CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1680

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/nsp31680N1680HN2498HnonsynAatCat1386138617757-7759
ORF1ab/nsp31680N1680NN2498NsynaaTaaC19319317757-7759
ORF1ab/nsp31680N1680SN2498SnonsynaAtaGt16716717757-7759
ORF1ab/nsp31680N1680delN2498deldelAAT---11011017757-7759
ORF1ab/nsp31680N1680KN2498KnonsynaaTaaA103750.7281557757-7759
ORF1ab/nsp31680N1680KN2498KnonsynaaTaaG103280.2718457757-7759
ORF1ab/nsp31680N1680DN2498DnonsynAatGat56550.9821437757-7759
ORF1ab/nsp31680N1680DN2498DnonsynAaTGaC5610.01785717757-7759
ORF1ab/nsp31680N1680TN2498TnonsynaAtaCt484817757-7759
ORF1ab/nsp31680N1680IN2498InonsynaAtaTt343417757-7759
ORF1ab/nsp31680N1680YN2498YnonsynAatTat1070.77757-7759
ORF1ab/nsp31680N1680YN2498YnonsynAaTTaC1030.37757-7759
ORF1ab/nsp31680N1680del2N2498del2delaATa--3317757-7759
ORF1ab/nsp31680N1680del1N2498del1delAat-at320.6666677757-7759
ORF1ab/nsp31680N1680del1N2498del1delaATaG-310.3333337757-7759
ORF1ab/nsp31680N1680EN2498EnonsynAaTGaA2217757-7759
ORF1ab/nsp31680N1680AN2498AnonsynAATGCA1117757-7759
ORF1ab/nsp31680N1680RN2498RnonsynaATaGA1117757-7759
ORF1ab/nsp31680N1680XN2498XnonsynAATTGA1117757-7759
ORF1ab/nsp31680N1680MN2498MnonsynaATaTG1117757-7759

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/nsp31680N1680HAatCat13861386All0.000265
ORF1ab/nsp31680N1680HAatCat13331333AY.40.002075
ORF1ab/nsp31680N1680NaaTaaC193193All0.000037
ORF1ab/nsp31680N1680SaAtaGt167167All0.000032
ORF1ab/nsp31680N1680delAAT---110110All0.000021
ORF1ab/nsp31680N1680KaaTaaA75103All0.000014
ORF1ab/nsp31680N1680KaaTaaG28103All0.000005
ORF1ab/nsp31680N1680SaAtaGt6161B.1.1.70.000055
ORF1ab/nsp31680N1680DAatGat5556All0.000011
ORF1ab/nsp31680N1680DAaTGaC156All0
ORF1ab/nsp31680N1680delAAT---4949B.1.1.70.000044
ORF1ab/nsp31680N1680TaAtaCt4848All0.000009
ORF1ab/nsp31680N1680IaAtaTt3434All0.000007
ORF1ab/nsp31680N1680IaAtaTt2727B.1.1.70.000024
ORF1ab/nsp31680N1680NaaTaaC2727B.1.1.70.000024
ORF1ab/nsp31680N1680KaaTaaA2427B.1.1.70.000021
ORF1ab/nsp31680N1680KaaTaaG327B.1.1.70.000003
ORF1ab/nsp31680N1680KaaTaaA2424B.1.1.4160.021719
ORF1ab/nsp31680N1680HAatCat2020B.1.2100.042644
ORF1ab/nsp31680N1680NaaTaaC1515AY.1130.002136
ORF1ab/nsp31680N1680NaaTaaC1414AY.850.00598
ORF1ab/nsp31680N1680KaaTaaG1414B.1.362.10.933333
ORF1ab/nsp31680N1680TaAtaCt1313AY.40.00002
ORF1ab/nsp31680N1680NaaTaaC1313B.1.5260.000306
ORF1ab/nsp31680N1680KaaTaaA1212B.1.1.2220.002448
ORF1ab/nsp31680N1680NaaTaaC1111AY.40.000017
ORF1ab/nsp31680N1680TaAtaCt1111AY.46.60.000794
ORF1ab/nsp31680N1680DAatGat1111B.1.1.70.00001
ORF1ab/nsp31680N1680YAatTat710All0.000001
ORF1ab/nsp31680N1680YAaTTaC310All0.000001
ORF1ab/nsp31680N1680KaaTaaG1010B.1.3620.015408
ORF1ab/nsp31680N1680NaaTaaC99AY.250.000054
ORF1ab/nsp31680N1680SaAtaGt99AY.250.000054
ORF1ab/nsp31680N1680NaaTaaC88AY.1030.00005
ORF1ab/nsp31680N1680SaAtaGt88B.1.3610.010309
ORF1ab/nsp31680N1680NaaTaaC88B.1.5250.000905
ORF1ab/nsp31680N1680SaAtaGt77AY.1030.000043
ORF1ab/nsp31680N1680HAatCat77AY.430.000031
ORF1ab/nsp31680N1680SaAtaGt77AY.430.000031
ORF1ab/nsp31680N1680NaaTaaC77B.1.5750.002124
ORF1ab/nsp31680N1680NaaTaaC77B.1.617.20.000026
ORF1ab/nsp31680N1680SaAtaGt66AY.40.000009
ORF1ab/nsp31680N1680NaaTaaC66AY.60.000247
ORF1ab/nsp31680N1680SaAtaGt66B.1.177.820.002864
ORF1ab/nsp31680N1680NaaTaaC66B.1.20.000053
ORF1ab/nsp31680N1680HAatCat66B.1.617.20.000023
ORF1ab/nsp31680N1680DAatGat45AY.30.00004
ORF1ab/nsp31680N1680DAaTGaC15AY.30.00001
ORF1ab/nsp31680N1680DAatGat55AY.40.000008
ORF1ab/nsp31680N1680KaaTaaA55AY.430.000022
ORF1ab/nsp31680N1680NaaTaaC55AY.440.00003
ORF1ab/nsp31680N1680SaAtaGt55B.1.1.5190.000199
ORF1ab/nsp31680N1680SaAtaGt55B.1.20.000044
ORF1ab/nsp31680N1680HAatCat55B.1.2320.002687
ORF1ab/nsp31680N1680delAAT---55B.1.617.20.000019
ORF1ab/nsp31680N1680NaaTaaC55P.10.000079
ORF1ab/nsp31680N1680delAAT---44AY.40.000006
ORF1ab/nsp31680N1680NaaTaaC44B.10.000037
ORF1ab/nsp31680N1680TaAtaCt44B.1.1.70.000004
ORF1ab/nsp31680N1680HAatCat44B.1.1.70.000004
ORF1ab/nsp31680N1680SaAtaGt44B.1.1080.023256
ORF1ab/nsp31680N1680SaAtaGt44B.1.617.20.000015
ORF1ab/nsp31680N1680DAatGat33A.23.10.002113
ORF1ab/nsp31680N1680del2aATa--33All0.000001
ORF1ab/nsp31680N1680del1Aat-at23All0
ORF1ab/nsp31680N1680del1aATaG-13All0
ORF1ab/nsp31680N1680SaAtaGt33AY.1200.000112
ORF1ab/nsp31680N1680DAatGat33AY.250.000018
ORF1ab/nsp31680N1680SaAtaGt33AY.440.000018
ORF1ab/nsp31680N1680NaaTaaC33AY.470.000093
ORF1ab/nsp31680N1680SaAtaGt33AY.7.10.000338
ORF1ab/nsp31680N1680SaAtaGt33B.10.000027
ORF1ab/nsp31680N1680TaAtaCt33B.10.000027
ORF1ab/nsp31680N1680SaAtaGt33B.1.1.2220.000612
ORF1ab/nsp31680N1680DAatGat33B.1.1.5190.000119
ORF1ab/nsp31680N1680YAaTTaC33B.1.1.70.000003
ORF1ab/nsp31680N1680delAAT---33B.1.1770.00004
ORF1ab/nsp31680N1680HAatCat33B.1.20.000026
ORF1ab/nsp31680N1680NaaTaaC33B.1.2360.00616
ORF1ab/nsp31680N1680NaaTaaC33B.1.4290.000071
ORF1ab/nsp31680N1680SaAtaGt33B.1.4560.009804
ORF1ab/nsp31680N1680NaaTaaC33Q.30.000435
ORF1ab/nsp31680N1680EAaTGaA220.111111
ORF1ab/nsp31680N1680NaaTaaC220.111111
ORF1ab/nsp31680N1680SaAtaGt220.111111
ORF1ab/nsp31680N1680EAaTGaA22All0
ORF1ab/nsp31680N1680delAAT---22AY.1110.000366
ORF1ab/nsp31680N1680delAAT---22AY.1200.000074
ORF1ab/nsp31680N1680delAAT---22AY.190.002281
ORF1ab/nsp31680N1680NaaTaaC22AY.200.000078
ORF1ab/nsp31680N1680NaaTaaC22AY.30.00002
ORF1ab/nsp31680N1680IaAtaTt22AY.3.10.000171
ORF1ab/nsp31680N1680DAatGat22AY.34.10.00102
ORF1ab/nsp31680N1680NaaTaaC22AY.390.000049
ORF1ab/nsp31680N1680YAatTat22AY.410.000588
ORF1ab/nsp31680N1680NaaTaaC22AY.430.000009
ORF1ab/nsp31680N1680DAatGat22AY.430.000009
ORF1ab/nsp31680N1680delAAT---22AY.46.20.001271
ORF1ab/nsp31680N1680SaAtaGt22AY.470.000062
ORF1ab/nsp31680N1680DAatGat22AY.650.001066
ORF1ab/nsp31680N1680SaAtaGt22AY.9.20.000073
ORF1ab/nsp31680N1680delAAT---22B.10.000018
ORF1ab/nsp31680N1680TaAtaCt22B.1.10.000036
ORF1ab/nsp31680N1680delAAT---22B.1.1.2360.013793
ORF1ab/nsp31680N1680NaaTaaC22B.1.1.4090.005666
ORF1ab/nsp31680N1680DAatGat22B.1.110.30.001437
ORF1ab/nsp31680N1680delAAT---22B.1.177.210.000153
ORF1ab/nsp31680N1680NaaTaaC22B.1.177.540.001213
ORF1ab/nsp31680N1680delAAT---22B.1.177.60.001953
ORF1ab/nsp31680N1680KaaTaaA22B.1.177.750.002081
ORF1ab/nsp31680N1680DAatGat22B.1.20.000018
ORF1ab/nsp31680N1680del1Aat-at12B.1.20.000009
ORF1ab/nsp31680N1680del1aATaG-12B.1.20.000009
ORF1ab/nsp31680N1680delAAT---22B.1.2580.000133
ORF1ab/nsp31680N1680TaAtaCt22B.1.2980.004228
ORF1ab/nsp31680N1680HAatCat22P.10.000032
ORF1ab/nsp31680N1680SaAtaGt22P.10.000032
ORF1ab/nsp31680N1680TaAtaCt22P.10.000032
ORF1ab/nsp31680N1680delAAT---11A0.000387
ORF1ab/nsp31680N1680HAatCat11A.20.000662
ORF1ab/nsp31680N1680TaAtaCt11A.2.30.004739
ORF1ab/nsp31680N1680MaATaTG11All0
ORF1ab/nsp31680N1680XAATTGA11All0
ORF1ab/nsp31680N1680RaATaGA11All0
ORF1ab/nsp31680N1680AAATGCA11All0
ORF1ab/nsp31680N1680NaaTaaC11AY.10.000396
ORF1ab/nsp31680N1680SaAtaGt11AY.1000.000046
ORF1ab/nsp31680N1680NaaTaaC11AY.1000.000046
ORF1ab/nsp31680N1680DAatGat11AY.1020.000027
ORF1ab/nsp31680N1680SaAtaGt11AY.1020.000027
ORF1ab/nsp31680N1680HAatCat11AY.1030.000006
ORF1ab/nsp31680N1680KaaTaaA11AY.1030.000006
ORF1ab/nsp31680N1680TaAtaCt11AY.1030.000006
ORF1ab/nsp31680N1680NaaTaaC11AY.1140.000231
ORF1ab/nsp31680N1680DAatGat11AY.1190.000035
ORF1ab/nsp31680N1680DAatGat11AY.1200.000037
ORF1ab/nsp31680N1680HAatCat11AY.1200.000037
ORF1ab/nsp31680N1680IaAtaTt11AY.200.000039
ORF1ab/nsp31680N1680delAAT---11AY.250.000006
ORF1ab/nsp31680N1680SaAtaGt11AY.260.000028
ORF1ab/nsp31680N1680HAatCat11AY.270.000065
ORF1ab/nsp31680N1680NaaTaaC11AY.290.000016
ORF1ab/nsp31680N1680DAatGat11AY.290.000016
ORF1ab/nsp31680N1680YAatTat11AY.30.00001
ORF1ab/nsp31680N1680SaAtaGt11AY.30.00001
ORF1ab/nsp31680N1680NaaTaaC11AY.3.10.000085
ORF1ab/nsp31680N1680DAatGat11AY.3.10.000085
ORF1ab/nsp31680N1680delAAT---11AY.330.000067
ORF1ab/nsp31680N1680SaAtaGt11AY.340.000097
ORF1ab/nsp31680N1680SaAtaGt11AY.380.000499
ORF1ab/nsp31680N1680TaAtaCt11AY.390.000025
ORF1ab/nsp31680N1680SaAtaGt11AY.39.10.00004
ORF1ab/nsp31680N1680NaaTaaC11AY.39.10.00004
ORF1ab/nsp31680N1680SaAtaGt11AY.4.20.000022
ORF1ab/nsp31680N1680NaaTaaC11AY.4.20.000022
ORF1ab/nsp31680N1680NaaTaaC11AY.4.50.000107
ORF1ab/nsp31680N1680delAAT---11AY.4.50.000107
ORF1ab/nsp31680N1680RaATaGA11AY.430.000004
ORF1ab/nsp31680N1680XAATTGA11AY.430.000004
ORF1ab/nsp31680N1680delAAT---11AY.430.000004
ORF1ab/nsp31680N1680delAAT---11AY.440.000006
ORF1ab/nsp31680N1680TaAtaCt11AY.440.000006
ORF1ab/nsp31680N1680KaaTaaG11AY.460.000104
ORF1ab/nsp31680N1680SaAtaGt11AY.46.60.000072
ORF1ab/nsp31680N1680NaaTaaC11AY.46.60.000072
ORF1ab/nsp31680N1680delAAT---11AY.50.000021
ORF1ab/nsp31680N1680SaAtaGt11AY.50.000021
ORF1ab/nsp31680N1680delAAT---11AY.520.000814
ORF1ab/nsp31680N1680delAAT---11AY.60.000041
ORF1ab/nsp31680N1680NaaTaaC11AY.640.000595
ORF1ab/nsp31680N1680HAatCat11AY.660.00107
ORF1ab/nsp31680N1680SaAtaGt11AY.740.000116
ORF1ab/nsp31680N1680SaAtaGt11AY.750.000056
ORF1ab/nsp31680N1680DAatGat11AY.750.000056
ORF1ab/nsp31680N1680delAAT---11AY.810.001992
ORF1ab/nsp31680N1680delAAT---11AY.840.000437
ORF1ab/nsp31680N1680delAAT---11AY.90.000068
ORF1ab/nsp31680N1680SaAtaGt11AY.98.10.000048
ORF1ab/nsp31680N1680DAatGat11AY.98.10.000048
ORF1ab/nsp31680N1680NaaTaaC11AY.98.10.000048
ORF1ab/nsp31680N1680del2aATa--11AY.990.001049
ORF1ab/nsp31680N1680KaaTaaA11B.10.000009
ORF1ab/nsp31680N1680del1Aat-at11B.10.000009
ORF1ab/nsp31680N1680DAatGat11B.10.000009
ORF1ab/nsp31680N1680IaAtaTt11B.10.000009
ORF1ab/nsp31680N1680NaaTaaC11B.1.10.000018
ORF1ab/nsp31680N1680DAatGat11B.1.10.000018
ORF1ab/nsp31680N1680AAATGCA11B.1.10.000018
ORF1ab/nsp31680N1680KaaTaaA11B.1.10.000018
ORF1ab/nsp31680N1680delAAT---11B.1.1.1700.001247
ORF1ab/nsp31680N1680TaAtaCt11B.1.1.250.000569
ORF1ab/nsp31680N1680DAatGat11B.1.1.2790.001121
ORF1ab/nsp31680N1680SaAtaGt11B.1.1.3060.000438
ORF1ab/nsp31680N1680YAatTat11B.1.1.3110.000358
ORF1ab/nsp31680N1680KaaTaaA11B.1.1.3120.001912
ORF1ab/nsp31680N1680SaAtaGt11B.1.1.4190.007407
ORF1ab/nsp31680N1680delAAT---11B.1.1.460.004367
ORF1ab/nsp31680N1680IaAtaTt11B.1.1.470.005348
ORF1ab/nsp31680N1680IaAtaTt11B.1.1600.000031
ORF1ab/nsp31680N1680HAatCat11B.1.160.280.002924
ORF1ab/nsp31680N1680IaAtaTt11B.1.1770.000013
ORF1ab/nsp31680N1680NaaTaaC11B.1.1770.000013
ORF1ab/nsp31680N1680DAatGat11B.1.1770.000013
ORF1ab/nsp31680N1680delAAT---11B.1.177.180.00116
ORF1ab/nsp31680N1680delAAT---11B.1.177.40.000211
ORF1ab/nsp31680N1680delAAT---11B.1.177.540.000606
ORF1ab/nsp31680N1680delAAT---11B.1.177.570.000281
ORF1ab/nsp31680N1680DAatGat11B.1.177.640.090909
ORF1ab/nsp31680N1680delAAT---11B.1.177.70.000165
ORF1ab/nsp31680N1680delAAT---11B.1.1790.003759
ORF1ab/nsp31680N1680TaAtaCt11B.1.20.000009
ORF1ab/nsp31680N1680KaaTaaA11B.1.20.000009
ORF1ab/nsp31680N1680YAatTat11B.1.2210.000071
ORF1ab/nsp31680N1680TaAtaCt11B.1.2210.000071
ORF1ab/nsp31680N1680NaaTaaC11B.1.2340.000132
ORF1ab/nsp31680N1680NaaTaaC11B.1.2400.000216
ORF1ab/nsp31680N1680delAAT---11B.1.258.100.011364
ORF1ab/nsp31680N1680DAatGat11B.1.258.170.000104
ORF1ab/nsp31680N1680NaaTaaC11B.1.3510.00003
ORF1ab/nsp31680N1680SaAtaGt11B.1.3510.00003
ORF1ab/nsp31680N1680DAatGat11B.1.351.30.000876
ORF1ab/nsp31680N1680DAatGat11B.1.3560.001727
ORF1ab/nsp31680N1680NaaTaaC11B.1.360.000146
ORF1ab/nsp31680N1680delAAT---11B.1.360.000146
ORF1ab/nsp31680N1680SaAtaGt11B.1.360.000146
ORF1ab/nsp31680N1680NaaTaaC11B.1.36.100.004785
ORF1ab/nsp31680N1680TaAtaCt11B.1.36.220.001208
ORF1ab/nsp31680N1680delAAT---11B.1.4090.000781
ORF1ab/nsp31680N1680DAatGat11B.1.4110.003704
ORF1ab/nsp31680N1680delAAT---11B.1.416.10.001563
ORF1ab/nsp31680N1680NaaTaaC11B.1.4270.00005
ORF1ab/nsp31680N1680TaAtaCt11B.1.4290.000024
ORF1ab/nsp31680N1680del2aATa--11B.1.5010.007353
ORF1ab/nsp31680N1680delAAT---11B.1.5610.000397
ORF1ab/nsp31680N1680SaAtaGt11B.1.5610.000397
ORF1ab/nsp31680N1680delAAT---11B.1.5960.000087
ORF1ab/nsp31680N1680delAAT---11B.1.6060.006024
ORF1ab/nsp31680N1680TaAtaCt11B.1.617.20.000004
ORF1ab/nsp31680N1680KaaTaaA11B.1.617.20.000004
ORF1ab/nsp31680N1680del2aATa--11B.1.617.20.000004
ORF1ab/nsp31680N1680NaaTaaC11B.1.6360.006711
ORF1ab/nsp31680N1680NaaTaaC11B.1.6370.000073
ORF1ab/nsp31680N1680delAAT---11B.4.40.018868
ORF1ab/nsp31680N1680SaAtaGt11C.270.018519
ORF1ab/nsp31680N1680MaATaTG11C.350.000774
ORF1ab/nsp31680N1680KaaTaaA11P.10.000016
ORF1ab/nsp31680N1680delAAT---11P.10.000016
ORF1ab/nsp31680N1680delAAT---11P.1.10.000318
ORF1ab/nsp31680N1680KaaTaaA11P.1.170.000162
ORF1ab/nsp31680N1680NaaTaaC11P.20.000187
ORF1ab/nsp31680N1680YAatTat11P.20.000187
ORF1ab/nsp31680N1680delAAT---11Q.10.000126
ORF1ab/nsp31680N1680TaAtaCt11Q.10.000126
ORF1ab/nsp31680N1680YAatTat11Q.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.