breseq  version 0.32.1  revision aa8f2595a244
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
MC JC 257,908 Δ776 bp [crl] [crl]
RA 380,022 (G)10→9 intergenic (‑141/+47) frmR ← / ← yaiO regulator protein that represses frmRAB operon/outer membrane protein
RA 1,026,864 A→G L51S (TTA→TCA)  mgsA ← methylglyoxal synthase
RA 1,028,652 C→T V24M (GTG→ATG)  hspQ ← heat shock protein involved in degradation of mutant DnaA, hemimethylated oriC DNA‑binding protein
RA 1,228,320 T→C L81P (CTG→CCG)  ycgM → putative isomerase/hydrolase
MC JC 1,299,499 Δ1,199 bp intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
RA 1,458,617 A→G A118A (GCA→GCG)  paaG → 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming
RA 1,595,427 A→G pseudogene (2561/3861 nt) yneO ← pseudogene, AidA homolog
RA 1,904,586 T→C V231A (GTC→GCC)  manZ → mannose‑specific enzyme IID component of PTS
MC JC 1,978,503 Δ776 bp insB1–insA insB1, insA
RA 2,126,422 C→T A257T (GCG→ACG)  wcaG ← bifunctional GDP‑fucose synthetase: GDP‑4‑dehydro‑6‑deoxy‑D‑mannose epimerase/ GDP‑4‑dehydro‑6‑L‑deoxygalactose reductase
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 2,401,103 G→A T151T (ACC→ACT)  nuoF ← NADH:ubiquinone oxidoreductase, chain F
RA 2,763,869 (T)7→8 coding (1285/1617 nt) yfjL ← CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein
RA 2,842,591 T→C L151L (TTA→TTG)  hycI ← protease involved in processing C‑terminal end of HycE
RA 2,937,802 A→G D112G (GAC→GGC)  fucK → L‑fuculokinase
RA 2,963,498 G→A T73T (ACC→ACT)  ppdB ← putative prepilin peptidase‑dependent protein
RA 3,139,583 G→A R286H (CGT→CAT)  yghU → putative S‑transferase
RA 3,271,600 (C)5→6 coding (171/1146 nt) garK ← glycerate kinase I
RA 3,366,953 G→A G10R (GGA→AGA)  yhcF → putative transcriptional regulator
RA 3,457,094 A→G I240V (ATC→GTC)  gspD → general secretory pathway component, cryptic
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 3,640,548 T→C intergenic (+3/‑314) uspA → / → dtpB universal stress global response regulator/dipeptide and tripeptide permease B
RA 3,791,004 A→G G114G (GGT→GGC)  tdh ← L‑threonine 3‑dehydrogenase, NAD(P)‑binding
RA 3,901,765 G→A G152G (GGC→GGT)  bglH ← carbohydrate‑specific outer membrane porin, cryptic
RA 3,936,381 C→T T35M (ACG→ATG)  rbsB → D‑ribose ABC transporter periplasmic binding protein, ribose chemotaxis receptor
RA 4,281,472 A→G E498G (GAG→GGG)  yjcE → putative cation/proton antiporter
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,490,935 A→G L69L (TTG→CTG)  idnR ← transcriptional repressor, 5‑gluconate‑binding
RA 4,538,491 C→T G92D (GGC→GAC)  nanM ← N‑acetylneuraminic acid mutarotase
RA 4,574,259 A→G pseudogene (341/2937 nt) yjiV → pseudogene, conserved hypothetical protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 84067 84080 14 7 [1] [1] 3 leuL/leuO leu operon leader peptide/global transcription factor
* * ÷ NC_000913 807337 810360 3024 3 [2] [1] 4 ybhB–[bioB] ybhB, bioA, [bioB]
* * ÷ NC_000913 954749 954790 42 3 [1] [0] 4 focA/ycaO formate channel/ribosomal protein S12 methylthiotransferase accessory factor
* * ÷ NC_000913 2033827 2033897 71 6 [2] [1] 3 rseX/yedS sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology, putative outer membrane protein
* * ÷ NC_000913 2857138 2859629 2492 4 [0] [2] 4 mutS methyl‑directed mismatch repair protein
* * ÷ NC_000913 3423784–3424231 3424523–3424244 14–740 4 [2] [2] 3 [rrfD]–[rrlD] [rrfD], [rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =3 (0.100)44 (1.630) 29/202 0.1 92.1% coding (290/630 nt) stfP e14 prophage, uncharacterized protein
?NC_000913 1209619 = 5 (0.190)pseudogene (1/501 nt) stfE pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
* ? NC_000913 = 12078053 (0.100)13 (0.480) 10/202 1.1 77.4% coding (305/630 nt) stfP e14 prophage, uncharacterized protein
?NC_000913 = 1209602 5 (0.190)pseudogene (18/501 nt) stfE pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
* ? NC_000913 4542682 =12 (0.380)13 (0.450) 9/216 1.3 49.9% intergenic (+49/‑433) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?NC_000913 4542996 = 15 (0.520)intergenic (+363/‑119) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
* ? NC_000913 = 454269012 (0.380)4 (0.140) 4/216 2.4 23.5% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?NC_000913 = 4542986 15 (0.520)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)