Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,819,3130GA54.2% 3.9 / 25.1 24intergenic (‑119/+84)ves/spyenvironmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone Spy
Reads supporting (aligned to +/- strand):  ref base G (11/0);  new base A (0/13);  total (11/13)
Fisher's exact test for biased strand distribution p-value = 4.01e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.68e-06
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

AGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATT  >  NZ_CP009273/1819232‑1819401
                                                                                 |                                                                                        
aGGTAACCGGGGATGGGTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCGTTTTTTACAGCTGGTTGAGAGGagaaaagaaa                                                                                  >  2:316701/1‑90 (MQ=255)
 ggTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTGAGAAGAgaaaagaaaa                                                                                 >  2:207534/1‑90 (MQ=255)
    aaCCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAAccg                                                                              >  1:311708/1‑90 (MQ=255)
      ccGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAAccgcc                                                                            >  2:171491/1‑90 (MQ=255)
           gATGGTTATGGGCACCTCGGGTGATTTACGTTAGTGGTGATCAGGTTTTTTTTACAACTGTTTGAAAAGAAAAAAAAAAACCGCCGATcc                                                                       <  1:171491/90‑1 (MQ=255)
                ttATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAACCGCCGATCCTGTcc                                                                  >  2:210845/1‑90 (MQ=255)
                   tgggCACCTGGGGTGATTTACTTTAGGGGTGATCGGGTTTTTTTTACAACTGTTTGAAAAGAAAAAAAAAACCCGCCGATCCTGTCCAcc                                                               <  1:194314/88‑1 (MQ=255)
                        aaCTGGGGTGATTTACGTTAGTGGTGATCAGTTTTTTTTTACAACTTTTTGAGAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCAtt                                                          <  2:103194/90‑1 (MQ=255)
                        aaCTGGGGTGATTTACGTTAGTGGTGATCAGGTTTTTTTTACAACTTTTTGAGAAGAAAAAAGAAAACCGCCGATCCTGTCCACCGCAtt                                                          <  1:18219/90‑1 (MQ=255)
                         aCTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTa                                                         >  2:5092/1‑90 (MQ=255)
                         aCTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTa                                                         >  2:194314/1‑90 (MQ=255)
                         aCTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTa                                                         >  1:245989/1‑90 (MQ=255)
                          ctggggTGTTTTACGTTAGTGGTGATCAGGTTTTTTTTACAACTTTTTGAGAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTAc                                                        <  1:416952/87‑1 (MQ=255)
                             gggTGTTTTACGTTGGGGGTGATCGGTTTTTTTTTACAATTTTTTGAGAAGAAAAAAAAAACCCGCCGATCCTGTCCACCGCATTACTGc                                                     <  2:311708/90‑1 (MQ=255)
                               gtattttACGTTAGGGGTGATCGGGTTTTTTTTACATTTTTTTGAAAAGAAAAAAAAAACCCGCCGATCCTGTCCACCGCATTACTGCaa                                                   <  2:407424/86‑1 (MQ=255)
                               gtaaTTTCCGTTAGTGGTCACCGGTTTTTTTTTACATCTTTTGGAAAAAAAAAAAAAAACCCGCCGATCCTGTCCACCGCATTACTGCaa                                                   <  2:239544/87‑1 (MQ=255)
                               gTGATTTACGTTAGTGGTGATCAGGTTTTTTTTACAACTGTTTGAAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCaa                                                   <  1:90370/90‑1 (MQ=255)
                               aagATTTACGTTAGGGGTGATCGGGTTTTTTTTACATTTGTTTGAAAAGAAAAAAAAAACCCGCCGATCCTGTCCACCGCATTACTGCaa                                                   <  2:271477/88‑1 (MQ=255)
                                  ttttAGGTTAGTGGTGATCGGTTTTTTTTTAAAACTTTTTGAAAAAAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGt                                                <  2:168320/89‑1 (MQ=255)
                                    ttACGTTAGTGGTGATCGGGTTTTTTTTACAACTGTTTGAAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAg                                              <  1:327692/90‑1 (MQ=255)
                                         ttAGTGGTGATCAGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGAc                                         >  2:209557/1‑90 (MQ=255)
                                            gtggtgATCAGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGAcctg                                      >  1:271477/1‑87 (MQ=255)
                                                tgATCAGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACcg                                  >  2:247696/1‑90 (MQ=255)
                                                 gATCAGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACcgg                                 >  2:415899/1‑90 (MQ=255)
                                                   tCAGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACcggcg                               >  1:277403/1‑90 (MQ=255)
                                                                  aaCTGTTTGAAAAGAAAAAAAAAACCCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTg                <  1:407513/90‑1 (MQ=255)
                                                                                agaaaagaaaACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGattatt  >  1:25087/1‑90 (MQ=255)
                                                                                 |                                                                                        
AGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATT  >  NZ_CP009273/1819232‑1819401

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑