New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 = 90728145 (0.860)5 (0.100) 3/240 NT 10.5% intergenic (+390/‑39) USA300HOU_0865/USA300HOU_0866 hypothetical protein/hypothetical protein
?CP000730 = 907290 44 (0.910)intergenic (+399/‑30) USA300HOU_0865/USA300HOU_0866 hypothetical protein/hypothetical protein

AATATTGGTGGGTTTGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAGAAAATGAAAATTATTATAATATC  >  CP000730/907150‑907430
                                                                                                                                            |                                                                                                                                            
aataTTGGTGGGTTTGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAACTGTATTGTATTTATAACGATCTAGCCATAACTCAATTCgg                                                                                                                                              >  2:211853/1‑141 (MQ=255)
aataTTGGTGGGCTTGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCgg                                                                                                                                              <  1:412661/141‑1 (MQ=255)
     tggtggGTTTGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGgttat                                                                                                                                         >  1:360257‑M2/1‑136 (MQ=255)
      ggtggGTTTGAGGAGCAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGgttatg                                                                                                                                        <  1:452910‑M2/141‑7 (MQ=255)
         tggtTTGAGGAGGAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGgttatggct                                                                                                                                     >  1:181536‑M2/2‑132 (MQ=255)
             ttGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACtt                                                                                                                                 <  1:20107/141‑1 (MQ=255)
               gaggagTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACtttt                                                                                                                               >  2:452992/1‑141 (MQ=255)
                   agTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAg                                                                                                                           <  1:96353/141‑1 (MQ=255)
                    gTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATATAGCCATAACTATATTCGGGTTATGGCTACTTTTATAgg                                                                                                                          >  1:7368/1‑141 (MQ=255)
                        cAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTa                                                                                                                      >  2:251100/1‑141 (MQ=255)
                         aataaaataaAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTaa                                                                                                                     <  2:508840/141‑1 (MQ=255)
                         aataaaataaAGGAGGTAATTGTGTAAAATACCCCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTat                                                                                                                     <  2:405138/141‑2 (MQ=255)
                          ataaaataaaGGAGGTAATTTTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTaaa                                                                                                                    <  2:408405/141‑1 (MQ=255)
                          ataaaataaaGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTaaa                                                                                                                    >  2:604817/1‑141 (MQ=255)
                              aataaaGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTaagatta                                                                                                                >  1:230725/1‑136 (MQ=255)
                                  aaGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGaa                                                                                                            >  1:84823/1‑141 (MQ=255)
                                      aggTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCa                                                                                                        >  1:462021/1‑141 (MQ=255)
                                           aTTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGa                                                                                                   >  2:363375/1‑141 (MQ=255)
                                                 gaaaaTATGTTCTTTTGTTATTTCTTATTTATTTACCACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCa                                                                                             <  1:112315/140‑1 (MQ=255)
                                                   aaaTATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACCCGAATAGAgttatggctagatcgttatatatataatacatttaattttatcggttgtaa                                                                                           >  1:382133‑M2/1‑90 (MQ=255)
                                                         ctctTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAAc                                                                                     <  1:14911/141‑1 (MQ=255)
                                                             ttttGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAAtt                                                                                 >  2:528609/1‑141 (MQ=255)
                                                             ttttGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAAtt                                                                                 >  1:515240/1‑141 (MQ=255)
                                                               tttttcttttatattgatttacaaccgacaAAATTAAATGTATTATATATATAACGATCTAGCCATAACCCGAATAGAgttatggctagatcgttatatatataatacatttaattttatcggttgtaaataaataagaaa                                                                               >  2:343542‑M2/12‑78 (MQ=255)
                                                               ttttTATTTCGTATTAATTTACAACCGATAAAATTAAATGTATGATATATATAACGATCTAGCCATAACCCGAATAGAgttatggctagatcgttatatatataatacatttaattttatcggttgtaaataaataagaaa                                                                               >  2:538581‑M2/1‑78 (MQ=255)
                                                                     tttCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAAGTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTc                                                                         <  1:574078/141‑1 (MQ=255)
                                                                      ttCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCt                                                                        <  1:93672/141‑1 (MQ=255)
                                                                          tatttattTACAACCGATAAAATTAAATCTATTATAAAGATAACGATCTAGCCATAACTCGATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAAGAAACAATTCAAAATTCTaaga                                                                    <  1:316819/141‑1 (MQ=255)
                                                                            tttatttaCAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTaagaag                                                                  >  1:244150/1‑141 (MQ=255)
                                                                             taatttaCAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTAAAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTaagaaga                                                                 <  2:578370/139‑1 (MQ=255)
                                                                                     aaCCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAAt                                                         <  1:533768/141‑1 (MQ=255)
                                                                                            aaaaTTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTa                                                  <  2:452910/141‑1 (MQ=255)
                                                                                              aaTTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTAcc                                                <  1:540004/141‑1 (MQ=255)
                                                                                              aaTTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAAATTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTAcc                                                >  2:217949/1‑141 (MQ=255)
                                                                                                  aaaTGTATTATATATATAACGATCTAGCCATAACTCTATTAGGGTTATGGCTACTTATATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATGGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGaga                                            >  2:99197/1‑140 (MQ=255)
                                                                                                   aaTGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGagta                                           <  2:515240/141‑1 (MQ=255)
                                                                                                   aaTGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTGTTAGAAGGGTAAATTTATGAAGCCATTTGACAGTCGTCATCAACAATTGCAAATTCTAAGAATAAGAGGAATGGAAGTACCGagta                                           >  1:507677/1‑141 (MQ=255)
                                                                                                     tGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATCGAAGTACCGagtagt                                         <  1:452992/141‑1 (MQ=255)
                                                                                                     tGTATTATATATATAACGATCTAGCCAAAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGagtagt                                         <  1:204188/141‑1 (MQ=255)
                                                                                                        attatATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGGGGAATGGAAGTACCGAGTAGTGCt                                      >  1:421771/1‑141 (MQ=255)
                                                                                                         ttatATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTa                                     <  1:241635/141‑1 (MQ=255)
                                                                                                                tataACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAgaga                              >  1:489564/1‑141 (MQ=255)
                                                                                                                tataACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAgaga                              >  1:271846/1‑141 (MQ=255)
                                                                                                                    aCGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTa                          >  2:411570/1‑141 (MQ=255)
                                                                                                                    aCGATCCAGCCATAAATGTAGCCGGGTGATAGCTACTTTTAGAGGGGTAAATTTATGAAGCCATTTGTAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTa                          <  1:9663/141‑1 (MQ=255)
                                                                                                                        tCTAGCCATAACTCTATTCGTGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAgaaa                      >  1:373216/1‑141 (MQ=255)
                                                                                                                         cTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAgaaaa                     <  2:236325/141‑1 (MQ=255)
                                                                                                                         cTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAgaaaa                     >  1:162234/1‑141 (MQ=255)
                                                                                                                           aGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAgaaaatg                   >  2:397629/1‑141 (MQ=255)
                                                                                                                             ccATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAgaaaatgaa                 >  2:427865/1‑141 (MQ=255)
                                                                                                                             ccATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCCAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAgaaaatgaa                 <  1:25065/141‑1 (MQ=255)
                                                                                                                               aTAACTTTATTCGGGTTGTGGCCACTTTTAAAGGAGTAAAATTATGAAGCCACTTGAAAGTCATAATAAACAATTGCAAATTTTGCGAAGAAGGGGAAGCGGAGTTCCAATGAGTGCTAAAAGAGATTTAgaaaatgaaaa               <  2:431174/141‑1 (MQ=255)
                                                                                                                                 acctctATTTCGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAGAAAATGAAAatt             <  1:62448/139‑1 (MQ=255)
                                                                                                                                    tctATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGGAGTACCGAGTAATGCTAAAAGAGATTTAGAAAATGAAAattatt          >  2:178994/1‑141 (MQ=255)
                                                                                                                                       aTTCGGgttatggctagatcgttatatatataatacatttaattttatcggttgtaaataaataagaaataacaaaaagagatattttacacaattacctcctttattttattgctactcctcaaacccaccaatattatc       <  1:361909‑M2/141‑136 (MQ=255)
                                                                                                                                       aTTCGGgttatggctagatcgttatatatataatacatttaattttatcggttgtaaataaataagaaataacaaaaagagatattttacacaattacctcctttattttattgctactcctcaaacccaccaatattatc       <  2:289330‑M2/141‑136 (MQ=255)
                                                                                                                                         tCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAGAAAATGAAAATTATTataat     <  1:25578/141‑1 (MQ=255)
                                                                                                                                            ggTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAGAAAATGAAAATTATTATAATATc  >  1:64377/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                            
AATATTGGTGGGTTTGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAGAAAATGAAAATTATTATAATATC  >  CP000730/907150‑907430

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.