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 | 16,704 | T→C | intergenic (+147/+47) | insL1 → / ← hokC | IS186/IS421 family transposase/protein HokC |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| 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 | 803,662 | C→A | L54I (CTT→ATT) | ybhJ → | putative hydratase YbhJ |
| RA | 844,900 | T→C | D194G (GAC→GGC) | ybiO ← | moderate conductance mechanosensitive channel YbiO |
| RA | 958,173 | A→G | D174G (GAC→GGC) | serC → | phosphoserine/phosphohydroxythreonine aminotransferase |
| RA | 981,850 | (G)6→5 | coding (804/1848 nt) | ldtD → | L,D‑transpeptidase LdtD |
| 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 | 1,185,245 | (T)6→5 | coding (350/1137 nt) | potA ← | spermidine preferential ABC transporter ATP binding subunit |
| RA | 1,552,362 | T→C | intergenic (+371/+36) | fdnI → / ← yddM | formate dehydrogenase N subunit gamma/DNA‑binding transcriptional regulator YddM |
| RA | 1,652,177 | G→A | intergenic (+2192/+551) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,739,489 | G→A | P104S (CCA→TCA) | punR ← | DNA‑binding transcriptional activator PunR |
| 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 | 2,196,426 | Δ46,519 bp | yehF–[yeiB] | 37 genes yehF, yehI, yehK, yehL, yehM, yehP, yehQ, yehR, yehS, btsR, btsS, mlrA, yohO, yehW, yehX, yehY, osmF, bglX, dld, pbpG, yohC, yohD, yohF, yohP, dusC, yohJ, yohK, cdd, sanA, yeiS, preT, preA, mglC, mglA, mglB, galS, [yeiB] |
|
| RA | 2,242,968 | G→T | intergenic (‑1/+16) | yeiB ← / ← folE | DUF418 domain‑containing protein YeiB/GTP cyclohydrolase 1 |
| RA | 2,243,185 | C→T | T156T (ACG→ACA) | folE ← | GTP cyclohydrolase 1 |
| 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] |
|
| JC | 2,449,820 | (GGA)3→2 | coding (228‑230/822 nt) | yfcO ← | DUF2544 domain‑containing protein YfcO |
| 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 | 3,096,175 | T→C | V119A (GTA→GCA) | yggT → | uncharacterized protein YggT |
| RA | 3,216,473 | A→G | Y7H (TAC→CAC) | nfeF ← | NADPH‑dependent ferric‑chelate reductase |
| RA | 3,216,481 | (G)6→7 | coding (11/765 nt) | 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 | 3,277,959 | T→C | D236G (GAT→GGT) | agaR ← | DNA‑binding transcriptional repressor AgaR |
| RA | 3,304,813 | (C)7→8 | coding (1005/1245 nt) | mtr ← | tryptophan:H(+) symporter Mtr |
| 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 | 3,876,476 | T→C | E159E (GAA→GAG) | yidA ← | sugar phosphatase YidA |
| RA | 4,008,439 | (T)5→4 | coding (621/621 nt) | rhtB ← | L‑homoserine/L‑homoserine lactone/L‑threonine exporter |
| RA | 4,072,544 | T→C | A36A (GCA→GCG) | yihT ← | 6‑deoxy‑6‑sulfofructose‑1‑phosphate aldolase |
| RA | 4,104,554 | T→C | Y141C (TAC→TGC) | cpxA ← | sensor histidine kinase CpxA |
| 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 | 4,278,657 | 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 | 3423881–3424231 | 3424429–3424238 | 8–549 | 7 [5] | [6] 7 | rrlD | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 3619008 | 3718313 | 99306 | 9 [0] | [0] 9 | 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 | 1207790 = | 18 (0.320) | 11 (0.210) | 10/456 | 2.0 | 42.4% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 13 (0.250) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 17 (0.300) | 30 (0.570) | 29/456 | 0.5 | 67.5% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 13 (0.250) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 27 (0.490) | 23/480 | 0.8 | 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 | |||||