New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE = 280894202 (1.060)18 (0.110)
+TTAATTGGGAGTA		 7/134 NT 10.5% intergenic (‑146/+11) USA300HOU_RS01225/USA300HOU_RS01230 hypothetical protein/hypothetical protein
?USA300TCH1516_ALE 855632 = 165 (0.870)intergenic (+163/‑597) zipA_1/cggR Cell division protein ZipA/Central glycolytic genes regulator

TAAAAAACAGCCATGACAAAGTAAAGTCATAGCTGTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/280856‑280894
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGACAGAAATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCA  >  USA300TCH1516_ALE/855632‑855678
                                       |||||||||||||                                               
TAAAAAACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTC          >  2:1425246/1‑91
  AAAAACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCC        >  2:2223709/1‑91
   AAAACAGCCATGACAAAGTAAAGTCATGGCTGATTCTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCA       >  1:1708963/1‑91
   AAAACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCA       >  2:1236222/1‑91
     AACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACC     >  1:3303534/1‑91
     AACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACC     >  1:3303553/1‑91
     AACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACC     >  2:3751139/1‑91
     AACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACC     >  2:3749866/1‑91
      ACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCa    >  1:3714947/1‑90
      ACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCa    >  2:1393099/1‑90
      ACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGCAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCa    >  2:3099870/1‑90
       CAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCac   >  1:1468992/1‑89
        AGCGATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCACACCaca  >  2:3443833/1‑88
        AGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCaca  >  2:601394/1‑88
        AGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCaca  >  1:3732492/1‑88
        AGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCACA  >  2:3652858/1‑91
        AGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCACA  >  2:2142134/1‑91
        AGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCACAAAATTTATTTGGTCGTCCCACCaca  >  1:168196/1‑88
                                       |||||||||||||                                               
TAAAAAACAGCCATGACAAAGTAAAGTCATAGCTGTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/280856‑280894
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGACAGAAATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCA  >  USA300TCH1516_ALE/855632‑855678

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ 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.