New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_002947 319208 =48 (0.750)4 (0.060) 4/246 NT 7.7% coding (534/1815 nt) PP_0264 sensor histidine kinase
?NC_002947 319244 = 49 (0.790)coding (498/1815 nt) PP_0264 sensor histidine kinase

GTCGGTCAGCGTGCGGGTAGCACGGAAGCGCCAGTCGGGCCGCGAAGTCAGGATGACCACGCCATTGTGATCGGTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTCGTTGAAGTAAGGGCGGAAGGCGAAGTTTCGGCCGACGAA  >  NC_002947/319061‑319354
                                                                                                                                                   |                                                                                                                                                  
accttggccgcctcgaactgggacaagcacgacagcttcgtcggccgaaacttcgccttccgcccttacttcaacgaagccatggccggccaccttggccgcttcttcggccacggcaccacctcggccaagcgcggctactactttGc                                                                                                                                                   <  4:169704‑M1/2‑1 (MQ=255)
  cttggccgcctcgaactgggacaagcacgacagcttcgtcggccgaaacttcgccttccgcccttacttcaacgaagccatggccggccaccttggccgcttcttcggccagggcaccacctcggccaagcgcggctacttctttGCcg                                                                                                                                                 <  8:255627‑M1/4‑1 (MQ=255)
  cttggccgcctcgaactgggacaagcacgacagcttcgtcggccgaaacttcgccttccgcccttacttcaacgaagccatggccggccaccttggccgcttcttcggccagggcaccacctcggccaagcgcggctacttctttGCcg                                                                                                                                                 <  4:67413‑M1/4‑1 (MQ=255)
   ggTCAGCGTGCGGGTAGCACGGAAGCGCCAGTCGGGCCGCGAAGTCAGGATGACCACGCCATTGTGATCGGTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCcga                                                                                                                                                <  2:147939/149‑1 (MQ=255)
    gTCAGCGTGCGGGTAGCACGGAAGCGCCAGTCGGGCCGCGAAGTCAGGATGACCACGCCATTGTGATCGGTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCcgac                                                                                                                                               <  6:83954/149‑1 (MQ=255)
    gTCAGCGTGCGGGTAGCACGGAAGCGCCAGTCGGGCCGCGAAGTCAGGATGACCACGCCATTGTGATCGGTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCcgac                                                                                                                                               >  5:363483/1‑149 (MQ=255)
    gTCAGCGTGCGGGTAGCACGGAAGCGCCAGTCGGGCCGCGAAGTCAGGATGACCACGCCATTGTGATCGGTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCcgac                                                                                                                                               >  5:83954/1‑149 (MQ=255)
       aGCGTGCGGGTAGCACGGAAGCGCCAGTCGGGCCGCGAAGTCAGGATGACCACGCCATTGTGATCGGTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCcgacga                                                                                                                                             <  5:125637/148‑1 (MQ=255)
       aGCGTGCGGGTAGCACGGAAGCGCCAGTCGGGCCGCGAAGTCAGGATGACCACGCCATTGTGATCGGTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTGACCACCAGCACGCCGACGATc                                                                                                                                           <  7:177211/149‑1 (MQ=255)
          gTGCGGGTAGCACGGAAGCGCCAGTCGGGCCGCGAAGTCAGGATGACCACGCCATTGTGATCGGTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCg                                                                                                                                         >  8:164049/1‑149 (MQ=255)
                    cACGGAAGCGCCAGTCGGGCCGCGAAGTCAGGATGACCACGCCATTGTGATCGGTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTcg                                                                                                                               >  5:142992/1‑149 (MQ=255)
                          gcacgacagcttcgtcggccgaaacttcgccttccgcccttacttcaacgaagccatggccggccaccttggccgcttcttcggccagggcaccacctcggccaagcgcggctacttctttGCCGACGATCCGCTCGCGGTCGCGCACg                                                                                                                         <  6:356484‑M1/28‑1 (MQ=255)
                                    gggCCGCGAAGTCAGGATGACCACGCCATTGTGATCGGTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCa                                                                                                                >  7:299414/1‑148 (MQ=255)
                                         gcgAAGTCAGGATGACCACGCCATTGTGATCGGTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATc                                                                                                                                           >  2:280275/1‑116 (MQ=255)
                                          ggccgaaacttcgccttccgcccttacttcaacgaagccatggccggccaccttggccgcttcttcggccagggcaccacctcggccaagcgcggctacttctttGCCGACGATCCGCTCTCGGTCGCGCACGGCCGCGGCAaagaag                                                                                                          >  5:356484‑M1/106‑148 (MQ=255)
                                              gaaacttcgccttccgcccttacttcaacgaagccatggccggccaccttggccgcttcttcggccagggcaccacctcggccaagcgcggctacttctttGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAaag                                                                                                             <  6:114432‑M1/40‑1 (MQ=255)
                                              gaaacttcgccttccgcccttacttcaacgaagccatggccggccaccttggccgcttcttcggccagggcaccacctcggccaagcgcggctacttctttGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAaag                                                                                                             >  5:114432‑M1/102‑141 (MQ=255)
                                                   gATGACCACGCCATTGTGATCGGTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCt                                                                                                >  3:81394/1‑149 (MQ=255)
                                                     tGACCACGCCATTGTGATCGGTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTg                                                                                              <  7:164049/149‑1 (MQ=255)
                                                         cACGCCATTGTGATCGGTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGcc                                                                                           >  3:199347/1‑148 (MQ=255)
                                                         cACGCCATTGTGATCGGTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGcc                                                                                           >  3:181791/1‑148 (MQ=255)
                                                         cACGCCATTGTGATCGGTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCg                                                                                          <  6:142992/149‑1 (MQ=255)
                                                              cATTGTGATCGGTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAggtg                                                                                     >  4:160566/1‑149 (MQ=255)
                                                                  gtgATCGGTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGgtggtg                                                                                  <  3:160566/148‑1 (MQ=255)
                                                                     aTCGGTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAgg                                                                                       >  6:231669/1‑140 (MQ=255)
                                                                     aTCGGTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAgg                                                                                       <  5:231669/140‑1 (MQ=255)
                                                                        ggTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTgg                                                                            <  8:76373/148‑1 (MQ=255)
                                                                         gTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGcc                                                                          >  3:182205/1‑149 (MQ=255)
                                                                                    ctgctCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGCTCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGGGGTGCCCTGGCCGAAGAAGCGGc                                                               >  8:12299/1‑149 (MQ=255)
                                                                                       ctCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCaa                                                            <  4:199347/149‑1 (MQ=255)
                                                                                          gggCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGt                                                         <  4:182205/149‑1 (MQ=255)
                                                                                                  ggCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCgaa                                                                       <  1:359754/127‑1 (MQ=255)
                                                                                                  ggCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCgaa                                                                       >  2:359754/1‑127 (MQ=255)
                                                                                                  ggCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTggccggc                                                  >  5:296453/1‑148 (MQ=255)
                                                                                                  ggCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTggccggc                                                  >  3:302447/1‑148 (MQ=255)
                                                                                                      ccACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTg                                                                                              >  6:46415/1‑100 (MQ=255)
                                                                                                      ccACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTg                                                                                              <  5:46415/100‑1 (MQ=255)
                                                                                                      ccACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATgg                                             >  6:406825/1‑149 (MQ=255)
                                                                                                          aGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTc                                         >  4:95599/1‑149 (MQ=255)
                                                                                                                  ggTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTCGTTGAAg                                  >  1:174711/1‑148 (MQ=255)
                                                                                                                   gtgtGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTCGTTGaa                                   <  3:186629/146‑1 (MQ=255)
                                                                                                                   gtgtGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTCGTTGaa                                   >  4:186629/1‑146 (MQ=255)
                                                                                                                    tgtgGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTCGTTGAAGTaa                               <  3:95599/149‑1 (MQ=255)
                                                                                                                      tgGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGGGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTCg                                        >  1:288249/1‑138 (MQ=255)
                                                                                                                      tgGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTCg                                        <  2:288249/138‑1 (MQ=255)
                                                                                                                      tgGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTCGTTGAAGTAAgg                             <  4:81394/149‑1 (MQ=255)
                                                                                                                      tgGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTCGTTGAAGTAAgg                             <  2:174711/149‑1 (MQ=255)
                                                                                                                         tCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTCGTTGAAGTAAGGGCg                          >  3:169704/1‑149 (MQ=255)
                                                                                                                             gaTCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTCGTTGAAGTAAGGGCGGAAg                      >  3:67413/1‑149 (MQ=255)
                                                                                                                                  aCTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTCGTTGAAGTAAGGGCGGAAGGCGaa                 <  4:181791/149‑1 (MQ=255)
                                                                                                                                   cTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTCGTTGAAGTAAGGGCGGAAGGCGAAg                >  3:298164/1‑149 (MQ=255)
                                                                                                                                        accaccAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTCGTTGAAGTAAGGGCGGAAGGCGAAGTTTCg           <  6:296453/149‑1 (MQ=255)
                                                                                                                                         ccaccaGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTCGTTGAAGTAAGGGCGGAAGGCGAAGTTTCgg          >  7:158578/1‑149 (MQ=255)
                                                                                                                                         ccaccaGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTCGTTGAAGTAAGGGCGGAAGGCGAAGTTTCgg          >  5:145098/1‑149 (MQ=255)
                                                                                                                                          caccaGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTCGTTGAAGTAAGGGCGGAAGGCGAAGTTTCGGc         >  5:220814/1‑149 (MQ=255)
                                                                                                                                           accaGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTCGTTGAAGTAAGGGCGGAAGGCGAAGTTTCGGcc        >  5:263125/1‑149 (MQ=255)
                                                                                                                                                 aCGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTCGTTGAAGTAAGGGCGGAAGGCGAAGTTTCGGCcgacg    >  1:46994/1‑147 (MQ=255)
                                                                                                                                                 aCGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTCGTTGAAGTAAGGGCGGAAGGCGAAGTTTCGGCCGACGaa  <  6:363483/149‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                                  
GTCGGTCAGCGTGCGGGTAGCACGGAAGCGCCAGTCGGGCCGCGAAGTCAGGATGACCACGCCATTGTGATCGGTCAGCAACAGCTGCTCGGGCGTACGGCCCCACAGGGTTTCGGTGTGGTCGAGATCGACTTTGACCACCAGCACGCCGACGATCCGCTCGCGGTCGCGCACGGCCGCGGCAAAGAAGTAGCCGCGCTTGGCCGAGGTGGTGCCCTGGCCGAAGAAGCGGCCAAGGTGGCCGGCCATGGCTTCGTTGAAGTAAGGGCGGAAGGCGAAGTTTCGGCCGACGAA  >  NC_002947/319061‑319354

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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.