CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1288

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	1288	T1288I	T2106I	nonsyn	aCt	aTt	4933	4929	0.999189	6581-6583
ORF1ab/nsp3	1288	T1288I	T2106I	nonsyn	aCT	aTC	4933	4	0.000810866	6581-6583
ORF1ab/nsp3	1288	T1288del	T2106del	del	ACT	---	309	309	1	6581-6583
ORF1ab/nsp3	1288	T1288S	T2106S	nonsyn	aCt	aGt	112	103	0.919643	6581-6583
ORF1ab/nsp3	1288	T1288S	T2106S	nonsyn	Act	Tct	112	6	0.0535714	6581-6583
ORF1ab/nsp3	1288	T1288S	T2106S	nonsyn	aCT	aGC	112	2	0.0178571	6581-6583
ORF1ab/nsp3	1288	T1288S	T2106S	nonsyn	AcT	TcC	112	1	0.00892857	6581-6583
ORF1ab/nsp3	1288	T1288T	T2106T	syn	acT	acC	95	67	0.705263	6581-6583
ORF1ab/nsp3	1288	T1288T	T2106T	syn	acT	acA	95	21	0.221053	6581-6583
ORF1ab/nsp3	1288	T1288T	T2106T	syn	acT	acG	95	7	0.0736842	6581-6583
ORF1ab/nsp3	1288	T1288A	T2106A	nonsyn	Act	Gct	69	68	0.985507	6581-6583
ORF1ab/nsp3	1288	T1288A	T2106A	nonsyn	AcT	GcC	69	1	0.0144928	6581-6583
ORF1ab/nsp3	1288	T1288N	T2106N	nonsyn	aCt	aAt	43	38	0.883721	6581-6583
ORF1ab/nsp3	1288	T1288N	T2106N	nonsyn	aCT	aAC	43	5	0.116279	6581-6583
ORF1ab/nsp3	1288	T1288del1	T2106del1	del	acT	ac-	12	6	0.5	6581-6583
ORF1ab/nsp3	1288	T1288del1	T2106del1	del	Act	-ct	12	4	0.333333	6581-6583
ORF1ab/nsp3	1288	T1288del1	T2106del1	del	ACt	-Mt	12	1	0.0833333	6581-6583
ORF1ab/nsp3	1288	T1288del1	T2106del1	del	aCt	a-t	12	1	0.0833333	6581-6583
ORF1ab/nsp3	1288	T1288P	T2106P	nonsyn	Act	Cct	6	6	1	6581-6583
ORF1ab/nsp3	1288	T1288L	T2106L	nonsyn	ACt	CTt	2	2	1	6581-6583
ORF1ab/nsp3	1288	T1288F	T2106F	nonsyn	ACT	TTC	2	1	0.5	6581-6583
ORF1ab/nsp3	1288	T1288F	T2106F	nonsyn	ACt	TTt	2	1	0.5	6581-6583
ORF1ab/nsp3	1288	T1288del2	T2106del2	del	ACt	--t	1	1	1	6581-6583
ORF1ab/nsp3	1288	T1288V	T2106V	nonsyn	ACt	GTt	1	1	1	6581-6583

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	1288	T1288I	aCt	aTt	4929	4933	All	0.000943
ORF1ab/nsp3	1288	T1288I	aCT	aTC	4	4933	All	0.000001
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1158	1158	AY.4	0.001802
ORF1ab/nsp3	1288	T1288I	aCt	aTt	874	874	B.1.1.7	0.000782
ORF1ab/nsp3	1288	T1288I	aCt	aTt	312	312	B.1.258	0.020763
ORF1ab/nsp3	1288	T1288del	ACT	---	309	309	All	0.000059
ORF1ab/nsp3	1288	T1288I	aCt	aTt	213	213	B.1.2	0.001876
ORF1ab/nsp3	1288	T1288I	aCt	aTt	194	194	AY.4.2.1	0.028903
ORF1ab/nsp3	1288	T1288I	aCt	aTt	188	188	AY.103	0.001167
ORF1ab/nsp3	1288	T1288I	aCt	aTt	136	136	B.1.617.2	0.000512
ORF1ab/nsp3	1288	T1288del	ACT	---	127	127	B.1.1.7	0.000114
ORF1ab/nsp3	1288	T1288I	aCt	aTt	124	124	P.1	0.001953
ORF1ab/nsp3	1288	T1288I	aCt	aTt	117	117	AY.43	0.000518
ORF1ab/nsp3	1288	T1288I	aCt	aTt	115	115	AY.44	0.0007
ORF1ab/nsp3	1288	T1288S	aCt	aGt	103	112	All	0.00002
ORF1ab/nsp3	1288	T1288S	Act	Tct	6	112	All	0.000001
ORF1ab/nsp3	1288	T1288S	aCT	aGC	2	112	All	0
ORF1ab/nsp3	1288	T1288S	AcT	TcC	1	112	All	0
ORF1ab/nsp3	1288	T1288S	aCt	aGt	100	101	AY.3	0.000995
ORF1ab/nsp3	1288	T1288S	Act	Tct	1	101	AY.3	0.00001
ORF1ab/nsp3	1288	T1288T	acT	acC	67	95	All	0.000013
ORF1ab/nsp3	1288	T1288T	acT	acA	21	95	All	0.000004
ORF1ab/nsp3	1288	T1288T	acT	acG	7	95	All	0.000001
ORF1ab/nsp3	1288	T1288I	aCt	aTt	91	91	AY.75	0.005098
ORF1ab/nsp3	1288	T1288I	aCt	aTt	85	85	B.1.1.134	0.965909
ORF1ab/nsp3	1288	T1288I	aCt	aTt	85	85	B.1.377	0.388128
ORF1ab/nsp3	1288	T1288A	Act	Gct	68	69	All	0.000013
ORF1ab/nsp3	1288	T1288A	AcT	GcC	1	69	All	0
ORF1ab/nsp3	1288	T1288I	aCt	aTt	63	63	B.1.177	0.00083
ORF1ab/nsp3	1288	T1288I	aCt	aTt	63	63	B.1.221	0.004475
ORF1ab/nsp3	1288	T1288I	aCt	aTt	63	63	B.1.369	0.017969
ORF1ab/nsp3	1288	T1288I	aCt	aTt	60	60	AY.102	0.001591
ORF1ab/nsp3	1288	T1288I	aCt	aTt	55	55	AY.27	0.00356
ORF1ab/nsp3	1288	T1288I	aCt	aTt	50	50	B.1.1.519	0.001986
ORF1ab/nsp3	1288	T1288I	aCt	aTt	48	48	AY.3	0.000477
ORF1ab/nsp3	1288	T1288I	aCt	aTt	47	47	B.1.160.21	0.959184
ORF1ab/nsp3	1288	T1288I	aCt	aTt	45	46	B.1	0.000412
ORF1ab/nsp3	1288	T1288I	aCT	aTC	1	46	B.1	0.000009
ORF1ab/nsp3	1288	T1288N	aCt	aAt	38	43	All	0.000007
ORF1ab/nsp3	1288	T1288N	aCT	aAC	5	43	All	0.000001
ORF1ab/nsp3	1288	T1288del	ACT	---	40	40	AY.26	0.001132
ORF1ab/nsp3	1288	T1288I	aCt	aTt	32	32	AY.4.5	0.00344
ORF1ab/nsp3	1288	T1288I	aCt	aTt	32	32	P.1.1	0.010165
ORF1ab/nsp3	1288	T1288I	aCt	aTt	28	28	AY.25	0.000168
ORF1ab/nsp3	1288	T1288I	aCt	aTt	28	28	B.1.1	0.000508
ORF1ab/nsp3	1288	T1288A	Act	Gct	28	28	B.1.177	0.000369
ORF1ab/nsp3	1288	T1288I	aCt	aTt	26	26	AY.20	0.00101
ORF1ab/nsp3	1288	T1288T	acT	acA	11	23	B.1.1.7	0.00001
ORF1ab/nsp3	1288	T1288T	acT	acC	11	23	B.1.1.7	0.00001
ORF1ab/nsp3	1288	T1288T	acT	acG	1	23	B.1.1.7	0.000001
ORF1ab/nsp3	1288	T1288I	aCt	aTt	20	20	B.1.110.3	0.014368
ORF1ab/nsp3	1288	T1288I	aCt	aTt	20	20	B.1.234	0.002639
ORF1ab/nsp3	1288	T1288I	aCt	aTt	20	20	B.1.324	0.032103
ORF1ab/nsp3	1288	T1288I	aCt	aTt	20	20	B.1.526	0.00047
ORF1ab/nsp3	1288	T1288del	ACT	---	19	19	B.1.177	0.00025
ORF1ab/nsp3	1288	T1288N	aCt	aAt	17	17	AY.4	0.000026
ORF1ab/nsp3	1288	T1288I	aCt	aTt	17	17	AY.47	0.000529
ORF1ab/nsp3	1288	T1288A	Act	Gct	16	16	B.1.1.7	0.000014
ORF1ab/nsp3	1288	T1288I	aCt	aTt	16	16	B.1.429	0.000376
ORF1ab/nsp3	1288	T1288del	ACT	---	15	15	AY.4	0.000023
ORF1ab/nsp3	1288	T1288I	aCt	aTt	15	15	AY.4.2	0.000325
ORF1ab/nsp3	1288	T1288I	aCt	aTt	14	14	AY.39	0.000346
ORF1ab/nsp3	1288	T1288I	aCt	aTt	14	14	B.1.621	0.001239
ORF1ab/nsp3	1288	T1288I	aCt	aTt	13	13	AY.26	0.000368
ORF1ab/nsp3	1288	T1288del1	acT	ac-	6	12	All	0.000001
ORF1ab/nsp3	1288	T1288del1	Act	-ct	4	12	All	0.000001
ORF1ab/nsp3	1288	T1288del1	ACt	-Mt	1	12	All	0
ORF1ab/nsp3	1288	T1288del1	aCt	a-t	1	12	All	0
ORF1ab/nsp3	1288	T1288I	aCt	aTt	12	12	AY.39.1	0.000475
ORF1ab/nsp3	1288	T1288I	aCt	aTt	12	12	B.1.427	0.000606
ORF1ab/nsp3	1288	T1288I	aCt	aTt	12	12	N.4	0.051064
ORF1ab/nsp3	1288	T1288I	aCt	aTt	11	11	B.1.177.75	0.011446
ORF1ab/nsp3	1288	T1288I	aCt	aTt	10	10	AY.118	0.000626
ORF1ab/nsp3	1288	T1288I	aCt	aTt	10	10	B.1.160	0.000312
ORF1ab/nsp3	1288	T1288I	aCt	aTt	10	10	B.1.351	0.000297
ORF1ab/nsp3	1288	T1288I	aCt	aTt	10	10	B.1.577	0.006873
ORF1ab/nsp3	1288	T1288I	aCt	aTt	10	10	B.1.628	0.003524
ORF1ab/nsp3	1288	T1288I	aCt	aTt	10	10	C.37	0.001161
ORF1ab/nsp3	1288	T1288I	aCt	aTt	9	9	B.1.596	0.000784
ORF1ab/nsp3	1288	T1288I	aCt	aTt	9	9	Q.1	0.001137
ORF1ab/nsp3	1288	T1288del	ACT	---	8	8	AY.4.5	0.00086
ORF1ab/nsp3	1288	T1288A	Act	Gct	7	8	AY.44	0.000043
ORF1ab/nsp3	1288	T1288A	AcT	GcC	1	8	AY.44	0.000006
ORF1ab/nsp3	1288	T1288I	aCt	aTt	8	8	AY.5	0.000165
ORF1ab/nsp3	1288	T1288I	aCt	aTt	8	8	R.1	0.00072
ORF1ab/nsp3	1288	T1288del	ACT	---	7	7	AY.43	0.000031
ORF1ab/nsp3	1288	T1288T	acT	acC	6	7	AY.44	0.000037
ORF1ab/nsp3	1288	T1288T	acT	acA	1	7	AY.44	0.000006
ORF1ab/nsp3	1288	T1288I	aCt	aTt	7	7	B.1.243	0.000487
ORF1ab/nsp3	1288	T1288I	aCt	aTt	7	7	B.1.346	0.009174
ORF1ab/nsp3	1288	T1288del	ACT	---	7	7	B.1.617.2	0.000026
ORF1ab/nsp3	1288	T1288I	aCt	aTt	3	6		0.166667
ORF1ab/nsp3	1288	T1288I	aCT	aTC	3	6		0.166667
ORF1ab/nsp3	1288	T1288P	Act	Cct	6	6	All	0.000001
ORF1ab/nsp3	1288	T1288T	acT	acA	6	6	AY.25	0.000036
ORF1ab/nsp3	1288	T1288I	aCt	aTt	6	6	AY.45	0.00073
ORF1ab/nsp3	1288	T1288I	aCt	aTt	6	6	B.1.1.28	0.001867
ORF1ab/nsp3	1288	T1288I	aCt	aTt	6	6	B.1.1.398	0.019355
ORF1ab/nsp3	1288	T1288I	aCt	aTt	6	6	B.1.306	0.034286
ORF1ab/nsp3	1288	T1288I	aCt	aTt	6	6	B.1.466.2	0.002347
ORF1ab/nsp3	1288	T1288I	aCt	aTt	5	5	AY.104	0.009921
ORF1ab/nsp3	1288	T1288I	aCt	aTt	5	5	AY.119	0.000177
ORF1ab/nsp3	1288	T1288N	aCt	aAt	5	5	AY.3	0.00005
ORF1ab/nsp3	1288	T1288I	aCt	aTt	5	5	AY.79	0.006053
ORF1ab/nsp3	1288	T1288T	acT	acG	2	5	B.1	0.000018
ORF1ab/nsp3	1288	T1288T	acT	acC	2	5	B.1	0.000018
ORF1ab/nsp3	1288	T1288T	acT	acA	1	5	B.1	0.000009
ORF1ab/nsp3	1288	T1288I	aCt	aTt	5	5	B.1.1.214	0.000277
ORF1ab/nsp3	1288	T1288I	aCt	aTt	5	5	B.1.1.222	0.00102
ORF1ab/nsp3	1288	T1288T	acT	acC	5	5	B.1.36	0.00073
ORF1ab/nsp3	1288	T1288I	aCt	aTt	5	5	B.1.617.1	0.000645
ORF1ab/nsp3	1288	T1288T	acT	acC	4	5	B.1.617.2	0.000015
ORF1ab/nsp3	1288	T1288T	acT	acA	1	5	B.1.617.2	0.000004
ORF1ab/nsp3	1288	T1288I	aCt	aTt	5	5	B.1.619	0.004355
ORF1ab/nsp3	1288	T1288S	aCT	aGC	2	4		0.111111
ORF1ab/nsp3	1288	T1288S	Act	Tct	1	4		0.055556
ORF1ab/nsp3	1288	T1288S	AcT	TcC	1	4		0.055556
ORF1ab/nsp3	1288	T1288I	aCt	aTt	4	4	A.23.1	0.002817
ORF1ab/nsp3	1288	T1288I	aCt	aTt	4	4	AY.4.4	0.001637
ORF1ab/nsp3	1288	T1288T	acT	acC	3	4	AY.43	0.000013
ORF1ab/nsp3	1288	T1288T	acT	acG	1	4	AY.43	0.000004
ORF1ab/nsp3	1288	T1288I	aCt	aTt	4	4	AY.61	0.000419
ORF1ab/nsp3	1288	T1288I	aCt	aTt	4	4	AY.98	0.000316
ORF1ab/nsp3	1288	T1288I	aCt	aTt	4	4	AY.99.2	0.000369
ORF1ab/nsp3	1288	T1288del	ACT	---	4	4	B.1.1	0.000073
ORF1ab/nsp3	1288	T1288I	aCt	aTt	4	4	B.1.1.297	0.008949
ORF1ab/nsp3	1288	T1288I	aCt	aTt	4	4	B.1.177.21	0.000306
ORF1ab/nsp3	1288	T1288I	aCt	aTt	4	4	B.1.36	0.000584
ORF1ab/nsp3	1288	T1288I	aCt	aTt	4	4	B.1.36.16	0.005698
ORF1ab/nsp3	1288	T1288N	aCt	aAt	4	4	B.1.617.2	0.000015
ORF1ab/nsp3	1288	T1288I	aCt	aTt	4	4	P.1.14	0.000191
ORF1ab/nsp3	1288	T1288I	aCt	aTt	3	3	AY.100	0.000138
ORF1ab/nsp3	1288	T1288T	acT	acC	3	3	AY.103	0.000019
ORF1ab/nsp3	1288	T1288I	aCt	aTt	3	3	AY.106	0.001005
ORF1ab/nsp3	1288	T1288I	aCt	aTt	3	3	AY.113	0.000427
ORF1ab/nsp3	1288	T1288I	aCt	aTt	3	3	AY.117	0.000254
ORF1ab/nsp3	1288	T1288I	aCt	aTt	3	3	AY.120	0.000112
ORF1ab/nsp3	1288	T1288I	aCt	aTt	3	3	AY.34	0.000291
ORF1ab/nsp3	1288	T1288T	acT	acC	3	3	AY.4	0.000005
ORF1ab/nsp3	1288	T1288I	aCt	aTt	3	3	AY.42	0.000121
ORF1ab/nsp3	1288	T1288P	Act	Cct	3	3	AY.43	0.000013
ORF1ab/nsp3	1288	T1288I	aCt	aTt	3	3	AY.86	0.00249
ORF1ab/nsp3	1288	T1288I	aCt	aTt	3	3	AY.91	0.002191
ORF1ab/nsp3	1288	T1288del	ACT	---	3	3	B.1	0.000027
ORF1ab/nsp3	1288	T1288N	aCt	aAt	2	3	B.1.1	0.000036
ORF1ab/nsp3	1288	T1288N	aCT	aAC	1	3	B.1.1	0.000018
ORF1ab/nsp3	1288	T1288del	ACT	---	3	3	B.1.1.1	0.00098
ORF1ab/nsp3	1288	T1288I	aCt	aTt	3	3	B.1.1.318	0.000905
ORF1ab/nsp3	1288	T1288del	ACT	---	3	3	B.1.177.7	0.000495
ORF1ab/nsp3	1288	T1288I	aCt	aTt	3	3	B.1.258.17	0.000312
ORF1ab/nsp3	1288	T1288I	aCt	aTt	3	3	B.1.309	0.142857
ORF1ab/nsp3	1288	T1288del	ACT	---	3	3	B.1.36.17	0.001482
ORF1ab/nsp3	1288	T1288I	aCt	aTt	3	3	P.1.7	0.000958
ORF1ab/nsp3	1288	T1288L	ACt	CTt	2	2		0.111111
ORF1ab/nsp3	1288	T1288N	aCT	aAC	2	2		0.111111
ORF1ab/nsp3	1288	T1288F	ACt	TTt	1	2		0.055556
ORF1ab/nsp3	1288	T1288F	ACT	TTC	1	2		0.055556
ORF1ab/nsp3	1288	T1288L	ACt	CTt	2	2	All	0
ORF1ab/nsp3	1288	T1288F	ACT	TTC	1	2	All	0
ORF1ab/nsp3	1288	T1288F	ACt	TTt	1	2	All	0
ORF1ab/nsp3	1288	T1288A	Act	Gct	2	2	AY.103	0.000012
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	AY.116	0.000574
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	AY.14	0.000176
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	AY.19	0.002281
ORF1ab/nsp3	1288	T1288del	ACT	---	2	2	AY.19	0.002281
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	AY.23	0.000139
ORF1ab/nsp3	1288	T1288del	ACT	---	2	2	AY.25	0.000012
ORF1ab/nsp3	1288	T1288A	Act	Gct	2	2	AY.29	0.000032
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	AY.29	0.000032
ORF1ab/nsp3	1288	T1288T	acT	acC	2	2	AY.3	0.00002
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	AY.33	0.000134
ORF1ab/nsp3	1288	T1288N	aCt	aAt	2	2	AY.39	0.000049
ORF1ab/nsp3	1288	T1288T	acT	acC	2	2	AY.39.1	0.000079
ORF1ab/nsp3	1288	T1288del1	acT	ac-	1	2	AY.4	0.000002
ORF1ab/nsp3	1288	T1288del1	Act	-ct	1	2	AY.4	0.000002
ORF1ab/nsp3	1288	T1288T	acT	acC	2	2	AY.42	0.00008
ORF1ab/nsp3	1288	T1288N	aCt	aAt	2	2	AY.43	0.000009
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	AY.46.6	0.000144
ORF1ab/nsp3	1288	T1288del	ACT	---	2	2	AY.5	0.000041
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	AY.51	0.001818
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	AY.54	0.000191
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	AY.63	0.000774
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	AY.74	0.000231
ORF1ab/nsp3	1288	T1288del	ACT	---	2	2	AY.75.1	0.000361
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	AY.84	0.000875
ORF1ab/nsp3	1288	T1288del	ACT	---	2	2	AY.9	0.000135
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	AY.90	0.001369
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	AY.98.1	0.000097
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	B.1.1.311	0.000716
ORF1ab/nsp3	1288	T1288del	ACT	---	2	2	B.1.1.37	0.000386
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	B.1.1.420	0.002012
ORF1ab/nsp3	1288	T1288N	aCT	aAC	2	2	B.1.1.7	0.000002
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	B.1.1.70	0.000682
ORF1ab/nsp3	1288	T1288del	ACT	---	2	2	B.1.160	0.000062
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	B.1.177.12	0.000303
ORF1ab/nsp3	1288	T1288del	ACT	---	2	2	B.1.177.4	0.000422
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	B.1.177.73	0.001133
ORF1ab/nsp3	1288	T1288del1	Act	-ct	1	2	B.1.2	0.000009
ORF1ab/nsp3	1288	T1288del1	aCt	a-t	1	2	B.1.2	0.000009
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	B.1.289	0.005319
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	B.1.351.2	0.000605
ORF1ab/nsp3	1288	T1288T	acT	acC	2	2	B.1.351.3	0.001753
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	B.1.525	0.000226
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	B.1.561	0.000794
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	B.1.623	0.001073
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	B.1.637	0.000146
ORF1ab/nsp3	1288	T1288T	acT	acC	2	2	D.2	0.00015
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	D.2	0.00015
ORF1ab/nsp3	1288	T1288T	acT	acC	1	2	P.1	0.000016
ORF1ab/nsp3	1288	T1288T	acT	acG	1	2	P.1	0.000016
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	P.1.4	0.001953
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	P.2	0.000373
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	P.7	0.008734
ORF1ab/nsp3	1288	T1288I	aCt	aTt	2	2	Q.8	0.00033
ORF1ab/nsp3	1288	T1288T	acT	acC	1	1		0.055556
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	A.2.5	0.000499
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	A.3	0.002096
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	AD.2	0.000219
ORF1ab/nsp3	1288	T1288V	ACt	GTt	1	1	All	0
ORF1ab/nsp3	1288	T1288del2	ACt	--t	1	1	All	0
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	AU.2	0.002421
ORF1ab/nsp3	1288	T1288T	acT	acC	1	1	AY.106	0.000335
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	AY.109	0.00074
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	AY.113	0.000142
ORF1ab/nsp3	1288	T1288T	acT	acG	1	1	AY.113	0.000142
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	AY.114	0.000231
ORF1ab/nsp3	1288	T1288N	aCt	aAt	1	1	AY.118	0.000063
ORF1ab/nsp3	1288	T1288N	aCt	aAt	1	1	AY.119	0.000035
ORF1ab/nsp3	1288	T1288S	aCt	aGt	1	1	AY.119	0.000035
ORF1ab/nsp3	1288	T1288T	acT	acC	1	1	AY.119	0.000035
ORF1ab/nsp3	1288	T1288P	Act	Cct	1	1	AY.119	0.000035
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	AY.12	0.000316
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	AY.120	0.000037
ORF1ab/nsp3	1288	T1288T	acT	acC	1	1	AY.14	0.000088
ORF1ab/nsp3	1288	T1288T	acT	acA	1	1	AY.23	0.00007
ORF1ab/nsp3	1288	T1288A	Act	Gct	1	1	AY.25	0.000006
ORF1ab/nsp3	1288	T1288T	acT	acC	1	1	AY.37	0.000316
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	AY.38	0.000499
ORF1ab/nsp3	1288	T1288T	acT	acC	1	1	AY.39	0.000025
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	AY.39.2	0.001541
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	AY.4.1	0.000737
ORF1ab/nsp3	1288	T1288A	Act	Gct	1	1	AY.4.2	0.000022
ORF1ab/nsp3	1288	T1288del1	Act	-ct	1	1	AY.4.5	0.000107
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	AY.40	0.000964
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	AY.44	0.000006
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	AY.46.2	0.000635
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	AY.46.4	0.000165
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	AY.46.5	0.000198
ORF1ab/nsp3	1288	T1288N	aCt	aAt	1	1	AY.46.6	0.000072
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	AY.47	0.000031
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	AY.5.4	0.000277
ORF1ab/nsp3	1288	T1288T	acT	acC	1	1	AY.50	0.000799
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	AY.59	0.00053
ORF1ab/nsp3	1288	T1288A	Act	Gct	1	1	AY.6	0.000041
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	AY.6	0.000041
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	AY.60	0.000938
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	AY.60	0.000938
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	AY.62	0.000436
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	AY.68	0.000274
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	AY.7	0.000196
ORF1ab/nsp3	1288	T1288T	acT	acC	1	1	AY.70	0.000209
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	AY.71	0.000475
ORF1ab/nsp3	1288	T1288del1	acT	ac-	1	1	AY.75	0.000056
ORF1ab/nsp3	1288	T1288A	Act	Gct	1	1	AY.75	0.000056
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	AY.77	0.001127
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	AY.84	0.000437
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	AY.87	0.000833
ORF1ab/nsp3	1288	T1288A	Act	Gct	1	1	AY.88	0.000884
ORF1ab/nsp3	1288	T1288T	acT	acC	1	1	AY.9.1	0.000084
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	AY.9.2	0.000037
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	AY.92	0.000287
ORF1ab/nsp3	1288	T1288T	acT	acC	1	1	AY.95	0.000761
ORF1ab/nsp3	1288	T1288T	acT	acG	1	1	AY.99	0.001049
ORF1ab/nsp3	1288	T1288del1	acT	ac-	1	1	B	0.000128
ORF1ab/nsp3	1288	T1288A	Act	Gct	1	1	B.1	0.000009
ORF1ab/nsp3	1288	T1288P	Act	Cct	1	1	B.1	0.000009
ORF1ab/nsp3	1288	T1288del1	acT	ac-	1	1	B.1	0.000009
ORF1ab/nsp3	1288	T1288S	aCt	aGt	1	1	B.1.1	0.000018
ORF1ab/nsp3	1288	T1288A	Act	Gct	1	1	B.1.1	0.000018
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.1.128	0.007092
ORF1ab/nsp3	1288	T1288T	acT	acC	1	1	B.1.1.129	0.009174
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.1.141	0.002012
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.1.170	0.001247
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.1.220	0.001859
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.1.221	0.010101
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.1.243	0.004082
ORF1ab/nsp3	1288	T1288T	acT	acC	1	1	B.1.1.25	0.000569
ORF1ab/nsp3	1288	T1288S	Act	Tct	1	1	B.1.1.257	0.009709
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.1.258	0.003257
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.1.277	0.000759
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.1.291	0.000742
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.1.306	0.000438
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.1.311	0.000358
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.1.312	0.001912
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.1.317	0.000412
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.1.33	0.000421
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.1.348	0.000796
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.1.361	0.045455
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.1.37	0.000193
ORF1ab/nsp3	1288	T1288T	acT	acC	1	1	B.1.1.385	0.004464
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.1.39	0.00051
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.1.39	0.00051
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.1.409	0.002833
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.1.44	0.00241
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.1.487	0.005587
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.1.51	0.001718
ORF1ab/nsp3	1288	T1288N	aCt	aAt	1	1	B.1.1.519	0.00004
ORF1ab/nsp3	1288	T1288S	Act	Tct	1	1	B.1.1.63	0.000386
ORF1ab/nsp3	1288	T1288S	Act	Tct	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1288	T1288del1	acT	ac-	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1288	T1288P	Act	Cct	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1288	T1288del2	ACt	--t	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1288	T1288V	ACt	GTt	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.1.70	0.000341
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.112	0.005181
ORF1ab/nsp3	1288	T1288S	Act	Tct	1	1	B.1.160	0.000031
ORF1ab/nsp3	1288	T1288del1	ACt	-Mt	1	1	B.1.177	0.000013
ORF1ab/nsp3	1288	T1288T	acT	acC	1	1	B.1.177	0.000013
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.177.11	0.001698
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.177.15	0.000631
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.177.16	0.000664
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.177.17	0.000821
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.177.31	0.011494
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.177.51	0.004566
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.177.52	0.001757
ORF1ab/nsp3	1288	T1288A	Act	Gct	1	1	B.1.177.53	0.002392
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.177.56	0.000668
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.177.60	0.000218
ORF1ab/nsp3	1288	T1288del1	Act	-ct	1	1	B.1.177.63	0.002703
ORF1ab/nsp3	1288	T1288A	Act	Gct	1	1	B.1.177.7	0.000165
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.177.81	0.000189
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.177.86	0.000183
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.177.87	0.000728
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.177.9	0.001332
ORF1ab/nsp3	1288	T1288N	aCt	aAt	1	1	B.1.2	0.000009
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.2	0.000009
ORF1ab/nsp3	1288	T1288A	Act	Gct	1	1	B.1.2	0.000009
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.206	0.000816
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.221	0.000071
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.221.1	0.002907
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.221.1	0.002907
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.258	0.000067
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.258.10	0.011364
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.258.21	0.007752
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.279	0.000514
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.314	0.007519
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.340	0.004292
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.349	0.000715
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.35	0.008475
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.36.17	0.000494
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.36.18	0.00042
ORF1ab/nsp3	1288	T1288A	Act	Gct	1	1	B.1.36.27	0.000763
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.36.29	0.000517
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.36.39	0.002217
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.36.8	0.001
ORF1ab/nsp3	1288	T1288T	acT	acC	1	1	B.1.377	0.004566
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.389	0.001002
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.409	0.000781
ORF1ab/nsp3	1288	T1288del1	acT	ac-	1	1	B.1.409	0.000781
ORF1ab/nsp3	1288	T1288T	acT	acC	1	1	B.1.429	0.000024
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.452	0.013699
ORF1ab/nsp3	1288	T1288T	acT	acC	1	1	B.1.456	0.003268
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.470	0.001404
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.491	0.052632
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.499	0.00105
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.509	0.000866
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.526	0.000024
ORF1ab/nsp3	1288	T1288T	acT	acC	1	1	B.1.548	0.035714
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.564	0.000426
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.575	0.000303
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.576	0.000907
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.585	0.027778
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.588	0.00091
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.1.595	0.000261
ORF1ab/nsp3	1288	T1288S	aCt	aGt	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1288	T1288A	Act	Gct	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.617.3	0.002985
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.621	0.000089
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.1.630	0.005236
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.11	0.005128
ORF1ab/nsp3	1288	T1288N	aCt	aAt	1	1	B.23	0.002924
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	B.34	0.013699
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	B.55	0.00295
ORF1ab/nsp3	1288	T1288A	Act	Gct	1	1	C.37	0.000116
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	C.4	0.01
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	L.2	0.011364
ORF1ab/nsp3	1288	T1288T	acT	acC	1	1	N.5	0.001767
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	P.1	0.000016
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	P.1.10	0.000269
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	P.1.12	0.000484
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	P.1.15	0.000232
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	P.1.17	0.000162
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	P.1.17.1	0.000875
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	P.3	0.001595
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	Q.1	0.000126
ORF1ab/nsp3	1288	T1288del	ACT	---	1	1	U.3	0.003861
ORF1ab/nsp3	1288	T1288I	aCt	aTt	1	1	Y.1	0.012821

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.