Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273341,0390CA54.5% 2.9 / 14.5 11intergenic (+337/‑76)BW25113_RS01680/BW25113_RS01685hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (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.

TTTGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGG  >  NZ_CP009273/340966‑341109
                                                                         |                                                                      
tttGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGc                                                        >  1:208109/1‑90 (MQ=255)
        gggTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAgg                                                >  1:214188/1‑90 (MQ=255)
                             cATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGa                           >  1:292581/1‑90 (MQ=255)
                              aTCGCACTAACGCCTAAAAAAAAATATGCTGAAAGGCTAATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAt                          <  2:193910/90‑1 (MQ=255)
                                 gcccTCAACCCTGAAAAAAAATATGCTGTAAGGCTCATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAttgt                       <  2:127167/87‑1 (MQ=255)
                                 ccccTCAAGCCTAAAAAAAAATGTGTTGAAAGGCTAATAAAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAttgt                       <  1:30390/87‑1 (MQ=255)
                                 ccacacaACCCTGAAAAAAAATGTGCTGAAAGGCTCAAAAAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAttgt                       <  1:180266/89‑1 (MQ=255)
                                      cAAGCCTGAAAAAAAATATGCTGAAAGGCTAATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTAt                  <  2:160367/90‑1 (MQ=255)
                                           cTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTAc             >  1:130610/1‑90 (MQ=255)
                                           cTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTAc             >  2:151204/1‑90 (MQ=255)
                                                      tatGTTGTAAGGCTAAAATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAgg  <  2:306964/90‑1 (MQ=255)
                                                                         |                                                                      
TTTGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGG  >  NZ_CP009273/340966‑341109

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑