CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp12 : CodonNum = 38

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/nsp1238Y38YY4430YsyntaCtaT40694069113552-13554
ORF1ab/nsp1238Y38HY4430HnonsynTacCac5858113552-13554
ORF1ab/nsp1238Y38delY4430deldelTAC---4545113552-13554
ORF1ab/nsp1238Y38XY4430XnonsyntaCtaA540.813552-13554
ORF1ab/nsp1238Y38XY4430XnonsyntACtGA510.213552-13554
ORF1ab/nsp1238Y38CY4430CnonsyntActGc44113552-13554
ORF1ab/nsp1238Y38FY4430FnonsyntActTc430.7513552-13554
ORF1ab/nsp1238Y38NY4430NnonsynTacAac430.7513552-13554
ORF1ab/nsp1238Y38del1Y4430del1deltAct-c420.513552-13554
ORF1ab/nsp1238Y38NY4430NnonsynTaCAaT410.2513552-13554
ORF1ab/nsp1238Y38del1Y4430del1delTac-ac410.2513552-13554
ORF1ab/nsp1238Y38del1Y4430del1deltaCta-410.2513552-13554
ORF1ab/nsp1238Y38FY4430FnonsyntACtTT410.2513552-13554
ORF1ab/nsp1238Y38DY4430DnonsynTacGac33113552-13554
ORF1ab/nsp1238Y38VY4430VnonsynTACGTA11113552-13554
ORF1ab/nsp1238Y38KY4430KnonsynTaCAaA11113552-13554

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/nsp1238Y38YtaCtaT40694069All0.000778
ORF1ab/nsp1238Y38YtaCtaT11991199B.1.10.021751
ORF1ab/nsp1238Y38YtaCtaT825825B.1.1.70.000739
ORF1ab/nsp1238Y38YtaCtaT462462AY.40.000719
ORF1ab/nsp1238Y38YtaCtaT185185AY.440.001126
ORF1ab/nsp1238Y38YtaCtaT8181AY.50.001673
ORF1ab/nsp1238Y38YtaCtaT6666B.1.617.20.000249
ORF1ab/nsp1238Y38YtaCtaT6666P.10.00104
ORF1ab/nsp1238Y38YtaCtaT6565AY.250.000391
ORF1ab/nsp1238Y38YtaCtaT6060B.1.1.3361
ORF1ab/nsp1238Y38HTacCac5858All0.000011
ORF1ab/nsp1238Y38YtaCtaT5858B.1.1.3381
ORF1ab/nsp1238Y38YtaCtaT5353B.1.1.5220.913793
ORF1ab/nsp1238Y38delTAC---4545All0.000009
ORF1ab/nsp1238Y38YtaCtaT4343P.1.140.002055
ORF1ab/nsp1238Y38YtaCtaT4141B.10.000376
ORF1ab/nsp1238Y38YtaCtaT4040B.1.20.000352
ORF1ab/nsp1238Y38YtaCtaT3939AY.430.000173
ORF1ab/nsp1238Y38HTacCac3939B.1.10.000707
ORF1ab/nsp1238Y38YtaCtaT3939B.1.2210.00277
ORF1ab/nsp1238Y38YtaCtaT3636AY.620.015686
ORF1ab/nsp1238Y38YtaCtaT3535B.1.1770.000461
ORF1ab/nsp1238Y38YtaCtaT3333B.1.36.160.047009
ORF1ab/nsp1238Y38YtaCtaT2929AY.90.00196
ORF1ab/nsp1238Y38YtaCtaT2626AY.750.001457
ORF1ab/nsp1238Y38YtaCtaT2525AY.1030.000155
ORF1ab/nsp1238Y38YtaCtaT2525B.1.1.5190.000993
ORF1ab/nsp1238Y38YtaCtaT2525B.1.4290.000588
ORF1ab/nsp1238Y38YtaCtaT1818B.1.1.10.00588
ORF1ab/nsp1238Y38YtaCtaT1818B.1.2580.001198
ORF1ab/nsp1238Y38YtaCtaT1818B.1.3110.004942
ORF1ab/nsp1238Y38YtaCtaT1717AY.1020.000451
ORF1ab/nsp1238Y38YtaCtaT1717B.1.1.3190.298246
ORF1ab/nsp1238Y38YtaCtaT1616Y.10.205128
ORF1ab/nsp1238Y38YtaCtaT1515B.1.177.860.002752
ORF1ab/nsp1238Y38delTAC---1414B.1.1.70.000013
ORF1ab/nsp1238Y38YtaCtaT1414B.1.110.30.010057
ORF1ab/nsp1238Y38YtaCtaT1313B.1.3510.000386
ORF1ab/nsp1238Y38YtaCtaT1010AY.30.000099
ORF1ab/nsp1238Y38YtaCtaT99B.1.1.2220.001836
ORF1ab/nsp1238Y38YtaCtaT99B.1.1.2690.012179
ORF1ab/nsp1238Y38YtaCtaT88AY.98.10.000387
ORF1ab/nsp1238Y38YtaCtaT88B.1.1.2240.114286
ORF1ab/nsp1238Y38YtaCtaT88B.1.1.4090.022663
ORF1ab/nsp1238Y38YtaCtaT77AY.200.000272
ORF1ab/nsp1238Y38YtaCtaT77AY.4.20.000152
ORF1ab/nsp1238Y38YtaCtaT77B.1.1.4470.25
ORF1ab/nsp1238Y38YtaCtaT77B.1.5260.000165
ORF1ab/nsp1238Y38YtaCtaT66AY.340.000582
ORF1ab/nsp1238Y38YtaCtaT66AY.390.000148
ORF1ab/nsp1238Y38YtaCtaT66B.1.1.3050.023166
ORF1ab/nsp1238Y38YtaCtaT66B.1.177.70.000989
ORF1ab/nsp1238Y38XtaCtaA45All0.000001
ORF1ab/nsp1238Y38XtACtGA15All0
ORF1ab/nsp1238Y38YtaCtaT55AY.20.001781
ORF1ab/nsp1238Y38YtaCtaT55AY.46.60.000361
ORF1ab/nsp1238Y38YtaCtaT55B.1.1.100.005574
ORF1ab/nsp1238Y38YtaCtaT55B.1.1.1940.024752
ORF1ab/nsp1238Y38YtaCtaT55B.1.5960.000436
ORF1ab/nsp1238Y38YtaCtaT55B.1.6210.000443
ORF1ab/nsp1238Y38YtaCtaT55P.1.70.001596
ORF1ab/nsp1238Y38CtActGc44All0.000001
ORF1ab/nsp1238Y38FtActTc34All0.000001
ORF1ab/nsp1238Y38NTacAac34All0.000001
ORF1ab/nsp1238Y38del1tAct-c24All0
ORF1ab/nsp1238Y38FtACtTT14All0
ORF1ab/nsp1238Y38NTaCAaT14All0
ORF1ab/nsp1238Y38del1Tac-ac14All0
ORF1ab/nsp1238Y38del1taCta-14All0
ORF1ab/nsp1238Y38YtaCtaT44AY.1200.000149
ORF1ab/nsp1238Y38YtaCtaT44AY.290.000063
ORF1ab/nsp1238Y38YtaCtaT44AY.3.10.000341
ORF1ab/nsp1238Y38YtaCtaT44AY.610.000419
ORF1ab/nsp1238Y38YtaCtaT44AY.9.20.000147
ORF1ab/nsp1238Y38YtaCtaT44B.1.1.2770.003035
ORF1ab/nsp1238Y38YtaCtaT44B.1.177.770.002905
ORF1ab/nsp1238Y38YtaCtaT44B.1.360.000584
ORF1ab/nsp1238Y38YtaCtaT44B.1.4700.005618
ORF1ab/nsp1238Y38DTacGac33All0.000001
ORF1ab/nsp1238Y38YtaCtaT33AY.1000.000138
ORF1ab/nsp1238Y38YtaCtaT33AY.230.000209
ORF1ab/nsp1238Y38YtaCtaT33AY.330.0002
ORF1ab/nsp1238Y38YtaCtaT33AY.39.10.000119
ORF1ab/nsp1238Y38delTAC---33AY.430.000013
ORF1ab/nsp1238Y38YtaCtaT33AY.540.000286
ORF1ab/nsp1238Y38YtaCtaT33AY.710.001425
ORF1ab/nsp1238Y38YtaCtaT33AY.980.000237
ORF1ab/nsp1238Y38YtaCtaT33B.1.1.4160.002715
ORF1ab/nsp1238Y38YtaCtaT33B.1.1.4300.125
ORF1ab/nsp1238Y38HTacCac33B.1.1.70.000003
ORF1ab/nsp1238Y38YtaCtaT33B.1.2430.000209
ORF1ab/nsp1238Y38YtaCtaT33B.1.2790.001541
ORF1ab/nsp1238Y38HTacCac33B.1.3510.000089
ORF1ab/nsp1238Y38YtaCtaT33B.1.5820.001472
ORF1ab/nsp1238Y38YtaCtaT33B.1.621.10.001517
ORF1ab/nsp1238Y38YtaCtaT33Q.30.000435
ORF1ab/nsp1238Y38YtaCtaT22A.280.005291
ORF1ab/nsp1238Y38YtaCtaT22AD.20.000438
ORF1ab/nsp1238Y38YtaCtaT22AE.80.000978
ORF1ab/nsp1238Y38YtaCtaT22AY.1050.001286
ORF1ab/nsp1238Y38YtaCtaT22AY.1190.000071
ORF1ab/nsp1238Y38YtaCtaT22AY.130.000322
ORF1ab/nsp1238Y38YtaCtaT22AY.260.000057
ORF1ab/nsp1238Y38delTAC---22AY.40.000003
ORF1ab/nsp1238Y38delTAC---22AY.4.50.000215
ORF1ab/nsp1238Y38YtaCtaT22AY.420.00008
ORF1ab/nsp1238Y38YtaCtaT22AY.460.000208
ORF1ab/nsp1238Y38YtaCtaT22AY.60.000082
ORF1ab/nsp1238Y38CtActGc22AY.610.00021
ORF1ab/nsp1238Y38YtaCtaT22AY.630.000774
ORF1ab/nsp1238Y38YtaCtaT22AY.7.20.001119
ORF1ab/nsp1238Y38YtaCtaT22AY.870.001665
ORF1ab/nsp1238Y38delTAC---22AY.990.002099
ORF1ab/nsp1238Y38YtaCtaT22AY.99.20.000184
ORF1ab/nsp1238Y38delTAC---22B.1.10.000036
ORF1ab/nsp1238Y38YtaCtaT22B.1.1.1980.002937
ORF1ab/nsp1238Y38YtaCtaT22B.1.1.2140.000111
ORF1ab/nsp1238Y38YtaCtaT22B.1.1.2160.001781
ORF1ab/nsp1238Y38YtaCtaT22B.1.1.2540.022472
ORF1ab/nsp1238Y38YtaCtaT22B.1.1.2980.001724
ORF1ab/nsp1238Y38YtaCtaT22B.1.1.3060.000877
ORF1ab/nsp1238Y38YtaCtaT22B.1.1.3700.025316
ORF1ab/nsp1238Y38YtaCtaT22B.1.1.3850.008929
ORF1ab/nsp1238Y38YtaCtaT22B.1.1.4190.014815
ORF1ab/nsp1238Y38YtaCtaT22B.1.1.80.007168
ORF1ab/nsp1238Y38YtaCtaT22B.1.1600.000062
ORF1ab/nsp1238Y38YtaCtaT22B.1.160.140.004237
ORF1ab/nsp1238Y38del1tAct-c22B.1.1770.000026
ORF1ab/nsp1238Y38YtaCtaT22B.1.177.440.001038
ORF1ab/nsp1238Y38YtaCtaT22B.1.177.600.000437
ORF1ab/nsp1238Y38YtaCtaT22B.1.177.730.001133
ORF1ab/nsp1238Y38YtaCtaT22B.1.177.810.000379
ORF1ab/nsp1238Y38HTacCac22B.1.20.000018
ORF1ab/nsp1238Y38YtaCtaT22B.1.4990.002101
ORF1ab/nsp1238Y38YtaCtaT22B.1.5170.000854
ORF1ab/nsp1238Y38YtaCtaT22B.1.5240.002813
ORF1ab/nsp1238Y38YtaCtaT22B.1.5610.000794
ORF1ab/nsp1238Y38YtaCtaT22B.1.6250.004706
ORF1ab/nsp1238Y38YtaCtaT22C.370.000232
ORF1ab/nsp1238Y38delTAC---22P.10.000032
ORF1ab/nsp1238Y38delTAC---22P.1.150.000465
ORF1ab/nsp1238Y38YtaCtaT22R.10.00018
ORF1ab/nsp1238Y38NTacAac11A.2.20.001689
ORF1ab/nsp1238Y38HTacCac11A.23.10.000704
ORF1ab/nsp1238Y38KTaCAaA11All0
ORF1ab/nsp1238Y38VTACGTA11All0
ORF1ab/nsp1238Y38YtaCtaT11AU.20.002421
ORF1ab/nsp1238Y38delTAC---11AY.1000.000046
ORF1ab/nsp1238Y38YtaCtaT11AY.1070.000466
ORF1ab/nsp1238Y38YtaCtaT11AY.1080.001103
ORF1ab/nsp1238Y38YtaCtaT11AY.1100.000113
ORF1ab/nsp1238Y38YtaCtaT11AY.116.10.000311
ORF1ab/nsp1238Y38delTAC---11AY.1190.000035
ORF1ab/nsp1238Y38YtaCtaT11AY.120.000316
ORF1ab/nsp1238Y38delTAC---11AY.1200.000037
ORF1ab/nsp1238Y38YtaCtaT11AY.140.000088
ORF1ab/nsp1238Y38HTacCac11AY.140.000088
ORF1ab/nsp1238Y38YtaCtaT11AY.16.10.00047
ORF1ab/nsp1238Y38YtaCtaT11AY.240.000431
ORF1ab/nsp1238Y38HTacCac11AY.240.000431
ORF1ab/nsp1238Y38delTAC---11AY.250.000006
ORF1ab/nsp1238Y38HTacCac11AY.250.000006
ORF1ab/nsp1238Y38HTacCac11AY.30.00001
ORF1ab/nsp1238Y38CtActGc11AY.30.00001
ORF1ab/nsp1238Y38FtActTc11AY.330.000067
ORF1ab/nsp1238Y38NTacAac11AY.40.000002
ORF1ab/nsp1238Y38HTacCac11AY.40.000002
ORF1ab/nsp1238Y38YtaCtaT11AY.4.2.10.000149
ORF1ab/nsp1238Y38YtaCtaT11AY.450.000122
ORF1ab/nsp1238Y38YtaCtaT11AY.46.20.000635
ORF1ab/nsp1238Y38YtaCtaT11AY.46.50.000198
ORF1ab/nsp1238Y38YtaCtaT11AY.470.000031
ORF1ab/nsp1238Y38YtaCtaT11AY.510.000909
ORF1ab/nsp1238Y38YtaCtaT11AY.590.00053
ORF1ab/nsp1238Y38delTAC---11AY.60.000041
ORF1ab/nsp1238Y38delTAC---11AY.660.00107
ORF1ab/nsp1238Y38YtaCtaT11AY.670.000464
ORF1ab/nsp1238Y38YtaCtaT11AY.680.000274
ORF1ab/nsp1238Y38YtaCtaT11AY.7.10.000113
ORF1ab/nsp1238Y38YtaCtaT11AY.840.000437
ORF1ab/nsp1238Y38FtACtTT11AY.9.20.000037
ORF1ab/nsp1238Y38HTacCac11AY.9.20.000037
ORF1ab/nsp1238Y38YtaCtaT11AY.960.002075
ORF1ab/nsp1238Y38XtACtGA11AY.98.10.000048
ORF1ab/nsp1238Y38YtaCtaT11AZ.20.000821
ORF1ab/nsp1238Y38YtaCtaT11B0.000128
ORF1ab/nsp1238Y38HTacCac11B0.000128
ORF1ab/nsp1238Y38del1taCta-11B.10.000009
ORF1ab/nsp1238Y38FtActTc11B.10.000009
ORF1ab/nsp1238Y38DTacGac11B.1.10.000018
ORF1ab/nsp1238Y38XtaCtaA11B.1.1.10.000327
ORF1ab/nsp1238Y38delTAC---11B.1.1.10.000327
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.1220.045455
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.1340.011364
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.1370.0125
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.1450.037037
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.1480.008772
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.1610.003534
ORF1ab/nsp1238Y38HTacCac11B.1.1.1740.003378
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.1860.003436
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.2070.001182
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.2440.015385
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.2790.001121
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.2990.012195
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.3150.008475
ORF1ab/nsp1238Y38delTAC---11B.1.1.3480.000796
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.3480.000796
ORF1ab/nsp1238Y38delTAC---11B.1.1.370.000193
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.3880.045455
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.390.00051
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.3970.002252
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.3980.003226
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.4070.041667
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.4100.037037
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.4170.002703
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.4220.045455
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.4620.008621
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.500.000679
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.540.003021
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.560.017857
ORF1ab/nsp1238Y38XtaCtaA11B.1.1.70.000001
ORF1ab/nsp1238Y38delTAC---11B.1.1.700.000341
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.700.000341
ORF1ab/nsp1238Y38YtaCtaT11B.1.1.890.006061
ORF1ab/nsp1238Y38YtaCtaT11B.1.1390.000733
ORF1ab/nsp1238Y38YtaCtaT11B.1.160.180.007299
ORF1ab/nsp1238Y38HTacCac11B.1.1770.000013
ORF1ab/nsp1238Y38YtaCtaT11B.1.177.210.000076
ORF1ab/nsp1238Y38HTacCac11B.1.177.210.000076
ORF1ab/nsp1238Y38YtaCtaT11B.1.177.350.000691
ORF1ab/nsp1238Y38YtaCtaT11B.1.177.520.001757
ORF1ab/nsp1238Y38DTacGac11B.1.177.70.000165
ORF1ab/nsp1238Y38YtaCtaT11B.1.1820.007246
ORF1ab/nsp1238Y38YtaCtaT11B.1.1890.004292
ORF1ab/nsp1238Y38NTaCAaT11B.1.20.000009
ORF1ab/nsp1238Y38delTAC---11B.1.20.000009
ORF1ab/nsp1238Y38KTaCAaA11B.1.20.000009
ORF1ab/nsp1238Y38YtaCtaT11B.1.2030.0625
ORF1ab/nsp1238Y38YtaCtaT11B.1.2340.000132
ORF1ab/nsp1238Y38YtaCtaT11B.1.2400.000216
ORF1ab/nsp1238Y38YtaCtaT11B.1.3440.008197
ORF1ab/nsp1238Y38YtaCtaT11B.1.3560.001727
ORF1ab/nsp1238Y38XtaCtaA11B.1.360.000146
ORF1ab/nsp1238Y38XtaCtaA11B.1.36.290.000517
ORF1ab/nsp1238Y38YtaCtaT11B.1.3960.000706
ORF1ab/nsp1238Y38DTacGac11B.1.4150.014286
ORF1ab/nsp1238Y38CtActGc11B.1.4290.000024
ORF1ab/nsp1238Y38YtaCtaT11B.1.4560.003268
ORF1ab/nsp1238Y38NTacAac11B.1.4620.007246
ORF1ab/nsp1238Y38delTAC---11B.1.5250.000113
ORF1ab/nsp1238Y38VTACGTA11B.1.5250.000113
ORF1ab/nsp1238Y38YtaCtaT11B.1.5510.00129
ORF1ab/nsp1238Y38YtaCtaT11B.1.5870.001898
ORF1ab/nsp1238Y38YtaCtaT11B.1.617.10.000129
ORF1ab/nsp1238Y38del1Tac-ac11B.1.617.20.000004
ORF1ab/nsp1238Y38delTAC---11B.1.617.20.000004
ORF1ab/nsp1238Y38YtaCtaT11B.1.6370.000073
ORF1ab/nsp1238Y38delTAC---11C.170.055556
ORF1ab/nsp1238Y38delTAC---11C.370.000116
ORF1ab/nsp1238Y38FtActTc11D.20.000075
ORF1ab/nsp1238Y38YtaCtaT11P.1.10.000318
ORF1ab/nsp1238Y38YtaCtaT11P.1.100.000269
ORF1ab/nsp1238Y38YtaCtaT11P.1.120.000484
ORF1ab/nsp1238Y38YtaCtaT11P.1.130.000898
ORF1ab/nsp1238Y38YtaCtaT11P.1.60.001946
ORF1ab/nsp1238Y38delTAC---11P.20.000187
ORF1ab/nsp1238Y38YtaCtaT11P.20.000187
ORF1ab/nsp1238Y38YtaCtaT11Q.10.000126
ORF1ab/nsp1238Y38YtaCtaT11Q.70.001111

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.