Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,947,829	0	G	A	47.1%	50.1 / 26.0	51	L47F (CTT→TTT)	hdfR	flhDC operon transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base G (7/20);  new base A (24/0);  total (31/20)
Fisher's exact test for biased strand distribution p-value = 1.16e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCACCGATAGAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGT  >  NC_000913/3947683‑3947970                                                                                                                                                    |                                                                                                                                               ggCACCGATAGAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAGGTTc                                                                                                                                            <  2:493591/151‑1 (MQ=255)     ccGATAGAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAGGTTCtcac                                                                                                                                        <  2:307969/151‑1 (MQ=255)            aaaaCTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAGGTTCACACCCA‑GTTg                                                                                                                                <  1:209373/151‑1 (MQ=255)             aaaCTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGG‑GAAAAAGGTCACCCCCC‑GTTg                                                                                                                                >  1:899630/1‑150 (MQ=255)                cTCGTTATGTCGTGAGGTATGCGCCTCCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAGGTTCACACCCA‑GTTg                                                                                                                                <  2:689571/147‑1 (MQ=255)                 tCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAAGGTCACACCCC‑GATGAtttt                                                                                                                           >  1:372002/1‑151 (MQ=255)                    ttATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGG‑GAAAAAGGTTACACCCA‑CTTGAttt                                                                                                                            >  1:35206/1‑147 (MQ=255)                      aTGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAAGGTTACACCCA‑GTTGGtttttccg                                                                                                                       >  1:473246/1‑146 (MQ=255)                      aTGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGG‑GAAAAGGGTTACACCCC‑GTTGATTTTTCAGt                                                                                                                      >  2:160241/1‑151 (MQ=255)                       tGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAAGGTTACAACCA‑GTTGATTTTTCAGtt                                                                                                                     >  2:900815/1‑151 (MQ=255)                        gTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GGAAAAGATCCCACCCC‑GGTGTttttttcgtt                                                                                                                     >  1:237142/1‑144 (MQ=255)                          cGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAAGGTGACAACCA‑GTTGGTTTTTCAAtttt                                                                                                                   >  2:3380/1‑148 (MQ=255)                               ggTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGAtt                                                                                                             <  2:389672/151‑1 (MQ=255)                                         aCCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCa                                                                                                   <  2:838349/151‑1 (MQ=255)                                                           tGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GGAAAAGGTCCCACCCA‑AGTGATTTTTTAGTTGTCTGTTTTGCAAGCTCACAACTGCCTGGGt                                                                                      >  1:530912/1‑146 (MQ=255)                                                           tGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAAGGTCACACCCC‑GTTGATTTTTCAGTTGTCTTATTCGAAAACTCACTGCTGACTggg                                                                                       >  1:320166/1‑145 (MQ=255)                                                             ccAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGa                                                                                  <  1:87347/148‑1 (MQ=255)                                                             ccAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGG‑GAAAAAGTTCACACCCC‑GGTTATTTTTCCGTTGTTTGCTTTGAAAAATCACCGCTGACTGGGTCAGa                                                                                  >  2:431415/1‑148 (MQ=255)                                                              cAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGG‑GAAAAAGGTTACACCCC‑GTTGGTTTTTCTGTTGTTTGATTTGAAAACGCACTGCTGACTGGGTCa                                                                                    >  1:64465/1‑145 (MQ=255)                                                                  tGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAAAGTCAACCCCAGGTTGTTTTTCC‑GTTGTCTGATTTGTAAAATCACTGCTGACTGGGGGAGATagag                                                                             >  1:726319/1‑148 (MQ=255)                                                                   gCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGa                                                                          <  2:261735/150‑1 (MQ=255)                                                                   gCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAAGATCACACCCC‑GGTGATTTTTCAGTTTTCTGATTTGAAAAAACACTTCCGACTGGGGGCGATAGAGCGAt                                                                         >  1:585847/1‑151 (MQ=255)                                                                    cTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGG‑GAAAAAGTTCACACCCA‑GGTGATTTTTCAGTTGTCTGATTCGAAAACTCACTGCTGACTGGGGCAGATAGAGCGAtt                                                                        >  2:307216/1‑151 (MQ=255)                                                                     tCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGG‑GAAAAAGGTCAAACCCC‑GTTGATTTTTCCGTTGTCTGATTTGAAAACTCACTGCTGGCTGGGGCAGATAGAGCGAtt                                                                        >  2:285653/1‑150 (MQ=255)                                                                     tCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGC‑GAAAAAGGTCACAACCA‑GCTGCTTTTTCAGTTTTCTGCTTTCAAAACCCACCGCTGGCTGGGGTAGATAGAGCGAtt                                                                        >  2:709670/1‑150 (MQ=255)                                                                             gTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGG‑GAAAAGGGTCACCCCCA‑GTTGGTTTTCCTGGTTTTTGGATCCAAAACTCGCTGGTGGCTGGGTCCGAAAGAGCGATTTAGCCGccc                                                               >  2:480059/1‑149 (MQ=255)                                                                                    cATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGG‑GAAAAAGGTCACACCCC‑GTTGATTTTTCCGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGAcc                                                           >  2:236340/1‑148 (MQ=255)                                                                                     aTAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGG‑GGAAAAGGTCCCACCCC‑CTTGATTTTTCAAGTTTCTTATTCGAAAACTCACTGCTGACTGGGTCAGATAGAGCGATTTAGCCCCCCGACCaaa                                                        >  2:101904/1‑150 (MQ=255)                                                                                     aTAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGG‑GAAAAAGGTCACACCCA‑GGTGGTTTTTCCGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGGCAGATAGAGCGATTTAGCCGCTCGACCcaa                                                        >  2:571115/1‑150 (MQ=255)                                                                                               agtTTTTCACCGGCAGTGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGtt                                              <  1:336068/150‑1 (MQ=255)                                                                                               agtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGtt                                              <  2:66316/150‑1 (MQ=255)                                                                                               agtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGtt                                              <  1:165898/150‑1 (MQ=255)                                                                                                gtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAGGGTGACAACCA‑GGTGGTTTTTCAGTTTTTTGGTTTGAAAGCTCCCCGCTGACTGGGGGAGATAGAGAGATTTAGCCGCTCGACCAAAGAGAagcggt                                              >  1:953208/1‑147 (MQ=255)                                                                                                gtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAAGGTCACAACCA‑GTTGATTTTTCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGGCAGATAGAGCGATTTAGCCGCCCGACCAAAGTGAcgcggt                                              >  2:883286/1‑147 (MQ=255)                                                                                                   tttCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAAGGTCACACCCA‑GGTGGTTTTTCCGTTGTCTTATTTGAAAACTCACTGCTGGCTGGGGCAGATAGAGGGATTCCGCCGCCCGACCAAAAGGAcgcggt                                              >  2:75608/1‑144 (MQ=255)                                                                                                     tCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAAGGTTACACCCC‑GTTGATTTTTCCGTTTTTTGGTTTGAAAACTCACTGCTGGCTGGGTCAGATAGAGCGGTTTAGCCGCTCGACCAAAAAGAcgcg                                                >  1:694424/1‑142 (MQ=255)                                                                                                            cAGCGGTTAAACGGATATTGTTTCTGTGGCGGGG‑GAAAAAGGTCACACCCA‑GTTGATTTTTCAGTTGTCTGATTTGAAAACTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCCAAGTGAAGCGTTCGGCTAAcat                                    >  2:570675/1‑145 (MQ=255)                                                                                                               cGGTTAAACGGATATTGTTTCTGTGGCGGGTGGAAAAGGTT‑ACACCCC‑GTTGATTTTTCAGTTTTCTGATTCGAAAGCTCACTGCTGACTGGGGCAGATAGAGCGATTCCGCCGCCCGACCAAAGAGAAGCGTTCGGCTAACTTCCCgg                               >  2:370243/1‑149 (MQ=255)                                                                                                                    aaaCGGATATTGTTTCTGTGGCGGGT‑GAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGtt                         <  2:951205/150‑1 (MQ=255)                                                                                                                     aaCGGATATTGTTTCTGTGGCGGGT‑GGAAAAGTTCACACCCC‑CTTGATTTTTCAGTTGTTTGGTTTGAAAGCTCAATGCTGGCTGGGGCAGATAGAGCGATTTAGCCGCTCGACCCAAATGACGCGTTCGGCTAACTTCCCGGGAAGgttt                       >  1:642794/1‑151 (MQ=255)                                                                                                                     aaCGGATATTGTTTCTGTGGCGGGT‑GAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGtttt                       <  2:28082/151‑1 (MQ=255)                                                                                                                     aaCGGATATTGTTTCTGTGGCGGGT‑GAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGtttt                       <  1:591364/151‑1 (MQ=255)                                                                                                                         gATATTGTTTCTGTGGCGGGG‑GAAAAGGGTCACACCCC‑GGTGATTTTTCAGTTGTCTGATTTGAAAAACCACTGCTGACTGGGGTAGAAAGAGCGATTTCGCCGCCCCACCAAAGGGAAGCGGTCGGCTAACTTCCCGGAAAGgtttt                      >  1:356119/1‑148 (MQ=255)                                                                                                                            atTGTTTCTGTGGCGGGT‑GAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACaa                 <  1:741346/150‑1 (MQ=255)                                                                                                                              tGTTTCTGTGGCGGGT‑GAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAAtt               <  1:628979/150‑1 (MQ=255)                                                                                                                               gTTTCTGTGGCGGGT‑GAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTc              <  2:446135/150‑1 (MQ=255)                                                                                                                                tttCTGTGGCGGGT‑GAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTGACTTCCAGGAAAGTTTTTAACAATTcc             <  2:190110/150‑1 (MQ=255)                                                                                                                                        gCGGGT‑GAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCcac     >  1:183271/1‑150 (MQ=255)                                                                                                                                          gggT‑GAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGGTTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGt  <  2:279067/151‑1 (MQ=255)                                                                                                                                          gggT‑GAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAg   <  2:834735/150‑1 (MQ=255)                                                                                                                                          gggT‑GAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGt  >  2:438973/1‑151 (MQ=255)                                                                                                                                                    |                                                                                                                                               GGCACCGATAGAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGT  >  NC_000913/3947683‑3947970

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: ‑