New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	52489 =	136 (1.380)	7 (0.070)	5/160	NT	7.3%	intergenic (+99/‑574)	USA300HOU_RS00215/USA300HOU_RS00220	hypothetical protein/hypothetical protein
	?	USA300TCH1516_ALE	52811 =	41 (0.420)					intergenic (+421/‑252)	USA300HOU_RS00215/USA300HOU_RS00220	hypothetical protein/hypothetical protein

TTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGCGATTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/52578‑52489 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TCGCGCGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAAT  >  USA300TCH1516_ALE/52811‑52854                                                                                                                                        TTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGCGATTTT                                             >  1:1504354/1‑91    CAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGCGATTTTCGC                                          >  1:311858/1‑91        CGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGCGATTTTCGCGCGA                                      >  1:2816643/1‑91                                     CGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGAAAATCGCGTGAAATAATCAGAGGAATCGT         >  1:3630648/1‑91                                      GCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGAAAATCCCGTGAAATAATCAGAGGAATCGTT        >  1:1616877/1‑91                                      GCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGAAAATCACGTGAAATAATCAGAGGAATCGTT        >  1:1522995/1‑91                                      GCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGCGATTTTCGCGCGACCATCACGTGAAATAATCAGAGGAAGCGct        >  1:1857200/1‑89                                        GCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGAAAATCGCGTGAAATAATCAGAGGAATCGTTTG      >  1:2589474/1‑91                                            TTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGAAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAAT  >  1:4065322/1‑91                                                                                                                                        TTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGCGATTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/52578‑52489 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TCGCGCGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAAT  >  USA300TCH1516_ALE/52811‑52854

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