Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,175,9570AT54.2% 12.6 / 29.6 24I17F (ATT→TTT) zupTzinc transporter ZupT
Reads supporting (aligned to +/- strand):  ref base A (2/9);  new base T (13/0);  total (15/9)
Fisher's exact test for biased strand distribution p-value = 4.21e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.43e-04
Rejected as consensus: Frequency below/above cutoff threshold.

GCCTGAAGGTGAAGATTTATAAGGAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGCAGCCA‑CGTTTATTGGCGC‑GTTTCTCGGCGTTCT‑CGGGC‑AAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGG  >  NZ_CP009273/3175877‑3176033
                                                                                 |                                                                               
gCCTGAAGGTGAAGATTTATAAGGAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGCAGCCA‑CGTTTATTGGCGC‑Gt                                                                       <  2:39082/90‑1 (MQ=255)
          gAAGATTTATAAGGAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGGGGCCA‑CGGTTTTTGGGGG‑GTTTTTCTGCgg                                                             >  2:548131/1‑89 (MQ=255)
          gAAGATTTATAAGGAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGCGGCCC‑CGGTTTTTTGGGC‑GGTTCTTCGCGt                                                             >  1:421777/1‑90 (MQ=255)
                      ggAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGCAGCCA‑CGTTTATTGGCGC‑GTTTCTCGGCGTTCT‑CGGGC‑aaaa                                               <  2:165515/90‑1 (MQ=255)
                       gAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGCAGCCA‑CGTTTTTTGGGGC‑GTTTTTCGGCGGTCT‑CGGGC‑aaaaa                                              >  1:257401/1‑90 (MQ=255)
                         gTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGGGGCCA‑CGGTTTTTTGCGC‑GGTTTTCCGCGTTTTCCGGGC‑AAAAAc                                             >  2:100911/1‑90 (MQ=255)
                         gTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGCAGCCA‑CGTTTTTTTGCGC‑GGTTCTCGGCGTTCT‑CCGGC‑aaaaaac                                            >  1:737989/1‑88 (MQ=255)
                            gTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGGAGCCC‑CGTTTTTTTGGGCGGTTTTTTGGGTTTTT‑CGGGC‑AAAAAcccc                                          >  2:539672/1‑89 (MQ=255)
                                 tGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGCAGCCC‑CGCTTATTTGCGC‑GTTTCTCTGCGTTCT‑CCGGC‑AAAAAACCCCGAAcc                                    >  1:643248/1‑90 (MQ=255)
                                 tGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGCAGCCA‑CGTTTATTGGCGC‑GTTTCTCGGCGTTCT‑CGGGC‑AAAAACCCTCGAAcc                                    <  1:107568/90‑1 (MQ=255)
                                      gTACCTCTCATTCTGACCATACTGGCGGGGGGGGCCC‑CGTTTTTTTGCGC‑GGTTTTTGGCGGTTT‑CGGGG‑AAAAAACCCCCGACCGCTTa                               >  2:774118/1‑90 (MQ=255)
                                      gTACCTCTCATTCTGACCATACTGGCGGGGGGAGCCA‑CGTTTTTTTGGGC‑GTTTTTCGGCGTTCT‑CGGGC‑AAAAAACCCCCAAACCCTTa                               >  2:230199/1‑90 (MQ=255)
                                            ctcATTCTGACCATACTGGCGGGGGGAGGCC‑CGTTTTTTTGGGC‑GGTTCTCTGCGTTCT‑CGGGG‑GAAAAACCCCGAACCGCTTTCTGGCg                         >  2:598492/1‑90 (MQ=255)
                                              cATTCTGACCATACTGGCGGGGGGAGCCA‑CGGTTATTTGCGC‑GGTTTTCGTCGTTCT‑CGGGC‑AAAAAACCTCGCACCGCTTACTGGCGtt                       >  2:525681/1‑90 (MQ=255)
                                                ttCTGACCATACTGGCGGGGGGAGCCC‑CGTTTTTTTGCGC‑GGTTTTCGGCGGTCT‑CGGGC‑AAAAAACCCCCAACCGCTTACTTGCGgttt                     >  1:748265/1‑90 (MQ=255)
                                                ttCTGACCATACTGGCGGGGGGAGCCACCGTTTTTTGGGGG‑GTTT‑TTGGCGTTCT‑CCGGC‑CAAAAACCCCGAACCCCCTACTGGGGtttt                     >  1:412420/1‑90 (MQ=255)
                                                     aCCATACTGGCGGGGGCAGCCA‑CGTTTATTGGCGC‑GTTTCTCGGCGTTCT‑CGGGC‑AAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTa                <  1:240196/90‑1 (MQ=255)
                                                        aTACTGGCGGGGGGGGCCC‑CGTCTTTTTGCGG‑GTTTCTTCTCGGTCT‑CGGGCAAAAAACCCCCGACCCCCTT‑CTTGCGTTTTCTCCAGGt             >  2:726610/1‑90 (MQ=255)
                                                        aTACTGGCGGGGGGAGCCC‑CGGTTTTTTGCGC‑GTTTTTCGGCGTTCT‑CGGGC‑AAAAAACCCCCAACCGCTTTCTGGCGGTTTTGCTACGt             >  2:312172/1‑90 (MQ=255)
                                                                 ggggCAGCCA‑CGTTTATTGGCGC‑GTTTCTCGGCGTTCT‑CGGGC‑AAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGTTTTTgcggcg    <  2:704609/90‑1 (MQ=255)
                                                                 ggggCAGCCA‑CGTTTATTGGCGC‑GTTTCTCGGCGTTCT‑CGGGC‑AAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTgcggcg    <  2:676368/90‑1 (MQ=255)
                                                                 ggggCAGCCA‑CGTTTATTGGCGC‑GTTTCTCGGCGTTCT‑CGGGC‑AAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTgcggcg    <  2:708998/90‑1 (MQ=255)
                                                                 ggggCAGCCA‑CGTTTATTGGCGC‑GTTTCTCGGCGTTCT‑CGGGC‑AAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTgcggcg    <  1:394355/90‑1 (MQ=255)
                                                                   ggCAGCCA‑CGTTTATTGGCGC‑GTTTCTCGGCGTTCT‑CGGGC‑AAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCggg  <  2:421777/90‑1 (MQ=255)
                                                                                 |                                                                               
GCCTGAAGGTGAAGATTTATAAGGAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGCAGCCA‑CGTTTATTGGCGC‑GTTTCTCGGCGTTCT‑CGGGC‑AAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGG  >  NZ_CP009273/3175877‑3176033

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑