CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF3a : CodonNum = 46

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
ORF3a	46	L46F		nonsyn	Ctt	Ttt	2420	2420	1	25528-25530
ORF3a	46	L46del		del	CTT	---	871	871	1	25528-25530
ORF3a	46	L46I		nonsyn	Ctt	Att	328	327	0.996951	25528-25530
ORF3a	46	L46I		nonsyn	CtT	AtA	328	1	0.00304878	25528-25530
ORF3a	46	L46L		syn	ctT	ctC	228	207	0.907895	25528-25530
ORF3a	46	L46L		syn	ctT	ctA	228	16	0.0701754	25528-25530
ORF3a	46	L46L		syn	ctT	ctG	228	5	0.0219298	25528-25530
ORF3a	46	L46V		nonsyn	Ctt	Gtt	94	94	1	25528-25530
ORF3a	46	L46P		nonsyn	cTt	cCt	65	63	0.969231	25528-25530
ORF3a	46	L46P		nonsyn	cTT	cCC	65	2	0.0307692	25528-25530
ORF3a	46	L46H		nonsyn	cTt	cAt	53	53	1	25528-25530
ORF3a	46	L46R		nonsyn	cTt	cGt	14	14	1	25528-25530
ORF3a	46	L46C		nonsyn	CTt	TGt	12	12	1	25528-25530
ORF3a	46	L46del1		del	CtT	-tA	10	4	0.4	25528-25530
ORF3a	46	L46del1		del	cTT	c-N	10	2	0.2	25528-25530
ORF3a	46	L46del1		del	cTt	c-t	10	2	0.2	25528-25530
ORF3a	46	L46del1		del	CTT	-NN	10	1	0.1	25528-25530
ORF3a	46	L46del1		del	CtT	Tt-	10	1	0.1	25528-25530
ORF3a	46	L46del2		del	cTT	c--	6	2	0.333333	25528-25530
ORF3a	46	L46del2		del	CTt	--t	6	2	0.333333	25528-25530
ORF3a	46	L46del2		del	CTT	--A	6	1	0.166667	25528-25530
ORF3a	46	L46del2		del	CTT	--N	6	1	0.166667	25528-25530
ORF3a	46	L46N		nonsyn	CTt	AAt	2	2	1	25528-25530
ORF3a	46	L46Y		nonsyn	CTt	TAt	2	2	1	25528-25530

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
ORF3a	46	L46F	Ctt	Ttt	2420	2420	All	0.000463
ORF3a	46	L46del	CTT	---	871	871	All	0.000167
ORF3a	46	L46F	Ctt	Ttt	552	552	B.1.1.326	0.971831
ORF3a	46	L46I	Ctt	Att	327	328	All	0.000063
ORF3a	46	L46I	CtT	AtA	1	328	All	0
ORF3a	46	L46F	Ctt	Ttt	317	317	B.1.2	0.002791
ORF3a	46	L46F	Ctt	Ttt	277	277	B.1.1.8	0.992832
ORF3a	46	L46L	ctT	ctC	207	228	All	0.00004
ORF3a	46	L46L	ctT	ctA	16	228	All	0.000003
ORF3a	46	L46L	ctT	ctG	5	228	All	0.000001
ORF3a	46	L46del	CTT	---	187	187	AY.26	0.005294
ORF3a	46	L46I	Ctt	Att	171	171	B.1.1.397	0.385135
ORF3a	46	L46L	ctT	ctC	139	153	B.1.1.7	0.000124
ORF3a	46	L46L	ctT	ctA	12	153	B.1.1.7	0.000011
ORF3a	46	L46L	ctT	ctG	2	153	B.1.1.7	0.000002
ORF3a	46	L46del	CTT	---	153	153	B.1.630	0.801047
ORF3a	46	L46F	Ctt	Ttt	134	134	B.1.617.2	0.000505
ORF3a	46	L46F	Ctt	Ttt	130	130	B.1.1.7	0.000116
ORF3a	46	L46F	Ctt	Ttt	96	96	AY.44	0.000584
ORF3a	46	L46V	Ctt	Gtt	94	94	All	0.000018
ORF3a	46	L46I	Ctt	Att	88	88	AY.4	0.000137
ORF3a	46	L46F	Ctt	Ttt	82	82	AY.25	0.000493
ORF3a	46	L46F	Ctt	Ttt	79	79	AY.4	0.000123
ORF3a	46	L46del	CTT	---	78	78	AY.75	0.00437
ORF3a	46	L46V	Ctt	Gtt	77	77	B.1.1.176	0.033831
ORF3a	46	L46F	Ctt	Ttt	77	77	B.1.1.519	0.003058
ORF3a	46	L46P	cTt	cCt	63	65	All	0.000012
ORF3a	46	L46P	cTT	cCC	2	65	All	0
ORF3a	46	L46H	cTt	cAt	53	53	All	0.00001
ORF3a	46	L46F	Ctt	Ttt	50	50	AY.102	0.001326
ORF3a	46	L46F	Ctt	Ttt	48	48	B.1.429	0.001129
ORF3a	46	L46F	Ctt	Ttt	45	45	P.1	0.000709
ORF3a	46	L46del	CTT	---	39	39	AY.4	0.000061
ORF3a	46	L46F	Ctt	Ttt	39	39	B.1.1.93	1
ORF3a	46	L46F	Ctt	Ttt	39	39	B.1.537	0.78
ORF3a	46	L46F	Ctt	Ttt	38	38	AY.43	0.000168
ORF3a	46	L46del	CTT	---	38	38	B.1.1.7	0.000034
ORF3a	46	L46H	cTt	cAt	37	37	AY.3	0.000368
ORF3a	46	L46del	CTT	---	36	36	B.1.177	0.000474
ORF3a	46	L46F	Ctt	Ttt	35	35	AY.119	0.001236
ORF3a	46	L46del	CTT	---	35	35	AY.43	0.000155
ORF3a	46	L46F	Ctt	Ttt	33	33	B.1.525	0.003734
ORF3a	46	L46del	CTT	---	29	29	AY.25	0.000174
ORF3a	46	L46F	Ctt	Ttt	26	26	B.1	0.000238
ORF3a	46	L46F	Ctt	Ttt	25	25	AY.3.1	0.002131
ORF3a	46	L46del	CTT	---	23	23	B.1.1	0.000417
ORF3a	46	L46del	CTT	---	20	20	B.1.526	0.00047
ORF3a	46	L46F	Ctt	Ttt	20	20	B.1.595	0.005219
ORF3a	46	L46F	Ctt	Ttt	18	18	AY.100	0.000828
ORF3a	46	L46F	Ctt	Ttt	18	18	AY.5	0.000372
ORF3a	46	L46del	CTT	---	17	17	AY.3	0.000169
ORF3a	46	L46F	Ctt	Ttt	16	16	AY.26	0.000453
ORF3a	46	L46I	Ctt	Att	16	16	AY.4.5	0.00172
ORF3a	46	L46F	Ctt	Ttt	15	15	AY.3	0.000149
ORF3a	46	L46F	Ctt	Ttt	15	15	AY.39	0.000371
ORF3a	46	L46del	CTT	---	15	15	B.1.617.2	0.000056
ORF3a	46	L46R	cTt	cGt	14	14	All	0.000003
ORF3a	46	L46F	Ctt	Ttt	14	14	AY.120	0.000521
ORF3a	46	L46F	Ctt	Ttt	13	13	AY.24	0.005603
ORF3a	46	L46P	cTt	cCt	13	13	B.1.1.7	0.000012
ORF3a	46	L46C	CTt	TGt	12	12	All	0.000002
ORF3a	46	L46P	cTt	cCt	12	12	B.1.1.406	0.077922
ORF3a	46	L46V	Ctt	Gtt	12	12	B.1.369	0.003423
ORF3a	46	L46del1	CtT	-tA	4	10	All	0.000001
ORF3a	46	L46del1	cTt	c-t	2	10	All	0
ORF3a	46	L46del1	cTT	c-N	2	10	All	0
ORF3a	46	L46del1	CTT	-NN	1	10	All	0
ORF3a	46	L46del1	CtT	Tt-	1	10	All	0
ORF3a	46	L46del	CTT	---	10	10	AY.103	0.000062
ORF3a	46	L46del	CTT	---	10	10	AY.44	0.000061
ORF3a	46	L46F	Ctt	Ttt	10	10	B.1.1	0.000181
ORF3a	46	L46L	ctT	ctC	7	9	AY.4	0.000011
ORF3a	46	L46L	ctT	ctA	1	9	AY.4	0.000002
ORF3a	46	L46L	ctT	ctG	1	9	AY.4	0.000002
ORF3a	46	L46del	CTT	---	9	9	B.1.1.274	0.045455
ORF3a	46	L46F	Ctt	Ttt	9	9	B.1.177	0.000119
ORF3a	46	L46del	CTT	---	9	9	B.1.258	0.000599
ORF3a	46	L46del	CTT	---	8	8	AY.39	0.000198
ORF3a	46	L46F	Ctt	Ttt	7	7	AY.103	0.000043
ORF3a	46	L46L	ctT	ctC	7	7	AY.43	0.000031
ORF3a	46	L46F	Ctt	Ttt	7	7	B.1.596	0.00061
ORF3a	46	L46del2	CTt	--t	2	6	All	0
ORF3a	46	L46del2	cTT	c--	2	6	All	0
ORF3a	46	L46del2	CTT	--A	1	6	All	0
ORF3a	46	L46del2	CTT	--N	1	6	All	0
ORF3a	46	L46del	CTT	---	6	6	AY.5	0.000124
ORF3a	46	L46del	CTT	---	6	6	B.1	0.000055
ORF3a	46	L46L	ctT	ctC	4	6	B.1	0.000037
ORF3a	46	L46L	ctT	ctA	1	6	B.1	0.000009
ORF3a	46	L46L	ctT	ctG	1	6	B.1	0.000009
ORF3a	46	L46del	CTT	---	6	6	B.1.160	0.000187
ORF3a	46	L46H	cTt	cAt	6	6	B.1.258.17	0.000624
ORF3a	46	L46P	cTt	cCt	5	5	AY.103	0.000031
ORF3a	46	L46del1	CtT	-tA	4	5	AY.26	0.000113
ORF3a	46	L46del1	CTT	-NN	1	5	AY.26	0.000028
ORF3a	46	L46I	Ctt	Att	5	5	B.1	0.000046
ORF3a	46	L46P	cTt	cCt	4	5	B.1.177	0.000053
ORF3a	46	L46P	cTT	cCC	1	5	B.1.177	0.000013
ORF3a	46	L46L	ctT	ctC	5	5	B.1.240	0.001078
ORF3a	46	L46del	CTT	---	5	5	B.1.438.1	0.000536
ORF3a	46	L46F	Ctt	Ttt	5	5	B.1.438.1	0.000536
ORF3a	46	L46L	ctT	ctC	4	4	AY.26	0.000113
ORF3a	46	L46P	cTt	cCt	4	4	AY.4	0.000006
ORF3a	46	L46del	CTT	---	4	4	AY.4.5	0.00043
ORF3a	46	L46L	ctT	ctC	4	4	AY.46.6	0.000289
ORF3a	46	L46I	Ctt	Att	4	4	AY.8	0.002424
ORF3a	46	L46I	Ctt	Att	4	4	AY.9	0.00027
ORF3a	46	L46del	CTT	---	4	4	AY.9.1	0.000335
ORF3a	46	L46P	cTt	cCt	4	4	B.1	0.000037
ORF3a	46	L46I	Ctt	Att	4	4	B.1.1.519	0.000159
ORF3a	46	L46I	Ctt	Att	4	4	B.1.1.7	0.000004
ORF3a	46	L46F	Ctt	Ttt	4	4	B.1.206	0.003263
ORF3a	46	L46P	cTt	cCt	3	4	B.1.221	0.000213
ORF3a	46	L46P	cTT	cCC	1	4	B.1.221	0.000071
ORF3a	46	L46F	Ctt	Ttt	4	4	B.1.340	0.017167
ORF3a	46	L46F	Ctt	Ttt	4	4	B.1.36.8	0.004
ORF3a	46	L46F	Ctt	Ttt	4	4	B.1.526	0.000094
ORF3a	46	L46F	Ctt	Ttt	4	4	B.1.617.1	0.000516
ORF3a	46	L46L	ctT	ctC	4	4	B.1.617.2	0.000015
ORF3a	46	L46del	CTT	---	4	4	P.1.9	0.019231
ORF3a	46	L46F	Ctt	Ttt	3	3	AY.110	0.000338
ORF3a	46	L46I	Ctt	Att	3	3	AY.13	0.000483
ORF3a	46	L46F	Ctt	Ttt	3	3	AY.13	0.000483
ORF3a	46	L46del	CTT	---	3	3	AY.39.1	0.000119
ORF3a	46	L46del	CTT	---	3	3	AY.4.2	0.000065
ORF3a	46	L46L	ctT	ctC	3	3	AY.42	0.000121
ORF3a	46	L46F	Ctt	Ttt	3	3	AY.42	0.000121
ORF3a	46	L46del	CTT	---	3	3	AY.45	0.000365
ORF3a	46	L46I	Ctt	Att	3	3	AY.69	0.00056
ORF3a	46	L46del	CTT	---	3	3	AY.74	0.000347
ORF3a	46	L46P	cTt	cCt	3	3	AY.9.2	0.00011
ORF3a	46	L46del	CTT	---	3	3	AY.98	0.000237
ORF3a	46	L46L	ctT	ctC	3	3	B.1.1	0.000054
ORF3a	46	L46F	Ctt	Ttt	3	3	B.1.1.222	0.000612
ORF3a	46	L46del	CTT	---	3	3	B.1.160.24	0.013274
ORF3a	46	L46F	Ctt	Ttt	3	3	B.1.177.2	0.013636
ORF3a	46	L46F	Ctt	Ttt	3	3	B.1.234	0.000396
ORF3a	46	L46del	CTT	---	3	3	B.1.36.17	0.001482
ORF3a	46	L46F	Ctt	Ttt	3	3	B.1.427	0.000151
ORF3a	46	L46I	Ctt	Att	3	3	B.1.617.2	0.000011
ORF3a	46	L46F	Ctt	Ttt	3	3	B.1.621	0.000266
ORF3a	46	L46del	CTT	---	3	3	B.1.637	0.000219
ORF3a	46	L46L	ctT	ctC	3	3	P.1	0.000047
ORF3a	46	L46F	Ctt	Ttt	3	3	Q.3	0.000435
ORF3a	46	L46del	CTT	---	3	3	U.3	0.011583
ORF3a	46	L46H	cTt	cAt	2	2		0.111111
ORF3a	46	L46N	CTt	AAt	2	2		0.111111
ORF3a	46	L46Y	CTt	TAt	2	2		0.111111
ORF3a	46	L46I	Ctt	Att	2	2		0.111111
ORF3a	46	L46Y	CTt	TAt	2	2	All	0
ORF3a	46	L46N	CTt	AAt	2	2	All	0
ORF3a	46	L46del	CTT	---	2	2	AY.100	0.000092
ORF3a	46	L46L	ctT	ctC	2	2	AY.103	0.000012
ORF3a	46	L46H	cTt	cAt	2	2	AY.103	0.000012
ORF3a	46	L46del	CTT	---	2	2	AY.113	0.000285
ORF3a	46	L46del	CTT	---	2	2	AY.118	0.000125
ORF3a	46	L46del	CTT	---	2	2	AY.119	0.000071
ORF3a	46	L46del	CTT	---	2	2	AY.120	0.000074
ORF3a	46	L46F	Ctt	Ttt	2	2	AY.14	0.000176
ORF3a	46	L46P	cTt	cCt	2	2	AY.20	0.000078
ORF3a	46	L46P	cTt	cCt	2	2	AY.25	0.000012
ORF3a	46	L46L	ctT	ctC	2	2	AY.25	0.000012
ORF3a	46	L46del	CTT	---	2	2	AY.29	0.000032
ORF3a	46	L46F	Ctt	Ttt	2	2	AY.29	0.000032
ORF3a	46	L46del	CTT	---	2	2	AY.33	0.000134
ORF3a	46	L46F	Ctt	Ttt	2	2	AY.34	0.000194
ORF3a	46	L46del	CTT	---	2	2	AY.34	0.000194
ORF3a	46	L46F	Ctt	Ttt	2	2	AY.38	0.000999
ORF3a	46	L46del2	cTT	c--	1	2	AY.4	0.000002
ORF3a	46	L46del2	CTt	--t	1	2	AY.4	0.000002
ORF3a	46	L46V	Ctt	Gtt	2	2	AY.43	0.000009
ORF3a	46	L46F	Ctt	Ttt	2	2	AY.45	0.000243
ORF3a	46	L46del	CTT	---	2	2	AY.46.2	0.001271
ORF3a	46	L46F	Ctt	Ttt	2	2	AY.46.5	0.000397
ORF3a	46	L46del	CTT	---	2	2	AY.54	0.000191
ORF3a	46	L46del	CTT	---	2	2	AY.6	0.000082
ORF3a	46	L46del	CTT	---	2	2	AY.67	0.000929
ORF3a	46	L46F	Ctt	Ttt	2	2	AY.73	0.001331
ORF3a	46	L46F	Ctt	Ttt	2	2	AY.75	0.000112
ORF3a	46	L46del	CTT	---	2	2	AY.81	0.003984
ORF3a	46	L46L	ctT	ctC	2	2	AY.85	0.000854
ORF3a	46	L46F	Ctt	Ttt	2	2	AY.9.2	0.000073
ORF3a	46	L46F	Ctt	Ttt	2	2	AY.93	0.000546
ORF3a	46	L46F	Ctt	Ttt	2	2	AY.98.1	0.000097
ORF3a	46	L46C	CTt	TGt	2	2	B.1	0.000018
ORF3a	46	L46R	cTt	cGt	2	2	B.1	0.000018
ORF3a	46	L46I	Ctt	Att	2	2	B.1.1.129	0.018349
ORF3a	46	L46C	CTt	TGt	2	2	B.1.1.291	0.001485
ORF3a	46	L46R	cTt	cGt	2	2	B.1.1.291	0.001485
ORF3a	46	L46I	Ctt	Att	2	2	B.1.1.437	0.020833
ORF3a	46	L46del	CTT	---	2	2	B.1.1.464	0.002946
ORF3a	46	L46del	CTT	---	2	2	B.1.1.519	0.000079
ORF3a	46	L46H	cTt	cAt	2	2	B.1.1.7	0.000002
ORF3a	46	L46F	Ctt	Ttt	2	2	B.1.160	0.000062
ORF3a	46	L46del	CTT	---	2	2	B.1.160.33	0.00885
ORF3a	46	L46C	CTt	TGt	2	2	B.1.169	0.029851
ORF3a	46	L46del	CTT	---	2	2	B.1.2	0.000018
ORF3a	46	L46C	CTt	TGt	2	2	B.1.2	0.000018
ORF3a	46	L46del	CTT	---	2	2	B.1.221	0.000142
ORF3a	46	L46del	CTT	---	2	2	B.1.36.38	0.003284
ORF3a	46	L46del	CTT	---	2	2	B.1.427	0.000101
ORF3a	46	L46del	CTT	---	2	2	B.1.429	0.000047
ORF3a	46	L46F	Ctt	Ttt	2	2	B.1.521	0.00995
ORF3a	46	L46del	CTT	---	2	2	B.1.525	0.000226
ORF3a	46	L46del	CTT	---	2	2	B.1.537	0.04
ORF3a	46	L46F	Ctt	Ttt	2	2	B.1.581	0.018868
ORF3a	46	L46F	Ctt	Ttt	2	2	B.1.609	0.000959
ORF3a	46	L46L	ctT	ctC	2	2	B.1.621	0.000177
ORF3a	46	L46del	CTT	---	2	2	B.1.621	0.000177
ORF3a	46	L46F	Ctt	Ttt	2	2	D.2	0.00015
ORF3a	46	L46del	CTT	---	2	2	D.2	0.00015
ORF3a	46	L46del	CTT	---	2	2	P.1	0.000032
ORF3a	46	L46I	Ctt	Att	2	2	P.1	0.000032
ORF3a	46	L46F	Ctt	Ttt	2	2	P.1.14	0.000096
ORF3a	46	L46L	ctT	ctC	2	2	P.1.14	0.000096
ORF3a	46	L46F	Ctt	Ttt	2	2	Q.7	0.002222
ORF3a	46	L46C	CTt	TGt	1	1	A.1	0.000282
ORF3a	46	L46del	CTT	---	1	1	AH.3	0.003802
ORF3a	46	L46F	Ctt	Ttt	1	1	AY.1	0.000396
ORF3a	46	L46L	ctT	ctC	1	1	AY.101	0.00049
ORF3a	46	L46L	ctT	ctC	1	1	AY.102	0.000027
ORF3a	46	L46del	CTT	---	1	1	AY.102	0.000027
ORF3a	46	L46del	CTT	---	1	1	AY.110	0.000113
ORF3a	46	L46del	CTT	---	1	1	AY.111	0.000183
ORF3a	46	L46del	CTT	---	1	1	AY.114	0.000231
ORF3a	46	L46del2	CTT	--N	1	1	AY.117	0.000085
ORF3a	46	L46F	Ctt	Ttt	1	1	AY.117	0.000085
ORF3a	46	L46P	cTt	cCt	1	1	AY.120	0.000037
ORF3a	46	L46I	Ctt	Att	1	1	AY.120	0.000037
ORF3a	46	L46del	CTT	---	1	1	AY.14	0.000088
ORF3a	46	L46F	Ctt	Ttt	1	1	AY.20	0.000039
ORF3a	46	L46del2	CTt	--t	1	1	AY.20	0.000039
ORF3a	46	L46I	Ctt	Att	1	1	AY.23	0.00007
ORF3a	46	L46F	Ctt	Ttt	1	1	AY.23	0.00007
ORF3a	46	L46del	CTT	---	1	1	AY.23	0.00007
ORF3a	46	L46F	Ctt	Ttt	1	1	AY.23.1	0.000417
ORF3a	46	L46del2	CTT	--A	1	1	AY.26	0.000028
ORF3a	46	L46L	ctT	ctA	1	1	AY.28	0.00189
ORF3a	46	L46F	Ctt	Ttt	1	1	AY.28	0.00189
ORF3a	46	L46del	CTT	---	1	1	AY.29.1	0.000221
ORF3a	46	L46L	ctT	ctC	1	1	AY.3	0.00001
ORF3a	46	L46del1	cTT	c-N	1	1	AY.3	0.00001
ORF3a	46	L46del	CTT	---	1	1	AY.3.1	0.000085
ORF3a	46	L46F	Ctt	Ttt	1	1	AY.33	0.000067
ORF3a	46	L46R	cTt	cGt	1	1	AY.33	0.000067
ORF3a	46	L46F	Ctt	Ttt	1	1	AY.4.2	0.000022
ORF3a	46	L46P	cTt	cCt	1	1	AY.4.2	0.000022
ORF3a	46	L46F	Ctt	Ttt	1	1	AY.4.5	0.000107
ORF3a	46	L46del	CTT	---	1	1	AY.42	0.00004
ORF3a	46	L46I	Ctt	Att	1	1	AY.43	0.000004
ORF3a	46	L46I	Ctt	Att	1	1	AY.44	0.000006
ORF3a	46	L46L	ctT	ctA	1	1	AY.44	0.000006
ORF3a	46	L46V	Ctt	Gtt	1	1	AY.44	0.000006
ORF3a	46	L46F	Ctt	Ttt	1	1	AY.46.2	0.000635
ORF3a	46	L46del	CTT	---	1	1	AY.46.4	0.000165
ORF3a	46	L46del1	cTT	c-N	1	1	AY.5	0.000021
ORF3a	46	L46L	ctT	ctC	1	1	AY.54	0.000095
ORF3a	46	L46I	Ctt	Att	1	1	AY.58	0.000907
ORF3a	46	L46del	CTT	---	1	1	AY.59	0.00053
ORF3a	46	L46F	Ctt	Ttt	1	1	AY.6	0.000041
ORF3a	46	L46P	cTt	cCt	1	1	AY.6	0.000041
ORF3a	46	L46F	Ctt	Ttt	1	1	AY.61	0.000105
ORF3a	46	L46del	CTT	---	1	1	AY.65	0.000533
ORF3a	46	L46F	Ctt	Ttt	1	1	AY.65	0.000533
ORF3a	46	L46R	cTt	cGt	1	1	AY.69	0.000187
ORF3a	46	L46F	Ctt	Ttt	1	1	AY.69	0.000187
ORF3a	46	L46del	CTT	---	1	1	AY.7	0.000196
ORF3a	46	L46del	CTT	---	1	1	AY.7.1	0.000113
ORF3a	46	L46F	Ctt	Ttt	1	1	AY.74	0.000116
ORF3a	46	L46L	ctT	ctC	1	1	AY.75	0.000056
ORF3a	46	L46P	cTt	cCt	1	1	AY.75	0.000056
ORF3a	46	L46del	CTT	---	1	1	AY.75.1	0.00018
ORF3a	46	L46F	Ctt	Ttt	1	1	AY.79	0.001211
ORF3a	46	L46F	Ctt	Ttt	1	1	AY.82	0.001357
ORF3a	46	L46I	Ctt	Att	1	1	AY.87	0.000833
ORF3a	46	L46del	CTT	---	1	1	AY.9	0.000068
ORF3a	46	L46L	ctT	ctC	1	1	AY.9.2	0.000037
ORF3a	46	L46del	CTT	---	1	1	AY.9.2	0.000037
ORF3a	46	L46del	CTT	---	1	1	AY.90	0.000684
ORF3a	46	L46del	CTT	---	1	1	AY.91	0.00073
ORF3a	46	L46del	CTT	---	1	1	AY.93	0.000273
ORF3a	46	L46del	CTT	---	1	1	AY.94	0.000443
ORF3a	46	L46del	CTT	---	1	1	AY.98.1	0.000048
ORF3a	46	L46del	CTT	---	1	1	AY.99	0.001049
ORF3a	46	L46del	CTT	---	1	1	AY.99.2	0.000092
ORF3a	46	L46F	Ctt	Ttt	1	1	AY.99.2	0.000092
ORF3a	46	L46del	CTT	---	1	1	B	0.000128
ORF3a	46	L46del1	cTt	c-t	1	1	B.1	0.000009
ORF3a	46	L46H	cTt	cAt	1	1	B.1.1	0.000018
ORF3a	46	L46del1	cTt	c-t	1	1	B.1.1	0.000018
ORF3a	46	L46R	cTt	cGt	1	1	B.1.1.128	0.007092
ORF3a	46	L46del1	CtT	Tt-	1	1	B.1.1.139	0.022727
ORF3a	46	L46I	Ctt	Att	1	1	B.1.1.203	0.016949
ORF3a	46	L46del	CTT	---	1	1	B.1.1.214	0.000055
ORF3a	46	L46del	CTT	---	1	1	B.1.1.225	0.007194
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.1.240	0.004695
ORF3a	46	L46R	cTt	cGt	1	1	B.1.1.257	0.009709
ORF3a	46	L46L	ctT	ctC	1	1	B.1.1.263	0.001558
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.1.265	0.003155
ORF3a	46	L46del	CTT	---	1	1	B.1.1.279	0.001121
ORF3a	46	L46del	CTT	---	1	1	B.1.1.28	0.000311
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.1.306	0.000438
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.1.33	0.000421
ORF3a	46	L46L	ctT	ctC	1	1	B.1.1.372	0.000689
ORF3a	46	L46del	CTT	---	1	1	B.1.1.409	0.002833
ORF3a	46	L46I	Ctt	Att	1	1	B.1.1.434	0.000349
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.1.464	0.001473
ORF3a	46	L46del	CTT	---	1	1	B.1.1.50	0.000679
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.1.50	0.000679
ORF3a	46	L46I	Ctt	Att	1	1	B.1.1.524	0.020833
ORF3a	46	L46R	cTt	cGt	1	1	B.1.1.7	0.000001
ORF3a	46	L46P	cTt	cCt	1	1	B.1.1.70	0.000341
ORF3a	46	L46C	CTt	TGt	1	1	B.1.1.8	0.003584
ORF3a	46	L46P	cTt	cCt	1	1	B.1.127	0.002198
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.139	0.000733
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.160.17	0.001701
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.160.18	0.007299
ORF3a	46	L46R	cTt	cGt	1	1	B.1.177	0.000013
ORF3a	46	L46del2	cTT	c--	1	1	B.1.177	0.000013
ORF3a	46	L46L	ctT	ctC	1	1	B.1.177	0.000013
ORF3a	46	L46del	CTT	---	1	1	B.1.177.12	0.000152
ORF3a	46	L46L	ctT	ctG	1	1	B.1.177.16	0.000664
ORF3a	46	L46del	CTT	---	1	1	B.1.177.21	0.000076
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.177.42	0.000894
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.177.57	0.000281
ORF3a	46	L46del	CTT	---	1	1	B.1.177.6	0.000977
ORF3a	46	L46I	Ctt	Att	1	1	B.1.2	0.000009
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.221	0.000071
ORF3a	46	L46L	ctT	ctC	1	1	B.1.221	0.000071
ORF3a	46	L46R	cTt	cGt	1	1	B.1.240	0.000216
ORF3a	46	L46del	CTT	---	1	1	B.1.241	0.000812
ORF3a	46	L46L	ctT	ctC	1	1	B.1.243	0.00007
ORF3a	46	L46C	CTt	TGt	1	1	B.1.243	0.00007
ORF3a	46	L46H	cTt	cAt	1	1	B.1.258	0.000067
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.258	0.000067
ORF3a	46	L46P	cTt	cCt	1	1	B.1.258	0.000067
ORF3a	46	L46I	Ctt	Att	1	1	B.1.302	0.013333
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.311	0.000275
ORF3a	46	L46C	CTt	TGt	1	1	B.1.333	0.010526
ORF3a	46	L46I	Ctt	Att	1	1	B.1.349	0.000715
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.351	0.00003
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.36	0.000146
ORF3a	46	L46del	CTT	---	1	1	B.1.36.24	0.006173
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.36.29	0.000517
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.391	0.001127
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.409	0.000781
ORF3a	46	L46H	cTt	cAt	1	1	B.1.427	0.00005
ORF3a	46	L46L	ctT	ctC	1	1	B.1.429	0.000024
ORF3a	46	L46R	cTt	cGt	1	1	B.1.446	0.02
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.462	0.007246
ORF3a	46	L46I	Ctt	Att	1	1	B.1.509	0.000866
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.546	0.003704
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.564	0.000426
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.573	0.006098
ORF3a	46	L46R	cTt	cGt	1	1	B.1.574	0.002151
ORF3a	46	L46R	cTt	cGt	1	1	B.1.576	0.000907
ORF3a	46	L46L	ctT	ctC	1	1	B.1.595	0.000261
ORF3a	46	L46del	CTT	---	1	1	B.1.596	0.000087
ORF3a	46	L46H	cTt	cAt	1	1	B.1.617.2	0.000004
ORF3a	46	L46V	Ctt	Gtt	1	1	B.1.617.2	0.000004
ORF3a	46	L46P	cTt	cCt	1	1	B.1.617.2	0.000004
ORF3a	46	L46I	CtT	AtA	1	1	B.1.630	0.005236
ORF3a	46	L46F	Ctt	Ttt	1	1	B.1.637	0.000073
ORF3a	46	L46del	CTT	---	1	1	B.1.638	0.052632
ORF3a	46	L46P	cTt	cCt	1	1	B.55	0.00295
ORF3a	46	L46F	Ctt	Ttt	1	1	C.33	0.058824
ORF3a	46	L46F	Ctt	Ttt	1	1	N.5	0.001767
ORF3a	46	L46P	cTt	cCt	1	1	P.1	0.000016
ORF3a	46	L46I	Ctt	Att	1	1	P.1.1	0.000318
ORF3a	46	L46V	Ctt	Gtt	1	1	P.1.1	0.000318
ORF3a	46	L46F	Ctt	Ttt	1	1	P.1.10	0.000269
ORF3a	46	L46F	Ctt	Ttt	1	1	P.1.12	0.000484
ORF3a	46	L46L	ctT	ctC	1	1	P.1.12	0.000484
ORF3a	46	L46del	CTT	---	1	1	P.1.14	0.000048
ORF3a	46	L46del	CTT	---	1	1	P.1.15	0.000232
ORF3a	46	L46P	cTt	cCt	1	1	P.1.17	0.000162
ORF3a	46	L46F	Ctt	Ttt	1	1	P.1.7	0.000319
ORF3a	46	L46F	Ctt	Ttt	1	1	Q.4	0.000455

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.