Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,947,831	0	T	G	54.8%	30.7 / 50.5	43	N46T (AAC→ACC)	hdfR	flhDC operon transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base T (8/11);  new base G (23/0);  total (32/11)
Fisher's exact test for biased strand distribution p-value = 1.77e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.72e-06

CACCGATAGAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTC  >  NC_000913/3947685‑3947974                                                                                                                                                   |                                                                                                                                                 cACCGATAGAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGGAAAGGGTca                                                                                                                                               >  1:284343/1‑150 (MQ=255) cACCGATAGAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAGGGTca                                                                                                                                               >  1:837022/1‑150 (MQ=255)           aaaCTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAAGGTCACACCCAGTTgg                                                                                                                                    >  2:729037/1‑150 (MQ=255)              cTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAGGGTTACACCCCGGTGAttt                                                                                                                                 >  2:549670/1‑151 (MQ=255)                   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                                      <  1:159817/150‑1 (MQ=255)                                                                                                         gCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTcc                                      <  1:851917/150‑1 (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)                                                                                                                                                   |                                                                                                                                                 CACCGATAGAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTC‑GAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTC  >  NC_000913/3947685‑3947974

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: ‑