Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 3,416,545 C→T 6.8% H505Y (CAC→TAC)  acrF → multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,416,5450CT 6.8% 182.2 / 3.3 59H505Y (CAC→TAC) acrFmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base C (34/21);  new base T (2/2);  total (36/23)
Fisher's exact test for biased strand distribution p-value = 6.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.54e-01

TCTTCGGCGGTTCTACTGGGGCAATTTATCGCCAGTTCTCTATCACCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCGGATCCACAGGACGATATTTACTGATCTATGCGCTGATTGTTGCAGGAATGGTGGTGT  >  NC_000913/3416405‑3416692
                                                                                                                                            |                                                                                                                                                   
tcttcGGCGGTTCTACTGGGGCAATTTATCGCCAGTTCTCTATCACCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGaaaa                                                                                                                                              >  6:211589/1‑148 (MQ=255)
     ggcggTTCTACTGGGGCAATTTATCGCCAGTTCTCTATCACCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAgg                                                                                                                                         <  2:222409/148‑1 (MQ=255)
         gTTCTACTGGGGCAATTTATCGCCAGTTCTCTATCACCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGt                                                                                                                                    <  5:27073/149‑1 (MQ=255)
                  gggCAATTTATCGCCAGTTCTCTATCACCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCggt                                                                                                                           >  3:66651/1‑149 (MQ=255)
                  gggCAATTTATCGCCAGTTCTCTATCACCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCggt                                                                                                                           >  1:61389/1‑149 (MQ=255)
                  gggCAATTTATCGCCAGTTCTCTATCACCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCg                                                                                                                             <  2:708/147‑1 (MQ=255)
                   ggCAATTTATCGCCAGTTCTCTATCACCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGa                                                                                                                                                 <  8:281251/126‑1 (MQ=255)
                   ggCAATTTATCGCCAGTTCTCTATCACCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGa                                                                                                                                                 >  7:281251/1‑126 (MQ=255)
                    gCAATTTATCGCCAGTTCTCTATCACCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCggttg                                                                                                                         >  8:50299/1‑149 (MQ=255)
                      aaTTTATCGCCAGTTCTCTATCACCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGCCATTCATACTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCggttggt                                                                                                                       >  1:102675/1‑149 (MQ=255)
                       aTTTATCGCCAGTTCTCTATCACCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCggttggtt                                                                                                                      <  1:97610/149‑1 (MQ=255)
                              gCCAGCTCTCTAACACCATCGTTTCCGCAATGGCGCTTTCTGTCCTGGTGCCATTGATGCATACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCCTCACGAAAATAAGGGCGGGTGCTTCGGTTGGGTTAATacc                                                                                                               <  4:199692/149‑1 (MQ=255)
                                cAGTTCTCTATCACCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATaccac                                                                                                             <  1:179885/149‑1 (MQ=255)
                                      tctATCCCCATCGTTTCGGCACTGGCGCGGTCTGTTCTGGTGGCAGTGCTTCTTACCACTGCGTTATGTGCAACGCTGCTTACACCCGTCTCTGAGGAGCATCACGAAACTAAGGGCGTTGTCTGCGGTTGGTTTAATACAACCTTCgc                                                                                                       >  6:231451/1‑148 (MQ=255)
                                         aTCACCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCa                                                                                                    >  8:1902/1‑149 (MQ=255)
                                          tCACCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATc                                                                                                     <  2:61389/147‑1 (MQ=255)
                                            aCCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAg                                                                                                 >  2:248030/1‑149 (MQ=255)
                                                tCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGt                                                                                              >  1:12389/1‑148 (MQ=255)
                                                   tttCGGCAATGGCGCTTTCTGTTCTGGGGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAAc                                                                                          <  5:211589/149‑1 (MQ=255)
                                                      cGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCa                                                                                        <  5:134738/148‑1 (MQ=255)
                                                      cGGCAATGGCGCTGTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCa                                                                                        <  7:314039/148‑1 (MQ=255)
                                                        gCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTa                                                                                     >  8:198238/1‑149 (MQ=255)
                                                           aTGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTacac                                                                                  <  6:336859/149‑1 (MQ=255)
                                                                      tgttctgGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCg                                                                       >  3:308174/1‑149 (MQ=255)
                                                                      tgttctgGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCg                                                                       >  7:279192/1‑149 (MQ=255)
                                                                      tgttctgGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCg                                                                       >  6:89767/1‑149 (MQ=255)
                                                                        gtctgGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGc                                                                     <  6:188307/148‑1 (MQ=255)
                                                                         tctgGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGc                                                                     >  2:58389/1‑148 (MQ=255)
                                                                             gtggCATTGATTCTTACCCCTGCGTTAAGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCAAAGCGTTACCCACTACACCAACAGCGTCGGCAAAAt                                                                >  6:93651/1‑149 (MQ=255)
                                                                             gtggCATTGATTCTTACCAATGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGACCATCACGAATATAAGGGCGGTTTCTTAGGTTGGTTTAATACAAACTTAGATCATAGAGTTAACCACTACAACAACAGCGTCGGCAAAAt                                                                >  2:96669/1‑149 (MQ=255)
                                                                               ggCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATTACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATcc                                                              >  1:199440/1‑149 (MQ=255)
                                                                               ggCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATTACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATcc                                                              >  7:336482/1‑149 (MQ=255)
                                                                                gCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCCCTACACCAACAGCGTCGGCAAAATCCt                                                             >  8:176935/1‑149 (MQ=255)
                                                                                  aTTGATTCTTACCCCTGCGTTATGTGCTACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATTCCACCTTCGAGCATATCGTTAACCACTACACCCTCAGCTTGGGCAAAATCCtag                                                           >  7:170642/1‑147 (MQ=255)
                                                                                  aTTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCg                                                           >  1:344144/1‑149 (MQ=255)
                                                                                  aTTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATAACACCTTCGATCATAGCGTTAAACACTAAACCAACAGCGTCGGCAAAATCCTCg                                                           >  5:8966/1‑149 (MQ=255)
                                                                                  aTTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGACTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCGTCGGTTGGTCTAAt                                                                                                                  >  4:67301/1‑94 (MQ=255)
                                                                                   ttGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCg                                                           >  5:143941/1‑148 (MQ=255)
                                                                                   ttGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCg                                                           >  7:70142/1‑148 (MQ=255)
                                                                                     gATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCGGa                                                         <  7:198238/148‑1 (MQ=255)
                                                                                          ttACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCGTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCGGATCca                                                     >  2:263986/1‑147 (MQ=255)
                                                                                              cccTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCGGATCCACAGGAc                                               >  5:31097/1‑149 (MQ=255)
                                                                                                 tGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCGGATCCACAGGACGa                                             >  8:348029/1‑148 (MQ=255)
                                                                                                     ttATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATc                                                                                                     <  5:313495/88‑1 (MQ=255)
                                                                                                       aTGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATATCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCGGATCCACAGGACGATATTTAc                                      >  1:35929/1‑149 (MQ=255)
                                                                                                       aTGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCGGATCCACAGGACGATATTTa                                       <  5:89767/148‑1 (MQ=255)
                                                                                                          tgCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCGGATCCACAGGACGATATTTACTGa                                   >  5:318042/1‑149 (MQ=255)
                                                                                                            cAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCGGATCCACAGGACGATATTTACTGAt                                  >  7:227332/1‑148 (MQ=255)
                                                                                                                            cGTCTCTGCTGAGCATTACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCGGATCCACAGGACGATATTTACTGATCTATGCGCTGAttgttg                 <  2:199440/149‑1 (MQ=255)
                                                                                                                            cGTCTCTGCTGAGCATTACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCGGATCCACAGGACGATATTTACTGATCTATGCGCTGAttgttg                 <  8:336482/149‑1 (MQ=255)
                                                                                                                            cGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCGGATCCACAGGACGATATTTACTGATCTATGCGCTGAttgttg                 <  1:248030/149‑1 (MQ=255)
                                                                                                                              tctcTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCGGATCCACAGGACGATATTTACTGATCTATGCGCTGAttgttg                 >  2:140528/1‑147 (MQ=255)
                                                                                                                              tctcTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCGGATCCACAGGACGATATTTACTGATCTATGCGCTGAttgttg                 >  8:7521/1‑147 (MQ=255)
                                                                                                                                   tctgATCATCAAGAATATATTGGCTGTTTGTTCGGTTGGTTTAATTCCTCCTTCGATGATATAGTTAACGACTACACCATCTGTGTCGGCAAAATCCTCGGATCGACTGGACGATATTTACTGTTCTATGCGGTGATTGTTGCAGGaa           <  4:308174/147‑1 (MQ=255)
                                                                                                                                     tgAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCGGATCCACAGGACGATATTTACTGa                                   <  2:166872/122‑1 (MQ=255)
                                                                                                                                     tgAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCGGATCCACAGGACGATATTTACTGa                                   >  1:166872/1‑122 (MQ=255)
                                                                                                                                        gCATCACGAAAATAAGGGCGGTTTCTGCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCGGATCCACAGGACGATATTTACTGATCTATGCGCTGATTGTTGCAGGAAtggtgg     <  4:12324/149‑1 (MQ=255)
                                                                                                                                         cATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCGGATCCACAGGACGATATTTACTGATCTATGCGCTGATTGTTGCAGGAATggtggt    >  1:28170/1‑149 (MQ=255)
                                                                                                                                           tCACGAAAATAAGGGCGGTTTCTTCGGTTTGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGGCGGCAAAATCCTCGGATCCACAGGACGATATTTACTGATCTATGCGCTGATTGTTGCAGGAATGGTGgtgt  <  4:66651/149‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                                   
TCTTCGGCGGTTCTACTGGGGCAATTTATCGCCAGTTCTCTATCACCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCGGATCCACAGGACGATATTTACTGATCTATGCGCTGATTGTTGCAGGAATGGTGGTGT  >  NC_000913/3416405‑3416692

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: