Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 2,221,358 A→T 7.7% L90M (TTG→ATG)  PP_1960 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029472,221,3580AT 7.7% 149.0 / 2.8 52L90M (TTG→ATG) PP_1960hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (23/25);  new base T (2/2);  total (25/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.50e-01

TCAACATTCGATTTATACCCTTTAATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCGGTATAACATGCTTATGATGCTGGAGTAGCGCGAAGACGTCCGAAGGGAGGCTCGGGCCGTGTCGTGAAGAAAA  >  NC_002947/2221213‑2221506
                                                                                                                                                 |                                                                                                                                                    
tcAACATTCGATTTATACCCTTTAATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTc                                                                                                                                                   >  1:76957/1‑149 (MQ=255)
     aTTCGATTTATACCCTTTAATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGt                                                                                                                                              >  7:61272/1‑149 (MQ=255)
         gATTTATACCCTTTAATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTc                                                                                                                                          <  2:291305/149‑1 (MQ=255)
                  ccTTTAATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGt                                                                                                                                              >  4:193793/1‑136 (MQ=255)
                  ccTTTAATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGt                                                                                                                                              <  3:193793/136‑1 (MQ=255)
                      tAATGTTCAACCAGTGAAAATAGTTGAGGATAATGTTTAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGt                                                                                                                               <  1:78441/147‑1 (MQ=255)
                       aaTGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGa                                                                                                                             >  1:319902/1‑148 (MQ=255)
                          gTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATAtt                                                                                                                         >  3:26931/1‑149 (MQ=255)
                              aaCCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTg                                                                                                                              >  8:153027/1‑140 (MQ=255)
                              aaCCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTg                                                                                                                              <  7:153027/140‑1 (MQ=255)
                              aaCCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATtgtg                                                                                                                      <  8:61272/148‑1 (MQ=255)
                                       aaaTAGTTGAGGATAATCTTTAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCaa                                                                                                                                                      >  6:324627/1‑107 (MQ=255)
                                       aaaTAGTTGAGGATAATCTTTAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCaa                                                                                                                                                      <  5:324627/107‑1 (MQ=255)
                                        aaTAGTTGAGGATAATCTTTAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTaa                                                                                                           >  6:89283/1‑149 (MQ=255)
                                         aTAGTTGAGGATAATCTTTAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAAt                                                                                                          <  2:333326/149‑1 (MQ=255)
                                            gTTGAGGATAATCTTTAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTTGTAATTa                                                                                                        <  2:319902/148‑1 (MQ=255)
                                             ttGAGGATAATCTTTAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGc                                                                                                      >  2:179441/1‑149 (MQ=255)
                                                  gATAATCTTTAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTAtt                                                                                                 >  8:156449/1‑149 (MQ=255)
                                                   aTAATCTTTAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTAttt                                                                                                <  5:89283/149‑1 (MQ=255)
                                                           tAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGgtt                                                                                           <  8:13716/146‑1 (MQ=255)
                                                                  tCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAg                                                                                 >  8:306637/1‑149 (MQ=255)
                                                                    aTAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTg                                                                                              <  4:176870/134‑1 (MQ=255)
                                                                    aTAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTg                                                                                              >  3:176870/1‑134 (MQ=255)
                                                                      aGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGc                                                                                >  6:2387/1‑146 (MQ=255)
                                                                      aGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGc                                                                                <  5:2387/146‑1 (MQ=255)
                                                                        aCTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCaa                                                                                  <  2:180156/142‑1 (MQ=255)
                                                                        aCTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCaa                                                                                  >  1:180156/1‑142 (MQ=255)
                                                                          tGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTgg                                                                                     >  7:88792/1‑137 (MQ=255)
                                                                          tGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTgg                                                                                     <  8:88792/137‑1 (MQ=255)
                                                                          tGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTATGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGTGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCATCgg                                                                          >  5:265055/1‑148 (MQ=255)
                                                                                  aGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCGGTATAAc                                                                    <  1:179441/146‑1 (MQ=255)
                                                                                  aGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCGGTATAAc                                                                    <  2:76957/146‑1 (MQ=255)
                                                                                   ggAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCGGTATAACATGc                                                                <  7:306637/149‑1 (MQ=255)
                                                                                      aGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCGGTATAACATGCTTa                                                             <  7:156449/149‑1 (MQ=255)
                                                                                       ggCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTg                                                                                      >  1:49296/1‑123 (MQ=255)
                                                                                       ggCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTg                                                                                      <  2:49296/123‑1 (MQ=255)
                                                                                         cTTAATGCGCTGGGTCTCAACGCGTAAAACTTTTCTGTCGACTTGCCATCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGTGTCGTAATTAGCGTATTTTGGTTGTTTTGCAAGCCAGCGGTATAACATGCTTatga                                                          <  6:265055/149‑1 (MQ=255)
                                                                                                  ctGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATtgtg                                                                                                                      >  4:303629/1‑80 (MQ=255)
                                                                                                  ctGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATtgtg                                                                                                                      <  3:303629/80‑1 (MQ=255)
                                                                                                     ggTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCATGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCGGTATAACATGCTTATGATGCt                                                      <  1:305344/141‑1 (MQ=255)
                                                                                                     ggTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCATGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCGGTATAACATGCTTATGATGCt                                                      <  1:310136/141‑1 (MQ=255)
                                                                                                     ggTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCATGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCGGTATAACATGCTTATGATGCt                                                      >  2:310136/1‑141 (MQ=255)
                                                                                                     ggTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCATGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCGGTATAACATGCTTATGATGCt                                                      >  2:305344/1‑141 (MQ=255)
                                                                                                            aCGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCGGTATAACATGCTTATGATGCTGGAGTAGCGCGAAGa                                       >  2:260586/1‑149 (MQ=255)
                                                                                                                gTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCGGTATAACATGCTTATGATGCTGGAGTAGCGCGAAGAc                                      >  6:45518/1‑146 (MQ=255)
                                                                                                                gTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCGGTATAACATGCTTATGATGCTGGAGTAGCGCGAAGAc                                      <  5:45518/146‑1 (MQ=255)
                                                                                                                      cTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCGGTATAACATGCTTATGATGCTGGAGTAGCGCGAAGACGTCCGAAgg                             <  1:260586/149‑1 (MQ=255)
                                                                                                                           ctgtcGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCg                                                                           <  3:209247/98‑1 (MQ=255)
                                                                                                                           ctgtcGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCg                                                                           >  4:209247/1‑98 (MQ=255)
                                                                                                                           ctgtcGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCGGTATAACATGCTTATGATGCTGGAGTAGCGCGAAGACGTCCGAAGGGAGGc                        >  1:259867/1‑149 (MQ=255)
                                                                                                                                      ccAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCGGTATAACATGCTTATGATGCTGGAGTAGCGCGAAGACGTCCGAAGGGa                           <  7:162056/135‑1 (MQ=255)
                                                                                                                                      ccAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCGGTATAACATGCTTATGATGCTGGAGTAGCGCGAAGACGTCCGAAGGGa                           >  8:162056/1‑135 (MQ=255)
                                                                                                                                            cTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCGGTATAACATGCTTATGATGCTGGAGTAGCGCGAAGACGTCCGAAGGGAGGCTCGGGCCGTGTCGTgaa       >  1:272964/1‑149 (MQ=255)
                                                                                                                                             ttCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCGGTATAACATGCTTATGATGCTGGAGTAGCGCGAAGACGTCCGAAGGGAGGCTCGGGCCGTGTCGTgaag      <  2:259867/149‑1 (MQ=255)
                                                                                                                                                 aGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCGGTATAACATGCTTATGATGCTGGAGTAGCGCGAAGACGTCCGAAGGGAGGCTCGGGCCGTGTCGTGAAGaaaa  <  3:303112/149‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                                    
TCAACATTCGATTTATACCCTTTAATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACTGTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTCAACGCGTAAAACTTGTCTGTCGACTTGCCAGCGCTTCAAGTCCCGGTTGTCCACGAGTGCGTGATATTGTGTGGGGTCGTAATTAGCGTATTTTGGTTGTTTGGCAAGCCAGCGGTATAACATGCTTATGATGCTGGAGTAGCGCGAAGACGTCCGAAGGGAGGCTCGGGCCGTGTCGTGAAGAAAA  >  NC_002947/2221213‑2221506

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: ‑