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 495,400 A→G V213V (GTA→GTG)  CJ019_00444 → hypothetical protein
RA 3,061,793 G→A S592N (AGC→AAC)  qedA_2 → Quinoprotein alcohol dehydrogenase (cytochromec)
RA 3,440,343 A→C S18R (AGC→CGC)  CJ019_03266 → hypothetical protein
RA 3,957,351 G→A H100Y (CAC→TAC)  dmlR_13 ← HTH‑type transcriptional regulator DmlR
RA 4,257,309 C→T intergenic (‑238/‑44) CJ019_03991 ← / → tsaM1 putative ABC transporter ATP‑binding protein/Toluene‑4‑sulfonate monooxygenase systemiron‑sulfur subunit TsaM1
RA 4,425,093 G→A V38V (GTG→GTA)  fabG_6 → 3‑oxoacyl‑[acyl‑carrier‑protein] reductase FabG
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 87979 88047 69 9 [7] [8] 9 [CJ019_00094]–[CJ019_00095] [CJ019_00094],[CJ019_00095]
* * ÷ KT2440 161232 161376–161317 86–145 11 [8] [8] 9 [uctC_1] [uctC_1]
* * ÷ KT2440 213578 213692 115 9 [6] [8] 9 [CJ019_00185] [CJ019_00185]
* * ÷ KT2440 277599 277688 90 10 [8] [8] 9 [betT2]–[tauD_2] [betT2],[tauD_2]
* * ÷ KT2440 309042 309094 53 9 [7] [6] 9 cysQ/CJ019_00284 3'(2'),5'‑bisphosphate nucleotidase CysQ/hypothetical protein
* * ÷ KT2440 346104 346229 126 9 [8] [8] 9 [btuD_1] [btuD_1]
* * ÷ KT2440 517190 517426 237 11 [6] [7] 10 tyrS/birA Tyrosine‑‑tRNA ligase/Bifunctional ligase/repressor BirA
* * ÷ KT2440 607271 607405 135 10 [8] [8] 10 dxs/ispA 1‑deoxy‑D‑xylulose‑5‑phosphate synthase/Farnesyl diphosphate synthase
* * ÷ KT2440 674284 674402 119 9 [8] [8] 9 [nimR_1]–[mcpH_2] [nimR_1],[mcpH_2]
* * ÷ KT2440 686599 686698 100 9 [7] [8] 9 metR_1 HTH‑type transcriptional regulator MetR
* * ÷ KT2440 711475 711576 102 9 [7] [8] 9 [thiO]–[aam] [thiO],[aam]
* * ÷ KT2440 856896 856981 86 9 [8] [6] 9 [hemH]–[uraA] [hemH],[uraA]
* * ÷ KT2440 908086 908218 133 9 [8] [7] 11 fruA/CJ019_00870 PTS system fructose‑specific EIIB'BC component/hypothetical protein
* * ÷ KT2440 1106821 1106955 135 10 [8] [8] 9 [hupB_1]–[rlmF] [hupB_1],[rlmF]
* * ÷ KT2440 1149264 1149498 235 10 [8] [8] 10 [sasA_4] [sasA_4]
* * ÷ KT2440 1304768 1304870 103 9 [8] [8] 9 [rapA] [rapA]
* * ÷ KT2440 1376293 1376329 37 11 [4] [8] 9 CJ019_01289 hypothetical protein
* * ÷ KT2440 1457227 1457305 79 9 [8] [8] 9 [algX] [algX]
* * ÷ KT2440 1563437 1563505 69 9 [7] [8] 10 [pcaF_1] [pcaF_1]
* * ÷ KT2440 1585617 1585691 75 10 [8] [8] 9 CJ019_01493 hypothetical protein
* * ÷ KT2440 1608711 1608799 89 9 [7] [8] 9 CJ019_01513 hypothetical protein
* * ÷ KT2440 1697667 1697723 57 10 [7] [8] 9 [CJ019_01593] [CJ019_01593]
* * ÷ KT2440 1705096 1705190 95 9 [8] [8] 10 ppc/adk Phosphoenolpyruvate carboxylase/Adenylate kinase
* * ÷ KT2440 1773099 1773169 71 9 [8] [7] 9 nhaK/dapL_1 Sodium, potassium, lithium and rubidium/H( )antiporter/LL‑diaminopimelate aminotransferase
* * ÷ KT2440 1833104 1833176 73 9 [8] [8] 11 [resA_1]–[CJ019_01751] [resA_1],[CJ019_01751]
* * ÷ KT2440 1896722 1896810 89 9 [8] [8] 9 [nasD] [nasD]
* * ÷ KT2440 1914575 1914654 80 10 [8] [8] 9 [ppsC_1]–[CJ019_01830] [ppsC_1],[CJ019_01830]
* * ÷ KT2440 1923416 1923500 85 9 [8] [7] 11 [apeB] [apeB]
* * ÷ KT2440 1925604 1925691 88 9 [8] [7] 9 rluA/minE Dual‑specificity RNA pseudouridine synthaseRluA/Cell division topological specificity factor
* * ÷ KT2440 1940816 1940908 93 10 [8] [7] 9 CJ019_01857/gshAB hypothetical protein/Glutathione biosynthesis bifunctional proteinGshAB
* * ÷ KT2440 2234313 2234419 107 9 [8] [8] 11 gltX/PP_RS08750 Glutamate‑‑tRNA ligase/tRNA‑Val
* * ÷ KT2440 2288820 2288928 109 9 [6] [8] 9 CJ019_02171/CJ019_02172 hypothetical protein/hypothetical protein
* * ÷ KT2440 2393574 2393614 41 9 [7] [7] 11 [dgt] [dgt]
* * ÷ KT2440 2471443 2471539 97 9 [8] [8] 9 [CJ019_02330] [CJ019_02330]
* * ÷ KT2440 2786767 2786823 57 9 [8] [8] 9 CJ019_02632/CJ019_02633 hypothetical protein/hypothetical protein
* * ÷ KT2440 2830122 2830230 109 9 [8] [7] 9 gabD1/namA_3 Succinate‑semialdehyde dehydrogenase [NADP( )]1/NADPH dehydrogenase
* * ÷ KT2440 2858506 2858553 48 9 [8] [7] 9 nicP_5/galA Porin‑like protein NicP/Gallate dioxygenase
* * ÷ KT2440 3046225 3046347 123 9 [8] [8] 10 [rcsC_5]–[degU_2] [rcsC_5],[degU_2]
* * ÷ KT2440 3145293 3145386 94 9 [8] [8] 9 livH_4 High‑affinity branched‑chain amino acidtransport system permease protein LivH
* * ÷ KT2440 3459875 3459934 60 10 [7] [8] 10 CJ019_03284 hypothetical protein
* * ÷ KT2440 3769398 3769477 80 9 [7] [8] 9 CJ019_03581/CJ019_03582 hypothetical protein/hypothetical protein
* * ÷ KT2440 3944707 3944818 112 10 [6] [8] 9 CJ019_03729/CJ019_03730 hypothetical protein/hypothetical protein
* * ÷ KT2440 4163759 4163873 115 10 [8] [7] 9 katG/leuO_2 Catalase‑peroxidase/HTH‑type transcriptional regulator LeuO
* * ÷ KT2440 4332101 4332173 73 9 [7] [8] 11 [CJ019_04068] [CJ019_04068]
* * ÷ KT2440 4333684 4333780 97 11 [7] [8] 10 ribBA_2/potD_2 Riboflavin biosynthesis protein RibBA/Spermidine/putrescine‑binding periplasmicprotein
* * ÷ KT2440 4346804 4346854 51 9 [7] [8] 9 nmoA Nitronate monooxygenase
* * ÷ KT2440 4436216 4436310 95 10 [8] [8] 9 nicP_12/nicT_2 Porin‑like protein NicP/Putative metabolite transport protein NicT
* * ÷ KT2440 4523645 4523754 110 10 [6] [8] 9 CJ019_04289/topB Acetyltransferase/DNA topoisomerase 3
* * ÷ KT2440 4566844 4566923 80 9 [8] [6] 9 CJ019_04323/glgX hypothetical protein/Glycogen operon protein GlgX
* * ÷ KT2440 4668950 4669028 79 9 [7] [5] 10 btuB_4/chrR Vitamin B12 transporter BtuB/Quinone reductase
* * ÷ KT2440 4734429 4734506 78 10 [8] [6] 9 gltA/CJ019_04468 Citrate synthase/hypothetical protein
* * ÷ KT2440 4801794 4802183 390 11 [6] [7] 9 CJ019_04509/dsbD_2 hypothetical protein/Thiol:disulfide interchange protein DsbD
* * ÷ KT2440 4838994 4839065 72 9 [5] [8] 9 CJ019_04536/copA_3 hypothetical protein/putative copper‑importing P‑type ATPase A
* * ÷ KT2440 4842387 4842449 63 13 [8] [5] 9 [CJ019_04539] [CJ019_04539]
* * ÷ KT2440 4846223 4846317 95 9 [8] [8] 9 recR/ybaB Recombination protein RecR/Nucleoid‑associated protein YbaB
* * ÷ KT2440 4883389 4883485 97 10 [6] [7] 9 hyi/glxR Hydroxypyruvate isomerase/2‑hydroxy‑3‑oxopropionate reductase
* * ÷ KT2440 4944755 4944847 93 9 [7] [8] 9 [CJ019_04642] [CJ019_04642]
* * ÷ KT2440 4954761 4954839 79 11 [6] [8] 9 fliE/atoC_3 Flagellar hook‑basal body complex protein FliE/Regulatory protein AtoC
* * ÷ KT2440 5193425 5193530 106 9 [8] [8] 13 [gltR_4]–[CJ019_04888] [gltR_4],[CJ019_04888]
* * ÷ KT2440 5232505 5232594 90 9 [8] [7] 9 psiE/CJ019_04928 Protein PsiE/hypothetical protein
* * ÷ KT2440 5250642 5250712 71 10 [8] [7] 9 [CJ019_04947] [CJ019_04947]
* * ÷ KT2440 5338266 5338375 110 9 [8] [8] 10 pgi_2/acsA_4 Glucose‑6‑phosphate isomerase/Acetyl‑coenzyme A synthetase
* * ÷ KT2440 5424176 5424244 69 9 [8] [7] 9 CJ019_05101/CJ019_05102 hypothetical protein/hypothetical protein
* * ÷ KT2440 5433086 5433174 89 11 [8] [5] 9 rluE Ribosomal large subunit pseudouridine synthaseE
* * ÷ KT2440 5500275 5500467 193 9 [7] [8] 9 [CJ019_05176] [CJ019_05176]
* * ÷ KT2440 5551636 5551785 150 9 [6] [8] 9 CJ019_05227/purA hypothetical protein/Adenylosuccinate synthetase
* * ÷ KT2440 5675179 5675308 130 10 [8] [8] 9 CJ019_05328/CJ019_05329 hypothetical protein/hypothetical protein
* * ÷ KT2440 5690435 5690556 122 11 [8] [8] 10 [hslV] [hslV]
* * ÷ KT2440 5810663 5810816 154 10 [8] [8] 9 [pilT] [pilT]
* * ÷ KT2440 5891553 5891631 79 9 [6] [8] 10 CJ019_05517/czcA_3 hypothetical protein/Cobalt‑zinc‑cadmium resistance protein CzcA
* * ÷ KT2440 5896969 5897039 71 9 [8] [7] 9 [CJ019_05521] [CJ019_05521]
* * ÷ KT2440 5978234 5978333 100 9 [8] [8] 11 [sasA_19]–[ycaC_2] [sasA_19],[ycaC_2]
* * ÷ KT2440 6002965 6002998 34 10 [8] [7] 13 mdtK/CJ019_05620 Multidrug resistance protein MdtK/hypothetical protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? KT2440 4918800 =1 (0.030)54 (1.480) 24/244 0.4 98.2% 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 = 49188011 (0.030)32 (0.870) 24/246 0.4 97.0% 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