Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,246,443 A→T 9.3% Q233L (CAG→CTG)  PP_2841 → site‑specific recombinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,246,4430AT 9.3% 119.8 / 2.4 43Q233L (CAG→CTG) PP_2841site‑specific recombinase
Reads supporting (aligned to +/- strand):  ref base A (21/18);  new base T (2/2);  total (23/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

TTGAACTGCGCCGCCAGGACCTGCCTGCCGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGACCACGGCCATCTATGACCGGCGTGATGACAAC  >  NC_002947/3246302‑3246588
                                                                                                                                             |                                                                                                                                                  
ttGAACTGCGCCGCCAGGACCTGCCTGCCGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTgggg                                                                                                                                             >  6:264285/1‑149 (MQ=255)
   aaCTGCGCCGCCAGGACCTGCCTGCCGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTg                                                                                                                                          <  1:189433/149‑1 (MQ=255)
         gccgccAGGACCTGCCTGCCGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATc                                                                                                                                    <  7:74074/149‑1 (MQ=255)
          ccgccAGGACCTGCCTGCCGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAg                                                                                                                                                   <  6:24947/133‑1 (MQ=255)
          ccgccAGGACCTGCCTGCCGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAg                                                                                                                                                   >  5:24947/1‑133 (MQ=255)
            gccAGGACCTGCCTGCCGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑g                                                                                                                                >  5:113126/1‑149 (MQ=255)
                    ctgcctgcCGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGa                                                                                                                        >  2:228037/1‑149 (MQ=255)
                      gcctgccGGCGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCAATACAAAGCATGCGATCTACTACATTGCCAGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGAtt                                                                                                                      >  4:300547/1‑149 (MQ=255)
                         tgccGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGAGTGAAGATCAT‑GCCGCACGATTTTc                                                                                                                   >  4:119791/1‑149 (MQ=255)
                         tgccGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCAGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTc                                                                                                                   >  5:212489/1‑149 (MQ=255)
                                         gACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTAc                                                                                                   >  3:10323/1‑149 (MQ=255)
                                            ccGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCTGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCg                                                                                                >  7:297716/1‑149 (MQ=255)
                                            ccGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCg                                                                                                >  1:284152/1‑149 (MQ=255)
                                            ccGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCg                                                                                                >  1:59935/1‑149 (MQ=255)
                                                       cAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGaa                                                                                      <  5:236657/148‑1 (MQ=255)
                                                         aCCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATAGCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAaga                                                                                    <  1:231931/149‑1 (MQ=255)
                                                                         cAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTc                                                                        <  5:253376/144‑1 (MQ=255)
                                                                         cAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTc                                                                        >  6:253376/1‑144 (MQ=255)
                                                                          aaCCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTgc                                                                  <  2:66037/149‑1 (MQ=255)
                                                                          aaCCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTgc                                                                  >  4:161394/1‑149 (MQ=255)
                                                                           aCCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCGTTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTgcg                                                                 <  2:193899/149‑1 (MQ=255)
                                                                           aCCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTgcg                                                                 <  3:161394/149‑1 (MQ=255)
                                                                              acaTTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAg                                                              <  6:113126/149‑1 (MQ=255)
                                                                                     ccGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTgg                                                       >  1:679/1‑149 (MQ=255)
                                                                                     ccGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTgg                                                       <  2:59935/149‑1 (MQ=255)
                                                                                                  aCCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCaa                                          >  2:260865/1‑149 (MQ=255)
                                                                                                   ccAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCaa                                          <  3:298822/148‑1 (MQ=255)
                                                                                                     aaGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAata                                        >  5:187530/1‑148 (MQ=255)
                                                                                                     aaGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAata                                        <  6:187530/148‑1 (MQ=255)
                                                                                                      cgCATGCGATCTACTACATTGCCCGCCAGCCCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCTCGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATc                                      <  2:295619/148‑1 (MQ=255)
                                                                                                         aTGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAg                                   <  2:284152/149‑1 (MQ=255)
                                                                                                          tGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGa                                  >  1:60386/1‑149 (MQ=255)
                                                                                                             gATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTGCTCAGCAGCTGGCGCACCATGACAATATCCAGACCa                               >  7:281843/1‑149 (MQ=255)
                                                                                                                   ctacATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGACCACgg                            <  8:297716/146‑1 (MQ=255)
                                                                                                                       aTTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGACCACGGCCATCTa                     <  2:60386/149‑1 (MQ=255)
                                                                                                                        ttGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCCGACCACGGCCATCTAt                    <  1:228037/149‑1 (MQ=255)
                                                                                                                                ctgcgcgccgcgCTGGCGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGACCACGGCCATCTATGACCGGCg            >  1:24743/3‑149 (MQ=255)
                                                                                                                                ctgcgcgccgcgCTGGCCGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATAGCGCAGAAGCTGGCGCACCATGCCAATATCCAGACAACGGCCATCTATGACCGGCg            >  7:42561/3‑149 (MQ=255)
                                                                                                                                    gcggcgcgCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGACCACGGCCATCTATGACCGGCGtgat        >  4:130344/1‑149 (MQ=255)
                                                                                                                                       gcgcgcAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGACCACGGCCATCTATGACCGGCGtgatta      >  8:259683/1‑146 (MQ=255)
                                                                                                                                          cgcTGGCGGGGGTGAAGATCAT‑GCCGCACGATTTTGGCCGTGCTTTGATTACCCGGGTGATCGAAGAGCACGAGCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGACCACGGCGATCTTTGACGGGCGTGATGACAAc  <  8:42561/149‑1 (MQ=255)
                                                                                                                                          cgcTGGCGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGACCACGGCCATCTATGACCGGCGTGATGACAAc  <  2:24743/149‑1 (MQ=255)
                                                                                                                                          cgcAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGACCACGGCCATCTATGACCGGCGTGATGACAAc  >  4:42589/1‑149 (MQ=255)
                                                                                                                                             |                                                                                                                                                  
TTGAACTGCGCCGCCAGGACCTGCCTGCCGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCAT‑GCCGCACGATTTTCGCCGGGCATTCATTACCCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGACCACGGCCATCTATGACCGGCGTGATGACAAC  >  NC_002947/3246302‑3246588

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑