New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 = 1463497NA (NA)10 (0.200) 9/272 NT 21.7% noncoding (1/1331 nt) IS2 repeat region
?CP009273 = 1584819 36 (0.730)intergenic (‑26/+292) yneL/hipA pseudogene, AraC family/inactivating GltX kinase facilitating persister formation; toxin of HipAB TA pair; autokinase

TTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAATGAGACGAACATTTACAGCAGA  >  CP009273/1463354‑1463637
                                                                                                                                               |                                                                                                                                            
ttttCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGCTTCAGGGGGCCGGTCTAAAccc                                                                                                                                         >  2:323502/1‑149 (MQ=14)
     cTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCCGGGGGTCCGTCTAAACCCCAGaa                                                                                                                                    >  1:417268/1‑149 (MQ=255)
      tgtgtgGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATCCAGGGGGCCAGTCTAAACCCCAGAac                                                                                                                                   >  1:605148/1‑149 (MQ=25)
            gTACGCCGTCTGCGTTTCTCCGGCCCTAAGTCATCAATCATGTGTTACGCTTCTACTGGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAacttactt                                                                                                                             <  2:414204/149‑1 (MQ=14)
                   gTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGa                                                                                                                      >  1:837279/1‑149 (MQ=255)
                     cTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGAtt                                                                                                                    >  2:725264/1‑149 (MQ=255)
                     cTGCGGTTCTCCGGCCCTAAGACATCAATCATCAGTTCTCCAATGGCTAGTCTAAAAACTAGTATTAAGACTATCACTTATTGAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACACCCCACAACTTACTTATGCTGAtt                                                                                                                    >  1:220523/1‑149 (MQ=14)
                      tGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTTGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACGTATGCTGATTc                                                                                                                   >  1:741238/1‑149 (MQ=255)
                          tttCTGCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGt                                                                                                               <  1:302162/149‑1 (MQ=255)
                                 ggCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCAGGTGCGaaaa                                                                                                        >  2:456522/1‑149 (MQ=255)
                                           cATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTtaataa                                                                                              <  2:829998/149‑1 (MQ=255)
                                                      tGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTGCTTGTa                                                                                   >  1:433108/1‑149 (MQ=255)
                                                       gTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTTTAg                                                                                  >  1:607299/1‑149 (MQ=255)
                                                       gTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAg                                                                                  >  2:662384/1‑149 (MQ=255)
                                                       gTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAg                                                                                  <  2:427616/149‑1 (MQ=255)
                                                       gTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAg                                                                                  <  2:260696/149‑1 (MQ=255)
                                                            ccAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGGTTCa                                                                             >  1:135775/1‑149 (MQ=255)
                                                             cAATGACTAGTCTAAAAACTAGTATTAAGACTTTCACTTATTTAAGTGAGATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCGAAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATACAGGTACTTGTAGATTCaa                                                                            <  1:278576/149‑1 (MQ=21)
                                                                tGACTAGCCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTg                                                                         <  2:232174/149‑1 (MQ=255)
                                                                      ggcTAAAAATTAGGACTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGGAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAAc                                                                   <  2:173822/147‑1 (MQ=255)
                                                                      gTCCAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAAc                                                                   <  2:176013/149‑1 (MQ=255)
                                                                          aaaaaCTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCaa                                                               >  2:203896/1‑149 (MQ=255)
                                                                            aaaCTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACa                                                             <  2:709109/149‑1 (MQ=255)
                                                                                 agaaTTAAGCCTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTAt                                                        <  1:764097/146‑1 (MQ=255)
                                                                                    aTTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATCAAGGTACTTGTAGATTCAATTGGTCAACGCAACCGTTAtgtg                                                     >  2:415676/1‑149 (MQ=255)
                                                                                    aTTAAGACTATCAATTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTCTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTAtgtg                                                     >  1:529355/1‑149 (MQ=255)
                                                                                                  ttATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTGAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTg                                       >  2:173713/1‑149 (MQ=255)
                                                                                                   tATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGc                                      <  1:824646/149‑1 (MQ=255)
                                                                                                    aTTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCg                                     <  2:41765/149‑1 (MQ=255)
                                                                                                           tGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTGGCGGAGGttt                              >  2:230805/1‑149 (MQ=255)
                                                                                                              tatTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGtttttt                           <  2:135775/149‑1 (MQ=255)
                                                                                                              tatTGGTTGGCTGGAGATGCAGGGCGCCAGTCTACACCCCAGAACTTACGTCTGCTGATGCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATCCAATTGGTCAACGCAACAGTTATGTGAAAACACGGGGTTGCGGAGGtttttt                           <  1:571833/149‑1 (MQ=25)
                                                                                                              gatTTGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGtttttt                           <  1:241118/148‑1 (MQ=255)
                                                                                                                      gTCTGGAGATTCAGGGTGCCAGTCTAAACACCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAGTTGGTCAACGCAACAGTTATGTGAAAACAGGGGGATGCGGAGGTTTTTTGAATgaga                   >  2:550890/1‑149 (MQ=37)
                                                                                                                         tGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCACCATTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAATGAGACGa                <  2:771132/149‑1 (MQ=255)
                                                                                                                                       gCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAATGAGACGAACATTTACAGCaga  <  2:50908/149‑1 (MQ=255)
                                                                                                                                               |                                                                                                                                            
TTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAATGAGACGAACATTTACAGCAGA  >  CP009273/1463354‑1463637

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.