New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	566777 =	NA (NA)	2317 (43.360)	256/260	NT	97.8%	noncoding (1/1258 nt)	IS3	repeat region
	?	NC_000913	= 572471	52 (0.970)					coding (6/456 nt)	ybcN	DLP12 prophage; DNA base‑flipping protein

GAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCC  >  NC_000913/566636‑566910                                                                                                                                              |                                                                                                                                      gAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTg                                                                                                                                      >  1:113890/1‑143 (MQ=255)   aGATCGCAGAAATTAAAGCTAAGTTCGTACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGTGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGAt                                                                                                                                    <  2:939437/143‑1 (MQ=255)    gATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATc                                                                                                                                   <  1:829311/143‑1 (MQ=255)    gATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATc                                                                                                                                   <  1:445255/143‑1 (MQ=255)       cGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTAAAAACACAAAAAAACAACAAACCACAAAACATCACCGCGGTAACAGGCGCAACCGTAATCTGATCTTa                                                                                                                                <  1:19883/143‑1 (MQ=255)          aGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTATGAGCACAAGTGGTTCCCGCGGTAACAGGCGCAACAGTAATCTGATCTTAccc                                                                                                                             >  2:219127/1‑143 (MQ=255)            aaaTTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAg                                                                                                                           <  1:614755/143‑1 (MQ=255)                   aGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCCTAAGAGCTTCTGTGCACAGGGCGTTGTCGCGGTAACCGGCGCCACCGTAATCCGCTCTTACCCAGccagagc                                                                                                                    >  2:949223/1‑137 (MQ=255)                   aGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGt                                                                                                                    <  2:352148/143‑1 (MQ=255)                           tctgACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACAcgc                                                                                                            <  1:1008166/140‑1 (MQ=255)                              gACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGc                                                                                                         >  1:71502/1‑143 (MQ=255)                                 tGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTaa                                                                                                      >  2:684500/1‑143 (MQ=255)                                 tGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTaa                                                                                                      >  2:759592/1‑143 (MQ=255)                                     acgAGCAAGTGGATGACGGGCAAAGAGGCAATTCTTCATTACCTTGGGGTGCATATGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGa                                                                                                  <  2:686782/141‑1 (MQ=38)                                          cAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGAGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTaaa                                                                                             >  2:488934/1‑143 (MQ=255)                                           aaGTGTATGCCGAGCAAAGCGGCAATTAGTCATTACCTGAGGACGCATAAGAGCTTCTGTTCACAGCACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTATCCAGCACTAGTGGACACGCGGCTAAGTGAGTAAAc                                                                                            <  1:614217/143‑1 (MQ=37)                                               gtATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACtctc                                                                                        <  1:137241/143‑1 (MQ=255)                                                ttgggcGGGCAAGGAGTCAATTCTTCATTACCTGGGGTTGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCtca                                                                                       <  2:984666/138‑1 (MQ=37)                                                tATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCtca                                                                                       <  1:779466/143‑1 (MQ=255)                                                   gACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCtcagtc                                                                                    >  2:1048763/1‑143 (MQ=255)                                                    aCGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCtcagtca                                                                                   <  1:682295/143‑1 (MQ=255)                                                     cGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGTACGTTACCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCtcagtcag                                                                                  >  1:517834/1‑143 (MQ=255)                                                      gggCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCaga                                                                                 <  2:864670/143‑1 (MQ=255)                                                                gCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTcac                                                                       >  1:506472/1‑143 (MQ=255)                                                                  aaTTATTCATTACCTGGGGACGCATAAGCGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGTGTAAACTCTCAGTCCGAGGTGACTCACAt                                                                     >  2:581061/1‑143 (MQ=255)                                                                  aaTTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACAt                                                                     >  2:870995/1‑143 (MQ=255)                                                                  aaTTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACAt                                                                     >  1:899652/1‑143 (MQ=255)                                                                  aaTTATGCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACAt                                                                     <  1:404063/143‑1 (MQ=255)                                                                    ttattCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCACTAGTGGACACGCGGCGAAGTGAGGAAACTCTCAGGCAGCGGCGACTGACAtaa                                                                   >  1:308270/1‑141 (MQ=37)                                                                       ttCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACaa                                                                >  1:668400/1‑143 (MQ=255)                                                                           ttACCTGGGGACGCATAAGCGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAAc                                                            <  1:247607/143‑1 (MQ=255)                                                                           ttACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCCTCCCCAGCAATAGTGGAAACGCGGCTAAGTGAGCAAACTCGCAGTCAGAGTGGACTCACATGACACAAAc                                                            >  1:355378/1‑143 (MQ=255)                                                                              ccTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCagag                                                                                <  1:786346/120‑1 (MQ=255)                                                                              ccTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCagag                                                                                >  2:786346/1‑120 (MQ=255)                                                                                 ggggACGCATAAGAGCTTCTGTGCACAGGGCGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATc                                                      <  1:1028569/143‑1 (MQ=255)                                                                                 ggggACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGATAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTAta                                                      >  1:693119/1‑142 (MQ=255)                                                                                   ggACGAATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGTCACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCaa                                                    >  2:874075/1‑143 (MQ=255)                                                                                    gACGCATAAGAGCTGCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAAc                                                   <  1:1015031/143‑1 (MQ=255)                                                                                      cGCATCACAGCTTCTGTGCACAGGACGTTCCCGCGGATGCACGCGCAACCGTAATCTGATCTTACCCAGCAATCGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCa                                                 <  2:1018625/143‑1 (MQ=17)                                                                                      cGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTCATCTAATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCa                                                 >  1:289084/1‑143 (MQ=255)                                                                                         aTAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACACGCCCATCCGTAATCTGATCTTACCCGGCAAGCGTCTACACCCGGCGAAGTGAGTAAACTCGCATTCAGAGGTGAGTCACATAACAAAAAGAGTAACAACCAGTa                                              >  2:918431/1‑143 (MQ=255)                                                                                          tAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTag                                             >  1:135796/1‑142 (MQ=255)                                                                                           aaGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGCACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTaaa                                            <  1:643974/143‑1 (MQ=255)                                                                                              agCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTaaaaaa                                         <  1:449290/143‑1 (MQ=255)                                                                                                cTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAAcc                                       >  2:565210/1‑143 (MQ=255)                                                                                                  tCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAAcccc                                     >  2:568417/1‑143 (MQ=255)                                                                                                  tCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAAcccc                                     >  2:568759/1‑143 (MQ=255)                                                                                                      tgCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTTGAGTTTAAACCACAGTCGACTCACATGACAAAAACAGTATACACCAGTAAAAAACCCCGTaa                                 >  1:240345/1‑143 (MQ=18)                                                                                                         acaGGACGTTGCCGCGGCAACAGGCGCAACCGTAATCTGCTCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCACAGTCAGAGGTGACTCACACGACAAAAAAAGTATAAACCACAAAAAAACCACGTCAACa                              >  2:108559/1‑143 (MQ=17)                                                                                                              aCGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCAtt                         >  1:908997/1‑143 (MQ=255)                                                                                                                      gcgGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGaa                 <  2:103312/143‑1 (MQ=255)                                                                                                                          tAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTc             >  1:625524/1‑143 (MQ=40)                                                                                                                          gaaCAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTc             <  1:76306/142‑1 (MQ=40)                                                                                                                            aCAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGc           <  1:565210/143‑1 (MQ=39)                                                                                                                             cAGGCGCAACCGTAATCTGATCATACCCAGCAATAGTGGACACGCGGCTAAGTTAGTAAACTCTCAGTCAGAGGGGACTCACAGGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCa          <  2:175614/143‑1 (MQ=255)                                                                                                                             cAGGCACAACCTTAATCTGATCTTACCCAGCAATAGTGTACACGCGACTAAGTGAGCAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCa          <  1:156828/143‑1 (MQ=11)                                                                                                                               ggCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGt        <  1:759592/143‑1 (MQ=37)                                                                                                                                gcgcAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTCAACAGCATTCGCCTGAATTTCGCCGTg       >  1:790639/1‑143 (MQ=25)                                                                                                                                     aCCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGcc  <  2:138113/143‑1 (MQ=32)                                                                                                                                     aCCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGcc  >  2:650732/1‑143 (MQ=32)                                                                                                                                              |                                                                                                                                      GAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCC  >  NC_000913/566636‑566910

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.