New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 = 1391494NA (NA)19 (0.370) 11/164 1.7 73.3% intergenic (+145/‑128) BW25113_RS06980/ynaJ IS5‑like element IS5 family transposase/DUF2534 family protein
?NZ_CP009273 1972747 = 7 (0.130)intergenic (‑293/‑487) flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC

AACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATG  >  NZ_CP009273/1972658‑1972833
                                                                                         |                                                                                      
gcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcc                                                                                        <  1:1195231‑M2/1‑1 (MQ=255)
gcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcc                                                                                        <  2:1119080‑M2/1‑1 (MQ=255)
 catttactggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcct                                                                                       <  1:1448562‑M2/2‑1 (MQ=255)
 catttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcct                                                                                       <  1:258013‑M2/2‑1 (MQ=255)
  cTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACtt                                                                                      <  2:1026209/90‑1 (MQ=255)
  atttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcctt                                                                                      <  2:730716‑M2/3‑1 (MQ=255)
  atttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcctt                                                                                      <  2:1489956‑M2/3‑1 (MQ=255)
   tttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTa                                                                                     >  1:1007034‑M2/87‑90 (MQ=255)
   tttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTa                                                                                     >  2:99723‑M2/87‑90 (MQ=255)
   tttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTa                                                                                     >  2:155955‑M2/87‑90 (MQ=255)
    ttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTaa                                                                                    >  1:1121334‑M2/86‑90 (MQ=255)
      aCTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAgg                                                                                  >  2:60200‑M1/1‑88 (MQ=255)
       cTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAgga                                                                                 <  1:184784‑M1/90‑4 (MQ=255)
        tCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATa                                                                                <  1:579334/90‑1 (MQ=255)
        gggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATa                                                                                <  1:1295741‑M2/9‑1 (MQ=255)
         ggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATaa                                                                               <  2:1007034‑M2/10‑1 (MQ=255)
         cGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaag                                                                               >  1:1220830‑M1/1‑85 (MQ=255)
         cGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaag                                                                               >  2:576206‑M1/1‑85 (MQ=255)
         cGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaag                                                                               >  1:828672‑M1/1‑85 (MQ=255)
           tCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggt                                                                             >  1:645915‑M1/1‑83 (MQ=255)
           tCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggt                                                                             >  2:1179329‑M1/1‑83 (MQ=255)
            cACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtg                                                                            <  2:954931‑M1/90‑9 (MQ=255)
              cTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcg                                                                          >  1:663800‑M1/1‑80 (MQ=255)
                 cacGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaac                                                                       >  2:1524366‑M1/1‑77 (MQ=255)
                   cGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaa                                                                     <  1:60200‑M1/90‑16 (MQ=255)
                    cggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGtat                                                                         >  2:369188‑M2/70‑85 (MQ=255)
                    cggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGtat                                                                         <  1:369188‑M2/16‑1 (MQ=255)
                     cacaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagt                                                                   >  2:312191‑M1/1‑73 (MQ=255)
                     cacaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagt                                                                   >  2:1195733‑M1/1‑73 (MQ=255)
                     cacaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagt                                                                   <  2:1430688‑M1/90‑18 (MQ=255)
                     cacaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagt                                                                   >  2:173091‑M1/1‑73 (MQ=255)
                      gctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCAt                                                                  >  1:1064504‑M2/68‑90 (MQ=255)
                        aTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccc                                                                >  2:53366‑M1/1‑70 (MQ=255)
                        aTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccc                                                                >  1:542206‑M1/1‑70 (MQ=255)
                        aTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccc                                                                <  1:53366‑M1/90‑21 (MQ=255)
                             aCGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgata                                                           <  1:742030‑M1/90‑26 (MQ=255)
                               ggAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACttttgtt                                                         >  1:1430725/1‑90 (MQ=255)
                                 aGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCAt                                                                  <  1:227690/79‑1 (MQ=255)
                                 aGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCAt                                                                  >  2:227690/1‑79 (MQ=255)
                                      ggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcat                                                  <  1:990233‑M1/90‑35 (MQ=255)
                                       gCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatg                                                 >  2:722516‑M1/1‑55 (MQ=255)
                                         tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtt                                               <  1:533063‑M1/90‑38 (MQ=255)
                                          gCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgttt                                              >  1:874516‑M1/1‑52 (MQ=255)
                                             gactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCa                                           >  1:1393306‑M2/45‑90 (MQ=255)
                                               tttCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcat                                         >  2:291693‑M1/1‑47 (MQ=255)
                                                tgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATc                                        <  2:271460‑M2/49‑1 (MQ=255)
                                                 gagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCt                                       <  1:1174136‑M2/50‑1 (MQ=255)
                                                    ataatGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctgga                                    <  1:548195‑M1/90‑49 (MQ=255)
                                                    ataatGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctgga                                    <  1:930229‑M1/90‑49 (MQ=255)
                                                      agccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaa                                  <  1:200354‑M2/55‑1 (MQ=255)
                                                      aatGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagc                                  <  2:645915‑M1/90‑51 (MQ=255)
                                                       atGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagcc                                 >  2:68923‑M1/1‑39 (MQ=255)
                                                         gCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccat                               <  1:312191‑M1/90‑54 (MQ=255)
                                                         gCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccat                               <  1:1195733‑M1/90‑54 (MQ=255)
                                                            tGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGtt                            >  2:68077/1‑90 (MQ=255)
                                                              aTGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaac                          >  2:1426373‑M1/1‑32 (MQ=255)
                                                              aTGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGtttt                          >  1:1369908/1‑90 (MQ=255)
                                                               tGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaaca                         <  2:535018‑M1/90‑60 (MQ=255)
                                                               tGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaaca                         <  1:120095‑M1/90‑60 (MQ=255)
                                                               tGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaaca                         <  2:542206‑M1/90‑60 (MQ=255)
                                                               tGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaaca                         <  1:1524366‑M1/90‑60 (MQ=255)
                                                               tGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaaca                         <  1:291693‑M1/90‑60 (MQ=255)
                                                                  tttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgc                      <  1:99723‑M2/67‑1 (MQ=255)
                                                                   gATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggt                     <  1:173091‑M1/90‑64 (MQ=255)
                                                                   gATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggt                     >  2:1307459‑M1/1‑27 (MQ=255)
                                                                   gATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggt                     <  1:221366‑M1/90‑64 (MQ=255)
                                                                   gATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggt                     <  1:1179329‑M1/90‑64 (MQ=255)
                                                                        cacaAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatc                >  1:609751‑M1/1‑22 (MQ=255)
                                                                        cacaAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatc                >  2:213371‑M1/1‑22 (MQ=255)
                                                                        cacaAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatc                >  1:630447‑M1/1‑22 (MQ=255)
                                                                        cacaAAACACTCAATTACTTAAggaaggtgcgaacaagtccc                                                                >  1:1267405‑M1/1‑22 (MQ=255)
                                                                        cacaAAACACTCAATTACTTAAggaaggtgcgaacaagtccc                                                                <  2:1267405‑M1/42‑21 (MQ=255)
                                                                          caAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcat              >  2:187766‑M1/1‑20 (MQ=255)
                                                                           aaaaCACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatg             <  1:1466526‑M1/90‑72 (MQ=255)
                                                                            aaaCACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatga            >  2:488448‑M1/1‑18 (MQ=255)
                                                                             aaCACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgag           >  2:461322‑M1/1‑17 (MQ=255)
                                                                             aaCACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgag           >  1:632168‑M1/1‑17 (MQ=255)
                                                                               cacTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtc         <  2:828672‑M1/90‑76 (MQ=255)
                                                                                acTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtca        >  2:633472‑M1/1‑14 (MQ=255)
                                                                                 cTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcat       >  1:1095124‑M1/1‑13 (MQ=255)
                                                                                      ttcCTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATg  <  2:850927‑M2/87‑1 (MQ=255)
                                                                                         |                                                                                      
AACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATG  >  NZ_CP009273/1972658‑1972833

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ 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.