CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp12 : CodonNum = 500

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	500	K500K	K4892K	syn	aaA	aaG	344	344	1	14938-14940
ORF1ab/nsp12	500	K500del	K4892del	del	AAA	---	39	39	1	14938-14940
ORF1ab/nsp12	500	K500R	K4892R	nonsyn	aAa	aGa	20	19	0.95	14938-14940
ORF1ab/nsp12	500	K500R	K4892R	nonsyn	aAA	aGG	20	1	0.05	14938-14940
ORF1ab/nsp12	500	K500del1	K4892del1	del	Aaa	-aa	10	6	0.6	14938-14940
ORF1ab/nsp12	500	K500del1	K4892del1	del	aAA	aG-	10	2	0.2	14938-14940
ORF1ab/nsp12	500	K500del1	K4892del1	del	aaA	aa-	10	1	0.1	14938-14940
ORF1ab/nsp12	500	K500del1	K4892del1	del	AAA	-NN	10	1	0.1	14938-14940
ORF1ab/nsp12	500	K500T	K4892T	nonsyn	aAa	aCa	7	7	1	14938-14940
ORF1ab/nsp12	500	K500I	K4892I	nonsyn	aAa	aTa	6	4	0.666667	14938-14940
ORF1ab/nsp12	500	K500I	K4892I	nonsyn	aAA	aTC	6	2	0.333333	14938-14940
ORF1ab/nsp12	500	K500N	K4892N	nonsyn	aaA	aaC	5	3	0.6	14938-14940
ORF1ab/nsp12	500	K500N	K4892N	nonsyn	aaA	aaT	5	2	0.4	14938-14940
ORF1ab/nsp12	500	K500L	K4892L	nonsyn	AAa	CTa	3	2	0.666667	14938-14940
ORF1ab/nsp12	500	K500L	K4892L	nonsyn	AAa	TTa	3	1	0.333333	14938-14940
ORF1ab/nsp12	500	K500M	K4892M	nonsyn	aAA	aTG	2	2	1	14938-14940
ORF1ab/nsp12	500	K500D	K4892D	nonsyn	AaA	GaC	1	1	1	14938-14940
ORF1ab/nsp12	500	K500del2	K4892del2	del	AAa	--a	1	1	1	14938-14940

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	500	K500K	aaA	aaG	344	344	All	0.000066
ORF1ab/nsp12	500	K500K	aaA	aaG	86	86	B.1	0.000788
ORF1ab/nsp12	500	K500K	aaA	aaG	63	63	B.1.1.7	0.000056
ORF1ab/nsp12	500	K500K	aaA	aaG	43	43	B.20	1
ORF1ab/nsp12	500	K500del	AAA	---	39	39	All	0.000007
ORF1ab/nsp12	500	K500R	aAa	aGa	19	20	All	0.000004
ORF1ab/nsp12	500	K500R	aAA	aGG	1	20	All	0
ORF1ab/nsp12	500	K500K	aaA	aaG	20	20	B.1.617.2	0.000075
ORF1ab/nsp12	500	K500K	aaA	aaG	14	14	AY.61	0.001467
ORF1ab/nsp12	500	K500del1	Aaa	-aa	6	10	All	0.000001
ORF1ab/nsp12	500	K500del1	aAA	aG-	2	10	All	0
ORF1ab/nsp12	500	K500del1	aaA	aa-	1	10	All	0
ORF1ab/nsp12	500	K500del1	AAA	-NN	1	10	All	0
ORF1ab/nsp12	500	K500del	AAA	---	10	10	B.1.1.7	0.000009
ORF1ab/nsp12	500	K500K	aaA	aaG	8	8	AY.103	0.00005
ORF1ab/nsp12	500	K500T	aAa	aCa	7	7	All	0.000001
ORF1ab/nsp12	500	K500K	aaA	aaG	7	7	AY.43	0.000031
ORF1ab/nsp12	500	K500K	aaA	aaG	7	7	AY.75	0.000392
ORF1ab/nsp12	500	K500I	aAa	aTa	4	6	All	0.000001
ORF1ab/nsp12	500	K500I	aAA	aTC	2	6	All	0
ORF1ab/nsp12	500	K500K	aaA	aaG	6	6	AY.26	0.00017
ORF1ab/nsp12	500	K500N	aaA	aaC	3	5	All	0.000001
ORF1ab/nsp12	500	K500N	aaA	aaT	2	5	All	0
ORF1ab/nsp12	500	K500K	aaA	aaG	5	5	AY.4	0.000008
ORF1ab/nsp12	500	K500R	aAa	aGa	4	4	AY.103	0.000025
ORF1ab/nsp12	500	K500K	aaA	aaG	4	4	AY.25	0.000024
ORF1ab/nsp12	500	K500K	aaA	aaG	4	4	AY.3	0.00004
ORF1ab/nsp12	500	K500R	aAa	aGa	4	4	B.1.1.7	0.000004
ORF1ab/nsp12	500	K500L	AAa	CTa	2	3	All	0
ORF1ab/nsp12	500	K500L	AAa	TTa	1	3	All	0
ORF1ab/nsp12	500	K500K	aaA	aaG	3	3	AY.119	0.000106
ORF1ab/nsp12	500	K500K	aaA	aaG	3	3	AY.69	0.00056
ORF1ab/nsp12	500	K500K	aaA	aaG	3	3	B.1.1	0.000054
ORF1ab/nsp12	500	K500K	aaA	aaG	3	3	B.1.160	0.000094
ORF1ab/nsp12	500	K500K	aaA	aaG	3	3	B.1.2	0.000026
ORF1ab/nsp12	500	K500K	aaA	aaG	3	3	B.1.429	0.000071
ORF1ab/nsp12	500	K500K	aaA	aaG	3	3	B.1.526	0.000071
ORF1ab/nsp12	500	K500K	aaA	aaG	3	3	B.1.637	0.000219
ORF1ab/nsp12	500	K500M	aAA	aTG	2	2		0.111111
ORF1ab/nsp12	500	K500L	AAa	CTa	2	2		0.111111
ORF1ab/nsp12	500	K500del1	aAA	aG-	2	2		0.111111
ORF1ab/nsp12	500	K500T	aAa	aCa	2	2		0.111111
ORF1ab/nsp12	500	K500M	aAA	aTG	2	2	All	0
ORF1ab/nsp12	500	K500K	aaA	aaG	2	2	AY.102	0.000053
ORF1ab/nsp12	500	K500R	aAa	aGa	2	2	AY.102	0.000053
ORF1ab/nsp12	500	K500del	AAA	---	2	2	AY.43	0.000009
ORF1ab/nsp12	500	K500del1	Aaa	-aa	2	2	B.1	0.000018
ORF1ab/nsp12	500	K500del	AAA	---	2	2	B.1.1	0.000036
ORF1ab/nsp12	500	K500K	aaA	aaG	2	2	B.1.1.39	0.001019
ORF1ab/nsp12	500	K500K	aaA	aaG	2	2	B.1.177	0.000026
ORF1ab/nsp12	500	K500del1	Aaa	-aa	2	2	B.1.2	0.000018
ORF1ab/nsp12	500	K500K	aaA	aaG	2	2	B.1.258.17	0.000208
ORF1ab/nsp12	500	K500K	aaA	aaG	2	2	B.1.351	0.000059
ORF1ab/nsp12	500	K500K	aaA	aaG	2	2	B.1.427	0.000101
ORF1ab/nsp12	500	K500K	aaA	aaG	2	2	B.1.597	0.009259
ORF1ab/nsp12	500	K500K	aaA	aaG	2	2	C.26	0.014706
ORF1ab/nsp12	500	K500del	AAA	---	2	2	P.1	0.000032
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	A.1	0.000282
ORF1ab/nsp12	500	K500N	aaA	aaT	1	1	A.2.4	0.003367
ORF1ab/nsp12	500	K500del2	AAa	--a	1	1	All	0
ORF1ab/nsp12	500	K500D	AaA	GaC	1	1	All	0
ORF1ab/nsp12	500	K500del	AAA	---	1	1	AY.107	0.000466
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	AY.113	0.000142
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	AY.116	0.000287
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	AY.121	0.000135
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	AY.13	0.000161
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	AY.14	0.000088
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	AY.16.1	0.00047
ORF1ab/nsp12	500	K500R	aAa	aGa	1	1	AY.23	0.00007
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	AY.23	0.00007
ORF1ab/nsp12	500	K500del	AAA	---	1	1	AY.25	0.000006
ORF1ab/nsp12	500	K500R	aAa	aGa	1	1	AY.26	0.000028
ORF1ab/nsp12	500	K500R	aAa	aGa	1	1	AY.3	0.00001
ORF1ab/nsp12	500	K500del	AAA	---	1	1	AY.3	0.00001
ORF1ab/nsp12	500	K500del	AAA	---	1	1	AY.35	0.000233
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	AY.36	0.000148
ORF1ab/nsp12	500	K500del	AAA	---	1	1	AY.38	0.000499
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	AY.39	0.000025
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	AY.4.2	0.000022
ORF1ab/nsp12	500	K500del	AAA	---	1	1	AY.4.5	0.000107
ORF1ab/nsp12	500	K500del	AAA	---	1	1	AY.42	0.00004
ORF1ab/nsp12	500	K500I	aAA	aTC	1	1	AY.43	0.000004
ORF1ab/nsp12	500	K500D	AaA	GaC	1	1	AY.43	0.000004
ORF1ab/nsp12	500	K500T	aAa	aCa	1	1	AY.43	0.000004
ORF1ab/nsp12	500	K500R	aAa	aGa	1	1	AY.43	0.000004
ORF1ab/nsp12	500	K500N	aaA	aaT	1	1	AY.43	0.000004
ORF1ab/nsp12	500	K500R	aAa	aGa	1	1	AY.44	0.000006
ORF1ab/nsp12	500	K500N	aaA	aaC	1	1	AY.44	0.000006
ORF1ab/nsp12	500	K500del	AAA	---	1	1	AY.44	0.000006
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	AY.45	0.000122
ORF1ab/nsp12	500	K500del	AAA	---	1	1	AY.46	0.000104
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	AY.46.3	0.000934
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	AY.5	0.000021
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	AY.65	0.000533
ORF1ab/nsp12	500	K500L	AAa	TTa	1	1	AY.67	0.000464
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	AY.75.1	0.00018
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	AY.78	0.001541
ORF1ab/nsp12	500	K500R	aAA	aGG	1	1	AY.84	0.000437
ORF1ab/nsp12	500	K500del2	AAa	--a	1	1	AY.9	0.000068
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	AY.9.1	0.000084
ORF1ab/nsp12	500	K500del	AAA	---	1	1	AY.99	0.001049
ORF1ab/nsp12	500	K500del	AAA	---	1	1	AY.99.1	0.001553
ORF1ab/nsp12	500	K500N	aaA	aaC	1	1	B.1	0.000009
ORF1ab/nsp12	500	K500T	aAa	aCa	1	1	B.1	0.000009
ORF1ab/nsp12	500	K500R	aAa	aGa	1	1	B.1	0.000009
ORF1ab/nsp12	500	K500del	AAA	---	1	1	B.1	0.000009
ORF1ab/nsp12	500	K500del1	AAA	-NN	1	1	B.1.1	0.000018
ORF1ab/nsp12	500	K500I	aAA	aTC	1	1	B.1.1	0.000018
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	B.1.1.10	0.001115
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	B.1.1.141	0.002012
ORF1ab/nsp12	500	K500del	AAA	---	1	1	B.1.1.159	0.004673
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	B.1.1.161	0.003534
ORF1ab/nsp12	500	K500I	aAa	aTa	1	1	B.1.1.174	0.003378
ORF1ab/nsp12	500	K500del	AAA	---	1	1	B.1.1.25	0.000569
ORF1ab/nsp12	500	K500del	AAA	---	1	1	B.1.1.306	0.000438
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	B.1.1.311	0.000358
ORF1ab/nsp12	500	K500R	aAa	aGa	1	1	B.1.1.39	0.00051
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	B.1.1.523	0.001563
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	B.1.1.63	0.000386
ORF1ab/nsp12	500	K500N	aaA	aaC	1	1	B.1.1.7	0.000001
ORF1ab/nsp12	500	K500I	aAa	aTa	1	1	B.1.1.7	0.000001
ORF1ab/nsp12	500	K500del1	aaA	aa-	1	1	B.1.1.7	0.000001
ORF1ab/nsp12	500	K500del	AAA	---	1	1	B.1.160.23	0.004831
ORF1ab/nsp12	500	K500del	AAA	---	1	1	B.1.177	0.000013
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	B.1.177.44	0.000519
ORF1ab/nsp12	500	K500del	AAA	---	1	1	B.1.177.68	0.015152
ORF1ab/nsp12	500	K500del	AAA	---	1	1	B.1.177.76	0.002494
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	B.1.177.85	0.005435
ORF1ab/nsp12	500	K500T	aAa	aCa	1	1	B.1.177.9	0.001332
ORF1ab/nsp12	500	K500I	aAa	aTa	1	1	B.1.2	0.000009
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	B.1.236	0.002053
ORF1ab/nsp12	500	K500del	AAA	---	1	1	B.1.258	0.000067
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	B.1.356	0.001727
ORF1ab/nsp12	500	K500R	aAa	aGa	1	1	B.1.36.29	0.000517
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	B.1.36.31	0.001751
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	B.1.361	0.001289
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	B.1.380	0.006623
ORF1ab/nsp12	500	K500del1	Aaa	-aa	1	1	B.1.396	0.000706
ORF1ab/nsp12	500	K500T	aAa	aCa	1	1	B.1.416	0.001269
ORF1ab/nsp12	500	K500I	aAa	aTa	1	1	B.1.429	0.000024
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	B.1.459	0.004082
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	B.1.523	0.002451
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	B.1.596	0.000087
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	B.1.609	0.000479
ORF1ab/nsp12	500	K500R	aAa	aGa	1	1	B.1.617.2	0.000004
ORF1ab/nsp12	500	K500T	aAa	aCa	1	1	B.1.617.2	0.000004
ORF1ab/nsp12	500	K500del	AAA	---	1	1	B.13	0.045455
ORF1ab/nsp12	500	K500del	AAA	---	1	1	C.36	0.000911
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	C.36.3.1	0.002717
ORF1ab/nsp12	500	K500K	aaA	aaG	1	1	P.1	0.000016
ORF1ab/nsp12	500	K500del1	Aaa	-aa	1	1	P.1	0.000016
ORF1ab/nsp12	500	K500del	AAA	---	1	1	P.1.4	0.000977

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.