New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 280894	206 (1.010)	15 (0.090) +TTAATTGGGAGTA	5/134	NT	8.8%	intergenic (‑146/+11)	USA300HOU_RS01225/USA300HOU_RS01230	hypothetical protein/hypothetical protein
	?	USA300TCH1516_ALE	855632 =	165 (0.810)					intergenic (+163/‑597)	zipA_1/cggR	Cell division protein ZipA/Central glycolytic genes regulator

AACAGCCATGACAAAGTAAAGTCATAGCTGTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/280861‑280894 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGACAGAAATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACT  >  USA300TCH1516_ALE/855632‑855681                                   |||||||||||||                                                   AACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACC        >  1:122241/1‑91  ACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCa       >  1:1338304/1‑90  ACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCa       >  1:1734055/1‑90  ACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCa       >  1:2543426/1‑90  ACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCa       >  1:3910179/1‑90  ACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCa       >  2:1014165/1‑90  ACAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCa       >  2:3302195/1‑90   CAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCac      >  1:2049961/1‑89   CAGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCac      >  1:2182743/1‑89    AGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGATATGATATTTTCGCTAAATTTATTTGGTCGTCCCGCCaca     >  1:3674875/1‑88    AGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCaca     >  1:3699678/1‑88    AGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCaca     >  1:797358/1‑88    AGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCaca     >  1:797661/1‑88    AGCCATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCACA     >  1:797548/1‑91       CATGACAAAGTAAAGTCATAGCTGTTTTTTAATTGGGAGTAGGACAGAGATGATATTTTCGCAAAATTTATTTGGTCGTCCCACCACAACa  >  2:1983311/1‑90                                   |||||||||||||                                                   AACAGCCATGACAAAGTAAAGTCATAGCTGTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/280861‑280894 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGACAGAAATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACT  >  USA300TCH1516_ALE/855632‑855681

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.