Predicted mutation
evidence seq id position mutation freq annotation gene description
RA REL606 1,901,913 A→T 13.8% intergenic (‑367/+28) pphA ← / ← yebY serine/threonine‑specific protein phosphatase 1/hypothetical protein

Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6061,901,9130A→T13.8% 2.2 ‑2.3 0.025intergenic (‑367/+28)pphA/yebYserine/threonine‑specific protein phosphatase 1/hypothetical protein
Reads supporting (aligned to +/- strand):  new base (4/0):  ref base (9/12):  total (13/12)
Fisher's exact test strand distribution p-value = 9.57e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 1.00e+00

GCCCGTTCTGGTGAAAGAACTGAGGCGGTTTTTTTATTGGAAATCAAAAGGCTATTTAGGTAATTAACAGA  >  REL606/1901878‑1901948
                                   |                                   
gCCCGTACTGGTGAAAGAACTGAGGCGGTTTTTTTa                                     <  1:90221/36‑1 (MQ=255)
   cgatCTGGTGAAAGAACTGTGGCGGTTTTTTTATTg                                  <  1:5892408/33‑1 (MQ=37)
     ttCTGGTGAAAGAACTGAGGCGGTTTTTTTTttttt                                >  1:4248251/1‑33 (MQ=37)
     ttCTGGTGAAAGAACTGAGGCGGTTTTTTTATTGGa                                <  1:3523114/36‑1 (MQ=255)
      tCTGGTGAAAGAACTGAGGCGGTTTTTTTATTGGaa                               <  1:468205/36‑1 (MQ=255)
      tCTGGTGAAAGAACTGAGGCGGTTTTTTTATTGGaa                               <  1:1354649/36‑1 (MQ=255)
        tGGTGAAAGAACTGAGGCGGTTTTTTTTTTTGGAAt                             >  1:681921/1‑36 (MQ=21)
        tGGTGAAAGAACTGAGGCGGTTTTTTTATTGGAAAt                             <  1:3110149/36‑1 (MQ=255)
         ggTGAAAGAACTGAGGCGGTTTTTTTATTGGAAATc                            <  1:4458330/36‑1 (MQ=255)
          gTGAAAGAACTGAGGCGGTTTTTTTATTGGAAATCa                           <  1:3640255/36‑1 (MQ=255)
           tGAAAGAACTGAGGCGGTTTTTTTATTGGAAATCaa                          <  1:367026/36‑1 (MQ=255)
             aaaGAACTGAGGCGGTTTTTTTATTGGAAATCaaaa                        <  1:3188939/36‑1 (MQ=255)
                   cTGAGGCGGTTTTTTTATTGGAAATCAAAAGGCTAt                  <  1:4286941/36‑1 (MQ=255)
                     gAGGCGGTTTTTTTTTTTTTAACCAAAAAGCTAttt                >  1:5484844/1‑36 (MQ=2)
                      aGGCGGTTTTTTTTTTTGAAATCAAAAGGGTATTTa               >  1:4297615/1‑36 (MQ=25)
                         cGGTTTTTTTATTGGAAATCAAAAGGCTATTTAGGt            >  1:2937219/1‑36 (MQ=255)
                           gTTTTTTTATTGGAAATCAAAAGGCTATTTAGGTaa          >  1:5154656/1‑36 (MQ=255)
                            tttttttATTGGAAATCAAAAGGCTATTTAGGTAAt         >  1:4716398/1‑36 (MQ=255)
                             ttttttATTGGAAATCAAAAGGCTATTTAGGTAAtt        >  1:4137904/1‑36 (MQ=255)
                             ttttttATTGGAAATCAAAAGGCTATTTAGGTAAtt        <  1:4381857/36‑1 (MQ=255)
                             ttttttATTGGAAATCAAAAGGCTATTTAGGTAAtt        >  1:1581223/1‑36 (MQ=255)
                             ttttttATTGGAAATCAAAAGGCTATTTAGGTAAtt        >  1:2719732/1‑36 (MQ=255)
                              tttttATTGGAAATCAAAAGGCTATTTAGGTAATTa       <  1:3642482/36‑1 (MQ=255)
                               ttttATTGGAAATCAAAAGGCTATTTAGGTAATTaa      >  1:41363/1‑36 (MQ=255)
                               ttttATTGGAAATCAAAAGGCTATTTAGGAAATTaa      >  1:3655652/1‑36 (MQ=255)
                                 ttATTGGAAATCAAAAGGCTATTTAGGTAATTAACa    >  1:1594625/1‑36 (MQ=255)
                                   aTTGGAAATCAAAAGGCTATTTAGGTAATTAACaga  >  1:228232/1‑36 (MQ=255)
                                   |                                   
GCCCGTTCTGGTGAAAGAACTGAGGCGGTTTTTTTATTGGAAATCAAAAGGCTATTTAGGTAATTAACAGA  >  REL606/1901878‑1901948

Base quality scores:  ATCG  < 3 ≤  ATCG  < 10 ≤  ATCG  < 22 ≤  ATCG  < 32 ≤  ATCG  < 37 ≤  ATCG