New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2731894	28 (0.840)	5 (0.150) +ATTATAAACA	4/242	2.7	15.2%	intergenic (‑22/‑111)	USA300HOU_RS14060/cocE	hypothetical protein/Cocaine esterase
	?	USA300TCH1516_ALE	2731895 =	30 (0.840)					intergenic (‑23/‑110)	USA300HOU_RS14060/cocE	hypothetical protein/Cocaine esterase
Rejected: Frequency below/above cutoff threshold.

AAATCTGCAATTTGTTGCACAGTAATCTCTTCTAATTGGTGTTGATGTAAAAGTTCAATAAATGCATTTCTCATTGCAACTTGTGATTTTCTAATACGTCGATCTATAGTCATTTATATCAAGTCCTCCCCAATG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2731760‑2731894 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ATTATAAACGTTATGTTCATTATCCCACAAATCTCCAACATTGATGATTGGCACACAATGTTTACCTGTTTAATATAGGT  >  USA300TCH1516_ALE/2731895‑2731974                                                                                                                                        ||||||||||                                                                                 AAATCTGCAATTTGTTGCACAGTAATCTCTTCTAATTGGTGTTGATGTAAAAGTTCAATAAATGCATTTCTCATTGCAACTTGTGATTTTCTAATACGTCGATCTATAGTCATTTATATCAAGTCCTCCCCAATGATTATA                                                                                      <  1:143180/141‑1       GCAATTTGTTGCACAGTAATCTCTTCTAATTGGTGTTGATGTAAAAGTTCAATAAATGCATTTCTCATTGCAACTTGTGATTTTCTAATACGTCGATCTATAGTCATTTATATCAAGTCCTCCCCAATGATTATAAACAAT                                                                                >  1:320248/1‑141            TTGTTGCACAGTAATCTCTTCTAATTGGTGTTGATGTAAAAGTTCAATAAATGCATTTCTCATTGCAACTTGTGATTTTCTAATACGTCGATCTATAGTCATTTATATCAAGTCCTCCCCAATGATTATAAACAATTATAA                                                                           <  2:253202/141‑1                                                                  ATTTCTCATTGCAACTTGTGATTTTCTAATACGTCGATCTATAGTCATTTATATCAAGTCCTCCCCAATGATTATAAACAATTATAAACGTTATGTTCATTATCCCACAAATCTCCAACATTGATGATTGGCACACAATGT                     >  1:13316/1‑141                                                                                     GATTTTCTAATACGTCGATCTATAGTCATTTATATCAAGTCCTCCCCAATGATTATAAACAATTATAAACGTTATGTTCATTATCCCACAAATCTCCAACATTGATGATTGGCACACAATGTTTACCTGTTTAATATAGGT  <  2:320248/141‑1                                                                                                                                        ||||||||||                                                                                 AAATCTGCAATTTGTTGCACAGTAATCTCTTCTAATTGGTGTTGATGTAAAAGTTCAATAAATGCATTTCTCATTGCAACTTGTGATTTTCTAATACGTCGATCTATAGTCATTTATATCAAGTCCTCCCCAATG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2731760‑2731894 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ATTATAAACGTTATGTTCATTATCCCACAAATCTCCAACATTGATGATTGGCACACAATGTTTACCTGTTTAATATAGGT  >  USA300TCH1516_ALE/2731895‑2731974

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.