New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2090980	183 (1.040)	14 (0.130) +AATGGTTATTAATTTAATCTTTAATCTAAAATAGC	9/110	12.7	12.0%	intergenic (‑214/+324)	USA300HOU_RS10575/USA300HOU_RS10590	hypothetical protein/hypothetical protein
	?	USA300TCH1516_ALE	= 2265579	155 (0.880)					intergenic (+442/+587)	USA300HOU_RS11590/hin_3	hypothetical protein/DNA‑invertase hin
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TAAATTAATAACCATTTAACCATCGAAACCAGCCAAAGTTAGCGATGGTTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2090930‑2090980 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CACCGTCTTTTTAACGGGCTCATTAGGGTAA  <  USA300TCH1516_ALE/2265579‑2265549                                                    |||||||||||||||||||||||||||||||||||                                TAAATTAATAACCATTTAACCATCGAAACCAGCCAAAGTTAGCGATGGTTAAATGGTTATTAATTTAATCTTTAATCTAAAATAGCCACCG                            >  2:1448434/1‑91  AAATTAATAACCATTTAACCATCGAAACCAGCCAAAGTTAGCG‑‑‑‑‑‑‑‑ATGGTTATTAATTTAATCTTTAATCTAAAATAGCCACCGTCTTTTTAA                   >  2:1822637/1‑91                   ACCATCGAAACCAGCCAAAGTTAGCGATGGTTAAATGGTTATTAATTTAATCTTTAATCTAAAATAGCCACCGTCTTTTTAACGGGCTCAT          >  2:1653034/1‑91                     CATCGAAACCAGCCAAAGTTAGCGATGGTTAAATGGTTATTAATTTAATCTTTAATCTAAAATAGCCACCGTCTTTTTAACGGGCTCATTA        >  2:2804127/1‑91                      ATCGAAACCAGCCAAAGTTAGCGATGGTTAAATGGTTATTAATTTAATCTTTAATCTAAAATAGCCACCGTCTTTTTAACGGGCTCATTAG       >  1:2052244/1‑91                      ATCGAAACCAGCCAAAGTTAGCGATGGTTAAATGGTTATTAATTTAATCTTTAATCTAAAATAGCCACCGTCTTTTTAACGGGCTCATTAG       >  2:2151511/1‑91                       TCGAAACCAGCCAAAGTTAGCGATGGTTAAATGGTTATTAATTTAATCTTTAATCTAAAATAGCCACCGTCTTTTTAACGGGCTCATTAGG      >  1:1763178/1‑91                       TCGAAACCAGCCAAAGTTAGCGATGGTTAAATGGTTATTAATTTAATCTTTAATCTAAAATAGCCACCGTCTTTTTAACGGGCTCATTAGG      >  1:1835691/1‑91                       TCGAAACCAGCCAAAGTTAGCGATGGTTAAATGGTTATTAATTTAATCTTTAATCTAAAATAGCCACCGTCTTTTTAACGGGCTCATTAGG      >  1:2078258/1‑91                       TCGAAACCAGCCAAAGTTAGCGATGGTTAAATGGTTATTAATTTAATCTTTAATCTAAAATAGCCACCGTCTTTTTAACGGGCTCATTAGG      >  2:1660745/1‑91                        CGAAACCAGCCAAAGTTAGCGATGGTTAAATGGTTATTAATTTAATCTTTAATCTAAAATAGCCACCGTCTTTTTAACGGGCTCATTAGGG     >  1:1024887/1‑91                          AAACCAGCCAAAGTTAGCGATGGTTAAATGGTTATTAATTTAATCTTTAATCTAAAATAGCCACCGTCTTTTTAACGGGCTCATTAGGGTA   >  2:2459792/1‑91                          AAACCAGCCAAAGTTAGCGATGGTTAAATGGTTATTAATTTAATCTTTAATCTAAAATAGCCACCGTCTTTTTAACGGGCTCATTAGGGTA   >  2:2459911/1‑91                           AACCAGCCAAAGTTAGCGATGGTTAAATGGTTATTAATTTAATCTTTAATCTAAAATAGCCACCGTCTTTTTAACGGGCTCATTAGGGTAA  >  2:1438481/1‑91                                                    |||||||||||||||||||||||||||||||||||                                TAAATTAATAACCATTTAACCATCGAAACCAGCCAAAGTTAGCGATGGTTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2090930‑2090980 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CACCGTCTTTTTAACGGGCTCATTAGGGTAA  <  USA300TCH1516_ALE/2265579‑2265549

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