New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	2455823 =	2 (0.040)	43 (0.910)	36/296	0.3	95.6%	coding (1039/1341 nt)	fadL	long‑chain fatty acid outer membrane transporter
	?	CP009273	3576788 =	NA (NA)					intergenic (+10/‑55)	yrhA/insA	pseudogene, interrupted by IS1E/IS1 repressor TnpA

TAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT‑CAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCT  >  CP009273/3576640‑3576930                                                                                                                                                     |                                                                                                                                                tAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAACTGAATTTTATAGAAATAATGATGATTTCATCAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAg                                                                                                                                                 <  1:621472/149‑1 (MQ=255)   gCCTCTCGAGTCCAGAACCTTCAGTAAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACCAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGt                                                                                                                                               <  2:265643/149‑1 (MQ=255)    ccTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTg                                                                                                                                              >  2:315702/1‑149 (MQ=255)     ctccCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGa                                                                                                                                             <  2:655118/149‑1 (MQ=255)        tcGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGTTGAtgc                                                                                                                                          >  2:549210/1‑149 (MQ=255)         cGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGAtgct                                                                                                                                         <  2:584406/149‑1 (MQ=255)           aTTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGAtgctgc                                                                                                                                       <  1:195630/149‑1 (MQ=255)               cAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGATATGCTGCCAAc                                                                                                                                   >  1:684283/1‑149 (MQ=255)                  aaCCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTa                                                                                                                                <  2:51198/149‑1 (MQ=255)                  aaCCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAACGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGCTGCTGCCAACTTa                                                                                                                                >  1:505128/1‑149 (MQ=255)                   acattgaGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTAc                                                                                                                               <  1:526414/143‑1 (MQ=255)                   aCCTTCAGTGAAAAACCTTTTTGCCGTAAATGAATTTTATAGAGATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTAc                                                                                                                               <  1:81439/149‑1 (MQ=255)                    ccTTCAGGTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACt                                                                                                                              <  1:271144/149‑1 (MQ=255)                      ttCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGGGATCGGGGAACAAACCACTGCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGa                                                                                                                            >  2:725728/1‑149 (MQ=255)                       tCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCGTGATCTACAAGAACGGGTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAAATTACTGAt                                                                                                                           >  1:91629/1‑149 (MQ=255)                         aGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGAttt                                                                                                                         <  2:12846/149‑1 (MQ=255)                            tAAAAACCTTTTTGTCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTCGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAgt                                                                                                                      <  1:87642/149‑1 (MQ=255)                             aaaaaCCTTTTTGCCGTAAATGAGTTTTCTAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAGTATTTACTTATGACATTAAAGGTGATGCTGCCACCTTACTGATTCAgtg                                                                                                                     >  1:530571/1‑149 (MQ=255)                             aaaaaCCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAgtg                                                                                                                     <  2:616025/149‑1 (MQ=255)                                    tttttGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGCTTTAGTGTatgatg                                                                                                              >  2:210120/1‑149 (MQ=255)                                    tttttGCCGTAAATGAATTTTATAGAAATAATAATGATTTCATAAACCCTGATCTTCAAGTACGGTTAGTGCTCGGTGATTATAAAATTGCCCTATTTACTTATGCCGTTAAAGGTGTTGCTGTCAAGTTACTGATTTAGTGTatgatg                                                                                                              >  1:338251/1‑149 (MQ=255)                                    tttttGCAGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTatgatg                                                                                                              <  2:108811/149‑1 (MQ=255)                                      tttGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGgt                                                                                                            <  2:464529/149‑1 (MQ=255)                                               aattaattTTATATAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTCACTGCTTTAGTGTATGATGGTGTTTTTGAg                                                                                                   <  2:398861/149‑1 (MQ=255)                                                aTGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAgg                                                                                                  <  2:719554/149‑1 (MQ=255)                                                    aTTTTATAGAAATAATTATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCt                                                                                              <  1:185377/149‑1 (MQ=255)                                                       ttATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCa                                                                                           <  2:167870/149‑1 (MQ=255)                                                       ttATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGGGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCa                                                                                           <  1:585430/149‑1 (MQ=255)                                                         ataGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGt                                                                                         <  1:631233/149‑1 (MQ=255)                                                               atactgcggttgtgaTAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTc                                                                                   >  1:8214/15‑149 (MQ=255)                                                                    gatgatTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGttt                                                                              <  2:113980/149‑1 (MQ=255)                                                                    gactgtttCCTAATCCCTGATCCACAAGAACTGTTAGGTATCTGGGACTATAGCATTTCAATATTTACTTATGACATTAAATGTGATGCTGCCGACTTACTGATTTAGTGTATGATGGTGTTTTTTAGTTGCTTCAGTGGCTTCTGttt                                                                              <  1:310971/144‑1 (MQ=21)                                                                        atTTCATAATCCCTAATCCACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAt                                                                          <  2:245792/149‑1 (MQ=255)                                                                        atTTCATAAACCCTGATCTTCAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAt                                                                          <  2:2678/149‑1 (MQ=255)                                                                          ttCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT‑Ca                                                                       >  1:617342/1‑149 (MQ=255)                                                                               aaaCCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT‑CAGCTGt                                                                  <  2:455558/149‑1 (MQ=255)                                                                               aaaCCCTGAACTAGAAGGACGGTTAGGGGTCGGTGATTGTAGTGCTTCAATACTGACTTTTGCCATTAAAGGCGATGCGGCCAGCTTCTTCATTTAGTGTATGATGGTGTTTTTGAGTTCCTCCAGCGGCTGCTGTTTCGGT‑CAGCTGt                                                                  <  1:200068/149‑1 (MQ=12)                                                                                 aCCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT‑CAGCTGTcc                                                                >  1:239521/1‑149 (MQ=255)                                                                                  cccTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTAGGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTATAT‑CAGCTGTccc                                                               >  2:25907/1‑149 (MQ=255)                                                                                   ccTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGAAATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT‑CAGCTGTCcct                                                              >  2:768461/1‑149 (MQ=255)                                                                                    cTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT‑CAGCTGTCcctc                                                             <  2:448175/149‑1 (MQ=255)                                                                                          tACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT‑CAGCTGTCCCTCCTGTTc                                                       <  2:338251/149‑1 (MQ=255)                                                                                           aCAAGAACGGTGAGTGATCGGGGATTATAGCAGTACAATATTTACTTATGACATTGAGGGTGATGATGCCAACTGAGTGATTTAGTGTATGATGGGGTTTTTGAGGTGCGCCGGTGGCGTCTGTCTCTAT‑CGGGTGTACCTCACGTTCa                                                      >  1:642839/1‑149 (MQ=255)                                                                                             aaGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT‑CAGCTGTCCCTCCTGTTCAGc                                                    <  2:588428/149‑1 (MQ=255)                                                                                             aaGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT‑CAGCTGTCCCTCCTGTTCAGc                                                    <  1:676893/149‑1 (MQ=255)                                                                                                    gTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT‑CAGCTGTCCCTCCTGTTCAGCTACTGAc                                             >  2:156279/1‑149 (MQ=255)                                                                                                           aTCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT‑CAGCTGTCCCTCCTGTTCAGCTACTGACGGggtgg                                      >  1:329953/1‑149 (MQ=255)                                                                                                            ttggggATTATAGCTGTTCAATATTTACTTATGACATTAAAGGTTATGCTGCCAACTTACTGATTTAGTGTATGATTGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT‑CAGCTGTCCCTCCTGTTCAGCTACTGACGGggtggt                                     <  1:25528/147‑1 (MQ=255)                                                                                                            gcGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTAAGATGGTGTTTTTGAGGTGCTCCAGTGGTTTCTGTTTCGAT‑CAGCTGTCCCTCCTGTTCAGCTACTGACGGggtggt                                     <  1:404489/148‑1 (MQ=255)                                                                                                              ggggATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGGTTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTCCTGTTTCTAT‑CAGCTGTCCCTCCTGCTCAGCTACTGCCgggaggttgc                                   >  2:644224/1‑142 (MQ=18)                                                                                                                         cATTTCAATATTTACTTATGCCATTAAATTTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT‑CAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCaaa                        >  1:393323/1‑149 (MQ=255)                                                                                                                               aaTATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGCTTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTG‑TTCTATGCACCGGTCTCTCCTGTTCAGCTACTGACGGGGTGGTGCGTCATGGCAAAAGCAcc                  >  2:179906/1‑149 (MQ=14)                                                                                                                               aaTATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT‑CAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCAcc                  <  1:210120/149‑1 (MQ=255)                                                                                                                                atatTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT‑CAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCAccg                 <  1:156279/149‑1 (MQ=255)                                                                                                                                   tttACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTGTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT‑CAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAACCAccgccg              >  2:268972/1‑149 (MQ=255)                                                                                                                                        ttATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT‑CAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGGGCGTAACGCGCAAAGCAAAGCCggcgat         >  1:704615/1‑145 (MQ=14)                                                                                                                                               aTTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT‑CAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCt  >  2:621655/1‑149 (MQ=33)                                                                                                                                                     |                                                                                                                                                TAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT‑CAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCT  >  CP009273/3576640‑3576930

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ 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.