CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp9 : CodonNum = 55

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/nsp9	55	R55R	R4195R	syn	agA	agG	3371	3022	0.89647	12848-12850
ORF1ab/nsp9	55	R55R	R4195R	syn	Aga	Cga	3371	349	0.10353	12848-12850
ORF1ab/nsp9	55	R55K	R4195K	nonsyn	aGa	aAa	93	93	1	12848-12850
ORF1ab/nsp9	55	R55del	R4195del	del	AGA	---	50	50	1	12848-12850
ORF1ab/nsp9	55	R55I	R4195I	nonsyn	aGa	aTa	28	28	1	12848-12850
ORF1ab/nsp9	55	R55G	R4195G	nonsyn	Aga	Gga	10	10	1	12848-12850
ORF1ab/nsp9	55	R55T	R4195T	nonsyn	aGa	aCa	6	6	1	12848-12850
ORF1ab/nsp9	55	R55S	R4195S	nonsyn	agA	agT	6	5	0.833333	12848-12850
ORF1ab/nsp9	55	R55S	R4195S	nonsyn	agA	agC	6	1	0.166667	12848-12850
ORF1ab/nsp9	55	R55X	R4195X	nonsyn	Aga	Tga	2	2	1	12848-12850
ORF1ab/nsp9	55	R55del2	R4195del2	del	AGa	--a	2	1	0.5	12848-12850
ORF1ab/nsp9	55	R55del2	R4195del2	del	aGA	a--	2	1	0.5	12848-12850
ORF1ab/nsp9	55	R55del1	R4195del1	del	AGA	GA-	2	1	0.5	12848-12850
ORF1ab/nsp9	55	R55del1	R4195del1	del	aGa	a-a	2	1	0.5	12848-12850

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/nsp9	55	R55R	agA	agG	3022	3371	All	0.000578
ORF1ab/nsp9	55	R55R	Aga	Cga	349	3371	All	0.000067
ORF1ab/nsp9	55	R55R	agA	agG	2286	2286	B.1.517	0.976089
ORF1ab/nsp9	55	R55R	Aga	Cga	339	440	AY.4	0.000528
ORF1ab/nsp9	55	R55R	agA	agG	101	440	AY.4	0.000157
ORF1ab/nsp9	55	R55R	agA	agG	190	190	B.1.517.1	1
ORF1ab/nsp9	55	R55R	agA	agG	124	125	B.1.1.7	0.000111
ORF1ab/nsp9	55	R55R	Aga	Cga	1	125	B.1.1.7	0.000001
ORF1ab/nsp9	55	R55K	aGa	aAa	93	93	All	0.000018
ORF1ab/nsp9	55	R55del	AGA	---	50	50	All	0.00001
ORF1ab/nsp9	55	R55R	agA	agG	50	50	AY.46.5	0.009921
ORF1ab/nsp9	55	R55R	agA	agG	45	45	B.1	0.000412
ORF1ab/nsp9	55	R55I	aGa	aTa	28	28	All	0.000005
ORF1ab/nsp9	55	R55K	aGa	aAa	25	25	B.1.617.2	0.000094
ORF1ab/nsp9	55	R55del	AGA	---	19	19	B.1.1.7	0.000017
ORF1ab/nsp9	55	R55R	agA	agG	14	19	B.1.617.2	0.000053
ORF1ab/nsp9	55	R55R	Aga	Cga	5	19	B.1.617.2	0.000019
ORF1ab/nsp9	55	R55R	agA	agG	16	16	B.1.429	0.000376
ORF1ab/nsp9	55	R55K	aGa	aAa	12	12	AY.103	0.000075
ORF1ab/nsp9	55	R55K	aGa	aAa	12	12	AY.4	0.000019
ORF1ab/nsp9	55	R55R	agA	agG	11	12	AY.43	0.000049
ORF1ab/nsp9	55	R55R	Aga	Cga	1	12	AY.43	0.000004
ORF1ab/nsp9	55	R55R	agA	agG	12	12	B.1.351	0.000357
ORF1ab/nsp9	55	R55R	agA	agG	11	11	B.1.2	0.000097
ORF1ab/nsp9	55	R55G	Aga	Gga	10	10	All	0.000002
ORF1ab/nsp9	55	R55R	agA	agG	10	10	AY.44	0.000061
ORF1ab/nsp9	55	R55R	agA	agG	9	9	B.1.526	0.000212
ORF1ab/nsp9	55	R55I	aGa	aTa	9	9	P.1	0.000142
ORF1ab/nsp9	55	R55R	agA	agG	7	7	AY.25	0.000042
ORF1ab/nsp9	55	R55R	agA	agG	7	7	B.1.577	0.004811
ORF1ab/nsp9	55	R55R	agA	agG	7	7	P.1.15	0.001626
ORF1ab/nsp9	55	R55T	aGa	aCa	6	6	All	0.000001
ORF1ab/nsp9	55	R55S	agA	agT	5	6	All	0.000001
ORF1ab/nsp9	55	R55S	agA	agC	1	6	All	0
ORF1ab/nsp9	55	R55R	agA	agG	6	6	AY.103	0.000037
ORF1ab/nsp9	55	R55I	aGa	aTa	6	6	B.1.1.7	0.000005
ORF1ab/nsp9	55	R55R	agA	agG	6	6	B.1.473	0.115385
ORF1ab/nsp9	55	R55R	agA	agG	6	6	P.1.14	0.000287
ORF1ab/nsp9	55	R55R	agA	agG	6	6	P.1.17	0.000971
ORF1ab/nsp9	55	R55R	agA	agG	5	5	B.1.1	0.000091
ORF1ab/nsp9	55	R55K	aGa	aAa	5	5	B.1.1.7	0.000004
ORF1ab/nsp9	55	R55R	agA	agG	4	4	AY.4.5	0.00043
ORF1ab/nsp9	55	R55R	agA	agG	4	4	B.1.1.519	0.000159
ORF1ab/nsp9	55	R55del	AGA	---	4	4	B.1.177	0.000053
ORF1ab/nsp9	55	R55K	aGa	aAa	4	4	B.1.258.17	0.000416
ORF1ab/nsp9	55	R55R	agA	agG	3	3	A.21	0.00831
ORF1ab/nsp9	55	R55K	aGa	aAa	3	3	AY.25	0.000018
ORF1ab/nsp9	55	R55R	agA	agG	3	3	AY.3	0.00003
ORF1ab/nsp9	55	R55del	AGA	---	3	3	AY.4	0.000005
ORF1ab/nsp9	55	R55K	aGa	aAa	3	3	AY.44	0.000018
ORF1ab/nsp9	55	R55I	aGa	aTa	3	3	B.1	0.000027
ORF1ab/nsp9	55	R55K	aGa	aAa	3	3	B.1	0.000027
ORF1ab/nsp9	55	R55R	agA	agG	3	3	B.1.1.306	0.001315
ORF1ab/nsp9	55	R55R	agA	agG	3	3	B.1.1.318	0.000905
ORF1ab/nsp9	55	R55R	agA	agG	3	3	B.1.177	0.00004
ORF1ab/nsp9	55	R55K	aGa	aAa	3	3	B.1.400	0.001287
ORF1ab/nsp9	55	R55R	agA	agG	3	3	B.1.637	0.000219
ORF1ab/nsp9	55	R55R	agA	agG	3	3	Q.8	0.000495
ORF1ab/nsp9	55	R55X	Aga	Tga	2	2	All	0
ORF1ab/nsp9	55	R55del1	AGA	GA-	1	2	All	0
ORF1ab/nsp9	55	R55del1	aGa	a-a	1	2	All	0
ORF1ab/nsp9	55	R55del2	AGa	--a	1	2	All	0
ORF1ab/nsp9	55	R55del2	aGA	a--	1	2	All	0
ORF1ab/nsp9	55	R55G	Aga	Gga	2	2	AY.101	0.000981
ORF1ab/nsp9	55	R55K	aGa	aAa	2	2	AY.26	0.000057
ORF1ab/nsp9	55	R55I	aGa	aTa	2	2	AY.4	0.000003
ORF1ab/nsp9	55	R55del	AGA	---	2	2	AY.4.5	0.000215
ORF1ab/nsp9	55	R55R	agA	agG	2	2	AY.42	0.00008
ORF1ab/nsp9	55	R55del	AGA	---	2	2	AY.43	0.000009
ORF1ab/nsp9	55	R55R	Aga	Cga	1	2	AY.54	0.000095
ORF1ab/nsp9	55	R55R	agA	agG	1	2	AY.54	0.000095
ORF1ab/nsp9	55	R55R	agA	agG	2	2	AY.73	0.001331
ORF1ab/nsp9	55	R55R	agA	agG	2	2	AY.74	0.000231
ORF1ab/nsp9	55	R55K	aGa	aAa	2	2	B.1.1	0.000036
ORF1ab/nsp9	55	R55R	agA	agG	2	2	B.1.1.269	0.002706
ORF1ab/nsp9	55	R55R	Aga	Cga	2	2	B.1.1.398	0.006452
ORF1ab/nsp9	55	R55R	agA	agG	2	2	B.1.1.523	0.003125
ORF1ab/nsp9	55	R55T	aGa	aCa	2	2	B.1.1.7	0.000002
ORF1ab/nsp9	55	R55G	Aga	Gga	2	2	B.1.1.7	0.000002
ORF1ab/nsp9	55	R55R	agA	agG	2	2	B.1.160	0.000062
ORF1ab/nsp9	55	R55G	Aga	Gga	2	2	B.1.160	0.000062
ORF1ab/nsp9	55	R55G	Aga	Gga	2	2	B.1.177	0.000026
ORF1ab/nsp9	55	R55R	agA	agG	2	2	B.1.221	0.000142
ORF1ab/nsp9	55	R55I	aGa	aTa	2	2	B.1.596	0.000174
ORF1ab/nsp9	55	R55R	agA	agG	2	2	B.1.621	0.000177
ORF1ab/nsp9	55	R55K	aGa	aAa	2	2	B.10	0.016529
ORF1ab/nsp9	55	R55S	agA	agT	2	2	D.2	0.00015
ORF1ab/nsp9	55	R55R	agA	agG	2	2	P.1	0.000032
ORF1ab/nsp9	55	R55I	aGa	aTa	1	1	A	0.000387
ORF1ab/nsp9	55	R55K	aGa	aAa	1	1	A	0.000387
ORF1ab/nsp9	55	R55R	agA	agG	1	1	A.23.1	0.000704
ORF1ab/nsp9	55	R55K	aGa	aAa	1	1	AE.8	0.000489
ORF1ab/nsp9	55	R55R	agA	agG	1	1	AY.100	0.000046
ORF1ab/nsp9	55	R55R	agA	agG	1	1	AY.102	0.000027
ORF1ab/nsp9	55	R55del	AGA	---	1	1	AY.103	0.000006
ORF1ab/nsp9	55	R55R	agA	agG	1	1	AY.120	0.000037
ORF1ab/nsp9	55	R55R	agA	agG	1	1	AY.120.2.1	0.000498
ORF1ab/nsp9	55	R55R	agA	agG	1	1	AY.16	0.00038
ORF1ab/nsp9	55	R55R	agA	agG	1	1	AY.23	0.00007
ORF1ab/nsp9	55	R55K	aGa	aAa	1	1	AY.23	0.00007
ORF1ab/nsp9	55	R55R	agA	agG	1	1	AY.26	0.000028
ORF1ab/nsp9	55	R55R	agA	agG	1	1	AY.27	0.000065
ORF1ab/nsp9	55	R55K	aGa	aAa	1	1	AY.27	0.000065
ORF1ab/nsp9	55	R55R	agA	agG	1	1	AY.32	0.000532
ORF1ab/nsp9	55	R55R	agA	agG	1	1	AY.33	0.000067
ORF1ab/nsp9	55	R55T	aGa	aCa	1	1	AY.34	0.000097
ORF1ab/nsp9	55	R55del	AGA	---	1	1	AY.34	0.000097
ORF1ab/nsp9	55	R55T	aGa	aCa	1	1	AY.39	0.000025
ORF1ab/nsp9	55	R55T	aGa	aCa	1	1	AY.4	0.000002
ORF1ab/nsp9	55	R55X	Aga	Tga	1	1	AY.42	0.00004
ORF1ab/nsp9	55	R55del1	aGa	a-a	1	1	AY.43	0.000004
ORF1ab/nsp9	55	R55del2	aGA	a--	1	1	AY.43	0.000004
ORF1ab/nsp9	55	R55K	aGa	aAa	1	1	AY.46	0.000104
ORF1ab/nsp9	55	R55S	agA	agC	1	1	AY.46	0.000104
ORF1ab/nsp9	55	R55R	agA	agG	1	1	AY.46.6	0.000072
ORF1ab/nsp9	55	R55R	agA	agG	1	1	AY.47	0.000031
ORF1ab/nsp9	55	R55R	agA	agG	1	1	AY.5	0.000021
ORF1ab/nsp9	55	R55S	agA	agT	1	1	AY.5	0.000021
ORF1ab/nsp9	55	R55del	AGA	---	1	1	AY.5.3	0.000337
ORF1ab/nsp9	55	R55R	agA	agG	1	1	AY.57	0.000656
ORF1ab/nsp9	55	R55R	agA	agG	1	1	AY.61	0.000105
ORF1ab/nsp9	55	R55R	agA	agG	1	1	AY.64	0.000595
ORF1ab/nsp9	55	R55del1	AGA	GA-	1	1	AY.67	0.000464
ORF1ab/nsp9	55	R55R	agA	agG	1	1	AY.68	0.000274
ORF1ab/nsp9	55	R55R	agA	agG	1	1	AY.7.1	0.000113
ORF1ab/nsp9	55	R55del	AGA	---	1	1	AY.72	0.001361
ORF1ab/nsp9	55	R55R	agA	agG	1	1	AY.75	0.000056
ORF1ab/nsp9	55	R55R	agA	agG	1	1	AY.75.1	0.00018
ORF1ab/nsp9	55	R55K	aGa	aAa	1	1	AY.9	0.000068
ORF1ab/nsp9	55	R55R	agA	agG	1	1	AY.9.2	0.000037
ORF1ab/nsp9	55	R55del	AGA	---	1	1	B.1	0.000009
ORF1ab/nsp9	55	R55I	aGa	aTa	1	1	B.1.1	0.000018
ORF1ab/nsp9	55	R55del	AGA	---	1	1	B.1.1.1	0.000327
ORF1ab/nsp9	55	R55K	aGa	aAa	1	1	B.1.1.122	0.045455
ORF1ab/nsp9	55	R55G	Aga	Gga	1	1	B.1.1.214	0.000055
ORF1ab/nsp9	55	R55R	agA	agG	1	1	B.1.1.216	0.00089
ORF1ab/nsp9	55	R55R	agA	agG	1	1	B.1.1.298	0.000862
ORF1ab/nsp9	55	R55R	agA	agG	1	1	B.1.1.309	0.005848
ORF1ab/nsp9	55	R55R	agA	agG	1	1	B.1.1.328	0.016949
ORF1ab/nsp9	55	R55R	agA	agG	1	1	B.1.1.33	0.000421
ORF1ab/nsp9	55	R55del	AGA	---	1	1	B.1.1.348	0.000796
ORF1ab/nsp9	55	R55del2	AGa	--a	1	1	B.1.1.7	0.000001
ORF1ab/nsp9	55	R55del	AGA	---	1	1	B.1.160	0.000031
ORF1ab/nsp9	55	R55K	aGa	aAa	1	1	B.1.177	0.000013
ORF1ab/nsp9	55	R55del	AGA	---	1	1	B.1.177.11	0.001698
ORF1ab/nsp9	55	R55del	AGA	---	1	1	B.1.177.15	0.000631
ORF1ab/nsp9	55	R55del	AGA	---	1	1	B.1.177.4	0.000211
ORF1ab/nsp9	55	R55R	agA	agG	1	1	B.1.177.4	0.000211
ORF1ab/nsp9	55	R55del	AGA	---	1	1	B.1.177.60	0.000218
ORF1ab/nsp9	55	R55R	agA	agG	1	1	B.1.177.73	0.000566
ORF1ab/nsp9	55	R55del	AGA	---	1	1	B.1.177.81	0.000189
ORF1ab/nsp9	55	R55del	AGA	---	1	1	B.1.177.83	0.001481
ORF1ab/nsp9	55	R55I	aGa	aTa	1	1	B.1.2	0.000009
ORF1ab/nsp9	55	R55K	aGa	aAa	1	1	B.1.2	0.000009
ORF1ab/nsp9	55	R55S	agA	agT	1	1	B.1.2	0.000009
ORF1ab/nsp9	55	R55R	agA	agG	1	1	B.1.258	0.000067
ORF1ab/nsp9	55	R55del	AGA	---	1	1	B.1.258.3	0.001675
ORF1ab/nsp9	55	R55del	AGA	---	1	1	B.1.311	0.000275
ORF1ab/nsp9	55	R55R	agA	agG	1	1	B.1.324	0.001605
ORF1ab/nsp9	55	R55T	aGa	aCa	1	1	B.1.351	0.00003
ORF1ab/nsp9	55	R55R	agA	agG	1	1	B.1.36	0.000146
ORF1ab/nsp9	55	R55K	aGa	aAa	1	1	B.1.36.1	0.00114
ORF1ab/nsp9	55	R55R	agA	agG	1	1	B.1.369	0.000285
ORF1ab/nsp9	55	R55R	agA	agG	1	1	B.1.375	0.00082
ORF1ab/nsp9	55	R55R	agA	agG	1	1	B.1.396	0.000706
ORF1ab/nsp9	55	R55I	aGa	aTa	1	1	B.1.413	0.004255
ORF1ab/nsp9	55	R55K	aGa	aAa	1	1	B.1.416.1	0.001563
ORF1ab/nsp9	55	R55X	Aga	Tga	1	1	B.1.429	0.000024
ORF1ab/nsp9	55	R55K	aGa	aAa	1	1	B.1.429	0.000024
ORF1ab/nsp9	55	R55I	aGa	aTa	1	1	B.1.429	0.000024
ORF1ab/nsp9	55	R55K	aGa	aAa	1	1	B.1.509	0.000866
ORF1ab/nsp9	55	R55del	AGA	---	1	1	B.1.525	0.000113
ORF1ab/nsp9	55	R55K	aGa	aAa	1	1	B.1.526	0.000024
ORF1ab/nsp9	55	R55R	agA	agG	1	1	B.1.580	0.004065
ORF1ab/nsp9	55	R55R	agA	agG	1	1	B.1.617.1	0.000129
ORF1ab/nsp9	55	R55G	Aga	Gga	1	1	B.1.617.2	0.000004
ORF1ab/nsp9	55	R55R	agA	agG	1	1	B.1.634	0.003425
ORF1ab/nsp9	55	R55K	aGa	aAa	1	1	B.1.637	0.000073
ORF1ab/nsp9	55	R55R	agA	agG	1	1	B.20	0.023256
ORF1ab/nsp9	55	R55K	aGa	aAa	1	1	B.40	0.000364
ORF1ab/nsp9	55	R55I	aGa	aTa	1	1	B.6	0.00091
ORF1ab/nsp9	55	R55R	agA	agG	1	1	C.3	0.007634
ORF1ab/nsp9	55	R55R	agA	agG	1	1	C.37	0.000116
ORF1ab/nsp9	55	R55del	AGA	---	1	1	D.2	0.000075
ORF1ab/nsp9	55	R55del	AGA	---	1	1	N.4	0.004255
ORF1ab/nsp9	55	R55K	aGa	aAa	1	1	P.1	0.000016
ORF1ab/nsp9	55	R55R	agA	agG	1	1	P.1.12	0.000484
ORF1ab/nsp9	55	R55R	agA	agG	1	1	P.3	0.001595
ORF1ab/nsp9	55	R55R	agA	agG	1	1	Q.1	0.000126
ORF1ab/nsp9	55	R55R	agA	agG	1	1	Q.4	0.000455
ORF1ab/nsp9	55	R55S	agA	agT	1	1	R.1	0.00009
ORF1ab/nsp9	55	R55del	AGA	---	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.