New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2713224	51 (1.100)	3 (0.070)	3/242	NT	5.6%	intergenic (‑322/+286)	isaA/USA300HOU_RS13945	putative transglycosylase IsaA/hypothetical protein
	?	USA300TCH1516_ALE	= 2713244	53 (1.230)					intergenic (‑342/+266)	isaA/USA300HOU_RS13945	putative transglycosylase IsaA/hypothetical protein

TTTTATACTGTAATGTGAAATATGTGCCCTTTAGAATCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATCAACAAATATGTTTCTACACATGTATTGATTGCTATTATTGTTGTATATTCAAAGTTTTAAAACACACATCTTTTGT  >  USA300TCH1516_ALE/2713105‑2713384                                                                                                                                            |                                                                                                                                             ttttATACTGTAATGTGAAATATGTGCCCTTTAGAATCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGc                                                                                                                                             >  1:361692‑M2/1‑140 (MQ=255)     ataCTGTAATGTGAAATATGTGCCCTTTAGAATCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGctgta                                                                                                                                         <  1:168443‑M2/141‑6 (MQ=255)               gtgAAATATGTGCCCTTTAGAATCCAATCAACCCTTGAAGTAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGa                                                                                                                               >  1:21413/1‑141 (MQ=255)                 gAAATATGTGCCCTTTAGAATCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACa                                                                                                                             <  1:250376/141‑1 (MQ=255)                  aaaTATGTGCCCTTTAGAATCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACAt                                                                                                                            >  2:176838/1‑141 (MQ=255)                  aaaTATGTGCCCTTTAGAATCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACAt                                                                                                                            >  1:661676/1‑141 (MQ=255)                     tatGTGCCCTTTAGAATCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTa                                                                                                                         <  1:675525/141‑1 (MQ=255)                      atGTGCCCTTTAGAATCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTaa                                                                                                                        >  1:651391/1‑141 (MQ=255)                       tgtgCCCTTTAGAATCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAAc                                                                                                                       >  1:228291/1‑141 (MQ=255)                        gtgCCCTTTAGAATCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACt                                                                                                                      >  2:94529/1‑141 (MQ=255)                          gCCCTTTAGAATCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTtc                                                                                                                    >  1:507991/1‑141 (MQ=255)                          gCCCTTTAGAATCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTtc                                                                                                                    <  1:309513/141‑1 (MQ=255)                           cccTTTAGAATCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTtct                                                                                                                   <  1:264198/141‑1 (MQ=255)                              tttAGAATCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCtt                                                                                                                <  1:779846/141‑1 (MQ=255)                                 aGAATCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTAtt                                                                                                             >  1:171591/1‑141 (MQ=255)                                     tCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCg                                                                                                         >  1:716283/1‑141 (MQ=255)                                     tCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCg                                                                                                         <  1:707916/141‑1 (MQ=255)                                       cAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTa                                                                                                       >  1:372378/1‑141 (MQ=255)                                          tCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACAt                                                                                                    <  1:211551/141‑1 (MQ=255)                                            aaCCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTa                                                                                                  >  1:262273/1‑141 (MQ=255)                                               ccTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAAc                                                                                               <  1:708682/141‑1 (MQ=255)                                                 ttGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGc                                                                                             <  2:308525/141‑1 (MQ=255)                                                 ttGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGc                                                                                             >  1:724100/1‑141 (MQ=255)                                                  tGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCa                                                                                            >  1:128280/1‑141 (MQ=255)                                                  tGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTATCGTAATATTACAGATTGTATTTTTGTTACATAGctgtaatattacgaaagctgtaatagatgagctaaatatagtaaaaatct                                                                                            <  1:226234‑M2/141‑51 (MQ=255)                                                   gAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCaa                                                                                           >  1:500874/1‑141 (MQ=255)                                                     aaTAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATCTCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAAtt                                                                                         >  1:601280/1‑141 (MQ=255)                                                       tAGTCTTTAACACATAAGATTTTTACTATATTTATCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTaa                                                                                       <  1:478496/141‑1 (MQ=255)                                                        aGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTaaa                                                                                      >  2:104806/1‑141 (MQ=255)                                                         gTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTaaaa                                                                                     >  1:432334/1‑141 (MQ=255)                                                          tCTTTAACACATAAGATTTTTACTATATTTAGCTGAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTaaaaa                                                                                    <  1:727970/141‑1 (MQ=255)                                                          tCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTaaaaa                                                                                    <  2:95798/141‑1 (MQ=255)                                                          tCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTaaaaa                                                                                    <  1:541156/141‑1 (MQ=255)                                                            tttAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGc                                                                                  <  2:92520/141‑1 (MQ=255)                                                              tAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCaa                                                                                <  2:310434/141‑1 (MQ=255)                                                               aaCACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAAt                                                                               >  1:203886/1‑141 (MQ=255)                                                                  acaTAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATcaa                                                                            <  1:134006/141‑1 (MQ=255)                                                                     tAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGctgtaatattacgaaagctgtaatagttgagctaaatatagtaaaaatctaatgtgttaaagactattt                                                                         <  1:261190‑M2/141‑70 (MQ=255)                                                                         aTTTTTACTATATTTAGCGCAACTAGTACTACTGTCTGATTATCACATAGTGGTTGGTTTTTACAGATCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATCAACAAatat                                                                     <  2:282187/141‑1 (MQ=255)                                                                                     tttAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATCAACAAATATGTTTCTACACAt                                                         >  1:258716/1‑141 (MQ=255)                                                                                     tttAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATCAACAAATATGTTTCTACACAt                                                         <  1:204395/141‑1 (MQ=255)                                                                                       tAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATCAACAAATATGTTTCTACACATGt                                                       <  2:284970/141‑1 (MQ=255)                                                                                          cTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATCAACAAATATGTTTCTACACATGTatt                                                    >  1:502604/1‑141 (MQ=255)                                                                                           tCAACTATTACAGCTTTCATAATATTACAGATGGTATTTTTGTTACATAGCTGCAACTTTTCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATCAACAAATATGTTTCTACACATGTattg                                                   <  1:173762/141‑1 (MQ=255)                                                                                              aCTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATCAACAAATATGTTTCTACACATGTattgatt                                                <  1:596719/141‑1 (MQ=255)                                                                                               cTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATCAACAAATATGTTTCTACACATGTattgattg                                               <  1:561839/141‑1 (MQ=255)                                                                                                 aTTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCACTTAAAAAGCAATCAACAAATATGTTTCTACACATGTATTGATTGCt                                             >  1:594672/1‑141 (MQ=255)                                                                                                 aTTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATCAACAAATATGTTTCTACACATGTATTGATTGCt                                             <  1:395740/141‑1 (MQ=255)                                                                                                    aCAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATCAACAAATATGTTTCTACACATGTATTGATTGCtatt                                          >  1:328526/1‑141 (MQ=255)                                                                                                        cTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATCAACAAATATGTTTCTACACATGTATTGATTGCTATTAttg                                      <  1:301727/141‑1 (MQ=255)                                                                                                            cGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATCAACAAATATGTTTCTACACATGTATTGATTGCTATTATtgttgt                                  <  1:636048/141‑1 (MQ=255)                                                                                                            cGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATCAACAAATATGTTTCTACACATGTATTGATTGCTATTATtgttgt                                  <  1:82090/141‑1 (MQ=255)                                                                                                                  atTACAGATTGTATTTTTGTTACATAGctgtaatattacgaaagctgtaatagttgagctaaatatagtaaaaatcttatgtgttaaagactatttcaagggttgattggattctaaagggcacatatttcacattacagt                            <  1:562104‑M2/141‑115 (MQ=255)                                                                                                                  atTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATCAACAAATATGTTTCTACACATGTATTGATTGCTATTATTGTTGTATATTc                            >  1:319345/1‑141 (MQ=255)                                                                                                                       aGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATCAACAAATATGTTTCTACACATGTATTGATTGCTATTATTGTTGTATATTCAAAGt                       <  1:503716/141‑1 (MQ=255)                                                                                                                                   tGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAACCGCAATTAAAAAGCAATCAACAAATATGTTTCTACACATGTATTGATTGCTATTATTGTTGTATATTCAAAGTTTTAAAacacac           <  1:156166/141‑1 (MQ=255)                                                                                                                                    gTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATCAACAAATATGTTTCTACACATGTATTGATTGCTATTATTGTTGTATATTCCAAGTTTTAAAAcacaca          >  1:205656/1‑141 (MQ=255)                                                                                                                                      tACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATCAACAAATATGTTTCTACACATGTATTGATTGCTATTATTGTTGTATATTCAAAGTTTTAAAACACACATc        >  2:193479/1‑141 (MQ=255)                                                                                                                                          tAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATCAACAAATATGTTTCTACACATGTATTGATTGCTATTATTGTTGTNTATTCAAAGTTTNAAAACACACATCtttt    <  1:657326/141‑1 (MQ=255)                                                                                                                                            gCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATCAACAAATATGTTTCTACACATGTATTGATTGCTATTATTGTTGTATATTCAAAGTTTTAAAACACACATCTTTtgt  <  1:569695/141‑1 (MQ=255)                                                                                                                                            |                                                                                                                                             TTTTATACTGTAATGTGAAATATGTGCCCTTTAGAATCCAATCAACCCTTGAAATAGTCTTTAACACATAAGATTTTTACTATATTTAGCTCAACTATTACAGCTTTCGTAATATTACAGATTGTATTTTTGTTACATAGCTGTAATATATCTGACATGTAACTTCTCTTATTTTCGTACATTAAACGCAATTAAAAAGCAATCAACAAATATGTTTCTACACATGTATTGATTGCTATTATTGTTGTATATTCAAAGTTTTAAAACACACATCTTTTGT  >  USA300TCH1516_ALE/2713105‑2713384

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ 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.