Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,578,431 T→A 14.0% intergenic (+108/‑216) PP_3158 → / → PP_5589 hypothetical protein/rhs repeat‑associated core domain‑containing protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,578,4310TA14.0% 125.0 / 10.2 50intergenic (+108/‑216)PP_3158/PP_5589hypothetical protein/rhs repeat‑associated core domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base T (17/26);  new base A (5/2);  total (22/28)
Fisher's exact test for biased strand distribution p-value = 2.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

GCAGAGCCTGTTGCTGATGAACTTCCTGCCGGTGCAGTAAGAGGCCTCTGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGATGGCCATTGCTCCGTGTTGAAGTACAATG  >  NC_002947/3578284‑3578575
                                                                                                                                                   |                                                                                                                                                
gcAGAGCCTGTTGCTGATGAACTTCCTGCCGGTGCAGTAAGAGGCCTCTGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCAttttt                                                                                                                                                 <  2:31495/149‑1 (MQ=255)
      ccTGTTGCTGATGAACTTCCTGCCGGTGCAGTAAGAGGCCTCTGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCGTGAGCGAATCAACGTTTCGTCGGGCTTCAAATGGCATTTTTGACAGt                                                                                                                                           >  2:268307/1‑149 (MQ=255)
        tGTTGCTGATGAACTTCCTGCCGGTGCAGTAAGAGGCCTCTGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAAATGGCATTTTTTACAGTTg                                                                                                                                         >  6:127425/1‑149 (MQ=255)
          ttGCTGATGAACTTCCTGCCGGTGCAGTAAGAGGCCTCTGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGc                                                                                                                                               <  7:86490/141‑1 (MQ=255)
          ttGCTGATGAACTTCCTGCCGGTGCAGTAAGAGGCCTCTGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGc                                                                                                                                               >  8:86490/1‑141 (MQ=255)
                atgaACTTCCTGCCGGTGCAGTAAGAGGCCTCTGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAgt                                                                                                                                 <  3:339632/149‑1 (MQ=255)
                  gaACTTCCTGCCGGTGCAGTAAGAGGCCTCTGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCAGTTTTGGCAGTTGGAGCGAgtgt                                                                                                                               >  1:248106/1‑149 (MQ=255)
                    aCTTCCTGCCGGTGCAGTAAGAGGCCTCTGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTAt                                                                                                                             <  7:129518/149‑1 (MQ=255)
                    aCTTCCTGCCGGTGCAGTAAGAGGCCTCTGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGGTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCTGTTGCAGCGAGTGTAt                                                                                                                             <  5:371395/149‑1 (MQ=255)
                     cTTCCTGCCGGTGCAGTAAGAGGCCTCTGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTAt                                                                                                                             >  5:317771/1‑148 (MQ=255)
                      ttCCTGCCGGTGCAGTAAGAGGCCTCTGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGGTGCAACAGGGATTTTTTCCAGGTGGAGCGCTTGTATg                                                                                                                            >  8:301403/1‑148 (MQ=255)
                          tGCCGGTGCAGTAAGAGGCCTCTGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGGAGCGAGTGTATTACacc                                                                                                                       >  2:290503/1‑147 (MQ=255)
                           gCCGGTGCGGTAAGAGGCCTCTGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGcc                                                                                                                      >  5:101163/1‑149 (MQ=255)
                             cGGTGCAGTAAGAGGCCTCTGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAACCTa                                                                                                                    <  1:290503/149‑1 (MQ=255)
                                     tAAGAGGCCTCTGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTc                                                                                                              >  1:69433/1‑147 (MQ=255)
                                      aaGAGGCCTCTGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCaa                                                                                                            <  3:67614/148‑1 (MQ=255)
                                       agagGCCTCTGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAgg                                                                                                          >  7:276250/1‑149 (MQ=255)
                                          ggCCTCTGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGaa                                                                                                       <  1:132185/149‑1 (MQ=255)
                                           gCCTCTGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGaaa                                                                                                      <  6:101163/149‑1 (MQ=255)
                                             ctctGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATg                                                                                                    <  2:285462/149‑1 (MQ=255)
                                             ctctGCCGAACGCCCTTTGCGTAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATg                                                                                                    <  1:314275/149‑1 (MQ=255)
                                                  ccGCACGCCCTTTGAGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGgtg                                                                                                 <  5:328712/147‑1 (MQ=255)
                                                    gCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTtct                                                                                             <  5:127425/149‑1 (MQ=255)
                                                                cGAAATGCCCATACATGAATCAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCAtt                                                                                  <  6:263082/148‑1 (MQ=255)
                                                                         cATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTTGCAGTTGGAGCGAGTGTATGACAGCCTAGAAATGAAGGGAAATGGTGTTATCTAAGGTCATTTATCGTGaa                                                                         >  4:252124/1‑148 (MQ=255)
                                                                          aTACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAAc                                                                       <  5:326048/149‑1 (MQ=255)
                                                                              atgaatgaGGATTGAGTTTATGAGTGTTCGTGAGCGAATCAACGTTTCGTCGGGCTGCAACTTGCATTTTTGACAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTc                                                                   <  1:268307/149‑1 (MQ=255)
                                                                              atgaatgaGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTc                                                                   <  3:252124/149‑1 (MQ=255)
                                                                              atgaatgaGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTc                                                                   <  6:317771/149‑1 (MQ=255)
                                                                                     aGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGc                                                             <  8:276250/148‑1 (MQ=255)
                                                                                      ggATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGt                                                           <  2:69433/149‑1 (MQ=255)
                                                                                               tgatgaGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAAtt                                                                                                               <  7:133332/88‑1 (MQ=255)
                                                                                                            tGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTg                                     <  7:301403/149‑1 (MQ=255)
                                                                                                              cgctaaTCAAGGTTTCGGCGTGCTTCAACTGGCATTTTTGCCTGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGAGCTATTTggg                                   <  2:353546/145‑1 (MQ=255)
                                                                                                               gCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCg                                                                             <  3:220114/106‑1 (MQ=255)
                                                                                                                 gAATCAACGTTTCGTCGGGCTGCAACAGGCATTTTTTGCAGTTGGAGCGAGTGTATGAAAGCCGAGAATTCAAGGGAAATGGTGTTATGTAAGGTGATTTATCGTGAATCGTTGGCAAGCGTACACGCCCCACGGCGGTATTTTGGGTg                                >  4:95393/1‑149 (MQ=255)
                                                                                                                       aCGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGa                               <  3:130743/144‑1 (MQ=255)
                                                                                                                       aCGTTTCGTCGGGCTGCAACAGGCATTTTTTCCAGTTGCAGCGAGTGTATGACAGCCTATAATTAAAGGGAAATGGTGTTATATAAGGTCATTAATAGTGAAACCTTAGCAAACGTAAACCCCCAACGGCGCTAATTTGGGTGAtata                           >  4:130743/1‑145 (MQ=255)
                                                                                                                               actcgCTGCAACTGGCAAAAATGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTggg                                   <  5:75394/128‑1 (MQ=39)
                                                                                                                               actcgCTGCAACTGGCAAAAATGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTggg                                   >  6:75394/5‑132 (MQ=39)
                                                                                                                                  ggCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGATGGCCATTGCTCCgtg               >  8:99714/1‑149 (MQ=255)
                                                                                                                                   gCTGCAACTGGCAAAAATGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGATGGCCATTGCTCCgt                <  1:40365/147‑1 (MQ=255)
                                                                                                                                    cTGCAACTGGCAAAAATGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGATGGCCATTGCTCCGTGtt             >  7:93394/1‑149 (MQ=255)
                                                                                                                                     tGCAACTGGCAAAAATGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGATGGCCATTGCTCCGTGtt             >  6:114124/1‑148 (MQ=255)
                                                                                                                                     tGCAACTGGCAAAAATGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGATGGCCATTGCTCCGTGtt             >  5:163020/1‑148 (MQ=255)
                                                                                                                                       cAACTGGCAAAAATGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGATGGCCATTGCTCCGTGTTg            >  1:317646/1‑147 (MQ=255)
                                                                                                                                        aaCTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCTCAAGCTTACACGCCCTACGGCTCTATTTTGGGTCATGGCCATTGCTCCGTTTTGaat         >  4:5880/1‑148 (MQ=255)
                                                                                                                                        aaCTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTATCTAAGGTAATTAATCTTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGTGTGATGGCCATTGCTCCGTGTTGaa          <  3:312856/148‑1 (MQ=255)
                                                                                                                                           tGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGATGGCCATTGCTCCGTGTTGAAGTa       >  3:179972/1‑148 (MQ=255)
                                                                                                                                           tGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGATGGCCATTGCTCCGTGTTGAAGTa       >  1:76528/1‑148 (MQ=255)
                                                                                                                                               aTTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGATGGCCATTGCTCCGTGTTGAAGTACAATg  <  7:99714/149‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                                
GCAGAGCCTGTTGCTGATGAACTTCCTGCCGGTGCAGTAAGAGGCCTCTGCCGCACGCCCTTTGCGAAATGCCCATACATGAATGAGGATTGAGTTGATGAGTGTTCATGAGCGAATCAACGTTTCGTCGGGCTGCAACTGGCATTTTTGCCAGTTGCAGCGAGTGTATGACAGCCTAGAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGATGGCCATTGCTCCGTGTTGAAGTACAATG  >  NC_002947/3578284‑3578575

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑