Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273832,2120TG54.5% 15.5 / 24.7 22F136V (TTT→GTT) hcxBhydroxycarboxylate dehydrogenase HcXB
Reads supporting (aligned to +/- strand):  ref base T (4/6);  new base G (12/0);  total (16/6)
Fisher's exact test for biased strand distribution p-value = 2.81e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.77e-03
Rejected as consensus: Frequency below/above cutoff threshold.

CACGGTATTGCCGCCGTGGCGCTACATAACTCGCATCATATCGGCCGTATCGGTTACTGGGCGGAGCAGTGTGCAGCGGCGGGGTTTGTCTCTATCCACTTTGTTAGCGTGGTCGGTATTCCAATGGTCGCGCCGTTCCACGGTCGCGACAGCCGCTTTGGCACCAATCC  >  NZ_CP009273/832128‑832297
                                                                                    |                                                                                     
cACGGTATTGCCGCCGTGGCGCTACATAACTCGCATCATATCGGCCGTATCGGTTACTGGGCGGAGCAGTGTGCAGCGGCGGGGTTTGtc                                                                                  <  1:596630/90‑1 (MQ=255)
            gccgTGGCGCTACATAACTCGCATCATATCGGCCGTATCGGTTACTGGGCGGAGCAGTGTGCAGCGGCGGGGGTTGTTTCTTTCCACttt                                                                      >  2:701322/1‑90 (MQ=255)
              cgTGGCGCTACATAACTCGCATCATATCGGCCGTATCGGTTACTGGGCGGAGCAGTGTGCAGCGGCGGGGGTTTTCTCTTTCCCCttttt                                                                    >  2:545479/1‑88 (MQ=255)
                            aCTCGCATCATATCGGCCGTATCGGTTACTGGGCGGAGCAGTGTGCAGCGGCGGGGTTTGTCTCTATCCACTTTGTTAGCGTGGTCGGTa                                                      <  2:46105/90‑1 (MQ=255)
                            aCTCGCATCATATCGGCCGTATCGGTTACTGGGCGGAGCAGTGTGCAGCGGCGGGGTTTGTCTCTATCCACTTTGTTAGCGTGGTCGGTa                                                      <  2:201645/90‑1 (MQ=255)
                            aCTCGCATCATATCGGCCGTATCGGTTACTGGGCGGAGCAGTGTGCAGCGGCGGGGGTTGTCTCTTTCCACTTTGTTTGCGGGGGCgggg                                                      >  2:140767/1‑88 (MQ=255)
                               cGCATCATATCGGCCGTATCGGTTACTGGGCGGAGCAGTGTGCAGCGGCGGGGGTTGTCTCTATCCACTTTGTTAGCGTGGGCGGGATTc                                                   >  1:103877/1‑90 (MQ=255)
                                 catcatATCGGCCGTATCGGTTACTGGGCGGAGCAGTGTGCAGCGGCGGGGGTTGTTTCTATCCCCTTTGTTTGCGTGGGCGGGATTCCa                                                 >  2:271380/1‑90 (MQ=255)
                                              gTATCGGTTACTGGGCGGAGCAGTGTGCAGCGGCGGGGTTTGTCTCTATCCACTTTGTTAGCGTgg                                                            >  1:293112/1‑66 (MQ=255)
                                              gTATCGGTTACTGGGCGGAGCAGTGTGCAGCGGCGGGGTTTGTCTCTATCCACTTTGTTAGCGTgg                                                            <  2:293112/66‑1 (MQ=255)
                                               tATCGGTTACTGGGCGGAGCAGTGTGCAGCGGCGGGGTTTGTCTCTATcc                                                                           <  2:422270/50‑1 (MQ=255)
                                               tATCGGTTACTGGGCGGAGCAGTGTGCAGCGGCGGGGTTTGTCTCTATcc                                                                           >  1:422270/1‑50 (MQ=255)
                                                   ggTTACTGGGCGGAGCAGTGTGCAGCGGCGGGGTTTGTCTCTATCCACTTTGTTAGCGTGGTCGGTATTCCAATGGTCGCGCCGTTCCAc                               >  1:352378/1‑90 (MQ=255)
                                                            gCGGAGCAGTGTGCAGCGGCGGGGTTTGTCTCTATCCAc                                                                         <  1:699505/39‑1 (MQ=255)
                                                            gCGGAGCAGTGTGCAGCGGCGGGGGTTGTCTCTATCCAc                                                                         >  2:699505/1‑39 (MQ=255)
                                                                 gCAGTGTGCAGCGGCGGGGGTTGTCTTTATCCCCTTTTTTAGCGGGGGCGGGATTCCAATGGGCGCGCCGGTCCACGGGCGCGACAGCCg                 >  2:802620/1‑90 (MQ=255)
                                                                      gtgCAGCGGCGGGGTTTGTCTCTATCCACTTTGTTAGCGTGGTCGGGATTCCAATGGTCGCGCCGTTCCACGGTCGCGACAGCCGCTTTg            >  1:621790/1‑90 (MQ=255)
                                                                      gtgCAGCGGCGGGGGTTTTCTCTATCCACTTTGTTTGCGTGGGCGGTATTCCAAAGGGCGCGCCGTTCCCCGGGCGCGACAGCCGCTTTg            >  2:864019/1‑90 (MQ=255)
                                                                      gtgCAGCGGCGGGGGTTGTCTCTATCCACTTTGTTAGCGTGGTCGGTATTCCAATGGTCGCGCCGTTCCACGGGCGCGACAGCCGCTTTg            >  1:472209/1‑90 (MQ=255)
                                                                         cAGCGGCGGGGGTTGTCTCTATCCACTTAGTTAGCGTGGGCGGGATTCCAAAGGGCGCGCCGGTCCCCGGTCGCGGCAACCGCCTTTGCa         >  2:353582/1‑90 (MQ=255)
                                                                           gcggcgGGGGTTGTCTCTATCCACTTTTTTAGCGTGGGCGGTATTCCAATGGTCGCGCCGTTCCACGGGCGCGACAGCCGCCTTGGCAcc       >  2:334116/1‑90 (MQ=255)
                                                                                ggggGTTGTCTCTATCCACTTTTTTAGGGTGGGCGGTATTCCCATGGTCGCGCCCTTCCCCGGGCGCGGCAGCCGCGTTTGCACCAATcc  >  2:588395/1‑90 (MQ=255)
                                                                                    |                                                                                     
CACGGTATTGCCGCCGTGGCGCTACATAACTCGCATCATATCGGCCGTATCGGTTACTGGGCGGAGCAGTGTGCAGCGGCGGGGTTTGTCTCTATCCACTTTGTTAGCGTGGTCGGTATTCCAATGGTCGCGCCGTTCCACGGTCGCGACAGCCGCTTTGGCACCAATCC  >  NZ_CP009273/832128‑832297

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑