breseq  version 0.26.1  
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 367,852 (GC)6→5 coding (568‑569/834 nt) mhpR ← mhp operon transcriptional activator
RA 380,022 (G)10→9 intergenic (‑141/+47) frmR ← / ← yaiO regulator protein that represses frmRAB operon/outer membrane protein
RA 525,276 C→T G672G (GGC→GGT)  rhsD → Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
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 1,351,196 (G)7→6 intergenic (‑157/+211) fabI ← / ← ycjD enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein
RA 1,642,981 G→C I87M (ATC→ATG)  quuQ ← Qin prophage; putative antitermination protein Q
RA 1,745,706 T→C E141G (GAG→GGG)  ydhQ ← autotransporter adhesin‑related protein
RA 1,807,657 G→A T86T (ACG→ACA)  ydiZ → uncharacterized protein
RA 1,978,440 (G)6→7 intergenic (‑243/+78) flhD ← / ← insB1 flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
MC JC 1,978,503 Δ776 bp insB1–insA insB1, insA
JC JC 1,979,486 IS5 (+) +4 bp intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
RA 2,051,535 G→A A2200T (GCC→ACC)  yeeJ → putative adhesin
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 2,183,397 (T)5→4 coding (255/819 nt) yegX ← putative family 25 glycosyl hydrolase
RA 2,245,845 G→A P309S (CCG→TCG)  cirA ← colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter
RA 2,620,434 (T)6→7 coding (439/627 nt) upp ← uracil phosphoribosyltransferase
RA 2,857,648 G→T E186* (GAA→TAA)  mutS → methyl‑directed mismatch repair protein
RA 2,905,539 T→C intergenic (‑121/‑18) queE ← / → yqcG 7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis/membrane stress resistance protein
RA 3,229,827 A→G N314D (AAC→GAC)  ygjK → alpha‑glucosidase
RA 3,342,107 (G)6→7 coding (842/987 nt) kdsD → D‑arabinose 5‑phosphate isomerase
RA 3,459,879 T→C A21A (GCT→GCC)  gspF → 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 3,595,025 +A coding (456/1278 nt) livM ← branched‑chain amino acid ABC transporter permease
RA 3,619,150 T→C intergenic (+161/‑42) nikR → / → rhsB transcriptional repressor, Ni‑binding/Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
RA 3,622,299 G→A T1036T (ACG→ACA)  rhsB → Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
RA 3,622,314 G→A R1041R (AGG→AGA)  rhsB → Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
RA 3,622,316 G→C S1042T (AGC→ACC)  rhsB → Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
RA 3,735,003 A→G T9A (ACA→GCA)  xylR → xylose divergent operon transcriptional activator
RA 3,777,535 C→T T46M (ACG→ATG)  lldP → L‑lactate permease
MC JC 3,815,859 Δ82 bp [rph]–[rph] [rph], [rph]
RA 3,928,930 G→A A225V (GCC→GTC)  viaA ← stimulator of RavA ATPase activity; von Willebrand factor domain protein
RA 3,966,553 G→A G46D (GGC→GAC)  rho → transcription termination factor
RA 4,060,920 T→C L158L (CTT→CTC)  yihL → putative DNA‑binding transcriptional regulator
RA 4,275,912 A→G M148V (ATG→GTG)  yjcC → putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,453,435 (G)5→4 coding (865/1026 nt) ytfT → putative sugar ABC transporter permease
RA 4,464,163 (T)6→5 coding (547/1656 nt) treC ← trehalose‑6‑P hydrolase
RA 4,597,488 A→G W652R (TGG→CGG)  opgB ← OPG periplasmic biosynthetic phosphoglycerol transferases I (membrane‑bound) and II (soluble)
RA 4,609,336 (C)7→8 intergenic (+13/‑78) yjjG → / → prfC dUMP phosphatase/peptide chain release factor RF‑3

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 2469147 2469801 655 41 [37] [31] 43 gtrS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
* * ÷ NC_000913 3423751–3424556 3424556 1–806 39 [38] [38] 39 [rrfD]–[rrlD] [rrfD], [rrlD]
* * ÷ NC_000913 4037910–4038686 4040521–4039392 707–2612 39 [38] [37] 40 [rrlA]–[rrfA] [rrlA], [rrfA]

Unassigned new junction evidence...
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =14 (0.150)98 (1.160) 56/272 0.2 90.9% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 7 (0.080)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780514 (0.150)67 (0.790) 46/272 0.6 87.3% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 7 (0.080)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related