Predicted mutation
evidence seq id position mutation freq annotation gene description
RA REL606 4,573,670 C→A 10.9% L199F (TTG→TTT hpaX ← hypothetical 4‑hydroxyphenylacetate permease

Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6064,573,6700C→A10.9% 4.4 ‑4.1 0.048597hpaXhypothetical 4‑hydroxyphenylacetate permease
Reads supporting (aligned to +/- strand):  new base (1/5):  ref base (30/12):  total (31/17)
Fisher's exact test strand distribution p-value = 1.66e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 1.00e+00

ATGACGCCGAGTAATACCGACGGGAAGCCTTCCAGCAAAAACAGCCACTGCCAGCCTTTTAATGCCATTAC  >  REL606/4573635‑4573705
                                   |                                   
aTGACGCCGAGTAATACCGACGGGAAGCCTTCCAGc                                     <  1:2814666/36‑1 (MQ=255)
aTGACGCCGAGTAATACCGACGGGAAGCCTTCCAGc                                     >  1:6992898/1‑36 (MQ=255)
aTGACGCCGAGTAATACCGACGGGAAGCCTTCCAGc                                     >  1:2262007/1‑36 (MQ=255)
 tGACGCCGAGTAATACCGACGGGAAGCCTTCCAGCa                                    <  1:6187871/36‑1 (MQ=255)
  gACGCCGAGTAATACCGGCGGGAAGCCGTCCAGCaa                                   <  1:8147132/36‑1 (MQ=37)
  gACGCCGAGTAATACCGACGGGAAGCCTTCCAGCaa                                   >  1:4171630/1‑36 (MQ=255)
  gACGCCGAGTAATACCGACGGGAAGCCTTCCAGCaa                                   <  1:3255001/36‑1 (MQ=255)
  gACGCCGAGTAATACCGACGGGAAGCCTTCCAGCaa                                   >  1:1778495/1‑36 (MQ=255)
  gACGCCGAGTAATACCGACGGGAAGCCTTCCAGCaa                                   <  1:7379917/36‑1 (MQ=255)
   aCGCCGAGTAATACCGACGGGAAGCCTTCCAGCaaa                                  <  1:7873971/36‑1 (MQ=255)
   aCGCCGAGTAATACCGACGGGAAGCCTTCCAGCaaa                                  <  1:5489978/36‑1 (MQ=255)
   aCGCCGAGTAATACCGACGGGAAGCCTTCCAGCaaa                                  >  1:1499541/1‑36 (MQ=255)
    cGCCGAGTAATACCGACGGGAAGCCTTCCAGCaaaa                                 <  1:6515030/36‑1 (MQ=255)
     gCCGAGTAATACCGACGGGAAGCCTTCCAGCaaaaa                                <  1:6857246/36‑1 (MQ=255)
     gCCGAGTAATACCGACGGGAAGACTTCCAGCcaaaa                                >  1:6764422/1‑36 (MQ=37)
      ccGAGTAATACCGACGGGAAGCCTTCCAGCAAAAAc                               >  1:7386819/1‑36 (MQ=255)
      ccGAGTAATACCGACGGGAAGCCTTCCAGCAAAAAc                               <  1:7919377/36‑1 (MQ=255)
       cGAGTAATACCGACGGGAAGCCTTCCAGCAAAAACa                              >  1:7965687/1‑36 (MQ=255)
        gAGTAATACCGACGGGAAGCCTTCCAGCAAAAACAg                             <  1:5939179/36‑1 (MQ=255)
         aGTAATACCGACGGGAAGCCTTCCAGCAAAAACAGc                            >  1:5534094/1‑36 (MQ=255)
         aGTAATACCGACGGGAAGCCTTCCAGCAAAAACAGc                            <  1:1336045/36‑1 (MQ=255)
         aGTAATACCGACGGGAAGCCTTCCAGCAAAAACAGc                            >  1:2186881/1‑36 (MQ=255)
         aGTAATACCGACGGGAAGCCTCCCAGCAAAAACAGc                            <  1:4779094/36‑1 (MQ=255)
          gTAATACCGACGGGAAGCCTTCCAGCAAAAAAAGcc                           >  1:191733/1‑36 (MQ=255)
            aaTACCGACGGGAAGCCTTCCAGCAAAAACAGCCAc                         >  1:671150/1‑36 (MQ=255)
             aTACCGACGGGAAGCCTTCCAGCAAAAACAGCCACt                        >  1:4843505/1‑36 (MQ=255)
              tcccGACGGGAACCCTCCCAAAAAAACCAGCCACTg                       <  1:1910735/34‑1 (MQ=9)
               aCCGACGGGAAGCCTTCCAGCAAAAACAGCCACTGc                      >  1:81193/1‑36 (MQ=255)
                ccGACGGGAAGCCTTCCAGCAAAAACAGCCACTGcc                     >  1:1466423/1‑36 (MQ=255)
                 cGACGGGAACCCTCCCAGAAAAACCAGCCACTGCCa                    <  1:2493254/36‑1 (MQ=16)
                  gACGGGAACCCTTAAAAAAAAAACAGCCACTGCCAg                   <  1:2339763/36‑1 (MQ=16)
                   aCGGGAAGCCTTCCAGCAAAAACAGCCACTGCCAGc                  >  1:1337597/1‑36 (MQ=255)
                   aCGGGAAGCCTTCCAGCAAAAACAGCCACTGCCAGc                  >  1:3633979/1‑36 (MQ=255)
                    cGGGAAGCCTTCCAGCAAAAACAGCCACTGCCAGcc                 >  1:7131138/1‑36 (MQ=255)
                    cGGGAAGCCTTCCAGCAAAAACAACCACTGCCAGcc                 >  1:5339305/1‑36 (MQ=255)
                    cGGGAAGCATCCCAAAAAAACCAGCCACTGCCAGcc                 <  1:6245407/36‑1 (MQ=9)
                    cGGAAAGCCTCCCACAAAAAACAGCCACTGCCAGcc                 <  1:5467826/36‑1 (MQ=16)
                     gggAAGCCTTCCAGCAAAAACAGCCACTGCCAGCCt                >  1:5221159/1‑36 (MQ=255)
                     gggAAGCCTTCCAGCAAAAACAGCCACTGCCAGCCt                >  1:2427118/1‑36 (MQ=255)
                     gggAAGCCTTCCAGAAAAAACAGCCACTGCCAGCCt                >  1:4952844/1‑36 (MQ=255)
                        aaGCCTTCCAGCAAAAACAGCCACTGCCAGCCtttt             >  1:4692/1‑36 (MQ=255)
                        aaGCCTTCCAGCAAAAACAGCCACTGCCAGCCtttt             >  1:4159040/1‑36 (MQ=255)
                        aaGCCTTCCAGCAAAAACAGCCACTGCCAGCCtttt             >  1:8066309/1‑36 (MQ=255)
                         aGCCTTCCAGCAAAAACAGCCACTTCCAGCCTTTTa            >  1:595210/1‑36 (MQ=255)
                         aGCCTTCCAGCAAAAACAGCCACTGCCAGCCTTTTa            >  1:4916725/1‑36 (MQ=255)
                           ccTTCCAGCAAAAACAGCCACTGCCAGCCTTTTAAt          >  1:4472358/1‑36 (MQ=255)
                            cTTCCAGCAAAAACAGCCACTGCCAGCCTTTTAATg         >  1:1399209/1‑36 (MQ=255)
                             ttCCAGCAAAAACAGCCACTGCCAGCCTTTTAATGc        >  1:8284847/1‑36 (MQ=255)
                               ccAGCAAAAACAGCCACTGCCAGCCTTTTAATGCCa      >  1:5938754/1‑36 (MQ=255)
                                cAGCAAAAACAGCCACTGCCAGCCTTTTAATGCCAt     >  1:3429166/1‑36 (MQ=255)
                                  gCAAAAACAGCCACTGCCAGCCTTTTAATGCCATTa   >  1:2109393/1‑36 (MQ=255)
                                   cAAAAACAGCCACTGCCAGCCTTTTAATGCCATTAc  >  1:3187259/1‑36 (MQ=255)
                                   cAAAAACAGCCACTGCCAGCCTTTTAATGCCATTAc  >  1:8305550/1‑36 (MQ=255)
                                   |                                   
ATGACGCCGAGTAATACCGACGGGAAGCCTTCCAGCAAAAACAGCCACTGCCAGCCTTTTAATGCCATTAC  >  REL606/4573635‑4573705

Base quality scores:  ATCG  < 3 ≤  ATCG  < 11 ≤  ATCG  < 22 ≤  ATCG  < 30 ≤  ATCG  < 37 ≤  ATCG