CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF3a : CodonNum = 104

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	104	P104S		nonsyn	Cct	Tct	32762	32757	0.999847	25702-25704
ORF3a	104	P104S		nonsyn	CcT	TcA	32762	2	0.0000610463	25702-25704
ORF3a	104	P104S		nonsyn	CcT	TcC	32762	2	0.0000610463	25702-25704
ORF3a	104	P104S		nonsyn	CcT	TcG	32762	1	0.0000305232	25702-25704
ORF3a	104	P104L		nonsyn	cCt	cTt	14679	14665	0.999046	25702-25704
ORF3a	104	P104L		nonsyn	cCT	cTC	14679	7	0.000476872	25702-25704
ORF3a	104	P104L		nonsyn	cCT	cTA	14679	3	0.000204374	25702-25704
ORF3a	104	P104L		nonsyn	CCT	TTA	14679	2	0.000136249	25702-25704
ORF3a	104	P104L		nonsyn	cCT	cTG	14679	2	0.000136249	25702-25704
ORF3a	104	P104F		nonsyn	CCt	TTt	2449	2448	0.999592	25702-25704
ORF3a	104	P104F		nonsyn	CCT	TTC	2449	1	0.00040833	25702-25704
ORF3a	104	P104P		syn	ccT	ccG	1144	856	0.748252	25702-25704
ORF3a	104	P104P		syn	ccT	ccC	1144	268	0.234266	25702-25704
ORF3a	104	P104P		syn	ccT	ccA	1144	20	0.0174825	25702-25704
ORF3a	104	P104H		nonsyn	cCt	cAt	190	189	0.994737	25702-25704
ORF3a	104	P104H		nonsyn	cCT	cAC	190	1	0.00526316	25702-25704
ORF3a	104	P104T		nonsyn	Cct	Act	154	152	0.987013	25702-25704
ORF3a	104	P104T		nonsyn	CcT	AcG	154	1	0.00649351	25702-25704
ORF3a	104	P104T		nonsyn	CcT	AcC	154	1	0.00649351	25702-25704
ORF3a	104	P104del		del	CCT	---	141	141	1	25702-25704
ORF3a	104	P104R		nonsyn	cCt	cGt	58	58	1	25702-25704
ORF3a	104	P104A		nonsyn	Cct	Gct	25	21	0.84	25702-25704
ORF3a	104	P104A		nonsyn	CcT	GcC	25	3	0.12	25702-25704
ORF3a	104	P104A		nonsyn	CcT	GcA	25	1	0.04	25702-25704
ORF3a	104	P104del1		del	ccT	cc-	14	14	1	25702-25704
ORF3a	104	P104del2		del	cCT	c--	5	4	0.8	25702-25704
ORF3a	104	P104del2		del	CCt	--t	5	1	0.2	25702-25704
ORF3a	104	P104C		nonsyn	CCt	TGt	4	4	1	25702-25704
ORF3a	104	P104I		nonsyn	CCt	ATt	2	1	0.5	25702-25704
ORF3a	104	P104I		nonsyn	CCT	ATC	2	1	0.5	25702-25704
ORF3a	104	P104K		nonsyn	CCT	AAG	1	1	1	25702-25704
ORF3a	104	P104N		nonsyn	CCt	AAt	1	1	1	25702-25704
ORF3a	104	P104Q		nonsyn	cCT	cAA	1	1	1	25702-25704
ORF3a	104	P104X		nonsyn	CCT	TAG	1	1	1	25702-25704
ORF3a	104	P104D		nonsyn	CCt	GAt	1	1	1	25702-25704
ORF3a	104	P104W		nonsyn	CCT	TGG	1	1	1	25702-25704
ORF3a	104	P104Y		nonsyn	CCt	TAt	1	1	1	25702-25704
ORF3a	104	P104V		nonsyn	CCt	GTt	1	1	1	25702-25704

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	104	P104S	Cct	Tct	32757	32762	All	0.006265
ORF3a	104	P104S	CcT	TcC	2	32762	All	0
ORF3a	104	P104S	CcT	TcA	2	32762	All	0
ORF3a	104	P104S	CcT	TcG	1	32762	All	0
ORF3a	104	P104S	Cct	Tct	24446	24446	AY.103	0.151787
ORF3a	104	P104L	cCt	cTt	14665	14679	All	0.002805
ORF3a	104	P104L	cCT	cTC	7	14679	All	0.000001
ORF3a	104	P104L	cCT	cTA	3	14679	All	0.000001
ORF3a	104	P104L	cCT	cTG	2	14679	All	0
ORF3a	104	P104L	CCT	TTA	2	14679	All	0
ORF3a	104	P104L	cCt	cTt	8482	8488	B.1.637	0.619803
ORF3a	104	P104L	cCT	cTC	6	8488	B.1.637	0.000438
ORF3a	104	P104S	Cct	Tct	2653	2653	B.1.1.7	0.002375
ORF3a	104	P104F	CCt	TTt	2448	2449	All	0.000468
ORF3a	104	P104F	CCT	TTC	1	2449	All	0
ORF3a	104	P104S	Cct	Tct	2265	2265	AY.24	0.976293
ORF3a	104	P104F	CCt	TTt	2177	2177	B.1.637	0.159079
ORF3a	104	P104L	cCt	cTt	1500	1500	B.1.526	0.035257
ORF3a	104	P104S	Cct	Tct	1392	1392	B.1.617.2	0.005241
ORF3a	104	P104L	cCt	cTt	1155	1155	B.1.1.7	0.001034
ORF3a	104	P104P	ccT	ccG	856	1144	All	0.000164
ORF3a	104	P104P	ccT	ccC	268	1144	All	0.000051
ORF3a	104	P104P	ccT	ccA	20	1144	All	0.000004
ORF3a	104	P104S	Cct	Tct	528	528	AY.4	0.000822
ORF3a	104	P104L	cCt	cTt	463	463	AY.4	0.000721
ORF3a	104	P104L	cCt	cTt	458	459	B.1	0.004195
ORF3a	104	P104L	cCT	cTA	1	459	B.1	0.000009
ORF3a	104	P104P	ccT	ccG	330	338	AY.4	0.000514
ORF3a	104	P104P	ccT	ccC	8	338	AY.4	0.000012
ORF3a	104	P104L	cCt	cTt	297	297	B.1.1.4	0.883929
ORF3a	104	P104P	ccT	ccG	190	244	B.1.1.7	0.00017
ORF3a	104	P104P	ccT	ccC	52	244	B.1.1.7	0.000047
ORF3a	104	P104P	ccT	ccA	2	244	B.1.1.7	0.000002
ORF3a	104	P104L	cCt	cTt	231	231	B.1.177	0.003042
ORF3a	104	P104L	cCt	cTt	214	214	AY.44	0.001303
ORF3a	104	P104H	cCt	cAt	189	190	All	0.000036
ORF3a	104	P104H	cCT	cAC	1	190	All	0
ORF3a	104	P104F	CCt	TTt	163	163	AY.103	0.001012
ORF3a	104	P104L	cCt	cTt	158	158	AY.25	0.00095
ORF3a	104	P104S	Cct	Tct	156	156	AY.108	0.171996
ORF3a	104	P104T	Cct	Act	152	154	All	0.000029
ORF3a	104	P104T	CcT	AcG	1	154	All	0
ORF3a	104	P104T	CcT	AcC	1	154	All	0
ORF3a	104	P104del	CCT	---	141	141	All	0.000027
ORF3a	104	P104S	Cct	Tct	141	141	AY.6	0.005799
ORF3a	104	P104L	cCt	cTt	139	139	B.1.617.2	0.000523
ORF3a	104	P104L	cCt	cTt	91	91	B.1.2	0.000801
ORF3a	104	P104S	Cct	Tct	89	89	AY.43	0.000394
ORF3a	104	P104L	cCt	cTt	88	88	P.1	0.001386
ORF3a	104	P104S	Cct	Tct	87	87	AY.25	0.000523
ORF3a	104	P104S	Cct	Tct	85	85	B.1.258	0.005656
ORF3a	104	P104L	cCt	cTt	85	85	B.1.429	0.002
ORF3a	104	P104S	Cct	Tct	82	82	B.1	0.000751
ORF3a	104	P104S	Cct	Tct	74	74	B.1.2	0.000652
ORF3a	104	P104F	CCt	TTt	71	71	B.1	0.00065
ORF3a	104	P104L	cCt	cTt	66	66	AY.43	0.000292
ORF3a	104	P104R	cCt	cGt	58	58	All	0.000011
ORF3a	104	P104S	Cct	Tct	54	54	AY.44	0.000329
ORF3a	104	P104L	cCt	cTt	47	47	B.1.1.353	0.979167
ORF3a	104	P104L	cCt	cTt	47	47	B.1.177.60	0.010266
ORF3a	104	P104L	cCt	cTt	44	44	AY.3	0.000438
ORF3a	104	P104S	Cct	Tct	44	44	B.1.160	0.001372
ORF3a	104	P104L	cCt	cTt	44	44	B.1.221	0.003125
ORF3a	104	P104H	cCt	cAt	41	41	AY.6	0.001686
ORF3a	104	P104L	cCt	cTt	41	41	B.1.1	0.000744
ORF3a	104	P104P	ccT	ccG	38	40	P.1	0.000599
ORF3a	104	P104P	ccT	ccC	2	40	P.1	0.000032
ORF3a	104	P104L	cCt	cTt	39	39	B.1.1.486	0.061514
ORF3a	104	P104P	ccT	ccC	34	37	AY.34	0.003297
ORF3a	104	P104P	ccT	ccG	3	37	AY.34	0.000291
ORF3a	104	P104del	CCT	---	37	37	B.1.1.7	0.000033
ORF3a	104	P104L	cCt	cTt	34	34	AY.103	0.000211
ORF3a	104	P104S	Cct	Tct	34	34	AY.33	0.00227
ORF3a	104	P104H	cCt	cAt	34	34	AY.4	0.000053
ORF3a	104	P104P	ccT	ccG	33	33	AY.46.6	0.002383
ORF3a	104	P104S	Cct	Tct	33	33	B.1.177	0.000435
ORF3a	104	P104P	ccT	ccG	19	31	B.1.617.2	0.000072
ORF3a	104	P104P	ccT	ccC	6	31	B.1.617.2	0.000023
ORF3a	104	P104P	ccT	ccA	6	31	B.1.617.2	0.000023
ORF3a	104	P104L	cCt	cTt	30	30	AY.102	0.000795
ORF3a	104	P104T	Cct	Act	29	29	AY.39	0.000717
ORF3a	104	P104L	cCt	cTt	29	29	P.1.14	0.001386
ORF3a	104	P104L	cCt	cTt	27	27	B.1.177.4	0.005699
ORF3a	104	P104L	cCt	cTt	27	27	B.1.525	0.003055
ORF3a	104	P104S	Cct	Tct	26	26	AY.117	0.002197
ORF3a	104	P104S	Cct	Tct	26	26	C.37	0.003018
ORF3a	104	P104L	cCt	cTt	26	26	D.2	0.001951
ORF3a	104	P104S	Cct	Tct	26	26	P.1	0.00041
ORF3a	104	P104A	Cct	Gct	21	25	All	0.000004
ORF3a	104	P104A	CcT	GcC	3	25	All	0.000001
ORF3a	104	P104A	CcT	GcA	1	25	All	0
ORF3a	104	P104L	cCt	cTt	25	25	AY.20	0.000972
ORF3a	104	P104S	Cct	Tct	24	24	AY.3	0.000239
ORF3a	104	P104H	cCt	cAt	23	23	AY.103	0.000143
ORF3a	104	P104L	cCt	cTt	23	23	AY.120.2.1	0.01146
ORF3a	104	P104P	ccT	ccC	13	23	AY.43	0.000058
ORF3a	104	P104P	ccT	ccG	10	23	AY.43	0.000044
ORF3a	104	P104R	cCt	cGt	23	23	B.1.1.7	0.000021
ORF3a	104	P104L	cCt	cTt	22	22	AY.39	0.000544
ORF3a	104	P104L	cCt	cTt	22	22	AY.61	0.002305
ORF3a	104	P104L	cCt	cTt	22	22	B.1.320	0.027397
ORF3a	104	P104L	cCt	cTt	20	20	B.1.1.519	0.000794
ORF3a	104	P104L	cCt	cTt	20	20	B.1.351	0.000595
ORF3a	104	P104L	cCt	cTt	19	19	AY.100	0.000874
ORF3a	104	P104L	cCt	cTt	18	18	AY.120	0.000669
ORF3a	104	P104P	ccT	ccC	11	18	AY.44	0.000067
ORF3a	104	P104P	ccT	ccG	7	18	AY.44	0.000043
ORF3a	104	P104P	ccT	ccG	10	17	AY.4.2	0.000217
ORF3a	104	P104P	ccT	ccC	7	17	AY.4.2	0.000152
ORF3a	104	P104L	cCt	cTt	16	16	AY.106	0.005358
ORF3a	104	P104P	ccT	ccC	10	16	AY.25	0.00006
ORF3a	104	P104P	ccT	ccG	6	16	AY.25	0.000036
ORF3a	104	P104S	Cct	Tct	16	16	B.1.1	0.00029
ORF3a	104	P104P	ccT	ccC	14	16	B.1.177	0.000184
ORF3a	104	P104P	ccT	ccG	2	16	B.1.177	0.000026
ORF3a	104	P104T	Cct	Act	16	16	R.1	0.00144
ORF3a	104	P104L	cCt	cTt	15	15	B.1.1.302	0.03112
ORF3a	104	P104L	cCt	cTt	15	15	B.1.160	0.000468
ORF3a	104	P104P	ccT	ccG	15	15	B.1.526	0.000353
ORF3a	104	P104P	ccT	ccG	12	15	B.1.621	0.001062
ORF3a	104	P104P	ccT	ccC	3	15	B.1.621	0.000266
ORF3a	104	P104S	Cct	Tct	15	15	Q.8	0.002474
ORF3a	104	P104del1	ccT	cc-	14	14	All	0.000003
ORF3a	104	P104L	cCt	cTt	14	14	AY.119	0.000494
ORF3a	104	P104L	cCt	cTt	14	14	AY.29	0.000221
ORF3a	104	P104P	ccT	ccG	11	14	AY.3	0.000109
ORF3a	104	P104P	ccT	ccC	3	14	AY.3	0.00003
ORF3a	104	P104P	ccT	ccC	10	14	B.1.1	0.000181
ORF3a	104	P104P	ccT	ccA	2	14	B.1.1	0.000036
ORF3a	104	P104P	ccT	ccG	2	14	B.1.1	0.000036
ORF3a	104	P104L	cCt	cTt	14	14	B.1.177.7	0.002308
ORF3a	104	P104L	cCt	cTt	14	14	P.2	0.002613
ORF3a	104	P104S	Cct	Tct	13	13	AY.20	0.000505
ORF3a	104	P104L	cCt	cTt	13	13	AY.84	0.005687
ORF3a	104	P104T	Cct	Act	13	13	B.1.177	0.000171
ORF3a	104	P104del	CCT	---	13	13	B.1.177	0.000171
ORF3a	104	P104A	Cct	Gct	13	13	B.1.2	0.000114
ORF3a	104	P104L	cCt	cTt	13	13	C.16	0.013786
ORF3a	104	P104T	Cct	Act	12	12	AY.25	0.000072
ORF3a	104	P104L	cCt	cTt	12	12	AY.26	0.00034
ORF3a	104	P104S	Cct	Tct	12	12	AY.62	0.005229
ORF3a	104	P104L	cCt	cTt	12	12	B	0.001534
ORF3a	104	P104del	CCT	---	12	12	B.1	0.00011
ORF3a	104	P104L	cCt	cTt	12	12	B.1.36.36	0.007225
ORF3a	104	P104P	ccT	ccG	12	12	Q.3	0.00174
ORF3a	104	P104L	cCt	cTt	5	11		0.277778
ORF3a	104	P104L	CCT	TTA	2	11		0.111111
ORF3a	104	P104L	cCT	cTG	2	11		0.111111
ORF3a	104	P104L	cCT	cTA	2	11		0.111111
ORF3a	104	P104S	Cct	Tct	11	11	AY.26	0.000311
ORF3a	104	P104S	Cct	Tct	11	11	AY.5	0.000227
ORF3a	104	P104P	ccT	ccG	11	11	AY.98	0.000869
ORF3a	104	P104L	cCt	cTt	11	11	B.1.1.214	0.00061
ORF3a	104	P104H	cCt	cAt	11	11	B.1.1.7	0.00001
ORF3a	104	P104S	Cct	Tct	11	11	B.1.258.17	0.001144
ORF3a	104	P104S	Cct	Tct	11	11	B.1.596	0.000959
ORF3a	104	P104P	ccT	ccG	11	11	P.1.10	0.002964
ORF3a	104	P104P	ccT	ccG	6	10	AY.103	0.000037
ORF3a	104	P104P	ccT	ccC	4	10	AY.103	0.000025
ORF3a	104	P104L	cCt	cTt	10	10	AY.54	0.000953
ORF3a	104	P104T	Cct	Act	10	10	B.1.2	0.000088
ORF3a	104	P104S	Cct	Tct	10	10	B.1.637	0.000731
ORF3a	104	P104S	Cct	Tct	10	10	Q.1	0.001263
ORF3a	104	P104P	ccT	ccG	9	9	AY.111	0.001648
ORF3a	104	P104P	ccT	ccG	9	9	AY.120	0.000335
ORF3a	104	P104P	ccT	ccG	9	9	AY.13	0.001449
ORF3a	104	P104S	Cct	Tct	9	9	AY.23	0.000628
ORF3a	104	P104H	cCt	cAt	9	9	AY.29	0.000142
ORF3a	104	P104S	Cct	Tct	9	9	AY.37	0.002845
ORF3a	104	P104L	cCt	cTt	9	9	AY.6	0.00037
ORF3a	104	P104P	ccT	ccC	6	9	AY.6	0.000247
ORF3a	104	P104P	ccT	ccG	3	9	AY.6	0.000123
ORF3a	104	P104P	ccT	ccC	7	9	B.1	0.000064
ORF3a	104	P104P	ccT	ccA	2	9	B.1	0.000018
ORF3a	104	P104T	Cct	Act	9	9	B.1.1.7	0.000008
ORF3a	104	P104L	cCt	cTt	9	9	B.1.177.53	0.021531
ORF3a	104	P104L	cCt	cTt	9	9	B.1.234	0.001187
ORF3a	104	P104S	Cct	Tct	9	9	B.1.264.1	0.428571
ORF3a	104	P104S	Cct	Tct	9	9	B.1.351	0.000268
ORF3a	104	P104S	Cct	Tct	9	9	B.1.427	0.000454
ORF3a	104	P104L	cCt	cTt	8	8	AU.1	0.010127
ORF3a	104	P104S	Cct	Tct	8	8	AY.118	0.000501
ORF3a	104	P104P	ccT	ccG	8	8	AY.2	0.002849
ORF3a	104	P104H	cCt	cAt	8	8	AY.25	0.000048
ORF3a	104	P104L	cCt	cTt	8	8	AY.5	0.000165
ORF3a	104	P104P	ccT	ccG	8	8	AY.5	0.000165
ORF3a	104	P104S	Cct	Tct	8	8	AY.9	0.000541
ORF3a	104	P104F	CCt	TTt	8	8	B.1.1.189	0.012103
ORF3a	104	P104S	Cct	Tct	8	8	B.1.1.519	0.000318
ORF3a	104	P104S	Cct	Tct	8	8	B.1.237	0.039801
ORF3a	104	P104S	Cct	Tct	8	8	B.1.621	0.000708
ORF3a	104	P104S	Cct	Tct	4	7		0.222222
ORF3a	104	P104S	CcT	TcA	2	7		0.111111
ORF3a	104	P104S	CcT	TcC	1	7		0.055556
ORF3a	104	P104L	cCt	cTt	7	7	AY.117	0.000592
ORF3a	104	P104S	Cct	Tct	7	7	AY.119	0.000247
ORF3a	104	P104L	cCt	cTt	7	7	AY.39.1	0.000277
ORF3a	104	P104H	cCt	cAt	7	7	AY.44	0.000043
ORF3a	104	P104S	Cct	Tct	7	7	AY.45	0.000852
ORF3a	104	P104L	cCt	cTt	7	7	AY.46	0.000729
ORF3a	104	P104P	ccT	ccC	5	7	AY.47	0.000156
ORF3a	104	P104P	ccT	ccG	2	7	AY.47	0.000062
ORF3a	104	P104S	Cct	Tct	7	7	B.1.1.25	0.00398
ORF3a	104	P104L	cCt	cTt	7	7	B.1.1.525	0.038251
ORF3a	104	P104T	Cct	Act	7	7	B.1.351	0.000208
ORF3a	104	P104T	Cct	Act	7	7	B.1.429	0.000165
ORF3a	104	P104S	Cct	Tct	7	7	B.1.429	0.000165
ORF3a	104	P104S	Cct	Tct	7	7	B.1.526	0.000165
ORF3a	104	P104H	cCt	cAt	7	7	B.1.617.2	0.000026
ORF3a	104	P104L	cCt	cTt	7	7	B.1.636	0.04698
ORF3a	104	P104P	ccT	ccG	6	6	AY.75	0.000336
ORF3a	104	P104L	cCt	cTt	6	6	AY.75	0.000336
ORF3a	104	P104L	cCt	cTt	6	6	AZ.3	0.009119
ORF3a	104	P104S	Cct	Tct	6	6	B.1.1.216	0.005343
ORF3a	104	P104L	cCt	cTt	6	6	B.1.1.507	0.052174
ORF3a	104	P104P	ccT	ccC	6	6	B.1.243	0.000418
ORF3a	104	P104R	cCt	cGt	6	6	B.1.351	0.000178
ORF3a	104	P104S	Cct	Tct	6	6	B.1.36	0.000875
ORF3a	104	P104R	cCt	cGt	6	6	B.1.617.2	0.000023
ORF3a	104	P104T	Cct	Act	6	6	B.1.617.2	0.000023
ORF3a	104	P104P	ccT	ccC	6	6	D.2	0.00045
ORF3a	104	P104P	ccT	ccC	3	5		0.166667
ORF3a	104	P104P	ccT	ccA	2	5		0.111111
ORF3a	104	P104del2	cCT	c--	4	5	All	0.000001
ORF3a	104	P104del2	CCt	--t	1	5	All	0
ORF3a	104	P104L	cCt	cTt	5	5	AY.111	0.000916
ORF3a	104	P104P	ccT	ccG	5	5	AY.118	0.000313
ORF3a	104	P104P	ccT	ccG	5	5	AY.14	0.00044
ORF3a	104	P104L	cCt	cTt	5	5	AY.23	0.000349
ORF3a	104	P104P	ccT	ccG	3	5	AY.26	0.000085
ORF3a	104	P104P	ccT	ccC	2	5	AY.26	0.000057
ORF3a	104	P104P	ccT	ccC	2	5	AY.39	0.000049
ORF3a	104	P104P	ccT	ccG	2	5	AY.39	0.000049
ORF3a	104	P104P	ccT	ccA	1	5	AY.39	0.000025
ORF3a	104	P104T	Cct	Act	5	5	AY.4	0.000008
ORF3a	104	P104S	Cct	Tct	5	5	AY.4.2.1	0.000745
ORF3a	104	P104del	CCT	---	5	5	AY.43	0.000022
ORF3a	104	P104T	Cct	Act	5	5	AY.44	0.00003
ORF3a	104	P104L	cCt	cTt	5	5	AY.46.4	0.000823
ORF3a	104	P104L	cCt	cTt	5	5	AY.47	0.000156
ORF3a	104	P104S	Cct	Tct	5	5	AY.60	0.00469
ORF3a	104	P104S	Cct	Tct	5	5	AY.70	0.001043
ORF3a	104	P104S	Cct	Tct	5	5	AY.98.1	0.000242
ORF3a	104	P104S	Cct	Tct	5	5	B	0.000639
ORF3a	104	P104P	ccT	ccC	5	5	B.1.1.176	0.002197
ORF3a	104	P104L	cCt	cTt	5	5	B.1.177.19	0.007153
ORF3a	104	P104H	cCt	cAt	5	5	B.1.2	0.000044
ORF3a	104	P104L	cCt	cTt	5	5	B.1.240	0.001078
ORF3a	104	P104L	cCt	cTt	5	5	B.1.36.29	0.002587
ORF3a	104	P104del	CCT	---	5	5	B.1.525	0.000566
ORF3a	104	P104L	cCt	cTt	5	5	B.1.596	0.000436
ORF3a	104	P104S	Cct	Tct	5	5	B.1.609	0.002397
ORF3a	104	P104del	CCT	---	5	5	B.1.617.2	0.000019
ORF3a	104	P104F	CCt	TTt	5	5	B.1.617.2	0.000019
ORF3a	104	P104L	cCt	cTt	5	5	C.37	0.00058
ORF3a	104	P104S	Cct	Tct	5	5	P.1.12	0.00242
ORF3a	104	P104S	Cct	Tct	5	5	Q.3	0.000725
ORF3a	104	P104L	cCt	cTt	5	5	Q.4	0.002274
ORF3a	104	P104L	cCt	cTt	5	5	Q.8	0.000825
ORF3a	104	P104C	CCt	TGt	4	4	All	0.000001
ORF3a	104	P104C	CCt	TGt	4	4	AY.103	0.000025
ORF3a	104	P104S	Cct	Tct	4	4	AY.116	0.001147
ORF3a	104	P104S	Cct	Tct	4	4	AY.13	0.000644
ORF3a	104	P104P	ccT	ccC	4	4	AY.20	0.000155
ORF3a	104	P104del	CCT	---	4	4	AY.25	0.000024
ORF3a	104	P104L	cCt	cTt	4	4	AY.37	0.001264
ORF3a	104	P104S	Cct	Tct	4	4	AY.39	0.000099
ORF3a	104	P104del	CCT	---	4	4	AY.4	0.000006
ORF3a	104	P104S	Cct	Tct	4	4	AY.4.2	0.000087
ORF3a	104	P104L	cCt	cTt	4	4	AY.40	0.003857
ORF3a	104	P104S	Cct	Tct	4	4	AY.42	0.000161
ORF3a	104	P104H	cCt	cAt	4	4	AY.43	0.000018
ORF3a	104	P104S	Cct	Tct	4	4	AY.46	0.000416
ORF3a	104	P104S	Cct	Tct	4	4	AY.47	0.000124
ORF3a	104	P104L	cCt	cTt	4	4	AY.58	0.00363
ORF3a	104	P104P	ccT	ccG	4	4	AY.61	0.000419
ORF3a	104	P104L	cCt	cTt	4	4	AY.92	0.001149
ORF3a	104	P104F	CCt	TTt	4	4	B.1.1	0.000073
ORF3a	104	P104L	cCt	cTt	4	4	B.1.1.157	0.003653
ORF3a	104	P104S	Cct	Tct	4	4	B.1.1.263	0.006231
ORF3a	104	P104L	cCt	cTt	4	4	B.1.1.316	0.0037
ORF3a	104	P104L	cCt	cTt	4	4	B.1.177.17	0.003284
ORF3a	104	P104S	Cct	Tct	4	4	B.1.177.40	0.020619
ORF3a	104	P104L	cCt	cTt	4	4	B.1.177.65	0.002661
ORF3a	104	P104L	cCt	cTt	4	4	B.1.177.73	0.002265
ORF3a	104	P104P	ccT	ccC	3	4	B.1.2	0.000026
ORF3a	104	P104P	ccT	ccG	1	4	B.1.2	0.000009
ORF3a	104	P104P	ccT	ccC	4	4	B.1.221	0.000284
ORF3a	104	P104S	Cct	Tct	4	4	B.1.234	0.000528
ORF3a	104	P104L	cCt	cTt	4	4	B.1.497	0.001259
ORF3a	104	P104S	Cct	Tct	4	4	B.1.525	0.000453
ORF3a	104	P104T	Cct	Act	4	4	B.1.526	0.000094
ORF3a	104	P104L	cCt	cTt	4	4	B.1.618	0.016129
ORF3a	104	P104L	cCt	cTt	4	4	B.1.621	0.000354
ORF3a	104	P104S	Cct	Tct	2	4	B.1.91	0.004149
ORF3a	104	P104T	Cct	Act	2	4	B.1.91	0.004149
ORF3a	104	P104T	CcT	AcC	1	4	B.1.91	0.002075
ORF3a	104	P104T	CcT	AcG	1	4	B.1.91	0.002075
ORF3a	104	P104S	CcT	TcC	1	4	B.1.91	0.002075
ORF3a	104	P104S	CcT	TcG	1	4	B.1.91	0.002075
ORF3a	104	P104del	CCT	---	4	4	P.1	0.000063
ORF3a	104	P104S	Cct	Tct	4	4	P.1.15	0.000929
ORF3a	104	P104del	CCT	---	4	4	P.1.15	0.000929
ORF3a	104	P104L	cCt	cTt	4	4	P.1.15	0.000929
ORF3a	104	P104T	Cct	Act	3	3	A.23.1	0.002113
ORF3a	104	P104L	cCt	cTt	3	3	AD.2	0.000657
ORF3a	104	P104P	ccT	ccA	2	3	AY.102	0.000053
ORF3a	104	P104P	ccT	ccC	1	3	AY.102	0.000027
ORF3a	104	P104S	Cct	Tct	3	3	AY.113	0.000427
ORF3a	104	P104T	Cct	Act	3	3	AY.117	0.000254
ORF3a	104	P104L	cCt	cTt	3	3	AY.118	0.000188
ORF3a	104	P104R	cCt	cGt	3	3	AY.26	0.000085
ORF3a	104	P104H	cCt	cAt	3	3	AY.3	0.00003
ORF3a	104	P104S	Cct	Tct	3	3	AY.32	0.001597
ORF3a	104	P104T	Cct	Act	3	3	AY.34	0.000291
ORF3a	104	P104A	CcT	GcC	3	3	AY.34	0.000291
ORF3a	104	P104S	Cct	Tct	3	3	AY.34	0.000291
ORF3a	104	P104P	ccT	ccG	3	3	AY.35	0.000699
ORF3a	104	P104H	cCt	cAt	3	3	AY.39	0.000074
ORF3a	104	P104del2	cCT	c--	3	3	AY.4	0.000005
ORF3a	104	P104L	cCt	cTt	3	3	AY.42	0.000121
ORF3a	104	P104L	cCt	cTt	3	3	AY.46.1	0.00308
ORF3a	104	P104S	Cct	Tct	3	3	AY.67	0.001393
ORF3a	104	P104L	cCt	cTt	3	3	AY.74	0.000347
ORF3a	104	P104S	Cct	Tct	3	3	AY.75	0.000168
ORF3a	104	P104L	cCt	cTt	3	3	AY.9	0.000203
ORF3a	104	P104L	cCt	cTt	3	3	AY.9.2	0.00011
ORF3a	104	P104S	Cct	Tct	3	3	AY.9.2	0.00011
ORF3a	104	P104L	cCt	cTt	3	3	AY.91.1	0.012195
ORF3a	104	P104S	Cct	Tct	3	3	AY.92	0.000862
ORF3a	104	P104L	cCt	cTt	3	3	AY.99	0.003148
ORF3a	104	P104R	cCt	cGt	3	3	B.1	0.000027
ORF3a	104	P104L	cCt	cTt	3	3	B.1.1.1	0.00098
ORF3a	104	P104S	Cct	Tct	3	3	B.1.1.189	0.004539
ORF3a	104	P104H	cCt	cAt	3	3	B.1.1.234	0.036145
ORF3a	104	P104L	cCt	cTt	3	3	B.1.1.317	0.001235
ORF3a	104	P104P	ccT	ccG	3	3	B.1.1.318	0.000905
ORF3a	104	P104del1	ccT	cc-	3	3	B.1.1.7	0.000003
ORF3a	104	P104F	CCt	TTt	3	3	B.1.1.7	0.000003
ORF3a	104	P104L	cCt	cTt	3	3	B.1.177.32	0.004049
ORF3a	104	P104R	cCt	cGt	3	3	B.1.2	0.000026
ORF3a	104	P104L	cCt	cTt	3	3	B.1.243	0.000209
ORF3a	104	P104P	ccT	ccC	3	3	B.1.36	0.000438
ORF3a	104	P104S	Cct	Tct	3	3	B.1.36.27	0.00229
ORF3a	104	P104L	cCt	cTt	3	3	B.1.427	0.000151
ORF3a	104	P104S	Cct	Tct	3	3	B.1.575	0.00091
ORF3a	104	P104del	CCT	---	3	3	B.1.621	0.000266
ORF3a	104	P104H	cCt	cAt	3	3	B.1.637	0.000219
ORF3a	104	P104S	Cct	Tct	3	3	C.14	0.012987
ORF3a	104	P104S	Cct	Tct	3	3	P.1.1	0.000953
ORF3a	104	P104S	Cct	Tct	3	3	P.1.14	0.000143
ORF3a	104	P104L	cCt	cTt	3	3	P.1.16	0.001122
ORF3a	104	P104S	Cct	Tct	3	3	P.1.2	0.003468
ORF3a	104	P104S	Cct	Tct	3	3	P.2	0.00056
ORF3a	104	P104H	cCt	cAt	3	3	P.2	0.00056
ORF3a	104	P104F	CCt	TTt	2	2		0.111111
ORF3a	104	P104L	cCt	cTt	2	2	A.1	0.000564
ORF3a	104	P104I	CCt	ATt	1	2	All	0
ORF3a	104	P104I	CCT	ATC	1	2	All	0
ORF3a	104	P104P	ccT	ccG	2	2	AY.1	0.000791
ORF3a	104	P104H	cCt	cAt	2	2	AY.102	0.000053
ORF3a	104	P104T	Cct	Act	2	2	AY.108	0.002205
ORF3a	104	P104A	Cct	Gct	2	2	AY.108	0.002205
ORF3a	104	P104del	CCT	---	2	2	AY.108	0.002205
ORF3a	104	P104L	cCt	cTt	2	2	AY.114	0.000462
ORF3a	104	P104L	cCt	cTt	2	2	AY.12	0.000632
ORF3a	104	P104H	cCt	cAt	2	2	AY.120.1	0.000642
ORF3a	104	P104del	CCT	---	2	2	AY.23	0.000139
ORF3a	104	P104T	Cct	Act	2	2	AY.26	0.000057
ORF3a	104	P104H	cCt	cAt	2	2	AY.26	0.000057
ORF3a	104	P104del	CCT	---	2	2	AY.29	0.000032
ORF3a	104	P104L	cCt	cTt	2	2	AY.3.1	0.000171
ORF3a	104	P104H	cCt	cAt	2	2	AY.33	0.000134
ORF3a	104	P104P	ccT	ccG	2	2	AY.38	0.000999
ORF3a	104	P104R	cCt	cGt	2	2	AY.4	0.000003
ORF3a	104	P104L	cCt	cTt	2	2	AY.4.2	0.000043
ORF3a	104	P104P	ccT	ccG	2	2	AY.4.2.1	0.000298
ORF3a	104	P104L	cCt	cTt	2	2	AY.4.4	0.000818
ORF3a	104	P104del	CCT	---	2	2	AY.4.5	0.000215
ORF3a	104	P104P	ccT	ccG	1	2	AY.42	0.00004
ORF3a	104	P104P	ccT	ccC	1	2	AY.42	0.00004
ORF3a	104	P104A	CcT	GcA	1	2	AY.43	0.000004
ORF3a	104	P104A	Cct	Gct	1	2	AY.43	0.000004
ORF3a	104	P104S	Cct	Tct	2	2	AY.46.4	0.000329
ORF3a	104	P104P	ccT	ccG	2	2	AY.46.5	0.000397
ORF3a	104	P104L	cCt	cTt	2	2	AY.48	0.00093
ORF3a	104	P104L	cCt	cTt	2	2	AY.55	0.001835
ORF3a	104	P104S	Cct	Tct	2	2	AY.57	0.001312
ORF3a	104	P104S	Cct	Tct	2	2	AY.58	0.001815
ORF3a	104	P104P	ccT	ccC	2	2	AY.60	0.001876
ORF3a	104	P104P	ccT	ccG	1	2	AY.62	0.000436
ORF3a	104	P104P	ccT	ccC	1	2	AY.62	0.000436
ORF3a	104	P104S	Cct	Tct	2	2	AY.74	0.000231
ORF3a	104	P104L	cCt	cTt	2	2	AY.75.1	0.000361
ORF3a	104	P104L	cCt	cTt	2	2	AY.81	0.003984
ORF3a	104	P104L	cCt	cTt	2	2	AY.88	0.001768
ORF3a	104	P104L	cCt	cTt	2	2	AY.9.1	0.000167
ORF3a	104	P104P	ccT	ccG	2	2	AY.96	0.004149
ORF3a	104	P104S	Cct	Tct	2	2	AY.98	0.000158
ORF3a	104	P104S	Cct	Tct	2	2	AY.99.2	0.000184
ORF3a	104	P104L	cCt	cTt	2	2	AY.99.2	0.000184
ORF3a	104	P104del1	ccT	cc-	2	2	B.1	0.000018
ORF3a	104	P104H	cCt	cAt	2	2	B.1	0.000018
ORF3a	104	P104T	Cct	Act	2	2	B.1	0.000018
ORF3a	104	P104A	Cct	Gct	2	2	B.1.1	0.000036
ORF3a	104	P104L	cCt	cTt	2	2	B.1.1.153	0.002191
ORF3a	104	P104S	Cct	Tct	2	2	B.1.1.214	0.000111
ORF3a	104	P104L	cCt	cTt	2	2	B.1.1.265	0.006309
ORF3a	104	P104L	cCt	cTt	2	2	B.1.1.28	0.000622
ORF3a	104	P104L	cCt	cTt	2	2	B.1.1.284	0.000215
ORF3a	104	P104L	cCt	cTt	2	2	B.1.1.294	0.002532
ORF3a	104	P104S	Cct	Tct	2	2	B.1.1.317	0.000823
ORF3a	104	P104P	ccT	ccA	1	2	B.1.1.33	0.000421
ORF3a	104	P104P	ccT	ccC	1	2	B.1.1.33	0.000421
ORF3a	104	P104P	ccT	ccG	2	2	B.1.1.337	0.007194
ORF3a	104	P104S	Cct	Tct	2	2	B.1.1.39	0.001019
ORF3a	104	P104L	cCt	cTt	2	2	B.1.1.434	0.000697
ORF3a	104	P104F	CCt	TTt	2	2	B.1.1.507	0.017391
ORF3a	104	P104L	cCt	cTt	2	2	B.1.147	0.001512
ORF3a	104	P104P	ccT	ccC	2	2	B.1.177.15	0.001262
ORF3a	104	P104P	ccT	ccC	2	2	B.1.177.16	0.001329
ORF3a	104	P104L	cCt	cTt	2	2	B.1.177.44	0.001038
ORF3a	104	P104L	cCt	cTt	2	2	B.1.177.57	0.000562
ORF3a	104	P104S	Cct	Tct	2	2	B.1.177.57	0.000562
ORF3a	104	P104L	cCt	cTt	2	2	B.1.177.79	0.004684
ORF3a	104	P104S	Cct	Tct	2	2	B.1.177.83	0.002963
ORF3a	104	P104del	CCT	---	2	2	B.1.2	0.000018
ORF3a	104	P104L	cCt	cTt	2	2	B.1.214.2	0.001199
ORF3a	104	P104S	Cct	Tct	2	2	B.1.221	0.000142
ORF3a	104	P104del	CCT	---	2	2	B.1.240	0.000431
ORF3a	104	P104L	cCt	cTt	2	2	B.1.241	0.001623
ORF3a	104	P104L	cCt	cTt	2	2	B.1.258	0.000133
ORF3a	104	P104L	cCt	cTt	2	2	B.1.258.17	0.000208
ORF3a	104	P104L	cCt	cTt	2	2	B.1.311	0.000549
ORF3a	104	P104F	CCt	TTt	2	2	B.1.351	0.000059
ORF3a	104	P104H	cCt	cAt	2	2	B.1.351	0.000059
ORF3a	104	P104P	ccT	ccG	1	2	B.1.351	0.00003
ORF3a	104	P104P	ccT	ccC	1	2	B.1.351	0.00003
ORF3a	104	P104L	cCt	cTt	2	2	B.1.36	0.000292
ORF3a	104	P104L	cCt	cTt	2	2	B.1.36.22	0.002415
ORF3a	104	P104S	Cct	Tct	2	2	B.1.369	0.00057
ORF3a	104	P104L	cCt	cTt	2	2	B.1.397	0.009709
ORF3a	104	P104L	cCt	cTt	2	2	B.1.400	0.000858
ORF3a	104	P104L	cCt	cTt	2	2	B.1.413	0.008511
ORF3a	104	P104L	cCt	cTt	2	2	B.1.426	0.002018
ORF3a	104	P104S	Cct	Tct	2	2	B.1.451	0.016393
ORF3a	104	P104R	cCt	cGt	2	2	B.1.595	0.000522
ORF3a	104	P104L	cCt	cTt	2	2	B.1.595	0.000522
ORF3a	104	P104S	Cct	Tct	2	2	B.1.621.1	0.001012
ORF3a	104	P104P	ccT	ccG	2	2	B.1.625	0.004706
ORF3a	104	P104P	ccT	ccG	2	2	B.1.628	0.000705
ORF3a	104	P104P	ccT	ccG	2	2	B.1.631	0.006734
ORF3a	104	P104F	CCt	TTt	1	2	B.1.91	0.002075
ORF3a	104	P104L	cCt	cTt	1	2	B.1.91	0.002075
ORF3a	104	P104F	CCT	TTC	1	2	B.1.91	0.002075
ORF3a	104	P104L	cCT	cTC	1	2	B.1.91	0.002075
ORF3a	104	P104I	CCt	ATt	1	2	B.1.91	0.002075
ORF3a	104	P104I	CCT	ATC	1	2	B.1.91	0.002075
ORF3a	104	P104S	Cct	Tct	2	2	B.52	0.020202
ORF3a	104	P104S	Cct	Tct	2	2	C.35	0.001548
ORF3a	104	P104P	ccT	ccG	1	2	C.37	0.000116
ORF3a	104	P104P	ccT	ccC	1	2	C.37	0.000116
ORF3a	104	P104S	Cct	Tct	2	2	P.1.10	0.000539
ORF3a	104	P104F	CCt	TTt	2	2	P.1.17	0.000324
ORF3a	104	P104L	cCt	cTt	2	2	P.1.17	0.000324
ORF3a	104	P104P	ccT	ccG	2	2	P.1.17	0.000324
ORF3a	104	P104L	cCt	cTt	2	2	R.1	0.00018
ORF3a	104	P104del	CCT	---	1	1	A	0.000387
ORF3a	104	P104L	cCt	cTt	1	1	A	0.000387
ORF3a	104	P104S	Cct	Tct	1	1	A.12	0.166667
ORF3a	104	P104H	cCt	cAt	1	1	A.2.2	0.001689
ORF3a	104	P104P	ccT	ccG	1	1	A.2.5	0.000499
ORF3a	104	P104S	Cct	Tct	1	1	A.2.5.1	0.004808
ORF3a	104	P104S	Cct	Tct	1	1	AD.2	0.000219
ORF3a	104	P104del	CCT	---	1	1	AH.3	0.003802
ORF3a	104	P104Y	CCt	TAt	1	1	All	0
ORF3a	104	P104W	CCT	TGG	1	1	All	0
ORF3a	104	P104X	CCT	TAG	1	1	All	0
ORF3a	104	P104N	CCt	AAt	1	1	All	0
ORF3a	104	P104D	CCt	GAt	1	1	All	0
ORF3a	104	P104Q	cCT	cAA	1	1	All	0
ORF3a	104	P104V	CCt	GTt	1	1	All	0
ORF3a	104	P104K	CCT	AAG	1	1	All	0
ORF3a	104	P104S	Cct	Tct	1	1	AM.1	0.111111
ORF3a	104	P104L	cCt	cTt	1	1	AM.4	0.003571
ORF3a	104	P104del	CCT	---	1	1	AV.1	0.005051
ORF3a	104	P104S	Cct	Tct	1	1	AY.100	0.000046
ORF3a	104	P104del	CCT	---	1	1	AY.100	0.000046
ORF3a	104	P104R	cCt	cGt	1	1	AY.100	0.000046
ORF3a	104	P104P	ccT	ccG	1	1	AY.100	0.000046
ORF3a	104	P104S	Cct	Tct	1	1	AY.101	0.00049
ORF3a	104	P104L	cCt	cTt	1	1	AY.104	0.001984
ORF3a	104	P104L	cCt	cTt	1	1	AY.105	0.000643
ORF3a	104	P104del	CCT	---	1	1	AY.106	0.000335
ORF3a	104	P104L	cCt	cTt	1	1	AY.107	0.000466
ORF3a	104	P104F	CCt	TTt	1	1	AY.108	0.001103
ORF3a	104	P104del	CCT	---	1	1	AY.111	0.000183
ORF3a	104	P104L	cCt	cTt	1	1	AY.113	0.000142
ORF3a	104	P104L	cCt	cTt	1	1	AY.116	0.000287
ORF3a	104	P104S	Cct	Tct	1	1	AY.116.1	0.000311
ORF3a	104	P104P	ccT	ccG	1	1	AY.119	0.000035
ORF3a	104	P104P	ccT	ccC	1	1	AY.12	0.000316
ORF3a	104	P104S	Cct	Tct	1	1	AY.16	0.00038
ORF3a	104	P104del	CCT	---	1	1	AY.20	0.000039
ORF3a	104	P104T	Cct	Act	1	1	AY.23	0.00007
ORF3a	104	P104del2	CCt	--t	1	1	AY.23	0.00007
ORF3a	104	P104L	cCt	cTt	1	1	AY.24	0.000431
ORF3a	104	P104L	cCt	cTt	1	1	AY.27	0.000065
ORF3a	104	P104S	Cct	Tct	1	1	AY.29.1	0.000221
ORF3a	104	P104L	cCt	cTt	1	1	AY.30	0.000396
ORF3a	104	P104P	ccT	ccG	1	1	AY.30	0.000396
ORF3a	104	P104P	ccT	ccA	1	1	AY.31	0.018519
ORF3a	104	P104L	cCt	cTt	1	1	AY.33	0.000067
ORF3a	104	P104R	cCt	cGt	1	1	AY.33	0.000067
ORF3a	104	P104del	CCT	---	1	1	AY.33	0.000067
ORF3a	104	P104L	cCt	cTt	1	1	AY.34	0.000097
ORF3a	104	P104del	CCT	---	1	1	AY.34.1	0.00051
ORF3a	104	P104S	Cct	Tct	1	1	AY.35	0.000233
ORF3a	104	P104L	cCt	cTt	1	1	AY.35	0.000233
ORF3a	104	P104del	CCT	---	1	1	AY.35	0.000233
ORF3a	104	P104L	cCt	cTt	1	1	AY.36	0.000148
ORF3a	104	P104P	ccT	ccG	1	1	AY.37	0.000316
ORF3a	104	P104R	cCt	cGt	1	1	AY.39	0.000025
ORF3a	104	P104del	CCT	---	1	1	AY.39	0.000025
ORF3a	104	P104S	Cct	Tct	1	1	AY.39.1	0.00004
ORF3a	104	P104T	Cct	Act	1	1	AY.39.1	0.00004
ORF3a	104	P104A	Cct	Gct	1	1	AY.4	0.000002
ORF3a	104	P104P	ccT	ccG	1	1	AY.4.1	0.000737
ORF3a	104	P104S	Cct	Tct	1	1	AY.4.3	0.000842
ORF3a	104	P104P	ccT	ccG	1	1	AY.4.4	0.000409
ORF3a	104	P104L	cCt	cTt	1	1	AY.4.5	0.000107
ORF3a	104	P104del1	ccT	cc-	1	1	AY.43	0.000004
ORF3a	104	P104R	cCt	cGt	1	1	AY.44	0.000006
ORF3a	104	P104L	cCt	cTt	1	1	AY.45	0.000122
ORF3a	104	P104P	ccT	ccG	1	1	AY.45	0.000122
ORF3a	104	P104H	cCt	cAt	1	1	AY.45	0.000122
ORF3a	104	P104P	ccT	ccC	1	1	AY.46	0.000104
ORF3a	104	P104P	ccT	ccC	1	1	AY.46.2	0.000635
ORF3a	104	P104S	Cct	Tct	1	1	AY.46.6	0.000072
ORF3a	104	P104S	Cct	Tct	1	1	AY.48	0.000465
ORF3a	104	P104P	ccT	ccG	1	1	AY.48	0.000465
ORF3a	104	P104S	Cct	Tct	1	1	AY.5.3	0.000337
ORF3a	104	P104L	cCt	cTt	1	1	AY.5.4	0.000277
ORF3a	104	P104S	Cct	Tct	1	1	AY.53	0.000288
ORF3a	104	P104S	Cct	Tct	1	1	AY.54	0.000095
ORF3a	104	P104P	ccT	ccG	1	1	AY.54	0.000095
ORF3a	104	P104P	ccT	ccG	1	1	AY.56	0.001605
ORF3a	104	P104S	Cct	Tct	1	1	AY.61	0.000105
ORF3a	104	P104T	Cct	Act	1	1	AY.62	0.000436
ORF3a	104	P104S	Cct	Tct	1	1	AY.63	0.000387
ORF3a	104	P104L	cCt	cTt	1	1	AY.67	0.000464
ORF3a	104	P104del	CCT	---	1	1	AY.68	0.000274
ORF3a	104	P104S	Cct	Tct	1	1	AY.69	0.000187
ORF3a	104	P104L	cCt	cTt	1	1	AY.69	0.000187
ORF3a	104	P104P	ccT	ccG	1	1	AY.7	0.000196
ORF3a	104	P104L	cCt	cTt	1	1	AY.7.1	0.000113
ORF3a	104	P104L	cCt	cTt	1	1	AY.72	0.001361
ORF3a	104	P104L	cCt	cTt	1	1	AY.73	0.000665
ORF3a	104	P104S	Cct	Tct	1	1	AY.75.1	0.00018
ORF3a	104	P104L	cCt	cTt	1	1	AY.79	0.001211
ORF3a	104	P104S	Cct	Tct	1	1	AY.84	0.000437
ORF3a	104	P104P	ccT	ccC	1	1	AY.85	0.000427
ORF3a	104	P104S	Cct	Tct	1	1	AY.86	0.00083
ORF3a	104	P104P	ccT	ccC	1	1	AY.9	0.000068
ORF3a	104	P104del2	cCT	c--	1	1	AY.9.1	0.000084
ORF3a	104	P104P	ccT	ccG	1	1	AY.9.2	0.000037
ORF3a	104	P104H	cCt	cAt	1	1	AY.90	0.000684
ORF3a	104	P104P	ccT	ccG	1	1	AY.90	0.000684
ORF3a	104	P104S	Cct	Tct	1	1	AY.91	0.00073
ORF3a	104	P104L	cCt	cTt	1	1	AY.93	0.000273
ORF3a	104	P104L	cCt	cTt	1	1	AY.94	0.000443
ORF3a	104	P104S	Cct	Tct	1	1	AY.95	0.000761
ORF3a	104	P104L	cCt	cTt	1	1	AY.98	0.000079
ORF3a	104	P104L	cCt	cTt	1	1	AZ.1	0.000867
ORF3a	104	P104P	ccT	ccG	1	1	AZ.3	0.00152
ORF3a	104	P104del	CCT	---	1	1	B	0.000128
ORF3a	104	P104F	CCt	TTt	1	1	B	0.000128
ORF3a	104	P104A	Cct	Gct	1	1	B.1	0.000009
ORF3a	104	P104T	Cct	Act	1	1	B.1.1	0.000018
ORF3a	104	P104D	CCt	GAt	1	1	B.1.1	0.000018
ORF3a	104	P104V	CCt	GTt	1	1	B.1.1	0.000018
ORF3a	104	P104del1	ccT	cc-	1	1	B.1.1	0.000018
ORF3a	104	P104del	CCT	---	1	1	B.1.1	0.000018
ORF3a	104	P104R	cCt	cGt	1	1	B.1.1	0.000018
ORF3a	104	P104S	Cct	Tct	1	1	B.1.1.171	0.003676
ORF3a	104	P104L	cCt	cTt	1	1	B.1.1.189	0.001513
ORF3a	104	P104T	Cct	Act	1	1	B.1.1.194	0.00495
ORF3a	104	P104del	CCT	---	1	1	B.1.1.204	0.00304
ORF3a	104	P104S	Cct	Tct	1	1	B.1.1.207	0.001182
ORF3a	104	P104P	ccT	ccC	1	1	B.1.1.214	0.000055
ORF3a	104	P104R	cCt	cGt	1	1	B.1.1.216	0.00089
ORF3a	104	P104del1	ccT	cc-	1	1	B.1.1.216	0.00089
ORF3a	104	P104S	Cct	Tct	1	1	B.1.1.222	0.000204
ORF3a	104	P104L	cCt	cTt	1	1	B.1.1.222	0.000204
ORF3a	104	P104L	cCt	cTt	1	1	B.1.1.243	0.004082
ORF3a	104	P104L	cCt	cTt	1	1	B.1.1.266	0.012195
ORF3a	104	P104L	cCt	cTt	1	1	B.1.1.279	0.001121
ORF3a	104	P104P	ccT	ccC	1	1	B.1.1.28	0.000311
ORF3a	104	P104L	cCt	cTt	1	1	B.1.1.280	0.003086
ORF3a	104	P104L	cCt	cTt	1	1	B.1.1.291	0.000742
ORF3a	104	P104F	CCt	TTt	1	1	B.1.1.301	0.001179
ORF3a	104	P104L	cCt	cTt	1	1	B.1.1.306	0.000438
ORF3a	104	P104S	Cct	Tct	1	1	B.1.1.311	0.000358
ORF3a	104	P104P	ccT	ccG	1	1	B.1.1.311	0.000358
ORF3a	104	P104L	cCt	cTt	1	1	B.1.1.311	0.000358
ORF3a	104	P104del	CCT	---	1	1	B.1.1.312	0.001912
ORF3a	104	P104S	Cct	Tct	1	1	B.1.1.312	0.001912
ORF3a	104	P104del	CCT	---	1	1	B.1.1.315	0.008475
ORF3a	104	P104H	cCt	cAt	1	1	B.1.1.318	0.000302
ORF3a	104	P104L	cCt	cTt	1	1	B.1.1.318	0.000302
ORF3a	104	P104L	cCt	cTt	1	1	B.1.1.328	0.016949
ORF3a	104	P104S	Cct	Tct	1	1	B.1.1.329	0.003846
ORF3a	104	P104Q	cCT	cAA	1	1	B.1.1.33	0.000421
ORF3a	104	P104H	cCT	cAC	1	1	B.1.1.33	0.000421
ORF3a	104	P104S	Cct	Tct	1	1	B.1.1.344	0.010753
ORF3a	104	P104L	cCt	cTt	1	1	B.1.1.348	0.000796
ORF3a	104	P104S	Cct	Tct	1	1	B.1.1.351	0.002793
ORF3a	104	P104P	ccT	ccG	1	1	B.1.1.369	0.000446
ORF3a	104	P104P	ccT	ccC	1	1	B.1.1.37	0.000193
ORF3a	104	P104L	cCt	cTt	1	1	B.1.1.372	0.000689
ORF3a	104	P104S	Cct	Tct	1	1	B.1.1.385	0.004464
ORF3a	104	P104L	cCt	cTt	1	1	B.1.1.388	0.045455
ORF3a	104	P104L	cCt	cTt	1	1	B.1.1.39	0.00051
ORF3a	104	P104P	ccT	ccC	1	1	B.1.1.39	0.00051
ORF3a	104	P104del	CCT	---	1	1	B.1.1.409	0.002833
ORF3a	104	P104del	CCT	---	1	1	B.1.1.420	0.001006
ORF3a	104	P104H	cCt	cAt	1	1	B.1.1.432	0.001266
ORF3a	104	P104L	cCt	cTt	1	1	B.1.1.446	0.076923
ORF3a	104	P104L	cCt	cTt	1	1	B.1.1.448	0.002033
ORF3a	104	P104S	Cct	Tct	1	1	B.1.1.47	0.005348
ORF3a	104	P104L	cCt	cTt	1	1	B.1.1.50	0.000679
ORF3a	104	P104S	Cct	Tct	1	1	B.1.1.515	0.02
ORF3a	104	P104T	Cct	Act	1	1	B.1.1.519	0.00004
ORF3a	104	P104del1	ccT	cc-	1	1	B.1.1.519	0.00004
ORF3a	104	P104L	cCt	cTt	1	1	B.1.1.524	0.020833
ORF3a	104	P104R	cCt	cGt	1	1	B.1.1.526	0.003546
ORF3a	104	P104L	cCt	cTt	1	1	B.1.1.528	0.004808
ORF3a	104	P104A	Cct	Gct	1	1	B.1.1.7	0.000001
ORF3a	104	P104W	CCT	TGG	1	1	B.1.1.7	0.000001
ORF3a	104	P104L	cCt	cTt	1	1	B.1.1.70	0.000341
ORF3a	104	P104S	Cct	Tct	1	1	B.1.115	0.021739
ORF3a	104	P104L	cCt	cTt	1	1	B.1.139	0.000733
ORF3a	104	P104P	ccT	ccA	1	1	B.1.14	0.017544
ORF3a	104	P104del	CCT	---	1	1	B.1.140	0.018868
ORF3a	104	P104H	cCt	cAt	1	1	B.1.147	0.000756
ORF3a	104	P104del	CCT	---	1	1	B.1.157	0.002985
ORF3a	104	P104del	CCT	---	1	1	B.1.160	0.000031
ORF3a	104	P104P	ccT	ccG	1	1	B.1.160	0.000031
ORF3a	104	P104L	cCt	cTt	1	1	B.1.160.14	0.002119
ORF3a	104	P104P	ccT	ccG	1	1	B.1.160.15	0.00495
ORF3a	104	P104del	CCT	---	1	1	B.1.160.23	0.004831
ORF3a	104	P104S	Cct	Tct	1	1	B.1.160.25	0.011111
ORF3a	104	P104L	cCt	cTt	1	1	B.1.160.32	0.004292
ORF3a	104	P104H	cCt	cAt	1	1	B.1.177	0.000013
ORF3a	104	P104del	CCT	---	1	1	B.1.177.18	0.00116
ORF3a	104	P104L	cCt	cTt	1	1	B.1.177.21	0.000076
ORF3a	104	P104P	ccT	ccG	1	1	B.1.177.32	0.00135
ORF3a	104	P104S	Cct	Tct	1	1	B.1.177.41	0.0025
ORF3a	104	P104P	ccT	ccC	1	1	B.1.177.44	0.000519
ORF3a	104	P104S	Cct	Tct	1	1	B.1.177.44	0.000519
ORF3a	104	P104L	cCt	cTt	1	1	B.1.177.50	0.004695
ORF3a	104	P104P	ccT	ccC	1	1	B.1.177.50	0.004695
ORF3a	104	P104del	CCT	---	1	1	B.1.177.51	0.004566
ORF3a	104	P104L	cCt	cTt	1	1	B.1.177.52	0.001757
ORF3a	104	P104del	CCT	---	1	1	B.1.177.62	0.001192
ORF3a	104	P104L	cCt	cTt	1	1	B.1.177.62	0.001192
ORF3a	104	P104L	cCt	cTt	1	1	B.1.177.75	0.001041
ORF3a	104	P104S	Cct	Tct	1	1	B.1.177.75	0.001041
ORF3a	104	P104L	cCt	cTt	1	1	B.1.177.83	0.001481
ORF3a	104	P104H	cCt	cAt	1	1	B.1.177.86	0.000183
ORF3a	104	P104L	cCt	cTt	1	1	B.1.177.86	0.000183
ORF3a	104	P104L	cCt	cTt	1	1	B.1.177.87	0.000728
ORF3a	104	P104F	CCt	TTt	1	1	B.1.2	0.000009
ORF3a	104	P104F	CCt	TTt	1	1	B.1.214	0.003663
ORF3a	104	P104L	cCt	cTt	1	1	B.1.218	0.005155
ORF3a	104	P104P	ccT	ccC	1	1	B.1.234	0.000132
ORF3a	104	P104P	ccT	ccC	1	1	B.1.236	0.002053
ORF3a	104	P104T	Cct	Act	1	1	B.1.243	0.00007
ORF3a	104	P104R	cCt	cGt	1	1	B.1.243	0.00007
ORF3a	104	P104L	cCt	cTt	1	1	B.1.243.1	0.022222
ORF3a	104	P104S	Cct	Tct	1	1	B.1.258.11	0.000396
ORF3a	104	P104P	ccT	ccC	1	1	B.1.258.11	0.000396
ORF3a	104	P104S	Cct	Tct	1	1	B.1.258.12	0.007874
ORF3a	104	P104L	cCt	cTt	1	1	B.1.258.15	0.018868
ORF3a	104	P104P	ccT	ccC	1	1	B.1.258.17	0.000104
ORF3a	104	P104L	cCt	cTt	1	1	B.1.298	0.002114
ORF3a	104	P104L	cCt	cTt	1	1	B.1.318	0.038462
ORF3a	104	P104P	ccT	ccC	1	1	B.1.320	0.001245
ORF3a	104	P104L	cCt	cTt	1	1	B.1.324	0.001605
ORF3a	104	P104L	cCt	cTt	1	1	B.1.336	0.002439
ORF3a	104	P104S	Cct	Tct	1	1	B.1.336	0.002439
ORF3a	104	P104L	cCt	cTt	1	1	B.1.340	0.004292
ORF3a	104	P104L	cCt	cTt	1	1	B.1.350	0.002933
ORF3a	104	P104L	cCt	cTt	1	1	B.1.356	0.001727
ORF3a	104	P104H	cCt	cAt	1	1	B.1.362	0.001541
ORF3a	104	P104del	CCT	---	1	1	B.1.362	0.001541
ORF3a	104	P104del1	ccT	cc-	1	1	B.1.362	0.001541
ORF3a	104	P104L	cCt	cTt	1	1	B.1.367	0.000792
ORF3a	104	P104F	CCt	TTt	1	1	B.1.367	0.000792
ORF3a	104	P104S	Cct	Tct	1	1	B.1.367	0.000792
ORF3a	104	P104L	cCt	cTt	1	1	B.1.375	0.00082
ORF3a	104	P104H	cCt	cAt	1	1	B.1.381	0.007812
ORF3a	104	P104S	Cct	Tct	1	1	B.1.391	0.001127
ORF3a	104	P104L	cCt	cTt	1	1	B.1.396	0.000706
ORF3a	104	P104S	Cct	Tct	1	1	B.1.399	0.001934
ORF3a	104	P104L	cCt	cTt	1	1	B.1.399	0.001934
ORF3a	104	P104L	cCt	cTt	1	1	B.1.401	0.008197
ORF3a	104	P104T	Cct	Act	1	1	B.1.408	0.00369
ORF3a	104	P104S	Cct	Tct	1	1	B.1.409	0.000781
ORF3a	104	P104del	CCT	---	1	1	B.1.416.1	0.001563
ORF3a	104	P104S	Cct	Tct	1	1	B.1.422	0.000812
ORF3a	104	P104T	Cct	Act	1	1	B.1.425	0.002994
ORF3a	104	P104H	cCt	cAt	1	1	B.1.429	0.000024
ORF3a	104	P104P	ccT	ccC	1	1	B.1.429	0.000024
ORF3a	104	P104S	Cct	Tct	1	1	B.1.438.1	0.000107
ORF3a	104	P104L	cCt	cTt	1	1	B.1.438.1	0.000107
ORF3a	104	P104P	ccT	ccG	1	1	B.1.438.1	0.000107
ORF3a	104	P104T	Cct	Act	1	1	B.1.459	0.004082
ORF3a	104	P104S	Cct	Tct	1	1	B.1.466.2	0.000391
ORF3a	104	P104S	Cct	Tct	1	1	B.1.470	0.001404
ORF3a	104	P104L	cCt	cTt	1	1	B.1.474	0.001901
ORF3a	104	P104S	Cct	Tct	1	1	B.1.499	0.00105
ORF3a	104	P104L	cCt	cTt	1	1	B.1.509	0.000866
ORF3a	104	P104L	cCt	cTt	1	1	B.1.530	0.007143
ORF3a	104	P104L	cCt	cTt	1	1	B.1.533	0.009615
ORF3a	104	P104S	Cct	Tct	1	1	B.1.555	0.022222
ORF3a	104	P104L	cCt	cTt	1	1	B.1.560	0.00463
ORF3a	104	P104L	cCt	cTt	1	1	B.1.564	0.000426
ORF3a	104	P104L	cCt	cTt	1	1	B.1.565	0.00081
ORF3a	104	P104S	Cct	Tct	1	1	B.1.565	0.00081
ORF3a	104	P104L	cCt	cTt	1	1	B.1.576	0.000907
ORF3a	104	P104S	Cct	Tct	1	1	B.1.580	0.004065
ORF3a	104	P104S	Cct	Tct	1	1	B.1.582	0.000491
ORF3a	104	P104S	Cct	Tct	1	1	B.1.595	0.000261
ORF3a	104	P104P	ccT	ccC	1	1	B.1.595	0.000261
ORF3a	104	P104del	CCT	---	1	1	B.1.596	0.000087
ORF3a	104	P104R	cCt	cGt	1	1	B.1.596	0.000087
ORF3a	104	P104P	ccT	ccC	1	1	B.1.606	0.006024
ORF3a	104	P104L	cCt	cTt	1	1	B.1.617.1	0.000129
ORF3a	104	P104P	ccT	ccC	1	1	B.1.617.1	0.000129
ORF3a	104	P104S	Cct	Tct	1	1	B.1.617.1	0.000129
ORF3a	104	P104del	CCT	---	1	1	B.1.617.1	0.000129
ORF3a	104	P104del1	ccT	cc-	1	1	B.1.617.2	0.000004
ORF3a	104	P104S	Cct	Tct	1	1	B.1.620	0.000946
ORF3a	104	P104del1	ccT	cc-	1	1	B.1.621	0.000089
ORF3a	104	P104L	cCt	cTt	1	1	B.1.621.1	0.000506
ORF3a	104	P104P	ccT	ccG	1	1	B.1.621.1	0.000506
ORF3a	104	P104L	cCt	cTt	1	1	B.1.623	0.000536
ORF3a	104	P104L	cCt	cTt	1	1	B.1.627	0.00202
ORF3a	104	P104L	cCt	cTt	1	1	B.1.628	0.000352
ORF3a	104	P104F	CCt	TTt	1	1	B.1.628	0.000352
ORF3a	104	P104S	Cct	Tct	1	1	B.1.631	0.003367
ORF3a	104	P104del	CCT	---	1	1	B.1.638	0.052632
ORF3a	104	P104L	cCt	cTt	1	1	B.1.9.4	0.006135
ORF3a	104	P104L	cCt	cTt	1	1	B.1.9.5	0.005682
ORF3a	104	P104N	CCt	AAt	1	1	B.1.91	0.002075
ORF3a	104	P104X	CCT	TAG	1	1	B.1.91	0.002075
ORF3a	104	P104Y	CCt	TAt	1	1	B.1.91	0.002075
ORF3a	104	P104K	CCT	AAG	1	1	B.1.91	0.002075
ORF3a	104	P104P	ccT	ccC	1	1	B.1.91	0.002075
ORF3a	104	P104L	cCt	cTt	1	1	B.3	0.000831
ORF3a	104	P104T	Cct	Act	1	1	B.40	0.000364
ORF3a	104	P104L	cCt	cTt	1	1	B.40	0.000364
ORF3a	104	P104H	cCt	cAt	1	1	B.55	0.00295
ORF3a	104	P104L	cCt	cTt	1	1	B.6	0.00091
ORF3a	104	P104L	cCt	cTt	1	1	C.14	0.004329
ORF3a	104	P104L	cCt	cTt	1	1	C.2	0.016129
ORF3a	104	P104del1	ccT	cc-	1	1	C.36.3	0.000567
ORF3a	104	P104S	Cct	Tct	1	1	C.36.3	0.000567
ORF3a	104	P104L	cCt	cTt	1	1	C.36.3.1	0.002717
ORF3a	104	P104S	Cct	Tct	1	1	C.39	0.018868
ORF3a	104	P104F	CCt	TTt	1	1	P.1	0.000016
ORF3a	104	P104L	cCt	cTt	1	1	P.1.1	0.000318
ORF3a	104	P104L	cCt	cTt	1	1	P.1.12	0.000484
ORF3a	104	P104P	ccT	ccG	1	1	P.1.12	0.000484
ORF3a	104	P104P	ccT	ccC	1	1	P.1.14	0.000048
ORF3a	104	P104R	cCt	cGt	1	1	P.1.14	0.000048
ORF3a	104	P104H	cCt	cAt	1	1	P.1.17	0.000162
ORF3a	104	P104S	Cct	Tct	1	1	P.1.17	0.000162
ORF3a	104	P104L	cCt	cTt	1	1	P.1.7	0.000319
ORF3a	104	P104P	ccT	ccC	1	1	P.2	0.000187
ORF3a	104	P104P	ccT	ccG	1	1	Q.1	0.000126
ORF3a	104	P104del	CCT	---	1	1	Q.4	0.000455
ORF3a	104	P104T	Cct	Act	1	1	Q.8	0.000165
ORF3a	104	P104S	Cct	Tct	1	1	R.1	0.00009
ORF3a	104	P104del1	ccT	cc-	1	1	R.1	0.00009
ORF3a	104	P104del	CCT	---	1	1	U.3	0.003861

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.