Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,947,850	0	C	T	57.1%	12.6 / 49.3	42	E40K (GAA→AAA)	hdfR	flhDC operon transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base C (6/12);  new base T (24/0);  total (30/12)
Fisher's exact test for biased strand distribution p-value = 1.68e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.29e-05

TATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATG  >  NC_000913/3947703‑3947998                                                                                                                                                    |                                                                                                                                                      tATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAg                                                                                                                                                    <  2:868093/151‑1 (MQ=255)   tGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAAGGTCACACCCAGTTGATTTTTCAGtt                                                                                                                                                  >  2:396943/1‑151 (MQ=255)    gTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGGTTACAACCAGTTGATTTTTCAGTTg                                                                                                                                                 >  2:740057/1‑151 (MQ=255)    gTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAAGGTTACACCCAGTTGATTTTTCAGttt                                                                                                                                                 >  1:273002/1‑150 (MQ=255)    gTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAAGGTCACACCCAGTTGATTTTTCAGTTg                                                                                                                                                 >  2:353680/1‑151 (MQ=255)           ggTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGGAAAGGGTTACAACCAGTTGGTTTTTCCGTTGTCttttt                                                                                                                                          >  1:169245/1‑147 (MQ=255)            gTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAAGGTCACACCCCGTTGATTTTTCAGTTTTTTGAttt                                                                                                                                         >  1:796840/1‑150 (MQ=255)            gTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAAGTTCACACCCCATTTGTTTTTCAGttttttgttt                                                                                                                                          >  1:504394/1‑142 (MQ=255)            gTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAGGGTCACACCCAGTTGATTTTTCAGTTGTCTGAttt                                                                                                                                         >  2:209091/1‑150 (MQ=255)            gTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAAGTTCACACCCAGTTGATTTTTCCGTTGTCTGAttt                                                                                                                                         >  1:367297/1‑150 (MQ=255)                         cctTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGGTCACACCCAGTTGATTTTTCAGTTGTCTGATTT‑GAAAGCTCActg                                                                                                                            >  2:583326/1‑150 (MQ=255)                         cctTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAGGGTCACACCCCGTTGATTTTTCAGTTGTCTGATTC‑GAAAGCTCActg                                                                                                                            >  1:372084/1‑150 (MQ=255)                              cGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACt                                                                                                                      <  1:315035/151‑1 (MQ=255)                                    gcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGGTCAAACCCCGTTGTTTTTTCAGTTGTTTGATTT‑GCAAACTCACTGCTGAGTggggga                                                                                                                >  2:8693/1‑148 (MQ=255)                                       tGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGAt                                                                                                             <  1:809320/151‑1 (MQ=255)                                       tGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGAt                                                                                                             <  1:396941/151‑1 (MQ=255)                                        gCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAGGGTCACACCCAGTTGATTTTCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGGCAGATa                                                                                                            >  2:708311/1‑151 (MQ=255)                                        gCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAAGTTCACACCCAGTTGATTTTTCAGTTGTCTGATTT‑GAAAGCTCACTGCTGACTGGGTCAGATa                                                                                                            >  1:330195/1‑151 (MQ=255)                                             gTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAAGGTCACACCCAGTTGGTTTTTCAGTTGTCTGGTTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCg                                                                                                       >  1:609471/1‑151 (MQ=255)                                               gCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAAGTTCACACCCCGTTGATTTTCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCGAt                                                                                                     >  2:860125/1‑151 (MQ=255)                                                          tttCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTTCAGTTGTCTGATTC‑GAAAACTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCg                                                                                          >  2:762532/1‑151 (MQ=255)                                                          tttCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAAGGTTACACCCAAGTGATTTTTCAGTTGTTTGATTT‑GAAAACTCACTGCTGACTCGGTCCGATAGAGAGATTCAGCCGCTc                                                                                           >  1:514768/1‑150 (MQ=255)                                                          tttCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAAGGTCACACCCAGTTGGTTTTTCAGTTGTTTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCCCg                                                                                          >  1:350162/1‑151 (MQ=255)                                                                    aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGGAAAGGGTCACACCCCGGTGGTTTTTCAGTTGTCTGATTCTGAAAG‑TCACTGCCGACTGGGGCAGAAAGAGCGATTCTACCGCCCGACCaaaaaga                                                                                >  2:255472/1‑147 (MQ=255)                                                                    aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGGTCACACCCAGTTGATTTTTCCGTTGTCTGATTT‑GAAAACTCACTGCTGACTGGGGCAGATAGAGGGATTTAGCCGCTCGACCAAAGTGa                                                                                >  2:835222/1‑151 (MQ=255)                                                                       cAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGAcg                                                                              <  2:196790/150‑1 (MQ=255)                                                                                       gCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTcc                                                              <  1:851917/150‑1 (MQ=255)                                                                                       gCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTcc                                                              <  1:159817/150‑1 (MQ=255)                                                                                             gTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAAGATCACACCCAGGTGATTTTTCAGTTGTCTGATTT‑GAAAACTCACTGCTGACTGGGGCAGATAGAGCGGTTTAGCCGCTCGACCAAAGAGACGCGTTCGGGTAAATTCCAGGaaaa                                                       >  1:61507/1‑150 (MQ=255)                                                                                             gTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAAGGTCACACCCAGTTGATTTTTCAGTTGTTTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTTAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTTCAGGAAAg                                                       >  1:613836/1‑151 (MQ=255)                                                                                                   cGGATATTGTTTCTGTGGCGGGTGAAAAGGGTCACACCCAGGTGGTTTTTCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGGCAGATAGAGGGATTTAGCCGCTCGACCAAAAGGACGCGGTCGGCTAAATTCCAGGAAAGgttttt                                                 >  1:385774/1‑150 (MQ=255)                                                                                                   cGGATATTGTTTCTGTGGCGGGTGAAAAAGGTTACACCCCGTTGATTTTTCAGTTTTTTGATTC‑GAAAGCTCACTGCTGACTGGGGCAGATAGAGCGATTCAGCCGCCCGACCAAAGTGACGCGTTCGGCTAAATTCCAGGAAAGgttttt                                                 >  1:122894/1‑150 (MQ=255)                                                                                                   cGGATATTGTTTCTGTGGCGGGGGAAAAAGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTa                                                 >  2:868362/1‑151 (MQ=255)                                                                                                     gATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTTCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCCCGACCAAAGAGACGCGTTCGGCTAACTTCCAGGAAAGATTTTaa                                                >  2:646095/1‑150 (MQ=255)                                                                                                               cTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTAt                                     <  1:304008/151‑1 (MQ=255)                                                                                                                    gCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCcac                                 <  1:747531/150‑1 (MQ=255)                                                                                                                         tGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGc                            <  1:643245/150‑1 (MQ=255)                                                                                                                               ggTTCACACCCAGTTGATTTTCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGctc                          <  2:587180/146‑1 (MQ=255)                                                                                                                               ggTTCACACCCAGTTGATTTTCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGctc                          >  1:587174/1‑146 (MQ=255)                                                                                                                                     cacCCAGTTGATTTTCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAatt               >  1:795712/1‑151 (MQ=255)                                                                                                                                                  ttCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATg  >  2:138052/1‑151 (MQ=255)                                                                                                                                                  ttCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATg  <  1:638713/151‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                      TATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATG  >  NC_000913/3947703‑3947998

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑