Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6063,280,8840C→A 8.5% 0.8 ‑2.7 0.077933rpoNDNA‑directed RNA polymerase subunit N
Rejected: E-value exceeds prediction threshold.
Reads supporting (aligned to +/- strand):  new base (1/8):  ref base (32/36):  total (33/44)
Fisher's exact test strand distribution p-value = 6.97e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 1.00e+00

AACCAGCACTACGCCTCGATGTGCAATAACGCGCGCAACGATGGTGACAGCCAGTTTATCCGCAGCAATCT  >  REL606/3280849‑3280919
                                   |                                   
aaCCAGCACTACGCCTCGATGTGCAATAACgcgcgc                                     >  1:4442470/1‑36 (MQ=255)
aaCCAGCACTACGCCTCGATGTGCAATAACgcgcgc                                     >  1:6831029/1‑36 (MQ=255)
aaCCAGCACTACGCCTCGATGTGCAATAACgcgcgc                                     >  1:6286649/1‑36 (MQ=255)
aaCCAGCACTACGCCTCGATGTGCAATAACgcgcgc                                     <  1:6866030/36‑1 (MQ=255)
aaCCAGCACTACGCCTCGATGTGCAATAACgcgcgc                                     >  1:3665606/1‑36 (MQ=255)
 aCCAGCACTACGCCTCGATGTGCAATAACGCGCGCa                                    <  1:2257544/36‑1 (MQ=255)
 aCCAGCACTACGCCTCGATGTGCAATAACGCGCGCa                                    >  1:6770019/1‑36 (MQ=255)
 aCCAGCACTACGCCTCGATGTGCAATAACGCGCGCa                                    <  1:1679387/36‑1 (MQ=255)
 aCCAGCACTACGCCTCGATGTGCAATAACGCGCGCa                                    >  1:4929718/1‑36 (MQ=255)
 aCCAGCACTACGCCTCGATGTGCAATAACGCGCGCa                                    <  1:1240144/36‑1 (MQ=255)
 aCCAGCACTACGCCTCGATGTGCAATAACGCGCGCa                                    >  1:514562/1‑36 (MQ=255)
 aCCAGCACTACGCCTCGATGTGCAATAACGCGCGCa                                    >  1:5171/1‑36 (MQ=255)
  ccAGCACTACGCCTCGATGTGCAATAACGCGCGCaa                                   >  1:3785484/1‑36 (MQ=255)
  ccAGCACTACGCCTCGATGTGCAATAACGCGCGCaa                                   <  1:3174145/36‑1 (MQ=255)
  ccAGCACTACGCCTCGATGTGCAATAACGCGCGCaa                                   <  1:2540161/36‑1 (MQ=255)
   cAGCACTACGCCTCGATGTGCAATAACGCGCGCAAc                                  >  1:3921831/1‑36 (MQ=255)
    aGCACTACGCCTCGATGTGCAATAACGCGCGCAACg                                 <  1:4745264/36‑1 (MQ=255)
    aGCACTACGCCTCGATGTGCAATAACGCGCGCAACg                                 >  1:1690327/1‑36 (MQ=255)
    aGCACTACGCCTCGATGTGCAATAACGCGCGCAACg                                 >  1:7314564/1‑36 (MQ=255)
      cACTACGCCTCGCTGTGCAATAACGCGCGAAACGAt                               >  1:6670672/1‑36 (MQ=37)
      cACTACGCCTCGATGTGCAATAACGCGCGCAACGAt                               <  1:3811234/36‑1 (MQ=255)
      cACTACGCCTCGATGTGCAATAACGCGCGCAACGAt                               <  1:348429/36‑1 (MQ=255)
      cACTACGCCTCGATGTGCAATAACGCGCGCAACGAt                               <  1:5740252/36‑1 (MQ=255)
      cACTACGCCTCGATGTGCAATAACGCGCGCAACGAt                               <  1:5806174/36‑1 (MQ=255)
      cACTACGCCTCGATGTGCAATAACGCGCGCAACGAt                               <  1:7149066/36‑1 (MQ=255)
      cACTACGCCTCGATATGCAATAACGCGCGCAACGAt                               <  1:4688564/36‑1 (MQ=255)
       aCTACGCCTCGATGTGCAATAACGCGCGCAACGATg                              >  1:2207588/1‑36 (MQ=255)
       aCTACGCCTCGATGTGCAATAACGCGCGCAACGATg                              >  1:1469568/1‑36 (MQ=255)
        cTACGCCTCGATGTGCAATAACGCGCGCAACGATgg                             >  1:3613163/1‑36 (MQ=255)
        cTACGCCTCGATGTGCAATAACGCGCGCAACGATgg                             >  1:3155643/1‑36 (MQ=255)
         tACGCCTCGATGTGCAATAACGCGCGCAACGATGGt                            <  1:7160223/36‑1 (MQ=255)
         tACGCCTCGATGTGCAATAACGCGCGCAACGATGGt                            >  1:1443152/1‑36 (MQ=255)
         tACGCCTCGATGTGCAATAACGCGCGCAACGATGGt                            <  1:1693486/36‑1 (MQ=255)
         tACGCCTCGATGTGCAATAACGCGCGCAACGATGGt                            <  1:2420073/36‑1 (MQ=255)
          aCGCCTCGATGTGCAATAACGCGCGCAACGATGGTg                           >  1:3884107/1‑36 (MQ=255)
           cGCCTCGATGTGCAATAACGCGCGCAACGATGGTGa                          <  1:6180330/36‑1 (MQ=255)
           cGCCTCGATGTGCAATAACGCGCGCAACGATGGTGa                          >  1:2038063/1‑36 (MQ=255)
            gCCTCGATGTGCAATAACGCGCGCAACGATGGTGAc                         <  1:3474463/36‑1 (MQ=255)
            gCCTCGATGTGCAATAACGCGCGCAACGATGGTGAc                         <  1:6551938/36‑1 (MQ=255)
            gCCTCGATGTGCAATAACGCGCGCAACGATGGTGAc                         >  1:5352191/1‑36 (MQ=255)
             ccTCGATGTGCAATAACGCGCGCAACGATGGTGACa                        <  1:4644470/36‑1 (MQ=255)
             ccTCGATGTGCAATAACGCGCGCAACGATGGTGACa                        <  1:6021665/36‑1 (MQ=255)
             ccTCGATGTGCAATAACGCGCGCAACGATGGTGACa                        <  1:1435258/36‑1 (MQ=255)
             ccTCGATGTGCAATAACGCGCGCAACGATGGTGACa                        >  1:3542674/1‑36 (MQ=255)
             ccTCGATGTGCAATAACGCGCGCAACGATGGTGACa                        <  1:6903153/36‑1 (MQ=255)
             ccTCGATGTGCAATAACGCGCGCAACGATGGTGACa                        <  1:6035503/36‑1 (MQ=255)
              cTCGATGTGCAATAACGCGCGCAACGATGGTGACAg                       <  1:3397848/36‑1 (MQ=255)
              cTCGATGTGCAATAACGCGCGCAACGATGGTGACAg                       <  1:5628665/36‑1 (MQ=255)
                cGATGTGCAATAACGCGCGCAACGATGGTGACAGcc                     >  1:6673956/1‑36 (MQ=255)
                cGATGTGCAATAACGCGCGCAACGATGGTGACAGcc                     <  1:168882/36‑1 (MQ=255)
                cGATGTGCAATAACGCGCGCAACGATGGTGACAGcc                     <  1:5350388/36‑1 (MQ=255)
                 gATGTGCAATAACGCGCGCAACGATGGTGACAGCCa                    >  1:7472619/1‑36 (MQ=255)
                  aTGTGCAATAACGCGCGCAACGATGGTGACAGCCAg                   >  1:5397969/1‑36 (MQ=255)
                  aTGTGCAATAACGCGCGCAACGATGGTGACAGCCAg                   <  1:2114344/36‑1 (MQ=255)
                  aTGTGCAATAACGCGCGCAACGATGGTGACAGCCAg                   <  1:131702/36‑1 (MQ=255)
                  aTGTGCAATAACGCGAGCAACGATGGTGACAGCCAg                   >  1:1482337/1‑36 (MQ=255)
                   tgtgCAATAACGCGCGCAACGATGGTGACAGCCAGt                  >  1:3903947/1‑36 (MQ=255)
                   tgtgCAATAACGCGCGCAACGATGGTGACAGCCAGt                  >  1:6489654/1‑36 (MQ=255)
                   tgtgCAATAACGCGCGCAACGATGGTGACAGCCAGt                  >  1:5861893/1‑36 (MQ=255)
                   tgtgAAATAACGCGCGAAACGAGGGTGACAGCCAGt                  <  1:6062980/36‑1 (MQ=25)
                    gtgCAATAACGCGCGCAACGATGGTGACAGCCAGtt                 >  1:431443/1‑36 (MQ=255)
                    gtgCAATAACGCGCGCAACGATGGTGACAGCCAGtt                 >  1:4029173/1‑36 (MQ=255)
                    gtgCAATAACGCGCGCAACGATGGTGACAGCCAGtt                 <  1:833815/36‑1 (MQ=255)
                     tgCAATAACGCGCGCAGCGATGGTGACAGCCAGttt                <  1:4378912/36‑1 (MQ=255)
                     tgCAATAACGCGCGAAACGATGGTGACAGCCAGttt                <  1:2355880/36‑1 (MQ=255)
                     tgCAATAACGCGCGAAAAGATGGTGACAGCCAGttt                <  1:1186456/36‑1 (MQ=25)
                      gCAATAACGCGCGCAACGATGGTGACAGCCAGTTTa               >  1:5288322/1‑36 (MQ=255)
                      gCAATAACGCGCGCAACGATGGTGACAGCCAGTTTa               >  1:2300759/1‑36 (MQ=255)
                        aaTAACGCGCGCAACGATGGTGACAGCCAGTTTATc             >  1:6225153/1‑36 (MQ=255)
                        aaTAACGCGCGCAACGATGGTGACAGCCAGTTTATc             <  1:3345852/36‑1 (MQ=255)
                        aaTAACGCGCGAAACGATGGTGACAGCCAGTTTATc             <  1:6702591/36‑1 (MQ=255)
                         aTAACGCGCGCAACGATGGTGACAGCCAGTTTCTcc            >  1:2921822/1‑36 (MQ=255)
                         aTAACGCGCGCAACGATGGTGACAGCCAGTTTATcc            <  1:4636266/36‑1 (MQ=255)
                         aTAACGCGCGAAACGATGGTGACAGCCAGTTTATcc            <  1:2293662/36‑1 (MQ=255)
                         aTAACGCGCGAAACCACGGTCACAGCCAGTTTATcc            <  1:7317952/36‑1 (MQ=19)
                          tAACGCGCGCAACGATGGGGACAGCCAGTTTATcag           >  1:5384315/1‑34 (MQ=37)
                          tAACGCGCGAAACGATGGTGACAGCCAGTTTATCCg           <  1:2045907/36‑1 (MQ=255)
                          aaaCGCGCGCAACGATGGTGACAGCCAGTTTATCCg           <  1:4738382/35‑1 (MQ=255)
                           aaCGCGCGCAACGATGGTAACAGCCAGTTTATCCgc          <  1:4787275/36‑1 (MQ=255)
                            aCGCGCGCAACGATGGTGACAGCCAGTTTATCCgca         <  1:7287392/36‑1 (MQ=255)
                            aCGCGCGCAACGATGGTGACAGCCAGTTTATCCgca         >  1:6870801/1‑36 (MQ=255)
                             cgcgcgAAACGATGGTGACAGCCAGTTTATCCgcag        <  1:7439685/36‑1 (MQ=255)
                              gcgcgcAACGATGGTGACAGCCAGTTTATCCgcagc       >  1:1138908/1‑36 (MQ=255)
                              gcgcgcAACGATGGTGACAGCCAGTTTATCCgcagc       >  1:1214483/1‑36 (MQ=255)
                              gcgcgcAACGATGGTGACAGCCAGTTTATCCgcagc       >  1:1429335/1‑36 (MQ=255)
                              gcgcgcAACGAGGGTGACAGCCAGTTTATCCgcagc       <  1:5038819/36‑1 (MQ=255)
                              gcgcgcAACGAGGGTGACAGCCAGTTTATCCgcagc       <  1:6484344/36‑1 (MQ=255)
                              acgcggAACAATGGTGGCAGCCAGTTTATCCgcagc       <  1:177853/35‑1 (MQ=25)
                               cgcgaAACGATGGTGACAGCCAGTTTATCCgcagca      <  1:1022703/36‑1 (MQ=255)
                                gcgcAACGATGGTGACAGCGAGTTTATCCGCAGCaa     >  1:6867857/1‑36 (MQ=255)
                                gcgcAACGATGGTGACAGCCAGTTTATCCGCAGCaa     >  1:5758622/1‑36 (MQ=255)
                                gcgcAACGATGGTGACAGCCAGTTTATCCGCAGCaa     >  1:583578/1‑36 (MQ=255)
                                 cgcAACGATGGTGACAGCCAGTTTATCCGCAGCAAt    >  1:4021539/1‑36 (MQ=255)
                                  gcAACGATGGTGACAGCCAGTTTATCCGCAGCAATc   >  1:7233871/1‑36 (MQ=255)
                                  gcAACGATGGTGACAGCCAGTTTATCCGCAGCAATc   <  1:3556165/36‑1 (MQ=255)
                                  gcAACGATGGTGACAGCCAGTTTATCCGCAGCAATc   <  1:5194533/36‑1 (MQ=255)
                                   cAAGGATGGTGACAGCCAGTTTATCCGCAGCAATCt  <  1:1699927/36‑1 (MQ=255)
                                   cAACGATGGTGACAGCTAGTTTGTCCGCAGCAATCt  <  1:2576566/36‑1 (MQ=37)
                                   |                                   
AACCAGCACTACGCCTCGATGTGCAATAACGCGCGCAACGATGGTGACAGCCAGTTTATCCGCAGCAATCT  >  REL606/3280849‑3280919

Base quality scores:  ATCG  < 3 ≤  ATCG  < 11 ≤  ATCG  < 22 ≤  ATCG  < 30 ≤  ATCG  < 37 ≤  ATCG