CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp13 : CodonNum = 88

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/nsp1388Q88HQ5412HnonsyncaAcaC42717426520.99847816498-16500
ORF1ab/nsp1388Q88HQ5412HnonsyncaAcaT42717650.0015216416498-16500
ORF1ab/nsp1388Q88delQ5412deldelCAA---448448116498-16500
ORF1ab/nsp1388Q88QQ5412QsyncaAcaG145145116498-16500
ORF1ab/nsp1388Q88XQ5412XnonsynCaaTaa4545116498-16500
ORF1ab/nsp1388Q88LQ5412LnonsyncAacTa32290.9062516498-16500
ORF1ab/nsp1388Q88LQ5412LnonsynCAaTTa3220.062516498-16500
ORF1ab/nsp1388Q88LQ5412LnonsyncAAcTT3210.0312516498-16500
ORF1ab/nsp1388Q88RQ5412RnonsyncAacGa2828116498-16500
ORF1ab/nsp1388Q88YQ5412YnonsynCaATaC16150.937516498-16500
ORF1ab/nsp1388Q88YQ5412YnonsynCaATaT1610.062516498-16500
ORF1ab/nsp1388Q88KQ5412KnonsynCaaAaa1313116498-16500
ORF1ab/nsp1388Q88del1Q5412del1delCAA-NN760.85714316498-16500
ORF1ab/nsp1388Q88del1Q5412del1delcAAc-T710.14285716498-16500
ORF1ab/nsp1388Q88del2Q5412del2delCAA--N66116498-16500
ORF1ab/nsp1388Q88PQ5412PnonsyncAacCa44116498-16500
ORF1ab/nsp1388Q88EQ5412EnonsynCaaGaa22116498-16500
ORF1ab/nsp1388Q88FQ5412FnonsynCAATTT22116498-16500
ORF1ab/nsp1388Q88SQ5412SnonsynCAaTCa11116498-16500

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/nsp1388Q88HcaAcaC4265242717All0.008158
ORF1ab/nsp1388Q88HcaAcaT6542717All0.000012
ORF1ab/nsp1388Q88HcaAcaC4184641897B.1.5260.98357
ORF1ab/nsp1388Q88HcaAcaT5141897B.1.5260.001199
ORF1ab/nsp1388Q88delCAA---448448All0.000086
ORF1ab/nsp1388Q88HcaAcaC308311B.1.1.70.000276
ORF1ab/nsp1388Q88HcaAcaT3311B.1.1.70.000003
ORF1ab/nsp1388Q88delCAA---297297B.1.1.70.000266
ORF1ab/nsp1388Q88HcaAcaC288290B.10.002638
ORF1ab/nsp1388Q88HcaAcaT2290B.10.000018
ORF1ab/nsp1388Q88QcaAcaG145145All0.000028
ORF1ab/nsp1388Q88XCaaTaa4545All0.000009
ORF1ab/nsp1388Q88HcaAcaC3940B.1.10.000707
ORF1ab/nsp1388Q88HcaAcaT140B.1.10.000018
ORF1ab/nsp1388Q88delCAA---3737B.1.1770.000487
ORF1ab/nsp1388Q88LcAacTa2932All0.000006
ORF1ab/nsp1388Q88LCAaTTa232All0
ORF1ab/nsp1388Q88LcAAcTT132All0
ORF1ab/nsp1388Q88delCAA---3131AZ.20.025452
ORF1ab/nsp1388Q88RcAacGa2828All0.000005
ORF1ab/nsp1388Q88HcaAcaC2828B.1.6230.015021
ORF1ab/nsp1388Q88HcaAcaC2424AY.200.000933
ORF1ab/nsp1388Q88HcaAcaC2424B.1.177.730.01359
ORF1ab/nsp1388Q88QcaAcaG2222B.1.1.70.00002
ORF1ab/nsp1388Q88HcaAcaC1919B.1.20.000167
ORF1ab/nsp1388Q88YCaATaC1516All0.000003
ORF1ab/nsp1388Q88YCaATaT116All0
ORF1ab/nsp1388Q88QcaAcaG1616B.1.1.4160.01448
ORF1ab/nsp1388Q88QcaAcaG1515B.10.000137
ORF1ab/nsp1388Q88YCaATaC1515B.1.5260.000353
ORF1ab/nsp1388Q88delCAA---1414B.1.10.000254
ORF1ab/nsp1388Q88KCaaAaa1313All0.000002
ORF1ab/nsp1388Q88XCaaTaa1111B.1.1.70.00001
ORF1ab/nsp1388Q88QcaAcaG1010AY.290.000158
ORF1ab/nsp1388Q88QcaAcaG1010B.1.258.170.00104
ORF1ab/nsp1388Q88QcaAcaG1010B.1.617.20.000038
ORF1ab/nsp1388Q88QcaAcaG99AY.440.000055
ORF1ab/nsp1388Q88QcaAcaG99AY.860.007469
ORF1ab/nsp1388Q88HcaAcaC99B.1.1.3120.017208
ORF1ab/nsp1388Q88delCAA---77AD.20.001533
ORF1ab/nsp1388Q88del1CAA-NN67All0.000001
ORF1ab/nsp1388Q88del1cAAc-T17All0
ORF1ab/nsp1388Q88LcAacTa77AY.440.000043
ORF1ab/nsp1388Q88delCAA---77B.1.1.440.016867
ORF1ab/nsp1388Q88QcaAcaG77B.1.177.520.012302
ORF1ab/nsp1388Q88del2CAA--N66All0.000001
ORF1ab/nsp1388Q88RcAacGa66AY.40.000009
ORF1ab/nsp1388Q88HcaAcaC66B.1.6250.014118
ORF1ab/nsp1388Q88XCaaTaa66D.20.00045
ORF1ab/nsp1388Q88LcAacTa55AY.200.000194
ORF1ab/nsp1388Q88RcAacGa55AY.430.000022
ORF1ab/nsp1388Q88XCaaTaa55B.1.10.000091
ORF1ab/nsp1388Q88KCaaAaa55B.1.1.70.000004
ORF1ab/nsp1388Q88del1CAA-NN55B.1.1.70.000004
ORF1ab/nsp1388Q88HcaAcaC55P.10.000079
ORF1ab/nsp1388Q88PcAacCa44All0.000001
ORF1ab/nsp1388Q88delCAA---44AY.430.000018
ORF1ab/nsp1388Q88delCAA---44B.10.000037
ORF1ab/nsp1388Q88HcaAcaC44B.1.1.2200.007435
ORF1ab/nsp1388Q88del2CAA--N44B.1.1.70.000004
ORF1ab/nsp1388Q88HcaAcaC44B.1.5750.001214
ORF1ab/nsp1388Q88RcAacGa33AY.250.000018
ORF1ab/nsp1388Q88LcAAcTT13AY.250.000006
ORF1ab/nsp1388Q88LCAaTTa13AY.250.000006
ORF1ab/nsp1388Q88LcAacTa13AY.250.000006
ORF1ab/nsp1388Q88LcAacTa33AY.30.00003
ORF1ab/nsp1388Q88XCaaTaa33B.10.000027
ORF1ab/nsp1388Q88delCAA---33B.1.1.3050.011583
ORF1ab/nsp1388Q88delCAA---33B.1.1.3150.025424
ORF1ab/nsp1388Q88HcaAcaC33B.1.1.5070.026087
ORF1ab/nsp1388Q88LcAacTa33B.1.1.70.000003
ORF1ab/nsp1388Q88QcaAcaG33B.1.466.20.001174
ORF1ab/nsp1388Q88HcaAcaC33B.1.5670.01
ORF1ab/nsp1388Q88HcaAcaC33B.1.5960.000261
ORF1ab/nsp1388Q88delCAA---33Q.10.000379
ORF1ab/nsp1388Q88delCAA---220.111111
ORF1ab/nsp1388Q88QcaAcaG220.111111
ORF1ab/nsp1388Q88FCAATTT22All0
ORF1ab/nsp1388Q88ECaaGaa22All0
ORF1ab/nsp1388Q88QcaAcaG22AY.1000.000092
ORF1ab/nsp1388Q88QcaAcaG22AY.1030.000012
ORF1ab/nsp1388Q88QcaAcaG22AY.1130.000285
ORF1ab/nsp1388Q88HcaAcaT22AY.250.000012
ORF1ab/nsp1388Q88LCAaTTa12AY.260.000028
ORF1ab/nsp1388Q88LcAacTa12AY.260.000028
ORF1ab/nsp1388Q88QcaAcaG22AY.30.00002
ORF1ab/nsp1388Q88QcaAcaG22AY.40.000003
ORF1ab/nsp1388Q88HcaAcaC22AY.40.000003
ORF1ab/nsp1388Q88delCAA---22AY.440.000012
ORF1ab/nsp1388Q88delCAA---22AY.90.000135
ORF1ab/nsp1388Q88HcaAcaC22B0.000256
ORF1ab/nsp1388Q88RcAacGa22B.10.000018
ORF1ab/nsp1388Q88HcaAcaT22B.1.1.2220.000408
ORF1ab/nsp1388Q88delCAA---22B.1.1.700.000682
ORF1ab/nsp1388Q88XCaaTaa22B.1.1770.000026
ORF1ab/nsp1388Q88QcaAcaG22B.1.177.530.004785
ORF1ab/nsp1388Q88HcaAcaC22B.1.177.70.00033
ORF1ab/nsp1388Q88XCaaTaa22B.1.20.000018
ORF1ab/nsp1388Q88QcaAcaG22B.1.20.000018
ORF1ab/nsp1388Q88LcAacTa22B.1.20.000018
ORF1ab/nsp1388Q88LcAacTa22B.1.2210.000142
ORF1ab/nsp1388Q88HcaAcaC22B.1.2430.000139
ORF1ab/nsp1388Q88delCAA---22B.1.2580.000133
ORF1ab/nsp1388Q88HcaAcaC22B.1.4270.000101
ORF1ab/nsp1388Q88HcaAcaC22B.1.4290.000047
ORF1ab/nsp1388Q88HcaAcaC22B.1.5610.000794
ORF1ab/nsp1388Q88HcaAcaC22B.1.5800.00813
ORF1ab/nsp1388Q88RcAacGa22B.1.617.20.000008
ORF1ab/nsp1388Q88delCAA---22B.1.617.20.000008
ORF1ab/nsp1388Q88LcAacTa22B.1.617.20.000008
ORF1ab/nsp1388Q88HcaAcaC12B.1.617.20.000004
ORF1ab/nsp1388Q88HcaAcaT12B.1.617.20.000004
ORF1ab/nsp1388Q88QcaAcaG22C.36.30.001134
ORF1ab/nsp1388Q88HcaAcaC22P.1.120.000968
ORF1ab/nsp1388Q88QcaAcaG22P.1.70.000639
ORF1ab/nsp1388Q88QcaAcaG11A0.000387
ORF1ab/nsp1388Q88XCaaTaa11A.2.20.001689
ORF1ab/nsp1388Q88LcAacTa11A.2.40.003367
ORF1ab/nsp1388Q88PcAacCa11A.2.40.003367
ORF1ab/nsp1388Q88SCAaTCa11All0
ORF1ab/nsp1388Q88delCAA---11AT.10.005128
ORF1ab/nsp1388Q88HcaAcaC11AT.10.005128
ORF1ab/nsp1388Q88QcaAcaG11AU.30.00211
ORF1ab/nsp1388Q88delCAA---11AY.1020.000027
ORF1ab/nsp1388Q88HcaAcaC11AY.1020.000027
ORF1ab/nsp1388Q88delCAA---11AY.1110.000183
ORF1ab/nsp1388Q88FCAATTT11AY.120.10.000321
ORF1ab/nsp1388Q88RcAacGa11AY.200.000039
ORF1ab/nsp1388Q88RcAacGa11AY.220.002092
ORF1ab/nsp1388Q88QcaAcaG11AY.230.00007
ORF1ab/nsp1388Q88KCaaAaa11AY.23.10.000417
ORF1ab/nsp1388Q88FCAATTT11AY.250.000006
ORF1ab/nsp1388Q88del1cAAc-T11AY.250.000006
ORF1ab/nsp1388Q88YCaATaT11AY.250.000006
ORF1ab/nsp1388Q88XCaaTaa11AY.250.000006
ORF1ab/nsp1388Q88XCaaTaa11AY.260.000028
ORF1ab/nsp1388Q88RcAacGa11AY.270.000065
ORF1ab/nsp1388Q88KCaaAaa11AY.270.000065
ORF1ab/nsp1388Q88RcAacGa11AY.290.000016
ORF1ab/nsp1388Q88LcAacTa11AY.290.000016
ORF1ab/nsp1388Q88XCaaTaa11AY.30.00001
ORF1ab/nsp1388Q88RcAacGa11AY.390.000025
ORF1ab/nsp1388Q88delCAA---11AY.40.000002
ORF1ab/nsp1388Q88QcaAcaG11AY.420.00004
ORF1ab/nsp1388Q88QcaAcaG11AY.430.000004
ORF1ab/nsp1388Q88HcaAcaC11AY.430.000004
ORF1ab/nsp1388Q88KCaaAaa11AY.430.000004
ORF1ab/nsp1388Q88RcAacGa11AY.440.000006
ORF1ab/nsp1388Q88HcaAcaT11AY.440.000006
ORF1ab/nsp1388Q88delCAA---11AY.460.000104
ORF1ab/nsp1388Q88ECaaGaa11AY.50.000021
ORF1ab/nsp1388Q88QcaAcaG11AY.60.000041
ORF1ab/nsp1388Q88delCAA---11AY.75.10.00018
ORF1ab/nsp1388Q88del2CAA--N11AY.90.000068
ORF1ab/nsp1388Q88del1CAA-NN11AY.90.000068
ORF1ab/nsp1388Q88KCaaAaa11B0.000128
ORF1ab/nsp1388Q88SCAaTCa11B.1.10.000018
ORF1ab/nsp1388Q88PcAacCa11B.1.10.000018
ORF1ab/nsp1388Q88XCaaTaa11B.1.1.1680.026316
ORF1ab/nsp1388Q88delCAA---11B.1.1.1970.037037
ORF1ab/nsp1388Q88delCAA---11B.1.1.2310.003096
ORF1ab/nsp1388Q88QcaAcaG11B.1.1.2370.005405
ORF1ab/nsp1388Q88KCaaAaa11B.1.1.2370.005405
ORF1ab/nsp1388Q88delCAA---11B.1.1.3060.000438
ORF1ab/nsp1388Q88XCaaTaa11B.1.1.3110.000358
ORF1ab/nsp1388Q88delCAA---11B.1.1.3180.000302
ORF1ab/nsp1388Q88HcaAcaC11B.1.1.3720.000689
ORF1ab/nsp1388Q88RcAacGa11B.1.1.4160.000905
ORF1ab/nsp1388Q88delCAA---11B.1.1.510.001718
ORF1ab/nsp1388Q88HcaAcaC11B.1.1.5190.00004
ORF1ab/nsp1388Q88delCAA---11B.1.1.5210.005348
ORF1ab/nsp1388Q88ECaaGaa11B.1.1.70.000001
ORF1ab/nsp1388Q88RcAacGa11B.1.1.70.000001
ORF1ab/nsp1388Q88QcaAcaG11B.1.1.720.030303
ORF1ab/nsp1388Q88LcAacTa11B.1.1180.006711
ORF1ab/nsp1388Q88delCAA---11B.1.1400.018868
ORF1ab/nsp1388Q88delCAA---11B.1.1600.000031
ORF1ab/nsp1388Q88HcaAcaC11B.1.1600.000031
ORF1ab/nsp1388Q88HcaAcaC11B.1.1700.00431
ORF1ab/nsp1388Q88PcAacCa11B.1.1770.000013
ORF1ab/nsp1388Q88del2CAA--N11B.1.1770.000013
ORF1ab/nsp1388Q88QcaAcaG11B.1.1770.000013
ORF1ab/nsp1388Q88RcAacGa11B.1.177.200.001517
ORF1ab/nsp1388Q88KCaaAaa11B.1.177.430.001477
ORF1ab/nsp1388Q88HcaAcaT11B.1.177.440.000519
ORF1ab/nsp1388Q88delCAA---11B.1.177.730.000566
ORF1ab/nsp1388Q88delCAA---11B.1.177.830.001481
ORF1ab/nsp1388Q88delCAA---11B.1.20.000009
ORF1ab/nsp1388Q88HcaAcaC11B.1.2140.003663
ORF1ab/nsp1388Q88QcaAcaG11B.1.2210.000071
ORF1ab/nsp1388Q88XCaaTaa11B.1.2340.000132
ORF1ab/nsp1388Q88delCAA---11B.1.2420.018868
ORF1ab/nsp1388Q88KCaaAaa11B.1.2430.00007
ORF1ab/nsp1388Q88HcaAcaC11B.1.243.10.022222
ORF1ab/nsp1388Q88XCaaTaa11B.1.2580.000067
ORF1ab/nsp1388Q88delCAA---11B.1.258.170.000104
ORF1ab/nsp1388Q88HcaAcaC11B.1.2760.016949
ORF1ab/nsp1388Q88delCAA---11B.1.3110.000275
ORF1ab/nsp1388Q88delCAA---11B.1.3510.00003
ORF1ab/nsp1388Q88HcaAcaC11B.1.3510.00003
ORF1ab/nsp1388Q88delCAA---11B.1.351.20.000303
ORF1ab/nsp1388Q88delCAA---11B.1.360.000146
ORF1ab/nsp1388Q88XCaaTaa11B.1.3690.000285
ORF1ab/nsp1388Q88QcaAcaG11B.1.3690.000285
ORF1ab/nsp1388Q88delCAA---11B.1.416.10.001563
ORF1ab/nsp1388Q88KCaaAaa11B.1.5250.000113
ORF1ab/nsp1388Q88HcaAcaC11B.1.5300.007143
ORF1ab/nsp1388Q88HcaAcaC11B.1.5440.006024
ORF1ab/nsp1388Q88XCaaTaa11B.1.5510.00129
ORF1ab/nsp1388Q88XCaaTaa11B.1.5710.009709
ORF1ab/nsp1388Q88PcAacCa11B.1.5820.000491
ORF1ab/nsp1388Q88XCaaTaa11B.1.5820.000491
ORF1ab/nsp1388Q88HcaAcaC11B.1.5850.027778
ORF1ab/nsp1388Q88HcaAcaT11B.1.617.10.000129
ORF1ab/nsp1388Q88QcaAcaG11B.1.6210.000089
ORF1ab/nsp1388Q88QcaAcaG11B.1.6280.000352
ORF1ab/nsp1388Q88HcaAcaC11B.1.6370.000073
ORF1ab/nsp1388Q88XCaaTaa11B.4.50.011905
ORF1ab/nsp1388Q88XCaaTaa11B.6.60.000889
ORF1ab/nsp1388Q88HcaAcaC11C.1.20.004255
ORF1ab/nsp1388Q88XCaaTaa11C.300.001727
ORF1ab/nsp1388Q88QcaAcaG11C.350.000774
ORF1ab/nsp1388Q88HcaAcaC11C.36.3.10.002717
ORF1ab/nsp1388Q88HcaAcaC11C.370.000116
ORF1ab/nsp1388Q88RcAacGa11D.20.000075
ORF1ab/nsp1388Q88delCAA---11P.1.10.000318
ORF1ab/nsp1388Q88HcaAcaC11P.1.10.000318
ORF1ab/nsp1388Q88HcaAcaC11P.1.170.000162
ORF1ab/nsp1388Q88XCaaTaa11Q.30.000145
ORF1ab/nsp1388Q88delCAA---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

CoV-GLUE uses sequence data from GISAID. GISAID data provided via this web application is subject to GISAID's Terms and Conditions.