Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273883,4700TG61.5% 5.0 / 10.1 13intergenic (+55/+120)rcdA/ybjLDNA‑binding transcriptional regulator RcdA/aspartate:alanine antiporter
Reads supporting (aligned to +/- strand):  ref base T (0/5);  new base G (8/0);  total (8/5)
Fisher's exact test for biased strand distribution p-value = 7.77e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.13e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GAGGGTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGC  >  NZ_CP009273/883400‑883536
                                                                      |                                                                  
gagGGTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGGTGATGGGCTCCCCaaaaag                                                 >  1:385847/1‑88 (MQ=255)
   ggTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATgggg                                              <  1:84536/90‑1 (MQ=255)
   ggTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATgggg                                              <  1:98158/90‑1 (MQ=255)
     ttGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGGTGGTGGGGTCCCCAAAATgggggc                                            >  1:521591/1‑88 (MQ=255)
     ttGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGGTGATGGGCTCCACAAAAAgggggc                                            >  2:462233/1‑88 (MQ=255)
                      aGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGGTGATGGGGTCCACAAAAAGGGGGCATCAAAAAAAAACAGTg                           >  2:260363/1‑90 (MQ=255)
                      aGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGGTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTg                           >  1:204124/1‑90 (MQ=255)
                      aGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGGTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAACAGTg                           >  1:55375/1‑90 (MQ=255)
                         tttAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGGTGATGGGGTCCACAAAAAAGGGAAATCAAAGAAAAACAggggga                        >  2:367854/1‑88 (MQ=255)
                          ttAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCAc                       <  1:462233/90‑1 (MQ=255)
                                 aCAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGGTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGGGGCACTAATTaa                >  1:239105/1‑90 (MQ=255)
                                            aTCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGccc     <  2:521591/90‑1 (MQ=255)
                                               aaCCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGc  <  2:54135/90‑1 (MQ=255)
                                                                      |                                                                  
GAGGGTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGC  >  NZ_CP009273/883400‑883536

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑