Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6061,274,3300G→T 9.0% 0.7 ‑5.3 ‑0.069256ychPpredicted invasin
Rejected: E-value exceeds prediction threshold.
Reads supporting (aligned to +/- strand):  new base (7/0):  ref base (27/35):  total (34/35)
Fisher's exact test strand distribution p-value = 4.99e-03
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 9.97e-01

AGGTCATTTTACCGGCAGTCGTGGAAGCTGGTTTGTGCCGTTACAAGATAATGATCGTTATCTCACCTGG  >  REL606/1274296‑1274365
                                  |                                   
aGGTCTTTTTACCGGCAGTCGTGGAAGCTGGTTtgt                                    <  1:6729334/36‑1 (MQ=255)
aGGTCATTTTACCGGCAGTCGTGGAAGCTGGTTtgt                                    <  1:1589644/36‑1 (MQ=255)
  gTCATTTTACCGGCAGCCTTGGGAGCTGGCTTTTGc                                  >  1:1381621/1‑36 (MQ=12)
    cATTTTACCGGCAGTCGTTGAAGCTGGTTTTTGCCg                                >  1:6751320/1‑36 (MQ=37)
    cATTTTACCGGCAGTCGTGGAAGCTGGTTTGTGcca                                <  1:3215654/36‑2 (MQ=255)
    cATTTTACCGGCAGTCGTGGAAGCTGGTTTGTGCCg                                <  1:5994087/36‑1 (MQ=255)
    cATTTTACCGGCAGTCGTGGAAGCTGGTTTGTGCCg                                <  1:642552/36‑1 (MQ=255)
     aTTTTGCCGGCAGTCGTGGAAGCTGGTTTGTGCCGt                               <  1:5045410/36‑1 (MQ=255)
      ttttACCGGCAGTCGTGGAAGCTGGTTTGTGCCGtt                              <  1:1909680/36‑1 (MQ=255)
       tttACCGGCAGTCGTGGAAGCTGGTTTTTTCCGTTa                             >  1:557790/1‑36 (MQ=37)
       tttACCGGCAGTCGTGGAAGCTGGTTTGTGCCGTTa                             <  1:2036932/36‑1 (MQ=255)
        ttACCGGCAGTCGTTGAAGCTGGTTTTTGCCGttta                            >  1:5931980/1‑34 (MQ=25)
        ttACCGGCAGTCGTGGGAGCTGGGTTTTGCGGttta                            >  1:5163451/1‑34 (MQ=12)
        ttACCGGCAGTCGTGGAAGCTGGTTTGTGCCGTTAc                            <  1:2558281/36‑1 (MQ=255)
        ttACCGGCAGTCGTGGAAGCTGGTTTGTGCCGTTAc                            <  1:2702094/36‑1 (MQ=255)
         tACCGGCATTCGTGGAAGCTGGTTTGTGCCGTTACa                           <  1:2741177/36‑1 (MQ=255)
         tACCGGCAGTCGTGGAAGGTGGTTTTTGTCGTTACa                           >  1:6572105/1‑36 (MQ=25)
         tACCGGCAGTCGTGGAAGCTGGTTTGTGCCGTTACa                           <  1:3919132/36‑1 (MQ=255)
          aCCGGCAGTCGTGGAAGCTGGTTTTTGCCGTTACaa                          >  1:5442797/1‑36 (MQ=255)
          aCCGGCAGTCGTGGAAGCTGGTTTGTGCCGTTACaa                          <  1:3922449/36‑1 (MQ=255)
          aCCGGCAGTCGTGGAAGCTGGTTTGTGCCGTTACaa                          <  1:6735222/36‑1 (MQ=255)
           ccGGCAGTCGTGGAAGCTGGTTTGTGCCGTTACAAg                         >  1:5100737/1‑36 (MQ=255)
           ccGGCAGTCGTGGAAGCTGGTTTGTGCCGTTACAAg                         >  1:4185074/1‑36 (MQ=255)
           ccGGCAGTCGTGGAAGCTGGTTTGTGCCGTTACAAg                         >  1:6663754/1‑36 (MQ=255)
           ccGGCAGTCGTGGAAGCTGGTTTGAGCCGTTAcccg                         >  1:7928267/1‑33 (MQ=38)
            cGGCAGTCGTGGAAGCTGGTTTGTGCCGTTACAAGa                        <  1:5662835/36‑1 (MQ=255)
            cGGCAGTCGTGGAAGCTGGTTTGTGCCGTTACAAGa                        >  1:5329337/1‑36 (MQ=255)
            cGGCAGTCGTGGAAGCTGGTTTGTGCCGTTACAAGa                        >  1:1338084/1‑36 (MQ=255)
             ggCAGTCGTGGAAGCTGGTTTGTGCCGTTACAAGAt                       <  1:7345288/36‑1 (MQ=255)
              gCAGTCGTGGAAGCTGGTTTGTGCCGTTACAAGATa                      >  1:3487367/1‑36 (MQ=255)
              gCAGTCGTGGAAGCTGGTTTGTGCCGTTACAAGATa                      <  1:773732/36‑1 (MQ=255)
               cAGTCGTGGAAGCTGGTTTGTGCCGTTACAAGATaa                     <  1:4309462/36‑1 (MQ=255)
                aGTCGTGGAAGCTGGTTTGTGCCGTTACAAGATAAt                    >  1:4865192/1‑36 (MQ=255)
                aGTCGTGGAAGCTGGTTTGTGCCGTTACAAGATAAt                    >  1:1045968/1‑36 (MQ=255)
                aGTCGTGGAAGCTGGTTTGTGCCGTTACAAGATAAt                    <  1:2928305/36‑1 (MQ=255)
                 gTCGTGGAAGCTGGTTTGTGCCGTTACAAGATAATg                   >  1:916958/1‑36 (MQ=255)
                 gTCGTGGAAGCTGGTTTGTGCCGTTACAAGATAATg                   <  1:1880990/36‑1 (MQ=255)
                 gTCGTGGAAGCTGGTTTGTGCCGTTACAAGATAATg                   >  1:7435499/1‑36 (MQ=255)
                  tCGTGGAAGCTGGTTTGTGCCGTTACAAGATAATGa                  <  1:2974545/36‑1 (MQ=255)
                  tCGTGGAAGCTGGTTTGTGCCGTTACAAGATAATGa                  <  1:6998782/36‑1 (MQ=255)
                   cGTGGAAGCTGGTTTGTGCCGTTACAAGATAATGAt                 >  1:5257721/1‑36 (MQ=255)
                   cGTGGAAGCTGGTTTGTGCCGTTACAAGATAATGAt                 <  1:3008470/36‑1 (MQ=255)
                    gTGGAAGCTGGTTTGTGCCGTTACAAGATAATGATc                >  1:5986413/1‑36 (MQ=255)
                    gTGGAAGCTGGTTTGTGCCGTTACAAGATAATGATc                >  1:2477151/1‑36 (MQ=255)
                     tGGAAGCTGGTTTGTGCCGTTACAAGATAATGAtag               >  1:403084/1‑34 (MQ=255)
                     tGGAAGCTGGTTTGTGCCGTTACAAGATAATGATCg               <  1:574350/36‑1 (MQ=255)
                      ggAAGCTGGTTTGTGCCGTTACAAGATAATGATCGt              >  1:3652689/1‑36 (MQ=255)
                      ggAAGCTGGTTTGTGCCGTTACAAGATAATGATCGt              >  1:7329033/1‑36 (MQ=255)
                       gAAGCTGGTTTGTGCCGTTACAAGATAATGATCGtt             <  1:7640455/36‑1 (MQ=255)
                       gAAGCTGGTTTGTGCCGTTACAAGATAATGATCGtt             >  1:7272964/1‑36 (MQ=255)
                       gAAGCTGGTTTGTGCCGTTACAAGATAATGATCGtt             <  1:602366/36‑1 (MQ=255)
                        aaGCTGGTTTGTGCCGTTACAAGATAATGATCGTTa            <  1:6241047/36‑1 (MQ=255)
                         aGCTGGTTTGTGCCGTTACAAGATAATGATCGTTAt           <  1:5871386/36‑1 (MQ=255)
                         aGCTGGTTTGTGCCGTTACAAGATAATGATCGTTAt           >  1:3548420/1‑36 (MQ=255)
                         aGCTGGTTTGTGCCGTTACAAGATAATGATCGTTAt           >  1:962252/1‑36 (MQ=255)
                          gCTGGTTTGTGCCGTTACAAGATAATGATCGTTAtc          <  1:730139/36‑1 (MQ=255)
                          gCTGGTTTGTGCCGTTACAAGATAATGATCGTTAtc          <  1:1459396/36‑1 (MQ=255)
                          gCTGGTTTGTGCCGTTACAAGATAATGATCGTTAtc          >  1:6715253/1‑36 (MQ=255)
                          gCTGGTTTGTGCCGTTACAAGATAATGATCGTTAtc          <  1:6634223/36‑1 (MQ=255)
                            tGGTTTGTGCCGTTACAAGATAATGATCGTTAtctc        >  1:3773886/1‑36 (MQ=255)
                             ggTTTGTGCCGTTACAAGATAATGATCGTTATCTCa       <  1:5239746/36‑1 (MQ=255)
                             ggTTTGTGCCGTTACAAGATAATGATCGTTATCTCa       <  1:7229032/36‑1 (MQ=255)
                              gTTTGTGCCGTTACAAGATAATGATCGTTATCTCAc      >  1:6798763/1‑36 (MQ=255)
                              gTTTGTGCCGTTACAAGATAATGATCGTTATCTCAc      <  1:542527/36‑1 (MQ=255)
                              gTTTGTGCCGTTACAAGATAATGATCGTTATCTCAc      >  1:3178259/1‑36 (MQ=255)
                              gTTTGTGCCGTTACAAGATAATGATCGTTATCTCAc      <  1:6310509/36‑1 (MQ=255)
                              gTTTGCGCCGTTACAAGGTAATGATCGTTATCTCaa      >  1:2328647/1‑35 (MQ=37)
                               tttGTGCCGTTACAAGATAATGATCGTTATCTCAcc     >  1:5005526/1‑36 (MQ=255)
                                ttGTGCCGTTACAAGATAATGATCGTTATCTCACCt    <  1:7177932/36‑1 (MQ=255)
                                ttGTGCCGTTACAAGATAATGATCGTTATCTCACCt    >  1:7138723/1‑36 (MQ=255)
                                ttGTGCCGTTACAAGATAATGATCGTTATCTCACCt    <  1:2071333/36‑1 (MQ=255)
                                 tgtgCCGTTACAAGATAATGATCGTTATCTCACCTg   <  1:2989056/36‑1 (MQ=255)
                                 tgtgCCGTTACAAGATAATGATCGTTATCTCACCTg   >  1:4744107/1‑36 (MQ=255)
                                  gtgCCGTTACAAGATAATGATCGTTATCTCACCTgg  >  1:5392202/1‑36 (MQ=255)
                                  gtgCCGTTACAAGATAATGATCGTTATCTCACCTgg  >  1:7041913/1‑36 (MQ=255)
                                  |                                   
AGGTCATTTTACCGGCAGTCGTGGAAGCTGGTTTGTGCCGTTACAAGATAATGATCGTTATCTCACCTGG  >  REL606/1274296‑1274365

Base quality scores:  ATCG  < 3 ≤  ATCG  < 12 ≤  ATCG  < 22 ≤  ATCG  < 30 ≤  ATCG  < 37 ≤  ATCG