Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,947,850	0	C	T	43.1%	58.0 / 30.2	51	E40K (GAA→AAA)	hdfR	flhDC operon transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base C (4/25);  new base T (22/0);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 1.11e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTA  >  NC_000913/3947709‑3947996                                                                                                                                               |                                                                                                                                                   gTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCt                                                                                                                                           <  2:80125/151‑1 (MQ=255)  tGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCTCCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGG‑GAAAAGGTCACACCCCGGTGATTTTTCCGTTGTCt                                                                                                                                           >  1:644281/1‑150 (MQ=255)              cACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGG‑GAAAAGGTCACACCCCGGTGATTTTTCCGTTGTCTGATTTGAAAACTc                                                                                                                              >  1:767456/1‑151 (MQ=255)                    ctTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGG‑GAAAAGTTAACACCCCGCTGATTTTTCAGTTTTTTGGTTCTAAAGCTccat                                                                                                                           >  1:128633/1‑145 (MQ=255)                       aCGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGAc                                                                                                                     <  1:869398/151‑1 (MQ=255)                        cGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACt                                                                                                                    <  2:155584/151‑1 (MQ=255)                           gcggcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAAGGTCACACCCCGTTGATTTTTCAGTTGTCTGATTCGAAAACTCACTGCTGACTggg                                                                                                                 >  2:35117/1‑151 (MQ=255)                               ccTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAg                                                                                                             <  1:837847/151‑1 (MQ=255)                                  gCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGAt                                                                                                           <  1:102756/150‑1 (MQ=255)                                    cAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑TAAAGGTTCACCCCCAGGTGATTTTTCAGTTTTTTGTTTCTGAAACTCCCCGCTCACTTGGTCAGa                                                                                                            >  1:375930/1‑147 (MQ=255)                                    cAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATaga                                                                                                        <  1:482673/151‑1 (MQ=255)                                    cAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGG‑AAAAGGATCACACCCCGTTGGTTTTTCAGTTGGCTGTTTTGGAAGCTCACTGTTCACTGGGGCAggt                                                                                                           >  1:772969/1‑146 (MQ=255)                                     aGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATagag                                                                                                       <  2:846672/151‑1 (MQ=255)                                       gTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCg                                                                                                     <  1:185493/151‑1 (MQ=255)                                        tGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGG‑AAAAAGGTCACACCCCGTTGATTTTTCCGTTGTTTGATTTGAAAACTCACTGCTGACTGGGGCAGATAGAGCg                                                                                                     >  2:486048/1‑150 (MQ=255)                                           tCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAAGGTTC‑CACCCAGTTGGTTTTTTAGTTTTTTGTTTCGAAAAATCACTGCTGACTGGGGCAGATAGAGGGAtt                                                                                                  >  1:148515/1‑150 (MQ=255)                                            cATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGG‑AAAAAGGTCACACCCCGTTGATTTTTCCGTTTTCTGATTCGAAAGCTCACTGCTGACTGGGGCAGATAGAGGGAtt                                                                                                  >  2:764007/1‑149 (MQ=255)                                                aGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAGGGTCACACCCAGTTGATTTTTCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGcc                                                                                             >  2:282995/1‑150 (MQ=255)                                                   gTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAAGGTCACACCCAAATGGGTTTTCCGGTCTCTTATTCGGAAATCCACTGCTTACTTGGGCCGATAGAGGGATTCAGCCGccc                                                                                         >  2:731244/1‑149 (MQ=255)                                                         gCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCa                                                                                    <  1:457059/150‑1 (MQ=255)                                                         gCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGG‑AAAAAGTTCACACCCAGTTGATTTTTCCGTTGTCTGATTCGAAAGCTCACTGCTGAATGGGTCAGATAGAGGGATTTAGGCGCTCGAACa                                                                                    >  2:289059/1‑150 (MQ=255)                                                                 cAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGG‑AAAAGGTTCACACCCAGTTGATTTTTCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGGCAGATAGAGCGATTCAGCCGCTCGACCAAAgag                                                                               >  2:405851/1‑145 (MQ=255)                                                                 cAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGG‑AAAAAGGTTACCCCCCGGTGATTTTTCAGTTTTTTGATTTGAAAAATCACTGCTGGCTGGGGCCGATAGAGCGATTTAGCCGCCCGACCaaaagggcg                                                                            >  1:367879/1‑144 (MQ=255)                                                                     agtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTc                                                                       <  1:156556/151‑1 (MQ=255)                                                                        ttttCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCgg                                                                     <  2:881529/150‑1 (MQ=255)                                                                         tttCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGc                                                                    <  2:935790/150‑1 (MQ=255)                                                                         tttCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGc                                                                    <  1:103717/150‑1 (MQ=255)                                                                          ttCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCt                                                                   <  1:300595/150‑1 (MQ=255)                                                                              ccGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACtt                                                              <  2:361574/151‑1 (MQ=255)                                                                                ggCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑GAAAAGGTCACCCCCAAGTGGTTTTTCCTTTTTTTGCTTTGCAAACTCACTGCCGACTGGGTCCGATAGAGCGATTCAGCCGCCCGACCAAAGAGACACGGTCGGCTAACtt                                                              >  1:609239/1‑149 (MQ=255)                                                                                ggCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTcc                                                            <  2:23187/151‑1 (MQ=255)                                                                                        ttAAACGGATATTGTTTCTGTGGCGGGGG‑GAAAGGTTCACCCCCCGTTGATTTTTCCGTTGTTTGATTCGAAAACTCACTGCTGACCGGGGTAGAAAAAGCGATTCAGCCCCCCGACCAAAATGACGCGGTCGGGTAAAtttccgggaa                                                      >  1:676192/1‑141 (MQ=255)                                                                                         tAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAAGGTCACACCCAGTTGATTTTTCAGTTGTTTGATTCGAAAACTCACTGCTGACTGGGTCAGATAGAGCGATTTAGCCGCCCGACCAAAAGGACGCGTTCGGCTAACTTCCAGGaaaagt                                                   >  2:248334/1‑148 (MQ=255)                                                                                         tAAACGGATATTGTTTCTGTGGCGGGGG‑AAAAAGGTCACACCCAGTTGATTTTTCCGGTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCCCGACCAAAGGGACGCGTTCGGCTAACTTCCAGGaaa                                                      >  2:517754/1‑148 (MQ=255)                                                                                            aCGGATATTGTTTCTGTGGCGGGGG‑AAAAGGGTTACACCCCGATGATTTTTCTGTTGTTTGATTTTAAAACTCCCCTCTTCCTGGGGTAGGTAGAGCGATTTAGCCGGCCGACCAAAGAAAACCGGTCGGCTAACTTCCCGGAAAAatttt                                                >  1:169506/1‑151 (MQ=255)                                                                                              ggATATTGTTTCTGTGGCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTaa                                              <  2:388207/151‑1 (MQ=255)                                                                                                atatTGTTTCTGTGGCGGGGG‑GAAAAGGTCACACCCCGTTGGTTTTTCCGTTTTCTGATTTGGAAGATCACTGCTGACTGGGTCAGATAGAGCGATTTAGCCGCTCGACCCAAATGACGCGGTTGGGTAACTTTCAGGGAAGttttt                                                >  1:129145/1‑147 (MQ=255)                                                                                                    tGTTTCTGTGGCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAAtt                                         <  1:348433/150‑1 (MQ=255)                                                                                                    tGTTTCTGTGGCGGGGG‑AAAAAGGTTACACCCCGTTGATTTTTCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCCCGACCAAAATGACGCGGTCGGCTAACTTCCAGGGAAGGTTTTTACaaat                                         >  1:773397/1‑148 (MQ=255)                                                                                                     gTTTCTGTGGCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTcc                                       <  1:807569/151‑1 (MQ=255)                                                                                                     gTTTCTGTGGCGGGGG‑AAAAGGGTCACACCCCGTTGATTTTTCCGTTTTCTGATTTGAAAGCTCACTGCTGACTGGGGCAGATAGAGCGATTTAGCCGCCCGACCAAAGTGACGCGTTCGGCTAACTTCCCGGAAAGTTTTTTACaaat                                         >  1:512038/1‑147 (MQ=255)                                                                                                             ggCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGCCGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATacac                               >  1:895969/1‑151 (MQ=255)                                                                                                             ggCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCca                                <  2:62442/150‑1 (MQ=255)                                                                                                                 ggTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTg                           <  1:479975/151‑1 (MQ=255)                                                                                                                        aaGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTcc                     >  1:305559/1‑151 (MQ=255)                                                                                                                         aGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCg                    >  2:885753/1‑151 (MQ=255)                                                                                                                           gTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGc                   >  2:200170/1‑150 (MQ=255)                                                                                                                               acacCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCaaa                <  1:812356/149‑1 (MQ=255)                                                                                                                                      gTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACGGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACGTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGt       <  1:894216/151‑1 (MQ=255)                                                                                                                                         gaatttCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTCACGCGTGCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGCCg     <  1:901485/147‑1 (MQ=255)                                                                                                                                            tttCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTa  <  2:436635/150‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                   GTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTG‑AAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTA  >  NC_000913/3947709‑3947996

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: ‑