Predicted mutation
evidence seq id position mutation freq annotation gene description
RA REL606 1,168,138 A→G 25.8% R90R (CGA→CGG)  ‡ pabC → 4‑amino‑4‑deoxychorismate lyase

Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6061,168,1380A→G25.8% 3.8 ‑2.5 0.027270pabC4‑amino‑4‑deoxychorismate lyase
Reads supporting (aligned to +/- strand):  new base (6/1):  ref base (8/11):  total (15/12)
Fisher's exact test strand distribution p-value = 8.09e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 1.00e+00

AAGTCGTGATCAGTCGCGGTAGTGGCGGGCGAGGGTACAGCACATTGAACAGCGGACCAGCAACGCG  >  REL606/1168107‑1168173
                               |                                   
aaGTCGTGATCAGTCGCGGTAGTGGCGGGGGGgggg                                 >  1:1954491/1‑35 (MQ=37)
aaGTCGTGATCAGTCGCGGTAGTGGCGGGCGGgggg                                 >  1:1789389/1‑35 (MQ=255)
aaGTCGTGATCAGTCGCGGTAGTGGCGGGCGAGGGt                                 <  1:33180/36‑1 (MQ=255)
 aGTCGTGATCAGTCGCGGTAGTGGCGGGGGGggggg                                >  1:3499161/1‑34 (MQ=25)
 aGTCGTGATCAGTCGCGGTAGTGGCGGGGGGggggg                                >  1:189200/1‑34 (MQ=25)
 aGTCGTGATCAGTCGCGGTAGTGGCGGGCGAGGGTa                                <  1:5016397/36‑1 (MQ=255)
        aTCAGTCGCGGTAGTGGCGGGCGAGGGTACAGcaca                         <  1:2215117/36‑1 (MQ=255)
         tCAGTCGCGGTAGTGGCGGGCGAGGGTACAGcactt                        <  1:2727851/36‑3 (MQ=255)
              cgcgGTAGTGGCGGGCTGGTGTACAGCACATTGAAc                   <  1:667143/36‑1 (MQ=25)
              cgcgGTAGTGGCGGGCGAGGGTACAGCACATTGAAc                   <  1:5130302/36‑1 (MQ=255)
              cgcgGTAGTGGCGGGCGAGGGTACAGCACATTGAAc                   <  1:1737914/36‑1 (MQ=255)
               gcgGTAGTGGCGGGGGGGGGGGGAGCACAATGaaaa                  >  1:3816148/1‑34 (MQ=9)
                cgGTAGTGGCGGGCGGGGGGACAGGACAATGAAAAg                 >  1:261073/1‑36 (MQ=16)
                    aGTGGCGGGCGAGGGTACAGCACATTGAACAGCGGa             <  1:477321/36‑1 (MQ=255)
                     gTGGCGGGCGTGGGTACAGCCCATTGAACAGCGGAc            >  1:1161171/1‑36 (MQ=37)
                      tGGCGGGCGAGGGTACAGCACATTGATCAGCGGAcc           <  1:3865600/36‑1 (MQ=255)
                      tGGCGGGCGAGGGTACAGCACATTGAACAGCGGAcc           >  1:5363078/1‑36 (MQ=255)
                      tGGCGGGCGAGGGTACAGCACATGGAACAGCGGAcc           >  1:4334752/1‑36 (MQ=255)
                        gcgggcgAGGGTACAGCACATTGAACAGCGGACCAg         <  1:4865052/36‑1 (MQ=255)
                        gcgggcgAGGGTACAGCACATTGAACAGCGGAACAg         >  1:2175603/1‑36 (MQ=255)
                          gggcgAGGGTACAGCACATTGAACAGCGGCCCAGcc       <  1:3714672/36‑2 (MQ=255)
                          gggcgAGGGTACAACACATTGAACAGCGGACCAGCa       >  1:3108442/1‑36 (MQ=255)
                            gcgAGGGTACAGCACATTGAACAGCGGACCAGCAAc     >  1:549268/1‑36 (MQ=255)
                            gcgAGGGTACAGCACATTGAACAGCGGACCAGCAAc     >  1:5791935/1‑36 (MQ=255)
                             cgAGGGTACAGCACATTGAACAGCGGACCAGCAAcg    >  1:5844205/1‑36 (MQ=255)
                              gAGGGTACAGCACATTGAACAGCGGACCAGCAAcgc   >  1:1397868/1‑36 (MQ=255)
                              gAGGGTACAGCACATTGAACAGCGGACCAGCAAcgc   <  1:5929570/36‑1 (MQ=255)
                               aGGGTACAGCACATTGAACAGCGGACCAGCAAcgcg  >  1:4676462/1‑36 (MQ=255)
                               aGGGTACAGCACATTGAACAGCGGACCAGCAAcgcg  >  1:3314733/1‑36 (MQ=255)
                               aGGGTACAGCACATTGAACAGCGGACCAGCAAcgcg  >  1:3253904/1‑36 (MQ=255)
                               aGGGTACAGCACATTGAACAGCGGACCAGCAAcgcg  <  1:5248322/36‑1 (MQ=255)
                               aGGGTACAGCACATTGAACAGCGGACCAGCAAcgcg  <  1:1852567/36‑1 (MQ=255)
                               aGGGTACAGAACATTGAATAGCGGACCAGCAAcggg  >  1:1657213/1‑34 (MQ=37)
                               |                                   
AAGTCGTGATCAGTCGCGGTAGTGGCGGGCGAGGGTACAGCACATTGAACAGCGGACCAGCAACGCG  >  REL606/1168107‑1168173

Base quality scores:  ATCG  < 3 ≤  ATCG  < 7 ≤  ATCG  < 16 ≤  ATCG  < 27 ≤  ATCG  < 37 ≤  ATCG