Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273172,9200CA57.1% 2.9 / 11.6 14P443T (CCG→ACG) clcAH(+)/Cl(‑) exchange transporter ClcA
Reads supporting (aligned to +/- strand):  ref base C (3/3);  new base A (8/0);  total (11/3)
Fisher's exact test for biased strand distribution p-value = 5.49e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.20e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

ATGACCGATAACTACCAGCTCATTTTGCCAATGATTATTACCGGTCTTGGCGCAACACTATTAGCGCAATTTACCGGCGGGAAACCGCTATACTCGGCGATTCTTGCGCGCACGCTGGCAAAACAGGAAGCTGAGCAACTGGCGCGAAGC  >  NZ_CP009273/172836‑172985
                                                                                    |                                                                 
aTGACCGATAACTACCAGCTCATTTTGCCAATGATTATTACCGGTCTTGGCGCAACACTATTAGCGCAATTTACCGGCGGGAAACCGCta                                                              >  2:546422/1‑90 (MQ=255)
    ccGATAACTACCAGCTCATTTTGCCAATGATTATTACCGGTCTTGGCGCAACACTATTAGCGCAATTTACCGGCGGGAAAACGCTATACt                                                          >  2:347686/1‑90 (MQ=255)
                aGCTCATTTTGCCAATGATTATTACCGGTCTTGGCGCAACACTATTAGCGCAATTTACCGGCGGGAAAACGCCATATTCGGCGATttttt                                              >  1:512946/1‑89 (MQ=255)
                 gCTCATTTTGCCAATGATTATTACCGGTCTTGGCGCAACACTATTAGCGCAATTTACCGGCGGGAAACCGCTATACTCTGCGGTTCTTgc                                             >  2:376270/1‑90 (MQ=255)
                 gCTCATTTTGCCAATGATTATTACCGGTCTTGGCGCAACACTATTAGCGCAATTTACCGGCGGGAAAACGCTATACTCCGCGATTCtttc                                             >  1:548700/1‑88 (MQ=255)
                     aTTTTGCCAATGATTATTACCGGTCTTGGCGCAACACTATTAGCGCAATTTACCGGCGGGAAACCGCTATACTCGGCGATTCTTgcgcgc                                         <  1:149962/90‑1 (MQ=255)
                                    attaCCGGTCTTGGCGCAACACTATTAGCGCAATTTACCGGCGGGAAAACGCTATACTCGGCGATTCTTGCGCGCACGCTGGCAAAACAg                          >  2:307636/1‑90 (MQ=255)
                                         cGGTCTTGGCGCAACACTATTAGCGCAATTTACCGGCGGGAAAACCCCATACTCCGCGATTCTTTCGCGCACGCTGGCAAAACAGGAAGc                     >  1:417465/1‑90 (MQ=255)
                                          ggTCTTGGCGCAACACTATTAGCGCAATTTACCGGCGGGAAAACCCTATTCTCCGTGATTTTTCTGGGCACCCCGGCGAAAAAGGaaacc                    >  1:334649/1‑87 (MQ=255)
                                          ggTCTTGGCGCAACACTATTAGCGCAATTTACCGGCGGGAAAACCCTATATTTGGCGCTTTTTTCGCGCCCCCTGGCCAAAAAAGaaagt                    >  2:221986/1‑87 (MQ=255)
                                               tGGCGCAACACTATTAGCGCAATTTACCGGCGGGGAACCGCTATTCGCGGAGATTCTTGGGCGCACGCTGGCTAAAAAGGAAGCTGAgta               >  2:363627/1‑88 (MQ=255)
                                               tGGCGCAACACTATTAGCGCAATTTACCGGCGGGAAAACGCTATACTCCGCGATTTTTGCGCGCCCGCTGGCAAAAAAGGAAGCTGAGCa               >  1:616181/1‑90 (MQ=255)
                                                       cacTATTAGCGCAATTTACCGGCGGGAAACCGCTATACTCGGCGATTCTTGCGCGCACGCTGGCAAAACAGGAAGCTGAGCAACTGgcgc       <  2:512946/90‑1 (MQ=255)
                                                            ttAGCGCAATTTACCGGCGGGAAACCGCTATACTCGGCGATTCTTGCGCGCACGCTGGCAAAACAGGAAGCTGAGCAACTGGCGCGAAGc  <  2:616181/90‑1 (MQ=255)
                                                                                    |                                                                 
ATGACCGATAACTACCAGCTCATTTTGCCAATGATTATTACCGGTCTTGGCGCAACACTATTAGCGCAATTTACCGGCGGGAAACCGCTATACTCGGCGATTCTTGCGCGCACGCTGGCAAAACAGGAAGCTGAGCAACTGGCGCGAAGC  >  NZ_CP009273/172836‑172985

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑