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.

GTTAAATACATTACTGTTGTTAAGTTGTTTTTGTAATTCAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATGTATGATTCAAATTACGTAATGAAAACAATCCAATATAT  >  USA300TCH1516_ALE/456162‑456423                                                                                                                                     |                                                                                                                                  gtTAAATACATTACTGTTGTTAAGTTGTTTTTGTAATTCAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAACTAATGAAAGTCATTTAACCTGAACATTaa                                                                                                                                 >  2:91340/1‑135 (MQ=255)   tAAATACATTACTGATGTTAAGTAGTTTTTGTAATTCAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTaaaa                                                                                                                               >  1:608548/1‑135 (MQ=255)    aaaTACATTACTGTTGTTAAGTTGTTTTTGTAATTCAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAat                                                                                                                              >  2:545916/1‑135 (MQ=255)    aaaTACATTACTGTTGTTAAGTTGTTTTTGTAATTCAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAat                                                                                                                              <  1:546869/135‑1 (MQ=255)    aaaTACATTACTGTTGTTAAGTTGTTTTTGTAATTAAAAGAGCAAAACAGAGTAACAGCATCAGTTGTAGTAAGCGGTAATCCGGTAAAACAACTAAATGAAGGAAGGAAAGTCATTTAAACACAACATTAAAat                                                                                                                              >  2:415592/1‑135 (MQ=255)    aaaTACATTACTGTTGTTAAGTTGATTTTGTAATTCAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAat                                                                                                                              >  1:661706/1‑135 (MQ=255)     aaTACATTACTGTTGTTAAATTGTTTTTGTAATTCAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAata                                                                                                                             >  1:498191/1‑135 (MQ=255)     aaTAAATTACTGTTGTTAAGTTGTTTTTGTAATTAAAAGAGCAGAACAGAGTAACATCCTCACTTGTAGTAAACGCTCATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAata                                                                                                                             >  2:154411/1‑135 (MQ=255)      aTACATTACTGTTGTTAAGTTGTTTTTGTAATTCAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAatat                                                                                                                            >  1:466015/1‑135 (MQ=255)          aTTACTGTTGTTAAGTTGTTTTTGTAATTCAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAATAGTAAAATATAttt                                                                                                                        <  1:671370/135‑1 (MQ=255)            tACTGTTGTTAAGTTGTTTTTGTAATTCAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTGt                                                                                                                      <  2:524242/135‑1 (MQ=255)                gttgttAAGTTGTTTTTGTAATTCAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTGttttt                                                                                                                  >  2:155749/1‑135 (MQ=255)                gttgttAAGTTGTTTTTGTAATTCAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACAATAATCCGGTAAAACAACTAGATGAAATAATGAAAGTCATTTAACCAGAACATTAAAATATATTTAttttt                                                                                                                  >  2:212466/1‑135 (MQ=255)                   gttAAGTTGTTTTTGTAATTCAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCAt                                                                                                               <  2:300112/135‑1 (MQ=255)                       aGTTGTTTTTGTAATTTAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAATCTGAACATTAAAATATATTTGTTTTTCATTAAg                                                                                                           <  1:130970/135‑1 (MQ=255)                             ttttGTAATTCAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTTAACATTAAAATATATTTGTTTTTCATTAAGaataat                                                                                                     <  1:35528/135‑1 (MQ=255)                             ttttGTAATTCAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGaataat                                                                                                     <  2:509566/135‑1 (MQ=255)                                   aaTTCAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATTTTTTTTTTTCATTAAGAATAATTCAAGt                                                                                               <  1:142214/135‑1 (MQ=255)                                                     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)                                                                                                                                     |                                                                                                                                  GTTAAATACATTACTGTTGTTAAGTTGTTTTTGTAATTCAAAGAGCAGAACAGAGTAACATCATCAGTTGTAGTAAACGATAATCCGGTAAAACAACTAAATGAAATAATGAAAGTCATTTAACCTGAACATTAAAATATATTTGTTTTTCATTAAGAATAATTCAAGTATATTTAAATCGAGGTTAATTATCGTATGAAACGATGCACGTTATAATAAAAATGTATGATTCAAATTACGTAATGAAAACAATCCAATATAT  >  USA300TCH1516_ALE/456162‑456423

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.