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 3,061,793 G→A S592N (AGC→AAC)  qedA_2 → Quinoprotein alcohol dehydrogenase (cytochromec)
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 88058 58 14 [13] [13] 16 [CJ019_00094]–[CJ019_00095] [CJ019_00094],[CJ019_00095]
* * ÷ KT2440 213560 213676 117 14 [13] [13] 16 [CJ019_00185] [CJ019_00185]
* * ÷ KT2440 277599 277690 92 14 [13] [12] 14 [betT2]–[tauD_2] [betT2],[tauD_2]
* * ÷ KT2440 329244 329373 130 14 [13] [13] 15 CJ019_00302/CJ019_00303 hypothetical protein/hypothetical protein
* * ÷ KT2440 346095 346230 136 14 [12] [13] 14 [btuD_1] [btuD_1]
* * ÷ KT2440 492234 492337 104 18 [11] [13] 14 uvrY/potA_1 Response regulator UvrY/Spermidine/putrescine import ATP‑binding proteinPotA
* * ÷ KT2440 517190 517295 106 18 [11] [12] 14 tyrS/birA Tyrosine‑‑tRNA ligase/Bifunctional ligase/repressor BirA
* * ÷ KT2440 607293 607400 108 14 [12] [12] 14 dxs/ispA 1‑deoxy‑D‑xylulose‑5‑phosphate synthase/Farnesyl diphosphate synthase
* * ÷ KT2440 661102 661239 138 21 [9] [13] 15 [CJ019_00619] [CJ019_00619]
* * ÷ KT2440 674245 674387 143 15 [12] [13] 15 [nimR_1]–[mcpH_2] [nimR_1],[mcpH_2]
* * ÷ KT2440 789821 789954 134 14 [13] [13] 14 [CJ019_00751] [CJ019_00751]
* * ÷ KT2440 876846 876994 149 14 [13] [11] 14 CJ019_00843/malT putative protein/HTH‑type transcriptional regulator MalT
* * ÷ KT2440 1304774 1304852 79 15 [13] [11] 16 CJ019_01223/rapA putative signaling protein/RNA polymerase‑associated protein RapA
* * ÷ KT2440 1360613 1360944 332 15 [13] [13] 14 [CJ019_01275] [CJ019_01275]
* * ÷ KT2440 1376283 1376336 54 14 [13] [13] 19 CJ019_01289 hypothetical protein
* * ÷ KT2440 1396586 1396685 100 15 [13] [13] 14 [CJ019_01313]–[mcpU_1] [CJ019_01313],[mcpU_1]
* * ÷ KT2440 1457206 1457287 82 14 [11] [13] 14 [algL]–[algX] [algL],[algX]
* * ÷ KT2440 1585633 1585722 90 14 [10] [13] 14 CJ019_01493 hypothetical protein
* * ÷ KT2440 1697643 1697718 76 16 [11] [10] 14 [CJ019_01593] [CJ019_01593]
* * ÷ KT2440 1914560 1914658 99 16 [13] [13] 14 [ppsC_1]–[CJ019_01830] [ppsC_1],[CJ019_01830]
* * ÷ KT2440 2092960 2093072 113 14 [13] [13] 17 rcsC_3/CJ019_01993 Sensor histidine kinase RcsC/hypothetical protein
* * ÷ KT2440 2229973 2230094 122 15 [11] [12] 15 [emrB_1] [emrB_1]
* * ÷ KT2440 2288824 2288932 109 14 [13] [10] 14 CJ019_02171/CJ019_02172 hypothetical protein/hypothetical protein
* * ÷ KT2440 2422930 2423046 117 15 [13] [12] 14 [slt] [slt]
* * ÷ KT2440 3046180 3046347 168 14 [13] [13] 14 [rcsC_5]–[degU_2] [rcsC_5],[degU_2]
* * ÷ KT2440 3069088 3069195 108 14 [13] [13] 16 [CJ019_02881]–[CJ019_02882] [CJ019_02881],[CJ019_02882]
* * ÷ KT2440 3145288 3145405 118 14 [13] [13] 15 livH_4 High‑affinity branched‑chain amino acidtransport system permease protein LivH
* * ÷ KT2440 3280231 3280364 134 16 [11] [13] 14 [CJ019_03085]–[xthA_2] [CJ019_03085],[xthA_2]
* * ÷ KT2440 3305673 3305811 139 14 [13] [13] 15 [CJ019_03107] [CJ019_03107]
* * ÷ KT2440 3769381 3769516 136 15 [13] [13] 14 CJ019_03581/CJ019_03582 hypothetical protein/hypothetical protein
* * ÷ KT2440 3944696 3944825 130 14 [13] [12] 17 CJ019_03729/CJ019_03730 hypothetical protein/hypothetical protein
* * ÷ KT2440 4163782 4163880 99 14 [13] [13] 15 katG/leuO_2 Catalase‑peroxidase/HTH‑type transcriptional regulator LeuO
* * ÷ KT2440 4332108 4332175 68 14 [13] [13] 14 [CJ019_04068] [CJ019_04068]
* * ÷ KT2440 4333683 4333783 101 16 [13] [13] 14 ribBA_2/potD_2 Riboflavin biosynthesis protein RibBA/Spermidine/putrescine‑binding periplasmicprotein
* * ÷ KT2440 4346803 4346881 79 17 [10] [11] 17 nmoA Nitronate monooxygenase
* * ÷ KT2440 4436221 4436304 84 14 [13] [13] 14 nicP_12/nicT_2 Porin‑like protein NicP/Putative metabolite transport protein NicT
* * ÷ KT2440 4497385 4497479 95 19 [12] [12] 14 [xanP]–[dsrE] [xanP],[dsrE]
* * ÷ KT2440 4523635 4523750 116 15 [13] [13] 15 [CJ019_04289] [CJ019_04289]
* * ÷ KT2440 4545591 4545697 107 14 [10] [10] 14 preA/rutR_2 NAD‑dependent dihydropyrimidine dehydrogenasesubunit PreA/HTH‑type transcriptional regulator RutR
* * ÷ KT2440 4668903 4669033 131 15 [13] [13] 14 [btuB_4] [btuB_4]
* * ÷ KT2440 4734442 4734517 76 14 [13] [13] 14 gltA/CJ019_04468 Citrate synthase/hypothetical protein
* * ÷ KT2440 4790200 4790309 110 16 [13] [12] 14 [qseC_3] [qseC_3]
* * ÷ KT2440 4842381 4842451 71 16 [12] [11] 14 [CJ019_04539] [CJ019_04539]
* * ÷ KT2440 4846232 4846359 128 16 [12] [12] 16 recR/ybaB Recombination protein RecR/Nucleoid‑associated protein YbaB
* * ÷ KT2440 4944724 4944837 114 14 [13] [11] 14 [CJ019_04642] [CJ019_04642]
* * ÷ KT2440 5188668 5188796 129 15 [13] [13] 14 [CJ019_04882]–[pxpC_2] [CJ019_04882],[pxpC_2]
* * ÷ KT2440 5193414 5193549 136 14 [12] [11] 14 [gltR_4]–[CJ019_04888] [gltR_4],[CJ019_04888]
* * ÷ KT2440 5500274 5500461 188 15 [12] [12] 14 [CJ019_05176] [CJ019_05176]
* * ÷ KT2440 5551618 5551788 171 14 [12] [13] 16 CJ019_05227/purA hypothetical protein/Adenylosuccinate synthetase
* * ÷ KT2440 5810692 5810973 282 15 [11] [13] 14 [pilT] [pilT]
* * ÷ KT2440 5896938 5897040 103 14 [12] [12] 18 [CJ019_05521] [CJ019_05521]
* * ÷ KT2440 5914023 5914114 92 14 [13] [13] 14 CJ019_05537 hypothetical protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? KT2440 4918800 =0 (0.000)55 (1.160) 28/248 0.5 100% 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)48 (1.010) 34/250 0.2 100% 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