Predicted mutation
evidence seq id position mutation freq annotation gene description
RA REL606 3,909,619 +G 6.9% coding (149/840 nt) hdfR ← transcriptional regulator HdfR

Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6063,909,6191.→G 6.9% 2.8 ‑1.6 ‑0.029coding (149/840 nt)hdfRtranscriptional regulator HdfR
Reads supporting (aligned to +/- strand):  new base (2/0):  ref base (11/16):  total (13/16)
Fisher's exact test strand distribution p-value = 1.92e-01
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 9.99e-01

CACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC.GG.GTGAAAAGGTTCACACCCAGTTGATTTTCCAG  >  REL606/3909584‑3909653
                                    |                                   
cACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGc                                      <  1:983098/36‑1 (MQ=255)
cACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGc                                      <  1:1322784/36‑1 (MQ=255)
cACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGc                                      <  1:1749228/36‑1 (MQ=255)
 aCCGGCAGCGGTTAAACGGATATTGTTTTTGTGGC.g                                    >  1:4992099/1‑36 (MQ=255)
 aCCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC.g                                    >  1:5705192/1‑36 (MQ=255)
   cGGCAGCGGTTAAACGGATATTGTTTCTGTGGC.gg.g                                 <  1:2348839/36‑1 (MQ=255)
       aGCGGTTAAACGGATATTGTTTCTGTGGC.GG.GTGaa                             <  1:4360451/36‑1 (MQ=255)
        gCGGTTAAACGGATATTGTTTCTGTGGC.GG.GTGaaa                            <  1:756228/36‑1 (MQ=255)
           gTTAAACGGATATTGTTTCTGTGGC.GG.GTGGAAAgg                         >  1:1047979/1‑36 (MQ=255)
           gTTAAACGGATATTGTTTCTGTGGC.GG.GTGAAAAgg                         <  1:1790727/36‑1 (MQ=255)
            ttAAACGGCTATTGTTTCTGTGGC.GG.GTGAAAAGGt                        <  1:4237900/36‑1 (MQ=255)
            ttAAACGGATATTGTTTCTGTGGC.GG.GGGGAAAAGt                        >  1:3335453/1‑36 (MQ=25)
            ttAAACGGATATTGTTTCTGTGGC.GG.GGGGAAAAGt                        >  1:2663704/1‑36 (MQ=25)
             tAAACGGATATTGTTTCTGTGGCGGG.GGGAAAAGGt                        >  1:3387531/1‑36 (MQ=25)
             tAAACGGATATTGTTTCTGTGGC.GGCGGGAAAAgtt                        >  1:4728953/1‑34 (MQ=21)
             tAAACGGATATTGTTTCTGTGGC.GG.GGGGAAAAGtt                       >  1:4663695/1‑36 (MQ=25)
                 cGGATATTGTTTCTGTGGC.GG.GTGAAAAGGTTcaca                   <  1:1720539/36‑1 (MQ=255)
                 cGGATATTGTTTCTGTGGC.GG.GGGGAAAAGTTtaca                   >  1:4852760/1‑36 (MQ=19)
                  ggATATTGTTTCTGTGGCGGG.GTGAAAAGGTTccac                   >  1:3349363/1‑33 (MQ=25)
                  ggATATTGTTTCTGTGGC.GG.GTGAAAAGGTTCacac                  <  1:5263008/36‑1 (MQ=255)
                   gATATTGTTTCTGTGGC.GG.GTGAAAAGGTTCACAcc                 <  1:2767218/36‑1 (MQ=255)
                      atTGTTTCTGTGGC.GG.GTGAAAAGGTTCACACCCAg              <  1:1000607/36‑1 (MQ=255)
                      atTGTTTCTGTGGC.GG.GTGAAAAAGGTTACAccccg              >  1:5381391/1‑34 (MQ=18)
                       ttGTTTCTGTGGC.GG.GTGAAAAGGTTCACACCCAGt             <  1:4054931/36‑1 (MQ=255)
                       ttGTTTCTGTGGC.GG.GTGAAAAGGTTCACACCCAGt             <  1:5005392/36‑1 (MQ=255)
                        tGTTTCTGTGGC.GG.GGGGAAAAGTTCTCACCCCGtt            >  1:2724418/1‑36 (MQ=16)
                         gTTTCTGTGGC.GG.GTGGAAAGGGTCACACCCCGttt           >  1:1498180/1‑35 (MQ=25)
                           ttCTGTGGC.GG.GTGAAAAGGTTCACACCCAGTTGAt         >  1:5458245/1‑36 (MQ=255)
                           ttCTGTGGC.GG.GTGAAAAGGTTCACACCCAGTTGAt         <  1:5864125/36‑1 (MQ=255)
                             cTGTGGC.GG.GTGAAAAGGTTCACACCCAGTTGAttt       <  1:4001072/36‑1 (MQ=255)
                              tgtgGC.GG.GTGAAAAGGTTCACACCCAGTTGAtttt      <  1:5557209/36‑1 (MQ=255)
                                tgGC.GG.GTGAAAAGGTTCACACCCAGTTGATTTTcc    <  1:3724488/36‑1 (MQ=255)
                                 ggC.GG.GTGAAAAGGTTCACACCCAGTTGATTTTCCa   <  1:4060708/36‑1 (MQ=255)
                                 ggC.GG.GTGAAAAGGTTCACACCCAGATGGTTTTcc  >  1:3831694/1‑35 (MQ=37)
                                  gC.GG.GTGAAAAGGTTCACACCCAGTTGATTTTCCAg  <  1:4084987/36‑1 (MQ=255)
                                    |                                   
CACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC.GG.GTGAAAAGGTTCACACCCAGTTGATTTTCCAG  >  REL606/3909584‑3909653

Base quality scores:  ATCG  < 3 ≤  ATCG  < 7 ≤  ATCG  < 16 ≤  ATCG  < 29 ≤  ATCG  < 37 ≤  ATCG