CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = N : CodonNum = 162 & Codon = Tct

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	P162S		nonsyn	Cct	Tct	1136	889	0.78257	28757-28759

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	162	P162S	Cct	Tct	889	1136	All	0.00017
N	162	P162S	Cct	Tct	236	238	B.1.1.7	0.000211
N	162	P162S	Cct	Tct	106	215	B.1	0.000971
N	162	P162S	Cct	Tct	62	93	B.1.177	0.000816
N	162	P162S	Cct	Tct	39	61	B.1.1	0.000707
N	162	P162S	Cct	Tct	54	54	AY.4	0.000084
N	162	P162S	Cct	Tct	37	37	AY.44	0.000225
N	162	P162S	Cct	Tct	24	24	B.1.429	0.000565
N	162	P162S	Cct	Tct	23	23	AY.46.6	0.001661
N	162	P162S	Cct	Tct	17	23	B.1.2	0.00015
N	162	P162S	Cct	Tct	20	20	B.1.617.2	0.000075
N	162	P162S	Cct	Tct	10	19	B.1.160	0.000312
N	162	P162S	Cct	Tct	11	19	B.1.177.44	0.005708
N	162	P162S	Cct	Tct	9	18	B.1.258	0.000599
N	162	P162S	Cct	Tct	10	17	B.1.1.39	0.005097
N	162	P162S	Cct	Tct	15	15	AY.103	0.000093
N	162	P162S	Cct	Tct	13	13	AY.39.1	0.000515
N	162	P162S	Cct	Tct	11	11	AY.14	0.000968
N	162	P162S	Cct	Tct	11	11	B.1.575	0.003337
N	162	P162S	Cct	Tct	10	10	AY.3	0.000099
N	162	P162S	Cct	Tct	7	10	B.1.221	0.000497
N	162	P162S	Cct	Tct	9	9	AY.117	0.000761
N	162	P162S	Cct	Tct	5	9	B.1.1.385	0.022321
N	162	P162S	Cct	Tct	8	8	AY.78	0.012327
N	162	P162S	Cct	Tct	8	8	P.1.2	0.009249
N	162	P162S	Cct	Tct	4	7	B.1.258.11	0.001585
N	162	P162S	Cct	Tct	6	6	AY.43	0.000027
N	162	P162S	Cct	Tct	2	5	B.1.1.170	0.002494
N	162	P162S	Cct	Tct	2	5	B.1.1.372	0.001377
N	162	P162S	Cct	Tct	3	5	B.1.177.77	0.002179
N	162	P162S	Cct	Tct	2	5	B.1.609	0.000959
N	162	P162S	Cct	Tct	4	4	AY.26	0.000113
N	162	P162S	Cct	Tct	3	4	B.1.1.277	0.002276
N	162	P162S	Cct	Tct	3	4	C.35	0.002322
N	162	P162S	Cct	Tct	3	4	K.1	0.071429
N	162	P162S	Cct	Tct	3	3	AY.25	0.000018
N	162	P162S	Cct	Tct	3	3	AY.35	0.000699
N	162	P162S	Cct	Tct	3	3	AY.46.4	0.000494
N	162	P162S	Cct	Tct	2	3	B.1.1.189	0.003026
N	162	P162S	Cct	Tct	1	3	B.1.1.301	0.001179
N	162	P162S	Cct	Tct	1	3	B.1.1.515	0.02
N	162	P162S	Cct	Tct	2	3	B.1.177.86	0.000367
N	162	P162S	Cct	Tct	1	3	B.1.293	0.0125
N	162	P162S	Cct	Tct	2	3	B.1.351	0.000059
N	162	P162S	Cct	Tct	1	3	B.1.78	0.008547
N	162	P162S	Cct	Tct	3	3	B.1.9.4	0.018405
N	162	P162S	Cct	Tct	3	3	D.2	0.000225
N	162	P162S	Cct	Tct	2	2	AY.114	0.000462
N	162	P162S	Cct	Tct	2	2	AY.20	0.000078
N	162	P162S	Cct	Tct	2	2	AY.29	0.000032
N	162	P162S	Cct	Tct	2	2	AY.56	0.00321
N	162	P162S	Cct	Tct	2	2	AY.6	0.000082
N	162	P162S	Cct	Tct	2	2	AY.8	0.001212
N	162	P162S	Cct	Tct	1	2	B.1.1.193	0.111111
N	162	P162S	Cct	Tct	2	2	B.1.1.222	0.000408
N	162	P162S	Cct	Tct	2	2	B.1.1.317	0.000823
N	162	P162S	Cct	Tct	2	2	B.1.1.519	0.000079
N	162	P162S	Cct	Tct	1	2	B.1.1.70	0.000341
N	162	P162S	Cct	Tct	2	2	B.1.146	0.008475
N	162	P162S	Cct	Tct	1	2	B.1.177.33	0.001645
N	162	P162S	Cct	Tct	1	2	B.1.177.50	0.004695
N	162	P162S	Cct	Tct	1	2	B.1.177.75	0.001041
N	162	P162S	Cct	Tct	2	2	B.1.177.81	0.000379
N	162	P162S	Cct	Tct	1	2	B.1.284	0.013158
N	162	P162S	Cct	Tct	2	2	B.1.427	0.000101
N	162	P162S	Cct	Tct	1	2	B.1.576	0.000907
N	162	P162S	Cct	Tct	2	2	B.1.582	0.000981
N	162	P162S	Cct	Tct	1	2	C.30	0.001727
N	162	P162S	Cct	Tct	2	2	C.37	0.000232
N	162	P162S	Cct	Tct	2	2	Q.1	0.000253
N	162	P162S	Cct	Tct	1	1		0.055556
N	162	P162S	Cct	Tct	1	1	A.21	0.00277
N	162	P162S	Cct	Tct	1	1	AY.100	0.000046
N	162	P162S	Cct	Tct	1	1	AY.102	0.000027
N	162	P162S	Cct	Tct	1	1	AY.116	0.000287
N	162	P162S	Cct	Tct	1	1	AY.27	0.000065
N	162	P162S	Cct	Tct	1	1	AY.33	0.000067
N	162	P162S	Cct	Tct	1	1	AY.37	0.000316
N	162	P162S	Cct	Tct	1	1	AY.38	0.000499
N	162	P162S	Cct	Tct	1	1	AY.4.2	0.000022
N	162	P162S	Cct	Tct	1	1	AY.45	0.000122
N	162	P162S	Cct	Tct	1	1	AY.46	0.000104
N	162	P162S	Cct	Tct	1	1	AY.48	0.000465
N	162	P162S	Cct	Tct	1	1	AY.5	0.000021
N	162	P162S	Cct	Tct	1	1	AY.7	0.000196
N	162	P162S	Cct	Tct	1	1	AY.85	0.000427
N	162	P162S	Cct	Tct	1	1	AY.9	0.000068
N	162	P162S	Cct	Tct	1	1	AY.90	0.000684
N	162	P162S	Cct	Tct	1	1	B.1.1.129	0.009174
N	162	P162S	Cct	Tct	1	1	B.1.1.157	0.000913
N	162	P162S	Cct	Tct	1	1	B.1.1.200	0.007463
N	162	P162S	Cct	Tct	1	1	B.1.1.318	0.000302
N	162	P162S	Cct	Tct	1	1	B.1.1.33	0.000421
N	162	P162S	Cct	Tct	1	1	B.1.1.413	0.006897
N	162	P162S	Cct	Tct	1	1	B.1.177.35	0.000691
N	162	P162S	Cct	Tct	1	1	B.1.177.83	0.001481
N	162	P162S	Cct	Tct	1	1	B.1.222	0.001692
N	162	P162S	Cct	Tct	1	1	B.1.232	0.000537
N	162	P162S	Cct	Tct	1	1	B.1.349	0.000715
N	162	P162S	Cct	Tct	1	1	B.1.36	0.000146
N	162	P162S	Cct	Tct	1	1	B.1.36.1	0.00114
N	162	P162S	Cct	Tct	1	1	B.1.36.24	0.006173
N	162	P162S	Cct	Tct	1	1	B.1.525	0.000113
N	162	P162S	Cct	Tct	1	1	B.1.526	0.000024
N	162	P162S	Cct	Tct	1	1	B.1.565	0.00081
N	162	P162S	Cct	Tct	1	1	B.1.617.1	0.000129
N	162	P162S	Cct	Tct	1	1	B.1.9.5	0.005682
N	162	P162S	Cct	Tct	1	1	B.3	0.000831
N	162	P162S	Cct	Tct	1	1	P.1.14	0.000048

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.