New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 907281	45 (0.870)	4 (0.080)	3/240	NT	8.6%	intergenic (+390/‑39)	USA300HOU_RS04490/USA300HOU_RS04495	hypothetical protein/hypothetical protein
	?	USA300TCH1516_ALE	= 907290	44 (0.920)					intergenic (+399/‑30)	USA300HOU_RS04490/USA300HOU_RS04495	hypothetical protein/hypothetical protein

GATAATATTGGTGGGTTTGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAGAAAATGAAAATT  >  USA300TCH1516_ALE/907147‑907419                                                                                                                                       |                                                                                                                                           gATAATATTGGTGGGTTTGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACccgaat                                                                                                                                      <  1:361909‑M1/141‑7 (MQ=255) gATAATATTGGTGGGTTTGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACccgaat                                                                                                                                      <  2:289330‑M1/141‑7 (MQ=255)    aataTTGGTGGGTTTGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAACTGTATTGTATTTATAACGATCTAGCCATAACTCAATTCgg                                                                                                                                   >  2:211853/1‑141 (MQ=255)    aataTTGGTGGGCTTGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCgg                                                                                                                                   <  1:412661/141‑1 (MQ=255)         tggtggGTTTGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGgttat                                                                                                                              >  1:360257‑M2/1‑136 (MQ=255)          ggtggGTTTGAGGAGCAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGgttatg                                                                                                                             <  1:452910‑M2/141‑7 (MQ=255)             tggtTTGAGGAGGAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGgttatggct                                                                                                                          >  1:181536‑M2/2‑132 (MQ=255)                 ttGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACtt                                                                                                                      <  1:20107/141‑1 (MQ=255)                   gaggagTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACtttt                                                                                                                    >  2:452992/1‑141 (MQ=255)                       agTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAg                                                                                                                <  1:96353/141‑1 (MQ=255)                        gTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATATAGCCATAACTATATTCGGGTTATGGCTACTTTTATAgg                                                                                                               >  1:7368/1‑141 (MQ=255)                            cAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTa                                                                                                           >  2:251100/1‑141 (MQ=255)                             aataaaataaAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTaa                                                                                                          <  2:508840/141‑1 (MQ=255)                             aataaaataaAGGAGGTAATTGTGTAAAATACCCCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTat                                                                                                          <  2:405138/141‑2 (MQ=255)                              ataaaataaaGGAGGTAATTTTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTaaa                                                                                                         <  2:408405/141‑1 (MQ=255)                              ataaaataaaGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTaaa                                                                                                         >  2:604817/1‑141 (MQ=255)                                  aataaaGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTaagatta                                                                                                     >  1:230725/1‑136 (MQ=255)                                      aaGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGaa                                                                                                 >  1:84823/1‑141 (MQ=255)                                          aggTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCa                                                                                             >  1:462021/1‑141 (MQ=255)                                               aTTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGa                                                                                        >  2:363375/1‑141 (MQ=255)                                                     gaaaaTATGTTCTTTTGTTATTTCTTATTTATTTACCACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCa                                                                                  <  1:112315/140‑1 (MQ=255)                                                       aaaTATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACCCGAATAGAgttatggctagatcgttatatatataatacatttaattttatcggttgtaa                                                                                >  1:382133‑M2/1‑90 (MQ=255)                                                             ctctTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAAc                                                                          <  1:14911/141‑1 (MQ=255)                                                                 ttttGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAAtt                                                                      >  2:528609/1‑141 (MQ=255)                                                                 ttttGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAAtt                                                                      >  1:515240/1‑141 (MQ=255)                                                                   ttttTATTTCGTATTAATTTACAACCGATAAAATTAAATGTATGATATATATAACGATCTAGCCATAACCCGAATAGAgttatggctagatcgttatatatataatacatttaattttatcggttgtaaataaataagaaa                                                                    >  2:538581‑M2/1‑78 (MQ=255)                                                                         tttCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACtctattcgggttatggctagatcgttatatatatcatacatttaattttatcggttgtaaattaatacgaaataaaaa                                                              >  2:538581‑M1/1‑63 (MQ=255)                                                                         tttCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAAGTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTc                                                              <  1:574078/141‑1 (MQ=255)                                                                          ttCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCt                                                             <  1:93672/141‑1 (MQ=255)                                                                              tatttattTACAACCGATAAAATTAAATCTATTATAAAGATAACGATCTAGCCATAACTCGATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAAGAAACAATTCAAAATTCTaaga                                                         <  1:316819/141‑1 (MQ=255)                                                                                tttatttaCAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTaagaag                                                       >  1:244150/1‑141 (MQ=255)                                                                                 taatttaCAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTAAAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTaagaaga                                                      <  2:578370/139‑1 (MQ=255)                                                                                     ttaCAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACtctattcgggttatggctagatcgttatatatataatacatttaattttatcggttgtaaataaataagaaataacaaaaagagatattt                                                  >  1:382133‑M1/1‑51 (MQ=255)                                                                                         aaCCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAAt                                              <  1:533768/141‑1 (MQ=255)                                                                                                aaaaTTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTa                                       <  2:452910/141‑1 (MQ=255)                                                                                                  aaTTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTAcc                                     <  1:540004/141‑1 (MQ=255)                                                                                                  aaTTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAAATTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTAcc                                     >  2:217949/1‑141 (MQ=255)                                                                                                      aaaTGTATTATATATATAACGATCTAGCCATAACTCTATTAGGGTTATGGCTACTTATATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATGGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGaga                                 >  2:99197/1‑140 (MQ=255)                                                                                                       aaTGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGagta                                <  2:515240/141‑1 (MQ=255)                                                                                                       aaTGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTGTTAGAAGGGTAAATTTATGAAGCCATTTGACAGTCGTCATCAACAATTGCAAATTCTAAGAATAAGAGGAATGGAAGTACCGagta                                >  1:507677/1‑141 (MQ=255)                                                                                                         tGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATCGAAGTACCGagtagt                              <  1:452992/141‑1 (MQ=255)                                                                                                         tGTATTATATATATAACGATCTAGCCAAAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGagtagt                              <  1:204188/141‑1 (MQ=255)                                                                                                            attatATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGGGGAATGGAAGTACCGAGTAGTGCt                           >  1:421771/1‑141 (MQ=255)                                                                                                             ttatATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTa                          <  1:241635/141‑1 (MQ=255)                                                                                                                    tataACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAgaga                   >  1:489564/1‑141 (MQ=255)                                                                                                                    tataACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAgaga                   >  1:271846/1‑141 (MQ=255)                                                                                                                        aCGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTa               >  2:411570/1‑141 (MQ=255)                                                                                                                        aCGATCCAGCCATAAATGTAGCCGGGTGATAGCTACTTTTAGAGGGGTAAATTTATGAAGCCATTTGTAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTa               <  1:9663/141‑1 (MQ=255)                                                                                                                            tCTAGCCATAACTCTATTCGTGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAgaaa           >  1:373216/1‑141 (MQ=255)                                                                                                                             cTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAgaaaa          >  1:162234/1‑141 (MQ=255)                                                                                                                             cTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAgaaaa          <  2:236325/141‑1 (MQ=255)                                                                                                                               aGCCATAACccgaatagagttatggctagatcgttatatatataatacatttaattttatcggttgtaaataaataagaaataacaaaaagagatattttacacaattacctcctttattttattgctcctcctcaaacca        >  1:181536‑M1/1‑9 (MQ=255)                                                                                                                               aGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAgaaaatg        >  2:397629/1‑141 (MQ=255)                                                                                                                                 ccATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAgaaaatgaa      >  2:427865/1‑141 (MQ=255)                                                                                                                                 ccATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCCAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAgaaaatgaa      <  1:25065/141‑1 (MQ=255)                                                                                                                                  cATAACccgaatagagttatggctagatcgttatatatataatacatttaattttatcggttgtaaataaataagaaataacaaaaagagatattttacacaattacctcctttattttattgctgctcctcaaacccacc     <  1:452910‑M1/141‑136 (MQ=255)                                                                                                                                   aTAACccgaatagagttatggctagatcgttatatatataatacatttaattttatcggttgtaaataaataagaaataacaaaaagagatattttacacaattacctcctttattttattgctactcctcaaacccacca    >  1:360257‑M1/1‑5 (MQ=255)                                                                                                                                   aTAACTTTATTCGGGTTGTGGCCACTTTTAAAGGAGTAAAATTATGAAGCCACTTGAAAGTCATAATAAACAATTGCAAATTTTGCGAAGAAGGGGAAGCGGAGTTCCAATGAGTGCTAAAAGAGATTTAgaaaatgaaaa    <  2:431174/141‑1 (MQ=255)                                                                                                                                     acctctATTTCGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAGAAAATGAAAatt  <  1:62448/139‑1 (MQ=255)                                                                                                                                       |                                                                                                                                           GATAATATTGGTGGGTTTGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAGAAAATGAAAATT  >  USA300TCH1516_ALE/907147‑907419

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.