Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP00927329,4960TA54.5% ‑0.8 / 13.3 11intergenic (+301/‑155)dapB/carA4‑hydroxy‑tetrahydrodipicolinate reductase/glutamine‑hydrolyzing carbamoyl‑phosphate synthase small subunit
Reads supporting (aligned to +/- strand):  ref base T (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.

GCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTG  >  NZ_CP009273/29417‑29582
                                                                               |                                                                                      
gcAAGCTTTTTCCAGAACAGTTTAAATTATTTTTTTGTCGTTTAATGCTTGTAAAACATGCATGACCCACAAAATAATAAAAAAAAcccc                                                                              <  2:238602/90‑1 (MQ=255)
gcAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATccc                                                                              >  2:334209/1‑90 (MQ=255)
                   ggTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTa                                                           >  1:555304/1‑90 (MQ=255)
                     ttAGATGTTTTTTTTGTCGTTTAATGCCTGAAAAACATGAAGGACCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAgc                                                         <  1:461716/90‑1 (MQ=255)
                                ttttGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATAtctc                                              >  2:257602/1‑90 (MQ=255)
                                                           gcatgAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATtc                   >  2:391484/1‑90 (MQ=255)
                                                           gcatgACCCAAAAAAAAAAAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATtc                   <  1:428472/90‑1 (MQ=255)
                                                             atgACCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATtcgt                 <  1:534788/90‑1 (MQ=255)
                                                                    acaAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAg          >  2:23159/1‑90 (MQ=255)
                                                                          aaataAAAAAACCCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGAtt    <  1:334209/89‑1 (MQ=255)
                                                                          aaataAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGAtt    <  1:362820/89‑1 (MQ=255)
                                                                            atatAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTg  >  1:213007/1‑90 (MQ=255)
                                                                               |                                                                                      
GCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTG  >  NZ_CP009273/29417‑29582

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑