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 1978503–1979270 1979278 9–776 28 [1] [0] 29 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 = 19785021 (0.030)27 (0.730) 25/264 0.6 98.3% 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

TTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAAT  >  NC_000913_3_pae_tpiA/1978366‑1978649
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tttACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatac                                                                                                                                         <  2:93258‑M1/149‑13 (MQ=255)
      cTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgt                                                                                                                                   <  1:571785‑M1/149‑19 (MQ=255)
       ttATCTAAGATTTTTCCTAAATCGTCGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtt                                                                                                                                  >  1:102623‑M1/1‑130 (MQ=255)
                       cTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtttttggtgtatttcaat                                                                                                                  >  2:467528‑M1/1‑114 (MQ=255)
                        tAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatc                                                                                                                 >  2:342145‑M1/1‑113 (MQ=255)
                                                 cTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATACATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgcta                                                                                        <  1:486044‑M1/149‑62 (MQ=255)
                                                  tACCCGGACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctag                                                                                       <  1:636037‑M1/149‑63 (MQ=255)
                                                  tACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctag                                                                                       >  2:70510‑M1/1‑87 (MQ=255)
                                                     acGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaa                                                                                    >  1:354872‑M1/1‑84 (MQ=255)
                                                              cAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacccgaccaagcaaaaatg                                                                           >  1:328881‑M1/1‑75 (MQ=255)
                                                               aaCGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatga                                                                          >  1:116403‑M1/1‑74 (MQ=255)
                                                                     ggggcgCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagg                                                                    <  2:634687‑M1/149‑82 (MQ=255)
                                                                            tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgtgtgtatttcaatctgttaaaaagtttttcgctatgctagcaagcaaaaatgaaacaggaatactc                                                             >  2:650888‑M1/1‑61 (MQ=255)
                                                                            tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatc                                                             >  2:347228‑M1/1‑61 (MQ=255)
                                                                                   ttCAATAATGCGTGATGCAGATCACACAAACCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgtgtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaacgg                                                      <  1:8373‑M1/149‑96 (MQ=255)
                                                                                                      gATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctatcatgaaaatcagaaagaggaataatcgaaatgggatgttgcgaacagtcaaa                                   >  2:146116‑M1/1‑35 (MQ=255)
                                                                                                              aaaaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcg                                                                                                >  1:187674‑M1/1‑27 (MQ=255)
                                                                                                              aaaaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcg                                                                                                <  2:187674‑M1/80‑54 (MQ=255)
                                                                                                               aaaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcac                          >  1:59067‑M1/1‑26 (MQ=255)
                                                                                                                       aaTTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaata                  >  2:629691‑M1/1‑18 (MQ=255)
                                                                                                                            cTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcat             <  1:62627‑M1/149‑137 (MQ=255)
                                                                                                                             ttAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatc            >  1:367055‑M1/1‑12 (MQ=255)
                                                                                                                              tAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttg                                               <  2:12542‑M1/113‑103 (MQ=255)
                                                                                                                              tAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttg                                               >  1:12542‑M1/1‑11 (MQ=255)
                                                                                                                              tAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgatacgctagcaaggaaaaatgaaacaggaagaatcgaaatgggatgttgcgcacagtcaaaataacttaccgtaaataatgatct           >  2:529575‑M1/1‑11 (MQ=255)
                                                                                                                               aaCATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctg          >  1:86247‑M1/1‑10 (MQ=255)
                                                                                                                                aCATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgc         >  1:569765‑M1/1‑9 (MQ=255)
                                                                                                                                       cgggTAATGACTCCAACTTCTTGATAGCGTTTTATGTACAGATACTGCCCGATGACTTTGTCATGCAGCCCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGAGTCAGGTTATCCCCCCCAAt  >  2:578061/2‑149 (MQ=11)
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TTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAAT  >  NC_000913_3_pae_tpiA/1978366‑1978649

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: