CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF7a : CodonNum = 102

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	102	L102del		del	CTT	---	9467	9467	1	27697-27699
ORF7a	102	L102F		nonsyn	Ctt	Ttt	1066	1064	0.998124	27697-27699
ORF7a	102	L102F		nonsyn	CtT	TtC	1066	2	0.00187617	27697-27699
ORF7a	102	L102del1		del	Ctt	-tt	759	714	0.940711	27697-27699
ORF7a	102	L102del1		del	ctT	ct-	759	37	0.0487484	27697-27699
ORF7a	102	L102del1		del	CtT	-tN	759	3	0.00395257	27697-27699
ORF7a	102	L102del1		del	CtT	Tt-	759	3	0.00395257	27697-27699
ORF7a	102	L102del1		del	CTT	-NN	759	2	0.00263505	27697-27699
ORF7a	102	L102P		nonsyn	cTt	cCt	254	251	0.988189	27697-27699
ORF7a	102	L102P		nonsyn	cTT	cCA	254	2	0.00787402	27697-27699
ORF7a	102	L102P		nonsyn	cTT	cCC	254	1	0.00393701	27697-27699
ORF7a	102	L102L		syn	ctT	ctC	162	138	0.851852	27697-27699
ORF7a	102	L102L		syn	ctT	ctA	162	13	0.0802469	27697-27699
ORF7a	102	L102L		syn	ctT	ctG	162	6	0.037037	27697-27699
ORF7a	102	L102L		syn	CtT	TtG	162	4	0.0246914	27697-27699
ORF7a	102	L102L		syn	CtT	TtA	162	1	0.00617284	27697-27699
ORF7a	102	L102I		nonsyn	Ctt	Att	71	67	0.943662	27697-27699
ORF7a	102	L102I		nonsyn	CtT	AtA	71	4	0.056338	27697-27699
ORF7a	102	L102V		nonsyn	Ctt	Gtt	29	29	1	27697-27699
ORF7a	102	L102R		nonsyn	cTt	cGt	23	23	1	27697-27699
ORF7a	102	L102del2		del	cTT	c--	19	12	0.631579	27697-27699
ORF7a	102	L102del2		del	CTt	--t	19	7	0.368421	27697-27699
ORF7a	102	L102H		nonsyn	cTt	cAt	14	14	1	27697-27699
ORF7a	102	L102N		nonsyn	CTt	AAt	9	9	1	27697-27699
ORF7a	102	L102S		nonsyn	CTT	TCC	7	6	0.857143	27697-27699
ORF7a	102	L102K		nonsyn	CTT	AAG	7	4	0.571429	27697-27699
ORF7a	102	L102K		nonsyn	CTT	AAA	7	3	0.428571	27697-27699
ORF7a	102	L102S		nonsyn	CTT	TCA	7	1	0.142857	27697-27699
ORF7a	102	L102Y		nonsyn	CTt	TAt	6	5	0.833333	27697-27699
ORF7a	102	L102Y		nonsyn	CTT	TAC	6	1	0.166667	27697-27699
ORF7a	102	L102M		nonsyn	CtT	AtG	5	5	1	27697-27699
ORF7a	102	L102Q		nonsyn	cTT	cAA	4	4	1	27697-27699
ORF7a	102	L102X		nonsyn	CTT	TAG	4	4	1	27697-27699
ORF7a	102	L102T		nonsyn	CTt	ACt	4	3	0.75	27697-27699
ORF7a	102	L102T		nonsyn	CTT	ACA	4	1	0.25	27697-27699
ORF7a	102	L102C		nonsyn	CTt	TGt	1	1	1	27697-27699

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	102	L102del	CTT	---	9467	9467	All	0.001811
ORF7a	102	L102del	CTT	---	1764	1764	B.1.1.7	0.001579
ORF7a	102	L102del	CTT	---	1136	1136	AY.39.1.1	0.823188
ORF7a	102	L102F	Ctt	Ttt	1064	1066	All	0.000204
ORF7a	102	L102F	CtT	TtC	2	1066	All	0
ORF7a	102	L102del	CTT	---	877	877	AY.4	0.001365
ORF7a	102	L102del	CTT	---	800	800	AY.25	0.004812
ORF7a	102	L102del1	Ctt	-tt	714	759	All	0.000137
ORF7a	102	L102del1	ctT	ct-	37	759	All	0.000007
ORF7a	102	L102del1	CtT	-tN	3	759	All	0.000001
ORF7a	102	L102del1	CtT	Tt-	3	759	All	0.000001
ORF7a	102	L102del1	CTT	-NN	2	759	All	0
ORF7a	102	L102del	CTT	---	570	570	B.1.617.2	0.002146
ORF7a	102	L102del	CTT	---	337	337	AY.102	0.008935
ORF7a	102	L102F	Ctt	Ttt	308	310	B.1.1.7	0.000276
ORF7a	102	L102F	CtT	TtC	2	310	B.1.1.7	0.000002
ORF7a	102	L102del	CTT	---	292	292	AY.43	0.001294
ORF7a	102	L102del	CTT	---	279	279	AY.39.1	0.011052
ORF7a	102	L102del	CTT	---	259	259	AY.75	0.01451
ORF7a	102	L102P	cTt	cCt	251	254	All	0.000048
ORF7a	102	L102P	cTT	cCA	2	254	All	0
ORF7a	102	L102P	cTT	cCC	1	254	All	0
ORF7a	102	L102del	CTT	---	246	246	AY.44	0.001497
ORF7a	102	L102del	CTT	---	195	195	AY.103	0.001211
ORF7a	102	L102del	CTT	---	179	179	AY.4.2	0.003882
ORF7a	102	L102del1	Ctt	-tt	164	168	AY.4	0.000255
ORF7a	102	L102del1	ctT	ct-	4	168	AY.4	0.000006
ORF7a	102	L102L	ctT	ctC	138	162	All	0.000026
ORF7a	102	L102L	ctT	ctA	13	162	All	0.000002
ORF7a	102	L102L	ctT	ctG	6	162	All	0.000001
ORF7a	102	L102L	CtT	TtG	4	162	All	0.000001
ORF7a	102	L102L	CtT	TtA	1	162	All	0
ORF7a	102	L102del	CTT	---	161	161	AY.3	0.001601
ORF7a	102	L102P	cTt	cCt	130	130	AY.119	0.00459
ORF7a	102	L102del	CTT	---	112	112	AY.33	0.007479
ORF7a	102	L102del1	Ctt	-tt	99	107	B.1.1.7	0.000089
ORF7a	102	L102del1	ctT	ct-	7	107	B.1.1.7	0.000006
ORF7a	102	L102del1	CTT	-NN	1	107	B.1.1.7	0.000001
ORF7a	102	L102del	CTT	---	97	97	AY.39	0.002397
ORF7a	102	L102del	CTT	---	89	89	B.1	0.000815
ORF7a	102	L102del1	Ctt	-tt	81	81	AY.120	0.003011
ORF7a	102	L102del	CTT	---	77	77	P.1.10	0.020749
ORF7a	102	L102del	CTT	---	75	75	B.1.2	0.00066
ORF7a	102	L102I	Ctt	Att	67	71	All	0.000013
ORF7a	102	L102I	CtT	AtA	4	71	All	0.000001
ORF7a	102	L102del	CTT	---	70	70	P.1	0.001103
ORF7a	102	L102F	Ctt	Ttt	69	69	AY.25	0.000415
ORF7a	102	L102del	CTT	---	69	69	AY.29	0.001088
ORF7a	102	L102del	CTT	---	69	69	AY.46	0.007182
ORF7a	102	L102del	CTT	---	67	67	AY.5	0.001383
ORF7a	102	L102del1	Ctt	-tt	66	66	B.1.628	0.023256
ORF7a	102	L102del	CTT	---	63	63	AY.46.4	0.010364
ORF7a	102	L102del1	Ctt	-tt	58	62	B.1.617.2	0.000218
ORF7a	102	L102del1	ctT	ct-	3	62	B.1.617.2	0.000011
ORF7a	102	L102del1	CtT	-tN	1	62	B.1.617.2	0.000004
ORF7a	102	L102del	CTT	---	54	54	B.1.621	0.00478
ORF7a	102	L102del	CTT	---	52	52	AY.120	0.001933
ORF7a	102	L102del	CTT	---	47	47	AY.26	0.001331
ORF7a	102	L102del	CTT	---	47	47	B.1.177	0.000619
ORF7a	102	L102F	Ctt	Ttt	45	45	AY.7.1	0.005072
ORF7a	102	L102del	CTT	---	44	44	B.1.1.519	0.001747
ORF7a	102	L102del	CTT	---	43	43	B.1.526	0.001011
ORF7a	102	L102L	ctT	ctC	40	40	AY.4	0.000062
ORF7a	102	L102del	CTT	---	40	40	AY.47	0.001244
ORF7a	102	L102del	CTT	---	39	39	AY.7	0.007644
ORF7a	102	L102del	CTT	---	37	37	AY.118	0.002318
ORF7a	102	L102L	ctT	ctC	36	37	B.1.1.7	0.000032
ORF7a	102	L102L	ctT	ctG	1	37	B.1.1.7	0.000001
ORF7a	102	L102F	Ctt	Ttt	37	37	B.1.351	0.0011
ORF7a	102	L102del	CTT	---	35	35	AY.36	0.005187
ORF7a	102	L102del	CTT	---	34	34	AY.74	0.003932
ORF7a	102	L102del	CTT	---	34	34	B.1.1	0.000617
ORF7a	102	L102F	Ctt	Ttt	33	33	B.1.2	0.000291
ORF7a	102	L102F	Ctt	Ttt	32	32	P.1	0.000504
ORF7a	102	L102V	Ctt	Gtt	29	29	All	0.000006
ORF7a	102	L102F	Ctt	Ttt	29	29	B.1.429	0.000682
ORF7a	102	L102F	Ctt	Ttt	28	28	B.1.617.2	0.000105
ORF7a	102	L102del	CTT	---	27	27	AY.53	0.007763
ORF7a	102	L102del	CTT	---	26	26	AY.119	0.000918
ORF7a	102	L102del1	Ctt	-tt	25	26	AY.25	0.00015
ORF7a	102	L102del1	ctT	ct-	1	26	AY.25	0.000006
ORF7a	102	L102del	CTT	---	25	25	AY.100	0.00115
ORF7a	102	L102del	CTT	---	25	25	AY.42	0.001006
ORF7a	102	L102P	cTt	cCt	24	25	B.1.1.7	0.000021
ORF7a	102	L102P	cTT	cCC	1	25	B.1.1.7	0.000001
ORF7a	102	L102F	Ctt	Ttt	24	24	B.1.177	0.000316
ORF7a	102	L102del1	ctT	ct-	13	24	B.1.526	0.000306
ORF7a	102	L102del1	Ctt	-tt	11	24	B.1.526	0.000259
ORF7a	102	L102R	cTt	cGt	23	23	All	0.000004
ORF7a	102	L102del	CTT	---	22	22	B.1.1.214	0.00122
ORF7a	102	L102del1	Ctt	-tt	22	22	B.1.325	0.151724
ORF7a	102	L102del	CTT	---	22	22	B.1.427	0.001111
ORF7a	102	L102del	CTT	---	21	21	AY.9.1	0.001758
ORF7a	102	L102F	Ctt	Ttt	21	21	Q.1	0.002653
ORF7a	102	L102F	Ctt	Ttt	20	20	AY.4	0.000031
ORF7a	102	L102del	CTT	---	20	20	AY.7.2	0.011186
ORF7a	102	L102del	CTT	---	20	20	B.1.36.39	0.044346
ORF7a	102	L102del2	cTT	c--	12	19	All	0.000002
ORF7a	102	L102del2	CTt	--t	7	19	All	0.000001
ORF7a	102	L102F	Ctt	Ttt	19	19	AY.111	0.00348
ORF7a	102	L102F	Ctt	Ttt	19	19	AY.3	0.000189
ORF7a	102	L102del	CTT	---	19	19	AY.9	0.001284
ORF7a	102	L102F	Ctt	Ttt	19	19	AY.92	0.005458
ORF7a	102	L102F	Ctt	Ttt	19	19	B.1.596	0.001656
ORF7a	102	L102P	cTt	cCt	18	18	AY.4	0.000028
ORF7a	102	L102del1	Ctt	-tt	17	18	AY.44	0.000103
ORF7a	102	L102del1	CtT	Tt-	1	18	AY.44	0.000006
ORF7a	102	L102del	CTT	---	18	18	B.1.351	0.000535
ORF7a	102	L102del	CTT	---	17	17	AY.121	0.0023
ORF7a	102	L102del	CTT	---	16	16	AY.46.1	0.016427
ORF7a	102	L102del1	Ctt	-tt	16	16	AY.95	0.012177
ORF7a	102	L102I	Ctt	Att	16	16	B.1.637	0.001169
ORF7a	102	L102del	CTT	---	15	15	AY.34	0.001454
ORF7a	102	L102P	cTt	cCt	15	15	AY.47	0.000467
ORF7a	102	L102I	Ctt	Att	15	15	B.1.1.7	0.000013
ORF7a	102	L102H	cTt	cAt	14	14	All	0.000003
ORF7a	102	L102del1	Ctt	-tt	10	14	AY.102	0.000265
ORF7a	102	L102del1	ctT	ct-	3	14	AY.102	0.00008
ORF7a	102	L102del1	CtT	-tN	1	14	AY.102	0.000027
ORF7a	102	L102del	CTT	---	14	14	AY.9.2	0.000514
ORF7a	102	L102F	Ctt	Ttt	14	14	B.1	0.000128
ORF7a	102	L102del	CTT	---	14	14	B.1.1.37	0.0027
ORF7a	102	L102del	CTT	---	13	13	AY.113	0.001851
ORF7a	102	L102del	CTT	---	13	13	AY.6	0.000535
ORF7a	102	L102del	CTT	---	13	13	AY.98.1	0.00063
ORF7a	102	L102del	CTT	---	13	13	AY.99.2	0.001198
ORF7a	102	L102del	CTT	---	13	13	B.1.160	0.000405
ORF7a	102	L102F	Ctt	Ttt	13	13	B.1.160	0.000405
ORF7a	102	L102L	ctT	ctC	13	13	B.1.177.21	0.000994
ORF7a	102	L102del	CTT	---	13	13	B.1.177.62	0.015495
ORF7a	102	L102del	CTT	---	13	13	C.37	0.001509
ORF7a	102	L102del	CTT	---	12	12	AY.111	0.002198
ORF7a	102	L102del	CTT	---	12	12	AY.120.1	0.003852
ORF7a	102	L102del1	Ctt	-tt	12	12	AY.43	0.000053
ORF7a	102	L102del	CTT	---	12	12	AY.85	0.005126
ORF7a	102	L102del	CTT	---	12	12	B.1.637	0.000877
ORF7a	102	L102del1	Ctt	-tt	11	11	AY.26	0.000311
ORF7a	102	L102del	CTT	---	11	11	AY.91	0.008035
ORF7a	102	L102F	Ctt	Ttt	11	11	B.1.637	0.000804
ORF7a	102	L102F	Ctt	Ttt	10	10	AY.102	0.000265
ORF7a	102	L102del	CTT	---	10	10	AY.45	0.001217
ORF7a	102	L102F	Ctt	Ttt	10	10	B.1.1	0.000181
ORF7a	102	L102F	Ctt	Ttt	10	10	B.1.177.42	0.008945
ORF7a	102	L102del	CTT	---	10	10	B.1.234	0.001319
ORF7a	102	L102del	CTT	---	10	10	B.1.243	0.000696
ORF7a	102	L102F	Ctt	Ttt	10	10	B.1.369	0.002852
ORF7a	102	L102N	CTt	AAt	9	9	All	0.000002
ORF7a	102	L102del1	Ctt	-tt	9	9	AY.118	0.000564
ORF7a	102	L102del	CTT	---	9	9	AY.16	0.003417
ORF7a	102	L102del	CTT	---	9	9	AY.23	0.000628
ORF7a	102	L102F	Ctt	Ttt	9	9	AY.26	0.000255
ORF7a	102	L102del	CTT	---	9	9	AY.3.1	0.000767
ORF7a	102	L102F	Ctt	Ttt	9	9	AY.43	0.00004
ORF7a	102	L102del	CTT	---	9	9	AY.46.6	0.00065
ORF7a	102	L102F	Ctt	Ttt	9	9	B.1.177.86	0.001651
ORF7a	102	L102del1	Ctt	-tt	9	9	B.1.2	0.000079
ORF7a	102	L102del	CTT	---	9	9	B.1.429	0.000212
ORF7a	102	L102P	cTt	cCt	8	8	AY.103	0.00005
ORF7a	102	L102F	Ctt	Ttt	8	8	AY.14	0.000704
ORF7a	102	L102del	CTT	---	8	8	AY.20	0.000311
ORF7a	102	L102F	Ctt	Ttt	8	8	AY.47	0.000249
ORF7a	102	L102del1	Ctt	-tt	8	8	AY.70	0.001668
ORF7a	102	L102del	CTT	---	8	8	B	0.001022
ORF7a	102	L102del	CTT	---	8	8	B.1.1.284	0.000859
ORF7a	102	L102del	CTT	---	8	8	B.1.1.318	0.002414
ORF7a	102	L102del2	cTT	c--	5	8	B.1.1.7	0.000004
ORF7a	102	L102del2	CTt	--t	3	8	B.1.1.7	0.000003
ORF7a	102	L102F	Ctt	Ttt	8	8	B.1.177.83	0.011852
ORF7a	102	L102I	Ctt	Att	4	7		0.222222
ORF7a	102	L102I	CtT	AtA	3	7		0.166667
ORF7a	102	L102S	CTT	TCC	6	7	All	0.000001
ORF7a	102	L102K	CTT	AAG	4	7	All	0.000001
ORF7a	102	L102K	CTT	AAA	3	7	All	0.000001
ORF7a	102	L102S	CTT	TCA	1	7	All	0
ORF7a	102	L102del	CTT	---	7	7	AY.117	0.000592
ORF7a	102	L102del1	Ctt	-tt	7	7	AY.119	0.000247
ORF7a	102	L102del	CTT	---	7	7	AY.29.1	0.001544
ORF7a	102	L102S	CTT	TCC	6	7	AY.4	0.000009
ORF7a	102	L102S	CTT	TCA	1	7	AY.4	0.000002
ORF7a	102	L102del	CTT	---	7	7	AY.54	0.000667
ORF7a	102	L102del	CTT	---	7	7	AY.86	0.005809
ORF7a	102	L102del	CTT	---	7	7	B.1.160.16	0.006506
ORF7a	102	L102del	CTT	---	7	7	B.1.221	0.000497
ORF7a	102	L102del	CTT	---	7	7	B.1.240	0.001509
ORF7a	102	L102del	CTT	---	7	7	B.1.525	0.000792
ORF7a	102	L102del	CTT	---	7	7	D.2	0.000525
ORF7a	102	L102F	Ctt	Ttt	7	7	L.3	0.024823
ORF7a	102	L102R	cTt	cGt	6	6	A	0.002322
ORF7a	102	L102del	CTT	---	6	6	AD.2	0.001314
ORF7a	102	L102Y	CTt	TAt	5	6	All	0.000001
ORF7a	102	L102Y	CTT	TAC	1	6	All	0
ORF7a	102	L102del	CTT	---	6	6	AY.14	0.000528
ORF7a	102	L102del	CTT	---	6	6	AY.19	0.006842
ORF7a	102	L102del	CTT	---	6	6	AY.27	0.000388
ORF7a	102	L102del1	Ctt	-tt	6	6	AY.3	0.00006
ORF7a	102	L102P	cTt	cCt	6	6	AY.3	0.00006
ORF7a	102	L102del1	Ctt	-tt	4	6	AY.39	0.000099
ORF7a	102	L102del1	CtT	-tN	1	6	AY.39	0.000025
ORF7a	102	L102del1	CTT	-NN	1	6	AY.39	0.000025
ORF7a	102	L102F	Ctt	Ttt	6	6	AY.44	0.000037
ORF7a	102	L102del	CTT	---	6	6	AY.46.5	0.00119
ORF7a	102	L102del	CTT	---	6	6	AY.68	0.001642
ORF7a	102	L102del	CTT	---	6	6	AY.98	0.000474
ORF7a	102	L102del	CTT	---	6	6	B.1.258	0.000399
ORF7a	102	L102del	CTT	---	6	6	B.1.422	0.004874
ORF7a	102	L102del	CTT	---	6	6	B.1.617.1	0.000774
ORF7a	102	L102del	CTT	---	6	6	B.1.8	0.011834
ORF7a	102	L102F	Ctt	Ttt	6	6	B.4.1	0.113208
ORF7a	102	L102del	CTT	---	6	6	P.1.1	0.001906
ORF7a	102	L102del	CTT	---	6	6	P.1.15	0.001394
ORF7a	102	L102F	Ctt	Ttt	6	6	P.1.16	0.002245
ORF7a	102	L102del	CTT	---	6	6	Q.4	0.002729
ORF7a	102	L102F	Ctt	Ttt	6	6	Q.8	0.000989
ORF7a	102	L102M	CtT	AtG	5	5	All	0.000001
ORF7a	102	L102L	ctT	ctC	5	5	AY.103	0.000031
ORF7a	102	L102F	Ctt	Ttt	5	5	AY.103	0.000031
ORF7a	102	L102P	cTt	cCt	5	5	AY.113	0.000712
ORF7a	102	L102V	Ctt	Gtt	5	5	AY.25	0.00003
ORF7a	102	L102del	CTT	---	5	5	AY.30	0.001979
ORF7a	102	L102del	CTT	---	5	5	AY.4.5	0.000537
ORF7a	102	L102L	ctT	ctC	5	5	AY.44	0.00003
ORF7a	102	L102del	CTT	---	5	5	AY.79	0.006053
ORF7a	102	L102F	Ctt	Ttt	5	5	AY.84	0.002187
ORF7a	102	L102F	Ctt	Ttt	5	5	AY.9	0.000338
ORF7a	102	L102del	CTT	---	5	5	B.1.1.486	0.007886
ORF7a	102	L102V	Ctt	Gtt	5	5	B.1.1.7	0.000004
ORF7a	102	L102del	CTT	---	5	5	B.1.177.60	0.001092
ORF7a	102	L102del	CTT	---	5	5	B.1.177.7	0.000824
ORF7a	102	L102R	cTt	cGt	5	5	B.1.351	0.000149
ORF7a	102	L102F	Ctt	Ttt	5	5	B.1.525	0.000566
ORF7a	102	L102del	CTT	---	5	5	B.1.596	0.000436
ORF7a	102	L102del	CTT	---	5	5	P.1.14	0.000239
ORF7a	102	L102del	CTT	---	5	5	P.2	0.000933
ORF7a	102	L102N	CTt	AAt	4	4		0.222222
ORF7a	102	L102H	cTt	cAt	4	4		0.222222
ORF7a	102	L102Q	cTT	cAA	4	4	All	0.000001
ORF7a	102	L102X	CTT	TAG	4	4	All	0.000001
ORF7a	102	L102T	CTt	ACt	3	4	All	0.000001
ORF7a	102	L102T	CTT	ACA	1	4	All	0
ORF7a	102	L102del1	Ctt	-tt	3	4	AY.103	0.000019
ORF7a	102	L102del1	CtT	Tt-	1	4	AY.103	0.000006
ORF7a	102	L102del	CTT	---	4	4	AY.105	0.002572
ORF7a	102	L102P	cTt	cCt	4	4	AY.106	0.00134
ORF7a	102	L102del	CTT	---	4	4	AY.12	0.001264
ORF7a	102	L102del	CTT	---	4	4	AY.13	0.000644
ORF7a	102	L102del	CTT	---	4	4	AY.21	0.00759
ORF7a	102	L102N	CTt	AAt	4	4	AY.26	0.000113
ORF7a	102	L102del	CTT	---	4	4	AY.35	0.000932
ORF7a	102	L102del	CTT	---	4	4	AY.5.3	0.00135
ORF7a	102	L102del	CTT	---	4	4	AY.7.1	0.000451
ORF7a	102	L102del	CTT	---	4	4	AY.73	0.002661
ORF7a	102	L102F	Ctt	Ttt	4	4	AY.9.1	0.000335
ORF7a	102	L102del1	Ctt	-tt	3	4	B.1	0.000027
ORF7a	102	L102del1	CtT	Tt-	1	4	B.1	0.000009
ORF7a	102	L102del1	Ctt	-tt	4	4	B.1.1	0.000073
ORF7a	102	L102P	cTt	cCt	4	4	B.1.1.519	0.000159
ORF7a	102	L102del	CTT	---	4	4	B.1.177.86	0.000734
ORF7a	102	L102F	Ctt	Ttt	4	4	B.1.210	0.008529
ORF7a	102	L102F	Ctt	Ttt	4	4	B.1.221	0.000284
ORF7a	102	L102F	Ctt	Ttt	4	4	B.1.240	0.000862
ORF7a	102	L102F	Ctt	Ttt	4	4	B.1.243	0.000278
ORF7a	102	L102del	CTT	---	4	4	B.1.258.11	0.001585
ORF7a	102	L102del	CTT	---	4	4	B.1.258.17	0.000416
ORF7a	102	L102del	CTT	---	4	4	B.1.287	0.121212
ORF7a	102	L102P	cTt	cCt	4	4	B.1.617.2	0.000015
ORF7a	102	L102L	ctT	ctC	4	4	B.1.617.2	0.000015
ORF7a	102	L102del	CTT	---	4	4	B.1.628	0.001409
ORF7a	102	L102del	CTT	---	4	4	N.7	0.117647
ORF7a	102	L102I	Ctt	Att	4	4	P.1	0.000063
ORF7a	102	L102del1	Ctt	-tt	3	4	P.1	0.000047
ORF7a	102	L102del1	ctT	ct-	1	4	P.1	0.000016
ORF7a	102	L102del	CTT	---	4	4	P.1.17	0.000647
ORF7a	102	L102del	CTT	---	4	4	Q.1	0.000505
ORF7a	102	L102F	Ctt	Ttt	4	4	Q.4	0.001819
ORF7a	102	L102del1	Ctt	-tt	4	4	Q.8	0.00066
ORF7a	102	L102del	CTT	---	4	4	Q.8	0.00066
ORF7a	102	L102Q	cTT	cAA	3	3		0.166667
ORF7a	102	L102L	ctT	ctA	3	3		0.166667
ORF7a	102	L102K	CTT	AAA	3	3		0.166667
ORF7a	102	L102L	ctT	ctC	3	3	AY.102	0.00008
ORF7a	102	L102I	Ctt	Att	3	3	AY.103	0.000019
ORF7a	102	L102del	CTT	---	3	3	AY.108	0.003308
ORF7a	102	L102del	CTT	---	3	3	AY.116	0.00086
ORF7a	102	L102del1	Ctt	-tt	3	3	AY.2	0.001068
ORF7a	102	L102del1	Ctt	-tt	3	3	AY.23	0.000209
ORF7a	102	L102del	CTT	---	3	3	AY.24	0.001293
ORF7a	102	L102X	CTT	TAG	3	3	AY.26	0.000085
ORF7a	102	L102I	Ctt	Att	3	3	AY.26	0.000085
ORF7a	102	L102Y	CTt	TAt	3	3	AY.26	0.000085
ORF7a	102	L102L	CtT	TtG	3	3	AY.26	0.000085
ORF7a	102	L102K	CTT	AAG	3	3	AY.26	0.000085
ORF7a	102	L102M	CtT	AtG	3	3	AY.26	0.000085
ORF7a	102	L102F	Ctt	Ttt	3	3	AY.29	0.000047
ORF7a	102	L102del	CTT	---	3	3	AY.37	0.000948
ORF7a	102	L102P	cTt	cCt	3	3	AY.39.1	0.000119
ORF7a	102	L102del1	Ctt	-tt	3	3	AY.4.2	0.000065
ORF7a	102	L102F	Ctt	Ttt	3	3	AY.42	0.000121
ORF7a	102	L102del	CTT	---	3	3	AY.46.2	0.001906
ORF7a	102	L102L	ctT	ctC	3	3	AY.5	0.000062
ORF7a	102	L102del1	Ctt	-tt	2	3	AY.6	0.000082
ORF7a	102	L102del1	ctT	ct-	1	3	AY.6	0.000041
ORF7a	102	L102del	CTT	---	3	3	AY.61	0.000314
ORF7a	102	L102del	CTT	---	3	3	AY.64	0.001786
ORF7a	102	L102V	Ctt	Gtt	3	3	AY.75.1	0.000541
ORF7a	102	L102del	CTT	---	3	3	AY.75.1	0.000541
ORF7a	102	L102del	CTT	---	3	3	AY.99	0.003148
ORF7a	102	L102P	cTt	cCt	3	3	B.1.1.1	0.00098
ORF7a	102	L102F	Ctt	Ttt	3	3	B.1.1.153	0.003286
ORF7a	102	L102del	CTT	---	3	3	B.1.1.170	0.003741
ORF7a	102	L102del	CTT	---	3	3	B.1.1.58	0.016129
ORF7a	102	L102R	cTt	cGt	3	3	B.1.1.7	0.000003
ORF7a	102	L102del	CTT	---	3	3	B.1.13	0.007126
ORF7a	102	L102P	cTt	cCt	3	3	B.1.177	0.00004
ORF7a	102	L102F	Ctt	Ttt	3	3	B.1.177.12	0.000455
ORF7a	102	L102del	CTT	---	3	3	B.1.177.57	0.000843
ORF7a	102	L102F	Ctt	Ttt	3	3	B.1.214.2	0.001799
ORF7a	102	L102del	CTT	---	3	3	B.1.311	0.000824
ORF7a	102	L102F	Ctt	Ttt	3	3	B.1.324	0.004815
ORF7a	102	L102del	CTT	---	3	3	B.1.351.2	0.000908
ORF7a	102	L102del	CTT	---	3	3	B.1.36	0.000438
ORF7a	102	L102del	CTT	---	3	3	B.1.36.17	0.001482
ORF7a	102	L102del	CTT	---	3	3	B.1.389	0.003006
ORF7a	102	L102F	Ctt	Ttt	3	3	B.1.427	0.000151
ORF7a	102	L102F	Ctt	Ttt	3	3	B.1.497	0.000944
ORF7a	102	L102F	Ctt	Ttt	3	3	B.1.526	0.000071
ORF7a	102	L102del	CTT	---	3	3	B.1.575	0.00091
ORF7a	102	L102F	Ctt	Ttt	3	3	B.1.595	0.000783
ORF7a	102	L102del	CTT	---	3	3	B.1.595	0.000783
ORF7a	102	L102I	Ctt	Att	2	3	B.1.617.2	0.000008
ORF7a	102	L102I	CtT	AtA	1	3	B.1.617.2	0.000004
ORF7a	102	L102del	CTT	---	3	3	B.1.626	0.017143
ORF7a	102	L102del	CTT	---	3	3	B.1.634	0.010274
ORF7a	102	L102del	CTT	---	3	3	B.31	0.011194
ORF7a	102	L102del1	Ctt	-tt	3	3	C.37	0.000348
ORF7a	102	L102F	Ctt	Ttt	3	3	C.37	0.000348
ORF7a	102	L102F	Ctt	Ttt	3	3	D.2	0.000225
ORF7a	102	L102F	Ctt	Ttt	3	3	Q.3	0.000435
ORF7a	102	L102del	CTT	---	3	3	Q.3	0.000435
ORF7a	102	L102del	CTT	---	3	3	R.1	0.00027
ORF7a	102	L102del	CTT	---	2	2		0.111111
ORF7a	102	L102P	cTT	cCA	1	2		0.055556
ORF7a	102	L102P	cTt	cCt	1	2		0.055556
ORF7a	102	L102T	CTt	ACt	1	2		0.055556
ORF7a	102	L102T	CTT	ACA	1	2		0.055556
ORF7a	102	L102del	CTT	---	2	2	A.2.5	0.000998
ORF7a	102	L102F	Ctt	Ttt	2	2	A.23.1	0.001408
ORF7a	102	L102del	CTT	---	2	2	A.28	0.005291
ORF7a	102	L102del	CTT	---	2	2	AY.10	0.00106
ORF7a	102	L102F	Ctt	Ttt	2	2	AY.100	0.000092
ORF7a	102	L102del1	Ctt	-tt	2	2	AY.101	0.000981
ORF7a	102	L102del2	cTT	c--	1	2	AY.103	0.000006
ORF7a	102	L102del2	CTt	--t	1	2	AY.103	0.000006
ORF7a	102	L102del	CTT	---	2	2	AY.104	0.003968
ORF7a	102	L102del	CTT	---	2	2	AY.106	0.00067
ORF7a	102	L102del	CTT	---	2	2	AY.107	0.000932
ORF7a	102	L102del	CTT	---	2	2	AY.109	0.001479
ORF7a	102	L102L	ctT	ctC	2	2	AY.11	0.002677
ORF7a	102	L102del	CTT	---	2	2	AY.114	0.000462
ORF7a	102	L102L	ctT	ctA	2	2	AY.116	0.000574
ORF7a	102	L102del2	cTT	c--	2	2	AY.14	0.000176
ORF7a	102	L102del1	Ctt	-tt	2	2	AY.14	0.000176
ORF7a	102	L102del1	ctT	ct-	1	2	AY.19	0.00114
ORF7a	102	L102del1	Ctt	-tt	1	2	AY.19	0.00114
ORF7a	102	L102P	cTt	cCt	2	2	AY.20	0.000078
ORF7a	102	L102P	cTt	cCt	2	2	AY.25	0.000012
ORF7a	102	L102L	CtT	TtG	1	2	AY.25	0.000006
ORF7a	102	L102L	ctT	ctC	1	2	AY.25	0.000006
ORF7a	102	L102I	Ctt	Att	2	2	AY.3	0.00002
ORF7a	102	L102F	Ctt	Ttt	2	2	AY.33	0.000134
ORF7a	102	L102F	Ctt	Ttt	2	2	AY.35	0.000466
ORF7a	102	L102del1	Ctt	-tt	2	2	AY.36	0.000296
ORF7a	102	L102del2	CTt	--t	2	2	AY.4	0.000003
ORF7a	102	L102R	cTt	cGt	2	2	AY.42	0.00008
ORF7a	102	L102P	cTt	cCt	2	2	AY.43	0.000009
ORF7a	102	L102H	cTt	cAt	2	2	AY.43	0.000009
ORF7a	102	L102R	cTt	cGt	2	2	AY.43	0.000009
ORF7a	102	L102P	cTt	cCt	2	2	AY.46.6	0.000144
ORF7a	102	L102V	Ctt	Gtt	2	2	AY.5	0.000041
ORF7a	102	L102del	CTT	---	2	2	AY.59	0.001059
ORF7a	102	L102F	Ctt	Ttt	2	2	AY.61	0.00021
ORF7a	102	L102del1	Ctt	-tt	2	2	AY.7	0.000392
ORF7a	102	L102del	CTT	---	2	2	AY.70	0.000417
ORF7a	102	L102del1	Ctt	-tt	2	2	AY.75.1	0.000361
ORF7a	102	L102del	CTT	---	2	2	AY.77	0.002255
ORF7a	102	L102del	CTT	---	2	2	AY.8	0.001212
ORF7a	102	L102del	CTT	---	2	2	AY.84	0.000875
ORF7a	102	L102del	CTT	---	2	2	AY.87	0.001665
ORF7a	102	L102del	CTT	---	2	2	AY.92	0.000575
ORF7a	102	L102del	CTT	---	2	2	AZ.6	0.016807
ORF7a	102	L102L	ctT	ctC	2	2	B.1	0.000018
ORF7a	102	L102V	Ctt	Gtt	2	2	B.1.1	0.000036
ORF7a	102	L102del1	Ctt	-tt	2	2	B.1.1.1	0.000653
ORF7a	102	L102del	CTT	---	2	2	B.1.1.155	0.142857
ORF7a	102	L102F	Ctt	Ttt	2	2	B.1.1.198	0.002937
ORF7a	102	L102del1	ctT	ct-	2	2	B.1.1.214	0.000111
ORF7a	102	L102F	Ctt	Ttt	2	2	B.1.1.216	0.001781
ORF7a	102	L102del	CTT	---	2	2	B.1.1.28	0.000622
ORF7a	102	L102del	CTT	---	2	2	B.1.1.317	0.000823
ORF7a	102	L102del	CTT	---	2	2	B.1.1.33	0.000842
ORF7a	102	L102del	CTT	---	2	2	B.1.1.348	0.001592
ORF7a	102	L102F	Ctt	Ttt	2	2	B.1.1.39	0.001019
ORF7a	102	L102del	CTT	---	2	2	B.1.1.449	0.045455
ORF7a	102	L102del1	Ctt	-tt	2	2	B.1.1.519	0.000079
ORF7a	102	L102del	CTT	---	2	2	B.1.1.63	0.000772
ORF7a	102	L102F	Ctt	Ttt	2	2	B.1.147	0.001512
ORF7a	102	L102del1	Ctt	-tt	2	2	B.1.160	0.000062
ORF7a	102	L102I	Ctt	Att	2	2	B.1.177	0.000026
ORF7a	102	L102del	CTT	---	2	2	B.1.177.12	0.000303
ORF7a	102	L102F	Ctt	Ttt	2	2	B.1.177.33	0.003289
ORF7a	102	L102del	CTT	---	2	2	B.1.177.4	0.000422
ORF7a	102	L102F	Ctt	Ttt	2	2	B.1.177.69	0.002967
ORF7a	102	L102del	CTT	---	2	2	B.1.177.80	0.003824
ORF7a	102	L102I	Ctt	Att	2	2	B.1.221	0.000142
ORF7a	102	L102F	Ctt	Ttt	2	2	B.1.258.17	0.000208
ORF7a	102	L102L	ctT	ctC	2	2	B.1.258.17	0.000208
ORF7a	102	L102del	CTT	---	2	2	B.1.306	0.011429
ORF7a	102	L102del	CTT	---	2	2	B.1.350	0.005865
ORF7a	102	L102L	ctT	ctC	1	2	B.1.351	0.00003
ORF7a	102	L102L	ctT	ctG	1	2	B.1.351	0.00003
ORF7a	102	L102F	Ctt	Ttt	2	2	B.1.36	0.000292
ORF7a	102	L102L	ctT	ctC	2	2	B.1.36.18	0.00084
ORF7a	102	L102F	Ctt	Ttt	2	2	B.1.400	0.000858
ORF7a	102	L102del1	Ctt	-tt	1	2	B.1.429	0.000024
ORF7a	102	L102del1	ctT	ct-	1	2	B.1.429	0.000024
ORF7a	102	L102F	Ctt	Ttt	2	2	B.1.439	0.011834
ORF7a	102	L102del	CTT	---	2	2	B.1.466.2	0.000782
ORF7a	102	L102F	Ctt	Ttt	2	2	B.1.577	0.001375
ORF7a	102	L102del	CTT	---	2	2	B.1.612	0.005305
ORF7a	102	L102del	CTT	---	2	2	B.1.621.1	0.001012
ORF7a	102	L102del	CTT	---	2	2	B.4.5	0.02381
ORF7a	102	L102del1	Ctt	-tt	2	2	P.1.12	0.000968
ORF7a	102	L102F	Ctt	Ttt	2	2	P.1.15	0.000465
ORF7a	102	L102del	CTT	---	2	2	P.1.7	0.000639
ORF7a	102	L102F	Ctt	Ttt	2	2	P.2	0.000373
ORF7a	102	L102V	Ctt	Gtt	2	2	Q.4	0.00091
ORF7a	102	L102I	Ctt	Att	2	2	R.1	0.00018
ORF7a	102	L102F	Ctt	Ttt	1	1		0.055556
ORF7a	102	L102V	Ctt	Gtt	1	1	A	0.000387
ORF7a	102	L102del	CTT	---	1	1	A	0.000387
ORF7a	102	L102del	CTT	---	1	1	A.1	0.000282
ORF7a	102	L102del	CTT	---	1	1	A.2.2	0.001689
ORF7a	102	L102R	cTt	cGt	1	1	A.2.2	0.001689
ORF7a	102	L102P	cTt	cCt	1	1	A.2.4	0.003367
ORF7a	102	L102F	Ctt	Ttt	1	1	A.2.5	0.000499
ORF7a	102	L102del	CTT	---	1	1	A.21	0.00277
ORF7a	102	L102del	CTT	---	1	1	A.23	0.010526
ORF7a	102	L102del1	Ctt	-tt	1	1	A.6	0.005128
ORF7a	102	L102L	ctT	ctC	1	1	A.6	0.005128
ORF7a	102	L102F	Ctt	Ttt	1	1	AD.1	0.004115
ORF7a	102	L102F	Ctt	Ttt	1	1	AD.2	0.000219
ORF7a	102	L102del	CTT	---	1	1	AH.3	0.003802
ORF7a	102	L102C	CTt	TGt	1	1	All	0
ORF7a	102	L102del	CTT	---	1	1	AW.1	0.003049
ORF7a	102	L102L	ctT	ctC	1	1	AY.10	0.00053
ORF7a	102	L102del1	Ctt	-tt	1	1	AY.100	0.000046
ORF7a	102	L102R	cTt	cGt	1	1	AY.103	0.000006
ORF7a	102	L102del	CTT	---	1	1	AY.11	0.001339
ORF7a	102	L102P	cTt	cCt	1	1	AY.110	0.000113
ORF7a	102	L102L	ctT	ctC	1	1	AY.117	0.000085
ORF7a	102	L102F	Ctt	Ttt	1	1	AY.118	0.000063
ORF7a	102	L102I	Ctt	Att	1	1	AY.119	0.000035
ORF7a	102	L102F	Ctt	Ttt	1	1	AY.12	0.000316
ORF7a	102	L102L	ctT	ctG	1	1	AY.12	0.000316
ORF7a	102	L102F	Ctt	Ttt	1	1	AY.120	0.000037
ORF7a	102	L102F	Ctt	Ttt	1	1	AY.121	0.000135
ORF7a	102	L102H	cTt	cAt	1	1	AY.14	0.000088
ORF7a	102	L102L	ctT	ctA	1	1	AY.19	0.00114
ORF7a	102	L102F	Ctt	Ttt	1	1	AY.19	0.00114
ORF7a	102	L102L	ctT	ctC	1	1	AY.23	0.00007
ORF7a	102	L102F	Ctt	Ttt	1	1	AY.23	0.00007
ORF7a	102	L102I	Ctt	Att	1	1	AY.23	0.00007
ORF7a	102	L102del1	Ctt	-tt	1	1	AY.24	0.000431
ORF7a	102	L102X	CTT	TAG	1	1	AY.25	0.000006
ORF7a	102	L102M	CtT	AtG	1	1	AY.25	0.000006
ORF7a	102	L102I	Ctt	Att	1	1	AY.25	0.000006
ORF7a	102	L102H	cTt	cAt	1	1	AY.25	0.000006
ORF7a	102	L102T	CTt	ACt	1	1	AY.25	0.000006
ORF7a	102	L102K	CTT	AAG	1	1	AY.25	0.000006
ORF7a	102	L102N	CTt	AAt	1	1	AY.25	0.000006
ORF7a	102	L102Y	CTt	TAt	1	1	AY.25	0.000006
ORF7a	102	L102V	Ctt	Gtt	1	1	AY.26	0.000028
ORF7a	102	L102F	Ctt	Ttt	1	1	AY.27	0.000065
ORF7a	102	L102L	ctT	ctA	1	1	AY.3	0.00001
ORF7a	102	L102V	Ctt	Gtt	1	1	AY.3	0.00001
ORF7a	102	L102F	Ctt	Ttt	1	1	AY.3.1	0.000085
ORF7a	102	L102L	ctT	ctC	1	1	AY.30	0.000396
ORF7a	102	L102del	CTT	---	1	1	AY.32	0.000532
ORF7a	102	L102del1	Ctt	-tt	1	1	AY.33	0.000067
ORF7a	102	L102P	cTt	cCt	1	1	AY.34	0.000097
ORF7a	102	L102del	CTT	---	1	1	AY.34.1	0.00051
ORF7a	102	L102F	Ctt	Ttt	1	1	AY.37	0.000316
ORF7a	102	L102del2	cTT	c--	1	1	AY.38	0.000499
ORF7a	102	L102del	CTT	---	1	1	AY.38	0.000499
ORF7a	102	L102L	ctT	ctA	1	1	AY.39	0.000025
ORF7a	102	L102I	Ctt	Att	1	1	AY.4	0.000002
ORF7a	102	L102H	cTt	cAt	1	1	AY.4	0.000002
ORF7a	102	L102F	Ctt	Ttt	1	1	AY.4.2	0.000022
ORF7a	102	L102F	Ctt	Ttt	1	1	AY.4.5	0.000107
ORF7a	102	L102L	ctT	ctC	1	1	AY.42	0.00004
ORF7a	102	L102del2	cTT	c--	1	1	AY.43	0.000004
ORF7a	102	L102V	Ctt	Gtt	1	1	AY.43	0.000004
ORF7a	102	L102L	ctT	ctA	1	1	AY.43	0.000004
ORF7a	102	L102Y	CTT	TAC	1	1	AY.44	0.000006
ORF7a	102	L102P	cTt	cCt	1	1	AY.44	0.000006
ORF7a	102	L102I	Ctt	Att	1	1	AY.44	0.000006
ORF7a	102	L102P	cTt	cCt	1	1	AY.46	0.000104
ORF7a	102	L102del1	Ctt	-tt	1	1	AY.46	0.000104
ORF7a	102	L102F	Ctt	Ttt	1	1	AY.46	0.000104
ORF7a	102	L102P	cTt	cCt	1	1	AY.46.5	0.000198
ORF7a	102	L102del1	Ctt	-tt	1	1	AY.46.6	0.000072
ORF7a	102	L102del1	Ctt	-tt	1	1	AY.47	0.000031
ORF7a	102	L102del1	Ctt	-tt	1	1	AY.48	0.000465
ORF7a	102	L102del	CTT	---	1	1	AY.48	0.000465
ORF7a	102	L102del1	Ctt	-tt	1	1	AY.5	0.000021
ORF7a	102	L102F	Ctt	Ttt	1	1	AY.5	0.000021
ORF7a	102	L102P	cTt	cCt	1	1	AY.5	0.000021
ORF7a	102	L102H	cTt	cAt	1	1	AY.5.4	0.000277
ORF7a	102	L102del	CTT	---	1	1	AY.5.4	0.000277
ORF7a	102	L102del	CTT	---	1	1	AY.51	0.000909
ORF7a	102	L102L	ctT	ctC	1	1	AY.57	0.000656
ORF7a	102	L102del	CTT	---	1	1	AY.58	0.000907
ORF7a	102	L102del	CTT	---	1	1	AY.60	0.000938
ORF7a	102	L102del2	cTT	c--	1	1	AY.60	0.000938
ORF7a	102	L102del1	Ctt	-tt	1	1	AY.60	0.000938
ORF7a	102	L102L	ctT	ctC	1	1	AY.61	0.000105
ORF7a	102	L102del	CTT	---	1	1	AY.62	0.000436
ORF7a	102	L102F	Ctt	Ttt	1	1	AY.67	0.000464
ORF7a	102	L102I	Ctt	Att	1	1	AY.67	0.000464
ORF7a	102	L102del	CTT	---	1	1	AY.69	0.000187
ORF7a	102	L102L	ctT	ctA	1	1	AY.7.1	0.000113
ORF7a	102	L102F	Ctt	Ttt	1	1	AY.70	0.000209
ORF7a	102	L102del	CTT	---	1	1	AY.72	0.001361
ORF7a	102	L102I	Ctt	Att	1	1	AY.75	0.000056
ORF7a	102	L102P	cTt	cCt	1	1	AY.75.1	0.00018
ORF7a	102	L102F	Ctt	Ttt	1	1	AY.75.1	0.00018
ORF7a	102	L102del	CTT	---	1	1	AY.83	0.001724
ORF7a	102	L102H	cTt	cAt	1	1	AY.85	0.000427
ORF7a	102	L102del	CTT	---	1	1	AY.88	0.000884
ORF7a	102	L102del1	Ctt	-tt	1	1	AY.9	0.000068
ORF7a	102	L102L	ctT	ctA	1	1	AY.9.2	0.000037
ORF7a	102	L102del1	Ctt	-tt	1	1	AY.92	0.000287
ORF7a	102	L102del	CTT	---	1	1	AY.93	0.000273
ORF7a	102	L102F	Ctt	Ttt	1	1	AY.95	0.000761
ORF7a	102	L102del	CTT	---	1	1	AY.96	0.002075
ORF7a	102	L102del1	Ctt	-tt	1	1	AY.98	0.000079
ORF7a	102	L102L	ctT	ctC	1	1	AY.98.1	0.000048
ORF7a	102	L102V	Ctt	Gtt	1	1	AY.98.1	0.000048
ORF7a	102	L102del	CTT	---	1	1	AZ.2	0.000821
ORF7a	102	L102H	cTt	cAt	1	1	B.1	0.000009
ORF7a	102	L102P	cTt	cCt	1	1	B.1	0.000009
ORF7a	102	L102I	Ctt	Att	1	1	B.1	0.000009
ORF7a	102	L102Y	CTt	TAt	1	1	B.1.1	0.000018
ORF7a	102	L102C	CTt	TGt	1	1	B.1.1	0.000018
ORF7a	102	L102H	cTt	cAt	1	1	B.1.1	0.000018
ORF7a	102	L102P	cTT	cCA	1	1	B.1.1	0.000018
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.1.113	0.006993
ORF7a	102	L102del	CTT	---	1	1	B.1.1.121	0.002427
ORF7a	102	L102del	CTT	---	1	1	B.1.1.132	0.014925
ORF7a	102	L102del	CTT	---	1	1	B.1.1.168	0.026316
ORF7a	102	L102del	CTT	---	1	1	B.1.1.189	0.001513
ORF7a	102	L102del	CTT	---	1	1	B.1.1.216	0.00089
ORF7a	102	L102del1	Ctt	-tt	1	1	B.1.1.222	0.000204
ORF7a	102	L102del	CTT	---	1	1	B.1.1.222	0.000204
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.1.25	0.000569
ORF7a	102	L102del	CTT	---	1	1	B.1.1.258	0.003257
ORF7a	102	L102L	ctT	ctG	1	1	B.1.1.265	0.003155
ORF7a	102	L102del	CTT	---	1	1	B.1.1.265	0.003155
ORF7a	102	L102del	CTT	---	1	1	B.1.1.277	0.000759
ORF7a	102	L102del1	Ctt	-tt	1	1	B.1.1.28	0.000311
ORF7a	102	L102del	CTT	---	1	1	B.1.1.280	0.003086
ORF7a	102	L102del	CTT	---	1	1	B.1.1.294	0.001266
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.1.306	0.000438
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.1.311	0.000358
ORF7a	102	L102del	CTT	---	1	1	B.1.1.312	0.001912
ORF7a	102	L102del	CTT	---	1	1	B.1.1.316	0.000925
ORF7a	102	L102del1	Ctt	-tt	1	1	B.1.1.318	0.000302
ORF7a	102	L102L	ctT	ctC	1	1	B.1.1.318	0.000302
ORF7a	102	L102del	CTT	---	1	1	B.1.1.331	0.011628
ORF7a	102	L102del	CTT	---	1	1	B.1.1.369	0.000446
ORF7a	102	L102I	Ctt	Att	1	1	B.1.1.374	0.002375
ORF7a	102	L102del	CTT	---	1	1	B.1.1.376	0.005952
ORF7a	102	L102del	CTT	---	1	1	B.1.1.398	0.003226
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.1.409	0.002833
ORF7a	102	L102del	CTT	---	1	1	B.1.1.411	0.014706
ORF7a	102	L102P	cTt	cCt	1	1	B.1.1.416	0.000905
ORF7a	102	L102del	CTT	---	1	1	B.1.1.434	0.000349
ORF7a	102	L102del	CTT	---	1	1	B.1.1.437	0.010417
ORF7a	102	L102del	CTT	---	1	1	B.1.1.448	0.002033
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.1.51	0.001718
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.1.519	0.00004
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.1.523	0.001563
ORF7a	102	L102Q	cTT	cAA	1	1	B.1.1.7	0.000001
ORF7a	102	L102H	cTt	cAt	1	1	B.1.1.7	0.000001
ORF7a	102	L102del	CTT	---	1	1	B.1.1.70	0.000341
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.105	0.009615
ORF7a	102	L102del	CTT	---	1	1	B.1.115	0.021739
ORF7a	102	L102del	CTT	---	1	1	B.1.126	0.001276
ORF7a	102	L102del	CTT	---	1	1	B.1.157	0.002985
ORF7a	102	L102I	Ctt	Att	1	1	B.1.160	0.000031
ORF7a	102	L102I	Ctt	Att	1	1	B.1.160.26	0.002421
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.160.30	0.002976
ORF7a	102	L102del	CTT	---	1	1	B.1.160.7	0.002079
ORF7a	102	L102del1	Ctt	-tt	1	1	B.1.177	0.000013
ORF7a	102	L102del1	Ctt	-tt	1	1	B.1.177.10	0.000878
ORF7a	102	L102del2	CTt	--t	1	1	B.1.177.15	0.000631
ORF7a	102	L102L	ctT	ctC	1	1	B.1.177.15	0.000631
ORF7a	102	L102del	CTT	---	1	1	B.1.177.16	0.000664
ORF7a	102	L102del1	Ctt	-tt	1	1	B.1.177.16	0.000664
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.177.21	0.000076
ORF7a	102	L102del	CTT	---	1	1	B.1.177.21	0.000076
ORF7a	102	L102del1	Ctt	-tt	1	1	B.1.177.21	0.000076
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.177.41	0.0025
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.177.43	0.001477
ORF7a	102	L102del	CTT	---	1	1	B.1.177.43	0.001477
ORF7a	102	L102del2	cTT	c--	1	1	B.1.177.44	0.000519
ORF7a	102	L102del	CTT	---	1	1	B.1.177.50	0.004695
ORF7a	102	L102del1	Ctt	-tt	1	1	B.1.177.54	0.000606
ORF7a	102	L102del	CTT	---	1	1	B.1.177.54	0.000606
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.177.63	0.002703
ORF7a	102	L102del	CTT	---	1	1	B.1.177.69	0.001484
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.177.81	0.000189
ORF7a	102	L102L	ctT	ctG	1	1	B.1.2	0.000009
ORF7a	102	L102del	CTT	---	1	1	B.1.214.2	0.0006
ORF7a	102	L102L	ctT	ctC	1	1	B.1.221	0.000071
ORF7a	102	L102P	cTt	cCt	1	1	B.1.221	0.000071
ORF7a	102	L102T	CTt	ACt	1	1	B.1.221	0.000071
ORF7a	102	L102del	CTT	---	1	1	B.1.221.4	0.004167
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.234	0.000132
ORF7a	102	L102del	CTT	---	1	1	B.1.235	0.002519
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.237	0.004975
ORF7a	102	L102del1	Ctt	-tt	1	1	B.1.247	0.014925
ORF7a	102	L102del	CTT	---	1	1	B.1.258.9	0.005
ORF7a	102	L102del	CTT	---	1	1	B.1.265	0.001271
ORF7a	102	L102L	ctT	ctG	1	1	B.1.279	0.000514
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.291	0.019231
ORF7a	102	L102del	CTT	---	1	1	B.1.320	0.001245
ORF7a	102	L102R	cTt	cGt	1	1	B.1.329	0.000608
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.351.2	0.000303
ORF7a	102	L102del	CTT	---	1	1	B.1.351.3	0.000876
ORF7a	102	L102L	ctT	ctC	1	1	B.1.351.3	0.000876
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.351.5	0.0006
ORF7a	102	L102del	CTT	---	1	1	B.1.356	0.001727
ORF7a	102	L102del	CTT	---	1	1	B.1.36.10	0.004785
ORF7a	102	L102P	cTt	cCt	1	1	B.1.36.17	0.000494
ORF7a	102	L102del	CTT	---	1	1	B.1.36.18	0.00042
ORF7a	102	L102del	CTT	---	1	1	B.1.36.20	0.016949
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.36.29	0.000517
ORF7a	102	L102del	CTT	---	1	1	B.1.36.29	0.000517
ORF7a	102	L102del	CTT	---	1	1	B.1.362	0.001541
ORF7a	102	L102del1	Ctt	-tt	1	1	B.1.362	0.001541
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.366	0.004878
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.367	0.000792
ORF7a	102	L102del	CTT	---	1	1	B.1.371	0.001122
ORF7a	102	L102del	CTT	---	1	1	B.1.375	0.00082
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.396	0.000706
ORF7a	102	L102del	CTT	---	1	1	B.1.409	0.000781
ORF7a	102	L102P	cTt	cCt	1	1	B.1.411	0.003704
ORF7a	102	L102L	ctT	ctA	1	1	B.1.416	0.001269
ORF7a	102	L102del	CTT	---	1	1	B.1.416	0.001269
ORF7a	102	L102L	ctT	ctC	1	1	B.1.427	0.00005
ORF7a	102	L102L	ctT	ctC	1	1	B.1.429	0.000024
ORF7a	102	L102V	Ctt	Gtt	1	1	B.1.429	0.000024
ORF7a	102	L102del	CTT	---	1	1	B.1.459	0.004082
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.465	0.003802
ORF7a	102	L102V	Ctt	Gtt	1	1	B.1.466.2	0.000391
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.466.2	0.000391
ORF7a	102	L102del	CTT	---	1	1	B.1.468	0.005714
ORF7a	102	L102del	CTT	---	1	1	B.1.470	0.001404
ORF7a	102	L102L	ctT	ctA	1	1	B.1.497	0.000315
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.499	0.00105
ORF7a	102	L102del	CTT	---	1	1	B.1.503	0.002488
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.506	0.02381
ORF7a	102	L102del	CTT	---	1	1	B.1.517	0.000427
ORF7a	102	L102del	CTT	---	1	1	B.1.527	0.003704
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.539	0.017544
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.564	0.000426
ORF7a	102	L102del	CTT	---	1	1	B.1.567	0.003333
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.575.1	0.002439
ORF7a	102	L102I	Ctt	Att	1	1	B.1.577	0.000687
ORF7a	102	L102del	CTT	---	1	1	B.1.577	0.000687
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.581	0.009434
ORF7a	102	L102del	CTT	---	1	1	B.1.585	0.027778
ORF7a	102	L102del	CTT	---	1	1	B.1.588	0.00091
ORF7a	102	L102L	ctT	ctC	1	1	B.1.596	0.000087
ORF7a	102	L102del1	Ctt	-tt	1	1	B.1.596	0.000087
ORF7a	102	L102V	Ctt	Gtt	1	1	B.1.596	0.000087
ORF7a	102	L102R	cTt	cGt	1	1	B.1.596	0.000087
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.617.1	0.000129
ORF7a	102	L102V	Ctt	Gtt	1	1	B.1.617.2	0.000004
ORF7a	102	L102M	CtT	AtG	1	1	B.1.617.2	0.000004
ORF7a	102	L102R	cTt	cGt	1	1	B.1.617.2	0.000004
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.620	0.000946
ORF7a	102	L102del	CTT	---	1	1	B.1.620	0.000946
ORF7a	102	L102F	Ctt	Ttt	1	1	B.1.621	0.000089
ORF7a	102	L102del1	Ctt	-tt	1	1	B.1.636	0.006711
ORF7a	102	L102del1	Ctt	-tt	1	1	B.1.637	0.000073
ORF7a	102	L102del	CTT	---	1	1	B.1.638	0.052632
ORF7a	102	L102del	CTT	---	1	1	B.12	0.00641
ORF7a	102	L102del1	Ctt	-tt	1	1	B.40	0.000364
ORF7a	102	L102del	CTT	---	1	1	B.40	0.000364
ORF7a	102	L102F	Ctt	Ttt	1	1	C.16	0.00106
ORF7a	102	L102V	Ctt	Gtt	1	1	C.2.1	0.006667
ORF7a	102	L102L	ctT	ctC	1	1	C.35	0.000774
ORF7a	102	L102F	Ctt	Ttt	1	1	C.35	0.000774
ORF7a	102	L102del	CTT	---	1	1	C.36	0.000911
ORF7a	102	L102del	CTT	---	1	1	C.36.3	0.000567
ORF7a	102	L102L	ctT	ctC	1	1	D.2	0.000075
ORF7a	102	L102del	CTT	---	1	1	N.5	0.001767
ORF7a	102	L102L	ctT	ctC	1	1	P.1	0.000016
ORF7a	102	L102P	cTt	cCt	1	1	P.1	0.000016
ORF7a	102	L102del	CTT	---	1	1	P.1.12	0.000484
ORF7a	102	L102F	Ctt	Ttt	1	1	P.1.12	0.000484
ORF7a	102	L102L	CtT	TtA	1	1	P.1.14	0.000048
ORF7a	102	L102F	Ctt	Ttt	1	1	P.1.14	0.000048
ORF7a	102	L102del1	Ctt	-tt	1	1	P.1.15	0.000232
ORF7a	102	L102del	CTT	---	1	1	P.1.16	0.000374
ORF7a	102	L102F	Ctt	Ttt	1	1	P.1.17	0.000162
ORF7a	102	L102del	CTT	---	1	1	P.1.4	0.000977
ORF7a	102	L102F	Ctt	Ttt	1	1	P.1.6	0.001946
ORF7a	102	L102F	Ctt	Ttt	1	1	P.1.7	0.000319
ORF7a	102	L102del	CTT	---	1	1	Q.2	0.000613
ORF7a	102	L102P	cTt	cCt	1	1	Q.8	0.000165
ORF7a	102	L102del	CTT	---	1	1	U.3	0.003861
ORF7a	102	L102del	CTT	---	1	1	W.4	0.001351
ORF7a	102	L102del	CTT	---	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.