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 ← / ← sctC Monooxygenase, DszC family/sulfur compound ABC transporter ‑ ATP‑binding subunit
RA 307,866 +C intergenic (+881/‑988) hslO → / → 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) hisF → / ← cbcV Imidazole glycerol phosphate synthase subunit HisF/choline / betaine / carnitine ABC transporter ‑ ATP binding subunit
RA 499,203 A→G intergenic (+47/‑249) uhpA → / → PP_0411 DNA‑binding response regulator UhpA/Polyamine ABC transporter, ATP‑binding protein
RA 1,070,248 +GA intergenic (+48/+94) aroP‑I → / ← PP_0928 aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger related‑protein
RA 1,126,647 +C intergenic (‑101/+48) tdcG‑II ← / ← gcvP‑I 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) trpS → / → zapE Tryptophan‑‑tRNA ligase/putative enzyme with nucleoside triphosphate hydrolase domain
RA 1,499,498 1 bp→CG intergenic (+75/‑89) trpS → / → zapE Tryptophan‑‑tRNA ligase/putative enzyme with nucleoside triphosphate hydrolase domain
RA 1,499,508 +C intergenic (+85/‑79) trpS → / → zapE Tryptophan‑‑tRNA ligase/putative enzyme with nucleoside triphosphate hydrolase domain
RA 1,932,640 +C intergenic (‑107/+43) rluA ← / ← minE 23S rRNA (746) and tRNA (32) pseudouridine synthase/Cell division topological specificity factor
RA 3,845,705 +G intergenic (‑72/+26) PP_3394 ← / ← PP_3395 putative 3‑hydroxy‑3‑methylglutaryl‑CoA lyase/Transcriptional regulator, LysR family
RA 3,951,159 T→C intergenic (‑123/+72) PP_3486 ← / ← PP_3487 putative cytochrome c/conserved exported protein of unknown function
RA 3,951,161 A→T intergenic (‑125/+70) PP_3486 ← / ← PP_3487 putative cytochrome c/conserved exported protein of unknown function
RA 4,586,030 2 bp→TC intergenic (+113/+101) PP_4061 → / ← PP_4063 conserved protein of unknown function/putative Long‑chain‑fatty‑acid‑CoA ligase
RA 4,586,035 +G intergenic (+118/+97) PP_4061 → / ← PP_4063 conserved protein of unknown function/putative Long‑chain‑fatty‑acid‑CoA ligase
RA 4,586,057 +C intergenic (+140/+75) PP_4061 → / ← PP_4063 conserved protein of unknown function/putative Long‑chain‑fatty‑acid‑CoA ligase
RA 4,740,811 (T)7→6 intergenic (+48/+705) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,740,816 T→G intergenic (+53/+700) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,740,819 2 bp→CT intergenic (+56/+696) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,229 A→C intergenic (+466/+287) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,231 C→G intergenic (+468/+285) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,234 C→T intergenic (+471/+282) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,236 2 bp→TG intergenic (+473/+279) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,239 A→G intergenic (+476/+277) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,243 3 bp→TGC intergenic (+480/+271) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,255 C→T intergenic (+492/+261) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,257 A→C intergenic (+494/+259) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,260 2 bp→GC intergenic (+497/+255) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,263 A→C intergenic (+500/+253) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,272 A→G intergenic (+509/+244) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,274 A→C intergenic (+511/+242) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,276 G→C intergenic (+513/+240) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,278 C→T intergenic (+515/+238) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,283 +T intergenic (+520/+233) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,289 C→G intergenic (+526/+227) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,292 C→T intergenic (+529/+224) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,294 C→G intergenic (+531/+222) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,296 A→C intergenic (+533/+220) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,298 C→T intergenic (+535/+218) gltA → / ← yeiW citrate synthase/putative oxidoreductase
JC 4,980,585 +GGC intergenic (‑24/+44) PP_4387 ← / ← flgE conserved exported protein of unknown function/Flagellar hook protein FlgE
JC 5,555,608 +GCC intergenic (‑84/+87) PP_4887 ← / ← PP_4888 conserved protein of unknown function/putative methyl‑accepting chemotaxis transducer
RA 5,674,751 +G intergenic (+113/+27) rhlE‑II → / ← yceI ATP‑dependent RNA helicase/polyisoprene‑binding protein, acidic stress response factor
RA 5,674,753 G→C intergenic (+115/+25) rhlE‑II → / ← yceI ATP‑dependent RNA helicase/polyisoprene‑binding protein, acidic stress response factor
JC 5,681,415 +CGGG intergenic (‑133/+71) PP_4986 ← / ← PP_4987 Channel protein, hemolysin III family/putative Chemotaxis protein
RA 6,013,885 T→C intergenic (+90/+20) xpt → / ← PP_5266 Xanthine phosphoribosyltransferase/putative acetyl‑CoA hydrolase family protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ AE015451 432344 432365 22 10 [3] [3] 5 PP_0354/PP_0355 CBS domain protein/Response regulator
* * ÷ AE015451 441181 441359 179 4 [3] [2] 4 bioF 8‑amino‑7‑oxononanoate synthase
* * ÷ AE015451 486311 486429 119 4 [2] [2] 4 [apaG] [apaG]
* * ÷ AE015451 726774 726878 105 4 [3] [2] 4 PP_0620/PP_0621 GntR family transcriptional regulator/conserved protein of unknown function
* * ÷ AE015451 747579 747655 77 4 [3] [2] 4 PP_0638/PP_5448 transposase/conserved protein of unknown function
* * ÷ AE015451 790210 790338 129 4 [3] [2] 4 PP_0676 putative Transcription elongation factor
* * ÷ AE015451 926424 926527 104 4 [3] [3] 4 PP_0805 Outer membrane efflux protein
* * ÷ AE015451 965605 965676 72 4 [3] [3] 7 ptxC putative phosphonate transport system permease protein PtxC
* * ÷ AE015451 968779 968815 37 4 [2] [3] 5 PP_0831/PP_t68 hypothetical protein/tRNA‑Leu
* * ÷ AE015451 1156204 1156282 79 4 [2] [2] 8 PP_1013 Sensor histidine kinase
* * ÷ AE015451 1348660 1348748 89 4 [3] [3] 4 galP‑I/PP_1174 porin‑like protein/conserved protein of unknown function
* * ÷ AE015451 1367572 1367798 227 5 [3] [2] 4 PP_1193 conserved membrane protein of unknown function
* * ÷ AE015451 1421780 1422001 222 4 [3] [2] 9 PP_1246 conserved exported protein of unknown function
* * ÷ AE015451 1544307 1544427 121 5 [3] [2] 4 mdfA putative multidrug efflux MFS transporter
* * ÷ AE015451 1637426 1637550 125 4 [2] [3] 5 PP_1437 Heavy metal sensor histidine kinase
* * ÷ AE015451 1644725 1644826 102 4 [3] [3] 4 [lon‑I] [lon‑I]
* * ÷ AE015451 1664506 1664590 85 5 [2] [3] 5 yhjE/PP_1459 putative inner membrane metabolite transport protein YhjE/CBS domain protein
* * ÷ AE015451 1691059 1691251 193 4 [2] [3] 4 PP_1487 conserved protein of unknown function
* * ÷ AE015451 1907203 1907303 101 4 [3] [3] 4 PP_1707 D‑isomer specific 2‑hydroxyacid dehydrogenase family protein
* * ÷ AE015451 2027322 2027481 160 4 [2] [1] 5 wbpL Glycosyl transferase WbpL
* * ÷ AE015451 2029898 2030014 117 5 [3] [2] 4 wbpM Polysaccharide biosynthesis protein
* * ÷ AE015451 2038239 2038385 147 5 [3] [3] 4 [rffE] [rffE]
* * ÷ AE015451 2039509 2039668 160 4 [3] [3] 4 [PP_1812] [PP_1812]
* * ÷ AE015451 2053476 2053596 121 4 [2] [3] 4 PP_1828 conserved protein of unknown function
* * ÷ AE015451 2073369 2073477 109 5 [3] [3] 11 [PP_1847] [PP_1847]
* * ÷ AE015451 2083885 2083995 111 4 [3] [3] 4 PP_1862 conserved membrane protein of unknown function
* * ÷ AE015451 2095205 2095250 46 4 [2] [2] 5 htpX/alaA Protease HtpX/glutamate‑pyruvate aminotransferase
* * ÷ AE015451 2142378 2142467 90 5 [3] [3] 5 PP_1897 DNA internalization‑related competence protein ComEC/Rec2
* * ÷ AE015451 2388272 2388337 66 4 [2] [3] 5 pyrD/rmf Dihydroorotate dehydrogenase (quinone)/ribosome modulation factor
* * ÷ AE015451 2478389 2478515 127 4 [2] [3] 4 PP_2172 conserved exported protein of unknown function
* * ÷ AE015451 2563975 2564017 43 5 [3] [0] 4 PP_2248 putative transporter
* * ÷ AE015451 2569413 2569605 193 5 [2] [2] 4 [PP_2252] [PP_2252]
* * ÷ AE015451 2865424 2865506 83 4 [2] [3] 4 gllP/glllA porin‑like protein/gallate dioxygenase
* * ÷ AE015451 2960765 2961011 247 4 [3] [3] 4 PP_2590 Outer membrane ferric siderophore receptor
* * ÷ AE015451 2975872 2975997 126 5 [3] [3] 4 ligC putative 4‑carboxy‑2‑hydroxymuconate‑6‑semialdehyde dehydrogenase
* * ÷ AE015451 2997207 2997259 53 4 [3] [2] 4 PP_2621 conserved protein of unknown function
* * ÷ AE015451 3157723 3157850 128 4 [2] [3] 4 PP_2773/opuA conserved protein of unknown function/glycine betaine ABC transporter, ATPase/permease fusion protein
* * ÷ AE015451 3178888 3178931 44 4 [1] [1] 5 PP_2790 Sigma‑54 dependent sensory box protein
* * ÷ AE015451 3276157 3276200 44 4 [3] [3] 4 PP_2874 conserved protein of unknown function
* * ÷ AE015451 3287123 3287265 143 5 [3] [3] 4 [PP_2889] [PP_2889]
* * ÷ AE015451 3443466 3443610 145 4 [3] [2] 5 PP_3062 putative Pyocin R2_PP, tail length determination protein
* * ÷ AE015451 3461014 3461091 78 4 [3] [2] 4 PP_3076 putative ABC transporter permease protein
* * ÷ AE015451 3579963 3580041 79 4 [1] [1] 4 benR BenABC operon transcriptional activator
* * ÷ AE015451 3839772 3839921 150 4 [3] [2] 4 PP_3389 conserved membrane protein of unknown function
* * ÷ AE015451 3848874 3848917 44 4 [0] [1] 5 PP_3397 conserved exported protein of unknown function
* * ÷ AE015451 3852871 3852972 102 6 [2] [3] 5 alkB alpha‑ketoglutarate‑ and Fe(II)‑dependent dioxygenase
* * ÷ AE015451 3872787 3872826 40 5 [1] [3] 5 PP_3421 Sensor histidine kinase
* * ÷ AE015451 3929687 3929892 206 4 [2] [1] 4 [PP_3464]–[PP_5603] [PP_3464],[PP_5603]
* * ÷ AE015451 3975746 3975967 222 4 [3] [3] 4 [PP_3505]–[PP_3506] [PP_3505],[PP_3506]
* * ÷ AE015451 3985633 3985742 110 5 [0] [3] 4 [oplB] [oplB]
* * ÷ AE015451 4515353 4515502 150 4 [2] [3] 4 [aat] [aat]
* * ÷ AE015451 4648211 4648305 95 5 [3] [3] 4 PP_4112 Sulphate transporter
* * ÷ AE015451 4705297 4705365 69 4 [2] [3] 4 kdpF/PP_4162 potassium‑transporting ATPase F/conserved membrane protein of unknown function
* * ÷ AE015451 4805264 4805351 88 4 [3] [3] 7 PP_4234 Aldehyde oxidase and xanthine dehydrogenase
* * ÷ AE015451 4839237 4839336 100 4 [2] [2] 4 ccoP‑I/PP_4254 cytochrome c oxidase subunit, cbb3‑type/conserved protein of unknown function
* * ÷ AE015451 5168109 5168200 92 4 [2] [3] 4 hrpA/PP_4547 ATP‑dependent helicase HrpA/putative Glutamine synthetase
* * ÷ AE015451 5291046 5291112 67 4 [3] [3] 4 PP_4664 Transcriptional regulator, LysR family
* * ÷ AE015451 5343554 5343613 60 5 [3] [3] 4 pgi‑II glucose‑6‑phosphate isomerase
* * ÷ AE015451 5389437 5389568 132 4 [2] [3] 4 dld2/PP_4738 D‑lactate dehydrogenase/conserved exported protein of unknown function
* * ÷ AE015451 5401503 5401516 14 5 [0] [2] 4 PP_4743/PP_4745 conserved protein of unknown function/transposase
* * ÷ AE015451 5660620 5660662 43 4 [1] [1] 4 ligB DNA ligase B
* * ÷ AE015451 5696601 5696757 157 8 [3] [2] 4 pyrC'/hslV dihydroorotase‑like protein/peptidase component of the ATP‑dependent HslVU protease
* * ÷ AE015451 5812277 5812372 96 4 [3] [2] 4 priA primosome assembly protein
* * ÷ AE015451 5812409 5812502 94 4 [2] [3] 4 priA primosome assembly protein
* * ÷ AE015451 5816950 5817153 204 4 [3] [3] 5 pilT twitching motility protein
* * ÷ AE015451 5835165 5835279 115 5 [3] [3] 4 [PP_5113]–[PP_5114] [PP_5113],[PP_5114]
* * ÷ AE015451 5858373 5858471 99 4 [2] [3] 4 PP_5134 conserved protein of unknown function
* * ÷ AE015451 6005849 6005924 76 5 [3] [2] 4 ydcJ metalloprotein, putative enzyme
* * ÷ AE015451 6008612 6008748 137 4 [0] [3] 4 norM Probable multidrug resistance protein NorM

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? AE015451 1737987 =20 (0.890)4 (0.200) 3/282 2.4 21.7% coding (32/348 nt) yffB putative glutathione‑dependent thiol reductase
?AE015451 = 1777401 11 (0.550)intergenic (+135/+157) PP_5476/PP_1585 conserved protein of unknown function/putative Antidote protein
* ? AE015451 = 178006617 (0.760)10 (0.470) 10/302 0.9 37.6% intergenic (+25/+81) PP_1587/dapC NhaP‑type Na+/H+ and K+/H+ antiporters/N‑succinyl‑L,L‑diaminopimelate aminotransferase alternative
?AE015451 1780129 = 17 (0.790)intergenic (+88/+18) PP_1587/dapC NhaP‑type Na+/H+ and K+/H+ antiporters/N‑succinyl‑L,L‑diaminopimelate aminotransferase alternative
* ? AE015451 2301453 =19 (0.850)5 (0.230) 4/310 2.3 21.1% intergenic (‑97/‑234) sbcD/PP_5497 Exonuclease SbcD/conserved protein of unknown function with rhs repeat‑associated core domain
?AE015451 2925429 = NA (NA)intergenic (‑177/+388) PP_2563/PP_2564 putative Antibiotic biosynthesis protein/putative Quercetin 2,3‑dioxygenase
* ? AE015451 4808174 =0 (0.000)4 (0.230) 3/246 2.2 42.1% intergenic (‑283/‑272) PP_4234/dsbD‑II Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2
?AE015451 = 5988935 11 (0.630)intergenic (+229/‑317) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? AE015451 = 48081790 (0.000)8 (0.390) 4/292 2.2 61.5% intergenic (‑288/‑267) PP_4234/dsbD‑II Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2
?AE015451 5988765 = 10 (0.480)intergenic (+59/‑487) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? AE015451 = 52015679 (0.400)15 (0.680) 15/310 0.5 59.0% intergenic (‑53/‑127) PP_4582/PP_4583 conserved membrane protein of unknown function/putative Peptidase
?AE015451 5201666 = 12 (0.550)intergenic (‑152/‑28) PP_4582/PP_4583 conserved membrane protein of unknown function/putative Peptidase
* ? AE015451 = 598875711 (0.490)7 (0.330) 7/300 1.4 35.5% intergenic (+51/‑495) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
?AE015451 5988979 = 15 (0.700)intergenic (+273/‑273) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA