New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1427019	55 (0.700)	4 (0.050)	3/268	9.3	7.0%	intergenic (‑750/+222)	pstS/cvfB	Phosphate‑binding protein PstS/Conserved virulence factor B
	?	USA300TCH1516_ALE	= 1912404	53 (0.710)					coding (526/609 nt)	USA300HOU_RS15290	hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TTTATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1426885‑1427019 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cagctcGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGACGTTCGAGTTAAACCCAAAATAGCCTTCATAAATCCAAAAACAGGCTCTACATCAAT  <  USA300TCH1516_ALE/1912404‑1912266                                                                                                                                                                                                                                                                                    ttgATGTAGCGCCTGTTTTTGGATTTCTGAAGGCTATGTTGGGTTACACTCCGCGGGCGGTTCGAGGAATAAATAAAGTTAAAGGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCGTTGAG                                                                                                                                       <  1:26376/138‑1                        TTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGT                                                                                                                >  2:51799/1‑141                          TATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGC                                                                                                              <  2:802608/141‑1                                   TATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATAC                                                                                                     <  1:51799/141‑1                                                                                                                                  CAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGACGTTCGAGTTAAACCCAAAATAGCCTTCATAAATCCAAAAACAGGCTCTACAT      <  1:291192/141‑1                                                                                                                                  CAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGACGTTCGAGTTAAACCCAAAATAGCCTTCATAAATCCAAAAACAGGCTCTACAT      <  1:344253/141‑1                                                                                                                                      TCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGACGTTCGAGTTAAACCCAAAATAGCCTTCATAAATCCAAACACAGGCACTACATCAAT  >  2:291661/1‑141                                                                                                                                                                                                                                                                                    TTTATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1426885‑1427019 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cagctcGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGACGTTCGAGTTAAACCCAAAATAGCCTTCATAAATCCAAAAACAGGCTCTACATCAAT  <  USA300TCH1516_ALE/1912404‑1912266

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.