Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,872,136 G→A 7.5% S82L (TCG→TTG)  PP_3420 ← sensor histidine kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,872,1360GA 7.5% 150.3 / 2.5 53S82L (TCG→TTG) PP_3420sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base G (27/22);  new base A (2/2);  total (29/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.79e-01

CGGCAGGTGCTCGACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATGATCAACAGGCTGATCAC  >  NC_002947/3872006‑3872281
                                                                                                                                   |                                                                                                                                                 
cGGCAGGTGCTCGACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCt                                                                                                                                 >  3:3824/1‑149 (MQ=255)
 ggCAGGTGCTCGACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGTCCGGTGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTg                                                                                                                                <  4:223264/149‑1 (MQ=255)
  gCAGGTGCTCGACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTgg                                                                                                                               <  8:53023/149‑1 (MQ=255)
    aGGTGCTCGACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGc                                                                                                                             <  2:28122/149‑1 (MQ=255)
      gTGCTCGACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCa                                                                                                                           >  2:136271/1‑149 (MQ=255)
          tCGACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGc                                                                                                                       >  5:223022/1‑149 (MQ=255)
            gACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTgg                                                                                                                               <  3:243827/139‑1 (MQ=255)
            gACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTgg                                                                                                                               >  4:243827/1‑139 (MQ=255)
                   tCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGcc                                                                                                                            >  5:89208/1‑135 (MQ=255)
                   tCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGcc                                                                                                                            <  6:89208/135‑1 (MQ=255)
                      aGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTg                                                                                                           >  7:191982/1‑149 (MQ=255)
                          aCTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCATTCGCAATTGCCGc                                                                                                                                           <  4:46728/113‑1 (MQ=255)
                          aCTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCATTCGCAATTGCCGc                                                                                                                                           >  3:46728/1‑113 (MQ=255)
                              gATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGt                                                                                                     >  8:235222/1‑147 (MQ=255)
                              gATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTaa                                                                                                   <  1:136271/149‑1 (MQ=255)
                               aTCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGCACTGCGCGGTAAg                                                                                                  <  4:3824/149‑1 (MQ=255)
                                   gggTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATg                                                                                              <  7:235222/149‑1 (MQ=255)
                                   gggTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATg                                                                                              >  2:40364/1‑149 (MQ=255)
                                   gggTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATg                                                                                              <  1:43887/149‑1 (MQ=255)
                                                 aGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCAc                                                                                >  3:55915/1‑149 (MQ=255)
                                                             aCCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGca                                                                     <  5:21554/148‑1 (MQ=255)
                                                               cTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGcacca                                                                  <  6:223022/149‑1 (MQ=255)
                                                               cTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGcacca                                                                  >  2:243033/1‑149 (MQ=255)
                                                               cTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGcacca                                                                  >  5:101440/1‑149 (MQ=255)
                                                                 gCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTcgc                                                                        <  6:104731/141‑1 (MQ=255)
                                                                 gCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTcgc                                                                        >  5:104731/1‑141 (MQ=255)
                                                                  cAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGcaccac                                                                 <  4:55915/147‑1 (MQ=255)
                                                                           cAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTc                                                       <  1:243033/148‑1 (MQ=255)
                                                                             ggTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGa                                                     >  3:80553/1‑148 (MQ=255)
                                                                              gTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGGTTGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGa                                                     >  1:44361/1‑148 (MQ=255)
                                                                                   gCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTaa                                              >  1:129129/1‑149 (MQ=255)
                                                                                    ccGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAAc                                             <  2:129129/149‑1 (MQ=255)
                                                                                    ccGCGGGTCCAGAAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTTAGAATGCAGCACTTAGGCCTGGGCCATTGCATGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCAAGAAGCGCGTCGAAACGTAAc                                             >  2:241287/1‑149 (MQ=255)
                                                                                      gcgGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGACCTGCGCGGTAAGCATGGCATCGCGCTCCCCGCTGTCGCGCACCACGACGCGCGTCGAAACCTCAcc                                            >  5:195819/1‑148 (MQ=255)
                                                                                                    tCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCAc                             >  8:75291/1‑149 (MQ=255)
                                                                                                      gCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATg                                                                                              >  6:34854/1‑82 (MQ=255)
                                                                                                      gCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATg                                                                                              <  5:34854/82‑1 (MQ=255)
                                                                                                        ccATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAg                         >  2:218541/1‑149 (MQ=255)
                                                                                                         cATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAgg                        >  3:20216/1‑149 (MQ=255)
                                                                                                         cATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAgg                        >  6:99768/1‑149 (MQ=255)
                                                                                                            ggtgg‑tGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTaa                     >  7:47064/1‑149 (MQ=255)
                                                                                                              tgg‑tgCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAAt                    >  8:221884/1‑148 (MQ=255)
                                                                                                              tgg‑tgCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATg                   <  4:20216/149‑1 (MQ=255)
                                                                                                                  tgCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATGATc                <  2:44361/149‑1 (MQ=255)
                                                                                                                  tgCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATGATc                <  7:75291/149‑1 (MQ=255)
                                                                                                                    ccAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATGATCaa              >  2:177664/1‑149 (MQ=255)
                                                                                                                    aagtgcggcATTCGCAATTGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGt                                                        <  5:199786/103‑1 (MQ=255)
                                                                                                                    aagtgcggcATTCGCAATTGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGt                                                        >  6:199786/5‑107 (MQ=255)
                                                                                                                         cggcAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTg                                                                            <  6:252320/82‑1 (MQ=255)
                                                                                                                         cggcAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTg                                                                            >  5:252320/1‑82 (MQ=255)
                                                                                                                          ggcAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATGATCAACAGGCt        <  5:99768/149‑1 (MQ=255)
                                                                                                                               ttGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATGATCAACAGGCTGATCa   >  6:227350/1‑149 (MQ=255)
                                                                                                                                 gCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATGATCAACAGGCTGATCAc  <  1:105447/148‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                                 
CGGCAGGTGCTCGACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATGATCAACAGGCTGATCAC  >  NC_002947/3872006‑3872281

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: ‑