breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
RA 37,255 A→C 27.1% G190G (GGT→GGG caiC ← putative crotonobetaine/carnitine‑CoA ligase
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 342,510 C→G 12.5% intergenic (+3/‑374) yahJ → / → yahK putative metallo‑dependent hydrolase domain deaminase/broad specificity NADPH‑dependent aldehyde reductase, Zn‑containing
RA 425,249 T→G 11.1% V80G (GTG→GGG)  queA → S‑adenosylmethionine:tRNA ribosyltransferase‑isomerase
RA 429,830 T→G 21.5% V109G (GTG→GGG)  secF → SecYEG protein translocase auxillary subunit
RA 458,189 A→G 15.9% D255G (GAT→GGT)  clpX → ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease
JC JC 458,790 IS186 (–) +6 bp :: Δ1 bp 47.6% intergenic (+90/‑93) clpX → / → lon ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La
RA 467,118 T→C 16.3% G65G (GGA→GGG ybaE ← putative ABC transporter periplasmic binding protein
RA 489,597 T→G 13.4% V1021G (GTG→GGG)  mscK → mechanosensitive channel protein, intermediate conductance, K+ regulated
RA 760,032 A→C 17.5% T443P (ACC→CCC)  sucA → 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding
RA 776,058 T→G 11.4% G70G (GGT→GGG tolR → membrane spanning protein in TolA‑TolQ‑TolR complex
RA 1,065,745 A→G 19.0% E54G (GAG→GGG)  agp → glucose‑1‑phosphatase/inositol phosphatase
RA 1,078,659 T→G 19.9% H75P (CAC→CCC)  putA ← fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase
JC 1,195,194 Δ3 bp 9.3% coding (72‑74/1251 nt) icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
RA 1,196,131 G→A 20.4% A337T (GCC→ACC)  icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
RA 1,196,305 C→T 46.8% R395C (CGT→TGT)  icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
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
MC JC 1,299,499 Δ1,199 bp 100% intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
RA 1,378,289 A→C 12.4% T136P (ACT→CCT)  ycjT → putative family 65 glycosyl hydrolase
RA 1,406,283 T→G 21.5% V102G (GTG→GGG)  smrA → DNA endonuclease
RA 1,425,607 G→T 9.6% L77L (CTG→CTT ynaK → Rac prophage; conserved protein
RA 1,530,890 A→T 6.0% pseudogene (305/738 nt) yncI → pseudogene
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 2,126,514 T→C 18.0% E226G (GAG→GGG)  wcaG ← bifunctional GDP‑fucose synthetase: GDP‑4‑dehydro‑6‑deoxy‑D‑mannose epimerase/ GDP‑4‑dehydro‑6‑L‑deoxygalactose reductase
RA 2,132,787 A→C 100% I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
RA 2,173,360 Δ1 bp 14.0% pseudogene (3/442 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 2,173,361 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 2,216,209 T→A 13.7% I90F (ATT→TTT)  yehW ← putative ABC transporter permease
RA 2,274,349 T→G 24.7% G57G (GGT→GGG yejB → microcin C ABC transporter permease
RA 2,525,307 G→T 13.4% E61* (GAA→TAA)  yfeN → putative outer membrane protein
RA 2,745,097 G→C 12.8% G81G (GGC→GGG trmD ← tRNA m(1)G37 methyltransferase, SAM‑dependent
RA 2,849,513 T→G 23.8% T113P (ACC→CCC)  hycB ← hydrogenase 3, Fe‑S subunit
RA 2,950,173 A→G 18.6% E311G (GAG→GGG)  argA → amino acid N‑acetyltransferase and inactive acetylglutamate kinase
RA 3,006,050 G→A 10.6% intergenic (‑264/‑212) ygeV ← / → ygeW putative sigma‑54‑interacting transcriptional activator/putative carbamoyltransferase
RA 3,090,130 A→C 17.4% T126P (ACC→CCC)  yggI → Zn‑dependent metalloprotease‑related protein
RA 3,206,438 G→A 19.4% intergenic (‑182/‑25) ttdR ← / → ttdA transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
RA 3,216,975 T→G 19.7% V66G (GTG→GGG)  yqjI → PadR family putative transcriptional regulator
RA 3,251,685 A→G 11.6% E221G (GAG→GGG)  yqjG → putative S‑transferase
RA 3,277,500 T→G 17.2% V55G (GTG→GGG)  yhaV → toxin of the SohB(PrlF)‑YhaV toxin‑antitoxin system
RA 3,289,059 G→A 12.4% L82L (CTG→CTA yraJ → putative outer membrane protein
RA 3,289,078 C→A 16.0% Q89K (CAG→AAG)  yraJ → putative outer membrane protein
RA 3,296,181 A→T 11.3% I125F (ATT→TTT)  diaA → DnaA initiator‑associating factor for replication initiation
RA 3,429,967 A→C 12.3% C19W (TGT→TGG yrdB ← DUF1488 family protein
RA 3,514,938 T→G 11.8% H41P (CAC→CCC)  rpe ← D‑ribulose‑5‑phosphate 3‑epimerase
RA 3,532,543 A→T 10.3% intergenic (‑104/‑275) yhgE ← / → pck DUF4153 family putative inner membrane protein/phosphoenolpyruvate carboxykinase [ATP]
RA 3,532,595 C→A 13.3% intergenic (‑156/‑223) yhgE ← / → pck DUF4153 family putative inner membrane protein/phosphoenolpyruvate carboxykinase [ATP]
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 3,662,719 T→G 12.9% V769G (GTG→GGG)  mdtF → anaerobic multidrug efflux transporter, ArcA‑regulated
RA 3,665,652 G→A 16.7% F53F (TTC→TTT gadX ← acid resistance regulon transcriptional activator; autoactivator
RA 3,665,655 T→A 10.6% V52V (GTA→GTT gadX ← acid resistance regulon transcriptional activator; autoactivator
RA 3,665,707 A→C 20.0% V35G (GTT→GGT)  gadX ← acid resistance regulon transcriptional activator; autoactivator
RA 3,755,363 A→C 11.1% G383G (GGT→GGG aldB ← aldehyde dehydrogenase B
RA 3,757,532 G→A 15.7% S99F (TCT→TTT)  yiaY ← L‑threonine dehydrogenase
MC JC 3,815,859 Δ82 bp 100% [rph][rph] [rph], [rph]
RA 3,820,994 A→C 9.1% G59G (GGT→GGG ligB ← DNA ligase, NAD(+)‑dependent
RA 3,860,856 A→C 11.5% T192P (ACT→CCT)  yidL → AraC family putative transcriptional regulator
RA 3,891,533 A→C 9.3% intergenic (+50/‑82) tnaB → / → mdtL tryptophan transporter of low affinity/multidrug efflux system protein
RA 3,895,216 T→A 12.9% *189K (TAA→AAA)  chrR → chromate reductase, Class I, flavoprotein
RA 3,996,586 T→G 12.9% G100G (GGT→GGG xerC → site‑specific tyrosine recombinase
JC 4,001,645 Δ5 bp 100% coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,019,672 A→C 6.6% T17P (ACC→CCC)  ubiJ → aerobic ubiquinone synthesis protein, SCP2 family protein
RA 4,029,690 T→G 10.7% T428P (ACT→CCT)  fadB ← fused 3‑hydroxybutyryl‑CoA epimerase/delta(3)‑cis‑delta(2)‑trans‑enoyl‑CoA isomerase/enoyl‑CoA hydratase/3‑hydroxyacyl‑CoA dehydrogenase
RA 4,065,580 T→A 13.0% T63S (ACC→TCC)  yihO ← putative sulphoquinovose importer
RA 4,065,596 C→A 15.0% L57L (CTG→CTT yihO ← putative sulphoquinovose importer
RA 4,065,604 T→A 14.6% I55F (ATC→TTC)  yihO ← putative sulphoquinovose importer
RA 4,096,769 T→C 11.0% E227G (GAG→GGG)  rhaB ← rhamnulokinase
RA 4,103,633 A→C 16.1% V448G (GTG→GGG)  cpxA ← sensory histidine kinase in two‑component regulatory system with CpxR
RA 4,150,396 T→A 10.7% intergenic (‑131/+51) eptC ← / ← ppc LPS heptose I phosphoethanolamine transferase/phosphoenolpyruvate carboxylase
RA 4,184,543 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,241,801 C→A 12.6% A152S (GCG→TCG)  xylE ← D‑xylose transporter
RA 4,241,994 T→G 14.8% S87S (TCA→TCC xylE ← D‑xylose transporter
RA 4,242,022 C→A 12.8% C78F (TGC→TTC)  xylE ← D‑xylose transporter
RA 4,296,060 C→T 26.0% 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 4,297,510 A→C 11.6% G619G (GGT→GGG fdhF ← formate dehydrogenase‑H, selenopolypeptide subunit
RA 4,300,840 A→G 9.6% L64P (CTC→CCC)  mdtP ← outer membrane factor of efflux pump
RA 4,449,045 T→G 26.8% intergenic (+3/+77) chpB → / ← ppa toxin of the ChpB‑ChpS toxin‑antitoxin system/inorganic pyrophosphatase
RA 4,594,550 C→G 20.8% R58P (CGC→CCC)  lgoT ← putative L‑galactonate:H+ symporter
RA 4,617,666 A→G 17.0% E115G (GAG→GGG)  deoC → 2‑deoxyribose‑5‑phosphate aldolase, NAD(P)‑linked
RA 4,621,986 C→G 10.1% A73G (GCG→GGG)  yjjJ → putative protein kinase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 4233732 4235409 1678 21 [20] [20] 23 pgi pgi

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 225739 =160 (1.820)8 (0.090)
+ACTTCA
3/420 NT 5.6% intergenic (+164/‑20) alaV/rrlH tRNA‑Ala/23S ribosomal RNA of rrnH operon
?NC_000913 = 4037483 117 (1.330)intergenic (+148/‑36) alaT/rrlA tRNA‑Ala/23S ribosomal RNA of rrnA operon
* ? NC_000913 279163 =NA (NA)57 (0.650) 4/432 NT 50.0% noncoding (768/768 nt) IS1 repeat region
?NC_000913 = 2760086 57 (0.650)coding (1102/1410 nt) yfjI CP4‑57 prophage; uncharacterized protein
* ? NC_000913 1207790 =11 (0.120)58 (0.710) 46/400 NT 81.0% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 17 (0.210)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780512 (0.140)69 (0.850) 42/400 NT 83.1% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 17 (0.210)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 1470336 =25 (0.280)31 (0.350) 3/432 NT 55.4% noncoding (1041/1221 nt) IS30 repeat region
?NC_000913 = 1979270 NA (NA)noncoding (1/768 nt) IS1 repeat region