Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,947,850	0	C	T	50.0%	33.0 / 33.3	50	E40K (GAA→AAA)	hdfR	flhDC operon transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base C (8/17);  new base T (25/0);  total (33/17)
Fisher's exact test for biased strand distribution p-value = 2.20e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATGAT  >  NC_000913/3947707‑3948000                                                                                                                                                  |                                                                                                                                                       tCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GAAAAGGGTCACACCCAGTTGATTTTTCCGtt                                                                                                                                                   >  1:477/1‑149 (MQ=255)  cGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTc                                                                                                                                                <  1:580247/151‑1 (MQ=255)    tGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCCGTTGATTTTTCAGTTGTCt                                                                                                                                               >  1:171648/1‑150 (MQ=255)    tGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GAAAAAGGTTACACCCCATTGGTTTTTCAATTg                                                                                                                                                  >  1:147993/1‑147 (MQ=255)      aGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GGAAAGGTTCACACCCCGGTGATTTTTCACTTGTCTGAt                                                                                                                                            >  2:484976/1‑151 (MQ=255)      aGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GGAAAAGGTCACCCCCCGTTGATTTTTCAGtttttttgt                                                                                                                                            >  2:2849/1‑144 (MQ=255)                 aCCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCCGTTGGTTTTTCAGTTGTTTGATTCGAAAACTc                                                                                                                                  >  1:311564/1‑150 (MQ=255)                         aCGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGG‑GAAAAGGTT‑ACACCCCGGTGGTTTTTCAGTTGTTTGGTTCGAAAAACCActgct                                                                                                                            >  2:321459/1‑148 (MQ=255)                         aCGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAAGGTTACACCCAGTTGATTTTTCAGTTGTCTTGTTCGAAAACTCActgccg                                                                                                                           >  1:383598/1‑147 (MQ=255)                                     ccAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GGAAAAGGTCACACCCAGTTGATTTTTCAGTTTTCTGATTCGGAAGCACACTGCTGAcctggggagat                                                                                                               >  2:80280/1‑139 (MQ=255)                                       aGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GAAAAAGTTCACACCCAGTTGATTTTTCAGTTGTCTGATTCGAAAACTCACTGCTGACTGGGGCAGATa                                                                                                              >  1:212601/1‑148 (MQ=255)                                             tCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGG‑GAAAAGGTT‑ACACCCCGTTGATTTTTCCGTTGTCTTGTTCGGAAAACCCCTGCTGACCGGGTTAGATAGAGCGGttt                                                                                                     >  2:280180/1‑150 (MQ=255)                                              cATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAAGATCACACCCAGTTGATTTTTCAGTTGTCTGATTCGAAAAATCACTGCTGACTGGGGCAGATAGAGCGAtt                                                                                                      >  1:637709/1‑149 (MQ=255)                                                  aGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAAGGTCACACCCAGCTGATTTTCCAGCTGTCTGATTTGGAAGGTCACCGCTGAATGGGGCAGATAAAGCGATTCAGcc                                                                                                 >  1:661540/1‑150 (MQ=255)                                                    cGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAAGATCACACCCAGTTGATTTTTCAGTTGTTTGATTTGAAAACTCACTGCTGACTGGGGCAGAAAGAGCGATTCAGCCGc                                                                                               >  1:532650/1‑150 (MQ=255)                                                        tCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GGAAAAGGTCACACCCCATTGATTTTTCAGTTGTCTGTTTCGGAAGCTCACTGGCGACTGGGTCAGATAGAGCGATTTAGCCCCTCGAc                                                                                          >  2:577062/1‑151 (MQ=255)                                                             aTAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGA‑GAAAAGGTTCTCACCCCGTTTTTTTTTCTGTTTTCTGATTTGAAAGTTCACTTCTTCACGGGTCAGATAGAGTGATTCAACCCCCCGACCaa                                                                                       >  1:471497/1‑149 (MQ=255)                                                                       agtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGtt                                                                            <  2:646097/150‑1 (MQ=255)                                                                        gtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCg                                                                          <  2:537048/151‑1 (MQ=255)                                                                         tttttCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGGTTACACCCCGTTGGTTTTTCAGTTGTCTGATTCGAAAACTCACCGCTGACTGGGTCAGATAGAGCGATTCAGCCGCCCGCCCCAAAAGACGCGGTCgg                                                                         >  1:643626/1‑151 (MQ=255)                                                                           tttCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAACTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGc                                                                        <  2:193105/150‑1 (MQ=255)                                                                                ccGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACtt                                                                  <  1:437549/151‑1 (MQ=255)                                                                                ccGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACtt                                                                  <  1:430935/151‑1 (MQ=255)                                                                                ccGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGGTCACACCCCGATGGTTTTTCAGTTTTCTGATTTGAAAACTTACTGCTGGCTGGGGCAGATAAAAGGATTTAACCGCCCCGCCAAAAGGGCGCGGTTGGCttaatt                                                                  >  2:359844/1‑146 (MQ=255)                                                                                ccGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GAAAAGGGTCACACCCCGGTGGTTTTTCAGTTGTCTGATTTGAAAACTCACTGCTGACTGGGGCAGATAGAGCGATTCAGCCGCCCGACCAAAATGACGCGTTCGGCTAAc                                                                    >  2:396987/1‑149 (MQ=255)                                                                                    cAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GAAAAGGGTTACACCCAGTTTATTTTTCAGTTGTCTGATTCGAAAAGTCACTGCTGGCTGGGTCAGATAAAGCGATTCAGCCGCTCGACCCAAGTGACGCGTTCGGCTAAAtt                                                                  >  1:267263/1‑147 (MQ=255)                                                                                     aGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAgg                                                             <  1:241381/151‑1 (MQ=255)                                                                                        ggTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GGAAAATATCACACCCAGTTGATTTTTCAGTTGTCTGATTCGAAAACACACTGCTGACCGGGGCAGATAGAGGGATTCAGCCGCCCGAACAAAGGGACGCGTTCGGCTAACTTTCAgg                                                             >  1:154045/1‑148 (MQ=255)                                                                                        ggTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GAAAAGGGTTACACCCAGTTGATTTTTCAGTTTTCTGGTTCGAAAAATCACTGCTGACTGGGTCAGATAGAGAGATTCAGCCGCCCGACCCAAATGACGCGGTCGGCTAACTTCCAGGaa                                                           >  2:163334/1‑150 (MQ=255)                                                                                         gTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAAGTTCACACCCAGGTGATTTTTCAGTTGTCTGATTCGAAAACTCACTGCTGACTGGGGCAGATAGAGCGATTTAGCCGCCCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGaa                                                           >  1:673505/1‑149 (MQ=255)                                                                                            aaaCGGATATTGTTTCTGTGGC‑GGGG‑GAAAAGGTTCACACCCCGCTGGTTTTTCCGTTTTTTTATTTTGAAGGCCACTTCTGTCCGGGTCAGATAGAGGGATTTAGCCGCTCCACCAAAATGACGCGGTCGGCTAACTTTCAGGAAAAttt                                                      >  2:632287/1‑151 (MQ=255)                                                                                               cGGATATTGTTTGTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTa                                                   <  2:164946/151‑1 (MQ=255)                                                                                               cGGATATTGTTTCTGTGGC‑GGGTGGAAAAGGTT‑ACACCCCGGTGGTTTTTCAGTTGTCTGATTTGAAAACTCAATGCTGACTGGGGCAGATAGAGAGATTCAGCCGCTCGACCAAAAAGACGCGTTCGGCTAACTTCCCGGAAAGgtttt                                                    >  2:260008/1‑150 (MQ=255)                                                                                                   tatTGTTTCTGTGGC‑GGGT‑GGAAAGGTTCACACCCCGTTGATTTTTCCTTTTTCTGATTTGAAAACTCACTGCTGACTGGGTCAGATAGAGCGATTTAGCCGCTCGACCAAAGTGACGCGTTCGGGTAACTTCCCGGAAAGGTTTTAACa                                                >  2:180476/1‑150 (MQ=255)                                                                                                    atTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACaa                                               <  2:563130/150‑1 (MQ=255)                                                                                                       gTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGATTTTCTAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTcc                                           <  2:380128/151‑1 (MQ=255)                                                                                                         ttCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCg                                          <  1:155303/150‑1 (MQ=255)                                                                                                          tCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGt                                         <  1:541962/150‑1 (MQ=255)                                                                                                           cTGTGGC‑GGGG‑GAAAAGGGTCAAACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGATCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAATTTTTTAAAATTCCGTa                                        >  2:492536/1‑150 (MQ=255)                                                                                                             gtgGC‑GGGT‑GAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTa                                        <  2:563024/148‑1 (MQ=255)                                                                                                             gtgGC‑GGGT‑GAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCCCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATc                                      <  1:32759/150‑1 (MQ=255)                                                                                                                                 cacaCCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCaaa                    >  1:329513/1‑150 (MQ=255)                                                                                                                                    acCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAatta                <  2:644955/151‑1 (MQ=255)                                                                                                                                    acCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAatt                 >  1:201810/1‑150 (MQ=255)                                                                                                                                           tGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTc          <  1:667364/150‑1 (MQ=255)                                                                                                                                           tGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCg         >  1:11609/1‑151 (MQ=255)                                                                                                                                             aTTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGtt       <  1:45446/151‑1 (MQ=255)                                                                                                                                              ttttCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGtt       >  1:75119/1‑150 (MQ=255)                                                                                                                                                ttCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATg    >  1:551009/1‑151 (MQ=255)                                                                                                                                                ttCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATg    >  1:458069/1‑151 (MQ=255)                                                                                                                                                  ccAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATGa   <  1:649808/150‑1 (MQ=255)                                                                                                                                                  ccAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATGAt  <  2:490359/151‑1 (MQ=255)                                                                                                                                                  ccAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATGAt  <  1:306575/151‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                       TCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATGAT  >  NC_000913/3947707‑3948000

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: ‑