Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,663,7940TA53.8% 2.8 / 14.2 13H19L (CAT→CTT) ynfLLysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (0/6);  new base A (7/0);  total (7/6)
Fisher's exact test for biased strand distribution p-value = 5.83e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.13e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

AATTTGTTGCTCCAGCGCCTGAATCTGCTGACTTAGCGGCGGTTGCGAAATATTCAGGCGGGCAGCGGCGCGCCCGAAATGCAGCTCTTCCGCAACAGCAACAAAGTAACGCAGATGACGAAGTTCAATATTCATATTTAAAACATCTTATTTGAGATTATTAA  >  NZ_CP009273/1663715‑1663878
                                                                               |                                                                                    
aaTTTGTTGCTCCAGCGCCTGAATCTGCTGACTTAGCGGCGGTTGGGAAAAATTTAGGGGGGGGGGGGGGGGCCCCCAAAGCAGCCCTTc                                                                            >  2:1086687/1‑90 (MQ=255)
aaTTTGTTGCTCCAGCGCCTGAATCTGCTGACTTAGCGGCGGGTGCGGAATATTTAAGGGGGGGGCGGCGCGCCCGCAAAGCAGCTCTTc                                                                            >  1:492244/1‑90 (MQ=255)
       tgCTCCAGCGCCTGAATCTGCTGACTTAGCGGCGGTTGCGAAATATTCAGGCGGGCAGCGGCGCGCCCGAAATGCAGCTCTTCCgcaaca                                                                     <  2:211190/90‑1 (MQ=255)
        gCTCCAGCGCCTGAATCTGCTGACTTAGCGGCGGTTGCGGAAAATTTAGGCGGGGAGCGGCGCGCCCCCAAAGCAGCTCTTCCccaacag                                                                    >  1:268097/1‑90 (MQ=255)
                   tGAATCTGCTGACTTAGCGGCGGTTGCGAAAAATTTAGGCGGGGGGGGGCGCGCCCCAAAAGCAGCCCTTCCCCCACAACaaaaaaaaaa                                                         >  1:394097/1‑86 (MQ=255)
                   tGAATCTGCTGACTTAGCGGCGGGTGCGAAAAATTTAGGCGGGGGGGGGGGCGCCCCCAAAGCAGCTCTTCCCCCACAGCAACaaaaaaa                                                         >  1:882439/1‑86 (MQ=255)
                          gctgACTTAGCGGCGGTTGCGGAAAATTTAGGCGGGGAGCGGCGCGCCCCAAAAGCAGCCCTTCCCCCACAACAAAAAAAGAAAGCAGag                                                  >  2:689576/1‑89 (MQ=255)
                                    cggcggTTGCGAAATATTCAGGCGGGCAGCGGCGCGCCCGAAATGCAGCTCTTCCGCAACAGCAACAAAGTAACGCAGATGACGAAGTTc                                        <  1:200311/90‑1 (MQ=255)
                                    cggcggTTGCGAAATATTCAGGCGGGCAGCGGCGCGCCCGAAATGCAGCTCTTCCGCAACAGCAACAAAGTAACGCAGATGACGAAGTTc                                        <  1:591114/90‑1 (MQ=255)
                                       cggTTGCGAAATATTCAGGCGGGCCGCGGCGCGCCCCAAAAGCAGCTCTTCCCCCACAGCAACAAAAAAACGCAGATGACGAAGGTCAat                                     >  2:891335/1‑90 (MQ=255)
                                                      cAGGCGGGCAGCGGCGCGCCCGAAATGCAGCTCTTCCGCAACAGCAACAAAGTAACGCAGATGACGAAGTTCAATATTCATATTTAAAAc                      <  1:891335/90‑1 (MQ=255)
                                                                   gcgcgcCCGAAATGCAGCTCTTCCGCAACAGCAACAAAGTAACGCAGATGACGAAGTTCAATATTCATATTTAAAACATCTTATTTgaga         <  2:592914/90‑1 (MQ=255)
                                                                          cGAAATGCAGCTCTTCCGCAACAGCAACAAAGTAACGCAGATGACGAAGTTCAATATTCATATTTAAAACATCTTATTTGAGATTATTaa  <  1:593770/90‑1 (MQ=255)
                                                                               |                                                                                    
AATTTGTTGCTCCAGCGCCTGAATCTGCTGACTTAGCGGCGGTTGCGAAATATTCAGGCGGGCAGCGGCGCGCCCGAAATGCAGCTCTTCCGCAACAGCAACAAAGTAACGCAGATGACGAAGTTCAATATTCATATTTAAAACATCTTATTTGAGATTATTAA  >  NZ_CP009273/1663715‑1663878

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑