New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	1175069 =	47 (1.040)	5 (0.110)	5/240	NT	10.4%	coding (138/558 nt)	PP_1030	hypothetical protein
	?	NC_002947	1175092 =	41 (0.940)					coding (161/558 nt)	PP_1030	hypothetical protein

AGCATCATCGTTCCAAAGCTGTCTACCGTCCCGGTGCATGAAGCCCGTGCCCGCGCCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATCTATACCCCCACCGAAGGCTTCCTCGAAGAAGCCGGTTGCCCGGAGTGCCGGCGCGAGGTAG  >  NC_002947/1174944‑1175241                                                                                                                                                      |                                                                                                                                                      accggcttcttcgaggaagccttcggtgggggtatagatgcagcgtttgagcatcacttccaggccgttgaccggttcgccgaagggcagtttttccgggtgcagggccactttgcgcgcccctgCCGCATGGGCCATG‑CCCTGGCGGCa                                                                                                                                                      >  1:968995‑M1/126‑150 (MQ=255)   catcatCGTTCCAAAGCTGTCTACCGTCCCGGTGCATGAAGCCCGTGCCCGCGCCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAgg                                                                                                                                                    >  1:1026414/1‑150 (MQ=255)    atcatcGTTCCAAAGCTGTCTACCGTCCCGGTGCATGAAGCCCGTGCCCGCGCCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAggg                                                                                                                                                   >  1:1048804/1‑150 (MQ=255)       atcGTTCCAAAGCTGTCTACCGTCCCGGTGCATGAAGCCCGTGCCCGCGCCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGgcg                                                                                                                                                >  2:495363/1‑150 (MQ=255)               aaaGCTGTCTACCGTCCCGGTGCATGAAGCCCGTGCCCGCGCCATCCTGCGCTGGCTGGTGCGCGAAAAGGTGCTCGAGGAGCATCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGt                                                                                                                                        >  1:146235/1‑150 (MQ=255)                 aGCTGTCTACCGTCCCGGTGCATGAAGCCCGTGCCCGCGCCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTgg                                                                                                                                      <  2:139269/150‑1 (MQ=255)                   cgccttccgtggtgttatagatgctgcgtttgagcatcacttccaggccgttgaccggttcgccgaagggcagtttttccgggtgcagggccactttgcgcgcccctgccgcatgggccatgccctggcggCAGGGGCGCGCAAAGTGGc                                                                                                                                     <  2:670638‑M2/19‑1 (MQ=255)                   cTGTCTACCGTCCCGGTGCATGAAGCCCGTGCCCGCGCCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGcc                                                                                                                                    <  1:622677/150‑1 (MQ=255)                         aCCGTCCCGGTGCATGAAGCCCGTGCCCGCGCCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGc                                                                                                                                     <  2:171325/143‑1 (MQ=255)                         aCCGTCCCGGTGCATGAAGCCCGTGCCCGCGCCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGc                                                                                                                                     <  1:645237/143‑1 (MQ=255)                         aCCGTCCCGGTGCATGAAGCCCGTGCCCGCGCCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGc                                                                                                                                     >  2:645237/1‑143 (MQ=255)                         aCCGTCCCGGTGCATGAAGCCCGTGCCCGCGCCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGc                                                                                                                                     >  1:171325/1‑143 (MQ=255)                          ccGTCCCGGTGCATGAAGCCCGTGCCCGCGCCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCAcc                                                                                                                             <  2:1026414/150‑1 (MQ=255)                           cGTCCCGGTGCATGAAGCCCGTGCCCGCGCCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCAccc                                                                                                                            <  1:364963/150‑1 (MQ=255)                           cGTCCCGGTGCATGAAGCCCGTGCCCGCGCCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCAccc                                                                                                                            <  1:495363/150‑1 (MQ=255)                           cGTCCCGGTGCATGAAGCCCGTGCCCGCGCCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCAccc                                                                                                                            <  2:603730/150‑1 (MQ=255)                                  gTGCATGAAGCCCGTGCCCGCGCCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTAGAGGGGCAGCTGACCACGGTTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGaaaaa                                                                                                                     >  1:450296/1‑150 (MQ=255)                                      gagAAGCCCGTGCCCGCGCCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGc                                                                                                                 >  1:644901/3‑150 (MQ=255)                                      aTGAAGCCCGTGCCCGCGCCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGc                                                                                                                 <  1:931145/150‑1 (MQ=255)                                       tGAAGCCCGTGCCCGCGCCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGcc                                                                                                                >  1:1095656/1‑150 (MQ=255)                                                     gcgcCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCCTG‑CCCTGCCGCCAGGTGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCgg                                                                                                  >  1:445167/1‑150 (MQ=255)                                                     gcgcCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCgg                                                                                                  <  1:195597/150‑1 (MQ=255)                                                      cgcCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGTCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGt                                                                                                 <  1:13341/150‑1 (MQ=255)                                                         cATCCTGCGCTGGCTGGTTCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCaa                                                                                              >  2:352581/1‑150 (MQ=255)                                                         cATCCTGCGCGGGCTGGTACGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCaa                                                                                              >  2:352553/1‑150 (MQ=255)                                                                      ctggTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTg                                                                                 <  1:959449/150‑1 (MQ=255)                                                                          tGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGa                                                                                <  1:164317/147‑1 (MQ=255)                                                                          tGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGa                                                                                >  2:164317/1‑147 (MQ=255)                                                                          tGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGc                                                                             >  1:1003798/1‑150 (MQ=255)                                                                                ccgaagggcagtttttccgggtgcagggccactttgcgcgcccctgCCGCATGGGCCATG‑CCCTGGCGGCAggg                                                                                                                                                   <  2:886177‑M1/28‑1 (MQ=255)                                                                                ccgaagggcagtttttccgggtgcagggccactttgcgcgcccctgCCGCATGGGCCATG‑CCCTGGCGGCAggg                                                                                                                                                   >  1:886177‑M1/47‑74 (MQ=255)                                                                                        gtcgAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATc                                                               >  2:220011/1‑150 (MQ=255)                                                                                        gtcgAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAAACGCATGGGCAATG‑ACATACCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATc                                                               >  1:1053137/1‑150 (MQ=255)                                                                                              gagCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATCTATAcc                                                         <  2:1003798/150‑1 (MQ=255)                                                                                                  agcTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATCTATACCCCCa                                                     <  2:1053137/150‑1 (MQ=255)                                                                                                  agcTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATCTATACCCCCa                                                     >  1:149886/1‑150 (MQ=255)                                                                                                         caccTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTg                                                                   <  1:272994/129‑1 (MQ=255)                                                                                                         caccTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTg                                                                   >  2:272994/1‑129 (MQ=255)                                                                                                         caccTGTGGCCGCACCGGTAACCACATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATCTATACCCCCACCGAAgg                                              >  2:517993/1‑150 (MQ=255)                                                                                                           gccactttgcgcgcccctgCCGCCAGGGC‑ATGGCCCATGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCAGCATCTATAACACCACGGAAGgcg                                            <  2:670638‑M1/131‑2 (MQ=255)                                                                                                              gtgGCCGCACCGGTAACCGCTTGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATCTATGCCCCCACCGAAGGCTTcc                                         <  2:1153676/150‑1 (MQ=255)                                                                                                                  ccGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATCTATACCCCCACCGAAGGCTTCCTCga                                     >  1:107288/1‑150 (MQ=255)                                                                                                                   cGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATCTATACCCCCACCGAAGGCTTCCTCgaa                                    <  2:455960/150‑1 (MQ=255)                                                                                                                          gTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATCTATACCCCCACCGAAGGCTTc                                          >  2:348145/1‑137 (MQ=255)                                                                                                                          gTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATCTATACCCCCACCGAAGGCTTc                                          <  1:348145/137‑1 (MQ=255)                                                                                                                          ccctgccgccagggcatggcccatgcggCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCgg                                                                                                          >  1:886177‑M2/29‑74 (MQ=255)                                                                                                                          ccctgccgccagggcatggcccatgcggCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCgg                                                                                                          <  2:886177‑M2/46‑1 (MQ=255)                                                                                                                             tgccgccagggcatggcccatgcggCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATCTATACCCCCACCGAAGGCTTCCTCGAAGAAGCCGGt                           >  1:968995‑M2/26‑150 (MQ=255)                                                                                                                               CGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATCTATACCCCCACCGAAGGCTTCCTCGAAGAAGCCGGTTGc                        <  1:994644‑M1/150‑1 (MQ=255)                                                                                                                                  aTGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATCTATACCCCCACCGAAGGCTTCCTCGAAGAAGCCGGTTGCCCg                     >  2:166074/1‑150 (MQ=255)                                                                                                                                    gggCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATCTATACCCCCACCGAAGGCTTCCTCGAAGAAGCCGGTTGCCCGGa                   <  2:450296/150‑1 (MQ=255)                                                                                                                                    gggCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATCTATACCCCCACCGAAGGCTTCCTCGAAGAAGCCGGTTGCCCGGa                   <  1:220011/150‑1 (MQ=255)                                                                                                                                     gggcatggcccatgcggCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATCTATACCCCCACCGAAGGCTTCCTCGAAGAAGCCGGTTGCCCGGa                   <  1:670638‑M2/133‑1 (MQ=255)                                                                                                                                                 ggcggcAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATCTATACCCCCACCGAAGGCTTCCTCGAAGAAGCCGGTTGCCCGGAGTGCCGGCGCGa       <  2:445167/150‑1 (MQ=255)                                                                                                                                                  gcggCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATCTATACCCCCACCGAAGGCTTCCTCGAAGAAGCCGGTTGCCCGGAGTGCCGGCGCGAg      <  2:994644‑M2/146‑1 (MQ=255)                                                                                                                                                     gCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATCTATACCCCCACCGAAGGCTTCCTCGAAGAAGCCGGTTGCCCGGAGTGCCGGCGCGAGGTa   <  2:146235‑M2/149‑1 (MQ=255)                                                                                                                                                      cAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATCTATACCCCCACCGAAGGCTTCCTCGAAGAAGCCGGTTGCCCGGAGTGCCGGCGCGaggtag  <  1:166074/150‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                      AGCATCATCGTTCCAAAGCTGTCTACCGTCCCGGTGCATGAAGCCCGTGCCCGCGCCATCCTGCGCTGGCTGGTGCGCGAAAAGGTCGTCGAGGAGCAGCTGACCACCTGTGGCCGCACCGGTAACCGCATGGGCCATG‑CCCTGGCGGCAGGGGCGCGCAAAGTGGCCCTGCACCCGGAAAAACTGCCCTTCGGCGAACCGGTCAACGGCCTGGAAGTGATGCTCAAACGCTGCATCTATACCCCCACCGAAGGCTTCCTCGAAGAAGCCGGTTGCCCGGAGTGCCGGCGCGAGGTAG  >  NC_002947/1174944‑1175241

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.