Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6062,654,3620G→T 7.8% 0.2 ‑5.9 ‑0.0771220clpBprotein disaggregation chaperone
Rejected: E-value exceeds prediction threshold.
Reads supporting (aligned to +/- strand):  new base (7/0):  ref base (28/42):  total (35/42)
Fisher's exact test strand distribution p-value = 2.80e-03
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 9.90e-01

TACGACGATCGAGTCGGTCGAGTTCTTCTGGTTTTGAGTCAATCTGCATACGAATGCTGGATGCTGCTTC  >  REL606/2654327‑2654396
                                   |                                  
tACGACGATCGAGTCGGTCGAGTTCTTCTGGTTTTg                                    <  1:6922668/36‑1 (MQ=255)
 acgacgATCGAGTCGGTCGAGTTCTTCTGGTTTTGa                                   <  1:2367237/36‑1 (MQ=255)
 acgacgATCGAGTCGGTCGAGTTCTTCTGGTTTTGa                                   <  1:1707178/36‑1 (MQ=255)
  cgacgaTCGAGTCGGTCGGGTTCTTCTGGTTTTTAg                                  >  1:3481094/1‑36 (MQ=37)
  cgacgaTCGAGTCGGTCGATTTCTTCTGGTTTTGAg                                  <  1:7542130/36‑1 (MQ=255)
   gacgaTCGCGTCGGTCGAGTTCTTCTGGTTTTGAGt                                 <  1:1743422/36‑1 (MQ=255)
   gacgaTCGAGTCGGTCGGGTTTTTCTGGTTTTTAGt                                 >  1:1222188/1‑36 (MQ=25)
     cgaTCGAGTCGGTCGCGTTTTTTTGGTTTTTATTCa                               >  1:4038996/1‑36 (MQ=16)
     cgaTCGAGTCGGTCGAGTTCTTCTGGTTTTGAGTCa                               <  1:1554437/36‑1 (MQ=255)
     cgaTCGAGTCGGTCGAAGTCTTGTGGTTTTGGGTCa                               >  1:1254269/1‑36 (MQ=255)
      gaTCGAGTCGGTCGAGTTCTTTTTGTTTTTAGTCaa                              >  1:2721531/1‑36 (MQ=25)
      gaTCGAGTCGGTCGAGTTCTTCTGGTTTTTTGTCaa                              >  1:6875798/1‑36 (MQ=37)
       aTCGAGTCGGTCGAGTTCTTCTGGTTTTGAGTCAAt                             >  1:7475946/1‑36 (MQ=255)
       aTCGAGTCGGTCGAGTTCTTCTGGTTTTGAGTCAAt                             <  1:5228882/36‑1 (MQ=255)
       aTCGAGTCGGTCGAGTTCTTCTGGTTTTGAGTCAAt                             <  1:1201747/36‑1 (MQ=255)
        tCGAGTCGGTCGAGTTCTTCTGGTTTTGAGTCAATc                            <  1:3362217/36‑1 (MQ=255)
        tCGAGTCGGTCGAGTTCTTCTGGTTTTGAGTCAATc                            <  1:4314810/36‑1 (MQ=255)
         cGAGTCGGTCGAGTTCTTCTGGTTTTGAGTCAATCt                           <  1:2219475/36‑1 (MQ=255)
         cGAGTCGGTCGAGTTCTTCTGGTTTTGAGTCAATCt                           >  1:4957924/1‑36 (MQ=255)
          gAGTCGGTCGAGTTCTTCTTGTTTTTTGTCAATCtt                          >  1:3114052/1‑35 (MQ=25)
          gAGTCGGTCGAGTTCTTCTTGTTTTTAGTCAATCTg                          >  1:3041884/1‑36 (MQ=38)
           aGTCGGTCGAGTTCTTCTGGTTTTGAGTCAATCTGc                         <  1:2078030/36‑1 (MQ=255)
           aGTCGGTCGAATTCTTCTGGTTTTGAGTCAATCTGc                         <  1:4678159/36‑1 (MQ=255)
             tcggtcgAGTTCTTCTGGTTTTGAGTCAATCTGCAt                       >  1:5279198/1‑36 (MQ=255)
             tcggtcgAGTTCTTCTGGTTTTGAGTCAATCTGCAt                       <  1:5803341/36‑1 (MQ=255)
             tcggtcgAGTTCTTCTGGTTTTGAGTCAATCTGCAt                       <  1:666820/36‑1 (MQ=255)
             tcggtcgAGTTCTTCTGGTTTTGAGTCAATCTGCAt                       <  1:1050397/36‑1 (MQ=255)
              cggtcgAGTTCTTCTGGTTTTGAGTCAATCTGCATa                      <  1:48614/36‑1 (MQ=255)
               ggtcgAGTTCTTCTGGTTTTGAGTCAATCTGCATAc                     <  1:4854289/36‑1 (MQ=255)
               ggtcgAGTTCTTCTGGTTTTGAGTCAATCTGCATAc                     <  1:2322758/36‑1 (MQ=255)
               ggtcgAGTTCTTCTGGTTTTGAGTCAATCTGCATAc                     <  1:7576964/36‑1 (MQ=255)
               ggtcgAGTTCTTCTGGTTTTGAGTCAATCTGCATAc                     >  1:3031297/1‑36 (MQ=255)
                gtcgAGTTCTTCTGGTTTTGAGTCAATCTGCATACg                    >  1:4509236/1‑36 (MQ=255)
                gtcgAGTTCTTCTGGTTTTGAGTCAATCTGCATACg                    >  1:612387/1‑36 (MQ=255)
                gtcgAGTTCTTCTGGTTTTGAGTCAATCTGCATACg                    >  1:7739776/1‑36 (MQ=255)
                 tcgAGTTCTTCTGGTTTTGAGTCAATCTGCATACGa                   >  1:3061350/1‑36 (MQ=255)
                   gAGTTCTTCTGGTTTTGAGTCAATCTGCATACGAAt                 >  1:5576481/1‑36 (MQ=255)
                   gAGTTCTTCTGGTTTTGAGTCAATCTGCATACGAAt                 <  1:5145173/36‑1 (MQ=255)
                   gAGTTCTTCTGGTTTTGAGTCAATCTGCATACGAAt                 <  1:3255227/36‑1 (MQ=255)
                    aGTTCTTCTGGTTTTGAGTCAATCTGCATACGAATg                >  1:4255617/1‑36 (MQ=255)
                    aGTTCTTCTGGTTTTGAGTCAATCTGCATACGAATg                >  1:541290/1‑36 (MQ=255)
                     gTTCTTCTGGTTTTGAGTCAATCTGCATACGAATGc               <  1:4610887/36‑1 (MQ=255)
                      ttcttcTGGTTTTGAGTCAATCTGCATACGAATGCt              >  1:711835/1‑36 (MQ=255)
                      ttcttcTGGTTTTGAGTCAATCTGCATACGAATGCt              <  1:3510345/36‑1 (MQ=255)
                      ttcttcTGGTTTTGAGTCAATCTGCATACGAATGCt              <  1:5977446/36‑1 (MQ=255)
                      ttcttcTGGTTTTGAGTCAATCTGCATACGAATGCt              <  1:4669588/36‑1 (MQ=255)
                       tcttctGGTTTTGAGTCAATCTGCATGCGAATGATg             >  1:5290174/1‑36 (MQ=38)
                       tcttctGGTTTTGAGTCAATCTGCATACGAATGCTg             >  1:2894932/1‑36 (MQ=255)
                        cttctGGTTTTGAGGCAATGTGTATACGAATGCTgg            >  1:952184/1‑36 (MQ=25)
                           ctGGTTTTGAGTCAATCTGCATACGAATGCTGGAtg         <  1:1963078/36‑1 (MQ=255)
                           ctGGTTTTGAGTCAATCTGCATACGAATGCTGGAtg         <  1:5141663/36‑1 (MQ=255)
                            tGGTTTTGAGTCAATCTGCATACGAATGCTGGAtgc        <  1:1136104/36‑1 (MQ=255)
                            tGGTTTTGAGTCAATCTGCATACGAATGCTGGAtgc        >  1:7835570/1‑36 (MQ=255)
                             ggTTTTGAGTCAATCTGCATACGAATGCTGGAtgct       <  1:1123632/36‑1 (MQ=255)
                             ggTTTTGAGTCAATCTGCATACGAATGCTGGAtgct       <  1:5802890/36‑1 (MQ=255)
                             ggTTTTGAGTCAATCTGCATACGAATGCTGGAtgct       >  1:5659719/1‑36 (MQ=255)
                             ggTTTTGAGTCAATCTGCATACGAATGCTGGAtgct       <  1:4819756/36‑1 (MQ=255)
                             ggTTTTGAGTCAATCTGCATACGAATGCTGGAtgct       >  1:1366337/1‑36 (MQ=255)
                              gTTTTGAGTCAATCTGCATACGAATGCTGGAtgctg      >  1:4837936/1‑36 (MQ=255)
                              gTTTTGAGTCAATCTGCATACGAATGCTGGAtgctg      <  1:2827937/36‑1 (MQ=255)
                              gTTTTGAGTCAATCTGCATACGAATGCTGGAtgctg      <  1:1166146/36‑1 (MQ=255)
                              gTTTTGAGTCAATCTGCATACGAATGCTGGAtgctg      <  1:7849158/36‑1 (MQ=255)
                               ttttGAGTCAATCTGCATACGAATGCTGGAtgctgc     >  1:3294925/1‑36 (MQ=255)
                               ttttGAGTCAATCTGCATACGAATGCTGGAtgctgc     <  1:4847967/36‑1 (MQ=255)
                               ttttGAGTCAATCTGCATACGAATGCTGGAtgctgc     >  1:1331525/1‑36 (MQ=255)
                               ttttGAGTCAATCTGCATACGAATGCTGGAtgctgc     <  1:6573884/36‑1 (MQ=255)
                               ttttGAGTCAATCTGCATACGAATGCTGGAtgctgc     <  1:1304394/36‑1 (MQ=255)
                                tttGAGTCAATCTGCATACGAATGCTGGATgctgct    <  1:1912963/36‑1 (MQ=255)
                                tttGAGTCAATCTGCATACGAATGCTGGATgctgct    >  1:6976945/1‑36 (MQ=255)
                                 ttGAGTCAATCTGCATACGAATGCTGGATGCTGCtt   <  1:2770733/36‑1 (MQ=255)
                                 ttGAGTCAATCTGCATACGAATGCTGGATGCTGCtt   >  1:3086083/1‑36 (MQ=255)
                                 ttGAGTCAATCTGCATACGAATGCTGGATGCTGCtt   >  1:1952552/1‑36 (MQ=255)
                                 ttGAGTCAATCTGCATACGAATGCTGGATGCTGCtt   <  1:1662928/36‑1 (MQ=255)
                                 ttGAGTCAATCTGCATACGAATGCTGGATGCTGCtt   <  1:4903882/36‑1 (MQ=255)
                                 ttGAGTCAATCTGCATACGAATGCTGGATGCTGCtt   >  1:4859273/1‑36 (MQ=255)
                                  tGAGTCAATCTGCATACGAATGCTGGATGCTGCTTc  >  1:3389922/1‑36 (MQ=255)
                                  tGAGTCAATCTGCATACGAATGCTGGATGCTGCTTc  <  1:2311046/36‑1 (MQ=255)
                                  tGAGTCAATCTGCATACGAATGCTGGATGCTGCTTc  >  1:4880932/1‑36 (MQ=255)
                                   |                                  
TACGACGATCGAGTCGGTCGAGTTCTTCTGGTTTTGAGTCAATCTGCATACGAATGCTGGATGCTGCTTC  >  REL606/2654327‑2654396

Base quality scores:  ATCG  < 3 ≤  ATCG  < 11 ≤  ATCG  < 22 ≤  ATCG  < 32 ≤  ATCG  < 37 ≤  ATCG