New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 1973060 =5 (0.350)4 (0.280) 4/274 NT 44.4% intergenic (‑606/‑174) flhD/uspC flagellar class II regulon transcriptional activator, with FlhC/universal stress protein
?CP009273 = 3577555 NA (NA)intergenic (+15/‑1) insB1/yrhA IS1 transposase B/pseudogene, interrupted by IS1E

CCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCAT  >  CP009273/3577423‑3577667
                                                                                                                                    |                                                                                                                
ccTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGATGGAACTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTa                                                                                                     >  2:127340/1‑146 (MQ=255)
                            cTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGcaca                                                                     >  1:85510/1‑150 (MQ=255)
                             tGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGc                                                                        <  2:31266/146‑1 (MQ=255)
                                      aGTCGCTGTCTTCCTTAAAATCGGTGGAGGTGCATGACAAAGTCATCTGGCATTATCTGAACATAAAACACTATCAATAAATATGATTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAatatat                                                           <  1:74600/150‑1 (MQ=21)
                                                    tcAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGt                                             <  1:37195/150‑1 (MQ=255)
                                                                                  aTCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTTAACGAAAt                   >  2:52303/1‑146 (MQ=255)
                                                                                                   cATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAATTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGATGTTCat  >  2:223534/1‑146 (MQ=255)
                                                                                                                                    |                                                                                                                
CCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCAT  >  CP009273/3577423‑3577667

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: 
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.