New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 514610	NA (NA)	6 (0.050)	6/244	NT	23.2%	intergenic (+2678/‑4085)	recR/speA_2	Recombination protein RecR/Arginine decarboxylase
	?	USA300TCH1516_ALE	= 558903	21 (0.170)					intergenic (+116/+3686)	USA300TCH1516_00505/gabR	tRNA‑Ile/HTH‑type transcriptional regulatory protein GabR

TGCGAGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAgaacact‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/514471‑514610 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGGCCTAAGTGGACTCGAACCACCGAC  <  USA300TCH1516_ALE/558903‑558757                                                                                                                                                                                                                                                                                                 TGCGAGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAG                                                                                                                                                    >  3:112793/1‑141  GCGAGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGA                                                                                                                                                   <  2:317155/141‑1  GCGAGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGA                                                                                                                                                   <  2:35798/141‑1  GCGAGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGA                                                                                                                                                   <  3:425888/141‑1   aGAGGGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAA                                                                                                                                                  <  4:89490/140‑1   CGAGCGCTTGACTAAATAGAAATTGTACATTGGAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAAGAACGAGTTTTAAATAAGCTGGAATTCATAAGACATGATCGCTAGTGTTCGAGAGAA                                                                                                                                                  <  4:404232/141‑1   CGAGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAA                                                                                                                                                  >  3:331048/1‑141   CGAGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAA                                                                                                                                                  <  2:699284/141‑1   CGAGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAA                                                                                                                                                  >  3:242281/1‑141   CGAGCGCTTGACTAAAAAGAAATTGTACATAGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAA                                                                                                                                                  <  4:46726/141‑1    GAGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTCGATAAGTAAGTAAAATATAGATTTTACCAAGCAAGACCTTGTTAAGAAATAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAAC                                                                                                                                                 >  3:201039/1‑141    GAGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAAC                                                                                                                                                 >  1:997763/1‑141    GAGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAAC                                                                                                                                                 <  1:465863/141‑1    GAGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAAC                                                                                                                                                 <  3:304291/141‑1     cGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGTTTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACA                                                                                                                                                <  2:186098/140‑1     AGCGCTTGACTAAAAAGAAATTGTACATTGCAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACA                                                                                                                                                <  4:301200/141‑1     AGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACA                                                                                                                                                <  2:908804/141‑1     AGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACA                                                                                                                                                >  1:1015010/1‑141     AGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACA                                                                                                                                                <  2:567146/141‑1     AGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACA                                                                                                                                                >  4:378939/1‑141     AGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACA                                                                                                                                                >  2:796991/1‑141     AGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACA                                                                                                                                                <  1:203838/141‑1     AGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACA                                                                                                                                                <  4:352234/141‑1     AGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACA                                                                                                                                                <  1:757388/141‑1     AGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACA                                                                                                                                                <  1:448098/141‑1     AGCGCTTGAATAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATCAAGAGTTTTACCCTGGTAGTAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACA                                                                                                                                                <  1:792481/141‑1      GCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAGATAATCGCTAGTGTTCGAAAGAACAC                                                                                                                                               <  1:399842/141‑1      GCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACAC                                                                                                                                               <  2:37505/141‑1      GCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACAC                                                                                                                                               >  2:277084/1‑141      GCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACAC                                                                                                                                               <  2:1060769/141‑1      GCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACAC                                                                                                                                               <  3:416392/141‑1      GCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACAC                                                                                                                                               <  2:829925/141‑1      GCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACAC                                                                                                                                               <  2:531845/141‑1       cgtTTGACGAAAAAGAAACTGCACATTGAAAACTAGATAAGTAAGTAAAATAGAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGCTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACT                                                                                                                                              >  2:428175/4‑141       CGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACT                                                                                                                                              <  3:217355/141‑1       CGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACT                                                                                                                                              <  3:248409/141‑1       CGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAGAACACT                                                                                                                                              <  1:60783/141‑1            GACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGCGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCTTTCGAACACTAGCGA                                                                                                                                         <  1:294231/141‑1                      tatTTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCTTTCGAACACTAGCGACTATTTCTTA                                                                                                                               <  1:952710/138‑1                                             AAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACT                                                                                                        <  1:286816/141‑1                                                                                     AATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATT                                                                                                 <  3:250111/108‑1                                                                                     AATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCTTTCGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATT                                                                                                 >  4:250111/1‑108                                                                                                                              CGCTAGTGTTCGAAAGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGGCCT                       >  3:20670/1‑141                                                                                                                                      TTCGAAAGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGGCCTAAGTGGAC               >  1:658526/1‑141                                                                                                                                        CGAAAGAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGGCCTAAGTGGACTC             >  3:356067/1‑141                                                                                                                                             GAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGGCCTAAGTGGACTCGAACC        <  2:584246/141‑1                                                                                                                                               ACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGGCCTAAGTGGACTCGAACCAC      <  2:1019415/141‑1                                                                                                                                                 ACTAGCGATTATTTCTTATGAATTCAAGCGTATTTAAATCTCTTTATTCACTCGGTGTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACGAATAATGGTGGGCCTAAGTGGACTCGAACCACCG    <  4:99240/141‑1                                                                                                                                                  CTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAAGCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGGCCTAAGTGGACTCGAACCACCGA   >  1:352206/1‑141                                                                                                                                                   TAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGGCCTAAGTGGACTCGAACCACCGAC  >  2:693589/1‑141                                                                                                                                                   TAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGGCCTAAGTGGACTCGAACCACCGAC  >  2:387528/1‑141                                                                                                                                                                                                                                                                                                 TGCGAGCGCTTGACTAAAAAGAAATTGTACATTGAAAACTAGATAAGTAAGTAAAATATAGATTTTACCAAGCAAAACCGAGTGAATAAAGAGTTTTAAATAAGCTTGAATTCATAAGAAATAATCGCTAGTGTTCGAAAgaacact‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/514471‑514610 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GAACACTAGCGATTATTTCTTATGAATTCAAGCTTATTTAAAACTCTTTATTCACTCGGTTTTGCTTGGTAAAATCTATATTTTACTTACTTATCTAGTTTTCAATGTACAAATAATGGTGGGCCTAAGTGGACTCGAACCACCGAC  <  USA300TCH1516_ALE/558903‑558757

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.