New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	1205383 =	121 (1.070)	58 (0.630) +TTCCTAGGGTGCCGTCTCAGCCTCG	7/218	12.7	44.9%	intergenic (‑264/‑305)	USA300HOU_RS15290/lspA	hypothetical protein/Lipoprotein signal peptidase
	?	USA300TCH1516_ALE	2478476 =	54 (0.480)					intergenic (+363/‑212)	USA300HOU_RS12760/USA300HOU_RS12765	hypothetical protein/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.

TGCCCATCTGGCACATTACTGTAAAATTCTATAAATAGAATTTTTGATGACGGGTCCCTTCCTAGGGTGCCGTCTCAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAGCGACAAATT  >  USA300TCH1516_ALE/2478337‑2478616                                                                                                                                             |                                                                                                                                             tGCCCATCTGGCACATTACTGTAAAATTCTATAAATAGAATTTTTGATGACGGGTCCCTTCCTAGGGTGCCGTCTCAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGt                                                                                                                                             >  1:462868/1‑141 (MQ=35)  gCCCATCTGGCACATTACTGTAAAATTCTATAAATAGAATTTTTGATGACGGGTCCCTTCCTAGGGTGCCGTCTCAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTc                                                                                                                                            >  1:401832/1‑141 (MQ=35)  gCCCATCTGGCACATTACTGTAAAATTCTATAAATAGAATTTTTGATGACGGGTCCCTTCCTAGGGTGCCGTCTCAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTc                                                                                                                                            <  2:441837/141‑1 (MQ=35)     cATCTGGCACATTACTGTAAAATTCTATAAATAGAATTTTTGATGACGGGTCCCTTCCTAGGGTGCCGTCTCAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTc                                                                                                                                         >  4:311555/1‑141 (MQ=33)      aTCTGGCACATTACTGTAAAATTCTATAAATAGAATTTTTGATGACGGGTCCCTTCCTAGGGTGCCGTCTCAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCg                                                                                                                                        >  2:790755/1‑141 (MQ=33)        cTGGCACATTACTGTAAAATTCTATAAATAGAATTTTTGATGACGGGTCCCTTCCTAGGGTGCCGTCTCAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGAc                                                                                                                                      <  2:490246/141‑1 (MQ=32)         tGGCACATTACTGTAAAATTCTATAAATAGAATTTTTGATGACGGGTCCCTTCCTAGGGTGCCGTCTCAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCTCCTGTCTTCGACt                                                                                                                                     >  2:822552/1‑141 (MQ=17)           gCACATTCCTGTAAAATTCTATAAATAGAATTTTTGATGACGGGTCCCTTCCTAGGGTGCCGTCTCAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTgg                                                                                                                                   <  1:533877/141‑1 (MQ=11)                                                                          ctcAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAAt                                                                    >  2:546118/1‑141 (MQ=32)                                                                          ctcAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAAt                                                                    <  1:985853/141‑1 (MQ=32)                                                                          ctcAGCCACCCCAAACGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCACTGTCTTCGACTGGCACTGCTCACTCCGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAAt                                                                    >  2:874959/1‑141 (MQ=255)                                                                           tcAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATa                                                                   >  4:117786/1‑141 (MQ=32)                                                                           tcAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATa                                                                   >  3:275628/1‑141 (MQ=32)                                                                             aGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACt                                                                 >  2:575716/1‑141 (MQ=32)                                                                               ccatcccAACCGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACttt                                                               >  2:637852/5‑141 (MQ=25)                                                                                cACCCCAACCGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTa                                                              >  4:2212/1‑141 (MQ=35)                                                                                cACCCCAACCGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTa                                                              <  3:397150/141‑1 (MQ=35)                                                                                  ccccAACCGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACTTNTTAACAGGTAATTTTACTTTTAAATACTTTaaa                                                            <  1:790755/141‑1 (MQ=25)                                                                                      aaCCGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTaaaaaaa                                                        >  4:380060/1‑141 (MQ=39)                                                                                      aaCCGGCACATTGTTGTAAGCTGACTATAC‑GTCAGCTTCTGTGTTGGGGCCCCTGCCTTCGCCTGGCACTGCCCCCTCAGGCGTCTCGCCATTAATACTACGTATTAACATGTAATCTTACTTTTAAATACTTTacaacaa                                                        >  2:428515/1‑141 (MQ=11)                                                                                        ccGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATa                                                      >  1:601914/1‑141 (MQ=40)                                                                                         cGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATaa                                                     <  1:581090/141‑1 (MQ=255)                                                                                           gCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGa                                                   <  3:145749/141‑1 (MQ=255)                                                                                            cacaTTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGac                                                  >  4:402398/1‑141 (MQ=255)                                                                                             acaTTGTTGTAAGCTGACTATAT‑GTCAGCTCCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAACAAAATAAGaca                                                 >  2:788889/1‑141 (MQ=255)                                                                                                 tgttgtAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACttt                                             >  1:458700/1‑141 (MQ=255)                                                                                                      tAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGTACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCa                                        <  2:308814/141‑1 (MQ=255)                                                                                                      tAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCa                                        >  1:675236/1‑141 (MQ=255)                                                                                                      tAAGCTGACTATAT‑GTCAGCTTCAGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTCTTAAATACTTTCAAAAAATAAGACACTTTGGccc                                        >  2:877221/1‑140 (MQ=255)                                                                                                        aGCTGAC‑ATATAGTCAGCTTCTGTGTTTGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAAc                                      >  4:273404/1‑141 (MQ=255)                                                                                                               tataT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGcc                               <  1:178804/141‑1 (MQ=255)                                                                                                                atat‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCa                              >  2:928184/1‑141 (MQ=255)                                                                                                                 tatagTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAACTAAGACACTTTGGAACACTTCAGccg                              >  2:799995/5‑140 (MQ=14)                                                                                                                   t‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGa                           <  2:60687/141‑1 (MQ=255)                                                                                                                     gTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGAt                          <  2:86344/141‑1 (MQ=255)                                                                                                                      tCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATa                         <  3:7549/141‑1 (MQ=255)                                                                                                                        aGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACa                       >  3:139721/1‑141 (MQ=255)                                                                                                                         gCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTaa                                                                      >  2:390004/1‑93 (MQ=33)                                                                                                                         gCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTaa                                                                      <  1:390004/93‑1 (MQ=33)                                                                                                                         gCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACaa                      >  3:87324/1‑141 (MQ=255)                                                                                                                              tgtgTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTAc                 >  2:767961/1‑141 (MQ=255)                                                                                                                              tgtgTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTAc                 >  1:740028/1‑141 (MQ=255)                                                                                                                              tgtgTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTAc                 >  2:572296/1‑141 (MQ=255)                                                                                                                               gtgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGTAAAGATACAATTTACa                >  1:566493/1‑141 (MQ=255)                                                                                                                                 gtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACaaa              >  1:859596/1‑141 (MQ=255)                                                                                                                                    ggggCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAg           <  1:546118/141‑1 (MQ=255)                                                                                                                                     gggCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATaa                                                     <  2:358345/98‑1 (MQ=39)                                                                                                                                     gggCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATaa                                                     >  1:358345/1‑98 (MQ=39)                                                                                                                                       gCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAGCGa        <  2:993778/141‑1 (MQ=255)                                                                                                                                        ccccTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAGCGAc       <  1:306416/141‑1 (MQ=255)                                                                                                                                          ccTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAGCGACaa     <  4:360645/141‑1 (MQ=255)                                                                                                                                          ccTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAGCGACaa     >  1:476699/1‑141 (MQ=255)                                                                                                                                           cTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAGCGACaaa    >  4:17021/1‑141 (MQ=255)                                                                                                                                            tGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAGCGACAAAt   <  1:315465/141‑1 (MQ=255)                                                                                                                                             gTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAGCGACAAAtt  <  4:52795/141‑1 (MQ=255)                                                                                                                                             |                                                                                                                                             TGCCCATCTGGCACATTACTGTAAAATTCTATAAATAGAATTTTTGATGACGGGTCCCTTCCTAGGGTGCCGTCTCAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATAT‑GTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAGCGACAAATT  >  USA300TCH1516_ALE/2478337‑2478616

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