Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 4,475,797 C→T 8.2% intergenic (‑29/‑238) pepA ← / → lptF multifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor/lipopolysaccharide export ABC permease of the LptBFGC export complex

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092734,475,7970CT 8.2% 141.2 / 3.6 49intergenic (‑29/‑238)pepA/lptFmultifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor/lipopolysaccharide export ABC permease of the LptBFGC export complex
Reads supporting (aligned to +/- strand):  ref base C (24/21);  new base T (2/2);  total (26/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.93e-01

GCTGATTTTATCGAGCTGTTCTGCAATCGGAGAAAGGCGACGTGGTTCGAAGACGCCCACGACGATGCAGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAATCTGAGAGGTGAATCCGTTGAGTATAATTATCTTAGCGACG  >  CP009273/4475652‑4475945
                                                                                                                                                 |                                                                                                                                                    
gCTGATTTTATCGAGCTGTTCTGCAATCGGAGCAAGGCGACGTGGTTCGAAGACGCCCACGGCGATGCAGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGAACTACGCTCCTGAATCTTAAAGCCACcggc                                                                                                                                                   >  2:635336/1‑149 (MQ=255)
gCTGATTTTATCGAGCTGTTCTGCAATCGGAGAAAGGCGACGTGGTTCGAAGACGCCCACGACGATGCAGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAAcggc                                                                                                                                                   >  2:354290/1‑149 (MQ=255)
    aTTTTATCGAGCTGTTCTGCAATCGGAGAAAGGCGACGTGGTTCGAAGACGCCCACGACGATGCAGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCTTGAATCTTAAAGACAACGGCGGTg                                                                                                                                               <  2:647631/149‑1 (MQ=255)
      tttATCGAGCTGTTCTGCAATCGGAGAAAGGCGACGTGGTTCGAAGACGCCCACGACGATGCAGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGc                                                                                                                                             <  2:663116/149‑1 (MQ=255)
               cTGTTCTGCAATCGGAGAAAGGCGACGTGGTTCGAAGACGCCCACGACGATGCAGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAg                                                                                                                                    <  2:805214/149‑1 (MQ=255)
                  ttCTGCAATCGGAGAAAGGCGACGTGGTTCGAAGACGCCCACGACGATGCAGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAAt                                                                                                                                 <  1:265148/149‑1 (MQ=255)
                         aTCGGAGAAAGGCGACGTGGTTCGAAGACGCCCACGACGATGCAGGCACTCCGCTGTTTCTCCGCGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGc                                                                                                                          >  1:650908/1‑149 (MQ=255)
                            ggAGAAAGGCGACGTGGTTCGAAGACGCCCACGACGATGCAGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCttt                                                                                                                       >  2:438029/1‑149 (MQ=255)
                            ggAGAAAGGCGACGTGGTTCGAAGACGCCCACGACGATGCAGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCttt                                                                                                                       >  1:777868/1‑149 (MQ=255)
                            ggAGAAAGGCGACGTGGTTCGAAGACGCCCACGACGATGCAGGCACTCCGCGGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACACCGGCGGTGGCTACAGATAGAATTGCagccttg                                                                                                                       >  2:217408/1‑143 (MQ=255)
                              agaAAGGCGACGTGGTTCGAAGACGCCCACGACGATGCAGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCg                                                                                                                     <  1:827409/149‑1 (MQ=255)
                              agaAAGGCGACGTGGTTCGAAGACGCCCACGACGATGCAGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCg                                                                                                                     >  1:810504/1‑149 (MQ=255)
                              agaAAGGCGACGTGGTTCGAAGACGCCCACGACGATGCAGGCACTCCGCAGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCTATGCACAACGCACCTGAATCTTAGAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCg                                                                                                                     <  1:160537/149‑1 (MQ=255)
                                aaaGGCGACGTGGTTCGAAGACGCCCACGACGATGCAGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTa                                                                                                                   >  1:146463/1‑149 (MQ=255)
                                         gTGGTTCGAAGACGCCGACGACGATGCAGGCACTCCGGTGTTTCTCCGGGCTACCGCTTTGTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTc                                                                                                          >  2:553039/1‑149 (MQ=255)
                                           gtttCGAAGACGCCCACGACGATGCCGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGTCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCg                                                                                                        <  1:499699/147‑1 (MQ=255)
                                            gTTCGAAGCCGCCCACGACGATGCAGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTTCACTAAACTCCATGCACTATGCGCCTGAAGCTTAAAGACAACGGCGGTGGGTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGc                                                                                                       <  1:19267/149‑1 (MQ=255)
                                            gTTCGAAGACGCCCACGACGATGCAGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGc                                                                                                       <  2:505914/149‑1 (MQ=255)
                                             ttCGAAGACGCCCACGACGATGCAGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCt                                                                                                      <  1:291633/149‑1 (MQ=255)
                                              tCGAAGACGCCCACGACGATGCAGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTg                                                                                                     >  2:8530/1‑149 (MQ=255)
                                              tCGAAGACGCCCACGACGATGCAGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTg                                                                                                     >  2:619067/1‑149 (MQ=255)
                                                 aaGACGCCCACGACGATGCAGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAATGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTg                                                                                                  >  2:89325/1‑149 (MQ=255)
                                                 aaGACGCCCACGACGATGCAGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAATGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTg                                                                                                  >  2:89195/1‑149 (MQ=255)
                                                 aaGACGCCCACGACGATGCAGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTg                                                                                                  <  1:307280/149‑1 (MQ=255)
                                                            gacgaTGCCGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCg                                                                                       <  1:78677/149‑1 (MQ=255)
                                                                    aGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCCAGCTTTCGTAACTCCTGTCCGCTGTTGCGCTGACTTCGTGTTAATc                                                                               >  2:83204/1‑149 (MQ=255)
                                                                      gCACCCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCtt                                                                             <  1:87423/149‑1 (MQ=255)
                                                                             gCTGTTTCCCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTCCGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACGCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGtta                                                                      <  1:173771/149‑1 (MQ=255)
                                                                                gTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGttatta                                                                   >  2:336700/1‑149 (MQ=255)
                                                                                gTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGttatta                                                                   >  2:351498/1‑149 (MQ=255)
                                                                                gTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGttatta                                                                   >  1:418210/1‑149 (MQ=255)
                                                                                gTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGGGTTAATCTTAACGttatta                                                                   >  2:818585/1‑149 (MQ=255)
                                                                                 tttCTCCGGGCTACCGCTTTTTTTTTTTTTTTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGTTATTAc                                                                  >  1:700787/1‑149 (MQ=255)
                                                                                   tccccGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGTTATTACgg                                                                <  2:151320/146‑1 (MQ=255)
                                                                                       cGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTCCGACCGCTCCGTGTTAATCTTAACGTTATTACGGCAtt                                                            <  2:426126/149‑1 (MQ=255)
                                                                                       cGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCATGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGCCTTCGTGTTAATCTTAACGTTATTCCGGCCtt                                                            >  2:309955/1‑149 (MQ=255)
                                                                                       cGGGCTACCGCTTCTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGAAAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCAGTTGCAATGACTTCGTGTTAATCTTAATGTTATTACGGCAtt                                                            >  2:614685/1‑149 (MQ=255)
                                                                                           cTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTATAGACGACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGTTATTACGGCATTGGCa                                                        <  1:786188/149‑1 (MQ=255)
                                                                                                  tttttACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGa                                                 <  2:810504/149‑1 (MQ=255)
                                                                                                    tttACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAATGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAAc                                               <  1:89325/149‑1 (MQ=255)
                                                                                                    tttACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAATGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAAc                                               <  1:89195/149‑1 (MQ=255)
                                                                                                           tAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAATCt                                        >  1:138607/1‑149 (MQ=255)
                                                                                                             gaCTCCATGCCCTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAATCTga                                      <  2:279545/148‑1 (MQ=255)
                                                                                                             caCTCCATGCGCTACGCTCCTGAATCTTATAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAATCTga                                      <  1:553039/148‑1 (MQ=255)
                                                                                                                tCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGTTATTACGGCATTGGCCCGTCAGAACAAAATCTGagag                                   >  1:778455/1‑149 (MQ=255)
                                                                                                                    tGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAATCTGAGAGGTGa                               <  2:650908/149‑1 (MQ=255)
                                                                                                                                cTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAATCTGAGAGGTGAATCCGTTGAGta                   >  1:213506/1‑149 (MQ=255)
                                                                                                                                 tGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAACACCTGAGAGGAGAATTCGGTGAGtat                  >  2:580956/1‑149 (MQ=255)
                                                                                                                                     tCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAATCTGAGAGGTGAATACGTTGAGTATAAtt              >  1:420054/1‑149 (MQ=255)
                                                                                                                                       ttAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGTTATTCAGGACTTCTTACTTCAGAACACAATCTGAGAGGTGAATCCGTTGAGTATAATTAt            >  2:846972/1‑149 (MQ=255)
                                                                                                                                               aaCGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCCATGACTTCGTGTTAATCTTAACGTTATTACGGCATTGGCACGACAGAACAAAATCTGAGAGGTGAATCCGTTGAGTATAATTATCTTAGcga    >  1:569221/1‑149 (MQ=255)
                                                                                                                                                 cggcggTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAATCTGAGAGGTGAATCCGTTGAGTATAATTATCTTAGcgacg  <  2:822204/149‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                                    
GCTGATTTTATCGAGCTGTTCTGCAATCGGAGAAAGGCGACGTGGTTCGAAGACGCCCACGACGATGCAGGCACTCCGCTGTTTCTCCGGGCTACCGCTTTTTACACTAAACTCCATGCACTACGCTCCTGAATCTTAAAGACAACGGCGGTGGCTACAGATAGAATTGCAAGCTTTCGTAACTCATGTCCGCTGTTGCGATGACTTCGTGTTAATCTTAACGTTATTACGGCATTGGCACGTCAGAACAAAATCTGAGAGGTGAATCCGTTGAGTATAATTATCTTAGCGACG  >  CP009273/4475652‑4475945

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: ‑