Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,560,093 G→T intergenic (+27/‑164) intZ → / → yffL CPZ‑55 prophage; putative phage integrase IntZ/CPZ‑55 prophage; uncharacterized protein YffL

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,560,0930GT95.8% 75.9 / ‑3.0 24intergenic (+27/‑164)intZ/yffLCPZ‑55 prophage; putative phage integrase IntZ/CPZ‑55 prophage; uncharacterized protein YffL
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base T (9/14);  total (9/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

ATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCGCAATTTTGCATTTTGTATAAGTATTTGTTTTGTGTGGTTTAACTATCACCTGATAAGAAACCTGTATTCAATTTGCCGGATTCGTCCGGCTTTTCTTTTTCGCTAATTATTCCATTATTCCA  >  NC_000913/2559960‑2560215
                                                                                                                                     |                                                                                                                          
ataACCAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCTCAAttt                                                                                                                      >  2:65178/1‑140 (MQ=255)
    ccAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCa                                                                                                                  <  1:219598/140‑1 (MQ=255)
    ccAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCa                                                                                                                  <  1:90066/140‑1 (MQ=255)
        gCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCa                                                                                                                  >  2:366845/1‑136 (MQ=255)
        gCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCa                                                                                                                  <  1:366845/136‑1 (MQ=255)
        gCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCAtttt                                                                                                              >  2:249400/1‑140 (MQ=255)
                 cTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCATTTTGTATAAGTa                                                                                                     <  1:65178/140‑1 (MQ=255)
                      gCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCATTTTGTATAAGTAtttgt                                                                                                <  2:206488/140‑1 (MQ=255)
                      gCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCATTTTGTATAAGTAtttgt                                                                                                >  2:23810/1‑140 (MQ=255)
                          cGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCATTTTGTATAAGTAtttgttttg                                                                                            >  2:267577/1‑140 (MQ=255)
                           ggCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCATTTTGTATAAGTAtttgttttgt                                                                                           <  2:82702/140‑1 (MQ=255)
                                 cAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCATTTTGTATAAGTATTTGTTTTGTGTGGtt                                                                                     <  1:229100/140‑1 (MQ=255)
                                 cAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCATTTTGTATAAGTATTTGTTTTGTGTGGtt                                                                                     <  2:274224/140‑1 (MQ=255)
                                         cAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCATTTTGTATAAGTATTTGTTTTGTGTGGTTTAACTATc                                                                             >  1:12813/1‑140 (MQ=255)
                                         cAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCGCAATTTTGCATTTTGTATAAGTATTTGTTTTGTGTGGTTTAACTATc                                                                             >  2:112497/1‑140 (MQ=255)
                                             aTTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCATTTTGTATAAGTATTTGTTTTGTGTGGTTTAACTATCACCt                                                                         <  2:25447/140‑1 (MQ=255)
                                               tACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCGCAATTTTGCATTTTGTATAAGTATTTGTTTTGTGTGGTTTAACTATCACCTGa                                                                       <  1:112497/140‑1 (MQ=255)
                                                    cGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCATTTTGTATAAGTATTTGTTTTGTGTGGTTTAACTATCACCTGATAAGa                                                                  <  1:249400/140‑1 (MQ=255)
                                                      aCGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCATTTTGTATAAGTATTTGTTTTGTGTGGTTTAACTATCACCTGATAAGaaa                                                                >  2:289297/1‑140 (MQ=255)
                                                                          gCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCATTTTGTATAAGTATTTGTTTTGTGTGGTTTAACTATCACCTGATAAGAAACCTGTATTCAATTTGCCGGa                                            >  2:76043/1‑140 (MQ=255)
                                                                               tAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCATTTTGTATAAGTATTTGTTTTGTGTGGTTTAACTATCACCTGATAAGAAACCTGTATTCAATTTGCCGGATTCGt                                       >  1:304353/1‑140 (MQ=255)
                                                                                 aCGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCATTTTGTATAAGTATTTGTTTTGTGTGGTTTAACTATCACCTGATAAGAAACCTGTATTCAATTTGCCGGATTCGTcc                                     <  2:66700/140‑1 (MQ=255)
                                                                                             tAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCATTTTGTATAAGTATTTGTTTTGTGTGGTTTAACTATCACCTGATAAGAAACCTGTATTCAATTTGCCGGATTCGTCCGGcttttctttt                         <  2:304353/140‑1 (MQ=255)
                                                                                                            taatTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCATTTTGTATAAGTATTTGTTTTGTGTGGTTTAACTATCACCTGATAAGAAACCTGTATTCAATTTGCCGGATTCGTCCGGCTTTTCTTTTTCGCTAattattcca          <  1:23810/140‑1 (MQ=255)
                                                                                                             aatTAAGCGGCTTTTTTGCAAAGCTCAATTTTGCATTTTGTATAAGTATTTGTTTTGTGTGGTTTAACTATCACCTGATAAGAAACCTGTATTCAATTTGCCGGATTCGTCCGGCTTTTCTTTTTCGCTAattattccat         <  1:267577/140‑1 (MQ=255)
                                                                                                                    cGGCTTTTTTGCAAAGCTCAATTTTGCATTTTGTATAAGTATTTGTTTTGTGTGGTTTAACTATCACCTGATAAGAAACCTGTATTCAATTTGCCGGATTCGTCCGGCTTTTCTTTTTCGCTAAttattccattattcca  >  2:84798/1‑140 (MQ=255)
                                                                                                                                     |                                                                                                                          
ATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGCTTTTTTGCAAAGCGCAATTTTGCATTTTGTATAAGTATTTGTTTTGTGTGGTTTAACTATCACCTGATAAGAAACCTGTATTCAATTTGCCGGATTCGTCCGGCTTTTCTTTTTCGCTAATTATTCCATTATTCCA  >  NC_000913/2559960‑2560215

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑