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	7.1%	intergenic (‑750/+222)	pstS/cvfB	Phosphate‑binding protein PstS/Conserved virulence factor B
	?	USA300TCH1516_ALE	1442906 =	NA (NA)					intergenic (+139/+129)	USA300HOU_RS07165/USA300TCH1516_01342	TelA‑like protein/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TTTATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1426885‑1427019 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cagctcGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGACATTCGAGTGAAACCCAAAATAGCCTTCATAAATCCAAAAACAGGCTCTACATCAA  >  USA300TCH1516_ALE/1442906‑1443043                                                                                                                                                                                                                                                                                   ttgATGTAGCGCCTGTTTTTGGATTTCTGAAGGCTATGTTGGGTTACACTCCGCGGGCGGTTCGAGGAATAAATAAAGTTAAAGGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCGTTGAG                                                                                                                                      <  1:26376/138‑1                        TTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGT                                                                                                               >  2:51799/1‑141                          TATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGC                                                                                                             <  2:802608/141‑1                                   TATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATAC                                                                                                    <  1:51799/141‑1                                                                                                                                  CAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGACATTCGAGTGAAACCCAAAATAGCCTTCATAAATCCAAAAACAGGCTCTACAT     <  1:567196/141‑1                                                                                                                                   AGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGACATTCGAGTGAAACCCAAAATAGCCTTCATAAATCCAAAAACAGGCTCTACATC    <  2:801041/141‑1                                                                                                                                     tTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACACAACCTAGCTCTCGTTTAAGTTTATTTATTCCTCGAACTGACATTCGAGTGAAACCCAAAATAGCCTTCATAAATCCAAAAACAGGCTCTACATCAA  <  2:25694/140‑1                                                                                                                                     CTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGACATTCGAGTGAAACCCAAAATAGCCTTCATAAATCCAAAAACAGGCTCTACATCAA  >  1:354958/1‑141                                                                                                                                     CTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGACATTCGAGTGAAACCCAAAATAGCCTTCATAAATCCAAAAACAGGCTCTACATCAA  >  2:436184/1‑141                                                                                                                                                                                                                                                                                   TTTATGTAGAGCCTGTTTTTGGATTTATGAAGGCTATTTTGGGTTTCACTCGAATGTCAGTTCGAGGAATAAATAAAGTTAAACGAGAGCTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1426885‑1427019 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cagctcGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGACATTCGAGTGAAACCCAAAATAGCCTTCATAAATCCAAAAACAGGCTCTACATCAA  >  USA300TCH1516_ALE/1442906‑1443043

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.