CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1522

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/nsp31522V1522AV2340AnonsyngTagCa4994970.9959927283-7285
ORF1ab/nsp31522V1522AV2340AnonsyngTAgCC49920.004008027283-7285
ORF1ab/nsp31522V1522LV2340LnonsynGtaCta3813530.9265097283-7285
ORF1ab/nsp31522V1522LV2340LnonsynGtaTta381280.07349087283-7285
ORF1ab/nsp31522V1522IV2340InonsynGtaAta30630617283-7285
ORF1ab/nsp31522V1522VV2340VsyngtAgtG1691510.8934917283-7285
ORF1ab/nsp31522V1522VV2340VsyngtAgtT169120.07100597283-7285
ORF1ab/nsp31522V1522VV2340VsyngtAgtC16960.0355037283-7285
ORF1ab/nsp31522V1522delV2340deldelGTA---828217283-7285
ORF1ab/nsp31522V1522GV2340GnonsyngTagGa860.757283-7285
ORF1ab/nsp31522V1522GV2340GnonsyngTAgGT820.257283-7285
ORF1ab/nsp31522V1522EV2340EnonsyngTagAa7717283-7285
ORF1ab/nsp31522V1522XV2340XnonsynGTaTGa320.6666677283-7285
ORF1ab/nsp31522V1522XV2340XnonsynGTaTAa310.3333337283-7285
ORF1ab/nsp31522V1522del2V2340del2delgTAg--310.3333337283-7285
ORF1ab/nsp31522V1522del2V2340del2delGTA--T310.3333337283-7285
ORF1ab/nsp31522V1522del2V2340del2delGTAA--310.3333337283-7285
ORF1ab/nsp31522V1522CV2340CnonsynGTATGT2217283-7285
ORF1ab/nsp31522V1522FV2340FnonsynGtATtT2217283-7285
ORF1ab/nsp31522V1522DV2340DnonsyngTAgAC210.57283-7285
ORF1ab/nsp31522V1522DV2340DnonsyngTAgAT210.57283-7285
ORF1ab/nsp31522V1522YV2340YnonsynGTATAT1117283-7285
ORF1ab/nsp31522V1522del1V2340del1delGta-ta1117283-7285
ORF1ab/nsp31522V1522RV2340RnonsynGTaAGa1117283-7285

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/nsp31522V1522AgTagCa497499All0.000095
ORF1ab/nsp31522V1522AgTAgCC2499All0
ORF1ab/nsp31522V1522LGtaCta353381All0.000068
ORF1ab/nsp31522V1522LGtaTta28381All0.000005
ORF1ab/nsp31522V1522AgTagCa373373AY.40.000581
ORF1ab/nsp31522V1522IGtaAta306306All0.000059
ORF1ab/nsp31522V1522VgtAgtG151169All0.000029
ORF1ab/nsp31522V1522VgtAgtT12169All0.000002
ORF1ab/nsp31522V1522VgtAgtC6169All0.000001
ORF1ab/nsp31522V1522IGtaAta130130B.1.6320.872483
ORF1ab/nsp31522V1522LGtaCta9797B.1.20.000854
ORF1ab/nsp31522V1522LGtaCta9191B.1.4290.002141
ORF1ab/nsp31522V1522delGTA---8282All0.000016
ORF1ab/nsp31522V1522IGtaAta4646AY.430.000204
ORF1ab/nsp31522V1522IGtaAta4444B.1.1.70.000039
ORF1ab/nsp31522V1522AgTagCa3939B.1.1.70.000035
ORF1ab/nsp31522V1522LGtaCta3333B.1.4270.001666
ORF1ab/nsp31522V1522AgTagCa3030AY.30.000298
ORF1ab/nsp31522V1522VgtAgtG2727AY.40.000042
ORF1ab/nsp31522V1522VgtAgtG2023B.1.617.20.000075
ORF1ab/nsp31522V1522VgtAgtC223B.1.617.20.000008
ORF1ab/nsp31522V1522VgtAgtT123B.1.617.20.000004
ORF1ab/nsp31522V1522IGtaAta2121AY.4.2.10.003129
ORF1ab/nsp31522V1522LGtaCta1621B.1.1.70.000014
ORF1ab/nsp31522V1522LGtaTta521B.1.1.70.000004
ORF1ab/nsp31522V1522VgtAgtG1719B.1.1.70.000015
ORF1ab/nsp31522V1522VgtAgtT219B.1.1.70.000002
ORF1ab/nsp31522V1522LGtaCta1919B.1.2430.001322
ORF1ab/nsp31522V1522LGtaCta1415B.1.5960.00122
ORF1ab/nsp31522V1522LGtaTta115B.1.5960.000087
ORF1ab/nsp31522V1522AgTagCa1515B.1.617.20.000056
ORF1ab/nsp31522V1522VgtAgtG1313AY.250.000078
ORF1ab/nsp31522V1522delGTA---1313B.1.1.70.000012
ORF1ab/nsp31522V1522VgtAgtG811B.1.10.000145
ORF1ab/nsp31522V1522VgtAgtT311B.1.10.000054
ORF1ab/nsp31522V1522LGtaCta1010B.1.1.5190.000397
ORF1ab/nsp31522V1522IGtaAta99AY.40.000014
ORF1ab/nsp31522V1522IGtaAta99B.1.351.50.005396
ORF1ab/nsp31522V1522GgTagGa68All0.000001
ORF1ab/nsp31522V1522GgTAgGT28All0
ORF1ab/nsp31522V1522VgtAgtG88AY.430.000035
ORF1ab/nsp31522V1522LGtaCta78B.10.000064
ORF1ab/nsp31522V1522LGtaTta18B.10.000009
ORF1ab/nsp31522V1522VgtAgtG88B.1.438.10.000858
ORF1ab/nsp31522V1522delGTA---88B.1.617.20.00003
ORF1ab/nsp31522V1522IGtaAta77A.10.001973
ORF1ab/nsp31522V1522EgTagAa77All0.000001
ORF1ab/nsp31522V1522LGtaTta77AY.40.000011
ORF1ab/nsp31522V1522LGtaCta66B.1.2390.007326
ORF1ab/nsp31522V1522LGtaCta66B.1.243.10.133333
ORF1ab/nsp31522V1522delGTA---55B.10.000046
ORF1ab/nsp31522V1522LGtaCta55B.1.5510.006452
ORF1ab/nsp31522V1522LGtaCta55R.10.00045
ORF1ab/nsp31522V1522delGTA---440.222222
ORF1ab/nsp31522V1522GgTAgGT240.111111
ORF1ab/nsp31522V1522GgTagGa240.111111
ORF1ab/nsp31522V1522VgtAgtG44AY.1030.000025
ORF1ab/nsp31522V1522VgtAgtG44AY.470.000124
ORF1ab/nsp31522V1522VgtAgtG34B.10.000027
ORF1ab/nsp31522V1522VgtAgtT14B.10.000009
ORF1ab/nsp31522V1522delGTA---44B.1.10.000073
ORF1ab/nsp31522V1522IGtaAta44B.1.617.20.000015
ORF1ab/nsp31522V1522IGtaAta44B.1.6210.000354
ORF1ab/nsp31522V1522LGtaCta44P.20.000747
ORF1ab/nsp31522V1522XGTaTGa230.111111
ORF1ab/nsp31522V1522XGTaTAa130.055556
ORF1ab/nsp31522V1522XGTaTGa23All0
ORF1ab/nsp31522V1522del2GTAA--13All0
ORF1ab/nsp31522V1522del2gTAg--13All0
ORF1ab/nsp31522V1522XGTaTAa13All0
ORF1ab/nsp31522V1522del2GTA--T13All0
ORF1ab/nsp31522V1522VgtAgtG23AY.1020.000053
ORF1ab/nsp31522V1522VgtAgtT13AY.1020.000027
ORF1ab/nsp31522V1522IGtaAta33AY.250.000018
ORF1ab/nsp31522V1522VgtAgtG33AY.30.00003
ORF1ab/nsp31522V1522VgtAgtG33AY.4.20.000065
ORF1ab/nsp31522V1522AgTagCa33AY.430.000013
ORF1ab/nsp31522V1522delGTA---33AY.430.000013
ORF1ab/nsp31522V1522VgtAgtG33AY.440.000018
ORF1ab/nsp31522V1522LGtaCta33B.1.1.3480.002389
ORF1ab/nsp31522V1522VgtAgtG33B.1.1770.00004
ORF1ab/nsp31522V1522AgTagCa33B.1.1770.00004
ORF1ab/nsp31522V1522IGtaAta33B.1.177.390.046154
ORF1ab/nsp31522V1522LGtaCta33B.1.4040.003906
ORF1ab/nsp31522V1522delGTA---33B.1.4110.011111
ORF1ab/nsp31522V1522LGtaCta33B.1.6090.001438
ORF1ab/nsp31522V1522VgtAgtG33B.1.6370.000219
ORF1ab/nsp31522V1522LGtaTta220.111111
ORF1ab/nsp31522V1522AgTAgCC220.111111
ORF1ab/nsp31522V1522FGtATtT220.111111
ORF1ab/nsp31522V1522CGTATGT220.111111
ORF1ab/nsp31522V1522VgtAgtT220.111111
ORF1ab/nsp31522V1522CGTATGT22All0
ORF1ab/nsp31522V1522FGtATtT22All0
ORF1ab/nsp31522V1522DgTAgAC12All0
ORF1ab/nsp31522V1522DgTAgAT12All0
ORF1ab/nsp31522V1522AgTagCa22AY.1180.000125
ORF1ab/nsp31522V1522IGtaAta22AY.30.00002
ORF1ab/nsp31522V1522delGTA---22AY.40.000003
ORF1ab/nsp31522V1522AgTagCa22AY.410.000588
ORF1ab/nsp31522V1522delGTA---22AY.420.00008
ORF1ab/nsp31522V1522LGtaTta22AY.440.000012
ORF1ab/nsp31522V1522IGtaAta22AY.440.000012
ORF1ab/nsp31522V1522delGTA---22AY.9.20.000073
ORF1ab/nsp31522V1522IGtaAta22B.10.000018
ORF1ab/nsp31522V1522LGtaCta12B.1.10.000018
ORF1ab/nsp31522V1522LGtaTta12B.1.10.000018
ORF1ab/nsp31522V1522delGTA---22B.1.1.2180.015385
ORF1ab/nsp31522V1522LGtaCta22B.1.1.2220.000408
ORF1ab/nsp31522V1522AgTagCa22B.1.1.330.000842
ORF1ab/nsp31522V1522EgTagAa22B.1.1.70.000002
ORF1ab/nsp31522V1522AgTagCa22B.1.1600.000062
ORF1ab/nsp31522V1522delGTA---22B.1.1770.000026
ORF1ab/nsp31522V1522delGTA---22B.1.177.620.002384
ORF1ab/nsp31522V1522IGtaAta22B.1.20.000018
ORF1ab/nsp31522V1522AgTagCa22B.1.20.000018
ORF1ab/nsp31522V1522VgtAgtG22B.1.214.20.001199
ORF1ab/nsp31522V1522LGtaCta22B.1.2320.001075
ORF1ab/nsp31522V1522LGtaCta22B.1.2340.000264
ORF1ab/nsp31522V1522LGtaCta22B.1.3960.001411
ORF1ab/nsp31522V1522LGtaCta22B.1.4000.000858
ORF1ab/nsp31522V1522VgtAgtG22B.1.5260.000047
ORF1ab/nsp31522V1522LGtaCta22B.1.5610.000794
ORF1ab/nsp31522V1522delGTA---22B.1.617.10.000258
ORF1ab/nsp31522V1522EgTagAa22B.1.617.20.000008
ORF1ab/nsp31522V1522LGtaTta12B.1.617.20.000004
ORF1ab/nsp31522V1522LGtaCta12B.1.617.20.000004
ORF1ab/nsp31522V1522IGtaAta22B.1.6230.001073
ORF1ab/nsp31522V1522LGtaTta12D.20.000075
ORF1ab/nsp31522V1522LGtaCta12D.20.000075
ORF1ab/nsp31522V1522IGtaAta22P.10.000032
ORF1ab/nsp31522V1522IGtaAta22P.20.000373
ORF1ab/nsp31522V1522DgTAgAT110.055556
ORF1ab/nsp31522V1522YGTATAT110.055556
ORF1ab/nsp31522V1522EgTagAa110.055556
ORF1ab/nsp31522V1522VgtAgtG11A0.000387
ORF1ab/nsp31522V1522delGTA---11AD.20.000219
ORF1ab/nsp31522V1522RGTaAGa11All0
ORF1ab/nsp31522V1522del1Gta-ta11All0
ORF1ab/nsp31522V1522YGTATAT11All0
ORF1ab/nsp31522V1522AgTagCa11AN.10.02
ORF1ab/nsp31522V1522VgtAgtG11AY.1000.000046
ORF1ab/nsp31522V1522delGTA---11AY.1010.00049
ORF1ab/nsp31522V1522LGtaTta11AY.1020.000027
ORF1ab/nsp31522V1522delGTA---11AY.1030.000006
ORF1ab/nsp31522V1522VgtAgtG11AY.1090.00074
ORF1ab/nsp31522V1522LGtaTta11AY.1140.000231
ORF1ab/nsp31522V1522AgTagCa11AY.1170.000085
ORF1ab/nsp31522V1522VgtAgtG11AY.1170.000085
ORF1ab/nsp31522V1522IGtaAta11AY.1170.000085
ORF1ab/nsp31522V1522delGTA---11AY.1200.000037
ORF1ab/nsp31522V1522VgtAgtG11AY.230.00007
ORF1ab/nsp31522V1522AgTagCa11AY.250.000006
ORF1ab/nsp31522V1522LGtaTta11AY.250.000006
ORF1ab/nsp31522V1522delGTA---11AY.250.000006
ORF1ab/nsp31522V1522AgTagCa11AY.260.000028
ORF1ab/nsp31522V1522VgtAgtG11AY.290.000016
ORF1ab/nsp31522V1522AgTagCa11AY.330.000067
ORF1ab/nsp31522V1522AgTagCa11AY.340.000097
ORF1ab/nsp31522V1522delGTA---11AY.360.000148
ORF1ab/nsp31522V1522VgtAgtC11AY.390.000025
ORF1ab/nsp31522V1522LGtaCta11AY.390.000025
ORF1ab/nsp31522V1522GgTagGa11AY.40.000002
ORF1ab/nsp31522V1522delGTA---11AY.4.30.000842
ORF1ab/nsp31522V1522AgTagCa11AY.4.50.000107
ORF1ab/nsp31522V1522delGTA---11AY.4.50.000107
ORF1ab/nsp31522V1522VgtAgtG11AY.410.000294
ORF1ab/nsp31522V1522AgTagCa11AY.420.00004
ORF1ab/nsp31522V1522del2GTAA--11AY.430.000004
ORF1ab/nsp31522V1522LGtaCta11AY.430.000004
ORF1ab/nsp31522V1522delGTA---11AY.440.000006
ORF1ab/nsp31522V1522LGtaTta11AY.450.000122
ORF1ab/nsp31522V1522IGtaAta11AY.460.000104
ORF1ab/nsp31522V1522IGtaAta11AY.46.10.001027
ORF1ab/nsp31522V1522IGtaAta11AY.46.40.000165
ORF1ab/nsp31522V1522delGTA---11AY.50.000021
ORF1ab/nsp31522V1522AgTagCa11AY.540.000095
ORF1ab/nsp31522V1522delGTA---11AY.660.00107
ORF1ab/nsp31522V1522IGtaAta11AY.680.000274
ORF1ab/nsp31522V1522IGtaAta11AY.690.000187
ORF1ab/nsp31522V1522VgtAgtT11AY.690.000187
ORF1ab/nsp31522V1522VgtAgtG11AY.740.000116
ORF1ab/nsp31522V1522delGTA---11AY.760.004831
ORF1ab/nsp31522V1522delGTA---11AY.840.000437
ORF1ab/nsp31522V1522del2gTAg--11AY.90.000068
ORF1ab/nsp31522V1522AgTagCa11AY.90.000068
ORF1ab/nsp31522V1522IGtaAta11AY.98.10.000048
ORF1ab/nsp31522V1522GgTagGa11AY.990.001049
ORF1ab/nsp31522V1522LGtaCta11AZ.30.00152
ORF1ab/nsp31522V1522AgTagCa11B.10.000009
ORF1ab/nsp31522V1522AgTagCa11B.1.10.000018
ORF1ab/nsp31522V1522RGTaAGa11B.1.10.000018
ORF1ab/nsp31522V1522LGtaTta11B.1.1.100.001115
ORF1ab/nsp31522V1522delGTA---11B.1.1.1590.004673
ORF1ab/nsp31522V1522EgTagAa11B.1.1.1760.000439
ORF1ab/nsp31522V1522LGtaCta11B.1.1.3160.000925
ORF1ab/nsp31522V1522VgtAgtC11B.1.1.330.000421
ORF1ab/nsp31522V1522AgTagCa11B.1.1.3480.000796
ORF1ab/nsp31522V1522delGTA---11B.1.1.3540.004386
ORF1ab/nsp31522V1522delGTA---11B.1.1.370.000193
ORF1ab/nsp31522V1522AgTagCa11B.1.1.3970.002252
ORF1ab/nsp31522V1522delGTA---11B.1.1.460.004367
ORF1ab/nsp31522V1522delGTA---11B.1.1.5190.00004
ORF1ab/nsp31522V1522VgtAgtG11B.1.1.5190.00004
ORF1ab/nsp31522V1522delGTA---11B.1.1.5250.005464
ORF1ab/nsp31522V1522GgTagGa11B.1.1.70.000001
ORF1ab/nsp31522V1522del1Gta-ta11B.1.1.70.000001
ORF1ab/nsp31522V1522VgtAgtC11B.1.1240.007812
ORF1ab/nsp31522V1522AgTagCa11B.1.1460.004237
ORF1ab/nsp31522V1522VgtAgtG11B.1.177.160.000664
ORF1ab/nsp31522V1522AgTagCa11B.1.177.560.000668
ORF1ab/nsp31522V1522AgTagCa11B.1.177.620.001192
ORF1ab/nsp31522V1522VgtAgtG11B.1.20.000009
ORF1ab/nsp31522V1522delGTA---11B.1.2100.002132
ORF1ab/nsp31522V1522VgtAgtG11B.1.2210.000071
ORF1ab/nsp31522V1522LGtaCta11B.1.2400.000216
ORF1ab/nsp31522V1522VgtAgtG11B.1.2650.001271
ORF1ab/nsp31522V1522LGtaCta11B.1.2650.001271
ORF1ab/nsp31522V1522LGtaCta11B.1.3110.000275
ORF1ab/nsp31522V1522AgTagCa11B.1.3510.00003
ORF1ab/nsp31522V1522VgtAgtG11B.1.3510.00003
ORF1ab/nsp31522V1522LGtaCta11B.1.3510.00003
ORF1ab/nsp31522V1522AgTagCa11B.1.360.000146
ORF1ab/nsp31522V1522IGtaAta11B.1.36.220.001208
ORF1ab/nsp31522V1522AgTagCa11B.1.36.390.002217
ORF1ab/nsp31522V1522IGtaAta11B.1.3610.001289
ORF1ab/nsp31522V1522LGtaCta11B.1.3690.000285
ORF1ab/nsp31522V1522AgTagCa11B.1.3960.000706
ORF1ab/nsp31522V1522VgtAgtG11B.1.3990.001934
ORF1ab/nsp31522V1522VgtAgtG11B.1.4000.000429
ORF1ab/nsp31522V1522LGtaCta11B.1.4080.00369
ORF1ab/nsp31522V1522delGTA---11B.1.4150.014286
ORF1ab/nsp31522V1522delGTA---11B.1.416.10.001563
ORF1ab/nsp31522V1522LGtaCta11B.1.4230.010204
ORF1ab/nsp31522V1522AgTagCa11B.1.4270.00005
ORF1ab/nsp31522V1522IGtaAta11B.1.4290.000024
ORF1ab/nsp31522V1522delGTA---11B.1.4530.003236
ORF1ab/nsp31522V1522GgTagGa11B.1.466.20.000391
ORF1ab/nsp31522V1522delGTA---11B.1.4970.000315
ORF1ab/nsp31522V1522LGtaTta11B.1.5170.000427
ORF1ab/nsp31522V1522AgTagCa11B.1.5250.000113
ORF1ab/nsp31522V1522delGTA---11B.1.5260.000024
ORF1ab/nsp31522V1522LGtaCta11B.1.5670.003333
ORF1ab/nsp31522V1522LGtaCta11B.1.5680.001111
ORF1ab/nsp31522V1522LGtaCta11B.1.5750.000303
ORF1ab/nsp31522V1522delGTA---11B.1.575.10.002439
ORF1ab/nsp31522V1522AgTagCa11B.1.5890.007576
ORF1ab/nsp31522V1522LGtaCta11B.1.5950.000261
ORF1ab/nsp31522V1522VgtAgtT11B.1.617.10.000129
ORF1ab/nsp31522V1522del2GTA--T11B.1.617.20.000004
ORF1ab/nsp31522V1522DgTAgAC11B.1.617.20.000004
ORF1ab/nsp31522V1522delGTA---11B.1.6210.000089
ORF1ab/nsp31522V1522VgtAgtG11B.1.6270.00202
ORF1ab/nsp31522V1522LGtaCta11B.1.810.021277
ORF1ab/nsp31522V1522VgtAgtC11C.350.000774
ORF1ab/nsp31522V1522IGtaAta11D.20.000075
ORF1ab/nsp31522V1522LGtaTta11P.10.000016
ORF1ab/nsp31522V1522VgtAgtG11P.10.000016
ORF1ab/nsp31522V1522delGTA---11P.1.150.000232
ORF1ab/nsp31522V1522EgTagAa11Q.30.000145
ORF1ab/nsp31522V1522IGtaAta11Q.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.