New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 4727775	41 (1.290)	8 (0.270)	7/236	NT	16.5%	intergenic (‑348/+56)	brnQ/sucD	branched‑chain amino acid transporter/succinyl‑CoA synthetase subunit alpha
	?	NC_002947	= 4727812	42 (1.390)					intergenic (‑385/+19)	brnQ/sucD	branched‑chain amino acid transporter/succinyl‑CoA synthetase subunit alpha

CGGATTGAAACATTCGTCTGCGTGAAAATTCCTATCAAACCTATCGAAGAATCTCTATTGCCAGCACCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGTCAGCCAGGGAACGCACGGTTTTCACACCCGCGTCCTGCAGGGCGGCGAACTTCTCGTCCGCAGTGCCCTTGCCGCCGGA  >  NC_002947/4727670‑4727959                                                                                                                                                |                                                                                                                                                    cGGATTGAAACATTCGTCTGCGTGAAAATTCCTATCAAACCTATCGAAGAATCTCTATTGCCAGCACCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTggggg                                                                                                                                              <  1:659700/150‑1 (MQ=255) cGGATTGAAACATTCGTCTGCGTGAAAATTCCTATCAAACCTATCGAAGAATCTCTATTGCCAGCACCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTggggg                                                                                                                                              >  1:414469/1‑150 (MQ=255)      tGAAACATTCGTCTGCGTGAAAATTCCTATCAAACCTATCGAAGAATCTCTATTGCCAGCACCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTa                                                                                                                                         <  1:9608/150‑1 (MQ=255)        aaaCATTCGTCTGCGTGAAAATTCCTATCAAACCTATCGAAGAATCTCTATTGCCAGCACCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGc                                                                                                                                       >  1:790595/1‑150 (MQ=255)           cATTCGTCTGCGTGAAAATTCCTATCAAACCTATCGAAGAATCTCTATTGCCAGCACCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGt                                                                                                                                    <  1:356710/150‑1 (MQ=255)                 tCTGCGTGAAAATTCCTATCAAACCTATCGAAGAATCTCTATTGCCAGCACCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTAct                                                                                                                              >  1:722963/1‑150 (MQ=255)                      gTGAAAATTCCTATCAAACCTATCGAAGAATCTCTATTGCCAGCACCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTg                                                                                                                         >  1:652813/1‑150 (MQ=255)                           aaTTCCTATCAAACCTATCGAAGAATCTCTATTGCCAGCACCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTc                                                                                                                    >  2:52567/1‑150 (MQ=255)                            aTTCCTATCAAACCTATCGAAGAATCTCTATTGCCAGCACCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCa                                                                                                                                      <  1:113089/131‑1 (MQ=255)                            aTTCCTATCAAACCTATCGAAGAATCTCTATTGCCAGCACCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCa                                                                                                                                      >  2:113089/1‑131 (MQ=255)                            aTTCCTATCAAACCTATCGAAGAATCTCTATTGCCAGCACCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTcc                                                                                                                   <  2:461870/150‑1 (MQ=255)                             ttCCTATCAAACCTATCGAAGAATCTCTATTGCCAGCACCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTccc                                                                                                                  >  1:529838/1‑150 (MQ=255)                              tCCTATCAAACCTATCGAAGAATCTCTATTGCCAGCACCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCcca                                                                                                                 <  2:790595/150‑1 (MQ=255)                                cTATCAAACCTATCGAAGAATCTCTATTGCCAGCACCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCccagc                                                                                                               <  2:414469/150‑1 (MQ=255)                                     aaaCCTATCGAAGAATCTCTATTGCCAGCACCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTc                                                                                                          >  2:551435/1‑150 (MQ=255)                                                   aTCTCTATTGCCAGCACCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCa                                                                                                         >  1:323336/1‑137 (MQ=255)                                                   aTCGCTATTGCCAGCACCGGCCTCTTCGCGGGTAAACCCGCTCTTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCa                                                                                                         <  2:323336/137‑1 (MQ=255)                                                          ttGCCAGCACCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCg                                                                                     >  1:86578/1‑150 (MQ=255)                                                                gCACCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGTCa                                                                               <  1:67248/150‑1 (MQ=255)                                                                      gCCTCTTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGTCAGCCAgg                                                                         >  2:296027/1‑150 (MQ=255)                                                                         tctTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTTGCACGTGGCTTCCCAGACAGTCAGCTCGGCCAGGGCCTTGCCGATGTCAGCCAGGGaa                                                                      >  1:225940/1‑150 (MQ=255)                                                                           ttCGCGGGTAAACACGCTCGTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGTCAGCCAGGGAACg                                                                    >  1:246910/1‑150 (MQ=255)                                                                           ggagcgGGTTTACCCGCCCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGTCAGCCAGGGAACg                                                                    >  2:333061/4‑150 (MQ=255)                                                                              gcgGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGTCAGCCAGGGAACGCAc                                                                 >  1:442497/1‑150 (MQ=255)                                                                               cgGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGTCAGCCAGGGAACGCACg                                                                <  1:551435/150‑1 (MQ=255)                                                                                gggTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGTCAGCCCGGGAACGCACgg                                                               <  2:652813/150‑1 (MQ=255)                                                                                     aaCCCGCTCCTACGAACCCCACATACGACAAAGGCGACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCGGATGTCAGCCAGGGAACGCACGGtttta                                                          >  1:135055/1‑149 (MQ=255)                                                                                      aCCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGAt                                                                                   <  1:394504/124‑1 (MQ=255)                                                                                      aCCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGAt                                                                                   >  2:394504/1‑124 (MQ=255)                                                                                          gCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGTCAGCCAGGGAACGCACGGTTTTCACAcc                                                     >  2:772497/1‑150 (MQ=255)                                                                                           cTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGTCAGCCAGGGAACGCACGGTTTTCACAccc                                                    <  2:720914/150‑1 (MQ=255)                                                                                             ccTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGTCAGCCAGGGAACGCACGGTTTTCACACCcgc                                                  <  1:372236/150‑1 (MQ=255)                                                                                                  gAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCgtggggttcgtaggagcgggtttacccgcgaagaggccggtgctggcaatagagattcttcgataggtttgataggaattttcacgcagacgaatgtttcaatc                                             <  2:575769‑M2/150‑105 (MQ=255)                                                                                                  gAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCgtggggggttcgtaggagcgggtttacccgcgaagaggccggtgctggcaatagagattcttcgataggtttgataggaattttcacgcagacgaatgtttcaa                                             <  2:56520‑M2/150‑105 (MQ=255)                                                                                                   aaCCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCgtggggttcgtaggagcgggtttacccgcgaagaggccggtgctggcaatagagattcttcgataggtttgataggactttttacgcagacgaatg                                                     >  2:527637‑M2/1‑45 (MQ=255)                                                                                                   aaCCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCgtggggttcgtaggagcgggtttacccgcgaagaggccggtgctggcaatagagattcttcgataggtttgataggaattttcacgcagacgaatg                                                     <  1:527637‑M2/141‑97 (MQ=255)                                                                                                     ccccACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCgtggggttcgtaggagcgggtttacccgcgaagaggccggtgctggcaatagagattcttgtgtatgtttgataggaattttcacgcagacgaatgtttcaatccga                                          >  1:575769‑M2/1‑43 (MQ=255)                                                                                                      cccACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGTCAGCCAGGGAACGCACGGTTTTCACACCCGCGTCCTGCAg                                         >  1:51672/1‑150 (MQ=255)                                                                                                         acaTACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGTCAGCCAGGGAACGCACGGTTTTCACACCCGCGTCCTGCAGggc                                      <  2:529838/150‑1 (MQ=255)                                                                                                           aTACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGt                                                                                 >  1:64885/1‑105 (MQ=255)                                                                                                           aTACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGt                                                                                 <  2:64885/105‑1 (MQ=255)                                                                                                           aTACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGTCAGCCAGGGAACGCACGGTTTTCACACCCGCGTCCTGCAGggcgg                                    >  1:673469/1‑150 (MQ=255)                                                                                                             aCGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCgtggggggttcgtaggagcgggtttacccgcgaagaggccggtgctggcaatagagattcttcgataggtttgataggaattttcacgcagacgaatgtttcaatccgaggataa                                  >  1:56520‑M2/1‑35 (MQ=255)                                                                                                               gACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGACTTGCCAGTGTCAACCAGGGAACGCACGGTTTTCACACCCGCGTCCTGCAGGGCGGCGaa                                >  1:616901/1‑150 (MQ=255)                                                                                                                aCAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCccagcca                                                                                                             >  2:749327/1‑72 (MQ=255)                                                                                                                aCAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCccagcca                                                                                                             <  1:749327/72‑1 (MQ=255)                                                                                                                 cAAAGGCCACCCGAAGGTGGCCTCTGTCGTATgtggggttcgtaggagcgggtttacccgcgaagaggccggtgctggcaatagagattcttcgataggtttgataggaattttcacgcagacgaatgtttcaatc                                             <  2:716000‑M2/136‑105 (MQ=255)                                                                                                                 cAAAGGCCACCCGAAGGTGGCCTCTGTCGTATgtggggttcgtaggagcgggtttacccgcgaagaggccggtgctggcaatagagattcttcgataggtttgataggaattttcacgcagacgaatgtttcaatc                                             >  1:716000‑M2/1‑32 (MQ=255)                                                                                                                  aaaGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGTCAGCCAGGGAACGCACGGTTTTCACACCCGCGTCCTGCAGGGCGGCGAACtt                             >  2:680094/1‑150 (MQ=255)                                                                                                                             gAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGTCAGCCAGGGAACGCACGGTTTTCACACCCGCGTCCTGCAGGGCGGCGAACTTCTCGTCCGCAg                  <  1:772497/150‑1 (MQ=255)                                                                                                                                 gTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGTCAGCCAGGGAACGCACGGTTTTCACACCCGCGTCCTGCAGGGCGGCGAACTTCTCGTCCGCAGTGcc              <  2:442497/150‑1 (MQ=255)                                                                                                                                  tGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGTCAGCCAGGGAACGCACGGTTTTCACACCCGCGTCCTGCAGGGCGGCGAACTTCTCGTCCGCAGTGccc             <  2:722963/150‑1 (MQ=255)                                                                                                                                              cgcgTGGGGGGTGTAGTCGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGTCACGCCGGGCACGCACGGTTTTCACACCCTCGTCCTGCAGGGCAGCGAACTTCTCGTCCGCGGTGCCCTTGCCGCCGga  >  2:72237/1‑150 (MQ=255)                                                                                                                                              cgcgTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGTCAGCCAGGGAACGCACGGTTTTCACACCCGCGTCCTGCAGGGCGGCGAACTTCTCGTCCGCAGTGCCCTTGCCGCCGga  <  2:86578/150‑1 (MQ=255)                                                                                                                                                |                                                                                                                                                    CGGATTGAAACATTCGTCTGCGTGAAAATTCCTATCAAACCTATCGAAGAATCTCTATTGCCAGCACCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAACCCCACATACGACAAAGGCCACCCGAAGGTGGCCTCTGT‑GCGCGTGGGGGGTGTAGCAGTATTACTTCTTGGCTTCCCAGCCAGTCAGCTCGGCCAGGGCCTTGCCGATGTCAGCCAGGGAACGCACGGTTTTCACACCCGCGTCCTGCAGGGCGGCGAACTTCTCGTCCGCAGTGCCCTTGCCGCCGGA  >  NC_002947/4727670‑4727959

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.