CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : CodonNum = 76

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
N	76	T76I		nonsyn	aCc	aTc	292	292	1	28499-28501
N	76	T76T		syn	acC	acT	58	49	0.844828	28499-28501
N	76	T76T		syn	acC	acA	58	8	0.137931	28499-28501
N	76	T76T		syn	acC	acG	58	1	0.0172414	28499-28501
N	76	T76A		nonsyn	Acc	Gcc	24	24	1	28499-28501
N	76	T76del		del	ACC	---	17	17	1	28499-28501
N	76	T76S		nonsyn	Acc	Tcc	16	13	0.8125	28499-28501
N	76	T76S		nonsyn	aCc	aGc	16	2	0.125	28499-28501
N	76	T76S		nonsyn	AcC	TcG	16	1	0.0625	28499-28501
N	76	T76N		nonsyn	aCc	aAc	8	8	1	28499-28501
N	76	T76L		nonsyn	ACC	CTT	7	6	0.857143	28499-28501
N	76	T76L		nonsyn	ACc	CTc	7	1	0.142857	28499-28501
N	76	T76P		nonsyn	Acc	Ccc	1	1	1	28499-28501
N	76	T76F		nonsyn	ACc	TTc	1	1	1	28499-28501
N	76	T76del2		del	aCC	a--	1	1	1	28499-28501

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
N	76	T76I	aCc	aTc	292	292	All	0.000056
N	76	T76I	aCc	aTc	129	129	B.1.1.218	0.992308
N	76	T76T	acC	acT	49	58	All	0.000009
N	76	T76T	acC	acA	8	58	All	0.000002
N	76	T76T	acC	acG	1	58	All	0
N	76	T76I	aCc	aTc	33	33	B.1.1.7	0.00003
N	76	T76A	Acc	Gcc	24	24	All	0.000005
N	76	T76I	aCc	aTc	22	22	B.1	0.000202
N	76	T76del	ACC	---	17	17	All	0.000003
N	76	T76S	Acc	Tcc	13	16	All	0.000002
N	76	T76S	aCc	aGc	2	16	All	0
N	76	T76S	AcC	TcG	1	16	All	0
N	76	T76I	aCc	aTc	16	16	B.1.1.519	0.000635
N	76	T76I	aCc	aTc	11	11	P.1	0.000173
N	76	T76A	Acc	Gcc	10	10	AY.4	0.000016
N	76	T76N	aCc	aAc	8	8	All	0.000002
N	76	T76L	ACC	CTT	6	7	All	0.000001
N	76	T76L	ACc	CTc	1	7	All	0
N	76	T76S	Acc	Tcc	7	7	AY.103	0.000043
N	76	T76T	acC	acT	7	7	B.1.637	0.000512
N	76	T76I	aCc	aTc	6	6	AY.4	0.000009
N	76	T76T	acC	acT	6	6	B.1.1.214	0.000333
N	76	T76T	acC	acT	6	6	B.1.1.7	0.000005
N	76	T76I	aCc	aTc	5	5	AY.25	0.00003
N	76	T76I	aCc	aTc	5	5	B.1.596	0.000436
N	76	T76L	ACC	CTT	4	4		0.222222
N	76	T76I	aCc	aTc	4	4	AY.44	0.000024
N	76	T76I	aCc	aTc	4	4	B.1.1.464	0.005891
N	76	T76T	acC	acT	4	4	B.1.243	0.000278
N	76	T76I	aCc	aTc	3	3	AY.30	0.001187
N	76	T76T	acC	acT	3	3	AY.4	0.000005
N	76	T76T	acC	acA	2	3	B.1	0.000018
N	76	T76T	acC	acG	1	3	B.1	0.000009
N	76	T76T	acC	acT	3	3	B.1.1.291	0.002227
N	76	T76N	aCc	aAc	3	3	B.1.1.7	0.000003
N	76	T76I	aCc	aTc	3	3	B.1.2	0.000026
N	76	T76T	acC	acT	3	3	B.1.2	0.000026
N	76	T76I	aCc	aTc	3	3	B.1.427	0.000151
N	76	T76I	aCc	aTc	3	3	B.1.429	0.000071
N	76	T76T	acC	acT	3	3	B.1.526	0.000071
N	76	T76A	Acc	Gcc	3	3	B.1.617.2	0.000011
N	76	T76del	ACC	---	2	2		0.111111
N	76	T76S	Acc	Tcc	2	2	AY.43	0.000009
N	76	T76T	acC	acA	2	2	AY.43	0.000009
N	76	T76I	aCc	aTc	2	2	B.1.1.284	0.000215
N	76	T76I	aCc	aTc	2	2	B.1.1.337	0.007194
N	76	T76A	Acc	Gcc	2	2	B.1.177.54	0.001213
N	76	T76T	acC	acT	2	2	B.1.429	0.000047
N	76	T76I	aCc	aTc	2	2	P.2	0.000373
N	76	T76I	aCc	aTc	2	2	P.3	0.00319
N	76	T76F	ACc	TTc	1	1	All	0
N	76	T76del2	aCC	a--	1	1	All	0
N	76	T76P	Acc	Ccc	1	1	All	0
N	76	T76T	acC	acA	1	1	AY.102	0.000027
N	76	T76I	aCc	aTc	1	1	AY.103	0.000006
N	76	T76A	Acc	Gcc	1	1	AY.103	0.000006
N	76	T76I	aCc	aTc	1	1	AY.16.1	0.00047
N	76	T76I	aCc	aTc	1	1	AY.18	0.010101
N	76	T76T	acC	acT	1	1	AY.23	0.00007
N	76	T76N	aCc	aAc	1	1	AY.25	0.000006
N	76	T76S	Acc	Tcc	1	1	AY.25	0.000006
N	76	T76del	ACC	---	1	1	AY.3	0.00001
N	76	T76I	aCc	aTc	1	1	AY.3	0.00001
N	76	T76I	aCc	aTc	1	1	AY.34	0.000097
N	76	T76N	aCc	aAc	1	1	AY.4	0.000002
N	76	T76P	Acc	Ccc	1	1	AY.44	0.000006
N	76	T76N	aCc	aAc	1	1	AY.44	0.000006
N	76	T76A	Acc	Gcc	1	1	AY.46.4	0.000165
N	76	T76A	Acc	Gcc	1	1	AY.47	0.000031
N	76	T76I	aCc	aTc	1	1	AY.53	0.000288
N	76	T76I	aCc	aTc	1	1	AY.67	0.000464
N	76	T76T	acC	acA	1	1	AY.69	0.000187
N	76	T76T	acC	acT	1	1	AY.9	0.000068
N	76	T76del	ACC	---	1	1	AY.9.2	0.000037
N	76	T76T	acC	acT	1	1	AY.9.2	0.000037
N	76	T76del	ACC	---	1	1	AZ.2	0.000821
N	76	T76S	aCc	aGc	1	1	B.1	0.000009
N	76	T76del	ACC	---	1	1	B.1	0.000009
N	76	T76L	ACC	CTT	1	1	B.1.1	0.000018
N	76	T76A	Acc	Gcc	1	1	B.1.1	0.000018
N	76	T76del	ACC	---	1	1	B.1.1	0.000018
N	76	T76I	aCc	aTc	1	1	B.1.1.139	0.022727
N	76	T76del	ACC	---	1	1	B.1.1.139	0.022727
N	76	T76del	ACC	---	1	1	B.1.1.216	0.00089
N	76	T76N	aCc	aAc	1	1	B.1.1.218	0.007692
N	76	T76I	aCc	aTc	1	1	B.1.1.220	0.001859
N	76	T76I	aCc	aTc	1	1	B.1.1.28	0.000311
N	76	T76I	aCc	aTc	1	1	B.1.1.291	0.000742
N	76	T76S	Acc	Tcc	1	1	B.1.1.356	0.008547
N	76	T76A	Acc	Gcc	1	1	B.1.1.37	0.000193
N	76	T76I	aCc	aTc	1	1	B.1.1.372	0.000689
N	76	T76S	aCc	aGc	1	1	B.1.1.39	0.00051
N	76	T76I	aCc	aTc	1	1	B.1.1.406	0.006494
N	76	T76T	acC	acT	1	1	B.1.1.519	0.00004
N	76	T76del	ACC	---	1	1	B.1.1.63	0.000386
N	76	T76del	ACC	---	1	1	B.1.1.7	0.000001
N	76	T76A	Acc	Gcc	1	1	B.1.1.7	0.000001
N	76	T76L	ACC	CTT	1	1	B.1.1.7	0.000001
N	76	T76I	aCc	aTc	1	1	B.1.139	0.000733
N	76	T76I	aCc	aTc	1	1	B.1.146	0.004237
N	76	T76I	aCc	aTc	1	1	B.1.160	0.000031
N	76	T76T	acC	acT	1	1	B.1.160	0.000031
N	76	T76I	aCc	aTc	1	1	B.1.160.16	0.000929
N	76	T76T	acC	acT	1	1	B.1.177	0.000013
N	76	T76I	aCc	aTc	1	1	B.1.177	0.000013
N	76	T76A	Acc	Gcc	1	1	B.1.177.21	0.000076
N	76	T76I	aCc	aTc	1	1	B.1.177.31	0.011494
N	76	T76del	ACC	---	1	1	B.1.177.63	0.002703
N	76	T76I	aCc	aTc	1	1	B.1.177.7	0.000165
N	76	T76del2	aCC	a--	1	1	B.1.2	0.000009
N	76	T76T	acC	acT	1	1	B.1.240	0.000216
N	76	T76I	aCc	aTc	1	1	B.1.240	0.000216
N	76	T76A	Acc	Gcc	1	1	B.1.243	0.00007
N	76	T76T	acC	acT	1	1	B.1.311	0.000275
N	76	T76S	Acc	Tcc	1	1	B.1.325	0.006897
N	76	T76I	aCc	aTc	1	1	B.1.329	0.000608
N	76	T76T	acC	acA	1	1	B.1.351.5	0.0006
N	76	T76I	aCc	aTc	1	1	B.1.36.26	0.002857
N	76	T76I	aCc	aTc	1	1	B.1.409	0.000781
N	76	T76del	ACC	---	1	1	B.1.415	0.014286
N	76	T76del	ACC	---	1	1	B.1.427	0.00005
N	76	T76S	Acc	Tcc	1	1	B.1.438.1	0.000107
N	76	T76del	ACC	---	1	1	B.1.439	0.005917
N	76	T76T	acC	acT	1	1	B.1.453	0.003236
N	76	T76T	acC	acA	1	1	B.1.497	0.000315
N	76	T76I	aCc	aTc	1	1	B.1.526	0.000024
N	76	T76A	Acc	Gcc	1	1	B.1.526	0.000024
N	76	T76I	aCc	aTc	1	1	B.1.582	0.000491
N	76	T76I	aCc	aTc	1	1	B.1.595	0.000261
N	76	T76N	aCc	aAc	1	1	B.1.617.2	0.000004
N	76	T76L	ACc	CTc	1	1	B.1.617.2	0.000004
N	76	T76I	aCc	aTc	1	1	B.1.617.2	0.000004
N	76	T76F	ACc	TTc	1	1	B.1.617.3	0.002985
N	76	T76I	aCc	aTc	1	1	B.1.621	0.000089
N	76	T76S	AcC	TcG	1	1	B.1.621	0.000089
N	76	T76I	aCc	aTc	1	1	B.39	0.002331
N	76	T76I	aCc	aTc	1	1	C.37	0.000116
N	76	T76T	acC	acT	1	1	C.37	0.000116
N	76	T76T	acC	acT	1	1	D.2	0.000075
N	76	T76I	aCc	aTc	1	1	D.2	0.000075
N	76	T76del	ACC	---	1	1	P.1	0.000016
N	76	T76T	acC	acT	1	1	P.1	0.000016
N	76	T76I	aCc	aTc	1	1	P.1.1	0.000318
N	76	T76I	aCc	aTc	1	1	P.1.14	0.000048
N	76	T76I	aCc	aTc	1	1	P.1.15	0.000232
N	76	T76del	ACC	---	1	1	Q.2	0.000613
N	76	T76I	aCc	aTc	1	1	Q.8	0.000165
N	76	T76I	aCc	aTc	1	1	R.1	0.00009

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.