Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,399,366 A→T 8.6% N60I (AAC→ATC) ‡ PP_4743 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,399,3660AT 8.6% 164.7 / 6.0 58N60I (AAC→ATC) ‡PP_4743hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (29/24);  new base T (2/3);  total (31/27)
Fisher's exact test for biased strand distribution p-value = 6.56e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.53e-01

TAAAGCCAAACAATTCATCTGCAAAAAGCTAGGCATAAATAATCTCGGAATAACTAAGCCAGGAGGAAGAGGACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGTTAGCAGAGGGCTATTTTTCCTTGGAGGATCGCTACACCTTGTAT  >  NC_002947/5399220‑5399511
                                                                                                                                                  |                                                                                                                                                 
tAAAGCCAAACAATTCATCTGCAAAAAGCTAGGCATAAATAATCTCGGAATAACTAAGCCAGGAGGAAGAGGACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAAc                                                                                                                                                  >  3:316692/1‑148 (MQ=255)
  aaGCCAAACAATTCATCTGCAAAAAGCTAGGCATAAATAATCTCGGAATAACTAAGCCAGGAGGAAGAGGACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACaa                                                                                                                                                <  6:84829/148‑1 (MQ=255)
     ccATACAATTCATCTGCAAAAAGCTAGTCATAAATAATCTGGGAATAACTAAGCCAGCTGGAAGAGGACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGTAACAACTACAACATCATTAACAatga                                                                                                                                             <  6:171554/148‑1 (MQ=255)
         aCAATTCATCTGCAAAAAGCTAGGCATAAATAATCTCGGAATAACTAAGCCAGGAGGAAGAGGACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATgaga                                                                                                                                        <  3:243649/149‑1 (MQ=255)
           aaTTCATCTGCAAAAAGCTAGGCATAAATAATCTCGGAATAACTAAGCCAGGAGGAAGAGGACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACt                                                                                                                                      <  6:91019/149‑1 (MQ=255)
             ttCATCTGCAAAAAGCTAGGCATAAATAATCTCGGAATAACTAAGCCAGGAGGAAGAGGACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTGTTAatgatgttgtagt                                                                                                                                    <  6:268544/149‑8 (MQ=255)
                  cTGCAAAAAGCTAGGCATAAATAATCTCGGAATAACTAAGCCAGGAGGAAGAGGACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGc                                                                                                                                >  6:148124/1‑148 (MQ=255)
                          aGCTAGGCATAAATAATCTCGGAATAACTAAGCCAGGAGGAAGAGGACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGaaa                                                                                                                       <  4:316692/149‑1 (MQ=255)
                             tAGGCATAAATAATCTCGGAATAACTAAGCCAGGAGGAAGAGGACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTGTTAatgatgttg                                                                                                                                        >  8:158884/1‑126 (MQ=255)
                             tAGGCATAAATAATCTCGGAATAACTAAGCCAGGAGGAAGAGGACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTGTTAatgatgttg                                                                                                                                        <  7:158884/129‑4 (MQ=255)
                                gCATAAATAATCTCGGAATAACTAAGCCAGGAGGAAGAGGACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCg                                                                                                                 >  1:89804/1‑149 (MQ=255)
                                              ggAATAACTAAGCCAGGAGGAAGAGGACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACCCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGCCAATTACTaaaa                                                                                                    >  5:306025/1‑148 (MQ=255)
                                                aaTACCTAAGCCAGGAGGAAGAGGACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAatat                                                                                                 <  2:317202/149‑1 (MQ=255)
                                                      tAAGCCAGGAGGAAGAGGACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAata                                                                                                  >  6:337179/1‑142 (MQ=255)
                                                      tAAGCCAGGAGGAAGAGGACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAata                                                                                                  <  5:337179/142‑1 (MQ=255)
                                                      tAAGCCAGGAGGAAGAGGACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCtt                                                                                            >  6:326496/1‑148 (MQ=255)
                                                              gaggaAGAGGACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGcag                                                                                    >  4:36447/1‑146 (MQ=255)
                                                                ggaAGAGGACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAat                                                                                                   >  2:300581/1‑131 (MQ=255)
                                                                ggaAGAGGACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAat                                                                                                   <  1:300581/131‑1 (MQ=255)
                                                                    gagTACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAAt                                                                             <  5:148124/149‑1 (MQ=255)
                                                                         cTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGt                                                                        >  4:67400/1‑149 (MQ=255)
                                                                            aCTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAg                                                                     >  5:300626/1‑149 (MQ=255)
                                                                              tCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGc                                                                    >  6:107474/1‑148 (MQ=255)
                                                                              tCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACAACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGc                                                                    >  2:191584/1‑148 (MQ=255)
                                                                                  cccGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCaaga                                                               <  3:141962/149‑1 (MQ=255)
                                                                                  cccGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCaag                                                                >  1:244487/1‑148 (MQ=255)
                                                                                        gTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTg                                                          <  5:107474/148‑1 (MQ=255)
                                                                                        gTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTg                                                          <  1:196532/148‑1 (MQ=255)
                                                                                        gTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTg                                                          <  1:191584/148‑1 (MQ=255)
                                                                                         tAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTgg                                                         >  4:6116/1‑148 (MQ=255)
                                                                                               ttGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCaag                                                                >  4:72961/1‑135 (MQ=255)
                                                                                               ttGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCaag                                                                <  3:72961/135‑1 (MQ=255)
                                                                                                 gAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATgg                                                 <  2:244487/148‑1 (MQ=255)
                                                                                                    cTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGtt                                             <  2:89804/149‑1 (MQ=255)
                                                                                                            cccATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCAAAGAAGCTGGTAACATGGCGTTAGCAGAgg                                     >  5:77058/1‑149 (MQ=255)
                                                                                                             ccATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGTTAGCAGAggg                                    >  6:258477/1‑149 (MQ=255)
                                                                                                               aTTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGTTAGCaga                                       >  8:224094/1‑144 (MQ=255)
                                                                                                               aTTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGTTAGCaga                                       <  7:224094/144‑1 (MQ=255)
                                                                                                                        aaaGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATg                                                  <  1:321244/124‑1 (MQ=255)
                                                                                                                        aaaGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATg                                                  >  2:321244/1‑124 (MQ=255)
                                                                                                                          aGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGTTAGCa                                         <  4:46741/131‑1 (MQ=255)
                                                                                                                          aGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGTTAGCa                                         >  3:46741/1‑131 (MQ=255)
                                                                                                                              aaaCAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGTTAGCAGAGGGCTATTTTTCCTTggag                    >  5:187545/1‑148 (MQ=255)
                                                                                                                              aaaCAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGTTAGCAGAGGGCTATTTTTCCTTggag                    >  7:112449/1‑148 (MQ=255)
                                                                                                                              aaaCAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGTTAGCAGAGGGCAATTTTTCCTTggag                    >  3:202081/1‑148 (MQ=255)
                                                                                                                                acaacTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAAc                                                     >  3:72018/1‑113 (MQ=255)
                                                                                                                                acaacTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAAc                                                     <  4:72018/113‑1 (MQ=255)
                                                                                                                                 caacTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGTTAGCAGAGGGCTATTTTTCCTTGGAGGATc                <  5:326496/149‑1 (MQ=255)
                                                                                                                                   acTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGTTAGCAGAGGGCTATTTTTCCTTGGAGGATCGc              <  3:6116/149‑1 (MQ=255)
                                                                                                                                     tACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGTTAGCAGAGGGCTATTTTTCCTTgg                      >  3:219451/1‑139 (MQ=255)
                                                                                                                                     tACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGTTAGCAGAGGGCTATTTTTCCTTgg                      <  4:219451/139‑1 (MQ=255)
                                                                                                                                     tACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGTTAGCAGAGGGCTATTTTTCCTTGGAGGATCGCTa            >  4:281049/1‑149 (MQ=255)
                                                                                                                                       caacaTCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGTTAGCAGAGGGCTATTTTTCCTTGGAGGATCGCTaca          >  7:228464/1‑149 (MQ=255)
                                                                                                                                         tcatcatTGTTAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGTTAGCaga                                       <  7:138316/117‑1 (MQ=255)
                                                                                                                                         tcatcatTGTTAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGTTAGCaga                                       >  8:138316/2‑118 (MQ=255)
                                                                                                                                           atcatTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGTTAGCAGAGGGCTATTTTTCCTTGGAGGATCGCTACACCtt      <  3:67400/149‑1 (MQ=255)
                                                                                                                                            tcatTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGTTAGCAGAGGGCTATTTTTCCTTGGAGGATCGCTACACCTTg     >  6:92577/1‑149 (MQ=255)
                                                                                                                                               ttAACAATGATGAGACTGACCGCTACTGGAAACCAGCGCCCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGTTAGCAGAGGGCTATTTTTCCTTGGAGGATCGCTACACCTTGTAt  >  1:30987/1‑149 (MQ=255)
                                                                                                                                                  |                                                                                                                                                 
TAAAGCCAAACAATTCATCTGCAAAAAGCTAGGCATAAATAATCTCGGAATAACTAAGCCAGGAGGAAGAGGACTAACTCAACCCGTTGTAAAACTTGAACTTAAGCGCCCATTGTACGCAAAGGGAAACAACTACAACATCATTAACAATGATGAGACTGACCGCTACTGGAAACCAGCGGGCATTACTAAAATATTCCTTGACCGCCTAACAAATTGCGTCAGCCAAGAAGCTGGTAACATGGCGTTAGCAGAGGGCTATTTTTCCTTGGAGGATCGCTACACCTTGTAT  >  NC_002947/5399220‑5399511

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: ‑