New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2008942 =	40 (0.870)	3 (0.070)	3/232	NT	8.3%	intergenic (+70/+121)	USA300HOU_RS10115/USA300HOU_RS10125	hypothetical protein/Putative multidrug export ATP‑binding/permease protein
	?	USA300TCH1516_ALE	2008991 =	31 (0.750)					intergenic (+119/+72)	USA300HOU_RS10115/USA300HOU_RS10125	hypothetical protein/Putative multidrug export ATP‑binding/permease protein

TTTATATAGCATTCAAAACTTATAAAGTATTAGTTGTTTGACTTCAGTACAATCTTGAAGAGAAAATTTGTAACAGGATGGTGGGGTCATAACATAGAAAAAGCAGTAAGA‑GATTTTCTTAATT‑‑GAAAATAATCTTACTGCTTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2009087‑2008942 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tcttactgctttttCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCTATATAAATGCTCGTAAGCACCTTGTTTTGCAATCAATTCACGATGCGT  >  USA300TCH1516_ALE/2008991‑2009128                                                                                                                                                                                                                                                                                                 TTTATATAGCATTCAAAACTTATAAAGTATTAGTTGTTTGACTTCAGTACAATCTTGAAGAGAAAATTTGTAACAGGATGGTGGGGTCATAACATAGAAAAAGCAGTAAGA‑GATTTTCTTAATT‑‑GAAAATAATCTTACTGC                                                                                                                                                 <  1:105563/141‑1  TTATATAGCATTCAAAACTTATAAAGTATTAGTTGTTTGACTTCAGTACAATCTATACGAGAAAATTTGTAACAGGATGGTGGGGTCATAACATAGAAAAAGCAGTAAGA‑GATTTTCTTAATT‑‑GAAAATAATCTTACTGCT                                                                                                                                                <  1:173687/141‑1      ATAGCATTCAAAACTTATAAAGTATTAGTTGTTTGACTTCAGTACAATCTTGAAGAGAAAATTTGTAACAGGATGGTGGGGTCATAACATAGAAAAAGCAGTAAGA‑GATTTTCTTAATT‑‑GAAAATAATCTTACTGCTTTTT                                                                                                                                            <  1:60926/141‑1             TCAAAACTTATAAAGTATTAGTTTTTTGACTTCAGTACAATCTTGAAGAGAAAATTTGTAACAGGATGGTGGGGTCATAACATAGAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAAT‑CTCTTACTGCTTTTTCTATGTT                                                                                                                                     <  1:270153/141‑1                                                                                                  AAAAAGCAGTAAGA‑GATTTTCTTAATT‑‑GAAAATAATCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCTAT                                                >  1:109000/1‑141                                                                                                                   TTTTCTTAATT‑‑GAAAATAATCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCTAAATAAATGCTCGTAAGC                                >  1:507401/1‑141                                                                                                                                                 TTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGACGTCAAACAACCACTACCCTCTAAGCCTTCAATGCTATATAAATGCTCGTAAGCACCTTGTTTTGCAATCAATTCACGATGC    >  2:13212/1‑141                                                                                                                                                 TTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCTATATAAATGCTCGTAAGCACCTTGTTTTGCAATCAATTCACGATGC    >  1:714329/1‑141                                                                                                                                                 TTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTAAAGATTGTACTGAAGTCAAACAACTAACACTTTGTAAGTTTTTAATGCTATATAAATGCTCGTAAGCACCTTGTTTTGCAATCAATTCACGATGC    >  2:64524/1‑141                                                                                                                                                   TTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCTATATAAATGCTCGTAAGCACCTTGTTTTGCAATCAATTCACGATGCGT  <  1:500241/141‑1                                                                                                                                                                                                                                                                                                 TTTATATAGCATTCAAAACTTATAAAGTATTAGTTGTTTGACTTCAGTACAATCTTGAAGAGAAAATTTGTAACAGGATGGTGGGGTCATAACATAGAAAAAGCAGTAAGA‑GATTTTCTTAATT‑‑GAAAATAATCTTACTGCTTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2009087‑2008942 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tcttactgctttttCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCTATATAAATGCTCGTAAGCACCTTGTTTTGCAATCAATTCACGATGCGT  >  USA300TCH1516_ALE/2008991‑2009128

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.