CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF3a : Mut = F105L

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	105	F105L		nonsyn	Ttt	Ctt	833	756	0.907563	25705-25707
ORF3a	105	F105L		nonsyn	ttT	ttG	833	57	0.0684274	25705-25707
ORF3a	105	F105L		nonsyn	ttT	ttA	833	19	0.0228091	25705-25707
ORF3a	105	F105L		nonsyn	TtT	CtC	833	1	0.00120048	25705-25707

Details of the mutation F105L 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	105	F105L	Ttt	Ctt	756	833	All	0.000145
ORF3a	105	F105L	ttT	ttG	57	833	All	0.000011
ORF3a	105	F105L	ttT	ttA	19	833	All	0.000004
ORF3a	105	F105L	TtT	CtC	1	833	All	0
ORF3a	105	F105L	Ttt	Ctt	232	232	B.1.469	0.837545
ORF3a	105	F105L	Ttt	Ctt	134	134	AY.36	0.019861
ORF3a	105	F105L	Ttt	Ctt	74	74	B.1.351	0.0022
ORF3a	105	F105L	Ttt	Ctt	28	42	B.1.1.7	0.000025
ORF3a	105	F105L	ttT	ttG	7	42	B.1.1.7	0.000006
ORF3a	105	F105L	ttT	ttA	7	42	B.1.1.7	0.000006
ORF3a	105	F105L	ttT	ttG	34	38	AY.3	0.000338
ORF3a	105	F105L	Ttt	Ctt	4	38	AY.3	0.00004
ORF3a	105	F105L	Ttt	Ctt	32	34	B.1.2	0.000282
ORF3a	105	F105L	ttT	ttA	1	34	B.1.2	0.000009
ORF3a	105	F105L	ttT	ttG	1	34	B.1.2	0.000009
ORF3a	105	F105L	Ttt	Ctt	19	20	B.1.1	0.000345
ORF3a	105	F105L	ttT	ttG	1	20	B.1.1	0.000018
ORF3a	105	F105L	Ttt	Ctt	16	19	B.1	0.000147
ORF3a	105	F105L	ttT	ttG	2	19	B.1	0.000018
ORF3a	105	F105L	ttT	ttA	1	19	B.1	0.000009
ORF3a	105	F105L	Ttt	Ctt	19	19	B.1.177.44	0.00986
ORF3a	105	F105L	Ttt	Ctt	18	19	B.1.617.2	0.000068
ORF3a	105	F105L	ttT	ttG	1	19	B.1.617.2	0.000004
ORF3a	105	F105L	Ttt	Ctt	18	18	AY.102	0.000477
ORF3a	105	F105L	Ttt	Ctt	18	18	AY.113	0.002563
ORF3a	105	F105L	Ttt	Ctt	14	14	AY.34	0.001358
ORF3a	105	F105L	Ttt	Ctt	12	12	AY.103	0.000075
ORF3a	105	F105L	Ttt	Ctt	12	12	AY.29	0.000189
ORF3a	105	F105L	Ttt	Ctt	11	11	B.1.36	0.001605
ORF3a	105	F105L	Ttt	Ctt	9	10	AY.4	0.000014
ORF3a	105	F105L	ttT	ttA	1	10	AY.4	0.000002
ORF3a	105	F105L	Ttt	Ctt	10	10	B.1.177	0.000132
ORF3a	105	F105L	ttT	ttG	6	6	B.1.565	0.004862
ORF3a	105	F105L	Ttt	Ctt	3	4	AY.25	0.000018
ORF3a	105	F105L	ttT	ttG	1	4	AY.25	0.000006
ORF3a	105	F105L	Ttt	Ctt	4	4	AY.44	0.000024
ORF3a	105	F105L	Ttt	Ctt	4	4	B.1.160.10	0.032258
ORF3a	105	F105L	Ttt	Ctt	4	4	B.1.462	0.028986
ORF3a	105	F105L	Ttt	Ctt	4	4	B.1.544	0.024096
ORF3a	105	F105L	Ttt	Ctt	2	3		0.111111
ORF3a	105	F105L	TtT	CtC	1	3		0.055556
ORF3a	105	F105L	Ttt	Ctt	3	3	AY.43	0.000013
ORF3a	105	F105L	ttT	ttG	1	3	B.1.1.33	0.000421
ORF3a	105	F105L	ttT	ttA	1	3	B.1.1.33	0.000421
ORF3a	105	F105L	Ttt	Ctt	1	3	B.1.1.33	0.000421
ORF3a	105	F105L	Ttt	Ctt	3	3	B.1.177.60	0.000655
ORF3a	105	F105L	Ttt	Ctt	2	2	AY.23	0.000139
ORF3a	105	F105L	Ttt	Ctt	2	2	AY.39	0.000049
ORF3a	105	F105L	Ttt	Ctt	2	2	AY.46	0.000208
ORF3a	105	F105L	Ttt	Ctt	2	2	AY.54	0.000191
ORF3a	105	F105L	Ttt	Ctt	2	2	B.1.1.416	0.00181
ORF3a	105	F105L	Ttt	Ctt	2	2	B.1.221	0.000142
ORF3a	105	F105L	ttT	ttA	2	2	B.1.258.17	0.000208
ORF3a	105	F105L	ttT	ttG	1	2	B.1.333	0.010526
ORF3a	105	F105L	ttT	ttA	1	2	B.1.333	0.010526
ORF3a	105	F105L	Ttt	Ctt	2	2	B.1.466.2	0.000782
ORF3a	105	F105L	Ttt	Ctt	2	2	B.1.530	0.014286
ORF3a	105	F105L	ttT	ttG	2	2	B.1.621	0.000177
ORF3a	105	F105L	ttT	ttA	2	2	B.1.91	0.004149
ORF3a	105	F105L	Ttt	Ctt	2	2	P.1	0.000032
ORF3a	105	F105L	Ttt	Ctt	1	1	AY.26	0.000028
ORF3a	105	F105L	Ttt	Ctt	1	1	AY.29.1	0.000221
ORF3a	105	F105L	Ttt	Ctt	1	1	AY.56	0.001605
ORF3a	105	F105L	Ttt	Ctt	1	1	AY.59	0.00053
ORF3a	105	F105L	Ttt	Ctt	1	1	AY.62	0.000436
ORF3a	105	F105L	Ttt	Ctt	1	1	AY.7.1	0.000113
ORF3a	105	F105L	Ttt	Ctt	1	1	AY.9.2	0.000037
ORF3a	105	F105L	Ttt	Ctt	1	1	AY.98.1	0.000048
ORF3a	105	F105L	ttT	ttA	1	1	AY.99.2	0.000092
ORF3a	105	F105L	Ttt	Ctt	1	1	B	0.000128
ORF3a	105	F105L	Ttt	Ctt	1	1	B.1.1.189	0.001513
ORF3a	105	F105L	Ttt	Ctt	1	1	B.1.1.284	0.000107
ORF3a	105	F105L	Ttt	Ctt	1	1	B.1.1.306	0.000438
ORF3a	105	F105L	Ttt	Ctt	1	1	B.1.177.32	0.00135
ORF3a	105	F105L	Ttt	Ctt	1	1	B.1.232	0.000537
ORF3a	105	F105L	Ttt	Ctt	1	1	B.1.236	0.002053
ORF3a	105	F105L	Ttt	Ctt	1	1	B.1.243	0.00007
ORF3a	105	F105L	Ttt	Ctt	1	1	B.1.258.11	0.000396
ORF3a	105	F105L	Ttt	Ctt	1	1	B.1.349	0.000715
ORF3a	105	F105L	Ttt	Ctt	1	1	B.1.351.5	0.0006
ORF3a	105	F105L	Ttt	Ctt	1	1	B.1.36.7	0.004
ORF3a	105	F105L	Ttt	Ctt	1	1	B.1.391	0.001127
ORF3a	105	F105L	Ttt	Ctt	1	1	B.1.470	0.001404
ORF3a	105	F105L	Ttt	Ctt	1	1	B.1.515	0.014493
ORF3a	105	F105L	Ttt	Ctt	1	1	B.1.521	0.004975
ORF3a	105	F105L	Ttt	Ctt	1	1	B.1.526	0.000024
ORF3a	105	F105L	ttT	ttA	1	1	B.1.596	0.000087
ORF3a	105	F105L	Ttt	Ctt	1	1	B.1.609	0.000479
ORF3a	105	F105L	Ttt	Ctt	1	1	C.36.3	0.000567
ORF3a	105	F105L	Ttt	Ctt	1	1	N.3	0.005814
ORF3a	105	F105L	ttT	ttA	1	1	P.1.10	0.000269
ORF3a	105	F105L	Ttt	Ctt	1	1	P.1.15	0.000232
ORF3a	105	F105L	Ttt	Ctt	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.