New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2031785	70 (1.120)	4 (0.110) +ACACCCCAACTCGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTATGTTGGGGCCCC	3/162	7.2	9.4%	intergenic (+251/+239)	USA300HOU_RS10250/USA300HOU_RS10255	hypothetical protein/hypothetical protein
	?	USA300TCH1516_ALE	= 2031834	63 (1.000)					intergenic (+300/+190)	USA300HOU_RS10250/USA300HOU_RS10255	hypothetical protein/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

CTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2031736‑2031785 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TGACTGAACGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAG  <  USA300TCH1516_ALE/2031834‑2031790                                                   |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||                                              CTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTAGGGCCC‑CGCCCCAACTCGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTGAACGAAAATGCGCTTGTAATAAGCTTT              <  1:529923/141‑1         GTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTCGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTATGTTGGGGCCCCTGACTGAACGAAAATGCGCTTGTAACAAGCTTTTTTCAAT       <  1:804605/141‑1            TGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTCGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTATGTTGGGGCCCCTGACTGAACGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCT    <  1:941432/141‑1              TAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTCGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTATGTTGGGGCCCCTGACTGAACGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAG  <  1:108893/141‑1                                                   |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||                                              CTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2031736‑2031785 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TGACTGAACGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAG  <  USA300TCH1516_ALE/2031834‑2031790

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