Predicted mutation
evidence seq id position mutation freq annotation gene description
RA REL606 3,120,587 A→C 14.0% T119P (ACA→CCA)  yqiG → predicted outer membrane usher protein

Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6063,120,5870A→C14.0% 2.6 ‑4.5 ‑0.150355yqiGpredicted outer membrane usher protein
Reads supporting (aligned to +/- strand):  new base (7/0):  ref base (20/23):  total (27/23)
Fisher's exact test strand distribution p-value = 1.13e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 7.27e-01

ATGGTTGTTACCCTATCGAAAAAGAAAAACAAATTACAACTTATCTCGATAAAGGGAAAATGCAATTATCC  >  REL606/3120552‑3120622
                                   |                                   
aTGGTTGTTACCCTATCGAAAAAGAAAAACAAATTa                                     >  1:885037/1‑36 (MQ=255)
 tGGTTGTTACCCTATCGAAAAAGAAAAACAAATTAc                                    >  1:7142850/1‑36 (MQ=255)
 tGGTTGTTACCCTATCGAAAAAGAAAAACAAATTAc                                    >  1:1157050/1‑36 (MQ=255)
 tGGTTGTTACCCTATCGAAAAAGAAAAACAAATTAc                                    >  1:7828409/1‑36 (MQ=255)
 tGGTTGTTACACTATCGAAAAAGAAAAACAAATTAc                                    <  1:447136/36‑1 (MQ=255)
  ggTTGTTACCCTATCGAAAAAGAAAAACAAATTACa                                   >  1:6932787/1‑36 (MQ=255)
  ggTTGTTACCCTATCGAAAAAGAAAAACAAATTACa                                   >  1:7501615/1‑36 (MQ=255)
   gttgttACCCTATCGAAAAAGAAAAACAAATTACaa                                  >  1:2395384/1‑36 (MQ=255)
    ttgttACCCTATCGAAAAAGAAAAACAAATTACAAc                                 >  1:3053425/1‑36 (MQ=255)
    ttgttACCCTATCGAAAAAGAAAAACAAATTACAAc                                 <  1:975898/36‑1 (MQ=255)
     tgttACCCTATCGAAAAAGAAAAACAAATTACAACt                                <  1:450152/36‑1 (MQ=255)
     tgttACCCTATAGAAAAAGAAAAACAAATTACAACt                                <  1:224974/36‑1 (MQ=255)
       ttACCCTATCGAAAAAGAAAAACAAATTACAACTTa                              >  1:5111068/1‑36 (MQ=255)
        tACCCTATCGAAAAAGAAAAACAAATTACAACTTAt                             <  1:224803/36‑1 (MQ=255)
        tACCCTATCGAAAAAGAAAAACAAATTACAACTTAt                             <  1:1122082/36‑1 (MQ=255)
        tACACTATCGAAAAAGAAAAACAAATTACAACTTAt                             <  1:2393400/36‑1 (MQ=255)
         aCCCTATCGAAAAAGAAAAACAAATTCCAACTTAtc                            >  1:143395/1‑36 (MQ=255)
          cccTATCGAAAAAGAAAAACAAATTACAACTTAtct                           <  1:3098667/36‑1 (MQ=255)
           ccTATCGAAAAAGAAAAACAAATTACAACTTAtctc                          >  1:6923449/1‑36 (MQ=255)
             tATCGAAAAAGAAAAACAAATTACAACTTATCTCGa                        >  1:6587230/1‑36 (MQ=255)
             tATAGAAAAAGAAAAACAAATTACAACTTATCTCGa                        <  1:2439836/36‑1 (MQ=255)
              aTCGAAAAAGAAAAACAAATTACAACTTATCTCGAt                       <  1:2223980/36‑1 (MQ=255)
              aTCGAAAAAGAAAAACAAATTACAACTTATCTCGAt                       <  1:4568470/36‑1 (MQ=255)
               tCGAAAAAGAAAAACAAATTCCAACTTATCTCGATa                      >  1:4704903/1‑36 (MQ=255)
                cGAAAAAGAAAAACAAATTCCAACTTATCTCGATaa                     >  1:6744292/1‑36 (MQ=255)
                cGAAAAAGAAAAACAAATTACAACTTATCTCGATaa                     <  1:2422532/36‑1 (MQ=255)
                cGAAAAAGAAAAACAAATTACAACTTATCTCGATaa                     >  1:5780178/1‑36 (MQ=255)
                cGAAAAAGAAAAACAAATTACAACTTATCTCGATaa                     >  1:1183671/1‑36 (MQ=255)
                 gaaaaagaaaaaCAAATTCCAACTTATCTCGATaaa                    >  1:7878299/1‑36 (MQ=255)
                 gaaaaagaaaaaCAAATTACAACTTATCTCGATaaa                    >  1:2798517/1‑36 (MQ=255)
                  aaaaagaaaaaCAAATTCCAACTTATCTCGATAAAg                   >  1:7246552/1‑36 (MQ=255)
                  aaaaagaaaaaCAAATTACAACTTATCTCGATAAAg                   <  1:137242/36‑1 (MQ=255)
                   aaaagaaaaaCAAATTACAACTTATCTCGATAAAgg                  <  1:3307783/36‑1 (MQ=255)
                    aaagaaaaaCAAATTCCAACTTATCTCGATAAAggg                 >  1:3575684/1‑36 (MQ=255)
                     aagaaaaaCAAATTACAACTTATCTCGATAAAGGGa                <  1:5607005/36‑1 (MQ=255)
                     aagaaaaaCAAATTACAACTTATCTCGATAAAGGGa                >  1:1121367/1‑36 (MQ=255)
                      agaaaaaCAAATTACAACTTATATCGATAAAGGGaa               >  1:7253325/1‑36 (MQ=255)
                        aaaaaCAAATTACAACTTATCTCGATAAAGGGaaaa             >  1:222403/1‑36 (MQ=255)
                        aaaaaCAAATTACAACTTATCTCGATAAAGGGaaaa             <  1:7056615/36‑1 (MQ=255)
                        aaaaaCAAATTACAACTTATCTCGATAAAGGGaaaa             <  1:6665674/36‑1 (MQ=255)
                         aaaaCAAATTACAACTTATCTCGATAAAGGGAAAAt            >  1:4162425/1‑36 (MQ=255)
                          aaaCAAATTCCAACTTATCTCGATAAAGGGAAAATg           >  1:2694597/1‑36 (MQ=255)
                           aaCAAATTACAACTTATCTCGATAAAGGGAAAATGc          >  1:3759633/1‑36 (MQ=255)
                           aaCAAATTACAACTTATCTCGATAAAGGGAAAATGc          <  1:4263372/36‑1 (MQ=255)
                            aCAAATTACAACTTATCTCGATAAAGGGAAAATGCa         >  1:2381655/1‑36 (MQ=255)
                             cAAATTACAACTTATCTCGATAAAGGGAAAATGCaa        >  1:3714145/1‑36 (MQ=255)
                              aaaTTACAACTTATCTCGATAAAGGGAAAATGCAAt       <  1:7253790/36‑1 (MQ=255)
                              aaaTTACAACTTATCTCGATAAAGGGAAAATGCAAt       <  1:2375212/36‑1 (MQ=255)
                                  tACAACTTATCTCGATAAAGGGAAAATGCAATTATc   <  1:6716786/36‑1 (MQ=255)
                                  tACAACTTATCTCGATAAAGGGAAAATGCAATTATc   <  1:4756663/36‑1 (MQ=255)
                                  tACAACTTATCTCGATAAAGGGAAAATGCAATTATc   <  1:5327889/36‑1 (MQ=255)
                                   aCAACTTATCTCGATAAAGTGAAAATGCAATTATcc  <  1:1447210/36‑1 (MQ=255)
                                   aCAACTTATCTCGATAAAGGGAAAATGCAATTATcc  <  1:6559577/36‑1 (MQ=255)
                                   aCAACTTATCTCGATAAAGGGAAAATGCAATTATcc  <  1:2079288/36‑1 (MQ=255)
                                   |                                   
ATGGTTGTTACCCTATCGAAAAAGAAAAACAAATTACAACTTATCTCGATAAAGGGAAAATGCAATTATCC  >  REL606/3120552‑3120622

Base quality scores:  ATCG  < 3 ≤  ATCG  < 16 ≤  ATCG  < 27 ≤  ATCG  < 32 ≤  ATCG  < 37 ≤  ATCG