Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092735,1590GA57.1% ‑1.6 / 14.2 14intergenic (+139/‑75)thrC/yaaXthreonine synthase/DUF2502 domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base G (6/0);  new base A (0/8);  total (6/8)
Fisher's exact test for biased strand distribution p-value = 3.33e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.05e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAAT‑AAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGA  >  NZ_CP009273/5086‑5237
                                                                          |                                                                              
ttATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAAT‑AAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGtt                                                                >  2:989101/1‑90 (MQ=255)
    ggAAAAAAAGGGAAGGGAAAAGGGAG‑AATTCCGAATAAAAGGCGGTAACTTAAGGTTGAAGAGGGGGGAAAATAACAACCGCCGTTCTCa                                                            <  1:800769/90‑1 (MQ=255)
             ggACAGGAAAAAAGGAAAATTTCTAAAA‑AAAGGGGGTAATTTAGAGATTAGGATTGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAAt                                                   <  1:42984/89‑1 (MQ=255)
                       aaaGGAAAAATTCAAAAT‑AAATGCGGTAACTAAGATATTAGGATGGGGAAAAAAAACACCCGCCGTTCTCATCGAGTAATCTCCGGatat                                         <  1:869099/90‑1 (MQ=255)
                        aaGGAAAATTTCTAAAA‑AAATGGGGTAATTAAGAGATTAGGATTGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATc                                        <  2:202839/90‑1 (MQ=255)
                                  tctaAAT‑AAATGCTTTAATTTAGAGATTAGGTTGGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAAc                              <  1:177756/90‑1 (MQ=255)
                                        aaaaaGGCGGTAATTTAGAGATTAGGATGGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCa                         <  2:954144/88‑1 (MQ=255)
                                         aaaaTGGGGTAATTAAGAGATTGGGATGGGGGAAAAAAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCaa                        <  1:68120/89‑1 (MQ=255)
                                            aTGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGa                     >  2:246061/1‑90 (MQ=255)
                                                           gaTTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCt      >  2:423441/1‑90 (MQ=255)
                                                            aTTAGGTTGGCGAAAAAAAACACCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCtg     <  1:554587/90‑1 (MQ=255)
                                                             ttAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCtgt    >  2:116461/1‑90 (MQ=255)
                                                              tAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCtgtg   >  1:365218/1‑90 (MQ=255)
                                                               aGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGa  >  1:684528/1‑90 (MQ=255)
                                                                          |                                                                              
TTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAAT‑AAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGA  >  NZ_CP009273/5086‑5237

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: ‑