Predicted mutation
evidence seq id position mutation freq annotation gene description
JC JC CP009273 2,400,257 IS5 (+) +4 bp 87.2% intergenic (‑137/‑780) lrhA ← / → alaA transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 2282398 =NA (NA)18 (1.250) 15/274 NT 85.3% noncoding (1195/1195 nt) IS5 repeat region
?CP009273 2400257 = 3 (0.210)intergenic (‑137/‑783) lrhA/alaA transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2
* ? CP009273 = 2283592NA (NA)23 (1.590) 23/274 NT 88.2% noncoding (1/1195 nt) IS5 repeat region
?CP009273 = 2400260 3 (0.210)intergenic (‑140/‑780) lrhA/alaA transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2

ACTTATCATATATTATCACTTACTGGCGGCTCATACTGAGCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCCA  >  CP009273/2400112‑2400406
                                                                                                                                                    |                                                                                                                                                  
aactggggataacgccttaaatggcgaagaaacggtctaaataggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTaaa                                                                                                                                                   >  1:48601‑M2/146‑150 (MQ=255)
         taacgccttaaatggcgaagaaacggtctaaataggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACt                                                                                                                                          >  1:218768‑M2/137‑150 (MQ=255)
         taacgccttaaatggcgaagaaacggtctaaataggctgattcaaggcatttacgggagaaaaaataggctcaaccatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccgcgcCTAAAAAAGc                                                                                                                                              >  2:25470‑M2/137‑146 (MQ=255)
          tattatCACTTACTGGCGGCTCATACTGAGCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggtaggt                                                                                                                                             <  2:36139‑M2/146‑8 (MQ=255)
                  naatggcgaagaaacggtctaaataggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcacaccttccCTAAAAAAGCGACTCACATTGtt                                                                                                                                 >  1:165317‑M2/128‑150 (MQ=255)
                  aaatggcgaagaaacggtctaaataggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtctgccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACTCACAt                                                                                                                                     <  2:123649‑M2/19‑1 (MQ=255)
                        ggtggcTCATACTGAGCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACAAAggaaggtgcgaacaagtccct                                                                                                                               <  2:92971‑M2/146‑22 (MQ=255)
                                aTCCTGAGCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgag                                                                                                                       >  2:162468‑M2/1‑117 (MQ=255)
                                    ctaaataggctgattcaaggcatttacaggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAg                                                                                                               <  1:149764‑M2/41‑1 (MQ=255)
                                       gCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGaa                                                                                                                >  2:222979/1‑146 (MQ=255)
                                        cTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtt                                                                                                               >  2:123605‑M2/1‑109 (MQ=255)
                                          ggTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcat                                                                                                         <  1:242337‑M2/150‑44 (MQ=255)
                                           ggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttgcCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAg                                                                                                            >  2:159230‑M2/103‑146 (MQ=255)
                                                attcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATcac                                                                                                       >  2:115107‑M2/98‑146 (MQ=255)
                                                attcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCCAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGACGTAGATCCCGGaa                                                                                                   >  1:74122‑M2/98‑150 (MQ=255)
                                                     tgCACACACAAACAAGCAATTGCATTTGTAATGCGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagc                                                                                                  >  2:182824‑M2/1‑96 (MQ=255)
                                                     tgCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATAGGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAatatat                                                                                              <  1:188636/150‑1 (MQ=255)
                                                       cacacacaAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagcca                                                                                                <  2:234561‑M2/146‑53 (MQ=255)
                                                          tttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATc                                                                                             >  2:130468‑M2/88‑146 (MQ=255)
                                                              aaacaaGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggt                                                                                     >  1:238413‑M2/1‑87 (MQ=255)
                                                                   gaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCa                                                                                >  1:232979‑M2/79‑150 (MQ=255)
                                                                   aGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatc                                                                                >  1:130730‑M2/1‑82 (MQ=255)
                                                                   aGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggtt                                                                                    <  2:233011‑M2/146‑65 (MQ=255)
                                                                     cAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcat                                                                              >  1:33055‑M2/1‑80 (MQ=255)
                                                                       aTTCCATTTGCAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatga                                                                            >  1:40950‑M2/1‑78 (MQ=255)
                                                                        ttCCATTGGGAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgag                                                                           <  1:130025‑M2/150‑74 (MQ=255)
                                                                             tttGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatc                                                                      >  1:234695‑M2/1‑72 (MQ=255)
                                                                                gTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcat                                                                       >  2:173417‑M2/1‑69 (MQ=255)
                                                                                caaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTa                                                                       <  2:194043‑M2/81‑1 (MQ=255)
                                                                                     atgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTactca                                                              >  1:92066‑M2/61‑150 (MQ=255)
                                                                                        aagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTactcactc                                                           >  1:157071‑M2/58‑150 (MQ=255)
                                                                                          gaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCtt                                                         >  1:79821‑M2/56‑150 (MQ=255)
                                                                                              tgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCt                                                     <  1:25825‑M2/99‑1 (MQ=255)
                                                                                               ggCCGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCACATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgaca                                                    >  1:223411‑M2/1‑54 (MQ=255)
                                                                                                  atgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTCTAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTATTTTCTAttt                                                 >  1:255275‑M2/48‑150 (MQ=255)
                                                                                                   gTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaactcaccttcgccgcca                                                    <  2:122670‑M2/146‑97 (MQ=255)
                                                                                                        aTCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAGggaaggtgcgaacaagtcactgatatgagatcatgtttgtcatctggaaccatagaacagggatcatcatgagtcatcaacttaccttcgccgacagagaa                                               <  2:38544‑M2/146‑102 (MQ=255)
                                                                                                              atccgggACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagc                                         >  2:162341‑M2/3‑39 (MQ=255)
                                                                                                              aaCCCGGACGAAAGTAAAAATGCACATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagta                                     >  1:76002‑M2/1‑39 (MQ=255)
                                                                                                                cgagaagaatttccccgctgattcacaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATgcg                                       <  2:145035‑M2/113‑1 (MQ=255)
                                                                                                                  cGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcg                                 <  1:214303‑M2/150‑116 (MQ=255)
                                                                                                                           tccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaat                        <  1:110396‑M2/128‑1 (MQ=255)
                                                                                                                                aaTGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtcagaccagaa                   <  1:162482‑M2/150‑130 (MQ=255)
                                                                                                                                    cATATGAGTTGCACTAAAACAGCGTCACACACTTTTCCGTTTTGTTTTTATAATTAGATCACAGAATATATCTTCATGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAAtgtg               <  1:190975/150‑1 (MQ=255)
                                                                                                                                         gAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtcagaccagaaaagagattt          >  1:254578‑M2/1‑12 (MQ=255)
                                                                                                                                              gCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGtt     <  1:48290/150‑1 (MQ=255)
                                                                                                                                               ccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTAGGTCCTTGTTc    >  1:217310‑M2/3‑150 (MQ=255)
                                                                                                                                                cCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTg       <  2:207179‑M2/145‑1 (MQ=255)
                                                                                                                                                cCTAAAAAAGCGACTCACATTGTTCCGTTAGAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTcc   <  1:180790‑M2/149‑1 (MQ=255)
                                                                                                                                                aCTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtcagaccagaaaagagattttct       >  2:113121‑M2/1‑5 (MQ=255)
                                                                                                                                                 cTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtcagaccagaaaagagattttcttgtcc  <  1:200729‑M2/150‑147 (MQ=255)
                                                                                                                                                 cTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtcagaccagaaaagagattttctt      <  2:80593‑M2/146‑143 (MQ=255)
                                                                                                                                                    |                                                                                                                                                  
ACTTATCATATATTATCACTTACTGGCGGCTCATACTGAGCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCCA  >  CP009273/2400112‑2400406

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