Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,805,347 G→T 11.6% T259T (ACC→ACA)  secA2 ← Sec family Type I general secretory pathway protein SecA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,805,3470GT11.6% 119.8 / 2.9 55T259T (ACC→ACA) secA2Sec family Type I general secretory pathway protein SecA
Reads supporting (aligned to +/- strand):  ref base G (25/21);  new base T (4/3);  total (31/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTCAAACAAATATTGTGCGCGCAGTGCTAAATTAATATTACGCACTAGGACCATCGCTTGTTCGCTATATAAATCTTCAACATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATATGAAATAGATTTGATTGTAATCTTGGTGCACCCGAAATAACTAATGGTGTTTGAGCAGCATCTAAAATGATTGAA  >  CP000730/2805209‑2805482
                                                                                                                                          |                                                                                                                                       
ttCAAACAAATATTGTGCGCGCAGTGCTAAATTAATATTACGCACTAGGACCATCGCTTGTTCGCTATATAAATCTTCAACATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTgg                                                                                                                                        <  2:594542/140‑1 (MQ=255)
 tCAAACACATATTGTGCGCGCAGTGCTAAATTAATATTACGCACTAGGACCATCGCTTGTTCGCTATATAAATCTTCAACATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGt                                                                                                                                       >  2:243334/1‑140 (MQ=255)
  caaacaaaTTTTGTCCGCGCAGTGCTAAATTAACATTACGCACTAGGACCATCGCTTGTTCGCTATATAAATCTTCAACATTAAAGTATGATTGTGCGGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGtc                                                                                                                                      <  2:186963/140‑1 (MQ=255)
      caaaTATTGTGCGCGCAGTGCTAAATTAATATTACGCACTAGGACCATCGCTTGTTCGCTATATAAATCTTCAACATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTTGtcttct                                                                                                                                  <  1:415736/140‑1 (MQ=255)
             tgtgCGCGCAGTGCTAAATTAATATTACGCACTAGGACCATCGCTTGTTCGCTATATAAATCTTCAACATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCAtttt                                                                                                                           <  1:565897/140‑1 (MQ=255)
                gcgcgcAGTGCTAAATTAATATTACGCACTAGGGCCATCGCTTGTTCGCTATATAAATCTTCAACATTAAAGTATGATTGTGCCGCTTCAATAACTTGAGTTGACAGCCATATTTCTTTTTTAGTCTTCTTCATTTTaaa                                                                                                                        >  1:621227/1‑140 (MQ=255)
                      aGTGCTAAATTAATATTACGCACTAGGACCATCGCTTGTTCGCTATATAAATCTTCAACATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCAc                                                                                                                  <  1:512831/140‑1 (MQ=255)
                       ctaatAAATTAGTATTACGCACTAGGACCATCGCTTGTTCGCTATATAAATCTTCAACATTAAAGTATGATTGTGCCGCTTCACTACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTGCTTCATTTTaaaaaccaag                                                                                                                 >  2:78781/5‑134 (MQ=255)
                        tGCTAAATTAATATTACGCACTAGGACCATCGCTTGTTCGCTATATAAATCTTCAACATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGt                                                                                                                >  1:68255/1‑140 (MQ=255)
                        tGCTAAATTAATATTAAGCACTAGGACCATCGCTTGTTCGATATATAAATCTTCAACATTAACGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAACTgaccgt                                                                                                                >  2:93616/1‑135 (MQ=255)
                         gCTAAATTAATATTACGCACTAGGACCATCGCTTGTTCGCTATATAAAACTTCAACATTAAAGTAAGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTACTTCATTTAAAAAGGCACgac                                                                                                               >  1:195600/1‑138 (MQ=255)
                          cTAAATTAATATTACGCACTAGGACCATCGCTTGTTCGCTATATAAATCTTCAACATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCt                                                                                                              <  2:263424/140‑1 (MQ=255)
                          cTAAATTAATATTACGCACTAGGACCATCGCTTGTTCGCTATATAAATCTTCAACATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCt                                                                                                              <  2:462102/140‑1 (MQ=255)
                                    atTACGCACTAGGACCATCGCTTGTTCGCTATATAAATCTTCAACAGTAAAATAAGATTGTGCCACTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGTTCTTCTTCTTTTTAAAATGACAGTCTTCAATCAATg                                                                                                    >  2:258205/1‑140 (MQ=255)
                                     ttACGCCCTAGGACCATCGCTTGTTCGCTATATAAATCTTCAACATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGt                                                                                                   <  1:288323/140‑1 (MQ=255)
                                      tACGCACTAGGACCATCGCTTGTTCGCTATATAAATCTTCAACATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTa                                                                                                  <  1:353460/140‑1 (MQ=255)
                                        cGCTCTAGGACGATCGCTTGCTCGCTATATAACTCTTCCACATTAAAGTATGATTGTGCCTCTTCAATACCTTGATTTACCAGCTTTATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATc                                                                                                <  1:54850/140‑1 (MQ=255)
                                           aCTAGGACCATCGCTTATTCGCTACATAAAACATCAACACTAAATTATTATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCGTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTAc                                                                                             <  1:286325/140‑1 (MQ=255)
                                              aGGACCATCGCTTGTTCGCTATATACATCTTCAACATTAAAGTATGATTGTGCAGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACaaa                                                                                          >  1:182441/1‑140 (MQ=255)
                                              aGGACCATCGCTTGTTCGCTATATAAATCTTCAACATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAACTGCACGTCTTCAATCAATGTATCTACaac                                                                                          >  2:51079/1‑139 (MQ=255)
                                              aGGACCATCGCTTGTTCGCTATATAAATCTTCAACATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACaaa                                                                                          >  2:491538/1‑140 (MQ=255)
                                              aGGACCATCGCTTGTTCGCTATATAAATCTTCAACATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTATAAAATGCACGTCTTCAATCAATGTATCTACaaa                                                                                          >  1:78475/1‑140 (MQ=255)
                                                gACCATCGCTTGTTCGCTATATAAATCTTCAACATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAAct                                                                                        >  1:80994/1‑140 (MQ=255)
                                                gACCATCGCTTGTTCGCTATATAAATCTTCAACATTAAAGTATGATTATGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTAACTACAAAct                                                                                        >  2:427639/1‑140 (MQ=255)
                                                        cTTGTTCGCTATATAAATCTTCAACATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCAAGTCTTCAATCAATGTATCTACAAACTCTTTcaca                                                                                >  1:296526/1‑140 (MQ=255)
                                                          tGTTCGCTATATAAATCTTCAACATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAat                                                                              <  2:81108/140‑1 (MQ=255)
                                                               gCTATATAAATCTTCAACATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATATGaa                                                                         >  1:105062/1‑140 (MQ=255)
                                                                ccacataCATCTTCAACATTAAAGTATGATTGTGCCGCTTTAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATATGaaa                                                                        <  2:163798/136‑1 (MQ=255)
                                                                cTATATAAACCTTCAACATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATATGaaa                                                                        <  2:525968/140‑1 (MQ=255)
                                                                           ttCAACATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCCTTTTGACGTACACATCTTCAATCAATGTATGTACCAACTCAGTCACAATATGAAATAGATTTGAtt                                                             <  1:454620/140‑1 (MQ=255)
                                                                              aaCATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTTTTTTTTTTTTTTTTAAAATGCACGTATTCAATCATTGTTTTTACAAACTCTTTCACAATATGAAATATATTTGTTTTTa                                                          >  2:256817/1‑140 (MQ=255)
                                                                              aaCATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGAACATCTTCAATAAATGTATCTACAAACTCTTTCACAATATGAGATTGCTTTGAtttca                                                          >  2:555127/1‑137 (MQ=255)
                                                                               aCATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATATGAAATAGATTTGATTGTaa                                                         >  1:344111/1‑140 (MQ=255)
                                                                                cATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTTTTTTTTTTTATTTTAAAATGCACGTCTTCAATCAAGGTATCTACAAACTCTTTCACAATATGAATTTGATTTGTTTGTAAt                                                        >  2:662296/1‑140 (MQ=255)
                                                                                cATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATATGAAATAGATTTGATTGTAAt                                                        >  1:479211/1‑140 (MQ=255)
                                                                                cATTAAAGTATGATTGTGCCACTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTAGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATATGAAATAAATTTGATTGTAAt                                                        >  1:13067/1‑140 (MQ=255)
                                                                                    aaaGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTTTTTTTTTTCATTTTAAAATGCACGTCTTCAATCAATGTAACTACAAACTCTTTGTCACTGTGAAAAAGActtactgacaaccctg                                                    >  2:329509/1‑127 (MQ=255)
                                                                                        tATGATTGTGCCGCTTCAATACCTTGATTTAACATCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATATGAAATAGATTTGATTGTAATCTTGGTGc                                                <  1:439705/140‑1 (MQ=255)
                                                                                              tgtgCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATGTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATATGAAATAGATTTGATTGTAATCTTGGTGCGccgca                                          >  2:395025/1‑137 (MQ=255)
                                                                                              tgtaCCGCTTCAATACATTGATTTAACAGACATATTTCTTTTTTGATCTTCTTCATTTTAAAATGCACGTCTTCAATAAATGTATCTACAAACTCTTTCACAATATGAAATAGATTTGATTGAAATCTTGGTCCAcacaa                                          >  2:409487/1‑136 (MQ=255)
                                                                                                   cGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTTTTCTTTTTCATTTTAAAATGCACGTCTTCAATCAATGTATATACAAACTCTTTCACAGTATGGAATAGATTTGATTGTAATCTTGGTGACCCCGAAATaa                                     >  2:241931/1‑140 (MQ=255)
                                                                                                    gCTTAAATACATTGATTTAACAGCCATATTTCTTTTTTGGTACTCTTCATTTTAAAATGAAGGGCTTCAATCAATGTATCTACACACTATTTCACAATATAAAATAGATTTCATGGTAATCTTGGGGCACCCGAAATacc                                    >  2:153597/1‑138 (MQ=255)
                                                                                                        cAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATATGAAATAGATTTGATTGTAATCTTGGTGCACCCGAAATAACTAAt                                >  1:413057/1‑140 (MQ=255)
                                                                                                        cAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATATGAAATAGATTTGATTGTAATCTTGGTGCACCCGAAATAACTAAt                                >  1:412797/1‑140 (MQ=255)
                                                                                                                ttaTTTAACAACCATATTTCTTTTTTGGTCCTCTTCATTTTAAAATTCACGTTTTCAATCAATGTACCTAAAATCTACTTAACGATATTAAATAGATTTGATTGTAATCTTGGTGCACCCGAAATAACTAATGGTGTTTg                        <  2:271188/138‑1 (MQ=255)
                                                                                                                tGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATATGAAATAGATTTGATTGTAATCTTGGTGCACCCGAAATAACTAATGGTGTTTg                        <  2:80994/140‑1 (MQ=255)
                                                                                                                tGATTTAACAGCCATATTTCTTTTTGTGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATATGAAATAGATTTGATTGTAATCTTGGTGCACCCGAAATAACTAATGGTGTTTg                        <  2:197127/140‑1 (MQ=255)
                                                                                                                        cAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATATGAAATAGATTTGATTGTAATCTTGGTGCACCCGAAATAACTAATGGTGTTTGAGCAGCAt                >  2:288658/1‑140 (MQ=255)
                                                                                                                         agtcATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATATGAAATAGATTTGATTGTAATCTTGGTGCACCCGAAATAACTAATGGTGTTTGAGCAGCATc               <  1:307727/137‑1 (MQ=255)
                                                                                                                         aGCCATATTTCTTTTTTGGTCTTTTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACGCTTTCACAATATGAAATAGATTTGATTGTAATCTTGGTGCACCCGAAATAACTAATGGTGTTTGAGCAGCATc               <  2:54083/140‑1 (MQ=255)
                                                                                                                          gCCATTTTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATATGAAATAGATTTGATTGTAATCTTGGTGCACCCGAAATAACTAATGGTGTTTGAGCAGCATCt              <  2:649535/140‑1 (MQ=255)
                                                                                                                                 ttCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATATGAAATAGATTTGATTGTAATCTTGGTGCACCCGAAATAACTAATGGTGTTTGAGCAGCATCTAAAATGa       <  2:358947/140‑1 (MQ=255)
                                                                                                                                 ttCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATATGAAATAGATTTGATATTAAACGTGGTGCACCCGAAATAACTAATGGTGTTTGAGCAGCATCTAAAATGa       >  1:316085/1‑140 (MQ=255)
                                                                                                                                  ttttttttGCTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATATGAAATAGATTTGATTGTAATCTTGGTGCACCCGAAATAACTAATGGTGTTTGAGCAGCATCTAAAATGAt      <  2:379157/138‑1 (MQ=255)
                                                                                                                                  tCTTTTTTTGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATATGAAATAGATTTGATTGTAATCTTGGTGCACCCGAAATAACTAATTGTGTTTGAGCAGCATCTAAAATGAt      <  2:132466/140‑1 (MQ=255)
                                                                                                                                      ttatGGTCTTGTTCATTTTAAAAAACACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATAAGAAATAGATTTGATTGTAATCTAGGTGCACCCAAAATAACTAATGGTGTTGTAGCAGCATCTATAATGacttaa  >  2:533292/4‑135 (MQ=255)
                                                                                                                                          |                                                                                                                                       
TTCAAACAAATATTGTGCGCGCAGTGCTAAATTAATATTACGCACTAGGACCATCGCTTGTTCGCTATATAAATCTTCAACATTAAAGTATGATTGTGCCGCTTCAATACCTTGATTTAACAGCCATATTTCTTTTTTGGTCTTCTTCATTTTAAAATGCACGTCTTCAATCAATGTATCTACAAACTCTTTCACAATATGAAATAGATTTGATTGTAATCTTGGTGCACCCGAAATAACTAATGGTGTTTGAGCAGCATCTAAAATGATTGAA  >  CP000730/2805209‑2805482

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑