Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,199,8110CA55.6% 1.0 / 11.9 9intergenic (‑196/‑11)ttdR/ttdADNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha
Reads supporting (aligned to +/- strand):  ref base C (0/4);  new base A (5/0);  total (5/4)
Fisher's exact test for biased strand distribution p-value = 7.94e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.17e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCG  >  NZ_CP009273/3199733‑3199888
                                                                              |                                                                             
ttCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCa                                                                    <  1:242941/90‑1 (MQ=255)
              agatatAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGt                                                      <  1:388578/88‑1 (MQ=255)
                  ataAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAAACAAAAACAAAAAAAGGAAATTCCCAGATGAGGGAAAAtaaaa                                                  >  2:385383/1‑88 (MQ=255)
                        ccACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCCGACAAAAACAAAAAATGGAGGTGCCATGATGAGCGGAAGGAATAAGCaaa                                            >  2:81271/1‑89 (MQ=255)
                          acaTTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAACAAAAAATGGAGGTGGCATGATGGGGGAAAGTAATAAACaaaaa                                          >  1:54304/1‑87 (MQ=255)
                          acaTTTTTAGTGGTAGTTTGTGGCGGGGAATTTTTTCCGACAAAAAAAAAAAATTGAGGTTCCCTGATGAGGGGAAGAAAAAAACaaacc                                          >  2:388578/1‑87 (MQ=255)
                                   gTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAAt                                 <  2:76539/90‑1 (MQ=255)
                                     ggTAGTTTGTGGCGGTGAATTTTTTCAGACAAATAAAAAAAATGGAGGTGCCATGATGAGCGAAAGGAAAAAACAACAAGCAGTGAATaa                               >  2:302594/1‑90 (MQ=255)
                                                                  cAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCg  <  2:54304/90‑1 (MQ=255)
                                                                              |                                                                             
TTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCG  >  NZ_CP009273/3199733‑3199888

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑