Predicted mutation
evidence seq id position mutation freq annotation gene description
RA REL606 2,446,442 C→A 24.7% V164F (GTT→TTT)  mntH ← manganese transport protein MntH

Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6062,446,4420C→A24.7% 9.0 ‑4.2 ‑0.031490mntHmanganese transport protein MntH
Reads supporting (aligned to +/- strand):  new base (1/7):  ref base (15/8):  total (16/15)
Fisher's exact test strand distribution p-value = 1.55e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 9.72e-01

GGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCG  >  REL606/2446407‑2446477
                                   |                                   
ggAGAAAATCAACTCGACAATGTAAGCCGCGGcaac                                     <  1:202636/36‑1 (MQ=255)
ggAGAAAATCAACTCGACAATGTAAGCCGCGGcaac                                     >  1:516469/1‑36 (MQ=255)
ggAGAAAATCAACTCGACAATGTAAGCCCCGGcaac                                     >  1:2546442/1‑36 (MQ=255)
 gagaAAATCAACTCGACAATGTAAGCCGCGGaaaca                                    >  1:2982515/1‑36 (MQ=255)
    aaaaTCAACTCGACAATGTAAGCCGCGGCaccaaac                                 >  1:4926234/1‑36 (MQ=255)
    aaaaTCAACTCGACAATGTAAGCCGCGGCaacaaac                                 <  1:5558220/36‑1 (MQ=255)
    aaaaTCAACTCGACAATGTAAGCCGCGGCaacaaac                                 <  1:6504809/36‑1 (MQ=255)
    aaaaTCAACTCGACAATGTAAGCCGCGGCaacaaac                                 >  1:3566460/1‑36 (MQ=255)
     aaaTCAACTCGACAATGTAAGCCGCGGCaacaaaca                                >  1:4581506/1‑36 (MQ=255)
     aaaTAAACACGACAATGTAAGCCGCGGCaacaaaca                                <  1:3591411/36‑1 (MQ=38)
        tCAACTCGACAATGTAAGCCGCGGCAACAAacaaca                             <  1:7959309/36‑1 (MQ=255)
        tCAACTCGACAATGTAAGCCGCGGCAACAAacaaca                             >  1:2567856/1‑36 (MQ=255)
        tCAACTCGACAATGTAAGCCGCGGCAACAAacaaca                             <  1:7122933/36‑1 (MQ=255)
         cAACTCGACAATGTAAGCCGCGGCAACAAACAACAg                            >  1:3606769/1‑36 (MQ=255)
          aaCTCGACAATGTAAGCCGCGGCAACAAACAACAGt                           <  1:6299880/36‑1 (MQ=255)
          aaCTCGACAATGTAAGCCGCGGCAACAAACAACAGt                           >  1:6676767/1‑36 (MQ=255)
          aaCTCGACAATGTAAGCCGCGGCAACAAACAACAGt                           <  1:5641889/36‑1 (MQ=255)
          aaCTCGACAATGTAAGCCGCGGCAACAAACAACAGt                           >  1:4782699/1‑36 (MQ=255)
             tCGACAATGTAAGCCGCGGCAACAAACAACAGTAAc                        <  1:6661398/36‑1 (MQ=255)
             tCGACAATGTAAGCCGCGGCAACAAACAACAGTAAc                        >  1:716056/1‑36 (MQ=255)
              cGACAATGTAAGCCGCGGCAACAAACAACAGTAAcc                       <  1:4371990/36‑1 (MQ=255)
               gACAATGAAAGCCGCGGCAACAAACAACAGTAAccc                      >  1:620064/1‑36 (MQ=255)
                  aaggTAAGCCGCGGCAACAAACAACAGTAACCCGcc                   <  1:6410195/33‑1 (MQ=255)
                  aaTGTAAGCCGCGGCAACAAACAACAGTAACCCGcc                   >  1:7071755/1‑36 (MQ=255)
                  aaTGTAAGCCGCGGCAAAAAACAACAGTAACCCGcc                   <  1:6074133/36‑1 (MQ=255)
                   aTGTAAGCCGCGGCAACAAACAACAGTAACCCGCCa                  >  1:4147704/1‑36 (MQ=255)
                   aTGTAAGCCGCGGCAACAAACAACAGTAACCCGCCa                  <  1:3091959/36‑1 (MQ=255)
                      tAAGCCGCGGCAACAAACAACAGTAACCCGCCAATc               >  1:7042131/1‑36 (MQ=255)
                      tAAGCCGCGGCAAAAAACAACAGTAACCCGCCAATc               <  1:8431268/36‑1 (MQ=255)
                      tAAGCCGCGGCAAAAAACAACAGTAACACGCCAATc               >  1:1385518/1‑36 (MQ=37)
                      tAAGCCGCGGAAAAAAACAAAAGTAACCCGCCAATc               <  1:5883544/36‑1 (MQ=25)
                       aaGCCGCGGCAACAAACAACCGTAACCCGACAATCa              >  1:4335800/1‑36 (MQ=37)
                       aaGCCGCGGCAACAAACAACAGTAACCCGCCAATCa              >  1:6725883/1‑36 (MQ=255)
                       aaGCCGCGGAAAAAAAAAACAGTAACCCGCCAATCa              <  1:3658753/36‑1 (MQ=25)
                        aGCCGCGGCAACAAACAACAGTAACCCGCCAATCAc             >  1:5958985/1‑36 (MQ=255)
                        aGCCGCGGAAAAAAACAACAGTAACCCGCCAATCAc             <  1:2197138/36‑1 (MQ=37)
                          ccccgGAAAAAAAAAAAAGTAACCCGCCAATCACtt           <  1:3551607/33‑1 (MQ=16)
                          ccGCGGCAACAAACAACAGTAACCCGCCAATCACtt           >  1:1052724/1‑36 (MQ=255)
                           cgcgGAAAAAAACAACAGTAACCCGCCAATCACttt          <  1:4785809/36‑1 (MQ=37)
                             cgGCAACAAACAACAGTAACCCGCCAATCACTTtct        >  1:3861490/1‑36 (MQ=255)
                              ggCAACAAACAACAGTAACCCGCCAATCACTTtctc       >  1:7189157/1‑36 (MQ=255)
                                caacaaACAACAGTAACCCGCCAATCACTTTCTCCa     >  1:2756916/1‑36 (MQ=255)
                                   caaacaaCAGTAACGCGCCAATCACTTTCTCCAGCg  >  1:5500328/1‑36 (MQ=255)
                                   |                                   
GGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCG  >  REL606/2446407‑2446477

Base quality scores:  ATCG  < 3 ≤  ATCG  < 10 ≤  ATCG  < 20 ≤  ATCG  < 30 ≤  ATCG  < 37 ≤  ATCG