New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 514606	NA (NA)	29 (0.110)	21/146	NT	NA	intergenic (+2674/‑4089)	recR/speA_2	Recombination protein RecR/Arginine decarboxylase
	?	USA300TCH1516_ALE	= 514610	NA (NA)					intergenic (+2678/‑4085)	recR/speA_2	Recombination protein RecR/Arginine decarboxylase

AGAAATAATCGCTAGTGTTCGAAAGAACACTCACAAGATTAATAACGCGTTTAAATCTTTTTATAAAAGAACGTAACTTCATGTTAACGTT  >  USA300TCH1516_ALE/514587‑514677                    |                                                                        agtaataatCGCTAGTGTTCGAAAGAACACTCACAAGATTAATAACGCGTTTAAATCTTTTTATAAAAGAACGTAACTTCATGTTAACGtt  <  2:4984718/88‑1 (MQ=1)                    |                                                                        AGAAATAATCGCTAGTGTTCGAAAGAACACTCACAAGATTAATAACGCGTTTAAATCTTTTTATAAAAGAACGTAACTTCATGTTAACGTT  >  USA300TCH1516_ALE/514587‑514677

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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.