Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 4,426,685 C→T 8.8% P107S (CCG→TCG)  PP_3920 → putative Phage integrase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,426,6850CT 8.8% 158.4 / 3.3 56P107S (CCG→TCG) PP_3920putative Phage integrase
Reads supporting (aligned to +/- strand):  ref base C (28/23);  new base T (3/2);  total (31/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.65e-01

CAAGTCGGTGCCGAAGGAACTGACCACGATGAAGGGAATCTTCGACGAGTACCTGCTGAAGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTATTCAACACGGCGAGGGAATGGGGGCTTACAACCCGGGACAACCCGTGCCT  >  NC_002947/4426543‑4426833
                                                                                                                                              |                                                                                                                                                    
cAAGTCGGTGCCGAAGGAACTGACCACGATGAAGGGAATCTTCGACGAGTACCTGCTGAAGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATc                                                                                                                                                 >  5:327031/1‑148 (MQ=255)
 aaGTCGGTGCCGAAGGAACTGACCACGATGAAGGGAATCTTCGACGAGTACCTGCTGAAGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGa                                                                                                                                               >  1:337253/1‑149 (MQ=255)
        tGCCGAAGGAACTGACCACGATGAAGGGAATCTTCGACGAGTACCTGCTGAAGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGTCGATCGGCGccgag                                                                                                                                        <  1:39662/149‑4 (MQ=255)
        tGCCGAAGGAACTGACCACGATGAAGGGAATCTTCGACGAGTACCTGCTGAAGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATc                                                                                                                                        <  1:850/149‑1 (MQ=255)
        tGCCGAAGGAACTGACCACGATGAAGGGAATCTTCGACGAGTACCTGCTGAAGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATc                                                                                                                                        >  5:282826/1‑149 (MQ=255)
               ggAACTGACCACGATGAAGGGAATCTTCGACGAGTACCTGCTGAAGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCgg                                                                                                                                 <  6:36366/149‑1 (MQ=255)
                 aaCTGACCACGATGAAGGGAATCTTCGACGAGTACCTGCTGAAGATCGTCCAAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGcc                                                                                                                               >  6:47861/1‑149 (MQ=255)
                   cTGACCACGATGAAGGGAATCTTCGACGAGTACCTGCTGAAGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCAt                                                                                                                             >  5:57354/1‑149 (MQ=255)
                   cTGACCACGATGAAGGGAATCTTCGACGAGTACCTGCTGAAGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCAt                                                                                                                             <  7:196307/149‑1 (MQ=255)
                         aCGATGAAGGGAATCTTCGACGAGTACCTGCTGAAGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATcgc                                                                                                                       <  2:337253/149‑1 (MQ=255)
                                 gggAATCTTCGACGAGTACCTGCTGAAGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTAcc                                                                                                               >  2:142572/1‑149 (MQ=255)
                                            acgaGTACCTGCTGAAGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCgg                                                                                                    >  5:101121/1‑149 (MQ=255)
                                              gaGTACCTGCTGAAGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTc                                                                                                  >  3:262723/1‑149 (MQ=255)
                                                  aCCTGCTGAAGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGc                                                                                               >  2:75654/1‑148 (MQ=255)
                                                    ctgctgAAGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGaa                                                                                            <  2:244735/149‑1 (MQ=255)
                                                    ctgctgAAGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGaa                                                                                            <  8:223306/149‑1 (MQ=255)
                                                         gAAGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGcc                                                                                                                               >  2:258013/1‑109 (MQ=255)
                                                         gAAGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGcc                                                                                                                               <  1:258013/109‑1 (MQ=255)
                                                          aaGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATcgcg                                                                                                                      >  3:51782/1‑117 (MQ=255)
                                                          aaGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATcgcg                                                                                                                      <  4:51782/117‑1 (MQ=255)
                                                          aaGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGAcc                                                                                        <  4:310316/147‑1 (MQ=255)
                                                             aTCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGc                                                                                   <  6:327031/149‑1 (MQ=255)
                                                                 tCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCaaa                                                                                >  4:310770/1‑148 (MQ=255)
                                                                  cccAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGAGCAATGTGTTCTACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCaaa                                                                                >  6:270854/1‑147 (MQ=255)
                                                                     aGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAgg                                                                            >  7:291419/1‑148 (MQ=255)
                                                                       gCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGa                                                                          >  8:246953/1‑148 (MQ=255)
                                                                         aaGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAgg                                                                                     >  1:148036/1‑135 (MQ=255)
                                                                         aaGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAAt                                                                       >  8:212930/1‑149 (MQ=255)
                                                                          aGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATc                                                                      <  1:142572/149‑1 (MQ=255)
                                                                          aGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATc                                                                      >  8:214386/1‑149 (MQ=255)
                                                                               gTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGTCGCCGATCGACGCAATCACCCCGTCCATGATCGCGCAGTACAGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGTAAATCGCCCt                                                                 <  6:127613/149‑1 (MQ=255)
                                                                                tCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTg                                                                <  6:101121/149‑1 (MQ=255)
                                                                                       ccAGAAGGACAACATCTACGAGCTCAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTccc                                                         <  5:101182/149‑1 (MQ=255)
                                                                                         aGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCAc                                                       <  6:282826/149‑1 (MQ=255)
                                                                                         aGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCAc                                                       <  1:75654/149‑1 (MQ=255)
                                                                                              gACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTAtt                                                  >  8:238959/1‑149 (MQ=255)
                                                                                                caacaTCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTAATc                                                 >  2:16167/1‑148 (MQ=255)
                                                                                                 aacaTCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTATTCaa                                               >  2:186058/1‑149 (MQ=255)
                                                                                                  acaTCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTATTCAac                                              <  6:81434/149‑1 (MQ=255)
                                                                                                        aCGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTATTCAACACGGCg                                        >  3:214587/1‑149 (MQ=255)
                                                                                                          gAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTATTCAACACGGCGAg                                      >  5:306494/1‑149 (MQ=255)
                                                                                                           aGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTATTCAACACGGCGAgg                                     <  6:57354/149‑1 (MQ=255)
                                                                                                             cTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTATTCAACACGGCGAggg                                    >  3:323179/1‑148 (MQ=255)
                                                                                                                 agcagcTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTATTCAACACGGCGAGGGAATgg                               <  7:246953/149‑1 (MQ=255)
                                                                                                                  gcagcTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTATTCAACACGGCGAGGGAATggg                              <  8:291419/149‑1 (MQ=255)
                                                                                                                      cTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTATTCAACACGGCGAGGGAATGGGGGCt                          >  3:265966/1‑149 (MQ=255)
                                                                                                                          gcAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTATTCAACACGGCGAGGGAATGGGGGCTTAc                       >  6:38337/1‑148 (MQ=255)
                                                                                                                           cAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCAc                                                       >  5:24673/1‑115 (MQ=255)
                                                                                                                           cAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCAc                                                       <  6:24673/115‑1 (MQ=255)
                                                                                                                                tgtTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTATTCAACACGGCGAGGGAATGGGGGCTTACAACCCgg                <  7:212930/149‑1 (MQ=255)
                                                                                                                                tgtTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTATTCAACACGGCGAGGGAATGGGGGCTTACAACCCg                 <  7:214386/148‑1 (MQ=255)
                                                                                                                                     gACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTATTCAACACGGCGAGGGAATGGGGGCTTACAACCCGGGACaa           >  7:30418/1‑149 (MQ=255)
                                                                                                                                       gatggCGTCGATCGGCGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTATTCAACACGGCGAGGGAATGGGGGCt                          <  7:280070/129‑1 (MQ=255)
                                                                                                                                       gatggCGTCGATCGGCGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTATTCAACACGGCGAGGGAATGGGGGCt                          >  8:280070/4‑132 (MQ=255)
                                                                                                                                       gatggCGTCGATCGGCGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTATTCAACACGGCGAGGGAATGGGGGCTTACAACCCGGGACAAcc         >  2:12982/4‑149 (MQ=255)
                                                                                                                                        atggCGTCGATCGGCGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTATTCAACACGGCGAGGGAATGGGGGCTTACAACCCGGGACAAccc        >  8:263719/3‑149 (MQ=255)
                                                                                                                                             gcCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACACGGAAATCGCCCTGCTTTCCCCCGTAGTCAACACGGCGAGGGAATGGGGGCTTACAACCCGGGACAACCCGGGcc   >  2:242552/1‑149 (MQ=255)
                                                                                                                                              ccGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTATTCAACACGGCGAGGGAATGGGGGCTTACAACCCGGGACAACCCGTGCCt  >  3:157179/1‑149 (MQ=255)
                                                                                                                                              |                                                                                                                                                    
CAAGTCGGTGCCGAAGGAACTGACCACGATGAAGGGAATCTTCGACGAGTACCTGCTGAAGATCGTCCCAGGCAAGGCCGTCAGGACCCAGAAGGACAACATCTACGAGCTGAAGCAGCTGCGCAATGTGTTCGACTCGGCGCCGATCGACGCCATCACCCCGGCCATGATCGCGCAGTACCGCGACTCGCGGTCGGCGAAGACCAGGGCAAACAGGGAAATCGCCCTGCTTTCCCACGTATTCAACACGGCGAGGGAATGGGGGCTTACAACCCGGGACAACCCGTGCCT  >  NC_002947/4426543‑4426833

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: ‑