New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2080726 =	47 (1.020)	4 (0.100)	4/234	NT	9.0%	intergenic (‑194/‑347)	USA300HOU_RS10505/aspC	hypothetical protein/Aspartate aminotransferase
	?	USA300TCH1516_ALE	2080759 =	39 (0.940)					intergenic (‑227/‑314)	USA300HOU_RS10505/aspC	hypothetical protein/Aspartate aminotransferase

AAATAGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCTCCGTTCGACTAA  >  USA300TCH1516_ALE/2080628‑2080897                                                                                                                                    |                                                                                                                                           aaaTAGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTAtgtgt                                                                                                                                   >  1:154247/1‑141 (MQ=255) aaaTAGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTAtgtgt                                                                                                                                   >  1:178170/1‑141 (MQ=255) aaaTAGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTAtgtgt                                                                                                                                   >  1:226284/1‑141 (MQ=255)   aTAGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTTGTACCAGTAGACTTGGGGTTATTTATgtgtgt                                                                                                                                 <  1:578211/141‑1 (MQ=255)     aGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAg                                                                                                                               >  2:126059/1‑141 (MQ=255)        atgacacttattacaggtggcttactaattatttttcgactttggttagaactgaaatggaaaaataaaaaatgatcctacacacataaataaccccaagtctggtaccagcagacttggggttATTTATGTGTGTAGGAt                                                                                                                            <  1:619380‑M2/17‑1 (MQ=255)           acaaAACCATTCAATCAAAATGATTATTGATTGCGCTATATTATGTTCAATGATATTATTTAAGTGTCTCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGCTATTTATGTGTGCAGGATCAt                                                                                                                         >  1:677560/1‑141 (MQ=255)           acaaAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCAt                                                                                                                         <  1:722869/141‑1 (MQ=255)           acaaAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCAt                                                                                                                         >  2:159484/1‑141 (MQ=255)            ctattattncaggtggcttactaattatttttcgtctttggttngaactgaaatggaaaaataaaanatgatcctacacacataaataaccccaagtctggtaacggcggctttggggttATTTATGTGTGTAGGATCAtt                                                                                                                        <  2:175666‑M2/21‑1 (MQ=255)              aaaCCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCAtttt                                                                                                                      <  1:139806/141‑1 (MQ=255)                   aTTCAATCAAAATGATGATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTAtt                                                                                                                 <  1:281261/141‑1 (MQ=255)                        atcaaAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTcc                                                                                                            <  1:334993/141‑1 (MQ=255)                        atcaaAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTcc                                                                                                            >  1:347979/1‑141 (MQ=255)                            aaaTGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCACCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCAttt                                                                                                        <  1:657804/141‑1 (MQ=255)                                gATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGt                                                                                                    >  1:772557/1‑141 (MQ=255)                                  ttattGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTc                                                                                                  >  1:336904/1‑141 (MQ=255)                                           gCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAg                                                                                         <  1:109347/141‑1 (MQ=255)                                           gCGATATATTGTGTTCAATGATATTATTTAAGTGTAGCCACGGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAg                                                                                         >  1:21525/1‑141 (MQ=255)                                              atatatTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCg                                                                                      <  1:51473/141‑1 (MQ=255)                                               tatatTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGa                                                                                     <  1:364002/141‑1 (MQ=255)                                                atatTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGaa                                                                                    <  1:313124/141‑1 (MQ=255)                                                atatTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGaa                                                                                    <  1:639992/141‑1 (MQ=255)                                                atatTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGaa                                                                                    <  2:31571/141‑1 (MQ=255)                                                      tgtTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAaataa                                                                              <  1:355644/141‑1 (MQ=255)                                                           aaTGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGt                                                                         <  1:2218/141‑1 (MQ=255)                                                                    attTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCt                                                                >  1:325508/1‑141 (MQ=255)                                                                    attTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCt                                                                <  2:171085/141‑1 (MQ=255)                                                                    attTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCt                                                                <  1:196372/141‑1 (MQ=255)                                                                        aaGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGtaa                                                            <  1:340403/141‑1 (MQ=255)                                                                         aGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGtaat                                                           >  2:60134/1‑141 (MQ=255)                                                                         aGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGtaat                                                           >  1:155160/1‑141 (MQ=255)                                                                            gtATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAg                                                        >  1:710744/1‑141 (MQ=255)                                                                              aatgatcctacacacataaatAACCCCAAAGCCGCCGTTACCAGACTTGGGGTTATTTATGTGTGTAGGATCATNTTTTATTTTTCCATTTCAGTTCNAACCAAAGACGAAAAATAATTAGTAAGCCACctgnaataatag                                                      <  2:175666‑M1/120‑4 (MQ=255)                                                                                  atcctacacacataaatAACCCCAAGTCTGCTGGTACCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGtcat                                                  <  1:619380‑M1/124‑1 (MQ=255)                                                                                       aTTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATcc                                             <  1:535854/141‑1 (MQ=255)                                                                                        ttATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATccc                                            <  1:524801/141‑1 (MQ=255)                                                                                        ttATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATccc                                            >  1:250892/1‑141 (MQ=255)                                                                                          ataCTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCctt                                          <  1:13282/141‑1 (MQ=255)                                                                                                cacaACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGcc                                    <  1:606684/141‑1 (MQ=255)                                                                                                caaAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGcc                                    >  1:652369‑M1/4‑141 (MQ=255)                                                                                                   AACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGccacc                                 >  1:362607‑M1/1‑141 (MQ=255)                                                                                                    ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGccacca                                >  1:376534‑M1/1‑141 (MQ=255)                                                                                                       CCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCAcat                             >  2:199135‑M1/1‑141 (MQ=255)                                                                                                       CCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCAcat                             >  2:199130‑M1/1‑141 (MQ=255)                                                                                                         aagtctgctggtaccagacttggggttATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCAcatca                           >  1:304818‑M2/28‑141 (MQ=255)                                                                                                          AGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCAcatcat                          <  1:710183‑M1/141‑1 (MQ=255)                                                                                                               GGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTacac                     <  2:328321‑M1/141‑1 (MQ=255)                                                                                                                gTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATtacact                    >  2:119146/1‑141 (MQ=255)                                                                                                                gTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATtacact                    >  1:4821/1‑141 (MQ=255)                                                                                                                ctggtaccagacttggggttATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAAGTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATtacact                    >  2:155479‑M2/21‑141 (MQ=255)                                                                                                                 tACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATtacacta                   >  1:523669/1‑141 (MQ=255)                                                                                                                      gcagACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCt              >  1:692618/1‑141 (MQ=255)                                                                                                                        agacttggggttATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCTcc            >  1:162110‑M2/13‑141 (MQ=255)                                                                                                                          acttggggttATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCTCCGt          <  2:14312‑M2/131‑1 (MQ=255)                                                                                                                              ggggttATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCATTTCTAACCAATGTCGTAATATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCTCTTCTTGCCACCACATCATTACACTACACCTCCGTTCGa      <  1:25870‑M2/135‑1 (MQ=255)                                                                                                                                  ttATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCTCCGTTCGACTaa  <  2:84982‑M2/139‑1 (MQ=255)                                                                                                                                  ttATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCTCCGTTCGACTaa  <  1:55629‑M2/139‑1 (MQ=255)                                                                                                                                  ttATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACCACACCTCCGTTCGACTaa  <  1:427588‑M2/139‑1 (MQ=255)                                                                                                                                    |                                                                                                                                           AAATAGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCTCCGTTCGACTAA  >  USA300TCH1516_ALE/2080628‑2080897

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