Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,906,0070TG52.9% 13.4 / 19.1 17H276P (CAC→CCC) htpXprotease HtpX
Reads supporting (aligned to +/- strand):  ref base T (2/6);  new base G (9/0);  total (11/6)
Fisher's exact test for biased strand distribution p-value = 2.26e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.53e-03
Rejected as consensus: Frequency below/above cutoff threshold.

TTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGC  >  NZ_CP009273/1905941‑1906067
                                                                  |                                                            
tttACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAAATCACTGAGc                                       >  1:26985/1‑90 (MQ=255)
  tACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGa                                     >  2:396202/1‑90 (MQ=255)
  tACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCAAGAAAAAACCACTGAGCGa                                     >  2:952406/1‑90 (MQ=255)
           ttACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACtt                            <  1:97019/90‑1 (MQ=255)
             aCTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGGTTTTGACTTAc                          >  2:512258/1‑90 (MQ=255)
              cTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTAcc                         <  1:6799/90‑1 (MQ=255)
              cTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTAcc                         <  1:168133/90‑1 (MQ=255)
              cTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCATGAACAACTCACTGAGCGGTTTTGACTTAcc                         >  2:355511/1‑90 (MQ=255)
                tCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGt                       <  1:952406/90‑1 (MQ=255)
                  aGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGATTTCGACTTACCGTTa                     >  2:29877/1‑90 (MQ=255)
                           cccGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCagaga            <  2:702859/90‑1 (MQ=255)
                              gTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAAAAACTCACTGAGCGATTTTGACTTTCCGTTAATGCAGAGAGcc         >  1:206178/1‑90 (MQ=255)
                                     gagCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGc  <  1:844740/90‑1 (MQ=255)
                                     gagCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGGTTTCGACTTTCCGTTTATGCAGAGAGCCATCATGc  >  1:378468/1‑90 (MQ=255)
                                     gagCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGc  >  2:310886/1‑90 (MQ=255)
                                     gagCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACCGAGCGATTTTGACTTTCCGGTAATGGAGAGAGCCATCATGc  >  1:109850/1‑90 (MQ=255)
                                     gagCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAAAAACTCACTGAGCGGTTTTGACTTACCGTTAATGCAGAGAGCCATCATGc  >  2:911012/1‑90 (MQ=255)
                                                                  |                                                            
TTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGC  >  NZ_CP009273/1905941‑1906067

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑