New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 280894	103 (1.050)	11 (0.130) +TTAATTGGGAGTA	7/134	NT	11.2%	intergenic (‑146/+11)	USA300HOU_RS01225/USA300HOU_RS01230	hypothetical protein/hypothetical protein
	?	USA300TCH1516_ALE	855632 =	105 (1.070)					intergenic (+163/‑597)	zipA_1/cggR	Cell division protein ZipA/Central glycolytic genes regulator

ACTCCCAATTAAAAAACAGCCATGACAAAGTAAAGTCATAGCTGTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/280847‑280894 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGACAGAAATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACT  >  USA300TCH1516_ALE/855632‑855681                                                 |||||||||||||                                                   ACTCCCAATTAAAAAACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTAT                      >  1:2260544/1‑91              AAACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCAC         >  1:806688/1‑91              AAACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCAC         >  1:826931/1‑91                ACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCa       >  1:1157185/1‑90                ACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCa       >  1:1157705/1‑90                ACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCa       >  1:1157847/1‑90                ACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCa       >  1:384101/1‑90                 CAGCCATGACAACGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCac      >  1:3181955/1‑89                  AGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCaca     >  1:1354285/1‑88                   GCCATGACAAAGGAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCACAA    >  1:3181079/1‑91                     CATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCACAACa  >  1:2503252/1‑90                                                 |||||||||||||                                                   ACTCCCAATTAAAAAACAGCCATGACAAAGTAAAGTCATAGCTGTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/280847‑280894 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGACAGAAATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACT  >  USA300TCH1516_ALE/855632‑855681

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