Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6063,269,6450T→A 6.7% 1.1 ‑4.4 ‑0.087702ispBoctaprenyl diphosphate synthase
Rejected: E-value exceeds prediction threshold.
Reads supporting (aligned to +/- strand):  new base (0/7):  ref base (43/36):  total (44/43)
Fisher's exact test strand distribution p-value = 1.20e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 9.82e-01

TTAGGTAAAAACGTCGGCGACGATCTGAACGAAGGTAAACCGACGCTGCCGCTGCTGCATGCGATGCATC  >  REL606/3269610‑3269679
                                   |                                  
ttAAGTAAAAACGTCGGCGACGATCTGAACGAAGGt                                    <  1:6699101/36‑1 (MQ=255)
 tAGGTAAAAACGTCGGCGACGATCTGAACGAAGGTa                                   <  1:3431725/36‑1 (MQ=255)
 tAGGTAAAAACGTCGGCGACCATCTGAACGAAGGTa                                   >  1:5781492/1‑36 (MQ=255)
  aGGTAAAAACGTCGGCGACGATCTGAACGAAGGTaa                                  <  1:117813/36‑1 (MQ=255)
  aGGTAAAAACGTCGGCGACGATCTGAACGAAGGTaa                                  >  1:6056095/1‑36 (MQ=255)
  aGGTAAAAACGTCGGCGACGATCTGAACGAAGGTaa                                  >  1:2437896/1‑36 (MQ=255)
   ggTAAAAACGTCGGCGACGATCTGAACGAAGGTaaa                                 <  1:1367763/36‑1 (MQ=255)
   ggTAAAAACGTCGGCGACGATCTGAACGAAGGTaaa                                 <  1:6021263/36‑1 (MQ=255)
    gTAAAAATGGCGGCGCAGATCTGAACGAAGGTAAAc                                <  1:4220426/36‑1 (MQ=16)
    gTAAAAACGTCGGCGACGATCTGAACGAAGGTAAAc                                >  1:22364/1‑36 (MQ=255)
    gTAAAAACGTCGGCGACGATCTGAACGAAGGTAAAc                                >  1:6550808/1‑36 (MQ=255)
    gTAAAAACGTCGGCGACGATCTGAACGAAGGTAAAc                                >  1:5344024/1‑36 (MQ=255)
    gTAAAAACGTCGGCGACGATCTGAACGAAGGTAAAc                                >  1:1717211/1‑36 (MQ=255)
     tAAAAACGTCGGCGACGATCTGAACGAAGGTAAAcc                               <  1:362059/36‑1 (MQ=255)
     tAAAAACGTCGGCGACGATCTGAACGAAGGTAAAcc                               <  1:3475064/36‑1 (MQ=255)
      aaaaaCGTCGGCGACGATCTGAACGAAGGTAAACCg                              >  1:4681386/1‑36 (MQ=255)
       aaaaCGTCGGCGACGATCTGAACGAAGGTAAACCGa                             >  1:143817/1‑36 (MQ=255)
       aaaaCGTCGGCGAAGATCTGAACGAAGGTAAACCGa                             <  1:2336263/36‑1 (MQ=255)
        aaaCGTCGGCGACGATCTGAACGAAGGTAAACCGAc                            >  1:3818544/1‑36 (MQ=255)
        aaaCGTCGGCGACGATCTGAACGAAGGTAAACCGAc                            >  1:3418577/1‑36 (MQ=255)
        aaaCGTCGGCGACGATCTGAACGAAGGTAAACCGAc                            >  1:4516632/1‑36 (MQ=255)
        aaaCGTCGGCGACGATCTGAACGAAGGTAAACCGAc                            <  1:436665/36‑1 (MQ=255)
        aaaCGTCGGCGACGATCTGAACGAAGGTAAACCGAc                            <  1:6620126/36‑1 (MQ=255)
         aaCGTCGGCGACGATCTGAACGAAGGTAAACCGAcg                           >  1:2126234/1‑36 (MQ=255)
         aaCGTCGGCGACGATCTGAACGAAGGTAAACCGAcg                           <  1:3459069/36‑1 (MQ=255)
         aaCGTCGGCGACGATCTGAACGAAGGTAAACCGAcg                           <  1:1607498/36‑1 (MQ=255)
          aCGTCGGCGACGATCTGAACGAAGGTAAACCGActc                          >  1:6611650/1‑34 (MQ=255)
          aCGTCGGCGACGATCTCAACGAAGGTAAACCGAcgc                          >  1:6376832/1‑36 (MQ=255)
            gTCGGCGACGATCTGAACGAAGGTAAACCGAcgctg                        <  1:3036347/36‑1 (MQ=255)
             tCGGCGACGATCTGAACGAAGGTAAACCGAcgctgc                       >  1:1819734/1‑36 (MQ=255)
             tCGGCGACGATCTGAACAAAGGTAAACCGAcgctgc                       <  1:3556127/36‑1 (MQ=255)
             gcGGCGACGATCTGAACGAAGGTAAACCGAcgctgc                       <  1:4635624/35‑1 (MQ=255)
              cGGCGACTATCTGAACGAAGGTAAACCGAcgctgcc                      <  1:4071312/36‑1 (MQ=255)
              cGGCGACGATCTGAACGAAGGTAAACCGAcgctgcc                      <  1:6941158/36‑1 (MQ=255)
               ggCGACGATCTGAACGAAGGTAAACCGAcgctgccg                     >  1:3034824/1‑36 (MQ=255)
                gCGGCGATCTGAACGAAGGTAAACCGGcgctgccgc                    <  1:509634/36‑1 (MQ=37)
                gCGACGATCTGAACGAAGGTAAACCGAcgctgccgc                    >  1:1444141/1‑36 (MQ=255)
                gCGACGATCTGAACGAAGGTAAACCGAagctgccgc                    >  1:4721620/1‑36 (MQ=255)
                acgacgaTCTGAAGAACGGAAAGCCGAcgctgccgc                    <  1:642578/35‑1 (MQ=16)
                 cgacgaTCTGAACGAAGGTAAACCGAcgctgccgct                   <  1:6293989/36‑1 (MQ=255)
                 cgacgaTCTGAACGAAGGTAAACCGAcgctgccgct                   <  1:142548/36‑1 (MQ=255)
                 caacgtTCTGAAGGAAGGAAAACCGAcgctgccgct                   <  1:6371749/34‑1 (MQ=21)
                  gacgaTCTGAACGAAGGTAAACCGAcgctgccgctg                  >  1:1779538/1‑36 (MQ=255)
                  gacgaTCTGAACGAAGGTAAACCGAcgctgccgctg                  >  1:2148126/1‑36 (MQ=255)
                  gacgaTCTGAACGAAGGTAAACCGAcgctgccgctg                  >  1:4230664/1‑36 (MQ=255)
                  gacgaTCTGAACGAAGGTAAACCGAcgctgccgctg                  <  1:7127731/36‑1 (MQ=255)
                   acgaTCTGAACGAAGGTAAACCGAcgctgccgctgc                 <  1:4435461/36‑1 (MQ=255)
                   acgaTCTGAACGAAGGTAAACCGAcgctgccgctgc                 <  1:5127244/36‑1 (MQ=255)
                   acgaTCTGAACGAAGGTAAACCGAcgctgccgctgc                 >  1:425319/1‑36 (MQ=255)
                    cgaTCTGAACGAAGGTAAACCGACGCTGCCgctgct                <  1:3965098/36‑1 (MQ=255)
                    cgaTCTGAACGAAGGTAAACCGACGCTGCCgctgct                >  1:3604562/1‑36 (MQ=255)
                    cgaTCGGAACGAAGGTAAACCGACGCTGCCgctgct                <  1:7293780/36‑1 (MQ=255)
                     gaTCTGAACGAAGGTAAACCGACGCTGCCGctgctg               >  1:501386/1‑36 (MQ=255)
                      aTCTGAACGAAGGTAAACCGACGCTGCCGCtgctgc              <  1:5357731/36‑1 (MQ=255)
                      aTCTGAACGAAGGTAAACCGACGCTGCCGCtgctgc              >  1:2489094/1‑36 (MQ=255)
                      aTCTGAACGAAGGTAAACCGACGCTGCCGCtgctgc              >  1:2281114/1‑36 (MQ=255)
                       tCTGAACGAAGGTAAACCGACTCTGCCGCTGCTGCa             >  1:2325512/1‑36 (MQ=255)
                       tCTGAACGAAGGTAAACCGACGCTGCCGCTGCTGCa             <  1:3839600/36‑1 (MQ=255)
                       tCTGAACGAAGGTAAACCGACGCTGCCGCTGCTGCa             >  1:1589307/1‑36 (MQ=255)
                        cTGAGCAAAGGAAAACCGACACTGCCGCTGCTGCAt            <  1:1044252/36‑1 (MQ=19)
                        cTGAACGAAGGAAAACCGACGCTGCCGCTGCTGCAt            <  1:5734849/36‑1 (MQ=255)
                        cTGAACGAAGGAAAACCGACGCTGCCGCTGCTGCAt            <  1:6375830/36‑1 (MQ=255)
                         tGACCGAAGGTAAACCGACGCTGCCGCTGCTGCATg           <  1:7058839/36‑1 (MQ=255)
                         tGAACGAAGGTAAACCGACGCTGCCGCTGCTGCATg           <  1:7204421/36‑1 (MQ=255)
                          gAACGAAGGTAAACCGACGCTGCCGCTGCTGCATGc          <  1:1643237/36‑1 (MQ=255)
                          gAACGAAGGTAAACCGACGCTGCCGCTGCTGCAGGc          >  1:4563031/1‑36 (MQ=255)
                           aaCGAAGGTAAACCGACGCTGGCGCTGCTGCATGCg         >  1:1472195/1‑36 (MQ=255)
                           aaCGAAGGCAAACCGACGCTGCCGCTGCTGCATGCg         >  1:5310/1‑36 (MQ=255)
                            aCGAAGGTAAACCGACGCTGCCGCTGCTGCATGCGa        <  1:7347165/36‑1 (MQ=255)
                            aCGAAGGTAAACCGACGCTGCCGCTGCTGCATGCGa        >  1:7228493/1‑36 (MQ=255)
                            aCGAAGGTAAACCGACGCTGCCGCTGCTGCATGCGa        >  1:1571294/1‑36 (MQ=255)
                            aCGAAGGTAAACCGACGCTGCCGCTGCTGCATGCGa        >  1:211746/1‑36 (MQ=255)
                            aCGAAGGTAAACCGACGCTGCCGCTGCTGCATGCGa        >  1:2204137/1‑36 (MQ=255)
                            aCGAAGGTAAACCGACGCTGCCGCTGCTGCATGCGa        <  1:3689167/36‑1 (MQ=255)
                             ggAAGTTAAACGGACGCTGCCGCTGCTGCATGCGAt       <  1:5733241/35‑1 (MQ=25)
                             cGAAGGTAAACCGACGCTGCCGCTGCTGCATGCGAt       <  1:4037493/36‑1 (MQ=255)
                             cGAAGGTAAACCGACGCTGCCGCTGCTGCATGCGAt       >  1:7053189/1‑36 (MQ=255)
                              gAAGGTAAACCGACGCTGCCGCTGCTGCATGCGATg      >  1:6324894/1‑36 (MQ=255)
                              gAAGGTAAACCGACGCTGCCGCTGCTGCATGCGATg      >  1:7015003/1‑36 (MQ=255)
                              gAAGGTAAACCGACGCTGCCGCTGCTGCATGCGATg      >  1:6002138/1‑36 (MQ=255)
                              gAAGGTAAACCGACGCTGCCGCTGCTGCATGCGATg      >  1:4435003/1‑36 (MQ=255)
                               aaGGTAAACCGACGCTGCCGCTGCTGCATGCGATGc     >  1:6535921/1‑36 (MQ=255)
                               aaGGAAACCCGACGCTGCCGCTGCTGCATGCGATGc     <  1:3738177/36‑1 (MQ=25)
                               aaGGAAACCCGACGCTGCCGCCGCTGCATGCGATGc     <  1:4144614/36‑1 (MQ=25)
                                aGGTAAACCGACGCTGCCGCTGCTGCATGCGATGca    <  1:3389974/36‑1 (MQ=255)
                                 ggTAACCCGACGCTGCCGCTGCTGCATGCGATGcat   <  1:4614462/36‑1 (MQ=255)
                                 ggTAAACCGACGCTGCCGCTGCTGCATGCGATGcat   >  1:1350883/1‑36 (MQ=255)
                                  gTAAACCGACGCTGCCGCTGCTGCATGCGATGcatc  >  1:1567753/1‑36 (MQ=255)
                                   |                                  
TTAGGTAAAAACGTCGGCGACGATCTGAACGAAGGTAAACCGACGCTGCCGCTGCTGCATGCGATGCATC  >  REL606/3269610‑3269679

Base quality scores:  ATCG  < 3 ≤  ATCG  < 8 ≤  ATCG  < 18 ≤  ATCG  < 30 ≤  ATCG  < 37 ≤  ATCG