breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
MC JC 257,908 Δ776 bp insB9–[crl] insB9, insA9, [crl]
RA 1,152,159 T→G F74C (TTC→TGC)  fabF → beta‑ketoacyl‑[acyl carrier protein] synthase II
MC JC 1,397,381 Δ13,756 bp [ynaJ]–[ttcA] 16 genes
RA 1,618,806 Δ1 bp coding (103/666 nt) marC ← inner membrane protein MarC
MC JC 1,978,503 Δ776 bp insB‑5–insA‑5 insB‑5, insA‑5
RA 2,173,363 Δ2 bp pseudogene (915‑916/1358 nt) gatC ← galactitol‑specific PTS enzyme IIC component
RA 2,661,812 T→A H107L (CAC→CTC)  iscR ← DNA‑binding transcriptional dual regulator IscR

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 2939356 4641652 1702297 151 [149] [0] NA fucR–yjtD fucR,rlmM,ygdD,gcvA,gcvB,ygdI,csdA,csdE,tcdA,mltA,metZ,metW,metV,amiC,argA,recD,recB,ptrA,recC,ppdC,ygdB,ppdB,ppdA,thyA,lgt,ptsP,rppH,ygdT,mutH,ygdQ,ygdR,tas,lplT,aas,omrA,omrB,galR,lysA,lysR,ygeA,araE,kduD,kduI,yqeF,yqeG,yqeH,yqeI,yqeJ,yqeL,yqeK,ygeF,ygeG,ygeH,ygeI,pbl,ygeK,ygeL,ygeN,ygeO,insD‑4,insC‑4,ygeP,ygeQ,glyU,ygeR,xdhA,xdhB,xdhC,ygeV,ygeW,ygeX,ygeY,hyuA,yqeA,yqeB,yqeC,mocA,ygfK,ssnA,ygfM,xdhD,xanQ,guaD,ghxQ,ygfS,ygfT,uacT,yqfG,yqfH,idi,lysS,prfB,prfB,recJ,dsbC,xerD,fldB,ygfX,sdhE,ygfZ,yqfA,yqfB,bglA,ygfF,gcvP,gcvH,gcvT,yqfI,ubiI,ubiH,pepP,ygfB,zapA,ssrS,fau,sibC,ibsC,serA,rpiA,yqfE,argP,scpA,argK,scpB,scpC,ygfI,yggE,argO,mscS,fbaA,pgk,epd,yggC,fumE,yggF,yggP,cmtA,cmtB,tktA,loiP,speB,speA,yqgB,yqgC,yqgD,metK,galP,yggI,endA,rsmE,gshB,yqgE,yqgF,yggR,yggS,yggT,yggU,rdgB,yggW,yggM,ansB,yggN,yggL,trmI,mutY,yggX,mltC,nupG,speC,yqgA,pheV,yghD,yghE,yghF,yghG,pppA,yghJ,glcA,glcB,glcG,glcF,glcE,glcD,glcC,yghO,insH‑9,yghQ,yghR,yghS,yghT,pitB,gss,yghU,hybG,hybF,hybE,hybD,hybC,hybB,hybA,hybO,yghW,yghX,yqhI,gpr,yqhA,yghA,exbD,exbB,metC,yghB,yqhC,yqhD,dkgA,yqhG,yqhH,ygiQ,ftsP,plsC,parC,ygiS,mqsA,mqsR,ygiV,ygiW,qseB,qseC,ygiZ,mdaB,ygiN,parE,yqiA,cpdA,yqiB,nudF,tolC,ygiA,ygiB,ygiC,ygiD,zupT,yqiD,ribB,ubiK,ygiL,yqiG,insC‑5,insD‑5,yqiG,yqiH,yqiI,glgS,yqiJ,yqiK,sibD,ibsD,sibE,ibsE,rfaE,glnE,ygiF,ygiM,cca,bacA,folB,plsY,ttdR,ttdA,ttdB,ttdT,tsaD,rpsU,dnaG,rpoD,mug,ileX,nfeF,nfeR,aer,patA,ygjH,ebgR,ebgA,ebgC,ygjI,ygjJ,ygjK,fadH,higA,higB,rlmG,ygjP,ygjQ,ygjR,alx,sstT,ygjV,uxaA,uxaC,exuT,exuR,yqjA,mzrA,yqjC,yqjD,yqjE,yqjK,yqjF,yqjG,yhaH,yhaI,yhaJ,yhaK,yhaL,cyuA,cyuP,tdcG,tdcF,tdcE,tdcD,tdcC,tdcB,tdcA,tdcR,yhaB,yhaC,rnpB,garK,garR,garL,garP,garD,prlF,yhaV,agaR,kbaZ,agaV,agaW,agaA,agaS,kbaY,agaB,agaC,agaD,agaI,yraH,yraI,yraJ,yraK,rsmI,lpoA,yraN,diaA,yraP,yraQ,yraR,yhbO,yhbP,yhbQ,yhbS,yhbT,yhbU,yhbV,yhbW,mtr,deaD,yrbN,nlpI,pnp,sraG,rpsO,truB,rbfA,infB,nusA,rimP,metY,argG,yhbX,leuU,secG,glmM,folP,ftsH,rlmE,yhbY,greA,dacB,obgE,yhbE,rpmA,rplU,ispB,sfsB,murA,ibaG,mlaB,mlaC,mlaD,mlaE,mlaF,yrbG,kdsD,kdsC,lptC,lptA,lptB,rpoN,hpf,ptsN,rapZ,npr,yrbL,mtgA,elbB,arcZ,arcB,yhcC,gltB,gltD,gltF,yhcA,yhcD,yhcE,insH‑10,yhcE,yhcF,yhcG,yhcH,nanK,nanE,nanT,nanA,nanR,dcuD,sspB,sspA,rpsI,rplM,zapE,yhcB,degQ,degS,mdh,argR,yhcN,yhcO,aaeB,aaeA,aaeX,aaeR,tldD,yhdP,rng,yhdE,mreD,mreC,mreB,csrD,yhdH,accB,accC,yhdT,panF,prmA,dusB,fis,yhdJ,yhdU,envR,acrE,acrF,yhdV,yhdW,yhdX,yhdY,yhdZ,rrfF,thrV,rrfD,rrlD,alaU,ileU,rrsD,yrdA,yrdB,aroE,tsaC,yrdD,smg,smf,def,fmt,rsmB,trkA,mscL,arfA,zntR,yhdN,rplQ,rpoA,rpsD,rpsK,rpsM,rpmJ,secY,rplO,rpmD,rpsE,rplR,rplF,rpsH,rpsN,rplE,rplX,rplN,rpsQ,rpmC,rplP,rpsC,rplV,rpsS,rplB,rplW,rplD,rplC,rpsJ,gspB,gspA,gspC,gspD,gspE,gspF,gspG,gspH,gspI,gspJ,gspK,gspL,gspM,gspO,bfr,bfd,chiA,tufA,fusA,rpsG,rpsL,tusB,tusC,tusD,yheO,fkpA,slyX,slyD,yheV,kefB,kefG,yheS,yheT,yheU,prkB,yhfA,crp,yhfK,argD,pabA,fic,yhfG,ppiA,tsgA,nirB,nirD,nirC,cysG,yhfL,frlA,frlB,frlC,frlD,frlR,yhfS,yhfT,yhfU,php,yhfW,yhfX,yhfY,yhfZ,trpS,gph,rpe,dam,damX,aroB,aroK,hofQ,hofP,hofO,hofN,hofM,mrcA,nudE,igaA,yrfG,hslR,hslO,yhgE,pck,envZ,ompR,greB,yhgF,feoA,feoB,feoC,rpnA,bioH,yhgH,nfuA,gntT,malQ,malP,malT,rtcA,rtcB,rtcR,glpR,glpG,glpE,glpD,yzgL,glgP,glgA,glgC,glgX,glgB,asd,yhgN,gntU,gntK,gntR,yhhW,yhhX,ryhB,yhhY,yhhZ,yrhA,insA‑6,insB‑6,yrhA,yrhD,yrhB,ggt,yhhA,ugpQ,ugpC,ugpE,ugpA,ugpB,livF,livG,livM,livH,livK,panZ,livJ,rpoH,ftsX,ftsE,ftsY,rsmD,yhhL,yhhM,yhhN,zntA,tusA,yhhQ,dcrB,yhhS,yhhT,acpT,nikA,nikB,nikC,nikD,nikE,nikR,rhsB,yhhH,yhhI,yhhJ,rbbA,yhiI,yhiJ,yhiL,yhiM,yhiN,pitA,uspB,uspA,dtpB,rsmJ,prlC,rlmJ,gor,dinQ,agrA,agrB,arsR,arsB,arsC,yhiS,insH‑11,yhiS,slp,dctR,yhiD,hdeB,hdeA,hdeD,arrS,gadE,gadF,mdtE,mdtF,gadW,gadY,gadX,gadA,ccp,treF,yhjB,yhjC,yhjD,yhjE,yhjG,pdeH,kdgK,yhjJ,dctA,pdeK,bcsC,bcsZ,bcsB,bcsA,bcsQ,yhjR,bcsE,bcsF,bcsG,ldrD,rdlD,yhjV,dppF,dppD,dppC,dppB,dppA,proK,eptB,yhjX,yhjY,tag,yiaC,bisC,yiaD,ghrB,yiaF,yiaG,cspA,hokA,insJ,insK,glyS,glyQ,ysaB,wecH,yiaA,yiaB,xylB,xylA,xylF,xylG,xylH,xylR,bax,malS,avtA,ysaA,yiaJ,yiaK,yiaL,yiaM,yiaN,yiaO,lyxK,sgbH,sgbU,sgbE,yiaT,yiaU,yiaV,yiaW,aldB,yiaY,selB,selA,yibF,rhsA,yibA,yibJ,yibG,yibS,yibV,yibH,yibI,mtlA,mtlD,mtlR,yibT,yibL,lldP,lldR,lldD,trmL,cysE,gpsA,secB,grxC,yibN,gpmM,envC,yibQ,waaH,tdh,kbl,htrL,rfaD,waaF,waaC,waaL,waaU,waaZ,waaY,waaJ,waaO,waaB,waaS,waaP,waaG,waaQ,waaA,coaD,mutM,rpmG,rpmB,yicR,dfp,dut,slmA,pyrE,rph,yicC,dinD,yicG,ligB,gmk,rpoZ,spoT,trmH,recG,gltS,xanP,yicH,yicI,yicJ,selC,setC,yicL,nlpA,yicS,nepI,yicN,adeQ,adeD,uhpT,uhpC,uhpB,uhpA,ilvN,ilvB,ivbL,istR,istR,tisB,emrD,yidF,yidG,yidH,yidI,yidJ,yidK,yidL,glvG,glvB,glvC,yidP,yidE,ibpB,ibpA,yidQ,yidR,cbrA,dgoT,dgoD,dgoA,dgoK,dgoR,yidX,yidA,yidB,gyrB,recF,dnaN,dnaA,ysdD,rpmH,rnpA,yidD,yidC,mnmE,tnaC,tnaA,tnaB,mdtL,yidZ,yieE,yieF,adeP,yieH,cbrB,cbrC,yieK,yieL,bglH,bglB,bglF,bglG,phoU,pstB,pstA,pstC,pstS,glmS,glmU,atpC,atpD,atpG,atpA,atpH,atpF,atpE,atpB,atpI,rsmG,mnmG,mioC,asnC,asnA,viaA,ravA,kup,rbsD,rbsA,rbsC,rbsB,rbsK,rbsR,hsrA,yieP,rrsC,gltU,rrlC,rrfC,aspT,trpT,hdfR,maoP,yifB,ilvL,ilvX,ilvG,ilvM,ilvE,ilvD,ilvA,ilvY,ilvC,ppiC,yifN,rep,gpp,rhlB,trxA,rhoL,rho,rfe,wzzE,wecB,wecC,rffG,rffH,rffC,wecE,wzxE,rffT,wzyE,rffM,yifK,argX,hisR,leuT,proM,aslB,aslA,glmZ,hemY,hemX,hemD,hemC,cyaA,cyaY,yzcX,yifL,dapF,yigA,xerC,yigB,uvrD,yigE,corA,yigF,yigG,rarD,yigI,pldA,recQ,rhtC,rhtB,pldB,yigL,bioP,metR,metE,ysgA,udp,rmuC,ubiE,ubiJ,esrE,ubiB,tatA,tatB,tatC,tatD,rfaH,ubiD,fre,fadA,fadB,pepQ,yigZ,trkH,hemG,rrsA,ileT,alaT,rrlA,rrfA,mobB,mobA,yihD,srkA,dsbA,yihF,yihG,polA,spf,yihA,csrC,yihI,hemN,yshB,glnG,glnL,glnA,bipA,yihL,yihM,yihN,ompL,yihO,yihP,yihQ,yihR,yihS,yihT,yihU,yihV,yihW,yihX,yihY,dtd,yiiD,yiiE,yiiF,fdhE,fdoI,fdoH,fdoG,fdhD,yiiG,frvR,frvX,frvB,frvA,rhaM,rhaD,rhaA,rhaB,rhaS,rhaR,rhaT,sodA,kdgT,yiiM,cpxA,cpxR,cpxP,cpxQ,fieF,pfkA,sbp,cdh,tpiA,yiiQ,yiiR,yiiS,uspD,fpr,glpX,glpK,glpF,zapB,rraA,menA,hslU,hslV,ftsN,cytR,priA,rpmE,yiiX,metJ,metB,metL,metF,katG,yijE,yijF,gldA,fsaB,ptsA,frwC,frwB,pflD,pflC,frwD,yijO,eptC,ppc,argE,argC,argB,argH,oxyS,oxyR,sthA,fabR,yijD,trmA,btuB,murI,rrsB,gltT,rrlB,rrfB,murB,birA,coaA,thrU,tyrU,glyT,thrT,tufB,secE,nusG,rplK,rplA,rplJ,rplL,rpoB,rpoC,yjaZ,sroH,thiH,thiG,thiS,thiF,thiE,thiC,rsd,nudC,hemE,nfi,yjaG,hupA,yjaH,zraP,zraS,zraR,purD,purH,rrsE,gltV,rrlE,rrfE,yjaA,yjaB,metA,aceB,aceA,aceK,arpA,iclR,metH,yjbB,pepE,rluF,yjbD,lysC,pgi,yjbE,yjbF,yjbG,yjbH,yjbT,psiE,xylE,malG,malF,malE,malK,lamB,malM,yjbI,ubiC,ubiA,plsB,dgkA,lexA,dinF,yjbJ,zur,yjbL,yjbM,dusA,pspG,qorA,dnaB,alr,tyrB,yjbS,aphA,yjbQ,yjbR,uvrA,ssb,yjcB,pdeC,soxS,soxR,ryjA,ghxP,yjcE,yjcF,actP,yjcH,acs,nrfA,nrfB,nrfC,nrfD,nrfE,nrfF,nrfG,gltP,yjcO,fdhF,mdtP,mdtO,mdtN,ytcA,yjcS,alsK,alsE,alsC,alsA,alsB,alsR,rpiB,yjdP,phnP,phnO,phnN,phnM,phnL,phnK,phnJ,phnI,phnH,phnG,phnF,phnE,phnD,phnC,yjdN,yjdM,crfC,yjcZ,proP,pmrR,basS,basR,eptA,adiC,adiY,adiA,melR,melA,melB,yjdF,fumB,dcuB,dcuR,dcuS,yjdI,yjdJ,ghoS,ghoT,lysU,dtpC,cadA,cadB,cadC,pheU,yjdC,dsbD,cutA,dcuA,aspA,fxsA,yjeH,groS,groL,yjeI,yjeJ,epmB,efp,ecnA,ecnB,gdx,blc,ampC,frdD,frdC,frdB,frdA,epmA,yjeM,yjeN,yjeO,mscM,psd,rsgA,orn,glyV,glyX,glyY,yjeV,queG,nnr,tsaE,amiB,mutL,miaA,hfq,hflX,hflK,hflC,yjeT,purA,nsrR,rnr,rlmB,yjfI,yjfJ,yjfK,yjfL,yjfM,yjfC,aidB,yjfN,bsmA,yjfP,ulaR,ulaG,ulaA,ulaB,ulaC,ulaD,ulaE,ulaF,yjfY,rpsF,priB,rpsR,rplI,yjfZ,ytfA,ytfB,fklB,cycA,ytfE,ytfF,qorB,ytfH,cpdB,cysQ,ytfI,ytfJ,ytfK,ytfL,msrA,tamA,tamB,ytfP,yzfA,chpS,chpB,ppa,ytfQ,ytfR,ytfT,yjfF,fbp,mpl,yjgA,pmbA,nrdG,nrdD,treC,treB,treR,mgtL,mgtA,ridA,pyrI,pyrB,pyrL,yjgH,bdcA,bdcR,tabA,yjgL,argI,rraB,yjgM,yjgN,valS,holC,pepA,lptF,lptG,yjgR,idnR,idnT,idnO,idnD,idnK,ahr,leuX,intB,insC‑6,insD‑6,yjgX,yjgZ,insG,yjhB,yjhC,ythA,yjhD,yjhE,insO,insI‑3,insO,insO,yjhV,fecE,fecD,fecC,fecB,fecA,fecR,fecI,insA‑7,yjhU,yjhF,yjhG,yjhH,yjhI,sgcR,sgcE,sgcA,ryjB,sgcQ,sgcC,sgcB,sgcX,yjhP,yjhQ,topAI,yjhZ,yjhR,nanS,nanM,nanC,fimB,fimE,fimA,fimI,fimC,fimD,fimF,fimG,fimH,gntP,uxuA,uxuB,uxuR,yjiC,ytiC,ytiD,idlP,iraD,hypT,iadA,yjiG,yjiH,kptA,yjiJ,yjiK,ytiA,yjiL,yjiM,yjiN,mdtM,rpnD,yjiR,yjiS,yjiT,yjiV,mcrC,mcrB,symE,symR,hsdS,hsdM,hsdR,mrr,yjiA,yjiX,btsT,tsr,lgoT,lgoR,lgoD,opgB,yjjA,dnaC,dnaT,yjjB,yjjP,yjjQ,bglJ,fhuF,yjjZ,leuV,leuP,leuQ,rsmC,holD,rimI,yjjG,prfC,osmY,ytjA,yjjU,yjjV,yjjW,yjjI,deoC,deoA,deoB,deoD,yjjJ,lplA,ytjB,serB,radA,nadR,ettA,slt,trpR,yjjX,ytjC,rob,creA,creB,creC,creD,arcA,yjjY,yjtD

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =10 (0.040)248 (1.040) 157/260 0.0 97.1% coding (290/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 1209619 = 6 (0.030)pseudogene (37/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 = 120780511 (0.040)201 (0.850) 130/260 0.0 96.2% coding (305/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 = 1209602 6 (0.030)pseudogene (54/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 = 12994980 (0.000)317 (1.220) 182/284 0.0 99.8% intergenic (+253/‑33) ychE/insH21 putative inner membrane protein/IS5 transposase and trans‑activator
?NC_000913 1300698 = 1 (0.000)intergenic (+151/‑484) insH21/oppA IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein