Predicted mutation
evidence seq id position mutation freq annotation gene description
RA REL606 3,864,228 C→A 17.1% D580Y (GAT→TAT)  bglF ← fused beta‑glucoside‑specific PTS enzymes: IIA component/IIB component/IIC component

Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6063,864,2280C→A17.1% 10.8 ‑4.5 ‑0.0521738bglFfused beta‑glucoside‑specific PTS enzymes: IIA component/IIB component/IIC component
Reads supporting (aligned to +/- strand):  new base (1/9):  ref base (24/18):  total (25/27)
Fisher's exact test strand distribution p-value = 1.16e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 9.77e-01

CACATCAAATCCGGCCTCGCGAATAGCAGGGATATCAAAAGAAATCAGCCGATCGCCTGTATTGACCTTGT  >  REL606/3864193‑3864263
                                   |                                   
cacaTCAAACCCGGCCTCGCGAATAGCAGGGATATc                                     <  1:5679146/36‑1 (MQ=255)
     cAAATCCGGCCTCGCGAATAGCAGGGATATCAAAAg                                <  1:1810057/36‑1 (MQ=255)
      aaaTCCGGCCTCGCGAATAGCAGGGATATCAAAAGa                               >  1:908565/1‑36 (MQ=255)
      aaaTCCGGCCTCGCGAATAGCAGGGATATCAAAAGa                               >  1:7161348/1‑36 (MQ=255)
      aaaTCCGGCCTCGCGAATAGCAGGGATATCAAAAGa                               >  1:301042/1‑36 (MQ=255)
       aaTCCGGCCTCGCGAATAGCAGGGATATCAAAAGaa                              >  1:7147626/1‑36 (MQ=255)
       aaTCCGGCCTCGCGAATAGCAGGGATATCAAAAGaa                              >  1:2984170/1‑36 (MQ=255)
       aaTCCGGCCTCGCGAATAGCAGGGAGATCAAAAGaa                              >  1:6062661/1‑36 (MQ=255)
        aTCCGGCCTCGCGAATAGCAGGGATATCAAAAGaaa                             >  1:4453850/1‑36 (MQ=255)
         tCCGGCCTCGCGAATAGCAGGGATATCAAAAGAAAt                            <  1:4038316/36‑1 (MQ=255)
          ccGGCCTCGCGAATAGCAGGGATATCAAAAGAAATc                           <  1:915443/36‑1 (MQ=255)
          ccGGCCTCGCGAATAGCAGGGATATCAAAAGAAATc                           <  1:760308/36‑1 (MQ=255)
          ccGGCCTCGCGAATAGCAGGGATATCAAAAGAAATc                           <  1:2698235/36‑1 (MQ=255)
           cGGCCTCGCGAATAGCAGGGATATCAAAAGAAATCa                          <  1:4481511/36‑1 (MQ=255)
             gCCTCGCGAATAGCAGGGATATCAAAAGAAATCAGc                        <  1:4622739/36‑1 (MQ=255)
              ccTCGCGAATAGCAGGGATATCAAAAGAAATCAGcc                       >  1:7494608/1‑36 (MQ=255)
              ccTCGCGAATAGCAGGGATATCAAAAGAAATCAGcc                       >  1:1809140/1‑36 (MQ=255)
               cTCGCGAATAGCAGGGATATCAAAAGAAATCAGCCg                      <  1:1596142/36‑1 (MQ=255)
               cTCGAGAATAGCAGGGATATAAAAAGAAAACAGCCg                      >  1:2044699/1‑36 (MQ=25)
                 cgcgAATAGCAGGGATATCAAAAGAAATCAGCCGAt                    >  1:601998/1‑36 (MQ=255)
                 cgcgAATAGCAGGGATATCAAAAGAAATCAGCCGAt                    <  1:5902730/36‑1 (MQ=255)
                 cgcgAATAGCAGGGATATCAAAAGAAATCAGCCGAt                    <  1:2061860/36‑1 (MQ=255)
                  gcgAATAGCAGGGATATCAAAAGAAATCAGCCGATc                   <  1:2587340/36‑1 (MQ=255)
                   cgAATAGCAGGGATATCAAAAGAAATCAGCCGATCg                  >  1:6740070/1‑36 (MQ=255)
                   cgAATAGCAGGGATATCAAAAGAAATCAGCCGATCg                  <  1:6345295/36‑1 (MQ=255)
                   cgAATAGCAGGGATATCAAAAGAAATCAGCCGATCg                  >  1:606088/1‑36 (MQ=255)
                   cgAATAGCAGGGATATCAAAAGAAATCAGCCGATCg                  <  1:5074256/36‑1 (MQ=255)
                    gAATAGCAGGGATATCAAAAGAAATCAGCCGATCGc                 >  1:1410822/1‑36 (MQ=255)
                     aaTAGCAGGGATATCAAAAGAAATCAGCCGATCGcc                >  1:4117952/1‑36 (MQ=255)
                     aaTAGCAGGGATATCAAAAGAAATCAGCCGATCGcc                <  1:7479076/36‑1 (MQ=255)
                      aTAGCAGGGATATCAAAAGAAATCAGCCGATCGCCt               <  1:4455864/36‑1 (MQ=255)
                      aTAGCAGGGATATAAAAAGAAATCAGCCGATCGCCt               <  1:3954235/36‑1 (MQ=255)
                      aTAGCAGGAATATAAAAAGAAATCAGCGGATCGCCt               <  1:5178022/36‑1 (MQ=21)
                      aTAGAAGAGATATAAAAATAACTCAGCCGATCGCCt               <  1:2064326/36‑1 (MQ=16)
                       tAGCAGGGATATCAAAAGAAATCAGCCGATCGCCTg              >  1:1874643/1‑36 (MQ=255)
                       aaGCAGGGATATCAAAAGAAAAGAGCCGATCGCCTg              <  1:3780169/35‑1 (MQ=37)
                        aaaaGGAATATAAAAAAAAACAAGCCGATCGCCTGt             <  1:2419153/33‑1 (MQ=2)
                        aGCAGGGATATCAAAAGAAATCAGCCGATCGCCTGt             >  1:2290171/1‑36 (MQ=255)
                         gaaGGGATATAAAAAGAAATCAGCCGATCGCCTGTa            <  1:251327/34‑1 (MQ=38)
                         gCAGGGATATCAAAAGAAATCAGCCGATCGCCTGTa            >  1:4194731/1‑36 (MQ=255)
                          cAGGGATATCAAAAGAAATCAGCCGATCGCCTGTAt           <  1:2284504/36‑1 (MQ=255)
                          cAGGGATATCAAAAGAAATCAGCCGATCGCCTGTAt           >  1:5873915/1‑36 (MQ=255)
                           tgggATATAAAAATAAATCAGCCGATCGCCTGTAtt          <  1:5984441/35‑1 (MQ=37)
                            gggATATCAAAAGAAATCAGCCGATCGCCTGTATTg         <  1:6973366/36‑1 (MQ=255)
                            gggATATCAAAAGAAATCAGCCGATCGCCTGTATTg         >  1:2446682/1‑36 (MQ=255)
                             ggATATCAAAAGAAATCAGCCGATCGCCTGTATTGa        >  1:6789903/1‑36 (MQ=255)
                             ggATATCAAAAGAAATCAGCCGATCGCCTGTATTGa        >  1:4959196/1‑36 (MQ=255)
                             gaatatAAAAAAAAATCAGCCGATCGCCTGTATTGa        <  1:4023378/34‑1 (MQ=37)
                              gATATAAAAAGAAATCAGCCGATCGCCTGTATTGAc       <  1:1535701/36‑1 (MQ=255)
                               atatCAAAAGAAATCAGCCGATCGCCTGTATTGAcc      >  1:444280/1‑36 (MQ=255)
                               atatAAAAAAAAATCAGCCGATCGCCTGTATTGAcc      <  1:7169376/36‑1 (MQ=37)
                                tatCAAAAGAAATCAGCCGATCGCCTGTATTGACCt     >  1:1290717/1‑36 (MQ=255)
                                 atCAAAAGAAATCAGCCGATCGCCTGTATTGACCtt    >  1:277863/1‑36 (MQ=255)
                                   cAAAAGAAATCAGCCGATCGCCTGTATTGACCTTGt  >  1:5950255/1‑36 (MQ=255)
                                   |                                   
CACATCAAATCCGGCCTCGCGAATAGCAGGGATATCAAAAGAAATCAGCCGATCGCCTGTATTGACCTTGT  >  REL606/3864193‑3864263

Base quality scores:  ATCG  < 3 ≤  ATCG  < 11 ≤  ATCG  < 23 ≤  ATCG  < 32 ≤  ATCG  < 37 ≤  ATCG