Predicted mutation
evidence seq id position mutation annotation gene description
MC JC NC_000913_3_pae_tpiA 1,299,499 Δ1,199 bp intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein

Missing coverage evidence...
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913_3_pae_tpiA 1299499–1300695 1300697 3–1199 28 [0] [0] 28 ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_pae_tpiA = 12994980 (0.000)26 (0.860) 24/276 0.3 100% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913_3_pae_tpiA 1300698 = 0 (0.000)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein

TTCTCAAATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCC  >  NC_000913_3_pae_tpiA/1299351‑1299645
                                                                                                                                                   |                                                                                                                                                   
ttctCAAATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTGGAGGAAAGTGCTAAa                                                                                                                                                    >  1:77560‑M1/1‑148 (MQ=255)
 tctcAAATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTGAat                                                                                                                                                   >  1:99240‑M1/1‑147 (MQ=255)
    cAAATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataat                                                                                                                                                <  1:295512‑M1/149‑6 (MQ=255)
     aaaTTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACGGCCCTTGGTAAAGGACTGTGCTAAataata                                                                                                                                               >  1:3125‑M1/1‑143 (MQ=255)
        ttACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatc                                                                                                                                            <  2:240912‑M1/149‑10 (MQ=255)
                aggtataaggATTTCCTTAACTGCTTGGCCTCACCATCATGTTAGTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAGTAATTGACATGATATTATTAATTCCACTGCCTTTGGTAGAGGATAGTGCTAAataataatcaattgtta                                                                                                                                    <  1:417802‑M1/146‑18 (MQ=255)
                  ttaTAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCGAAataataatcaattgttaaa                                                                                                                                  >  1:426457‑M1/1‑130 (MQ=255)
                  ttaTAAGGATTTCCATAACTGCTTCTCTTCACTATCATGTTCATTTCAATCCAACATAATCCTGGGCTTGCTGAATAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaa                                                                                                                                  <  1:125711‑M1/149‑20 (MQ=255)
                          aTTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtg                                                                                                                          <  2:317133‑M1/149‑28 (MQ=255)
                              ccTTAACTGCTTCTCCTCACCATCATGTTATTTTAGCCACAGCAGAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatt                                                                                                                      >  1:270538‑M1/1‑118 (MQ=255)
                                           tcctcACCCTCATGGTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataatcatcaattgtttaattattgtgcatttcactactgtaat                                                                                                         >  2:511273‑M1/1‑105 (MQ=255)
                                                aCCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttaactactggaactgtaa                                                                                                    >  2:339364‑M1/1‑100 (MQ=255)
                                                      ttgTAATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAACTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaa                                                                                              >  2:417932‑M1/2‑94 (MQ=255)
                                                        gTTATTTTCGCCACATGATAATCCTGGGCTTACTGAAGAATAATTGAAATGATATTATTAATTCCACTGCATTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattatggtgcatttcagtaccggaactgtaataaacaca                                                                                            >  2:193798‑M1/1‑92 (MQ=255)
                                                           aTTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagat                                                                                         <  2:239405‑M1/149‑61 (MQ=255)
                                                                                    ctggcttAAGAATAATTGAAAGGAGATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataattaattgttaaattattgtgaatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctattt                                                                <  2:115647‑M1/146‑86 (MQ=255)
                                                                                      tGCTGAACAATTATTGAAATGATATTATTAATTCCACAGCCTTTGGTATAGGAAAGTGCTAAataataatcaagtgttaaatcattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttga                                                              <  2:191451‑M1/149‑88 (MQ=255)
                                                                                        gtgAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgatt                                                            <  1:286874‑M1/148‑90 (MQ=255)
                                                                                          gaagaaTAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattga                                                          <  1:233498‑M1/149‑92 (MQ=255)
                                                                                                  atTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaag                                                  <  1:277686‑M1/149‑100 (MQ=255)
                                                                                                   ttGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaaga                                                 >  2:317195‑M1/1‑49 (MQ=255)
                                                                                                    tGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaaga                                                                                          <  2:279287‑M1/107‑60 (MQ=255)
                                                                                                    tGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaaga                                                                                          >  1:279287‑M1/1‑48 (MQ=255)
                                                                                                    ggaaatgaaattATTAAGTCCAAGGCCTTTGGTAGAGGAAAGCGCTAAataataatcaattgttaaattattgtgcattcgactactggaactgtaatgagaaaagatagacatgcttagccaatctctatttgattgaattgaaagat                                                <  2:3125‑M1/148‑102 (MQ=255)
                                                                                                                attaATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggc                                    >  2:176535‑M1/1‑36 (MQ=255)
                                                                                                                                    tAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagatt                >  2:67015‑M1/1‑16 (MQ=255)
                                                                                                                                                 tAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaacacagtttgttaaggcatggatgcaagctatagattctgatacggtcaa   <  1:406513‑M1/149‑147 (MQ=255)
                                                                                                                                                  aaataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgaggtaataaaaactggggttttaaggcatggatgcaagctatagattctgatacggtcaat  <  1:406333‑M1/149‑148 (MQ=255)
                                                                                                                                                   |                                                                                                                                                   
TTCTCAAATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCC  >  NC_000913_3_pae_tpiA/1299351‑1299645

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: 
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.