CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1842

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/nsp31842Q1842HQ2660HnonsyncaAcaT4053400.8395068243-8245
ORF1ab/nsp31842Q1842HQ2660HnonsyncaAcaC405650.1604948243-8245
ORF1ab/nsp31842Q1842RQ2660RnonsyncAacGa16416418243-8245
ORF1ab/nsp31842Q1842QQ2660QsyncaAcaG10310318243-8245
ORF1ab/nsp31842Q1842delQ2660deldelCAA---606018243-8245
ORF1ab/nsp31842Q1842XQ2660XnonsynCaaTaa606018243-8245
ORF1ab/nsp31842Q1842KQ2660KnonsynCaaAaa42410.976198243-8245
ORF1ab/nsp31842Q1842KQ2660KnonsynCaAAaG4210.02380958243-8245
ORF1ab/nsp31842Q1842LQ2660LnonsyncAacTa28220.7857148243-8245
ORF1ab/nsp31842Q1842LQ2660LnonsynCAaTTa2830.1071438243-8245
ORF1ab/nsp31842Q1842LQ2660LnonsyncAAcTT2830.1071438243-8245
ORF1ab/nsp31842Q1842del1Q2660del1delCaa-aa540.88243-8245
ORF1ab/nsp31842Q1842del1Q2660del1delcAac-a510.28243-8245
ORF1ab/nsp31842Q1842PQ2660PnonsyncAacCa430.758243-8245
ORF1ab/nsp31842Q1842PQ2660PnonsyncAAcCT410.258243-8245
ORF1ab/nsp31842Q1842SQ2660SnonsynCAaTCa320.6666678243-8245
ORF1ab/nsp31842Q1842IQ2660InonsynCAaATa320.6666678243-8245
ORF1ab/nsp31842Q1842IQ2660InonsynCAAATT310.3333338243-8245
ORF1ab/nsp31842Q1842SQ2660SnonsynCAATCT310.3333338243-8245
ORF1ab/nsp31842Q1842FQ2660FnonsynCAATTT2218243-8245
ORF1ab/nsp31842Q1842YQ2660YnonsynCaATaT2218243-8245
ORF1ab/nsp31842Q1842EQ2660EnonsynCaaGaa2218243-8245
ORF1ab/nsp31842Q1842TQ2660TnonsynCAAACT210.58243-8245
ORF1ab/nsp31842Q1842TQ2660TnonsynCAaACa210.58243-8245
ORF1ab/nsp31842Q1842NQ2660NnonsynCaAAaT1118243-8245

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/nsp31842Q1842HcaAcaT340405All0.000065
ORF1ab/nsp31842Q1842HcaAcaC65405All0.000012
ORF1ab/nsp31842Q1842HcaAcaT328331AY.40.000511
ORF1ab/nsp31842Q1842HcaAcaC3331AY.40.000005
ORF1ab/nsp31842Q1842RcAacGa164164All0.000031
ORF1ab/nsp31842Q1842QcaAcaG103103All0.00002
ORF1ab/nsp31842Q1842RcAacGa7575B.1.1.2180.576923
ORF1ab/nsp31842Q1842XCaaTaa6060All0.000011
ORF1ab/nsp31842Q1842delCAA---6060All0.000011
ORF1ab/nsp31842Q1842KCaaAaa4142All0.000008
ORF1ab/nsp31842Q1842KCaAAaG142All0
ORF1ab/nsp31842Q1842HcaAcaC3030B.1.1.70.000027
ORF1ab/nsp31842Q1842LcAacTa2228All0.000004
ORF1ab/nsp31842Q1842LcAAcTT328All0.000001
ORF1ab/nsp31842Q1842LCAaTTa328All0.000001
ORF1ab/nsp31842Q1842QcaAcaG2424B.1.617.20.00009
ORF1ab/nsp31842Q1842RcAacGa2020B.1.1.70.000018
ORF1ab/nsp31842Q1842delCAA---1919B.1.1.70.000017
ORF1ab/nsp31842Q1842QcaAcaG1616AY.40.000025
ORF1ab/nsp31842Q1842KCaaAaa1313B.1.10.000236
ORF1ab/nsp31842Q1842HcaAcaC1112AY.1030.000068
ORF1ab/nsp31842Q1842HcaAcaT112AY.1030.000006
ORF1ab/nsp31842Q1842XCaaTaa99B.1.1.70.000008
ORF1ab/nsp31842Q1842KCaaAaa99B.1.1.70.000008
ORF1ab/nsp31842Q1842RcAacGa99B.1.617.20.000034
ORF1ab/nsp31842Q1842LcAacTa380.166667
ORF1ab/nsp31842Q1842LCAaTTa380.166667
ORF1ab/nsp31842Q1842LcAAcTT280.111111
ORF1ab/nsp31842Q1842RcAacGa88AY.1030.00005
ORF1ab/nsp31842Q1842QcaAcaG88AY.30.00008
ORF1ab/nsp31842Q1842XCaaTaa88B.10.000073
ORF1ab/nsp31842Q1842QcaAcaG88B.1.1.70.000007
ORF1ab/nsp31842Q1842HcaAcaC88C.360.007286
ORF1ab/nsp31842Q1842XCaaTaa77AY.40.000011
ORF1ab/nsp31842Q1842HcaAcaC47B.1.617.20.000015
ORF1ab/nsp31842Q1842HcaAcaT37B.1.617.20.000011
ORF1ab/nsp31842Q1842RcAacGa66AY.1200.000223
ORF1ab/nsp31842Q1842KCaaAaa66B.10.000055
ORF1ab/nsp31842Q1842XCaaTaa550.277778
ORF1ab/nsp31842Q1842del1Caa-aa45All0.000001
ORF1ab/nsp31842Q1842del1cAac-a15All0
ORF1ab/nsp31842Q1842LcAacTa55AY.40.000008
ORF1ab/nsp31842Q1842RcAacGa55AY.430.000022
ORF1ab/nsp31842Q1842QcaAcaG55B.1.20.000044
ORF1ab/nsp31842Q1842QcaAcaG55B.1.5820.002453
ORF1ab/nsp31842Q1842PcAacCa34All0.000001
ORF1ab/nsp31842Q1842PcAAcCT14All0
ORF1ab/nsp31842Q1842QcaAcaG44AY.1170.000338
ORF1ab/nsp31842Q1842RcAacGa44AY.200.000155
ORF1ab/nsp31842Q1842LcAacTa44AY.430.000018
ORF1ab/nsp31842Q1842RcAacGa44B.10.000037
ORF1ab/nsp31842Q1842delCAA---44B.10.000037
ORF1ab/nsp31842Q1842RcAacGa44B.1.1.4640.005891
ORF1ab/nsp31842Q1842PcAacCa230.111111
ORF1ab/nsp31842Q1842SCAaTCa230.111111
ORF1ab/nsp31842Q1842SCAATCT130.055556
ORF1ab/nsp31842Q1842PcAAcCT130.055556
ORF1ab/nsp31842Q1842ICAaATa23All0
ORF1ab/nsp31842Q1842SCAaTCa23All0
ORF1ab/nsp31842Q1842ICAAATT13All0
ORF1ab/nsp31842Q1842SCAATCT13All0
ORF1ab/nsp31842Q1842delCAA---33AY.40.000005
ORF1ab/nsp31842Q1842delCAA---33AY.4.50.000322
ORF1ab/nsp31842Q1842QcaAcaG33AY.930.000819
ORF1ab/nsp31842Q1842RcAacGa33B.1.10.000054
ORF1ab/nsp31842Q1842XCaaTaa33B.1.1770.00004
ORF1ab/nsp31842Q1842KCaaAaa33B.1.3510.000089
ORF1ab/nsp31842Q1842RcAacGa33B.1.36.290.001552
ORF1ab/nsp31842Q1842QcaAcaG33B.1.5260.000071
ORF1ab/nsp31842Q1842delCAA---33P.10.000047
ORF1ab/nsp31842Q1842YCaATaT220.111111
ORF1ab/nsp31842Q1842HcaAcaT220.111111
ORF1ab/nsp31842Q1842FCAATTT220.111111
ORF1ab/nsp31842Q1842TCAaACa120.055556
ORF1ab/nsp31842Q1842ICAaATa120.055556
ORF1ab/nsp31842Q1842TCAAACT120.055556
ORF1ab/nsp31842Q1842ICAAATT120.055556
ORF1ab/nsp31842Q1842YCaATaT22All0
ORF1ab/nsp31842Q1842FCAATTT22All0
ORF1ab/nsp31842Q1842ECaaGaa22All0
ORF1ab/nsp31842Q1842TCAAACT12All0
ORF1ab/nsp31842Q1842TCAaACa12All0
ORF1ab/nsp31842Q1842LcAacTa22AY.1000.000092
ORF1ab/nsp31842Q1842ECaaGaa22AY.1030.000012
ORF1ab/nsp31842Q1842QcaAcaG22AY.1180.000125
ORF1ab/nsp31842Q1842delCAA---22AY.250.000012
ORF1ab/nsp31842Q1842LcAacTa22AY.250.000012
ORF1ab/nsp31842Q1842RcAacGa22AY.360.000296
ORF1ab/nsp31842Q1842QcaAcaG22AY.39.10.000079
ORF1ab/nsp31842Q1842delCAA---22AY.430.000009
ORF1ab/nsp31842Q1842HcaAcaT12AY.430.000004
ORF1ab/nsp31842Q1842HcaAcaC12AY.430.000004
ORF1ab/nsp31842Q1842delCAA---22B.1.10.000036
ORF1ab/nsp31842Q1842KCaaAaa22B.1.1.1450.074074
ORF1ab/nsp31842Q1842LcAacTa22B.1.1.70.000002
ORF1ab/nsp31842Q1842delCAA---22B.1.177.160.001329
ORF1ab/nsp31842Q1842QcaAcaG22B.1.177.680.030303
ORF1ab/nsp31842Q1842RcAacGa22B.1.177.810.000379
ORF1ab/nsp31842Q1842RcAacGa22B.1.4290.000047
ORF1ab/nsp31842Q1842delCAA---22B.1.5960.000174
ORF1ab/nsp31842Q1842KCaaAaa110.055556
ORF1ab/nsp31842Q1842NCaAAaT110.055556
ORF1ab/nsp31842Q1842QcaAcaG11A0.000387
ORF1ab/nsp31842Q1842QcaAcaG11A.2.5.30.010309
ORF1ab/nsp31842Q1842HcaAcaT11AD.20.000219
ORF1ab/nsp31842Q1842XCaaTaa11AD.20.000219
ORF1ab/nsp31842Q1842NCaAAaT11All0
ORF1ab/nsp31842Q1842XCaaTaa11AP.10.001502
ORF1ab/nsp31842Q1842HcaAcaC11AY.1000.000046
ORF1ab/nsp31842Q1842XCaaTaa11AY.1030.000006
ORF1ab/nsp31842Q1842RcAacGa11AY.1180.000063
ORF1ab/nsp31842Q1842QcaAcaG11AY.1200.000037
ORF1ab/nsp31842Q1842QcaAcaG11AY.190.00114
ORF1ab/nsp31842Q1842delCAA---11AY.190.00114
ORF1ab/nsp31842Q1842QcaAcaG11AY.20.000356
ORF1ab/nsp31842Q1842HcaAcaT11AY.200.000039
ORF1ab/nsp31842Q1842QcaAcaG11AY.200.000039
ORF1ab/nsp31842Q1842QcaAcaG11AY.230.00007
ORF1ab/nsp31842Q1842QcaAcaG11AY.250.000006
ORF1ab/nsp31842Q1842KCaaAaa11AY.250.000006
ORF1ab/nsp31842Q1842XCaaTaa11AY.260.000028
ORF1ab/nsp31842Q1842RcAacGa11AY.30.00001
ORF1ab/nsp31842Q1842RcAacGa11AY.330.000067
ORF1ab/nsp31842Q1842LcAacTa11AY.370.000316
ORF1ab/nsp31842Q1842LcAacTa11AY.390.000025
ORF1ab/nsp31842Q1842QcaAcaG11AY.39.20.001541
ORF1ab/nsp31842Q1842del1Caa-aa11AY.40.000002
ORF1ab/nsp31842Q1842KCaaAaa11AY.40.000002
ORF1ab/nsp31842Q1842HcaAcaT11AY.4.20.000022
ORF1ab/nsp31842Q1842HcaAcaT11AY.420.00004
ORF1ab/nsp31842Q1842XCaaTaa11AY.420.00004
ORF1ab/nsp31842Q1842RcAacGa11AY.420.00004
ORF1ab/nsp31842Q1842XCaaTaa11AY.430.000004
ORF1ab/nsp31842Q1842KCaAAaG11AY.430.000004
ORF1ab/nsp31842Q1842XCaaTaa11AY.440.000006
ORF1ab/nsp31842Q1842LcAacTa11AY.440.000006
ORF1ab/nsp31842Q1842HcaAcaC11AY.440.000006
ORF1ab/nsp31842Q1842del1Caa-aa11AY.440.000006
ORF1ab/nsp31842Q1842QcaAcaG11AY.440.000006
ORF1ab/nsp31842Q1842KCaaAaa11AY.440.000006
ORF1ab/nsp31842Q1842RcAacGa11AY.450.000122
ORF1ab/nsp31842Q1842QcaAcaG11AY.460.000104
ORF1ab/nsp31842Q1842KCaaAaa11AY.460.000104
ORF1ab/nsp31842Q1842delCAA---11AY.46.20.000635
ORF1ab/nsp31842Q1842delCAA---11AY.50.000021
ORF1ab/nsp31842Q1842delCAA---11AY.520.000814
ORF1ab/nsp31842Q1842HcaAcaC11AY.550.000917
ORF1ab/nsp31842Q1842QcaAcaG11AY.550.000917
ORF1ab/nsp31842Q1842delCAA---11AY.60.000041
ORF1ab/nsp31842Q1842XCaaTaa11AY.680.000274
ORF1ab/nsp31842Q1842RcAacGa11AY.7.10.000113
ORF1ab/nsp31842Q1842RcAacGa11AY.710.000475
ORF1ab/nsp31842Q1842XCaaTaa11AY.930.000273
ORF1ab/nsp31842Q1842RcAacGa11AY.98.10.000048
ORF1ab/nsp31842Q1842RcAacGa11AY.990.001049
ORF1ab/nsp31842Q1842QcaAcaG11B0.000128
ORF1ab/nsp31842Q1842XCaaTaa11B0.000128
ORF1ab/nsp31842Q1842QcaAcaG11B.10.000009
ORF1ab/nsp31842Q1842HcaAcaC11B.10.000009
ORF1ab/nsp31842Q1842XCaaTaa11B.1.10.000018
ORF1ab/nsp31842Q1842delCAA---11B.1.1.1590.004673
ORF1ab/nsp31842Q1842delCAA---11B.1.1.3060.000438
ORF1ab/nsp31842Q1842delCAA---11B.1.1.3150.008475
ORF1ab/nsp31842Q1842QcaAcaG11B.1.1.370.000193
ORF1ab/nsp31842Q1842XCaaTaa11B.1.1.3720.000689
ORF1ab/nsp31842Q1842XCaaTaa11B.1.1.4160.000905
ORF1ab/nsp31842Q1842XCaaTaa11B.1.1.4320.001266
ORF1ab/nsp31842Q1842HcaAcaC11B.1.1.4660.008696
ORF1ab/nsp31842Q1842KCaaAaa11B.1.1.470.005348
ORF1ab/nsp31842Q1842QcaAcaG11B.1.1.500.000679
ORF1ab/nsp31842Q1842HcaAcaC11B.1.1.630.000386
ORF1ab/nsp31842Q1842PcAacCa11B.1.1.70.000001
ORF1ab/nsp31842Q1842del1Caa-aa11B.1.1.70.000001
ORF1ab/nsp31842Q1842ICAaATa11B.1.1.70.000001
ORF1ab/nsp31842Q1842RcAacGa11B.1.1.700.000341
ORF1ab/nsp31842Q1842XCaaTaa11B.1.160.160.000929
ORF1ab/nsp31842Q1842delCAA---11B.1.1770.000013
ORF1ab/nsp31842Q1842delCAA---11B.1.177.180.00116
ORF1ab/nsp31842Q1842XCaaTaa11B.1.177.440.000519
ORF1ab/nsp31842Q1842delCAA---11B.1.177.540.000606
ORF1ab/nsp31842Q1842XCaaTaa11B.1.177.810.000189
ORF1ab/nsp31842Q1842KCaaAaa11B.1.20.000009
ORF1ab/nsp31842Q1842XCaaTaa11B.1.20.000009
ORF1ab/nsp31842Q1842XCaaTaa11B.1.2060.000816
ORF1ab/nsp31842Q1842XCaaTaa11B.1.2210.000071
ORF1ab/nsp31842Q1842QcaAcaG11B.1.2340.000132
ORF1ab/nsp31842Q1842HcaAcaC11B.1.2430.00007
ORF1ab/nsp31842Q1842delCAA---11B.1.258.100.011364
ORF1ab/nsp31842Q1842XCaaTaa11B.1.258.140.00098
ORF1ab/nsp31842Q1842RcAacGa11B.1.2600.003344
ORF1ab/nsp31842Q1842del1cAac-a11B.1.2650.001271
ORF1ab/nsp31842Q1842RcAacGa11B.1.360.000146
ORF1ab/nsp31842Q1842delCAA---11B.1.36.220.001208
ORF1ab/nsp31842Q1842HcaAcaC11B.1.4160.001269
ORF1ab/nsp31842Q1842RcAacGa11B.1.4250.002994
ORF1ab/nsp31842Q1842XCaaTaa11B.1.4270.00005
ORF1ab/nsp31842Q1842QcaAcaG11B.1.4270.00005
ORF1ab/nsp31842Q1842QcaAcaG11B.1.4290.000024
ORF1ab/nsp31842Q1842XCaaTaa11B.1.5270.003704
ORF1ab/nsp31842Q1842XCaaTaa11B.1.5820.000491
ORF1ab/nsp31842Q1842QcaAcaG11B.1.5960.000087
ORF1ab/nsp31842Q1842XCaaTaa11B.1.5960.000087
ORF1ab/nsp31842Q1842RcAacGa11B.1.617.10.000129
ORF1ab/nsp31842Q1842XCaaTaa11B.1.617.10.000129
ORF1ab/nsp31842Q1842LcAAcTT11B.1.617.20.000004
ORF1ab/nsp31842Q1842XCaaTaa11B.1.617.20.000004
ORF1ab/nsp31842Q1842delCAA---11B.1.6380.052632
ORF1ab/nsp31842Q1842RcAacGa11B.400.000364
ORF1ab/nsp31842Q1842QcaAcaG11B.400.000364
ORF1ab/nsp31842Q1842LcAacTa11B.6.10.026316
ORF1ab/nsp31842Q1842delCAA---11C.170.055556
ORF1ab/nsp31842Q1842delCAA---11C.370.000116
ORF1ab/nsp31842Q1842RcAacGa11C.37.10.002618
ORF1ab/nsp31842Q1842XCaaTaa11D.20.000075
ORF1ab/nsp31842Q1842del1Caa-aa11D.20.000075
ORF1ab/nsp31842Q1842HcaAcaT11P.10.000016
ORF1ab/nsp31842Q1842RcAacGa11P.1.120.000484
ORF1ab/nsp31842Q1842KCaaAaa11P.1.150.000232
ORF1ab/nsp31842Q1842delCAA---11Q.10.000126
ORF1ab/nsp31842Q1842delCAA---11U.30.003861

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.