Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,570,3340CA55.6% 2.8 / 13.2 9D515Y (GAT→TAT) yddBTonB‑dependent receptor plug domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base C (4/0);  new base A (0/5);  total (4/5)
Fisher's exact test for biased strand distribution p-value = 7.94e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.17e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

AGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCATATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATC  >  NZ_CP009273/1570245‑1570403
                                                                                         |                                                                     
aGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCATATc                                                                       <  2:197287/90‑1 (MQ=255)
  gCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCATATCaa                                                                     >  2:210690/1‑90 (MQ=255)
                       gcgTAAGATTTTTATTACCTGATCCCGTTCCCGCCCAGTTATTGCGAATATCACGAAACCCAATAAAAAAAATATCCCCGCCATAGTAAc                                                <  2:330510/90‑1 (MQ=255)
                                        ccTGATCCCGATCCCTCCCAGTTATTGAGAATATCCAGTATTCCAATAAAAAAAATTTCCCCGCCATAGTAACGGTTATAACCTGCTGTa                               <  1:246686/90‑1 (MQ=255)
                                               ccGATCCCGCCCAGTTTTGGCGGATATCACGTAACCCCATATAAAAAATTTTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTg                        <  2:164767/90‑1 (MQ=255)
                                                cGATCCCGCCCAGTTATGGCGAATATCAAGTAATCCAATAAAAAAAATATCCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGa                       <  2:126362/90‑1 (MQ=255)
                                                 gATTCCGTCCAGCTATTGCGGATATCACGTAATCCCATATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAg                      >  1:126362/1‑90 (MQ=255)
                                                 gATTCCGTCCAGCTATTGCGGATATCACGTAATCCCATATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAg                      >  1:372059/1‑90 (MQ=255)
                                                         ccAGCTTTTGCGGATATCACTTAACCCAATATAAAAAATATCCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGAtt              <  2:453019/90‑1 (MQ=255)
                                                                     gATATCACGTAATCCCATATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATc  >  2:424336/1‑90 (MQ=255)
                                                                                         |                                                                     
AGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCATATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATC  >  NZ_CP009273/1570245‑1570403

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑