CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF7a : Mut = A79del

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	79	A79del		del	GCC	---	7865	7865	1	27628-27630

Details of the mutation A79del 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	79	A79del	GCC	---	7865	7865	All	0.001504
ORF7a	79	A79del	GCC	---	2805	2805	AY.4	0.004366
ORF7a	79	A79del	GCC	---	1231	1231	B.1.1.7	0.001102
ORF7a	79	A79del	GCC	---	411	411	AY.4.2	0.008914
ORF7a	79	A79del	GCC	---	304	304	B.1.617.2	0.001145
ORF7a	79	A79del	GCC	---	192	192	AY.103	0.001192
ORF7a	79	A79del	GCC	---	184	184	AY.43	0.000815
ORF7a	79	A79del	GCC	---	179	179	AY.3	0.00178
ORF7a	79	A79del	GCC	---	179	179	B.1.177.21	0.013688
ORF7a	79	A79del	GCC	---	176	176	AY.39	0.004349
ORF7a	79	A79del	GCC	---	161	161	AY.44	0.00098
ORF7a	79	A79del	GCC	---	124	124	AY.29	0.001956
ORF7a	79	A79del	GCC	---	96	96	AY.26	0.002718
ORF7a	79	A79del	GCC	---	87	87	AY.25	0.000523
ORF7a	79	A79del	GCC	---	78	78	AY.100	0.003589
ORF7a	79	A79del	GCC	---	73	73	AY.42	0.002937
ORF7a	79	A79del	GCC	---	72	72	AY.98	0.005688
ORF7a	79	A79del	GCC	---	71	71	B.1.526	0.001669
ORF7a	79	A79del	GCC	---	64	64	B.1.177	0.000843
ORF7a	79	A79del	GCC	---	62	62	AY.120	0.002305
ORF7a	79	A79del	GCC	---	60	60	B.1.2	0.000528
ORF7a	79	A79del	GCC	---	44	44	B.1.621	0.003895
ORF7a	79	A79del	GCC	---	43	43	B.1	0.000394
ORF7a	79	A79del	GCC	---	41	41	B.1.1.284	0.004403
ORF7a	79	A79del	GCC	---	40	40	P.1	0.00063
ORF7a	79	A79del	GCC	---	34	34	AY.3.1	0.002899
ORF7a	79	A79del	GCC	---	34	34	B.1.160	0.00106
ORF7a	79	A79del	GCC	---	32	32	AY.119	0.00113
ORF7a	79	A79del	GCC	---	32	32	AY.46.6	0.002311
ORF7a	79	A79del	GCC	---	32	32	AY.47	0.000995
ORF7a	79	A79del	GCC	---	29	29	AY.20	0.001127
ORF7a	79	A79del	GCC	---	29	29	AY.36	0.004298
ORF7a	79	A79del	GCC	---	29	29	AY.6	0.001193
ORF7a	79	A79del	GCC	---	27	27	B.1.351	0.000803
ORF7a	79	A79del	GCC	---	26	26	B.1.1.214	0.001442
ORF7a	79	A79del	GCC	---	25	25	AY.7.2	0.013982
ORF7a	79	A79del	GCC	---	25	25	B.1.637	0.001827
ORF7a	79	A79del	GCC	---	22	22	AY.5	0.000454
ORF7a	79	A79del	GCC	---	21	21	AY.46.4	0.003455
ORF7a	79	A79del	GCC	---	20	20	AY.102	0.00053
ORF7a	79	A79del	GCC	---	20	20	B.1.429	0.000471
ORF7a	79	A79del	GCC	---	19	19	AY.75	0.001064
ORF7a	79	A79del	GCC	---	16	16	AY.98.1	0.000775
ORF7a	79	A79del	GCC	---	15	15	AY.30	0.005936
ORF7a	79	A79del	GCC	---	15	15	C.37	0.001741
ORF7a	79	A79del	GCC	---	14	14	AY.117	0.001183
ORF7a	79	A79del	GCC	---	14	14	B.1.1.258	0.045603
ORF7a	79	A79del	GCC	---	13	13	AY.23	0.000907
ORF7a	79	A79del	GCC	---	13	13	B.1.1	0.000236
ORF7a	79	A79del	GCC	---	13	13	B.1.525	0.001471
ORF7a	79	A79del	GCC	---	13	13	R.1	0.00117
ORF7a	79	A79del	GCC	---	12	12	AY.116	0.003441
ORF7a	79	A79del	GCC	---	12	12	AY.121	0.001624
ORF7a	79	A79del	GCC	---	12	12	B.1.324	0.019262
ORF7a	79	A79del	GCC	---	11	11	AY.110	0.00124
ORF7a	79	A79del	GCC	---	11	11	AY.71	0.005226
ORF7a	79	A79del	GCC	---	11	11	AY.9	0.000744
ORF7a	79	A79del	GCC	---	11	11	B.1.596	0.000959
ORF7a	79	A79del	GCC	---	10	10	AY.39.1	0.000396
ORF7a	79	A79del	GCC	---	10	10	B.1.1.519	0.000397
ORF7a	79	A79del	GCC	---	10	10	Q.8	0.001649
ORF7a	79	A79del	GCC	---	9	9	B.1.427	0.000454
ORF7a	79	A79del	GCC	---	9	9	L.1	0.017143
ORF7a	79	A79del	GCC	---	8	8	AY.113	0.001139
ORF7a	79	A79del	GCC	---	8	8	AY.118	0.000501
ORF7a	79	A79del	GCC	---	8	8	AY.7	0.001568
ORF7a	79	A79del	GCC	---	8	8	AY.99.2	0.000737
ORF7a	79	A79del	GCC	---	8	8	B.1.1.231	0.024768
ORF7a	79	A79del	GCC	---	8	8	B.1.160.31	0.064516
ORF7a	79	A79del	GCC	---	7	7	AY.29.1	0.001544
ORF7a	79	A79del	GCC	---	7	7	AY.35	0.001631
ORF7a	79	A79del	GCC	---	7	7	AY.45	0.000852
ORF7a	79	A79del	GCC	---	6	6	AY.120.1	0.001926
ORF7a	79	A79del	GCC	---	6	6	B.1.258	0.000399
ORF7a	79	A79del	GCC	---	6	6	P.1.15	0.001394
ORF7a	79	A79del	GCC	---	5	5	AY.106	0.001674
ORF7a	79	A79del	GCC	---	5	5	AY.34	0.000485
ORF7a	79	A79del	GCC	---	5	5	AY.61	0.000524
ORF7a	79	A79del	GCC	---	5	5	AY.80	0.005643
ORF7a	79	A79del	GCC	---	5	5	AY.9.2	0.000184
ORF7a	79	A79del	GCC	---	5	5	B.1.1.1	0.001633
ORF7a	79	A79del	GCC	---	5	5	B.1.234	0.00066
ORF7a	79	A79del	GCC	---	5	5	B.1.375	0.004098
ORF7a	79	A79del	GCC	---	5	5	B.1.70	0.121951
ORF7a	79	A79del	GCC	---	5	5	P.2	0.000933
ORF7a	79	A79del	GCC	---	4	4	A	0.001548
ORF7a	79	A79del	GCC	---	4	4	AY.14	0.000352
ORF7a	79	A79del	GCC	---	4	4	AY.4.5	0.00043
ORF7a	79	A79del	GCC	---	4	4	AY.54	0.000381
ORF7a	79	A79del	GCC	---	4	4	AY.7.1	0.000451
ORF7a	79	A79del	GCC	---	4	4	B.1.1.369	0.001785
ORF7a	79	A79del	GCC	---	4	4	B.1.214.2	0.002398
ORF7a	79	A79del	GCC	---	4	4	B.1.243	0.000278
ORF7a	79	A79del	GCC	---	4	4	B.1.351.2	0.00121
ORF7a	79	A79del	GCC	---	3	3	AY.114	0.000693
ORF7a	79	A79del	GCC	---	3	3	AY.13	0.000483
ORF7a	79	A79del	GCC	---	3	3	AY.24	0.001293
ORF7a	79	A79del	GCC	---	3	3	AY.33	0.0002
ORF7a	79	A79del	GCC	---	3	3	AY.88	0.002653
ORF7a	79	A79del	GCC	---	3	3	AY.92	0.000862
ORF7a	79	A79del	GCC	---	3	3	B.1.1.121	0.007282
ORF7a	79	A79del	GCC	---	3	3	B.1.1.37	0.000579
ORF7a	79	A79del	GCC	---	3	3	B.1.160.16	0.002788
ORF7a	79	A79del	GCC	---	3	3	B.1.258.17	0.000312
ORF7a	79	A79del	GCC	---	3	3	B.1.575	0.00091
ORF7a	79	A79del	GCC	---	3	3	B.1.595	0.000783
ORF7a	79	A79del	GCC	---	3	3	B.1.626	0.017143
ORF7a	79	A79del	GCC	---	3	3	Q.1	0.000379
ORF7a	79	A79del	GCC	---	2	2	A.28	0.005291
ORF7a	79	A79del	GCC	---	2	2	AY.108	0.002205
ORF7a	79	A79del	GCC	---	2	2	AY.109	0.001479
ORF7a	79	A79del	GCC	---	2	2	AY.19	0.002281
ORF7a	79	A79del	GCC	---	2	2	AY.27	0.000129
ORF7a	79	A79del	GCC	---	2	2	AY.34.1	0.00102
ORF7a	79	A79del	GCC	---	2	2	AY.4.2.1	0.000298
ORF7a	79	A79del	GCC	---	2	2	AY.4.4	0.000818
ORF7a	79	A79del	GCC	---	2	2	AY.46	0.000208
ORF7a	79	A79del	GCC	---	2	2	AY.48	0.00093
ORF7a	79	A79del	GCC	---	2	2	AY.5.3	0.000675
ORF7a	79	A79del	GCC	---	2	2	AY.53	0.000575
ORF7a	79	A79del	GCC	---	2	2	AY.65	0.001066
ORF7a	79	A79del	GCC	---	2	2	AY.87	0.001665
ORF7a	79	A79del	GCC	---	2	2	AY.9.1	0.000167
ORF7a	79	A79del	GCC	---	2	2	AY.91	0.001461
ORF7a	79	A79del	GCC	---	2	2	AY.99	0.002099
ORF7a	79	A79del	GCC	---	2	2	B	0.000256
ORF7a	79	A79del	GCC	---	2	2	B.1.1.101	0.02
ORF7a	79	A79del	GCC	---	2	2	B.1.1.170	0.002494
ORF7a	79	A79del	GCC	---	2	2	B.1.1.220	0.003717
ORF7a	79	A79del	GCC	---	2	2	B.1.1.25	0.001137
ORF7a	79	A79del	GCC	---	2	2	B.1.1.521	0.010695
ORF7a	79	A79del	GCC	---	2	2	B.1.177.15	0.001262
ORF7a	79	A79del	GCC	---	2	2	B.1.177.55	0.004662
ORF7a	79	A79del	GCC	---	2	2	B.1.177.57	0.000562
ORF7a	79	A79del	GCC	---	2	2	B.1.177.60	0.000437
ORF7a	79	A79del	GCC	---	2	2	B.1.177.7	0.00033
ORF7a	79	A79del	GCC	---	2	2	B.1.177.81	0.000379
ORF7a	79	A79del	GCC	---	2	2	B.1.177.86	0.000367
ORF7a	79	A79del	GCC	---	2	2	B.1.221	0.000142
ORF7a	79	A79del	GCC	---	2	2	B.1.240	0.000431
ORF7a	79	A79del	GCC	---	2	2	B.1.258.11	0.000793
ORF7a	79	A79del	GCC	---	2	2	B.1.36	0.000292
ORF7a	79	A79del	GCC	---	2	2	B.1.499	0.002101
ORF7a	79	A79del	GCC	---	2	2	B.1.517.1	0.010526
ORF7a	79	A79del	GCC	---	2	2	B.1.621.1	0.001012
ORF7a	79	A79del	GCC	---	2	2	P.1.14	0.000096
ORF7a	79	A79del	GCC	---	1	1	A.1	0.000282
ORF7a	79	A79del	GCC	---	1	1	A.2.2	0.001689
ORF7a	79	A79del	GCC	---	1	1	A.23	0.010526
ORF7a	79	A79del	GCC	---	1	1	A.23.1	0.000704
ORF7a	79	A79del	GCC	---	1	1	AU.3	0.00211
ORF7a	79	A79del	GCC	---	1	1	AY.101	0.00049
ORF7a	79	A79del	GCC	---	1	1	AY.111	0.000183
ORF7a	79	A79del	GCC	---	1	1	AY.116.1	0.000311
ORF7a	79	A79del	GCC	---	1	1	AY.12	0.000316
ORF7a	79	A79del	GCC	---	1	1	AY.16	0.00038
ORF7a	79	A79del	GCC	---	1	1	AY.38	0.000499
ORF7a	79	A79del	GCC	---	1	1	AY.4.1	0.000737
ORF7a	79	A79del	GCC	---	1	1	AY.46.5	0.000198
ORF7a	79	A79del	GCC	---	1	1	AY.52	0.000814
ORF7a	79	A79del	GCC	---	1	1	AY.59	0.00053
ORF7a	79	A79del	GCC	---	1	1	AY.62	0.000436
ORF7a	79	A79del	GCC	---	1	1	AY.66	0.00107
ORF7a	79	A79del	GCC	---	1	1	AY.68	0.000274
ORF7a	79	A79del	GCC	---	1	1	AY.69	0.000187
ORF7a	79	A79del	GCC	---	1	1	AY.70	0.000209
ORF7a	79	A79del	GCC	---	1	1	AY.73	0.000665
ORF7a	79	A79del	GCC	---	1	1	AY.84	0.000437
ORF7a	79	A79del	GCC	---	1	1	AY.85	0.000427
ORF7a	79	A79del	GCC	---	1	1	AY.95	0.000761
ORF7a	79	A79del	GCC	---	1	1	AZ.2	0.000821
ORF7a	79	A79del	GCC	---	1	1	B.1.1.174	0.003378
ORF7a	79	A79del	GCC	---	1	1	B.1.1.192	0.002309
ORF7a	79	A79del	GCC	---	1	1	B.1.1.194	0.00495
ORF7a	79	A79del	GCC	---	1	1	B.1.1.205	0.003717
ORF7a	79	A79del	GCC	---	1	1	B.1.1.207	0.001182
ORF7a	79	A79del	GCC	---	1	1	B.1.1.265	0.003155
ORF7a	79	A79del	GCC	---	1	1	B.1.1.277	0.000759
ORF7a	79	A79del	GCC	---	1	1	B.1.1.301	0.001179
ORF7a	79	A79del	GCC	---	1	1	B.1.1.303	0.002762
ORF7a	79	A79del	GCC	---	1	1	B.1.1.317	0.000412
ORF7a	79	A79del	GCC	---	1	1	B.1.1.318	0.000302
ORF7a	79	A79del	GCC	---	1	1	B.1.1.33	0.000421
ORF7a	79	A79del	GCC	---	1	1	B.1.1.336	0.016667
ORF7a	79	A79del	GCC	---	1	1	B.1.1.366	0.015873
ORF7a	79	A79del	GCC	---	1	1	B.1.1.434	0.000349
ORF7a	79	A79del	GCC	---	1	1	B.1.1.437	0.010417
ORF7a	79	A79del	GCC	---	1	1	B.1.1.448	0.002033
ORF7a	79	A79del	GCC	---	1	1	B.1.1.70	0.000341
ORF7a	79	A79del	GCC	---	1	1	B.1.115	0.021739
ORF7a	79	A79del	GCC	---	1	1	B.1.177.10	0.000878
ORF7a	79	A79del	GCC	---	1	1	B.1.177.31	0.011494
ORF7a	79	A79del	GCC	---	1	1	B.1.177.4	0.000211
ORF7a	79	A79del	GCC	---	1	1	B.1.177.50	0.004695
ORF7a	79	A79del	GCC	---	1	1	B.1.177.6	0.000977
ORF7a	79	A79del	GCC	---	1	1	B.1.177.62	0.001192
ORF7a	79	A79del	GCC	---	1	1	B.1.221.1	0.002907
ORF7a	79	A79del	GCC	---	1	1	B.1.236	0.002053
ORF7a	79	A79del	GCC	---	1	1	B.1.252	0.006623
ORF7a	79	A79del	GCC	---	1	1	B.1.265	0.001271
ORF7a	79	A79del	GCC	---	1	1	B.1.319	0.003049
ORF7a	79	A79del	GCC	---	1	1	B.1.351.3	0.000876
ORF7a	79	A79del	GCC	---	1	1	B.1.36.17	0.000494
ORF7a	79	A79del	GCC	---	1	1	B.1.36.31	0.001751
ORF7a	79	A79del	GCC	---	1	1	B.1.371	0.001122
ORF7a	79	A79del	GCC	---	1	1	B.1.396	0.000706
ORF7a	79	A79del	GCC	---	1	1	B.1.406	0.006061
ORF7a	79	A79del	GCC	---	1	1	B.1.416.1	0.001563
ORF7a	79	A79del	GCC	---	1	1	B.1.459	0.004082
ORF7a	79	A79del	GCC	---	1	1	B.1.466.2	0.000391
ORF7a	79	A79del	GCC	---	1	1	B.1.468	0.005714
ORF7a	79	A79del	GCC	---	1	1	B.1.470	0.001404
ORF7a	79	A79del	GCC	---	1	1	B.1.535	0.028571
ORF7a	79	A79del	GCC	---	1	1	B.1.564.1	0.001577
ORF7a	79	A79del	GCC	---	1	1	B.1.568	0.001111
ORF7a	79	A79del	GCC	---	1	1	B.1.576	0.000907
ORF7a	79	A79del	GCC	---	1	1	B.1.582	0.000491
ORF7a	79	A79del	GCC	---	1	1	B.1.617.1	0.000129
ORF7a	79	A79del	GCC	---	1	1	B.1.628	0.000352
ORF7a	79	A79del	GCC	---	1	1	B.1.638	0.052632
ORF7a	79	A79del	GCC	---	1	1	B.1.88.1	0.004808
ORF7a	79	A79del	GCC	---	1	1	B.1.9.1	0.032258
ORF7a	79	A79del	GCC	---	1	1	B.1.93	0.000934
ORF7a	79	A79del	GCC	---	1	1	C.36.3	0.000567
ORF7a	79	A79del	GCC	---	1	1	D.2	0.000075
ORF7a	79	A79del	GCC	---	1	1	N.5	0.001767
ORF7a	79	A79del	GCC	---	1	1	P.1.1	0.000318
ORF7a	79	A79del	GCC	---	1	1	P.1.13	0.000898
ORF7a	79	A79del	GCC	---	1	1	P.1.16	0.000374
ORF7a	79	A79del	GCC	---	1	1	P.1.17	0.000162
ORF7a	79	A79del	GCC	---	1	1	P.1.3	0.034483
ORF7a	79	A79del	GCC	---	1	1	P.1.4	0.000977
ORF7a	79	A79del	GCC	---	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.