Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273172,7550AG61.5% 4.9 / 11.0 13T388A (ACG→GCG) clcAH(+)/Cl(‑) exchange transporter ClcA
Reads supporting (aligned to +/- strand):  ref base A (0/5);  new base G (8/0);  total (8/5)
Fisher's exact test for biased strand distribution p-value = 7.77e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.13e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GGCGCTGGGTACTGTGCTGGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATC  >  NZ_CP009273/172676‑172820
                                                                               |                                                                 
ggCGCTGGGTACTGTGCTGGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGGGGTTGCttt                                                         >  1:100814/1‑88 (MQ=255)
      gggTACTGTGCTGGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGGTTGCTATTTCCgg                                                   >  2:480615/1‑90 (MQ=255)
             gtgCTGGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATgggg                                            <  2:17498/90‑1 (MQ=255)
                  gggAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGTTTGCTATTGCCGGGATGGGGGGAtt                                       >  2:129442/1‑90 (MQ=255)
                  gggAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGTTTGCTATTGCCGGGATGGGGGGAtt                                       >  2:249289/1‑90 (MQ=255)
                       ccGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGTTTGCTTTTGCCGGGATGGGGGGATTACttg                                  >  2:224408/1‑88 (MQ=255)
                         gCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGGTTGCTATTGCCGGGATGGGGGGATTACTggcg                                >  2:240258/1‑90 (MQ=255)
                          cTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTggcgg                               <  1:266286/90‑1 (MQ=255)
                          cTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTggcgg                               <  2:100765/90‑1 (MQ=255)
                            ttCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCa                             <  1:87632/90‑1 (MQ=255)
                                    ggTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGTTTGCTATTGCCGGGATGGGGGGATTACTGGCGGGATCTAtttg                     >  1:162953/1‑88 (MQ=255)
                                    ggTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGGTTTCTGTTGCCGGGATGGGGGCATTACTTGCGGGATCTAtttg                     >  1:284587/1‑88 (MQ=255)
                                                       ccGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATc  <  2:100814/90‑1 (MQ=255)
                                                                               |                                                                 
GGCGCTGGGTACTGTGCTGGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATC  >  NZ_CP009273/172676‑172820

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑