CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 1130

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
S	1130	I1130M		nonsyn	atA	atG	409	409	1	24950-24952
S	1130	I1130V		nonsyn	Ata	Gta	268	268	1	24950-24952
S	1130	I1130I		syn	atA	atT	178	164	0.921348	24950-24952
S	1130	I1130I		syn	atA	atC	178	14	0.0786517	24950-24952
S	1130	I1130L		nonsyn	Ata	Cta	112	62	0.553571	24950-24952
S	1130	I1130L		nonsyn	Ata	Tta	112	47	0.419643	24950-24952
S	1130	I1130L		nonsyn	AtA	CtG	112	2	0.0178571	24950-24952
S	1130	I1130L		nonsyn	AtA	TtG	112	1	0.00892857	24950-24952
S	1130	I1130T		nonsyn	aTa	aCa	99	98	0.989899	24950-24952
S	1130	I1130T		nonsyn	aTA	aCG	99	1	0.010101	24950-24952
S	1130	I1130del		del	ATA	---	32	32	1	24950-24952
S	1130	I1130R		nonsyn	aTa	aGa	4	4	1	24950-24952
S	1130	I1130E		nonsyn	ATA	GAG	3	3	1	24950-24952
S	1130	I1130N		nonsyn	aTA	aAT	2	2	1	24950-24952
S	1130	I1130S		nonsyn	ATa	TCa	2	1	0.5	24950-24952
S	1130	I1130S		nonsyn	ATA	TCG	2	1	0.5	24950-24952
S	1130	I1130del2		del	aTA	a--	1	1	1	24950-24952
S	1130	I1130del1		del	atA	at-	1	1	1	24950-24952
S	1130	I1130K		nonsyn	aTa	aAa	1	1	1	24950-24952

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
S	1130	I1130M	atA	atG	409	409	All	0.000078
S	1130	I1130V	Ata	Gta	268	268	All	0.000051
S	1130	I1130V	Ata	Gta	197	197	AV.1	0.994949
S	1130	I1130I	atA	atT	164	178	All	0.000031
S	1130	I1130I	atA	atC	14	178	All	0.000003
S	1130	I1130M	atA	atG	158	158	AY.4	0.000246
S	1130	I1130L	Ata	Cta	62	112	All	0.000012
S	1130	I1130L	Ata	Tta	47	112	All	0.000009
S	1130	I1130L	AtA	CtG	2	112	All	0
S	1130	I1130L	AtA	TtG	1	112	All	0
S	1130	I1130T	aTa	aCa	98	99	All	0.000019
S	1130	I1130T	aTA	aCG	1	99	All	0
S	1130	I1130M	atA	atG	68	68	B.1.1.7	0.000061
S	1130	I1130I	atA	atT	35	35	B.1.617.2	0.000132
S	1130	I1130del	ATA	---	32	32	All	0.000006
S	1130	I1130T	aTa	aCa	28	28	B.1.1.7	0.000025
S	1130	I1130M	atA	atG	27	27	B.1.177.48	0.084375
S	1130	I1130I	atA	atT	25	26	B.1.1.7	0.000022
S	1130	I1130I	atA	atC	1	26	B.1.1.7	0.000001
S	1130	I1130L	Ata	Cta	17	23	B.1.1.7	0.000015
S	1130	I1130L	Ata	Tta	6	23	B.1.1.7	0.000005
S	1130	I1130I	atA	atT	20	20	AY.102	0.00053
S	1130	I1130L	Ata	Cta	19	19	AY.100	0.000874
S	1130	I1130I	atA	atT	14	14	AY.20	0.000544
S	1130	I1130M	atA	atG	12	12	AY.6	0.000494
S	1130	I1130M	atA	atG	12	12	B.1	0.00011
S	1130	I1130V	Ata	Gta	12	12	B.1.617.2	0.000045
S	1130	I1130M	atA	atG	11	11	AY.103	0.000068
S	1130	I1130V	Ata	Gta	11	11	AY.114	0.002542
S	1130	I1130M	atA	atG	11	11	AY.74	0.001272
S	1130	I1130T	aTa	aCa	11	11	B.1.351	0.000327
S	1130	I1130V	Ata	Gta	10	10	AY.4	0.000016
S	1130	I1130I	atA	atT	10	10	B.1.526	0.000235
S	1130	I1130L	Ata	Cta	6	10	B.1.617.2	0.000023
S	1130	I1130L	Ata	Tta	4	10	B.1.617.2	0.000015
S	1130	I1130T	aTa	aCa	9	9	AY.4	0.000014
S	1130	I1130M	atA	atG	8	8	AY.43	0.000035
S	1130	I1130I	atA	atT	7	7	AY.39	0.000173
S	1130	I1130I	atA	atT	5	7	B.1.2	0.000044
S	1130	I1130I	atA	atC	2	7	B.1.2	0.000018
S	1130	I1130M	atA	atG	7	7	B.1.617.2	0.000026
S	1130	I1130T	aTa	aCa	5	6		0.277778
S	1130	I1130T	aTA	aCG	1	6		0.055556
S	1130	I1130I	atA	atT	6	6	AY.4	0.000009
S	1130	I1130V	Ata	Gta	6	6	AY.43	0.000027
S	1130	I1130I	atA	atT	4	6	AY.43	0.000018
S	1130	I1130I	atA	atC	2	6	AY.43	0.000009
S	1130	I1130I	atA	atT	6	6	AY.44	0.000037
S	1130	I1130V	Ata	Gta	6	6	B.1.1.7	0.000005
S	1130	I1130M	atA	atG	6	6	B.1.400.1	0.090909
S	1130	I1130T	aTa	aCa	5	5	AY.25	0.00003
S	1130	I1130I	atA	atT	5	5	AY.42	0.000201
S	1130	I1130L	Ata	Tta	5	5	B.1.1	0.000091
S	1130	I1130T	aTa	aCa	5	5	B.1.617.2	0.000019
S	1130	I1130L	AtA	CtG	2	4		0.111111
S	1130	I1130L	Ata	Tta	1	4		0.055556
S	1130	I1130L	AtA	TtG	1	4		0.055556
S	1130	I1130R	aTa	aGa	4	4	All	0.000001
S	1130	I1130L	Ata	Tta	4	4	AY.1	0.001583
S	1130	I1130L	Ata	Cta	4	4	AY.19	0.004561
S	1130	I1130L	Ata	Tta	4	4	AY.4	0.000006
S	1130	I1130M	atA	atG	4	4	AY.44	0.000024
S	1130	I1130L	Ata	Tta	3	4	AY.44	0.000018
S	1130	I1130L	Ata	Cta	1	4	AY.44	0.000006
S	1130	I1130M	atA	atG	4	4	AY.98.1	0.000194
S	1130	I1130del	ATA	---	4	4	B.1.1.7	0.000004
S	1130	I1130M	atA	atG	4	4	B.1.177	0.000053
S	1130	I1130M	atA	atG	4	4	B.1.177.73	0.002265
S	1130	I1130M	atA	atG	4	4	B.1.177.81	0.000757
S	1130	I1130L	Ata	Cta	4	4	B.1.351	0.000119
S	1130	I1130L	Ata	Tta	4	4	B.1.400	0.001716
S	1130	I1130I	atA	atC	3	4	P.1	0.000047
S	1130	I1130I	atA	atT	1	4	P.1	0.000016
S	1130	I1130E	ATA	GAG	3	3	All	0.000001
S	1130	I1130L	Ata	Tta	2	3	AY.103	0.000012
S	1130	I1130L	Ata	Cta	1	3	AY.103	0.000006
S	1130	I1130T	aTa	aCa	3	3	AY.119	0.000106
S	1130	I1130L	Ata	Cta	3	3	AY.25	0.000018
S	1130	I1130M	atA	atG	3	3	AY.25	0.000018
S	1130	I1130I	atA	atT	3	3	AY.30	0.001187
S	1130	I1130M	atA	atG	3	3	AY.39	0.000074
S	1130	I1130T	aTa	aCa	3	3	AY.39	0.000074
S	1130	I1130M	atA	atG	3	3	AY.39.1	0.000119
S	1130	I1130del	ATA	---	3	3	AY.43	0.000013
S	1130	I1130V	Ata	Gta	3	3	B.1.1.214	0.000166
S	1130	I1130L	Ata	Tta	3	3	B.1.1.519	0.000119
S	1130	I1130M	atA	atG	3	3	B.1.2	0.000026
S	1130	I1130T	aTa	aCa	3	3	Q.8	0.000495
S	1130	I1130E	ATA	GAG	2	2		0.111111
S	1130	I1130S	ATa	TCa	1	2		0.055556
S	1130	I1130S	ATA	TCG	1	2		0.055556
S	1130	I1130N	aTA	aAT	2	2	All	0
S	1130	I1130S	ATA	TCG	1	2	All	0
S	1130	I1130S	ATa	TCa	1	2	All	0
S	1130	I1130M	atA	atG	2	2	AY.102	0.000053
S	1130	I1130T	aTa	aCa	2	2	AY.103	0.000012
S	1130	I1130del	ATA	---	2	2	AY.120	0.000074
S	1130	I1130I	atA	atT	2	2	AY.120	0.000074
S	1130	I1130M	atA	atG	2	2	AY.20	0.000078
S	1130	I1130I	atA	atT	2	2	AY.23	0.000139
S	1130	I1130L	Ata	Tta	2	2	AY.3	0.00002
S	1130	I1130M	atA	atG	2	2	AY.3	0.00002
S	1130	I1130I	atA	atT	2	2	AY.33	0.000134
S	1130	I1130del	ATA	---	2	2	AY.33	0.000134
S	1130	I1130T	aTa	aCa	2	2	AY.33	0.000134
S	1130	I1130M	atA	atG	2	2	AY.36	0.000296
S	1130	I1130I	atA	atT	2	2	AY.36	0.000296
S	1130	I1130L	Ata	Tta	2	2	AY.39	0.000049
S	1130	I1130del	ATA	---	2	2	AY.4	0.000003
S	1130	I1130M	atA	atG	2	2	AY.4.2	0.000043
S	1130	I1130del	ATA	---	2	2	AY.4.5	0.000215
S	1130	I1130T	aTa	aCa	2	2	AY.44	0.000012
S	1130	I1130I	atA	atC	1	2	AY.5	0.000021
S	1130	I1130I	atA	atT	1	2	AY.5	0.000021
S	1130	I1130M	atA	atG	2	2	AY.54	0.000191
S	1130	I1130M	atA	atG	2	2	B.1.1.157	0.001826
S	1130	I1130M	atA	atG	2	2	B.1.1.413	0.013793
S	1130	I1130M	atA	atG	2	2	B.1.160	0.000062
S	1130	I1130L	Ata	Cta	2	2	B.1.177	0.000026
S	1130	I1130M	atA	atG	2	2	B.1.177.60	0.000437
S	1130	I1130T	aTa	aCa	2	2	B.1.2	0.000018
S	1130	I1130M	atA	atG	2	2	B.1.351	0.000059
S	1130	I1130V	Ata	Gta	2	2	B.1.426	0.002018
S	1130	I1130L	Ata	Tta	2	2	B.1.525	0.000226
S	1130	I1130M	atA	atG	2	2	D.2	0.00015
S	1130	I1130del	ATA	---	2	2	P.1	0.000032
S	1130	I1130M	atA	atG	2	2	P.1.14	0.000096
S	1130	I1130V	Ata	Gta	2	2	P.1.14	0.000096
S	1130	I1130I	atA	atC	1	2	P.7	0.004367
S	1130	I1130I	atA	atT	1	2	P.7	0.004367
S	1130	I1130M	atA	atG	1	1		0.055556
S	1130	I1130K	aTa	aAa	1	1	All	0
S	1130	I1130del2	aTA	a--	1	1	All	0
S	1130	I1130del1	atA	at-	1	1	All	0
S	1130	I1130I	atA	atT	1	1	AY.100	0.000046
S	1130	I1130L	Ata	Tta	1	1	AY.102	0.000027
S	1130	I1130T	aTa	aCa	1	1	AY.102	0.000027
S	1130	I1130V	Ata	Gta	1	1	AY.102	0.000027
S	1130	I1130I	atA	atT	1	1	AY.103	0.000006
S	1130	I1130R	aTa	aGa	1	1	AY.103	0.000006
S	1130	I1130V	Ata	Gta	1	1	AY.103	0.000006
S	1130	I1130del	ATA	---	1	1	AY.108	0.001103
S	1130	I1130T	aTa	aCa	1	1	AY.110	0.000113
S	1130	I1130T	aTa	aCa	1	1	AY.111	0.000183
S	1130	I1130L	Ata	Cta	1	1	AY.113	0.000142
S	1130	I1130I	atA	atC	1	1	AY.113	0.000142
S	1130	I1130M	atA	atG	1	1	AY.118	0.000063
S	1130	I1130del	ATA	---	1	1	AY.118	0.000063
S	1130	I1130M	atA	atG	1	1	AY.119	0.000035
S	1130	I1130V	Ata	Gta	1	1	AY.119	0.000035
S	1130	I1130I	atA	atT	1	1	AY.119	0.000035
S	1130	I1130T	aTa	aCa	1	1	AY.120	0.000037
S	1130	I1130T	aTa	aCa	1	1	AY.20	0.000039
S	1130	I1130V	Ata	Gta	1	1	AY.25	0.000006
S	1130	I1130del	ATA	---	1	1	AY.3	0.00001
S	1130	I1130I	atA	atT	1	1	AY.3	0.00001
S	1130	I1130V	Ata	Gta	1	1	AY.3.1	0.000085
S	1130	I1130M	atA	atG	1	1	AY.30	0.000396
S	1130	I1130M	atA	atG	1	1	AY.32	0.000532
S	1130	I1130I	atA	atT	1	1	AY.34	0.000097
S	1130	I1130I	atA	atT	1	1	AY.39.1	0.00004
S	1130	I1130V	Ata	Gta	1	1	AY.39.1	0.00004
S	1130	I1130T	aTa	aCa	1	1	AY.4.5	0.000107
S	1130	I1130L	Ata	Tta	1	1	AY.43	0.000004
S	1130	I1130T	aTa	aCa	1	1	AY.43	0.000004
S	1130	I1130V	Ata	Gta	1	1	AY.44	0.000006
S	1130	I1130R	aTa	aGa	1	1	AY.44	0.000006
S	1130	I1130V	Ata	Gta	1	1	AY.45	0.000122
S	1130	I1130I	atA	atC	1	1	AY.46.2	0.000635
S	1130	I1130T	aTa	aCa	1	1	AY.46.4	0.000165
S	1130	I1130I	atA	atT	1	1	AY.46.6	0.000072
S	1130	I1130M	atA	atG	1	1	AY.47	0.000031
S	1130	I1130T	aTa	aCa	1	1	AY.47	0.000031
S	1130	I1130V	Ata	Gta	1	1	AY.5	0.000021
S	1130	I1130T	aTa	aCa	1	1	AY.5	0.000021
S	1130	I1130M	atA	atG	1	1	AY.5.3	0.000337
S	1130	I1130M	atA	atG	1	1	AY.53	0.000288
S	1130	I1130V	Ata	Gta	1	1	AY.54	0.000095
S	1130	I1130E	ATA	GAG	1	1	AY.62	0.000436
S	1130	I1130T	aTa	aCa	1	1	AY.65	0.000533
S	1130	I1130del	ATA	---	1	1	AY.67	0.000464
S	1130	I1130T	aTa	aCa	1	1	AY.67	0.000464
S	1130	I1130T	aTa	aCa	1	1	AY.70	0.000209
S	1130	I1130V	Ata	Gta	1	1	AY.78	0.001541
S	1130	I1130R	aTa	aGa	1	1	AY.79	0.001211
S	1130	I1130L	Ata	Cta	1	1	AY.84	0.000437
S	1130	I1130del	ATA	---	1	1	AY.85	0.000427
S	1130	I1130I	atA	atC	1	1	AY.85	0.000427
S	1130	I1130del	ATA	---	1	1	AY.9	0.000068
S	1130	I1130M	atA	atG	1	1	AY.92	0.000287
S	1130	I1130M	atA	atG	1	1	AY.98	0.000079
S	1130	I1130del	ATA	---	1	1	AY.99.2	0.000092
S	1130	I1130T	aTa	aCa	1	1	B.1	0.000009
S	1130	I1130R	aTa	aGa	1	1	B.1	0.000009
S	1130	I1130N	aTA	aAT	1	1	B.1	0.000009
S	1130	I1130L	Ata	Tta	1	1	B.1	0.000009
S	1130	I1130T	aTa	aCa	1	1	B.1.1	0.000018
S	1130	I1130M	atA	atG	1	1	B.1.1	0.000018
S	1130	I1130M	atA	atG	1	1	B.1.1.1	0.000327
S	1130	I1130M	atA	atG	1	1	B.1.1.222	0.000204
S	1130	I1130T	aTa	aCa	1	1	B.1.1.283	0.023256
S	1130	I1130I	atA	atT	1	1	B.1.1.31	0.066667
S	1130	I1130M	atA	atG	1	1	B.1.1.317	0.000412
S	1130	I1130M	atA	atG	1	1	B.1.1.453	0.008475
S	1130	I1130M	atA	atG	1	1	B.1.1.519	0.00004
S	1130	I1130M	atA	atG	1	1	B.1.1.526	0.003546
S	1130	I1130del1	atA	at-	1	1	B.1.1.7	0.000001
S	1130	I1130del2	aTA	a--	1	1	B.1.1.7	0.000001
S	1130	I1130M	atA	atG	1	1	B.1.160.32	0.004292
S	1130	I1130V	Ata	Gta	1	1	B.1.177	0.000013
S	1130	I1130M	atA	atG	1	1	B.1.177.15	0.000631
S	1130	I1130M	atA	atG	1	1	B.1.177.56	0.000668
S	1130	I1130M	atA	atG	1	1	B.1.177.65	0.000665
S	1130	I1130del	ATA	---	1	1	B.1.177.7	0.000165
S	1130	I1130V	Ata	Gta	1	1	B.1.177.81	0.000189
S	1130	I1130L	Ata	Cta	1	1	B.1.2	0.000009
S	1130	I1130V	Ata	Gta	1	1	B.1.2	0.000009
S	1130	I1130L	Ata	Tta	1	1	B.1.221	0.000071
S	1130	I1130T	aTa	aCa	1	1	B.1.252	0.006623
S	1130	I1130V	Ata	Gta	1	1	B.1.258.11	0.000396
S	1130	I1130V	Ata	Gta	1	1	B.1.258.21	0.007752
S	1130	I1130M	atA	atG	1	1	B.1.336	0.002439
S	1130	I1130M	atA	atG	1	1	B.1.337	0.005587
S	1130	I1130del	ATA	---	1	1	B.1.351	0.00003
S	1130	I1130M	atA	atG	1	1	B.1.36.29	0.000517
S	1130	I1130L	Ata	Cta	1	1	B.1.369	0.000285
S	1130	I1130M	atA	atG	1	1	B.1.400	0.000429
S	1130	I1130V	Ata	Gta	1	1	B.1.422	0.000812
S	1130	I1130M	atA	atG	1	1	B.1.427	0.00005
S	1130	I1130M	atA	atG	1	1	B.1.429.1	0.012048
S	1130	I1130I	atA	atT	1	1	B.1.438.1	0.000107
S	1130	I1130T	aTa	aCa	1	1	B.1.466.2	0.000391
S	1130	I1130I	atA	atT	1	1	B.1.466.2	0.000391
S	1130	I1130del	ATA	---	1	1	B.1.561	0.000397
S	1130	I1130I	atA	atT	1	1	B.1.564	0.000426
S	1130	I1130V	Ata	Gta	1	1	B.1.568	0.001111
S	1130	I1130M	atA	atG	1	1	B.1.575	0.000303
S	1130	I1130K	aTa	aAa	1	1	B.1.595	0.000261
S	1130	I1130I	atA	atT	1	1	B.1.595	0.000261
S	1130	I1130N	aTA	aAT	1	1	B.1.595	0.000261
S	1130	I1130I	atA	atT	1	1	B.1.596	0.000087
S	1130	I1130del	ATA	---	1	1	B.1.617.2	0.000004
S	1130	I1130M	atA	atG	1	1	B.1.627	0.00202
S	1130	I1130I	atA	atC	1	1	B.1.630	0.005236
S	1130	I1130del	ATA	---	1	1	B.1.630	0.005236
S	1130	I1130L	Ata	Tta	1	1	B.1.637	0.000073
S	1130	I1130V	Ata	Gta	1	1	C.37	0.000116
S	1130	I1130del	ATA	---	1	1	C.37	0.000116
S	1130	I1130M	atA	atG	1	1	C.37	0.000116
S	1130	I1130L	Ata	Cta	1	1	D.2	0.000075
S	1130	I1130M	atA	atG	1	1	P.1	0.000016
S	1130	I1130del	ATA	---	1	1	P.1.15	0.000232
S	1130	I1130del	ATA	---	1	1	Q.8	0.000165

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.