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

GATAATATTGGTGGGTTTGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAGAAAATGAAAATT  >  CP000730/907147‑907419
                                                                                                                                      |                                                                                                                                          
gATAATATTGGTGGGTTTGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACccgaat                                                                                                                                      <  2:289330‑M1/141‑7 (MQ=255)
gATAATATTGGTGGGTTTGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACccgaat                                                                                                                                      <  1:361909‑M1/141‑7 (MQ=255)
   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)
                                                                        tttCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACtctattcgggttatggctagatcgttatatatatcatacatttaattttatcggttgtaaattaatacgaaataaaaa                                                              >  2:538581‑M1/1‑63 (MQ=255)
                                                                        tttCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACtctattcgggttatggctagatcgttatatatataatacatttaattttgtcggttgtaaatcaatataaaagaaaaa                                                              >  2:343542‑M1/1‑63 (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)
                                                                                    ttaCAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACtctattcgggttatggctagatcgttatatatataatacatttaattttatcggttgtaaataaataagaaataacaaaaagagatattt                                                  >  1:382133‑M1/1‑51 (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)
                                                                                                                              aGCCATAACccgaatagagttatggctagatcgttatatatataatacatttaattttatcggttgtaaataaataagaaataacaaaaagagatattttacacaattacctcctttattttattgctcctcctcaaacca        >  1:181536‑M1/1‑9 (MQ=255)
                                                                                                                              aGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAgaaaatg        >  2:397629/1‑141 (MQ=255)
                                                                                                                                ccATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAgaaaatgaa      >  2:427865/1‑141 (MQ=255)
                                                                                                                                ccATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCCAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAgaaaatgaa      <  1:25065/141‑1 (MQ=255)
                                                                                                                                 cATAACccgaatagagttatggctagatcgttatatatataatacatttaattttatcggttgtaaataaataagaaataacaaaaagagatattttacacaattacctcctttattttattgctgctcctcaaacccacc     <  1:452910‑M1/141‑136 (MQ=255)
                                                                                                                                  aTAACccgaatagagttatggctagatcgttatatatataatacatttaattttatcggttgtaaataaataagaaataacaaaaagagatattttacacaattacctcctttattttattgctactcctcaaacccacca    >  1:360257‑M1/1‑5 (MQ=255)
                                                                                                                                  aTAACTTTATTCGGGTTGTGGCCACTTTTAAAGGAGTAAAATTATGAAGCCACTTGAAAGTCATAATAAACAATTGCAAATTTTGCGAAGAAGGGGAAGCGGAGTTCCAATGAGTGCTAAAAGAGATTTAgaaaatgaaaa    <  2:431174/141‑1 (MQ=255)
                                                                                                                                    acctctATTTCGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAGAAAATGAAAatt  <  1:62448/139‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                          
GATAATATTGGTGGGTTTGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAGAAAATGAAAATT  >  CP000730/907147‑907419

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.