New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1801134	44 (0.690)	4 (0.060)	4/254	NT	8.2%	coding (186/1122 nt)	citZ	Citrate synthase 2
	?	USA300TCH1516_ALE	= 1801146	47 (0.760)					coding (174/1122 nt)	citZ	Citrate synthase 2

TGTGCAATATATGATAATGACGTACGTAATGCTGTCATTGGATGCACGTGATCTGTAACATACTCCTCAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAGTC‑AATTGACTTTCAATAATTGAACTTATTTTAGTCTCCGCTGCGAT  >  USA300TCH1516_ALE/1801009‑1801286                                                                                                                                          |                                                                                                                                               tgtgCAATATATGATAATGACGTACGTTATGCTGTCATTGGATGCACGTGATCTGTAACATACTCCTCAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGATCTtct                                                                                                                                             <  2:342275‑M2/141‑4 (MQ=255) tgtgCAATATATGATAATGACGTACGTAATGCTGTCATTGGATGCACGTGATCTGTAACATACTCCCCAAAATGTGTCTACACACGAGGATTTAATGTCATGTATTCATTTAATTTCCCTTTTAGATAACCAAGCGCTtct                                                                                                                                             <  2:114383‑M2/141‑4 (MQ=255)  gtgCAATATATGATAATGACGTACGTAATGCTGTCATTGGATGCACGTGATCTGTAACATACTCCTCAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGATcttctt                                                                                                                                            >  2:487707/1‑141 (MQ=255)     cAATATATGATAATGACGTACGTAATGCTGTCATTGGATGCACGTGATCTGTAACATACTCCTCAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGt                                                                                                                                         <  1:393907/141‑1 (MQ=255)       atatatGATAATGACGTACGTAATGCTGTCATTGGATGCACGTGATCTGTAACATACTCCTCAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGttt                                                                                                                                       >  2:119320/1‑141 (MQ=255)         agatGATAATCACGTACGGAATGCTGTGATTGGATGCACGGGATCTGTAACATGCTCCTCAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTgg                                                                                                                                     <  2:367766/139‑1 (MQ=255)          tatGATAATGACGTACGTAATGCTGTCATTGGATGCACGTGATCTGTAACATACTCCTCAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGc                                                                                                                                    <  2:476227/141‑1 (MQ=255)          tatGATAATGACGTACGTAATGCTGTCATTGGATGCACGTGATCTGTAACATACTCCTCAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGc                                                                                                                                    <  1:77486/141‑1 (MQ=255)                  tGACGTACGTAATGCTGTCATTGGATGCACGTGATCTGTAACATACTCCTCAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCtata                                                                                                                            <  1:226638/141‑1 (MQ=255)                  tGACGTACGTAATGCTGTCATTGGATGCACGTGATCTGTAACATACTCCTCAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCtata                                                                                                                            <  1:68029/141‑1 (MQ=255)                    acgtacgtAATGCTGTCATTGGATGCACGTGATCTGTAACATACTCCTCAAAATGTGTATACACACGAGGCTTTTTAGGCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGt                                                                                                                          >  1:776069/1‑141 (MQ=255)                        acgtaATGCTGTCATTGGATGCACGTGATCTGTAACATACTCCTCAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCa                                                                                                                      <  2:90529/141‑1 (MQ=255)                                 tggcATGGGATGCACGTGATCTGTAACATACTCCTCAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTGAGTTGTCTATAGTTCCATAATAGGaa                                                                                                             <  2:641462/138‑1 (MQ=255)                                 tGTCATTGGATGCACGTGATCTGTAACATACTACTCAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTGGGCAATCTATAGTTGTATAATAGGaa                                                                                                             >  1:237271/1‑141 (MQ=255)                                       tGGATGCACGTGATCTGTAACATACTCCTCAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAAc                                                                                                       >  2:21583/1‑141 (MQ=255)                                           tGCACGTGATCTGTAACATACTCATCCAAATGTGTATTCACACGAGGATTTAATGTCATGTATTGATTTAATAGCCCGCTTAGATGAGCAAGGTCTTCTTCGTTTGGCAATCTATCGTTCCATAATAGGAAAATAActtct                                                                                                   <  2:51632/141‑1 (MQ=255)                                            gCACGTGATCTGTAACATACTCCTCAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAActtctt                                                                                                  >  1:283877/1‑141 (MQ=255)                                            gCACGTGATCTGTAACATACTCCTCAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAActtctt                                                                                                  >  2:424685/1‑141 (MQ=255)                                             cACGTGATCTGTAAGATACTCGTGAAAATGTGTATACAAAAAAGGAGTTAATGTCATATATTGATTTAATTTCCCTTTTAGATGAGCAAGGTATTCTTCGTTTGTCAAGATATAGTTACATAATAGGAAAATAActtctta                                                                                                 >  2:398615/1‑140 (MQ=255)                                             cACGTGATCGGTAACATACCCCTCAAAATGTGTATACACACGAGAGCTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACttcttc                                                                                                 <  1:66223/141‑1 (MQ=255)                                              aCGTGATCTGTAACATACTCCTCAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTACCTTTTAGAAAAGCTTGCTAAtctaaaagagaaattaaatcaatacatgacattaaatcctcatgtata                                                                                                <  2:34180‑M2/141‑49 (MQ=255)                                               cGTGATCTGTAACATACTCCTCAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCaa                                                                                               >  1:207424/1‑141 (MQ=255)                                                 tGATCTGTAACATACTCCTCAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTTGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAAt                                                                                             >  1:598161/1‑141 (MQ=255)                                                  gATCTGTAACATACTCCTCAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAAtt                                                                                            >  2:770185/1‑141 (MQ=255)                                                              tctccttcAAAGGTGTCTACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCTTTTTGCAAGAGCTTGCTCAtctaaaagggaaattaactcaatacatgacattaaatcctcgtgtgtatacacattttgaggag                                                                                >  1:687951‑M2/2‑77 (MQ=255)                                                               ctcctcAAAATTTGTATACACACTAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATTGTTCCATAATAGCAAAATAACTTCTTCAAATTGCGCATTTTCAGc                                                                               <  2:691436/141‑1 (MQ=255)                                                               ctcctcAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAga                                                                               >  2:66767/1‑140 (MQ=255)                                                               ctcctcAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGAAGAGCTTGCTCAtctaaaagggaaattaaatcaatacatgacattaaatcctaatgtgtataaacattttgaggagt                                                                               <  2:687951‑M2/141‑66 (MQ=255)                                                                 cctcAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTa                                                                             >  1:232802/1‑141 (MQ=255)                                                                 cctcAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTa                                                                             >  2:576096/1‑141 (MQ=255)                                                                      aaaTGTTTATACACAAGAGTATTAAATGTCATGTATTGATTTAATTTCTCTTTTATATGAGCAAGCTATTCTTCGTTTCGCAATCTATAGTTCTATGATATGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGatca                                                                        <  2:382265/141‑1 (MQ=255)                                                                              ataCACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATTTATAGTTCCATAATAGGACAACACACACAACAAATTGAGCATTCTGTGCGAGATAATCA‑AGATc                                                               >  2:162011/1‑141 (MQ=255)                                                                               tataCACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGAAGAGCTTGCTCAtctaaaagtgaaattaaatcaatacatgacattaaatcctcgtgtgtatacacattttgaggagtatgttacagatcacgt                                                               >  1:34180‑M2/1‑60 (MQ=255)                                                                                        ggATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCa                                                     <  2:339365/141‑1 (MQ=255)                                                                                         gATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCCGCTAGATCATCA‑ATATCATAGCCGGCAt                                                    >  1:466801/1‑141 (MQ=255)                                                                                           tttAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATaa                                                  >  1:97863/1‑141 (MQ=255)                                                                                           tttAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ACAACATCGCCCCCATaa                                                  >  2:142238/1‑141 (MQ=255)                                                                                           tttAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAAAAAATTCTTCAAGTTGCGCATGCCCAGCATGATCATCA‑ATATCATAGCCGGCATaa                                                  >  1:492563/1‑141 (MQ=255)                                                                                             tAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAGt                                                >  1:760839/1‑141 (MQ=255)                                                                                               aTGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAGTC‑a                                             >  2:477201/1‑141 (MQ=255)                                                                                                  tCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAGTC‑AAtt                                          <  1:624761/141‑1 (MQ=255)                                                                                                         ttGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATCGCGCATTTGGAGCTTGCTACTAA‑CTAGCATGGCCGGCATAAGTC‑AATTGACtttt                                   >  1:295985/1‑140 (MQ=255)                                                                                                            aTTTAATTTCCATTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAGTC‑AATTGACTTTCagt                                <  2:74388/141‑3 (MQ=255)                                                                                                               tAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAATTC‑AATTGACTTTCaataat                             >  2:596916/1‑141 (MQ=255)                                                                                                                 aTTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCT‑ATCTCCTAGCCGGCATAAGTC‑AATTGACTTTCATTAATTg                           >  2:637279/1‑141 (MQ=255)                                                                                                                 aTTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAGTC‑AATTGACTTTCAATAATTg                           <  1:477201/141‑1 (MQ=255)                                                                                                                  tttCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAGTC‑AATTGACTTTCAATAATTGa                          <  1:507815/141‑1 (MQ=255)                                                                                                                   ttCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAGTC‑AATTGACTTTCAATAATTGaa                         <  1:119320/141‑1 (MQ=255)                                                                                                                    tCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAGTC‑AATTGACTTTCAATAATTGAAc                        >  1:530411/1‑141 (MQ=255)                                                                                                                      ccTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAGTC‑AATTTACTTTCAATAATTCCACtt                      >  2:693903/1‑141 (MQ=255)                                                                                                                          ttAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAGTC‑AATTGACTTTCAATAATTGAACTTAttt                  >  1:525547/1‑141 (MQ=255)                                                                                                                          ttAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAGTC‑AATTGACTTTCAATAATTGAACTTAttt                  >  1:573905/1‑141 (MQ=255)                                                                                                                          ttAGACGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAGTC‑AATTGACTTTCAATAATTGAACTTAttt                  <  1:509029/141‑1 (MQ=255)                                                                                                                                   gaatcgcttcttCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAGTC‑AATTGACTTTCAATAATTGAACTTATTTTAGTCTCCg         <  2:161041/135‑1 (MQ=255)                                                                                                                                   cAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAGTC‑AATTGACTTTCAATAATTAAACTTATTTTAGTCTCCg         >  2:471389/1‑141 (MQ=255)                                                                                                                                     aGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAGTC‑AATTGACTTTCAATAATTGAACTTATTTTAGTCTCCGCt       <  1:464757/141‑1 (MQ=255)                                                                                                                                       ctctTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAGTC‑AATTGACTTTCATTATCATCACTTATCTTAGTCTCCGCTGc     >  2:125425/1‑141 (MQ=255)                                                                                                                                       ctctTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAGTC‑AATTGACTTTCAATAATTGAACTTATTTTAGTCTCCGCTGc     >  1:620375/1‑141 (MQ=255)                                                                                                                                       ctctTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAATC‑AATTGACTTTCAATAATTGAACTTATTTTAGTCTCCGCtcc     >  2:427640/1‑139 (MQ=255)                                                                                                                                       ctctTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCT‑GGCATTCAGGGAGCAGAGCAGG‑AAAAGACGTAGTGACGTTCAATAATTGAACTTATTTTAGTCTCCGCTGc     <  1:576096/141‑1 (MQ=255)                                                                                                                                          ttcttcGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAGTC‑AATTGACTTTCAATAATTGAACTTATTTTAGTCTCCGCTGCGAt  <  1:350949/141‑1 (MQ=255)                                                                                                                                          ttcttcGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATGGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAGTC‑AATTGACTTTCAATAATTGAACTTATTTTAGTCTCCGCTGCGAt  <  1:7665/141‑1 (MQ=255)                                                                                                                                          |                                                                                                                                               TGTGCAATATATGATAATGACGTACGTAATGCTGTCATTGGATGCACGTGATCTGTAACATACTCCTCAAAATGTGTATACACACGAGGATTTAATGTCATGTATTGATTTAATTTCCCTTTTAGATGAGCAAGCTCTTCTTCGTTTGGCAATCTATAGTTCCATAATAGGAAAATAACTTCTTCAAATTGCGCATTTTCAGCTAGATCATCA‑ATATCATAGCCGGCATAAGTC‑AATTGACTTTCAATAATTGAACTTATTTTAGTCTCCGCTGCGAT  >  USA300TCH1516_ALE/1801009‑1801286

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.