Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,906,0110TG65.2% 14.3 / 22.8 23T275P (ACC→CCC) htpXprotease HtpX
Reads supporting (aligned to +/- strand):  ref base T (0/8);  new base G (15/0);  total (15/8)
Fisher's exact test for biased strand distribution p-value = 2.04e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.94e-05
Rejected as consensus: Frequency below/above cutoff threshold.

ACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGCGGTTCATAGCTGGTTTT  >  NZ_CP009273/1905926‑1906098
                                                                                     |                                                                                       
aCGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATg                                                                                     <  1:471262/90‑1 (MQ=255)
 cgcgCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGa                                                                                    <  1:672029/90‑1 (MQ=255)
   cgcTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCATGaaa                                                                                  >  1:232555/1‑89 (MQ=255)
   cgcTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGaaa                                                                                  >  1:649398/1‑89 (MQ=255)
               tttACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGc                                                                      >  1:828671/1‑90 (MQ=255)
                      cATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGGGTGAGCAACTAACTATGCGGttttc                                                               >  2:1202503/1‑88 (MQ=255)
                           tACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTa                                                          <  2:283992/90‑1 (MQ=255)
                           tACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTa                                                          <  2:295925/90‑1 (MQ=255)
                                 aGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGATTTTGACTTACCGttt                                                    >  2:1173454/1‑89 (MQ=255)
                                  ggTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGGTTTCCACTTACCGTTaa                                                   >  1:343535/1‑90 (MQ=255)
                                       tCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACCCCCCGAGCGGTTTTGACTTTCCCTTAATGCag                                              >  2:932981/1‑90 (MQ=255)
                                          cccGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCagaga                                           <  2:803143/90‑1 (MQ=255)
                                             gTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGcc                                        >  1:457383/1‑90 (MQ=255)
                                             gTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCCTGAAAAAATCCCCTAGCGGTTTTGACTTACCGTTTATGGAGGGAGcc                                        >  2:905237/1‑90 (MQ=255)
                                             gTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGATTTTTACTTTCCGTTAATGCAGAGAGcc                                        >  2:961748/1‑90 (MQ=255)
                                             gTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAAATCACTTAGCGATTTTGACTTACCGTTTATGCAGAGAGcc                                        >  2:278036/1‑90 (MQ=255)
                                              tACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGAGGGGCATGAAAAACTCCCTGAGCGATTTTGACTTACCGGTAAAGCAGAGAGCca                                       >  1:597309/1‑90 (MQ=255)
                                                cGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCcatc                                     <  2:1020311/90‑1 (MQ=255)
                                                 gCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCcatca                                    <  1:891641/90‑1 (MQ=255)
                                                                gTTTATCCAGCGGCGGGGGGGGCATGAAAAACTCACTGAGCGATTTTGACTTACCGTTAATGCAGAGAGCCATCATGCTGGGTGcttctt                     >  1:674193/1‑90 (MQ=255)
                                                                gTTTATCCAGCGGCGGGGGGGGAATCAACAAATCACTGGGCGATTTTGGCTTACCGTTAATGGAGGGGGGCAATATGCTGGTTGgttctt                     >  1:1167533/1‑90 (MQ=255)
                                                                         gcggcgGGAGGGGCATGGAAAACACACCGAGCTATTTTGACTTCACCTTAAACCAGAGAGCCATCATGTTGGGTGGGTATTGGGGTTctt            >  2:995087/1‑88 (MQ=255)
                                                                             cggGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGCGGTTCATAGCt        <  1:995087/90‑1 (MQ=255)
                                                                                   ggtCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGCGGTTCATAGCTGGtttt  >  2:318895/1‑90 (MQ=255)
                                                                                     |                                                                                       
ACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGCGGTTCATAGCTGGTTTT  >  NZ_CP009273/1905926‑1906098

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑