Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,659,0460AT53.8% 5.8 / 16.9 13I42N (ATT→AAT) gadXacid resistance transcriptional activator GadX
Reads supporting (aligned to +/- strand):  ref base A (5/1);  new base T (0/7);  total (5/8)
Fisher's exact test for biased strand distribution p-value = 4.66e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.56e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATA  >  NZ_CP009273/3658966‑3659120
                                                                                |                                                                           
cctcctTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTg                                                                    >  2:457782/1‑90 (MQ=255)
      tGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCg                                                              >  2:246317/1‑90 (MQ=255)
         gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa                                                           <  2:200537/90‑1 (MQ=255)
                      aaatGAAAGCGGGTCCTTTGACACAAAAAAAAATTTTTCACCCCCCTTATCTACCCAATTTTGGCTTGCATCCGAAAAAACCA‑GGTCAcc                                             <  2:39832/89‑1 (MQ=255)
                       aatAAAAGCGTGTCCTTTGACACAAAAAAAAAATTTTCAACACACTTATCTACTCAATTTTGGCTTGCACCCGAAAAAACCA‑GGTCACCg                                            <  2:104370/90‑1 (MQ=255)
                              gCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTaa                                     >  2:48702/1‑90 (MQ=255)
                                      cTTGCCACGAATACAAATTTTTCAACACCTTTTTCTCCTCGATTTTGGTTTCCACCCCCAAAACCCA‑GGTCCCCGCCATTAAAATAGCGa                             <  1:200855/90‑1 (MQ=255)
                                       ttGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGat                            >  2:219334/1‑90 (MQ=255)
                                           cacaAATAAAAATTTTTCAACCCATTTATCTCCTCAATTTTGGCTTCCACCCGAAAAACCCA‑GGTCACCGCCATTAAAATAGCGATATTc                        <  1:370302/90‑1 (MQ=255)
                                               aaTACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCa                    >  2:370302/1‑90 (MQ=255)
                                                           caaccacatTTATCTCCTCAATTTTGGTTTGCACCCG‑AAAAACCAGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg        <  1:356236/86‑1 (MQ=255)
                                                                ccacTTATCTACTAAATTTTGGTTTGCACCCAAAAAAACCG‑GGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat   <  2:34902/89‑1 (MQ=255)
                                                                 cacTTATCTCCTCGATTTTGGTTTGCACCCGAAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAata  <  1:219334/90‑1 (MQ=255)
                                                                                |                                                                           
CCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATA  >  NZ_CP009273/3658966‑3659120

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: ‑