New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	3290190 =	47 (0.780)	5 (0.090)	3/254	NT	10.3%	coding (1222/1752 nt)	PP_2892	hypothetical protein
	?	NC_002947	3290226 =	42 (0.730)					coding (1258/1752 nt)	PP_2892	hypothetical protein

TGATTTCGCTCAAGTACCAACGCGAAGAATATCGCCTGGGTGACGACTCCGGTTTGAGCAACCTGCTGATGCCGGGCGTCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTTCTCGGACGCGTACAGTTTGGTGGCAGTGCAACCAATGGCTTCAAGAA  >  NC_002947/3290080‑3290371                                                                                                                                                   |                                                                                                                                                  gggcgtccgagaaagcggtggttgtggccgagtgtggtcaggcctttgagcaatacgttgccgtgcagcaggttggtgtcggacaccagcccttccttggcaccttgaacATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGtt                                                                                                                                                 >  4:176493‑M1/111‑149 (MQ=255)    tttCGCTCAAGTACCAACGCGAAGAATATCGCCTGGGTGACGACTCCGGTTTGAGCAACCTGCTGATGCCGGGCGTCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCaa                                                                                                                                              <  6:296284/149‑1 (MQ=255)    tttCGCTCAAGTACCAACGCGAAGAATATCGCCTGGGTGACGACTCCGGTTTGAGCAACCTGCTGATGCCGGGCGTCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCaa                                                                                                                                              <  6:304323/149‑1 (MQ=255)     ttCGCTCAAGTACCAACGCGAAGAATATCGCCTGGGTGACGACTCCGGTTTGAGCAACCTGCTGATGCCGGGCGTCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAg                                                                                                                                             >  6:141153/1‑149 (MQ=255)      tccgagaaagcggtggttgtggccgagtgtggtcaggcctttgagcaatacgttgccgtgcagcaggttggtgtcggacaccagcccttccttggcaccttgaacATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAgg                                                                                                                                            >  4:255347‑M1/106‑149 (MQ=255)      tccgagaaagcggtggttgtggccgagtgtggtcaggcctttgagcaatacgttgccgtgcagcaggttggtgtcggacaccagcccttccttggcaccttgaacATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAgg                                                                                                                                            >  8:316184‑M1/106‑149 (MQ=255)                  cAACGCGAAGAATATCGCCTGGGTGACGACTCCGGTTTGAGCAACCTGCTGATGCCGGGCGTCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCaaggaagg                                                                                                                                >  7:262866/1‑149 (MQ=255)                    aCGCGAAGAATATCGCCTGGGTGACGACTCCGGTTTGAGCAACCTGCTGATGCCGGGCGTCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGc                                                                                                                              <  8:205602/149‑1 (MQ=255)                      gcgAAGAATATCGCCTGGGTGACGACTCCGGTTTGAGCAACCTGCTGATGCCGGGCGTCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTg                                                                                                                            <  4:137796/149‑1 (MQ=255)                        gaagaaTATCGCCTGGGTGACGACTCCGGTTTGAGCAACCTGCTGATGCCGGGCGTCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGgt                                                                                                                          >  4:353760/1‑149 (MQ=255)                        gaagaaTATCGCCTGGGTGACGACTCCGGTTTGAGCAACCTGCTGATGCCGGGCGTCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGgt                                                                                                                          >  6:199346/1‑149 (MQ=255)                         aagaaTATCGCCTGGGTGACGACTCCGGTTTGAGCAACCTGCTGATGCCGGGCGTCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGgtg                                                                                                                         >  1:337172/1‑149 (MQ=255)                          agaaTATCGCCTGGGTGACGACTCCGGTTTGAGCAACCTGCTGATGCCGGGCGTCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGgtgt                                                                                                                        <  6:140596/149‑1 (MQ=255)                           gaaTATCGCCTGGGTGACGACTCCGGTTTGAGCAACCTGCTGATGCCGGGCGTCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTc                                                                                                                       <  8:262866/149‑1 (MQ=255)                              tatCGCCTGGGTGACGACTCCGGTTTGAGCAACCTGCTGATGCCGGGCGTCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGa                                                                                                                    >  4:79846/1‑149 (MQ=255)                                     tGGGTGACGACTCCGGTTTGAGCAACCTGCTGATGCCGGGCGTCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAAc                                                                                                             >  5:127926/1‑149 (MQ=255)                                      tcaggcctttgagcaatacgttgccgtgcagcaggttggtgtcggacaccagcccttccttggcaccttgaacATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAgg                                                                                                                                            >  2:180231‑M1/74‑117 (MQ=255)                                      tcaggcctttgagcaatacgttgccgtgcagcaggttggtgtcggacaccagcccttccttggcaccttgaacATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAgg                                                                                                                                            <  1:180231‑M1/44‑1 (MQ=255)                                             gacTCCGGTTTGAGCAACCTGCTGATGCCGGGCGTCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCa                                                                                                     >  6:301768/1‑149 (MQ=255)                                                           cAACCTGCTGATGCCGGGCGTCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGc                                                                                       <  5:301768/149‑1 (MQ=255)                                                            aaCCTGCTGATGCCGGGCGTCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCt                                                                                      <  6:127926/149‑1 (MQ=255)                                                            aaCCTGCTGATGCCGGGCGTCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCt                                                                                      >  1:55728/1‑149 (MQ=255)                                                                   tgATGCCGGGCTTCAGCTTTTCCTTCCTGCGCAGTTACAACCGTATCGATCCGCACAACGGCTATCGCCGGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGc                                                                               <  8:332367/149‑1 (MQ=255)                                                                   tgATGCCGGGCGTCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGc                                                                               >  5:220549/1‑149 (MQ=255)                                                                     aTGCCGGGCGTCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGc                                                                               <  3:353760/147‑1 (MQ=255)                                                                               tCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTc                                                                   >  7:223276/1‑149 (MQ=255)                                                                                    ttttCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCca                                                              >  5:175986/1‑149 (MQ=255)                                                                                        ccttcctGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGCCACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGAACCCACTCGGCCCCAac                                                          >  6:378937/1‑149 (MQ=255)                                                                                            cctGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGAc                                                                          >  6:73410/1‑129 (MQ=255)                                                                                            cctGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGAc                                                                          <  5:73410/129‑1 (MQ=255)                                                                                              tGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCTAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGAc                                                                          <  5:160777/127‑1 (MQ=255)                                                                                              tGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCTAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGAc                                                                          >  6:160777/1‑127 (MQ=255)                                                                                                 gcAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCt                                                                                                                             >  1:96337/1‑73 (MQ=255)                                                                                                 gcAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCt                                                                                                                             <  2:96337/73‑1 (MQ=255)                                                                                                    gTGACAACCGTATCGATCCGCACAACGTCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCAGACTCGGCCACAACCACTGCTTtctc                                              <  2:337172/149‑1 (MQ=255)                                                                                                    gTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTtctc                                              <  5:199346/149‑1 (MQ=255)                                                                                                    gTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTtctc                                              <  2:231113/149‑1 (MQ=255)                                                                                                     tGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTTCTCg                                             <  5:141153/149‑1 (MQ=255)                                                                                                       ccttgaacatcgaactgcaggcgatagccgttgtgcggatcgatGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGa                                                                           <  1:180231‑M2/73‑1 (MQ=255)                                                                                                       ccttgaacatcgaactgcaggcgatagccgttgtgcggatcgatGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGa                                                                           >  2:180231‑M2/45‑117 (MQ=255)                                                                                                       ccttgaacatcgaactgcaggcgatagccgttgtgcggatcgatGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTTCTCGGa                                           >  4:255347‑M2/45‑149 (MQ=255)                                                                                                       ccttgaacatcgaactgcaggcgatagccgttgtgcggatcgatGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTTCTCGGa                                           >  8:316184‑M2/45‑149 (MQ=255)                                                                                                         aaCCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTGTCTCGGCcg                                         >  4:281452/1‑149 (MQ=255)                                                                                                           ccGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTTCTCGGAcgcg                                       >  2:232517/1‑149 (MQ=255)                                                                                                            aacatcgaactgcaggcgatagccgttgtgcggatcgatGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTTCTCGgacgccc                                      >  4:176493‑M2/40‑147 (MQ=255)                                                                                                              tATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTGGGCCACAACCACCGCTTTCTCGGACGCGTAc                                    <  1:232517/149‑1 (MQ=255)                                                                                                               ATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGATCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTTCTCGGACGCGTa                                     <  7:170626‑M1/147‑1 (MQ=255)                                                                                                                   ATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACCCTCGGCCACAACCACCGCTTTCTCGGACGCGTACAGttt                               <  7:318977‑M1/149‑1 (MQ=255)                                                                                                                       gCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTTCTCGGACGCGTACAGTTtggtg                           >  4:150714/1‑149 (MQ=255)                                                                                                                        cacaACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTTCTCGGACGCGTACAGTTtggtgg                          <  6:175986/149‑1 (MQ=255)                                                                                                                           aaCGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTTCTCGGACGCGTACAGTTTGGTGGCAg                       >  7:188044/1‑149 (MQ=255)                                                                                                                               gCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTTCTCGGACGCGTACAGTTTGGTGGCAGTGc                    >  3:195988/1‑148 (MQ=255)                                                                                                                                      ccTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTTCTCGGACGCGTACAGTTTGGTGGCAGTGCAACCAATg            >  6:70328/1‑149 (MQ=255)                                                                                                                                       cTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTTCTCGGACGCGTACAGTTTGGTTGCACTGCCACCaaact           <  3:79846/149‑4 (MQ=255)                                                                                                                                         gCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTTCTCGGACGCGTACAGTTTGGTGGCAGTGCAACCAATGGCt         >  3:206963/1‑149 (MQ=255)                                                                                                                                         gCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTTCTCGGACGCGTACAGTTTGGTGGCAGTGCAACCAATGGCt         >  1:169202/1‑149 (MQ=255)                                                                                                                                                gatGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTTCTCGGACGCGTACAGTTTGGTGGCAGTGCAACCAATGGCTTCAAGaa  <  2:55728‑M2/146‑1 (MQ=255)                                                                                                                                                gatGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTTCTCGGACGCGTACAGTTTGGTGGCAGTGCAACCAATGGCTTCAAGaa  <  7:316184‑M2/146‑1 (MQ=255)                                                                                                                                                gatGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTTCTCGGACGCGTACAGTTTGGTGGCAGTGCAACCAATGGCTTCAAGaa  <  3:255347‑M2/146‑1 (MQ=255)                                                                                                                                                 atGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTTCTCGGACGCGTACAGTTTGGTGGCAGTGCAACCAATGGCTTCAAGaa  >  3:284176‑M2/3‑148 (MQ=255)                                                                                                                                                   |                                                                                                                                                  TGATTTCGCTCAAGTACCAACGCGAAGAATATCGCCTGGGTGACGACTCCGGTTTGAGCAACCTGCTGATGCCGGGCGTCAGCTTTTCCTTCCTGCGCAGTGACAACCGTATCGATCCGCACAACGGCTATCGCCTGCAGTTCGATGTTCAAGGTGCCAAGGAAGGGCTGGTGTCCGACACCAACCTGCTGCACGGCAACGTATTGCTCAAAGGCCTGACCACACTCGGCCACAACCACCGCTTTCTCGGACGCGTACAGTTTGGTGGCAGTGCAACCAATGGCTTCAAGAA  >  NC_002947/3290080‑3290371

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.