New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2278438 =	42 (0.910)	3 (0.070)	3/238	NT	6.9%	intergenic (+106/+213)	mtlD/ebh_3	Mannitol‑1‑phosphate 5‑dehydrogenase/Extracellular matrix‑binding protein ebh
	?	USA300TCH1516_ALE	2278497 =	43 (1.020)					intergenic (+165/+154)	mtlD/ebh_3	Mannitol‑1‑phosphate 5‑dehydrogenase/Extracellular matrix‑binding protein ebh

AAGTTTCCAACGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACTTGGTTACTTAGTAAGGAATATTTCCCTATGAAATAACTAGATGTTCACA  >  USA300TCH1516_ALE/2278358‑2278636                                                                                                                                            |                                                                                                                                            aagTTTCCAACGTTATNCGTTAACAATCANTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGc                                                                                                                                            >  1:740637/1‑141 (MQ=255)    tttCCAACGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGtt                                                                                                                                         >  1:441678/1‑141 (MQ=255)    tttCCAACGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGtt                                                                                                                                         >  1:340843/1‑141 (MQ=255)         aaCGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGTATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTtaataa                                                                                                                                    <  1:39747/141‑1 (MQ=255)           cGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAAtt                                                                                                                                  <  1:121742/141‑1 (MQ=255)                ttCGTTAACAATCAGTAATAATTTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGttt                                                                                                                             <  2:278188/141‑1 (MQ=255)                ttCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGttt                                                                                                                             >  2:284820/1‑141 (MQ=255)                ttCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGttt                                                                                                                             >  1:252198/1‑141 (MQ=255)                  cGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTa                                                                                                                           >  1:112239/1‑141 (MQ=255)                  cGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTa                                                                                                                           <  1:764756/141‑1 (MQ=255)                         aaTCCGTAATAATGTAGTAGTTCCCTTGAATTAACAATACTAAATTTCTGAACATAAACAATCCCCCCTTCCACATAGTCTCTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGa                                                                                                                    <  1:157350/141‑1 (MQ=255)                           tCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGagc                                                                                                                  <  1:528852/141‑1 (MQ=255)                           tCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGagc                                                                                                                  <  2:152099/141‑1 (MQ=255)                                  taatGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGagccacagcc                                                                                                           >  1:347578/1‑141 (MQ=255)                                    atGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGagccacagccac                                                                                                         <  2:153167/141‑1 (MQ=255)                                    atGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGagccacagccac                                                                                                         >  2:24115/1‑141 (MQ=255)                                     tGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCAcc                                                                                                        <  2:235955/141‑1 (MQ=255)                                     tGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCAcc                                                                                                        <  2:315018/141‑1 (MQ=255)                                      gtagtaGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCt                                                                                                       >  1:405311/1‑141 (MQ=255)                                          tagtGCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTc                                                                                                   <  1:627453/141‑1 (MQ=255)                                              tCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGATAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCacaa                                                                                               >  2:63412/1‑138 (MQ=255)                                                   tGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGCCACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTAt                                                                                          <  2:155346/141‑1 (MQ=255)                                                   tGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTAt                                                                                          <  1:553241/141‑1 (MQ=255)                                                          aCAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCAt                                                                                   >  2:50323/1‑141 (MQ=255)                                                          aCAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCAt                                                                                   >  1:53402/1‑141 (MQ=255)                                                             atatTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTAc                                                                                <  1:305970/141‑1 (MQ=255)                                                                   aaTTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAAc                                                                          >  1:350519/1‑141 (MQ=255)                                                                         tGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTc                                                                    >  1:145621/1‑141 (MQ=255)                                                                         tGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCAACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTc                                                                    >  1:583326/1‑141 (MQ=255)                                                                          gAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCa                                                                   >  1:615125/1‑141 (MQ=255)                                                                           aaCATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCat                                                                  >  1:36010/1‑141 (MQ=255)                                                                            aCATAAAAAATACTCCCTTCAACCTAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTACTTTCGAGCCACAGCCACCTATTCACTGGCTATTGGTCATTACTAAAACAAATTCata                                                                 >  1:579548/1‑141 (MQ=255)                                                                             cATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCatat                                                                >  1:168463/1‑141 (MQ=255)                                                                                aaaaaaTACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGGATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTaa                                                             >  2:109737/1‑141 (MQ=255)                                                                                 AAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAAc                                                            >  1:524149‑M1/1‑141 (MQ=255)                                                                                     ATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGtt                                                        >  1:24577‑M1/1‑141 (MQ=255)                                                                                       ACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAg                                                      <  1:80017‑M1/141‑1 (MQ=255)                                                                                        ctcctttcatacataacacaagttaagtgtctatgttgaagggagtatttttGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGa                                                     >  2:200384‑M2/53‑141 (MQ=255)                                                                                         TCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGAc                                                    <  1:456458‑M1/141‑1 (MQ=255)                                                                                          cctttcatacataacacaagttaagtgtctatgttgaagggagtatttttGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACt                                                   >  1:491100‑M2/51‑141 (MQ=255)                                                                                          CCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACt                                                   >  2:271444‑M1/1‑141 (MQ=255)                                                                                            cTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACTTg                                                 >  1:387311/1‑141 (MQ=255)                                                                                                 aCATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACTTGGTTAc                                            >  1:115117/1‑141 (MQ=255)                                                                                                   aTAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACTTGGTTACtt                                          >  1:25428/1‑141 (MQ=255)                                                                                                    tAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACTTGGTTACTTa                                         >  2:94866/1‑141 (MQ=255)                                                                                                          cTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACTTGGTTACTTAGTAAgg                                   <  1:543724/141‑1 (MQ=255)                                                                                                            tAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACTTGGTTACTTAGTAAGGaa                                 >  1:100549/1‑141 (MQ=255)                                                                                                            agttaagtgtctatgttgaagggagtatttttGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACTTGGTTACTTAGTAAGGaa                                 >  1:521641‑M2/33‑141 (MQ=255)                                                                                                              aCTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACTTGGTTACTTAGTAAGGAata                               >  1:141619/1‑141 (MQ=255)                                                                                                                  gtgtTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACTTGGTTACTTAGTAAGGAATATTTc                           >  1:257205/1‑141 (MQ=255)                                                                                                                    gtTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAGTTCATATTAACTGTTAGACTTGGTTACTTAGTAAGGAATATTTccc                         >  1:306074/1‑141 (MQ=255)                                                                                                                      tatgtatgAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACTTGGTTACTTAGTAAGGAATATTTCCCTa                       <  1:478146/141‑1 (MQ=255)                                                                                                                        tgtatgAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACACATTCATATTAACTGTTAGACTTGGTTACTTAGTAAGGAATATTTCCCTATg                     <  2:256511/141‑1 (MQ=255)                                                                                                                         gtatgAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACTTGGTTACTTAGTAAGGAATATTTCCCTATGa                    >  2:78019/1‑141 (MQ=255)                                                                                                                                    gtatttttGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACTTGGTTACTTAGTAAGGAATATTTCCCTATGAAATAACTAGAt         >  1:569265‑M2/9‑141 (MQ=255)                                                                                                                                      atttttGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACTTGGTTACTTAGTAAGGAATATTTCCCTATGAAATAACTAGATGt       >  1:425036‑M2/7‑141 (MQ=255)                                                                                                                                       tttttGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACTTGGTTACTTAGTAAGGAATATTTCCCTATGAAATAACTAGATGtt      <  1:113222‑M2/136‑1 (MQ=255)                                                                                                                                       tttttGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACTTGGTTACTTAGTAAGGAATATTTCCCTATGAAATAACTAGATGtt      >  2:75701‑M2/6‑141 (MQ=255)                                                                                                                                       tttttGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACTTGGTTACTTAGTAAGGAATATTTCCCTATGAAATAACTAGATGtt      <  1:262401‑M2/136‑1 (MQ=255)                                                                                                                                         tttGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACTTGGTTACTTAGTAAGGAATATTTCCCTATGAAATAACTAGATGTTca    >  1:60949‑M2/4‑141 (MQ=255)                                                                                                                                           tGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACTTGGTTACTTAGTAAGGAATATTTCCCTATGAAATAACTAGATGTTcaca  >  2:201490‑M2/2‑141 (MQ=255)                                                                                                                                            |                                                                                                                                            AAGTTTCCAACGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAACTGTTAGACTTGGTTACTTAGTAAGGAATATTTCCCTATGAAATAACTAGATGTTCACA  >  USA300TCH1516_ALE/2278358‑2278636

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.