Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,414,637 C→T 9.8% A535V (GCC→GTC)  PP_3026 → recombinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,414,6370CT 9.8% 133.8 / 4.8 51A535V (GCC→GTC) PP_3026recombinase
Reads supporting (aligned to +/- strand):  ref base C (21/25);  new base T (2/3);  total (23/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.12e-01

ATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGTGTGCACCACCAGGTGGCCTTGTCCCTCCCAGAAATTTTCCTGTACCTCGACGCATACACGCCAGGCGGCCCATGCGA  >  NC_002947/3414489‑3414784
                                                                                                                                                    |                                                                                                                                                   
atgatCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGcggcc                                                                                                                                                    <  2:1570283/150‑1 (MQ=255)
 tgatCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCACGCAGTTTAGGAAGACCGGAGAGTGGGcggccg                                                                                                                                                   <  1:1507445/150‑1 (MQ=255)
       aTACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCg                                                                                                                                             >  1:1784055/1‑150 (MQ=255)
            ttCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGTCGACGCCGGCCGc                                                                                                                                        <  2:486849/150‑1 (MQ=255)
               gATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGTCTACGCCGGCCGCCCa                                                                                                                                     <  1:1314085/150‑1 (MQ=255)
                    cATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCactctc                                                                                                                                >  2:1756079/1‑145 (MQ=255)
                      tCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCactctccg                                                                                                                              <  1:1756079/150‑8 (MQ=255)
                            tttACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTAc                                                                                                                        <  2:1313873/150‑1 (MQ=255)
                               aCATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGATAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCt                                                                                                                     <  2:1483172/150‑1 (MQ=255)
                               aCATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCt                                                                                                                     <  2:1784055/150‑1 (MQ=255)
                                cATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTg                                                                                                                    >  1:1385568/1‑150 (MQ=255)
                                 aTGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGCGCGGCCGGCGACGACCGCCCAGACTGATGTTTACGCTGa                                                                                                                   >  2:1343105/1‑150 (MQ=255)
                                     gtggtgTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTAc                                                                                                                        <  1:1284391/141‑1 (MQ=255)
                                     gtggtgTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTAc                                                                                                                        >  2:1284391/1‑141 (MQ=255)
                                         tgtAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGGTGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTgt                                                                                                           >  1:674460/1‑150 (MQ=255)
                                          gtAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTgtc                                                                                                          <  1:260665/150‑1 (MQ=255)
                                           tAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTgtcg                                                                                                         >  1:604868/1‑150 (MQ=255)
                                             gTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTgtcgtc                                                                                                       <  2:1473502/150‑1 (MQ=255)
                                                ccAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTAt                                                                                                    >  2:321825/1‑150 (MQ=255)
                                                     ggggCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGa                                                                                               >  2:254149/1‑150 (MQ=255)
                                                                    gTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAg                                                                                >  1:54224/1‑150 (MQ=255)
                                                                     tACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAgt                                                                               <  1:254149/150‑1 (MQ=255)
                                                                        aTCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGTCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGtgtg                                                                            >  1:176494/1‑150 (MQ=255)
                                                                          cGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGTGTGca                                                                          <  1:380655/150‑1 (MQ=255)
                                                                             tGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTgtc                                                                                                          <  1:379595/115‑1 (MQ=255)
                                                                             tGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTgtc                                                                                                          >  2:379595/1‑115 (MQ=255)
                                                                             tGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAg                                                                                              >  1:560794/1‑127 (MQ=255)
                                                                             tGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAg                                                                                              <  2:560794/127‑1 (MQ=255)
                                                                              gTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGTGTGcaccac                                                                      <  2:436409/150‑1 (MQ=255)
                                                                              gTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGTGTGcaccac                                                                      <  1:28606/150‑1 (MQ=255)
                                                                                 ttGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGTGTGCACCACCAg                                                                   >  2:1319101/1‑150 (MQ=255)
                                                                                  tGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCgg                                                                                         <  2:1490711/127‑1 (MQ=255)
                                                                                  tGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCgg                                                                                         >  1:1490711/1‑127 (MQ=255)
                                                                                  tGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGTGTGCACCACCAgg                                                                  <  1:1319101/150‑1 (MQ=255)
                                                                                    cTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGActtctt                                                                                                             <  2:1153778/105‑1 (MQ=255)
                                                                                    cTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGActtctt                                                                                                             >  1:1153778/1‑105 (MQ=255)
                                                                                     tGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACGGGAGAGTGGGAGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTTTTGGGAGGCCGGGTGGGCTAGTGTGCACCACCAGGTgg                                                               >  2:616401/1‑150 (MQ=255)
                                                                                       aTTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGTGTGCACCACCAGGTGGcc                                                             <  2:1137769/150‑1 (MQ=255)
                                                                                           ccAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGTCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGTGTGCACCACCAGGTGGCCTTGt                                                         <  2:176494/150‑1 (MQ=255)
                                                                                            cAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGTGTGCACCACCAGGTGGCCTTGtc                                                        <  1:321825/150‑1 (MQ=255)
                                                                                             aaGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGTGTGCACCACCAGGTGGCCTTGtcc                                                       >  2:1933004/1‑150 (MQ=255)
                                                                                               ggCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGTGTGCACCACCAGGTGGCCTTGtccct                                                     >  1:197535/1‑150 (MQ=255)
                                                                                                gCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGTGTGCACCACCAGGTGGCCTTGtccctc                                                    <  2:604868/150‑1 (MQ=255)
                                                                                                           gcgATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGCGCTAGTGTGCACCACCAGGTGGCCTTGTCCCTCCCAGAAAtttt                                         <  2:335639/150‑1 (MQ=255)
                                                                                                            cggtGGCTTAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTTACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGTGTGCACCACCAGGTGGCCTTGTCCCTCCCAGAAATTTTc                                        <  1:1343105/147‑1 (MQ=255)
                                                                                                             gATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGTCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGc                                                                                   >  1:1926000/1‑106 (MQ=255)
                                                                                                             gATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGTCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGc                                                                                   <  2:1926000/106‑1 (MQ=255)
                                                                                                             gATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGTGTGCACCACCAGGTGGCCTTGTCCCTCCCAGAAATTTTcc                                       <  1:96442/150‑1 (MQ=255)
                                                                                                                  cTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCgg                                                                                         >  2:1247959/1‑95 (MQ=255)
                                                                                                                  cTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCgg                                                                                         <  1:1247959/95‑1 (MQ=255)
                                                                                                                       ggTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGTGTGCACCACCAGGTGGCCTTGTCCCTCCCAGAAATTTTCCTGTACCTCGa                             >  2:1389231/1‑150 (MQ=255)
                                                                                                                                            gTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGTGTGCACCACCACGTTGAAACGGCTCGCCCAGAAATTTTCCTGTACCTCGACGCATACACGCCAGGCGGccc        <  2:1927753/150‑1 (MQ=255)
                                                                                                                                             tGGGCGGTCGACGCCGGCCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGTGTGCACCACCAGGTGGCCTTGTCCCTCCCAGAAATTTTCCTGTACCTCGACGCATACACGCCAGGCGGCCCa       >  2:515300/1‑150 (MQ=255)
                                                                                                                                               ggcggcCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGTGTGCACCACCAGGTGGCCTTGTCCCTCCCAGAAATTTTCCTGTACCTCGACGCATACACGCCAGGCGGCCCATg     >  1:1872861/1‑150 (MQ=255)
                                                                                                                                                gcggcCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGTGTGCACCACCAGGTGGCCTTGTCCCTCCCAGAAATTTTCCTGTACCTCGACGCATACACGCCAGGCGGCCCATGc    <  2:1385568/150‑1 (MQ=255)
                                                                                                                                                  ggccggcGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGTGTGCACCACCAGGTGGCCTTGTCCCTCCCAGAAATTTTCCTGTACCTCGACGCATACACGCCAGGCGGCCCATGCGa  >  2:1544864/1‑150 (MQ=255)
                                                                                                                                                    |                                                                                                                                                   
ATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTCGACCGCCCAGACTGATGTTTACGCTGACTTCTTGTCGTCTATTGGGAGGCCGGGTGGGCTAGTGTGCACCACCAGGTGGCCTTGTCCCTCCCAGAAATTTTCCTGTACCTCGACGCATACACGCCAGGCGGCCCATGCGA  >  NC_002947/3414489‑3414784

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: ‑