CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : 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/nsp3	109	P109L	P927L	nonsyn	cCa	cTa	8035	8033	0.999751	3044-3046
ORF1ab/nsp3	109	P109L	P927L	nonsyn	CCa	TTa	8035	2	0.000248911	3044-3046
ORF1ab/nsp3	109	P109P	P927P	syn	ccA	ccG	1531	1012	0.661006	3044-3046
ORF1ab/nsp3	109	P109P	P927P	syn	ccA	ccT	1531	376	0.245591	3044-3046
ORF1ab/nsp3	109	P109P	P927P	syn	ccA	ccC	1531	143	0.093403	3044-3046
ORF1ab/nsp3	109	P109S	P927S	nonsyn	Cca	Tca	554	551	0.994585	3044-3046
ORF1ab/nsp3	109	P109S	P927S	nonsyn	CcA	TcT	554	2	0.00361011	3044-3046
ORF1ab/nsp3	109	P109S	P927S	nonsyn	CcA	TcC	554	1	0.00180505	3044-3046
ORF1ab/nsp3	109	P109A	P927A	nonsyn	Cca	Gca	95	95	1	3044-3046
ORF1ab/nsp3	109	P109T	P927T	nonsyn	Cca	Aca	45	45	1	3044-3046
ORF1ab/nsp3	109	P109del	P927del	del	CCA	---	43	43	1	3044-3046
ORF1ab/nsp3	109	P109Q	P927Q	nonsyn	cCa	cAa	40	37	0.925	3044-3046
ORF1ab/nsp3	109	P109Q	P927Q	nonsyn	cCA	cAG	40	3	0.075	3044-3046
ORF1ab/nsp3	109	P109del1	P927del1	del	Cca	-ca	29	24	0.827586	3044-3046
ORF1ab/nsp3	109	P109del1	P927del1	del	ccA	cc-	29	5	0.172414	3044-3046
ORF1ab/nsp3	109	P109R	P927R	nonsyn	cCa	cGa	22	22	1	3044-3046
ORF1ab/nsp3	109	P109X	P927X	nonsyn	CCa	TAa	2	2	1	3044-3046
ORF1ab/nsp3	109	P109del2	P927del2	del	cCA	c--	2	1	0.5	3044-3046
ORF1ab/nsp3	109	P109del2	P927del2	del	CCA	--N	2	1	0.5	3044-3046
ORF1ab/nsp3	109	P109F	P927F	nonsyn	CCA	TTT	1	1	1	3044-3046
ORF1ab/nsp3	109	P109Y	P927Y	nonsyn	CCA	TAT	1	1	1	3044-3046
ORF1ab/nsp3	109	P109V	P927V	nonsyn	CCA	GTT	1	1	1	3044-3046
ORF1ab/nsp3	109	P109C	P927C	nonsyn	CCA	TGT	1	1	1	3044-3046

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	109	P109L	cCa	cTa	8033	8035	All	0.001536
ORF1ab/nsp3	109	P109L	CCa	TTa	2	8035	All	0
ORF1ab/nsp3	109	P109P	ccA	ccG	1012	1531	All	0.000194
ORF1ab/nsp3	109	P109P	ccA	ccT	376	1531	All	0.000072
ORF1ab/nsp3	109	P109P	ccA	ccC	143	1531	All	0.000027
ORF1ab/nsp3	109	P109L	cCa	cTa	1517	1517	B.1.1.7	0.001358
ORF1ab/nsp3	109	P109L	cCa	cTa	899	899	B.1.617.2	0.003385
ORF1ab/nsp3	109	P109L	cCa	cTa	789	789	AY.25	0.004746
ORF1ab/nsp3	109	P109S	Cca	Tca	551	554	All	0.000105
ORF1ab/nsp3	109	P109S	CcA	TcT	2	554	All	0
ORF1ab/nsp3	109	P109S	CcA	TcC	1	554	All	0
ORF1ab/nsp3	109	P109P	ccA	ccG	525	528	AY.103	0.00326
ORF1ab/nsp3	109	P109P	ccA	ccT	2	528	AY.103	0.000012
ORF1ab/nsp3	109	P109P	ccA	ccC	1	528	AY.103	0.000006
ORF1ab/nsp3	109	P109L	cCa	cTa	419	419	AY.4	0.000652
ORF1ab/nsp3	109	P109L	cCa	cTa	298	298	B.1.577	0.204811
ORF1ab/nsp3	109	P109L	cCa	cTa	284	284	AY.103	0.001763
ORF1ab/nsp3	109	P109L	cCa	cTa	282	282	AY.43	0.001249
ORF1ab/nsp3	109	P109L	cCa	cTa	264	264	AY.44	0.001607
ORF1ab/nsp3	109	P109L	cCa	cTa	174	174	AY.3	0.001731
ORF1ab/nsp3	109	P109P	ccA	ccT	126	167	B.1.1.7	0.000113
ORF1ab/nsp3	109	P109P	ccA	ccG	41	167	B.1.1.7	0.000037
ORF1ab/nsp3	109	P109L	cCa	cTa	165	165	AY.9.2	0.00606
ORF1ab/nsp3	109	P109L	cCa	cTa	158	158	AY.39	0.003904
ORF1ab/nsp3	109	P109L	cCa	cTa	134	134	B.1.177	0.001764
ORF1ab/nsp3	109	P109L	cCa	cTa	124	124	AY.109	0.091716
ORF1ab/nsp3	109	P109P	ccA	ccG	104	121	B.1.617.2	0.000392
ORF1ab/nsp3	109	P109P	ccA	ccT	10	121	B.1.617.2	0.000038
ORF1ab/nsp3	109	P109P	ccA	ccC	7	121	B.1.617.2	0.000026
ORF1ab/nsp3	109	P109S	Cca	Tca	112	112	B.1.1.7	0.0001
ORF1ab/nsp3	109	P109L	cCa	cTa	112	112	P.1	0.001764
ORF1ab/nsp3	109	P109L	cCa	cTa	109	109	AY.102	0.00289
ORF1ab/nsp3	109	P109S	Cca	Tca	107	107	AY.103	0.000664
ORF1ab/nsp3	109	P109L	cCa	cTa	107	107	B.1.2	0.000942
ORF1ab/nsp3	109	P109L	cCa	cTa	104	104	B.1	0.000953
ORF1ab/nsp3	109	P109L	cCa	cTa	101	101	B.1.1	0.001832
ORF1ab/nsp3	109	P109P	ccA	ccC	99	99	AY.109	0.073225
ORF1ab/nsp3	109	P109L	cCa	cTa	97	97	AY.88	0.085765
ORF1ab/nsp3	109	P109A	Cca	Gca	95	95	All	0.000018
ORF1ab/nsp3	109	P109P	ccA	ccT	76	91	AY.43	0.000337
ORF1ab/nsp3	109	P109P	ccA	ccG	15	91	AY.43	0.000066
ORF1ab/nsp3	109	P109L	cCa	cTa	87	87	AY.26	0.002463
ORF1ab/nsp3	109	P109L	cCa	cTa	78	78	AY.5.1	0.293233
ORF1ab/nsp3	109	P109L	cCa	cTa	70	70	AY.61	0.007334
ORF1ab/nsp3	109	P109L	cCa	cTa	66	66	B.1.526	0.001551
ORF1ab/nsp3	109	P109P	ccA	ccT	30	52	AY.4	0.000047
ORF1ab/nsp3	109	P109P	ccA	ccG	17	52	AY.4	0.000026
ORF1ab/nsp3	109	P109P	ccA	ccC	5	52	AY.4	0.000008
ORF1ab/nsp3	109	P109L	cCa	cTa	49	49	B.1.177.63	0.132432
ORF1ab/nsp3	109	P109L	cCa	cTa	47	47	B.1.621	0.00416
ORF1ab/nsp3	109	P109L	cCa	cTa	46	46	AY.20	0.001788
ORF1ab/nsp3	109	P109L	cCa	cTa	46	46	B.1.284	0.605263
ORF1ab/nsp3	109	P109T	Cca	Aca	45	45	All	0.000009
ORF1ab/nsp3	109	P109L	cCa	cTa	45	45	AY.5	0.000929
ORF1ab/nsp3	109	P109L	cCa	cTa	44	44	AY.4.2	0.000954
ORF1ab/nsp3	109	P109del	CCA	---	43	43	All	0.000008
ORF1ab/nsp3	109	P109L	cCa	cTa	41	41	R.1	0.00369
ORF1ab/nsp3	109	P109Q	cCa	cAa	37	40	All	0.000007
ORF1ab/nsp3	109	P109Q	cCA	cAG	3	40	All	0.000001
ORF1ab/nsp3	109	P109A	Cca	Gca	40	40	AY.4	0.000062
ORF1ab/nsp3	109	P109L	cCa	cTa	39	39	AY.116.1	0.012146
ORF1ab/nsp3	109	P109L	cCa	cTa	38	38	B.1.234	0.005014
ORF1ab/nsp3	109	P109P	ccA	ccG	28	37	P.1	0.000441
ORF1ab/nsp3	109	P109P	ccA	ccT	7	37	P.1	0.00011
ORF1ab/nsp3	109	P109P	ccA	ccC	2	37	P.1	0.000032
ORF1ab/nsp3	109	P109P	ccA	ccT	15	35	AY.25	0.00009
ORF1ab/nsp3	109	P109P	ccA	ccG	15	35	AY.25	0.00009
ORF1ab/nsp3	109	P109P	ccA	ccC	5	35	AY.25	0.00003
ORF1ab/nsp3	109	P109S	Cca	Tca	34	34	AY.4	0.000053
ORF1ab/nsp3	109	P109L	cCa	cTa	32	32	AY.47	0.000995
ORF1ab/nsp3	109	P109A	Cca	Gca	32	32	B.1.177	0.000421
ORF1ab/nsp3	109	P109L	cCa	cTa	31	31	B.1.438.1	0.003325
ORF1ab/nsp3	109	P109L	cCa	cTa	30	30	B.1.160	0.000936
ORF1ab/nsp3	109	P109L	cCa	cTa	30	30	B.1.429	0.000706
ORF1ab/nsp3	109	P109S	Cca	Tca	30	30	B.1.617.2	0.000113
ORF1ab/nsp3	109	P109del1	Cca	-ca	24	29	All	0.000005
ORF1ab/nsp3	109	P109del1	ccA	cc-	5	29	All	0.000001
ORF1ab/nsp3	109	P109L	cCa	cTa	29	29	AY.42	0.001167
ORF1ab/nsp3	109	P109L	cCa	cTa	29	29	B.1.1.214	0.001608
ORF1ab/nsp3	109	P109P	ccA	ccG	29	29	B.1.1.48	0.083333
ORF1ab/nsp3	109	P109L	cCa	cTa	28	28	AY.75	0.001569
ORF1ab/nsp3	109	P109L	cCa	cTa	25	25	B.1.1.519	0.000993
ORF1ab/nsp3	109	P109P	ccA	ccT	25	25	P.1.17	0.004044
ORF1ab/nsp3	109	P109S	Cca	Tca	23	23	AY.3	0.000229
ORF1ab/nsp3	109	P109P	ccA	ccG	12	23	AY.44	0.000073
ORF1ab/nsp3	109	P109P	ccA	ccT	8	23	AY.44	0.000049
ORF1ab/nsp3	109	P109P	ccA	ccC	3	23	AY.44	0.000018
ORF1ab/nsp3	109	P109S	Cca	Tca	23	23	AY.5	0.000475
ORF1ab/nsp3	109	P109P	ccA	ccG	23	23	B.1.177.82	0.010979
ORF1ab/nsp3	109	P109L	cCa	cTa	23	23	B.1.36.22	0.027778
ORF1ab/nsp3	109	P109R	cCa	cGa	22	22	All	0.000004
ORF1ab/nsp3	109	P109L	cCa	cTa	22	22	AY.119	0.000777
ORF1ab/nsp3	109	P109L	cCa	cTa	20	20	AE.4	0.869565
ORF1ab/nsp3	109	P109L	cCa	cTa	20	20	AY.46.6	0.001444
ORF1ab/nsp3	109	P109S	Cca	Tca	19	19	AY.118	0.00119
ORF1ab/nsp3	109	P109P	ccA	ccG	19	19	B.1.497	0.00598
ORF1ab/nsp3	109	P109R	cCa	cGa	18	18	AY.4	0.000028
ORF1ab/nsp3	109	P109L	cCa	cTa	18	18	B.1.1.318	0.005432
ORF1ab/nsp3	109	P109P	ccA	ccT	15	17	AY.102	0.000398
ORF1ab/nsp3	109	P109P	ccA	ccG	2	17	AY.102	0.000053
ORF1ab/nsp3	109	P109P	ccA	ccG	17	17	B.1.214.3	0.121429
ORF1ab/nsp3	109	P109L	cCa	cTa	17	17	P.1.14	0.000813
ORF1ab/nsp3	109	P109L	cCa	cTa	15	15	AY.117	0.001268
ORF1ab/nsp3	109	P109L	cCa	cTa	15	15	AY.29	0.000237
ORF1ab/nsp3	109	P109L	cCa	cTa	15	15	AY.98	0.001185
ORF1ab/nsp3	109	P109L	cCa	cTa	15	15	AY.99.2	0.001382
ORF1ab/nsp3	109	P109L	cCa	cTa	15	15	B.1.177.44	0.007784
ORF1ab/nsp3	109	P109L	cCa	cTa	14	14	AY.100	0.000644
ORF1ab/nsp3	109	P109L	cCa	cTa	14	14	AY.113	0.001993
ORF1ab/nsp3	109	P109L	cCa	cTa	14	14	AY.120	0.000521
ORF1ab/nsp3	109	P109P	ccA	ccG	9	14	AY.3	0.00009
ORF1ab/nsp3	109	P109P	ccA	ccC	3	14	AY.3	0.00003
ORF1ab/nsp3	109	P109P	ccA	ccT	2	14	AY.3	0.00002
ORF1ab/nsp3	109	P109L	cCa	cTa	14	14	B.1.177.69	0.020772
ORF1ab/nsp3	109	P109L	cCa	cTa	14	14	B.1.221	0.000994
ORF1ab/nsp3	109	P109L	cCa	cTa	14	14	B.1.243	0.000974
ORF1ab/nsp3	109	P109P	ccA	ccG	13	14	B.1.621	0.001151
ORF1ab/nsp3	109	P109P	ccA	ccC	1	14	B.1.621	0.000089
ORF1ab/nsp3	109	P109P	ccA	ccG	13	13	A.1	0.003664
ORF1ab/nsp3	109	P109L	cCa	cTa	13	13	AY.46	0.001353
ORF1ab/nsp3	109	P109L	cCa	cTa	13	13	AY.92	0.003735
ORF1ab/nsp3	109	P109T	Cca	Aca	13	13	B.1.1.7	0.000012
ORF1ab/nsp3	109	P109L	cCa	cTa	12	12	AY.39.1	0.000475
ORF1ab/nsp3	109	P109Q	cCa	cAa	12	12	B.1.1.7	0.000011
ORF1ab/nsp3	109	P109S	Cca	Tca	11	11	AY.100	0.000506
ORF1ab/nsp3	109	P109S	Cca	Tca	11	11	AY.111	0.002015
ORF1ab/nsp3	109	P109L	cCa	cTa	11	11	AY.30	0.004353
ORF1ab/nsp3	109	P109S	Cca	Tca	11	11	AY.44	0.000067
ORF1ab/nsp3	109	P109P	ccA	ccT	6	11	B.1	0.000055
ORF1ab/nsp3	109	P109P	ccA	ccG	4	11	B.1	0.000037
ORF1ab/nsp3	109	P109P	ccA	ccC	1	11	B.1	0.000009
ORF1ab/nsp3	109	P109L	cCa	cTa	11	11	B.1.1.348	0.008758
ORF1ab/nsp3	109	P109L	cCa	cTa	11	11	B.1.1.397	0.024775
ORF1ab/nsp3	109	P109L	cCa	cTa	11	11	B.1.177.60	0.002403
ORF1ab/nsp3	109	P109L	cCa	cTa	11	11	B.1.517	0.004697
ORF1ab/nsp3	109	P109L	cCa	cTa	10	10	AY.37	0.003161
ORF1ab/nsp3	109	P109P	ccA	ccG	9	10	AY.4.2	0.000195
ORF1ab/nsp3	109	P109P	ccA	ccC	1	10	AY.4.2	0.000022
ORF1ab/nsp3	109	P109P	ccA	ccG	10	10	AY.46.6	0.000722
ORF1ab/nsp3	109	P109P	ccA	ccT	10	10	AY.72	0.013605
ORF1ab/nsp3	109	P109L	cCa	cTa	10	10	AY.75.1	0.001803
ORF1ab/nsp3	109	P109P	ccA	ccG	10	10	B.1.2	0.000088
ORF1ab/nsp3	109	P109L	cCa	cTa	10	10	B.1.311	0.002746
ORF1ab/nsp3	109	P109P	ccA	ccG	10	10	B.1.429	0.000235
ORF1ab/nsp3	109	P109L	cCa	cTa	10	10	B.1.596	0.000871
ORF1ab/nsp3	109	P109S	Cca	Tca	9	10	D.2	0.000675
ORF1ab/nsp3	109	P109S	CcA	TcT	1	10	D.2	0.000075
ORF1ab/nsp3	109	P109L	cCa	cTa	9	9	AY.23	0.000628
ORF1ab/nsp3	109	P109L	cCa	cTa	9	9	AY.27	0.000582
ORF1ab/nsp3	109	P109P	ccA	ccT	6	9	AY.98	0.000474
ORF1ab/nsp3	109	P109P	ccA	ccG	3	9	AY.98	0.000237
ORF1ab/nsp3	109	P109P	ccA	ccG	8	9	B.1.1	0.000145
ORF1ab/nsp3	109	P109P	ccA	ccT	1	9	B.1.1	0.000018
ORF1ab/nsp3	109	P109L	cCa	cTa	9	9	B.1.1.222	0.001836
ORF1ab/nsp3	109	P109L	cCa	cTa	9	9	B.1.147	0.006803
ORF1ab/nsp3	109	P109L	cCa	cTa	9	9	B.1.525	0.001018
ORF1ab/nsp3	109	P109L	cCa	cTa	9	9	B.1.91	0.018672
ORF1ab/nsp3	109	P109L	cCa	cTa	8	8	AY.12	0.002528
ORF1ab/nsp3	109	P109P	ccA	ccG	8	8	AY.34	0.000776
ORF1ab/nsp3	109	P109L	cCa	cTa	8	8	AY.34	0.000776
ORF1ab/nsp3	109	P109S	Cca	Tca	8	8	AY.43	0.000035
ORF1ab/nsp3	109	P109L	cCa	cTa	7	8	AY.9.1	0.000586
ORF1ab/nsp3	109	P109L	CCa	TTa	1	8	AY.9.1	0.000084
ORF1ab/nsp3	109	P109S	Cca	Tca	8	8	B.1.1.369	0.00357
ORF1ab/nsp3	109	P109L	cCa	cTa	8	8	B.1.1.432	0.010127
ORF1ab/nsp3	109	P109S	Cca	Tca	8	8	B.1.2	0.00007
ORF1ab/nsp3	109	P109L	cCa	cTa	8	8	B.1.240	0.001725
ORF1ab/nsp3	109	P109P	ccA	ccG	8	8	B.1.351.3	0.007011
ORF1ab/nsp3	109	P109L	cCa	cTa	8	8	B.1.36	0.001167
ORF1ab/nsp3	109	P109L	cCa	cTa	8	8	B.44	0.8
ORF1ab/nsp3	109	P109L	cCa	cTa	8	8	Q.7	0.008889
ORF1ab/nsp3	109	P109L	cCa	cTa	7	7	AY.120.2	0.008997
ORF1ab/nsp3	109	P109T	Cca	Aca	7	7	AY.3	0.00007
ORF1ab/nsp3	109	P109L	cCa	cTa	7	7	AY.53	0.002013
ORF1ab/nsp3	109	P109L	cCa	cTa	7	7	AY.54	0.000667
ORF1ab/nsp3	109	P109L	cCa	cTa	7	7	C.37	0.000812
ORF1ab/nsp3	109	P109L	cCa	cTa	7	7	Q.3	0.001015
ORF1ab/nsp3	109	P109P	ccA	ccC	5	6	AY.100	0.00023
ORF1ab/nsp3	109	P109P	ccA	ccG	1	6	AY.100	0.000046
ORF1ab/nsp3	109	P109L	cCa	cTa	6	6	AY.118	0.000376
ORF1ab/nsp3	109	P109L	cCa	cTa	6	6	AY.13	0.000966
ORF1ab/nsp3	109	P109L	cCa	cTa	6	6	AY.19	0.006842
ORF1ab/nsp3	109	P109S	Cca	Tca	6	6	AY.23	0.000418
ORF1ab/nsp3	109	P109del1	Cca	-ca	6	6	AY.44	0.000037
ORF1ab/nsp3	109	P109L	cCa	cTa	6	6	AY.5.4	0.00166
ORF1ab/nsp3	109	P109T	Cca	Aca	6	6	B.1.1.416	0.00543
ORF1ab/nsp3	109	P109L	cCa	cTa	6	6	B.1.177.35	0.004147
ORF1ab/nsp3	109	P109del1	Cca	-ca	5	6	B.1.2	0.000044
ORF1ab/nsp3	109	P109del1	ccA	cc-	1	6	B.1.2	0.000009
ORF1ab/nsp3	109	P109L	cCa	cTa	6	6	B.1.351	0.000178
ORF1ab/nsp3	109	P109L	cCa	cTa	6	6	D.2	0.00045
ORF1ab/nsp3	109	P109L	cCa	cTa	5	5	AH.3	0.019011
ORF1ab/nsp3	109	P109P	ccA	ccG	5	5	AY.111	0.000916
ORF1ab/nsp3	109	P109S	Cca	Tca	5	5	AY.119	0.000177
ORF1ab/nsp3	109	P109L	cCa	cTa	5	5	AY.33	0.000334
ORF1ab/nsp3	109	P109S	Cca	Tca	5	5	AY.75	0.00028
ORF1ab/nsp3	109	P109L	cCa	cTa	5	5	AY.98.1	0.000242
ORF1ab/nsp3	109	P109del	CCA	---	5	5	B.1	0.000046
ORF1ab/nsp3	109	P109L	cCa	cTa	5	5	B.1.1.284	0.000537
ORF1ab/nsp3	109	P109S	Cca	Tca	5	5	B.1.1.374	0.011876
ORF1ab/nsp3	109	P109L	cCa	cTa	5	5	B.1.1.89	0.030303
ORF1ab/nsp3	109	P109L	cCa	cTa	5	5	B.1.177.82	0.002387
ORF1ab/nsp3	109	P109S	Cca	Tca	5	5	B.1.221	0.000355
ORF1ab/nsp3	109	P109L	cCa	cTa	5	5	B.1.258	0.000333
ORF1ab/nsp3	109	P109L	cCa	cTa	5	5	B.1.499	0.005252
ORF1ab/nsp3	109	P109P	ccA	ccT	3	5	B.1.526	0.000071
ORF1ab/nsp3	109	P109P	ccA	ccG	2	5	B.1.526	0.000047
ORF1ab/nsp3	109	P109A	Cca	Gca	5	5	B.1.617.2	0.000019
ORF1ab/nsp3	109	P109L	cCa	cTa	5	5	N.4	0.021277
ORF1ab/nsp3	109	P109S	Cca	Tca	5	5	P.1	0.000079
ORF1ab/nsp3	109	P109L	cCa	cTa	5	5	P.1.12	0.00242
ORF1ab/nsp3	109	P109L	cCa	cTa	5	5	Q.8	0.000825
ORF1ab/nsp3	109	P109del	CCA	---	4	4		0.222222
ORF1ab/nsp3	109	P109S	Cca	Tca	4	4	AY.102	0.000106
ORF1ab/nsp3	109	P109L	cCa	cTa	4	4	AY.114	0.000924
ORF1ab/nsp3	109	P109L	cCa	cTa	4	4	AY.14	0.000352
ORF1ab/nsp3	109	P109S	Cca	Tca	4	4	AY.15	0.008889
ORF1ab/nsp3	109	P109T	Cca	Aca	4	4	AY.23	0.000279
ORF1ab/nsp3	109	P109P	ccA	ccG	2	4	AY.33	0.000134
ORF1ab/nsp3	109	P109P	ccA	ccT	1	4	AY.33	0.000067
ORF1ab/nsp3	109	P109P	ccA	ccC	1	4	AY.33	0.000067
ORF1ab/nsp3	109	P109Q	cCa	cAa	4	4	AY.4	0.000006
ORF1ab/nsp3	109	P109L	cCa	cTa	4	4	AY.4.5	0.00043
ORF1ab/nsp3	109	P109L	cCa	cTa	4	4	AY.45	0.000487
ORF1ab/nsp3	109	P109L	cCa	cTa	4	4	AY.46.4	0.000658
ORF1ab/nsp3	109	P109L	cCa	cTa	4	4	AY.7.1	0.000451
ORF1ab/nsp3	109	P109L	cCa	cTa	4	4	AY.9	0.00027
ORF1ab/nsp3	109	P109L	cCa	cTa	4	4	B.1.1.205	0.01487
ORF1ab/nsp3	109	P109L	cCa	cTa	4	4	B.1.1.50	0.002716
ORF1ab/nsp3	109	P109S	Cca	Tca	4	4	B.1.1.71	0.024242
ORF1ab/nsp3	109	P109L	cCa	cTa	4	4	B.1.110.3	0.002874
ORF1ab/nsp3	109	P109P	ccA	ccG	4	4	B.1.177	0.000053
ORF1ab/nsp3	109	P109L	cCa	cTa	4	4	B.1.177.62	0.004768
ORF1ab/nsp3	109	P109L	cCa	cTa	4	4	B.1.177.81	0.000757
ORF1ab/nsp3	109	P109L	cCa	cTa	4	4	B.1.36.21	0.008639
ORF1ab/nsp3	109	P109L	cCa	cTa	4	4	B.1.617.1	0.000516
ORF1ab/nsp3	109	P109Q	cCa	cAa	4	4	B.1.617.2	0.000015
ORF1ab/nsp3	109	P109L	cCa	cTa	4	4	Q.1	0.000505
ORF1ab/nsp3	109	P109S	Cca	Tca	3	3	A	0.001161
ORF1ab/nsp3	109	P109L	cCa	cTa	3	3	A.2.5	0.001497
ORF1ab/nsp3	109	P109A	Cca	Gca	3	3	AY.102	0.00008
ORF1ab/nsp3	109	P109S	Cca	Tca	2	3	AY.105	0.001286
ORF1ab/nsp3	109	P109S	CcA	TcT	1	3	AY.105	0.000643
ORF1ab/nsp3	109	P109P	ccA	ccG	3	3	AY.119	0.000106
ORF1ab/nsp3	109	P109L	cCa	cTa	3	3	AY.120.1	0.000963
ORF1ab/nsp3	109	P109del1	Cca	-ca	3	3	AY.120.1	0.000963
ORF1ab/nsp3	109	P109L	cCa	cTa	3	3	AY.121	0.000406
ORF1ab/nsp3	109	P109S	Cca	Tca	3	3	AY.14	0.000264
ORF1ab/nsp3	109	P109S	Cca	Tca	3	3	AY.25	0.000018
ORF1ab/nsp3	109	P109L	cCa	cTa	3	3	AY.36	0.000445
ORF1ab/nsp3	109	P109del	CCA	---	3	3	AY.4	0.000005
ORF1ab/nsp3	109	P109S	Cca	Tca	3	3	AY.4.2	0.000065
ORF1ab/nsp3	109	P109Q	cCa	cAa	3	3	AY.43	0.000013
ORF1ab/nsp3	109	P109S	Cca	Tca	3	3	AY.48	0.001395
ORF1ab/nsp3	109	P109L	cCa	cTa	3	3	AY.69	0.00056
ORF1ab/nsp3	109	P109S	Cca	Tca	3	3	AY.98	0.000237
ORF1ab/nsp3	109	P109L	cCa	cTa	3	3	AY.99.1	0.004658
ORF1ab/nsp3	109	P109S	Cca	Tca	3	3	B.1	0.000027
ORF1ab/nsp3	109	P109L	cCa	cTa	3	3	B.1.1.316	0.002775
ORF1ab/nsp3	109	P109del	CCA	---	3	3	B.1.1.33	0.001263
ORF1ab/nsp3	109	P109L	cCa	cTa	3	3	B.1.1.342	0.1875
ORF1ab/nsp3	109	P109L	cCa	cTa	3	3	B.1.1.448	0.006098
ORF1ab/nsp3	109	P109L	cCa	cTa	3	3	B.1.1.51	0.005155
ORF1ab/nsp3	109	P109del	CCA	---	3	3	B.1.1.7	0.000003
ORF1ab/nsp3	109	P109P	ccA	ccT	2	3	B.1.177.57	0.000562
ORF1ab/nsp3	109	P109P	ccA	ccG	1	3	B.1.177.57	0.000281
ORF1ab/nsp3	109	P109L	cCa	cTa	3	3	B.1.177.73	0.001699
ORF1ab/nsp3	109	P109L	cCa	cTa	3	3	B.1.279	0.001541
ORF1ab/nsp3	109	P109P	ccA	ccG	3	3	B.1.351	0.000089
ORF1ab/nsp3	109	P109S	Cca	Tca	3	3	B.1.36	0.000438
ORF1ab/nsp3	109	P109L	cCa	cTa	3	3	B.1.428	0.003061
ORF1ab/nsp3	109	P109L	cCa	cTa	3	3	B.1.497	0.000944
ORF1ab/nsp3	109	P109S	Cca	Tca	3	3	B.1.596	0.000261
ORF1ab/nsp3	109	P109S	Cca	Tca	3	3	B.1.617.1	0.000387
ORF1ab/nsp3	109	P109del1	Cca	-ca	2	3	B.1.617.2	0.000008
ORF1ab/nsp3	109	P109del1	ccA	cc-	1	3	B.1.617.2	0.000004
ORF1ab/nsp3	109	P109L	cCa	cTa	3	3	B.1.618	0.012097
ORF1ab/nsp3	109	P109P	ccA	ccG	3	3	C.16	0.003181
ORF1ab/nsp3	109	P109L	cCa	cTa	3	3	C.36	0.002732
ORF1ab/nsp3	109	P109S	Cca	Tca	3	3	C.37	0.000348
ORF1ab/nsp3	109	P109P	ccA	ccT	3	3	D.2	0.000225
ORF1ab/nsp3	109	P109L	cCa	cTa	3	3	P.1.15	0.000697
ORF1ab/nsp3	109	P109L	cCa	cTa	3	3	P.1.17	0.000485
ORF1ab/nsp3	109	P109L	cCa	cTa	3	3	P.7	0.0131
ORF1ab/nsp3	109	P109P	ccA	ccT	2	3	Q.8	0.00033
ORF1ab/nsp3	109	P109P	ccA	ccG	1	3	Q.8	0.000165
ORF1ab/nsp3	109	P109A	Cca	Gca	2	2		0.111111
ORF1ab/nsp3	109	P109X	CCa	TAa	2	2	All	0
ORF1ab/nsp3	109	P109del2	CCA	--N	1	2	All	0
ORF1ab/nsp3	109	P109del2	cCA	c--	1	2	All	0
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	AY.10	0.00106
ORF1ab/nsp3	109	P109del1	Cca	-ca	2	2	AY.103	0.000012
ORF1ab/nsp3	109	P109X	CCa	TAa	2	2	AY.105	0.001286
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	AY.111	0.000366
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	AY.116	0.000574
ORF1ab/nsp3	109	P109P	ccA	ccG	2	2	AY.116	0.000574
ORF1ab/nsp3	109	P109S	Cca	Tca	2	2	AY.117	0.000169
ORF1ab/nsp3	109	P109A	Cca	Gca	2	2	AY.119	0.000071
ORF1ab/nsp3	109	P109P	ccA	ccT	2	2	AY.121	0.000271
ORF1ab/nsp3	109	P109P	ccA	ccC	1	2	AY.20	0.000039
ORF1ab/nsp3	109	P109P	ccA	ccT	1	2	AY.20	0.000039
ORF1ab/nsp3	109	P109S	Cca	Tca	2	2	AY.26	0.000057
ORF1ab/nsp3	109	P109P	ccA	ccG	1	2	AY.26	0.000028
ORF1ab/nsp3	109	P109P	ccA	ccC	1	2	AY.26	0.000028
ORF1ab/nsp3	109	P109P	ccA	ccT	2	2	AY.29	0.000032
ORF1ab/nsp3	109	P109del1	Cca	-ca	2	2	AY.3	0.00002
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	AY.32	0.001065
ORF1ab/nsp3	109	P109A	Cca	Gca	2	2	AY.4.2	0.000043
ORF1ab/nsp3	109	P109T	Cca	Aca	2	2	AY.42	0.00008
ORF1ab/nsp3	109	P109Q	cCa	cAa	2	2	AY.44	0.000012
ORF1ab/nsp3	109	P109P	ccA	ccT	1	2	AY.47	0.000031
ORF1ab/nsp3	109	P109P	ccA	ccG	1	2	AY.47	0.000031
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	AY.55	0.001835
ORF1ab/nsp3	109	P109P	ccA	ccC	1	2	AY.61	0.000105
ORF1ab/nsp3	109	P109P	ccA	ccG	1	2	AY.61	0.000105
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	AY.7	0.000392
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	AY.7.2	0.001119
ORF1ab/nsp3	109	P109S	Cca	Tca	2	2	AY.73	0.001331
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	AY.74	0.000231
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	AY.79	0.002421
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	AY.8	0.001212
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	AY.90	0.001369
ORF1ab/nsp3	109	P109P	ccA	ccT	1	2	AY.95	0.000761
ORF1ab/nsp3	109	P109P	ccA	ccC	1	2	AY.95	0.000761
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	AY.99	0.002099
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	AZ.1	0.001735
ORF1ab/nsp3	109	P109P	ccA	ccT	1	2	B	0.000128
ORF1ab/nsp3	109	P109P	ccA	ccG	1	2	B	0.000128
ORF1ab/nsp3	109	P109T	Cca	Aca	2	2	B.1	0.000018
ORF1ab/nsp3	109	P109S	Cca	Tca	2	2	B.1.1	0.000036
ORF1ab/nsp3	109	P109del	CCA	---	2	2	B.1.1	0.000036
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.1.1	0.000653
ORF1ab/nsp3	109	P109P	ccA	ccT	2	2	B.1.1.207	0.002364
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.1.207	0.002364
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.1.230	0.018349
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.1.312	0.003824
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.1.317	0.000823
ORF1ab/nsp3	109	P109del	CCA	---	2	2	B.1.1.348	0.001592
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.1.372	0.001377
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.1.385	0.008929
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.1.39	0.001019
ORF1ab/nsp3	109	P109S	Cca	Tca	2	2	B.1.1.411	0.029412
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.1.434	0.000697
ORF1ab/nsp3	109	P109S	Cca	Tca	2	2	B.1.1.519	0.000079
ORF1ab/nsp3	109	P109del1	ccA	cc-	1	2	B.1.1.7	0.000001
ORF1ab/nsp3	109	P109del1	Cca	-ca	1	2	B.1.1.7	0.000001
ORF1ab/nsp3	109	P109S	Cca	Tca	2	2	B.1.160	0.000062
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.160.7	0.004158
ORF1ab/nsp3	109	P109del	CCA	---	2	2	B.1.177	0.000026
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.177.24	0.002591
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.177.50	0.00939
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.177.7	0.00033
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.177.86	0.000367
ORF1ab/nsp3	109	P109del	CCA	---	2	2	B.1.2	0.000018
ORF1ab/nsp3	109	P109T	Cca	Aca	2	2	B.1.2	0.000018
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.214.2	0.001199
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.222	0.003384
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.232	0.001075
ORF1ab/nsp3	109	P109P	ccA	ccG	2	2	B.1.243	0.000139
ORF1ab/nsp3	109	P109S	Cca	Tca	2	2	B.1.243	0.000139
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.298	0.004228
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.36.8	0.002
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.369	0.00057
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.426	0.002018
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.427	0.000101
ORF1ab/nsp3	109	P109S	Cca	Tca	2	2	B.1.427	0.000101
ORF1ab/nsp3	109	P109S	Cca	Tca	2	2	B.1.429	0.000047
ORF1ab/nsp3	109	P109S	Cca	Tca	2	2	B.1.436	0.002058
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.466.2	0.000782
ORF1ab/nsp3	109	P109P	ccA	ccG	2	2	B.1.517	0.000854
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.561	0.000794
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.595	0.000522
ORF1ab/nsp3	109	P109P	ccA	ccT	2	2	B.1.609	0.000959
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.609	0.000959
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.628	0.000705
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.636	0.013423
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	B.1.637	0.000146
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	C.16	0.002121
ORF1ab/nsp3	109	P109L	cCa	cTa	2	2	N.5	0.003534
ORF1ab/nsp3	109	P109del	CCA	---	2	2	N.6	0.014184
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	A	0.000387
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	A.2.2	0.001689
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	A.2.5.2	0.001572
ORF1ab/nsp3	109	P109P	ccA	ccT	1	1	A.27	0.001656
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	A.6	0.005128
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AD.2	0.000219
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AE.8	0.000489
ORF1ab/nsp3	109	P109F	CCA	TTT	1	1	All	0
ORF1ab/nsp3	109	P109C	CCA	TGT	1	1	All	0
ORF1ab/nsp3	109	P109Y	CCA	TAT	1	1	All	0
ORF1ab/nsp3	109	P109V	CCA	GTT	1	1	All	0
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AS.1	0.009524
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	AU.2	0.002421
ORF1ab/nsp3	109	P109V	CCA	GTT	1	1	AY.100	0.000046
ORF1ab/nsp3	109	P109Q	cCa	cAa	1	1	AY.103	0.000006
ORF1ab/nsp3	109	P109A	Cca	Gca	1	1	AY.103	0.000006
ORF1ab/nsp3	109	P109Y	CCA	TAT	1	1	AY.105	0.000643
ORF1ab/nsp3	109	P109Q	cCa	cAa	1	1	AY.105	0.000643
ORF1ab/nsp3	109	P109L	CCa	TTa	1	1	AY.105	0.000643
ORF1ab/nsp3	109	P109F	CCA	TTT	1	1	AY.105	0.000643
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.106	0.000335
ORF1ab/nsp3	109	P109P	ccA	ccT	1	1	AY.106	0.000335
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.107	0.000466
ORF1ab/nsp3	109	P109S	CcA	TcC	1	1	AY.109	0.00074
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.11	0.001339
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.110	0.000113
ORF1ab/nsp3	109	P109A	Cca	Gca	1	1	AY.113	0.000142
ORF1ab/nsp3	109	P109P	ccA	ccT	1	1	AY.117	0.000085
ORF1ab/nsp3	109	P109P	ccA	ccC	1	1	AY.118	0.000063
ORF1ab/nsp3	109	P109del1	Cca	-ca	1	1	AY.120	0.000037
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	AY.120	0.000037
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	AY.120	0.000037
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.120.2.1	0.000498
ORF1ab/nsp3	109	P109Q	cCa	cAa	1	1	AY.121	0.000135
ORF1ab/nsp3	109	P109P	ccA	ccT	1	1	AY.13	0.000161
ORF1ab/nsp3	109	P109A	Cca	Gca	1	1	AY.13	0.000161
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	AY.14	0.000088
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.16	0.00038
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	AY.2	0.000356
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	AY.23	0.00007
ORF1ab/nsp3	109	P109Q	cCa	cAa	1	1	AY.25	0.000006
ORF1ab/nsp3	109	P109A	Cca	Gca	1	1	AY.25	0.000006
ORF1ab/nsp3	109	P109del	CCA	---	1	1	AY.25	0.000006
ORF1ab/nsp3	109	P109del1	Cca	-ca	1	1	AY.25	0.000006
ORF1ab/nsp3	109	P109del	CCA	---	1	1	AY.26	0.000028
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.28	0.00189
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	AY.29	0.000016
ORF1ab/nsp3	109	P109del2	cCA	c--	1	1	AY.3	0.00001
ORF1ab/nsp3	109	P109Q	cCA	cAG	1	1	AY.3	0.00001
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.3.1	0.000085
ORF1ab/nsp3	109	P109del	CCA	---	1	1	AY.30	0.000396
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.35	0.000233
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	AY.37	0.000316
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.38	0.000499
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	AY.39	0.000025
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	AY.39	0.000025
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	AY.39.1	0.00004
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.4.2.1	0.000149
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	AY.4.4	0.000409
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	AY.4.5	0.000107
ORF1ab/nsp3	109	P109del	CCA	---	1	1	AY.42	0.00004
ORF1ab/nsp3	109	P109del	CCA	---	1	1	AY.43	0.000004
ORF1ab/nsp3	109	P109A	Cca	Gca	1	1	AY.43	0.000004
ORF1ab/nsp3	109	P109C	CCA	TGT	1	1	AY.43	0.000004
ORF1ab/nsp3	109	P109R	cCa	cGa	1	1	AY.43	0.000004
ORF1ab/nsp3	109	P109T	Cca	Aca	1	1	AY.43	0.000004
ORF1ab/nsp3	109	P109del	CCA	---	1	1	AY.46	0.000104
ORF1ab/nsp3	109	P109Q	cCa	cAa	1	1	AY.46.2	0.000635
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	AY.46.4	0.000165
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.46.5	0.000198
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	AY.46.5	0.000198
ORF1ab/nsp3	109	P109T	Cca	Aca	1	1	AY.46.6	0.000072
ORF1ab/nsp3	109	P109T	Cca	Aca	1	1	AY.47	0.000031
ORF1ab/nsp3	109	P109del	CCA	---	1	1	AY.5	0.000021
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.5.3	0.000337
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	AY.50	0.000799
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	AY.53	0.000288
ORF1ab/nsp3	109	P109del1	Cca	-ca	1	1	AY.54	0.000095
ORF1ab/nsp3	109	P109P	ccA	ccT	1	1	AY.55	0.000917
ORF1ab/nsp3	109	P109P	ccA	ccT	1	1	AY.56	0.001605
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.59	0.00053
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	AY.59	0.00053
ORF1ab/nsp3	109	P109del1	ccA	cc-	1	1	AY.65	0.000533
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.68	0.000274
ORF1ab/nsp3	109	P109Q	cCa	cAa	1	1	AY.7	0.000196
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.71	0.000475
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	AY.74	0.000116
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.77	0.001127
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.78	0.001541
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	AY.79	0.001211
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.80	0.001129
ORF1ab/nsp3	109	P109P	ccA	ccC	1	1	AY.82	0.001357
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.84	0.000437
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.85	0.000427
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.87	0.000833
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	AY.9.1	0.000084
ORF1ab/nsp3	109	P109Q	cCA	cAG	1	1	AY.9.2	0.000037
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AY.93	0.000273
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	AY.96	0.002075
ORF1ab/nsp3	109	P109Q	cCa	cAa	1	1	AY.98	0.000079
ORF1ab/nsp3	109	P109R	cCa	cGa	1	1	AY.99	0.001049
ORF1ab/nsp3	109	P109R	cCa	cGa	1	1	AY.99.2	0.000092
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	AZ.2	0.000821
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B	0.000128
ORF1ab/nsp3	109	P109P	ccA	ccT	1	1	B.1.1.121	0.002427
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.1.170	0.001247
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.1.198	0.001468
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.1.216	0.00089
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	B.1.1.216	0.00089
ORF1ab/nsp3	109	P109P	ccA	ccT	1	1	B.1.1.241	0.00207
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.1.25	0.000569
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.1.253	0.002506
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.1.277	0.000759
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.1.28	0.000311
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.1.286	0.002899
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.1.289	0.002083
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	B.1.1.291	0.000742
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.1.294	0.001266
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.1.305	0.003861
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.1.306	0.000438
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.1.332	0.03125
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	B.1.1.344	0.010753
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.1.364	0.066667
ORF1ab/nsp3	109	P109del	CCA	---	1	1	B.1.1.369	0.000446
ORF1ab/nsp3	109	P109P	ccA	ccC	1	1	B.1.1.37	0.000193
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.1.37	0.000193
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	B.1.1.389	0.006061
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	B.1.1.39	0.00051
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.1.398	0.003226
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.1.420	0.001006
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	B.1.1.434	0.000349
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.1.440	0.011765
ORF1ab/nsp3	109	P109P	ccA	ccC	1	1	B.1.1.50	0.000679
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	B.1.1.506	0.037037
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	B.1.1.55	0.012987
ORF1ab/nsp3	109	P109P	ccA	ccT	1	1	B.1.1.63	0.000386
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.1.70	0.000341
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.1.71	0.006061
ORF1ab/nsp3	109	P109T	Cca	Aca	1	1	B.1.1.71	0.006061
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.111	0.001175
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.112	0.005181
ORF1ab/nsp3	109	P109Q	cCa	cAa	1	1	B.1.177	0.000013
ORF1ab/nsp3	109	P109T	Cca	Aca	1	1	B.1.177	0.000013
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	B.1.177	0.000013
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.177.10	0.000878
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.177.12	0.000152
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.177.15	0.000631
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.177.16	0.000664
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.177.17	0.000821
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	B.1.177.17	0.000821
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.177.19	0.001431
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.177.33	0.001645
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.177.4	0.000211
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	B.1.177.40	0.005155
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.177.41	0.0025
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	B.1.177.44	0.000519
ORF1ab/nsp3	109	P109T	Cca	Aca	1	1	B.1.177.44	0.000519
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	B.1.177.48	0.003125
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.177.48	0.003125
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	B.1.177.5	0.001242
ORF1ab/nsp3	109	P109A	Cca	Gca	1	1	B.1.177.62	0.001192
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	B.1.177.65	0.000665
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.177.79	0.002342
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.177.8	0.000752
ORF1ab/nsp3	109	P109Q	cCA	cAG	1	1	B.1.2	0.000009
ORF1ab/nsp3	109	P109Q	cCa	cAa	1	1	B.1.206	0.000816
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	B.1.214	0.003663
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.218	0.005155
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.219	0.009434
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	B.1.234	0.000132
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.237	0.004975
ORF1ab/nsp3	109	P109P	ccA	ccT	1	1	B.1.258	0.000067
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.258.17	0.000104
ORF1ab/nsp3	109	P109Q	cCa	cAa	1	1	B.1.284	0.013158
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.319	0.003049
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	B.1.328	0.03125
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.348	0.018182
ORF1ab/nsp3	109	P109del	CCA	---	1	1	B.1.349	0.000715
ORF1ab/nsp3	109	P109R	cCa	cGa	1	1	B.1.351	0.00003
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.351.2	0.000303
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.356	0.001727
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.36.1	0.00114
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.36.10	0.004785
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.36.18	0.00042
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.36.28	0.005747
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.36.29	0.000517
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	B.1.36.7	0.004
ORF1ab/nsp3	109	P109Q	cCa	cAa	1	1	B.1.369	0.000285
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	B.1.375	0.00082
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	B.1.38	0.032258
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.399	0.001934
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.404	0.001302
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.409	0.000781
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.416	0.001269
ORF1ab/nsp3	109	P109del	CCA	---	1	1	B.1.416.1	0.001563
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	B.1.426	0.001009
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	B.1.427	0.00005
ORF1ab/nsp3	109	P109T	Cca	Aca	1	1	B.1.427	0.00005
ORF1ab/nsp3	109	P109A	Cca	Gca	1	1	B.1.427	0.00005
ORF1ab/nsp3	109	P109del	CCA	---	1	1	B.1.429	0.000024
ORF1ab/nsp3	109	P109T	Cca	Aca	1	1	B.1.429	0.000024
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	B.1.433	0.003195
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.436	0.001029
ORF1ab/nsp3	109	P109P	ccA	ccT	1	1	B.1.438.1	0.000107
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.470	0.001404
ORF1ab/nsp3	109	P109Q	cCa	cAa	1	1	B.1.470	0.001404
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.523	0.002451
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	B.1.525	0.000113
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.538	0.008065
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.543	0.01
ORF1ab/nsp3	109	P109del	CCA	---	1	1	B.1.561	0.000397
ORF1ab/nsp3	109	P109P	ccA	ccT	1	1	B.1.561	0.000397
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.564	0.000426
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	B.1.565	0.00081
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.576	0.000907
ORF1ab/nsp3	109	P109del	CCA	---	1	1	B.1.577	0.000687
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.595.4	0.007299
ORF1ab/nsp3	109	P109P	ccA	ccC	1	1	B.1.599	0.00365
ORF1ab/nsp3	109	P109T	Cca	Aca	1	1	B.1.609	0.000479
ORF1ab/nsp3	109	P109del	CCA	---	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.623	0.000536
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.626	0.005714
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	B.1.637	0.000073
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.1.9.4	0.006135
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.40	0.000364
ORF1ab/nsp3	109	P109P	ccA	ccT	1	1	B.56	0.028571
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	B.6	0.00091
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	B.6.6	0.000889
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	C.35	0.000774
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	C.36.3	0.000567
ORF1ab/nsp3	109	P109A	Cca	Gca	1	1	C.37.1	0.002618
ORF1ab/nsp3	109	P109P	ccA	ccG	1	1	N.8	0.03125
ORF1ab/nsp3	109	P109del2	CCA	--N	1	1	P.1	0.000016
ORF1ab/nsp3	109	P109del	CCA	---	1	1	P.1	0.000016
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	P.1.1	0.000318
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	P.1.12	0.000484
ORF1ab/nsp3	109	P109A	Cca	Gca	1	1	P.1.17	0.000162
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	P.1.2	0.001156
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	P.1.4	0.000977
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	P.1.9	0.004808
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	P.2	0.000187
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	P.2	0.000187
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	P.3	0.001595
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	P.7	0.004367
ORF1ab/nsp3	109	P109P	ccA	ccT	1	1	Q.4	0.000455
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	Q.8	0.000165
ORF1ab/nsp3	109	P109del1	ccA	cc-	1	1	R.1	0.00009
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	R.1	0.00009
ORF1ab/nsp3	109	P109S	Cca	Tca	1	1	U.3	0.003861
ORF1ab/nsp3	109	P109L	cCa	cTa	1	1	Z.1	0.00289

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.