New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	556088 =	389 (1.090)	82 (0.240) +TA	15/156	NT	17.8%	intergenic (+556/‑129)	lysS/USA300TCH1516_00497	Lysine‑‑tRNA ligase/tRNA‑Val
	?	USA300TCH1516_ALE	561925 =	NA (NA)					intergenic (+3138/+664)	USA300TCH1516_00505/gabR	tRNA‑Ile/HTH‑type transcriptional regulatory protein GabR

CTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTCCCATGCCGAACACAGAAGTTA  >  USA300TCH1516_ALE/561914‑562004            |                                                                                ctgtCTAGTTTTGAATGTATAAGTTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTCCCATGCCGAACACAGAAGTTa  <  2:6602529/88‑1 (MQ=0)            |                                                                                CTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTCCCATGCCGAACACAGAAGTTA  >  USA300TCH1516_ALE/561914‑562004

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.