Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273539,9750AG66.7% 23.1 / 22.6 27D258D (GAT→GAC) allCallantoate deiminase
Reads supporting (aligned to +/- strand):  ref base A (5/4);  new base G (13/5);  total (18/9)
Fisher's exact test for biased strand distribution p-value = 4.23e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.64e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CAATCAATGGTGAACGTGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCGT  >  NZ_CP009273/539889‑540061
                                                                                      |                                                                                      
caatcaatGGTGAACGTGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCg                                                                                     >  1:227441/1‑90 (MQ=255)
            aaCGTGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTc                                                                         >  1:63432/1‑90 (MQ=255)
                tGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCtt                                                                     >  2:475633/1‑90 (MQ=255)
                 ggTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCttt                                                                    >  2:442091/1‑90 (MQ=255)
                            gCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACt                                                         >  2:820128/1‑90 (MQ=255)
                            gCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACt                                                         >  1:707368/1‑90 (MQ=255)
                            gCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGGCGCCCATCCTTTTCGCTTTTTCGACCGACt                                                         >  1:914808/1‑90 (MQ=255)
                             caccacATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTg                                                        <  2:1012042/90‑1 (MQ=255)
                             caccacATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTg                                                        <  2:441462/90‑1 (MQ=255)
                                 acaTTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGGCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATgg                                                    >  2:1633/1‑90 (MQ=255)
                                            aTTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGTTGGCAAATGCGACt                                         >  1:508292/1‑90 (MQ=255)
                                              tCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGa                                       <  1:475633/90‑1 (MQ=255)
                                                  gcgcGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGc                                   >  2:787992/1‑90 (MQ=255)
                                                      ggCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTaa                               >  1:16283/1‑90 (MQ=255)
                                                               ttGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCa                      >  1:650032/1‑90 (MQ=255)
                                                               ttGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCa                      <  2:753493/90‑1 (MQ=255)
                                                                 gCCAAAGGTCAGAACCAGCGGGTCGCCCATCATTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCacg                    >  1:664542/1‑90 (MQ=255)
                                                                 gCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCacg                    <  2:229166/90‑1 (MQ=255)
                                                                 gCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCacg                    >  2:717562/1‑90 (MQ=255)
                                                                 gCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCacg                    >  1:229166/1‑90 (MQ=255)
                                                                 gCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCacg                    >  1:899027/1‑90 (MQ=255)
                                                                       ggTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATa              <  1:586502/90‑1 (MQ=255)
                                                                               ccAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCg      <  2:707368/90‑1 (MQ=255)
                                                                               ccAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCg      <  1:163434/90‑1 (MQ=255)
                                                                                 aGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGc    >  1:70917/1‑90 (MQ=255)
                                                                                  gCGGATCGCCCGTCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCg   >  2:1146269/1‑90 (MQ=255)
                                                                                   cGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCgt  <  2:453755/90‑1 (MQ=255)
                                                                                      |                                                                                      
CAATCAATGGTGAACGTGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCGT  >  NZ_CP009273/539889‑540061

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑