New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1426689	10 (0.050)	11 (0.060)	7/146	NT	54.7%	intergenic (‑420/+552)	pstS/cvfB	Phosphate‑binding protein PstS/Conserved virulence factor B
	?	USA300TCH1516_ALE	= 1426728	NA (NA)					intergenic (‑459/+513)	pstS/cvfB	Phosphate‑binding protein PstS/Conserved virulence factor B

GCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATACAT  >  USA300TCH1516_ALE/1426721‑1426819        |                                                                                            gCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTg          >  1:1732508/1‑91 (MQ=31)  cTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGa         >  2:3131116/1‑91 (MQ=32)  cTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGa         >  2:2597297/1‑91 (MQ=32)  cTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGa         >  2:1611342/1‑91 (MQ=32)   ttCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGaa        <  2:1645748/91‑1 (MQ=33)    tCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGaaa       <  1:1400783/91‑1 (MQ=34)     cTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAAt      >  1:314960/1‑91 (MQ=34)     cTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAAt      >  2:217514/1‑91 (MQ=34)      tgtgTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATa     >  2:993048/1‑91 (MQ=34)      tgtgTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATa     >  1:1591806/1‑91 (MQ=33)      tgtgTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATa     >  1:1592823/1‑91 (MQ=34)      tgtgTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATa     >  1:3214647/1‑91 (MQ=34)      tgtgTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATa     >  1:2018259/1‑91 (MQ=34)      tgtgTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATa     >  1:1592837/1‑91 (MQ=34)       gtgtTGGGGCCCCTGTCTTTGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATAc    >  2:797297/1‑91 (MQ=18)       gtgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTCCGTATTAACATGTAATTTTACTTTGAAATAc    >  1:1077501/1‑91 (MQ=18)       gtgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATAc    >  1:2003862/1‑91 (MQ=33)       gtgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATAc    <  2:3828533/91‑1 (MQ=34)       gtgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATAc    <  2:3094184/91‑1 (MQ=34)       gtgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATAc    >  2:2222608/1‑91 (MQ=33)       gtgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATAc    <  2:1560992/91‑1 (MQ=34)       gtgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATAc    >  1:2931388/1‑91 (MQ=34)       gtgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATAc    >  1:2928917/1‑91 (MQ=34)       gtgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATAc    <  1:287832/91‑1 (MQ=34)       gtgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATAc    >  1:2588820/1‑91 (MQ=34)       gtgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATAc    >  1:2588435/1‑91 (MQ=34)       gtgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATAc    <  1:2301860/91‑1 (MQ=34)       gtgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAA‑‑TTACTTTGAAATACAt  >  1:2019631/1‑91 (MQ=255)       gtgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGCCCCGCCATTAATACTACGTATTCACATGTAACGTTACTCTGAAATAc    >  2:3098045/1‑91 (MQ=11)        tgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATACa   >  2:1653354/1‑91 (MQ=35)        tgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATACa   >  2:2265583/1‑91 (MQ=35)        |                                                                                            GCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTGAAATACAT  >  USA300TCH1516_ALE/1426721‑1426819

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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.