Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,336,227 G→A 10.0% R870H (CGC→CAC)  PP_4695 → two‑component system sensor histidine kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,336,2270GA10.0% 129.6 / 5.5 50R870H (CGC→CAC) PP_4695two‑component system sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base G (24/21);  new base A (2/3);  total (26/24)
Fisher's exact test for biased strand distribution p-value = 6.61e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.52e-01

GCAGCCACCAGAACAGCGAGGAGCCCGTGTGCCTGGCTGAAGTGGCACAAGATGCCATCGGTCTGCTGGCGTTGAACCGGCGCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGTTAACGAGCACACCGTCGACCTGATCGTCGAAGACGAAGGCAGCGGGATTCCGAAGAACATCA  >  NC_002947/5336080‑5336373
                                                                                                                                                   |                                                                                                                                                  
gcAGCCACCAGAACAGCGAGGAGCCCGTGTGCCTGGCTGAAGTGGCACAAGATGCCATCGGTCTGCTGGCGTTGAACCGGCTCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGGAGTGGACCCGCAGCGcc                                                                                                                                                  >  2:286662/1‑150 (MQ=255)
 cAGCCACCAGAACAGCGAGGAGCCCGTGTGCCTGGCTGAAGTGGCACAAGATGCCATCGGTCTGCTGGCGTTGAACCGGCGCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGcca                                                                                                                                                 <  2:242790/150‑2 (MQ=255)
     cacccGAACAGCGAGGAGCCCGTGTGCCTGGCTGAAGTGGCACAAGATGCCATCGGTCTGCTGGCGTTGAACCGGCGCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCACCTgggc                                                                                                                                             >  2:524700/1‑148 (MQ=255)
        caGAACAGCGAGGAGCCCGTGTGCCTGGCTGAAGTGGCACAAGATGCCATCGGTCTGCTGGCGTTGAACCGGCGCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAg                                                                                                                                          <  2:759372/150‑1 (MQ=255)
         aGAACAGCGAGGAGCCCGTGTGCCTGGCTGAAGTGGCACAAGATGCCATCGGTCTGCTGGCGTTGAACCGGCGCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAgg                                                                                                                                         >  2:1209362/1‑150 (MQ=255)
            aCAGCGAGGAGCCCGTGTGCCTGGCTGAAGTGGCACAAGATGCCATCGGTCTGCTGGCGTTGAACCGGCGCAATTTCGAAGTACGGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGc                                                                                                                                      <  1:303424/150‑1 (MQ=255)
             cAGCGAGGAGCCCGTGTGCCTGGCTGAAGTGGCACAAGATGCCATCGGTCTGCTGGCGTTGAACCGGCGCAATTGCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCt                                                                                                                                     <  1:1162510/150‑1 (MQ=255)
              aGCGAGGAGCCCGTGTGCCTGGCTGAAGTGGCACAAGATGCCATCGGTCTGCTGGCGTTGAACCGGCGCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCAGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTg                                                                                                                                    <  2:449679/150‑1 (MQ=255)
               gCGAGGAGCCCGTGTGCCTGGCTGAAGTGGCACAAGATGCCATCGGTCTGCTGTCGTTGAACCGGCGCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCAGTGGGCCGAAGGTGACCCGCAGCACCTGGGCCAGGCGCTgc                                                                                                                                   <  1:1361220/150‑2 (MQ=255)
               gCGAGGAGCCCGTGTGCCTGGCTGAAGTGGCACAAGATGCCATCGGTCTGCTGGCGTTGAACCGGCGCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCACCTGGGCCAGGCGCTgc                                                                                                                                   >  2:969953/1‑149 (MQ=255)
                 gaggagCCCGTGTGCCTGGCTGAAGTGGCACAAGATGCCATCGGTCTGCTGGCGTTGAACCGGCGCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGGCCCGCAGCACCTGGGCCAGGCGCTgcgg                                                                                                                                 <  1:969953/150‑4 (MQ=255)
                 gaggagCCCGTGTGCCTGGCTGAAGTGGCACAAGATGCCATCGGTCTGCTGGCGTTGAACCGGCGCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCACCTGGGCCAGGCGCTgcgg                                                                                                                                 <  1:524700/150‑4 (MQ=255)
                    gagCCCGTGTGCCTGGCTGAAGTGGCACAAGATGCCATCGGTCTGCTGGCGTTGAACCGGCGCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAAc                                                                                                                              <  2:742264/150‑1 (MQ=255)
                                cTGGCTGAAGTGGCACAAGATGCCATCGGTCTGCTGGCGTTGAACCGGCGCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTTGCTCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAAc                                                                                                                  <  2:1262190/150‑1 (MQ=255)
                                        aGTGGCACAAGATGCCATCGGTCTGCTGGCGTTGAACCGGCGCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGa                                                                                                          <  1:1209362/150‑1 (MQ=255)
                                              acaAGATGCCATCGGTCTGCTGGCGTTGAACCGGCGCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTc                                                                                                    >  2:431946/1‑150 (MQ=255)
                                              acaAGATGCCATCGGTCTGCTGGCGTTGAACCGGCGCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTc                                                                                                    <  1:491473/150‑1 (MQ=255)
                                                aaGATGCCATCGGTCTGCTGGCGTTGAACCGGCGCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTcgc                                                                                                  >  2:640099/1‑150 (MQ=255)
                                                     gCCATCGGTCTGCTGGCGTTGAACCGGCGCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGccc                                                                                             >  1:1080505/1‑150 (MQ=255)
                                                                    gCGTTGAACCGGCGCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCcgtgcgc                                                                              <  2:673507/150‑1 (MQ=255)
                                                                         gAACCGGCGCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCcgtgcgcgtgcg                                                                         >  1:551249/1‑150 (MQ=255)
                                                                            ccGGCGCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAg                                                                      >  1:845778/1‑150 (MQ=255)
                                                                               gcgcAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTTCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGa                                                                   <  1:286662/150‑1 (MQ=255)
                                                                                     tttCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGTTaa                                                             >  1:828563/1‑150 (MQ=255)
                                                                                             tACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGTTAACGAGcaca                                                     >  1:66656/1‑150 (MQ=255)
                                                                                             tACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGTTAACGAGcaca                                                     >  1:1303715/1‑150 (MQ=255)
                                                                                             tACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGTTAACGAGcaca                                                     >  2:168643/1‑150 (MQ=255)
                                                                                                aGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCa                                                                       <  2:435133/129‑1 (MQ=255)
                                                                                                aGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCa                                                                       >  1:435133/1‑129 (MQ=255)
                                                                                                     ttcAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCtctc                                                                                                                      >  2:366696/1‑77 (MQ=255)
                                                                                                     ttcAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCtctc                                                                                                                      <  1:366696/77‑1 (MQ=255)
                                                                                                     ttcAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGc                                                                                                       >  1:477269/1‑92 (MQ=255)
                                                                                                     ttcAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGc                                                                                                       <  2:477269/92‑1 (MQ=255)
                                                                                                     ttcAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGTTAACGAGCACACCGTCGAc                                             >  2:1384595/1‑150 (MQ=255)
                                                                                                     ttcAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGTTAACGAGCACACCGTCGAc                                             <  2:551249/150‑1 (MQ=255)
                                                                                                      tcAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGTTAACGAGCACACCGTCGAcc                                            >  1:1147651/1‑150 (MQ=255)
                                                                                                         aCCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGTTAACGAGCACACCGTCGACCTGa                                         >  2:1125969/1‑150 (MQ=255)
                                                                                                           cTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGTTAACGAGCACACCGTCGACCTGAtc                                       <  1:431946/150‑1 (MQ=255)
                                                                                                              tGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGTTAACGAGCACACCGTCGACCTGAtcgtc                                    >  1:235558/1‑150 (MQ=255)
                                                                                                                cGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGTTAACGAGCACACCGTCGACCTGATCGTCGa                                  >  1:1410474/1‑150 (MQ=255)
                                                                                                                 gACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGTTAACGAGCACACCGTCGACCTGATCGTCGaa                                 <  2:66656/150‑1 (MQ=255)
                                                                                                                      ggACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGTTAACGAGCACACCGTCGACCTGATCGTCGAAGACGa                            >  1:857872/1‑150 (MQ=255)
                                                                                                                       gtgcATTTGTCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGCTCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGTTAACGAGCACACCGTCGACCTGATCGTCGAAGACGaa                           <  2:655049/147‑1 (MQ=255)
                                                                                                                           aTTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGTTAACGAGCACACCGTCGACCTGATCGTCGAAGACGAAGGCa                       >  1:1072139/1‑150 (MQ=255)
                                                                                                                                      ggTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGTTAACGAGCACACCGTCGACCTGATCGTCGAAGACGAAGGCAGCGGGATTCCg            >  2:130087/1‑150 (MQ=255)
                                                                                                                                        tGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGTTAACGAGCACACCGTCGACCTGATCGTCGAAGACGAAGGCAGCGGGATTCCgaa          >  1:939936/1‑150 (MQ=255)
                                                                                                                                        tGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGTTAACGAGCACACCGTCGACCTGATCGTCGAAGACGAAGGCAGCGGGATTCCgaa          <  2:845778/150‑1 (MQ=255)
                                                                                                                                            ccGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGt                                                                >  2:1017950/1‑92 (MQ=255)
                                                                                                                                            ccGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGt                                                                <  1:1017950/92‑1 (MQ=255)
                                                                                                                                                aGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGTTAACGAGCACACCGTCGACCTGATCGTCGAAGACGAAGGCAGCGGGATTCCGAAGAAcatca  <  1:640099/150‑1 (MQ=255)
                                                                                                                                                   gcCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAg                                                                  <  2:702339/83‑1 (MQ=255)
                                                                                                                                                   gcCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAg                                                                  >  1:702339/1‑83 (MQ=255)
                                                                                                                                                   |                                                                                                                                                  
GCAGCCACCAGAACAGCGAGGAGCCCGTGTGCCTGGCTGAAGTGGCACAAGATGCCATCGGTCTGCTGGCGTTGAACCGGCGCAATTTCGAAGTACAGTTCTTCAACCTTTGCGACCCGGACCATTGGGCCGAAGGTGACCCGCAGCGCCTGGCCCAGGTGCTGATCAACCTGCTCTCCAACGCCCGCGATGCCTCGCCGCCCGGCAGCGCCGTGCGCGTGCGCAGCGAGGTTAACGAGCACACCGTCGACCTGATCGTCGAAGACGAAGGCAGCGGGATTCCGAAGAACATCA  >  NC_002947/5336080‑5336373

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑