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 37,250 A→C 21.8% V192G (GTG→GGG)  caiC ← putative crotonobetaine/carnitine‑CoA ligase
RA 71,877 A→G 25.4% E176G (GAG→GGG)  yabI → DedA family inner membrane protein
RA 75,091 G→T 37.4% D130E (GAC→GAA thiB ← thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein
RA 134,775 T→C 15.7% intergenic (+25/+13) yacL → / ← speD UPF0231 family protein/S‑adenosylmethionine decarboxylase
RA 151,821 A→G 11.3% T137T (ACT→ACC yadL ← putative fimbrial‑like adhesin protein
RA 159,258 G→T 21.7% V285V (GTC→GTA gluQ ← glutamyl‑Q tRNA(Asp) synthetase
RA 173,427 A→G 16.9% R656G (AGA→GGA)  fhuB → iron(3+)‑hydroxamate import ABC transporter permease
RA 194,997 C→A 12.0% A32E (GCA→GAA)  ispU → undecaprenyl pyrophosphate synthase
RA 209,270 T→G 18.8% V217G (GTG→GGG)  accA → acetyl‑CoA carboxylase, carboxytransferase, alpha subunit
RA 246,984 T→C 15.3% A91A (GCT→GCC yafL → putative lipoprotein and C40 family peptidase
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 345,302 C→A 12.2% intergenic (+311/‑102) yahL → / → yahM uncharacterized protein/uncharacterized protein
JC JC 458,790 IS186 (–) +6 bp :: Δ1 bp 100% intergenic (+90/‑93) clpX → / → lon ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La
RA 501,181 A→C 23.1% T353P (ACT→CCT)  gsk → inosine/guanosine kinase
RA 685,022 G→C 15.3% R78R (CGC→CGG gltL ← glutamate/aspartate ABC transporter ATPase
RA 742,267 T→C 13.9% E97G (GAG→GGG)  dtpD ← dipeptide and tripeptide permease D
RA 762,113 T→C 25.9% S198P (TCC→CCC)  sucB → dihydrolipoyltranssuccinase
RA 830,865 A→G 19.7% intergenic (‑222/‑7) ybiH ← / → rhlE DUF1956 domain‑containing tetR family putative transcriptional regulator/ATP‑dependent RNA helicase
RA 842,815 C→A 19.1% Q162K (CAA→AAA)  rlmF → 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent
RA 954,356 C→A 31.3% L37L (CTG→CTT focA ← formate channel
RA 1,027,203 T→G 6.8% T191P (ACA→CCA)  yccT ← UPF0319 family protein
RA 1,058,486 T→C 23.0% S135P (TCG→CCG)  torC → trimethylamine N‑oxide (TMAO) reductase I, cytochrome c‑type subunit
RA 1,074,669 C→G 15.2% A143G (GCG→GGG)  rutR → rut operon transcriptional repressor for
RA 1,132,071 T→C 10.1% L73P (CTC→CCC)  flgD → flagellar hook assembly protein
RA 1,196,305 C→T 100% R395C (CGT→TGT)  icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
RA 1,289,973 G→A 10.8% E243E (GAG→GAA rssA → putative patatin‑like family phospholipase
JC JC 1,293,032 IS1 (–) +8 bp 100% intergenic (‑110/‑488) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
RA 1,536,735 A→C 13.9% V192G (GTG→GGG)  narW ← nitrate reductase 2 (NRZ), delta subunit (assembly subunit)
MC JC 1,978,503 Δ776 bp 100% insB1insA insB1, insA
JC JC 1,979,486 IS5 (+) +4 bp 100% intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
RA 2,054,830 A→C 16.5% T396T (ACA→ACC shiA → shikimate transporter
RA 2,132,787 A→C 100% I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
RA 2,154,491 T→C 21.9% L159P (CTC→CCC)  mdtA → multidrug efflux system, subunit A
RA 2,169,668 A→C 15.6% intergenic (+57/+25) yegS → / ← gatR phosphatidylglycerol kinase, metal‑dependent/pseudogene, repressor for gat operon; interrupted by IS3; split galactitol utilization operon repressor, fragment 2; split galactitol utilization operon repressor, interrupted
RA 2,173,361 Δ2 bp 100% pseudogene (1‑2/442 nt) gatC ← pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA 2,209,353 T→G 14.2% pseudogene (254/2001 nt) yehQ → pseudogene
RA 2,507,677 T→C 13.5% E73G (GAG→GGG)  fryC ← putative enzyme IIC component of PTS
RA 2,509,880 A→C 14.2% D84A (GAC→GCC)  yfeO → putative ion channel protein
RA 2,561,294 T→C 13.5% intergenic (+396/‑74) yffL → / → yffM CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
RA 2,590,065 A→G 18.2% E824G (GAG→GGG)  acrD → aminoglycoside/multidrug efflux system
RA 2,732,138 A→C 13.6% V679G (GTG→GGG)  clpB ← protein disaggregation chaperone
RA 2,733,167 A→C 11.0% V336G (GTG→GGG)  clpB ← protein disaggregation chaperone
RA 2,739,684 T→C 18.3% E129G (GAG→GGG)  tyrA ← fused chorismate mutase T/prephenate dehydrogenase
RA 2,744,004 T→C 14.2% L127P (CTC→CCC)  yfiB → OM lipoprotein putative positive effector of YfiN activity
RA 2,795,328 T→G 14.9% V359G (GTA→GGA)  gabP → gamma‑aminobutyrate transporter
RA 2,796,104 C→T 15.0% S144F (TCT→TTT)  csiR → transcriptional repressor of csiD
RA 2,819,154 T→C 8.0% intergenic (‑8/+227) csrA ← / ← alaS pleiotropic regulatory protein for carbon source metabolism/alanyl‑tRNA synthetase
RA 2,820,820 G→A 7.9% L398L (CTG→TTG)  alaS ← alanyl‑tRNA synthetase
RA 2,822,002 T→C 6.8% S4G (AGC→GGC)  alaS ← alanyl‑tRNA synthetase
RA 2,935,069 A→G 15.4% S279G (AGC→GGC)  fucP → L‑fucose transporter
RA 2,959,174 A→C 13.1% G1085G (GGT→GGG recC ← exonuclease V (RecBCD complex), gamma chain
RA 2,969,479 T→G 19.4% intergenic (‑502/‑183) rppH ← / → mutH RNA pyrophosphohydrolase/methyl‑directed mismatch repair protein
RA 2,977,544 A→C 16.4% T316P (ACT→CCT)  galR → galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor
RA 3,027,731 A→G 18.3% E204G (GAG→GGG)  ghxQ → guanine/hypoxanthine permease, high affinity; guanine/hypoxanthine:H+ symporter
RA 3,066,865 A→T 8.8% Y103* (TAT→TAA ygfI ← putative DNA‑binding transcriptional regulator
RA 3,113,957 T→A 16.4% L132F (TTA→TTT pppA ← bifunctional prepilin leader peptidase/ methylase
RA 3,145,643 T→G 15.0% T207P (ACT→CCT)  hybO ← hydrogenase 2, small subunit
RA 3,265,360 T→C 17.2% G223G (GGA→GGG tdcB ← L‑threonine dehydratase, catabolic
RA 3,293,767 C→G 15.8% A123G (GCG→GGG)  lpoA → OM lipoprotein stimulator of MrcA transpeptidase
RA 3,329,773 A→G 16.6% S271G (AGC→GGC)  dacB → D‑alanyl‑D‑alanine carboxypeptidase
RA 3,373,350 A→G 17.9% L76P (CTC→CCC)  nanA ← N‑acetylneuraminate lyase
RA 3,373,358 C→T 12.3% K73K (AAG→AAA nanA ← N‑acetylneuraminate lyase
RA 3,479,689 G→A 15.8% L307F (CTC→TTC)  kefB ← potassium:proton antiporter
RA 3,489,862 A→G 15.5% S107P (TCC→CCC)  argD ← bifunctional acetylornithine aminotransferase and succinyldiaminopimelate aminotransferase
RA 3,523,993 A→G 14.6% S375G (AGT→GGT)  mrcA → penicillin‑binding protein 1a, murein transglycosylase and transpeptidase
JC 3,525,959 +GGATCA 44.8% coding (191/561 nt) nudE ← adenosine nucleotide hydrolase; Ap3A/Ap2A/ADP‑ribose/NADH hydrolase
RA 3,532,595 C→A 18.4% intergenic (‑156/‑223) yhgE ← / → pck DUF4153 family putative inner membrane protein/phosphoenolpyruvate carboxykinase [ATP]
RA 3,551,917 A→C 22.1% V186G (GTG→GGG)  malP ← maltodextrin phosphorylase
RA 3,560,455:1 +G 100% 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 3,686,539 T→C 14.0% S879G (AGC→GGC)  bcsC ← cellulose synthase subunit
MC JC 3,815,859 Δ82 bp 100% [rph][rph] [rph], [rph]
RA 3,875,521 T→C 18.7% A28A (GCT→GCC yidX → putative lipoprotein
RA 3,894,501 T→G 14.8% S207R (AGT→AGG yieE → phosphopantetheinyl transferase superfamily protein
RA 3,895,556 T→C 19.2% M352V (ATG→GTG)  adeP ← adenine permease, high affinity; adenine:H+ symporter
RA 3,966,914 A→C 14.2% S166S (TCA→TCC rho → transcription termination factor
JC 4,001,645 Δ5 bp 100% coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,017,526 T→C 11.3% L65P (CTC→CCC)  rmuC → DNA recombination protein
RA 4,087,251 T→G 19.3% C84G (TGC→GGC)  yiiG → DUF3829 family lipoprotein
RA 4,146,772 T→G 14.5% V172G (GTG→GGG)  pflC → putative [formate‑C‑acetyltransferase 2]‑activating enzyme; pyruvate formate‑lyase 1‑activating enzyme
RA 4,184,543 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,240,883 A→C 5.8% F458V (TTT→GTT)  xylE ← D‑xylose transporter
RA 4,241,829 T→A 12.9% L142F (TTA→TTT xylE ← D‑xylose transporter
RA 4,280,131 A→G 12.7% E51G (GAG→GGG)  yjcE → putative cation/proton antiporter
RA 4,280,577 A→G 22.9% S200G (AGC→GGC)  yjcE → putative cation/proton antiporter
RA 4,289,531 T→G 13.0% V96G (GTG→GGG)  nrfB → nitrite reductase, formate‑dependent, penta‑heme cytochrome c
RA 4,296,060 C→T 27.7% intergenic (+266/+376) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,380:1 +CG 100% intergenic (+586/+56) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,336,951 A→C 22.1% G27G (GGT→GGG adiC ← arginine:agmatine antiporter
RA 4,423,529 T→G 12.1% G228G (GGT→GGG ulaE → L‑xylulose 5‑phosphate 3‑epimerase
RA 4,446,969 T→G 17.6% V953G (GTG→GGG)  tamB → translocation and assembly module for autotransporter export, inner membrane subunit
RA 4,449,045 T→G 25.0% intergenic (+3/+77) chpB → / ← ppa toxin of the ChpB‑ChpS toxin‑antitoxin system/inorganic pyrophosphatase
RA 4,487,250 C→T 14.2% L345F (CTC→TTC)  lptF → lipopolysaccharide export ABC permease
RA 4,530,174 T→A 12.7% I24F (ATC→TTC)  sgcC ← putative PTS system EIIC permease component
RA 4,579,656 A→C 24.2% V62G (GTG→GGG)  symE ← toxic peptide regulated by antisense sRNA symR
RA 4,628,141 A→G 10.8% E276G (GAG→GGG)  nadR → trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 384787 385044 258 18 [14] [13] 18 yaiS/tauA putative PIG‑L family deacetylase/taurine ABC transporter periplasmic binding protein
* * ÷ NC_000913 584291 584589 299 18 [16] [16] 17 [appY] [appY]
* * ÷ NC_000913 1212036 1212633 598 17 [15] [14] 17 iraM/ycgX RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein
* * ÷ NC_000913 1544464 1545062 599 17 [15] [15] 17 [yddK]–[yddK] [yddK],[yddK]
* * ÷ NC_000913 2103927 2104162 236 18 [16] [14] 18 wbbK lipopolysaccharide biosynthesis protein
* * ÷ NC_000913 2469155 2469855 701 18 [10] [13] 17 gtrS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
* * ÷ NC_000913 3796978 3797746 769 17 [16] [16] 17 waaL O‑antigen ligase
* * ÷ NC_000913 4233769 4235416 1648 17 [15] [16] 18 [pgi] [pgi]
* * ÷ NC_000913 4374222 4374420 199 19 [16] [16] 22 [yjeJ] [yjeJ]
* * ÷ NC_000913 4542580 4542911 332 17 [16] [15] 18 [fimE] [fimE]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 279163 =NA (NA)51 (0.720) 3/438 NT 63.0% noncoding (768/768 nt) IS1 repeat region
?NC_000913 = 2760086 30 (0.420)coding (1102/1410 nt) yfjI CP4‑57 prophage; uncharacterized protein
* ? NC_000913 1207790 =9 (0.130)59 (0.900) 46/406 NT 82.3% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 17 (0.260)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12078058 (0.110)47 (0.720) 38/406 NT 79.4% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 17 (0.260)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)22 (0.320) 19/430 NT 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
* ? NC_000913 = 409433371 (1.010)4 (0.060) 3/432 NT 5.8% noncoding (18/402 nt) REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences
?NC_000913 = 4094466 59 (0.850)noncoding (151/402 nt) REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences