CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : CodonNum = 109

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	109	Y109Y		syn	taT	taC	3084	3084	1	28598-28600
N	109	Y109F		nonsyn	tAt	tTt	84	80	0.952381	28598-28600
N	109	Y109F		nonsyn	tAT	tTC	84	4	0.047619	28598-28600
N	109	Y109del		del	TAT	---	17	17	1	28598-28600
N	109	Y109H		nonsyn	Tat	Cat	12	12	1	28598-28600
N	109	Y109C		nonsyn	tAt	tGt	7	5	0.714286	28598-28600
N	109	Y109C		nonsyn	tAT	tGC	7	2	0.285714	28598-28600
N	109	Y109X		nonsyn	taT	taA	4	3	0.75	28598-28600
N	109	Y109X		nonsyn	taT	taG	4	1	0.25	28598-28600
N	109	Y109D		nonsyn	Tat	Gat	2	2	1	28598-28600
N	109	Y109N		nonsyn	Tat	Aat	1	1	1	28598-28600
N	109	Y109L		nonsyn	tAT	tTA	1	1	1	28598-28600
N	109	Y109I		nonsyn	TAT	ATC	1	1	1	28598-28600
N	109	Y109S		nonsyn	tAt	tCt	1	1	1	28598-28600
N	109	Y109del1		del	taT	ta-	1	1	1	28598-28600
N	109	Y109del2		del	TAt	--t	1	1	1	28598-28600

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	109	Y109Y	taT	taC	3084	3084	All	0.00059
N	109	Y109Y	taT	taC	1558	1558	B.1.619.1	0.999359
N	109	Y109Y	taT	taC	576	576	B.1.232	0.309511
N	109	Y109Y	taT	taC	326	326	AY.5	0.006732
N	109	Y109Y	taT	taC	202	202	B.1.561	0.080191
N	109	Y109F	tAt	tTt	80	84	All	0.000015
N	109	Y109F	tAT	tTC	4	84	All	0.000001
N	109	Y109Y	taT	taC	58	58	B.1	0.000531
N	109	Y109Y	taT	taC	45	45	B.1.1.7	0.00004
N	109	Y109F	tAt	tTt	43	43	B.1.1.7	0.000038
N	109	Y109Y	taT	taC	39	39	B.1.617.2	0.000147
N	109	Y109Y	taT	taC	32	32	AY.43	0.000142
N	109	Y109Y	taT	taC	31	31	AY.4	0.000048
N	109	Y109Y	taT	taC	26	26	B.1.2	0.000229
N	109	Y109del	TAT	---	17	17	All	0.000003
N	109	Y109Y	taT	taC	16	16	AY.1	0.006332
N	109	Y109H	Tat	Cat	12	12	All	0.000002
N	109	Y109Y	taT	taC	11	11	AY.44	0.000067
N	109	Y109F	tAt	tTt	11	11	B.1.2	0.000097
N	109	Y109Y	taT	taC	10	10	AY.39	0.000247
N	109	Y109Y	taT	taC	8	8	AY.23	0.000558
N	109	Y109Y	taT	taC	8	8	AY.79	0.009685
N	109	Y109C	tAt	tGt	5	7	All	0.000001
N	109	Y109C	tAT	tGC	2	7	All	0
N	109	Y109Y	taT	taC	7	7	AY.103	0.000043
N	109	Y109Y	taT	taC	7	7	B.1.619	0.006098
N	109	Y109F	tAt	tTt	7	7	Q.3	0.001015
N	109	Y109Y	taT	taC	6	6	AY.25	0.000036
N	109	Y109Y	taT	taC	6	6	AY.46.6	0.000433
N	109	Y109Y	taT	taC	6	6	B.1.351	0.000178
N	109	Y109Y	taT	taC	6	6	B.1.429	0.000141
N	109	Y109F	tAt	tTt	3	5		0.166667
N	109	Y109F	tAT	tTC	2	5		0.111111
N	109	Y109Y	taT	taC	5	5	AY.82	0.006784
N	109	Y109Y	taT	taC	5	5	B.1.281	0.108696
N	109	Y109Y	taT	taC	4	4		0.222222
N	109	Y109C	tAT	tGC	2	4		0.111111
N	109	Y109C	tAt	tGt	2	4		0.111111
N	109	Y109X	taT	taA	3	4	All	0.000001
N	109	Y109X	taT	taG	1	4	All	0
N	109	Y109Y	taT	taC	4	4	AY.3	0.00004
N	109	Y109Y	taT	taC	3	3	AY.102	0.00008
N	109	Y109F	tAt	tTt	3	3	AY.4	0.000005
N	109	Y109Y	taT	taC	3	3	AY.4.4	0.001227
N	109	Y109Y	taT	taC	3	3	P.1	0.000047
N	109	Y109del	TAT	---	2	2		0.111111
N	109	Y109D	Tat	Gat	2	2	All	0
N	109	Y109F	tAt	tTt	2	2	AY.103	0.000012
N	109	Y109Y	taT	taC	2	2	AY.2	0.000712
N	109	Y109H	Tat	Cat	2	2	AY.4	0.000003
N	109	Y109Y	taT	taC	2	2	AY.61	0.00021
N	109	Y109Y	taT	taC	2	2	AY.73	0.001331
N	109	Y109Y	taT	taC	2	2	AY.81	0.003984
N	109	Y109F	tAt	tTt	2	2	AY.82	0.002714
N	109	Y109Y	taT	taC	2	2	AY.9.1	0.000167
N	109	Y109Y	taT	taC	2	2	AY.9.2	0.000073
N	109	Y109Y	taT	taC	2	2	AY.98	0.000158
N	109	Y109Y	taT	taC	2	2	AY.99.2	0.000184
N	109	Y109Y	taT	taC	2	2	B.1.1	0.000036
N	109	Y109Y	taT	taC	2	2	B.1.1.135	0.00939
N	109	Y109Y	taT	taC	2	2	B.1.1.317	0.000823
N	109	Y109Y	taT	taC	2	2	B.1.1.397	0.004505
N	109	Y109del	TAT	---	2	2	B.1.1.7	0.000002
N	109	Y109Y	taT	taC	2	2	B.1.147	0.001512
N	109	Y109C	tAt	tGt	2	2	B.1.177	0.000026
N	109	Y109Y	taT	taC	2	2	B.1.22	0.002635
N	109	Y109Y	taT	taC	2	2	B.1.36.16	0.002849
N	109	Y109F	tAt	tTt	2	2	B.1.429	0.000047
N	109	Y109Y	taT	taC	2	2	B.1.466.2	0.000782
N	109	Y109del	TAT	---	2	2	B.1.617.2	0.000008
N	109	Y109Y	taT	taC	2	2	B.1.637	0.000146
N	109	Y109Y	taT	taC	2	2	C.36	0.001821
N	109	Y109Y	taT	taC	2	2	P.1.14	0.000096
N	109	Y109X	taT	taA	1	1		0.055556
N	109	Y109L	tAT	tTA	1	1		0.055556
N	109	Y109Y	taT	taC	1	1	A.2.5	0.000499
N	109	Y109L	tAT	tTA	1	1	All	0
N	109	Y109I	TAT	ATC	1	1	All	0
N	109	Y109S	tAt	tCt	1	1	All	0
N	109	Y109N	Tat	Aat	1	1	All	0
N	109	Y109del1	taT	ta-	1	1	All	0
N	109	Y109del2	TAt	--t	1	1	All	0
N	109	Y109F	tAt	tTt	1	1	AY.100	0.000046
N	109	Y109del1	taT	ta-	1	1	AY.100	0.000046
N	109	Y109del	TAT	---	1	1	AY.103	0.000006
N	109	Y109H	Tat	Cat	1	1	AY.110	0.000113
N	109	Y109Y	taT	taC	1	1	AY.117	0.000085
N	109	Y109C	tAt	tGt	1	1	AY.117	0.000085
N	109	Y109del	TAT	---	1	1	AY.118	0.000063
N	109	Y109Y	taT	taC	1	1	AY.119	0.000035
N	109	Y109Y	taT	taC	1	1	AY.121	0.000135
N	109	Y109Y	taT	taC	1	1	AY.14	0.000088
N	109	Y109H	Tat	Cat	1	1	AY.25	0.000006
N	109	Y109Y	taT	taC	1	1	AY.26	0.000028
N	109	Y109Y	taT	taC	1	1	AY.29	0.000016
N	109	Y109del	TAT	---	1	1	AY.3	0.00001
N	109	Y109H	Tat	Cat	1	1	AY.3	0.00001
N	109	Y109H	Tat	Cat	1	1	AY.33	0.000067
N	109	Y109Y	taT	taC	1	1	AY.37	0.000316
N	109	Y109H	Tat	Cat	1	1	AY.39	0.000025
N	109	Y109D	Tat	Gat	1	1	AY.43	0.000004
N	109	Y109del	TAT	---	1	1	AY.43	0.000004
N	109	Y109F	tAt	tTt	1	1	AY.43	0.000004
N	109	Y109F	tAT	tTC	1	1	AY.44	0.000006
N	109	Y109Y	taT	taC	1	1	AY.5.3	0.000337
N	109	Y109H	Tat	Cat	1	1	AY.5.3	0.000337
N	109	Y109del	TAT	---	1	1	AY.62	0.000436
N	109	Y109del	TAT	---	1	1	AY.67	0.000464
N	109	Y109Y	taT	taC	1	1	AY.72	0.001361
N	109	Y109H	Tat	Cat	1	1	AY.79	0.001211
N	109	Y109F	tAt	tTt	1	1	AY.9.2	0.000037
N	109	Y109Y	taT	taC	1	1	AY.99.1	0.001553
N	109	Y109Y	taT	taC	1	1	AZ.2	0.000821
N	109	Y109H	Tat	Cat	1	1	B	0.000128
N	109	Y109del2	TAt	--t	1	1	B.1	0.000009
N	109	Y109S	tAt	tCt	1	1	B.1	0.000009
N	109	Y109N	Tat	Aat	1	1	B.1	0.000009
N	109	Y109del	TAT	---	1	1	B.1.1	0.000018
N	109	Y109I	TAT	ATC	1	1	B.1.1	0.000018
N	109	Y109del	TAT	---	1	1	B.1.1.216	0.00089
N	109	Y109Y	taT	taC	1	1	B.1.1.234	0.012048
N	109	Y109Y	taT	taC	1	1	B.1.1.25	0.000569
N	109	Y109Y	taT	taC	1	1	B.1.1.306	0.000438
N	109	Y109Y	taT	taC	1	1	B.1.1.33	0.000421
N	109	Y109X	taT	taA	1	1	B.1.1.7	0.000001
N	109	Y109H	Tat	Cat	1	1	B.1.1.7	0.000001
N	109	Y109Y	taT	taC	1	1	B.1.177	0.000013
N	109	Y109Y	taT	taC	1	1	B.1.177.12	0.000152
N	109	Y109F	tAT	tTC	1	1	B.1.177.63	0.002703
N	109	Y109X	taT	taA	1	1	B.1.177.69	0.001484
N	109	Y109Y	taT	taC	1	1	B.1.177.73	0.000566
N	109	Y109H	Tat	Cat	1	1	B.1.2	0.000009
N	109	Y109del	TAT	---	1	1	B.1.2	0.000009
N	109	Y109F	tAt	tTt	1	1	B.1.234	0.000132
N	109	Y109Y	taT	taC	1	1	B.1.240	0.000216
N	109	Y109Y	taT	taC	1	1	B.1.241	0.000812
N	109	Y109Y	taT	taC	1	1	B.1.36	0.000146
N	109	Y109Y	taT	taC	1	1	B.1.369	0.000285
N	109	Y109F	tAt	tTt	1	1	B.1.369	0.000285
N	109	Y109Y	taT	taC	1	1	B.1.399	0.001934
N	109	Y109del	TAT	---	1	1	B.1.415	0.014286
N	109	Y109del	TAT	---	1	1	B.1.427	0.00005
N	109	Y109Y	taT	taC	1	1	B.1.459	0.004082
N	109	Y109Y	taT	taC	1	1	B.1.465	0.003802
N	109	Y109Y	taT	taC	1	1	B.1.567	0.003333
N	109	Y109X	taT	taG	1	1	B.1.617.2	0.000004
N	109	Y109F	tAt	tTt	1	1	B.1.617.2	0.000004
N	109	Y109Y	taT	taC	1	1	B.1.620	0.000946
N	109	Y109Y	taT	taC	1	1	B.1.621	0.000089
N	109	Y109Y	taT	taC	1	1	C.35	0.000774
N	109	Y109Y	taT	taC	1	1	D.2	0.000075
N	109	Y109F	tAt	tTt	1	1	P.1	0.000016
N	109	Y109D	Tat	Gat	1	1	P.1.1	0.000318
N	109	Y109Y	taT	taC	1	1	P.1.15	0.000232
N	109	Y109Y	taT	taC	1	1	P.2	0.000187
N	109	Y109Y	taT	taC	1	1	Q.1	0.000126
N	109	Y109Y	taT	taC	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.