Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 4,797,712 T→C 9.6% I91V (ATC→GTC) ‡ PP_4224 ← sensor histidine kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,797,7120TC 9.6% 136.9 / 5.1 52I91V (ATC→GTC) ‡PP_4224sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base T (24/23);  new base C (3/2);  total (27/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.63e-01

TCCATGTGCCGGTCAGCCGTGGTGATGCGCACATCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTGGCGGTCAGCGGCTGCGGCAGTTGGTCGATCAGCCCGGCGACCATACGCGCCGACG  >  NC_002947/4797567‑4797852
                                                                                                                                                 |                                                                                                                                            
tCCATGTGCCGGTCATCCGTGGTGATGCGCACATCGCCGTGGTTGTAGGTAAAGGTTCGCCAAAGCGCATCGTCGATTTTCTGGTCTCGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGAtctc                                                                                                                                           <  1:209237/149‑1 (MQ=39)
  cATGTGCCGGTCAGCCGTGGTGATGCGCACATCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCg                                                                                                                                          <  3:386195/148‑1 (MQ=255)
  cATGTGCCGGTCAGCCGTGGTGATGCGCACATCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGc                                                                                                                                         <  8:164137/149‑1 (MQ=255)
    tgtgCCGGTCAGCCGTGGTGATGCGCACATCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGATCCTCGCCa                                                                                                                                       <  3:228153/149‑1 (MQ=255)
      tgCCGGGCAGCCGTGGTGATGCGCACATCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCAc                                                                                                                                      <  5:191267/148‑1 (MQ=255)
        ccGGTCAGCCGTGGTGATGCGCACATCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATTGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGATCCTCGCCagca                                                                                                                                    <  5:271471/148‑4 (MQ=39)
         cGGTCAGCCGTGGTGATGCGCACATCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAg                                                                                                                                  <  1:140002/149‑1 (MQ=255)
            tCAGCCGTGGTGATGCGCACATCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGa                                                                                                                               <  7:344707/149‑1 (MQ=255)
            tCAGCCGTGGTGATGCGCACATCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGGCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGGGGATCTCGCCACGCAGCGa                                                                                                                               <  7:171538/149‑1 (MQ=255)
              aGCCGTGGTGATGCGCACATCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGc                                                                                                                             >  7:271621/1‑149 (MQ=255)
                ccGTGGTGATGCGCACATCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCt                                                                                                                            >  6:30140/1‑148 (MQ=255)
                   tggtgATGCGCACATCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCa                                                                                                                                   <  2:340437/138‑1 (MQ=255)
                   tggtgATGCGCACATCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCa                                                                                                                                   >  1:340437/1‑138 (MQ=255)
                      tgATGCGCACATCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTgg                                                                                                                     <  7:116385/149‑1 (MQ=255)
                      tgATGCGCACATCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTgg                                                                                                                     >  8:116385/1‑149 (MQ=255)
                           cgcACATCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGgc                                                                                                                >  7:175480/1‑149 (MQ=255)
                            gcACATCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGc                                                                                                                                 <  4:58160/131‑1 (MQ=255)
                            gcACATCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGc                                                                                                                                 >  3:58160/1‑131 (MQ=255)
                             cacaTCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCAGCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGgcca                                                                                                              >  1:285249/1‑149 (MQ=255)
                               caTCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGgccatg                                                                                                            <  5:30140/149‑1 (MQ=255)
                               caTCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGgccatg                                                                                                            <  3:107374/149‑1 (MQ=255)
                                    ccGTTGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTAGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTGGCCACGCAGCGAGCTGACCTGGCAGGCCTTGCCATc                                                                                                       <  2:284760/149‑1 (MQ=255)
                                              aGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGTAGGCCATGCCATCCGGTACGCt                                                                                              >  2:202892/1‑148 (MQ=255)
                                                 tAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGaa                                                                                           <  5:198900/148‑1 (MQ=255)
                                                   aaGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCACGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTg                                                                                        >  7:336406/1‑149 (MQ=255)
                                                           ccAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCgg                                                                                   >  2:333336/1‑146 (MQ=255)
                                                           ccAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCgg                                                                                   >  7:32792/1‑146 (MQ=255)
                                                            cAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAg                                                                                >  4:249843/1‑148 (MQ=255)
                                                                   cATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAAtcc                                                                        <  3:136356/149‑3 (MQ=255)
                                                                      cgtcgATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGcc                                                                     >  5:344147/1‑149 (MQ=255)
                                                                        tcgATGGTCTGGTCACGAAACCCGCTGAGCTCGTCGTACATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTc                                                                   >  5:115262/1‑149 (MQ=255)
                                                                              gtctggtcACGAAACCCGCTGCGCTCGTCGTCCATGGCGCAATGGTGCGTGTGGTTGCTGGCGAGCATCTCGCAACGCAGCGAGCTGACCTGGCAGGCAATGCCATCCGGTACGCTGAACTGGACGGCAGAAAAATTCGCCTCCCCGcc                                                             >  4:212712/1‑149 (MQ=18)
                                                                                 tggtcACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCtt                                                          >  4:372124/1‑149 (MQ=255)
                                                                                   gtcACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTgg                                                        <  8:32792/149‑1 (MQ=255)
                                                                                    tcACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTGGc                                                       >  3:310767/1‑149 (MQ=255)
                                                                                          aaCCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTGGCGGTCAg                                                 <  4:310767/149‑1 (MQ=255)
                                                                                           aCCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTGGCGGTCAGc                                                >  2:208558/1‑149 (MQ=255)
                                                                                           aCCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTGGCGGTCAGc                                                <  8:175480/149‑1 (MQ=255)
                                                                                               gCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGAGCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTGGCGGTCAGCGGCt                                            <  8:336406/149‑1 (MQ=255)
                                                                                                    gcTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTGGCGGTCAGCGGCTGCgg                                        >  4:68930/1‑148 (MQ=255)
                                                                                                     cTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTGGCGGTCAGCGGCTGCGGCa                                      <  3:249843/149‑1 (MQ=40)
                                                                                                      tcgtcgTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTGGCGGTCa                                                  >  7:5255/1‑136 (MQ=40)
                                                                                                      tcgtcgTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTGGCGGTCa                                                  <  8:5255/136‑1 (MQ=40)
                                                                                                           gtcCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTGGCGGTCAGCGGCTGCGGCAGTTGGt                                >  7:20356/1‑149 (MQ=255)
                                                                                                            tcCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTGGCGGTCAGCGGCTGCGGCAGTTGGTc                               <  5:262692/149‑1 (MQ=255)
                                                                                                                        tCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTGGCGGTCAGCGGCTGCGGCAGTTGGTCGATCAGCCCGGc                   >  6:322592/1‑149 (MQ=39)
                                                                                                                             cTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTGGCGGTCAGCGGCTGCGGCAGTTGGTCGATCAGCCCGGc                   <  2:90780/144‑1 (MQ=39)
                                                                                                                             cTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTGGCGGTCAGCGGCTGCGGCAGTTGGTCGATCAGCCCGGc                   >  1:90780/1‑144 (MQ=39)
                                                                                                                                   gTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTGGCGGTCAGCGGCTGCGGCAGTTGGTCGATCAGCCCGGCGACCATAcgc         <  6:344147/148‑1 (MQ=39)
                                                                                                                                    tgcgtGGCGAGATCCTCGCCA‑GCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTGGCGGTCAGCGGCTGCGGCAGTTGGTCGATCAGCCCGGCGACCATACGCGcc      >  1:151563/5‑149 (MQ=14)
                                                                                                                                       gtGGCGAGATCCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTGGCGGTCAGCGGCTGCGGCAGTTGGTCGATCAGCCCGGCGACCATACGCGCCGa    >  5:138765/2‑149 (MQ=255)
                                                                                                                                        tGGCGAGATCCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTCAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTGGCGGTCAGCGGCTGCGGCAGTTGGTCGATCAGCCCGGCGACCATACGCGCCGAc   >  1:47406/1‑149 (MQ=255)
                                                                                                                                         ggCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTGGCGGTCAGCGGCTGCGGCAGTTGGTCGATCAGCCCGGCGACCATACGCGCCGACg  >  1:11353/1‑149 (MQ=39)
                                                                                                                                                 |                                                                                                                                            
TCCATGTGCCGGTCAGCCGTGGTGATGCGCACATCGCCGTGGTTGTAGGTAAAGGTGCGCCAAAGCGCATCGTCGATGGTCTGGTCACGAAACCCGCTGCGCTCGTCGTCCATGGCGCCATCGTGCTTGTGGTTGCTGGCGAGGATCTCGCCACGCAGCGAGCTGACCTGGCAGGCCATGCCATCCGGTACGCTGAACTGGTCGGCAGAAAAATGCGCCTCCCCGCCCTTGGCGGTCAGCGGCTGCGGCAGTTGGTCGATCAGCCCGGCGACCATACGCGCCGACG  >  NC_002947/4797567‑4797852

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: ‑