CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp2 : CodonNum = 564

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/nsp2564G564GG744GsynggAggG10497540.718782495-2497
ORF1ab/nsp2564G564GG744GsynggAggT10492430.2316492495-2497
ORF1ab/nsp2564G564GG744GsynggAggC1049520.0495712495-2497
ORF1ab/nsp2564G564delG744deldelGGA---909012495-2497
ORF1ab/nsp2564G564VG744VnonsyngGagTa20190.952495-2497
ORF1ab/nsp2564G564VG744VnonsyngGAgTG2010.052495-2497
ORF1ab/nsp2564G564XG744XnonsynGgaTga131312495-2497
ORF1ab/nsp2564G564RG744RnonsynGgaAga12110.9166672495-2497
ORF1ab/nsp2564G564RG744RnonsynGgaCga1210.08333332495-2497
ORF1ab/nsp2564G564EG744EnonsyngGAgAG860.752495-2497
ORF1ab/nsp2564G564EG744EnonsyngGagAa820.252495-2497
ORF1ab/nsp2564G564KG744KnonsynGGaAAa420.52495-2497
ORF1ab/nsp2564G564KG744KnonsynGGAAAG420.52495-2497
ORF1ab/nsp2564G564del1G744del1delggAgg-2212495-2497
ORF1ab/nsp2564G564CG744CnonsynGgATgT210.52495-2497
ORF1ab/nsp2564G564CG744CnonsynGgATgC210.52495-2497
ORF1ab/nsp2564G564DG744DnonsyngGAgAC1112495-2497
ORF1ab/nsp2564G564IG744InonsynGGaATa1112495-2497
ORF1ab/nsp2564G564AG744AnonsyngGagCa1112495-2497
ORF1ab/nsp2564G564FG744FnonsynGGATTT1112495-2497
ORF1ab/nsp2564G564del2G744del2delgGAg--1112495-2497

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/nsp2564G564GggAggG7541049All0.000144
ORF1ab/nsp2564G564GggAggT2431049All0.000046
ORF1ab/nsp2564G564GggAggC521049All0.00001
ORF1ab/nsp2564G564GggAggG131133AY.460.013634
ORF1ab/nsp2564G564GggAggT2133AY.460.000208
ORF1ab/nsp2564G564GggAggG81129B.1.1.70.000073
ORF1ab/nsp2564G564GggAggT35129B.1.1.70.000031
ORF1ab/nsp2564G564GggAggC13129B.1.1.70.000012
ORF1ab/nsp2564G564GggAggG98117AY.40.000153
ORF1ab/nsp2564G564GggAggT18117AY.40.000028
ORF1ab/nsp2564G564GggAggC1117AY.40.000002
ORF1ab/nsp2564G564delGGA---9090All0.000017
ORF1ab/nsp2564G564GggAggG6266AY.200.00241
ORF1ab/nsp2564G564GggAggT466AY.200.000155
ORF1ab/nsp2564G564GggAggG5458B.1.4290.001271
ORF1ab/nsp2564G564GggAggC258B.1.4290.000047
ORF1ab/nsp2564G564GggAggT258B.1.4290.000047
ORF1ab/nsp2564G564GggAggT4257B.1.1.5190.001668
ORF1ab/nsp2564G564GggAggG1557B.1.1.5190.000596
ORF1ab/nsp2564G564GggAggG3451B.1.617.20.000128
ORF1ab/nsp2564G564GggAggT1351B.1.617.20.000049
ORF1ab/nsp2564G564GggAggC451B.1.617.20.000015
ORF1ab/nsp2564G564GggAggT3535AY.690.006534
ORF1ab/nsp2564G564GggAggG2333AY.430.000102
ORF1ab/nsp2564G564GggAggT933AY.430.00004
ORF1ab/nsp2564G564GggAggC133AY.430.000004
ORF1ab/nsp2564G564GggAggG2026B.1.1770.000263
ORF1ab/nsp2564G564GggAggT626B.1.1770.000079
ORF1ab/nsp2564G564GggAggG1525B.10.000137
ORF1ab/nsp2564G564GggAggT825B.10.000073
ORF1ab/nsp2564G564GggAggC225B.10.000018
ORF1ab/nsp2564G564VgGagTa1920All0.000004
ORF1ab/nsp2564G564VgGAgTG120All0
ORF1ab/nsp2564G564GggAggC1020AY.440.000061
ORF1ab/nsp2564G564GggAggG720AY.440.000043
ORF1ab/nsp2564G564GggAggT320AY.440.000018
ORF1ab/nsp2564G564GggAggG1119AY.390.000272
ORF1ab/nsp2564G564GggAggT719AY.390.000173
ORF1ab/nsp2564G564GggAggC119AY.390.000025
ORF1ab/nsp2564G564delGGA---1919B.1.1.70.000017
ORF1ab/nsp2564G564GggAggG814AY.1030.00005
ORF1ab/nsp2564G564GggAggT414AY.1030.000025
ORF1ab/nsp2564G564GggAggC214AY.1030.000012
ORF1ab/nsp2564G564GggAggG1014AY.30.000099
ORF1ab/nsp2564G564GggAggT214AY.30.00002
ORF1ab/nsp2564G564GggAggC214AY.30.00002
ORF1ab/nsp2564G564GggAggG1414B.1.2320.007523
ORF1ab/nsp2564G564XGgaTga1313All0.000002
ORF1ab/nsp2564G564GggAggG1213AY.1020.000318
ORF1ab/nsp2564G564GggAggT113AY.1020.000027
ORF1ab/nsp2564G564RGgaAga1112All0.000002
ORF1ab/nsp2564G564RGgaCga112All0
ORF1ab/nsp2564G564GggAggG712B.1.20.000062
ORF1ab/nsp2564G564GggAggT412B.1.20.000035
ORF1ab/nsp2564G564GggAggC112B.1.20.000009
ORF1ab/nsp2564G564GggAggG710B.1.10.000127
ORF1ab/nsp2564G564GggAggT310B.1.10.000054
ORF1ab/nsp2564G564GggAggG1010B.1.1.2770.007587
ORF1ab/nsp2564G564GggAggG99B.1.6090.004314
ORF1ab/nsp2564G564GggAggG79P.10.00011
ORF1ab/nsp2564G564GggAggT29P.10.000032
ORF1ab/nsp2564G564EgGAgAG68All0.000001
ORF1ab/nsp2564G564EgGagAa28All0
ORF1ab/nsp2564G564GggAggG78AY.250.000042
ORF1ab/nsp2564G564GggAggC18AY.250.000006
ORF1ab/nsp2564G564GggAggT48AY.610.000419
ORF1ab/nsp2564G564GggAggG48AY.610.000419
ORF1ab/nsp2564G564delGGA---88B.1.617.20.00003
ORF1ab/nsp2564G564GggAggG77B.1.1.3750.083333
ORF1ab/nsp2564G564GggAggG66B.1.4160.007614
ORF1ab/nsp2564G564GggAggG66P.30.009569
ORF1ab/nsp2564G564GggAggG45AY.260.000113
ORF1ab/nsp2564G564GggAggT15AY.260.000028
ORF1ab/nsp2564G564delGGA---55AY.40.000008
ORF1ab/nsp2564G564GggAggG35AY.99.20.000276
ORF1ab/nsp2564G564GggAggT25AY.99.20.000184
ORF1ab/nsp2564G564VgGagTa55B.10.000046
ORF1ab/nsp2564G564delGGA---55B.10.000046
ORF1ab/nsp2564G564GggAggG55B.1.4760.5
ORF1ab/nsp2564G564GggAggT35B.1.617.10.000387
ORF1ab/nsp2564G564GggAggG25B.1.617.10.000258
ORF1ab/nsp2564G564delGGA---440.222222
ORF1ab/nsp2564G564KGGaAAa240.111111
ORF1ab/nsp2564G564KGGAAAG240.111111
ORF1ab/nsp2564G564KGGAAAG24All0
ORF1ab/nsp2564G564KGGaAAa24All0
ORF1ab/nsp2564G564GggAggG44AY.1000.000184
ORF1ab/nsp2564G564GggAggG44AY.1170.000338
ORF1ab/nsp2564G564GggAggT34B0.000383
ORF1ab/nsp2564G564GggAggG14B0.000128
ORF1ab/nsp2564G564GggAggT24B.1.360.000292
ORF1ab/nsp2564G564GggAggG24B.1.360.000292
ORF1ab/nsp2564G564GggAggG44B.1.5610.001588
ORF1ab/nsp2564G564GggAggC44P.1.170.000647
ORF1ab/nsp2564G564GggAggG44R.10.00036
ORF1ab/nsp2564G564GggAggG33AY.840.001312
ORF1ab/nsp2564G564GggAggG23AY.90.000135
ORF1ab/nsp2564G564GggAggT13AY.90.000068
ORF1ab/nsp2564G564GggAggG33AY.920.000862
ORF1ab/nsp2564G564VgGagTa23B.1.10.000036
ORF1ab/nsp2564G564VgGAgTG13B.1.10.000018
ORF1ab/nsp2564G564GggAggT33B.1.1.10.00098
ORF1ab/nsp2564G564delGGA---33B.1.1.330.001263
ORF1ab/nsp2564G564GggAggG33B.1.1890.012876
ORF1ab/nsp2564G564GggAggT33B.1.4270.000151
ORF1ab/nsp2564G564GggAggG22AD.20.000438
ORF1ab/nsp2564G564del1ggAgg-22All0
ORF1ab/nsp2564G564CGgATgT12All0
ORF1ab/nsp2564G564CGgATgC12All0
ORF1ab/nsp2564G564GggAggT22AY.1200.000074
ORF1ab/nsp2564G564delGGA---22AY.250.000012
ORF1ab/nsp2564G564GggAggT12AY.290.000016
ORF1ab/nsp2564G564GggAggC12AY.290.000016
ORF1ab/nsp2564G564GggAggG22AY.420.00008
ORF1ab/nsp2564G564delGGA---22AY.430.000009
ORF1ab/nsp2564G564VgGagTa22AY.430.000009
ORF1ab/nsp2564G564RGgaAga22AY.440.000012
ORF1ab/nsp2564G564GggAggG22AY.930.000546
ORF1ab/nsp2564G564delGGA---22B.1.10.000036
ORF1ab/nsp2564G564GggAggT22B.1.1.1610.007067
ORF1ab/nsp2564G564delGGA---22B.1.1.3480.001592
ORF1ab/nsp2564G564GggAggT22B.1.1.3720.001377
ORF1ab/nsp2564G564VgGagTa22B.1.1.70.000002
ORF1ab/nsp2564G564RGgaAga22B.1.1.70.000002
ORF1ab/nsp2564G564XGgaTga22B.1.1.70.000002
ORF1ab/nsp2564G564EgGAgAG22B.1.1.70.000002
ORF1ab/nsp2564G564CGgATgC12B.1.1.70.000001
ORF1ab/nsp2564G564CGgATgT12B.1.1.70.000001
ORF1ab/nsp2564G564GggAggG22B.1.177.600.000437
ORF1ab/nsp2564G564EgGagAa12B.1.3510.00003
ORF1ab/nsp2564G564EgGAgAG12B.1.3510.00003
ORF1ab/nsp2564G564GggAggG22B.1.36.180.00084
ORF1ab/nsp2564G564GggAggG22B.1.36.290.001035
ORF1ab/nsp2564G564GggAggC22B.1.36.380.003284
ORF1ab/nsp2564G564delGGA---22B.1.4240.016129
ORF1ab/nsp2564G564delGGA---22B.1.4290.000047
ORF1ab/nsp2564G564delGGA---22N.60.014184
ORF1ab/nsp2564G564GggAggT22P.1.90.009615
ORF1ab/nsp2564G564del2gGAg--11All0
ORF1ab/nsp2564G564FGGATTT11All0
ORF1ab/nsp2564G564AgGagCa11All0
ORF1ab/nsp2564G564IGGaATa11All0
ORF1ab/nsp2564G564DgGAgAC11All0
ORF1ab/nsp2564G564GggAggG11AM.40.003571
ORF1ab/nsp2564G564VgGagTa11AY.1000.000046
ORF1ab/nsp2564G564RGgaAga11AY.1030.000006
ORF1ab/nsp2564G564delGGA---11AY.1080.001103
ORF1ab/nsp2564G564delGGA---11AY.1110.000183
ORF1ab/nsp2564G564delGGA---11AY.1130.000142
ORF1ab/nsp2564G564GggAggT11AY.1190.000035
ORF1ab/nsp2564G564GggAggG11AY.16.10.00047
ORF1ab/nsp2564G564delGGA---11AY.190.00114
ORF1ab/nsp2564G564GggAggG11AY.230.00007
ORF1ab/nsp2564G564XGgaTga11AY.250.000006
ORF1ab/nsp2564G564RGgaAga11AY.250.000006
ORF1ab/nsp2564G564delGGA---11AY.30.00001
ORF1ab/nsp2564G564RGgaAga11AY.30.00001
ORF1ab/nsp2564G564GggAggG11AY.360.000148
ORF1ab/nsp2564G564VgGagTa11AY.390.000025
ORF1ab/nsp2564G564GggAggC11AY.39.10.00004
ORF1ab/nsp2564G564XGgaTga11AY.40.000002
ORF1ab/nsp2564G564GggAggG11AY.4.30.000842
ORF1ab/nsp2564G564delGGA---11AY.4.50.000107
ORF1ab/nsp2564G564delGGA---11AY.420.00004
ORF1ab/nsp2564G564IGGaATa11AY.430.000004
ORF1ab/nsp2564G564RGgaAga11AY.430.000004
ORF1ab/nsp2564G564EgGAgAG11AY.440.000006
ORF1ab/nsp2564G564delGGA---11AY.440.000006
ORF1ab/nsp2564G564GggAggG11AY.450.000122
ORF1ab/nsp2564G564delGGA---11AY.460.000104
ORF1ab/nsp2564G564GggAggC11AY.46.20.000635
ORF1ab/nsp2564G564XGgaTga11AY.46.50.000198
ORF1ab/nsp2564G564GggAggG11AY.46.60.000072
ORF1ab/nsp2564G564delGGA---11AY.46.60.000072
ORF1ab/nsp2564G564delGGA---11AY.50.000021
ORF1ab/nsp2564G564GggAggG11AY.50.000021
ORF1ab/nsp2564G564GggAggT11AY.5.10.003759
ORF1ab/nsp2564G564GggAggG11AY.540.000095
ORF1ab/nsp2564G564GggAggG11AY.550.000917
ORF1ab/nsp2564G564GggAggT11AY.590.00053
ORF1ab/nsp2564G564delGGA---11AY.60.000041
ORF1ab/nsp2564G564GggAggT11AY.650.000533
ORF1ab/nsp2564G564GggAggG11AY.680.000274
ORF1ab/nsp2564G564GggAggG11AY.750.000056
ORF1ab/nsp2564G564GggAggG11AY.780.001541
ORF1ab/nsp2564G564delGGA---11AY.840.000437
ORF1ab/nsp2564G564XGgaTga11AY.90.000068
ORF1ab/nsp2564G564delGGA---11AY.9.20.000037
ORF1ab/nsp2564G564GggAggG11AY.910.00073
ORF1ab/nsp2564G564GggAggT11AY.940.000443
ORF1ab/nsp2564G564GggAggT11AY.950.000761
ORF1ab/nsp2564G564GggAggG11AY.98.10.000048
ORF1ab/nsp2564G564delGGA---11AY.990.001049
ORF1ab/nsp2564G564RGgaAga11B0.000128
ORF1ab/nsp2564G564del1ggAgg-11B.10.000009
ORF1ab/nsp2564G564RGgaAga11B.10.000009
ORF1ab/nsp2564G564XGgaTga11B.10.000009
ORF1ab/nsp2564G564RGgaAga11B.1.10.000018
ORF1ab/nsp2564G564del2gGAg--11B.1.10.000018
ORF1ab/nsp2564G564GggAggG11B.1.1.3020.002075
ORF1ab/nsp2564G564GggAggT11B.1.1.3330.001076
ORF1ab/nsp2564G564delGGA---11B.1.1.4160.000905
ORF1ab/nsp2564G564delGGA---11B.1.1.4480.002033
ORF1ab/nsp2564G564XGgaTga11B.1.1.470.005348
ORF1ab/nsp2564G564VgGagTa11B.1.1.700.000341
ORF1ab/nsp2564G564DgGAgAC11B.1.1600.000031
ORF1ab/nsp2564G564GggAggT11B.1.1600.000031
ORF1ab/nsp2564G564GggAggG11B.1.160.300.002976
ORF1ab/nsp2564G564GggAggG11B.1.1630.02439
ORF1ab/nsp2564G564delGGA---11B.1.1770.000013
ORF1ab/nsp2564G564GggAggG11B.1.177.190.001431
ORF1ab/nsp2564G564delGGA---11B.1.177.430.001477
ORF1ab/nsp2564G564delGGA---11B.1.177.570.000281
ORF1ab/nsp2564G564GggAggC11B.1.177.650.000665
ORF1ab/nsp2564G564GggAggG11B.1.177.730.000566
ORF1ab/nsp2564G564GggAggG11B.1.177.830.001481
ORF1ab/nsp2564G564delGGA---11B.1.177.830.001481
ORF1ab/nsp2564G564GggAggT11B.1.177.860.000183
ORF1ab/nsp2564G564delGGA---11B.1.1790.003759
ORF1ab/nsp2564G564VgGagTa11B.1.20.000009
ORF1ab/nsp2564G564EgGAgAG11B.1.20.000009
ORF1ab/nsp2564G564VgGagTa11B.1.2210.000071
ORF1ab/nsp2564G564del1ggAgg-11B.1.2210.000071
ORF1ab/nsp2564G564delGGA---11B.1.2210.000071
ORF1ab/nsp2564G564GggAggG11B.1.2410.000812
ORF1ab/nsp2564G564GggAggG11B.1.2430.00007
ORF1ab/nsp2564G564RGgaCga11B.1.2580.000067
ORF1ab/nsp2564G564GggAggG11B.1.2580.000067
ORF1ab/nsp2564G564delGGA---11B.1.258.30.001675
ORF1ab/nsp2564G564GggAggG11B.1.3110.000275
ORF1ab/nsp2564G564AgGagCa11B.1.3490.000715
ORF1ab/nsp2564G564GggAggT11B.1.3500.002933
ORF1ab/nsp2564G564GggAggG11B.1.3510.00003
ORF1ab/nsp2564G564EgGagAa11B.1.360.000146
ORF1ab/nsp2564G564delGGA---11B.1.36.180.00042
ORF1ab/nsp2564G564delGGA---11B.1.36.380.001642
ORF1ab/nsp2564G564GggAggG11B.1.4220.000812
ORF1ab/nsp2564G564GggAggG11B.1.4990.00105
ORF1ab/nsp2564G564GggAggT11B.1.5260.000024
ORF1ab/nsp2564G564GggAggG11B.1.5450.014493
ORF1ab/nsp2564G564delGGA---11B.1.5610.000397
ORF1ab/nsp2564G564XGgaTga11B.1.5820.000491
ORF1ab/nsp2564G564XGgaTga11B.1.5950.000261
ORF1ab/nsp2564G564EgGAgAG11B.1.617.10.000129
ORF1ab/nsp2564G564delGGA---11B.1.617.30.002985
ORF1ab/nsp2564G564delGGA---11B.1.6210.000089
ORF1ab/nsp2564G564XGgaTga11B.1.6270.00202
ORF1ab/nsp2564G564GggAggG11B.1.6280.000352
ORF1ab/nsp2564G564GggAggT11B.230.002924
ORF1ab/nsp2564G564XGgaTga11B.270.015385
ORF1ab/nsp2564G564delGGA---11B.570.015152
ORF1ab/nsp2564G564GggAggC11C.370.000116
ORF1ab/nsp2564G564VgGagTa11C.370.000116
ORF1ab/nsp2564G564XGgaTga11D.20.000075
ORF1ab/nsp2564G564GggAggC11D.20.000075
ORF1ab/nsp2564G564VgGagTa11D.20.000075
ORF1ab/nsp2564G564delGGA---11P.10.000016
ORF1ab/nsp2564G564FGGATTT11P.10.000016
ORF1ab/nsp2564G564VgGagTa11P.1.10.000318
ORF1ab/nsp2564G564GggAggG11P.1.140.000048
ORF1ab/nsp2564G564GggAggG11P.1.150.000232
ORF1ab/nsp2564G564GggAggG11P.1.20.001156
ORF1ab/nsp2564G564delGGA---11P.20.000187

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.