CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : Mut = S1699F

Details of the codons used for the mutation across all lineages (CodonProp is the proportion each codon is used for this AA mutation):

ORFCodonNumMutORF1abMutMutTypeRefCodonMutCodonAACountCodonCountCodonPropGenome Position
ORF1ab/nsp31699S1699FS2517FnonsyntCttTt1417141717814-7816

Details of the mutation S1699F within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):

ORFCodonNumMutRefCodonMutCodonCodonCountAACountLineageLineageCodonProp
ORF1ab/nsp31699S1699FtCttTt14171417All0.000271
ORF1ab/nsp31699S1699FtCttTt285285B.1.1.70.000255
ORF1ab/nsp31699S1699FtCttTt246246AY.40.000383
ORF1ab/nsp31699S1699FtCttTt131131B.1.3510.003894
ORF1ab/nsp31699S1699FtCttTt7878AY.360.011561
ORF1ab/nsp31699S1699FtCttTt6565L.10.12381
ORF1ab/nsp31699S1699FtCttTt6363B.1.4181
ORF1ab/nsp31699S1699FtCttTt5959B.1.1.2240.842857
ORF1ab/nsp31699S1699FtCttTt3636B.1.10.000653
ORF1ab/nsp31699S1699FtCttTt3535B.1.617.20.000132
ORF1ab/nsp31699S1699FtCttTt3131AY.500.02478
ORF1ab/nsp31699S1699FtCttTt2626B.10.000238
ORF1ab/nsp31699S1699FtCttTt2121AY.30.000209
ORF1ab/nsp31699S1699FtCttTt1919AY.250.000114
ORF1ab/nsp31699S1699FtCttTt1919B.1.36.10.021665
ORF1ab/nsp31699S1699FtCttTt1717AY.430.000075
ORF1ab/nsp31699S1699FtCttTt1515P.10.000236
ORF1ab/nsp31699S1699FtCttTt1414B.1.20.000123
ORF1ab/nsp31699S1699FtCttTt1212B.30.009967
ORF1ab/nsp31699S1699FtCttTt1111AY.1030.000068
ORF1ab/nsp31699S1699FtCttTt1111B.1.1600.000343
ORF1ab/nsp31699S1699FtCttTt1010B.1.4970.003148
ORF1ab/nsp31699S1699FtCttTt88AY.260.000226
ORF1ab/nsp31699S1699FtCttTt88B.1.1.2840.000859
ORF1ab/nsp31699S1699FtCttTt77AY.200.000272
ORF1ab/nsp31699S1699FtCttTt77B.1.4290.000165
ORF1ab/nsp31699S1699FtCttTt77B.1.617.10.000903
ORF1ab/nsp31699S1699FtCttTt66AY.1200.000223
ORF1ab/nsp31699S1699FtCttTt66AY.4.20.00013
ORF1ab/nsp31699S1699FtCttTt66B.1.360.000875
ORF1ab/nsp31699S1699FtCttTt55B.1.1.5190.000199
ORF1ab/nsp31699S1699FtCttTt55B.1.3750.004098
ORF1ab/nsp31699S1699FtCttTt55B.1.4740.009506
ORF1ab/nsp31699S1699FtCttTt55B.1.6190.004355
ORF1ab/nsp31699S1699FtCttTt55P.1.100.001347
ORF1ab/nsp31699S1699FtCttTt44AY.1020.000106
ORF1ab/nsp31699S1699FtCttTt44B.1.177.860.000734
ORF1ab/nsp31699S1699FtCttTt44B.1.3960.002823
ORF1ab/nsp31699S1699FtCttTt330.166667
ORF1ab/nsp31699S1699FtCttTt33AY.46.60.000217
ORF1ab/nsp31699S1699FtCttTt33AY.50.000062
ORF1ab/nsp31699S1699FtCttTt33B.1.1.1010.03
ORF1ab/nsp31699S1699FtCttTt33B.1.2340.000396
ORF1ab/nsp31699S1699FtCttTt33B.1.5960.000261
ORF1ab/nsp31699S1699FtCttTt33P.20.00056
ORF1ab/nsp31699S1699FtCttTt22AY.116.10.000623
ORF1ab/nsp31699S1699FtCttTt22AY.1170.000169
ORF1ab/nsp31699S1699FtCttTt22AY.380.000999
ORF1ab/nsp31699S1699FtCttTt22AY.470.000062
ORF1ab/nsp31699S1699FtCttTt22AY.590.001059
ORF1ab/nsp31699S1699FtCttTt22B0.000256
ORF1ab/nsp31699S1699FtCttTt22B.1.1.2650.006309
ORF1ab/nsp31699S1699FtCttTt22B.1.1.3060.000877
ORF1ab/nsp31699S1699FtCttTt22B.1.1.3800.019608
ORF1ab/nsp31699S1699FtCttTt22B.1.1770.000026
ORF1ab/nsp31699S1699FtCttTt22B.1.177.180.00232
ORF1ab/nsp31699S1699FtCttTt22B.1.2100.004264
ORF1ab/nsp31699S1699FtCttTt22B.1.2430.000139
ORF1ab/nsp31699S1699FtCttTt22B.1.36.360.001204
ORF1ab/nsp31699S1699FtCttTt22B.1.4700.002809
ORF1ab/nsp31699S1699FtCttTt22B.1.5240.002813
ORF1ab/nsp31699S1699FtCttTt22B.1.5250.000226
ORF1ab/nsp31699S1699FtCttTt22C.10.004785
ORF1ab/nsp31699S1699FtCttTt11AY.1000.000046
ORF1ab/nsp31699S1699FtCttTt11AY.1100.000113
ORF1ab/nsp31699S1699FtCttTt11AY.1130.000142
ORF1ab/nsp31699S1699FtCttTt11AY.1140.000231
ORF1ab/nsp31699S1699FtCttTt11AY.1180.000063
ORF1ab/nsp31699S1699FtCttTt11AY.1190.000035
ORF1ab/nsp31699S1699FtCttTt11AY.130.000161
ORF1ab/nsp31699S1699FtCttTt11AY.140.000088
ORF1ab/nsp31699S1699FtCttTt11AY.230.00007
ORF1ab/nsp31699S1699FtCttTt11AY.390.000025
ORF1ab/nsp31699S1699FtCttTt11AY.39.10.00004
ORF1ab/nsp31699S1699FtCttTt11AY.440.000006
ORF1ab/nsp31699S1699FtCttTt11AY.460.000104
ORF1ab/nsp31699S1699FtCttTt11AY.60.000041
ORF1ab/nsp31699S1699FtCttTt11AY.680.000274
ORF1ab/nsp31699S1699FtCttTt11AY.750.000056
ORF1ab/nsp31699S1699FtCttTt11AY.90.000068
ORF1ab/nsp31699S1699FtCttTt11AY.910.00073
ORF1ab/nsp31699S1699FtCttTt11AY.99.20.000092
ORF1ab/nsp31699S1699FtCttTt11AZ.20.000821
ORF1ab/nsp31699S1699FtCttTt11B.1.1.2160.00089
ORF1ab/nsp31699S1699FtCttTt11B.1.1.2250.007194
ORF1ab/nsp31699S1699FtCttTt11B.1.1.2690.001353
ORF1ab/nsp31699S1699FtCttTt11B.1.1.2750.011236
ORF1ab/nsp31699S1699FtCttTt11B.1.1.2790.001121
ORF1ab/nsp31699S1699FtCttTt11B.1.1.3010.001179
ORF1ab/nsp31699S1699FtCttTt11B.1.1.3120.001912
ORF1ab/nsp31699S1699FtCttTt11B.1.1.3340.016393
ORF1ab/nsp31699S1699FtCttTt11B.1.1.3660.015873
ORF1ab/nsp31699S1699FtCttTt11B.1.1.370.000193
ORF1ab/nsp31699S1699FtCttTt11B.1.1.3970.002252
ORF1ab/nsp31699S1699FtCttTt11B.1.1.4340.000349
ORF1ab/nsp31699S1699FtCttTt11B.1.1.440.00241
ORF1ab/nsp31699S1699FtCttTt11B.1.1420.002899
ORF1ab/nsp31699S1699FtCttTt11B.1.1570.002985
ORF1ab/nsp31699S1699FtCttTt11B.1.177.120.000152
ORF1ab/nsp31699S1699FtCttTt11B.1.177.410.0025
ORF1ab/nsp31699S1699FtCttTt11B.1.177.60.000977
ORF1ab/nsp31699S1699FtCttTt11B.1.177.90.001332
ORF1ab/nsp31699S1699FtCttTt11B.1.2210.000071
ORF1ab/nsp31699S1699FtCttTt11B.1.258.140.00098
ORF1ab/nsp31699S1699FtCttTt11B.1.2650.001271
ORF1ab/nsp31699S1699FtCttTt11B.1.2840.013158
ORF1ab/nsp31699S1699FtCttTt11B.1.3110.000275
ORF1ab/nsp31699S1699FtCttTt11B.1.36.170.000494
ORF1ab/nsp31699S1699FtCttTt11B.1.416.10.001563
ORF1ab/nsp31699S1699FtCttTt11B.1.4590.004082
ORF1ab/nsp31699S1699FtCttTt11B.1.4660.023256
ORF1ab/nsp31699S1699FtCttTt11B.1.5010.007353
ORF1ab/nsp31699S1699FtCttTt11B.1.5260.000024
ORF1ab/nsp31699S1699FtCttTt11B.1.5340.0125
ORF1ab/nsp31699S1699FtCttTt11B.1.5750.000303
ORF1ab/nsp31699S1699FtCttTt11B.1.5950.000261
ORF1ab/nsp31699S1699FtCttTt11B.1.6210.000089
ORF1ab/nsp31699S1699FtCttTt11B.1.6230.000536
ORF1ab/nsp31699S1699FtCttTt11B.1.6370.000073
ORF1ab/nsp31699S1699FtCttTt11D.20.000075
ORF1ab/nsp31699S1699FtCttTt11P.1.150.000232
ORF1ab/nsp31699S1699FtCttTt11P.1.160.000374
ORF1ab/nsp31699S1699FtCttTt11P.70.004367
ORF1ab/nsp31699S1699FtCttTt11Q.30.000145
ORF1ab/nsp31699S1699FtCttTt11Q.40.000455
ORF1ab/nsp31699S1699FtCttTt11Q.80.000165
ORF1ab/nsp31699S1699FtCttTt11W.40.001351

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

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