Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,588,4040TA53.3% 4.0 / 16.3 15Y146F (TAC→TTC) livMbranched chain amino acid ABC transporter permease LivM
Reads supporting (aligned to +/- strand):  ref base T (6/1);  new base A (0/8);  total (6/9)
Fisher's exact test for biased strand distribution p-value = 1.40e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.15e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CCCAAGCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAAGCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAG  >  NZ_CP009273/3588353‑3588492
                                                   |                                                                                        
cccAAGCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAAGCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGa                                                    >  1:23109/1‑90 (MQ=255)
cccAAGCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAAGCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGa                                                    >  2:476773/1‑90 (MQ=255)
 ccAAGCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAAGCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGAc                                                   >  2:70248/1‑90 (MQ=255)
   aaGCCGTAATAGTGATTGAGCAGCGAAAAAGTGTAAGCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACca                                                 <  2:481160/90‑1 (MQ=255)
               tGATTGACCAGCAAAAAATTGAAAGCGCCGAGGGCTAAAAACCCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTc                                     <  1:136932/90‑1 (MQ=255)
                      gcagcGAAAAAGTGAAAGCCCCGGTGGCGAAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCga                              <  1:101864/90‑1 (MQ=255)
                         gcgcAAAAGTGTAAGCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGAc                           >  2:344837/1‑90 (MQ=255)
                           gcAAAAGTGAAAGCGCGGATGGCGAAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCg                         <  1:192308/90‑1 (MQ=255)
                           caaaaaGTATAAGCGCCGATGGCGAAAAACCCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCg                         <  2:438159/88‑1 (MQ=255)
                                aGTGTAAGCGCCGATGGCGAAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGAt                    <  1:217740/90‑1 (MQ=255)
                                 gtgaAAGCGCGGAGGGCAAAAAACCCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATa                   <  1:202990/90‑1 (MQ=255)
                                     aaGCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGt               >  2:401015/1‑90 (MQ=255)
                                      aGCGCCGAGGGCGAAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTa              <  2:7376/90‑1 (MQ=255)
                                                gCGAAAAACCCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTc    <  2:375250/90‑1 (MQ=255)
                                                  gTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAg  >  2:316373/1‑90 (MQ=255)
                                                   |                                                                                        
CCCAAGCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAAGCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAG  >  NZ_CP009273/3588353‑3588492

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑