breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
RA 351,831 C→A 15.6% P400Q (CCG→CAG)  codB → cytosine transporter
RA 687,119 A→C 40.0% I41S (ATC→AGC)  ybeX ← putative ion transport
RA 1,820,438 G→T 17.3% P248Q (CCG→CAG)  astE ← succinylglutamate desuccinylase
RA 3,809,169 Δ1 bp 28.6% intergenic (‑41/+25) pyrE ← / ← rph orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
JC 3,809,219 Δ82 bp 57.7% [rph]–[rph] [rph], [rph]
RA 4,423,519 T→C 7.4% D108G (GAT→GGT)  qorB ← NAD(P)H:quinone oxidoreductase
RA 4,496,742 A→G 7.8% pseudogene (65/249 nt) yjhE → pseudogene, KpLE2 phage‑like element

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP009273 80522 80593 72 4 [3] [0] 4 leuL/leuO leu operon leader peptide/global transcription factor
* * ÷ CP009273 233672 233749 78 4 [3] [3] 4 aspV/yafT tRNA‑Asp/lipoprotein
* * ÷ CP009273 234932 234955 24 4 [3] [2] 4 ykfM lethality reduction protein, putative inner membrane protein
* * ÷ CP009273 234988 234998 11 4 [2] [2] 4 ykfM lethality reduction protein, putative inner membrane protein
* * ÷ CP009273 524119 524212 94 4 [3] [3] 4 ybbD pseudogene
* * ÷ CP009273 748273 748354 82 4 [3] [3] 4 ybgD/gltA putative fimbrial‑like adhesin protein/citrate synthase
* * ÷ CP009273 950151 950250 100 4 [3] [2] 4 focA/ycaO formate channel/ribosomal protein S12 methylthiotransferase accessory factor
* * ÷ CP009273 982713 982774 62 4 [2] [3] 5 ompF/asnS outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
* * ÷ CP009273 1046168 1046246 79 7 [3] [3] 4 insB1/cspH IS1 transposase B/stress protein, member of the CspA‑family
* * ÷ CP009273 1193089 1193273 185 5 [3] [3] 4 ymfE e14 prophage; putative inner membrane protein
* * ÷ CP009273 1193708 1193718 11 4 [2] [2] 4 ymfE/lit e14 prophage; putative inner membrane protein/e14 prophage; cell death peptidase, inhibitor of T4 late gene expression
* * ÷ CP009273 1207527 1207619 93 4 [0] [3] 4 iraM/ycgX RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein
* * ÷ CP009273 1431298 1431357 60 4 [2] [2] 4 ompN/micC outer membrane pore protein N, non‑specific/sRNA antisense regulator of OmpC translation, Hfq‑dependent
* * ÷ CP009273 1592510 1592623 114 4 [2] [2] 6 yneO/lsrK pseudogene, AidA homolog/autoinducer‑2 (AI‑2) kinase
* * ÷ CP009273 1807093 1807130 38 6 [3] [3] 4 ydjO uncharacterized protein
* * ÷ CP009273 1952431 1952614 184 4 [3] [3] 4 torY/cutC TMAO reductase III (TorYZ), cytochrome c‑type subunit/copper homeostasis protein
* * ÷ CP009273 2027296 2027454 159 5 [2] [2] 4 rseX/yedS sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology; putative outer membrane protein
* * ÷ CP009273 2100651 2100677 27 4 [2] [3] 4 wbbH O‑antigen polymerase
* * ÷ CP009273 2101563 2101662 100 4 [3] [3] 6 glf UDP‑galactopyranose mutase, FAD/NAD(P)‑binding
* * ÷ CP009273 2379173 2379386 214 4 [3] [3] 4 [yfbK]–[yfbL] [yfbK],[yfbL]
* * ÷ CP009273 2462779 2462848 70 4 [3] [3] 4 gtrS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
* * ÷ CP009273 2584436 2584528 93 4 [3] [2] 6 ypfM/yffB stress‑induced small enterobacterial protein/putative ArsC family reductase
* * ÷ CP009273 2779849 2779888 40 4 [3] [3] 4 ygaQ uncharacterized protein; putative enzyme
* * ÷ CP009273 2981757 2981794 38 4 [2] [3] 4 yqeH/yqeI putative LuxR family transcriptional regulator/putative transcriptional regulator
* * ÷ CP009273 3262621 3262708 88 4 [3] [1] 5 yhaC pentapetide repeats‑related protein
* * ÷ CP009273 3551467 3551558 92 4 [3] [3] 4 rtcB/rtcR RNA‑splicing ligase/sigma 54‑dependent transcriptional regulator of rtcBA expression
* * ÷ CP009273 3798424 3798459 36 4 [3] [3] 4 waaS lipopolysaccharide core biosynthesis protein
* * ÷ CP009273 4531517 4531539 23 4 [3] [3] 4 fimB/fimE tyrosine recombinase/inversion of on/off regulator of fimA/tyrosine recombinase/inversion of on/off regulator of fimA

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 360104 =29 (0.830)30 (0.860) 23/290 NT 52.6% intergenic (‑38/+557) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 360286 25 (0.720)intergenic (‑220/+375) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
* ? CP009273 1203246 =17 (0.490)24 (0.770) 18/258 NT 68.5% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 1205075 = 7 (0.230)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 120326117 (0.490)21 (0.680) 19/258 NT 65.5% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 = 1205058 7 (0.230)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 346350312 (0.340)4 (0.110) 4/290 NT 25.0% intergenic (‑291/+1) chiA/tufA periplasmic endochitinase/translation elongation factor EF‑Tu 1
?CP009273 = 3577555 NA (NA)intergenic (+15/‑1) insB1/yrhA IS1 transposase B/pseudogene, interrupted by IS1E