CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF3a : Mut = A72S

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	72	A72S		nonsyn	Gca	Tca	6068	6063	0.999176	25606-25608
ORF3a	72	A72S		nonsyn	GCA	AGC	6068	3	0.000494397	25606-25608
ORF3a	72	A72S		nonsyn	GcA	TcT	6068	2	0.000329598	25606-25608

Details of the mutation A72S 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	72	A72S	Gca	Tca	6063	6068	All	0.00116
ORF3a	72	A72S	GCA	AGC	3	6068	All	0.000001
ORF3a	72	A72S	GcA	TcT	2	6068	All	0
ORF3a	72	A72S	Gca	Tca	2765	2765	B.1.258	0.184002
ORF3a	72	A72S	Gca	Tca	563	563	B.1.1.7	0.000504
ORF3a	72	A72S	Gca	Tca	445	445	B.1.351	0.013228
ORF3a	72	A72S	Gca	Tca	329	329	B.1.160.14	0.697034
ORF3a	72	A72S	Gca	Tca	259	259	B.1	0.002372
ORF3a	72	A72S	Gca	Tca	245	245	AY.4	0.000381
ORF3a	72	A72S	Gca	Tca	124	124	B.1.617.2	0.000467
ORF3a	72	A72S	Gca	Tca	118	118	B.1.429	0.002776
ORF3a	72	A72S	Gca	Tca	90	90	B.1.151	1
ORF3a	72	A72S	Gca	Tca	73	73	AY.43	0.000323
ORF3a	72	A72S	Gca	Tca	70	70	AY.103	0.000435
ORF3a	72	A72S	Gca	Tca	68	68	AY.113	0.009682
ORF3a	72	A72S	Gca	Tca	64	64	B.1.177	0.000843
ORF3a	72	A72S	Gca	Tca	57	57	B.1.1	0.001034
ORF3a	72	A72S	Gca	Tca	51	51	P.1.14	0.002438
ORF3a	72	A72S	Gca	Tca	50	50	AY.44	0.000304
ORF3a	72	A72S	Gca	Tca	40	40	B.1.160	0.001248
ORF3a	72	A72S	Gca	Tca	31	31	B	0.003962
ORF3a	72	A72S	Gca	Tca	30	30	AY.4.2	0.000651
ORF3a	72	A72S	Gca	Tca	29	29	AY.39	0.000717
ORF3a	72	A72S	Gca	Tca	29	29	B.1.2	0.000255
ORF3a	72	A72S	Gca	Tca	27	27	AY.102	0.000716
ORF3a	72	A72S	Gca	Tca	20	20	P.1	0.000315
ORF3a	72	A72S	Gca	Tca	19	19	B.1.427	0.000959
ORF3a	72	A72S	Gca	Tca	18	18	B.1.1.333	0.019376
ORF3a	72	A72S	Gca	Tca	16	16	AY.26	0.000453
ORF3a	72	A72S	Gca	Tca	15	15	AY.25	0.00009
ORF3a	72	A72S	Gca	Tca	15	15	B.1.617.1	0.001934
ORF3a	72	A72S	Gca	Tca	14	14	AY.29	0.000221
ORF3a	72	A72S	Gca	Tca	13	13	AY.5	0.000268
ORF3a	72	A72S	Gca	Tca	12	12	AY.119	0.000424
ORF3a	72	A72S	Gca	Tca	11	11	A	0.004257
ORF3a	72	A72S	Gca	Tca	10	10	AY.16	0.003797
ORF3a	72	A72S	Gca	Tca	10	10	AY.3	0.000099
ORF3a	72	A72S	Gca	Tca	10	10	B.1.466.2	0.003912
ORF3a	72	A72S	Gca	Tca	8	8	AY.120	0.000297
ORF3a	72	A72S	Gca	Tca	8	8	AY.23	0.000558
ORF3a	72	A72S	Gca	Tca	7	7	AY.41	0.002058
ORF3a	72	A72S	Gca	Tca	2	6		0.111111
ORF3a	72	A72S	GCA	AGC	2	6		0.111111
ORF3a	72	A72S	GcA	TcT	2	6		0.111111
ORF3a	72	A72S	Gca	Tca	6	6	AY.20	0.000233
ORF3a	72	A72S	Gca	Tca	6	6	AY.98	0.000474
ORF3a	72	A72S	Gca	Tca	6	6	C.9	0.181818
ORF3a	72	A72S	Gca	Tca	5	5	AY.14	0.00044
ORF3a	72	A72S	Gca	Tca	5	5	AY.34	0.000485
ORF3a	72	A72S	Gca	Tca	5	5	AY.36	0.000741
ORF3a	72	A72S	Gca	Tca	5	5	B.1.526	0.000118
ORF3a	72	A72S	Gca	Tca	5	5	P.1.15	0.001162
ORF3a	72	A72S	Gca	Tca	4	4	AY.45	0.000487
ORF3a	72	A72S	Gca	Tca	4	4	AY.6	0.000165
ORF3a	72	A72S	Gca	Tca	4	4	B.1.1.397	0.009009
ORF3a	72	A72S	Gca	Tca	4	4	B.1.221	0.000284
ORF3a	72	A72S	Gca	Tca	4	4	B.1.243	0.000278
ORF3a	72	A72S	Gca	Tca	4	4	B.1.258.21	0.031008
ORF3a	72	A72S	Gca	Tca	4	4	B.1.36	0.000584
ORF3a	72	A72S	Gca	Tca	4	4	B.1.459	0.016327
ORF3a	72	A72S	Gca	Tca	4	4	B.1.469	0.01444
ORF3a	72	A72S	Gca	Tca	4	4	B.1.609	0.001918
ORF3a	72	A72S	Gca	Tca	4	4	P.3	0.00638
ORF3a	72	A72S	Gca	Tca	3	3	AY.108	0.003308
ORF3a	72	A72S	Gca	Tca	3	3	AY.27	0.000194
ORF3a	72	A72S	Gca	Tca	3	3	AY.33	0.0002
ORF3a	72	A72S	Gca	Tca	3	3	AY.46.5	0.000595
ORF3a	72	A72S	Gca	Tca	3	3	AY.5.4	0.00083
ORF3a	72	A72S	Gca	Tca	3	3	AY.75	0.000168
ORF3a	72	A72S	Gca	Tca	3	3	AY.78	0.004622
ORF3a	72	A72S	Gca	Tca	3	3	AY.9.2	0.00011
ORF3a	72	A72S	Gca	Tca	3	3	B.1.1.214	0.000166
ORF3a	72	A72S	Gca	Tca	3	3	B.1.1.39	0.001529
ORF3a	72	A72S	Gca	Tca	3	3	B.1.139	0.002199
ORF3a	72	A72S	Gca	Tca	3	3	B.1.177.12	0.000455
ORF3a	72	A72S	Gca	Tca	3	3	B.1.218	0.015464
ORF3a	72	A72S	Gca	Tca	3	3	B.1.222	0.005076
ORF3a	72	A72S	Gca	Tca	3	3	B.1.258.11	0.001189
ORF3a	72	A72S	Gca	Tca	3	3	B.1.359	0.068182
ORF3a	72	A72S	Gca	Tca	3	3	B.1.621	0.000266
ORF3a	72	A72S	Gca	Tca	3	3	B.26	0.044118
ORF3a	72	A72S	Gca	Tca	3	3	C.37	0.000348
ORF3a	72	A72S	Gca	Tca	3	3	P.1.7	0.000958
ORF3a	72	A72S	Gca	Tca	2	2	A.2	0.001324
ORF3a	72	A72S	Gca	Tca	2	2	A.23.1	0.001408
ORF3a	72	A72S	Gca	Tca	2	2	A.29	0.010638
ORF3a	72	A72S	Gca	Tca	2	2	AD.2	0.000438
ORF3a	72	A72S	Gca	Tca	2	2	AY.1	0.000791
ORF3a	72	A72S	Gca	Tca	2	2	AY.10	0.00106
ORF3a	72	A72S	Gca	Tca	2	2	AY.117	0.000169
ORF3a	72	A72S	Gca	Tca	2	2	AY.29.1	0.000441
ORF3a	72	A72S	Gca	Tca	2	2	AY.4.5	0.000215
ORF3a	72	A72S	Gca	Tca	2	2	AY.46	0.000208
ORF3a	72	A72S	Gca	Tca	2	2	AY.59	0.001059
ORF3a	72	A72S	Gca	Tca	2	2	AY.61	0.00021
ORF3a	72	A72S	Gca	Tca	2	2	AY.7.1	0.000225
ORF3a	72	A72S	Gca	Tca	2	2	AY.71	0.00095
ORF3a	72	A72S	Gca	Tca	2	2	AY.98.1	0.000097
ORF3a	72	A72S	Gca	Tca	2	2	AY.99	0.002099
ORF3a	72	A72S	Gca	Tca	2	2	B.1.1.153	0.002191
ORF3a	72	A72S	Gca	Tca	2	2	B.1.1.170	0.002494
ORF3a	72	A72S	Gca	Tca	2	2	B.1.1.204	0.006079
ORF3a	72	A72S	Gca	Tca	2	2	B.1.1.28	0.000622
ORF3a	72	A72S	Gca	Tca	2	2	B.1.1.306	0.000877
ORF3a	72	A72S	Gca	Tca	2	2	B.1.1.318	0.000604
ORF3a	72	A72S	Gca	Tca	2	2	B.1.1.375	0.02381
ORF3a	72	A72S	Gca	Tca	2	2	B.1.1.420	0.002012
ORF3a	72	A72S	Gca	Tca	2	2	B.1.1.434	0.000697
ORF3a	72	A72S	Gca	Tca	2	2	B.1.1.50	0.001358
ORF3a	72	A72S	Gca	Tca	2	2	B.1.1.70	0.000682
ORF3a	72	A72S	Gca	Tca	2	2	B.1.160.30	0.005952
ORF3a	72	A72S	Gca	Tca	2	2	B.1.177.60	0.000437
ORF3a	72	A72S	Gca	Tca	2	2	B.1.258.2	0.009009
ORF3a	72	A72S	Gca	Tca	2	2	B.1.351.2	0.000605
ORF3a	72	A72S	Gca	Tca	2	2	B.1.36.29	0.001035
ORF3a	72	A72S	Gca	Tca	2	2	B.1.369	0.00057
ORF3a	72	A72S	Gca	Tca	2	2	B.1.525	0.000226
ORF3a	72	A72S	Gca	Tca	2	2	Q.1	0.000253
ORF3a	72	A72S	Gca	Tca	1	1	A.1	0.000282
ORF3a	72	A72S	Gca	Tca	1	1	A.21	0.00277
ORF3a	72	A72S	Gca	Tca	1	1	AY.116	0.000287
ORF3a	72	A72S	Gca	Tca	1	1	AY.118	0.000063
ORF3a	72	A72S	Gca	Tca	1	1	AY.12	0.000316
ORF3a	72	A72S	Gca	Tca	1	1	AY.121	0.000135
ORF3a	72	A72S	Gca	Tca	1	1	AY.24	0.000431
ORF3a	72	A72S	Gca	Tca	1	1	AY.3.1	0.000085
ORF3a	72	A72S	Gca	Tca	1	1	AY.39.1	0.00004
ORF3a	72	A72S	Gca	Tca	1	1	AY.40	0.000964
ORF3a	72	A72S	Gca	Tca	1	1	AY.42	0.00004
ORF3a	72	A72S	Gca	Tca	1	1	AY.46.3	0.000934
ORF3a	72	A72S	Gca	Tca	1	1	AY.47	0.000031
ORF3a	72	A72S	Gca	Tca	1	1	AY.49	0.003195
ORF3a	72	A72S	Gca	Tca	1	1	AY.53	0.000288
ORF3a	72	A72S	Gca	Tca	1	1	AY.55	0.000917
ORF3a	72	A72S	Gca	Tca	1	1	AY.68	0.000274
ORF3a	72	A72S	Gca	Tca	1	1	AY.77	0.001127
ORF3a	72	A72S	Gca	Tca	1	1	AY.9	0.000068
ORF3a	72	A72S	Gca	Tca	1	1	AY.9.1	0.000084
ORF3a	72	A72S	Gca	Tca	1	1	AY.90	0.000684
ORF3a	72	A72S	Gca	Tca	1	1	AY.92	0.000287
ORF3a	72	A72S	Gca	Tca	1	1	AY.99.2	0.000092
ORF3a	72	A72S	Gca	Tca	1	1	B.1.1.1	0.000327
ORF3a	72	A72S	GCA	AGC	1	1	B.1.1.139	0.022727
ORF3a	72	A72S	Gca	Tca	1	1	B.1.1.174	0.003378
ORF3a	72	A72S	Gca	Tca	1	1	B.1.1.189	0.001513
ORF3a	72	A72S	Gca	Tca	1	1	B.1.1.216	0.00089
ORF3a	72	A72S	Gca	Tca	1	1	B.1.1.222	0.000204
ORF3a	72	A72S	Gca	Tca	1	1	B.1.1.241	0.00207
ORF3a	72	A72S	Gca	Tca	1	1	B.1.1.25	0.000569
ORF3a	72	A72S	Gca	Tca	1	1	B.1.1.301	0.001179
ORF3a	72	A72S	Gca	Tca	1	1	B.1.1.464	0.001473
ORF3a	72	A72S	Gca	Tca	1	1	B.1.1.519	0.00004
ORF3a	72	A72S	Gca	Tca	1	1	B.1.127	0.002198
ORF3a	72	A72S	Gca	Tca	1	1	B.1.157	0.002985
ORF3a	72	A72S	Gca	Tca	1	1	B.1.160.16	0.000929
ORF3a	72	A72S	Gca	Tca	1	1	B.1.160.23	0.004831
ORF3a	72	A72S	Gca	Tca	1	1	B.1.160.29	0.004219
ORF3a	72	A72S	Gca	Tca	1	1	B.1.177.16	0.000664
ORF3a	72	A72S	Gca	Tca	1	1	B.1.177.17	0.000821
ORF3a	72	A72S	Gca	Tca	1	1	B.1.177.44	0.000519
ORF3a	72	A72S	Gca	Tca	1	1	B.1.177.6	0.000977
ORF3a	72	A72S	Gca	Tca	1	1	B.1.177.75	0.001041
ORF3a	72	A72S	Gca	Tca	1	1	B.1.177.86	0.000183
ORF3a	72	A72S	Gca	Tca	1	1	B.1.210	0.002132
ORF3a	72	A72S	Gca	Tca	1	1	B.1.235	0.002519
ORF3a	72	A72S	Gca	Tca	1	1	B.1.258.12	0.007874
ORF3a	72	A72S	Gca	Tca	1	1	B.1.258.14	0.00098
ORF3a	72	A72S	Gca	Tca	1	1	B.1.258.15	0.018868
ORF3a	72	A72S	Gca	Tca	1	1	B.1.258.3	0.001675
ORF3a	72	A72S	Gca	Tca	1	1	B.1.284	0.013158
ORF3a	72	A72S	Gca	Tca	1	1	B.1.293	0.0125
ORF3a	72	A72S	Gca	Tca	1	1	B.1.326	0.007576
ORF3a	72	A72S	Gca	Tca	1	1	B.1.329	0.000608
ORF3a	72	A72S	Gca	Tca	1	1	B.1.349	0.000715
ORF3a	72	A72S	Gca	Tca	1	1	B.1.36.27	0.000763
ORF3a	72	A72S	Gca	Tca	1	1	B.1.36.35	0.002604
ORF3a	72	A72S	Gca	Tca	1	1	B.1.375	0.00082
ORF3a	72	A72S	Gca	Tca	1	1	B.1.40	0.019608
ORF3a	72	A72S	Gca	Tca	1	1	B.1.416.1	0.001563
ORF3a	72	A72S	Gca	Tca	1	1	B.1.437	0.020833
ORF3a	72	A72S	Gca	Tca	1	1	B.1.473	0.019231
ORF3a	72	A72S	Gca	Tca	1	1	B.1.499	0.00105
ORF3a	72	A72S	Gca	Tca	1	1	B.1.516	0.001957
ORF3a	72	A72S	Gca	Tca	1	1	B.1.527	0.003704
ORF3a	72	A72S	Gca	Tca	1	1	B.1.568	0.001111
ORF3a	72	A72S	Gca	Tca	1	1	B.1.575.1	0.002439
ORF3a	72	A72S	Gca	Tca	1	1	B.1.625	0.002353
ORF3a	72	A72S	Gca	Tca	1	1	B.1.627	0.00202
ORF3a	72	A72S	Gca	Tca	1	1	B.1.632	0.006711
ORF3a	72	A72S	Gca	Tca	1	1	B.1.78	0.008547
ORF3a	72	A72S	Gca	Tca	1	1	B.1.94	0.027027
ORF3a	72	A72S	Gca	Tca	1	1	B.3.1	0.001658
ORF3a	72	A72S	Gca	Tca	1	1	C.1.2	0.004255
ORF3a	72	A72S	Gca	Tca	1	1	D.2	0.000075
ORF3a	72	A72S	Gca	Tca	1	1	K.1	0.02381
ORF3a	72	A72S	Gca	Tca	1	1	P.1.12	0.000484
ORF3a	72	A72S	Gca	Tca	1	1	P.2	0.000187
ORF3a	72	A72S	Gca	Tca	1	1	Q.7	0.001111
ORF3a	72	A72S	Gca	Tca	1	1	Q.8	0.000165
ORF3a	72	A72S	Gca	Tca	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.