CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = M : Mut = F28L

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
M	28	F28L		nonsyn	Ttc	Ctc	20093	19901	0.990444	26604-26606
M	28	F28L		nonsyn	ttC	ttA	20093	182	0.00905788	26604-26606
M	28	F28L		nonsyn	TtC	CtT	20093	7	0.00034838	26604-26606
M	28	F28L		nonsyn	ttC	ttG	20093	3	0.000149306	26604-26606

Details of the mutation F28L 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
M	28	F28L	Ttc	Ctc	19901	20093	All	0.003806
M	28	F28L	ttC	ttA	182	20093	All	0.000035
M	28	F28L	TtC	CtT	7	20093	All	0.000001
M	28	F28L	ttC	ttG	3	20093	All	0.000001
M	28	F28L	Ttc	Ctc	11076	11078	R.1	0.99694
M	28	F28L	TtC	CtT	2	11078	R.1	0.00018
M	28	F28L	Ttc	Ctc	7941	7961	B.1.1.7	0.007109
M	28	F28L	ttC	ttA	14	7961	B.1.1.7	0.000013
M	28	F28L	TtC	CtT	4	7961	B.1.1.7	0.000004
M	28	F28L	ttC	ttG	2	7961	B.1.1.7	0.000002
M	28	F28L	Ttc	Ctc	316	317	B.1.1	0.005733
M	28	F28L	ttC	ttA	1	317	B.1.1	0.000018
M	28	F28L	ttC	ttA	154	154	B.1.621	0.013632
M	28	F28L	Ttc	Ctc	111	117	B.1	0.001017
M	28	F28L	ttC	ttA	5	117	B.1	0.000046
M	28	F28L	ttC	ttG	1	117	B.1	0.000009
M	28	F28L	Ttc	Ctc	101	101	B.1.1.220	0.187732
M	28	F28L	Ttc	Ctc	45	45	Q.8	0.007421
M	28	F28L	Ttc	Ctc	37	37	B.1.2	0.000326
M	28	F28L	Ttc	Ctc	34	34	B.1.1.525	0.185792
M	28	F28L	Ttc	Ctc	17	17	B.1.1.317	0.006999
M	28	F28L	Ttc	Ctc	15	15	B.1.1.25	0.008528
M	28	F28L	Ttc	Ctc	15	15	B.1.544	0.090361
M	28	F28L	Ttc	Ctc	14	14	Q.1	0.001769
M	28	F28L	Ttc	Ctc	13	13	B.1.416	0.016497
M	28	F28L	Ttc	Ctc	12	12	B.1.1.10	0.013378
M	28	F28L	Ttc	Ctc	11	11	AY.4.2	0.000239
M	28	F28L	Ttc	Ctc	10	10	P.1	0.000158
M	28	F28L	Ttc	Ctc	9	9	AY.4	0.000014
M	28	F28L	Ttc	Ctc	6	7	B.1.617.2	0.000023
M	28	F28L	ttC	ttA	1	7	B.1.617.2	0.000004
M	28	F28L	Ttc	Ctc	5	6	AY.44	0.00003
M	28	F28L	ttC	ttA	1	6	AY.44	0.000006
M	28	F28L	Ttc	Ctc	6	6	B.1.177.73	0.003398
M	28	F28L	Ttc	Ctc	5	5	B.1.375	0.004098
M	28	F28L	Ttc	Ctc	5	5	B.1.576	0.004533
M	28	F28L	Ttc	Ctc	4	4	AY.43	0.000018
M	28	F28L	Ttc	Ctc	4	4	B	0.000511
M	28	F28L	Ttc	Ctc	4	4	B.1.160	0.000125
M	28	F28L	Ttc	Ctc	4	4	B.1.258	0.000266
M	28	F28L	Ttc	Ctc	4	4	B.1.369	0.001141
M	28	F28L	Ttc	Ctc	4	4	B.1.526	0.000094
M	28	F28L	Ttc	Ctc	3	3	B.1.1.222	0.000612
M	28	F28L	Ttc	Ctc	3	3	B.1.1.311	0.001074
M	28	F28L	Ttc	Ctc	3	3	B.1.1.39	0.001529
M	28	F28L	Ttc	Ctc	3	3	B.1.1.521	0.016043
M	28	F28L	Ttc	Ctc	2	3	B.1.177	0.000026
M	28	F28L	ttC	ttA	1	3	B.1.177	0.000013
M	28	F28L	Ttc	Ctc	3	3	B.1.399	0.005803
M	28	F28L	Ttc	Ctc	3	3	B.1.429	0.000071
M	28	F28L	ttC	ttA	2	2		0.111111
M	28	F28L	Ttc	Ctc	2	2	AY.118	0.000125
M	28	F28L	Ttc	Ctc	2	2	AY.26	0.000057
M	28	F28L	Ttc	Ctc	2	2	AY.3	0.00002
M	28	F28L	Ttc	Ctc	2	2	B.1.1.153	0.002191
M	28	F28L	Ttc	Ctc	2	2	B.1.1.291	0.001485
M	28	F28L	Ttc	Ctc	2	2	B.1.1.51	0.003436
M	28	F28L	Ttc	Ctc	2	2	B.1.1.83	0.00542
M	28	F28L	Ttc	Ctc	2	2	B.1.177.8	0.001505
M	28	F28L	Ttc	Ctc	2	2	B.1.351	0.000059
M	28	F28L	Ttc	Ctc	2	2	B.1.596	0.000174
M	28	F28L	Ttc	Ctc	2	2	B.1.637	0.000146
M	28	F28L	Ttc	Ctc	1	1	A	0.000387
M	28	F28L	Ttc	Ctc	1	1	AY.116	0.000287
M	28	F28L	Ttc	Ctc	1	1	AY.25	0.000006
M	28	F28L	Ttc	Ctc	1	1	AY.42	0.00004
M	28	F28L	Ttc	Ctc	1	1	AY.52	0.000814
M	28	F28L	Ttc	Ctc	1	1	AY.9.1	0.000084
M	28	F28L	Ttc	Ctc	1	1	AY.9.2	0.000037
M	28	F28L	Ttc	Ctc	1	1	B.1.1.196	0.005714
M	28	F28L	Ttc	Ctc	1	1	B.1.1.198	0.001468
M	28	F28L	Ttc	Ctc	1	1	B.1.1.214	0.000055
M	28	F28L	Ttc	Ctc	1	1	B.1.1.236	0.006897
M	28	F28L	Ttc	Ctc	1	1	B.1.1.263	0.001558
M	28	F28L	Ttc	Ctc	1	1	B.1.1.277	0.000759
M	28	F28L	Ttc	Ctc	1	1	B.1.1.305	0.003861
M	28	F28L	Ttc	Ctc	1	1	B.1.1.33	0.000421
M	28	F28L	Ttc	Ctc	1	1	B.1.1.409	0.002833
M	28	F28L	Ttc	Ctc	1	1	B.1.1.464	0.001473
M	28	F28L	Ttc	Ctc	1	1	B.1.1.519	0.00004
M	28	F28L	Ttc	Ctc	1	1	B.1.1.522	0.017241
M	28	F28L	Ttc	Ctc	1	1	B.1.1.8	0.003584
M	28	F28L	Ttc	Ctc	1	1	B.1.161	0.017241
M	28	F28L	TtC	CtT	1	1	B.1.177.21	0.000076
M	28	F28L	Ttc	Ctc	1	1	B.1.177.84	0.006667
M	28	F28L	Ttc	Ctc	1	1	B.1.279	0.000514
M	28	F28L	Ttc	Ctc	1	1	B.1.36.18	0.00042
M	28	F28L	Ttc	Ctc	1	1	B.1.468	0.005714
M	28	F28L	Ttc	Ctc	1	1	B.1.497	0.000315
M	28	F28L	Ttc	Ctc	1	1	B.1.530	0.007143
M	28	F28L	Ttc	Ctc	1	1	B.1.533	0.009615
M	28	F28L	ttC	ttA	1	1	B.1.588	0.00091
M	28	F28L	Ttc	Ctc	1	1	B.1.609	0.000479
M	28	F28L	Ttc	Ctc	1	1	B.1.628	0.000352
M	28	F28L	ttC	ttA	1	1	B.6.6	0.000889
M	28	F28L	ttC	ttA	1	1	P.1.1	0.000318
M	28	F28L	Ttc	Ctc	1	1	P.2	0.000187

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.