CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 749

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	749	T749I	T1567I	nonsyn	aCt	aTt	15005	15003	0.999867	4964-4966
ORF1ab/nsp3	749	T749I	T1567I	nonsyn	aCT	aTC	15005	2	0.000133289	4964-4966
ORF1ab/nsp3	749	T749A	T1567A	nonsyn	Act	Gct	9905	9903	0.999798	4964-4966
ORF1ab/nsp3	749	T749A	T1567A	nonsyn	AcT	GcC	9905	1	0.000100959	4964-4966
ORF1ab/nsp3	749	T749A	T1567A	nonsyn	AcT	GcA	9905	1	0.000100959	4964-4966
ORF1ab/nsp3	749	T749T	T1567T	syn	acT	acC	273	266	0.974359	4964-4966
ORF1ab/nsp3	749	T749T	T1567T	syn	acT	acA	273	6	0.021978	4964-4966
ORF1ab/nsp3	749	T749T	T1567T	syn	acT	acG	273	1	0.003663	4964-4966
ORF1ab/nsp3	749	T749N	T1567N	nonsyn	aCt	aAt	78	76	0.974359	4964-4966
ORF1ab/nsp3	749	T749N	T1567N	nonsyn	aCT	aAC	78	2	0.025641	4964-4966
ORF1ab/nsp3	749	T749del	T1567del	del	ACT	---	39	39	1	4964-4966
ORF1ab/nsp3	749	T749V	T1567V	nonsyn	ACt	GTt	27	27	1	4964-4966
ORF1ab/nsp3	749	T749del1	T1567del1	del	aCt	a-t	15	10	0.666667	4964-4966
ORF1ab/nsp3	749	T749del1	T1567del1	del	acT	ac-	15	4	0.266667	4964-4966
ORF1ab/nsp3	749	T749del1	T1567del1	del	ACt	-Tt	15	1	0.0666667	4964-4966
ORF1ab/nsp3	749	T749S	T1567S	nonsyn	Act	Tct	9	5	0.555556	4964-4966
ORF1ab/nsp3	749	T749S	T1567S	nonsyn	AcT	TcC	9	2	0.222222	4964-4966
ORF1ab/nsp3	749	T749S	T1567S	nonsyn	AcT	TcA	9	1	0.111111	4964-4966
ORF1ab/nsp3	749	T749S	T1567S	nonsyn	aCt	aGt	9	1	0.111111	4964-4966
ORF1ab/nsp3	749	T749D	T1567D	nonsyn	ACT	GAC	5	3	0.6	4964-4966
ORF1ab/nsp3	749	T749D	T1567D	nonsyn	ACt	GAt	5	2	0.4	4964-4966
ORF1ab/nsp3	749	T749Y	T1567Y	nonsyn	ACt	TAt	4	3	0.75	4964-4966
ORF1ab/nsp3	749	T749Y	T1567Y	nonsyn	ACT	TAC	4	1	0.25	4964-4966
ORF1ab/nsp3	749	T749F	T1567F	nonsyn	ACT	TTC	2	1	0.5	4964-4966
ORF1ab/nsp3	749	T749F	T1567F	nonsyn	ACt	TTt	2	1	0.5	4964-4966
ORF1ab/nsp3	749	T749X	T1567X	nonsyn	ACT	TAA	1	1	1	4964-4966
ORF1ab/nsp3	749	T749E	T1567E	nonsyn	ACT	GAA	1	1	1	4964-4966
ORF1ab/nsp3	749	T749K	T1567K	nonsyn	aCT	aAA	1	1	1	4964-4966
ORF1ab/nsp3	749	T749del2	T1567del2	del	aCT	a--	1	1	1	4964-4966
ORF1ab/nsp3	749	T749P	T1567P	nonsyn	Act	Cct	1	1	1	4964-4966
ORF1ab/nsp3	749	T749L	T1567L	nonsyn	ACt	CTt	1	1	1	4964-4966

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	749	T749I	aCt	aTt	15003	15005	All	0.00287
ORF1ab/nsp3	749	T749I	aCT	aTC	2	15005	All	0
ORF1ab/nsp3	749	T749A	Act	Gct	9903	9905	All	0.001894
ORF1ab/nsp3	749	T749A	AcT	GcA	1	9905	All	0
ORF1ab/nsp3	749	T749A	AcT	GcC	1	9905	All	0
ORF1ab/nsp3	749	T749A	Act	Gct	7726	7726	B.1.1.7	0.006916
ORF1ab/nsp3	749	T749I	aCt	aTt	7464	7464	B.1.617.1	0.9626
ORF1ab/nsp3	749	T749I	aCt	aTt	2111	2111	B.1.1.7	0.00189
ORF1ab/nsp3	749	T749A	Act	Gct	2073	2073	Q.4	0.942701
ORF1ab/nsp3	749	T749I	aCt	aTt	1121	1121	B.1.367	0.888273
ORF1ab/nsp3	749	T749I	aCt	aTt	541	541	B.1.617.2	0.002037
ORF1ab/nsp3	749	T749I	aCt	aTt	495	495	AY.3	0.004923
ORF1ab/nsp3	749	T749I	aCt	aTt	415	415	B.1.620	0.392621
ORF1ab/nsp3	749	T749I	aCt	aTt	279	279	B.1	0.002556
ORF1ab/nsp3	749	T749I	aCt	aTt	277	277	AY.4	0.000431
ORF1ab/nsp3	749	T749T	acT	acC	266	273	All	0.000051
ORF1ab/nsp3	749	T749T	acT	acA	6	273	All	0.000001
ORF1ab/nsp3	749	T749T	acT	acG	1	273	All	0
ORF1ab/nsp3	749	T749I	aCt	aTt	165	165	AY.5.4	0.045656
ORF1ab/nsp3	749	T749I	aCt	aTt	152	152	AY.43	0.000673
ORF1ab/nsp3	749	T749T	acT	acC	130	130	AY.43	0.000576
ORF1ab/nsp3	749	T749I	aCt	aTt	112	112	B.1.1.133	0.949153
ORF1ab/nsp3	749	T749I	aCt	aTt	109	109	AA.7	1
ORF1ab/nsp3	749	T749I	aCt	aTt	96	96	B.1.234	0.012667
ORF1ab/nsp3	749	T749I	aCt	aTt	90	90	AY.103	0.000559
ORF1ab/nsp3	749	T749I	aCt	aTt	85	85	P.1	0.001339
ORF1ab/nsp3	749	T749I	aCt	aTt	81	81	AY.25	0.000487
ORF1ab/nsp3	749	T749N	aCt	aAt	76	78	All	0.000015
ORF1ab/nsp3	749	T749N	aCT	aAC	2	78	All	0
ORF1ab/nsp3	749	T749I	aCt	aTt	75	75	B.1.2	0.00066
ORF1ab/nsp3	749	T749I	aCt	aTt	71	71	B.1.177	0.000935
ORF1ab/nsp3	749	T749T	acT	acC	68	68	AY.4.2	0.001475
ORF1ab/nsp3	749	T749I	aCt	aTt	52	52	AY.44	0.000317
ORF1ab/nsp3	749	T749I	aCt	aTt	46	46	A.23.1	0.032394
ORF1ab/nsp3	749	T749I	aCt	aTt	41	41	B.1.1	0.000744
ORF1ab/nsp3	749	T749A	Act	Gct	40	40	Q.8	0.006596
ORF1ab/nsp3	749	T749del	ACT	---	39	39	All	0.000007
ORF1ab/nsp3	749	T749I	aCt	aTt	35	35	AY.99.2	0.003226
ORF1ab/nsp3	749	T749I	aCt	aTt	33	33	AY.26	0.000934
ORF1ab/nsp3	749	T749I	aCt	aTt	32	32	AY.101	0.015694
ORF1ab/nsp3	749	T749A	Act	Gct	29	29	B.1.1	0.000526
ORF1ab/nsp3	749	T749I	aCt	aTt	29	29	B.1.1.1	0.009474
ORF1ab/nsp3	749	T749I	aCt	aTt	29	29	B.1.1.373	0.690476
ORF1ab/nsp3	749	T749I	aCt	aTt	28	28	B.1.177.15	0.017666
ORF1ab/nsp3	749	T749V	ACt	GTt	27	27	All	0.000005
ORF1ab/nsp3	749	T749V	ACt	GTt	27	27	B.1.1.7	0.000024
ORF1ab/nsp3	749	T749I	aCt	aTt	26	26	AY.5	0.000537
ORF1ab/nsp3	749	T749T	acT	acC	23	24	B.1.1.7	0.000021
ORF1ab/nsp3	749	T749T	acT	acA	1	24	B.1.1.7	0.000001
ORF1ab/nsp3	749	T749N	aCt	aAt	23	23	B.1.139	0.016862
ORF1ab/nsp3	749	T749I	aCt	aTt	21	21	AY.75	0.001176
ORF1ab/nsp3	749	T749I	aCt	aTt	20	20	AY.4.2	0.000434
ORF1ab/nsp3	749	T749I	aCt	aTt	20	20	AY.42	0.000805
ORF1ab/nsp3	749	T749I	aCt	aTt	20	20	AY.98.1	0.000969
ORF1ab/nsp3	749	T749I	aCt	aTt	19	19	AY.29	0.0003
ORF1ab/nsp3	749	T749I	aCt	aTt	19	19	B	0.002428
ORF1ab/nsp3	749	T749del	ACT	---	19	19	B.1.1.7	0.000017
ORF1ab/nsp3	749	T749I	aCt	aTt	17	17	AY.33	0.001135
ORF1ab/nsp3	749	T749del1	aCt	a-t	10	15	All	0.000002
ORF1ab/nsp3	749	T749del1	acT	ac-	4	15	All	0.000001
ORF1ab/nsp3	749	T749del1	ACt	-Tt	1	15	All	0
ORF1ab/nsp3	749	T749I	aCt	aTt	15	15	B.1.1.333	0.016146
ORF1ab/nsp3	749	T749I	aCt	aTt	15	15	B.1.177.69	0.022255
ORF1ab/nsp3	749	T749I	aCt	aTt	15	15	B.1.243	0.001044
ORF1ab/nsp3	749	T749I	aCt	aTt	14	14	AY.46.3	0.013072
ORF1ab/nsp3	749	T749I	aCt	aTt	14	14	B.1.258	0.000932
ORF1ab/nsp3	749	T749I	aCt	aTt	14	14	B.1.429	0.000329
ORF1ab/nsp3	749	T749I	aCt	aTt	14	14	B.1.526	0.000329
ORF1ab/nsp3	749	T749I	aCt	aTt	13	13	AY.118	0.000814
ORF1ab/nsp3	749	T749I	aCt	aTt	13	13	AY.3.1	0.001108
ORF1ab/nsp3	749	T749I	aCt	aTt	13	13	AY.39	0.000321
ORF1ab/nsp3	749	T749I	aCt	aTt	13	13	AY.9.2	0.000477
ORF1ab/nsp3	749	T749I	aCt	aTt	13	13	B.1.177.34	0.684211
ORF1ab/nsp3	749	T749I	aCt	aTt	13	13	B.1.427	0.000656
ORF1ab/nsp3	749	T749I	aCt	aTt	12	12	AY.24	0.005172
ORF1ab/nsp3	749	T749I	aCt	aTt	12	12	B.1.369	0.003423
ORF1ab/nsp3	749	T749I	aCt	aTt	12	12	B.1.525	0.001358
ORF1ab/nsp3	749	T749I	aCt	aTt	11	11	AY.39.1	0.000436
ORF1ab/nsp3	749	T749I	aCt	aTt	11	11	AY.4.5	0.001182
ORF1ab/nsp3	749	T749N	aCt	aAt	11	11	B.1.1.7	0.00001
ORF1ab/nsp3	749	T749I	aCt	aTt	11	11	P.1.14	0.000526
ORF1ab/nsp3	749	T749I	aCt	aTt	10	10	AY.74	0.001156
ORF1ab/nsp3	749	T749I	aCt	aTt	10	10	B.1.1.319	0.175439
ORF1ab/nsp3	749	T749I	aCt	aTt	10	10	B.1.195	0.050251
ORF1ab/nsp3	749	T749S	Act	Tct	5	9	All	0.000001
ORF1ab/nsp3	749	T749S	AcT	TcC	2	9	All	0
ORF1ab/nsp3	749	T749S	aCt	aGt	1	9	All	0
ORF1ab/nsp3	749	T749S	AcT	TcA	1	9	All	0
ORF1ab/nsp3	749	T749I	aCt	aTt	9	9	B.1.1.434	0.003137
ORF1ab/nsp3	749	T749I	aCt	aTt	9	9	P.1.2	0.010405
ORF1ab/nsp3	749	T749I	aCt	aTt	8	8	AY.120	0.000297
ORF1ab/nsp3	749	T749I	aCt	aTt	8	8	AY.20	0.000311
ORF1ab/nsp3	749	T749T	acT	acC	7	8	AY.4	0.000011
ORF1ab/nsp3	749	T749T	acT	acG	1	8	AY.4	0.000002
ORF1ab/nsp3	749	T749I	aCt	aTt	8	8	B.1.1.28	0.00249
ORF1ab/nsp3	749	T749I	aCt	aTt	8	8	B.1.160	0.00025
ORF1ab/nsp3	749	T749I	aCt	aTt	8	8	B.1.177.73	0.00453
ORF1ab/nsp3	749	T749N	aCt	aAt	8	8	B.1.36	0.001167
ORF1ab/nsp3	749	T749I	aCt	aTt	8	8	B.1.568	0.008889
ORF1ab/nsp3	749	T749I	aCt	aTt	7	7	AY.117	0.000592
ORF1ab/nsp3	749	T749I	aCt	aTt	7	7	AY.119	0.000247
ORF1ab/nsp3	749	T749I	aCt	aTt	7	7	AY.14	0.000616
ORF1ab/nsp3	749	T749I	aCt	aTt	7	7	AY.23	0.000488
ORF1ab/nsp3	749	T749I	aCt	aTt	7	7	AY.45	0.000852
ORF1ab/nsp3	749	T749I	aCt	aTt	7	7	AY.9.1	0.000586
ORF1ab/nsp3	749	T749I	aCt	aTt	7	7	B.1.1.253	0.017544
ORF1ab/nsp3	749	T749I	aCt	aTt	7	7	B.1.1.33	0.002946
ORF1ab/nsp3	749	T749I	aCt	aTt	7	7	B.1.1.519	0.000278
ORF1ab/nsp3	749	T749I	aCt	aTt	7	7	B.1.564	0.002981
ORF1ab/nsp3	749	T749del1	aCt	a-t	7	7	B.1.617.1	0.000903
ORF1ab/nsp3	749	T749I	aCt	aTt	7	7	D.2	0.000525
ORF1ab/nsp3	749	T749I	aCt	aTt	6	6	A.7	0.333333
ORF1ab/nsp3	749	T749I	aCt	aTt	6	6	AY.104	0.011905
ORF1ab/nsp3	749	T749I	aCt	aTt	6	6	AZ.2	0.004926
ORF1ab/nsp3	749	T749I	aCt	aTt	6	6	B.1.1.284	0.000644
ORF1ab/nsp3	749	T749I	aCt	aTt	6	6	B.1.126	0.007653
ORF1ab/nsp3	749	T749I	aCt	aTt	6	6	B.1.214	0.021978
ORF1ab/nsp3	749	T749I	aCt	aTt	6	6	B.1.438.1	0.000644
ORF1ab/nsp3	749	T749N	aCt	aAt	6	6	B.1.525	0.000679
ORF1ab/nsp3	749	T749I	aCt	aTt	6	6	B.1.621	0.000531
ORF1ab/nsp3	749	T749I	aCt	aTt	6	6	Q.2	0.003681
ORF1ab/nsp3	749	T749T	acT	acA	3	5		0.166667
ORF1ab/nsp3	749	T749T	acT	acC	2	5		0.111111
ORF1ab/nsp3	749	T749D	ACT	GAC	3	5	All	0.000001
ORF1ab/nsp3	749	T749D	ACt	GAt	2	5	All	0
ORF1ab/nsp3	749	T749I	aCt	aTt	5	5	AY.12	0.00158
ORF1ab/nsp3	749	T749I	aCt	aTt	5	5	AY.34	0.000485
ORF1ab/nsp3	749	T749A	Act	Gct	5	5	AY.4	0.000008
ORF1ab/nsp3	749	T749I	aCt	aTt	5	5	AY.46.6	0.000361
ORF1ab/nsp3	749	T749I	aCt	aTt	5	5	AY.54	0.000477
ORF1ab/nsp3	749	T749I	aCt	aTt	5	5	AY.6	0.000206
ORF1ab/nsp3	749	T749I	aCt	aTt	5	5	B.1.1.528	0.024038
ORF1ab/nsp3	749	T749I	aCt	aTt	5	5	B.1.1.63	0.001929
ORF1ab/nsp3	749	T749I	aCt	aTt	5	5	B.1.221	0.000355
ORF1ab/nsp3	749	T749I	aCt	aTt	5	5	B.1.596	0.000436
ORF1ab/nsp3	749	T749I	aCt	aTt	5	5	B.1.628	0.001762
ORF1ab/nsp3	749	T749I	aCt	aTt	5	5	N.5	0.008834
ORF1ab/nsp3	749	T749I	aCt	aTt	5	5	P.1.1	0.001588
ORF1ab/nsp3	749	T749I	aCt	aTt	5	5	Q.1	0.000632
ORF1ab/nsp3	749	T749S	Act	Tct	2	4		0.111111
ORF1ab/nsp3	749	T749S	AcT	TcC	1	4		0.055556
ORF1ab/nsp3	749	T749S	AcT	TcA	1	4		0.055556
ORF1ab/nsp3	749	T749I	aCt	aTt	4	4	A.21	0.01108
ORF1ab/nsp3	749	T749Y	ACt	TAt	3	4	All	0.000001
ORF1ab/nsp3	749	T749Y	ACT	TAC	1	4	All	0
ORF1ab/nsp3	749	T749I	aCt	aTt	4	4	AY.108	0.00441
ORF1ab/nsp3	749	T749T	acT	acC	4	4	AY.42	0.000161
ORF1ab/nsp3	749	T749I	aCt	aTt	4	4	B.1.1.214	0.000222
ORF1ab/nsp3	749	T749I	aCt	aTt	4	4	B.1.1.216	0.003562
ORF1ab/nsp3	749	T749I	aCt	aTt	4	4	B.1.1.25	0.002274
ORF1ab/nsp3	749	T749I	aCt	aTt	4	4	B.1.1.39	0.002039
ORF1ab/nsp3	749	T749T	acT	acC	4	4	B.1.1.519	0.000159
ORF1ab/nsp3	749	T749I	aCt	aTt	4	4	B.1.160.16	0.003717
ORF1ab/nsp3	749	T749I	aCt	aTt	4	4	B.1.177.60	0.000874
ORF1ab/nsp3	749	T749I	aCt	aTt	4	4	B.1.258.17	0.000416
ORF1ab/nsp3	749	T749I	aCt	aTt	4	4	B.1.425	0.011976
ORF1ab/nsp3	749	T749I	aCt	aTt	4	4	C.37	0.000464
ORF1ab/nsp3	749	T749I	aCt	aTt	4	4	P.1.7	0.001277
ORF1ab/nsp3	749	T749Y	ACt	TAt	2	3		0.111111
ORF1ab/nsp3	749	T749N	aCt	aAt	2	3		0.111111
ORF1ab/nsp3	749	T749D	ACT	GAC	2	3		0.111111
ORF1ab/nsp3	749	T749Y	ACT	TAC	1	3		0.055556
ORF1ab/nsp3	749	T749N	aCT	aAC	1	3		0.055556
ORF1ab/nsp3	749	T749D	ACt	GAt	1	3		0.055556
ORF1ab/nsp3	749	T749T	acT	acC	3	3	AY.25	0.000018
ORF1ab/nsp3	749	T749I	aCt	aTt	3	3	AY.4.4	0.001227
ORF1ab/nsp3	749	T749A	Act	Gct	3	3	AY.44	0.000018
ORF1ab/nsp3	749	T749I	aCt	aTt	3	3	AY.46	0.000312
ORF1ab/nsp3	749	T749I	aCt	aTt	3	3	AY.46.2	0.001906
ORF1ab/nsp3	749	T749I	aCt	aTt	3	3	AY.47	0.000093
ORF1ab/nsp3	749	T749I	aCt	aTt	3	3	AY.9	0.000203
ORF1ab/nsp3	749	T749I	aCt	aTt	3	3	AY.98	0.000237
ORF1ab/nsp3	749	T749I	aCt	aTt	3	3	B.1.1.135	0.014085
ORF1ab/nsp3	749	T749N	aCt	aAt	3	3	B.1.177	0.00004
ORF1ab/nsp3	749	T749I	aCt	aTt	3	3	B.1.177.62	0.003576
ORF1ab/nsp3	749	T749I	aCt	aTt	3	3	B.1.177.81	0.000568
ORF1ab/nsp3	749	T749N	aCt	aAt	2	3	B.1.221	0.000142
ORF1ab/nsp3	749	T749N	aCT	aAC	1	3	B.1.221	0.000071
ORF1ab/nsp3	749	T749I	aCt	aTt	3	3	B.1.351	0.000089
ORF1ab/nsp3	749	T749T	acT	acC	3	3	B.1.429	0.000071
ORF1ab/nsp3	749	T749I	aCt	aTt	3	3	B.1.561	0.001191
ORF1ab/nsp3	749	T749I	aCt	aTt	3	3	B.1.575	0.00091
ORF1ab/nsp3	749	T749I	aCt	aTt	3	3	B.1.576	0.00272
ORF1ab/nsp3	749	T749A	Act	Gct	3	3	B.1.617.2	0.000011
ORF1ab/nsp3	749	T749I	aCt	aTt	3	3	B.1.621.1	0.001517
ORF1ab/nsp3	749	T749I	aCt	aTt	3	3	C.30	0.005181
ORF1ab/nsp3	749	T749I	aCt	aTt	3	3	P.1.15	0.000697
ORF1ab/nsp3	749	T749F	ACt	TTt	1	2		0.055556
ORF1ab/nsp3	749	T749I	aCt	aTt	1	2		0.055556
ORF1ab/nsp3	749	T749A	Act	Gct	1	2		0.055556
ORF1ab/nsp3	749	T749A	AcT	GcA	1	2		0.055556
ORF1ab/nsp3	749	T749I	aCT	aTC	1	2		0.055556
ORF1ab/nsp3	749	T749F	ACT	TTC	1	2		0.055556
ORF1ab/nsp3	749	T749F	ACT	TTC	1	2	All	0
ORF1ab/nsp3	749	T749F	ACt	TTt	1	2	All	0
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	AY.100	0.000092
ORF1ab/nsp3	749	T749A	Act	Gct	2	2	AY.102	0.000053
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	AY.102	0.000053
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	AY.106	0.00067
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	AY.113	0.000285
ORF1ab/nsp3	749	T749T	acT	acC	2	2	AY.20	0.000078
ORF1ab/nsp3	749	T749N	aCt	aAt	2	2	AY.4	0.000003
ORF1ab/nsp3	749	T749T	acT	acC	2	2	AY.44	0.000012
ORF1ab/nsp3	749	T749del1	acT	ac-	1	2	AY.44	0.000006
ORF1ab/nsp3	749	T749del1	aCt	a-t	1	2	AY.44	0.000006
ORF1ab/nsp3	749	T749N	aCt	aAt	2	2	AY.5	0.000041
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	AY.63	0.000774
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	AY.65	0.001066
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	AY.68	0.000547
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	AY.75.1	0.000361
ORF1ab/nsp3	749	T749A	Act	Gct	2	2	B.1	0.000018
ORF1ab/nsp3	749	T749N	aCt	aAt	2	2	B.1	0.000018
ORF1ab/nsp3	749	T749del1	aCt	a-t	1	2	B.1	0.000009
ORF1ab/nsp3	749	T749del1	acT	ac-	1	2	B.1	0.000009
ORF1ab/nsp3	749	T749T	acT	acA	1	2	B.1.1	0.000018
ORF1ab/nsp3	749	T749T	acT	acC	1	2	B.1.1	0.000018
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	B.1.1.222	0.000408
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	B.1.1.294	0.002532
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	B.1.1.351	0.005587
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	B.1.1.398	0.006452
ORF1ab/nsp3	749	T749del	ACT	---	2	2	B.1.177	0.000026
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	B.1.177.21	0.000153
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	B.1.177.36	0.032258
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	B.1.177.7	0.00033
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	B.1.177.8	0.001505
ORF1ab/nsp3	749	T749T	acT	acC	2	2	B.1.2	0.000018
ORF1ab/nsp3	749	T749D	ACt	GAt	1	2	B.1.221	0.000071
ORF1ab/nsp3	749	T749A	Act	Gct	1	2	B.1.221	0.000071
ORF1ab/nsp3	749	T749D	ACT	GAC	1	2	B.1.221	0.000071
ORF1ab/nsp3	749	T749A	AcT	GcC	1	2	B.1.221	0.000071
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	B.1.237	0.00995
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	B.1.349	0.00143
ORF1ab/nsp3	749	T749del	ACT	---	2	2	B.1.36	0.000292
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	B.1.36	0.000292
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	B.1.36.29	0.001035
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	B.1.362	0.003082
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	B.1.470	0.002809
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	B.1.517	0.000854
ORF1ab/nsp3	749	T749T	acT	acC	2	2	B.1.526	0.000047
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	B.1.582	0.000981
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	B.1.588	0.00182
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	C.35	0.001548
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	C.36.3	0.001134
ORF1ab/nsp3	749	T749I	aCt	aTt	2	2	P.1.17	0.000324
ORF1ab/nsp3	749	T749E	ACT	GAA	1	1		0.055556
ORF1ab/nsp3	749	T749X	ACT	TAA	1	1		0.055556
ORF1ab/nsp3	749	T749K	aCT	aAA	1	1		0.055556
ORF1ab/nsp3	749	T749del	ACT	---	1	1	A	0.000387
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	A	0.000387
ORF1ab/nsp3	749	T749del	ACT	---	1	1	A.2.2	0.001689
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	A.2.2	0.001689
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	A.28	0.002646
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	A.3	0.002096
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	A.5	0.001923
ORF1ab/nsp3	749	T749K	aCT	aAA	1	1	All	0
ORF1ab/nsp3	749	T749P	Act	Cct	1	1	All	0
ORF1ab/nsp3	749	T749L	ACt	CTt	1	1	All	0
ORF1ab/nsp3	749	T749del2	aCT	a--	1	1	All	0
ORF1ab/nsp3	749	T749X	ACT	TAA	1	1	All	0
ORF1ab/nsp3	749	T749E	ACT	GAA	1	1	All	0
ORF1ab/nsp3	749	T749del1	acT	ac-	1	1	AU.3	0.00211
ORF1ab/nsp3	749	T749A	Act	Gct	1	1	AY.100	0.000046
ORF1ab/nsp3	749	T749N	aCt	aAt	1	1	AY.100	0.000046
ORF1ab/nsp3	749	T749A	Act	Gct	1	1	AY.105	0.000643
ORF1ab/nsp3	749	T749T	acT	acC	1	1	AY.106	0.000335
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	AY.114	0.000231
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	AY.116.1	0.000311
ORF1ab/nsp3	749	T749A	Act	Gct	1	1	AY.117	0.000085
ORF1ab/nsp3	749	T749T	acT	acC	1	1	AY.120	0.000037
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	AY.13	0.000161
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	AY.16.1	0.00047
ORF1ab/nsp3	749	T749T	acT	acC	1	1	AY.29	0.000016
ORF1ab/nsp3	749	T749N	aCt	aAt	1	1	AY.29.1	0.000221
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	AY.29.1	0.000221
ORF1ab/nsp3	749	T749del1	ACt	-Tt	1	1	AY.3	0.00001
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	AY.32	0.000532
ORF1ab/nsp3	749	T749A	Act	Gct	1	1	AY.33	0.000067
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	AY.36	0.000148
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	AY.37	0.000316
ORF1ab/nsp3	749	T749del	ACT	---	1	1	AY.4	0.000002
ORF1ab/nsp3	749	T749P	Act	Cct	1	1	AY.4	0.000002
ORF1ab/nsp3	749	T749del2	aCT	a--	1	1	AY.4	0.000002
ORF1ab/nsp3	749	T749S	aCt	aGt	1	1	AY.44	0.000006
ORF1ab/nsp3	749	T749N	aCt	aAt	1	1	AY.46	0.000104
ORF1ab/nsp3	749	T749T	acT	acC	1	1	AY.46.4	0.000165
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	AY.49	0.003195
ORF1ab/nsp3	749	T749N	aCt	aAt	1	1	AY.5.3	0.000337
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	AY.55	0.000917
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	AY.59	0.00053
ORF1ab/nsp3	749	T749N	aCt	aAt	1	1	AY.62	0.000436
ORF1ab/nsp3	749	T749I	aCT	aTC	1	1	AY.67	0.000464
ORF1ab/nsp3	749	T749A	Act	Gct	1	1	AY.68	0.000274
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	AY.7.1	0.000113
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	AY.79	0.001211
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	AY.82	0.001357
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	AY.84	0.000437
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	AY.88	0.000884
ORF1ab/nsp3	749	T749T	acT	acC	1	1	AY.9	0.000068
ORF1ab/nsp3	749	T749T	acT	acC	1	1	AY.9.2	0.000037
ORF1ab/nsp3	749	T749A	Act	Gct	1	1	B	0.000128
ORF1ab/nsp3	749	T749S	Act	Tct	1	1	B.1	0.000009
ORF1ab/nsp3	749	T749S	Act	Tct	1	1	B.1.1	0.000018
ORF1ab/nsp3	749	T749N	aCt	aAt	1	1	B.1.1	0.000018
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.1.117	0.009709
ORF1ab/nsp3	749	T749del	ACT	---	1	1	B.1.1.139	0.022727
ORF1ab/nsp3	749	T749del	ACT	---	1	1	B.1.1.142	0.017544
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.1.186	0.003436
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.1.204	0.00304
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.1.220	0.001859
ORF1ab/nsp3	749	T749A	Act	Gct	1	1	B.1.1.228	0.003049
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.1.277	0.000759
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.1.291	0.000742
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.1.3	0.008696
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.1.306	0.000438
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.1.317	0.000412
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.1.338	0.017241
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.1.354	0.004386
ORF1ab/nsp3	749	T749T	acT	acC	1	1	B.1.1.362	0.005618
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.1.369	0.000446
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.1.391	0.008547
ORF1ab/nsp3	749	T749A	Act	Gct	1	1	B.1.1.409	0.002833
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.1.432	0.001266
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.1.433	0.001425
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.1.442	0.018519
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.1.486	0.001577
ORF1ab/nsp3	749	T749S	AcT	TcC	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.1.70	0.000341
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.128	0.000635
ORF1ab/nsp3	749	T749T	acT	acC	1	1	B.1.142	0.002899
ORF1ab/nsp3	749	T749del	ACT	---	1	1	B.1.157	0.002985
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.157	0.002985
ORF1ab/nsp3	749	T749del	ACT	---	1	1	B.1.160	0.000031
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.160.32	0.004292
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.162	0.005025
ORF1ab/nsp3	749	T749A	Act	Gct	1	1	B.1.170	0.00431
ORF1ab/nsp3	749	T749N	aCt	aAt	1	1	B.1.177.10	0.000878
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.177.10	0.000878
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.177.12	0.000152
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.177.17	0.000821
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.177.33	0.001645
ORF1ab/nsp3	749	T749del	ACT	---	1	1	B.1.177.54	0.000606
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.177.54	0.000606
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.177.6	0.000977
ORF1ab/nsp3	749	T749del	ACT	---	1	1	B.1.177.63	0.002703
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.177.63	0.002703
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.177.65	0.000665
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.177.75	0.001041
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.177.82	0.000477
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.177.83	0.001481
ORF1ab/nsp3	749	T749N	aCt	aAt	1	1	B.1.177.86	0.000183
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.177.86	0.000183
ORF1ab/nsp3	749	T749A	Act	Gct	1	1	B.1.2	0.000009
ORF1ab/nsp3	749	T749Y	ACt	TAt	1	1	B.1.2	0.000009
ORF1ab/nsp3	749	T749del1	acT	ac-	1	1	B.1.2	0.000009
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.206	0.000816
ORF1ab/nsp3	749	T749del1	aCt	a-t	1	1	B.1.214	0.003663
ORF1ab/nsp3	749	T749T	acT	acC	1	1	B.1.221	0.000071
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.221.2	0.004016
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.23	0.006061
ORF1ab/nsp3	749	T749N	aCt	aAt	1	1	B.1.234	0.000132
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.3	0.002618
ORF1ab/nsp3	749	T749del	ACT	---	1	1	B.1.319	0.003049
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.320	0.001245
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.348	0.018182
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.36.10	0.004785
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.36.38	0.001642
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.361	0.001289
ORF1ab/nsp3	749	T749N	aCt	aAt	1	1	B.1.378	0.006849
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.39	0.003906
ORF1ab/nsp3	749	T749T	acT	acC	1	1	B.1.404	0.001302
ORF1ab/nsp3	749	T749del	ACT	---	1	1	B.1.409	0.000781
ORF1ab/nsp3	749	T749del	ACT	---	1	1	B.1.415	0.014286
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.456	0.003268
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.466.2	0.000391
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.478	0.011765
ORF1ab/nsp3	749	T749A	Act	Gct	1	1	B.1.497	0.000315
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.509	0.000866
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.524	0.001406
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.537	0.02
ORF1ab/nsp3	749	T749N	aCt	aAt	1	1	B.1.541	0.004425
ORF1ab/nsp3	749	T749T	acT	acC	1	1	B.1.541	0.004425
ORF1ab/nsp3	749	T749A	Act	Gct	1	1	B.1.576	0.000907
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.597	0.00463
ORF1ab/nsp3	749	T749del	ACT	---	1	1	B.1.617.1	0.000129
ORF1ab/nsp3	749	T749A	Act	Gct	1	1	B.1.617.1	0.000129
ORF1ab/nsp3	749	T749del	ACT	---	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	749	T749L	ACt	CTt	1	1	B.1.620	0.000946
ORF1ab/nsp3	749	T749T	acT	acC	1	1	B.1.621	0.000089
ORF1ab/nsp3	749	T749N	aCt	aAt	1	1	B.1.621	0.000089
ORF1ab/nsp3	749	T749A	Act	Gct	1	1	B.1.623	0.000536
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.623	0.000536
ORF1ab/nsp3	749	T749N	aCt	aAt	1	1	B.1.636	0.006711
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.1.637	0.000073
ORF1ab/nsp3	749	T749del	ACT	---	1	1	B.15	0.017544
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.3.1	0.001658
ORF1ab/nsp3	749	T749A	Act	Gct	1	1	B.3.1	0.001658
ORF1ab/nsp3	749	T749T	acT	acA	1	1	B.40	0.000364
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.55	0.00295
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.6	0.00091
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	B.6.8	0.008264
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	C.1	0.002392
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	C.36.1	0.004149
ORF1ab/nsp3	749	T749A	Act	Gct	1	1	C.37	0.000116
ORF1ab/nsp3	749	T749S	Act	Tct	1	1	D.2	0.000075
ORF1ab/nsp3	749	T749T	acT	acC	1	1	D.2	0.000075
ORF1ab/nsp3	749	T749N	aCt	aAt	1	1	P.1	0.000016
ORF1ab/nsp3	749	T749A	Act	Gct	1	1	P.1	0.000016
ORF1ab/nsp3	749	T749del	ACT	---	1	1	P.1	0.000016
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	P.1.12	0.000484
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	P.1.13	0.000898
ORF1ab/nsp3	749	T749N	aCt	aAt	1	1	P.2	0.000187
ORF1ab/nsp3	749	T749I	aCt	aTt	1	1	P.2	0.000187
ORF1ab/nsp3	749	T749A	Act	Gct	1	1	Q.1	0.000126
ORF1ab/nsp3	749	T749I	aCt	aTt	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.