Predicted mutation
evidence seq id position mutation freq annotation gene description
RA REL606 3,909,619 +G 6.1% 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 6.1% 3.5 ‑1.5 ‑0.133coding (149/840 nt)hdfRtranscriptional regulator HdfR
Reads supporting (aligned to +/- strand):  new base (2/0):  ref base (14/17):  total (16/17)
Fisher's exact test strand distribution p-value = 2.27e-01
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 7.29e-01

CACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC.GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGT  >  REL606/3909584‑3909654
                                    |                                   
cACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGc                                      <  1:4069968/36‑1 (MQ=255)
 aCCGGCAGCGGTTAAACGGATATTGTTTCTGTTGC.g                                    >  1:136531/1‑36 (MQ=255)
 aCCGGCAGCGGTTAAACGGATATTGTTTCTGTTGC.g                                    >  1:7390018/1‑36 (MQ=255)
 aCCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC.g                                    <  1:1451685/36‑1 (MQ=255)
 aCCGGCAGCGGTTAAACGGATATTGTTTCTGTGCC.g                                    >  1:1468871/1‑36 (MQ=255)
  ccGGCAGCGGTTAAACGGATATTGTTTCTGTGGC.gg                                   <  1:823796/36‑1 (MQ=255)
  ccGGCAGCGGTTAAACGGATATTGTTTCTGTGGC.gg                                   <  1:823270/36‑1 (MQ=255)
  ccGGCAGCGGTTAAACGGATATTGTTTCTGTGGC.gg                                   >  1:6103313/1‑36 (MQ=255)
   cGGCAGCGGTTAAACGGATATTGTTTCTGTGGC.ggg                                  <  1:6590486/36‑1 (MQ=255)
    ggCAGCGGTTAAACGGATATTGTTTCTGTGGC.gggg                                 >  1:3837589/1‑35 (MQ=255)
     gCAGCGGTTAAACGGATATTGTTTCTGTGGC.ggggg                                >  1:423873/1‑34 (MQ=255)
      cAGCGGTTAAACGGATATTGTTTCTGTGGC.GGGTgt                               >  1:2899708/1‑35 (MQ=255)
      cAGCGGTTAAACGGATATTGTTTCTGTGGC.GGGTGa                               <  1:7355110/36‑1 (MQ=255)
       aacGGTTAAACGGATATTGTTTCTGTGGC.GGGTGaa                              <  1:6336529/34‑1 (MQ=255)
       aGCGGTTAAACGGATATTGTTTCTGTGGC.GGGTgga                              >  1:2195657/1‑34 (MQ=255)
         cGGTTAAACGGATATTGTTTCTGTGGC.GGGTGaaaa                            <  1:1732057/36‑1 (MQ=255)
          ggTTAAACGGATATTGTTTCTGTGGC.GGGTGGAAAg                           >  1:6999592/1‑36 (MQ=255)
             tAAACGGATATTGTTTCTGTGGCGGGGTGAAAAGGt                         >  1:2162278/1‑36 (MQ=37)
              aaaCGGATATTGTTTCTGTGGC.GGGGGGAAAGGttt                       >  1:4609162/1‑35 (MQ=37)
               aaCGGATATTGTTTCTGTGGCGGGGGGAAAAGGtta                       >  1:5889599/1‑35 (MQ=25)
               aaCGGATATTGTTTCTGTGGC.GGGTTGAAAGGTTct                      >  1:7248423/1‑35 (MQ=37)
               aaCGGATATTGTTTCTGTGGC.GGGTGAAAATGTTca                      <  1:7047042/36‑1 (MQ=255)
               aaCGGATATTGTTTCTGTGGC.GGGTGAAAAGGTTca                      <  1:1677004/36‑1 (MQ=255)
                aCGGATATTGTTTCTGTGGC.GGGTGAAAAAGTTtac                     >  1:6452558/1‑36 (MQ=37)
                aCGGATATTGTTTCTGTGGC.GGGGGGAAAAGTTtac                     >  1:4535924/1‑36 (MQ=19)
                 cGGATATTGTTTCTGTGGC.GGGTGAAAAAGTTtacc                    >  1:2331165/1‑35 (MQ=37)
                 cGGATATTGTTTCAGTGGC.GGGTGAAAAGGTTcaca                    >  1:3233220/1‑36 (MQ=255)
                  ggATATTGTTTCTGTGGC.GGGTGAAAAGGTTcacgc                   <  1:2866831/36‑3 (MQ=255)
                  ggATATTGTTTCTATGGC.GGGTGAAAAGGTTCacac                   <  1:94589/36‑1 (MQ=255)
                    atatTGTTTCTGTGGC.GGGTGAAAAGGTTCACAccc                 <  1:1858873/36‑1 (MQ=255)
                    atatTGTTTCTGAGCC.GGGTGAAAAAGTTATCAccc                 >  1:87944/1‑36 (MQ=16)
                      atTGTTTCTGTGGC.GGGTGAAAAGGTTCACACCCAg               <  1:5548566/36‑1 (MQ=255)
                       ttGTTTCTGTGGC.GGGTGAAAAGGTTCACACCCAGt              <  1:5894497/36‑1 (MQ=255)
                        tGTTTCTGTGGC.GGGTGAAAAGGTTCACACCCAGtt             <  1:4441405/36‑1 (MQ=255)
                        tGTTTCTGTGGC.GGGTGAAAAGGTTCACACCCAGtt             <  1:4377192/36‑1 (MQ=255)
                         gTTTCTGTGGC.GGGTGAAAAGGTTCACACCCAGTTg            >  1:7471795/1‑36 (MQ=255)
                          tttCTGTGGC.GGGTGAAAAGGTTCACACCCAGTTGa           <  1:7343561/36‑1 (MQ=255)
                           ttCTGTGGC.NGGTGAAAAGGTTCACACCCAGTTGAt          <  1:4531037/36‑1 (MQ=255)
                            tCTGTGGC.GGGTGAAAAGGTTCACACCCAGTTGAtt         <  1:2713196/36‑1 (MQ=255)
                               gtgGC.GGGTGAAAAGGTTCACACCCAGTTGATTTTc      <  1:1410965/36‑1 (MQ=255)
                                tgGC.GGGTGAAAAGGTTCACACCCAGTTGATTTTcc     <  1:2141430/36‑1 (MQ=255)
                                 ggC.GGGGGAAAAGGTTCACACCCAGTTGATTTTCCa    >  1:5432912/1‑36 (MQ=255)
                                  gC.GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAg   >  1:97208/1‑36 (MQ=255)
                                  gC.GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAg   >  1:4635590/1‑36 (MQ=255)
                                   c.GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGt  <  1:1194972/36‑1 (MQ=255)
                                   c.GGATGAAAAGGTTCGCGCCCAGTTGATTTTCCAGt  <  1:346181/36‑1 (MQ=25)
                                    |                                   
CACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC.GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGT  >  REL606/3909584‑3909654

Base quality scores:  ATCG  < 3 ≤  ATCG  < 7 ≤  ATCG  < 19 ≤  ATCG  < 30 ≤  ATCG  < 37 ≤  ATCG