New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451	= 4933879	29 (0.730)	5 (0.140)	5/304	NT	16.1%	coding (570/1308 nt)	flhF	Flagellar biosynthesis protein FlhF
	?	AE015451	= 4933863	26 (0.720)					coding (586/1308 nt)	flhF	Flagellar biosynthesis protein FlhF

AGGATGCGGCCCAGGGTCTTGAGCTGTTCCTGAGCGCCGATACGGAAGCTGTCCATGCTCACCAGCGCCAGGTTCTGCGCGCCGTACTTGAGCACGTAGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTCCAGGCCAGCGAACCGAGTTGCACTTCCAGCAGCTCGCGCAGGCCCGACAGCTCGGAGCGCATGGCATCGAACAGGCGTGGGTCAACCGGCGCAGCAGCC  >  AE015451/4933634‑4934098                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                            aGGATGCGGCCCAGGGTCTTGAGCTGTTCCTGAGCGCCGATACGGAAGCTGTCCATGCTCACCAGCGCCAGGTTCTGCGCGCCGTACTTGAGCACGTAGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCA                                                                                                                                                                                                                                       <  1:524942‑M1/236‑1 (MQ=255)            cAGGGTCTTGAGCTGTTCCTGAGCGCCGATACGGAAGCTGTCCATGCTCACCAGCGCCAGGTTCTGCGCGCCGTACTTGAGCACGTAGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCa                                                                                                                                                                                                                            <  1:483104‑M1/236‑2 (MQ=255)                                   cgcCGATACGGAAGCTGTCCATGCTCACCAGCGCCAGGTTCTGCGCGCCGTACTTGAGCACGTAGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAg                                                                                                                                                                                                      >  1:297935/1‑235 (MQ=255)                                        aTACGGAAGCTGTCCATGCTCACCAGCGCCAGGTTCTGCGCGCCGTACTTGAGCACGTAGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGG                                                                                                                                                                                                                                >  1:553887‑M1/1‑204 (MQ=255)                                        aTACGGAAGCTGTCCAGGCTCACCCGCGCCAGGTTCTGCGCGCCGTACTTGAGCACGTAGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATgcgccaggcctggcgcatgctgctggctcacttg                                                                                                                                                                                                           >  1:215484‑M2/1‑191 (MQ=255)                                                                      aGGTTCTGCGCGCCGTACTTGAGCACGTAGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGcc                                                                                                                                                                  <  1:51035/236‑1 (MQ=255)                                                                                 gcCGTACTTGAGCACGTAGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCa                                                                                                                                                       <  1:416888/236‑1 (MQ=255)                                                                                                    cgcgcgGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGt                                                                                                                                                                                                         >  2:273595/1‑167 (MQ=255)                                                                                                      cgcgGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGccc                                                                                                                                                                           <  2:525516/195‑1 (MQ=255)                                                                                                         ggCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCCCCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCggg                                                                                                                                                                                     <  1:234475/182‑1 (MQ=255)                                                                                                            cggctTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCatgctgctggctc                                                                                                                                                                                                                <  2:96084‑M1/150‑14 (MQ=255)                                                                                                             aGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCCATCTcg                                                                                                                                                                                                              >  2:228776/1‑153 (MQ=255)                                                                                                                tgggccAGGGTGGTGGTCTCGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCatgctgctggctcacttggcacggatgatc                                                                                                                                                                                               <  1:306551‑M1/163‑31 (MQ=255)                                                                                                                      aGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGcc                                                                                                                  <  1:160071/236‑1 (MQ=255)                                                                                                                            gtggtCTTGCCCCGGCCCGCCGGGCCGACCATGGCGATCCCCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCa                                                                                                             <  1:209948/235‑1 (MQ=255)                                                                                                                            gtggtCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGAtct                                                                                                                                                                                                                <  1:586778/136‑1 (MQ=255)                                                                                                                            gtggtCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGAtct                                                                                                                                                                                                                >  2:586777/1‑136 (MQ=255)                                                                                                                             tggtCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCCGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTcggcg                                                                                                                                                                                                           <  2:500300/140‑1 (MQ=255)                                                                                                                                    gCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGAtt                                                                                                      <  2:297934/234‑1 (MQ=255)                                                                                                                                     cccATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATgcgccaggcctggc                                                                                                                                                                                                                               >  1:128151‑M2/1‑98 (MQ=255)                                                                                                                                     cccATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGC                                                                                                                                                                                                                               >  2:128151‑M1/1‑112 (MQ=255)                                                                                                                                      ccATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCggg                                                                                                                                                                                     <  2:484792/153‑1 (MQ=255)                                                                                                                                             cgccgGGCCGACCATGGCGATCACCCCACCCTCGTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATgcgccaggcctggcgcatgctgctggctcacttggcacggatgatc                                                                                                                                                                                               >  2:82482‑M2/1‑90 (MQ=255)                                                                                                                                                  ggCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATg                                                                                                                                                                                                                                            <  2:425138‑M2/86‑2 (MQ=255)                                                                                                                                                  ggCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATG                                                                                                                                                                                                                                            <  1:425139‑M1/86‑1 (MQ=255)                                                                                                                                                               gATCACCCCCCCCTCTTCGATCGGCTCGATTTCCGGCACTTCGATCCTCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCggg                                                                                                                                                                                     <  2:240098/128‑1 (MQ=255)                                                                                                                                                                   accccacccTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAg                                                                                                                                                      <  2:671098/155‑1 (MQ=255)                                                                                                                                                                    ccccacccTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTCCAGGCCAGCGAACCGAGTTGCACTTCcagcag                                                                     >  1:266513/1‑235 (MQ=255)                                                                                                                                                                    ccccacccTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGACAAGTCAGCCAGCAGCATGCGCCAGGCCTGGCGCatgctgctggctcacttggcacggctgatcgaagtgcccgaaatcgagccgatcgcagagg                                                                                                                                                                >  2:320962‑M1/1‑83 (MQ=255)                                                                                                                                                                       cacccTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTCCAGGCCAGCGAACCGAGTTGCACTTCCAGCAGCTcg                                                                 <  1:418995/236‑1 (MQ=255)                                                                                                                                                                          ccTCTGCGATCGGCTCGATTTCGGGCACTTCGATCAGCCGTGCCAAGTGAGCCAGCAGCATgcgccaggcctggcgcatgctgctggctgacttgtcacggatgatcgaagtgcctgaaatcgagccgatcgaagagggtgggg                                                                                                                                                          >  2:320962‑M2/1‑61 (MQ=255)                                                                                                                                                                                  aTCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCCGGCCTGGCGCGGCTCTTCGATCTCGGCGGTcc                                                                                                                                                                                                       >  2:8756/1‑90 (MQ=255)                                                                                                                                                                                      gCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCggg                                                                                                                                                                                     <  2:264525/105‑1 (MQ=255)                                                                                                                                                                                      gCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCggg                                                                                                                                                                                     >  1:264526/1‑105 (MQ=255)                                                                                                                                                                                                       tCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTCCAGGCCAGCGAACCGAGTTGCACTTCCAGCAGCTCGCGCAGGCCCGACAGCTCGGAGCGCATGGCAt                                  <  1:668926/235‑1 (MQ=255)                                                                                                                                                                                                         gATCATCCGTGCCAAGTGGGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGATGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTCCAGGCCAGCGAACCGAGTTGCACTTCCAGCAGCTCGCGCAGGCCCGACAGCTCGGAGCGCATGGCATCg                                <  1:215356/235‑1 (MQ=255)                                                                                                                                                                                                         gATCATCCGTGCCAAGTGAGCCAGCAGCATgcgccaggcctggcgcatgctgctggctcacttggcacggatgatcgaagtgcctgaaatcgagccgatcgaagagggtggggtgatcgccatggtcggcccggcgggcatgggcgagaccaccaccctggccca                                                                                                      <  1:306551‑M2/165‑136 (MQ=255)                                                                                                                                                                                                         gATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCatgctgctggctcacttggcacggatgatcgaagtgcctgaaatcgagccgatcgacgagggtggggtgatcgccatggtcggcccggcg                                                                                                                                   >  2:82482‑M1/1‑46 (MQ=255)                                                                                                                                                                                                                     cAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCatgctgctggctcacttggcacggatgatcgaagtgcctgaaatcgagccgatcgaagagggtggggtgatcgccatggtcggcccggcgggcatgggcaagaccaccaccctggccaagctggccgcgcgctacgtgctcaagtacggcgcgcagaacctggcgcgggtgagcctggacagcttccgtat                              >  1:215484‑M1/1‑34 (MQ=255)                                                                                                                                                                                                                          gAGCCAGCAGCATgcgccaggcctggcgcatgctgctggctcacttggcacggatgatcgaagtgcctgaaatcgagccgatcgaagagggtggggtgatcgccatggtcggcccggcgggcatgggcaagaccaccaccctggccaagccg                                                                                                  <  2:96084‑M2/152‑140 (MQ=255)                                                                                                                                                                                                                              cagcggCAGGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGcc                                                                                                                  <  2:252431/132‑1 (MQ=255)                                                                                                                                                                                                                                gcagcaTGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTCCAGGCCAGCGAACCGAGTTGCACTTCCAGCAGCTCGCGCAGGCCCGACAGCTCgg                                              <  2:676275/198‑1 (MQ=255)                                                                                                                                                                                                                                gcagcaTGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTCCAGGCCAGCGAACCGAGTTGCACTTCCAGCAGCTCGCGCAGGCCCGACAGCTCgg                                              >  1:676276/1‑198 (MQ=255)                                                                                                                                                                                                                                    caTGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCa                                                                                                             <  1:92750/131‑1 (MQ=255)                                                                                                                                                                                                                                      tgcgccaggcctggcgcatgctgctggctcacttggcacggatgatcgaagtgcctgaaatcgagccgatcgaagagggtggggtgatcgccatggtcggcccggcgggcatgggcaagaccaccaccctggccaagctggccgcgcgctacgtgctcaagtacggcgcgcagaacctggcgctggtgagcatggacagcttccgtatcggcgctcaggaacagctcaagaccctg  <  1:483104‑M2/236‑236 (MQ=255)                                                                                                                                                                                                                                      tGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGcc                                                                                                                                                                  <  2:153741/76‑1 (MQ=255)                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                            AGGATGCGGCCCAGGGTCTTGAGCTGTTCCTGAGCGCCGATACGGAAGCTGTCCATGCTCACCAGCGCCAGGTTCTGCGCGCCGTACTTGAGCACGTAGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTCCAGGCCAGCGAACCGAGTTGCACTTCCAGCAGCTCGCGCAGGCCCGACAGCTCGGAGCGCATGGCATCGAACAGGCGTGGGTCAACCGGCGCAGCAGCC  >  AE015451/4933634‑4934098

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ 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.