Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,788,561 C→T 7.2% S25N (AGC→AAC)  PP_3350 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,788,5610CT 7.2% 159.4 / 2.5 55S25N (AGC→AAC) PP_3350hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (26/25);  new base T (2/2);  total (28/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.02e-01

CGAGTTGCAGCCAGGCCGACTCTGACAGCCGATGGTAGCGCAGGCCATCGAAAGGGGCAGTGGCCTTGGCGGGGTCGTCGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATCATCAGAATTTCCCTTCACTTGTTTTTATAATTGTTCTTACAAACTGGATAACTCTGTTAACGATTATTTTT  >  NC_002947/3788415‑3788703
                                                                                                                                                   |                                                                                                                                              
cGAGTTGCAGCCAGGCCGACTCTGACAGCCGATGGTAGCGCAGGCCATCGAAAGGGGCAGTGGCCTTGGCGGGGTCGTCGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTg                                                                                                                                              >  1:335239/1‑149 (MQ=255)
   cttGCAGCCAGGCCGACTCTGACAGCCGATGGTAGCGCACGCCATCGAAAGGGGCAGTGGCCTTGGCGGGGTCGACGAGAAAGCGGTACACCTCGAACCAGCCACGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCATCAAGCCGGCAGGcc                                                                                                                                           >  5:145191/2‑149 (MQ=255)
        ggCCAGGCCGTCTCTGACAGCCGATGGTAGCGCAGGCCATCGAAAGGGGCAGTGGCCTTGGCGGGGTCGTCGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTa                                                                                                                                      <  7:211406/148‑1 (MQ=255)
           cAGGCCGACTCTGACAGCCGATGGTAGCGCAGGCCATCGAAAGGGGCAGTGGCCTTGGCGGGGTCGTCGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGc                                                                                                                                   <  5:296810/149‑1 (MQ=255)
            aGGCCGACTCTGACAGCCGATGGTAGCGCAGGCCATCGAAAGGGGCAGTGGCCTTGGCGGGGTCGTCGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCg                                                                                                                                  <  7:11329/149‑1 (MQ=255)
             ggCCGACTCTGACAGCCGATGGTAGCGCAGGCCATCGAAAGGGGCAGTGGCCTTGGCGGGGTCGTCGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCgg                                                                                                                                 <  6:321965/149‑1 (MQ=255)
                cGACTCTGACAGCCGATGGTAGCGCAGGCCATCGAAAGGGGCAGTGGCCTTGGCGGGGTCGTCGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAAt                                                                                                                              >  3:120531/1‑149 (MQ=255)
                  aCTCTGACCGCCGATGGTAGCGCAGGCCAGCTAAAGGGGCAGTGGCCTTGGCGGGGTCGTCGAGAAAGCGGTAGGCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGTCTCTCTTCAAGCGGTCTGGCCGCGTAGGCGGAATgg                                                                                                                            <  6:134164/149‑1 (MQ=255)
                            ccGATGGTAGCGCAGGCCATCGAAAGGGGCAGTGGCCTTGGCGGGGTCGTCGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGa                                                                                                                    >  3:315704/1‑147 (MQ=255)
                                   tAGCGCAGGCCATCGAAAGGGGCAGTGGCCTTGGCGGGGTCGTCGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCAt                                                                                                           <  2:335239/149‑1 (MQ=255)
                                       gcAGGCCATCGAAAGGGGCAGTGGCCTTGGCGGGGTCGTCGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGTAATGGCACAGCGAAAGCACCATGAgg                                                                                                       <  1:274028/149‑1 (MQ=255)
                                           gCCATCGAAAGGGGCAGTGGCCTTGGCGGGGTCGTCGAGAAAGCGGTAGTCCTCGATCCAGTGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCg                                                                                                                     <  8:140258/131‑1 (MQ=255)
                                           gCCATCGAAAGGGGCAGTGGCCTTGGCGGGGTCGTCGAGAAAGCGGTAGTCCTCGATCCAGTGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCg                                                                                                                     >  7:140258/1‑131 (MQ=255)
                                             cATCGAAAGGGGCAGTGGCCTTGGCGGGGTCGTCGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGggcagg                                                                                                 >  4:258411/1‑149 (MQ=255)
                                                cGAAAGGGGCAGTGGCCTTGGCGGGGTCGTCGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGggcaggca                                                                                               >  4:56838/1‑148 (MQ=255)
                                                      gggCAGTGGCCTTGGCGGGGTCGTCGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCg                                                                                        >  4:105549/1‑149 (MQ=255)
                                                       ggCAGTGGCCTTGGCGGGGTCGTCGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGt                                                                                       <  1:61834/149‑1 (MQ=255)
                                                        gCAGTGGCCTTGGCGGGGTCGTCGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGtt                                                                                      >  2:290027/1‑149 (MQ=255)
                                                                cTTGGCGGGGTCGTCGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCt                                                                              <  1:321702/149‑1 (MQ=255)
                                                                   ggCGGGGTCGTCGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGa                                                                           >  5:306736/1‑149 (MQ=255)
                                                                     cGGGGTCGTCGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGatg                                                                         <  4:120531/149‑2 (MQ=255)
                                                                      ggggTCGTCGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGatga                                                                        >  2:258442/1‑147 (MQ=255)
                                                                      ggggTCGTCGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGatga                                                                        >  3:71115/1‑147 (MQ=255)
                                                                         gtcgtcGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGAtgatca                                                                     <  3:56838/149‑1 (MQ=255)
                                                                            gtcgAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATGATCAGaa                                                                  >  8:269650/1‑149 (MQ=255)
                                                                             tcgAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAg                                                                                                        <  3:317095/110‑1 (MQ=255)
                                                                             tcgAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAg                                                                                                        >  4:317095/1‑110 (MQ=255)
                                                                                    aggggTAGTCCTCGAGCGAGCGAGGGGCCCCTGGCCT‑CCGCGGCGGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGGGAAAGGACGTTGTGGGGCAGGCTTACCCCGTTCTACGGCTTGATGATCTGAATTTCGCtt                                                          <  6:145191/146‑1 (MQ=255)
                                                                                    aGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATGATCAGAATTTCCCtt                                                          <  7:269650/149‑1 (MQ=255)
                                                                                    aGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATGATCAGAATTTCCCtt                                                          <  6:306736/149‑1 (MQ=255)
                                                                                      cGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCAt                                                                                                           >  6:250044/1‑98 (MQ=255)
                                                                                      cGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCAt                                                                                                           <  5:250044/98‑1 (MQ=255)
                                                                                              cTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATGATCAGAATTTcc                                                             <  1:187110/136‑1 (MQ=255)
                                                                                              cTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATGATCAGAATTTcc                                                             >  2:187110/1‑136 (MQ=255)
                                                                                              cTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATGATCAGAATTTCCCTTCACTTGtttt                                                >  1:167639/1‑149 (MQ=255)
                                                                                               tCGATCCAGCGAGGGGCCCCTGGCCTGCCCCGGCCGGCTCTCTTCAAGCGGGTTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCATCGGCTTGa                                                                           >  1:2696/1‑122 (MQ=255)
                                                                                               tCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGTTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCATCGGCTTGa                                                                           <  2:2696/121‑1 (MQ=255)
                                                                                               tCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGTTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGa                                                                           <  2:112539/121‑1 (MQ=255)
                                                                                               tCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGTTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGa                                                                           >  1:112539/1‑121 (MQ=255)
                                                                                                   tCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATGATCAGAATTTCCCTTCACTTGTTTTTATaa                                           <  2:167639/149‑1 (MQ=255)
                                                                                                      aGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATGATCAGAATTTCCCTTCACTTGTTTTTATAATTg                                        >  4:27775/1‑149 (MQ=255)
                                                                                                       gCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATGATCAGAATTTCCCTTCACTTGTTTTTATAATTGt                                       >  1:323888/1‑149 (MQ=255)
                                                                                                          aGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATGATCAGAATTTCCCTTCACTTGTTTTTATAATTGTTCt                                    <  1:290027/149‑1 (MQ=255)
                                                                                                            gggCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATGATCAGAATTTCCCTTCACTTGTTTTTATAATTGTTCtt                                   >  8:263551/1‑148 (MQ=255)
                                                                                                            gggCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATGATCAGAATTTCCCTTCACTTGTTTTTATAATTGTTCTTa                                  <  3:258411/149‑1 (MQ=255)
                                                                                                            gggCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGACTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATGATCAGAATTTCCCTTCACTTGTTTTTATAATTGTTCtt                                   >  6:335345/1‑148 (MQ=255)
                                                                                                               ccccTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACAATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATGATCAGCATTTCCCTTCACTTGTTTTTATAATTGGTCTTACa                                >  1:215758/1‑148 (MQ=255)
                                                                                                                  cTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGTATACCCCGTTCAACGGCTTGATGATCAGAATTTCCCTTCACTTGTTTTTATAATTGTTCTTACAAACt                            <  4:315704/149‑1 (MQ=255)
                                                                                                                      ccT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATGATCAGAATTTCCCTTCACTTGTTTTTATAATTGTTCTTACAAACTGGa                         >  7:131806/1‑148 (MQ=255)
                                                                                                                           cccGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATGATCAGAATTTCCCTTCACTTGTTTTTATAATTGTTCTTACAAACTGGAt                        >  6:133327/1‑145 (MQ=255)
                                                                                                                           cccGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATGATCAGAATTTCCCTTCACTTGTTTTTATAATTGTTCTTACAAACTGGAt                        <  5:133327/145‑1 (MQ=255)
                                                                                                                           cccGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATGATCAGAATTTCCCTTCACTTGTTTTTATAATTGTTCTTACAAACTGGATAAct                    >  3:25502/1‑149 (MQ=255)
                                                                                                                                       tctTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATGATCAGAATTTCCCTTCACTTGTTTTTATAATTGTTCTTACAAACTGGATAACTCTGTTAACGat         >  5:183850/1‑148 (MQ=255)
                                                                                                                                             aGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATGATCAGAATTTCCCTTCACTTGTTTTTATAATTGTTCTTACAAACTGGATAACTCTGTTAACGATTAttttt  <  7:263551/149‑1 (MQ=255)
                                                                                                                                             aGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATGATCAGAATTTCCCTTCACTTGTTTTTATAATTGTTCTTACAAACTGGATAACTCTGTTAACGATTAttttt  <  3:27775/149‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                              
CGAGTTGCAGCCAGGCCGACTCTGACAGCCGATGGTAGCGCAGGCCATCGAAAGGGGCAGTGGCCTTGGCGGGGTCGTCGAGAAAGCGGTAGTCCTCGATCCAGCGAGGGGCCCCTGGCCT‑CCCCGGCCGGCTCTCTTCAAGCGGGCTGGCCGCGTAGGCGGAATGGCACAGCGAAAGCACCATGAGGGGCAGGCATACCCCGTTCAACGGCTTGATCATCAGAATTTCCCTTCACTTGTTTTTATAATTGTTCTTACAAACTGGATAACTCTGTTAACGATTATTTTT  >  NC_002947/3788415‑3788703

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: ‑