Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 2,851,857 C→T 9.1% A469V (GCG→GTG)  mutS → methyl‑directed mismatch repair protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092732,851,8570CT 9.1% 116.5 / 2.1 44A469V (GCG→GTG) mutSmethyl‑directed mismatch repair protein
Reads supporting (aligned to +/- strand):  ref base C (21/18);  new base T (2/2);  total (24/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.17e-01

CGACGGTGGTGTTATCGCATCGGGCTATAACGAAGAGCTGGATGAGTGGCGCGCGCTGGCTGACGGCGCGACCGATTATCTGGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTACATGCGTCGCCAGACGCTGAAAAACGCCGAGCGCTACATCATTCCAGAGCTAAAAGAGTACGAAGATAAAGTTCTCACCTC  >  CP009273/2851711‑2851998
                                                                                                                                                  |                                                                                                                                             
cgACGGTGGTGTTATCGCATCGGGCTATAACGAAGAGCTGGATGAGTGGCGCGCGCTGGCTGACGGCGCGACAGATTATCTGGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCgg                                                                                                                                             <  2:430102/149‑1 (MQ=255)
  aCGGTGGTGTTATCGCATCGGGCTATAACGAAGAGCTGGATGAGTGGCGCGCGCTGGCTGACGGCGCGACCGATTATCTGGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGTCTGGACACGCTGAAAGTTGGCTTTTATGCGGTg                                                                                                                                           <  2:317568/149‑1 (MQ=255)
            tATCGCATCGGGCCATAACGAAGAGCTGGAAGAGTGGCGCGAGCTGGCCGCCGGCGCGACCGATTATCTGGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGctact                                                                                                                                 <  2:42370/149‑1 (MQ=255)
               cGCATCGGGCTATAACGAAGAGCTGGATGAGTGGCGCGCGCTGGCTGACGGCGCGACCGATTATCTGGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTCTAATTCGGTGCActatc                                                                                                                                    <  1:336543/143‑5 (MQ=255)
                gCATCGGGCTATAACGAAGAGCTGGATGAGTGGCGCGCGCTGGCTGACGGCGCGACCGATTATCTGGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGTGGTGCACGGCTACTACAt                                                                                                                             >  2:308187/1‑149 (MQ=255)
                gCATCGGGCTATAACGAAGAGCTGGATGAGTGGCGCGCGCTGGCTGACGGCGCGACCGAATATCTGGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCGGAAAGTTGGCTTTAATGTGGTGCACGGCTACTACAt                                                                                                                             >  2:308174/1‑149 (MQ=255)
                   tCGGGCTATAACGAAGGGCGGGATGGGTGGCGGGCGCTGGCTGACGGCGCGGCCGATTATCTGGGGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGctacta                                                                                                                                <  1:10748/143‑1 (MQ=255)
                    cGGGCTATAACGAAGAGCTGGATGAGTGGCGCGCGCTGGCTGACGGCGCGACCGATTATCTGGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCtactac                                                                                                                               >  1:169465/1‑143 (MQ=255)
                         tataACGAAGAGCTGGATGAGTGGCGCGCGCTGGCTGACGGCGCGACCGATTATCTGGAGCGTCTGGAACTCCGCGAGCGTGAACGTACCGCCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCa                                                                                                                          >  1:346682/1‑143 (MQ=255)
                               gAAGAGCTGGATGAGTGGCGCGCGCTGGCTGACGGCGCGACCGATTATCTGGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAg                                                                                                                    >  1:49740/1‑143 (MQ=255)
                               gAAGAGCTGGATGAGTGGCGCGCGCTGGCTGACGGCGCGACCGATTATCTGGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGttg                                                                                                              >  2:402273/1‑147 (MQ=255)
                               gAAGAGCTGGATGAGTGGCGCGCGCTGGCTGACGGCGACACCGATTATCTGGAGCGTCTGGAAGTCCGCGAGCGTGCTCGTACCGGCCTGGGCGCGGTGTAAGCTGGCTGTAAGGGGGTGTACGCCTACCTCCTTCaactgaa                                                                                                                    >  1:83422/1‑138 (MQ=255)
                                    gCTGGATGAGTGGCGCGCGCTGGCTGGCGGCGCGACCGATTATCTGGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCaaa                                                                                                         <  2:242130/149‑1 (MQ=255)
                                        gATGAGTGGCGCGCGCTGGCTGACGGCGCGACCGATTATCTGGAGCGTCTGGAAGTCCGCGGACGTGAACGTACAGGCCTGGACACGAGGAAAGTTGGCGTTAATGCGGTGCACGGCACCTACATTCAAATCAGCCGTGGGCa                                                                                                           >  1:215850/1‑143 (MQ=255)
                                        gATGAGTGGCGCGCGCTGGCTGACGGCGCGACCGAGTATCTGGAGCGACTGGAAGTGCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCa                                                                                                     >  2:18292/1‑149 (MQ=255)
                                              tGGCGCGCGCTGGCTGACGGCGCGACCGATTATCTGGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGc                                                                                               >  2:388973/1‑149 (MQ=255)
                                               gccgcgcgcTGGCGGACGGCGCGACCGATTATCTGGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTCCATTCAAATTAGCCGTGGGCAAAGCCATCTGGCa                                                                                              <  2:218946/147‑1 (MQ=255)
                                                     cgcTGGCTGACGGCGCGACCGATTATCTGGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGTCACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCa                                                                                              <  1:29935/143‑1 (MQ=255)
                                                      gctggcggACGGCGCGACCGATTATCTGGGGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCAc                                                                                             <  1:122924/143‑1 (MQ=255)
                                                       ctggccgACGGCGCGACCTATTATCTGGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCaa                                                                                      <  2:151479/149‑1 (MQ=255)
                                                          gctgACGGCGCGACCGATTATCTGGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCAt                                                                                         >  1:65235/1‑143 (MQ=255)
                                                          gcggACGGCACTACCTATGTTCTGGAGCGTCTGGAAGCCCGCGTGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTTAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTa                                                                                   <  2:56307/146‑1 (MQ=255)
                                                            tgACGGCGCGACCGATTATCTGGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTACa                                                                                 >  2:324991/1‑149 (MQ=255)
                                                               cgtcgcgACCGATTATCTCGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAAATACATGc                                                                              <  2:432423/146‑1 (MQ=255)
                                                                  cgcgACCGATTATCTGGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTCCATGCGTc                                                                           >  2:350972/1‑149 (MQ=255)
                                                                              tCTGGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTACATGCGTCGCCAGa                                                                     >  1:187100/1‑143 (MQ=255)
                                                                                    gCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCACCTGGCACCCATCAACTACATGCGTCGCCAGACGCCGa                                                               >  1:360101/1‑143 (MQ=255)
                                                                                    gCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGGGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTACATGCGCCGCCAGACGCTGa                                                               >  1:359396/1‑143 (MQ=255)
                                                                                          ggAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTACATGCGTCGCCAGACGCTGAAAAACGCCGAgc                                                   <  2:53797/149‑1 (MQ=255)
                                                                                                 cgcgAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTACATGCGTCGCCAGACGCTGAAAAACGCCGAgcg                                                  <  1:15712/143‑1 (MQ=255)
                                                                                                 cgcgAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTACATGCGTCGCCAGACGCTGAAAAACGCCGAgcg                                                  >  1:147475/1‑143 (MQ=255)
                                                                                                           aaCGTACCGGTCTGGACACGCTGACAGTTCGCTTTAATGCGGTGCACGGCTACTACACTCAAATCAGCCGTGGGCAAAGCTATCTGGCACCCCTCAACTACATGCGTCGCCAGACGCTGAAAAACGCCGAGCGCTACATCATTCCagag                                  <  2:177566/149‑1 (MQ=255)
                                                                                                           aaCGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTACATGCGTCGCCAGACGCTGAAAAACGCCGAGCGCTACATCATTCCagag                                  <  2:201472/149‑1 (MQ=255)
                                                                                                                  cGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTACATGCGTCGCCAGACGCTGACAAACGCCGAGCGCTACATCATTCCAGAGCTAAAag                           >  2:382868/1‑149 (MQ=255)
                                                                                                                    gCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTACATGCGTCGCCAGACGCTGAAAAACGCCGAGCGCTACATCATTCCCGAGCTa                               >  1:327107/1‑143 (MQ=255)
                                                                                                                      cTGGACACGCTGAAAGTTGGCTTTAATGTGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTACATGCGTCGCCAGACGCTGAAAAACGCCGAGCGCTACATCATTCCAGAGCTaaa                             <  1:273079/143‑1 (MQ=255)
                                                                                                                      cTGGACACGCTGAAAGTTGGCTTTAATGTGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTACATGCGTCGCCAGACGCTGAAAAACGCCGAGCGCTACATCATTCCAGAGCTaaa                             <  1:273067/143‑1 (MQ=255)
                                                                                                                           cacGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTACATGCGTCGCCAGACGCTGAAAAACGCCGAGCGCTACATCATTCCAGAGCTAAAAGAGt                        <  1:146492/143‑1 (MQ=255)
                                                                                                                              gCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTACATGCGTCGCCAGACGCTGAAAAACGCCGAGCGCTACATCATTCCAGAGCTAAAAGAGTACGAAGATa               >  2:247215/1‑149 (MQ=255)
                                                                                                                                 gAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTACATGCGTCGCCAGACGCTGAAACACGCCGAGCGCTACATCATTCCAGAGCTAAAAGAGTACAAAg                  >  1:49608/1‑143 (MQ=255)
                                                                                                                                 gAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTACATGCGTCGCCAGACGCTGAAAAACGCCGAGCGCTACATCATTCCAGAGCTAAAAGAGTACGAAg                  >  1:362076/1‑143 (MQ=255)
                                                                                                                                          cTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTACATGCGTCGCCAGACGCTGAAAAACGCCGAGCGCTACATCATTCCAGAGCTAAAAGAGTACGAAGATAAAGTtc         >  1:315926/1‑143 (MQ=255)
                                                                                                                                           tttAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTACATGCGTCGCCAGACGCTGAAAAACGCCGAGCGCTACATCATTCCAGAGCTAAAAGAGTACGAAGATAAAGTTCTCACCTc  >  2:140050/1‑149 (MQ=255)
                                                                                                                                              aaTGCGGTGCACGGTCACTACAGTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTACATGCGTCGCCAGACGCTGAAAAACGCCGAGCGCTACATCATTCCAGAGCTAAAAGAGTACGAAGATAAAGTTCTCAc     <  1:289245/143‑1 (MQ=255)
                                                                                                                                                  |                                                                                                                                             
CGACGGTGGTGTTATCGCATCGGGCTATAACGAAGAGCTGGATGAGTGGCGCGCGCTGGCTGACGGCGCGACCGATTATCTGGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTTTAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTACATGCGTCGCCAGACGCTGAAAAACGCCGAGCGCTACATCATTCCAGAGCTAAAAGAGTACGAAGATAAAGTTCTCACCTC  >  CP009273/2851711‑2851998

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑