CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp4 : CodonNum = 478

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/nsp4478F478FF3241FsynttCttT2558255819986-9988
ORF1ab/nsp4478F478delF3241deldelTTC---666619986-9988
ORF1ab/nsp4478F478LF3241LnonsynTtcCtc22150.6818189986-9988
ORF1ab/nsp4478F478LF3241LnonsynttCttA2270.3181829986-9988
ORF1ab/nsp4478F478SF3241SnonsyntTctCc760.8571439986-9988
ORF1ab/nsp4478F478SF3241SnonsyntTCtCT710.1428579986-9988
ORF1ab/nsp4478F478YF3241YnonsyntTctAc6619986-9988
ORF1ab/nsp4478F478del1F3241del1delttCtt-420.59986-9988
ORF1ab/nsp4478F478del1F3241del1delTtc-tc420.59986-9988
ORF1ab/nsp4478F478IF3241InonsynTtcAtc3319986-9988
ORF1ab/nsp4478F478VF3241VnonsynTtcGtc2219986-9988
ORF1ab/nsp4478F478del2F3241del2deltTCt--1119986-9988
ORF1ab/nsp4478F478CF3241CnonsyntTctGc1119986-9988

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/nsp4478F478FttCttT25582558All0.000489
ORF1ab/nsp4478F478FttCttT12731273AY.90.086048
ORF1ab/nsp4478F478FttCttT231231A.280.611111
ORF1ab/nsp4478F478FttCttT193193B.1.1.70.000173
ORF1ab/nsp4478F478FttCttT7878Y.11
ORF1ab/nsp4478F478delTTC---6666All0.000013
ORF1ab/nsp4478F478FttCttT6464B.1.617.20.000241
ORF1ab/nsp4478F478FttCttT5353B.1.4290.001247
ORF1ab/nsp4478F478FttCttT4949AY.470.001524
ORF1ab/nsp4478F478FttCttT3535AY.40.000054
ORF1ab/nsp4478F478FttCttT3434AY.39.10.001347
ORF1ab/nsp4478F478FttCttT3131B.1.177.520.054482
ORF1ab/nsp4478F478FttCttT2929B.1.1770.000382
ORF1ab/nsp4478F478delTTC---2727B.1.1.70.000024
ORF1ab/nsp4478F478FttCttT2626AY.390.000642
ORF1ab/nsp4478F478FttCttT2424AY.430.000106
ORF1ab/nsp4478F478LTtcCtc1522All0.000003
ORF1ab/nsp4478F478LttCttA722All0.000001
ORF1ab/nsp4478F478FttCttT2121AY.30.000209
ORF1ab/nsp4478F478FttCttT2121B.10.000192
ORF1ab/nsp4478F478FttCttT2020AY.250.00012
ORF1ab/nsp4478F478FttCttT1818B.1.10.000327
ORF1ab/nsp4478F478FttCttT1818B.1.1.500.01222
ORF1ab/nsp4478F478FttCttT1818B.1.5950.004697
ORF1ab/nsp4478F478FttCttT1818P.10.000284
ORF1ab/nsp4478F478FttCttT1717B.1.1.2220.003468
ORF1ab/nsp4478F478FttCttT1515AY.10.005936
ORF1ab/nsp4478F478FttCttT1414AY.1030.000087
ORF1ab/nsp4478F478FttCttT1313AY.440.000079
ORF1ab/nsp4478F478FttCttT1313B.1.5750.003944
ORF1ab/nsp4478F478FttCttT99AY.130.001449
ORF1ab/nsp4478F478FttCttT88AY.1170.000676
ORF1ab/nsp4478F478FttCttT88AY.1190.000282
ORF1ab/nsp4478F478FttCttT88AY.120.10.002568
ORF1ab/nsp4478F478FttCttT88AY.910.005844
ORF1ab/nsp4478F478StTctCc67All0.000001
ORF1ab/nsp4478F478StTCtCT17All0
ORF1ab/nsp4478F478FttCttT77B.1.1600.000218
ORF1ab/nsp4478F478FttCttT77B.1.20.000062
ORF1ab/nsp4478F478YtTctAc66All0.000001
ORF1ab/nsp4478F478FttCttT66AY.75.10.001082
ORF1ab/nsp4478F478delTTC---66B.10.000055
ORF1ab/nsp4478F478FttCttT66B.1.1.3170.00247
ORF1ab/nsp4478F478FttCttT55AY.1000.00023
ORF1ab/nsp4478F478FttCttT55AY.1020.000133
ORF1ab/nsp4478F478FttCttT55AY.200.000194
ORF1ab/nsp4478F478FttCttT55AY.230.000349
ORF1ab/nsp4478F478FttCttT55AY.540.000477
ORF1ab/nsp4478F478FttCttT55AY.610.000524
ORF1ab/nsp4478F478FttCttT55B.1.177.670.038168
ORF1ab/nsp4478F478del1Ttc-tc24All0
ORF1ab/nsp4478F478del1ttCtt-24All0
ORF1ab/nsp4478F478FttCttT44AY.1130.00057
ORF1ab/nsp4478F478FttCttT44AY.260.000113
ORF1ab/nsp4478F478FttCttT44AY.4.20.000087
ORF1ab/nsp4478F478FttCttT44B0.000511
ORF1ab/nsp4478F478LTtcCtc24B.10.000018
ORF1ab/nsp4478F478LttCttA24B.10.000018
ORF1ab/nsp4478F478FttCttT44B.1.360.000584
ORF1ab/nsp4478F478FttCttT44B.1.4270.000202
ORF1ab/nsp4478F478FttCttT44C.370.000464
ORF1ab/nsp4478F478ITtcAtc33All0.000001
ORF1ab/nsp4478F478FttCttT33AY.290.000047
ORF1ab/nsp4478F478FttCttT33AY.3.10.000256
ORF1ab/nsp4478F478delTTC---33AY.430.000013
ORF1ab/nsp4478F478FttCttT33AY.46.50.000595
ORF1ab/nsp4478F478delTTC---33AY.750.000168
ORF1ab/nsp4478F478YtTctAc33B.10.000027
ORF1ab/nsp4478F478FttCttT33B.1.2400.000647
ORF1ab/nsp4478F478FttCttT33B.1.36.180.001261
ORF1ab/nsp4478F478FttCttT33B.1.5250.000339
ORF1ab/nsp4478F478FttCttT33B.1.5610.001191
ORF1ab/nsp4478F478FttCttT33B.1.6210.000266
ORF1ab/nsp4478F478FttCttT22AD.20.000438
ORF1ab/nsp4478F478VTtcGtc22All0
ORF1ab/nsp4478F478FttCttT22AY.1160.000574
ORF1ab/nsp4478F478FttCttT22AY.1200.000074
ORF1ab/nsp4478F478FttCttT22AY.340.000194
ORF1ab/nsp4478F478delTTC---22AY.40.000003
ORF1ab/nsp4478F478YtTctAc22AY.40.000003
ORF1ab/nsp4478F478delTTC---22AY.4.50.000215
ORF1ab/nsp4478F478FttCttT22AY.460.000208
ORF1ab/nsp4478F478FttCttT22AY.580.001815
ORF1ab/nsp4478F478FttCttT22AY.9.10.000167
ORF1ab/nsp4478F478FttCttT22AY.9.20.000073
ORF1ab/nsp4478F478FttCttT22AY.900.001369
ORF1ab/nsp4478F478delTTC---22B.1.10.000036
ORF1ab/nsp4478F478FttCttT22B.1.1.2690.002706
ORF1ab/nsp4478F478FttCttT22B.1.1.3480.001592
ORF1ab/nsp4478F478FttCttT22B.1.1.5190.000079
ORF1ab/nsp4478F478FttCttT22B.1.1.80.007168
ORF1ab/nsp4478F478delTTC---22B.1.1770.000026
ORF1ab/nsp4478F478LTtcCtc22B.1.2210.000142
ORF1ab/nsp4478F478FttCttT22B.1.3110.000549
ORF1ab/nsp4478F478FttCttT22B.1.5260.000047
ORF1ab/nsp4478F478FttCttT22B.1.5820.000981
ORF1ab/nsp4478F478LttCttA12B.1.5960.000087
ORF1ab/nsp4478F478LTtcCtc12B.1.5960.000087
ORF1ab/nsp4478F478del1Ttc-tc12B.1.617.20.000004
ORF1ab/nsp4478F478LTtcCtc12B.1.617.20.000004
ORF1ab/nsp4478F478LttCttA12B.1.617.20.000004
ORF1ab/nsp4478F478del1ttCtt-12B.1.617.20.000004
ORF1ab/nsp4478F478FttCttT22C.37.10.005236
ORF1ab/nsp4478F478delTTC---22P.10.000032
ORF1ab/nsp4478F478delTTC---22P.1.120.000968
ORF1ab/nsp4478F478FttCttT22P.1.140.000096
ORF1ab/nsp4478F478FttCttT110.055556
ORF1ab/nsp4478F478FttCttT11A0.000387
ORF1ab/nsp4478F478FttCttT11A.20.000662
ORF1ab/nsp4478F478del2tTCt--11All0
ORF1ab/nsp4478F478CtTctGc11All0
ORF1ab/nsp4478F478StTctCc11AY.1030.000006
ORF1ab/nsp4478F478FttCttT11AY.1140.000231
ORF1ab/nsp4478F478LTtcCtc11AY.1190.000035
ORF1ab/nsp4478F478StTCtCT11AY.1200.000037
ORF1ab/nsp4478F478FttCttT11AY.160.00038
ORF1ab/nsp4478F478FttCttT11AY.20.000356
ORF1ab/nsp4478F478delTTC---11AY.250.000006
ORF1ab/nsp4478F478FttCttT11AY.270.000065
ORF1ab/nsp4478F478FttCttT11AY.330.000067
ORF1ab/nsp4478F478FttCttT11AY.34.10.00051
ORF1ab/nsp4478F478YtTctAc11AY.390.000025
ORF1ab/nsp4478F478delTTC---11AY.390.000025
ORF1ab/nsp4478F478FttCttT11AY.4.50.000107
ORF1ab/nsp4478F478CtTctGc11AY.4.50.000107
ORF1ab/nsp4478F478FttCttT11AY.420.00004
ORF1ab/nsp4478F478LttCttA11AY.430.000004
ORF1ab/nsp4478F478FttCttT11AY.450.000122
ORF1ab/nsp4478F478delTTC---11AY.46.20.000635
ORF1ab/nsp4478F478FttCttT11AY.50.000021
ORF1ab/nsp4478F478delTTC---11AY.60.000041
ORF1ab/nsp4478F478FttCttT11AY.700.000209
ORF1ab/nsp4478F478FttCttT11AY.740.000116
ORF1ab/nsp4478F478FttCttT11AY.920.000287
ORF1ab/nsp4478F478FttCttT11AY.980.000079
ORF1ab/nsp4478F478delTTC---11AY.99.10.001553
ORF1ab/nsp4478F478FttCttT11AY.99.20.000092
ORF1ab/nsp4478F478LttCttA11B0.000128
ORF1ab/nsp4478F478VTtcGtc11B.10.000009
ORF1ab/nsp4478F478LTtcCtc11B.1.10.000018
ORF1ab/nsp4478F478ITtcAtc11B.1.10.000018
ORF1ab/nsp4478F478ITtcAtc11B.1.1.1390.022727
ORF1ab/nsp4478F478FttCttT11B.1.1.2070.001182
ORF1ab/nsp4478F478FttCttT11B.1.1.2730.006757
ORF1ab/nsp4478F478FttCttT11B.1.1.3120.001912
ORF1ab/nsp4478F478FttCttT11B.1.1.3160.000925
ORF1ab/nsp4478F478FttCttT11B.1.1.3330.001076
ORF1ab/nsp4478F478delTTC---11B.1.1.4090.002833
ORF1ab/nsp4478F478FttCttT11B.1.1.460.004367
ORF1ab/nsp4478F478FttCttT11B.1.1.4850.016667
ORF1ab/nsp4478F478StTctCc11B.1.1.500.000679
ORF1ab/nsp4478F478delTTC---11B.1.1.5280.004808
ORF1ab/nsp4478F478FttCttT11B.1.1.630.000386
ORF1ab/nsp4478F478LTtcCtc11B.1.1.70.000001
ORF1ab/nsp4478F478FttCttT11B.1.1110.001175
ORF1ab/nsp4478F478StTctCc11B.1.1770.000013
ORF1ab/nsp4478F478delTTC---11B.1.177.150.000631
ORF1ab/nsp4478F478delTTC---11B.1.177.40.000211
ORF1ab/nsp4478F478FttCttT11B.1.177.460.000918
ORF1ab/nsp4478F478VTtcGtc11B.1.177.540.000606
ORF1ab/nsp4478F478delTTC---11B.1.177.690.001484
ORF1ab/nsp4478F478delTTC---11B.1.177.70.000165
ORF1ab/nsp4478F478FttCttT11B.1.177.730.000566
ORF1ab/nsp4478F478delTTC---11B.1.177.810.000189
ORF1ab/nsp4478F478delTTC---11B.1.177.870.000728
ORF1ab/nsp4478F478delTTC---11B.1.1790.003759
ORF1ab/nsp4478F478del1Ttc-tc11B.1.20.000009
ORF1ab/nsp4478F478LTtcCtc11B.1.20.000009
ORF1ab/nsp4478F478FttCttT11B.1.2210.000071
ORF1ab/nsp4478F478FttCttT11B.1.2580.000067
ORF1ab/nsp4478F478FttCttT11B.1.2790.000514
ORF1ab/nsp4478F478delTTC---11B.1.36.180.00042
ORF1ab/nsp4478F478StTctCc11B.1.3890.001002
ORF1ab/nsp4478F478del1ttCtt-11B.1.3960.000706
ORF1ab/nsp4478F478FttCttT11B.1.4200.010417
ORF1ab/nsp4478F478StTctCc11B.1.4270.00005
ORF1ab/nsp4478F478LTtcCtc11B.1.4290.000024
ORF1ab/nsp4478F478StTctCc11B.1.466.20.000391
ORF1ab/nsp4478F478LTtcCtc11B.1.5440.006024
ORF1ab/nsp4478F478FttCttT11B.1.5640.000426
ORF1ab/nsp4478F478ITtcAtc11B.1.617.10.000129
ORF1ab/nsp4478F478FttCttT11B.1.6180.004032
ORF1ab/nsp4478F478FttCttT11B.1.6230.000536
ORF1ab/nsp4478F478FttCttT11B.1.6280.000352
ORF1ab/nsp4478F478FttCttT11B.1.6370.000073
ORF1ab/nsp4478F478LTtcCtc11B.4.50.011905
ORF1ab/nsp4478F478LttCttA11B.60.00091
ORF1ab/nsp4478F478FttCttT11C.110.010638
ORF1ab/nsp4478F478FttCttT11C.2.10.006667
ORF1ab/nsp4478F478del2tTCt--11C.350.000774
ORF1ab/nsp4478F478LTtcCtc11D.20.000075
ORF1ab/nsp4478F478LTtcCtc11P.10.000016
ORF1ab/nsp4478F478FttCttT11P.1.100.000269
ORF1ab/nsp4478F478FttCttT11Q.10.000126

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.