New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 558929	NA (NA)	3 (0.010)	3/144	NT	NA	intergenic (+142/+3660)	USA300TCH1516_00505/gabR	tRNA‑Ile/HTH‑type transcriptional regulatory protein GabR
	?	USA300TCH1516_ALE	= 558960	NA (NA)					intergenic (+173/+3629)	USA300TCH1516_00505/gabR	tRNA‑Ile/HTH‑type transcriptional regulatory protein GabR

ATAAGAAATAATCGCTAGTGTTCGAAAGAACACTCACAAGATTAATAACGCGTTTCCTGTAGGATGGAAACATAGATTAAGTTATTAAGGGCGCACGGTGGATGCCTTGGCACTAGAAGCCGATGAAGGACGTTACTAACGACGATATGCT  >  USA300TCH1516_ALE/558881‑559031                                                                                |                                                                        cgttattaatcttgtgAGTGTTCTTTCGAACACTCACAAGATTAATAACGCGTTTCCTGTAGGATGGAAACATAGATTAAGTTATTAAggg                                                              >  1:5316853‑M2/17‑91 (MQ=255)        aatcttgtgAGTGTTCTTTCGAACACTCACAAGATTAATAACGCGTTTCCTGTAGGATGGAAACATAGATTAAGTTATTAAGGGCGCACgg                                                       >  2:3352262‑M2/10‑91 (MQ=255)        aatcttgtgAGTGTTCTTTCGAACACTCACAAGATTAAGAACGCGTTTCCTGTAGGATGGAAACATAGATTAAGTTATTAAGGGCGCACgg                                                       >  2:3464020‑M2/10‑91 (MQ=255)         atcttgtgAGTGTTCTTTCGAACACTCACAAGATTAATAACGCGTTTCCTGTAGGATGGAAACATCGATTAAGTTATTAAGGGCGCACGGt                                                      >  1:5157446‑M2/9‑91 (MQ=255)           cttgtgAGTGTTCTTTCGAACACTCACAAGATTAATAACGCGTTTCCTGTAGGATGGAAACATAGATTAAGTTATTAAGGGCGCACGGTgg                                                    >  1:5305527‑M2/7‑91 (MQ=255)                                                             agtaTGGAAACATAGATTAAGTTATTAAGGGCGCACGGTGGATGCCTTGGCACTAGAAGCCGATGAAGGACGTTACTAACGACGATATGCt  <  2:5174687/88‑1 (MQ=1)                                                                                |                                                                        ATAAGAAATAATCGCTAGTGTTCGAAAGAACACTCACAAGATTAATAACGCGTTTCCTGTAGGATGGAAACATAGATTAAGTTATTAAGGGCGCACGGTGGATGCCTTGGCACTAGAAGCCGATGAAGGACGTTACTAACGACGATATGCT  >  USA300TCH1516_ALE/558881‑559031

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.