Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,941,2100CT45.6% 45.4 / 22.4 46E40K (GAA→AAA) hdfRHTH‑type transcriptional regulator HdfR
Reads supporting (aligned to +/- strand):  ref base C (7/18);  new base T (21/0);  total (28/18)
Fisher's exact test for biased strand distribution p-value = 2.24e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

ATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAAT  >  NZ_CP009273/3941076‑3941344
                                                                                                                                      |                                                                                                                                      
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)
                                                            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)
                                                                                                                       cacCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGct             <  1:251297/139‑1 (MQ=255)
                                                                                                                       cacCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGct             <  2:135368/139‑1 (MQ=255)
                                                                                                                                   tttCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAat  >  2:516465/1‑138 (MQ=255)
                                                                                                                                      |                                                                                                                                      
ATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAAT  >  NZ_CP009273/3941076‑3941344

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑