CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : Mut = T1288I

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/nsp31288T1288IT2106InonsynaCtaTt493349290.9991896581-6583
ORF1ab/nsp31288T1288IT2106InonsynaCTaTC493340.0008108666581-6583

Details of the mutation T1288I within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):

ORFCodonNumMutRefCodonMutCodonCodonCountAACountLineageLineageCodonProp
ORF1ab/nsp31288T1288IaCtaTt49294933All0.000943
ORF1ab/nsp31288T1288IaCTaTC44933All0.000001
ORF1ab/nsp31288T1288IaCtaTt11581158AY.40.001802
ORF1ab/nsp31288T1288IaCtaTt874874B.1.1.70.000782
ORF1ab/nsp31288T1288IaCtaTt312312B.1.2580.020763
ORF1ab/nsp31288T1288IaCtaTt213213B.1.20.001876
ORF1ab/nsp31288T1288IaCtaTt194194AY.4.2.10.028903
ORF1ab/nsp31288T1288IaCtaTt188188AY.1030.001167
ORF1ab/nsp31288T1288IaCtaTt136136B.1.617.20.000512
ORF1ab/nsp31288T1288IaCtaTt124124P.10.001953
ORF1ab/nsp31288T1288IaCtaTt117117AY.430.000518
ORF1ab/nsp31288T1288IaCtaTt115115AY.440.0007
ORF1ab/nsp31288T1288IaCtaTt9191AY.750.005098
ORF1ab/nsp31288T1288IaCtaTt8585B.1.1.1340.965909
ORF1ab/nsp31288T1288IaCtaTt8585B.1.3770.388128
ORF1ab/nsp31288T1288IaCtaTt6363B.1.1770.00083
ORF1ab/nsp31288T1288IaCtaTt6363B.1.2210.004475
ORF1ab/nsp31288T1288IaCtaTt6363B.1.3690.017969
ORF1ab/nsp31288T1288IaCtaTt6060AY.1020.001591
ORF1ab/nsp31288T1288IaCtaTt5555AY.270.00356
ORF1ab/nsp31288T1288IaCtaTt5050B.1.1.5190.001986
ORF1ab/nsp31288T1288IaCtaTt4848AY.30.000477
ORF1ab/nsp31288T1288IaCtaTt4747B.1.160.210.959184
ORF1ab/nsp31288T1288IaCtaTt4546B.10.000412
ORF1ab/nsp31288T1288IaCTaTC146B.10.000009
ORF1ab/nsp31288T1288IaCtaTt3232AY.4.50.00344
ORF1ab/nsp31288T1288IaCtaTt3232P.1.10.010165
ORF1ab/nsp31288T1288IaCtaTt2828AY.250.000168
ORF1ab/nsp31288T1288IaCtaTt2828B.1.10.000508
ORF1ab/nsp31288T1288IaCtaTt2626AY.200.00101
ORF1ab/nsp31288T1288IaCtaTt2020B.1.110.30.014368
ORF1ab/nsp31288T1288IaCtaTt2020B.1.2340.002639
ORF1ab/nsp31288T1288IaCtaTt2020B.1.3240.032103
ORF1ab/nsp31288T1288IaCtaTt2020B.1.5260.00047
ORF1ab/nsp31288T1288IaCtaTt1717AY.470.000529
ORF1ab/nsp31288T1288IaCtaTt1616B.1.4290.000376
ORF1ab/nsp31288T1288IaCtaTt1515AY.4.20.000325
ORF1ab/nsp31288T1288IaCtaTt1414AY.390.000346
ORF1ab/nsp31288T1288IaCtaTt1414B.1.6210.001239
ORF1ab/nsp31288T1288IaCtaTt1313AY.260.000368
ORF1ab/nsp31288T1288IaCtaTt1212AY.39.10.000475
ORF1ab/nsp31288T1288IaCtaTt1212B.1.4270.000606
ORF1ab/nsp31288T1288IaCtaTt1212N.40.051064
ORF1ab/nsp31288T1288IaCtaTt1111B.1.177.750.011446
ORF1ab/nsp31288T1288IaCtaTt1010AY.1180.000626
ORF1ab/nsp31288T1288IaCtaTt1010B.1.1600.000312
ORF1ab/nsp31288T1288IaCtaTt1010B.1.3510.000297
ORF1ab/nsp31288T1288IaCtaTt1010B.1.5770.006873
ORF1ab/nsp31288T1288IaCtaTt1010B.1.6280.003524
ORF1ab/nsp31288T1288IaCtaTt1010C.370.001161
ORF1ab/nsp31288T1288IaCtaTt99B.1.5960.000784
ORF1ab/nsp31288T1288IaCtaTt99Q.10.001137
ORF1ab/nsp31288T1288IaCtaTt88AY.50.000165
ORF1ab/nsp31288T1288IaCtaTt88R.10.00072
ORF1ab/nsp31288T1288IaCtaTt77B.1.2430.000487
ORF1ab/nsp31288T1288IaCtaTt77B.1.3460.009174
ORF1ab/nsp31288T1288IaCTaTC360.166667
ORF1ab/nsp31288T1288IaCtaTt360.166667
ORF1ab/nsp31288T1288IaCtaTt66AY.450.00073
ORF1ab/nsp31288T1288IaCtaTt66B.1.1.280.001867
ORF1ab/nsp31288T1288IaCtaTt66B.1.1.3980.019355
ORF1ab/nsp31288T1288IaCtaTt66B.1.3060.034286
ORF1ab/nsp31288T1288IaCtaTt66B.1.466.20.002347
ORF1ab/nsp31288T1288IaCtaTt55AY.1040.009921
ORF1ab/nsp31288T1288IaCtaTt55AY.1190.000177
ORF1ab/nsp31288T1288IaCtaTt55AY.790.006053
ORF1ab/nsp31288T1288IaCtaTt55B.1.1.2140.000277
ORF1ab/nsp31288T1288IaCtaTt55B.1.1.2220.00102
ORF1ab/nsp31288T1288IaCtaTt55B.1.617.10.000645
ORF1ab/nsp31288T1288IaCtaTt55B.1.6190.004355
ORF1ab/nsp31288T1288IaCtaTt44A.23.10.002817
ORF1ab/nsp31288T1288IaCtaTt44AY.4.40.001637
ORF1ab/nsp31288T1288IaCtaTt44AY.610.000419
ORF1ab/nsp31288T1288IaCtaTt44AY.980.000316
ORF1ab/nsp31288T1288IaCtaTt44AY.99.20.000369
ORF1ab/nsp31288T1288IaCtaTt44B.1.1.2970.008949
ORF1ab/nsp31288T1288IaCtaTt44B.1.177.210.000306
ORF1ab/nsp31288T1288IaCtaTt44B.1.360.000584
ORF1ab/nsp31288T1288IaCtaTt44B.1.36.160.005698
ORF1ab/nsp31288T1288IaCtaTt44P.1.140.000191
ORF1ab/nsp31288T1288IaCtaTt33AY.1000.000138
ORF1ab/nsp31288T1288IaCtaTt33AY.1060.001005
ORF1ab/nsp31288T1288IaCtaTt33AY.1130.000427
ORF1ab/nsp31288T1288IaCtaTt33AY.1170.000254
ORF1ab/nsp31288T1288IaCtaTt33AY.1200.000112
ORF1ab/nsp31288T1288IaCtaTt33AY.340.000291
ORF1ab/nsp31288T1288IaCtaTt33AY.420.000121
ORF1ab/nsp31288T1288IaCtaTt33AY.860.00249
ORF1ab/nsp31288T1288IaCtaTt33AY.910.002191
ORF1ab/nsp31288T1288IaCtaTt33B.1.1.3180.000905
ORF1ab/nsp31288T1288IaCtaTt33B.1.258.170.000312
ORF1ab/nsp31288T1288IaCtaTt33B.1.3090.142857
ORF1ab/nsp31288T1288IaCtaTt33P.1.70.000958
ORF1ab/nsp31288T1288IaCtaTt22AY.1160.000574
ORF1ab/nsp31288T1288IaCtaTt22AY.140.000176
ORF1ab/nsp31288T1288IaCtaTt22AY.190.002281
ORF1ab/nsp31288T1288IaCtaTt22AY.230.000139
ORF1ab/nsp31288T1288IaCtaTt22AY.290.000032
ORF1ab/nsp31288T1288IaCtaTt22AY.330.000134
ORF1ab/nsp31288T1288IaCtaTt22AY.46.60.000144
ORF1ab/nsp31288T1288IaCtaTt22AY.510.001818
ORF1ab/nsp31288T1288IaCtaTt22AY.540.000191
ORF1ab/nsp31288T1288IaCtaTt22AY.630.000774
ORF1ab/nsp31288T1288IaCtaTt22AY.740.000231
ORF1ab/nsp31288T1288IaCtaTt22AY.840.000875
ORF1ab/nsp31288T1288IaCtaTt22AY.900.001369
ORF1ab/nsp31288T1288IaCtaTt22AY.98.10.000097
ORF1ab/nsp31288T1288IaCtaTt22B.1.1.3110.000716
ORF1ab/nsp31288T1288IaCtaTt22B.1.1.4200.002012
ORF1ab/nsp31288T1288IaCtaTt22B.1.1.700.000682
ORF1ab/nsp31288T1288IaCtaTt22B.1.177.120.000303
ORF1ab/nsp31288T1288IaCtaTt22B.1.177.730.001133
ORF1ab/nsp31288T1288IaCtaTt22B.1.2890.005319
ORF1ab/nsp31288T1288IaCtaTt22B.1.351.20.000605
ORF1ab/nsp31288T1288IaCtaTt22B.1.5250.000226
ORF1ab/nsp31288T1288IaCtaTt22B.1.5610.000794
ORF1ab/nsp31288T1288IaCtaTt22B.1.6230.001073
ORF1ab/nsp31288T1288IaCtaTt22B.1.6370.000146
ORF1ab/nsp31288T1288IaCtaTt22D.20.00015
ORF1ab/nsp31288T1288IaCtaTt22P.1.40.001953
ORF1ab/nsp31288T1288IaCtaTt22P.20.000373
ORF1ab/nsp31288T1288IaCtaTt22P.70.008734
ORF1ab/nsp31288T1288IaCtaTt22Q.80.00033
ORF1ab/nsp31288T1288IaCtaTt11A.2.50.000499
ORF1ab/nsp31288T1288IaCtaTt11A.30.002096
ORF1ab/nsp31288T1288IaCtaTt11AU.20.002421
ORF1ab/nsp31288T1288IaCtaTt11AY.1090.00074
ORF1ab/nsp31288T1288IaCtaTt11AY.1140.000231
ORF1ab/nsp31288T1288IaCtaTt11AY.380.000499
ORF1ab/nsp31288T1288IaCtaTt11AY.39.20.001541
ORF1ab/nsp31288T1288IaCtaTt11AY.4.10.000737
ORF1ab/nsp31288T1288IaCtaTt11AY.400.000964
ORF1ab/nsp31288T1288IaCtaTt11AY.46.40.000165
ORF1ab/nsp31288T1288IaCtaTt11AY.46.50.000198
ORF1ab/nsp31288T1288IaCtaTt11AY.5.40.000277
ORF1ab/nsp31288T1288IaCtaTt11AY.600.000938
ORF1ab/nsp31288T1288IaCtaTt11AY.620.000436
ORF1ab/nsp31288T1288IaCtaTt11AY.680.000274
ORF1ab/nsp31288T1288IaCtaTt11AY.70.000196
ORF1ab/nsp31288T1288IaCtaTt11AY.710.000475
ORF1ab/nsp31288T1288IaCtaTt11AY.770.001127
ORF1ab/nsp31288T1288IaCtaTt11AY.870.000833
ORF1ab/nsp31288T1288IaCtaTt11AY.9.20.000037
ORF1ab/nsp31288T1288IaCtaTt11AY.920.000287
ORF1ab/nsp31288T1288IaCtaTt11B.1.1.1280.007092
ORF1ab/nsp31288T1288IaCtaTt11B.1.1.1410.002012
ORF1ab/nsp31288T1288IaCtaTt11B.1.1.1700.001247
ORF1ab/nsp31288T1288IaCtaTt11B.1.1.2200.001859
ORF1ab/nsp31288T1288IaCtaTt11B.1.1.2430.004082
ORF1ab/nsp31288T1288IaCtaTt11B.1.1.2770.000759
ORF1ab/nsp31288T1288IaCtaTt11B.1.1.2910.000742
ORF1ab/nsp31288T1288IaCtaTt11B.1.1.3060.000438
ORF1ab/nsp31288T1288IaCtaTt11B.1.1.3170.000412
ORF1ab/nsp31288T1288IaCtaTt11B.1.1.330.000421
ORF1ab/nsp31288T1288IaCtaTt11B.1.1.370.000193
ORF1ab/nsp31288T1288IaCtaTt11B.1.1.390.00051
ORF1ab/nsp31288T1288IaCtaTt11B.1.1.4870.005587
ORF1ab/nsp31288T1288IaCtaTt11B.1.1.510.001718
ORF1ab/nsp31288T1288IaCtaTt11B.1.1120.005181
ORF1ab/nsp31288T1288IaCtaTt11B.1.177.310.011494
ORF1ab/nsp31288T1288IaCtaTt11B.1.177.810.000189
ORF1ab/nsp31288T1288IaCtaTt11B.1.177.860.000183
ORF1ab/nsp31288T1288IaCtaTt11B.1.2060.000816
ORF1ab/nsp31288T1288IaCtaTt11B.1.221.10.002907
ORF1ab/nsp31288T1288IaCtaTt11B.1.258.210.007752
ORF1ab/nsp31288T1288IaCtaTt11B.1.3140.007519
ORF1ab/nsp31288T1288IaCtaTt11B.1.350.008475
ORF1ab/nsp31288T1288IaCtaTt11B.1.36.170.000494
ORF1ab/nsp31288T1288IaCtaTt11B.1.36.290.000517
ORF1ab/nsp31288T1288IaCtaTt11B.1.36.80.001
ORF1ab/nsp31288T1288IaCtaTt11B.1.4520.013699
ORF1ab/nsp31288T1288IaCtaTt11B.1.4700.001404
ORF1ab/nsp31288T1288IaCtaTt11B.1.4910.052632
ORF1ab/nsp31288T1288IaCtaTt11B.1.4990.00105
ORF1ab/nsp31288T1288IaCtaTt11B.1.5090.000866
ORF1ab/nsp31288T1288IaCtaTt11B.1.5640.000426
ORF1ab/nsp31288T1288IaCtaTt11B.1.5750.000303
ORF1ab/nsp31288T1288IaCtaTt11B.1.5760.000907
ORF1ab/nsp31288T1288IaCtaTt11B.1.5950.000261
ORF1ab/nsp31288T1288IaCtaTt11B.110.005128
ORF1ab/nsp31288T1288IaCtaTt11B.550.00295
ORF1ab/nsp31288T1288IaCtaTt11C.40.01
ORF1ab/nsp31288T1288IaCtaTt11L.20.011364
ORF1ab/nsp31288T1288IaCtaTt11P.1.100.000269
ORF1ab/nsp31288T1288IaCtaTt11P.1.120.000484
ORF1ab/nsp31288T1288IaCtaTt11P.1.170.000162
ORF1ab/nsp31288T1288IaCtaTt11P.1.17.10.000875
ORF1ab/nsp31288T1288IaCtaTt11P.30.001595
ORF1ab/nsp31288T1288IaCtaTt11Y.10.012821

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.