Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,240,7030GT55.6% 5.6 / 12.7 9E30* (GAA→TAA) BW25113_RS06225hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/4);  new base T (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.

GTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACCCGTTCGGCAATGCTTCAGTT  >  NZ_CP009273/1240616‑1240770
                                                                                       |                                                                   
gtgATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGaa                                                                   <  2:568140/90‑1 (MQ=255)
          aaataaatATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAAt                                                         <  1:536787/90‑1 (MQ=255)
                            gTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTTGGTGGGGTTTTTTAACAATTTTAATTGATTAATCCTTTTGGCa                                       >  1:261052/1‑90 (MQ=255)
                                 cAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTa                                  <  1:232452/90‑1 (MQ=255)
                                       ggCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTTGGTGCGCTTTTTTAAAATTTTGAAATTATCAATCCTTCTGGCCGATTAAGACaa                            >  1:260256/1‑90 (MQ=255)
                                       ggCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGGTGCGCTTTTTTAAAATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCaa                            >  1:492187/1‑90 (MQ=255)
                                        gCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTTGCTGCGCCTATTTAAAATTTTGAATTGATTAATCCCTCTTGGAGATTAAGCCaaa                           >  1:331180/1‑90 (MQ=255)
                                            tAAAAATGGGGCGGATAGTGAGGCGGTTTTTGCTGCGCTTTTTTAAAATTTTGAATTTATTAATCCTTCTGGCAGGTTAAGCCAAAAAAc                       >  1:57616/1‑90 (MQ=255)
                                                                 ggCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACCCGTTCGGCAATGCTTCAGtt  <  2:246723/90‑1 (MQ=255)
                                                                                       |                                                                   
GTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACCCGTTCGGCAATGCTTCAGTT  >  NZ_CP009273/1240616‑1240770

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑