Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,906,0070TG57.1% 12.4 / 17.4 21H276P (CAC→CCC) htpXprotease HtpX
Reads supporting (aligned to +/- strand):  ref base T (4/5);  new base G (12/0);  total (16/5)
Fisher's exact test for biased strand distribution p-value = 6.19e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.18e-02
Rejected as consensus: Frequency below/above cutoff threshold.

GATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGCG  >  NZ_CP009273/1905919‑1906082
                                                                                        |                                                                           
gATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCgggtg                                                                            <  2:80233/90‑1 (MQ=255)
gATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCgggtg                                                                            <  2:573634/90‑1 (MQ=255)
gATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCgggtg                                                                            <  1:704198/90‑1 (MQ=255)
           gcTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGaaca                                                                 <  1:776841/90‑1 (MQ=255)
           gcTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGaaca                                                                 >  2:334597/1‑90 (MQ=255)
                      tttACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACCCCCTTAGc                                                      >  2:432374/1‑90 (MQ=255)
                             cATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGAttttg                                               >  2:231225/1‑88 (MQ=255)
                                    cTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAAATCACTGAGCGATTTTGGCTTAcc                                        >  2:869326/1‑90 (MQ=255)
                                    cTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAAAAACCCACTGAGCGGTTTTGACTTAcc                                        >  1:55586/1‑90 (MQ=255)
                                      tCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCATGAACAACTCACTGAGCGATTTTGGCTTACCGt                                      >  2:575275/1‑90 (MQ=255)
                                        aGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGGCTGAAAAAATCACTTAGCCGCTTCGACTTACCGttt                                    >  1:656727/1‑89 (MQ=255)
                                            aTTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCATGAACAACTCACTGAGCGATTTCGACTTACCGGTAATGc                                >  2:135012/1‑90 (MQ=255)
                                             ttCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGGTTTTTACTTACCGTTAATGCa                               >  1:149293/1‑90 (MQ=255)
                                                 cccGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCagaga                           <  1:850969/90‑1 (MQ=255)
                                                    gTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGACTTCGACTTACCGTTAATGCAGAGAGcc                        >  2:754685/1‑90 (MQ=255)
                                                    gTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAAAAACTCACTGAGCGATTTTTACTTACCGGTTATGGCGAGAGcc                        >  2:532063/1‑90 (MQ=255)
                                                           gagCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGc                 >  2:675455/1‑90 (MQ=255)
                                                           gagCTTCAATTCGTTTATCCAGCGGCGGGGGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGc                 >  2:111891/1‑90 (MQ=255)
                                                           gagCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAAAAACTCACTGAGCGATTTTGACTTTCCGTTAATGGAGAGAGGCATCATGc                 >  1:498405/1‑90 (MQ=255)
                                                                     tCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGATTTTGACTTTCCGGTAATGCAGAGAGCCATCATGCTGGGTGcttt       >  1:377951/1‑89 (MQ=255)
                                                                     tCGTTTATCCAGCGGCGGGGGGGGCATGAACAAATCACTGAGCGATTTTGACTTTCCGTTAATGCAGAGAGCCATCATGCTGGTTGcttt       >  1:33198/1‑89 (MQ=255)
                                                                         ttATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGc   <  2:377951/90‑1 (MQ=255)
                                                                         ttATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGc   <  1:374662/90‑1 (MQ=255)
                                                                          tATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGCg  <  1:675455/90‑1 (MQ=255)
                                                                                        |                                                                           
GATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGCG  >  NZ_CP009273/1905919‑1906082

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑