Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,553,637 C→T 8.5% R102C (CGC→TGC)  PP_3138 → VirK domain‑containing protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,553,6370CT 8.5% 129.1 / 2.6 47R102C (CGC→TGC) PP_3138VirK domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base C (19/24);  new base T (2/2);  total (21/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.24e-01

GGTCTGCAGCGGCTGGGTGTGGATTGTATCGGTGTCGTGCAATGGCCTTACATCAGCCGATGCTGGGAGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCA  >  NC_002947/3553490‑3553784
                                                                                                                                                   |                                                                                                                                                   
ggTCTGCAGCGGCTGGGTGTGGATTGTATCGGTGTCGTGCAATGGCCTTACATCAGCCGATGCTGGGAGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGgc                                                                                                                                                     >  6:190697/1‑148 (MQ=255)
ggTCTGCAGCGGCTGGGTGTGGATTGTATCGGTGTCGTGCAATGGCCTTACATCAGCCGATGCTGGGAGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGgc                                                                                                                                                     <  5:190697/148‑1 (MQ=255)
  tCTGCAGCGGCTGGGTGTGGATTGTATCGGTGTCGTGCAATGGCCTTACATCAGCCGATGCTGGGAGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGgcgc                                                                                                                                                   >  2:21752/1‑148 (MQ=255)
      cAGCGGCTGGGTGTGGATTGTATCGGTGTCGTGCAATGGCCTTACATCAGCCGATGCTGGGAGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGcgacg                                                                                                                                               >  5:181507/1‑148 (MQ=255)
            cTGGGTGTGGATTGTATCGGTGTCGTGCAATGGCCTTACATCAGCCGATGCTGGGAGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCt                                                                                                                                        >  1:233637/1‑149 (MQ=255)
              gggTGTGGATTGTATCGGTGTCGTGCAATGGCCTTACATCAGCCGATGCTGGGAGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGa                                                                                                                                      <  1:21752/149‑1 (MQ=255)
                      aTTGTATCGGTGTCGTGCAATGGCCTTACATCAGCCGATGCTGGGAGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCtgtgt                                                                                                                              <  4:210566/149‑1 (MQ=255)
                          tATCGGTGTCGTGCAATGGCCTTACATCAGCCGATGCTGGGAGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGAc                                                                                                                           <  1:188499/148‑1 (MQ=255)
                           aTCGGTGTCGTGCAATGGCCTTACATCAGCCGATGCTGGGAGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGATGCTGTGTGACCt                                                                                                                         >  4:67019/1‑149 (MQ=255)
                               gtgtCGTGCAATGGCCTTACATCAGCCGATGCTGGGAGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTAGAATGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTcc                                                                                                                     <  6:120468/149‑1 (MQ=255)
                                       cAATGGCCTTACATCAGCCGATGCTGGGAGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACt                                                                                                              <  7:179145/148‑1 (MQ=255)
                                          tGGCCTTACATCAGCCGATGCTGGGAGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGATGCTGTGTGACCTGTCCAGCCACTCGcc                                                                                                          <  3:67019/149‑1 (MQ=255)
                                                    tCAGCCGATGCTGGGAGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGc                                                                                                >  4:177630/1‑149 (MQ=255)
                                                     cAGCCGATGCTGGGAGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGcc                                                                                               >  3:184008/1‑149 (MQ=255)
                                                      aGCCGATGCTGGGAGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGTCt                                                                                              <  7:125564/149‑1 (MQ=255)
                                                         cGATGCTGGGAGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGt                                                                                           <  2:233637/149‑1 (MQ=255)
                                                          gATGCTGGGAGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTg                                                                                          <  6:181507/149‑1 (MQ=255)
                                                               tGGGAGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCtta                                                                                                                                      <  7:199357/100‑3 (MQ=255)
                                                               tGGGAGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGa                                                                                                                                      >  8:199357/1‑100 (MQ=255)
                                                                   aGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTCCTGGACCgg                                                                                 >  3:197033/1‑149 (MQ=255)
                                                                      cgcCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGc                                                                                <  3:219040/147‑1 (MQ=255)
                                                                      cgcCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGc                                                                                >  4:219040/1‑147 (MQ=255)
                                                                         cacaGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATc                                                                           <  3:207427/149‑1 (MQ=255)
                                                                            tgCGTCTGGATGTGGTGGCTACGCAGTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTgg                                                                        <  4:197033/148‑1 (MQ=255)
                                                                            aGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTgg                                                                        <  7:186178/149‑1 (MQ=255)
                                                                             gCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGt                                                                       <  3:177630/149‑1 (MQ=255)
                                                                                   ggAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAgc                                                                 >  4:246882/1‑149 (MQ=255)
                                                                                        tggtggCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGcgcg                                                              >  3:63696/1‑147 (MQ=255)
                                                                                          gtggCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGTGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAgg                                                          >  5:78007/1‑149 (MQ=255)
                                                                                          gtggCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGTGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAgg                                                          >  5:82318/1‑149 (MQ=255)
                                                                                          gtggCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGaa                                                            <  3:181128/147‑1 (MQ=255)
                                                                                          gtggCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGaa                                                            >  4:181128/1‑147 (MQ=255)
                                                                                            ggCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGc                                                         >  6:134623/1‑148 (MQ=255)
                                                                                            ggCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGc                                                         >  1:106238/1‑148 (MQ=255)
                                                                                                 cGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGTGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCt                                                    <  6:82318/148‑1 (MQ=255)
                                                                                                 cGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGTGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCt                                                    <  6:78007/148‑1 (MQ=255)
                                                                                                     cTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGc                                               <  5:134623/149‑1 (MQ=255)
                                                                                                      tttGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCt                                              >  2:176617/1‑149 (MQ=255)
                                                                                                          aaCGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGaa                                           <  7:40246/148‑1 (MQ=255)
                                                                                                               gTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGtt                                     <  4:184008/149‑1 (MQ=255)
                                                                                                                tGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTc                                    <  3:246882/149‑1 (MQ=255)
                                                                                                                    tGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCa                                  >  4:115721/1‑147 (MQ=255)
                                                                                                                    tGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCa                                  <  3:115721/147‑1 (MQ=255)
                                                                                                                      ggCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGc                               <  1:176617/148‑1 (MQ=255)
                                                                                                                                ggCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTc                                    <  4:58266/133‑1 (MQ=255)
                                                                                                                                ggCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTc                                    >  3:58266/1‑133 (MQ=255)
                                                                                                                                             ctgGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCgtgt                   >  6:123790/1‑137 (MQ=255)
                                                                                                                                             ctgGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCgtgt                   <  5:123790/137‑1 (MQ=255)
                                                                                                                                              tgGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGcc      >  2:274069/1‑149 (MQ=255)
                                                                                                                                                gggCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGACCCTGTTCCAGGCCGACCTCCGTGTGGCATcccttccctt    >  4:202946/1‑149 (MQ=255)
                                                                                                                                                  gcgcGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCa  >  6:106358/1‑149 (MQ=255)
                                                                                                                                                   |                                                                                                                                                   
GGTCTGCAGCGGCTGGGTGTGGATTGTATCGGTGTCGTGCAATGGCCTTACATCAGCCGATGCTGGGAGGCGCCACAGCGTCTGGAGGTGGTGGCTACGCACTTTGAACGGGTGGCTGGGCAGTTCCCGGCGTTGCTGTTGCTGGGGCGCGACGAAAACCTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCA  >  NC_002947/3553490‑3553784

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑