Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273754,0340GT54.5% 1.6 / 12.4 11intergenic (+173/‑128)sdhB/sucAsuccinate dehydrogenase iron‑sulfur subunit SdhB/2‑oxoglutarate dehydrogenase E1 component
Reads supporting (aligned to +/- strand):  ref base G (4/1);  new base T (0/6);  total (4/7)
Fisher's exact test for biased strand distribution p-value = 1.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.05e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TGATAAGCGCAGCGCATCAGGCGTAACAAAGAAATGCAGGAAATCTTTAAAAACTG‑CCCCTGACACTAAGACAGTTTTTAAAGGTTCCTTCGCGAGCCACTACGTAGACAAGAGCTCGCAAGTGAACCCCGGCACGCACATCACTGTGCGTGGTAG  >  NZ_CP009273/753961‑754116
                                                                          |                                                                                  
tGATAAGCGCAGCGCATCAGGCGTAACAAAGAAATGCAGGAAATCTTTAAAAACTG‑CCCCTGACACTAAGACAGTTTTTAAAGGTTCCtt                                                                    >  2:118924/1‑90 (MQ=255)
     agcgcagcgcATCAGGCAAAAAAAAAAAAGGCAGAAAATTTTAAAAACCTC‑CCCCTGACACTAAGACATTTTTAAAAGTTTCCTTCGCGa                                                               <  2:124390/90‑1 (MQ=255)
            cgcaCCAGGCGAAAAAAAAAAGGGAAGGAAATCTTAAAAATCCG‑CCCCTGACACTAACACATTTTTAAAAGGTTCCTTCGCGAGCCACTa                                                        <  1:284851/90‑1 (MQ=255)
                     cGTAACAAAGAAATGCAGGAAATCTTTAAAAACTG‑CCCCTGACACTAAGACAGTTTTTAAAGGTTCCTTCGCGAGCCACTACGTAGACaa                                               >  1:396772/1‑90 (MQ=255)
                                 aTGCAGGAAATCTTTAAAAACTG‑CCCCTGACACTAAGACAGTTTTTAAAGGTTCCTTCGCGAGCCACTACGTAGACAAGAGCTCGCAAGt                                   >  2:215026/1‑90 (MQ=255)
                                 aTGCAGGAAATCTTTAAAAACTG‑CCCCTGACACTAAGACAGTTTTTAAAGGTTCCTTCGCGAGCCACTACGTAGACAAGAGCTCGCAAGt                                   >  2:386642/1‑90 (MQ=255)
                                          aTCTTAAAAACCTG‑CCCCTGACACTAAGACAGTTTTTAAAGGTTCCTTCGCGAGCCACTACGTAGACAAGAGCTCGCAAGTGAACCCCgg                          <  1:32356/90‑1 (MQ=255)
                                            tttaaaaaaCTC‑CCCCTGACACTAAGACATTTTTAAAAGGTTCCTTCGCGAGCCACTACGTAGACAAGAGCTCGCAAGTGAACCCCGgca                        <  1:102835/86‑1 (MQ=255)
                                             tttAAAAACCCCCCCCTGACACAAAGACTTTTTTAAAGGGTCCCTTCGGGAGCCACTACGTAGACAAGAGCTCGCAAGTGAACCCCGgca                        <  2:123091/90‑1 (MQ=255)
                                                       ccccccTAACACAAAGACATTTTTAAAAGTTTCCTCCGCGAGCCACTACGTAGACAAGAGCTCGCAAGTGAACCCCGGCACGCACATCAc              <  2:177423/88‑1 (MQ=255)
                                                                   tAAGACATTTTTAAAAGTTTCCTTCGCGAGCCACTACGTAGACAAGAGCTCGCAAGTGAACCCCGGCACGCACATCACTGTGCGTGgtag  <  1:215026/90‑1 (MQ=255)
                                                                          |                                                                                  
TGATAAGCGCAGCGCATCAGGCGTAACAAAGAAATGCAGGAAATCTTTAAAAACTG‑CCCCTGACACTAAGACAGTTTTTAAAGGTTCCTTCGCGAGCCACTACGTAGACAAGAGCTCGCAAGTGAACCCCGGCACGCACATCACTGTGCGTGGTAG  >  NZ_CP009273/753961‑754116

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑