CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp10 : CodonNum = 79

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/nsp1079C79CC4332CsyntgCtgT16561656113259-13261
ORF1ab/nsp1079C79SC4332SnonsynTgcAgc2282230.9780713259-13261
ORF1ab/nsp1079C79SC4332SnonsyntGctCc22840.017543913259-13261
ORF1ab/nsp1079C79SC4332SnonsyntGCtCA22810.0043859613259-13261
ORF1ab/nsp1079C79delC4332deldelTGC---3838113259-13261
ORF1ab/nsp1079C79del1C4332del1deltgCtg-23210.91304313259-13261
ORF1ab/nsp1079C79del1C4332del1deltGct-c2320.086956513259-13261
ORF1ab/nsp1079C79FC4332FnonsyntGctTc1414113259-13261
ORF1ab/nsp1079C79XC4332XnonsyntgCtgA1010113259-13261
ORF1ab/nsp1079C79YC4332YnonsyntGctAc88113259-13261
ORF1ab/nsp1079C79del2C4332del2deltGCt--66113259-13261
ORF1ab/nsp1079C79RC4332RnonsynTgcCgc66113259-13261
ORF1ab/nsp1079C79GC4332GnonsynTgcGgc33113259-13261
ORF1ab/nsp1079C79TC4332TnonsynTGCACT22113259-13261
ORF1ab/nsp1079C79WC4332WnonsyntgCtgG11113259-13261

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/nsp1079C79CtgCtgT16561656All0.000317
ORF1ab/nsp1079C79CtgCtgT322322B.1.1.70.000288
ORF1ab/nsp1079C79STgcAgc223228All0.000043
ORF1ab/nsp1079C79StGctCc4228All0.000001
ORF1ab/nsp1079C79StGCtCA1228All0
ORF1ab/nsp1079C79CtgCtgT141141B.1.617.20.000531
ORF1ab/nsp1079C79STgcAgc129129Q.30.018709
ORF1ab/nsp1079C79CtgCtgT119119B.1.20.001048
ORF1ab/nsp1079C79CtgCtgT100100AY.40.000156
ORF1ab/nsp1079C79CtgCtgT9797B.1.1.2320.176044
ORF1ab/nsp1079C79CtgCtgT9090AY.50.001858
ORF1ab/nsp1079C79CtgCtgT4848B.1.4290.001129
ORF1ab/nsp1079C79delTGC---3838All0.000007
ORF1ab/nsp1079C79CtgCtgT3737AY.1030.00023
ORF1ab/nsp1079C79CtgCtgT3333P.10.00052
ORF1ab/nsp1079C79CtgCtgT3232AY.430.000142
ORF1ab/nsp1079C79STgcAgc2930B.1.20.000255
ORF1ab/nsp1079C79StGctCc130B.1.20.000009
ORF1ab/nsp1079C79CtgCtgT2727AY.610.002829
ORF1ab/nsp1079C79CtgCtgT2525B.10.000229
ORF1ab/nsp1079C79CtgCtgT2424B.1.3510.000713
ORF1ab/nsp1079C79del1tgCtg-2123All0.000004
ORF1ab/nsp1079C79del1tGct-c223All0
ORF1ab/nsp1079C79CtgCtgT2323B.1.4050.283951
ORF1ab/nsp1079C79CtgCtgT2222AK.21
ORF1ab/nsp1079C79CtgCtgT2121AY.440.000128
ORF1ab/nsp1079C79CtgCtgT2121B.1.1770.000277
ORF1ab/nsp1079C79CtgCtgT2020AY.30.000199
ORF1ab/nsp1079C79CtgCtgT1616B.1.4330.051118
ORF1ab/nsp1079C79CtgCtgT1515AY.250.00009
ORF1ab/nsp1079C79FtGctTc1414All0.000003
ORF1ab/nsp1079C79CtgCtgT1414C.370.001625
ORF1ab/nsp1079C79STgcAgc1313B.1.1.3170.005352
ORF1ab/nsp1079C79CtgCtgT1313B.1.1.4130.089655
ORF1ab/nsp1079C79CtgCtgT1212B.1.2430.000835
ORF1ab/nsp1079C79CtgCtgT1212B.1.438.10.001287
ORF1ab/nsp1079C79CtgCtgT1111AY.140.000968
ORF1ab/nsp1079C79CtgCtgT1111Q.10.00139
ORF1ab/nsp1079C79XtgCtgA1010All0.000002
ORF1ab/nsp1079C79CtgCtgT1010AY.260.000283
ORF1ab/nsp1079C79CtgCtgT1010B.1.10.000181
ORF1ab/nsp1079C79CtgCtgT1010B.1.2580.000665
ORF1ab/nsp1079C79CtgCtgT99AY.1020.000239
ORF1ab/nsp1079C79CtgCtgT99AY.1130.001282
ORF1ab/nsp1079C79CtgCtgT99AY.330.000601
ORF1ab/nsp1079C79CtgCtgT99AY.360.001334
ORF1ab/nsp1079C79STgcAgc99AY.440.000055
ORF1ab/nsp1079C79CtgCtgT99B.1.1.4160.008145
ORF1ab/nsp1079C79delTGC---99B.1.1.70.000008
ORF1ab/nsp1079C79CtgCtgT99B.1.5770.006186
ORF1ab/nsp1079C79YtGctAc88All0.000002
ORF1ab/nsp1079C79CtgCtgT88AY.690.001493
ORF1ab/nsp1079C79del1tgCtg-78B.1.1.70.000006
ORF1ab/nsp1079C79del1tGct-c18B.1.1.70.000001
ORF1ab/nsp1079C79delTGC---77AY.250.000042
ORF1ab/nsp1079C79CtgCtgT77AY.290.00011
ORF1ab/nsp1079C79STgcAgc77B.1.2410.005682
ORF1ab/nsp1079C79CtgCtgT77B.1.36.190.064815
ORF1ab/nsp1079C79del2tGCt--66All0.000001
ORF1ab/nsp1079C79RTgcCgc66All0.000001
ORF1ab/nsp1079C79CtgCtgT66AY.750.000336
ORF1ab/nsp1079C79CtgCtgT66AY.98.10.000291
ORF1ab/nsp1079C79STgcAgc66B.1.10.000109
ORF1ab/nsp1079C79STgcAgc66B.1.2580.000399
ORF1ab/nsp1079C79CtgCtgT55AY.270.000324
ORF1ab/nsp1079C79STgcAgc55AY.30.00005
ORF1ab/nsp1079C79CtgCtgT55AY.740.000578
ORF1ab/nsp1079C79CtgCtgT55AY.9.20.000184
ORF1ab/nsp1079C79CtgCtgT55AY.99.20.000461
ORF1ab/nsp1079C79CtgCtgT55B.1.1.630.001929
ORF1ab/nsp1079C79CtgCtgT55P.1.130.004492
ORF1ab/nsp1079C79CtgCtgT44AY.1190.000141
ORF1ab/nsp1079C79CtgCtgT44AY.3.10.000341
ORF1ab/nsp1079C79CtgCtgT44AY.420.000161
ORF1ab/nsp1079C79CtgCtgT44AY.470.000124
ORF1ab/nsp1079C79CtgCtgT44AY.5.40.001107
ORF1ab/nsp1079C79CtgCtgT44AY.75.10.000721
ORF1ab/nsp1079C79CtgCtgT44B.1.1.260.020942
ORF1ab/nsp1079C79del2tGCt--44B.1.1.70.000004
ORF1ab/nsp1079C79STgcAgc44B.1.1.70.000004
ORF1ab/nsp1079C79del1tgCtg-34B.1.1770.00004
ORF1ab/nsp1079C79del1tGct-c14B.1.1770.000013
ORF1ab/nsp1079C79CtgCtgT44C.36.30.002269
ORF1ab/nsp1079C79CtgCtgT33A.2.50.001497
ORF1ab/nsp1079C79GTgcGgc33All0.000001
ORF1ab/nsp1079C79CtgCtgT33AY.1000.000138
ORF1ab/nsp1079C79CtgCtgT33AY.1200.000112
ORF1ab/nsp1079C79CtgCtgT33AY.200.000117
ORF1ab/nsp1079C79CtgCtgT33AY.230.000209
ORF1ab/nsp1079C79CtgCtgT33AY.4.20.000065
ORF1ab/nsp1079C79CtgCtgT33AY.46.40.000494
ORF1ab/nsp1079C79CtgCtgT33AY.490.009585
ORF1ab/nsp1079C79CtgCtgT33AY.7.10.000338
ORF1ab/nsp1079C79CtgCtgT33AY.980.000237
ORF1ab/nsp1079C79CtgCtgT33B.1.1.1700.003741
ORF1ab/nsp1079C79CtgCtgT33B.1.1.5190.000119
ORF1ab/nsp1079C79XtgCtgA33B.1.1.70.000003
ORF1ab/nsp1079C79CtgCtgT33B.1.5170.001281
ORF1ab/nsp1079C79CtgCtgT33B.1.5960.000261
ORF1ab/nsp1079C79CtgCtgT33B.1.6210.000266
ORF1ab/nsp1079C79CtgCtgT33B.1.621.10.001517
ORF1ab/nsp1079C79CtgCtgT33C.360.002732
ORF1ab/nsp1079C79CtgCtgT33L.30.010638
ORF1ab/nsp1079C79STgcAgc33N.50.0053
ORF1ab/nsp1079C79TTGCACT220.111111
ORF1ab/nsp1079C79YtGctAc220.111111
ORF1ab/nsp1079C79TTGCACT22All0
ORF1ab/nsp1079C79CtgCtgT22AY.1060.00067
ORF1ab/nsp1079C79CtgCtgT22AY.1160.000574
ORF1ab/nsp1079C79CtgCtgT22AY.130.000322
ORF1ab/nsp1079C79CtgCtgT22AY.16.10.00094
ORF1ab/nsp1079C79STgcAgc22AY.250.000012
ORF1ab/nsp1079C79StGctCc12AY.40.000002
ORF1ab/nsp1079C79STgcAgc12AY.40.000002
ORF1ab/nsp1079C79del1tgCtg-22AY.4.50.000215
ORF1ab/nsp1079C79delTGC---22AY.4.50.000215
ORF1ab/nsp1079C79del1tgCtg-22AY.430.000009
ORF1ab/nsp1079C79CtgCtgT22AY.450.000243
ORF1ab/nsp1079C79CtgCtgT22AY.460.000208
ORF1ab/nsp1079C79CtgCtgT22AY.500.001599
ORF1ab/nsp1079C79CtgCtgT22AY.540.000191
ORF1ab/nsp1079C79CtgCtgT22AY.620.000871
ORF1ab/nsp1079C79CtgCtgT22AY.650.001066
ORF1ab/nsp1079C79CtgCtgT22AY.670.000929
ORF1ab/nsp1079C79FtGctTc22B.10.000018
ORF1ab/nsp1079C79delTGC---22B.10.000018
ORF1ab/nsp1079C79StGCtCA12B.1.1.3060.000438
ORF1ab/nsp1079C79StGctCc12B.1.1.3060.000438
ORF1ab/nsp1079C79CtgCtgT22B.1.1.3360.033333
ORF1ab/nsp1079C79CtgCtgT22B.1.1.4340.000697
ORF1ab/nsp1079C79FtGctTc22B.1.1.70.000002
ORF1ab/nsp1079C79CtgCtgT22B.1.110.30.001437
ORF1ab/nsp1079C79CtgCtgT22B.1.1600.000062
ORF1ab/nsp1079C79CtgCtgT22B.1.177.720.00678
ORF1ab/nsp1079C79CtgCtgT22B.1.2470.029851
ORF1ab/nsp1079C79CtgCtgT22B.1.4260.002018
ORF1ab/nsp1079C79CtgCtgT22B.1.4320.022472
ORF1ab/nsp1079C79CtgCtgT22B.1.5260.000047
ORF1ab/nsp1079C79CtgCtgT22B.1.5680.002222
ORF1ab/nsp1079C79CtgCtgT22B.1.6310.006734
ORF1ab/nsp1079C79CtgCtgT22B.1.6370.000146
ORF1ab/nsp1079C79CtgCtgT22C.140.008658
ORF1ab/nsp1079C79CtgCtgT22C.160.002121
ORF1ab/nsp1079C79XtgCtgA22D.20.00015
ORF1ab/nsp1079C79CtgCtgT22D.20.00015
ORF1ab/nsp1079C79CtgCtgT22P.1.140.000096
ORF1ab/nsp1079C79CtgCtgT22P.1.70.000639
ORF1ab/nsp1079C79CtgCtgT11A0.000387
ORF1ab/nsp1079C79CtgCtgT11A.10.000282
ORF1ab/nsp1079C79STgcAgc11A.20.000662
ORF1ab/nsp1079C79del1tgCtg-11AH.30.003802
ORF1ab/nsp1079C79WtgCtgG11All0
ORF1ab/nsp1079C79CtgCtgT11AY.1010.00049
ORF1ab/nsp1079C79CtgCtgT11AY.1110.000183
ORF1ab/nsp1079C79delTGC---11AY.1110.000183
ORF1ab/nsp1079C79delTGC---11AY.1200.000037
ORF1ab/nsp1079C79CtgCtgT11AY.1210.000135
ORF1ab/nsp1079C79STgcAgc11AY.230.00007
ORF1ab/nsp1079C79XtgCtgA11AY.250.000006
ORF1ab/nsp1079C79delTGC---11AY.30.00001
ORF1ab/nsp1079C79XtgCtgA11AY.30.00001
ORF1ab/nsp1079C79GTgcGgc11AY.30.00001
ORF1ab/nsp1079C79CtgCtgT11AY.320.000532
ORF1ab/nsp1079C79CtgCtgT11AY.340.000097
ORF1ab/nsp1079C79CtgCtgT11AY.380.000499
ORF1ab/nsp1079C79CtgCtgT11AY.390.000025
ORF1ab/nsp1079C79CtgCtgT11AY.39.10.00004
ORF1ab/nsp1079C79del1tgCtg-11AY.40.000002
ORF1ab/nsp1079C79FtGctTc11AY.4.50.000107
ORF1ab/nsp1079C79STgcAgc11AY.420.00004
ORF1ab/nsp1079C79FtGctTc11AY.430.000004
ORF1ab/nsp1079C79delTGC---11AY.430.000004
ORF1ab/nsp1079C79YtGctAc11AY.430.000004
ORF1ab/nsp1079C79RTgcCgc11AY.440.000006
ORF1ab/nsp1079C79FtGctTc11AY.440.000006
ORF1ab/nsp1079C79YtGctAc11AY.440.000006
ORF1ab/nsp1079C79delTGC---11AY.46.20.000635
ORF1ab/nsp1079C79CtgCtgT11AY.46.60.000072
ORF1ab/nsp1079C79CtgCtgT11AY.5.30.000337
ORF1ab/nsp1079C79CtgCtgT11AY.590.00053
ORF1ab/nsp1079C79CtgCtgT11AY.60.000041
ORF1ab/nsp1079C79delTGC---11AY.600.000938
ORF1ab/nsp1079C79STgcAgc11AY.610.000105
ORF1ab/nsp1079C79delTGC---11AY.670.000464
ORF1ab/nsp1079C79YtGctAc11AY.670.000464
ORF1ab/nsp1079C79STgcAgc11AY.670.000464
ORF1ab/nsp1079C79CtgCtgT11AY.790.001211
ORF1ab/nsp1079C79CtgCtgT11AY.870.000833
ORF1ab/nsp1079C79RTgcCgc11AY.9.20.000037
ORF1ab/nsp1079C79CtgCtgT11AY.920.000287
ORF1ab/nsp1079C79delTGC---11AY.990.001049
ORF1ab/nsp1079C79YtGctAc11B0.000128
ORF1ab/nsp1079C79CtgCtgT11B0.000128
ORF1ab/nsp1079C79YtGctAc11B.10.000009
ORF1ab/nsp1079C79RTgcCgc11B.10.000009
ORF1ab/nsp1079C79StGctCc11B.10.000009
ORF1ab/nsp1079C79delTGC---11B.1.1.10.000327
ORF1ab/nsp1079C79CtgCtgT11B.1.1.1640.005155
ORF1ab/nsp1079C79CtgCtgT11B.1.1.2070.001182
ORF1ab/nsp1079C79del1tgCtg-11B.1.1.2360.006897
ORF1ab/nsp1079C79CtgCtgT11B.1.1.2770.000759
ORF1ab/nsp1079C79del1tgCtg-11B.1.1.2790.001121
ORF1ab/nsp1079C79CtgCtgT11B.1.1.2840.000107
ORF1ab/nsp1079C79XtgCtgA11B.1.1.3060.000438
ORF1ab/nsp1079C79del1tgCtg-11B.1.1.3110.000358
ORF1ab/nsp1079C79CtgCtgT11B.1.1.3260.001761
ORF1ab/nsp1079C79delTGC---11B.1.1.3480.000796
ORF1ab/nsp1079C79CtgCtgT11B.1.1.3480.000796
ORF1ab/nsp1079C79FtGctTc11B.1.1.3540.004386
ORF1ab/nsp1079C79CtgCtgT11B.1.1.3760.005952
ORF1ab/nsp1079C79WtgCtgG11B.1.1.70.000001
ORF1ab/nsp1079C79CtgCtgT11B.1.1.700.000341
ORF1ab/nsp1079C79XtgCtgA11B.1.1770.000013
ORF1ab/nsp1079C79delTGC---11B.1.1770.000013
ORF1ab/nsp1079C79YtGctAc11B.1.1770.000013
ORF1ab/nsp1079C79del2tGCt--11B.1.1770.000013
ORF1ab/nsp1079C79CtgCtgT11B.1.177.110.001698
ORF1ab/nsp1079C79CtgCtgT11B.1.177.150.000631
ORF1ab/nsp1079C79del1tgCtg-11B.1.177.170.000821
ORF1ab/nsp1079C79delTGC---11B.1.177.180.00116
ORF1ab/nsp1079C79del1tgCtg-11B.1.177.690.001484
ORF1ab/nsp1079C79CtgCtgT11B.1.177.810.000189
ORF1ab/nsp1079C79CtgCtgT11B.1.177.820.000477
ORF1ab/nsp1079C79delTGC---11B.1.177.830.001481
ORF1ab/nsp1079C79RTgcCgc11B.1.20.000009
ORF1ab/nsp1079C79FtGctTc11B.1.20.000009
ORF1ab/nsp1079C79RTgcCgc11B.1.2230.002778
ORF1ab/nsp1079C79CtgCtgT11B.1.2340.000132
ORF1ab/nsp1079C79GTgcGgc11B.1.2430.00007
ORF1ab/nsp1079C79CtgCtgT11B.1.258.110.000396
ORF1ab/nsp1079C79STgcAgc11B.1.3510.00003
ORF1ab/nsp1079C79CtgCtgT11B.1.351.20.000303
ORF1ab/nsp1079C79GTgcGgc11B.1.360.000146
ORF1ab/nsp1079C79CtgCtgT11B.1.360.000146
ORF1ab/nsp1079C79CtgCtgT11B.1.36.290.000517
ORF1ab/nsp1079C79del2tGCt--11B.1.36.380.001642
ORF1ab/nsp1079C79CtgCtgT11B.1.3670.000792
ORF1ab/nsp1079C79FtGctTc11B.1.3690.000285
ORF1ab/nsp1079C79CtgCtgT11B.1.3690.000285
ORF1ab/nsp1079C79CtgCtgT11B.1.4040.001302
ORF1ab/nsp1079C79CtgCtgT11B.1.4270.00005
ORF1ab/nsp1079C79STgcAgc11B.1.438.10.000107
ORF1ab/nsp1079C79FtGctTc11B.1.4730.019231
ORF1ab/nsp1079C79CtgCtgT11B.1.5250.000113
ORF1ab/nsp1079C79CtgCtgT11B.1.5510.00129
ORF1ab/nsp1079C79CtgCtgT11B.1.5650.00081
ORF1ab/nsp1079C79FtGctTc11B.1.5760.000907
ORF1ab/nsp1079C79delTGC---11B.1.5950.000261
ORF1ab/nsp1079C79CtgCtgT11B.1.5950.000261
ORF1ab/nsp1079C79CtgCtgT11B.1.6020.006536
ORF1ab/nsp1079C79CtgCtgT11B.1.617.10.000129
ORF1ab/nsp1079C79delTGC---11B.1.617.20.000004
ORF1ab/nsp1079C79RTgcCgc11B.1.617.20.000004
ORF1ab/nsp1079C79STgcAgc11B.1.617.20.000004
ORF1ab/nsp1079C79XtgCtgA11B.1.6270.00202
ORF1ab/nsp1079C79CtgCtgT11B.1.6280.000352
ORF1ab/nsp1079C79delTGC---11B.1.6300.005236
ORF1ab/nsp1079C79CtgCtgT11B.1.80.001972
ORF1ab/nsp1079C79FtGctTc11B.1.930.000934
ORF1ab/nsp1079C79CtgCtgT11B.1.940.027027
ORF1ab/nsp1079C79CtgCtgT11B.1.960.018868
ORF1ab/nsp1079C79CtgCtgT11B.30.000831
ORF1ab/nsp1079C79CtgCtgT11B.40.002208
ORF1ab/nsp1079C79CtgCtgT11B.400.000364
ORF1ab/nsp1079C79FtGctTc11B.60.00091
ORF1ab/nsp1079C79CtgCtgT11C.1.20.004255
ORF1ab/nsp1079C79STgcAgc11P.10.000016
ORF1ab/nsp1079C79delTGC---11P.10.000016
ORF1ab/nsp1079C79CtgCtgT11P.1.120.000484
ORF1ab/nsp1079C79CtgCtgT11P.1.170.000162
ORF1ab/nsp1079C79CtgCtgT11P.1.20.001156
ORF1ab/nsp1079C79CtgCtgT11P.1.80.004785
ORF1ab/nsp1079C79CtgCtgT11P.20.000187
ORF1ab/nsp1079C79delTGC---11Q.20.000613
ORF1ab/nsp1079C79CtgCtgT11Q.80.000165
ORF1ab/nsp1079C79CtgCtgT11R.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.