New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2746384	46 (1.000)	4 (0.090)	4/244	NT	8.2%	intergenic (‑632/+53)	mqo2/acsA_2	putative malate:quinone oxidoreductase 2/Acetyl‑coenzyme A synthetase
	?	USA300TCH1516_ALE	= 2746433	46 (1.060)					intergenic (‑681/+4)	mqo2/acsA_2	putative malate:quinone oxidoreductase 2/Acetyl‑coenzyme A synthetase

GTGATAGTAATGTGTTTTTATTAAACTGGGATATTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTT  >  USA300TCH1516_ALE/2746244‑2746522                                                                                                                                             |                                                                                                                                           gTGATAGTAATGTGTTTTTATTAAACTGGGATATTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACA                                                                                                                                            <  1:639600‑M1/141‑1 (MQ=255) gTGATAGTAATGTGTTTTTATTAAACTGGGATATTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATCTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACA                                                                                                                                            >  1:714237‑M1/1‑141 (MQ=255)    aTAGTAATGTGTTTTTATTAAACTGGGATATTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTG‑TCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCa                                                                                                                                        <  1:30903/141‑1 (MQ=255)      aGTAATGTGTTTTTATTAAACTGGGATATTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAg                                                                                                                                       >  1:39381/1‑141 (MQ=255)       gTAATGTGTTTTTATTAAACTGGGATATTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGt                                                                                                                                      >  1:462822/1‑141 (MQ=255)              gtTTTTATTAAACTGGGATATTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGc                                                                                                                               <  2:3645/141‑1 (MQ=255)                  ttattaAACTGGGATATTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTat                                                                                                                           <  2:40492/141‑1 (MQ=255)                     ttaAACTGGGATATTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTatcat                                                                                                                        >  1:65327/1‑141 (MQ=255)                        aaCTGGGATATTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATcatcat                                                                                                                     >  2:331597/1‑141 (MQ=255)                          cTGGGATATTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATAc                                                                                                                   >  1:592299/1‑141 (MQ=255)                              gATATTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTa                                                                                                               <  1:70496/141‑1 (MQ=255)                                 atTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGc                                                                                                            >  1:160939/1‑141 (MQ=255)                                  ttCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACagcagtccaatgcgtaaggtatgatgatacgca                                                                                                            <  2:226060‑M1/141‑34 (MQ=255)                                  ttCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAtagcaaagcagtccaatgcgtaaggtatgatga                                                                                                           <  2:282785‑M1/141‑34 (MQ=255)                                      aGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTgg                                                                                                       >  1:771125/1‑141 (MQ=255)                                           tAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGc                                                                                                  >  1:773787/1‑141 (MQ=255)                                           tAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGc                                                                                                  >  2:169579/1‑141 (MQ=255)                                             aCATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCtt                                                                                                <  1:169246/141‑1 (MQ=255)                                             aCATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGCATCATCATACCTTACGCATTGGACTGCtt                                                                                                >  1:13733/1‑141 (MQ=255)                                              cATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTATACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCttt                                                                                               >  1:470858/1‑141 (MQ=255)                                                tCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGc                                                                                             >  1:182412/1‑141 (MQ=255)                                                     tatTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGCACATCATAGATAAACAAGCAGTCCAGTGCGTAGCATCATACCTTACGCATTGGACTGCTTTGCTAtgt                                                                                        <  2:64344‑M2/141‑4 (MQ=255)                                                             cATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTattgat                                                                                >  1:501325/1‑141 (MQ=255)                                                              aTTCTTCATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAACAACATCATAAATAAACAtcgcaaagcagtccaatgcgtaaggtatgatgatacgcactggactgcttgtttatttatg                                                                               <  1:197024‑M1/141‑62 (MQ=255)                                                               ttCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTAAAATCTATATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTattgattg                                                                              >  1:575294/1‑141 (MQ=255)                                                                tCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGCCTGCTTTGCTATGTTTATTGATTGc                                                                             <  2:215828/141‑1 (MQ=255)                                                                 cTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAACCAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCt                                                                            <  1:575054/141‑1 (MQ=255)                                                                     aTACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGCCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCt                                                                        >  1:321567/1‑141 (MQ=255)                                                                      tACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCtt                                                                       <  1:786464/141‑1 (MQ=255)                                                                          ggTTGCGCTTATTTCTAAACTAATTTTAATTTTTATAACTAGACGACAAAGAACATCATAAATAAACagcagtccaatgcgtaaggtatgatgatacgcactggactgcttgtttatttatgatgttctttgtcgtctag                                                                    <  1:630947‑M1/141‑74 (MQ=255)                                                                                   tGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCa                                                          <  1:530982/141‑1 (MQ=255)                                                                                    gTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCAt                                                         >  1:232869/1‑141 (MQ=255)                                                                                       tCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCAtttt                                                      >  1:349204/1‑141 (MQ=255)                                                                                        cTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCAttttt                                                     >  1:258997/1‑141 (MQ=255)                                                                                         tAAACTAATTTTAATATTTATAACTAGACGACATAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTc                                                    >  1:409035/1‑141 (MQ=255)                                                                                           aaCTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGTTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTa                                                  <  2:205247/141‑1 (MQ=255)                                                                                              tAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTAttt                                               <  2:88934/141‑1 (MQ=255)                                                                                                aTTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCa                                             <  1:212410/141‑1 (MQ=255)                                                                                                  tttAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGc                                           >  1:178419/1‑141 (MQ=255)                                                                                                     aaTATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCAtc                                        <  1:377789/141‑1 (MQ=255)                                                                                                     aaTATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCAtc                                        >  2:210034/1‑141 (MQ=255)                                                                                                      atatTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTTCCATTTTTCTGTTTCAGCAtct                                       >  2:231780/1‑141 (MQ=255)                                                                                                       tatTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCAtctc                                      <  2:90290/141‑1 (MQ=255)                                                                                                          ttATAACTAGACGACANAGAACATCATAANTAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTa                                   >  2:246213/1‑141 (MQ=255)                                                                                                          ttATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTa                                   >  1:674211/1‑141 (MQ=255)                                                                                                                cTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTT‑‑‑‑tttatttatgatgttctttgtcgtctagttataaaaattaaaattagtttagaaataagcgcaacc                          <  1:630947‑M2/141‑67 (MQ=255)                                                                                                                  aGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAaca                           >  1:336036/1‑141 (MQ=255)                                                                                                                  aGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAaca                           <  1:12554/141‑1 (MQ=255)                                                                                                                     cgacAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACacga                        <  1:253277/141‑1 (MQ=255)                                                                                                                      gacAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACacgac                       <  2:269008/141‑1 (MQ=255)                                                                                                                      gacAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACacgac                       >  2:38129/1‑141 (MQ=255)                                                                                                                          aaGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTCCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGaaa                   >  2:170976/1‑140 (MQ=255)                                                                                                                               catcatAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGATCAACACGACGAATTTTAc              >  1:404329/1‑141 (MQ=255)                                                                                                                                atcatAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTAcc             >  1:632174/1‑141 (MQ=255)                                                                                                                                  catAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCGAtgtttatttatgatgttgtttgtcgtctagttataaatattaaaattagtttagaaacaagcgcaaccagtatgaagaat           <  1:197024‑M2/141‑81 (MQ=255)                                                                                                                                    taaataaaCATGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAg         <  2:196242/141‑1 (MQ=255)                                                                                                                                     aaataaaCAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAgt        <  1:268132/141‑1 (MQ=255)                                                                                                                                           aCAtagcaaagcagtccaatgcgtaaggtatgatgctacgcactggactgcttgtttatctatgatgtgctttgtcgtctagttataaatattaaaattagtttagaaacaagcgcaaccagtattaagaatgagaaaata  <  2:64344‑M1/141‑139 (MQ=255)                                                                                                                                             |                                                                                                                                           GTGATAGTAATGTGTTTTTATTAAACTGGGATATTCGAGGTTTAACATCTTATATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTT  >  USA300TCH1516_ALE/2746244‑2746522

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