New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 557240	NA (NA)	5 (0.010)	3/152	NT	NA	intergenic (+298/‑1471)	USA300TCH1516_00504/USA300TCH1516_00505	tRNA‑Ala/tRNA‑Ile
	?	USA300TCH1516_ALE	= 557277	NA (NA)					intergenic (+335/‑1434)	USA300TCH1516_00504/USA300TCH1516_00505	tRNA‑Ala/tRNA‑Ile

TTCTCTGATGTTAGCGGCGGACGGGTGAGTAACACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGCTAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTCTTGCTGTCA  >  USA300TCH1516_ALE/557151‑557291                                                                                          |                                                    ttttctGATGTTAGCGGCGGACGGGTGAGTAACACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGCTAATACCgg                                                    <  2:1951376/88‑1 (MQ=1)                        ggagAGTAACACGTGGATAACCGACCTAGAAGACTGGGATAACTTCGGGAAACCGGAGCTAATACCGGATAATATTTTGAACCGCATGGtt                             <  2:5641464/88‑1 (MQ=0)                                                   attaGACTGGGATAACTTCGGGAAACCGGAGCTAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTCTTGCTGTCa  <  2:6175323/88‑1 (MQ=1)                                                                                          |                                                    TTCTCTGATGTTAGCGGCGGACGGGTGAGTAACACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGCTAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTCTTGCTGTCA  >  USA300TCH1516_ALE/557151‑557291

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.