CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 39

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/nsp339C39CC857CsyntgCtgT2476247612834-2836
ORF1ab/nsp339C39XC857XnonsyntgCtgA45440.9777782834-2836
ORF1ab/nsp339C39XC857XnonsyntGCtAA4510.02222222834-2836
ORF1ab/nsp339C39delC857deldelTGC---404012834-2836
ORF1ab/nsp339C39FC857FnonsyntGctTc19180.9473682834-2836
ORF1ab/nsp339C39FC857FnonsyntGCtTT1910.05263162834-2836
ORF1ab/nsp339C39GC857GnonsynTgcGgc11100.9090912834-2836
ORF1ab/nsp339C39RC857RnonsynTgcCgc11100.9090912834-2836
ORF1ab/nsp339C39GC857GnonsynTgCGgT1110.09090912834-2836
ORF1ab/nsp339C39RC857RnonsynTgCAgA1110.09090912834-2836
ORF1ab/nsp339C39YC857YnonsyntGctAc760.8571432834-2836
ORF1ab/nsp339C39SC857SnonsynTgcAgc730.4285712834-2836
ORF1ab/nsp339C39SC857SnonsyntGctCc730.4285712834-2836
ORF1ab/nsp339C39SC857SnonsynTgCAgT710.1428572834-2836
ORF1ab/nsp339C39YC857YnonsyntGCtAT710.1428572834-2836
ORF1ab/nsp339C39del1C857del1deltgCtg-6612834-2836
ORF1ab/nsp339C39LC857LnonsyntGCtTA420.52834-2836
ORF1ab/nsp339C39LC857LnonsynTGCCTG410.252834-2836
ORF1ab/nsp339C39LC857LnonsynTGcCTc410.252834-2836
ORF1ab/nsp339C39HC857HnonsynTGcCAc2212834-2836
ORF1ab/nsp339C39VC857VnonsynTGCGTT210.52834-2836
ORF1ab/nsp339C39VC857VnonsynTGcGTc210.52834-2836
ORF1ab/nsp339C39IC857InonsynTGcATc210.52834-2836
ORF1ab/nsp339C39IC857InonsynTGCATT210.52834-2836
ORF1ab/nsp339C39AC857AnonsynTGCGCT1112834-2836
ORF1ab/nsp339C39WC857WnonsyntgCtgG1112834-2836

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/nsp339C39CtgCtgT24762476All0.000474
ORF1ab/nsp339C39CtgCtgT916916B.1.36.80.916
ORF1ab/nsp339C39CtgCtgT349349B.1.36.260.997143
ORF1ab/nsp339C39CtgCtgT188188B.1.36.310.329247
ORF1ab/nsp339C39CtgCtgT123123B.1.20.001083
ORF1ab/nsp339C39CtgCtgT107107B.1.1.70.000096
ORF1ab/nsp339C39CtgCtgT6363B.1.617.20.000237
ORF1ab/nsp339C39CtgCtgT5959B.1.1130.921875
ORF1ab/nsp339C39CtgCtgT5454AY.1030.000335
ORF1ab/nsp339C39CtgCtgT5353AY.40.000082
ORF1ab/nsp339C39XtgCtgA4445All0.000008
ORF1ab/nsp339C39XtGCtAA145All0
ORF1ab/nsp339C39CtgCtgT4343B.1.1770.000566
ORF1ab/nsp339C39CtgCtgT4141B.10.000376
ORF1ab/nsp339C39delTGC---4040All0.000008
ORF1ab/nsp339C39CtgCtgT3939AY.250.000235
ORF1ab/nsp339C39CtgCtgT3838AY.440.000231
ORF1ab/nsp339C39CtgCtgT3434AY.430.000151
ORF1ab/nsp339C39CtgCtgT2929B.1.360.004231
ORF1ab/nsp339C39CtgCtgT2323AY.30.000229
ORF1ab/nsp339C39XtgCtgA2222B.1.1.70.00002
ORF1ab/nsp339C39FtGctTc1819All0.000003
ORF1ab/nsp339C39FtGCtTT119All0
ORF1ab/nsp339C39CtgCtgT1919B.1.10.000345
ORF1ab/nsp339C39CtgCtgT1212B.1.1.500.008147
ORF1ab/nsp339C39GTgcGgc1011All0.000002
ORF1ab/nsp339C39RTgcCgc1011All0.000002
ORF1ab/nsp339C39GTgCGgT111All0
ORF1ab/nsp339C39RTgCAgA111All0
ORF1ab/nsp339C39CtgCtgT99AY.390.000222
ORF1ab/nsp339C39CtgCtgT99B.1.1840.529412
ORF1ab/nsp339C39CtgCtgT88B.1.2470.119403
ORF1ab/nsp339C39CtgCtgT88B.1.2580.000532
ORF1ab/nsp339C39YtGctAc67All0.000001
ORF1ab/nsp339C39StGctCc37All0.000001
ORF1ab/nsp339C39STgcAgc37All0.000001
ORF1ab/nsp339C39YtGCtAT17All0
ORF1ab/nsp339C39STgCAgT17All0
ORF1ab/nsp339C39CtgCtgT77AY.370.002212
ORF1ab/nsp339C39CtgCtgT77AY.98.10.000339
ORF1ab/nsp339C39CtgCtgT77B.1.1.3170.002882
ORF1ab/nsp339C39CtgCtgT77B.1.1.5190.000278
ORF1ab/nsp339C39XtgCtgA77B.1.1770.000092
ORF1ab/nsp339C39CtgCtgT77B.1.5260.000165
ORF1ab/nsp339C39del1tgCtg-66All0.000001
ORF1ab/nsp339C39CtgCtgT66B.1.36.100.028708
ORF1ab/nsp339C39CtgCtgT66B.1.36.170.002964
ORF1ab/nsp339C39CtgCtgT66B.1.4620.043478
ORF1ab/nsp339C39CtgCtgT66B.1.6210.000531
ORF1ab/nsp339C39CtgCtgT66Q.10.000758
ORF1ab/nsp339C39CtgCtgT55AY.1000.00023
ORF1ab/nsp339C39CtgCtgT55AY.1020.000133
ORF1ab/nsp339C39CtgCtgT55B0.000639
ORF1ab/nsp339C39delTGC---55B.10.000046
ORF1ab/nsp339C39CtgCtgT55B.1.4290.000118
ORF1ab/nsp339C39CtgCtgT55B.1.4560.01634
ORF1ab/nsp339C39delTGC---440.222222
ORF1ab/nsp339C39FtGctTc340.166667
ORF1ab/nsp339C39FtGCtTT140.055556
ORF1ab/nsp339C39LtGCtTA24All0
ORF1ab/nsp339C39LTGCCTG14All0
ORF1ab/nsp339C39LTGcCTc14All0
ORF1ab/nsp339C39CtgCtgT44AY.230.000279
ORF1ab/nsp339C39CtgCtgT44AY.90.00027
ORF1ab/nsp339C39CtgCtgT44B.1.1.4040.063492
ORF1ab/nsp339C39delTGC---44B.1.1.70.000004
ORF1ab/nsp339C39CtgCtgT44B.1.1600.000125
ORF1ab/nsp339C39CtgCtgT44B.1.177.410.01
ORF1ab/nsp339C39CtgCtgT44D.20.0003
ORF1ab/nsp339C39CtgCtgT44P.10.000063
ORF1ab/nsp339C39XtgCtgA330.166667
ORF1ab/nsp339C39CtgCtgT330.166667
ORF1ab/nsp339C39CtgCtgT33A0.001161
ORF1ab/nsp339C39CtgCtgT33AY.260.000085
ORF1ab/nsp339C39CtgCtgT33AY.330.0002
ORF1ab/nsp339C39XtgCtgA33AY.40.000005
ORF1ab/nsp339C39CtgCtgT33AY.50.000062
ORF1ab/nsp339C39CtgCtgT33AY.700.000626
ORF1ab/nsp339C39CtgCtgT33AY.720.004082
ORF1ab/nsp339C39CtgCtgT33AY.9.10.000251
ORF1ab/nsp339C39CtgCtgT33AY.9.20.00011
ORF1ab/nsp339C39delTGC---33B.1.1.330.001263
ORF1ab/nsp339C39delTGC---33B.1.1.3480.002389
ORF1ab/nsp339C39GTgcGgc33B.1.1.70.000003
ORF1ab/nsp339C39CtgCtgT33B.1.1430.06383
ORF1ab/nsp339C39XtgCtgA23B.1.2210.000142
ORF1ab/nsp339C39XtGCtAA13B.1.2210.000071
ORF1ab/nsp339C39HTGcCAc220.111111
ORF1ab/nsp339C39LtGCtTA220.111111
ORF1ab/nsp339C39VTGCGTT120.055556
ORF1ab/nsp339C39VTGcGTc120.055556
ORF1ab/nsp339C39GTgCGgT120.055556
ORF1ab/nsp339C39STgcAgc120.055556
ORF1ab/nsp339C39ITGcATc120.055556
ORF1ab/nsp339C39GTgcGgc120.055556
ORF1ab/nsp339C39STgCAgT120.055556
ORF1ab/nsp339C39ITGCATT120.055556
ORF1ab/nsp339C39HTGcCAc22All0
ORF1ab/nsp339C39VTGCGTT12All0
ORF1ab/nsp339C39ITGCATT12All0
ORF1ab/nsp339C39ITGcATc12All0
ORF1ab/nsp339C39VTGcGTc12All0
ORF1ab/nsp339C39CtgCtgT22AY.1060.00067
ORF1ab/nsp339C39CtgCtgT22AY.1200.000074
ORF1ab/nsp339C39CtgCtgT22AY.200.000078
ORF1ab/nsp339C39CtgCtgT22AY.3.10.000171
ORF1ab/nsp339C39CtgCtgT22AY.340.000194
ORF1ab/nsp339C39RTgcCgc22AY.40.000003
ORF1ab/nsp339C39CtgCtgT22AY.450.000243
ORF1ab/nsp339C39FtGctTc22B.1.10.000036
ORF1ab/nsp339C39delTGC---22B.1.10.000036
ORF1ab/nsp339C39CtgCtgT22B.1.1.2370.010811
ORF1ab/nsp339C39CtgCtgT22B.1.1.280.000622
ORF1ab/nsp339C39CtgCtgT22B.1.177.210.000153
ORF1ab/nsp339C39XtgCtgA22B.1.177.330.003289
ORF1ab/nsp339C39CtgCtgT22B.1.177.600.000437
ORF1ab/nsp339C39CtgCtgT22B.1.2210.000142
ORF1ab/nsp339C39YtGCtAT12B.1.2210.000071
ORF1ab/nsp339C39YtGctAc12B.1.2210.000071
ORF1ab/nsp339C39CtgCtgT22B.1.3510.000059
ORF1ab/nsp339C39CtgCtgT22B.1.36.290.001035
ORF1ab/nsp339C39delTGC---22B.1.4240.016129
ORF1ab/nsp339C39CtgCtgT22B.1.4270.000101
ORF1ab/nsp339C39delTGC---22B.1.4290.000047
ORF1ab/nsp339C39CtgCtgT22B.1.438.10.000215
ORF1ab/nsp339C39CtgCtgT22B.1.5750.000607
ORF1ab/nsp339C39CtgCtgT22B.1.5960.000174
ORF1ab/nsp339C39CtgCtgT22C.370.000232
ORF1ab/nsp339C39delTGC---22N.60.014184
ORF1ab/nsp339C39delTGC---22P.10.000032
ORF1ab/nsp339C39CtgCtgT22P.1.160.000748
ORF1ab/nsp339C39CtgCtgT22Q.40.00091
ORF1ab/nsp339C39CtgCtgT11A.10.000282
ORF1ab/nsp339C39WtgCtgG11All0
ORF1ab/nsp339C39ATGCGCT11All0
ORF1ab/nsp339C39FtGctTc11AY.1030.000006
ORF1ab/nsp339C39CtgCtgT11AY.1050.000643
ORF1ab/nsp339C39CtgCtgT11AY.1140.000231
ORF1ab/nsp339C39CtgCtgT11AY.1160.000287
ORF1ab/nsp339C39CtgCtgT11AY.1180.000063
ORF1ab/nsp339C39CtgCtgT11AY.1190.000035
ORF1ab/nsp339C39CtgCtgT11AY.16.10.00047
ORF1ab/nsp339C39CtgCtgT11AY.20.000356
ORF1ab/nsp339C39CtgCtgT11AY.300.000396
ORF1ab/nsp339C39FtGctTc11AY.330.000067
ORF1ab/nsp339C39CtgCtgT11AY.360.000148
ORF1ab/nsp339C39CtgCtgT11AY.380.000499
ORF1ab/nsp339C39CtgCtgT11AY.39.20.001541
ORF1ab/nsp339C39StGctCc11AY.40.000002
ORF1ab/nsp339C39FtGctTc11AY.40.000002
ORF1ab/nsp339C39CtgCtgT11AY.4.20.000022
ORF1ab/nsp339C39FtGctTc11AY.4.2.10.000149
ORF1ab/nsp339C39CtgCtgT11AY.4.2.10.000149
ORF1ab/nsp339C39STgcAgc11AY.420.00004
ORF1ab/nsp339C39XtgCtgA11AY.430.000004
ORF1ab/nsp339C39STgcAgc11AY.430.000004
ORF1ab/nsp339C39YtGctAc11AY.430.000004
ORF1ab/nsp339C39delTGC---11AY.430.000004
ORF1ab/nsp339C39YtGctAc11AY.440.000006
ORF1ab/nsp339C39RTgcCgc11AY.440.000006
ORF1ab/nsp339C39FtGctTc11AY.460.000104
ORF1ab/nsp339C39CtgCtgT11AY.46.40.000165
ORF1ab/nsp339C39CtgCtgT11AY.470.000031
ORF1ab/nsp339C39CtgCtgT11AY.540.000095
ORF1ab/nsp339C39CtgCtgT11AY.550.000917
ORF1ab/nsp339C39delTGC---11AY.60.000041
ORF1ab/nsp339C39CtgCtgT11AY.60.000041
ORF1ab/nsp339C39CtgCtgT11AY.610.000105
ORF1ab/nsp339C39CtgCtgT11AY.620.000436
ORF1ab/nsp339C39CtgCtgT11AY.650.000533
ORF1ab/nsp339C39CtgCtgT11AY.680.000274
ORF1ab/nsp339C39YtGctAc11AY.790.001211
ORF1ab/nsp339C39CtgCtgT11AY.790.001211
ORF1ab/nsp339C39delTGC---11AY.9.20.000037
ORF1ab/nsp339C39RTgcCgc11B0.000128
ORF1ab/nsp339C39FtGctTc11B0.000128
ORF1ab/nsp339C39WtgCtgG11B.10.000009
ORF1ab/nsp339C39LTGCCTG11B.10.000009
ORF1ab/nsp339C39XtgCtgA11B.10.000009
ORF1ab/nsp339C39YtGctAc11B.10.000009
ORF1ab/nsp339C39FtGctTc11B.10.000009
ORF1ab/nsp339C39del1tgCtg-11B.1.10.000018
ORF1ab/nsp339C39XtgCtgA11B.1.10.000018
ORF1ab/nsp339C39GTgcGgc11B.1.10.000018
ORF1ab/nsp339C39CtgCtgT11B.1.1.10.000327
ORF1ab/nsp339C39StGctCc11B.1.1.1530.001095
ORF1ab/nsp339C39CtgCtgT11B.1.1.160.055556
ORF1ab/nsp339C39CtgCtgT11B.1.1.1980.001468
ORF1ab/nsp339C39CtgCtgT11B.1.1.2160.00089
ORF1ab/nsp339C39CtgCtgT11B.1.1.2210.010101
ORF1ab/nsp339C39GTgcGgc11B.1.1.250.000569
ORF1ab/nsp339C39CtgCtgT11B.1.1.3030.002762
ORF1ab/nsp339C39CtgCtgT11B.1.1.3060.000438
ORF1ab/nsp339C39CtgCtgT11B.1.1.3180.000302
ORF1ab/nsp339C39CtgCtgT11B.1.1.3260.001761
ORF1ab/nsp339C39CtgCtgT11B.1.1.3690.000446
ORF1ab/nsp339C39CtgCtgT11B.1.1.370.000193
ORF1ab/nsp339C39delTGC---11B.1.1.4160.000905
ORF1ab/nsp339C39CtgCtgT11B.1.1.4190.007407
ORF1ab/nsp339C39RTgCAgA11B.1.1.460.004367
ORF1ab/nsp339C39delTGC---11B.1.1.460.004367
ORF1ab/nsp339C39CtgCtgT11B.1.1.4640.001473
ORF1ab/nsp339C39YtGctAc11B.1.1.500.000679
ORF1ab/nsp339C39LTGcCTc11B.1.1.5190.00004
ORF1ab/nsp339C39RTgcCgc11B.1.1.5190.00004
ORF1ab/nsp339C39FtGctTc11B.1.1.5190.00004
ORF1ab/nsp339C39CtgCtgT11B.1.1.5230.001563
ORF1ab/nsp339C39CtgCtgT11B.1.1.5260.003546
ORF1ab/nsp339C39CtgCtgT11B.1.1.630.000386
ORF1ab/nsp339C39del1tgCtg-11B.1.1.70.000001
ORF1ab/nsp339C39RTgcCgc11B.1.1.70.000001
ORF1ab/nsp339C39FtGctTc11B.1.1.70.000001
ORF1ab/nsp339C39delTGC---11B.1.1.700.000341
ORF1ab/nsp339C39CtgCtgT11B.1.1.700.000341
ORF1ab/nsp339C39CtgCtgT11B.1.1040.00369
ORF1ab/nsp339C39GTgcGgc11B.1.1600.000031
ORF1ab/nsp339C39CtgCtgT11B.1.160.160.000929
ORF1ab/nsp339C39RTgcCgc11B.1.1770.000013
ORF1ab/nsp339C39FtGctTc11B.1.1770.000013
ORF1ab/nsp339C39delTGC---11B.1.177.510.004566
ORF1ab/nsp339C39CtgCtgT11B.1.177.580.001332
ORF1ab/nsp339C39CtgCtgT11B.1.177.60.000977
ORF1ab/nsp339C39CtgCtgT11B.1.177.810.000189
ORF1ab/nsp339C39StGctCc11B.1.20.000009
ORF1ab/nsp339C39delTGC---11B.1.20.000009
ORF1ab/nsp339C39RTgcCgc11B.1.20.000009
ORF1ab/nsp339C39CtgCtgT11B.1.221.30.000833
ORF1ab/nsp339C39CtgCtgT11B.1.2320.000537
ORF1ab/nsp339C39del1tgCtg-11B.1.2470.014925
ORF1ab/nsp339C39XtgCtgA11B.1.258.140.00098
ORF1ab/nsp339C39CtgCtgT11B.1.258.170.000104
ORF1ab/nsp339C39FtGctTc11B.1.3110.000275
ORF1ab/nsp339C39CtgCtgT11B.1.351.30.000876
ORF1ab/nsp339C39CtgCtgT11B.1.36.160.001425
ORF1ab/nsp339C39del1tgCtg-11B.1.36.80.001
ORF1ab/nsp339C39CtgCtgT11B.1.466.20.000391
ORF1ab/nsp339C39CtgCtgT11B.1.5090.000866
ORF1ab/nsp339C39CtgCtgT11B.1.5330.009615
ORF1ab/nsp339C39CtgCtgT11B.1.5370.02
ORF1ab/nsp339C39CtgCtgT11B.1.5510.00129
ORF1ab/nsp339C39delTGC---11B.1.5610.000397
ORF1ab/nsp339C39CtgCtgT11B.1.575.20.004808
ORF1ab/nsp339C39RTgcCgc11B.1.5820.000491
ORF1ab/nsp339C39GTgcGgc11B.1.5880.00091
ORF1ab/nsp339C39FtGctTc11B.1.5950.000261
ORF1ab/nsp339C39CtgCtgT11B.1.6020.006536
ORF1ab/nsp339C39del1tgCtg-11B.1.617.10.000129
ORF1ab/nsp339C39XtgCtgA11B.1.617.10.000129
ORF1ab/nsp339C39ATGCGCT11B.1.617.20.000004
ORF1ab/nsp339C39delTGC---11B.1.617.20.000004
ORF1ab/nsp339C39FtGctTc11B.1.617.20.000004
ORF1ab/nsp339C39CtgCtgT11B.1.6200.000946
ORF1ab/nsp339C39CtgCtgT11B.400.000364
ORF1ab/nsp339C39delTGC---11B.570.015152
ORF1ab/nsp339C39GTgcGgc11B.570.015152
ORF1ab/nsp339C39GTgcGgc11D.20.000075
ORF1ab/nsp339C39CtgCtgT11N.30.005814
ORF1ab/nsp339C39del1tgCtg-11P.10.000016
ORF1ab/nsp339C39CtgCtgT11P.1.150.000232
ORF1ab/nsp339C39CtgCtgT11P.1.70.000319
ORF1ab/nsp339C39CtgCtgT11P.20.000187
ORF1ab/nsp339C39RTgcCgc11Q.20.000613

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.