Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,459,983 T→A 9.6% D141V (GAC→GTC)  PP_3075 ← transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,459,9830TA 9.6% 155.1 / 7.6 52D141V (GAC→GTC) PP_3075transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (20/27);  new base A (2/3);  total (22/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.18e-01

GCTTCCAGGCTGGGCGCGCTGCTGCCGACGAACTGGGCGAAGCTGTATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGACCACCAACGGCTCGTTCGGCGTGTCGAGCATGTCCAGCAGGATGGGCCGGCCATTGCTCACCACATCGCGCATCAG  >  NC_002947/3459839‑3460125
                                                                                                                                                |                                                                                                                                              
gCTTCCAGGCTGGGCGCGCTGCTGCCGACGAACTGGGCGAAGCTGTATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCTGTTCGACGAAc                                                                                                                                           >  2:66420/1‑150 (MQ=255)
gCTTCCAGGCTGGGCGCGCTGCTGCCGACGAACTGGGCGAAGCTGTATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTACTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAAc                                                                                                                                           >  1:9396/1‑150 (MQ=255)
  ttCCAGGCTGGGCGCGCTGCTGCCGACGAACTGGGCGAAGCTGTATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGacaca                                                                                                                                         >  2:520095/1‑146 (MQ=255)
    ccAGGCTGGGCGCGCTGCTGCCGACGAACTGGGCGAAGCTGTATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAgcg                                                                                                                                       <  2:623753/150‑1 (MQ=255)
      aGGCTGGGCGCGCTGCTGCCGACGAACTGGGCGAAGCTGTATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCTGTTCGACGAACTGCGCa                                                                                                                                     <  1:432570/150‑1 (MQ=255)
      aGGCTGGGCGCGCTGCTGCCGACGAACTGGGCGAAGCTGTATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCTGTTCGACGAACTGCGCa                                                                                                                                     <  1:66420/150‑1 (MQ=255)
             gcgcgcTGCTGCCGACGAACTGGGCGAAGCTGTATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGGGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCaa                                                                                                                              <  1:812017/150‑1 (MQ=255)
               gcgcTGCTGCCGACGAACTGGGCGAAGCTGTATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATg                                                                                                                            >  2:514843/1‑150 (MQ=255)
                cgcTGCTGCCGACGAACTGGGCGAAGCTGTATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATgg                                                                                                                           <  1:156523/150‑1 (MQ=255)
                      tgcCGACGAACTGGGCGAAGCTGTATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGa                                                                                                                     >  1:804040/1‑150 (MQ=255)
                      tgcCGACGAACTGGGCGAAGCTGTATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATACTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGa                                                                                                                     <  2:121981/150‑1 (MQ=255)
                       gcCGACGAACTGGGCGAAGCTGTATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCTGTTCGACGAACTGCGCa                                                                                                                                     <  2:630614/133‑1 (MQ=255)
                       gcCGACGAACTGGGCGAAGCTGTATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCTGTTCGACGAACTGCGCa                                                                                                                                     >  1:630614/1‑133 (MQ=255)
                               aCTGGGCGAAGCTGTATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAgcgcgc                                                                                                            >  2:91555/1‑150 (MQ=255)
                                  gggCGAAGCTGTATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCt                                                                                                         <  2:689628/150‑1 (MQ=255)
                                    gCGAAGCTGTATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTgg                                                                                                       <  1:520095/150‑1 (MQ=255)
                                    gCGAAGCTGTATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTgg                                                                                                       <  1:462951/150‑1 (MQ=255)
                                         gCTGTATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATc                                                                                                  >  1:299518/1‑150 (MQ=255)
                                           tGTATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGt                                                                                                >  2:489954/1‑150 (MQ=255)
                                             tATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTgg                                                                                              >  1:305623/1‑150 (MQ=255)
                                               tttGGCCTGGCGGGCGCGAAGTTGTGCGCGGGTCGAGGCCAGCTGCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGAt                                                                                            <  2:140938/150‑1 (MQ=255)
                                                       ggcgggcgCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGACGTGTGTTAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGgc                                                                                    <  1:650316/150‑1 (MQ=255)
                                                         cgggcgCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGgcgc                                                                                  <  1:317362/150‑1 (MQ=255)
                                                          gggcgCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGATGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCa                                                                                 <  2:652126/150‑1 (MQ=255)
                                                             cgcgcAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGa                                                                              <  1:595111/150‑1 (MQ=255)
                                                              gcgcAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGa                                                                                             >  1:176508/1‑134 (MQ=255)
                                                              gcgcAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGa                                                                                             <  2:176508/134‑1 (MQ=255)
                                                                               tCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGACCACCAACGGCTCGTTCg                                                            >  2:417187/1‑150 (MQ=255)
                                                                                   ggCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGACCACCAACGGCTCGTTCGGCgt                                                        <  1:489954/150‑1 (MQ=255)
                                                                                    gCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGgcgc                                                                                                                        <  2:108463/85‑1 (MQ=255)
                                                                                    gCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGgcgc                                                                                                                        >  1:108463/1‑85 (MQ=255)
                                                                                    gCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCAt                                                                                >  2:159844/1‑125 (MQ=255)
                                                                                    gCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCAt                                                                                <  1:159844/125‑1 (MQ=255)
                                                                                         ttCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGACCACCAACGGCTCGTTCGGCGTGTCGAg                                                  <  2:701524/150‑1 (MQ=255)
                                                                                            ctgctgCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGACCACCAACGGCTCGTTCGGCGTGTCGAGCAt                                               >  1:28993/1‑150 (MQ=255)
                                                                                             tgctgcATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGACCACCAACGGCTCGTTCGGCgtg                                                       <  2:174862/141‑1 (MQ=255)
                                                                                             tgctgcATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGACCACCAACGGCTCGTTCGGCgtg                                                       >  1:174862/1‑141 (MQ=255)
                                                                                             tgctgcATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGACCACCAACGGCTCGTTCGGCGTGTCGAGCATg                                              >  1:844519/1‑150 (MQ=255)
                                                                                              gctgcATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGACCACCAACGGCTCGTTCGGCGTGTCGAGCATGt                                             <  1:91555/150‑1 (MQ=255)
                                                                                                     gCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGACCACCAACGGCTCGTTCGGCGTGTCGAGCATGTCcagcag                                      <  2:851707/150‑1 (MQ=255)
                                                                                                       tGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGACCACCAACGGCTCGTTCGGCGTGTCGAGCATGTCCAGCAggg                                    >  2:476847/1‑149 (MQ=255)
                                                                                                       tGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGACCACCAACGGCTCGTTCGGCGTGTCGAGCATGTCCAGCAGGa                                    >  2:320304/1‑150 (MQ=255)
                                                                                                                       cagcGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGACCACCAACGGCTCGTTCGGCGTGTCGAGCATGTCCAGCAGGATGGGCCGGCCATTGCt                    >  2:388370/1‑150 (MQ=255)
                                                                                                                         gcggcgACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGACCACCAACGGCTCGTTCGGCGTGTCGAGCATGTCCAGCAGGATg                                  <  1:807604/134‑1 (MQ=255)
                                                                                                                         gcggcgACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGACCACCAACGGCTCGTTCGGCGTGTCGAGCATGTCCAGCAGGATg                                  >  2:807604/1‑134 (MQ=255)
                                                                                                                            gcgACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGACCACCAACGGCTCGTTCGGCGTGTCGAGCATGTCCAGCAGGATGGGCCGGCCATTGCTcacca               <  1:388370/150‑1 (MQ=255)
                                                                                                                                       cgcAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGACCACCAACGGCTCGTTCGGCGTGTCGAGCATGTCCAGCAGGATGGGCCGGCCATTGCTCACCACATCGCGCATc    <  1:417187/150‑1 (MQ=255)
                                                                                                                                       cgcAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGACCACCAACGGCTCGTTCGGCGTGTCGAGCATGTCCAGCAGGATGGGCCGGCCATTGCTCACCACATCGCGCATc    <  2:804040/150‑1 (MQ=255)
                                                                                                                                        gcAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGACCACCAACGGCTCGTTCGGCGTGTCGAGCATGTCCAGCAGGATGGGCCGGCCATTGCTCACCACATCGCGCATCa   <  2:299518/150‑1 (MQ=255)
                                                                                                                                         cAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGACCACCAACGGCTCGTTCGGCGTGTCGAGCATGTCCAGCAGGATGGGCCGGCCATTGCTCACCACATCGCGCATCAg  <  2:409815/150‑1 (MQ=255)
                                                                                                                                            ttCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATgg                                                                                          >  2:152296/1‑59 (MQ=255)
                                                                                                                                            ttCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATgg                                                                                          <  1:152296/59‑1 (MQ=255)
                                                                                                                                                |                                                                                                                                              
GCTTCCAGGCTGGGCGCGCTGCTGCCGACGAACTGGGCGAAGCTGTATTTGGCCTGGCGGGCGCGCAGTTGCGAGCGGGTCGAGGCCAGTTCCTGCTGCATGCTGGCGTAGCGCTTGAGCAGCGGCGACAGGCTGCGCAGTTCGTCGAACAGCGCAAAGCCAATGGCGCCGATCAGCGCGCCCTGGTCATCGTGGATGGGCAGGCGCATGACCACCAACGGCTCGTTCGGCGTGTCGAGCATGTCCAGCAGGATGGGCCGGCCATTGCTCACCACATCGCGCATCAG  >  NC_002947/3459839‑3460125

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑