CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF7a : CodonNum = 45

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
ORF7a	45	P45L		nonsyn	cCa	cTa	85277	70702	0.829086	27526-27528
ORF7a	45	P45L		nonsyn	CCa	TTa	85277	14535	0.170445	27526-27528
ORF7a	45	P45L		nonsyn	cCA	cTT	85277	35	0.000410427	27526-27528
ORF7a	45	P45L		nonsyn	cCA	cTG	85277	3	0.0000351795	27526-27528
ORF7a	45	P45L		nonsyn	cCA	cTC	85277	2	0.000023453	27526-27528
ORF7a	45	P45S		nonsyn	Cca	Tca	3288	3263	0.992397	27526-27528
ORF7a	45	P45S		nonsyn	CcA	TcT	3288	22	0.006691	27526-27528
ORF7a	45	P45S		nonsyn	CcA	TcC	3288	2	0.000608273	27526-27528
ORF7a	45	P45S		nonsyn	CCA	AGT	3288	1	0.000304136	27526-27528
ORF7a	45	P45del		del	CCA	---	3002	3002	1	27526-27528
ORF7a	45	P45R		nonsyn	cCa	cGa	1016	1012	0.996063	27526-27528
ORF7a	45	P45R		nonsyn	cCA	cGT	1016	2	0.0019685	27526-27528
ORF7a	45	P45R		nonsyn	CCa	AGa	1016	1	0.000984252	27526-27528
ORF7a	45	P45R		nonsyn	cCA	cGG	1016	1	0.000984252	27526-27528
ORF7a	45	P45P		syn	ccA	ccT	581	242	0.416523	27526-27528
ORF7a	45	P45P		syn	ccA	ccC	581	181	0.311532	27526-27528
ORF7a	45	P45P		syn	ccA	ccG	581	158	0.271945	27526-27528
ORF7a	45	P45del2		del	CCa	--a	181	117	0.646409	27526-27528
ORF7a	45	P45del2		del	cCA	c--	181	63	0.348066	27526-27528
ORF7a	45	P45del2		del	CCA	T--	181	1	0.00552486	27526-27528
ORF7a	45	P45Q		nonsyn	cCa	cAa	127	127	1	27526-27528
ORF7a	45	P45T		nonsyn	Cca	Aca	82	72	0.878049	27526-27528
ORF7a	45	P45T		nonsyn	CcA	AcT	82	10	0.121951	27526-27528
ORF7a	45	P45del1		del	ccA	cc-	65	59	0.907692	27526-27528
ORF7a	45	P45del1		del	CcA	Ac-	65	2	0.0307692	27526-27528
ORF7a	45	P45del1		del	CCA	TT-	65	2	0.0307692	27526-27528
ORF7a	45	P45del1		del	Cca	-ca	65	1	0.0153846	27526-27528
ORF7a	45	P45del1		del	CcA	-cN	65	1	0.0153846	27526-27528
ORF7a	45	P45F		nonsyn	CCA	TTT	47	42	0.893617	27526-27528
ORF7a	45	P45F		nonsyn	CCA	TTC	47	5	0.106383	27526-27528
ORF7a	45	P45A		nonsyn	Cca	Gca	34	23	0.676471	27526-27528
ORF7a	45	P45A		nonsyn	CcA	GcT	34	10	0.294118	27526-27528
ORF7a	45	P45A		nonsyn	CcA	GcC	34	1	0.0294118	27526-27528
ORF7a	45	P45K		nonsyn	CCa	AAa	26	26	1	27526-27528
ORF7a	45	P45V		nonsyn	CCA	GTT	25	15	0.6	27526-27528
ORF7a	45	P45V		nonsyn	CCa	GTa	25	7	0.28	27526-27528
ORF7a	45	P45V		nonsyn	CCA	GTC	25	3	0.12	27526-27528
ORF7a	45	P45I		nonsyn	CCA	ATT	22	13	0.590909	27526-27528
ORF7a	45	P45I		nonsyn	CCa	ATa	22	8	0.363636	27526-27528
ORF7a	45	P45I		nonsyn	CCA	ATC	22	1	0.0454545	27526-27528
ORF7a	45	P45X		nonsyn	CCa	TAa	18	17	0.944444	27526-27528
ORF7a	45	P45D		nonsyn	CCA	GAT	18	16	0.888889	27526-27528
ORF7a	45	P45Y		nonsyn	CCA	TAT	18	15	0.833333	27526-27528
ORF7a	45	P45Y		nonsyn	CCA	TAC	18	3	0.166667	27526-27528
ORF7a	45	P45D		nonsyn	CCA	GAC	18	2	0.111111	27526-27528
ORF7a	45	P45X		nonsyn	CCa	TGa	18	1	0.0555556	27526-27528
ORF7a	45	P45H		nonsyn	cCA	cAT	11	9	0.818182	27526-27528
ORF7a	45	P45H		nonsyn	cCA	cAC	11	2	0.181818	27526-27528
ORF7a	45	P45N		nonsyn	CCA	AAT	9	7	0.777778	27526-27528
ORF7a	45	P45N		nonsyn	CCA	AAC	9	2	0.222222	27526-27528
ORF7a	45	P45E		nonsyn	CCa	GAa	6	5	0.833333	27526-27528
ORF7a	45	P45E		nonsyn	CCA	GAG	6	1	0.166667	27526-27528
ORF7a	45	P45C		nonsyn	CCA	TGT	3	3	1	27526-27528
ORF7a	45	P45G		nonsyn	CCa	GGa	2	1	0.5	27526-27528
ORF7a	45	P45G		nonsyn	CCA	GGT	2	1	0.5	27526-27528

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
ORF7a	45	P45L	cCa	cTa	70702	85277	All	0.013523
ORF7a	45	P45L	CCa	TTa	14535	85277	All	0.00278
ORF7a	45	P45L	cCA	cTT	35	85277	All	0.000007
ORF7a	45	P45L	cCA	cTG	3	85277	All	0.000001
ORF7a	45	P45L	cCA	cTC	2	85277	All	0
ORF7a	45	P45L	cCa	cTa	37538	45921	B.1.617.2	0.141346
ORF7a	45	P45L	CCa	TTa	8361	45921	B.1.617.2	0.031483
ORF7a	45	P45L	cCA	cTT	18	45921	B.1.617.2	0.000068
ORF7a	45	P45L	cCA	cTG	3	45921	B.1.617.2	0.000011
ORF7a	45	P45L	cCA	cTC	1	45921	B.1.617.2	0.000004
ORF7a	45	P45L	cCa	cTa	18153	22482	AY.43	0.080426
ORF7a	45	P45L	CCa	TTa	4328	22482	AY.43	0.019175
ORF7a	45	P45L	cCA	cTT	1	22482	AY.43	0.000004
ORF7a	45	P45S	Cca	Tca	3263	3288	All	0.000624
ORF7a	45	P45S	CcA	TcT	22	3288	All	0.000004
ORF7a	45	P45S	CcA	TcC	2	3288	All	0
ORF7a	45	P45S	CCA	AGT	1	3288	All	0
ORF7a	45	P45del	CCA	---	3002	3002	All	0.000574
ORF7a	45	P45L	cCa	cTa	1910	2287	AY.44	0.011626
ORF7a	45	P45L	CCa	TTa	377	2287	AY.44	0.002295
ORF7a	45	P45L	cCa	cTa	2083	2088	B.1.1.7	0.001865
ORF7a	45	P45L	CCa	TTa	5	2088	B.1.1.7	0.000004
ORF7a	45	P45S	Cca	Tca	2050	2050	AY.4	0.003191
ORF7a	45	P45L	cCa	cTa	1750	1779	AY.4	0.002724
ORF7a	45	P45L	CCa	TTa	29	1779	AY.4	0.000045
ORF7a	45	P45L	cCa	cTa	1261	1275	AY.12	0.398546
ORF7a	45	P45L	CCa	TTa	14	1275	AY.12	0.004425
ORF7a	45	P45L	cCa	cTa	525	1041	AY.102	0.01392
ORF7a	45	P45L	CCa	TTa	516	1041	AY.102	0.013681
ORF7a	45	P45R	cCa	cGa	1012	1016	All	0.000194
ORF7a	45	P45R	cCA	cGT	2	1016	All	0
ORF7a	45	P45R	CCa	AGa	1	1016	All	0
ORF7a	45	P45R	cCA	cGG	1	1016	All	0
ORF7a	45	P45R	cCa	cGa	901	901	B.1.160	0.0281
ORF7a	45	P45L	cCa	cTa	595	695	AY.46	0.061928
ORF7a	45	P45L	CCa	TTa	100	695	AY.46	0.010408
ORF7a	45	P45L	cCa	cTa	590	590	AY.4.2	0.012796
ORF7a	45	P45P	ccA	ccT	242	581	All	0.000046
ORF7a	45	P45P	ccA	ccC	181	581	All	0.000035
ORF7a	45	P45P	ccA	ccG	158	581	All	0.00003
ORF7a	45	P45del	CCA	---	498	498	AY.25	0.002995
ORF7a	45	P45L	cCa	cTa	473	495	AY.119	0.016701
ORF7a	45	P45L	CCa	TTa	22	495	AY.119	0.000777
ORF7a	45	P45L	cCa	cTa	470	487	AY.111	0.086081
ORF7a	45	P45L	CCa	TTa	17	487	AY.111	0.003114
ORF7a	45	P45L	cCa	cTa	378	444	AY.39	0.009341
ORF7a	45	P45L	CCa	TTa	66	444	AY.39	0.001631
ORF7a	45	P45del	CCA	---	438	438	B.1.1.7	0.000392
ORF7a	45	P45L	cCa	cTa	381	401	AY.103	0.002366
ORF7a	45	P45L	CCa	TTa	20	401	AY.103	0.000124
ORF7a	45	P45del	CCA	---	290	290	B.1.617.2	0.001092
ORF7a	45	P45S	Cca	Tca	279	279	B.1.1.7	0.00025
ORF7a	45	P45del	CCA	---	265	265	AY.4	0.000412
ORF7a	45	P45L	cCa	cTa	218	250	AY.25	0.001311
ORF7a	45	P45L	CCa	TTa	17	250	AY.25	0.000102
ORF7a	45	P45L	cCA	cTT	14	250	AY.25	0.000084
ORF7a	45	P45L	cCA	cTC	1	250	AY.25	0.000006
ORF7a	45	P45L	cCa	cTa	213	237	AY.116	0.061084
ORF7a	45	P45L	CCa	TTa	24	237	AY.116	0.006883
ORF7a	45	P45L	cCa	cTa	196	222	AY.34.1	0.099949
ORF7a	45	P45L	CCa	TTa	26	222	AY.34.1	0.013259
ORF7a	45	P45L	cCa	cTa	165	186	AY.117	0.013945
ORF7a	45	P45L	CCa	TTa	21	186	AY.117	0.001775
ORF7a	45	P45del	CCA	---	182	182	B.1.177.21	0.013918
ORF7a	45	P45del2	CCa	--a	117	181	All	0.000022
ORF7a	45	P45del2	cCA	c--	63	181	All	0.000012
ORF7a	45	P45del2	CCA	T--	1	181	All	0
ORF7a	45	P45L	cCa	cTa	178	178	B.1.621	0.015756
ORF7a	45	P45L	cCa	cTa	142	159	AY.5.4	0.039292
ORF7a	45	P45L	CCa	TTa	17	159	AY.5.4	0.004704
ORF7a	45	P45L	cCa	cTa	72	142	AY.5.3	0.024291
ORF7a	45	P45L	CCa	TTa	70	142	AY.5.3	0.023617
ORF7a	45	P45S	Cca	Tca	127	134	B.1.617.2	0.000478
ORF7a	45	P45S	CcA	TcT	7	134	B.1.617.2	0.000026
ORF7a	45	P45L	cCa	cTa	133	133	AY.26	0.003765
ORF7a	45	P45L	cCa	cTa	118	133	AY.45	0.014359
ORF7a	45	P45L	CCa	TTa	15	133	AY.45	0.001825
ORF7a	45	P45L	cCa	cTa	108	132	AY.84	0.047244
ORF7a	45	P45L	CCa	TTa	24	132	AY.84	0.010499
ORF7a	45	P45Q	cCa	cAa	127	127	All	0.000024
ORF7a	45	P45S	Cca	Tca	123	123	AY.43	0.000545
ORF7a	45	P45L	cCa	cTa	118	118	AY.46.4	0.019411
ORF7a	45	P45L	CCa	TTa	92	108	AY.59	0.048729
ORF7a	45	P45L	cCa	cTa	16	108	AY.59	0.008475
ORF7a	45	P45L	cCa	cTa	103	103	AY.41	0.030276
ORF7a	45	P45L	cCa	cTa	90	103	AY.5	0.001858
ORF7a	45	P45L	CCa	TTa	13	103	AY.5	0.000268
ORF7a	45	P45del	CCA	---	102	102	AY.3	0.001015
ORF7a	45	P45del	CCA	---	98	98	AY.103	0.000608
ORF7a	45	P45L	cCa	cTa	69	98	AY.63	0.026692
ORF7a	45	P45L	CCa	TTa	29	98	AY.63	0.011219
ORF7a	45	P45L	cCa	cTa	89	90	AY.46.2	0.056544
ORF7a	45	P45L	CCa	TTa	1	90	AY.46.2	0.000635
ORF7a	45	P45L	cCa	cTa	90	90	P.1	0.001418
ORF7a	45	P45L	cCa	cTa	88	88	B.1.2	0.000775
ORF7a	45	P45L	cCa	cTa	85	87	B.1	0.000779
ORF7a	45	P45L	CCa	TTa	2	87	B.1	0.000018
ORF7a	45	P45S	Cca	Tca	86	86	AY.3	0.000855
ORF7a	45	P45L	cCa	cTa	66	83	AY.23	0.004603
ORF7a	45	P45L	CCa	TTa	17	83	AY.23	0.001186
ORF7a	45	P45T	Cca	Aca	72	82	All	0.000014
ORF7a	45	P45T	CcA	AcT	10	82	All	0.000002
ORF7a	45	P45del	CCA	---	80	80	AY.43	0.000354
ORF7a	45	P45S	Cca	Tca	79	79	AY.103	0.000491
ORF7a	45	P45L	cCa	cTa	72	74	AY.3	0.000716
ORF7a	45	P45L	CCa	TTa	1	74	AY.3	0.00001
ORF7a	45	P45L	cCA	cTT	1	74	AY.3	0.00001
ORF7a	45	P45L	cCa	cTa	49	72	AY.32	0.026092
ORF7a	45	P45L	CCa	TTa	23	72	AY.32	0.012247
ORF7a	45	P45L	cCa	cTa	72	72	B.1.177	0.000948
ORF7a	45	P45L	cCa	cTa	69	70	AY.33	0.004608
ORF7a	45	P45L	CCa	TTa	1	70	AY.33	0.000067
ORF7a	45	P45del	CCA	---	68	68	AY.39	0.00168
ORF7a	45	P45del	CCA	---	66	66	AY.44	0.000402
ORF7a	45	P45del1	ccA	cc-	59	65	All	0.000011
ORF7a	45	P45del1	CCA	TT-	2	65	All	0
ORF7a	45	P45del1	CcA	Ac-	2	65	All	0
ORF7a	45	P45del1	CcA	-cN	1	65	All	0
ORF7a	45	P45del1	Cca	-ca	1	65	All	0
ORF7a	45	P45del	CCA	---	63	63	AY.100	0.002898
ORF7a	45	P45del2	CCa	--a	62	62	AY.4	0.000096
ORF7a	45	P45L	cCa	cTa	54	62	AY.46.6	0.003899
ORF7a	45	P45L	CCa	TTa	8	62	AY.46.6	0.000578
ORF7a	45	P45L	CCa	TTa	36	61	AY.118	0.002255
ORF7a	45	P45L	cCa	cTa	25	61	AY.118	0.001566
ORF7a	45	P45L	cCa	cTa	57	61	AY.58	0.051724
ORF7a	45	P45L	CCa	TTa	4	61	AY.58	0.00363
ORF7a	45	P45S	Cca	Tca	43	60	AY.25	0.000259
ORF7a	45	P45S	CcA	TcT	15	60	AY.25	0.00009
ORF7a	45	P45S	CcA	TcC	1	60	AY.25	0.000006
ORF7a	45	P45S	CCA	AGT	1	60	AY.25	0.000006
ORF7a	45	P45L	CCa	TTa	49	59	AY.10	0.025967
ORF7a	45	P45L	cCa	cTa	10	59	AY.10	0.005299
ORF7a	45	P45L	cCa	cTa	59	59	B.1.1	0.00107
ORF7a	45	P45del	CCA	---	58	58	AY.39.1	0.002298
ORF7a	45	P45del	CCA	---	57	57	AY.29	0.000899
ORF7a	45	P45L	cCa	cTa	55	57	AY.98	0.004345
ORF7a	45	P45L	CCa	TTa	2	57	AY.98	0.000158
ORF7a	45	P45L	cCa	cTa	48	55	AY.105	0.030868
ORF7a	45	P45L	CCa	TTa	7	55	AY.105	0.004502
ORF7a	45	P45L	cCa	cTa	43	53	AY.89	0.210784
ORF7a	45	P45L	CCa	TTa	10	53	AY.89	0.04902
ORF7a	45	P45L	cCa	cTa	35	52	AY.42	0.001408
ORF7a	45	P45L	CCa	TTa	17	52	AY.42	0.000684
ORF7a	45	P45L	cCa	cTa	52	52	B.1.1.28	0.016184
ORF7a	45	P45P	ccA	ccC	26	52	B.1.2	0.000229
ORF7a	45	P45P	ccA	ccG	21	52	B.1.2	0.000185
ORF7a	45	P45P	ccA	ccT	5	52	B.1.2	0.000044
ORF7a	45	P45L	cCa	cTa	49	51	AY.88	0.043324
ORF7a	45	P45L	CCa	TTa	2	51	AY.88	0.001768
ORF7a	45	P45P	ccA	ccG	22	49	B.1.1.7	0.00002
ORF7a	45	P45P	ccA	ccT	15	49	B.1.1.7	0.000013
ORF7a	45	P45P	ccA	ccC	12	49	B.1.1.7	0.000011
ORF7a	45	P45F	CCA	TTT	42	47	All	0.000008
ORF7a	45	P45F	CCA	TTC	5	47	All	0.000001
ORF7a	45	P45L	cCa	cTa	39	47	AY.92	0.011204
ORF7a	45	P45L	CCa	TTa	8	47	AY.92	0.002298
ORF7a	45	P45L	cCa	cTa	40	46	AY.99	0.041973
ORF7a	45	P45L	CCa	TTa	6	46	AY.99	0.006296
ORF7a	45	P45L	cCa	cTa	32	45	AY.47	0.000995
ORF7a	45	P45L	CCa	TTa	13	45	AY.47	0.000404
ORF7a	45	P45L	cCa	cTa	44	44	AY.78	0.067797
ORF7a	45	P45L	cCa	cTa	41	43	AY.20	0.001593
ORF7a	45	P45L	CCa	TTa	2	43	AY.20	0.000078
ORF7a	45	P45L	cCa	cTa	35	42	AY.106	0.011721
ORF7a	45	P45L	CCa	TTa	7	42	AY.106	0.002344
ORF7a	45	P45L	cCa	cTa	35	42	AY.95	0.026636
ORF7a	45	P45L	CCa	TTa	7	42	AY.95	0.005327
ORF7a	45	P45del	CCA	---	41	41	AY.3.1	0.003496
ORF7a	45	P45P	ccA	ccT	33	41	B.1.429	0.000776
ORF7a	45	P45P	ccA	ccC	7	41	B.1.429	0.000165
ORF7a	45	P45P	ccA	ccG	1	41	B.1.429	0.000024
ORF7a	45	P45S	Cca	Tca	39	39	AY.44	0.000237
ORF7a	45	P45T	Cca	Aca	38	38	B.1.1.7	0.000034
ORF7a	45	P45del	CCA	---	37	37	B.1.1.284	0.003974
ORF7a	45	P45del	CCA	---	37	37	B.1.621	0.003275
ORF7a	45	P45L	cCa	cTa	36	36	AY.29	0.000568
ORF7a	45	P45R	cCa	cGa	35	36	B.1.617.2	0.000132
ORF7a	45	P45R	cCA	cGT	1	36	B.1.617.2	0.000004
ORF7a	45	P45A	Cca	Gca	23	34	All	0.000004
ORF7a	45	P45A	CcA	GcT	10	34	All	0.000002
ORF7a	45	P45A	CcA	GcC	1	34	All	0
ORF7a	45	P45del	CCA	---	34	34	B.1	0.000311
ORF7a	45	P45Q	cCa	cAa	34	34	B.1.1.7	0.00003
ORF7a	45	P45L	cCa	cTa	29	33	AY.19	0.033067
ORF7a	45	P45L	CCa	TTa	4	33	AY.19	0.004561
ORF7a	45	P45L	cCa	cTa	31	31	AY.108	0.034179
ORF7a	45	P45L	cCa	cTa	25	31	AY.113	0.00356
ORF7a	45	P45L	CCa	TTa	6	31	AY.113	0.000854
ORF7a	45	P45L	cCa	cTa	30	31	AY.120	0.001115
ORF7a	45	P45L	CCa	TTa	1	31	AY.120	0.000037
ORF7a	45	P45R	cCa	cGa	31	31	AY.61	0.003248
ORF7a	45	P45del	CCA	---	30	30	AY.102	0.000795
ORF7a	45	P45L	cCa	cTa	28	29	B.1.351	0.000832
ORF7a	45	P45L	CCa	TTa	1	29	B.1.351	0.00003
ORF7a	45	P45L	cCa	cTa	23	28	AY.100	0.001058
ORF7a	45	P45L	CCa	TTa	5	28	AY.100	0.00023
ORF7a	45	P45L	cCa	cTa	27	28	AY.46.1	0.027721
ORF7a	45	P45L	CCa	TTa	1	28	AY.46.1	0.001027
ORF7a	45	P45L	cCa	cTa	28	28	AY.56	0.044944
ORF7a	45	P45S	Cca	Tca	27	27	AY.39.1	0.00107
ORF7a	45	P45P	ccA	ccT	27	27	B.1.110.3	0.019397
ORF7a	45	P45L	cCa	cTa	27	27	B.1.429	0.000635
ORF7a	45	P45K	CCa	AAa	26	26	All	0.000005
ORF7a	45	P45del	CCA	---	26	26	AY.119	0.000918
ORF7a	45	P45P	ccA	ccG	15	26	AY.3	0.000149
ORF7a	45	P45P	ccA	ccT	10	26	AY.3	0.000099
ORF7a	45	P45P	ccA	ccC	1	26	AY.3	0.00001
ORF7a	45	P45V	CCA	GTT	15	25	All	0.000003
ORF7a	45	P45V	CCa	GTa	7	25	All	0.000001
ORF7a	45	P45V	CCA	GTC	3	25	All	0.000001
ORF7a	45	P45L	cCa	cTa	25	25	B.1.160	0.00078
ORF7a	45	P45F	CCA	TTT	20	24	AY.25	0.00012
ORF7a	45	P45F	CCA	TTC	4	24	AY.25	0.000024
ORF7a	45	P45L	cCa	cTa	24	24	AY.54	0.002288
ORF7a	45	P45L	cCa	cTa	22	24	AY.91	0.01607
ORF7a	45	P45L	CCa	TTa	2	24	AY.91	0.001461
ORF7a	45	P45Q	cCa	cAa	24	24	B.1.637	0.001754
ORF7a	45	P45S	Cca	Tca	23	23	AY.39	0.000568
ORF7a	45	P45L	cCa	cTa	23	23	AY.53	0.006613
ORF7a	45	P45L	cCa	cTa	23	23	AY.9	0.001555
ORF7a	45	P45del	CCA	---	23	23	B.1.1.214	0.001276
ORF7a	45	P45del1	ccA	cc-	23	23	B.1.2	0.000203
ORF7a	45	P45I	CCA	ATT	13	22	All	0.000002
ORF7a	45	P45I	CCa	ATa	8	22	All	0.000002
ORF7a	45	P45I	CCA	ATC	1	22	All	0
ORF7a	45	P45L	CCa	TTa	12	22	AY.14	0.001056
ORF7a	45	P45L	cCa	cTa	10	22	AY.14	0.00088
ORF7a	45	P45del2	CCa	--a	22	22	AY.25	0.000132
ORF7a	45	P45P	ccA	ccT	20	22	AY.46.6	0.001444
ORF7a	45	P45P	ccA	ccC	2	22	AY.46.6	0.000144
ORF7a	45	P45L	cCa	cTa	17	21	AY.121	0.0023
ORF7a	45	P45L	CCa	TTa	4	21	AY.121	0.000541
ORF7a	45	P45V	CCA	GTT	12	21	AY.25	0.000072
ORF7a	45	P45V	CCa	GTa	6	21	AY.25	0.000036
ORF7a	45	P45V	CCA	GTC	3	21	AY.25	0.000018
ORF7a	45	P45L	cCa	cTa	20	21	AY.67	0.009285
ORF7a	45	P45L	CCa	TTa	1	21	AY.67	0.000464
ORF7a	45	P45L	cCa	cTa	20	21	AY.98.1	0.000969
ORF7a	45	P45L	CCa	TTa	1	21	AY.98.1	0.000048
ORF7a	45	P45S	Cca	Tca	21	21	B.1.2	0.000185
ORF7a	45	P45L	cCa	cTa	16	20	AY.4.3	0.013468
ORF7a	45	P45L	CCa	TTa	4	20	AY.4.3	0.003367
ORF7a	45	P45S	Cca	Tca	20	20	AY.5	0.000413
ORF7a	45	P45S	Cca	Tca	20	20	B.1.429	0.000471
ORF7a	45	P45L	cCa	cTa	16	19	AY.110	0.001803
ORF7a	45	P45L	CCa	TTa	3	19	AY.110	0.000338
ORF7a	45	P45P	ccA	ccT	13	19	AY.25	0.000078
ORF7a	45	P45P	ccA	ccG	3	19	AY.25	0.000018
ORF7a	45	P45P	ccA	ccC	3	19	AY.25	0.000018
ORF7a	45	P45del	CCA	---	19	19	AY.42	0.000764
ORF7a	45	P45P	ccA	ccT	11	19	AY.43	0.000049
ORF7a	45	P45P	ccA	ccC	6	19	AY.43	0.000027
ORF7a	45	P45P	ccA	ccG	2	19	AY.43	0.000009
ORF7a	45	P45del	CCA	---	19	19	AY.46.4	0.003126
ORF7a	45	P45del	CCA	---	19	19	AY.7.2	0.010626
ORF7a	45	P45L	cCa	cTa	15	19	AY.77	0.016911
ORF7a	45	P45L	CCa	TTa	4	19	AY.77	0.00451
ORF7a	45	P45K	CCa	AAa	19	19	B.1.1.7	0.000017
ORF7a	45	P45X	CCa	TAa	17	18	All	0.000003
ORF7a	45	P45D	CCA	GAT	16	18	All	0.000003
ORF7a	45	P45Y	CCA	TAT	15	18	All	0.000003
ORF7a	45	P45Y	CCA	TAC	3	18	All	0.000001
ORF7a	45	P45D	CCA	GAC	2	18	All	0
ORF7a	45	P45X	CCa	TGa	1	18	All	0
ORF7a	45	P45Q	cCa	cAa	18	18	AY.25	0.000108
ORF7a	45	P45del	CCA	---	18	18	AY.98.1	0.000872
ORF7a	45	P45L	cCa	cTa	17	18	AY.99.2	0.001567
ORF7a	45	P45L	CCa	TTa	1	18	AY.99.2	0.000092
ORF7a	45	P45del	CCA	---	18	18	B.1.177	0.000237
ORF7a	45	P45L	cCa	cTa	18	18	C.37	0.002089
ORF7a	45	P45L	cCa	cTa	14	17	AY.114	0.003235
ORF7a	45	P45L	CCa	TTa	3	17	AY.114	0.000693
ORF7a	45	P45L	cCa	cTa	17	17	AY.51	0.015455
ORF7a	45	P45L	cCa	cTa	15	17	AY.74	0.001735
ORF7a	45	P45L	CCa	TTa	2	17	AY.74	0.000231
ORF7a	45	P45S	Cca	Tca	17	17	B.1.177	0.000224
ORF7a	45	P45P	ccA	ccC	7	17	B.1.617.2	0.000026
ORF7a	45	P45P	ccA	ccT	7	17	B.1.617.2	0.000026
ORF7a	45	P45P	ccA	ccG	3	17	B.1.617.2	0.000011
ORF7a	45	P45del2	CCa	--a	13	16	AY.103	0.000081
ORF7a	45	P45del2	cCA	c--	3	16	AY.103	0.000019
ORF7a	45	P45L	cCa	cTa	16	16	AY.109	0.011834
ORF7a	45	P45S	Cca	Tca	16	16	AY.26	0.000453
ORF7a	45	P45S	Cca	Tca	16	16	AY.33	0.001068
ORF7a	45	P45P	ccA	ccC	9	16	B.1	0.000082
ORF7a	45	P45P	ccA	ccT	6	16	B.1	0.000055
ORF7a	45	P45P	ccA	ccG	1	16	B.1	0.000009
ORF7a	45	P45L	cCa	cTa	16	16	B.1.177.57	0.004496
ORF7a	45	P45L	cCa	cTa	16	16	B.1.526	0.000376
ORF7a	45	P45Q	cCa	cAa	15	15	B.1.617.2	0.000056
ORF7a	45	P45L	cCa	cTa	13	14	AY.4.5	0.001397
ORF7a	45	P45L	CCa	TTa	1	14	AY.4.5	0.000107
ORF7a	45	P45P	ccA	ccT	10	14	AY.42	0.000402
ORF7a	45	P45P	ccA	ccG	4	14	AY.42	0.000161
ORF7a	45	P45del	CCA	---	14	14	AY.47	0.000435
ORF7a	45	P45L	cCa	cTa	14	14	B.1.1.337	0.05036
ORF7a	45	P45L	cCa	cTa	14	14	B.1.177.77	0.010167
ORF7a	45	P45F	CCA	TTT	13	14	B.1.617.2	0.000049
ORF7a	45	P45F	CCA	TTC	1	14	B.1.617.2	0.000004
ORF7a	45	P45del	CCA	---	14	14	B.1.637	0.001023
ORF7a	45	P45del	CCA	---	14	14	P.1	0.000221
ORF7a	45	P45S	Cca	Tca	13	13	AY.102	0.000345
ORF7a	45	P45S	Cca	Tca	13	13	AY.29	0.000205
ORF7a	45	P45L	cCa	cTa	10	13	AY.48	0.004651
ORF7a	45	P45L	CCa	TTa	3	13	AY.48	0.001395
ORF7a	45	P45L	cCa	cTa	12	13	AY.64	0.007143
ORF7a	45	P45L	CCa	TTa	1	13	AY.64	0.000595
ORF7a	45	P45L	cCa	cTa	12	13	AY.9.2	0.000441
ORF7a	45	P45L	CCa	TTa	1	13	AY.9.2	0.000037
ORF7a	45	P45S	Cca	Tca	13	13	AY.98.1	0.00063
ORF7a	45	P45S	Cca	Tca	12	13	B.1	0.00011
ORF7a	45	P45S	CcA	TcC	1	13	B.1	0.000009
ORF7a	45	P45del	CCA	---	13	13	C.37	0.001509
ORF7a	45	P45Y	CCA	TAT	9	12	AY.25	0.000054
ORF7a	45	P45A	CcA	GcT	7	12	AY.25	0.000042
ORF7a	45	P45A	Cca	Gca	4	12	AY.25	0.000024
ORF7a	45	P45Y	CCA	TAC	3	12	AY.25	0.000018
ORF7a	45	P45A	CcA	GcC	1	12	AY.25	0.000006
ORF7a	45	P45L	cCa	cTa	12	12	AY.34	0.001164
ORF7a	45	P45L	cCa	cTa	7	12	AY.35	0.001631
ORF7a	45	P45L	CCa	TTa	5	12	AY.35	0.001165
ORF7a	45	P45L	CCa	TTa	7	12	AY.52	0.0057
ORF7a	45	P45L	cCa	cTa	5	12	AY.52	0.004072
ORF7a	45	P45del2	cCA	c--	11	12	B.1.1.7	0.00001
ORF7a	45	P45del2	CCa	--a	1	12	B.1.1.7	0.000001
ORF7a	45	P45del	CCA	---	12	12	B.1.2	0.000106
ORF7a	45	P45L	cCa	cTa	12	12	B.1.311	0.003295
ORF7a	45	P45del	CCA	---	12	12	B.1.324	0.019262
ORF7a	45	P45P	ccA	ccT	12	12	B.1.346	0.015727
ORF7a	45	P45del	CCA	---	12	12	B.1.526	0.000282
ORF7a	45	P45L	cCa	cTa	12	12	Q.8	0.001979
ORF7a	45	P45H	cCA	cAT	9	11	All	0.000002
ORF7a	45	P45H	cCA	cAC	2	11	All	0
ORF7a	45	P45R	cCa	cGa	11	11	AY.102	0.000292
ORF7a	45	P45del	CCA	---	11	11	AY.26	0.000311
ORF7a	45	P45P	ccA	ccT	6	11	AY.4	0.000009
ORF7a	45	P45P	ccA	ccC	3	11	AY.4	0.000005
ORF7a	45	P45P	ccA	ccG	2	11	AY.4	0.000003
ORF7a	45	P45P	ccA	ccC	5	11	AY.44	0.00003
ORF7a	45	P45P	ccA	ccG	4	11	AY.44	0.000024
ORF7a	45	P45P	ccA	ccT	2	11	AY.44	0.000012
ORF7a	45	P45L	cCa	cTa	10	11	AY.82	0.013569
ORF7a	45	P45L	CCa	TTa	1	11	AY.82	0.001357
ORF7a	45	P45L	cCa	cTa	11	11	B.1.177.81	0.002083
ORF7a	45	P45del2	CCa	--a	11	11	B.1.221	0.000781
ORF7a	45	P45P	ccA	ccT	11	11	C.36.3	0.006239
ORF7a	45	P45P	ccA	ccG	11	11	D.2	0.000825
ORF7a	45	P45P	ccA	ccT	5	10	AY.103	0.000031
ORF7a	45	P45P	ccA	ccC	3	10	AY.103	0.000019
ORF7a	45	P45P	ccA	ccG	2	10	AY.103	0.000012
ORF7a	45	P45S	Cca	Tca	10	10	AY.116	0.002868
ORF7a	45	P45del	CCA	---	10	10	AY.20	0.000389
ORF7a	45	P45del	CCA	---	10	10	AY.23	0.000697
ORF7a	45	P45L	cCa	cTa	10	10	AY.27	0.000647
ORF7a	45	P45L	cCa	cTa	7	10	AY.39.1	0.000277
ORF7a	45	P45L	CCa	TTa	3	10	AY.39.1	0.000119
ORF7a	45	P45del	CCA	---	10	10	AY.5	0.000206
ORF7a	45	P45L	cCa	cTa	10	10	AY.70	0.002085
ORF7a	45	P45L	CCa	TTa	6	10	AY.75	0.000336
ORF7a	45	P45L	cCa	cTa	4	10	AY.75	0.000224
ORF7a	45	P45S	Cca	Tca	10	10	AY.9	0.000676
ORF7a	45	P45L	cCa	cTa	10	10	B.1.1.519	0.000397
ORF7a	45	P45A	Cca	Gca	10	10	B.1.1.7	0.000009
ORF7a	45	P45T	Cca	Aca	10	10	B.1.628	0.003524
ORF7a	45	P45N	CCA	AAT	7	9	All	0.000001
ORF7a	45	P45N	CCA	AAC	2	9	All	0
ORF7a	45	P45L	cCa	cTa	7	9	AY.11	0.009371
ORF7a	45	P45L	CCa	TTa	2	9	AY.11	0.002677
ORF7a	45	P45H	cCA	cAT	8	9	AY.25	0.000048
ORF7a	45	P45H	cCA	cAC	1	9	AY.25	0.000006
ORF7a	45	P45del	CCA	---	9	9	AY.34	0.000873
ORF7a	45	P45L	cCa	cTa	8	9	AY.87	0.006661
ORF7a	45	P45L	CCa	TTa	1	9	AY.87	0.000833
ORF7a	45	P45L	cCa	cTa	8	9	AY.9.1	0.00067
ORF7a	45	P45L	CCa	TTa	1	9	AY.9.1	0.000084
ORF7a	45	P45I	CCa	ATa	5	9	B.1.1.7	0.000004
ORF7a	45	P45I	CCA	ATT	4	9	B.1.1.7	0.000004
ORF7a	45	P45del	CCA	---	9	9	L.1	0.017143
ORF7a	45	P45L	cCa	cTa	9	9	P.1.15	0.002091
ORF7a	45	P45del	CCA	---	9	9	R.1	0.00081
ORF7a	45	P45D	CCA	GAT	6	8	AY.25	0.000036
ORF7a	45	P45D	CCA	GAC	2	8	AY.25	0.000012
ORF7a	45	P45L	cCa	cTa	8	8	AY.6	0.000329
ORF7a	45	P45L	cCa	cTa	7	8	AY.68	0.001916
ORF7a	45	P45L	CCa	TTa	1	8	AY.68	0.000274
ORF7a	45	P45L	cCa	cTa	7	8	AY.69	0.001307
ORF7a	45	P45L	CCa	TTa	1	8	AY.69	0.000187
ORF7a	45	P45S	Cca	Tca	8	8	AY.75	0.000448
ORF7a	45	P45del	CCA	---	8	8	AY.75	0.000448
ORF7a	45	P45del1	ccA	cc-	8	8	B.1	0.000073
ORF7a	45	P45del1	ccA	cc-	8	8	B.1.1.7	0.000007
ORF7a	45	P45D	CCA	GAT	8	8	B.1.177.21	0.000612
ORF7a	45	P45del2	cCA	c--	8	8	B.1.2	0.00007
ORF7a	45	P45S	Cca	Tca	8	8	B.1.427	0.000404
ORF7a	45	P45L	cCa	cTa	7	7	AY.1	0.00277
ORF7a	45	P45del	CCA	---	7	7	AY.120	0.00026
ORF7a	45	P45X	CCa	TAa	6	7	AY.25	0.000036
ORF7a	45	P45X	CCa	TGa	1	7	AY.25	0.000006
ORF7a	45	P45T	Cca	Aca	4	7	AY.4	0.000006
ORF7a	45	P45T	CcA	AcT	3	7	AY.4	0.000005
ORF7a	45	P45S	Cca	Tca	7	7	AY.45	0.000852
ORF7a	45	P45L	cCa	cTa	7	7	AY.7	0.001372
ORF7a	45	P45L	cCa	cTa	6	7	AY.7.1	0.000676
ORF7a	45	P45L	CCa	TTa	1	7	AY.7.1	0.000113
ORF7a	45	P45L	cCa	cTa	7	7	AY.99.1	0.01087
ORF7a	45	P45del	CCA	---	7	7	B.1.1	0.000127
ORF7a	45	P45R	cCa	cGa	7	7	B.1.1.7	0.000006
ORF7a	45	P45del	CCA	---	7	7	B.1.160	0.000218
ORF7a	45	P45del	CCA	---	7	7	B.1.429	0.000165
ORF7a	45	P45del	CCA	---	7	7	B.1.525	0.000792
ORF7a	45	P45P	ccA	ccG	4	7	B.1.617.1	0.000516
ORF7a	45	P45P	ccA	ccT	2	7	B.1.617.1	0.000258
ORF7a	45	P45P	ccA	ccC	1	7	B.1.617.1	0.000129
ORF7a	45	P45P	ccA	ccT	4	7	P.1	0.000063
ORF7a	45	P45P	ccA	ccG	2	7	P.1	0.000032
ORF7a	45	P45P	ccA	ccC	1	7	P.1	0.000016
ORF7a	45	P45del	CCA	---	7	7	P.1.15	0.001626
ORF7a	45	P45L	cCa	cTa	7	7	R.1	0.00063
ORF7a	45	P45E	CCa	GAa	5	6	All	0.000001
ORF7a	45	P45E	CCA	GAG	1	6	All	0
ORF7a	45	P45P	ccA	ccG	4	6	AY.102	0.000106
ORF7a	45	P45P	ccA	ccT	2	6	AY.102	0.000053
ORF7a	45	P45S	Cca	Tca	6	6	AY.111	0.001099
ORF7a	45	P45del	CCA	---	6	6	AY.120.1	0.001926
ORF7a	45	P45I	CCA	ATT	4	6	AY.25	0.000024
ORF7a	45	P45I	CCa	ATa	1	6	AY.25	0.000006
ORF7a	45	P45I	CCA	ATC	1	6	AY.25	0.000006
ORF7a	45	P45P	ccA	ccG	4	6	AY.33	0.000267
ORF7a	45	P45P	ccA	ccC	2	6	AY.33	0.000134
ORF7a	45	P45L	CCa	TTa	4	6	AY.37	0.001264
ORF7a	45	P45L	cCa	cTa	2	6	AY.37	0.000632
ORF7a	45	P45L	cCa	cTa	6	6	AY.40	0.005786
ORF7a	45	P45del2	cCA	c--	6	6	AY.47	0.000187
ORF7a	45	P45del	CCA	---	6	6	AY.54	0.000572
ORF7a	45	P45L	cCa	cTa	5	6	AY.61	0.000524
ORF7a	45	P45L	CCa	TTa	1	6	AY.61	0.000105
ORF7a	45	P45L	cCa	cTa	5	6	AY.85	0.002136
ORF7a	45	P45L	CCa	TTa	1	6	AY.85	0.000427
ORF7a	45	P45L	cCa	cTa	6	6	AZ.3	0.009119
ORF7a	45	P45P	ccA	ccG	3	6	B.1.1	0.000054
ORF7a	45	P45P	ccA	ccC	2	6	B.1.1	0.000036
ORF7a	45	P45P	ccA	ccT	1	6	B.1.1	0.000018
ORF7a	45	P45S	Cca	Tca	6	6	B.1.1.519	0.000238
ORF7a	45	P45del	CCA	---	6	6	B.1.351	0.000178
ORF7a	45	P45S	Cca	Tca	6	6	B.1.399	0.011605
ORF7a	45	P45del1	ccA	cc-	6	6	B.1.596	0.000523
ORF7a	45	P45P	ccA	ccC	4	6	B.1.596	0.000349
ORF7a	45	P45P	ccA	ccT	2	6	B.1.596	0.000174
ORF7a	45	P45L	cCa	cTa	6	6	C.36.3	0.003403
ORF7a	45	P45S	Cca	Tca	6	6	C.37.1	0.015707
ORF7a	45	P45S	Cca	Tca	6	6	P.1	0.000095
ORF7a	45	P45S	Cca	Tca	5	5	AY.109	0.003698
ORF7a	45	P45S	Cca	Tca	5	5	AY.120	0.000186
ORF7a	45	P45L	cCa	cTa	5	5	AY.16	0.001898
ORF7a	45	P45L	cCa	cTa	5	5	AY.21	0.009488
ORF7a	45	P45L	cCa	cTa	5	5	AY.3.1	0.000426
ORF7a	45	P45P	ccA	ccG	4	5	AY.39	0.000099
ORF7a	45	P45P	ccA	ccC	1	5	AY.39	0.000025
ORF7a	45	P45del	CCA	---	5	5	AY.4.2	0.000108
ORF7a	45	P45L	cCa	cTa	5	5	AY.4.2.1	0.000745
ORF7a	45	P45L	cCa	cTa	5	5	AY.4.4	0.002046
ORF7a	45	P45L	cCa	cTa	4	5	AY.60	0.003752
ORF7a	45	P45L	CCa	TTa	1	5	AY.60	0.000938
ORF7a	45	P45del	CCA	---	5	5	AY.92	0.001436
ORF7a	45	P45L	cCa	cTa	4	5	AY.93	0.001092
ORF7a	45	P45L	CCa	TTa	1	5	AY.93	0.000273
ORF7a	45	P45del2	cCA	c--	5	5	B.1	0.000046
ORF7a	45	P45Q	cCa	cAa	5	5	B.1	0.000046
ORF7a	45	P45S	Cca	Tca	5	5	B.1.1	0.000091
ORF7a	45	P45del	CCA	---	5	5	B.1.1.56	0.089286
ORF7a	45	P45L	cCa	cTa	5	5	B.1.1.70	0.001705
ORF7a	45	P45P	ccA	ccC	3	5	B.1.160	0.000094
ORF7a	45	P45P	ccA	ccG	2	5	B.1.160	0.000062
ORF7a	45	P45P	ccA	ccC	3	5	B.1.177	0.00004
ORF7a	45	P45P	ccA	ccT	2	5	B.1.177	0.000026
ORF7a	45	P45L	CCa	TTa	4	5	B.1.177.21	0.000306
ORF7a	45	P45L	cCa	cTa	1	5	B.1.177.21	0.000076
ORF7a	45	P45L	cCa	cTa	5	5	B.1.234	0.00066
ORF7a	45	P45L	cCa	cTa	5	5	B.1.243	0.000348
ORF7a	45	P45P	ccA	ccC	4	5	B.1.351	0.000119
ORF7a	45	P45P	ccA	ccG	1	5	B.1.351	0.00003
ORF7a	45	P45L	cCa	cTa	5	5	B.1.596	0.000436
ORF7a	45	P45del2	CCa	--a	2	5	B.1.617.2	0.000008
ORF7a	45	P45del2	cCA	c--	2	5	B.1.617.2	0.000008
ORF7a	45	P45del2	CCA	T--	1	5	B.1.617.2	0.000004
ORF7a	45	P45L	cCa	cTa	5	5	B.1.628	0.001762
ORF7a	45	P45L	cCa	cTa	5	5	D.2	0.000375
ORF7a	45	P45L	cCa	cTa	5	5	P.1.14	0.000239
ORF7a	45	P45L	cCa	cTa	4	4	A.23.1	0.002817
ORF7a	45	P45del	CCA	---	4	4	AY.121	0.000541
ORF7a	45	P45P	ccA	ccG	4	4	AY.20	0.000155
ORF7a	45	P45T	CcA	AcT	3	4	AY.25	0.000018
ORF7a	45	P45T	Cca	Aca	1	4	AY.25	0.000006
ORF7a	45	P45L	cCa	cTa	4	4	AY.30	0.001583
ORF7a	45	P45del	CCA	---	4	4	AY.33	0.000267
ORF7a	45	P45S	Cca	Tca	4	4	AY.34	0.000388
ORF7a	45	P45L	cCa	cTa	4	4	AY.36	0.000593
ORF7a	45	P45L	cCa	cTa	2	4	AY.38	0.000999
ORF7a	45	P45L	CCa	TTa	2	4	AY.38	0.000999
ORF7a	45	P45S	Cca	Tca	4	4	AY.4.2	0.000087
ORF7a	45	P45S	Cca	Tca	4	4	AY.4.5	0.00043
ORF7a	45	P45del	CCA	---	4	4	AY.40	0.003857
ORF7a	45	P45R	cCa	cGa	4	4	AY.43	0.000018
ORF7a	45	P45P	ccA	ccG	3	4	AY.5	0.000062
ORF7a	45	P45P	ccA	ccC	1	4	AY.5	0.000021
ORF7a	45	P45L	cCa	cTa	3	4	AY.57	0.001969
ORF7a	45	P45L	CCa	TTa	1	4	AY.57	0.000656
ORF7a	45	P45del	CCA	---	4	4	AY.9.2	0.000147
ORF7a	45	P45S	Cca	Tca	4	4	AY.93	0.001092
ORF7a	45	P45L	cCa	cTa	3	4	AY.96	0.006224
ORF7a	45	P45L	CCa	TTa	1	4	AY.96	0.002075
ORF7a	45	P45L	cCa	cTa	4	4	B.1.1.63	0.001543
ORF7a	45	P45X	CCa	TAa	4	4	B.1.1.7	0.000004
ORF7a	45	P45N	CCA	AAT	4	4	B.1.1.7	0.000004
ORF7a	45	P45S	Cca	Tca	4	4	B.1.177.12	0.000607
ORF7a	45	P45F	CCA	TTT	4	4	B.1.177.21	0.000306
ORF7a	45	P45S	Cca	Tca	4	4	B.1.221	0.000284
ORF7a	45	P45P	ccA	ccT	2	4	B.1.221	0.000142
ORF7a	45	P45P	ccA	ccC	2	4	B.1.221	0.000142
ORF7a	45	P45L	cCa	cTa	4	4	B.1.427	0.000202
ORF7a	45	P45L	cCa	cTa	4	4	B.1.525	0.000453
ORF7a	45	P45A	CcA	GcT	3	4	B.1.617.2	0.000011
ORF7a	45	P45A	Cca	Gca	1	4	B.1.617.2	0.000004
ORF7a	45	P45S	Cca	Tca	4	4	P.1.14	0.000191
ORF7a	45	P45P	ccA	ccG	4	4	P.1.14	0.000191
ORF7a	45	P45P	ccA	ccC	4	4	Q.3	0.00058
ORF7a	45	P45C	CCA	TGT	3	3	All	0.000001
ORF7a	45	P45P	ccA	ccG	2	3	AY.10	0.00106
ORF7a	45	P45P	ccA	ccT	1	3	AY.10	0.00053
ORF7a	45	P45S	Cca	Tca	3	3	AY.100	0.000138
ORF7a	45	P45T	Cca	Aca	3	3	AY.103	0.000019
ORF7a	45	P45del	CCA	---	3	3	AY.118	0.000188
ORF7a	45	P45S	Cca	Tca	3	3	AY.119	0.000106
ORF7a	45	P45S	Cca	Tca	3	3	AY.121	0.000406
ORF7a	45	P45E	CCa	GAa	3	3	AY.25	0.000018
ORF7a	45	P45N	CCA	AAT	2	3	AY.25	0.000012
ORF7a	45	P45N	CCA	AAC	1	3	AY.25	0.000006
ORF7a	45	P45R	cCa	cGa	3	3	AY.26	0.000085
ORF7a	45	P45P	ccA	ccC	2	3	AY.26	0.000057
ORF7a	45	P45P	ccA	ccG	1	3	AY.26	0.000028
ORF7a	45	P45del	CCA	---	3	3	AY.29.1	0.000662
ORF7a	45	P45del	CCA	---	3	3	AY.35	0.000699
ORF7a	45	P45del	CCA	---	3	3	AY.4.5	0.000322
ORF7a	45	P45del2	cCA	c--	3	3	AY.44	0.000018
ORF7a	45	P45del	CCA	---	3	3	AY.45	0.000365
ORF7a	45	P45P	ccA	ccC	2	3	AY.46	0.000208
ORF7a	45	P45P	ccA	ccT	1	3	AY.46	0.000104
ORF7a	45	P45del	CCA	---	3	3	AY.46.5	0.000595
ORF7a	45	P45S	Cca	Tca	3	3	AY.47	0.000093
ORF7a	45	P45L	cCa	cTa	3	3	AY.55	0.002752
ORF7a	45	P45del	CCA	---	3	3	AY.61	0.000314
ORF7a	45	P45P	ccA	ccG	2	3	AY.61	0.00021
ORF7a	45	P45P	ccA	ccT	1	3	AY.61	0.000105
ORF7a	45	P45L	cCa	cTa	3	3	AY.62	0.001307
ORF7a	45	P45L	cCa	cTa	3	3	AY.75.1	0.000541
ORF7a	45	P45L	cCa	cTa	3	3	AY.8	0.001818
ORF7a	45	P45L	cCa	cTa	2	3	AY.86	0.00166
ORF7a	45	P45L	CCa	TTa	1	3	AY.86	0.00083
ORF7a	45	P45del	CCA	---	3	3	AY.88	0.002653
ORF7a	45	P45del	CCA	---	3	3	AY.98	0.000237
ORF7a	45	P45L	cCa	cTa	3	3	B.1.1.1	0.00098
ORF7a	45	P45S	Cca	Tca	3	3	B.1.1.214	0.000166
ORF7a	45	P45del	CCA	---	3	3	B.1.1.25	0.001706
ORF7a	45	P45P	ccA	ccC	3	3	B.1.1.39	0.001529
ORF7a	45	P45F	CCA	TTT	3	3	B.1.1.7	0.000003
ORF7a	45	P45Y	CCA	TAT	3	3	B.1.1.7	0.000003
ORF7a	45	P45P	ccA	ccC	2	3	B.1.139	0.001466
ORF7a	45	P45P	ccA	ccT	1	3	B.1.139	0.000733
ORF7a	45	P45L	cCa	cTa	3	3	B.1.177.32	0.004049
ORF7a	45	P45L	cCa	cTa	3	3	B.1.177.43	0.004431
ORF7a	45	P45L	cCa	cTa	3	3	B.1.177.86	0.00055
ORF7a	45	P45L	cCa	cTa	3	3	B.1.222	0.005076
ORF7a	45	P45del	CCA	---	3	3	B.1.234	0.000396
ORF7a	45	P45P	ccA	ccC	2	3	B.1.234	0.000264
ORF7a	45	P45P	ccA	ccT	1	3	B.1.234	0.000132
ORF7a	45	P45L	cCa	cTa	3	3	B.1.258	0.0002
ORF7a	45	P45L	cCa	cTa	3	3	B.1.265	0.003812
ORF7a	45	P45P	ccA	ccC	2	3	B.1.291	0.038462
ORF7a	45	P45P	ccA	ccG	1	3	B.1.291	0.019231
ORF7a	45	P45S	Cca	Tca	3	3	B.1.351	0.000089
ORF7a	45	P45L	cCa	cTa	3	3	B.1.36	0.000438
ORF7a	45	P45S	Cca	Tca	3	3	B.1.428	0.003061
ORF7a	45	P45S	Cca	Tca	3	3	B.1.526	0.000071
ORF7a	45	P45L	cCa	cTa	3	3	B.1.564.1	0.004732
ORF7a	45	P45L	cCa	cTa	3	3	B.1.575	0.00091
ORF7a	45	P45L	cCa	cTa	3	3	B.1.595	0.000783
ORF7a	45	P45del	CCA	---	3	3	B.1.596	0.000261
ORF7a	45	P45X	CCa	TAa	3	3	B.1.617.2	0.000011
ORF7a	45	P45V	CCA	GTT	3	3	B.1.617.2	0.000011
ORF7a	45	P45I	CCA	ATT	3	3	B.1.617.2	0.000011
ORF7a	45	P45T	CcA	AcT	2	3	B.1.617.2	0.000008
ORF7a	45	P45T	Cca	Aca	1	3	B.1.617.2	0.000004
ORF7a	45	P45S	Cca	Tca	3	3	B.1.621	0.000266
ORF7a	45	P45del	CCA	---	3	3	B.1.626	0.017143
ORF7a	45	P45del2	CCa	--a	3	3	B.1.637	0.000219
ORF7a	45	P45L	cCa	cTa	3	3	B.1.637	0.000219
ORF7a	45	P45del	CCA	---	3	3	Q.8	0.000495
ORF7a	45	P45S	Cca	Tca	3	3	R.1	0.00027
ORF7a	45	P45A	Cca	Gca	2	2		0.111111
ORF7a	45	P45del	CCA	---	2	2	A	0.000774
ORF7a	45	P45P	ccA	ccC	1	2	A	0.000387
ORF7a	45	P45P	ccA	ccG	1	2	A	0.000387
ORF7a	45	P45P	ccA	ccG	1	2	A.1	0.000282
ORF7a	45	P45P	ccA	ccC	1	2	A.1	0.000282
ORF7a	45	P45L	cCa	cTa	2	2	A.2.5	0.000998
ORF7a	45	P45del	CCA	---	2	2	A.28	0.005291
ORF7a	45	P45L	cCa	cTa	2	2	A.28	0.005291
ORF7a	45	P45G	CCA	GGT	1	2	All	0
ORF7a	45	P45G	CCa	GGa	1	2	All	0
ORF7a	45	P45L	cCa	cTa	2	2	AU.2	0.004843
ORF7a	45	P45L	cCa	cTa	2	2	AY.107	0.000932
ORF7a	45	P45del	CCA	---	2	2	AY.108	0.002205
ORF7a	45	P45del	CCA	---	2	2	AY.109	0.001479
ORF7a	45	P45del	CCA	---	2	2	AY.110	0.000225
ORF7a	45	P45del	CCA	---	2	2	AY.114	0.000462
ORF7a	45	P45S	Cca	Tca	2	2	AY.117	0.000169
ORF7a	45	P45P	ccA	ccC	2	2	AY.118	0.000125
ORF7a	45	P45P	ccA	ccT	1	2	AY.119	0.000035
ORF7a	45	P45P	ccA	ccC	1	2	AY.119	0.000035
ORF7a	45	P45L	cCa	cTa	2	2	AY.13	0.000322
ORF7a	45	P45R	cCa	cGa	2	2	AY.16	0.000759
ORF7a	45	P45S	Cca	Tca	2	2	AY.20	0.000078
ORF7a	45	P45S	Cca	Tca	2	2	AY.23	0.000139
ORF7a	45	P45L	cCa	cTa	2	2	AY.24	0.000862
ORF7a	45	P45C	CCA	TGT	2	2	AY.25	0.000012
ORF7a	45	P45G	CCA	GGT	1	2	AY.25	0.000006
ORF7a	45	P45G	CCa	GGa	1	2	AY.25	0.000006
ORF7a	45	P45R	CCa	AGa	1	2	AY.25	0.000006
ORF7a	45	P45R	cCA	cGT	1	2	AY.25	0.000006
ORF7a	45	P45L	cCa	cTa	2	2	AY.29.1	0.000441
ORF7a	45	P45T	Cca	Aca	2	2	AY.3	0.00002
ORF7a	45	P45P	ccA	ccT	2	2	AY.34	0.000194
ORF7a	45	P45R	cCa	cGa	2	2	AY.36	0.000296
ORF7a	45	P45del2	cCA	c--	2	2	AY.39	0.000049
ORF7a	45	P45R	cCa	cGa	2	2	AY.4	0.000003
ORF7a	45	P45del2	cCA	c--	2	2	AY.4.2	0.000043
ORF7a	45	P45del	CCA	---	2	2	AY.4.2.1	0.000298
ORF7a	45	P45del	CCA	---	2	2	AY.4.3	0.001684
ORF7a	45	P45Q	cCa	cAa	2	2	AY.43	0.000009
ORF7a	45	P45del1	CCA	TT-	2	2	AY.43	0.000009
ORF7a	45	P45del2	cCA	c--	2	2	AY.43	0.000009
ORF7a	45	P45Q	cCa	cAa	2	2	AY.44	0.000012
ORF7a	45	P45T	Cca	Aca	2	2	AY.44	0.000012
ORF7a	45	P45S	Cca	Tca	2	2	AY.46	0.000208
ORF7a	45	P45L	cCa	cTa	2	2	AY.46.5	0.000397
ORF7a	45	P45Q	cCa	cAa	2	2	AY.47	0.000062
ORF7a	45	P45L	cCa	cTa	2	2	AY.49	0.00639
ORF7a	45	P45S	Cca	Tca	2	2	AY.5.4	0.000553
ORF7a	45	P45del	CCA	---	2	2	AY.53	0.000575
ORF7a	45	P45P	ccA	ccT	1	2	AY.67	0.000464
ORF7a	45	P45P	ccA	ccC	1	2	AY.67	0.000464
ORF7a	45	P45del	CCA	---	2	2	AY.7.1	0.000225
ORF7a	45	P45P	ccA	ccT	1	2	AY.7.1	0.000113
ORF7a	45	P45P	ccA	ccC	1	2	AY.7.1	0.000113
ORF7a	45	P45L	cCa	cTa	2	2	AY.72	0.002721
ORF7a	45	P45L	cCa	cTa	2	2	AY.73	0.001331
ORF7a	45	P45P	ccA	ccT	1	2	AY.84	0.000437
ORF7a	45	P45P	ccA	ccC	1	2	AY.84	0.000437
ORF7a	45	P45del	CCA	---	2	2	AY.9	0.000135
ORF7a	45	P45P	ccA	ccC	1	2	AY.9	0.000068
ORF7a	45	P45P	ccA	ccT	1	2	AY.9	0.000068
ORF7a	45	P45del	CCA	---	2	2	AY.9.1	0.000167
ORF7a	45	P45L	CCa	TTa	1	2	AY.90	0.000684
ORF7a	45	P45L	cCa	cTa	1	2	AY.90	0.000684
ORF7a	45	P45P	ccA	ccC	2	2	AY.98.1	0.000097
ORF7a	45	P45del	CCA	---	2	2	AY.99.2	0.000184
ORF7a	45	P45L	cCa	cTa	2	2	B	0.000256
ORF7a	45	P45P	ccA	ccC	2	2	B	0.000256
ORF7a	45	P45A	Cca	Gca	2	2	B.1	0.000018
ORF7a	45	P45R	cCa	cGa	2	2	B.1	0.000018
ORF7a	45	P45K	CCa	AAa	2	2	B.1.1	0.000036
ORF7a	45	P45Q	cCa	cAa	2	2	B.1.1	0.000036
ORF7a	45	P45del2	cCA	c--	2	2	B.1.1	0.000036
ORF7a	45	P45del	CCA	---	2	2	B.1.1.121	0.004854
ORF7a	45	P45L	cCa	cTa	2	2	B.1.1.214	0.000111
ORF7a	45	P45P	ccA	ccG	2	2	B.1.1.222	0.000408
ORF7a	45	P45L	cCa	cTa	2	2	B.1.1.222	0.000408
ORF7a	45	P45del	CCA	---	2	2	B.1.1.318	0.000604
ORF7a	45	P45L	cCa	cTa	2	2	B.1.1.33	0.000842
ORF7a	45	P45S	Cca	Tca	2	2	B.1.1.335	0.025974
ORF7a	45	P45P	ccA	ccT	1	2	B.1.1.409	0.002833
ORF7a	45	P45P	ccA	ccC	1	2	B.1.1.409	0.002833
ORF7a	45	P45L	cCa	cTa	2	2	B.1.1.464	0.002946
ORF7a	45	P45L	cCa	cTa	2	2	B.1.1.486	0.003155
ORF7a	45	P45P	ccA	ccT	1	2	B.1.146	0.004237
ORF7a	45	P45P	ccA	ccG	1	2	B.1.146	0.004237
ORF7a	45	P45Q	cCa	cAa	2	2	B.1.177	0.000026
ORF7a	45	P45X	CCa	TAa	2	2	B.1.177.21	0.000153
ORF7a	45	P45S	Cca	Tca	2	2	B.1.177.33	0.003289
ORF7a	45	P45P	ccA	ccC	2	2	B.1.177.43	0.002954
ORF7a	45	P45del	CCA	---	2	2	B.1.177.43	0.002954
ORF7a	45	P45L	cCa	cTa	2	2	B.1.177.62	0.002384
ORF7a	45	P45del	CCA	---	2	2	B.1.177.81	0.000379
ORF7a	45	P45del	CCA	---	2	2	B.1.177.86	0.000367
ORF7a	45	P45del	CCA	---	2	2	B.1.214.2	0.001199
ORF7a	45	P45del	CCA	---	2	2	B.1.221	0.000142
ORF7a	45	P45L	cCa	cTa	2	2	B.1.241	0.001623
ORF7a	45	P45S	Cca	Tca	2	2	B.1.243	0.000139
ORF7a	45	P45R	cCa	cGa	2	2	B.1.258	0.000133
ORF7a	45	P45del	CCA	---	2	2	B.1.258.11	0.000793
ORF7a	45	P45L	cCa	cTa	2	2	B.1.258.14	0.001961
ORF7a	45	P45S	Cca	Tca	2	2	B.1.258.21	0.015504
ORF7a	45	P45L	cCa	cTa	2	2	B.1.279	0.001027
ORF7a	45	P45del	CCA	---	2	2	B.1.351.2	0.000605
ORF7a	45	P45del	CCA	---	2	2	B.1.36	0.000292
ORF7a	45	P45L	cCa	cTa	1	2	B.1.375	0.00082
ORF7a	45	P45L	cCA	cTT	1	2	B.1.375	0.00082
ORF7a	45	P45P	ccA	ccT	1	2	B.1.466.2	0.000391
ORF7a	45	P45P	ccA	ccC	1	2	B.1.466.2	0.000391
ORF7a	45	P45P	ccA	ccG	2	2	B.1.470	0.002809
ORF7a	45	P45P	ccA	ccG	1	2	B.1.497	0.000315
ORF7a	45	P45P	ccA	ccC	1	2	B.1.497	0.000315
ORF7a	45	P45P	ccA	ccG	2	2	B.1.525	0.000226
ORF7a	45	P45del2	cCA	c--	2	2	B.1.526	0.000047
ORF7a	45	P45del1	ccA	cc-	2	2	B.1.526	0.000047
ORF7a	45	P45I	CCA	ATT	1	2	B.1.576	0.000907
ORF7a	45	P45I	CCa	ATa	1	2	B.1.576	0.000907
ORF7a	45	P45P	ccA	ccT	1	2	B.1.582	0.000491
ORF7a	45	P45P	ccA	ccC	1	2	B.1.582	0.000491
ORF7a	45	P45L	cCa	cTa	2	2	B.1.609	0.000959
ORF7a	45	P45L	cCa	cTa	2	2	B.1.617.1	0.000258
ORF7a	45	P45K	CCa	AAa	2	2	B.1.617.2	0.000008
ORF7a	45	P45D	CCA	GAT	2	2	B.1.617.2	0.000008
ORF7a	45	P45Y	CCA	TAT	2	2	B.1.617.2	0.000008
ORF7a	45	P45E	CCa	GAa	1	2	B.1.617.2	0.000004
ORF7a	45	P45E	CCA	GAG	1	2	B.1.617.2	0.000004
ORF7a	45	P45del	CCA	---	2	2	B.1.617.3	0.00597
ORF7a	45	P45L	cCa	cTa	2	2	B.1.623	0.001073
ORF7a	45	P45L	cCa	cTa	2	2	B.1.632	0.013423
ORF7a	45	P45P	ccA	ccG	2	2	B.1.637	0.000146
ORF7a	45	P45del	CCA	---	2	2	C.36.3	0.001134
ORF7a	45	P45S	Cca	Tca	2	2	C.37	0.000232
ORF7a	45	P45P	ccA	ccT	1	2	C.37	0.000116
ORF7a	45	P45P	ccA	ccC	1	2	C.37	0.000116
ORF7a	45	P45S	Cca	Tca	2	2	D.2	0.00015
ORF7a	45	P45del2	cCA	c--	2	2	P.1	0.000032
ORF7a	45	P45T	Cca	Aca	2	2	P.1	0.000032
ORF7a	45	P45S	Cca	Tca	2	2	P.1.17	0.000324
ORF7a	45	P45L	cCa	cTa	2	2	P.2	0.000373
ORF7a	45	P45S	Cca	Tca	2	2	Q.2	0.001227
ORF7a	45	P45L	cCa	cTa	2	2	Q.3	0.00029
ORF7a	45	P45P	ccA	ccG	1	2	Q.4	0.000455
ORF7a	45	P45P	ccA	ccC	1	2	Q.4	0.000455
ORF7a	45	P45del	CCA	---	1	1	A.1	0.000282
ORF7a	45	P45Q	cCa	cAa	1	1	A.1	0.000282
ORF7a	45	P45L	cCa	cTa	1	1	A.2	0.000662
ORF7a	45	P45T	Cca	Aca	1	1	A.2	0.000662
ORF7a	45	P45S	Cca	Tca	1	1	A.23.1	0.000704
ORF7a	45	P45del	CCA	---	1	1	A.23.1	0.000704
ORF7a	45	P45L	cCa	cTa	1	1	A.27	0.001656
ORF7a	45	P45L	cCa	cTa	1	1	AD.2	0.000219
ORF7a	45	P45del2	cCA	c--	1	1	AY.100	0.000046
ORF7a	45	P45L	cCa	cTa	1	1	AY.101	0.00049
ORF7a	45	P45R	cCa	cGa	1	1	AY.101	0.00049
ORF7a	45	P45del	CCA	---	1	1	AY.101	0.00049
ORF7a	45	P45Q	cCa	cAa	1	1	AY.102	0.000027
ORF7a	45	P45A	Cca	Gca	1	1	AY.103	0.000006
ORF7a	45	P45R	cCa	cGa	1	1	AY.103	0.000006
ORF7a	45	P45Q	cCa	cAa	1	1	AY.103	0.000006
ORF7a	45	P45S	Cca	Tca	1	1	AY.105	0.000643
ORF7a	45	P45S	Cca	Tca	1	1	AY.107	0.000466
ORF7a	45	P45P	ccA	ccG	1	1	AY.109	0.00074
ORF7a	45	P45E	CCa	GAa	1	1	AY.110	0.000113
ORF7a	45	P45del	CCA	---	1	1	AY.111	0.000183
ORF7a	45	P45del	CCA	---	1	1	AY.113	0.000142
ORF7a	45	P45S	Cca	Tca	1	1	AY.114	0.000231
ORF7a	45	P45del	CCA	---	1	1	AY.116	0.000287
ORF7a	45	P45P	ccA	ccT	1	1	AY.116	0.000287
ORF7a	45	P45del	CCA	---	1	1	AY.116.1	0.000311
ORF7a	45	P45P	ccA	ccT	1	1	AY.116.1	0.000311
ORF7a	45	P45S	Cca	Tca	1	1	AY.118	0.000063
ORF7a	45	P45del	CCA	---	1	1	AY.12	0.000316
ORF7a	45	P45P	ccA	ccC	1	1	AY.12	0.000316
ORF7a	45	P45P	ccA	ccC	1	1	AY.120	0.000037
ORF7a	45	P45del2	CCa	--a	1	1	AY.120.1	0.000321
ORF7a	45	P45T	Cca	Aca	1	1	AY.120.1	0.000321
ORF7a	45	P45P	ccA	ccC	1	1	AY.121	0.000135
ORF7a	45	P45T	Cca	Aca	1	1	AY.13	0.000161
ORF7a	45	P45del	CCA	---	1	1	AY.13	0.000161
ORF7a	45	P45P	ccA	ccC	1	1	AY.14	0.000088
ORF7a	45	P45S	Cca	Tca	1	1	AY.14	0.000088
ORF7a	45	P45P	ccA	ccT	1	1	AY.16	0.00038
ORF7a	45	P45del	CCA	---	1	1	AY.16	0.00038
ORF7a	45	P45S	Cca	Tca	1	1	AY.16.1	0.00047
ORF7a	45	P45del	CCA	---	1	1	AY.16.1	0.00047
ORF7a	45	P45Q	cCa	cAa	1	1	AY.20	0.000039
ORF7a	45	P45L	cCa	cTa	1	1	AY.22	0.002092
ORF7a	45	P45R	cCa	cGa	1	1	AY.23	0.00007
ORF7a	45	P45P	ccA	ccC	1	1	AY.23	0.00007
ORF7a	45	P45S	Cca	Tca	1	1	AY.23.1	0.000417
ORF7a	45	P45L	cCa	cTa	1	1	AY.23.1	0.000417
ORF7a	45	P45K	CCa	AAa	1	1	AY.25	0.000006
ORF7a	45	P45del1	ccA	cc-	1	1	AY.26	0.000028
ORF7a	45	P45Q	cCa	cAa	1	1	AY.29	0.000016
ORF7a	45	P45P	ccA	ccT	1	1	AY.29	0.000016
ORF7a	45	P45del2	cCA	c--	1	1	AY.29	0.000016
ORF7a	45	P45Q	cCa	cAa	1	1	AY.29.1	0.000221
ORF7a	45	P45del2	cCA	c--	1	1	AY.3	0.00001
ORF7a	45	P45Q	cCa	cAa	1	1	AY.3	0.00001
ORF7a	45	P45del1	ccA	cc-	1	1	AY.3	0.00001
ORF7a	45	P45I	CCA	ATT	1	1	AY.3.1	0.000085
ORF7a	45	P45del	CCA	---	1	1	AY.30	0.000396
ORF7a	45	P45del1	ccA	cc-	1	1	AY.30	0.000396
ORF7a	45	P45N	CCA	AAC	1	1	AY.33	0.000067
ORF7a	45	P45S	Cca	Tca	1	1	AY.35	0.000233
ORF7a	45	P45T	Cca	Aca	1	1	AY.37	0.000316
ORF7a	45	P45del	CCA	---	1	1	AY.38	0.000499
ORF7a	45	P45del1	CcA	Ac-	1	1	AY.4	0.000002
ORF7a	45	P45P	ccA	ccT	1	1	AY.4.2	0.000022
ORF7a	45	P45S	Cca	Tca	1	1	AY.4.4	0.000409
ORF7a	45	P45S	Cca	Tca	1	1	AY.41	0.000294
ORF7a	45	P45T	Cca	Aca	1	1	AY.42	0.00004
ORF7a	45	P45del2	CCa	--a	1	1	AY.42	0.00004
ORF7a	45	P45S	Cca	Tca	1	1	AY.42	0.00004
ORF7a	45	P45H	cCA	cAC	1	1	AY.43	0.000004
ORF7a	45	P45I	CCa	ATa	1	1	AY.43	0.000004
ORF7a	45	P45A	Cca	Gca	1	1	AY.43	0.000004
ORF7a	45	P45T	CcA	AcT	1	1	AY.43	0.000004
ORF7a	45	P45V	CCa	GTa	1	1	AY.44	0.000006
ORF7a	45	P45R	cCa	cGa	1	1	AY.44	0.000006
ORF7a	45	P45del1	CcA	Ac-	1	1	AY.44	0.000006
ORF7a	45	P45del1	ccA	cc-	1	1	AY.45	0.000122
ORF7a	45	P45P	ccA	ccG	1	1	AY.45	0.000122
ORF7a	45	P45del	CCA	---	1	1	AY.46	0.000104
ORF7a	45	P45S	Cca	Tca	1	1	AY.46.2	0.000635
ORF7a	45	P45P	ccA	ccC	1	1	AY.46.2	0.000635
ORF7a	45	P45del2	cCA	c--	1	1	AY.46.4	0.000165
ORF7a	45	P45S	Cca	Tca	1	1	AY.46.6	0.000072
ORF7a	45	P45T	CcA	AcT	1	1	AY.5.4	0.000277
ORF7a	45	P45Q	cCa	cAa	1	1	AY.5.4	0.000277
ORF7a	45	P45L	cCa	cTa	1	1	AY.50	0.000799
ORF7a	45	P45S	Cca	Tca	1	1	AY.55	0.000917
ORF7a	45	P45S	Cca	Tca	1	1	AY.63	0.000387
ORF7a	45	P45L	cCa	cTa	1	1	AY.66	0.00107
ORF7a	45	P45del	CCA	---	1	1	AY.66	0.00107
ORF7a	45	P45S	Cca	Tca	1	1	AY.67	0.000464
ORF7a	45	P45del	CCA	---	1	1	AY.68	0.000274
ORF7a	45	P45S	Cca	Tca	1	1	AY.68	0.000274
ORF7a	45	P45del	CCA	---	1	1	AY.7	0.000196
ORF7a	45	P45S	Cca	Tca	1	1	AY.7.1	0.000113
ORF7a	45	P45del	CCA	---	1	1	AY.71	0.000475
ORF7a	45	P45del2	cCA	c--	1	1	AY.71	0.000475
ORF7a	45	P45del	CCA	---	1	1	AY.73	0.000665
ORF7a	45	P45del	CCA	---	1	1	AY.74	0.000116
ORF7a	45	P45P	ccA	ccG	1	1	AY.75.1	0.00018
ORF7a	45	P45S	Cca	Tca	1	1	AY.75.1	0.00018
ORF7a	45	P45S	Cca	Tca	1	1	AY.77	0.001127
ORF7a	45	P45P	ccA	ccG	1	1	AY.77	0.001127
ORF7a	45	P45del	CCA	---	1	1	AY.79	0.001211
ORF7a	45	P45del	CCA	---	1	1	AY.80	0.001129
ORF7a	45	P45L	cCa	cTa	1	1	AY.81	0.001992
ORF7a	45	P45Q	cCa	cAa	1	1	AY.82	0.001357
ORF7a	45	P45L	cCa	cTa	1	1	AY.83	0.001724
ORF7a	45	P45S	Cca	Tca	1	1	AY.84	0.000437
ORF7a	45	P45del	CCA	---	1	1	AY.85	0.000427
ORF7a	45	P45A	Cca	Gca	1	1	AY.87	0.000833
ORF7a	45	P45S	Cca	Tca	1	1	AY.88	0.000884
ORF7a	45	P45P	ccA	ccG	1	1	AY.9.1	0.000084
ORF7a	45	P45S	Cca	Tca	1	1	AY.9.1	0.000084
ORF7a	45	P45P	ccA	ccC	1	1	AY.9.2	0.000037
ORF7a	45	P45S	Cca	Tca	1	1	AY.90	0.000684
ORF7a	45	P45del	CCA	---	1	1	AY.91	0.00073
ORF7a	45	P45L	cCa	cTa	1	1	AY.91.1	0.004065
ORF7a	45	P45L	cCa	cTa	1	1	AY.94	0.000443
ORF7a	45	P45del	CCA	---	1	1	AY.94	0.000443
ORF7a	45	P45P	ccA	ccG	1	1	AY.95	0.000761
ORF7a	45	P45P	ccA	ccT	1	1	AY.96	0.002075
ORF7a	45	P45S	Cca	Tca	1	1	AY.98	0.000079
ORF7a	45	P45R	cCa	cGa	1	1	AY.98	0.000079
ORF7a	45	P45P	ccA	ccG	1	1	AY.99.2	0.000092
ORF7a	45	P45del	CCA	---	1	1	AZ.2	0.000821
ORF7a	45	P45del	CCA	---	1	1	B	0.000128
ORF7a	45	P45X	CCa	TAa	1	1	B.1.1	0.000018
ORF7a	45	P45R	cCa	cGa	1	1	B.1.1	0.000018
ORF7a	45	P45del1	ccA	cc-	1	1	B.1.1	0.000018
ORF7a	45	P45T	Cca	Aca	1	1	B.1.1	0.000018
ORF7a	45	P45del1	ccA	cc-	1	1	B.1.1.1	0.000327
ORF7a	45	P45P	ccA	ccT	1	1	B.1.1.121	0.002427
ORF7a	45	P45L	cCa	cTa	1	1	B.1.1.121	0.002427
ORF7a	45	P45del	CCA	---	1	1	B.1.1.157	0.000913
ORF7a	45	P45S	Cca	Tca	1	1	B.1.1.170	0.001247
ORF7a	45	P45L	cCa	cTa	1	1	B.1.1.176	0.000439
ORF7a	45	P45del	CCA	---	1	1	B.1.1.192	0.002309
ORF7a	45	P45del	CCA	---	1	1	B.1.1.207	0.001182
ORF7a	45	P45del2	cCA	c--	1	1	B.1.1.214	0.000055
ORF7a	45	P45L	cCa	cTa	1	1	B.1.1.218	0.007692
ORF7a	45	P45P	ccA	ccC	1	1	B.1.1.226	0.005814
ORF7a	45	P45P	ccA	ccT	1	1	B.1.1.228	0.003049
ORF7a	45	P45P	ccA	ccC	1	1	B.1.1.231	0.003096
ORF7a	45	P45L	cCa	cTa	1	1	B.1.1.236	0.006897
ORF7a	45	P45S	Cca	Tca	1	1	B.1.1.241	0.00207
ORF7a	45	P45S	Cca	Tca	1	1	B.1.1.253	0.002506
ORF7a	45	P45del	CCA	---	1	1	B.1.1.277	0.000759
ORF7a	45	P45S	Cca	Tca	1	1	B.1.1.284	0.000107
ORF7a	45	P45L	cCa	cTa	1	1	B.1.1.284	0.000107
ORF7a	45	P45L	cCa	cTa	1	1	B.1.1.294	0.001266
ORF7a	45	P45del	CCA	---	1	1	B.1.1.304	0.002809
ORF7a	45	P45L	cCa	cTa	1	1	B.1.1.312	0.001912
ORF7a	45	P45P	ccA	ccC	1	1	B.1.1.318	0.000302
ORF7a	45	P45del	CCA	---	1	1	B.1.1.33	0.000421
ORF7a	45	P45Q	cCa	cAa	1	1	B.1.1.33	0.000421
ORF7a	45	P45P	ccA	ccC	1	1	B.1.1.334	0.016393
ORF7a	45	P45L	cCa	cTa	1	1	B.1.1.344	0.010753
ORF7a	45	P45P	ccA	ccC	1	1	B.1.1.356	0.008547
ORF7a	45	P45L	cCa	cTa	1	1	B.1.1.37	0.000193
ORF7a	45	P45Q	cCa	cAa	1	1	B.1.1.374	0.002375
ORF7a	45	P45P	ccA	ccC	1	1	B.1.1.376	0.005952
ORF7a	45	P45P	ccA	ccC	1	1	B.1.1.377	0.001381
ORF7a	45	P45S	Cca	Tca	1	1	B.1.1.378	0.007299
ORF7a	45	P45L	cCa	cTa	1	1	B.1.1.385	0.004464
ORF7a	45	P45L	cCa	cTa	1	1	B.1.1.398	0.003226
ORF7a	45	P45Q	cCa	cAa	1	1	B.1.1.398	0.003226
ORF7a	45	P45P	ccA	ccC	1	1	B.1.1.412	0.007634
ORF7a	45	P45P	ccA	ccC	1	1	B.1.1.434	0.000349
ORF7a	45	P45P	ccA	ccC	1	1	B.1.1.448	0.002033
ORF7a	45	P45S	Cca	Tca	1	1	B.1.1.481	0.071429
ORF7a	45	P45Q	cCa	cAa	1	1	B.1.1.519	0.00004
ORF7a	45	P45del	CCA	---	1	1	B.1.1.519	0.00004
ORF7a	45	P45del	CCA	---	1	1	B.1.1.522	0.017241
ORF7a	45	P45L	cCa	cTa	1	1	B.1.1.523	0.001563
ORF7a	45	P45P	ccA	ccC	1	1	B.1.1.70	0.000341
ORF7a	45	P45L	cCa	cTa	1	1	B.1.1.74	0.00431
ORF7a	45	P45L	cCa	cTa	1	1	B.1.1.98	0.018519
ORF7a	45	P45S	Cca	Tca	1	1	B.1.112	0.005181
ORF7a	45	P45del	CCA	---	1	1	B.1.115	0.021739
ORF7a	45	P45L	cCa	cTa	1	1	B.1.126	0.001276
ORF7a	45	P45P	ccA	ccG	1	1	B.1.128	0.000635
ORF7a	45	P45L	cCa	cTa	1	1	B.1.128	0.000635
ORF7a	45	P45L	cCa	cTa	1	1	B.1.131	0.008772
ORF7a	45	P45del	CCA	---	1	1	B.1.140	0.018868
ORF7a	45	P45P	ccA	ccT	1	1	B.1.160.10	0.008065
ORF7a	45	P45L	cCa	cTa	1	1	B.1.160.14	0.002119
ORF7a	45	P45R	cCa	cGa	1	1	B.1.160.14	0.002119
ORF7a	45	P45P	ccA	ccT	1	1	B.1.160.26	0.002421
ORF7a	45	P45R	cCa	cGa	1	1	B.1.160.33	0.004425
ORF7a	45	P45del2	cCA	c--	1	1	B.1.177	0.000013
ORF7a	45	P45F	CCA	TTT	1	1	B.1.177	0.000013
ORF7a	45	P45S	Cca	Tca	1	1	B.1.177.16	0.000664
ORF7a	45	P45P	ccA	ccC	1	1	B.1.177.23	0.003236
ORF7a	45	P45L	cCa	cTa	1	1	B.1.177.35	0.000691
ORF7a	45	P45S	Cca	Tca	1	1	B.1.177.4	0.000211
ORF7a	45	P45del	CCA	---	1	1	B.1.177.50	0.004695
ORF7a	45	P45L	cCa	cTa	1	1	B.1.177.52	0.001757
ORF7a	45	P45P	ccA	ccG	1	1	B.1.177.53	0.002392
ORF7a	45	P45P	ccA	ccC	1	1	B.1.177.54	0.000606
ORF7a	45	P45S	Cca	Tca	1	1	B.1.177.58	0.001332
ORF7a	45	P45P	ccA	ccT	1	1	B.1.177.6	0.000977
ORF7a	45	P45L	cCa	cTa	1	1	B.1.177.60	0.000218
ORF7a	45	P45del	CCA	---	1	1	B.1.177.62	0.001192
ORF7a	45	P45P	ccA	ccC	1	1	B.1.177.63	0.002703
ORF7a	45	P45Q	cCa	cAa	1	1	B.1.177.7	0.000165
ORF7a	45	P45del	CCA	---	1	1	B.1.177.83	0.001481
ORF7a	45	P45T	Cca	Aca	1	1	B.1.2	0.000009
ORF7a	45	P45S	Cca	Tca	1	1	B.1.206	0.000816
ORF7a	45	P45L	cCa	cTa	1	1	B.1.210	0.002132
ORF7a	45	P45L	cCa	cTa	1	1	B.1.214.2	0.0006
ORF7a	45	P45L	cCa	cTa	1	1	B.1.221	0.000071
ORF7a	45	P45S	Cca	Tca	1	1	B.1.234	0.000132
ORF7a	45	P45L	cCa	cTa	1	1	B.1.239	0.001221
ORF7a	45	P45T	Cca	Aca	1	1	B.1.240	0.000216
ORF7a	45	P45L	cCa	cTa	1	1	B.1.240	0.000216
ORF7a	45	P45del	CCA	---	1	1	B.1.240	0.000216
ORF7a	45	P45P	ccA	ccC	1	1	B.1.241	0.000812
ORF7a	45	P45del	CCA	---	1	1	B.1.243	0.00007
ORF7a	45	P45del2	cCA	c--	1	1	B.1.243	0.00007
ORF7a	45	P45L	cCa	cTa	1	1	B.1.258.11	0.000396
ORF7a	45	P45P	ccA	ccT	1	1	B.1.258.16	0.001637
ORF7a	45	P45L	cCa	cTa	1	1	B.1.258.17	0.000104
ORF7a	45	P45del	CCA	---	1	1	B.1.258.17	0.000104
ORF7a	45	P45Q	cCa	cAa	1	1	B.1.258.17	0.000104
ORF7a	45	P45P	ccA	ccT	1	1	B.1.311	0.000275
ORF7a	45	P45P	ccA	ccC	1	1	B.1.320	0.001245
ORF7a	45	P45P	ccA	ccG	1	1	B.1.334	0.018182
ORF7a	45	P45P	ccA	ccC	1	1	B.1.336	0.002439
ORF7a	45	P45L	cCa	cTa	1	1	B.1.349	0.000715
ORF7a	45	P45R	cCA	cGG	1	1	B.1.351	0.00003
ORF7a	45	P45del1	ccA	cc-	1	1	B.1.351	0.00003
ORF7a	45	P45T	Cca	Aca	1	1	B.1.351	0.00003
ORF7a	45	P45L	cCa	cTa	1	1	B.1.351.2	0.000303
ORF7a	45	P45P	ccA	ccG	1	1	B.1.36	0.000146
ORF7a	45	P45L	cCa	cTa	1	1	B.1.36.18	0.00042
ORF7a	45	P45L	cCa	cTa	1	1	B.1.36.29	0.000517
ORF7a	45	P45P	ccA	ccT	1	1	B.1.36.29	0.000517
ORF7a	45	P45L	cCa	cTa	1	1	B.1.36.31	0.001751
ORF7a	45	P45P	ccA	ccT	1	1	B.1.36.37	0.002778
ORF7a	45	P45Q	cCa	cAa	1	1	B.1.36.8	0.001
ORF7a	45	P45L	cCa	cTa	1	1	B.1.36.8	0.001
ORF7a	45	P45L	cCa	cTa	1	1	B.1.361	0.001289
ORF7a	45	P45L	cCa	cTa	1	1	B.1.362	0.001541
ORF7a	45	P45L	cCa	cTa	1	1	B.1.367	0.000792
ORF7a	45	P45P	ccA	ccC	1	1	B.1.369	0.000285
ORF7a	45	P45del	CCA	---	1	1	B.1.371	0.001122
ORF7a	45	P45del	CCA	---	1	1	B.1.375	0.00082
ORF7a	45	P45L	cCa	cTa	1	1	B.1.391	0.001127
ORF7a	45	P45S	Cca	Tca	1	1	B.1.396	0.000706
ORF7a	45	P45P	ccA	ccC	1	1	B.1.399	0.001934
ORF7a	45	P45P	ccA	ccC	1	1	B.1.413	0.004255
ORF7a	45	P45L	cCa	cTa	1	1	B.1.416	0.001269
ORF7a	45	P45del2	cCA	c--	1	1	B.1.416	0.001269
ORF7a	45	P45P	ccA	ccC	1	1	B.1.426	0.001009
ORF7a	45	P45del2	cCA	c--	1	1	B.1.427	0.00005
ORF7a	45	P45del	CCA	---	1	1	B.1.427	0.00005
ORF7a	45	P45P	ccA	ccC	1	1	B.1.427	0.00005
ORF7a	45	P45del1	ccA	cc-	1	1	B.1.429	0.000024
ORF7a	45	P45del2	cCA	c--	1	1	B.1.429	0.000024
ORF7a	45	P45del	CCA	---	1	1	B.1.438.1	0.000107
ORF7a	45	P45L	cCa	cTa	1	1	B.1.438.1	0.000107
ORF7a	45	P45L	cCa	cTa	1	1	B.1.456	0.003268
ORF7a	45	P45del	CCA	---	1	1	B.1.459	0.004082
ORF7a	45	P45del	CCA	---	1	1	B.1.466.2	0.000391
ORF7a	45	P45L	cCa	cTa	1	1	B.1.466.2	0.000391
ORF7a	45	P45P	ccA	ccG	1	1	B.1.467	0.04
ORF7a	45	P45del	CCA	---	1	1	B.1.468	0.005714
ORF7a	45	P45L	cCa	cTa	1	1	B.1.470	0.001404
ORF7a	45	P45del	CCA	---	1	1	B.1.470	0.001404
ORF7a	45	P45R	cCa	cGa	1	1	B.1.473	0.019231
ORF7a	45	P45P	ccA	ccC	1	1	B.1.503	0.002488
ORF7a	45	P45P	ccA	ccG	1	1	B.1.517	0.000427
ORF7a	45	P45del	CCA	---	1	1	B.1.517	0.000427
ORF7a	45	P45S	Cca	Tca	1	1	B.1.525	0.000113
ORF7a	45	P45Q	cCa	cAa	1	1	B.1.526	0.000024
ORF7a	45	P45del	CCA	---	1	1	B.1.535	0.028571
ORF7a	45	P45S	Cca	Tca	1	1	B.1.538	0.008065
ORF7a	45	P45L	cCa	cTa	1	1	B.1.540	0.009709
ORF7a	45	P45P	ccA	ccC	1	1	B.1.551	0.00129
ORF7a	45	P45L	cCa	cTa	1	1	B.1.561	0.000397
ORF7a	45	P45S	Cca	Tca	1	1	B.1.565	0.00081
ORF7a	45	P45del1	ccA	cc-	1	1	B.1.568	0.001111
ORF7a	45	P45F	CCA	TTT	1	1	B.1.576	0.000907
ORF7a	45	P45Q	cCa	cAa	1	1	B.1.576	0.000907
ORF7a	45	P45N	CCA	AAT	1	1	B.1.576	0.000907
ORF7a	45	P45X	CCa	TAa	1	1	B.1.576	0.000907
ORF7a	45	P45Y	CCA	TAT	1	1	B.1.576	0.000907
ORF7a	45	P45L	CCa	TTa	1	1	B.1.576	0.000907
ORF7a	45	P45K	CCa	AAa	1	1	B.1.576	0.000907
ORF7a	45	P45L	cCa	cTa	1	1	B.1.582	0.000491
ORF7a	45	P45del	CCA	---	1	1	B.1.582	0.000491
ORF7a	45	P45L	cCa	cTa	1	1	B.1.588	0.00091
ORF7a	45	P45S	Cca	Tca	1	1	B.1.588	0.00091
ORF7a	45	P45del2	cCA	c--	1	1	B.1.595	0.000261
ORF7a	45	P45P	ccA	ccC	1	1	B.1.595	0.000261
ORF7a	45	P45S	Cca	Tca	1	1	B.1.596	0.000087
ORF7a	45	P45Q	cCa	cAa	1	1	B.1.596	0.000087
ORF7a	45	P45S	Cca	Tca	1	1	B.1.597	0.00463
ORF7a	45	P45del1	ccA	cc-	1	1	B.1.606	0.006024
ORF7a	45	P45P	ccA	ccC	1	1	B.1.609	0.000479
ORF7a	45	P45S	Cca	Tca	1	1	B.1.617.1	0.000129
ORF7a	45	P45C	CCA	TGT	1	1	B.1.617.2	0.000004
ORF7a	45	P45del1	Cca	-ca	1	1	B.1.617.2	0.000004
ORF7a	45	P45H	cCA	cAT	1	1	B.1.617.2	0.000004
ORF7a	45	P45del	CCA	---	1	1	B.1.620	0.000946
ORF7a	45	P45del2	CCa	--a	1	1	B.1.621	0.000089
ORF7a	45	P45del1	ccA	cc-	1	1	B.1.621.1	0.000506
ORF7a	45	P45S	Cca	Tca	1	1	B.1.621.1	0.000506
ORF7a	45	P45del	CCA	---	1	1	B.1.636	0.006711
ORF7a	45	P45S	Cca	Tca	1	1	B.1.637	0.000073
ORF7a	45	P45del	CCA	---	1	1	B.1.638	0.052632
ORF7a	45	P45S	Cca	Tca	1	1	B.1.83	0.015385
ORF7a	45	P45S	Cca	Tca	1	1	B.1.88.1	0.004808
ORF7a	45	P45del	CCA	---	1	1	B.1.9.1	0.032258
ORF7a	45	P45L	cCa	cTa	1	1	B.1.91	0.002075
ORF7a	45	P45L	cCa	cTa	1	1	B.40	0.000364
ORF7a	45	P45S	Cca	Tca	1	1	B.40	0.000364
ORF7a	45	P45del	CCA	---	1	1	B.55	0.00295
ORF7a	45	P45Q	cCa	cAa	1	1	B.6	0.00091
ORF7a	45	P45P	ccA	ccC	1	1	C.1	0.002392
ORF7a	45	P45P	ccA	ccT	1	1	C.16	0.00106
ORF7a	45	P45L	cCa	cTa	1	1	C.16	0.00106
ORF7a	45	P45L	cCa	cTa	1	1	C.22	0.071429
ORF7a	45	P45P	ccA	ccC	1	1	C.35	0.000774
ORF7a	45	P45A	Cca	Gca	1	1	C.35	0.000774
ORF7a	45	P45R	cCa	cGa	1	1	C.36.3	0.000567
ORF7a	45	P45del2	cCA	c--	1	1	C.37	0.000116
ORF7a	45	P45del	CCA	---	1	1	K.3	0.006173
ORF7a	45	P45L	cCa	cTa	1	1	N.5	0.001767
ORF7a	45	P45Q	cCa	cAa	1	1	P.1	0.000016
ORF7a	45	P45K	CCa	AAa	1	1	P.1	0.000016
ORF7a	45	P45del	CCA	---	1	1	P.1.1	0.000318
ORF7a	45	P45S	Cca	Tca	1	1	P.1.12	0.000484
ORF7a	45	P45L	cCa	cTa	1	1	P.1.12	0.000484
ORF7a	45	P45del1	CcA	-cN	1	1	P.1.15	0.000232
ORF7a	45	P45S	Cca	Tca	1	1	P.1.15	0.000232
ORF7a	45	P45del	CCA	---	1	1	P.1.16	0.000374
ORF7a	45	P45L	cCa	cTa	1	1	P.1.16	0.000374
ORF7a	45	P45L	cCa	cTa	1	1	P.1.17	0.000162
ORF7a	45	P45L	cCa	cTa	1	1	P.1.2	0.001156
ORF7a	45	P45del	CCA	---	1	1	P.1.3	0.034483
ORF7a	45	P45del	CCA	---	1	1	P.1.4	0.000977
ORF7a	45	P45L	cCa	cTa	1	1	P.1.7	0.000319
ORF7a	45	P45P	ccA	ccT	1	1	P.1.7	0.000319
ORF7a	45	P45del	CCA	---	1	1	P.2	0.000187
ORF7a	45	P45del1	ccA	cc-	1	1	P.2	0.000187
ORF7a	45	P45S	Cca	Tca	1	1	Q.1	0.000126
ORF7a	45	P45del	CCA	---	1	1	Q.7	0.001111

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.