Predicted mutation
evidence seq id position mutation freq annotation gene description
JC JC CP009273 2,400,257 IS5 (+) +4 bp 51.9% 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)13 (0.600) 12/272 NT 49.2% noncoding (1195/1195 nt) IS5 repeat region
?CP009273 2400257 = 13 (0.620)intergenic (‑137/‑783) lrhA/alaA transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2
* ? CP009273 = 2283592NA (NA)15 (0.690) 11/272 NT 52.8% noncoding (1/1195 nt) IS5 repeat region
?CP009273 = 2400260 13 (0.620)intergenic (‑140/‑780) lrhA/alaA transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2

GCACTTATCATATATTATCACTTACTGGCGGCTCATACTGAGCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCC  >  CP009273/2400110‑2400405
                                                                                                                                                   |                                                                                                                                                    
aaaactggggataacgccttaaatggcgaagaaacggtctaaataggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCt                                                                                                                                                     >  1:304368‑M2/148‑149 (MQ=255)
  aactggggataacgccttaaatggcgaagaaacggtctaaataggctgattcacggcaaacttgcgagaaaaaatcggctcaaccatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTaa                                                                                                                                                   <  1:389243‑M2/4‑1 (MQ=255)
  aactggggataacgccttaaatggcgaagaaacggtctaaataggctgattcaaggcatttgcgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTaa                                                                                                                                                   >  1:13268‑M2/146‑149 (MQ=255)
      ggggataacgccttaaatggcgaagaaacggtctaaataggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagctgagaagaatttccccacttattcgcaccttccCTaaaaaa                                                                                                                                               <  1:56966‑M2/8‑1 (MQ=255)
        ggataacgccttaaatggcgaagaaacggtctaaataggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTaaa                                                                                                                                                  <  2:290341‑M2/5‑1 (MQ=255)
         atatatTATCACTTACTGGCGGCTCATACTGAGCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCCCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCg                                                                                                                                            >  1:275323/1‑149 (MQ=255)
             acgccttaaatggcgaagaaacggtctaaataggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGc                                                                                                                                             <  2:341455‑M2/10‑1 (MQ=255)
                     aatggcgaagaaacggtctaaataggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACTcaca                                                                                                                                     <  2:358172‑M2/18‑1 (MQ=255)
                            aagaaacggtttaaataggctgattcaaggcattgacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTtat                                                                                                                         <  1:382339‑M2/30‑1 (MQ=255)
                                   tACTGAGCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGGATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATaa                                                                                                                       >  2:40605/1‑144 (MQ=255)
                                      tGAGCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGATGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgt                                                                                                               <  1:233158‑M2/149‑37 (MQ=255)
                                       taaataggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGcc                                                                                                                   >  2:203005‑M2/109‑144 (MQ=255)
                                       gAGCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGcc                                                                                                                   <  2:279099/144‑1 (MQ=255)
                                        aGCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCCTCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCt                                                                                                                  >  2:23737/1‑144 (MQ=255)
                                        aGCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatca                                                                                                                  <  2:338778‑M2/144‑34 (MQ=255)
                                        aGCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagaaca                                                                                                                  <  2:201667‑M2/144‑34 (MQ=255)
                                         gCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgataggggatcatgtttg                                                                                                            <  1:150981‑M2/149‑40 (MQ=255)
                                         gCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagcccctgatatgagttcatgtttg                                                                                                            <  1:150959‑M2/149‑40 (MQ=255)
                                                tgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGAtcacc                                                                                                     >  1:204549‑M2/100‑148 (MQ=255)
                                                      gtgCACACACAAACAAGCAATTCTATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAg                                                                                                    >  2:240803/1‑144 (MQ=255)
                                                      aaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAatat                                                                                               <  1:126067‑M2/56‑1 (MQ=255)
                                                        gCACACACAAACAAGCAATTCCAGTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggag                                                                                                  >  2:25422‑M2/1‑95 (MQ=255)
                                                                    aaGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAATAGCTACCAGAATATATAttaggg                                                                                      >  2:106855/1‑140 (MQ=255)
                                                                        aaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATGACAGAATATATCTTCAGGGATCGCata                                                                             >  1:363546‑M2/76‑149 (MQ=255)
                                                                              aTTTGGAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttgaacatt                                                                            <  2:247891‑M2/144‑72 (MQ=255)
                                                                                ttGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACCCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCt                                                                          <  2:343962/144‑1 (MQ=255)
                                                                                 tGTAATGTGCCTCCCTGGCAGTTTCCTCCGGATCCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcgtcatgagtcatca                                                                    >  1:271241‑M2/1‑70 (MQ=255)
                                                                                 tGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatca                                                                    >  1:957‑M2/1‑70 (MQ=255)
                                                                                      catgaagaaatgaaatgactgagtcagccgagaagaatgtccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAg                                                                    <  2:70849‑M2/83‑1 (MQ=255)
                                                                                         gCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTa                                                                 <  2:100167/144‑1 (MQ=255)
                                                                                                tgaaatgactgagtcagccgagaagaacttccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTactcactc                                                          <  2:178352‑M2/93‑1 (MQ=255)
                                                                                                      tttcgtccgggttccGGATGAAAGTAAAAATGCATATGAGTTGCACTAAAAAGGCGCAGCAGAATTTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTa                                               >  1:252890/14‑149 (MQ=255)
                                                                                                       ttCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgaca                                                   >  2:200575‑M2/1‑48 (MQ=255)
                                                                                                         cATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagt                                                 <  2:225438‑M2/144‑99 (MQ=255)
                                                                                                                  cccGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATg                                        <  2:245240/144‑1 (MQ=255)
                                                                                                                    cGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggagcgaacaagtccctgatatgagcacatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcag                                      <  2:324986‑M2/144‑110 (MQ=255)
                                                                                                                      aagaatttccccgcttagtcgcaccttgcCTAAAAGAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGttt                               <  1:348778‑M2/120‑1 (MQ=255)
                                                                                                                         gAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgt                            >  1:228777‑M2/1‑30 (MQ=255)
                                                                                                                               cccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAAAATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatg                      >  1:198417‑M2/21‑149 (MQ=255)
                                                                                                                                         atGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaaat                 >  2:105903/1‑144 (MQ=255)
                                                                                                                                            aGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTcc         >  1:64056/1‑149 (MQ=255)
                                                                                                                                            aGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTACAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTcc         >  1:240580/1‑149 (MQ=255)
                                                                                                                                             ccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCTTGTATGTATAAATGTAAATGTGAGTCCt        <  1:297624‑M2/143‑1 (MQ=255)
                                                                                                                                              ttGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCtt       <  1:76650/149‑1 (MQ=255)
                                                                                                                                               tGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtcagaccagaaaagagattttct      >  1:228036‑M2/1‑8 (MQ=255)
                                                                                                                                               tGCAATAAggaaggggccaacaagtccctgatatgagatcatgtttgtcatctggagccatagcacagggttcatcatgagtcagcaacttaccttcgccgacagtgaattcagcaggaagcgccgtcagaccagaaaagagattttct      >  1:375655‑M2/1‑8 (MQ=255)
                                                                                                                                                   cTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtcagaccagaacaggggttttcttgtc  <  1:10297‑M2/149‑146 (MQ=255)
                                                                                                                                                   cTAAggaaggtgcgaacaagtccctgatatgagatcatgtgtgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtcagaccagaaaagagattttcttgtc  >  1:275418‑M2/1‑4 (MQ=255)
                                                                                                                                                   |                                                                                                                                                    
GCACTTATCATATATTATCACTTACTGGCGGCTCATACTGAGCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCC  >  CP009273/2400110‑2400405

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.