CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF3a : CodonNum = 77

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	77	V77F		nonsyn	Gtt	Ttt	17528	17528	1	25621-25623
ORF3a	77	V77I		nonsyn	Gtt	Att	1343	1343	1	25621-25623
ORF3a	77	V77V		syn	gtT	gtC	891	826	0.927048	25621-25623
ORF3a	77	V77V		syn	gtT	gtG	891	35	0.0392817	25621-25623
ORF3a	77	V77V		syn	gtT	gtA	891	30	0.03367	25621-25623
ORF3a	77	V77A		nonsyn	gTt	gCt	477	477	1	25621-25623
ORF3a	77	V77L		nonsyn	Gtt	Ctt	76	74	0.973684	25621-25623
ORF3a	77	V77L		nonsyn	GtT	CtG	76	2	0.0263158	25621-25623
ORF3a	77	V77del		del	GTT	---	45	45	1	25621-25623
ORF3a	77	V77G		nonsyn	gTt	gGt	10	9	0.9	25621-25623
ORF3a	77	V77G		nonsyn	gTT	gGG	10	1	0.1	25621-25623
ORF3a	77	V77del2		del	GTt	--t	5	3	0.6	25621-25623
ORF3a	77	V77del2		del	GTT	--N	5	1	0.2	25621-25623
ORF3a	77	V77del2		del	gTT	g--	5	1	0.2	25621-25623
ORF3a	77	V77D		nonsyn	gTt	gAt	4	4	1	25621-25623
ORF3a	77	V77H		nonsyn	GTt	CAt	4	2	0.5	25621-25623
ORF3a	77	V77H		nonsyn	GTT	CAC	4	2	0.5	25621-25623
ORF3a	77	V77del1		del	Gtt	-tt	3	3	1	25621-25623
ORF3a	77	V77E		nonsyn	gTT	gAG	2	2	1	25621-25623
ORF3a	77	V77Q		nonsyn	GTT	CAG	2	2	1	25621-25623
ORF3a	77	V77S		nonsyn	GTt	TCt	2	2	1	25621-25623
ORF3a	77	V77C		nonsyn	GTt	TGt	1	1	1	25621-25623
ORF3a	77	V77Y		nonsyn	GTt	TAt	1	1	1	25621-25623

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	77	V77F	Gtt	Ttt	17528	17528	All	0.003352
ORF3a	77	V77F	Gtt	Ttt	4569	4569	B.1.177.60	0.998034
ORF3a	77	V77F	Gtt	Ttt	3016	3016	B.1.1.7	0.0027
ORF3a	77	V77F	Gtt	Ttt	1889	1889	B.1.617.2	0.007113
ORF3a	77	V77F	Gtt	Ttt	1407	1407	AY.102	0.037305
ORF3a	77	V77I	Gtt	Att	1343	1343	All	0.000257
ORF3a	77	V77F	Gtt	Ttt	1241	1241	AY.44	0.007554
ORF3a	77	V77V	gtT	gtC	826	891	All	0.000158
ORF3a	77	V77V	gtT	gtG	35	891	All	0.000007
ORF3a	77	V77V	gtT	gtA	30	891	All	0.000006
ORF3a	77	V77F	Gtt	Ttt	849	849	AY.4	0.001321
ORF3a	77	V77F	Gtt	Ttt	611	611	B.1.177	0.008045
ORF3a	77	V77V	gtT	gtC	575	577	AY.4	0.000895
ORF3a	77	V77V	gtT	gtA	2	577	AY.4	0.000003
ORF3a	77	V77A	gTt	gCt	477	477	All	0.000091
ORF3a	77	V77F	Gtt	Ttt	450	450	B.1.36.25	0.993377
ORF3a	77	V77F	Gtt	Ttt	427	427	B.1.177.79	1
ORF3a	77	V77F	Gtt	Ttt	256	256	U.3	0.988417
ORF3a	77	V77A	gTt	gCt	255	255	AY.44	0.001552
ORF3a	77	V77I	Gtt	Att	250	250	AY.51	0.227273
ORF3a	77	V77I	Gtt	Att	238	238	B.1.1.216	0.211932
ORF3a	77	V77F	Gtt	Ttt	189	189	R.1	0.017012
ORF3a	77	V77I	Gtt	Att	185	185	AY.44	0.001126
ORF3a	77	V77F	Gtt	Ttt	178	178	B.1.1.222	0.036312
ORF3a	77	V77F	Gtt	Ttt	161	161	B.1.258.17	0.016739
ORF3a	77	V77F	Gtt	Ttt	134	134	AY.39	0.003311
ORF3a	77	V77F	Gtt	Ttt	130	130	AY.43	0.000576
ORF3a	77	V77F	Gtt	Ttt	114	114	U.2	1
ORF3a	77	V77I	Gtt	Att	90	90	AY.47	0.002799
ORF3a	77	V77I	Gtt	Att	88	88	B.1.1.7	0.000079
ORF3a	77	V77I	Gtt	Att	88	88	B.1.36	0.012839
ORF3a	77	V77F	Gtt	Ttt	87	87	AY.75	0.004874
ORF3a	77	V77F	Gtt	Ttt	86	86	B.1.2	0.000757
ORF3a	77	V77F	Gtt	Ttt	84	84	B.1	0.000769
ORF3a	77	V77F	Gtt	Ttt	80	80	AY.34	0.007757
ORF3a	77	V77F	Gtt	Ttt	78	78	U.1	1
ORF3a	77	V77L	Gtt	Ctt	74	76	All	0.000014
ORF3a	77	V77L	GtT	CtG	2	76	All	0
ORF3a	77	V77F	Gtt	Ttt	76	76	B.1.258	0.005058
ORF3a	77	V77F	Gtt	Ttt	73	73	AY.103	0.000453
ORF3a	77	V77I	Gtt	Att	61	61	B.1.617.2	0.00023
ORF3a	77	V77A	gTt	gCt	58	58	B.1.1	0.001052
ORF3a	77	V77F	Gtt	Ttt	56	56	AY.121	0.007578
ORF3a	77	V77F	Gtt	Ttt	55	55	AY.3	0.000547
ORF3a	77	V77V	gtT	gtC	34	54	AY.14	0.002992
ORF3a	77	V77V	gtT	gtA	20	54	AY.14	0.00176
ORF3a	77	V77A	gTt	gCt	50	50	AY.4	0.000078
ORF3a	77	V77F	Gtt	Ttt	50	50	B.1.1	0.000907
ORF3a	77	V77F	Gtt	Ttt	47	47	AY.42	0.001891
ORF3a	77	V77F	Gtt	Ttt	47	47	D.2	0.003527
ORF3a	77	V77del	GTT	---	45	45	All	0.000009
ORF3a	77	V77F	Gtt	Ttt	45	45	B.1.596	0.003921
ORF3a	77	V77F	Gtt	Ttt	44	44	B.1.438.4	0.93617
ORF3a	77	V77I	Gtt	Att	43	43	B.1	0.000394
ORF3a	77	V77F	Gtt	Ttt	40	40	AY.25	0.000241
ORF3a	77	V77V	gtT	gtC	36	36	AY.43	0.000159
ORF3a	77	V77F	Gtt	Ttt	33	33	AY.9.2	0.001212
ORF3a	77	V77F	Gtt	Ttt	32	32	AY.46	0.003331
ORF3a	77	V77F	Gtt	Ttt	29	29	B.1.526	0.000682
ORF3a	77	V77F	Gtt	Ttt	28	28	P.1	0.000441
ORF3a	77	V77I	Gtt	Att	27	27	AY.4	0.000042
ORF3a	77	V77F	Gtt	Ttt	27	27	AY.45	0.003285
ORF3a	77	V77V	gtT	gtC	26	26	B.1.526	0.000611
ORF3a	77	V77F	Gtt	Ttt	24	24	B.1.351	0.000713
ORF3a	77	V77F	Gtt	Ttt	23	23	AY.111	0.004212
ORF3a	77	V77I	Gtt	Att	23	23	B.1.517	0.009821
ORF3a	77	V77F	Gtt	Ttt	23	23	P.2	0.004293
ORF3a	77	V77I	Gtt	Att	20	20	AY.100	0.00092
ORF3a	77	V77V	gtT	gtC	20	20	B.1.1.203	0.338983
ORF3a	77	V77F	Gtt	Ttt	19	19	B.1.1.519	0.000755
ORF3a	77	V77I	Gtt	Att	18	18	AY.25	0.000108
ORF3a	77	V77F	Gtt	Ttt	18	18	AY.98.1	0.000872
ORF3a	77	V77I	Gtt	Att	18	18	B.1.2	0.000158
ORF3a	77	V77F	Gtt	Ttt	18	18	B.1.243	0.001253
ORF3a	77	V77V	gtT	gtC	17	18	B.1.617.2	0.000064
ORF3a	77	V77V	gtT	gtG	1	18	B.1.617.2	0.000004
ORF3a	77	V77F	Gtt	Ttt	18	18	P.1.14	0.00086
ORF3a	77	V77I	Gtt	Att	17	17	AY.104	0.03373
ORF3a	77	V77F	Gtt	Ttt	17	17	AY.9.1	0.001423
ORF3a	77	V77F	Gtt	Ttt	16	16	AY.26	0.000453
ORF3a	77	V77F	Gtt	Ttt	16	16	AY.33	0.001068
ORF3a	77	V77F	Gtt	Ttt	16	16	AY.34.1	0.008159
ORF3a	77	V77V	gtT	gtG	16	16	AY.75	0.000896
ORF3a	77	V77F	Gtt	Ttt	16	16	B.1.36	0.002334
ORF3a	77	V77F	Gtt	Ttt	15	15	AY.4.2	0.000325
ORF3a	77	V77F	Gtt	Ttt	15	15	B.1.1.317	0.006175
ORF3a	77	V77V	gtT	gtC	14	15	P.1	0.000221
ORF3a	77	V77V	gtT	gtG	1	15	P.1	0.000016
ORF3a	77	V77F	Gtt	Ttt	14	14	AY.99	0.01469
ORF3a	77	V77V	gtT	gtC	11	14	B.1.1.7	0.00001
ORF3a	77	V77V	gtT	gtG	2	14	B.1.1.7	0.000002
ORF3a	77	V77V	gtT	gtA	1	14	B.1.1.7	0.000001
ORF3a	77	V77F	Gtt	Ttt	14	14	B.1.429	0.000329
ORF3a	77	V77A	gTt	gCt	13	13	AY.119	0.000459
ORF3a	77	V77I	Gtt	Att	13	13	AY.65	0.00693
ORF3a	77	V77del	GTT	---	13	13	B.1.1.7	0.000012
ORF3a	77	V77F	Gtt	Ttt	12	12	AY.120	0.000446
ORF3a	77	V77A	gTt	gCt	12	12	P.1	0.000189
ORF3a	77	V77F	Gtt	Ttt	11	11	AY.98	0.000869
ORF3a	77	V77A	gTt	gCt	11	11	B.1.1.7	0.00001
ORF3a	77	V77F	Gtt	Ttt	11	11	P.1.17	0.001779
ORF3a	77	V77G	gTt	gGt	9	10	All	0.000002
ORF3a	77	V77G	gTT	gGG	1	10	All	0
ORF3a	77	V77I	Gtt	Att	10	10	AY.120	0.000372
ORF3a	77	V77F	Gtt	Ttt	10	10	AY.36	0.001482
ORF3a	77	V77F	Gtt	Ttt	10	10	AY.46.2	0.006353
ORF3a	77	V77F	Gtt	Ttt	10	10	B.1.1.312	0.01912
ORF3a	77	V77A	gTt	gCt	10	10	B.1.617.2	0.000038
ORF3a	77	V77L	Gtt	Ctt	9	9	AY.103	0.000056
ORF3a	77	V77F	Gtt	Ttt	9	9	AY.16	0.003417
ORF3a	77	V77F	Gtt	Ttt	9	9	AY.20	0.00035
ORF3a	77	V77F	Gtt	Ttt	9	9	AY.46.6	0.00065
ORF3a	77	V77F	Gtt	Ttt	9	9	AY.5	0.000186
ORF3a	77	V77F	Gtt	Ttt	9	9	AY.84	0.003937
ORF3a	77	V77I	Gtt	Att	9	9	B.1.1	0.000163
ORF3a	77	V77F	Gtt	Ttt	9	9	B.1.160	0.000281
ORF3a	77	V77F	Gtt	Ttt	9	9	B.1.160.16	0.008364
ORF3a	77	V77F	Gtt	Ttt	9	9	B.1.177.81	0.001704
ORF3a	77	V77F	Gtt	Ttt	9	9	B.1.456	0.029412
ORF3a	77	V77F	Gtt	Ttt	9	9	B.1.625	0.021176
ORF3a	77	V77I	Gtt	Att	8	8	AM.1	0.888889
ORF3a	77	V77F	Gtt	Ttt	8	8	AY.100	0.000368
ORF3a	77	V77V	gtT	gtC	8	8	AY.103	0.00005
ORF3a	77	V77I	Gtt	Att	8	8	AY.37	0.002528
ORF3a	77	V77L	Gtt	Ctt	8	8	AY.44	0.000049
ORF3a	77	V77V	gtT	gtC	5	8	B.1	0.000046
ORF3a	77	V77V	gtT	gtA	2	8	B.1	0.000018
ORF3a	77	V77V	gtT	gtG	1	8	B.1	0.000009
ORF3a	77	V77V	gtT	gtC	8	8	B.1.1.291	0.005939
ORF3a	77	V77I	Gtt	Att	8	8	B.1.1.519	0.000318
ORF3a	77	V77L	Gtt	Ctt	8	8	B.1.1.7	0.000007
ORF3a	77	V77A	gTt	gCt	8	8	R.1	0.00072
ORF3a	77	V77I	Gtt	Att	7	7	AY.103	0.000043
ORF3a	77	V77F	Gtt	Ttt	7	7	AY.108	0.007718
ORF3a	77	V77F	Gtt	Ttt	7	7	AY.118	0.000439
ORF3a	77	V77I	Gtt	Att	7	7	AY.3	0.00007
ORF3a	77	V77F	Gtt	Ttt	7	7	AY.54	0.000667
ORF3a	77	V77I	Gtt	Att	7	7	AY.9.2	0.000257
ORF3a	77	V77A	gTt	gCt	7	7	B.1	0.000064
ORF3a	77	V77F	Gtt	Ttt	7	7	B.1.177.21	0.000535
ORF3a	77	V77A	gTt	gCt	7	7	B.1.2	0.000062
ORF3a	77	V77V	gtT	gtC	7	7	B.1.2	0.000062
ORF3a	77	V77F	Gtt	Ttt	7	7	B.1.400	0.003003
ORF3a	77	V77F	Gtt	Ttt	7	7	B.1.427	0.000353
ORF3a	77	V77F	Gtt	Ttt	7	7	P.1.7	0.002235
ORF3a	77	V77I	Gtt	Att	6	6	AY.105	0.003859
ORF3a	77	V77F	Gtt	Ttt	6	6	AY.117	0.000507
ORF3a	77	V77V	gtT	gtC	6	6	AY.20	0.000233
ORF3a	77	V77F	Gtt	Ttt	6	6	AY.23	0.000418
ORF3a	77	V77F	Gtt	Ttt	6	6	AY.29	0.000095
ORF3a	77	V77F	Gtt	Ttt	6	6	AY.3.1	0.000512
ORF3a	77	V77I	Gtt	Att	6	6	AY.43	0.000027
ORF3a	77	V77F	Gtt	Ttt	6	6	AY.61	0.000629
ORF3a	77	V77A	gTt	gCt	6	6	AY.91	0.004383
ORF3a	77	V77L	Gtt	Ctt	6	6	B.1	0.000055
ORF3a	77	V77L	Gtt	Ctt	6	6	B.1.1.187	0.053097
ORF3a	77	V77F	Gtt	Ttt	6	6	C.37	0.000696
ORF3a	77	V77L	Gtt	Ctt	5	5	A.2.5.3	0.051546
ORF3a	77	V77del2	GTt	--t	3	5	All	0.000001
ORF3a	77	V77del2	GTT	--N	1	5	All	0
ORF3a	77	V77del2	gTT	g--	1	5	All	0
ORF3a	77	V77L	Gtt	Ctt	5	5	AY.102	0.000133
ORF3a	77	V77F	Gtt	Ttt	5	5	AY.119	0.000177
ORF3a	77	V77F	Gtt	Ttt	5	5	AY.39.1	0.000198
ORF3a	77	V77L	Gtt	Ctt	5	5	AY.4	0.000008
ORF3a	77	V77F	Gtt	Ttt	5	5	AY.77	0.005637
ORF3a	77	V77F	Gtt	Ttt	5	5	AY.99.2	0.000461
ORF3a	77	V77F	Gtt	Ttt	5	5	B.1.1.294	0.006329
ORF3a	77	V77F	Gtt	Ttt	5	5	B.1.1.306	0.002192
ORF3a	77	V77del	GTT	---	5	5	B.1.177	0.000066
ORF3a	77	V77F	Gtt	Ttt	5	5	B.1.221	0.000355
ORF3a	77	V77F	Gtt	Ttt	5	5	B.1.236	0.010267
ORF3a	77	V77F	Gtt	Ttt	5	5	B.1.438	0.03268
ORF3a	77	V77F	Gtt	Ttt	5	5	C.35	0.00387
ORF3a	77	V77F	Gtt	Ttt	5	5	L.3	0.01773
ORF3a	77	V77L	GtT	CtG	2	4		0.111111
ORF3a	77	V77L	Gtt	Ctt	2	4		0.111111
ORF3a	77	V77D	gTt	gAt	4	4	All	0.000001
ORF3a	77	V77H	GTT	CAC	2	4	All	0
ORF3a	77	V77H	GTt	CAt	2	4	All	0
ORF3a	77	V77F	Gtt	Ttt	4	4	AY.17	0.032787
ORF3a	77	V77V	gtT	gtG	2	4	AY.26	0.000057
ORF3a	77	V77V	gtT	gtC	2	4	AY.26	0.000057
ORF3a	77	V77I	Gtt	Att	4	4	AY.39	0.000099
ORF3a	77	V77V	gtT	gtG	2	4	AY.39	0.000049
ORF3a	77	V77V	gtT	gtC	2	4	AY.39	0.000049
ORF3a	77	V77A	gTt	gCt	4	4	AY.39.1	0.000158
ORF3a	77	V77V	gtT	gtG	3	4	AY.44	0.000018
ORF3a	77	V77V	gtT	gtC	1	4	AY.44	0.000006
ORF3a	77	V77F	Gtt	Ttt	4	4	AY.59	0.002119
ORF3a	77	V77I	Gtt	Att	4	4	AY.61	0.000419
ORF3a	77	V77F	Gtt	Ttt	4	4	B.1.1.174	0.013514
ORF3a	77	V77V	gtT	gtC	4	4	B.1.1.222	0.000816
ORF3a	77	V77F	Gtt	Ttt	4	4	B.1.1.28	0.001245
ORF3a	77	V77F	Gtt	Ttt	4	4	B.1.1.39	0.002039
ORF3a	77	V77V	gtT	gtC	3	4	B.1.177	0.00004
ORF3a	77	V77V	gtT	gtA	1	4	B.1.177	0.000013
ORF3a	77	V77F	Gtt	Ttt	4	4	B.1.177.6	0.003906
ORF3a	77	V77V	gtT	gtC	4	4	B.1.351	0.000119
ORF3a	77	V77F	Gtt	Ttt	4	4	B.1.36.39	0.008869
ORF3a	77	V77F	Gtt	Ttt	4	4	B.1.525	0.000453
ORF3a	77	V77L	Gtt	Ctt	4	4	B.1.617.2	0.000015
ORF3a	77	V77F	Gtt	Ttt	4	4	B.1.619.1	0.002566
ORF3a	77	V77I	Gtt	Att	4	4	C.37	0.000464
ORF3a	77	V77F	Gtt	Ttt	4	4	P.1.12	0.001936
ORF3a	77	V77D	gTt	gAt	3	3		0.166667
ORF3a	77	V77V	gtT	gtG	3	3		0.166667
ORF3a	77	V77V	gtT	gtC	3	3	A	0.001161
ORF3a	77	V77F	Gtt	Ttt	3	3	A.2.4	0.010101
ORF3a	77	V77del1	Gtt	-tt	3	3	All	0.000001
ORF3a	77	V77F	Gtt	Ttt	3	3	AY.11	0.004016
ORF3a	77	V77F	Gtt	Ttt	3	3	AY.110	0.000338
ORF3a	77	V77A	gTt	gCt	3	3	AY.113	0.000427
ORF3a	77	V77F	Gtt	Ttt	3	3	AY.16.1	0.00141
ORF3a	77	V77A	gTt	gCt	3	3	AY.20	0.000117
ORF3a	77	V77A	gTt	gCt	3	3	AY.3	0.00003
ORF3a	77	V77F	Gtt	Ttt	3	3	AY.47	0.000093
ORF3a	77	V77F	Gtt	Ttt	3	3	AY.56	0.004815
ORF3a	77	V77F	Gtt	Ttt	3	3	AY.7.2	0.001678
ORF3a	77	V77I	Gtt	Att	3	3	AY.94	0.001328
ORF3a	77	V77F	Gtt	Ttt	3	3	AY.96	0.006224
ORF3a	77	V77V	gtT	gtC	3	3	B.1.1	0.000054
ORF3a	77	V77F	Gtt	Ttt	3	3	B.1.1.1	0.00098
ORF3a	77	V77F	Gtt	Ttt	3	3	B.1.1.169	0.054545
ORF3a	77	V77V	gtT	gtC	3	3	B.1.1.176	0.001318
ORF3a	77	V77V	gtT	gtC	3	3	B.1.1.192	0.006928
ORF3a	77	V77F	Gtt	Ttt	3	3	B.1.1.25	0.001706
ORF3a	77	V77I	Gtt	Att	3	3	B.1.1.355	0.046154
ORF3a	77	V77F	Gtt	Ttt	3	3	B.1.177.10	0.002634
ORF3a	77	V77F	Gtt	Ttt	3	3	B.1.240	0.000647
ORF3a	77	V77I	Gtt	Att	3	3	B.1.243	0.000209
ORF3a	77	V77F	Gtt	Ttt	3	3	B.1.351.3	0.002629
ORF3a	77	V77F	Gtt	Ttt	3	3	B.1.568	0.003333
ORF3a	77	V77F	Gtt	Ttt	3	3	B.52	0.030303
ORF3a	77	V77F	Gtt	Ttt	3	3	Q.3	0.000435
ORF3a	77	V77F	Gtt	Ttt	3	3	Q.8	0.000495
ORF3a	77	V77del	GTT	---	3	3	U.3	0.011583
ORF3a	77	V77F	Gtt	Ttt	2	2		0.111111
ORF3a	77	V77E	gTT	gAG	2	2		0.111111
ORF3a	77	V77H	GTt	CAt	2	2		0.111111
ORF3a	77	V77Q	GTT	CAG	2	2		0.111111
ORF3a	77	V77L	Gtt	Ctt	2	2	A.2.5	0.000998
ORF3a	77	V77Q	GTT	CAG	2	2	All	0
ORF3a	77	V77S	GTt	TCt	2	2	All	0
ORF3a	77	V77E	gTT	gAG	2	2	All	0
ORF3a	77	V77F	Gtt	Ttt	2	2	AY.1	0.000791
ORF3a	77	V77L	Gtt	Ctt	2	2	AY.100	0.000092
ORF3a	77	V77I	Gtt	Att	2	2	AY.102	0.000053
ORF3a	77	V77F	Gtt	Ttt	2	2	AY.106	0.00067
ORF3a	77	V77F	Gtt	Ttt	2	2	AY.116	0.000574
ORF3a	77	V77V	gtT	gtC	2	2	AY.120	0.000074
ORF3a	77	V77I	Gtt	Att	2	2	AY.120.2.1	0.000997
ORF3a	77	V77F	Gtt	Ttt	2	2	AY.13	0.000322
ORF3a	77	V77F	Gtt	Ttt	2	2	AY.14	0.000176
ORF3a	77	V77I	Gtt	Att	2	2	AY.20	0.000078
ORF3a	77	V77del	GTT	---	2	2	AY.23	0.000139
ORF3a	77	V77I	Gtt	Att	2	2	AY.26	0.000057
ORF3a	77	V77V	gtT	gtC	2	2	AY.29	0.000032
ORF3a	77	V77I	Gtt	Att	2	2	AY.39.1	0.000079
ORF3a	77	V77del	GTT	---	2	2	AY.4	0.000003
ORF3a	77	V77V	gtT	gtC	2	2	AY.4.4	0.000818
ORF3a	77	V77del	GTT	---	2	2	AY.4.5	0.000215
ORF3a	77	V77I	Gtt	Att	2	2	AY.5	0.000041
ORF3a	77	V77I	Gtt	Att	2	2	AY.55	0.001835
ORF3a	77	V77F	Gtt	Ttt	2	2	AY.55	0.001835
ORF3a	77	V77I	Gtt	Att	2	2	AY.6	0.000082
ORF3a	77	V77F	Gtt	Ttt	2	2	AY.60	0.001876
ORF3a	77	V77F	Gtt	Ttt	2	2	AY.63	0.000774
ORF3a	77	V77F	Gtt	Ttt	2	2	AY.68	0.000547
ORF3a	77	V77F	Gtt	Ttt	2	2	AY.69	0.000373
ORF3a	77	V77I	Gtt	Att	2	2	AY.7.2	0.001119
ORF3a	77	V77I	Gtt	Att	2	2	AY.75.1	0.000361
ORF3a	77	V77F	Gtt	Ttt	2	2	AY.75.1	0.000361
ORF3a	77	V77F	Gtt	Ttt	2	2	AY.89	0.009804
ORF3a	77	V77I	Gtt	Att	2	2	AY.9.1	0.000167
ORF3a	77	V77I	Gtt	Att	2	2	AY.98.1	0.000097
ORF3a	77	V77F	Gtt	Ttt	2	2	B	0.000256
ORF3a	77	V77del	GTT	---	2	2	B.1	0.000018
ORF3a	77	V77G	gTT	gGG	1	2	B.1	0.000009
ORF3a	77	V77G	gTt	gGt	1	2	B.1	0.000009
ORF3a	77	V77I	Gtt	Att	2	2	B.1.1.1	0.000653
ORF3a	77	V77I	Gtt	Att	2	2	B.1.1.10	0.00223
ORF3a	77	V77F	Gtt	Ttt	2	2	B.1.1.214	0.000111
ORF3a	77	V77F	Gtt	Ttt	2	2	B.1.1.216	0.001781
ORF3a	77	V77I	Gtt	Att	2	2	B.1.1.28	0.000622
ORF3a	77	V77I	Gtt	Att	2	2	B.1.1.311	0.000716
ORF3a	77	V77F	Gtt	Ttt	2	2	B.1.1.372	0.001377
ORF3a	77	V77G	gTt	gGt	2	2	B.1.1.7	0.000002
ORF3a	77	V77F	Gtt	Ttt	2	2	B.1.177.7	0.00033
ORF3a	77	V77F	Gtt	Ttt	2	2	B.1.177.86	0.000367
ORF3a	77	V77V	gtT	gtC	2	2	B.1.22	0.002635
ORF3a	77	V77F	Gtt	Ttt	2	2	B.1.22	0.002635
ORF3a	77	V77I	Gtt	Att	2	2	B.1.232	0.001075
ORF3a	77	V77F	Gtt	Ttt	2	2	B.1.234	0.000264
ORF3a	77	V77I	Gtt	Att	2	2	B.1.258	0.000133
ORF3a	77	V77F	Gtt	Ttt	2	2	B.1.36.1	0.002281
ORF3a	77	V77I	Gtt	Att	2	2	B.1.36.38	0.003284
ORF3a	77	V77V	gtT	gtC	1	2	B.1.396	0.000706
ORF3a	77	V77V	gtT	gtA	1	2	B.1.396	0.000706
ORF3a	77	V77V	gtT	gtG	2	2	B.1.427	0.000101
ORF3a	77	V77F	Gtt	Ttt	2	2	B.1.507	0.022472
ORF3a	77	V77F	Gtt	Ttt	2	2	B.1.527	0.007407
ORF3a	77	V77F	Gtt	Ttt	2	2	B.1.540	0.019417
ORF3a	77	V77F	Gtt	Ttt	2	2	B.1.595.1	0.011696
ORF3a	77	V77F	Gtt	Ttt	2	2	B.1.597	0.009259
ORF3a	77	V77del	GTT	---	2	2	B.1.617.2	0.000008
ORF3a	77	V77F	Gtt	Ttt	2	2	C.28	0.08
ORF3a	77	V77V	gtT	gtC	2	2	C.37	0.000232
ORF3a	77	V77I	Gtt	Att	2	2	P.1	0.000032
ORF3a	77	V77V	gtT	gtC	2	2	Q.8	0.00033
ORF3a	77	V77S	GTt	TCt	2	2	R.1	0.00018
ORF3a	77	V77G	gTt	gGt	1	1		0.055556
ORF3a	77	V77Y	GTt	TAt	1	1		0.055556
ORF3a	77	V77C	GTt	TGt	1	1		0.055556
ORF3a	77	V77F	Gtt	Ttt	1	1	A	0.000387
ORF3a	77	V77A	gTt	gCt	1	1	A.27	0.001656
ORF3a	77	V77F	Gtt	Ttt	1	1	AA.6	0.016129
ORF3a	77	V77del2	GTt	--t	1	1	AD.2	0.000219
ORF3a	77	V77D	gTt	gAt	1	1	AD.2	0.000219
ORF3a	77	V77del	GTT	---	1	1	AH.3	0.003802
ORF3a	77	V77Y	GTt	TAt	1	1	All	0
ORF3a	77	V77C	GTt	TGt	1	1	All	0
ORF3a	77	V77A	gTt	gCt	1	1	AY.100	0.000046
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.101	0.00049
ORF3a	77	V77V	gtT	gtG	1	1	AY.102	0.000027
ORF3a	77	V77A	gTt	gCt	1	1	AY.102	0.000027
ORF3a	77	V77A	gTt	gCt	1	1	AY.103	0.000006
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.104	0.001984
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.105	0.000643
ORF3a	77	V77I	Gtt	Att	1	1	AY.107	0.000466
ORF3a	77	V77V	gtT	gtC	1	1	AY.107	0.000466
ORF3a	77	V77I	Gtt	Att	1	1	AY.108	0.001103
ORF3a	77	V77del	GTT	---	1	1	AY.111	0.000183
ORF3a	77	V77del1	Gtt	-tt	1	1	AY.113	0.000142
ORF3a	77	V77V	gtT	gtC	1	1	AY.12	0.000316
ORF3a	77	V77I	Gtt	Att	1	1	AY.120.1	0.000321
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.19	0.00114
ORF3a	77	V77A	gTt	gCt	1	1	AY.23	0.00007
ORF3a	77	V77I	Gtt	Att	1	1	AY.24	0.000431
ORF3a	77	V77del	GTT	---	1	1	AY.25	0.000006
ORF3a	77	V77A	gTt	gCt	1	1	AY.25	0.000006
ORF3a	77	V77V	gtT	gtA	1	1	AY.25	0.000006
ORF3a	77	V77A	gTt	gCt	1	1	AY.26	0.000028
ORF3a	77	V77I	Gtt	Att	1	1	AY.27	0.000065
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.27	0.000065
ORF3a	77	V77L	Gtt	Ctt	1	1	AY.3	0.00001
ORF3a	77	V77del2	GTT	--N	1	1	AY.3	0.00001
ORF3a	77	V77I	Gtt	Att	1	1	AY.3.1	0.000085
ORF3a	77	V77V	gtT	gtC	1	1	AY.32	0.000532
ORF3a	77	V77del	GTT	---	1	1	AY.33	0.000067
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.35	0.000233
ORF3a	77	V77L	Gtt	Ctt	1	1	AY.39	0.000025
ORF3a	77	V77del	GTT	---	1	1	AY.39	0.000025
ORF3a	77	V77A	gTt	gCt	1	1	AY.39	0.000025
ORF3a	77	V77G	gTt	gGt	1	1	AY.4	0.000002
ORF3a	77	V77I	Gtt	Att	1	1	AY.4.2	0.000022
ORF3a	77	V77del2	GTt	--t	1	1	AY.4.2	0.000022
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.4.2.1	0.000149
ORF3a	77	V77L	Gtt	Ctt	1	1	AY.4.5	0.000107
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.4.5	0.000107
ORF3a	77	V77V	gtT	gtC	1	1	AY.40	0.000964
ORF3a	77	V77V	gtT	gtC	1	1	AY.41	0.000294
ORF3a	77	V77A	gTt	gCt	1	1	AY.42	0.00004
ORF3a	77	V77del	GTT	---	1	1	AY.43	0.000004
ORF3a	77	V77I	Gtt	Att	1	1	AY.45	0.000122
ORF3a	77	V77I	Gtt	Att	1	1	AY.46	0.000104
ORF3a	77	V77I	Gtt	Att	1	1	AY.46.2	0.000635
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.46.4	0.000165
ORF3a	77	V77V	gtT	gtC	1	1	AY.46.4	0.000165
ORF3a	77	V77V	gtT	gtG	1	1	AY.47	0.000031
ORF3a	77	V77I	Gtt	Att	1	1	AY.49	0.003195
ORF3a	77	V77L	Gtt	Ctt	1	1	AY.5	0.000021
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.5.3	0.000337
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.51	0.000909
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.52	0.000814
ORF3a	77	V77V	gtT	gtC	1	1	AY.54	0.000095
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.58	0.000907
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.6	0.000041
ORF3a	77	V77A	gTt	gCt	1	1	AY.63	0.000387
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.64	0.000595
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.66	0.00107
ORF3a	77	V77G	gTt	gGt	1	1	AY.67	0.000464
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.70	0.000209
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.71	0.000475
ORF3a	77	V77I	Gtt	Att	1	1	AY.72	0.001361
ORF3a	77	V77A	gTt	gCt	1	1	AY.74	0.000116
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.74	0.000116
ORF3a	77	V77L	Gtt	Ctt	1	1	AY.75	0.000056
ORF3a	77	V77I	Gtt	Att	1	1	AY.75	0.000056
ORF3a	77	V77I	Gtt	Att	1	1	AY.77	0.001127
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.78	0.001541
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.85	0.000427
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.88	0.000884
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.9	0.000068
ORF3a	77	V77V	gtT	gtC	1	1	AY.9	0.000068
ORF3a	77	V77A	gTt	gCt	1	1	AY.9.1	0.000084
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.91	0.00073
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.92	0.000287
ORF3a	77	V77A	gTt	gCt	1	1	AY.92	0.000287
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.93	0.000273
ORF3a	77	V77I	Gtt	Att	1	1	AY.95	0.000761
ORF3a	77	V77I	Gtt	Att	1	1	AY.98	0.000079
ORF3a	77	V77F	Gtt	Ttt	1	1	AY.99.1	0.001553
ORF3a	77	V77del1	Gtt	-tt	1	1	B.1	0.000009
ORF3a	77	V77H	GTT	CAC	1	1	B.1	0.000009
ORF3a	77	V77H	GTT	CAC	1	1	B.1.1	0.000018
ORF3a	77	V77L	Gtt	Ctt	1	1	B.1.1	0.000018
ORF3a	77	V77A	gTt	gCt	1	1	B.1.1.1	0.000327
ORF3a	77	V77A	gTt	gCt	1	1	B.1.1.134	0.011364
ORF3a	77	V77L	Gtt	Ctt	1	1	B.1.1.170	0.001247
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.1.189	0.001513
ORF3a	77	V77I	Gtt	Att	1	1	B.1.1.196	0.005714
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.1.198	0.001468
ORF3a	77	V77A	gTt	gCt	1	1	B.1.1.216	0.00089
ORF3a	77	V77V	gtT	gtC	1	1	B.1.1.220	0.001859
ORF3a	77	V77del	GTT	---	1	1	B.1.1.236	0.006897
ORF3a	77	V77I	Gtt	Att	1	1	B.1.1.261	0.008621
ORF3a	77	V77I	Gtt	Att	1	1	B.1.1.262	0.015152
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.1.284	0.000107
ORF3a	77	V77A	gTt	gCt	1	1	B.1.1.284	0.000107
ORF3a	77	V77A	gTt	gCt	1	1	B.1.1.291	0.000742
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.1.304	0.002809
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.1.307	0.002532
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.1.316	0.000925
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.1.318	0.000302
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.1.33	0.000421
ORF3a	77	V77A	gTt	gCt	1	1	B.1.1.348	0.000796
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.1.375	0.011905
ORF3a	77	V77A	gTt	gCt	1	1	B.1.1.398	0.003226
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.1.403	0.025641
ORF3a	77	V77del	GTT	---	1	1	B.1.1.409	0.002833
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.1.409	0.002833
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.1.420	0.001006
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.1.432	0.001266
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.1.448	0.002033
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.1.46	0.004367
ORF3a	77	V77V	gtT	gtC	1	1	B.1.1.50	0.000679
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.1.53	0.013699
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.1.54	0.003021
ORF3a	77	V77del2	gTT	g--	1	1	B.1.1.7	0.000001
ORF3a	77	V77del1	Gtt	-tt	1	1	B.1.1.7	0.000001
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.110.3	0.000718
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.111	0.001175
ORF3a	77	V77G	gTt	gGt	1	1	B.1.13	0.002375
ORF3a	77	V77V	gtT	gtC	1	1	B.1.160.16	0.000929
ORF3a	77	V77del2	GTt	--t	1	1	B.1.161	0.017241
ORF3a	77	V77A	gTt	gCt	1	1	B.1.177	0.000013
ORF3a	77	V77I	Gtt	Att	1	1	B.1.177	0.000013
ORF3a	77	V77L	Gtt	Ctt	1	1	B.1.177	0.000013
ORF3a	77	V77del	GTT	---	1	1	B.1.177.17	0.000821
ORF3a	77	V77A	gTt	gCt	1	1	B.1.177.31	0.011494
ORF3a	77	V77G	gTt	gGt	1	1	B.1.177.73	0.000566
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.177.73	0.000566
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.177.75	0.001041
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.178	0.02381
ORF3a	77	V77I	Gtt	Att	1	1	B.1.195	0.005025
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.214	0.003663
ORF3a	77	V77I	Gtt	Att	1	1	B.1.221	0.000071
ORF3a	77	V77V	gtT	gtC	1	1	B.1.232	0.000537
ORF3a	77	V77A	gTt	gCt	1	1	B.1.232	0.000537
ORF3a	77	V77V	gtT	gtC	1	1	B.1.243	0.00007
ORF3a	77	V77L	Gtt	Ctt	1	1	B.1.243	0.00007
ORF3a	77	V77V	gtT	gtC	1	1	B.1.258	0.000067
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.311	0.000275
ORF3a	77	V77A	gTt	gCt	1	1	B.1.315	0.006061
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.320	0.001245
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.349	0.000715
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.351.2	0.000303
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.36.22	0.001208
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.36.24	0.006173
ORF3a	77	V77A	gTt	gCt	1	1	B.1.36.29	0.000517
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.36.8	0.001
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.36.9	0.003215
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.380	0.006623
ORF3a	77	V77L	Gtt	Ctt	1	1	B.1.389	0.001002
ORF3a	77	V77L	Gtt	Ctt	1	1	B.1.391	0.001127
ORF3a	77	V77del	GTT	---	1	1	B.1.415	0.014286
ORF3a	77	V77V	gtT	gtC	1	1	B.1.429	0.000024
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.466.1	0.007194
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.471	0.002732
ORF3a	77	V77A	gTt	gCt	1	1	B.1.517	0.000427
ORF3a	77	V77V	gtT	gtC	1	1	B.1.517	0.000427
ORF3a	77	V77L	Gtt	Ctt	1	1	B.1.525	0.000113
ORF3a	77	V77I	Gtt	Att	1	1	B.1.538	0.008065
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.576	0.000907
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.581	0.009434
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.582	0.000491
ORF3a	77	V77del	GTT	---	1	1	B.1.585	0.027778
ORF3a	77	V77V	gtT	gtC	1	1	B.1.596	0.000087
ORF3a	77	V77I	Gtt	Att	1	1	B.1.609	0.000479
ORF3a	77	V77A	gTt	gCt	1	1	B.1.609	0.000479
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.617.1	0.000129
ORF3a	77	V77I	Gtt	Att	1	1	B.1.621	0.000089
ORF3a	77	V77V	gtT	gtA	1	1	B.1.621	0.000089
ORF3a	77	V77del	GTT	---	1	1	B.1.627	0.00202
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.628	0.000352
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.637	0.000073
ORF3a	77	V77del	GTT	---	1	1	B.1.638	0.052632
ORF3a	77	V77F	Gtt	Ttt	1	1	B.1.8	0.001972
ORF3a	77	V77F	Gtt	Ttt	1	1	B.40	0.000364
ORF3a	77	V77F	Gtt	Ttt	1	1	B.6	0.00091
ORF3a	77	V77I	Gtt	Att	1	1	C.30	0.001727
ORF3a	77	V77V	gtT	gtC	1	1	D.2	0.000075
ORF3a	77	V77G	gTt	gGt	1	1	D.2	0.000075
ORF3a	77	V77F	Gtt	Ttt	1	1	D.3	0.005917
ORF3a	77	V77V	gtT	gtA	1	1	P.1.14	0.000048
ORF3a	77	V77del	GTT	---	1	1	P.1.15	0.000232
ORF3a	77	V77F	Gtt	Ttt	1	1	P.6	0.003145
ORF3a	77	V77F	Gtt	Ttt	1	1	Q.1	0.000126
ORF3a	77	V77F	Gtt	Ttt	1	1	Q.4	0.000455
ORF3a	77	V77I	Gtt	Att	1	1	Q.7	0.001111

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.