Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,213,8470GT58.3% 5.6 / 15.3 12C355F (TGT→TTT) pdeGcyclic diguanylate phosphodiesterase
Reads supporting (aligned to +/- strand):  ref base G (4/1);  new base T (0/7);  total (4/8)
Fisher's exact test for biased strand distribution p-value = 1.01e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.93e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GAGTAAATTGCCGGAAGGTTTTCATATTGGAATTAATTTTAGCGCTTCGCATATTATTTCGCCGACGTTTGTCGACGAGTGTTTAAATTTCCGTGACAGTTTTACCCGCCGCGATTTAAACCTTGTTCTGGAAGTCACCGAGCGTGAGCCATTGAA  >  NZ_CP009273/1213767‑1213922
                                                                                |                                                                           
gAGTAAATTGCCGGAAGGTTTTCATATTGGAATTAATTTTAGCGCTTCGCATATTATTTCGCCGACGTTTGTCGACGAGTGTTTAAAttt                                                                    >  1:572781/1‑90 (MQ=255)
      aTTGCCGGAAGGTTTTCATATTGGAATTAATTTTAGCGCTTCGCATATTATTTCGCCGACGTTTGTCGACGAGTGTTTAAATTTCCGTGa                                                              <  2:621091/90‑1 (MQ=255)
              aaGGTTTTCATATTGGAATTAATTTTAGCGCTTCGCATATTATTTCGCCGACGTTTGTCGACGAGTGTTTAAATTTCCGTGACAGTTTTa                                                      >  2:58412/1‑90 (MQ=255)
                   tttCATATTGGAATTAATTTTAGCGCTTCGCATATTATTTCGCCGACGTTTGTCGACGAGTGTTTAAATTTCCGTGACAGTTTTACccgc                                                 >  1:547562/1‑90 (MQ=255)
                      cATTTTGAATTTATTTTTAGCGTTTCGTATTTTTTTTCGCCGACGTTTGTCGACGATTTTTTAATTTTCCGTGACATTTTTCCCcgccgc                                              <  1:262396/90‑1 (MQ=255)
                                 tatttttAGCTTTTCGTATTTTTTTTCGCCGCTGTTTGTCGACGAGTTTTTAATTTTCCGTGACATTTTTCCCCGCCGCGATTTAAACCt                                   <  1:58412/87‑1 (MQ=255)
                                  atttttAGCTCTTCGCTTTTTTTTCCGCCGACGTTTGTCGAGGAGTTTTTAATTTTCCGTGACATTTTTCCCCGCCGCGATTTAAACCtt                                  <  1:465166/88‑1 (MQ=255)
                                              tCGCATATTATTTCGCCGACGTTTGTCGACGAGTGTTTAAATTTCCGTGACAGTTTTACCCGCCGCGATTTAAACCTTGTTCTGGAAGTc                      >  1:153493/1‑90 (MQ=255)
                                                         tccGCCGACGTTTGTCGACGAGTTTTTAATTTTCCGTGACATTTTTCCCCGCCGCGATTTAAACCTTGTTCTGGAAGTCACCGAGCGTGa           <  2:140759/88‑1 (MQ=255)
                                                           cGCCGACTTTTGTCGAGGATTTTTTAATTTTCCGTGACATTTTTCCCCGCCGCGATTTAAACCTTGTTCTGGAAGTCACCGAGCGTGAGc         <  1:172021/90‑1 (MQ=255)
                                                           cGCCGACTTTTGTCGACGAGTTTTTAAATTTCCGTGACAGTTTTACCCGCCGCGATTTAAACCTTGTTCTGGAAGTCACCGAGCGTGAGc         <  2:228023/90‑1 (MQ=255)
                                                                  ttttGTCGACGATTTTTTAATTTTCCGTGACTTTTTTCCCCGCCGCGATTTAAACCTTGTTCTGGAAGTCACCGAGCGTGAGCCATTGaa  <  1:237267/89‑1 (MQ=255)
                                                                                |                                                                           
GAGTAAATTGCCGGAAGGTTTTCATATTGGAATTAATTTTAGCGCTTCGCATATTATTTCGCCGACGTTTGTCGACGAGTGTTTAAATTTCCGTGACAGTTTTACCCGCCGCGATTTAAACCTTGTTCTGGAAGTCACCGAGCGTGAGCCATTGAA  >  NZ_CP009273/1213767‑1213922

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑