Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,579,1180TG58.3% 10.1 / 13.0 13K542N (AAA→AAC) ydePacid resistance putative oxidoreductase YdeP
Reads supporting (aligned to +/- strand):  ref base T (2/3);  new base G (7/0);  total (10/3)
Fisher's exact test for biased strand distribution p-value = 4.55e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.93e-03
Rejected as consensus: Frequency below/above cutoff threshold.

TACCACGCTCTGGGGTAGTGCTGCCTGCGCGATTCCCGCGACCACTGCACACTCTGATTTCAGCATTACACCGGCGGGTTTTAACACGCCACGCGAGGCATGAATCATCGACATTGAATCCTCAACGGTTACCGCCTGCGCACCGT  >  NZ_CP009273/1579040‑1579185
                                                                              |                                                                   
tACCACGCTCTGGGGTAGTGCTGCCTGCGCGATTCCCGCGACCACTGCACACTCTGATTTCAGCATTACACCGGCGGGGTTTTAcacgcc                                                          >  2:484443/1‑90 (MQ=255)
 aCCACGCTCTGGGGTAGTGCTGCCTGCGCGATTCCCGCGACCACTGCACACTCTGATTTCAGCATTACACCGGCGGGTTTTTAcacgccc                                                         >  1:427560/1‑89 (MQ=255)
       ctctGGGGTAGTGCTGCCTGCGCGATTCCCGCGACCACTGCACACTCTGATTTCAGCATTACACCGGCGGGGTTTAACACGCCACGCGAg                                                   >  2:639593/1‑90 (MQ=255)
         ctGGGGTAGTGCTGCCTGCGCGATTCCCGCGACCACTGCACACTCTGATTTCAGCATTACACCGGCGGGTTTTAACACGCCACGCGAGGc                                                 >  2:677885/1‑90 (MQ=255)
                   gctgcCTGCGCGATTCCCGCGACCACTGCACACTCTGATTTCAGCATTACACCGGCGGGGTTTTAAACGCCACGCGCGGCAAGAaacaac                                       >  1:398285/1‑88 (MQ=255)
                                  cccGCGACCACTGCACACTCTGATTTCAGCATTACACCGGCGGGTTTTAACACGCCACGCGAGGCATGAATCATCGACATTGAATCCTCa                        <  2:637829/90‑1 (MQ=255)
                                    cgcgACCACTGCACACTCTGATTTCAGCATTACACCGGCGGGTTTTAACACGCCACGCGAGGCATGAATCATCGACATTGAATCCTCAAc                      <  1:677885/90‑1 (MQ=255)
                                    cgcgACCACTGCACACTCTGATTTCAGCATTACACCGGCGGGTTTTAACACGCCACGCGAGGCATGAATCATCGACATTGAATCCTCAAc                      <  2:318330/90‑1 (MQ=255)
                                    cgcgACCACTGCACACTCTGATTTCAGCATTACACCGGCGGGGTTTAACACGCCACGCGAGGCATGAATCATCGACATTGAATCCTCAAc                      >  2:312410/1‑90 (MQ=255)
                                                   ctctGATTTCAGCATTACACCGGCGGGGTTTAACACGCCACGCGAGGCATGAATCATCGACATTGAATCCTCAACGGTTACCGCCTgcgc       >  1:13395/1‑90 (MQ=255)
                                                   ctctGAGTTCAGCATTACACCGGCGGGCTTTAACACCGCACGCGGGGGGAGAATCATCGGCACTTAATCCTCAACGGGTTCACCCTgcgc       >  1:122347/1‑90 (MQ=255)
                                                      tGATTTCAGCATTACACCGGCGGGGTTTAACACGCCACGCGGGGCATGAATCATCGACATTTAATCCCCAAAGGTTAACGCCCGCGCAcc    >  1:614520/1‑90 (MQ=255)
                                                        aTTTCAGCATTACACCGGCGGGGTTTAACACGCCACGCGAGGCATGAATAATCGACATTGAATCCTCAACGGTTACCGCCCGCGCACCGt  >  1:294882/1‑90 (MQ=255)
                                                                              |                                                                   
TACCACGCTCTGGGGTAGTGCTGCCTGCGCGATTCCCGCGACCACTGCACACTCTGATTTCAGCATTACACCGGCGGGTTTTAACACGCCACGCGAGGCATGAATCATCGACATTGAATCCTCAACGGTTACCGCCTGCGCACCGT  >  NZ_CP009273/1579040‑1579185

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑