Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,673,5610AC60.0% 10.2 / 15.5 20Y293S (TAC→TCC) ydgHDUF1471 family protein YdgH
Reads supporting (aligned to +/- strand):  ref base A (5/3);  new base C (0/12);  total (5/15)
Fisher's exact test for biased strand distribution p-value = 3.61e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.27e-03
Rejected as consensus: Frequency below/above cutoff threshold.

GCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTCAGTTACTCCTATAA  >  NZ_CP009273/1673474‑1673648
                                                                                       |                                                                                       
gCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTAcc                                                                                       >  1:169047/1‑90 (MQ=255)
                      cGGCAACATGCCCAAAGCCTCCTATCGGGTTGCAAACCGGGCCGAGAAGAAGGGTGCTAAGTTTTCCCACACCCCCCGCCAGTGGCAGGa                                                                 <  2:841421/90‑1 (MQ=255)
                        gCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAAc                                                               >  2:801981/1‑90 (MQ=255)
                        gCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAAc                                                               >  2:335964/1‑90 (MQ=255)
                          aaCATGCCCGAAGTCTCCTATCAGGTTGCAAAACGTGCCGCGAAGAAAGGTGCTAAGTATTCCCACATCACCCGCCAGTGGCAGGAACGt                                                             <  1:681313/90‑1 (MQ=255)
                          aaCATGCCCGAAGCCCCCTATCAGGTTGCAAAACGTGCCGAAAAGAAGGGTGCTAAGTATTACCACATCCCCCGCCAGTGGCAGGAACGt                                                             <  2:425892/90‑1 (MQ=255)
                          aaCATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCAAAGAAGGGTGCAAAATTTTCCCACATCACCCGCCAGTGGCAGGAACGt                                                             <  1:550184/90‑1 (MQ=255)
                                  cGAAGTCTCCTATCGGGTTGCAAAACGGGCCGGGAAAAAAGGTGCAAATTTTTCCCACACCCCCCGCCAGTGGCAGGAACGTGGtaataa                                                     <  2:226634/90‑1 (MQ=255)
                                            taccAGGTTGCGAACCGGGCCGAGAAAAAAGGTGCTAAGTATTCCCACACCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTc                                           <  2:198124/87‑1 (MQ=255)
                                            tATCAGGTGGCGAAACGTGCCGCGAAAAAGGGTGCTAAGTTTTCCCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTc                                           <  1:624317/90‑1 (MQ=255)
                                                 ggTTGCGAACCGTGCGGGGAAGAAGGGTGCTAAGTTTTCCCCCACCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAgcgc                                      <  2:931705/90‑1 (MQ=255)
                                                 ggTTGCGAAACGTGCCGCGAAAAAAGGTGCTAAGTATTACCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAgcgc                                      <  1:138695/90‑1 (MQ=255)
                                                 ggTGGCGAACCGTGCCGCGAAAAAAGGTGCAAAGTATTCCCACACCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAgcgc                                      <  1:910519/90‑1 (MQ=255)
                                                    tGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGGAATAACCTGACCGTCAGCGCAGa                                   >  1:500619/1‑90 (MQ=255)
                                                      caaaaCGTGCCGCAAAGAAAGGTGCTAAGTATTCCCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATc                                 <  1:262786/88‑1 (MQ=255)
                                                      cGAAACGTGCCGCGAAAAAAGGTGCAAAGTATTCCCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATc                                 <  1:546879/90‑1 (MQ=255)
                                                        aaaCGTGCCGCGAAAAAAGGTGATAAGTATTCCCACACCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTg                               <  2:232850/90‑1 (MQ=255)
                                                          aCGTGCAGCAAGGAAAGAGGCAAATTATCACCACCCCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGta                             <  1:471568/90‑1 (MQ=255)
                                                                          gttGCTAAGTTTTCCCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTCAGt             <  1:87193/88‑1 (MQ=255)
                                                                                     ttACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTCAGTTACTCCTATaa  >  1:229295/1‑90 (MQ=255)
                                                                                       |                                                                                       
GCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTCAGTTACTCCTATAA  >  NZ_CP009273/1673474‑1673648

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑