Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,454,1460TC54.5% 4.1 / 10.7 11F324S (TTC→TCC) gspFtype II secretion system inner membrane protein GspF
Reads supporting (aligned to +/- strand):  ref base T (4/1);  new base C (0/6);  total (4/7)
Fisher's exact test for biased strand distribution p-value = 1.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.05e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GTAACAGCATTCATCTTTCGCTGGAACAAACCGCAATTTTCCCGCCGATGATGCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATAAC  >  NZ_CP009273/3454107‑3454228
                                       |                                                                                  
gaaaCAGCTTTCATCTTCCGCGGAAAAAACCCGCATTTTCCCCGCCGATGATGCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCAGc                                  <  2:314235/88‑1 (MQ=255)
  aaCAGCATTCTTCTTTCGCTGAAACAACCCGCATTTTTCCCGCCGATGATGCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCAGCTc                                <  2:248201/90‑1 (MQ=255)
       cctccATCTTTCGTTGAAACACACCGCAATTTCCCCGCCGATGATGCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGcac                           <  1:263772/86‑1 (MQ=255)
       cATTCTTCTTGCGCTGAAACAACCCAAATTTTCCCCGCCGATGATGCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGcac                           <  1:263286/90‑1 (MQ=255)
        aTTCATCTTTCGCTGGAACAAACCGCAATTTTCCCGCCGATGATGCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGcaca                          >  1:258981/1‑90 (MQ=255)
        aTTCATCTTTCGCTGGAACAAACCGCAATTTTCCCGCCGATGATGCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGcaca                          >  1:314235/1‑90 (MQ=255)
            atttttCGCGGAAACAACCCGAATTTTCCCCGCCGATGATGCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTaa                      <  2:227458/87‑1 (MQ=255)
                ttCGCTGGAACAAACCGCAATTTTCCCGCCGATGATGCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGt                  >  2:149816/1‑90 (MQ=255)
                 tCGCTGAAACAACCCGAATTTTCCCCGCCGATGATGCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAGTGGTc                 <  2:103672/90‑1 (MQ=255)
                       aaacaacCCGAAATTTCCCCGCCGATGATGCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGcc           <  2:32488/89‑1 (MQ=255)
                                gCAATTTTCCCGCCGATGATGCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATAAc  >  1:10783/1‑90 (MQ=255)
                                       |                                                                                  
GTAACAGCATTCATCTTTCGCTGGAACAAACCGCAATTTTCCCGCCGATGATGCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATAAC  >  NZ_CP009273/3454107‑3454228

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: ‑