New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2376100	37 (1.040)	5 (0.140)	3/280	3.5	10.8%	intergenic (‑77/‑110)	topB/USA300HOU_RS12205	DNA topoisomerase 3/hypothetical protein
	?	USA300TCH1516_ALE	2376113 =	46 (1.290)					intergenic (‑90/‑97)	topB/USA300HOU_RS12205	DNA topoisomerase 3/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

ATAAATTATCCTTTCTCATACGTTCTTTTATTTCGAACGTGCTTCATCTATTCCACTAATCTTTGATTTAAATTCAATG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2376022‑2376100 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GTGTTAAATGTATTGTAACATGTTAATATCACTATTAACTTTCATTTCAGTTGAAATACTATATAATAAAAGTAACAAAAAGTACGGAGGTAATGACATGAGCATAGTTCAGTTATATGATATTA  >  USA300TCH1516_ALE/2376113‑2376237                                                                                                                                                                                                              ATAAATTATCCTTTCTCATACGTTCTTTTATTTCGAACGTGCTTCATCTATTCCACTAATCTTTGATTTAAATTCAATGGTGTTAAATGTATTGTAACATGTTAATATCACTATTAACTTTCATTTCAGTTGAAATACTAT                                                                 >  2:240926/1‑141                                    AACTTGCTTCATCTATTCCACTAATCTTTGATTTAAATTCAATGGTGTTAAATGTATTGTAACATGTTAATATCACTATTAACTTTCATTTCAGTTGAAATACTATATAATAAAAGTAACAAAAAGTACGGAGGTAATGAC                              <  2:6454/141‑1                                    AACGTGCTTCATCTATTCCACTAATCTTTGATTTAAATTCAATGGTGTTAAATGTATTGTAACATGTTAATATCACTATTAACTTTCATTTCAGTTGAAATACTATATAATAAAAGTAACAAAAAGTACGGAGGTAATGAC                              <  2:401932/141‑1                                    AACGTGATTCATCTATTCCACTAATCTTTGATTTAAATTCAATGGTGTTAAATGTATTGTAACATGTTAATATCACTATTAACTTTCATTTCAGTTGAAATACTATATAAAAAAAAAAAAAAAAAGTACGGAGGTAATGAC                              <  2:401988/141‑1                                                                TGATTTAAATTCAATGGTGTTAAATGTATTGTAACATGTTAATATCACTATTAACTTTCATTTCAGTTGAAATACTATATAATAAAAGTAACAAAAAGTACGGAGGTAATGACATGAGCATAGTTCAGTTATATGATATTA  >  2:188313/1‑141                                                                                                                                                                                                              ATAAATTATCCTTTCTCATACGTTCTTTTATTTCGAACGTGCTTCATCTATTCCACTAATCTTTGATTTAAATTCAATG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2376022‑2376100 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GTGTTAAATGTATTGTAACATGTTAATATCACTATTAACTTTCATTTCAGTTGAAATACTATATAATAAAAGTAACAAAAAGTACGGAGGTAATGACATGAGCATAGTTCAGTTATATGATATTA  >  USA300TCH1516_ALE/2376113‑2376237

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ 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.