New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	1100713 =	54 (0.950)	4 (0.080)	3/238	NT	8.0%	intergenic (‑277/+53)	USA300HOU_1033/pdf1	hypothetical protein/formylmethionine deformylase
	?	CP000730	1100746 =	43 (0.830)					intergenic (‑310/+20)	USA300HOU_1033/pdf1	hypothetical protein/formylmethionine deformylase

GATTTTATATGAAACGGTAAAATTTAAATGAGGGGATAAAAAGTTTGGTAGAAAGGTGAATATATTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCATAGAACATTACACCATTTAAATGGTCAATTTCATGTTGGAAAACAATTGCTGGATATCCT  >  CP000730/1100613‑1100883                                                                                                                                       |                                                                                                                                          gATTTTATATGAAACGGTAAAATTTAAATGAGGGGATAAAAAGTTTGGTAGAAAGGTGAATATATTTAACTGTTGTTTATTCGAAAAAGATGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTa                                                                                                                                    >  2:196154/1‑141 (MQ=255)  aTTTTATATGAAACGGTAAAATTTAAATGAGGGGATAAAAAGTTTGGTAGAAAGGTGAATATATTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAg                                                                                                                                   >  1:72584/1‑141 (MQ=255)         ttGAAACGGTAAAATTTAAATGAGGGGATAAAAAGTTTGGTAGAAAGGTGAATATATTTAACTGTTGTTTATTCGAAAAAGTTGTAATAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAGAAtg                                                                                                                            <  2:407114/140‑1 (MQ=255)         tggtgtaatgttctatgatcacattgacaaagatcacccattacaaccacatacagatgcagtagaagtttaaaacacatttttctaattatcaaagcttaggacatcatatttatcctaagctttGATAATTAGAAAAAt                                                                                                                             >  1:541602‑M2/127‑141 (MQ=255)                   aaaaTTTAAATGAGGGGATAAAAAGTTTGGTAGAAAGGTGAATATATTTAACTGTTGATTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAAc                                                                                                                  >  2:404173/1‑141 (MQ=255)                    aaaTTTAAATGAGGGGATAAAAAGTTTGGTAGAAAGGTGAATATATTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGGAAAATGTGTTTTAAACt                                                                                                                 >  2:330704/1‑141 (MQ=255)                    aaaTTTAAATGAGGGGATAAAAAGTTTGGTAGAAAGGTGAATATATTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAGCt                                                                                                                 >  1:461080/1‑141 (MQ=255)                           aaTGAGGGGATAAAAAGTTTGGTAGAAAGGTGAATATATTTAACTGTTGTTTATCAGCAGGAGCTGTACAATTATAAGCTTAGGACATCATATT‑TATCCTAAGCTTGGATAATTAGAAAAATGTGTTTTAAACTTCTACTg                                                                                                          >  1:156797/1‑141 (MQ=255)                            aTGAGGGGATAAAAAGTTTGGTAGAACGGTGAATATATTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGCACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGc                                                                                                         <  1:410354/141‑1 (MQ=255)                                ggggATAAAAAGTTTGGTAGAAAGGTGTATATATTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGGAAAGCTTAGGACATCCTATT‑TATCCTAAGCTTTGGTAATTAGAAAAATGGGTTGTAAAATTCTACTGCAtac                                                                                                     >  1:31365/1‑139 (MQ=255)                                 gggATAAAAAGTTTGGTAGAAAGGTGAATATATTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTg                                                                                                    <  1:27379/141‑1 (MQ=255)                                   gATAAAAAGTTTGGTAGAAAGGTGAATATATTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCCTCGGTa                                                                                                  >  1:618615/1‑141 (MQ=255)                                     tAAAAAGTTTGGTAGAAAGGTGAATATATTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTAtg                                                                                                <  1:32262/141‑1 (MQ=255)                                        aaaGTGTGGTAGAAAGGTGAATATATTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTgg                                                                                             <  2:66726/141‑1 (MQ=255)                                         atcacccattacaaccacatacagatgcagtagaagtttaaaacacatttttctaattatcaaagcttaggacatcatatttatcctaagctttGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTgg                                                                                             <  2:541602‑M2/47‑1 (MQ=255)                                         aaGTTTGGTAGAAAGGTGAATATATTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGt                                                                                            >  2:134866/1‑141 (MQ=255)                                          aGTTTGGTAGAAAGGTGAATATATTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTGTGTGGtt                                                                                           >  1:603288/1‑141 (MQ=255)                                          aGTTTGGTAGAAAGGTGAATATATTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGtt                                                                                           <  1:551920/141‑1 (MQ=255)                                               ggTAGAAAGGTGAATATATTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAACAGCTTAGGACATCATATT‑TATCCTAAGCTTCGCCGAGAAAAAAGAACTGATTTAAACTTCTACTCCATCTGTATGTGGTTGTaag                                                                                      >  1:652246/1‑140 (MQ=255)                                               ggTAGAAAGGTGAATATATTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAAt                                                                                      >  2:187602/1‑141 (MQ=255)                                                gTAGAAAGGTGAATATATTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATg                                                                                     >  2:535068/1‑141 (MQ=255)                                                     aaGGTGAATATATTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGa                                                                                <  2:648589/141‑1 (MQ=255)                                                     aaGGTGAATATATTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTAATGCATCTGTATGTGGTTGTAATGGGTGa                                                                                >  2:34764/1‑141 (MQ=255)                                                      ccacatacagatgcagtagaagtttaaaacacatttttctaattatcAAAGCTTAGGATAA‑ATATGATGTCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGAt                                                                               <  2:541602‑M1/94‑1 (MQ=255)                                                       ggTGAATATATTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATc                                                                              <  1:257489/141‑1 (MQ=255)                                                           aaTATATTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTg                                                                          >  2:239277/1‑141 (MQ=255)                                                            atatatTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGt                                                                         >  2:584674/1‑141 (MQ=255)                                                            agatatTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGt                                                                         <  2:164167/139‑1 (MQ=255)                                                             tatatTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTc                                                                        <  2:639661/141‑1 (MQ=255)                                                             tagatTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTc                                                                        <  2:136814/138‑1 (MQ=255)                                                                       tgttgtTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCa                                                              >  1:338736/1‑141 (MQ=255)                                                                        gttgttTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCAt                                                             <  2:247051/141‑1 (MQ=255)                                                                            tttATTCGAAAAACTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCATAGaa                                                         <  2:480722/141‑1 (MQ=255)                                                                                  cGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATACTAGAACATTac                                                   >  2:486364/1‑141 (MQ=255)                                                                                     aaaaGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTTTTAATTAGAAAAATGTGTTTTAAAGTTCTACTGCATATGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATATTATAACATTACAcc                                                >  2:234444/1‑141 (MQ=255)                                                                                     aaaaGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCATTGTGATCATAGTAGTTTacagc                                                >  2:318122/1‑139 (MQ=255)                                                                                      atttttctaattatcAAAGCTTAGGATAA‑ATATGATGTCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCATAGAACATTACACCa                                               >  1:541602‑M1/16‑141 (MQ=255)                                                                                        aGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCATAGAACATTACACCAtt                                             >  1:466562/1‑141 (MQ=255)                                                                                         gTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCATAGAACATTACAACAttt                                            >  1:143349/1‑141 (MQ=255)                                                                                           tGTAAAAGTAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCATAGAACATTACACCATTTaa                                          <  2:651279/141‑1 (MQ=255)                                                                                           tGTAAAAGGAAAAGCTTAGGCCATCATATT‑TATCCTAAGCTTTGCTAATTAGANAAATTTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTCTGTCAATTTGATCATAGACCATTACACCATTTaa                                          >  1:406502/1‑141 (MQ=255)                                                                                            gTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCATAGAACATTCCACCATTTaaa                                         >  2:440475/1‑141 (MQ=255)                                                                                                aaGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCATAGAACATTACACCATTTAAATGGt                                     >  1:33757/1‑141 (MQ=255)                                                                                                   gAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTTAATGTGATCATAGAACATTACACCATTTAAATGGTCaa                                  <  1:429531/141‑1 (MQ=255)                                                                                                    aaaaGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCATAGAACATTACACCATTTAAATGGTCAAt                                 >  1:504053/1‑141 (MQ=255)                                                                                                      AAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCATAGAACATTACACCATTTAAATGGTCAAttt                               <  2:338658‑M1/141‑1 (MQ=255)                                                                                                       AGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCATAGAACATTACACCATTTAAATGGTCAATTTc                              <  1:520158‑M1/141‑1 (MQ=255)                                                                                                            agtaCATCATATT‑TATCCTAAGTTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGAGCATAGAACATTACACCATTTAAATGGTCAATTTCATGtt                         <  2:274868/138‑1 (MQ=255)                                                                                                            AGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCATAGAACATTACACCATTTAAATGGTCAATTTCATGtt                         >  1:262923‑M1/1‑141 (MQ=255)                                                                                                             aggataaatatgatgtcctaagctttGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCATAGAACATTACACCATTTAAATGGTCAATTTCATGtt                         >  1:464094‑M2/27‑141 (MQ=255)                                                                                                             aggataaatatgatgtcctaagctttGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCATAGAACATTACACCATTTAAATGGTCAATTTCATGtt                         >  1:464102‑M2/27‑141 (MQ=255)                                                                                                               agaacagatT‑TATTCTAAGCTTTGATAATTAGGAAAACGTGTTTTAAACTTCTACTGCATAAGTATGTGGTTGTAATGGGTGATCTTTATAAATGTGATCATAGAACATTAAACCATTTAAATGGTCAATTTAATGTTgca                      >  2:505492/8‑139 (MQ=255)                                                                                                                catcatATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTGTTTAATGTGATCATAGAACATTACACCATTTAAATGGTCAATTTCATGTTGGaa                     >  1:484901/1‑141 (MQ=255)                                                                                                                          tATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCATAGAACATTACACCAGTTAAATGTTGAAGTTCATGTTGGAAAACAATTGc            <  2:143349/141‑1 (MQ=255)                                                                                                                                 agctttGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCATAGAACATTACACCATTTAAATGGTCAATTTCATGTTGGAAAACAATTGCTGGatat     <  1:91803‑M2/135‑1 (MQ=255)                                                                                                                                    tttGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCATAGACCATTACACCATTTAAATGGTCAATTTCATGTTGGAAAACAATTGCTGGATATCCt  <  2:574102‑M2/138‑1 (MQ=255)                                                                                                                                    tttGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCATAGAACATTACACCATTTAAATGGTCAATTTCATGTTGGAAAACAATTGCTGGATATCCt  <  2:218568‑M2/138‑1 (MQ=255)                                                                                                                                    tttGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCCGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCATAGAACATTACACCATTTAAATGGTCAATTTCATGTTGGAAAACAATTGCTGGATATCCt  <  2:624837‑M2/138‑1 (MQ=255)                                                                                                                                       |                                                                                                                                          GATTTTATATGAAACGGTAAAATTTAAATGAGGGGATAAAAAGTTTGGTAGAAAGGTGAATATATTTAACTGTTGTTTATTCGAAAAAGTTGTAAAAGGAAAAGCTTAGGACATCATATT‑TATCCTAAGCTTTGATAATTAGAAAAATGTGTTTTAAACTTCTACTGCATCTGTATGTGGTTGTAATGGGTGATCTTTGTCAATGTGATCATAGAACATTACACCATTTAAATGGTCAATTTCATGTTGGAAAACAATTGCTGGATATCCT  >  CP000730/1100613‑1100883

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.