breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
RA 278,744 +A intergenic (‑239/+75) PP_0224 ← / ← PP_0225 Monooxygenase, DszC family/sulfur compound ABC transporter ‑ ATP‑binding subunit
RA 307,866 +C intergenic (+881/‑988) PP_0252 → / → PP_0254 33 kDa chaperonin/conserved protein of unknown function
RA 336,125 +T coding (210/237 nt) PP_0278 → conserved protein of unknown function
RA 353,067 A→G intergenic (+34/+84) PP_0293 → / ← PP_0294 Imidazole glycerol phosphate synthase subunit HisF/choline / betaine / carnitine ABC transporter ‑ ATP binding subunit
RA 499,203 A→G intergenic (+47/‑249) PP_0410 → / → PP_0411 DNA‑binding response regulator UhpA/Polyamine ABC transporter, ATP‑binding protein
RA 1,070,248 +GA intergenic (+48/+94) PP_0927 → / ← PP_0928 aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger related‑protein
RA 1,126,647 +C intergenic (‑101/+48) PP_0987 ← / ← PP_0988 L‑serine dehydratase/glycine dehydrogenase
RA 1,419,549 +C intergenic (‑38/+98) PP_1242 ← / ← PP_1244 conserved protein of unknown function/conserved protein of unknown function
RA 1,499,480 2 bp→AC intergenic (+57/‑106) PP_1311 → / → PP_1312 Tryptophan‑‑tRNA ligase/putative enzyme with nucleoside triphosphate hydrolase domain
RA 1,499,498 1 bp→CG intergenic (+75/‑89) PP_1311 → / → PP_1312 Tryptophan‑‑tRNA ligase/putative enzyme with nucleoside triphosphate hydrolase domain
RA 1,499,508 +C intergenic (+85/‑79) PP_1311 → / → PP_1312 Tryptophan‑‑tRNA ligase/putative enzyme with nucleoside triphosphate hydrolase domain
RA 1,646,782 T→C S2P (TCC→CCC)  araC (Ppu opt) → L‑arabinonate dehydratase
RA 1,938,272 +C intergenic (‑107/+43) PP_1731 ← / ← PP_1732 23S rRNA (746) and tRNA (32) pseudouridine synthase/Cell division topological specificity factor
RA 2,964,155 C→T A428V (GCA→GTA)  PP_2589 → Aldehyde dehydrogenase family protein
RA 3,074,368 G→A S592N (AGC→AAC)  PP_2679 → quinoprotein ethanol dehydrogenase
RA 3,283,603 T→C Y179C (TAC→TGC)  xylE (Ppu opt) ←
RA 3,284,241 +T intergenic (‑103/‑105) xylE (Ppu opt) ← / → xylA (Ppu opt) –/–
RA 3,857,849 +G intergenic (‑72/+26) PP_3394 ← / ← PP_3395 putative 3‑hydroxy‑3‑methylglutaryl‑CoA lyase/Transcriptional regulator, LysR family
RA 3,963,303 T→C intergenic (‑123/+72) PP_3486 ← / ← PP_3487 putative cytochrome c/conserved exported protein of unknown function
RA 3,963,305 A→T intergenic (‑125/+70) PP_3486 ← / ← PP_3487 putative cytochrome c/conserved exported protein of unknown function
RA 4,598,174 2 bp→TC intergenic (+113/+101) PP_4061 → / ← PP_4063 conserved protein of unknown function/putative Long‑chain‑fatty‑acid‑CoA ligase
RA 4,598,179 +G intergenic (+118/+97) PP_4061 → / ← PP_4063 conserved protein of unknown function/putative Long‑chain‑fatty‑acid‑CoA ligase
RA 4,598,201 +C intergenic (+140/+75) PP_4061 → / ← PP_4063 conserved protein of unknown function/putative Long‑chain‑fatty‑acid‑CoA ligase
MC JC 4,725,879 Δ93 bp coding (1967‑2059/2115 nt) PP_4171 → conserved exported protein of unknown function
RA 4,752,955 (T)7→6 intergenic (+48/+705) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,752,960 T→G intergenic (+53/+700) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,752,963 2 bp→CT intergenic (+56/+696) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,753,373 A→C intergenic (+466/+287) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,753,375 C→G intergenic (+468/+285) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,753,378 C→T intergenic (+471/+282) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,753,380 2 bp→TG intergenic (+473/+279) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,753,383 A→G intergenic (+476/+277) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,753,387 3 bp→TGC intergenic (+480/+271) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,753,399 C→T intergenic (+492/+261) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,753,401 A→C intergenic (+494/+259) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,753,404 2 bp→GC intergenic (+497/+255) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,753,407 A→C intergenic (+500/+253) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,753,416 A→G intergenic (+509/+244) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,753,418 A→C intergenic (+511/+242) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,753,420 G→C intergenic (+513/+240) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,753,422 C→T intergenic (+515/+238) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,753,427 +T intergenic (+520/+233) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,753,433 C→G intergenic (+526/+227) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,753,436 C→T intergenic (+529/+224) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,753,438 C→G intergenic (+531/+222) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,753,440 A→C intergenic (+533/+220) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
RA 4,753,442 C→T intergenic (+535/+218) PP_4194 → / ← PP_4195 citrate synthase/putative oxidoreductase
JC 4,992,729 +GGC intergenic (‑24/+44) PP_4387 ← / ← PP_4388 conserved exported protein of unknown function/Flagellar hook protein FlgE
JC 5,566,684 +GCC intergenic (‑84/+87) PP_4887 ← / ← PP_4888 conserved protein of unknown function/putative methyl‑accepting chemotaxis transducer
RA 5,685,827 +G intergenic (+113/+27) PP_4980 → / ← PP_4981 ATP‑dependent RNA helicase/polyisoprene‑binding protein, acidic stress response factor
RA 5,685,829 G→C intergenic (+115/+25) PP_4980 → / ← PP_4981 ATP‑dependent RNA helicase/polyisoprene‑binding protein, acidic stress response factor
JC 5,692,491 +CGGG intergenic (‑133/+71) PP_4986 ← / ← PP_4987 Channel protein, hemolysin III family/putative Chemotaxis protein
RA 6,024,961 T→C intergenic (+90/+20) PP_5265 → / ← PP_5266 Xanthine phosphoribosyltransferase/putative acetyl‑CoA hydrolase family protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ JE3692‑4 171329–176339 176339 1–5011 43 [41] [40] 44 PP_16SA–[PP_5SA] PP_16SA,PP_23SA,[PP_5SA]
* * ÷ JE3692‑4 176607–181731 181731 1–5125 46 [40] [35] 43 PP_16SB–[PP_r01] PP_16SB,PP_23SB,[PP_r01]
* * ÷ JE3692‑4 1652986 1652986 1 79 [0] [0] 80 nahF (Ppu opt)/PP_1445 –/carbohydrate‑selective porin
* * ÷ JE3692‑4 4820304 4820346 43 67 [0] [40] 43 PP_4234/PP_4235 Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? JE3692‑4 = 65278273 (0.700)52 (0.630) 30/156 2.3 64.2% coding (1961/1962 nt) PP_0562 Methyl‑accepting chemotaxis protein CtpL
?JE3692‑4 = 4820303 0 (0.000)intergenic (‑268/‑287) PP_4234/PP_4235 Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2
* ? JE3692‑4 = 16449990 (0.000)78 (0.760) 58/194 0.7 100% intergenic (‑258/‑188) PP_1443/araE (Ppu opt) DNA‑binding, ATP‑dependent protease/–
?JE3692‑4 = 1652985 0 (0.000)intergenic (+174/+34) nahF (Ppu opt)/PP_1445 –/carbohydrate‑selective porin
* ? JE3692‑4 1644999 =0 (0.000)76 (0.740) 58/194 0.7 100% intergenic (‑258/‑188) PP_1443/araE (Ppu opt) DNA‑binding, ATP‑dependent protease/–
?JE3692‑4 1652987 = 0 (0.000)intergenic (+176/+32) nahF (Ppu opt)/PP_1445 –/carbohydrate‑selective porin
* ? JE3692‑4 = 494387932 (0.320)76 (0.770)
+CCTTC
59/176 0.4 70.9% coding (483/741 nt) PP_4341 RNA polymerase sigma 28 (sigma F) factor for class III flagellar operons
?JE3692‑4 4943880 = 32 (0.310)coding (482/741 nt) PP_4341 RNA polymerase sigma 28 (sigma F) factor for class III flagellar operons