CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF3a : CodonNum = 240

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
ORF3a	240	P240S		nonsyn	Cct	Tct	17374	17372	0.999885	26110-26112
ORF3a	240	P240S		nonsyn	CcT	TcC	17374	2	0.000115115	26110-26112
ORF3a	240	P240L		nonsyn	cCt	cTt	10428	10421	0.999329	26110-26112
ORF3a	240	P240L		nonsyn	cCT	cTA	10428	7	0.00067127	26110-26112
ORF3a	240	P240P		syn	ccT	ccC	901	830	0.921199	26110-26112
ORF3a	240	P240P		syn	ccT	ccA	901	54	0.0599334	26110-26112
ORF3a	240	P240P		syn	ccT	ccG	901	17	0.0188679	26110-26112
ORF3a	240	P240H		nonsyn	cCt	cAt	827	827	1	26110-26112
ORF3a	240	P240R		nonsyn	cCt	cGt	103	103	1	26110-26112
ORF3a	240	P240T		nonsyn	Cct	Act	88	87	0.988636	26110-26112
ORF3a	240	P240T		nonsyn	CcT	AcG	88	1	0.0113636	26110-26112
ORF3a	240	P240del		del	CCT	---	44	44	1	26110-26112
ORF3a	240	P240F		nonsyn	CCt	TTt	7	7	1	26110-26112
ORF3a	240	P240A		nonsyn	Cct	Gct	6	6	1	26110-26112
ORF3a	240	P240del1		del	ccT	cc-	5	2	0.4	26110-26112
ORF3a	240	P240del1		del	Cct	-ct	5	2	0.4	26110-26112
ORF3a	240	P240del1		del	CcT	-cA	5	1	0.2	26110-26112
ORF3a	240	P240V		nonsyn	CCt	GTt	2	2	1	26110-26112
ORF3a	240	P240D		nonsyn	CCt	GAt	1	1	1	26110-26112
ORF3a	240	P240Q		nonsyn	cCT	cAA	1	1	1	26110-26112

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
ORF3a	240	P240S	Cct	Tct	17372	17374	All	0.003323
ORF3a	240	P240S	CcT	TcC	2	17374	All	0
ORF3a	240	P240S	Cct	Tct	11525	11525	B.1.1.7	0.010317
ORF3a	240	P240L	cCt	cTt	10421	10428	All	0.001993
ORF3a	240	P240L	cCT	cTA	7	10428	All	0.000001
ORF3a	240	P240L	cCt	cTt	1931	1931	AY.4	0.003005
ORF3a	240	P240L	cCt	cTt	1599	1603	B.1.1.7	0.001431
ORF3a	240	P240L	cCT	cTA	4	1603	B.1.1.7	0.000004
ORF3a	240	P240L	cCt	cTt	917	917	AY.42	0.036891
ORF3a	240	P240P	ccT	ccC	830	901	All	0.000159
ORF3a	240	P240P	ccT	ccA	54	901	All	0.00001
ORF3a	240	P240P	ccT	ccG	17	901	All	0.000003
ORF3a	240	P240H	cCt	cAt	827	827	All	0.000158
ORF3a	240	P240L	cCt	cTt	753	753	AY.44	0.004583
ORF3a	240	P240L	cCt	cTt	743	743	B.1.2	0.006542
ORF3a	240	P240S	Cct	Tct	669	669	AY.3	0.006654
ORF3a	240	P240H	cCt	cAt	614	614	B.1.617.2	0.002312
ORF3a	240	P240L	cCt	cTt	600	600	B.1.617.2	0.002259
ORF3a	240	P240S	Cct	Tct	516	516	AY.4	0.000803
ORF3a	240	P240S	Cct	Tct	426	426	B.1	0.003902
ORF3a	240	P240S	Cct	Tct	390	390	B.1.240	0.08407
ORF3a	240	P240L	cCt	cTt	382	382	B.1.427	0.01929
ORF3a	240	P240P	ccT	ccC	315	315	AY.23	0.021971
ORF3a	240	P240S	Cct	Tct	313	313	AY.119	0.011051
ORF3a	240	P240S	Cct	Tct	258	258	Q.8	0.042546
ORF3a	240	P240S	Cct	Tct	246	246	B.1.617.2	0.000926
ORF3a	240	P240L	cCt	cTt	223	223	AY.103	0.001385
ORF3a	240	P240S	Cct	Tct	208	208	AY.49	0.664537
ORF3a	240	P240L	cCt	cTt	173	173	AY.43	0.000766
ORF3a	240	P240L	cCt	cTt	167	167	AY.39	0.004127
ORF3a	240	P240S	Cct	Tct	157	157	AY.103	0.000975
ORF3a	240	P240S	Cct	Tct	152	152	P.1	0.002395
ORF3a	240	P240S	Cct	Tct	147	148	AY.25	0.000884
ORF3a	240	P240S	CcT	TcC	1	148	AY.25	0.000006
ORF3a	240	P240L	cCt	cTt	143	143	AY.25	0.00086
ORF3a	240	P240L	cCt	cTt	141	141	B.1	0.001291
ORF3a	240	P240S	Cct	Tct	134	134	B.1.1	0.002431
ORF3a	240	P240L	cCt	cTt	133	133	B.1.466.1	0.956835
ORF3a	240	P240S	Cct	Tct	126	126	AY.43	0.000558
ORF3a	240	P240S	Cct	Tct	126	126	B.1.2	0.001109
ORF3a	240	P240L	cCt	cTt	118	118	AY.46.4	0.019411
ORF3a	240	P240S	Cct	Tct	116	116	B.1.1.219	0.58
ORF3a	240	P240P	ccT	ccC	114	114	C.38	0.919355
ORF3a	240	P240L	cCt	cTt	109	109	B.1.596	0.009498
ORF3a	240	P240L	cCt	cTt	106	106	AY.29	0.001672
ORF3a	240	P240R	cCt	cGt	103	103	All	0.00002
ORF3a	240	P240S	Cct	Tct	102	102	B.1.571	0.990291
ORF3a	240	P240P	ccT	ccC	99	99	AY.47	0.003079
ORF3a	240	P240T	Cct	Act	87	88	All	0.000017
ORF3a	240	P240T	CcT	AcG	1	88	All	0
ORF3a	240	P240S	Cct	Tct	87	87	AY.44	0.00053
ORF3a	240	P240L	cCt	cTt	85	85	B.1.1.141	0.171026
ORF3a	240	P240L	cCt	cTt	84	85	P.1	0.001323
ORF3a	240	P240L	cCT	cTA	1	85	P.1	0.000016
ORF3a	240	P240L	cCt	cTt	83	83	B.1.526	0.001951
ORF3a	240	P240L	cCt	cTt	78	78	B.1.438.1	0.008366
ORF3a	240	P240L	cCt	cTt	74	74	AY.102	0.001962
ORF3a	240	P240S	Cct	Tct	74	74	Q.3	0.010732
ORF3a	240	P240L	cCt	cTt	70	70	B.1.351.2	0.02118
ORF3a	240	P240L	cCt	cTt	66	66	AY.14	0.005809
ORF3a	240	P240L	cCt	cTt	66	66	B.1.429	0.001553
ORF3a	240	P240L	cCt	cTt	63	63	B.1.1	0.001143
ORF3a	240	P240S	Cct	Tct	62	62	B.1.177	0.000816
ORF3a	240	P240S	Cct	Tct	60	60	AY.46.2	0.038119
ORF3a	240	P240S	Cct	Tct	52	52	AY.29	0.00082
ORF3a	240	P240S	Cct	Tct	48	48	B.1.221	0.00341
ORF3a	240	P240L	cCt	cTt	48	48	B.1.604	0.827586
ORF3a	240	P240S	Cct	Tct	47	47	B.1.160	0.001466
ORF3a	240	P240L	cCt	cTt	47	47	B.1.177	0.000619
ORF3a	240	P240del	CCT	---	44	44	All	0.000008
ORF3a	240	P240L	cCt	cTt	44	44	AY.116.1	0.013703
ORF3a	240	P240S	Cct	Tct	44	44	AY.5	0.000909
ORF3a	240	P240L	cCt	cTt	43	43	AY.3	0.000428
ORF3a	240	P240R	cCt	cGt	43	43	AY.43	0.000191
ORF3a	240	P240L	cCt	cTt	42	43	B.1.351	0.001249
ORF3a	240	P240L	cCT	cTA	1	43	B.1.351	0.00003
ORF3a	240	P240L	cCt	cTt	42	42	C.37	0.004875
ORF3a	240	P240L	cCt	cTt	41	41	AY.39.1	0.001624
ORF3a	240	P240S	Cct	Tct	41	41	B.1.258	0.002728
ORF3a	240	P240L	cCt	cTt	40	40	AY.47	0.001244
ORF3a	240	P240S	Cct	Tct	40	40	B.1.351	0.001189
ORF3a	240	P240P	ccT	ccC	21	39	B.1.1.7	0.000019
ORF3a	240	P240P	ccT	ccA	18	39	B.1.1.7	0.000016
ORF3a	240	P240P	ccT	ccC	26	37	B.1.617.2	0.000098
ORF3a	240	P240P	ccT	ccA	11	37	B.1.617.2	0.000041
ORF3a	240	P240S	Cct	Tct	35	36	AY.23	0.002441
ORF3a	240	P240S	CcT	TcC	1	36	AY.23	0.00007
ORF3a	240	P240L	cCt	cTt	36	36	AY.26	0.001019
ORF3a	240	P240P	ccT	ccC	35	36	AY.3	0.000348
ORF3a	240	P240P	ccT	ccA	1	36	AY.3	0.00001
ORF3a	240	P240L	cCt	cTt	34	34	B.1.1.214	0.001886
ORF3a	240	P240L	cCt	cTt	34	34	B.1.1.519	0.00135
ORF3a	240	P240S	Cct	Tct	34	34	B.1.234	0.004486
ORF3a	240	P240S	Cct	Tct	34	34	B.1.639	0.73913
ORF3a	240	P240S	Cct	Tct	32	32	AY.118	0.002005
ORF3a	240	P240S	Cct	Tct	30	30	B.1.427	0.001515
ORF3a	240	P240S	Cct	Tct	29	29	AY.4.2	0.000629
ORF3a	240	P240L	cCt	cTt	29	29	B.1.621	0.002567
ORF3a	240	P240T	Cct	Act	29	29	P.1	0.000457
ORF3a	240	P240S	Cct	Tct	28	28	B.1.1.519	0.001112
ORF3a	240	P240L	cCt	cTt	27	27	AY.119	0.000953
ORF3a	240	P240H	cCt	cAt	27	27	AY.3	0.000269
ORF3a	240	P240L	cCt	cTt	27	27	P.2	0.005039
ORF3a	240	P240L	cCt	cTt	26	26	AY.5	0.000537
ORF3a	240	P240S	Cct	Tct	26	26	Q.1	0.003284
ORF3a	240	P240H	cCt	cAt	25	25	AY.43	0.000111
ORF3a	240	P240S	Cct	Tct	25	25	B.1.177.81	0.004733
ORF3a	240	P240L	cCt	cTt	25	25	B.1.36	0.003648
ORF3a	240	P240L	cCt	cTt	24	24	AY.100	0.001104
ORF3a	240	P240L	cCt	cTt	24	24	AY.32	0.01278
ORF3a	240	P240H	cCt	cAt	24	24	B.1.1.7	0.000021
ORF3a	240	P240L	cCt	cTt	24	24	B.1.177.24	0.031088
ORF3a	240	P240S	Cct	Tct	23	23	AY.26	0.000651
ORF3a	240	P240P	ccT	ccC	23	23	AY.34.1	0.011729
ORF3a	240	P240L	cCt	cTt	23	23	B.1.243	0.0016
ORF3a	240	P240S	Cct	Tct	22	22	AY.39	0.000544
ORF3a	240	P240P	ccT	ccC	22	22	B.1.160	0.000686
ORF3a	240	P240S	Cct	Tct	22	22	B.1.243	0.001531
ORF3a	240	P240S	Cct	Tct	21	21	AY.20	0.000816
ORF3a	240	P240P	ccT	ccC	21	21	AY.75.1	0.003787
ORF3a	240	P240P	ccT	ccC	20	20	AY.34	0.001939
ORF3a	240	P240L	cCt	cTt	20	20	AY.4.4	0.008183
ORF3a	240	P240L	cCt	cTt	19	19	AY.20	0.000738
ORF3a	240	P240L	cCt	cTt	19	19	AY.9.2	0.000698
ORF3a	240	P240L	cCt	cTt	19	19	B.1.221	0.00135
ORF3a	240	P240L	cCt	cTt	19	19	B.1.258	0.001264
ORF3a	240	P240S	Cct	Tct	19	19	B.1.429	0.000447
ORF3a	240	P240S	Cct	Tct	18	18	A.27	0.029801
ORF3a	240	P240L	cCt	cTt	18	18	AY.118	0.001128
ORF3a	240	P240H	cCt	cAt	18	18	AY.4	0.000028
ORF3a	240	P240R	cCt	cGt	18	18	B.1.1.7	0.000016
ORF3a	240	P240L	cCt	cTt	18	18	B.1.160	0.000561
ORF3a	240	P240H	cCt	cAt	18	18	B.1.177.86	0.003302
ORF3a	240	P240S	Cct	Tct	17	17	AY.117	0.001437
ORF3a	240	P240L	cCt	cTt	17	17	AY.120	0.000632
ORF3a	240	P240S	Cct	Tct	17	17	AY.47	0.000529
ORF3a	240	P240T	Cct	Act	17	17	AY.54	0.001621
ORF3a	240	P240S	Cct	Tct	17	17	B.1.1.216	0.015138
ORF3a	240	P240S	Cct	Tct	17	17	B.1.637	0.001242
ORF3a	240	P240S	Cct	Tct	16	16	AY.102	0.000424
ORF3a	240	P240L	cCt	cTt	16	16	AY.107	0.007456
ORF3a	240	P240P	ccT	ccC	16	16	AY.33	0.001068
ORF3a	240	P240L	cCt	cTt	16	16	AY.4.2	0.000347
ORF3a	240	P240S	Cct	Tct	16	16	AY.54	0.001526
ORF3a	240	P240S	Cct	Tct	16	16	AY.98	0.001264
ORF3a	240	P240S	Cct	Tct	16	16	B.1.1.28	0.00498
ORF3a	240	P240L	cCt	cTt	16	16	B.1.470	0.022472
ORF3a	240	P240L	cCt	cTt	16	16	B.1.637	0.001169
ORF3a	240	P240L	cCt	cTt	15	15	AY.88	0.013263
ORF3a	240	P240S	Cct	Tct	14	14	AY.46	0.001457
ORF3a	240	P240L	cCt	cTt	14	14	AY.59	0.007415
ORF3a	240	P240S	Cct	Tct	14	14	B.1.1.214	0.000776
ORF3a	240	P240S	Cct	Tct	14	14	B.1.177.73	0.007928
ORF3a	240	P240P	ccT	ccC	10	13	AY.43	0.000044
ORF3a	240	P240P	ccT	ccA	3	13	AY.43	0.000013
ORF3a	240	P240P	ccT	ccC	12	13	AY.44	0.000073
ORF3a	240	P240P	ccT	ccA	1	13	AY.44	0.000006
ORF3a	240	P240S	Cct	Tct	13	13	B.1.526	0.000306
ORF3a	240	P240S	Cct	Tct	12	12	AY.114	0.002773
ORF3a	240	P240S	Cct	Tct	12	12	AY.121	0.001624
ORF3a	240	P240S	Cct	Tct	12	12	AY.16	0.004556
ORF3a	240	P240H	cCt	cAt	12	12	AY.4.2	0.00026
ORF3a	240	P240L	cCt	cTt	12	12	AY.9.1	0.001005
ORF3a	240	P240S	Cct	Tct	12	12	B.1.177.21	0.000918
ORF3a	240	P240S	Cct	Tct	12	12	B.1.177.62	0.014303
ORF3a	240	P240L	cCt	cTt	12	12	B.1.234	0.001583
ORF3a	240	P240S	Cct	Tct	12	12	B.1.497	0.003777
ORF3a	240	P240L	cCt	cTt	12	12	B.1.575	0.003641
ORF3a	240	P240L	cCt	cTt	12	12	B.1.617.1	0.001548
ORF3a	240	P240L	cCt	cTt	12	12	P.1.14	0.000574
ORF3a	240	P240L	cCt	cTt	12	12	Q.8	0.001979
ORF3a	240	P240L	cCt	cTt	11	11	AY.45	0.001339
ORF3a	240	P240L	cCt	cTt	11	11	AY.61	0.001153
ORF3a	240	P240L	cCt	cTt	11	11	B.1.1.241	0.022774
ORF3a	240	P240S	Cct	Tct	11	11	B.1.1.63	0.004244
ORF3a	240	P240S	Cct	Tct	11	11	B.1.177.79	0.025761
ORF3a	240	P240S	Cct	Tct	11	11	B.1.258.17	0.001144
ORF3a	240	P240S	Cct	Tct	11	11	B.1.36.29	0.005691
ORF3a	240	P240P	ccT	ccG	10	11	C.37	0.001161
ORF3a	240	P240P	ccT	ccC	1	11	C.37	0.000116
ORF3a	240	P240R	cCt	cGt	11	11	P.1	0.000173
ORF3a	240	P240S	Cct	Tct	11	11	P.1.10	0.002964
ORF3a	240	P240T	Cct	Act	10	10	AY.4	0.000016
ORF3a	240	P240P	ccT	ccC	6	10	AY.4	0.000009
ORF3a	240	P240P	ccT	ccA	3	10	AY.4	0.000005
ORF3a	240	P240P	ccT	ccG	1	10	AY.4	0.000002
ORF3a	240	P240L	cCt	cTt	10	10	AY.46	0.001041
ORF3a	240	P240H	cCt	cAt	10	10	B.1	0.000092
ORF3a	240	P240H	cCt	cAt	10	10	B.1.1.216	0.008905
ORF3a	240	P240S	Cct	Tct	10	10	B.1.1.222	0.00204
ORF3a	240	P240L	cCt	cTt	10	10	B.1.1.33	0.004209
ORF3a	240	P240S	Cct	Tct	10	10	B.1.177.12	0.001517
ORF3a	240	P240P	ccT	ccC	10	10	B.1.2	0.000088
ORF3a	240	P240S	Cct	Tct	9	9	AY.100	0.000414
ORF3a	240	P240P	ccT	ccC	7	9	AY.103	0.000043
ORF3a	240	P240P	ccT	ccG	1	9	AY.103	0.000006
ORF3a	240	P240P	ccT	ccA	1	9	AY.103	0.000006
ORF3a	240	P240L	cCt	cTt	9	9	AY.24	0.003879
ORF3a	240	P240L	cCt	cTt	9	9	B.1.1.265	0.028391
ORF3a	240	P240S	Cct	Tct	9	9	B.1.1.316	0.008326
ORF3a	240	P240S	Cct	Tct	9	9	B.1.438.1	0.000965
ORF3a	240	P240S	Cct	Tct	9	9	B.1.596	0.000784
ORF3a	240	P240S	Cct	Tct	9	9	B.1.609	0.004314
ORF3a	240	P240S	Cct	Tct	9	9	C.37	0.001045
ORF3a	240	P240L	cCt	cTt	8	8	AY.23	0.000558
ORF3a	240	P240L	cCt	cTt	8	8	AY.3.1	0.000682
ORF3a	240	P240del	CCT	---	8	8	AY.5	0.000165
ORF3a	240	P240L	cCt	cTt	8	8	AY.54	0.000763
ORF3a	240	P240S	Cct	Tct	8	8	B.1.1.464	0.011782
ORF3a	240	P240L	cCt	cTt	8	8	B.1.400	0.003432
ORF3a	240	P240F	CCt	TTt	7	7	All	0.000001
ORF3a	240	P240P	ccT	ccC	7	7	AY.25	0.000042
ORF3a	240	P240S	Cct	Tct	7	7	AY.36	0.001037
ORF3a	240	P240H	cCt	cAt	7	7	AY.44	0.000043
ORF3a	240	P240L	cCt	cTt	7	7	AY.5.3	0.002362
ORF3a	240	P240P	ccT	ccC	7	7	AY.74	0.00081
ORF3a	240	P240S	Cct	Tct	7	7	AY.75	0.000392
ORF3a	240	P240L	cCt	cTt	7	7	AY.92	0.002011
ORF3a	240	P240L	cCt	cTt	7	7	B.1.1.216	0.006233
ORF3a	240	P240T	Cct	Act	7	7	B.1.243	0.000487
ORF3a	240	P240S	Cct	Tct	7	7	B.1.466	0.162791
ORF3a	240	P240L	cCt	cTt	7	7	B.1.582	0.003435
ORF3a	240	P240S	Cct	Tct	7	7	B.1.617.1	0.000903
ORF3a	240	P240S	Cct	Tct	7	7	B.1.621	0.00062
ORF3a	240	P240L	cCt	cTt	7	7	P.1.15	0.001626
ORF3a	240	P240S	Cct	Tct	7	7	P.1.2	0.008092
ORF3a	240	P240A	Cct	Gct	6	6	All	0.000001
ORF3a	240	P240L	cCt	cTt	6	6	AY.113	0.000854
ORF3a	240	P240S	Cct	Tct	6	6	AY.13	0.000966
ORF3a	240	P240L	cCt	cTt	6	6	AY.75.1	0.001082
ORF3a	240	P240L	cCt	cTt	6	6	AY.98	0.000474
ORF3a	240	P240S	Cct	Tct	6	6	AZ.2	0.004926
ORF3a	240	P240S	Cct	Tct	6	6	B.1.1.33	0.002525
ORF3a	240	P240L	cCt	cTt	6	6	B.1.1.417	0.016216
ORF3a	240	P240S	Cct	Tct	6	6	B.1.128	0.003812
ORF3a	240	P240S	Cct	Tct	6	6	B.1.369	0.001711
ORF3a	240	P240S	Cct	Tct	6	6	B.1.462	0.043478
ORF3a	240	P240S	Cct	Tct	6	6	B.1.595	0.001566
ORF3a	240	P240L	cCt	cTt	6	6	C.36.2	0.206897
ORF3a	240	P240H	cCt	cAt	6	6	C.37	0.000696
ORF3a	240	P240L	cCt	cTt	6	6	P.1.7	0.001916
ORF3a	240	P240L	cCt	cTt	5	5	A	0.001935
ORF3a	240	P240del1	Cct	-ct	2	5	All	0
ORF3a	240	P240del1	ccT	cc-	2	5	All	0
ORF3a	240	P240del1	CcT	-cA	1	5	All	0
ORF3a	240	P240S	Cct	Tct	5	5	AY.120	0.000186
ORF3a	240	P240L	cCt	cTt	5	5	AY.2	0.001781
ORF3a	240	P240S	Cct	Tct	5	5	AY.24	0.002155
ORF3a	240	P240L	cCt	cTt	5	5	AY.33	0.000334
ORF3a	240	P240L	cCt	cTt	5	5	AY.36	0.000741
ORF3a	240	P240R	cCt	cGt	5	5	AY.4	0.000008
ORF3a	240	P240P	ccT	ccC	5	5	AY.46	0.00052
ORF3a	240	P240L	cCt	cTt	5	5	B.1.1.192	0.011547
ORF3a	240	P240H	cCt	cAt	5	5	B.1.1.269	0.006766
ORF3a	240	P240S	Cct	Tct	5	5	B.1.1.349	0.051546
ORF3a	240	P240L	cCt	cTt	5	5	B.1.177.16	0.003322
ORF3a	240	P240L	cCt	cTt	5	5	B.1.177.21	0.000382
ORF3a	240	P240S	Cct	Tct	5	5	B.1.36	0.00073
ORF3a	240	P240L	cCt	cTt	5	5	B.1.587	0.009488
ORF3a	240	P240T	Cct	Act	5	5	B.1.617.2	0.000019
ORF3a	240	P240L	cCt	cTt	5	5	B.28	0.016393
ORF3a	240	P240H	cCt	cAt	5	5	P.1	0.000079
ORF3a	240	P240P	ccT	ccC	3	5	P.1	0.000047
ORF3a	240	P240P	ccT	ccG	1	5	P.1	0.000016
ORF3a	240	P240P	ccT	ccA	1	5	P.1	0.000016
ORF3a	240	P240del	CCT	---	4	4		0.222222
ORF3a	240	P240L	cCt	cTt	4	4	AD.2	0.000876
ORF3a	240	P240P	ccT	ccA	2	4	AY.102	0.000053
ORF3a	240	P240P	ccT	ccC	2	4	AY.102	0.000053
ORF3a	240	P240L	cCt	cTt	4	4	AY.12	0.001264
ORF3a	240	P240P	ccT	ccC	4	4	AY.39	0.000099
ORF3a	240	P240del	CCT	---	4	4	AY.43	0.000018
ORF3a	240	P240L	cCt	cTt	4	4	AY.48	0.00186
ORF3a	240	P240L	cCt	cTt	4	4	AY.9	0.00027
ORF3a	240	P240S	Cct	Tct	4	4	B	0.000511
ORF3a	240	P240P	ccT	ccC	3	4	B.1	0.000027
ORF3a	240	P240P	ccT	ccA	1	4	B.1	0.000009
ORF3a	240	P240P	ccT	ccA	4	4	B.1.1	0.000073
ORF3a	240	P240L	cCt	cTt	4	4	B.1.1.164	0.020619
ORF3a	240	P240L	cCt	cTt	4	4	B.1.1.222	0.000816
ORF3a	240	P240L	cCt	cTt	4	4	B.1.1.306	0.001754
ORF3a	240	P240S	Cct	Tct	4	4	B.1.1.39	0.002039
ORF3a	240	P240P	ccT	ccC	4	4	B.1.1.519	0.000159
ORF3a	240	P240F	CCt	TTt	4	4	B.1.1.7	0.000004
ORF3a	240	P240T	Cct	Act	4	4	B.1.1.7	0.000004
ORF3a	240	P240del	CCT	---	4	4	B.1.1.7	0.000004
ORF3a	240	P240S	Cct	Tct	4	4	B.1.210	0.008529
ORF3a	240	P240S	Cct	Tct	4	4	B.1.214.2	0.002398
ORF3a	240	P240L	cCt	cTt	4	4	B.1.258.17	0.000416
ORF3a	240	P240L	cCt	cTt	4	4	B.1.260	0.013378
ORF3a	240	P240del	CCT	---	4	4	B.1.351	0.000119
ORF3a	240	P240S	Cct	Tct	4	4	B.1.396	0.002823
ORF3a	240	P240H	cCt	cAt	4	4	B.1.400	0.001716
ORF3a	240	P240S	Cct	Tct	4	4	B.1.517	0.001708
ORF3a	240	P240L	cCt	cTt	4	4	B.1.525	0.000453
ORF3a	240	P240del	CCT	---	4	4	B.1.525	0.000453
ORF3a	240	P240S	Cct	Tct	4	4	B.1.575	0.001214
ORF3a	240	P240L	cCt	cTt	4	4	B.1.576	0.003626
ORF3a	240	P240S	Cct	Tct	4	4	B.1.576	0.003626
ORF3a	240	P240S	Cct	Tct	4	4	B.1.628	0.001409
ORF3a	240	P240L	cCt	cTt	4	4	B.1.631	0.013468
ORF3a	240	P240L	cCt	cTt	4	4	Q.3	0.00058
ORF3a	240	P240L	cCt	cTt	3	3	A.2.5	0.001497
ORF3a	240	P240R	cCt	cGt	3	3	AY.102	0.00008
ORF3a	240	P240R	cCt	cGt	3	3	AY.103	0.000019
ORF3a	240	P240L	cCt	cTt	3	3	AY.105	0.001929
ORF3a	240	P240L	cCt	cTt	3	3	AY.116	0.00086
ORF3a	240	P240L	cCt	cTt	3	3	AY.117	0.000254
ORF3a	240	P240P	ccT	ccA	2	3	AY.120	0.000074
ORF3a	240	P240P	ccT	ccC	1	3	AY.120	0.000037
ORF3a	240	P240L	cCt	cTt	3	3	AY.13	0.000483
ORF3a	240	P240L	cCt	cTt	3	3	AY.16.1	0.00141
ORF3a	240	P240del	CCT	---	3	3	AY.25	0.000018
ORF3a	240	P240del1	Cct	-ct	1	3	AY.25	0.000006
ORF3a	240	P240del1	ccT	cc-	1	3	AY.25	0.000006
ORF3a	240	P240del1	CcT	-cA	1	3	AY.25	0.000006
ORF3a	240	P240L	cCt	cTt	3	3	AY.27	0.000194
ORF3a	240	P240R	cCt	cGt	3	3	AY.29	0.000047
ORF3a	240	P240S	Cct	Tct	3	3	AY.3.1	0.000256
ORF3a	240	P240P	ccT	ccC	3	3	AY.3.1	0.000256
ORF3a	240	P240S	Cct	Tct	3	3	AY.33	0.0002
ORF3a	240	P240L	cCt	cTt	3	3	AY.34.1	0.00153
ORF3a	240	P240S	Cct	Tct	3	3	AY.34.1	0.00153
ORF3a	240	P240S	Cct	Tct	3	3	AY.42	0.000121
ORF3a	240	P240H	cCt	cAt	3	3	AY.42	0.000121
ORF3a	240	P240S	Cct	Tct	3	3	AY.45	0.000365
ORF3a	240	P240S	Cct	Tct	3	3	AY.5.4	0.00083
ORF3a	240	P240S	Cct	Tct	3	3	AY.61	0.000314
ORF3a	240	P240L	cCt	cTt	3	3	AY.62	0.001307
ORF3a	240	P240L	cCt	cTt	3	3	AY.69	0.00056
ORF3a	240	P240L	cCt	cTt	3	3	AY.7.1	0.000338
ORF3a	240	P240S	Cct	Tct	3	3	AY.84	0.001312
ORF3a	240	P240S	Cct	Tct	3	3	AY.9.2	0.00011
ORF3a	240	P240S	Cct	Tct	3	3	AY.92	0.000862
ORF3a	240	P240L	cCt	cTt	3	3	AY.98.1	0.000145
ORF3a	240	P240S	Cct	Tct	3	3	AY.99.2	0.000276
ORF3a	240	P240L	cCt	cTt	3	3	B.1.1.1	0.00098
ORF3a	240	P240S	Cct	Tct	3	3	B.1.1.25	0.001706
ORF3a	240	P240S	Cct	Tct	3	3	B.1.1.306	0.001315
ORF3a	240	P240S	Cct	Tct	3	3	B.1.1.317	0.001235
ORF3a	240	P240S	Cct	Tct	3	3	B.1.1.318	0.000905
ORF3a	240	P240S	Cct	Tct	3	3	B.1.1.326	0.005282
ORF3a	240	P240L	cCt	cTt	3	3	B.1.1.380	0.029412
ORF3a	240	P240S	Cct	Tct	3	3	B.1.1.420	0.003018
ORF3a	240	P240S	Cct	Tct	3	3	B.1.111	0.003525
ORF3a	240	P240L	cCt	cTt	3	3	B.1.160.11	0.017143
ORF3a	240	P240L	cCt	cTt	3	3	B.1.160.16	0.002788
ORF3a	240	P240L	cCt	cTt	3	3	B.1.177.81	0.000568
ORF3a	240	P240P	ccT	ccC	3	3	B.1.177.86	0.00055
ORF3a	240	P240T	Cct	Act	3	3	B.1.258.17	0.000312
ORF3a	240	P240L	cCt	cTt	3	3	B.1.311	0.000824
ORF3a	240	P240L	cCt	cTt	3	3	B.1.349	0.002144
ORF3a	240	P240H	cCt	cAt	3	3	B.1.351	0.000089
ORF3a	240	P240S	Cct	Tct	3	3	B.1.36.18	0.001261
ORF3a	240	P240L	cCt	cTt	3	3	B.1.395	0.021127
ORF3a	240	P240L	cCt	cTt	3	3	B.1.396	0.002117
ORF3a	240	P240L	cCt	cTt	3	3	B.1.398	0.008929
ORF3a	240	P240S	Cct	Tct	3	3	B.1.425	0.008982
ORF3a	240	P240S	Cct	Tct	3	3	B.1.466.2	0.001174
ORF3a	240	P240S	Cct	Tct	3	3	B.1.564	0.001278
ORF3a	240	P240L	cCt	cTt	3	3	B.1.595	0.000783
ORF3a	240	P240H	cCt	cAt	3	3	C.36	0.002732
ORF3a	240	P240S	Cct	Tct	3	3	D.2	0.000225
ORF3a	240	P240S	Cct	Tct	3	3	K.2	0.12
ORF3a	240	P240S	Cct	Tct	3	3	L.3	0.010638
ORF3a	240	P240S	Cct	Tct	3	3	P.1.17	0.000485
ORF3a	240	P240S	Cct	Tct	3	3	P.1.7	0.000958
ORF3a	240	P240S	Cct	Tct	3	3	P.2	0.00056
ORF3a	240	P240L	cCt	cTt	3	3	P.6	0.009434
ORF3a	240	P240L	cCt	cTt	3	3	U.3	0.011583
ORF3a	240	P240V	CCt	GTt	2	2		0.111111
ORF3a	240	P240S	Cct	Tct	2	2	A.23	0.021053
ORF3a	240	P240L	cCt	cTt	2	2	A.28	0.005291
ORF3a	240	P240V	CCt	GTt	2	2	All	0
ORF3a	240	P240L	cCt	cTt	2	2	AU.2	0.004843
ORF3a	240	P240S	Cct	Tct	2	2	AY.105	0.001286
ORF3a	240	P240S	Cct	Tct	2	2	AY.110	0.000225
ORF3a	240	P240L	cCt	cTt	2	2	AY.111	0.000366
ORF3a	240	P240S	Cct	Tct	2	2	AY.116	0.000574
ORF3a	240	P240L	cCt	cTt	2	2	AY.16	0.000759
ORF3a	240	P240S	Cct	Tct	2	2	AY.22	0.004184
ORF3a	240	P240P	ccT	ccC	2	2	AY.24	0.000862
ORF3a	240	P240H	cCt	cAt	2	2	AY.25	0.000012
ORF3a	240	P240S	Cct	Tct	2	2	AY.27	0.000129
ORF3a	240	P240S	Cct	Tct	2	2	AY.29.1	0.000441
ORF3a	240	P240L	cCt	cTt	2	2	AY.29.1	0.000441
ORF3a	240	P240R	cCt	cGt	2	2	AY.3	0.00002
ORF3a	240	P240S	Cct	Tct	2	2	AY.32	0.001065
ORF3a	240	P240L	cCt	cTt	2	2	AY.35	0.000466
ORF3a	240	P240H	cCt	cAt	2	2	AY.36	0.000296
ORF3a	240	P240H	cCt	cAt	2	2	AY.39	0.000049
ORF3a	240	P240S	Cct	Tct	2	2	AY.39.1	0.000079
ORF3a	240	P240del	CCT	---	2	2	AY.4	0.000003
ORF3a	240	P240R	cCt	cGt	2	2	AY.44	0.000012
ORF3a	240	P240S	Cct	Tct	2	2	AY.46.4	0.000329
ORF3a	240	P240S	Cct	Tct	2	2	AY.46.6	0.000144
ORF3a	240	P240S	Cct	Tct	2	2	AY.6	0.000082
ORF3a	240	P240S	Cct	Tct	2	2	AY.65	0.001066
ORF3a	240	P240L	cCT	cTA	1	2	AY.65	0.000533
ORF3a	240	P240L	cCt	cTt	1	2	AY.65	0.000533
ORF3a	240	P240S	Cct	Tct	2	2	AY.68	0.000547
ORF3a	240	P240L	cCt	cTt	2	2	AY.68	0.000547
ORF3a	240	P240S	Cct	Tct	2	2	AY.7.1	0.000225
ORF3a	240	P240L	cCt	cTt	2	2	AY.74	0.000231
ORF3a	240	P240P	ccT	ccC	2	2	AY.75	0.000112
ORF3a	240	P240H	cCt	cAt	2	2	AY.75.1	0.000361
ORF3a	240	P240S	Cct	Tct	2	2	AY.9.1	0.000167
ORF3a	240	P240S	Cct	Tct	2	2	AY.93	0.000546
ORF3a	240	P240L	cCt	cTt	2	2	AY.94	0.000885
ORF3a	240	P240S	Cct	Tct	2	2	AY.98.1	0.000097
ORF3a	240	P240L	cCt	cTt	2	2	B	0.000256
ORF3a	240	P240T	Cct	Act	2	2	B.1	0.000018
ORF3a	240	P240S	Cct	Tct	2	2	B.1.1.121	0.004854
ORF3a	240	P240S	Cct	Tct	2	2	B.1.1.176	0.000879
ORF3a	240	P240S	Cct	Tct	2	2	B.1.1.205	0.007435
ORF3a	240	P240L	cCt	cTt	2	2	B.1.1.220	0.003717
ORF3a	240	P240L	cCt	cTt	2	2	B.1.1.28	0.000622
ORF3a	240	P240L	cCt	cTt	2	2	B.1.1.284	0.000215
ORF3a	240	P240S	Cct	Tct	2	2	B.1.1.289	0.004167
ORF3a	240	P240L	cCt	cTt	2	2	B.1.1.307	0.005063
ORF3a	240	P240S	Cct	Tct	2	2	B.1.1.311	0.000716
ORF3a	240	P240L	cCt	cTt	2	2	B.1.1.326	0.003521
ORF3a	240	P240L	cCt	cTt	2	2	B.1.1.372	0.001377
ORF3a	240	P240L	cCt	cTt	2	2	B.1.1.374	0.004751
ORF3a	240	P240L	cCt	cTt	2	2	B.1.1.39	0.001019
ORF3a	240	P240L	cCt	cTt	2	2	B.1.1.413	0.013793
ORF3a	240	P240S	Cct	Tct	2	2	B.1.1.487	0.011173
ORF3a	240	P240L	cCt	cTt	2	2	B.1.1.63	0.000772
ORF3a	240	P240L	cCt	cTt	2	2	B.1.1.70	0.000682
ORF3a	240	P240L	cCt	cTt	2	2	B.1.111	0.00235
ORF3a	240	P240S	Cct	Tct	2	2	B.1.143	0.042553
ORF3a	240	P240S	Cct	Tct	2	2	B.1.160.32	0.008584
ORF3a	240	P240P	ccT	ccC	2	2	B.1.177	0.000026
ORF3a	240	P240L	cCt	cTt	2	2	B.1.177.54	0.001213
ORF3a	240	P240P	ccT	ccA	2	2	B.1.177.60	0.000437
ORF3a	240	P240S	Cct	Tct	2	2	B.1.195	0.01005
ORF3a	240	P240H	cCt	cAt	2	2	B.1.2	0.000018
ORF3a	240	P240del	CCT	---	2	2	B.1.2	0.000018
ORF3a	240	P240S	Cct	Tct	2	2	B.1.208	0.08
ORF3a	240	P240L	cCt	cTt	2	2	B.1.214.2	0.001199
ORF3a	240	P240P	ccT	ccG	1	2	B.1.221	0.000071
ORF3a	240	P240P	ccT	ccC	1	2	B.1.221	0.000071
ORF3a	240	P240S	Cct	Tct	2	2	B.1.232	0.001075
ORF3a	240	P240R	cCt	cGt	2	2	B.1.258	0.000133
ORF3a	240	P240S	Cct	Tct	2	2	B.1.325	0.013793
ORF3a	240	P240L	cCt	cTt	2	2	B.1.36.22	0.002415
ORF3a	240	P240S	Cct	Tct	2	2	B.1.36.27	0.001527
ORF3a	240	P240L	cCt	cTt	2	2	B.1.399	0.003868
ORF3a	240	P240S	Cct	Tct	2	2	B.1.400	0.000858
ORF3a	240	P240S	Cct	Tct	2	2	B.1.404	0.002604
ORF3a	240	P240L	cCt	cTt	2	2	B.1.428	0.002041
ORF3a	240	P240L	cCt	cTt	2	2	B.1.460	0.035714
ORF3a	240	P240F	CCt	TTt	2	2	B.1.466.1	0.014388
ORF3a	240	P240L	cCt	cTt	2	2	B.1.478	0.023529
ORF3a	240	P240S	Cct	Tct	2	2	B.1.480	0.004975
ORF3a	240	P240S	Cct	Tct	2	2	B.1.499	0.002101
ORF3a	240	P240L	cCt	cTt	2	2	B.1.517	0.000854
ORF3a	240	P240T	Cct	Act	2	2	B.1.525	0.000226
ORF3a	240	P240H	cCt	cAt	2	2	B.1.526	0.000047
ORF3a	240	P240L	cCt	cTt	2	2	B.1.527	0.007407
ORF3a	240	P240S	Cct	Tct	2	2	B.1.532	0.012422
ORF3a	240	P240S	Cct	Tct	2	2	B.1.575.1	0.004878
ORF3a	240	P240L	cCt	cTt	2	2	B.1.609	0.000959
ORF3a	240	P240P	ccT	ccC	2	2	C.36.3.1	0.005435
ORF3a	240	P240L	cCt	cTt	2	2	D.2	0.00015
ORF3a	240	P240L	cCt	cTt	2	2	N.5	0.003534
ORF3a	240	P240H	cCt	cAt	2	2	P.1.1	0.000635
ORF3a	240	P240L	cCt	cTt	2	2	P.1.10	0.000539
ORF3a	240	P240S	Cct	Tct	2	2	P.1.14	0.000096
ORF3a	240	P240L	cCt	cTt	2	2	Q.1	0.000253
ORF3a	240	P240S	Cct	Tct	2	2	Q.7	0.002222
ORF3a	240	P240S	Cct	Tct	2	2	R.1	0.00018
ORF3a	240	P240L	cCt	cTt	2	2	R.1	0.00018
ORF3a	240	P240S	Cct	Tct	2	2	S.1	0.009901
ORF3a	240	P240S	Cct	Tct	1	1	A	0.000387
ORF3a	240	P240L	cCt	cTt	1	1	A.1	0.000282
ORF3a	240	P240S	Cct	Tct	1	1	A.2.2	0.001689
ORF3a	240	P240S	Cct	Tct	1	1	A.2.5	0.000499
ORF3a	240	P240S	Cct	Tct	1	1	A.2.5.1	0.004808
ORF3a	240	P240L	cCt	cTt	1	1	A.2.5.2	0.001572
ORF3a	240	P240L	cCt	cTt	1	1	A.24	0.071429
ORF3a	240	P240S	Cct	Tct	1	1	AE.1	0.011364
ORF3a	240	P240D	CCt	GAt	1	1	All	0
ORF3a	240	P240Q	cCT	cAA	1	1	All	0
ORF3a	240	P240S	Cct	Tct	1	1	AM.2	0.111111
ORF3a	240	P240L	cCt	cTt	1	1	AT.1	0.005128
ORF3a	240	P240H	cCt	cAt	1	1	AU.3	0.00211
ORF3a	240	P240S	Cct	Tct	1	1	AV.1	0.005051
ORF3a	240	P240L	cCt	cTt	1	1	AY.1	0.000396
ORF3a	240	P240S	Cct	Tct	1	1	AY.1	0.000396
ORF3a	240	P240del1	Cct	-ct	1	1	AY.1	0.000396
ORF3a	240	P240S	Cct	Tct	1	1	AY.10	0.00053
ORF3a	240	P240S	Cct	Tct	1	1	AY.104	0.001984
ORF3a	240	P240S	Cct	Tct	1	1	AY.111	0.000183
ORF3a	240	P240P	ccT	ccC	1	1	AY.113	0.000142
ORF3a	240	P240S	Cct	Tct	1	1	AY.113	0.000142
ORF3a	240	P240L	cCt	cTt	1	1	AY.114	0.000231
ORF3a	240	P240H	cCt	cAt	1	1	AY.117	0.000085
ORF3a	240	P240R	cCt	cGt	1	1	AY.118	0.000063
ORF3a	240	P240H	cCt	cAt	1	1	AY.119	0.000035
ORF3a	240	P240H	cCt	cAt	1	1	AY.121	0.000135
ORF3a	240	P240L	cCt	cTt	1	1	AY.121	0.000135
ORF3a	240	P240S	Cct	Tct	1	1	AY.14	0.000088
ORF3a	240	P240S	Cct	Tct	1	1	AY.16.1	0.00047
ORF3a	240	P240S	Cct	Tct	1	1	AY.19	0.00114
ORF3a	240	P240S	Cct	Tct	1	1	AY.2	0.000356
ORF3a	240	P240H	cCt	cAt	1	1	AY.20	0.000039
ORF3a	240	P240L	cCt	cTt	1	1	AY.22	0.002092
ORF3a	240	P240S	Cct	Tct	1	1	AY.23.1	0.000417
ORF3a	240	P240R	cCt	cGt	1	1	AY.25	0.000006
ORF3a	240	P240P	ccT	ccC	1	1	AY.27	0.000065
ORF3a	240	P240S	Cct	Tct	1	1	AY.30	0.000396
ORF3a	240	P240H	cCt	cAt	1	1	AY.30	0.000396
ORF3a	240	P240H	cCt	cAt	1	1	AY.33	0.000067
ORF3a	240	P240A	Cct	Gct	1	1	AY.35	0.000233
ORF3a	240	P240L	cCt	cTt	1	1	AY.38	0.000499
ORF3a	240	P240R	cCt	cGt	1	1	AY.39	0.000025
ORF3a	240	P240H	cCt	cAt	1	1	AY.39.1	0.00004
ORF3a	240	P240R	cCt	cGt	1	1	AY.39.1	0.00004
ORF3a	240	P240P	ccT	ccA	1	1	AY.4.2	0.000022
ORF3a	240	P240H	cCt	cAt	1	1	AY.4.4	0.000409
ORF3a	240	P240L	cCt	cTt	1	1	AY.4.5	0.000107
ORF3a	240	P240P	ccT	ccC	1	1	AY.46.1	0.001027
ORF3a	240	P240L	cCt	cTt	1	1	AY.46.3	0.000934
ORF3a	240	P240R	cCt	cGt	1	1	AY.46.3	0.000934
ORF3a	240	P240L	cCt	cTt	1	1	AY.46.6	0.000072
ORF3a	240	P240P	ccT	ccC	1	1	AY.46.6	0.000072
ORF3a	240	P240H	cCt	cAt	1	1	AY.47	0.000031
ORF3a	240	P240S	Cct	Tct	1	1	AY.5.3	0.000337
ORF3a	240	P240S	Cct	Tct	1	1	AY.53	0.000288
ORF3a	240	P240P	ccT	ccC	1	1	AY.53	0.000288
ORF3a	240	P240P	ccT	ccG	1	1	AY.54	0.000095
ORF3a	240	P240L	cCt	cTt	1	1	AY.55	0.000917
ORF3a	240	P240L	cCt	cTt	1	1	AY.56	0.001605
ORF3a	240	P240L	cCt	cTt	1	1	AY.57	0.000656
ORF3a	240	P240P	ccT	ccC	1	1	AY.58	0.000907
ORF3a	240	P240L	cCt	cTt	1	1	AY.6	0.000041
ORF3a	240	P240P	ccT	ccG	1	1	AY.6	0.000041
ORF3a	240	P240H	cCt	cAt	1	1	AY.61	0.000105
ORF3a	240	P240S	Cct	Tct	1	1	AY.62	0.000436
ORF3a	240	P240S	Cct	Tct	1	1	AY.63	0.000387
ORF3a	240	P240A	Cct	Gct	1	1	AY.67	0.000464
ORF3a	240	P240del	CCT	---	1	1	AY.68	0.000274
ORF3a	240	P240P	ccT	ccC	1	1	AY.69	0.000187
ORF3a	240	P240del	CCT	---	1	1	AY.7	0.000196
ORF3a	240	P240S	Cct	Tct	1	1	AY.73	0.000665
ORF3a	240	P240S	Cct	Tct	1	1	AY.75.1	0.00018
ORF3a	240	P240L	cCt	cTt	1	1	AY.77	0.001127
ORF3a	240	P240H	cCt	cAt	1	1	AY.82	0.001357
ORF3a	240	P240P	ccT	ccC	1	1	AY.84	0.000437
ORF3a	240	P240L	cCt	cTt	1	1	AY.84	0.000437
ORF3a	240	P240L	cCt	cTt	1	1	AY.85	0.000427
ORF3a	240	P240S	Cct	Tct	1	1	AY.85	0.000427
ORF3a	240	P240S	Cct	Tct	1	1	AY.87	0.000833
ORF3a	240	P240P	ccT	ccC	1	1	AY.9.2	0.000037
ORF3a	240	P240T	Cct	Act	1	1	AY.91	0.00073
ORF3a	240	P240del1	ccT	cc-	1	1	AY.93	0.000273
ORF3a	240	P240S	Cct	Tct	1	1	AY.95	0.000761
ORF3a	240	P240P	ccT	ccC	1	1	AY.98	0.000079
ORF3a	240	P240T	Cct	Act	1	1	B	0.000128
ORF3a	240	P240P	ccT	ccC	1	1	B	0.000128
ORF3a	240	P240A	Cct	Gct	1	1	B.1	0.000009
ORF3a	240	P240A	Cct	Gct	1	1	B.1.1	0.000018
ORF3a	240	P240R	cCt	cGt	1	1	B.1.1	0.000018
ORF3a	240	P240L	cCt	cTt	1	1	B.1.1.10	0.001115
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.141	0.002012
ORF3a	240	P240L	cCt	cTt	1	1	B.1.1.153	0.001095
ORF3a	240	P240L	cCt	cTt	1	1	B.1.1.157	0.000913
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.160	0.02381
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.181	0.004545
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.189	0.001513
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.210	0.005714
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.221	0.010101
ORF3a	240	P240T	Cct	Act	1	1	B.1.1.232	0.001815
ORF3a	240	P240L	cCt	cTt	1	1	B.1.1.236	0.006897
ORF3a	240	P240L	cCt	cTt	1	1	B.1.1.258	0.003257
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.258	0.003257
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.265	0.003155
ORF3a	240	P240L	cCt	cTt	1	1	B.1.1.269	0.001353
ORF3a	240	P240L	cCt	cTt	1	1	B.1.1.277	0.000759
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.279	0.001121
ORF3a	240	P240F	CCt	TTt	1	1	B.1.1.28	0.000311
ORF3a	240	P240T	Cct	Act	1	1	B.1.1.28	0.000311
ORF3a	240	P240L	cCt	cTt	1	1	B.1.1.280	0.003086
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.297	0.002237
ORF3a	240	P240L	cCt	cTt	1	1	B.1.1.302	0.002075
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.305	0.003861
ORF3a	240	P240del	CCT	---	1	1	B.1.1.306	0.000438
ORF3a	240	P240D	CCt	GAt	1	1	B.1.1.306	0.000438
ORF3a	240	P240del	CCT	---	1	1	B.1.1.311	0.000358
ORF3a	240	P240L	cCt	cTt	1	1	B.1.1.315	0.008475
ORF3a	240	P240L	cCt	cTt	1	1	B.1.1.317	0.000412
ORF3a	240	P240L	cCt	cTt	1	1	B.1.1.318	0.000302
ORF3a	240	P240H	cCt	cAt	1	1	B.1.1.329	0.003846
ORF3a	240	P240del	CCT	---	1	1	B.1.1.33	0.000421
ORF3a	240	P240Q	cCT	cAA	1	1	B.1.1.33	0.000421
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.331	0.011628
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.335	0.012987
ORF3a	240	P240L	cCt	cTt	1	1	B.1.1.340	0.045455
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.348	0.000796
ORF3a	240	P240L	cCt	cTt	1	1	B.1.1.352	0.03125
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.354	0.004386
ORF3a	240	P240L	cCt	cTt	1	1	B.1.1.37	0.000193
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.385	0.004464
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.397	0.002252
ORF3a	240	P240L	cCt	cTt	1	1	B.1.1.406	0.006494
ORF3a	240	P240L	cCt	cTt	1	1	B.1.1.409	0.002833
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.409	0.002833
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.429	0.004608
ORF3a	240	P240P	ccT	ccC	1	1	B.1.1.432	0.001266
ORF3a	240	P240L	cCt	cTt	1	1	B.1.1.448	0.002033
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.486	0.001577
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.50	0.000679
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.507	0.008696
ORF3a	240	P240T	Cct	Act	1	1	B.1.1.519	0.00004
ORF3a	240	P240H	cCt	cAt	1	1	B.1.1.519	0.00004
ORF3a	240	P240A	Cct	Gct	1	1	B.1.1.521	0.005348
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.521	0.005348
ORF3a	240	P240L	cCt	cTt	1	1	B.1.1.521	0.005348
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.525	0.005464
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.526	0.003546
ORF3a	240	P240L	cCt	cTt	1	1	B.1.1.526	0.003546
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.528	0.004808
ORF3a	240	P240S	Cct	Tct	1	1	B.1.1.70	0.000341
ORF3a	240	P240L	cCt	cTt	1	1	B.1.110.2	0.166667
ORF3a	240	P240L	cCt	cTt	1	1	B.1.118	0.006711
ORF3a	240	P240L	cCt	cTt	1	1	B.1.119	0.010526
ORF3a	240	P240L	cCt	cTt	1	1	B.1.139	0.000733
ORF3a	240	P240R	cCt	cGt	1	1	B.1.147	0.000756
ORF3a	240	P240S	Cct	Tct	1	1	B.1.147	0.000756
ORF3a	240	P240S	Cct	Tct	1	1	B.1.160.10	0.008065
ORF3a	240	P240T	Cct	Act	1	1	B.1.160.9	0.007194
ORF3a	240	P240del	CCT	---	1	1	B.1.177	0.000013
ORF3a	240	P240L	cCt	cTt	1	1	B.1.177.12	0.000152
ORF3a	240	P240P	ccT	ccA	1	1	B.1.177.17	0.000821
ORF3a	240	P240S	Cct	Tct	1	1	B.1.177.24	0.001295
ORF3a	240	P240S	Cct	Tct	1	1	B.1.177.32	0.00135
ORF3a	240	P240S	Cct	Tct	1	1	B.1.177.35	0.000691
ORF3a	240	P240S	Cct	Tct	1	1	B.1.177.4	0.000211
ORF3a	240	P240S	Cct	Tct	1	1	B.1.177.44	0.000519
ORF3a	240	P240L	cCt	cTt	1	1	B.1.177.44	0.000519
ORF3a	240	P240L	cCt	cTt	1	1	B.1.177.5	0.001242
ORF3a	240	P240S	Cct	Tct	1	1	B.1.177.52	0.001757
ORF3a	240	P240L	cCt	cTt	1	1	B.1.177.60	0.000218
ORF3a	240	P240L	cCt	cTt	1	1	B.1.177.62	0.001192
ORF3a	240	P240S	Cct	Tct	1	1	B.1.177.69	0.001484
ORF3a	240	P240L	cCt	cTt	1	1	B.1.177.7	0.000165
ORF3a	240	P240L	cCt	cTt	1	1	B.1.177.73	0.000566
ORF3a	240	P240del	CCT	---	1	1	B.1.177.73	0.000566
ORF3a	240	P240S	Cct	Tct	1	1	B.1.177.82	0.000477
ORF3a	240	P240L	cCt	cTt	1	1	B.1.177.82	0.000477
ORF3a	240	P240L	cCt	cTt	1	1	B.1.177.86	0.000183
ORF3a	240	P240L	cCt	cTt	1	1	B.1.199	0.004132
ORF3a	240	P240S	Cct	Tct	1	1	B.1.239	0.001221
ORF3a	240	P240L	cCt	cTt	1	1	B.1.239	0.001221
ORF3a	240	P240L	cCt	cTt	1	1	B.1.240	0.000216
ORF3a	240	P240L	cCt	cTt	1	1	B.1.241	0.000812
ORF3a	240	P240P	ccT	ccA	1	1	B.1.258	0.000067
ORF3a	240	P240S	Cct	Tct	1	1	B.1.258.14	0.00098
ORF3a	240	P240S	Cct	Tct	1	1	B.1.264	0.012346
ORF3a	240	P240L	cCt	cTt	1	1	B.1.265	0.001271
ORF3a	240	P240L	cCt	cTt	1	1	B.1.284	0.013158
ORF3a	240	P240L	cCt	cTt	1	1	B.1.301	0.005917
ORF3a	240	P240L	cCt	cTt	1	1	B.1.320	0.001245
ORF3a	240	P240L	cCt	cTt	1	1	B.1.330	0.028571
ORF3a	240	P240L	cCt	cTt	1	1	B.1.335	0.010309
ORF3a	240	P240L	cCt	cTt	1	1	B.1.346	0.001311
ORF3a	240	P240T	Cct	Act	1	1	B.1.351	0.00003
ORF3a	240	P240P	ccT	ccC	1	1	B.1.351	0.00003
ORF3a	240	P240R	cCt	cGt	1	1	B.1.351	0.00003
ORF3a	240	P240S	Cct	Tct	1	1	B.1.351.2	0.000303
ORF3a	240	P240S	Cct	Tct	1	1	B.1.351.3	0.000876
ORF3a	240	P240L	cCt	cTt	1	1	B.1.356	0.001727
ORF3a	240	P240L	cCt	cTt	1	1	B.1.36.10	0.004785
ORF3a	240	P240L	cCt	cTt	1	1	B.1.36.16	0.001425
ORF3a	240	P240L	cCt	cTt	1	1	B.1.36.18	0.00042
ORF3a	240	P240L	cCt	cTt	1	1	B.1.36.29	0.000517
ORF3a	240	P240S	Cct	Tct	1	1	B.1.36.35	0.002604
ORF3a	240	P240S	Cct	Tct	1	1	B.1.36.39	0.002217
ORF3a	240	P240S	Cct	Tct	1	1	B.1.36.7	0.004
ORF3a	240	P240P	ccT	ccA	1	1	B.1.36.8	0.001
ORF3a	240	P240S	Cct	Tct	1	1	B.1.36.8	0.001
ORF3a	240	P240L	cCt	cTt	1	1	B.1.36.9	0.003215
ORF3a	240	P240S	Cct	Tct	1	1	B.1.362.2	0.004717
ORF3a	240	P240L	cCt	cTt	1	1	B.1.369	0.000285
ORF3a	240	P240L	cCt	cTt	1	1	B.1.371	0.001122
ORF3a	240	P240S	Cct	Tct	1	1	B.1.375	0.00082
ORF3a	240	P240L	cCt	cTt	1	1	B.1.377	0.004566
ORF3a	240	P240S	Cct	Tct	1	1	B.1.382	0.008929
ORF3a	240	P240L	cCt	cTt	1	1	B.1.389	0.001002
ORF3a	240	P240A	Cct	Gct	1	1	B.1.400	0.000429
ORF3a	240	P240L	cCt	cTt	1	1	B.1.400.1	0.015152
ORF3a	240	P240L	cCt	cTt	1	1	B.1.408	0.00369
ORF3a	240	P240S	Cct	Tct	1	1	B.1.408	0.00369
ORF3a	240	P240S	Cct	Tct	1	1	B.1.411	0.003704
ORF3a	240	P240S	Cct	Tct	1	1	B.1.416.1	0.001563
ORF3a	240	P240S	Cct	Tct	1	1	B.1.426	0.001009
ORF3a	240	P240T	Cct	Act	1	1	B.1.427	0.00005
ORF3a	240	P240R	cCt	cGt	1	1	B.1.429	0.000024
ORF3a	240	P240P	ccT	ccC	1	1	B.1.429	0.000024
ORF3a	240	P240S	Cct	Tct	1	1	B.1.451	0.008197
ORF3a	240	P240L	cCt	cTt	1	1	B.1.462	0.007246
ORF3a	240	P240L	cCt	cTt	1	1	B.1.466.2	0.000391
ORF3a	240	P240L	cCt	cTt	1	1	B.1.468	0.005714
ORF3a	240	P240S	Cct	Tct	1	1	B.1.468	0.005714
ORF3a	240	P240S	Cct	Tct	1	1	B.1.474	0.001901
ORF3a	240	P240H	cCt	cAt	1	1	B.1.497	0.000315
ORF3a	240	P240T	CcT	AcG	1	1	B.1.497	0.000315
ORF3a	240	P240del	CCT	---	1	1	B.1.497	0.000315
ORF3a	240	P240P	ccT	ccC	1	1	B.1.523	0.002451
ORF3a	240	P240S	Cct	Tct	1	1	B.1.525	0.000113
ORF3a	240	P240L	cCt	cTt	1	1	B.1.538	0.008065
ORF3a	240	P240S	Cct	Tct	1	1	B.1.551	0.00129
ORF3a	240	P240L	cCt	cTt	1	1	B.1.561	0.000397
ORF3a	240	P240S	Cct	Tct	1	1	B.1.564.1	0.001577
ORF3a	240	P240L	cCt	cTt	1	1	B.1.565	0.00081
ORF3a	240	P240S	Cct	Tct	1	1	B.1.565	0.00081
ORF3a	240	P240S	Cct	Tct	1	1	B.1.568	0.001111
ORF3a	240	P240P	ccT	ccC	1	1	B.1.576	0.000907
ORF3a	240	P240S	Cct	Tct	1	1	B.1.577	0.000687
ORF3a	240	P240H	cCt	cAt	1	1	B.1.580	0.004065
ORF3a	240	P240S	Cct	Tct	1	1	B.1.582	0.000491
ORF3a	240	P240P	ccT	ccC	1	1	B.1.596	0.000087
ORF3a	240	P240L	cCt	cTt	1	1	B.1.597	0.00463
ORF3a	240	P240S	Cct	Tct	1	1	B.1.606	0.006024
ORF3a	240	P240R	cCt	cGt	1	1	B.1.617.2	0.000004
ORF3a	240	P240S	Cct	Tct	1	1	B.1.619	0.000871
ORF3a	240	P240L	cCt	cTt	1	1	B.1.620	0.000946
ORF3a	240	P240S	Cct	Tct	1	1	B.1.620	0.000946
ORF3a	240	P240L	cCt	cTt	1	1	B.1.623	0.000536
ORF3a	240	P240P	ccT	ccC	1	1	B.1.628	0.000352
ORF3a	240	P240S	Cct	Tct	1	1	B.1.631	0.003367
ORF3a	240	P240P	ccT	ccC	1	1	B.1.637	0.000073
ORF3a	240	P240S	Cct	Tct	1	1	B.1.8	0.001972
ORF3a	240	P240S	Cct	Tct	1	1	B.1.93	0.000934
ORF3a	240	P240S	Cct	Tct	1	1	B.28	0.003279
ORF3a	240	P240L	cCt	cTt	1	1	B.3	0.000831
ORF3a	240	P240S	Cct	Tct	1	1	B.3	0.000831
ORF3a	240	P240L	cCt	cTt	1	1	B.3.1	0.001658
ORF3a	240	P240L	cCt	cTt	1	1	B.4	0.002208
ORF3a	240	P240L	cCt	cTt	1	1	B.40	0.000364
ORF3a	240	P240S	Cct	Tct	1	1	B.40	0.000364
ORF3a	240	P240P	ccT	ccC	1	1	B.45	0.003831
ORF3a	240	P240S	Cct	Tct	1	1	B.6	0.00091
ORF3a	240	P240H	cCt	cAt	1	1	B.6.6	0.000889
ORF3a	240	P240L	cCt	cTt	1	1	C.1	0.002392
ORF3a	240	P240L	cCt	cTt	1	1	C.1.2	0.004255
ORF3a	240	P240L	cCt	cTt	1	1	C.16	0.00106
ORF3a	240	P240L	cCt	cTt	1	1	C.23	0.005814
ORF3a	240	P240S	Cct	Tct	1	1	C.35	0.000774
ORF3a	240	P240S	Cct	Tct	1	1	C.36	0.000911
ORF3a	240	P240L	cCt	cTt	1	1	C.37.1	0.002618
ORF3a	240	P240L	cCt	cTt	1	1	N.3	0.005814
ORF3a	240	P240L	cCt	cTt	1	1	N.9	0.005952
ORF3a	240	P240L	cCt	cTt	1	1	P.1.1	0.000318
ORF3a	240	P240R	cCt	cGt	1	1	P.1.10	0.000269
ORF3a	240	P240L	cCt	cTt	1	1	P.1.12	0.000484
ORF3a	240	P240S	Cct	Tct	1	1	P.1.12	0.000484
ORF3a	240	P240H	cCt	cAt	1	1	P.1.14	0.000048
ORF3a	240	P240S	Cct	Tct	1	1	P.1.15	0.000232
ORF3a	240	P240H	cCt	cAt	1	1	P.1.17	0.000162
ORF3a	240	P240P	ccT	ccG	1	1	P.1.2	0.001156
ORF3a	240	P240S	Cct	Tct	1	1	P.1.6	0.001946
ORF3a	240	P240S	Cct	Tct	1	1	P.3	0.001595
ORF3a	240	P240P	ccT	ccC	1	1	Q.1	0.000126
ORF3a	240	P240L	cCt	cTt	1	1	Q.4	0.000455
ORF3a	240	P240del	CCT	---	1	1	R.1	0.00009
ORF3a	240	P240L	cCt	cTt	1	1	S.1	0.00495

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.