New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 193444 =45 (0.240)5 (0.030) 4/218 NT 10.3% intergenic (+15/‑77) frr/dxr ribosome recycling factor/1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase
?NC_000913 193489 = 46 (0.270)intergenic (+60/‑32) frr/dxr ribosome recycling factor/1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase

GGACGATGTACAGAAACTGACTGATGCTGCAATCAAGAAAATTGAAGCGGCGCTGGCAGACAAAGAAGCAGAACTGATGCAGTTCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAAT  >  NC_000913/193342‑193634
                                                                                                                                                   |                                                                                                                                                 
ggACGATGTACAGAAACTGACTGATGCTGCAATCAAGAAAATTGAAGCGGCGCTGGCAGACAAAGAAGCAGAACTGATGCAGTTCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGc                                                                                                                                                  >  4:1541911/1‑149 (MQ=255)
        tACAGAAACTGACTGATGCTGCAATCAAGAAAATTGAAGCGGCGCTGGCAGACAAAGAAGCAGAACTGATGCAGTTCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTAtt                                                                                                                                          >  4:198510/1‑149 (MQ=255)
           aGAAACTGACTGATGCTGCAATCAAGAAAATTGAAGCGGCGCTGGCAGACAAAGAAGCAGAACTGATGCAGTTCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTg                                                                                                                                       <  3:1338697/149‑1 (MQ=255)
               actgactgATGCTGCAATCAAGAAAATTGAAGCGGCGCTGGCAGACAAAGAAGCAGAACTGATGCAGTTCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGtctc                                                                                                                                   >  1:654978/1‑149 (MQ=255)
                                    gAAAATTGAAGCGGCGCTGGCAGACAAAGAAGCAGAACTGATGCAGTTCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAg                                                                                                              >  2:633515/1‑149 (MQ=255)
                                     aaaaTTGAAGCGGCGCTGGCAGACAAAGAAGCAGAACTGATGCAGTTCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTc                                                                                                                                         <  1:1541816/121‑1 (MQ=255)
                                     aaaaTTGAAGCGGCGCTGGCAGACAAAGAAGCAGAACTGATGCAGTTCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTc                                                                                                                                         >  2:1541816/1‑121 (MQ=255)
                                                 gcgcTGGCAGACAAAGAAGCAGAACTGATGCAGTTCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTc                                                                                                 <  1:633515/149‑1 (MQ=255)
                                                          gACAAAGAAGCAGAACTGATGCAGTTCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCAGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGa                                                                                        >  3:1279175/1‑149 (MQ=255)
                                                               agaagCAGAACTGATGCAGTTCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGc                                                                                            >  1:1248299/1‑140 (MQ=255)
                                                               agaagCAGAACTGATGCAGTTCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGc                                                                                            <  2:1248299/140‑1 (MQ=255)
                                                                gaagCAGAACTGATGCAGTTCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCt                                                                                  <  3:198510/149‑1 (MQ=255)
                                                                           gATGCAGTTCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTgc                                                                       <  3:1541911/149‑1 (MQ=255)
                                                                                  ttCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTAt                                                                                                                                           <  1:139907/74‑1 (MQ=255)
                                                                                  ttCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTAt                                                                                                                                           >  2:139907/1‑74 (MQ=255)
                                                                                    cTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGAtt                                                                             >  4:1744412/1‑134 (MQ=255)
                                                                                    cTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGAtt                                                                             <  3:1744412/134‑1 (MQ=255)
                                                                                        tttCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTgca                                                                      <  1:989030/137‑1 (MQ=255)
                                                                                        tttCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTgca                                                                      >  2:989030/1‑137 (MQ=255)
                                                                                             tGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACgtggtg                                                     <  2:1289441/149‑1 (MQ=255)
                                                                                                  gACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACt                                                                                                         <  3:85241/92‑1 (MQ=255)
                                                                                                  gACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACt                                                                                                         >  4:85241/1‑92 (MQ=255)
                                                                                                     aaaaaCGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACgtggt                                                      <  3:870668/140‑1 (MQ=255)
                                                                                                     aaaaaCGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACgtggt                                                      >  4:870668/1‑140 (MQ=255)
                                                                                                        aacgccgccagccgatccgcaaggatctactgagcggcgttttGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTgg                                                                                              <  4:506153‑M2/54‑1 (MQ=255)
                                                                                                        aacgccgccagccgatccgcaaggatctactgagcggcgttttGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTgg                                                                                              >  3:506153‑M2/44‑97 (MQ=255)
                                                                                                          CGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGt                                                                          <  2:1156‑M1/115‑1 (MQ=255)
                                                                                                          CGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGt                                                                          >  1:1156‑M1/1‑115 (MQ=255)
                                                                                                             CGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGaa                                      <  3:395241‑M1/148‑1 (MQ=255)
                                                                                                             CGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGaa                                      >  4:395241‑M1/1‑148 (MQ=255)
                                                                                                              gccagccgatccgcaaggatctactgagcggcgttttGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGt                                                                          >  3:906059‑M2/38‑111 (MQ=255)
                                                                                                              gccagccgatccgcaaggatctactgagcggcgttttGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGt                                                                          <  4:906059‑M2/74‑1 (MQ=255)
                                                                                                              gccagccgatccgcaaggatctactgagcggcgttttGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAaca                                    >  4:548343‑M2/38‑149 (MQ=255)
                                                                                                              GCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCaa                                                                                                                                 <  4:332327‑M1/56‑1 (MQ=255)
                                                                                                              GCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCaa                                                                                                                                 >  3:332327‑M1/1‑56 (MQ=255)
                                                                                                                tCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGa                                                                                                                          <  1:125168/61‑1 (MQ=255)
                                                                                                                tCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGa                                                                                                                          >  2:125168/1‑61 (MQ=255)
                                                                                                                tCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCa                                                <  1:431130/135‑1 (MQ=255)
                                                                                                                tCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCa                                                >  2:431130/1‑135 (MQ=255)
                                                                                                                  cataattCCTTGCGGATCGGCTGGCGGTTTTTTGCTTTTTTTTTTGTCCCAACTCTGGATTTTTCATAAAGAACCCCACCTTCCGGGCCTCCACCGGCTAGTTTGGTTGCAGCCCGGTGGACGTTGTGCGCAAAAACCCCGAACACTTc                                <  2:1318414/143‑1 (MQ=255)
                                                                                                                  aGTAGATCCTTGCGGATCGGCTGGCAGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTc                                <  4:1279175/149‑1 (MQ=255)
                                                                                                                   gTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTca                               >  1:1318414/1‑148 (MQ=255)
                                                                                                                    tAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCcg                              >  2:151584/1‑149 (MQ=255)
                                                                                                                     aGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCcgc                             >  1:1770555/1‑149 (MQ=255)
                                                                                                                      gATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGt                                                                          <  4:663013/103‑1 (MQ=255)
                                                                                                                      gATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGt                                                                          >  3:663013/1‑103 (MQ=255)
                                                                                                                       aTCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGt                           >  1:1292148/1‑149 (MQ=255)
                                                                                                                        tCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGaa                                      <  1:1325390/137‑1 (MQ=255)
                                                                                                                        tCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGaa                                      >  2:1325390/1‑137 (MQ=255)
                                                                                                                           ttGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTgca                                                                      >  1:396025/1‑102 (MQ=255)
                                                                                                                           ttGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTgca                                                                      <  2:396025/102‑1 (MQ=255)
                                                                                                                                gATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCt                                                                                  >  1:289558/1‑85 (MQ=255)
                                                                                                                                gATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCt                                                                                  <  2:289558/85‑1 (MQ=255)
                                                                                                                                gATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCt                  >  1:341450/1‑149 (MQ=255)
                                                                                                                                 aTCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCtg                 >  3:767857/1‑149 (MQ=255)
                                                                                                                                 aTCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCtg                 >  1:975397/1‑149 (MQ=255)
                                                                                                                                  tCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGAc                                                           <  4:1168764/106‑1 (MQ=255)
                                                                                                                                  tCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGAc                                                           >  3:1168764/1‑106 (MQ=255)
                                                                                                                                       tGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTggca           >  3:1405153/1‑149 (MQ=255)
                                                                                                                                              gttttGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTggcag          >  1:1495356‑M2/6‑143 (MQ=255)
                                                                                                                                              gttttGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTggcag          <  2:1495356‑M2/138‑1 (MQ=255)
                                                                                                                                               ttttGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCaaaaa   >  1:1629977‑M2/5‑149 (MQ=255)
                                                                                                                                               ttttGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAACAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCaaaaa   >  3:1233721‑M2/5‑149 (MQ=255)
                                                                                                                                                tttGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAAt  <  2:1770555‑M2/146‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                                 
GGACGATGTACAGAAACTGACTGATGCTGCAATCAAGAAAATTGAAGCGGCGCTGGCAGACAAAGAAGCAGAACTGATGCAGTTCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAAT  >  NC_000913/193342‑193634

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ 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.