New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	2749540 =	39 (0.650)	4 (0.070)	4/260	NT	7.9%	intergenic (+13/+101)	PP_2405/PP_2406	hypothetical protein/quinate/shikimate dehydrogenase
	?	NC_002947	2749629 =	55 (0.940)					intergenic (+102/+12)	PP_2405/PP_2406	hypothetical protein/quinate/shikimate dehydrogenase

TGCCTGGGGCAACCAGTTCTGGCCGGCGCATTACTTTGTCGACCGCAAGGGGCAGGTGCGCCATGTGCACTTTGGCGAGGGGGATTATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCGAAGAAGCCAACACTTTTCTATCAGGTGAAACTGGCAAAGTGCGCCTGCATCCGCGCCGCATCCGCCT  >  NC_002947/2749392‑2749687                                                                                                                                                     |                                                                                                                                                          tGCCTGGGGCAACCAGTTCTGGCCGGCGCATTACTTTGTCGACCGCAAGGGGCAGGTGCGCCATGTGCACTTTGGCGAGGGGGATTATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCg                                                                                                                                                           >  4:76737/1‑149 (MQ=255)   cccgggcactgggctgccgcacgctggatggcagcaacatggcggtgttccaggcggtgaaggcattcgagctgttcagcgggcggcaggcggatgcggcgcggatgcaggcgcactttgccagtttcacctgatagaaaagtgttGGc                                                                                                                                                         >  5:348429‑M1/147‑149 (MQ=255)   ccTGTGGCAACCAGTGCTGGCCGGCGCATTACTTTGTCGACCGCCAGGGGCAGGTGCGCCATGTGCACGTTGGCGAGGGGGATTATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGTTGATGCTCCTGTACCGGc                                                                                                                                                         <  4:35753/149‑1 (MQ=255)    cTGGGGCAACCAGTTCTGGCCGGCGCATTACTTTGTCGACCGCAAGGGGCAGGTGCGCCATGTGCACTTCGGCGAGGGGGATTATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGcc                                                                                                                                                        >  6:25283/1‑149 (MQ=255)         gCAACCAGTTCTGGCCGGCGCATTACTTTGTCGACCGCAAGGGGCAGGTGCGCCATGTGCACTTTGGCGAGGGGGATTATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTc                                                                                                                                                   >  7:161985/1‑149 (MQ=255)           aaCCAGTTCTGGCCGGCGCATTACTTTGTCGACCGCAAGGGGCAGGTGCGCCATGTGCACTTTGGCGAGGGGGATTATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTcgc                                                                                                                                                 <  2:222397/149‑1 (MQ=255)           aaCCAGTTCTGGCCGGCGCATTACTTTGTCGACCGCAAGGGGCACGTGCGCCATGTGCACTTTGGCGAGGGGGATTATGGTGGCCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTcgc                                                                                                                                                 >  5:369054/1‑149 (MQ=255)            aCCAGTTCTGGCCGGCGCATTACTTTGTCGACCGCAAGGGGCAGGTGCGCCATGTGCACTTTGGCGAGGGGGATTATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTcgcg                                                                                                                                                >  1:140056/1‑149 (MQ=255)                gTTCTGGCCGGCGCATTACTTTGTCGACCGCAAGGGGCAGGTGCGCCATGTGCACTTTGGCGAGGGGGATTATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCa                                                                                                                                            <  2:140056/149‑1 (MQ=255)                     gcacgctggatggcagcaacatggcggtgttccaggcggtgaaggcattcgagctgttcagcgggcggcaggcggatgcggcgcggatgcaggcgcactttgccagtttcacctgatagaaaagtgttGGc                                                                                                                                                         <  5:280055‑M1/3‑1 (MQ=255)                     gcacgctggatggcagcaacatggcggtgttccaggcggtgaaggcattcgagctgttcagcgggcggcaggcggatgcggcgcggatgcaggcgcactttgccagtttcacctgatagaaaagtgttGGc                                                                                                                                                         >  6:280055‑M1/129‑131 (MQ=255)                      gCCGGCGCATTACTTTGTCGACCGCAAGGGGCAGGTGCGCCATGTGCACTTTGGCGAGGGGGATTATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGccc                                                                                                                                       <  3:76737/148‑1 (MQ=255)                            gcATTACTTTGTCGACCGCAAGGGGCAGGTGCGCCATGTGCACTTTGGCGAGGGGGATTATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAgg                                                                                                                            >  7:349302/1‑148 (MQ=255)                            gcATTACTTTGTCGACCGCAAGGGGCAGGTGCGCCATGTGCACTTTGGCGAGGGGGATTATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAgg                                                                                                                            >  7:62700/1‑148 (MQ=255)                                     tGTCGACCGCAAGGGGCAGGTGCGCCATGTGCACTTTGGCGAGGGGGATTATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑caca                                                                                                                              >  7:330687/1‑137 (MQ=255)                                     tGTCGACCGCAAGGGGCAGGTGCGCCATGTGCACTTTGGCGAGGGGGATTATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑caca                                                                                                                              <  8:330687/137‑1 (MQ=255)                                        cGACCGCAAGGGGCAGGTGCGCCATGTGCACTTTGGCGAGGGGGATTATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAAt                                                                                                                 >  4:184762/1‑147 (MQ=255)                                                  gtgCAGGTGCGCCATGTGCACTTTGGCGAGGGGGATTATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTg                                                                                                     <  8:161985/147‑1 (MQ=255)                                                                  tgCACTTTGGCGAGGGGGATTATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGa                                                                                     <  4:240516/149‑1 (MQ=255)                                                                     aCTTTGGCGAGGGGGATTATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCg                                                                                  >  8:9984/1‑149 (MQ=255)                                                                            cGAGGGGGATTATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGc                                                                          <  7:9984/149‑1 (MQ=255)                                                                             ttcagcgggcggcaggcggatgcggcgcggatgcaggcgcactttgccagtttcacctgatagaaaagtgttGGCTTCTTCGCGGGCACGCCCGCTCCCACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCgg                                                                                 >  1:28662‑M1/73‑147 (MQ=255)                                                                               gggggATTATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTCTGGGAGCGG‑GCGTGCCcg                                                                       >  3:85403/1‑149 (MQ=255)                                                                                agcgggcggcaggcggatgcggcgcggatgcaggcgcactttgccagtttcacctgatagaaaagtgttGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCcgc                                                                      >  2:232366‑M1/70‑149 (MQ=255)                                                                                   gATTATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCgaa                                                                   <  8:345613/149‑1 (MQ=255)                                                                                     ttATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTAc                                                                                             >  4:258338/1‑122 (MQ=255)                                                                                     ttATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTAc                                                                                             <  3:258338/122‑1 (MQ=255)                                                                                     ttATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTATCCTGTACCGGCCTATTCGCCGGCATGCCC‑‑‑‑‑CACAGGGACAGTTCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCgaag                                                                  >  1:62263/1‑148 (MQ=255)                                                                                        tggtggCCAGCAACAGGGGATCCAGGCTTTGCTGCATCAAAACGGGTCATTCTCCTGTCCCGCCCTCTTCGCGGGTTTGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCGAAGAAGc                                                              <  1:115744/149‑1 (MQ=37)                                                                                           tggGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCGAAGAAGCCaa                                                           <  8:349302/149‑1 (MQ=255)                                                                                           tggGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCGAAGAAGCCaa                                                           >  5:307272/1‑149 (MQ=255)                                                                                              ggatgcggcgcggatgcaggcgcactttgccagtttcacctgatagaaaagtgttGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCcgcg                                                                     >  1:287551‑M1/56‑136 (MQ=255)                                                                                              ggatgcggcgcggatgcaggcgcactttgccagtttcacctgatagaaaagtgttGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCcgcg                                                                     <  2:287551‑M1/81‑1 (MQ=255)                                                                                                  gAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGGAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCGAAGAAGCCAACACtttt                                                    <  6:369054/149‑1 (MQ=255)                                                                                                        gTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCGAAGAAGCCAACACTTTTCTATCa                                              <  2:197507/149‑1 (MQ=255)                                                                                                           aTACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCGAAGAAGCCAACACTTTTCTATCAgg                                            <  1:173418/148‑1 (MQ=255)                                                                                                             aCAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCGAAGAAGCCAACACTTTTCTATCAGGTg                                          >  6:170502/1‑148 (MQ=255)                                                                                                               aGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCGAAGAAGCCAACACTTTTCTATCAGGTGaaa                                       <  5:25283/149‑1 (MQ=255)                                                                                                               aGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCGAAGAAGCCAACACTTTTCTATCAGGTGaaa                                       >  1:70417/1‑149 (MQ=255)                                                                                                                     tGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGGCGCGTGCCCGCGAAGAAGCCAACACTTTTCTATCAGGTGAAACTgg                                   <  1:76362/148‑1 (MQ=255)                                                                                                                         ggATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACTTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCGAAGAAGCCAACACTTTTCTATCa                                              <  5:255065/132‑1 (MQ=255)                                                                                                                         ggATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCGAAGAAGCCAACACTTTTCTATCa                                              >  6:255065/1‑132 (MQ=255)                                                                                                                              aaaatGTGTGATTCTGCTGTACGGGACTCTTCGCGGGCATGCTG‑‑‑‑‑CACAGGGTCAGTGCATTCAGTAACGTTTGCGGAGTAGCTGTGGGAGCGG‑TCGTGCCCTCGAAGAAGCCATCACTTTTCTATCAGGTGAAACTGGCTTAGTgcgc                         <  4:85403/148‑1 (MQ=255)                                                                                                                               aaaaGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCGAAGAAGCCAACACTTTTCTATCAGGTGAAACTGGCAAAGTGCGCCt                       <  5:170502/149‑1 (MQ=255)                                                                                                                               aaaaGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCGAAGAAGCCAACACTTTTCTATCAGGTGAAACTGGCAAAGTGCGCCt                       <  6:307272/149‑1 (MQ=255)                                                                                                                                      tGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCGAAGAAGCCAACACTTTTCTATCAGGTGAAACTGGCAAAGTGCGCCTGCATCcg                >  8:72362/1‑149 (MQ=255)                                                                                                                                       gATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCGAAGAAGCCAACACTTTTCTATCAGGTGAAACTGGCAAAGTGCGCCTGCATCcgc               <  8:62700/149‑1 (MQ=255)                                                                                                                                         ttCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCGAAGAAGCCAACACTTTTCTATCAGGTGAAACTGGCAAAGTGCGCCTGCATCCgcgc             >  7:301818/1‑149 (MQ=255)                                                                                                                                            tcCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCGAAGAAGCCAACACTTTTCTATCAGGTGAAACTGGCAAAGTGCGCCTGCATCCGcgccg           >  7:273578/1‑148 (MQ=255)                                                                                                                                                    cGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCGAAGAAGCCAACACTTTTCTATCAGGTGAAACTGGCAAAGTGCGCCTGCATCCGCGCCGCATCCGCCt  >  6:380720/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                          TGCCTGGGGCAACCAGTTCTGGCCGGCGCATTACTTTGTCGACCGCAAGGGGCAGGTGCGCCATGTGCACTTTGGCGAGGGGGATTATGGTGGGCAGGAACAGGTGATACAGGCTTTGCTGGATGAAAAAGGGTGATTCTCCTGTACCGGCCTCTTCGCGGGCATGCCC‑‑‑‑‑CACAGGGACAGTGCAATCAGTAACGTTTGCGCAGTACCTGTGGGAGCGG‑GCGTGCCCGCGAAGAAGCCAACACTTTTCTATCAGGTGAAACTGGCAAAGTGCGCCTGCATCCGCGCCGCATCCGCCT  >  NC_002947/2749392‑2749687

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ 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.