Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,498,4400CT54.2% 13.0 / 31.1 24E314K (GAA→AAA) yhfSaminotransferase class I/II‑fold pyridoxal phosphate‑dependent enzyme
Reads supporting (aligned to +/- strand):  ref base C (1/10);  new base T (13/0);  total (14/10)
Fisher's exact test for biased strand distribution p-value = 5.61e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.28e-05
Rejected as consensus: Frequency below/above cutoff threshold.

TCGGGTTAATGCGAATCGCACAATGTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTCATATTTCGACTCTGCACCCACCGGGTAAGGCAAGGCACCGCGCTTTT‑GCGCCTCTTCCAGCACTCTGGCGGCAAT  >  NZ_CP009273/3498353‑3498515
                                                                                       |                                                                            
tCGGGTTAATGCGAATCGCACAATGTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTCat                                                                            <  2:448057/90‑1 (MQ=255)
        aTGCGAATCGCACAATGTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGGTTTTATAttttggc                                                                    >  2:213861/1‑86 (MQ=255)
        aTGCGAATCGCACAATGTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGGATTTATATTTTGAc                                                                    >  1:495848/1‑90 (MQ=255)
            gAATCGCACAATGTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTTATATTTTGACTCTg                                                                >  2:8762/1‑90 (MQ=255)
             aaTCGCACAATGTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGGTTTTATATTTTGACTCTGc                                                               >  1:885485/1‑90 (MQ=255)
             aaTCGCACAATGTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGGTTTTATATTTTGACTCTGc                                                               >  1:843197/1‑90 (MQ=255)
             aaTCGCACAATGTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGGTTTTATATTTCGACTCTGc                                                               >  1:282242/1‑90 (MQ=255)
                 gCACAATGTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGGTTTTATATTTTGACTCTTcaccc                                                           >  1:248070/1‑90 (MQ=255)
                   acaATGTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTCATATTTCGACTCTGcacccac                                                         <  1:846518/90‑1 (MQ=255)
                   acaATGTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTCATATTTCGACTCTGcacccac                                                         <  1:34905/90‑1 (MQ=255)
                   acaATGTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTCATATTTCGACTCTGcacccac                                                         <  2:838847/90‑1 (MQ=255)
                        gTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTCATATTTCGACTCTGCACCCACCGGGt                                                    <  2:819516/90‑1 (MQ=255)
                         ttCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGGTTTTCTATTTTTACTCTGCACCCCCCCGGTa                                                   >  1:825251/1‑90 (MQ=255)
                          tCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTCATATTTCGACTCTGCACCCACCGGGTaa                                                  <  1:523898/90‑1 (MQ=255)
                          tCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTCATATTTCGACTCTGCACCCACCGGGTaa                                                  <  1:2539/90‑1 (MQ=255)
                                tgtgGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGGGTTTATATTTCGACTCCTCGCCCCCCCGGTaacgcaag                                            >  2:864565/1‑90 (MQ=255)
                                  tgGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTTATATTTTGACTCTGCACCCACCCGGGtaggcaatgg                                          >  2:673047/1‑87 (MQ=255)
                                  tgGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTCATATTTCGACTCTGCACCCACCGGGTaaggcaaggc                                          <  1:208263/90‑1 (MQ=255)
                                       tCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGGTTTTATATTTTGACTCTGCCCCCACCCGGGAAGGCAAAGGACcgc                                     >  1:652164/1‑90 (MQ=255)
                                       tCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTTATATTTTGACTCTGCACCCCCCCGGGAAGGGAAGGCACcgc                                     >  2:229800/1‑90 (MQ=255)
                                       tCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTCATATTTCGACTCTGCACCCACCGGGTAAGGCAAGGCACcgc                                     <  2:242286/90‑1 (MQ=255)
                                                       tCCGGAAAGGCGATAAAAGAGCGGCGGGAATTCGTATTTCTTCTCTGCACCCACCCGGGAAGGCAAGGGCCAGCCCTTTTGGCGCCCCtt                     >  2:408473/1‑90 (MQ=255)
                                                                   aTAAAAGAGCGGCGGGATTTCATATTTCGACTCTGCACCCACCGGGTAAGGCAAGGCACCGCGCTTTT‑GCGCCTCTTCCAGCACTCTggc        <  1:334783/90‑1 (MQ=255)
                                                                         gagCGGCGGGGTTTTATATTTTTACTCTGCCCCCCCCCGGGAAAGGAAGGCACCGCGCTTTT‑TTGCCCCTTCCCGCCCCCCGGCGGCaaa  >  1:766135/1‑89 (MQ=255)
                                                                                       |                                                                            
TCGGGTTAATGCGAATCGCACAATGTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTCATATTTCGACTCTGCACCCACCGGGTAAGGCAAGGCACCGCGCTTTT‑GCGCCTCTTCCAGCACTCTGGCGGCAAT  >  NZ_CP009273/3498353‑3498515

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑