New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	5165795 =	45 (0.840)	4 (0.080)	4/254	NT	7.7%	coding (2085/3906 nt)	hrpA	ATP‑dependent helicase HrpA
	?	NC_002947	5165832 =	53 (1.020)					coding (2048/3906 nt)	hrpA	ATP‑dependent helicase HrpA

CGAGGTCGCCGGGTCGATCGGGCCGTAGTGCACCGGCCGACGGCCGACCAGGATCAGCCCGTAGAGCGTGATCTGCTCGTAGGCCACCACCTGCCCGCGCTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGCCCGAAGATGGATGCACCCAGAAGCGCCGCTGACG  >  NC_002947/5165648‑5165941                                                                                                                                                     |                                                                                                                                                   cgAGGTCGCCGGGTCGATCGGGCCGTAGTGCACCGGCCGACGGCCGACCAGGATCAGCCCGTAGAGCGTGATCTGCTCGTAGGCCACCACCTGCCCGCGCTTCTTCTCCCAGTGCGGCCTCGAAATGGTTCTTCTTGATCAGGTggccg                                                                                                                                                    <  1:35707/149‑1 (MQ=255)  tggccagaagaccgaagagggagactaccagggcgcccgtcagcggcgcttctgggtgcatccatcttcgggcctggggcgcaagcgcccgcagtgggtcatggctgccgagctggtcgaaaccaccaagctgtatgcgcgcatggtgg                                                                                                                                                   <  3:227808‑M1/2‑1 (MQ=255)   ggccagaagaccgaagagggcgactaccagggcgcccgtcagcggcgcttctgggtgcatccatcttcgggcctggggcgcaagcgcccgcagtgggtcatggctgccgagctggtcgaaaccaccaagctgtatgcgcgcatggtgg                                                                                                                                                   >  7:32441‑M1/147‑148 (MQ=255)        gaagaccgaagagggcgactaccagggcgcccgtcagcggcgcttctgggtgcatccatcttcgggcctggggcgcaagcgcccgcagtgggtcatggctgccgagctggtcgaaaccaccaagctgtatgcgcgcatggtGGcc                                                                                                                                                 <  1:202908‑M1/4‑1 (MQ=255)           gggTCGATCGGGCCGTAGTGCACCGGCCGACGGCCGACCAGGATCAGCCCGTAGAGCGTGATCTGCTCGTAGGCCACCACCTGCCCGCGCTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGcgc                                                                                                                                         <  2:276539/149‑3 (MQ=255)           gaccgaagagggcgactaccagggcgcccgtcagcggcgcttctgggtgcatccatcttcgggcctggggcgcaagcgcccgcagtgggtcatggctgccgagctggtcgaaaccaccaagctgtatgcgcgcatggtGGCCAGCGGCt                                                                                                                                          <  4:234780‑M1/11‑1 (MQ=255)             gTCGATCGGGCCGTAGTGCACCGGCCGACGGCCGACCAGGATCAGCCCGTAGAGCGTGATCTGCTCGTAGGCCACCACCTGCCCGCGCTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGa                                                                                                                                       <  4:18473/149‑1 (MQ=255)                gATCGGGCCGTAGTGCACCGGCCGACGGCCGACCAGGATCAGCCCGTAGAGCGTGATCTGCTCGTAGGCCACCACCTGCCCGCGCTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATc                                                                                                                                     <  7:139509/148‑1 (MQ=255)                               cACCGGCCGACGGCCGACCAGGATCAGCCCGTAGAGCGTGATCTGCTCGTAGGCCACCACCTGCCCGCGCTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCt                                                                                                                     >  5:204442/1‑149 (MQ=255)                                 ccGGCCGACGGCCGACCAGGATCAGCCCGTAGAGCGTGATCTGCTCGTAGGCCACCACCTGCCCGCGCTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTg                                                                                                                   >  4:23602/1‑149 (MQ=255)                                   ggccgacggccgacCAGGATCAGCCCGTAGAGCGTGATCTGCTCGTAGGCCACCACCTGCCCGCGCTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGc                                                                                                                 >  3:316333/1‑149 (MQ=255)                                           agcggcgcttctgggtgcatccatcttcgggcctggggcgcaagcgcccgcagtgggtcatggctgccgagctggtcgaaaccaccaagctgtatgcgcgcatggtGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCAt                                                                                                           >  3:234780‑M1/107‑148 (MQ=255)                                               gcgcttctgggtgcatccatcttcgggcctggggcgcaagcgcccgcagtgggtcatggctgccgagctggtcgaaaccaccaagctgtatgcgcgcatggtGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATgc                                                                                                         >  4:261562‑M1/103‑146 (MQ=255)                                               gcgcttctgggtgcatccatcttcgggcctggggcgcaagcgcccgcagtgggtcatggctgccgagctggtcgaaaccaccaagctgtatgcgcgcatggtGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATgc                                                                                                         <  3:261562‑M1/44‑1 (MQ=255)                                                    gATCAGCCCGTAGAGCGTGATCTGCTCGTAGGCCACCACCTGCCCGCGCTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATa                                                                                                  >  1:78628/1‑147 (MQ=255)                                                                gagCGTGATCTGCTCGTAGGCCACCACCTGCCCGCGCTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGttt                                                                                    <  2:237748/149‑1 (MQ=255)                                                                      gATCTGCTCGTAGGCCACCACCTGCCCGCGCTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGAc                                                                                >  8:168039/1‑147 (MQ=255)                                                                             tCGTAGGCCACCACCTGCCCGCGCTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCgg                                                                        >  3:213861/1‑148 (MQ=255)                                                                                 aGGCCACCACCTGCCCGCGCTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGc                                                                    >  1:59423/1‑148 (MQ=255)                                                                                   gCCACCACCTGCCCGCGCTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCAt                                                                 >  1:181472/1‑149 (MQ=255)                                                                                     caccacCTGCCCGCGCTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGa                                                               >  2:49116/1‑149 (MQ=255)                                                                                      accaccTGCCCGCGCTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGAc                                                              >  7:58329/1‑149 (MQ=255)                                                                                         accTGCCCGCGCTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCa                                                           <  8:58329/149‑1 (MQ=255)                                                                                          ccTGCCCGCGCTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCAc                                                          >  4:227808/1‑149 (MQ=255)                                                                                              cccGCGCTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTg                                                        <  2:59423/147‑1 (MQ=255)                                                                                                 gcgcTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGtt                                                                                     >  3:77034/1‑115 (MQ=255)                                                                                                 gcgcTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGtt                                                                                     <  4:77034/115‑1 (MQ=255)                                                                                                   gcTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGgcgc                                                 >  3:286959/1‑149 (MQ=255)                                                                                                     ttcttcTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCtt                                               >  7:186676/1‑149 (MQ=255)                                                                                                            cccAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGccc                                         >  3:261699/1‑148 (MQ=255)                                                                                                             ccAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGccc                                         >  1:211016/1‑147 (MQ=255)                                                                                                             ccAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGccc                                         >  5:301867/1‑147 (MQ=255)                                                                                                                gTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGc                                    >  4:325550/1‑149 (MQ=255)                                                                                                                 tGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGcc                                   <  2:78628/149‑1 (MQ=255)                                                                                                                     g‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGCCCGaa                               <  3:23602/149‑1 (MQ=255)                                                                                                                     g‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGCCCGaa                               <  3:98914/149‑1 (MQ=255)                                                                                                                       cTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGCCCg                                 >  4:257662/1‑146 (MQ=255)                                                                                                                        tCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGCCCg                                 >  4:228769/1‑145 (MQ=255)                                                                                                                        tCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCAAGCGcccgcagt                                    <  2:287336/142‑6 (MQ=255)                                                                                                                          gAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGCCCGAAgatg                           >  2:202908/1‑149 (MQ=255)                                                                                                                          gAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGCCCGAAga                             <  3:228769/147‑1 (MQ=255)                                                                                                                           aaaTGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGCCCGAAgatgg                          <  2:211016/149‑1 (MQ=255)                                                                                                                            aaTGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGCCCGAAgatgga                         <  6:301867/149‑1 (MQ=255)                                                                                                                                gTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGCCCGAAGATGGATGCa                     >  7:55557/1‑149 (MQ=255)                                                                                                                                  tcttctTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGCCCGAAGATGGATGCAcc                   >  4:5405/1‑149 (MQ=255)                                                                                                                                  tcttctTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGCCCGAAGATGGATGCAcc                   >  8:300668/1‑149 (MQ=255)                                                                                                                                         gATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGATCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGCCCGAAGATGGATGCACCCAGAAgc            >  3:79327/1‑149 (MQ=255)                                                                                                                                         gATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGCCCGAAGATGGATGCACCCAGaa              <  3:325550/147‑1 (MQ=255)                                                                                                                                         gATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGCCCGAAGATGGATGCACCCAGAAgc            >  2:39206/1‑149 (MQ=255)                                                                                                                                         gATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGCCCGAAGATGGATGCACCCAGAAgc            >  2:33946/1‑149 (MQ=255)                                                                                                                                             aGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGATCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGCCCGAAGATGGATGCTCCCAGAAGcgcc         <  4:79327/148‑1 (MQ=255)                                                                                                                                               gTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGc                                    <  4:27778/119‑1 (MQ=255)                                                                                                                                               gTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGc                                    >  3:27778/1‑119 (MQ=255)                                                                                                                                                   ccggccAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGCCCGAAGATGGATGCACCCAGAAGCGCCGCTGACg  <  4:316333/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                   CGAGGTCGCCGGGTCGATCGGGCCGTAGTGCACCGGCCGACGGCCGACCAGGATCAGCCCGTAGAGCGTGATCTGCTCGTAGGCCACCACCTGCCCGCGCTTCTTCTCCCAGTGCGG‑CTCGAAATGGTTCTTCTTGATCAGGTGGCCGGCCAGCGGCTCGATCCAGTCCGGCTCGATCTTGGCCACCATGCGCGCATACAGCTTGGTGGTTTCGACCAGCTCGGCAGCCATGACCCACTGCGGGCGCTTGCGCCCCAGGCCCGAAGATGGATGCACCCAGAAGCGCCGCTGACG  >  NC_002947/5165648‑5165941

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.