New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	729254 =	47 (1.020)	3 (0.070)	3/236	NT	6.8%	intergenic (+55/‑96)	USA300HOU_RS03535/aes	hypothetical protein/Acetyl esterase
	?	USA300TCH1516_ALE	729295 =	40 (0.950)					intergenic (+96/‑55)	USA300HOU_RS03535/aes	hypothetical protein/Acetyl esterase

TTACAGTTATAAAAAGCGCAGTTATCATCGTCCATTTATTATCTTTATTCATTACATCGTACCTCTCTATTTGTTAGACGCTCATATTAATAGACTGAATAAATATAAAAAGCAATTCGCCCGATAAGAGTAGAGACGAATTGCTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/729401‑729254 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgaattgcttttTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGATAATAAATGGACGATGATAACTGCGCTTTTTATAACTGTAATCAGTGTATTGTTAGCATTTCATCTGAAACA  >  USA300TCH1516_ALE/729295‑729432                                                                                                                                                                                                                                                                                                TTACAGTTATAAAAAGCGCAGTTATCATCGTCCATTTATTATCTTTATTCATTACATCGTACCTCTCTATTTGTTAGACGCTCATATTAATAGACTGAATAAATATAAAAAGCAATTCGCCCGATAAGAGTAGAGACGAAT                                                                                                                                                   >  2:176277/1‑141  TACAGTTATAAAAAGCGCAGTTATCATCGTCCATTTATTATCTTTATTCATTACATCGTACCTCTCTATTTGTTAGACGCTCATATTAATAGACTGAATAAATATAAAAAGCAATTCGCCCGATAAGAGTAGAGACGAATT                                                                                                                                                  <  1:386311/141‑1                                           CTTTATTCATTACATCGTACCTCTCTATTTGTTAGACACTCATATTAATAGACTGAATAAATATAAAAAGCAATTCGCCCGATAAGAGTAGAGACGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAAC                                                                                                         >  1:568981/1‑141                                                                                                  AATAAATATAAAAAGCAATTCGCCCGATAAGAGTAGAGACGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGATAATAAATGGACGATGATAACTGC                                                  >  2:144276/1‑141                                                                                                                   ATTCGCCCGATAAGAGTAGAGACGAATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGATAATAAATGGACGATGATAACTGCGCTTTTTATAACTGTAA                                 >  1:750174/1‑141                                                                                                                                           AATTGCTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGATAATAAATGGACGATGATAACTGCGCTTTTTATAACTGTAATCAGTGTATTGTTAGCATTTCATC         <  2:222640/141‑1                                                                                                                                                CTTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGATAATAAATGGACGATGATAACTGCGCTTTTTATAACTGTAATCAGTGTATTGTTAGCATTTCATCTGAAA    <  1:238115/141‑1                                                                                                                                                 TTTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGATAATAAATGGACGATGATAACTGCGCTTTTTATAACTGTAATCAGTGTATTGTTAGCATTTCATCTGAAAC   >  1:407426/1‑141                                                                                                                                                  TTTTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGATAATAAATGGACGATGATAACTGCGCTTTTTATAACTGTAATCAGTGTATTGTTAGCATTTCATCTGAAACA  <  1:68977/141‑1                                                                                                                                                                                                                                                                                                TTACAGTTATAAAAAGCGCAGTTATCATCGTCCATTTATTATCTTTATTCATTACATCGTACCTCTCTATTTGTTAGACGCTCATATTAATAGACTGAATAAATATAAAAAGCAATTCGCCCGATAAGAGTAGAGACGAATTGCTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/729401‑729254 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgaattgcttttTATATTTATTCAGTCTATTAATATGAGCGTCTAACAAATAGAGAGGTACGATGTAATGAATAAAGATAATAAATGGACGATGATAACTGCGCTTTTTATAACTGTAATCAGTGTATTGTTAGCATTTCATCTGAAACA  >  USA300TCH1516_ALE/729295‑729432

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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.