New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2478424	7 (0.030)	6 (0.030)	4/146	NT	48.5%	intergenic (+311/‑264)	USA300HOU_RS12760/USA300HOU_RS12765	hypothetical protein/hypothetical protein
	?	USA300TCH1516_ALE	= 2478463	NA (NA)					intergenic (+350/‑225)	USA300HOU_RS12760/USA300HOU_RS12765	hypothetical protein/hypothetical protein

GCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACT  >  USA300TCH1516_ALE/2478456‑2478553        |                                                                                           gCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACtttt         <  2:95089/91‑1 (MQ=31) gCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACtttt         <  1:240830/91‑1 (MQ=31)  cTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTa        <  2:3797942/91‑1 (MQ=32)   ttCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTaa       >  2:2927463/1‑91 (MQ=33)   ttCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTCTTaa       <  1:3126092/91‑1 (MQ=17)     cTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCGGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAAt     >  1:1612426/1‑91 (MQ=21)     cTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAAt     <  2:343211/91‑1 (MQ=33)     cTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAAt     <  1:2227520/91‑1 (MQ=34)      tgtgTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAACTa    >  2:2633531/1‑91 (MQ=18)       gtgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATAc   >  2:742177/1‑91 (MQ=33)       gtgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATAc   <  2:874604/91‑1 (MQ=34)       gtgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATAc   >  1:1016890/1‑91 (MQ=34)        tgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACt  <  1:735581/91‑1 (MQ=35)        tgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACt  >  2:1909013/1‑91 (MQ=35)        tgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACt  <  2:1940904/91‑1 (MQ=35)        tgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACt  <  2:606711/91‑1 (MQ=35)        tgtTGGGGCCCCTGTCTTCGACTGGCACTGCCCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACt  >  1:601964/1‑91 (MQ=21)        |                                                                                           GCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACT  >  USA300TCH1516_ALE/2478456‑2478553

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ 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.