Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,906,0070TG59.1% 13.5 / 22.6 22H276P (CAC→CCC) htpXprotease HtpX
Reads supporting (aligned to +/- strand):  ref base T (2/7);  new base G (13/0);  total (15/7)
Fisher's exact test for biased strand distribution p-value = 2.11e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.24e-04
Rejected as consensus: Frequency below/above cutoff threshold.

GATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGCGGTTCATAGCT  >  NZ_CP009273/1905919‑1906092
                                                                                        |                                                                                     
gATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCgggtg                                                                                      <  1:958078/90‑1 (MQ=255)
   cAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCgggtgggt                                                                                   <  2:766650/90‑1 (MQ=255)
        cgcgCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATg                                                                               <  2:438557/89‑1 (MQ=255)
        cgcgCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCATg                                                                               >  1:438557/1‑89 (MQ=255)
                      tttACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGGATGAACAACTCCCTGGGc                                                                >  2:125269/1‑90 (MQ=255)
                        tACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGTCATGAACAAATCACTGAGCGa                                                              >  2:284321/1‑90 (MQ=255)
                        tACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACCGAGCGa                                                              >  1:311186/1‑90 (MQ=255)
                            tCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAAATCACTGAGCGGtttt                                                          >  2:117097/1‑89 (MQ=255)
                             cATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAAAAAATCACTTAGCGAttttg                                                         >  1:360813/1‑88 (MQ=255)
                                    cTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCgggtg                                                                                      <  2:497288/54‑1 (MQ=255)
                                    cTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCgggtg                                                                                      >  1:497288/1‑54 (MQ=255)
                                    cTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTAcc                                                  <  1:831737/90‑1 (MQ=255)
                                       cAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGtt                                               <  1:682601/90‑1 (MQ=255)
                                        aGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCgggtg                                                                                      <  2:298273/50‑1 (MQ=255)
                                        aGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTa                                              >  2:302187/1‑90 (MQ=255)
                                        aGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGGGATTTTGACTTACCGTTa                                              >  2:548315/1‑90 (MQ=255)
                                        aGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGATTTTGACTTACCGTTa                                              >  2:934605/1‑90 (MQ=255)
                                              tCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGTGGGCATGATCAACTCACTGAGCGTTTTCGACCTAACCTTAAtcgag                                        >  2:658464/1‑86 (MQ=255)
                                              tCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAAAAAATCCCTGAGCGATTTTGACTTACCGGTTATTCag                                        >  1:83327/1‑90 (MQ=255)
                                                 cccGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCagaga                                     <  2:530122/90‑1 (MQ=255)
                                                    gTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGTCATGAACAACTCACCCAGCGATTTTGACTTTCCGTTTATGCAGAGAGcc                                  >  2:589577/1‑90 (MQ=255)
                                                           gagCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGc                           <  1:420000/90‑1 (MQ=255)
                                                           gagCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCACTGAGCGATTTTGACTTACCGTTTATGCAGAGAGCCATCATGc                           >  1:236107/1‑90 (MQ=255)
                                                           gagCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAAAAAACCCCTGAGCGATTTTGACTTTCCGTTAATTCAGAGAGCCATCATGc                           >  1:331709/1‑90 (MQ=255)
                                                                       gTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTAcc                                                  >  2:357383/1‑55 (MQ=255)
                                                                       gTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTAcc                                                  <  1:357383/55‑1 (MQ=255)
                                                                                    cggGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGCGGTTCATAGCt  <  1:400953/90‑1 (MQ=255)
                                                                                        |                                                                                     
GATCAGGACGCGCTTTTTAGTATTTACTTCATATTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGCGGTTCATAGCT  >  NZ_CP009273/1905919‑1906092

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑