New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	566777 =	NA (NA)	1625 (35.760)	247/262	NT	97.2%	noncoding (1/1258 nt)	IS3	repeat region
	?	NC_000913	= 572471	48 (1.050)					coding (6/456 nt)	ybcN	DLP12 prophage; DNA base‑flipping protein

ATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCT  >  NC_000913/566640‑566912                                                                                                                                          |                                                                                                                                         aTCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCt                                                                                                                                     >  1:182432/1‑143 (MQ=255)     cAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGAGCAAAGAGGCAATTGTTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAACCTGATCTTAcc                                                                                                                                 >  2:404205/1‑143 (MQ=255)             aaggCTAAGTGCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATa                                                                                                                         <  2:458787/140‑1 (MQ=255)             aacgcggaGTGCGGACGGTATGGGGCAAGTGTATGACGGGCAAAGAGGCAATTATTCAGTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATa                                                                                                                         <  2:337910/136‑1 (MQ=255)               tgCTAAGTTCGGAGTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGt                                                                                                                       <  2:812400/142‑1 (MQ=255)               atcTAAGTTCCGACTGTAAGGAGCAAGTGTATGCCGGGGAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGt                                                                                                                       <  2:850419/141‑1 (MQ=255)                  tAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑a                                                                                                                   <  2:131415/143‑1 (MQ=255)                  tAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑a                                                                                                                   <  1:599602/143‑1 (MQ=255)                    aggtCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑aca                                                                                                                 <  2:892405/140‑1 (MQ=255)                     gTTCGGAGTGAAAGGAGGAGGTGTATGACGGGCACAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑acac                                                                                                                <  1:121987/143‑1 (MQ=255)                      ttCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACAcg                                                                                                               >  2:119179/1‑143 (MQ=255)                       tCGGACTGAGAGGAGGAGGTGTATGACGGGCAATGAGGCAATTATTCATTTCCTGGGGACGCATAAGTGCGTCTGTTCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACAcgc                                                                                                              <  2:28993/143‑1 (MQ=38)                          gACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGGCGCATAAGAGCTTCAGTGCACAGGACGTTGCCGCCGTAACAGGCGCAACCGTAATCTGATCTTACACAGCAATAGTGG‑ACACGCGGc                                                                                                           >  2:873370/1‑143 (MQ=255)                          gACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCGTACCCAGCAATAGTGG‑ACACGCGGc                                                                                                           >  2:758430/1‑143 (MQ=255)                             tGAAAGGAGCAAGTGTATGTTGGGGAAAGACTCAAGTATTCGTTACCTGGGGAAGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTaa                                                                                                        >  1:912552/1‑143 (MQ=38)                              gAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAg                                                                                                       <  2:514312/143‑1 (MQ=255)                               aaaGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTCATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTACGt                                                                                                      >  2:732468/1‑143 (MQ=255)                               aaaGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGt                                                                                                      <  1:772357/143‑1 (MQ=255)                               aaaGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGt                                                                                                      >  1:871467/1‑143 (MQ=255)                                 aGGAGCAAGTGTATGACGGGCAAAGAGGAAATTATTCAGTACCTGGGGACGCATAACAACCTCACTGAAAGGGTCGTTGCCGCGGTAACAGGCGCGACCGTAATCTGATCTTACCCAGCAGTAGTGG‑ACACGCGGCTAAGTGa                                                                                                    >  2:191782/1‑143 (MQ=25)                                    ggacaGTGTAGGAACGGCAAAGCGGCGGTGGTCCGTTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTa                                                                                                 <  2:786057/139‑1 (MQ=25)                                      gaggtggATGACGGGGAAAGAGGCATTTATCCATTCCCCGGGGACGCATAAGAGCTTCTGTGGACAGCACCGTGCGGCGCTGACAGGCGCTAGCGTGATCTGATCGGACCCAGGAATAGTGG‑ACACGCGGCTAAGGGAGTaaa                                                                                               <  2:656095/140‑1 (MQ=19)                                       aaGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAAAAGAGG‑ACACGCGGCTAAGGGacgaaaa                                                                                              >  2:102081/1‑137 (MQ=39)                                       aaGTGTATGACGGGCAAAGAGGCAATTATGCATGATCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAAc                                                                                              <  1:422461/143‑1 (MQ=255)                                                  gggCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCCTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCaga                                                                                   <  2:613825/143‑1 (MQ=255)                                                     cAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGt                                                                                <  1:449542/143‑1 (MQ=255)                                                            gCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACCAGCGGCCAAGTGAGTAAACTCTCAGTCAGAGGTGACTcac                                                                         >  1:862088/1‑143 (MQ=255)                                                              aaTTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGGAATCTGATCTTACCCAGCAATAGTCG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGCATCACAt                                                                       >  2:61614/1‑143 (MQ=255)                                                               actattCTGTACGTGGTGACGCATAAGGTCTTACGTGCGCAGTGCGTTGCCGCGGTAACAGGCGCAAACGTAAGCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATg                                                                      <  2:310666/141‑1 (MQ=17)                                                                       ttACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGCAATCTGATCGTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGCCAGGAGGAACCCACATGACacacac                                                              >  2:458397/1‑138 (MQ=25)                                                                            tGGGGCGGCACAAGGCCTTCTGTGCACGGGAGGTTGCCGCGGTAACAGGCGCAACCGTAAGCTGATCTTACTCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTAt                                                         <  2:586331/143‑1 (MQ=18)                                                                            tGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTAt                                                         >  1:40440/1‑143 (MQ=255)                                                                               ggACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATGGTGG‑ACACGCGGCTAAGTGAGTAAGCTCGCAGTCAGAGGTGGCTCACATGCACCACACAGTATCaa                                                      >  2:667832/1‑143 (MQ=21)                                                                                gACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAAc                                                     <  1:772677/143‑1 (MQ=255)                                                                                  cGCATAAGAGCTGCCGTGCACAGGACCTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCa                                                   <  1:737504/143‑1 (MQ=255)                                                                                  cGCAGAAGGGCTTCTGTGCGCAGGTCGTTGCCGCGTTAACAGGCGCAACCGTAATCTGATCTTACCCATCATTAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCa                                                   <  2:469511/143‑1 (MQ=18)                                                                                   gCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAg                                                  >  1:472430/1‑143 (MQ=255)                                                                                    cATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATAGTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCAGATGACAAAAACAGTAACAAGCaat                                                 >  2:777398/1‑141 (MQ=21)                                                                                      tAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAAGCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACCGGATCAACCAGTaa                                               >  1:469507/1‑143 (MQ=255)                                                                                              tttttgCACAGGGCGTTGCCGGGGTAAGAGGCGCAACCGTAAACGGAGCGGACCCAGCAAGAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAAcccc                                       <  1:518826/139‑1 (MQ=17)                                                                                               cTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCg                                      >  1:888761/1‑143 (MQ=255)                                                                                                     agaGGACGTTGCCGCGGTAACAGGCGCAACCGTAACGTGATCTTACCCAGCAATAGTGGAATAAAACGTTCTG‑GAGTAAACTATCCGGATGAAGTGACGCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACa                                <  1:911537/141‑1 (MQ=12)                                                                                                         gACGTTGCCGCGGTAACAGGCGCAACAGAAATCTGGTCTTACCCAGGAAAAGTGG‑ACAAGCGGCTAAGTGAGTAAACTCACAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAACAACGCCGAACACAGCAt                            >  2:496889/1‑143 (MQ=17)                                                                                                             ttGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGc                        <  1:409573/143‑1 (MQ=255)                                                                                                                 cgcgGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGa                    >  1:67152/1‑143 (MQ=255)                                                                                                                  gcgGTAGCAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGaa                   <  1:887887/143‑1 (MQ=255)                                                                                                                         cAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGACTTTCGCa            >  1:536878/1‑143 (MQ=38)                                                                                                                          aGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATAACAAAAACAGTATCAACCAGTAAAAAACCCAGTAAACAGCATCCGACTCCAGTTCGCAg           >  2:96834/1‑143 (MQ=11)                                                                                                                           cggggaaCCGTGAACTGATGTTACCCAGCAATAGTGG‑ACACGCGGCTGTGATGCAAAACTGTCTGTCAGGGTTGACGCACATGACAAAAACAGTATCAACCAGTAAAAAACCCGGTAAACAGCATTCGCCTGAATTTCGCAGt          <  2:403058/138‑1 (MQ=11)                                                                                                                              ggaaCCGTGCTCTGATATGACCCAGCAATACTGT‑ACACGCGGCTAAGAGAGTAAACTCTCAGTAATAGCTGACTCACATTACAAAAACAGTATCAACCAGTAAAAAACCCCTTAAACAGCATTCGCCTGAATTTCGCAGTGaa       <  2:89455/141‑1 (MQ=11)                                                                                                                              gcAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGaa       <  2:40440/143‑1 (MQ=34)                                                                                                                                aaCCGAAATCTGATCTAACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGc     <  1:389010/143‑1 (MQ=17)                                                                                                                                  ccGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAAccc   >  1:844309/1‑143 (MQ=14)                                                                                                                                   cGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCt  >  2:213844/1‑143 (MQ=11)                                                                                                                                   cGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCCCCTGACTTTCGCAGTGCAGCCCt  >  1:321723/1‑143 (MQ=2)                                                                                                                                   cGTAAGCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCt  <  1:287675/143‑1 (MQ=11)                                                                                                                                          |                                                                                                                                         ATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGG‑ACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCT  >  NC_000913/566640‑566912

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.