CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = M : CodonNum = 22

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	22	L22L		syn	Cta	Tta	2430	2205	0.907407	26586-26588
M	22	L22L		syn	ctA	ctG	2430	143	0.0588477	26586-26588
M	22	L22L		syn	ctA	ctT	2430	60	0.0246914	26586-26588
M	22	L22L		syn	ctA	ctC	2430	21	0.00864198	26586-26588
M	22	L22L		syn	CtA	TtG	2430	1	0.000411523	26586-26588
M	22	L22I		nonsyn	Cta	Ata	56	56	1	26586-26588
M	22	L22del		del	CTA	---	38	38	1	26586-26588
M	22	L22P		nonsyn	cTa	cCa	12	11	0.916667	26586-26588
M	22	L22P		nonsyn	cTA	cCT	12	1	0.0833333	26586-26588
M	22	L22del1		del	CtA	Tt-	11	5	0.454545	26586-26588
M	22	L22del1		del	cTa	c-a	11	3	0.272727	26586-26588
M	22	L22del1		del	CtA	Nt-	11	1	0.0909091	26586-26588
M	22	L22del1		del	Cta	-ta	11	1	0.0909091	26586-26588
M	22	L22del1		del	CTa	-Ga	11	1	0.0909091	26586-26588
M	22	L22V		nonsyn	Cta	Gta	8	6	0.75	26586-26588
M	22	L22V		nonsyn	CtA	GtG	8	1	0.125	26586-26588
M	22	L22V		nonsyn	CtA	GtT	8	1	0.125	26586-26588
M	22	L22S		nonsyn	CTa	TCa	7	5	0.714286	26586-26588
M	22	L22S		nonsyn	CTA	TCT	7	2	0.285714	26586-26588
M	22	L22R		nonsyn	cTa	cGa	5	3	0.6	26586-26588
M	22	L22R		nonsyn	CTa	AGa	5	1	0.2	26586-26588
M	22	L22R		nonsyn	cTA	cGG	5	1	0.2	26586-26588
M	22	L22Q		nonsyn	cTa	cAa	3	3	1	26586-26588
M	22	L22G		nonsyn	CTA	GGG	2	1	0.5	26586-26588
M	22	L22G		nonsyn	CTa	GGa	2	1	0.5	26586-26588
M	22	L22del2		del	CTa	--a	1	1	1	26586-26588
M	22	L22F		nonsyn	CtA	TtT	1	1	1	26586-26588

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	22	L22L	Cta	Tta	2205	2430	All	0.000422
M	22	L22L	ctA	ctG	143	2430	All	0.000027
M	22	L22L	ctA	ctT	60	2430	All	0.000011
M	22	L22L	ctA	ctC	21	2430	All	0.000004
M	22	L22L	CtA	TtG	1	2430	All	0
M	22	L22L	Cta	Tta	1669	1671	AY.4	0.002598
M	22	L22L	ctA	ctC	1	1671	AY.4	0.000002
M	22	L22L	ctA	ctG	1	1671	AY.4	0.000002
M	22	L22L	Cta	Tta	79	94	B.1.1.7	0.000071
M	22	L22L	ctA	ctT	9	94	B.1.1.7	0.000008
M	22	L22L	ctA	ctG	5	94	B.1.1.7	0.000004
M	22	L22L	CtA	TtG	1	94	B.1.1.7	0.000001
M	22	L22L	ctA	ctG	75	86	AY.43	0.000332
M	22	L22L	Cta	Tta	9	86	AY.43	0.00004
M	22	L22L	ctA	ctT	2	86	AY.43	0.000009
M	22	L22L	Cta	Tta	77	77	B.1.1.273	0.52027
M	22	L22I	Cta	Ata	56	56	All	0.000011
M	22	L22L	ctA	ctG	43	46	B.1.525	0.004866
M	22	L22L	Cta	Tta	2	46	B.1.525	0.000226
M	22	L22L	ctA	ctT	1	46	B.1.525	0.000113
M	22	L22L	Cta	Tta	45	45	AY.42	0.00181
M	22	L22del	CTA	---	38	38	All	0.000007
M	22	L22L	Cta	Tta	36	38	B.1.617.2	0.000136
M	22	L22L	ctA	ctT	1	38	B.1.617.2	0.000004
M	22	L22L	ctA	ctG	1	38	B.1.617.2	0.000004
M	22	L22L	Cta	Tta	26	29	AY.25	0.000156
M	22	L22L	ctA	ctT	3	29	AY.25	0.000018
M	22	L22L	ctA	ctC	12	17	B.1.2	0.000106
M	22	L22L	ctA	ctG	2	17	B.1.2	0.000018
M	22	L22L	Cta	Tta	2	17	B.1.2	0.000018
M	22	L22L	ctA	ctT	1	17	B.1.2	0.000009
M	22	L22L	Cta	Tta	17	17	C.39	0.320755
M	22	L22L	Cta	Tta	11	16	AY.44	0.000067
M	22	L22L	ctA	ctC	3	16	AY.44	0.000018
M	22	L22L	ctA	ctT	2	16	AY.44	0.000012
M	22	L22L	Cta	Tta	12	14	AY.29	0.000189
M	22	L22L	ctA	ctT	1	14	AY.29	0.000016
M	22	L22L	ctA	ctG	1	14	AY.29	0.000016
M	22	L22L	Cta	Tta	13	13	AY.84	0.005687
M	22	L22P	cTa	cCa	11	12	All	0.000002
M	22	L22P	cTA	cCT	1	12	All	0
M	22	L22del1	CtA	Tt-	5	11	All	0.000001
M	22	L22del1	cTa	c-a	3	11	All	0.000001
M	22	L22del1	Cta	-ta	1	11	All	0
M	22	L22del1	CtA	Nt-	1	11	All	0
M	22	L22del1	CTa	-Ga	1	11	All	0
M	22	L22L	Cta	Tta	11	11	AT.1	0.05641
M	22	L22L	Cta	Tta	11	11	AY.54	0.001049
M	22	L22L	Cta	Tta	6	11	B.1	0.000055
M	22	L22L	ctA	ctT	4	11	B.1	0.000037
M	22	L22L	ctA	ctG	1	11	B.1	0.000009
M	22	L22L	Cta	Tta	8	11	B.1.351	0.000238
M	22	L22L	ctA	ctT	3	11	B.1.351	0.000089
M	22	L22L	Cta	Tta	7	10	AY.20	0.000272
M	22	L22L	ctA	ctT	3	10	AY.20	0.000117
M	22	L22L	Cta	Tta	10	10	B.1.1	0.000181
M	22	L22L	Cta	Tta	6	9	AY.85	0.002563
M	22	L22L	ctA	ctT	2	9	AY.85	0.000854
M	22	L22L	ctA	ctG	1	9	AY.85	0.000427
M	22	L22L	Cta	Tta	9	9	B.1.1.519	0.000357
M	22	L22L	Cta	Tta	9	9	C.13	0.230769
M	22	L22V	Cta	Gta	6	8	All	0.000001
M	22	L22V	CtA	GtG	1	8	All	0
M	22	L22V	CtA	GtT	1	8	All	0
M	22	L22S	CTa	TCa	5	7	All	0.000001
M	22	L22S	CTA	TCT	2	7	All	0
M	22	L22I	Cta	Ata	7	7	B.1.1.7	0.000006
M	22	L22I	Cta	Ata	7	7	B.1.526	0.000165
M	22	L22I	Cta	Ata	6	6	AY.43	0.000027
M	22	L22L	Cta	Tta	4	6	B.1.177	0.000053
M	22	L22L	ctA	ctT	2	6	B.1.177	0.000026
M	22	L22L	Cta	Tta	6	6	C.37	0.000696
M	22	L22R	cTa	cGa	3	5	All	0.000001
M	22	L22R	cTA	cGG	1	5	All	0
M	22	L22R	CTa	AGa	1	5	All	0
M	22	L22L	Cta	Tta	4	5	AY.102	0.000106
M	22	L22L	ctA	ctG	1	5	AY.102	0.000027
M	22	L22L	Cta	Tta	4	5	AY.103	0.000025
M	22	L22L	ctA	ctG	1	5	AY.103	0.000006
M	22	L22L	ctA	ctC	3	5	AY.36	0.000445
M	22	L22L	Cta	Tta	2	5	AY.36	0.000296
M	22	L22L	ctA	ctG	3	5	AY.39	0.000074
M	22	L22L	Cta	Tta	2	5	AY.39	0.000049
M	22	L22del	CTA	---	5	5	B.1.1.7	0.000004
M	22	L22L	Cta	Tta	2	4	AY.119	0.000071
M	22	L22L	ctA	ctT	2	4	AY.119	0.000071
M	22	L22L	Cta	Tta	4	4	AY.47	0.000124
M	22	L22del	CTA	---	4	4	B.1	0.000037
M	22	L22P	cTa	cCa	3	4	B.1	0.000027
M	22	L22P	cTA	cCT	1	4	B.1	0.000009
M	22	L22L	Cta	Tta	4	4	B.1.160	0.000125
M	22	L22L	ctA	ctT	4	4	B.1.320	0.004981
M	22	L22L	Cta	Tta	3	4	B.1.617.1	0.000387
M	22	L22L	ctA	ctG	1	4	B.1.617.1	0.000129
M	22	L22L	Cta	Tta	4	4	P.1	0.000063
M	22	L22Q	cTa	cAa	3	3	All	0.000001
M	22	L22L	ctA	ctT	2	3	AY.35	0.000466
M	22	L22L	Cta	Tta	1	3	AY.35	0.000233
M	22	L22I	Cta	Ata	3	3	AY.4	0.000005
M	22	L22L	Cta	Tta	2	3	AY.5	0.000041
M	22	L22L	ctA	ctG	1	3	AY.5	0.000021
M	22	L22I	Cta	Ata	3	3	B.1	0.000027
M	22	L22L	Cta	Tta	3	3	B.1.1.63	0.001157
M	22	L22del1	CtA	Tt-	2	3	B.1.1.7	0.000002
M	22	L22del1	CtA	Nt-	1	3	B.1.1.7	0.000001
M	22	L22I	Cta	Ata	3	3	B.1.177	0.00004
M	22	L22del1	CtA	Tt-	3	3	B.1.177.21	0.000229
M	22	L22L	Cta	Tta	2	3	B.1.177.21	0.000153
M	22	L22L	ctA	ctT	1	3	B.1.177.21	0.000076
M	22	L22del	CTA	---	3	3	B.1.2	0.000026
M	22	L22L	ctA	ctC	2	3	B.1.427	0.000101
M	22	L22L	Cta	Tta	1	3	B.1.427	0.00005
M	22	L22L	Cta	Tta	3	3	B.1.497	0.000944
M	22	L22L	Cta	Tta	3	3	B.1.582	0.001472
M	22	L22I	Cta	Ata	3	3	B.1.617.1	0.000387
M	22	L22L	Cta	Tta	3	3	B.1.621	0.000266
M	22	L22L	ctA	ctT	3	3	P.1.14	0.000143
M	22	L22L	Cta	Tta	3	3	P.2	0.00056
M	22	L22del	CTA	---	2	2		0.111111
M	22	L22G	CTa	GGa	1	2	All	0
M	22	L22G	CTA	GGG	1	2	All	0
M	22	L22L	Cta	Tta	2	2	AY.100	0.000092
M	22	L22L	ctA	ctG	2	2	AY.26	0.000057
M	22	L22L	Cta	Tta	2	2	AY.39.1	0.000079
M	22	L22L	Cta	Tta	2	2	AY.4.2	0.000043
M	22	L22del1	cTa	c-a	2	2	AY.43	0.000009
M	22	L22I	Cta	Ata	2	2	AY.44	0.000012
M	22	L22L	Cta	Tta	2	2	AY.55	0.001835
M	22	L22L	Cta	Tta	1	2	AY.6	0.000041
M	22	L22L	ctA	ctT	1	2	AY.6	0.000041
M	22	L22V	Cta	Gta	1	2	AY.85	0.000427
M	22	L22R	cTa	cGa	1	2	AY.85	0.000427
M	22	L22R	cTA	cGG	1	2	AY.85	0.000427
M	22	L22G	CTA	GGG	1	2	AY.85	0.000427
M	22	L22V	CtA	GtG	1	2	AY.85	0.000427
M	22	L22G	CTa	GGa	1	2	AY.85	0.000427
M	22	L22S	CTA	TCT	1	2	AY.99	0.001049
M	22	L22S	CTa	TCa	1	2	AY.99	0.001049
M	22	L22S	CTa	TCa	1	2	B.1	0.000009
M	22	L22S	CTA	TCT	1	2	B.1	0.000009
M	22	L22L	Cta	Tta	2	2	B.1.1.1	0.000653
M	22	L22L	ctA	ctT	2	2	B.1.1.306	0.000877
M	22	L22V	CtA	GtT	1	2	B.1.1.7	0.000001
M	22	L22V	Cta	Gta	1	2	B.1.1.7	0.000001
M	22	L22I	Cta	Ata	2	2	B.1.243	0.000139
M	22	L22L	Cta	Tta	2	2	B.1.243	0.000139
M	22	L22L	Cta	Tta	2	2	B.1.258	0.000133
M	22	L22L	ctA	ctT	2	2	B.1.258.17	0.000208
M	22	L22L	ctA	ctT	1	2	B.1.36	0.000146
M	22	L22L	Cta	Tta	1	2	B.1.36	0.000146
M	22	L22L	Cta	Tta	2	2	B.1.36.31	0.003503
M	22	L22L	Cta	Tta	2	2	B.1.499	0.002101
M	22	L22I	Cta	Ata	2	2	B.1.525	0.000226
M	22	L22L	Cta	Tta	2	2	B.1.575	0.000607
M	22	L22L	Cta	Tta	2	2	B.1.596	0.000174
M	22	L22P	cTa	cCa	2	2	B.1.617.2	0.000008
M	22	L22I	Cta	Ata	2	2	B.1.617.2	0.000008
M	22	L22del	CTA	---	2	2	P.1	0.000032
M	22	L22L	Cta	Tta	2	2	P.1.1	0.000635
M	22	L22L	Cta	Tta	2	2	Q.8	0.00033
M	22	L22F	CtA	TtT	1	1	All	0
M	22	L22del2	CTa	--a	1	1	All	0
M	22	L22I	Cta	Ata	1	1	AY.100	0.000046
M	22	L22L	ctA	ctT	1	1	AY.101	0.00049
M	22	L22S	CTa	TCa	1	1	AY.103	0.000006
M	22	L22L	Cta	Tta	1	1	AY.107	0.000466
M	22	L22del1	Cta	-ta	1	1	AY.108	0.001103
M	22	L22P	cTa	cCa	1	1	AY.113	0.000142
M	22	L22S	CTa	TCa	1	1	AY.113	0.000142
M	22	L22L	Cta	Tta	1	1	AY.113	0.000142
M	22	L22del	CTA	---	1	1	AY.120	0.000037
M	22	L22I	Cta	Ata	1	1	AY.121	0.000135
M	22	L22L	Cta	Tta	1	1	AY.121	0.000135
M	22	L22del	CTA	---	1	1	AY.14	0.000088
M	22	L22I	Cta	Ata	1	1	AY.16	0.00038
M	22	L22I	Cta	Ata	1	1	AY.23	0.00007
M	22	L22L	Cta	Tta	1	1	AY.23	0.00007
M	22	L22I	Cta	Ata	1	1	AY.25	0.000006
M	22	L22I	Cta	Ata	1	1	AY.27	0.000065
M	22	L22S	CTa	TCa	1	1	AY.3	0.00001
M	22	L22P	cTa	cCa	1	1	AY.3	0.00001
M	22	L22L	Cta	Tta	1	1	AY.3	0.00001
M	22	L22L	ctA	ctG	1	1	AY.30	0.000396
M	22	L22L	Cta	Tta	1	1	AY.37	0.000316
M	22	L22L	Cta	Tta	1	1	AY.38	0.000499
M	22	L22del	CTA	---	1	1	AY.39	0.000025
M	22	L22I	Cta	Ata	1	1	AY.39.1	0.00004
M	22	L22V	Cta	Gta	1	1	AY.4	0.000002
M	22	L22del	CTA	---	1	1	AY.4	0.000002
M	22	L22I	Cta	Ata	1	1	AY.4.2	0.000022
M	22	L22del	CTA	---	1	1	AY.4.5	0.000107
M	22	L22del	CTA	---	1	1	AY.43	0.000004
M	22	L22Q	cTa	cAa	1	1	AY.44	0.000006
M	22	L22L	Cta	Tta	1	1	AY.45	0.000122
M	22	L22L	Cta	Tta	1	1	AY.46	0.000104
M	22	L22L	Cta	Tta	1	1	AY.46.6	0.000072
M	22	L22del1	CTa	-Ga	1	1	AY.46.6	0.000072
M	22	L22L	Cta	Tta	1	1	AY.58	0.000907
M	22	L22P	cTa	cCa	1	1	AY.6	0.000041
M	22	L22L	Cta	Tta	1	1	AY.61	0.000105
M	22	L22L	Cta	Tta	1	1	AY.62	0.000436
M	22	L22L	Cta	Tta	1	1	AY.67	0.000464
M	22	L22del	CTA	---	1	1	AY.68	0.000274
M	22	L22del	CTA	---	1	1	AY.75	0.000056
M	22	L22L	ctA	ctG	1	1	AY.75	0.000056
M	22	L22L	Cta	Tta	1	1	AY.76	0.004831
M	22	L22L	Cta	Tta	1	1	AY.8	0.000606
M	22	L22del	CTA	---	1	1	AY.84	0.000437
M	22	L22P	cTa	cCa	1	1	AY.9.2	0.000037
M	22	L22I	Cta	Ata	1	1	AY.98	0.000079
M	22	L22L	Cta	Tta	1	1	AY.99.2	0.000092
M	22	L22R	CTa	AGa	1	1	B.1	0.000009
M	22	L22L	Cta	Tta	1	1	B.1.1.198	0.001468
M	22	L22L	Cta	Tta	1	1	B.1.1.207	0.001182
M	22	L22I	Cta	Ata	1	1	B.1.1.214	0.000055
M	22	L22L	Cta	Tta	1	1	B.1.1.216	0.00089
M	22	L22L	ctA	ctT	1	1	B.1.1.219	0.005
M	22	L22L	ctA	ctG	1	1	B.1.1.222	0.000204
M	22	L22L	Cta	Tta	1	1	B.1.1.25	0.000569
M	22	L22del	CTA	---	1	1	B.1.1.288	0.001916
M	22	L22del	CTA	---	1	1	B.1.1.312	0.001912
M	22	L22L	Cta	Tta	1	1	B.1.1.329	0.003846
M	22	L22del	CTA	---	1	1	B.1.1.343	0.020833
M	22	L22L	Cta	Tta	1	1	B.1.1.370	0.012658
M	22	L22L	ctA	ctT	1	1	B.1.1.420	0.001006
M	22	L22L	ctA	ctT	1	1	B.1.1.432	0.001266
M	22	L22L	Cta	Tta	1	1	B.1.1.448	0.002033
M	22	L22L	Cta	Tta	1	1	B.1.1.46	0.004367
M	22	L22I	Cta	Ata	1	1	B.1.1.519	0.00004
M	22	L22L	Cta	Tta	1	1	B.1.1.523	0.001563
M	22	L22R	cTa	cGa	1	1	B.1.1.7	0.000001
M	22	L22P	cTa	cCa	1	1	B.1.1.7	0.000001
M	22	L22Q	cTa	cAa	1	1	B.1.1.7	0.000001
M	22	L22del	CTA	---	1	1	B.1.1.70	0.000341
M	22	L22del	CTA	---	1	1	B.1.160.33	0.004425
M	22	L22del	CTA	---	1	1	B.1.161	0.017241
M	22	L22F	CtA	TtT	1	1	B.1.177.21	0.000076
M	22	L22del	CTA	---	1	1	B.1.177.21	0.000076
M	22	L22L	ctA	ctT	1	1	B.1.177.56	0.000668
M	22	L22L	Cta	Tta	1	1	B.1.177.83	0.001481
M	22	L22I	Cta	Ata	1	1	B.1.2	0.000009
M	22	L22P	cTa	cCa	1	1	B.1.2	0.000009
M	22	L22L	ctA	ctG	1	1	B.1.234	0.000132
M	22	L22V	Cta	Gta	1	1	B.1.243	0.00007
M	22	L22L	Cta	Tta	1	1	B.1.258.14	0.00098
M	22	L22L	Cta	Tta	1	1	B.1.336	0.002439
M	22	L22L	Cta	Tta	1	1	B.1.337	0.005587
M	22	L22I	Cta	Ata	1	1	B.1.36.29	0.000517
M	22	L22del	CTA	---	1	1	B.1.396	0.000706
M	22	L22L	Cta	Tta	1	1	B.1.404	0.001302
M	22	L22L	Cta	Tta	1	1	B.1.416.1	0.001563
M	22	L22I	Cta	Ata	1	1	B.1.427	0.00005
M	22	L22L	ctA	ctT	1	1	B.1.429	0.000024
M	22	L22I	Cta	Ata	1	1	B.1.429	0.000024
M	22	L22V	Cta	Gta	1	1	B.1.429	0.000024
M	22	L22L	ctA	ctT	1	1	B.1.517	0.000427
M	22	L22L	Cta	Tta	1	1	B.1.524	0.001406
M	22	L22L	ctA	ctT	1	1	B.1.526	0.000024
M	22	L22L	Cta	Tta	1	1	B.1.561	0.000397
M	22	L22del	CTA	---	1	1	B.1.577	0.000687
M	22	L22del1	cTa	c-a	1	1	B.1.580	0.004065
M	22	L22del	CTA	---	1	1	B.1.595	0.000261
M	22	L22V	Cta	Gta	1	1	B.1.596	0.000087
M	22	L22del	CTA	---	1	1	B.1.609	0.000479
M	22	L22R	cTa	cGa	1	1	B.1.609	0.000479
M	22	L22del2	CTa	--a	1	1	B.1.617.2	0.000004
M	22	L22L	Cta	Tta	1	1	B.1.625	0.002353
M	22	L22del	CTA	---	1	1	B.1.627	0.00202
M	22	L22L	Cta	Tta	1	1	B.1.637	0.000073
M	22	L22Q	cTa	cAa	1	1	B.1.637	0.000073
M	22	L22L	Cta	Tta	1	1	C.1	0.002392
M	22	L22L	Cta	Tta	1	1	C.35	0.000774
M	22	L22L	Cta	Tta	1	1	C.36.3	0.000567
M	22	L22L	Cta	Tta	1	1	D.2	0.000075
M	22	L22del	CTA	---	1	1	P.1.15	0.000232
M	22	L22I	Cta	Ata	1	1	Q.3	0.000145
M	22	L22L	Cta	Tta	1	1	Q.7	0.001111
M	22	L22L	Cta	Tta	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.