New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2742800 =	54 (0.820)	4 (0.060)	4/246	NT	7.5%	coding (167/417 nt)	USA300HOU_RS14120	hypothetical protein
	?	USA300TCH1516_ALE	2742840 =	47 (0.750)					coding (207/417 nt)	USA300HOU_RS14120	hypothetical protein

TTGCTGCTATTTTCATATCATTCATGTTGCTATGGATGACCATGTTGTTTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCTTATTTATAGCATTGTATCCCTTTTTAGT  >  USA300TCH1516_ALE/2742662‑2742935                                                                                                                                           |                                                                                                                                        tctgtcacactaaattgaaaaattggacgttgcgcaataaatactaaaaagggatacaatgctataaataagaaaaataaagggatataacatagatagtaaagccttttagaagtatgaaacagcaacacaaatacaaa                                                                                                                                        >  1:755330‑M1/139‑140 (MQ=255)   gctgctATTTTCATATCATTCATGTTGCTATGGATGACCATGTTGTTTGTCTTAATAAGCAATCTCTCCCATTTAAAAGCTGTATTATTGAATTTAGATTTTCTACTTCCTTCTGACAACACACCATATATTCTAGAaat                                                                                                                                      <  2:611853/140‑1 (MQ=255)   gctgctATTTTCATATCATTCATGTTGCTATGGATGACCATGTTGTTTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAaat                                                                                                                                      >  1:212229/1‑140 (MQ=255)   gctgctATTTTCATATCATTCATGTTGCTATGGATGACCATGTTGTTTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAaat                                                                                                                                      <  1:605269/140‑1 (MQ=255)   gctgctATTGTCATATCAGTCATGTTGCTATGGATGACCATGTTGTTTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAaat                                                                                                                                      <  1:86768/140‑1 (MQ=255)             tCATATCATTCATGTTGCTATGGATGACCATGCTGTTTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCACATATTCTAGAAATAATATGTCAc                                                                                                                            >  1:792010/1‑140 (MQ=255)                tatCATTCATGTTGCTATGGATGACCATGTTGTTTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTa                                                                                                                         <  2:208516/140‑1 (MQ=255)                tatCATTCATGTTGCTATGGATGACCATGTTGTTTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTa                                                                                                                         <  1:324444/140‑1 (MQ=255)                   cattcatGTTGCTATGGATGACCATGTTGTTTGACTTAATAAGCAATCAATCTCATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATCTGTCACTTACTa                                                                                                                      >  2:172670/1‑140 (MQ=255)                         tGTTGCTATGGATGACCATGTTGTTTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGt                                                                                                                >  1:759859/1‑140 (MQ=255)                          gTTGCTATGGATGACCATGTTGTTTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTa                                                                                                               >  1:349510/1‑140 (MQ=255)                              cTATGTATGACAATGTTGTTTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGt                                                                                                           <  1:114481/140‑1 (MQ=255)                              cTATGGATGACCATGTTGTTTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGt                                                                                                           <  1:783349/140‑1 (MQ=255)                                 tGGATGACCATGTTGTTTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCat                                                                                                        <  1:430922/140‑1 (MQ=255)                                    atgcgcATGTTGTATGAGTGAATAAGCAATTAATCACATTTCAAAGCTTTATTAGTTGATTTAGATTTTCTCATTCTTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATCGGTAGCGTCattta                                                                                                     <  2:480989/135‑1 (MQ=255)                                    aTGACCATGTTGTTTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCattta                                                                                                     >  1:112531/1‑140 (MQ=255)                                     tGACCATGTTGTTTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCatttat                                                                                                    <  1:49528/140‑1 (MQ=255)                                     tGACCATGTTGTTTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCatttat                                                                                                    <  1:441416/140‑1 (MQ=255)                                        ccATGTTGTTTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTACTTGGTAGCGTCATTTAtttt                                                                                                 >  1:14951/1‑140 (MQ=255)                                         cATGTTGTTTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTg                                                                                                >  1:768870/1‑140 (MQ=255)                                          aTGTTGTTTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGt                                                                                               >  1:734284/1‑140 (MQ=255)                                               gttTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCGTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTtg                                                                                          >  1:425986/1‑140 (MQ=255)                                               gttTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCATTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTtg                                                                                          >  1:426211/1‑140 (MQ=255)                                                 ttGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTtgtg                                                                                        <  2:476963/140‑1 (MQ=255)                                                  tGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTgtgt                                                                                       <  1:88522/140‑1 (MQ=255)                                                    aCTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTg                                                                                     <  2:556458/140‑1 (MQ=255)                                                     cTTAATAAGCAGTCAATTACATTTAACAGCTTTATTATTCAATTTATATTTTCTAATTCCTTCTGACAATACACTATATATTCTTGATATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGc                                                                                    <  2:80957/140‑1 (MQ=255)                                                       taataaGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTg                                                                                  >  1:44189/1‑140 (MQ=255)                                                         ataaGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCtttt                                                                                >  2:80018/1‑140 (MQ=255)                                                         ataaGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGtt                                                                                <  2:308143/140‑1 (MQ=255)                                                         ataaGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTACTTGTGACATTACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTTTATTTGTGTTGCTAtt                                                                                >  2:653908/1‑140 (MQ=255)                                                           aaGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTc                                                                              >  1:234033/1‑140 (MQ=255)                                                            aGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTACTCTGTAATTGTGTTGCTGTTTCa                                                                             >  2:466365/1‑140 (MQ=255)                                                                   catcaTATTTAAAAGCTTTATTATTCAATTTATATTTTCTAATTCCTTCTGACAATACACCATTTATTCTAGAAATTATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTCCt                                                                      <  2:577958/139‑1 (MQ=255)                                                                   attctcaTTTATATGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCt                                                                      <  2:798850/135‑1 (MQ=255)                                                                     tcaCATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTaa                                                                    <  2:772193/140‑1 (MQ=255)                                                                     tcaCATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTaa                                                                    >  1:530311/1‑140 (MQ=255)                                                                     tcaCATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTaa                                                                    <  2:136681/140‑1 (MQ=255)                                                                      cacaTTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTaaa                                                                   <  2:379584/140‑1 (MQ=255)                                                                       acaTTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTaaaa                                                                  <  1:648152/140‑1 (MQ=255)                                                                        gaaaaataaagggatataacatagatagtaaagccttttagaagtatgaaacagcaacacaaatacaAAATAATATGTCACTTACTAATTGGTAGCATCATTTATATTGTATTTGTGTTGCTGTTTCATACTTCTAAAAg                                                                 <  2:508624‑M1/73‑1 (MQ=255)                                                                          tttAAAATCTTTATTATTTAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGc                                                               <  2:731062/140‑1 (MQ=255)                                                                               aaGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTAc                                                          >  2:385489/1‑140 (MQ=255)                                                                                aGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTAct                                                         <  1:691141/140‑1 (MQ=255)                                                                                  cTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTActat                                                       <  1:576537/140‑1 (MQ=255)                                                                                    ttattaTTGAATTTAGATTTTCTAATTCCTTCTTACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTActatct                                                     <  2:331566/140‑1 (MQ=255)                                                                                      attattGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTActatctat                                                   <  2:210263/140‑1 (MQ=255)                                                                                         attGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTCTCTATGtt                                                >  1:270184/1‑140 (MQ=255)                                                                                                 tAGATTTTCTAATTCCTTCTGTCAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCt                                        <  2:720470/140‑1 (MQ=255)                                                                                                     ttttCTGCTTCCTTCTGCCAATTCACAATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTAt                                    <  1:240935/140‑1 (MQ=255)                                                                                                     ttttCTAATTCCTTCTGATAATACACTATATATTCTATAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTAt                                    <  2:485026/140‑1 (MQ=255)                                                                                                      tttCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAACTGGCGTTGCTCTCTATGTTATATCTCTTTAtt                                   >  1:503163/1‑140 (MQ=255)                                                                                                       ttCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTAttt                                  <  1:555010/140‑1 (MQ=255)                                                                                                          cttttagaagtatgaaacagcaacacaaatacaAAATAATATGTCACTTACTAATTGGTAGCGTc                                                                                                          <  2:671247‑M1/32‑1 (MQ=255)                                                                                                          cttttagaagtatgaaacagcaacacaaatacaAAATAATATGTCACTTACTAATTGGTAGCGTc                                                                                                          >  1:671247‑M1/34‑65 (MQ=255)                                                                                                          ctgttagaagtatgaaacagcaacacaaatacaAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTTCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTc                               >  1:508624‑M1/34‑140 (MQ=255)                                                                                                            aTTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAACAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCtt                             <  1:768440/140‑1 (MQ=255)                                                                                                                       cAATACACCATATATTCTAGAAATAATATGTCACTTACTACTTGGTAGCGTCATATATTTTGTCTTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCACTCTATATTTCTTATTTATAGCAt                  >  2:374244/1‑140 (MQ=255)                                                                                                                       cAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTGATTTTTCTTATTTTTAGAAt                  >  2:15627/1‑140 (MQ=255)                                                                                                                          tACCCCATATCTTCTAGAAATAATATGTCACTGACTATTTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCTTATTTATAGCATTGt               <  2:9176/140‑1 (MQ=255)                                                                                                                                 tatatTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCTTATTTATAGCATTGTATCCCtt        <  1:258816/140‑1 (MQ=255)                                                                                                                                   tatTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCTTATTTATAGCATTGTATCCCtttt      <  1:83661/140‑1 (MQ=255)                                                                                                                                   tatTCTAGAAATAATATCTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATTTTATATCCCTTTATTTTTCTTATTTATAGCATTGTATCCCtttt      <  1:593123/140‑1 (MQ=255)                                                                                                                                       cTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCTTATTTATAGCATTGTATCCCTTTTTAGt  <  2:768870/140‑1 (MQ=255)                                                                                                                                       cTAGAAATAATATGTCACTTACTAATTGGGAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTATACTCTATACGTTATATCCCTTTATTTTTCTTATTTATAGCATTGTATCCCTTTTTAGt  <  1:550581/140‑1 (MQ=255)                                                                                                                                           |                                                                                                                                        TTGCTGCTATTTTCATATCATTCATGTTGCTATGGATGACCATGTTGTTTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCTTATTTATAGCATTGTATCCCTTTTTAGT  >  USA300TCH1516_ALE/2742662‑2742935

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.