Predicted mutation
evidence seq id position mutation freq annotation gene description
RA REL606 4,117,709 A→T 9.2% L19* (TTA→TAA)  yijF ← hypothetical protein

Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6064,117,7090A→T 9.2% 2.4 ‑3.0 ‑0.24456yijFhypothetical protein
Reads supporting (aligned to +/- strand):  new base (4/0):  ref base (17/22):  total (21/23)
Fisher's exact test strand distribution p-value = 4.85e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 6.21e-01

TTTGTACCACGGTTGGTGGAACGGCGGGAGATTTTAAGGAGTGGCTGGTAAATGCCGTTAGCAGGCTGAGC  >  REL606/4117674‑4117744
                                   |                                   
tttGTACCCCGGTTGGTGGAACGGCGGGAGATTTTa                                     <  1:5789797/36‑1 (MQ=255)
tttGTACCACGGTTGTTGGAACGGCGGGAGATTTTa                                     <  1:4206573/36‑1 (MQ=255)
   gTACCACGGTTGGTGGAACGGCGGGAGGTTTTAAgg                                  >  1:5849731/1‑36 (MQ=255)
    tACCACGGTTGGTGGAACGGCGGGTGTTTTTAAGGa                                 >  1:5528345/1‑36 (MQ=37)
    tACCACGGTTGGTGGAACGGCGGGGGGTTTTTAggg                                 >  1:4390338/1‑35 (MQ=25)
     aCCACGGTTGGTGGAACGGCGGGAGATTTTAAGGAg                                <  1:2939541/36‑1 (MQ=255)
        aCGGTTGGTGGAACGGCGGGGGGTTTTTAGGAGGgg                             >  1:3663821/1‑36 (MQ=19)
        aCGGTTGGTGGAACGGCGGGGGATTTTTAGGAGGgg                             >  1:3500635/1‑36 (MQ=37)
         cGGTTGGTGGAACGGCGGGAGATTTTAAGGAGTGGc                            <  1:4377862/36‑1 (MQ=255)
         cGGTTGGTGGAACGGCGGGAGATTTTAAGGAGTGGc                            <  1:4680043/36‑1 (MQ=255)
          ggTTGGTGGAACGGCGGGGGGTTTTAAGGAGTGGCt                           >  1:2306569/1‑36 (MQ=37)
          ggTTGGTGGAACGGCGGGCGGTTTTAAGGGGTgggt                           >  1:3915893/1‑34 (MQ=21)
          ggTTGGTGGAACGGCGGGAGGTTTTTAGGAGTgggt                           >  1:3443491/1‑34 (MQ=25)
          ggTTGGTGGAACGGCGGGAGATTTTAAGGAGTgggt                           >  1:4223425/1‑34 (MQ=255)
          ggTTGGTGGAACGGCGGGAGATTTTAAGGAGTGGCt                           <  1:4932630/36‑1 (MQ=255)
           gTTGGTGGAACGGCGGGGGATTTTAAGGGGTgggcg                          >  1:616989/1‑33 (MQ=25)
           gTTGGTGGAACGGCGGGAGATTTTAAGGAGTGGCTg                          <  1:1302706/36‑1 (MQ=255)
             tggtggAACGGCGGGTGATTTTAAAGAGTGGGTggg                        >  1:4912516/1‑35 (MQ=25)
             tggtggAACGGCGGGAGATTTTAAGGAGTGGCTGGt                        <  1:2889518/36‑1 (MQ=255)
               gtggAAGGGCGGGAGATTTTAAGTAGTGGCTGGTaa                      <  1:2280385/36‑1 (MQ=37)
               gtggAACGGCGGGAGATTTTAAGGAGTGGCTGGTaa                      <  1:2092049/36‑1 (MQ=255)
                tggAACGGCGGGAGATTTTAAGGAGTGGCTGGTaaa                     <  1:4073265/36‑1 (MQ=255)
                tggAACGGCGGGAGATTTTAAGGAGTGGCTGGTaaa                     <  1:4072925/36‑1 (MQ=255)
                   aaCGGCGGGAGATTTTGAGGAGTGGCTGGTAAATGc                  <  1:2767603/36‑1 (MQ=255)
                   aaCGGCGGGAGATTTTAAGGAGTGGCTGGTAAATGc                  <  1:1093339/36‑1 (MQ=255)
                    aCGGCGGGAGATTTTAAGGAGTGGCTGGTAAATGcc                 <  1:2990401/36‑1 (MQ=255)
                       gcggGATATTTTACGGAGTGGCTGGTAAATGCCGtt              <  1:1289355/36‑1 (MQ=37)
                       gcggGAGATTTTAAGGAGTTGCTGGTAAATGCCGtt              <  1:3307502/36‑1 (MQ=255)
                       gcggGAGATTTTAAGGAGTGGCTGGTAAATGCCGtt              <  1:3764797/36‑1 (MQ=255)
                       gcggGAGATTTTAAGGAGTGGCTGGTAAATGCCGtt              <  1:3435110/36‑1 (MQ=255)
                       gcggGAGATTTTAAGGAGTGGCTGGTAAATGCCGtt              <  1:4256814/36‑1 (MQ=255)
                         gggAGATTTTAAGGAGTGGCTGGTAAATGCCGCTAg            >  1:5720743/1‑36 (MQ=255)
                         gggAGATTTTAAGCAGTGGCTGGTAAATTCCGTTAg            >  1:2492477/1‑36 (MQ=37)
                          ggAGATTTTAAGGAGTGGCTGGTAAATGCCGTTAGc           <  1:4280914/36‑1 (MQ=255)
                          ggAGATTTTAAGGAGTGGCTGGGAAATGCCGTTAGc           >  1:1675831/1‑36 (MQ=255)
                           gagaTTTTAAGGAGTGGCTGGGAAAAGCCGTTAGCa          >  1:271871/1‑36 (MQ=37)
                            tgaTTTGAAGGAGTGCCTGGTAAGTGCCGTTAGccg         <  1:5031023/35‑3 (MQ=19)
                            agaTTTTAAGGAGTGGCTGGTAAATGCCGTTAGCAg         <  1:2881228/36‑1 (MQ=255)
                            agaTTTTAAGGAGTGGCTGGTAAATGCCGTTAGCAg         <  1:2811394/36‑1 (MQ=255)
                            agaTTTTAAGGAGTGGCTGGTAAATGCCGTTAGCAg         >  1:4899733/1‑36 (MQ=255)
                            agaTTTTAAGGAGTGGCTGGGAAAAGCCGTTGGCAg         >  1:81075/1‑36 (MQ=21)
                               ttttAAGGATTGGCTGGTAAATGACGTTATCAGGCt      <  1:5419439/36‑1 (MQ=25)
                                tttAAGGAGTGGCTGGTAAATGCCGTTAGCAGGCTg     >  1:5191501/1‑36 (MQ=255)
                                 ttAAGGAGTGGCTGGTAAATGCCGTTAGCAGGCTGa    >  1:5723925/1‑36 (MQ=255)
                                  tAAGGAGTGGCTGGTAAATGCCGTTAGCAGGCTGag   >  1:5682650/1‑36 (MQ=255)
                                  tAAGGAGTGGCTGGGAAATGGCGTTAGCAGGCTGag   >  1:382919/1‑36 (MQ=37)
                                   aaGGAGTGGCTGGTAAATGCCGTTAGGAGGCTGagc  >  1:1825939/1‑36 (MQ=255)
                                   aaGGAGTGGCTGGTAAATGCCGGTAGCAGGGTGagg  >  1:2406854/1‑35 (MQ=37)
                                   aaGGAGTGGCTGGTAAAGACCGTTAGCAGGCTGagc  >  1:5355098/1‑36 (MQ=37)
                                   |                                   
TTTGTACCACGGTTGGTGGAACGGCGGGAGATTTTAAGGAGTGGCTGGTAAATGCCGTTAGCAGGCTGAGC  >  REL606/4117674‑4117744

Base quality scores:  ATCG  < 3 ≤  ATCG  < 7 ≤  ATCG  < 12 ≤  ATCG  < 26 ≤  ATCG  < 37 ≤  ATCG