Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913_3_pae_pgi 130,072 C→T 8.9% A397T (GCC→ACC)  yacH ← DUF3300 family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_pgi130,0720CT 8.9% 126.5 / 4.1 52A397T (GCC→ACC) yacHDUF3300 family protein
Reads supporting (aligned to +/- strand):  ref base C (26/21);  new base T (2/3);  total (28/24)
Fisher's exact test for biased strand distribution p-value = 6.52e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.08e-01

AAGTCGTCATAGCTCCCATAGTGTTCAGCTTCATTAAACCGCTGTGCCGCTGCCTGACGTTGGGTATCTCGTGTAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAACCGCTTTGCCATATCCTGATCATGATAGGGCACACCATTACGGTAGTTTGGATTGTGCCGCCATGCCATATTCTTATCAGTAAGATGCTCACCGGTGA  >  NC_000913_3_pae_pgi/129924‑130218
                                                                                                                                                    |                                                                                                                                                  
aaGTCGTCATAGCTCCCATAGTGTTCAGCTTCATTAAACCGCTGTGCCGCTGCCTGACGTTGGGTATCTCGTGTAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGc                                                                                                                                                    <  2:951178/149‑1 (MQ=255)
   tcgtcATAGCTCCCATAGTGTTCATCTTCATTAAACCTCTGTGCCGCTGCCTAACGTTGGGTATCTCGTGCAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTCGGGCAgg                                                                                                                                                 <  1:928740/149‑1 (MQ=255)
        aTAGCTCCCATAGTGTTCAGCTTCATTAGACCGCTGTGCCGCTGCCTGACGTTGGGTGTCTCGTGTAATGACTGGTACGGCGGTTGGTGGTTGCTGAAACTGCTGTGCTGGCGCCTGACGCTGCCTGTCGCGCGATGGGGCAgagcatg                                                                                                                                            >  2:604305/1‑143 (MQ=255)
          aGCTCCCATAGTGTTCAGCTTCATTAAACCGCTGTGCCGCTGCCTGACGTTGGGTATCTCGTGTAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGc                                                                                                                                          >  1:805148/1‑149 (MQ=255)
            cTCCCATAGTGTTCAGCTTCATTAAACCGCTGTGCCGCTGCCTGACGTTGGGTATCTCGTGTAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGt                                                                                                                                        >  2:702843/1‑149 (MQ=255)
               ccATAGTGTTCAGCTTCATTAAACCGCTGCACGGTGGGCTTGGGTGGGGTATCTCGTGTAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACACTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTgac                                                                                                                                     >  1:240577/1‑147 (MQ=255)
                cATAGTGTTCAGCTTCATTAAACCGCTGTGCCGCTGCCTGACGTTGGGTATCTCGTGTAATGACTGGTGCGGCGTGTGTTCGTTGCGGAAACTGCTTTGCTGCCGCCTGACGCTGGCTGTCGCGAGGTGGGTCCGGTAATTGCGTGgcg                                                                                                                                    >  2:890861/1‑149 (MQ=255)
                       ttaaGCTTCATTAAAACGCTGTGGGGCTGCCTGGCGTGGGGTGTCGCGTGTAGTGACTGGTGCGGGGGGGGTTGGTTGCTGAAATTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGGGGTCATTc                                                                                                                             >  2:744394/4‑149 (MQ=255)
                         cAGCTTCATTAAACCGCTGTGCCGCTGCCTGACGTTGGGTATCTCGTGTAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAgg                                                                                                                                                 >  2:362360/1‑127 (MQ=255)
                         cAGCTTCATTAAACCGCTGTGCCGCTGCCTGACGTTGGGTATCTCGTGTAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAgg                                                                                                                                                 <  1:362360/127‑1 (MQ=255)
                                attgacccGCTGTGCCGCTGCCTGTCGTTGGGTATCGCGTGTAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGa                                                                                                                    <  1:96642/143‑1 (MQ=255)
                                aTTAAACCGCTGTGCCGCTGCCTGACGTCCGGCAACTCGTGTAATGACTGGTGCGGGGTGTGTTCGTTGCTGAAGCTGATTTGCTGCCGCCTGACGCTGGCTGTCGCCCGTTGGGGCAGCACGTTGCGTGGCGACCATTCCCCAGTTGa                                                                                                                    >  2:217970/1‑149 (MQ=255)
                                 ttAAACCGCTGTGCCGCTGCCTGACGTTGGGTATCTCGTGTAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGAc                                                                                                                   <  1:627612/149‑1 (MQ=255)
                                    aaCCGCTGTGCCGCTGCCTGACGTTGGGTATCTCGTGTAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATc                                                                                                                >  1:273872/1‑149 (MQ=255)
                                           gtgCCGTTGCCTGACGTTGGGTATCTCGTGTAATGACTGGTGCGGCGTGTGTTTGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGTTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTtga                                                                                                         <  2:868033/149‑1 (MQ=255)
                                           gtgCAGCTGCCTGGCGTTGGGTATCTCGTGGAATGACTGGTGCGGTGTGTGTTCGTTGCTGACACTGATTTGCTGCCGACTGACGTTCGCTGTCCCGCCTTGGGTCAGGTTATTGCGTGCCGCTCATTCCGCCGTTGACATCGGTTtga                                                                                                         <  1:849131/149‑1 (MQ=255)
                                              ccGCTGCCTGACGTTGGGTATCTCGTGTAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTtgatga                                                                                                      >  1:939530/1‑149 (MQ=255)
                                                gCTGCCTGACGTTGGGTATCTCGTGTAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTGATTCCGACGTTGACATCGGTTTGATGaaa                                                                                                    >  1:935193/1‑149 (MQ=255)
                                                gCTGCCTGACGTTGGGTATCTCGTGTAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGaaa                                                                                                    >  1:494513/1‑149 (MQ=255)
                                                     cTGACGTTGGGTATCTCGTGTAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTCATCAAACCgat                                                                                               <  2:273872/149‑3 (MQ=255)
                                                          gTTGGGTATCTCGTGTAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCATGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAACCGCTTTGcc                                                                                          >  1:771003/1‑149 (MQ=255)
                                                              ggTATCTCGTGTAATGACTGGTGCGGCGTGTGTGCGTTGCGGAAACTGAATCGCGGCCGCCTGAGGCTGCGTGGCGCGAGTTACAGCAGGTAAATGCGGGGCGCTCCTGCCGCCGTTGACAACAAATAGATGAAACAGATTTGCCatat                                                                                      >  2:98507/1‑149 (MQ=255)
                                                                tATCTCGTGTAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAACCGCTTTGCCATATcc                                                                                    >  1:762842/1‑149 (MQ=255)
                                                                    tcGTGTAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAAACGCTTTGCCATATCCTGAt                                                                                >  1:201316/1‑149 (MQ=255)
                                                                      gtgtAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTCCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAACCGCTTTGCCATAACCTGATCa                                                                              >  1:61595/1‑149 (MQ=255)
                                                                       tgtAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAACCGCTTTGCCATATCCTGATCAt                                                                             <  2:532154/149‑1 (MQ=255)
                                                                       tgtAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAACCGCTTTGCCATATCCTGATCAt                                                                             <  2:807937/149‑1 (MQ=255)
                                                                            tGACTGGTGCGGCGGGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAACCGCTTTGCCATATCCTGATCATGATAg                                                                        <  2:898361/149‑1 (MQ=255)
                                                                             gcccggTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCAGTTGACAGCGGTTTGATGAAACCGCTTTGCCAGATCCTGATCATGATAgg                                                                       <  1:237412/145‑1 (MQ=255)
                                                                               cTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCTCGTTGGGGCATGTAATTGCGTGGCGCTCATTCCGCGGTTGACATCGGTTTGATGAAACCCCTTTGCCAAATCCTGATCATATTAGGGc                                                                     >  2:176103/1‑149 (MQ=255)
                                                                               cTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTAGGGGCAGGCGATTGCGGTTCTCTAATGCCGCCGTTGACATCGGTTTGATGAAACCGCTTTGCCATATCCTGCGCATGATAGTGc                                                                     >  2:112257/1‑149 (MQ=255)
                                                                                        cgTGTTTTCGGTGCTGAAACTGAGTTCCGGCGGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGATAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTATGATGAAACCGCTTTGCCATATCCCGATCATGATAGGGCACACCATTa                                                            <  2:508839/149‑1 (MQ=255)
                                                                                          tgtgtTCGTTGGTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCTTTGACATCGGTTTGATGAAACCGCTTTGCCATATCCTGATCATGATAGGGCACCCCATTaat                                                          <  2:928965/149‑3 (MQ=255)
                                                                                          tgtgtTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAACCGCTTTGCCATATCCTGATCATGATAGGGCACACCATTACg                                                          <  1:9211/149‑1 (MQ=255)
                                                                                            tgtTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGTAGGTAATTGCGTGGCGCTCATTCCGCCGt                                                                                                                       <  2:294964/86‑1 (MQ=255)
                                                                                            tgtTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGTAGGTAATTGCGTGGCGCTCATTCCGCCGt                                                                                                                       <  2:295168/86‑1 (MQ=255)
                                                                                            tgtTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGTAGGTAATTGCGTGGCGCTCATTCCGCCGt                                                                                                                       >  1:294964/1‑86 (MQ=255)
                                                                                            tgtTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGTAGGTAATTGCGTGGCGCTCATTCCGCCGt                                                                                                                       >  1:295168/1‑86 (MQ=255)
                                                                                                gggtGCTGAAACTGATTTTCTGCAGCCTGACGCTGGCTGTCGGCCGTTGGGCCAGGTAATTGCGTGGCGCTTATTCCGCCGTTGTCATCGGTTTGATAAAACCGCTTTGCCATATCCTGATCATGATCGGGCACACCATTACGGTAGtt                                                    <  2:129605/146‑1 (MQ=255)
                                                                                                 gTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAACCGCTTTGCCATATCCTGATCATGATAGGGCACACCATTACGGTAGttt                                                   <  2:934247/149‑1 (MQ=255)
                                                                                                  ttGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAACCGCTTTGCCATATCCTGATCATGATAGGGCACACCATTACGGTAGTTTg                                                  <  2:939530/149‑1 (MQ=255)
                                                                                                      tGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAACCGCTTTGCCATATCCTGATCATGATAGGGCACACCATTACGGTATTTTGGAtt                                              >  1:738384/1‑149 (MQ=255)
                                                                                                             tatgtgctgcCGCATGACGCTGGCTGTCGCGCGTTGCGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTGGACATCGGTTTGATGAAACCGCTTTGCCATATCCTGATCATGATAGGGCACACCATTACGGTCGTTTCGATTGTgcagc                                       >  2:290560/5‑149 (MQ=255)
                                                                                                               tttGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAACCGCTTTGCCATATCCTGATCATGATAGGGCACACCATTACGGTAGTTTGGATTGTGCCgcca                                     >  1:528866/1‑149 (MQ=255)
                                                                                                                ttGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAACCGCTTTGCCATATCCTGATCATGATAGGGCACACCATTACGGTAGTTTGGATTGTGCCgccat                                    >  2:306041/1‑149 (MQ=255)
                                                                                                                        gccTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAACCGCTTTGCCATATCCTGATCATGATAGGGCACACCATTACGGTAGATTGGATTGTGCCGCCATGCCATAtt                            >  1:275898/1‑149 (MQ=255)
                                                                                                                        ccctgcggctggctgCCGCGCTTTGGTGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAACCGCTTTGCCATATCCTGATCATGATAGGGCACACCATTACGGTAGTTTGGATTGTGCCGCCATGCCATAtt                            <  2:47683/142‑1 (MQ=255)
                                                                                                                         ccTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAACCGCTTTGCCATATCCTGATCATGATAGGGCACACCATTACGGTAGTTTGGATTGTGCCGCCATGCCATATTc                           <  1:543318/149‑1 (MQ=255)
                                                                                                                           tGACGCTGGCTGTCGCGCGTTGGGGTAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAACCGCTTTGCCATATCCTGATCATGATAGGGCACACCATTACGGTAGTTTGGATTGTGCCGCCATGCCATATTCtt                         <  1:193331/149‑1 (MQ=255)
                                                                                                                           tGACACTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAACCGCTTTGCCATATCCTGATCATGATAGGGCACACCATTACGGTAGTTTGGATTGTGCCGCCATGCCATATTCtt                         >  2:764018/1‑149 (MQ=255)
                                                                                                                              cGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAACCGCTTTg                                                                                            >  1:127539/1‑79 (MQ=255)
                                                                                                                              cGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAACCGCTTTg                                                                                            <  2:127539/79‑1 (MQ=255)
                                                                                                                                                  ggCAGGGAATGGCGTGGCGCTCATTCCGCCGTTGACATCGGGTTGGGGAAACCGCTTTGCCATATCCTGATCATGATAGGGCACACCATTACGGTAGTTTGGATTGTGCCGCCATGCCATATTCTTATCAGTAAGATGCTCACCGGTGa  <  1:79825/149‑1 (MQ=255)
                                                                                                                                                    |                                                                                                                                                  
AAGTCGTCATAGCTCCCATAGTGTTCAGCTTCATTAAACCGCTGTGCCGCTGCCTGACGTTGGGTATCTCGTGTAATGACTGGTGCGGCGTGTGTTCGTTGCTGAAACTGATTTGCTGCCGCCTGACGCTGGCTGTCGCGCGTTGGGGCAGGTAATTGCGTGGCGCTCATTCCGCCGTTGACATCGGTTTGATGAAACCGCTTTGCCATATCCTGATCATGATAGGGCACACCATTACGGTAGTTTGGATTGTGCCGCCATGCCATATTCTTATCAGTAAGATGCTCACCGGTGA  >  NC_000913_3_pae_pgi/129924‑130218

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑