CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF3a : CodonNum = 12

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	12	T12I		nonsyn	aCt	aTt	5302	5300	0.999623	25426-25428
ORF3a	12	T12I		nonsyn	aCT	aTC	5302	2	0.000377216	25426-25428
ORF3a	12	T12del		del	ACT	---	889	889	1	25426-25428
ORF3a	12	T12T		syn	acT	acC	181	134	0.740331	25426-25428
ORF3a	12	T12T		syn	acT	acA	181	40	0.220994	25426-25428
ORF3a	12	T12T		syn	acT	acG	181	7	0.038674	25426-25428
ORF3a	12	T12A		nonsyn	Act	Gct	150	150	1	25426-25428
ORF3a	12	T12N		nonsyn	aCt	aAt	58	58	1	25426-25428
ORF3a	12	T12S		nonsyn	aCt	aGt	58	54	0.931035	25426-25428
ORF3a	12	T12S		nonsyn	Act	Tct	58	4	0.0689655	25426-25428
ORF3a	12	T12P		nonsyn	Act	Cct	57	57	1	25426-25428
ORF3a	12	T12del1		del	acT	ac-	11	7	0.636364	25426-25428
ORF3a	12	T12del1		del	Act	-ct	11	3	0.272727	25426-25428
ORF3a	12	T12del1		del	ACt	-Tt	11	1	0.0909091	25426-25428
ORF3a	12	T12Q		nonsyn	ACT	CAA	6	6	1	25426-25428
ORF3a	12	T12del2		del	aCT	a--	3	2	0.666667	25426-25428
ORF3a	12	T12del2		del	ACt	--t	3	1	0.333333	25426-25428
ORF3a	12	T12K		nonsyn	aCT	aAA	2	2	1	25426-25428
ORF3a	12	T12R		nonsyn	ACT	CGA	2	2	1	25426-25428
ORF3a	12	T12X		nonsyn	ACT	TGA	1	1	1	25426-25428

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	12	T12I	aCt	aTt	5300	5302	All	0.001014
ORF3a	12	T12I	aCT	aTC	2	5302	All	0
ORF3a	12	T12I	aCt	aTt	3212	3214	B.1.1.7	0.002875
ORF3a	12	T12I	aCT	aTC	2	3214	B.1.1.7	0.000002
ORF3a	12	T12del	ACT	---	889	889	All	0.00017
ORF3a	12	T12I	aCt	aTt	346	346	P.1	0.005451
ORF3a	12	T12I	aCt	aTt	316	316	AY.4	0.000492
ORF3a	12	T12del	ACT	---	258	258	B.1.1.7	0.000231
ORF3a	12	T12I	aCt	aTt	241	241	B.1.160	0.007516
ORF3a	12	T12T	acT	acC	134	181	All	0.000026
ORF3a	12	T12T	acT	acA	40	181	All	0.000008
ORF3a	12	T12T	acT	acG	7	181	All	0.000001
ORF3a	12	T12A	Act	Gct	150	150	All	0.000029
ORF3a	12	T12del	ACT	---	114	114	B.1.177	0.001501
ORF3a	12	T12I	aCt	aTt	97	97	AY.25	0.000583
ORF3a	12	T12del	ACT	---	76	76	AY.4	0.000118
ORF3a	12	T12I	aCt	aTt	64	64	B.1.2	0.000564
ORF3a	12	T12I	aCt	aTt	59	59	B.1.177	0.000777
ORF3a	12	T12N	aCt	aAt	58	58	All	0.000011
ORF3a	12	T12S	aCt	aGt	54	58	All	0.00001
ORF3a	12	T12S	Act	Tct	4	58	All	0.000001
ORF3a	12	T12P	Act	Cct	57	57	All	0.000011
ORF3a	12	T12I	aCt	aTt	56	56	B.1.617.2	0.000211
ORF3a	12	T12A	Act	Gct	53	53	AY.3	0.000527
ORF3a	12	T12P	Act	Cct	40	40	B.1.1.7	0.000036
ORF3a	12	T12I	aCt	aTt	39	39	AY.44	0.000237
ORF3a	12	T12T	acT	acC	36	39	B.1.1.7	0.000032
ORF3a	12	T12T	acT	acA	2	39	B.1.1.7	0.000002
ORF3a	12	T12T	acT	acG	1	39	B.1.1.7	0.000001
ORF3a	12	T12I	aCt	aTt	39	39	B.1.621	0.003452
ORF3a	12	T12I	aCt	aTt	38	38	AY.4.2	0.000824
ORF3a	12	T12I	aCt	aTt	38	38	AY.43	0.000168
ORF3a	12	T12I	aCt	aTt	38	38	Q.1	0.0048
ORF3a	12	T12I	aCt	aTt	37	37	AY.113	0.005268
ORF3a	12	T12I	aCt	aTt	37	37	B.1.1	0.000671
ORF3a	12	T12T	acT	acC	34	34	AY.51	0.030909
ORF3a	12	T12I	aCt	aTt	34	34	B.1.526	0.000799
ORF3a	12	T12T	acT	acA	32	32	B.1.1.214	0.001775
ORF3a	12	T12I	aCt	aTt	27	27	B.1	0.000247
ORF3a	12	T12del	ACT	---	27	27	B.1	0.000247
ORF3a	12	T12I	aCt	aTt	26	26	AY.103	0.000161
ORF3a	12	T12S	aCt	aGt	25	25	B.1.258	0.001664
ORF3a	12	T12del	ACT	---	25	25	B.1.526	0.000588
ORF3a	12	T12del	ACT	---	24	24	AY.8	0.014545
ORF3a	12	T12I	aCt	aTt	22	22	AY.39	0.000544
ORF3a	12	T12del	ACT	---	22	22	AY.43	0.000097
ORF3a	12	T12I	aCt	aTt	22	22	B.1.351	0.000654
ORF3a	12	T12I	aCt	aTt	19	19	AY.3	0.000189
ORF3a	12	T12del	ACT	---	18	18	B.1.617.2	0.000068
ORF3a	12	T12I	aCt	aTt	17	17	AY.14	0.001496
ORF3a	12	T12I	aCt	aTt	17	17	P.1.14	0.000813
ORF3a	12	T12A	Act	Gct	16	16	AY.3.1	0.001364
ORF3a	12	T12A	Act	Gct	16	16	B.1.1.7	0.000014
ORF3a	12	T12del	ACT	---	16	16	B.1.2	0.000141
ORF3a	12	T12del	ACT	---	16	16	P.1	0.000252
ORF3a	12	T12N	aCt	aAt	15	15	B.1.426	0.015136
ORF3a	12	T12I	aCt	aTt	15	15	B.1.637	0.001096
ORF3a	12	T12del	ACT	---	14	14	AY.25	0.000084
ORF3a	12	T12del	ACT	---	14	14	AY.44	0.000085
ORF3a	12	T12I	aCt	aTt	14	14	B.1.243	0.000974
ORF3a	12	T12del	ACT	---	13	13	AY.29	0.000205
ORF3a	12	T12T	acT	acC	13	13	AY.44	0.000079
ORF3a	12	T12I	aCt	aTt	12	12	AE.7	1
ORF3a	12	T12I	aCt	aTt	12	12	AY.102	0.000318
ORF3a	12	T12I	aCt	aTt	12	12	AY.118	0.000752
ORF3a	12	T12I	aCt	aTt	12	12	B.1.1.519	0.000477
ORF3a	12	T12del1	acT	ac-	7	11	All	0.000001
ORF3a	12	T12del1	Act	-ct	3	11	All	0.000001
ORF3a	12	T12del1	ACt	-Tt	1	11	All	0
ORF3a	12	T12I	aCt	aTt	11	11	AY.117	0.00093
ORF3a	12	T12I	aCt	aTt	11	11	AY.119	0.000388
ORF3a	12	T12I	aCt	aTt	11	11	AY.62	0.004793
ORF3a	12	T12N	aCt	aAt	11	11	W.3	0.057895
ORF3a	12	T12del	ACT	---	10	10	AY.4.5	0.001075
ORF3a	12	T12I	aCt	aTt	10	10	AY.42	0.000402
ORF3a	12	T12I	aCt	aTt	10	10	AY.5	0.000206
ORF3a	12	T12I	aCt	aTt	9	9	AY.120	0.000335
ORF3a	12	T12P	Act	Cct	9	9	AY.25	0.000054
ORF3a	12	T12del	ACT	---	9	9	AY.3	0.00009
ORF3a	12	T12del	ACT	---	9	9	B.1.1	0.000163
ORF3a	12	T12I	aCt	aTt	9	9	B.1.1.316	0.008326
ORF3a	12	T12del	ACT	---	9	9	B.1.234	0.001187
ORF3a	12	T12I	aCt	aTt	9	9	B.1.429	0.000212
ORF3a	12	T12A	Act	Gct	9	9	P.1	0.000142
ORF3a	12	T12I	aCt	aTt	8	8	AY.75	0.000448
ORF3a	12	T12I	aCt	aTt	8	8	B.1.177.33	0.013158
ORF3a	12	T12I	aCt	aTt	7	7	AY.100	0.000322
ORF3a	12	T12del	ACT	---	7	7	B.1.1.317	0.002882
ORF3a	12	T12I	aCt	aTt	7	7	B.1.427	0.000353
ORF3a	12	T12del	ACT	---	7	7	B.1.540	0.067961
ORF3a	12	T12Q	ACT	CAA	6	6	All	0.000001
ORF3a	12	T12I	aCt	aTt	6	6	AY.29	0.000095
ORF3a	12	T12del	ACT	---	6	6	AZ.1	0.005204
ORF3a	12	T12T	acT	acC	5	6	B.1	0.000046
ORF3a	12	T12T	acT	acG	1	6	B.1	0.000009
ORF3a	12	T12I	aCt	aTt	6	6	B.1.1.1	0.00196
ORF3a	12	T12del	ACT	---	6	6	B.1.160	0.000187
ORF3a	12	T12del	ACT	---	6	6	B.1.177.7	0.000989
ORF3a	12	T12del	ACT	---	6	6	B.1.561	0.002382
ORF3a	12	T12del	ACT	---	6	6	B.1.609	0.002876
ORF3a	12	T12I	aCt	aTt	6	6	P.2	0.00112
ORF3a	12	T12T	acT	acC	5	5	AY.103	0.000031
ORF3a	12	T12I	aCt	aTt	5	5	AY.20	0.000194
ORF3a	12	T12A	Act	Gct	5	5	AY.44	0.00003
ORF3a	12	T12T	acT	acC	5	5	AY.47	0.000156
ORF3a	12	T12I	aCt	aTt	5	5	AY.5.3	0.001687
ORF3a	12	T12N	aCt	aAt	5	5	B.1.1.7	0.000004
ORF3a	12	T12Q	ACT	CAA	5	5	B.1.1.98	0.092593
ORF3a	12	T12S	aCt	aGt	5	5	B.1.2	0.000044
ORF3a	12	T12I	aCt	aTt	5	5	B.1.234	0.00066
ORF3a	12	T12del	ACT	---	5	5	B.1.258	0.000333
ORF3a	12	T12I	aCt	aTt	5	5	B.1.258.4	0.017241
ORF3a	12	T12I	aCt	aTt	5	5	B.1.36.36	0.00301
ORF3a	12	T12del	ACT	---	5	5	B.1.429	0.000118
ORF3a	12	T12I	aCt	aTt	5	5	B.1.525	0.000566
ORF3a	12	T12I	aCt	aTt	5	5	B.1.596	0.000436
ORF3a	12	T12I	aCt	aTt	5	5	B.1.617.1	0.000645
ORF3a	12	T12I	aCt	aTt	4	4	AY.26	0.000113
ORF3a	12	T12N	aCt	aAt	4	4	AY.4	0.000006
ORF3a	12	T12I	aCt	aTt	4	4	AY.87	0.003331
ORF3a	12	T12I	aCt	aTt	4	4	AY.99.2	0.000369
ORF3a	12	T12del	ACT	---	4	4	B.1.1.214	0.000222
ORF3a	12	T12del	ACT	---	4	4	B.1.1.222	0.000816
ORF3a	12	T12del	ACT	---	4	4	B.1.1.28	0.001245
ORF3a	12	T12S	aCt	aGt	3	4	B.1.1.7	0.000003
ORF3a	12	T12S	Act	Tct	1	4	B.1.1.7	0.000001
ORF3a	12	T12del	ACT	---	4	4	B.1.177.4	0.000844
ORF3a	12	T12I	aCt	aTt	4	4	B.1.221	0.000284
ORF3a	12	T12T	acT	acC	4	4	B.1.258	0.000266
ORF3a	12	T12I	aCt	aTt	4	4	B.1.258	0.000266
ORF3a	12	T12T	acT	acC	4	4	B.1.617.2	0.000015
ORF3a	12	T12I	aCt	aTt	4	4	B.1.619.1	0.002566
ORF3a	12	T12I	aCt	aTt	4	4	P.1.12	0.001936
ORF3a	12	T12A	Act	Gct	4	4	P.2	0.000747
ORF3a	12	T12del2	aCT	a--	2	3	All	0
ORF3a	12	T12del2	ACt	--t	1	3	All	0
ORF3a	12	T12T	acT	acC	3	3	AY.118	0.000188
ORF3a	12	T12S	aCt	aGt	3	3	AY.20	0.000117
ORF3a	12	T12A	Act	Gct	3	3	AY.25	0.000018
ORF3a	12	T12S	aCt	aGt	3	3	AY.25	0.000018
ORF3a	12	T12A	Act	Gct	3	3	AY.26	0.000085
ORF3a	12	T12I	aCt	aTt	3	3	AY.3.1	0.000256
ORF3a	12	T12I	aCt	aTt	3	3	AY.33	0.0002
ORF3a	12	T12I	aCt	aTt	3	3	AY.34	0.000291
ORF3a	12	T12A	Act	Gct	3	3	AY.42	0.000121
ORF3a	12	T12N	aCt	aAt	3	3	AY.43	0.000013
ORF3a	12	T12I	aCt	aTt	3	3	AY.5.4	0.00083
ORF3a	12	T12I	aCt	aTt	3	3	AY.75.1	0.000541
ORF3a	12	T12A	Act	Gct	3	3	B.1	0.000027
ORF3a	12	T12del	ACT	---	3	3	B.1.1.133	0.025424
ORF3a	12	T12I	aCt	aTt	3	3	B.1.1.214	0.000166
ORF3a	12	T12del	ACT	---	3	3	B.1.1.519	0.000119
ORF3a	12	T12del	ACT	---	3	3	B.1.126	0.003827
ORF3a	12	T12del	ACT	---	3	3	B.1.177.20	0.004552
ORF3a	12	T12I	aCt	aTt	3	3	B.1.177.21	0.000229
ORF3a	12	T12A	Act	Gct	3	3	B.1.177.35	0.002073
ORF3a	12	T12del	ACT	---	3	3	B.1.177.60	0.000655
ORF3a	12	T12I	aCt	aTt	3	3	B.1.177.77	0.002179
ORF3a	12	T12del	ACT	---	3	3	B.1.221	0.000213
ORF3a	12	T12I	aCt	aTt	3	3	B.1.240	0.000647
ORF3a	12	T12del	ACT	---	3	3	B.1.36.18	0.001261
ORF3a	12	T12I	aCt	aTt	3	3	B.1.375	0.002459
ORF3a	12	T12I	aCt	aTt	3	3	B.1.453	0.009709
ORF3a	12	T12I	aCt	aTt	3	3	B.1.469	0.01083
ORF3a	12	T12del	ACT	---	3	3	B.1.510	0.078947
ORF3a	12	T12I	aCt	aTt	3	3	B.1.577	0.002062
ORF3a	12	T12A	Act	Gct	3	3	B.1.617.1	0.000387
ORF3a	12	T12del	ACT	---	3	3	B.1.637	0.000219
ORF3a	12	T12del	ACT	---	3	3	C.37	0.000348
ORF3a	12	T12N	aCt	aAt	3	3	P.1	0.000047
ORF3a	12	T12T	acT	acA	2	3	P.1	0.000032
ORF3a	12	T12T	acT	acC	1	3	P.1	0.000016
ORF3a	12	T12I	aCt	aTt	3	3	Q.8	0.000495
ORF3a	12	T12R	ACT	CGA	2	2		0.111111
ORF3a	12	T12K	aCT	aAA	2	2		0.111111
ORF3a	12	T12T	acT	acG	2	2		0.111111
ORF3a	12	T12del	ACT	---	2	2	AD.2	0.000438
ORF3a	12	T12I	aCt	aTt	2	2	AD.2	0.000438
ORF3a	12	T12R	ACT	CGA	2	2	All	0
ORF3a	12	T12K	aCT	aAA	2	2	All	0
ORF3a	12	T12del	ACT	---	2	2	AY.103	0.000012
ORF3a	12	T12I	aCt	aTt	2	2	AY.116.1	0.000623
ORF3a	12	T12I	aCt	aTt	2	2	AY.16	0.000759
ORF3a	12	T12P	Act	Cct	2	2	AY.20	0.000078
ORF3a	12	T12I	aCt	aTt	2	2	AY.23	0.000139
ORF3a	12	T12A	Act	Gct	2	2	AY.23	0.000139
ORF3a	12	T12N	aCt	aAt	2	2	AY.25	0.000012
ORF3a	12	T12S	aCt	aGt	2	2	AY.26	0.000057
ORF3a	12	T12del	ACT	---	2	2	AY.27	0.000129
ORF3a	12	T12I	aCt	aTt	2	2	AY.36	0.000296
ORF3a	12	T12T	acT	acC	2	2	AY.4	0.000003
ORF3a	12	T12P	Act	Cct	2	2	AY.4	0.000003
ORF3a	12	T12T	acT	acC	2	2	AY.4.4	0.000818
ORF3a	12	T12T	acT	acC	2	2	AY.43	0.000009
ORF3a	12	T12I	aCt	aTt	2	2	AY.45	0.000243
ORF3a	12	T12I	aCt	aTt	2	2	AY.46	0.000208
ORF3a	12	T12T	acT	acC	2	2	AY.46.3	0.001867
ORF3a	12	T12I	aCt	aTt	2	2	AY.46.6	0.000144
ORF3a	12	T12del	ACT	---	2	2	AY.47	0.000062
ORF3a	12	T12I	aCt	aTt	2	2	AY.47	0.000062
ORF3a	12	T12del	ACT	---	2	2	AY.5	0.000041
ORF3a	12	T12A	Act	Gct	2	2	AY.5	0.000041
ORF3a	12	T12I	aCt	aTt	2	2	AY.6	0.000082
ORF3a	12	T12S	aCt	aGt	2	2	AY.61	0.00021
ORF3a	12	T12del	ACT	---	2	2	AY.75	0.000112
ORF3a	12	T12S	aCt	aGt	2	2	AY.75.1	0.000361
ORF3a	12	T12I	aCt	aTt	2	2	AY.9	0.000135
ORF3a	12	T12del	ACT	---	2	2	AY.90	0.001369
ORF3a	12	T12I	aCt	aTt	2	2	AY.98.1	0.000097
ORF3a	12	T12I	aCt	aTt	2	2	B.1.1.153	0.002191
ORF3a	12	T12I	aCt	aTt	2	2	B.1.1.170	0.002494
ORF3a	12	T12I	aCt	aTt	2	2	B.1.1.210	0.011429
ORF3a	12	T12I	aCt	aTt	2	2	B.1.1.28	0.000622
ORF3a	12	T12del	ACT	---	2	2	B.1.1.301	0.002358
ORF3a	12	T12I	aCt	aTt	2	2	B.1.1.302	0.004149
ORF3a	12	T12I	aCt	aTt	2	2	B.1.1.370	0.025316
ORF3a	12	T12I	aCt	aTt	2	2	B.1.1.521	0.010695
ORF3a	12	T12del1	Act	-ct	2	2	B.1.1.7	0.000002
ORF3a	12	T12del2	aCT	a--	2	2	B.1.1.7	0.000002
ORF3a	12	T12I	aCt	aTt	2	2	B.1.1.70	0.000682
ORF3a	12	T12del1	ACt	-Tt	1	2	B.1.177	0.000013
ORF3a	12	T12del1	acT	ac-	1	2	B.1.177	0.000013
ORF3a	12	T12del	ACT	---	2	2	B.1.177.32	0.002699
ORF3a	12	T12I	aCt	aTt	2	2	B.1.177.7	0.00033
ORF3a	12	T12I	aCt	aTt	2	2	B.1.177.73	0.001133
ORF3a	12	T12del	ACT	---	2	2	B.1.177.83	0.002963
ORF3a	12	T12I	aCt	aTt	2	2	B.1.189	0.008584
ORF3a	12	T12T	acT	acC	2	2	B.1.221	0.000142
ORF3a	12	T12I	aCt	aTt	2	2	B.1.258.17	0.000208
ORF3a	12	T12del	ACT	---	2	2	B.1.258.3	0.00335
ORF3a	12	T12I	aCt	aTt	2	2	B.1.351.3	0.001753
ORF3a	12	T12I	aCt	aTt	2	2	B.1.36	0.000292
ORF3a	12	T12A	Act	Gct	2	2	B.1.36.1	0.002281
ORF3a	12	T12del	ACT	---	2	2	B.1.427	0.000101
ORF3a	12	T12A	Act	Gct	2	2	B.1.429	0.000047
ORF3a	12	T12del	ACT	---	2	2	B.1.453	0.006472
ORF3a	12	T12del	ACT	---	2	2	B.1.506	0.047619
ORF3a	12	T12del	ACT	---	2	2	B.1.525	0.000226
ORF3a	12	T12A	Act	Gct	2	2	B.1.526	0.000047
ORF3a	12	T12I	aCt	aTt	2	2	B.1.575	0.000607
ORF3a	12	T12del	ACT	---	2	2	B.1.582	0.000981
ORF3a	12	T12del	ACT	---	2	2	B.1.596	0.000174
ORF3a	12	T12A	Act	Gct	2	2	B.1.617.2	0.000008
ORF3a	12	T12S	aCt	aGt	2	2	B.1.617.2	0.000008
ORF3a	12	T12I	aCt	aTt	2	2	B.1.620	0.001892
ORF3a	12	T12T	acT	acC	2	2	B.1.621	0.000177
ORF3a	12	T12I	aCt	aTt	2	2	B.23	0.005848
ORF3a	12	T12I	aCt	aTt	2	2	C.36	0.001821
ORF3a	12	T12del	ACT	---	2	2	C.36.3	0.001134
ORF3a	12	T12I	aCt	aTt	2	2	C.37	0.000232
ORF3a	12	T12I	aCt	aTt	2	2	D.2	0.00015
ORF3a	12	T12I	aCt	aTt	2	2	P.1.10.1	0.01626
ORF3a	12	T12del	ACT	---	2	2	P.1.14	0.000096
ORF3a	12	T12I	aCt	aTt	2	2	Q.7	0.002222
ORF3a	12	T12del	ACT	---	2	2	R.1	0.00018
ORF3a	12	T12del	ACT	---	2	2	U.3	0.007722
ORF3a	12	T12del	ACT	---	1	1	A.2.5	0.000499
ORF3a	12	T12I	aCt	aTt	1	1	A.27	0.001656
ORF3a	12	T12I	aCt	aTt	1	1	AL.1	0.012987
ORF3a	12	T12X	ACT	TGA	1	1	All	0
ORF3a	12	T12I	aCt	aTt	1	1	AY.1	0.000396
ORF3a	12	T12del	ACT	---	1	1	AY.100	0.000046
ORF3a	12	T12I	aCt	aTt	1	1	AY.101	0.00049
ORF3a	12	T12N	aCt	aAt	1	1	AY.102	0.000027
ORF3a	12	T12A	Act	Gct	1	1	AY.103	0.000006
ORF3a	12	T12del1	Act	-ct	1	1	AY.103	0.000006
ORF3a	12	T12del	ACT	---	1	1	AY.105	0.000643
ORF3a	12	T12I	aCt	aTt	1	1	AY.110	0.000113
ORF3a	12	T12del	ACT	---	1	1	AY.111	0.000183
ORF3a	12	T12T	acT	acA	1	1	AY.111	0.000183
ORF3a	12	T12T	acT	acC	1	1	AY.113	0.000142
ORF3a	12	T12A	Act	Gct	1	1	AY.113	0.000142
ORF3a	12	T12I	aCt	aTt	1	1	AY.114	0.000231
ORF3a	12	T12del	ACT	---	1	1	AY.117	0.000085
ORF3a	12	T12A	Act	Gct	1	1	AY.117	0.000085
ORF3a	12	T12P	Act	Cct	1	1	AY.119	0.000035
ORF3a	12	T12A	Act	Gct	1	1	AY.119	0.000035
ORF3a	12	T12del	ACT	---	1	1	AY.14	0.000088
ORF3a	12	T12S	aCt	aGt	1	1	AY.16	0.00038
ORF3a	12	T12del	ACT	---	1	1	AY.19	0.00114
ORF3a	12	T12I	aCt	aTt	1	1	AY.2	0.000356
ORF3a	12	T12del	ACT	---	1	1	AY.20	0.000039
ORF3a	12	T12del	ACT	---	1	1	AY.23	0.00007
ORF3a	12	T12T	acT	acC	1	1	AY.25	0.000006
ORF3a	12	T12del	ACT	---	1	1	AY.26	0.000028
ORF3a	12	T12N	aCt	aAt	1	1	AY.26	0.000028
ORF3a	12	T12N	aCt	aAt	1	1	AY.29	0.000016
ORF3a	12	T12del	ACT	---	1	1	AY.29.1	0.000221
ORF3a	12	T12X	ACT	TGA	1	1	AY.3	0.00001
ORF3a	12	T12del1	acT	ac-	1	1	AY.3	0.00001
ORF3a	12	T12del	ACT	---	1	1	AY.3.1	0.000085
ORF3a	12	T12S	Act	Tct	1	1	AY.30	0.000396
ORF3a	12	T12del	ACT	---	1	1	AY.33	0.000067
ORF3a	12	T12A	Act	Gct	1	1	AY.33	0.000067
ORF3a	12	T12T	acT	acG	1	1	AY.34	0.000097
ORF3a	12	T12del	ACT	---	1	1	AY.35	0.000233
ORF3a	12	T12A	Act	Gct	1	1	AY.36	0.000148
ORF3a	12	T12A	Act	Gct	1	1	AY.37	0.000316
ORF3a	12	T12I	aCt	aTt	1	1	AY.38	0.000499
ORF3a	12	T12del	ACT	---	1	1	AY.39	0.000025
ORF3a	12	T12N	aCt	aAt	1	1	AY.39	0.000025
ORF3a	12	T12del1	acT	ac-	1	1	AY.4	0.000002
ORF3a	12	T12del2	ACt	--t	1	1	AY.4	0.000002
ORF3a	12	T12A	Act	Gct	1	1	AY.4	0.000002
ORF3a	12	T12I	aCt	aTt	1	1	AY.4.3	0.000842
ORF3a	12	T12I	aCt	aTt	1	1	AY.4.5	0.000107
ORF3a	12	T12del	ACT	---	1	1	AY.42	0.00004
ORF3a	12	T12S	Act	Tct	1	1	AY.43	0.000004
ORF3a	12	T12P	Act	Cct	1	1	AY.43	0.000004
ORF3a	12	T12N	aCt	aAt	1	1	AY.45	0.000122
ORF3a	12	T12I	aCt	aTt	1	1	AY.46.2	0.000635
ORF3a	12	T12N	aCt	aAt	1	1	AY.46.6	0.000072
ORF3a	12	T12S	aCt	aGt	1	1	AY.47	0.000031
ORF3a	12	T12N	aCt	aAt	1	1	AY.47	0.000031
ORF3a	12	T12del	ACT	---	1	1	AY.5.4	0.000277
ORF3a	12	T12I	aCt	aTt	1	1	AY.51	0.000909
ORF3a	12	T12T	acT	acC	1	1	AY.54	0.000095
ORF3a	12	T12I	aCt	aTt	1	1	AY.55	0.000917
ORF3a	12	T12del	ACT	---	1	1	AY.6	0.000041
ORF3a	12	T12A	Act	Gct	1	1	AY.6	0.000041
ORF3a	12	T12del	ACT	---	1	1	AY.60	0.000938
ORF3a	12	T12I	aCt	aTt	1	1	AY.61	0.000105
ORF3a	12	T12T	acT	acC	1	1	AY.61	0.000105
ORF3a	12	T12A	Act	Gct	1	1	AY.61	0.000105
ORF3a	12	T12I	aCt	aTt	1	1	AY.63	0.000387
ORF3a	12	T12I	aCt	aTt	1	1	AY.64	0.000595
ORF3a	12	T12A	Act	Gct	1	1	AY.75.1	0.00018
ORF3a	12	T12A	Act	Gct	1	1	AY.78	0.001541
ORF3a	12	T12del	ACT	---	1	1	AY.81	0.001992
ORF3a	12	T12I	aCt	aTt	1	1	AY.86	0.00083
ORF3a	12	T12N	aCt	aAt	1	1	AY.9	0.000068
ORF3a	12	T12del	ACT	---	1	1	AY.9	0.000068
ORF3a	12	T12I	aCt	aTt	1	1	AY.9.1	0.000084
ORF3a	12	T12A	Act	Gct	1	1	AY.9.2	0.000037
ORF3a	12	T12I	aCt	aTt	1	1	AY.9.2	0.000037
ORF3a	12	T12del	ACT	---	1	1	AY.9.2	0.000037
ORF3a	12	T12del	ACT	---	1	1	AY.92	0.000287
ORF3a	12	T12I	aCt	aTt	1	1	AY.92	0.000287
ORF3a	12	T12T	acT	acA	1	1	AY.94	0.000443
ORF3a	12	T12I	aCt	aTt	1	1	AY.95	0.000761
ORF3a	12	T12N	aCt	aAt	1	1	AY.98	0.000079
ORF3a	12	T12I	aCt	aTt	1	1	AY.99	0.001049
ORF3a	12	T12del	ACT	---	1	1	AY.99	0.001049
ORF3a	12	T12I	aCt	aTt	1	1	AZ.1	0.000867
ORF3a	12	T12I	aCt	aTt	1	1	B	0.000128
ORF3a	12	T12del1	acT	ac-	1	1	B.1	0.000009
ORF3a	12	T12S	aCt	aGt	1	1	B.1	0.000009
ORF3a	12	T12N	aCt	aAt	1	1	B.1.1	0.000018
ORF3a	12	T12S	aCt	aGt	1	1	B.1.1	0.000018
ORF3a	12	T12del	ACT	---	1	1	B.1.1.1	0.000327
ORF3a	12	T12del	ACT	---	1	1	B.1.1.10	0.001115
ORF3a	12	T12I	aCt	aTt	1	1	B.1.1.158	0.012195
ORF3a	12	T12T	acT	acC	1	1	B.1.1.176	0.000439
ORF3a	12	T12I	aCt	aTt	1	1	B.1.1.207	0.001182
ORF3a	12	T12I	aCt	aTt	1	1	B.1.1.216	0.00089
ORF3a	12	T12del	ACT	---	1	1	B.1.1.220	0.001859
ORF3a	12	T12I	aCt	aTt	1	1	B.1.1.229	0.005747
ORF3a	12	T12del	ACT	---	1	1	B.1.1.234	0.012048
ORF3a	12	T12I	aCt	aTt	1	1	B.1.1.25	0.000569
ORF3a	12	T12I	aCt	aTt	1	1	B.1.1.269	0.001353
ORF3a	12	T12S	aCt	aGt	1	1	B.1.1.294	0.001266
ORF3a	12	T12I	aCt	aTt	1	1	B.1.1.301	0.001179
ORF3a	12	T12I	aCt	aTt	1	1	B.1.1.306	0.000438
ORF3a	12	T12del	ACT	---	1	1	B.1.1.312	0.001912
ORF3a	12	T12T	acT	acG	1	1	B.1.1.33	0.000421
ORF3a	12	T12I	aCt	aTt	1	1	B.1.1.33	0.000421
ORF3a	12	T12I	aCt	aTt	1	1	B.1.1.337	0.003597
ORF3a	12	T12del	ACT	---	1	1	B.1.1.37	0.000193
ORF3a	12	T12I	aCt	aTt	1	1	B.1.1.37	0.000193
ORF3a	12	T12I	aCt	aTt	1	1	B.1.1.400	0.05
ORF3a	12	T12del	ACT	---	1	1	B.1.1.409	0.002833
ORF3a	12	T12N	aCt	aAt	1	1	B.1.1.434	0.000349
ORF3a	12	T12A	Act	Gct	1	1	B.1.1.464	0.001473
ORF3a	12	T12del	ACT	---	1	1	B.1.1.486	0.001577
ORF3a	12	T12Q	ACT	CAA	1	1	B.1.1.52	0.012195
ORF3a	12	T12I	aCt	aTt	1	1	B.1.1.523	0.001563
ORF3a	12	T12I	aCt	aTt	1	1	B.1.1.57	0.011494
ORF3a	12	T12I	aCt	aTt	1	1	B.1.1.89	0.006061
ORF3a	12	T12del	ACT	---	1	1	B.1.1.98	0.018519
ORF3a	12	T12del	ACT	---	1	1	B.1.128	0.000635
ORF3a	12	T12del	ACT	---	1	1	B.1.142	0.002899
ORF3a	12	T12A	Act	Gct	1	1	B.1.160	0.000031
ORF3a	12	T12del	ACT	---	1	1	B.1.160.16	0.000929
ORF3a	12	T12del	ACT	---	1	1	B.1.160.23	0.004831
ORF3a	12	T12del	ACT	---	1	1	B.1.160.32	0.004292
ORF3a	12	T12I	aCt	aTt	1	1	B.1.170	0.00431
ORF3a	12	T12T	acT	acC	1	1	B.1.177	0.000013
ORF3a	12	T12T	acT	acC	1	1	B.1.177.10	0.000878
ORF3a	12	T12I	aCt	aTt	1	1	B.1.177.16	0.000664
ORF3a	12	T12del	ACT	---	1	1	B.1.177.19	0.001431
ORF3a	12	T12I	aCt	aTt	1	1	B.1.177.35	0.000691
ORF3a	12	T12I	aCt	aTt	1	1	B.1.177.54	0.000606
ORF3a	12	T12I	aCt	aTt	1	1	B.1.177.56	0.000668
ORF3a	12	T12del	ACT	---	1	1	B.1.177.57	0.000281
ORF3a	12	T12del	ACT	---	1	1	B.1.177.58	0.001332
ORF3a	12	T12del1	acT	ac-	1	1	B.1.177.6	0.000977
ORF3a	12	T12I	aCt	aTt	1	1	B.1.177.60	0.000218
ORF3a	12	T12del	ACT	---	1	1	B.1.177.69	0.001484
ORF3a	12	T12del	ACT	---	1	1	B.1.177.73	0.000566
ORF3a	12	T12del	ACT	---	1	1	B.1.177.76	0.002494
ORF3a	12	T12T	acT	acC	1	1	B.1.177.8	0.000752
ORF3a	12	T12I	aCt	aTt	1	1	B.1.177.81	0.000189
ORF3a	12	T12T	acT	acC	1	1	B.1.177.81	0.000189
ORF3a	12	T12S	aCt	aGt	1	1	B.1.177.81	0.000189
ORF3a	12	T12I	aCt	aTt	1	1	B.1.177.86	0.000183
ORF3a	12	T12T	acT	acC	1	1	B.1.177.86	0.000183
ORF3a	12	T12del	ACT	---	1	1	B.1.195	0.005025
ORF3a	12	T12del1	acT	ac-	1	1	B.1.2	0.000009
ORF3a	12	T12A	Act	Gct	1	1	B.1.2	0.000009
ORF3a	12	T12T	acT	acA	1	1	B.1.2	0.000009
ORF3a	12	T12del	ACT	---	1	1	B.1.221.1	0.002907
ORF3a	12	T12I	aCt	aTt	1	1	B.1.221.3	0.000833
ORF3a	12	T12I	aCt	aTt	1	1	B.1.232	0.000537
ORF3a	12	T12del1	acT	ac-	1	1	B.1.240	0.000216
ORF3a	12	T12I	aCt	aTt	1	1	B.1.241	0.000812
ORF3a	12	T12del	ACT	---	1	1	B.1.243	0.00007
ORF3a	12	T12del	ACT	---	1	1	B.1.258.17	0.000104
ORF3a	12	T12N	aCt	aAt	1	1	B.1.265	0.001271
ORF3a	12	T12I	aCt	aTt	1	1	B.1.265	0.001271
ORF3a	12	T12T	acT	acC	1	1	B.1.351	0.00003
ORF3a	12	T12del	ACT	---	1	1	B.1.351	0.00003
ORF3a	12	T12I	aCt	aTt	1	1	B.1.36.22	0.001208
ORF3a	12	T12I	aCt	aTt	1	1	B.1.36.7	0.004
ORF3a	12	T12I	aCt	aTt	1	1	B.1.36.9	0.003215
ORF3a	12	T12I	aCt	aTt	1	1	B.1.362	0.001541
ORF3a	12	T12del	ACT	---	1	1	B.1.363	0.012987
ORF3a	12	T12I	aCt	aTt	1	1	B.1.369	0.000285
ORF3a	12	T12del	ACT	---	1	1	B.1.375	0.00082
ORF3a	12	T12del	ACT	---	1	1	B.1.378	0.006849
ORF3a	12	T12del	ACT	---	1	1	B.1.408	0.00369
ORF3a	12	T12del	ACT	---	1	1	B.1.409	0.000781
ORF3a	12	T12T	acT	acG	1	1	B.1.416.1	0.001563
ORF3a	12	T12del	ACT	---	1	1	B.1.422	0.000812
ORF3a	12	T12I	aCt	aTt	1	1	B.1.425	0.002994
ORF3a	12	T12I	aCt	aTt	1	1	B.1.466.2	0.000391
ORF3a	12	T12del	ACT	---	1	1	B.1.500	0.052632
ORF3a	12	T12I	aCt	aTt	1	1	B.1.509	0.000866
ORF3a	12	T12T	acT	acC	1	1	B.1.516	0.001957
ORF3a	12	T12N	aCt	aAt	1	1	B.1.526	0.000024
ORF3a	12	T12S	aCt	aGt	1	1	B.1.561	0.000397
ORF3a	12	T12del	ACT	---	1	1	B.1.577	0.000687
ORF3a	12	T12T	acT	acA	1	1	B.1.587	0.001898
ORF3a	12	T12I	aCt	aTt	1	1	B.1.588	0.00091
ORF3a	12	T12I	aCt	aTt	1	1	B.1.590	0.004545
ORF3a	12	T12del	ACT	---	1	1	B.1.595	0.000261
ORF3a	12	T12I	aCt	aTt	1	1	B.1.595	0.000261
ORF3a	12	T12I	aCt	aTt	1	1	B.1.609	0.000479
ORF3a	12	T12del	ACT	---	1	1	B.1.617.1	0.000129
ORF3a	12	T12N	aCt	aAt	1	1	B.1.617.2	0.000004
ORF3a	12	T12I	aCt	aTt	1	1	B.1.623	0.000536
ORF3a	12	T12del	ACT	---	1	1	B.1.623	0.000536
ORF3a	12	T12del	ACT	---	1	1	B.1.628	0.000352
ORF3a	12	T12del	ACT	---	1	1	B.1.638	0.052632
ORF3a	12	T12I	aCt	aTt	1	1	B.1.8	0.001972
ORF3a	12	T12I	aCt	aTt	1	1	B.1.9.5	0.005682
ORF3a	12	T12I	aCt	aTt	1	1	B.1.93	0.000934
ORF3a	12	T12del	ACT	---	1	1	B.3.1	0.001658
ORF3a	12	T12del	ACT	---	1	1	B.40	0.000364
ORF3a	12	T12I	aCt	aTt	1	1	B.58	0.010204
ORF3a	12	T12A	Act	Gct	1	1	B.60	0.015873
ORF3a	12	T12I	aCt	aTt	1	1	C.35	0.000774
ORF3a	12	T12del	ACT	---	1	1	C.36	0.000911
ORF3a	12	T12I	aCt	aTt	1	1	K.1	0.02381
ORF3a	12	T12P	Act	Cct	1	1	P.1	0.000016
ORF3a	12	T12I	aCt	aTt	1	1	P.1.1	0.000318
ORF3a	12	T12del	ACT	---	1	1	P.1.10	0.000269
ORF3a	12	T12I	aCt	aTt	1	1	P.1.10	0.000269
ORF3a	12	T12I	aCt	aTt	1	1	P.1.13	0.000898
ORF3a	12	T12N	aCt	aAt	1	1	P.1.14	0.000048
ORF3a	12	T12S	Act	Tct	1	1	P.1.14	0.000048
ORF3a	12	T12I	aCt	aTt	1	1	P.1.15	0.000232
ORF3a	12	T12del	ACT	---	1	1	P.1.15	0.000232
ORF3a	12	T12del	ACT	---	1	1	P.1.16	0.000374
ORF3a	12	T12P	Act	Cct	1	1	P.1.7	0.000319
ORF3a	12	T12del	ACT	---	1	1	P.1.7	0.000319
ORF3a	12	T12I	aCt	aTt	1	1	P.1.7	0.000319
ORF3a	12	T12del	ACT	---	1	1	P.2	0.000187
ORF3a	12	T12del	ACT	---	1	1	Q.2	0.000613
ORF3a	12	T12I	aCt	aTt	1	1	Q.4	0.000455
ORF3a	12	T12del	ACT	---	1	1	Q.4	0.000455
ORF3a	12	T12del	ACT	---	1	1	Q.8	0.000165

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.