CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp2 : CodonNum = 409

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/nsp2409D409GD589GnonsyngAtgGt342134190.9994152030-2032
ORF1ab/nsp2409D409GD589GnonsyngATgGG342110.0002923122030-2032
ORF1ab/nsp2409D409GD589GnonsyngATgGC342110.0002923122030-2032
ORF1ab/nsp2409D409AD589AnonsyngAtgCt33233212030-2032
ORF1ab/nsp2409D409DD589DsyngaTgaC27527512030-2032
ORF1ab/nsp2409D409ND589NnonsynGatAat20720712030-2032
ORF1ab/nsp2409D409YD589YnonsynGatTat10910912030-2032
ORF1ab/nsp2409D409ED589EnonsyngaTgaG41360.8780492030-2032
ORF1ab/nsp2409D409ED589EnonsyngaTgaA4150.1219512030-2032
ORF1ab/nsp2409D409delD589deldelGAT---393912030-2032
ORF1ab/nsp2409D409VD589VnonsyngAtgTt313112030-2032
ORF1ab/nsp2409D409del1D589del1delgaTga-430.752030-2032
ORF1ab/nsp2409D409del1D589del1delgATgG-410.252030-2032
ORF1ab/nsp2409D409ID589InonsynGAtATt1112030-2032
ORF1ab/nsp2409D409SD589SnonsynGAtAGt1112030-2032
ORF1ab/nsp2409D409HD589HnonsynGatCat1112030-2032

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/nsp2409D409GgAtgGt34193421All0.000654
ORF1ab/nsp2409D409GgATgGC13421All0
ORF1ab/nsp2409D409GgATgGG13421All0
ORF1ab/nsp2409D409GgAtgGt17881789B.1.1.3170.736105
ORF1ab/nsp2409D409GgATgGC11789B.1.1.3170.000412
ORF1ab/nsp2409D409GgAtgGt745745AY.40.00116
ORF1ab/nsp2409D409AgAtgCt332332All0.000063
ORF1ab/nsp2409D409GgAtgGt275276B.1.1.70.000246
ORF1ab/nsp2409D409GgATgGG1276B.1.1.70.000001
ORF1ab/nsp2409D409DgaTgaC275275All0.000053
ORF1ab/nsp2409D409GgAtgGt245245B.10.002244
ORF1ab/nsp2409D409NGatAat207207All0.00004
ORF1ab/nsp2409D409AgAtgCt184184B.1.1.70.000165
ORF1ab/nsp2409D409YGatTat109109All0.000021
ORF1ab/nsp2409D409AgAtgCt103103AY.40.00016
ORF1ab/nsp2409D409DgaTgaC7171B.1.1.70.000064
ORF1ab/nsp2409D409GgAtgGt6363AS.20.984375
ORF1ab/nsp2409D409GgAtgGt5959B.1.10.00107
ORF1ab/nsp2409D409NGatAat5858B.1.1.70.000052
ORF1ab/nsp2409D409NGatAat5555B.1.617.20.000207
ORF1ab/nsp2409D409NGatAat4747B.1.3990.090909
ORF1ab/nsp2409D409EgaTgaG3641All0.000007
ORF1ab/nsp2409D409EgaTgaA541All0.000001
ORF1ab/nsp2409D409GgAtgGt4141B.1.617.20.000154
ORF1ab/nsp2409D409YGatTat4141B.1.617.20.000154
ORF1ab/nsp2409D409DgaTgaC4040AY.40.000062
ORF1ab/nsp2409D409delGAT---3939All0.000007
ORF1ab/nsp2409D409DgaTgaC3939AY.430.000173
ORF1ab/nsp2409D409VgAtgTt3131All0.000006
ORF1ab/nsp2409D409GgAtgGt1818AY.440.00011
ORF1ab/nsp2409D409YGatTat1717AY.40.000026
ORF1ab/nsp2409D409GgAtgGt1616AY.430.000071
ORF1ab/nsp2409D409DgaTgaC1616AY.730.010645
ORF1ab/nsp2409D409DgaTgaC1212B.1.2430.000835
ORF1ab/nsp2409D409DgaTgaC1111B.1.617.20.000041
ORF1ab/nsp2409D409DgaTgaC1010AY.260.000283
ORF1ab/nsp2409D409GgAtgGt99AY.250.000054
ORF1ab/nsp2409D409VgAtgTt99AY.40.000014
ORF1ab/nsp2409D409EgaTgaG99B.10.000082
ORF1ab/nsp2409D409GgAtgGt99B.1.3610.011598
ORF1ab/nsp2409D409NGatAat88AY.430.000035
ORF1ab/nsp2409D409EgaTgaG78B.1.1.70.000006
ORF1ab/nsp2409D409EgaTgaA18B.1.1.70.000001
ORF1ab/nsp2409D409GgAtgGt88B.1.20.00007
ORF1ab/nsp2409D409NGatAat77B.10.000064
ORF1ab/nsp2409D409GgAtgGt77B.1.1.1610.024735
ORF1ab/nsp2409D409VgAtgTt77B.1.1.70.000006
ORF1ab/nsp2409D409DgaTgaC77B.1.360.001021
ORF1ab/nsp2409D409GgAtgGt77B.1.36.170.003458
ORF1ab/nsp2409D409NGatAat66AY.250.000036
ORF1ab/nsp2409D409GgAtgGt66AY.340.000582
ORF1ab/nsp2409D409DgaTgaC66B.1.110.30.00431
ORF1ab/nsp2409D409DgaTgaC66B.1.36.120.057692
ORF1ab/nsp2409D409GgAtgGt66B.1.4290.000141
ORF1ab/nsp2409D409AgAtgCt66B.1.5750.00182
ORF1ab/nsp2409D409GgAtgGt66P.10.000095
ORF1ab/nsp2409D409AgAtgCt55AY.1030.000031
ORF1ab/nsp2409D409GgAtgGt55AY.1030.000031
ORF1ab/nsp2409D409GgAtgGt55AY.1190.000177
ORF1ab/nsp2409D409AgAtgCt55AY.1190.000177
ORF1ab/nsp2409D409DgaTgaC55AY.250.00003
ORF1ab/nsp2409D409delGAT---55B.10.000046
ORF1ab/nsp2409D409delGAT---55B.1.1.70.000004
ORF1ab/nsp2409D409GgAtgGt55B.1.1770.000066
ORF1ab/nsp2409D409VgAtgTt55B.1.1770.000066
ORF1ab/nsp2409D409EgaTgaG55B.1.617.20.000019
ORF1ab/nsp2409D409del1gaTga-34All0.000001
ORF1ab/nsp2409D409del1gATgG-14All0
ORF1ab/nsp2409D409YGatTat44AY.1020.000106
ORF1ab/nsp2409D409GgAtgGt44AY.3.10.000341
ORF1ab/nsp2409D409NGatAat44AY.40.000006
ORF1ab/nsp2409D409AgAtgCt44AY.430.000018
ORF1ab/nsp2409D409DgaTgaC44AY.440.000024
ORF1ab/nsp2409D409YGatTat44AY.470.000124
ORF1ab/nsp2409D409DgaTgaC44B.1.1.330.001684
ORF1ab/nsp2409D409GgAtgGt33AY.1020.00008
ORF1ab/nsp2409D409EgaTgaG23AY.1030.000012
ORF1ab/nsp2409D409EgaTgaA13AY.1030.000006
ORF1ab/nsp2409D409YGatTat33AY.250.000018
ORF1ab/nsp2409D409GgAtgGt33AY.390.000074
ORF1ab/nsp2409D409EgaTgaG33AY.40.000005
ORF1ab/nsp2409D409YGatTat33AY.430.000013
ORF1ab/nsp2409D409GgAtgGt33AY.75.10.000541
ORF1ab/nsp2409D409NGatAat33AY.840.001312
ORF1ab/nsp2409D409DgaTgaC33AY.850.001282
ORF1ab/nsp2409D409GgAtgGt33AY.90.000203
ORF1ab/nsp2409D409AgAtgCt33B.10.000027
ORF1ab/nsp2409D409NGatAat33B.1.10.000054
ORF1ab/nsp2409D409delGAT---33B.1.1.330.001263
ORF1ab/nsp2409D409GgAtgGt33B.1.1.5190.000119
ORF1ab/nsp2409D409YGatTat33B.1.1.70.000003
ORF1ab/nsp2409D409GgAtgGt33B.1.177.70.000495
ORF1ab/nsp2409D409GgAtgGt33B.1.2430.000209
ORF1ab/nsp2409D409DgaTgaC33B.1.2580.0002
ORF1ab/nsp2409D409GgAtgGt33B.1.4080.01107
ORF1ab/nsp2409D409GgAtgGt33B.1.466.20.001174
ORF1ab/nsp2409D409GgAtgGt22AE.20.117647
ORF1ab/nsp2409D409DgaTgaC22AY.1030.000012
ORF1ab/nsp2409D409DgaTgaC22AY.116.10.000623
ORF1ab/nsp2409D409NGatAat22AY.1200.000074
ORF1ab/nsp2409D409NGatAat22AY.260.000057
ORF1ab/nsp2409D409GgAtgGt22AY.300.000791
ORF1ab/nsp2409D409GgAtgGt22AY.330.000134
ORF1ab/nsp2409D409NGatAat22AY.330.000134
ORF1ab/nsp2409D409GgAtgGt22AY.34.10.00102
ORF1ab/nsp2409D409NGatAat22AY.390.000049
ORF1ab/nsp2409D409YGatTat22AY.390.000049
ORF1ab/nsp2409D409delGAT---22AY.40.000003
ORF1ab/nsp2409D409DgaTgaC22AY.4.2.10.000298
ORF1ab/nsp2409D409GgAtgGt22AY.420.00008
ORF1ab/nsp2409D409YGatTat22AY.420.00008
ORF1ab/nsp2409D409YGatTat22AY.440.000012
ORF1ab/nsp2409D409GgAtgGt22AY.70.000392
ORF1ab/nsp2409D409YGatTat22AY.7.10.000225
ORF1ab/nsp2409D409DgaTgaC22AY.880.001768
ORF1ab/nsp2409D409GgAtgGt22AY.9.20.000073
ORF1ab/nsp2409D409AgAtgCt22AY.99.20.000184
ORF1ab/nsp2409D409YGatTat22B.10.000018
ORF1ab/nsp2409D409DgaTgaC22B.10.000018
ORF1ab/nsp2409D409delGAT---22B.1.1.3480.001592
ORF1ab/nsp2409D409GgAtgGt22B.1.1.3700.025316
ORF1ab/nsp2409D409DgaTgaC22B.1.1.4200.002012
ORF1ab/nsp2409D409GgAtgGt22B.1.1.5210.010695
ORF1ab/nsp2409D409AgAtgCt22B.1.1920.018519
ORF1ab/nsp2409D409AgAtgCt22B.1.20.000018
ORF1ab/nsp2409D409EgaTgaG22B.1.20.000018
ORF1ab/nsp2409D409DgaTgaC22B.1.2320.001075
ORF1ab/nsp2409D409YGatTat22B.1.2580.000133
ORF1ab/nsp2409D409GgAtgGt22B.1.4200.020833
ORF1ab/nsp2409D409delGAT---22B.1.4240.016129
ORF1ab/nsp2409D409GgAtgGt22B.1.4270.000101
ORF1ab/nsp2409D409DgaTgaC22B.1.5260.000047
ORF1ab/nsp2409D409DgaTgaC22B.1.5960.000174
ORF1ab/nsp2409D409YGatTat22B.1.617.10.000258
ORF1ab/nsp2409D409AgAtgCt22B.1.617.20.000008
ORF1ab/nsp2409D409YGatTat22B.1.621.10.001012
ORF1ab/nsp2409D409YGatTat22B.1.6270.00404
ORF1ab/nsp2409D409delGAT---22N.60.014184
ORF1ab/nsp2409D409NGatAat22P.10.000032
ORF1ab/nsp2409D409DgaTgaC22P.1.140.000096
ORF1ab/nsp2409D409delGAT---22P.20.000373
ORF1ab/nsp2409D409GgAtgGt22Q.80.00033
ORF1ab/nsp2409D409GgAtgGt11A.2.50.000499
ORF1ab/nsp2409D409HGatCat11All0
ORF1ab/nsp2409D409IGAtATt11All0
ORF1ab/nsp2409D409SGAtAGt11All0
ORF1ab/nsp2409D409VgAtgTt11AS.20.015625
ORF1ab/nsp2409D409GgAtgGt11AY.1000.000046
ORF1ab/nsp2409D409VgAtgTt11AY.1010.00049
ORF1ab/nsp2409D409DgaTgaC11AY.1020.000027
ORF1ab/nsp2409D409delGAT---11AY.1030.000006
ORF1ab/nsp2409D409YGatTat11AY.1060.000335
ORF1ab/nsp2409D409GgAtgGt11AY.1070.000466
ORF1ab/nsp2409D409GgAtgGt11AY.1090.00074
ORF1ab/nsp2409D409GgAtgGt11AY.1160.000287
ORF1ab/nsp2409D409NGatAat11AY.1180.000063
ORF1ab/nsp2409D409YGatTat11AY.1210.000135
ORF1ab/nsp2409D409YGatTat11AY.16.10.00047
ORF1ab/nsp2409D409delGAT---11AY.16.10.00047
ORF1ab/nsp2409D409NGatAat11AY.200.000039
ORF1ab/nsp2409D409NGatAat11AY.230.00007
ORF1ab/nsp2409D409EgaTgaG11AY.240.000431
ORF1ab/nsp2409D409YGatTat11AY.240.000431
ORF1ab/nsp2409D409VgAtgTt11AY.250.000006
ORF1ab/nsp2409D409EgaTgaG11AY.260.000028
ORF1ab/nsp2409D409GgAtgGt11AY.290.000016
ORF1ab/nsp2409D409GgAtgGt11AY.30.00001
ORF1ab/nsp2409D409EgaTgaG11AY.30.00001
ORF1ab/nsp2409D409AgAtgCt11AY.330.000067
ORF1ab/nsp2409D409AgAtgCt11AY.390.000025
ORF1ab/nsp2409D409DgaTgaC11AY.390.000025
ORF1ab/nsp2409D409GgAtgGt11AY.39.10.00004
ORF1ab/nsp2409D409GgAtgGt11AY.4.20.000022
ORF1ab/nsp2409D409delGAT---11AY.4.50.000107
ORF1ab/nsp2409D409DgaTgaC11AY.400.000964
ORF1ab/nsp2409D409EgaTgaG11AY.410.000294
ORF1ab/nsp2409D409EgaTgaA11AY.430.000004
ORF1ab/nsp2409D409VgAtgTt11AY.430.000004
ORF1ab/nsp2409D409del1gaTga-11AY.440.000006
ORF1ab/nsp2409D409IGAtATt11AY.440.000006
ORF1ab/nsp2409D409AgAtgCt11AY.440.000006
ORF1ab/nsp2409D409NGatAat11AY.440.000006
ORF1ab/nsp2409D409EgaTgaG11AY.440.000006
ORF1ab/nsp2409D409GgAtgGt11AY.46.50.000198
ORF1ab/nsp2409D409DgaTgaC11AY.470.000031
ORF1ab/nsp2409D409DgaTgaC11AY.50.000021
ORF1ab/nsp2409D409GgAtgGt11AY.5.30.000337
ORF1ab/nsp2409D409GgAtgGt11AY.5.40.000277
ORF1ab/nsp2409D409delGAT---11AY.540.000095
ORF1ab/nsp2409D409GgAtgGt11AY.60.000041
ORF1ab/nsp2409D409AgAtgCt11AY.7.10.000113
ORF1ab/nsp2409D409YGatTat11AY.740.000116
ORF1ab/nsp2409D409DgaTgaC11AY.740.000116
ORF1ab/nsp2409D409GgAtgGt11AY.750.000056
ORF1ab/nsp2409D409VgAtgTt11AY.750.000056
ORF1ab/nsp2409D409DgaTgaC11AY.75.10.00018
ORF1ab/nsp2409D409GgAtgGt11AY.770.001127
ORF1ab/nsp2409D409delGAT---11AY.9.20.000037
ORF1ab/nsp2409D409DgaTgaC11AY.980.000079
ORF1ab/nsp2409D409GgAtgGt11AY.98.10.000048
ORF1ab/nsp2409D409YGatTat11AY.99.10.001553
ORF1ab/nsp2409D409YGatTat11B0.000128
ORF1ab/nsp2409D409VgAtgTt11B.10.000009
ORF1ab/nsp2409D409DgaTgaC11B.1.10.000018
ORF1ab/nsp2409D409AgAtgCt11B.1.10.000018
ORF1ab/nsp2409D409del1gaTga-11B.1.10.000018
ORF1ab/nsp2409D409delGAT---11B.1.10.000018
ORF1ab/nsp2409D409GgAtgGt11B.1.1.100.001115
ORF1ab/nsp2409D409GgAtgGt11B.1.1.1590.004673
ORF1ab/nsp2409D409GgAtgGt11B.1.1.1760.000439
ORF1ab/nsp2409D409GgAtgGt11B.1.1.1980.001468
ORF1ab/nsp2409D409AgAtgCt11B.1.1.2220.000204
ORF1ab/nsp2409D409GgAtgGt11B.1.1.2220.000204
ORF1ab/nsp2409D409NGatAat11B.1.1.250.000569
ORF1ab/nsp2409D409EgaTgaA11B.1.1.2580.003257
ORF1ab/nsp2409D409GgAtgGt11B.1.1.2910.000742
ORF1ab/nsp2409D409GgAtgGt11B.1.1.3260.001761
ORF1ab/nsp2409D409VgAtgTt11B.1.1.330.000421
ORF1ab/nsp2409D409GgAtgGt11B.1.1.3470.018182
ORF1ab/nsp2409D409AgAtgCt11B.1.1.3720.000689
ORF1ab/nsp2409D409GgAtgGt11B.1.1.3980.003226
ORF1ab/nsp2409D409delGAT---11B.1.1.4160.000905
ORF1ab/nsp2409D409YGatTat11B.1.1.5190.00004
ORF1ab/nsp2409D409HGatCat11B.1.1.70.000001
ORF1ab/nsp2409D409EgaTgaG11B.1.1.700.000341
ORF1ab/nsp2409D409del1gATgG-11B.1.110.30.000718
ORF1ab/nsp2409D409GgAtgGt11B.1.1600.000031
ORF1ab/nsp2409D409NGatAat11B.1.1770.000013
ORF1ab/nsp2409D409YGatTat11B.1.1770.000013
ORF1ab/nsp2409D409delGAT---11B.1.177.180.00116
ORF1ab/nsp2409D409GgAtgGt11B.1.177.210.000076
ORF1ab/nsp2409D409VgAtgTt11B.1.177.500.004695
ORF1ab/nsp2409D409AgAtgCt11B.1.177.530.002392
ORF1ab/nsp2409D409DgaTgaC11B.1.177.570.000281
ORF1ab/nsp2409D409GgAtgGt11B.1.177.600.000218
ORF1ab/nsp2409D409AgAtgCt11B.1.177.70.000165
ORF1ab/nsp2409D409delGAT---11B.1.1790.003759
ORF1ab/nsp2409D409DgaTgaC11B.1.20.000009
ORF1ab/nsp2409D409SGAtAGt11B.1.20.000009
ORF1ab/nsp2409D409DgaTgaC11B.1.2210.000071
ORF1ab/nsp2409D409delGAT---11B.1.2340.000132
ORF1ab/nsp2409D409GgAtgGt11B.1.2580.000067
ORF1ab/nsp2409D409GgAtgGt11B.1.3240.001605
ORF1ab/nsp2409D409DgaTgaC11B.1.3500.002933
ORF1ab/nsp2409D409AgAtgCt11B.1.3510.00003
ORF1ab/nsp2409D409YGatTat11B.1.351.20.000303
ORF1ab/nsp2409D409GgAtgGt11B.1.360.000146
ORF1ab/nsp2409D409YGatTat11B.1.4160.001269
ORF1ab/nsp2409D409GgAtgGt11B.1.4170.028571
ORF1ab/nsp2409D409delGAT---11B.1.4290.000024
ORF1ab/nsp2409D409YGatTat11B.1.4410.009615
ORF1ab/nsp2409D409YGatTat11B.1.4850.014925
ORF1ab/nsp2409D409DgaTgaC11B.1.5250.000113
ORF1ab/nsp2409D409GgAtgGt11B.1.5260.000024
ORF1ab/nsp2409D409GgAtgGt11B.1.5580.004566
ORF1ab/nsp2409D409delGAT---11B.1.5610.000397
ORF1ab/nsp2409D409GgAtgGt11B.1.5640.000426
ORF1ab/nsp2409D409VgAtgTt11B.1.5670.003333
ORF1ab/nsp2409D409AgAtgCt11B.1.5960.000087
ORF1ab/nsp2409D409GgAtgGt11B.1.5960.000087
ORF1ab/nsp2409D409GgAtgGt11B.1.617.10.000129
ORF1ab/nsp2409D409delGAT---11B.1.617.20.000004
ORF1ab/nsp2409D409del1gaTga-11B.1.617.20.000004
ORF1ab/nsp2409D409GgAtgGt11B.1.6280.000352
ORF1ab/nsp2409D409DgaTgaC11B.1.6370.000073
ORF1ab/nsp2409D409AgAtgCt11B.1.6370.000073
ORF1ab/nsp2409D409EgaTgaA11B.40.002208
ORF1ab/nsp2409D409EgaTgaG11B.400.000364
ORF1ab/nsp2409D409delGAT---11B.570.015152
ORF1ab/nsp2409D409YGatTat11B.60.00091
ORF1ab/nsp2409D409GgAtgGt11C.36.10.004149
ORF1ab/nsp2409D409VgAtgTt11D.20.000075
ORF1ab/nsp2409D409DgaTgaC11D.20.000075
ORF1ab/nsp2409D409YGatTat11D.20.000075
ORF1ab/nsp2409D409AgAtgCt11D.20.000075
ORF1ab/nsp2409D409EgaTgaG11N.50.001767
ORF1ab/nsp2409D409GgAtgGt11N.50.001767
ORF1ab/nsp2409D409delGAT---11P.10.000016
ORF1ab/nsp2409D409DgaTgaC11P.10.000016
ORF1ab/nsp2409D409YGatTat11P.1.140.000048
ORF1ab/nsp2409D409DgaTgaC11P.1.170.000162
ORF1ab/nsp2409D409delGAT---11Q.10.000126
ORF1ab/nsp2409D409GgAtgGt11Q.10.000126
ORF1ab/nsp2409D409AgAtgCt11Q.80.000165

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.