Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,058,9400TA64.3% ‑5.9 / 10.7 14T63S (ACC→TCC) yihOMFS transporter
Reads supporting (aligned to +/- strand):  ref base T (3/2);  new base A (0/9);  total (3/11)
Fisher's exact test for biased strand distribution p-value = 2.75e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.63e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

AAATAAAGGGACGAAATTTGCCTTTAGGCCCAATATTTTTCCGCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGATAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATA  >  NZ_CP009273/4058856‑4059006
                                                                                    |                                                                  
aaataaaGGGACGAAATTTGCCTTTAGGCCCAATATTTTTCCGCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTaaaaa                                                               >  2:79714/1‑90 (MQ=255)
        ggACGAAATTTGCCTTTAGGCCCAATATTTTTCCGCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGcc                                                       <  1:17451/90‑1 (MQ=255)
         gACGAAATTTGCCTTTAGGCCCAATATTTTTCCGCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGcca                                                      <  1:79714/90‑1 (MQ=255)
                   gCCTTGAGGCCAAATATTTTCCCGCGAGTGGAGAAAAAACCCGGTGAGCATATCGGTAAACGGGGAAAAAACCTCCCCCACCAAAAAGaa                                            <  2:341313/90‑2 (MQ=255)
                      tttAGCCCAAATTTTTTCCCGCGAGTCGAGAAAAAATCCGGTGAGCATATCGGTAAACGCGGAAAAAACCTTCCCCACCAAAAAGATaac                                         <  2:101943/90‑2 (MQ=255)
                          gccccAATTTTTTCCCGCGAGTCGAGAAAAAACCGGGTGAGCATATCGGAAAACGCGGAAAAAACCTTCCCCACCAAAAAGATAATCCCg                                     <  2:5683/88‑1 (MQ=255)
                           gCCAAATATTTTCCCGCGAGTCGAGAAAAAACCCGGTGAGCATATCGGAAACCGCGGAAAAAACCTTCGCCACAAAAAAGATAATCCCGc                                    <  2:303264/90‑1 (MQ=255)
                                         cgcgAGTCGAGAAAAAACCGGGTGAGCATATGGGTAAACGGGGAAAAAAACTTCCCCCCCAGAAAGATTACCCCGCCATAGTAAGCAGGc                      <  1:476020/90‑1 (MQ=255)
                                          gcgAGTGGAAAAAAAACCGGGTGAGCATATCGGAAAACGGGGAAAAAAACTCCCCCCCCAAAAAAATAACCCCGCCATAGTAAGCAGGCa                     <  2:76617/90‑1 (MQ=255)
                                                      aaaaCCCGGTGACAATATCGAAAAACGCGAAAAAAACCTCCCCCACAAAAAAAAAAACCCCGCCATAGTAAGCAGGCATCCCTAATTCAt         <  2:61045/90‑1 (MQ=255)
                                                       aaaCCCGGGGACCATATCGGAAAACGCGGAAAAAACCTCCCCCACAAAAAAAATAACCCCGCCATAGTAAGCAGGCATCCCTAATTCATc        <  2:364860/90‑1 (MQ=255)
                                                        aacccGGTGAGCATACGGGAAAACGCGGAAAAAACCTCCCCCACAAAAAAAATAACCCCGCCATAGTAAGCAGGCATCCCTAATTCATCg       <  2:83694/87‑1 (MQ=255)
                                                            cGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGATAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGtat   >  1:61045/1‑90 (MQ=255)
                                                             ggTGAGCATATAGGAAAACGCGGTAACAACCATCACCATGAGATGGATATTCCAGACATAGGACGCAGGCATCGCTAATTCATCGGtata  >  2:426582/1‑90 (MQ=255)
                                                                                    |                                                                  
AAATAAAGGGACGAAATTTGCCTTTAGGCCCAATATTTTTCCGCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGATAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATA  >  NZ_CP009273/4058856‑4059006

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑