Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,872,131 A→T 7.5% L84M (TTG→ATG)  PP_3420 ← sensor histidine kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,872,1310AT 7.5% 159.6 / 3.3 53L84M (TTG→ATG) PP_3420sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base A (27/22);  new base T (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 = 7.35e-01

CATTGGCCAGCAAGGTGTCCGGCAGGTGCTCGACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATGATCAACAGGCT  >  NC_002947/3871987‑3872275
                                                                                                                                                 |                                                                                                                                                
cATTGGCCAGCAAGGTGTCCGGCAGGTGCTCGACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGc                                                                                                                                              <  3:148125/149‑1 (MQ=255)
 aTTGGCCAGCAAGGTGTCCGGCAGGTGCTCGACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGc                                                                                                                                              >  6:21554/1‑148 (MQ=255)
                   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                                                                                                                      <  6:89208/135‑1 (MQ=255)
                                      tCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGcc                                                                                                                      >  5:89208/1‑135 (MQ=255)
                                         aGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTg                                                                                                     >  7:191982/1‑149 (MQ=255)
                                             aCTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCATTCGCAATTGCCGc                                                                                                                                     >  3:46728/1‑113 (MQ=255)
                                             aCTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCATTCGCAATTGCCGc                                                                                                                                     <  4:46728/113‑1 (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                                                                                        >  2:40364/1‑149 (MQ=255)
                                                      gggTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATg                                                                                        <  7:235222/149‑1 (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                                                            >  2:243033/1‑149 (MQ=255)
                                                                                  cTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGcacca                                                            <  6:223022/149‑1 (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                                                                                        <  5:34854/82‑1 (MQ=255)
                                                                                                                         gCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATg                                                                                        >  6:34854/1‑82 (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          <  7:75291/149‑1 (MQ=255)
                                                                                                                                     tgCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATGATc          <  2:44361/149‑1 (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)
                                                                                                                                                 |                                                                                                                                                
CATTGGCCAGCAAGGTGTCCGGCAGGTGCTCGACATGATCGAGGAACTCGATCCGGGTCGATTCGGCCAGGGCCGGGGTGACCTGCAAGTGCTGCAGGTCCAGCCGCGGGTCCAGCAACTCGCCCATGGTGG‑TGCCAGGCGGCAATTGCGAATGCCGCACTTCGGCCTGGGCCATTGCCTGAATGAACTGCGCGGTAAGCATGGCATCGCGCTCCACGCTGTCGCGCACCACGAAGCGCGTCGAAACGTAACCCAGCCCACCTGCCACCGAGGTAATGATCAACAGGCT  >  NC_002947/3871987‑3872275

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: ‑