Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,287,9110CA54.5% 9.0 / 18.1 11intergenic (+90/+54)galU/hnsUTP‑‑glucose‑1‑phosphate uridylyltransferase GalU/DNA‑binding transcriptional regulator H‑NS
Reads supporting (aligned to +/- strand):  ref base C (5/0);  new base A (0/6);  total (5/6)
Fisher's exact test for biased strand distribution p-value = 2.16e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.28e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TATCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTT  >  NZ_CP009273/1287837‑1287997
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tATCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCccgc                                                                         >  2:32121/1‑90 (MQ=255)
                       aTCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGt                                                  >  1:1105658/1‑90 (MQ=255)
                           ccGCCTTTTTTTTATATTTTTTTTTTTTAAAATTTTTTAAAACCGGAAAAAAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCaa                                              <  2:1288656/89‑1 (MQ=255)
                            ggCCTTTTTTTTATAGCTTTTTTTTATAAAATTTTTTAAAACCGAAAAAAAAAAATCCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAAt                                             <  1:870647/89‑1 (MQ=255)
                                     tttATAGCTTATTCTTATAAAATTGTCTAAACCCGGAAAAAAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAg                                    <  2:67565/90‑1 (MQ=255)
                                              ttttcttattAAATTGTTTAAAACCGGAAAAAAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCt                           <  2:1207132/88‑1 (MQ=255)
                                                    tattaAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCa                     >  1:1387706/1‑90 (MQ=255)
                                                     attaAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAg                    >  2:1297737/1‑90 (MQ=255)
                                                          aTTGTCTAAACCCGAAAAAAAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAAt               <  2:1037378/90‑1 (MQ=255)
                                                                      cGGAAAAAAAAAACTCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGAtt   <  2:1176225/90‑1 (MQ=255)
                                                                       ggACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGAttt  >  2:963112/1‑90 (MQ=255)
                                                                          |                                                                                      
TATCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTT  >  NZ_CP009273/1287837‑1287997

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑