New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1979486 =	1 (0.020)	62 (1.470)	44/284	0.0	98.4%	intergenic (‑271/‑267)	insA/uspC	IS1 repressor TnpA/universal stress protein
	?	NC_000913	2101749 =	NA (NA)					intergenic (‑5/+146)	wbbL/insH1	pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator

TCTTCACAGTACATAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTAT  >  NC_000913/2101607‑2101885                                                                                                                                               |                                                                                                                                          tCTTCACAGTACATAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTaag                                                                                                                                           <  2:604274/143‑1 (MQ=255)    taacaGTACATAAAGTAACCGTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGAAACAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACCTTCTTTAGGAATTTTTGGTCTATCaaagaa                                                                                                                                        >  1:663764/3‑143 (MQ=255)      acaGTACATAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGACTTTCTGCTTGTTGacggaagg                                                                                                                                      >  2:175739/1‑143 (MQ=255)             aTAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAACTTTTGCTTTATTAAGAAAGGTGCGAAt                                                                                                                               >  2:41881/1‑143 (MQ=255)              tAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATa                                                                                                                              <  2:19015/143‑1 (MQ=255)                       cTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATTAGAATAGAGACAATCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGaa                                                                                                                     >  1:335242/1‑143 (MQ=255)                       cTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGTAGGTGCGAATAAGCGGGGaa                                                                                                                     >  2:370425/1‑143 (MQ=255)                       cTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTACGAATAAGCGGGGac                                                                                                                     >  1:564047/1‑142 (MQ=255)                        ttGATCGAAGCCAGTTACACGCACAAAATCCGAAACACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGaaa                                                                                                                    <  2:648058/143‑1 (MQ=255)                        atcagcacaGCCATTTACACGCACAAAGTCCAAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAAGAGAGACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGaaa                                                                                                                    <  2:648184/135‑1 (MQ=255)                          gATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCATTAAAAAAAATTTTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAAtt                                                                                                                  <  2:325645/143‑1 (MQ=255)                           aTCGAAGCCATTTACACGCACAATATCTGAACAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAAttc                                                                                                                 <  1:141808/143‑1 (MQ=255)                           aTCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAAttc                                                                                                                 <  2:99466/143‑1 (MQ=255)                              gAAGCCATTTACACGCACAAAATCTGAAAAACGTACTAGCATAAATGATCCTGCGCACCAATCAACAACCGTCTCAGAATAGATAATTGTTTTAGGAATTTTTGTTGTATTACGGAAGGTGCAAATAAGCGCAGAAAttcttc                                                                                                              >  2:165603/1‑143 (MQ=255)                                    atcttcgctcacaAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCt                                                                                                        <  1:54552/134‑1 (MQ=255)                                     tttACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGACTTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAACTTCtgctgtgctg                                                                                                       >  1:256217/1‑143 (MQ=255)                                       tACACGCACAAAATCTGAAAAAGGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGAc                                                                                                     <  2:619625/143‑1 (MQ=255)                                        acacTCACAAACTCCGAAAAACGTACCATCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACt                                                                                                    <  2:236862/143‑1 (MQ=255)                                          acGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCa                                                                                                  <  1:34512/143‑1 (MQ=255)                                            gCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATAAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGtctctgc                                                                                                >  1:506694/1‑140 (MQ=255)                                            gCACAAAATCTGAAAAACGTACCAGCATAAATGAGCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGt                                                                                                >  1:731805/1‑143 (MQ=255)                                                aaaaTCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcatt                                                                                            >  1:603087/1‑143 (MQ=255)                                                   aTCTGAAAAACGTACCATCATAAATGATCCTGCGCACCAACCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGCAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcatttca                                                                                         <  2:312465/143‑1 (MQ=255)                                                        aaattcGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑Tttct                                                                                   <  1:20398/138‑1 (MQ=255)                                                        aaaaaCGTACCAGCATAAATAATCCTGCGCAGCCATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑Tttct                                                                                   <  1:99080/143‑1 (MQ=255)                                                               tACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGACTTCTTGTTTACTTACGGAAGGTGCAAATAAGAGGGGAGATTCTTCTCGGCTGAGGCAGTCAATTGA‑TGTCGTCgtgta                                                                            >  2:133887/1‑142 (MQ=255)                                                               tACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCGTTTCA‑TTTCATGATGtt                                                                            >  2:248090/1‑143 (MQ=255)                                                               tACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGtt                                                                            <  2:81558/143‑1 (MQ=255)                                                                aCCAGCATAAATGATCCTGCGCACCAAGCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGttt                                                                           <  1:250178/143‑1 (MQ=255)                                                                  cAGGATAAATGATCCTGCGCACCAATGAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGa                                                                         <  2:58300/143‑1 (MQ=255)                                                                  cAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCCTGTTTGa                                                                         >  2:101413/1‑143 (MQ=255)                                                                  cAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGa                                                                         <  1:657930/143‑1 (MQ=255)                                                                    gCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGGATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTGTGAGc                                                                       >  2:591450/1‑143 (MQ=255)                                                                     cATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAATTTCTTCTCGGCTGACTCAGTAGTTTCA‑TTTCTTCATTTTTGAgtg                                                                      >  2:144506/1‑141 (MQ=255)                                                                     cATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGAGcc                                                                      >  1:280473/1‑143 (MQ=255)                                                                         aaTGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTACGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGAGTCAGTCATTTCA‑TTTCTTCATGTTTGTGCCGAtt                                                                  >  2:4631/1‑143 (MQ=255)                                                                            gATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTATGAATTTTTGTTTTATTAAGTAAGGTGCGAATAAGCGGGTAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGAGCCGAttttt                                                               <  1:556016/143‑1 (MQ=255)                                                                                cTGCGCACCAATCAACACCCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGGGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGAGCCGATTTTTtctc                                                           <  1:775/143‑1 (MQ=255)                                                                                 tGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGAGCCGATTTTATGTcc                                                          >  1:265405/1‑143 (MQ=255)                                                                                   cgcACCACTCAACGACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGCTTTATTACGGAAGGTGCGCATAAGCGGGGAAATTCTTCTCGGCTGACTCAGCCATTTTA‑TTGCTTCATGTTTGAGCCGATTTTTTCTCCCg                                                        <  2:14055/143‑1 (MQ=21)                                                                                         aaTCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCCTTTCA‑TTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATg                                                  >  1:664465/1‑143 (MQ=255)                                                                                             aacaacCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCtt                                              <  1:675871/143‑1 (MQ=255)                                                                                              acaacCGTATAAGAATAGATACTTTCTTTAGGAATTTTTGATTTATTAAGGAAAGTACGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAACTGCCTTg                                             >  1:156220/1‑143 (MQ=18)                                                                                               caacCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGa                                            <  1:422792/143‑1 (MQ=255)                                                                                                aacCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGaa                                           >  1:214686/1‑143 (MQ=255)                                                                                                         aGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTAt                                  >  1:569465/1‑143 (MQ=255)                                                                                                          gAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGCCTCAGTCATTCCA‑TTTCTTCCTGTTTGAGCCGATTTTTTCTACCGTCAATTCCGTgtaccgacccctt                                 >  1:226826/1‑131 (MQ=18)                                                                                                             tAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAg                              >  1:514557/1‑143 (MQ=255)                                                                                                             gaGATACGTTCTTTAGAAATTTTTGTTTTATCAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTAACTCAGTCATTTCA‑TTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAg                              <  2:81186/142‑1 (MQ=255)                                                                                                                        tttAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTttcttc                   <  1:148164/143‑1 (MQ=255)                                                                                                                          tAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGc                 <  2:335242/143‑1 (MQ=255)                                                                                                                             gAATTTTTTTTTTTTTTTTTAAGGTGCGAATAAGCGGGGAAATTCTTCTCTGCTGACTCAGTCATTTCA‑TTTCTTCTTGTTTGCGCCGATTTTTTCTCTCGTATATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCAt              >  2:569946/1‑143 (MQ=11)                                                                                                                             gAATTTTTGTTTTATTACGGAAGGTGCGAATAAGTGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCa               <  2:324731/143‑1 (MQ=255)                                                                                                                             gAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTGA‑TGTCTTCATGTTTGAGCCGCTTTTTTATCCCGTTTATGTCTTTAATGTCTCTCTTTAGCCCGTttctctgacgt              >  2:547305/1‑136 (MQ=14)                                                                                                                             gAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCAt              >  2:130001/1‑143 (MQ=255)                                                                                                                                  tttGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAg         <  1:653623/143‑1 (MQ=38)                                                                                                                                   ttGTTCTATTAAGGAAGGTGCGAATAAGCGGTGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAgg        <  2:256217/143‑1 (MQ=21)                                                                                                                                       tttATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGtt    >  1:214485/1‑143 (MQ=33)                                                                                                                                       tttATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGtt    >  1:145335/1‑143 (MQ=33)                                                                                                                                         tattaAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGCGCCGATTTTTTCTCCCGTAAATGCCTTGAATCATCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTag  >  2:619676/1‑142 (MQ=17)                                                                                                                                               |                                                                                                                                          TCTTCACAGTACATAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCA‑TTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTAT  >  NC_000913/2101607‑2101885

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