Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,941,1910TG41.3% 59.5 / 11.4 47N46T (AAC→ACC) hdfRHTH‑type transcriptional regulator HdfR
Reads supporting (aligned to +/- strand):  ref base T (9/18);  new base G (19/0);  total (29/18)
Fisher's exact test for biased strand distribution p-value = 1.78e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

ACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAG  >  NZ_CP009273/3941057‑3941329
                                                                                                                                      |                                                                                                                                          
aCTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTcac                                                                                                                                        <  2:315369/139‑1 (MQ=255)
    gTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGGTTCTGTGGCGGGTGAAAAGGGTCACAacc                                                                                                                                    >  1:338264/1‑139 (MQ=255)
              gAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAAGGTCACACCCCGGTGGtttt                                                                                                                          >  2:482979/1‑139 (MQ=255)
                   aTGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGGTTACACCCAGTTGATTTTTCAgc                                                                                                                     >  2:508799/1‑138 (MQ=255)
                    tGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGGAAAGGGTCACACCCCGTTGATTTTTTAGtt                                                                                                                    >  2:157642/1‑139 (MQ=255)
                      cgcCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAAGGTTACACCCCAGTGGTTTTTCAGtttt                                                                                                                  >  2:66005/1‑137 (MQ=255)
                        ccACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCt                                                                                                                <  2:630292/139‑1 (MQ=255)
                           cctcctTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAGGGTCACACCCCGGTGGTTTTTCAGTTGTGTGAt                                                                                                             >  2:399457/1‑139 (MQ=255)
                            ctcctTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGGAAAGGGTCACACCCCGTTGATTTTTTCGTTGTTTGAtt                                                                                                            >  2:118889/1‑139 (MQ=255)
                                 tACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAAGTTCACACCCCGTTTATTTTTCCGTTGTCTGATTCGaa                                                                                                        >  2:741894/1‑138 (MQ=255)
                                    gggCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCt                                                                                                    <  1:102361/139‑1 (MQ=255)
                                    gggCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCt                                                                                                    <  1:361352/139‑1 (MQ=255)
                                     ggcggcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAAGGTTACACCCAGTTGTTTTTTCAGTTGTCTGTTTCGAAAACTc                                                                                                   >  2:953053/1‑139 (MQ=255)
                                       cggcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAGGGTCACACCCAGGTGGTTTTTCAGGTGTCTGATTCGGAAGCTCAc                                                                                                 >  2:102606/1‑139 (MQ=255)
                                         gcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCActg                                                                                               <  2:354314/139‑1 (MQ=255)
                                         gcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGGTCACACCCAGTTGTTTTTCCAGTTGTCTGATTCGAAAGCTCCctg                                                                                               >  1:734598/1‑139 (MQ=255)
                                         gcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAGGTTCACACCCAGCTGATTTTCCAGTTGTCTGATTCGAAAGCTCActg                                                                                               >  1:922370/1‑139 (MQ=255)
                                              ccAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGa                                                                                           <  2:649970/138‑1 (MQ=255)
                                              ccAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGa                                                                                           <  2:680091/138‑1 (MQ=255)
                                                   tGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGt                                                                                     <  1:899999/139‑1 (MQ=255)
                                                    gCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGGAAAGGGTCACACCCAGTTGGTTTTCCAGTTGTTTGATTCGAAAACTCACTGCTGACTGGGt                                                                                     >  2:795823/1‑138 (MQ=255)
                                                       cATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGGTAACACCCAGTTGATTTTTCAGTTGTCTGTTTTGGAAGCTCACTGCTGACTGGGt                                                                                     >  2:86207/1‑135 (MQ=255)
                                                        aTGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAAGTTTAAACCCCGTTGGTTTTTCAGTTGTCTGATTCGAAAGATCACTGCTGGCTGGGGCAGa                                                                                 >  2:540409/1‑138 (MQ=255)
                                                             cGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAGGTTTAGACCCAGTTGATTTTTCAGTTGTCTGATTCGAAAGCGCACTGCTGACTGGGGCGGATAGAGc                                                                           >  1:295251/1‑139 (MQ=255)
                                                                       tAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCg                                                                 <  1:540409/139‑1 (MQ=255)
                                                                         aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCt                                                               <  1:885784/139‑1 (MQ=255)
                                                                          ggCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGTAAAGGGTCACACCCAGATGGTTTTTCCGTTTGCTGGTTCGAAAGGTCACTGCTGACTGGGTCAGATAGAGCGGTTCAGACggcc                                                              >  2:158235/1‑136 (MQ=255)
                                                                          ggCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAGGGTCACACCCAGTTGATTTTTCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGccc                                                              >  1:244661/1‑137 (MQ=255)
                                                                               tagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTcaca                                                                                                                                       <  2:146964/61‑1 (MQ=255)
                                                                               tagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTcaca                                                                                                                                       >  1:146964/1‑61 (MQ=255)
                                                                               tagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGCACCCACCCTGCTGATTTTTCACTTTTCTTATTCGCAAGCTCACCGCTGCCTGGGTCCCACAGAGCGATTCACCCGCTCCAcc                                                          >  1:742068/1‑138 (MQ=255)
                                                                               tagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAAGGTCACACCCAGTTGATTTTTCCGTTGTCTGATTCGAAAACTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGAcc                                                          >  1:285655/1‑138 (MQ=255)
                                                                                    tttCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAAGGTCACACCCCGTTGGTTTTTCCGTTGTCTGATTCGAAAACTCACTGCTGACTGGGTCAGATAGAGCGATTTAGCCGCTCGACCCAAGTg                                                    >  2:322566/1‑139 (MQ=255)
                                                                                    tttCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAAGGTCACACCCAGTTGATTTTTCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGGCAGATAGAGCGATTCAGCCGCCCGACCaaa                                                       >  1:504865/1‑136 (MQ=255)
                                                                                            gCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAAGTTCACACCCAGTTGATTTTTTACTTGTGTGATTCGAAAGCACACTGGTGGCAGGGGCAGAAAGAGGGATTCAACCGCCCGGCCCAAGTGACGCGttt                                            >  2:444334/1‑138 (MQ=255)
                                                                                                           atatTGTTTCTGTGGCGGGTGAAAAGGTTCACCCCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGa                             <  2:338264/139‑1 (MQ=255)
                                                                                                           atatTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCCGTTGATTTTTCAGTTGTCTGATTCGAAAACTCACTGCCGACTGGGTTCGATAGAGCGATTCAGCCGCCCGACCAAAATGACGCGTTTGGCTAACTTCCAgg                              >  2:358734/1‑138 (MQ=255)
                                                                                                           atatTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGa                             <  2:244661/139‑1 (MQ=255)
                                                                                                            tatTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCCGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGa                             >  1:855651/1‑138 (MQ=255)
                                                                                                             atTGTTTCTGTGGCGGGTGAAAAGGGTCACACCCAGTTGATTTTTCAGTTGTCTGATTTGAAAACTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTTCAGGa                             >  1:915636/1‑137 (MQ=255)
                                                                                                                           ggggGAAAAGGTTCACACCCAGTTGATTTTCTAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCCCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTc             >  1:281000/1‑139 (MQ=255)
                                                                                                                           gggTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTc             <  2:790844/139‑1 (MQ=255)
                                                                                                                            ggTGAAAAGGGTCACACCCAGTTGATTTTTCAGTTGTCTGATTCGAAAACTCAATGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTcc            >  2:332290/1‑139 (MQ=255)
                                                                                                                              tGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGt          <  1:399457/139‑1 (MQ=255)
                                                                                                                                   aGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCca     <  1:66005/139‑1 (MQ=255)
                                                                                                                                    ggTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCcac    <  1:524156/139‑1 (MQ=255)
                                                                                                                                     gTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCcaca   <  2:775095/139‑1 (MQ=255)
                                                                                                                                      ttCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAg  >  2:597215/1‑139 (MQ=255)
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ACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAG  >  NZ_CP009273/3941057‑3941329

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑