Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273353,6010CA59.3% ‑4.9 / 22.0 27L267F (TTG→TTTcynRtranscriptional regulator CynR
Reads supporting (aligned to +/- strand):  ref base C (9/2);  new base A (0/16);  total (9/18)
Fisher's exact test for biased strand distribution p-value = 1.17e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.06e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

ATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTG  >  NZ_CP009273/353514‑353677
                                                                                         |                                                                             
aTTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑‑CCGCCGcaacaa                                                                             >  1:117104/1‑90 (MQ=255)
   tCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑‑CCGCCGCAACAAAAc                                                                         >  2:515193/1‑90 (MQ=255)
          acaacCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTCCCAGCTATTTTT‑‑CCGCCGCAACAAAACCGCCGtt                                                                  >  1:481757/1‑90 (MQ=255)
           cacccGCGCTTTTCCCCAACCCCTTGTAAAAAAATCCCTCCGCGGCGGCTGTCTGCCAGTTTTTTTC‑‑CCCCCGAAAAAAAACCGCCGTtc                                                                 <  1:309093/87‑1 (MQ=12)
           cacccGCGCTTTTACCCACCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTC‑‑CCGCCGCAACAAAACCGCCGTtc                                                                 <  2:154200/87‑1 (MQ=25)
           cacccGCGCATTTACCCAACGCCATGTGAAAAAATGCCTTCGGGGCGGCTGTCTGCCAGCTTTTTTC‑‑CCGCCGCAAAAAAACCGCCGTtc                                                                 <  2:146748/87‑1 (MQ=21)
               cgcgCTTTTACCCACCCCCATGTCAAAAAATCCCTCCGCGGCGGCTGTCTGCCAGCTTTTTCC‑‑CCGCCGCAAAAAAACCGCCGTtctctc                                                             <  2:181815/90‑1 (MQ=19)
                ccgcTTTTACCCACCCCCATGTGAAAAAATCCTTCCGGGGGGGTTGTCTCCCAGTTTTTTTC‑‑CCCCCGAAAAAAAACCGCCGTTCTCTcc                                                            <  2:434435/89‑1 (MQ=255)
                 cgcATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑‑CCGCCGCAACAAAACCGCCGTTCTCTCCa                                                           >  2:409890/1‑90 (MQ=255)
                       tATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTg                                                     >  2:374280/1‑90 (MQ=255)
                       tATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTg                                                     >  2:50568/1‑90 (MQ=255)
                             aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                               >  1:462313/1‑90 (MQ=255)
                             aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                               >  1:282907/1‑90 (MQ=255)
                             aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                               >  2:535079/1‑90 (MQ=255)
                             aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgctg                                               >  1:244944/1‑87 (MQ=255)
                               gCCTTGTGAAAAAATGCCTGCGCGGCGGCTGTCTGCCAGTTTTTTTT‑‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCa                                             <  2:448543/90‑1 (MQ=37)
                               cccATGTGAAAAAATGCCTTCGCGGGGGCTGTCGGCCAGCTTTTTTC‑‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCa                                             <  2:217010/89‑1 (MQ=255)
                                 caggtgAAAAAATGCCTTCGGGGCGGCTGTCTGCCAGCTTTTTTC‑‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                           <  2:38254/87‑1 (MQ=37)
                                       aaaaaaTCCCTCCGGGGGGGCTTTCCCCCAGTTTTTTTC‑‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt                                     <  2:370102/89‑1 (MQ=255)
                                        aaaaaTGCCTTCGCGGCGGCTGTCTGCCAGCTTTTTTC‑‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa                                    <  2:68689/90‑1 (MQ=38)
                                                 tccgcgGCGGCTTCATCCAGTATTTTTCCCCCCCGCAACAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc                          <  1:390488/88‑1 (MQ=255)
                                                       ggggcTGTCTGCCAGTTTTTTTC‑‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCa                     <  2:586366/88‑1 (MQ=255)
                                                       gcggtTGTCGGCCATTTTTTTTC‑‑CCGCCAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCa                     <  1:139378/90‑1 (MQ=255)
                                                          gcTGTCCCCCCGTTATTTTC‑‑CCCCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgt                  <  2:367800/90‑1 (MQ=255)
                                                                        tttttc‑‑CCCCCACAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc    <  2:351433/89‑1 (MQ=255)
                                                                         ttttt‑‑CCCCCCAAAAAAAACCCGCCGCTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc    <  1:75147/90‑1 (MQ=255)
                                                                          tttc‑‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg  <  2:46727/90‑1 (MQ=255)
                                                                          tttc‑‑CCCCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg  <  2:608272/90‑1 (MQ=255)
                                                                                         |                                                                             
ATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTG  >  NZ_CP009273/353514‑353677

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: