ata	Gta	1	1	B.1.177	0.000013
M	48	I48V	Ata	Gta	1	1	B.1.177.21	0.000076
M	48	I48M	atA	atG	1	1	B.1.177.44	0.000519
M	48	I48V	Ata	Gta	1	1	B.1.177.57	0.000281
M	48	I48T	aTa	aCa	1	1	B.1.2	0.000009
M	48	I48del1	aTa	a-a	1	1	B.1.2	0.000009
M	48	I48M	atA	atG	1	1	B.1.2	0.000009
M	48	I48K	aTa	aAa	1	1	B.1.2	0.000009
M	48	I48V	Ata	Gta	1	1	B.1.221	0.000071
M	48	I48V	Ata	Gta	1	1	B.1.243	0.00007
M	48	I48del	ATA	---	1	1	B.1.258.11	0.000396
M	48	I48L	Ata	Cta	1	1	B.1.311	0.000275
M	48	I48V	Ata	Gta	1	1	B.1.382	0.008929
M	48	I48del1	aTa	a-a	1	1	B.1.39	0.003906
M	48	I48L	Ata	Cta	1	1	B.1.416	0.001269
M	48	I48L	Ata	Cta	1	1	B.1.428	0.00102
M	48	I48K	aTa	aAa	1	1	B.1.501	0.007353
M	48	I48L	Ata	Cta	1	1	B.1.525	0.000113
M	48	I48L	Ata	Cta	1	1	B.1.526	0.000024
M	48	I48V	Ata	Gta	1	1	B.1.526	0.000024
M	48	I48del	ATA	---	1	1	B.1.577	0.000687
M	48	I48del	ATA	---	1	1	B.1.595	0.000261
M	48	I48V	Ata	Gta	1	1	B.1.596	0.000087
M	48	I48L	Ata	Cta	1	1	B.1.617.1	0.000129
M	48	I48L	Ata	Cta	1	1	B.1.617.2	0.000004
M	48	I48M	atA	atG	1	1	B.1.617.2	0.000004
M	48	I48del	ATA	---	1	1	B.1.627	0.00202
M	48	I48L	Ata	Cta	1	1	B.1.637	0.000073
M	48	I48L	Ata	Cta	1	1	B.40	0.000364
M	48	I48L	Ata	Cta	1	1	B.61	0.005747
M	48	I48del	ATA	---	1	1	P.1	0.000016
M	48	I48V	Ata	Gta	1	1	P.1	0.000016
M	48	I48V	Ata	Gta	1	1	P.1.12	0.000484
M	48	I48del	ATA	---	1	1	P.1.15	0.000232
M	48	I48V	Ata	Gta	1	1	P.2	0.000187
M	48	I48T	aTa	aCa	1	1	Q.1	0.000126

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.