Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,175,9570AT53.8% 3.8 / 16.0 13I17F (ATT→TTT) zupTzinc transporter ZupT
Reads supporting (aligned to +/- strand):  ref base A (0/6);  new base T (7/0);  total (7/6)
Fisher's exact test for biased strand distribution p-value = 5.83e-04
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.

ACGATCTGCCTGAAGGTGAAGATTTATAAGGAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGCAGCCACGTTTATTGGCGCGTTTCTCGGCGTTCTCGGGCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGAT  >  NZ_CP009273/3175870‑3176036
                                                                                       |                                                                               
aCGATCTGCCTGAAGGTGAAGATTTATAAGGAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGCAGCCACGTTTAtt                                                                               <  2:353947/90‑1 (MQ=255)
         cTGAAGGTGAAGATTTATAAGGAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGGAGCCACGTTTTTTGGCGCGttt                                                                      >  1:170266/1‑90 (MQ=255)
                             ggAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGCAGCCACGTTTATTGGCGCGTTTCTCGGCGTTCTCGGGCaaaa                                                  <  2:152807/90‑1 (MQ=255)
                              gAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGGAGCCCCGGTTTTTGGGGCGTTTTTCCGCCGTCTCCGGCaaaaa                                                 >  2:8724/1‑90 (MQ=255)
                                gTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGGGGCCCCGGTTTTTTGGGCGTTTTTCCGCGCTCTCCGGCaaaaaac                                               >  2:555603/1‑88 (MQ=255)
                                                  tctcATTCTGACCATACTGGCGGGGGGAGCCCCGTTTTTTTGCGCGGTTTTCTGCGTTCTCGGGGGAAAAACCCCCCACAGCTTTCTGGc                             >  2:452824/1‑90 (MQ=255)
                                                  tctcATTCTGACCATACTGGCGGGGGGAGCCACGGTTTTTTGCGCGTTTTTCCGCGTTCTCGGGCAAAAAAACTCGAACCGCTTTCTGGc                             >  1:53621/1‑90 (MQ=255)
                                                           gACCATACTGGCGGGGGGAGCCCCGTTTTTTTGGGCGTTTTTCCGCGTTCTCCGGCGAAAAACCCCCAACCGCTTTCTGGGGGTTTCggt                    >  2:315681/1‑88 (MQ=255)
                                                            aCCATACTGGCGGGGGCAGCCACGTTTATTGGCGCGTTTCTCGGCGTTCTCGGGCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTa                   <  1:383997/90‑1 (MQ=255)
                                                            aCCATACTGGCGGGGGCAGCCACGTTTATTGGCGCGTTTCTCGGCGTTCTCGGGCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTa                   <  2:358556/90‑1 (MQ=255)
                                                                       gggggCAGCCACGTTTTTTTGCGCGGTTTTCGGCGTTCTCGGGCAAAAAACCCCGAACCCCTTACTGGCGTTTTTGCTGGGGTTTgcggc        >  2:27607/1‑90 (MQ=255)
                                                                             aGCCACGTTTATTGGCGCGTTTCTCGGCGTTCTCGGGCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGAt  <  1:324304/90‑1 (MQ=255)
                                                                             aGCCACGTTTATTGGCGCGTTTCTCGGCGTTCTCGGGCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGAt  <  2:64982/90‑1 (MQ=255)
                                                                                       |                                                                               
ACGATCTGCCTGAAGGTGAAGATTTATAAGGAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGCAGCCACGTTTATTGGCGCGTTTCTCGGCGTTCTCGGGCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGAT  >  NZ_CP009273/3175870‑3176036

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑