CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF7a : CodonNum = 68

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	68	P68del		del	CCT	---	30502	30502	1	27595-27597
ORF7a	68	P68P		syn	ccT	ccC	1503	988	0.657352	27595-27597
ORF7a	68	P68P		syn	ccT	ccA	1503	422	0.280772	27595-27597
ORF7a	68	P68P		syn	ccT	ccG	1503	93	0.0618762	27595-27597
ORF7a	68	P68L		nonsyn	cCt	cTt	774	769	0.99354	27595-27597
ORF7a	68	P68L		nonsyn	cCT	cTG	774	3	0.00387597	27595-27597
ORF7a	68	P68L		nonsyn	cCT	cTC	774	1	0.00129199	27595-27597
ORF7a	68	P68L		nonsyn	cCT	cTA	774	1	0.00129199	27595-27597
ORF7a	68	P68S		nonsyn	Cct	Tct	539	534	0.990724	27595-27597
ORF7a	68	P68S		nonsyn	CcT	TcA	539	2	0.00371058	27595-27597
ORF7a	68	P68S		nonsyn	CcT	TcC	539	2	0.00371058	27595-27597
ORF7a	68	P68S		nonsyn	CcT	TcG	539	1	0.00185529	27595-27597
ORF7a	68	P68H		nonsyn	cCt	cAt	185	184	0.994595	27595-27597
ORF7a	68	P68H		nonsyn	cCT	cAC	185	1	0.00540541	27595-27597
ORF7a	68	P68del2		del	CCt	--t	62	56	0.903226	27595-27597
ORF7a	68	P68del2		del	CCT	--N	62	3	0.0483871	27595-27597
ORF7a	68	P68del2		del	cCT	c--	62	3	0.0483871	27595-27597
ORF7a	68	P68del1		del	Cct	-ct	55	27	0.490909	27595-27597
ORF7a	68	P68del1		del	ccT	cc-	55	24	0.436364	27595-27597
ORF7a	68	P68del1		del	CCT	-NN	55	2	0.0363636	27595-27597
ORF7a	68	P68del1		del	CCT	NT-	55	1	0.0181818	27595-27597
ORF7a	68	P68del1		del	CCt	-Gt	55	1	0.0181818	27595-27597
ORF7a	68	P68R		nonsyn	cCt	cGt	30	28	0.933333	27595-27597
ORF7a	68	P68R		nonsyn	cCT	cGA	30	1	0.0333333	27595-27597
ORF7a	68	P68R		nonsyn	cCT	cGC	30	1	0.0333333	27595-27597
ORF7a	68	P68T		nonsyn	Cct	Act	26	25	0.961538	27595-27597
ORF7a	68	P68T		nonsyn	CcT	AcA	26	1	0.0384615	27595-27597
ORF7a	68	P68C		nonsyn	CCt	TGt	24	24	1	27595-27597
ORF7a	68	P68V		nonsyn	CCT	GTC	23	20	0.869565	27595-27597
ORF7a	68	P68V		nonsyn	CCt	GTt	23	3	0.130435	27595-27597
ORF7a	68	P68A		nonsyn	Cct	Gct	11	9	0.818182	27595-27597
ORF7a	68	P68A		nonsyn	CcT	GcC	11	1	0.0909091	27595-27597
ORF7a	68	P68A		nonsyn	CcT	GcA	11	1	0.0909091	27595-27597
ORF7a	68	P68F		nonsyn	CCt	TTt	5	4	0.8	27595-27597
ORF7a	68	P68F		nonsyn	CCT	TTC	5	1	0.2	27595-27597
ORF7a	68	P68G		nonsyn	CCT	GGC	4	2	0.5	27595-27597
ORF7a	68	P68G		nonsyn	CCT	GGA	4	1	0.25	27595-27597
ORF7a	68	P68G		nonsyn	CCt	GGt	4	1	0.25	27595-27597
ORF7a	68	P68Q		nonsyn	cCT	cAA	3	3	1	27595-27597
ORF7a	68	P68I		nonsyn	CCt	ATt	2	2	1	27595-27597
ORF7a	68	P68D		nonsyn	CCT	GAC	2	1	0.5	27595-27597
ORF7a	68	P68X		nonsyn	CCT	TAA	2	1	0.5	27595-27597
ORF7a	68	P68X		nonsyn	CCT	TGA	2	1	0.5	27595-27597
ORF7a	68	P68D		nonsyn	CCt	GAt	2	1	0.5	27595-27597
ORF7a	68	P68K		nonsyn	CCT	AAA	1	1	1	27595-27597
ORF7a	68	P68Y		nonsyn	CCt	TAt	1	1	1	27595-27597
ORF7a	68	P68E		nonsyn	CCT	GAA	1	1	1	27595-27597

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	68	P68del	CCT	---	30502	30502	All	0.005834
ORF7a	68	P68del	CCT	---	12354	12354	AY.4	0.019228
ORF7a	68	P68del	CCT	---	2711	2711	B.1.617.2	0.010208
ORF7a	68	P68del	CCT	---	2537	2537	AY.44	0.015442
ORF7a	68	P68del	CCT	---	2298	2298	B.1.1.7	0.002057
ORF7a	68	P68P	ccT	ccC	988	1503	All	0.000189
ORF7a	68	P68P	ccT	ccA	422	1503	All	0.000081
ORF7a	68	P68P	ccT	ccG	93	1503	All	0.000018
ORF7a	68	P68del	CCT	---	1187	1187	AY.43	0.005259
ORF7a	68	P68del	CCT	---	1186	1186	AY.25	0.007134
ORF7a	68	P68L	cCt	cTt	769	774	All	0.000147
ORF7a	68	P68L	cCT	cTG	3	774	All	0.000001
ORF7a	68	P68L	cCT	cTC	1	774	All	0
ORF7a	68	P68L	cCT	cTA	1	774	All	0
ORF7a	68	P68del	CCT	---	607	607	AY.103	0.003769
ORF7a	68	P68del	CCT	---	589	589	AY.3	0.005858
ORF7a	68	P68del	CCT	---	553	553	AY.120	0.02056
ORF7a	68	P68S	Cct	Tct	534	539	All	0.000102
ORF7a	68	P68S	CcT	TcC	2	539	All	0
ORF7a	68	P68S	CcT	TcA	2	539	All	0
ORF7a	68	P68S	CcT	TcG	1	539	All	0
ORF7a	68	P68del	CCT	---	484	484	AY.4.2	0.010497
ORF7a	68	P68del	CCT	---	448	448	AY.3.1	0.038196
ORF7a	68	P68del	CCT	---	435	435	AY.39	0.010749
ORF7a	68	P68P	ccT	ccC	405	424	B.1.1.7	0.000363
ORF7a	68	P68P	ccT	ccA	13	424	B.1.1.7	0.000012
ORF7a	68	P68P	ccT	ccG	6	424	B.1.1.7	0.000005
ORF7a	68	P68del	CCT	---	400	400	AY.26	0.011324
ORF7a	68	P68del	CCT	---	261	261	AY.102	0.00692
ORF7a	68	P68del	CCT	---	223	223	AY.29	0.003518
ORF7a	68	P68P	ccT	ccA	216	216	B.1.1.318	0.065178
ORF7a	68	P68del	CCT	---	206	206	B.1.351	0.006124
ORF7a	68	P68L	cCt	cTt	188	188	AY.4	0.000293
ORF7a	68	P68del	CCT	---	187	187	B.1.177.21	0.0143
ORF7a	68	P68H	cCt	cAt	184	185	All	0.000035
ORF7a	68	P68H	cCT	cAC	1	185	All	0
ORF7a	68	P68L	cCt	cTt	166	166	B.1.1.7	0.000149
ORF7a	68	P68P	ccT	ccC	163	164	AY.44	0.000992
ORF7a	68	P68P	ccT	ccA	1	164	AY.44	0.000006
ORF7a	68	P68P	ccT	ccA	153	158	AY.25	0.00092
ORF7a	68	P68P	ccT	ccC	5	158	AY.25	0.00003
ORF7a	68	P68del	CCT	---	158	158	AY.6	0.006498
ORF7a	68	P68del	CCT	---	138	138	AY.100	0.006349
ORF7a	68	P68del	CCT	---	133	133	B.1.2	0.001171
ORF7a	68	P68del	CCT	---	123	123	B.1.526	0.002891
ORF7a	68	P68del	CCT	---	120	120	AY.46.6	0.008665
ORF7a	68	P68L	cCt	cTt	118	118	B.1.617.2	0.000444
ORF7a	68	P68del	CCT	---	117	117	AY.119	0.004131
ORF7a	68	P68del	CCT	---	112	112	B.1.177	0.001475
ORF7a	68	P68P	ccT	ccC	104	110	B.1.1	0.001887
ORF7a	68	P68P	ccT	ccG	4	110	B.1.1	0.000073
ORF7a	68	P68P	ccT	ccA	2	110	B.1.1	0.000036
ORF7a	68	P68del	CCT	---	103	103	AY.47	0.003204
ORF7a	68	P68del	CCT	---	92	92	B.1	0.000843
ORF7a	68	P68del	CCT	---	89	89	AY.5	0.001838
ORF7a	68	P68S	Cct	Tct	89	89	B.1.177.21	0.006806
ORF7a	68	P68del	CCT	---	85	85	AY.46.4	0.013983
ORF7a	68	P68del	CCT	---	76	76	P.1	0.001197
ORF7a	68	P68P	ccT	ccC	70	70	B.1.1.251	0.555556
ORF7a	68	P68del	CCT	---	64	64	AY.113	0.009113
ORF7a	68	P68del	CCT	---	64	64	B.1.621	0.005665
ORF7a	68	P68del	CCT	---	63	63	AY.20	0.002449
ORF7a	68	P68del2	CCt	--t	56	62	All	0.000011
ORF7a	68	P68del2	cCT	c--	3	62	All	0.000001
ORF7a	68	P68del2	CCT	--N	3	62	All	0.000001
ORF7a	68	P68del	CCT	---	61	61	AY.75	0.003417
ORF7a	68	P68del	CCT	---	56	56	AY.42	0.002253
ORF7a	68	P68del1	Cct	-ct	27	55	All	0.000005
ORF7a	68	P68del1	ccT	cc-	24	55	All	0.000005
ORF7a	68	P68del1	CCT	-NN	2	55	All	0
ORF7a	68	P68del1	CCt	-Gt	1	55	All	0
ORF7a	68	P68del1	CCT	NT-	1	55	All	0
ORF7a	68	P68L	cCt	cTt	54	54	AY.43	0.000239
ORF7a	68	P68del	CCT	---	53	53	AY.23	0.003697
ORF7a	68	P68del	CCT	---	53	53	AY.39.1	0.0021
ORF7a	68	P68P	ccT	ccC	42	52	AY.4	0.000065
ORF7a	68	P68P	ccT	ccG	6	52	AY.4	0.000009
ORF7a	68	P68P	ccT	ccA	4	52	AY.4	0.000006
ORF7a	68	P68del	CCT	---	50	50	AY.46	0.005204
ORF7a	68	P68del	CCT	---	50	50	B.1.1.284	0.00537
ORF7a	68	P68del	CCT	---	49	49	AY.33	0.003272
ORF7a	68	P68del	CCT	---	49	49	B.1.429	0.001153
ORF7a	68	P68H	cCt	cAt	48	48	AY.83	0.082759
ORF7a	68	P68P	ccT	ccC	40	48	B.1.617.2	0.000151
ORF7a	68	P68P	ccT	ccA	6	48	B.1.617.2	0.000023
ORF7a	68	P68P	ccT	ccG	2	48	B.1.617.2	0.000008
ORF7a	68	P68S	Cct	Tct	46	46	B.1.1.7	0.000041
ORF7a	68	P68del	CCT	---	44	44	AY.117	0.003719
ORF7a	68	P68del	CCT	---	43	43	AY.86	0.035685
ORF7a	68	P68del	CCT	---	42	42	AY.107	0.019571
ORF7a	68	P68del	CCT	---	42	42	B.1.160	0.00131
ORF7a	68	P68S	Cct	Tct	40	40	AY.103	0.000248
ORF7a	68	P68P	ccT	ccG	31	39	AY.43	0.000137
ORF7a	68	P68P	ccT	ccA	5	39	AY.43	0.000022
ORF7a	68	P68P	ccT	ccC	3	39	AY.43	0.000013
ORF7a	68	P68del	CCT	---	39	39	B.1.637	0.00285
ORF7a	68	P68S	Cct	Tct	37	38	AY.4	0.000058
ORF7a	68	P68S	CcT	TcA	1	38	AY.4	0.000002
ORF7a	68	P68S	Cct	Tct	38	38	B.1.617.2	0.000143
ORF7a	68	P68del	CCT	---	37	37	AY.45	0.004502
ORF7a	68	P68del	CCT	---	36	36	B.1.1	0.000653
ORF7a	68	P68S	Cct	Tct	35	35	AY.43	0.000155
ORF7a	68	P68del	CCT	---	35	35	AY.54	0.003337
ORF7a	68	P68del	CCT	---	35	35	B.1.1.214	0.001941
ORF7a	68	P68del	CCT	---	35	35	B.1.628	0.012333
ORF7a	68	P68del	CCT	---	35	35	C.37	0.004062
ORF7a	68	P68del	CCT	---	34	34	AY.98	0.002686
ORF7a	68	P68del	CCT	---	33	33	AY.36	0.004891
ORF7a	68	P68del	CCT	---	33	33	AY.37	0.01043
ORF7a	68	P68H	cCt	cAt	32	32	AY.4	0.00005
ORF7a	68	P68del	CCT	---	32	32	AY.7	0.006272
ORF7a	68	P68del	CCT	---	31	31	AY.34	0.003006
ORF7a	68	P68del	CCT	---	31	31	AY.98.1	0.001501
ORF7a	68	P68R	cCt	cGt	28	30	All	0.000005
ORF7a	68	P68R	cCT	cGA	1	30	All	0
ORF7a	68	P68R	cCT	cGC	1	30	All	0
ORF7a	68	P68del	CCT	---	30	30	AY.5.4	0.008301
ORF7a	68	P68del	CCT	---	30	30	AY.99.2	0.002765
ORF7a	68	P68del	CCT	---	29	29	AY.118	0.001817
ORF7a	68	P68S	Cct	Tct	29	29	AY.44	0.000177
ORF7a	68	P68H	cCt	cAt	29	29	P.1	0.000457
ORF7a	68	P68del2	CCt	--t	28	28	AY.60	0.026266
ORF7a	68	P68del	CCT	---	28	28	AY.7.2	0.01566
ORF7a	68	P68T	Cct	Act	25	26	All	0.000005
ORF7a	68	P68T	CcT	AcA	1	26	All	0
ORF7a	68	P68S	Cct	Tct	26	26	AY.4.2	0.000564
ORF7a	68	P68del	CCT	---	26	26	AY.9	0.001757
ORF7a	68	P68L	cCt	cTt	26	26	B.1.2	0.000229
ORF7a	68	P68del	CCT	---	25	25	AY.110	0.002817
ORF7a	68	P68del	CCT	---	25	25	AY.114	0.005778
ORF7a	68	P68del	CCT	---	25	25	AY.121	0.003383
ORF7a	68	P68del	CCT	---	25	25	B.1.1.519	0.000993
ORF7a	68	P68del	CCT	---	25	25	B.1.596	0.002178
ORF7a	68	P68C	CCt	TGt	24	24	All	0.000005
ORF7a	68	P68L	cCt	cTt	24	24	AY.25	0.000144
ORF7a	68	P68V	CCT	GTC	20	23	All	0.000004
ORF7a	68	P68V	CCt	GTt	3	23	All	0.000001
ORF7a	68	P68del	CCT	---	22	22	AY.9.1	0.001842
ORF7a	68	P68del	CCT	---	22	22	B.1.427	0.001111
ORF7a	68	P68del	CCT	---	22	22	R.1	0.00198
ORF7a	68	P68del	CCT	---	21	21	AY.9.2	0.000771
ORF7a	68	P68del	CCT	---	20	20	AY.106	0.006698
ORF7a	68	P68H	cCt	cAt	20	20	B.1.617.2	0.000075
ORF7a	68	P68del	CCT	---	19	19	AY.35	0.004428
ORF7a	68	P68del1	ccT	cc-	17	19	AY.44	0.000103
ORF7a	68	P68del1	Cct	-ct	2	19	AY.44	0.000012
ORF7a	68	P68P	ccT	ccG	11	19	AY.5	0.000227
ORF7a	68	P68P	ccT	ccC	8	19	AY.5	0.000165
ORF7a	68	P68del	CCT	---	19	19	AY.61	0.001991
ORF7a	68	P68P	ccT	ccG	19	19	AY.9.2	0.000698
ORF7a	68	P68S	Cct	Tct	19	19	AY.98.1	0.00092
ORF7a	68	P68P	ccT	ccC	18	18	AY.119	0.000636
ORF7a	68	P68del	CCT	---	17	17	AY.30	0.006727
ORF7a	68	P68S	Cct	Tct	16	16	B.1.1	0.00029
ORF7a	68	P68P	ccT	ccC	15	16	B.1.1.222	0.00306
ORF7a	68	P68P	ccT	ccA	1	16	B.1.1.222	0.000204
ORF7a	68	P68P	ccT	ccC	16	16	B.1.1.261	0.137931
ORF7a	68	P68del	CCT	---	15	15	AY.111	0.002747
ORF7a	68	P68del	CCT	---	15	15	AY.120.1	0.004815
ORF7a	68	P68del	CCT	---	15	15	AY.87	0.01249
ORF7a	68	P68S	Cct	Tct	15	15	B.1.525	0.001697
ORF7a	68	P68L	cCt	cTt	14	14	AY.47	0.000435
ORF7a	68	P68P	ccT	ccC	11	14	B.1	0.000101
ORF7a	68	P68P	ccT	ccA	3	14	B.1	0.000027
ORF7a	68	P68del	CCT	---	14	14	B.1.1.258	0.045603
ORF7a	68	P68del	CCT	---	13	13	AY.116	0.003728
ORF7a	68	P68del	CCT	---	13	13	AY.68	0.003559
ORF7a	68	P68S	Cct	Tct	13	13	B.1.526	0.000306
ORF7a	68	P68del	CCT	---	13	13	P.1.14	0.000621
ORF7a	68	P68del	CCT	---	12	12	AY.12	0.003793
ORF7a	68	P68del	CCT	---	12	12	AY.14	0.001056
ORF7a	68	P68del	CCT	---	12	12	AY.46.2	0.007624
ORF7a	68	P68del	CCT	---	12	12	AY.84	0.005249
ORF7a	68	P68del	CCT	---	12	12	AY.99	0.012592
ORF7a	68	P68del	CCT	---	12	12	B.1.324	0.019262
ORF7a	68	P68A	Cct	Gct	9	11	All	0.000002
ORF7a	68	P68A	CcT	GcC	1	11	All	0
ORF7a	68	P68A	CcT	GcA	1	11	All	0
ORF7a	68	P68L	cCt	cTt	11	11	AY.103	0.000068
ORF7a	68	P68del	CCT	---	11	11	B.1.177.15	0.00694
ORF7a	68	P68S	Cct	Tct	11	11	B.1.177.16	0.007309
ORF7a	68	P68del	CCT	---	11	11	B.1.234	0.001451
ORF7a	68	P68del	CCT	---	11	11	Q.8	0.001814
ORF7a	68	P68R	cCt	cGt	11	11	R.1	0.00099
ORF7a	68	P68del	CCT	---	10	10	AY.13	0.00161
ORF7a	68	P68S	Cct	Tct	10	10	AY.25	0.00006
ORF7a	68	P68C	CCt	TGt	10	10	AY.3.1	0.000853
ORF7a	68	P68L	cCt	cTt	9	10	AY.44	0.000055
ORF7a	68	P68L	cCT	cTG	1	10	AY.44	0.000006
ORF7a	68	P68del	CCT	---	10	10	AY.46.5	0.001984
ORF7a	68	P68del	CCT	---	10	10	AY.71	0.004751
ORF7a	68	P68del	CCT	---	10	10	B.1.525	0.001132
ORF7a	68	P68H	cCt	cAt	9	9	AY.102	0.000239
ORF7a	68	P68P	ccT	ccC	9	9	AY.115	0.046875
ORF7a	68	P68L	cCt	cTt	9	9	AY.3	0.00009
ORF7a	68	P68del	CCT	---	9	9	AY.4.2.1	0.001341
ORF7a	68	P68del	CCT	---	9	9	AY.7.1	0.001014
ORF7a	68	P68del	CCT	---	9	9	AY.74	0.001041
ORF7a	68	P68S	Cct	Tct	9	9	B.1.2	0.000079
ORF7a	68	P68P	ccT	ccG	6	9	B.1.2	0.000053
ORF7a	68	P68P	ccT	ccA	2	9	B.1.2	0.000018
ORF7a	68	P68P	ccT	ccC	1	9	B.1.2	0.000009
ORF7a	68	P68del	CCT	---	9	9	B.1.258.9	0.045
ORF7a	68	P68L	cCt	cTt	9	9	B.1.621	0.000797
ORF7a	68	P68del	CCT	---	9	9	L.1	0.017143
ORF7a	68	P68S	Cct	Tct	9	9	P.1	0.000142
ORF7a	68	P68del	CCT	---	8	8	AY.10	0.00424
ORF7a	68	P68del	CCT	---	8	8	AY.4.5	0.00086
ORF7a	68	P68del	CCT	---	8	8	B.1.1.231	0.024768
ORF7a	68	P68L	cCt	cTt	8	8	P.1	0.000126
ORF7a	68	P68del	CCT	---	8	8	P.1.15	0.001859
ORF7a	68	P68del	CCT	---	7	7	AY.19	0.007982
ORF7a	68	P68del2	CCt	--t	6	7	AY.25	0.000036
ORF7a	68	P68del2	CCT	--N	1	7	AY.25	0.000006
ORF7a	68	P68P	ccT	ccC	7	7	AY.3	0.00007
ORF7a	68	P68del	CCT	---	7	7	AY.34.1	0.00357
ORF7a	68	P68del	CCT	---	7	7	AY.49	0.022364
ORF7a	68	P68del	CCT	---	7	7	AY.59	0.003708
ORF7a	68	P68L	cCt	cTt	7	7	B.1.240	0.001509
ORF7a	68	P68del	CCT	---	7	7	B.1.243	0.000487
ORF7a	68	P68P	ccT	ccC	6	6	AY.100	0.000276
ORF7a	68	P68P	ccT	ccC	4	6	AY.120	0.000149
ORF7a	68	P68P	ccT	ccG	2	6	AY.120	0.000074
ORF7a	68	P68S	Cct	Tct	6	6	AY.120.1	0.001926
ORF7a	68	P68del	CCT	---	6	6	AY.16	0.002278
ORF7a	68	P68del	CCT	---	6	6	AY.29.1	0.001323
ORF7a	68	P68L	cCt	cTt	6	6	AY.39.1	0.000238
ORF7a	68	P68del	CCT	---	6	6	AY.40	0.005786
ORF7a	68	P68L	cCt	cTt	6	6	AY.46.5	0.00119
ORF7a	68	P68del	CCT	---	6	6	AY.65	0.003198
ORF7a	68	P68del	CCT	---	6	6	AY.73	0.003992
ORF7a	68	P68L	cCt	cTt	6	6	AY.99.2	0.000553
ORF7a	68	P68L	cCt	cTt	6	6	B.1.1	0.000109
ORF7a	68	P68del	CCT	---	6	6	B.1.1.33	0.002525
ORF7a	68	P68H	cCt	cAt	6	6	B.1.1.7	0.000005
ORF7a	68	P68del1	Cct	-ct	5	6	B.1.1.7	0.000004
ORF7a	68	P68del1	ccT	cc-	1	6	B.1.1.7	0.000001
ORF7a	68	P68del	CCT	---	6	6	B.1.214.2	0.003597
ORF7a	68	P68del	CCT	---	5	5	A	0.001935
ORF7a	68	P68F	CCt	TTt	4	5	All	0.000001
ORF7a	68	P68F	CCT	TTC	1	5	All	0
ORF7a	68	P68S	Cct	Tct	5	5	AY.102	0.000133
ORF7a	68	P68del	CCT	---	5	5	AY.109	0.003698
ORF7a	68	P68L	cCt	cTt	5	5	AY.20	0.000194
ORF7a	68	P68del	CCT	---	5	5	AY.24	0.002155
ORF7a	68	P68del	CCT	---	5	5	AY.27	0.000324
ORF7a	68	P68del	CCT	---	5	5	AY.46.1	0.005133
ORF7a	68	P68del	CCT	---	5	5	AY.62	0.002179
ORF7a	68	P68del	CCT	---	5	5	AY.80	0.005643
ORF7a	68	P68S	Cct	Tct	5	5	AY.9.2	0.000184
ORF7a	68	P68del	CCT	---	5	5	AY.91	0.003652
ORF7a	68	P68del	CCT	---	5	5	AY.95	0.003805
ORF7a	68	P68S	Cct	Tct	5	5	B.1	0.000046
ORF7a	68	P68L	cCt	cTt	4	5	B.1	0.000037
ORF7a	68	P68L	cCT	cTA	1	5	B.1	0.000009
ORF7a	68	P68del	CCT	---	5	5	B.1.1.56	0.089286
ORF7a	68	P68T	Cct	Act	5	5	B.1.1.7	0.000004
ORF7a	68	P68P	ccT	ccC	5	5	B.1.177	0.000066
ORF7a	68	P68del	CCT	---	5	5	B.1.375	0.004098
ORF7a	68	P68S	Cct	Tct	5	5	B.1.438.1	0.000536
ORF7a	68	P68del	CCT	---	5	5	B.1.595	0.001305
ORF7a	68	P68del	CCT	---	5	5	B.1.623	0.002682
ORF7a	68	P68del	CCT	---	5	5	B.1.70	0.121951
ORF7a	68	P68P	ccT	ccG	3	5	P.1	0.000047
ORF7a	68	P68P	ccT	ccA	1	5	P.1	0.000016
ORF7a	68	P68P	ccT	ccC	1	5	P.1	0.000016
ORF7a	68	P68S	Cct	Tct	5	5	P.1.14	0.000239
ORF7a	68	P68del	CCT	---	5	5	P.1.7	0.001596
ORF7a	68	P68del	CCT	---	5	5	P.2	0.000933
ORF7a	68	P68del	CCT	---	5	5	Q.1	0.000632
ORF7a	68	P68L	cCT	cTG	2	4		0.111111
ORF7a	68	P68L	cCT	cTC	1	4		0.055556
ORF7a	68	P68L	cCt	cTt	1	4		0.055556
ORF7a	68	P68G	CCT	GGC	2	4	All	0
ORF7a	68	P68G	CCT	GGA	1	4	All	0
ORF7a	68	P68G	CCt	GGt	1	4	All	0
ORF7a	68	P68P	ccT	ccC	4	4	AY.116	0.001147
ORF7a	68	P68L	cCt	cTt	4	4	AY.119	0.000141
ORF7a	68	P68H	cCt	cAt	4	4	AY.120	0.000149
ORF7a	68	P68del	CCT	---	4	4	AY.120.2	0.005141
ORF7a	68	P68del	CCT	---	4	4	AY.2	0.001425
ORF7a	68	P68S	Cct	Tct	4	4	AY.20	0.000155
ORF7a	68	P68H	cCt	cAt	4	4	AY.23	0.000279
ORF7a	68	P68H	cCt	cAt	4	4	AY.3	0.00004
ORF7a	68	P68L	cCt	cTt	4	4	AY.39	0.000099
ORF7a	68	P68del	CCT	---	4	4	AY.5.2	0.009852
ORF7a	68	P68del	CCT	---	4	4	AY.5.3	0.00135
ORF7a	68	P68L	cCt	cTt	4	4	AY.52	0.003257
ORF7a	68	P68del	CCT	---	4	4	AY.66	0.004278
ORF7a	68	P68L	cCt	cTt	4	4	AY.75	0.000224
ORF7a	68	P68del	CCT	---	4	4	AY.88	0.003537
ORF7a	68	P68del	CCT	---	4	4	AY.92	0.001149
ORF7a	68	P68del	CCT	---	4	4	AY.93	0.001092
ORF7a	68	P68del	CCT	---	4	4	B.1.1.1	0.001307
ORF7a	68	P68del	CCT	---	4	4	B.1.1.164	0.020619
ORF7a	68	P68del	CCT	---	4	4	B.1.1.37	0.000771
ORF7a	68	P68L	cCt	cTt	4	4	B.1.160.30	0.011905
ORF7a	68	P68S	Cct	Tct	4	4	B.1.177	0.000053
ORF7a	68	P68P	ccT	ccC	4	4	B.1.240	0.000862
ORF7a	68	P68del	CCT	---	4	4	B.1.258	0.000266
ORF7a	68	P68L	cCt	cTt	4	4	B.1.351	0.000119
ORF7a	68	P68del	CCT	---	4	4	B.1.351.2	0.00121
ORF7a	68	P68del	CCT	---	4	4	B.1.36	0.000584
ORF7a	68	P68del	CCT	---	4	4	B.1.466.2	0.001565
ORF7a	68	P68del	CCT	---	4	4	B.1.577	0.002749
ORF7a	68	P68del1	Cct	-ct	4	4	B.1.617.2	0.000015
ORF7a	68	P68S	Cct	Tct	4	4	B.1.621	0.000354
ORF7a	68	P68del	CCT	---	4	4	D.2	0.0003
ORF7a	68	P68Q	cCT	cAA	3	3	All	0.000001
ORF7a	68	P68L	cCt	cTt	3	3	AY.102	0.00008
ORF7a	68	P68del	CCT	---	3	3	AY.105	0.001929
ORF7a	68	P68del	CCT	---	3	3	AY.116.1	0.000934
ORF7a	68	P68S	Cct	Tct	3	3	AY.120	0.000112
ORF7a	68	P68P	ccT	ccC	3	3	AY.20	0.000117
ORF7a	68	P68R	cCt	cGt	3	3	AY.25	0.000018
ORF7a	68	P68L	cCt	cTt	3	3	AY.29	0.000047
ORF7a	68	P68del2	CCt	--t	3	3	AY.3	0.00003
ORF7a	68	P68L	cCt	cTt	3	3	AY.36	0.000445
ORF7a	68	P68del2	CCt	--t	3	3	AY.39.1	0.000119
ORF7a	68	P68T	Cct	Act	3	3	AY.4	0.000005
ORF7a	68	P68H	cCt	cAt	2	3	AY.43	0.000009
ORF7a	68	P68del1	Cct	-ct	2	3	AY.43	0.000009
ORF7a	68	P68del1	CCT	NT-	1	3	AY.43	0.000004
ORF7a	68	P68G	CCt	GGt	1	3	AY.43	0.000004
ORF7a	68	P68R	cCt	cGt	1	3	AY.43	0.000004
ORF7a	68	P68G	CCT	GGA	1	3	AY.43	0.000004
ORF7a	68	P68A	CcT	GcC	1	3	AY.43	0.000004
ORF7a	68	P68H	cCT	cAC	1	3	AY.43	0.000004
ORF7a	68	P68A	CcT	GcA	1	3	AY.43	0.000004
ORF7a	68	P68R	cCT	cGC	1	3	AY.43	0.000004
ORF7a	68	P68R	cCT	cGA	1	3	AY.43	0.000004
ORF7a	68	P68G	CCT	GGC	1	3	AY.43	0.000004
ORF7a	68	P68A	Cct	Gct	1	3	AY.43	0.000004
ORF7a	68	P68H	cCt	cAt	3	3	AY.44	0.000018
ORF7a	68	P68del1	Cct	-ct	1	3	AY.46.6	0.000072
ORF7a	68	P68del1	ccT	cc-	1	3	AY.46.6	0.000072
ORF7a	68	P68del1	CCt	-Gt	1	3	AY.46.6	0.000072
ORF7a	68	P68del	CCT	---	3	3	AY.48	0.001395
ORF7a	68	P68T	Cct	Act	3	3	AY.5	0.000062
ORF7a	68	P68del	CCT	---	3	3	AY.64	0.001786
ORF7a	68	P68del	CCT	---	3	3	AY.69	0.00056
ORF7a	68	P68S	Cct	Tct	3	3	AY.73	0.001996
ORF7a	68	P68del	CCT	---	3	3	AY.85	0.001282
ORF7a	68	P68del	CCT	---	3	3	AY.90	0.002053
ORF7a	68	P68H	cCt	cAt	3	3	AY.92	0.000862
ORF7a	68	P68V	CCT	GTC	3	3	B.1.1	0.000054
ORF7a	68	P68del	CCT	---	3	3	B.1.1.121	0.007282
ORF7a	68	P68del	CCT	---	3	3	B.1.1.189	0.004539
ORF7a	68	P68del	CCT	---	3	3	B.1.1.222	0.000612
ORF7a	68	P68del	CCT	---	3	3	B.1.1.25	0.001706
ORF7a	68	P68del	CCT	---	3	3	B.1.1.318	0.000905
ORF7a	68	P68R	cCt	cGt	3	3	B.1.1.7	0.000003
ORF7a	68	P68del	CCT	---	3	3	B.1.177.57	0.000843
ORF7a	68	P68del	CCT	---	3	3	B.1.177.6	0.00293
ORF7a	68	P68del	CCT	---	3	3	B.1.177.7	0.000495
ORF7a	68	P68del	CCT	---	3	3	B.1.221	0.000213
ORF7a	68	P68del	CCT	---	3	3	B.1.258.17	0.000312
ORF7a	68	P68del	CCT	---	3	3	B.1.311	0.000824
ORF7a	68	P68V	CCT	GTC	3	3	B.1.36.1	0.003421
ORF7a	68	P68del	CCT	---	3	3	B.1.36.36	0.001806
ORF7a	68	P68del	CCT	---	3	3	B.1.369	0.000856
ORF7a	68	P68P	ccT	ccC	3	3	B.1.466.2	0.001174
ORF7a	68	P68del	CCT	---	3	3	B.1.575	0.00091
ORF7a	68	P68del	CCT	---	3	3	B.1.617.1	0.000387
ORF7a	68	P68del	CCT	---	3	3	B.1.626	0.017143
ORF7a	68	P68S	Cct	Tct	1	2		0.055556
ORF7a	68	P68S	CcT	TcC	1	2		0.055556
ORF7a	68	P68F	CCt	TTt	1	2		0.055556
ORF7a	68	P68F	CCT	TTC	1	2		0.055556
ORF7a	68	P68del	CCT	---	2	2	A.28	0.005291
ORF7a	68	P68del	CCT	---	2	2	AD.2	0.000438
ORF7a	68	P68I	CCt	ATt	2	2	All	0
ORF7a	68	P68D	CCt	GAt	1	2	All	0
ORF7a	68	P68D	CCT	GAC	1	2	All	0
ORF7a	68	P68X	CCT	TGA	1	2	All	0
ORF7a	68	P68X	CCT	TAA	1	2	All	0
ORF7a	68	P68del	CCT	---	2	2	AY.1	0.000791
ORF7a	68	P68L	cCt	cTt	2	2	AY.100	0.000092
ORF7a	68	P68del	CCT	---	2	2	AY.101	0.000981
ORF7a	68	P68P	ccT	ccC	1	2	AY.102	0.000027
ORF7a	68	P68P	ccT	ccA	1	2	AY.102	0.000027
ORF7a	68	P68C	CCt	TGt	2	2	AY.103	0.000012
ORF7a	68	P68del1	Cct	-ct	2	2	AY.103	0.000012
ORF7a	68	P68H	cCt	cAt	2	2	AY.103	0.000012
ORF7a	68	P68P	ccT	ccC	1	2	AY.103	0.000006
ORF7a	68	P68del2	cCT	c--	1	2	AY.103	0.000006
ORF7a	68	P68del2	CCt	--t	1	2	AY.103	0.000006
ORF7a	68	P68P	ccT	ccA	1	2	AY.103	0.000006
ORF7a	68	P68del	CCT	---	2	2	AY.108	0.002205
ORF7a	68	P68L	cCt	cTt	2	2	AY.120	0.000074
ORF7a	68	P68del	CCT	---	2	2	AY.22	0.004184
ORF7a	68	P68L	cCt	cTt	2	2	AY.23	0.000139
ORF7a	68	P68T	Cct	Act	2	2	AY.24	0.000862
ORF7a	68	P68del1	CCT	-NN	1	2	AY.25	0.000006
ORF7a	68	P68del1	Cct	-ct	1	2	AY.25	0.000006
ORF7a	68	P68S	Cct	Tct	2	2	AY.26	0.000057
ORF7a	68	P68del2	CCt	--t	2	2	AY.26	0.000057
ORF7a	68	P68C	CCt	TGt	2	2	AY.29	0.000032
ORF7a	68	P68del	CCT	---	2	2	AY.38	0.000999
ORF7a	68	P68del2	CCt	--t	2	2	AY.39	0.000049
ORF7a	68	P68P	ccT	ccC	2	2	AY.39	0.000049
ORF7a	68	P68del2	CCT	--N	1	2	AY.4	0.000002
ORF7a	68	P68del2	CCt	--t	1	2	AY.4	0.000002
ORF7a	68	P68P	ccT	ccC	1	2	AY.4.2.1	0.000149
ORF7a	68	P68P	ccT	ccA	1	2	AY.4.2.1	0.000149
ORF7a	68	P68del	CCT	---	2	2	AY.4.4	0.000818
ORF7a	68	P68del	CCT	---	2	2	AY.41	0.000588
ORF7a	68	P68del2	CCt	--t	2	2	AY.43	0.000009
ORF7a	68	P68D	CCt	GAt	1	2	AY.43	0.000004
ORF7a	68	P68D	CCT	GAC	1	2	AY.43	0.000004
ORF7a	68	P68del2	cCT	c--	1	2	AY.44	0.000006
ORF7a	68	P68del2	CCt	--t	1	2	AY.44	0.000006
ORF7a	68	P68P	ccT	ccC	2	2	AY.45	0.000243
ORF7a	68	P68P	ccT	ccC	2	2	AY.47	0.000062
ORF7a	68	P68del	CCT	---	2	2	AY.51	0.001818
ORF7a	68	P68del	CCT	---	2	2	AY.52	0.001629
ORF7a	68	P68del	CCT	---	2	2	AY.53	0.000575
ORF7a	68	P68S	Cct	Tct	2	2	AY.58	0.001815
ORF7a	68	P68P	ccT	ccC	2	2	AY.61	0.00021
ORF7a	68	P68del	CCT	---	2	2	AY.70	0.000417
ORF7a	68	P68P	ccT	ccC	2	2	AY.75	0.000112
ORF7a	68	P68del	CCT	---	2	2	AY.75.1	0.000361
ORF7a	68	P68del	CCT	---	2	2	AY.79	0.002421
ORF7a	68	P68del	CCT	---	2	2	AY.8	0.001212
ORF7a	68	P68S	Cct	Tct	2	2	AY.81	0.003984
ORF7a	68	P68del	CCT	---	2	2	AY.82	0.002714
ORF7a	68	P68L	cCt	cTt	2	2	AY.9.2	0.000073
ORF7a	68	P68del	CCT	---	2	2	AZ.2	0.001642
ORF7a	68	P68H	cCt	cAt	2	2	B.1	0.000018
ORF7a	68	P68del	CCT	---	2	2	B.1.1.101	0.02
ORF7a	68	P68del	CCT	---	2	2	B.1.1.163	0.015267
ORF7a	68	P68del	CCT	---	2	2	B.1.1.170	0.002494
ORF7a	68	P68del	CCT	---	2	2	B.1.1.192	0.004619
ORF7a	68	P68P	ccT	ccC	1	2	B.1.1.214	0.000055
ORF7a	68	P68P	ccT	ccA	1	2	B.1.1.214	0.000055
ORF7a	68	P68del	CCT	---	2	2	B.1.1.220	0.003717
ORF7a	68	P68del	CCT	---	2	2	B.1.1.265	0.006309
ORF7a	68	P68del	CCT	---	2	2	B.1.1.303	0.005525
ORF7a	68	P68del	CCT	---	2	2	B.1.1.311	0.000716
ORF7a	68	P68del	CCT	---	2	2	B.1.1.317	0.000823
ORF7a	68	P68del	CCT	---	2	2	B.1.1.372	0.001377
ORF7a	68	P68del	CCT	---	2	2	B.1.1.432	0.002532
ORF7a	68	P68L	cCt	cTt	2	2	B.1.1.519	0.000079
ORF7a	68	P68del	CCT	---	2	2	B.1.1.521	0.010695
ORF7a	68	P68V	CCT	GTC	2	2	B.1.1.7	0.000002
ORF7a	68	P68C	CCt	TGt	2	2	B.1.1.7	0.000002
ORF7a	68	P68S	Cct	Tct	2	2	B.1.110.3	0.001437
ORF7a	68	P68del	CCT	---	2	2	B.1.128	0.001271
ORF7a	68	P68del	CCT	---	2	2	B.1.139	0.001466
ORF7a	68	P68C	CCt	TGt	2	2	B.1.160	0.000062
ORF7a	68	P68del	CCT	---	2	2	B.1.160.16	0.001859
ORF7a	68	P68del	CCT	---	2	2	B.1.160.30	0.005952
ORF7a	68	P68del	CCT	---	2	2	B.1.177.10	0.001756
ORF7a	68	P68del	CCT	---	2	2	B.1.177.4	0.000422
ORF7a	68	P68del	CCT	---	2	2	B.1.177.55	0.004662
ORF7a	68	P68del	CCT	---	2	2	B.1.177.81	0.000379
ORF7a	68	P68del	CCT	---	2	2	B.1.177.82	0.000955
ORF7a	68	P68del	CCT	---	2	2	B.1.177.86	0.000367
ORF7a	68	P68del	CCT	---	2	2	B.1.190	0.02
ORF7a	68	P68P	ccT	ccA	2	2	B.1.221.1	0.005814
ORF7a	68	P68S	Cct	Tct	2	2	B.1.221.4	0.008333
ORF7a	68	P68S	Cct	Tct	2	2	B.1.234	0.000264
ORF7a	68	P68del	CCT	---	2	2	B.1.240	0.000431
ORF7a	68	P68S	Cct	Tct	2	2	B.1.243	0.000139
ORF7a	68	P68del	CCT	---	2	2	B.1.258.11	0.000793
ORF7a	68	P68del	CCT	---	2	2	B.1.349	0.00143
ORF7a	68	P68V	CCT	GTC	2	2	B.1.351	0.000059
ORF7a	68	P68del	CCT	---	2	2	B.1.356	0.003454
ORF7a	68	P68del	CCT	---	2	2	B.1.36.9	0.006431
ORF7a	68	P68del	CCT	---	2	2	B.1.396	0.001411
ORF7a	68	P68S	Cct	Tct	2	2	B.1.439	0.011834
ORF7a	68	P68del	CCT	---	2	2	B.1.499	0.002101
ORF7a	68	P68del	CCT	---	2	2	B.1.561	0.000794
ORF7a	68	P68S	Cct	Tct	2	2	B.1.582	0.000981
ORF7a	68	P68S	CcT	TcA	1	2	B.1.617.1	0.000129
ORF7a	68	P68S	Cct	Tct	1	2	B.1.617.1	0.000129
ORF7a	68	P68V	CCt	GTt	2	2	B.1.617.2	0.000008
ORF7a	68	P68T	CcT	AcA	1	2	B.1.617.2	0.000004
ORF7a	68	P68T	Cct	Act	1	2	B.1.617.2	0.000004
ORF7a	68	P68del	CCT	---	2	2	B.1.621.1	0.001012
ORF7a	68	P68del	CCT	---	2	2	C.36.3	0.001134
ORF7a	68	P68del	CCT	---	2	2	P.1.1	0.000635
ORF7a	68	P68del	CCT	---	2	2	P.1.13	0.001797
ORF7a	68	P68del	CCT	---	2	2	P.1.17.1	0.00175
ORF7a	68	P68del	CCT	---	2	2	P.1.2	0.002312
ORF7a	68	P68del	CCT	---	2	2	Q.4	0.00091
ORF7a	68	P68P	ccT	ccC	2	2	Q.8	0.00033
ORF7a	68	P68P	ccT	ccC	1	1		0.055556
ORF7a	68	P68del	CCT	---	1	1	A.1	0.000282
ORF7a	68	P68P	ccT	ccC	1	1	A.1	0.000282
ORF7a	68	P68T	Cct	Act	1	1	A.1	0.000282
ORF7a	68	P68P	ccT	ccC	1	1	A.2.2	0.001689
ORF7a	68	P68L	cCt	cTt	1	1	A.2.5	0.000499
ORF7a	68	P68del	CCT	---	1	1	A.2.5	0.000499
ORF7a	68	P68del	CCT	---	1	1	A.23	0.010526
ORF7a	68	P68del	CCT	---	1	1	A.23.1	0.000704
ORF7a	68	P68del2	cCT	c--	1	1	AA.2	0.007692
ORF7a	68	P68Y	CCt	TAt	1	1	All	0
ORF7a	68	P68K	CCT	AAA	1	1	All	0
ORF7a	68	P68E	CCT	GAA	1	1	All	0
ORF7a	68	P68L	cCt	cTt	1	1	AU.2	0.002421
ORF7a	68	P68del	CCT	---	1	1	AU.3	0.00211
ORF7a	68	P68S	Cct	Tct	1	1	AY.100	0.000046
ORF7a	68	P68A	Cct	Gct	1	1	AY.102	0.000027
ORF7a	68	P68T	Cct	Act	1	1	AY.103	0.000006
ORF7a	68	P68del	CCT	---	1	1	AY.104	0.001984
ORF7a	68	P68R	cCt	cGt	1	1	AY.108	0.001103
ORF7a	68	P68del1	Cct	-ct	1	1	AY.108	0.001103
ORF7a	68	P68L	cCt	cTt	1	1	AY.11	0.001339
ORF7a	68	P68S	Cct	Tct	1	1	AY.110	0.000113
ORF7a	68	P68L	cCt	cTt	1	1	AY.111	0.000183
ORF7a	68	P68S	Cct	Tct	1	1	AY.114	0.000231
ORF7a	68	P68del2	CCt	--t	1	1	AY.114	0.000231
ORF7a	68	P68del1	ccT	cc-	1	1	AY.117	0.000085
ORF7a	68	P68S	Cct	Tct	1	1	AY.118	0.000063
ORF7a	68	P68S	Cct	Tct	1	1	AY.119	0.000035
ORF7a	68	P68del	CCT	---	1	1	AY.120.2.1	0.000498
ORF7a	68	P68R	cCt	cGt	1	1	AY.121	0.000135
ORF7a	68	P68L	cCt	cTt	1	1	AY.13	0.000161
ORF7a	68	P68C	CCt	TGt	1	1	AY.16	0.00038
ORF7a	68	P68del1	Cct	-ct	1	1	AY.20	0.000039
ORF7a	68	P68P	ccT	ccC	1	1	AY.23	0.00007
ORF7a	68	P68del1	Cct	-ct	1	1	AY.23	0.00007
ORF7a	68	P68del	CCT	---	1	1	AY.23.1	0.000417
ORF7a	68	P68P	ccT	ccC	1	1	AY.23.1	0.000417
ORF7a	68	P68L	cCt	cTt	1	1	AY.24	0.000431
ORF7a	68	P68T	Cct	Act	1	1	AY.25	0.000006
ORF7a	68	P68A	Cct	Gct	1	1	AY.25	0.000006
ORF7a	68	P68P	ccT	ccC	1	1	AY.26	0.000028
ORF7a	68	P68P	ccT	ccC	1	1	AY.27	0.000065
ORF7a	68	P68del	CCT	---	1	1	AY.28	0.00189
ORF7a	68	P68P	ccT	ccG	1	1	AY.29	0.000016
ORF7a	68	P68del1	Cct	-ct	1	1	AY.3	0.00001
ORF7a	68	P68H	cCt	cAt	1	1	AY.3.1	0.000085
ORF7a	68	P68H	cCt	cAt	1	1	AY.32	0.000532
ORF7a	68	P68del	CCT	---	1	1	AY.32	0.000532
ORF7a	68	P68P	ccT	ccC	1	1	AY.33	0.000067
ORF7a	68	P68S	Cct	Tct	1	1	AY.33	0.000067
ORF7a	68	P68del2	CCt	--t	1	1	AY.33	0.000067
ORF7a	68	P68L	cCt	cTt	1	1	AY.34	0.000097
ORF7a	68	P68L	cCt	cTt	1	1	AY.34.1	0.00051
ORF7a	68	P68del2	CCT	--N	1	1	AY.36	0.000148
ORF7a	68	P68L	cCt	cTt	1	1	AY.37	0.000316
ORF7a	68	P68R	cCt	cGt	1	1	AY.37	0.000316
ORF7a	68	P68S	CcT	TcC	1	1	AY.39	0.000025
ORF7a	68	P68I	CCt	ATt	1	1	AY.39	0.000025
ORF7a	68	P68G	CCT	GGC	1	1	AY.39	0.000025
ORF7a	68	P68L	cCt	cTt	1	1	AY.39.2	0.001541
ORF7a	68	P68del	CCT	---	1	1	AY.39.2	0.001541
ORF7a	68	P68R	cCt	cGt	1	1	AY.4	0.000002
ORF7a	68	P68A	Cct	Gct	1	1	AY.4	0.000002
ORF7a	68	P68del1	CCT	-NN	1	1	AY.4	0.000002
ORF7a	68	P68H	cCt	cAt	1	1	AY.4.1	0.000737
ORF7a	68	P68del	CCT	---	1	1	AY.4.1	0.000737
ORF7a	68	P68L	cCt	cTt	1	1	AY.4.2	0.000022
ORF7a	68	P68del	CCT	---	1	1	AY.4.3	0.000842
ORF7a	68	P68P	ccT	ccC	1	1	AY.4.5	0.000107
ORF7a	68	P68L	cCt	cTt	1	1	AY.41	0.000294
ORF7a	68	P68P	ccT	ccC	1	1	AY.42	0.00004
ORF7a	68	P68Q	cCT	cAA	1	1	AY.43	0.000004
ORF7a	68	P68E	CCT	GAA	1	1	AY.43	0.000004
ORF7a	68	P68C	CCt	TGt	1	1	AY.44	0.000006
ORF7a	68	P68T	Cct	Act	1	1	AY.44	0.000006
ORF7a	68	P68L	cCt	cTt	1	1	AY.45	0.000122
ORF7a	68	P68S	Cct	Tct	1	1	AY.46	0.000104
ORF7a	68	P68L	cCt	cTt	1	1	AY.46	0.000104
ORF7a	68	P68P	ccT	ccC	1	1	AY.46.2	0.000635
ORF7a	68	P68L	cCt	cTt	1	1	AY.46.4	0.000165
ORF7a	68	P68S	Cct	Tct	1	1	AY.46.4	0.000165
ORF7a	68	P68L	cCt	cTt	1	1	AY.46.6	0.000072
ORF7a	68	P68del2	CCt	--t	1	1	AY.46.6	0.000072
ORF7a	68	P68R	cCt	cGt	1	1	AY.46.6	0.000072
ORF7a	68	P68C	CCt	TGt	1	1	AY.47	0.000031
ORF7a	68	P68S	Cct	Tct	1	1	AY.5	0.000021
ORF7a	68	P68H	cCt	cAt	1	1	AY.5	0.000021
ORF7a	68	P68del2	CCt	--t	1	1	AY.5	0.000021
ORF7a	68	P68L	cCt	cTt	1	1	AY.5.3	0.000337
ORF7a	68	P68S	Cct	Tct	1	1	AY.5.3	0.000337
ORF7a	68	P68S	Cct	Tct	1	1	AY.5.4	0.000277
ORF7a	68	P68A	Cct	Gct	1	1	AY.5.4	0.000277
ORF7a	68	P68del	CCT	---	1	1	AY.50	0.000799
ORF7a	68	P68V	CCt	GTt	1	1	AY.54	0.000095
ORF7a	68	P68R	cCt	cGt	1	1	AY.6	0.000041
ORF7a	68	P68L	cCt	cTt	1	1	AY.61	0.000105
ORF7a	68	P68H	cCt	cAt	1	1	AY.61	0.000105
ORF7a	68	P68del	CCT	---	1	1	AY.63	0.000387
ORF7a	68	P68H	cCt	cAt	1	1	AY.65	0.000533
ORF7a	68	P68del1	Cct	-ct	1	1	AY.65	0.000533
ORF7a	68	P68del	CCT	---	1	1	AY.67	0.000464
ORF7a	68	P68P	ccT	ccG	1	1	AY.67	0.000464
ORF7a	68	P68S	Cct	Tct	1	1	AY.7	0.000196
ORF7a	68	P68C	CCt	TGt	1	1	AY.7.1	0.000113
ORF7a	68	P68P	ccT	ccA	1	1	AY.72	0.001361
ORF7a	68	P68L	cCt	cTt	1	1	AY.74	0.000116
ORF7a	68	P68del1	ccT	cc-	1	1	AY.74	0.000116
ORF7a	68	P68P	ccT	ccA	1	1	AY.75.1	0.00018
ORF7a	68	P68del	CCT	---	1	1	AY.78	0.001541
ORF7a	68	P68del	CCT	---	1	1	AY.81	0.001992
ORF7a	68	P68H	cCt	cAt	1	1	AY.84	0.000437
ORF7a	68	P68S	CcT	TcG	1	1	AY.85	0.000427
ORF7a	68	P68L	cCt	cTt	1	1	AY.85	0.000427
ORF7a	68	P68del	CCT	---	1	1	AY.89	0.004902
ORF7a	68	P68H	cCt	cAt	1	1	AY.9	0.000068
ORF7a	68	P68del1	Cct	-ct	1	1	AY.9.2	0.000037
ORF7a	68	P68H	cCt	cAt	1	1	AY.9.2	0.000037
ORF7a	68	P68L	cCt	cTt	1	1	AY.9.2.1	0.001976
ORF7a	68	P68del	CCT	---	1	1	AY.94	0.000443
ORF7a	68	P68L	cCt	cTt	1	1	AY.98	0.000079
ORF7a	68	P68H	cCt	cAt	1	1	AY.98	0.000079
ORF7a	68	P68P	ccT	ccC	1	1	AY.98	0.000079
ORF7a	68	P68del	CCT	---	1	1	B	0.000128
ORF7a	68	P68T	Cct	Act	1	1	B	0.000128
ORF7a	68	P68L	cCt	cTt	1	1	B	0.000128
ORF7a	68	P68S	Cct	Tct	1	1	B	0.000128
ORF7a	68	P68del2	CCt	--t	1	1	B.1	0.000009
ORF7a	68	P68del1	ccT	cc-	1	1	B.1	0.000009
ORF7a	68	P68X	CCT	TAA	1	1	B.1	0.000009
ORF7a	68	P68V	CCT	GTC	1	1	B.1	0.000009
ORF7a	68	P68F	CCt	TTt	1	1	B.1.1	0.000018
ORF7a	68	P68A	Cct	Gct	1	1	B.1.1	0.000018
ORF7a	68	P68del	CCT	---	1	1	B.1.1.10	0.001115
ORF7a	68	P68del	CCT	---	1	1	B.1.1.123	0.017857
ORF7a	68	P68del	CCT	---	1	1	B.1.1.135	0.004695
ORF7a	68	P68P	ccT	ccC	1	1	B.1.1.135	0.004695
ORF7a	68	P68del	CCT	---	1	1	B.1.1.141	0.002012
ORF7a	68	P68del	CCT	---	1	1	B.1.1.174	0.003378
ORF7a	68	P68L	cCt	cTt	1	1	B.1.1.176	0.000439
ORF7a	68	P68V	CCT	GTC	1	1	B.1.1.189	0.001513
ORF7a	68	P68del	CCT	---	1	1	B.1.1.194	0.00495
ORF7a	68	P68L	cCt	cTt	1	1	B.1.1.198	0.001468
ORF7a	68	P68del	CCT	---	1	1	B.1.1.205	0.003717
ORF7a	68	P68del	CCT	---	1	1	B.1.1.207	0.001182
ORF7a	68	P68del	CCT	---	1	1	B.1.1.209	0.008929
ORF7a	68	P68H	cCt	cAt	1	1	B.1.1.214	0.000055
ORF7a	68	P68S	Cct	Tct	1	1	B.1.1.214	0.000055
ORF7a	68	P68A	Cct	Gct	1	1	B.1.1.214	0.000055
ORF7a	68	P68S	Cct	Tct	1	1	B.1.1.222	0.000204
ORF7a	68	P68del	CCT	---	1	1	B.1.1.241	0.00207
ORF7a	68	P68del	CCT	---	1	1	B.1.1.253	0.002506
ORF7a	68	P68L	cCt	cTt	1	1	B.1.1.274	0.005051
ORF7a	68	P68del	CCT	---	1	1	B.1.1.277	0.000759
ORF7a	68	P68S	Cct	Tct	1	1	B.1.1.279	0.001121
ORF7a	68	P68V	CCT	GTC	1	1	B.1.1.282	0.011628
ORF7a	68	P68S	Cct	Tct	1	1	B.1.1.291	0.000742
ORF7a	68	P68del	CCT	---	1	1	B.1.1.298	0.000862
ORF7a	68	P68del	CCT	---	1	1	B.1.1.301	0.001179
ORF7a	68	P68V	CCT	GTC	1	1	B.1.1.305	0.003861
ORF7a	68	P68H	cCt	cAt	1	1	B.1.1.306	0.000438
ORF7a	68	P68A	Cct	Gct	1	1	B.1.1.326	0.001761
ORF7a	68	P68del	CCT	---	1	1	B.1.1.366	0.015873
ORF7a	68	P68del	CCT	---	1	1	B.1.1.383	0.0625
ORF7a	68	P68del	CCT	---	1	1	B.1.1.39	0.00051
ORF7a	68	P68P	ccT	ccC	1	1	B.1.1.420	0.001006
ORF7a	68	P68del	CCT	---	1	1	B.1.1.437	0.010417
ORF7a	68	P68del	CCT	---	1	1	B.1.1.523	0.001563
ORF7a	68	P68del1	Cct	-ct	1	1	B.1.1.70	0.000341
ORF7a	68	P68del	CCT	---	1	1	B.1.115	0.021739
ORF7a	68	P68L	cCt	cTt	1	1	B.1.160	0.000031
ORF7a	68	P68L	cCt	cTt	1	1	B.1.160.9	0.007194
ORF7a	68	P68R	cCt	cGt	1	1	B.1.177	0.000013
ORF7a	68	P68H	cCt	cAt	1	1	B.1.177	0.000013
ORF7a	68	P68Q	cCT	cAA	1	1	B.1.177	0.000013
ORF7a	68	P68L	cCt	cTt	1	1	B.1.177	0.000013
ORF7a	68	P68V	CCT	GTC	1	1	B.1.177	0.000013
ORF7a	68	P68del	CCT	---	1	1	B.1.177.16	0.000664
ORF7a	68	P68S	Cct	Tct	1	1	B.1.177.18	0.00116
ORF7a	68	P68K	CCT	AAA	1	1	B.1.177.21	0.000076
ORF7a	68	P68P	ccT	ccA	1	1	B.1.177.21	0.000076
ORF7a	68	P68X	CCT	TGA	1	1	B.1.177.21	0.000076
ORF7a	68	P68Q	cCT	cAA	1	1	B.1.177.21	0.000076
ORF7a	68	P68del	CCT	---	1	1	B.1.177.50	0.004695
ORF7a	68	P68P	ccT	ccC	1	1	B.1.177.51	0.004566
ORF7a	68	P68T	Cct	Act	1	1	B.1.177.57	0.000281
ORF7a	68	P68del	CCT	---	1	1	B.1.177.60	0.000218
ORF7a	68	P68del	CCT	---	1	1	B.1.177.62	0.001192
ORF7a	68	P68L	cCt	cTt	1	1	B.1.177.65	0.000665
ORF7a	68	P68L	cCt	cTt	1	1	B.1.177.7	0.000165
ORF7a	68	P68P	ccT	ccC	1	1	B.1.177.79	0.002342
ORF7a	68	P68del	CCT	---	1	1	B.1.177.83	0.001481
ORF7a	68	P68T	Cct	Act	1	1	B.1.2	0.000009
ORF7a	68	P68del1	ccT	cc-	1	1	B.1.2	0.000009
ORF7a	68	P68H	cCt	cAt	1	1	B.1.2	0.000009
ORF7a	68	P68del	CCT	---	1	1	B.1.201	0.005682
ORF7a	68	P68del	CCT	---	1	1	B.1.206	0.000816
ORF7a	68	P68del	CCT	---	1	1	B.1.220	0.01087
ORF7a	68	P68P	ccT	ccA	1	1	B.1.221	0.000071
ORF7a	68	P68L	cCt	cTt	1	1	B.1.221	0.000071
ORF7a	68	P68T	Cct	Act	1	1	B.1.221.4	0.004167
ORF7a	68	P68del	CCT	---	1	1	B.1.236	0.002053
ORF7a	68	P68V	CCT	GTC	1	1	B.1.242	0.018868
ORF7a	68	P68del1	ccT	cc-	1	1	B.1.243	0.00007
ORF7a	68	P68L	cCt	cTt	1	1	B.1.258	0.000067
ORF7a	68	P68S	Cct	Tct	1	1	B.1.258	0.000067
ORF7a	68	P68P	ccT	ccC	1	1	B.1.258.14	0.00098
ORF7a	68	P68P	ccT	ccA	1	1	B.1.258.17	0.000104
ORF7a	68	P68Y	CCt	TAt	1	1	B.1.258.9	0.005
ORF7a	68	P68del	CCT	---	1	1	B.1.265	0.001271
ORF7a	68	P68H	cCt	cAt	1	1	B.1.311	0.000275
ORF7a	68	P68del	CCT	---	1	1	B.1.319	0.003049
ORF7a	68	P68P	ccT	ccC	1	1	B.1.320	0.001245
ORF7a	68	P68P	ccT	ccA	1	1	B.1.351	0.00003
ORF7a	68	P68del	CCT	---	1	1	B.1.351.3	0.000876
ORF7a	68	P68V	CCT	GTC	1	1	B.1.36	0.000146
ORF7a	68	P68L	cCt	cTt	1	1	B.1.36	0.000146
ORF7a	68	P68del	CCT	---	1	1	B.1.36.17	0.000494
ORF7a	68	P68del	CCT	---	1	1	B.1.36.35	0.002604
ORF7a	68	P68del	CCT	---	1	1	B.1.36.38	0.001642
ORF7a	68	P68R	cCt	cGt	1	1	B.1.367	0.000792
ORF7a	68	P68del	CCT	---	1	1	B.1.371	0.001122
ORF7a	68	P68del	CCT	---	1	1	B.1.380	0.006623
ORF7a	68	P68del	CCT	---	1	1	B.1.389	0.001002
ORF7a	68	P68L	cCt	cTt	1	1	B.1.396	0.000706
ORF7a	68	P68del	CCT	---	1	1	B.1.406	0.006061
ORF7a	68	P68del1	Cct	-ct	1	1	B.1.409	0.000781
ORF7a	68	P68del	CCT	---	1	1	B.1.416	0.001269
ORF7a	68	P68I	CCt	ATt	1	1	B.1.416	0.001269
ORF7a	68	P68del	CCT	---	1	1	B.1.416.1	0.001563
ORF7a	68	P68P	ccT	ccA	1	1	B.1.416.1	0.001563
ORF7a	68	P68P	ccT	ccA	1	1	B.1.427	0.00005
ORF7a	68	P68L	cCt	cTt	1	1	B.1.428	0.00102
ORF7a	68	P68P	ccT	ccC	1	1	B.1.429	0.000024
ORF7a	68	P68L	cCt	cTt	1	1	B.1.429	0.000024
ORF7a	68	P68T	Cct	Act	1	1	B.1.429	0.000024
ORF7a	68	P68del	CCT	---	1	1	B.1.433	0.003195
ORF7a	68	P68L	cCt	cTt	1	1	B.1.433	0.003195
ORF7a	68	P68V	CCT	GTC	1	1	B.1.438	0.006536
ORF7a	68	P68L	cCt	cTt	1	1	B.1.438.1	0.000107
ORF7a	68	P68del	CCT	---	1	1	B.1.438.1	0.000107
ORF7a	68	P68del	CCT	---	1	1	B.1.443	0.004673
ORF7a	68	P68del	CCT	---	1	1	B.1.459	0.004082
ORF7a	68	P68del	CCT	---	1	1	B.1.468	0.005714
ORF7a	68	P68V	CCT	GTC	1	1	B.1.469	0.00361
ORF7a	68	P68del	CCT	---	1	1	B.1.470	0.001404
ORF7a	68	P68del	CCT	---	1	1	B.1.471	0.002732
ORF7a	68	P68L	cCt	cTt	1	1	B.1.497	0.000315
ORF7a	68	P68P	ccT	ccG	1	1	B.1.497	0.000315
ORF7a	68	P68F	CCt	TTt	1	1	B.1.497	0.000315
ORF7a	68	P68L	cCt	cTt	1	1	B.1.503	0.002488
ORF7a	68	P68del	CCT	---	1	1	B.1.509	0.000866
ORF7a	68	P68L	cCt	cTt	1	1	B.1.517	0.000427
ORF7a	68	P68del	CCT	---	1	1	B.1.517	0.000427
ORF7a	68	P68V	CCT	GTC	1	1	B.1.525	0.000113
ORF7a	68	P68del	CCT	---	1	1	B.1.535	0.028571
ORF7a	68	P68del	CCT	---	1	1	B.1.545	0.014493
ORF7a	68	P68S	Cct	Tct	1	1	B.1.546	0.003704
ORF7a	68	P68P	ccT	ccA	1	1	B.1.551	0.00129
ORF7a	68	P68del	CCT	---	1	1	B.1.560	0.00463
ORF7a	68	P68S	Cct	Tct	1	1	B.1.564	0.000426
ORF7a	68	P68del	CCT	---	1	1	B.1.564	0.000426
ORF7a	68	P68del	CCT	---	1	1	B.1.564.1	0.001577
ORF7a	68	P68del	CCT	---	1	1	B.1.568	0.001111
ORF7a	68	P68P	ccT	ccC	1	1	B.1.574	0.002151
ORF7a	68	P68del	CCT	---	1	1	B.1.576	0.000907
ORF7a	68	P68del	CCT	---	1	1	B.1.582	0.000491
ORF7a	68	P68P	ccT	ccC	1	1	B.1.582	0.000491
ORF7a	68	P68del	CCT	---	1	1	B.1.588	0.00091
ORF7a	68	P68P	ccT	ccC	1	1	B.1.595	0.000261
ORF7a	68	P68S	Cct	Tct	1	1	B.1.596	0.000087
ORF7a	68	P68del1	Cct	-ct	1	1	B.1.596	0.000087
ORF7a	68	P68T	Cct	Act	1	1	B.1.609	0.000479
ORF7a	68	P68T	Cct	Act	1	1	B.1.612	0.002653
ORF7a	68	P68del1	Cct	-ct	1	1	B.1.617.1	0.000129
ORF7a	68	P68R	cCt	cGt	1	1	B.1.617.1	0.000129
ORF7a	68	P68R	cCt	cGt	1	1	B.1.617.2	0.000004
ORF7a	68	P68del2	CCt	--t	1	1	B.1.617.2	0.000004
ORF7a	68	P68F	CCt	TTt	1	1	B.1.617.2	0.000004
ORF7a	68	P68del	CCT	---	1	1	B.1.617.3	0.002985
ORF7a	68	P68del	CCT	---	1	1	B.1.627	0.00202
ORF7a	68	P68H	cCt	cAt	1	1	B.1.628	0.000352
ORF7a	68	P68C	CCt	TGt	1	1	B.1.637	0.000073
ORF7a	68	P68L	cCt	cTt	1	1	B.1.637	0.000073
ORF7a	68	P68del	CCT	---	1	1	B.1.638	0.052632
ORF7a	68	P68del	CCT	---	1	1	B.1.88.1	0.004808
ORF7a	68	P68del	CCT	---	1	1	B.1.9.1	0.032258
ORF7a	68	P68S	Cct	Tct	1	1	B.11	0.005128
ORF7a	68	P68del	CCT	---	1	1	B.11	0.005128
ORF7a	68	P68L	cCt	cTt	1	1	B.11	0.005128
ORF7a	68	P68del	CCT	---	1	1	B.40	0.000364
ORF7a	68	P68P	ccT	ccC	1	1	C.16	0.00106
ORF7a	68	P68del	CCT	---	1	1	C.30	0.001727
ORF7a	68	P68del	CCT	---	1	1	C.36.3.1	0.002717
ORF7a	68	P68L	cCt	cTt	1	1	C.37	0.000116
ORF7a	68	P68P	ccT	ccC	1	1	C.37	0.000116
ORF7a	68	P68P	ccT	ccC	1	1	D.2	0.000075
ORF7a	68	P68del	CCT	---	1	1	K.3	0.006173
ORF7a	68	P68del	CCT	---	1	1	N.5	0.001767
ORF7a	68	P68C	CCt	TGt	1	1	P.1	0.000016
ORF7a	68	P68del2	CCt	--t	1	1	P.1	0.000016
ORF7a	68	P68del	CCT	---	1	1	P.1.10	0.000269
ORF7a	68	P68del	CCT	---	1	1	P.1.12	0.000484
ORF7a	68	P68L	cCt	cTt	1	1	P.1.14	0.000048
ORF7a	68	P68L	cCt	cTt	1	1	P.1.15	0.000232
ORF7a	68	P68del	CCT	---	1	1	P.1.16	0.000374
ORF7a	68	P68L	cCt	cTt	1	1	P.1.17	0.000162
ORF7a	68	P68del	CCT	---	1	1	P.1.17	0.000162
ORF7a	68	P68A	Cct	Gct	1	1	P.1.17.1	0.000875
ORF7a	68	P68del	CCT	---	1	1	P.1.3	0.034483
ORF7a	68	P68del	CCT	---	1	1	P.1.4	0.000977
ORF7a	68	P68del	CCT	---	1	1	P.1.8	0.004785
ORF7a	68	P68L	cCt	cTt	1	1	Q.1	0.000126
ORF7a	68	P68del	CCT	---	1	1	Q.7	0.001111
ORF7a	68	P68del	CCT	---	1	1	Z.1	0.00289

CoV-GLUE is still in development. CoV-GLUE was originally developed as part of COG-UK by Josh Singer using the GLUE framework at the MRC-University of Glasgow Centre for Virus Research (CVR). In 2021 it was redeveloped by Richard Orton to scale to the millions of genome sequences available. We acknowledge support from the MRC (MC_UU_12014/12), WT (220977/Z/20/Z) and UKRI G2P (MR/W005611/1). Please contact Richard Orton with any queries: Richard.Orton@glasgow.ac.uk

CoV-GLUE uses sequence data from GISAID. GISAID data provided via this web application is subject to GISAID's Terms and Conditions.