CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : Mut = P162L

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	162	P162L		nonsyn	cCt	cTt	1013	702	0.692991	28757-28759
N	162	P162L		nonsyn	cCT	cTC	1013	102	0.100691	28757-28759
N	162	P162L		nonsyn	CCT	TTA	1013	85	0.0839092	28757-28759
N	162	P162L		nonsyn	cCT	cTA	1013	84	0.082922	28757-28759
N	162	P162L		nonsyn	cCT	cTG	1013	21	0.0207305	28757-28759
N	162	P162L		nonsyn	CCT	TTG	1013	19	0.0187562	28757-28759

Details of the mutation P162L 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	162	P162L	cCt	cTt	702	1013	All	0.000134
N	162	P162L	cCT	cTC	102	1013	All	0.00002
N	162	P162L	CCT	TTA	85	1013	All	0.000016
N	162	P162L	cCT	cTA	84	1013	All	0.000016
N	162	P162L	cCT	cTG	21	1013	All	0.000004
N	162	P162L	CCT	TTG	19	1013	All	0.000004
N	162	P162L	cCt	cTt	90	235	B.1	0.000824
N	162	P162L	cCT	cTC	51	235	B.1	0.000467
N	162	P162L	cCT	cTA	35	235	B.1	0.000321
N	162	P162L	CCT	TTA	35	235	B.1	0.000321
N	162	P162L	cCT	cTG	12	235	B.1	0.00011
N	162	P162L	CCT	TTG	12	235	B.1	0.00011
N	162	P162L	cCt	cTt	115	116	B.1.1.7	0.000103
N	162	P162L	CCT	TTA	1	116	B.1.1.7	0.000001
N	162	P162L	cCt	cTt	71	71	AY.4	0.000111
N	162	P162L	cCt	cTt	23	62	B.1.177	0.000303
N	162	P162L	cCT	cTC	12	62	B.1.177	0.000158
N	162	P162L	cCT	cTA	12	62	B.1.177	0.000158
N	162	P162L	CCT	TTA	12	62	B.1.177	0.000158
N	162	P162L	cCT	cTG	2	62	B.1.177	0.000026
N	162	P162L	CCT	TTG	1	62	B.1.177	0.000013
N	162	P162L	cCt	cTt	30	58	B.1.1	0.000544
N	162	P162L	cCT	cTC	7	58	B.1.1	0.000127
N	162	P162L	CCT	TTA	7	58	B.1.1	0.000127
N	162	P162L	cCT	cTA	7	58	B.1.1	0.000127
N	162	P162L	cCT	cTG	4	58	B.1.1	0.000073
N	162	P162L	CCT	TTG	3	58	B.1.1	0.000054
N	162	P162L	cCt	cTt	33	33	AY.47	0.001026
N	162	P162L	cCt	cTt	22	33	B.1.258	0.001464
N	162	P162L	cCT	cTC	5	33	B.1.258	0.000333
N	162	P162L	CCT	TTA	3	33	B.1.258	0.0002
N	162	P162L	cCT	cTA	3	33	B.1.258	0.0002
N	162	P162L	cCt	cTt	26	26	AY.25	0.000156
N	162	P162L	cCt	cTt	11	23	B.1.160	0.000343
N	162	P162L	CCT	TTA	3	23	B.1.160	0.000094
N	162	P162L	cCT	cTA	3	23	B.1.160	0.000094
N	162	P162L	cCT	cTC	2	23	B.1.160	0.000062
N	162	P162L	CCT	TTG	2	23	B.1.160	0.000062
N	162	P162L	cCT	cTG	2	23	B.1.160	0.000062
N	162	P162L	cCt	cTt	20	20	B.6.6	0.017778
N	162	P162L	cCt	cTt	19	19	B.1.637	0.001388
N	162	P162L	cCt	cTt	17	17	Q.3	0.002466
N	162	P162L	cCt	cTt	11	16	B.1.221	0.000781
N	162	P162L	cCT	cTA	2	16	B.1.221	0.000142
N	162	P162L	CCT	TTA	2	16	B.1.221	0.000142
N	162	P162L	cCT	cTC	1	16	B.1.221	0.000071
N	162	P162L	cCt	cTt	5	15	B.1.2	0.000044
N	162	P162L	CCT	TTA	4	15	B.1.2	0.000035
N	162	P162L	cCT	cTA	4	15	B.1.2	0.000035
N	162	P162L	cCT	cTC	2	15	B.1.2	0.000018
N	162	P162L	cCt	cTt	12	12	AY.103	0.000075
N	162	P162L	cCt	cTt	12	12	AY.26	0.00034
N	162	P162L	cCt	cTt	12	12	AY.44	0.000073
N	162	P162L	cCt	cTt	11	11	AY.118	0.000689
N	162	P162L	cCt	cTt	6	11	B.1.1.39	0.003058
N	162	P162L	cCT	cTC	3	11	B.1.1.39	0.001529
N	162	P162L	CCT	TTA	1	11	B.1.1.39	0.00051
N	162	P162L	cCT	cTA	1	11	B.1.1.39	0.00051
N	162	P162L	cCt	cTt	5	11	B.1.177.44	0.002595
N	162	P162L	cCT	cTC	4	11	B.1.177.44	0.002076
N	162	P162L	cCT	cTA	1	11	B.1.177.44	0.000519
N	162	P162L	CCT	TTA	1	11	B.1.177.44	0.000519
N	162	P162L	cCt	cTt	4	10	B.1.1.385	0.017857
N	162	P162L	cCT	cTC	2	10	B.1.1.385	0.008929
N	162	P162L	CCT	TTA	2	10	B.1.1.385	0.008929
N	162	P162L	cCT	cTA	2	10	B.1.1.385	0.008929
N	162	P162L	cCt	cTt	10	10	B.1.1.519	0.000397
N	162	P162L	cCt	cTt	10	10	B.1.617.2	0.000038
N	162	P162L	cCt	cTt	8	8	AY.39	0.000198
N	162	P162L	cCt	cTt	4	8	B.1.258.11	0.001585
N	162	P162L	cCT	cTC	2	8	B.1.258.11	0.000793
N	162	P162L	cCT	cTA	1	8	B.1.258.11	0.000396
N	162	P162L	CCT	TTA	1	8	B.1.258.11	0.000396
N	162	P162L	cCt	cTt	7	7	AY.43	0.000031
N	162	P162L	CCT	TTA	2	7	B.1.1.170	0.002494
N	162	P162L	cCt	cTt	2	7	B.1.1.170	0.002494
N	162	P162L	cCT	cTA	2	7	B.1.1.170	0.002494
N	162	P162L	cCT	cTC	1	7	B.1.1.170	0.001247
N	162	P162L	cCt	cTt	2	7	B.1.1.372	0.001377
N	162	P162L	CCT	TTA	2	7	B.1.1.372	0.001377
N	162	P162L	cCT	cTA	2	7	B.1.1.372	0.001377
N	162	P162L	cCT	cTC	1	7	B.1.1.372	0.000689
N	162	P162L	cCt	cTt	6	6	AY.5	0.000124
N	162	P162L	cCt	cTt	2	6	B.1.609	0.000959
N	162	P162L	cCT	cTG	1	6	B.1.609	0.000479
N	162	P162L	CCT	TTA	1	6	B.1.609	0.000479
N	162	P162L	cCT	cTA	1	6	B.1.609	0.000479
N	162	P162L	CCT	TTG	1	6	B.1.609	0.000479
N	162	P162L	cCt	cTt	5	5	AY.119	0.000177
N	162	P162L	cCt	cTt	5	5	AY.39.1	0.000198
N	162	P162L	cCt	cTt	5	5	AY.6	0.000206
N	162	P162L	cCt	cTt	5	5	B.1.617.1	0.000645
N	162	P162L	cCt	cTt	4	4	AY.3	0.00004
N	162	P162L	cCt	cTt	4	4	AY.50	0.003197
N	162	P162L	cCt	cTt	2	4	B.1.1.277	0.001517
N	162	P162L	CCT	TTA	1	4	B.1.1.277	0.000759
N	162	P162L	cCT	cTA	1	4	B.1.1.277	0.000759
N	162	P162L	cCt	cTt	1	4	B.1.1.301	0.001179
N	162	P162L	cCT	cTC	1	4	B.1.1.301	0.001179
N	162	P162L	cCT	cTA	1	4	B.1.1.301	0.001179
N	162	P162L	CCT	TTA	1	4	B.1.1.301	0.001179
N	162	P162L	CCT	TTA	1	4	B.1.1.515	0.02
N	162	P162L	cCT	cTA	1	4	B.1.1.515	0.02
N	162	P162L	cCT	cTC	1	4	B.1.1.515	0.02
N	162	P162L	cCt	cTt	1	4	B.1.1.515	0.02
N	162	P162L	cCt	cTt	1	4	B.1.293	0.0125
N	162	P162L	cCT	cTA	1	4	B.1.293	0.0125
N	162	P162L	CCT	TTA	1	4	B.1.293	0.0125
N	162	P162L	cCT	cTC	1	4	B.1.293	0.0125
N	162	P162L	cCt	cTt	4	4	B.1.404	0.005208
N	162	P162L	cCT	cTC	1	4	B.1.78	0.008547
N	162	P162L	cCT	cTA	1	4	B.1.78	0.008547
N	162	P162L	CCT	TTA	1	4	B.1.78	0.008547
N	162	P162L	cCt	cTt	1	4	B.1.78	0.008547
N	162	P162L	cCt	cTt	3	3	AY.4.2	0.000065
N	162	P162L	cCT	cTA	1	3	B.1.1.193	0.111111
N	162	P162L	cCt	cTt	1	3	B.1.1.193	0.111111
N	162	P162L	CCT	TTA	1	3	B.1.1.193	0.111111
N	162	P162L	CCT	TTA	1	3	B.1.177.33	0.001645
N	162	P162L	cCT	cTA	1	3	B.1.177.33	0.001645
N	162	P162L	cCt	cTt	1	3	B.1.177.33	0.001645
N	162	P162L	cCt	cTt	2	3	B.1.177.77	0.001452
N	162	P162L	cCT	cTC	1	3	B.1.177.77	0.000726
N	162	P162L	cCt	cTt	1	3	B.1.284	0.013158
N	162	P162L	CCT	TTA	1	3	B.1.284	0.013158
N	162	P162L	cCT	cTA	1	3	B.1.284	0.013158
N	162	P162L	cCt	cTt	2	3	C.35	0.001548
N	162	P162L	cCT	cTC	1	3	C.35	0.000774
N	162	P162L	cCt	cTt	2	2	A	0.000774
N	162	P162L	cCt	cTt	2	2	AY.102	0.000053
N	162	P162L	cCt	cTt	2	2	AY.120	0.000074
N	162	P162L	cCt	cTt	2	2	AY.20	0.000078
N	162	P162L	cCt	cTt	2	2	AY.27	0.000129
N	162	P162L	cCt	cTt	2	2	AY.4.4	0.000818
N	162	P162L	cCt	cTt	2	2	AY.63	0.000774
N	162	P162L	cCT	cTC	1	2	B.1.1.70	0.000341
N	162	P162L	cCt	cTt	1	2	B.1.1.70	0.000341
N	162	P162L	cCT	cTC	1	2	B.1.177.75	0.001041
N	162	P162L	cCt	cTt	1	2	B.1.177.75	0.001041
N	162	P162L	cCt	cTt	1	2	B.1.177.86	0.000183
N	162	P162L	cCT	cTC	1	2	B.1.177.86	0.000183
N	162	P162L	cCt	cTt	2	2	B.1.526	0.000047
N	162	P162L	cCt	cTt	2	2	B.1.621	0.000177
N	162	P162L	cCt	cTt	2	2	Q.8	0.00033
N	162	P162L	cCt	cTt	1	1	AY.16.1	0.00047
N	162	P162L	cCt	cTt	1	1	AY.45	0.000122
N	162	P162L	cCt	cTt	1	1	AY.9	0.000068
N	162	P162L	cCt	cTt	1	1	AY.91	0.00073
N	162	P162L	cCt	cTt	1	1	AY.98.1	0.000048
N	162	P162L	cCt	cTt	1	1	B.1.1.297	0.002237
N	162	P162L	cCt	cTt	1	1	B.1.1.312	0.001912
N	162	P162L	cCt	cTt	1	1	B.1.1.317	0.000412
N	162	P162L	cCt	cTt	1	1	B.1.1.374	0.002375
N	162	P162L	cCt	cTt	1	1	B.1.127	0.002198
N	162	P162L	cCt	cTt	1	1	B.1.146	0.004237
N	162	P162L	cCt	cTt	1	1	B.1.177.35	0.000691
N	162	P162L	cCt	cTt	1	1	B.1.177.81	0.000189
N	162	P162L	cCt	cTt	1	1	B.1.234	0.000132
N	162	P162L	cCt	cTt	1	1	B.1.243	0.00007
N	162	P162L	cCt	cTt	1	1	B.1.36	0.000146
N	162	P162L	cCt	cTt	1	1	B.1.36.24	0.006173
N	162	P162L	cCt	cTt	1	1	B.1.36.38	0.001642
N	162	P162L	cCt	cTt	1	1	B.1.425	0.002994
N	162	P162L	cCt	cTt	1	1	B.1.427	0.00005
N	162	P162L	cCt	cTt	1	1	B.1.567	0.003333
N	162	P162L	cCt	cTt	1	1	B.1.9.4	0.006135
N	162	P162L	cCt	cTt	1	1	C.37	0.000116
N	162	P162L	cCt	cTt	1	1	K.1	0.02381
N	162	P162L	cCt	cTt	1	1	P.1.16	0.000374

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.