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

CCATGTTGTTTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCTTATTTATAGCATTGTATCCCTTTTTAGTATTTATTGCGCAACGTCCAATTTTTCAATTTAGTGTGACAGAAT  >  USA300TCH1516_ALE/2742701‑2742979                                                                                                                                            |                                                                                                                                            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                                                                                                                <  2:136681/140‑1 (MQ=255)                              tcaCATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTaa                                                                                                                >  1:530311/1‑140 (MQ=255)                               cacaTTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTaaa                                                                                                               <  2:379584/140‑1 (MQ=255)                                acaTTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTaaaa                                                                                                              <  1:648152/140‑1 (MQ=255)                                 gaaaaataaagggatataacatagatagtaaagccttttagaagtatgaaacagcaacacaaatacaAAATAATATGTCACTTACTAATTGGTAGCATCATTTATATTGTATTTGTGTTGCTGTTTCATACTTCTAAAAg                                                                                                             <  2:508624‑M1/73‑1 (MQ=255)                                 gaaaaataaagggatataacatagatagtaaagccttttagaagtatgaaacagaaacacaaatacaaaataaatgacgctaccaattagtaagtgacatattatttTGTATTTGTGTTGCTGTTTCATACTTCTAACAg                                                                                                             >  1:508624‑M2/108‑140 (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)                                                                   cttttagaagtatgaaacagcaacacaaatacaatataaatgatgctaccaattagtaagtgacatattatttTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTc                                                                           <  2:508624‑M2/67‑1 (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)                                                                                                     AATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATATATGTTATATCCCTTTATTTTTCTTATTTATAGCATTGTATCCCTTTTTAGtattta                                         <  1:395368‑M1/140‑1 (MQ=255)                                                                                                      ATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTGTGTTATATCCCTTTATTTTTCTTATTTTTATCATTGTATTCCTTTTTAGtctttat                                        <  2:623208‑M1/140‑1 (MQ=255)                                                                                                       TAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCTTATTTATAGCATTGTATCCCTTTTTAGtatttatt                                       <  1:637946‑M1/140‑1 (MQ=255)                                                                                                       TAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCTTATTTATAGCATTGTATCCCTTTTTAGtatttatt                                       <  1:519206‑M1/140‑1 (MQ=255)                                                                                                          tatGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCTTATTTATAGCATTGTATCCCTTTTTAGTATTTATTgcg                                    >  1:210395/1‑140 (MQ=255)                                                                                                            gacgctaccaattagtaagtgacatattatttTGTATTTGTGTTGCTGTTTCATACTTCTAAAAg                                                                                                             >  1:671247‑M2/33‑65 (MQ=255)                                                                                                            gacgctaccaattagtaagtgacatattatttTGTATTTGTGTTGCTGTTTCATACTTCTAAAAg                                                                                                             <  2:671247‑M2/33‑1 (MQ=255)                                                                                                             gTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCTTATTTATAGCATTGTATCCCTTTTTAGTATTTATTGCGCaa                                 >  1:224141/1‑140 (MQ=255)                                                                                                                  ttACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCTTATTTATAACATTGTATCCCTTTTTAGTATTTATTGCGCCATGTca                            >  2:270034/1‑139 (MQ=255)                                                                                                                        aTTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCTTATTTATAGCATTGTATCCCTTTTTAGTATTTATTGCGCAACGTCCAAtttt                      <  2:539614/140‑1 (MQ=255)                                                                                                                           ggTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCTTCTTTATAGCATTGTATCCGTTTTTCAGATTTAGGGTGCACCGTCCCATCTTTCa                   >  1:334935/1‑140 (MQ=255)                                                                                                                            gTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCTTTTTTATAGCATTGTATTCTTTTTTATTTTTTTTTGCTCATAGTCCAATTTTTcga                  >  2:725076/1‑138 (MQ=255)                                                                                                                               gCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCTTATTTATAGCATTGTATCCCTTTTTAGTATTTATTGCGCAACGTCCAATTTTTCAAttt               >  1:802196/1‑140 (MQ=255)                                                                                                                                     tttatttTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCTTATTTATAGCATTGTATCCCTTTTTAGTATTTATTGCGCAACGTCCAATTTTTCAATTTAGtgtg         >  1:202926/1‑140 (MQ=255)                                                                                                                                     tttatttTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCTTATTTATAGCATTGTATCCCTTTTTAGTATTTATTGCGCAACGTCCAATTTTTCAATTTAGtgtg         >  1:355628/1‑140 (MQ=255)                                                                                                                                          ttTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCTTATTTATAGCATTGTATCCCTTTTTAGTATTTATTGCGCAACGTCCAATTTTTCAATTTAGTGTGACAGa    >  1:755330‑M2/3‑140 (MQ=255)                                                                                                                                            tGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCTTATTTATAGCATTGTATCCCTTTTTAGTATTTATTGCGCAACGTCCAATTTTTCAATTTAGTGTGACAGAAt  <  2:212229/140‑1 (MQ=255)                                                                                                                                            |                                                                                                                                            CCATGTTGTTTGACTTAATAAGCAATCAATCACATTTAAAAGCTTTATTATTGAATTTAGATTTTCTAATTCCTTCTGACAATACACCATATATTCTAGAAATAATATGTCACTTACTAATTGGTAGCGTCATTTATTTTGTATTTGTGTTGCTGTTTCATACTTCTAAAAGGCTTTACTATCTATGTTATATCCCTTTATTTTTCTTATTTATAGCATTGTATCCCTTTTTAGTATTTATTGCGCAACGTCCAATTTTTCAATTTAGTGTGACAGAAT  >  USA300TCH1516_ALE/2742701‑2742979

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.