CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = M : CodonNum = 73

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	73	I73L		nonsyn	Ata	Cta	383	374	0.976501	26739-26741
M	73	I73L		nonsyn	Ata	Tta	383	7	0.0182768	26739-26741
M	73	I73L		nonsyn	AtA	TtG	383	2	0.00522193	26739-26741
M	73	I73I		syn	atA	atT	332	321	0.966867	26739-26741
M	73	I73I		syn	atA	atC	332	11	0.0331325	26739-26741
M	73	I73M		nonsyn	atA	atG	249	249	1	26739-26741
M	73	I73V		nonsyn	Ata	Gta	137	136	0.992701	26739-26741
M	73	I73V		nonsyn	AtA	GtG	137	1	0.00729927	26739-26741
M	73	I73del		del	ATA	---	72	72	1	26739-26741
M	73	I73T		nonsyn	aTa	aCa	8	8	1	26739-26741
M	73	I73K		nonsyn	aTa	aAa	6	6	1	26739-26741
M	73	I73F		nonsyn	AtA	TtC	4	2	0.5	26739-26741
M	73	I73F		nonsyn	AtA	TtT	4	2	0.5	26739-26741
M	73	I73G		nonsyn	ATA	GGC	2	2	1	26739-26741
M	73	I73R		nonsyn	aTa	aGa	2	2	1	26739-26741
M	73	I73N		nonsyn	aTA	aAT	1	1	1	26739-26741
M	73	I73A		nonsyn	ATa	GCa	1	1	1	26739-26741
M	73	I73del1		del	atA	at-	1	1	1	26739-26741

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	73	I73L	Ata	Cta	374	383	All	0.000072
M	73	I73L	Ata	Tta	7	383	All	0.000001
M	73	I73L	AtA	TtG	2	383	All	0
M	73	I73L	Ata	Cta	333	333	AY.25	0.002003
M	73	I73I	atA	atT	321	332	All	0.000061
M	73	I73I	atA	atC	11	332	All	0.000002
M	73	I73M	atA	atG	249	249	All	0.000048
M	73	I73I	atA	atT	228	231	B.1.1.7	0.000204
M	73	I73I	atA	atC	3	231	B.1.1.7	0.000003
M	73	I73M	atA	atG	144	144	B.1.1.413	0.993103
M	73	I73V	Ata	Gta	136	137	All	0.000026
M	73	I73V	AtA	GtG	1	137	All	0
M	73	I73del	ATA	---	72	72	All	0.000014
M	73	I73del	ATA	---	50	50	B.1.177.21	0.003824
M	73	I73V	Ata	Gta	44	44	B.1.1.7	0.000039
M	73	I73M	atA	atG	18	18	AY.4	0.000028
M	73	I73I	atA	atT	14	17	AY.4	0.000022
M	73	I73I	atA	atC	3	17	AY.4	0.000005
M	73	I73M	atA	atG	14	14	B.1.1.7	0.000013
M	73	I73V	Ata	Gta	14	14	B.1.2	0.000123
M	73	I73M	atA	atG	13	13	B.1.1	0.000236
M	73	I73M	atA	atG	12	12	AY.3	0.000119
M	73	I73V	Ata	Gta	12	12	AY.4	0.000019
M	73	I73I	atA	atT	12	12	B.1.1.133	0.101695
M	73	I73M	atA	atG	12	12	B.1.637	0.000877
M	73	I73V	Ata	Gta	12	12	P.1	0.000189
M	73	I73del	ATA	---	11	11	B.1.1.7	0.00001
M	73	I73I	atA	atT	10	10	B.1	0.000092
M	73	I73I	atA	atT	10	10	B.1.2	0.000088
M	73	I73T	aTa	aCa	8	8	All	0.000002
M	73	I73L	Ata	Cta	8	8	B.1.617.2	0.00003
M	73	I73V	Ata	Gta	8	8	B.1.617.2	0.00003
M	73	I73V	Ata	Gta	7	7	AY.20	0.000272
M	73	I73K	aTa	aAa	6	6	All	0.000001
M	73	I73L	Ata	Cta	6	6	AY.53	0.001725
M	73	I73L	Ata	Cta	4	6	B.1.1.7	0.000004
M	73	I73L	Ata	Tta	2	6	B.1.1.7	0.000002
M	73	I73M	atA	atG	6	6	B.1.177	0.000079
M	73	I73V	Ata	Gta	5	5	AY.113	0.000712
M	73	I73I	atA	atT	5	5	AY.120	0.000186
M	73	I73I	atA	atT	5	5	B.1.1	0.000091
M	73	I73I	atA	atT	5	5	B.1.160	0.000156
M	73	I73I	atA	atC	5	5	C.37	0.00058
M	73	I73M	atA	atG	5	5	P.1.14	0.000239
M	73	I73I	atA	atT	5	5	P.1.4	0.004883
M	73	I73T	aTa	aCa	4	4		0.222222
M	73	I73F	AtA	TtC	2	4		0.111111
M	73	I73F	AtA	TtT	2	4		0.111111
M	73	I73F	AtA	TtC	2	4	All	0
M	73	I73F	AtA	TtT	2	4	All	0
M	73	I73V	Ata	Gta	4	4	AY.25	0.000024
M	73	I73M	atA	atG	4	4	B.1	0.000037
M	73	I73V	Ata	Gta	4	4	B.1.429	0.000094
M	73	I73L	Ata	Cta	2	3	AY.4	0.000003
M	73	I73L	Ata	Tta	1	3	AY.4	0.000002
M	73	I73V	Ata	Gta	2	3	B.1	0.000018
M	73	I73V	AtA	GtG	1	3	B.1	0.000009
M	73	I73M	atA	atG	3	3	B.1.1.222	0.000612
M	73	I73I	atA	atT	3	3	B.1.617.1	0.000387
M	73	I73L	AtA	TtG	2	2		0.111111
M	73	I73K	aTa	aAa	2	2		0.111111
M	73	I73G	ATA	GGC	2	2	All	0
M	73	I73R	aTa	aGa	2	2	All	0
M	73	I73V	Ata	Gta	2	2	AY.102	0.000053
M	73	I73M	atA	atG	2	2	AY.103	0.000012
M	73	I73L	Ata	Cta	2	2	AY.116	0.000574
M	73	I73M	atA	atG	2	2	AY.118	0.000125
M	73	I73I	atA	atT	2	2	AY.13	0.000322
M	73	I73V	Ata	Gta	2	2	AY.42	0.00008
M	73	I73I	atA	atT	2	2	AY.43	0.000009
M	73	I73L	Ata	Tta	1	2	AY.43	0.000004
M	73	I73L	Ata	Cta	1	2	AY.43	0.000004
M	73	I73L	Ata	Cta	2	2	AY.44	0.000012
M	73	I73V	Ata	Gta	2	2	AY.44	0.000012
M	73	I73L	Ata	Cta	2	2	B.1.1	0.000036
M	73	I73L	Ata	Cta	2	2	B.1.1.519	0.000079
M	73	I73I	atA	atT	2	2	B.1.110.3	0.001437
M	73	I73V	Ata	Gta	2	2	B.1.149	0.006849
M	73	I73V	Ata	Gta	2	2	B.1.160	0.000062
M	73	I73G	ATA	GGC	2	2	B.1.177.21	0.000153
M	73	I73R	aTa	aGa	2	2	B.1.177.21	0.000153
M	73	I73M	atA	atG	2	2	B.1.260	0.006689
M	73	I73L	Ata	Cta	2	2	B.1.351	0.000059
M	73	I73I	atA	atT	2	2	B.1.617.2	0.000008
M	73	I73I	atA	atT	2	2	B.1.621	0.000177
M	73	I73I	atA	atT	2	2	B.1.621.1	0.001012
M	73	I73V	Ata	Gta	2	2	C.36.3	0.001134
M	73	I73L	Ata	Cta	2	2	Q.8	0.00033
M	73	I73N	aTA	aAT	1	1	All	0
M	73	I73A	ATa	GCa	1	1	All	0
M	73	I73del1	atA	at-	1	1	All	0
M	73	I73V	Ata	Gta	1	1	AY.100	0.000046
M	73	I73M	atA	atG	1	1	AY.100	0.000046
M	73	I73M	atA	atG	1	1	AY.104	0.001984
M	73	I73V	Ata	Gta	1	1	AY.109	0.00074
M	73	I73I	atA	atT	1	1	AY.117	0.000085
M	73	I73L	Ata	Cta	1	1	AY.117	0.000085
M	73	I73I	atA	atT	1	1	AY.119	0.000035
M	73	I73del	ATA	---	1	1	AY.120	0.000037
M	73	I73L	Ata	Cta	1	1	AY.20	0.000039
M	73	I73V	Ata	Gta	1	1	AY.23	0.00007
M	73	I73I	atA	atT	1	1	AY.24	0.000431
M	73	I73I	atA	atT	1	1	AY.29.1	0.000221
M	73	I73L	Ata	Cta	1	1	AY.39	0.000025
M	73	I73V	Ata	Gta	1	1	AY.43	0.000004
M	73	I73M	atA	atG	1	1	AY.44	0.000006
M	73	I73K	aTa	aAa	1	1	AY.44	0.000006
M	73	I73L	Ata	Cta	1	1	AY.46	0.000104
M	73	I73V	Ata	Gta	1	1	AY.54	0.000095
M	73	I73I	atA	atT	1	1	AY.72	0.001361
M	73	I73L	Ata	Tta	1	1	AY.75	0.000056
M	73	I73M	atA	atG	1	1	B	0.000128
M	73	I73L	Ata	Cta	1	1	B	0.000128
M	73	I73T	aTa	aCa	1	1	B.1	0.000009
M	73	I73del	ATA	---	1	1	B.1	0.000009
M	73	I73K	aTa	aAa	1	1	B.1.1	0.000018
M	73	I73N	aTA	aAT	1	1	B.1.1	0.000018
M	73	I73L	Ata	Tta	1	1	B.1.1.164	0.005155
M	73	I73M	atA	atG	1	1	B.1.1.174	0.003378
M	73	I73L	Ata	Cta	1	1	B.1.1.239	0.032258
M	73	I73M	atA	atG	1	1	B.1.1.326	0.001761
M	73	I73del	ATA	---	1	1	B.1.1.372	0.000689
M	73	I73V	Ata	Gta	1	1	B.1.1.398	0.003226
M	73	I73M	atA	atG	1	1	B.1.1.432	0.001266
M	73	I73T	aTa	aCa	1	1	B.1.1.7	0.000001
M	73	I73M	atA	atG	1	1	B.1.1.99	0.02381
M	73	I73del	ATA	---	1	1	B.1.160	0.000031
M	73	I73L	Ata	Cta	1	1	B.1.160.8	0.001289
M	73	I73del	ATA	---	1	1	B.1.161	0.017241
M	73	I73I	atA	atT	1	1	B.1.177	0.000013
M	73	I73T	aTa	aCa	1	1	B.1.177.21	0.000076
M	73	I73V	Ata	Gta	1	1	B.1.177.32	0.00135
M	73	I73V	Ata	Gta	1	1	B.1.177.4	0.000211
M	73	I73I	atA	atT	1	1	B.1.177.76	0.002494
M	73	I73M	atA	atG	1	1	B.1.2	0.000009
M	73	I73K	aTa	aAa	1	1	B.1.2	0.000009
M	73	I73del1	atA	at-	1	1	B.1.2	0.000009
M	73	I73V	Ata	Gta	1	1	B.1.210	0.002132
M	73	I73L	Ata	Tta	1	1	B.1.234	0.000132
M	73	I73I	atA	atT	1	1	B.1.254	0.025
M	73	I73del	ATA	---	1	1	B.1.258.11	0.000396
M	73	I73V	Ata	Gta	1	1	B.1.351	0.00003
M	73	I73M	atA	atG	1	1	B.1.36	0.000146
M	73	I73M	atA	atG	1	1	B.1.36.29	0.000517
M	73	I73I	atA	atT	1	1	B.1.428	0.00102
M	73	I73A	ATa	GCa	1	1	B.1.446	0.02
M	73	I73I	atA	atT	1	1	B.1.499	0.00105
M	73	I73V	Ata	Gta	1	1	B.1.524	0.001406
M	73	I73M	atA	atG	1	1	B.1.533	0.009615
M	73	I73del	ATA	---	1	1	B.1.577	0.000687
M	73	I73I	atA	atT	1	1	B.1.596	0.000087
M	73	I73del	ATA	---	1	1	B.1.596	0.000087
M	73	I73del	ATA	---	1	1	B.1.617.2	0.000004
M	73	I73K	aTa	aAa	1	1	B.1.617.2	0.000004
M	73	I73del	ATA	---	1	1	B.1.627	0.00202
M	73	I73L	Ata	Cta	1	1	P.1	0.000016
M	73	I73T	aTa	aCa	1	1	P.1	0.000016
M	73	I73del	ATA	---	1	1	P.1.15	0.000232
M	73	I73I	atA	atT	1	1	P.2	0.000187
M	73	I73V	Ata	Gta	1	1	P.2	0.000187

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.