Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,199,7940CT58.3% ‑2.2 / 11.8 12intergenic (‑179/‑28)ttdR/ttdADNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha
Reads supporting (aligned to +/- strand):  ref base C (0/5);  new base T (7/0);  total (7/5)
Fisher's exact test for biased strand distribution p-value = 1.26e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.93e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAG  >  NZ_CP009273/3199706‑3199867
                                                                                        |                                                                         
gTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTcc                                                                          <  1:417070/90‑1 (MQ=255)
  tGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAg                                                                        <  1:335226/90‑1 (MQ=255)
                      aCATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGt                                                    <  2:17778/90‑1 (MQ=255)
                         tatTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAAAAAAAAATGGAGGTgg                                                 >  1:64397/1‑89 (MQ=255)
                         tatTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAAAAAAAAAAAAAAAATTGAGGTGc                                                 >  1:256436/1‑90 (MQ=255)
                           ttCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGGAATTTTTCAAAAAAAAAAAAAAAATAGAGTTGGCa                                               >  1:324742/1‑90 (MQ=255)
                                 gTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAAACAAAAACAAAAAATGGAGTTGCCctgattg                                         >  1:429588/1‑88 (MQ=255)
                                   ggCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGc                                       <  1:93503/90‑1 (MQ=255)
                                      aaaaaaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGaa                                    <  2:489866/90‑1 (MQ=255)
                                                              gTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAAt            <  2:324742/90‑1 (MQ=255)
                                                                   aGTTTGTGGCGGTGAATTTTTTCAGACAAAAACAAAAAATGGAGTTGCCCTGATGAGGGAAAGGAATAAGCAACAGGGAGTGAATAAGtt       >  1:85425/1‑90 (MQ=255)
                                                                        gtgGCGGTGAATTTTTTCAGACAAAAAAAAAAAATGGGGGTGGCATGGTGGGGGAAAATAAAAAAAAAAAGGCAGGGAAAAAATTTACag  >  2:625010/1‑90 (MQ=255)
                                                                        gtgGCGGTGAATTTTTTCAGACAAAAAAAAAAAATGGAGTTGCCCTGATGAGGGGAAGAAATAAGCAACAAGCCGGGGAAAAATTGACag  >  1:443135/1‑90 (MQ=255)
                                                                                        |                                                                         
GTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAG  >  NZ_CP009273/3199706‑3199867

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑