CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp6 : CodonNum = 222

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/nsp6	222	T222T	T3791T	syn	acT	acC	313	277	0.884984	11636-11638
ORF1ab/nsp6	222	T222T	T3791T	syn	acT	acG	313	31	0.0990415	11636-11638
ORF1ab/nsp6	222	T222T	T3791T	syn	acT	acA	313	5	0.0159744	11636-11638
ORF1ab/nsp6	222	T222del	T3791del	del	ACT	---	103	103	1	11636-11638
ORF1ab/nsp6	222	T222N	T3791N	nonsyn	aCt	aAt	52	50	0.961538	11636-11638
ORF1ab/nsp6	222	T222N	T3791N	nonsyn	aCT	aAC	52	2	0.0384615	11636-11638
ORF1ab/nsp6	222	T222I	T3791I	nonsyn	aCt	aTt	24	24	1	11636-11638
ORF1ab/nsp6	222	T222S	T3791S	nonsyn	Act	Tct	14	14	1	11636-11638
ORF1ab/nsp6	222	T222A	T3791A	nonsyn	Act	Gct	11	11	1	11636-11638
ORF1ab/nsp6	222	T222del2	T3791del2	del	aCT	a--	7	4	0.571429	11636-11638
ORF1ab/nsp6	222	T222del2	T3791del2	del	ACt	--t	7	2	0.285714	11636-11638
ORF1ab/nsp6	222	T222del2	T3791del2	del	ACT	G--	7	1	0.142857	11636-11638
ORF1ab/nsp6	222	T222P	T3791P	nonsyn	Act	Cct	5	3	0.6	11636-11638
ORF1ab/nsp6	222	T222P	T3791P	nonsyn	AcT	CcC	5	2	0.4	11636-11638
ORF1ab/nsp6	222	T222H	T3791H	nonsyn	ACT	CAC	4	2	0.5	11636-11638
ORF1ab/nsp6	222	T222H	T3791H	nonsyn	ACt	CAt	4	2	0.5	11636-11638
ORF1ab/nsp6	222	T222del1	T3791del1	del	Act	-ct	3	2	0.666667	11636-11638
ORF1ab/nsp6	222	T222del1	T3791del1	del	ACt	G-t	3	1	0.333333	11636-11638
ORF1ab/nsp6	222	T222K	T3791K	nonsyn	aCT	aAG	2	1	0.5	11636-11638
ORF1ab/nsp6	222	T222K	T3791K	nonsyn	aCT	aAA	2	1	0.5	11636-11638
ORF1ab/nsp6	222	T222V	T3791V	nonsyn	ACT	GTG	1	1	1	11636-11638
ORF1ab/nsp6	222	T222Y	T3791Y	nonsyn	ACt	TAt	1	1	1	11636-11638

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/nsp6	222	T222T	acT	acC	277	313	All	0.000053
ORF1ab/nsp6	222	T222T	acT	acG	31	313	All	0.000006
ORF1ab/nsp6	222	T222T	acT	acA	5	313	All	0.000001
ORF1ab/nsp6	222	T222T	acT	acC	164	164	B.1.1.71	0.993939
ORF1ab/nsp6	222	T222del	ACT	---	103	103	All	0.00002
ORF1ab/nsp6	222	T222N	aCt	aAt	50	52	All	0.00001
ORF1ab/nsp6	222	T222N	aCT	aAC	2	52	All	0
ORF1ab/nsp6	222	T222N	aCt	aAt	27	27	AY.4.2.1	0.004023
ORF1ab/nsp6	222	T222T	acT	acC	14	26	B.1.1.7	0.000013
ORF1ab/nsp6	222	T222T	acT	acG	12	26	B.1.1.7	0.000011
ORF1ab/nsp6	222	T222I	aCt	aTt	24	24	All	0.000005
ORF1ab/nsp6	222	T222T	acT	acC	19	21	AY.4	0.00003
ORF1ab/nsp6	222	T222T	acT	acA	1	21	AY.4	0.000002
ORF1ab/nsp6	222	T222T	acT	acG	1	21	AY.4	0.000002
ORF1ab/nsp6	222	T222del	ACT	---	20	20	B.1.617.2	0.000075
ORF1ab/nsp6	222	T222T	acT	acC	19	19	B.1.1.409	0.053824
ORF1ab/nsp6	222	T222del	ACT	---	16	16	B.1.1.7	0.000014
ORF1ab/nsp6	222	T222T	acT	acC	11	15	B.1	0.000101
ORF1ab/nsp6	222	T222T	acT	acA	2	15	B.1	0.000018
ORF1ab/nsp6	222	T222T	acT	acG	2	15	B.1	0.000018
ORF1ab/nsp6	222	T222S	Act	Tct	14	14	All	0.000003
ORF1ab/nsp6	222	T222A	Act	Gct	11	11	All	0.000002
ORF1ab/nsp6	222	T222del	ACT	---	10	10	B.1	0.000092
ORF1ab/nsp6	222	T222T	acT	acC	8	9	AY.45	0.000973
ORF1ab/nsp6	222	T222T	acT	acG	1	9	AY.45	0.000122
ORF1ab/nsp6	222	T222T	acT	acC	7	8	B.1.177	0.000092
ORF1ab/nsp6	222	T222T	acT	acG	1	8	B.1.177	0.000013
ORF1ab/nsp6	222	T222del2	aCT	a--	4	7	All	0.000001
ORF1ab/nsp6	222	T222del2	ACt	--t	2	7	All	0
ORF1ab/nsp6	222	T222del2	ACT	G--	1	7	All	0
ORF1ab/nsp6	222	T222del	ACT	---	6	6	AY.75.1	0.001082
ORF1ab/nsp6	222	T222P	Act	Cct	3	5	All	0.000001
ORF1ab/nsp6	222	T222P	AcT	CcC	2	5	All	0
ORF1ab/nsp6	222	T222del	ACT	---	5	5	AY.4	0.000008
ORF1ab/nsp6	222	T222N	aCt	aAt	5	5	AY.42	0.000201
ORF1ab/nsp6	222	T222del	ACT	---	5	5	AY.43	0.000022
ORF1ab/nsp6	222	T222T	acT	acC	5	5	B.1.1	0.000091
ORF1ab/nsp6	222	T222T	acT	acC	5	5	B.1.2	0.000044
ORF1ab/nsp6	222	T222H	ACt	CAt	2	4		0.111111
ORF1ab/nsp6	222	T222N	aCt	aAt	2	4		0.111111
ORF1ab/nsp6	222	T222N	aCT	aAC	2	4		0.111111
ORF1ab/nsp6	222	T222H	ACT	CAC	2	4		0.111111
ORF1ab/nsp6	222	T222P	AcT	CcC	2	4		0.111111
ORF1ab/nsp6	222	T222P	Act	Cct	2	4		0.111111
ORF1ab/nsp6	222	T222H	ACT	CAC	2	4	All	0
ORF1ab/nsp6	222	T222H	ACt	CAt	2	4	All	0
ORF1ab/nsp6	222	T222del	ACT	---	4	4	AY.9.2	0.000147
ORF1ab/nsp6	222	T222I	aCt	aTt	4	4	B.1	0.000037
ORF1ab/nsp6	222	T222S	Act	Tct	4	4	P.1	0.000063
ORF1ab/nsp6	222	T222del1	Act	-ct	2	3	All	0
ORF1ab/nsp6	222	T222del1	ACt	G-t	1	3	All	0
ORF1ab/nsp6	222	T222T	acT	acG	2	3	AY.102	0.000053
ORF1ab/nsp6	222	T222T	acT	acC	1	3	AY.102	0.000027
ORF1ab/nsp6	222	T222del	ACT	---	3	3	AY.26	0.000085
ORF1ab/nsp6	222	T222del	ACT	---	3	3	AY.33	0.0002
ORF1ab/nsp6	222	T222A	Act	Gct	3	3	AY.4	0.000005
ORF1ab/nsp6	222	T222I	aCt	aTt	3	3	B.1.1.7	0.000003
ORF1ab/nsp6	222	T222A	Act	Gct	3	3	B.1.1.7	0.000003
ORF1ab/nsp6	222	T222del	ACT	---	3	3	B.1.2	0.000026
ORF1ab/nsp6	222	T222T	acT	acC	2	3	B.1.526	0.000047
ORF1ab/nsp6	222	T222T	acT	acG	1	3	B.1.526	0.000024
ORF1ab/nsp6	222	T222N	aCt	aAt	3	3	B.1.617.2	0.000011
ORF1ab/nsp6	222	T222T	acT	acC	2	3	B.1.617.2	0.000008
ORF1ab/nsp6	222	T222T	acT	acG	1	3	B.1.617.2	0.000004
ORF1ab/nsp6	222	T222T	acT	acG	3	3	B.1.621	0.000266
ORF1ab/nsp6	222	T222T	acT	acC	2	2		0.111111
ORF1ab/nsp6	222	T222K	aCT	aAA	1	2	All	0
ORF1ab/nsp6	222	T222K	aCT	aAG	1	2	All	0
ORF1ab/nsp6	222	T222N	aCt	aAt	2	2	AY.12	0.000632
ORF1ab/nsp6	222	T222T	acT	acG	2	2	AY.120	0.000074
ORF1ab/nsp6	222	T222del	ACT	---	2	2	AY.42	0.00008
ORF1ab/nsp6	222	T222T	acT	acC	1	2	AY.44	0.000006
ORF1ab/nsp6	222	T222T	acT	acG	1	2	AY.44	0.000006
ORF1ab/nsp6	222	T222del	ACT	---	2	2	AY.65	0.001066
ORF1ab/nsp6	222	T222del	ACT	---	2	2	AY.71	0.00095
ORF1ab/nsp6	222	T222N	aCt	aAt	2	2	B.1.1.7	0.000002
ORF1ab/nsp6	222	T222I	aCt	aTt	2	2	B.1.2	0.000018
ORF1ab/nsp6	222	T222S	Act	Tct	2	2	B.1.429	0.000047
ORF1ab/nsp6	222	T222T	acT	acC	2	2	P.1	0.000032
ORF1ab/nsp6	222	T222S	Act	Tct	1	1	A	0.000387
ORF1ab/nsp6	222	T222del	ACT	---	1	1	A	0.000387
ORF1ab/nsp6	222	T222N	aCt	aAt	1	1	A.2.5.3	0.010309
ORF1ab/nsp6	222	T222Y	ACt	TAt	1	1	All	0
ORF1ab/nsp6	222	T222V	ACT	GTG	1	1	All	0
ORF1ab/nsp6	222	T222T	acT	acC	1	1	AM.4	0.003571
ORF1ab/nsp6	222	T222T	acT	acC	1	1	AU.3	0.00211
ORF1ab/nsp6	222	T222N	aCt	aAt	1	1	AY.102	0.000027
ORF1ab/nsp6	222	T222T	acT	acC	1	1	AY.103	0.000006
ORF1ab/nsp6	222	T222I	aCt	aTt	1	1	AY.103	0.000006
ORF1ab/nsp6	222	T222del	ACT	---	1	1	AY.24	0.000431
ORF1ab/nsp6	222	T222del2	ACT	G--	1	1	AY.24	0.000431
ORF1ab/nsp6	222	T222T	acT	acC	1	1	AY.25	0.000006
ORF1ab/nsp6	222	T222S	Act	Tct	1	1	AY.25	0.000006
ORF1ab/nsp6	222	T222T	acT	acC	1	1	AY.26	0.000028
ORF1ab/nsp6	222	T222T	acT	acG	1	1	AY.3	0.00001
ORF1ab/nsp6	222	T222del	ACT	---	1	1	AY.34	0.000097
ORF1ab/nsp6	222	T222del	ACT	---	1	1	AY.37	0.000316
ORF1ab/nsp6	222	T222del2	aCT	a--	1	1	AY.38	0.000499
ORF1ab/nsp6	222	T222N	aCt	aAt	1	1	AY.4.2	0.000022
ORF1ab/nsp6	222	T222A	Act	Gct	1	1	AY.4.2	0.000022
ORF1ab/nsp6	222	T222del	ACT	---	1	1	AY.4.5	0.000107
ORF1ab/nsp6	222	T222del2	aCT	a--	1	1	AY.43	0.000004
ORF1ab/nsp6	222	T222T	acT	acC	1	1	AY.43	0.000004
ORF1ab/nsp6	222	T222A	Act	Gct	1	1	AY.44	0.000006
ORF1ab/nsp6	222	T222K	aCT	aAA	1	1	AY.44	0.000006
ORF1ab/nsp6	222	T222N	aCt	aAt	1	1	AY.44	0.000006
ORF1ab/nsp6	222	T222P	Act	Cct	1	1	AY.47	0.000031
ORF1ab/nsp6	222	T222N	aCt	aAt	1	1	AY.47	0.000031
ORF1ab/nsp6	222	T222del	ACT	---	1	1	AY.47	0.000031
ORF1ab/nsp6	222	T222T	acT	acG	1	1	AY.5	0.000021
ORF1ab/nsp6	222	T222V	ACT	GTG	1	1	AY.55	0.000917
ORF1ab/nsp6	222	T222del	ACT	---	1	1	AY.62	0.000436
ORF1ab/nsp6	222	T222T	acT	acC	1	1	AY.67	0.000464
ORF1ab/nsp6	222	T222T	acT	acC	1	1	AY.7	0.000196
ORF1ab/nsp6	222	T222del	ACT	---	1	1	AY.75	0.000056
ORF1ab/nsp6	222	T222T	acT	acC	1	1	AY.75	0.000056
ORF1ab/nsp6	222	T222del	ACT	---	1	1	AY.78	0.001541
ORF1ab/nsp6	222	T222N	aCt	aAt	1	1	AY.9	0.000068
ORF1ab/nsp6	222	T222del	ACT	---	1	1	AY.9	0.000068
ORF1ab/nsp6	222	T222del	ACT	---	1	1	AY.9.1	0.000084
ORF1ab/nsp6	222	T222del2	aCT	a--	1	1	AY.9.1	0.000084
ORF1ab/nsp6	222	T222Y	ACt	TAt	1	1	AY.9.2	0.000037
ORF1ab/nsp6	222	T222A	Act	Gct	1	1	AY.9.2	0.000037
ORF1ab/nsp6	222	T222T	acT	acC	1	1	AY.98	0.000079
ORF1ab/nsp6	222	T222del	ACT	---	1	1	AY.98.1	0.000048
ORF1ab/nsp6	222	T222I	aCt	aTt	1	1	B	0.000128
ORF1ab/nsp6	222	T222del	ACT	---	1	1	B	0.000128
ORF1ab/nsp6	222	T222T	acT	acC	1	1	B	0.000128
ORF1ab/nsp6	222	T222del1	Act	-ct	1	1	B.1	0.000009
ORF1ab/nsp6	222	T222del	ACT	---	1	1	B.1.1.1	0.000327
ORF1ab/nsp6	222	T222I	aCt	aTt	1	1	B.1.1.15	0.013514
ORF1ab/nsp6	222	T222S	Act	Tct	1	1	B.1.1.207	0.001182
ORF1ab/nsp6	222	T222T	acT	acG	1	1	B.1.1.263	0.001558
ORF1ab/nsp6	222	T222I	aCt	aTt	1	1	B.1.1.284	0.000107
ORF1ab/nsp6	222	T222I	aCt	aTt	1	1	B.1.1.39	0.00051
ORF1ab/nsp6	222	T222I	aCt	aTt	1	1	B.1.1.417	0.002703
ORF1ab/nsp6	222	T222del	ACT	---	1	1	B.1.1.432	0.001266
ORF1ab/nsp6	222	T222I	aCt	aTt	1	1	B.1.1.519	0.00004
ORF1ab/nsp6	222	T222S	Act	Tct	1	1	B.1.1.7	0.000001
ORF1ab/nsp6	222	T222S	Act	Tct	1	1	B.1.1.70	0.000341
ORF1ab/nsp6	222	T222del	ACT	---	1	1	B.1.1.71	0.006061
ORF1ab/nsp6	222	T222I	aCt	aTt	1	1	B.1.160	0.000031
ORF1ab/nsp6	222	T222T	acT	acC	1	1	B.1.160.26	0.002421
ORF1ab/nsp6	222	T222del	ACT	---	1	1	B.1.161	0.017241
ORF1ab/nsp6	222	T222S	Act	Tct	1	1	B.1.177.15	0.000631
ORF1ab/nsp6	222	T222T	acT	acC	1	1	B.1.177.21	0.000076
ORF1ab/nsp6	222	T222del	ACT	---	1	1	B.1.177.83	0.001481
ORF1ab/nsp6	222	T222S	Act	Tct	1	1	B.1.2	0.000009
ORF1ab/nsp6	222	T222del2	ACt	--t	1	1	B.1.2	0.000009
ORF1ab/nsp6	222	T222I	aCt	aTt	1	1	B.1.23	0.006061
ORF1ab/nsp6	222	T222N	aCt	aAt	1	1	B.1.243	0.00007
ORF1ab/nsp6	222	T222I	aCt	aTt	1	1	B.1.338	0.008621
ORF1ab/nsp6	222	T222T	acT	acG	1	1	B.1.36	0.000146
ORF1ab/nsp6	222	T222I	aCt	aTt	1	1	B.1.375	0.00082
ORF1ab/nsp6	222	T222T	acT	acC	1	1	B.1.400	0.000429
ORF1ab/nsp6	222	T222del1	ACt	G-t	1	1	B.1.428	0.00102
ORF1ab/nsp6	222	T222N	aCt	aAt	1	1	B.1.429	0.000024
ORF1ab/nsp6	222	T222T	acT	acC	1	1	B.1.525	0.000113
ORF1ab/nsp6	222	T222I	aCt	aTt	1	1	B.1.525	0.000113
ORF1ab/nsp6	222	T222T	acT	acA	1	1	B.1.528	0.047619
ORF1ab/nsp6	222	T222I	aCt	aTt	1	1	B.1.585	0.027778
ORF1ab/nsp6	222	T222del2	aCT	a--	1	1	B.1.596	0.000087
ORF1ab/nsp6	222	T222N	aCt	aAt	1	1	B.1.596	0.000087
ORF1ab/nsp6	222	T222I	aCt	aTt	1	1	B.1.606	0.006024
ORF1ab/nsp6	222	T222del1	Act	-ct	1	1	B.1.617.2	0.000004
ORF1ab/nsp6	222	T222S	Act	Tct	1	1	B.1.617.2	0.000004
ORF1ab/nsp6	222	T222A	Act	Gct	1	1	B.1.617.2	0.000004
ORF1ab/nsp6	222	T222K	aCT	aAG	1	1	B.1.619	0.000871
ORF1ab/nsp6	222	T222I	aCt	aTt	1	1	B.1.637	0.000073
ORF1ab/nsp6	222	T222T	acT	acA	1	1	B.40	0.000364
ORF1ab/nsp6	222	T222A	Act	Gct	1	1	B.6.6	0.000889
ORF1ab/nsp6	222	T222del	ACT	---	1	1	C.36	0.000911
ORF1ab/nsp6	222	T222del	ACT	---	1	1	N.4	0.004255
ORF1ab/nsp6	222	T222del2	ACt	--t	1	1	P.1	0.000016
ORF1ab/nsp6	222	T222del	ACT	---	1	1	P.1.1	0.000318
ORF1ab/nsp6	222	T222del	ACT	---	1	1	Q.2	0.000613

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.