CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp9 : CodonNum = 25

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/nsp925D25GD4165GnonsyngAtgGt7447430.99865612758-12760
ORF1ab/nsp925D25GD4165GnonsyngATgGC74410.0013440912758-12760
ORF1ab/nsp925D25DD4165DsyngaTgaC547547112758-12760
ORF1ab/nsp925D25ND4165NnonsynGatAat172172112758-12760
ORF1ab/nsp925D25AD4165AnonsyngAtgCt135135112758-12760
ORF1ab/nsp925D25delD4165deldelGAT---5252112758-12760
ORF1ab/nsp925D25YD4165YnonsynGatTat4949112758-12760
ORF1ab/nsp925D25ED4165EnonsyngaTgaA22160.72727312758-12760
ORF1ab/nsp925D25ED4165EnonsyngaTgaG2260.27272712758-12760
ORF1ab/nsp925D25del2D4165del2delGAt--t1111112758-12760
ORF1ab/nsp925D25VD4165VnonsyngAtgTt66112758-12760
ORF1ab/nsp925D25HD4165HnonsynGatCat650.83333312758-12760
ORF1ab/nsp925D25HD4165HnonsynGaTCaC610.16666712758-12760
ORF1ab/nsp925D25del1D4165del1delGat-at310.33333312758-12760
ORF1ab/nsp925D25del1D4165del1delgAtg-t310.33333312758-12760
ORF1ab/nsp925D25del1D4165del1delgaTga-310.33333312758-12760
ORF1ab/nsp925D25TD4165TnonsynGATACA11112758-12760

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/nsp925D25GgAtgGt743744All0.000142
ORF1ab/nsp925D25GgATgGC1744All0
ORF1ab/nsp925D25DgaTgaC547547All0.000105
ORF1ab/nsp925D25GgAtgGt479479B.1.2360.983573
ORF1ab/nsp925D25DgaTgaC250250B.1.1.70.000224
ORF1ab/nsp925D25NGatAat172172All0.000033
ORF1ab/nsp925D25AgAtgCt135135All0.000026
ORF1ab/nsp925D25DgaTgaC8989AY.120.10.028571
ORF1ab/nsp925D25NGatAat8585AY.910.062089
ORF1ab/nsp925D25AgAtgCt8181AY.40.000126
ORF1ab/nsp925D25DgaTgaC6565B.1.1.3740.154394
ORF1ab/nsp925D25delGAT---5252All0.00001
ORF1ab/nsp925D25YGatTat4949All0.000009
ORF1ab/nsp925D25GgAtgGt4444AY.260.001246
ORF1ab/nsp925D25GgAtgGt3131B.1.1180.208054
ORF1ab/nsp925D25EgaTgaA1622All0.000003
ORF1ab/nsp925D25EgaTgaG622All0.000001
ORF1ab/nsp925D25NGatAat2121B.1.1.70.000019
ORF1ab/nsp925D25AgAtgCt1616AY.260.000453
ORF1ab/nsp925D25GgAtgGt1516B.10.000137
ORF1ab/nsp925D25GgATgGC116B.10.000009
ORF1ab/nsp925D25GgAtgGt1616B.1.1.70.000014
ORF1ab/nsp925D25GgAtgGt1616B.1.1580.380952
ORF1ab/nsp925D25GgAtgGt1515AY.40.000023
ORF1ab/nsp925D25NGatAat1313AY.40.00002
ORF1ab/nsp925D25GgAtgGt1212B.1.617.20.000045
ORF1ab/nsp925D25del2GAt--t1111All0.000002
ORF1ab/nsp925D25delGAT---1111AY.750.000616
ORF1ab/nsp925D25YGatTat1111B.1.1.70.00001
ORF1ab/nsp925D25DgaTgaC1010AY.30.000099
ORF1ab/nsp925D25DgaTgaC1010AY.40.000016
ORF1ab/nsp925D25DgaTgaC1010B.1.617.20.000038
ORF1ab/nsp925D25YGatTat1010P.10.000158
ORF1ab/nsp925D25DgaTgaC99AY.430.00004
ORF1ab/nsp925D25DgaTgaC99B.1.20.000079
ORF1ab/nsp925D25GgAtgGt99P.10.000142
ORF1ab/nsp925D25GgAtgGt88B.1.1770.000105
ORF1ab/nsp925D25DgaTgaC88B.1.3510.000238
ORF1ab/nsp925D25GgAtgGt77AY.440.000043
ORF1ab/nsp925D25AgAtgCt77B.1.1.70.000006
ORF1ab/nsp925D25delGAT---77B.1.1600.000218
ORF1ab/nsp925D25VgAtgTt66All0.000001
ORF1ab/nsp925D25HGatCat56All0.000001
ORF1ab/nsp925D25HGaTCaC16All0
ORF1ab/nsp925D25GgAtgGt66AY.200.000233
ORF1ab/nsp925D25del2GAt--t66AY.250.000036
ORF1ab/nsp925D25delGAT---66AY.250.000036
ORF1ab/nsp925D25NGatAat66AY.250.000036
ORF1ab/nsp925D25NGatAat66B.10.000055
ORF1ab/nsp925D25delGAT---66B.1.1770.000079
ORF1ab/nsp925D25GgAtgGt66B.1.177.430.008863
ORF1ab/nsp925D25GgAtgGt66B.1.20.000053
ORF1ab/nsp925D25DgaTgaC55AY.1020.000133
ORF1ab/nsp925D25YGatTat55AY.40.000008
ORF1ab/nsp925D25DgaTgaC55B.1.10.000091
ORF1ab/nsp925D25DgaTgaC55B.1.177.870.003639
ORF1ab/nsp925D25GgAtgGt55C.36.30.002836
ORF1ab/nsp925D25DgaTgaC44AY.140.000352
ORF1ab/nsp925D25DgaTgaC44AY.250.000024
ORF1ab/nsp925D25NGatAat44AY.440.000024
ORF1ab/nsp925D25DgaTgaC44AY.440.000024
ORF1ab/nsp925D25GgAtgGt44AY.610.000419
ORF1ab/nsp925D25YGatTat44B.10.000037
ORF1ab/nsp925D25DgaTgaC44B.10.000037
ORF1ab/nsp925D25NGatAat44B.1.1600.000125
ORF1ab/nsp925D25AgAtgCt44B.1.20.000035
ORF1ab/nsp925D25DgaTgaC44B.1.2220.006768
ORF1ab/nsp925D25del1gaTga-13All0
ORF1ab/nsp925D25del1gAtg-t13All0
ORF1ab/nsp925D25del1Gat-at13All0
ORF1ab/nsp925D25DgaTgaC33AY.98.10.000145
ORF1ab/nsp925D25AgAtgCt33B.10.000027
ORF1ab/nsp925D25EgaTgaA33B.10.000027
ORF1ab/nsp925D25GgAtgGt33B.1.10.000054
ORF1ab/nsp925D25DgaTgaC33B.1.1.280.000934
ORF1ab/nsp925D25del2GAt--t33B.1.1.70.000003
ORF1ab/nsp925D25DgaTgaC33B.1.1600.000094
ORF1ab/nsp925D25GgAtgGt33B.1.2580.0002
ORF1ab/nsp925D25AgAtgCt33B.1.360.000438
ORF1ab/nsp925D25GgAtgGt33B.1.4290.000071
ORF1ab/nsp925D25DgaTgaC33B.1.5070.033708
ORF1ab/nsp925D25AgAtgCt33B.1.617.20.000011
ORF1ab/nsp925D25YGatTat33B.1.617.20.000011
ORF1ab/nsp925D25NGatAat33B.1.6210.000266
ORF1ab/nsp925D25GgAtgGt22AY.1000.000092
ORF1ab/nsp925D25YGatTat22AY.1020.000053
ORF1ab/nsp925D25GgAtgGt22AY.1030.000012
ORF1ab/nsp925D25DgaTgaC22AY.1030.000012
ORF1ab/nsp925D25DgaTgaC22AY.1180.000125
ORF1ab/nsp925D25GgAtgGt22AY.1190.000071
ORF1ab/nsp925D25GgAtgGt22AY.1200.000074
ORF1ab/nsp925D25DgaTgaC22AY.1200.000074
ORF1ab/nsp925D25DgaTgaC22AY.120.2.10.000997
ORF1ab/nsp925D25NGatAat22AY.200.000078
ORF1ab/nsp925D25GgAtgGt22AY.250.000012
ORF1ab/nsp925D25DgaTgaC22AY.260.000057
ORF1ab/nsp925D25DgaTgaC22AY.270.000129
ORF1ab/nsp925D25NGatAat22AY.30.00002
ORF1ab/nsp925D25DgaTgaC22AY.3.10.000171
ORF1ab/nsp925D25DgaTgaC22AY.390.000049
ORF1ab/nsp925D25delGAT---22AY.40.000003
ORF1ab/nsp925D25EgaTgaA12AY.40.000002
ORF1ab/nsp925D25EgaTgaG12AY.40.000002
ORF1ab/nsp925D25DgaTgaC22AY.4.20.000043
ORF1ab/nsp925D25GgAtgGt22AY.4.50.000215
ORF1ab/nsp925D25GgAtgGt22AY.420.00008
ORF1ab/nsp925D25YGatTat22AY.430.000009
ORF1ab/nsp925D25GgAtgGt22AY.470.000062
ORF1ab/nsp925D25GgAtgGt22AY.50.000041
ORF1ab/nsp925D25GgAtgGt22B0.000256
ORF1ab/nsp925D25EgaTgaA22B.1.1.1610.007067
ORF1ab/nsp925D25EgaTgaA22B.1.1.3010.002358
ORF1ab/nsp925D25delGAT---22B.1.1.390.001019
ORF1ab/nsp925D25DgaTgaC22B.1.1770.000026
ORF1ab/nsp925D25VgAtgTt22B.1.177.540.001213
ORF1ab/nsp925D25AgAtgCt22B.1.2840.026316
ORF1ab/nsp925D25YGatTat22B.1.3510.000059
ORF1ab/nsp925D25GgAtgGt22B.1.36.390.004435
ORF1ab/nsp925D25AgAtgCt22B.1.36.80.002
ORF1ab/nsp925D25NGatAat22B.1.4290.000047
ORF1ab/nsp925D25GgAtgGt22B.1.5760.001813
ORF1ab/nsp925D25delGAT---22B.1.617.20.000008
ORF1ab/nsp925D25NGatAat22C.370.000232
ORF1ab/nsp925D25NGatAat22P.10.000032
ORF1ab/nsp925D25GgAtgGt11A.210.00277
ORF1ab/nsp925D25GgAtgGt11AD.20.000219
ORF1ab/nsp925D25TGATACA11All0
ORF1ab/nsp925D25DgaTgaC11AY.1000.000046
ORF1ab/nsp925D25VgAtgTt11AY.1000.000046
ORF1ab/nsp925D25del1gAtg-t11AY.1020.000027
ORF1ab/nsp925D25VgAtgTt11AY.1030.000006
ORF1ab/nsp925D25delGAT---11AY.1110.000183
ORF1ab/nsp925D25GgAtgGt11AY.1160.000287
ORF1ab/nsp925D25DgaTgaC11AY.1170.000085
ORF1ab/nsp925D25AgAtgCt11AY.1190.000035
ORF1ab/nsp925D25DgaTgaC11AY.1190.000035
ORF1ab/nsp925D25YGatTat11AY.1210.000135
ORF1ab/nsp925D25GgAtgGt11AY.190.00114
ORF1ab/nsp925D25HGatCat11AY.200.000039
ORF1ab/nsp925D25AgAtgCt11AY.250.000006
ORF1ab/nsp925D25EgaTgaA11AY.250.000006
ORF1ab/nsp925D25YGatTat11AY.250.000006
ORF1ab/nsp925D25TGATACA11AY.250.000006
ORF1ab/nsp925D25NGatAat11AY.260.000028
ORF1ab/nsp925D25EgaTgaG11AY.29.10.000221
ORF1ab/nsp925D25GgAtgGt11AY.30.00001
ORF1ab/nsp925D25GgAtgGt11AY.3.10.000085
ORF1ab/nsp925D25DgaTgaC11AY.300.000396
ORF1ab/nsp925D25NGatAat11AY.360.000148
ORF1ab/nsp925D25NGatAat11AY.390.000025
ORF1ab/nsp925D25GgAtgGt11AY.390.000025
ORF1ab/nsp925D25YGatTat11AY.39.10.00004
ORF1ab/nsp925D25HGatCat11AY.40.000002
ORF1ab/nsp925D25delGAT---11AY.4.20.000022
ORF1ab/nsp925D25GgAtgGt11AY.400.000964
ORF1ab/nsp925D25DgaTgaC11AY.420.00004
ORF1ab/nsp925D25GgAtgGt11AY.430.000004
ORF1ab/nsp925D25AgAtgCt11AY.430.000004
ORF1ab/nsp925D25EgaTgaA11AY.430.000004
ORF1ab/nsp925D25del2GAt--t11AY.430.000004
ORF1ab/nsp925D25NGatAat11AY.430.000004
ORF1ab/nsp925D25AgAtgCt11AY.440.000006
ORF1ab/nsp925D25NGatAat11AY.46.50.000198
ORF1ab/nsp925D25delGAT---11AY.46.60.000072
ORF1ab/nsp925D25NGatAat11AY.480.000465
ORF1ab/nsp925D25HGatCat11AY.50.000021
ORF1ab/nsp925D25GgAtgGt11AY.5.30.000337
ORF1ab/nsp925D25delGAT---11AY.5.40.000277
ORF1ab/nsp925D25DgaTgaC11AY.540.000095
ORF1ab/nsp925D25AgAtgCt11AY.580.000907
ORF1ab/nsp925D25EgaTgaG11AY.60.000041
ORF1ab/nsp925D25NGatAat11AY.620.000436
ORF1ab/nsp925D25NGatAat11AY.640.000595
ORF1ab/nsp925D25DgaTgaC11AY.670.000464
ORF1ab/nsp925D25DgaTgaC11AY.750.000056
ORF1ab/nsp925D25NGatAat11AY.750.000056
ORF1ab/nsp925D25NGatAat11AY.880.000884
ORF1ab/nsp925D25AgAtgCt11AY.90.000068
ORF1ab/nsp925D25DgaTgaC11AY.90.000068
ORF1ab/nsp925D25delGAT---11AY.9.20.000037
ORF1ab/nsp925D25GgAtgGt11AY.9.20.000037
ORF1ab/nsp925D25NGatAat11AY.98.10.000048
ORF1ab/nsp925D25delGAT---11AY.990.001049
ORF1ab/nsp925D25del1gaTga-11B0.000128
ORF1ab/nsp925D25HGatCat11B.10.000009
ORF1ab/nsp925D25delGAT---11B.10.000009
ORF1ab/nsp925D25AgAtgCt11B.1.10.000018
ORF1ab/nsp925D25YGatTat11B.1.10.000018
ORF1ab/nsp925D25delGAT---11B.1.1.1390.022727
ORF1ab/nsp925D25NGatAat11B.1.1.1600.02381
ORF1ab/nsp925D25DgaTgaC11B.1.1.1610.003534
ORF1ab/nsp925D25GgAtgGt11B.1.1.1610.003534
ORF1ab/nsp925D25DgaTgaC11B.1.1.1860.003436
ORF1ab/nsp925D25AgAtgCt11B.1.1.1920.002309
ORF1ab/nsp925D25NGatAat11B.1.1.2140.000055
ORF1ab/nsp925D25GgAtgGt11B.1.1.2220.000204
ORF1ab/nsp925D25DgaTgaC11B.1.1.2220.000204
ORF1ab/nsp925D25NGatAat11B.1.1.2290.005747
ORF1ab/nsp925D25EgaTgaA11B.1.1.2670.010101
ORF1ab/nsp925D25delGAT---11B.1.1.280.000311
ORF1ab/nsp925D25AgAtgCt11B.1.1.3000.010753
ORF1ab/nsp925D25EgaTgaA11B.1.1.3070.002532
ORF1ab/nsp925D25GgAtgGt11B.1.1.330.000421
ORF1ab/nsp925D25delGAT---11B.1.1.3480.000796
ORF1ab/nsp925D25GgAtgGt11B.1.1.3720.000689
ORF1ab/nsp925D25GgAtgGt11B.1.1.470.005348
ORF1ab/nsp925D25GgAtgGt11B.1.1.4860.001577
ORF1ab/nsp925D25DgaTgaC11B.1.1.5190.00004
ORF1ab/nsp925D25HGaTCaC11B.1.1.5190.00004
ORF1ab/nsp925D25DgaTgaC11B.1.1.5230.001563
ORF1ab/nsp925D25GgAtgGt11B.1.1.580.005376
ORF1ab/nsp925D25VgAtgTt11B.1.1.70.000001
ORF1ab/nsp925D25EgaTgaG11B.1.1.70.000001
ORF1ab/nsp925D25delGAT---11B.1.1.70.000001
ORF1ab/nsp925D25del1Gat-at11B.1.1.70.000001
ORF1ab/nsp925D25GgAtgGt11B.1.1.700.000341
ORF1ab/nsp925D25GgAtgGt11B.1.1460.004237
ORF1ab/nsp925D25GgAtgGt11B.1.1600.000031
ORF1ab/nsp925D25GgAtgGt11B.1.177.230.003236
ORF1ab/nsp925D25GgAtgGt11B.1.177.440.000519
ORF1ab/nsp925D25GgAtgGt11B.1.177.500.004695
ORF1ab/nsp925D25NGatAat11B.1.20.000009
ORF1ab/nsp925D25GgAtgGt11B.1.2060.000816
ORF1ab/nsp925D25GgAtgGt11B.1.2340.000132
ORF1ab/nsp925D25DgaTgaC11B.1.2410.000812
ORF1ab/nsp925D25DgaTgaC11B.1.2430.00007
ORF1ab/nsp925D25YGatTat11B.1.2430.00007
ORF1ab/nsp925D25GgAtgGt11B.1.2430.00007
ORF1ab/nsp925D25delGAT---11B.1.2580.000067
ORF1ab/nsp925D25AgAtgCt11B.1.258.110.000396
ORF1ab/nsp925D25NGatAat11B.1.258.40.003448
ORF1ab/nsp925D25delGAT---11B.1.3110.000275
ORF1ab/nsp925D25VgAtgTt11B.1.3510.00003
ORF1ab/nsp925D25delGAT---11B.1.3510.00003
ORF1ab/nsp925D25DgaTgaC11B.1.36.310.001751
ORF1ab/nsp925D25EgaTgaA11B.1.36.80.001
ORF1ab/nsp925D25YGatTat11B.1.3990.001934
ORF1ab/nsp925D25GgAtgGt11B.1.4040.001302
ORF1ab/nsp925D25GgAtgGt11B.1.4270.00005
ORF1ab/nsp925D25YGatTat11B.1.4290.000024
ORF1ab/nsp925D25AgAtgCt11B.1.4530.003236
ORF1ab/nsp925D25AgAtgCt11B.1.5250.000113
ORF1ab/nsp925D25EgaTgaA11B.1.5960.000087
ORF1ab/nsp925D25YGatTat11B.1.617.10.000129
ORF1ab/nsp925D25HGatCat11B.1.617.20.000004
ORF1ab/nsp925D25EgaTgaG11B.1.617.20.000004
ORF1ab/nsp925D25NGatAat11B.1.617.20.000004
ORF1ab/nsp925D25NGatAat11B.1.6250.002353
ORF1ab/nsp925D25AgAtgCt11B.400.000364
ORF1ab/nsp925D25NGatAat11B.410.008
ORF1ab/nsp925D25EgaTgaA11B.550.00295
ORF1ab/nsp925D25EgaTgaA11B.610.005747
ORF1ab/nsp925D25GgAtgGt11C.230.005814
ORF1ab/nsp925D25AgAtgCt11C.370.000116
ORF1ab/nsp925D25YGatTat11D.20.000075
ORF1ab/nsp925D25DgaTgaC11D.20.000075
ORF1ab/nsp925D25NGatAat11D.20.000075
ORF1ab/nsp925D25delGAT---11N.40.004255
ORF1ab/nsp925D25DgaTgaC11P.10.000016
ORF1ab/nsp925D25delGAT---11P.10.000016
ORF1ab/nsp925D25YGatTat11P.1.140.000048
ORF1ab/nsp925D25GgAtgGt11P.1.150.000232
ORF1ab/nsp925D25EgaTgaG11P.20.000187
ORF1ab/nsp925D25DgaTgaC11Q.10.000126
ORF1ab/nsp925D25del2GAt--t11Q.20.000613

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.