CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF7a : CodonNum = 34

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	34	P34S		nonsyn	Cct	Tct	10644	10644	1	27493-27495
ORF7a	34	P34L		nonsyn	cCt	cTt	6977	6977	1	27493-27495
ORF7a	34	P34del		del	CCT	---	1241	1241	1	27493-27495
ORF7a	34	P34P		syn	ccT	ccC	637	454	0.712716	27493-27495
ORF7a	34	P34P		syn	ccT	ccG	637	139	0.21821	27493-27495
ORF7a	34	P34P		syn	ccT	ccA	637	44	0.0690738	27493-27495
ORF7a	34	P34H		nonsyn	cCt	cAt	167	166	0.994012	27493-27495
ORF7a	34	P34H		nonsyn	cCT	cAC	167	1	0.00598802	27493-27495
ORF7a	34	P34R		nonsyn	cCt	cGt	140	139	0.992857	27493-27495
ORF7a	34	P34R		nonsyn	CCT	AGA	140	1	0.00714286	27493-27495
ORF7a	34	P34F		nonsyn	CCt	TTt	88	88	1	27493-27495
ORF7a	34	P34T		nonsyn	Cct	Act	44	43	0.977273	27493-27495
ORF7a	34	P34T		nonsyn	CcT	AcC	44	1	0.0227273	27493-27495
ORF7a	34	P34del2		del	cCT	c--	16	9	0.5625	27493-27495
ORF7a	34	P34del2		del	CCt	--t	16	5	0.3125	27493-27495
ORF7a	34	P34del2		del	CCT	T--	16	1	0.0625	27493-27495
ORF7a	34	P34del2		del	CCT	--N	16	1	0.0625	27493-27495
ORF7a	34	P34del1		del	ccT	cc-	6	3	0.5	27493-27495
ORF7a	34	P34del1		del	Cct	-ct	6	3	0.5	27493-27495
ORF7a	34	P34I		nonsyn	CCt	ATt	4	3	0.75	27493-27495
ORF7a	34	P34I		nonsyn	CCT	ATA	4	1	0.25	27493-27495
ORF7a	34	P34A		nonsyn	Cct	Gct	3	3	1	27493-27495
ORF7a	34	P34E		nonsyn	CCT	GAA	1	1	1	27493-27495
ORF7a	34	P34X		nonsyn	CCT	TAG	1	1	1	27493-27495

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	34	P34S	Cct	Tct	10644	10644	All	0.002036
ORF7a	34	P34L	cCt	cTt	6977	6977	All	0.001334
ORF7a	34	P34S	Cct	Tct	4171	4171	B.1.1.7	0.003734
ORF7a	34	P34L	cCt	cTt	2137	2137	B.1.1.7	0.001913
ORF7a	34	P34L	cCt	cTt	1750	1750	AY.4	0.002724
ORF7a	34	P34S	Cct	Tct	1259	1259	AY.103	0.007817
ORF7a	34	P34del	CCT	---	1241	1241	All	0.000237
ORF7a	34	P34S	Cct	Tct	646	646	AY.4	0.001005
ORF7a	34	P34P	ccT	ccC	454	637	All	0.000087
ORF7a	34	P34P	ccT	ccG	139	637	All	0.000027
ORF7a	34	P34P	ccT	ccA	44	637	All	0.000008
ORF7a	34	P34S	Cct	Tct	500	500	B.1.617.2	0.001883
ORF7a	34	P34S	Cct	Tct	484	484	AY.43	0.002144
ORF7a	34	P34S	Cct	Tct	348	348	AY.46	0.03622
ORF7a	34	P34del	CCT	---	303	303	AY.4	0.000472
ORF7a	34	P34L	cCt	cTt	295	295	B.1.617.2	0.001111
ORF7a	34	P34del	CCT	---	276	276	B.1.1.7	0.000247
ORF7a	34	P34P	ccT	ccC	273	273	AY.111	0.05
ORF7a	34	P34S	Cct	Tct	265	265	B.1.637	0.019364
ORF7a	34	P34S	Cct	Tct	213	213	AY.25	0.001281
ORF7a	34	P34S	Cct	Tct	202	202	AY.5	0.004171
ORF7a	34	P34S	Cct	Tct	189	189	AY.29	0.002981
ORF7a	34	P34del	CCT	---	179	179	B.1.177.21	0.013688
ORF7a	34	P34S	Cct	Tct	171	171	B.1.618	0.689516
ORF7a	34	P34H	cCt	cAt	166	167	All	0.000032
ORF7a	34	P34H	cCT	cAC	1	167	All	0
ORF7a	34	P34S	Cct	Tct	156	156	AY.44	0.00095
ORF7a	34	P34L	cCt	cTt	155	155	AY.103	0.000962
ORF7a	34	P34R	cCt	cGt	139	140	All	0.000027
ORF7a	34	P34R	CCT	AGA	1	140	All	0
ORF7a	34	P34L	cCt	cTt	138	138	B.1.2	0.001215
ORF7a	34	P34L	cCt	cTt	135	135	AY.44	0.000822
ORF7a	34	P34L	cCt	cTt	128	128	AY.3	0.001273
ORF7a	34	P34L	cCt	cTt	123	123	B.1.577	0.084536
ORF7a	34	P34L	cCt	cTt	120	120	AY.43	0.000532
ORF7a	34	P34S	Cct	Tct	113	113	B.1.438.1	0.012121
ORF7a	34	P34S	Cct	Tct	97	97	P.1	0.001528
ORF7a	34	P34S	Cct	Tct	93	93	B.1.177	0.001225
ORF7a	34	P34P	ccT	ccG	65	91	B.1.1.7	0.000058
ORF7a	34	P34P	ccT	ccC	26	91	B.1.1.7	0.000023
ORF7a	34	P34F	CCt	TTt	88	88	All	0.000017
ORF7a	34	P34S	Cct	Tct	87	87	AY.3	0.000865
ORF7a	34	P34L	cCt	cTt	87	87	P.1	0.001371
ORF7a	34	P34S	Cct	Tct	82	82	B.1.2	0.000722
ORF7a	34	P34L	cCt	cTt	79	79	AY.5	0.001631
ORF7a	34	P34L	cCt	cTt	68	68	B.1.526	0.001598
ORF7a	34	P34P	ccT	ccC	60	67	AY.43	0.000266
ORF7a	34	P34P	ccT	ccA	4	67	AY.43	0.000018
ORF7a	34	P34P	ccT	ccG	3	67	AY.43	0.000013
ORF7a	34	P34S	Cct	Tct	65	65	AY.33	0.004341
ORF7a	34	P34del	CCT	---	64	64	AY.25	0.000385
ORF7a	34	P34L	cCt	cTt	64	64	B.1.619.1	0.041052
ORF7a	34	P34L	cCt	cTt	62	62	AY.25	0.000373
ORF7a	34	P34F	CCt	TTt	62	62	B.1.1.7	0.000056
ORF7a	34	P34S	Cct	Tct	59	59	C.37	0.006848
ORF7a	34	P34H	cCt	cAt	58	58	AY.4	0.00009
ORF7a	34	P34L	cCt	cTt	58	58	AY.4.2	0.001258
ORF7a	34	P34L	cCt	cTt	58	58	B.1	0.000531
ORF7a	34	P34L	cCt	cTt	57	57	P.1.10	0.01536
ORF7a	34	P34L	cCt	cTt	56	56	AY.98	0.004424
ORF7a	34	P34S	Cct	Tct	55	55	B.1	0.000504
ORF7a	34	P34S	Cct	Tct	55	55	B.1.429	0.001294
ORF7a	34	P34S	Cct	Tct	54	54	AY.36	0.008004
ORF7a	34	P34R	cCt	cGt	53	53	B.1.1.7	0.000047
ORF7a	34	P34L	cCt	cTt	50	50	B.1.429	0.001176
ORF7a	34	P34L	cCt	cTt	50	50	B.1.635	0.877193
ORF7a	34	P34S	Cct	Tct	48	48	AY.39	0.001186
ORF7a	34	P34S	Cct	Tct	45	45	AY.6	0.001851
ORF7a	34	P34S	Cct	Tct	45	45	B.1.177.21	0.003441
ORF7a	34	P34T	Cct	Act	43	44	All	0.000008
ORF7a	34	P34T	CcT	AcC	1	44	All	0
ORF7a	34	P34del	CCT	---	43	43	AY.3	0.000428
ORF7a	34	P34L	cCt	cTt	43	43	B.1.177	0.000566
ORF7a	34	P34L	cCt	cTt	42	42	B.1.351	0.001249
ORF7a	34	P34S	Cct	Tct	40	40	B.1.351	0.001189
ORF7a	34	P34del	CCT	---	38	38	AY.29	0.000599
ORF7a	34	P34L	cCt	cTt	36	36	B.1.1.311	0.012894
ORF7a	34	P34del	CCT	---	34	34	AY.44	0.000207
ORF7a	34	P34S	Cct	Tct	34	34	AY.75	0.001905
ORF7a	34	P34L	cCt	cTt	33	33	AY.119	0.001165
ORF7a	34	P34L	cCt	cTt	33	33	AY.29	0.000521
ORF7a	34	P34S	Cct	Tct	32	32	AY.98	0.002528
ORF7a	34	P34L	cCt	cTt	31	31	AY.26	0.000878
ORF7a	34	P34L	cCt	cTt	31	31	B.1.427	0.001565
ORF7a	34	P34S	Cct	Tct	31	31	C.36.3	0.017584
ORF7a	34	P34L	cCt	cTt	30	30	AY.102	0.000795
ORF7a	34	P34del	CCT	---	29	29	AY.103	0.00018
ORF7a	34	P34S	Cct	Tct	29	29	AY.119	0.001024
ORF7a	34	P34L	cCt	cTt	28	28	AY.100	0.001288
ORF7a	34	P34S	Cct	Tct	28	28	AY.4.2	0.000607
ORF7a	34	P34L	cCt	cTt	28	28	B.1.1	0.000508
ORF7a	34	P34S	Cct	Tct	27	27	AY.102	0.000716
ORF7a	34	P34L	cCt	cTt	27	27	AY.91	0.019722
ORF7a	34	P34S	Cct	Tct	27	27	B.1.596	0.002353
ORF7a	34	P34L	cCt	cTt	26	26	AY.64	0.015476
ORF7a	34	P34S	Cct	Tct	23	23	B.1.1	0.000417
ORF7a	34	P34P	ccT	ccA	23	23	B.1.617.1	0.002966
ORF7a	34	P34S	Cct	Tct	22	22	AY.111	0.004029
ORF7a	34	P34L	cCt	cTt	22	22	AY.20	0.000855
ORF7a	34	P34L	cCt	cTt	22	22	AY.46.6	0.001589
ORF7a	34	P34P	ccT	ccG	22	22	AY.53	0.006325
ORF7a	34	P34P	ccT	ccG	19	21	AY.3	0.000189
ORF7a	34	P34P	ccT	ccC	1	21	AY.3	0.00001
ORF7a	34	P34P	ccT	ccA	1	21	AY.3	0.00001
ORF7a	34	P34H	cCt	cAt	21	21	B.1.2	0.000185
ORF7a	34	P34P	ccT	ccC	16	21	B.1.2	0.000141
ORF7a	34	P34P	ccT	ccG	4	21	B.1.2	0.000035
ORF7a	34	P34P	ccT	ccA	1	21	B.1.2	0.000009
ORF7a	34	P34del	CCT	---	21	21	U.1	0.269231
ORF7a	34	P34S	Cct	Tct	20	20	B.1.160	0.000624
ORF7a	34	P34L	cCt	cTt	19	19	B.1.160	0.000593
ORF7a	34	P34S	Cct	Tct	19	19	P.1.14	0.000908
ORF7a	34	P34S	Cct	Tct	18	18	AY.3.1	0.001535
ORF7a	34	P34L	cCt	cTt	18	18	AY.39	0.000445
ORF7a	34	P34S	Cct	Tct	18	18	AY.46.6	0.0013
ORF7a	34	P34H	cCt	cAt	18	18	B.1.1.7	0.000016
ORF7a	34	P34T	Cct	Act	18	18	B.1.1.7	0.000016
ORF7a	34	P34L	cCt	cTt	18	18	B.1.177.86	0.003302
ORF7a	34	P34S	Cct	Tct	18	18	B.1.346	0.023591
ORF7a	34	P34L	cCt	cTt	18	18	B.1.621	0.001593
ORF7a	34	P34R	cCt	cGt	17	17	B.1.2	0.00015
ORF7a	34	P34P	ccT	ccC	14	17	B.1.617.2	0.000053
ORF7a	34	P34P	ccT	ccG	3	17	B.1.617.2	0.000011
ORF7a	34	P34del2	cCT	c--	9	16	All	0.000002
ORF7a	34	P34del2	CCt	--t	5	16	All	0.000001
ORF7a	34	P34del2	CCT	--N	1	16	All	0
ORF7a	34	P34del2	CCT	T--	1	16	All	0
ORF7a	34	P34S	Cct	Tct	16	16	AY.118	0.001002
ORF7a	34	P34L	cCt	cTt	16	16	AY.45	0.001947
ORF7a	34	P34del	CCT	---	16	16	AY.7.2	0.008949
ORF7a	34	P34S	Cct	Tct	16	16	B.1.1.519	0.000635
ORF7a	34	P34S	Cct	Tct	16	16	B.1.177.60	0.003495
ORF7a	34	P34S	Cct	Tct	16	16	B.1.526	0.000376
ORF7a	34	P34L	cCt	cTt	15	15	AY.117	0.001268
ORF7a	34	P34L	cCt	cTt	15	15	AY.74	0.001735
ORF7a	34	P34del	CCT	---	15	15	B.1.1.214	0.000832
ORF7a	34	P34S	Cct	Tct	15	15	B.1.240	0.003233
ORF7a	34	P34L	cCt	cTt	15	15	B.1.438.1	0.001609
ORF7a	34	P34S	Cct	Tct	15	15	B.1.561	0.005955
ORF7a	34	P34L	cCt	cTt	14	14	AY.33	0.000935
ORF7a	34	P34del	CCT	---	14	14	AY.43	0.000062
ORF7a	34	P34L	cCt	cTt	14	14	AY.87	0.011657
ORF7a	34	P34S	Cct	Tct	14	14	B.1.177.57	0.003934
ORF7a	34	P34S	Cct	Tct	14	14	B.1.234	0.001847
ORF7a	34	P34L	cCt	cTt	14	14	C.37	0.001625
ORF7a	34	P34L	cCt	cTt	14	14	P.1.14	0.000669
ORF7a	34	P34L	cCt	cTt	14	14	Q.8	0.002309
ORF7a	34	P34S	Cct	Tct	13	13	AY.12	0.004109
ORF7a	34	P34L	cCt	cTt	13	13	AY.9.2	0.000477
ORF7a	34	P34L	cCt	cTt	13	13	AY.98.1	0.00063
ORF7a	34	P34S	Cct	Tct	13	13	B.1.1.265	0.041009
ORF7a	34	P34R	cCt	cGt	13	13	B.1.160	0.000405
ORF7a	34	P34R	cCt	cGt	13	13	B.1.177	0.000171
ORF7a	34	P34L	cCt	cTt	13	13	B.1.221	0.000923
ORF7a	34	P34L	cCt	cTt	13	13	B.1.595	0.003392
ORF7a	34	P34del	CCT	---	13	13	B.1.617.2	0.000049
ORF7a	34	P34L	cCt	cTt	12	12	AY.120	0.000446
ORF7a	34	P34L	cCt	cTt	12	12	AY.47	0.000373
ORF7a	34	P34S	Cct	Tct	12	12	AY.47	0.000373
ORF7a	34	P34L	cCt	cTt	12	12	AY.99.2	0.001106
ORF7a	34	P34L	cCt	cTt	12	12	B.1.1.214	0.000665
ORF7a	34	P34L	cCt	cTt	12	12	B.1.1.519	0.000477
ORF7a	34	P34S	Cct	Tct	12	12	B.1.177.65	0.007984
ORF7a	34	P34L	cCt	cTt	12	12	B.1.36.18	0.005042
ORF7a	34	P34S	Cct	Tct	12	12	B.1.427	0.000606
ORF7a	34	P34L	cCt	cTt	12	12	B.1.637	0.000877
ORF7a	34	P34S	Cct	Tct	11	11	AY.23	0.000767
ORF7a	34	P34T	Cct	Act	11	11	AY.4	0.000017
ORF7a	34	P34S	Cct	Tct	11	11	AY.85	0.004699
ORF7a	34	P34S	Cct	Tct	11	11	AY.9	0.000744
ORF7a	34	P34S	Cct	Tct	11	11	B.1.619	0.009582
ORF7a	34	P34S	Cct	Tct	11	11	B.1.621	0.000974
ORF7a	34	P34L	cCt	cTt	11	11	R.1	0.00099
ORF7a	34	P34S	Cct	Tct	10	10	AY.117	0.000845
ORF7a	34	P34L	cCt	cTt	10	10	AY.23	0.000697
ORF7a	34	P34L	cCt	cTt	10	10	AY.34	0.00097
ORF7a	34	P34S	Cct	Tct	10	10	B.1.367	0.007924
ORF7a	34	P34H	cCt	cAt	10	10	B.1.617.2	0.000038
ORF7a	34	P34S	Cct	Tct	9	9	AY.106	0.003014
ORF7a	34	P34L	cCt	cTt	9	9	AY.121	0.001218
ORF7a	34	P34S	Cct	Tct	9	9	AY.20	0.00035
ORF7a	34	P34P	ccT	ccC	8	9	AY.36	0.001186
ORF7a	34	P34P	ccT	ccA	1	9	AY.36	0.000148
ORF7a	34	P34del	CCT	---	9	9	AY.39	0.000222
ORF7a	34	P34L	cCt	cTt	9	9	AY.39.1	0.000357
ORF7a	34	P34S	Cct	Tct	9	9	AY.42	0.000362
ORF7a	34	P34del	CCT	---	9	9	B.1	0.000082
ORF7a	34	P34del	CCT	---	9	9	B.1.1.284	0.000967
ORF7a	34	P34del2	cCT	c--	4	9	B.1.1.7	0.000004
ORF7a	34	P34del2	CCt	--t	3	9	B.1.1.7	0.000003
ORF7a	34	P34del2	CCT	T--	1	9	B.1.1.7	0.000001
ORF7a	34	P34del2	CCT	--N	1	9	B.1.1.7	0.000001
ORF7a	34	P34P	ccT	ccG	6	9	B.1.177	0.000079
ORF7a	34	P34P	ccT	ccC	2	9	B.1.177	0.000026
ORF7a	34	P34P	ccT	ccA	1	9	B.1.177	0.000013
ORF7a	34	P34L	cCt	cTt	9	9	B.1.243	0.000626
ORF7a	34	P34S	Cct	Tct	9	9	B.1.258	0.000599
ORF7a	34	P34del	CCT	---	9	9	C.37	0.001045
ORF7a	34	P34del	CCT	---	9	9	P.1	0.000142
ORF7a	34	P34L	cCt	cTt	9	9	P.1.15	0.002091
ORF7a	34	P34L	cCt	cTt	9	9	P.1.7	0.002874
ORF7a	34	P34L	cCt	cTt	9	9	Q.3	0.001305
ORF7a	34	P34S	Cct	Tct	9	9	Q.3	0.001305
ORF7a	34	P34S	Cct	Tct	9	9	Q.8	0.001484
ORF7a	34	P34R	cCt	cGt	8	8	AY.103	0.00005
ORF7a	34	P34L	cCt	cTt	8	8	AY.118	0.000501
ORF7a	34	P34S	Cct	Tct	8	8	AY.39.1	0.000317
ORF7a	34	P34H	cCt	cAt	8	8	AY.45	0.000973
ORF7a	34	P34L	cCt	cTt	8	8	AY.5.4	0.002214
ORF7a	34	P34S	Cct	Tct	8	8	AY.63	0.003095
ORF7a	34	P34S	Cct	Tct	8	8	AY.98.1	0.000387
ORF7a	34	P34H	cCt	cAt	8	8	B.1.351	0.000238
ORF7a	34	P34L	cCt	cTt	8	8	B.1.525	0.000905
ORF7a	34	P34L	cCt	cTt	8	8	B.1.596	0.000697
ORF7a	34	P34L	cCt	cTt	8	8	B.1.628	0.002819
ORF7a	34	P34S	Cct	Tct	7	7	AY.116.1	0.00218
ORF7a	34	P34S	Cct	Tct	7	7	AY.120	0.00026
ORF7a	34	P34S	Cct	Tct	7	7	AY.39.2	0.010786
ORF7a	34	P34L	cCt	cTt	7	7	AY.4.3	0.005892
ORF7a	34	P34R	cCt	cGt	6	7	AY.43	0.000027
ORF7a	34	P34R	CCT	AGA	1	7	AY.43	0.000004
ORF7a	34	P34del	CCT	---	7	7	AY.47	0.000218
ORF7a	34	P34S	Cct	Tct	7	7	AY.59	0.003708
ORF7a	34	P34L	cCt	cTt	7	7	AY.6	0.000288
ORF7a	34	P34L	cCt	cTt	7	7	AY.7	0.001372
ORF7a	34	P34L	cCt	cTt	7	7	AY.9.1	0.000586
ORF7a	34	P34P	ccT	ccC	7	7	AY.95	0.005327
ORF7a	34	P34S	Cct	Tct	7	7	B	0.000895
ORF7a	34	P34P	ccT	ccA	5	7	B.1	0.000046
ORF7a	34	P34P	ccT	ccG	1	7	B.1	0.000009
ORF7a	34	P34P	ccT	ccC	1	7	B.1	0.000009
ORF7a	34	P34S	Cct	Tct	7	7	B.1.160.16	0.006506
ORF7a	34	P34L	cCt	cTt	7	7	B.1.160.23	0.033816
ORF7a	34	P34S	Cct	Tct	7	7	B.1.177.32	0.009447
ORF7a	34	P34S	Cct	Tct	7	7	B.1.177.4	0.001477
ORF7a	34	P34del	CCT	---	7	7	B.1.2	0.000062
ORF7a	34	P34L	cCt	cTt	7	7	B.1.234	0.000924
ORF7a	34	P34H	cCt	cAt	7	7	B.1.628	0.002467
ORF7a	34	P34L	cCt	cTt	7	7	D.2	0.000525
ORF7a	34	P34S	Cct	Tct	7	7	P.1.17	0.001132
ORF7a	34	P34del1	Cct	-ct	3	6	All	0.000001
ORF7a	34	P34del1	ccT	cc-	3	6	All	0.000001
ORF7a	34	P34S	Cct	Tct	6	6	AY.120.1	0.001926
ORF7a	34	P34S	Cct	Tct	6	6	AY.26	0.00017
ORF7a	34	P34L	cCt	cTt	6	6	AY.36	0.000889
ORF7a	34	P34del	CCT	---	6	6	B.1.177.44	0.003114
ORF7a	34	P34S	Cct	Tct	6	6	B.1.214.2	0.003597
ORF7a	34	P34S	Cct	Tct	6	6	B.1.221	0.000426
ORF7a	34	P34L	cCt	cTt	6	6	B.1.258.2	0.027027
ORF7a	34	P34S	Cct	Tct	6	6	D.2	0.00045
ORF7a	34	P34S	Cct	Tct	6	6	Q.1	0.000758
ORF7a	34	P34L	cCt	cTt	5	5	AY.12	0.00158
ORF7a	34	P34del	CCT	---	5	5	AY.20	0.000194
ORF7a	34	P34P	ccT	ccG	3	5	AY.25	0.000018
ORF7a	34	P34P	ccT	ccC	2	5	AY.25	0.000012
ORF7a	34	P34P	ccT	ccC	5	5	AY.26	0.000142
ORF7a	34	P34S	Cct	Tct	5	5	AY.27	0.000324
ORF7a	34	P34H	cCt	cAt	5	5	AY.43	0.000022
ORF7a	34	P34L	cCt	cTt	5	5	AY.52	0.004072
ORF7a	34	P34S	Cct	Tct	5	5	AY.62	0.002179
ORF7a	34	P34L	cCt	cTt	5	5	AY.75.1	0.000902
ORF7a	34	P34S	Cct	Tct	5	5	AY.9.2	0.000184
ORF7a	34	P34H	cCt	cAt	5	5	B.1	0.000046
ORF7a	34	P34S	Cct	Tct	5	5	B.1.1.214	0.000277
ORF7a	34	P34L	cCt	cTt	5	5	B.1.1.222	0.00102
ORF7a	34	P34L	cCt	cTt	5	5	B.1.1.28	0.001556
ORF7a	34	P34L	cCt	cTt	5	5	B.1.258	0.000333
ORF7a	34	P34del	CCT	---	5	5	B.1.429	0.000118
ORF7a	34	P34S	Cct	Tct	5	5	B.1.499	0.005252
ORF7a	34	P34del	CCT	---	5	5	B.1.526	0.000118
ORF7a	34	P34L	cCt	cTt	5	5	B.1.588	0.00455
ORF7a	34	P34S	Cct	Tct	5	5	B.1.595	0.001305
ORF7a	34	P34L	cCt	cTt	5	5	B.1.597	0.023148
ORF7a	34	P34L	cCt	cTt	5	5	B.1.617.1	0.000645
ORF7a	34	P34P	ccT	ccG	2	5	P.1	0.000032
ORF7a	34	P34P	ccT	ccC	2	5	P.1	0.000032
ORF7a	34	P34P	ccT	ccA	1	5	P.1	0.000016
ORF7a	34	P34L	cCt	cTt	5	5	P.1.12	0.00242
ORF7a	34	P34L	cCt	cTt	4	4	AD.2	0.000876
ORF7a	34	P34I	CCt	ATt	3	4	All	0.000001
ORF7a	34	P34I	CCT	ATA	1	4	All	0
ORF7a	34	P34S	Cct	Tct	4	4	AY.100	0.000184
ORF7a	34	P34del	CCT	---	4	4	AY.100	0.000184
ORF7a	34	P34P	ccT	ccC	4	4	AY.103	0.000025
ORF7a	34	P34T	Cct	Act	4	4	AY.103	0.000025
ORF7a	34	P34L	cCt	cTt	4	4	AY.116.1	0.001246
ORF7a	34	P34del	CCT	---	4	4	AY.121	0.000541
ORF7a	34	P34S	Cct	Tct	4	4	AY.13	0.000644
ORF7a	34	P34del	CCT	---	4	4	AY.26	0.000113
ORF7a	34	P34R	cCt	cGt	4	4	AY.29	0.000063
ORF7a	34	P34S	Cct	Tct	4	4	AY.29.1	0.000882
ORF7a	34	P34L	cCt	cTt	4	4	AY.3.1	0.000341
ORF7a	34	P34L	cCt	cTt	4	4	AY.32	0.00213
ORF7a	34	P34S	Cct	Tct	4	4	AY.35	0.000932
ORF7a	34	P34P	ccT	ccC	2	4	AY.4	0.000003
ORF7a	34	P34P	ccT	ccG	2	4	AY.4	0.000003
ORF7a	34	P34F	CCt	TTt	4	4	AY.43	0.000018
ORF7a	34	P34P	ccT	ccA	2	4	AY.44	0.000012
ORF7a	34	P34P	ccT	ccC	2	4	AY.44	0.000012
ORF7a	34	P34L	cCt	cTt	4	4	AY.46	0.000416
ORF7a	34	P34S	Cct	Tct	4	4	AY.48	0.00186
ORF7a	34	P34S	Cct	Tct	4	4	AY.5.3	0.00135
ORF7a	34	P34L	cCt	cTt	4	4	AY.54	0.000381
ORF7a	34	P34L	cCt	cTt	4	4	AY.61	0.000419
ORF7a	34	P34L	cCt	cTt	4	4	AY.77	0.00451
ORF7a	34	P34del	CCT	---	4	4	AY.98.1	0.000194
ORF7a	34	P34L	cCt	cTt	4	4	B	0.000511
ORF7a	34	P34L	cCt	cTt	4	4	B.1.1.284	0.00043
ORF7a	34	P34L	cCt	cTt	4	4	B.1.1.416	0.00362
ORF7a	34	P34S	Cct	Tct	4	4	B.1.1.433	0.005698
ORF7a	34	P34L	cCt	cTt	4	4	B.1.177.82	0.001909
ORF7a	34	P34L	cCt	cTt	4	4	B.1.258.17	0.000416
ORF7a	34	P34L	cCt	cTt	4	4	B.1.311	0.001098
ORF7a	34	P34S	Cct	Tct	4	4	B.1.351.3	0.003506
ORF7a	34	P34L	cCt	cTt	4	4	B.1.400	0.001716
ORF7a	34	P34L	cCt	cTt	4	4	B.1.497	0.001259
ORF7a	34	P34T	Cct	Act	4	4	B.1.617.2	0.000015
ORF7a	34	P34del	CCT	---	4	4	B.1.637	0.000292
ORF7a	34	P34L	cCt	cTt	4	4	P.1.1	0.001271
ORF7a	34	P34S	Cct	Tct	4	4	P.2	0.000747
ORF7a	34	P34L	cCt	cTt	4	4	Q.1	0.000505
ORF7a	34	P34L	cCt	cTt	3	3	A.23.1	0.002113
ORF7a	34	P34S	Cct	Tct	3	3	AD.2	0.000657
ORF7a	34	P34A	Cct	Gct	3	3	All	0.000001
ORF7a	34	P34S	Cct	Tct	3	3	AY.1	0.001187
ORF7a	34	P34F	CCt	TTt	3	3	AY.103	0.000019
ORF7a	34	P34del	CCT	---	3	3	AY.106	0.001005
ORF7a	34	P34S	Cct	Tct	3	3	AY.109	0.002219
ORF7a	34	P34del	CCT	---	3	3	AY.118	0.000188
ORF7a	34	P34P	ccT	ccG	3	3	AY.121	0.000406
ORF7a	34	P34S	Cct	Tct	3	3	AY.14	0.000264
ORF7a	34	P34L	cCt	cTt	3	3	AY.16	0.001139
ORF7a	34	P34H	cCt	cAt	3	3	AY.25	0.000018
ORF7a	34	P34L	cCt	cTt	3	3	AY.30	0.001187
ORF7a	34	P34S	Cct	Tct	3	3	AY.37	0.000948
ORF7a	34	P34R	cCt	cGt	3	3	AY.4	0.000005
ORF7a	34	P34F	CCt	TTt	3	3	AY.4	0.000005
ORF7a	34	P34S	Cct	Tct	3	3	AY.4.2.1	0.000447
ORF7a	34	P34L	cCt	cTt	3	3	AY.40	0.002893
ORF7a	34	P34L	cCt	cTt	3	3	AY.41	0.000882
ORF7a	34	P34L	cCt	cTt	3	3	AY.42	0.000121
ORF7a	34	P34S	Cct	Tct	3	3	AY.45	0.000365
ORF7a	34	P34S	Cct	Tct	3	3	AY.5.4	0.00083
ORF7a	34	P34S	Cct	Tct	3	3	AY.53	0.000863
ORF7a	34	P34L	cCt	cTt	3	3	AY.68	0.000821
ORF7a	34	P34P	ccT	ccC	3	3	AY.7.2	0.001678
ORF7a	34	P34L	cCt	cTt	3	3	AY.9	0.000203
ORF7a	34	P34S	Cct	Tct	3	3	AY.9.1	0.000251
ORF7a	34	P34S	Cct	Tct	3	3	AY.91	0.002191
ORF7a	34	P34S	Cct	Tct	3	3	AY.92	0.000862
ORF7a	34	P34S	Cct	Tct	3	3	AY.99.2	0.000276
ORF7a	34	P34P	ccT	ccC	2	3	B.1.1	0.000036
ORF7a	34	P34P	ccT	ccG	1	3	B.1.1	0.000018
ORF7a	34	P34del	CCT	---	3	3	B.1.1.25	0.001706
ORF7a	34	P34S	Cct	Tct	3	3	B.1.1.284	0.000322
ORF7a	34	P34S	Cct	Tct	3	3	B.1.1.434	0.001046
ORF7a	34	P34del1	Cct	-ct	2	3	B.1.1.7	0.000002
ORF7a	34	P34del1	ccT	cc-	1	3	B.1.1.7	0.000001
ORF7a	34	P34P	ccT	ccC	3	3	B.1.165	0.035714
ORF7a	34	P34S	Cct	Tct	3	3	B.1.177.44	0.001557
ORF7a	34	P34S	Cct	Tct	3	3	B.1.177.53	0.007177
ORF7a	34	P34S	Cct	Tct	3	3	B.1.177.58	0.003995
ORF7a	34	P34L	cCt	cTt	3	3	B.1.177.69	0.004451
ORF7a	34	P34S	Cct	Tct	3	3	B.1.177.81	0.000568
ORF7a	34	P34P	ccT	ccA	3	3	B.1.221	0.000213
ORF7a	34	P34del	CCT	---	3	3	B.1.234	0.000396
ORF7a	34	P34L	cCt	cTt	3	3	B.1.240	0.000647
ORF7a	34	P34S	Cct	Tct	3	3	B.1.258.17	0.000312
ORF7a	34	P34del	CCT	---	3	3	B.1.351	0.000089
ORF7a	34	P34S	Cct	Tct	3	3	B.1.351.2	0.000908
ORF7a	34	P34L	cCt	cTt	3	3	B.1.428	0.003061
ORF7a	34	P34F	CCt	TTt	3	3	B.1.470	0.004213
ORF7a	34	P34S	Cct	Tct	3	3	B.1.525	0.000339
ORF7a	34	P34H	cCt	cAt	3	3	B.1.526	0.000071
ORF7a	34	P34L	cCt	cTt	3	3	B.1.564	0.001278
ORF7a	34	P34L	cCt	cTt	3	3	B.1.576	0.00272
ORF7a	34	P34S	Cct	Tct	3	3	B.1.582	0.001472
ORF7a	34	P34S	Cct	Tct	3	3	B.1.595.1	0.017544
ORF7a	34	P34R	cCt	cGt	3	3	B.1.617.2	0.000011
ORF7a	34	P34L	cCt	cTt	3	3	B.1.619	0.002613
ORF7a	34	P34L	cCt	cTt	3	3	B.1.621.1	0.001517
ORF7a	34	P34del	CCT	---	3	3	B.1.626	0.017143
ORF7a	34	P34S	Cct	Tct	3	3	B.1.628	0.001057
ORF7a	34	P34S	Cct	Tct	3	3	N.4	0.012766
ORF7a	34	P34F	CCt	TTt	3	3	P.1	0.000047
ORF7a	34	P34H	cCt	cAt	3	3	P.1	0.000047
ORF7a	34	P34S	Cct	Tct	3	3	P.1.10	0.000808
ORF7a	34	P34S	Cct	Tct	3	3	P.1.15	0.000697
ORF7a	34	P34S	Cct	Tct	3	3	P.1.16	0.001122
ORF7a	34	P34L	cCt	cTt	3	3	P.2	0.00056
ORF7a	34	P34del	CCT	---	3	3	Q.8	0.000495
ORF7a	34	P34S	Cct	Tct	3	3	R.1	0.00027
ORF7a	34	P34S	Cct	Tct	2	2	A	0.000774
ORF7a	34	P34del	CCT	---	2	2	A.28	0.005291
ORF7a	34	P34R	cCt	cGt	2	2	AY.109	0.001479
ORF7a	34	P34L	cCt	cTt	2	2	AY.11	0.002677
ORF7a	34	P34S	Cct	Tct	2	2	AY.110	0.000225
ORF7a	34	P34L	cCt	cTt	2	2	AY.110	0.000225
ORF7a	34	P34L	cCt	cTt	2	2	AY.111	0.000366
ORF7a	34	P34L	cCt	cTt	2	2	AY.113	0.000285
ORF7a	34	P34L	cCt	cTt	2	2	AY.114	0.000462
ORF7a	34	P34del	CCT	---	2	2	AY.119	0.000071
ORF7a	34	P34L	cCt	cTt	2	2	AY.13	0.000322
ORF7a	34	P34L	cCt	cTt	2	2	AY.14	0.000176
ORF7a	34	P34S	Cct	Tct	2	2	AY.16	0.000759
ORF7a	34	P34L	cCt	cTt	2	2	AY.17	0.016393
ORF7a	34	P34del2	cCT	c--	2	2	AY.20	0.000078
ORF7a	34	P34T	CcT	AcC	1	2	AY.26	0.000028
ORF7a	34	P34T	Cct	Act	1	2	AY.26	0.000028
ORF7a	34	P34del	CCT	---	2	2	AY.29.1	0.000441
ORF7a	34	P34S	Cct	Tct	2	2	AY.30	0.000791
ORF7a	34	P34del	CCT	---	2	2	AY.33	0.000134
ORF7a	34	P34S	Cct	Tct	2	2	AY.34.1	0.00102
ORF7a	34	P34L	cCt	cTt	2	2	AY.34.1	0.00102
ORF7a	34	P34L	cCt	cTt	2	2	AY.37	0.000632
ORF7a	34	P34L	cCt	cTt	2	2	AY.4.2.1	0.000298
ORF7a	34	P34L	cCt	cTt	2	2	AY.4.4	0.000818
ORF7a	34	P34S	Cct	Tct	2	2	AY.4.5	0.000215
ORF7a	34	P34L	cCt	cTt	2	2	AY.4.5	0.000215
ORF7a	34	P34del	CCT	---	2	2	AY.42	0.00008
ORF7a	34	P34R	cCt	cGt	2	2	AY.44	0.000012
ORF7a	34	P34H	cCt	cAt	2	2	AY.44	0.000012
ORF7a	34	P34L	cCt	cTt	2	2	AY.46.4	0.000329
ORF7a	34	P34S	Cct	Tct	2	2	AY.46.4	0.000329
ORF7a	34	P34L	cCt	cTt	2	2	AY.46.5	0.000397
ORF7a	34	P34F	CCt	TTt	2	2	AY.46.6	0.000144
ORF7a	34	P34L	cCt	cTt	2	2	AY.60	0.001876
ORF7a	34	P34S	Cct	Tct	2	2	AY.7	0.000392
ORF7a	34	P34S	Cct	Tct	2	2	AY.7.1	0.000225
ORF7a	34	P34L	cCt	cTt	2	2	AY.7.2	0.001119
ORF7a	34	P34L	cCt	cTt	2	2	AY.70	0.000417
ORF7a	34	P34L	cCt	cTt	2	2	AY.73	0.001331
ORF7a	34	P34del	CCT	---	2	2	AY.75	0.000112
ORF7a	34	P34L	cCt	cTt	2	2	AY.75	0.000112
ORF7a	34	P34S	Cct	Tct	2	2	AY.75.1	0.000361
ORF7a	34	P34P	ccT	ccC	2	2	AY.75.1	0.000361
ORF7a	34	P34S	Cct	Tct	2	2	AY.77	0.002255
ORF7a	34	P34del	CCT	---	2	2	AY.9	0.000135
ORF7a	34	P34L	cCt	cTt	2	2	AY.90	0.001369
ORF7a	34	P34S	Cct	Tct	2	2	AY.99	0.002099
ORF7a	34	P34A	Cct	Gct	2	2	B.1	0.000018
ORF7a	34	P34del	CCT	---	2	2	B.1.1	0.000036
ORF7a	34	P34L	cCt	cTt	2	2	B.1.1.1	0.000653
ORF7a	34	P34S	Cct	Tct	2	2	B.1.1.222	0.000408
ORF7a	34	P34L	cCt	cTt	2	2	B.1.1.241	0.004141
ORF7a	34	P34S	Cct	Tct	2	2	B.1.1.33	0.000842
ORF7a	34	P34S	Cct	Tct	2	2	B.1.1.37	0.000386
ORF7a	34	P34L	cCt	cTt	2	2	B.1.1.37	0.000386
ORF7a	34	P34P	ccT	ccC	2	2	B.1.1.37	0.000386
ORF7a	34	P34L	cCt	cTt	2	2	B.1.1.372	0.001377
ORF7a	34	P34S	Cct	Tct	2	2	B.1.1.416	0.00181
ORF7a	34	P34S	Cct	Tct	2	2	B.1.1.420	0.002012
ORF7a	34	P34S	Cct	Tct	2	2	B.1.1.432	0.002532
ORF7a	34	P34L	cCt	cTt	2	2	B.1.1.44	0.004819
ORF7a	34	P34L	cCt	cTt	2	2	B.1.1.486	0.003155
ORF7a	34	P34S	Cct	Tct	2	2	B.1.1.50	0.001358
ORF7a	34	P34del	CCT	---	2	2	B.1.177	0.000026
ORF7a	34	P34S	Cct	Tct	2	2	B.1.177.15	0.001262
ORF7a	34	P34L	cCt	cTt	2	2	B.1.177.21	0.000153
ORF7a	34	P34S	Cct	Tct	2	2	B.1.177.48	0.00625
ORF7a	34	P34S	Cct	Tct	2	2	B.1.177.69	0.002967
ORF7a	34	P34del	CCT	---	2	2	B.1.177.86	0.000367
ORF7a	34	P34S	Cct	Tct	2	2	B.1.206	0.001631
ORF7a	34	P34L	cCt	cTt	2	2	B.1.214.3	0.014286
ORF7a	34	P34S	Cct	Tct	2	2	B.1.22	0.002635
ORF7a	34	P34S	Cct	Tct	2	2	B.1.223	0.005556
ORF7a	34	P34L	cCt	cTt	2	2	B.1.241	0.001623
ORF7a	34	P34del	CCT	---	2	2	B.1.258	0.000133
ORF7a	34	P34del	CCT	---	2	2	B.1.258.11	0.000793
ORF7a	34	P34S	Cct	Tct	2	2	B.1.298	0.004228
ORF7a	34	P34del	CCT	---	2	2	B.1.36	0.000292
ORF7a	34	P34L	cCt	cTt	2	2	B.1.36.1	0.002281
ORF7a	34	P34S	Cct	Tct	2	2	B.1.36.18	0.00084
ORF7a	34	P34L	cCt	cTt	2	2	B.1.36.22	0.002415
ORF7a	34	P34L	cCt	cTt	2	2	B.1.361	0.002577
ORF7a	34	P34R	cCt	cGt	2	2	B.1.429	0.000047
ORF7a	34	P34S	Cct	Tct	2	2	B.1.575	0.000607
ORF7a	34	P34S	Cct	Tct	2	2	B.1.576	0.001813
ORF7a	34	P34S	Cct	Tct	2	2	B.1.617.1	0.000258
ORF7a	34	P34F	CCt	TTt	2	2	B.1.621	0.000177
ORF7a	34	P34R	cCt	cGt	2	2	B.1.637	0.000146
ORF7a	34	P34L	cCt	cTt	2	2	C.1	0.004785
ORF7a	34	P34L	cCt	cTt	2	2	C.14	0.008658
ORF7a	34	P34S	Cct	Tct	2	2	C.16	0.002121
ORF7a	34	P34del	CCT	---	2	2	C.36.3	0.001134
ORF7a	34	P34S	Cct	Tct	2	2	P.1.12	0.000968
ORF7a	34	P34L	cCt	cTt	2	2	P.1.4	0.001953
ORF7a	34	P34S	Cct	Tct	2	2	P.1.7	0.000639
ORF7a	34	P34del	CCT	---	1	1	A	0.000387
ORF7a	34	P34L	cCt	cTt	1	1	A	0.000387
ORF7a	34	P34S	Cct	Tct	1	1	A.1	0.000282
ORF7a	34	P34del2	cCT	c--	1	1	A.1	0.000282
ORF7a	34	P34L	cCt	cTt	1	1	A.2.2	0.001689
ORF7a	34	P34L	cCt	cTt	1	1	A.2.5	0.000499
ORF7a	34	P34L	cCt	cTt	1	1	A.2.5.2	0.001572
ORF7a	34	P34L	cCt	cTt	1	1	AB.1	0.008197
ORF7a	34	P34E	CCT	GAA	1	1	All	0
ORF7a	34	P34X	CCT	TAG	1	1	All	0
ORF7a	34	P34L	cCt	cTt	1	1	AY.1	0.000396
ORF7a	34	P34H	cCT	cAC	1	1	AY.100	0.000046
ORF7a	34	P34T	Cct	Act	1	1	AY.100	0.000046
ORF7a	34	P34F	CCt	TTt	1	1	AY.100	0.000046
ORF7a	34	P34del2	cCT	c--	1	1	AY.100	0.000046
ORF7a	34	P34L	cCt	cTt	1	1	AY.101	0.00049
ORF7a	34	P34H	cCt	cAt	1	1	AY.103	0.000006
ORF7a	34	P34L	cCt	cTt	1	1	AY.106	0.000335
ORF7a	34	P34L	cCt	cTt	1	1	AY.107	0.000466
ORF7a	34	P34S	Cct	Tct	1	1	AY.108	0.001103
ORF7a	34	P34del	CCT	---	1	1	AY.108	0.001103
ORF7a	34	P34del	CCT	---	1	1	AY.110	0.000113
ORF7a	34	P34del	CCT	---	1	1	AY.113	0.000142
ORF7a	34	P34L	cCt	cTt	1	1	AY.116	0.000287
ORF7a	34	P34del2	CCt	--t	1	1	AY.118	0.000063
ORF7a	34	P34F	CCt	TTt	1	1	AY.119	0.000035
ORF7a	34	P34P	ccT	ccG	1	1	AY.120	0.000037
ORF7a	34	P34del	CCT	---	1	1	AY.120	0.000037
ORF7a	34	P34L	cCt	cTt	1	1	AY.120.1	0.000321
ORF7a	34	P34del	CCT	---	1	1	AY.120.1	0.000321
ORF7a	34	P34P	ccT	ccC	1	1	AY.120.1	0.000321
ORF7a	34	P34S	Cct	Tct	1	1	AY.120.2.1	0.000498
ORF7a	34	P34del	CCT	---	1	1	AY.19	0.00114
ORF7a	34	P34L	cCt	cTt	1	1	AY.2	0.000356
ORF7a	34	P34del1	Cct	-ct	1	1	AY.20	0.000039
ORF7a	34	P34L	cCt	cTt	1	1	AY.23.1	0.000417
ORF7a	34	P34S	Cct	Tct	1	1	AY.23.1	0.000417
ORF7a	34	P34H	cCt	cAt	1	1	AY.26	0.000028
ORF7a	34	P34H	cCt	cAt	1	1	AY.29	0.000016
ORF7a	34	P34L	cCt	cTt	1	1	AY.29.1	0.000221
ORF7a	34	P34I	CCT	ATA	1	1	AY.3	0.00001
ORF7a	34	P34H	cCt	cAt	1	1	AY.3.1	0.000085
ORF7a	34	P34S	Cct	Tct	1	1	AY.32	0.000532
ORF7a	34	P34del	CCT	---	1	1	AY.34	0.000097
ORF7a	34	P34del	CCT	---	1	1	AY.34.1	0.00051
ORF7a	34	P34L	cCt	cTt	1	1	AY.38	0.000499
ORF7a	34	P34H	cCt	cAt	1	1	AY.39	0.000025
ORF7a	34	P34P	ccT	ccC	1	1	AY.39	0.000025
ORF7a	34	P34X	CCT	TAG	1	1	AY.39	0.000025
ORF7a	34	P34del	CCT	---	1	1	AY.39.1	0.00004
ORF7a	34	P34I	CCt	ATt	1	1	AY.4	0.000002
ORF7a	34	P34P	ccT	ccC	1	1	AY.4.2	0.000022
ORF7a	34	P34del	CCT	---	1	1	AY.4.2	0.000022
ORF7a	34	P34T	Cct	Act	1	1	AY.40	0.000964
ORF7a	34	P34P	ccT	ccC	1	1	AY.42	0.00004
ORF7a	34	P34F	CCt	TTt	1	1	AY.42	0.00004
ORF7a	34	P34T	Cct	Act	1	1	AY.43	0.000004
ORF7a	34	P34del1	ccT	cc-	1	1	AY.43	0.000004
ORF7a	34	P34T	Cct	Act	1	1	AY.44	0.000006
ORF7a	34	P34del	CCT	---	1	1	AY.45	0.000122
ORF7a	34	P34R	cCt	cGt	1	1	AY.46	0.000104
ORF7a	34	P34H	cCt	cAt	1	1	AY.46	0.000104
ORF7a	34	P34L	cCt	cTt	1	1	AY.46.3	0.000934
ORF7a	34	P34S	Cct	Tct	1	1	AY.46.5	0.000198
ORF7a	34	P34L	cCt	cTt	1	1	AY.48	0.000465
ORF7a	34	P34H	cCt	cAt	1	1	AY.5	0.000021
ORF7a	34	P34del	CCT	---	1	1	AY.5	0.000021
ORF7a	34	P34P	ccT	ccC	1	1	AY.5	0.000021
ORF7a	34	P34L	cCt	cTt	1	1	AY.5.3	0.000337
ORF7a	34	P34del	CCT	---	1	1	AY.5.4	0.000277
ORF7a	34	P34L	cCt	cTt	1	1	AY.51	0.000909
ORF7a	34	P34S	Cct	Tct	1	1	AY.54	0.000095
ORF7a	34	P34del	CCT	---	1	1	AY.54	0.000095
ORF7a	34	P34S	Cct	Tct	1	1	AY.55	0.000917
ORF7a	34	P34L	cCt	cTt	1	1	AY.59	0.00053
ORF7a	34	P34del	CCT	---	1	1	AY.6	0.000041
ORF7a	34	P34S	Cct	Tct	1	1	AY.61	0.000105
ORF7a	34	P34L	cCt	cTt	1	1	AY.62	0.000436
ORF7a	34	P34P	ccT	ccC	1	1	AY.62	0.000436
ORF7a	34	P34L	cCt	cTt	1	1	AY.65	0.000533
ORF7a	34	P34P	ccT	ccC	1	1	AY.66	0.00107
ORF7a	34	P34del	CCT	---	1	1	AY.66	0.00107
ORF7a	34	P34S	Cct	Tct	1	1	AY.69	0.000187
ORF7a	34	P34del	CCT	---	1	1	AY.7.1	0.000113
ORF7a	34	P34S	Cct	Tct	1	1	AY.7.2	0.000559
ORF7a	34	P34S	Cct	Tct	1	1	AY.73	0.000665
ORF7a	34	P34P	ccT	ccC	1	1	AY.75	0.000056
ORF7a	34	P34R	cCt	cGt	1	1	AY.75	0.000056
ORF7a	34	P34del	CCT	---	1	1	AY.76	0.004831
ORF7a	34	P34del	CCT	---	1	1	AY.79	0.001211
ORF7a	34	P34S	Cct	Tct	1	1	AY.79	0.001211
ORF7a	34	P34S	Cct	Tct	1	1	AY.8	0.000606
ORF7a	34	P34L	cCt	cTt	1	1	AY.80	0.001129
ORF7a	34	P34L	cCt	cTt	1	1	AY.81	0.001992
ORF7a	34	P34L	cCt	cTt	1	1	AY.82	0.001357
ORF7a	34	P34S	Cct	Tct	1	1	AY.84	0.000437
ORF7a	34	P34L	cCt	cTt	1	1	AY.84	0.000437
ORF7a	34	P34L	cCt	cTt	1	1	AY.86	0.00083
ORF7a	34	P34L	cCt	cTt	1	1	AY.89	0.004902
ORF7a	34	P34del	CCT	---	1	1	AY.9.1	0.000084
ORF7a	34	P34L	cCt	cTt	1	1	AY.91.1	0.004065
ORF7a	34	P34P	ccT	ccG	1	1	AY.92	0.000287
ORF7a	34	P34S	Cct	Tct	1	1	AY.93	0.000273
ORF7a	34	P34L	cCt	cTt	1	1	AY.93	0.000273
ORF7a	34	P34P	ccT	ccG	1	1	AY.93	0.000273
ORF7a	34	P34L	cCt	cTt	1	1	AY.95	0.000761
ORF7a	34	P34P	ccT	ccC	1	1	AY.98	0.000079
ORF7a	34	P34L	cCt	cTt	1	1	AY.99	0.001049
ORF7a	34	P34L	cCt	cTt	1	1	AY.99.1	0.001553
ORF7a	34	P34del	CCT	---	1	1	AY.99.2	0.000092
ORF7a	34	P34L	cCt	cTt	1	1	AZ.1	0.000867
ORF7a	34	P34P	ccT	ccC	1	1	B	0.000128
ORF7a	34	P34F	CCt	TTt	1	1	B.1	0.000009
ORF7a	34	P34R	cCt	cGt	1	1	B.1	0.000009
ORF7a	34	P34S	Cct	Tct	1	1	B.1.1.1	0.000327
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.121	0.002427
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.139	0.022727
ORF7a	34	P34S	Cct	Tct	1	1	B.1.1.157	0.000913
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.176	0.000439
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.189	0.001513
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.192	0.002309
ORF7a	34	P34S	Cct	Tct	1	1	B.1.1.194	0.00495
ORF7a	34	P34S	Cct	Tct	1	1	B.1.1.196	0.005714
ORF7a	34	P34S	Cct	Tct	1	1	B.1.1.207	0.001182
ORF7a	34	P34del	CCT	---	1	1	B.1.1.207	0.001182
ORF7a	34	P34R	cCt	cGt	1	1	B.1.1.214	0.000055
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.220	0.001859
ORF7a	34	P34del	CCT	---	1	1	B.1.1.222	0.000204
ORF7a	34	P34S	Cct	Tct	1	1	B.1.1.25	0.000569
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.25	0.000569
ORF7a	34	P34P	ccT	ccG	1	1	B.1.1.254	0.011236
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.263	0.001558
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.265	0.003155
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.274	0.005051
ORF7a	34	P34R	cCt	cGt	1	1	B.1.1.28	0.000311
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.288	0.001916
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.289	0.002083
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.294	0.001266
ORF7a	34	P34S	Cct	Tct	1	1	B.1.1.294	0.001266
ORF7a	34	P34S	Cct	Tct	1	1	B.1.1.307	0.002532
ORF7a	34	P34S	Cct	Tct	1	1	B.1.1.311	0.000358
ORF7a	34	P34R	cCt	cGt	1	1	B.1.1.311	0.000358
ORF7a	34	P34S	Cct	Tct	1	1	B.1.1.317	0.000412
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.318	0.000302
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.326	0.001761
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.33	0.000421
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.354	0.004386
ORF7a	34	P34S	Cct	Tct	1	1	B.1.1.397	0.002252
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.398	0.003226
ORF7a	34	P34S	Cct	Tct	1	1	B.1.1.4	0.002976
ORF7a	34	P34S	Cct	Tct	1	1	B.1.1.429	0.004608
ORF7a	34	P34S	Cct	Tct	1	1	B.1.1.448	0.002033
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.45	0.014085
ORF7a	34	P34S	Cct	Tct	1	1	B.1.1.464	0.001473
ORF7a	34	P34del	CCT	---	1	1	B.1.1.519	0.00004
ORF7a	34	P34del	CCT	---	1	1	B.1.1.522	0.017241
ORF7a	34	P34S	Cct	Tct	1	1	B.1.1.528	0.004808
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.63	0.000386
ORF7a	34	P34E	CCT	GAA	1	1	B.1.1.7	0.000001
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.70	0.000341
ORF7a	34	P34L	cCt	cTt	1	1	B.1.1.8	0.003584
ORF7a	34	P34S	Cct	Tct	1	1	B.1.104	0.00369
ORF7a	34	P34S	Cct	Tct	1	1	B.1.110.3	0.000718
ORF7a	34	P34L	cCt	cTt	1	1	B.1.111	0.001175
ORF7a	34	P34S	Cct	Tct	1	1	B.1.111	0.001175
ORF7a	34	P34del	CCT	---	1	1	B.1.115	0.021739
ORF7a	34	P34S	Cct	Tct	1	1	B.1.124	0.007812
ORF7a	34	P34L	cCt	cTt	1	1	B.1.147	0.000756
ORF7a	34	P34del	CCT	---	1	1	B.1.160	0.000031
ORF7a	34	P34del2	CCt	--t	1	1	B.1.160	0.000031
ORF7a	34	P34S	Cct	Tct	1	1	B.1.160.30	0.002976
ORF7a	34	P34H	cCt	cAt	1	1	B.1.177	0.000013
ORF7a	34	P34del2	cCT	c--	1	1	B.1.177	0.000013
ORF7a	34	P34S	Cct	Tct	1	1	B.1.177.10	0.000878
ORF7a	34	P34S	Cct	Tct	1	1	B.1.177.12	0.000152
ORF7a	34	P34L	cCt	cTt	1	1	B.1.177.15	0.000631
ORF7a	34	P34S	Cct	Tct	1	1	B.1.177.16	0.000664
ORF7a	34	P34L	cCt	cTt	1	1	B.1.177.17	0.000821
ORF7a	34	P34S	Cct	Tct	1	1	B.1.177.18	0.00116
ORF7a	34	P34L	cCt	cTt	1	1	B.1.177.24	0.001295
ORF7a	34	P34S	Cct	Tct	1	1	B.1.177.24	0.001295
ORF7a	34	P34L	cCt	cTt	1	1	B.1.177.32	0.00135
ORF7a	34	P34S	Cct	Tct	1	1	B.1.177.35	0.000691
ORF7a	34	P34S	Cct	Tct	1	1	B.1.177.40	0.005155
ORF7a	34	P34L	cCt	cTt	1	1	B.1.177.43	0.001477
ORF7a	34	P34S	Cct	Tct	1	1	B.1.177.46	0.000918
ORF7a	34	P34L	cCt	cTt	1	1	B.1.177.50	0.004695
ORF7a	34	P34S	Cct	Tct	1	1	B.1.177.52	0.001757
ORF7a	34	P34L	cCt	cTt	1	1	B.1.177.54	0.000606
ORF7a	34	P34P	ccT	ccC	1	1	B.1.177.54	0.000606
ORF7a	34	P34S	Cct	Tct	1	1	B.1.177.56	0.000668
ORF7a	34	P34I	CCt	ATt	1	1	B.1.177.63	0.002703
ORF7a	34	P34L	cCt	cTt	1	1	B.1.177.7	0.000165
ORF7a	34	P34R	cCt	cGt	1	1	B.1.177.7	0.000165
ORF7a	34	P34S	Cct	Tct	1	1	B.1.177.7	0.000165
ORF7a	34	P34S	Cct	Tct	1	1	B.1.177.73	0.000566
ORF7a	34	P34L	cCt	cTt	1	1	B.1.177.73	0.000566
ORF7a	34	P34S	Cct	Tct	1	1	B.1.177.77	0.000726
ORF7a	34	P34S	Cct	Tct	1	1	B.1.177.8	0.000752
ORF7a	34	P34L	cCt	cTt	1	1	B.1.177.80	0.001912
ORF7a	34	P34P	ccT	ccA	1	1	B.1.177.80	0.001912
ORF7a	34	P34del	CCT	---	1	1	B.1.177.80	0.001912
ORF7a	34	P34del	CCT	---	1	1	B.1.177.81	0.000189
ORF7a	34	P34L	cCt	cTt	1	1	B.1.177.81	0.000189
ORF7a	34	P34S	Cct	Tct	1	1	B.1.177.82	0.000477
ORF7a	34	P34del	CCT	---	1	1	B.1.177.83	0.001481
ORF7a	34	P34S	Cct	Tct	1	1	B.1.177.86	0.000183
ORF7a	34	P34L	cCt	cTt	1	1	B.1.189	0.004292
ORF7a	34	P34S	Cct	Tct	1	1	B.1.195	0.005025
ORF7a	34	P34P	ccT	ccC	1	1	B.1.206	0.000816
ORF7a	34	P34S	Cct	Tct	1	1	B.1.210	0.002132
ORF7a	34	P34L	cCt	cTt	1	1	B.1.214.1	0.02
ORF7a	34	P34L	cCt	cTt	1	1	B.1.214.2	0.0006
ORF7a	34	P34del	CCT	---	1	1	B.1.221	0.000071
ORF7a	34	P34H	cCt	cAt	1	1	B.1.232	0.000537
ORF7a	34	P34S	Cct	Tct	1	1	B.1.232	0.000537
ORF7a	34	P34S	Cct	Tct	1	1	B.1.239	0.001221
ORF7a	34	P34del	CCT	---	1	1	B.1.240	0.000216
ORF7a	34	P34P	ccT	ccC	1	1	B.1.241	0.000812
ORF7a	34	P34L	cCt	cTt	1	1	B.1.245	0.03125
ORF7a	34	P34L	cCt	cTt	1	1	B.1.252	0.006623
ORF7a	34	P34S	Cct	Tct	1	1	B.1.252	0.006623
ORF7a	34	P34del	CCT	---	1	1	B.1.258.17	0.000104
ORF7a	34	P34L	cCt	cTt	1	1	B.1.267	0.018519
ORF7a	34	P34S	Cct	Tct	1	1	B.1.284	0.013158
ORF7a	34	P34L	cCt	cTt	1	1	B.1.305	0.002151
ORF7a	34	P34S	Cct	Tct	1	1	B.1.306	0.005714
ORF7a	34	P34S	Cct	Tct	1	1	B.1.311	0.000275
ORF7a	34	P34L	cCt	cTt	1	1	B.1.336	0.002439
ORF7a	34	P34L	cCt	cTt	1	1	B.1.338	0.008621
ORF7a	34	P34L	cCt	cTt	1	1	B.1.349	0.000715
ORF7a	34	P34S	Cct	Tct	1	1	B.1.349	0.000715
ORF7a	34	P34R	cCt	cGt	1	1	B.1.351	0.00003
ORF7a	34	P34H	cCt	cAt	1	1	B.1.36	0.000146
ORF7a	34	P34L	cCt	cTt	1	1	B.1.36	0.000146
ORF7a	34	P34S	Cct	Tct	1	1	B.1.36.1	0.00114
ORF7a	34	P34L	cCt	cTt	1	1	B.1.36.10	0.004785
ORF7a	34	P34L	cCt	cTt	1	1	B.1.36.19	0.009259
ORF7a	34	P34S	Cct	Tct	1	1	B.1.36.27	0.000763
ORF7a	34	P34L	cCt	cTt	1	1	B.1.36.29	0.000517
ORF7a	34	P34A	Cct	Gct	1	1	B.1.36.29	0.000517
ORF7a	34	P34L	cCt	cTt	1	1	B.1.36.31	0.001751
ORF7a	34	P34S	Cct	Tct	1	1	B.1.36.39	0.002217
ORF7a	34	P34P	ccT	ccA	1	1	B.1.36.8	0.001
ORF7a	34	P34S	Cct	Tct	1	1	B.1.361	0.001289
ORF7a	34	P34H	cCt	cAt	1	1	B.1.362	0.001541
ORF7a	34	P34L	cCt	cTt	1	1	B.1.369	0.000285
ORF7a	34	P34S	Cct	Tct	1	1	B.1.369	0.000285
ORF7a	34	P34S	Cct	Tct	1	1	B.1.371	0.001122
ORF7a	34	P34L	cCt	cTt	1	1	B.1.375	0.00082
ORF7a	34	P34S	Cct	Tct	1	1	B.1.375	0.00082
ORF7a	34	P34S	Cct	Tct	1	1	B.1.389	0.001002
ORF7a	34	P34S	Cct	Tct	1	1	B.1.398	0.002976
ORF7a	34	P34L	cCt	cTt	1	1	B.1.416	0.001269
ORF7a	34	P34L	cCt	cTt	1	1	B.1.421	0.007463
ORF7a	34	P34del	CCT	---	1	1	B.1.427	0.00005
ORF7a	34	P34H	cCt	cAt	1	1	B.1.429	0.000024
ORF7a	34	P34T	Cct	Act	1	1	B.1.429	0.000024
ORF7a	34	P34del	CCT	---	1	1	B.1.438.1	0.000107
ORF7a	34	P34del	CCT	---	1	1	B.1.459	0.004082
ORF7a	34	P34L	cCt	cTt	1	1	B.1.466.2	0.000391
ORF7a	34	P34del	CCT	---	1	1	B.1.466.2	0.000391
ORF7a	34	P34P	ccT	ccC	1	1	B.1.466.2	0.000391
ORF7a	34	P34S	Cct	Tct	1	1	B.1.466.2	0.000391
ORF7a	34	P34del	CCT	---	1	1	B.1.468	0.005714
ORF7a	34	P34del	CCT	---	1	1	B.1.470	0.001404
ORF7a	34	P34L	cCt	cTt	1	1	B.1.471	0.002732
ORF7a	34	P34S	Cct	Tct	1	1	B.1.471	0.002732
ORF7a	34	P34S	Cct	Tct	1	1	B.1.479	0.038462
ORF7a	34	P34S	Cct	Tct	1	1	B.1.509	0.000866
ORF7a	34	P34L	cCt	cTt	1	1	B.1.517	0.000427
ORF7a	34	P34S	Cct	Tct	1	1	B.1.517	0.000427
ORF7a	34	P34R	cCt	cGt	1	1	B.1.526	0.000024
ORF7a	34	P34S	Cct	Tct	1	1	B.1.540	0.009709
ORF7a	34	P34S	Cct	Tct	1	1	B.1.544	0.006024
ORF7a	34	P34S	Cct	Tct	1	1	B.1.546	0.003704
ORF7a	34	P34S	Cct	Tct	1	1	B.1.556	0.007519
ORF7a	34	P34L	cCt	cTt	1	1	B.1.561	0.000397
ORF7a	34	P34S	Cct	Tct	1	1	B.1.565	0.00081
ORF7a	34	P34L	cCt	cTt	1	1	B.1.570	0.002941
ORF7a	34	P34L	cCt	cTt	1	1	B.1.575	0.000303
ORF7a	34	P34S	Cct	Tct	1	1	B.1.577	0.000687
ORF7a	34	P34del	CCT	---	1	1	B.1.596	0.000087
ORF7a	34	P34S	Cct	Tct	1	1	B.1.609	0.000479
ORF7a	34	P34L	cCt	cTt	1	1	B.1.609	0.000479
ORF7a	34	P34F	CCt	TTt	1	1	B.1.617.2	0.000004
ORF7a	34	P34I	CCt	ATt	1	1	B.1.617.2	0.000004
ORF7a	34	P34del1	ccT	cc-	1	1	B.1.617.2	0.000004
ORF7a	34	P34del	CCT	---	1	1	B.1.617.3	0.002985
ORF7a	34	P34H	cCt	cAt	1	1	B.1.619	0.000871
ORF7a	34	P34S	Cct	Tct	1	1	B.1.619.1	0.000641
ORF7a	34	P34del	CCT	---	1	1	B.1.620	0.000946
ORF7a	34	P34L	cCt	cTt	1	1	B.1.623	0.000536
ORF7a	34	P34L	cCt	cTt	1	1	B.1.626	0.005714
ORF7a	34	P34del	CCT	---	1	1	B.1.630	0.005236
ORF7a	34	P34del	CCT	---	1	1	B.1.636	0.006711
ORF7a	34	P34S	Cct	Tct	1	1	B.1.8	0.001972
ORF7a	34	P34S	Cct	Tct	1	1	B.1.91	0.002075
ORF7a	34	P34S	Cct	Tct	1	1	B.1.93	0.000934
ORF7a	34	P34L	cCt	cTt	1	1	B.1.94	0.027027
ORF7a	34	P34S	Cct	Tct	1	1	B.18	0.043478
ORF7a	34	P34S	Cct	Tct	1	1	B.38	0.02381
ORF7a	34	P34L	cCt	cTt	1	1	B.4.7	0.010101
ORF7a	34	P34S	Cct	Tct	1	1	B.40	0.000364
ORF7a	34	P34S	Cct	Tct	1	1	B.55	0.00295
ORF7a	34	P34L	cCt	cTt	1	1	B.58	0.010204
ORF7a	34	P34L	cCt	cTt	1	1	B.6.6	0.000889
ORF7a	34	P34S	Cct	Tct	1	1	B.6.6	0.000889
ORF7a	34	P34P	ccT	ccC	1	1	C.14	0.004329
ORF7a	34	P34L	cCt	cTt	1	1	C.16	0.00106
ORF7a	34	P34P	ccT	ccC	1	1	C.16	0.00106
ORF7a	34	P34L	cCt	cTt	1	1	C.30	0.001727
ORF7a	34	P34S	Cct	Tct	1	1	C.35	0.000774
ORF7a	34	P34L	cCt	cTt	1	1	C.36.3	0.000567
ORF7a	34	P34P	ccT	ccC	1	1	C.37	0.000116
ORF7a	34	P34F	CCt	TTt	1	1	D.2	0.000075
ORF7a	34	P34L	cCt	cTt	1	1	N.9	0.005952
ORF7a	34	P34S	Cct	Tct	1	1	N.9	0.005952
ORF7a	34	P34R	cCt	cGt	1	1	P.1	0.000016
ORF7a	34	P34S	Cct	Tct	1	1	P.1.1	0.000318
ORF7a	34	P34H	cCt	cAt	1	1	P.1.14	0.000048
ORF7a	34	P34R	cCt	cGt	1	1	P.1.15	0.000232
ORF7a	34	P34H	cCt	cAt	1	1	P.1.15	0.000232
ORF7a	34	P34L	cCt	cTt	1	1	P.1.17	0.000162
ORF7a	34	P34S	Cct	Tct	1	1	P.1.2	0.001156
ORF7a	34	P34P	ccT	ccG	1	1	P.2	0.000187
ORF7a	34	P34del	CCT	---	1	1	Q.2	0.000613
ORF7a	34	P34L	cCt	cTt	1	1	Q.4	0.000455
ORF7a	34	P34S	Cct	Tct	1	1	Q.7	0.001111
ORF7a	34	P34del	CCT	---	1	1	R.1	0.00009
ORF7a	34	P34S	Cct	Tct	1	1	Y.1	0.012821

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.