CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF7a : CodonNum = 59

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	59	F59del		del	TTT	---	32671	32671	1	27568-27570
ORF7a	59	F59del2		del	tTT	t--	1008	956	0.948413	27568-27570
ORF7a	59	F59del2		del	TTt	--t	1008	50	0.0496032	27568-27570
ORF7a	59	F59del2		del	TTT	C--	1008	1	0.000992064	27568-27570
ORF7a	59	F59del2		del	TTT	--A	1008	1	0.000992064	27568-27570
ORF7a	59	F59del1		del	ttT	tt-	357	294	0.823529	27568-27570
ORF7a	59	F59del1		del	Ttt	-tt	357	53	0.148459	27568-27570
ORF7a	59	F59del1		del	TTT	-NN	357	6	0.0168067	27568-27570
ORF7a	59	F59del1		del	TtT	-tN	357	2	0.00560224	27568-27570
ORF7a	59	F59del1		del	TTt	-Nt	357	1	0.00280112	27568-27570
ORF7a	59	F59del1		del	TtT	Ct-	357	1	0.00280112	27568-27570
ORF7a	59	F59L		nonsyn	ttT	ttA	301	173	0.574751	27568-27570
ORF7a	59	F59L		nonsyn	Ttt	Ctt	301	107	0.355482	27568-27570
ORF7a	59	F59L		nonsyn	ttT	ttG	301	13	0.0431894	27568-27570
ORF7a	59	F59L		nonsyn	TtT	CtG	301	3	0.00996678	27568-27570
ORF7a	59	F59L		nonsyn	TtT	CtA	301	3	0.00996678	27568-27570
ORF7a	59	F59L		nonsyn	TtT	CtC	301	2	0.00664452	27568-27570
ORF7a	59	F59S		nonsyn	tTt	tCt	147	138	0.938776	27568-27570
ORF7a	59	F59S		nonsyn	TTt	AGt	147	5	0.0340136	27568-27570
ORF7a	59	F59S		nonsyn	tTT	tCC	147	2	0.0136054	27568-27570
ORF7a	59	F59S		nonsyn	tTT	tCG	147	1	0.00680272	27568-27570
ORF7a	59	F59S		nonsyn	tTT	tCA	147	1	0.00680272	27568-27570
ORF7a	59	F59F		syn	ttT	ttC	104	104	1	27568-27570
ORF7a	59	F59Y		nonsyn	tTt	tAt	54	50	0.925926	27568-27570
ORF7a	59	F59Y		nonsyn	tTT	tAC	54	4	0.0740741	27568-27570
ORF7a	59	F59V		nonsyn	Ttt	Gtt	51	47	0.921569	27568-27570
ORF7a	59	F59V		nonsyn	TtT	GtA	51	3	0.0588235	27568-27570
ORF7a	59	F59V		nonsyn	TtT	GtG	51	1	0.0196078	27568-27570
ORF7a	59	F59I		nonsyn	Ttt	Att	33	28	0.848485	27568-27570
ORF7a	59	F59I		nonsyn	TtT	AtA	33	3	0.0909091	27568-27570
ORF7a	59	F59I		nonsyn	TtT	AtC	33	2	0.0606061	27568-27570
ORF7a	59	F59N		nonsyn	TTt	AAt	15	12	0.8	27568-27570
ORF7a	59	F59N		nonsyn	TTT	AAC	15	3	0.2	27568-27570
ORF7a	59	F59Q		nonsyn	TTT	CAG	14	12	0.857143	27568-27570
ORF7a	59	F59Q		nonsyn	TTT	CAA	14	2	0.142857	27568-27570
ORF7a	59	F59C		nonsyn	tTt	tGt	12	11	0.916667	27568-27570
ORF7a	59	F59C		nonsyn	tTT	tGC	12	1	0.0833333	27568-27570
ORF7a	59	F59X		nonsyn	tTT	tAA	9	7	0.777778	27568-27570
ORF7a	59	F59X		nonsyn	tTT	tAG	9	1	0.111111	27568-27570
ORF7a	59	F59X		nonsyn	tTT	tGA	9	1	0.111111	27568-27570
ORF7a	59	F59P		nonsyn	TTT	CCA	7	2	0.285714	27568-27570
ORF7a	59	F59P		nonsyn	TTt	CCt	7	2	0.285714	27568-27570
ORF7a	59	F59P		nonsyn	TTT	CCC	7	2	0.285714	27568-27570
ORF7a	59	F59P		nonsyn	TTT	CCG	7	1	0.142857	27568-27570
ORF7a	59	F59K		nonsyn	TTT	AAA	6	6	1	27568-27570
ORF7a	59	F59T		nonsyn	TTt	ACt	5	2	0.4	27568-27570
ORF7a	59	F59T		nonsyn	TTT	ACC	5	2	0.4	27568-27570
ORF7a	59	F59T		nonsyn	TTT	ACA	5	1	0.2	27568-27570
ORF7a	59	F59H		nonsyn	TTT	CAC	4	2	0.5	27568-27570
ORF7a	59	F59H		nonsyn	TTt	CAt	4	2	0.5	27568-27570
ORF7a	59	F59D		nonsyn	TTt	GAt	2	2	1	27568-27570
ORF7a	59	F59E		nonsyn	TTT	GAA	2	2	1	27568-27570

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	59	F59del	TTT	---	32671	32671	All	0.006249
ORF7a	59	F59del	TTT	---	12150	12150	AY.4	0.018911
ORF7a	59	F59del	TTT	---	4130	4130	B.1.1.7	0.003697
ORF7a	59	F59del	TTT	---	3432	3432	B.1.617.2	0.012923
ORF7a	59	F59del	TTT	---	1666	1666	AY.120.1	0.534831
ORF7a	59	F59del	TTT	---	1591	1591	AY.25	0.00957
ORF7a	59	F59del2	tTT	t--	956	1008	All	0.000183
ORF7a	59	F59del2	TTt	--t	50	1008	All	0.00001
ORF7a	59	F59del2	TTT	--A	1	1008	All	0
ORF7a	59	F59del2	TTT	C--	1	1008	All	0
ORF7a	59	F59del	TTT	---	968	968	AY.43	0.004289
ORF7a	59	F59del	TTT	---	662	662	AY.103	0.00411
ORF7a	59	F59del	TTT	---	586	586	AY.44	0.003567
ORF7a	59	F59del	TTT	---	494	494	AY.3	0.004914
ORF7a	59	F59del	TTT	---	441	441	AY.26	0.012485
ORF7a	59	F59del	TTT	---	390	390	AY.39	0.009637
ORF7a	59	F59del1	ttT	tt-	294	357	All	0.000056
ORF7a	59	F59del1	Ttt	-tt	53	357	All	0.00001
ORF7a	59	F59del1	TTT	-NN	6	357	All	0.000001
ORF7a	59	F59del1	TtT	-tN	2	357	All	0
ORF7a	59	F59del1	TTt	-Nt	1	357	All	0
ORF7a	59	F59del1	TtT	Ct-	1	357	All	0
ORF7a	59	F59del	TTT	---	337	337	AY.102	0.008935
ORF7a	59	F59L	ttT	ttA	173	301	All	0.000033
ORF7a	59	F59L	Ttt	Ctt	107	301	All	0.00002
ORF7a	59	F59L	ttT	ttG	13	301	All	0.000002
ORF7a	59	F59L	TtT	CtA	3	301	All	0.000001
ORF7a	59	F59L	TtT	CtG	3	301	All	0.000001
ORF7a	59	F59L	TtT	CtC	2	301	All	0
ORF7a	59	F59del2	tTT	t--	276	279	B.1.1.7	0.000247
ORF7a	59	F59del2	TTt	--t	3	279	B.1.1.7	0.000003
ORF7a	59	F59del2	tTT	t--	256	278	AY.4	0.000398
ORF7a	59	F59del2	TTt	--t	22	278	AY.4	0.000034
ORF7a	59	F59del	TTT	---	276	276	AY.46.5	0.054762
ORF7a	59	F59del	TTT	---	273	273	AY.29	0.004306
ORF7a	59	F59del	TTT	---	257	257	AY.4.2	0.005574
ORF7a	59	F59del	TTT	---	225	225	AY.120	0.008365
ORF7a	59	F59del	TTT	---	216	216	B.1.351	0.006421
ORF7a	59	F59del	TTT	---	185	185	B.1.177.21	0.014147
ORF7a	59	F59del	TTT	---	174	174	AY.98	0.013745
ORF7a	59	F59del	TTT	---	158	158	B.1.526	0.003714
ORF7a	59	F59S	tTt	tCt	138	147	All	0.000026
ORF7a	59	F59S	TTt	AGt	5	147	All	0.000001
ORF7a	59	F59S	tTT	tCC	2	147	All	0
ORF7a	59	F59S	tTT	tCG	1	147	All	0
ORF7a	59	F59S	tTT	tCA	1	147	All	0
ORF7a	59	F59del	TTT	---	147	147	AY.5	0.003035
ORF7a	59	F59del	TTT	---	134	134	B.1	0.001227
ORF7a	59	F59del	TTT	---	130	130	AY.54	0.012395
ORF7a	59	F59del	TTT	---	126	126	AY.47	0.003919
ORF7a	59	F59del	TTT	---	125	125	AY.100	0.005751
ORF7a	59	F59del	TTT	---	124	124	B.1.177	0.001633
ORF7a	59	F59del	TTT	---	116	116	AY.119	0.004096
ORF7a	59	F59del	TTT	---	115	115	AY.7.1	0.012961
ORF7a	59	F59F	ttT	ttC	104	104	All	0.00002
ORF7a	59	F59del	TTT	---	89	89	AY.46.4	0.014641
ORF7a	59	F59del	TTT	---	86	86	B.1.2	0.000757
ORF7a	59	F59del	TTT	---	81	81	AY.33	0.005409
ORF7a	59	F59del	TTT	---	77	77	AY.46.6	0.00556
ORF7a	59	F59del	TTT	---	68	68	AY.3.1	0.005798
ORF7a	59	F59del	TTT	---	64	64	AY.42	0.002575
ORF7a	59	F59del	TTT	---	64	64	AY.5.4	0.017709
ORF7a	59	F59del	TTT	---	60	60	AY.45	0.007301
ORF7a	59	F59del	TTT	---	59	59	AY.113	0.008401
ORF7a	59	F59del	TTT	---	59	59	AY.6	0.002427
ORF7a	59	F59del	TTT	---	58	58	AY.46	0.006037
ORF7a	59	F59del	TTT	---	58	58	P.1	0.000914
ORF7a	59	F59del	TTT	---	57	57	AY.39.1	0.002258
ORF7a	59	F59del	TTT	---	57	57	AY.75	0.003193
ORF7a	59	F59Y	tTt	tAt	50	54	All	0.00001
ORF7a	59	F59Y	tTT	tAC	4	54	All	0.000001
ORF7a	59	F59del	TTT	---	53	53	AY.20	0.00206
ORF7a	59	F59del	TTT	---	53	53	AY.23	0.003697
ORF7a	59	F59del1	ttT	tt-	40	53	AY.4	0.000062
ORF7a	59	F59del1	Ttt	-tt	11	53	AY.4	0.000017
ORF7a	59	F59del1	TTT	-NN	1	53	AY.4	0.000002
ORF7a	59	F59del1	TTt	-Nt	1	53	AY.4	0.000002
ORF7a	59	F59del1	ttT	tt-	53	53	AY.6	0.00218
ORF7a	59	F59V	Ttt	Gtt	47	51	All	0.000009
ORF7a	59	F59V	TtT	GtA	3	51	All	0.000001
ORF7a	59	F59V	TtT	GtG	1	51	All	0
ORF7a	59	F59L	ttT	ttA	38	51	B.1.1.7	0.000034
ORF7a	59	F59L	Ttt	Ctt	12	51	B.1.1.7	0.000011
ORF7a	59	F59L	ttT	ttG	1	51	B.1.1.7	0.000001
ORF7a	59	F59del	TTT	---	51	51	B.1.621	0.004514
ORF7a	59	F59del2	tTT	t--	46	46	B.1.177.4	0.009709
ORF7a	59	F59del	TTT	---	45	45	AY.13	0.007244
ORF7a	59	F59del1	ttT	tt-	43	45	B.1.1.7	0.000038
ORF7a	59	F59del1	Ttt	-tt	1	45	B.1.1.7	0.000001
ORF7a	59	F59del1	TtT	-tN	1	45	B.1.1.7	0.000001
ORF7a	59	F59del	TTT	---	44	44	AY.107	0.020503
ORF7a	59	F59del	TTT	---	44	44	AY.9.2	0.001616
ORF7a	59	F59del	TTT	---	44	44	AY.98.1	0.002131
ORF7a	59	F59del2	tTT	t--	42	42	AY.116.1	0.01308
ORF7a	59	F59del	TTT	---	40	40	AY.118	0.002506
ORF7a	59	F59del	TTT	---	40	40	AY.4.2.1	0.005959
ORF7a	59	F59del	TTT	---	40	40	B.1.1.284	0.004296
ORF7a	59	F59del	TTT	---	39	39	AY.110	0.004395
ORF7a	59	F59del	TTT	---	39	39	P.1.14	0.001864
ORF7a	59	F59del	TTT	---	38	38	B.1.1	0.000689
ORF7a	59	F59del	TTT	---	37	37	AY.117	0.003127
ORF7a	59	F59del	TTT	---	35	35	AY.34	0.003394
ORF7a	59	F59del	TTT	---	35	35	AY.7	0.00686
ORF7a	59	F59del	TTT	---	35	35	AY.9	0.002366
ORF7a	59	F59del	TTT	---	35	35	B.1.160	0.001092
ORF7a	59	F59I	Ttt	Att	28	33	All	0.000005
ORF7a	59	F59I	TtT	AtA	3	33	All	0.000001
ORF7a	59	F59I	TtT	AtC	2	33	All	0
ORF7a	59	F59del2	tTT	t--	31	33	B.1.617.2	0.000117
ORF7a	59	F59del2	TTT	C--	1	33	B.1.617.2	0.000004
ORF7a	59	F59del2	TTt	--t	1	33	B.1.617.2	0.000004
ORF7a	59	F59del	TTT	---	32	32	B.1.1.214	0.001775
ORF7a	59	F59del	TTT	---	30	30	AY.91	0.021914
ORF7a	59	F59del	TTT	---	29	29	AY.99.2	0.002673
ORF7a	59	F59del	TTT	---	28	28	AY.60	0.026266
ORF7a	59	F59del2	tTT	t--	24	27	AY.25	0.000144
ORF7a	59	F59del2	TTt	--t	3	27	AY.25	0.000018
ORF7a	59	F59S	tTt	tCt	27	27	B.1.400	0.011583
ORF7a	59	F59del1	ttT	tt-	25	26	AY.103	0.000155
ORF7a	59	F59del1	Ttt	-tt	1	26	AY.103	0.000006
ORF7a	59	F59del	TTT	---	26	26	AY.19	0.029647
ORF7a	59	F59L	ttT	ttA	19	26	AY.25	0.000114
ORF7a	59	F59L	Ttt	Ctt	2	26	AY.25	0.000012
ORF7a	59	F59L	ttT	ttG	2	26	AY.25	0.000012
ORF7a	59	F59L	TtT	CtG	1	26	AY.25	0.000006
ORF7a	59	F59L	TtT	CtA	1	26	AY.25	0.000006
ORF7a	59	F59L	TtT	CtC	1	26	AY.25	0.000006
ORF7a	59	F59del	TTT	---	26	26	AY.61	0.002724
ORF7a	59	F59del	TTT	---	26	26	AY.9.1	0.002177
ORF7a	59	F59del	TTT	---	26	26	B.1.637	0.0019
ORF7a	59	F59L	Ttt	Ctt	14	25	AY.44	0.000085
ORF7a	59	F59L	ttT	ttA	10	25	AY.44	0.000061
ORF7a	59	F59L	ttT	ttG	1	25	AY.44	0.000006
ORF7a	59	F59del	TTT	---	24	24	AY.121	0.003248
ORF7a	59	F59S	tTt	tCt	24	24	AY.4	0.000037
ORF7a	59	F59L	ttT	ttA	16	24	AY.43	0.000071
ORF7a	59	F59L	Ttt	Ctt	7	24	AY.43	0.000031
ORF7a	59	F59L	ttT	ttG	1	24	AY.43	0.000004
ORF7a	59	F59del	TTT	---	24	24	AY.7.2	0.013423
ORF7a	59	F59del	TTT	---	23	23	C.37	0.002669
ORF7a	59	F59del	TTT	---	22	22	AY.30	0.008706
ORF7a	59	F59del	TTT	---	22	22	AY.36	0.003261
ORF7a	59	F59del2	tTT	t--	22	22	AY.43	0.000097
ORF7a	59	F59del	TTT	---	22	22	B.1.429	0.000518
ORF7a	59	F59L	Ttt	Ctt	12	22	B.1.617.2	0.000045
ORF7a	59	F59L	ttT	ttA	8	22	B.1.617.2	0.00003
ORF7a	59	F59L	ttT	ttG	1	22	B.1.617.2	0.000004
ORF7a	59	F59L	TtT	CtG	1	22	B.1.617.2	0.000004
ORF7a	59	F59del	TTT	---	21	21	AY.106	0.007033
ORF7a	59	F59del2	tTT	t--	19	21	AY.44	0.000116
ORF7a	59	F59del2	TTt	--t	2	21	AY.44	0.000012
ORF7a	59	F59del	TTT	---	19	19	AY.116	0.005449
ORF7a	59	F59Y	tTt	tAt	19	19	AY.42	0.000764
ORF7a	59	F59del	TTT	---	19	19	B.1.1.222	0.003876
ORF7a	59	F59del2	tTT	t--	19	19	B.1.177	0.00025
ORF7a	59	F59del	TTT	---	19	19	B.1.214.2	0.011391
ORF7a	59	F59del1	ttT	tt-	14	19	B.1.617.2	0.000053
ORF7a	59	F59del1	Ttt	-tt	3	19	B.1.617.2	0.000011
ORF7a	59	F59del1	TTT	-NN	2	19	B.1.617.2	0.000008
ORF7a	59	F59L	ttT	ttA	18	18	AY.103	0.000112
ORF7a	59	F59del	TTT	---	18	18	AY.111	0.003297
ORF7a	59	F59L	Ttt	Ctt	13	17	AY.3	0.000129
ORF7a	59	F59L	ttT	ttA	4	17	AY.3	0.00004
ORF7a	59	F59del	TTT	---	17	17	AY.4.5	0.001827
ORF7a	59	F59del	TTT	---	17	17	AY.74	0.001966
ORF7a	59	F59del	TTT	---	17	17	R.1	0.00153
ORF7a	59	F59del	TTT	---	16	16	AY.1	0.006332
ORF7a	59	F59del2	tTT	t--	15	16	AY.3	0.000149
ORF7a	59	F59del2	TTt	--t	1	16	AY.3	0.00001
ORF7a	59	F59del	TTT	---	16	16	AY.37	0.005057
ORF7a	59	F59del	TTT	---	16	16	AY.62	0.006972
ORF7a	59	F59del	TTT	---	16	16	B.1.427	0.000808
ORF7a	59	F59N	TTt	AAt	12	15	All	0.000002
ORF7a	59	F59N	TTT	AAC	3	15	All	0.000001
ORF7a	59	F59del2	tTT	t--	15	15	AY.120	0.000558
ORF7a	59	F59del	TTT	---	15	15	AY.14	0.00132
ORF7a	59	F59del	TTT	---	15	15	AY.46.2	0.00953
ORF7a	59	F59del	TTT	---	15	15	B.1.596	0.001307
ORF7a	59	F59S	tTt	tCt	15	15	Q.7	0.016667
ORF7a	59	F59Q	TTT	CAG	12	14	All	0.000002
ORF7a	59	F59Q	TTT	CAA	2	14	All	0
ORF7a	59	F59del	TTT	---	14	14	AY.114	0.003235
ORF7a	59	F59del2	tTT	t--	14	14	AY.119	0.000494
ORF7a	59	F59del	TTT	---	14	14	B.1.1.258	0.045603
ORF7a	59	F59del	TTT	---	14	14	B.1.243	0.000974
ORF7a	59	F59del	TTT	---	13	13	AY.68	0.003559
ORF7a	59	F59del	TTT	---	13	13	AY.84	0.005687
ORF7a	59	F59del	TTT	---	13	13	B.1.1.519	0.000516
ORF7a	59	F59F	ttT	ttC	13	13	B.1.1.7	0.000012
ORF7a	59	F59del	TTT	---	13	13	B.1.525	0.001471
ORF7a	59	F59del1	ttT	tt-	13	13	B.1.621	0.001151
ORF7a	59	F59C	tTt	tGt	11	12	All	0.000002
ORF7a	59	F59C	tTT	tGC	1	12	All	0
ORF7a	59	F59F	ttT	ttC	12	12	AY.4	0.000019
ORF7a	59	F59del1	ttT	tt-	10	12	AY.44	0.000061
ORF7a	59	F59del1	Ttt	-tt	2	12	AY.44	0.000012
ORF7a	59	F59del	TTT	---	12	12	AY.90	0.008214
ORF7a	59	F59del	TTT	---	12	12	B.1.324	0.019262
ORF7a	59	F59del	TTT	---	12	12	Q.8	0.001979
ORF7a	59	F59del	TTT	---	11	11	AY.12	0.003477
ORF7a	59	F59Q	TTT	CAG	11	11	AY.4	0.000017
ORF7a	59	F59F	ttT	ttC	11	11	AY.43	0.000049
ORF7a	59	F59del	TTT	---	11	11	AY.87	0.009159
ORF7a	59	F59del	TTT	---	11	11	AY.99	0.011542
ORF7a	59	F59del	TTT	---	11	11	B.1.177.60	0.002403
ORF7a	59	F59S	tTt	tCt	11	11	B.1.549	0.079137
ORF7a	59	F59I	Ttt	Att	11	11	C.16	0.011665
ORF7a	59	F59del	TTT	---	10	10	AY.35	0.00233
ORF7a	59	F59L	ttT	ttA	6	10	AY.4	0.000009
ORF7a	59	F59L	Ttt	Ctt	3	10	AY.4	0.000005
ORF7a	59	F59L	ttT	ttG	1	10	AY.4	0.000002
ORF7a	59	F59L	Ttt	Ctt	10	10	B.1.177	0.000132
ORF7a	59	F59del	TTT	---	10	10	B.1.177.56	0.006676
ORF7a	59	F59F	ttT	ttC	10	10	B.1.351	0.000297
ORF7a	59	F59del	TTT	---	10	10	B.1.391	0.011274
ORF7a	59	F59X	tTT	tAA	7	9	All	0.000001
ORF7a	59	F59X	tTT	tAG	1	9	All	0
ORF7a	59	F59X	tTT	tGA	1	9	All	0
ORF7a	59	F59del	TTT	---	9	9	AY.109	0.006657
ORF7a	59	F59del2	tTT	t--	9	9	AY.29	0.000142
ORF7a	59	F59V	Ttt	Gtt	8	9	AY.4	0.000012
ORF7a	59	F59V	TtT	GtG	1	9	AY.4	0.000002
ORF7a	59	F59Y	tTt	tAt	9	9	B.1.2	0.000079
ORF7a	59	F59L	ttT	ttA	7	9	B.1.2	0.000062
ORF7a	59	F59L	Ttt	Ctt	2	9	B.1.2	0.000018
ORF7a	59	F59del	TTT	---	9	9	B.1.258.9	0.045
ORF7a	59	F59del2	tTT	t--	9	9	B.1.526	0.000212
ORF7a	59	F59del2	tTT	t--	9	9	D.2	0.000675
ORF7a	59	F59del	TTT	---	9	9	L.1	0.017143
ORF7a	59	F59del	TTT	---	8	8	A.21	0.022161
ORF7a	59	F59del	TTT	---	8	8	AY.10	0.00424
ORF7a	59	F59del2	tTT	t--	8	8	AY.111	0.001465
ORF7a	59	F59del	TTT	---	8	8	AY.27	0.000518
ORF7a	59	F59del	TTT	---	8	8	AY.29.1	0.001764
ORF7a	59	F59del1	ttT	tt-	8	8	AY.5.4	0.002214
ORF7a	59	F59del	TTT	---	8	8	AY.52	0.006515
ORF7a	59	F59del	TTT	---	8	8	AY.85	0.003417
ORF7a	59	F59S	tTt	tCt	5	8	B.1	0.000046
ORF7a	59	F59S	TTt	AGt	3	8	B.1	0.000027
ORF7a	59	F59del	TTT	---	8	8	B.1.1.231	0.024768
ORF7a	59	F59del2	TTt	--t	7	8	B.1.1.284	0.000752
ORF7a	59	F59del2	tTT	t--	1	8	B.1.1.284	0.000107
ORF7a	59	F59S	tTt	tCt	8	8	B.1.243	0.000557
ORF7a	59	F59del2	tTT	t--	7	8	B.1.596	0.00061
ORF7a	59	F59del2	TTt	--t	1	8	B.1.596	0.000087
ORF7a	59	F59del	TTT	---	8	8	P.1.15	0.001859
ORF7a	59	F59del	TTT	---	8	8	Q.1	0.001011
ORF7a	59	F59P	TTt	CCt	2	7	All	0
ORF7a	59	F59P	TTT	CCC	2	7	All	0
ORF7a	59	F59P	TTT	CCA	2	7	All	0
ORF7a	59	F59P	TTT	CCG	1	7	All	0
ORF7a	59	F59del1	Ttt	-tt	6	7	AY.102	0.000159
ORF7a	59	F59del1	ttT	tt-	1	7	AY.102	0.000027
ORF7a	59	F59del2	tTT	t--	7	7	AY.103	0.000043
ORF7a	59	F59del2	tTT	t--	6	7	AY.26	0.00017
ORF7a	59	F59del2	TTT	--A	1	7	AY.26	0.000028
ORF7a	59	F59del1	ttT	tt-	6	7	AY.4.2	0.00013
ORF7a	59	F59del1	Ttt	-tt	1	7	AY.4.2	0.000022
ORF7a	59	F59V	Ttt	Gtt	7	7	AY.43	0.000031
ORF7a	59	F59del	TTT	---	7	7	AY.65	0.003731
ORF7a	59	F59del	TTT	---	7	7	AY.71	0.003325
ORF7a	59	F59del	TTT	---	7	7	AY.75.1	0.001262
ORF7a	59	F59del	TTT	---	7	7	AY.92	0.002011
ORF7a	59	F59del2	tTT	t--	7	7	B.1.1.3	0.06087
ORF7a	59	F59S	tTt	tCt	7	7	B.1.617.2	0.000026
ORF7a	59	F59V	Ttt	Gtt	6	7	B.1.617.2	0.000023
ORF7a	59	F59V	TtT	GtA	1	7	B.1.617.2	0.000004
ORF7a	59	F59del	TTT	---	7	7	B.1.628	0.002467
ORF7a	59	F59K	TTT	AAA	6	6	All	0.000001
ORF7a	59	F59L	Ttt	Ctt	5	6	AY.102	0.000133
ORF7a	59	F59L	ttT	ttA	1	6	AY.102	0.000027
ORF7a	59	F59del	TTT	---	6	6	AY.108	0.006615
ORF7a	59	F59del	TTT	---	6	6	AY.116.1	0.001869
ORF7a	59	F59del	TTT	---	6	6	AY.32	0.003195
ORF7a	59	F59del	TTT	---	6	6	AY.34.1	0.00306
ORF7a	59	F59del2	tTT	t--	6	6	AY.4.2	0.00013
ORF7a	59	F59S	tTt	tCt	6	6	AY.44	0.000037
ORF7a	59	F59del	TTT	---	6	6	AY.46.1	0.00616
ORF7a	59	F59del2	tTT	t--	6	6	AY.9.2	0.00022
ORF7a	59	F59F	ttT	ttC	6	6	B.1	0.000055
ORF7a	59	F59del1	ttT	tt-	4	6	B.1.177	0.000053
ORF7a	59	F59del1	Ttt	-tt	2	6	B.1.177	0.000026
ORF7a	59	F59del	TTT	---	6	6	B.1.177.20	0.009105
ORF7a	59	F59del1	ttT	tt-	4	6	B.1.2	0.000035
ORF7a	59	F59del1	TTT	-NN	2	6	B.1.2	0.000018
ORF7a	59	F59S	tTt	tCt	3	6	B.1.351	0.000089
ORF7a	59	F59S	tTT	tCC	2	6	B.1.351	0.000059
ORF7a	59	F59S	tTT	tCA	1	6	B.1.351	0.00003
ORF7a	59	F59F	ttT	ttC	6	6	B.1.617.2	0.000023
ORF7a	59	F59del2	tTT	t--	6	6	P.1	0.000095
ORF7a	59	F59V	Ttt	Gtt	6	6	P.1.17	0.000971
ORF7a	59	F59del2	tTT	t--	6	6	Q.8	0.000989
ORF7a	59	F59T	TTt	ACt	2	5	All	0
ORF7a	59	F59T	TTT	ACC	2	5	All	0
ORF7a	59	F59T	TTT	ACA	1	5	All	0
ORF7a	59	F59del1	ttT	tt-	5	5	AY.120	0.000186
ORF7a	59	F59del	TTT	---	5	5	AY.16	0.001898
ORF7a	59	F59F	ttT	ttC	5	5	AY.25	0.00003
ORF7a	59	F59del1	Ttt	-tt	4	5	AY.25	0.000024
ORF7a	59	F59Y	tTt	tAt	4	5	AY.25	0.000024
ORF7a	59	F59S	tTt	tCt	4	5	AY.25	0.000024
ORF7a	59	F59S	tTT	tCG	1	5	AY.25	0.000006
ORF7a	59	F59del1	ttT	tt-	1	5	AY.25	0.000006
ORF7a	59	F59Y	tTT	tAC	1	5	AY.25	0.000006
ORF7a	59	F59del	TTT	---	5	5	AY.4.4	0.002046
ORF7a	59	F59del	TTT	---	5	5	AY.48	0.002326
ORF7a	59	F59del	TTT	---	5	5	AY.66	0.005348
ORF7a	59	F59del	TTT	---	5	5	AY.80	0.005643
ORF7a	59	F59F	ttT	ttC	5	5	AY.91	0.003652
ORF7a	59	F59del	TTT	---	5	5	AY.93	0.001365
ORF7a	59	F59del	TTT	---	5	5	AY.95	0.003805
ORF7a	59	F59del2	tTT	t--	5	5	AY.99.2	0.000461
ORF7a	59	F59del1	ttT	tt-	5	5	B.1	0.000046
ORF7a	59	F59L	Ttt	Ctt	3	5	B.1	0.000027
ORF7a	59	F59L	ttT	ttA	2	5	B.1	0.000018
ORF7a	59	F59del	TTT	---	5	5	B.1.1.56	0.089286
ORF7a	59	F59S	tTt	tCt	5	5	B.1.1.7	0.000004
ORF7a	59	F59N	TTt	AAt	3	5	B.1.351	0.000089
ORF7a	59	F59I	Ttt	Att	2	5	B.1.351	0.000059
ORF7a	59	F59T	TTT	ACC	2	5	B.1.351	0.000059
ORF7a	59	F59I	TtT	AtC	2	5	B.1.351	0.000059
ORF7a	59	F59T	TTt	ACt	2	5	B.1.351	0.000059
ORF7a	59	F59N	TTT	AAC	2	5	B.1.351	0.000059
ORF7a	59	F59T	TTT	ACA	1	5	B.1.351	0.00003
ORF7a	59	F59I	TtT	AtA	1	5	B.1.351	0.00003
ORF7a	59	F59del	TTT	---	5	5	B.1.375	0.004098
ORF7a	59	F59del	TTT	---	5	5	B.1.595	0.001305
ORF7a	59	F59del	TTT	---	5	5	B.1.70	0.121951
ORF7a	59	F59del	TTT	---	5	5	P.2	0.000933
ORF7a	59	F59del	TTT	---	4	4	A	0.001548
ORF7a	59	F59H	TTT	CAC	2	4	All	0
ORF7a	59	F59H	TTt	CAt	2	4	All	0
ORF7a	59	F59del	TTT	---	4	4	AY.101	0.001962
ORF7a	59	F59del2	tTT	t--	3	4	AY.102	0.00008
ORF7a	59	F59del2	TTt	--t	1	4	AY.102	0.000027
ORF7a	59	F59V	Ttt	Gtt	4	4	AY.103	0.000025
ORF7a	59	F59del	TTT	---	4	4	AY.22	0.008368
ORF7a	59	F59del1	ttT	tt-	3	4	AY.3	0.00003
ORF7a	59	F59del1	Ttt	-tt	1	4	AY.3	0.00001
ORF7a	59	F59del2	TTt	--t	2	4	AY.39	0.000049
ORF7a	59	F59del2	tTT	t--	2	4	AY.39	0.000049
ORF7a	59	F59del2	tTT	t--	4	4	AY.47	0.000124
ORF7a	59	F59del1	ttT	tt-	3	4	AY.47	0.000093
ORF7a	59	F59del1	Ttt	-tt	1	4	AY.47	0.000031
ORF7a	59	F59L	ttT	ttA	4	4	AY.5	0.000083
ORF7a	59	F59del	TTT	---	4	4	AY.53	0.00115
ORF7a	59	F59del	TTT	---	4	4	AY.59	0.002119
ORF7a	59	F59del	TTT	---	4	4	AY.70	0.000834
ORF7a	59	F59del	TTT	---	4	4	AY.73	0.002661
ORF7a	59	F59del	TTT	---	4	4	AY.79	0.004843
ORF7a	59	F59F	ttT	ttC	4	4	AY.85	0.001709
ORF7a	59	F59del	TTT	---	4	4	B.1.1.318	0.001207
ORF7a	59	F59del1	ttT	tt-	3	4	B.1.160	0.000094
ORF7a	59	F59del1	Ttt	-tt	1	4	B.1.160	0.000031
ORF7a	59	F59N	TTt	AAt	4	4	B.1.177.21	0.000306
ORF7a	59	F59L	ttT	ttA	3	4	B.1.177.21	0.000229
ORF7a	59	F59L	TtT	CtA	1	4	B.1.177.21	0.000076
ORF7a	59	F59F	ttT	ttC	4	4	B.1.2	0.000035
ORF7a	59	F59del	TTT	---	4	4	B.1.234	0.000528
ORF7a	59	F59Y	tTt	tAt	2	4	B.1.351	0.000059
ORF7a	59	F59Y	tTT	tAC	2	4	B.1.351	0.000059
ORF7a	59	F59L	TtT	CtA	1	4	B.1.351	0.00003
ORF7a	59	F59L	ttT	ttA	1	4	B.1.351	0.00003
ORF7a	59	F59L	TtT	CtC	1	4	B.1.351	0.00003
ORF7a	59	F59L	Ttt	Ctt	1	4	B.1.351	0.00003
ORF7a	59	F59F	ttT	ttC	4	4	B.1.525	0.000453
ORF7a	59	F59del1	ttT	tt-	4	4	B.1.526	0.000094
ORF7a	59	F59del	TTT	---	4	4	D.2	0.0003
ORF7a	59	F59del1	ttT	tt-	3	4	P.1	0.000047
ORF7a	59	F59L	ttT	ttA	3	4	P.1	0.000047
ORF7a	59	F59L	Ttt	Ctt	1	4	P.1	0.000016
ORF7a	59	F59del1	Ttt	-tt	1	4	P.1	0.000016
ORF7a	59	F59del	TTT	---	3	3	A.23.1	0.002113
ORF7a	59	F59del1	ttT	tt-	3	3	AY.100	0.000138
ORF7a	59	F59del2	TTt	--t	2	3	AY.100	0.000092
ORF7a	59	F59del2	tTT	t--	1	3	AY.100	0.000046
ORF7a	59	F59del2	tTT	t--	3	3	AY.118	0.000188
ORF7a	59	F59L	ttT	ttA	3	3	AY.118	0.000188
ORF7a	59	F59L	ttT	ttA	2	3	AY.120	0.000074
ORF7a	59	F59L	Ttt	Ctt	1	3	AY.120	0.000037
ORF7a	59	F59del	TTT	---	3	3	AY.120.2	0.003856
ORF7a	59	F59del	TTT	---	3	3	AY.120.2.1	0.001495
ORF7a	59	F59del2	tTT	t--	3	3	AY.20	0.000117
ORF7a	59	F59del	TTT	---	3	3	AY.24	0.001293
ORF7a	59	F59V	Ttt	Gtt	2	3	AY.25	0.000012
ORF7a	59	F59X	tTT	tAA	2	3	AY.25	0.000012
ORF7a	59	F59V	TtT	GtA	1	3	AY.25	0.000006
ORF7a	59	F59X	tTT	tAG	1	3	AY.25	0.000006
ORF7a	59	F59V	Ttt	Gtt	3	3	AY.26	0.000085
ORF7a	59	F59del1	ttT	tt-	3	3	AY.33	0.0002
ORF7a	59	F59del1	ttT	tt-	2	3	AY.34	0.000194
ORF7a	59	F59del1	Ttt	-tt	1	3	AY.34	0.000097
ORF7a	59	F59del1	Ttt	-tt	3	3	AY.36	0.000445
ORF7a	59	F59del1	ttT	tt-	3	3	AY.39	0.000074
ORF7a	59	F59del	TTT	---	3	3	AY.4.3	0.002525
ORF7a	59	F59del	TTT	---	3	3	AY.40	0.002893
ORF7a	59	F59del	TTT	---	3	3	AY.41	0.000882
ORF7a	59	F59del1	ttT	tt-	3	3	AY.42	0.000121
ORF7a	59	F59del1	ttT	tt-	2	3	AY.43	0.000009
ORF7a	59	F59del1	Ttt	-tt	1	3	AY.43	0.000004
ORF7a	59	F59Y	tTt	tAt	3	3	AY.45	0.000365
ORF7a	59	F59del	TTT	---	3	3	AY.5.3	0.001012
ORF7a	59	F59del2	tTT	t--	3	3	AY.54	0.000286
ORF7a	59	F59del	TTT	---	3	3	AY.64	0.001786
ORF7a	59	F59del	TTT	---	3	3	AY.69	0.00056
ORF7a	59	F59del1	Ttt	-tt	3	3	AY.7.1	0.000338
ORF7a	59	F59del2	TTt	--t	2	3	AY.75	0.000112
ORF7a	59	F59del2	tTT	t--	1	3	AY.75	0.000056
ORF7a	59	F59del	TTT	---	3	3	AY.86	0.00249
ORF7a	59	F59del	TTT	---	3	3	AY.88	0.002653
ORF7a	59	F59del2	tTT	t--	3	3	AY.98	0.000237
ORF7a	59	F59del2	tTT	t--	3	3	B.1	0.000027
ORF7a	59	F59S	tTt	tCt	3	3	B.1.1	0.000054
ORF7a	59	F59del	TTT	---	3	3	B.1.1.118	0.030612
ORF7a	59	F59del	TTT	---	3	3	B.1.1.121	0.007282
ORF7a	59	F59del	TTT	---	3	3	B.1.1.25	0.001706
ORF7a	59	F59del	TTT	---	3	3	B.1.1.33	0.001263
ORF7a	59	F59L	ttT	ttA	3	3	B.1.1.37	0.000579
ORF7a	59	F59I	Ttt	Att	3	3	B.1.1.7	0.000003
ORF7a	59	F59del	TTT	---	3	3	B.1.160.16	0.002788
ORF7a	59	F59del	TTT	---	3	3	B.1.177.10	0.002634
ORF7a	59	F59Y	tTt	tAt	3	3	B.1.177.21	0.000229
ORF7a	59	F59del	TTT	---	3	3	B.1.177.57	0.000843
ORF7a	59	F59del	TTT	---	3	3	B.1.177.6	0.00293
ORF7a	59	F59del	TTT	---	3	3	B.1.177.62	0.003576
ORF7a	59	F59del	TTT	---	3	3	B.1.177.81	0.000568
ORF7a	59	F59V	Ttt	Gtt	3	3	B.1.2	0.000026
ORF7a	59	F59del	TTT	---	3	3	B.1.221	0.000213
ORF7a	59	F59del	TTT	---	3	3	B.1.258	0.0002
ORF7a	59	F59del	TTT	---	3	3	B.1.258.17	0.000312
ORF7a	59	F59C	tTt	tGt	3	3	B.1.351	0.000089
ORF7a	59	F59P	TTT	CCC	1	3	B.1.351	0.00003
ORF7a	59	F59P	TTt	CCt	1	3	B.1.351	0.00003
ORF7a	59	F59P	TTT	CCA	1	3	B.1.351	0.00003
ORF7a	59	F59del	TTT	---	3	3	B.1.351.2	0.000908
ORF7a	59	F59del	TTT	---	3	3	B.1.36	0.000438
ORF7a	59	F59I	Ttt	Att	3	3	B.1.416	0.003807
ORF7a	59	F59del2	tTT	t--	3	3	B.1.466.2	0.001174
ORF7a	59	F59del	TTT	---	3	3	B.1.575	0.00091
ORF7a	59	F59del	TTT	---	3	3	B.1.582	0.001472
ORF7a	59	F59S	tTt	tCt	3	3	B.1.609	0.001438
ORF7a	59	F59del	TTT	---	3	3	B.1.617.1	0.000387
ORF7a	59	F59Y	tTt	tAt	2	3	B.1.617.2	0.000008
ORF7a	59	F59Y	tTT	tAC	1	3	B.1.617.2	0.000004
ORF7a	59	F59del	TTT	---	3	3	B.1.621.1	0.001517
ORF7a	59	F59del	TTT	---	3	3	B.1.626	0.017143
ORF7a	59	F59del2	tTT	t--	3	3	B.1.628	0.001057
ORF7a	59	F59V	Ttt	Gtt	3	3	P.1	0.000047
ORF7a	59	F59del	TTT	---	3	3	P.1.16	0.001122
ORF7a	59	F59del1	ttT	tt-	3	3	Q.3	0.000435
ORF7a	59	F59I	Ttt	Att	2	2		0.111111
ORF7a	59	F59Y	tTt	tAt	2	2		0.111111
ORF7a	59	F59L	Ttt	Ctt	2	2		0.111111
ORF7a	59	F59N	TTt	AAt	2	2		0.111111
ORF7a	59	F59del	TTT	---	2	2	A.28	0.005291
ORF7a	59	F59del	TTT	---	2	2	AD.2	0.000438
ORF7a	59	F59L	Ttt	Ctt	2	2	AD.2	0.000438
ORF7a	59	F59D	TTt	GAt	2	2	All	0
ORF7a	59	F59E	TTT	GAA	2	2	All	0
ORF7a	59	F59del2	tTT	t--	2	2	AY.14	0.000176
ORF7a	59	F59del	TTT	---	2	2	AY.2	0.000712
ORF7a	59	F59I	Ttt	Att	2	2	AY.25	0.000012
ORF7a	59	F59H	TTt	CAt	1	2	AY.25	0.000006
ORF7a	59	F59P	TTt	CCt	1	2	AY.25	0.000006
ORF7a	59	F59P	TTT	CCG	1	2	AY.25	0.000006
ORF7a	59	F59H	TTT	CAC	1	2	AY.25	0.000006
ORF7a	59	F59del1	Ttt	-tt	1	2	AY.26	0.000028
ORF7a	59	F59del1	TtT	Ct-	1	2	AY.26	0.000028
ORF7a	59	F59L	Ttt	Ctt	2	2	AY.29	0.000032
ORF7a	59	F59F	ttT	ttC	2	2	AY.39	0.000049
ORF7a	59	F59L	ttT	ttG	1	2	AY.39	0.000025
ORF7a	59	F59L	ttT	ttA	1	2	AY.39	0.000025
ORF7a	59	F59del	TTT	---	2	2	AY.39.2	0.003082
ORF7a	59	F59del2	tTT	t--	2	2	AY.4.4	0.000818
ORF7a	59	F59C	tTt	tGt	1	2	AY.44	0.000006
ORF7a	59	F59C	tTT	tGC	1	2	AY.44	0.000006
ORF7a	59	F59del2	tTT	t--	2	2	AY.45	0.000243
ORF7a	59	F59del2	tTT	t--	2	2	AY.46.5	0.000397
ORF7a	59	F59del	TTT	---	2	2	AY.49	0.00639
ORF7a	59	F59del	TTT	---	2	2	AY.51	0.001818
ORF7a	59	F59I	Ttt	Att	2	2	AY.53	0.000575
ORF7a	59	F59L	Ttt	Ctt	1	2	AY.54	0.000095
ORF7a	59	F59L	ttT	ttG	1	2	AY.54	0.000095
ORF7a	59	F59del	TTT	---	2	2	AY.57	0.001312
ORF7a	59	F59del2	tTT	t--	2	2	AY.6	0.000082
ORF7a	59	F59del1	ttT	tt-	2	2	AY.7	0.000392
ORF7a	59	F59del	TTT	---	2	2	AY.72	0.002721
ORF7a	59	F59del	TTT	---	2	2	AY.8	0.001212
ORF7a	59	F59L	Ttt	Ctt	1	2	B.1.1	0.000018
ORF7a	59	F59L	ttT	ttG	1	2	B.1.1	0.000018
ORF7a	59	F59del	TTT	---	2	2	B.1.1.1	0.000653
ORF7a	59	F59del	TTT	---	2	2	B.1.1.170	0.002494
ORF7a	59	F59del	TTT	---	2	2	B.1.1.219	0.01
ORF7a	59	F59del	TTT	---	2	2	B.1.1.220	0.003717
ORF7a	59	F59del1	Ttt	-tt	2	2	B.1.1.227	0.008696
ORF7a	59	F59del	TTT	---	2	2	B.1.1.37	0.000386
ORF7a	59	F59del	TTT	---	2	2	B.1.1.372	0.001377
ORF7a	59	F59del	TTT	---	2	2	B.1.1.521	0.010695
ORF7a	59	F59F	ttT	ttC	2	2	B.1.1.523	0.003125
ORF7a	59	F59V	Ttt	Gtt	2	2	B.1.1.7	0.000002
ORF7a	59	F59C	tTt	tGt	2	2	B.1.1.7	0.000002
ORF7a	59	F59L	ttT	ttA	2	2	B.1.160	0.000062
ORF7a	59	F59del	TTT	---	2	2	B.1.177.16	0.001329
ORF7a	59	F59X	tTT	tAA	2	2	B.1.177.21	0.000153
ORF7a	59	F59del	TTT	---	2	2	B.1.177.43	0.002954
ORF7a	59	F59del	TTT	---	2	2	B.1.177.5	0.002484
ORF7a	59	F59del	TTT	---	2	2	B.1.177.55	0.004662
ORF7a	59	F59del	TTT	---	2	2	B.1.177.86	0.000367
ORF7a	59	F59del	TTT	---	2	2	B.1.190	0.02
ORF7a	59	F59del2	tTT	t--	2	2	B.1.2	0.000018
ORF7a	59	F59F	ttT	ttC	2	2	B.1.221.4	0.008333
ORF7a	59	F59del	TTT	---	2	2	B.1.258.11	0.000793
ORF7a	59	F59F	ttT	ttC	2	2	B.1.260	0.006689
ORF7a	59	F59del	TTT	---	2	2	B.1.264	0.024691
ORF7a	59	F59del	TTT	---	2	2	B.1.311	0.000549
ORF7a	59	F59del	TTT	---	2	2	B.1.349	0.00143
ORF7a	59	F59H	TTt	CAt	1	2	B.1.351	0.00003
ORF7a	59	F59H	TTT	CAC	1	2	B.1.351	0.00003
ORF7a	59	F59del	TTT	---	2	2	B.1.369	0.00057
ORF7a	59	F59del	TTT	---	2	2	B.1.401	0.016393
ORF7a	59	F59L	ttT	ttA	2	2	B.1.415.1	0.015152
ORF7a	59	F59del2	tTT	t--	2	2	B.1.429	0.000047
ORF7a	59	F59del1	ttT	tt-	2	2	B.1.429	0.000047
ORF7a	59	F59del	TTT	---	2	2	B.1.470	0.002809
ORF7a	59	F59del	TTT	---	2	2	B.1.497	0.00063
ORF7a	59	F59del	TTT	---	2	2	B.1.576	0.001813
ORF7a	59	F59del1	ttT	tt-	2	2	B.1.596	0.000174
ORF7a	59	F59I	TtT	AtA	2	2	B.1.617.2	0.000008
ORF7a	59	F59X	tTT	tAA	2	2	B.1.617.2	0.000008
ORF7a	59	F59N	TTt	AAt	1	2	B.1.617.2	0.000004
ORF7a	59	F59N	TTT	AAC	1	2	B.1.617.2	0.000004
ORF7a	59	F59del	TTT	---	2	2	B.1.617.3	0.00597
ORF7a	59	F59del2	TTt	--t	1	2	B.1.621	0.000089
ORF7a	59	F59del2	tTT	t--	1	2	B.1.621	0.000089
ORF7a	59	F59del	TTT	---	2	2	B.1.627	0.00404
ORF7a	59	F59L	ttT	ttA	1	2	B.40	0.000364
ORF7a	59	F59L	ttT	ttG	1	2	B.40	0.000364
ORF7a	59	F59del	TTT	---	2	2	C.36.3	0.001134
ORF7a	59	F59S	tTt	tCt	2	2	P.1	0.000032
ORF7a	59	F59del1	ttT	tt-	2	2	P.1.14	0.000096
ORF7a	59	F59del	TTT	---	2	2	P.1.17.1	0.00175
ORF7a	59	F59del	TTT	---	2	2	P.1.2	0.002312
ORF7a	59	F59del2	tTT	t--	2	2	P.1.7	0.000639
ORF7a	59	F59del2	tTT	t--	2	2	R.1	0.00018
ORF7a	59	F59del	TTT	---	1	1	A.1	0.000282
ORF7a	59	F59del	TTT	---	1	1	A.2.5.3	0.010309
ORF7a	59	F59del	TTT	---	1	1	A.23	0.010526
ORF7a	59	F59del2	tTT	t--	1	1	AA.7	0.009174
ORF7a	59	F59del	TTT	---	1	1	AU.3	0.00211
ORF7a	59	F59C	tTt	tGt	1	1	AY.1	0.000396
ORF7a	59	F59L	ttT	ttA	1	1	AY.1	0.000396
ORF7a	59	F59X	tTT	tGA	1	1	AY.1	0.000396
ORF7a	59	F59F	ttT	ttC	1	1	AY.100	0.000046
ORF7a	59	F59C	tTt	tGt	1	1	AY.102	0.000027
ORF7a	59	F59F	ttT	ttC	1	1	AY.102	0.000027
ORF7a	59	F59F	ttT	ttC	1	1	AY.103	0.000006
ORF7a	59	F59S	tTt	tCt	1	1	AY.103	0.000006
ORF7a	59	F59del	TTT	---	1	1	AY.104	0.001984
ORF7a	59	F59del	TTT	---	1	1	AY.105	0.000643
ORF7a	59	F59del	TTT	---	1	1	AY.11	0.001339
ORF7a	59	F59del2	tTT	t--	1	1	AY.110	0.000113
ORF7a	59	F59N	TTt	AAt	1	1	AY.111	0.000183
ORF7a	59	F59L	Ttt	Ctt	1	1	AY.116	0.000287
ORF7a	59	F59del2	tTT	t--	1	1	AY.117	0.000085
ORF7a	59	F59L	ttT	ttA	1	1	AY.117	0.000085
ORF7a	59	F59F	ttT	ttC	1	1	AY.119	0.000035
ORF7a	59	F59L	ttT	ttA	1	1	AY.121	0.000135
ORF7a	59	F59del1	ttT	tt-	1	1	AY.13	0.000161
ORF7a	59	F59del	TTT	---	1	1	AY.16.1	0.00047
ORF7a	59	F59V	Ttt	Gtt	1	1	AY.16.1	0.00047
ORF7a	59	F59Y	tTt	tAt	1	1	AY.20	0.000039
ORF7a	59	F59del1	ttT	tt-	1	1	AY.23	0.00007
ORF7a	59	F59del2	tTT	t--	1	1	AY.23	0.00007
ORF7a	59	F59L	Ttt	Ctt	1	1	AY.23	0.00007
ORF7a	59	F59Q	TTT	CAA	1	1	AY.25	0.000006
ORF7a	59	F59D	TTt	GAt	1	1	AY.25	0.000006
ORF7a	59	F59N	TTt	AAt	1	1	AY.25	0.000006
ORF7a	59	F59E	TTT	GAA	1	1	AY.25	0.000006
ORF7a	59	F59L	ttT	ttA	1	1	AY.26	0.000028
ORF7a	59	F59S	tTt	tCt	1	1	AY.26	0.000028
ORF7a	59	F59F	ttT	ttC	1	1	AY.26	0.000028
ORF7a	59	F59S	tTt	tCt	1	1	AY.27	0.000065
ORF7a	59	F59L	Ttt	Ctt	1	1	AY.27	0.000065
ORF7a	59	F59V	Ttt	Gtt	1	1	AY.29	0.000016
ORF7a	59	F59del1	ttT	tt-	1	1	AY.3.1	0.000085
ORF7a	59	F59F	ttT	ttC	1	1	AY.3.1	0.000085
ORF7a	59	F59del2	TTt	--t	1	1	AY.30	0.000396
ORF7a	59	F59del2	tTT	t--	1	1	AY.32	0.000532
ORF7a	59	F59del2	tTT	t--	1	1	AY.33	0.000067
ORF7a	59	F59S	tTt	tCt	1	1	AY.33	0.000067
ORF7a	59	F59del1	ttT	tt-	1	1	AY.34.1	0.00051
ORF7a	59	F59del2	tTT	t--	1	1	AY.35	0.000233
ORF7a	59	F59del1	ttT	tt-	1	1	AY.37	0.000316
ORF7a	59	F59del	TTT	---	1	1	AY.38	0.000499
ORF7a	59	F59S	tTt	tCt	1	1	AY.39	0.000025
ORF7a	59	F59del1	Ttt	-tt	1	1	AY.39.1	0.00004
ORF7a	59	F59del2	tTT	t--	1	1	AY.39.1	0.00004
ORF7a	59	F59I	Ttt	Att	1	1	AY.4	0.000002
ORF7a	59	F59del1	ttT	tt-	1	1	AY.4.1	0.000737
ORF7a	59	F59L	ttT	ttA	1	1	AY.4.2	0.000022
ORF7a	59	F59del2	tTT	t--	1	1	AY.4.5	0.000107
ORF7a	59	F59L	ttT	ttA	1	1	AY.42	0.00004
ORF7a	59	F59Q	TTT	CAG	1	1	AY.43	0.000004
ORF7a	59	F59F	ttT	ttC	1	1	AY.44	0.000006
ORF7a	59	F59V	Ttt	Gtt	1	1	AY.44	0.000006
ORF7a	59	F59del	TTT	---	1	1	AY.46.3	0.000934
ORF7a	59	F59del2	tTT	t--	1	1	AY.46.3	0.000934
ORF7a	59	F59del2	tTT	t--	1	1	AY.46.4	0.000165
ORF7a	59	F59L	ttT	ttA	1	1	AY.46.4	0.000165
ORF7a	59	F59del1	ttT	tt-	1	1	AY.46.5	0.000198
ORF7a	59	F59S	tTt	tCt	1	1	AY.47	0.000031
ORF7a	59	F59del1	ttT	tt-	1	1	AY.49	0.003195
ORF7a	59	F59del1	ttT	tt-	1	1	AY.5	0.000021
ORF7a	59	F59del2	tTT	t--	1	1	AY.5.3	0.000337
ORF7a	59	F59del1	ttT	tt-	1	1	AY.53	0.000288
ORF7a	59	F59S	tTt	tCt	1	1	AY.57	0.000656
ORF7a	59	F59del2	tTT	t--	1	1	AY.61	0.000105
ORF7a	59	F59L	ttT	ttA	1	1	AY.61	0.000105
ORF7a	59	F59del1	Ttt	-tt	1	1	AY.62	0.000436
ORF7a	59	F59L	Ttt	Ctt	1	1	AY.65	0.000533
ORF7a	59	F59del2	tTT	t--	1	1	AY.7.1	0.000113
ORF7a	59	F59V	TtT	GtA	1	1	AY.7.2	0.000559
ORF7a	59	F59del2	tTT	t--	1	1	AY.70	0.000209
ORF7a	59	F59del2	tTT	t--	1	1	AY.74	0.000116
ORF7a	59	F59F	ttT	ttC	1	1	AY.74	0.000116
ORF7a	59	F59L	ttT	ttA	1	1	AY.74	0.000116
ORF7a	59	F59L	ttT	ttA	1	1	AY.75	0.000056
ORF7a	59	F59del1	ttT	tt-	1	1	AY.75	0.000056
ORF7a	59	F59del	TTT	---	1	1	AY.81	0.001992
ORF7a	59	F59del1	ttT	tt-	1	1	AY.86	0.00083
ORF7a	59	F59del	TTT	---	1	1	AY.89	0.004902
ORF7a	59	F59F	ttT	ttC	1	1	AY.9	0.000068
ORF7a	59	F59L	ttT	ttA	1	1	AY.9	0.000068
ORF7a	59	F59del1	TTT	-NN	1	1	AY.9.2	0.000037
ORF7a	59	F59del2	tTT	t--	1	1	AY.91	0.00073
ORF7a	59	F59del	TTT	---	1	1	AY.94	0.000443
ORF7a	59	F59del1	Ttt	-tt	1	1	AY.94	0.000443
ORF7a	59	F59del1	Ttt	-tt	1	1	AY.98.1	0.000048
ORF7a	59	F59L	Ttt	Ctt	1	1	AY.99.2	0.000092
ORF7a	59	F59del	TTT	---	1	1	AZ.2	0.000821
ORF7a	59	F59del	TTT	---	1	1	B	0.000128
ORF7a	59	F59Y	tTt	tAt	1	1	B.1	0.000009
ORF7a	59	F59del2	tTT	t--	1	1	B.1.1	0.000018
ORF7a	59	F59F	ttT	ttC	1	1	B.1.1	0.000018
ORF7a	59	F59C	tTt	tGt	1	1	B.1.1	0.000018
ORF7a	59	F59del1	ttT	tt-	1	1	B.1.1	0.000018
ORF7a	59	F59I	Ttt	Att	1	1	B.1.1.1	0.000327
ORF7a	59	F59del2	tTT	t--	1	1	B.1.1.1	0.000327
ORF7a	59	F59del1	ttT	tt-	1	1	B.1.1.10	0.001115
ORF7a	59	F59del	TTT	---	1	1	B.1.1.10	0.001115
ORF7a	59	F59del2	tTT	t--	1	1	B.1.1.135	0.004695
ORF7a	59	F59del	TTT	---	1	1	B.1.1.157	0.000913
ORF7a	59	F59del	TTT	---	1	1	B.1.1.174	0.003378
ORF7a	59	F59del1	ttT	tt-	1	1	B.1.1.192	0.002309
ORF7a	59	F59del	TTT	---	1	1	B.1.1.192	0.002309
ORF7a	59	F59del	TTT	---	1	1	B.1.1.194	0.00495
ORF7a	59	F59del	TTT	---	1	1	B.1.1.205	0.003717
ORF7a	59	F59del	TTT	---	1	1	B.1.1.207	0.001182
ORF7a	59	F59del	TTT	---	1	1	B.1.1.209	0.008929
ORF7a	59	F59L	ttT	ttA	1	1	B.1.1.214	0.000055
ORF7a	59	F59L	ttT	ttG	1	1	B.1.1.225	0.007194
ORF7a	59	F59del	TTT	---	1	1	B.1.1.240	0.004695
ORF7a	59	F59del	TTT	---	1	1	B.1.1.241	0.00207
ORF7a	59	F59del2	TTt	--t	1	1	B.1.1.25	0.000569
ORF7a	59	F59del	TTT	---	1	1	B.1.1.277	0.000759
ORF7a	59	F59del	TTT	---	1	1	B.1.1.298	0.000862
ORF7a	59	F59L	ttT	ttG	1	1	B.1.1.303	0.002762
ORF7a	59	F59del	TTT	---	1	1	B.1.1.303	0.002762
ORF7a	59	F59del	TTT	---	1	1	B.1.1.311	0.000358
ORF7a	59	F59L	ttT	ttA	1	1	B.1.1.317	0.000412
ORF7a	59	F59del2	tTT	t--	1	1	B.1.1.317	0.000412
ORF7a	59	F59del1	Ttt	-tt	1	1	B.1.1.318	0.000302
ORF7a	59	F59del	TTT	---	1	1	B.1.1.329	0.003846
ORF7a	59	F59S	tTt	tCt	1	1	B.1.1.33	0.000421
ORF7a	59	F59del	TTT	---	1	1	B.1.1.348	0.000796
ORF7a	59	F59del	TTT	---	1	1	B.1.1.366	0.015873
ORF7a	59	F59del	TTT	---	1	1	B.1.1.368	0.003086
ORF7a	59	F59F	ttT	ttC	1	1	B.1.1.372	0.000689
ORF7a	59	F59del	TTT	---	1	1	B.1.1.376	0.005952
ORF7a	59	F59L	Ttt	Ctt	1	1	B.1.1.377	0.001381
ORF7a	59	F59del	TTT	---	1	1	B.1.1.39	0.00051
ORF7a	59	F59L	Ttt	Ctt	1	1	B.1.1.409	0.002833
ORF7a	59	F59del	TTT	---	1	1	B.1.1.409	0.002833
ORF7a	59	F59del	TTT	---	1	1	B.1.1.432	0.001266
ORF7a	59	F59del	TTT	---	1	1	B.1.1.434	0.000349
ORF7a	59	F59del	TTT	---	1	1	B.1.1.437	0.010417
ORF7a	59	F59del	TTT	---	1	1	B.1.1.486	0.001577
ORF7a	59	F59L	ttT	ttA	1	1	B.1.1.50	0.000679
ORF7a	59	F59del1	ttT	tt-	1	1	B.1.1.519	0.00004
ORF7a	59	F59del	TTT	---	1	1	B.1.1.525	0.005464
ORF7a	59	F59Y	tTt	tAt	1	1	B.1.1.7	0.000001
ORF7a	59	F59K	TTT	AAA	1	1	B.1.1.7	0.000001
ORF7a	59	F59del	TTT	---	1	1	B.1.1.70	0.000341
ORF7a	59	F59del	TTT	---	1	1	B.1.115	0.021739
ORF7a	59	F59del	TTT	---	1	1	B.1.128	0.000635
ORF7a	59	F59del	TTT	---	1	1	B.1.140	0.018868
ORF7a	59	F59L	Ttt	Ctt	1	1	B.1.149	0.003425
ORF7a	59	F59del	TTT	---	1	1	B.1.160.26	0.002421
ORF7a	59	F59del1	ttT	tt-	1	1	B.1.160.29	0.004219
ORF7a	59	F59del2	tTT	t--	1	1	B.1.160.7	0.002079
ORF7a	59	F59C	tTt	tGt	1	1	B.1.177	0.000013
ORF7a	59	F59P	TTT	CCA	1	1	B.1.177	0.000013
ORF7a	59	F59del	TTT	---	1	1	B.1.177.12	0.000152
ORF7a	59	F59L	ttT	ttA	1	1	B.1.177.12	0.000152
ORF7a	59	F59del	TTT	---	1	1	B.1.177.15	0.000631
ORF7a	59	F59K	TTT	AAA	1	1	B.1.177.21	0.000076
ORF7a	59	F59I	Ttt	Att	1	1	B.1.177.21	0.000076
ORF7a	59	F59del	TTT	---	1	1	B.1.177.4	0.000211
ORF7a	59	F59del	TTT	---	1	1	B.1.177.50	0.004695
ORF7a	59	F59del	TTT	---	1	1	B.1.177.53	0.002392
ORF7a	59	F59S	tTt	tCt	1	1	B.1.177.54	0.000606
ORF7a	59	F59L	TtT	CtG	1	1	B.1.177.63	0.002703
ORF7a	59	F59del	TTT	---	1	1	B.1.177.7	0.000165
ORF7a	59	F59S	tTt	tCt	1	1	B.1.177.77	0.000726
ORF7a	59	F59del	TTT	---	1	1	B.1.177.8	0.000752
ORF7a	59	F59del	TTT	---	1	1	B.1.177.83	0.001481
ORF7a	59	F59del	TTT	---	1	1	B.1.177.9	0.001332
ORF7a	59	F59P	TTT	CCC	1	1	B.1.2	0.000009
ORF7a	59	F59K	TTT	AAA	1	1	B.1.2	0.000009
ORF7a	59	F59S	tTt	tCt	1	1	B.1.234	0.000132
ORF7a	59	F59del	TTT	---	1	1	B.1.236	0.002053
ORF7a	59	F59del	TTT	---	1	1	B.1.240	0.000216
ORF7a	59	F59L	ttT	ttA	1	1	B.1.258	0.000067
ORF7a	59	F59L	Ttt	Ctt	1	1	B.1.258.11	0.000396
ORF7a	59	F59del	TTT	---	1	1	B.1.265	0.001271
ORF7a	59	F59del	TTT	---	1	1	B.1.320	0.001245
ORF7a	59	F59S	TTt	AGt	1	1	B.1.333	0.010526
ORF7a	59	F59del2	tTT	t--	1	1	B.1.351	0.00003
ORF7a	59	F59K	TTT	AAA	1	1	B.1.351	0.00003
ORF7a	59	F59Q	TTT	CAA	1	1	B.1.351	0.00003
ORF7a	59	F59X	tTT	tAA	1	1	B.1.351	0.00003
ORF7a	59	F59del	TTT	---	1	1	B.1.351.3	0.000876
ORF7a	59	F59L	Ttt	Ctt	1	1	B.1.36	0.000146
ORF7a	59	F59F	ttT	ttC	1	1	B.1.36	0.000146
ORF7a	59	F59Y	tTt	tAt	1	1	B.1.36	0.000146
ORF7a	59	F59del	TTT	---	1	1	B.1.36.19	0.009259
ORF7a	59	F59del	TTT	---	1	1	B.1.36.35	0.002604
ORF7a	59	F59del	TTT	---	1	1	B.1.361	0.001289
ORF7a	59	F59S	tTt	tCt	1	1	B.1.367	0.000792
ORF7a	59	F59del	TTT	---	1	1	B.1.371	0.001122
ORF7a	59	F59F	ttT	ttC	1	1	B.1.375	0.00082
ORF7a	59	F59L	Ttt	Ctt	1	1	B.1.389	0.001002
ORF7a	59	F59del	TTT	---	1	1	B.1.389	0.001002
ORF7a	59	F59del1	Ttt	-tt	1	1	B.1.396	0.000706
ORF7a	59	F59L	Ttt	Ctt	1	1	B.1.398	0.002976
ORF7a	59	F59S	tTt	tCt	1	1	B.1.398	0.002976
ORF7a	59	F59del2	tTT	t--	1	1	B.1.404	0.001302
ORF7a	59	F59del	TTT	---	1	1	B.1.406	0.006061
ORF7a	59	F59del	TTT	---	1	1	B.1.409	0.000781
ORF7a	59	F59Y	tTt	tAt	1	1	B.1.416.1	0.001563
ORF7a	59	F59del	TTT	---	1	1	B.1.416.1	0.001563
ORF7a	59	F59del2	tTT	t--	1	1	B.1.427	0.00005
ORF7a	59	F59L	ttT	ttA	1	1	B.1.429	0.000024
ORF7a	59	F59S	tTt	tCt	1	1	B.1.438.1	0.000107
ORF7a	59	F59del	TTT	---	1	1	B.1.438.1	0.000107
ORF7a	59	F59S	TTt	AGt	1	1	B.1.446	0.02
ORF7a	59	F59del	TTT	---	1	1	B.1.459	0.004082
ORF7a	59	F59del	TTT	---	1	1	B.1.466.2	0.000391
ORF7a	59	F59del	TTT	---	1	1	B.1.468	0.005714
ORF7a	59	F59C	tTt	tGt	1	1	B.1.497	0.000315
ORF7a	59	F59del1	ttT	tt-	1	1	B.1.509	0.000866
ORF7a	59	F59del	TTT	---	1	1	B.1.517	0.000427
ORF7a	59	F59K	TTT	AAA	1	1	B.1.526	0.000024
ORF7a	59	F59del	TTT	---	1	1	B.1.534	0.0125
ORF7a	59	F59del	TTT	---	1	1	B.1.535	0.028571
ORF7a	59	F59del	TTT	---	1	1	B.1.564	0.000426
ORF7a	59	F59del	TTT	---	1	1	B.1.565	0.00081
ORF7a	59	F59del	TTT	---	1	1	B.1.568	0.001111
ORF7a	59	F59del	TTT	---	1	1	B.1.577	0.000687
ORF7a	59	F59del1	Ttt	-tt	1	1	B.1.595	0.000261
ORF7a	59	F59Y	tTt	tAt	1	1	B.1.596	0.000087
ORF7a	59	F59del1	TtT	-tN	1	1	B.1.599	0.00365
ORF7a	59	F59del	TTT	---	1	1	B.1.609	0.000479
ORF7a	59	F59K	TTT	AAA	1	1	B.1.617.2	0.000004
ORF7a	59	F59D	TTt	GAt	1	1	B.1.617.2	0.000004
ORF7a	59	F59E	TTT	GAA	1	1	B.1.617.2	0.000004
ORF7a	59	F59del	TTT	---	1	1	B.1.623	0.000536
ORF7a	59	F59L	ttT	ttA	1	1	B.1.630	0.005236
ORF7a	59	F59del2	tTT	t--	1	1	B.1.637	0.000073
ORF7a	59	F59del	TTT	---	1	1	B.1.638	0.052632
ORF7a	59	F59del	TTT	---	1	1	B.1.9.1	0.032258
ORF7a	59	F59del	TTT	---	1	1	B.11	0.005128
ORF7a	59	F59del2	tTT	t--	1	1	B.3	0.000831
ORF7a	59	F59del	TTT	---	1	1	B.39	0.002331
ORF7a	59	F59F	ttT	ttC	1	1	C.16	0.00106
ORF7a	59	F59del	TTT	---	1	1	C.28	0.04
ORF7a	59	F59del2	tTT	t--	1	1	C.30	0.001727
ORF7a	59	F59del2	tTT	t--	1	1	C.37	0.000116
ORF7a	59	F59L	Ttt	Ctt	1	1	D.2	0.000075
ORF7a	59	F59del	TTT	---	1	1	K.3	0.006173
ORF7a	59	F59F	ttT	ttC	1	1	P.1	0.000016
ORF7a	59	F59del	TTT	---	1	1	P.1.1	0.000318
ORF7a	59	F59del2	tTT	t--	1	1	P.1.10	0.000269
ORF7a	59	F59del2	tTT	t--	1	1	P.1.12	0.000484
ORF7a	59	F59del	TTT	---	1	1	P.1.13	0.000898
ORF7a	59	F59del2	tTT	t--	1	1	P.1.14	0.000048
ORF7a	59	F59del	TTT	---	1	1	P.1.17	0.000162
ORF7a	59	F59del	TTT	---	1	1	P.1.3	0.034483
ORF7a	59	F59L	ttT	ttA	1	1	P.1.4	0.000977
ORF7a	59	F59del	TTT	---	1	1	P.1.4	0.000977
ORF7a	59	F59S	tTt	tCt	1	1	P.2	0.000187
ORF7a	59	F59del2	tTT	t--	1	1	Q.1	0.000126
ORF7a	59	F59del2	tTT	t--	1	1	Q.3	0.000145
ORF7a	59	F59del1	ttT	tt-	1	1	Q.4	0.000455
ORF7a	59	F59del	TTT	---	1	1	Q.7	0.001111
ORF7a	59	F59F	ttT	ttC	1	1	Q.8	0.000165
ORF7a	59	F59del	TTT	---	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.