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 | 155,463 | A→T | *247K (TAA→AAA) | yadV ← | putative fimbrial chaperone YadV |
| MC JC | 244,301 | Δ9,446 bp | yafJ–yafP | yafJ, dpaA, yafQ, dinJ, yafL, rayT, dinB, yafN, yafO, yafP | |
| RA | 254,249 | A→T | intergenic (+1088/+10) | yafP → / ← pepD | putative N‑acetyltransferase YafP/peptidase D |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 389,601 | C→T | D43N (GAC→AAC) | hemB ← | porphobilinogen synthase |
| RA | 389,867 | T→C | intergenic (‑140/‑384) | hemB ← / → yaiT | porphobilinogen synthase/putative autotransporter YaiT |
| MC JC | 390,251 | Δ14,565 bp | [yaiT]–[dgcC] | 16 genes [yaiT], ytiB, insF2, insE2, yaiT, iprA, ampH, sbmA, yaiW, yaiY, yaiZ, ddlA, iraP, phoA, psiF, [dgcC] |
|
| MC JC | 519,143 | Δ14,682 bp | [ybbO]–[allZ] | [ybbO], [tesA], ybbA, ybbP, rhsD, ybbC, ylbG, selU, allS, allA, [allR], [allZ] | |
| RA | 535,337 | T→C | A474A (GCT→GCC) | gcl → | glyoxylate carboligase |
| RA | 536,173 | T→C | L155P (CTC→CCC) | hyi → | hydroxypyruvate isomerase |
| RA | 536,492 | A→G | intergenic (+6/‑94) | hyi → / → glxR | hydroxypyruvate isomerase/tartronate semialdehyde reductase 2 |
| RA | 536,549 | T→C | intergenic (+63/‑37) | hyi → / → glxR | hydroxypyruvate isomerase/tartronate semialdehyde reductase 2 |
| MC JC | 536,617 | Δ14,712 bp | [glxR]–[ybcF] | [glxR], ybbW, allB, ybbY, glxK, allE, allC, allD, fdrA, ylbE, ylbF, [ybcF] | |
| RA | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| MC JC | 565,054 | 44181 bp→TGA | [intD]–insL2 | 52 genes [intD], renD, insE3, insF3, renD, emrE, ylcJ, ybcK, ybcL, ybcM, ylcH, ybcN, ninE, ybcO, rusA, ylcG, quuD, nmpC, insH2, nmpC, essD, rrrD, rzpD, rzoD, borD, ybcV, ybcW, ylcI, nohD, tfaD, tfaX, appY, ompT, envY, ybcH, nfrA, nfrB, cusS, cusR, cusC, cusF, cusB, cusA, pheP, ybdG, nfsB, ybdF, ybdJ, ybdK, sokE, hokE, insL2 |
|
| RA | 670,635 | A→T | L324Q (CTG→CAG) | holA ← | DNA polymerase III subunit delta |
| RA | 1,048,596 | G→A | G32G (GGC→GGT) | gfcC ← | capsule biosynthesis GfcC family protein |
| MC JC | 1,048,805 | Δ48,085 bp | [gfcB]–ycdU | 45 genes [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 |
|
| JC JC | 1,105,376 | IS2 (–) +5 bp | intergenic (+83/‑34) | csgC → / → ymdA | curlin chaperone/uncharacterized protein YmdA |
| MC JC | 1,196,861 | 27046 bp→5 bp | ymfD–ymgJ | 37 genes ymfD, ymfE, lit, intE, xisE, ymfH, ymfI, ymfJ, ymfK, ymfT, ymfL, ymfM, ymfN, ymfR, beeE, ymfQ, ycfK, tfaP, tfaE, pinE, mcrA, iraM, ymgK, ymgL, ycgX, bluR, bluF, ycgZ, ymgA, ariR, ymgC, pdeG, ymgF, ymgD, ymgG, ymgI, ymgJ |
|
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,301,917 | C→T | Q246Y (CAG→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,301,919 | G→T | Q246Y (CAG→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,628,332 | T→C | intergenic (+69/‑20) | ydfG → / → rspR | 3‑hydroxy acid dehydrogenase YdfG/DNA‑binding transcriptional repressor RspR |
| MC JC | 1,628,340 | Δ10,127 bp | rspR–[cspI] | 17 genes rspR, ydfZ, ydfI, ydfJ, ynfT, ydfK, pinQ, tfaQ, stfQ, nohA, ynfO, ydfO, gnsB, ynfN, ynfR, ynfQ, [cspI] |
|
| RA | 1,638,571 | G→A | H33Y (CAT→TAT) | cspI ← | cold shock‑like protein CspI |
| RA | 1,640,045 | +C | coding (13/534 nt) | rrrQ ← | putative lysozyme |
| MC JC | 1,640,057 | Δ7,591 bp | [rrrQ]–[dicC] | 18 genes [rrrQ], [ydfR], essQ, ynfU, cspB, cspF, ynfS, ydfT, ydfU, rem, hokD, relE, relB, ydfV, flxA, ydfW, ydfX, [dicC] |
|
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| JC JC | 1,853,797 | IS1 (–) +9 bp | coding (175‑183/1359 nt) | ydjE ← | putative transporter YdjE |
| MC JC | 1,961,950 | Δ28,129 bp | yecT–[tyrP] | 33 genes yecT, flhE, flhA, flhB, cheZ, cheY, cheB, cheR, tap, tar, cheW, cheA, cheA, motB, motA, motR, flhC, flhD, insB5, insA5, uspC, otsA, otsB, araH, araG, araF, ftnB, yecJ, azuC, yecR, ftnA, yecH, [tyrP] |
|
| MC JC | 1,993,664 | Δ31,548 bp | [uvrC]–[yodD] | 40 genes [uvrC], uvrY, yecU, yecF, sdiA, sdsN, tcyN, tcyL, dcyD, tcyJ, fliZ, fliA, fliX, fliC, fliD, fliS, fliT, amyA, yedD, yedE, yedF, yedK, yedL, fliE, fliF, fliG, fliH, fliI, fliJ, fliK, fliL, fliM, fliN, fliO, fliP, fliQ, fliR, rcsA, dsrB, [yodD] |
|
| MC JC | 2,030,451 | Δ10,928 bp | [yedA]–[zinT] | [yedA], [vsr], dcm, yedJ, drpB, rseX, hchA, hprS, hprR, hiuH, msrP, msrQ, [zinT] | |
| RA | 2,041,467 | A→G | K31K (AAA→AAG) | zinT → | metal‑binding protein ZinT |
| MC JC | 2,066,152 | Δ12,778 bp | insH6–[yoeF] | insH6, yoeA, insD3, insC3, yoeA, isrC, flu, yeeR, yeeS, yeeT, cbeA, cbtA, yeeW, [yoeF] | |
| RA | 2,078,954 | A→G | intergenic (+23/+78) | yoeF → / ← tmaR | putative uncharacterized protein YoeF/PTS system regulator TmaR |
| MC JC | 2,101,395 | Δ11,672 bp | wbbL–rfbB | wbbL, insH7, wbbL, wbbK, wbbJ, wbbI, wbbH, glf, rfbX, rfbC, rfbA, rfbD, rfbB | |
| RA | 2,113,177 | A→G | intergenic (‑116/+257) | rfbB ← / ← galF | dTDP‑glucose 4,6‑dehydratase 1/UTP:glucose‑1‑phosphate uridylyltransferase, low activity |
| MC JC | 2,143,266 | Δ40,395 bp | [dgcE]–yegX | 38 genes [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 |
|
| MC JC | 2,196,474 | Δ29,182 bp | [yehF]–yohC | 21 genes [yehF], yehI, yehK, yehL, yehM, yehP, yehQ, yehR, yehS, btsR, btsS, mlrA, yohO, yehW, yehX, yehY, osmF, bglX, dld, pbpG, yohC |
|
| MC JC | 2,251,701 | Δ7,597 bp | [yeiI]–psuK | [yeiI], nupX, rihB, yeiL, psuT, psuG, psuK | |
| RA | 2,730,870 | T→C | noncoding (288/1542 nt) | rrsG ← | 16S ribosomal RNA |
| MC JC | 2,756,159 | Δ33,804 bp | [intA]–[glaH] | 28 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] |
|
| RA | 2,790,153 | C→T | P58S (CCC→TCC) | lhgD → | L‑2‑hydroxyglutarate dehydrogenase |
| RA | 2,790,310 | C→T | A110V (GCG→GTG) | lhgD → | L‑2‑hydroxyglutarate dehydrogenase |
| MC JC | 2,795,656 | Δ5,717 bp | glaR–[nrdE] | glaR, kbp, yqaE, ygaV, ygaP, stpA, alaE, ygaC, ygaM, nrdH, [nrdI], [nrdE] | |
| MC JC | 2,804,790 | Δ5,840 bp | proV–[ygaH] | proV, proW, proX, ygaZ, [ygaH] | |
| MC JC | 2,825,796 | Δ4,947 bp | srlA–[gutQ] | srlA, srlE, srlB, srlD, gutM, srlR, [gutQ] | |
| RA | 2,867,454 | 2 bp→AA | coding (97‑98/993 nt) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,985,726 | A→G | intergenic (‑134/‑121) | yqeF ← / → yqeG | putative acyltransferase/putative transporter YqeG |
| RA | 2,985,816 | T→C | intergenic (‑224/‑31) | yqeF ← / → yqeG | putative acyltransferase/putative transporter YqeG |
| MC JC | 2,985,842 | Δ47,769 bp | yqeG–[idi] | 39 genes yqeG, yqeH, yqeI, yqeJ, yqeL, yqeK, ygeG, ygeH, ygeI, insD4, insC4, ygeQ, glyU, actS, 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] |
|
| MC JC | 3,077,568 | Δ1,832 bp | [cmtA]–cmtB | [cmtA], cmtB | |
| MC JC | 3,110,591 | Δ24,234 bp | [yghD]–yghT | 20 genes [yghD], yghE, yqhJ, yghF, yghG, pppA, yghJ, glcA, glcB, glcG, glcF, glcE, glcD, glcC, yghO, insH9, yghQ, yghR, yghS, yghT |
|
| MC JC | 3,281,895 | Δ27 bp | intergenic (+1205/‑55) | agaV → / → agaS | N‑acetyl‑D‑galactosamine specific PTS enzyme IIB component/putative galactosamine‑6‑phosphate deaminase/isomerase |
| MC JC | 3,361,226 | Δ9,811 bp | [gltF]–[nanE] | [gltF], yhcA, yhcD, yhcE, insH10, yhcE, yhcF, yhcG, nanQ, nanK, [nanE] | |
| RA | 3,486,205 | C→A | T29K (ACG→AAG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| JC JC | 3,707,484 | IS3 (+) +3 bp | coding (220‑222/1608 nt) | dppA ← | dipeptide ABC transporter periplasmic binding protein |
| JC JC | 3,720,136 | IS3 (–) +3 bp :: +TCA | coding (88‑90/213 nt) | cspA → | cold shock protein CspA |
| MC JC | 3,855,159 | Δ11,170 bp | [yidF]–yidE | [yidF], yidG, yidH, yidI, yidJ, yidK, yidL, glvB, glvC, yidP, yidE | |
| RA | 3,867,576 | G→T | intergenic (‑154/‑152) | ibpA ← / → yidQ | small heat shock protein IbpA/DUF1375 domain‑containing putative lipoprotein YidQ |
| MC JC | 3,867,599 | Δ9,908 bp | yidQ–yidB | yidQ, yidR, cbrA, dgoT, dgoD, dgoA, dgoK, dgoR, yidX, yidA, yidB | |
| JC JC | 3,890,411 | IS1 (–) +9 bp | coding (176‑184/1248 nt) | tnaB → | tryptophan:H(+) symporter TnaB |
| MC JC | 3,927,155 | Δ12,222 bp | [asnA]–[hsrA] | [asnA], viaA, ravA, kup, rbsD, rbsA, rbsC, rbsB, rbsZ, rbsK, rbsR, [hsrA] | |
| MC JC | 4,060,444 | Δ19,761 bp | yihL–yiiF | 19 genes yihL, yihM, yihN, ompL, yihO, yihP, yihQ, yihR, yihS, yihT, yihU, yihV, csqR, yihX, yihY, dtd, fabY, yiiE, yiiF |
|
| MC JC | 4,086,996 | Δ13,531 bp | yiiG–rhaT | yiiG, frvR, frvX, frvB, frvA, rhaM, rhaD, rhaA, rhaB, rhaS, rhaR, rhaT | |
| RA | 4,139,288 | C→T | D141N (GAC→AAC) | fsaB ← | fructose‑6‑phosphate aldolase 2 |
| RA | 4,139,511 | Δ1 bp | coding (198/663 nt) | fsaB ← | fructose‑6‑phosphate aldolase 2 |
| MC JC | 4,139,771 | 10483 bp→TG | [ptsA]–[eptC] | [ptsA], frwC, frwB, pflD, pflC, frwD, yijO, [eptC] | |
| RA | 4,235,651 | T→C | intergenic (+244/‑255) | pgi → / → yjbE | glucose‑6‑phosphate isomerase/uncharacterized protein YjbE |
| MC JC | 4,235,905 | 16376 bp→52 bp | yjbE–malM | yjbE, yjbF, yjbG, yjbH, yjbT, psiE, xylE, malH, malG, malF, malE, malK, lamB, malM | |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| MC JC | 4,299,522 | Δ12,535 bp | mdtP–alsB | mdtP, mdtO, mdtN, ytcA, yjcS, alsK, alsE, alsC, alsA, alsB | |
| RA | 4,312,070 | Δ1 bp | intergenic (‑28/+31) | alsB ← / ← alsR | D‑allose ABC transporter periplasmic binding protein/DNA‑binding transcriptional repressor AlsR |
| RA | 4,312,151 | G→C | Q281E (CAA→GAA) | alsR ← | DNA‑binding transcriptional repressor AlsR |
| RA | 4,312,215 | A→G | T259T (ACT→ACC) | alsR ← | DNA‑binding transcriptional repressor AlsR |
| RA | 4,312,219 | A→G | L258P (CTA→CCA) | alsR ← | DNA‑binding transcriptional repressor AlsR |
| RA | 4,312,289 | A→G | Y235H (TAT→CAT) | alsR ← | DNA‑binding transcriptional repressor AlsR |
| RA | 4,312,498 | C→G | R165P (CGC→CCC) | alsR ← | DNA‑binding transcriptional repressor AlsR |
| RA | 4,313,027 | T→G | intergenic (‑36/‑323) | alsR ← / → rpiB | DNA‑binding transcriptional repressor AlsR/allose‑6‑phosphate isomerase/ribose‑5‑phosphate isomerase B |
| MC JC | 4,313,864 | Δ16,405 bp | yjdP–rdcB | 18 genes yjdP, phnP, phnO, phnN, phnM, phnL, phnK, phnJ, phnI, phnH, phnG, phnF, phnD, phnC, yjdN, yjdM, rdcA, rdcB |
|
| RA | 4,558,907 | T→A | K207M (AAG→ATG) | iadA ← | isoaspartyl dipeptidase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 263076 | 315228 | 52153 | 56 [0] | [0] 62 | ykfI–ykgR | ykfI,yafW,ykfH,ykfG,yafX,ykfF,ykfB,yafY,yafZ,ykfA,perR,insN,insI1,insN,eyeA,ykfC,insH1,mmuP,mmuM,afuC,insB2,insA2,yagB,yagA,yagE,yagF,yagG,yagH,xynR,argF,argL,ykgS,insB3,insA3,yagJ,yagK,yagL,yagM,ykgV,yagN,intF,yagP,paoD,paoC,paoB,paoA,yagU,ykgJ,ecpE,ecpD,ecpC,ecpB,ecpA,matA,ykgL,ykgO,ykgM,ykgR |
| * | * | ÷ | NC_000913 | 315404–316476 | 388643 | 72168–73240 | 14 [13] | [0] 56 | [insE1]–[tauD] | [insE1],insF1,rclC,rclB,rclA,rclR,ykgE,ykgF,ykgG,ykgH,betA,betB,betI,betT,yahV,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,frmB,frmA,frmR,yaiO,yaiX,insC1,insD1,yaiX,yaiP,ykiC,yaiS,tauA,tauB,tauC,[tauD] |
| * | * | ÷ | NC_000913 | 2406788 | 2407179 | 392 | 64 [0] | [0] 41 | lrhA/alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| * | * | ÷ | NC_000913 | 3423877–3424234 | 3424448–3424238 | 5–572 | 14 [13] | [12] 15 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 263075 | 0 (0.000) | 56 (0.940) | 51/490 | 0.1 | 100% | intergenic (+129/+253) | thrW/ykfI | tRNA‑Thr/toxin of the YkfI‑YafW toxin‑antitoxin system |
| ? | NC_000913 | 388644 = | 0 (0.000) | coding (850/852 nt) | tauD | taurine dioxygenase | |||||
| * | ? | NC_000913 | 1978503 = | NA (NA) | 64 (1.070) | 59/492 | 0.0 | 100% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 2406787 | 0 (0.000) | intergenic (‑146/‑774) | lrhA/alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 18 (0.300) | 17/494 | 2.0 | 28.1% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 2421268 | 46 (0.770) | coding (648/648 nt) | yfcG | disulfide bond oxidoreductase YfcG | |||||
| * | ? | NC_000913 | 2407180 = | 0 (0.000) | 41 (0.690) | 40/492 | 0.3 | 100% | intergenic (‑539/‑381) | lrhA/alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| ? | NC_000913 | 3583428 = | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||