New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 482715 =53 (0.860)3 (0.050) 3/244 NT 6.2% intergenic (+512/‑171) USA300HOU_RS02285/USA300HOU_RS02295 hypothetical protein/hypothetical protein
?USA300TCH1516_ALE 482748 = 41 (0.710)intergenic (+545/‑138) USA300HOU_RS02285/USA300HOU_RS02295 hypothetical protein/hypothetical protein

ATAGGGGTAAAGAATCTAACTAATGTAATGATTAACGCTATATAGACAAAAATAACTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATAACATTTGTAAAATGAAAATGATGATACGAGGAGATTGTAAGA  >  USA300TCH1516_ALE/482610‑482886
                                                                                                                                           |                                                                                                                                          
aTAGGGGTAAAGAATCTAACTAATGTAATGATTAACGTTATATAGACAAAAATAACTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATtata                                                                                                                                          <  1:397106/141‑1 (MQ=255)
aTAGGGGTAAAGAATCTAACTAATGTAATGATTAACGCTATATAGACAAAAATAACTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATtata                                                                                                                                          >  1:674518/1‑141 (MQ=255)
 gaGGGGTAAAGAATCTAACTAATGTAATGATTAACGCTATATAGACAAAAATAACTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATAc                                                                                                                                         <  1:186204/140‑1 (MQ=255)
   ggggTAAAGAATCTAACTAATGTAATGATTAACGCTATATAGACAAAAATAACTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAACAAAATATTGTTATTTCAATTATaaaa                                                                                                                                       >  1:382200/1‑141 (MQ=255)
     atgttatccataatatcaatgtgccacaaatttcactttaccgacaatatcaaaattataaagttcatattgttatgtatattgcaaataaaacattgtataattgaaaatagcaaaatattgttatttcaattATACAAt                                                                                                                                      <  2:285225‑M2/7‑1 (MQ=255)
      gTAAAGAATCTAACTAATGTAATGATTAACGCTATATAGACAAAAATAACTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGt                                                                                                                                    <  2:446581/141‑1 (MQ=255)
                taactaaTGTAATGATTAACGCTATATAGACAAAAATAACTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTAATAAATTGAAAATAGCAAACCATCGTTATCTCAAACAGACAAtattttatttaaa                                                                                                                          >  1:106486/1‑138 (MQ=255)
                  actaaTGTAATGATGAACTCTATATAGACAAAAATAACTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAat                                                                                                                        >  2:276231/1‑141 (MQ=255)
                       atgtgccacaaatttcactttaccgacaatatcaaaattataaagttcatattgttatatatatttcaaataaaacattgtataattgaaataataatattttgctatttttaattATTCTATATTTTATTTACAatttaa                                                                                                                    >  1:229725‑M2/117‑140 (MQ=255)
                       atgtgccacaaatttcactttaccgacaatatcaaaattataaagttcatattgttatatatattgcaaataaaacattatataattgaaaatagcaaaatattattatttcaattATACAATATTTTATTTACAatataa                                                                                                                    >  2:229725‑M2/117‑140 (MQ=255)
                             gATTAACGCTATATAGACAAAAATAACTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATTGCAAAATATTGTTATTTCAATTATACAATGATTTATTTGCAATATACATAACaa                                                                                                             >  2:74584/1‑141 (MQ=255)
                             gATTAACGCTATATAGACAAAAATAACTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACaa                                                                                                             >  1:464626/1‑141 (MQ=255)
                               ttAACGCTATATAGACAAAAATAACTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAata                                                                                                           >  1:363853/1‑141 (MQ=255)
                                       atataGACAAAAATAACTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACttt                                                                                                   >  2:625040/1‑141 (MQ=255)
                                        tataGACAAAAATAACTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTta                                                                                                  <  1:644070/141‑1 (MQ=255)
                                            gACAAAAATAACTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAAt                                                                                              >  1:566797/1‑141 (MQ=255)
                                             aCAAAAATAACTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAAtt                                                                                             <  2:578494/141‑1 (MQ=255)
                                                   aTAACTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAACTCCTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGata                                                                                       >  1:393186/1‑141 (MQ=255)
                                                    tAACTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGatat                                                                                      >  1:56304/1‑141 (MQ=255)
                                                     aaCTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATACCAATATGAACTTTATAATTTTGATAtt                                                                                     >  1:693800/1‑141 (MQ=255)
                                                     aaCTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATATTTTTGATAtt                                                                                     >  2:193467/1‑141 (MQ=255)
                                                     aaCTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATAtt                                                                                     >  2:375951/1‑141 (MQ=255)
                                                     aaCTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTACTTGCATTGTATATAACAATATGAACTTTATAATTTTTATAtt                                                                                     >  2:6669/1‑141 (MQ=255)
                                                        tctATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTc                                                                                  >  1:669643/1‑141 (MQ=255)
                                                                  cGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGa                                                                        >  1:689223/1‑141 (MQ=255)
                                                                     cTTATCCGCTCTGTATAATAAATATAAATAGTACTATATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAAt                                                                     <  2:712094/141‑1 (MQ=255)
                                                                       tACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAAttt                                                                   >  2:32168/1‑141 (MQ=255)
                                                                          ccactctGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTtgtg                                                                <  2:435399/138‑1 (MQ=255)
                                                                            ccTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAACCATTGTTTTTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGc                                                              <  1:429961/141‑1 (MQ=255)
                                                                              tctGTATAATAAATATAAATCGTACTATATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGcac                                                            <  2:518561/141‑1 (MQ=255)
                                                                              tctGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGcac                                                            <  2:311971/141‑1 (MQ=255)
                                                                                ttatattgtaaataaaatattgtatAATTGAAATAATAATATTTTGCTATTTTCAATTATATAATGTTTTATTTGCAATATATATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACAt                                                          >  2:229725‑M1/26‑141 (MQ=255)
                                                                                ttaaattgtaaataaaatatagaatAATTAAAAATAGCAAAATATTATTATTTCAATTATACAATGTTTTATTTGAAATATATATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACAt                                                          >  1:229725‑M1/26‑141 (MQ=255)
                                                                                tGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACGTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACAt                                                          <  1:212093/141‑1 (MQ=255)
                                                                                 ttataATAAATATAAATCTTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACAtt                                                         <  2:372112/140‑1 (MQ=255)
                                                                                  tataATCAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTg                                                        <  1:340922/141‑1 (MQ=255)
                                                                                   ataataAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGa                                                       <  1:104139/141‑1 (MQ=255)
                                                                                      ataaatataaatCGTACTAAATTGAAAATAGCAAAATATTGTCAGGATAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGatat                                                    <  1:141275/141‑1 (MQ=255)
                                                                                         aatataaatCGTACTAAATGGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGAtattat                                                 <  2:82197/141‑1 (MQ=255)
                                                                                               aatCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATaa                                           >  1:246498/1‑141 (MQ=255)
                                                                                               aatCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATaa                                           >  2:701485/1‑141 (MQ=255)
                                                                                               aatCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGAACATTGATATTATGGATaa                                           >  1:708706/1‑141 (MQ=255)
                                                                                                atCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATAAc                                          >  1:117708/1‑141 (MQ=255)
                                                                                                atCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATAAc                                          >  1:195227/1‑141 (MQ=255)
                                                                                                 tCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATAACa                                         <  2:99852/141‑1 (MQ=255)
                                                                                                 tCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATAACa                                         <  2:508957/141‑1 (MQ=255)
                                                                                                 aagtaggaaaTTGAAAATAGCAAAATATGGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATAACa                                         <  1:623650/134‑1 (MQ=255)
                                                                                                  attgtatAATTGAAATAACAATATTTTGCTATTTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATAACAt                                        <  2:285225‑M1/134‑1 (MQ=255)
                                                                                                          ATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCTGTAAATTGAAATTTGTGGCAAATTGATATTATGGATATTAtttgttata                                <  2:449315‑M1/141‑5 (MQ=255)
                                                                                                          ATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATAATATTTTTaaaa                                <  2:422917‑M1/141‑1 (MQ=255)
                                                                                                           ttcacAATAGCTAAATATTGATAATGAAATTATACAATGTTTTATTTGCAATATACATAACAATTTGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATAACATTTGTAAAAt                               >  1:385062‑M1/6‑141 (MQ=255)
                                                                                                           TTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATAACATTTGTAAAAt                               >  1:192226‑M1/1‑141 (MQ=255)
                                                                                                              AAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATAACATTTGTAAAATGaa                            <  1:366466‑M1/141‑1 (MQ=255)
                                                                                                                  tAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTTTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATAACATTTGTaaaatgaaaatg                        >  2:556011/1‑141 (MQ=255)
                                                                                                                    gCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATAACATTTGTAAAATGAAAatgat                      >  1:443378/1‑141 (MQ=255)
                                                                                                                              gTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGTACATTGATATTATGGATAACATTTGTAAAATGAAAATGATGATACgagga            <  1:423205/141‑1 (MQ=255)
                                                                                                                              gTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGTATAACATTTGTAAAATGAAAATGATGATACgagga            >  2:288509/1‑141 (MQ=255)
                                                                                                                              gTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATAACATTTGTAAAATGAAAATGATGATACgagga            >  2:681066/1‑141 (MQ=255)
                                                                                                                               ttATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATAACATTTGTAAAATGAAAATGATTATACgaggag           >  2:440588/1‑141 (MQ=255)
                                                                                                                                         ttATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATAACATTTGTAAAATGAAAATGATGATACGAGGAGATTGTAAGa  >  2:541503‑M2/3‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                          
ATAGGGGTAAAGAATCTAACTAATGTAATGATTAACGCTATATAGACAAAAATAACTCTATTGATACGCCTTACCCCCTCTGTATAATAAATATAAATCGTACTAAATTGAAAATAGCAAAATATTGTTATTTCAATTATACAATGTTTTATTTGCAATATACATAACAATATGAACTTTATAATTTTGATATTGTCGGTAAAGTGAAATTTGTGGCACATTGATATTATGGATAACATTTGTAAAATGAAAATGATGATACGAGGAGATTGTAAGA  >  USA300TCH1516_ALE/482610‑482886

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.