Predicted mutation
evidence seq id position mutation freq annotation gene description
RA REL606 3,448,149 A→T 12.8% *413K (TAA→AAA)  hofQ ← predicted fimbrial transporter

Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6063,448,1490A→T12.8% 3.4 ‑2.2 0.0501237hofQpredicted fimbrial transporter
Reads supporting (aligned to +/- strand):  new base (6/1):  ref base (21/22):  total (27/23)
Fisher's exact test strand distribution p-value = 1.07e-01
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 1.00e+00

AGCGTAAAAACATTACCGCTTTTACGGCTGTTTACTCACTGGAAACCAGTCGTGGCGTGATAAACACCA  >  REL606/3448116‑3448184
                                 |                                   
aGCGTAAAAACATTACCGCTTTTACGGCTGTTTACt                                   <  1:1919911/36‑1 (MQ=255)
 gCGTAAAAACATTACCGCTTTTACGGCTGTTTACTc                                  <  1:1564847/36‑1 (MQ=255)
   gTAAAAACATTACCGCTTTTACNGCTGTTTACTCAc                                <  1:2584027/36‑1 (MQ=255)
    tAAAAACATTACCGCTTTTACGGCTGTTTACTCACt                               <  1:4779423/36‑1 (MQ=255)
    tAAAAACATTACCGCTTTTACGGCTGTTTACTCACt                               <  1:4233609/36‑1 (MQ=255)
    tAAAAACATTACCGCTTTTACGGCTGTTTACTCACt                               <  1:3962557/36‑1 (MQ=255)
    tAAAAACATTACCGCTTTTACGGCTGTTTACTCACt                               <  1:6447702/36‑1 (MQ=255)
     aaaaaCATTACCGCTTTTACGGCTGTTTACTCACTg                              <  1:5955515/36‑1 (MQ=255)
     aaaaaCATTACCGCTTTTACGGCTGGTTTCTCCCtt                              >  1:3049587/1‑35 (MQ=21)
      aaaaCATTACCGCTTTTACGGCTGTTTACTCCCTgg                             >  1:6539837/1‑36 (MQ=255)
       aaaCATTACCGCTTTTACGGCTGTTTACTCACTGGa                            <  1:2311673/36‑1 (MQ=255)
       aaaCATTACCGCTTTTACGGCTGGTTTCTCTCTggt                            >  1:6209834/1‑35 (MQ=21)
       aaaCATTACCGCTTTTACGGCTGGTTACTCACttta                            >  1:1690156/1‑33 (MQ=37)
        aaCATTACCGCTTTTACGGCTGTTTACTCACTGGaa                           <  1:1657100/36‑1 (MQ=255)
           atgaCCGCGTTTACGGCTGTTTACTCACTGGAAAcc                        <  1:7478585/33‑1 (MQ=37)
           aTTACCGCTTTTACGGCTGTTTTCTTCCTGGGAAca                        >  1:4607048/1‑35 (MQ=16)
           aTTACCGCTTTTACGGCTGGTTTCTTCCTTGAAAcc                        >  1:1758215/1‑36 (MQ=12)
             tACCGCTTTTACGGCTGTTTTTTTACTGGAAAACaa                      >  1:6167094/1‑35 (MQ=16)
             tACCGCTTTTACGGCTGTTTACTCACTTGAAAACAg                      >  1:7428450/1‑36 (MQ=37)
              aCCGCTTTTACGGCTGTTTTCTCACTTGAAACCAGt                     >  1:5490124/1‑36 (MQ=37)
              aCCGCTTTTACGGCTGTTTACTCACTGGAAACCAGt                     <  1:6597273/36‑1 (MQ=255)
               ccGCTTTTACGGCTGTTTACTCACTGGAAACCAGTc                    <  1:1997353/36‑1 (MQ=255)
               ccGCTTTTACGGCTGTTTACTCACTGGAAACCAGTc                    <  1:715395/36‑1 (MQ=255)
               ccGCTTTTACGGCTGTTTACTCACTGGAAACCAGTc                    <  1:5504359/36‑1 (MQ=255)
                cGCTTTTACGGCTGTTTTCTCACTGGAAACCAGTCg                   <  1:530806/36‑1 (MQ=255)
                 gCTTTTACGGCTGTTTATTCACTTGAAAACAATCGt                  >  1:4223294/1‑36 (MQ=16)
                 gCTTTTACGGCTGGTTATTTACTTTAAACCAGTCGt                  >  1:1880382/1‑36 (MQ=16)
                  cTTTTACGGCTGTTTACTCACTGGAAACCAGTCGTg                 >  1:5953721/1‑36 (MQ=255)
                  cTTTTACGGCTGGTTAATTCCTGGAAACCAGTCGTg                 >  1:4098104/1‑36 (MQ=16)
                   ttttACGGCTGTTTACTCCCTGGAAACCAGTCGTgg                >  1:1011725/1‑36 (MQ=255)
                   ttttACGGCTGTTTACTCACTTGAAACCAGTCGTgg                >  1:868329/1‑36 (MQ=255)
                    tttACGGCTGTTTACTCACTGGAAACCAGTCGTGGc               <  1:7169882/36‑1 (MQ=255)
                     ttACGGCTGTTTACTCACTGGAAACCAGTCGTGGCg              <  1:2611449/36‑1 (MQ=255)
                      tACGGCTGTTTACTCACTGGAAACCAGTCGTGGCGt             <  1:705592/36‑1 (MQ=255)
                        cGGCTGTTTACTCACTGGAAACCAGTCGTGGCGTGa           >  1:4489131/1‑36 (MQ=255)
                         ggCTGTTTACTCACTGGAAGCCAGTCGTGGCGTGAt          <  1:4119452/36‑1 (MQ=255)
                         ggCTGTTTACTCACTGGAAACCAGTCGTGGCGTGAt          >  1:2743453/1‑36 (MQ=255)
                         ggCTGTTTACTCACTGGAAACCAGTCGTGGCGTGAt          >  1:2230898/1‑36 (MQ=255)
                          gCTGTTTACTCACTGGAAACCAGTCGTGGCGTGATa         >  1:5032649/1‑36 (MQ=255)
                          gCTGTTTACTCACTGGAAACCAGTCGTGGCGTGATa         >  1:4112168/1‑36 (MQ=255)
                           cTGTTTACTCACTGGAAACCAGTCGTGGCGTGATaa        >  1:1533589/1‑36 (MQ=255)
                            tGTTTACTCACTGGAACCTAGTCGTGGCGTGATaaa       <  1:7433442/36‑1 (MQ=37)
                            tGTTTACTCACTGGAAACCAGTCGTGGCGTGATaaa       >  1:6808264/1‑36 (MQ=255)
                            tGTTTACTCACTGGAAACCAGTCGTGGCGTGATaaa       >  1:611023/1‑36 (MQ=255)
                             gTTTACTCACTGGAAACCAGTCGTGGCGTGATAAac      >  1:5823661/1‑36 (MQ=255)
                              tttACTCACTGGAAACCAGTCGTGGCGTGATAAaca     <  1:119123/36‑1 (MQ=255)
                               ttACTCACTGGAAACCAGTCGTGGCGTGATAAacac    >  1:7342858/1‑36 (MQ=255)
                               ttACTCACTGGAAACCAGTCGTGGCGTGATAAacac    >  1:942804/1‑36 (MQ=255)
                                tACTCACTGGAAACCAGTCGTGGCGTGATAAAcacc   >  1:6663749/1‑36 (MQ=255)
                                tACTCACTGGAAACCAGTCGTGGCGTGATAAAcacc   <  1:3348423/36‑1 (MQ=255)
                                 aCTCACTGGAAACCAGTCGTGGCGTGATAAAcacca  <  1:108730/36‑1 (MQ=255)
                                 aCTCACTGGAAACCAGTCGTGGCGTGATAAAcacca  >  1:4451721/1‑36 (MQ=255)
                                 |                                   
AGCGTAAAAACATTACCGCTTTTACGGCTGTTTACTCACTGGAAACCAGTCGTGGCGTGATAAACACCA  >  REL606/3448116‑3448184

Base quality scores:  ATCG  < 3 ≤  ATCG  < 7 ≤  ATCG  < 16 ≤  ATCG  < 30 ≤  ATCG  < 37 ≤  ATCG