Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,947,850	0	C	T	44.0%	64.1 / 25.9	50	E40K (GAA→AAA)	hdfR	flhDC operon transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base C (7/21);  new base T (22/0);  total (29/21)
Fisher's exact test for biased strand distribution p-value = 2.63e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑G‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATGAT  >  NC_000913/3947700‑3948000                                                                                                                                                          |                                                                                                                                                       cGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑G‑AAAAGGTTCACACCCAGTTGATTTTc                                                                                                                                                        <  2:310024/151‑1 (MQ=255)                    cgcCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑G‑AAAAGGGTCACACCCAGTTGGTTTTTCCGGTTTCTGGTTTGaaa                                                                                                                                      >  1:6128/1‑150 (MQ=255)                      ccACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑G‑AAAAAGGTCACACCCCGTTGATTTTTCAGTTGTCTGATTCGaaa                                                                                                                                      >  1:437260/1‑148 (MQ=255)                       cACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑G‑AAAAGGGTCACACCCAGTTGATTTTTCAGTTGTCTGATTCGa                                                                                                                                        >  1:639740/1‑145 (MQ=255)                         cctcctTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑G‑AAAAAGTTTACACCCCGGTGGTTTTTCAGTTGTTTGGTTCGAAAGCTc                                                                                                                                  >  1:737551/1‑149 (MQ=255)                         cctcctTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑G‑AAAAAGGTTACACCCCGGTTATTTTTCAGTTTTTTTATTCGGAAACTc                                                                                                                                  >  2:51871/1‑149 (MQ=255)                         cctcctTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑G‑AAAAAGGTTACACCCAGTTGGTTTTTCCGTTGTCTGATTTGAAAGCTc                                                                                                                                  >  1:87274/1‑149 (MQ=255)                            cctTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑G‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCActgc                                                                                                                             <  2:512519/151‑1 (MQ=255)                                    gcggcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGG‑AAAAGGTT‑ACACCCCGGTGATTTTTCCGTTTTCTGATTTTAAAACTCACTGCTGACTgg                                                                                                                      >  2:290217/1‑150 (MQ=255)                                      ggcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑G‑AAAAGGGTCACACCCAGGTGATTTTTCAGTTGTCTGATTCGAAAACTCACCGCTGACTggg                                                                                                                     >  1:262101/1‑149 (MQ=255)                                          tGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑G‑AAAAAGGTCACACCCAGTTGATTTTTCAGTTGTCTGATTCGAAAGCTCACTGCTGACTggg                                                                                                                     >  1:285359/1‑145 (MQ=255)                                           gCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑G‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGa                                                                                                                <  2:526716/149‑1 (MQ=255)                                              aGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGG‑AAAAGGTT‑ACACCCCATTGGTTTTTCAGTTTTTTTGTTTGAAAAATCCctgctggccgg                                                                                                                      >  2:678507/1‑135 (MQ=255)                                              aGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑G‑AAAAAGGTCACACCCAGCTGATTTTTCCGTTTTTTGATTTGAAAACTCACCGCTGACTggg                                                                                                                     >  2:269635/1‑141 (MQ=255)                                                gTGCTCATGAGCGCTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGTATATTGTTTCTGTGGC‑GGGT‑G‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTTACTGGGTCAGATaga                                                                                                            <  1:691078/148‑1 (MQ=255)                                                  gCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑G‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGa                                                                                                        <  1:728329/150‑1 (MQ=255)                                                     cATGAGCGTTTCTGCATACGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGC‑G‑AAAAGGGTCAAACCCCGGTGGTTTTTCCGCTGTTTGAATCGGAGGCACACTACTGCCAGGGGCGGATaaa                                                                                                            >  2:485965/1‑141 (MQ=255)                                                      aTGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGG‑G‑AAAAGGTT‑ACACCCAATTGATTTTTCAGTTTTTTGGTTTGAAAACTCACTGCTGACTGGGGGCGATAGAGCGAtt                                                                                                      >  1:417188/1‑148 (MQ=255)                                                        gAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑G‑AAAAGGGTTACACCCCGATGGTTTTTCCATTTTTTGTTTTGAAAAACCACTGCTGGCTGGGGCAGATAGAGGGATTCAGcc                                                                                                 >  1:73425/1‑151 (MQ=255)                                                         aGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑G‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCg                                                                                                <  1:304341/151‑1 (MQ=255)                                                          gCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑G‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGc                                                                                               <  2:819796/151‑1 (MQ=255)                                                            gTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑G‑GAAAAGGTCACAACCCGTTGATTTTTCTGTTTTCTGATTTGGAAAATCACTGCTGGCTGGGGCAGAAAGAGCGATTCAGCCGCTc                                                                                             >  2:147644/1‑151 (MQ=255)                                                              ttCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑G‑AAAAGGGTCACAACCAGTTGATTTTTCAGTTTTCTGATTCGAAAGCTTACCGCTGACTGGGTCAGATAGAAAGATTCacac                                                                                                 >  1:225382/1‑142 (MQ=255)                                                                              agtTTTTCACCGGCAGCGGTTAAACGGCTATTGTTTCTGTGGC‑GGGC‑G‑TAAATGTTCAAAACCCGTTGATTTTTCCGTTGTTTGATTCTAAAGCTCAATGTTGACTGGGGCAGGTAGAGGGCTTCAGCCGCTCGGCCCAAGTGACGCGtt                                                                            >  1:322893/1‑150 (MQ=255)                                                                              agtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑G‑GAAAAGGTCGCACCCCGTTGATTTTTCAGTTGTCTGGTTCGAAAACACACTGCTGAATGGGGCAGATAGAGCGATTCAGACGCCCGAACCAAGTGAagcggt                                                                            >  2:338986/1‑148 (MQ=255)                                                                              agtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑G‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGtt                                                                            <  1:91877/150‑1 (MQ=255)                                                                              agtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑G‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTc                                                                           <  2:788962/151‑1 (MQ=255)                                                                               gtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑G‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCg                                                                          <  1:413138/151‑1 (MQ=255)                                                                                 ttttCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑G‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCgg                                                                         <  2:393486/150‑1 (MQ=255)                                                                                    tCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑G‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTa                                                                      <  2:127920/150‑1 (MQ=255)                                                                                     cACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑G‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAAc                                                                    <  1:869517/151‑1 (MQ=255)                                                                                     cACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑G‑GAAAGGGTCACACCCAGATGGTTTTTTCGTTTTTTGATTTGAAAACTTACTGCTGACTGGGTGAGATAGAGCGGTTCTGCCGCCCGACCCAAGAGACGCGGTCGGCCaa                                                                     >  2:279/1‑150 (MQ=255)                                                                                          gCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGC‑T‑GAAAGGGTCACACCCCGTTGGTTTTTCCGTTGTGTGTTTCGGAAGCTCACTGGTGACTTGGTTCGAGAAAGGGATTCATCCGCTCCACCCAAGTGAAACGTTCGGCTTAc                                                                    >  1:225033/1‑146 (MQ=255)                                                                                           cAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑G‑AAAAAGGTCACACCCAGTTGGTTTTTCAGTTGTCTGATTCGAAAACTCACTGCTGACTGGGGCAGATAGAGCGATTCAGCCGCCCGACCAAAGAGGGGCGGTCGGCTAAATTcccg                                                              >  1:657509/1‑149 (MQ=255)                                                                                               ggTTAAACGGATATTGTTTCTGTGGC‑GGGT‑G‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGaaa                                                          <  2:756332/151‑1 (MQ=255)                                                                                                   aaaCGGATATTGTTTCTGTGGC‑GGGT‑G‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGtt                                                       <  2:574197/150‑1 (MQ=255)                                                                                                         atatTGTTTCTGTGGC‑GGGT‑G‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACa                                                <  1:302618/151‑1 (MQ=255)                                                                                                         atatTGTTTCTGTGGC‑GGGG‑G‑AAAAAGGTCACACCCAGTTGATTTTCCAGTTTTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAATGACGCGTTCGGCTAAATTCCAGGAAAGTTTTTaa                                                  >  1:879073/1‑149 (MQ=255)                                                                                                          tatTGTTTCTGTGGC‑GGGT‑GAAAAAAGTTACCCCCCCATTG‑TTTTTCTGTTTTTTGATTTGGAAAATCACCTCTTACTTGGGCAGATAGAGGGATTTCGACGCCCCACCAAAAGTACGCGTTCGGCTTACTTCCAGGAAAGattttta                                                  >  2:502528/1‑146 (MQ=255)                                                                                                              gTTTCTGTGGC‑GGGT‑G‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTcc                                           <  2:41549/151‑1 (MQ=255)                                                                                                                    gtgGC‑GGGT‑G‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTa                                        <  1:128867/148‑1 (MQ=255)                                                                                                                        c‑GGGT‑G‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCcac                                   >  2:273507/1‑149 (MQ=255)                                                                                                                               g‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGctc                            >  2:509333/1‑151 (MQ=255)                                                                                                                                   aaGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTcc                         >  2:446753/1‑151 (MQ=255)                                                                                                                                           cacCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAatt                 >  2:835648/1‑151 (MQ=255)                                                                                                                                            acCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAatta                <  2:85747/151‑1 (MQ=255)                                                                                                                                                 gTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGt           <  2:201618/151‑1 (MQ=255)                                                                                                                                                    gATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGt        >  1:342723/1‑151 (MQ=255)                                                                                                                                                       tttCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTa      <  2:794536/150‑1 (MQ=255)                                                                                                                                                         tCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATg    <  1:579796/150‑1 (MQ=255)                                                                                                                                                         tCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATg    >  1:595207/1‑150 (MQ=255)                                                                                                                                                          ccAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATGAt  >  2:683844/1‑151 (MQ=255)                                                                                                                                                          ccAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATGAt  >  2:319423/1‑151 (MQ=255)                                                                                                                                                          |                                                                                                                                                       CGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑G‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATGAT  >  NC_000913/3947700‑3948000

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: ‑