Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,429,9840GA54.5% ‑2.0 / 11.4 11intergenic (‑108/+33)uspF/ompNuniversal stress protein UspF/porin OmpN
Reads supporting (aligned to +/- strand):  ref base G (5/0);  new base A (0/6);  total (5/6)
Fisher's exact test for biased strand distribution p-value = 2.16e-03
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.

CCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAA  >  NZ_CP009273/1429897‑1430041
                                                                                       |                                                         
ccGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGaa                                                         >  2:276942/1‑90 (MQ=255)
       aaGTGTAACGCCAGATAACTTTTTTTGTGAAAGGAGGGATTTCACTTTTTTAATTAAGAAAAAAGGAGAAAAAAAAAGAAAAAAAAGccc                                                  <  1:198432/90‑1 (MQ=255)
       aaGTGTAACCACAAATGACTTTTTTTGTGAAATGACGGAGTTCACTTTTTTAATTAAGAAAAAGGGAGAAAAAAAAAGAAAAAAAAcccc                                                  <  1:907817/90‑1 (MQ=255)
            tAACGCCAGATGACTTTTTTTGTGAAATGAGGGAGTTCAATTTTTTATTTTAGAAAAAAGGAGAAAAAAAAAGAAAAAAAAGCCCGCCAt                                             <  2:831166/90‑1 (MQ=255)
            tAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCAt                                             >  1:110522/1‑90 (MQ=255)
                 ccAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAg                                        >  2:51335/1‑90 (MQ=255)
                   aGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCg                                      >  2:653201/1‑90 (MQ=255)
                           cTTTTTGTGAAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAAAAAAAGCAAAAAAAGCCCGCCATAACAGCGGGCaggag                              <  2:270732/90‑1 (MQ=255)
                                    aaaTGACGGAGTCCACTTTTTTAATTTAGAAAAAAGGAGGAAGAAAAAGCAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGaa                     <  2:419244/89‑1 (MQ=255)
                                     aaTGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAAc                    >  1:862961/1‑90 (MQ=255)
                                                       ttaaaTTAAGAAAAAAGGAGAAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTaaa  <  2:706363/87‑1 (MQ=255)
                                                                                       |                                                         
CCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAA  >  NZ_CP009273/1429897‑1430041

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑