breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
Predicted mutations | |||||
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evidence | position | mutation | annotation | gene | description |
MC JC | 15,389 | Δ5,175 bp | insL‑1–insA‑1 | insL‑1, hokC, mokC, sokC, nhaA, nhaR, insB‑1, insA‑1 | |
RA | 119,028 | T→C | V99A (GTC→GCC) | ampD → | 1,6‑anhydro‑N‑acetylmuramoyl‑L‑alanine amidase |
MC JC | 167,484 | Δ5,964 bp | [fhuA]–fhuB | [fhuA], fhuC, fhuD, fhuB | |
RA | 257,794 | T→C | intergenic (+23/‑35) | frsA → / → crl | fermentation‑respiration switch protein/RNA polymerase holoenzyme assembly factor Crl |
MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
MC JC | 263,514 | Δ61,897 bp | [ykfI]–ykgH | 71 genes [ykfI], yafW, ykfH, ykfG, yafX, ykfF, ykfB, yafY, yafZ, ykfA, perR, insN, insI‑1, insN, eyeA, ykfC, insH‑1, mmuP, mmuM, afuC, afuB, insB‑2, insA‑2, yagB, yagA, yagE, yagF, yagG, yagH, xynR, argF, ykgS, insB‑3, insA‑3, yagJ, yagK, yagL, yagM, ykgV, yagN, intF, yagP, paoD, paoC, paoB, paoA, yagU, ykgJ, ecpE, ecpD, ecpC, ecpB, ecpA, ecpR, ykgL, ykgO, ykgM, ykgR, ykgP, eaeH, insE‑1, insF‑1, ykgA, rclC, rclB, rclA, rclR, ykgE, ykgF, ykgG, ykgH |
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MC JC | 332,366 | Δ44,951 bp | pdeL–yaiL | 39 genes pdeL, yahB, yahC, yahD, yahE, yahF, yahG, yahH, yahI, yahJ, yahK, yahL, yahM, yahN, yahO, prpR, prpB, prpC, prpD, prpE, codB, codA, cynR, cynT, cynS, cynX, lacA, lacY, lacZ, lacI, mhpR, mhpA, mhpB, mhpC, mhpD, mhpF, mhpE, mhpT, yaiL |
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MC JC | 389,898 | Δ9,908 bp | yaiT–[yaiZ] | yaiT, insF‑2, insE‑2, yaiT, iprA, ampH, sbmA, yaiW, yaiY, [yaiZ] | |
MC JC | 508,873 | Δ40,744 bp | copA–[ylbE] | 37 genes copA, copA, copA, glsA, ybaT, cueR, ybbJ, qmcA, fetA, fetB, cnoX, ybbO, tesA, ybbA, ybbP, rhsD, ybbC, ylbH, ybbD, ylbI, ylbG, selU, allS, allA, allR, gcl, hyi, glxR, ybbW, allB, ybbY, glxK, allE, allC, allD, fdrA, [ylbE] |
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MC JC | 565,055 | Δ21,054 bp | [intD]–ompT | 37 genes [intD], xisD, exoD, renD, insE‑3, insF‑3, renD, emrE, ylcJ, ybcK, ybcL, ybcM, ylcH, ybcN, ninE, ybcO, rusA, ylcG, ybcQ, nmpC, insH‑2, nmpC, essD, rrrD, rzpD, rzoD, borD, ybcV, ybcW, ylcI, nohD, aaaD, tfaD, ybcY, tfaX, appY, ompT |
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MC JC | 603,467 | Δ5,885 bp | [ybdG]–insL‑2 | [ybdG], nfsB, ybdF, ybdJ, ybdK, sokE, hokE, insL‑2 | |
MC JC | 675,552 | Δ7,819 bp | ybeQ–[hscC] | ybeQ, ybeR, djlB, ybeT, ybeU, djlC, [hscC] | |
MC JC | 687,860 | Δ1,185 bp | IS5‑mediated | insH‑3 | insH‑3 |
MC JC | 729,365 | Δ9,598 bp | rhsC–ybfD | rhsC, ybfB, ybfO, ybfC, ybfQ, ybfL, ybfD | |
RA | 765,191 | Δ1 bp | coding (685/723 nt) | mngR ← | DNA‑binding transcriptional repressor MngR |
MC JC | 765,208 | Δ5,405 bp | [mngR]–mngB | [mngR], mngA, mngB | |
MC JC | 819,776 | Δ62,977 bp | ybhL–deoR | 57 genes ybhL, ybhM, ybhN, clsB, ybhP, ybhQ, ybhR, ybhS, ybhF, ybhG, cecR, rhlE, ybiA, dinG, ybiB, hcxB, ybiJ, ybiI, ybiX, fiu, mcbA, rlmF, ybiO, glnQ, glnP, glnH, dps, rhtA, yliM, ompX, opgE, rybA, mntS, mntR, ybiR, ldtB, ybiT, ybiU, ybiV, ybiW, ybiY, fsaA, moeB, moeA, iaaA, gsiA, gsiB, gsiC, gsiD, pdeI, dgcI, rimO, bssR, yliI, gstB, dacC, deoR |
|
RA | 988,499 | G→A | P163S (CCA→TCA) | asnS ← | asparagine‑‑tRNA ligase |
MC JC | 997,868 | Δ6,818 bp | [elfA]–ycbF | [elfA], elfD, elfC, elfG, ycbU, ycbV, ycbF | |
MC JC | 1,040,502 | Δ73,763 bp | [appX]–[mdtG] | 75 genes [appX], appA, etk, etp, gfcE, gfcD, gfcC, gfcB, gfcA, insA‑4, insB‑4, 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, efeU, efeO, efeB, phoH, pgaD, pgaC, pgaB, pgaA, dgcT, insF‑4, insE‑4, ymdE, ycdU, serX, ghrA, ycdX, ycdY, ycdZ, csgG, csgF, csgE, csgD, csgB, csgA, csgC, ymdA, ymdB, clsC, opgC, opgG, opgH, yceK, msyB, [mdtG] |
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MC JC | 1,129,397 | Δ11,591 bp | flgN–flgL | flgN, flgM, flgA, flgB, flgC, flgD, flgE, flgF, flgG, flgH, flgI, flgJ, flgK, flgL | |
MC JC | 1,197,137 | 25956 bp→12 bp | [ymfD]–[ymgI] | 42 genes [ymfD], ymfE, lit, intE, xisE, ymfH, ymfI, ymfJ, ymfK, ymfT, ymfL, ymfM, oweE, ymfN, aaaE, ymfR, beeE, jayE, ymfQ, ycfK, tfaP, tfaE, stfE, pinE, mcrA, icdC, iraM, ymgK, ymgL, ycgX, bluR, bluF, ycgZ, ymgA, ariR, ymgC, pdeG, ymgF, ycgH, ymgD, ymgG, [ymgI] |
|
RA | 1,270,811 | C→T | V347M (GTG→ATG) | chaA ← | Na(+)/K(+):H(+) antiporter ChaA |
MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
RA | 1,382,555 | C→T | S203S (AGC→AGT) | ompG → | outer membrane porin G |
MC JC | 1,388,889 | Δ9,734 bp | ycjG–[uspE] | ycjG, mpaA, ymjC, ymjD, ycjY, pgrR, mppA, ynaI, insH‑4, ynaJ, [uspE] | |
RA | 1,400,309 | Δ1 bp | coding (1465/1527 nt) | abgT ← | p‑aminobenzoyl glutamate:H(+) symporter |
RA | 1,400,314 | Δ1 bp | coding (1460/1527 nt) | abgT ← | p‑aminobenzoyl glutamate:H(+) symporter |
MC JC | 1,400,325 | Δ81,931 bp | [abgT]–[azoR] | 87 genes [abgT], abgB, abgA, abgR, mcaS, smrA, dgcM, zntB, fnrS, ynaL, dbpA, ttcA, intR, xisR, rcbA, ralA, ralR, recT, recE, racC, ydaE, kilR, sieB, ydaF, ydaG, racR, ydaS, ydaT, ydaU, ydaV, ydaW, rzpR, rzoR, trkG, ynaK, ydaY, ynaA, lomR, insH‑5, lomR, stfR, tfaR, pinR, ynaE, ynaM, ttcC, uspF, ompN, micC, ydbK, ydbJ, hslJ, ldhA, ydbH, ynbE, ydbL, feaR, feaB, tynA, paaZ, paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK, paaX, paaY, ynbG, ydbA, insD‑2, insC‑2, ydbA, insI‑2, ydbA, pdxI, ydbD, ynbA, ynbB, ynbC, ynbD, [azoR] |
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MC JC | 1,509,562 | Δ46,201 bp | [hicB]–maeA | 43 genes [hicB], ydcR, ydcS, ydcT, ydcU, ydcV, patD, yncL, ortT, ydcY, ydcZ, mnaT, curA, mcbR, yncD, yncE, ansP, yncG, yncH, rhsE, ydcD, yncO, yncI, ydcC, pptA, yddH, nhoA, yddE, narV, narW, narY, narZ, narU, yddJ, yddK, yddL, yddG, fdnG, fdnH, fdnI, yddM, adhP, maeA |
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MC JC | 1,627,518 | Δ25,244 bp | [ydfG]–[ynfP] | 48 genes [ydfG], ydfH, ydfZ, ydfI, ydfJ, ynfT, ydfK, pinQ, tfaQ, ydfN, nohA, ynfO, ydfO, gnsB, ynfN, ynfR, ynfQ, cspI, rzpQ, rzoQ, rrrQ, ydfR, essQ, cspB, cspF, ynfS, ydfT, ydfU, rem, hokD, relE, relB, ydfV, flxA, ydfW, ydfX, dicC, dicA, ydfA, ydfB, ydfC, dicF, dicB, ydfD, ydfE, insD‑7, intQ, [ynfP] |
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RA | 1,742,755 | G→C | P163R (CCG→CGG) | ribC ← | riboflavin synthase |
MC JC | 1,872,030 | Δ1,437 bp | [dgcJ] | [dgcJ] | |
MC JC | 1,962,566 | Δ16,764 bp | flhE–insA‑5 | 17 genes flhE, flhA, flhB, cheZ, cheY, cheB, cheR, tap, tar, cheW, cheA, motB, motA, flhC, flhD, insB‑5, insA‑5 |
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MC JC | 1,997,112 | Δ26,567 bp | [tcyN]–[fliR] | 32 genes [tcyN], tcyL, dcyD, tcyJ, fliZ, fliA, fliC, fliD, fliS, fliT, amyA, yedD, yedE, yedF, yedK, yedL, yedN, intG, fliE, fliF, fliG, fliH, fliI, fliJ, fliK, fliL, fliM, fliN, fliO, fliP, fliQ, [fliR] |
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MC JC | 2,101,397 | Δ36,321 bp | [wbbL]–wza | 34 genes [wbbL], insH‑7, 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 |
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MC JC | 2,165,151 | Δ12,060 bp | yegP–gatY | 17 genes yegP, yegQ, cyaR, ogrK, yegZ, yegR, yegS, gatR, insE‑5, insF‑5, gatR, gatD, gatC, gatB, gatA, gatZ, gatY |
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MC JC | 2,204,350 | Δ32,368 bp | yehL–preA | 30 genes yehL, yehM, yehP, yehQ, yehR, yehS, btsR, btsS, mlrA, yohO, yehW, yehX, yehY, osmF, bglX, dld, pbpG, yohC, yohD, yohF, mdtQ, yohP, dusC, yohJ, yohK, cdd, sanA, yeiS, preT, preA |
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MC JC | 2,286,401 | Δ3,780 bp | [yejO]–[yejO] | [yejO], insH‑8, [yejO] | |
MC JC | 2,320,144 | Δ16,489 bp | [atoS]–[yfaA] | [atoS], atoC, atoD, atoA, atoE, atoB, yfaP, yfaQ, yfaS, yfaT, [yfaA] | |
MC JC | 2,466,545 | Δ9,634 bp | [intS]–[ypdJ] | 15 genes [intS], yfdG, yfdH, yfdI, yfdK, yfdL, yfdM, yfdN, yfdO, yfdP, yfdQ, yfdR, yfdS, [yfdT], [ypdJ] |
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MC JC | 2,509,631 | Δ8,319 bp | [yfeO]–pdeA | [yfeO], ypeC, mntH, nupC, insL‑3, pdeA | |
MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
MC JC | 2,601,201 | Δ13,595 bp | [hyfA]–focB | [hyfA], hyfB, hyfC, hyfD, hyfE, hyfF, hyfG, hyfH, hyfI, hyfJ, hyfR, focB | |
RA | 2,756,138 | Δ1 bp | intergenic (+183/‑21) | ssrA → / → intA | tmRNA/CP4‑57 prophage; integrase |
MC JC | 2,756,160 | Δ35,091 bp | [intA]–[lhgO] | 33 genes [intA], yfjH, alpA, yfjI, yfjJ, abpB, abpA, yfjM, rnlA, rnlB, yfjP, yfjQ, yfjR, ypjK, yfjS, yfjT, yfjU, yfjV, yfjW, ypjI, yfjX, yfjY, ypjJ, yfjZ, ypjF, ypjA, pinH, ypjB, ypjC, ileY, ygaQ, csiD, [lhgO] |
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RA | 2,843,412 | C→T | R12H (CGT→CAT) | hycH ← | formate hydrogenlyase assembly protein |
MC JC | 2,994,992 | Δ3,877 bp | [ygeL]–ygeQ | [ygeL], ygeN, ygeO, insD‑4, insC‑4, ygeP, ygeQ | |
RA | 3,090,282 | C→T | intergenic (+30/‑65) | yggI → / → endA | conserved protein YggI/DNA‑specific endonuclease I |
RA | 3,090,341 | Δ1 bp | intergenic (+89/‑6) | yggI → / → endA | conserved protein YggI/DNA‑specific endonuclease I |
MC JC | 3,090,347 | Δ708 bp | coding (1‑708/708 nt) | endA → | DNA‑specific endonuclease I |
RA | 3,091,305 | A→G | S58G (AGC→GGC) | rsmE → | 16S rRNA m(3)U1498 methyltransferase |
MC JC | 3,110,680 | 25702 bp→GA | [yghD]–pitB | 20 genes [yghD], yghE, yghF, yghG, pppA, yghJ, glcA, glcB, glcG, glcF, glcE, glcD, glcC, yghO, insH‑9, yghQ, yghR, yghS, yghT, pitB |
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MC JC | 3,184,782 | Δ6,916 bp | ubiK–yqiI | ubiK, ygiL, yqiG, insC‑5, insD‑5, yqiG, yqiH, yqiI | |
MC JC | 3,362,162 | Δ5,481 bp | [yhcA]–[yhcF] | [yhcA], yhcD, yhcE, insH‑10, yhcE, [yhcF] | |
MC JC | 3,453,928 | Δ15,926 bp | gspA–[chiA] | 16 genes gspA, gspC, gspD, gspE, gspF, gspG, gspH, gspI, gspJ, gspK, gspL, gspM, gspO, bfr, bfd, [chiA] |
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RA | 3,477,150 | C→T | K90K (AAG→AAA) | fkpA ← | peptidyl‑prolyl cis‑trans isomerase FkpA |
RA | 3,513,003 | A→G | D212D (GAT→GAC) | trpS ← | tryptophan‑‑tRNA ligase |
MC JC | 3,581,139 | 3915 bp→6 bp | [yhhY]–yrhB | [yhhY], yhhZ, yrhA, insA‑6, insB‑6, yrhA, yrhD, yrhB | |
MC JC | 3,618,992 | Δ6,688 bp | rhsB–[yhhJ] | rhsB, yhhH, yhhI, [yhhJ] | |
MC JC | 3,651,293 | Δ2,422 bp | [yhiS]–yhiS | [yhiS], insH‑11, yhiS | |
RA | 3,720,597 | Δ1 bp | coding (4/153 nt) | hokA ← | small toxic polypeptide |
MC JC | 3,720,634 | Δ1,442 bp | IS150‑mediated | insJ–insK | insJ, insK |
MC JC | 3,761,993 | Δ8,250 bp | rhsA–yibV | rhsA, yibA, yibJ, yibG, yibS, yibV | |
RA | 3,801,078 | (T)7→6 | coding (922/1017 nt) | waaJ ← | UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase |
MC JC | 3,888,432 | Δ18,167 bp | tnaC–bglG | 17 genes tnaC, tnaA, tnaB, mdtL, yidZ, yieE, yieF, adeP, yieH, cbrB, cbrC, yieK, yieL, bglH, bglB, bglF, bglG |
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RA | 4,093,223 | A→G | V72V (GTT→GTC) | rhaM ← | L‑rhamnose mutarotase |
MC JC | 4,299,628 | Δ25,538 bp | [mdtP]–[phnC] | 27 genes [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] |
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RA | 4,354,915 | G→A | intergenic (‑198/+39) | lysU ← / ← dtpC | lysine‑‑tRNA ligase/Ap4A synthetase/Ap3A synthetase/dipeptide/tripeptide:H(+) symporter DtpC |
RA | 4,438,124 | T→C | W140R (TGG→CGG) | ytfI → | protein YtfI |
RA | 4,485,906 | C→A | A16S (GCC→TCC) | pepA ← | aminopeptidase A/I |
MC JC | 4,496,676 | Δ53,036 bp | intB–fimH | 54 genes 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 |
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MC JC | 4,555,491 | Δ41,523 bp | [yjiC]–lgoD | 37 genes [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 |
Unassigned missing coverage evidence | ||||||||||
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seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NC_000913 | 380112 | 388670 | 8559 | 46 [0] | [18] 21 | [yaiO]–tauD | [yaiO],yaiX,insC‑1,insD‑1,yaiX,yaiP,ykiC,yaiS,tauA,tauB,tauC,tauD |
* | * | ÷ | NC_000913 | 2066213–2066304 | 2080591 | 14288–14379 | 25 [19] | [0] 89 | insH‑6–[yeeA] | insH‑6,yoeA,insD‑3,insC‑3,yoeA,yeeP,isrC,flu,yeeR,yeeS,yeeT,cbeA,cbtA,yeeW,yoeF,yeeX,[yeeA] |
* | * | ÷ | NC_000913 | 3423698–3424234 | 3426808–3424653 | 420–3111 | 25 [16] | [16] 20 | [rrfD]–rrlD | [rrfD],rrlD |
Unassigned new junction evidence | |||||||||||
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seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NC_000913 | = 380111 | 0 (0.000) | 38 (0.600) +CGAGAT |
25/86 | 0.6 | 58.7% | coding (732/774 nt) | yaiO | outer membrane protein YaiO |
? | NC_000913 | 4070444 = | 61 (0.840) | intergenic (‑43/+71) | yihR/yihS | putative aldose 1‑epimerase YihR/sulfoquinovose isomerase | |||||
* | ? | NC_000913 | = 2066304 | NA (NA) | 87 (1.200) | 52/98 | 0.0 | 100% | noncoding (1050/1195 nt) | IS5 | repeat region |
? | NC_000913 | 2080592 = | 0 (0.000) | intergenic (‑1/+197) | yeeA/sbmC | putative transporter YeeA/DNA gyrase inhibitor | |||||
* | ? | NC_000913 | 2798364 = | 45 (0.620) | 25 (0.420) | 21/80 | 0.8 | 39.5% | coding (132/405 nt) | stpA | DNA‑binding transcriptional repressor StpA with RNA chaperone activity |
? | NC_000913 | = 2798360 | 40 (0.680) | coding (136/405 nt) | stpA | DNA‑binding transcriptional repressor StpA with RNA chaperone activity | |||||
* | ? | NC_000913 | = 2846300 | 31 (0.430) | 23 (0.340) | 21/92 | 1.2 | 40.7% | coding (172/1710 nt) | hycE | formate hydrogenlyase subunit HycE |
? | NC_000913 | 2867269 = | 38 (0.560) | coding (283/993 nt) | rpoS | RNA polymerase, sigma S (sigma 38) factor | |||||
* | ? | NC_000913 | = 3593298 | 30 (0.410) | 28 (0.390) | 23/98 | 1.1 | 49.6% | coding (140/714 nt) | livF | branched chain amino acid/phenylalanine ABC transporter ATP binding subunit LivF |
? | NC_000913 | 3593309 = | 27 (0.370) | coding (129/714 nt) | livF | branched chain amino acid/phenylalanine ABC transporter ATP binding subunit LivF | |||||
* | ? | NC_000913 | = 4400288 | 47 (0.650) | 53 (0.760) | 42/94 | 0.1 | 54.4% | coding (1/309 nt) | hfq | RNA‑binding protein Hfq |
? | NC_000913 | 4400296 = | 44 (0.630) | coding (9/309 nt) | hfq | RNA‑binding protein Hfq |