New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451	= 4933879	30 (0.730)	6 (0.160)	6/304	NT	17.9%	coding (570/1308 nt)	flhF	Flagellar biosynthesis protein FlhF
	?	AE015451	= 4933863	28 (0.760)					coding (586/1308 nt)	flhF	Flagellar biosynthesis protein FlhF

CTGAGCGCCGATACGGAAGCTGTCCATGCTCACCAGCGCCAGGTTCTGCGCGCCGTACTTGAGCACGTAGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTCCAGGCCAGCGAACCGAGTTGCACTTCCAGCAGCTCGCGCAGGCCCGACAGCTCGGAGCGCATGGCATCGAACAGGCGTGGGTCAACCGGCGCAGCAGCCGGTACGGCGGCGGCCT  >  AE015451/4933663‑4934114                                                                                                                                                                                                                         |                                                                                                                                                                                                                                            cTGAGCGCCGATACGGAAGCTGTCCATGCTCACCAGCGCCAGGTTCTGCGCGCCGTACTTGAGCACGTAGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCCCCTCGATCCcgg                                                                                                                                                                                                                             >  2:360325/1‑233 (MQ=255)                       tCCATGCTCACCAGCGCCAGGTTCTGCGCGCCGTACTTGAGCACGTAGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCggg                                                                                                                                                                                                     <  1:587122/235‑1 (MQ=255)                             cTCACCAGCGCCAGGTTCTGCGCGCCGTACTTGAGCACGTAGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGctc                                                                                                                                                                                                                                        >  1:299178/1‑194 (MQ=255)                                  cAGCGCCAGGTTCTGCGCGCCGTACTTGAGCACGTAGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTc                                                                                                                                                                                                                   <  2:671816/210‑1 (MQ=255)                                    gcgcCAGGTTCTGCGCGCCGTACTTGAGCACGTAGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGa                                                                                                                                                                                        >  1:462959/1‑235 (MQ=255)                                     cgcCAGGTTCTGCGCGCCGTACTTGAGCACGTAGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACa                                                                                                                                                                                      <  1:567023/236‑1 (MQ=255)                                        cAGGTTCTGCGCGCCGTACTTGAGCACGTAGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGc                                                                                                                                                                                   >  1:281956/1‑236 (MQ=255)                                             tCTGCGCGCCGTACTTGAGCACGTAGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGc                                                                                                                                                                                                    >  1:636286/1‑214 (MQ=255)                                                      cGTACTTGAGCACGTAGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCACGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGc                                                                                                                                                                                                    <  1:83481/205‑1 (MQ=255)                                                                   gTAGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCCAGTGAGCCAGCAGCACGCGCCCGGCCTGGCGCGGCCCTTCGAt                                                                                                                                                                                                                                  >  2:83481/1‑162 (MQ=255)                                                                     aGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCatgctgctggc                                                                                                                                                                                                                                  <  1:348685‑M1/160‑12 (MQ=255)                                                                     aGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCatgctgctggc                                                                                                                                                                                                                                  >  2:348684‑M1/1‑149 (MQ=255)                                                                          gcgGCCAGCTTGGCCAGGGTGGTGGTCTTGCCGATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTcggcg                                                                                                                                                                                                                           <  1:314833/162‑1 (MQ=255)                                                                                                        cccATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTcc                                                                                                                    <  1:360326/235‑1 (MQ=255)                                                                                                        cccATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGGTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTcc                                                                                                                    >  1:507106/1‑235 (MQ=255)                                                                                                          cATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTCAGCCAGCCGCCTGCGCCAGGCCTGGCGCGGCCCCTCgct                                                                                                                                                                                                                                  >  2:104387/1‑121 (MQ=255)                                                                                                             gCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTCCAGGcc                                                                                                               >  1:324145/1‑235 (MQ=255)                                                                                                               ccgccgGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTcggcggg                                                                                                                                                                                                                         >  1:147321/1‑126 (MQ=255)                                                                                                                          aCCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTCCAGGCCAGCGAACCGAGtt                                                                                                  >  1:429126/1‑235 (MQ=255)                                                                                                                              tGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTcggcg                                                                                                                                                                                                                           >  1:103546/1‑110 (MQ=255)                                                                                                                                               tctTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCggg                                                                                                                                                                                                     <  2:201985/115‑1 (MQ=255)                                                                                                                                                      tCGGCTCGATTTCAGTCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTCCAGGCCAGCGAACCGAGTTGCACTTCcag                                                                                        <  2:724222/217‑1 (MQ=255)                                                                                                                                                        ggCTCGATTTCAGGCACTGCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCa                                                                                                                             <  2:580278/178‑1 (MQ=255)                                                                                                                                                         gCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCatgctgctggctcacttggcacggatgatcgaagtgcctgaaatcgagccgatcgaagagggtggggtgatcgccatggtcggcccggcgggcatgggcaaga                                                                                                                                      >  2:646698‑M1/1‑65 (MQ=255)                                                                                                                                                            cGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCCGCATGCGCCAGGCCCGGCGCctgctgctggctcacctggcacggatgatcgaagtgcctgaagtcgagccgatcgcagagggtggggcc                                                                                                                                                                        >  2:551174‑M1/1‑62 (MQ=255)                                                                                                                                                              aTTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCatgctgctggctcacttggcacggatgatcgaagtgcctgaaatcgagccgatcgaagagggtggggtga                                                                                                                                                                       >  1:485007‑M1/1‑60 (MQ=255)                                                                                                                                                                            gATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCatgctgctggcgcacttg                                                                                                                                                                                                                           <  2:59970‑M1/64‑19 (MQ=255)                                                                                                                                                                            gATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCCGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCCtg                                                                                                                                       >  1:211778/1‑148 (MQ=255)                                                                                                                                                                                      gCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAgg                                                                                                                                                                                                                     >  2:198377/1‑60 (MQ=255)                                                                                                                                                                                        cAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCCGGTCCAGCAGCTCGCGGGCGATCGGCCCGGGCAGGCCGATGCGCTGCAGGCGGCGCCCAAGGGTGGc                                                                                                                                                    >  1:232034/1‑123 (MQ=255)                                                                                                                                                                                        cAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTCCAGGCCAGCGAACCGAGTTGCACTTCCAGCAGCTCGCGCAGGCCCGa                                                                      >  1:1954/1‑201 (MQ=255)                                                                                                                                                                                         aaGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTCCAGGCCAGCGAACCGAGTTGCACTTCCAGCAGCTCGCGCAGGCCCGACAGCTCGGAGCGCATGGCATCGAACAGGCGTGGGt                                   >  1:63836/1‑235 (MQ=255)                                                                                                                                                                                              aGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTCCAGGCCAGCGAAcc                                                                                                       <  2:579343/162‑1 (MQ=255)                                                                                                                                                                                               gCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTCCAGGCCAGCGAACCGAGTTGCACTTCCAGCAGCTCGCGCAGGCCCGACAGCTCGGAGCGCATGGCATCGAACAGGCGTGGGTCAACCg                             >  1:500793/1‑235 (MQ=255)                                                                                                                                                                                                    cagcaTGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTCCAGGCCAGCGAACCGAGTTGCACTTCCAGCAGCTCGCGCAGGCCCGACAGCTCGGAGCGCATGGCATCGAACAGGCGTGGGTCAACCGGCgca                        <  1:404144/235‑1 (MQ=255)                                                                                                                                                                                                       caTGCGCCAGGCCTGGCGCatgctgctggctcacttggcacggatgatcgaagtgcctgaaatcgagccgatcgaagagggtggggtgatcgccatggtcggcccggcgggcatgggcaagaccaccaccctggccaagctggccgcgcgctacgtgctcaagtacggcgcgcagaacctggcgctggtgagcatggacagcttccgtatcggcgctcaggaacagctcaagac                      >  1:277661‑M1/1‑19 (MQ=255)                                                                                                                                                                                                         ggcgccAGGCCTGGCGCatgctgctggctcacttggcacggatgatcgaagtgcctgaaatcgagccgatcgaagagggtggggtgatcgccatggtcggcccggcgggcatgtgcaagaccaccaccctggccaagctggccgcgcgct                                                                                                        <  2:36816‑M1/149‑134 (MQ=255)                                                                                                                                                                                                             ccAGGCCTGGCGCatgctgctggctcacttggcacggatgatcgaagtgcctgaaatcgagccgatcgaagagggtggggtgatcgccatggtcggcccggcgggcatgggcaagaccaccaccctggccaagctggccgcgcgctacgtgctcaagtacggcgcgcagaacctggcgctggtgagcatggacagcttccgtat                                              <  1:501404‑M1/204‑192 (MQ=255)                                                                                                                                                                                                                 gCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTCCAGGCCAGCGAACCGAGTTGCACTTCCAGCAGCTCGCGCAGGCCCGACAGCTCGGAGCGCATGGCAt                                                  >  1:743870/1‑196 (MQ=255)                                                                                                                                                                                                                    tGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTCCAGGCCAGCGAACCGAGTTGCACTTCCAGCAGCTCGCGCAGGCCCGACAGCTCGGAgcg                                                          >  1:2311/1‑185 (MQ=255)                                                                                                                                                                                                                     ggCGCatgctgctggctcacttggcacggatgatcgaagtgcctgaaatcgagccgatcgaagagggtggggtgatcgccatggtcggcccggcgggcatgggcaagaccaccaccctggccaagctggccgcgcgctacgtgctcaagtacggcgcgcaga                                                                                <  1:5549‑M1/162‑158 (MQ=255)                                                                                                                                                                                                                         cgGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTCCAGGCCAGCGAACCGAGTTGCACTTCCAGCAGCTCGCGCAGGCCCGACAGCTCGGAGCGCATGGCATCGAACAGGCGTGGGTCAACCGGCGCAGCAGCCGGTACGGCGGCGGCCt  >  1:256136/1‑236 (MQ=255)                                                                                                                                                                                                                         |                                                                                                                                                                                                                                            CTGAGCGCCGATACGGAAGCTGTCCATGCTCACCAGCGCCAGGTTCTGCGCGCCGTACTTGAGCACGTAGCGCGCGGCCAGCTTGGCCAGGGTGGTGGTCTTGCCCATGCCCGCCGGGCCGACCATGGCGATCACCCCACCCTCTTCGATCGGCTCGATTTCAGGCACTTCGATCATCCGTGCCAAGTGAGCCAGCAGCATGCGCCAGGCCTGGCGCGGCTCTTCGATCTCGGCGGTCAGGTCCAGCAGCTCGCGGGCGATCGGCCCGGACAGGCCGATGCGCTGCAGGCGGCGCCAAAGGTTGGCCTGCTGCGGCTTGCTGCCCTGCAGCTGATTCCAGGCCAGCGAACCGAGTTGCACTTCCAGCAGCTCGCGCAGGCCCGACAGCTCGGAGCGCATGGCATCGAACAGGCGTGGGTCAACCGGCGCAGCAGCCGGTACGGCGGCGGCCT  >  AE015451/4933663‑4934114

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.