New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 456294	44 (0.770)	3 (0.050)	3/262	6.0	7.1%	intergenic (+216/‑150)	speC_5/tst_4	Exotoxin type C/Toxic shock syndrome toxin‑1
	?	USA300TCH1516_ALE	= 456337	35 (0.630)					intergenic (+259/‑107)	speC_5/tst_4	Exotoxin type C/Toxic shock syndrome toxin‑1
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

GAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATGTATGATTCAAATTACGTAATGAAAACAATCCAATATATTAAGATTGGAGCAAATAAATATGAAATTTACAGCATTAGCAAAAGC  >  USA300TCH1516_ALE/456214‑456469                                                                                                                            |                                                                                                                                     gagTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTTTTTTTTTTTTTTTCAATTATATTTAAATCAAGtttt                                                                                                                           >  2:422028/1‑134 (MQ=255)        atcatcAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCg                                                                                                                    >  1:631173/1‑135 (MQ=255)         tcatcaGTTGTGGTAATCGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATAGTTATATCGAGTTTAATTATCGt                                                                                                                   >  1:289564/1‑135 (MQ=255)           atcaGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTAt                                                                                                                 <  2:532772/135‑1 (MQ=255)             caGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGTGGTTAATTATCGTATGa                                                                                                               <  1:569872/135‑1 (MQ=255)                ttGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAAc                                                                                                            <  1:581997/135‑1 (MQ=255)                   taataAACGAGAATCACGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGAt                                                                                                         <  2:466015/132‑1 (MQ=255)                             tAATCCGGTAAAACCACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTtata                                                                                               >  1:342825/1‑135 (MQ=255)                             tAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTtata                                                                                               >  1:137379/1‑135 (MQ=255)                             tAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTtata                                                                                               >  1:396143/1‑135 (MQ=255)                             tAATCCGGTAAAACAAATAAATCACAAAAAAAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTtata                                                                                               >  1:132089/1‑135 (MQ=255)                              aaTCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTataa                                                                                              >  1:217858/1‑135 (MQ=255)                                tCCGGTAAAACAACTAAATGAAAGTATTAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTataata                                                                                            <  2:631173/135‑1 (MQ=255)                                   ggTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATaaaa                                                                                         <  2:217858/135‑1 (MQ=255)                                   ggTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAAAGATGCACGTTATAATaaaa                                                                                         >  1:649160/1‑135 (MQ=255)                                      aaaaCATCTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATGTTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATg                                                                                      <  2:362380/135‑1 (MQ=255)                                                         atGAAAGGCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATGTATGATTCAAATTACGTaa                                                                   <  1:154411/135‑1 (MQ=255)                                                          tGAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATGTATGATTCAAATTACGTAAt                                                                  <  1:402681/135‑1 (MQ=255)                                                              aGTTATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGATTAATTCAAGTATATTTAAATCGAGGTTAATTATCGAATGACACGATGCACGTTATAATATAAATGTATGATTCAAATTACGTAATGaaa                                                              >  2:461860/1‑135 (MQ=255)                                                              aGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATGTATGATTCAAATTAACTAATGaaa                                                              >  2:458249/1‑135 (MQ=255)                                                               gTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATGTATGATTCCAATTACGTAATAaaaa                                                             >  2:534270/1‑135 (MQ=255)                                                                       aCCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATGTATGATTCCAATTACGTAATGAAAACAATCCaa                                                     <  2:237989/135‑1 (MQ=255)                                                                       aCCTGAACATTAAAATATATTTGTTGTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATGTATGATTCAAATTACGTAATGAAAACAATCCaa                                                     <  1:305192/135‑1 (MQ=255)                                                                        ccTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTTAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATGTATGATTCAAATTACGTAATGAAAACAATCCAat                                                    <  1:545916/135‑1 (MQ=255)                                                                        ccTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATGTATGATTCAAATTACGTAATGAAAACAATCCAat                                                    <  2:661706/135‑1 (MQ=255)                                                                            aaCATTAAAATATATTTGTTTTTCCTAAAAAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATGTATGATTCAAATTACGTAATGAAAACAATCCAatatat                                                >  1:272792/1‑135 (MQ=255)                                                                                       atatTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATGTATGATTCAAATTACGTAATGAAAACAATCCAATATATTAAGATTGGAg                                     >  1:371165/1‑135 (MQ=255)                                                                                              tttttCAATAAAAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATGTATGATTCAAATTACGTAATGAAAACAATCCAATATATTAAGATTGGAGCaaataa                              <  1:373497/135‑1 (MQ=255)                                                                                                     ttAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATGTATGATTCAAATTACGTAATGAAAACAATCCAATTTATTAAGATTGGAGCAAATAAATATGaa                       <  1:464686/135‑1 (MQ=255)                                                                                                     ttAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATGTATGATTCAAATTACGTAATGAAAACAATCCAATATTTTTAGTTTGGAGCAAATAAATATGaa                       <  1:476529/135‑1 (MQ=255)                                                                                                           ataatTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATGTATGATTCAAATTACGTAATGAAAACAATCCAATATATTAAGATTGGAGCAAATAAATATGAAATTTAc                 <  2:396143/135‑1 (MQ=255)                                                                                                           ataatTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATGTATGATTCAAATTACGTAATGAAAACAATCCAATATATTAAGATTGGAGCAAATAAATATGAAATTTAc                 <  2:608548/135‑1 (MQ=255)                                                                                                           ataatTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATGTATGATTCAAAGTACGTAATGAAAACAATCCAATATATTAAGATTGGAGCAAATAAATATGAAATTTAc                 <  2:137379/135‑1 (MQ=255)                                                                                                                        atTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATGTATGATTCAAATTACGTAATGAAAACAATCCAATATATTAAGATTGGAGCAAATAAATATGAAATTTACAGCATTAGCaaaa    >  1:413337/1‑135 (MQ=255)                                                                                                                          ttAAATAGAGGTCAAACATCGTTTGAAACGATGCACGTTATAATAAAAATGTATGATTCAAATTACGTAATGAAAACAATCCAATATATAAAGATTGGAGCAAATAAATATGAAATTTACAGCATTAGCAAAAGc  <  2:414544/135‑1 (MQ=38)                                                                                                                            |                                                                                                                                     GAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATGTATGATTCAAATTACGTAATGAAAACAATCCAATATATTAAGATTGGAGCAAATAAATATGAAATTTACAGCATTAGCAAAAGC  >  USA300TCH1516_ALE/456214‑456469

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