New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	848604 =	19 (0.590)	3 (0.100)	3/244	NT	14.3%	intergenic (+609/‑271)	trxB/USA300HOU_RS04145	Thioredoxin reductase/Nucleotide‑binding protein
	?	USA300TCH1516_ALE	848625 =	18 (0.600)					intergenic (+630/‑250)	trxB/USA300HOU_RS04145	Thioredoxin reductase/Nucleotide‑binding protein

TTAAAAGGAGCTTGGGACATAAATCAATGTCCTAGGGTCTATAATATTATATTGCTAGTAGTTGACTGAATGAAAATGCGCTTGCAACAAGCTTTTTTCAACTCTAGTCAGGGGCCCCAACACAGAGAATTTCGAAAAGAAATTCT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/848749‑848604 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gaaattctCTGTGTTGGGGCCCCTGACTAGAGTTGAAAAAAGCTTGTTGCAAGCGCATTTTCATTCAGTCAACTACTAGCAATATAATATTATAGACCCTAGGACATTGATTTATGTCCCAAGCTCCTTTTAAATGATGTATATTT  >  USA300TCH1516_ALE/848625‑848762                                                                                                                                                                                                                                                                                              TTAAAAGGAGCTTGGGACATAAATCAATGTCCTAGGGTCTATAATATTATATTGCTAGTAGTTGACTGAATGAAAATGCGCTTGCAACAAGCTTTTTTCAACTCTAGTCAGGGGCCCCAACACAGAGAATTTCGAAAAGAA                                                                                                                                                 <  1:13902/141‑1     AAGGAGTGTGGGACATAAATCAATGTCCTAGGGTCTATAATATTATATTGCTAGTAGTTGACTGAATGAAAATGCGCTTGCAACAAGCTTTTTTAAACGCTAGACAGGGGCGACAACACAGAGAATTTAGAAAAGAAATTa                                                                                                                                             >  2:163408/1‑140      AGGAGCTTGGGACATAAATCAATGTCCTAGGGTCTATAATATTATATTGCTAGTAGTTGACTGAATGAAAATGCGCTTGCAACAAGCTTTTTTCAACTCTAGTCAGGGGCCCCAACACAGCGAATTTCGAAAAGCAATccc                                                                                                                                            >  2:167515/1‑138      AGGAGCTTGGGACATAAATCAATGTCCTAGGGTCTATAATATTATATTGCTAGTAGTTGACTGAATGAAAATGCGCTTGCAACAAGCTTTTTTCAACTCTAGTCAGGGGCCCCAACACAGAGAATTTCGAAAAGAAATTCT                                                                                                                                            >  1:136987/1‑141                       ATCAATGTCCTAGGGTCTATAATATTATATTGCTAGTAGTTGACTGAATGAAAATGCGCTTGCAACAAGCTTTTTTCAACTCTAGTCAGGGGCCCCAACACAGAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTG                                                                                                                           <  1:349927/141‑1                               CCTAGAGTCTATAATATTATATTGCTAGTAGTTGACTGAATGAAAATGCGGTTGCAACAAGCTTTTTTCAACTCTAGTCAGGGGCCCCAACACAGAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAGT                                                                                                                   <  1:74083/141‑1                                                                                                                                    TCGAACAGAAATTATCTGTGTTGGGGCCCCTGCCTAGAGTTGAAAAAAGCTTGTTGCAAGCGCATTTTCATTCAGTCAACTACTAGCAATATAATCTTATCGACACTAGGACCTTGATATATGTCCCACGCTCCTTTTAAA              >  2:24173/1‑141                                                                                                                                                TCTCTGTGTTGGGGCCCCTGACTAGAGTTGAAAAAAGCTTGTTGCAAGCGCATTTGCATTCAGTCAACTACTAGCAATCTAAGCTTATAGACCCTAGGCCATTGGTTGATGTCCCAAGATACTTTTAAATGATATATATTT  >  2:4799/1‑141                                                                                                                                                                                                                                                                                              TTAAAAGGAGCTTGGGACATAAATCAATGTCCTAGGGTCTATAATATTATATTGCTAGTAGTTGACTGAATGAAAATGCGCTTGCAACAAGCTTTTTTCAACTCTAGTCAGGGGCCCCAACACAGAGAATTTCGAAAAGAAATTCT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/848749‑848604 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gaaattctCTGTGTTGGGGCCCCTGACTAGAGTTGAAAAAAGCTTGTTGCAAGCGCATTTTCATTCAGTCAACTACTAGCAATATAATATTATAGACCCTAGGACATTGATTTATGTCCCAAGCTCCTTTTAAATGATGTATATTT  >  USA300TCH1516_ALE/848625‑848762

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.