Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6064,182,4570A→G10.5% 3.6 ‑16.9 0.075926zraSsensory histidine kinase in two‑component regulatory system with ZraR
Rejected: Polymorphism prediction not supported by minimum number of reads on both strands.
Reads supporting (aligned to +/- strand):  new base (9/0):  ref base (6/59):  total (16/59)
Fisher's exact test strand distribution p-value = 4.53e-08
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 1.00e+00

GGTTAGGCCAACGCATCTGGCTTTGCAGGCGGTGGATCTCAACACGCTGATTAACCACTCATTACAGCTGG  >  REL606/4182422‑4182492
                                   |                                   
ggTTAGGCCAACGCATCTGGCTTTGCAGGCGGTGGa                                     <  1:3232485/36‑1 (MQ=255)
 gTTAGGCCAACGCATCTGTCTTTGCAGGCGGTGGAt                                    <  1:4164187/36‑1 (MQ=255)
 gTTAGGCCAACGCATCTGGCTTTGCAGGCGGTGGAt                                    <  1:4827526/36‑1 (MQ=255)
  ttAGGCCAACGCATCTGGCTTTGCAGGCGGTGGAtc                                   <  1:4015106/36‑1 (MQ=255)
  ttAGGCCAACGCATCTGGCTTTGCAGGCGGTGGAtc                                   <  1:3361425/36‑1 (MQ=255)
   tAGGCGAACGCATCTGGCTTTGCAGGCGGTGGAtct                                  <  1:3991907/36‑1 (MQ=255)
    aGGCCAACGTATCTGGCTTTGCTGGCGGTGTAtctc                                 <  1:7344859/36‑1 (MQ=25)
    aGGCCAACGCATCTGGCTTTGCAGGCGGTGGGtctt                                 >  1:4919555/1‑35 (MQ=255)
    aGGCCAACGCATCTGGCTTTGCAGGCGGTGGAtctc                                 <  1:1530899/36‑1 (MQ=255)
     ggCCAACGCATCTGGCTTTGCAGGCGGTGGATCTCa                                <  1:1632066/36‑1 (MQ=255)
     ggCCAACGCATCTGGCTTTGCAGGCGGTGGATCTCa                                <  1:1639855/36‑1 (MQ=255)
      gCCAACGCATCTGGCTTTGCAGGCGGTGGATTTCaa                               >  1:7901724/1‑36 (MQ=255)
      gCCAACGCATCTGGCTTTGCAGGCGGTGGATCTCaa                               <  1:7914973/36‑1 (MQ=255)
      gCCAACGCATCTGGCTTTGCAGGCGGTGGATCTCaa                               <  1:342581/36‑1 (MQ=255)
      gCCAACGCATCTGGCTTTGCAGGCGGTGGATCTCaa                               <  1:4444316/36‑1 (MQ=255)
      gCCAACGCATCTGGCTTAGCAGGCGGTGGATCTCaa                               <  1:6017922/36‑1 (MQ=255)
       ccAACGCATCTGGCTTTGCAGGCGGTGGATCTCAac                              <  1:4511437/36‑1 (MQ=255)
        cAACGCATCTGGCTTTGCAGGCGGTGGGTCTCTnca                             >  1:4541932/1‑36 (MQ=37)
        cAACGCATCTGGCTTTGCAGGCGGTGGGTCTCAaca                             >  1:4290815/1‑36 (MQ=255)
        cAACGCATCTGGCTTTGCAGGCGGTGGATCTCAaca                             <  1:7309063/36‑1 (MQ=255)
        cAACGCATCTGGCTTTGCAGGCGGTGGATCTCAaca                             <  1:127005/36‑1 (MQ=255)
        cAACGCATCTGGCTTTGCAGGCGGTGGATCTCAaca                             <  1:4789998/36‑1 (MQ=255)
        cAACGCATCTGGCTTTGCAGCCGGTGGGTCTCAaca                             >  1:1261255/1‑36 (MQ=37)
         aaCGCATCTGGCTTTGCAGGCGGTGGATCTCAacac                            <  1:7814131/36‑1 (MQ=255)
         aaCGCATCTGGCTTTGCAGGCGGCGGGTTTCAacac                            >  1:520649/1‑36 (MQ=25)
          aCGCATCTGGCTTTGCAGGCGGTGGGTTTCAACACg                           >  1:1509494/1‑36 (MQ=37)
          aCGCATCTGGCTTTGCAGGCGGTGGATCTCAACACg                           <  1:2370728/36‑1 (MQ=255)
          aCGCATCTGGCTTTGCAGGCGGTGGATCTCAACACg                           <  1:7164850/36‑1 (MQ=255)
           cGCATCTGGCTTTGCAGGCGGTGGATCTCAACACGc                          <  1:4774603/36‑1 (MQ=255)
           cGCATCTGGCTTTGCAGGCGGTGGATCTCAACACGc                          <  1:7210991/36‑1 (MQ=255)
            gCATCTGGCTTTGCAGGCGGTGGGTTTCAAAACGCt                         >  1:4268065/1‑36 (MQ=25)
            gCATCTGGCTTTGCAGGCGGTGGATCTCAACACGCt                         <  1:1369157/36‑1 (MQ=255)
            gCATCTGGCTTTGCAGGCGGTGGATCTCAACACGCt                         <  1:3105664/36‑1 (MQ=255)
            gCATCTGGCTTTGCAGGCGGTGGATCTCAACACGCt                         <  1:6661327/36‑1 (MQ=255)
             cATCTGGCTTTGCAGGCGGTGGGTCTTAACACGCTg                        >  1:1490141/1‑36 (MQ=37)
             cATCTGGCTTTGCAGGCGGTGGATCTCAACACGCTg                        <  1:1723471/36‑1 (MQ=255)
             cATCTGGCTTTGCAGGCGGTGGATCTCAACACGCTg                        <  1:7010065/36‑1 (MQ=255)
             cATCTGGCTTTGCAGGCGGTGGATCTCAACACGCTg                        <  1:6691922/36‑1 (MQ=255)
              aTCTGGCTTTGCAGGCGGTGGGTTTCAACACGCTgt                       >  1:5807532/1‑35 (MQ=37)
              aTCTGGCTTTGCAGGCGGTGGATCTCAACACGCTGa                       <  1:4677008/36‑1 (MQ=255)
               tCTGGCTTTGCAGGCGGTGGATCTCAACACGCTGAt                      <  1:2539005/36‑1 (MQ=255)
               tCTGGCTTTGCAGGCGGTGGATCTCAACACGCTGAt                      <  1:6462788/36‑1 (MQ=255)
               tCTGACTTTGCAGGCGGTGGATCTCAACACGCTGAt                      <  1:1509942/36‑1 (MQ=255)
                cTGGCTTTGCAGGCGGTGGATCTCAACACGCTGAtt                     <  1:961564/36‑1 (MQ=255)
                cTGGCTTTGCAGGCGGTGGATCTCAACACGCTGAtt                     <  1:7091844/36‑1 (MQ=255)
                cTGGCTTTGCAGGCGGTGGATCTCAACACGCTGAtt                     <  1:5971898/36‑1 (MQ=255)
                 tGGCTTTGCAGGCGGTGGTTTTCAAAACACCGAttt                    >  1:4090013/1‑35 (MQ=9)
                 tGGCTTTGCAGGCGGTGGATCTCAACACGCTGATTa                    <  1:6275200/36‑1 (MQ=255)
                  ggCTTTGCAGGCGGTGGATCTCAACACGCTGATTaa                   <  1:1316399/36‑1 (MQ=255)
                   gCTTTGCAGGCGGTGGATCTCAACACGCTGATTAAc                  <  1:3435176/36‑1 (MQ=255)
                    cTTTGCAGGCGGTGGATCTCAACACGCTGATTAAcc                 <  1:7655249/36‑1 (MQ=255)
                     tttGCAGGCGGTGGATCTCAACACGCTGATTAACCa                <  1:6348650/36‑1 (MQ=255)
                     tttGCAGGCGGTGGATCTCAACACGCTGATTAACCa                <  1:3139322/36‑1 (MQ=255)
                        gCAGGCGGTGGATCTCAACACGCTGATTAACCACTc             <  1:7656327/36‑1 (MQ=255)
                        gCAGGCGGTGGATCTCAACACGCTGATTAACCACTc             <  1:2164403/36‑1 (MQ=255)
                        gCAGGCGGTGGATCTCAACACGCTGATTAACCACTc             <  1:1623590/36‑1 (MQ=255)
                           ggCGGTGGATCTCAACACGCTGATTAACCACTCAtt          <  1:2141138/36‑1 (MQ=255)
                            gCGGTGGATCTCAACACGCTGATTAACCACTCATTa         <  1:2112411/36‑1 (MQ=255)
                            gCGGTGGATCTCAACACGCTGATTAACCACTCATTa         <  1:6092904/36‑1 (MQ=255)
                            gCGGTGGATCTCAACACGCTGATTAACCACTCATTa         <  1:2313304/36‑1 (MQ=255)
                             cGGTGGATCTCAACACGCTGATTAACCACTCATTAc        >  1:643346/1‑36 (MQ=255)
                              ggTGGATCTCAACACGCTGATTAACCACTCATTACa       <  1:5365340/36‑1 (MQ=255)
                              ggTGGATCACAACACGCTGATTAACCACTCATTACa       <  1:6585787/36‑1 (MQ=255)
                               gTGGATCTCAACACGCTGATTAACCACTCATTACAg      <  1:5962565/36‑1 (MQ=255)
                               gTGGATCTCAACACGCTGATTAACCACTCATTACAg      <  1:7453133/36‑1 (MQ=255)
                               gTGGATCTCAACACGCTGATTAACCACTCATTACAg      <  1:1893204/36‑1 (MQ=255)
                               gTGGATCTCAACACGCTGATTAACCACTCATTACAg      >  1:4772334/1‑36 (MQ=255)
                                tGGATCTCAACACGCTGATTAACCACTCATTACAGc     >  1:6992650/1‑36 (MQ=255)
                                tGGATCTCAACACGCTGATTAACCACTCATTACAGc     <  1:7424833/36‑1 (MQ=255)
                                 ggATCTCAACACGCTGATTAACCACTCATTACAGCt    <  1:3105497/36‑1 (MQ=255)
                                 ggATCTCAACACGCTGATTAACCACTCATTACAGCt    <  1:6539341/36‑1 (MQ=255)
                                 ggATCTCAACACGCTGATTAACCACTCATTACAGCt    >  1:4936145/1‑36 (MQ=255)
                                 ggATCTCAACACGCTGATTAACCACTCATTACAGCt    <  1:1905850/36‑1 (MQ=255)
                                  gATCTCAACACGCTGATTAACCACTCATTACAGCTg   <  1:7321374/36‑1 (MQ=255)
                                  gATCTCAACACGCTGATTAACCACTCATTACAGCTg   <  1:7461222/36‑1 (MQ=255)
                                  gATCTCAACACGCTGATTAACCACTCATTACAGCTg   >  1:762467/1‑36 (MQ=255)
                                   aTCTCAACACGCTGATTAACCACTCATTACAGCTgg  >  1:7636960/1‑36 (MQ=255)
                                   aTCTCAACACGCTGATTAACCACTCATTACAGCTgg  >  1:4003992/1‑36 (MQ=255)
                                   |                                   
GGTTAGGCCAACGCATCTGGCTTTGCAGGCGGTGGATCTCAACACGCTGATTAACCACTCATTACAGCTGG  >  REL606/4182422‑4182492

Base quality scores:  ATCG  < 3 ≤  ATCG  < 10 ≤  ATCG  < 22 ≤  ATCG  < 30 ≤  ATCG  < 37 ≤  ATCG