New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2633273	78 (0.790)	11 (0.110) +GC	6/156	NT	13.6%	coding (2675/3057 nt)	fnbA_2	Fibronectin‑binding protein A
	?	USA300TCH1516_ALE	= 2633349	65 (0.660)					coding (2599/3057 nt)	fnbA_2	Fibronectin‑binding protein A

TGGTGGCGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAACACTATTGTGTCCACCGAATTGATAACTTGGTT  >  USA300TCH1516_ALE/2633260‑2633438                                                                                          |                                                                                          tggtggCGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGtt                                                                                          >  1:1101701/1‑91 (MQ=40) tggtggCGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGtt                                                                                          >  1:2431862/1‑91 (MQ=40)    tggCGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTttgt                                                                                       >  1:1287977/1‑91 (MQ=39)     ggCGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTttgtt                                                                                      >  1:626972/1‑91 (MQ=38)       cGTTGGTGTTTCCGGCCCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGCTTGGAGGAGTTGTATCTTCTTCAATCGTTTGTTGa                                                                                    >  1:459704/1‑91 (MQ=255)         ttGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGAcc                                                                                  <  1:2160439/91‑1 (MQ=34)          tGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCt                                                                                 <  1:3621146/91‑1 (MQ=33)           ggTGTTTCCGGCTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCtt                                                                                <  1:832809/91‑1 (MQ=34)           ggTGTTTCCGGCTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCtt                                                                                >  1:2431200/1‑91 (MQ=33)           ggTGTTTCCGGCTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCtt                                                                                >  1:2431213/1‑91 (MQ=34)            gtgtTTCCGGCTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGCGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTc                                                                               >  1:238482/1‑91 (MQ=21)               tttCCGGCTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCAtt                                                                            >  1:11955/1‑91 (MQ=34)                 tCCGGCTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCAtttt                                                                          >  1:2993853/1‑91 (MQ=37)                  ccGGCTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTg                                                                         >  1:2564237/1‑91 (MQ=38)                  ccGGCTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTg                                                                         >  1:3547511/1‑91 (MQ=38)                  ccGGCTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTg                                                                         >  1:3546491/1‑91 (MQ=38)                  ccGGCTCACCTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTg                                                                         <  1:2155373/91‑1 (MQ=255)                     gCTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGcc                                                                      >  1:2415949/1‑91 (MQ=255)                      cTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCg                                                                     <  1:1871772/91‑1 (MQ=255)                        cACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCt                                                                   <  1:3901715/91‑1 (MQ=255)                        cACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCt                                                                   <  1:1645374/91‑1 (MQ=255)                        cACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCt                                                                   <  1:1819726/91‑1 (MQ=255)                        cACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCt                                                                   <  1:1820657/91‑1 (MQ=255)                         aCTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGTCCGCtt                                                                  <  1:3223246/91‑1 (MQ=255)                           ttGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTAc                                                                >  1:3904817/1‑91 (MQ=255)                            tGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACt                                                               <  1:4106760/91‑1 (MQ=255)                            tGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACt                                                               >  1:4128937/1‑91 (MQ=255)                             ggTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACtt                                                              <  1:1051733/91‑1 (MQ=255)                              gTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACttt                                                             <  1:674806/91‑1 (MQ=255)                              gTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACttt                                                             <  1:937491/91‑1 (MQ=255)                               tACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACtttt                                                            <  1:2050640/91‑1 (MQ=255)                                 cTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTgg                                                          <  1:3886913/91‑1 (MQ=255)                                  ttCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGa                                                         >  1:2991369/1‑91 (MQ=255)                                   tCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTGCTTTTAGaa                                                        >  1:3727140/1‑91 (MQ=255)                                   tCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGaa                                                        <  1:1069240/91‑1 (MQ=255)                                   tCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGaa                                                        >  1:1137851/1‑91 (MQ=255)                                     tGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAgt                                                      >  1:2012773/1‑91 (MQ=255)                                      ggTGTCGGTGGCGTTGGTGGCACGATTGGAGTTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAgtg                                                     <  1:1228249/91‑1 (MQ=255)                                      ggTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAgtg                                                     <  1:1256645/91‑1 (MQ=255)                                      ggTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAgtg                                                     <  1:2168127/91‑1 (MQ=255)                                      ggTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAgtg                                                     <  1:1228668/91‑1 (MQ=255)                                      ggTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAgtg                                                     <  1:844552/91‑1 (MQ=255)                                        tgtCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTa                                                   <  1:611568/91‑1 (MQ=255)                                        tgtCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTa                                                   <  1:1542317/91‑1 (MQ=255)                                          tCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTAtc                                                 >  1:337087/1‑91 (MQ=255)                                           cGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGATGTGTAtct                                                >  1:899146/1‑91 (MQ=255)                                           cGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTAtct                                                >  1:11477/1‑91 (MQ=255)                                             gTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTAtcttc                                              >  1:1306885/1‑91 (MQ=255)                                                  gTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCaa                                         <  1:2295574/91‑1 (MQ=255)                                                   ttGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCaaa                                        >  1:2187055/1‑91 (MQ=255)                                                      gtggCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTc                                     <  1:2635678/91‑1 (MQ=255)                                                      gtggCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTc                                     <  1:1190469/91‑1 (MQ=255)                                                         gCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCatt                                  <  1:3184558/91‑3 (MQ=255)                                                          cACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAaca                                 >  1:141518/1‑91 (MQ=255)                                                             gATTGGAGGTGTTGTATCTTCTTCAATCGTgccaccaacgccaccgacaccagaagtaccaagcgagccggaaacaccaacaccaccgaca                              <  1:1695590‑M2/91‑62 (MQ=255)                                                             gATTGGAGGTGTTGTATCTTCTTCAATCGTgccaccaacgccaccgacaccagaagtaccaagcgagccggaaacaccaacaccaccgaca                              <  1:1695648‑M2/91‑62 (MQ=255)                                                               ttGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAACACTAtt                            >  1:3470473/1‑91 (MQ=255)                                                                tGGAGGTGTTGTATCTTCTTCAATCGTgccaccaacgccaccgacaccagaagtaccaagtgagccggaaacaccaacgccaccaacacca                           <  1:1835178‑M2/91‑65 (MQ=255)                                                                 ggAGGTGTTGTATCTTCTTCAATCGTgccaccaacgcgaccgacaccagaagtaccaagtgagccggaaacaccaacgccaccaacaccag                          <  1:3513455‑M2/91‑66 (MQ=255)                                                                 ggAGGTGTTGTATCTTCTTCAATCGTgccaccaacgccaccgacaccagaagtaccaagcgagccggaaacaccaacaccaccgacaccag                          <  1:2014165‑M2/91‑66 (MQ=255)                                                                  gAGGTGTTGTATCTTCTTCAATCGTgccaccaacgccaccgacaccagaagtaccaagtgagccggaaacaccaacgccaccaacaccaga                         <  1:3245700‑M2/91‑67 (MQ=255)                                                                  gAGGTGTTGTATCTTCTTCAATCGTgccaccaacgccaccgacaccagaagtaccaagcgagccggaaacaccaacaccaccgacaccaga                         <  1:2075677‑M2/91‑67 (MQ=255)                                                                   aGGTGTTGTATCTTCTTCAATCGTgccaccaacgccaccgactccagaagtaccaagcgagccggaaacaccaacaccacccacaccagaa                        <  1:1417366‑M2/91‑68 (MQ=255)                                                                   aGGTGTTGTATCTTCTTCAATCGTgccaccaacgccaccgacaccagaagtaccaagcgagccggaaacaccaacaccaccgacaccagaa                        <  1:1407413‑M2/91‑68 (MQ=255)                                                                    ggTGTTGTATCTTCTTCAATCGTgccaccaacgccaccgacaccagaagtaccaagtgagccggaaacaccaacgccaccaacaccagaag                       <  1:1643919‑M2/91‑69 (MQ=255)                                                                    ggTGTTGTATCTTCTTCAATCGTgccaccaacgccaccgacaccagaagtaccaagcgagccggaaacaccaacaccaccgacaccagaag                       <  1:1084614‑M2/91‑69 (MQ=255)                                                                    ggTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAACACTATTGTGTc                       >  1:3526706/1‑91 (MQ=255)                                                                    ggTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAACACTATTGTGTc                       <  1:2108254/91‑1 (MQ=255)                                                                               ttcttcAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAACACTATTGTGTCCACCGAATTGa            <  1:556763/91‑1 (MQ=255)                                                                               ttcttcAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAACACTATTGTGTCCACCGAATTGa            >  1:1235008/1‑91 (MQ=255)                                                                               ttcttcAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAACACTATTGTGTCCACCGAATTGa            <  1:2870094/91‑1 (MQ=255)                                                                                tcttcAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAACACTATTGTGTCCACCGAATTGAt           >  1:2707558/1‑91 (MQ=255)                                                                                 cttcAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAACACTATTGTGTCCACCGAATTGATa          >  1:3729919/1‑91 (MQ=255)                                                                                   tcAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAACACTATTGTGTCCACCGAATTGATAAc        >  1:1938009/1‑91 (MQ=255)                                                                                   tcAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAACACTATTGTGTCCACCGAATTGATAAc        >  1:722223/1‑91 (MQ=255)                                                                                   tcAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAACACTATTGTGTCCACCGAATTGATAAc        >  1:1875479/1‑91 (MQ=255)                                                                                    cAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAACACTATTGTGTCCACCGAATTGATAACt       <  1:1689459/91‑1 (MQ=255)                                                                                    cAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAACACTATTGTGTCCACCGAATTGATAACt       >  1:3251603/1‑91 (MQ=255)                                                                                    cAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAACACTATTGTGTCCACCGAATTGATAACt       >  1:1174068/1‑91 (MQ=255)                                                                                     aaTCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAACACTATTGTGTCCACCGAATTGATAACtt      <  1:4008292/91‑1 (MQ=255)                                                                                       tCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAACACTATTGTGTCCACCGAATTGATAACTTgg    >  1:2038845/1‑91 (MQ=255)                                                                                       tCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAACACTATTGTGTCCACCGAATTGATAACTTgg    <  1:3168712/91‑1 (MQ=255)                                                                                       tCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAACACTATTGTGTCCACCGAATTGATAACTTgg    >  1:3261161/1‑91 (MQ=255)                                                                                         gTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAACACTATTGTGTCCACCGAATTGATAACTTGGtt  <  1:147312/91‑1 (MQ=255)                                                                                          |                                                                                          TGGTGGCGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTGGAGGTGTTGTATCTTCTTCAATCGTTTGTTGACCTTCATTTTGGCCGCTTACTTTTGGAAGTGTATCTTCTTCAAAGTCAACACTATTGTGTCCACCGAATTGATAACTTGGTT  >  USA300TCH1516_ALE/2633260‑2633438

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.