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 201,101 C→T 14.3% A41V (GCC→GTC)  rnhB → ribonuclease HII, degrades RNA of DNA‑RNA hybrids
RA 481,176 Δ1 bp 100% intergenic (‑101/‑41) acrA ← / → acrR multidrug efflux system/transcriptional repressor
JC JC 982,331 IS2 (–) +5 bp 100% coding (104‑108/1089 nt) ompF ← outer membrane porin 1a (Ia;b;F)
RA 1,191,676 C→T 100% H366H (CAC→CAT)  icd → e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA 1,191,688 C→T 100% T370T (ACC→ACT)  icd → e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA 1,999,185 C→A 19.9% D134E (GAC→GAA)  fliS → flagellar protein potentiates polymerization
RA 2,065,990 G→A 20.0% G324D (GGC→GAC)  flu → CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
RA 2,332,641 C→A 100% D87Y (GAC→TAC)  gyrA ← DNA gyrase (type II topoisomerase), subunit A
MC JC 2,332,651 Δ3 bp 100% coding (247‑249/2628 nt) gyrA ← DNA gyrase (type II topoisomerase), subunit A
RA 2,707,297 C→A 100% A348E (GCA→GAA)  srmB → ATP‑dependent RNA helicase
RA 2,956,956 C→A 18.3% T40T (ACG→ACT)  ppdB ← putative prepilin peptidase‑dependent protein
MC JC 2,960,899 Δ1,189 bp 100% [ptsP]–[rppH] [ptsP], [rppH]
RA 3,017,648 A→G 24.7% intergenic (+103/‑62) xdhD → / → xanQ putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding/xanthine permease
RA 3,167,378 C→T 100% E460K (GAA→AAA)  parE ← DNA topoisomerase IV, subunit B
RA 3,529,363 Δ1 bp 100% coding (581/720 nt) ompR ← response regulator in two‑component regulatory system with EnvZ
RA 3,657,830 C→A 13.8% R50L (CGA→CTA)  gadW ← transcriptional activator of gadA and gadBC; repressor of gadX
RA 3,808,039 G→T 12.9% L62L (CTG→CTT)  slmA → nucleoid occlusion factor, anti‑FtsZ division inhibitor
RA 3,826,195 C→T 8.7% R568H (CGC→CAC)  yicI ← putative alpha‑glucosidase
RA 3,834,441 G→T 10.4% A220E (GCA→GAA)  nepI ← putative transporter
RA 4,051,806 G→T 100% V14L (GTA→TTA)  typA → GTP‑binding protein
RA 4,335,568 G→A 19.4% L526L (CTG→TTG)  fumB ← anaerobic class I fumarate hydratase (fumarase B)

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP009273 42026 42051 26 3 [2] [2] 4 caiT/fixA putative transporter/anaerobic carnitine reduction putative electron transfer flavoprotein subunit
* * ÷ CP009273 153599 153728 130 3 [2] [2] 3 yadN/folK putative fimbrial‑like adhesin protein/2‑amino‑4‑hydroxy‑6‑hydroxymethyldihyropteridine pyrophosphokinase
* * ÷ CP009273 295813 295834 22 3 [2] [2] 3 paoC PaoABC aldehyde oxidoreductase, Moco‑containing subunit
* * ÷ CP009273 574677 574714 38 3 [2] [1] 4 ybcV DLP12 prophage; uncharacterized protein
* * ÷ CP009273 579508 579520 13 3 [2] [2] 3 appY global transcriptional activator; DLP12 prophage
* * ÷ CP009273 748508 748589 82 3 [2] [2] 3 ybgD/gltA putative fimbrial‑like adhesin protein/citrate synthase
* * ÷ CP009273 950129 950253 125 3 [2] [1] 3 focA/ycaO formate channel/ribosomal protein S12 methylthiotransferase accessory factor
* * ÷ CP009273 1098874 1098973 100 3 [2] [2] 3 csgD/csgB csgBAC operon transcriptional regulator/curlin nucleator protein, minor subunit in curli complex
* * ÷ CP009273 1174508 1174525 18 4 [2] [2] 3 nagK N‑acetyl‑D‑glucosamine kinase
* * ÷ CP009273 1192329 1193074 746 3 [2] [2] 3 [ymfD]–[ymfE] [ymfD],[ymfE]
* * ÷ CP009273 1193117 1193335 219 3 [2] [2] 3 ymfE e14 prophage; putative inner membrane protein
* * ÷ CP009273 1193350 1193690 341 3 [2] [2] 3 ymfE e14 prophage; putative inner membrane protein
* * ÷ CP009273 1193725 1194610 886 3 [2] [2] 3 [lit] [lit]
* * ÷ CP009273 1194691 1196362 1672 3 [2] [2] 3 [lit]–[xisE] [lit],intE,[xisE]
* * ÷ CP009273 1196525 1196708 184 3 [2] [2] 3 xisE/ymfI e14 prophage; putative excisionase/e14 prophage; uncharacterized protein
* * ÷ CP009273 1196765 1197565 801 3 [2] [2] 3 ymfI–ymfJ ymfI,ymfJ
* * ÷ CP009273 1197897 1198868 972 3 [2] [2] 3 [cohE]–[ymfL] [cohE],croE,[ymfL]
* * ÷ CP009273 1198994 1199785 792 3 [2] [2] 3 [ymfL]–[oweE] [ymfL],ymfM,[oweE]
* * ÷ CP009273 1199863 1200095 233 3 [2] [2] 3 aaaE pseudogene, phage terminase protein A family, e14 prophage;Phage or Prophage Related
* * ÷ CP009273 1200390 1200928 539 3 [2] [2] 3 aaaE pseudogene, phage terminase protein A family, e14 prophage;Phage or Prophage Related
* * ÷ CP009273 1201109 1201602 494 3 [2] [2] 3 [ymfR]–[jayE] [ymfR],beeE,[jayE]
* * ÷ CP009273 1201965 1203943 1979 3 [2] [2] 3 [jayE]–[tfaP] [jayE],ymfQ,stfP,[tfaP]
* * ÷ CP009273 1204221 1206677 2457 3 [2] [2] 3 [tfaE]–mcrA [tfaE],stfE,pinE,mcrA
* * ÷ CP009273 1206762 1206868 107 3 [2] [0] 3 mcrA/icdC putative 5‑methylcytosine/5‑hydroxymethylcytosine‑specific restriction nuclease; 5‑methylcytosine DNA binding protein; e14 prophage gene/pseudogene, isocitrate dehydrogenase C‑terminal gene fragment; idcC' is a 54 codon 3' gene fragment created during e14 prophage insertion
* * ÷ CP009273 1431306 1431372 67 3 [2] [0] 4 ompN/micC outer membrane pore protein N, non‑specific/sRNA antisense regulator of OmpC translation, Hfq‑dependent
* * ÷ CP009273 1494786 1494824 39 3 [2] [2] 3 ydcK/tehA uncharacterized protein/potassium‑tellurite ethidium and proflavin transporter
* * ÷ CP009273 1524310 1524426 117 4 [1] [2] 3 ydcD uncharacterized protein
* * ÷ CP009273 1540291 1540420 130 3 [2] [2] 3 yddL/yddG putative lipoprotein;putative membrane; Not classified; putative outer membrane porin protein/aromatic amino acid exporter
* * ÷ CP009273 1577922 1577974 53 3 [2] [2] 3 [ydeO] [ydeO]
* * ÷ CP009273 1592494 1592628 135 3 [2] [2] 3 yneO/lsrK pseudogene, AidA homolog/autoinducer‑2 (AI‑2) kinase
* * ÷ CP009273 1618903 1618977 75 3 [2] [2] 3 ydeI/ydeJ hydrogen peroxide resistance OB fold protein; putative periplasmic protein/inactive PncC family protein
* * ÷ CP009273 1797628 1797645 18 4 [0] [2] 3 arpB pseudogene, ankyrin repeats
* * ÷ CP009273 2037484 2037541 58 3 [1] [2] 3 mtfA anti‑repressor for DgsA(Mlc)
* * ÷ CP009273 2097482 2097579 98 3 [2] [2] 3 wbbK lipopolysaccharide biosynthesis protein
* * ÷ CP009273 2099583 2099687 105 3 [2] [2] 3 wbbH O‑antigen polymerase
* * ÷ CP009273 2379321 2379385 65 3 [2] [2] 4 [yfbL] [yfbL]
* * ÷ CP009273 2400560 2400668 109 3 [2] [2] 3 lrhA/alaA transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2
* * ÷ CP009273 2435962 2436002 41 3 [2] [2] 3 mnmC fused 5‑methylaminomethyl‑2‑thiouridine‑forming enzyme methyltransferase and FAD‑dependent demodification enzyme
* * ÷ CP009273 2456440 2456457 18 3 [2] [2] 3 fadL/yfdF long‑chain fatty acid outer membrane transporter/uncharacterized protein
* * ÷ CP009273 2462630 2462697 68 4 [2] [2] 3 gtrS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
* * ÷ CP009273 2463044 2463250 207 3 [2] [2] 3 gtrS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
* * ÷ CP009273 2463618 2463800 183 3 [2] [2] 3 gtrS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
* * ÷ CP009273 2584443 2584515 73 4 [2] [2] 5 ypfM/yffB stress‑induced small enterobacterial protein/putative ArsC family reductase
* * ÷ CP009273 2735066 2735078 13 3 [2] [2] 3 yfiL lipoprotein
* * ÷ CP009273 2767043 2767079 37 3 [2] [0] 3 yfjW CP4‑57 prophage; putative inner membrane protein
* * ÷ CP009273 2792289 2792324 36 4 [1] [2] 3 stpA/alaE DNA binding protein, nucleoid‑associated/alanine exporter, alanine‑inducible, stress‑responsive
* * ÷ CP009273 2975768 2975780 13 3 [2] [2] 4 araE/kduD arabinose transporter/hexuronate dehydrogenase; hexuronate utilization in high osmolarity
* * ÷ CP009273 3492781 3492801 21 3 [2] [2] 5 cysG/yhfL fused siroheme synthase 1,3‑dimethyluroporphyriongen III dehydrogenase and siroheme ferrochelatase/uroporphyrinogen methyltransferase/small lipoprotein
* * ÷ CP009273 3647062 3647117 56 4 [2] [2] 3 [yhiS] [yhiS]
* * ÷ CP009273 3763037 3763264 228 3 [2] [1] 4 [yibV] [yibV]
* * ÷ CP009273 3792824 3792865 42 3 [2] [2] 3 waaZ lipopolysaccharide core biosynthesis protein
* * ÷ CP009273 3798341 3798488 148 3 [2] [2] 3 [waaS] [waaS]
* * ÷ CP009273 4241549 4241639 91 3 [2] [2] 3 yjbI pseudogene, SopA‑related, pentapeptide repeats‑containing
* * ÷ CP009273 4294370 4294422 53 3 [2] [2] 3 ytcA/yjcS putative inner membrane DUF1656 family protein; efflux pump associated/metallo‑beta‑lactamase superfamily protein
* * ÷ CP009273 4316803 4316896 94 3 [1] [2] 3 yjdM/crfC zinc‑ribbon family protein/clamp‑binding sister replication fork colocalization protein, dynamin‑related
* * ÷ CP009273 4532510 4532586 77 3 [2] [2] 3 fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 360104 =11 (0.470)20 (0.860) 19/296 NT 54.1% intergenic (‑38/+557) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 360286 23 (0.990)intergenic (‑220/+375) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor