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 4,140 A→T 18.2% D136V (GAT→GTT)  thrC → L‑threonine synthase
RA 193,951 A→G 9.6% K307E (AAA→GAA)  rseP → inner membrane zinc RIP metalloprotease; RpoE activator, by degrading RseA; cleaved signal peptide endoprotease
RA 864,305 G→T 9.8% A444S (GCG→TCG)  gsiA → glutathione transporter ATP‑binding protein, ABC superfamily
JC JC 981,963 IS1 (+) +9 bp 100% coding (468‑476/1089 nt) ompF ← outer membrane porin 1a (Ia;b;F)
RA 3,207,739 A→C 100% D445A (GAT→GCT)  rpoD → RNA polymerase, sigma 70 (sigma D) factor
RA 3,365,908 G→A 100% P9L (CCG→CTG)  nanT ← sialic acid transporter
RA 3,778,863 A→T 18.6% T82S (ACT→TCT)  gpmM → phosphoglycero mutase III, cofactor‑independent
RA 3,983,589 C→A 14.8% E180* (GAG→TAG)  hemC ← hydroxymethylbilane synthase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP009273 233710 233755 46 2 [1] [1] 2 aspV/yafT tRNA‑Asp/lipoprotein
* * ÷ CP009273 1098837 1098848 12 2 [1] [1] 2 csgD/csgB csgBAC operon transcriptional regulator/curlin nucleator protein, minor subunit in curli complex
* * ÷ CP009273 1158867 1158919 53 2 [1] [1] 2 thiK thiamine kinase
* * ÷ CP009273 1161536 1161550 15 2 [1] [1] 2 [ndh] [ndh]
* * ÷ CP009273 1164264 1164309 46 2 [1] [1] 2 [ycfQ] [ycfQ]
* * ÷ CP009273 1164343 1164425 83 2 [1] [1] 2 ycfQ/bhsA repressor for bhsA(ycfR)/biofilm, cell surface and signaling protein
* * ÷ CP009273 1193236 1193258 23 2 [1] [0] 2 ymfE e14 prophage; putative inner membrane protein
* * ÷ CP009273 1225897 1225975 79 2 [1] [1] 2 hlyE/umuD hemolysin E/DNA polymerase V, subunit D
* * ÷ CP009273 1268432 1268455 24 2 [1] [1] 2 chaC cation transport regulator
* * ÷ CP009273 1311564 1311580 17 2 [1] [1] 2 trpB tryptophan synthase, beta subunit
* * ÷ CP009273 1320841 1320946 106 2 [1] [1] 2 [yciQ] [yciQ]
* * ÷ CP009273 1326259 1326263 5 2 [1] [1] 3 topA DNA topoisomerase I, omega subunit
* * ÷ CP009273 1333929 1333952 24 2 [1] [1] 2 pgpB phosphatidylglycerophosphatase B
* * ÷ CP009273 1539478 1539491 14 2 [1] [1] 2 yddK pseudogene, leucine‑rich protein; putative glycoportein
* * ÷ CP009273 1541497 1541509 13 2 [1] [1] 2 yddG/fdnG aromatic amino acid exporter/formate dehydrogenase‑N, alpha subunit, nitrate‑inducible
* * ÷ CP009273 1748981 1749132 152 2 [1] [1] 2 ydhY/ydhZ putative 4Fe‑4S ferridoxin‑type protein; FNR, Nar, NarP‑regulated protein; putative subunit of YdhYVWXUT oxidoreductase complex/uncharacterized protein
* * ÷ CP009273 1806966 1806974 9 2 [1] [1] 3 ydjO uncharacterized protein
* * ÷ CP009273 1807097 1807125 29 2 [0] [1] 2 ydjO uncharacterized protein
* * ÷ CP009273 1990339 1990372 34 2 [1] [1] 2 sdiA/yecC quorum‑sensing transcriptional activator/putative ABC superfamily transporter ATP‑binding subunit
* * ÷ CP009273 2004753 2004803 51 2 [1] [1] 2 yedN pseudogene, IpaH/YopM family
* * ÷ CP009273 2027080 2027143 64 2 [1] [1] 2 [rseX] [rseX]
* * ÷ CP009273 2027411 2027422 12 2 [1] [1] 2 rseX/yedS sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology; putative outer membrane protein
* * ÷ CP009273 2097529 2097557 29 2 [1] [1] 2 wbbK lipopolysaccharide biosynthesis protein
* * ÷ CP009273 2185824 2185923 100 2 [1] [1] 2 yehD/yehE putative fimbrial‑like adhesin protein/DUF2574 family protein
* * ÷ CP009273 2300305 2300350 46 2 [1] [1] 2 mqo/yojI malate dehydrogenase, FAD/NAD(P)‑binding domain/microcin J25 efflux pump, TolC‑dependent; fused ABC transporter permease and ATP‑binding components
* * ÷ CP009273 2337811 2337834 24 2 [1] [1] 2 yfaL/nrdA adhesin/ribonucleoside‑diphosphate reductase 1, alpha subunit
* * ÷ CP009273 2359300 2359313 14 2 [1] [0] 3 ais/arnB putative LPS core heptose(II)‑phosphate phosphatase/uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent
* * ÷ CP009273 2463185 2463227 43 2 [1] [1] 2 gtrS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
* * ÷ CP009273 2491966 2492003 38 2 [1] [1] 2 alaC/ypdA valine‑pyruvate aminotransferase 3/sensor kinase regulating yhjX; pyruvate‑responsive YpdAB two‑component system
* * ÷ CP009273 2622973 2623012 40 2 [1] [1] 2 yfgG/yfgH uncharacterized protein/outer membrane integrity lipoprotein
* * ÷ CP009273 2686955 2686971 17 2 [1] [1] 2 purL phosphoribosylformyl‑glycineamide synthetase
* * ÷ CP009273 2767739 2767751 13 2 [1] [1] 2 yfjW CP4‑57 prophage; putative inner membrane protein
* * ÷ CP009273 2877653 2877667 15 2 [1] [1] 2 casA/ygcB CRISP RNA (crRNA) containing Cascade antiviral complex protein/R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
* * ÷ CP009273 2898989 2899002 14 2 [1] [1] 3 yqcG uncharacterized protein
* * ÷ CP009273 2988529 2988633 105 2 [1] [1] 2 ygeK/ygeN pseudogene; putative 2‑component transcriptional regulator/pseudogene
* * ÷ CP009273 3260815 3260861 47 2 [1] [1] 3 tdcR L‑threonine dehydratase operon activator protein
* * ÷ CP009273 3262546 3262611 66 2 [1] [1] 2 yhaC pentapetide repeats‑related protein
* * ÷ CP009273 3368038 3368050 13 2 [1] [1] 2 nanR/dcuD transcriptional repressor of the nan operon, induced by sialic acid/putative transporter
* * ÷ CP009273 3406926 3406967 42 2 [0] [0] 2 acrS/acrE acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein
* * ÷ CP009273 3575483 3575511 29 2 [1] [1] 2 yhhZ putative Hcp1 family polymorphic toxin protein; putative colicin‑like DNase/tRNase activity
* * ÷ CP009273 3644308 3644320 13 2 [1] [1] 2 arsC/yhiS arsenate reductase/pseudogene
* * ÷ CP009273 3787053 3787109 57 3 [1] [1] 4 yibB/hldD YibB family protein, function unknown/ADP‑L‑glycero‑D‑mannoheptose‑6‑epimerase, NAD(P)‑binding
* * ÷ CP009273 3794421 3794428 8 3 [0] [1] 2 waaJ UDP‑D‑glucose:(galactosyl)lipopolysaccharide glucosyltransferase
* * ÷ CP009273 3830092 3830113 22 2 [1] [1] 2 yicT/setC pseudogene/putative arabinose efflux transporter
* * ÷ CP009273 3900139 3900185 47 2 [1] [1] 2 bglG/phoU transcriptional antiterminator of the bgl operon/negative regulator of PhoR/PhoB two‑component regulator

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 19796 =NA (NA)143 (5.530) 78/268 NT 85.6% noncoding (768/768 nt) IS1 repeat region
?CP009273 4317405 = 24 (0.930)coding (454/2229 nt) crfC clamp‑binding sister replication fork colocalization protein, dynamin‑related
* ? CP009273 = 20563NA (NA)9 (0.350) 9/266 NT 90.1% noncoding (1/768 nt) IS1 repeat region
?CP009273 1503915 = 1 (0.040)noncoding (755/1748 nt) IS609 repeat region
* ? CP009273 360104 =14 (0.540)25 (0.970) 23/268 NT 68.5% intergenic (‑38/+557) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 360286 9 (0.350)intergenic (‑220/+375) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
* ? CP009273 1203246 =9 (0.350)4 (0.180) 4/236 NT 28.6% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 1205075 = 12 (0.530)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 15039231 (0.040)22 (0.850) 19/268 NT 95.7% noncoding (763/1748 nt) IS609 repeat region
?CP009273 = 3577555 NA (NA)intergenic (+15/‑1) insB1/yrhA IS1 transposase B/pseudogene, interrupted by IS1E
* ? CP009273 3576788 =NA (NA)157 (6.070) 88/268 NT 84.9% intergenic (+10/‑55) yrhA/insA pseudogene, interrupted by IS1E/IS1 repressor TnpA
?CP009273 = 4372249 28 (1.080)intergenic (‑114/‑211) frdA/epmA fumarate reductase (anaerobic) catalytic and NAD/flavoprotein subunit/Elongation Factor P Lys34 lysyltransferase
* ? CP009273 = 45325074 (0.150)4 (0.170) 4/250 NT 26.0% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?CP009273 = 4532803 19 (0.790)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)