New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	566777 =	NA (NA)	2081 (40.730)	250/260	NT	97.2%	noncoding (1/1258 nt)	IS3	repeat region
	?	NC_000913	= 572471	60 (1.170)					coding (6/456 nt)	ybcN	DLP12 prophage; DNA base‑flipping protein

GAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCT  >  NC_000913/566636‑566912                                                                                                                                              |                                                                                                                                        gAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCAGTACCTGGGGACGCATAAGAGCTTCTATGCACAGGACGTTGCCGCGGTAACAGGCGCAAACGTCATCTg                                                                                                                                        >  2:964935/1‑143 (MQ=255)   agagCGCAGAAATTAAAGCTAAGTTCGGACTGAATGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGAt                                                                                                                                      <  2:473173/143‑1 (MQ=255)   aGATCTCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGAt                                                                                                                                      <  2:243905/143‑1 (MQ=255)   aGATCGCAGAAATTAAAGCTAAGTGCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGAt                                                                                                                                      <  2:799061/143‑1 (MQ=255)   aGATCGCAGAAAGTAACGCTAGGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGAt                                                                                                                                      <  1:5576/143‑1 (MQ=255)     aTCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGctct                                                                                                                                    >  2:742647/1‑143 (MQ=255)       cGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTa                                                                                                                                  <  1:477146/143‑1 (MQ=255)                    gCTAAGTCCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTg                                                                                                                     <  1:647492/143‑1 (MQ=255)                     cTAAGTGCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTgg                                                                                                                    <  2:433055/143‑1 (MQ=255)                        aGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTACTCTGTTCTTACCCAGATATAGCGGaca                                                                                                                 >  1:733231/1‑143 (MQ=255)                                cTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTCACAGGCGCAACCGTAATCTGCTCTTACCCAGCAATAGTGGACACGCGGCtc                                                                                                         >  1:931758/1‑142 (MQ=255)                                   aaaGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATACATTACCTGGGGGGGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAAGCTGATCTTACCCAGCCAGAGTGGCCACGCGGCAAAGt                                                                                                      >  2:827095/1‑143 (MQ=255)                                         gCACGTGTATGACGGGCAAAGAGTCAATTATTTCTTTCTTGGTTACTCATAAGAGCTTTTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTaa                                                                                                <  1:814403/143‑1 (MQ=25)                                            aGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAAct                                                                                             >  2:222780/1‑143 (MQ=255)                                                      gggCACAGAGGCAGTTACTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCaga                                                                                   <  1:91714/143‑1 (MQ=255)                                                      gggCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAg                                                                                                                             >  1:418711/1‑101 (MQ=255)                                                      gggCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAg                                                                                                                             <  2:418711/101‑1 (MQ=255)                                                       ggCAACGAGGTAATTCTTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCagag                                                                                  <  1:628278/143‑1 (MQ=255)                                                       ggCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTTCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCagag                                                                                  <  1:570462/143‑1 (MQ=255)                                                          aaaGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTg                                                                               >  2:956730/1‑143 (MQ=255)                                                           aaGAGGTAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGa                                                                              <  1:29523/143‑1 (MQ=255)                                                               ggCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAGACTCTCAGTCAGAGGTGACTca                                                                          >  1:870942/1‑143 (MQ=255)                                                               ggCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGAAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTca                                                                          <  2:524924/143‑1 (MQ=255)                                                                gCAATTGTTTTTTCCTTGTGGACGCATAAGCGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTcac                                                                         <  1:585538/143‑1 (MQ=21)                                                                gCAATTATTCATTACCTGGGGACTCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTcac                                                                         <  2:800531/143‑1 (MQ=255)                                                                 cAATTATTCATTGCCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTcaca                                                                        <  1:24814/143‑1 (MQ=255)                                                                 cAATTATTCATTACCTGGGGACGCTTAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTcaca                                                                        <  1:349534/143‑1 (MQ=255)                                                                        tCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGCCaaa                                                                 >  2:612809/1‑143 (MQ=255)                                                                          aTTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGGCAGAGGTGACTCACATGACaaaaa                                                               <  1:217703/143‑1 (MQ=255)                                                                          aTTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTCCCGCGGTAACCGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGGCACGCGGCTCAGTGAGTAAGCTCAAAGTCAGCGGTGACTCACATGCCaaaaa                                                               >  2:114231/1‑143 (MQ=25)                                                                            tACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACa                                                             <  1:670387/143‑1 (MQ=255)                                                                            tACCTGGGGACGCATAAGAGCGTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACa                                                             <  2:190047/143‑1 (MQ=255)                                                                                  gggACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCa                                                       >  1:763151/1‑143 (MQ=255)                                                                                   ggACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCaa                                                      >  2:569908/1‑143 (MQ=255)                                                                                      cGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCa                                                   <  1:621654/143‑1 (MQ=255)                                                                                           cagagCGTCTGTGCACAGGACGTTGCCGTGGTAACAGGCGCGACCGTAACCTGATCTTACCCAGCAATAGTGGACACTCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTaaa                                              <  2:631747/142‑1 (MQ=18)                                                                                                  tcgctgCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGGTCTTCCCGAGCAACAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAAcccc                                       <  1:1006442/139‑1 (MQ=18)                                                                                                  tCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAAcccc                                       >  1:933601/1‑143 (MQ=255)                                                                                                       gCACAGGACGTTGCCGCGGTAACAGGCGCAGCCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCGAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTaaa                                  <  2:972625/143‑1 (MQ=255)                                                                                                        cacaGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAGACCCCGTAAAc                                 >  1:391067/1‑143 (MQ=255)                                                                                                         acaGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTGACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCCCAGTCAGAGGTGACTCACATGACAAAAACAGCATGCACACGTAGAGAACCCCGTAcaca                                >  2:149284/1‑143 (MQ=17)                                                                                                           aGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGAAATAGTGGACAAGCGACTAAGTGAATAAACTCTCAGAAAGAAATGACTCACATAACAAAAACACTATAAACCAGTAAAAAACCACCTAAAAAga                              >  2:879011/1‑142 (MQ=255)                                                                                                                 ttGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGc                        <  2:870942/143‑1 (MQ=255)                                                                                                                  tGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATAAACAAGTAAAAAACCCCGAAAACAACATTAGcc                       >  1:14895/1‑143 (MQ=17)                                                                                                                   gCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCt                      <  2:496264/143‑1 (MQ=255)                                                                                                                     cgcgGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGa                    >  1:263097/1‑143 (MQ=255)                                                                                                                      ccgGTCACAGGCGCCAACGTAATCTGATCTTACCGAGGAGTAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGaa                   <  2:931758/142‑1 (MQ=11)                                                                                                                         gTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAACTGAGTAAACTCTCAGTCAGAGGGGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATACGCCTGCAtta                >  2:701721/1‑142 (MQ=255)                                                                                                                             cAGGCGCAACCGTAATCTTATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCa            <  1:496368/143‑1 (MQ=38)                                                                                                                                gcgcAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCCCATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTg         >  1:617793/1‑143 (MQ=25)                                                                                                                                  tcAACCATAATCTGATCTTACCCAGCAAGAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGATGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGaa       <  2:921113/142‑1 (MQ=12)                                                                                                                                  gcAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGaa       <  1:206555/143‑1 (MQ=34)                                                                                                                                    gaCCGTAAGCTGATAGTAACCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGc     <  2:270420/142‑1 (MQ=255)                                                                                                                                    aaCCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATCCGCCTGAATTTCGCAGTGAAGc     >  2:370593/1‑143 (MQ=17)                                                                                                                                       cGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGCCAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCCGAACTTCGCAGTGAAGcccc  >  2:895856/1‑142 (MQ=2)                                                                                                                                       cGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGacgacgt  >  1:623063/1‑137 (MQ=11)                                                                                                                                       cGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCACAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCACCTGAAATTCGCAGTGAAGACCt  >  2:452157/1‑143 (MQ=2)                                                                                                                                       cGTAATCTGATCTTACCCAGCAATACTGGACACGAGTCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCACGTAACCAGCATTCGCCTGAAGTTCGCAGTGAAAccca  >  2:993872/1‑142 (MQ=11)                                                                                                                                              |                                                                                                                                        GAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCT  >  NC_000913/566636‑566912

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.