New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 = 120532363 (0.980)3 (0.050)
+AGCGAA
3/248 NT 6.2% intergenic (+459/‑365) USA300HOU_1131/lspA possible lactoylglutathione lyase/A8 family signal peptidase II
?CP000730 = 1893309 33 (0.510)intergenic (‑1303/+177) rot/USA300HOU_1755 repressor of toxins Rot/lysophospholipase

ATTTATTAAATTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAAC  >  CP000730/1893169‑1893408
                                                                                                                                             |                                                                                                   
atttattAAATTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTGAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGc                                                                                                     >  1:112198/1‑141 (MQ=255)
 tttattAAATTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCg                                                                                                    >  1:323586/1‑141 (MQ=255)
 tttattAAATTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTACGTGCAAGTTGGGAAAAATGTCTTATTTTATCGAAGTATTGAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCg                                                                                                    <  1:337196/141‑1 (MQ=255)
 tttattAAATTATAAGAAGGGACGCAACAGAGAAAATTCATTTTATTGAATTTTACATTTATGGGCAAGTTGGGAAAAATGTCTTATTTTTTTAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCg                                                                                                    <  1:337513/141‑1 (MQ=11)
   tattaAATTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCgag                                                                                                  <  1:351706/141‑1 (MQ=255)
    attaAATTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATAGTGCATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCgaga                                                                                                 >  1:597545/1‑141 (MQ=255)
      taAATTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTTTTAATGGCGAGACt                                                                                               >  1:126387/1‑141 (MQ=255)
       aaaTTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTc                                                                                              <  1:527173/141‑1 (MQ=255)
        aaTTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTcc                                                                                             >  2:441069/1‑141 (MQ=255)
        aaTTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTAAATGGTAATACGTAGTATTAATGGCGAGACTcc                                                                                             <  2:701915/141‑1 (MQ=255)
         aTTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCt                                                                                            <  1:349461/141‑1 (MQ=255)
              aCGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTGAATGGCttcgctttcctag                                                                                        <  1:507450‑M2/141‑14 (MQ=255)
               cGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGTCGAGACTCCTGATGGa                                                                                      >  2:231178/1‑141 (MQ=255)
               cGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGa                                                                                      >  1:115742/1‑141 (MQ=255)
                   gggACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAg                                                                                  >  2:236768/1‑141 (MQ=255)
                     gACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTg                                                                                >  2:34217/1‑141 (MQ=255)
                       cccAACACAGAAAATTCATTTTATTGGATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGcc                                                                              <  2:510685/141‑1 (MQ=255)
                        ccAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCa                                                                             >  2:546808/1‑141 (MQ=255)
                                    aTTCATTTTATTGAATTTTGCGTTAATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGa                                                                 >  2:544455/1‑141 (MQ=255)
                                      tCATTTTATTGAATTTTACATTTATGTGCAAGTGGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACCCCTGAGGGAGCAGCGCCAGGCGAAGACCGAgg                                                               <  2:184002/141‑1 (MQ=255)
                                        aTTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCt                                                             >  2:69237/1‑141 (MQ=255)
                                            tATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTgaga                                                         <  2:574933/141‑1 (MQ=255)
                                                    tttACATTTATGTGCAAGTTGGGATAAATGTCTTATTTTTTCAAAGTTTTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCGGTGCCAGTCGGAGTCCGAGGCTGAGACGGCAccc                                                 >  1:184822/1‑141 (MQ=14)
                                                    tttACATTTATGTGCAAGATGGCGTAGATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCAccc                                                 >  1:184885/1‑141 (MQ=14)
                                                       aCATTTATGTGCAAGTTGGGTAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAACTTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAg                                              >  1:51595/1‑141 (MQ=255)
                                                         aTTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAATTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGa                                            >  2:385039/1‑141 (MQ=255)
                                                            tATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAg                                         >  1:65801/1‑141 (MQ=255)
                                                              tgtgCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCg                                       <  1:34217/141‑1 (MQ=255)
                                                                 gCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAg                                    <  2:115742/141‑1 (MQ=255)
                                                                 gCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTGAATACGTAGTATTAATGGCGAGACTCCTGAGTGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAg                                    <  2:224360/141‑1 (MQ=255)
                                                                 gCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATGTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCttcgctttcctagggtgccgtctcagcctcggtcttcgactggcactgctccctcaggagtctcg                                    >  1:589907‑M2/1‑76 (MQ=255)
                                                                         ggAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCaa                            >  1:60824/1‑141 (MQ=255)
                                                                               aTGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAATCGAAGCCATTCAATActtc                      <  1:88650/141‑4 (MQ=25)
                                                                               aTGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGGGAAGCCATTCAATACGaa                      >  2:170145/1‑141 (MQ=25)
                                                                                       atttttttttttttttAAAAGTAAAATTACATGTTAATACGTAGTATTATTGGCGGGATTTCTGAGGGTGCAGTGCCTGTCGAAGAGCGAGGCTGGGTCGGCGCTCTAGGAAAGTGATGCTATTCATTTCGAGGTATGGtt              >  2:193044/14‑140 (MQ=2)
                                                                                         ttttCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGtata            <  1:65546/141‑1 (MQ=35)
                                                                                         ttttCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGtata            <  1:364143/141‑1 (MQ=35)
                                                                                           ttCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATaaa          >  2:146449/1‑141 (MQ=34)
                                                                                           ttCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATaaa          >  1:80185/1‑141 (MQ=35)
                                                                                            tCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTGAATGGCttcgctttcctagggtgccgtctcagcctcggtcttcgactggcactgctccctcagaagtctcgccatcaatactacgtattaacatgta          >  2:507450‑M2/1‑50 (MQ=255)
                                                                                                aGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATagag     >  1:357347/1‑141 (MQ=32)
                                                                                                   ttttAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAATACCGAGGCTGTGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAAc  >  2:667177/2‑141 (MQ=14)
                                                                                                                                             |                                                                                                   
ATTTATTAAATTATACGAAGGGACCCAACACAGAAAATTCATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAATGTCTTATTTTTTCAAAGTATTTAAAAGTAAAATTACATGTTAATACGTAGTATTAATGGCGAGACTCCTGAGGGAGCAGTGCCAGTCGAAGACCGAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAAC  >  CP000730/1893169‑1893408

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.