Predicted mutation
evidence seq id position mutation freq annotation gene description
RA REL606 3,381,587 G→T 14.5% F82L (TTC→TTA pioO ← part of gsp divergon involved in type II protein secretion

Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6063,381,5870G→T14.5% 3.1 ‑4.4 ‑0.027246pioOpart of gsp divergon involved in type II protein secretion
Reads supporting (aligned to +/- strand):  new base (4/0):  ref base (6/17):  total (10/17)
Fisher's exact test strand distribution p-value = 1.20e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 9.87e-01

TCGACGGATTCGACGACGGGGAGTGGCTGTTTTTTGAAGAAATAGTGTTGTGTTGATTGTTTAAAAGCGGG  >  REL606/3381552‑3381622
                                   |                                   
tcGACGGATTCGACGACGGGGAGTGGCTGTTTTTTg                                     <  1:3585346/36‑1 (MQ=255)
  gACGGATTCGACGACGGGGAGTGGCTGTTTTTTgaa                                   <  1:484227/36‑1 (MQ=255)
    cGGATTCGACGACGGGGAGTGGCTGTTTTTTgaata                                 <  1:4074452/36‑3 (MQ=255)
     ggATTCGACGACGTGGAGTGGCTGTTTTTTgaagaa                                <  1:4742716/36‑1 (MQ=255)
        atCGGCGACGGGGAGTGGCTGTTTTTTGAAGAAATa                             <  1:141601/35‑1 (MQ=255)
           gacgacGGGGAGTGGCTGGTTTTTTTAGAAATAttg                          >  1:1068395/1‑36 (MQ=16)
           gacgacGGGGAGTGGCTGGGTTTTTTAGAAATAgtg                          >  1:231145/1‑36 (MQ=16)
            gcgacgGGGAGTGGCTGTTTTTTGAAGAAATAgtgt                         <  1:66368/35‑1 (MQ=255)
             cgacgGGGAGTGGCTGTTTTTTGAAGAAATAgtgtt                        <  1:5622545/36‑1 (MQ=255)
              gacgGGGAGTGGCTGGTTTTTTTTGGAAAAgtgttg                       >  1:5770304/1‑36 (MQ=9)
                 ggggAGTGGCTGTTTTTTGAAGAAATAgtgttgtgt                    <  1:1952550/36‑1 (MQ=255)
                 ggggAGTGGCTGGTTTTTTTAGAAAAAgtgttgtgt                    >  1:2240238/1‑36 (MQ=19)
                  gggAGTGGCTGTTTTTTGAAGAGATAgtgttgtgtt                   <  1:5155169/36‑1 (MQ=255)
                  gggAGTGGCTGTTTTTTGAAGAAATAgtgttgtgtt                   <  1:5565953/36‑1 (MQ=255)
                     aGTGGCTGTTTTTTGAAGAAATAGTGTTGTGTTGAt                <  1:1346627/36‑1 (MQ=255)
                     aGTGGCTGTTTTTTGAAGAAATAGTGTTGTGTTGAt                <  1:4000306/36‑1 (MQ=255)
                      gTGGCTGTTTTTTGAAGAAATAGTGTTGTGTTGAtt               <  1:118445/36‑1 (MQ=255)
                        ggCTGTTTTTTGAAGAAATAGTGTTGTGTTGATTGt             >  1:742052/1‑36 (MQ=255)
                        ggCTGTTTTTTGAAGAAATAGTGTTGTGTTGATTGt             <  1:4053055/36‑1 (MQ=255)
                         gCTGTTTTTTGAAGAAATAGTGTTGTGTTGATTGtt            >  1:3490170/1‑36 (MQ=255)
                          cTGTTTTTTGAAGAAATAGTGTTGTGTTGATTGttt           <  1:3828250/36‑1 (MQ=255)
                          cTGTTTTTTGAAGAAATAGTGTTGTGTTGATTGttt           <  1:4729519/36‑1 (MQ=255)
                          cTGTTTTTTGAAGAAATAGTGTTGTGTTGATTGttt           <  1:2379116/36‑1 (MQ=255)
                          cTGTTTTTTGAAGAAATAGTGTTGTGTTGATTGttt           <  1:64925/36‑1 (MQ=255)
                           tGTTTTTTGAGGAAATAGTGTTGTGTTGATTGTTTa          <  1:2729185/36‑1 (MQ=255)
                           tGTTTATTGCAGAAATAGTGTTGTGTTGATTGTTTa          <  1:2158453/36‑1 (MQ=38)
                            gTTTTTTGAAGAAATAGTGTTGTGTTGATTGTTTaa         >  1:5852783/1‑36 (MQ=255)
                            gTTTTTTGAAGAAATAGTGTTGTGTTGATTGTTTaa         >  1:1380875/1‑36 (MQ=255)
                             ttttttGAAGAAATAGTGTTGTGTTGATTGTTTaaa        >  1:1962797/1‑36 (MQ=255)
                              tttttGCAGACATAGTGTTGTGTTGATTGTTTaaaa       <  1:3259138/36‑1 (MQ=37)
                                tttGAAGAAATAGTGTTGTGTTGATTGTTTAAAAGc     >  1:3518084/1‑36 (MQ=255)
                                   gaagaaATAGGGTTGTGGTGATTGTTTAAAAGCagg  >  1:5327824/1‑36 (MQ=25)
                                   |                                   
TCGACGGATTCGACGACGGGGAGTGGCTGTTTTTTGAAGAAATAGTGTTGTGTTGATTGTTTAAAAGCGGG  >  REL606/3381552‑3381622

Base quality scores:  ATCG  < 3 ≤  ATCG  < 7 ≤  ATCG  < 18 ≤  ATCG  < 28 ≤  ATCG  < 37 ≤  ATCG