Predicted mutation
evidence seq id position mutation freq annotation gene description
JC JC CP009273 2,400,257 IS5 (+) +4 bp 63.6% 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)5 (0.280) 5/270 NT 44.7% noncoding (1195/1195 nt) IS5 repeat region
?CP009273 2400257 = 6 (0.340)intergenic (‑137/‑783) lrhA/alaA transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2
* ? CP009273 = 2283592NA (NA)16 (0.890) 13/270 NT 72.1% noncoding (1/1195 nt) IS5 repeat region
?CP009273 = 2400260 6 (0.340)intergenic (‑140/‑780) lrhA/alaA transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2

TCACTTACTGGCGGCTCATACTGAGCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCCA  >  CP009273/2400127‑2400406
                                                                                                                                     |                                                                                                                                                  
tCACTTACTGGCGGCTCATACTGAGCTGGTTAATGCTGTTTACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaa                                                                                                                                     >  1:143786‑M2/1‑134 (MQ=255)
      aCTGGCGGCTCATACTGAGCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACAt                                                                                                                                     <  2:49141/143‑1 (MQ=255)
            ggcTCATACTGAGCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTcc                                                                                                                               >  2:240188/1‑143 (MQ=255)
             gcTCATACTGAGCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctg                                                                                                                              <  2:172118‑M2/143‑23 (MQ=255)
                cATACGGAGCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgata                                                                                                                           >  2:270113‑M2/1‑118 (MQ=255)
                acggtctaaataggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGc                                                                                                                     <  1:176777‑M2/35‑1 (MQ=255)
                   aCTTAGCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatga                                                                                                                        >  2:236759‑M2/1‑115 (MQ=255)
                      taaataggcggaatcaaagcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAg                                                                                                               <  1:165250‑M2/41‑1 (MQ=255)
                             gctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGt                                                                                                              >  2:298338‑M2/102‑143 (MQ=255)
                               aaTGCTTTGGCTACGCAATCAAGCAATTCCATTTTTCATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGCACCAAAGAAAAAATGTATATGAGTTGCACTAAggaaggtgcgaacaagtccttgatatgagatcatgtttgtcatctg                                                                                                      >  1:128681‑M2/1‑103 (MQ=255)
                               aaTGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctg                                                                                                      <  1:67977‑M2/149‑47 (MQ=255)
                                 tGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTCCACTAAggaaggtgcgaacaattccctgatatgagatcaagtttgtca                                                                                                          <  2:137178‑M2/143‑43 (MQ=255)
                                         acacacaAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAat                                                                                                  >  2:241721/1‑143 (MQ=255)
                                             acaaacaaGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAg                                                                                        <  1:256545/149‑1 (MQ=255)
                                                aacaaGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaa                                                                                           <  2:142651‑M2/143‑58 (MQ=255)
                                                          tCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgag                                                                           <  1:102176‑M2/149‑74 (MQ=255)
                                                                      atgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTactc                                                               <  1:330460‑M2/89‑1 (MQ=255)
                                                                               tGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcgtcaacttaccttcgccga                                                      >  1:195127‑M2/1‑55 (MQ=255)
                                                                                     tttcgtccgggttccggatgaaagtaaaAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccga                                                      <  2:294514‑M2/130‑95 (MQ=255)
                                                                                         aTCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagt                                                  <  2:32480‑M2/143‑99 (MQ=255)
                                                                                              gAACCCGGACGAAAGTAAAACTGCCTATGAGTTGCCCTAAggaaggtgcgaacaagtccctgatatgagaccatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaagttaccttcgcccacggtttatt                                             >  2:50776‑M2/1‑40 (MQ=255)
                                                                                               atcacGGACGAAAGTAAAAATGCATATGAAGTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGAc                                            <  2:88417/139‑1 (MQ=255)
                                                                                                        gAAAGGAAAAATGCATATGAGTTGCACTAAggaaggggcgaacacgtccctgatatgagatcatgtttgtcatctggagccatagaacagggtgcatcatgagtcaacaacttaccctcgccgacagtgaattcagcagtaag                                   >  2:178128‑M2/1‑30 (MQ=255)
                                                                                                         aaaGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCgtgt                                  <  2:222931/143‑1 (MQ=255)
                                                                                                           ttccccgcttattcgcaccttccCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGttt                                <  2:290697‑M2/120‑1 (MQ=255)
                                                                                                                   ggcATATGAGTTGCACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtcagaccagaaa                  >  1:156619‑M2/2‑19 (MQ=255)
                                                                                                                    gaaaactgtggtatctaaggaaggttcgaacaagcccctgatatgagatcatgtttgtcatctggagtcatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtcagaccagaaaa                 >  1:3824‑M2/15‑18 (MQ=255)
                                                                                                                                cACTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtcagaccagaaaagagattttcttg     <  1:169466‑M2/149‑144 (MQ=255)
                                                                                                                                cACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGGGTc           >  2:505/1‑143 (MQ=255)
                                                                                                                                cACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTc           >  2:517/1‑143 (MQ=255)
                                                                                                                                  cTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtcagaccagaaaagagatattcttgtc   <  1:270012‑M2/149‑146 (MQ=255)
                                                                                                                                   tAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtcagaccagaaaagagattttcttgtcc  <  1:253412‑M2/149‑147 (MQ=255)
                                                                                                                                     aggagggtgcgaacaagtccctgagatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtcagaccagaaaagagattttctt      >  2:107739‑M2/1‑1 (MQ=255)
                                                                                                                                     aggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatataacagggttcatcatgagtcatcaacttaccgtcgccgacagtgaattcagcagtaagcgccgtcagaccagaaaagagattttctt      >  2:16555‑M2/1‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                                  
TCACTTACTGGCGGCTCATACTGAGCTGGTTAATGCTGTGCACACACAAACAAGCAATTCCATTTGTAATGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCCA  >  CP009273/2400127‑2400406

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.