CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : Mut = Y1323del

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
ORF1ab/nsp3	1323	Y1323del	Y2141del	del	TAT	---	753	753	1	6686-6688

Details of the mutation Y1323del 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
ORF1ab/nsp3	1323	Y1323del	TAT	---	753	753	All	0.000144
ORF1ab/nsp3	1323	Y1323del	TAT	---	116	116	B.1.1.7	0.000104
ORF1ab/nsp3	1323	Y1323del	TAT	---	93	93	B.1.617.2	0.00035
ORF1ab/nsp3	1323	Y1323del	TAT	---	68	68	AY.103	0.000422
ORF1ab/nsp3	1323	Y1323del	TAT	---	68	68	AY.44	0.000414
ORF1ab/nsp3	1323	Y1323del	TAT	---	49	49	AY.43	0.000217
ORF1ab/nsp3	1323	Y1323del	TAT	---	39	39	AY.4	0.000061
ORF1ab/nsp3	1323	Y1323del	TAT	---	37	37	AY.25	0.000223
ORF1ab/nsp3	1323	Y1323del	TAT	---	17	17	B.1.177	0.000224
ORF1ab/nsp3	1323	Y1323del	TAT	---	13	13	AY.36	0.001927
ORF1ab/nsp3	1323	Y1323del	TAT	---	13	13	B.1	0.000119
ORF1ab/nsp3	1323	Y1323del	TAT	---	11	11	AY.29	0.000174
ORF1ab/nsp3	1323	Y1323del	TAT	---	10	10	AY.26	0.000283
ORF1ab/nsp3	1323	Y1323del	TAT	---	10	10	AY.34.1	0.005099
ORF1ab/nsp3	1323	Y1323del	TAT	---	9	9	AY.102	0.000239
ORF1ab/nsp3	1323	Y1323del	TAT	---	8	8	AY.119	0.000282
ORF1ab/nsp3	1323	Y1323del	TAT	---	8	8	AY.3	0.00008
ORF1ab/nsp3	1323	Y1323del	TAT	---	7	7	AY.4.5	0.000752
ORF1ab/nsp3	1323	Y1323del	TAT	---	7	7	B.1.2	0.000062
ORF1ab/nsp3	1323	Y1323del	TAT	---	6	6	AY.111	0.001099
ORF1ab/nsp3	1323	Y1323del	TAT	---	6	6	AY.20	0.000233
ORF1ab/nsp3	1323	Y1323del	TAT	---	6	6	AY.47	0.000187
ORF1ab/nsp3	1323	Y1323del	TAT	---	6	6	AY.75	0.000336
ORF1ab/nsp3	1323	Y1323del	TAT	---	5	5	AY.5	0.000103
ORF1ab/nsp3	1323	Y1323del	TAT	---	5	5	AY.74	0.000578
ORF1ab/nsp3	1323	Y1323del	TAT	---	4	4	AY.100	0.000184
ORF1ab/nsp3	1323	Y1323del	TAT	---	4	4	AY.39	0.000099
ORF1ab/nsp3	1323	Y1323del	TAT	---	4	4	AY.46.6	0.000289
ORF1ab/nsp3	1323	Y1323del	TAT	---	3	3	AY.23	0.000209
ORF1ab/nsp3	1323	Y1323del	TAT	---	3	3	AY.39.1	0.000119
ORF1ab/nsp3	1323	Y1323del	TAT	---	3	3	AY.61	0.000314
ORF1ab/nsp3	1323	Y1323del	TAT	---	3	3	B.1.1	0.000054
ORF1ab/nsp3	1323	Y1323del	TAT	---	3	3	B.1.1.351	0.00838
ORF1ab/nsp3	1323	Y1323del	TAT	---	3	3	B.1.36.17	0.001482
ORF1ab/nsp3	1323	Y1323del	TAT	---	3	3	B.1.596	0.000261
ORF1ab/nsp3	1323	Y1323del	TAT	---	2	2	AY.1	0.000791
ORF1ab/nsp3	1323	Y1323del	TAT	---	2	2	AY.38	0.000999
ORF1ab/nsp3	1323	Y1323del	TAT	---	2	2	AY.65	0.001066
ORF1ab/nsp3	1323	Y1323del	TAT	---	2	2	AY.92	0.000575
ORF1ab/nsp3	1323	Y1323del	TAT	---	2	2	AY.99.2	0.000184
ORF1ab/nsp3	1323	Y1323del	TAT	---	2	2	B.1.1.153	0.002191
ORF1ab/nsp3	1323	Y1323del	TAT	---	2	2	B.1.1.39	0.001019
ORF1ab/nsp3	1323	Y1323del	TAT	---	2	2	B.1.160	0.000062
ORF1ab/nsp3	1323	Y1323del	TAT	---	2	2	B.1.177.17	0.001642
ORF1ab/nsp3	1323	Y1323del	TAT	---	2	2	B.1.177.56	0.001335
ORF1ab/nsp3	1323	Y1323del	TAT	---	2	2	B.1.36	0.000292
ORF1ab/nsp3	1323	Y1323del	TAT	---	2	2	B.1.588	0.00182
ORF1ab/nsp3	1323	Y1323del	TAT	---	2	2	B.1.595	0.000522
ORF1ab/nsp3	1323	Y1323del	TAT	---	2	2	P.1	0.000032
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	A.1	0.000282
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.113	0.000142
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.114	0.000231
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.118	0.000063
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.14	0.000088
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.16	0.00038
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.19	0.00114
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.21	0.001898
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.27	0.000065
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.3.1	0.000085
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.32	0.000532
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.33	0.000067
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.35	0.000233
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.37	0.000316
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.42	0.00004
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.45	0.000122
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.46.2	0.000635
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.55	0.000917
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.59	0.00053
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.6	0.000041
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.60	0.000938
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.68	0.000274
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.7	0.000196
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.70	0.000209
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.72	0.001361
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.75.1	0.00018
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.84	0.000437
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.9	0.000068
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.98.1	0.000048
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.99	0.001049
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	AY.99.1	0.001553
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.1.216	0.00089
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.1.284	0.000107
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.1.311	0.000358
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.1.312	0.001912
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.1.348	0.000796
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.1.37	0.000193
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.1.409	0.002833
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.1.416	0.000905
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.1.424	0.045455
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.1.432	0.001266
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.1.434	0.000349
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.1.47	0.005348
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.1.63	0.000386
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.160.30	0.002976
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.177.15	0.000631
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.177.16	0.000664
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.177.18	0.00116
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.177.4	0.000211
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.177.44	0.000519
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.177.45	0.000381
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.177.58	0.001332
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.177.6	0.000977
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.177.69	0.001484
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.177.7	0.000165
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.177.81	0.000189
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.177.87	0.000728
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.210	0.002132
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.243	0.00007
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.258.10	0.011364
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.258.14	0.00098
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.399	0.001934
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.526	0.000024
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.605	0.005952
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.621	0.000089
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.630	0.005236
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	B.1.9.5	0.005682
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	C.35	0.000774
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	C.36.3	0.000567
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	C.37	0.000116
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	D.2	0.000075
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	P.1.15	0.000232
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	Q.1	0.000126
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	Q.4	0.000455
ORF1ab/nsp3	1323	Y1323del	TAT	---	1	1	U.3	0.003861

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.