Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,356,9000TC63.6% ‑4.1 / 11.8 22G71G (GGA→GGG) yfaYnicotinamide mononucleotide deamidase‑related protein YfaY
Reads supporting (aligned to +/- strand):  ref base T (7/1);  new base C (0/14);  total (7/15)
Fisher's exact test for biased strand distribution p-value = 4.69e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.84e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TTGAGCCAGGCTTCATGCAGCACCAGGCCTTCACCTTTTGCTGTCGCAGCGGCGAGTGCGCTTAAATCATCGCTGGTCGGTCCCAGCCCGCCGTTAACGATCAGCACATCGGCGTGCTGACTACGTTCGCGAAGAATGGTGACTAAGTCATCAAGGT  >  NZ_CP009273/2356820‑2356976
                                                                                |                                                                            
ttGAGCCAGGCTTCATGCAGCACCAGGCCTTCACCTTTTGCTGTCGCAGCGGCGAGTGCGCTTAAATCATCGCTGGTCGGTCCCAGCccg                                                                     >  1:367173/1‑90 (MQ=255)
      cAGGCTTCATGCAGCACCAGGCCTTCACCTTTTGCTGTCGCAGCGGCGAGTGCGCTTAAATCATCGCTGGTCGGTCCCAGCCCGCCGTTa                                                               >  1:298181/1‑90 (MQ=255)
       aGGTTTCAGGCACCCCCGGCCCTTCCCTTTTTGCTGCCGCGGGGGGGGGTGCGTTAAAATCATCGCTGGTCGGCCCCAGCCCGCCGTTaa                                                              <  2:361438/90‑1 (MQ=255)
       aGGCTTCATGCAGCACCAGGCCTTCACCTTTTGCTGTCGCAGCGGCGAGTGCGCTTAAATCATCGCTGGTCGGTCCCAGCCCGCCGTTaa                                                              >  2:221604/1‑90 (MQ=255)
        ggCTTCATGCAGCACCAGGCCTTCACCTTTTGCTGTCGCAGCGGCGAGTGCGCTTAAATCATCGCTGGTCGGTCCCAGCCCGCCGTTAAc                                                             >  2:241376/1‑90 (MQ=255)
            tCATGCAGCCCCAGCCCTTCCCTTTTTGCTGTCGCGGGGGCGAGTGCGTTAAAATCATCGCTGGTCGGCCCCAGCCCGCCGTTAACGATc                                                         <  1:954708/90‑1 (MQ=255)
              aTGCACCACCGGCCCTTCCCTTTTTGCTGCCGCGGGGGCGGGTGCGCTAAAATCATCGCTGGTCGGCCCCAGCCCGCCGTTAACGATCAg                                                       <  2:298181/90‑1 (MQ=255)
                  agcaCCAGGCCTTCACCTTTTGCTGTCGCAGCGGCGAGTGCGCTTAAATCATCGCTGGTCGGTCCCAGCCCGCCGTTAACGATCAGcaca                                                   >  1:602548/1‑90 (MQ=255)
                   gcaCCAGGCCTTCACCTTTTGCTGTCGCAGCGGCGAGTGCGCTTAAATCATCGCTGGTCGGTCCCAGCCCGCCGTTAACGATCAGCACAt                                                  >  1:484019/1‑90 (MQ=255)
                           ccTTCCCTTTTTGCTGCCGCGGGGGGGAGGGCGTTAAAATCCTCGCGGGGCGGCCCCACCCCGCCGTTAACGATCAGCACATCGGCGTGc                                          <  2:367173/90‑1 (MQ=255)
                             ttCACCTTTTGCTGTCGCAGCGGCGAGTGCGCTTAAATCATCGCTGGTCGGTCCCAGCCCGCCGTTAACGATCAGCACATCGGCGTGCTg                                        >  2:978986/1‑90 (MQ=255)
                                       gCTGTCGCGGCGGCGAGTGCCTTTAAACCATCGCGGGTGGGCCCCAGCCCGCCGTTAACGATCAGCACATCGGCGTGCTGACTACGTTcg                              <  1:390827/90‑1 (MQ=255)
                                          gTCGCGGGGGGGGGTGCGCTAAAATCATCGCGGGTGGGTCCCAGCCCGCCGTTAACGATCAGCACATCGGCGTGCTGACTACGTTCGCga                           <  1:221604/90‑1 (MQ=255)
                                           tCGCGGGGGCGAGTGCTTTAAAACCGCCGCTGGTGGGCCCCAGCCCGCCGTTAACGATCAGCACATCGGCGTGCTGACTACGTTCGCgaa                          <  2:169015/90‑1 (MQ=255)
                                                 gggcgGGTGCTTTAAAATCTTCGCGGGTCGCCCCCAGCCCGCCGTTAACGATCAGCACATCGGCGTGCTGACTACGTTCGCGAAGAATgg                    <  2:433272/89‑1 (MQ=255)
                                                              tAAATCGCCGCGGGTCGCCCCCAACCCGCCGTTAACGATCAGCACATCGGCGTGCTGACTACGTTCGCGAAGAATGGTGACTAAGtcatc       <  1:978986/90‑1 (MQ=255)
                                                              aaaaTCGTCGCTGGTCGGCCCCCCCCCGCCGTTAACGATCAGCACATCGGCGTGCTGACTACGTTCGCGAAGAATGGTGACTAAGtcatc       <  2:204372/89‑1 (MQ=255)
                                                              aaaaTCGCCGCGGGTCGGCCCCACCCCGCCGTTAACGATCAGCACATCGGCGTGCTGACTACGTTCGCGAAGAATGGTGACTAAGtcatc       <  2:499995/89‑1 (MQ=255)
                                                              aaaaTCCTCGCTGGTCGCCCCCACCCCGCCGTTAACGATCAGCACATCGGCGTGCTGACTACGTTCGCGAAGAATGGTGACTAAGtcatc       <  1:386818/89‑1 (MQ=255)
                                                              aaaaTCCTCGCGGGTCGGCCCCAGCCCGCCGTTAACGATCAGCACATCGGCGTGCTGACTACGTTCGCGAAGAATGGTGACTAAGtcatc       <  1:1003183/89‑1 (MQ=255)
                                                              aaaaTCATCGCTGGTCGGCCCCAGCCCGCCGTTAACGATCAGCACATCGGCGTGCTGACTACGTTCGCGAAGAATGGTGACTAAGtcatc       <  1:424693/89‑1 (MQ=255)
                                                                   cttcGCTGGCCGGCCCCACCCCGCCGTTAACGATCAGCACATCGGCGTGCTGACTACGTTCGCGAAGAATGGTGACTAAGTCATCAAGGt  <  2:1110864/88‑1 (MQ=255)
                                                                          ggtcggtcCCAGCCCGCCGTTAACGATCAGCACATCgg                                               >  2:298560/1‑38 (MQ=255)
                                                                          ggtcggtcCCAGCCCGCCGTTAACGATCAGCACATCgg                                               <  1:298560/38‑1 (MQ=255)
                                                                                |                                                                            
TTGAGCCAGGCTTCATGCAGCACCAGGCCTTCACCTTTTGCTGTCGCAGCGGCGAGTGCGCTTAAATCATCGCTGGTCGGTCCCAGCCCGCCGTTAACGATCAGCACATCGGCGTGCTGACTACGTTCGCGAAGAATGGTGACTAAGTCATCAAGGT  >  NZ_CP009273/2356820‑2356976

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑