CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1010

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/nsp31010T1010AT1828AnonsynActGct1797179715747-5749
ORF1ab/nsp31010T1010TT1828TsynacTacC6706390.9537315747-5749
ORF1ab/nsp31010T1010TT1828TsynacTacG670160.02388065747-5749
ORF1ab/nsp31010T1010TT1828TsynacTacA670150.02238815747-5749
ORF1ab/nsp31010T1010IT1828InonsynaCtaTt5265190.9866925747-5749
ORF1ab/nsp31010T1010IT1828InonsynaCTaTC52650.00950575747-5749
ORF1ab/nsp31010T1010IT1828InonsynaCTaTA52620.003802285747-5749
ORF1ab/nsp31010T1010NT1828NnonsynaCtaAt3293280.996965747-5749
ORF1ab/nsp31010T1010NT1828NnonsynaCTaAC32910.003039515747-5749
ORF1ab/nsp31010T1010delT1828deldelACT---181815747-5749
ORF1ab/nsp31010T1010ST1828SnonsynActTct420.55747-5749
ORF1ab/nsp31010T1010ST1828SnonsynaCtaGt420.55747-5749
ORF1ab/nsp31010T1010LT1828LnonsynACTCTA210.55747-5749
ORF1ab/nsp31010T1010LT1828LnonsynACTCTC210.55747-5749
ORF1ab/nsp31010T1010KT1828KnonsynaCTaAA1115747-5749
ORF1ab/nsp31010T1010VT1828VnonsynACTGTC1115747-5749
ORF1ab/nsp31010T1010del1T1828del1delaCta-t1115747-5749
ORF1ab/nsp31010T1010HT1828HnonsynACTCAC1115747-5749
ORF1ab/nsp31010T1010QT1828QnonsynACTCAA1115747-5749

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/nsp31010T1010AActGct17971797All0.000344
ORF1ab/nsp31010T1010AActGct969969B.1.3750.794262
ORF1ab/nsp31010T1010TacTacC639670All0.000122
ORF1ab/nsp31010T1010TacTacG16670All0.000003
ORF1ab/nsp31010T1010TacTacA15670All0.000003
ORF1ab/nsp31010T1010AActGct642642B.1.1.70.000575
ORF1ab/nsp31010T1010TacTacC560560B.1.6370.040921
ORF1ab/nsp31010T1010IaCtaTt519526All0.000099
ORF1ab/nsp31010T1010IaCTaTC5526All0.000001
ORF1ab/nsp31010T1010IaCTaTA2526All0
ORF1ab/nsp31010T1010NaCtaAt328329All0.000063
ORF1ab/nsp31010T1010NaCTaAC1329All0
ORF1ab/nsp31010T1010NaCtaAt128128B.1.4290.003012
ORF1ab/nsp31010T1010IaCtaTt113113B.1.4290.002659
ORF1ab/nsp31010T1010IaCtaTt9494AY.40.000146
ORF1ab/nsp31010T1010AActGct7575AY.250.000451
ORF1ab/nsp31010T1010NaCtaAt7272AY.40.000112
ORF1ab/nsp31010T1010IaCtaTt4444B.1.1.3680.135802
ORF1ab/nsp31010T1010IaCtaTt4141B.1.1.5210.219251
ORF1ab/nsp31010T1010AActGct2727B.1.36.210.058315
ORF1ab/nsp31010T1010IaCtaTt2525B.1.1.70.000022
ORF1ab/nsp31010T1010NaCtaAt2222B.1.1.70.00002
ORF1ab/nsp31010T1010AActGct2121B.10.000192
ORF1ab/nsp31010T1010NaCtaAt2020B.1.617.20.000075
ORF1ab/nsp31010T1010TacTacC819B.1.1.70.000007
ORF1ab/nsp31010T1010TacTacA719B.1.1.70.000006
ORF1ab/nsp31010T1010TacTacG419B.1.1.70.000004
ORF1ab/nsp31010T1010delACT---1818All0.000003
ORF1ab/nsp31010T1010IaCtaTt1616B.1.160.300.047619
ORF1ab/nsp31010T1010IaCtaTt1616B.1.3510.000476
ORF1ab/nsp31010T1010IaCtaTt1515B.10.000137
ORF1ab/nsp31010T1010NaCtaAt1414B.1.1770.000184
ORF1ab/nsp31010T1010TacTacC1313P.10.000205
ORF1ab/nsp31010T1010NaCtaAt1212AY.1030.000075
ORF1ab/nsp31010T1010IaCtaTt1212B.1.1.5190.000477
ORF1ab/nsp31010T1010IaCtaTt1212B.1.5960.001046
ORF1ab/nsp31010T1010TacTacC1212B.1.617.20.000045
ORF1ab/nsp31010T1010AActGct1111B.1.3510.000327
ORF1ab/nsp31010T1010AActGct1010AY.430.000044
ORF1ab/nsp31010T1010IaCtaTt1010B.1.36.160.014245
ORF1ab/nsp31010T1010NaCtaAt1010B.1.5250.001132
ORF1ab/nsp31010T1010IaCtaTt1010B.1.5650.008104
ORF1ab/nsp31010T1010TacTacC69B.10.000055
ORF1ab/nsp31010T1010TacTacG29B.10.000018
ORF1ab/nsp31010T1010TacTacA19B.10.000009
ORF1ab/nsp31010T1010IaCtaTt77AY.1030.000043
ORF1ab/nsp31010T1010IaCtaTt77B.1.1.2190.035
ORF1ab/nsp31010T1010TacTacC77B.1.1.250.00398
ORF1ab/nsp31010T1010IaCtaTt66AY.430.000027
ORF1ab/nsp31010T1010NaCtaAt66AY.430.000027
ORF1ab/nsp31010T1010delACT---66B.1.1.70.000005
ORF1ab/nsp31010T1010IaCtaTt55AY.790.006053
ORF1ab/nsp31010T1010IaCtaTt55B.1.10.000091
ORF1ab/nsp31010T1010IaCtaTt55B.1.1600.000156
ORF1ab/nsp31010T1010TacTacC45B.1.20.000035
ORF1ab/nsp31010T1010TacTacG15B.1.20.000009
ORF1ab/nsp31010T1010TacTacC55B.1.36.290.002587
ORF1ab/nsp31010T1010NaCtaAt55B.1.4270.000252
ORF1ab/nsp31010T1010AActGct55B.1.617.20.000019
ORF1ab/nsp31010T1010SaCtaGt24All0
ORF1ab/nsp31010T1010SActTct24All0
ORF1ab/nsp31010T1010TacTacC44AY.1030.000025
ORF1ab/nsp31010T1010IaCtaTt44AY.390.000099
ORF1ab/nsp31010T1010AActGct44AY.40.000006
ORF1ab/nsp31010T1010TacTacC44AY.430.000018
ORF1ab/nsp31010T1010IaCtaTt44AY.50.000083
ORF1ab/nsp31010T1010NaCtaAt44B.1.1.2840.00043
ORF1ab/nsp31010T1010NaCtaAt44B.1.20.000035
ORF1ab/nsp31010T1010AActGct44B.1.3670.00317
ORF1ab/nsp31010T1010AActGct44B.1.5650.003241
ORF1ab/nsp31010T1010IaCtaTt44B.1.617.20.000015
ORF1ab/nsp31010T1010IaCtaTt44B.1.6370.000292
ORF1ab/nsp31010T1010IaCTaTC24P.10.000032
ORF1ab/nsp31010T1010IaCtaTt24P.10.000032
ORF1ab/nsp31010T1010AActGct33AY.1030.000019
ORF1ab/nsp31010T1010NaCtaAt33AY.1070.001398
ORF1ab/nsp31010T1010IaCtaTt33AY.230.000209
ORF1ab/nsp31010T1010TacTacC23AY.3.10.000171
ORF1ab/nsp31010T1010TacTacA13AY.3.10.000085
ORF1ab/nsp31010T1010NaCtaAt33AY.380.001498
ORF1ab/nsp31010T1010TacTacC23AY.40.000003
ORF1ab/nsp31010T1010TacTacG13AY.40.000002
ORF1ab/nsp31010T1010AActGct33AY.460.000312
ORF1ab/nsp31010T1010IaCtaTt33AY.460.000312
ORF1ab/nsp31010T1010IaCtaTt33B.1.20.000026
ORF1ab/nsp31010T1010IaCtaTt33P.1.140.000143
ORF1ab/nsp31010T1010LACTCTC12All0
ORF1ab/nsp31010T1010LACTCTA12All0
ORF1ab/nsp31010T1010IaCTaTC22AY.1010.000981
ORF1ab/nsp31010T1010NaCtaAt22AY.1020.000053
ORF1ab/nsp31010T1010IaCtaTt22AY.1020.000053
ORF1ab/nsp31010T1010NaCtaAt22AY.250.000012
ORF1ab/nsp31010T1010IaCtaTt22AY.250.000012
ORF1ab/nsp31010T1010IaCtaTt22AY.30.00002
ORF1ab/nsp31010T1010IaCtaTt22AY.440.000012
ORF1ab/nsp31010T1010TacTacG22AY.460.000208
ORF1ab/nsp31010T1010TacTacG22AY.470.000062
ORF1ab/nsp31010T1010SaCtaGt22B.10.000018
ORF1ab/nsp31010T1010IaCtaTt22B.1.1.2140.000111
ORF1ab/nsp31010T1010IaCtaTt22B.1.1.330.000842
ORF1ab/nsp31010T1010AActGct22B.1.20.000018
ORF1ab/nsp31010T1010delACT---22B.1.360.000292
ORF1ab/nsp31010T1010AActGct22B.1.4270.000101
ORF1ab/nsp31010T1010IaCtaTt22B.1.5250.000226
ORF1ab/nsp31010T1010NaCtaAt22B.1.5260.000047
ORF1ab/nsp31010T1010IaCtaTt22B.1.6090.000959
ORF1ab/nsp31010T1010IaCtaTt22B.1.621.10.001012
ORF1ab/nsp31010T1010LACTCTA12P.1.150.000232
ORF1ab/nsp31010T1010LACTCTC12P.1.150.000232
ORF1ab/nsp31010T1010IaCTaTC12P.1.150.000232
ORF1ab/nsp31010T1010IaCTaTA12P.1.150.000232
ORF1ab/nsp31010T1010TacTacG22P.20.000373
ORF1ab/nsp31010T1010NaCtaAt110.055556
ORF1ab/nsp31010T1010delACT---11A.2.20.001689
ORF1ab/nsp31010T1010QACTCAA11All0
ORF1ab/nsp31010T1010KaCTaAA11All0
ORF1ab/nsp31010T1010VACTGTC11All0
ORF1ab/nsp31010T1010del1aCta-t11All0
ORF1ab/nsp31010T1010HACTCAC11All0
ORF1ab/nsp31010T1010IaCtaTt11AY.100.00053
ORF1ab/nsp31010T1010AActGct11AY.1020.000027
ORF1ab/nsp31010T1010IaCtaTt11AY.1070.000466
ORF1ab/nsp31010T1010AActGct11AY.140.000088
ORF1ab/nsp31010T1010NaCtaAt11AY.190.00114
ORF1ab/nsp31010T1010NaCtaAt11AY.23.10.000417
ORF1ab/nsp31010T1010TacTacG11AY.240.000431
ORF1ab/nsp31010T1010IaCtaTt11AY.260.000028
ORF1ab/nsp31010T1010IaCtaTt11AY.270.000065
ORF1ab/nsp31010T1010TacTacC11AY.30.00001
ORF1ab/nsp31010T1010TacTacC11AY.330.000067
ORF1ab/nsp31010T1010NaCtaAt11AY.330.000067
ORF1ab/nsp31010T1010NaCtaAt11AY.34.10.00051
ORF1ab/nsp31010T1010AActGct11AY.390.000025
ORF1ab/nsp31010T1010TacTacA11AY.390.000025
ORF1ab/nsp31010T1010NaCtaAt11AY.39.20.001541
ORF1ab/nsp31010T1010IaCtaTt11AY.4.20.000022
ORF1ab/nsp31010T1010NaCtaAt11AY.4.50.000107
ORF1ab/nsp31010T1010NaCtaAt11AY.420.00004
ORF1ab/nsp31010T1010TacTacA11AY.420.00004
ORF1ab/nsp31010T1010NaCtaAt11AY.440.000006
ORF1ab/nsp31010T1010AActGct11AY.450.000122
ORF1ab/nsp31010T1010NaCtaAt11AY.460.000104
ORF1ab/nsp31010T1010IaCtaTt11AY.470.000031
ORF1ab/nsp31010T1010del1aCta-t11AY.480.000465
ORF1ab/nsp31010T1010IaCtaTt11AY.540.000095
ORF1ab/nsp31010T1010TacTacC11AY.610.000105
ORF1ab/nsp31010T1010IaCTaTA11AY.620.000436
ORF1ab/nsp31010T1010IaCtaTt11AY.680.000274
ORF1ab/nsp31010T1010TacTacA11AY.690.000187
ORF1ab/nsp31010T1010IaCtaTt11AY.740.000116
ORF1ab/nsp31010T1010delACT---11AY.750.000056
ORF1ab/nsp31010T1010TacTacC11AY.75.10.00018
ORF1ab/nsp31010T1010delACT---11AY.850.000427
ORF1ab/nsp31010T1010AActGct11AY.90.000068
ORF1ab/nsp31010T1010AActGct11AY.98.10.000048
ORF1ab/nsp31010T1010AActGct11AY.99.20.000092
ORF1ab/nsp31010T1010delACT---11B0.000128
ORF1ab/nsp31010T1010IaCtaTt11B0.000128
ORF1ab/nsp31010T1010NaCtaAt11B.10.000009
ORF1ab/nsp31010T1010TacTacC11B.1.10.000018
ORF1ab/nsp31010T1010AActGct11B.1.10.000018
ORF1ab/nsp31010T1010AActGct11B.1.1.100.001115
ORF1ab/nsp31010T1010delACT---11B.1.1.1390.022727
ORF1ab/nsp31010T1010delACT---11B.1.1.1420.017544
ORF1ab/nsp31010T1010IaCtaTt11B.1.1.2290.005747
ORF1ab/nsp31010T1010IaCtaTt11B.1.1.250.000569
ORF1ab/nsp31010T1010IaCtaTt11B.1.1.2540.011236
ORF1ab/nsp31010T1010TacTacA11B.1.1.3060.000438
ORF1ab/nsp31010T1010IaCtaTt11B.1.1.3440.010753
ORF1ab/nsp31010T1010TacTacA11B.1.1.5190.00004
ORF1ab/nsp31010T1010NaCtaAt11B.1.1.5190.00004
ORF1ab/nsp31010T1010TacTacC11B.1.1770.000013
ORF1ab/nsp31010T1010IaCtaTt11B.1.177.730.000566
ORF1ab/nsp31010T1010NaCtaAt11B.1.2210.000071
ORF1ab/nsp31010T1010IaCtaTt11B.1.2430.00007
ORF1ab/nsp31010T1010IaCtaTt11B.1.2580.000067
ORF1ab/nsp31010T1010IaCtaTt11B.1.3240.001605
ORF1ab/nsp31010T1010TacTacC11B.1.3510.00003
ORF1ab/nsp31010T1010IaCtaTt11B.1.351.30.000876
ORF1ab/nsp31010T1010AActGct11B.1.3700.008
ORF1ab/nsp31010T1010NaCtaAt11B.1.3770.004566
ORF1ab/nsp31010T1010NaCtaAt11B.1.3960.000706
ORF1ab/nsp31010T1010TacTacC11B.1.4090.000781
ORF1ab/nsp31010T1010TacTacC11B.1.4270.00005
ORF1ab/nsp31010T1010IaCtaTt11B.1.4270.00005
ORF1ab/nsp31010T1010IaCtaTt11B.1.4970.000315
ORF1ab/nsp31010T1010AActGct11B.1.5170.000427
ORF1ab/nsp31010T1010TacTacA11B.1.5250.000113
ORF1ab/nsp31010T1010IaCtaTt11B.1.5260.000024
ORF1ab/nsp31010T1010TacTacC11B.1.5260.000024
ORF1ab/nsp31010T1010AActGct11B.1.5260.000024
ORF1ab/nsp31010T1010TacTacG11B.1.5610.000397
ORF1ab/nsp31010T1010NaCtaAt11B.1.5750.000303
ORF1ab/nsp31010T1010NaCtaAt11B.1.5960.000087
ORF1ab/nsp31010T1010AActGct11B.1.5960.000087
ORF1ab/nsp31010T1010delACT---11B.1.617.20.000004
ORF1ab/nsp31010T1010SActTct11B.1.617.20.000004
ORF1ab/nsp31010T1010VACTGTC11B.1.617.20.000004
ORF1ab/nsp31010T1010delACT---11B.150.017544
ORF1ab/nsp31010T1010delACT---11B.340.013699
ORF1ab/nsp31010T1010IaCtaTt11C.350.000774
ORF1ab/nsp31010T1010delACT---11C.370.000116
ORF1ab/nsp31010T1010IaCtaTt11D.20.000075
ORF1ab/nsp31010T1010TacTacC11D.20.000075
ORF1ab/nsp31010T1010SActTct11D.20.000075
ORF1ab/nsp31010T1010TacTacC11D.30.005917
ORF1ab/nsp31010T1010NaCtaAt11L.10.001905
ORF1ab/nsp31010T1010NaCtaAt11P.10.000016
ORF1ab/nsp31010T1010IaCtaTt11P.1.100.000269
ORF1ab/nsp31010T1010IaCtaTt11P.1.120.000484
ORF1ab/nsp31010T1010AActGct11P.1.150.000232
ORF1ab/nsp31010T1010HACTCAC11P.1.150.000232
ORF1ab/nsp31010T1010QACTCAA11P.1.150.000232
ORF1ab/nsp31010T1010NaCTaAC11P.1.150.000232
ORF1ab/nsp31010T1010KaCTaAA11P.1.150.000232
ORF1ab/nsp31010T1010AActGct11P.20.000187
ORF1ab/nsp31010T1010IaCtaTt11Q.10.000126
ORF1ab/nsp31010T1010IaCtaTt11R.10.00009

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.