Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,976,0100CA55.6% 0.3 / 12.8 9intergenic (‑142/+25)otsB/araHtrehalose‑phosphatase/arabinose ABC transporter permease AraH
Reads supporting (aligned to +/- strand):  ref base C (0/4);  new base A (5/0);  total (5/4)
Fisher's exact test for biased strand distribution p-value = 7.94e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.17e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACA  >  NZ_CP009273/1975939‑1976041
                                                                       |                               
gtgtGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGGTATGGGGGGGAAAAAAGGTAAAATTTTTGAGaaa               >  2:46362/1‑90 (MQ=255)
gtgtGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGGTATGGGGGGGAAAAAAACTAAAATGTTTTAGaaa               >  2:529529/1‑90 (MQ=255)
gtgtGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGGGGGGTTTTGGGGGGAAAAAAACTTAAATGGTGTAGaaa               >  1:428716/1‑90 (MQ=255)
 tgtgACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGGGGGGTAGGGGGGGGAAAAAAGCCAAAAAGTTGTAGaaaa              >  1:199677/1‑90 (MQ=255)
  gtgACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGaaaaa             <  1:276440/90‑1 (MQ=255)
  gtgACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGaaaaa             <  1:527322/90‑1 (MQ=255)
  gtgACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGaaaaa             <  2:39012/90‑1 (MQ=255)
          ggTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTTGGTATGGGGGGGAAAAAAACTAAATTGTTTCAGAAAAAAAAATCAg     >  2:276440/1‑90 (MQ=255)
             cGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACa  <  2:290515/90‑1 (MQ=255)
                                                                       |                               
GTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACA  >  NZ_CP009273/1975939‑1976041

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑