breseq  version 0.27.1  revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
JC 1,673,557 Δ120 bp intergenic (‑56/‑237) mdtJ ← / → tqsA multidrug efflux system transporter/pheromone AI‑2 transporter
RA 2,173,363 Δ2 bp intergenic (‑1/+1) gatC ← / ← gatC pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA 3,560,455 +G intergenic (‑2/+1) glpR ← / ← glpR pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
RA 3,815,883 +C pseudogene (667/669 nt) rph ← ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 1673489 1676609 3121 358 [355] [354] 360 [mdtJ]–[pntA] [mdtJ], tqsA, pntB, [pntA]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 25790742 (0.080)490 (1.030) 230/284 0.0 96.1% intergenic (+8/‑769) crl/crl pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers
?NC_000913 258684 = 0 (0.000)pseudogene (9/331 nt) crl pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers
* ? NC_000913 273955 =NA (NA)375 (0.750) 174/300 2.9 58.3% noncoding (1195/1195 nt) IS5 repeat region
?NC_000913 = 565828 268 (0.530)coding (151/1164 nt) intD DLP12 prophage; putative phage integrase
* ? NC_000913 1207790 =76 (0.150)336 (0.750) 183/268 0.5 83.1% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 69 (0.150)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780575 (0.150)395 (0.880) 192/268 0.2 85.3% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 69 (0.150)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)537 (1.100) 236/292 0.0 99.8% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913 1300698 = 2 (0.000)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913 = 197850229 (0.060)540 (1.140) 233/284 0.0 97.5% intergenic (‑305/+16) flhD/insB1 flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
?NC_000913 1979279 = 0 (0.000)intergenic (‑64/‑474) insA/uspC IS1 repressor TnpA/universal stress protein
* ? NC_000913 = 2558698254 (0.510)259 (0.550) 171/284 2.2 53.3% intergenic (‑19/‑160) eutB/intZ ethanolamine ammonia‑lyase, large subunit, heavy chain/CPZ‑55 prophage; putative phage integrase
?NC_000913 2565489 = 213 (0.450)coding (1396/1404 nt) eutA reactivating factor for ethanolamine ammonia lyase
* ? NC_000913 = 3393157287 (0.570)312 (0.620) 180/300 2.3 52.1% coding (3102/3801 nt) yhdP DUF3971‑AsmA2 domains protein
?NC_000913 3583428 = NA (NA)noncoding (1/768 nt) IS1 repeat region
* ? NC_000913 3583428 =NA (NA)309 (0.620) 176/298 2.6 46.7% noncoding (1/768 nt) IS1 repeat region
?NC_000913 = 4542049 353 (0.710)coding (13/597 nt) fimE tyrosine recombinase/inversion of on/off regulator of fimA
* ? NC_000913 4542682 =272 (0.540)318 (0.670) 185/282 1.0 55.7% intergenic (+49/‑433) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?NC_000913 4542996 = 250 (0.530)intergenic (+363/‑119) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
* ? NC_000913 = 4542690272 (0.540)296 (0.630) 179/282 1.4 53.9% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?NC_000913 = 4542986 250 (0.530)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)