Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,199,7940CT53.8% ‑2.3 / 12.7 13intergenic (‑179/‑28)ttdR/ttdADNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha
Reads supporting (aligned to +/- strand):  ref base C (1/5);  new base T (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 = 1.13e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTG  >  NZ_CP009273/3199707‑3199863
                                                                                       |                                                                      
ttGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGGGGATTTTTTCa                                                                      >  2:372570/1‑90 (MQ=255)
   aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGAc                                                                   <  1:336605/90‑1 (MQ=255)
    ttCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGAC‑a                                                                 <  2:120972/90‑1 (MQ=255)
                        tatTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGAA‑AAAAACAAAAAATGGAGTTGc                                             >  2:236557/1‑90 (MQ=255)
                        tatTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGGGGATTTTTTCAGAC‑AAAAAAAAAAAAAGGAGGTgg                                             >  1:128253/1‑89 (MQ=255)
                        tatTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGGGAATTTTTTCAAAA‑AAAAAAAAAAAAAGGAGGTgg                                             >  1:11766/1‑89 (MQ=255)
                               ggTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGAC‑AAATACAAAAACTGGAGTTGCCatgatg                                      <  2:56689/90‑1 (MQ=255)
                                     aaaaaaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGaa                                <  2:239914/90‑1 (MQ=255)
                                     aaaaaaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGaa                                <  2:76261/90‑1 (MQ=255)
                                                    acaTTTTTAGTGGTAGTTTGTGGCGGGGAATTTTTTCCGAC‑AAAAAAAAAAAAAGGGGGTGGCCTGATGAGGGAAAGAAATAAACaaaaa                 >  2:363056/1‑87 (MQ=255)
                                                            agaggTAGTTTGTGGCGGTGAATTTTTTCTGACAAAAAAAAAAAAATGGGTTTGCC‑TTATGAGGGAAAAAAAAAAGCAAAAAGCAGGGaa         >  2:535842/4‑90 (MQ=255)
                                                                 tAGTTTGTGGCGGGGGATTTTTTCAGAC‑AAAAAAAAAAAATGGGGGTGGCCTGGTGGGCGAAAATAATAAAAAACAGGCAGGGAATAAGt    >  1:250196/1‑90 (MQ=255)
                                                                   gTTTGTGGCGGTGAATTTTTCCAGAC‑AAAAAAAAAAAATGGGGGTGCCATGATGAGCGGAAGAAATAAGAAAAAAGCAGTGGATAAATTg  >  2:58142/1‑90 (MQ=255)
                                                                                       |                                                                      
TTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTG  >  NZ_CP009273/3199707‑3199863

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑