New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	221933 =	35 (1.410)	3 (0.130)	3/266	3.0	9.2%	coding (1341/2046 nt)	ptsG_1	PTS system glucose‑specific EIICBA component
	?	USA300TCH1516_ALE	222024 =	26 (1.100)					coding (1250/2046 nt)	ptsG_1	PTS system glucose‑specific EIICBA component
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

CAGGTCGTGAAGATAAACAATCACAAGCGGCTACTGCTTCAGCAACTGAATTACCATATGCAGTATTAGAAGCTATGGGTGGCAAAGCAAACATTAAACATTTAGACGCTTGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/222045‑221933 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgcttgtGATTGTTTATCTTCACGACCTGGTGTTTTGTATTTTAATTTTACAATTAAGAATCGGAATACGAAGTAGTAAATAACTGCG  >  USA300TCH1516_ALE/222024‑222104                                                                                                                                                                                                    CAGGTCGTGAAGATAAACAATCACAAGCGGCTACTGCTTCAGCAACTGAATTACCATATGCAGTATTAGAAGCTGTGTGTGGCAAAGCAAACATTAAACATTTAGACGCTTGTGATTGTTTATCTTCACGACCTGGTGTTT                                                       >  1:134835/1‑141                              GCTACTGCTTCAGCAACTGAATTACCATATGCAGTATTAGAAGCTATGGGTGGCAAAGCAAACATTAAACATTTAGACGCTTGTGATTGTTTATCTTCACGACCTGGTGTTTTGTATTTTAATTTTACAATTAAGAATCGG                          >  1:136509/1‑141                                                      CCATATGCAGTATTAGAAGCTATGGGTGGCAAAGCAAACATTAAACATTTAGACGCTTGTGATTGTTTATCTTCACGACCTGGTGTTTTGTATTTTAATTTTACAATTAAGAATCGGAATACGAAGTAGTAAATAACTGCG  <  2:134835/141‑1                                                                                                                                                                                                    CAGGTCGTGAAGATAAACAATCACAAGCGGCTACTGCTTCAGCAACTGAATTACCATATGCAGTATTAGAAGCTATGGGTGGCAAAGCAAACATTAAACATTTAGACGCTTGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/222045‑221933 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgcttgtGATTGTTTATCTTCACGACCTGGTGTTTTGTATTTTAATTTTACAATTAAGAATCGGAATACGAAGTAGTAAATAACTGCG  >  USA300TCH1516_ALE/222024‑222104

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