Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273172,1030TG54.2% 15.1 / 29.9 24G170G (GGT→GGG) clcAH(+)/Cl(‑) exchange transporter ClcA
Reads supporting (aligned to +/- strand):  ref base T (5/6);  new base G (13/0);  total (18/6)
Fisher's exact test for biased strand distribution p-value = 3.43e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.61e-04
Rejected as consensus: Frequency below/above cutoff threshold.

GGTGTTGGGGCGCGAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGTGACGAAGCTCGCCATACGCTGCTGGCAACCGGTGCTGCTGCGGGGCTGGCTGCGGCCTTTAACGCGCCGCTGGCG  >  NZ_CP009273/172022‑172178
                                                                                 |                                                                           
ggTGTTGGGGCGCGAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGGATGGGGCTTGATATTTTCCGCCTGAAAGGGGACGAAGc                                                                     >  2:35144/1‑90 (MQ=255)
     tGGGGCGCGAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGGCGGATGGGGGTTGATATTTTCCGCCTGAAAGGGGACGAAGCTCGcc                                                                >  2:445651/1‑90 (MQ=255)
           gcgAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGGGACGAAGCTCGCCATACgc                                                          >  1:363730/1‑90 (MQ=255)
           gcgAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGGGACGAAACTCGCCATACgc                                                          >  1:267091/1‑90 (MQ=255)
           gcgAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGGATGGGGGTTGATATTTTTCGCCTGAAAGGGGACGAAGCTCGCCATACgc                                                          >  2:278452/1‑90 (MQ=255)
           gcgAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGGATGGGGCTTGATATTTTTCGCCTGAAAGGGGACGAAGCTCGCCATACgc                                                          >  2:193653/1‑90 (MQ=255)
           gcgAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGGATGGGGCTTGATATTTTCCGCCTGAAAGGGGACGAAGCTCGCCATACgc                                                          >  2:167118/1‑90 (MQ=255)
           gcgAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGGATGGGGCTTGATATTTTCCGCCCGAAAGGGGACGAAGCTCGCCATACgc                                                          >  2:9247/1‑90 (MQ=255)
           gcgAAGGGCCAACCGTGCAGATCGGCGGGAACATTTGTCGGATGGTGGTTGATATTTTTCGCCTCAAAGGGGACGAAGCTGGCCATAAgc                                                          >  2:359148/1‑90 (MQ=255)
                    cAACCGTGCAGATCGGCGGTAACATTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGTGACGAAGCTCGCCATACGCTGCTGGCaa                                                 <  1:359148/90‑1 (MQ=255)
                          tGCAGATCGGCGGTAACATTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGGGACGAAGCTCGCCATACCCTGCTGGCAACCCGtg                                           >  1:326322/1‑90 (MQ=255)
                          tGCAGATCGGCGGTAACATTGGCCGTATGGGGCTTGATATTTTCCGCCTGAAAGGTGACGAAGCTCGCCATACGCTGCTGGCAACCGGtg                                           >  1:386982/1‑90 (MQ=255)
                           gCAGATCGGCGGTAACATTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGGGACGAAGCTCGCCATACGCTGCTGGCAACCGGtgc                                          >  1:268850/1‑90 (MQ=255)
                              gATCGGCGGTAACATTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGTGACGAAGCTCGCCATACGCTGCTGGCAACCGGtgctgc                                       <  1:35144/90‑1 (MQ=255)
                                tCGGCGGTAACATTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGTGACGAAGCTCGCCATACGCTGCTGGCAAcc                                               <  1:11675/80‑1 (MQ=255)
                                tCGGCGGTAACATTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGGGACGAAGCTCGCCATACGCTGCTGGCAAcc                                               >  2:11675/1‑80 (MQ=255)
                                   gcggTAACATTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGTGACGAAGCTCGCCATACGCTGCTGGCAACCGGTGCTGCTGCgg                                  >  1:1713/1‑90 (MQ=255)
                                           aTTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGTGACGAAGCTCGCCATACGCTGCTGGCAACCGGtgc                                          <  1:235248/74‑1 (MQ=255)
                                           aTTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGGGACGAAGCTCGCCATACGCTGCTGGCAACCGGtgc                                          >  2:235248/1‑74 (MQ=255)
                                                        tGCTTGATATTTTCCGCCTGAAAGGTGACGAAGCTCGCCATACGCTGCTGGCAACCGGTGCTGCTGCGGGGCTGGCTGCGGCCTTTAAcg             >  1:358599/1‑90 (MQ=255)
                                                                 ttttCCGCCTGAAAGGTGACGAAGCTCGCCATACGCTGCTGGCAACCGGtgc                                          >  2:146959/1‑52 (MQ=255)
                                                                 ttttCCGCCTGAAAGGTGACGAAGCTCGCCATACGCTGCTGGCAACCGGtgc                                          <  1:146959/52‑1 (MQ=255)
                                                                  tttCCGCCTGAAAGGTGACGAAGCTCGCCATACGCTGCTGGCAACCGGTGCTGCTGCGGGGCTGGCTGCGGCCTTTAACGCGCCGCTGGc   <  2:386982/90‑1 (MQ=255)
                                                                   ttCCGCCTGAAAGGTGACGAAGCCCGCCATACGCTGCTGGCAACCGGTGCTGCTGCGGGGCTGGCTGCGGCCTTTAACGCGCCGCTGGCg  >  2:278054/1‑90 (MQ=255)
                                                                                 |                                                                           
GGTGTTGGGGCGCGAAGGGCCAACCGTGCAGATCGGCGGTAACATTGGCCGTATGGTGCTTGATATTTTCCGCCTGAAAGGTGACGAAGCTCGCCATACGCTGCTGGCAACCGGTGCTGCTGCGGGGCTGGCTGCGGCCTTTAACGCGCCGCTGGCG  >  NZ_CP009273/172022‑172178

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑