Predicted mutation
evidence seq id position mutation freq annotation gene description
RA REL606 1,454,373 T→A 27.0% F642Y (TTC→TAC)  hrpA → ATP‑dependent helicase

Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6061,454,3730T→A27.0% 7.6 ‑4.4 0.0221925hrpAATP‑dependent helicase
Reads supporting (aligned to +/- strand):  new base (0/6):  ref base (11/5):  total (11/11)
Fisher's exact test strand distribution p-value = 1.24e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 1.00e+00

CGCGCGTTTCTCCATCTTCCCCGGTTCTGG.TTTATTCAAAAAACCGCCGAAATGGGTAATGGTGGCGGAAC  >  REL606/1454338‑1454408
                                    |                                   
cgcgcgTTTCTCCATCTTCCCCGGTTCTGG.TTTAtt                                     <  1:2546404/36‑1 (MQ=255)
 gcgcgTTTCTCCATCTTCCCCGGTTCTGG.TTTATTc                                    >  1:1196303/1‑36 (MQ=255)
 gcgcgTTTCTCCATCTTCCCCGGTTCTGG.TTTATTc                                    <  1:2830299/36‑1 (MQ=255)
   gcgTTTCTCCATCTTCCCCGGTTCTGG.TTTATTCaa                                  <  1:3221787/36‑1 (MQ=255)
   gcgTTTCTCCATCTTCCCCGGTTCTGG.TTTATTCaa                                  >  1:7921987/1‑36 (MQ=255)
    cgTTTCTCCATCTTCCCCGGTTCTGG.TTTATTCaaa                                 <  1:2746040/36‑1 (MQ=255)
    cgTTTCTCCATCTTCCCCGGTTCTGG.TTTATTCaaa                                 <  1:7709099/36‑1 (MQ=255)
     gTTTCTCCATCTTCCCCGGTTCTGG.TTTATTCaaaa                                >  1:7179155/1‑36 (MQ=255)
     gTTTCTCCATCTTCCCCGGTTCTGG.TTTATTCaaaa                                >  1:5283739/1‑36 (MQ=255)
         ctcCATCTTCCCCGGTTCTGG.TTTATTCAAAAAAcc                            <  1:3790592/36‑1 (MQ=255)
         ctcCATCTTCCCCGGTTCTGG.TTTATTCAAAAAAcc                            >  1:7879355/1‑36 (MQ=255)
             aTCTTCCCCGGTTCTGG.TTTATTCAAAAAAccgccg                        >  1:7339367/1‑36 (MQ=255)
                ttCCCCGGTTCTGG.TTTATTCAAAAAACCGCCGaaa                     >  1:4078842/1‑36 (MQ=255)
                ctCCCCGGTTTTGGTTTTATAAAAAAAACCGCCGaa                      <  1:3420790/35‑1 (MQ=9)
                   cccGGTTCTGG.TTTATTCAAAAAACCGCCGAAATgg                  >  1:3604627/1‑36 (MQ=255)
                    ccGATTCTGT.TTAATAAAAAAAACCGCCGAAATggg                 <  1:3594640/36‑1 (MQ=12)
                     gggTTTTGT.TTTATAAAAAAACCCGCCGAAATGGGt                <  1:5276852/35‑1 (MQ=2)
                      gtttCTGT.TTTATAAAAAAAACCGCCGAAATGGGTa               <  1:544380/34‑1 (MQ=18)
                      ggTTTTGG.TTAATAAAAAAAACCGCCGAAATGGGTa               <  1:5305018/36‑1 (MQ=16)
                        ttCTGG.TTTATTCAAAAAACCGCCGAAATGGGTAAt             >  1:5228410/1‑36 (MQ=255)
                             g.TTTATTCAAAAAACCGCCGAAATGGGTAAtggtgg        >  1:6058975/1‑36 (MQ=255)
                              ttttATAAAAAAAACCGCCGAAATGGGTAAtggtgg        <  1:4189920/35‑1 (MQ=25)
                               tttATTCAAAAAACCGCCGAAATGGGTAATGGTGGc       >  1:719379/1‑36 (MQ=255)
                                    tCAAAAAACCGCCGAAATGGGTAATGGTGGCGGAAc  >  1:4090516/1‑36 (MQ=255)
                                    tCAAAAAACCGCCGAAATGGGTAATGGTGGCGGAAc  >  1:8210226/1‑36 (MQ=255)
                                    |                                   
CGCGCGTTTCTCCATCTTCCCCGGTTCTGG.TTTATTCAAAAAACCGCCGAAATGGGTAATGGTGGCGGAAC  >  REL606/1454338‑1454408

Base quality scores:  ATCG  < 3 ≤  ATCG  < 6 ≤  ATCG  < 21 ≤  ATCG  < 32 ≤  ATCG  < 37 ≤  ATCG