breseq  version 0.27.1  revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
RA 1,903 G→A E523K (GAA→AAA)  thrA → Bifunctional aspartokinase/homoserine dehydrogenase 1
RA 10,696 C→T A221T (GCC→ACC)  yaaW ← UPF0174 family protein
RA 23,501 C→T L371L (CTG→TTG)  ileS → isoleucyl‑tRNA synthetase
RA 31,683 C→T N289N (AAC→AAT)  carB → carbamoyl‑phosphate synthase large subunit
RA 42,108 G→A intergenic (‑177/‑295) caiT ← / → fixA putative transporter/anaerobic carnitine reduction putative electron transfer flavoprotein subunit
RA 59,968 C→T V127I (GTC→ATC)  rluA ← dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent
RA 76,249 G→A Q351* (CAA→TAA)  sgrR ← transcriptional DNA‑binding transcriptional activator of sgrS sRNA
RA 88,571 G→A V182M (GTG→ATG)  cra → transcriptional repressor‑activator for carbon metabolism
RA 113,695 G→A W84* (TGG→TGA)  guaC → GMP reductase
RA 156,068 A→G V45A (GTA→GCA)  yadV ← putative periplasmic pilin chaperone
RA 157,585 C→T D50N (GAT→AAT)  folK ← 2‑amino‑4‑hydroxy‑6‑hydroxymethyldihyropteridine pyrophosphokinase
MC JC 257,908 Δ776 bp [crl] [crl]
RA 276,899 G→A G62E (GGG→GAG)  mmuM → CP4‑6 prophage; S‑methylmethionine:homocysteine methyltransferase
RA 281,291 G→A I231I (ATC→ATT)  yagA ← CP4‑6 prophage; putative DNA‑binding transcriptional regulator
RA 283,338 G→A M46I (ATG→ATA)  yagF → CP4‑6 prophage; dehydratase family protein
RA 284,535 T→G A445A (GCT→GCG)  yagF → CP4‑6 prophage; dehydratase family protein
RA 286,569 G→A S392N (AGC→AAC)  yagG → CP4‑6 prophage; putative sugar transporter
RA 290,175 G→A T44I (ACC→ATC)  argF ← ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage
RA 292,433 G→A F172F (TTC→TTT)  yagK ← CP4‑6 prophage; conserved protein
JC JC 295,082 IS5 (–) +4 bp intergenic (‑283/+54) yagM ← / ← yagN CP4‑6 prophage; uncharacterized protein/CP4‑6 prophage; uncharacterized protein
RA 298,441 G→A R96C (CGC→TGC)  paoD ← moco insertion factor for PaoABC aldehyde oxidoreductase
RA 303,541 G→A R184K (AGA→AAA)  yagU → DUF1440 family inner membrane acid resistance protein
RA 306,023 G→A T265T (ACC→ACT)  ecpD ← polymerized tip adhesin of ECP fibers
RA 311,717 G→A intergenic (‑381/‑395) ecpR ← / → ykgL putative transcriptional regulator for the ecp operon/uncharacterized protein
RA 312,865 G→A intergenic (‑88/+276) ykgM ← / ← ykgR 50S ribosomal protein L31 type B; alternative zinc‑limitation L31 protein/uncharacterized protein
RA 313,543 G→A intergenic (‑301/+173) ykgR ← / ← ykgP uncharacterized protein/pseudogene, oxidoreductase family
RA 317,788 C→T A178T (GCG→ACG)  rclC ← reactive chlorine species (RCS) stress resistance inner membrane protein
RA 325,394 G→A intergenic (‑30/+183) ykgH ← / ← betA putative inner membrane protein/choline dehydrogenase, a flavoprotein
RA 327,999 G→A S245S (TCC→TCT)  betB ← betaine aldehyde dehydrogenase, NAD‑dependent
RA 331,879 G→A intergenic (+383/‑492) betT → / → yahA choline transporter of high affinity/c‑di‑GMP‑specific phosphodiesterase
RA 338,656 G→A C111Y (TGC→TAC)  yahG → DUF1116 family protein
RA 340,202 G→A S13N (AGC→AAC)  yahI → carbamate kinase‑like protein
RA 340,248 G→A E28E (GAG→GAA)  yahI → carbamate kinase‑like protein
RA 343,523 G→A A214T (GCA→ACA)  yahK → broad specificity NADPH‑dependent aldehyde reductase, Zn‑containing
RA 349,013 G→A G111E (GGA→GAA)  prpB → 2‑methylisocitrate lyase
RA 358,484 G→A S69S (AGC→AGT)  cynR ← transcriptional activator of cyn operon; autorepressor
RA 358,962 G→A G55D (GGC→GAC)  cynT → carbonic anhydrase
RA 362,730 G→A G150G (GGC→GGT)  lacY ← lactose permease
RA 365,307 G→A F333F (TTC→TTT)  lacZ ← beta‑D‑galactosidase
RA 367,812 G→A G203G (GGC→GGT)  mhpR ← mhp operon transcriptional activator
RA 377,450 T→A intergenic (+139/+85) yaiL → / ← frmB DUF2058 family protein/S‑formylglutathione hydrolase
RA 377,474 C→T intergenic (+163/+61) yaiL → / ← frmB DUF2058 family protein/S‑formylglutathione hydrolase
RA 377,478 C→T intergenic (+167/+57) yaiL → / ← frmB DUF2058 family protein/S‑formylglutathione hydrolase
RA 377,492 G→A intergenic (+181/+43) yaiL → / ← frmB DUF2058 family protein/S‑formylglutathione hydrolase
RA 390,087 G→A intergenic (‑360/‑164) hemB ← / → yaiT 5‑aminolevulinate dehydratase (porphobilinogen synthase)/pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
RA 466,148 G→A P389S (CCA→TCA)  ybaE ← putative ABC transporter periplasmic binding protein
RA 469,271 G→A G134E (GGG→GAG)  mdlA → putative multidrug ABC transporter ATPase
RA 480,295 2 bp→AA coding (13‑14/219 nt) hha ← modulator of gene expression, with H‑NS
RA 502,232 G→A T336I (ACC→ATC)  ybaL ← inner membrane putative NAD(P)‑binding transporter
RA 662,269 C→T D4N (GAT→AAT)  lipB ← octanoyltransferase; octanoyl‑[ACP]:protein N‑octanoyltransferase
RA 784,677 G→A A49A (GCC→GCT)  zitB ← zinc efflux system
RA 881,531 A→T I269F (ATC→TTC)  dacC → D‑alanyl‑D‑alanine carboxypeptidase; penicillin‑binding protein 6a
JC JC 1,091,173 IS5 (–) +4 bp coding (1114‑1117/2424 nt) pgaA ← biofilm adhesin polysaccharide PGA secretin; OM porin; poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein
RA 1,147,196 C→T P135S (CCG→TCG)  yceD → DUF177 family protein
RA 1,148,873 A→C I39L (ATC→CTC)  fabH → 3‑oxoacyl‑[acyl‑carrier‑protein] synthase III
RA 1,156,913 G→A G46D (GGT→GAT)  ycfH → putative DNase
RA 1,169,836 A→G L180P (CTG→CCG)  ldtC ← L,D‑transpeptidase linking Lpp to murein
RA 1,189,980 A→G T156T (ACT→ACC)  phoP ← response regulator in two‑component regulatory system with PhoQ
RA 1,190,776 T→G K404T (AAG→ACG)  purB ← adenylosuccinate lyase
RA 1,191,644 C→T E115K (GAA→AAA)  purB ← adenylosuccinate lyase
JC JC 1,199,869 IS3 (+) +3 bp coding (936‑938/1128 nt) intE ← e14 prophage; putative integrase
RA 1,282,627 C→T Q922* (CAG→TAG)  narG → nitrate reductase 1, alpha subunit
RA 1,290,669 G→A W143* (TGG→TAG)  rssB → PcnB‑degradosome interaction factor; response regulator
RA 1,297,496 G→A A209V (GCT→GTT)  adhE ← fused acetaldehyde‑CoA dehydrogenase/iron‑dependent alcohol dehydrogenase/pyruvate‑formate lyase deactivase
MC JC 1,299,499 Δ1,199 bp intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
RA 1,301,992 A→T N271Y (AAT→TAT)  oppA → oligopeptide ABC transporter periplasmic binding protein
RA 1,306,736 T→G S325A (TCC→GCC)  oppF → oligopeptide ABC transporter ATPase
JC JC 1,308,693 IS1 (–) +9 bp intergenic (‑48/‑87) clsA ← / → yciY cardiolipin synthase 1/uncharacterized protein
RA 1,311,610 2 bp→AG coding (522‑523/720 nt) tonB → membrane spanning protein in TonB‑ExbB‑ExbD transport complex
RA 1,322,759 G→A A63V (GCT→GTT)  trpE ← component I of anthranilate synthase
RA 1,337,394 A→G S522G (AGC→GGC)  acnA → aconitate hydratase 1; aconitase A
RA 1,358,859 T→C Y110C (TAT→TGT)  puuP ← putrescine importer
RA 1,384,652 A→G D179G (GAC→GGC)  ycjX → DUF463 family protein, puatative P‑loop NTPase
JC JC 1,399,590 IS5 (+) +4 bp intergenic (‑64/+128) fnr ← / ← ogt oxygen‑sensing anaerobic growth regulon transcriptional regulator FNR; autorepressor/O‑6‑alkylguanine‑DNA:cysteine‑protein methyltransferase
RA 1,401,893 G→A Q455* (CAA→TAA)  abgB ← p‑aminobenzoyl‑glutamate hydrolase, B subunit
RA 1,453,992 G→A W22* (TGG→TGA)  paaA → ring 1,2‑phenylacetyl‑CoA epoxidase subunit
RA 1,597,364 T→C pseudogene (624/3861 nt) yneO ← pseudogene, AidA homolog
RA 1,643,679 A→T L209Q (CTG→CAG)  ydfU ← Qin prophage; uncharacterized protein
RA 1,652,331 T→C pseudogene (781/1158 nt) intQ → pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related
RA 1,776,100 G→A E172K (GAA→AAA)  ydiF → putative acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit/beta subunit
RA 1,894,839 T→C L12P (CTC→CCC)  pabB → aminodeoxychorismate synthase, subunit I
RA 1,907,411 T→G K9Q (AAG→CAG)  cspC ← stress protein, member of the CspA‑family
JC JC 1,909,925 IS5 (+) +4 bp coding (172‑175/792 nt) kdgR ← KDG regulon transcriptional repressor
RA 1,955,010 G→A D666D (GAC→GAT)  torZ ← trimethylamine N‑oxide reductase system III, catalytic subunit
MC JC 1,978,503 Δ776 bp insB1–insA insB1, insA
RA 1,994,637 A→G Y24H (TAC→CAC)  uvrC ← excinuclease UvrABC, endonuclease subunit
RA 2,040,433 C→A A319D (GCC→GAC)  yedY → membrane‑anchored, periplasmic TMAO, DMSO reductase
RA 2,041,411 G→A G13S (GGT→AGT)  zinT → zinc and cadmium binding protein, periplasmic
RA 2,046,506 G→T V523V (GTG→GTT)  yeeJ → putative adhesin
RA 2,085,319 G→A A69A (GCC→GCT)  yeeE ← UPF0394 family inner membrane protein
RA 2,086,634 G→A A143A (GCC→GCT)  plaP ← putrescine importer, low affinity
RA 2,103,891 G→A P207S (CCA→TCA)  wbbK ← lipopolysaccharide biosynthesis protein
RA 2,111,259 Δ1 bp coding (718/900 nt) rfbD ← dTDP‑L‑rhamnose synthase, NAD(P)‑dependent dTDP‑4‑dehydrorhamnose reductase subunit
RA 2,122,908 G→A I24I (ATC→ATT)  cpsG ← phosphomannomutase
RA 2,134,498 G→A V385V (GTC→GTT)  wzc ← colanic acid production tyrosine‑protein kinase; autokinase; Ugd phosphorylase
RA 2,137,543 G→A intergenic (‑300/‑359) wza ← / → yegH colanic acid export protein; outer membrane auxillary lipoprotein/inner membrane protein
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 2,173,448 C→T pseudogene (831/914 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
JC JC 2,174,359 IS5 (+) +4 bp coding (205‑208/285 nt) gatB ← galactitol‑specific enzyme IIB component of PTS
RA 2,188,087 T→C T110A (ACG→GCG)  yehA ← putative fimbrial‑like adhesin protein
RA 2,329,209 A→G W197R (TGG→CGG)  yfaQ ← tandem DUF2300 domain protein, putative host defense protein
RA 2,339,162 C→T D87N (GAC→AAC)  gyrA ← DNA gyrase (type II topoisomerase), subunit A
RA 2,384,808 C→T K305K (AAG→AAA)  yfbK ← Von Willebrand factor domain putative lipoprotein
RA 2,410,419 G→A L312L (CTG→TTG)  yfbS ← putative transporter
RA 2,484,827 C→T L152F (CTT→TTT)  evgS → hybrid sensory histidine kinase in two‑component regulatory system with EvgA
RA 2,510,609 C→T P327L (CCG→CTG)  yfeO → putative ion channel protein
RA 2,587,112 C→T A461V (GCA→GTA)  narQ → sensory histidine kinase in two‑component regulatory system with NarP
RA 2,598,893 C→T G290S (GGT→AGT)  dapA ← dihydrodipicolinate synthase
RA 2,732,992 G→A I394I (ATC→ATT)  clpB ← protein disaggregation chaperone
RA 2,804,133 C→T S211F (TCT→TTT)  nrdF → ribonucleoside‑diphosphate reductase 2, beta subunit, ferritin‑like protein
RA 2,814,459 Δ1 bp coding (275/516 nt) luxS ← S‑ribosylhomocysteine lyase
RA 2,814,461 C→T L91L (CTG→CTA)  luxS ← S‑ribosylhomocysteine lyase
RA 2,817,197 G→A R103C (CGC→TGC)  yqaB ← fructose‑1‑P and 6‑phosphogluconate phosphatase
RA 2,823,288 C→T G161D (GGC→GAC)  recA ← DNA recombination and repair protein; ssDNA‑dependent ATPase; synaptase; ssDNA and dsDNA binding protein; ATP‑dependent homologous DNA strand exchanger; recombinase A; LexA autocleavage cofactor
RA 2,867,454 T→A Q33L (CAG→CTG)  rpoS ← RNA polymerase, sigma S (sigma 38) factor
RA 2,871,153 T→G N51T (AAC→ACC)  truD ← tRNA(Glu) pseudouridine(13) synthase
RA 2,926,543 2 bp→TT coding (236‑237/1365 nt) ygdH → UPF0717 family protein
RA 2,926,772 C→A G155G (GGC→GGA)  ygdH → UPF0717 family protein
RA 3,028,546 G→A A156V (GCC→GTC)  ygfS ← putative 4Fe‑4S ferredoxin‑type oxidoreductase subunit
RA 3,050,472 G→A L66L (CTG→TTG)  gcvT ← aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex
RA 3,061,916 C→T A356V (GCC→GTC)  scpA → methylmalonyl‑CoA mutase
RA 3,065,449 G→A L216L (TTG→TTA)  scpC → propionyl‑CoA:succinate CoA transferase
RA 3,065,861 G→A V354I (GTC→ATC)  scpC → propionyl‑CoA:succinate CoA transferase
RA 3,089,260 T→C V326A (GTG→GCG)  galP → D‑galactose transporter
RA 3,090,968 G→A E208K (GAG→AAG)  endA → DNA‑specific endonuclease I
RA 3,104,887 G→A S152N (AGC→AAC)  mltC → membrane‑bound lytic murein transglycosylase C
RA 3,120,786 G→A T165I (ACT→ATT)  glcA ← glycolate transporter
RA 3,121,033 T→C I83V (ATT→GTT)  glcA ← glycolate transporter
RA 3,127,981 G→A P14L (CCC→CTC)  glcD ← glycolate oxidase subunit, FAD‑linked
RA 3,130,161 G→A intergenic (‑18/‑17) yghO ← / → insH1 pseudogene, IS‑interrupted/IS5 transposase and trans‑activator
RA 3,132,077 G→A A111V (GCG→GTG)  yghQ ← putative inner membrane polysaccharide flippase
RA 3,133,175 G→A T13I (ACC→ATC)  yghR ← putative ATP‑binding protein
RA 3,134,263 G→A A45T (GCC→ACC)  yghT → putative ATP‑binding protein
RA 3,145,944 G→A L106L (CTC→CTT)  hybO ← hydrogenase 2, small subunit
RA 3,150,316 G→A E219K (GAG→AAG)  yghA → putative oxidoreductase
RA 3,162,216 G→A Q152* (CAG→TAG)  ftsP ← septal ring component that protects the divisome from stress; multicopy suppressor of ftsI(Ts)
RA 3,176,625 G→A S70F (TCC→TTC)  cpdA ← 3',5' cAMP phosphodiesterase
RA 3,179,383 G→A K423K (AAG→AAA)  tolC → transport channel
RA 3,193,351 G→A G163E (GGG→GAG)  yqiK → PHB family membrane protein, function unknown
RA 3,204,617 G→A intergenic (‑28/‑77) folB ← / → plsY dihydroneopterin aldolase and dihydroneopterin triphosphate 2'‑epimerase/putative glycerol‑3‑phosphate acyltransferase
RA 3,207,549 Δ1 bp coding (179/606 nt) ttdB → L‑tartrate dehydratase, beta subunit
RA 3,219,128 G→A intergenic (‑52/‑366) aer ← / → patA fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component/putrescine:2‑oxoglutaric acid aminotransferase, PLP‑dependent
RA 3,224,895 C→T L755L (CTG→TTG)  ebgA → evolved beta‑D‑galactosidase, alpha subunit
RA 3,227,339 C→T T369I (ACC→ATC)  ygjI → putative transporter
RA 3,240,423 C→T G160G (GGC→GGT)  sstT → sodium:serine/threonine symporter
RA 3,256,157 C→T Q165Q (CAG→CAA)  yhaM ← putative L‑serine dehydratase alpha chain
RA 3,259,283 G→A H123Y (CAT→TAT)  tdcG ← L‑serine dehydratase 3, anaerobic
RA 3,270,497 C→T intergenic (+895/+128) yhaC → / ← garK pentapetide repeats‑related protein/glycerate kinase I
RA 3,275,902 A→T E207D (GAA→GAT)  garD → D‑galactarate dehydrogenase
RA 3,292,312 C→T P324P (CCC→CCT)  yraK → putative fimbrial‑like adhesin protein
RA 3,304,647 T→C I391V (ATT→GTT)  mtr ← tryptophan transporter of high affinity
RA 3,329,743 G→T D261Y (GAT→TAT)  dacB → D‑alanyl‑D‑alanine carboxypeptidase
RA 3,388,041 T→G T50P (ACG→CCG)  aaeB ← p‑hydroxybenzoic acid efflux system component
RA 3,506,393 T→C D315G (GAC→GGC)  yhfT ← inner membrane protein
RA 3,524,184 C→T A438A (GCC→GCT)  mrcA → penicillin‑binding protein 1a, murein transglycosylase and transpeptidase
RA 3,558,291 C→T G8G (GGC→GGT)  rtcR → sigma 54‑dependent transcriptional regulator of rtcBA expression
RA 3,559,621 C→T P452S (CCC→TCC)  rtcR → sigma 54‑dependent transcriptional regulator of rtcBA expression
RA 3,560,119 A→G pseudogene (335/606 nt) glpR ← pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
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 3,579,050 G→A A199V (GCC→GTC)  yhhW ← quercetinase activity in vitro
RA 3,581,316 G→A G60E (GGA→GAA)  yhhY → aminoacyl nucleotide detoxifying acetyltransferase
RA 3,581,850 G→A intergenic (+224/‑13) yhhY → / → yhhZ aminoacyl nucleotide detoxifying acetyltransferase/putative Hcp1 family polymorphic toxin protein; putative colicin‑like DNase/tRNase activity
RA 3,585,517 G→A A436V (GCC→GTC)  ggt ← gamma‑glutamyltranspeptidase
RA 3,587,531 G→A L195F (CTC→TTC)  ugpQ ← glycerophosphodiester phosphodiesterase, cytosolic
RA 3,588,787 G→A P132S (CCG→TCG)  ugpC ← sn‑glycerol‑3‑phosphate ABC transporter ATPase
RA 3,589,956 G→A L24L (CTC→CTT)  ugpE ← sn‑glycerol‑3‑phosphate ABC transporter permease
RA 3,621,090 C→T R633R (CGC→CGT)  rhsB → Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
RA 3,647,677 C→T intergenic (+26/+28) gor → / ← dinQ glutathione oxidoreductase/UV‑inducible membrane toxin, DinQ‑AgrB type I toxin‑antitoxin system
RA 3,707,947 C→A intergenic (‑242/+669) dppA ← / ← proK dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro
RA 3,725,176 T→G E48A (GAG→GCG)  glyQ ← glycine tRNA synthetase, alpha subunit
RA 3,815,883 +C pseudogene (667/669 nt) rph ← ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
RA 3,827,026 C→T A606V (GCG→GTG)  recG → ATP‑dependent DNA helicase
RA 3,927,292 T→C D46D (GAT→GAC)  asnA → asparagine synthetase A
RA 3,937,909 G→A A206T (GCG→ACG)  rbsK → ribokinase
RA 3,937,997 G→A G235D (GGT→GAT)  rbsK → ribokinase
RA 3,938,441 Δ1 bp coding (215/993 nt) rbsR → transcriptional repressor of ribose metabolism
RA 3,941,874 C→T noncoding (67/1542 nt) rrsC → 16S ribosomal RNA of rrnC operon
RA 3,946,246 G→A noncoding (2543/2904 nt) rrlC → 23S ribosomal RNA of rrnC operon
RA 3,950,099 C→T intergenic (‑130/‑223) yifB ← / → ilvL magnesium chelatase family protein and putative transcriptional regulator/ilvG operon leader peptide
RA 3,956,003 G→A D225N (GAT→AAT)  ilvA → l‑threonine dehydratase, biosynthetic; also known as threonine deaminase
RA 3,966,598 G→A G61E (GGA→GAA)  rho → transcription termination factor
RA 4,084,932 G→T F297L (TTC→TTA)  fdoG ← formate dehydrogenase‑O, large subunit
RA 4,139,298 G→A A137A (GCC→GCT)  fsaB ← fructose‑6‑phosphate aldolase 2
RA 4,160,157 G→A L212L (CTG→TTG)  sthA ← pyridine nucleotide transhydrogenase, soluble
RA 4,175,827 C→T noncoding (74/76 nt) thrT → tRNA‑Thr
RA 4,178,883 C→T A2V (GCT→GTT)  rplA → 50S ribosomal subunit protein L1
RA 4,179,001 C→T S41S (AGC→AGT)  rplA → 50S ribosomal subunit protein L1
RA 4,185,777 C→T S143F (TCC→TTC)  rpoC → RNA polymerase, beta prime subunit
RA 4,193,177 C→T E134K (GAG→AAG)  thiF ← adenylyltransferase, modifies ThiS C‑terminus
RA 4,193,820 C→T G129R (GGA→AGA)  thiE ← thiamine phosphate synthase (thiamine phosphate pyrophosphorylase)
RA 4,219,752 C→T S386F (TCC→TTC)  aceK → isocitrate dehydrogenase kinase/phosphatase
RA 4,222,743 C→T intergenic (‑256/+61) arpA ← / ← iclR ankyrin repeat protein/transcriptional repressor
RA 4,223,638 T→C intergenic (‑10/‑190) iclR ← / → metH transcriptional repressor/homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA 4,224,483 C→T S219F (TCC→TTC)  metH → homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA 4,234,479 C→T A241V (GCG→GTG)  pgi → glucosephosphate isomerase
RA 4,249,684 C→T A44V (GCT→GTT)  malM → maltose regulon periplasmic protein
RA 4,265,668 C→T T452I (ACC→ATC)  dnaB → replicative DNA helicase
RA 4,269,449 C→T C12C (TGC→TGT)  aphA → acid phosphatase/phosphotransferase, class B, non‑specific
RA 4,271,130 C→T E914E (GAG→GAA)  uvrA ← ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC
RA 4,278,488 C→T P4S (CCA→TCA)  ghxP → guanine/hypoxanthine permease, high affinity; guanine/hypoxanthine:H+ symporter
RA 4,282,536 C→T Q180Q (CAG→CAA)  yjcF ← pentapeptide repeats protein
RA 4,284,077 C→T A276T (GCG→ACG)  actP ← acetate transporter
RA 4,286,033 C→T A447T (GCG→ACG)  acs ← acetyl‑CoA synthetase
RA 4,296,187 C→T intergenic (+393/+249) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,300 C→T intergenic (+506/+136) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,297,469 C→T G633D (GGC→GAC)  fdhF ← formate dehydrogenase‑H, selenopolypeptide subunit
RA 4,298,199 C→T A390T (GCA→ACA)  fdhF ← formate dehydrogenase‑H, selenopolypeptide subunit
RA 4,301,071 C→T A670T (GCA→ACA)  mdtO ← membrane translocase (MDR) of MdtNOP efflux pump, PET family
RA 4,303,755 C→T V119I (GTT→ATT)  mdtN ← membrane fusion protein of efflux pump
RA 4,311,337 C→T A236T (GCA→ACA)  alsB ← D‑allose ABC transporter periplasmic binding protein
RA 4,320,079 C→T Q195Q (CAG→CAA)  phnI ← ribophosphonate triphosphate synthase complex putative catalytic subunit
RA 4,320,785 C→T E155K (GAG→AAG)  phnH ← ribophosphonate triphosphate synthase subunit
RA 4,322,605 C→T pseudogene (210/372 nt) phnE ← defective phosphonate ABC transporter permease;transport; Transport of small molecules: Anions; membrane channel protein component of Pn transporter; membrane component of ABC superfamily
RA 4,325,644 C→T S33N (AGC→AAC)  yjdN ← metalloprotein superfamily protein
RA 4,325,837 C→T intergenic (‑96/+562) yjdN ← / ← yjdM metalloprotein superfamily protein/zinc‑ribbon family protein
RA 4,332,310 C→T G321G (GGG→GGA)  basS ← sensory histidine kinase in two‑component regulatory system with BasR
RA 4,337,864 C→T V22V (GTG→GTA)  adiY ← adi system transcriptional activator
RA 4,342,825 C→T N305N (AAC→AAT)  melA → alpha‑galactosidase, NAD(P)‑binding
RA 4,349,259 C→T intergenic (‑515/+56) dcuB ← / ← dcuR C4‑dicarboxylate transporter, anaerobic; DcuS co‑sensor/response regulator in two‑component regulatory system with DcuS
RA 4,351,519 C→T T48T (ACG→ACA)  dcuS ← sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration
RA 4,351,590 C→T V25I (GTC→ATC)  dcuS ← sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration
RA 4,359,909 C→T W41* (TGG→TGA)  cadB ← putative lysine/cadaverine transporter
RA 4,364,798 C→T G82D (GGC→GAC)  dsbD ← thiol:disulfide interchange protein and activator of DsbC
RA 4,366,668 C→T A36T (GCC→ACC)  dcuA ← C4‑dicarboxylate antiporter
RA 4,371,401 C→T A126V (GCT→GTT)  groL → Cpn60 chaperonin GroEL, large subunit of GroESL
RA 4,373,421 C→T A272T (GCG→ACG)  yjeJ ← uncharacterized protein
RA 4,376,844 C→T intergenic (+145/‑31) ecnB → / → sugE entericidin B membrane lipoprotein/multidrug efflux system protein
RA 4,380,469 C→T E17K (GAA→AAA)  frdB ← fumarate reductase (anaerobic), Fe‑S subunit
RA 4,388,120 C→T A417A (GCG→GCA)  mscM ← mechanosensitive channel protein, miniconductance
RA 4,389,838 C→T V175M (GTG→ATG)  psd ← phosphatidylserine decarboxylase
RA 4,401,607 C→T T312T (ACC→ACT)  hflX → GTPase, stimulated by 50S subunit binding; Mn(2+) homeostasis regulator
RA 4,403,010 C→T R325C (CGT→TGT)  hflK → modulator for HflB protease specific for phage lambda cII repressor
RA 4,407,045 C→T A131V (GCT→GTT)  rnr → exoribonuclease R, RNase R
RA 4,414,625 C→T R117R (CGC→CGT)  aidB → DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase
RA 4,418,862 C→T G255D (GGT→GAT)  ulaG ← L‑ascorbate 6‑phosphate lactonase
RA 4,426,929 C→T C165Y (TGC→TAC)  yjfZ ← uncharacterized protein
RA 4,433,459 C→T G189D (GGC→GAC)  qorB ← NAD(P)H:quinone oxidoreductase
RA 4,435,124 C→T W481* (TGG→TAG)  cpdB ← 2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase
RA 4,435,750 C→T G272G (GGG→GGA)  cpdB ← 2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase
RA 4,451,280 C→T P75S (CCG→TCG)  ytfR → putative sugar ABC transporter ATPase
RA 4,457,392 C→T E158E (GAG→GAA)  yjgA ← ribosome‑associated UPF0307 family protein
RA 4,482,901 C→T V313M (GTG→ATG)  valS ← valyl‑tRNA synthetase
RA 4,486,869 T→A L218M (TTG→ATG)  lptF → lipopolysaccharide export ABC permease
RA 4,487,022 C→T R269C (CGT→TGT)  lptF → lipopolysaccharide export ABC permease
RA 4,489,775 C→T V97M (GTG→ATG)  yjgR ← DUF853 family protein with NTPase fold
RA 4,494,499 C→T intergenic (‑93/‑124) idnD ← / → idnK L‑idonate 5‑dehydrogenase, NAD‑binding/D‑gluconate kinase, thermosensitive
RA 4,501,500 C→T L81L (CTG→TTG)  yjgZ → uncharacterized protein
RA 4,510,238 T→G intergenic (+105/+452) yjhV → / ← fecE pseudogene, KpLE2 phage‑like element/ferric citrate ABC transporter ATPase
RA 4,517,355 C→T Q121Q (CAG→CAA)  fecR ← anti‑sigma transmembrane signal transducer for ferric citrate transport; periplasmic FecA‑bound ferric citrate sensor and cytoplasmic FecI ECF sigma factor activator
RA 4,524,401 C→T G204S (GGC→AGC)  yjhH ← putative lyase/synthase
RA 4,524,596 C→T D139N (GAT→AAT)  yjhH ← putative lyase/synthase
RA 4,529,039 C→T G402D (GGT→GAT)  sgcC ← putative PTS system EIIC permease component
RA 4,530,797 C→T Q285Q (CAG→CAA)  sgcX ← putative endoglucanase with Zn‑dependent exopeptidase domain
RA 4,541,261 C→T A102V (GCT→GTT)  fimB → tyrosine recombinase/inversion of on/off regulator of fimA
JC JC 4,542,042 IS1 (+) +8 bp coding (6‑13/597 nt) fimE → tyrosine recombinase/inversion of on/off regulator of fimA
RA 4,553,671 C→T F257F (TTC→TTT)  uxuB → D‑mannonate oxidoreductase, NAD‑dependent
RA 4,564,385 C→T S102N (AGC→AAC)  yjiL ← putative ATPase, activator of (R)‑hydroxyglutaryl‑CoA dehydratase
RA 4,570,550 C→T S342N (AGC→AAC)  yjiR ← putative DNA‑binding transcriptional regulator/putative aminotransferase
RA 4,571,280 C→T E99K (GAG→AAG)  yjiR ← putative DNA‑binding transcriptional regulator/putative aminotransferase
RA 4,585,673 C→T W363* (TGG→TGA)  hsdR ← endonuclease R Type I restriction enzyme
RA 4,587,365 C→T S139S (AGC→AGT)  mrr → methylated adenine and cytosine restriction protein
RA 4,604,517 C→T L120L (CTG→TTG)  bglJ → bgl operon transcriptional activator
RA 4,630,295 C→T Q76Q (CAG→CAA)  ettA ← energy‑dependent translational throttle A
RA 4,636,925 G→C R77P (CGC→CCC)  creC → sensory histidine kinase in two‑component regulatory system with CreB or PhoB
RA 4,638,058 C→T L455L (CTG→TTG)  creC → sensory histidine kinase in two‑component regulatory system with CreB or PhoB
RA 4,638,240 G→A L21L (TTG→TTA)  creD → inner membrane protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 3423676–3424234 3424620–3424238 5–945 291 [290] [289] 291 [rrfD]–[rrlD] [rrfD], [rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 273955 =NA (NA)341 (0.810) 177/300 1.2 97.4% noncoding (1195/1195 nt) IS5 repeat region
?NC_000913 = 565828 9 (0.020)coding (151/1164 nt) intD DLP12 prophage; putative phage integrase
* ? NC_000913 = 275149NA (NA)372 (0.880) 196/300 0.3 95.9% noncoding (1/1195 nt) IS5 repeat region
?NC_000913 577188 = 16 (0.040)intergenic (‑363/‑210) nmpC/essD DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage/DLP12 prophage; putative phage lysis protein
* ? NC_000913 1207790 =110 (0.260)261 (0.690) 160/268 1.0 71.9% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 106 (0.280)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 1207805112 (0.270)273 (0.720) 166/268 0.7 72.6% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 106 (0.280)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 1978503 =NA (NA)361 (0.860) 196/300 0.3 NA noncoding (768/768 nt) IS1 repeat region
?NC_000913 = 4434636 NA (NA)coding (1930/1944 nt) cpdB 2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase
* ? NC_000913 = 255869813 (0.030)414 (1.040) 214/284 0.0 96.9% intergenic (‑19/‑160) eutB/intZ ethanolamine ammonia‑lyase, large subunit, heavy chain/CPZ‑55 prophage; putative phage integrase
?NC_000913 2565489 = 14 (0.040)coding (1396/1404 nt) eutA reactivating factor for ethanolamine ammonia lyase
* ? NC_000913 3583428 =NA (NA)405 (0.960) 212/300 0.0 90.8% noncoding (1/768 nt) IS1 repeat region
?NC_000913 4434629 = 41 (0.100)coding (1937/1944 nt) cpdB 2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase