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 44,301 (T)9→8 intergenic (+132/‑359) oprD_1 → / → czcR_2 Porin D/Transcriptional activator protein CzcR
RA 120,983 (T)9→8 intergenic (+280/+92) polA → / ← engB DNA polymerase I/putative GTP‑binding protein EngB
RA 179,484 T→C C316R (TGC→CGC)  CJ019_00182 → hypothetical protein
RA 1,806,731 G→T K10N (AAG→AAT)  yeiG → S‑formylglutathione hydrolase YeiG
RA 3,061,793 G→A S592N (AGC→AAC)  qedA_2 → Quinoprotein alcohol dehydrogenase (cytochromec)
RA 3,957,351 G→A H100Y (CAC→TAC)  dmlR_13 ← HTH‑type transcriptional regulator DmlR
RA 5,757,239 (A)6→5 coding (781/834 nt) CJ019_05400 → hypothetical protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ KT2440 88001 88083 83 7 [6] [6] 7 [CJ019_00094]–[CJ019_00095] [CJ019_00094],[CJ019_00095]
* * ÷ KT2440 161229 161284 56 7 [6] [4] 7 [uctC_1] [uctC_1]
* * ÷ KT2440 277601 277674 74 7 [5] [5] 8 [betT2]–[tauD_2] [betT2],[tauD_2]
* * ÷ KT2440 309043 309107 65 11 [6] [5] 8 cysQ/CJ019_00284 3'(2'),5'‑bisphosphate nucleotidase CysQ/hypothetical protein
* * ÷ KT2440 346105 346216 112 7 [4] [6] 7 [btuD_1] [btuD_1]
* * ÷ KT2440 492248 492333 86 7 [6] [6] 7 uvrY/potA_1 Response regulator UvrY/Spermidine/putrescine import ATP‑binding proteinPotA
* * ÷ KT2440 517198 517293 96 8 [4] [6] 7 tyrS/birA Tyrosine‑‑tRNA ligase/Bifunctional ligase/repressor BirA
* * ÷ KT2440 607285 607387 103 7 [6] [4] 7 dxs/ispA 1‑deoxy‑D‑xylulose‑5‑phosphate synthase/Farnesyl diphosphate synthase
* * ÷ KT2440 641248 641348 101 10 [6] [6] 7 [acoR_2] [acoR_2]
* * ÷ KT2440 674245 674387 143 9 [6] [6] 7 [nimR_1]–[mcpH_2] [nimR_1],[mcpH_2]
* * ÷ KT2440 690110 690256 147 7 [6] [5] 10 [bauC] [bauC]
* * ÷ KT2440 711479 711559 81 7 [6] [5] 7 [thiO]–[aam] [thiO],[aam]
* * ÷ KT2440 908062 908207 146 8 [6] [5] 7 [fruA] [fruA]
* * ÷ KT2440 1000527 1000620 94 7 [6] [6] 7 [fecA_1] [fecA_1]
* * ÷ KT2440 1006276 1006328 53 8 [6] [6] 7 prfC/spuD_1 Peptide chain release factor RF3/Putrescine‑binding periplasmic protein SpuD
* * ÷ KT2440 1117560 1117659 100 8 [6] [6] 8 gcvT_1 Aminomethyltransferase
* * ÷ KT2440 1119661 1119697 37 7 [5] [3] 8 tdcG_2/gcvP_1 L‑serine dehydratase TdcG/Glycine dehydrogenase (decarboxylating)
* * ÷ KT2440 1277773 1277891 119 9 [6] [6] 7 [pal_2] [pal_2]
* * ÷ KT2440 1304753 1304838 86 7 [6] [5] 7 CJ019_01223/rapA putative signaling protein/RNA polymerase‑associated protein RapA
* * ÷ KT2440 1351801 1351924 124 8 [6] [4] 7 entD Enterobactin synthase component D
* * ÷ KT2440 1360664 1360953 290 7 [6] [4] 7 CJ019_01275 hypothetical protein
* * ÷ KT2440 1402162 1402180 19 8 [0] [2] 7 ydgA/nadA Protein YdgA/Quinolinate synthase A
* * ÷ KT2440 1411273 1411322 50 7 [6] [6] 8 [purC] [purC]
* * ÷ KT2440 1457214 1457305 92 7 [6] [6] 7 [algL]–[algX] [algL],[algX]
* * ÷ KT2440 1480089 1480247 159 7 [6] [6] 7 [degS] [degS]
* * ÷ KT2440 1492467 1492581 115 11 [6] [3] 10 [CJ019_01406] [CJ019_01406]
* * ÷ KT2440 1499953 1500058 106 7 [5] [5] 7 [sspA] [sspA]
* * ÷ KT2440 1524800 1524857 58 7 [6] [6] 8 CJ019_01439 hypothetical protein
* * ÷ KT2440 1537410 1537552 143 8 [6] [6] 7 [mdfA] [mdfA]
* * ÷ KT2440 1563451 1563512 62 7 [5] [5] 7 pcaF_1/kgtP_1 Beta‑ketoadipyl‑CoA thiolase/Alpha‑ketoglutarate permease
* * ÷ KT2440 1585616 1585700 85 8 [6] [6] 8 CJ019_01493 hypothetical protein
* * ÷ KT2440 1608705 1608777 73 8 [6] [6] 7 CJ019_01513 hypothetical protein
* * ÷ KT2440 1697657 1697723 67 7 [5] [5] 7 [CJ019_01593] [CJ019_01593]
* * ÷ KT2440 1833103 1833176 74 8 [6] [6] 8 [resA_1]–[CJ019_01751] [resA_1],[CJ019_01751]
* * ÷ KT2440 1914575 1914690 116 7 [6] [6] 8 [ppsC_1]–[CJ019_01830] [ppsC_1],[CJ019_01830]
* * ÷ KT2440 1923421 1923500 80 7 [6] [6] 10 [apeB] [apeB]
* * ÷ KT2440 1935378 1935465 88 7 [6] [4] 8 [CJ019_01850] [CJ019_01850]
* * ÷ KT2440 1940827 1940915 89 7 [6] [6] 9 CJ019_01857/gshAB hypothetical protein/Glutathione biosynthesis bifunctional proteinGshAB
* * ÷ KT2440 2043559 2043700 142 7 [6] [6] 8 [smrA] [smrA]
* * ÷ KT2440 2092962 2093085 124 8 [6] [6] 8 rcsC_3/CJ019_01993 Sensor histidine kinase RcsC/hypothetical protein
* * ÷ KT2440 2234336 2234409 74 7 [6] [5] 7 gltX/PP_RS08750 Glutamate‑‑tRNA ligase/tRNA‑Val
* * ÷ KT2440 2275822 2275839 18 10 [6] [0] 7 yodB_1/PP_RS08750 Cytochrome b561/tRNA‑Val
* * ÷ KT2440 2288822 2288929 108 9 [5] [6] 7 CJ019_02171/CJ019_02172 hypothetical protein/hypothetical protein
* * ÷ KT2440 3046223 3046308 86 7 [6] [4] 7 [rcsC_5]–[degU_2] [rcsC_5],[degU_2]
* * ÷ KT2440 3069126 3069190 65 7 [6] [6] 7 [CJ019_02882] [CJ019_02882]
* * ÷ KT2440 3145280 3145399 120 7 [6] [6] 8 livH_4 High‑affinity branched‑chain amino acidtransport system permease protein LivH
* * ÷ KT2440 3280231 3280350 120 11 [6] [4] 7 [CJ019_03085] [CJ019_03085]
* * ÷ KT2440 3305703 3305771 69 7 [6] [6] 7 [CJ019_03107] [CJ019_03107]
* * ÷ KT2440 3459865 3459927 63 7 [6] [6] 7 CJ019_03284 hypothetical protein
* * ÷ KT2440 3581173 3581210 38 7 [0] [6] 9 catA_1/ydcO_3 Catechol 1,2‑dioxygenase/Inner membrane protein YdcO
* * ÷ KT2440 3769389 3769472 84 8 [6] [6] 7 CJ019_03581/CJ019_03582 hypothetical protein/hypothetical protein
* * ÷ KT2440 3784628 3784744 117 7 [6] [6] 7 dmdC_4 3‑methylmercaptopropionyl‑CoA dehydrogenase
* * ÷ KT2440 4025799 4025841 43 7 [6] [6] 7 dmdC_5/CJ019_03801 3‑methylmercaptopropionyl‑CoA dehydrogenase/hypothetical protein
* * ÷ KT2440 4143636 4143810 175 8 [6] [6] 7 [lrp_3] [lrp_3]
* * ÷ KT2440 4163781 4163880 100 7 [6] [6] 9 katG/leuO_2 Catalase‑peroxidase/HTH‑type transcriptional regulator LeuO
* * ÷ KT2440 4332105 4332180 76 7 [6] [6] 7 [CJ019_04068] [CJ019_04068]
* * ÷ KT2440 4346808 4346844 37 7 [6] [5] 7 nmoA Nitronate monooxygenase
* * ÷ KT2440 4523628 4523712 85 7 [5] [6] 7 [CJ019_04289] [CJ019_04289]
* * ÷ KT2440 4698963 4699096 134 7 [4] [6] 8 [ydiK_3] [ydiK_3]
* * ÷ KT2440 4734464 4734565 102 7 [3] [5] 7 [CJ019_04468] [CJ019_04468]
* * ÷ KT2440 4801806 4802039 234 7 [6] [6] 7 CJ019_04509/dsbD_2 hypothetical protein/Thiol:disulfide interchange protein DsbD
* * ÷ KT2440 4846248 4846313 66 7 [6] [4] 8 recR/ybaB Recombination protein RecR/Nucleoid‑associated protein YbaB
* * ÷ KT2440 4883360 4883485 126 7 [6] [6] 10 [hyi] [hyi]
* * ÷ KT2440 4944704 4944835 132 7 [6] [6] 7 [CJ019_04642] [CJ019_04642]
* * ÷ KT2440 4954765 4954834 70 7 [5] [6] 7 fliE/atoC_3 Flagellar hook‑basal body complex protein FliE/Regulatory protein AtoC
* * ÷ KT2440 5193440 5193528 89 7 [6] [6] 9 [gltR_4]–[CJ019_04888] [gltR_4],[CJ019_04888]
* * ÷ KT2440 5195428 5195503 76 7 [6] [5] 7 CJ019_04890/dapb1 hypothetical protein/Dipeptidyl aminopeptidase BI
* * ÷ KT2440 5204030 5204098 69 7 [6] [3] 13 rnd/eptA_2 Ribonuclease D/Phosphoethanolamine transferase EptA
* * ÷ KT2440 5251708 5251748 41 7 [5] [6] 7 CJ019_04948/fabV hypothetical protein/Enoyl‑[acyl‑carrier‑protein] reductase [NADH]
* * ÷ KT2440 5338246 5338360 115 8 [6] [4] 7 [pgi_2] [pgi_2]
* * ÷ KT2440 5433093 5433160 68 7 [6] [6] 8 rluE Ribosomal large subunit pseudouridine synthaseE
* * ÷ KT2440 5478934 5479028 95 7 [6] [4] 7 purH/purD Bifunctional purine biosynthesis protein PurH/Phosphoribosylamine‑‑glycine ligase
* * ÷ KT2440 5500305 5500462 158 7 [5] [6] 7 [CJ019_05176] [CJ019_05176]
* * ÷ KT2440 5530858 5530931 74 7 [5] [5] 7 nadE/CJ019_05208 NH(3)‑dependent NAD( ) synthetase/Azurin
* * ÷ KT2440 5532366 5532442 77 7 [6] [5] 7 CJ019_05209/CJ019_05210 Putative cytokinin riboside 5'‑monophosphate phosphoribohydrolase/hypothetical protein
* * ÷ KT2440 5549390 5549531 142 11 [5] [6] 7 [CJ019_05227] [CJ019_05227]
* * ÷ KT2440 5551624 5551800 177 10 [6] [6] 7 [purA] [purA]
* * ÷ KT2440 5587917 5587991 75 10 [6] [6] 7 CJ019_05260/thiC hypothetical protein/Phosphomethylpyrimidine synthase
* * ÷ KT2440 5646789 5646820 32 7 [5] [6] 7 CJ019_05302/CJ019_05303 hypothetical protein/hypothetical protein
* * ÷ KT2440 5727850 5727931 82 7 [6] [6] 8 proY_2/hutH Proline‑specific permease ProY/Histidine ammonia‑lyase
* * ÷ KT2440 5891539 5891651 113 7 [6] [6] 8 CJ019_05517/czcA_3 hypothetical protein/Cobalt‑zinc‑cadmium resistance protein CzcA
* * ÷ KT2440 5896945 5897041 97 8 [6] [5] 8 [CJ019_05521] [CJ019_05521]
* * ÷ KT2440 5899312 5899385 74 7 [5] [6] 7 potH Putrescine transport system permease proteinPotH
* * ÷ KT2440 6026606 6026689 84 7 [6] [6] 7 dppA_4/CJ019_05642 Periplasmic dipeptide transport protein/hypothetical protein
* * ÷ KT2440 6092135 6092348 214 8 [6] [6] 7 hexR_2 HTH‑type transcriptional regulator HexR

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? KT2440 4918800 =0 (0.000)51 (1.590) 30/246 0.1 100% coding (7/789 nt) soj_1 Sporulation initiation inhibitor protein Soj
?KT2440 = 5539492 NA (NA)intergenic (‑358/+71) CJ019_03622/rlmB IS110 family transposase ISPpu9/23S rRNA (guanosine‑2'‑O‑)‑methyltransferaseRlmB
* ? KT2440 = 49188010 (0.000)34 (1.050) 23/248 0.3 100% coding (6/789 nt) soj_1 Sporulation initiation inhibitor protein Soj
?KT2440 5216408 = NA (NA)intergenic (‑50/+386) rhaS_5/CJ019_01212 HTH‑type transcriptional activator RhaS/IS110 family transposase ISPpu9