Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 2,398,162 G→T 7.7% L499I (CTC→ATC)  PP_2100 ← two‑component system sensor protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029472,398,1620GT 7.7% 152.4 / 3.0 52L499I (CTC→ATC) PP_2100two‑component system sensor protein
Reads supporting (aligned to +/- strand):  ref base G (25/23);  new base T (2/2);  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 = 8.55e-01

AACAAAAGCACGGCCGTGGCCAGCACCACCTGCAGGGCCAGGCGGCTGTAGCCTTTGGAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCGGATGACCAGTTCTGGGTTGCTGGCCAGGGCGTGATTGGCGTCGATCAGGGTGGTGATCACCGCATCGA  >  NC_002947/2398014‑2398305
                                                                                                                                                    |                                                                                                                                               
aacaaAAGCACGGCCGTGGCCAGCACCACCTGCAGGGCCAGGCGGCTGTAGCCTTTGGAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAg                                                                                                                                                 >  8:246063/1‑149 (MQ=255)
   aaaaGCACGGCCGTGGCCAGCACCACCTGCAGGGCCAGGCGGCTGTAGCCTTTGGAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGAt                                                                                                                                              <  8:284977/149‑1 (MQ=255)
   aaaaGCACGGCCGTGGCCAGCACCACCTGCAGGGCCAGGCGGCTGTAGCCTTTGGAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGAt                                                                                                                                              <  8:193329/149‑1 (MQ=255)
       gCACGGCCGTGGCCAGCACCACCTGCAGGGCCAGGCGGCTGTAGCCTTTGGAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGa                                                                                                                                           >  7:106251/1‑148 (MQ=255)
          cggcggTGGCCAGCACCTCCTGCAGGGCCAGGCGGCGGTAGCCTTTGGAGTTGTCATCCTCATGCGTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTGAGCAAAGCTTTGTCGATCCTCGacaaa                                                                                                                                       <  4:289753/149‑2 (MQ=255)
           ggCCGTGGCCAGCACCACCTGCAGGGCCAGGCGGCTGTAGCCTTTGGAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGacaaca                                                                                                                                      <  1:210449/149‑1 (MQ=255)
             ccGTGGCCAGCACCACCTGCAGGGCCAGGCGGCTGTAGCCTTTGGAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAgc                                                                                                                                    >  5:113987/1‑149 (MQ=255)
              cGTGGCCAGCACCACCTGCAGGGCCAGGCGGCTGTAGCCTTTGGAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAgcg                                                                                                                                   <  8:191132/149‑1 (MQ=255)
                          caccTGCAGGGCCAGGCGGCTGTAGCCTTTGGAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACgggg                                                                                                                       >  4:280397/1‑149 (MQ=255)
                           accTGCAGGGCCAGTCGGCTGTAGCCTTTGGAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACgggg                                                                                                                       >  8:206527/1‑148 (MQ=255)
                            ccTGCAGGGCCAGGCGGCTGTAGCCTTTGGAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGATCCTCGacaaa                                                                                                                                       >  8:191424/1‑130 (MQ=255)
                            ccTGCAGGGCCAGGCGGCTGTAGCCTTTGGAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGATCCTCGacaaa                                                                                                                                       <  7:191424/131‑2 (MQ=255)
                            ccTGCAGGGCCAGGCGGCTGTAGCCTTTGGAGTTGTCATCCTCATGCCAGCCAAAGACACGCCAGCGGTTGTTGATTACCCCCAGCTCTACCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGAGCGACAACAGCGCCGGTGACggggg                                                                                                                      >  8:181027/1‑147 (MQ=255)
                                cAGGGCCAGGCGGCTGTAGCCTTTGGAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAAtgg                                                                                                                 >  4:274832/1‑149 (MQ=255)
                                    gCCAGGCGGCTGTAGCCTTTGGAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAAt                                                                                                                   <  2:210700/143‑1 (MQ=255)
                                    gCCAGGCGGCTGTAGCCTTTGGAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAAt                                                                                                                   >  1:210700/1‑143 (MQ=255)
                                               gTAGCCTTTGGAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCAGGTGACgggg                                                                                                                       >  6:140467/1‑128 (MQ=255)
                                                 aGCCTTTGGAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGtt                                                                                                 <  8:106251/148‑1 (MQ=255)
                                                   ccTTTGGAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGc                                                                                              <  2:132499/149‑1 (MQ=255)
                                                    cTTTGGAGTTGTCATCCTCATTCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCg                                                                                             <  6:18360/149‑1 (MQ=255)
                                                    cTTTGGAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCg                                                                                             >  3:203058/1‑149 (MQ=255)
                                                    cTTTGGAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCg                                                                                             >  6:47561/1‑149 (MQ=255)
                                                         gAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTc                                                                                        >  6:68193/1‑149 (MQ=255)
                                                               tCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATACTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCAGcc                                                                                  <  1:241354/149‑1 (MQ=255)
                                                                 aTCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACgg                                                                                                                         >  2:270290/1‑108 (MQ=255)
                                                                 aTCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACgg                                                                                                                         <  1:270290/108‑1 (MQ=255)
                                                                 aTCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGccga                                                                                <  3:274832/149‑1 (MQ=255)
                                                                       aTGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAg                                                                           <  5:47561/148‑1 (MQ=255)
                                                                       aTGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCAGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAgg                                                                          >  2:145996/1‑149 (MQ=255)
                                                                          cctgccAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGc                                                                       >  6:264591/1‑149 (MQ=255)
                                                                           ctgccAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCg                                                                      <  8:262715/149‑1 (MQ=255)
                                                                              ccAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCGGa                                                                    <  4:295475/148‑1 (MQ=255)
                                                                                aaaGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCGGATGa                                                                 <  3:280397/149‑1 (MQ=255)
                                                                                aaaGCCACGCCAGCGGTTGTTGATTACCCACAGCACTTCCGGTGAGATGCTCACCAAAGCTTTGTCGAGGATCAACAACAGCGCCGGTGACGGGGCAATGCTGGCCATGGCGAAGTTGGCGGTTTCGCTGCCGACCGCTCTGCGGATGa                                                                 >  7:305221/1‑149 (MQ=255)
                                                                                   gCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCGGATGACCa                                                              <  7:206527/149‑1 (MQ=255)
                                                                                    ccACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATc                                                                                                                                             >  1:210938/1‑69 (MQ=255)
                                                                                    ccACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATc                                                                                                                                             <  2:210938/69‑1 (MQ=255)
                                                                                    ccACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCGGATGACCAg                                                             >  1:135361/1‑149 (MQ=255)
                                                                                            gCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGACAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCGGATGACCAGTTCTGGGt                                                     >  8:57111/1‑149 (MQ=255)
                                                                                                  gttgATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCGGATGACCAGTTCTGGGTTGCTg                                                <  6:113987/148‑1 (MQ=255)
                                                                                                      aTTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCGGATGACCAGTTCTGGGTTGCTGGCCAg                                           >  2:207408/1‑149 (MQ=255)
                                                                                                            cccAGCGCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCGGATGACCAGTTCTGGGTTGCTGGCCAGGGCGTg                                     <  5:68193/149‑1 (MQ=255)
                                                                                                                 ctctTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGACAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCGGATGACCAGTTCTGGGTTGCTGGCCAGGGCGTGATTgg                                <  7:57111/149‑1 (MQ=255)
                                                                                                                        ggTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCGGATGACCAGTTCTGGGTTGCTGGCCAGGGCGTGATTGGCGTCGAt                         >  3:236655/1‑149 (MQ=255)
                                                                                                                         gTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCGGATGACCAGTTCTGGGTTGCTGGCCAGGGCGTGATTGGCGTCGAt                         >  1:86629/1‑148 (MQ=255)
                                                                                                                                 cTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCGGATGACCAGTTCTGGGTTGCTGGCCAGGGCGTGATTGGCGTCGATCAGggtgg                 <  7:246063/148‑1 (MQ=255)
                                                                                                                                  tCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCGGATGACCAGTTCTGGGTTGCTGGCCCGGGCGTGATTGGCGTCGATCAGggtggt                >  6:262936/1‑148 (MQ=255)
                                                                                                                                    aGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCGGATGACCAGTTCTGGGTTGCTGGCCAGGGCGTGATTGGCGTCGATCAGGgtggtg               <  2:135361/147‑1 (MQ=255)
                                                                                                                                    aGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCGGATGACCAGTTCTGGGTTGCTGGCCAGGGCGTGATTGGCGTCGATCAGGGTGGTGAt             >  4:226869/1‑149 (MQ=255)
                                                                                                                                      cAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCGGATGACCAGTTCTGGGTTGCTGGCCAGGGCGTGATTGGCGTCGATCAGggt                   >  6:69563/1‑141 (MQ=255)
                                                                                                                                      cAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCGGATGACCAGTTCTGGGTTGCTGGCCAGGGCGTGATTGGCGTCGATCAGggt                   <  5:69563/141‑1 (MQ=255)
                                                                                                                                            gttGTCGATCCTCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCGGATGACCAGTTCTGGGTTGCTGGCCAGGGCGTGATTGGCGTCGATCAGGGTGGTGATCACCGCAt     >  5:114238/2‑149 (MQ=255)
                                                                                                                                               gTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCGGATGACCAGTTCTGGGTTGCTGGCCAGGGCGTGATTGGCGTCGATCAGGGTGGTGATCACCGCATCGa  >  5:289850/1‑149 (MQ=255)
                                                                                                                                                    |                                                                                                                                               
AACAAAAGCACGGCCGTGGCCAGCACCACCTGCAGGGCCAGGCGGCTGTAGCCTTTGGAGTTGTCATCCTCATGCCTGCCAAAGCCACGCCAGCGGTTGTTGATTACCCCCAGCTCTTCCGGTGAGATGCTCAGCAAAGCTTTGTCGAGGATCGACAACAGCGCCGGTGACGGGGCAATGGTGGCCATGGCGAAGTTGGCGGGTTCGCTGCCGACCGAGGTGCGGATGACCAGTTCTGGGTTGCTGGCCAGGGCGTGATTGGCGTCGATCAGGGTGGTGATCACCGCATCGA  >  NC_002947/2398014‑2398305

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: ‑