New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 5965485	49 (0.930)	3 (0.060)	3/244	NT	6.3%	coding (679/696 nt)	had	(S)‑2‑haloacid dehalogenase
	?	NC_002947	= 5965530	42 (0.830)					intergenic (+28/+72)	had/PP_5232	(S)‑2‑haloacid dehalogenase/hypothetical protein

CGCCGGTTTGCGCGCGGTGTGGTTCAACCCGCAGGGCAAGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTGCCGTACTTGTTGTCTGGCTTCTTGGGCGGGTCAGCGACCACGTTGGCCTCGACTTCCTGC  >  NC_002947/5965382‑5965677                                                                                                                                                      |                                                                                                                                                    cgcCGGTTTGCGCGCGGTGTGGTTCAACCCGCAGGGCAAGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGcgg                                                                                                                                                     <  7:125691/149‑1 (MQ=255)    cGGTTTGCGCGCGGTGTGGTTCAACCCGCAGGGCAAGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGgca                                                                                                                                                  <  2:148293‑M2/149‑4 (MQ=255)      gTTTGCGCGCGGTGTGGTTCAACCCGCAGGGCAAGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGTCGCGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGgcacg                                                                                                                                                >  7:167370‑M2/1‑144 (MQ=255)      gTTTGCGCGCGGTGTGGTTCAACCCGCAGGGCAAGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGgcacg                                                                                                                                                >  1:156160‑M2/1‑144 (MQ=255)       tttGCGCGCGGTGTGGTTCAACCCGCAGGGCAAGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGcgggcacgg                                                                                                                                               <  7:173063/149‑1 (MQ=255)                  tgtgGTTCAACCCGCAGGGCAAGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACaaaa                                                                                                                                    <  6:196271/149‑1 (MQ=255)                    tgGTTCAACCCGCAGGGCAAGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAAcc                                                                                                                                  >  4:15298/1‑149 (MQ=255)                      gTTCAACCCGCAGGGCAAGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGcgggcacgggc                                                                                                                                             <  4:40893/136‑1 (MQ=255)                      gTTCAACCCGCAGGGCAAGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGcgggcacgggc                                                                                                                                             >  3:40893/1‑136 (MQ=255)                      gTTCAACCCGCAGGGCAAGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCca                                                                                                                                <  8:67424/149‑1 (MQ=255)                       ttCAACCCGCAGGGCAAGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCAAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCca                                                                                                                                >  5:323091/1‑148 (MQ=255)                        acaccgcGCAGGGCAAGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAAc                                                                                                                                   >  2:304158/7‑144 (MQ=255)                          aaCCCGCAGGGCAAGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAg                                                                                                                             <  3:15298/148‑1 (MQ=255)                          aaCCCGCAGGGCAAGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAg                                                                                                                             <  8:32322/148‑1 (MQ=255)                          aaCCCGCAGGGCAAGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCAAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAgg                                                                                                                            <  6:323091/149‑1 (MQ=255)                             ccGCAGGGCAAGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAg                                                                                                                             <  7:19922/145‑1 (MQ=255)                             ccGCAGGGCAAGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAg                                                                                                                             >  8:19922/1‑145 (MQ=255)                               gCAGGGCAAGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAGACGCGTGTCGAGCCTGCCGGCCTTGATCCCGCGCTGGGGATGCCGGGAGCCGGTTTGCGGCCCATTCGCGGGCCCGGGCACCACAAAACCCCCAGGctt                                                                                                                         >  1:82821/1‑146 (MQ=255)                               gCAGGGCAAGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATaa                                                                                                                       <  7:260377/149‑1 (MQ=255)                                      aaGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGcc                                                                                                                <  3:326822/149‑1 (MQ=255)                                         gCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAgg                                                                                                                            >  2:270339/1‑134 (MQ=255)                                         gCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAgg                                                                                                                            <  1:270339/134‑1 (MQ=255)                                           cTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAg                                                                                                           >  8:279456/1‑149 (MQ=255)                                                   gCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGAcggcg                                                                                                   >  6:349969/1‑149 (MQ=255)                                                      aTCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGc                                                                                                >  3:326845/1‑149 (MQ=255)                                                               cGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCg                                                                                       <  4:326845/149‑1 (MQ=255)                                                                  aTGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGAt                                                                                     >  2:21684/1‑148 (MQ=255)                                                                             cAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACATAACCCACAGGCATATATAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCAGTCAgg                                                                         >  7:126496/1‑148 (MQ=255)                                                                               g‑cgcCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGa                                                                         >  3:295126/1‑147 (MQ=255)                                                                                         gCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTg                                                              >  7:157458/1‑149 (MQ=255)                                                                                           aGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTGcc                                                            <  6:351855/149‑1 (MQ=255)                                                                                                 ccGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGgcacgtcgggcagctgcgacaggcgctggatttcggcatccggcgcctgatcgccagtccaggccttgccctgcgggttgaaccacaccgcgcg                                                       <  4:115064‑M2/148‑95 (MQ=255)                                                                                                  cGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTGCCGTACttg                                                     <  4:295126/149‑1 (MQ=255)                                                                                                   gACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGgcacgtcgggcagctgcgacaggcgctggatttcggcatccggcgcctgatcgccagtccaggccttgccctgcgggttgaa                                                                   >  3:162511‑M2/1‑52 (MQ=255)                                                                                                   gACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGgcacgtcgggcagctgcgacaggcgctggatttcggcatccggcgcctgatcgccagtccaggccttgccctgcgggttgaa                                                                   <  4:162511‑M2/134‑83 (MQ=255)                                                                                                      gTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTGcc                                                            <  2:155866/138‑1 (MQ=255)                                                                                                      gTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTGcc                                                            >  1:155866/1‑138 (MQ=255)                                                                                                         cTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTGCCGTACTTGTTGTCTg                                              <  5:349969/149‑1 (MQ=255)                                                                                                          tCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTGCCGTACTTGTTGTc                                                >  3:235785/1‑146 (MQ=255)                                                                                                          tCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTGCCGTACTTGTTGTc                                                <  4:235785/146‑1 (MQ=255)                                                                                                                    gcgctgACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTGCCGTACTTGTTGTCTGGCTTCTTgg                                     <  8:157458/147‑1 (MQ=255)                                                                                                                      gctgACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTGCCGTACTTGTTGTCTGGCTTCTTGGGCgg                                 <  2:82821/149‑1 (MQ=255)                                                                                                                      gctgACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTGCCGTACTTGTTGTCTGGCTTCTTGGGCgg                                 >  4:179683/1‑149 (MQ=255)                                                                                                                          aCGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTGCCGTACTTGTTGTCTGGCTTCTTGGGCGGGt                               <  1:21684/147‑1 (MQ=255)                                                                                                                          aCGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTGCCGTACTTGTTGTCTGGCTTCTTGGGCGGGTCa                             <  7:279456/149‑1 (MQ=255)                                                                                                                            gggAGCCGCTTTGCGGCCCATTCGCGGGCTCGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTg                                                              >  7:90209/1‑114 (MQ=255)                                                                                                                            gggAGCCGCTTTGCGGCCCATTCGCGGGCTCGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTg                                                              <  8:90209/114‑1 (MQ=255)                                                                                                                                 ccGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCATAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTGCCGTACTTGTTGTCTGGCTTCTTGGGc                                   <  8:334844/136‑1 (MQ=255)                                                                                                                                 ccGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCAGAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTGCCGTACTTGTTGTCTGGCTTCTTGGGc                                   >  7:334844/1‑136 (MQ=255)                                                                                                                                 ccGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTGCCGTACTTGTTGTCTGGCTTCTTGGGCGGGTCAGCGACCa                      >  8:128992/1‑149 (MQ=255)                                                                                                                                           gCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTGCCGTACTTGTTGTCTGGCTTCTTGGGCGGGTCAGCGACCACGTTGGCCTc            <  6:361395/149‑1 (MQ=255)                                                                                                                                           gCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTGCCGTACTTGTTGTCTGGCTTCTTGGGCGGGTCAGCGACCACGTTGGCCTc            >  5:361395/1‑149 (MQ=255)                                                                                                                                                     gggcacgtcgggcagctgcgacaggcgctggatttcggcatccggcgcctgatcgccagtccaggccttgccctgcgggttgaaccacaccgcgcgcaaaccggcgcgctgggcaccggcaatgtcatcgccagggtgatcgccgatgt  >  3:115064‑M2/1‑2 (MQ=255)                                                                                                                                                      |                                                                                                                                                    CGCCGGTTTGCGCGCGGTGTGGTTCAACCCGCAGGGCAAGGCCTGGACTGGCGATCAGGCGCCGGATGCCGAAATCCAG‑CGCCTGTCGCAGCTGCCCGACGTGCTCGCGCGCTGGCGCTGACGGGAGCCGCTTTGCGGCCCATTCGCGGGCACGGGCAACACAAAACCCACAGGCATAAAAAAGCCCGCAGCGACGGCGGGCTTTTTTGCGATCAGCCACTCAGATAGGGCGGCTGCCGTACTTGTTGTCTGGCTTCTTGGGCGGGTCAGCGACCACGTTGGCCTCGACTTCCTGC  >  NC_002947/5965382‑5965677

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.