CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF7a : Mut = A79V

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	A79V		nonsyn	gCc	gTc	1012	988	0.976285	27628-27630
ORF7a	79	A79V		nonsyn	gCC	gTT	1012	23	0.0227273	27628-27630
ORF7a	79	A79V		nonsyn	gCC	gTA	1012	1	0.000988142	27628-27630

Details of the mutation A79V 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	A79V	gCc	gTc	988	1012	All	0.000189
ORF7a	79	A79V	gCC	gTT	23	1012	All	0.000004
ORF7a	79	A79V	gCC	gTA	1	1012	All	0
ORF7a	79	A79V	gCc	gTc	208	210	B.1.1.7	0.000186
ORF7a	79	A79V	gCC	gTT	2	210	B.1.1.7	0.000002
ORF7a	79	A79V	gCc	gTc	184	184	AY.4	0.000286
ORF7a	79	A79V	gCc	gTc	102	102	AY.46.6	0.007365
ORF7a	79	A79V	gCc	gTc	78	78	AY.4.5	0.008384
ORF7a	79	A79V	gCc	gTc	32	32	AY.103	0.000199
ORF7a	79	A79V	gCc	gTc	30	30	B.1.2	0.000264
ORF7a	79	A79V	gCc	gTc	27	27	B.1.617.2	0.000102
ORF7a	79	A79V	gCc	gTc	19	19	AY.99.2	0.001751
ORF7a	79	A79V	gCc	gTc	18	19	B.1	0.000165
ORF7a	79	A79V	gCC	gTT	1	19	B.1	0.000009
ORF7a	79	A79V	gCc	gTc	18	18	AY.25	0.000108
ORF7a	79	A79V	gCc	gTc	14	18	B.1.1	0.000254
ORF7a	79	A79V	gCC	gTT	4	18	B.1.1	0.000073
ORF7a	79	A79V	gCc	gTc	15	15	AY.9.1	0.001256
ORF7a	79	A79V	gCc	gTc	13	15	B.1.351	0.000386
ORF7a	79	A79V	gCC	gTT	2	15	B.1.351	0.000059
ORF7a	79	A79V	gCc	gTc	12	12	AY.44	0.000073
ORF7a	79	A79V	gCc	gTc	10	10	AY.39	0.000247
ORF7a	79	A79V	gCc	gTc	10	10	AY.4.2.1	0.00149
ORF7a	79	A79V	gCc	gTc	10	10	AY.43	0.000044
ORF7a	79	A79V	gCc	gTc	8	8	AY.61	0.000838
ORF7a	79	A79V	gCc	gTc	8	8	B.1.1.348	0.006369
ORF7a	79	A79V	gCc	gTc	6	7	B.1.177	0.000079
ORF7a	79	A79V	gCC	gTT	1	7	B.1.177	0.000013
ORF7a	79	A79V	gCc	gTc	7	7	B.1.526	0.000165
ORF7a	79	A79V	gCc	gTc	7	7	P.1	0.00011
ORF7a	79	A79V	gCc	gTc	7	7	Q.1	0.000884
ORF7a	79	A79V	gCc	gTc	6	6	AY.23	0.000418
ORF7a	79	A79V	gCc	gTc	6	6	AY.3	0.00006
ORF7a	79	A79V	gCc	gTc	6	6	B.1.1.519	0.000238
ORF7a	79	A79V	gCc	gTc	5	5	AY.102	0.000133
ORF7a	79	A79V	gCc	gTc	5	5	AY.3.1	0.000426
ORF7a	79	A79V	gCc	gTc	4	4	AY.16	0.001519
ORF7a	79	A79V	gCc	gTc	4	4	AY.27	0.000259
ORF7a	79	A79V	gCc	gTc	4	4	B.1.1.271	0.222222
ORF7a	79	A79V	gCc	gTc	4	4	B.1.243	0.000278
ORF7a	79	A79V	gCc	gTc	4	4	B.1.427	0.000202
ORF7a	79	A79V	gCc	gTc	4	4	B.1.429	0.000094
ORF7a	79	A79V	gCc	gTc	3	3	AY.116.1	0.000934
ORF7a	79	A79V	gCc	gTc	3	3	AY.39.1	0.000119
ORF7a	79	A79V	gCc	gTc	3	3	AY.47	0.000093
ORF7a	79	A79V	gCc	gTc	3	3	AY.99.1	0.004658
ORF7a	79	A79V	gCc	gTc	3	3	B.1.177.32	0.004049
ORF7a	79	A79V	gCC	gTT	3	3	B.1.36.1	0.003421
ORF7a	79	A79V	gCc	gTc	3	3	B.1.620	0.002838
ORF7a	79	A79V	gCc	gTc	2	2	A.2.5	0.000998
ORF7a	79	A79V	gCc	gTc	2	2	AY.106	0.00067
ORF7a	79	A79V	gCc	gTc	2	2	AY.119	0.000071
ORF7a	79	A79V	gCc	gTc	2	2	AY.29	0.000032
ORF7a	79	A79V	gCc	gTc	2	2	AY.46.5	0.000397
ORF7a	79	A79V	gCc	gTc	2	2	AY.78	0.003082
ORF7a	79	A79V	gCc	gTc	2	2	AY.9.2	0.000073
ORF7a	79	A79V	gCc	gTc	2	2	B.1.411	0.007407
ORF7a	79	A79V	gCc	gTc	2	2	B.6	0.00182
ORF7a	79	A79V	gCc	gTc	2	2	P.1.10	0.000539
ORF7a	79	A79V	gCc	gTc	2	2	P.1.14	0.000096
ORF7a	79	A79V	gCc	gTc	1	1	A.19	0.009434
ORF7a	79	A79V	gCc	gTc	1	1	AS.2	0.015625
ORF7a	79	A79V	gCc	gTc	1	1	AY.100	0.000046
ORF7a	79	A79V	gCc	gTc	1	1	AY.120	0.000037
ORF7a	79	A79V	gCc	gTc	1	1	AY.13	0.000161
ORF7a	79	A79V	gCc	gTc	1	1	AY.14	0.000088
ORF7a	79	A79V	gCc	gTc	1	1	AY.20	0.000039
ORF7a	79	A79V	gCc	gTc	1	1	AY.26	0.000028
ORF7a	79	A79V	gCc	gTc	1	1	AY.32	0.000532
ORF7a	79	A79V	gCc	gTc	1	1	AY.33	0.000067
ORF7a	79	A79V	gCc	gTc	1	1	AY.37	0.000316
ORF7a	79	A79V	gCc	gTc	1	1	AY.4.2	0.000022
ORF7a	79	A79V	gCc	gTc	1	1	AY.4.3	0.000842
ORF7a	79	A79V	gCc	gTc	1	1	AY.42	0.00004
ORF7a	79	A79V	gCc	gTc	1	1	AY.5	0.000021
ORF7a	79	A79V	gCc	gTc	1	1	AY.53	0.000288
ORF7a	79	A79V	gCc	gTc	1	1	AY.6	0.000041
ORF7a	79	A79V	gCc	gTc	1	1	AY.75	0.000056
ORF7a	79	A79V	gCc	gTc	1	1	AY.85	0.000427
ORF7a	79	A79V	gCc	gTc	1	1	AY.9	0.000068
ORF7a	79	A79V	gCc	gTc	1	1	AY.98	0.000079
ORF7a	79	A79V	gCc	gTc	1	1	AY.98.1	0.000048
ORF7a	79	A79V	gCc	gTc	1	1	B	0.000128
ORF7a	79	A79V	gCc	gTc	1	1	B.1.1.121	0.002427
ORF7a	79	A79V	gCc	gTc	1	1	B.1.1.157	0.000913
ORF7a	79	A79V	gCc	gTc	1	1	B.1.1.176	0.000439
ORF7a	79	A79V	gCC	gTT	1	1	B.1.1.189	0.001513
ORF7a	79	A79V	gCC	gTT	1	1	B.1.1.25	0.000569
ORF7a	79	A79V	gCC	gTT	1	1	B.1.1.282	0.011628
ORF7a	79	A79V	gCc	gTc	1	1	B.1.1.291	0.000742
ORF7a	79	A79V	gCC	gTT	1	1	B.1.1.305	0.003861
ORF7a	79	A79V	gCc	gTc	1	1	B.1.1.306	0.000438
ORF7a	79	A79V	gCc	gTc	1	1	B.1.1.326	0.001761
ORF7a	79	A79V	gCc	gTc	1	1	B.1.1.37	0.000193
ORF7a	79	A79V	gCc	gTc	1	1	B.1.1.70	0.000341
ORF7a	79	A79V	gCc	gTc	1	1	B.1.160	0.000031
ORF7a	79	A79V	gCc	gTc	1	1	B.1.177.15	0.000631
ORF7a	79	A79V	gCc	gTc	1	1	B.1.177.21	0.000076
ORF7a	79	A79V	gCc	gTc	1	1	B.1.177.43	0.001477
ORF7a	79	A79V	gCC	gTA	1	1	B.1.177.63	0.002703
ORF7a	79	A79V	gCc	gTc	1	1	B.1.177.81	0.000189
ORF7a	79	A79V	gCc	gTc	1	1	B.1.221	0.000071
ORF7a	79	A79V	gCc	gTc	1	1	B.1.236	0.002053
ORF7a	79	A79V	gCc	gTc	1	1	B.1.240	0.000216
ORF7a	79	A79V	gCC	gTT	1	1	B.1.242	0.018868
ORF7a	79	A79V	gCc	gTc	1	1	B.1.311	0.000275
ORF7a	79	A79V	gCc	gTc	1	1	B.1.349	0.000715
ORF7a	79	A79V	gCC	gTT	1	1	B.1.36	0.000146
ORF7a	79	A79V	gCc	gTc	1	1	B.1.36.31	0.001751
ORF7a	79	A79V	gCc	gTc	1	1	B.1.36.9	0.003215
ORF7a	79	A79V	gCc	gTc	1	1	B.1.362	0.001541
ORF7a	79	A79V	gCC	gTT	1	1	B.1.438	0.006536
ORF7a	79	A79V	gCc	gTc	1	1	B.1.444	0.015873
ORF7a	79	A79V	gCC	gTT	1	1	B.1.469	0.00361
ORF7a	79	A79V	gCc	gTc	1	1	B.1.509	0.000866
ORF7a	79	A79V	gCC	gTT	1	1	B.1.525	0.000113
ORF7a	79	A79V	gCc	gTc	1	1	B.1.596	0.000087
ORF7a	79	A79V	gCc	gTc	1	1	B.6.6	0.000889
ORF7a	79	A79V	gCc	gTc	1	1	C.1.2	0.004255
ORF7a	79	A79V	gCc	gTc	1	1	P.1.1	0.000318
ORF7a	79	A79V	gCc	gTc	1	1	P.1.17	0.000162
ORF7a	79	A79V	gCC	gTT	1	1	P.1.17.1	0.000875
ORF7a	79	A79V	gCc	gTc	1	1	P.1.2	0.001156
ORF7a	79	A79V	gCc	gTc	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.