breseq  version 0.32.1  revision aa8f2595a244
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 375,067 A→G intergenic (+186/‑392) mhpE → / → mhpT 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter
RA 375,075 G→A intergenic (+194/‑384) mhpE → / → mhpT 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter
RA 380,021 (G)10→8 intergenic (‑140/+47) frmR ← / ← yaiO regulator protein that represses frmRAB operon/outer membrane protein
RA 404,123 (C)5→4 coding (421/1116 nt) yaiC → diguanylate cyclase, cellulose regualtor
RA 467,458 C→T P16L (CCC→CTC)  cof → thiamine pyrimidine pyrophosphate hydrolase, HMP‑PP phosphatase
RA 543,768 A→G T93T (ACT→ACC allE ← S‑ureidoglycine aminohydrolase
RA 573,440 C→T R24C (CGC→TGC)  rusA → DLP12 prophage, endonuclease RUS
RA 585,317 C→T W106* (TGG→TAG)  ompT ← DLP12 prophage, outer membrane protease VII, outer membrane protein 3b
RA 593,467 T→G D435A (GAC→GCC)  cusS ← copper‑sensing histidine kinase in two‑component regulatory system with CusR
RA 600,470 C→T A586V (GCG→GTG)  cusA → copper/silver efflux system, membrane component
RA 738,087 A→G intergenic (+126/‑5) ybfL → / → ybfD pseudogene, DDE domain transposase family,putative factor, Not classified, putative receptor protein/H repeat‑associated putative transposase
RA 746,063 A→G Q43Q (CAA→CAG nei → endonuclease VIII and 5‑formyluracil/5‑hydroxymethyluracil DNA glycosylase
RA 807,343 C→G intergenic (‑62/+90) ybhC ← / ← ybhB acyl‑CoA thioesterase, lipoprotein/kinase inhibitor homolog, UPF0098 family
RA 857,298 C→T R446W (CGG→TGG)  ybiT → ABC‑F family putative regulatory ATPase
RA 867,319 A→G Y251C (TAC→TGC)  iaaA → Isoaspartyl peptidase
RA 936,202 C→T T993T (ACC→ACT ftsK → DNA translocase at septal ring sorting daughter chromsomes
RA 989,319 (G)5→6 coding (1038/1203 nt) pncB ← nicotinate phosphoribosyltransferase
RA 1,036,083 C→T A105V (GCG→GTG)  hyaD → hydrogenase 1 maturation protease
RA 1,077,868 G→A R339C (CGC→TGC)  putA ← fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase
JC 1,198,498 (AATGATGA)6→5 intergenic (‑261/‑190) ymfE ← / → lit e14 prophage, putative inner membrane protein/T4 phage exclusion protein, cell death peptidase, e14 prophage
RA 1,276,337 G→A R428C (CGC→TGC)  narX ← sensory histidine kinase in two‑component regulatory system with NarL
RA 1,287,826 C→T A267T (GCA→ACA)  purU ← formyltetrahydrofolate hydrolase
RA 1,351,196 (G)7→8 intergenic (‑157/+211) fabI ← / ← ycjD enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein
RA 1,421,650 (C)7→8 coding (532/858 nt) ydaU → Rac prophage, conserved protein
RA 1,428,875 T→C pseudogene (80/189 nt) lomR → pseudogene, Rac prophage lom homolog,Phage or Prophage Related, interrupted by IS5 and N‑ter deletion
RA 1,458,617 A→G A118A (GCA→GCG paaG → 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming
RA 1,504,515 C→T R267C (CGC→TGC)  insQ → IS609 transposase B
RA 1,595,427 A→G pseudogene (2561/3861 nt) yneO ← pseudogene, AidA homolog
RA 1,702,700 T→C F156F (TTT→TTC add → adenosine deaminase
RA 1,722,854 T→C L245P (CTC→CCC)  ydhK → putative efflux protein (PET) component of YdhJK efflux pump
RA 1,873,602 C→T T10M (ACG→ATG)  yeaK → aminoacyl‑tRNA editing domain protein
RA 1,904,586 T→C V231A (GTC→GCC)  manZ → mannose‑specific enzyme IID component of PTS
MC JC 1,978,503 Δ776 bp insB1insA insB1, insA
RA 1,995,320 G→A R14C (CGC→TGC)  uvrY ← response regulator in two‑component regulatory system with BarA
RA 2,073,094 T→C L519P (CTG→CCG)  flu → CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
RA 2,166,540 T→C R291R (CGT→CGC yegQ → putative peptidase
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 2,185,875 (G)7→6 intergenic (‑79/‑42) rcnR ← / → rcnA transcriptional repressor of rcnA/membrane protein conferring nickel and cobalt resistance
RA 2,238,421 T→C E290G (GAG→GGG)  mglA ← methyl‑galactoside ABC transporter ATPase
RA 2,277,291 C→T A331V (GCG→GTG)  yejF → microcin C ABC transporter ATPase
RA 2,314,922 T→C S479P (TCC→CCC)  rcsD → phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
RA 2,380,852 T→C D59G (GAC→GGC)  elaB ← putative membrane‑anchored DUF883 family ribosome‑binding protein
RA 2,401,103 G→A T151T (ACC→ACT nuoF ← NADH:ubiquinone oxidoreductase, chain F
RA 2,631,531 G→A G335G (GGC→GGT guaA ← GMP synthetase (glutamine aminotransferase)
RA 2,763,869 (T)7→8 coding (1285/1617 nt) yfjL ← CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein
RA 2,771,806 A→T intergenic (+191/+196) yfjT → / ← yfjU CP4‑57 prophage, putative periplasmic protein/CP4‑57 prophage, conserved protein,Phage or Prophage Related
RA 2,829,493 G→A S149S (TCG→TCA srlR → sorbitol‑inducible srl operon transcriptional repressor
RA 2,834,077 G→A A56T (GCC→ACC)  norW → NADH:flavorubredoxin oxidoreductase
RA 2,842,591 T→C L151L (TTA→TTG hycI ← protease involved in processing C‑terminal end of HycE
RA 2,937,802 A→G D112G (GAC→GGC)  fucK → L‑fuculokinase
RA 2,968,916 T→C Q21R (CAG→CGG)  rppH ← RNA pyrophosphohydrolase
RA 3,066,288 T→C T296A (ACG→GCG)  ygfI ← putative DNA‑binding transcriptional regulator
RA 3,139,583 G→A R286H (CGT→CAT)  yghU → putative S‑transferase
RA 3,177,274 G→A R3C (CGT→TGT)  yqiB ← DUF1249 protein YqiB
RA 3,194,362 (G)6→7 coding (1499/1662 nt) yqiK → PHB family membrane protein, function unknown
RA 3,271,600 (C)5→7 coding (171/1146 nt) garK ← glycerate kinase I
RA 3,366,953 G→A G10R (GGA→AGA)  yhcF → putative transcriptional regulator
RA 3,457,094 A→G I240V (ATC→GTC)  gspD → 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 3,638,618 T→C V326A (GTG→GCG)  pitA → phosphate transporter, low‑affinity, tellurite importer
RA 3,709,561 (C)6→7 coding (915/1692 nt) eptB ← KDO phosphoethanolamine transferase, Ca(2+)‑inducible
RA 3,720,202 T→C S52P (TCC→CCC)  cspA → RNA chaperone and antiterminator, cold‑inducible
RA 3,728,118 (C)8→9 coding (1254/1455 nt) xylB ← xylulokinase
RA 3,790,538 A→G S270P (TCT→CCT)  tdh ← L‑threonine 3‑dehydrogenase, NAD(P)‑binding
RA 3,791,004 A→G G114G (GGT→GGC tdh ← L‑threonine 3‑dehydrogenase, NAD(P)‑binding
RA 3,815,813 A→G intergenic (‑45/+21) pyrE ← / ← rph orotate phosphoribosyltransferase/ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH
RA 3,901,765 G→A G152G (GGC→GGT bglH ← carbohydrate‑specific outer membrane porin, cryptic
RA 3,920,872 G→A T6I (ACA→ATA)  atpF ← F0 sector of membrane‑bound ATP synthase, subunit b
RA 3,932,121 A→G N269S (AAC→AGC)  kup → potassium transporter
RA 3,936,381 C→T T35M (ACG→ATG)  rbsB → D‑ribose ABC transporter periplasmic binding protein, ribose chemotaxis receptor
RA 3,959,758 A→G L19P (CTG→CCG)  ppiC ← peptidyl‑prolyl cis‑trans isomerase C (rotamase C)
RA 4,183,238 C→T A665V (GCG→GTG)  rpoB → RNA polymerase, beta subunit
RA 4,281,472 A→G E498G (GAG→GGG)  yjcE → putative cation/proton antiporter
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,304,888 A→G N570N (AAT→AAC yjcS ← metallo‑beta‑lactamase superfamily protein
RA 4,351,093 G→A G190G (GGC→GGT dcuS ← sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration
RA 4,490,935 A→G L69L (TTG→CTG)  idnR ← transcriptional repressor, 5‑gluconate‑binding
RA 4,538,491 C→T G92D (GGC→GAC)  nanM ← N‑acetylneuraminic acid mutarotase
RA 4,574,259 A→G pseudogene (341/2937 nt) yjiV → pseudogene, conserved hypothetical protein
RA 4,606,215 (G)8→9 noncoding (72/87 nt) leuP ← tRNA‑Leu

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 807347 810368 3022 9 [0] [7] 9 ybhB–[bioB] ybhB, bioA, [bioB]
* * ÷ NC_000913 2857138 2859626 2489 12 [0] [8] 9 mutS methyl‑directed mismatch repair protein
* * ÷ NC_000913 3423785–3424233 3424530–3424241 9–746 9 [7] [7] 9 [rrfD]–[rrlD] [rrfD], [rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =59 (1.170)20 (0.460) 19/192 0.9 32.4% coding (290/630 nt) stfP e14 prophage, uncharacterized protein
?NC_000913 1209619 = 33 (0.760)pseudogene (1/501 nt) stfE pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)78 (1.600) 52/216 0.0 100% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913 1300698 = 0 (0.000)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein