New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	3478034 =	52 (0.870)	5 (0.080)	5/240	NT	7.8%	intergenic (‑26/+70)	PP_3088/PP_3089	hypothetical protein/hypothetical protein
	?	NC_002947	3478063 =	66 (1.100)					intergenic (‑55/+41)	PP_3088/PP_3089	hypothetical protein/hypothetical protein

TCCGCCCGGCGTGCCTCCTTGATCTGATCGAACAAGGCAGAGAAGCTCAAGTCTTCGCCACTGCCACCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCT  >  NC_002947/3477887‑3478180                                                                                                                                                    |                                                                                                                                                   tttgaccGGCGTGCCTCCTTGATCTGATCGAACAAGGCAGAGAAGCTCAAGTCTTCGCCACTGCCACCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGaa                                                                                                                                                    <  1:1371561/143‑1 (MQ=255) tttgaccGGCGTGCCTCCTTGATCTGATCGAACAAGGCAGAGAAGCTCAAGTCTTCGCCACTGCCACCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGaa                                                                                                                                                    >  2:1371561/6‑148 (MQ=255)        ggCGTGCCTCCTTGATCTGATCGAACAAGGCAGAGAAGCTCAAGTCTTCGCCACTGCCACCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGcc                                                                                                                                           <  1:901557/150‑1 (MQ=255)              cctccgTGATCTGAGCGAACAAGGCAGAGAAGCTCAAGTCTTCGCCACTGCCACCCTCGCTAGGGGCGACCAGTGTGGCCAGCGAGAGGGCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCGAGTGAATAGCGCGCCGGaaaa                                                                                                                                     >  2:275751/1‑150 (MQ=255)                 cctTGATCTGATCGAACAAGGCAGAGAAGCTCAAGTCTTCGCCACTGCCACCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAAccc                                                                                                                                  <  2:1553563/150‑1 (MQ=255)                 cctTGATCTGATCGAACAAGGCAGAGAAGCTCAAGTCTTCGCCACTGCCACCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAAccc                                                                                                                                  >  1:303088/1‑150 (MQ=255)                      atctgatcGAACAAGGCAGAGAAGCTCAAGTCTTCGCCACTGCCACCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGgcgc                                                                                                                             <  1:975332/150‑1 (MQ=255)                       acccagcagaaccgcaccgacggccaggccggcggcaacatcgtgggtggctgggaccgcaccgcgaacaaagtgtttgcctaagcacgtaccgaaccatgggccgcttcggcggcctgtgttccGCAGCGCGCCGGAAAACCCGgcgcg                                                                                                                            >  2:72763‑M1/126‑150 (MQ=255)                               aaCAAGGCAGAGAAGCTCAAGTCTTCGCCACTGCCACCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGaa                                                                                                                    >  1:681200/1‑150 (MQ=255)                                  aaGGCAGAGAAGCTCAAGTCTTCGCCACTGCCACCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAgcac                                                                                                                 >  2:89889/1‑150 (MQ=255)                                   aGGCAGAGAAGCTCAAGTCTTCGCCACTGCCACCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCAGGAAAACCCGGCGCGCTGCGGAAcaca                                                                                                                <  2:640794/150‑1 (MQ=255)                                     gCAGAGAAGCTCAAGTCTTCGCCACTGCCACCCTCGATAGGGGCGAACAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACggg                                                                                                              >  1:402526/1‑150 (MQ=255)                                      cAGAGAAGCTCAAGTCTTCGCCACTGCCACCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGCGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGgc                                                                                                             >  2:9142/1‑150 (MQ=255)                                             gCTCAAGTCTTCGCCACTGCCACCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGaa                                                                                                      <  1:703899/150‑1 (MQ=255)                                                 aaGTCTTCGCCACTGCCACCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCgg                                                                                                  <  1:1635409/150‑1 (MQ=255)                                                    tCTTCGCCACTGCCACCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGccc                                                                                               >  2:1316495/1‑150 (MQ=255)                                                         gCCACTGCCACCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGt                                                                                          >  1:724522/1‑150 (MQ=255)                                                          ccACTGCCACCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGtt                                                                                         >  1:554415/1‑150 (MQ=255)                                                           cACTGCCACCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTc                                                                                        <  1:1195569/150‑1 (MQ=255)                                                            aCTGCCACCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCg                                                                                       >  1:1085687/1‑150 (MQ=255)                                                                 cACCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACg                                                                                  >  1:1037146/1‑150 (MQ=255)                                                                 cACCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACg                                                                                  >  2:739458/1‑150 (MQ=255)                                                                  aCCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCCGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGt                                                                                 <  2:681200/150‑1 (MQ=255)                                                                       cggtAGGGGCGACCAGTGTGGCCACCGAGAGGGCATTGAGAATTTCAGGCATAGAACACTGTGGACAGGGCTAGTGAACAGCGCGCAGCAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTa                                                                            <  1:275751/147‑1 (MQ=255)                                                                              ggCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAac                                                                     >  2:446518/1‑150 (MQ=255)                                                                                  aCCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACtt                                                                 >  1:1022941/1‑150 (MQ=255)                                                                                   ccAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGc                                                                                                                        <  2:189171/94‑1 (MQ=255)                                                                                   ccAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGc                                                                                                                        >  1:189171/1‑94 (MQ=255)                                                                                   ccAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACttt                                                                <  1:330454/150‑1 (MQ=255)                                                                                      gtgtGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGtt                                                             >  2:1051661/1‑150 (MQ=255)                                                                                          ggCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTcgcg                                                         >  1:1180023/1‑150 (MQ=255)                                                                                          ggCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTcgcg                                                         <  2:747935/150‑1 (MQ=255)                                                                                           gCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCgcgg                                                        <  2:334763/150‑1 (MQ=255)                                                                                            aaagtgtttgcctaagcacgtaccgaaccatgggccgcttcggcggcctgtgttccACAGCGCGCCGGAAAACCCGGCGCGCTGCGGaa                                                                                                                    >  1:1314062‑M1/57‑89 (MQ=255)                                                                                            aaagtgtttgcctaagcacgtaccgaaccatgggccgcttcggcggcctgtgttccACAGCGCGCCGGAAAACCCGGCGCGCTGCGGaa                                                                                                                    <  2:1314062‑M1/33‑1 (MQ=255)                                                                                                 gtttgcctaagcacgtaccgaaccatgggccgcttcggcggcctgtgttccACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAg                                                                                                               <  2:493777‑M1/38‑1 (MQ=255)                                                                                                 gtttgcctaagcacgtaccgaaccatgggccgcttcggcggcctgtgttccACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAg                                                                                                               >  1:493777‑M1/52‑89 (MQ=255)                                                                                                     ggTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCa                                              <  2:1022941/150‑1 (MQ=255)                                                                                                      gTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAg                                             >  2:1103417/1‑150 (MQ=255)                                                                                                          ttGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTa                                                                            >  2:635953/1‑115 (MQ=255)                                                                                                          ttGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTa                                                                            <  1:635953/115‑1 (MQ=255)                                                                                                          ttGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGccac                                         <  1:739458/150‑1 (MQ=255)                                                                                                                 tttCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGAt                                  >  1:408549/1‑150 (MQ=255)                                                                                                                    cAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGtt                               <  1:446518/150‑1 (MQ=255)                                                                                                                         aTAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTgccgc                          >  2:348525/1‑150 (MQ=255)                                                                                                                             aaCACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTcgcg                                                         <  1:1382831/115‑1 (MQ=255)                                                                                                                             aaCACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTcgcg                                                         >  2:1382831/1‑115 (MQ=255)                                                                                                                             aaCACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAg                                             >  1:206133/1‑127 (MQ=255)                                                                                                                             aaCACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAg                                             <  2:206133/127‑1 (MQ=255)                                                                                                                             aaCACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGc                      >  1:975984/1‑150 (MQ=255)                                                                                                                             aaCACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGATCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGc                      >  2:716120/1‑150 (MQ=255)                                                                                                                                  tctGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGc                 >  2:1527677/1‑150 (MQ=255)                                                                                                                                  tctGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGc                 >  2:963886/1‑150 (MQ=255)                                                                                                                                         aTGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCg            >  2:1173945/1‑148 (MQ=255)                                                                                                                                         aTGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCg            <  1:1173945/148‑1 (MQ=255)                                                                                                                                           ggCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCAGGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGc        >  1:1398170/1‑150 (MQ=255)                                                                                                                                              tAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTc                                                                                        >  2:341062/1‑67 (MQ=255)                                                                                                                                              tAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTc                                                                                        <  1:341062/67‑1 (MQ=255)                                                                                                                                              tAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGt     >  1:312468/1‑150 (MQ=255)                                                                                                                                                 ggAAGAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACATAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTct  <  2:303088/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                   TCCGCCCGGCGTGCCTCCTTGATCTGATCGAACAAGGCAGAGAAGCTCAAGTCTTCGCCACTGCCACCCTCGATAGGGGCGACCAGTGTGGCCAGCGAGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCT  >  NC_002947/3477887‑3478180

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ 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.