Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,175,9570AT51.6% 19.4 / 40.9 31I17F (ATT→TTT) zupTzinc transporter ZupT
Reads supporting (aligned to +/- strand):  ref base A (6/9);  new base T (16/0);  total (22/9)
Fisher's exact test for biased strand distribution p-value = 2.48e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.42e-04
Rejected as consensus: Frequency below/above cutoff threshold.

TCTGCCTGAAGGTGAAGATTTATAAGGAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGCAG‑CCACG‑TTTATTGGCGCGTTTCTCGGCGTTC‑T‑C‑GGGCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGATC  >  NZ_CP009273/3175874‑3176037
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tCTGCCTGAAGGTGAAGATTTATAAGGAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGGAG‑GCACC‑tttttttggg                                                                               >  2:635385/1‑86 (MQ=255)
        aaGGTGAAGATTTATAAGGAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGCAG‑CCACG‑TTTATTGGCGCGTTtctc                                                                       <  1:673255/90‑1 (MQ=255)
             gAAGATTTATAAGGAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGGGG‑CCCCG‑TTTTTTTGGGCGGTTTTCGGCGt                                                                  >  1:291574/1‑90 (MQ=255)
             gAAGATTTATAAGGAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGCAG‑CCACG‑TTTTTTTGCGCGTTTCTCGGCGt                                                                  >  2:166637/1‑90 (MQ=255)
                         ggAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGCAG‑CCACG‑TTTATTGGCGCGTTTCTCGGCGTTC‑T‑C‑GGGCaaaa                                                   <  2:701072/90‑1 (MQ=255)
                         ggAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGCAG‑CCACG‑TTTATTGGCGCGTTTCTCGGCGTTC‑T‑C‑GGGCaaaa                                                   <  2:489548/90‑1 (MQ=255)
                         ggAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGCAG‑CCACG‑TTTATTGGCGCGTTTCTCGGCGTTC‑T‑C‑GGGCaaaa                                                   <  2:161380/90‑1 (MQ=255)
                         ggAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGCAG‑CCACG‑TTTATTGGCGCGTTTCTCGGCGTTC‑T‑C‑GGGCaaaa                                                   <  2:495693/90‑1 (MQ=255)
                          gAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGGGG‑CCCCG‑GTTTTTGGGGCGGTTTTCCGCGGTT‑T‑C‑CGGCcaaaa                                                  >  1:219709/1‑90 (MQ=255)
                            gTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGGGG‑CCACG‑GTTTTTTGGGCGTTTTTTGGCGGTC‑T‑CTGGGGAAAAAc                                                 >  1:947345/1‑90 (MQ=255)
                              tGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGGAG‑CCCCG‑CTTTTTTGGGCGTTTTTCGGCGTTC‑T‑C‑CGGCAAAAAcccc                                              >  2:984295/1‑89 (MQ=255)
                                      tCAGTACCTCTCATTCTGACCATACTGGCGGGGGGAG‑CCACG‑TTTTTTTGGGCGTTTTTCCGCGTTC‑T‑C‑GGGCAAAAAACCCCGAAcccc                                      >  2:935321/1‑88 (MQ=255)
                                         gTACCTCTCATTCTGACCATACTGGCGGGGGGAG‑GCCCGCTTTTTTGGGGGGTTT‑TTGGCGTTT‑T‑C‑GGGCAAAAAACCCCCAACCCCttc                                   >  2:1259428/1‑89 (MQ=255)
                                              tctcATTCTGACCATACTGGCGGGGGGGG‑CCACG‑TTTTTTTGGGCGGTTTTTTGCGTTCTT‑T‑GGGGAAAAACCC‑CCAACCGCTTTCttgg                              >  1:853406/1‑87 (MQ=255)
                                              tctcATTCTGACCATACTGGCGGGGGGAG‑CCACG‑TTTTTTGGCGCGTTTTTCGGCGTTC‑T‑C‑GGGCAAAAAACCTCGGACCGCTTACTGGc                              >  2:1181359/1‑90 (MQ=255)
                                              tctcATTCTGACCATACTGGCGGGGGCAG‑CCCCG‑TTTATTTGCGCGTTTTTCCGCGTTC‑T‑C‑GGGCAAAAACCCCCGAACCGCCTACTGGc                              >  2:383810/1‑90 (MQ=255)
                                              tctcATTCTGACCATACTGGCGGGGGCAG‑CCACG‑TTTTTTTGCGCGGTTTTCCGCGTTC‑T‑C‑GGGCAAAAAACCCCCAACCCCTTACTGGc                              >  1:439499/1‑90 (MQ=255)
                                                 cATTCTGACCATACTGGCGGGGGGAG‑CCACG‑TTTTTTTGCGCGTTTTTCGGCGTTC‑T‑C‑CGGCAAAAACCCCCCAACCGCCTTCTgggggt                           >  1:567701/1‑86 (MQ=255)
                                                      tGACCATACTGGCGGGGGCAG‑CCACG‑GTTATTTGCGCGTTTTTCGGCGGTC‑T‑C‑GGGCAAAAAACCTCGAAACGCCTTCTGGGGttttttc                      >  2:125420/1‑87 (MQ=255)
                                                       gACCATACTGGCGGGGGGAGCCCCCG‑TTTTTTGG‑GCGGTTTTCCGCGCTC‑T‑C‑GGGGCAAAACCCCCGAAACGCCTCCTTGCGTTTTTGCt                     >  1:720584/1‑90 (MQ=255)
                                                       gACCATACTGGCGGGGGGAG‑CCCCG‑CTTTTTTGGGCGGTTTTTCGCGTTC‑TCC‑GGGCAAAAACCC‑CCAACCCCCTACTTGCGTTTTTGCt                     >  1:1437470/1‑90 (MQ=255)
                                                       gACCATACTGGCGGGGGCAG‑CCCCG‑TTTTTTTGCGCGTTTTTCCGCGTTC‑T‑C‑GGGCAAAAACCCCCGAACCGCTTTCTTGCGGTTTTGCt                     >  2:141527/1‑90 (MQ=255)
                                                       gACCATACTGGCGGGGGCAG‑CCACG‑TTTATTGGCGCGTTTCTCGGCGTTC‑T‑C‑GGGCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCt                     <  2:224122/90‑1 (MQ=255)
                                                        aCCATACTGGCGGGGGCAG‑CCACG‑TTTATTGGCGCGTTTCTCGGCGTTC‑T‑C‑GGGCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTa                    <  2:205122/90‑1 (MQ=255)
                                                           aTACTGGCGGGGGCCG‑CCACG‑GTTATTTGCGCGTTTTTCGGCGTTC‑T‑C‑CGGCAAAAAACCCCCAACCGCCTTCTCGGGTTTTCCCTTggg                 >  2:207541/1‑89 (MQ=255)
                                                           aTACTGGCGGGGGCAG‑CCACG‑TTTATTGGCGCGTTTCTCGGCGTTC‑T‑C‑GGGCAAAAAACCTCGAACCCCTTACTGGCGGTTTCGCTAggg                 >  2:578319/1‑89 (MQ=255)
                                                                 gCGGGGGGAG‑CCACG‑GTTTTTGGGGCGGTTTTCGGCGGTC‑T‑C‑GGGGAAAAAACCTCGAACCGCTTACTGGGGGTTTTGCTGGGGTTTtcg           >  1:27857/1‑90 (MQ=255)
                                                                   gggggCAG‑CCCCG‑TTTTTTGGGGCGGTTTTCGGCGTTC‑T‑C‑GGGCAAAAAACCCCGAACCCCTTACTGGCGTTTTTGCTCGGTTTTtcggg         >  1:1155664/1‑89 (MQ=255)
                                                                         aG‑CCACG‑TTTATTGGCGCGTTTCTCGGCGTTC‑T‑C‑GGGCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGAt   <  2:567701/90‑1 (MQ=255)
                                                                          g‑CCACG‑TTTATTGGCGCGTTTCTCGGCGTTC‑T‑C‑GGGCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCggggggc  >  2:1435067/1‑87 (MQ=255)
                                                                                g‑TTTATTGGCGCGTTTCTCGGCGTTC‑T‑C‑GGGCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTg             >  2:315765/1‑74 (MQ=255)
                                                                                g‑TTTATTGGCGCGTTTCTCGGCGTTC‑T‑C‑GGGCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTg             <  1:315765/74‑1 (MQ=255)
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TCTGCCTGAAGGTGAAGATTTATAAGGAGTTGTCGATGTCAGTACCTCTCATTCTGACCATACTGGCGGGGGCAG‑CCACG‑TTTATTGGCGCGTTTCTCGGCGTTC‑T‑C‑GGGCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGATC  >  NZ_CP009273/3175874‑3176037

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑