New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 = 244282146 (0.880)5 (0.110) 5/228 NT 11.3% intergenic (+18/+40) USA300HOU_2304/USA300HOU_2305 transcriptional regulator/hypothetical protein
?CP000730 = 2442838 38 (0.830)intergenic (+35/+23) USA300HOU_2304/USA300HOU_2305 transcriptional regulator/hypothetical protein

AGTAACACATTCTACTTAACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATATTCTTTTTTCTTTTGC  >  CP000730/2442681‑2442957
                                                                                                                                            |                                                                                                                                        
aGTAACACATTCTACTTAACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGAT                                                                                                                                          <  1:36227‑M1/141‑1 (MQ=255)
  tAACACATTCTACTTAACTGATGAGACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGAttt                                                                                                                                        <  2:358140/141‑1 (MQ=255)
     cacaTTCTACTTAACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAAt                                                                                                                                     <  1:569024/141‑1 (MQ=255)
      acaTTCTACTTAACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATg                                                                                                                                    >  2:422456/1‑141 (MQ=255)
         ttCTACTTAACTGATGGTACAGACTATTCTAGCTTCATGAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGcc                                                                                                                                 >  1:392625/1‑141 (MQ=255)
         ttCTACTTAACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGcc                                                                                                                                 >  1:219348/1‑141 (MQ=255)
         ttCTACTTAACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGcc                                                                                                                                 <  1:152840/141‑1 (MQ=255)
           cTACTTAACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTAGACTCAGAGTTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCtt                                                                                                                               <  1:443875/141‑1 (MQ=255)
                 aaCTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCt                                                                                                                         >  2:357726/1‑141 (MQ=255)
                 aaCTAATGGTACCGACCATTCTAGCTTTATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTATTACATAATGATATTTCAAATTATATAAAAGGAAGTTATGATaggctcaaggccattaa                                                                                                                         <  1:40815‑M1/141‑18 (MQ=255)
                   ctgctcgTACAGCTTATTCTAGCTTCATCAGGTATTATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCATATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTAt                                                                                                                       <  2:173295/135‑1 (MQ=255)
                           aCAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTatcataaatt                                                                                                               <  1:576655‑M2/141‑11 (MQ=255)
                                cTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATACTGCGTATTTACTACATAAAGAATTATCAAATTAGAAAAAAGGAAGTTATGATTTACTGGCCTTGAGCCTatcataacttccttt                                                                                                          <  2:218520‑M2/141‑16 (MQ=255)
                                   ttttAGCTTCATAAGGAATGATAGAGTCTTGGAAACACTTATAGGAAAAGTTAATGAGTATTTTCCACATATTGATATTAAAAAAAAAAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTAt                                                                                                       <  2:103404/138‑1 (MQ=255)
                                   ttCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTAt                                                                                                       <  1:300020/141‑1 (MQ=255)
                                   ttCTAGCTCCATTAGTTATCATATATACCTTGAAACCCTTGTAAGAAAATATAAGGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATagtctcaaggccattcaatcataacttcctttttt                                                                                                       <  2:272561‑M1/141‑36 (MQ=255)
                                     cTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAACAATAATGTTTTTGTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCa                                                                                                     <  1:114966/141‑1 (MQ=255)
                                      tAGTTTCATCAGTTATCTTATCTTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTCTGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCAt                                                                                                    <  1:75936/141‑1 (MQ=255)
                                        gCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCAttt                                                                                                  >  1:490120/1‑141 (MQ=255)
                                        gCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCAttt                                                                                                  <  2:317977/141‑1 (MQ=255)
                                           tcatcaGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTAt                                                                                               <  2:391017/141‑1 (MQ=255)
                                             atcaGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTAttg                                                                                             <  2:543924/141‑1 (MQ=255)
                                                  ttATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATtgttgtg                                                                                        <  1:573287/141‑1 (MQ=255)
                                                     tCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCCTGAGCCTATCATAACTTCCTTTTATCCTTTTAttgttttgttt                                                                                     >  1:587052/1‑140 (MQ=255)
                                                     tCATATATTCTTTGAAACACTTGTAAAAAAATATAATGAGTATTTATTACATAATGATATTTCAAATTAGAAAAAAGAAGTTATGATaggctcaaggccattaaatcataacttccttttttctaatttgaaatatcatta                                                                                    <  2:31997‑M1/141‑55 (MQ=255)
                                                      tcactatttctacaaaCACTTTTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTTCTTTTATCATTTTATTGTTGTGTTGa                                                                                    <  1:135342/128‑1 (MQ=255)
                                                               tttGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGAt                                                                           <  1:217514/141‑1 (MQ=255)
                                                                ttGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATaggctcaaggccattaaatcataacttccttttttctaatttgaaatatcattatgtagtaaat                                                                          >  2:156228‑M1/1‑77 (MQ=255)
                                                                ttGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTatcataacttccttttttctaatttgaaatatcattatgtagtaaat                                                                          <  1:156228‑M2/141‑48 (MQ=255)
                                                                ttGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATa                                                                          >  2:561322/1‑141 (MQ=255)
                                                                 tGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGAtga                                                                         >  2:81844/1‑139 (MQ=255)
                                                                 tGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATat                                                                         >  1:175182/1‑140 (MQ=255)
                                                                  gAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAAc                                                                        <  1:183122/141‑1 (MQ=255)
                                                                     acacTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTGTCGATAACTTg                                                                     >  2:475825/1‑141 (MQ=255)
                                                                        cTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGCTa                                                                  >  2:445538/1‑141 (MQ=255)
                                                                          tGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTCCa                                                                >  2:149744/1‑141 (MQ=255)
                                                                           gTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACAt                                                               <  1:599294/141‑1 (MQ=255)
                                                                            tAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATc                                                              <  2:77853/141‑1 (MQ=255)
                                                                                    tataATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCaaa                                                      >  2:253477/1‑141 (MQ=255)
                                                                                              aTTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATaggctcaaggccattaaatcataacttccttttttctaatttgaaatatcattatgtagtaaatactcattatattttcttacaagtgtttcaa                                            <  1:156228‑M1/141‑95 (MQ=255)
                                                                                              aTTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTatcataacttccttttttctaatttgaaatatcattatgtagtaaatactcattatattttcttacaagtgtttcaa                                            >  2:156228‑M2/1‑64 (MQ=255)
                                                                                              aTTTACTACATAATGAAATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCg                                            <  1:76824/141‑1 (MQ=255)
                                                                                               tttACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGa                                           <  1:357726/141‑1 (MQ=255)
                                                                                               tttACTACATAATGATATTTAAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGa                                           <  2:91942/141‑1 (MQ=255)
                                                                                                  actacATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAAc                                        >  2:267555/1‑141 (MQ=255)
                                                                                                   ctaaATAAAGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAACCGCTTATCACTTCCTTTTATCATTTTATTATTGTGTTGATATTTCGATAACGTTGTACATCTTCTCAAACATCAATTCGataac                                       >  2:155419/1‑137 (MQ=255)
                                                                                                    tacATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCa                                      <  1:49443/141‑1 (MQ=255)
                                                                                                        tAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTatcataacttcttttttctaatttgaaatatcattatgtaataaatactcattatatttttttacaagtgtttcaaagaatatatga                                  <  2:31997‑M2/141‑88 (MQ=255)
                                                                                                             atatTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATg                             >  2:461397/1‑141 (MQ=255)
                                                                                                             atatTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATg                             >  2:602189/1‑141 (MQ=255)
                                                                                                                    aaaTTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCGCCATGTcatcat                      >  1:71798/1‑141 (MQ=255)
                                                                                                                         aGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGatat                 >  1:596631/1‑141 (MQ=255)
                                                                                                                         aGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCGTATATCATTTTATTGTTGTGTTGATGCTTCGATAACGTGGTACATCTTATAAAACAGCAATTCGAAACCATGCACCCTCGCACCATGatat                 >  2:478350/1‑141 (MQ=255)
                                                                                                                           aaaaaaGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATAttc               <  1:101518/141‑1 (MQ=255)
                                                                                                                           aaaaaaGGAAGTTATGATTGAATGGCCTTGAGACTatcataacttccttttttctaatttgaaatatcattatgtagtaaatactccttatattttcttacaagggtttcaaggtatatatgataactaatggagctagaa               <  2:272561‑M2/141‑107 (MQ=255)
                                                                                                                            aaaaaGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATAttct              >  2:485592/1‑141 (MQ=255)
                                                                                                                             aaaaGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATAttctt             >  2:113307/1‑141 (MQ=255)
                                                                                                                              aaaGGAAGTTATGATaggctcaaggccagtaaatcataacttccttttttctaatttgataattctttatgtagtaaatacgcagtatattttcttacaagtgtttcaaagaatatatgataactgatgaagctagaatag            <  2:218520‑M1/141‑127 (MQ=255)
                                                                                                                                   aatttatgATaggctcaaggccattaaatcataacttccttttttctaatttgaaatatcattatgtagtaaatactcattatattttcttacaagtgtttcaaagaatatatgataactgatgaagctagaatagtctgt       <  1:576655‑M1/138‑132 (MQ=255)
                                                                                                                                   aaGTTATTATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATAttcttttttct       <  1:179595/141‑1 (MQ=255)
                                                                                                                                    aGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGGGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATAttcttttttctt      >  1:327620/1‑141 (MQ=255)
                                                                                                                                       tATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATATTCTTTTTTCTTTTg   <  1:580207/141‑1 (MQ=255)
                                                                                                                                        aTGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATATTCTTTTTTCTTTTGc  <  1:74251/141‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                        
AGTAACACATTCTACTTAACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATATTCTTTTTTCTTTTGC  >  CP000730/2442681‑2442957

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.