New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 2522101	49 (1.000)	4 (0.080)	4/242	NT	6.9%	coding (3309/4446 nt)	PP_2212	leucine‑rich repeat‑containing protein
	?	NC_002947	= 2522133	60 (1.260)					coding (3341/4446 nt)	PP_2212	leucine‑rich repeat‑containing protein

CGGTTGGCGCATAACGAGATACGCCTCGACGCCCAGGCGATCAGCGTTCTGCATGGTTTGTCCAACCTTGTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTGCGCAACAACCAACTCCGCGAAGTGCCCACCGAGATCCAGCTGATGCCTTATGCATTTCGACAGGC  >  NC_002947/2521964‑2522250                                                                                                                                          |                                                                                                                                                       cGGTTGGCGCATAACGAGATACGCCTCGACGCCCAGGCGATCAGCGTTCTGCATGGTTTGTCCAACCTTGTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAAc                                                                                                                                           <  1:518422/150‑1 (MQ=255)   gTTGGCGCATAACGAGATACGCCTCGACGCCCAGGCGATCAGCGTTCTGCATGGTTTGTCCAACCTTGTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCt                                                                                                                                         <  1:668013/150‑1 (MQ=255)         gcATAACGAGATACGCCTCGACGCCCAGGCGATCAGCGTTCTGCATGGTTTGTCCAACCTTGTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCa                                                                                                                                   >  1:960048/1‑150 (MQ=255)                  gaTACGCCTCTACGCCCAGGCGATCAGCGTTCTGCATGGTTTGTCCAACCTTGTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCt                                                                                                                          >  1:460665/1‑150 (MQ=255)                  gaTACGCCTCGACGCCCAGGCGATCAGCGTTCTGCATGGTTTGTCCAACCTTGTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCt                                                                                                                          >  1:925436/1‑150 (MQ=255)                       gCCTCGACGCCCAGGCGATCAGCGTTCTGCATGGTTTGTCCAACCTTGTGCATCTTGATCTCAGTCATAACCAGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTgggga                                                                                                                     >  2:420514/1‑148 (MQ=255)                            gACGCCCAGGCGATCAGCGTTCTGCATGGTTTGTCCAACCTTGTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGAACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTgg                                                                                                                >  1:170906/1‑150 (MQ=255)                              cGCCCAGGCGATCAGCGTTCTGCATGGTTTGTCCAACCTTGTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGcc                                                                                                              <  2:460665/150‑1 (MQ=255)                                           aGCGTTATGCATGGTTTGTCCAACCTTGTGCATCTTGATCTCAGTCATAACTGGTTGGGAGCGGTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAg                                                                                                 >  2:280114/1‑150 (MQ=255)                                                  tGCATGGTTTGTCCAACCTTGTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCtgtg                                                                                          <  1:1202760/150‑1 (MQ=255)                                                   gCATGGTTTGTCCAACCTTTTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTg                                                                                                    <  1:198907/139‑1 (MQ=255)                                                   gCATGGTTTGTCCAACCTTGTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTg                                                                                                    >  2:198907/1‑139 (MQ=255)                                                       ggTTTGTCCAACCTTGTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGcc                                                                                                      >  2:1148522/1‑133 (MQ=255)                                                       ggTTTGTCCAACCTTGTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGcc                                                                                                      <  1:1148522/133‑1 (MQ=255)                                                         tttGTCCAACCTTGTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACt                                                                                   <  1:38629/150‑1 (MQ=255)                                                             tCCAACCTTGTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGaa                                                                               >  1:260744/1‑150 (MQ=255)                                                             tCCAACCTTGTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGaa                                                                               >  1:133494/1‑150 (MQ=255)                                                              ccAACCTTGTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAAc                                                                              >  2:1091249/1‑150 (MQ=255)                                                               cAACCTTGTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACg                                                                             >  1:1152443/1‑150 (MQ=255)                                                                aaCCTTGTGCATCTTGATCTCAGTTATCACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCCTCGCCGGCTAGGCACCTGGCCGCGTCGCCTGGAACTCTGTCATCGACTTGAACGt                                                                            <  2:502480/150‑1 (MQ=255)                                                                aaCCTTGTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGt                                                                            >  2:863526/1‑150 (MQ=255)                                                                aaCCTTGTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGt                                                                            >  1:207000/1‑150 (MQ=255)                                                                  ccTTGTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGc                                                                          <  1:820987/150‑1 (MQ=255)                                                                     tgtgCATCTTGATCTCAGTCATAACCGGCTGGAAGCCCCCAACCTGCCCTTCGGCCATCTTTCTCGGCTGCACCTG‑GTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGa                                                                       <  1:926703/150‑1 (MQ=255)                                                                      gtgCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGTTGAc                                                                      <  1:1237738/150‑1 (MQ=255)                                                                         cATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTGcccagccgacaatgacgcaggttcaggctggtcagccgagaaa                                                                                                             >  1:948929‑M1/1‑66 (MQ=255)                                                                         cATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTGcccagccgacaatgacgcaggttcaggctggtcagccgagaaa                                                                                                             <  2:948929‑M1/109‑44 (MQ=255)                                                                          aTCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTgc                                                                  <  2:902011/150‑1 (MQ=255)                                                                           tCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTgcg                                                                 <  2:960048/150‑1 (MQ=255)                                                                              tGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTGcccagccgacaatgacgcaggttcaggctggtcagc                                                                                                                    >  1:37810‑M1/1‑61 (MQ=255)                                                                              tGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTGcccagccgacaatgacgcaggttcaggctggtcagc                                                                                                                    <  2:37810‑M1/97‑37 (MQ=255)                                                                                 tctcAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTGCGcaacaa                                                           >  1:991445/1‑150 (MQ=255)                                                                                 tctcAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTGCGcaacaa                                                           <  2:260744/150‑1 (MQ=255)                                                                                 cctcAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTATCAGTGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTGCGcaacaa                                                           <  1:79251/149‑1 (MQ=255)                                                                                             ccGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTGCGcaac                                                             <  2:587498/136‑1 (MQ=255)                                                                                             ccGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTGCGcaac                                                             >  1:587498/1‑136 (MQ=255)                                                                                              cGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTg                                                                           <  2:1133521/121‑1 (MQ=255)                                                                                              cGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTg                                                                           >  1:1133521/1‑121 (MQ=255)                                                                                              cGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTGCGCAACAACCAACTCCGCGaa                                              >  2:1023720/1‑150 (MQ=255)                                                                                                  tGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTGCGCAACAACCAACTCCGCGAAGTGc                                          >  2:957715/1‑150 (MQ=255)                                                                                                    gAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTGCGCAACAACCAACTCCGCGAAGTGccc                                        >  2:408576/1‑150 (MQ=255)                                                                                                           tGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTGCGCAACAACCAACTCCGCGAAGTGCCCACCgaga                                 <  2:1152443/150‑1 (MQ=255)                                                                                                             gACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAAc                                                                              <  1:999456/103‑1 (MQ=255)                                                                                                             gACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAAc                                                                              >  2:999456/1‑103 (MQ=255)                                                                                                               cATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTGCGCAACAACCAACTCCGCGAAGTGCCCACCGAGATCCa                             >  2:356484/1‑150 (MQ=255)                                                                                                                  gAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTGCGCAACAACCAACTCCGCGAAGTGCCCACCGAGATCCAGCt                          >  2:159170/1‑150 (MQ=255)                                                                                                                    gCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTGCGCAACAACCAACTCCGCGAAGTGCCCACCGAGATCCAGCTGa                        <  1:356484/150‑1 (MQ=255)                                                                                                                          accaACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTGCGCAACAACCAACTCCGCGAAGTGCCCACCGAGATCCAGCTGATGCCtt                  >  2:1105640/1‑150 (MQ=255)                                                                                                                            caACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTGCGCAACAACCAACTCCGCGAAGTGCCCACCGAGATCCAGCTGATGCCTTAt                <  1:408576/150‑1 (MQ=255)                                                                                                                               cTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTGCGCAACAACCAACTCCGCGAAGTGCCCACCGAGATCCAGCTGATGCCTTa                 <  2:220932/146‑1 (MQ=255)                                                                                                                               cTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTGCGCAACAACCAACTCCGCGAAGTGCCCACCGAGATCCAGCTGATGCCTTa                 >  1:220932/1‑146 (MQ=255)                                                                                                                                tttCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGcagccgagaaagttggtggaagctcatgtccagcgcttccagccggttatgactgagatcaagatg                                                     >  1:948929‑M2/1‑43 (MQ=255)                                                                                                                                tttCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGcagccgagaaagttggtggaagctcatgtccagcgcttccagccggttatgactgagatcaagatg                                                     <  2:948929‑M2/109‑67 (MQ=255)                                                                                                                                    tcGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTGCGCAACAACCAACTCCGCGAAGTGCCCACCGAGATCCAGCTGATGCCTTATGCATTTCg        >  2:322304/1‑150 (MQ=255)                                                                                                                                     cGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTGCGCAACAACCAACTCCGCGAAGTGCCCACCGAGATCCAGCTGATGCCTTATGCATTTCGa       <  2:1280546/150‑1 (MQ=255)                                                                                                                                       gCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGcagccgagaaagttggtggaagctcatgtccagcgcttccagccggttatgactgagatca                                                          <  2:37810‑M2/97‑62 (MQ=255)                                                                                                                                       gCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGcagccgagaaagttggtggaagctcatgtccagcgcttccagccggttatgactgagatca                                                          >  1:37810‑M2/1‑36 (MQ=255)                                                                                                                                        cTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACATGCGCAACAACCAACTCCGCGAAGTGCCCACCGAGATCCAGCTGATGCCTTATGCATTTCGACAg    <  2:925436/150‑1 (MQ=255)                                                                                                                                          g‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGACCGTGCTGACTTGCGCAACAACTATCTTCGCGCGGTGCCCACCGAGATCCAGCTGATGCCTTATGCATTTCGACAGGc  <  2:170906/150‑1 (MQ=255)                                                                                                                                          |                                                                                                                                                       CGGTTGGCGCATAACGAGATACGCCTCGACGCCCAGGCGATCAGCGTTCTGCATGGTTTGTCCAACCTTGTGCATCTTGATCTCAGTCATAACCGGCTGGAAGCGCTGGACATGAGCTTCCACCAACTTTCTCGGCTG‑ACCAGCCTGAACCTGCGTCATTGTCGGCTGGGCAGCTGGCCGCGTCGCCTGGAGCTCTGTGGTCTACTTGAACGTGCTGACTTGCGCAACAACCAACTCCGCGAAGTGCCCACCGAGATCCAGCTGATGCCTTATGCATTTCGACAGGC  >  NC_002947/2521964‑2522250

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