CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp4 : CodonNum = 384

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/nsp4384C384FC3147FnonsyntGttTt47747719704-9706
ORF1ab/nsp4384C384CC3147CsyntgTtgC25025019704-9706
ORF1ab/nsp4384C384LC3147LnonsynTGtCTt100950.959704-9706
ORF1ab/nsp4384C384LC3147LnonsyntGTtTG10020.029704-9706
ORF1ab/nsp4384C384LC3147LnonsyntGTtTA10020.029704-9706
ORF1ab/nsp4384C384LC3147LnonsynTGTCTG10010.019704-9706
ORF1ab/nsp4384C384delC3147deldelTGT---949419704-9706
ORF1ab/nsp4384C384SC3147SnonsynTgtAgt23190.8260879704-9706
ORF1ab/nsp4384C384SC3147SnonsyntGttCt2340.1739139704-9706
ORF1ab/nsp4384C384YC3147YnonsyntGttAt222219704-9706
ORF1ab/nsp4384C384RC3147RnonsynTgtCgt1170.6363649704-9706
ORF1ab/nsp4384C384XC3147XnonsyntgTtgA1150.4545459704-9706
ORF1ab/nsp4384C384XC3147XnonsyntGTtAA1140.3636369704-9706
ORF1ab/nsp4384C384RC3147RnonsynTgTAgG1120.1818189704-9706
ORF1ab/nsp4384C384XC3147XnonsyntGTtAG1120.1818189704-9706
ORF1ab/nsp4384C384RC3147RnonsynTgTAgA1120.1818189704-9706
ORF1ab/nsp4384C384GC3147GnonsynTgtGgt950.5555569704-9706
ORF1ab/nsp4384C384GC3147GnonsynTgTGgA920.2222229704-9706
ORF1ab/nsp4384C384GC3147GnonsynTgTGgG920.2222229704-9706
ORF1ab/nsp4384C384WC3147WnonsyntgTtgG6619704-9706
ORF1ab/nsp4384C384VC3147VnonsynTGTGTG620.3333339704-9706
ORF1ab/nsp4384C384VC3147VnonsynTGTGTA620.3333339704-9706
ORF1ab/nsp4384C384VC3147VnonsynTGtGTt620.3333339704-9706
ORF1ab/nsp4384C384IC3147InonsynTGtATt530.69704-9706
ORF1ab/nsp4384C384IC3147InonsynTGTATA520.49704-9706
ORF1ab/nsp4384C384EC3147EnonsynTGTGAA420.59704-9706
ORF1ab/nsp4384C384EC3147EnonsynTGTGAG420.59704-9706
ORF1ab/nsp4384C384KC3147KnonsynTGTAAG420.59704-9706
ORF1ab/nsp4384C384KC3147KnonsynTGTAAA420.59704-9706
ORF1ab/nsp4384C384DC3147DnonsynTGtGAt2219704-9706
ORF1ab/nsp4384C384MC3147MnonsynTGTATG2219704-9706
ORF1ab/nsp4384C384NC3147NnonsynTGtAAt2219704-9706
ORF1ab/nsp4384C384del2C3147del2delTGt--t1119704-9706
ORF1ab/nsp4384C384del1C3147del1delTgt-gt1119704-9706

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/nsp4384C384FtGttTt477477All0.000091
ORF1ab/nsp4384C384FtGttTt314314B.1.4250.94012
ORF1ab/nsp4384C384CtgTtgC250250All0.000048
ORF1ab/nsp4384C384LTGtCTt95100All0.000018
ORF1ab/nsp4384C384LtGTtTA2100All0
ORF1ab/nsp4384C384LtGTtTG2100All0
ORF1ab/nsp4384C384LTGTCTG1100All0
ORF1ab/nsp4384C384delTGT---9494All0.000018
ORF1ab/nsp4384C384CtgTtgC9191AY.1030.000565
ORF1ab/nsp4384C384CtgTtgC6565B.1.1.70.000058
ORF1ab/nsp4384C384LTGtCTt5151AY.920.014651
ORF1ab/nsp4384C384delTGT---4444B.1.1.70.000039
ORF1ab/nsp4384C384FtGttTt3636AY.40.000056
ORF1ab/nsp4384C384CtgTtgC2929B.1.3510.000862
ORF1ab/nsp4384C384STgtAgt1923All0.000004
ORF1ab/nsp4384C384StGttCt423All0.000001
ORF1ab/nsp4384C384YtGttAt2222All0.000004
ORF1ab/nsp4384C384CtgTtgC2020B.1.20.000176
ORF1ab/nsp4384C384FtGttTt1616B.1.1.70.000014
ORF1ab/nsp4384C384FtGttTt1616B.1.6280.005638
ORF1ab/nsp4384C384STgtAgt1212B.1.4290.000282
ORF1ab/nsp4384C384RTgtCgt711All0.000001
ORF1ab/nsp4384C384XtgTtgA511All0.000001
ORF1ab/nsp4384C384XtGTtAA411All0.000001
ORF1ab/nsp4384C384RTgTAgG211All0
ORF1ab/nsp4384C384RTgTAgA211All0
ORF1ab/nsp4384C384XtGTtAG211All0
ORF1ab/nsp4384C384FtGttTt1111B.1.20.000097
ORF1ab/nsp4384C384XtGTtAA4100.222222
ORF1ab/nsp4384C384XtgTtgA4100.222222
ORF1ab/nsp4384C384XtGTtAG2100.111111
ORF1ab/nsp4384C384FtGttTt1010AY.1170.000845
ORF1ab/nsp4384C384GTgtGgt59All0.000001
ORF1ab/nsp4384C384GTgTGgG29All0
ORF1ab/nsp4384C384GTgTGgA29All0
ORF1ab/nsp4384C384FtGttTt99B.1.10.000163
ORF1ab/nsp4384C384LTGtCTt88B.1.360.001167
ORF1ab/nsp4384C384delTGT---77AY.4.50.000752
ORF1ab/nsp4384C384GTgtGgt260.111111
ORF1ab/nsp4384C384VTGTGTA260.111111
ORF1ab/nsp4384C384VTGtGTt260.111111
ORF1ab/nsp4384C384VTGTGTG260.111111
ORF1ab/nsp4384C384GTgTGgG260.111111
ORF1ab/nsp4384C384GTgTGgA260.111111
ORF1ab/nsp4384C384WtgTtgG66All0.000001
ORF1ab/nsp4384C384VTGtGTt26All0
ORF1ab/nsp4384C384VTGTGTG26All0
ORF1ab/nsp4384C384VTGTGTA26All0
ORF1ab/nsp4384C384delTGT---66B.1.1770.000079
ORF1ab/nsp4384C384LTGtCTt66B.1.4270.000303
ORF1ab/nsp4384C384FtGttTt66B.1.617.20.000023
ORF1ab/nsp4384C384ITGtATt35All0.000001
ORF1ab/nsp4384C384ITGTATA25All0
ORF1ab/nsp4384C384FtGttTt55AY.230.000349
ORF1ab/nsp4384C384CtgTtgC55AY.40.000008
ORF1ab/nsp4384C384FtGttTt55B.10.000046
ORF1ab/nsp4384C384LTGtCTt55B.1.1.2220.00102
ORF1ab/nsp4384C384YtGttAt440.222222
ORF1ab/nsp4384C384WtgTtgG440.222222
ORF1ab/nsp4384C384KTGTAAG240.111111
ORF1ab/nsp4384C384RTgTAgG240.111111
ORF1ab/nsp4384C384KTGTAAA240.111111
ORF1ab/nsp4384C384ITGTATA240.111111
ORF1ab/nsp4384C384ITGtATt240.111111
ORF1ab/nsp4384C384ETGTGAA240.111111
ORF1ab/nsp4384C384ETGTGAG240.111111
ORF1ab/nsp4384C384LtGTtTG240.111111
ORF1ab/nsp4384C384LtGTtTA240.111111
ORF1ab/nsp4384C384RTgTAgA240.111111
ORF1ab/nsp4384C384KTGTAAG24All0
ORF1ab/nsp4384C384ETGTGAG24All0
ORF1ab/nsp4384C384KTGTAAA24All0
ORF1ab/nsp4384C384ETGTGAA24All0
ORF1ab/nsp4384C384CtgTtgC44AY.30.00004
ORF1ab/nsp4384C384delTGT---44AY.40.000006
ORF1ab/nsp4384C384CtgTtgC44AY.4.20.000087
ORF1ab/nsp4384C384delTGT---44AY.430.000018
ORF1ab/nsp4384C384CtgTtgC44B.10.000037
ORF1ab/nsp4384C384LTGtCTt44B.1.4290.000094
ORF1ab/nsp4384C384YtGttAt44B.1.617.20.000015
ORF1ab/nsp4384C384FtGttTt330.166667
ORF1ab/nsp4384C384FtGttTt33AY.120.000948
ORF1ab/nsp4384C384YtGttAt33AY.250.000018
ORF1ab/nsp4384C384CtgTtgC33AY.260.000085
ORF1ab/nsp4384C384YtGttAt33AY.40.000005
ORF1ab/nsp4384C384FtGttTt33AY.440.000018
ORF1ab/nsp4384C384FtGttTt33B.1.1.5190.000119
ORF1ab/nsp4384C384LTGtCTt33B.1.20.000026
ORF1ab/nsp4384C384LTGtCTt33B.1.2580.0002
ORF1ab/nsp4384C384FtGttTt33B.1.5640.001278
ORF1ab/nsp4384C384DTGtGAt220.111111
ORF1ab/nsp4384C384MTGTATG220.111111
ORF1ab/nsp4384C384NTGtAAt220.111111
ORF1ab/nsp4384C384STgtAgt220.111111
ORF1ab/nsp4384C384MTGTATG22All0
ORF1ab/nsp4384C384NTGtAAt22All0
ORF1ab/nsp4384C384DTGtGAt22All0
ORF1ab/nsp4384C384CtgTtgC22AY.1020.000053
ORF1ab/nsp4384C384CtgTtgC22AY.1040.003968
ORF1ab/nsp4384C384FtGttTt22AY.200.000078
ORF1ab/nsp4384C384FtGttTt22AY.260.000057
ORF1ab/nsp4384C384FtGttTt22AY.30.00002
ORF1ab/nsp4384C384LTGtCTt22AY.30.00002
ORF1ab/nsp4384C384CtgTtgC22AY.320.001065
ORF1ab/nsp4384C384FtGttTt22AY.39.10.000079
ORF1ab/nsp4384C384FtGttTt22AY.430.000009
ORF1ab/nsp4384C384CtgTtgC22AY.50.000041
ORF1ab/nsp4384C384CtgTtgC22AY.9.10.000167
ORF1ab/nsp4384C384CtgTtgC22AY.91.10.00813
ORF1ab/nsp4384C384RTgtCgt22B.10.000018
ORF1ab/nsp4384C384YtGttAt22B.10.000018
ORF1ab/nsp4384C384StGttCt12B.1.10.000018
ORF1ab/nsp4384C384STgtAgt12B.1.10.000018
ORF1ab/nsp4384C384STgtAgt22B.1.1.70.000002
ORF1ab/nsp4384C384LTGtCTt22B.1.1770.000026
ORF1ab/nsp4384C384CtgTtgC22B.1.177.120.000303
ORF1ab/nsp4384C384delTGT---22B.1.177.690.002967
ORF1ab/nsp4384C384FtGttTt22B.1.177.820.000955
ORF1ab/nsp4384C384delTGT---22B.1.20.000018
ORF1ab/nsp4384C384LTGtCTt22B.1.3510.000059
ORF1ab/nsp4384C384delTGT---22B.1.617.20.000008
ORF1ab/nsp4384C384LTGtCTt22B.1.617.20.000008
ORF1ab/nsp4384C384LTGtCTt11A.10.000282
ORF1ab/nsp4384C384del1Tgt-gt11All0
ORF1ab/nsp4384C384del2TGt--t11All0
ORF1ab/nsp4384C384FtGttTt11AY.1020.000027
ORF1ab/nsp4384C384YtGttAt11AY.1030.000006
ORF1ab/nsp4384C384delTGT---11AY.1060.000335
ORF1ab/nsp4384C384CtgTtgC11AY.1090.00074
ORF1ab/nsp4384C384FtGttTt11AY.1110.000183
ORF1ab/nsp4384C384FtGttTt11AY.1140.000231
ORF1ab/nsp4384C384YtGttAt11AY.1170.000085
ORF1ab/nsp4384C384YtGttAt11AY.1180.000063
ORF1ab/nsp4384C384YtGttAt11AY.1190.000035
ORF1ab/nsp4384C384delTGT---11AY.190.00114
ORF1ab/nsp4384C384CtgTtgC11AY.200.000039
ORF1ab/nsp4384C384FtGttTt11AY.220.002092
ORF1ab/nsp4384C384FtGttTt11AY.240.000431
ORF1ab/nsp4384C384CtgTtgC11AY.250.000006
ORF1ab/nsp4384C384LTGtCTt11AY.260.000028
ORF1ab/nsp4384C384RTgtCgt11AY.260.000028
ORF1ab/nsp4384C384YtGttAt11AY.290.000016
ORF1ab/nsp4384C384RTgtCgt11AY.30.00001
ORF1ab/nsp4384C384LTGtCTt11AY.330.000067
ORF1ab/nsp4384C384FtGttTt11AY.340.000097
ORF1ab/nsp4384C384FtGttTt11AY.390.000025
ORF1ab/nsp4384C384YtGttAt11AY.39.10.00004
ORF1ab/nsp4384C384GTgtGgt11AY.40.000002
ORF1ab/nsp4384C384LTGtCTt11AY.40.000002
ORF1ab/nsp4384C384FtGttTt11AY.420.00004
ORF1ab/nsp4384C384CtgTtgC11AY.430.000004
ORF1ab/nsp4384C384LTGtCTt11AY.450.000122
ORF1ab/nsp4384C384FtGttTt11AY.460.000104
ORF1ab/nsp4384C384CtgTtgC11AY.460.000104
ORF1ab/nsp4384C384delTGT---11AY.46.20.000635
ORF1ab/nsp4384C384FtGttTt11AY.470.000031
ORF1ab/nsp4384C384FtGttTt11AY.50.000021
ORF1ab/nsp4384C384StGttCt11AY.590.00053
ORF1ab/nsp4384C384delTGT---11AY.60.000041
ORF1ab/nsp4384C384del2TGt--t11AY.670.000464
ORF1ab/nsp4384C384delTGT---11AY.680.000274
ORF1ab/nsp4384C384delTGT---11AY.90.000068
ORF1ab/nsp4384C384delTGT---11AY.9.20.000037
ORF1ab/nsp4384C384delTGT---11AY.99.10.001553
ORF1ab/nsp4384C384StGttCt11B.10.000009
ORF1ab/nsp4384C384ITGtATt11B.1.10.000018
ORF1ab/nsp4384C384delTGT---11B.1.10.000018
ORF1ab/nsp4384C384RTgtCgt11B.1.10.000018
ORF1ab/nsp4384C384delTGT---11B.1.1.1390.022727
ORF1ab/nsp4384C384delTGT---11B.1.1.2360.006897
ORF1ab/nsp4384C384GTgtGgt11B.1.1.2630.001558
ORF1ab/nsp4384C384FtGttTt11B.1.1.280.000311
ORF1ab/nsp4384C384LTGtCTt11B.1.1.280.000311
ORF1ab/nsp4384C384FtGttTt11B.1.1.3070.002532
ORF1ab/nsp4384C384RTgtCgt11B.1.1.3070.002532
ORF1ab/nsp4384C384CtgTtgC11B.1.1.3110.000358
ORF1ab/nsp4384C384GTgtGgt11B.1.1.3260.001761
ORF1ab/nsp4384C384LTGTCTG11B.1.1.3720.000689
ORF1ab/nsp4384C384WtgTtgG11B.1.1.70.000001
ORF1ab/nsp4384C384XtgTtgA11B.1.1.70.000001
ORF1ab/nsp4384C384delTGT---11B.1.1.700.000341
ORF1ab/nsp4384C384CtgTtgC11B.1.1770.000013
ORF1ab/nsp4384C384del1Tgt-gt11B.1.1770.000013
ORF1ab/nsp4384C384delTGT---11B.1.177.110.001698
ORF1ab/nsp4384C384FtGttTt11B.1.177.120.000152
ORF1ab/nsp4384C384STgtAgt11B.1.177.160.000664
ORF1ab/nsp4384C384delTGT---11B.1.177.170.000821
ORF1ab/nsp4384C384delTGT---11B.1.177.40.000211
ORF1ab/nsp4384C384delTGT---11B.1.177.550.002331
ORF1ab/nsp4384C384delTGT---11B.1.177.560.000668
ORF1ab/nsp4384C384delTGT---11B.1.177.580.001332
ORF1ab/nsp4384C384delTGT---11B.1.177.760.002494
ORF1ab/nsp4384C384StGttCt11B.1.20.000009
ORF1ab/nsp4384C384CtgTtgC11B.1.3460.001311
ORF1ab/nsp4384C384FtGttTt11B.1.3510.00003
ORF1ab/nsp4384C384delTGT---11B.1.36.380.001642
ORF1ab/nsp4384C384FtGttTt11B.1.4000.000429
ORF1ab/nsp4384C384FtGttTt11B.1.4270.00005
ORF1ab/nsp4384C384FtGttTt11B.1.4290.000024
ORF1ab/nsp4384C384CtgTtgC11B.1.617.10.000129
ORF1ab/nsp4384C384WtgTtgG11B.1.617.10.000129
ORF1ab/nsp4384C384FtGttTt11B.1.6210.000089
ORF1ab/nsp4384C384FtGttTt11B.1.6270.00202
ORF1ab/nsp4384C384CtgTtgC11B.1.6370.000073
ORF1ab/nsp4384C384RTgtCgt11B.1.930.000934
ORF1ab/nsp4384C384LTGtCTt11B.400.000364
ORF1ab/nsp4384C384delTGT---11C.350.000774
ORF1ab/nsp4384C384STgtAgt11D.20.000075
ORF1ab/nsp4384C384CtgTtgC11D.20.000075
ORF1ab/nsp4384C384FtGttTt11P.10.000016
ORF1ab/nsp4384C384FtGttTt11P.30.001595
ORF1ab/nsp4384C384delTGT---11Q.10.000126
ORF1ab/nsp4384C384delTGT---11U.30.003861

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.