Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6063,292,4780A→. 2.6% 1.6 ‑0.7 ‑0.177coding (2612/4554 nt)gltBglutamate synthase, large subunit
Rejected: E-value exceeds prediction threshold.
Reads supporting (aligned to +/- strand):  new base (0/2):  ref base (38/37):  total (38/39)
Fisher's exact test strand distribution p-value = 4.94e-01
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 8.56e-01

CACGCTGCGCGATCTGCTGGCAATTACGCCGGGTGAAAACGCGGTCAACATTGCTGATGTTGAACCGGCAA  >  REL606/3292443‑3292513
                                   |                                   
cACGCTGCGCGATCTGCTGGCAATTACGCCGGGTGa                                     >  1:3797025/1‑36 (MQ=255)
 aCGCGGCGCGATCTGCTGGCAATTACGCCGGGTGaa                                    >  1:4836270/1‑36 (MQ=255)
  cGCTGCGCGATCTGCTGGCAATTACGCCGGGTGaaa                                   <  1:4971148/36‑1 (MQ=255)
   gCTGCGCGATCTGCTGGCAATTACGCCGGGTGaaaa                                  <  1:7060209/36‑1 (MQ=255)
   gCTGCGCGATCTGCTGGCAATTACGCCGGGTGaaaa                                  >  1:7429249/1‑36 (MQ=255)
    cTGCGCGATCTGCTGGCAATTACGCCGGGTGAAAAc                                 >  1:2760866/1‑36 (MQ=255)
      gcgcGATCTGCTGGCAATTACGCCGGGTGAAATcgc                               >  1:4030874/1‑36 (MQ=255)
      gcgcGATCTGCTGGCAATTACGCCGGGTGAAAAcgc                               >  1:919838/1‑36 (MQ=255)
        gcgATCTGCTGGCAATTACGCCGGGTGAAAACGCgg                             >  1:4016435/1‑36 (MQ=255)
        gcgATCTGCTGGCAATTACGCCGGGTGAAAACGCgg                             <  1:7923255/36‑1 (MQ=255)
         cggtCTGATGGTAATTACGCCGGGTGAAAACGCGGt                            <  1:2310525/33‑1 (MQ=25)
         cgATCTGCTGGCAATTACGCCGGGTG.AAACGCGGTc                           <  1:646302/36‑1 (MQ=38)
         cgATCTGCTGGCAATTACGCCGGGTG.AAACGCGGTc                           <  1:619931/36‑1 (MQ=38)
          gATCTGCTGGCAATTACGCCGGGTGAAAACGCGGTc                           >  1:3047977/1‑36 (MQ=255)
          gATCTGCTGGCAATTACGCCGGGTGAAAACGCGGTc                           >  1:2399319/1‑36 (MQ=255)
          gATCTGCTGGCAATTACGCCGGGTGAAAACGCGGTc                           >  1:2245818/1‑36 (MQ=255)
          gATCTGCTGGCAATTACGCCGGGTGAAAACGCGGTc                           <  1:6332754/36‑1 (MQ=255)
           aTCTGCTGGCAATTACGCCGGGTGAAAACGCGGTCa                          <  1:7463818/36‑1 (MQ=255)
           aTCTGCTGGCAATTACGCCGGGTGAAAACGCGGTCa                          <  1:5686497/36‑1 (MQ=255)
           aTCTGCTGGCAATTACGCCGGGTGAAAACGCGGTCa                          <  1:7223803/36‑1 (MQ=255)
           aTCTGCTGGCAATTACGCCGGGTGAAAACGCGGTCa                          <  1:720585/36‑1 (MQ=255)
           aTCTGCTGGCAATTACGCCGGGTGAAAACGCGGTCa                          <  1:3963736/36‑1 (MQ=255)
           aTCTGCTGGCAATTACGCCGGGTGAAAACGCGGTCa                          <  1:6690880/36‑1 (MQ=255)
           aTCTGCTGGCAATTACGCCGGGTGAAAACGCGGTCa                          >  1:2936535/1‑36 (MQ=255)
            tCTGCTGGCAATTACGCCGGGTGAAAACGCGGTCaa                         <  1:1948364/36‑1 (MQ=255)
            tCTGCTGGCAATTACGCCGGGTGAAAACGCGGTCaa                         <  1:7475427/36‑1 (MQ=255)
            tCTGCTGGCAATTACGCCGGGTGAAAACGCGGTCaa                         >  1:555178/1‑36 (MQ=255)
            tCTGCTGGCAATTACGCCGGGTGAAAACGCGGTCaa                         <  1:2916616/36‑1 (MQ=255)
            tCTGCTGGCAATTACGCCGGGTGAAAACGCGGTCaa                         <  1:3220582/36‑1 (MQ=255)
              tgctgGCAATTACGCCGGGTGAAAACGCGGTCAACa                       <  1:3472343/36‑1 (MQ=255)
              tgctgGCAATTACGCCGGGTGAAAACGCGGTCAACa                       >  1:7599709/1‑36 (MQ=255)
              tgctgGCAATTACGCCGGGTGAAAACGCGGTCAACa                       <  1:266193/36‑1 (MQ=255)
              tgctgGCAATTACGCCGGGTGAAAACGCGGTCAACa                       <  1:955004/36‑1 (MQ=255)
               gctgGCAATTACGCCGGGTGAAAACGCGGTCAACAt                      >  1:3440170/1‑36 (MQ=255)
               gctgGCAATTACGCCGGGTGAAAACGCGGTCAACAt                      >  1:7203049/1‑36 (MQ=255)
               gctgGCAATTACGCCGGGTGAAAACGCGGTCAACAt                      >  1:1373674/1‑36 (MQ=255)
               gctgGCAATTACGCCGGGTGAAAACGCGGTCAACAt                      >  1:5748196/1‑36 (MQ=255)
                ctgGTAATTACGCCGGGTGAAAACGCGGTCAACAtt                     <  1:4742207/36‑1 (MQ=255)
                ctgGCAATTACGCCGGGTGAAAACGCGGTCAACAtt                     >  1:720576/1‑36 (MQ=255)
                ctgGCAATTACGCCGGGTGAAAACGCGGTCAACAtt                     >  1:1491114/1‑36 (MQ=255)
                 tgGCAATTACGCCGGGTGAAAACGCGGTCAACATTg                    >  1:1804955/1‑36 (MQ=255)
                 tgGCAATTACGCCGGGTGAAAACGCGGTCAACATTg                    >  1:6988801/1‑36 (MQ=255)
                 tgGCAATTACGCCGGGTGAAAACGCGGTCAACATTg                    >  1:7689182/1‑36 (MQ=255)
                  ggCAATTACGCCGGGTGAAAACGCGGTCAACATTGc                   <  1:7587748/36‑1 (MQ=255)
                  ggCAATTACGCCGGGTGAAAACGCGGTCAACATTGc                   <  1:1539862/36‑1 (MQ=255)
                  ggCAATTACGCCGGGTGAAAACGCGGTCAACATTGc                   >  1:7282271/1‑36 (MQ=255)
                   gCAATTACGCCGGGTGAAAACGCGGTCAACATTGCt                  >  1:2412130/1‑36 (MQ=255)
                    cAATTACGCCGGGTGAAAACGCGGTCAACATTGCTg                 >  1:3965029/1‑36 (MQ=255)
                    cAATTACGCCGGGTGAAAACGCGGTCAACATTGCTg                 <  1:2433356/36‑1 (MQ=255)
                     aaTTACGCCGGGTGAAAACGCGGGCAACATTGCTGa                >  1:1196853/1‑36 (MQ=255)
                      aTTACGCCGGGTGAAAACGCGGTCAACATTGCTGAt               <  1:4087377/36‑1 (MQ=255)
                       ttACGCCGGGTGAAAACGCGGTCAACATTGCTGATg              <  1:2916542/36‑1 (MQ=255)
                       ttACGCCGGGTGAAAACGCGGTCAACATTGCTGATg              >  1:1250603/1‑36 (MQ=255)
                        tACGCCGGGTGAAAACGCGGTCAACATTGCTGATGt             <  1:3110441/36‑1 (MQ=255)
                        tACGCCGGGTGAAAACGCGGTCAACATTGCTGATGt             >  1:6678402/1‑36 (MQ=255)
                         actccGGGTGAAAACGCTGTCAACATTGCTGATGtt            <  1:3268524/33‑1 (MQ=37)
                         aagCCGGGTGAAAACGCGGTCAACATTGCTGATGtt            <  1:5568215/34‑1 (MQ=255)
                         aCGCCGGGTGAAAACGCGGTCAACATTGCTGATGtt            <  1:2457879/36‑1 (MQ=255)
                         aCGCCGGGTGAAAACGCGGTCAACATTGCTGATGtt            <  1:4740002/36‑1 (MQ=255)
                         aCGCCGGGTGAAAACGCGGTCAACATTGCTGATGtt            >  1:7352291/1‑36 (MQ=255)
                         aCGCCGGGTGAAAACGCGGTCAACATTGCTGATGtt            <  1:1054602/36‑1 (MQ=255)
                          cGCCGGGTGAAAACGCGGTCAACATTGCTGATGTTg           >  1:655975/1‑36 (MQ=255)
                          cGCCGGGTGAAAACGCGGTCAACATTGCTGATGTTg           >  1:504576/1‑36 (MQ=255)
                           gCCGGGTGAAAACGCGGTCAACATTGCTGATGTTGa          <  1:5778116/36‑1 (MQ=255)
                           gCCGGGTGAAAACGCGGTCAACATTGCTGATGTTGa          >  1:7676143/1‑36 (MQ=255)
                            ccGGGTGAAAACGCGGTCAACATTGCTGATGTTGaa         >  1:5545743/1‑36 (MQ=255)
                             cGGGTGAAAACGCGGTCAACATTGCTGATGTTGAAc        <  1:6009127/36‑1 (MQ=255)
                             cGGGTGAAAACGCGGTCAACATTGCTGATGTTGAAc        >  1:5794450/1‑36 (MQ=255)
                             cGGGTGAAAACGCGGTCAACATTGCTGATGTTGAAc        >  1:7241189/1‑36 (MQ=255)
                             cGGGTGAAAACGCGGTCAACATTGCTGATGTTGAAc        <  1:7321319/36‑1 (MQ=255)
                             cGGGTGAAAACGCGGTCAACATTGCTGATGTTGAAc        >  1:3639653/1‑36 (MQ=255)
                              gggTGAAAACGCGGTCAACATTGCTGATGTTGAAcc       >  1:1226424/1‑36 (MQ=255)
                              gggTGAAAACGCGGTCAACATTGCTGATGTTGAAcc       <  1:2103207/36‑1 (MQ=255)
                              gggTGAAAACGCGGTCAACATTGCTGATGTTGAAcc       >  1:4930064/1‑36 (MQ=255)
                              gggTGAAAACGCGGTCAACATTGCTGATGTTGAAcc       <  1:549654/36‑1 (MQ=255)
                              gggTGAAAACGCGGTCAACATTGCTGATGTTGAAcc       <  1:6659139/36‑1 (MQ=255)
                                gTGAAAACGCGGTCAACATTGCTGATGTTGAACCgg     <  1:5535148/36‑1 (MQ=255)
                                gTGAAAACGCGGTCAACATTGCTGATGTTGAACCgg     >  1:310478/1‑36 (MQ=255)
                                 tGAAAACGCGGTCAACATTGCTGATGTTGAACCGGc    >  1:937382/1‑36 (MQ=255)
                                  gAAAACGCGGTCAACATTGCTGATGTTGAACCGGCa   >  1:7425545/1‑36 (MQ=255)
                                  gAAAACGCGGTCAACATTGCTGATGTTGAACCGGCa   <  1:5947371/36‑1 (MQ=255)
                                  gAAAACGCGGTCAACATTGCTGATGTTGAACCGGCa   <  1:1028506/36‑1 (MQ=255)
                                   aaaaCGCGGTCAACATTGCTGATGTTGAACCGGCaa  <  1:7466961/36‑1 (MQ=255)
                                   aaaaCGCGGTCAACATTGCTGATGTTGAACCGGCaa  >  1:3907266/1‑36 (MQ=255)
                                   |                                   
CACGCTGCGCGATCTGCTGGCAATTACGCCGGGTGAAAACGCGGTCAACATTGCTGATGTTGAACCGGCAA  >  REL606/3292443‑3292513

Base quality scores:  ATCG  < 3 ≤  ATCG  < 16 ≤  ATCG  < 23 ≤  ATCG  < 30 ≤  ATCG  < 37 ≤  ATCG