Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,125,8250TC58.3% 6.2 / 11.8 12G165G (GGA→GGG) flgAflagellar basal body P‑ring formation chaperone FlgA
Reads supporting (aligned to +/- strand):  ref base T (5/0);  new base C (0/7);  total (5/7)
Fisher's exact test for biased strand distribution p-value = 1.26e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.93e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GTTCAGCGCCTGACCTTCTGCGTTGGCGCTAAACCCATCACCGCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATCGCGCAGGCTAATG  >  NZ_CP009273/1125759‑1125903
                                                                  |                                                                              
gTTCAGCGCCTGACCTTCTGCGTTGGCGCTAAACCCATCACCGCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGCCATGCCTg                                                         >  2:468374/1‑90 (MQ=255)
  tCAGCGCCTGCCCTTCTGCGTTGGCGCTAACCCCACCCCCGCGGGCGATCACATTGACGCGTTGCCCCGCTTTTACCCGCCATGCCTGGc                                                       <  2:88469/90‑1 (MQ=255)
           gcccTTCTGCGTTGGCGCAAACCCCCCCCCCGCGGGCGATCACATTGCCGCGTTGCCCCGTTTTTCCCCGCCATGCCTGGCGAAACTggg                                              <  1:524633/88‑1 (MQ=255)
                     gTTGGCGCAAACCCCACCACCCCTGGGGATCACATTGACGCGTTGCCCCGTTTTTCCCCGCCATGCCTGGCGAAACTGGGTTAACTGGAt                                    <  1:255437/90‑1 (MQ=255)
                       tGGCGCTAAACCCATCACCGCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAg                                  >  2:431178/1‑90 (MQ=255)
                             tAAACCCATCACCGCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGCTgtc                            >  1:452320/1‑88 (MQ=255)
                              aacccccTCCCCGGTGGCGATCACTTTGGCGTTTTGCCCCGTTTTCCCCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATc                           <  1:416150/87‑1 (MQ=255)
                               accccACCCCCGCTGGCGATCACATTGACGCGTTGCCCCGCTTTTACCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCg                          <  2:35079/88‑1 (MQ=255)
                                        ccGCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGa                 >  2:94052/1‑90 (MQ=255)
                                              gCGATCACATTGGCGCGTTGCCCCTTTTTTCCCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATCgcgc           <  1:468374/90‑1 (MQ=255)
                                                     caTTGACGGGTTGCCCCGTTTTTCCCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATCGCGCAGGCTaa    <  2:482023/90‑1 (MQ=255)
                                                       ttGACGCGTTGTCCCGCTTTTACCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATCGCGCAGGCTAATg  >  1:77190/1‑90 (MQ=255)
                                                                  |                                                                              
GTTCAGCGCCTGACCTTCTGCGTTGGCGCTAAACCCATCACCGCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATCGCGCAGGCTAATG  >  NZ_CP009273/1125759‑1125903

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑