Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6064,311,0271.→A 6.4% 4.4 ‑3.4 0.047coding (960/1092 nt)basSsensory histidine kinase in two‑component regulatory system with BasR
Rejected: Polymorphism prediction not supported by minimum number of reads on both strands.
Reads supporting (aligned to +/- strand):  new base (0/3):  ref base (31/13):  total (31/16)
Fisher's exact test strand distribution p-value = 3.45e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 1.00e+00

TGCAACTGTGTAATGCGGCTGACAATACTTAACCCC.AGACCAATCCCGCCATAACGGCTGTCCATACGTA  >  REL606/4310992‑4311061
                                    |                                  
tGCAACTGTGTAATGCGGCTGACAATACTTAAcccc                                     >  1:1309710/1‑36 (MQ=255)
tGCAACTGTGTAATGCGGCTGACAATACTTAAcccc                                     <  1:2722498/36‑1 (MQ=255)
 gCAACTGTGTAATGCGGCTGACAATACTTAACCCC.a                                   <  1:2169063/36‑1 (MQ=255)
 gCAACTGTGTAATGCGGCTGACAATACTTAACCCC.a                                   <  1:1960503/36‑1 (MQ=255)
  cAACTGTGTAATGCGGCTGACAATACTTAACCCC.Ag                                  >  1:4900327/1‑36 (MQ=255)
  cAACTGTGTAATGCGGCTGACAATACTTAACCCC.Ag                                  >  1:3762647/1‑36 (MQ=255)
   aaCTGTGTAATGCGGCTGACAATACTTAACCCC.AGa                                 <  1:2467804/36‑1 (MQ=255)
    aCTGTGTAATGCGGCTGACAATACTTAACCCC.AGAc                                >  1:5893658/1‑36 (MQ=255)
    aCTGTGTAATGCGGCTGACAATACTTAACCCC.AGAc                                >  1:1853719/1‑36 (MQ=255)
     cTGTGTAATGCGGCTGACAATACTTAACCCC.AGAcc                               >  1:2402705/1‑36 (MQ=255)
     cTGTGTAATGCGGCTGACAATACTTAACCCC.AGAcc                               <  1:2655021/36‑1 (MQ=255)
     cTGTGTAATGCGGCTGACAATACTTAACCCC.AGAcc                               <  1:1557544/36‑1 (MQ=255)
      tgtgTAATGCGGCTGACAATACTTAACCCC.AGACCa                              >  1:1446013/1‑36 (MQ=255)
      tgtgTAATGCGGCTGACAATACTTAACCCC.AGACCa                              <  1:4225669/36‑1 (MQ=255)
      tgtgTAATGCGGCTGACAATACTTAACCCC.AGACCa                              >  1:4898326/1‑36 (MQ=255)
      tgtgTAATGCGGCTGACAATACTTAACCCC.AGACCa                              >  1:7110245/1‑36 (MQ=255)
      tgtgTAATGCGGCTGACAATACTTAACCCC.AGACCa                              >  1:872734/1‑36 (MQ=255)
       gtgtAATGCGGCTGACAATACTTAACCCC.AGACCaa                             >  1:3142979/1‑36 (MQ=255)
       gtgtAATGCGGCTGACAATACTTAACCCC.AGACCaa                             >  1:2299682/1‑36 (MQ=255)
        tgtAATGCGGCTGACAATACTTAACCCC.AGACCAAt                            >  1:4499515/1‑36 (MQ=255)
        tgtAATGAGGCTGACAATACTTAACCCC.AGACCAAt                            <  1:74802/36‑1 (MQ=255)
          tAATGCGGCTGACAATACTTAACCCC.AGACCAATcc                          <  1:1358736/36‑1 (MQ=255)
          tAATGCGGCTGACAATACTTAACCCC.AGACCAATcc                          >  1:2882448/1‑36 (MQ=255)
           aaTGCGGCTGACACTACTTAACCCC.AGACCAATccc                         >  1:3192389/1‑36 (MQ=255)
           aaTGCGGCTGACAATACTTAACCCC.AGACCAATccc                         <  1:22644/36‑1 (MQ=255)
             tGCGGCTGACAATACTTAACCCC.AGACCAATCCCGc                       <  1:2302295/36‑1 (MQ=255)
              gCGGCTGACAATACTTAACCCC.AGACCAATCCCGcc                      <  1:311274/36‑1 (MQ=255)
              gCGGCTGACAATACTTAACCCC.AGACCAATCCCGcc                      <  1:6235978/36‑1 (MQ=255)
               cGGCTGACAATACTTAACCCC.AGACCAATCCCGCCa                     <  1:1314730/36‑1 (MQ=255)
               cGGCTGACAATACTTAACCCC.AGACCAATCCCGCCa                     >  1:4104166/1‑36 (MQ=255)
                ggCTGACAATACTTAACCCC.AGACCAATCCCGCCAt                    >  1:1133246/1‑36 (MQ=255)
                 gCTGACAATACTTAACCCC.AGACCAATCCCGCCATa                   >  1:4462062/1‑36 (MQ=255)
                   tGACAATACTTAACCCC.AGACCAATCCCGCCATAAc                 >  1:1310850/1‑36 (MQ=255)
                   tGACAATACTTAACCCC.AGACCAATCCCGCCATAAc                 >  1:1388073/1‑36 (MQ=255)
                     aCAATACTTAACCCC.AGACCAATCCCGCCATAACgg               >  1:6051614/1‑36 (MQ=255)
                     aCAATACTTAACCCC.AGACCAATCCCGCCATAACgg               >  1:2916437/1‑36 (MQ=255)
                      cAATACTTAACCCC.AGACCAATCCCGCCATAACGGc              >  1:6646304/1‑36 (MQ=255)
                       aaTACTTAACCCC.AGACCAATCCCGCCATAACGGCt             >  1:4530888/1‑36 (MQ=255)
                         tACTTAACCCC.AGACCAATCCCGCCATAACGGCTGt           >  1:382495/1‑36 (MQ=255)
                          aCTTAACCCC.AGACCAATCACGCCATAACGGCTGTc          >  1:2134037/1‑36 (MQ=255)
                           cTTAACCCC.AGACCAATCCCGCCATAACGGCTGTcc         >  1:467041/1‑36 (MQ=255)
                           cTTAACCCC.AGACCAATCCCGCCATAACGGCTGTcc         >  1:5068454/1‑36 (MQ=255)
                           actAACCCCAAAACAAATCCCGCCATAACGGCTGTc          <  1:655051/34‑1 (MQ=16)
                            ttAACCCC.AGACCAATCCCGCCATAACGGCTGTCCa        >  1:4651056/1‑36 (MQ=255)
                             tAACCCCAAAACAAACCCCGCCATAACGGCTGTCCa        <  1:1452943/36‑1 (MQ=12)
                             tAACCCCAAAACAAACCCCGCCATAACGGCTGTCCa        <  1:3377401/36‑1 (MQ=12)
                             tAACCCC.AGCCCAAGCCCGCCCTAACGGCTGCCCAt       >  1:2030704/1‑36 (MQ=19)
                             tAACCCC.AGACCAATCCCGCCATAACGGCTGTccct       >  1:6803842/1‑34 (MQ=255)
                             aaaCCCA.ACACAAACCCCGCCATAACGGCTGTCCAt       <  1:5016984/35‑1 (MQ=16)
                              aaCCCC.AGACCAATCCCGCAATGACGGCTGTGCaga      >  1:1469408/1‑34 (MQ=21)
                              aaCCCA.AAACAATTCCCGCCATAACGGCTTTCCATa      <  1:4266501/36‑1 (MQ=16)
                                cccc.AGACCAATCCCGCCATAACGGCTGTCCATACg    >  1:6979950/1‑36 (MQ=255)
                                 ccc.AGACCAATCCCGCCATAACGGCTGTCCATACGt   >  1:2831327/1‑36 (MQ=255)
                                  cc.AGACCAATCCCGCCATAACGGCTGTCCATAccca  >  1:5962587/1‑33 (MQ=255)
                                  cc.AGACCAATCCCGCCATAACGGCTGTCCATACGTa  >  1:124119/1‑36 (MQ=255)
                                    |                                  
TGCAACTGTGTAATGCGGCTGACAATACTTAACCCC.AGACCAATCCCGCCATAACGGCTGTCCATACGTA  >  REL606/4310992‑4311061

Base quality scores:  ATCG  < 3 ≤  ATCG  < 9 ≤  ATCG  < 21 ≤  ATCG  < 30 ≤  ATCG  < 37 ≤  ATCG