CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp8 : Mut = S4S

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/nsp84S4SS3946SsyntcAtcG10559540.90426512101-12103
ORF1ab/nsp84S4SS3946SsyntcAtcT1055860.081516612101-12103
ORF1ab/nsp84S4SS3946SsyntcAtcC1055140.013270112101-12103
ORF1ab/nsp84S4SS3946SsynTCAAGC105510.00094786712101-12103

Details of the mutation S4S within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):

ORFCodonNumMutRefCodonMutCodonCodonCountAACountLineageLineageCodonProp
ORF1ab/nsp84S4StcAtcG9541055All0.000182
ORF1ab/nsp84S4StcAtcT861055All0.000016
ORF1ab/nsp84S4StcAtcC141055All0.000003
ORF1ab/nsp84S4STCAAGC11055All0
ORF1ab/nsp84S4StcAtcG584584AP.10.876877
ORF1ab/nsp84S4StcAtcG7186B.1.1.70.000064
ORF1ab/nsp84S4StcAtcT1486B.1.1.70.000013
ORF1ab/nsp84S4StcAtcC186B.1.1.70.000001
ORF1ab/nsp84S4StcAtcG6771AY.40.000104
ORF1ab/nsp84S4StcAtcT371AY.40.000005
ORF1ab/nsp84S4StcAtcC171AY.40.000002
ORF1ab/nsp84S4StcAtcT3150B.1.617.20.000117
ORF1ab/nsp84S4StcAtcG1950B.1.617.20.000072
ORF1ab/nsp84S4StcAtcG2424B.10.00022
ORF1ab/nsp84S4StcAtcG2022B.1.10.000363
ORF1ab/nsp84S4StcAtcT222B.1.10.000036
ORF1ab/nsp84S4StcAtcG2020B.1.177.730.011325
ORF1ab/nsp84S4StcAtcT1218AY.430.000053
ORF1ab/nsp84S4StcAtcG518AY.430.000022
ORF1ab/nsp84S4StcAtcC118AY.430.000004
ORF1ab/nsp84S4StcAtcG1616B.1.5260.000376
ORF1ab/nsp84S4StcAtcG1315AY.1030.000081
ORF1ab/nsp84S4StcAtcT215AY.1030.000012
ORF1ab/nsp84S4StcAtcG1414AY.1100.001578
ORF1ab/nsp84S4StcAtcG99AY.980.000711
ORF1ab/nsp84S4StcAtcG68AY.30.00006
ORF1ab/nsp84S4StcAtcT28AY.30.00002
ORF1ab/nsp84S4StcAtcT37AY.440.000018
ORF1ab/nsp84S4StcAtcG37AY.440.000018
ORF1ab/nsp84S4StcAtcC17AY.440.000006
ORF1ab/nsp84S4StcAtcG66AY.23.10.002504
ORF1ab/nsp84S4StcAtcG56AY.4.20.000108
ORF1ab/nsp84S4StcAtcT16AY.4.20.000022
ORF1ab/nsp84S4StcAtcG66B.1.1.3170.00247
ORF1ab/nsp84S4StcAtcG56B.1.1600.000156
ORF1ab/nsp84S4StcAtcT16B.1.1600.000031
ORF1ab/nsp84S4StcAtcG66B.1.4290.000141
ORF1ab/nsp84S4StcAtcG55AY.250.00003
ORF1ab/nsp84S4StcAtcT35B.1.20.000026
ORF1ab/nsp84S4StcAtcG25B.1.20.000018
ORF1ab/nsp84S4StcAtcG45P.10.000063
ORF1ab/nsp84S4StcAtcC15P.10.000016
ORF1ab/nsp84S4StcAtcC340.166667
ORF1ab/nsp84S4STCAAGC140.055556
ORF1ab/nsp84S4StcAtcT34AY.1190.000106
ORF1ab/nsp84S4StcAtcG14AY.1190.000035
ORF1ab/nsp84S4StcAtcG23AY.450.000243
ORF1ab/nsp84S4StcAtcC13AY.450.000122
ORF1ab/nsp84S4StcAtcT23AY.50.000041
ORF1ab/nsp84S4StcAtcG13AY.50.000021
ORF1ab/nsp84S4StcAtcT22AY.1020.000053
ORF1ab/nsp84S4StcAtcG12AY.3.10.000085
ORF1ab/nsp84S4StcAtcC12AY.3.10.000085
ORF1ab/nsp84S4StcAtcG22AY.420.00008
ORF1ab/nsp84S4StcAtcG22B0.000256
ORF1ab/nsp84S4StcAtcG22B.1.1.10.000653
ORF1ab/nsp84S4StcAtcG22B.1.1770.000026
ORF1ab/nsp84S4StcAtcG22B.1.177.170.001642
ORF1ab/nsp84S4StcAtcG22B.1.6210.000177
ORF1ab/nsp84S4StcAtcG22C.370.000232
ORF1ab/nsp84S4StcAtcG12P.1.140.000048
ORF1ab/nsp84S4StcAtcT12P.1.140.000048
ORF1ab/nsp84S4StcAtcC11A0.000387
ORF1ab/nsp84S4StcAtcT11AY.1170.000085
ORF1ab/nsp84S4StcAtcG11AY.1200.000037
ORF1ab/nsp84S4StcAtcG11AY.1210.000135
ORF1ab/nsp84S4StcAtcG11AY.140.000088
ORF1ab/nsp84S4StcAtcG11AY.160.00038
ORF1ab/nsp84S4StcAtcG11AY.300.000396
ORF1ab/nsp84S4StcAtcG11AY.320.000532
ORF1ab/nsp84S4StcAtcT11AY.340.000097
ORF1ab/nsp84S4StcAtcG11AY.360.000148
ORF1ab/nsp84S4StcAtcG11AY.390.000025
ORF1ab/nsp84S4StcAtcG11AY.4.50.000107
ORF1ab/nsp84S4StcAtcT11AY.460.000104
ORF1ab/nsp84S4StcAtcG11AY.470.000031
ORF1ab/nsp84S4StcAtcG11AY.60.000041
ORF1ab/nsp84S4StcAtcG11AY.710.000475
ORF1ab/nsp84S4StcAtcG11AY.9.20.000037
ORF1ab/nsp84S4StcAtcT11AY.98.10.000048
ORF1ab/nsp84S4StcAtcG11AY.99.20.000092
ORF1ab/nsp84S4StcAtcG11B.1.1.2370.005405
ORF1ab/nsp84S4StcAtcC11B.1.1.2420.043478
ORF1ab/nsp84S4StcAtcG11B.1.1.280.000311
ORF1ab/nsp84S4StcAtcC11B.1.1.390.00051
ORF1ab/nsp84S4StcAtcG11B.1.1.5280.004808
ORF1ab/nsp84S4StcAtcG11B.1.177.560.000668
ORF1ab/nsp84S4StcAtcG11B.1.2210.000071
ORF1ab/nsp84S4StcAtcG11B.1.2320.000537
ORF1ab/nsp84S4StcAtcG11B.1.2580.000067
ORF1ab/nsp84S4StcAtcC11B.1.466.20.000391
ORF1ab/nsp84S4StcAtcG11B.1.5250.000113
ORF1ab/nsp84S4StcAtcG11B.1.5760.000907
ORF1ab/nsp84S4StcAtcG11B.1.6370.000073

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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