New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 954748	128 (1.150)	3 (0.040) +TTGGCATTTACGAAGTTTAAATGTGCAATTAGAATATATGTATAACAATATT	3/172	13.1	4.0%	intergenic (+402/+101)	gluD/glpQ_1	NAD‑specific glutamate dehydrogenase/Glycerophosphodiester phosphodiesterase
	?	USA300TCH1516_ALE	2830190 =	104 (0.940)					intergenic (+18/+429)	icaC/lipA_2	putative poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein/Lipase 1
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

GGGACGACGAAATAAATTTTGCGAAAATATCATTTCTGTCCCACTCCCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/954700‑954748 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAACACGCGGTGGGCGAAATCAGTTTGAATTGACTGACTTCGTTTT  >  USA300TCH1516_ALE/2830190‑2830235                                                  ||||||||||||||||||||||||||||||||||||||||||||||||||||                                               GGGACGACGAAATAAATTTTGCGAAAATATCATTTCTGTCCCACTCCCATTGGCATTTACGAAGTTTAAATGTGCAATTAGAATATATGTATAACAATATTAAACACGCGGTGGGCCAAATCAGTTTGAATTGACTGACTT        <  1:810884/141‑1     CGACGAAATAAATTTTGCGAAAATATCATTTCTGTCCCACTCCCATTGGCATTTACGAAGTTTAAATGTGCAATTAGAATATATGTATAACAATATTAAACACGCGGTGGGCGAAATCAGTTTGAATTGACTGACTTCGTT    <  2:144670/141‑1       ACGAAATAAATTTTGCGAAAATATCATTTCTGTCCCACTCCCATTGGCATTTACGAAGTTTAAATGTGCAATTAGAATATATGTATAACAATATTAAACACGCGGTGGGCGAAATCAGTTTGAATTGACTGACTTCGTTTT  <  1:208338/141‑1                                                  ||||||||||||||||||||||||||||||||||||||||||||||||||||                                               GGGACGACGAAATAAATTTTGCGAAAATATCATTTCTGTCCCACTCCCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/954700‑954748 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAACACGCGGTGGGCGAAATCAGTTTGAATTGACTGACTTCGTTTT  >  USA300TCH1516_ALE/2830190‑2830235

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.