New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	514600 =	NA (NA)	12 (0.040)	7/146	NT	NA	intergenic (+2668/‑4095)	recR/speA_2	Recombination protein RecR/Arginine decarboxylase
	?	USA300TCH1516_ALE	514618 =	NA (NA)					intergenic (+2686/‑4077)	recR/speA_2	Recombination protein RecR/Arginine decarboxylase

AATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACTCACAAGATTAATAACGCGTTTAAATCTTTTTATAAAAGAACG  >  USA300TCH1516_ALE/514569‑514659                                |                                                            aaaaaGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACTCACAAGATTAATAACGCCTGGAAGTATTTTTATAAAAGAACg  <  1:2906449/88‑1 (MQ=1)                                |                                                            AATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACTCACAAGATTAATAACGCGTTTAAATCTTTTTATAAAAGAACG  >  USA300TCH1516_ALE/514569‑514659

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ 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.