CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : Mut = L1299L

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/nsp31299L1299LL2117LsynttAttG391234630.8852256614-6616
ORF1ab/nsp31299L1299LL2117LsynTtaCta39124490.1147756614-6616

Details of the mutation L1299L within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):

ORFCodonNumMutRefCodonMutCodonCodonCountAACountLineageLineageCodonProp
ORF1ab/nsp31299L1299LttAttG34633912All0.000662
ORF1ab/nsp31299L1299LTtaCta4493912All0.000086
ORF1ab/nsp31299L1299LttAttG725725AY.39.10.02872
ORF1ab/nsp31299L1299LttAttG421456B.1.1.70.000377
ORF1ab/nsp31299L1299LTtaCta35456B.1.1.70.000031
ORF1ab/nsp31299L1299LttAttG303345AY.40.000472
ORF1ab/nsp31299L1299LTtaCta42345AY.40.000065
ORF1ab/nsp31299L1299LTtaCta248330AY.440.00151
ORF1ab/nsp31299L1299LttAttG82330AY.440.000499
ORF1ab/nsp31299L1299LttAttG163163B.1.5730.993902
ORF1ab/nsp31299L1299LttAttG156159AY.470.004852
ORF1ab/nsp31299L1299LTtaCta3159AY.470.000093
ORF1ab/nsp31299L1299LttAttG77114B.1.617.20.00029
ORF1ab/nsp31299L1299LTtaCta37114B.1.617.20.000139
ORF1ab/nsp31299L1299LttAttG109112B.10.000998
ORF1ab/nsp31299L1299LTtaCta3112B.10.000027
ORF1ab/nsp31299L1299LttAttG100100B.1.10.001814
ORF1ab/nsp31299L1299LttAttG9494B.1.4290.002212
ORF1ab/nsp31299L1299LttAttG6869B.1.1770.000895
ORF1ab/nsp31299L1299LTtaCta169B.1.1770.000013
ORF1ab/nsp31299L1299LttAttG6767B.1.1.4340.023353
ORF1ab/nsp31299L1299LttAttG6162AY.1030.000379
ORF1ab/nsp31299L1299LTtaCta162AY.1030.000006
ORF1ab/nsp31299L1299LttAttG5861B.1.5260.001363
ORF1ab/nsp31299L1299LTtaCta361B.1.5260.000071
ORF1ab/nsp31299L1299LttAttG5160AY.430.000226
ORF1ab/nsp31299L1299LTtaCta960AY.430.00004
ORF1ab/nsp31299L1299LttAttG5959AY.30.000587
ORF1ab/nsp31299L1299LttAttG4455B.1.20.000387
ORF1ab/nsp31299L1299LTtaCta1155B.1.20.000097
ORF1ab/nsp31299L1299LttAttG5252P.10.000819
ORF1ab/nsp31299L1299LttAttG4747AY.200.001827
ORF1ab/nsp31299L1299LttAttG4045AY.250.000241
ORF1ab/nsp31299L1299LTtaCta545AY.250.00003
ORF1ab/nsp31299L1299LttAttG3941AY.1200.00145
ORF1ab/nsp31299L1299LTtaCta241AY.1200.000074
ORF1ab/nsp31299L1299LttAttG4040AY.390.000988
ORF1ab/nsp31299L1299LttAttG3535B.1.1950.175879
ORF1ab/nsp31299L1299LttAttG2929B.1.2210.00206
ORF1ab/nsp31299L1299LttAttG2727AY.1100.003043
ORF1ab/nsp31299L1299LttAttG2626B.1.36.380.042693
ORF1ab/nsp31299L1299LttAttG2424B.1.1.1000.96
ORF1ab/nsp31299L1299LttAttG2222B.1.3510.000654
ORF1ab/nsp31299L1299LttAttG2121AY.9.20.000771
ORF1ab/nsp31299L1299LttAttG1919B.1.1600.000593
ORF1ab/nsp31299L1299LttAttG1216AY.260.00034
ORF1ab/nsp31299L1299LTtaCta416AY.260.000113
ORF1ab/nsp31299L1299LttAttG1516B.1.4270.000757
ORF1ab/nsp31299L1299LTtaCta116B.1.4270.00005
ORF1ab/nsp31299L1299LttAttG1414AY.320.007455
ORF1ab/nsp31299L1299LttAttG1314B.1.1.5190.000516
ORF1ab/nsp31299L1299LTtaCta114B.1.1.5190.00004
ORF1ab/nsp31299L1299LttAttG1212AY.98.10.000581
ORF1ab/nsp31299L1299LttAttG1212B.1.1.5120.342857
ORF1ab/nsp31299L1299LttAttG1212B.1.177.820.005728
ORF1ab/nsp31299L1299LttAttG911AY.290.000142
ORF1ab/nsp31299L1299LTtaCta211AY.290.000032
ORF1ab/nsp31299L1299LttAttG1111B.1.1.2220.002244
ORF1ab/nsp31299L1299LttAttG1111B.1.350.09322
ORF1ab/nsp31299L1299LttAttG910AY.4.20.000195
ORF1ab/nsp31299L1299LTtaCta110AY.4.20.000022
ORF1ab/nsp31299L1299LttAttG89AY.50.000165
ORF1ab/nsp31299L1299LTtaCta19AY.50.000021
ORF1ab/nsp31299L1299LttAttG99AY.610.000943
ORF1ab/nsp31299L1299LttAttG99AY.750.000504
ORF1ab/nsp31299L1299LttAttG99B.1.5750.002731
ORF1ab/nsp31299L1299LttAttG88AY.1020.000212
ORF1ab/nsp31299L1299LttAttG88C.370.000929
ORF1ab/nsp31299L1299LttAttG46AY.1130.00057
ORF1ab/nsp31299L1299LTtaCta26AY.1130.000285
ORF1ab/nsp31299L1299LTtaCta66AY.1170.000507
ORF1ab/nsp31299L1299LttAttG66AY.230.000418
ORF1ab/nsp31299L1299LttAttG46AY.340.000388
ORF1ab/nsp31299L1299LTtaCta26AY.340.000194
ORF1ab/nsp31299L1299LTtaCta46AY.460.000416
ORF1ab/nsp31299L1299LttAttG26AY.460.000208
ORF1ab/nsp31299L1299LTtaCta56AY.540.000477
ORF1ab/nsp31299L1299LttAttG16AY.540.000095
ORF1ab/nsp31299L1299LttAttG66B.260.088235
ORF1ab/nsp31299L1299LttAttG55AY.140.00044
ORF1ab/nsp31299L1299LttAttG55AY.810.00996
ORF1ab/nsp31299L1299LttAttG45B.1.6210.000354
ORF1ab/nsp31299L1299LTtaCta15B.1.6210.000089
ORF1ab/nsp31299L1299LttAttG44AY.590.002119
ORF1ab/nsp31299L1299LttAttG44AY.60.000165
ORF1ab/nsp31299L1299LttAttG44AY.75.10.000721
ORF1ab/nsp31299L1299LttAttG34B.1.2580.0002
ORF1ab/nsp31299L1299LTtaCta14B.1.2580.000067
ORF1ab/nsp31299L1299LttAttG44B.1.36.180.001681
ORF1ab/nsp31299L1299LttAttG44B.1.4130.017021
ORF1ab/nsp31299L1299LTtaCta24B.1.438.10.000215
ORF1ab/nsp31299L1299LttAttG24B.1.438.10.000215
ORF1ab/nsp31299L1299LttAttG44B.1.466.10.028777
ORF1ab/nsp31299L1299LttAttG33AY.1000.000138
ORF1ab/nsp31299L1299LttAttG33AY.1180.000188
ORF1ab/nsp31299L1299LttAttG33AY.1210.000406
ORF1ab/nsp31299L1299LttAttG33AY.4.40.001227
ORF1ab/nsp31299L1299LttAttG23AY.99.20.000184
ORF1ab/nsp31299L1299LTtaCta13AY.99.20.000092
ORF1ab/nsp31299L1299LttAttG33B.1.1.2320.005445
ORF1ab/nsp31299L1299LttAttG33B.1.1.2840.000322
ORF1ab/nsp31299L1299LttAttG33B.1.1.3180.000905
ORF1ab/nsp31299L1299LttAttG33B.1.1.4160.002715
ORF1ab/nsp31299L1299LttAttG33B.1.1.700.001023
ORF1ab/nsp31299L1299LttAttG33B.1.2340.000396
ORF1ab/nsp31299L1299LttAttG33B.1.5170.001281
ORF1ab/nsp31299L1299LttAttG23B.1.5250.000226
ORF1ab/nsp31299L1299LTtaCta13B.1.5250.000113
ORF1ab/nsp31299L1299LttAttG33P.1.100.000808
ORF1ab/nsp31299L1299LTtaCta33P.20.00056
ORF1ab/nsp31299L1299LttAttG22A.23.10.001408
ORF1ab/nsp31299L1299LttAttG22AY.3.10.000171
ORF1ab/nsp31299L1299LttAttG22AY.4.50.000215
ORF1ab/nsp31299L1299LttAttG22AY.420.00008
ORF1ab/nsp31299L1299LttAttG12AY.5.30.000337
ORF1ab/nsp31299L1299LTtaCta12AY.5.30.000337
ORF1ab/nsp31299L1299LttAttG22B.1.1.3160.00185
ORF1ab/nsp31299L1299LttAttG22B.1.1.3170.000823
ORF1ab/nsp31299L1299LttAttG22B.1.1490.006849
ORF1ab/nsp31299L1299LTtaCta22B.1.177.520.003515
ORF1ab/nsp31299L1299LttAttG22B.1.2320.001075
ORF1ab/nsp31299L1299LttAttG22B.1.36.310.003503
ORF1ab/nsp31299L1299LttAttG22B.1.4330.00639
ORF1ab/nsp31299L1299LttAttG22B.1.5770.001375
ORF1ab/nsp31299L1299LttAttG22B.1.6370.000146
ORF1ab/nsp31299L1299LttAttG22B.1.80.003945
ORF1ab/nsp31299L1299LttAttG22C.160.002121
ORF1ab/nsp31299L1299LttAttG22C.360.001821
ORF1ab/nsp31299L1299LttAttG22P.1.140.000096
ORF1ab/nsp31299L1299LttAttG22Q.10.000253
ORF1ab/nsp31299L1299LttAttG22Q.80.00033
ORF1ab/nsp31299L1299LttAttG22R.10.00018
ORF1ab/nsp31299L1299LttAttG22W.40.002703
ORF1ab/nsp31299L1299LttAttG110.055556
ORF1ab/nsp31299L1299LttAttG11A.10.000282
ORF1ab/nsp31299L1299LttAttG11A.20.000662
ORF1ab/nsp31299L1299LttAttG11A.2.50.000499
ORF1ab/nsp31299L1299LTtaCta11AY.1050.000643
ORF1ab/nsp31299L1299LttAttG11AY.1070.000466
ORF1ab/nsp31299L1299LttAttG11AY.1190.000035
ORF1ab/nsp31299L1299LTtaCta11AY.120.20.001285
ORF1ab/nsp31299L1299LttAttG11AY.160.00038
ORF1ab/nsp31299L1299LttAttG11AY.16.10.00047
ORF1ab/nsp31299L1299LttAttG11AY.270.000065
ORF1ab/nsp31299L1299LttAttG11AY.300.000396
ORF1ab/nsp31299L1299LttAttG11AY.330.000067
ORF1ab/nsp31299L1299LttAttG11AY.370.000316
ORF1ab/nsp31299L1299LttAttG11AY.39.1.10.000725
ORF1ab/nsp31299L1299LttAttG11AY.4.2.10.000149
ORF1ab/nsp31299L1299LttAttG11AY.46.60.000072
ORF1ab/nsp31299L1299LTtaCta11AY.620.000436
ORF1ab/nsp31299L1299LttAttG11AY.660.00107
ORF1ab/nsp31299L1299LttAttG11AY.700.000209
ORF1ab/nsp31299L1299LttAttG11AY.710.000475
ORF1ab/nsp31299L1299LttAttG11AY.850.000427
ORF1ab/nsp31299L1299LttAttG11AY.880.000884
ORF1ab/nsp31299L1299LttAttG11AZ.20.000821
ORF1ab/nsp31299L1299LttAttG11B0.000128
ORF1ab/nsp31299L1299LttAttG11B.1.1.1090.04
ORF1ab/nsp31299L1299LttAttG11B.1.1.1210.002427
ORF1ab/nsp31299L1299LttAttG11B.1.1.1890.001513
ORF1ab/nsp31299L1299LttAttG11B.1.1.2050.003717
ORF1ab/nsp31299L1299LttAttG11B.1.1.2160.00089
ORF1ab/nsp31299L1299LttAttG11B.1.1.250.000569
ORF1ab/nsp31299L1299LttAttG11B.1.1.2770.000759
ORF1ab/nsp31299L1299LTtaCta11B.1.1.2790.001121
ORF1ab/nsp31299L1299LttAttG11B.1.1.3120.001912
ORF1ab/nsp31299L1299LTtaCta11B.1.1.3260.001761
ORF1ab/nsp31299L1299LttAttG11B.1.1.3350.012987
ORF1ab/nsp31299L1299LttAttG11B.1.1.3690.000446
ORF1ab/nsp31299L1299LttAttG11B.1.1.3700.012658
ORF1ab/nsp31299L1299LttAttG11B.1.1.3710.010417
ORF1ab/nsp31299L1299LttAttG11B.1.1.3720.000689
ORF1ab/nsp31299L1299LttAttG11B.1.1.3760.005952
ORF1ab/nsp31299L1299LttAttG11B.1.1.4020.011111
ORF1ab/nsp31299L1299LttAttG11B.1.1.740.00431
ORF1ab/nsp31299L1299LttAttG11B.1.1.820.038462
ORF1ab/nsp31299L1299LttAttG11B.1.1280.000635
ORF1ab/nsp31299L1299LttAttG11B.1.1630.02439
ORF1ab/nsp31299L1299LttAttG11B.1.177.170.000821
ORF1ab/nsp31299L1299LttAttG11B.1.177.420.000894
ORF1ab/nsp31299L1299LttAttG11B.1.177.440.000519
ORF1ab/nsp31299L1299LttAttG11B.1.177.50.001242
ORF1ab/nsp31299L1299LttAttG11B.1.177.580.001332
ORF1ab/nsp31299L1299LttAttG11B.1.177.860.000183
ORF1ab/nsp31299L1299LttAttG11B.1.2330.014085
ORF1ab/nsp31299L1299LttAttG11B.1.258.170.000104
ORF1ab/nsp31299L1299LttAttG11B.1.351.20.000303
ORF1ab/nsp31299L1299LttAttG11B.1.351.50.0006
ORF1ab/nsp31299L1299LttAttG11B.1.3610.001289
ORF1ab/nsp31299L1299LttAttG11B.1.3690.000285
ORF1ab/nsp31299L1299LTtaCta11B.1.4020.009804
ORF1ab/nsp31299L1299LttAttG11B.1.4080.00369
ORF1ab/nsp31299L1299LttAttG11B.1.466.20.000391
ORF1ab/nsp31299L1299LTtaCta11B.1.4670.04
ORF1ab/nsp31299L1299LttAttG11B.1.4700.001404
ORF1ab/nsp31299L1299LttAttG11B.1.5200.021739
ORF1ab/nsp31299L1299LttAttG11B.1.5240.001406
ORF1ab/nsp31299L1299LttAttG11B.1.5330.009615
ORF1ab/nsp31299L1299LttAttG11B.1.5540.004405
ORF1ab/nsp31299L1299LttAttG11B.1.5610.000397
ORF1ab/nsp31299L1299LttAttG11B.1.5960.000087
ORF1ab/nsp31299L1299LttAttG11B.1.6060.006024
ORF1ab/nsp31299L1299LttAttG11B.1.6090.000479
ORF1ab/nsp31299L1299LttAttG11B.1.617.10.000129
ORF1ab/nsp31299L1299LttAttG11B.1.6310.003367
ORF1ab/nsp31299L1299LttAttG11B.230.002924
ORF1ab/nsp31299L1299LttAttG11B.280.003279
ORF1ab/nsp31299L1299LttAttG11B.290.003509
ORF1ab/nsp31299L1299LttAttG11B.390.002331
ORF1ab/nsp31299L1299LTtaCta11B.400.000364
ORF1ab/nsp31299L1299LttAttG11C.20.016129
ORF1ab/nsp31299L1299LttAttG11C.36.30.000567
ORF1ab/nsp31299L1299LttAttG11D.20.000075
ORF1ab/nsp31299L1299LttAttG11P.1.150.000232
ORF1ab/nsp31299L1299LttAttG11P.1.70.000319
ORF1ab/nsp31299L1299LttAttG11Q.30.000145

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.