New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	482715 =	53 (0.860)	3 (0.050)	3/244	NT	6.2%	intergenic (+512/‑171)	USA300HOU_RS02285/USA300HOU_RS02295	hypothetical protein/hypothetical protein
	?	USA300TCH1516_ALE	482748 =	41 (0.710)					intergenic (+545/‑138)	USA300HOU_RS02285/USA300HOU_RS02295	hypothetical protein/hypothetical protein

TTCATTTTACAAATGTTATCCATAATATCAATGTGCCACAAATTTCACTTTACCGACAATATCAAAATTATAAAGTTCATATTGTTATGTATATTGCAAATAAAACATTGTATAATTG‑AAATAACAATATTTTGCTATTTTCAATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/482860‑482715 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tttcaattATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATAACATTTGTAAAATGAAAATGATGATACGAGGAGATTGTAAGA  >  USA300TCH1516_ALE/482748‑482886                                                                                                                                                                                                                                                                                                TTCATTTTACAAATGTTATCCATAATATCAATGTGCCACAAATTTCACTTTACCGACAATATCAAAATTATAAAGTTCATATTGTTATGTATATTGCAAATAAAACATTGTATAATTG‑AAATAACAATATTTTGCTATTTT                                                                                                                                                  <  1:366466/141‑1    ATTTTACAAATGTTATCCATAATATCAATGTGCCACAAATTTCACTTTACCGACAATATCAAAATTATAAAGTTCATATTGTTATGTATATTGCAAATAAAACATTGTATAATTG‑AAATAACAATATTTTGCTATTTTCAA                                                                                                                                               >  1:192226/1‑141    ATTTTACAAATGTTATCCATAATATCAATGTGCCACAAATTTCACTTTACCGACAATATCAAAATTATAAAGTTCAAATTGTTATGTATATTGCAAATAAAACATTGTATAATTT‑CATTATCAATATTTAGCTATTgtgaa                                                                                                                                               >  1:385062/1‑136     tataACAAATAATATCCATAATATCAATTTGCCACAAATTTCAATTTACAGACAATATCAAAATTATAAAGTTCATATTGTTATGTATATTGCAAATAAAACATTGTATAATTG‑AAATAACAATATTTTGCTATTTTCAAT                                                                                                                                              <  2:449315/137‑1     TTTTAAAAATATTATCCATAATATCAATGTGCCACAAATTTCACTTTACCGACAATATCAAAATTATAAAGTTCATATTGTTATGTATATTGCAAATAAAACATTGTATAATTG‑AAATAACAATATTTTGCTATTTTCAAT                                                                                                                                              <  2:422917/141‑1             ATGTTATCCATAATATCAATGTGCCACAAATTTCACTTTACCGACAATATCAAAATTATAAAGTTCATATTGTTATGTATATTGCAAATAAAACATTGTATAATTGAAAATAGCAAAATATTGTTA‑TTTCAATTATACAAT                                                                                                                                      <  2:285225/141‑1                               ATGTGCCACAAATTTCACTTTACCGACAATATCAAAATTATAAAGTTCATATTGTTATATATATTTCAAATAAAACATTGTATAATTG‑AAATAATAATATTTTGCTATTTTTAATTATTCTATATTTTATTTACAATTTAa                                                                                                                    >  1:229725/1‑140                               ATGTGCCACAAATTTCACTTTACCGACAATATCAAAATTATAAAGTTCATATTGTTATATATATTGCAAATAAAACATTATATAATTGAAAATAGCAAAATATTATTA‑TTTCAATTATACAATATTTTATTTACAATATAa                                                                                                                    >  2:229725/1‑140                                                                                                                                                  TTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATAACATTTGTAAAATGAAAATGATGATACGAGGAGATTGTAAGA  >  2:541503/1‑141                                                                                                                                                                                                                                                                                                TTCATTTTACAAATGTTATCCATAATATCAATGTGCCACAAATTTCACTTTACCGACAATATCAAAATTATAAAGTTCATATTGTTATGTATATTGCAAATAAAACATTGTATAATTG‑AAATAACAATATTTTGCTATTTTCAATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/482860‑482715 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tttcaattATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATAACATTTGTAAAATGAAAATGATGATACGAGGAGATTGTAAGA  >  USA300TCH1516_ALE/482748‑482886

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.