Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,002,576 A→T 7.9% I105F (ATT→TTT)  PP_4409 → site‑specific recombinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,002,5760AT 7.9% 148.9 / 4.7 51I105F (ATT→TTT) PP_4409site‑specific recombinase
Reads supporting (aligned to +/- strand):  ref base A (25/22);  new base T (2/2);  total (27/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.18e-01

CTTACATAATGCCAACTTCATCGACTTCTTCGAAGAAGGTCTCAAGCATATTGAGCCGAGCAAATCCGAAGTAAACACCCTGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCTTTCCTGAAGAGCCTTGGTAATTACTTCCAGAAATACAAAGACTACTGCGAGAACGGGCTGGTAATTGAAA  >  NC_002947/5002431‑5002717
                                                                                                                                                 |                                                                                                                                             
cTTACATAATGCCAACTTCATCGACTTCTTCGAAGAAGGTCTCAAGCATATTGAGCCGAGCAAATCCGAAGTAAACACCCTGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTg                                                                                                                                           <  2:257256/150‑1 (MQ=255)
cTTACATAATGCCAACTTCATCGACTTCTTCGAAGAAGGTCTCAAGCATATTGAGCCGAGCAAATCCGAAGTAAACACCCTGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTg                                                                                                                                           <  1:884225/150‑1 (MQ=255)
 ttACATAATGCCAACTTCATCGACTTCTTCGAAGAAGGTCTCAAGCATATTGAGCCGAGCAAATCCGAAGTAAACACCCTGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGc                                                                                                                                          <  2:743432/150‑1 (MQ=255)
     aTAATGCCAACTTCATCGACTTCTTCGAAGAAGGTCTCAAGCATATTGAGCCGAGCAAATCCGAAGTAACCACCCTGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGaaa                                                                                                                                      >  2:412774/1‑149 (MQ=255)
               cTTCATCGACTTCTTCGAAGAAGGTCTCAAGCATATTGAGCCGAGCAAATCCGAAGTAAACACCCTGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTc                                                                                                                            >  2:568752/1‑150 (MQ=255)
                      gACTTCTTCGAAGAAGGTCTCAAGCATATTGAGCCGAGCAAATCCGAAGTAAACACCCTGTATCGAGAGGATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATg                                                                                                                     <  1:568752/150‑1 (MQ=255)
                      gACTTCTTCGAAGAAGGTCTCAAGCATATTGAGCCGAGCAAATCCGAAGTAAACAACCTGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCCAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATg                                                                                                                     <  1:757075/150‑1 (MQ=255)
                           cttcGAAGAAGGTCTCAAGCATATTGAGCCGAGCAAATCCTAAGTAAACACCCTGTATCGAGAGTATCACTAATTCACGACAGTTGGCAGCTCCAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAg                                                                                                                <  1:135571/150‑1 (MQ=255)
                            ttcGAGGAAGGCCTCAAGCATATTGAGCCGAGCAAATCCGAAGTAAACACCCTGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGc                                                                                                               >  1:151371/1‑150 (MQ=255)
                            ttcGAAGAAGGTCTCAAGCATATTGAGCCGAGCAAATCCGAAGTAAACACCCTGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTcc                                                                                                                           <  2:92014/138‑1 (MQ=255)
                            ttcGAAGAAGGTCTCAAGCATATTGAGCCGAGCAAATCCGAAGTAAACACCCTGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTcc                                                                                                                           >  1:92014/1‑138 (MQ=255)
                            ttcGAAGAAGGTCTCAAGCATATTGAGCCGAGCAAATCCGAAGGAAACACCCTGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGc                                                                                                               >  2:434903/1‑150 (MQ=255)
                               gaagaaGGTCTCAAGCATATTGAGCCGAGCAAATCCGAAGTAAACACCCTGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACg                                                                                                            <  1:83321/150‑1 (MQ=255)
                                aagaagGTCTCAAGCATATTGAGCCGAGCAAATCCGAAGTAAACACCCTGTGTCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACgg                                                                                                           >  1:357658/1‑150 (MQ=255)
                                aagaagGTCTCAAGCATATTGAGCCGAGCAAATCCGAAGTAAACACCCTGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACgg                                                                                                           >  1:904354/1‑150 (MQ=255)
                                               atatTGAGCCGAGCAAATCCGAAGTAAACACCCTGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAat                                                                                            >  1:196860/1‑150 (MQ=255)
                                                  ttGAGCCGAGCAAATCCGAAGTAAACACCCTGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATc                                                                                         >  1:401568/1‑150 (MQ=255)
                                                     aGCCGAGCAAATCCGAAGTAAACACCCTGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACg                                                                                      <  1:1094755/150‑1 (MQ=255)
                                                           gCAAATCCGAAGTAAACACCCTGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAat                                                                                            <  2:213449/138‑1 (MQ=255)
                                                           gCAAATCCGAAGTAAACACCCTGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAat                                                                                            >  1:213449/1‑138 (MQ=255)
                                                                    aaGTAAACACCCTGTATCGAGAGTATCACTCACACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCtt                                                                       >  2:625597/1‑150 (MQ=255)
                                                                        aaaCACCCTGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATCCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCTTTCCt                                                                   >  2:681156/1‑150 (MQ=255)
                                                                              ccTGTATCGAGAGTATCACTCATACTTGTCAGTTGGCAGCGCGAGCAATTCAACAGGTGTTCGCAAAATTTGCGAAGCTAAACCGTACCCAATGGTAAGGACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCTTTCCTGAagag                                                             >  2:582987/1‑150 (MQ=255)
                                                                              ccTGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCTTTCCTGAagag                                                             <  2:196860/150‑1 (MQ=255)
                                                                                tGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCTTTCCTGAAGAGcc                                                           >  2:71436/1‑150 (MQ=255)
                                                                                    tCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATCCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCTTTCCTGAAGAGCCTTgg                                                       <  1:681156/150‑1 (MQ=255)
                                                                                       agagTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATg                                                                                                                     >  2:626183/1‑85 (MQ=255)
                                                                                       agagTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATg                                                                                                                     <  1:626183/85‑1 (MQ=255)
                                                                                       agagTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCTTTCCTGAAGAGCCTTGGTaa                                                    <  1:434903/150‑1 (MQ=255)
                                                                                               aCTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATc                                                                                                       <  2:107438/91‑1 (MQ=255)
                                                                                               aCTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATc                                                                                                       >  1:107438/1‑91 (MQ=255)
                                                                                                cTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAat                                                                                            >  2:84504/1‑101 (MQ=255)
                                                                                                cTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAat                                                                                            <  1:84504/101‑1 (MQ=255)
                                                                                                   gtACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCTTTCCTGAAGAGCCTTGGTAATTACTTc                                             >  1:1062622/2‑145 (MQ=255)
                                                                                                   aTACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCTTTCCTGAAGAGCCTTGGTAATTACTTc                                             <  2:1062622/145‑1 (MQ=255)
                                                                                                       ttGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCGCACGTCCAGCCTTTCCTGAAGAGCCTTGGTAATTACTTCCAGAAATAc                                    >  2:85180/1‑150 (MQ=255)
                                                                                                       ttGACAGTTGGCAGCGCGAACAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATc                                                                                         <  1:909484/97‑1 (MQ=255)
                                                                                                       ttGACAGTTGGCAGCGCGAACAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATc                                                                                         >  2:909484/1‑97 (MQ=255)
                                                                                                               tGGCAGCGCGAGCAATTCAACAGTTGTTCGAAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCTTTCCTGAAGAGCCTTGGTAATTACTTCCAGAAATACAAAGacta                            <  2:357658/150‑1 (MQ=255)
                                                                                                                  cAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCTTTCCTGAAGAGCCTTGGTAATTACTTCCAGAAATACAAAGACTACTg                         >  1:735083/1‑150 (MQ=255)
                                                                                                                   aGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCTTTCCTGAAGAGCCTTGGTAATTACTTCCAGAAATACAAAGACTACTGc                        >  2:1062678/1‑150 (MQ=255)
                                                                                                                    gcgcGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCTTTCCTGAAGAGCCTTGGTAATTACTTCCAGAAATACAAAGACTACTGCg                       >  1:1058704/1‑150 (MQ=255)
                                                                                                                              ttCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCTTTCCTGAAGAGCCTTGGTAATTACTTCCAGAAATACAAAGACTACTGCGAGAACggcat             >  2:790427/1‑147 (MQ=255)
                                                                                                                                cAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCTTTCCTGAAGAGCCTTGGTAATTACTTCCAGAAATACAAAGACTACTGCGAGAACGGGCTgg           <  2:604676/150‑1 (MQ=255)
                                                                                                                                  aCAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCTTTCCTGAAGAGCCTTGGTAATTACTTCCAGAAATACAAAGACTACTGCGAGAACGGGCTGGTa         >  2:983905/1‑150 (MQ=255)
                                                                                                                                   cAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCTTTCCTGAAGAGCCTTGGTAATTACTTCCAGAAATACAAAGACTACTGCGAGAACGGGCTGGTaa        <  1:71436/150‑1 (MQ=255)
                                                                                                                                     gttgttCGCAAGATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCTTTCCTGCAGAGCCTTGGTAATTACTCCCAGAAATACAAAGACTACTGCGAGAACGGGCTGGTAAtt      <  1:412774/150‑1 (MQ=255)
                                                                                                                                        cttCGCAAATTTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCTTTCCTGAAGAGCCTTGGTAATTACTTCCAGAAATACAAAGACTACTg                         >  1:457575/2‑128 (MQ=255)
                                                                                                                                        cttCGCAAATTTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCTTTCCTGAAGAGCCTTGGTAATTACTTCCAGAAATACAAAGACTACTg                         <  2:457575/127‑1 (MQ=255)
                                                                                                                                        cttCGCAAATTTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATACCACGCTCAAGTCCAGCCTTTCCTGAAGAGCCTTGGTAATTACTTCCAGAAATACAAAGACTACTGCGAGAACGGGCTGGTAATTGaa   >  1:582327/2‑150 (MQ=255)
                                                                                                                                         ttCGCAAATTTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATACCACGCTCAAGTCCAGCCTTTCCTGAAGAGCCTTGGTAATTACTTCCAGAAATACAAAGACTACTGCGAGAACGGGCTGGTAATTGaaa  <  2:582327/150‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                             
CTTACATAATGCCAACTTCATCGACTTCTTCGAAGAAGGTCTCAAGCATATTGAGCCGAGCAAATCCGAAGTAAACACCCTGTATCGAGAGTATCACTCATACTTGACAGTTGGCAGCGCGAGCAATTCAACAGTTGTTCGCAAAATTTGCGAAGCTAAACCGTCCCCAATGGTAAGCACGGCATCGTCAAAAAAATATCACGCTCAAGTCCAGCCTTTCCTGAAGAGCCTTGGTAATTACTTCCAGAAATACAAAGACTACTGCGAGAACGGGCTGGTAATTGAAA  >  NC_002947/5002431‑5002717

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑