Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 2,223,369 G→C 9.3% P393R (CCG→CGG)  PP_1962 ← site‑specific recombinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029472,223,3690GC 9.3% 146.3 / 7.6 54P393R (CCG→CGG) PP_1962site‑specific recombinase
Reads supporting (aligned to +/- strand):  ref base G (23/26);  new base C (2/3);  total (25/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.21e-01

AATGGTGGCCGAACAGCAGACGGATCAGGTCAATATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAGAGCGGAGCGTTCTCAGAGATTTAATGGTTTCACCAACAAATTTAGGTAGAGGGAGGC  >  NC_002947/2223226‑2223510
                                                                                                                                               |                                                                                                                                             
aaTGGTGGCCGAACAGCAGACGGATCAGGTCAATATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGAAGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGc                                                                                                                                          >  6:302911/1‑149 (MQ=255)
    gtggCCGAACAGCAGTCGGATCAGGTCAATATTTCGTTCGCTCCAATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCg                                                                                                                                      <  1:5716/149‑1 (MQ=255)
        ccGAACAGCAGACGGATCAGGTCAATATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGaa                                                                                                                                   >  4:256548/1‑148 (MQ=255)
        ccGAACAGCAGACGGATCAGGTCAATATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAac                                                                                                                                  <  8:168087/149‑1 (MQ=255)
         cGAACAGCAGACGGATCAGGTCAATATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGGTGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAaca                                                                                                                                 >  7:204634/1‑149 (MQ=255)
         cGAACAGCAGACGGATCAGGTCAATATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGc                                                                                                                                       >  4:159980/1‑143 (MQ=255)
         cGAACAGCAGACGGATCAGGTCAATATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGc                                                                                                                                       <  3:159980/143‑1 (MQ=255)
         cGAACAGCAGACGGATCAGGTCAATATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAaca                                                                                                                                 >  5:75931/1‑149 (MQ=255)
         cGAACAGCAGACGGATCACGTCAATATTTCGTTAGCTCCCATTGAACAGCATTTCTGCAATCGTTTTCGGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATAAATGATTGTGTTCGGCAGATGCGGaaga                                                                                                                                 >  8:157415/1‑147 (MQ=255)
          gAACAGCAGACGGATCAGGGCAATATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAacac                                                                                                                                <  5:114492/149‑1 (MQ=255)
            aCAGCAGACGGATCAGGTCAATATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATAGGTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCCGCAGCTGCCGAacacaa                                                                                                                              <  8:81691/149‑3 (MQ=255)
                cagACGGATCAGGTCAATATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTgg                                                                                                                          <  5:302911/149‑1 (MQ=255)
                    cGGATCAGGTCAATATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTAc                                                                                                                      <  2:283545/149‑1 (MQ=255)
                        tCAGGTCAATATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCtt                                                                                                                   <  2:172754/148‑1 (MQ=255)
                        tCAGGTCAATATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCtt                                                                                                                   >  5:113780/1‑148 (MQ=255)
                        tCAGGTCAATATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTg                                                                                                                  >  5:108985/1‑149 (MQ=255)
                            gTCAATATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCttt                                                                                                                            <  7:325393/135‑1 (MQ=255)
                            gTCAATATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCCTTTTCAGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACATCTTCGAGATAATCAATGATTGAGTTCGGCAGCTGCGGAACACCatt                                                                                                                            >  8:325393/1‑135 (MQ=255)
                              cAATATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCgat                                                                                                            >  1:195400/1‑149 (MQ=255)
                               aaTATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCgat                                                                                                            <  6:113780/148‑1 (MQ=255)
                               aaTATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCgat                                                                                                            <  6:108985/148‑1 (MQ=255)
                                 tatTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCgatgat                                                                                                         >  1:100380/1‑149 (MQ=255)
                                      cgttcgCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGGTGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAg                                                                                                     <  8:204634/148‑1 (MQ=255)
                                      cgttcgCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAg                                                                                                     >  6:85078/1‑148 (MQ=255)
                                          cgCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCAct                                                                                                 <  6:75931/148‑1 (MQ=255)
                                           gCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGctctct                                                                                               >  5:168720/1‑149 (MQ=255)
                                                 aTTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGaaaaa                                                                                         <  2:100380/149‑1 (MQ=255)
                                                     aTCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATg                                                                                       >  4:314380/1‑147 (MQ=255)
                                                     aTCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGaa                                                                                     <  3:314380/149‑1 (MQ=255)
                                                         ggATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAg                                                                                                     <  4:237671/129‑1 (MQ=255)
                                                         ggATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAg                                                                                                     >  3:237671/1‑129 (MQ=255)
                                                              tCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGccctccc                                                                             <  2:195400/148‑1 (MQ=255)
                                                                  cAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAg                                                                        <  5:125764/149‑1 (MQ=255)
                                                                       gTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAgg                                                                    <  3:256548/148‑1 (MQ=255)
                                                                                   cGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAgagcg                                                       >  2:217604/1‑149 (MQ=255)
                                                                                    gATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAgagcg                                                       >  8:254282/1‑148 (MQ=255)
                                                                                    gATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAgagcg                                                       <  3:305078/148‑1 (MQ=255)
                                                                                          gATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAGAGCGGAGCGtt                                                <  3:245673/149‑1 (MQ=255)
                                                                                              gAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAGAGCGGAGCGTTCTCa                                            <  1:217604/149‑1 (MQ=255)
                                                                                                  cgcTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAGAGCGGAGCGTTCTCAgaga                                        <  6:168720/149‑1 (MQ=255)
                                                                                                   gcTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCgatga                                                                                                          >  1:214425/1‑82 (MQ=255)
                                                                                                   gcTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCgatga                                                                                                          <  2:214425/82‑1 (MQ=255)
                                                                                                   gcTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAGAGCGGAGCGTTCTCAGAGAt                                       >  6:223974/1‑149 (MQ=255)
                                                                                                                         gagaTAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAGAGCGGAGCGTTCTCAGAGATTTAATGGTTTCACCAACAAAtt                 >  2:27214/1‑149 (MQ=255)
                                                                                                                           gaTAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAGAGCGGAGCGTTCTCa                                            <  3:243191/120‑1 (MQ=255)
                                                                                                                           gaTAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAGAGCGGAGCGTTCTCa                                            >  4:243191/1‑120 (MQ=255)
                                                                                                                               aTCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAGAGCGGAGCGTTCTCAGAGATTTAATGGTTTCACCAACAAATTTAGGTa           >  8:41885/1‑149 (MQ=255)
                                                                                                                                  aaTGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAGAGCGGAGCGTTCTCAGAGATTTAATGGTTTCACCAACAAATTTAGGTagag        <  7:254282/149‑1 (MQ=255)
                                                                                                                                  aaTGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAGAGCGGAGCGTTCTCAGAGATTTAATGGTTTCACCAACAAATTTAGGTagag        >  5:277776/1‑149 (MQ=255)
                                                                                                                                     aaaggtgtTCCGCAGCTGCCGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAGAGCGGAGCGTTCTCAGAGATTTAATGGTTTCACCAACAAATTTa               >  7:274470/5‑139 (MQ=255)
                                                                                                                                     aaaggtgtTCCGCAGCTGCCGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAGAGCGGAGCGTTCTCAGAGATTTAATGGTTTCACCAACAAATTTa               <  8:274470/135‑1 (MQ=255)
                                                                                                                                      aaggtgtTCCGCAGCTGCCGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAgagcgga                                                     <  6:273723/97‑1 (MQ=255)
                                                                                                                                      aaggtgtTCCGCAGCTGCCGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAgagcgga                                                     >  5:273723/4‑100 (MQ=255)
                                                                                                                                         gtgtTCGGCAGCTGCTGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGTAGCCCTCCCTGTAGAAGGTCCACGTAGAGCGGAGCGTTCTCTGAGATTTAATGGTTTCACCAACAAATTTAGGTAGAGGGAGGc  <  7:157415/148‑1 (MQ=255)
                                                                                                                                               |                                                                                                                                             
AATGGTGGCCGAACAGCAGACGGATCAGGTCAATATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAGAGCGGAGCGTTCTCAGAGATTTAATGGTTTCACCAACAAATTTAGGTAGAGGGAGGC  >  NC_002947/2223226‑2223510

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: ‑