Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,819,3180GA45.0% 12.9 / 12.7 20intergenic (‑124/+79)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 (0/9);  total (11/9)
Fisher's exact test for biased strand distribution p-value = 5.95e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

AGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATT  >  NZ_CP009273/1819232‑1819401
                                                                                      |                                                                                   
aGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTGAGAAGagaaaagaaa                                                                                  >  1:282617/1‑90 (MQ=255)
aGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTGAGAAGagaaaagaaa                                                                                  >  1:566943/1‑90 (MQ=255)
      ccGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAAccgcc                                                                            >  1:736709/1‑90 (MQ=255)
      ccGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAAAAAAccgcc                                                                            <  2:566943/90‑1 (MQ=255)
           gttGGTTACCGCCACCTGGGGTATTTTACTTTAGTGGTAATCGGTTTTTTTTTAAAATTTTTAAAAAAGAAAAAAAAAAACCGCCGATcc                                                                       <  1:922775/88‑1 (MQ=255)
            aTGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAACCGCCGATCCt                                                                      >  1:1087123/1‑90 (MQ=255)
               gTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAACCGCCGATCCTGTc                                                                   >  1:511485/1‑90 (MQ=255)
                ttATCGCCAACTGGGGTGATTTACTTTAGTGGTGATCAGGTTTTTTTTACAACTGTTTGAGAAGAAAAAAAAAAACCGCCGATCCTGTcc                                                                  <  2:659954/90‑1 (MQ=255)
                          ctggggTGTTTTATTTTAGTGGTGATCAGTTTTTTTTTACACTTTTTTGAGAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTAc                                                        <  2:1502119/87‑1 (MQ=255)
                          cgggggTGTTTTACGTTGGGGGTGATAGGGTTTTTTTTAAAATTGTTTGAAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTAc                                                        <  2:1087123/87‑1 (MQ=255)
                               gtgtTTTTCGTTAGTGGTGATCGGGCTTTTTTTAAAACTTTTTGAAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCaa                                                   <  2:282617/90‑1 (MQ=255)
                                   tttACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTa                                               >  2:172093/1‑90 (MQ=255)
                                    ttACGTTAGGGGTGACAGGGTTTTTTTTACAATTTTTTGAAAAAAAAAAAAAAAGCCGCCGATCCTGTCCACCGCATTACTGCAAGGTAg                                              <  2:736709/90‑1 (MQ=255)
                                        gTTAGTGGTGATCAGTTTTTTTTTACACTTTTTGGAAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGa                                          <  1:1104842/90‑1 (MQ=255)
                                                 gATCAGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACcgg                                 >  1:465371/1‑90 (MQ=255)
                                                   tCAGGTTTTTTTTACAATTTTTTGAGAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACcggcg                               <  2:465371/90‑1 (MQ=255)
                                                     aGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGt                             >  1:250644/1‑90 (MQ=255)
                                                     aGGCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGt                             >  2:810362/1‑90 (MQ=255)
                                                      ggCTTTTTTTACAACTGTTTGAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTc                            >  1:276686/1‑90 (MQ=255)
                                                           tttttACAACTGTTTGAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAg                       >  1:400337/1‑90 (MQ=255)
                                                                aCAACTGTTTGAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAAttttt                  >  1:470553/1‑90 (MQ=255)
                                                                           agaagagaaAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGGCTTAAGTTTTTTGGCTGAAAGa       >  2:392901/1‑90 (MQ=255)
                                                                                agaaaagaaaACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGattatt  >  2:1388993/1‑90 (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 < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑