New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 2515612NA (NA)66 (1.050) 49/280 0.2 95.7% intergenic (+171/+29) insL1/yfeA IS186 transposase/putative diguanylate cyclase
?NC_000913 2536308 = 3 (0.050)coding (477/510 nt) crr glucose‑specific enzyme IIA component of PTS

GAGCTTACAGGTGGCCATTCGTGGGACAGTATCCCTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCGAGCTTATGCAATAGCGCCTGCTGCTGTTGCGTCTCGACAAACTCCGCGACCA  >  NC_000913/2515475‑2515750
                                                                                                                                         |                                                                                                                                          
gAGCTTACAGGTGGCCATTCGTGGGACAGTATCCCTGGCAGCGTACAAAACGCACTTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATa                                                                                                                                       <  2:488907/143‑1 (MQ=2)
     tACAGGTGGCCATTCGTGGGACAGTATCCCTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGCTAATTcc                                                                                                                                  >  2:458365/1‑143 (MQ=18)
        aGGTGGCCATTCGTGGGACAGTATCCCTGACAGCCTACAAAACGCAATTGCATCACGCGAGGCATCGTCTTCTCTAGGCACCGTGGCGTCGACTTCTTCAGATGCTTCAACCCTTGACCTAGCCGTCCTGGGCTAATTCGCCg                                                                                                                               >  2:465806/1‑143 (MQ=2)
        aGGTGGCCATTCGTGGGACAGTATCCCTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCCTCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGATTAAAAAATTAAATAAGCGCTTATGAGATAATACCCCg                                                                                                                               >  1:867734/1‑143 (MQ=11)
        aGGTGGCCATTCGTGGGACAGTATCCCTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCg                                                                                                                               <  2:194292/143‑1 (MQ=35)
          gTGGCCATTCGTGGGACAGTATCCCTGACAGCCTACAAAACGCAATTGAAGAACGAGAGGCATCGTCTTAACGAGGCACCGAGGCATCGCATTGTTCAGATGGTTCCACCCTTCAGTTAGCGCTTATGAGATAATTCCCCGGt                                                                                                                             >  2:562019/1‑143 (MQ=11)
              ccATTCGTGGGACAGTATCCCTGACAGCCTACAAAACGCAATTGTAGTTCGCGTGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGttttt                                                                                                                         <  1:367159/143‑1 (MQ=255)
                aTTCGTGGGACAGTATCCCTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATCATTCCCCGGtgttttt                                                                                                                       >  2:800741/1‑143 (MQ=18)
                      tggATAGTATCTTTGACAGTCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCTTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCt                                                                                                                 <  2:568604/142‑1 (MQ=14)
                      gggCCAGTATCCCTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCt                                                                                                                 <  2:588387/143‑1 (MQ=255)
                        gACAGTATCCCTGACAGTCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGt                                                                                                               <  2:898152/143‑1 (MQ=255)
                        gACAGTATCCCTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCCTCGTCTTCACGAGGCCCCGACGCGTCGCATTCTTCAGATGGTTCAACCCTTACGTTCGCGCTTATGGGATAATTCCCCGGGTCTTTTCCGccact                                                                                                               >  2:118733/1‑140 (MQ=11)
                             tATCCCTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCCTATGGGATAATTGCCCGGATTTTTTACGCCAGTTCAta                                                                                                          >  2:165299/1‑142 (MQ=14)
                               tCCCTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAg                                                                                                        <  1:187328/143‑1 (MQ=255)
                                  cTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGCCTAAACAACGCACCGAGGCGTCGCATCCTGCATATCGTTCAACCCTGAAGTTAGCGCTTATGCGATAATCCCCCGGTCTTCCTACGCCTGTTCACCCGCTa                                                                                                     >  2:92661/1‑143 (MQ=14)
                                       aGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACGCTTAAGGTAGCGCTTGTGGGATAATTCCCCGGTTTTTTTCCGGCGGTAAATGACCTAATGGc                                                                                                >  2:779708/1‑143 (MQ=14)
                                       aGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCGTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTGATCAGCTAAtagg                                                                                                >  2:651476/1‑140 (MQ=255)
                                          cTACAAAACGCGATTGAAGATCGCGATGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGc                                                                                             <  1:882693/143‑1 (MQ=255)
                                           tACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGACGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCAGTCAATCAGCTAATGGCTGCg                                                                                            >  1:838596/1‑143 (MQ=255)
                                            aCAAACCGCACTTGCAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCgg                                                                                           <  1:71395/143‑1 (MQ=255)
                                              aaaaCGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATGATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGc                                                                                         >  1:1075663/1‑143 (MQ=255)
                                              aaaaCGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGc                                                                                         >  1:1095137/1‑143 (MQ=255)
                                                    cAATTGAAGAACTCGTGGGATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCaa                                                                                   <  1:871198/143‑1 (MQ=255)
                                                    cAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTATTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCaa                                                                                   >  1:11355/1‑143 (MQ=255)
                                                      aTTGAAGAACGCGAGGCAACGTCTGAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATc                                                                                 <  1:4821/143‑1 (MQ=255)
                                                           agacCGCGAGGCATCGTCTTAACGACGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATa                                                                            <  1:365094/143‑1 (MQ=255)
                                                           agaaCGGGACGCACCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATa                                                                            <  1:935869/143‑1 (MQ=255)
                                                            gaaCGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATAc                                                                           >  1:483564/1‑143 (MQ=255)
                                                              aCGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATAccc                                                                         <  2:333250/143‑1 (MQ=255)
                                                                gcgAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCACTCATATCCCCtt                                                                       >  1:135633/1‑143 (MQ=255)
                                                                 cggggCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAGGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTCATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTg                                                                      <  2:544434/140‑1 (MQ=255)
                                                                  gAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTCATCCGCTAATGGCTTCTGGCGACCAATCAAATACACttac                                                                     >  1:380618/1‑141 (MQ=21)
                                                                          gTCTTAACGAGACACCGAGGCGTCGCATTCTTCAGATGGATCAACCCTTAAGTTAGCGCTTATGGGATAATTCACCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCACTCAAATACCCTTGCAGatatct                                                             >  2:191032/1‑141 (MQ=255)
                                                                            cTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACTCCTGTTAATCAGCTAATGGCTGCGGGTGACCAATCACATTCTCTTGCAGATATTGCa                                                           >  2:1022852/1‑143 (MQ=25)
                                                                                aCGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCCGCGGGCGACCAACCTAATACCCTCGCAGCTATTGCGccac                                                       >  2:213714/1‑141 (MQ=25)
                                                                                   aGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCGAg                                                    <  2:444322/143‑1 (MQ=255)
                                                                                    ggCACCGAGGCGTCGCATTCGTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCGAGc                                                   <  2:567245/143‑1 (MQ=255)
                                                                                        ccGAGGCGTCGCATTCTTCAGATGGTGCAACCCTTAAGTTAGCGATTATGAGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCGAGCTTAt                                               <  1:1055618/143‑1 (MQ=255)
                                                                                         cGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCGGGGCTTATg                                              >  2:920244/1‑143 (MQ=255)
                                                                                         cGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCGAGCTTATg                                              <  2:534707/143‑1 (MQ=255)
                                                                                            gccgcgggagttctcAGATGGTTCGACCCTGAAGTGAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCGAGCTTATGCaa                                           <  2:244711/130‑1 (MQ=255)
                                                                                              cGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCGAGCTTCTGCAATa                                         >  1:886036/1‑143 (MQ=255)
                                                                                               gtctgaTTCTTCAGATGGTTCATCCCTTAACTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCGAGCTTATGCAATAg                                        <  2:869611/138‑1 (MQ=255)
                                                                                                tCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATATCCTTCCAGATATTGCACCAAGAGCTTACGCAATAgc                                       >  2:285214/1‑143 (MQ=38)
                                                                                                 cGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATCGGATAATTCCCCGGTTTTTTTACTCCTGTTTATCAGCTAATGCCTGCGGGCGTCCAATCAAATACCCCTCCACCCATTGCCCCCCGCGCTTATGCaacaccc                                      >  2:314715/1‑138 (MQ=25)
                                                                                                    aTTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAGTACCGTTGCAGATATTGCACCCGGAGCTTATGCAATGGCGCct                                   >  1:881029/1‑143 (MQ=255)
                                                                                                        ttcAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCGAGCTTATGCAATAGCGCctgctg                               >  1:921186/1‑143 (MQ=255)
                                                                                                            ggtGGTTCAAGCCTTAAGTTAGCGCTTATGGGATAATTCCGCGGTTTTTGTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCGAGCTTATGCAATAGCGCCTGCTGCTGt                           <  2:1082586/141‑1 (MQ=255)
                                                                                                             aTGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCGAGCTTCTGCCATAGCGCCCGCTGCTGtt                          >  1:564786/1‑143 (MQ=255)
                                                                                                               ggTTCAACCGTTAAGGTAGCGCTTATGGGATAATTCCCCGGTTTTCTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCGAGCTTATGCAATAGCGCCTGCTGCTGTTGc                        <  1:69795/143‑1 (MQ=255)
                                                                                                               ggTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCGAGCTTATGCAATAGCGCCTGCTGCTGTTGc                        <  2:521767/143‑1 (MQ=255)
                                                                                                                gTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCGAGCTTATGCAATAGCGCCTGCTGCTGTTGCg                       >  1:997139/1‑143 (MQ=255)
                                                                                                                 ttcagtccgtAAGTGAGCGCTTATGGGATAAGTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGAGATGGCGCCCCGAGCTTATGCAATAGCGCCTGCTGCTGTTGCGt                      <  2:445964/134‑1 (MQ=255)
                                                                                                                   cAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCGCCCTGCTCTTATGCAATAGCGCCTGCTGCTGTTGCGtct                    <  2:796392/143‑1 (MQ=255)
                                                                                                                    ctcccTTCAATGAGCACTTCTGGCATAATTCCCCCGTTTTTTTACGCATGTTAATCAGCTAATGGCTGCGGCCGACCAATCAAATTCCCTTGCAGATATTGCACCCCGATCTTATTCAATAGCCCCTGCTGCTGTTGCGtctc                   <  2:827062/141‑1 (MQ=255)
                                                                                                                     aCCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCGAGCTTATGCAATAGCGCCTGCTGCTGTTGCGTCTCg                  >  1:81107/1‑143 (MQ=255)
                                                                                                                     aCCCTGAAGTCAGCGCTTATGCGCTAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCACATACCCTTGCAGTTATTGCACCCCGAGCTTATGCAATAGCGCCTGCTGCTGTTGCGTCTCg                  <  1:125044/143‑1 (MQ=255)
                                                                                                                     aCCCGTAAGTTAGCGCTGATGGGATAATTCCCCGGTTGTCTTACGCCTGTTACTCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCGAGCTTATGCAATAGCGCCTGCTGCTGTTGCGTCTCg                  <  1:125528/143‑1 (MQ=255)
                                                                                                                        cTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCGAGCGTATGCAATAGCGCCTGCTGCTGTTGCGTATCGACa               >  1:1001/1‑143 (MQ=255)
                                                                                                                                     ttATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCGAGCTTATGCAATAGCGCCTGCTGCTGTTGCGTCTCGACAAACTCCGCGACca  <  2:483564/143‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                          
GAGCTTACAGGTGGCCATTCGTGGGACAGTATCCCTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCGAGCTTATGCAATAGCGCCTGCTGCTGTTGCGTCTCGACAAACTCCGCGACCA  >  NC_000913/2515475‑2515750

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.