Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 2,223,378 G→C 9.8% P390R (CCG→CGG)  PP_1962 ← site‑specific recombinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029472,223,3780GC 9.8% 143.3 / 7.5 51P390R (CCG→CGG) PP_1962site‑specific recombinase
Reads supporting (aligned to +/- strand):  ref base G (22/23);  new base C (2/3);  total (24/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01

GTGGCCGAACAGCAGACGGATCAGGTCAATATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAGAGCGGAGCGTTCTCAGAGATTTAATGGTTTCACCAACAAATTTAGGTAGAGGGAGGCGTTCAGTCTCAC  >  NC_002947/2223230‑2223522
                                                                                                                                                    |                                                                                                                                                
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)
     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                                                                                                                 >  3:237671/1‑129 (MQ=255)
                                                     ggATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAg                                                                                                                 <  4:237671/129‑1 (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                                                                   <  3:305078/148‑1 (MQ=255)
                                                                                gATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAgagcg                                                                   >  8:254282/1‑148 (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                                                        >  4:243191/1‑120 (MQ=255)
                                                                                                                       gaTAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAGAGCGGAGCGTTCTCa                                                        <  3:243191/120‑1 (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                                                                 >  5:273723/4‑100 (MQ=255)
                                                                                                                                  aaggtgtTCCGCAGCTGCCGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAgagcgga                                                                 <  6:273723/97‑1 (MQ=255)
                                                                                                                                     gtgtTCGGCAGCTGCTGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGTAGCCCTCCCTGTAGAAGGTCCACGTAGAGCGGAGCGTTCTCTGAGATTTAATGGTTTCACCAACAAATTTAGGTAGAGGGAGGc              <  7:157415/148‑1 (MQ=255)
                                                                                                                                                 tGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAGAGCGGAGCGTTCTCAGAGATTTAATGGTTTCACCAACAAATTTAGGTAGAGGGAGGCGTTCAGTCTCAc  >  2:56844/1‑148 (MQ=255)
                                                                                                                                                    |                                                                                                                                                
GTGGCCGAACAGCAGACGGATCAGGTCAATATTTCGTTCGCTCCGATTGATCAGGATTTCTGCAATCGTTTTCCGAAAGCGATGCGGATGGAGGCGCTCGATCCCCGTCACTTCTTCGAGATAATCAATGATTGTGTTCGGCAGCTGCGGAACACCTTTGGTTACCTTGATCGATGATGAAGCACTCTGAAAAATGAAGCCCTCCCTGTAGAAGGTCCACGTAGAGCGGAGCGTTCTCAGAGATTTAATGGTTTCACCAACAAATTTAGGTAGAGGGAGGCGTTCAGTCTCAC  >  NC_002947/2223230‑2223522

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: ‑