CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp9 : CodonNum = 109

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/nsp9	109	T109I	T4249I	nonsyn	aCa	aTa	8492	8492	1	13010-13012
ORF1ab/nsp9	109	T109T	T4249T	syn	acA	acG	222	125	0.563063	13010-13012
ORF1ab/nsp9	109	T109T	T4249T	syn	acA	acT	222	81	0.364865	13010-13012
ORF1ab/nsp9	109	T109T	T4249T	syn	acA	acC	222	16	0.0720721	13010-13012
ORF1ab/nsp9	109	T109del	T4249del	del	ACA	---	46	46	1	13010-13012
ORF1ab/nsp9	109	T109A	T4249A	nonsyn	Aca	Gca	10	10	1	13010-13012
ORF1ab/nsp9	109	T109P	T4249P	nonsyn	Aca	Cca	9	9	1	13010-13012
ORF1ab/nsp9	109	T109S	T4249S	nonsyn	Aca	Tca	7	7	1	13010-13012
ORF1ab/nsp9	109	T109del1	T4249del1	del	acA	ac-	6	5	0.833333	13010-13012
ORF1ab/nsp9	109	T109K	T4249K	nonsyn	aCa	aAa	6	5	0.833333	13010-13012
ORF1ab/nsp9	109	T109K	T4249K	nonsyn	aCA	aAG	6	1	0.166667	13010-13012
ORF1ab/nsp9	109	T109del1	T4249del1	del	Aca	-ca	6	1	0.166667	13010-13012
ORF1ab/nsp9	109	T109R	T4249R	nonsyn	aCa	aGa	5	5	1	13010-13012
ORF1ab/nsp9	109	T109del2	T4249del2	del	ACa	--a	1	1	1	13010-13012

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/nsp9	109	T109I	aCa	aTa	8492	8492	All	0.001624
ORF1ab/nsp9	109	T109I	aCa	aTa	2166	2166	B.1.1.7	0.001939
ORF1ab/nsp9	109	T109I	aCa	aTa	1339	1339	AY.4	0.002084
ORF1ab/nsp9	109	T109I	aCa	aTa	695	695	B.1.617.2	0.002617
ORF1ab/nsp9	109	T109I	aCa	aTa	550	550	AY.25	0.003308
ORF1ab/nsp9	109	T109T	acA	acG	125	222	All	0.000024
ORF1ab/nsp9	109	T109T	acA	acT	81	222	All	0.000015
ORF1ab/nsp9	109	T109T	acA	acC	16	222	All	0.000003
ORF1ab/nsp9	109	T109I	aCa	aTa	204	204	AY.44	0.001242
ORF1ab/nsp9	109	T109I	aCa	aTa	200	200	AY.43	0.000886
ORF1ab/nsp9	109	T109I	aCa	aTa	182	182	AY.26	0.005152
ORF1ab/nsp9	109	T109I	aCa	aTa	174	174	AY.103	0.00108
ORF1ab/nsp9	109	T109I	aCa	aTa	171	171	B.1.626	0.977143
ORF1ab/nsp9	109	T109I	aCa	aTa	170	170	AY.3	0.001691
ORF1ab/nsp9	109	T109I	aCa	aTa	156	156	B.1.177	0.002054
ORF1ab/nsp9	109	T109I	aCa	aTa	99	99	B.1.526	0.002327
ORF1ab/nsp9	109	T109I	aCa	aTa	90	90	AY.102	0.002386
ORF1ab/nsp9	109	T109I	aCa	aTa	84	84	AY.59	0.044492
ORF1ab/nsp9	109	T109I	aCa	aTa	82	82	B.1	0.000751
ORF1ab/nsp9	109	T109I	aCa	aTa	81	81	B.1.2	0.000713
ORF1ab/nsp9	109	T109I	aCa	aTa	80	80	AY.29	0.001262
ORF1ab/nsp9	109	T109I	aCa	aTa	73	73	AY.5	0.001507
ORF1ab/nsp9	109	T109I	aCa	aTa	67	67	AY.118	0.004197
ORF1ab/nsp9	109	T109T	acA	acG	66	67	B.1.1.7	0.000059
ORF1ab/nsp9	109	T109T	acA	acT	1	67	B.1.1.7	0.000001
ORF1ab/nsp9	109	T109T	acA	acT	66	66	B.1.2	0.000581
ORF1ab/nsp9	109	T109I	aCa	aTa	60	60	B.1.177.75	0.062435
ORF1ab/nsp9	109	T109I	aCa	aTa	56	56	AY.98	0.004424
ORF1ab/nsp9	109	T109I	aCa	aTa	54	54	AY.110	0.006085
ORF1ab/nsp9	109	T109I	aCa	aTa	49	49	B.1.1	0.000889
ORF1ab/nsp9	109	T109del	ACA	---	46	46	All	0.000009
ORF1ab/nsp9	109	T109I	aCa	aTa	45	45	B.1.460	0.803571
ORF1ab/nsp9	109	T109I	aCa	aTa	44	44	B.1.429	0.001035
ORF1ab/nsp9	109	T109I	aCa	aTa	43	43	AY.100	0.001978
ORF1ab/nsp9	109	T109I	aCa	aTa	41	41	AY.13	0.0066
ORF1ab/nsp9	109	T109I	aCa	aTa	41	41	AY.39	0.001013
ORF1ab/nsp9	109	T109I	aCa	aTa	39	39	AY.113	0.005553
ORF1ab/nsp9	109	T109I	aCa	aTa	38	38	AY.119	0.001342
ORF1ab/nsp9	109	T109I	aCa	aTa	37	37	AY.20	0.001438
ORF1ab/nsp9	109	T109I	aCa	aTa	34	34	B.1.351	0.001011
ORF1ab/nsp9	109	T109I	aCa	aTa	33	33	B.1.177.6	0.032227
ORF1ab/nsp9	109	T109I	aCa	aTa	32	32	B.1.96	0.603774
ORF1ab/nsp9	109	T109I	aCa	aTa	31	31	AY.52	0.025244
ORF1ab/nsp9	109	T109I	aCa	aTa	29	29	AY.9.2	0.001065
ORF1ab/nsp9	109	T109T	acA	acG	28	28	AY.4	0.000044
ORF1ab/nsp9	109	T109I	aCa	aTa	28	28	B.1.177.44	0.01453
ORF1ab/nsp9	109	T109I	aCa	aTa	27	27	AY.3.1	0.002302
ORF1ab/nsp9	109	T109I	aCa	aTa	27	27	AY.4.5	0.002902
ORF1ab/nsp9	109	T109I	aCa	aTa	27	27	AY.92	0.007756
ORF1ab/nsp9	109	T109I	aCa	aTa	26	26	AY.75	0.001457
ORF1ab/nsp9	109	T109I	aCa	aTa	26	26	B.1.36.16	0.037037
ORF1ab/nsp9	109	T109I	aCa	aTa	24	24	AY.46.6	0.001733
ORF1ab/nsp9	109	T109I	aCa	aTa	24	24	AY.9	0.001622
ORF1ab/nsp9	109	T109I	aCa	aTa	21	21	AY.42	0.000845
ORF1ab/nsp9	109	T109I	aCa	aTa	20	20	D.2	0.001501
ORF1ab/nsp9	109	T109I	aCa	aTa	19	19	AY.108	0.020948
ORF1ab/nsp9	109	T109I	aCa	aTa	19	19	AY.4.2	0.000412
ORF1ab/nsp9	109	T109I	aCa	aTa	19	19	B.1.427	0.000959
ORF1ab/nsp9	109	T109I	aCa	aTa	18	18	AY.101	0.008828
ORF1ab/nsp9	109	T109I	aCa	aTa	18	18	AY.54	0.001716
ORF1ab/nsp9	109	T109I	aCa	aTa	18	18	B.1.1.141	0.036217
ORF1ab/nsp9	109	T109I	aCa	aTa	18	18	P.1	0.000284
ORF1ab/nsp9	109	T109I	aCa	aTa	17	17	B.1.1.519	0.000675
ORF1ab/nsp9	109	T109I	aCa	aTa	16	16	AY.117	0.001352
ORF1ab/nsp9	109	T109I	aCa	aTa	16	16	AY.23	0.001116
ORF1ab/nsp9	109	T109I	aCa	aTa	16	16	AY.98.1	0.000775
ORF1ab/nsp9	109	T109I	aCa	aTa	15	15	AY.120	0.000558
ORF1ab/nsp9	109	T109I	aCa	aTa	15	15	AY.45	0.001825
ORF1ab/nsp9	109	T109I	aCa	aTa	15	15	AY.75.1	0.002705
ORF1ab/nsp9	109	T109I	aCa	aTa	14	14	AY.47	0.000435
ORF1ab/nsp9	109	T109I	aCa	aTa	14	14	AY.5.3	0.004723
ORF1ab/nsp9	109	T109I	aCa	aTa	14	14	AY.6	0.000576
ORF1ab/nsp9	109	T109I	aCa	aTa	14	14	AY.84	0.006124
ORF1ab/nsp9	109	T109I	aCa	aTa	12	12	AY.121	0.001624
ORF1ab/nsp9	109	T109I	aCa	aTa	12	12	AY.69	0.00224
ORF1ab/nsp9	109	T109del	ACA	---	12	12	B.1.1.7	0.000011
ORF1ab/nsp9	109	T109I	aCa	aTa	12	12	B.1.227	0.571429
ORF1ab/nsp9	109	T109I	aCa	aTa	11	11	AY.61	0.001153
ORF1ab/nsp9	109	T109I	aCa	aTa	11	11	AY.85	0.004699
ORF1ab/nsp9	109	T109I	aCa	aTa	11	11	B.1.234	0.001451
ORF1ab/nsp9	109	T109I	aCa	aTa	11	11	P.1.7	0.003512
ORF1ab/nsp9	109	T109A	Aca	Gca	10	10	All	0.000002
ORF1ab/nsp9	109	T109I	aCa	aTa	10	10	AY.99.2	0.000922
ORF1ab/nsp9	109	T109I	aCa	aTa	10	10	B.1.177.57	0.00281
ORF1ab/nsp9	109	T109I	aCa	aTa	10	10	B.1.243	0.000696
ORF1ab/nsp9	109	T109I	aCa	aTa	10	10	Q.1	0.001263
ORF1ab/nsp9	109	T109P	Aca	Cca	9	9	All	0.000002
ORF1ab/nsp9	109	T109I	aCa	aTa	9	9	B	0.00115
ORF1ab/nsp9	109	T109I	aCa	aTa	9	9	B.1.1.222	0.001836
ORF1ab/nsp9	109	T109I	aCa	aTa	9	9	B.1.596	0.000784
ORF1ab/nsp9	109	T109I	aCa	aTa	8	8	AY.34	0.000776
ORF1ab/nsp9	109	T109I	aCa	aTa	8	8	AY.39.1	0.000317
ORF1ab/nsp9	109	T109I	aCa	aTa	8	8	AY.70	0.001668
ORF1ab/nsp9	109	T109I	aCa	aTa	8	8	B.1.149	0.027397
ORF1ab/nsp9	109	T109S	Aca	Tca	7	7	All	0.000001
ORF1ab/nsp9	109	T109T	acA	acT	3	7	AY.44	0.000018
ORF1ab/nsp9	109	T109T	acA	acC	3	7	AY.44	0.000018
ORF1ab/nsp9	109	T109T	acA	acG	1	7	AY.44	0.000006
ORF1ab/nsp9	109	T109I	aCa	aTa	7	7	AY.90	0.004791
ORF1ab/nsp9	109	T109I	aCa	aTa	7	7	B.1.617.1	0.000903
ORF1ab/nsp9	109	T109del1	acA	ac-	5	6	All	0.000001
ORF1ab/nsp9	109	T109K	aCa	aAa	5	6	All	0.000001
ORF1ab/nsp9	109	T109K	aCA	aAG	1	6	All	0
ORF1ab/nsp9	109	T109del1	Aca	-ca	1	6	All	0
ORF1ab/nsp9	109	T109I	aCa	aTa	6	6	AY.46	0.000624
ORF1ab/nsp9	109	T109I	aCa	aTa	6	6	AY.93	0.001638
ORF1ab/nsp9	109	T109I	aCa	aTa	6	6	AY.99	0.006296
ORF1ab/nsp9	109	T109I	aCa	aTa	6	6	B.1.1.214	0.000333
ORF1ab/nsp9	109	T109I	aCa	aTa	6	6	B.1.1.37	0.001157
ORF1ab/nsp9	109	T109I	aCa	aTa	6	6	B.1.1.427	0.857143
ORF1ab/nsp9	109	T109I	aCa	aTa	6	6	B.1.497	0.001889
ORF1ab/nsp9	109	T109I	aCa	aTa	6	6	B.1.575	0.00182
ORF1ab/nsp9	109	T109I	aCa	aTa	6	6	B.1.625	0.014118
ORF1ab/nsp9	109	T109I	aCa	aTa	6	6	P.2	0.00112
ORF1ab/nsp9	109	T109R	aCa	aGa	5	5	All	0.000001
ORF1ab/nsp9	109	T109I	aCa	aTa	5	5	AY.116	0.001434
ORF1ab/nsp9	109	T109I	aCa	aTa	5	5	AY.63	0.001934
ORF1ab/nsp9	109	T109I	aCa	aTa	5	5	AY.73	0.003327
ORF1ab/nsp9	109	T109I	aCa	aTa	5	5	AY.74	0.000578
ORF1ab/nsp9	109	T109I	aCa	aTa	5	5	B.1.160	0.000156
ORF1ab/nsp9	109	T109I	aCa	aTa	4	4	AY.16	0.001519
ORF1ab/nsp9	109	T109T	acA	acG	4	4	AY.20	0.000155
ORF1ab/nsp9	109	T109T	acA	acG	3	4	AY.25	0.000018
ORF1ab/nsp9	109	T109T	acA	acT	1	4	AY.25	0.000006
ORF1ab/nsp9	109	T109T	acA	acC	4	4	AY.26	0.000113
ORF1ab/nsp9	109	T109I	aCa	aTa	4	4	AY.27	0.000259
ORF1ab/nsp9	109	T109I	aCa	aTa	4	4	AY.33	0.000267
ORF1ab/nsp9	109	T109I	aCa	aTa	4	4	AY.34.1	0.00204
ORF1ab/nsp9	109	T109I	aCa	aTa	4	4	AY.4.2.1	0.000596
ORF1ab/nsp9	109	T109I	aCa	aTa	4	4	AY.46.5	0.000794
ORF1ab/nsp9	109	T109T	acA	acC	4	4	AY.5	0.000083
ORF1ab/nsp9	109	T109I	aCa	aTa	4	4	AY.55	0.00367
ORF1ab/nsp9	109	T109I	aCa	aTa	4	4	AY.79	0.004843
ORF1ab/nsp9	109	T109I	aCa	aTa	4	4	AY.9.1	0.000335
ORF1ab/nsp9	109	T109I	aCa	aTa	4	4	B.1.1.180	0.043011
ORF1ab/nsp9	109	T109del1	acA	ac-	3	4	B.1.1.7	0.000003
ORF1ab/nsp9	109	T109del1	Aca	-ca	1	4	B.1.1.7	0.000001
ORF1ab/nsp9	109	T109del	ACA	---	4	4	B.1.177	0.000053
ORF1ab/nsp9	109	T109I	aCa	aTa	4	4	B.1.177.4	0.000844
ORF1ab/nsp9	109	T109I	aCa	aTa	4	4	B.1.177.56	0.00267
ORF1ab/nsp9	109	T109I	aCa	aTa	4	4	B.1.177.86	0.000734
ORF1ab/nsp9	109	T109I	aCa	aTa	4	4	B.1.221	0.000284
ORF1ab/nsp9	109	T109I	aCa	aTa	4	4	B.1.525	0.000453
ORF1ab/nsp9	109	T109I	aCa	aTa	4	4	B.1.595	0.001044
ORF1ab/nsp9	109	T109T	acA	acG	4	4	B.1.617.2	0.000015
ORF1ab/nsp9	109	T109I	aCa	aTa	4	4	B.1.621.1	0.002023
ORF1ab/nsp9	109	T109I	aCa	aTa	4	4	Q.8	0.00066
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	AD.2	0.000657
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	AY.10	0.00159
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	AY.14	0.000264
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	AY.36	0.000445
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	AY.4.1	0.002212
ORF1ab/nsp9	109	T109del	ACA	---	3	3	AY.4.5	0.000322
ORF1ab/nsp9	109	T109del	ACA	---	3	3	AY.43	0.000013
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	AY.46.4	0.000494
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	AY.62	0.001307
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	AY.68	0.000821
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	AY.7	0.000588
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	AY.7.2	0.001678
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	B.1.1.28	0.000934
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	B.1.1.33	0.001263
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	B.1.1.416	0.002715
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	B.1.1.48	0.008621
ORF1ab/nsp9	109	T109K	aCa	aAa	3	3	B.1.1.7	0.000003
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	B.1.126	0.003827
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	B.1.177.21	0.000229
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	B.1.240	0.000647
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	B.1.258	0.0002
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	B.1.361	0.003866
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	B.1.470	0.004213
ORF1ab/nsp9	109	T109del	ACA	---	3	3	B.1.617.2	0.000011
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	B.1.621	0.000266
ORF1ab/nsp9	109	T109I	aCa	aTa	3	3	P.1.14	0.000143
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	A.2.5	0.000998
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	AN.1	0.04
ORF1ab/nsp9	109	T109T	acA	acG	2	2	AY.100	0.000092
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	AY.109	0.001479
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	AY.114	0.000462
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	AY.16.1	0.00094
ORF1ab/nsp9	109	T109T	acA	acG	2	2	AY.24	0.000862
ORF1ab/nsp9	109	T109T	acA	acG	2	2	AY.3	0.00002
ORF1ab/nsp9	109	T109T	acA	acT	1	2	AY.39	0.000025
ORF1ab/nsp9	109	T109T	acA	acG	1	2	AY.39	0.000025
ORF1ab/nsp9	109	T109A	Aca	Gca	2	2	AY.46	0.000208
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	AY.65	0.001066
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	AY.7.1	0.000225
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	AY.86	0.00166
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	AY.88	0.001768
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	AY.95	0.001522
ORF1ab/nsp9	109	T109T	acA	acG	2	2	AY.95	0.001522
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	B.1.1.398	0.006452
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	B.1.1.448	0.004065
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	B.1.1.525	0.010929
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	B.1.110.3	0.001437
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	B.1.128	0.001271
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	B.1.139	0.001466
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	B.1.162	0.01005
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	B.1.258.17	0.000208
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	B.1.279	0.001027
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	B.1.311	0.000549
ORF1ab/nsp9	109	T109del	ACA	---	2	2	B.1.311	0.000549
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	B.1.36	0.000292
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	B.1.437	0.041667
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	B.1.438.1	0.000215
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	B.1.480	0.004975
ORF1ab/nsp9	109	T109T	acA	acT	2	2	B.1.497	0.00063
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	B.1.570	0.005882
ORF1ab/nsp9	109	T109S	Aca	Tca	2	2	B.1.617.2	0.000008
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	B.1.628	0.000705
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	B.1.637	0.000146
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	B.46	0.041667
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	C.37	0.000232
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	P.1.15	0.000465
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	P.1.16	0.000748
ORF1ab/nsp9	109	T109I	aCa	aTa	2	2	W.4	0.002703
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	A	0.000387
ORF1ab/nsp9	109	T109T	acA	acC	1	1	A.2	0.000662
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	A.3	0.002096
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AA.7	0.009174
ORF1ab/nsp9	109	T109R	aCa	aGa	1	1	AD.2	0.000219
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AK.1	0.012658
ORF1ab/nsp9	109	T109del2	ACa	--a	1	1	All	0
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AU.2	0.002421
ORF1ab/nsp9	109	T109A	Aca	Gca	1	1	AY.102	0.000027
ORF1ab/nsp9	109	T109S	Aca	Tca	1	1	AY.102	0.000027
ORF1ab/nsp9	109	T109T	acA	acC	1	1	AY.102	0.000027
ORF1ab/nsp9	109	T109T	acA	acG	1	1	AY.103	0.000006
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AY.107	0.000466
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AY.111	0.000183
ORF1ab/nsp9	109	T109T	acA	acG	1	1	AY.119	0.000035
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AY.120.1	0.000321
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AY.19	0.00114
ORF1ab/nsp9	109	T109P	Aca	Cca	1	1	AY.23	0.00007
ORF1ab/nsp9	109	T109T	acA	acT	1	1	AY.23	0.00007
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AY.23.1	0.000417
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AY.24	0.000431
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AY.29.1	0.000221
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AY.32	0.000532
ORF1ab/nsp9	109	T109S	Aca	Tca	1	1	AY.33	0.000067
ORF1ab/nsp9	109	T109P	Aca	Cca	1	1	AY.33	0.000067
ORF1ab/nsp9	109	T109A	Aca	Gca	1	1	AY.33	0.000067
ORF1ab/nsp9	109	T109del	ACA	---	1	1	AY.34	0.000097
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AY.37	0.000316
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AY.38	0.000499
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AY.39.2	0.001541
ORF1ab/nsp9	109	T109del	ACA	---	1	1	AY.4	0.000002
ORF1ab/nsp9	109	T109T	acA	acG	1	1	AY.4.2	0.000022
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AY.40	0.000964
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AY.41	0.000294
ORF1ab/nsp9	109	T109A	Aca	Gca	1	1	AY.42	0.00004
ORF1ab/nsp9	109	T109P	Aca	Cca	1	1	AY.42	0.00004
ORF1ab/nsp9	109	T109S	Aca	Tca	1	1	AY.43	0.000004
ORF1ab/nsp9	109	T109T	acA	acG	1	1	AY.43	0.000004
ORF1ab/nsp9	109	T109S	Aca	Tca	1	1	AY.44	0.000006
ORF1ab/nsp9	109	T109S	Aca	Tca	1	1	AY.46	0.000104
ORF1ab/nsp9	109	T109del	ACA	---	1	1	AY.46.2	0.000635
ORF1ab/nsp9	109	T109P	Aca	Cca	1	1	AY.5	0.000021
ORF1ab/nsp9	109	T109T	acA	acC	1	1	AY.5.3	0.000337
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AY.56	0.001605
ORF1ab/nsp9	109	T109del	ACA	---	1	1	AY.6	0.000041
ORF1ab/nsp9	109	T109T	acA	acT	1	1	AY.61	0.000105
ORF1ab/nsp9	109	T109del	ACA	---	1	1	AY.72	0.001361
ORF1ab/nsp9	109	T109del	ACA	---	1	1	AY.75	0.000056
ORF1ab/nsp9	109	T109T	acA	acT	1	1	AY.75	0.000056
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AY.77	0.001127
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AY.8	0.000606
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AY.82	0.001357
ORF1ab/nsp9	109	T109T	acA	acG	1	1	AY.9	0.000068
ORF1ab/nsp9	109	T109K	aCA	aAG	1	1	AY.9.2	0.000037
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AY.94	0.000443
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	AY.96	0.002075
ORF1ab/nsp9	109	T109P	Aca	Cca	1	1	AY.96	0.002075
ORF1ab/nsp9	109	T109del	ACA	---	1	1	AY.99	0.001049
ORF1ab/nsp9	109	T109del	ACA	---	1	1	AY.99.1	0.001553
ORF1ab/nsp9	109	T109T	acA	acT	1	1	AY.99.2	0.000092
ORF1ab/nsp9	109	T109P	Aca	Cca	1	1	B.1	0.000009
ORF1ab/nsp9	109	T109A	Aca	Gca	1	1	B.1	0.000009
ORF1ab/nsp9	109	T109del	ACA	---	1	1	B.1.1	0.000018
ORF1ab/nsp9	109	T109del	ACA	---	1	1	B.1.1.1	0.000327
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.1.121	0.002427
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.1.176	0.000439
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.1.200	0.007463
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.1.207	0.001182
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.1.277	0.000759
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.1.294	0.001266
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.1.306	0.000438
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.1.318	0.000302
ORF1ab/nsp9	109	T109T	acA	acG	1	1	B.1.1.326	0.001761
ORF1ab/nsp9	109	T109del	ACA	---	1	1	B.1.1.348	0.000796
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.1.359	0.027778
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.1.369	0.000446
ORF1ab/nsp9	109	T109del	ACA	---	1	1	B.1.1.37	0.000193
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.1.378	0.007299
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.1.39	0.00051
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.1.409	0.002833
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.1.41	0.006329
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.1.429	0.004608
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.1.432	0.001266
ORF1ab/nsp9	109	T109T	acA	acG	1	1	B.1.1.519	0.00004
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.1.523	0.001563
ORF1ab/nsp9	109	T109P	Aca	Cca	1	1	B.1.1.7	0.000001
ORF1ab/nsp9	109	T109R	aCa	aGa	1	1	B.1.1.7	0.000001
ORF1ab/nsp9	109	T109A	Aca	Gca	1	1	B.1.1.7	0.000001
ORF1ab/nsp9	109	T109del2	ACa	--a	1	1	B.1.1.7	0.000001
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.1.70	0.000341
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.160.28	0.002924
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.160.30	0.002976
ORF1ab/nsp9	109	T109T	acA	acG	1	1	B.1.177	0.000013
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.177.15	0.000631
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.177.16	0.000664
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.177.24	0.001295
ORF1ab/nsp9	109	T109R	aCa	aGa	1	1	B.1.177.32	0.00135
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.177.32	0.00135
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.177.33	0.001645
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.177.41	0.0025
ORF1ab/nsp9	109	T109T	acA	acG	1	1	B.1.177.57	0.000281
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.177.81	0.000189
ORF1ab/nsp9	109	T109T	acA	acC	1	1	B.1.177.81	0.000189
ORF1ab/nsp9	109	T109del	ACA	---	1	1	B.1.177.83	0.001481
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.189	0.004292
ORF1ab/nsp9	109	T109del	ACA	---	1	1	B.1.2	0.000009
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.206	0.000816
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.221.3	0.000833
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.23	0.006061
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.232	0.000537
ORF1ab/nsp9	109	T109K	aCa	aAa	1	1	B.1.234	0.000132
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.245	0.03125
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.258.14	0.00098
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.274	0.011905
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.335	0.010309
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.338	0.008621
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.341	0.022727
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.346	0.001311
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.351.2	0.000303
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.36.29	0.000517
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.36.36	0.000602
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.36.9	0.003215
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.362.2	0.004717
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.369	0.000285
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.400	0.000429
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.408	0.00369
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.409	0.000781
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.413	0.004255
ORF1ab/nsp9	109	T109del1	acA	ac-	1	1	B.1.415	0.014286
ORF1ab/nsp9	109	T109R	aCa	aGa	1	1	B.1.416	0.001269
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.428	0.00102
ORF1ab/nsp9	109	T109A	Aca	Gca	1	1	B.1.429	0.000024
ORF1ab/nsp9	109	T109T	acA	acT	1	1	B.1.429	0.000024
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.485	0.014925
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.504	0.03125
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.516	0.001957
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.535	0.028571
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.538	0.008065
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.564.1	0.001577
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.565	0.00081
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.576	0.000907
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.582	0.000491
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.597	0.00463
ORF1ab/nsp9	109	T109K	aCa	aAa	1	1	B.1.609	0.000479
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.609	0.000479
ORF1ab/nsp9	109	T109del	ACA	---	1	1	B.1.617.1	0.000129
ORF1ab/nsp9	109	T109A	Aca	Gca	1	1	B.1.617.2	0.000004
ORF1ab/nsp9	109	T109P	Aca	Cca	1	1	B.1.617.2	0.000004
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.617.3	0.002985
ORF1ab/nsp9	109	T109T	acA	acT	1	1	B.1.621	0.000089
ORF1ab/nsp9	109	T109A	Aca	Gca	1	1	B.1.625	0.002353
ORF1ab/nsp9	109	T109del	ACA	---	1	1	B.1.630	0.005236
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.1.631	0.003367
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.31	0.003731
ORF1ab/nsp9	109	T109del	ACA	---	1	1	B.34	0.013699
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	B.6	0.00091
ORF1ab/nsp9	109	T109T	acA	acC	1	1	B.6	0.00091
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	C.1.2	0.004255
ORF1ab/nsp9	109	T109del1	acA	ac-	1	1	C.17	0.055556
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	C.36.1	0.004149
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	C.36.3	0.000567
ORF1ab/nsp9	109	T109R	aCa	aGa	1	1	D.2	0.000075
ORF1ab/nsp9	109	T109T	acA	acG	1	1	D.2	0.000075
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	L.1	0.001905
ORF1ab/nsp9	109	T109del	ACA	---	1	1	N.4	0.004255
ORF1ab/nsp9	109	T109T	acA	acT	1	1	P.1	0.000016
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	P.1.17	0.000162
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	P.1.8	0.004785
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	P.4	0.003802
ORF1ab/nsp9	109	T109P	Aca	Cca	1	1	Q.1	0.000126
ORF1ab/nsp9	109	T109del	ACA	---	1	1	Q.2	0.000613
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	Q.4	0.000455
ORF1ab/nsp9	109	T109I	aCa	aTa	1	1	U.2	0.008772

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.