CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp8 : CodonNum = 4

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
ORF1ab/nsp84S4LS3946LnonsyntCatTa664664112101-12103
ORF1ab/nsp84S4AS3946AnonsynTcaGca272272112101-12103
ORF1ab/nsp84S4TS3946TnonsynTcaAca1161150.99137912101-12103
ORF1ab/nsp84S4TS3946TnonsynTcAAcC11610.0086206912101-12103
ORF1ab/nsp84S4PS3946PnonsynTcaCca88112101-12103
ORF1ab/nsp84S4delS3946deldelTCA---66112101-12103
ORF1ab/nsp84S4XS3946XnonsyntCatAa430.7512101-12103
ORF1ab/nsp84S4del1S3946del1delTca-ca420.512101-12103
ORF1ab/nsp84S4del1S3946del1deltcAtc-420.512101-12103
ORF1ab/nsp84S4XS3946XnonsyntCatGa410.2512101-12103
ORF1ab/nsp84S4CS3946CnonsyntCAtGT320.66666712101-12103
ORF1ab/nsp84S4CS3946CnonsyntCAtGC310.33333312101-12103
ORF1ab/nsp84S4del2S3946del2delTCAC--210.512101-12103
ORF1ab/nsp84S4del2S3946del2delTCa--a210.512101-12103
ORF1ab/nsp84S4YS3946YnonsyntCAtAC11112101-12103
ORF1ab/nsp84S4RS3946RnonsynTCaAGa11112101-12103
ORF1ab/nsp84S4NS3946NnonsynTCAAAC11112101-12103
ORF1ab/nsp84S4KS3946KnonsynTCaAAa11112101-12103

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/nsp84S4StcAtcG9541055All0.000182
ORF1ab/nsp84S4StcAtcT861055All0.000016
ORF1ab/nsp84S4StcAtcC141055All0.000003
ORF1ab/nsp84S4STCAAGC11055All0
ORF1ab/nsp84S4LtCatTa664664All0.000127
ORF1ab/nsp84S4StcAtcG584584AP.10.876877
ORF1ab/nsp84S4ATcaGca272272All0.000052
ORF1ab/nsp84S4ATcaGca215215AY.260.006087
ORF1ab/nsp84S4LtCatTa125125B.1.1.70.000112
ORF1ab/nsp84S4TTcaAca115116All0.000022
ORF1ab/nsp84S4TTcAAcC1116All0
ORF1ab/nsp84S4StcAtcG7186B.1.1.70.000064
ORF1ab/nsp84S4StcAtcT1486B.1.1.70.000013
ORF1ab/nsp84S4StcAtcC186B.1.1.70.000001
ORF1ab/nsp84S4LtCatTa8585B.1.5260.001998
ORF1ab/nsp84S4TTcaAca7676B.1.36.380.124795
ORF1ab/nsp84S4StcAtcG6771AY.40.000104
ORF1ab/nsp84S4StcAtcT371AY.40.000005
ORF1ab/nsp84S4StcAtcC171AY.40.000002
ORF1ab/nsp84S4LtCatTa6464AY.40.0001
ORF1ab/nsp84S4StcAtcT3150B.1.617.20.000117
ORF1ab/nsp84S4StcAtcG1950B.1.617.20.000072
ORF1ab/nsp84S4LtCatTa3434B.1.617.20.000128
ORF1ab/nsp84S4LtCatTa2626B.10.000238
ORF1ab/nsp84S4LtCatTa2626B.1.1.1810.118182
ORF1ab/nsp84S4StcAtcG2424B.10.00022
ORF1ab/nsp84S4StcAtcG2022B.1.10.000363
ORF1ab/nsp84S4StcAtcT222B.1.10.000036
ORF1ab/nsp84S4LtCatTa2121AY.30.000209
ORF1ab/nsp84S4LtCatTa2020AY.290.000315
ORF1ab/nsp84S4StcAtcG2020B.1.177.730.011325
ORF1ab/nsp84S4StcAtcT1218AY.430.000053
ORF1ab/nsp84S4StcAtcG518AY.430.000022
ORF1ab/nsp84S4StcAtcC118AY.430.000004
ORF1ab/nsp84S4LtCatTa1717P.10.000268
ORF1ab/nsp84S4LtCatTa1616AY.250.000096
ORF1ab/nsp84S4StcAtcG1616B.1.5260.000376
ORF1ab/nsp84S4StcAtcG1315AY.1030.000081
ORF1ab/nsp84S4StcAtcT215AY.1030.000012
ORF1ab/nsp84S4LtCatTa1515AY.430.000066
ORF1ab/nsp84S4StcAtcG1414AY.1100.001578
ORF1ab/nsp84S4LtCatTa1414AY.740.001619
ORF1ab/nsp84S4LtCatTa1414B.1.10.000254
ORF1ab/nsp84S4LtCatTa1212AY.440.000073
ORF1ab/nsp84S4ATcaGca1111AY.40.000017
ORF1ab/nsp84S4TTcaAca1010B.1.1.70.000009
ORF1ab/nsp84S4LtCatTa99AY.390.000222
ORF1ab/nsp84S4StcAtcG99AY.980.000711
ORF1ab/nsp84S4LtCatTa99B.1.1770.000119
ORF1ab/nsp84S4PTcaCca88All0.000002
ORF1ab/nsp84S4ATcaGca88AY.250.000048
ORF1ab/nsp84S4ATcaGca88AY.290.000126
ORF1ab/nsp84S4StcAtcG68AY.30.00006
ORF1ab/nsp84S4StcAtcT28AY.30.00002
ORF1ab/nsp84S4LtCatTa88B.1.20.00007
ORF1ab/nsp84S4TTcaAca77AY.40.000011
ORF1ab/nsp84S4StcAtcG37AY.440.000018
ORF1ab/nsp84S4StcAtcT37AY.440.000018
ORF1ab/nsp84S4StcAtcC17AY.440.000006
ORF1ab/nsp84S4LtCatTa77AY.50.000145
ORF1ab/nsp84S4ATcaGca77B.1.1.70.000006
ORF1ab/nsp84S4delTCA---66All0.000001
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/nsp84S4LtCatTa55B.1.4290.000118
ORF1ab/nsp84S4LtCatTa55B.1.438.10.000536
ORF1ab/nsp84S4StcAtcG45P.10.000063
ORF1ab/nsp84S4StcAtcC15P.10.000016
ORF1ab/nsp84S4StcAtcC340.166667
ORF1ab/nsp84S4STCAAGC140.055556
ORF1ab/nsp84S4XtCatAa34All0.000001
ORF1ab/nsp84S4del1Tca-ca24All0
ORF1ab/nsp84S4del1tcAtc-24All0
ORF1ab/nsp84S4XtCatGa14All0
ORF1ab/nsp84S4LtCatTa44AY.1030.000025
ORF1ab/nsp84S4LtCatTa44AY.1180.000251
ORF1ab/nsp84S4StcAtcT34AY.1190.000106
ORF1ab/nsp84S4StcAtcG14AY.1190.000035
ORF1ab/nsp84S4LtCatTa44AY.9.10.000335
ORF1ab/nsp84S4LtCatTa44B.1.1.500.002716
ORF1ab/nsp84S4LtCatTa44B.1.2210.000284
ORF1ab/nsp84S4PTcaCca330.166667
ORF1ab/nsp84S4CtCAtGT23All0
ORF1ab/nsp84S4CtCAtGC13All0
ORF1ab/nsp84S4TTcaAca33AY.120.2.10.001495
ORF1ab/nsp84S4LtCatTa33AY.130.000483
ORF1ab/nsp84S4LtCatTa33AY.260.000085
ORF1ab/nsp84S4LtCatTa33AY.330.0002
ORF1ab/nsp84S4TTcaAca33AY.430.000013
ORF1ab/nsp84S4StcAtcG23AY.450.000243
ORF1ab/nsp84S4StcAtcC13AY.450.000122
ORF1ab/nsp84S4LtCatTa33AY.470.000093
ORF1ab/nsp84S4StcAtcT23AY.50.000041
ORF1ab/nsp84S4StcAtcG13AY.50.000021
ORF1ab/nsp84S4ATcaGca33B.1.1.280.000934
ORF1ab/nsp84S4ATcaGca33B.1.1260.003827
ORF1ab/nsp84S4TTcaAca33B.1.1770.00004
ORF1ab/nsp84S4LtCatTa33B.1.5250.000339
ORF1ab/nsp84S4LtCatTa33L.10.005714
ORF1ab/nsp84S4ATcaGca220.111111
ORF1ab/nsp84S4XtCatGa120.055556
ORF1ab/nsp84S4TTcaAca120.055556
ORF1ab/nsp84S4TTcAAcC120.055556
ORF1ab/nsp84S4XtCatAa120.055556
ORF1ab/nsp84S4del2TCa--a12All0
ORF1ab/nsp84S4del2TCAC--12All0
ORF1ab/nsp84S4StcAtcT22AY.1020.000053
ORF1ab/nsp84S4LtCatTa22AY.1020.000053
ORF1ab/nsp84S4LtCatTa22AY.1100.000225
ORF1ab/nsp84S4ATcaGca22AY.1190.000071
ORF1ab/nsp84S4StcAtcC12AY.3.10.000085
ORF1ab/nsp84S4StcAtcG12AY.3.10.000085
ORF1ab/nsp84S4LtCatTa22AY.39.10.000079
ORF1ab/nsp84S4StcAtcG22AY.420.00008
ORF1ab/nsp84S4LtCatTa22AY.420.00008
ORF1ab/nsp84S4TTcaAca22AY.440.000012
ORF1ab/nsp84S4LtCatTa22AY.600.001876
ORF1ab/nsp84S4LtCatTa22AY.75.10.000361
ORF1ab/nsp84S4LtCatTa22AY.980.000158
ORF1ab/nsp84S4LtCatTa22AY.98.10.000097
ORF1ab/nsp84S4StcAtcG22B0.000256
ORF1ab/nsp84S4StcAtcG22B.1.1.10.000653
ORF1ab/nsp84S4LtCatTa22B.1.1.5190.000079
ORF1ab/nsp84S4delTCA---22B.1.1.70.000002
ORF1ab/nsp84S4ATcaGca22B.1.1770.000026
ORF1ab/nsp84S4StcAtcG22B.1.1770.000026
ORF1ab/nsp84S4StcAtcG22B.1.177.170.001642
ORF1ab/nsp84S4LtCatTa22B.1.177.810.000379
ORF1ab/nsp84S4ATcaGca22B.1.20.000018
ORF1ab/nsp84S4LtCatTa22B.1.2430.000139
ORF1ab/nsp84S4LtCatTa22B.1.3510.000059
ORF1ab/nsp84S4LtCatTa22B.1.351.20.000605
ORF1ab/nsp84S4LtCatTa22B.1.4270.000101
ORF1ab/nsp84S4LtCatTa22B.1.617.10.000258
ORF1ab/nsp84S4TTcaAca22B.1.617.20.000008
ORF1ab/nsp84S4ATcaGca22B.1.617.20.000008
ORF1ab/nsp84S4StcAtcG22B.1.6210.000177
ORF1ab/nsp84S4StcAtcG22C.370.000232
ORF1ab/nsp84S4LtCatTa22D.20.00015
ORF1ab/nsp84S4StcAtcT12P.1.140.000048
ORF1ab/nsp84S4StcAtcG12P.1.140.000048
ORF1ab/nsp84S4CtCAtGC110.055556
ORF1ab/nsp84S4YtCAtAC110.055556
ORF1ab/nsp84S4NTCAAAC110.055556
ORF1ab/nsp84S4RTCaAGa110.055556
ORF1ab/nsp84S4KTCaAAa110.055556
ORF1ab/nsp84S4StcAtcC11A0.000387
ORF1ab/nsp84S4LtCatTa11AA.70.009174
ORF1ab/nsp84S4KTCaAAa11All0
ORF1ab/nsp84S4RTCaAGa11All0
ORF1ab/nsp84S4YtCAtAC11All0
ORF1ab/nsp84S4NTCAAAC11All0
ORF1ab/nsp84S4TTcaAca11AY.1000.000046
ORF1ab/nsp84S4ATcaGca11AY.1100.000113
ORF1ab/nsp84S4LtCatTa11AY.1170.000085
ORF1ab/nsp84S4StcAtcT11AY.1170.000085
ORF1ab/nsp84S4LtCatTa11AY.1190.000035
ORF1ab/nsp84S4LtCatTa11AY.120.000316
ORF1ab/nsp84S4TTcaAca11AY.1200.000037
ORF1ab/nsp84S4LtCatTa11AY.1200.000037
ORF1ab/nsp84S4StcAtcG11AY.1200.000037
ORF1ab/nsp84S4StcAtcG11AY.1210.000135
ORF1ab/nsp84S4LtCatTa11AY.1210.000135
ORF1ab/nsp84S4StcAtcG11AY.140.000088
ORF1ab/nsp84S4StcAtcG11AY.160.00038
ORF1ab/nsp84S4LtCatTa11AY.200.000039
ORF1ab/nsp84S4LtCatTa11AY.23.10.000417
ORF1ab/nsp84S4del1Tca-ca11AY.250.000006
ORF1ab/nsp84S4LtCatTa11AY.270.000065
ORF1ab/nsp84S4LtCatTa11AY.29.10.000221
ORF1ab/nsp84S4TTcaAca11AY.30.00001
ORF1ab/nsp84S4LtCatTa11AY.300.000396
ORF1ab/nsp84S4StcAtcG11AY.300.000396
ORF1ab/nsp84S4StcAtcG11AY.320.000532
ORF1ab/nsp84S4StcAtcT11AY.340.000097
ORF1ab/nsp84S4LtCatTa11AY.34.10.00051
ORF1ab/nsp84S4StcAtcG11AY.360.000148
ORF1ab/nsp84S4ATcaGca11AY.390.000025
ORF1ab/nsp84S4StcAtcG11AY.390.000025
ORF1ab/nsp84S4ATcaGca11AY.4.10.000737
ORF1ab/nsp84S4LtCatTa11AY.4.2.10.000149
ORF1ab/nsp84S4StcAtcG11AY.4.50.000107
ORF1ab/nsp84S4ATcaGca11AY.430.000004
ORF1ab/nsp84S4del2TCAC--11AY.440.000006
ORF1ab/nsp84S4ATcaGca11AY.450.000122
ORF1ab/nsp84S4StcAtcT11AY.460.000104
ORF1ab/nsp84S4LtCatTa11AY.46.10.001027
ORF1ab/nsp84S4StcAtcG11AY.470.000031
ORF1ab/nsp84S4LtCatTa11AY.520.000814
ORF1ab/nsp84S4LtCatTa11AY.530.000288
ORF1ab/nsp84S4LtCatTa11AY.540.000095
ORF1ab/nsp84S4TTcaAca11AY.550.000917
ORF1ab/nsp84S4StcAtcG11AY.60.000041
ORF1ab/nsp84S4LtCatTa11AY.60.000041
ORF1ab/nsp84S4LtCatTa11AY.660.00107
ORF1ab/nsp84S4LtCatTa11AY.7.10.000113
ORF1ab/nsp84S4LtCatTa11AY.700.000209
ORF1ab/nsp84S4StcAtcG11AY.710.000475
ORF1ab/nsp84S4LtCatTa11AY.860.00083
ORF1ab/nsp84S4LtCatTa11AY.90.000068
ORF1ab/nsp84S4StcAtcG11AY.9.20.000037
ORF1ab/nsp84S4LtCatTa11AY.950.000761
ORF1ab/nsp84S4ATcaGca11AY.980.000079
ORF1ab/nsp84S4StcAtcT11AY.98.10.000048
ORF1ab/nsp84S4StcAtcG11AY.99.20.000092
ORF1ab/nsp84S4XtCatAa11B.10.000009
ORF1ab/nsp84S4PTcaCca11B.10.000009
ORF1ab/nsp84S4TTcaAca11B.10.000009
ORF1ab/nsp84S4delTCA---11B.10.000009
ORF1ab/nsp84S4del1tcAtc-11B.10.000009
ORF1ab/nsp84S4delTCA---11B.1.10.000018
ORF1ab/nsp84S4TTcaAca11B.1.10.000018
ORF1ab/nsp84S4LtCatTa11B.1.1.10.000327
ORF1ab/nsp84S4LtCatTa11B.1.1.1700.001247
ORF1ab/nsp84S4LtCatTa11B.1.1.1760.000439
ORF1ab/nsp84S4LtCatTa11B.1.1.1980.001468
ORF1ab/nsp84S4StcAtcG11B.1.1.2370.005405
ORF1ab/nsp84S4StcAtcC11B.1.1.2420.043478
ORF1ab/nsp84S4LtCatTa11B.1.1.250.000569
ORF1ab/nsp84S4LtCatTa11B.1.1.280.000311
ORF1ab/nsp84S4StcAtcG11B.1.1.280.000311
ORF1ab/nsp84S4LtCatTa11B.1.1.3060.000438
ORF1ab/nsp84S4LtCatTa11B.1.1.3160.000925
ORF1ab/nsp84S4LtCatTa11B.1.1.3550.015385
ORF1ab/nsp84S4StcAtcC11B.1.1.390.00051
ORF1ab/nsp84S4LtCatTa11B.1.1.3910.008547
ORF1ab/nsp84S4LtCatTa11B.1.1.5000.02
ORF1ab/nsp84S4StcAtcG11B.1.1.5280.004808
ORF1ab/nsp84S4LtCatTa11B.1.1.580.005376
ORF1ab/nsp84S4del2TCa--a11B.1.1.70.000001
ORF1ab/nsp84S4CtCAtGT11B.1.1.70.000001
ORF1ab/nsp84S4PTcaCca11B.1.1.70.000001
ORF1ab/nsp84S4LtCatTa11B.1.177.100.000878
ORF1ab/nsp84S4LtCatTa11B.1.177.210.000076
ORF1ab/nsp84S4LtCatTa11B.1.177.410.0025
ORF1ab/nsp84S4LtCatTa11B.1.177.420.000894
ORF1ab/nsp84S4LtCatTa11B.1.177.520.001757
ORF1ab/nsp84S4StcAtcG11B.1.177.560.000668
ORF1ab/nsp84S4TTcaAca11B.1.177.570.000281
ORF1ab/nsp84S4delTCA---11B.1.177.860.000183
ORF1ab/nsp84S4LtCatTa11B.1.177.860.000183
ORF1ab/nsp84S4LtCatTa11B.1.1820.007246
ORF1ab/nsp84S4XtCatAa11B.1.20.000009
ORF1ab/nsp84S4PTcaCca11B.1.20.000009
ORF1ab/nsp84S4LtCatTa11B.1.220.001318
ORF1ab/nsp84S4StcAtcG11B.1.2210.000071
ORF1ab/nsp84S4StcAtcG11B.1.2320.000537
ORF1ab/nsp84S4PTcaCca11B.1.2340.000132
ORF1ab/nsp84S4StcAtcG11B.1.2580.000067
ORF1ab/nsp84S4LtCatTa11B.1.2600.003344
ORF1ab/nsp84S4LtCatTa11B.1.3110.000275
ORF1ab/nsp84S4CtCAtGT11B.1.360.000146
ORF1ab/nsp84S4LtCatTa11B.1.360.000146
ORF1ab/nsp84S4LtCatTa11B.1.3780.006849
ORF1ab/nsp84S4ATcaGca11B.1.4290.000024
ORF1ab/nsp84S4PTcaCca11B.1.4590.004082
ORF1ab/nsp84S4LtCatTa11B.1.4600.017857
ORF1ab/nsp84S4LtCatTa11B.1.466.20.000391
ORF1ab/nsp84S4StcAtcC11B.1.466.20.000391
ORF1ab/nsp84S4LtCatTa11B.1.4700.001404
ORF1ab/nsp84S4StcAtcG11B.1.5250.000113
ORF1ab/nsp84S4StcAtcG11B.1.5760.000907
ORF1ab/nsp84S4del1Tca-ca11B.1.5950.000261
ORF1ab/nsp84S4LtCatTa11B.1.5960.000087
ORF1ab/nsp84S4LtCatTa11B.1.6020.006536
ORF1ab/nsp84S4del1tcAtc-11B.1.617.10.000129
ORF1ab/nsp84S4LtCatTa11B.1.6280.000352
ORF1ab/nsp84S4LtCatTa11B.1.6340.003425
ORF1ab/nsp84S4StcAtcG11B.1.6370.000073
ORF1ab/nsp84S4LtCatTa11B.400.000364
ORF1ab/nsp84S4LtCatTa11C.160.00106
ORF1ab/nsp84S4LtCatTa11C.190.027027
ORF1ab/nsp84S4delTCA---11N.40.004255
ORF1ab/nsp84S4TTcaAca11P.1.120.000484
ORF1ab/nsp84S4LtCatTa11P.1.150.000232
ORF1ab/nsp84S4LtCatTa11P.1.170.000162
ORF1ab/nsp84S4LtCatTa11P.1.80.004785
ORF1ab/nsp84S4LtCatTa11Q.10.000126

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.