New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 5238639	53 (1.070)	4 (0.080)	4/250	NT	7.4%	coding (151/204 nt)	PP_5701	hypothetical protein
	?	NC_002947	= 5238748	48 (1.000)					intergenic (+56/‑225)	PP_5701/PP_4616	hypothetical protein/hypothetical protein

CCAGGAACTTCGCACTAAGGCTGGTTAACGTGCCGGAAGGGCCGGCCTCTTCGCGGGCTCGCCCGCTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGTTTCGGGCAAATGGTTCCTGGCAAAGGCGCTCCCGCAGCGCTCGGTCTGTGCCACGCTACAATTTCTGCTTGCGAA  >  NC_002947/5238604‑5238896                                                                                                                                                 |                                                                                                                                                       ccAGGAACTTCGCACTAAGGCTGGTTAACGTGCCGGAAGGGCCGGCCTCTTCGCGGGCTCGCCCCCACCCCCAGCGGTCACCACAGTAGTCAAGACTTGCACACTACCATTGGGAGCGGGCGTGCCCGCGAAACGGCCCGACCTGCCGa                                                                                                                                                    >  8:108632/1‑149 (MQ=38)  cAGGAACTTCGCACTAAGGCTGGTTAACGTGCCGGAAGGGCCGGCCTCTTCGCGGGCTCGCCCCCTCCCACAGCCGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCCAAAGGGCCCGCCCTGCCGa                                                                                                                                                    >  3:150416/1‑148 (MQ=38)           cGCACTAAGGCTGGTTAACGTGCCGGAAGGGCCGGCCTCTTCGCGGGCTCGCCCGCTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATcc                                                                                                                                           <  2:108801/148‑1 (MQ=255)             cACTAAGGCGGGTTACCGGGCCGCCTGGCCGGGCCTCTTCGCGGGCTCCCCGGCGCCCACCGCGGTCACCACAGATCCCAACACTTGCACATTCCCGGTGGGTGCGGGCGAGCCCGCTAAAGGGCCGGACCTGCCGACAAATATCCCCg                                                                                                                                        <  4:150416/149‑1 (MQ=255)                    gCTGGTTAACGTGCCGGAAGGGCCGGCCTCTTCGCGGGCTCGCCCGCTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGGGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGc                                                                                                                                 <  6:270993/149‑1 (MQ=255)                     cTGGTTAACGTGCCGGAAGGGCCGGCCTCTTCGCGGGCTCGCCCGCTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCa                                                                                                                                <  4:127499/149‑1 (MQ=255)                     cTGGTTAACGTGCCGGAAGGGCCGGCCTCTTCGCGGGCTCGCCCGCTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCa                                                                                                                                <  6:232958/149‑1 (MQ=255)                      tGGTTAACGTGCCGGAAGGGCCGGCCTCTTCGCGGGCTCGCCCGCTCCCGCAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCAc                                                                                                                               >  1:84865/1‑149 (MQ=255)                           aaCGTGCCGGAAGGGCCGGCCTCTTCGCGGGCTCGCCCGCTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCGGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCg                                                                                                                          >  5:169404/1‑149 (MQ=255)                             cGTGCCGGAAGGGCCGGCCTCTTCGCGGGCTCGCCCGCTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCa                                                                                                                        <  7:108632/149‑1 (MQ=255)                                gCCGGAAGGGCCGGCCTCTTCGCGGGCTCGCCCGCTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAgcc                                                                                                                     >  1:104491/1‑149 (MQ=255)                                           cggccTCTTCGCGGGCTCGCCCGCTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCAtt                                                                                                        >  7:61845/1‑149 (MQ=255)                                              ccTCTTCGCGGGCTCGCCCGCTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCAt                                                                                                                                   <  5:170089/121‑1 (MQ=255)                                              ccTCTTCGCGGGCTCGCCCGCTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCAt                                                                                                                                   >  6:170089/1‑121 (MQ=255)                                               ctctTCGCGGGCTCGCCCGCTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTcgcg                                                                                                    <  2:104491/149‑1 (MQ=255)                                                tctTCGCGGGCTCGCCCGCTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGCCCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCgg                                                                                                   >  6:167430/1‑149 (MQ=255)                                                tctTCGCGGGCTCGCCCGCTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCAccc                                                                                                            <  7:20625/140‑1 (MQ=255)                                                tctTCGCGGGCTCGCCCGCTCCCACACCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCAccc                                                                                                            >  8:20625/1‑140 (MQ=255)                                                  ttCGCGGGCTCGCCCGCTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCGGCC‑‑GCCACCCCATTCGCggg                                                                                                  >  2:101649/1‑148 (MQ=255)                                                           tCGCCCGCTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCtgtg                                                                                        >  5:165475/1‑149 (MQ=255)                                                             gCCCGCTCCCCCAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGc                                                                                       <  2:84865/148‑1 (MQ=255)                                                             gCCCGCTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCGGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCtgtg                                                                                        <  6:169404/147‑1 (MQ=255)                                                             gCCCGCTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGcc                                                                                      >  3:21064/1‑149 (MQ=255)                                                               ccGCTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGccggcacgttaaccagccttagtgcgaagttcctgggctcagcggacat                                                                                                       <  3:255233‑M2/132‑50 (MQ=255)                                                               ccGCTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGccggcacgttaaccagccttagtgcgaagttcctgggctcagcggacat                                                                                                       >  4:255233‑M2/1‑83 (MQ=255)                                                                  cTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACaa                                                                                 <  7:270193/149‑1 (MQ=255)                                                                     ccACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACt                                                                               <  5:167430/148‑1 (MQ=255)                                                                     ccACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTg                                                                              >  6:210193/1‑149 (MQ=255)                                                                      cacaGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGccggcacgttaaccagccttagtgcgaagttcctgggctcagcggacatctgcacctgaaccagcgccgact                                                                                <  3:119379‑M2/148‑73 (MQ=255)                                                                      cacaGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGt                                                                             <  5:210193/149‑1 (MQ=255)                                                                       acaGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCAc                                                                                                              <  3:159279/115‑1 (MQ=255)                                                                       acaGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCAc                                                                                                              >  4:159279/1‑115 (MQ=255)                                                                                      gtagtCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGTTTCGGGCAAATGGTTc                                                             <  6:165475/149‑1 (MQ=255)                                                                                       tagtCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACAGTTTCGGGCAAATGGTTcc                                                            >  3:11956/1‑149 (MQ=255)                                                                                         gtCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCACCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCATACAACAGTTTCGGGCAAATGCTTACTg                                                          >  4:211898/1‑149 (MQ=38)                                                                                            aaGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGccggcacgttaaccagccttagtgcgaagttcctgggctcagcggacatctgcacctgaaccagcgccgactcaagaagaggccgcagcgcctc                                                          >  4:119379‑M2/1‑54 (MQ=255)                                                                                            aaGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGTTTCGGGCAAATGGTTCCTGGc                                                        >  5:110797/1‑148 (MQ=255)                                                                                            aaGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGTTTCGGGCAAATGGTTCCTGGc                                                        >  5:229691/1‑148 (MQ=255)                                                                                              gACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTAc                                                                                   <  6:94660/119‑1 (MQ=255)                                                                                              gACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGTTTCGGGCAAATGGTTCCTGGCa                                                       >  3:275231/1‑147 (MQ=255)                                                                                              gACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGTTTCGGGCAAATGGTTCCTGGCa                                                       >  8:69242/1‑147 (MQ=255)                                                                                                      caGTACCTGTGGGAGCGGACGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGTTTCGGGCAAATGGTTCCTGGCAAAGGCGCTcc                                             >  1:196800/1‑149 (MQ=255)                                                                                                         tACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGTTTCGGGCAAATGGTTCCTGGCAAAGGCGCTCCCGc                                          <  4:21064/149‑1 (MQ=255)                                                                                                                   aGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGTTTCGGGCAAATGGTTCCTGGCAAAGGCGCTCCCGCAGCGCTCGGt                                <  8:61845/149‑1 (MQ=255)                                                                                                                        gCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGTTTCGGGCAAATGGTTCCTGGCAAAGGCGCTCCCGCAGCGCTCGGTCtgtg                           >  4:139668/1‑149 (MQ=255)                                                                                                                        gCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGTTTCGGGCAAATGGTTCCTGGCAAAGGCGCTCCCGCAGCGCTCGGTCtgtg                           >  7:56412/1‑149 (MQ=255)                                                                                                                                gcgAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACGGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGTTTCGGGCAAATGGTTCCTGGCAAAGGCGCTCCCGCAGCGCTCGGTCTGTGCCACGCt                    >  1:60475/1‑148 (MQ=255)                                                                                                                                  gAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGTTTCGGGCAAATGGTTCCTGGCAAAGGCGCTCCCGCAGCGCTCGGTCTGTGCCACGCTAc                  >  5:156967/1‑148 (MQ=255)                                                                                                                                   aaaGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCTGGCAAGACTGTGCCTACAACTGTTTCGTGATAATGGTTCGTGCCAAAGGCGCTCCCTCAGCGCTCGGACTCTGCCAAGCTaaa                 >  2:253951/1‑146 (MQ=255)                                                                                                                                         ccGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCATCCCGGCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGTTTCGGGCAAATGGTTCCTGGCAAAGGCGCTCCCGCAGCGCTCGGTCTGTGCCACGCTACAATTTc            <  1:263837/149‑1 (MQ=255)                                                                                                                                           ggACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGTTTCGGGCAAATGGTTCCTGGCAAAGGCGCTCCCGCAGCGCTCGGTCTGTGc                          >  2:293169/1‑131 (MQ=255)                                                                                                                                           ggACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGTTTCGGGCAAATGGTTCCTGGCAAAGGCGCTCCCGCAGCGCTCGGTCTGTGc                          <  1:293169/131‑1 (MQ=255)                                                                                                                                            gACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGTTTCGGGCAAATGGTTCCTGGCAAAGGCGCTCCCGCAGCGCTCGGTCTGTGCCACGCTACAATTTCTGCtt       <  2:60475/149‑1 (MQ=255)                                                                                                                                            gACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGTTTCGGGCAAATGGTTCCTGGCAAAGGCGCTCCCGCAGCGCTCGGTCTGTGCCACGCTACAATTTCTGCtt       <  8:129923/149‑1 (MQ=255)                                                                                                                                             aCCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGTTTCGGGCAAATGGTTCCTGGCAAAGGCGCTCCCGCAGCGCTCGGTCTGTGCCACGCTACAATTTCTGCTTg      >  1:67437/1‑149 (MQ=255)                                                                                                                                             aCCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCAGTGCCTACAACTGTTTCGCGCAAATGGTTCCTGGCAAAGGCGCTCCCCCAGCGCTCGGTCTGTGCCACGCTACAATTTCTGCTTg      >  1:62948/1‑149 (MQ=255)                                                                                                                                                 gCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGTTTCGGGCAAATGGTTCCTGGCAAAGGCGCTCCCGCAGCGCTCGGTCTGTGCCACGCTACAATTTCTGCTTGCGaa  >  2:77952/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                                       CCAGGAACTTCGCACTAAGGCTGGTTAACGTGCCGGAAGGGCCGGCCTCTTCGCGGGCTCGCCCGCTCCCACAGCGGTCACCACAGTAGTCAAGACTTGCACAGTACCTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGACCTGCCGACAAATATCCCCGGCCATGCACCGTCGCAGCC‑‑GCCACCCCATTCGCGGGCAAGCCTGTGCCTACAACTGTTTCGGGCAAATGGTTCCTGGCAAAGGCGCTCCCGCAGCGCTCGGTCTGTGCCACGCTACAATTTCTGCTTGCGAA  >  NC_002947/5238604‑5238896

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ 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.