CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1867

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	1867	P1867T	P2685T	nonsyn	Ccc	Acc	5347	5346	0.999813	8318-8320
ORF1ab/nsp3	1867	P1867T	P2685T	nonsyn	CcC	AcT	5347	1	0.000187021	8318-8320
ORF1ab/nsp3	1867	P1867P	P2685P	syn	ccC	ccT	3612	3384	0.936877	8318-8320
ORF1ab/nsp3	1867	P1867P	P2685P	syn	ccC	ccA	3612	166	0.0459579	8318-8320
ORF1ab/nsp3	1867	P1867P	P2685P	syn	ccC	ccG	3612	62	0.017165	8318-8320
ORF1ab/nsp3	1867	P1867S	P2685S	nonsyn	Ccc	Tcc	1536	1535	0.999349	8318-8320
ORF1ab/nsp3	1867	P1867S	P2685S	nonsyn	CcC	TcT	1536	1	0.000651042	8318-8320
ORF1ab/nsp3	1867	P1867del	P2685del	del	CCC	---	111	111	1	8318-8320
ORF1ab/nsp3	1867	P1867L	P2685L	nonsyn	cCc	cTc	22	20	0.909091	8318-8320
ORF1ab/nsp3	1867	P1867L	P2685L	nonsyn	cCC	cTG	22	2	0.0909091	8318-8320
ORF1ab/nsp3	1867	P1867del1	P2685del1	del	Ccc	-cc	18	10	0.555556	8318-8320
ORF1ab/nsp3	1867	P1867del1	P2685del1	del	ccC	cc-	18	7	0.388889	8318-8320
ORF1ab/nsp3	1867	P1867del1	P2685del1	del	CcC	-cN	18	1	0.0555556	8318-8320
ORF1ab/nsp3	1867	P1867A	P2685A	nonsyn	Ccc	Gcc	13	13	1	8318-8320
ORF1ab/nsp3	1867	P1867H	P2685H	nonsyn	cCc	cAc	9	8	0.888889	8318-8320
ORF1ab/nsp3	1867	P1867H	P2685H	nonsyn	cCC	cAT	9	1	0.111111	8318-8320
ORF1ab/nsp3	1867	P1867del2	P2685del2	del	cCC	c--	6	6	1	8318-8320
ORF1ab/nsp3	1867	P1867R	P2685R	nonsyn	cCc	cGc	1	1	1	8318-8320

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	1867	P1867T	Ccc	Acc	5346	5347	All	0.001022
ORF1ab/nsp3	1867	P1867T	CcC	AcT	1	5347	All	0
ORF1ab/nsp3	1867	P1867P	ccC	ccT	3384	3612	All	0.000647
ORF1ab/nsp3	1867	P1867P	ccC	ccA	166	3612	All	0.000032
ORF1ab/nsp3	1867	P1867P	ccC	ccG	62	3612	All	0.000012
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1535	1536	All	0.000294
ORF1ab/nsp3	1867	P1867S	CcC	TcT	1	1536	All	0
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1101	1108	B.1.1.7	0.000986
ORF1ab/nsp3	1867	P1867P	ccC	ccA	6	1108	B.1.1.7	0.000005
ORF1ab/nsp3	1867	P1867P	ccC	ccG	1	1108	B.1.1.7	0.000001
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	875	875	AY.4.3	0.736532
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	839	839	B.1.1.7	0.000751
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	815	815	B.1.1.279	0.913677
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	610	610	B.1.1.7	0.000546
ORF1ab/nsp3	1867	P1867P	ccC	ccT	404	409	AY.4	0.000629
ORF1ab/nsp3	1867	P1867P	ccC	ccA	5	409	AY.4	0.000008
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	307	307	AY.62	0.133769
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	302	302	AY.57	0.198163
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	280	280	AY.4	0.000436
ORF1ab/nsp3	1867	P1867P	ccC	ccT	262	262	B.1.429	0.006165
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	212	213	B.1.617.2	0.000798
ORF1ab/nsp3	1867	P1867T	CcC	AcT	1	213	B.1.617.2	0.000004
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	197	197	AY.25	0.001185
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	148	148	AY.103	0.000919
ORF1ab/nsp3	1867	P1867P	ccC	ccT	139	139	B.1.2	0.001224
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	133	133	AY.44	0.00081
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	130	130	AY.4	0.000202
ORF1ab/nsp3	1867	P1867P	ccC	ccT	70	120	P.1	0.001103
ORF1ab/nsp3	1867	P1867P	ccC	ccA	50	120	P.1	0.000788
ORF1ab/nsp3	1867	P1867del	CCC	---	111	111	All	0.000021
ORF1ab/nsp3	1867	P1867P	ccC	ccT	56	107	AY.44	0.000341
ORF1ab/nsp3	1867	P1867P	ccC	ccG	48	107	AY.44	0.000292
ORF1ab/nsp3	1867	P1867P	ccC	ccA	3	107	AY.44	0.000018
ORF1ab/nsp3	1867	P1867P	ccC	ccT	100	102	B.1.617.2	0.000377
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	102	B.1.617.2	0.000004
ORF1ab/nsp3	1867	P1867P	ccC	ccG	1	102	B.1.617.2	0.000004
ORF1ab/nsp3	1867	P1867P	ccC	ccT	77	98	B.1	0.000705
ORF1ab/nsp3	1867	P1867P	ccC	ccA	18	98	B.1	0.000165
ORF1ab/nsp3	1867	P1867P	ccC	ccG	3	98	B.1	0.000027
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	94	94	P.1	0.001481
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	93	93	AY.43	0.000412
ORF1ab/nsp3	1867	P1867P	ccC	ccT	80	92	AY.25	0.000481
ORF1ab/nsp3	1867	P1867P	ccC	ccA	12	92	AY.25	0.000072
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	92	92	B.1.1	0.001669
ORF1ab/nsp3	1867	P1867P	ccC	ccT	87	87	AY.53	0.025014
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	83	83	B.1.2	0.000731
ORF1ab/nsp3	1867	P1867P	ccC	ccT	39	72	AY.29	0.000615
ORF1ab/nsp3	1867	P1867P	ccC	ccA	33	72	AY.29	0.000521
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	70	70	B.1.429	0.001647
ORF1ab/nsp3	1867	P1867P	ccC	ccT	67	67	AY.103	0.000416
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	56	57	B.1.617.2	0.000211
ORF1ab/nsp3	1867	P1867S	CcC	TcT	1	57	B.1.617.2	0.000004
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	56	56	B.1	0.000513
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	56	56	B.1.1.186	0.19244
ORF1ab/nsp3	1867	P1867P	ccC	ccT	52	54	AY.43	0.00023
ORF1ab/nsp3	1867	P1867P	ccC	ccA	2	54	AY.43	0.000009
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	53	53	Q.3	0.007687
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	50	50	B.1.351	0.001486
ORF1ab/nsp3	1867	P1867del	CCC	---	45	45	B.1.1.7	0.00004
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	44	44	AY.100	0.002024
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	43	43	AY.103	0.000267
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	43	43	AY.3	0.000428
ORF1ab/nsp3	1867	P1867P	ccC	ccT	41	41	AY.4.2	0.000889
ORF1ab/nsp3	1867	P1867P	ccC	ccT	40	40	B.1.1.222	0.00816
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	38	38	B.1.177.81	0.007194
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	38	38	R.1	0.00342
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	34	34	B.1.1.159	0.158879
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	32	32	AY.102	0.000848
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	32	32	B.1.221	0.002273
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	30	30	B.1.177.82	0.01432
ORF1ab/nsp3	1867	P1867P	ccC	ccT	30	30	B.1.439	0.177515
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	29	29	B.1.258.17	0.003015
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	28	28	AY.29	0.000442
ORF1ab/nsp3	1867	P1867P	ccC	ccT	27	27	AY.9	0.001825
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	27	27	B.1.160	0.000842
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	25	25	AY.42	0.001006
ORF1ab/nsp3	1867	P1867P	ccC	ccT	24	24	AY.45	0.00292
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	24	24	B.1.177	0.000316
ORF1ab/nsp3	1867	P1867P	ccC	ccT	24	24	B.1.258.17	0.002495
ORF1ab/nsp3	1867	P1867P	ccC	ccT	17	24	B.1.351	0.000505
ORF1ab/nsp3	1867	P1867P	ccC	ccG	7	24	B.1.351	0.000208
ORF1ab/nsp3	1867	P1867P	ccC	ccT	22	23	AY.102	0.000583
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	23	AY.102	0.000027
ORF1ab/nsp3	1867	P1867P	ccC	ccT	23	23	B.1.160	0.000717
ORF1ab/nsp3	1867	P1867L	cCc	cTc	20	22	All	0.000004
ORF1ab/nsp3	1867	P1867L	cCC	cTG	2	22	All	0
ORF1ab/nsp3	1867	P1867P	ccC	ccT	18	22	AY.3	0.000179
ORF1ab/nsp3	1867	P1867P	ccC	ccA	4	22	AY.3	0.00004
ORF1ab/nsp3	1867	P1867P	ccC	ccT	21	21	AY.110	0.002366
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	21	21	AY.20	0.000816
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	21	21	B.1.1.33	0.008838
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	21	21	B.1.1.425	0.954545
ORF1ab/nsp3	1867	P1867P	ccC	ccT	18	21	B.1.177	0.000237
ORF1ab/nsp3	1867	P1867P	ccC	ccA	3	21	B.1.177	0.00004
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	20	20	AY.25	0.00012
ORF1ab/nsp3	1867	P1867P	ccC	ccT	19	19	AY.23	0.001325
ORF1ab/nsp3	1867	P1867P	ccC	ccT	19	19	B.1.1	0.000345
ORF1ab/nsp3	1867	P1867del1	Ccc	-cc	10	18	All	0.000002
ORF1ab/nsp3	1867	P1867del1	ccC	cc-	7	18	All	0.000001
ORF1ab/nsp3	1867	P1867del1	CcC	-cN	1	18	All	0
ORF1ab/nsp3	1867	P1867P	ccC	ccT	18	18	B.1.336	0.043902
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	17	17	AY.75	0.000952
ORF1ab/nsp3	1867	P1867P	ccC	ccT	16	16	AY.39	0.000395
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	16	16	B.1.177	0.000211
ORF1ab/nsp3	1867	P1867P	ccC	ccT	15	15	AY.26	0.000425
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	15	15	B.1.1	0.000272
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	15	15	B.1.279	0.007704
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	14	14	AY.44	0.000085
ORF1ab/nsp3	1867	P1867A	Ccc	Gcc	13	13	All	0.000002
ORF1ab/nsp3	1867	P1867P	ccC	ccT	13	13	B.1.1.519	0.000516
ORF1ab/nsp3	1867	P1867P	ccC	ccT	11	13	B.1.177.73	0.006229
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	13	B.1.177.73	0.000566
ORF1ab/nsp3	1867	P1867P	ccC	ccG	1	13	B.1.177.73	0.000566
ORF1ab/nsp3	1867	P1867P	ccC	ccT	13	13	B.1.575	0.003944
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	12	12	AY.24	0.005172
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	12	12	B.1	0.00011
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	12	12	B.1.1.433	0.017094
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	12	12	B.1.1.63	0.00463
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	12	12	B.1.164	0.179104
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	12	12	B.1.243	0.000835
ORF1ab/nsp3	1867	P1867P	ccC	ccT	12	12	B.1.596	0.001046
ORF1ab/nsp3	1867	P1867P	ccC	ccT	11	11	AY.1	0.004353
ORF1ab/nsp3	1867	P1867A	Ccc	Gcc	11	11	AY.20	0.000428
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	11	11	AY.23	0.000767
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	11	11	AY.47	0.000342
ORF1ab/nsp3	1867	P1867P	ccC	ccT	11	11	B.1.582	0.005397
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	11	11	P.2	0.002053
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	10	10	AY.39	0.000247
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	10	10	AY.6	0.000411
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	10	10	AY.98.1	0.000484
ORF1ab/nsp3	1867	P1867P	ccC	ccT	10	10	B.1.1.10	0.011148
ORF1ab/nsp3	1867	P1867P	ccC	ccT	10	10	B.1.1.311	0.003582
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	10	10	B.1.2	0.000088
ORF1ab/nsp3	1867	P1867H	cCc	cAc	8	9	All	0.000002
ORF1ab/nsp3	1867	P1867H	cCC	cAT	1	9	All	0
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	9	9	AY.4.2	0.000195
ORF1ab/nsp3	1867	P1867P	ccC	ccT	9	9	AY.4.4	0.003682
ORF1ab/nsp3	1867	P1867P	ccC	ccT	9	9	B.1.1.46	0.039301
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	9	9	B.1.526	0.000212
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	9	9	B.1.596	0.000784
ORF1ab/nsp3	1867	P1867P	ccC	ccT	8	8	AY.100	0.000368
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	8	8	AY.100	0.000368
ORF1ab/nsp3	1867	P1867P	ccC	ccT	8	8	AY.24	0.003448
ORF1ab/nsp3	1867	P1867P	ccC	ccT	8	8	AY.39.1	0.000317
ORF1ab/nsp3	1867	P1867P	ccC	ccT	7	8	AY.42	0.000282
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	8	AY.42	0.00004
ORF1ab/nsp3	1867	P1867P	ccC	ccT	8	8	AY.47	0.000249
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	8	8	AY.78	0.012327
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	8	8	B.1.1.50	0.005431
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	8	8	B.1.1.519	0.000318
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	8	8	B.1.177.21	0.000612
ORF1ab/nsp3	1867	P1867P	ccC	ccT	8	8	B.1.416.1	0.0125
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	8	8	B.1.575.1	0.019512
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	7	7	AY.116.1	0.00218
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	7	7	AY.39	0.000173
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	7	7	AY.43	0.000031
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	7	7	AY.46	0.000729
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	7	7	AY.47	0.000218
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	7	7	AY.67	0.00325
ORF1ab/nsp3	1867	P1867P	ccC	ccT	7	7	AY.75	0.000392
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	7	7	AY.83	0.012069
ORF1ab/nsp3	1867	P1867P	ccC	ccT	7	7	AY.98.1	0.000339
ORF1ab/nsp3	1867	P1867P	ccC	ccT	7	7	B.1.1.28	0.002179
ORF1ab/nsp3	1867	P1867P	ccC	ccT	7	7	B.1.177.81	0.001325
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	7	7	B.1.36	0.001021
ORF1ab/nsp3	1867	P1867P	ccC	ccT	7	7	B.1.36.18	0.002941
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	7	7	B.1.361	0.009021
ORF1ab/nsp3	1867	P1867P	ccC	ccT	7	7	B.1.525	0.000792
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	7	7	P.1.14	0.000335
ORF1ab/nsp3	1867	P1867del2	cCC	c--	6	6	All	0.000001
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	6	6	AY.102	0.000159
ORF1ab/nsp3	1867	P1867P	ccC	ccT	6	6	AY.20	0.000233
ORF1ab/nsp3	1867	P1867del	CCC	---	6	6	AY.4.5	0.000645
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	6	6	AY.5	0.000124
ORF1ab/nsp3	1867	P1867P	ccC	ccT	6	6	AY.67	0.002786
ORF1ab/nsp3	1867	P1867P	ccC	ccT	6	6	AY.92	0.001724
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	6	6	AY.98	0.000474
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	6	6	B.1.1.222	0.001224
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	6	6	B.1.1.348	0.004777
ORF1ab/nsp3	1867	P1867del1	ccC	cc-	5	6	B.1.1.7	0.000004
ORF1ab/nsp3	1867	P1867del1	Ccc	-cc	1	6	B.1.1.7	0.000001
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	6	6	B.1.1.70	0.002046
ORF1ab/nsp3	1867	P1867del	CCC	---	6	6	B.1.177	0.000079
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	6	6	B.1.240	0.001293
ORF1ab/nsp3	1867	P1867P	ccC	ccT	6	6	B.1.346	0.007864
ORF1ab/nsp3	1867	P1867P	ccC	ccT	6	6	B.1.36	0.000875
ORF1ab/nsp3	1867	P1867P	ccC	ccT	6	6	B.1.438.1	0.000644
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	6	6	B.1.466.2	0.002347
ORF1ab/nsp3	1867	P1867P	ccC	ccT	6	6	B.1.526	0.000141
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	6	6	C.37	0.000696
ORF1ab/nsp3	1867	P1867P	ccC	ccA	3	6	P.1.12	0.001452
ORF1ab/nsp3	1867	P1867P	ccC	ccT	3	6	P.1.12	0.001452
ORF1ab/nsp3	1867	P1867P	ccC	ccT	6	6	P.1.14	0.000287
ORF1ab/nsp3	1867	P1867P	ccC	ccA	5	5	AY.21	0.009488
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	5	5	AY.26	0.000142
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	5	5	AY.3	0.00005
ORF1ab/nsp3	1867	P1867del	CCC	---	5	5	AY.4	0.000008
ORF1ab/nsp3	1867	P1867L	cCc	cTc	5	5	AY.4	0.000008
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	5	5	AY.42	0.000201
ORF1ab/nsp3	1867	P1867del	CCC	---	5	5	AY.43	0.000022
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	5	5	AY.45	0.000608
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	5	5	AY.46	0.00052
ORF1ab/nsp3	1867	P1867P	ccC	ccT	5	5	AY.5	0.000103
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	5	5	AY.54	0.000477
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	5	5	AY.61	0.000524
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	5	5	AY.84	0.002187
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	5	5	AY.85	0.002136
ORF1ab/nsp3	1867	P1867P	ccC	ccT	5	5	AY.9.1	0.000419
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	5	5	AY.99.2	0.000461
ORF1ab/nsp3	1867	P1867del2	cCC	c--	5	5	B.1.1.7	0.000004
ORF1ab/nsp3	1867	P1867L	cCc	cTc	5	5	B.1.1.7	0.000004
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	5	5	B.1.390	0.053191
ORF1ab/nsp3	1867	P1867P	ccC	ccT	3	5	B.1.427	0.000151
ORF1ab/nsp3	1867	P1867P	ccC	ccG	1	5	B.1.427	0.00005
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	5	B.1.427	0.00005
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	4	4	AY.118	0.000251
ORF1ab/nsp3	1867	P1867P	ccC	ccT	4	4	AY.119	0.000141
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	4	4	AY.119	0.000141
ORF1ab/nsp3	1867	P1867P	ccC	ccT	4	4	AY.16.1	0.00188
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	4	4	AY.3.1	0.000341
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	4	4	AY.33	0.000267
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	4	4	AY.34	0.000388
ORF1ab/nsp3	1867	P1867P	ccC	ccT	4	4	AY.98	0.000316
ORF1ab/nsp3	1867	P1867del	CCC	---	4	4	B.1	0.000037
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	4	4	B.1.1.176	0.001757
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	4	4	B.1.1.519	0.000159
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	4	4	B.1.160	0.000125
ORF1ab/nsp3	1867	P1867P	ccC	ccT	4	4	B.1.177.77	0.002905
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	4	4	B.1.177.81	0.000757
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	4	4	B.1.221	0.000284
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	4	4	B.1.369	0.001141
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	4	4	B.1.429	0.000094
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	4	4	B.1.561	0.001588
ORF1ab/nsp3	1867	P1867P	ccC	ccT	4	4	B.1.589	0.030303
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	4	4	B.1.595	0.001044
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	4	4	B.1.621	0.000354
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	4	4	B.1.637	0.000292
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	4	4	C.35	0.003096
ORF1ab/nsp3	1867	P1867P	ccC	ccT	4	4	Q.8	0.00066
ORF1ab/nsp3	1867	P1867P	ccC	ccT	3	3	A.27	0.004967
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	3	3	AY.12	0.000948
ORF1ab/nsp3	1867	P1867P	ccC	ccT	3	3	AY.120	0.000112
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	3	3	AY.120	0.000112
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	3	3	AY.121	0.000406
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	3	3	AY.20	0.000117
ORF1ab/nsp3	1867	P1867P	ccC	ccT	3	3	AY.27	0.000194
ORF1ab/nsp3	1867	P1867P	ccC	ccT	3	3	AY.29.1	0.000662
ORF1ab/nsp3	1867	P1867P	ccC	ccT	3	3	AY.3.1	0.000256
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	3	3	AY.30	0.001187
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	3	3	AY.32	0.001597
ORF1ab/nsp3	1867	P1867P	ccC	ccT	3	3	AY.33	0.0002
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	3	3	AY.36	0.000445
ORF1ab/nsp3	1867	P1867P	ccC	ccT	3	3	AY.37	0.000948
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	3	3	AY.4.2.1	0.000447
ORF1ab/nsp3	1867	P1867P	ccC	ccT	3	3	AY.46.6	0.000217
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	3	3	AY.46.6	0.000217
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	3	AY.6	0.000082
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	3	AY.6	0.000041
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	3	3	AY.60	0.002814
ORF1ab/nsp3	1867	P1867P	ccC	ccT	3	3	AY.71	0.001425
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	3	3	AY.75	0.000168
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	3	3	AY.91	0.002191
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	3	3	AZ.2	0.002463
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	3	3	B.1.1.306	0.001315
ORF1ab/nsp3	1867	P1867P	ccC	ccT	3	3	B.1.1.416	0.002715
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	3	3	B.1.160.24	0.013274
ORF1ab/nsp3	1867	P1867P	ccC	ccT	3	3	B.1.177.7	0.000495
ORF1ab/nsp3	1867	P1867P	ccC	ccT	3	3	B.1.232	0.001612
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	3	3	B.1.258.17	0.000312
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	3	3	B.1.340	0.012876
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	3	3	B.1.36.29	0.001552
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	3	B.1.36.29	0.001035
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	3	B.1.36.29	0.000517
ORF1ab/nsp3	1867	P1867P	ccC	ccT	3	3	B.1.36.8	0.003
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	3	B.1.369	0.00057
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	3	B.1.369	0.000285
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	3	3	B.1.427	0.000151
ORF1ab/nsp3	1867	P1867P	ccC	ccT	3	3	B.1.564	0.001278
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	3	3	B.1.623	0.001609
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	3	3	N.5	0.0053
ORF1ab/nsp3	1867	P1867del1	Ccc	-cc	3	3	P.1	0.000047
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	3	3	P.1	0.000047
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	3	3	Q.2	0.00184
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	3	3	Q.8	0.000495
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	2	2	A.2.5	0.000998
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	A.2.5	0.000998
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	2	2	AY.10	0.00106
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	2	2	AY.106	0.00067
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	AY.117	0.000169
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	2	2	AY.120	0.000074
ORF1ab/nsp3	1867	P1867L	cCc	cTc	2	2	AY.120.2.1	0.000997
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	AY.121	0.000271
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	AY.19	0.002281
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	2	2	AY.23	0.000139
ORF1ab/nsp3	1867	P1867del	CCC	---	2	2	AY.25	0.000012
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	2	2	AY.3.1	0.000171
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	2	2	AY.38	0.000999
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	2	2	AY.4.2	0.000043
ORF1ab/nsp3	1867	P1867del1	Ccc	-cc	2	2	AY.44	0.000012
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	AY.46	0.000208
ORF1ab/nsp3	1867	P1867del	CCC	---	2	2	AY.5	0.000041
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	2	2	AY.5	0.000041
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	2	AY.52	0.000814
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	2	AY.52	0.000814
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	2	2	AY.61	0.00021
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	2	2	AY.75.1	0.000361
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	2	2	AY.9.1	0.000167
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	AY.9.2	0.000073
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	AY.99.2	0.000184
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	B	0.000256
ORF1ab/nsp3	1867	P1867H	cCc	cAc	2	2	B.1	0.000018
ORF1ab/nsp3	1867	P1867del	CCC	---	2	2	B.1.1	0.000036
ORF1ab/nsp3	1867	P1867del1	Ccc	-cc	1	2	B.1.1	0.000018
ORF1ab/nsp3	1867	P1867del1	ccC	cc-	1	2	B.1.1	0.000018
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	B.1.1.216	0.001781
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	B.1.1.220	0.003717
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	2	2	B.1.1.25	0.001137
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	2	2	B.1.1.306	0.000877
ORF1ab/nsp3	1867	P1867del	CCC	---	2	2	B.1.1.311	0.000716
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	2	B.1.1.318	0.000302
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	2	B.1.1.318	0.000302
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	2	2	B.1.1.418	0.045455
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	2	2	B.1.1.523	0.003125
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	2	2	B.1.1.525	0.010929
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	B.1.111	0.00235
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	2	2	B.1.177.12	0.000303
ORF1ab/nsp3	1867	P1867L	cCc	cTc	2	2	B.1.177.12	0.000303
ORF1ab/nsp3	1867	P1867del	CCC	---	2	2	B.1.177.17	0.001642
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	2	2	B.1.177.33	0.003289
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	2	2	B.1.177.55	0.004662
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	2	2	B.1.177.73	0.001133
ORF1ab/nsp3	1867	P1867del	CCC	---	2	2	B.1.177.87	0.001456
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	B.1.214.2	0.001199
ORF1ab/nsp3	1867	P1867L	cCC	cTG	2	2	B.1.235	0.005038
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	B.1.241	0.001623
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	B.1.258	0.000133
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	2	2	B.1.258	0.000133
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	B.1.258.11	0.000793
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	2	2	B.1.258.4	0.006897
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	B.1.298	0.004228
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	2	2	B.1.351	0.000059
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	2	2	B.1.362	0.003082
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	B.1.409	0.001563
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	B.1.466.2	0.000782
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	B.1.499	0.002101
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	2	2	B.1.525	0.000226
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	B.1.588	0.00182
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	B.1.609	0.000959
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	2	2	B.1.617.1	0.000258
ORF1ab/nsp3	1867	P1867del	CCC	---	2	2	B.1.617.2	0.000008
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	2	2	B.1.621	0.000177
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	B.1.637	0.000146
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	B.4	0.004415
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	2	2	N.6	0.014184
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	2	2	P.1.14	0.000096
ORF1ab/nsp3	1867	P1867P	ccC	ccT	2	2	P.1.15	0.000465
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	2	2	P.1.15	0.000465
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	2	P.2	0.000187
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	2	P.2	0.000187
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	2	2	R.1	0.00018
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	2	2	W.4	0.002703
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	A.1	0.000282
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	A.19	0.009434
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	1	A.2	0.000662
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	1	A.2.4	0.003367
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	A.21	0.00277
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	A.28	0.002646
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	AD.2	0.000219
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AD.2	0.000219
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AE.8	0.000489
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AH.3	0.003802
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	AH.3	0.003802
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AL.1	0.012987
ORF1ab/nsp3	1867	P1867R	cCc	cGc	1	1	All	0
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.101	0.00049
ORF1ab/nsp3	1867	P1867del1	ccC	cc-	1	1	AY.101	0.00049
ORF1ab/nsp3	1867	P1867H	cCc	cAc	1	1	AY.103	0.000006
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	AY.104	0.001984
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.108	0.001103
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.111	0.000183
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.111	0.000183
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.113	0.000142
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.114	0.000231
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.116	0.000287
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.116	0.000287
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.116.1	0.000311
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.118	0.000063
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.118	0.000063
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	AY.120	0.000037
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.120.2	0.001285
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.13	0.000161
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.14	0.000088
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.16.1	0.00047
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	AY.19	0.00114
ORF1ab/nsp3	1867	P1867H	cCc	cAc	1	1	AY.23	0.00007
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	1	AY.23.1	0.000417
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	AY.29.1	0.000221
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.32	0.000532
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	AY.33	0.000067
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.34.1	0.00051
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.35	0.000233
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.36	0.000148
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.38	0.000499
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.39.1	0.00004
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	AY.39.1	0.00004
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.4.4	0.000409
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.4.5	0.000107
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.4.5	0.000107
ORF1ab/nsp3	1867	P1867A	Ccc	Gcc	1	1	AY.4.5	0.000107
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.40	0.000964
ORF1ab/nsp3	1867	P1867L	cCc	cTc	1	1	AY.44	0.000006
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.46.2	0.000635
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.46.3	0.000934
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.46.4	0.000165
ORF1ab/nsp3	1867	P1867del1	CcC	-cN	1	1	AY.46.6	0.000072
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.5.3	0.000337
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.51	0.000909
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.53	0.000288
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.54	0.000095
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.56	0.001605
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.58	0.000907
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	AY.59	0.00053
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.59	0.00053
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	AY.6	0.000041
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	AY.60	0.000938
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.61	0.000105
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.65	0.000533
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.65	0.000533
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.68	0.000274
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.69	0.000187
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	AY.7.1	0.000113
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.7.1	0.000113
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.70	0.000209
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	AY.72	0.001361
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	1	AY.74	0.000116
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	AY.74	0.000116
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	AY.75.1	0.00018
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.79	0.001211
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	AY.81	0.001992
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.87	0.000833
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	AY.89	0.004902
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	AY.9	0.000068
ORF1ab/nsp3	1867	P1867L	cCc	cTc	1	1	AY.9	0.000068
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.9	0.000068
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.9.2	0.000037
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	AY.90	0.000684
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	AY.92	0.000287
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	AY.98	0.000079
ORF1ab/nsp3	1867	P1867L	cCc	cTc	1	1	AY.99.2	0.000092
ORF1ab/nsp3	1867	P1867R	cCc	cGc	1	1	B	0.000128
ORF1ab/nsp3	1867	P1867L	cCc	cTc	1	1	B.1	0.000009
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.1.1	0.000327
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.1.10	0.001115
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.1.141	0.002012
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.1.153	0.001095
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.1.157	0.000913
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	B.1.1.159	0.004673
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.1.159	0.004673
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.1.164	0.005155
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.1.214	0.000055
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.1.231	0.003096
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.1.232	0.001815
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	B.1.1.236	0.006897
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.1.263	0.001558
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.1.277	0.000759
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.1.301	0.001179
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	B.1.1.306	0.000438
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.1.306	0.000438
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.1.311	0.000358
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.1.312	0.001912
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.1.317	0.000412
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	B.1.1.317	0.000412
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.1.317	0.000412
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.1.320	0.018182
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	B.1.1.33	0.000421
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.1.333	0.001076
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.1.344	0.010753
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	B.1.1.369	0.000446
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.1.369	0.000446
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	1	B.1.1.37	0.000193
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.1.372	0.000689
ORF1ab/nsp3	1867	P1867del2	cCC	c--	1	1	B.1.1.372	0.000689
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.1.397	0.002252
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.1.416	0.000905
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.1.433	0.001425
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.1.448	0.002033
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	B.1.1.46	0.004367
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.1.461	0.012048
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	1	B.1.1.464	0.001473
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.1.528	0.004808
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.1.61	0.008772
ORF1ab/nsp3	1867	P1867H	cCc	cAc	1	1	B.1.1.7	0.000001
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	B.1.1.97	0.029412
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.110	0.004525
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.110.3	0.000718
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	B.1.115	0.021739
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.157	0.002985
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.160.26	0.002421
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.167	0.007812
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	B.1.177.10	0.000878
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	B.1.177.15	0.000631
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	B.1.177.16	0.000664
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.177.17	0.000821
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	B.1.177.18	0.00116
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	B.1.177.21	0.000076
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.177.5	0.001242
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	B.1.177.51	0.004566
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.177.55	0.002331
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.177.56	0.000668
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.177.60	0.000218
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	B.1.177.63	0.002703
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.177.7	0.000165
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	B.1.177.7	0.000165
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.177.77	0.000726
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.177.82	0.000477
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	B.1.177.86	0.000183
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	B.1.177.9	0.001332
ORF1ab/nsp3	1867	P1867del1	Ccc	-cc	1	1	B.1.2	0.000009
ORF1ab/nsp3	1867	P1867H	cCc	cAc	1	1	B.1.2	0.000009
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.214	0.003663
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.221	0.000071
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.221.4	0.004167
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	1	B.1.221.4	0.004167
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	1	B.1.222	0.001692
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.239	0.001221
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.243	0.00007
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.263	0.047619
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.265	0.001271
ORF1ab/nsp3	1867	P1867H	cCc	cAc	1	1	B.1.265	0.001271
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.311	0.000275
ORF1ab/nsp3	1867	P1867A	Ccc	Gcc	1	1	B.1.351	0.00003
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.351.2	0.000303
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	B.1.36.1	0.00114
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.36.17	0.000494
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.36.22	0.001208
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.36.27	0.000763
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.36.31	0.001751
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	B.1.36.31	0.001751
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	B.1.36.38	0.001642
ORF1ab/nsp3	1867	P1867L	cCc	cTc	1	1	B.1.367	0.000792
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.416	0.001269
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	B.1.416.1	0.001563
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.426	0.001009
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.456	0.003268
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.459	0.004082
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.485	0.014925
ORF1ab/nsp3	1867	P1867H	cCc	cAc	1	1	B.1.526	0.000024
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.532	0.006211
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.550	0.013699
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.551	0.00129
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	B.1.575	0.000303
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	1	B.1.577	0.000687
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.588	0.00091
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	B.1.595.4	0.007299
ORF1ab/nsp3	1867	P1867del1	Ccc	-cc	1	1	B.1.596	0.000087
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	1	B.1.617.1	0.000129
ORF1ab/nsp3	1867	P1867H	cCC	cAT	1	1	B.1.617.2	0.000004
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.1.621	0.000089
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.628	0.000352
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.1.631	0.003367
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	B.1.637	0.000073
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	B.34	0.013699
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	B.34	0.013699
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	B.6	0.00091
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	C.14	0.004329
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	C.17	0.055556
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	C.35	0.000774
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	C.35	0.000774
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	C.37	0.000116
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	C.37	0.000116
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	C.37	0.000116
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	C.6	0.037037
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	D.2	0.000075
ORF1ab/nsp3	1867	P1867L	cCc	cTc	1	1	D.2	0.000075
ORF1ab/nsp3	1867	P1867P	ccC	ccA	1	1	K.1	0.02381
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	L.1	0.001905
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	N.5	0.001767
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	P.1	0.000016
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	P.1.1	0.000318
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	P.1.10	0.000269
ORF1ab/nsp3	1867	P1867del1	Ccc	-cc	1	1	P.1.14	0.000048
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	P.1.2	0.001156
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	P.1.7	0.000319
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	P.2	0.000187
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	Q.1	0.000126
ORF1ab/nsp3	1867	P1867del	CCC	---	1	1	Q.1	0.000126
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	Q.1	0.000126
ORF1ab/nsp3	1867	P1867T	Ccc	Acc	1	1	Q.1	0.000126
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	Q.3	0.000145
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	Q.4	0.000455
ORF1ab/nsp3	1867	P1867S	Ccc	Tcc	1	1	Q.8	0.000165
ORF1ab/nsp3	1867	P1867P	ccC	ccT	1	1	R.1	0.00009

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.