Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273883,4700TG54.5% 6.7 / 11.0 11intergenic (+55/+120)rcdA/ybjLDNA‑binding transcriptional regulator RcdA/aspartate:alanine antiporter
Reads supporting (aligned to +/- strand):  ref base T (1/4);  new base G (6/0);  total (7/4)
Fisher's exact test for biased strand distribution p-value = 1.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.28e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

AGGATGGTTGAGAGGGTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAG  >  NZ_CP009273/883389‑883523
                                                                                 |                                                     
aGGATGGTTGAGAGGGTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGc                                               <  1:407701/90‑1 (MQ=255)
     ggTTGAGAGGGTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGGTGATGGGCTCcac                                          >  1:601179/1‑90 (MQ=255)
         gagaGGGTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACaaaa                                      >  2:329413/1‑90 (MQ=255)
                ttGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGGTGATGGGCTCCACAAAATGGGGAc                               >  2:224503/1‑90 (MQ=255)
                ttGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGGTGATGGGCTCCACAAAATAGGGAc                               >  2:495960/1‑90 (MQ=255)
                         agtagATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGGTGATGGGCTCCACAAAATGGGGACATCAAAGaa                      >  2:23913/1‑90 (MQ=255)
                               tAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGGTTGTGGGTTCCACAAAAATGGGGCAACAAAAAAAAGCAg                >  1:226962/1‑90 (MQ=255)
                                     ttAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCAc          <  2:558573/90‑1 (MQ=255)
                                     ttAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCAc          <  2:601179/90‑1 (MQ=255)
                                            aCAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGGTGGTGGGCGCCGCAAAAAGGGGGCAACAAAAAAAAACAGAGGCACTTATTaa   >  1:344235/1‑90 (MQ=255)
                                             cAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAg  <  1:329413/90‑1 (MQ=255)
                                                                                 |                                                     
AGGATGGTTGAGAGGGTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAG  >  NZ_CP009273/883389‑883523

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑