CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp13 : CodonNum = 252

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/nsp13252L252LL5576LsynttAttG7976080.76286116990-16992
ORF1ab/nsp13252L252LL5576LsynTtaCta7971880.23588516990-16992
ORF1ab/nsp13252L252LL5576LsynTtACtG79710.0012547116990-16992
ORF1ab/nsp13252L252VL5576VnonsynTtaGta2929116990-16992
ORF1ab/nsp13252L252delL5576deldelTTA---2020116990-16992
ORF1ab/nsp13252L252IL5576InonsynTtaAta15140.93333316990-16992
ORF1ab/nsp13252L252IL5576InonsynTtAAtT1510.066666716990-16992
ORF1ab/nsp13252L252SL5576SnonsyntTatCa970.77777816990-16992
ORF1ab/nsp13252L252SL5576SnonsyntTAtCT910.11111116990-16992
ORF1ab/nsp13252L252SL5576SnonsyntTAtCG910.11111116990-16992
ORF1ab/nsp13252L252FL5576FnonsynttAttT420.516990-16992
ORF1ab/nsp13252L252XL5576XnonsyntTatGa420.516990-16992
ORF1ab/nsp13252L252FL5576FnonsynttAttC420.516990-16992
ORF1ab/nsp13252L252XL5576XnonsyntTatAa420.516990-16992
ORF1ab/nsp13252L252TL5576TnonsynTTaACa320.66666716990-16992
ORF1ab/nsp13252L252TL5576TnonsynTTAACG310.33333316990-16992
ORF1ab/nsp13252L252PL5576PnonsynTTaCCa22116990-16992
ORF1ab/nsp13252L252QL5576QnonsynTTACAG22116990-16992
ORF1ab/nsp13252L252RL5576RnonsynTTaAGa210.516990-16992
ORF1ab/nsp13252L252RL5576RnonsynTTAAGG210.516990-16992
ORF1ab/nsp13252L252ML5576MnonsynTtAAtG11116990-16992
ORF1ab/nsp13252L252WL5576WnonsyntTAtGG11116990-16992

Details of the mutation no within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):

ORFCodonNumMutRefCodonMutCodonCodonCountAACountLineageLineageCodonProp
ORF1ab/nsp13252L252LttAttG608797All0.000116
ORF1ab/nsp13252L252LTtaCta188797All0.000036
ORF1ab/nsp13252L252LTtACtG1797All0
ORF1ab/nsp13252L252LttAttG139139AY.260.003935
ORF1ab/nsp13252L252LttAttG8586B.1.2580.005656
ORF1ab/nsp13252L252LTtaCta186B.1.2580.000067
ORF1ab/nsp13252L252LttAttG4073B.1.1.70.000036
ORF1ab/nsp13252L252LTtaCta3373B.1.1.70.00003
ORF1ab/nsp13252L252LttAttG7171B.1.3630.922078
ORF1ab/nsp13252L252LttAttG2344B.1.1600.000717
ORF1ab/nsp13252L252LTtaCta2144B.1.1600.000655
ORF1ab/nsp13252L252LTtaCta4242B.1.1.250.023877
ORF1ab/nsp13252L252LTtaCta2541AY.1030.000155
ORF1ab/nsp13252L252LttAttG1641AY.1030.000099
ORF1ab/nsp13252L252LttAttG2330AY.40.000036
ORF1ab/nsp13252L252LTtaCta730AY.40.000011
ORF1ab/nsp13252L252VTtaGta2929All0.000006
ORF1ab/nsp13252L252LttAttG2225B.10.000202
ORF1ab/nsp13252L252LTtaCta325B.10.000027
ORF1ab/nsp13252L252LttAttG1923AY.250.000114
ORF1ab/nsp13252L252LTtaCta423AY.250.000024
ORF1ab/nsp13252L252LttAttG2122AY.1020.000557
ORF1ab/nsp13252L252LTtaCta122AY.1020.000027
ORF1ab/nsp13252L252delTTA---2020All0.000004
ORF1ab/nsp13252L252LttAttG1719B.1.617.20.000064
ORF1ab/nsp13252L252LTtaCta219B.1.617.20.000008
ORF1ab/nsp13252L252LTtaCta916AY.30.00009
ORF1ab/nsp13252L252LttAttG716AY.30.00007
ORF1ab/nsp13252L252ITtaAta1415All0.000003
ORF1ab/nsp13252L252ITtAAtT115All0
ORF1ab/nsp13252L252LttAttG814B.1.20.00007
ORF1ab/nsp13252L252LTtaCta614B.1.20.000053
ORF1ab/nsp13252L252LttAttG813AY.430.000035
ORF1ab/nsp13252L252LTtaCta413AY.430.000018
ORF1ab/nsp13252L252LTtACtG113AY.430.000004
ORF1ab/nsp13252L252LttAttG1313AY.460.001353
ORF1ab/nsp13252L252LttAttG1313B.1.5260.000306
ORF1ab/nsp13252L252LTtaCta1111AY.330.000735
ORF1ab/nsp13252L252StTatCa79All0.000001
ORF1ab/nsp13252L252StTAtCG19All0
ORF1ab/nsp13252L252StTAtCT19All0
ORF1ab/nsp13252L252ITtaAta99AY.140.000792
ORF1ab/nsp13252L252LttAttG57AY.200.000194
ORF1ab/nsp13252L252LTtaCta27AY.200.000078
ORF1ab/nsp13252L252delTTA---66B.1.1.70.000005
ORF1ab/nsp13252L252VTtaGta66B.1.4270.000303
ORF1ab/nsp13252L252LttAttG45B.1.10.000073
ORF1ab/nsp13252L252LTtaCta15B.1.10.000018
ORF1ab/nsp13252L252delTTA---440.222222
ORF1ab/nsp13252L252StTatCa340.166667
ORF1ab/nsp13252L252StTAtCG140.055556
ORF1ab/nsp13252L252XtTatGa24All0
ORF1ab/nsp13252L252FttAttT24All0
ORF1ab/nsp13252L252XtTatAa24All0
ORF1ab/nsp13252L252FttAttC24All0
ORF1ab/nsp13252L252LTtaCta44AY.1080.00441
ORF1ab/nsp13252L252LttAttG44AY.740.000463
ORF1ab/nsp13252L252LttAttG44B.1.1.3110.001433
ORF1ab/nsp13252L252LttAttG44B.1.5900.018182
ORF1ab/nsp13252L252TTTaACa23All0
ORF1ab/nsp13252L252TTTAACG13All0
ORF1ab/nsp13252L252VTtaGta33AY.1180.000188
ORF1ab/nsp13252L252LttAttG33AY.290.000047
ORF1ab/nsp13252L252VTtaGta33AY.40.000005
ORF1ab/nsp13252L252LttAttG33AY.4.2.10.000447
ORF1ab/nsp13252L252LttAttG33AY.440.000018
ORF1ab/nsp13252L252LttAttG33AY.470.000093
ORF1ab/nsp13252L252LttAttG33B.1.1.3970.006757
ORF1ab/nsp13252L252ITtaAta33B.1.1.70.000003
ORF1ab/nsp13252L252VTtaGta33B.1.1.70.000003
ORF1ab/nsp13252L252VTtaGta33P.10.000047
ORF1ab/nsp13252L252RTTAAGG120.055556
ORF1ab/nsp13252L252TTTAACG120.055556
ORF1ab/nsp13252L252TTTaACa120.055556
ORF1ab/nsp13252L252RTTaAGa120.055556
ORF1ab/nsp13252L252QTTACAG22All0
ORF1ab/nsp13252L252PTTaCCa22All0
ORF1ab/nsp13252L252RTTAAGG12All0
ORF1ab/nsp13252L252RTTaAGa12All0
ORF1ab/nsp13252L252VTtaGta22AY.1170.000169
ORF1ab/nsp13252L252LttAttG22AY.1200.000074
ORF1ab/nsp13252L252LttAttG22AY.300.000791
ORF1ab/nsp13252L252LttAttG22AY.390.000049
ORF1ab/nsp13252L252LTtaCta12AY.420.00004
ORF1ab/nsp13252L252LttAttG12AY.420.00004
ORF1ab/nsp13252L252LttAttG22AY.450.000243
ORF1ab/nsp13252L252LttAttG22AY.540.000191
ORF1ab/nsp13252L252delTTA---22AY.670.000929
ORF1ab/nsp13252L252LttAttG22AY.690.000373
ORF1ab/nsp13252L252LttAttG22AY.98.10.000097
ORF1ab/nsp13252L252LttAttG22B.1.1.2220.000408
ORF1ab/nsp13252L252LttAttG12B.1.1.5190.00004
ORF1ab/nsp13252L252LTtaCta12B.1.1.5190.00004
ORF1ab/nsp13252L252LTtaCta22B.1.177.860.000367
ORF1ab/nsp13252L252VTtaGta22B.1.20.000018
ORF1ab/nsp13252L252LttAttG22R.10.00018
ORF1ab/nsp13252L252XtTatGa110.055556
ORF1ab/nsp13252L252LttAttG110.055556
ORF1ab/nsp13252L252ITtaAta110.055556
ORF1ab/nsp13252L252WtTAtGG110.055556
ORF1ab/nsp13252L252MTtAAtG110.055556
ORF1ab/nsp13252L252WtTAtGG11All0
ORF1ab/nsp13252L252MTtAAtG11All0
ORF1ab/nsp13252L252LTtaCta11AY.1000.000046
ORF1ab/nsp13252L252VTtaGta11AY.1030.000006
ORF1ab/nsp13252L252delTTA---11AY.1080.001103
ORF1ab/nsp13252L252LttAttG11AY.1130.000142
ORF1ab/nsp13252L252LTtaCta11AY.140.000088
ORF1ab/nsp13252L252LttAttG11AY.230.00007
ORF1ab/nsp13252L252ITtaAta11AY.250.000006
ORF1ab/nsp13252L252XtTatGa11AY.250.000006
ORF1ab/nsp13252L252VTtaGta11AY.30.00001
ORF1ab/nsp13252L252LttAttG11AY.3.10.000085
ORF1ab/nsp13252L252LTtaCta11AY.340.000097
ORF1ab/nsp13252L252StTatCa11AY.350.000233
ORF1ab/nsp13252L252LttAttG11AY.360.000148
ORF1ab/nsp13252L252LTtaCta11AY.39.10.00004
ORF1ab/nsp13252L252LttAttG11AY.4.20.000022
ORF1ab/nsp13252L252PTTaCCa11AY.420.00004
ORF1ab/nsp13252L252StTatCa11AY.420.00004
ORF1ab/nsp13252L252TTTaACa11AY.430.000004
ORF1ab/nsp13252L252QTTACAG11AY.440.000006
ORF1ab/nsp13252L252VTtaGta11AY.440.000006
ORF1ab/nsp13252L252delTTA---11AY.440.000006
ORF1ab/nsp13252L252VTtaGta11AY.470.000031
ORF1ab/nsp13252L252LttAttG11AY.50.000021
ORF1ab/nsp13252L252LttAttG11AY.60.000041
ORF1ab/nsp13252L252LttAttG11AY.610.000105
ORF1ab/nsp13252L252LTtaCta11AY.650.000533
ORF1ab/nsp13252L252delTTA---11AY.720.001361
ORF1ab/nsp13252L252StTAtCT11AY.750.000056
ORF1ab/nsp13252L252LttAttG11AY.75.10.00018
ORF1ab/nsp13252L252LTtaCta11AY.910.00073
ORF1ab/nsp13252L252VTtaGta11AY.98.10.000048
ORF1ab/nsp13252L252delTTA---11AY.990.001049
ORF1ab/nsp13252L252XtTatAa11B.10.000009
ORF1ab/nsp13252L252VTtaGta11B.10.000009
ORF1ab/nsp13252L252XtTatAa11B.1.10.000018
ORF1ab/nsp13252L252VTtaGta11B.1.10.000018
ORF1ab/nsp13252L252LttAttG11B.1.1.2160.00089
ORF1ab/nsp13252L252LttAttG11B.1.1.4330.001425
ORF1ab/nsp13252L252LttAttG11B.1.1150.021739
ORF1ab/nsp13252L252LttAttG11B.1.1770.000013
ORF1ab/nsp13252L252StTatCa11B.1.1770.000013
ORF1ab/nsp13252L252FttAttT11B.1.1770.000013
ORF1ab/nsp13252L252LttAttG11B.1.177.770.000726
ORF1ab/nsp13252L252LttAttG11B.1.214.20.0006
ORF1ab/nsp13252L252ITtAAtT11B.1.2420.018868
ORF1ab/nsp13252L252LttAttG11B.1.2430.00007
ORF1ab/nsp13252L252FttAttC11B.1.2580.000067
ORF1ab/nsp13252L252LttAttG11B.1.360.000146
ORF1ab/nsp13252L252delTTA---11B.1.36.180.00042
ORF1ab/nsp13252L252LttAttG11B.1.36.290.000517
ORF1ab/nsp13252L252LttAttG11B.1.3800.006623
ORF1ab/nsp13252L252LTtaCta11B.1.4220.000812
ORF1ab/nsp13252L252delTTA---11B.1.4270.00005
ORF1ab/nsp13252L252LttAttG11B.1.4290.000024
ORF1ab/nsp13252L252FttAttT11B.1.4730.019231
ORF1ab/nsp13252L252LttAttG11B.1.5880.00091
ORF1ab/nsp13252L252LttAttG11B.1.5960.000087
ORF1ab/nsp13252L252delTTA---11B.1.617.20.000004
ORF1ab/nsp13252L252FttAttC11B.1.617.20.000004
ORF1ab/nsp13252L252PTTaCCa11B.1.617.20.000004
ORF1ab/nsp13252L252LttAttG11B.1.6210.000089
ORF1ab/nsp13252L252LttAttG11B.1.6370.000073
ORF1ab/nsp13252L252LTtaCta11B.6.60.000889
ORF1ab/nsp13252L252QTTACAG11C.170.055556
ORF1ab/nsp13252L252StTatCa11C.36.30.000567
ORF1ab/nsp13252L252LttAttG11P.10.000016
ORF1ab/nsp13252L252LttAttG11P.1.150.000232
ORF1ab/nsp13252L252delTTA---11Q.80.000165

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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