Predicted mutation
evidence seq id position mutation freq annotation gene description
RA REL606 4,311,831 G→T 10.9% R52R (CGC→CGA basS ← sensory histidine kinase in two‑component regulatory system with BasR

Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6064,311,8310G→T10.9% 2.2 ‑4.5 0.077156basSsensory histidine kinase in two‑component regulatory system with BasR
Reads supporting (aligned to +/- strand):  new base (10/0):  ref base (38/28):  total (49/28)
Fisher's exact test strand distribution p-value = 1.09e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 1.00e+00

CGCGGATCTCACGCATGATGTGGCGATCGTTGTTGCGATTGTCGCGTAGCGCCTGCTCAAACAGCTGAAT  >  REL606/4311797‑4311866
                                  |                                   
cgcgGATCTCACGCATGATGTGGCGATCGTTGTTGc                                    <  1:7053433/36‑1 (MQ=255)
cgcgGATCTCACGCATGATGTGGCGATCGTTGTTGc                                    >  1:5544816/1‑36 (MQ=255)
 gcgGATCTCACGCATGATGTGGCGATCGTTGTTGCg                                   >  1:7360403/1‑36 (MQ=255)
 gcgGATCTCACGCATGATGTGGCGATCGTTGTTGCg                                   >  1:7734266/1‑36 (MQ=255)
 gcgGATCTCACGCATGATGTGGCGATCGTTGTTGCg                                   >  1:1299115/1‑36 (MQ=255)
 gcgGATCTCACGCATGATGTGGCGATCGTTGTTGCg                                   >  1:7233784/1‑36 (MQ=255)
  cgGATCTCACGCATGATGTGGCGATTGCTGTTGCGa                                  >  1:5379820/1‑36 (MQ=25)
  cgGATCTCACGCATGATGTGGCGATCGTTGTTGCGa                                  >  1:3061467/1‑36 (MQ=255)
   ggATCTCACGCATGATGTGGCGATCGTTGTTGCGAt                                 <  1:511994/36‑1 (MQ=255)
   ggATCTCACGCATGATGTGGCGATCGTTGTTGCGAt                                 <  1:585300/36‑1 (MQ=255)
    tttctcACGCGGGATGTGGCGATCGTTGTTGCGAtt                                <  1:5411034/34‑1 (MQ=37)
    gttctcACTTATGATGTGGCGGTCGTTGTTGCTAtt                                <  1:2167943/34‑1 (MQ=16)
    gATCTCACGCATGATGTGGCGATCGTTGTTGCGAtt                                <  1:7479161/36‑1 (MQ=255)
    gATCTCACGCATGATGTGGCGATCGTTGTTGCGAtt                                >  1:2715029/1‑36 (MQ=255)
    gATCTCACGCATGATGTGGCGATCGTTGTTGCGAtt                                <  1:6702080/36‑1 (MQ=255)
    gATCTCACGCATGATCTGGCGACCGTCGTTTGGAtt                                >  1:5593773/1‑36 (MQ=12)
     aTCTCACGCATGATGTGGCGATCGTTTTTTCGGttt                               >  1:2062796/1‑35 (MQ=25)
      tctcACGCATGATGTGGCGATCTTTGTTTCGTtttt                              >  1:4617558/1‑34 (MQ=25)
      tctcACGCATGATGTGGCGATCTTTGTTTCGATTGt                              >  1:3314676/1‑36 (MQ=38)
      tctcACGCATGATGTGGCGATCGTTGTTGCGATTGt                              >  1:1174085/1‑36 (MQ=255)
      tctcACGCATGATGTGGCGATCGTTGTTGCGATTGt                              >  1:3293626/1‑36 (MQ=255)
      tctcACGCATGATGTGGCGATCGTTGTTGCGATTGt                              >  1:4032086/1‑36 (MQ=255)
       ctcACGCATGATGTGGCGATCGTTGTTGCGATTGTc                             <  1:1931455/36‑1 (MQ=255)
       ctcACGCATGATGTGGCGATCGTTGTTGCGATTGTc                             <  1:1612378/36‑1 (MQ=255)
        tcACGCATGATGTGGCGATCGTTTTTTCGATTGttg                            >  1:3758001/1‑34 (MQ=37)
         cACGCATGATGTGGCGATCGTTGTTGGGATTGTcgc                           >  1:787135/1‑36 (MQ=255)
         cACGCATGATGTGGCGATCGTTGTTGCGATTGTcgc                           <  1:1469972/36‑1 (MQ=255)
          aCGCATGATGTGGCGATCGTTGTTGCGATTGTcgcg                          <  1:4557890/36‑1 (MQ=255)
          aCGCATGATGTGGCGATCGTTGTTGCGATTGTcgcg                          <  1:4556522/36‑1 (MQ=255)
           cGCATGATGTGGCGATCGTTGTTGCGATTGTCGCGt                         <  1:1826748/36‑1 (MQ=255)
           cGCATGATGTGGCGATCGTTGTTGCGATTGTCGCGt                         <  1:4088273/36‑1 (MQ=255)
            gCATGATGTGGCGATCGTTTTTTCGATTTTTGCGTa                        >  1:5838892/1‑36 (MQ=19)
            gCATGATGTGGCGATCGTTTTTACGATTGTCGCGtg                        >  1:7190552/1‑35 (MQ=37)
            gCATGATGTGGCGATCGTTGTTGCGATTGTCGCTTa                        >  1:5105113/1‑36 (MQ=255)
            gCATGATGTGGCGATCGTTGTTGCGATTGTCGCGTa                        >  1:314228/1‑36 (MQ=255)
             cATGATGTGGCGATCGTTGTTTCTATTGTTGCGGAg                       >  1:7704998/1‑36 (MQ=16)
             cATGATGTGGCGATCGTTGTTGCGATTGTCGGGTAg                       >  1:5965290/1‑36 (MQ=255)
             cATGATGTGGCGATCGTTGTTGCGATTGTCGCGTAg                       >  1:1575022/1‑36 (MQ=255)
             cATGATGTGGCGATCGTTGTTGCGATTGTCGCGTAg                       >  1:6276972/1‑36 (MQ=255)
             cATGATGTGGCGATCGTTGTTGCGATTGTCGCGTAg                       <  1:7241369/36‑1 (MQ=255)
             cATGATGTGGCGATCGTTGTTGCGATTGTCGCGTAg                       <  1:2433922/36‑1 (MQ=255)
              atgatgTGGCGATCGTTGTTTTGCTTTTCGCGTGgc                      >  1:4856306/1‑36 (MQ=12)
              atgatgTGGCGATCGTTGTTTCGATTTTCGCGTAgc                      >  1:7025729/1‑36 (MQ=37)
              atgatgTGGCGATCGTTGTTGCGATTGTCGCGTAgc                      <  1:4440794/36‑1 (MQ=255)
               tgatgTGGCGATCGTTGTTGCGATTGTCGCGTAgcg                     >  1:5132687/1‑36 (MQ=255)
               tgatgTGGCGATCGTTGTTGCGATTGTCGCGTAgcg                     <  1:351125/36‑1 (MQ=255)
                gatgTGGCGATCGTTGTTGTGATTTTCGCGTAgcgc                    >  1:3684672/1‑36 (MQ=38)
                gatgTGGCGATCGTTGTTGCGATTGTCGGGTAtcgc                    >  1:5261371/1‑36 (MQ=37)
                gatgTGGCGATCGTTGTTGCGATTGTCGCGTAgcgc                    <  1:6567327/36‑1 (MQ=255)
                gatgTGGCGATCGTTGTTGCGATTGTCGCGTAgcgc                    >  1:3782297/1‑36 (MQ=255)
                 atgTGGCGATCGTTGTTGCGATTGTCGCGTAGCGcc                   >  1:4834041/1‑36 (MQ=255)
                 atgTGGCGATCGTTGTTGCGATTGTCGCGTAGCGcc                   <  1:4257060/36‑1 (MQ=255)
                 atgTGGCGATCGTTGTTGCGATTGTCGCGTAGCGcc                   >  1:1515757/1‑36 (MQ=255)
                 atgTGGCGATCGTTGTTGCGATTGTCGCGTAGCGcc                   >  1:1427340/1‑36 (MQ=255)
                  tgtgGCGATCGTTTTTTCGATTTTTGGGTAGCGCCt                  >  1:2820831/1‑36 (MQ=16)
                   gtgGCGATCGTTGTTGCGATTGTCGCGTAGCGCCTg                 <  1:1264135/36‑1 (MQ=255)
                    tgGCGATCGTTGTTGCGATTGTCGCGTAGCGCCTGc                >  1:5610865/1‑36 (MQ=255)
                     ggCGATCGTTGTTGCGATTGTCGCGTAGCGCCTGCt               <  1:7636175/36‑1 (MQ=255)
                      gCGATCGTTGTTGCGATTGTCGCGTAGCGCCTGCTc              >  1:7361635/1‑36 (MQ=255)
                      gCGATCGTTGTTGCGATTGTCGCGTAGCGCCTGCTc              <  1:909669/36‑1 (MQ=255)
                      gCGATCGTTGTTGCGATTGTCGCGTAGCGCCTGCTc              <  1:1374970/36‑1 (MQ=255)
                       cGATCGTTGTTGCGATTGTCGCGTAGCGCCTGCTCa             >  1:879024/1‑36 (MQ=255)
                       cGATCGTTGTTGCGATTGTCGCGTAGCGCCTGCTCa             >  1:4388153/1‑36 (MQ=255)
                       cGATCGTTGTTGCGATTGTCGCGTAGCGCCTGCTCa             >  1:2830611/1‑36 (MQ=255)
                        gATCGTTGTTGCGCTTGTCGCGTAGCGCCTGCTCaa            <  1:2684185/36‑1 (MQ=255)
                        gATCGTTGTTGCGATTGTCGCGTAGCGCCTGCTcta            >  1:1772334/1‑34 (MQ=255)
                        gATCGTTGTTGCGATTGTCGCGTAGCGCCTGCTCaa            >  1:5833127/1‑36 (MQ=255)
                        gATCGTTGTTGCGATTGTCGCGTAGCGCCTGCTCaa            <  1:5043993/36‑1 (MQ=255)
                         aTCGTTGTTGCGATTGTCGCGTAGCGCCTGCTCaaa           <  1:6343886/36‑1 (MQ=255)
                          tCGTTGTTGCGATTGTCGCGTAGCGCCTGCTCAAAc          <  1:5753582/36‑1 (MQ=255)
                          tCGTTGTTGCGATTGTCGCGTAGCGCCTGCTCAAAc          >  1:136544/1‑36 (MQ=255)
                           cGTTGTTGCGATTGTCGCGTAGCGCCTGCTCAAACa         >  1:1016097/1‑36 (MQ=255)
                           cGTTGTTGCGATTGTCGCGTAGCGCCTGCTCAAACa         >  1:4798774/1‑36 (MQ=255)
                            gttgttGCGATTGTCGCGTAGCGCCTGCTCAAACAg        >  1:1004625/1‑36 (MQ=255)
                            gttgttGCGATTGTCGCGTAGCGCCTGCTCAAACAg        >  1:4231645/1‑36 (MQ=255)
                            gttgttGCGATTGTCGCGTAGCGCCTGCTCAAACAg        >  1:6238921/1‑36 (MQ=255)
                            gttgttGCGATTGTCGCGTAGCGCCTGCTCAAACAg        >  1:5744494/1‑36 (MQ=255)
                             ttgttgCGATTGTCGCGTAGCGCCTGCTCAAACAGc       <  1:6570407/36‑1 (MQ=255)
                              tgttgCGATTGTCGCTTAGCGCCTGCTCAAACAGCt      <  1:6729269/36‑1 (MQ=255)
                               gttgCGATTGTCGCGTAGCGCCTGCTCACACAGCTg     >  1:1295653/1‑36 (MQ=255)
                               gttgCGATTGTCGCGTAGCGCCTGCTCAAACAGCTg     <  1:6128469/36‑1 (MQ=255)
                                ttgCGATTGTCGCGTAGCGCCTGCTCAAACAGCTGa    >  1:403849/1‑36 (MQ=255)
                                ttgCGATTGTCGCGTAGCGCCTGCTCAAACAGCTGa    >  1:2577704/1‑36 (MQ=255)
                                ttgCGATTGTCGCGTAGCGCCTGCTCAAACAGCTGa    <  1:1816545/36‑1 (MQ=255)
                                ttgCGATTGTCGCGTAGCGCCTGCTCAAACAGCTGa    >  1:4365190/1‑36 (MQ=255)
                                 tgCGATTGTCGCGTAGCGCCTGCTCAAACAGCTGaa   <  1:2961086/36‑1 (MQ=255)
                                  gCGATTGTCGCGTAGCGCCTGCTCAAACAGCTGAAt  <  1:4843850/36‑1 (MQ=255)
                                  |                                   
CGCGGATCTCACGCATGATGTGGCGATCGTTGTTGCGATTGTCGCGTAGCGCCTGCTCAAACAGCTGAAT  >  REL606/4311797‑4311866

Base quality scores:  ATCG  < 3 ≤  ATCG  < 7 ≤  ATCG  < 16 ≤  ATCG  < 29 ≤  ATCG  < 37 ≤  ATCG