CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF7a : CodonNum = 49

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	49	L49del		del	CTA	---	5048	5048	1	27538-27540
ORF7a	49	L49P		nonsyn	cTa	cCa	4393	4381	0.997268	27538-27540
ORF7a	49	L49P		nonsyn	cTA	cCT	4393	8	0.00182108	27538-27540
ORF7a	49	L49P		nonsyn	cTA	cCC	4393	4	0.000910539	27538-27540
ORF7a	49	L49L		syn	Cta	Tta	3310	2969	0.896979	27538-27540
ORF7a	49	L49L		syn	ctA	ctG	3310	250	0.0755287	27538-27540
ORF7a	49	L49L		syn	ctA	ctT	3310	66	0.0199396	27538-27540
ORF7a	49	L49L		syn	CtA	TtG	3310	15	0.00453172	27538-27540
ORF7a	49	L49L		syn	ctA	ctC	3310	10	0.00302115	27538-27540
ORF7a	49	L49I		nonsyn	Cta	Ata	320	308	0.9625	27538-27540
ORF7a	49	L49I		nonsyn	CtA	AtT	320	11	0.034375	27538-27540
ORF7a	49	L49I		nonsyn	CtA	AtC	320	1	0.003125	27538-27540
ORF7a	49	L49V		nonsyn	Cta	Gta	124	121	0.975806	27538-27540
ORF7a	49	L49V		nonsyn	CtA	GtT	124	3	0.0241935	27538-27540
ORF7a	49	L49del1		del	ctA	ct-	59	49	0.830508	27538-27540
ORF7a	49	L49del1		del	Cta	-ta	59	6	0.101695	27538-27540
ORF7a	49	L49del1		del	cTA	cC-	59	2	0.0338983	27538-27540
ORF7a	49	L49del1		del	cTA	c-N	59	1	0.0169492	27538-27540
ORF7a	49	L49del1		del	CTA	-NN	59	1	0.0169492	27538-27540
ORF7a	49	L49Q		nonsyn	cTa	cAa	48	45	0.9375	27538-27540
ORF7a	49	L49Q		nonsyn	cTA	cAG	48	3	0.0625	27538-27540
ORF7a	49	L49X		nonsyn	CTa	TAa	31	19	0.612903	27538-27540
ORF7a	49	L49X		nonsyn	CTA	TAG	31	6	0.193548	27538-27540
ORF7a	49	L49X		nonsyn	CTa	TGa	31	6	0.193548	27538-27540
ORF7a	49	L49del2		del	cTA	c--	25	18	0.72	27538-27540
ORF7a	49	L49R		nonsyn	cTa	cGa	25	11	0.44	27538-27540
ORF7a	49	L49R		nonsyn	CTa	AGa	25	10	0.4	27538-27540
ORF7a	49	L49del2		del	CTA	--N	25	5	0.2	27538-27540
ORF7a	49	L49R		nonsyn	cTA	cGG	25	2	0.08	27538-27540
ORF7a	49	L49R		nonsyn	CTA	AGG	25	1	0.04	27538-27540
ORF7a	49	L49del2		del	CTA	--T	25	1	0.04	27538-27540
ORF7a	49	L49R		nonsyn	cTA	cGT	25	1	0.04	27538-27540
ORF7a	49	L49del2		del	CTa	--a	25	1	0.04	27538-27540
ORF7a	49	L49S		nonsyn	CTa	TCa	23	13	0.565217	27538-27540
ORF7a	49	L49S		nonsyn	CTA	TCT	23	6	0.26087	27538-27540
ORF7a	49	L49S		nonsyn	CTA	TCC	23	1	0.0434783	27538-27540
ORF7a	49	L49S		nonsyn	CTA	AGT	23	1	0.0434783	27538-27540
ORF7a	49	L49S		nonsyn	CTA	TCG	23	1	0.0434783	27538-27540
ORF7a	49	L49S		nonsyn	CTA	AGC	23	1	0.0434783	27538-27540
ORF7a	49	L49F		nonsyn	CtA	TtT	18	14	0.777778	27538-27540
ORF7a	49	L49F		nonsyn	CtA	TtC	18	4	0.222222	27538-27540
ORF7a	49	L49K		nonsyn	CTa	AAa	16	14	0.875	27538-27540
ORF7a	49	L49K		nonsyn	CTA	AAG	16	2	0.125	27538-27540
ORF7a	49	L49H		nonsyn	cTA	cAT	12	8	0.666667	27538-27540
ORF7a	49	L49H		nonsyn	cTA	cAC	12	4	0.333333	27538-27540
ORF7a	49	L49Y		nonsyn	CTA	TAT	8	7	0.875	27538-27540
ORF7a	49	L49Y		nonsyn	CTA	TAC	8	1	0.125	27538-27540
ORF7a	49	L49N		nonsyn	CTA	AAT	7	4	0.571429	27538-27540
ORF7a	49	L49N		nonsyn	CTA	AAC	7	3	0.428571	27538-27540
ORF7a	49	L49C		nonsyn	CTA	TGT	5	4	0.8	27538-27540
ORF7a	49	L49T		nonsyn	CTa	ACa	5	3	0.6	27538-27540
ORF7a	49	L49T		nonsyn	CTA	ACC	5	2	0.4	27538-27540
ORF7a	49	L49C		nonsyn	CTA	TGC	5	1	0.2	27538-27540
ORF7a	49	L49E		nonsyn	CTa	GAa	4	4	1	27538-27540
ORF7a	49	L49A		nonsyn	CTA	GCT	4	3	0.75	27538-27540
ORF7a	49	L49A		nonsyn	CTa	GCa	4	1	0.25	27538-27540
ORF7a	49	L49D		nonsyn	CTA	GAT	2	2	1	27538-27540
ORF7a	49	L49G		nonsyn	CTa	GGa	2	2	1	27538-27540
ORF7a	49	L49M		nonsyn	CtA	AtG	1	1	1	27538-27540

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	49	L49del	CTA	---	5048	5048	All	0.000965
ORF7a	49	L49P	cTa	cCa	4381	4393	All	0.000838
ORF7a	49	L49P	cTA	cCT	8	4393	All	0.000002
ORF7a	49	L49P	cTA	cCC	4	4393	All	0.000001
ORF7a	49	L49L	Cta	Tta	2969	3310	All	0.000568
ORF7a	49	L49L	ctA	ctG	250	3310	All	0.000048
ORF7a	49	L49L	ctA	ctT	66	3310	All	0.000013
ORF7a	49	L49L	CtA	TtG	15	3310	All	0.000003
ORF7a	49	L49L	ctA	ctC	10	3310	All	0.000002
ORF7a	49	L49P	cTa	cCa	2440	2443	B.1.617.2	0.009188
ORF7a	49	L49P	cTA	cCC	2	2443	B.1.617.2	0.000008
ORF7a	49	L49P	cTA	cCT	1	2443	B.1.617.2	0.000004
ORF7a	49	L49del	CTA	---	1337	1337	B.1.617.2	0.005034
ORF7a	49	L49P	cTa	cCa	1090	1090	AY.102	0.0289
ORF7a	49	L49L	Cta	Tta	625	636	AY.4	0.000973
ORF7a	49	L49L	ctA	ctG	10	636	AY.4	0.000016
ORF7a	49	L49L	ctA	ctT	1	636	AY.4	0.000002
ORF7a	49	L49del	CTA	---	558	558	B.1.1.7	0.0005
ORF7a	49	L49del	CTA	---	416	416	AY.25	0.002502
ORF7a	49	L49L	Cta	Tta	390	390	B.1.1.121	0.946602
ORF7a	49	L49L	Cta	Tta	347	373	B.1.617.2	0.001307
ORF7a	49	L49L	ctA	ctG	22	373	B.1.617.2	0.000083
ORF7a	49	L49L	ctA	ctT	2	373	B.1.617.2	0.000008
ORF7a	49	L49L	CtA	TtG	2	373	B.1.617.2	0.000008
ORF7a	49	L49I	Cta	Ata	308	320	All	0.000059
ORF7a	49	L49I	CtA	AtT	11	320	All	0.000002
ORF7a	49	L49I	CtA	AtC	1	320	All	0
ORF7a	49	L49del	CTA	---	303	303	AY.4	0.000472
ORF7a	49	L49L	Cta	Tta	289	289	AY.26	0.008182
ORF7a	49	L49I	Cta	Ata	256	256	AY.4	0.000398
ORF7a	49	L49del	CTA	---	221	221	AY.102	0.00586
ORF7a	49	L49L	Cta	Tta	113	215	B.1.1.7	0.000101
ORF7a	49	L49L	ctA	ctG	96	215	B.1.1.7	0.000086
ORF7a	49	L49L	ctA	ctC	4	215	B.1.1.7	0.000004
ORF7a	49	L49L	ctA	ctT	2	215	B.1.1.7	0.000002
ORF7a	49	L49P	cTa	cCa	199	199	AY.39	0.004918
ORF7a	49	L49del	CTA	---	197	197	AY.43	0.000873
ORF7a	49	L49L	Cta	Tta	189	192	AY.103	0.001174
ORF7a	49	L49L	ctA	ctT	3	192	AY.103	0.000019
ORF7a	49	L49del	CTA	---	180	180	B.1.177.21	0.013765
ORF7a	49	L49L	Cta	Tta	152	155	AY.44	0.000925
ORF7a	49	L49L	ctA	ctT	2	155	AY.44	0.000012
ORF7a	49	L49L	ctA	ctG	1	155	AY.44	0.000006
ORF7a	49	L49L	Cta	Tta	137	137	AY.75.1	0.024702
ORF7a	49	L49del	CTA	---	126	126	AY.103	0.000782
ORF7a	49	L49V	Cta	Gta	121	124	All	0.000023
ORF7a	49	L49V	CtA	GtT	3	124	All	0.000001
ORF7a	49	L49del	CTA	---	120	120	AY.39	0.002965
ORF7a	49	L49P	cTa	cCa	120	120	AY.43	0.000532
ORF7a	49	L49del	CTA	---	108	108	AY.3	0.001074
ORF7a	49	L49del	CTA	---	96	96	AY.44	0.000584
ORF7a	49	L49L	Cta	Tta	74	83	AY.25	0.000445
ORF7a	49	L49L	ctA	ctT	5	83	AY.25	0.00003
ORF7a	49	L49L	ctA	ctC	2	83	AY.25	0.000012
ORF7a	49	L49L	CtA	TtG	2	83	AY.25	0.000012
ORF7a	49	L49del	CTA	---	81	81	AY.120	0.003011
ORF7a	49	L49del	CTA	---	74	74	AY.26	0.002095
ORF7a	49	L49L	Cta	Tta	70	72	AY.43	0.00031
ORF7a	49	L49L	ctA	ctG	2	72	AY.43	0.000009
ORF7a	49	L49del	CTA	---	69	69	AY.46.4	0.011351
ORF7a	49	L49del	CTA	---	67	67	AY.29	0.001057
ORF7a	49	L49del	CTA	---	64	64	AY.100	0.002944
ORF7a	49	L49del1	ctA	ct-	49	59	All	0.000009
ORF7a	49	L49del1	Cta	-ta	6	59	All	0.000001
ORF7a	49	L49del1	cTA	cC-	2	59	All	0
ORF7a	49	L49del1	CTA	-NN	1	59	All	0
ORF7a	49	L49del1	cTA	c-N	1	59	All	0
ORF7a	49	L49L	Cta	Tta	59	59	AY.111	0.010806
ORF7a	49	L49P	cTa	cCa	58	58	AY.46.4	0.009541
ORF7a	49	L49del	CTA	---	55	55	AY.47	0.001711
ORF7a	49	L49P	cTa	cCa	53	53	AY.120	0.00197
ORF7a	49	L49Q	cTa	cAa	45	48	All	0.000009
ORF7a	49	L49Q	cTA	cAG	3	48	All	0.000001
ORF7a	49	L49del	CTA	---	48	48	AY.3.1	0.004092
ORF7a	49	L49del	CTA	---	48	48	B.1.2	0.000423
ORF7a	49	L49P	cTa	cCa	47	47	AY.5.4	0.013005
ORF7a	49	L49L	Cta	Tta	35	45	B.1.2	0.000308
ORF7a	49	L49L	ctA	ctG	9	45	B.1.2	0.000079
ORF7a	49	L49L	ctA	ctT	1	45	B.1.2	0.000009
ORF7a	49	L49del	CTA	---	44	44	B.1	0.000403
ORF7a	49	L49L	Cta	Tta	42	43	AY.3	0.000418
ORF7a	49	L49L	ctA	ctG	1	43	AY.3	0.00001
ORF7a	49	L49P	cTa	cCa	37	37	AY.46	0.003851
ORF7a	49	L49del	CTA	---	37	37	B.1.1.284	0.003974
ORF7a	49	L49del	CTA	---	37	37	B.1.621	0.003275
ORF7a	49	L49V	Cta	Gta	34	34	P.1	0.000536
ORF7a	49	L49X	CTa	TAa	19	31	All	0.000004
ORF7a	49	L49X	CTA	TAG	6	31	All	0.000001
ORF7a	49	L49X	CTa	TGa	6	31	All	0.000001
ORF7a	49	L49L	ctA	ctG	20	31	B.1.1.519	0.000794
ORF7a	49	L49L	Cta	Tta	11	31	B.1.1.519	0.000437
ORF7a	49	L49P	cTa	cCa	29	30	AY.44	0.000177
ORF7a	49	L49P	cTA	cCT	1	30	AY.44	0.000006
ORF7a	49	L49L	Cta	Tta	26	29	AY.102	0.000689
ORF7a	49	L49L	ctA	ctG	1	29	AY.102	0.000027
ORF7a	49	L49L	ctA	ctC	1	29	AY.102	0.000027
ORF7a	49	L49L	ctA	ctT	1	29	AY.102	0.000027
ORF7a	49	L49P	cTa	cCa	29	29	AY.117	0.002451
ORF7a	49	L49del	CTA	---	29	29	AY.54	0.002765
ORF7a	49	L49del	CTA	---	28	28	AY.42	0.001126
ORF7a	49	L49L	Cta	Tta	27	27	B.1.1.176	0.011863
ORF7a	49	L49del2	cTA	c--	18	25	All	0.000003
ORF7a	49	L49R	cTa	cGa	11	25	All	0.000002
ORF7a	49	L49R	CTa	AGa	10	25	All	0.000002
ORF7a	49	L49del2	CTA	--N	5	25	All	0.000001
ORF7a	49	L49R	cTA	cGG	2	25	All	0
ORF7a	49	L49R	cTA	cGT	1	25	All	0
ORF7a	49	L49R	CTA	AGG	1	25	All	0
ORF7a	49	L49del2	CTA	--T	1	25	All	0
ORF7a	49	L49del2	CTa	--a	1	25	All	0
ORF7a	49	L49del	CTA	---	25	25	P.1	0.000394
ORF7a	49	L49del	CTA	---	24	24	AY.119	0.000847
ORF7a	49	L49del	CTA	---	24	24	B.1.1.214	0.001331
ORF7a	49	L49V	Cta	Gta	24	24	B.1.1.7	0.000021
ORF7a	49	L49L	ctA	ctT	24	24	B.1.177.4	0.005065
ORF7a	49	L49S	CTa	TCa	13	23	All	0.000002
ORF7a	49	L49S	CTA	TCT	6	23	All	0.000001
ORF7a	49	L49S	CTA	AGC	1	23	All	0
ORF7a	49	L49S	CTA	AGT	1	23	All	0
ORF7a	49	L49S	CTA	TCG	1	23	All	0
ORF7a	49	L49S	CTA	TCC	1	23	All	0
ORF7a	49	L49P	cTa	cCa	21	22	B.1.1.7	0.000019
ORF7a	49	L49P	cTA	cCC	1	22	B.1.1.7	0.000001
ORF7a	49	L49Q	cTa	cAa	20	22	B.1.617.2	0.000075
ORF7a	49	L49Q	cTA	cAG	2	22	B.1.617.2	0.000008
ORF7a	49	L49del	CTA	---	21	21	AY.7.2	0.011745
ORF7a	49	L49L	Cta	Tta	21	21	AY.9.2	0.000771
ORF7a	49	L49del	CTA	---	19	19	B.1.177	0.00025
ORF7a	49	L49F	CtA	TtT	14	18	All	0.000003
ORF7a	49	L49F	CtA	TtC	4	18	All	0.000001
ORF7a	49	L49del	CTA	---	18	18	B.1.526	0.000423
ORF7a	49	L49del	CTA	---	17	17	AY.5	0.000351
ORF7a	49	L49K	CTa	AAa	14	16	All	0.000003
ORF7a	49	L49K	CTA	AAG	2	16	All	0
ORF7a	49	L49P	cTa	cCa	16	16	AY.22	0.033473
ORF7a	49	L49X	CTa	TAa	10	16	AY.25	0.00006
ORF7a	49	L49X	CTA	TAG	3	16	AY.25	0.000018
ORF7a	49	L49X	CTa	TGa	3	16	AY.25	0.000018
ORF7a	49	L49L	Cta	Tta	11	16	B.1	0.000101
ORF7a	49	L49L	ctA	ctG	4	16	B.1	0.000037
ORF7a	49	L49L	CtA	TtG	1	16	B.1	0.000009
ORF7a	49	L49L	CtA	TtG	10	16	B.1.177.21	0.000765
ORF7a	49	L49L	ctA	ctT	6	16	B.1.177.21	0.000459
ORF7a	49	L49del	CTA	---	16	16	C.37	0.001857
ORF7a	49	L49del	CTA	---	15	15	AY.20	0.000583
ORF7a	49	L49P	cTa	cCa	15	15	AY.45	0.001825
ORF7a	49	L49L	Cta	Tta	15	15	AY.61	0.001572
ORF7a	49	L49L	Cta	Tta	9	15	B.1.1	0.000163
ORF7a	49	L49L	ctA	ctG	6	15	B.1.1	0.000109
ORF7a	49	L49X	CTa	TAa	9	15	B.1.617.2	0.000034
ORF7a	49	L49R	CTa	AGa	8	15	B.1.617.2	0.00003
ORF7a	49	L49R	cTa	cGa	5	15	B.1.617.2	0.000019
ORF7a	49	L49X	CTa	TGa	3	15	B.1.617.2	0.000011
ORF7a	49	L49X	CTA	TAG	3	15	B.1.617.2	0.000011
ORF7a	49	L49R	CTA	AGG	1	15	B.1.617.2	0.000004
ORF7a	49	L49R	cTA	cGG	1	15	B.1.617.2	0.000004
ORF7a	49	L49L	ctA	ctG	12	15	D.2	0.0009
ORF7a	49	L49L	Cta	Tta	3	15	D.2	0.000225
ORF7a	49	L49L	Cta	Tta	14	14	AY.118	0.000877
ORF7a	49	L49P	cTa	cCa	14	14	AY.37	0.004425
ORF7a	49	L49L	ctA	ctG	10	14	AY.5	0.000206
ORF7a	49	L49L	Cta	Tta	4	14	AY.5	0.000083
ORF7a	49	L49P	cTa	cCa	14	14	AY.73	0.009315
ORF7a	49	L49del	CTA	---	14	14	B.1.351	0.000416
ORF7a	49	L49del	CTA	---	14	14	B.1.596	0.00122
ORF7a	49	L49del	CTA	---	14	14	B.1.637	0.001023
ORF7a	49	L49P	cTa	cCa	13	13	AY.14	0.001144
ORF7a	49	L49L	Cta	Tta	13	13	AY.23	0.000907
ORF7a	49	L49Q	cTa	cAa	13	13	AY.25	0.000078
ORF7a	49	L49del	CTA	---	13	13	AY.68	0.003559
ORF7a	49	L49H	cTA	cAT	8	12	All	0.000002
ORF7a	49	L49H	cTA	cAC	4	12	All	0.000001
ORF7a	49	L49P	cTa	cCa	12	12	AY.106	0.004019
ORF7a	49	L49del	CTA	---	12	12	AY.110	0.001352
ORF7a	49	L49L	Cta	Tta	12	12	AY.68	0.003285
ORF7a	49	L49del	CTA	---	12	12	AY.98.1	0.000581
ORF7a	49	L49I	Cta	Ata	12	12	B.1.1.369	0.005355
ORF7a	49	L49P	cTa	cCa	12	12	B.1.12	0.096
ORF7a	49	L49del	CTA	---	12	12	B.1.324	0.019262
ORF7a	49	L49del1	ctA	ct-	11	11	AY.119	0.000388
ORF7a	49	L49L	Cta	Tta	11	11	AY.16	0.004176
ORF7a	49	L49del	CTA	---	11	11	AY.23	0.000767
ORF7a	49	L49P	cTa	cCa	7	11	AY.25	0.000042
ORF7a	49	L49P	cTA	cCT	3	11	AY.25	0.000018
ORF7a	49	L49P	cTA	cCC	1	11	AY.25	0.000006
ORF7a	49	L49del	CTA	---	11	11	AY.35	0.002564
ORF7a	49	L49del	CTA	---	11	11	AY.37	0.003477
ORF7a	49	L49L	Cta	Tta	11	11	AY.4.2	0.000239
ORF7a	49	L49L	Cta	Tta	11	11	B.1.1.37	0.002122
ORF7a	49	L49del	CTA	---	10	10	AY.106	0.003349
ORF7a	49	L49del	CTA	---	10	10	AY.120.1	0.00321
ORF7a	49	L49P	cTa	cCa	10	10	AY.20	0.000389
ORF7a	49	L49L	Cta	Tta	8	10	AY.47	0.000249
ORF7a	49	L49L	ctA	ctG	2	10	AY.47	0.000062
ORF7a	49	L49L	Cta	Tta	10	10	C.16	0.010604
ORF7a	49	L49L	ctA	ctG	6	10	P.1	0.000095
ORF7a	49	L49L	Cta	Tta	4	10	P.1	0.000063
ORF7a	49	L49del	CTA	---	10	10	R.1	0.0009
ORF7a	49	L49K	CTa	AAa	8	9	AY.25	0.000048
ORF7a	49	L49I	Cta	Ata	6	9	AY.25	0.000036
ORF7a	49	L49I	CtA	AtT	2	9	AY.25	0.000012
ORF7a	49	L49K	CTA	AAG	1	9	AY.25	0.000006
ORF7a	49	L49I	CtA	AtC	1	9	AY.25	0.000006
ORF7a	49	L49del	CTA	---	9	9	AY.45	0.001095
ORF7a	49	L49del	CTA	---	9	9	AY.46.2	0.005718
ORF7a	49	L49L	Cta	Tta	9	9	AY.57	0.005906
ORF7a	49	L49del1	ctA	ct-	9	9	AY.75	0.000504
ORF7a	49	L49L	Cta	Tta	8	9	B.1.177	0.000105
ORF7a	49	L49L	ctA	ctC	1	9	B.1.177	0.000013
ORF7a	49	L49del	CTA	---	9	9	L.1	0.017143
ORF7a	49	L49Y	CTA	TAT	7	8	All	0.000001
ORF7a	49	L49Y	CTA	TAC	1	8	All	0
ORF7a	49	L49del1	ctA	ct-	6	8	AY.102	0.000159
ORF7a	49	L49del1	cTA	cC-	1	8	AY.102	0.000027
ORF7a	49	L49del1	CTA	-NN	1	8	AY.102	0.000027
ORF7a	49	L49P	cTa	cCa	8	8	AY.111	0.001465
ORF7a	49	L49del	CTA	---	8	8	AY.116	0.002294
ORF7a	49	L49del	CTA	---	8	8	AY.118	0.000501
ORF7a	49	L49del2	cTA	c--	8	8	AY.25	0.000048
ORF7a	49	L49H	cTA	cAT	6	8	AY.25	0.000036
ORF7a	49	L49S	CTa	TCa	4	8	AY.25	0.000024
ORF7a	49	L49S	CTA	TCT	2	8	AY.25	0.000012
ORF7a	49	L49H	cTA	cAC	2	8	AY.25	0.000012
ORF7a	49	L49S	CTA	AGT	1	8	AY.25	0.000006
ORF7a	49	L49S	CTA	TCG	1	8	AY.25	0.000006
ORF7a	49	L49L	Cta	Tta	8	8	AY.29	0.000126
ORF7a	49	L49I	CtA	AtT	8	8	AY.3.1	0.000682
ORF7a	49	L49del	CTA	---	8	8	AY.30	0.003166
ORF7a	49	L49P	cTa	cCa	8	8	AY.33	0.000534
ORF7a	49	L49del	CTA	---	8	8	AY.34	0.000776
ORF7a	49	L49V	Cta	Gta	8	8	AY.43	0.000035
ORF7a	49	L49P	cTa	cCa	8	8	AY.46.2	0.005083
ORF7a	49	L49del	CTA	---	8	8	B.1.525	0.000905
ORF7a	49	L49del1	ctA	ct-	7	8	B.1.617.2	0.000026
ORF7a	49	L49S	CTa	TCa	4	8	B.1.617.2	0.000015
ORF7a	49	L49S	CTA	TCT	2	8	B.1.617.2	0.000008
ORF7a	49	L49S	CTA	AGC	1	8	B.1.617.2	0.000004
ORF7a	49	L49del1	cTA	c-N	1	8	B.1.617.2	0.000004
ORF7a	49	L49S	CTA	TCC	1	8	B.1.617.2	0.000004
ORF7a	49	L49V	Cta	Gta	8	8	P.1.14	0.000382
ORF7a	49	L49N	CTA	AAT	4	7	All	0.000001
ORF7a	49	L49N	CTA	AAC	3	7	All	0.000001
ORF7a	49	L49L	Cta	Tta	7	7	AY.110	0.000789
ORF7a	49	L49del	CTA	---	7	7	AY.113	0.000997
ORF7a	49	L49L	Cta	Tta	7	7	AY.119	0.000247
ORF7a	49	L49L	Cta	Tta	6	7	AY.33	0.000401
ORF7a	49	L49L	ctA	ctG	1	7	AY.33	0.000067
ORF7a	49	L49del	CTA	---	7	7	AY.39.1	0.000277
ORF7a	49	L49P	cTa	cCa	7	7	AY.54	0.000667
ORF7a	49	L49del	CTA	---	7	7	AY.98	0.000553
ORF7a	49	L49L	ctA	ctT	7	7	B.1.1.39	0.003568
ORF7a	49	L49Q	cTa	cAa	7	7	B.1.1.7	0.000006
ORF7a	49	L49del	CTA	---	7	7	B.1.160	0.000218
ORF7a	49	L49del	CTA	---	7	7	B.1.429	0.000165
ORF7a	49	L49L	Cta	Tta	7	7	B.1.617.1	0.000903
ORF7a	49	L49del	CTA	---	7	7	P.1.15	0.001626
ORF7a	49	L49P	cTa	cCa	6	6	AY.103	0.000037
ORF7a	49	L49del1	ctA	ct-	6	6	AY.121	0.000812
ORF7a	49	L49del	CTA	---	6	6	AY.121	0.000812
ORF7a	49	L49P	cTa	cCa	6	6	AY.16	0.002278
ORF7a	49	L49Y	CTA	TAT	6	6	AY.25	0.000036
ORF7a	49	L49L	Cta	Tta	6	6	AY.39	0.000148
ORF7a	49	L49L	Cta	Tta	6	6	AY.71	0.00285
ORF7a	49	L49del	CTA	---	6	6	AY.75	0.000336
ORF7a	49	L49del	CTA	---	6	6	AY.9.1	0.000502
ORF7a	49	L49P	cTa	cCa	6	6	AY.98	0.000474
ORF7a	49	L49del	CTA	---	6	6	B.1.1	0.000109
ORF7a	49	L49L	Cta	Tta	6	6	B.1.177.81	0.001136
ORF7a	49	L49L	Cta	Tta	6	6	B.1.526	0.000141
ORF7a	49	L49K	CTa	AAa	5	6	B.1.617.2	0.000019
ORF7a	49	L49K	CTA	AAG	1	6	B.1.617.2	0.000004
ORF7a	49	L49L	ctA	ctG	6	6	Q.1	0.000758
ORF7a	49	L49C	CTA	TGT	4	5	All	0.000001
ORF7a	49	L49T	CTa	ACa	3	5	All	0.000001
ORF7a	49	L49T	CTA	ACC	2	5	All	0
ORF7a	49	L49C	CTA	TGC	1	5	All	0
ORF7a	49	L49del	CTA	---	5	5	AY.14	0.00044
ORF7a	49	L49N	CTA	AAT	3	5	AY.25	0.000018
ORF7a	49	L49V	Cta	Gta	3	5	AY.25	0.000018
ORF7a	49	L49V	CtA	GtT	2	5	AY.25	0.000012
ORF7a	49	L49N	CTA	AAC	2	5	AY.25	0.000012
ORF7a	49	L49L	Cta	Tta	5	5	AY.27	0.000324
ORF7a	49	L49L	Cta	Tta	4	5	AY.36	0.000593
ORF7a	49	L49L	ctA	ctG	1	5	AY.36	0.000148
ORF7a	49	L49del	CTA	---	5	5	AY.4.2	0.000108
ORF7a	49	L49del	CTA	---	5	5	AY.46.1	0.005133
ORF7a	49	L49P	cTa	cCa	5	5	AY.46.6	0.000361
ORF7a	49	L49del	CTA	---	5	5	AY.61	0.000524
ORF7a	49	L49L	Cta	Tta	5	5	AY.7	0.00098
ORF7a	49	L49del	CTA	---	5	5	AY.74	0.000578
ORF7a	49	L49L	Cta	Tta	2	5	AY.75	0.000112
ORF7a	49	L49L	ctA	ctG	2	5	AY.75	0.000112
ORF7a	49	L49L	ctA	ctC	1	5	AY.75	0.000056
ORF7a	49	L49P	cTa	cCa	5	5	AY.84	0.002187
ORF7a	49	L49del	CTA	---	5	5	AY.88	0.004421
ORF7a	49	L49del	CTA	---	5	5	AY.9.2	0.000184
ORF7a	49	L49del	CTA	---	5	5	B.1.1.56	0.089286
ORF7a	49	L49del	CTA	---	5	5	B.1.234	0.00066
ORF7a	49	L49V	Cta	Gta	5	5	B.1.351	0.000149
ORF7a	49	L49L	Cta	Tta	5	5	B.1.466.2	0.001956
ORF7a	49	L49V	Cta	Gta	5	5	B.1.617.2	0.000019
ORF7a	49	L49L	ctA	ctG	5	5	P.2	0.000933
ORF7a	49	L49S	CTA	TCT	2	4		0.111111
ORF7a	49	L49L	ctA	ctT	2	4		0.111111
ORF7a	49	L49P	cTa	cCa	2	4		0.111111
ORF7a	49	L49S	CTa	TCa	2	4		0.111111
ORF7a	49	L49L	Cta	Tta	2	4		0.111111
ORF7a	49	L49P	cTA	cCT	2	4		0.111111
ORF7a	49	L49E	CTa	GAa	4	4	All	0.000001
ORF7a	49	L49A	CTA	GCT	3	4	All	0.000001
ORF7a	49	L49A	CTa	GCa	1	4	All	0
ORF7a	49	L49del	CTA	---	4	4	AY.107	0.001864
ORF7a	49	L49del	CTA	---	4	4	AY.111	0.000733
ORF7a	49	L49L	ctA	ctT	3	4	AY.116	0.00086
ORF7a	49	L49L	Cta	Tta	1	4	AY.116	0.000287
ORF7a	49	L49L	Cta	Tta	4	4	AY.120	0.000149
ORF7a	49	L49L	Cta	Tta	4	4	AY.14	0.000352
ORF7a	49	L49F	CtA	TtT	4	4	AY.25	0.000024
ORF7a	49	L49R	CTa	AGa	2	4	AY.25	0.000012
ORF7a	49	L49R	cTa	cGa	1	4	AY.25	0.000006
ORF7a	49	L49R	cTA	cGT	1	4	AY.25	0.000006
ORF7a	49	L49P	cTa	cCa	4	4	AY.4	0.000006
ORF7a	49	L49L	Cta	Tta	4	4	AY.46.6	0.000289
ORF7a	49	L49I	Cta	Ata	4	4	AY.52	0.003257
ORF7a	49	L49L	Cta	Tta	4	4	AY.6	0.000165
ORF7a	49	L49del	CTA	---	4	4	AY.66	0.004278
ORF7a	49	L49L	Cta	Tta	4	4	AY.84	0.00175
ORF7a	49	L49del	CTA	---	4	4	AY.85	0.001709
ORF7a	49	L49del	CTA	---	4	4	AY.91	0.002922
ORF7a	49	L49del	CTA	---	4	4	AY.99	0.004197
ORF7a	49	L49del1	ctA	ct-	3	4	B.1.1.7	0.000003
ORF7a	49	L49del1	Cta	-ta	1	4	B.1.1.7	0.000001
ORF7a	49	L49L	Cta	Tta	4	4	B.1.160	0.000125
ORF7a	49	L49L	Cta	Tta	4	4	B.1.234	0.000528
ORF7a	49	L49L	Cta	Tta	2	4	B.1.351	0.000059
ORF7a	49	L49L	ctA	ctG	1	4	B.1.351	0.00003
ORF7a	49	L49L	ctA	ctT	1	4	B.1.351	0.00003
ORF7a	49	L49L	Cta	Tta	3	4	B.1.429	0.000071
ORF7a	49	L49L	ctA	ctG	1	4	B.1.429	0.000024
ORF7a	49	L49F	CtA	TtT	4	4	B.1.617.2	0.000015
ORF7a	49	L49H	cTA	cAC	2	4	B.1.617.2	0.000008
ORF7a	49	L49H	cTA	cAT	2	4	B.1.617.2	0.000008
ORF7a	49	L49V	Cta	Gta	4	4	P.2	0.000747
ORF7a	49	L49L	ctA	ctG	2	3	AY.100	0.000092
ORF7a	49	L49L	Cta	Tta	1	3	AY.100	0.000046
ORF7a	49	L49I	Cta	Ata	3	3	AY.103	0.000019
ORF7a	49	L49P	cTa	cCa	3	3	AY.105	0.001929
ORF7a	49	L49del	CTA	---	3	3	AY.114	0.000693
ORF7a	49	L49del	CTA	---	3	3	AY.117	0.000254
ORF7a	49	L49L	ctA	ctG	2	3	AY.117	0.000169
ORF7a	49	L49L	Cta	Tta	1	3	AY.117	0.000085
ORF7a	49	L49L	ctA	ctG	3	3	AY.13	0.000483
ORF7a	49	L49P	cTa	cCa	3	3	AY.23	0.000209
ORF7a	49	L49E	CTa	GAa	3	3	AY.25	0.000018
ORF7a	49	L49T	CTa	ACa	2	3	AY.25	0.000012
ORF7a	49	L49T	CTA	ACC	1	3	AY.25	0.000006
ORF7a	49	L49del	CTA	---	3	3	AY.29.1	0.000662
ORF7a	49	L49L	Cta	Tta	3	3	AY.3.1	0.000256
ORF7a	49	L49P	cTa	cCa	3	3	AY.32	0.001597
ORF7a	49	L49del	CTA	---	3	3	AY.33	0.0002
ORF7a	49	L49P	cTa	cCa	3	3	AY.34.1	0.00153
ORF7a	49	L49P	cTa	cCa	3	3	AY.36	0.000445
ORF7a	49	L49V	Cta	Gta	3	3	AY.39	0.000074
ORF7a	49	L49L	ctA	ctG	3	3	AY.39.1	0.000119
ORF7a	49	L49del	CTA	---	3	3	AY.4.5	0.000322
ORF7a	49	L49del	CTA	---	3	3	AY.40	0.002893
ORF7a	49	L49L	Cta	Tta	3	3	AY.42	0.000121
ORF7a	49	L49L	ctA	ctG	1	3	AY.45	0.000122
ORF7a	49	L49L	Cta	Tta	1	3	AY.45	0.000122
ORF7a	49	L49L	ctA	ctT	1	3	AY.45	0.000122
ORF7a	49	L49del	CTA	---	3	3	AY.46	0.000312
ORF7a	49	L49L	Cta	Tta	2	3	AY.46	0.000208
ORF7a	49	L49L	ctA	ctT	1	3	AY.46	0.000104
ORF7a	49	L49L	Cta	Tta	3	3	AY.62	0.001307
ORF7a	49	L49P	cTa	cCa	3	3	AY.77	0.003382
ORF7a	49	L49del	CTA	---	3	3	AY.84	0.001312
ORF7a	49	L49P	cTa	cCa	3	3	AY.86	0.00249
ORF7a	49	L49del	CTA	---	3	3	AY.92	0.000862
ORF7a	49	L49del	CTA	---	3	3	AY.95	0.002283
ORF7a	49	L49R	cTa	cGa	3	3	B.1	0.000027
ORF7a	49	L49del	CTA	---	3	3	B.1.1.121	0.007282
ORF7a	49	L49L	ctA	ctG	1	3	B.1.1.216	0.00089
ORF7a	49	L49L	ctA	ctC	1	3	B.1.1.216	0.00089
ORF7a	49	L49L	Cta	Tta	1	3	B.1.1.216	0.00089
ORF7a	49	L49del	CTA	---	3	3	B.1.1.25	0.001706
ORF7a	49	L49F	CtA	TtT	3	3	B.1.177.21	0.000229
ORF7a	49	L49del	CTA	---	3	3	B.1.214.2	0.001799
ORF7a	49	L49del	CTA	---	3	3	B.1.427	0.000151
ORF7a	49	L49del2	cTA	c--	3	3	B.1.617.2	0.000011
ORF7a	49	L49I	Cta	Ata	3	3	B.1.617.2	0.000011
ORF7a	49	L49L	Cta	Tta	3	3	B.1.620	0.002838
ORF7a	49	L49del	CTA	---	3	3	B.1.626	0.017143
ORF7a	49	L49del	CTA	---	3	3	P.1.14	0.000143
ORF7a	49	L49L	ctA	ctG	2	3	P.1.14	0.000096
ORF7a	49	L49L	Cta	Tta	1	3	P.1.14	0.000048
ORF7a	49	L49F	CtA	TtT	2	2		0.111111
ORF7a	49	L49G	CTa	GGa	2	2		0.111111
ORF7a	49	L49del	CTA	---	2	2	A	0.000774
ORF7a	49	L49del	CTA	---	2	2	A.28	0.005291
ORF7a	49	L49D	CTA	GAT	2	2	All	0
ORF7a	49	L49G	CTa	GGa	2	2	All	0
ORF7a	49	L49del	CTA	---	2	2	AY.1	0.000791
ORF7a	49	L49del2	cTA	c--	1	2	AY.103	0.000006
ORF7a	49	L49del2	CTa	--a	1	2	AY.103	0.000006
ORF7a	49	L49L	Cta	Tta	2	2	AY.106	0.00067
ORF7a	49	L49L	Cta	Tta	2	2	AY.107	0.000932
ORF7a	49	L49del	CTA	---	2	2	AY.108	0.002205
ORF7a	49	L49del	CTA	---	2	2	AY.109	0.001479
ORF7a	49	L49P	cTa	cCa	2	2	AY.119	0.000071
ORF7a	49	L49del	CTA	---	2	2	AY.19	0.002281
ORF7a	49	L49L	ctA	ctG	2	2	AY.19	0.002281
ORF7a	49	L49L	Cta	Tta	2	2	AY.20	0.000078
ORF7a	49	L49del	CTA	---	2	2	AY.24	0.000862
ORF7a	49	L49D	CTA	GAT	2	2	AY.25	0.000012
ORF7a	49	L49C	CTA	TGT	2	2	AY.25	0.000012
ORF7a	49	L49del1	ctA	ct-	2	2	AY.25	0.000012
ORF7a	49	L49A	CTA	GCT	1	2	AY.25	0.000006
ORF7a	49	L49A	CTa	GCa	1	2	AY.25	0.000006
ORF7a	49	L49I	Cta	Ata	2	2	AY.26	0.000057
ORF7a	49	L49L	Cta	Tta	2	2	AY.30	0.000791
ORF7a	49	L49del	CTA	---	2	2	AY.34.1	0.00102
ORF7a	49	L49del	CTA	---	2	2	AY.36	0.000296
ORF7a	49	L49del1	Cta	-ta	1	2	AY.4	0.000002
ORF7a	49	L49del1	ctA	ct-	1	2	AY.4	0.000002
ORF7a	49	L49del	CTA	---	2	2	AY.4.2.1	0.000298
ORF7a	49	L49L	Cta	Tta	2	2	AY.4.5	0.000215
ORF7a	49	L49I	Cta	Ata	2	2	AY.44	0.000012
ORF7a	49	L49P	cTa	cCa	2	2	AY.46.1	0.002053
ORF7a	49	L49L	Cta	Tta	2	2	AY.46.2	0.001271
ORF7a	49	L49V	Cta	Gta	2	2	AY.46.6	0.000144
ORF7a	49	L49P	cTa	cCa	2	2	AY.47	0.000062
ORF7a	49	L49P	cTa	cCa	2	2	AY.5	0.000041
ORF7a	49	L49L	Cta	Tta	2	2	AY.53	0.000575
ORF7a	49	L49P	cTa	cCa	2	2	AY.53	0.000575
ORF7a	49	L49del	CTA	---	2	2	AY.53	0.000575
ORF7a	49	L49del	CTA	---	2	2	AY.57	0.001312
ORF7a	49	L49P	cTa	cCa	2	2	AY.68	0.000547
ORF7a	49	L49del	CTA	---	2	2	AY.7	0.000392
ORF7a	49	L49L	Cta	Tta	2	2	AY.7.1	0.000225
ORF7a	49	L49L	Cta	Tta	2	2	AY.70	0.000417
ORF7a	49	L49V	Cta	Gta	2	2	AY.71	0.00095
ORF7a	49	L49del	CTA	---	2	2	AY.71	0.00095
ORF7a	49	L49P	cTa	cCa	2	2	AY.71	0.00095
ORF7a	49	L49del	CTA	---	2	2	AY.73	0.001331
ORF7a	49	L49del2	cTA	c--	2	2	AY.75	0.000112
ORF7a	49	L49L	ctA	ctT	2	2	AY.77	0.002255
ORF7a	49	L49del	CTA	---	2	2	AY.9	0.000135
ORF7a	49	L49P	cTa	cCa	2	2	AY.9.2	0.000073
ORF7a	49	L49P	cTa	cCa	2	2	AY.92	0.000575
ORF7a	49	L49L	Cta	Tta	2	2	AY.98.1	0.000097
ORF7a	49	L49del2	CTA	--N	2	2	AY.99.2	0.000184
ORF7a	49	L49L	Cta	Tta	2	2	AY.99.2	0.000184
ORF7a	49	L49del	CTA	---	2	2	AY.99.2	0.000184
ORF7a	49	L49P	cTa	cCa	2	2	B.1	0.000018
ORF7a	49	L49Q	cTa	cAa	1	2	B.1	0.000009
ORF7a	49	L49Q	cTA	cAG	1	2	B.1	0.000009
ORF7a	49	L49V	Cta	Gta	2	2	B.1.1.189	0.003026
ORF7a	49	L49V	Cta	Gta	2	2	B.1.1.28	0.000622
ORF7a	49	L49L	Cta	Tta	1	2	B.1.1.28	0.000311
ORF7a	49	L49L	ctA	ctG	1	2	B.1.1.28	0.000311
ORF7a	49	L49del	CTA	---	2	2	B.1.1.318	0.000604
ORF7a	49	L49L	ctA	ctG	1	2	B.1.1.33	0.000421
ORF7a	49	L49L	Cta	Tta	1	2	B.1.1.33	0.000421
ORF7a	49	L49L	Cta	Tta	2	2	B.1.1.413	0.013793
ORF7a	49	L49del	CTA	---	2	2	B.1.1.519	0.000079
ORF7a	49	L49A	CTA	GCT	2	2	B.1.1.7	0.000002
ORF7a	49	L49I	Cta	Ata	2	2	B.1.1.7	0.000002
ORF7a	49	L49L	Cta	Tta	2	2	B.1.1.70	0.000682
ORF7a	49	L49L	ctA	ctG	2	2	B.1.160.25	0.022222
ORF7a	49	L49V	Cta	Gta	2	2	B.1.177	0.000026
ORF7a	49	L49P	cTa	cCa	1	2	B.1.177.21	0.000076
ORF7a	49	L49P	cTA	cCT	1	2	B.1.177.21	0.000076
ORF7a	49	L49del	CTA	---	2	2	B.1.177.43	0.002954
ORF7a	49	L49del	CTA	---	2	2	B.1.177.81	0.000379
ORF7a	49	L49del	CTA	---	2	2	B.1.177.86	0.000367
ORF7a	49	L49I	Cta	Ata	2	2	B.1.2	0.000018
ORF7a	49	L49del	CTA	---	2	2	B.1.221	0.000142
ORF7a	49	L49del	CTA	---	2	2	B.1.243	0.000139
ORF7a	49	L49del	CTA	---	2	2	B.1.258.11	0.000793
ORF7a	49	L49del1	Cta	-ta	2	2	B.1.36	0.000292
ORF7a	49	L49F	CtA	TtC	2	2	B.1.36	0.000292
ORF7a	49	L49L	ctA	ctG	1	2	B.1.36	0.000146
ORF7a	49	L49L	Cta	Tta	1	2	B.1.36	0.000146
ORF7a	49	L49del	CTA	---	2	2	B.1.375	0.001639
ORF7a	49	L49V	Cta	Gta	2	2	B.1.416	0.002538
ORF7a	49	L49del	CTA	---	2	2	B.1.575	0.000607
ORF7a	49	L49L	Cta	Tta	2	2	B.1.596	0.000174
ORF7a	49	L49T	CTA	ACC	1	2	B.1.617.2	0.000004
ORF7a	49	L49Y	CTA	TAC	1	2	B.1.617.2	0.000004
ORF7a	49	L49N	CTA	AAC	1	2	B.1.617.2	0.000004
ORF7a	49	L49N	CTA	AAT	1	2	B.1.617.2	0.000004
ORF7a	49	L49Y	CTA	TAT	1	2	B.1.617.2	0.000004
ORF7a	49	L49T	CTa	ACa	1	2	B.1.617.2	0.000004
ORF7a	49	L49del	CTA	---	2	2	B.1.617.3	0.00597
ORF7a	49	L49del	CTA	---	2	2	B.1.621.1	0.001012
ORF7a	49	L49L	Cta	Tta	1	2	B.1.637	0.000073
ORF7a	49	L49L	ctA	ctG	1	2	B.1.637	0.000073
ORF7a	49	L49del	CTA	---	2	2	C.36.3	0.001134
ORF7a	49	L49L	Cta	Tta	2	2	P.1.15	0.000465
ORF7a	49	L49V	Cta	Gta	2	2	P.1.17	0.000324
ORF7a	49	L49L	Cta	Tta	2	2	P.1.4	0.001953
ORF7a	49	L49del	CTA	---	2	2	P.2	0.000373
ORF7a	49	L49L	ctA	ctG	1	1	A.1	0.000282
ORF7a	49	L49del	CTA	---	1	1	A.1	0.000282
ORF7a	49	L49del	CTA	---	1	1	A.23.1	0.000704
ORF7a	49	L49I	Cta	Ata	1	1	A.29	0.005319
ORF7a	49	L49L	ctA	ctT	1	1	A.3	0.002096
ORF7a	49	L49L	Cta	Tta	1	1	AD.2	0.000219
ORF7a	49	L49M	CtA	AtG	1	1	All	0
ORF7a	49	L49P	cTa	cCa	1	1	AY.10	0.00053
ORF7a	49	L49P	cTa	cCa	1	1	AY.100	0.000046
ORF7a	49	L49del	CTA	---	1	1	AY.101	0.00049
ORF7a	49	L49V	Cta	Gta	1	1	AY.102	0.000027
ORF7a	49	L49del2	cTA	c--	1	1	AY.102	0.000027
ORF7a	49	L49L	Cta	Tta	1	1	AY.105	0.000643
ORF7a	49	L49I	Cta	Ata	1	1	AY.105	0.000643
ORF7a	49	L49L	Cta	Tta	1	1	AY.109	0.00074
ORF7a	49	L49P	cTa	cCa	1	1	AY.110	0.000113
ORF7a	49	L49L	Cta	Tta	1	1	AY.113	0.000142
ORF7a	49	L49P	cTa	cCa	1	1	AY.114	0.000231
ORF7a	49	L49del	CTA	---	1	1	AY.116.1	0.000311
ORF7a	49	L49P	cTa	cCa	1	1	AY.118	0.000063
ORF7a	49	L49C	CTA	TGC	1	1	AY.119	0.000035
ORF7a	49	L49del2	cTA	c--	1	1	AY.120	0.000037
ORF7a	49	L49L	Cta	Tta	1	1	AY.120.2	0.001285
ORF7a	49	L49L	Cta	Tta	1	1	AY.121	0.000135
ORF7a	49	L49del	CTA	---	1	1	AY.13	0.000161
ORF7a	49	L49del	CTA	---	1	1	AY.16	0.00038
ORF7a	49	L49P	cTa	cCa	1	1	AY.19	0.00114
ORF7a	49	L49L	Cta	Tta	1	1	AY.2	0.000356
ORF7a	49	L49del	CTA	---	1	1	AY.22	0.002092
ORF7a	49	L49V	Cta	Gta	1	1	AY.23	0.00007
ORF7a	49	L49P	cTa	cCa	1	1	AY.23.1	0.000417
ORF7a	49	L49M	CtA	AtG	1	1	AY.25	0.000006
ORF7a	49	L49F	CtA	TtC	1	1	AY.26	0.000028
ORF7a	49	L49Q	cTa	cAa	1	1	AY.29	0.000016
ORF7a	49	L49L	ctA	ctT	1	1	AY.29.1	0.000221
ORF7a	49	L49I	Cta	Ata	1	1	AY.3	0.00001
ORF7a	49	L49V	CtA	GtT	1	1	AY.3.1	0.000085
ORF7a	49	L49L	ctA	ctG	1	1	AY.32	0.000532
ORF7a	49	L49P	cTa	cCa	1	1	AY.34	0.000097
ORF7a	49	L49del2	CTA	--N	1	1	AY.36	0.000148
ORF7a	49	L49L	Cta	Tta	1	1	AY.37	0.000316
ORF7a	49	L49del	CTA	---	1	1	AY.38	0.000499
ORF7a	49	L49del1	ctA	ct-	1	1	AY.39	0.000025
ORF7a	49	L49V	Cta	Gta	1	1	AY.4	0.000002
ORF7a	49	L49R	cTa	cGa	1	1	AY.4.2	0.000022
ORF7a	49	L49I	Cta	Ata	1	1	AY.4.2	0.000022
ORF7a	49	L49L	Cta	Tta	1	1	AY.4.2.1	0.000149
ORF7a	49	L49P	cTa	cCa	1	1	AY.4.2.1	0.000149
ORF7a	49	L49P	cTa	cCa	1	1	AY.42	0.00004
ORF7a	49	L49R	cTA	cGG	1	1	AY.43	0.000004
ORF7a	49	L49I	Cta	Ata	1	1	AY.43	0.000004
ORF7a	49	L49F	CtA	TtT	1	1	AY.43	0.000004
ORF7a	49	L49V	Cta	Gta	1	1	AY.44	0.000006
ORF7a	49	L49L	Cta	Tta	1	1	AY.46.3	0.000934
ORF7a	49	L49I	Cta	Ata	1	1	AY.47	0.000031
ORF7a	49	L49del2	CTA	--T	1	1	AY.47	0.000031
ORF7a	49	L49P	cTa	cCa	1	1	AY.48	0.000465
ORF7a	49	L49P	cTa	cCa	1	1	AY.5.3	0.000337
ORF7a	49	L49del	CTA	---	1	1	AY.5.3	0.000337
ORF7a	49	L49del	CTA	---	1	1	AY.5.4	0.000277
ORF7a	49	L49L	Cta	Tta	1	1	AY.54	0.000095
ORF7a	49	L49del2	cTA	c--	1	1	AY.54	0.000095
ORF7a	49	L49S	CTa	TCa	1	1	AY.54	0.000095
ORF7a	49	L49P	cTa	cCa	1	1	AY.56	0.001605
ORF7a	49	L49I	Cta	Ata	1	1	AY.57	0.000656
ORF7a	49	L49P	cTa	cCa	1	1	AY.58	0.000907
ORF7a	49	L49P	cTa	cCa	1	1	AY.59	0.00053
ORF7a	49	L49del	CTA	---	1	1	AY.59	0.00053
ORF7a	49	L49V	Cta	Gta	1	1	AY.59	0.00053
ORF7a	49	L49P	cTa	cCa	1	1	AY.6	0.000041
ORF7a	49	L49del	CTA	---	1	1	AY.62	0.000436
ORF7a	49	L49P	cTa	cCa	1	1	AY.63	0.000387
ORF7a	49	L49del	CTA	---	1	1	AY.65	0.000533
ORF7a	49	L49L	Cta	Tta	1	1	AY.67	0.000464
ORF7a	49	L49I	Cta	Ata	1	1	AY.7	0.000196
ORF7a	49	L49P	cTa	cCa	1	1	AY.7	0.000196
ORF7a	49	L49del	CTA	---	1	1	AY.7.1	0.000113
ORF7a	49	L49P	cTa	cCa	1	1	AY.7.1	0.000113
ORF7a	49	L49P	cTa	cCa	1	1	AY.70	0.000209
ORF7a	49	L49P	cTa	cCa	1	1	AY.74	0.000116
ORF7a	49	L49L	Cta	Tta	1	1	AY.74	0.000116
ORF7a	49	L49I	Cta	Ata	1	1	AY.75	0.000056
ORF7a	49	L49P	cTa	cCa	1	1	AY.75	0.000056
ORF7a	49	L49L	ctA	ctG	1	1	AY.78	0.001541
ORF7a	49	L49del	CTA	---	1	1	AY.79	0.001211
ORF7a	49	L49del	CTA	---	1	1	AY.8	0.000606
ORF7a	49	L49del	CTA	---	1	1	AY.81	0.001992
ORF7a	49	L49del	CTA	---	1	1	AY.82	0.001357
ORF7a	49	L49P	cTa	cCa	1	1	AY.82	0.001357
ORF7a	49	L49P	cTa	cCa	1	1	AY.87	0.000833
ORF7a	49	L49P	cTa	cCa	1	1	AY.88	0.000884
ORF7a	49	L49del	CTA	---	1	1	AY.89	0.004902
ORF7a	49	L49I	Cta	Ata	1	1	AY.9	0.000068
ORF7a	49	L49P	cTa	cCa	1	1	AY.9.1	0.000084
ORF7a	49	L49L	Cta	Tta	1	1	AY.90	0.000684
ORF7a	49	L49del	CTA	---	1	1	AY.90	0.000684
ORF7a	49	L49P	cTa	cCa	1	1	AY.91	0.00073
ORF7a	49	L49del2	cTA	c--	1	1	AY.91	0.00073
ORF7a	49	L49L	Cta	Tta	1	1	AY.92	0.000287
ORF7a	49	L49del1	Cta	-ta	1	1	AY.92	0.000287
ORF7a	49	L49L	Cta	Tta	1	1	AY.93	0.000273
ORF7a	49	L49del	CTA	---	1	1	AY.94	0.000443
ORF7a	49	L49P	cTa	cCa	1	1	AY.96	0.002075
ORF7a	49	L49L	Cta	Tta	1	1	AY.98	0.000079
ORF7a	49	L49P	cTa	cCa	1	1	AY.98.1	0.000048
ORF7a	49	L49del	CTA	---	1	1	AZ.2	0.000821
ORF7a	49	L49del	CTA	---	1	1	B	0.000128
ORF7a	49	L49L	Cta	Tta	1	1	B.1.1.1	0.000327
ORF7a	49	L49L	Cta	Tta	1	1	B.1.1.117	0.009709
ORF7a	49	L49del	CTA	---	1	1	B.1.1.157	0.000913
ORF7a	49	L49L	Cta	Tta	1	1	B.1.1.174	0.003378
ORF7a	49	L49del	CTA	---	1	1	B.1.1.174	0.003378
ORF7a	49	L49del	CTA	---	1	1	B.1.1.192	0.002309
ORF7a	49	L49L	Cta	Tta	1	1	B.1.1.192	0.002309
ORF7a	49	L49L	Cta	Tta	1	1	B.1.1.222	0.000204
ORF7a	49	L49V	Cta	Gta	1	1	B.1.1.282	0.011628
ORF7a	49	L49L	Cta	Tta	1	1	B.1.1.311	0.000358
ORF7a	49	L49L	Cta	Tta	1	1	B.1.1.318	0.000302
ORF7a	49	L49del	CTA	---	1	1	B.1.1.33	0.000421
ORF7a	49	L49L	ctA	ctG	1	1	B.1.1.348	0.000796
ORF7a	49	L49V	Cta	Gta	1	1	B.1.1.411	0.014706
ORF7a	49	L49L	ctA	ctG	1	1	B.1.1.50	0.000679
ORF7a	49	L49I	Cta	Ata	1	1	B.1.1.519	0.00004
ORF7a	49	L49C	CTA	TGT	1	1	B.1.1.7	0.000001
ORF7a	49	L49del1	cTA	cC-	1	1	B.1.1.70	0.000341
ORF7a	49	L49L	Cta	Tta	1	1	B.1.1.89	0.006061
ORF7a	49	L49del	CTA	---	1	1	B.1.115	0.021739
ORF7a	49	L49del	CTA	---	1	1	B.1.140	0.018868
ORF7a	49	L49K	CTa	AAa	1	1	B.1.177	0.000013
ORF7a	49	L49P	cTa	cCa	1	1	B.1.177	0.000013
ORF7a	49	L49C	CTA	TGT	1	1	B.1.177	0.000013
ORF7a	49	L49del	CTA	---	1	1	B.1.177.10	0.000878
ORF7a	49	L49I	Cta	Ata	1	1	B.1.177.21	0.000076
ORF7a	49	L49Q	cTa	cAa	1	1	B.1.177.21	0.000076
ORF7a	49	L49P	cTa	cCa	1	1	B.1.177.44	0.000519
ORF7a	49	L49del	CTA	---	1	1	B.1.177.5	0.001242
ORF7a	49	L49del	CTA	---	1	1	B.1.177.50	0.004695
ORF7a	49	L49del	CTA	---	1	1	B.1.177.62	0.001192
ORF7a	49	L49S	CTa	TCa	1	1	B.1.177.63	0.002703
ORF7a	49	L49del	CTA	---	1	1	B.1.177.83	0.001481
ORF7a	49	L49L	Cta	Tta	1	1	B.1.177.86	0.000183
ORF7a	49	L49Q	cTa	cAa	1	1	B.1.2	0.000009
ORF7a	49	L49P	cTa	cCa	1	1	B.1.2	0.000009
ORF7a	49	L49V	Cta	Gta	1	1	B.1.2	0.000009
ORF7a	49	L49del2	CTA	--N	1	1	B.1.2	0.000009
ORF7a	49	L49L	ctA	ctG	1	1	B.1.222	0.001692
ORF7a	49	L49V	Cta	Gta	1	1	B.1.234	0.000132
ORF7a	49	L49del	CTA	---	1	1	B.1.240	0.000216
ORF7a	49	L49L	Cta	Tta	1	1	B.1.241	0.000812
ORF7a	49	L49I	Cta	Ata	1	1	B.1.258	0.000067
ORF7a	49	L49I	Cta	Ata	1	1	B.1.258.17	0.000104
ORF7a	49	L49del	CTA	---	1	1	B.1.258.17	0.000104
ORF7a	49	L49P	cTa	cCa	1	1	B.1.258.17	0.000104
ORF7a	49	L49V	Cta	Gta	1	1	B.1.258.20	0.015873
ORF7a	49	L49L	Cta	Tta	1	1	B.1.258.9	0.005
ORF7a	49	L49L	Cta	Tta	1	1	B.1.298	0.002114
ORF7a	49	L49E	CTa	GAa	1	1	B.1.351	0.00003
ORF7a	49	L49Q	cTa	cAa	1	1	B.1.351	0.00003
ORF7a	49	L49del	CTA	---	1	1	B.1.351.2	0.000303
ORF7a	49	L49del	CTA	---	1	1	B.1.356	0.001727
ORF7a	49	L49L	ctA	ctG	1	1	B.1.36.29	0.000517
ORF7a	49	L49P	cTa	cCa	1	1	B.1.370	0.008
ORF7a	49	L49del	CTA	---	1	1	B.1.371	0.001122
ORF7a	49	L49L	Cta	Tta	1	1	B.1.389	0.001002
ORF7a	49	L49del	CTA	---	1	1	B.1.416	0.001269
ORF7a	49	L49del	CTA	---	1	1	B.1.416.1	0.001563
ORF7a	49	L49P	cTa	cCa	1	1	B.1.416.1	0.001563
ORF7a	49	L49L	Cta	Tta	1	1	B.1.416.1	0.001563
ORF7a	49	L49I	Cta	Ata	1	1	B.1.427	0.00005
ORF7a	49	L49del	CTA	---	1	1	B.1.438.1	0.000107
ORF7a	49	L49del	CTA	---	1	1	B.1.459	0.004082
ORF7a	49	L49del	CTA	---	1	1	B.1.466.2	0.000391
ORF7a	49	L49F	CtA	TtC	1	1	B.1.468	0.005714
ORF7a	49	L49del	CTA	---	1	1	B.1.470	0.001404
ORF7a	49	L49L	Cta	Tta	1	1	B.1.499	0.00105
ORF7a	49	L49del1	Cta	-ta	1	1	B.1.525	0.000113
ORF7a	49	L49L	ctA	ctG	1	1	B.1.525	0.000113
ORF7a	49	L49P	cTa	cCa	1	1	B.1.526	0.000024
ORF7a	49	L49del	CTA	---	1	1	B.1.535	0.028571
ORF7a	49	L49del	CTA	---	1	1	B.1.568	0.001111
ORF7a	49	L49L	Cta	Tta	1	1	B.1.575.1	0.002439
ORF7a	49	L49del	CTA	---	1	1	B.1.576	0.000907
ORF7a	49	L49del1	ctA	ct-	1	1	B.1.576	0.000907
ORF7a	49	L49del	CTA	---	1	1	B.1.582	0.000491
ORF7a	49	L49del	CTA	---	1	1	B.1.595	0.000261
ORF7a	49	L49I	CtA	AtT	1	1	B.1.617.1	0.000129
ORF7a	49	L49S	CTa	TCa	1	1	B.1.617.1	0.000129
ORF7a	49	L49del1	ctA	ct-	1	1	B.1.621	0.000089
ORF7a	49	L49L	Cta	Tta	1	1	B.1.621	0.000089
ORF7a	49	L49R	cTa	cGa	1	1	B.1.637	0.000073
ORF7a	49	L49I	Cta	Ata	1	1	B.1.637	0.000073
ORF7a	49	L49V	Cta	Gta	1	1	B.1.637	0.000073
ORF7a	49	L49del	CTA	---	1	1	B.1.638	0.052632
ORF7a	49	L49del	CTA	---	1	1	B.1.9.1	0.032258
ORF7a	49	L49del	CTA	---	1	1	B.55	0.00295
ORF7a	49	L49L	Cta	Tta	1	1	C.36	0.000911
ORF7a	49	L49V	Cta	Gta	1	1	C.36.3	0.000567
ORF7a	49	L49P	cTa	cCa	1	1	D.2	0.000075
ORF7a	49	L49del	CTA	---	1	1	K.3	0.006173
ORF7a	49	L49del2	CTA	--N	1	1	P.1	0.000016
ORF7a	49	L49del1	ctA	ct-	1	1	P.1	0.000016
ORF7a	49	L49del	CTA	---	1	1	P.1.1	0.000318
ORF7a	49	L49L	Cta	Tta	1	1	P.1.11	0.010204
ORF7a	49	L49V	Cta	Gta	1	1	P.1.12	0.000484
ORF7a	49	L49del	CTA	---	1	1	P.1.13	0.000898
ORF7a	49	L49L	ctA	ctG	1	1	P.1.16	0.000374
ORF7a	49	L49del	CTA	---	1	1	P.1.16	0.000374
ORF7a	49	L49L	Cta	Tta	1	1	P.1.17	0.000162
ORF7a	49	L49del	CTA	---	1	1	P.1.3	0.034483
ORF7a	49	L49del	CTA	---	1	1	P.1.4	0.000977
ORF7a	49	L49del	CTA	---	1	1	Q.7	0.001111
ORF7a	49	L49L	Cta	Tta	1	1	Q.8	0.000165
ORF7a	49	L49P	cTa	cCa	1	1	R.1	0.00009

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.