Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273172,0780TG58.3% 5.9 / 19.3 24V162G (GTG→GGG) clcAH(+)/Cl(‑) exchange transporter ClcA
Reads supporting (aligned to +/- strand):  ref base T (5/5);  new base G (14/0);  total (19/5)
Fisher's exact test for biased strand distribution p-value = 5.93e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.50e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GGCGGAGGCATGGTGTTGGGGCGCGAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGTGACGAAGCTCGCCATACGCTGCTGGCAACCGGTGCTGCTGCGGGGCTGGCTGCGG  >  NZ_CP009273/172011‑172158
                                                                   |                                                                                
ggcggAGGCATGGTGTTGGGGCGCGAAGGGCCAACCGGGCAGATCGGCGGGAACATTGGGCGGATGGGGGGTGATATTTTCCGCCTGaaa                                                            >  2:236311/1‑90 (MQ=255)
 gcggAGGCATGGTGTTGGGGCGCGAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGTATGGGGCTTGATATTTTCCGCCTGAAAg                                                           >  1:140315/1‑90 (MQ=255)
       gCATGGTGTTGGGGCGCGAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGGCGGATGGGGGTTGGTATTTTTCGCCTGAAAGGGGACg                                                     >  2:535060/1‑90 (MQ=255)
         aTGGTGTTGGGGCGCGAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGTATGGGGCTTGATATTTTCCGCCTGAAAGGTGACGaa                                                   >  1:93143/1‑90 (MQ=255)
           ggTGTTGGGGCGCGAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGTGACGAAGc                                                 <  2:223145/90‑1 (MQ=255)
           ggTGTTGGGGCGCGAAGGGCCAACCGTGCAGATCGGCGGGAACATTGGCCGGATGGGGGGTTATATTTTTCGCCTGAAAGGGGGCGAAGc                                                 >  2:659311/1‑90 (MQ=255)
                tGGGGCGCGAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGTGACGAAg                                                  >  1:144049/1‑84 (MQ=255)
                tGGGGCGCGAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGTGACGAAg                                                  <  2:144049/84‑1 (MQ=255)
                      gcgAAGGGCCAACCGTGCAGATCGGCGGTAACGTTGGCCGGATTGGGGTTTAAATTTTCCGCCTGAAAGGGGGCGGAGCCCGCCCTAccc                                      >  2:559521/1‑88 (MQ=255)
                      gcgAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGTGACGAAGCTCGCCATACgc                                      <  1:209778/90‑1 (MQ=255)
                      gcgAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGGGACGAAGCTCGCCATACgc                                      >  1:103923/1‑90 (MQ=255)
                      gcgAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGTATGGGGCTTGGTATTTTCCGCCTGAAAGGGGACGAAGCTCGCCATACgc                                      >  1:657046/1‑90 (MQ=255)
                      gcgAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGTATGGGGCTTGATATTTTCCGCCTGAAAGGGGACGAAGCTCGCCATACgc                                      >  1:316240/1‑90 (MQ=255)
                      gcgAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGTATGGGGCTTGATATTTTCCGCCTGAAAGGGGACGAAGCTCGCCATACgc                                      >  2:36849/1‑90 (MQ=255)
                      gcgAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGGATGGGGCTTGATATTTTCCGCCTGAAAGGAGACGAAGCTCGCCATACgc                                      >  1:419206/1‑90 (MQ=255)
                      gcgAAGGGCCAACCGTGCAGATCGGCGGTAAAATTGGCCGGATGGGGCTTTGAATTTTTCGCCTGGAAGGGGACGAAGCTCGCCCTAAgc                                      >  2:305607/1‑90 (MQ=255)
                      gcgAAGGGCCAACCGTGCAGATCGGCGGGAACATTGGCCGTTTGGGGCTTGGAATTTTCCGGCCGAAAGGGGACGCAGCCCGCCacaccc                                      >  2:499063/1‑88 (MQ=255)
                                     tGCAGATCGGCGGTAAAATTGGCCGTATGGGGGTTGATATTTTCCCCCTGAAAGGGGACGAAACGCGCCATACGCTGCTGGCAACCgggg                       >  1:316811/1‑88 (MQ=255)
                                      gCAGATCGGCGGTAACATTGGCCGTATGGGGCTTGAGATTTTTCTGCTGAAACGGGACGAAGCTCCCCCTACGCAGCTGGACACCGGggc                      >  1:695178/1‑90 (MQ=255)
                                         gATCGGCGGTAACATTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGTGACGAAGCTCGCCATACGCTGCTGGCAACCGGtgctgc                   <  2:272797/90‑1 (MQ=255)
                                            cggcggTAACATTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGGGACGAAGCTCGCCATACGCTGCTGGCAACCGGggctgctgc                >  2:16279/1‑90 (MQ=255)
                                              gcggTAACATTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGGGACGAAGCTCGCCATACGCTGCTGGCAACCGGGGCTGCTGCgg              >  1:644564/1‑90 (MQ=255)
                                                          gCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGTGACGAAGCTCGCCATACGCTGCTGGCAACCGGTGCTGCTGCGGGGCTGGCTGCgg  <  1:685384/90‑1 (MQ=255)
                                                          gCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGTGACGAAGCTCGCCATACGCTGCTGGCAACCGGTGCTGCTGCGGGGCTGGCTGCgg  >  1:475371/1‑90 (MQ=255)
                                                                   |                                                                                
GGCGGAGGCATGGTGTTGGGGCGCGAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGTGACGAAGCTCGCCATACGCTGCTGGCAACCGGTGCTGCTGCGGGGCTGGCTGCGG  >  NZ_CP009273/172011‑172158

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑