Predicted mutation
evidence seq id position mutation annotation gene description
MC JC NC_000913_3_pae_tpiA 1,978,503 Δ776 bp insB1insA insB1, insA

Missing coverage evidence...
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913_3_pae_tpiA 1978503 1979278 776 55 [0] [0] 55 insB1–insA insB1,insA

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_pae_tpiA = 19785020 (0.000)55 (1.020) 48/270 0.1 100% intergenic (‑305/+16) flhD/insB1 flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
?NC_000913_3_pae_tpiA 1979279 = 0 (0.000)intergenic (‑64/‑474) insA/uspC IS1 repressor TnpA/universal stress protein

ATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGC  >  NC_000913_3_pae_tpiA/1979135‑1979418
                                                                                                                                                |                                                                                                                                           
atgtgtccttacacttatccaatatttttcctaactcgacgcaactgtacccgtcactacacacacatacaacggaggggggcagcgattttcaataacgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATaa                                                                                                                                         <  1:162339‑M2/5‑1 (MQ=255)
atgggtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATaa                                                                                                                                         <  2:174165‑M2/5‑1 (MQ=255)
     tctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactaaacgacacccacacggaggggggctgcgattttcaataatgcgtgatgcagaacacacaaaacactcaattacttaacataaatgTATAAGTGAt                                                                                                                                    >  1:746162‑M2/140‑149 (MQ=255)
            acttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacctaaaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacctacatgTCTAAGTCATACttttg                                                                                                                             >  2:833640‑M2/133‑149 (MQ=255)
                  ctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                       <  1:920175‑M2/23‑1 (MQ=255)
                   taagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTCAAATTCATACTTTTGTTTTggg                                                                                                                      >  2:204305‑M2/126‑149 (MQ=255)
                   taagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTggg                                                                                                                      >  2:981508‑M2/126‑149 (MQ=255)
                    aagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGgt                                                                                                                     <  1:645220‑M2/25‑1 (MQ=255)
                      gatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGgtgt                                                                                                                   >  1:262866‑M2/123‑149 (MQ=255)
                        tttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAt                                                                                                                 >  2:950237‑M2/121‑149 (MQ=255)
                                 aatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCACTCTg                                                                                                        >  1:251113‑M2/112‑149 (MQ=255)
                                  atcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGt                                                                                                       <  2:746162‑M2/39‑1 (MQ=255)
                                  atcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGt                                                                                                       <  2:565000‑M2/39‑1 (MQ=255)
                                   tcgacgcaagtgtactggtcactacacgcacatagaacggaggggggctgcgattttcaataatgcgtgatgcagttcacacaaaacactcaattacttaacataaatgTATATGTCATACTTTTGTTTTGGGTGTATTTCAATCTGtt                                                                                                      <  2:490667‑M2/40‑1 (MQ=255)
                                        gcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaaa                                                                                                 <  1:935646‑M2/45‑1 (MQ=255)
                                        gcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTAATACTATTGTTTTGGGTGTATTTCAATCTGTTaaaaa                                                                                                 >  1:943258‑M2/105‑149 (MQ=255)
                                              gtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGttttt                                                                                           <  1:124099‑M2/51‑1 (MQ=255)
                                               tactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTc                                                                                          >  1:348583‑M2/98‑149 (MQ=255)
                                                  tcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTTAATCTGTTAAAAAGTTTTTcgct                                                                                       >  1:685591‑M2/95‑149 (MQ=255)
                                                  tcgtcactacacgcacaaacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgct                                                                                       <  2:138253‑M2/55‑1 (MQ=255)
                                                           cacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTcgca                                                                              >  1:422677‑M2/86‑149 (MQ=255)
                                                            acgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGATACGCTagcaa                                                                             >  2:622004‑M2/85‑149 (MQ=255)
                                                              gcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattgcttaacataaatgTTTAGGTCATACTTTTGCGTTGGGTGTATTTCAATCTGTTAAACCGTTTTTCGCTACCCTagcatgc                                                                           >  2:619510‑M2/83‑149 (MQ=255)
                                                                acatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACtttt                                                                                                                              <  2:822467‑M2/16‑1 (MQ=255)
                                                                acatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACtttt                                                                                                                              >  1:822467‑M2/81‑96 (MQ=255)
                                                                acatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAACGTTTTTAACTACGCtagtaagcac                                                                         >  2:402030‑M2/81‑148 (MQ=255)
                                                                  atacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacgctcaattgcttaacataaatgTATAAGTCATACTTTTGGTTTGGGTTTATTTCACTGTGTAAAAAAGTTTTTCGCTACGCTAGCAAGCaaaa                                                                       >  1:87918‑M2/79‑149 (MQ=255)
                                                                  atacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaa                                                                       >  2:756586‑M2/79‑149 (MQ=255)
                                                                      aacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacgtaaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTCTTTCGCTACGCTAGCGATCAAAgataa                                                                   >  1:449626‑M2/75‑147 (MQ=255)
                                                                      aacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGa                                                                   >  1:391168‑M2/75‑149 (MQ=255)
                                                                           aggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAg                                                              <  1:950237‑M2/80‑1 (MQ=255)
                                                                              ggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaa                                                           <  2:962525‑M2/83‑1 (MQ=255)
                                                                                  ctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaataat                                                       <  1:722067‑M2/87‑1 (MQ=255)
                                                                                         tttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATCCTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATg                                                >  1:140700‑M2/56‑149 (MQ=255)
                                                                                          ttaaataatgcgtgatgcagatcacacaaaacactcaaatacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATgg                                               <  2:17261‑M2/95‑1 (MQ=255)
                                                                                           tcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATggg                                              >  1:245310‑M2/54‑149 (MQ=255)
                                                                                                aatgcgagatgcagatcacacaaaacactcaatcagataacataaatgTAGACATCATACTCTTGTCTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGtt                                         <  2:813259‑M2/101‑1 (MQ=255)
                                                                                                      tgatgcagatcacacaaaacactcaattacttaacatacatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGTATGTTGCGcac                                   >  2:679720‑M2/43‑149 (MQ=255)
                                                                                                       gatgcagatcacacaaaaaactcaattacttaccataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcaca                                  <  1:204305‑M2/108‑1 (MQ=255)
                                                                                                        atgcagatcacacacaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAg                                 <  1:781946‑M2/109‑1 (MQ=255)
                                                                                                          gcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGAAGTTGCGCACAGTc                               >  1:255154‑M2/39‑149 (MQ=255)
                                                                                                          gcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTACATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAATc                               >  2:265782‑M2/39‑149 (MQ=255)
                                                                                                              atcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaaaa                           >  1:574585‑M2/35‑149 (MQ=255)
                                                                                                                 acacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATaa                        >  1:253416‑M2/32‑149 (MQ=255)
                                                                                                                   acaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACt                      >  1:216638‑M2/30‑149 (MQ=255)
                                                                                                                     aaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGGTGTTGCGCACAGTCAAAATAACTCa                    >  2:399811‑M2/28‑149 (MQ=255)
                                                                                                                      aaacactcaattacttaacataaatgTATAAGTCATACTTTTGGTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCAc                   <  1:318490‑M2/123‑1 (MQ=255)
                                                                                                                         cactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAGTTCAATATGTTAAAAAGTTTTTGGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGACATGGGATGTTACGCACAGTCAAAATAACTCACcga                >  2:312402‑M2/24‑148 (MQ=255)
                                                                                                                          actcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCCAAAATGAAACAGGAATAATCGAAATGGGATGTTAGGCACAGTCAAAataaatcgcagga               >  1:1008506‑M2/23‑143 (MQ=255)
                                                                                                                              aattacttaacataaataTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTGGCAAGCAAAAATGAAACAGGAATAATCGAAATTGGATGTTGCCAACAGACAAAATAACTAACAGTAaata           >  2:586593‑M2/19‑149 (MQ=255)
                                                                                                                                   cttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAatcat      <  1:978993‑M2/136‑1 (MQ=255)
                                                                                                                                    ttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTc                     <  2:100306‑M2/121‑1 (MQ=255)
                                                                                                                                    ttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTc                     >  1:100306‑M2/13‑133 (MQ=255)
                                                                                                                                     taacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGACATGGGGTGTTGCGCACAGTGAAAATAACTCACCGTAAATAATCATCt    <  1:399811‑M2/138‑1 (MQ=255)
                                                                                                                                       acataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGc  >  1:163758‑M2/10‑149 (MQ=255)
                                                                                                                                                |                                                                                                                                           
ATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGC  >  NC_000913_3_pae_tpiA/1979135‑1979418

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: