CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp12 : CodonNum = 807

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	807	K807R	K5199R	nonsyn	aAa	aGa	280	280	1	15859-15861
ORF1ab/nsp12	807	K807N	K5199N	nonsyn	aaA	aaC	156	145	0.929487	15859-15861
ORF1ab/nsp12	807	K807N	K5199N	nonsyn	aaA	aaT	156	11	0.0705128	15859-15861
ORF1ab/nsp12	807	K807K	K5199K	syn	aaA	aaG	130	130	1	15859-15861
ORF1ab/nsp12	807	K807E	K5199E	nonsyn	Aaa	Gaa	48	48	1	15859-15861
ORF1ab/nsp12	807	K807T	K5199T	nonsyn	aAa	aCa	15	15	1	15859-15861
ORF1ab/nsp12	807	K807del1	K5199del1	del	aaA	aa-	14	7	0.5	15859-15861
ORF1ab/nsp12	807	K807del1	K5199del1	del	Aaa	-aa	14	6	0.428571	15859-15861
ORF1ab/nsp12	807	K807del1	K5199del1	del	AaA	Ga-	14	1	0.0714286	15859-15861
ORF1ab/nsp12	807	K807del	K5199del	del	AAA	---	9	9	1	15859-15861
ORF1ab/nsp12	807	K807Q	K5199Q	nonsyn	Aaa	Caa	7	7	1	15859-15861
ORF1ab/nsp12	807	K807X	K5199X	nonsyn	Aaa	Taa	4	4	1	15859-15861
ORF1ab/nsp12	807	K807I	K5199I	nonsyn	aAa	aTa	3	3	1	15859-15861
ORF1ab/nsp12	807	K807G	K5199G	nonsyn	AAA	GGT	1	1	1	15859-15861
ORF1ab/nsp12	807	K807del2	K5199del2	del	aAA	a--	1	1	1	15859-15861
ORF1ab/nsp12	807	K807L	K5199L	nonsyn	AAa	CTa	1	1	1	15859-15861
ORF1ab/nsp12	807	K807D	K5199D	nonsyn	AaA	GaC	1	1	1	15859-15861

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	807	K807R	aAa	aGa	280	280	All	0.000054
ORF1ab/nsp12	807	K807N	aaA	aaC	145	156	All	0.000028
ORF1ab/nsp12	807	K807N	aaA	aaT	11	156	All	0.000002
ORF1ab/nsp12	807	K807R	aAa	aGa	140	140	R.1	0.012601
ORF1ab/nsp12	807	K807K	aaA	aaG	130	130	All	0.000025
ORF1ab/nsp12	807	K807N	aaA	aaC	66	66	AY.9	0.004461
ORF1ab/nsp12	807	K807E	Aaa	Gaa	48	48	All	0.000009
ORF1ab/nsp12	807	K807E	Aaa	Gaa	30	30	B.1.1.320	0.545455
ORF1ab/nsp12	807	K807R	aAa	aGa	25	25	B.1.387	1
ORF1ab/nsp12	807	K807R	aAa	aGa	21	21	B.1.1.7	0.000019
ORF1ab/nsp12	807	K807K	aaA	aaG	18	18	B.1	0.000165
ORF1ab/nsp12	807	K807K	aaA	aaG	18	18	B.1.396	0.012703
ORF1ab/nsp12	807	K807K	aaA	aaG	17	17	B.1.1.7	0.000015
ORF1ab/nsp12	807	K807T	aAa	aCa	15	15	All	0.000003
ORF1ab/nsp12	807	K807R	aAa	aGa	15	15	B.1.2	0.000132
ORF1ab/nsp12	807	K807del1	aaA	aa-	7	14	All	0.000001
ORF1ab/nsp12	807	K807del1	Aaa	-aa	6	14	All	0.000001
ORF1ab/nsp12	807	K807del1	AaA	Ga-	1	14	All	0
ORF1ab/nsp12	807	K807R	aAa	aGa	13	13	AY.4	0.00002
ORF1ab/nsp12	807	K807N	aaA	aaC	13	13	B.1.2	0.000114
ORF1ab/nsp12	807	K807K	aaA	aaG	12	12	AY.103	0.000075
ORF1ab/nsp12	807	K807R	aAa	aGa	12	12	B.1.1	0.000218
ORF1ab/nsp12	807	K807N	aaA	aaC	12	12	B.1.1.7	0.000011
ORF1ab/nsp12	807	K807N	aaA	aaC	10	10	AY.4	0.000016
ORF1ab/nsp12	807	K807N	aaA	aaC	9	10	B.1.177	0.000119
ORF1ab/nsp12	807	K807N	aaA	aaT	1	10	B.1.177	0.000013
ORF1ab/nsp12	807	K807del	AAA	---	9	9	All	0.000002
ORF1ab/nsp12	807	K807K	aaA	aaG	9	9	B.1.617.2	0.000034
ORF1ab/nsp12	807	K807N	aaA	aaC	8	9	B.1.617.2	0.00003
ORF1ab/nsp12	807	K807N	aaA	aaT	1	9	B.1.617.2	0.000004
ORF1ab/nsp12	807	K807E	Aaa	Gaa	8	8	AY.3	0.00008
ORF1ab/nsp12	807	K807Q	Aaa	Caa	7	7	All	0.000001
ORF1ab/nsp12	807	K807E	Aaa	Gaa	7	7	AY.4	0.000011
ORF1ab/nsp12	807	K807N	aaA	aaC	6	7	B.1.1	0.000109
ORF1ab/nsp12	807	K807N	aaA	aaT	1	7	B.1.1	0.000018
ORF1ab/nsp12	807	K807K	aaA	aaG	7	7	B.1.2	0.000062
ORF1ab/nsp12	807	K807R	aAa	aGa	6	6	AY.33	0.000401
ORF1ab/nsp12	807	K807K	aaA	aaG	6	6	AY.4	0.000009
ORF1ab/nsp12	807	K807R	aAa	aGa	6	6	B.1.617.2	0.000023
ORF1ab/nsp12	807	K807T	aAa	aCa	5	5	AY.39.1	0.000198
ORF1ab/nsp12	807	K807K	aaA	aaG	5	5	B.1.1	0.000091
ORF1ab/nsp12	807	K807del1	aaA	aa-	4	5	B.1.1.7	0.000004
ORF1ab/nsp12	807	K807del1	Aaa	-aa	1	5	B.1.1.7	0.000001
ORF1ab/nsp12	807	K807N	aaA	aaC	4	5	P.1	0.000063
ORF1ab/nsp12	807	K807N	aaA	aaT	1	5	P.1	0.000016
ORF1ab/nsp12	807	K807X	Aaa	Taa	4	4	All	0.000001
ORF1ab/nsp12	807	K807R	aAa	aGa	4	4	AY.103	0.000025
ORF1ab/nsp12	807	K807R	aAa	aGa	4	4	AY.25	0.000024
ORF1ab/nsp12	807	K807N	aaA	aaC	3	4	AY.3	0.00003
ORF1ab/nsp12	807	K807N	aaA	aaT	1	4	AY.3	0.00001
ORF1ab/nsp12	807	K807K	aaA	aaG	4	4	AY.44	0.000024
ORF1ab/nsp12	807	K807R	aAa	aGa	4	4	AY.44	0.000024
ORF1ab/nsp12	807	K807R	aAa	aGa	4	4	AY.98.1	0.000194
ORF1ab/nsp12	807	K807R	aAa	aGa	4	4	B.1.177.56	0.00267
ORF1ab/nsp12	807	K807I	aAa	aTa	3	3	All	0.000001
ORF1ab/nsp12	807	K807N	aaA	aaC	3	3	AY.103	0.000019
ORF1ab/nsp12	807	K807R	aAa	aGa	3	3	B.1.526	0.000071
ORF1ab/nsp12	807	K807N	aaA	aaC	2	2	AY.102	0.000053
ORF1ab/nsp12	807	K807N	aaA	aaC	2	2	AY.23	0.000139
ORF1ab/nsp12	807	K807N	aaA	aaT	2	2	AY.25	0.000012
ORF1ab/nsp12	807	K807del1	aaA	aa-	2	2	AY.25	0.000012
ORF1ab/nsp12	807	K807R	aAa	aGa	2	2	AY.29	0.000032
ORF1ab/nsp12	807	K807Q	Aaa	Caa	2	2	AY.3	0.00002
ORF1ab/nsp12	807	K807T	aAa	aCa	2	2	AY.4	0.000003
ORF1ab/nsp12	807	K807N	aaA	aaT	1	2	AY.43	0.000004
ORF1ab/nsp12	807	K807N	aaA	aaC	1	2	AY.43	0.000004
ORF1ab/nsp12	807	K807K	aaA	aaG	2	2	AY.5	0.000041
ORF1ab/nsp12	807	K807R	aAa	aGa	2	2	B.1.1.306	0.000877
ORF1ab/nsp12	807	K807K	aaA	aaG	2	2	B.1.1.306	0.000877
ORF1ab/nsp12	807	K807T	aAa	aCa	2	2	B.1.1.7	0.000002
ORF1ab/nsp12	807	K807del	AAA	---	2	2	B.1.1.7	0.000002
ORF1ab/nsp12	807	K807K	aaA	aaG	2	2	B.1.351	0.000059
ORF1ab/nsp12	807	K807R	aAa	aGa	2	2	B.1.596	0.000174
ORF1ab/nsp12	807	K807K	aaA	aaG	2	2	B.1.617.1	0.000258
ORF1ab/nsp12	807	K807Q	Aaa	Caa	2	2	B.1.617.2	0.000008
ORF1ab/nsp12	807	K807del1	Aaa	-aa	2	2	B.1.617.2	0.000008
ORF1ab/nsp12	807	K807K	aaA	aaG	2	2	P.1	0.000032
ORF1ab/nsp12	807	K807K	aaA	aaG	2	2	P.1.10	0.000539
ORF1ab/nsp12	807	K807K	aaA	aaG	2	2	Q.8	0.00033
ORF1ab/nsp12	807	K807N	aaA	aaC	1	1	A.2.2	0.001689
ORF1ab/nsp12	807	K807K	aaA	aaG	1	1	AE.2	0.058824
ORF1ab/nsp12	807	K807D	AaA	GaC	1	1	All	0
ORF1ab/nsp12	807	K807G	AAA	GGT	1	1	All	0
ORF1ab/nsp12	807	K807L	AAa	CTa	1	1	All	0
ORF1ab/nsp12	807	K807del2	aAA	a--	1	1	All	0
ORF1ab/nsp12	807	K807N	aaA	aaC	1	1	AY.1	0.000396
ORF1ab/nsp12	807	K807N	aaA	aaT	1	1	AY.114	0.000231
ORF1ab/nsp12	807	K807R	aAa	aGa	1	1	AY.118	0.000063
ORF1ab/nsp12	807	K807T	aAa	aCa	1	1	AY.118	0.000063
ORF1ab/nsp12	807	K807I	aAa	aTa	1	1	AY.120	0.000037
ORF1ab/nsp12	807	K807R	aAa	aGa	1	1	AY.16	0.00038
ORF1ab/nsp12	807	K807K	aaA	aaG	1	1	AY.20	0.000039
ORF1ab/nsp12	807	K807K	aaA	aaG	1	1	AY.23	0.00007
ORF1ab/nsp12	807	K807K	aaA	aaG	1	1	AY.25	0.000006
ORF1ab/nsp12	807	K807del2	aAA	a--	1	1	AY.25	0.000006
ORF1ab/nsp12	807	K807N	aaA	aaC	1	1	AY.29	0.000016
ORF1ab/nsp12	807	K807K	aaA	aaG	1	1	AY.3	0.00001
ORF1ab/nsp12	807	K807T	aAa	aCa	1	1	AY.3	0.00001
ORF1ab/nsp12	807	K807N	aaA	aaC	1	1	AY.33	0.000067
ORF1ab/nsp12	807	K807R	aAa	aGa	1	1	AY.39	0.000025
ORF1ab/nsp12	807	K807K	aaA	aaG	1	1	AY.39	0.000025
ORF1ab/nsp12	807	K807del1	aaA	aa-	1	1	AY.4	0.000002
ORF1ab/nsp12	807	K807T	aAa	aCa	1	1	AY.4.5	0.000107
ORF1ab/nsp12	807	K807K	aaA	aaG	1	1	AY.43	0.000004
ORF1ab/nsp12	807	K807T	aAa	aCa	1	1	AY.43	0.000004
ORF1ab/nsp12	807	K807R	aAa	aGa	1	1	AY.43	0.000004
ORF1ab/nsp12	807	K807Q	Aaa	Caa	1	1	AY.44	0.000006
ORF1ab/nsp12	807	K807del1	AaA	Ga-	1	1	AY.44	0.000006
ORF1ab/nsp12	807	K807E	Aaa	Gaa	1	1	AY.46.6	0.000072
ORF1ab/nsp12	807	K807K	aaA	aaG	1	1	AY.59	0.00053
ORF1ab/nsp12	807	K807K	aaA	aaG	1	1	AY.60	0.000938
ORF1ab/nsp12	807	K807R	aAa	aGa	1	1	AY.75	0.000056
ORF1ab/nsp12	807	K807L	AAa	CTa	1	1	AY.85	0.000427
ORF1ab/nsp12	807	K807N	aaA	aaT	1	1	AY.9.1	0.000084
ORF1ab/nsp12	807	K807I	aAa	aTa	1	1	AY.98.1	0.000048
ORF1ab/nsp12	807	K807R	aAa	aGa	1	1	AY.99.2	0.000092
ORF1ab/nsp12	807	K807K	aaA	aaG	1	1	B	0.000128
ORF1ab/nsp12	807	K807del1	Aaa	-aa	1	1	B.1	0.000009
ORF1ab/nsp12	807	K807del	AAA	---	1	1	B.1.1	0.000018
ORF1ab/nsp12	807	K807G	AAA	GGT	1	1	B.1.1	0.000018
ORF1ab/nsp12	807	K807X	Aaa	Taa	1	1	B.1.1.216	0.00089
ORF1ab/nsp12	807	K807E	Aaa	Gaa	1	1	B.1.1.282	0.011628
ORF1ab/nsp12	807	K807R	aAa	aGa	1	1	B.1.1.369	0.000446
ORF1ab/nsp12	807	K807K	aaA	aaG	1	1	B.1.1.398	0.003226
ORF1ab/nsp12	807	K807R	aAa	aGa	1	1	B.1.1.416	0.000905
ORF1ab/nsp12	807	K807D	AaA	GaC	1	1	B.1.1.464	0.001473
ORF1ab/nsp12	807	K807Q	Aaa	Caa	1	1	B.1.1.7	0.000001
ORF1ab/nsp12	807	K807I	aAa	aTa	1	1	B.1.1.7	0.000001
ORF1ab/nsp12	807	K807K	aaA	aaG	1	1	B.1.177	0.000013
ORF1ab/nsp12	807	K807R	aAa	aGa	1	1	B.1.177.20	0.001517
ORF1ab/nsp12	807	K807K	aaA	aaG	1	1	B.1.177.40	0.005155
ORF1ab/nsp12	807	K807N	aaA	aaC	1	1	B.1.177.60	0.000218
ORF1ab/nsp12	807	K807R	aAa	aGa	1	1	B.1.177.7	0.000165
ORF1ab/nsp12	807	K807del1	Aaa	-aa	1	1	B.1.177.73	0.000566
ORF1ab/nsp12	807	K807del	AAA	---	1	1	B.1.177.83	0.001481
ORF1ab/nsp12	807	K807X	Aaa	Taa	1	1	B.1.2	0.000009
ORF1ab/nsp12	807	K807del1	Aaa	-aa	1	1	B.1.2	0.000009
ORF1ab/nsp12	807	K807K	aaA	aaG	1	1	B.1.234	0.000132
ORF1ab/nsp12	807	K807T	aAa	aCa	1	1	B.1.234	0.000132
ORF1ab/nsp12	807	K807K	aaA	aaG	1	1	B.1.236	0.002053
ORF1ab/nsp12	807	K807N	aaA	aaT	1	1	B.1.258	0.000067
ORF1ab/nsp12	807	K807K	aaA	aaG	1	1	B.1.36.29	0.000517
ORF1ab/nsp12	807	K807K	aaA	aaG	1	1	B.1.416	0.001269
ORF1ab/nsp12	807	K807K	aaA	aaG	1	1	B.1.470	0.001404
ORF1ab/nsp12	807	K807K	aaA	aaG	1	1	B.1.596	0.000087
ORF1ab/nsp12	807	K807T	aAa	aCa	1	1	B.1.617.1	0.000129
ORF1ab/nsp12	807	K807Q	Aaa	Caa	1	1	B.1.617.1	0.000129
ORF1ab/nsp12	807	K807N	aaA	aaC	1	1	B.1.617.1	0.000129
ORF1ab/nsp12	807	K807X	Aaa	Taa	1	1	B.1.617.1	0.000129
ORF1ab/nsp12	807	K807del	AAA	---	1	1	B.1.617.2	0.000004
ORF1ab/nsp12	807	K807E	Aaa	Gaa	1	1	B.1.617.2	0.000004
ORF1ab/nsp12	807	K807X	Aaa	Taa	1	1	B.1.621	0.000089
ORF1ab/nsp12	807	K807del	AAA	---	1	1	C.36	0.000911
ORF1ab/nsp12	807	K807R	aAa	aGa	1	1	D.2	0.000075
ORF1ab/nsp12	807	K807K	aaA	aaG	1	1	D.2	0.000075
ORF1ab/nsp12	807	K807del	AAA	---	1	1	P.1.1	0.000318
ORF1ab/nsp12	807	K807R	aAa	aGa	1	1	P.1.14	0.000048
ORF1ab/nsp12	807	K807del	AAA	---	1	1	Q.1	0.000126
ORF1ab/nsp12	807	K807del	AAA	---	1	1	Q.2	0.000613
ORF1ab/nsp12	807	K807R	aAa	aGa	1	1	Q.3	0.000145

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.