CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp12 : CodonNum = 77

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/nsp1277F77FF4469FsynttCttT24012401113669-13671
ORF1ab/nsp1277F77LF4469LnonsynTtcCtc149980.65771813669-13671
ORF1ab/nsp1277F77LF4469LnonsynttCttA149500.3355713669-13671
ORF1ab/nsp1277F77LF4469LnonsynTtCCtT14910.0067114113669-13671
ORF1ab/nsp1277F77SF4469SnonsyntTctCc1161140.98275913669-13671
ORF1ab/nsp1277F77SF4469SnonsyntTCtCT11610.0086206913669-13671
ORF1ab/nsp1277F77SF4469SnonsyntTCtCA11610.0086206913669-13671
ORF1ab/nsp1277F77YF4469YnonsyntTctAc71700.98591513669-13671
ORF1ab/nsp1277F77YF4469YnonsyntTCtAT7110.014084513669-13671
ORF1ab/nsp1277F77CF4469CnonsyntTctGc6464113669-13671
ORF1ab/nsp1277F77VF4469VnonsynTtcGtc41390.95121913669-13671
ORF1ab/nsp1277F77VF4469VnonsynTtCGtT4110.024390213669-13671
ORF1ab/nsp1277F77VF4469VnonsynTtCGtA4110.024390213669-13671
ORF1ab/nsp1277F77delF4469deldelTTC---2222113669-13671
ORF1ab/nsp1277F77IF4469InonsynTtcAtc44113669-13671
ORF1ab/nsp1277F77del2F4469del2deltTCt--33113669-13671
ORF1ab/nsp1277F77XF4469XnonsyntTCtAA320.66666713669-13671
ORF1ab/nsp1277F77XF4469XnonsyntTCtGA310.33333313669-13671
ORF1ab/nsp1277F77DF4469DnonsynTTCGAT210.513669-13671
ORF1ab/nsp1277F77DF4469DnonsynTTcGAc210.513669-13671
ORF1ab/nsp1277F77del1F4469del1delTtc-tc210.513669-13671
ORF1ab/nsp1277F77del1F4469del1delttCtt-210.513669-13671
ORF1ab/nsp1277F77EF4469EnonsynTTCGAA11113669-13671

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/nsp1277F77FttCttT24012401All0.000459
ORF1ab/nsp1277F77FttCttT12201220B.1.177.730.690827
ORF1ab/nsp1277F77FttCttT510510B.1.1770.006715
ORF1ab/nsp1277F77FttCttT269269B.1.177.230.87055
ORF1ab/nsp1277F77FttCttT209209B.1.1.70.000187
ORF1ab/nsp1277F77LTtcCtc98149All0.000019
ORF1ab/nsp1277F77LttCttA50149All0.00001
ORF1ab/nsp1277F77LTtCCtT1149All0
ORF1ab/nsp1277F77StTctCc114116All0.000022
ORF1ab/nsp1277F77StTCtCT1116All0
ORF1ab/nsp1277F77StTCtCA1116All0
ORF1ab/nsp1277F77YtTctAc7071All0.000013
ORF1ab/nsp1277F77YtTCtAT171All0
ORF1ab/nsp1277F77YtTctAc6666B.1.1.70.000059
ORF1ab/nsp1277F77CtTctGc6464All0.000012
ORF1ab/nsp1277F77CtTctGc5151B.1.20.000449
ORF1ab/nsp1277F77VTtcGtc3941All0.000007
ORF1ab/nsp1277F77VTtCGtA141All0
ORF1ab/nsp1277F77VTtCGtT141All0
ORF1ab/nsp1277F77FttCttT3131AY.40.000048
ORF1ab/nsp1277F77LTtcCtc2929AY.30.000288
ORF1ab/nsp1277F77StTctCc2525B.1.1.3690.011156
ORF1ab/nsp1277F77delTTC---2222All0.000004
ORF1ab/nsp1277F77LttCttA1720AY.40.000026
ORF1ab/nsp1277F77LTtcCtc320AY.40.000005
ORF1ab/nsp1277F77VTtcGtc2020B.1.1.70.000018
ORF1ab/nsp1277F77FttCttT1717B.10.000156
ORF1ab/nsp1277F77FttCttT1515B.1.10.000272
ORF1ab/nsp1277F77FttCttT1414B.1.617.20.000053
ORF1ab/nsp1277F77StTctCc1414P.10.000221
ORF1ab/nsp1277F77StTctCc1313AY.260.000368
ORF1ab/nsp1277F77LTtcCtc1213B.1.1.70.000011
ORF1ab/nsp1277F77LttCttA113B.1.1.70.000001
ORF1ab/nsp1277F77FttCttT1111B.1.4290.000259
ORF1ab/nsp1277F77LTtcCtc711B.1.617.20.000026
ORF1ab/nsp1277F77LttCttA411B.1.617.20.000015
ORF1ab/nsp1277F77StTctCc1010B.1.1.70.000009
ORF1ab/nsp1277F77StTctCc99AY.40.000014
ORF1ab/nsp1277F77LTtcCtc88AY.1000.000368
ORF1ab/nsp1277F77VTtcGtc88AY.440.000049
ORF1ab/nsp1277F77FttCttT88B.1.3510.000238
ORF1ab/nsp1277F77StTctCc88B.1.6210.000708
ORF1ab/nsp1277F77FttCttT77AY.250.000042
ORF1ab/nsp1277F77LTtcCtc77AY.4.20.000152
ORF1ab/nsp1277F77LttCttA47B.10.000037
ORF1ab/nsp1277F77LTtcCtc37B.10.000027
ORF1ab/nsp1277F77delTTC---77B.1.1.70.000006
ORF1ab/nsp1277F77FttCttT77B.1.220.009223
ORF1ab/nsp1277F77StTctCc66AY.1020.000159
ORF1ab/nsp1277F77LTtcCtc56AY.1030.000031
ORF1ab/nsp1277F77LttCttA16AY.1030.000006
ORF1ab/nsp1277F77LttCttA66B.1.1.5190.000238
ORF1ab/nsp1277F77FttCttT55AY.1030.000031
ORF1ab/nsp1277F77FttCttT55AY.30.00005
ORF1ab/nsp1277F77LTtcCtc55AY.340.000485
ORF1ab/nsp1277F77VTtcGtc35B.10.000027
ORF1ab/nsp1277F77VTtCGtT15B.10.000009
ORF1ab/nsp1277F77VTtCGtA15B.10.000009
ORF1ab/nsp1277F77CtTctGc55B.1.1.70.000004
ORF1ab/nsp1277F77LttCttA45B.1.20.000035
ORF1ab/nsp1277F77LTtcCtc15B.1.20.000009
ORF1ab/nsp1277F77ITtcAtc44All0.000001
ORF1ab/nsp1277F77LTtcCtc44AY.250.000024
ORF1ab/nsp1277F77StTctCc34B.10.000027
ORF1ab/nsp1277F77StTCtCT14B.10.000009
ORF1ab/nsp1277F77FttCttT44B.1.1600.000125
ORF1ab/nsp1277F77FttCttT44B.1.160.200.035714
ORF1ab/nsp1277F77LTtcCtc34P.10.000047
ORF1ab/nsp1277F77LttCttA14P.10.000016
ORF1ab/nsp1277F77del2tTCt--33All0.000001
ORF1ab/nsp1277F77XtTCtAA23All0
ORF1ab/nsp1277F77XtTCtGA13All0
ORF1ab/nsp1277F77FttCttT33AY.1000.000138
ORF1ab/nsp1277F77CtTctGc33AY.290.000047
ORF1ab/nsp1277F77FttCttT33AY.99.20.000276
ORF1ab/nsp1277F77FttCttT33B0.000383
ORF1ab/nsp1277F77LTtcCtc23B.1.1770.000026
ORF1ab/nsp1277F77LttCttA13B.1.1770.000013
ORF1ab/nsp1277F77FttCttT33B.1.360.000438
ORF1ab/nsp1277F77StTctCc33D.20.000225
ORF1ab/nsp1277F77DTTCGAT12All0
ORF1ab/nsp1277F77DTTcGAc12All0
ORF1ab/nsp1277F77del1Ttc-tc12All0
ORF1ab/nsp1277F77del1ttCtt-12All0
ORF1ab/nsp1277F77FttCttT22AY.200.000078
ORF1ab/nsp1277F77FttCttT22AY.230.000139
ORF1ab/nsp1277F77LttCttA12AY.420.00004
ORF1ab/nsp1277F77LTtcCtc12AY.420.00004
ORF1ab/nsp1277F77StTctCc22AY.430.000009
ORF1ab/nsp1277F77FttCttT22AY.440.000012
ORF1ab/nsp1277F77del2tTCt--22AY.440.000012
ORF1ab/nsp1277F77VTtcGtc22AY.450.000243
ORF1ab/nsp1277F77FttCttT22AY.930.000546
ORF1ab/nsp1277F77FttCttT22AY.98.10.000097
ORF1ab/nsp1277F77YtTCtAT12B.10.000009
ORF1ab/nsp1277F77XtTCtAA12B.10.000009
ORF1ab/nsp1277F77YtTctAc12B.10.000009
ORF1ab/nsp1277F77XtTCtGA12B.10.000009
ORF1ab/nsp1277F77DTTcGAc12B.10.000009
ORF1ab/nsp1277F77DTTCGAT12B.10.000009
ORF1ab/nsp1277F77LttCttA22B.1.10.000036
ORF1ab/nsp1277F77VTtcGtc22B.1.1.170.033333
ORF1ab/nsp1277F77LttCttA22B.1.1.2220.000408
ORF1ab/nsp1277F77StTctCc12B.1.2210.000071
ORF1ab/nsp1277F77StTCtCA12B.1.2210.000071
ORF1ab/nsp1277F77FttCttT22B.1.2410.001623
ORF1ab/nsp1277F77StTctCc22B.1.2430.000139
ORF1ab/nsp1277F77FttCttT22B.1.2930.025
ORF1ab/nsp1277F77StTctCc22B.1.617.20.000008
ORF1ab/nsp1277F77FttCttT22P.1.10.000635
ORF1ab/nsp1277F77FttCttT11A.210.00277
ORF1ab/nsp1277F77StTctCc11AE.50.018519
ORF1ab/nsp1277F77ETTCGAA11All0
ORF1ab/nsp1277F77FttCttT11AY.1020.000027
ORF1ab/nsp1277F77delTTC---11AY.1080.001103
ORF1ab/nsp1277F77FttCttT11AY.1160.000287
ORF1ab/nsp1277F77LTtcCtc11AY.1180.000063
ORF1ab/nsp1277F77FttCttT11AY.1180.000063
ORF1ab/nsp1277F77FttCttT11AY.1190.000035
ORF1ab/nsp1277F77StTctCc11AY.1190.000035
ORF1ab/nsp1277F77delTTC---11AY.1200.000037
ORF1ab/nsp1277F77StTctCc11AY.1200.000037
ORF1ab/nsp1277F77delTTC---11AY.120.10.000321
ORF1ab/nsp1277F77FttCttT11AY.1210.000135
ORF1ab/nsp1277F77LttCttA11AY.160.00038
ORF1ab/nsp1277F77FttCttT11AY.160.00038
ORF1ab/nsp1277F77StTctCc11AY.200.000039
ORF1ab/nsp1277F77LTtcCtc11AY.230.00007
ORF1ab/nsp1277F77CtTctGc11AY.23.10.000417
ORF1ab/nsp1277F77delTTC---11AY.250.000006
ORF1ab/nsp1277F77StTctCc11AY.250.000006
ORF1ab/nsp1277F77ITtcAtc11AY.250.000006
ORF1ab/nsp1277F77FttCttT11AY.260.000028
ORF1ab/nsp1277F77StTctCc11AY.390.000025
ORF1ab/nsp1277F77LTtcCtc11AY.390.000025
ORF1ab/nsp1277F77FttCttT11AY.390.000025
ORF1ab/nsp1277F77VTtcGtc11AY.40.000002
ORF1ab/nsp1277F77FttCttT11AY.4.20.000022
ORF1ab/nsp1277F77StTctCc11AY.4.20.000022
ORF1ab/nsp1277F77FttCttT11AY.4.50.000107
ORF1ab/nsp1277F77FttCttT11AY.430.000004
ORF1ab/nsp1277F77StTctCc11AY.440.000006
ORF1ab/nsp1277F77ITtcAtc11AY.440.000006
ORF1ab/nsp1277F77StTctCc11AY.450.000122
ORF1ab/nsp1277F77FttCttT11AY.50.000021
ORF1ab/nsp1277F77delTTC---11AY.50.000021
ORF1ab/nsp1277F77del1ttCtt-11AY.540.000095
ORF1ab/nsp1277F77LTtcCtc11AY.580.000907
ORF1ab/nsp1277F77FttCttT11AY.60.000041
ORF1ab/nsp1277F77delTTC---11AY.660.00107
ORF1ab/nsp1277F77LTtcCtc11AY.680.000274
ORF1ab/nsp1277F77CtTctGc11AY.730.000665
ORF1ab/nsp1277F77LttCttA11AY.750.000056
ORF1ab/nsp1277F77LTtCCtT11AY.790.001211
ORF1ab/nsp1277F77ITtcAtc11AY.9.20.000037
ORF1ab/nsp1277F77delTTC---11AY.990.001049
ORF1ab/nsp1277F77del1Ttc-tc11B.10.000009
ORF1ab/nsp1277F77CtTctGc11B.10.000009
ORF1ab/nsp1277F77ETTCGAA11B.10.000009
ORF1ab/nsp1277F77delTTC---11B.1.1.10.000327
ORF1ab/nsp1277F77FttCttT11B.1.1.10.000327
ORF1ab/nsp1277F77delTTC---11B.1.1.1390.022727
ORF1ab/nsp1277F77FttCttT11B.1.1.1700.001247
ORF1ab/nsp1277F77StTctCc11B.1.1.2220.000204
ORF1ab/nsp1277F77FttCttT11B.1.1.2310.003096
ORF1ab/nsp1277F77LTtcCtc11B.1.1.250.000569
ORF1ab/nsp1277F77FttCttT11B.1.1.2940.001266
ORF1ab/nsp1277F77delTTC---11B.1.1.3480.000796
ORF1ab/nsp1277F77StTctCc11B.1.1.370.000193
ORF1ab/nsp1277F77FttCttT11B.1.1.370.000193
ORF1ab/nsp1277F77FttCttT11B.1.1.5180.006329
ORF1ab/nsp1277F77FttCttT11B.1.1.5210.005348
ORF1ab/nsp1277F77ITtcAtc11B.1.1.70.000001
ORF1ab/nsp1277F77StTctCc11B.1.1.830.00271
ORF1ab/nsp1277F77LTtcCtc11B.1.1600.000031
ORF1ab/nsp1277F77FttCttT11B.1.160.160.000929
ORF1ab/nsp1277F77FttCttT11B.1.160.260.002421
ORF1ab/nsp1277F77FttCttT11B.1.160.310.008065
ORF1ab/nsp1277F77delTTC---11B.1.1610.017241
ORF1ab/nsp1277F77StTctCc11B.1.1770.000013
ORF1ab/nsp1277F77FttCttT11B.1.177.270.009434
ORF1ab/nsp1277F77FttCttT11B.1.177.310.011494
ORF1ab/nsp1277F77FttCttT11B.1.177.430.001477
ORF1ab/nsp1277F77FttCttT11B.1.177.440.000519
ORF1ab/nsp1277F77FttCttT11B.1.177.60.000977
ORF1ab/nsp1277F77FttCttT11B.1.177.750.001041
ORF1ab/nsp1277F77StTctCc11B.1.20.000009
ORF1ab/nsp1277F77LttCttA11B.1.2210.000071
ORF1ab/nsp1277F77YtTctAc11B.1.2210.000071
ORF1ab/nsp1277F77XtTCtAA11B.1.2210.000071
ORF1ab/nsp1277F77StTctCc11B.1.2340.000132
ORF1ab/nsp1277F77VTtcGtc11B.1.2400.000216
ORF1ab/nsp1277F77YtTctAc11B.1.2400.000216
ORF1ab/nsp1277F77FttCttT11B.1.258.170.000104
ORF1ab/nsp1277F77LttCttA11B.1.3320.003497
ORF1ab/nsp1277F77YtTctAc11B.1.3510.00003
ORF1ab/nsp1277F77LttCttA11B.1.3510.00003
ORF1ab/nsp1277F77CtTctGc11B.1.36.380.001642
ORF1ab/nsp1277F77delTTC---11B.1.4150.014286
ORF1ab/nsp1277F77FttCttT11B.1.4200.010417
ORF1ab/nsp1277F77VTtcGtc11B.1.4240.008065
ORF1ab/nsp1277F77LTtcCtc11B.1.4290.000024
ORF1ab/nsp1277F77VTtcGtc11B.1.4990.00105
ORF1ab/nsp1277F77FttCttT11B.1.5170.000427
ORF1ab/nsp1277F77CtTctGc11B.1.617.20.000004
ORF1ab/nsp1277F77delTTC---11B.1.617.20.000004
ORF1ab/nsp1277F77del2tTCt--11B.1.617.20.000004
ORF1ab/nsp1277F77delTTC---11B.1.6300.005236
ORF1ab/nsp1277F77StTctCc11B.1.6370.000073
ORF1ab/nsp1277F77FttCttT11B.400.000364
ORF1ab/nsp1277F77LttCttA11B.6.30.026316
ORF1ab/nsp1277F77delTTC---11C.170.055556
ORF1ab/nsp1277F77FttCttT11P.10.000016
ORF1ab/nsp1277F77FttCttT11Q.80.000165
ORF1ab/nsp1277F77FttCttT11R.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.