Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,673,5610AC57.6% 20.8 / 26.7 33Y293S (TAC→TCC) ydgHDUF1471 family protein YdgH
Reads supporting (aligned to +/- strand):  ref base A (7/7);  new base C (0/19);  total (7/26)
Fisher's exact test for biased strand distribution p-value = 8.03e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.35e-03
Rejected as consensus: Frequency below/above cutoff threshold.

GGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTCAGTTACTCCTATAA  >  NZ_CP009273/1673488‑1673648
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ggCAACTACGGCAACATGCCCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTCCCACATCACCCGCCAg                                                                         <  2:405668/90‑1 (MQ=255)
     agaCGGAAACCTGGCCGAAGCCTCCTCCCAGGTTGGGAAAGGGGCCGGGAAGAAAGGTGCTAAGTATTACCCCACCGCCCGCCAGTGGCa                                                                    <  1:567166/88‑1 (MQ=255)
          gCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAAc                                                               >  2:437780/1‑90 (MQ=255)
          gCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAAc                                                               >  1:804770/1‑90 (MQ=255)
          gCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAAc                                                               >  1:683114/1‑90 (MQ=255)
            aaaaTGACCGAAGTCTCCTATCGGGTGGCGAACCGGGCCGAGAAAAAGGGTGATAATTATTCCCACACCCCCCGCCAGTGGCAGGAACGt                                                             <  1:545972/87‑1 (MQ=255)
            aaCATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTCCCACATCACCCGCCAGTGGCAGGAACGt                                                             <  2:228713/90‑1 (MQ=255)
            aaCATGACCGAAGTCTCCTATAGGGTGGCAAAAGGGGCGGGGAAAAAGGGTGATAAGTTTTCCCACACCCCCCGCCAGTGGCAGGAACGt                                                             <  1:829792/90‑1 (MQ=255)
            aaCATCACCGAAGTTTCCTATCGGGTTGCAAAAGGGGCCGGGAAAAAGGGTACTAATTATTACCACACCCCCCGCCAGTGGCAGGAACGt                                                             <  1:1031333/90‑1 (MQ=255)
                tGACCAAAGTCTCCTATCAGGTTGCAAACCGTGCCGCAAAGAAAGGTGCTAAGTATTCCCACATCCCCCGCCAGTGGCAGGAACGTGGta                                                         <  1:437780/90‑1 (MQ=255)
                  aCCGAAGTCCCCTATCAGGTTGCGAAACGTGCCGCAAAGAAAGGTGCAAAGTATTCCCACACCCCCCGCCAGTGGCAGGAACGTGGtaat                                                       <  1:456403/90‑1 (MQ=255)
                              tATCAGGTTGCGAAACGTGCCGCGAAAAAAGGTGCTAAGTATTACCACACCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTc                                           <  2:865559/90‑1 (MQ=255)
                                   ggTTGCGAAACGTGCCGCGAAAAAAGGTGCTAAGTATTCCCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAgcgc                                      <  2:203542/90‑1 (MQ=255)
                                   ggTTGCAAAACGTGCCGCAAAGAAAGGTGCTAAGTATTCCCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAgcgc                                      <  2:87676/90‑1 (MQ=255)
                                   ggTGGCGAAACGTGCCGCGAAAAAAGGTGTTAAGTATTCCCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAgcgc                                      <  2:683114/90‑1 (MQ=255)
                                     ttGCAAACCGTGCCGCAAAAAAGGGTGTTAAGTTTTCCCACACCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAg                                    <  1:417524/90‑1 (MQ=255)
                                        caaaaCGGGCCGCAAAAAAAGGTGCTAAGTTTTACCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATc                                 <  2:918924/88‑1 (MQ=255)
                                          aaccGTCCCGCAAAAAAAGGTGCTAAGTATTCCCCCACCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTg                               <  2:936510/87‑1 (MQ=255)
                                          aaaCGTGCCGCGAAGAAGGGTGCTAAGTATTCCCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTg                               <  2:408521/90‑1 (MQ=255)
                                          aaaCGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTg                               <  2:149871/90‑1 (MQ=255)
                                             cGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGtat                            >  2:622584/1‑90 (MQ=255)
                                               tGCCGGAAAGAAGGGTGCTAAGTTTTCCCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTataa                          <  1:408966/90‑1 (MQ=255)
                                                        aaaaGGTGAAAAGTATTCCCACCTCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTAtt                 <  2:578107/89‑1 (MQ=255)
                                                             gtacTAAGTTTTCCCACACCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTCAGtt            <  1:847603/87‑1 (MQ=255)
                                                             gTGCTAAGTATTCCCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTCAGtt            <  2:335793/90‑1 (MQ=255)
                                                             gTGCTAAGTATTACCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTCAGtt            <  2:17724/90‑1 (MQ=255)
                                                             gTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTCAGtt            <  2:804770/90‑1 (MQ=255)
                                                               gCTAAGTATTCCCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTCAGTTAc          <  2:335322/90‑1 (MQ=255)
                                                               gCTAAGTATTCCCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTCAGTTAc          <  2:367893/90‑1 (MQ=255)
                                                                cTAAGTATTCCCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTCAGTTACt         <  2:680060/90‑1 (MQ=255)
                                                                  aaGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGGAATAACCTGACCGTCAGCGCCGATCTGTATAAATAACTATTCAGGTACTcc       >  1:501394/1‑90 (MQ=255)
                                                                    gTATTACCACATCACCCGCCAGTGGCAGGGACGTGGGAATAACCGGACCTTCTACGCCGATCTGTATAAATAACTATTCAGTTACTCCta     >  1:990651/1‑90 (MQ=255)
                                                                       ttACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTCAGTTACTCCTATaa  >  1:437861/1‑90 (MQ=255)
                                                                         |                                                                                       
GGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTCAGTTACTCCTATAA  >  NZ_CP009273/1673488‑1673648

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑