mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 124,078 | C→T | D354D (GAC→GAT) | aceE → | pyruvate dehydrogenase E1 component |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 403,205 | (T)7→8 | intergenic (+43/‑76) | phoA → / → psiF | alkaline phosphatase/phosphate starvation‑inducible protein PsiF |
| RA | 421,256 | A→G | T91A (ACC→GCC) | proY → | putative transporter ProY |
| RA | 498,116 | C→T | P21L (CCT→CTT) | hemH → | ferrochelatase |
| RA | 498,809 | A→G | K252R (AAA→AGA) | hemH → | ferrochelatase |
| RA | 499,060 | T→G | D305A (GAC→GCC) | aes ← | acetylesterase |
| MC JC | 499,082 | Δ52,248 bp | [aes]–[ybcF] | 46 genes [aes], gsk, ybaL, fsr, ushA, ybaK, chiX, ybaP, ybaQ, copA, copA, copA, glsA, ybaT, cueR, ybbJ, qmcA, fetA, fetB, cnoX, ybbO, tesA, ybbA, ybbP, rhsD, ybbC, ylbG, selU, allS, allA, allR, allZ, gcl, hyi, glxR, ybbW, allB, ybbY, glxK, allE, allC, allD, fdrA, ylbE, ylbF, [ybcF] |
|
| RA | 694,721 | C→T | G79S (GGC→AGC) | miaB ← | isopentenyl‑adenosine A37 tRNA methylthiolase |
| RA | 709,364 | A→G | D344G (GAT→GGT) | chiP → | chitooligosaccharide outer membrane channel |
| RA | 723,528 | (T)8→7 | coding (887/2685 nt) | kdpD ← | sensor histidine kinase KdpD |
| RA | 803,662 | C→A | L54I (CTT→ATT) | ybhJ → | putative hydratase YbhJ |
| RA | 851,631 | A→G | Y323H (TAC→CAC) | opgE ← | phosphoethanolamine transferase OpgE |
| MC JC | 1,042,956 | Δ72,555 bp | [etk]–mdtG | 71 genes [etk], etp, gfcE, gfcD, gfcC, gfcB, gfcA, insA4, insB4, cspH, cspG, ymcF, ymcE, gnsA, yccM, torS, torT, torR, torC, torA, torD, cbpM, cbpA, yccE, agp, yccJ, wrbA, ymdF, rutG, rutF, rutE, rutD, rutC, rutB, rutA, rutR, putA, ymdG, putP, efeO, efeB, phoH, pgaD, pgaC, pgaB, pgaA, dgcT, insF4, insE4, ycdU, serX, ghrA, ycdX, ycdY, ycdZ, csgG, csgF, csgE, csgD, csgB, csgA, csgC, ymdA, ymdB, clsC, opgC, opgG, opgH, yceK, msyB, mdtG |
|
| RA | 1,552,453 | G→A | A77V (GCA→GTA) | yddM ← | DNA‑binding transcriptional regulator YddM |
| RA | 1,905,761 | G→A | G25D (GGT→GAT) | mntP → | Mn(2(+)) exporter |
| MC JC | 1,978,503 | Δ776 bp | insB5–insA5 | insB5, insA5 | |
| MC JC | 2,085,042 | Δ109,115 bp | [tsuA]–[mrp] | 106 genes [tsuA], plaP, yoeI, yeeY, yeeZ, yoeB, yefM, hisL, hisG, hisD, hisC, hisB, hisH, hisA, hisF, hisI, wzzB, ugd, gnd, wbbL, insH7, wbbL, wbbK, wbbJ, wbbI, wbbH, glf, rfbX, rfbC, rfbA, rfbD, rfbB, galF, wcaM, wcaL, wcaK, wzxC, wcaJ, cpsG, cpsB, wcaI, gmm, fcl, gmd, wcaF, wcaE, wcaD, wcaC, wcaB, wcaA, wzc, wzb, wza, yegH, asmA, dcd, udk, dgcE, alkA, yegD, yegI, yegJ, pphC, yegL, sibA, ibsA, sibB, ibsB, mdtA, mdtB, mdtC, mdtD, baeS, baeR, yegP, trhP, cyaR, ogrK, yegR, yegS, gatR, insE5, insF5, gatR, gatD, gatB, gatA, gatZ, gatY, fbaB, yegT, yegU, yegV, yegW, yegX, thiD, thiM, rcnR, rcnA, rcnB, yehA, yehB, yehC, yehD, yehE, [mrp] |
|
| MC JC | 2,286,372 | Δ22,969 bp | yejO–[alkB] | 24 genes yejO, insH8, yejO, narP, ccmH, ccmG, ccmF, ccmE, ccmD, ccmC, ccmB, ccmA, napC, napB, napH, napG, napA, napD, napF, yojO, eco, mqo, yojI, [alkB] |
|
| RA | 2,311,650 | A→G | F367S (TTC→TCC) | ompC ← | outer membrane porin C |
| MC JC | 2,312,100 | 24707 bp→A | [ompC]–[gyrA] | 16 genes [ompC], micF, rcsD, rcsB, rcsC, atoS, atoC, atoD, atoA, atoE, atoB, yfaP, yfaQ, yfaT, yfaA, [gyrA] |
|
| MC JC | 2,348,550 | Δ41,411 bp | [yfaE]–[yfbP] | 40 genes [yfaE], inaA, glpQ, glpT, glpA, glpB, glpC, rpnE, yfaU, yfaV, rhmD, yfaX, yfaY, yfaZ, nudI, ais, arnB, arnC, arnA, arnD, arnT, arnE, arnF, pmrD, menE, menC, menB, menH, menD, menF, elaB, elaA, rbn, elaD, yfbK, yfbL, yfbM, yfbN, yfbO, [yfbP] |
|
| RA | 2,389,974 | T→G | intergenic (+10/+74) | yfbP → / ← nuoN | uncharacterized protein YfbP/NADH:quinone oxidoreductase subunit N |
| RA | 2,390,295 | T→G | Q404P (CAG→CCG) | nuoN ← | NADH:quinone oxidoreductase subunit N |
| RA | 2,424,640 | T→C | Q198Q (CAA→CAG) | hisM ← | lysine/arginine/ornithine ABC transporter/histidine ABC transporter, membrane subunit HisM |
| RA | 2,531,483 | T→A | S7S (TCT→TCA) | cysZ → | sulfate:H(+) symporter |
| RA | 2,756,045 | T→C | intergenic (+90/‑114) | ssrA → / → intA | tmRNA/integrase IntA |
| RA | 2,756,047 | T→C | intergenic (+92/‑112) | ssrA → / → intA | tmRNA/integrase IntA |
| MC JC | 2,756,415 | Δ57,799 bp | [intA]–emrB | 53 genes [intA], yfjH, alpA, yfjI, yfjJ, abpB, abpA, yfjM, rnlA, rnlB, yfjP, yfjQ, yfjR, ypjK, yfjS, yfjT, yfjU, yfjW, yfjX, yfjY, ypjJ, yfjZ, ypjF, ypjA, ypjB, ypjC, ileY, glaH, lhgD, gabD, gabT, gabP, glaR, kbp, yqaE, ygaV, ygaP, stpA, alaE, ygaC, ygaM, nrdH, nrdI, nrdE, nrdF, proV, proW, proX, ygaZ, ygaH, mprA, emrA, emrB |
|
| RA | 2,823,802 | A→G | intergenic (‑33/+47) | recA ← / ← pncC | DNA recombination/repair protein RecA/NMN aminohydrolase |
| MC JC | 2,823,891 | Δ42,638 bp | [pncC]–ygbN | 41 genes [pncC], mltB, srlA, srlE, srlB, srlD, gutM, srlR, gutQ, norR, norV, norW, hypF, hydN, ascG, ascF, ascB, hycI, hycH, hycG, hycF, hycE, hycD, hycC, hycB, hycA, hypA, hypB, hypC, hypD, hypE, fhlA, ygbA, mutS, pphB, ygbI, ygbJ, ygbK, ygbL, ygbM, ygbN |
|
| RA | 3,194,362 | (G)6→7 | coding (1499/1662 nt) | yqiK → | flotillin family inner membrane protein YqiK |
| RA | 3,214,325 | T→C | F427L (TTC→CTC) | rpoD → | RNA polymerase sigma factor RpoD |
| RA | 3,216,473 | A→G | Y7H (TAC→CAC) | nfeF ← | NADPH‑dependent ferric‑chelate reductase |
| MC JC | 3,216,779 | 53253 bp→GTC | [nfeR]–yhaC | 50 genes [nfeR], aer, patA, ygjH, ebgR, ebgA, ebgC, ygjI, ygjJ, ygjK, fadH, higA, higB, rlmG, ygjP, ygjQ, ygjR, alx, sstT, ygjV, uxaA, uxaC, exuT, exuR, yqiM, 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 |
|
| RA | 3,321,967 | A→G | intergenic (‑354/+105) | yhbX ← / ← leuU | putative hydrolase YhbX/tRNA‑Leu |
| RA | 3,436,697 | G→A | E60E (GAG→GAA) | trkA → | NAD‑binding component of Trk potassium transporters |
| RA | 3,449,779 | G→A | S35S (AGC→AGT) | rpsC ← | 30S ribosomal subunit protein S3 |
| RA | 3,468,768 | C→T | W362* (TGG→TGA) | chiA ← | endochitinase |
| RA | 3,474,425 | T→C | K43R (AAA→AGA) | rpsL ← | 30S ribosomal subunit protein S12 |
| RA | 3,523,800 | C→G | Y310* (TAC→TAG) | mrcA → | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcA |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,718,336 | A→C | *237E (TAA→GAA) | yiaF ← | DUF3053 domain‑containing protein YiaF |
| RA | 3,725,393 | G→A | intergenic (‑75/+20) | glyQ ← / ← ysaB | glycine‑‑tRNA ligase subunit alpha/putative lipoprotein YsaB |
| RA | 3,725,582 | C→A | C44F (TGC→TTC) | ysaB ← | putative lipoprotein YsaB |
| MC JC | 3,725,590 | 46159 bp→ATCG | [ysaB]–yibI | 41 genes [ysaB], wecH, yiaA, yiaB, xylB, xylZ, xylA, xylF, xylG, xylH, xylR, bax, baxL, malS, avtA, ysaA, plaR, yiaK, yiaL, yiaM, yiaN, yiaO, lyxK, sgbH, sgbU, sgbE, yiaT, yiaU, yiaV, yiaW, aldB, yiaY, selB, selA, yibF, rhsA, yibA, yibG, yibV, yibH, yibI |
|
| RA | 3,854,281 | A→G | L120L (TTA→TTG) | emrD → | multidrug efflux pump EmrD |
| RA | 3,922,994 | T→C | intergenic (‑554/+63) | atpI ← / ← rsmG | ATP synthase accessory factor AtpI/16S rRNA m(7)G527 methyltransferase |
| RA | 4,106,199 | A→G | E127G (GAG→GGG) | cpxP → | periplasmic protein CpxP |
| RA | 4,123,930 | A→T | V176E (GTA→GAA) | cytR ← | DNA‑binding transcriptional repressor CytR |
| RA | 4,174,041 | A→T | E320D (GAA→GAT) | birA → | DNA‑binding transcriptional repressor/biotin‑[acetyl‑CoA‑carboxylase] ligase BirA |
| RA | 4,204,890 | C→T | G348S (GGT→AGT) | purD ← | phosphoribosylamine‑‑glycine ligase |
| RA | 4,241,235 | A→G | G340G (GGT→GGC) | xylE ← | D‑xylose:H(+) symporter |
| RA | 4,278,657 | T→C | V60A (GTT→GCT) | ghxP → | guanine/hypoxanthine transporter GhxP |
| RA | 4,278,682 | C→T | A68A (GCC→GCT) | ghxP → | guanine/hypoxanthine transporter GhxP |
| RA | 4,279,023 | T→C | F182S (TTC→TCC) | ghxP → | guanine/hypoxanthine transporter GhxP |
| RA | 4,279,034 | Δ2 bp | coding (556‑557/1350 nt) | ghxP → | guanine/hypoxanthine transporter GhxP |
| MC JC | 4,279,050 | Δ82,373 bp | [ghxP]–[cadC] | 72 genes [ghxP], yjcE, yjcF, actP, yjcH, acs, ytcB, 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, phnD, phnC, yjdN, yjdM, rdcA, rdcB, 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] |
|
| RA | 4,362,045 | T→C | intergenic (‑111/+506) | cadC ← / ← pheU | DNA‑binding transcriptional activator CadC/tRNA‑Phe |
| MC JC | 4,488,473 | Δ111,735 bp | yjgR–yjjA | 100 genes yjgR, idnR, idnT, idnO, idnD, idnK, ahr, leuX, insC6, insD6, yjgZ, insG, nanX, nanY, ythA, insO, insI3, insO, insO, fecE, fecD, fecC, fecB, fecA, fecR, fecI, ykiE, insA7, yjhU, yjhF, yjhG, yjhH, yjhI, sgcR, sgcE, sgcA, ryjB, sgcQ, sgcC, sgcB, sgcX, yjhP, yjhQ, topAI, ythB, 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, ytiE, yjiR, yjiS, yjiT, mcrC, mcrB, mcrB, symE, symR, hsdS, hsdM, hsdR, mrr, yjiA, yjiX, btsT, tsr, lgoT, lgoR, lgoD, opgB, yjjA |
|
| RA | 4,600,215 | +C | intergenic (‑26/+23) | yjjA ← / ← dnaC | DUF2501 domain‑containing protein YjjA/DNA replication protein DnaC |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3619008 | 3718313 | 99306 | 10 [0] | [2] 17 | rhsB–ghrB | rhsB,yhhH,yhhI,yhhJ,rbbA,yhiI,yhiY,yhiJ,yhiM,yhiN,pitA,uspB,uspA,yriA,yriB,dtpB,rsmJ,prlC,rlmJ,gor,dinQ,agrA,agrB,arsR,arsB,arsC,yhiS,insH11,yhiS,slp,dctR,yhiD,hdeB,hdeA,hdeD,arrS,gadE,gadF,mdtE,mdtF,gadW,gadY,gadX,gadA,ccp,treF,yhjB,rcdB,yhjD,yhjE,yhjG,pdeH,kdgK,yhjJ,dctA,pdeK,bcsC,bcsZ,bcsB,bcsA,yhjR,bcsE,bcsF,bcsG,ldrD,rdlD,yhjV,dppF,dppD,dppC,dppB,dppA,proK,eptB,yhjX,yhjY,tag,yiaC,bisC,yiaD,ghrB |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 15911 | NA (NA) | 9 (0.130) +TGTTTTCAA |
9/472 | 2.4 | NA | noncoding (525/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 15922 = | NA (NA) | noncoding (536/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 45 (0.630) | 15 (0.230) | 13/458 | 1.8 | 35.3% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 13 (0.200) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 44 (0.620) | 22 (0.330) | 21/458 | 1.1 | 44.8% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 13 (0.200) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 33 (0.470) | 33/482 | 0.6 | 100% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||