New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 825232	50 (0.940)	4 (0.080)	4/250	NT	7.5%	coding (24/1056 nt)	tagO	putative undecaprenyl‑phosphate N‑acetylglucosaminyl 1‑phosphate transferase
	?	USA300TCH1516_ALE	= 825273	51 (1.000)					coding (65/1056 nt)	tagO	putative undecaprenyl‑phosphate N‑acetylglucosaminyl 1‑phosphate transferase

AGATATATCATTCTATAAAGACAATATTAAATAAATATAACGTTAAAAACAATTAATATCGATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTCTCTTTTCATTTTTAATAGGTATTTGGATTGGTCATCCTATTGAAACA  >  USA300TCH1516_ALE/825134‑825412                                                                                                                                            |                                                                                                                                            aGATATATCATTCTATAAAGACAATATTAAATAAATATAACGTTAAAAACAATTAATATCGATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATt                                                                                                                                            >  2:497846‑M2/1‑140 (MQ=255)     atatCATTCTATAAAGAGAATATTAAATAAATATAACGTTAAAAACAATTAATAGCGATGAAGGTGAATAAATGGTTACATTATTACTAGTTACAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATtgcaa                                                                                                                                        >  2:633691‑M2/1‑136 (MQ=255)     atatCATTCTATAAAGACAATATTAAATAAATATAACGTTAAAAACAATTAATATCGATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATtgcaa                                                                                                                                        >  2:275815‑M2/1‑136 (MQ=255)       atCATTCTATAAAGACAATATTAAATAAATATAACGTTAAAAACAATTAATATCGATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAata                                                                                                                                      >  1:146471/1‑141 (MQ=255)          actCTATAAAGCCAATACTAAATAAATAAAACGCTAAAAACAATTAATATCGATGAATGTGAATAAATGGTTACATTATCACCAGTTGCAGTAACAATGATTGTCATTTTGACGATAACACCAATTGTTATTGCAATATCg                                                                                                                                   <  1:183822/139‑1 (MQ=255)             cTATAAAGACAATATTAAATAAATATAACGTTAAAAACAATTAATATCGATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATtgcaaatagtaat                                                                                                                                <  1:509822‑M2/141‑14 (MQ=255)                  aaGACAATATTAAATAAATATAACGTTAAAAACAATTAATATCGATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGAtt                                                                                                                           >  1:362942/1‑141 (MQ=255)                    gACAATATTAAATAAATATAACGTTAAAAACAATTAATATCGATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACATCAATTGTTATTGCAATATCGAAAAGATTaa                                                                                                                         >  2:53447/1‑141 (MQ=255)                    gACAATATTAAATAAATATAACGTTAAAAACAATTAATATCGATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACAACCATTGTAATTGCAATCTAGAAACGATTaa                                                                                                                         >  2:359976/1‑141 (MQ=255)                      cAATATTAAATAAATATAACGTTAAAAACAATTAATATCGATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAAt                                                                                                                       <  1:288274/141‑1 (MQ=255)                       aaTATTAAATAAATATAACGTTAAAAACAATTAATATCGATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATtgcaactagtaataatgtaacca                                                                                                                      <  1:501379‑M2/141‑24 (MQ=255)                          atTAAATAAATATAACGTTAAAAACAATTAATATCGATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTAAGTTCGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAg                                                                                                                   <  2:332043/141‑1 (MQ=255)                          atTAAACAAATATAACGTTAAAAACAATTAATATCGATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAAGTGTTATTGCAATATCGAAAAGATTAAATTTAg                                                                                                                   <  1:164022/141‑1 (MQ=255)                              aataaataTAAAGTTAAAAACAATTAATATCGATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGa                                                                                                               <  2:24598/141‑1 (MQ=255)                                   atatAACGTTAAAAACAATTAATATCGATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAAc                                                                                                          >  2:86032/1‑141 (MQ=255)                                   atatAACGTTAAAAACAATTAATATCGATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAAc                                                                                                          <  1:282143/141‑1 (MQ=255)                                   atatAACGGTAAAAACAATTAATATCGATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAAc                                                                                                          <  1:282031/141‑1 (MQ=255)                                    tataACGTTAAAAAAAATTAATATCGATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAAcc                                                                                                         >  1:356121/1‑141 (MQ=255)                                        aCGTTAAAAACAATTAATATCGATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAAt                                                                                                     <  2:415124/141‑1 (MQ=255)                                            tAAAAACAATTAATATCGATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTa                                                                                                 >  2:72068/1‑141 (MQ=255)                                                             gATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTaaa                                                                                >  1:120694/1‑141 (MQ=255)                                                             gATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTaaa                                                                                <  1:86032/141‑1 (MQ=255)                                                                     ggAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTc                                                                        <  1:280670/140‑1 (MQ=255)                                                                           aaTGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTAAATTaa                                                                  >  1:204247/1‑140 (MQ=255)                                                                             tGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATtgcaactagtaataatgtaaccatttattcaccttcatcgatattaattgtttttaacgttatatttatttaatatt                                                                >  2:501379‑M2/1‑64 (MQ=255)                                                                                  aCATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGGTAGGggtggt                                                           <  2:146471/141‑1 (MQ=255)                                                                                   cATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTa                                                          >  2:352458/1‑141 (MQ=255)                                                                                      tattaCTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAg                                                       <  2:245092/141‑1 (MQ=255)                                                                                       attaCTAGTTGCAGTAATAATGATTGTCAGTTTGACGATAACACCAATTGTTATtgcaactagtaataatgtaaccatttattcaccttcatcgatattaattgtttttaacgttatatttatttaatattgtctttatag                                                      >  2:509822‑M2/1‑54 (MQ=255)                                                                                       attaCTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATGTCAGTTATGGGTGGTACAGt                                                      <  1:406317/141‑1 (MQ=255)                                                                                         taCTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTgt                                                    >  2:624751/1‑140 (MQ=255)                                                                                           cTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGAtt                                                  >  1:309859/1‑141 (MQ=255)                                                                                            tAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATtc                                                 <  2:488528/141‑1 (MQ=255)                                                                                             aGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAACGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGGGGTACAGTGTTtct                                                >  1:508702/1‑141 (MQ=255)                                                                                             aGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATtct                                                >  2:480621/1‑141 (MQ=255)                                                                                             aGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATtct                                                >  2:341500/1‑141 (MQ=255)                                                                                             aGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATtct                                                >  1:605812/1‑141 (MQ=255)                                                                                               ttGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTctct                                              >  2:239274/1‑141 (MQ=255)                                                                                                tGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTCTCtt                                             <  1:72068/141‑1 (MQ=255)                                                                                                tGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTCTCtt                                             >  2:36415/1‑141 (MQ=255)                                                                                                       aCAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTCTCTTTTCAttt                                      >  1:171948/1‑141 (MQ=255)                                                                                                       aCAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATGTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTCTCTTTTCAttt                                      >  1:606301/1‑141 (MQ=255)                                                                                                            gATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTCTCTTTTCATTTTTAAt                                 <  2:476633/141‑1 (MQ=255)                                                                                                                    gTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTCTCTTTTCATTTTTAATAGGTAttt                         <  1:549228/141‑1 (MQ=255)                                                                                                                      ttGACTATAACACAAATTGTTATTGCAATATCTAAAATGTTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTCTCTTTTCATTTTTAATAGGTATTTgg                       <  2:187071/141‑1 (MQ=255)                                                                                                                      ttGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTCTCTTTTCATTTTTAATAGGTATTTgg                       <  2:393204/141‑1 (MQ=255)                                                                                                                        taCGATAACACCCATTGATATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTCTCTTTTCATTTTTAATAGGTATTTGGAt                     <  1:376028/140‑1 (MQ=255)                                                                                                                        gACGATAAGACCATTTGTAATTGCAAAATCGAAAAGATAAAATTGAGTTGCTAAACTAAATTGTAGAAAAGTACACATGAAACCTATTTCAGTGATGGGTGGTACAGTGATTCTCTTTTCATTGTTAATAGGTATTTGAAt                     <  2:242738/141‑1 (MQ=255)                                                                                                                        gACGATAACACCAATTGTTATTGCAATAGCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTCTCTTTTCATTTTTAATAGGTATTTGGAt                     <  1:375969/141‑1 (MQ=255)                                                                                                                        aaCGATAACAACAATTGTTATTGCAATATCAAAAAGATTAAATTTAGTTTATAAACCAAATTTTAGAAAAGTACACACTAATCCTATTTCATTTATTGTTGGTACAGTGATTCTCTTTTCATTTTTAATAGGTATTTGGAt                     <  2:650895/140‑1 (MQ=255)                                                                                                                          cGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATGTCAGTTATGGGTGGTACAGTGATTCTCTTTTCATTTTTAATAGGTATTTGGATTg                   >  2:365578/1‑141 (MQ=255)                                                                                                                          agATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTCTCTTTTCATTTTTAATAGGTATTTGGATTg                   <  2:379023/140‑1 (MQ=255)                                                                                                                            aTAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTCTCTTTTCATTTTTAATAGGTATTTGGATTGGt                 <  2:361460/141‑1 (MQ=255)                                                                                                                             tAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTCTCTTTTCATTTTTAATAGGTATTTGGATTGGTc                >  1:462622/1‑141 (MQ=255)                                                                                                                             tAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTCTCTTTTCATTTTTAATAGGTATTTGGATTGGTc                >  1:420612/1‑141 (MQ=255)                                                                                                                             tAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGAGCAACCAAATCTTAGAAAAGTACACACTAAACCTATTTCAGTAAGGGGTGGTACAGTTATTATCCTTTCATCTTTAATAGGCATTTggctggggc                >  1:420701/1‑134 (MQ=255)                                                                                                                                 acCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTCTCTTTTCATTTTTAATAGGTATTTGGa                      <  1:234971/131‑1 (MQ=255)                                                                                                                                 acCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTCTCTTTTCATTTTTAATAGGTATTTGGa                      >  2:234971/1‑131 (MQ=255)                                                                                                                                       tGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTCTCTTTTCATTTTTAATAGGTATTTGGTTTGGTCATCCTATTGa      >  2:499380/1‑141 (MQ=255)                                                                                                                                       tGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTCTCTTTTCATTTTTAATAGGTATTTGGGTTGGTCATCCTATTGa      >  2:251299/1‑141 (MQ=255)                                                                                                                                           gttGCAATATAGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTCTTTTTTCATTTTTTATTGGTATTTGGGTTGTTCTTCTTTTTGTAACa  >  2:209791/2‑141 (MQ=255)                                                                                                                                            |                                                                                                                                            AGATATATCATTCTATAAAGACAATATTAAATAAATATAACGTTAAAAACAATTAATATCGATGAAGGTGAATAAATGGTTACATTATTACTAGTTGCAGTAACAATGATTGTCAGTTTGACGATAACACCAATTGTTATTGCAATATCGAAAAGATTAAATTTAGTTGATAAACCAAATTTTAGAAAAGTACACACTAAACCTATTTCAGTTATGGGTGGTACAGTGATTCTCTTTTCATTTTTAATAGGTATTTGGATTGGTCATCCTATTGAAACA  >  USA300TCH1516_ALE/825134‑825412

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