CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp12 : CodonNum = 401

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/nsp12	401	L401F	L4793F	nonsyn	Ctt	Ttt	419	419	1	14641-14643
ORF1ab/nsp12	401	L401L	L4793L	syn	ctT	ctC	402	401	0.997512	14641-14643
ORF1ab/nsp12	401	L401L	L4793L	syn	ctT	ctG	402	1	0.00248756	14641-14643
ORF1ab/nsp12	401	L401del	L4793del	del	CTT	---	33	33	1	14641-14643
ORF1ab/nsp12	401	L401I	L4793I	nonsyn	Ctt	Att	10	10	1	14641-14643
ORF1ab/nsp12	401	L401P	L4793P	nonsyn	cTt	cCt	8	6	0.75	14641-14643
ORF1ab/nsp12	401	L401P	L4793P	nonsyn	cTT	cCC	8	2	0.25	14641-14643
ORF1ab/nsp12	401	L401R	L4793R	nonsyn	cTt	cGt	1	1	1	14641-14643
ORF1ab/nsp12	401	L401del1	L4793del1	del	cTT	c-N	1	1	1	14641-14643
ORF1ab/nsp12	401	L401S	L4793S	nonsyn	CTt	TCt	1	1	1	14641-14643
ORF1ab/nsp12	401	L401V	L4793V	nonsyn	CtT	GtA	1	1	1	14641-14643

Details of the mutation no 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/nsp12	401	L401F	Ctt	Ttt	419	419	All	0.00008
ORF1ab/nsp12	401	L401L	ctT	ctC	401	402	All	0.000077
ORF1ab/nsp12	401	L401L	ctT	ctG	1	402	All	0
ORF1ab/nsp12	401	L401F	Ctt	Ttt	281	281	AY.4	0.000437
ORF1ab/nsp12	401	L401L	ctT	ctC	102	102	B.1.402	1
ORF1ab/nsp12	401	L401L	ctT	ctC	75	75	AY.106	0.025117
ORF1ab/nsp12	401	L401L	ctT	ctC	44	44	B.1.617.2	0.000166
ORF1ab/nsp12	401	L401L	ctT	ctC	42	42	B.1	0.000385
ORF1ab/nsp12	401	L401L	ctT	ctC	37	37	AY.102	0.000981
ORF1ab/nsp12	401	L401del	CTT	---	33	33	All	0.000006
ORF1ab/nsp12	401	L401F	Ctt	Ttt	17	17	AY.105	0.010932
ORF1ab/nsp12	401	L401del	CTT	---	17	17	B.1.1.7	0.000015
ORF1ab/nsp12	401	L401L	ctT	ctC	12	12	AY.43	0.000053
ORF1ab/nsp12	401	L401F	Ctt	Ttt	12	12	B.1.617.2	0.000045
ORF1ab/nsp12	401	L401I	Ctt	Att	10	10	All	0.000002
ORF1ab/nsp12	401	L401F	Ctt	Ttt	10	10	AY.102	0.000265
ORF1ab/nsp12	401	L401L	ctT	ctC	10	10	B.1.429	0.000235
ORF1ab/nsp12	401	L401F	Ctt	Ttt	9	9	B.1.1.157	0.008219
ORF1ab/nsp12	401	L401F	Ctt	Ttt	9	9	B.1.1.519	0.000357
ORF1ab/nsp12	401	L401L	ctT	ctC	9	9	B.1.1.7	0.000008
ORF1ab/nsp12	401	L401P	cTt	cCt	6	8	All	0.000001
ORF1ab/nsp12	401	L401P	cTT	cCC	2	8	All	0
ORF1ab/nsp12	401	L401L	ctT	ctC	8	8	B.1.1.1	0.002614
ORF1ab/nsp12	401	L401F	Ctt	Ttt	8	8	B.1.595	0.002088
ORF1ab/nsp12	401	L401L	ctT	ctC	7	7	AY.120	0.00026
ORF1ab/nsp12	401	L401L	ctT	ctC	6	6	AY.4	0.000009
ORF1ab/nsp12	401	L401F	Ctt	Ttt	5	5	AY.103	0.000031
ORF1ab/nsp12	401	L401F	Ctt	Ttt	5	5	AY.3	0.00005
ORF1ab/nsp12	401	L401L	ctT	ctC	5	5	B.1.111	0.005875
ORF1ab/nsp12	401	L401F	Ctt	Ttt	5	5	B.1.177	0.000066
ORF1ab/nsp12	401	L401L	ctT	ctC	4	4	AY.103	0.000025
ORF1ab/nsp12	401	L401L	ctT	ctC	4	4	AY.25	0.000024
ORF1ab/nsp12	401	L401L	ctT	ctC	4	4	AY.39	0.000099
ORF1ab/nsp12	401	L401L	ctT	ctC	4	4	AY.4.5	0.00043
ORF1ab/nsp12	401	L401F	Ctt	Ttt	4	4	AY.44	0.000024
ORF1ab/nsp12	401	L401L	ctT	ctC	4	4	AY.44	0.000024
ORF1ab/nsp12	401	L401F	Ctt	Ttt	3	3	AY.25	0.000018
ORF1ab/nsp12	401	L401F	Ctt	Ttt	3	3	AY.32	0.001597
ORF1ab/nsp12	401	L401F	Ctt	Ttt	3	3	AY.39	0.000074
ORF1ab/nsp12	401	L401F	Ctt	Ttt	3	3	AY.46.1	0.00308
ORF1ab/nsp12	401	L401P	cTt	cCt	3	3	B.1.1.7	0.000003
ORF1ab/nsp12	401	L401F	Ctt	Ttt	3	3	B.1.429	0.000071
ORF1ab/nsp12	401	L401F	Ctt	Ttt	3	3	B.1.561	0.001191
ORF1ab/nsp12	401	L401F	Ctt	Ttt	2	2	A.2.5	0.000998
ORF1ab/nsp12	401	L401I	Ctt	Att	2	2	AY.103	0.000012
ORF1ab/nsp12	401	L401F	Ctt	Ttt	2	2	AY.104	0.003968
ORF1ab/nsp12	401	L401F	Ctt	Ttt	2	2	AY.116	0.000574
ORF1ab/nsp12	401	L401L	ctT	ctC	2	2	AY.16	0.000759
ORF1ab/nsp12	401	L401F	Ctt	Ttt	2	2	AY.29	0.000032
ORF1ab/nsp12	401	L401I	Ctt	Att	2	2	AY.3	0.00002
ORF1ab/nsp12	401	L401P	cTT	cCC	1	2	B.1	0.000009
ORF1ab/nsp12	401	L401P	cTt	cCt	1	2	B.1	0.000009
ORF1ab/nsp12	401	L401F	Ctt	Ttt	2	2	B.1.1	0.000036
ORF1ab/nsp12	401	L401L	ctT	ctC	2	2	B.1.1.178	0.083333
ORF1ab/nsp12	401	L401F	Ctt	Ttt	2	2	B.1.2	0.000018
ORF1ab/nsp12	401	L401F	Ctt	Ttt	2	2	B.1.605	0.011905
ORF1ab/nsp12	401	L401F	Ctt	Ttt	2	2	R.1	0.00018
ORF1ab/nsp12	401	L401F	Ctt	Ttt	1	1	A.2.5.1	0.004808
ORF1ab/nsp12	401	L401R	cTt	cGt	1	1	All	0
ORF1ab/nsp12	401	L401V	CtT	GtA	1	1	All	0
ORF1ab/nsp12	401	L401del1	cTT	c-N	1	1	All	0
ORF1ab/nsp12	401	L401S	CTt	TCt	1	1	All	0
ORF1ab/nsp12	401	L401del	CTT	---	1	1	AY.100	0.000046
ORF1ab/nsp12	401	L401F	Ctt	Ttt	1	1	AY.106	0.000335
ORF1ab/nsp12	401	L401del	CTT	---	1	1	AY.111	0.000183
ORF1ab/nsp12	401	L401L	ctT	ctC	1	1	AY.113	0.000142
ORF1ab/nsp12	401	L401L	ctT	ctC	1	1	AY.121	0.000135
ORF1ab/nsp12	401	L401F	Ctt	Ttt	1	1	AY.14	0.000088
ORF1ab/nsp12	401	L401L	ctT	ctC	1	1	AY.20	0.000039
ORF1ab/nsp12	401	L401F	Ctt	Ttt	1	1	AY.20	0.000039
ORF1ab/nsp12	401	L401I	Ctt	Att	1	1	AY.25	0.000006
ORF1ab/nsp12	401	L401del	CTT	---	1	1	AY.25	0.000006
ORF1ab/nsp12	401	L401L	ctT	ctC	1	1	AY.3	0.00001
ORF1ab/nsp12	401	L401F	Ctt	Ttt	1	1	AY.33	0.000067
ORF1ab/nsp12	401	L401L	ctT	ctC	1	1	AY.34.1	0.00051
ORF1ab/nsp12	401	L401del	CTT	---	1	1	AY.4	0.000002
ORF1ab/nsp12	401	L401del	CTT	---	1	1	AY.4.5	0.000107
ORF1ab/nsp12	401	L401F	Ctt	Ttt	1	1	AY.40	0.000964
ORF1ab/nsp12	401	L401F	Ctt	Ttt	1	1	AY.43	0.000004
ORF1ab/nsp12	401	L401P	cTT	cCC	1	1	AY.44	0.000006
ORF1ab/nsp12	401	L401L	ctT	ctC	1	1	AY.45	0.000122
ORF1ab/nsp12	401	L401del	CTT	---	1	1	AY.46.2	0.000635
ORF1ab/nsp12	401	L401L	ctT	ctC	1	1	AY.46.4	0.000165
ORF1ab/nsp12	401	L401L	ctT	ctC	1	1	AY.47	0.000031
ORF1ab/nsp12	401	L401L	ctT	ctC	1	1	AY.48	0.000465
ORF1ab/nsp12	401	L401F	Ctt	Ttt	1	1	AY.61	0.000105
ORF1ab/nsp12	401	L401del	CTT	---	1	1	AY.68	0.000274
ORF1ab/nsp12	401	L401L	ctT	ctC	1	1	AY.75	0.000056
ORF1ab/nsp12	401	L401L	ctT	ctC	1	1	AY.84	0.000437
ORF1ab/nsp12	401	L401F	Ctt	Ttt	1	1	AY.9	0.000068
ORF1ab/nsp12	401	L401L	ctT	ctC	1	1	AY.9.1	0.000084
ORF1ab/nsp12	401	L401F	Ctt	Ttt	1	1	AY.9.2	0.000037
ORF1ab/nsp12	401	L401del	CTT	---	1	1	AY.9.2	0.000037
ORF1ab/nsp12	401	L401L	ctT	ctC	1	1	AY.9.2	0.000037
ORF1ab/nsp12	401	L401del1	cTT	c-N	1	1	AY.98.1	0.000048
ORF1ab/nsp12	401	L401del	CTT	---	1	1	AY.99.1	0.001553
ORF1ab/nsp12	401	L401S	CTt	TCt	1	1	B	0.000128
ORF1ab/nsp12	401	L401F	Ctt	Ttt	1	1	B	0.000128
ORF1ab/nsp12	401	L401F	Ctt	Ttt	1	1	B.1	0.000009
ORF1ab/nsp12	401	L401L	ctT	ctC	1	1	B.1.1	0.000018
ORF1ab/nsp12	401	L401del	CTT	---	1	1	B.1.1	0.000018
ORF1ab/nsp12	401	L401I	Ctt	Att	1	1	B.1.1.174	0.003378
ORF1ab/nsp12	401	L401L	ctT	ctC	1	1	B.1.1.214	0.000055
ORF1ab/nsp12	401	L401del	CTT	---	1	1	B.1.1.306	0.000438
ORF1ab/nsp12	401	L401I	Ctt	Att	1	1	B.1.1.434	0.000349
ORF1ab/nsp12	401	L401del	CTT	---	1	1	B.1.1.46	0.004367
ORF1ab/nsp12	401	L401F	Ctt	Ttt	1	1	B.1.1.58	0.005376
ORF1ab/nsp12	401	L401V	CtT	GtA	1	1	B.1.1.7	0.000001
ORF1ab/nsp12	401	L401F	Ctt	Ttt	1	1	B.1.1.7	0.000001
ORF1ab/nsp12	401	L401del	CTT	---	1	1	B.1.160	0.000031
ORF1ab/nsp12	401	L401P	cTt	cCt	1	1	B.1.177	0.000013
ORF1ab/nsp12	401	L401del	CTT	---	1	1	B.1.177.16	0.000664
ORF1ab/nsp12	401	L401F	Ctt	Ttt	1	1	B.1.177.21	0.000076
ORF1ab/nsp12	401	L401I	Ctt	Att	1	1	B.1.177.33	0.001645
ORF1ab/nsp12	401	L401del	CTT	---	1	1	B.1.177.54	0.000606
ORF1ab/nsp12	401	L401L	ctT	ctC	1	1	B.1.243	0.00007
ORF1ab/nsp12	401	L401F	Ctt	Ttt	1	1	B.1.265	0.001271
ORF1ab/nsp12	401	L401I	Ctt	Att	1	1	B.1.36.1	0.00114
ORF1ab/nsp12	401	L401F	Ctt	Ttt	1	1	B.1.36.38	0.001642
ORF1ab/nsp12	401	L401F	Ctt	Ttt	1	1	B.1.377	0.004566
ORF1ab/nsp12	401	L401R	cTt	cGt	1	1	B.1.433	0.003195
ORF1ab/nsp12	401	L401I	Ctt	Att	1	1	B.1.517	0.000427
ORF1ab/nsp12	401	L401L	ctT	ctC	1	1	B.1.595	0.000261
ORF1ab/nsp12	401	L401L	ctT	ctC	1	1	B.1.596	0.000087
ORF1ab/nsp12	401	L401L	ctT	ctC	1	1	B.1.609	0.000479
ORF1ab/nsp12	401	L401del	CTT	---	1	1	B.1.617.2	0.000004
ORF1ab/nsp12	401	L401P	cTt	cCt	1	1	B.1.617.2	0.000004
ORF1ab/nsp12	401	L401L	ctT	ctC	1	1	B.1.621	0.000089
ORF1ab/nsp12	401	L401F	Ctt	Ttt	1	1	B.28	0.003279
ORF1ab/nsp12	401	L401L	ctT	ctG	1	1	C.37	0.000116
ORF1ab/nsp12	401	L401F	Ctt	Ttt	1	1	D.2	0.000075

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.