Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,659,0580TC54.5% 6.9 / 11.6 11D38G (GAT→GGT) gadXacid resistance transcriptional activator GadX
Reads supporting (aligned to +/- strand):  ref base T (3/2);  new base C (0/6);  total (3/8)
Fisher's exact test for biased strand distribution p-value = 6.06e-02
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.

GCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAC  >  NZ_CP009273/3658975‑3659138
                                                                                   |                                                                                
gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa                                                                            <  1:23434/90‑1 (MQ=255)
   tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaaa                                                                         >  1:275800/1‑90 (MQ=255)
     gggAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAAcc                                                                       <  1:262363/90‑1 (MQ=255)
                   aaGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCAtt                                                         >  1:263830/1‑90 (MQ=255)
                       gtgtCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTaaaa                                                     >  2:60588/1‑90 (MQ=255)
                        tttCCTTTAACACAAATAAAAAATTTCCAACACACTTATCTTCTAAATTTTGGCTTCCACCCCAAAAACCCAGCTCCCCGCCATTAAAAt                                                    <  2:263830/88‑1 (MQ=255)
                        ttccccTTGACACAAATAAAAAATTTCCACCACACTTATCTACTCAATTTTGGCTTCCACCCGAAAAAACCAGGCCACCGCCATTAAAAt                                                    <  1:250320/87‑1 (MQ=255)
                                  cacaAATAAAAAATTTTCAACACACTTATCTACTCAATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTc                                          <  1:85950/90‑1 (MQ=255)
                                                  tCAACACACTTATCTACTCAATTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg                          <  1:340116/90‑1 (MQ=255)
                                                                          tgtcTTGCACCCAAAAAAACCAGGCCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc  <  2:63230/87‑1 (MQ=255)
                                                                          tGGTTTGCACCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc  <  1:57437/90‑1 (MQ=255)
                                                                                   |                                                                                
GCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAC  >  NZ_CP009273/3658975‑3659138

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑