CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 839

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/nsp3839K839EK1657EnonsynAaaGaa2933293315234-5236
ORF1ab/nsp3839K839RK1657RnonsynaAaaGa9089070.9988995234-5236
ORF1ab/nsp3839K839RK1657RnonsynaAAaGG90810.001101325234-5236
ORF1ab/nsp3839K839KK1657KsynaaAaaG61761715234-5236
ORF1ab/nsp3839K839QK1657QnonsynAaaCaa858515234-5236
ORF1ab/nsp3839K839TK1657TnonsynaAaaCa80780.9755234-5236
ORF1ab/nsp3839K839TK1657TnonsynaAAaCT8020.0255234-5236
ORF1ab/nsp3839K839delK1657deldelAAA---494915234-5236
ORF1ab/nsp3839K839NK1657NnonsynaaAaaC47310.6595745234-5236
ORF1ab/nsp3839K839NK1657NnonsynaaAaaT47160.3404265234-5236
ORF1ab/nsp3839K839del1K1657del1delAaa-aa29250.8620695234-5236
ORF1ab/nsp3839K839del1K1657del1delAaAGa-2910.03448285234-5236
ORF1ab/nsp3839K839del1K1657del1delAaA-aN2910.03448285234-5236
ORF1ab/nsp3839K839del1K1657del1delAAa-Na2910.03448285234-5236
ORF1ab/nsp3839K839del1K1657del1delaaAaa-2910.03448285234-5236
ORF1ab/nsp3839K839IK1657InonsynaAaaTa141415234-5236
ORF1ab/nsp3839K839XK1657XnonsynAaaTaa3315234-5236
ORF1ab/nsp3839K839HK1657HnonsynAaACaC2215234-5236
ORF1ab/nsp3839K839del2K1657del2delaAAa--210.55234-5236
ORF1ab/nsp3839K839del2K1657del2delAAa--a210.55234-5236
ORF1ab/nsp3839K839VK1657VnonsynAAaGTa1115234-5236

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/nsp3839K839EAaaGaa29332933All0.000561
ORF1ab/nsp3839K839EAaaGaa18851885A.2.50.940619
ORF1ab/nsp3839K839RaAaaGa907908All0.000173
ORF1ab/nsp3839K839RaAAaGG1908All0
ORF1ab/nsp3839K839KaaAaaG617617All0.000118
ORF1ab/nsp3839K839EAaaGaa585585A.2.5.20.919811
ORF1ab/nsp3839K839RaAaaGa524524AY.1030.003254
ORF1ab/nsp3839K839RaAaaGa288288AY.40.000448
ORF1ab/nsp3839K839EAaaGaa204204A.2.5.10.980769
ORF1ab/nsp3839K839KaaAaaG9696B.1.6370.007015
ORF1ab/nsp3839K839EAaaGaa9191A.2.5.30.938144
ORF1ab/nsp3839K839QAaaCaa8585All0.000016
ORF1ab/nsp3839K839KaaAaaG8383AY.50.001714
ORF1ab/nsp3839K839TaAaaCa7880All0.000015
ORF1ab/nsp3839K839TaAAaCT280All0
ORF1ab/nsp3839K839KaaAaaG6565R.10.005851
ORF1ab/nsp3839K839KaaAaaG6464B.1.617.20.000241
ORF1ab/nsp3839K839EAaaGaa5959AY.40.000092
ORF1ab/nsp3839K839KaaAaaG5353AY.40.000082
ORF1ab/nsp3839K839delAAA---4949All0.000009
ORF1ab/nsp3839K839NaaAaaC3147All0.000006
ORF1ab/nsp3839K839NaaAaaT1647All0.000003
ORF1ab/nsp3839K839KaaAaaG3939B.1.1.70.000035
ORF1ab/nsp3839K839TaAaaCa3030B.1.1600.000936
ORF1ab/nsp3839K839del1Aaa-aa2529All0.000005
ORF1ab/nsp3839K839del1AaA-aN129All0
ORF1ab/nsp3839K839del1aaAaa-129All0
ORF1ab/nsp3839K839del1AaAGa-129All0
ORF1ab/nsp3839K839del1AAa-Na129All0
ORF1ab/nsp3839K839QAaaCaa2828AY.440.00017
ORF1ab/nsp3839K839KaaAaaG2424B.1.20.000211
ORF1ab/nsp3839K839KaaAaaG2121AY.30.000209
ORF1ab/nsp3839K839KaaAaaG2020AY.390.000494
ORF1ab/nsp3839K839KaaAaaG1919AY.250.000114
ORF1ab/nsp3839K839EAaaGaa1616AY.1030.000099
ORF1ab/nsp3839K839RaAaaGa1516B.1.1.70.000013
ORF1ab/nsp3839K839RaAAaGG116B.1.1.70.000001
ORF1ab/nsp3839K839NaaAaaC1515B.1.1.70.000013
ORF1ab/nsp3839K839IaAaaTa1414All0.000003
ORF1ab/nsp3839K839KaaAaaG1414B.1.1.2970.03132
ORF1ab/nsp3839K839QAaaCaa1414B.1.1.4320.017722
ORF1ab/nsp3839K839RaAaaGa1414B.1.617.20.000053
ORF1ab/nsp3839K839del1Aaa-aa1314P.10.000205
ORF1ab/nsp3839K839del1AAa-Na114P.10.000016
ORF1ab/nsp3839K839KaaAaaG1313B.10.000119
ORF1ab/nsp3839K839RaAaaGa1212AY.260.00034
ORF1ab/nsp3839K839RaAaaGa1212AY.30.000119
ORF1ab/nsp3839K839TaAaaCa1212AY.40.000019
ORF1ab/nsp3839K839TaAaaCa1111AY.1030.000068
ORF1ab/nsp3839K839KaaAaaG1111AY.1030.000068
ORF1ab/nsp3839K839QAaaCaa1111AY.39.10.000436
ORF1ab/nsp3839K839QAaaCaa1111AY.98.10.000533
ORF1ab/nsp3839K839KaaAaaG1111B.1.4270.000555
ORF1ab/nsp3839K839KaaAaaG1111P.1.100.002964
ORF1ab/nsp3839K839EAaaGaa1010B.10.000092
ORF1ab/nsp3839K839delAAA---1010B.1.1.70.000009
ORF1ab/nsp3839K839RaAaaGa99AY.1190.000318
ORF1ab/nsp3839K839NaaAaaT77B.1.1.3190.122807
ORF1ab/nsp3839K839KaaAaaG77B.1.1770.000092
ORF1ab/nsp3839K839KaaAaaG77B.1.3510.000208
ORF1ab/nsp3839K839EAaaGaa66AY.1000.000276
ORF1ab/nsp3839K839TaAaaCa66B.1.1.70.000005
ORF1ab/nsp3839K839EAaaGaa66B.1.1.70.000005
ORF1ab/nsp3839K839delAAA---55AY.40.000008
ORF1ab/nsp3839K839del1Aaa-aa45AY.99.20.000369
ORF1ab/nsp3839K839del1AaA-aN15AY.99.20.000092
ORF1ab/nsp3839K839QAaaCaa55B.10.000046
ORF1ab/nsp3839K839EAaaGaa55B.1.10.000091
ORF1ab/nsp3839K839EAaaGaa55B.1.1770.000066
ORF1ab/nsp3839K839RaAaaGa55B.1.5260.000118
ORF1ab/nsp3839K839EAaaGaa55B.1.617.20.000019
ORF1ab/nsp3839K839RaAaaGa55P.10.000079
ORF1ab/nsp3839K839KaaAaaG55P.10.000079
ORF1ab/nsp3839K839EAaaGaa44AY.1200.000149
ORF1ab/nsp3839K839KaaAaaG44AY.330.000267
ORF1ab/nsp3839K839NaaAaaC44AY.430.000018
ORF1ab/nsp3839K839KaaAaaG44AY.440.000024
ORF1ab/nsp3839K839delAAA---44B.10.000037
ORF1ab/nsp3839K839del1Aaa-aa24B.1.1.70.000002
ORF1ab/nsp3839K839del1aaAaa-14B.1.1.70.000001
ORF1ab/nsp3839K839del1AaAGa-14B.1.1.70.000001
ORF1ab/nsp3839K839NaaAaaT44B.1.4270.000202
ORF1ab/nsp3839K839QAaaCaa44B.1.617.20.000015
ORF1ab/nsp3839K839TaAaaCa44B.1.617.20.000015
ORF1ab/nsp3839K839NaaAaaC44B.1.617.20.000015
ORF1ab/nsp3839K839XAaaTaa33All0.000001
ORF1ab/nsp3839K839TaAaaCa33AY.1020.00008
ORF1ab/nsp3839K839KaaAaaG33AY.1190.000106
ORF1ab/nsp3839K839RaAaaGa33AY.250.000018
ORF1ab/nsp3839K839RaAaaGa33B.10.000027
ORF1ab/nsp3839K839IaAaaTa33B.1.1.70.000003
ORF1ab/nsp3839K839EAaaGaa33B.1.2390.003663
ORF1ab/nsp3839K839delAAA---33B.1.617.20.000011
ORF1ab/nsp3839K839TaAAaCT220.111111
ORF1ab/nsp3839K839delAAA---220.111111
ORF1ab/nsp3839K839HAaACaC22All0
ORF1ab/nsp3839K839del2aAAa--12All0
ORF1ab/nsp3839K839del2AAa--a12All0
ORF1ab/nsp3839K839RaAaaGa22AY.1000.000092
ORF1ab/nsp3839K839EAaaGaa22AY.160.000759
ORF1ab/nsp3839K839EAaaGaa22AY.250.000012
ORF1ab/nsp3839K839KaaAaaG22AY.290.000032
ORF1ab/nsp3839K839NaaAaaC22AY.30.00002
ORF1ab/nsp3839K839EAaaGaa22AY.390.000049
ORF1ab/nsp3839K839RaAaaGa22AY.390.000049
ORF1ab/nsp3839K839IaAaaTa22AY.40.000003
ORF1ab/nsp3839K839KaaAaaG22AY.420.00008
ORF1ab/nsp3839K839delAAA---22AY.430.000009
ORF1ab/nsp3839K839KaaAaaG22AY.430.000009
ORF1ab/nsp3839K839TaAaaCa22AY.440.000012
ORF1ab/nsp3839K839RaAaaGa22AY.440.000012
ORF1ab/nsp3839K839KaaAaaG22AY.450.000243
ORF1ab/nsp3839K839EAaaGaa22AY.46.10.002053
ORF1ab/nsp3839K839KaaAaaG22AY.470.000062
ORF1ab/nsp3839K839EAaaGaa22AY.540.000191
ORF1ab/nsp3839K839IaAaaTa22AY.750.000112
ORF1ab/nsp3839K839KaaAaaG22AY.770.002255
ORF1ab/nsp3839K839KaaAaaG22B.1.10.000036
ORF1ab/nsp3839K839EAaaGaa22B.1.1570.00597
ORF1ab/nsp3839K839delAAA---22B.1.1770.000026
ORF1ab/nsp3839K839IaAaaTa22B.1.20.000018
ORF1ab/nsp3839K839TaAaaCa22B.1.20.000018
ORF1ab/nsp3839K839delAAA---22B.1.360.000292
ORF1ab/nsp3839K839KaaAaaG22B.1.36.180.00084
ORF1ab/nsp3839K839EAaaGaa22B.1.4290.000047
ORF1ab/nsp3839K839del1Aaa-aa22B.1.617.20.000008
ORF1ab/nsp3839K839KaaAaaG22P.1.170.000324
ORF1ab/nsp3839K839RaAaaGa22R.10.00018
ORF1ab/nsp3839K839EAaaGaa11A.10.000282
ORF1ab/nsp3839K839KaaAaaG11A.20.000662
ORF1ab/nsp3839K839EAaaGaa11A.20.000662
ORF1ab/nsp3839K839delAAA---11A.2.20.001689
ORF1ab/nsp3839K839delAAA---11AH.30.003802
ORF1ab/nsp3839K839VAAaGTa11All0
ORF1ab/nsp3839K839KaaAaaG11AY.10.000396
ORF1ab/nsp3839K839KaaAaaG11AY.1020.000027
ORF1ab/nsp3839K839QAaaCaa11AY.1030.000006
ORF1ab/nsp3839K839TaAaaCa11AY.1100.000113
ORF1ab/nsp3839K839KaaAaaG11AY.1130.000142
ORF1ab/nsp3839K839KaaAaaG11AY.1160.000287
ORF1ab/nsp3839K839EAaaGaa11AY.116.10.000311
ORF1ab/nsp3839K839KaaAaaG11AY.1170.000085
ORF1ab/nsp3839K839RaAaaGa11AY.1170.000085
ORF1ab/nsp3839K839KaaAaaG11AY.1180.000063
ORF1ab/nsp3839K839EAaaGaa11AY.1190.000035
ORF1ab/nsp3839K839del2AAa--a11AY.1190.000035
ORF1ab/nsp3839K839EAaaGaa11AY.20.000356
ORF1ab/nsp3839K839EAaaGaa11AY.200.000039
ORF1ab/nsp3839K839KaaAaaG11AY.200.000039
ORF1ab/nsp3839K839KaaAaaG11AY.230.00007
ORF1ab/nsp3839K839delAAA---11AY.250.000006
ORF1ab/nsp3839K839EAaaGaa11AY.260.000028
ORF1ab/nsp3839K839del1Aaa-aa11AY.260.000028
ORF1ab/nsp3839K839KaaAaaG11AY.260.000028
ORF1ab/nsp3839K839TaAaaCa11AY.260.000028
ORF1ab/nsp3839K839QAaaCaa11AY.340.000097
ORF1ab/nsp3839K839TaAaaCa11AY.370.000316
ORF1ab/nsp3839K839IaAaaTa11AY.390.000025
ORF1ab/nsp3839K839XAaaTaa11AY.40.000002
ORF1ab/nsp3839K839NaaAaaC11AY.40.000002
ORF1ab/nsp3839K839QAaaCaa11AY.40.000002
ORF1ab/nsp3839K839delAAA---11AY.4.50.000107
ORF1ab/nsp3839K839RaAaaGa11AY.420.00004
ORF1ab/nsp3839K839QAaaCaa11AY.430.000004
ORF1ab/nsp3839K839TaAaaCa11AY.430.000004
ORF1ab/nsp3839K839HAaACaC11AY.430.000004
ORF1ab/nsp3839K839EAaaGaa11AY.440.000006
ORF1ab/nsp3839K839NaaAaaT11AY.440.000006
ORF1ab/nsp3839K839TaAaaCa11AY.450.000122
ORF1ab/nsp3839K839delAAA---11AY.46.20.000635
ORF1ab/nsp3839K839QAaaCaa11AY.46.60.000072
ORF1ab/nsp3839K839EAaaGaa11AY.470.000031
ORF1ab/nsp3839K839NaaAaaC11AY.5.40.000277
ORF1ab/nsp3839K839KaaAaaG11AY.60.000041
ORF1ab/nsp3839K839NaaAaaT11AY.60.000041
ORF1ab/nsp3839K839EAaaGaa11AY.60.000041
ORF1ab/nsp3839K839NaaAaaC11AY.610.000105
ORF1ab/nsp3839K839KaaAaaG11AY.690.000187
ORF1ab/nsp3839K839delAAA---11AY.750.000056
ORF1ab/nsp3839K839KaaAaaG11AY.9.10.000084
ORF1ab/nsp3839K839EAaaGaa11AY.9.20.000037
ORF1ab/nsp3839K839TaAaaCa11AY.9.20.000037
ORF1ab/nsp3839K839QAaaCaa11AY.940.000443
ORF1ab/nsp3839K839KaaAaaG11AY.98.10.000048
ORF1ab/nsp3839K839EAaaGaa11B0.000128
ORF1ab/nsp3839K839XAaaTaa11B.10.000009
ORF1ab/nsp3839K839TaAaaCa11B.1.10.000018
ORF1ab/nsp3839K839del1Aaa-aa11B.1.10.000018
ORF1ab/nsp3839K839NaaAaaC11B.1.10.000018
ORF1ab/nsp3839K839IaAaaTa11B.1.10.000018
ORF1ab/nsp3839K839del1Aaa-aa11B.1.1.1280.007092
ORF1ab/nsp3839K839delAAA---11B.1.1.1420.017544
ORF1ab/nsp3839K839EAaaGaa11B.1.1.2220.000204
ORF1ab/nsp3839K839EAaaGaa11B.1.1.2650.003155
ORF1ab/nsp3839K839EAaaGaa11B.1.1.3070.002532
ORF1ab/nsp3839K839delAAA---11B.1.1.3150.008475
ORF1ab/nsp3839K839EAaaGaa11B.1.1.3180.000302
ORF1ab/nsp3839K839NaaAaaC11B.1.1.3780.007299
ORF1ab/nsp3839K839KaaAaaG11B.1.1.4130.006897
ORF1ab/nsp3839K839EAaaGaa11B.1.1.4640.001473
ORF1ab/nsp3839K839delAAA---11B.1.1.5190.00004
ORF1ab/nsp3839K839VAAaGTa11B.1.1.70.000001
ORF1ab/nsp3839K839XAaaTaa11B.1.1.70.000001
ORF1ab/nsp3839K839del2aAAa--11B.1.1.70.000001
ORF1ab/nsp3839K839QAaaCaa11B.1.1.70.000001
ORF1ab/nsp3839K839KaaAaaG11B.1.1600.000031
ORF1ab/nsp3839K839QAaaCaa11B.1.1770.000013
ORF1ab/nsp3839K839KaaAaaG11B.1.177.160.000664
ORF1ab/nsp3839K839EAaaGaa11B.1.177.170.000821
ORF1ab/nsp3839K839delAAA---11B.1.177.210.000076
ORF1ab/nsp3839K839delAAA---11B.1.177.620.001192
ORF1ab/nsp3839K839KaaAaaG11B.1.177.650.000665
ORF1ab/nsp3839K839EAaaGaa11B.1.177.650.000665
ORF1ab/nsp3839K839delAAA---11B.1.177.680.015152
ORF1ab/nsp3839K839QAaaCaa11B.1.177.810.000189
ORF1ab/nsp3839K839delAAA---11B.1.177.810.000189
ORF1ab/nsp3839K839RaAaaGa11B.1.20.000009
ORF1ab/nsp3839K839EAaaGaa11B.1.20.000009
ORF1ab/nsp3839K839QAaaCaa11B.1.20.000009
ORF1ab/nsp3839K839NaaAaaT11B.1.20.000009
ORF1ab/nsp3839K839KaaAaaG11B.1.2140.003663
ORF1ab/nsp3839K839QAaaCaa11B.1.2210.000071
ORF1ab/nsp3839K839EAaaGaa11B.1.2210.000071
ORF1ab/nsp3839K839KaaAaaG11B.1.2430.00007
ORF1ab/nsp3839K839RaAaaGa11B.1.2430.00007
ORF1ab/nsp3839K839RaAaaGa11B.1.2580.000067
ORF1ab/nsp3839K839delAAA---11B.1.3190.003049
ORF1ab/nsp3839K839RaAaaGa11B.1.3250.006897
ORF1ab/nsp3839K839EAaaGaa11B.1.3360.002439
ORF1ab/nsp3839K839KaaAaaG11B.1.351.20.000303
ORF1ab/nsp3839K839KaaAaaG11B.1.360.000146
ORF1ab/nsp3839K839EAaaGaa11B.1.360.000146
ORF1ab/nsp3839K839EAaaGaa11B.1.36.10.00114
ORF1ab/nsp3839K839NaaAaaT11B.1.36.160.001425
ORF1ab/nsp3839K839EAaaGaa11B.1.3910.001127
ORF1ab/nsp3839K839KaaAaaG11B.1.4090.000781
ORF1ab/nsp3839K839delAAA---11B.1.416.10.001563
ORF1ab/nsp3839K839EAaaGaa11B.1.4220.000812
ORF1ab/nsp3839K839IaAaaTa11B.1.4270.00005
ORF1ab/nsp3839K839RaAaaGa11B.1.4290.000024
ORF1ab/nsp3839K839EAaaGaa11B.1.4620.007246
ORF1ab/nsp3839K839EAaaGaa11B.1.5040.03125
ORF1ab/nsp3839K839KaaAaaG11B.1.5260.000024
ORF1ab/nsp3839K839RaAaaGa11B.1.5820.000491
ORF1ab/nsp3839K839KaaAaaG11B.1.6090.000479
ORF1ab/nsp3839K839IaAaaTa11B.1.617.20.000004
ORF1ab/nsp3839K839HAaACaC11B.1.617.20.000004
ORF1ab/nsp3839K839delAAA---11B.1.6210.000089
ORF1ab/nsp3839K839EAaaGaa11B.1.6230.000536
ORF1ab/nsp3839K839EAaaGaa11B.1.6280.000352
ORF1ab/nsp3839K839delAAA---11B.1.6300.005236
ORF1ab/nsp3839K839delAAA---11B.150.017544
ORF1ab/nsp3839K839QAaaCaa11B.6.30.026316
ORF1ab/nsp3839K839RaAaaGa11B.6.80.008264
ORF1ab/nsp3839K839TaAaaCa11C.36.30.000567
ORF1ab/nsp3839K839delAAA---11C.370.000116
ORF1ab/nsp3839K839NaaAaaT11C.370.000116
ORF1ab/nsp3839K839EAaaGaa11D.20.000075
ORF1ab/nsp3839K839EAaaGaa11P.10.000016
ORF1ab/nsp3839K839EAaaGaa11P.1.140.000048
ORF1ab/nsp3839K839NaaAaaC11P.20.000187
ORF1ab/nsp3839K839del1Aaa-aa11P.20.000187
ORF1ab/nsp3839K839EAaaGaa11Q.10.000126
ORF1ab/nsp3839K839IaAaaTa11Q.30.000145
ORF1ab/nsp3839K839EAaaGaa11R.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.