New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2080223 =	19 (0.530)	3 (0.090)	3/264	3.4	14.0%	intergenic (‑131/+133)	ytrA/USA300HOU_RS10505	HTH‑type transcriptional repressor YtrA/hypothetical protein
	?	USA300TCH1516_ALE	= 2080217	19 (0.560)					intergenic (‑125/+139)	ytrA/USA300HOU_RS10505	HTH‑type transcriptional repressor YtrA/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

AAGACATTCGTTTTAGCAGTCTTTTTTATTGAAGTAGACAATGCAAGATTAAATGGTAGTGTCATTTCATTTTATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2080298‑2080223 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑attttattCAACTGCTAGTAATACAATACTCAGTGTTATTTCTGAAGACTGGTTGATAATGAGACATGCATATTTAC  <  USA300TCH1516_ALE/2080217‑2080149                                                                                                                                                   AAGACATTCGTTTTAGCAGTCTTTTTTATTGAAGTAGACAATGCAAGATTAAATGGTAGTGTCATTTCATTTTATTCAACTGCTAGTAATACAATACTCAGTGTTATTTCTGAAGACTGGTTGATAATGAGACATGCATAT      <  1:400954/141‑1   GACATTCGTTTTAGCAGTCTTTTTTATTGAAGTAGACAATGCAAGATTAAATGGTAGTGTCATTTCATTTTATTCAACTGCTAGTAATACAATACTCAGTGTTATTTCTGAAGACTGGTTGATAATG‑GACATGCATATTTA   <  1:381470/141‑1    ACATTCGTTTTAGCAGTCTTTTTTATTGAAGTAGACAATGCAAGATTAAATGGTAGTGTCATTTCATTTTATTCAACTGCTAGTAATACAATACTCAGTGTTATTTCTGAAGACTGGTTGATAATG‑GACATGCATATTTAC  <  1:204676/141‑1                                                                                                                                                   AAGACATTCGTTTTAGCAGTCTTTTTTATTGAAGTAGACAATGCAAGATTAAATGGTAGTGTCATTTCATTTTATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2080298‑2080223 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑attttattCAACTGCTAGTAATACAATACTCAGTGTTATTTCTGAAGACTGGTTGATAATGAGACATGCATATTTAC  <  USA300TCH1516_ALE/2080217‑2080149

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