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

TATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTTTTGGTAAGTCGTCAACGAATTCAATCTCTCTCGGATATTTATATGGTGCAA  >  USA300TCH1516_ALE/2746296‑2746573                                                                                                                                          |                                                                                                                                             tatTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGCACATCATAGATAAACAAGCAGTCCAGTGCGTAGCATCATACCTTACGCATTGGACTGCTTTGCTAtgt                                                                                                                                           <  2:64344‑M2/141‑4 (MQ=255)         cATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTattgat                                                                                                                                   >  1:501325/1‑141 (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)                               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                                                                              <  1:12554/141‑1 (MQ=255)                                                              aGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAaca                                                                              >  1:336036/1‑141 (MQ=255)                                                                 cgacAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACacga                                                                           <  1:253277/141‑1 (MQ=255)                                                                  gacAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACacgac                                                                          >  2:38129/1‑141 (MQ=255)                                                                  gacAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACacgac                                                                          <  2:269008/141‑1 (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)                                                                                          aGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTTTTg                                                  <  2:329201/141‑1 (MQ=255)                                                                                          aGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTTTTg                                                  >  1:612737/1‑141 (MQ=255)                                                                                            cAGTCCAGTGCGTATCATCATACCTTACGCATTGGTCTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTTTTGGt                                                <  1:359939/141‑1 (MQ=255)                                                                                             aGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTTTTGGTa                                               <  1:573946/141‑1 (MQ=255)                                                                                              gTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTTTTGGTaa                                              <  1:375487/141‑1 (MQ=255)                                                                                               tCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTCTCGGAGTTTGTTTTTGGTAAg                                             >  2:254319/1‑141 (MQ=255)                                                                                                ccAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTTTTGGTAAgt                                            >  1:423959/1‑141 (MQ=255)                                                                                                   gTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTTTTGGTAAgtcgt                                         <  2:281913/141‑1 (MQ=255)                                                                                                    tGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTTTTGGTAAgtcgtc                                        >  2:149674/1‑141 (MQ=255)                                                                                                    tGCGTATCATCATACCTTACGCATTGGACTGCTT‑‑‑‑tttatttatgatgttctttgtcgtctagttataaatattaaaattagtttagaaacaagcgcaaccagtattaagaatgagaaaatataagatgttaaacctcgaa                                     <  2:226060‑M2/141‑107 (MQ=255)                                                                                                      cGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTTTTGGTAAGTCGTCaa                                      >  2:49233/1‑141 (MQ=255)                                                                                                       gTATCATAATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTTTTGGTAAGTCGTCAAc                                     >  2:294838/1‑141 (MQ=255)                                                                                                        tATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCGTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTTTTGGTAAGTCGTCAACg                                    >  1:401524/1‑141 (MQ=255)                                                                                                          tcatcaTACCTTACGCATTGGACTGCTTTGCTAtgtttatttatgatgttctttgtcgtctagttataaatattaaaattagtttagaaacaagcgcaaccagtattaagaatgagaaaatataagatgttaaacctcgaa                                  <  2:282785‑M2/141‑109 (MQ=255)                                                                                                          tcatcaTACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTTTTGGTAAGTCGTCAACGaa                                  <  1:648953/141‑1 (MQ=255)                                                                                                          tcatcaTACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTTTTGGTAAGTCGTCAACGaa                                  >  1:247531/1‑141 (MQ=255)                                                                                                                         cATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTTTTGGTAAGTCGTCAACGAATTCAATCTCTCTCgg                   >  1:598406/1‑141 (MQ=255)                                                                                                                         cATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTTTTGGTAAGTCGTCAACGAATTCAATCTCTCTCgg                   >  1:4573/1‑141 (MQ=255)                                                                                                                          aTTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTTTTGGTAAGTCGTCAACGAATTCAATCTCTCTCGGa                  >  1:533984/1‑141 (MQ=255)                                                                                                                                       gCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTTTTGGTAAGTCGTCAACGAATTCAATCTCTCTCGGATATTTATATGGTg     >  1:606313/1‑141 (MQ=255)                                                                                                                                          aTGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTTTTGGTAAGTCGTCAACGAATTCAATCTCTCTCGGATATTTATATGGTGCaa  >  2:105455/1‑141 (MQ=255)                                                                                                                                          |                                                                                                                                             TATTTTCTCATTCTTAATACTGGTTGCGCTTGTTTCTAAACTAATTTTAATATTTATAACTAGACGACAAAGAACATCATAAATAAACAAGCAGTCCAGTGCGTATCATCATACCTTACGCATTGGACTGCTTTGCTATGTTTATTGATTGCTATCTTTTTGTTGTTGCCATTTTTCTATTTCAGCATCTCGTAGTTCAACACGACGAATTTTACCTGAGTTTGTTTTTGGTAAGTCGTCAACGAATTCAATCTCTCTCGGATATTTATATGGTGCAA  >  USA300TCH1516_ALE/2746296‑2746573

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.