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

Predicted mutation
evidence position mutation annotation gene description
RA 2,399,955 C→A E56* (GAA→TAA)  lrhA ← transcriptional repressor of flagellar, motility and chemotaxis genes

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP009273 80542 80613 72 2 [1] [1] 2 leuL/leuO leu operon leader peptide/global transcription factor
* * ÷ CP009273 153676 153872 197 2 [1] [0] 2 [folK] [folK]
* * ÷ CP009273 340589 340635 47 2 [1] [0] 2 yahL uncharacterized protein
* * ÷ CP009273 559276 559343 68 3 [1] [1] 2 [sfmF]–[sfmZ] [sfmF],[sfmZ]
* * ÷ CP009273 653424 653471 48 2 [1] [1] 2 flc/ybeM fluoride efflux channel, dual topology membrane protein/pseudogene, C‑N hydrolase superfamily homology;putative enzyme; Not classified; putative amidase
* * ÷ CP009273 993170 993214 45 2 [0] [1] 2 ssuE/elfA NAD(P)H‑dependent FMN reductase/laminin‑binding fimbrin subunit
* * ÷ CP009273 1072420 1072465 46 2 [0] [1] 2 putA fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase
* * ÷ CP009273 1205059 1205074 16 15 [0] [0] 14 stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* * ÷ CP009273 1350036 1350079 44 3 [1] [0] 2 sapA antimicrobial peptide transport ABC transporter periplasmic binding protein
* * ÷ CP009273 1385065 1385112 48 2 [1] [1] 2 ymjC pseudogene
* * ÷ CP009273 1459362 1459541 180 2 [1] [1] 2 ynbG ynbG
* * ÷ CP009273 1647402 1647409 8 4 [0] [0] 2 rspB putative Zn‑dependent NAD(P)‑binding oxidoreductase
* * ÷ CP009273 1725468 1725543 76 2 [1] [0] 2 lhr putative ATP‑dependent helicase
* * ÷ CP009273 1726383 1726415 33 3 [1] [0] 2 lhr putative ATP‑dependent helicase
* * ÷ CP009273 1783742 1783774 33 3 [0] [1] 3 aroH/ydiE 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible/hemin uptake protein HemP homolog
* * ÷ CP009273 1819132 1819163 32 3 [1] [1] 2 ves cold‑ and stress‑inducible protein
* * ÷ CP009273 1842432 1842481 50 2 [1] [0] 2 ydjA putative oxidoreductase
* * ÷ CP009273 1942448 1942460 13 2 [0] [0] 3 nudB dihydroneopterin triphosphate pyrophosphatase
* * ÷ CP009273 1944734 1944784 51 2 [1] [1] 2 [aspS] [aspS]
* * ÷ CP009273 2027296 2027415 120 2 [1] [1] 2 rseX/yedS sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology; putative outer membrane protein
* * ÷ CP009273 2051074 2051224 151 2 [0] [1] 2 yeeN/asnW UPF0082 family protein/tRNA‑Asn
* * ÷ CP009273 2118378 2118434 57 3 [0] [1] 4 wcaI putative glycosyl transferase
* * ÷ CP009273 2179065 2179089 25 2 [1] [1] 3 rcnR transcriptional repressor of rcnA
* * ÷ CP009273 2201126 2201188 63 3 [1] [1] 6 yehM uncharacterized protein
* * ÷ CP009273 2208322 2208788 467 2 [1] [1] 2 [mlrA] [mlrA]
* * ÷ CP009273 2208850 2209085 236 2 [1] [0] 2 [mlrA] [mlrA]
* * ÷ CP009273 2463688 2463744 57 2 [0] [0] 2 gtrS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
* * ÷ CP009273 2568664 2568694 31 6 [0] [1] 2 eutP putative P‑loop NTPase ethanolamine utilization protein
* * ÷ CP009273 2569405 2569429 25 2 [0] [1] 2 eutS/maeB putative ethanol utilization carboxysome structural protein/malic enzyme: putative oxidoreductase/putative phosphotransacetylase
* * ÷ CP009273 2636976 2637008 33 3 [0] [1] 2 rlmN dual specificity 23S rRNA m(2)A2503, tRNA m(2)A37 methyltransferase, SAM‑dependent
* * ÷ CP009273 2853082 2853089 8 2 [0] [1] 3 mutS/pphB methyl‑directed mismatch repair protein/serine/threonine‑specific protein phosphatase 2
* * ÷ CP009273 3354276 3354296 21 2 [0] [0] 3 gltD/gltF glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
* * ÷ CP009273 3448775 3448865 91 3 [1] [0] 10 gspA/gspC general secretory pathway component, cryptic/general secretory pathway component, cryptic
* * ÷ CP009273 3629073 3629086 14 3 [0] [1] 2 yhiM acid resistance protein, inner membrane
* * ÷ CP009273 3745281 3745398 118 2 [0] [1] 2 [yiaU] [yiaU]
* * ÷ CP009273 3750355 3750357 3 2 [0] [1] 2 yiaY putative Fe‑containing alcohol dehydrogenase, Pfam00465 family
* * ÷ CP009273 3787017 3787111 95 2 [0] [1] 2 [yibB] [yibB]
* * ÷ CP009273 3797648 3797810 163 3 [1] [1] 2 waaS lipopolysaccharide core biosynthesis protein
* * ÷ CP009273 3805715 3805725 11 3 [0] [0] 2 yicR UPF0758 family protein
* * ÷ CP009273 4036008 4036098 91 2 [1] [1] 2 srkA stress response kinase A; MazF antagonist; Thr/Ser kinase involved in Cpx stress response
* * ÷ CP009273 4137111 4137123 13 2 [1] [1] 3 frwD putative enzyme IIB component of PTS
* * ÷ CP009273 4294365 4294421 57 6 [0] [1] 3 ytcA/yjcS putative inner membrane DUF1656 family protein; efflux pump associated/metallo‑beta‑lactamase superfamily protein
* * ÷ CP009273 4374142 4374154 13 2 [1] [1] 2 yjeM putative transporter

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 360104 =15 (0.800)13 (0.700) 9/268 0.4 46.4% intergenic (‑38/+557) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 360286 NA (NA)intergenic (‑220/+375) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
* ? CP009273 1203246 =6 (0.320)14 (0.850) 9/236 0.3 84.1% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 1205075 = 0 (0.000)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 12032616 (0.320)14 (0.850) 11/236 0.2 84.1% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 = 1205058 0 (0.000)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 3923686 =16 (0.860)5 (0.270) 3/266 1.3 23.9% coding (768/1497 nt) ravA hexameric AAA+ MoxR family ATPase, putative molecular chaperone
?CP009273 4033280 = NA (NA)noncoding (2402/2905 nt) rrlA 23S ribosomal RNA of rrnA operon
* ? CP009273 4363113 =15 (0.860)12 (0.690) 3/248 1.2 44.6% intergenic (+134/+69) yjeI/yjeJ DUF4156 family lipoprotein/uncharacterized protein
?CP009273 4364315 = NA (NA)noncoding (1/99 nt) RIP329 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site RIP329 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site