CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF7a : CodonNum = 47

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	47	H47Y		nonsyn	Cat	Tat	5223	5214	0.998277	27532-27534
ORF7a	47	H47Y		nonsyn	CaT	TaC	5223	9	0.00172315	27532-27534
ORF7a	47	H47del		del	CAT	---	3238	3238	1	27532-27534
ORF7a	47	H47N		nonsyn	Cat	Aat	1603	1593	0.993762	27532-27534
ORF7a	47	H47N		nonsyn	CaT	AaC	1603	10	0.0062383	27532-27534
ORF7a	47	H47H		syn	caT	caC	1553	1553	1	27532-27534
ORF7a	47	H47R		nonsyn	cAt	cGt	375	358	0.954667	27532-27534
ORF7a	47	H47R		nonsyn	CAT	AGA	375	10	0.0266667	27532-27534
ORF7a	47	H47R		nonsyn	cAT	cGC	375	4	0.0106667	27532-27534
ORF7a	47	H47R		nonsyn	CAT	AGG	375	1	0.00266667	27532-27534
ORF7a	47	H47R		nonsyn	cAT	cGG	375	1	0.00266667	27532-27534
ORF7a	47	H47R		nonsyn	cAT	cGA	375	1	0.00266667	27532-27534
ORF7a	47	H47L		nonsyn	cAt	cTt	177	152	0.858757	27532-27534
ORF7a	47	H47L		nonsyn	CAT	TTA	177	9	0.0508475	27532-27534
ORF7a	47	H47L		nonsyn	cAT	cTC	177	5	0.0282486	27532-27534
ORF7a	47	H47L		nonsyn	CAT	TTG	177	5	0.0282486	27532-27534
ORF7a	47	H47L		nonsyn	cAT	cTA	177	4	0.0225989	27532-27534
ORF7a	47	H47L		nonsyn	cAT	cTG	177	2	0.0112994	27532-27534
ORF7a	47	H47Q		nonsyn	caT	caA	155	91	0.587097	27532-27534
ORF7a	47	H47Q		nonsyn	caT	caG	155	64	0.412903	27532-27534
ORF7a	47	H47del1		del	caT	ca-	118	57	0.483051	27532-27534
ORF7a	47	H47del1		del	Cat	-at	118	54	0.457627	27532-27534
ORF7a	47	H47del1		del	cAt	c-t	118	4	0.0338983	27532-27534
ORF7a	47	H47del1		del	CAT	-NN	118	2	0.0169492	27532-27534
ORF7a	47	H47del1		del	cAT	c-N	118	1	0.00847458	27532-27534
ORF7a	47	H47D		nonsyn	Cat	Gat	64	60	0.9375	27532-27534
ORF7a	47	H47D		nonsyn	CaT	GaC	64	4	0.0625	27532-27534
ORF7a	47	H47P		nonsyn	cAt	cCt	56	50	0.892857	27532-27534
ORF7a	47	H47P		nonsyn	cAT	cCA	56	3	0.0535714	27532-27534
ORF7a	47	H47P		nonsyn	cAT	cCC	56	2	0.0357143	27532-27534
ORF7a	47	H47P		nonsyn	cAT	cCG	56	1	0.0178571	27532-27534
ORF7a	47	H47F		nonsyn	CAt	TTt	32	24	0.75	27532-27534
ORF7a	47	H47F		nonsyn	CAT	TTC	32	8	0.25	27532-27534
ORF7a	47	H47del2		del	cAT	c--	30	18	0.6	27532-27534
ORF7a	47	H47S		nonsyn	CAT	TCA	30	11	0.366667	27532-27534
ORF7a	47	H47del2		del	CAt	--t	30	11	0.366667	27532-27534
ORF7a	47	H47S		nonsyn	CAt	TCt	30	6	0.2	27532-27534
ORF7a	47	H47S		nonsyn	CAt	AGt	30	5	0.166667	27532-27534
ORF7a	47	H47S		nonsyn	CAT	AGC	30	3	0.1	27532-27534
ORF7a	47	H47S		nonsyn	CAT	TCG	30	3	0.1	27532-27534
ORF7a	47	H47S		nonsyn	CAT	TCC	30	2	0.0666667	27532-27534
ORF7a	47	H47del2		del	CAT	--W	30	1	0.0333333	27532-27534
ORF7a	47	H47X		nonsyn	CaT	TaA	24	11	0.458333	27532-27534
ORF7a	47	H47X		nonsyn	CAT	TGA	24	9	0.375	27532-27534
ORF7a	47	H47X		nonsyn	CaT	TaG	24	4	0.166667	27532-27534
ORF7a	47	H47K		nonsyn	CaT	AaA	21	14	0.666667	27532-27534
ORF7a	47	H47T		nonsyn	CAT	ACA	21	11	0.52381	27532-27534
ORF7a	47	H47K		nonsyn	CaT	AaG	21	7	0.333333	27532-27534
ORF7a	47	H47T		nonsyn	CAt	ACt	21	6	0.285714	27532-27534
ORF7a	47	H47T		nonsyn	CAT	ACG	21	3	0.142857	27532-27534
ORF7a	47	H47T		nonsyn	CAT	ACC	21	1	0.047619	27532-27534
ORF7a	47	H47C		nonsyn	CAt	TGt	20	17	0.85	27532-27534
ORF7a	47	H47C		nonsyn	CAT	TGC	20	3	0.15	27532-27534
ORF7a	47	H47I		nonsyn	CAT	ATA	17	8	0.470588	27532-27534
ORF7a	47	H47I		nonsyn	CAt	ATt	17	7	0.411765	27532-27534
ORF7a	47	H47I		nonsyn	CAT	ATC	17	2	0.117647	27532-27534
ORF7a	47	H47E		nonsyn	CaT	GaG	14	13	0.928571	27532-27534
ORF7a	47	H47E		nonsyn	CaT	GaA	14	1	0.0714286	27532-27534
ORF7a	47	H47V		nonsyn	CAT	GTG	12	6	0.5	27532-27534
ORF7a	47	H47V		nonsyn	CAt	GTt	12	4	0.333333	27532-27534
ORF7a	47	H47V		nonsyn	CAT	GTC	12	1	0.0833333	27532-27534
ORF7a	47	H47V		nonsyn	CAT	GTA	12	1	0.0833333	27532-27534
ORF7a	47	H47G		nonsyn	CAT	GGG	6	3	0.5	27532-27534
ORF7a	47	H47G		nonsyn	CAt	GGt	6	2	0.333333	27532-27534
ORF7a	47	H47G		nonsyn	CAT	GGC	6	1	0.166667	27532-27534
ORF7a	47	H47M		nonsyn	CAT	ATG	2	2	1	27532-27534
ORF7a	47	H47W		nonsyn	CAT	TGG	2	2	1	27532-27534
ORF7a	47	H47A		nonsyn	CAT	GCA	1	1	1	27532-27534

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	47	H47Y	Cat	Tat	5214	5223	All	0.000997
ORF7a	47	H47Y	CaT	TaC	9	5223	All	0.000002
ORF7a	47	H47del	CAT	---	3238	3238	All	0.000619
ORF7a	47	H47N	Cat	Aat	1593	1603	All	0.000305
ORF7a	47	H47N	CaT	AaC	10	1603	All	0.000002
ORF7a	47	H47H	caT	caC	1553	1553	All	0.000297
ORF7a	47	H47Y	Cat	Tat	1544	1546	B.1.1.7	0.001382
ORF7a	47	H47Y	CaT	TaC	2	1546	B.1.1.7	0.000002
ORF7a	47	H47N	Cat	Aat	672	672	B.1.1.7	0.000602
ORF7a	47	H47del	CAT	---	553	553	B.1.1.7	0.000495
ORF7a	47	H47del	CAT	---	418	418	AY.25	0.002514
ORF7a	47	H47R	cAt	cGt	358	375	All	0.000068
ORF7a	47	H47R	CAT	AGA	10	375	All	0.000002
ORF7a	47	H47R	cAT	cGC	4	375	All	0.000001
ORF7a	47	H47R	CAT	AGG	1	375	All	0
ORF7a	47	H47R	cAT	cGA	1	375	All	0
ORF7a	47	H47R	cAT	cGG	1	375	All	0
ORF7a	47	H47Y	Cat	Tat	360	360	AY.4	0.00056
ORF7a	47	H47N	Cat	Aat	317	317	AY.4	0.000493
ORF7a	47	H47H	caT	caC	296	296	B.1.551	0.381935
ORF7a	47	H47del	CAT	---	288	288	AY.4	0.000448
ORF7a	47	H47del	CAT	---	272	272	B.1.617.2	0.001024
ORF7a	47	H47Y	Cat	Tat	243	243	B.1.2	0.00214
ORF7a	47	H47H	caT	caC	216	216	B.1.1.186	0.742268
ORF7a	47	H47H	caT	caC	203	203	AY.4	0.000316
ORF7a	47	H47Y	Cat	Tat	181	181	B.1.177	0.002383
ORF7a	47	H47del	CAT	---	180	180	B.1.177.21	0.013765
ORF7a	47	H47L	cAt	cTt	152	177	All	0.000029
ORF7a	47	H47L	CAT	TTA	9	177	All	0.000002
ORF7a	47	H47L	CAT	TTG	5	177	All	0.000001
ORF7a	47	H47L	cAT	cTC	5	177	All	0.000001
ORF7a	47	H47L	cAT	cTA	4	177	All	0.000001
ORF7a	47	H47L	cAT	cTG	2	177	All	0
ORF7a	47	H47Y	Cat	Tat	175	175	AY.103	0.001087
ORF7a	47	H47Y	Cat	Tat	169	169	AY.26	0.004784
ORF7a	47	H47Y	Cat	Tat	166	168	B.1.617.2	0.000625
ORF7a	47	H47Y	CaT	TaC	2	168	B.1.617.2	0.000008
ORF7a	47	H47Y	Cat	Tat	167	167	AY.43	0.00074
ORF7a	47	H47Q	caT	caA	91	155	All	0.000017
ORF7a	47	H47Q	caT	caG	64	155	All	0.000012
ORF7a	47	H47Y	Cat	Tat	148	148	B.1.429	0.003482
ORF7a	47	H47H	caT	caC	147	147	AY.25	0.000884
ORF7a	47	H47Y	Cat	Tat	137	141	AY.25	0.000824
ORF7a	47	H47Y	CaT	TaC	4	141	AY.25	0.000024
ORF7a	47	H47del	CAT	---	122	122	AY.103	0.000758
ORF7a	47	H47del1	caT	ca-	57	118	All	0.000011
ORF7a	47	H47del1	Cat	-at	54	118	All	0.00001
ORF7a	47	H47del1	cAt	c-t	4	118	All	0.000001
ORF7a	47	H47del1	CAT	-NN	2	118	All	0
ORF7a	47	H47del1	cAT	c-N	1	118	All	0
ORF7a	47	H47Y	Cat	Tat	114	114	R.1	0.010261
ORF7a	47	H47N	Cat	Aat	106	106	P.1	0.00167
ORF7a	47	H47del	CAT	---	104	104	AY.3	0.001034
ORF7a	47	H47H	caT	caC	103	103	B.1.1.7	0.000092
ORF7a	47	H47del	CAT	---	96	96	AY.43	0.000425
ORF7a	47	H47Y	Cat	Tat	95	95	AY.44	0.000578
ORF7a	47	H47Y	Cat	Tat	94	94	AY.3	0.000935
ORF7a	47	H47del	CAT	---	75	75	AY.26	0.002123
ORF7a	47	H47Y	Cat	Tat	74	74	C.37	0.008589
ORF7a	47	H47del	CAT	---	72	72	AY.44	0.000438
ORF7a	47	H47Y	Cat	Tat	71	71	B.1.1	0.001288
ORF7a	47	H47R	cAt	cGt	70	70	AY.4	0.000109
ORF7a	47	H47Y	Cat	Tat	70	70	AY.47	0.002177
ORF7a	47	H47H	caT	caC	67	67	AY.44	0.000408
ORF7a	47	H47R	cAt	cGt	66	66	B.1.1.7	0.000059
ORF7a	47	H47Y	Cat	Tat	65	65	B.1.1.170	0.081047
ORF7a	47	H47D	Cat	Gat	60	64	All	0.000011
ORF7a	47	H47D	CaT	GaC	4	64	All	0.000001
ORF7a	47	H47del	CAT	---	63	63	AY.100	0.002898
ORF7a	47	H47H	caT	caC	63	63	B.1.617.2	0.000237
ORF7a	47	H47Y	Cat	Tat	61	61	B.1	0.000559
ORF7a	47	H47del	CAT	---	58	58	AY.29	0.000915
ORF7a	47	H47Y	Cat	Tat	57	57	B.1.160	0.001778
ORF7a	47	H47P	cAt	cCt	50	56	All	0.00001
ORF7a	47	H47P	cAT	cCA	3	56	All	0.000001
ORF7a	47	H47P	cAT	cCC	2	56	All	0
ORF7a	47	H47P	cAT	cCG	1	56	All	0
ORF7a	47	H47Y	Cat	Tat	54	54	P.1	0.000851
ORF7a	47	H47H	caT	caC	53	53	AY.43	0.000235
ORF7a	47	H47del	CAT	---	52	52	AY.47	0.001617
ORF7a	47	H47del	CAT	---	51	51	B.1.2	0.000449
ORF7a	47	H47Y	Cat	Tat	50	50	B.1.1.266	0.609756
ORF7a	47	H47N	Cat	Aat	49	49	AD.2	0.010729
ORF7a	47	H47del	CAT	---	48	48	AY.3.1	0.004092
ORF7a	47	H47del	CAT	---	46	46	B.1	0.000421
ORF7a	47	H47del	CAT	---	45	45	AY.39	0.001112
ORF7a	47	H47Y	Cat	Tat	42	42	B.1.160.18	0.306569
ORF7a	47	H47N	Cat	Aat	42	42	B.1.525	0.004753
ORF7a	47	H47L	cAt	cTt	38	38	AY.4	0.000059
ORF7a	47	H47del	CAT	---	37	37	B.1.1.284	0.003974
ORF7a	47	H47del	CAT	---	37	37	B.1.621	0.003275
ORF7a	47	H47R	cAt	cGt	23	36	AY.25	0.000138
ORF7a	47	H47R	CAT	AGA	7	36	AY.25	0.000042
ORF7a	47	H47R	cAT	cGC	3	36	AY.25	0.000018
ORF7a	47	H47R	CAT	AGG	1	36	AY.25	0.000006
ORF7a	47	H47R	cAT	cGG	1	36	AY.25	0.000006
ORF7a	47	H47R	cAT	cGA	1	36	AY.25	0.000006
ORF7a	47	H47Y	Cat	Tat	35	35	AY.39	0.000865
ORF7a	47	H47Y	Cat	Tat	34	34	AY.5	0.000702
ORF7a	47	H47N	Cat	Aat	34	34	B.1.2	0.000299
ORF7a	47	H47Y	Cat	Tat	34	34	B.1.349	0.024303
ORF7a	47	H47N	Cat	Aat	27	34	B.1.617.2	0.000102
ORF7a	47	H47N	CaT	AaC	7	34	B.1.617.2	0.000026
ORF7a	47	H47F	CAt	TTt	24	32	All	0.000005
ORF7a	47	H47F	CAT	TTC	8	32	All	0.000002
ORF7a	47	H47Y	Cat	Tat	32	32	B.1.1.214	0.001775
ORF7a	47	H47N	Cat	Aat	32	32	B.1.234	0.004222
ORF7a	47	H47del2	cAT	c--	18	30	All	0.000003
ORF7a	47	H47S	CAT	TCA	11	30	All	0.000002
ORF7a	47	H47del2	CAt	--t	11	30	All	0.000002
ORF7a	47	H47S	CAt	TCt	6	30	All	0.000001
ORF7a	47	H47S	CAt	AGt	5	30	All	0.000001
ORF7a	47	H47S	CAT	AGC	3	30	All	0.000001
ORF7a	47	H47S	CAT	TCG	3	30	All	0.000001
ORF7a	47	H47S	CAT	TCC	2	30	All	0
ORF7a	47	H47del2	CAT	--W	1	30	All	0
ORF7a	47	H47Y	Cat	Tat	28	28	AY.42	0.001126
ORF7a	47	H47Y	Cat	Tat	28	28	B.1.36.18	0.011765
ORF7a	47	H47L	cAt	cTt	27	27	B.1.637	0.001973
ORF7a	47	H47L	CAT	TTA	8	26	AY.25	0.000048
ORF7a	47	H47L	cAt	cTt	8	26	AY.25	0.000048
ORF7a	47	H47L	cAT	cTA	4	26	AY.25	0.000024
ORF7a	47	H47L	CAT	TTG	4	26	AY.25	0.000024
ORF7a	47	H47L	cAT	cTC	2	26	AY.25	0.000012
ORF7a	47	H47P	cAt	cCt	25	26	AY.36	0.003705
ORF7a	47	H47P	cAT	cCC	1	26	AY.36	0.000148
ORF7a	47	H47Y	Cat	Tat	25	25	B.1.407	0.892857
ORF7a	47	H47X	CaT	TaA	11	24	All	0.000002
ORF7a	47	H47X	CAT	TGA	9	24	All	0.000002
ORF7a	47	H47X	CaT	TaG	4	24	All	0.000001
ORF7a	47	H47del1	Cat	-at	24	24	AY.4.2	0.000521
ORF7a	47	H47del	CAT	---	24	24	B.1.1.214	0.001331
ORF7a	47	H47Y	Cat	Tat	24	24	B.1.234	0.003167
ORF7a	47	H47Y	Cat	Tat	23	23	AY.102	0.00061
ORF7a	47	H47S	CAT	TCA	8	23	AY.25	0.000048
ORF7a	47	H47S	CAt	TCt	4	23	AY.25	0.000024
ORF7a	47	H47S	CAT	AGC	3	23	AY.25	0.000018
ORF7a	47	H47S	CAT	TCG	3	23	AY.25	0.000018
ORF7a	47	H47S	CAt	AGt	3	23	AY.25	0.000018
ORF7a	47	H47S	CAT	TCC	2	23	AY.25	0.000012
ORF7a	47	H47H	caT	caC	22	22	AY.26	0.000623
ORF7a	47	H47Y	Cat	Tat	22	22	B.1.232	0.011822
ORF7a	47	H47R	cAt	cGt	22	22	B.1.526	0.000517
ORF7a	47	H47del	CAT	---	22	22	P.1	0.000347
ORF7a	47	H47K	CaT	AaA	14	21	All	0.000003
ORF7a	47	H47T	CAT	ACA	11	21	All	0.000002
ORF7a	47	H47K	CaT	AaG	7	21	All	0.000001
ORF7a	47	H47T	CAt	ACt	6	21	All	0.000001
ORF7a	47	H47T	CAT	ACG	3	21	All	0.000001
ORF7a	47	H47T	CAT	ACC	1	21	All	0
ORF7a	47	H47del1	caT	ca-	21	21	AY.26	0.000595
ORF7a	47	H47H	caT	caC	21	21	B.1	0.000192
ORF7a	47	H47H	caT	caC	21	21	B.1.2	0.000185
ORF7a	47	H47Y	Cat	Tat	21	21	B.1.36.24	0.12963
ORF7a	47	H47C	CAt	TGt	17	20	All	0.000003
ORF7a	47	H47C	CAT	TGC	3	20	All	0.000001
ORF7a	47	H47Y	Cat	Tat	20	20	AY.120	0.000744
ORF7a	47	H47Y	Cat	Tat	20	20	AY.24	0.008621
ORF7a	47	H47del	CAT	---	20	20	AY.46.4	0.00329
ORF7a	47	H47H	caT	caC	20	20	C.37	0.002321
ORF7a	47	H47Y	Cat	Tat	20	20	P.1.15	0.004647
ORF7a	47	H47del	CAT	---	19	19	AY.42	0.000764
ORF7a	47	H47del	CAT	---	19	19	AY.7.2	0.010626
ORF7a	47	H47Q	caT	caA	19	19	B.1.177	0.00025
ORF7a	47	H47del	CAT	---	19	19	B.1.177	0.00025
ORF7a	47	H47N	Cat	Aat	19	19	B.1.637	0.001388
ORF7a	47	H47H	caT	caC	18	18	AY.103	0.000112
ORF7a	47	H47Y	Cat	Tat	18	18	AY.20	0.0007
ORF7a	47	H47del	CAT	---	18	18	B.1.526	0.000423
ORF7a	47	H47H	caT	caC	18	18	B.1.575	0.005461
ORF7a	47	H47I	CAT	ATA	8	17	All	0.000002
ORF7a	47	H47I	CAt	ATt	7	17	All	0.000001
ORF7a	47	H47I	CAT	ATC	2	17	All	0
ORF7a	47	H47Y	Cat	Tat	17	17	AY.100	0.000782
ORF7a	47	H47Y	Cat	Tat	17	17	AY.4.2	0.000369
ORF7a	47	H47Y	Cat	Tat	17	17	AY.85	0.007262
ORF7a	47	H47Q	caT	caA	14	17	B.1	0.000128
ORF7a	47	H47Q	caT	caG	3	17	B.1	0.000027
ORF7a	47	H47del	CAT	---	16	16	AY.119	0.000565
ORF7a	47	H47N	Cat	Aat	16	16	AY.14	0.001408
ORF7a	47	H47X	CaT	TaA	7	16	AY.25	0.000042
ORF7a	47	H47X	CAT	TGA	6	16	AY.25	0.000036
ORF7a	47	H47X	CaT	TaG	3	16	AY.25	0.000018
ORF7a	47	H47N	Cat	Aat	16	16	B.1	0.000147
ORF7a	47	H47Q	caT	caA	12	16	B.1.1.7	0.000011
ORF7a	47	H47Q	caT	caG	4	16	B.1.1.7	0.000004
ORF7a	47	H47del	CAT	---	16	16	C.37	0.001857
ORF7a	47	H47Y	Cat	Tat	16	16	P.1.14	0.000765
ORF7a	47	H47T	CAT	ACA	8	15	AY.25	0.000048
ORF7a	47	H47T	CAT	ACG	3	15	AY.25	0.000018
ORF7a	47	H47T	CAt	ACt	3	15	AY.25	0.000018
ORF7a	47	H47T	CAT	ACC	1	15	AY.25	0.000006
ORF7a	47	H47N	Cat	Aat	15	15	AY.26	0.000425
ORF7a	47	H47del	CAT	---	15	15	AY.5	0.00031
ORF7a	47	H47Y	Cat	Tat	15	15	B.1.351	0.000446
ORF7a	47	H47del	CAT	---	15	15	B.1.351	0.000446
ORF7a	47	H47Y	Cat	Tat	15	15	B.1.427	0.000757
ORF7a	47	H47Q	caT	caA	8	15	B.1.617.2	0.00003
ORF7a	47	H47Q	caT	caG	7	15	B.1.617.2	0.000026
ORF7a	47	H47E	CaT	GaG	13	14	All	0.000002
ORF7a	47	H47E	CaT	GaA	1	14	All	0
ORF7a	47	H47R	cAt	cGt	14	14	AY.3	0.000139
ORF7a	47	H47Y	Cat	Tat	14	14	B.1.1.519	0.000556
ORF7a	47	H47del	CAT	---	14	14	B.1.596	0.00122
ORF7a	47	H47N	Cat	Aat	14	14	B.1.596	0.00122
ORF7a	47	H47R	cAt	cGt	10	14	B.1.617.2	0.000038
ORF7a	47	H47R	CAT	AGA	3	14	B.1.617.2	0.000011
ORF7a	47	H47R	cAT	cGC	1	14	B.1.617.2	0.000004
ORF7a	47	H47del	CAT	---	14	14	B.1.637	0.001023
ORF7a	47	H47Y	Cat	Tat	13	13	AY.119	0.000459
ORF7a	47	H47del	CAT	---	13	13	AY.20	0.000505
ORF7a	47	H47H	caT	caC	13	13	AY.23	0.000907
ORF7a	47	H47H	caT	caC	13	13	B.1.1.33	0.005471
ORF7a	47	H47H	caT	caC	13	13	B.1.1.519	0.000516
ORF7a	47	H47L	cAt	cTt	13	13	B.1.1.7	0.000012
ORF7a	47	H47Y	Cat	Tat	13	13	B.1.243	0.000905
ORF7a	47	H47N	Cat	Aat	13	13	P.1.14	0.000621
ORF7a	47	H47V	CAT	GTG	6	12	All	0.000001
ORF7a	47	H47V	CAt	GTt	4	12	All	0.000001
ORF7a	47	H47V	CAT	GTA	1	12	All	0
ORF7a	47	H47V	CAT	GTC	1	12	All	0
ORF7a	47	H47del	CAT	---	12	12	AY.102	0.000318
ORF7a	47	H47I	CAT	ATA	8	12	AY.25	0.000048
ORF7a	47	H47I	CAt	ATt	3	12	AY.25	0.000018
ORF7a	47	H47I	CAT	ATC	1	12	AY.25	0.000006
ORF7a	47	H47D	Cat	Gat	12	12	AY.4	0.000019
ORF7a	47	H47Q	caT	caG	11	12	AY.4	0.000017
ORF7a	47	H47Q	caT	caA	1	12	AY.4	0.000002
ORF7a	47	H47R	cAt	cGt	12	12	AY.59	0.006356
ORF7a	47	H47R	cAt	cGt	12	12	AY.99.2	0.001106
ORF7a	47	H47Y	Cat	Tat	12	12	B.1.177.35	0.008293
ORF7a	47	H47N	Cat	Aat	12	12	B.1.221	0.000852
ORF7a	47	H47del	CAT	---	12	12	B.1.324	0.019262
ORF7a	47	H47H	caT	caC	12	12	B.1.499	0.012605
ORF7a	47	H47Y	Cat	Tat	12	12	B.1.596	0.001046
ORF7a	47	H47del	CAT	---	11	11	AY.120	0.000409
ORF7a	47	H47K	CaT	AaA	8	11	AY.25	0.000048
ORF7a	47	H47N	Cat	Aat	8	11	AY.25	0.000048
ORF7a	47	H47del1	Cat	-at	7	11	AY.25	0.000042
ORF7a	47	H47del1	caT	ca-	4	11	AY.25	0.000024
ORF7a	47	H47K	CaT	AaG	3	11	AY.25	0.000018
ORF7a	47	H47N	CaT	AaC	3	11	AY.25	0.000018
ORF7a	47	H47del	CAT	---	11	11	AY.35	0.002564
ORF7a	47	H47R	cAt	cGt	11	11	AY.44	0.000067
ORF7a	47	H47H	caT	caC	11	11	AY.46	0.001145
ORF7a	47	H47D	Cat	Gat	11	11	B.1.1.7	0.00001
ORF7a	47	H47N	Cat	Aat	11	11	B.1.177	0.000145
ORF7a	47	H47F	CAT	TTC	7	11	B.1.177.21	0.000535
ORF7a	47	H47F	CAt	TTt	4	11	B.1.177.21	0.000306
ORF7a	47	H47Y	Cat	Tat	11	11	B.1.258	0.000732
ORF7a	47	H47Y	Cat	Tat	11	11	B.1.311	0.00302
ORF7a	47	H47del	CAT	---	11	11	B.1.429	0.000259
ORF7a	47	H47R	cAt	cGt	11	11	D.2	0.000825
ORF7a	47	H47H	caT	caC	11	11	P.1	0.000173
ORF7a	47	H47D	Cat	Gat	10	10	AY.12	0.003161
ORF7a	47	H47del2	CAt	--t	6	10	AY.3	0.00006
ORF7a	47	H47del2	cAT	c--	4	10	AY.3	0.00004
ORF7a	47	H47N	Cat	Aat	10	10	AY.39	0.000247
ORF7a	47	H47H	caT	caC	10	10	AY.39.1	0.000396
ORF7a	47	H47Y	Cat	Tat	10	10	AY.51	0.009091
ORF7a	47	H47Y	Cat	Tat	10	10	AY.6	0.000411
ORF7a	47	H47del1	caT	ca-	6	10	B.1.1.7	0.000005
ORF7a	47	H47del1	Cat	-at	3	10	B.1.1.7	0.000003
ORF7a	47	H47del1	cAt	c-t	1	10	B.1.1.7	0.000001
ORF7a	47	H47R	cAt	cGt	10	10	B.1.177.4	0.002111
ORF7a	47	H47Y	Cat	Tat	10	10	B.1.36.29	0.005173
ORF7a	47	H47Y	Cat	Tat	10	10	B.1.526	0.000235
ORF7a	47	H47L	cAt	cTt	5	10	B.1.617.2	0.000019
ORF7a	47	H47L	cAT	cTC	2	10	B.1.617.2	0.000008
ORF7a	47	H47L	cAT	cTG	2	10	B.1.617.2	0.000008
ORF7a	47	H47L	CAT	TTA	1	10	B.1.617.2	0.000004
ORF7a	47	H47del	CAT	---	10	10	R.1	0.0009
ORF7a	47	H47P	cAt	cCt	4	9	AY.25	0.000024
ORF7a	47	H47P	cAT	cCA	3	9	AY.25	0.000018
ORF7a	47	H47P	cAT	cCC	1	9	AY.25	0.000006
ORF7a	47	H47P	cAT	cCG	1	9	AY.25	0.000006
ORF7a	47	H47Y	Cat	Tat	9	9	AY.29	0.000142
ORF7a	47	H47del	CAT	---	9	9	AY.34	0.000873
ORF7a	47	H47N	Cat	Aat	9	9	AY.44	0.000055
ORF7a	47	H47del	CAT	---	9	9	AY.54	0.000858
ORF7a	47	H47P	cAt	cCt	9	9	B.1.1.7	0.000008
ORF7a	47	H47C	CAt	TGt	8	9	B.1.617.2	0.00003
ORF7a	47	H47C	CAT	TGC	1	9	B.1.617.2	0.000004
ORF7a	47	H47N	Cat	Aat	9	9	B.1.621	0.000797
ORF7a	47	H47del	CAT	---	9	9	L.1	0.017143
ORF7a	47	H47H	caT	caC	8	8	AY.102	0.000212
ORF7a	47	H47Q	caT	caG	8	8	AY.119	0.000282
ORF7a	47	H47L	cAt	cTt	8	8	AY.120	0.000297
ORF7a	47	H47del	CAT	---	8	8	AY.120.1	0.002568
ORF7a	47	H47C	CAt	TGt	6	8	AY.25	0.000036
ORF7a	47	H47C	CAT	TGC	2	8	AY.25	0.000012
ORF7a	47	H47Y	Cat	Tat	8	8	AY.3.1	0.000682
ORF7a	47	H47F	CAt	TTt	8	8	AY.3.1	0.000682
ORF7a	47	H47del	CAT	---	8	8	AY.98.1	0.000387
ORF7a	47	H47Y	Cat	Tat	8	8	AY.99.2	0.000737
ORF7a	47	H47E	CaT	GaG	8	8	B.1.177.21	0.000612
ORF7a	47	H47N	Cat	Aat	8	8	B.1.429	0.000188
ORF7a	47	H47H	caT	caC	8	8	B.1.429	0.000188
ORF7a	47	H47N	Cat	Aat	8	8	B.1.438.1	0.000858
ORF7a	47	H47del	CAT	---	8	8	B.1.525	0.000905
ORF7a	47	H47X	CaT	TaA	4	8	B.1.617.2	0.000015
ORF7a	47	H47X	CAT	TGA	3	8	B.1.617.2	0.000011
ORF7a	47	H47X	CaT	TaG	1	8	B.1.617.2	0.000004
ORF7a	47	H47Y	Cat	Tat	8	8	B.1.93	0.00747
ORF7a	47	H47del	CAT	---	7	7	AY.116	0.002007
ORF7a	47	H47Y	Cat	Tat	7	7	AY.116.1	0.00218
ORF7a	47	H47R	cAt	cGt	7	7	AY.20	0.000272
ORF7a	47	H47Q	caT	caA	5	7	AY.25	0.00003
ORF7a	47	H47Q	caT	caG	2	7	AY.25	0.000012
ORF7a	47	H47del	CAT	---	7	7	AY.39.1	0.000277
ORF7a	47	H47del2	cAT	c--	7	7	AY.4	0.000011
ORF7a	47	H47del	CAT	---	7	7	AY.4.2	0.000152
ORF7a	47	H47Y	Cat	Tat	7	7	AY.61	0.000733
ORF7a	47	H47del	CAT	---	7	7	B.1.1	0.000127
ORF7a	47	H47L	cAt	cTt	7	7	B.1.1.519	0.000278
ORF7a	47	H47H	caT	caC	7	7	B.1.160	0.000218
ORF7a	47	H47del	CAT	---	7	7	B.1.160	0.000218
ORF7a	47	H47R	cAt	cGt	7	7	B.1.160.8	0.009021
ORF7a	47	H47Y	Cat	Tat	7	7	B.1.162	0.035176
ORF7a	47	H47Y	Cat	Tat	7	7	B.1.221	0.000497
ORF7a	47	H47Y	Cat	Tat	7	7	B.1.438.1	0.000751
ORF7a	47	H47S	CAT	TCA	3	7	B.1.617.2	0.000011
ORF7a	47	H47S	CAt	AGt	2	7	B.1.617.2	0.000008
ORF7a	47	H47S	CAt	TCt	2	7	B.1.617.2	0.000008
ORF7a	47	H47Y	Cat	Tat	7	7	B.1.634	0.023973
ORF7a	47	H47N	Cat	Aat	7	7	C.36.3	0.003971
ORF7a	47	H47del	CAT	---	7	7	P.1.15	0.001626
ORF7a	47	H47G	CAT	GGG	3	6	All	0.000001
ORF7a	47	H47G	CAt	GGt	2	6	All	0
ORF7a	47	H47G	CAT	GGC	1	6	All	0
ORF7a	47	H47Y	Cat	Tat	6	6	AY.117	0.000507
ORF7a	47	H47del	CAT	---	6	6	AY.118	0.000376
ORF7a	47	H47Y	Cat	Tat	6	6	AY.118	0.000376
ORF7a	47	H47H	caT	caC	6	6	AY.14	0.000528
ORF7a	47	H47R	cAt	cGt	6	6	AY.16	0.002278
ORF7a	47	H47del	CAT	---	6	6	AY.23	0.000418
ORF7a	47	H47F	CAt	TTt	6	6	AY.25	0.000036
ORF7a	47	H47G	CAT	GGG	3	6	AY.25	0.000018
ORF7a	47	H47G	CAt	GGt	2	6	AY.25	0.000012
ORF7a	47	H47G	CAT	GGC	1	6	AY.25	0.000006
ORF7a	47	H47Y	Cat	Tat	6	6	AY.36	0.000889
ORF7a	47	H47H	caT	caC	6	6	AY.39	0.000148
ORF7a	47	H47Y	Cat	Tat	6	6	AY.4.5	0.000645
ORF7a	47	H47R	cAt	cGt	6	6	AY.43	0.000027
ORF7a	47	H47Y	Cat	Tat	6	6	AY.46.6	0.000433
ORF7a	47	H47Y	Cat	Tat	6	6	AY.54	0.000572
ORF7a	47	H47Y	Cat	Tat	6	6	AY.98	0.000474
ORF7a	47	H47Y	Cat	Tat	6	6	AY.98.1	0.000291
ORF7a	47	H47L	cAt	cTt	6	6	B.1	0.000055
ORF7a	47	H47H	caT	caC	6	6	B.1.1	0.000109
ORF7a	47	H47Q	caT	caA	6	6	B.1.160	0.000187
ORF7a	47	H47Y	Cat	Tat	6	6	B.1.160.29	0.025316
ORF7a	47	H47H	caT	caC	6	6	B.1.177.42	0.005367
ORF7a	47	H47del	CAT	---	6	6	B.1.234	0.000792
ORF7a	47	H47N	Cat	Aat	6	6	B.1.241	0.00487
ORF7a	47	H47Y	Cat	Tat	6	6	B.1.36.8	0.006
ORF7a	47	H47L	cAt	cTt	6	6	B.1.517	0.002562
ORF7a	47	H47Y	Cat	Tat	6	6	B.1.563	0.101695
ORF7a	47	H47K	CaT	AaA	6	6	B.1.617.2	0.000023
ORF7a	47	H47D	Cat	Gat	3	6	B.1.617.2	0.000011
ORF7a	47	H47V	CAT	GTG	3	6	B.1.617.2	0.000011
ORF7a	47	H47D	CaT	GaC	3	6	B.1.617.2	0.000011
ORF7a	47	H47V	CAT	GTC	1	6	B.1.617.2	0.000004
ORF7a	47	H47V	CAT	GTA	1	6	B.1.617.2	0.000004
ORF7a	47	H47V	CAt	GTt	1	6	B.1.617.2	0.000004
ORF7a	47	H47Y	Cat	Tat	6	6	B.1.621	0.000531
ORF7a	47	H47Y	Cat	Tat	6	6	Q.1	0.000758
ORF7a	47	H47H	caT	caC	6	6	R.1	0.00054
ORF7a	47	H47Y	Cat	Tat	5	5	AY.120.1	0.001605
ORF7a	47	H47Y	Cat	Tat	5	5	AY.23	0.000349
ORF7a	47	H47H	caT	caC	5	5	AY.29	0.000079
ORF7a	47	H47H	caT	caC	5	5	AY.3	0.00005
ORF7a	47	H47Y	Cat	Tat	5	5	AY.33	0.000334
ORF7a	47	H47Q	caT	caG	5	5	AY.44	0.00003
ORF7a	47	H47del	CAT	---	5	5	AY.45	0.000608
ORF7a	47	H47del	CAT	---	5	5	AY.61	0.000524
ORF7a	47	H47del	CAT	---	5	5	AY.9.1	0.000419
ORF7a	47	H47del	CAT	---	5	5	AY.9.2	0.000184
ORF7a	47	H47del1	caT	ca-	4	5	B.1	0.000037
ORF7a	47	H47del1	cAt	c-t	1	5	B.1	0.000009
ORF7a	47	H47Y	Cat	Tat	5	5	B.1.1.189	0.007564
ORF7a	47	H47H	caT	caC	5	5	B.1.1.47	0.026738
ORF7a	47	H47H	caT	caC	5	5	B.1.1.526	0.01773
ORF7a	47	H47del	CAT	---	5	5	B.1.1.56	0.089286
ORF7a	47	H47Y	Cat	Tat	5	5	B.1.258.21	0.03876
ORF7a	47	H47Y	Cat	Tat	5	5	B.1.525	0.000566
ORF7a	47	H47Y	Cat	Tat	5	5	B.1.587	0.009488
ORF7a	47	H47Y	Cat	Tat	5	5	B.1.617.1	0.000645
ORF7a	47	H47T	CAT	ACA	3	5	B.1.617.2	0.000011
ORF7a	47	H47T	CAt	ACt	2	5	B.1.617.2	0.000008
ORF7a	47	H47Y	Cat	Tat	5	5	B.1.628	0.001762
ORF7a	47	H47N	Cat	Aat	5	5	D.2	0.000375
ORF7a	47	H47H	caT	caC	5	5	Q.3	0.000725
ORF7a	47	H47L	cAt	cTt	4	4	AY.11	0.005355
ORF7a	47	H47del	CAT	---	4	4	AY.113	0.00057
ORF7a	47	H47Y	Cat	Tat	4	4	AY.114	0.000924
ORF7a	47	H47H	caT	caC	4	4	AY.119	0.000141
ORF7a	47	H47del	CAT	---	4	4	AY.121	0.000541
ORF7a	47	H47V	CAT	GTG	2	4	AY.25	0.000012
ORF7a	47	H47V	CAt	GTt	2	4	AY.25	0.000012
ORF7a	47	H47R	cAt	cGt	4	4	AY.29	0.000063
ORF7a	47	H47N	Cat	Aat	4	4	AY.3	0.00004
ORF7a	47	H47del	CAT	---	4	4	AY.33	0.000267
ORF7a	47	H47D	Cat	Gat	4	4	AY.33	0.000267
ORF7a	47	H47Y	Cat	Tat	4	4	AY.39.1	0.000158
ORF7a	47	H47L	cAt	cTt	4	4	AY.4.2	0.000087
ORF7a	47	H47N	Cat	Aat	4	4	AY.43	0.000018
ORF7a	47	H47D	Cat	Gat	4	4	AY.43	0.000018
ORF7a	47	H47Q	caT	caG	3	4	AY.43	0.000013
ORF7a	47	H47del1	caT	ca-	3	4	AY.43	0.000013
ORF7a	47	H47Q	caT	caA	1	4	AY.43	0.000004
ORF7a	47	H47del1	Cat	-at	1	4	AY.43	0.000004
ORF7a	47	H47Y	Cat	Tat	4	4	AY.45	0.000487
ORF7a	47	H47Y	Cat	Tat	4	4	AY.7	0.000784
ORF7a	47	H47del	CAT	---	4	4	AY.75	0.000224
ORF7a	47	H47Y	Cat	Tat	4	4	AY.75	0.000224
ORF7a	47	H47del	CAT	---	4	4	AY.91	0.002922
ORF7a	47	H47Y	Cat	Tat	4	4	B	0.000511
ORF7a	47	H47Y	Cat	Tat	4	4	B.1.1.70	0.001364
ORF7a	47	H47N	Cat	Aat	4	4	B.1.160	0.000125
ORF7a	47	H47R	cAt	cGt	4	4	B.1.177	0.000053
ORF7a	47	H47Y	Cat	Tat	4	4	B.1.177.52	0.00703
ORF7a	47	H47Y	Cat	Tat	4	4	B.1.258.17	0.000416
ORF7a	47	H47Y	Cat	Tat	4	4	B.1.36	0.000584
ORF7a	47	H47N	Cat	Aat	4	4	B.1.36.29	0.002069
ORF7a	47	H47Y	Cat	Tat	4	4	B.1.362	0.006163
ORF7a	47	H47Y	Cat	Tat	4	4	B.1.459	0.016327
ORF7a	47	H47N	Cat	Aat	4	4	B.1.526	0.000094
ORF7a	47	H47Y	Cat	Tat	4	4	B.1.595	0.001044
ORF7a	47	H47H	caT	caC	4	4	B.1.596	0.000349
ORF7a	47	H47H	caT	caC	4	4	B.1.609	0.001918
ORF7a	47	H47E	CaT	GaG	3	4	B.1.617.2	0.000011
ORF7a	47	H47E	CaT	GaA	1	4	B.1.617.2	0.000004
ORF7a	47	H47R	cAt	cGt	4	4	B.1.637	0.000292
ORF7a	47	H47N	Cat	Aat	4	4	C.37	0.000464
ORF7a	47	H47Y	Cat	Tat	4	4	P.1.2	0.004624
ORF7a	47	H47Y	Cat	Tat	4	4	P.1.7	0.001277
ORF7a	47	H47Y	Cat	Tat	4	4	Q.8	0.00066
ORF7a	47	H47Y	Cat	Tat	3	3	AE.7	0.25
ORF7a	47	H47N	Cat	Aat	3	3	AY.100	0.000138
ORF7a	47	H47N	Cat	Aat	3	3	AY.102	0.00008
ORF7a	47	H47Q	caT	caG	3	3	AY.103	0.000019
ORF7a	47	H47del1	Cat	-at	2	3	AY.103	0.000012
ORF7a	47	H47del1	CAT	-NN	1	3	AY.103	0.000006
ORF7a	47	H47del	CAT	---	3	3	AY.107	0.001398
ORF7a	47	H47del	CAT	---	3	3	AY.110	0.000338
ORF7a	47	H47Y	Cat	Tat	3	3	AY.111	0.000549
ORF7a	47	H47Y	Cat	Tat	3	3	AY.113	0.000427
ORF7a	47	H47del1	Cat	-at	3	3	AY.118	0.000188
ORF7a	47	H47R	cAt	cGt	3	3	AY.120	0.000112
ORF7a	47	H47Y	Cat	Tat	3	3	AY.2	0.001068
ORF7a	47	H47H	caT	caC	3	3	AY.20	0.000117
ORF7a	47	H47D	Cat	Gat	2	3	AY.25	0.000012
ORF7a	47	H47D	CaT	GaC	1	3	AY.25	0.000006
ORF7a	47	H47del	CAT	---	3	3	AY.29.1	0.000662
ORF7a	47	H47H	caT	caC	3	3	AY.3.1	0.000256
ORF7a	47	H47Y	Cat	Tat	3	3	AY.34	0.000291
ORF7a	47	H47P	cAt	cCt	3	3	AY.4	0.000005
ORF7a	47	H47del1	Cat	-at	2	3	AY.4	0.000003
ORF7a	47	H47del1	CAT	-NN	1	3	AY.4	0.000002
ORF7a	47	H47del	CAT	---	3	3	AY.4.5	0.000322
ORF7a	47	H47L	cAt	cTt	3	3	AY.44	0.000018
ORF7a	47	H47del1	cAT	c-N	1	3	AY.44	0.000006
ORF7a	47	H47del1	Cat	-at	1	3	AY.44	0.000006
ORF7a	47	H47del1	caT	ca-	1	3	AY.44	0.000006
ORF7a	47	H47Y	Cat	Tat	3	3	AY.46	0.000312
ORF7a	47	H47Y	Cat	Tat	3	3	AY.46.5	0.000595
ORF7a	47	H47Y	Cat	Tat	3	3	AY.68	0.000821
ORF7a	47	H47H	caT	caC	3	3	AY.75	0.000168
ORF7a	47	H47R	cAt	cGt	3	3	AY.79	0.003632
ORF7a	47	H47del	CAT	---	3	3	AY.88	0.002653
ORF7a	47	H47H	caT	caC	3	3	AY.9.1	0.000251
ORF7a	47	H47Y	Cat	Tat	3	3	AY.9.2	0.00011
ORF7a	47	H47del	CAT	---	3	3	AY.92	0.000862
ORF7a	47	H47H	caT	caC	3	3	AY.98	0.000237
ORF7a	47	H47del	CAT	---	3	3	AY.99	0.003148
ORF7a	47	H47R	cAt	cGt	3	3	B.1	0.000027
ORF7a	47	H47N	Cat	Aat	3	3	B.1.1	0.000054
ORF7a	47	H47Q	caT	caG	2	3	B.1.1	0.000036
ORF7a	47	H47Q	caT	caA	1	3	B.1.1	0.000018
ORF7a	47	H47del	CAT	---	3	3	B.1.1.121	0.007282
ORF7a	47	H47Y	Cat	Tat	3	3	B.1.1.216	0.002671
ORF7a	47	H47Y	Cat	Tat	3	3	B.1.1.232	0.005445
ORF7a	47	H47del	CAT	---	3	3	B.1.1.25	0.001706
ORF7a	47	H47Y	Cat	Tat	3	3	B.1.1.306	0.001315
ORF7a	47	H47H	caT	caC	3	3	B.1.1.397	0.006757
ORF7a	47	H47Y	Cat	Tat	3	3	B.1.1.464	0.004418
ORF7a	47	H47Y	Cat	Tat	3	3	B.1.1.487	0.01676
ORF7a	47	H47K	CaT	AaG	3	3	B.1.1.7	0.000003
ORF7a	47	H47N	Cat	Aat	3	3	B.1.177.21	0.000229
ORF7a	47	H47Y	Cat	Tat	3	3	B.1.177.21	0.000229
ORF7a	47	H47N	Cat	Aat	3	3	B.1.177.54	0.001819
ORF7a	47	H47Y	Cat	Tat	3	3	B.1.177.86	0.00055
ORF7a	47	H47R	cAt	cGt	3	3	B.1.2	0.000026
ORF7a	47	H47H	caT	caC	3	3	B.1.258	0.0002
ORF7a	47	H47N	Cat	Aat	3	3	B.1.427	0.000151
ORF7a	47	H47del	CAT	---	3	3	B.1.427	0.000151
ORF7a	47	H47Y	Cat	Tat	3	3	B.1.466.2	0.001174
ORF7a	47	H47H	caT	caC	3	3	B.1.466.2	0.001174
ORF7a	47	H47Y	Cat	Tat	3	3	B.1.576	0.00272
ORF7a	47	H47Y	Cat	Tat	3	3	B.1.577	0.002062
ORF7a	47	H47del1	cAt	c-t	1	3	B.1.617.2	0.000004
ORF7a	47	H47del1	caT	ca-	1	3	B.1.617.2	0.000004
ORF7a	47	H47del1	Cat	-at	1	3	B.1.617.2	0.000004
ORF7a	47	H47del	CAT	---	3	3	B.1.626	0.017143
ORF7a	47	H47Y	Cat	Tat	3	3	B.1.637	0.000219
ORF7a	47	H47Y	Cat	Tat	3	3	D.2	0.000225
ORF7a	47	H47R	cAt	cGt	3	3	P.1	0.000047
ORF7a	47	H47Y	Cat	Tat	3	3	P.1.1	0.000953
ORF7a	47	H47Y	Cat	Tat	3	3	P.2	0.00056
ORF7a	47	H47Y	Cat	Tat	3	3	Q.3	0.000435
ORF7a	47	H47C	CAt	TGt	2	2		0.111111
ORF7a	47	H47Y	Cat	Tat	2	2		0.111111
ORF7a	47	H47R	cAt	cGt	2	2		0.111111
ORF7a	47	H47del	CAT	---	2	2	A	0.000774
ORF7a	47	H47R	cAt	cGt	2	2	A.2.5	0.000998
ORF7a	47	H47N	Cat	Aat	2	2	A.2.5	0.000998
ORF7a	47	H47N	Cat	Aat	2	2	A.23.1	0.001408
ORF7a	47	H47del	CAT	---	2	2	A.28	0.005291
ORF7a	47	H47M	CAT	ATG	2	2	All	0
ORF7a	47	H47W	CAT	TGG	2	2	All	0
ORF7a	47	H47H	caT	caC	2	2	AY.100	0.000092
ORF7a	47	H47D	Cat	Gat	2	2	AY.102	0.000053
ORF7a	47	H47R	cAt	cGt	2	2	AY.103	0.000012
ORF7a	47	H47N	Cat	Aat	2	2	AY.103	0.000012
ORF7a	47	H47del	CAT	---	2	2	AY.108	0.002205
ORF7a	47	H47del	CAT	---	2	2	AY.109	0.001479
ORF7a	47	H47del	CAT	---	2	2	AY.114	0.000462
ORF7a	47	H47Y	Cat	Tat	2	2	AY.121	0.000271
ORF7a	47	H47R	cAt	cGt	2	2	AY.121	0.000271
ORF7a	47	H47Y	Cat	Tat	2	2	AY.14	0.000176
ORF7a	47	H47del	CAT	---	2	2	AY.14	0.000176
ORF7a	47	H47Y	Cat	Tat	2	2	AY.16	0.000759
ORF7a	47	H47N	Cat	Aat	2	2	AY.20	0.000078
ORF7a	47	H47N	Cat	Aat	2	2	AY.23	0.000139
ORF7a	47	H47E	CaT	GaG	2	2	AY.25	0.000012
ORF7a	47	H47W	CAT	TGG	2	2	AY.25	0.000012
ORF7a	47	H47M	CAT	ATG	2	2	AY.25	0.000012
ORF7a	47	H47del2	CAt	--t	1	2	AY.25	0.000006
ORF7a	47	H47del2	cAT	c--	1	2	AY.25	0.000006
ORF7a	47	H47Y	Cat	Tat	2	2	AY.27	0.000129
ORF7a	47	H47R	cAt	cGt	2	2	AY.27	0.000129
ORF7a	47	H47L	cAt	cTt	2	2	AY.29	0.000032
ORF7a	47	H47del1	caT	ca-	2	2	AY.29	0.000032
ORF7a	47	H47H	caT	caC	2	2	AY.29.1	0.000441
ORF7a	47	H47del1	Cat	-at	2	2	AY.3.1	0.000171
ORF7a	47	H47del	CAT	---	2	2	AY.30	0.000791
ORF7a	47	H47Y	Cat	Tat	2	2	AY.32	0.001065
ORF7a	47	H47N	Cat	Aat	2	2	AY.33	0.000134
ORF7a	47	H47del1	caT	ca-	2	2	AY.36	0.000296
ORF7a	47	H47H	caT	caC	2	2	AY.4.2	0.000043
ORF7a	47	H47del	CAT	---	2	2	AY.4.2.1	0.000298
ORF7a	47	H47del	CAT	---	2	2	AY.4.3	0.001684
ORF7a	47	H47Y	Cat	Tat	2	2	AY.4.4	0.000818
ORF7a	47	H47Y	Cat	Tat	2	2	AY.41	0.000588
ORF7a	47	H47P	cAt	cCt	2	2	AY.43	0.000009
ORF7a	47	H47L	CAT	TTG	1	2	AY.43	0.000004
ORF7a	47	H47L	cAt	cTt	1	2	AY.43	0.000004
ORF7a	47	H47Y	Cat	Tat	2	2	AY.46.4	0.000329
ORF7a	47	H47H	caT	caC	2	2	AY.47	0.000062
ORF7a	47	H47Q	caT	caG	2	2	AY.5	0.000041
ORF7a	47	H47N	Cat	Aat	2	2	AY.5	0.000041
ORF7a	47	H47Y	Cat	Tat	2	2	AY.56	0.00321
ORF7a	47	H47del	CAT	---	2	2	AY.57	0.001312
ORF7a	47	H47H	caT	caC	2	2	AY.6	0.000082
ORF7a	47	H47Y	Cat	Tat	2	2	AY.63	0.000774
ORF7a	47	H47del	CAT	---	2	2	AY.66	0.002139
ORF7a	47	H47del	CAT	---	2	2	AY.71	0.00095
ORF7a	47	H47N	Cat	Aat	2	2	AY.75	0.000112
ORF7a	47	H47Y	Cat	Tat	2	2	AY.75.1	0.000361
ORF7a	47	H47del	CAT	---	2	2	AY.85	0.000854
ORF7a	47	H47H	caT	caC	2	2	AY.88	0.001768
ORF7a	47	H47Y	Cat	Tat	2	2	AY.88	0.001768
ORF7a	47	H47H	caT	caC	2	2	AY.9	0.000135
ORF7a	47	H47N	Cat	Aat	2	2	AY.9	0.000135
ORF7a	47	H47del	CAT	---	2	2	AY.9	0.000135
ORF7a	47	H47P	cAt	cCt	2	2	AY.9.1	0.000167
ORF7a	47	H47del2	cAT	c--	2	2	AY.95	0.001522
ORF7a	47	H47R	cAt	cGt	2	2	AY.98.1	0.000097
ORF7a	47	H47N	Cat	Aat	2	2	AY.98.1	0.000097
ORF7a	47	H47H	caT	caC	2	2	AY.98.1	0.000097
ORF7a	47	H47del2	cAT	c--	2	2	AY.99.2	0.000184
ORF7a	47	H47Y	Cat	Tat	2	2	B.1.1.1	0.000653
ORF7a	47	H47Y	Cat	Tat	2	2	B.1.1.133	0.016949
ORF7a	47	H47R	cAt	cGt	2	2	B.1.1.153	0.002191
ORF7a	47	H47R	cAt	cGt	2	2	B.1.1.214	0.000111
ORF7a	47	H47Y	Cat	Tat	2	2	B.1.1.236	0.013793
ORF7a	47	H47Y	Cat	Tat	2	2	B.1.1.294	0.002532
ORF7a	47	H47Y	Cat	Tat	2	2	B.1.1.318	0.000604
ORF7a	47	H47del	CAT	---	2	2	B.1.1.318	0.000604
ORF7a	47	H47N	Cat	Aat	2	2	B.1.1.359	0.055556
ORF7a	47	H47Q	caT	caA	2	2	B.1.1.39	0.001019
ORF7a	47	H47Y	Cat	Tat	2	2	B.1.1.402	0.022222
ORF7a	47	H47del	CAT	---	2	2	B.1.1.519	0.000079
ORF7a	47	H47H	caT	caC	2	2	B.1.1.61	0.017544
ORF7a	47	H47N	Cat	Aat	2	2	B.1.160.17	0.003401
ORF7a	47	H47L	cAt	cTt	2	2	B.1.177	0.000026
ORF7a	47	H47H	caT	caC	2	2	B.1.177	0.000026
ORF7a	47	H47Y	Cat	Tat	2	2	B.1.177.4	0.000422
ORF7a	47	H47del	CAT	---	2	2	B.1.177.43	0.002954
ORF7a	47	H47Y	Cat	Tat	2	2	B.1.177.44	0.001038
ORF7a	47	H47Q	caT	caA	2	2	B.1.177.44	0.001038
ORF7a	47	H47Y	Cat	Tat	2	2	B.1.177.7	0.00033
ORF7a	47	H47R	cAt	cGt	2	2	B.1.177.7	0.00033
ORF7a	47	H47Y	Cat	Tat	2	2	B.1.177.81	0.000379
ORF7a	47	H47del	CAT	---	2	2	B.1.177.81	0.000379
ORF7a	47	H47del	CAT	---	2	2	B.1.177.86	0.000367
ORF7a	47	H47Q	caT	caG	2	2	B.1.2	0.000018
ORF7a	47	H47del	CAT	---	2	2	B.1.214.2	0.001199
ORF7a	47	H47Y	Cat	Tat	2	2	B.1.239	0.002442
ORF7a	47	H47Y	Cat	Tat	2	2	B.1.240	0.000431
ORF7a	47	H47del	CAT	---	2	2	B.1.243	0.000139
ORF7a	47	H47R	cAt	cGt	2	2	B.1.243	0.000139
ORF7a	47	H47del	CAT	---	2	2	B.1.258.11	0.000793
ORF7a	47	H47H	caT	caC	2	2	B.1.258.17	0.000208
ORF7a	47	H47H	caT	caC	2	2	B.1.311	0.000549
ORF7a	47	H47H	caT	caC	2	2	B.1.323	0.041667
ORF7a	47	H47Q	caT	caA	1	2	B.1.351	0.00003
ORF7a	47	H47Q	caT	caG	1	2	B.1.351	0.00003
ORF7a	47	H47N	Cat	Aat	2	2	B.1.36.36	0.001204
ORF7a	47	H47H	caT	caC	2	2	B.1.369	0.00057
ORF7a	47	H47del	CAT	---	2	2	B.1.375	0.001639
ORF7a	47	H47Q	caT	caG	1	2	B.1.416.1	0.001563
ORF7a	47	H47Q	caT	caA	1	2	B.1.416.1	0.001563
ORF7a	47	H47Y	Cat	Tat	2	2	B.1.468	0.011429
ORF7a	47	H47Y	Cat	Tat	2	2	B.1.524	0.002813
ORF7a	47	H47H	caT	caC	2	2	B.1.526	0.000047
ORF7a	47	H47del	CAT	---	2	2	B.1.575	0.000607
ORF7a	47	H47N	Cat	Aat	2	2	B.1.617.1	0.000258
ORF7a	47	H47F	CAt	TTt	2	2	B.1.617.2	0.000008
ORF7a	47	H47I	CAt	ATt	1	2	B.1.617.2	0.000004
ORF7a	47	H47I	CAT	ATC	1	2	B.1.617.2	0.000004
ORF7a	47	H47del	CAT	---	2	2	B.1.617.3	0.00597
ORF7a	47	H47Y	Cat	Tat	2	2	B.1.619	0.001742
ORF7a	47	H47del	CAT	---	2	2	B.1.621.1	0.001012
ORF7a	47	H47Y	Cat	Tat	2	2	B.1.621.1	0.001012
ORF7a	47	H47H	caT	caC	2	2	B.1.637	0.000146
ORF7a	47	H47N	Cat	Aat	2	2	C.16	0.002121
ORF7a	47	H47del	CAT	---	2	2	C.36.3	0.001134
ORF7a	47	H47del	CAT	---	2	2	P.1.14	0.000096
ORF7a	47	H47Y	Cat	Tat	2	2	P.1.4	0.001953
ORF7a	47	H47del	CAT	---	2	2	P.2	0.000373
ORF7a	47	H47del	CAT	---	2	2	Q.8	0.00033
ORF7a	47	H47H	caT	caC	1	1	A	0.000387
ORF7a	47	H47Q	caT	caG	1	1	A	0.000387
ORF7a	47	H47Q	caT	caA	1	1	A.1	0.000282
ORF7a	47	H47del	CAT	---	1	1	A.1	0.000282
ORF7a	47	H47del1	Cat	-at	1	1	A.2	0.000662
ORF7a	47	H47Y	Cat	Tat	1	1	A.2.5	0.000499
ORF7a	47	H47N	Cat	Aat	1	1	A.2.5.2	0.001572
ORF7a	47	H47N	Cat	Aat	1	1	A.2.5.3	0.010309
ORF7a	47	H47Y	Cat	Tat	1	1	A.2.5.3	0.010309
ORF7a	47	H47Y	Cat	Tat	1	1	A.23.1	0.000704
ORF7a	47	H47del	CAT	---	1	1	A.23.1	0.000704
ORF7a	47	H47H	caT	caC	1	1	AA.1	0.007246
ORF7a	47	H47Y	Cat	Tat	1	1	AE.3	0.032258
ORF7a	47	H47Y	Cat	Tat	1	1	AE.8	0.000489
ORF7a	47	H47A	CAT	GCA	1	1	All	0
ORF7a	47	H47R	cAt	cGt	1	1	AY.1	0.000396
ORF7a	47	H47Q	caT	caA	1	1	AY.100	0.000046
ORF7a	47	H47del	CAT	---	1	1	AY.101	0.00049
ORF7a	47	H47R	cAt	cGt	1	1	AY.102	0.000027
ORF7a	47	H47del1	Cat	-at	1	1	AY.102	0.000027
ORF7a	47	H47del2	cAT	c--	1	1	AY.103	0.000006
ORF7a	47	H47R	cAt	cGt	1	1	AY.104	0.001984
ORF7a	47	H47Y	Cat	Tat	1	1	AY.105	0.000643
ORF7a	47	H47Y	Cat	Tat	1	1	AY.106	0.000335
ORF7a	47	H47P	cAt	cCt	1	1	AY.107	0.000466
ORF7a	47	H47R	cAt	cGt	1	1	AY.109	0.00074
ORF7a	47	H47R	cAt	cGt	1	1	AY.110	0.000113
ORF7a	47	H47Q	caT	caG	1	1	AY.111	0.000183
ORF7a	47	H47H	caT	caC	1	1	AY.113	0.000142
ORF7a	47	H47H	caT	caC	1	1	AY.114	0.000231
ORF7a	47	H47H	caT	caC	1	1	AY.116.1	0.000311
ORF7a	47	H47del	CAT	---	1	1	AY.116.1	0.000311
ORF7a	47	H47D	Cat	Gat	1	1	AY.117	0.000085
ORF7a	47	H47H	caT	caC	1	1	AY.117	0.000085
ORF7a	47	H47D	Cat	Gat	1	1	AY.118	0.000063
ORF7a	47	H47D	Cat	Gat	1	1	AY.121	0.000135
ORF7a	47	H47A	CAT	GCA	1	1	AY.13	0.000161
ORF7a	47	H47del	CAT	---	1	1	AY.13	0.000161
ORF7a	47	H47H	caT	caC	1	1	AY.13	0.000161
ORF7a	47	H47del1	caT	ca-	1	1	AY.14	0.000088
ORF7a	47	H47H	caT	caC	1	1	AY.16	0.00038
ORF7a	47	H47del	CAT	---	1	1	AY.16	0.00038
ORF7a	47	H47L	cAt	cTt	1	1	AY.20	0.000039
ORF7a	47	H47Q	caT	caG	1	1	AY.20	0.000039
ORF7a	47	H47del1	caT	ca-	1	1	AY.23	0.00007
ORF7a	47	H47del	CAT	---	1	1	AY.24	0.000431
ORF7a	47	H47R	cAt	cGt	1	1	AY.26	0.000028
ORF7a	47	H47H	caT	caC	1	1	AY.27	0.000065
ORF7a	47	H47N	Cat	Aat	1	1	AY.29	0.000016
ORF7a	47	H47D	Cat	Gat	1	1	AY.29	0.000016
ORF7a	47	H47del1	Cat	-at	1	1	AY.3	0.00001
ORF7a	47	H47D	Cat	Gat	1	1	AY.3	0.00001
ORF7a	47	H47N	Cat	Aat	1	1	AY.3.1	0.000085
ORF7a	47	H47L	cAt	cTt	1	1	AY.3.1	0.000085
ORF7a	47	H47Q	caT	caG	1	1	AY.33	0.000067
ORF7a	47	H47H	caT	caC	1	1	AY.33	0.000067
ORF7a	47	H47Y	Cat	Tat	1	1	AY.35	0.000233
ORF7a	47	H47R	cAt	cGt	1	1	AY.36	0.000148
ORF7a	47	H47del2	cAT	c--	1	1	AY.36	0.000148
ORF7a	47	H47H	caT	caC	1	1	AY.36	0.000148
ORF7a	47	H47N	Cat	Aat	1	1	AY.37	0.000316
ORF7a	47	H47del	CAT	---	1	1	AY.38	0.000499
ORF7a	47	H47Q	caT	caA	1	1	AY.39	0.000025
ORF7a	47	H47D	Cat	Gat	1	1	AY.39	0.000025
ORF7a	47	H47N	Cat	Aat	1	1	AY.39.1	0.00004
ORF7a	47	H47R	cAt	cGt	1	1	AY.4.2	0.000022
ORF7a	47	H47L	cAt	cTt	1	1	AY.4.2.1	0.000149
ORF7a	47	H47P	cAt	cCt	1	1	AY.4.2.1	0.000149
ORF7a	47	H47N	Cat	Aat	1	1	AY.4.5	0.000107
ORF7a	47	H47Y	Cat	Tat	1	1	AY.40	0.000964
ORF7a	47	H47Q	caT	caA	1	1	AY.42	0.00004
ORF7a	47	H47H	caT	caC	1	1	AY.42	0.00004
ORF7a	47	H47del2	CAt	--t	1	1	AY.43	0.000004
ORF7a	47	H47V	CAT	GTG	1	1	AY.43	0.000004
ORF7a	47	H47D	Cat	Gat	1	1	AY.44	0.000006
ORF7a	47	H47H	caT	caC	1	1	AY.45	0.000122
ORF7a	47	H47N	Cat	Aat	1	1	AY.45	0.000122
ORF7a	47	H47del	CAT	---	1	1	AY.46	0.000104
ORF7a	47	H47R	cAt	cGt	1	1	AY.46.4	0.000165
ORF7a	47	H47del1	Cat	-at	1	1	AY.46.6	0.000072
ORF7a	47	H47D	Cat	Gat	1	1	AY.47	0.000031
ORF7a	47	H47N	Cat	Aat	1	1	AY.47	0.000031
ORF7a	47	H47R	cAt	cGt	1	1	AY.47	0.000031
ORF7a	47	H47H	caT	caC	1	1	AY.48	0.000465
ORF7a	47	H47H	caT	caC	1	1	AY.5	0.000021
ORF7a	47	H47del1	Cat	-at	1	1	AY.5	0.000021
ORF7a	47	H47del	CAT	---	1	1	AY.5.3	0.000337
ORF7a	47	H47del	CAT	---	1	1	AY.5.4	0.000277
ORF7a	47	H47Y	Cat	Tat	1	1	AY.53	0.000288
ORF7a	47	H47N	Cat	Aat	1	1	AY.53	0.000288
ORF7a	47	H47del	CAT	---	1	1	AY.53	0.000288
ORF7a	47	H47C	CAt	TGt	1	1	AY.54	0.000095
ORF7a	47	H47R	cAt	cGt	1	1	AY.54	0.000095
ORF7a	47	H47H	caT	caC	1	1	AY.54	0.000095
ORF7a	47	H47Q	caT	caG	1	1	AY.54	0.000095
ORF7a	47	H47H	caT	caC	1	1	AY.57	0.000656
ORF7a	47	H47Y	Cat	Tat	1	1	AY.59	0.00053
ORF7a	47	H47del	CAT	---	1	1	AY.59	0.00053
ORF7a	47	H47R	cAt	cGt	1	1	AY.6	0.000041
ORF7a	47	H47L	cAt	cTt	1	1	AY.60	0.000938
ORF7a	47	H47L	cAt	cTt	1	1	AY.61	0.000105
ORF7a	47	H47R	cAt	cGt	1	1	AY.61	0.000105
ORF7a	47	H47H	caT	caC	1	1	AY.61	0.000105
ORF7a	47	H47Y	Cat	Tat	1	1	AY.62	0.000436
ORF7a	47	H47H	caT	caC	1	1	AY.64	0.000595
ORF7a	47	H47H	caT	caC	1	1	AY.67	0.000464
ORF7a	47	H47Y	Cat	Tat	1	1	AY.67	0.000464
ORF7a	47	H47del	CAT	---	1	1	AY.68	0.000274
ORF7a	47	H47Y	Cat	Tat	1	1	AY.69	0.000187
ORF7a	47	H47N	Cat	Aat	1	1	AY.69	0.000187
ORF7a	47	H47del	CAT	---	1	1	AY.7	0.000196
ORF7a	47	H47L	cAt	cTt	1	1	AY.7.1	0.000113
ORF7a	47	H47H	caT	caC	1	1	AY.7.1	0.000113
ORF7a	47	H47Y	CaT	TaC	1	1	AY.7.1	0.000113
ORF7a	47	H47del	CAT	---	1	1	AY.7.1	0.000113
ORF7a	47	H47del1	caT	ca-	1	1	AY.7.2	0.000559
ORF7a	47	H47Y	Cat	Tat	1	1	AY.70	0.000209
ORF7a	47	H47Y	Cat	Tat	1	1	AY.71	0.000475
ORF7a	47	H47H	caT	caC	1	1	AY.71	0.000475
ORF7a	47	H47Y	Cat	Tat	1	1	AY.73	0.000665
ORF7a	47	H47del	CAT	---	1	1	AY.73	0.000665
ORF7a	47	H47H	caT	caC	1	1	AY.74	0.000116
ORF7a	47	H47del	CAT	---	1	1	AY.74	0.000116
ORF7a	47	H47Y	Cat	Tat	1	1	AY.74	0.000116
ORF7a	47	H47Q	caT	caA	1	1	AY.75	0.000056
ORF7a	47	H47del1	caT	ca-	1	1	AY.75	0.000056
ORF7a	47	H47H	caT	caC	1	1	AY.75.1	0.00018
ORF7a	47	H47Q	caT	caG	1	1	AY.75.1	0.00018
ORF7a	47	H47del	CAT	---	1	1	AY.79	0.001211
ORF7a	47	H47Y	Cat	Tat	1	1	AY.79	0.001211
ORF7a	47	H47del	CAT	---	1	1	AY.8	0.000606
ORF7a	47	H47R	cAt	cGt	1	1	AY.85	0.000427
ORF7a	47	H47N	Cat	Aat	1	1	AY.9.2	0.000037
ORF7a	47	H47H	caT	caC	1	1	AY.9.2	0.000037
ORF7a	47	H47R	cAt	cGt	1	1	AY.9.2	0.000037
ORF7a	47	H47Y	Cat	Tat	1	1	AY.91	0.00073
ORF7a	47	H47Y	Cat	Tat	1	1	AY.93	0.000273
ORF7a	47	H47del	CAT	---	1	1	AY.94	0.000443
ORF7a	47	H47del2	CAt	--t	1	1	AY.98	0.000079
ORF7a	47	H47del	CAT	---	1	1	AY.98	0.000079
ORF7a	47	H47del1	caT	ca-	1	1	AY.99	0.001049
ORF7a	47	H47Q	caT	caA	1	1	AY.99.2	0.000092
ORF7a	47	H47H	caT	caC	1	1	AY.99.2	0.000092
ORF7a	47	H47del	CAT	---	1	1	AY.99.2	0.000092
ORF7a	47	H47del	CAT	---	1	1	AZ.2	0.000821
ORF7a	47	H47del	CAT	---	1	1	B	0.000128
ORF7a	47	H47Q	caT	caA	1	1	B	0.000128
ORF7a	47	H47F	CAT	TTC	1	1	B.1	0.000009
ORF7a	47	H47R	cAt	cGt	1	1	B.1.1	0.000018
ORF7a	47	H47N	Cat	Aat	1	1	B.1.1.135	0.004695
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.1.152	0.04
ORF7a	47	H47H	caT	caC	1	1	B.1.1.157	0.000913
ORF7a	47	H47N	Cat	Aat	1	1	B.1.1.157	0.000913
ORF7a	47	H47del	CAT	---	1	1	B.1.1.157	0.000913
ORF7a	47	H47H	caT	caC	1	1	B.1.1.172	0.018182
ORF7a	47	H47del	CAT	---	1	1	B.1.1.174	0.003378
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.1.176	0.000439
ORF7a	47	H47del	CAT	---	1	1	B.1.1.192	0.002309
ORF7a	47	H47N	Cat	Aat	1	1	B.1.1.216	0.00089
ORF7a	47	H47del1	caT	ca-	1	1	B.1.1.216	0.00089
ORF7a	47	H47N	Cat	Aat	1	1	B.1.1.240	0.004695
ORF7a	47	H47N	Cat	Aat	1	1	B.1.1.25	0.000569
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.1.25	0.000569
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.1.255	0.00303
ORF7a	47	H47R	cAt	cGt	1	1	B.1.1.263	0.001558
ORF7a	47	H47N	Cat	Aat	1	1	B.1.1.279	0.001121
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.1.28	0.000311
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.1.284	0.000107
ORF7a	47	H47N	Cat	Aat	1	1	B.1.1.284	0.000107
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.1.302	0.002075
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.1.304	0.002809
ORF7a	47	H47N	Cat	Aat	1	1	B.1.1.304	0.002809
ORF7a	47	H47L	cAt	cTt	1	1	B.1.1.306	0.000438
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.1.309	0.005848
ORF7a	47	H47L	cAt	cTt	1	1	B.1.1.317	0.000412
ORF7a	47	H47Q	caT	caA	1	1	B.1.1.33	0.000421
ORF7a	47	H47N	Cat	Aat	1	1	B.1.1.33	0.000421
ORF7a	47	H47del	CAT	---	1	1	B.1.1.33	0.000421
ORF7a	47	H47H	caT	caC	1	1	B.1.1.334	0.016393
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.1.368	0.003086
ORF7a	47	H47N	Cat	Aat	1	1	B.1.1.37	0.000193
ORF7a	47	H47N	Cat	Aat	1	1	B.1.1.374	0.002375
ORF7a	47	H47H	caT	caC	1	1	B.1.1.387	0.058824
ORF7a	47	H47H	caT	caC	1	1	B.1.1.409	0.002833
ORF7a	47	H47Q	caT	caA	1	1	B.1.1.445	0.037037
ORF7a	47	H47R	cAt	cGt	1	1	B.1.1.486	0.001577
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.1.486	0.001577
ORF7a	47	H47N	Cat	Aat	1	1	B.1.1.487	0.005587
ORF7a	47	H47R	cAt	cGt	1	1	B.1.1.521	0.005348
ORF7a	47	H47del	CAT	---	1	1	B.1.1.522	0.017241
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.1.523	0.001563
ORF7a	47	H47N	Cat	Aat	1	1	B.1.1.523	0.001563
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.1.63	0.000386
ORF7a	47	H47del2	CAt	--t	1	1	B.1.1.7	0.000001
ORF7a	47	H47I	CAt	ATt	1	1	B.1.1.7	0.000001
ORF7a	47	H47F	CAt	TTt	1	1	B.1.1.7	0.000001
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.105	0.009615
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.110.3	0.000718
ORF7a	47	H47del	CAT	---	1	1	B.1.115	0.021739
ORF7a	47	H47Q	caT	caG	1	1	B.1.139	0.000733
ORF7a	47	H47H	caT	caC	1	1	B.1.139	0.000733
ORF7a	47	H47del	CAT	---	1	1	B.1.140	0.018868
ORF7a	47	H47L	cAt	cTt	1	1	B.1.160.10	0.008065
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.160.16	0.000929
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.160.22	0.006757
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.160.28	0.002924
ORF7a	47	H47Q	caT	caA	1	1	B.1.160.29	0.004219
ORF7a	47	H47P	cAt	cCt	1	1	B.1.160.29	0.004219
ORF7a	47	H47del1	caT	ca-	1	1	B.1.160.30	0.002976
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.160.32	0.004292
ORF7a	47	H47Q	caT	caA	1	1	B.1.160.32	0.004292
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.160.8	0.001289
ORF7a	47	H47Q	caT	caG	1	1	B.1.170	0.00431
ORF7a	47	H47F	CAt	TTt	1	1	B.1.177	0.000013
ORF7a	47	H47del1	caT	ca-	1	1	B.1.177	0.000013
ORF7a	47	H47I	CAt	ATt	1	1	B.1.177	0.000013
ORF7a	47	H47R	cAt	cGt	1	1	B.1.177.11	0.001698
ORF7a	47	H47N	Cat	Aat	1	1	B.1.177.12	0.000152
ORF7a	47	H47R	cAt	cGt	1	1	B.1.177.12	0.000152
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.177.12	0.000152
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.177.20	0.001517
ORF7a	47	H47K	CaT	AaG	1	1	B.1.177.21	0.000076
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.177.40	0.005155
ORF7a	47	H47Q	caT	caA	1	1	B.1.177.43	0.001477
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.177.43	0.001477
ORF7a	47	H47del	CAT	---	1	1	B.1.177.50	0.004695
ORF7a	47	H47N	Cat	Aat	1	1	B.1.177.51	0.004566
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.177.51	0.004566
ORF7a	47	H47H	caT	caC	1	1	B.1.177.56	0.000668
ORF7a	47	H47N	Cat	Aat	1	1	B.1.177.60	0.000218
ORF7a	47	H47del	CAT	---	1	1	B.1.177.62	0.001192
ORF7a	47	H47N	Cat	Aat	1	1	B.1.177.62	0.001192
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.177.73	0.000566
ORF7a	47	H47N	Cat	Aat	1	1	B.1.177.75	0.001041
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.177.77	0.000726
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.177.8	0.000752
ORF7a	47	H47N	Cat	Aat	1	1	B.1.177.82	0.000477
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.177.83	0.001481
ORF7a	47	H47del	CAT	---	1	1	B.1.177.83	0.001481
ORF7a	47	H47N	Cat	Aat	1	1	B.1.177.86	0.000183
ORF7a	47	H47H	caT	caC	1	1	B.1.177.87	0.000728
ORF7a	47	H47T	CAt	ACt	1	1	B.1.2	0.000009
ORF7a	47	H47del1	cAt	c-t	1	1	B.1.2	0.000009
ORF7a	47	H47L	cAt	cTt	1	1	B.1.2	0.000009
ORF7a	47	H47D	Cat	Gat	1	1	B.1.2	0.000009
ORF7a	47	H47N	Cat	Aat	1	1	B.1.214	0.003663
ORF7a	47	H47H	caT	caC	1	1	B.1.22	0.001318
ORF7a	47	H47Q	caT	caA	1	1	B.1.221	0.000071
ORF7a	47	H47H	caT	caC	1	1	B.1.221	0.000071
ORF7a	47	H47del	CAT	---	1	1	B.1.221	0.000071
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.223	0.002778
ORF7a	47	H47L	cAt	cTt	1	1	B.1.232	0.000537
ORF7a	47	H47N	Cat	Aat	1	1	B.1.237	0.004975
ORF7a	47	H47del	CAT	---	1	1	B.1.240	0.000216
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.241	0.000812
ORF7a	47	H47H	caT	caC	1	1	B.1.243	0.00007
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.258.12	0.007874
ORF7a	47	H47del	CAT	---	1	1	B.1.258.17	0.000104
ORF7a	47	H47N	Cat	Aat	1	1	B.1.279	0.000514
ORF7a	47	H47H	caT	caC	1	1	B.1.301	0.005917
ORF7a	47	H47H	caT	caC	1	1	B.1.304	0.023256
ORF7a	47	H47H	caT	caC	1	1	B.1.320	0.001245
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.338	0.008621
ORF7a	47	H47L	cAt	cTt	1	1	B.1.351	0.00003
ORF7a	47	H47R	cAt	cGt	1	1	B.1.351	0.00003
ORF7a	47	H47V	CAt	GTt	1	1	B.1.351	0.00003
ORF7a	47	H47D	Cat	Gat	1	1	B.1.351	0.00003
ORF7a	47	H47H	caT	caC	1	1	B.1.351	0.00003
ORF7a	47	H47N	Cat	Aat	1	1	B.1.351	0.00003
ORF7a	47	H47del	CAT	---	1	1	B.1.351.2	0.000303
ORF7a	47	H47H	caT	caC	1	1	B.1.351.2	0.000303
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.351.3	0.000876
ORF7a	47	H47N	Cat	Aat	1	1	B.1.351.3	0.000876
ORF7a	47	H47del	CAT	---	1	1	B.1.356	0.001727
ORF7a	47	H47H	caT	caC	1	1	B.1.36	0.000146
ORF7a	47	H47N	Cat	Aat	1	1	B.1.36	0.000146
ORF7a	47	H47H	caT	caC	1	1	B.1.36.10	0.004785
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.36.16	0.001425
ORF7a	47	H47H	caT	caC	1	1	B.1.36.22	0.001208
ORF7a	47	H47del1	caT	ca-	1	1	B.1.36.29	0.000517
ORF7a	47	H47del2	CAt	--t	1	1	B.1.361	0.001289
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.361	0.001289
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.369	0.000285
ORF7a	47	H47del	CAT	---	1	1	B.1.371	0.001122
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.375	0.00082
ORF7a	47	H47N	Cat	Aat	1	1	B.1.396	0.000706
ORF7a	47	H47H	caT	caC	1	1	B.1.396	0.000706
ORF7a	47	H47Q	caT	caG	1	1	B.1.398	0.002976
ORF7a	47	H47Q	caT	caA	1	1	B.1.399	0.001934
ORF7a	47	H47N	Cat	Aat	1	1	B.1.400	0.000429
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.406	0.006061
ORF7a	47	H47H	caT	caC	1	1	B.1.415	0.014286
ORF7a	47	H47del	CAT	---	1	1	B.1.416	0.001269
ORF7a	47	H47del1	caT	ca-	1	1	B.1.416.1	0.001563
ORF7a	47	H47del1	Cat	-at	1	1	B.1.427	0.00005
ORF7a	47	H47L	cAt	cTt	1	1	B.1.427	0.00005
ORF7a	47	H47H	caT	caC	1	1	B.1.427	0.00005
ORF7a	47	H47D	Cat	Gat	1	1	B.1.438.1	0.000107
ORF7a	47	H47del	CAT	---	1	1	B.1.438.1	0.000107
ORF7a	47	H47N	Cat	Aat	1	1	B.1.445	0.011765
ORF7a	47	H47del	CAT	---	1	1	B.1.459	0.004082
ORF7a	47	H47del	CAT	---	1	1	B.1.466.2	0.000391
ORF7a	47	H47Q	caT	caA	1	1	B.1.468	0.005714
ORF7a	47	H47del1	caT	ca-	1	1	B.1.468	0.005714
ORF7a	47	H47N	Cat	Aat	1	1	B.1.468	0.005714
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.469	0.00361
ORF7a	47	H47del	CAT	---	1	1	B.1.470	0.001404
ORF7a	47	H47H	caT	caC	1	1	B.1.470	0.001404
ORF7a	47	H47Q	caT	caA	1	1	B.1.473	0.019231
ORF7a	47	H47P	cAt	cCt	1	1	B.1.497	0.000315
ORF7a	47	H47N	Cat	Aat	1	1	B.1.497	0.000315
ORF7a	47	H47Q	caT	caA	1	1	B.1.497	0.000315
ORF7a	47	H47Q	caT	caA	1	1	B.1.520	0.021739
ORF7a	47	H47del1	caT	ca-	1	1	B.1.525	0.000113
ORF7a	47	H47H	caT	caC	1	1	B.1.525	0.000113
ORF7a	47	H47L	cAt	cTt	1	1	B.1.526	0.000024
ORF7a	47	H47del	CAT	---	1	1	B.1.535	0.028571
ORF7a	47	H47N	Cat	Aat	1	1	B.1.545	0.014493
ORF7a	47	H47H	caT	caC	1	1	B.1.548	0.035714
ORF7a	47	H47H	caT	caC	1	1	B.1.558	0.004566
ORF7a	47	H47N	Cat	Aat	1	1	B.1.564.1	0.001577
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.565	0.00081
ORF7a	47	H47del	CAT	---	1	1	B.1.568	0.001111
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.575.1	0.002439
ORF7a	47	H47I	CAt	ATt	1	1	B.1.576	0.000907
ORF7a	47	H47del	CAT	---	1	1	B.1.576	0.000907
ORF7a	47	H47N	Cat	Aat	1	1	B.1.576	0.000907
ORF7a	47	H47F	CAt	TTt	1	1	B.1.576	0.000907
ORF7a	47	H47N	Cat	Aat	1	1	B.1.579	0.011236
ORF7a	47	H47del	CAT	---	1	1	B.1.582	0.000491
ORF7a	47	H47H	caT	caC	1	1	B.1.588	0.00091
ORF7a	47	H47del	CAT	---	1	1	B.1.595	0.000261
ORF7a	47	H47N	Cat	Aat	1	1	B.1.609	0.000479
ORF7a	47	H47del1	caT	ca-	1	1	B.1.617.1	0.000129
ORF7a	47	H47F	CAt	TTt	1	1	B.1.617.1	0.000129
ORF7a	47	H47Q	caT	caG	1	1	B.1.617.1	0.000129
ORF7a	47	H47del2	CAT	--W	1	1	B.1.617.2	0.000004
ORF7a	47	H47N	Cat	Aat	1	1	B.1.620	0.000946
ORF7a	47	H47Y	Cat	Tat	1	1	B.1.635	0.017544
ORF7a	47	H47del	CAT	---	1	1	B.1.638	0.052632
ORF7a	47	H47del	CAT	---	1	1	B.1.9.1	0.032258
ORF7a	47	H47Y	Cat	Tat	1	1	B.3	0.000831
ORF7a	47	H47Y	Cat	Tat	1	1	B.4	0.002208
ORF7a	47	H47Y	Cat	Tat	1	1	B.40	0.000364
ORF7a	47	H47del	CAT	---	1	1	B.55	0.00295
ORF7a	47	H47H	caT	caC	1	1	B.6	0.00091
ORF7a	47	H47L	cAt	cTt	1	1	B.6.6	0.000889
ORF7a	47	H47R	cAt	cGt	1	1	C.31	0.017857
ORF7a	47	H47Y	Cat	Tat	1	1	C.35	0.000774
ORF7a	47	H47Y	Cat	Tat	1	1	C.36	0.000911
ORF7a	47	H47del1	Cat	-at	1	1	C.37	0.000116
ORF7a	47	H47Y	Cat	Tat	1	1	C.37.1	0.002618
ORF7a	47	H47H	caT	caC	1	1	D.2	0.000075
ORF7a	47	H47L	cAt	cTt	1	1	D.2	0.000075
ORF7a	47	H47del	CAT	---	1	1	K.3	0.006173
ORF7a	47	H47N	Cat	Aat	1	1	N.5	0.001767
ORF7a	47	H47L	cAt	cTt	1	1	N.5	0.001767
ORF7a	47	H47R	cAt	cGt	1	1	N.5	0.001767
ORF7a	47	H47L	cAt	cTt	1	1	P.1	0.000016
ORF7a	47	H47del	CAT	---	1	1	P.1.1	0.000318
ORF7a	47	H47N	Cat	Aat	1	1	P.1.1	0.000318
ORF7a	47	H47Y	Cat	Tat	1	1	P.1.11	0.010204
ORF7a	47	H47Y	Cat	Tat	1	1	P.1.12	0.000484
ORF7a	47	H47del	CAT	---	1	1	P.1.13	0.000898
ORF7a	47	H47N	Cat	Aat	1	1	P.1.15	0.000232
ORF7a	47	H47P	cAt	cCt	1	1	P.1.15	0.000232
ORF7a	47	H47D	Cat	Gat	1	1	P.1.15	0.000232
ORF7a	47	H47del	CAT	---	1	1	P.1.16	0.000374
ORF7a	47	H47del1	Cat	-at	1	1	P.1.17	0.000162
ORF7a	47	H47Y	Cat	Tat	1	1	P.1.17	0.000162
ORF7a	47	H47N	Cat	Aat	1	1	P.1.17	0.000162
ORF7a	47	H47del	CAT	---	1	1	P.1.3	0.034483
ORF7a	47	H47del	CAT	---	1	1	P.1.4	0.000977
ORF7a	47	H47H	caT	caC	1	1	P.2	0.000187
ORF7a	47	H47Y	Cat	Tat	1	1	P.4	0.003802
ORF7a	47	H47Y	Cat	Tat	1	1	P.7	0.004367
ORF7a	47	H47N	Cat	Aat	1	1	Q.3	0.000145
ORF7a	47	H47L	cAT	cTC	1	1	Q.4	0.000455
ORF7a	47	H47del	CAT	---	1	1	Q.7	0.001111
ORF7a	47	H47N	Cat	Aat	1	1	Q.8	0.000165
ORF7a	47	H47N	Cat	Aat	1	1	R.1	0.00009
ORF7a	47	H47Y	Cat	Tat	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.