breseq  version 0.35.4  revision f352f80f4bc9
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 264,098 G→T L50L (CTC→CTA)  ykfH ← uncharacterized protein
RA 272,881 C→T pseudogene (35/1108 nt) ykfC → CP4‑6 prophage; conserved protein;Phage or Prophage Related
RA 275,065 G→A T18I (ACC→ATC)  insH1 ← IS5 transposase and trans‑activator
RA 314,816 (G)5→6 pseudogene (460/872 nt) eaeH → pseudogene, attaching and effacing protein homology;factor; Not classified
RA 482,230 G→A P725L (CCG→CTG)  acrB ← multidrug efflux system protein
RA 913,000 C→T G272D (GGC→GAC)  hcp ← hybrid‑cluster [4Fe‑2S‑2O] subunit of anaerobic terminal reductases
RA 1,197,502 C→T G11R (GGA→AGA)  ymfD ← e14 prophage; putative SAM‑dependent methyltransferase
RA 1,220,766 C→T pseudogene (1166/2574 nt) ycgH → pseudogene; putative ATP‑binding component of a transport system
RA 1,500,163 A→G V96A (GTC→GCC)  ydcK ← uncharacterized protein
RA 1,544,022 1 bp→AA coding (39/1389 nt) narU ← nitrate/nitrite transporter
RA 1,591,093 (T)7→8 coding (1084/1323 nt) hipA ← inactivating GltX kinase facilitating persister formation; toxin of HipAB TA pair; autokinase
RA 1,743,960 G→A L168L (CTG→CTA)  mdtK → multidrug efflux system transporter
MC JC 1,978,503 Δ776 bp insB1–insA insB1, insA
RA 2,052,148 A→G intergenic (+134/+128) yeeJ → / ← yeeL putative adhesin/pseudogene, glycosyltransferase homology
RA 2,106,741 A→T S162S (TCT→TCA)  wbbH ← O‑antigen polymerase
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 2,670,017 G→A G329D (GGC→GAC)  hcaE → 3‑phenylpropionate dioxygenase, large (alpha) subunit
RA 2,679,525 G→T A1074D (GCT→GAT)  yphG ← DUF4380 domain‑containing TPR repeat protein
RA 2,740,078 T→C intergenic (‑9/+2) tyrA ← / ← aroF fused chorismate mutase T/prephenate dehydrogenase/3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tyrosine‑repressible
RA 2,759,615 G→A E211K (GAA→AAA)  yfjI → CP4‑57 prophage; uncharacterized protein
RA 2,795,396 C→A Q382K (CAG→AAG)  gabP → gamma‑aminobutyrate transporter
RA 2,817,170 C→A E112* (GAA→TAA)  yqaB ← fructose‑1‑P and 6‑phosphogluconate phosphatase
RA 3,075,359 T→C N275S (AAC→AGC)  yggF ← fructose 1,6 bisphosphatase isozyme
RA 3,215,447 C→A G9G (GGG→GGT)  mug ← G/U mismatch‑specific DNA glycosylase; xanthine DNA glycosylase
RA 3,309,006 (C)6→7 intergenic (‑82/+27) nlpI ← / ← pnp lipoprotein involved in osmotic sensitivity and filamentation/polynucleotide phosphorylase/polyadenylase
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 3,815,810 Δ1 bp intergenic (‑42/+24) pyrE ← / ← rph orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
RA 4,110,747 G→C intergenic (+62/+784) cdh → / ← yiiQ CDP‑diacylglycerol phosphotidylhydrolase/DUF1454 family putative periplasmic protein
RA 4,111,596 G→A L179L (CTG→TTG)  yiiQ ← DUF1454 family putative periplasmic protein
RA 4,158,984 G→T M193I (ATG→ATT)  oxyR → oxidative and nitrosative stress transcriptional regulator
RA 4,171,489 G→A intergenic (+29/‑64) rrlB → / → rrfB 23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon
RA 4,184,711 C→T T1184M (ACG→ATG)  rpoB → RNA polymerase, beta subunit
RA 4,296,297 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,397,330 G→T M1M (ATG→ATT) † mutL → methyl‑directed mismatch repair protein
RA 4,472,342 (A)8→9 coding (108/135 nt) pyrL ← pyrBI operon leader peptide
RA 4,604,632 C→A A186E (GCA→GAA)  bglJ → bgl operon transcriptional activator
RA 4,619,320 G→A Q392Q (CAG→CAA)  deoA → thymidine phosphorylase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913_3_pae_tpiA 3423732–3424234 3424559–3424238 5–828 36 [35] [35] 36 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913_3_pae_tpiA 4166293–4168136 4171466–4168488 353–5174 36 [35] [35] 36 rrsB–rrlB rrsB,gltT,rrlB

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_pae_tpiA = 120780517 (0.220)56 (0.840) 48/240 0.5 86.2% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913_3_pae_tpiA = 1209602 3 (0.040)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913_3_pae_tpiA = 12994980 (0.000)76 (1.030) 63/264 0.2 100% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913_3_pae_tpiA 1300698 = 0 (0.000)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein