New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 2085296 =54 (0.690)13 (0.190) 12/232 NT 18.6% intergenic (‑558/‑400) mapW2/USA300HOU_1944 cell surface protein MapW2/hypothetical protein
?CP000730 = 2128343 66 (0.950)intergenic (+57/+1062) int/USA300HOU_2011 bacteriophage integrase/possible leukocidin subunit

TGTAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP000730/2085449‑2085296
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccagtttggatacaTAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATGTAG  <  CP000730/2128343‑2128204
                                                                                                                                                                                                                                                                                                      
tgcAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTGTATATGAGGTATTATTGATAATGATAAAGATATAAATCGTTATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTC                                                                                                                                                           <  1:27904/138‑1
TGTAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTACAAGTCTC                                                                                                                                                           <  2:552082/141‑1
TGTAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTC                                                                                                                                                           <  1:388543/141‑1
 tTAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCC                                                                                                                                                          <  1:288950/140‑1
 GTAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCC                                                                                                                                                          <  1:699162/141‑1
 GTAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCC                                                                                                                                                          <  1:807030/141‑1
    ATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGT                                                                                                                                                       >  1:804921/1‑141
        TAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTCCTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCCGTTTGG                                                                                                                                                   >  1:879204/1‑141
          AATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGAT                                                                                                                                                 <  1:716757/141‑1
                                  TAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTGGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGT                                                                                                                         >  2:53550/1‑141
                                      ATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTT                                                                                                                     >  2:732063/1‑141
                                             TTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGT                                                                                                              <  1:68754/141‑1
                                                         ATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTA                                                                                                  <  1:8202/141‑1
                                                          TTATTGATAATGATAAAGTTACAAACCTTGATATTATGCTGTTTTAATTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAA                                                                                                 <  1:766219/141‑1
                                                                                     TTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAA                                                                      >  1:372142/1‑141
                                                                                                        CTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTG                                                   <  2:301040/141‑1
                                                                                                                  gctgAGTACTTTTATGTTAAAAGTCTCCAGTTTTGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGGCCCTAAGGGGTCCCTAAATTACATACTTTCAAATATTTTATTTTTTTTTTTGTCCTCTTCAT                                         <  1:225832/137‑1
                                                                                                                  GATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCAT                                         >  2:581303/1‑141
                                                                                                                   ATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTACATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATT                                        <  2:155671/141‑1
                                                                                                                    TAATTAATTTTATGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAACTTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTA                                       <  2:532806/141‑1
                                                                                                                                TGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCT                           >  1:20827/1‑141
                                                                                                                                TGTTAAAAGTCTCCAGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCT                           >  1:20902/1‑141
                                                                                                                                              AGTTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATA             <  1:97128/141‑1
                                                                                                                                                TTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACA           <  1:429869/141‑1
                                                                                                                                                TTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACA           <  2:229093/141‑1
                                                                                                                                                TTTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACA           <  2:721239/141‑1
                                                                                                                                                 TTGGATACATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACAC          <  1:663541/141‑1
                                                                                                                                                         ATAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATGTAG  <  1:761372/141‑1
                                                                                                                                                                                                                                                                                                      
TGTAATTTTAAATTTAAAGTCCCTAAAAAGTCCCTAAAATTTTATTTTATATGAGGTATTATTGATAATGATAAAGTTATAAACCTTGATATTATGCTGTTTTACTTTTTGAATGATAAGTAATTTTATGTTAAAAGTCTCCAGTTTGGATACA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP000730/2085449‑2085296
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccagtttggatacaTAGAAACCTTGTAACAACAGTATTTATTGGGTTTGGAGTCCCTAATGGGTCCCTAAATTACATACTTTCTAAAATTTTAGTTGTTTTTTTGTCCTCTTCATTAAATTTTTCTTCTAACAAATGAGAATACACGGATGTAG  <  CP000730/2128343‑2128204

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.