Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,906,0070TG57.9% 10.1 / 20.0 19H276P (CAC→CCC) htpXprotease HtpX
Reads supporting (aligned to +/- strand):  ref base T (1/7);  new base G (11/0);  total (12/7)
Fisher's exact test for biased strand distribution p-value = 1.59e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.32e-04
Rejected as consensus: Frequency below/above cutoff threshold.

AGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGCGGTTCATAGCT  >  NZ_CP009273/1905923‑1906092
                                                                                    |                                                                                     
aGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCggggggggc                                                                                  >  2:573513/1‑88 (MQ=255)
   aCGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATg                                                                               <  1:207472/90‑1 (MQ=255)
      cgcTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGaac                                                                            >  2:410142/1‑90 (MQ=255)
                tATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGTCATGAAAAAATCCCtca                                                                  >  1:25292/1‑88 (MQ=255)
                           tatTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAAAAAATCACTGAGCGATTTTGAc                                                       >  1:442065/1‑90 (MQ=255)
                              tACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGGTTTTGACttt                                                    >  2:124703/1‑89 (MQ=255)
                                    aGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGTCATGAAAAACCCACTGAGCGATTTTGACTTACCGTTa                                              >  1:276500/1‑90 (MQ=255)
                                             cccGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCagaga                                     <  2:38401/90‑1 (MQ=255)
                                             cccGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGATTTTGACTTACCCTTAATGCagaga                                     >  2:11782/1‑90 (MQ=255)
                                                gTACGCAGAGCTTCAATTCGTTTATCCAGCGGCgggtg                                                                                      <  1:64245/38‑1 (MQ=255)
                                                gTACGCAGAGCTTCAATTCGTTTATCCAGCGGCgggtg                                                                                      >  2:64245/1‑38 (MQ=255)
                                                gTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCATTAAAAACTCACTGGGGGATTTTTACCTACCGATAAATCagcgaggc                                  >  2:580093/1‑88 (MQ=255)
                                                gTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGGTTTCGACTTTACGTTAATGCagagaggc                                  >  2:134893/1‑88 (MQ=255)
                                                       gagCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGc                           <  1:553905/90‑1 (MQ=255)
                                                       gagCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGGTTTTGACTTACCGTTAATGCAGAGAGCCATCATGc                           >  2:616785/1‑90 (MQ=255)
                                                       gagCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAAATCACTGAGGGATTTCGACTTACCGTTAATGCAGAGGGCCATCATGc                           >  2:199250/1‑90 (MQ=255)
                                                             cAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTg                     <  2:560549/90‑1 (MQ=255)
                                                                 tCGTTTATCCAGCGGCGGGGGGGGCATGAACAAATCACTGAGCGGTTTTTACTTTCCGTTAATGCAGAGAGCCATCATGCTGGTTGcttt                 >  1:310336/1‑89 (MQ=255)
                                                                     ttATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGc             <  1:408934/90‑1 (MQ=255)
                                                                       aTCCAGCGGCGGGGGGGGCATGAAAAAATCCCTGAGCGATTTTGTCTTTCCGCTAATGCAGAGGGGCAACATGCTGGTTGGTTTTTTCgg           >  1:182491/1‑90 (MQ=255)
                                                                                cggGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGCGGTTCATAGCt  <  1:573513/90‑1 (MQ=255)
                                                                                cggGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGCGGTTCATAGCt  <  2:442065/90‑1 (MQ=255)
                                                                                    |                                                                                     
AGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGCGGTTCATAGCT  >  NZ_CP009273/1905923‑1906092

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑