CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp6 : CodonNum = 54

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/nsp654A54SA3623SnonsynGctTct94379437111132-11134
ORF1ab/nsp654A54AA3623AsyngcTgcC6985120.73352411132-11134
ORF1ab/nsp654A54AA3623AsyngcTgcA6981620.23209211132-11134
ORF1ab/nsp654A54AA3623AsyngcTgcG698240.03438411132-11134
ORF1ab/nsp654A54delA3623deldelGCT---5555111132-11134
ORF1ab/nsp654A54VA3623VnonsyngCtgTt3939111132-11134
ORF1ab/nsp654A54TA3623TnonsynGctAct29280.96551711132-11134
ORF1ab/nsp654A54TA3623TnonsynGcTAcC2910.034482811132-11134
ORF1ab/nsp654A54del1A3623del1delgcTgc-15120.811132-11134
ORF1ab/nsp654A54del1A3623del1delGct-ct1530.211132-11134
ORF1ab/nsp654A54GA3623GnonsyngCtgGt1060.611132-11134
ORF1ab/nsp654A54GA3623GnonsyngCTgGG1020.211132-11134
ORF1ab/nsp654A54GA3623GnonsyngCTgGC1020.211132-11134
ORF1ab/nsp654A54FA3623FnonsynGCtTTt77111132-11134
ORF1ab/nsp654A54EA3623EnonsyngCTgAG22111132-11134
ORF1ab/nsp654A54DA3623DnonsyngCTgAC22111132-11134
ORF1ab/nsp654A54PA3623PnonsynGctCct22111132-11134
ORF1ab/nsp654A54NA3623NnonsynGCtAAt11111132-11134
ORF1ab/nsp654A54del2A3623del2delgCTg--11111132-11134
ORF1ab/nsp654A54LA3623LnonsynGCtCTt11111132-11134

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/nsp654A54SGctTct94379437All0.001805
ORF1ab/nsp654A54SGctTct67516751B.1.1770.088894
ORF1ab/nsp654A54SGctTct15191519B.1.177.150.95836
ORF1ab/nsp654A54AgcTgcC512698All0.000098
ORF1ab/nsp654A54AgcTgcA162698All0.000031
ORF1ab/nsp654A54AgcTgcG24698All0.000005
ORF1ab/nsp654A54AgcTgcC281281B.1.1.2580.915309
ORF1ab/nsp654A54SGctTct164164B.1.177.141
ORF1ab/nsp654A54SGctTct136136AA.10.985507
ORF1ab/nsp654A54SGctTct128128AA.20.984615
ORF1ab/nsp654A54SGctTct110110AA.41
ORF1ab/nsp654A54SGctTct109109AA.71
ORF1ab/nsp654A54SGctTct103103B.1.177.781
ORF1ab/nsp654A54AgcTgcA9194B.1.617.20.000343
ORF1ab/nsp654A54AgcTgcG294B.1.617.20.000008
ORF1ab/nsp654A54AgcTgcC194B.1.617.20.000004
ORF1ab/nsp654A54SGctTct6262AA.51
ORF1ab/nsp654A54SGctTct6161AA.60.983871
ORF1ab/nsp654A54SGctTct5858B.10.000531
ORF1ab/nsp654A54delGCT---5555All0.000011
ORF1ab/nsp654A54AgcTgcA4950AY.350.011419
ORF1ab/nsp654A54AgcTgcC150AY.350.000233
ORF1ab/nsp654A54AgcTgcC4848B.10.00044
ORF1ab/nsp654A54SGctTct4545AA.81
ORF1ab/nsp654A54VgCtgTt3939All0.000007
ORF1ab/nsp654A54SGctTct3737AA.31
ORF1ab/nsp654A54SGctTct3232B.1.160.300.095238
ORF1ab/nsp654A54AgcTgcC2730AY.40.000042
ORF1ab/nsp654A54AgcTgcG330AY.40.000005
ORF1ab/nsp654A54TGctAct2829All0.000005
ORF1ab/nsp654A54TGcTAcC129All0
ORF1ab/nsp654A54AgcTgcC1923B.1.1.70.000017
ORF1ab/nsp654A54AgcTgcG323B.1.1.70.000003
ORF1ab/nsp654A54AgcTgcA123B.1.1.70.000001
ORF1ab/nsp654A54AgcTgcC2323B.1.177.720.077966
ORF1ab/nsp654A54SGctTct1818B.1.1600.000561
ORF1ab/nsp654A54del1gcTgc-1215All0.000002
ORF1ab/nsp654A54del1Gct-ct315All0.000001
ORF1ab/nsp654A54AgcTgcC1515C.340.555556
ORF1ab/nsp654A54TGctAct1212B.1.1.70.000011
ORF1ab/nsp654A54AgcTgcC811B.1.20.00007
ORF1ab/nsp654A54AgcTgcG311B.1.20.000026
ORF1ab/nsp654A54GgCtgGt610All0.000001
ORF1ab/nsp654A54GgCTgGG210All0
ORF1ab/nsp654A54GgCTgGC210All0
ORF1ab/nsp654A54SGctTct1010B.1.10.000181
ORF1ab/nsp654A54VgCtgTt1010B.1.1.70.000009
ORF1ab/nsp654A54AgcTgcC1010B.1.1770.000132
ORF1ab/nsp654A54AgcTgcG88AY.260.000226
ORF1ab/nsp654A54delGCT---88B.1.1.70.000007
ORF1ab/nsp654A54SGctTct88B.1.177.440.004152
ORF1ab/nsp654A54FGCtTTt77All0.000001
ORF1ab/nsp654A54SGctTct77B.1.177.690.010386
ORF1ab/nsp654A54AgcTgcC66AY.29.10.001323
ORF1ab/nsp654A54TGctAct66AY.40.000009
ORF1ab/nsp654A54FGCtTTt66B.1.1770.000079
ORF1ab/nsp654A54SGctTct66B.1.177.620.007151
ORF1ab/nsp654A54AgcTgcC66B.1.5760.00544
ORF1ab/nsp654A54AgcTgcC66B.1.5960.000523
ORF1ab/nsp654A54AgcTgcA55AY.16.10.00235
ORF1ab/nsp654A54SGctTct55B.1.2360.010267
ORF1ab/nsp654A54AgcTgcC55D.20.000375
ORF1ab/nsp654A54GgCTgGG240.111111
ORF1ab/nsp654A54GgCTgGC240.111111
ORF1ab/nsp654A54delGCT---44AY.250.000024
ORF1ab/nsp654A54AgcTgcC34AY.440.000018
ORF1ab/nsp654A54AgcTgcA14AY.440.000006
ORF1ab/nsp654A54VgCtgTt44AY.470.000124
ORF1ab/nsp654A54VgCtgTt44B.10.000037
ORF1ab/nsp654A54SGctTct44B.1.177.310.045977
ORF1ab/nsp654A54SGctTct44B.1.2210.000284
ORF1ab/nsp654A54AgcTgcC33AY.1030.000019
ORF1ab/nsp654A54AgcTgcC33AY.250.000018
ORF1ab/nsp654A54delGCT---33AY.430.000013
ORF1ab/nsp654A54AgcTgcA33AY.480.001395
ORF1ab/nsp654A54SGctTct33B0.000383
ORF1ab/nsp654A54SGctTct33B.1.177.570.000843
ORF1ab/nsp654A54SGctTct33B.1.177.650.001996
ORF1ab/nsp654A54SGctTct33B.1.177.750.003122
ORF1ab/nsp654A54AgcTgcC33B.1.4290.000071
ORF1ab/nsp654A54AgcTgcC33B.1.5950.000783
ORF1ab/nsp654A54delGCT---33B.1.617.20.000011
ORF1ab/nsp654A54VgCtgTt33B.1.617.20.000011
ORF1ab/nsp654A54TGctAct220.111111
ORF1ab/nsp654A54DgCTgAC220.111111
ORF1ab/nsp654A54EgCTgAG220.111111
ORF1ab/nsp654A54delGCT---22A.280.005291
ORF1ab/nsp654A54PGctCct22All0
ORF1ab/nsp654A54DgCTgAC22All0
ORF1ab/nsp654A54EgCTgAG22All0
ORF1ab/nsp654A54SGctTct22AY.140.000176
ORF1ab/nsp654A54AgcTgcC12AY.230.00007
ORF1ab/nsp654A54AgcTgcA12AY.230.00007
ORF1ab/nsp654A54VgCtgTt22AY.30.00002
ORF1ab/nsp654A54SGctTct22AY.300.000791
ORF1ab/nsp654A54GgCtgGt22AY.40.000003
ORF1ab/nsp654A54AgcTgcC22B0.000256
ORF1ab/nsp654A54delGCT---22B.10.000018
ORF1ab/nsp654A54AgcTgcC22B.1.10.000036
ORF1ab/nsp654A54AgcTgcC22B.1.1.2200.003717
ORF1ab/nsp654A54SGctTct22B.1.1.70.000002
ORF1ab/nsp654A54del1gcTgc-22B.1.1.70.000002
ORF1ab/nsp654A54SGctTct22B.1.177.40.000422
ORF1ab/nsp654A54SGctTct22B.1.177.400.010309
ORF1ab/nsp654A54SGctTct22B.1.177.430.002954
ORF1ab/nsp654A54SGctTct22B.1.177.540.001213
ORF1ab/nsp654A54SGctTct22B.1.177.70.00033
ORF1ab/nsp654A54SGctTct22B.1.177.860.000367
ORF1ab/nsp654A54delGCT---22B.1.20.000018
ORF1ab/nsp654A54SGctTct22B.1.20.000018
ORF1ab/nsp654A54SGctTct22B.1.2220.003384
ORF1ab/nsp654A54AgcTgcC22B.1.2430.000139
ORF1ab/nsp654A54AgcTgcC22B.1.2890.005319
ORF1ab/nsp654A54AgcTgcC22B.1.3510.000059
ORF1ab/nsp654A54VgCtgTt22B.1.3610.002577
ORF1ab/nsp654A54delGCT---22B.1.4270.000101
ORF1ab/nsp654A54AgcTgcC22B.1.4270.000101
ORF1ab/nsp654A54delGCT---22B.1.5260.000047
ORF1ab/nsp654A54AgcTgcC22B.1.5820.000981
ORF1ab/nsp654A54del1gcTgc-22B.1.6270.00404
ORF1ab/nsp654A54AgcTgcG22B.1.6370.000146
ORF1ab/nsp654A54AgcTgcC11A.20.000662
ORF1ab/nsp654A54AgcTgcC11A.2.20.001689
ORF1ab/nsp654A54SGctTct11AD.20.000219
ORF1ab/nsp654A54NGCtAAt11All0
ORF1ab/nsp654A54del2gCTg--11All0
ORF1ab/nsp654A54LGCtCTt11All0
ORF1ab/nsp654A54AgcTgcC11AU.20.002421
ORF1ab/nsp654A54PGctCct11AY.1020.000027
ORF1ab/nsp654A54delGCT---11AY.1080.001103
ORF1ab/nsp654A54delGCT---11AY.1110.000183
ORF1ab/nsp654A54SGctTct11AY.1200.000037
ORF1ab/nsp654A54TGctAct11AY.120.10.000321
ORF1ab/nsp654A54AgcTgcA11AY.190.00114
ORF1ab/nsp654A54del2gCTg--11AY.250.000006
ORF1ab/nsp654A54VgCtgTt11AY.250.000006
ORF1ab/nsp654A54AgcTgcC11AY.30.00001
ORF1ab/nsp654A54GgCtgGt11AY.30.00001
ORF1ab/nsp654A54delGCT---11AY.30.00001
ORF1ab/nsp654A54AgcTgcC11AY.330.000067
ORF1ab/nsp654A54del1gcTgc-11AY.390.000025
ORF1ab/nsp654A54AgcTgcC11AY.39.10.00004
ORF1ab/nsp654A54delGCT---11AY.40.000002
ORF1ab/nsp654A54SGctTct11AY.40.000002
ORF1ab/nsp654A54delGCT---11AY.4.50.000107
ORF1ab/nsp654A54delGCT---11AY.420.00004
ORF1ab/nsp654A54AgcTgcG11AY.430.000004
ORF1ab/nsp654A54SGctTct11AY.440.000006
ORF1ab/nsp654A54AgcTgcA11AY.450.000122
ORF1ab/nsp654A54AgcTgcA11AY.470.000031
ORF1ab/nsp654A54AgcTgcA11AY.50.000021
ORF1ab/nsp654A54SGctTct11AY.50.000021
ORF1ab/nsp654A54AgcTgcA11AY.540.000095
ORF1ab/nsp654A54AgcTgcA11AY.550.000917
ORF1ab/nsp654A54AgcTgcC11AY.610.000105
ORF1ab/nsp654A54delGCT---11AY.660.00107
ORF1ab/nsp654A54AgcTgcC11AY.710.000475
ORF1ab/nsp654A54delGCT---11AY.750.000056
ORF1ab/nsp654A54VgCtgTt11AY.75.10.00018
ORF1ab/nsp654A54AgcTgcA11AY.9.20.000037
ORF1ab/nsp654A54TGctAct11B0.000128
ORF1ab/nsp654A54delGCT---11B0.000128
ORF1ab/nsp654A54GgCtgGt11B.10.000009
ORF1ab/nsp654A54del1gcTgc-11B.10.000009
ORF1ab/nsp654A54NGCtAAt11B.1.10.000018
ORF1ab/nsp654A54delGCT---11B.1.10.000018
ORF1ab/nsp654A54VgCtgTt11B.1.10.000018
ORF1ab/nsp654A54del1gcTgc-11B.1.10.000018
ORF1ab/nsp654A54del1Gct-ct11B.1.1.1370.0125
ORF1ab/nsp654A54delGCT---11B.1.1.1420.017544
ORF1ab/nsp654A54AgcTgcC11B.1.1.1710.003676
ORF1ab/nsp654A54TGctAct11B.1.1.1890.001513
ORF1ab/nsp654A54delGCT---11B.1.1.2140.000055
ORF1ab/nsp654A54AgcTgcA11B.1.1.250.000569
ORF1ab/nsp654A54AgcTgcC11B.1.1.290.010309
ORF1ab/nsp654A54SGctTct11B.1.1.3150.008475
ORF1ab/nsp654A54TGctAct11B.1.1.3690.000446
ORF1ab/nsp654A54AgcTgcC11B.1.1.3770.001381
ORF1ab/nsp654A54SGctTct11B.1.1.390.00051
ORF1ab/nsp654A54AgcTgcC11B.1.1.5190.00004
ORF1ab/nsp654A54GgCtgGt11B.1.1.70.000001
ORF1ab/nsp654A54SGctTct11B.1.1.700.000341
ORF1ab/nsp654A54del1gcTgc-11B.1.1600.000031
ORF1ab/nsp654A54FGCtTTt11B.1.1600.000031
ORF1ab/nsp654A54SGctTct11B.1.160.200.008929
ORF1ab/nsp654A54VgCtgTt11B.1.160.200.008929
ORF1ab/nsp654A54SGctTct11B.1.160.280.002924
ORF1ab/nsp654A54SGctTct11B.1.160.90.007194
ORF1ab/nsp654A54VgCtgTt11B.1.1770.000013
ORF1ab/nsp654A54LGCtCTt11B.1.1770.000013
ORF1ab/nsp654A54AgcTgcC11B.1.177.120.000152
ORF1ab/nsp654A54SGctTct11B.1.177.210.000076
ORF1ab/nsp654A54delGCT---11B.1.177.40.000211
ORF1ab/nsp654A54AgcTgcC11B.1.177.450.000381
ORF1ab/nsp654A54SGctTct11B.1.177.60.000977
ORF1ab/nsp654A54AgcTgcC11B.1.177.70.000165
ORF1ab/nsp654A54SGctTct11B.1.177.730.000566
ORF1ab/nsp654A54delGCT---11B.1.177.760.002494
ORF1ab/nsp654A54SGctTct11B.1.177.770.000726
ORF1ab/nsp654A54SGctTct11B.1.177.830.001481
ORF1ab/nsp654A54del1gcTgc-11B.1.20.000009
ORF1ab/nsp654A54VgCtgTt11B.1.20.000009
ORF1ab/nsp654A54AgcTgcC11B.1.2060.000816
ORF1ab/nsp654A54del1gcTgc-11B.1.2060.000816
ORF1ab/nsp654A54AgcTgcA11B.1.2210.000071
ORF1ab/nsp654A54VgCtgTt11B.1.2210.000071
ORF1ab/nsp654A54TGcTAcC11B.1.2360.002053
ORF1ab/nsp654A54AgcTgcC11B.1.2370.004975
ORF1ab/nsp654A54del1Gct-ct11B.1.2580.000067
ORF1ab/nsp654A54delGCT---11B.1.2580.000067
ORF1ab/nsp654A54delGCT---11B.1.258.30.001675
ORF1ab/nsp654A54VgCtgTt11B.1.3110.000275
ORF1ab/nsp654A54AgcTgcA11B.1.3320.003497
ORF1ab/nsp654A54delGCT---11B.1.3510.00003
ORF1ab/nsp654A54delGCT---11B.1.36.290.000517
ORF1ab/nsp654A54delGCT---11B.1.36.310.001751
ORF1ab/nsp654A54SGctTct11B.1.3620.001541
ORF1ab/nsp654A54VgCtgTt11B.1.3690.000285
ORF1ab/nsp654A54SGctTct11B.1.3750.00082
ORF1ab/nsp654A54delGCT---11B.1.3960.000706
ORF1ab/nsp654A54TGctAct11B.1.3960.000706
ORF1ab/nsp654A54SGctTct11B.1.4160.001269
ORF1ab/nsp654A54SGctTct11B.1.416.10.001563
ORF1ab/nsp654A54VgCtgTt11B.1.4270.00005
ORF1ab/nsp654A54VgCtgTt11B.1.4290.000024
ORF1ab/nsp654A54PGctCct11B.1.4290.000024
ORF1ab/nsp654A54AgcTgcC11B.1.5170.000427
ORF1ab/nsp654A54delGCT---11B.1.5250.000113
ORF1ab/nsp654A54AgcTgcC11B.1.5260.000024
ORF1ab/nsp654A54AgcTgcC11B.1.5640.000426
ORF1ab/nsp654A54del1Gct-ct11B.1.5640.000426
ORF1ab/nsp654A54AgcTgcC11B.1.5690.014493
ORF1ab/nsp654A54GgCtgGt11B.1.5950.000261
ORF1ab/nsp654A54TGctAct11B.1.5960.000087
ORF1ab/nsp654A54delGCT---11B.1.5970.00463
ORF1ab/nsp654A54SGctTct11B.1.6000.005848
ORF1ab/nsp654A54del1gcTgc-11B.1.6060.006024
ORF1ab/nsp654A54del1gcTgc-11B.1.617.20.000004
ORF1ab/nsp654A54SGctTct11B.1.617.20.000004
ORF1ab/nsp654A54TGctAct11B.1.6210.000089
ORF1ab/nsp654A54AgcTgcC11B.1.6230.000536
ORF1ab/nsp654A54AgcTgcG11B.1.6270.00202
ORF1ab/nsp654A54SGctTct11B.1.780.008547
ORF1ab/nsp654A54AgcTgcC11B.400.000364
ORF1ab/nsp654A54VgCtgTt11B.400.000364
ORF1ab/nsp654A54TGctAct11D.20.000075
ORF1ab/nsp654A54delGCT---11N.40.004255
ORF1ab/nsp654A54SGctTct11P.10.000016
ORF1ab/nsp654A54AgcTgcG11P.10.000016
ORF1ab/nsp654A54delGCT---11P.1.10.000318
ORF1ab/nsp654A54AgcTgcC11P.1.100.000269
ORF1ab/nsp654A54VgCtgTt11P.1.140.000048
ORF1ab/nsp654A54delGCT---11P.1.150.000232
ORF1ab/nsp654A54VgCtgTt11P.1.150.000232
ORF1ab/nsp654A54AgcTgcA11P.1.20.001156
ORF1ab/nsp654A54SGctTct11Q.10.000126
ORF1ab/nsp654A54delGCT---11Q.20.000613
ORF1ab/nsp654A54delGCT---11U.30.003861
ORF1ab/nsp654A54SGctTct11Z.10.00289

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.