Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092737,1320AC53.8% 4.6 / 12.5 13G276G (GGT→GGG) yaaJsodium:alanine symporter family protein
Reads supporting (aligned to +/- strand):  ref base A (4/2);  new base C (0/7);  total (4/9)
Fisher's exact test for biased strand distribution p-value = 2.10e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.70e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

ATCTGGACAATCCCTTGCGCTGCCGGATGCGGAGGCCAGGACGCCGCTGCCGCTGCCGCGTTTGGCGTCGAACCCATTCCCGCCTCATTGGAAAACATACTGCGCTGAAAACCGTTAGTAATCGCCTGGCTTAAGGTATATCC  >  NZ_CP009273/7061‑7203
                                                                       |                                                                       
atcTGGACAACCCCTTGCGCTGCCGGAGCCGGGGGCCAGGCCGCCGCTGCCGCTGCCGGGTTTGGCGTCGACCCCATTCCCGCCTCATTg                                                       <  1:497967/90‑1 (MQ=255)
   gggACAACCCCTGGCGCTGCCGGATGGGGGGGCCGGGACGCCGCTGCCGCTGCCGCGTTTGGCGTCGACCCCATTCCCGCCTCATTGGaa                                                    <  1:453138/89‑1 (MQ=255)
                gcgcTGCCGGATGCGGAGGCCAGGACGCCGCTGCCGCTGCCGCGTTTGGCGTCGAACCCATTCCCGCCTCATTGGAAAACATACTGCGCt                                       >  1:110083/1‑90 (MQ=255)
                gcgcTGCCGGATGCGGAGGCCAGGACGCCGCTGCCGCTGCCGCGTTTGGCGTCGAACCCATTCCCGCCTCATTGGAAAACATACTGCGCt                                       >  1:522268/1‑90 (MQ=255)
                    tGCCGGATGCGGAGGCCAGGACGCCGCTGCCGCTGCCGCGTTTGGCGTCGACCCCATTCCCGCCTCATTGGAAAACATACTGCGCTGaaa                                   <  2:240987/90‑1 (MQ=255)
                                    cgggACGCCCCTGCCGCTGCCGCGTTTGGCGTCGACCCCATTCCCGCCTCATTGGAAAACATACTGCGCTGAAAACCGTTAGTAATCGcc                   <  1:55024/88‑1 (MQ=255)
                                     aGGCCGCCGCTGCCGCTGCCGCTTTTGGCGTCGACCCCATTCCCGCCTCATTGGAAAACATACTGCGCTGAAAACCGTTAGTAATCGCCt                  <  2:361178/90‑1 (MQ=255)
                                     aGGCCGCCGCTGCCCCTCCCGCGTTTGGAGTCGACCCCATTCCCGCCTCATTGGAAAACATACTGCGCTGAAAACCGTTAGTAATCGCCt                  <  2:110083/90‑1 (MQ=255)
                                     aGGACGCCGCTGCCGCTGCCGCGTTTGGCGTCGAACCCATTCCCGCCTCATTGGAAAACATACTGCGCTGAAAACCGTTAGTAATCGCCt                  <  2:522268/90‑1 (MQ=255)
                                           ccgctgccgctgCCGCGTTTGGCGTCGACCCCATTCCCGCCTCATTGGAAAACATACTGCGCTGAAAACCGTTAGTAATCGCCTGGCTTa            <  2:327228/90‑1 (MQ=255)
                                           ccgctgccgctgCCGCGTTTGGCGTCGAACCCATTCCCGCCTCATTGGAAAACATACTGCGCTGAAAACCGTTAGTAATCGCCTGGCTTa            >  1:254036/1‑90 (MQ=255)
                                           ccgcggccgctgCCGTGTTTGGCGTCGAACCCATTCCCGCCTCATTGGAAAACATACTGCGCTGAAAACCGTTAGTAATCGCCTGGCTTa            <  1:291963/90‑1 (MQ=255)
                                                     tgccgcGTTTGGCGTCGAACCCATTCCCGCCTCATTGGAAAACATACTGCGCTGAAAACCGTTAGTAATCGCCTGGCTTAAGGTATATcc  >  1:507374/1‑90 (MQ=255)
                                                                       |                                                                       
ATCTGGACAATCCCTTGCGCTGCCGGATGCGGAGGCCAGGACGCCGCTGCCGCTGCCGCGTTTGGCGTCGAACCCATTCCCGCCTCATTGGAAAACATACTGCGCTGAAAACCGTTAGTAATCGCCTGGCTTAAGGTATATCC  >  NZ_CP009273/7061‑7203

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑