Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,994,3580AG65.5% 28.9 / 25.4 29S50P (TCC→CCC) fliZflagella biosynthesis regulatory protein FliZ
Reads supporting (aligned to +/- strand):  ref base A (6/4);  new base G (8/11);  total (14/15)
Fisher's exact test for biased strand distribution p-value = 4.50e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

AAGCCGATAATATCGAAAAAATCACTCTGCGTTTTGCAATGTAAATCACCGCAAAATCGGCACAATGCCGCCCATGA‑TTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTCTGGCTGTGTTTAAAGTCTTTAAGATAGCGGCTTAATGGCCGTCTTT  >  NZ_CP009273/1994231‑1994486
                                                                                                                                |                                                                                                                                
aaGCCGATAATATCGAAAAAATCACTCTGCGTTTTGCAATGTAAATCACCGCAAAATCGGCACAATGCCGCCCATGATTTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGGAATCTCGAtt                                                                                                                        <  2:456783/139‑1 (MQ=255)
     gATAATATCGAAAAAATCACTCTGCGTTTTGCAATGTAAATCACCGCAAAATCGGCACAATGCCGCCCATGA‑TTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGGAATCTCGATTTTATTc                                                                                                                  <  1:421938/139‑1 (MQ=255)
                    aTCACTCTGCGTTTTGCAATGTAAATCACCGCAAAATCGGCACAATGCCGCCCATGA‑TTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGAAATCTCGATTTTATTCACTATTTTGCCGTcg                                                                                                   <  1:403716/139‑1 (MQ=255)
                       aCTCTGCGTTTTGCAATGTAAATCACCGCAAAATCGGCACAATGCCGCCCATGA‑TTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGGAATCTCGATTTTATTCACTATTTTGCCGTcgcg                                                                                                 <  2:245238/138‑1 (MQ=255)
                                       tGTAAATCACCGCAAAATCGGCACAATGCCGCCCATGA‑TTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGTACTAAGGCAATGCGAt                                                                                >  2:443700/1‑139 (MQ=255)
                                                 cGCAAAATCGGCACAATGCCGCCCATGA‑TTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAAtt                                                                       >  2:512121/1‑138 (MQ=255)
                                                   cAAAATCGGCACAATGCCGCCCATGA‑TTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGGAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTAc                                                                    >  1:204166/1‑139 (MQ=255)
                                                   cAAAATCGGCACAATGCCGCCCATGA‑TTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTAc                                                                    >  2:286549/1‑139 (MQ=255)
                                                   cAAAATCGGCACAATGCCGCCCATGA‑TTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTAc                                                                    >  1:474627/1‑139 (MQ=255)
                                                            cacaATGCCGCCCATGA‑TTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGGAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATgcg                                                           <  1:26229/139‑1 (MQ=255)
                                                                aTGCCGCCCATGA‑TTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGGAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCa                                                       <  1:537586/139‑1 (MQ=255)
                                                                           gA‑TTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGGAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTCTGGc                                            >  1:451525/1‑139 (MQ=255)
                                                                            a‑TTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTCTGGCt                                           <  1:286549/139‑1 (MQ=255)
                                                                                    ttCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGGAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTCTGGCTGTGTTTa                                    <  2:451525/139‑1 (MQ=255)
                                                                                    ttCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGGAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTCTGGCTGTGTTTa                                    <  2:311818/139‑1 (MQ=255)
                                                                                      ccGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGGAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGGAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTCTGGCTGTGTTTa                                    >  2:324018/1‑137 (MQ=255)
                                                                                       cGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGGAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTCTGGCTGTGTTTaaa                                  <  2:143905/138‑1 (MQ=255)
                                                                                       cGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGGAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTCTGGCTGTGTTTAAAg                                 >  1:143905/1‑139 (MQ=255)
                                                                                       cGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTCTGGCTGTGTTTaaa                                  <  1:119947/138‑1 (MQ=255)
                                                                                         tttGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACt                                                                                             >  2:528258/1‑77 (MQ=255)
                                                                                         tttGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACt                                                                                             <  1:528258/77‑1 (MQ=255)
                                                                                                 ccaTTTTCATCAAGCAGCGTGTCCAGGCGGGGAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTAct                                                                   >  2:142552/1‑94 (MQ=255)
                                                                                                 ccaTTTTCATCAAGCAGCGTGTCCAGGCGGGGAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTAct                                                                   <  1:142552/95‑2 (MQ=255)
                                                                                                                agcGTGTCCAGGCGGGGAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTCTGGCTGTGTTTAAAGTCTTTAAGATAGCGGCTTAATGGcc        <  2:204166/139‑1 (MQ=255)
                                                                                                                agcGTGTCCAGGCGGGGAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTCTGGCTGTGTTTAAAGTCTTTAAGATAGCGGCTTAATGGcc        <  1:364347/139‑1 (MQ=255)
                                                                                                                  cGTGTCCAGGCGGGGAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTCTGGCTGTGTTTAAAGTCTTTAAGATAGCGGCTTAATGGCCGt      >  1:478932/1‑139 (MQ=255)
                                                                                                                  cGTGTCCAGGCGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTCTGGCTGTGTTTAAAGTCTTTAAGATAGCGGCTTAATGGCCGt      >  2:118032/1‑139 (MQ=255)
                                                                                                                      tCCAGGCGGGGAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTCTGGCTGTGTTTAAAGTCTTTAAGATAGCGGCTTAATGGCCGTCttt  >  2:161472/1‑139 (MQ=255)
                                                                                                                      tCCAGGCGGGGAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTCTGGCTGTGTTTAAAGTCTTTAAGATAGCGGCTTAATGGCCGTCttt  >  1:163436/1‑139 (MQ=255)
                                                                                                                                aaaTCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGa                                                                                 >  2:43718/1‑50 (MQ=255)
                                                                                                                                aaaTCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGa                                                                                 <  1:43718/50‑1 (MQ=255)
                                                                                                                                |                                                                                                                                
AAGCCGATAATATCGAAAAAATCACTCTGCGTTTTGCAATGTAAATCACCGCAAAATCGGCACAATGCCGCCCATGA‑TTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTCTGGCTGTGTTTAAAGTCTTTAAGATAGCGGCTTAATGGCCGTCTTT  >  NZ_CP009273/1994231‑1994486

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑