New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	5432710 =	52 (1.060)	3 (0.060)	3/254	NT	5.1%	intergenic (+45/+25)	PP_5713/hrpB	hypothetical protein/ATP‑dependent helicase HrpB
	?	NC_002947	5432794 =	62 (1.310)					coding (2470/2529 nt)	hrpB	ATP‑dependent helicase HrpB

GGAGTGGGGAGTGGGTAGCCTGGCTCAACGTCGAGGAAGGCGAAGTGATCACGTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGTAGTGCTTCGGATATCGCCCTTTCAGGTCTTTCTTCACCTCGGCATAGGTCGTGCG  >  NC_002947/5432562‑5432851                                                                                                                                                     |                                                                                                                                              ggagtggggagtggGTAGCCTGGCTCAACGTCGAGGAAGGCGAAGTGATCACGTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCg                                                                                                                                               >  1:168063/1‑149 (MQ=255) ggagtggggagtggGTAGCCTGGCTCAACGTCGAGGAAGGCGAAGTGATCACGTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCg                                                                                                                                               <  7:64712/149‑1 (MQ=255) atcgccaatggccggcagcaggtcaagctgcacctgctgtcaccggcgcgtcggccggtgcaggtgacccaggacctggccagtttctggcgcacgccctatgccgaggtgaagaaagacctgaaagggcgatatccgaagcactactg                                                                                                                                               <  4:175036‑M1/1‑1 (MQ=255)    gccaatggccggcagcaggtcaagctgcacctgctgtcaccggcgcgtcggccggtgcaggtgacccaggacctggccagtttctggcgcccgacctatgccgaggtgaagcaagacctgcaagggcgctatccgcagcactactGGcc                                                                                                                                            <  8:285747‑M1/4‑1 (MQ=255)              ggTAGCCTGGCTCAACGTCGAGGAAGGCGAAGTGATCACGTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTc                                                                                                                                  <  1:129921/149‑1 (MQ=255)                  gCCTGGCTCAACGTCGAGGAAGGCGAAGTGATCACGTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCggtg                                                                                                                              <  2:209784/149‑1 (MQ=255)                  gCCTGGCTCAACGTCGAGGAAGGCGAAGTGATCACGTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCggtg                                                                                                                              <  2:168063/149‑1 (MQ=255)                   ccTGGCTCAACGTCGAGGAAGGCGAAGTGATCTCGTTGCTATTGAGGCAGGGAGTTCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCggtg                                                                                                                              <  1:123311/148‑1 (MQ=255)                    cTGGCTCAACGTCGAGGAAGGCGAAGTGATCACGTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCggtggt                                                                                                                            <  4:60618/149‑1 (MQ=255)                         tCAACGTCGAGGAAGGCGAAGTGATCACGTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCa                                                                                                                       >  4:218229/1‑149 (MQ=255)                         tCAACGTCGAGGAAGGCGAAGTGATCACGTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCa                                                                                                                       >  7:285354/1‑149 (MQ=255)                                 gAGGAAGGCGAAGTGATCACGTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTcc                                                                                                               <  3:218229/149‑1 (MQ=255)                                 gAGGAAGGCGAAGTGATCACGTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTcc                                                                                                               <  5:25063/149‑1 (MQ=255)                                 gAGGAAGGCGAAGTGATCACGTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTcc                                                                                                               <  3:202979/149‑1 (MQ=255)                                    gAAGGCGAAGTGATCACGTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCctc                                                                                                            >  8:169357/1‑149 (MQ=255)                                    gAAGGCGAAGTGATCACGTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCctc                                                                                                            >  5:33120/1‑149 (MQ=255)                                       ggCGAAGTGATCACGTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCg                                                                                                         <  6:57369/149‑1 (MQ=255)                                        gCGAAGTGATCACGTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCgg                                                                                                        <  7:169357/149‑1 (MQ=255)                                          gAAGTGATCACGTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCt                                                                                                      >  5:44294/1‑149 (MQ=255)                                               gATCACGTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGgtgt                                                                                                                          <  8:14974/124‑1 (MQ=255)                                               gATCACGTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGgtgt                                                                                                                          >  7:14974/1‑124 (MQ=255)                                                 tCACGTTACTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCt                                                                                               <  1:48193/149‑1 (MQ=255)                                                   aCGTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTg                                                                                              <  8:285354/148‑1 (MQ=255)                                                     gTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTc                                                                                                                >  8:267454/1‑128 (MQ=255)                                                     gTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTc                                                                                                                <  7:267454/128‑1 (MQ=255)                                                        ccTTTTGAGGCAGGCAGTTCGAGCTTCACTGGACGTGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGt                                                                                         <  7:39337/148‑1 (MQ=255)                                                           tgcaggtgacccaggacctggccagtttctggcgcacgacctatgccgaggtgaagaaagacctgaaagggcgatatccgaagcactactGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGcc                                                                                     <  7:288410‑M1/59‑1 (MQ=255)                                                                 gcaggcagATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGc                                                                                >  1:73140/1‑148 (MQ=255)                                                                         aTCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAgg                                                                       >  4:188561/1‑149 (MQ=255)                                                                                ttCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTcc                                                                >  1:68757/1‑149 (MQ=255)                                                                                          gcgcacgacctatgccgaggtgaagaaagacctgaaagggcgatatccgaagcactactGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCagtagt                                                      >  8:288410‑M1/60‑149 (MQ=255)                                                                                          gcgcacgacctatgccgaggtgaagaaagacctgaaagggcgatatccgaagcactactGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCagt                                                         >  1:120118‑M1/60‑146 (MQ=255)                                                                                           gggCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGTAGTg                                                     <  7:58853/149‑1 (MQ=255)                                                                                                 tACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGTAGTGCTTCg                                                >  6:297693/1‑148 (MQ=255)                                                                                                   cGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCagt                                                         >  3:18463/1‑137 (MQ=255)                                                                                                   cGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCagt                                                         <  4:18463/137‑1 (MQ=255)                                                                                                    gATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAgg                                                                       >  3:158002/1‑122 (MQ=255)                                                                                                    gATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAgg                                                                       <  4:158002/122‑1 (MQ=255)                                                                                                    gATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGTAGTGCTTCGGata                                            >  3:87583/1‑149 (MQ=255)                                                                                                         aTGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGTAGTGCTTCGGATATCGcc                                       >  1:43280/1‑149 (MQ=255)                                                                                                         aTGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGTAGTGCTTCGGATATCGcc                                       <  2:73140/149‑1 (MQ=255)                                                                                                         aTGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGAAGTGCTTCGGATATCGcc                                       >  5:296180/1‑149 (MQ=255)                                                                                                              aCGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCCTCCGGCCAGTAGTGCTTCGGATATCGCCCttt                                   >  1:245374/1‑148 (MQ=255)                                                                                                               cGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGTAGTGCTTCGGATATCGCCCTTTCa                                 <  6:33120/149‑1 (MQ=255)                                                                                                                gACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGTAGTGCTTCGGATATCGCCCTTTCAg                                >  6:178962/1‑149 (MQ=255)                                                                                                                gACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGTAGTGCTTCGGATATCGCCCTTTCAg                                <  4:75038/149‑1 (MQ=255)                                                                                                                        acacGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGTAGTGCTTCGGATATCGCCCTTTCAg                                <  4:10802/141‑1 (MQ=255)                                                                                                                        acacGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGTAGTGCTTCGGATATCGCCCTTTCAg                                >  3:10802/1‑141 (MQ=255)                                                                                                                        acacGTCGTGGCCAGCGCATGATTTTTTCGGCCAGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGTAGTGCTTCGGATATCGCCCTTTCAGGtctttct                        >  1:196961/1‑149 (MQ=255)                                                                                                                         cacGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGTAGTGCTTCGGATATCGCCCTTTCAGGtctttctt                       <  6:44294/149‑1 (MQ=255)                                                                                                                         cacGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGTAGTGCTTCGGATATCGCCCTTTCAGGtctttctt                       <  2:245374/149‑1 (MQ=255)                                                                                                                             tcgtGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGTAGTGCTTc                                                 >  4:151713/1‑119 (MQ=255)                                                                                                                                  gCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGTAGTGCTTCGGATATCGCCCTTTCAGGTCTTTCTTCACCTCgg               <  5:178962/148‑1 (MQ=255)                                                                                                                                       cgcATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCg                                                               <  3:266421/95‑1 (MQ=255)                                                                                                                                       cgcATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCg                                                               >  4:266421/1‑95 (MQ=255)                                                                                                                                            gATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGTAGTGCTTCGGATATCGCCCTTTCAGGTCTTTCTTCACCTCGGCATAGGTCGTg    >  6:278362/1‑149 (MQ=255)                                                                                                                                             aTTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGTAGTGCTTCGGATATCGCCCTTTCAGGTCTTTCTTCACCTCGGCATAGGTCGTg    <  4:87583/148‑1 (MQ=255)                                                                                                                                              ttttttCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGTAGTGCTTCGGATATCGCCCTTTCAGGTCTTTCTTCACCTCGGCATAGGTCGTgcg  >  1:179855/1‑149 (MQ=255)                                                                                                                                              ttttttCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGTAGTGCTTCGGATATCGCCCTTTCAGGTCTTTCTTCACCTCGGCATAGGTCGTgc   <  3:188561/148‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                              GGAGTGGGGAGTGGGTAGCCTGGCTCAACGTCGAGGAAGGCGAAGTGATCACGTTCCTATTGAGGCAGGCAGATCGAGCTTCACTGGCCGGGGCAATACGATGAATGGCACGACCACTGACACGTCGTGGCCAGCGCATGATTTTTTCGGCCTGCCGCACTCGGTGGTGTGCATCAGCTCCCTCTCGGCTTGGCCCTGGCGGTAGCCTCGGCCACCAGAGGGTCGTCCGGCCAGTAGTGCTTCGGATATCGCCCTTTCAGGTCTTTCTTCACCTCGGCATAGGTCGTGCG  >  NC_002947/5432562‑5432851

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.