Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273172,7720AG54.5% 5.6 / 12.6 11G393G (GGA→GGG) clcAH(+)/Cl(‑) exchange transporter ClcA
Reads supporting (aligned to +/- strand):  ref base A (1/4);  new base G (6/0);  total (7/4)
Fisher's exact test for biased strand distribution p-value = 1.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.28e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATCATTCT  >  NZ_CP009273/172694‑172825
                                                                              |                                                     
gggAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGTTTGCTATTGCCCGGATGGGGGCCtt                                            >  1:79290/1‑90 (MQ=255)
gggAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGGTTTCTTTTTCCGGGATggggggttt                                            >  2:145215/1‑86 (MQ=255)
     ccGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGTTTGCTTTTTCCGGGATGGGGGGATTTCttg                                       >  2:106592/1‑88 (MQ=255)
     ccGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGTTTGCTATTGCCGGGATTGGGGGATTTCttg                                       >  1:58053/1‑88 (MQ=255)
     ccGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGGTTGCTATTGCCGGGATGGGGGGATTACttg                                       >  2:233022/1‑88 (MQ=255)
     ccGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGAGGGTTGGTATTGCCGGGATGGGGGGGTTACttg                                       >  2:3548/1‑88 (MQ=255)
      cGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAGTGGGGGCATTACTggc                                      <  2:470023/90‑1 (MQ=255)
                                         aaTATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATCAttc   <  1:298418/90‑1 (MQ=255)
                                          atatCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATCAttct  <  1:450845/90‑1 (MQ=255)
                                                                       ttGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGcc                    <  1:251411/43‑1 (MQ=255)
                                                                       ttGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGcc                    >  2:251411/1‑43 (MQ=255)
                                                                              |                                                     
GGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATCATTCT  >  NZ_CP009273/172694‑172825

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑