Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273172,7550AG53.8% 5.9 / 14.6 13T388A (ACG→GCG) clcAH(+)/Cl(‑) exchange transporter ClcA
Reads supporting (aligned to +/- strand):  ref base A (1/5);  new base G (7/0);  total (8/5)
Fisher's exact test for biased strand distribution p-value = 4.66e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.56e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

ACTGTGCTGGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATCATTCTGGTTC  >  NZ_CP009273/172686‑172830
                                                                     |                                                                           
aCTGTGCTGGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATg                                                         <  1:174961/90‑1 (MQ=255)
   gtgCTGGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGtt                                                                         <  1:414170/71‑1 (MQ=255)
   gtgCTGGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGtt                                                                         >  2:414170/1‑71 (MQ=255)
        gggAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGGGTTTGGTATTTCCGGGATGGGGGGAtt                                                 >  1:275881/1‑90 (MQ=255)
        gggAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGTTTGCTTTTGCCCGGAAGGGGGGAtt                                                 >  2:355047/1‑90 (MQ=255)
        gggAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGGTTGCTATTTCCGGGATGGGGGGAtt                                                 >  1:55771/1‑90 (MQ=255)
        gggAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGGTTGCTATTGCCGGGATGGGGGGAtt                                                 >  1:184399/1‑90 (MQ=255)
             ccGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGGTTTGTATTGCCGGAATGGGGGGATTACTgg                                            >  1:51415/1‑90 (MQ=255)
             ccGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGAGTTTTCTTTTGCCGGGATGGGGGGATTACttg                                            >  2:394736/1‑88 (MQ=255)
                                     aGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGGTTGCTATTGCCGGGATGGGGGCGTTACTGGGGGGATCTATTCGCGGGGCGTTaa                    >  1:31000/1‑90 (MQ=255)
                                       cTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACg                  <  1:355047/90‑1 (MQ=255)
                                                  atatCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATCAttct       <  2:341057/90‑1 (MQ=255)
                                                       aCCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATCAttctggttc  <  2:236005/90‑1 (MQ=255)
                                                                     |                                                                           
ACTGTGCTGGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATCATTCTGGTTC  >  NZ_CP009273/172686‑172830

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑