Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,995,457	0	T	G	44.0%	78.1 / 11.4	50	G232G (GGT→GGG)	dapF	diaminopimelate epimerase
Reads supporting (aligned to +/- strand):  ref base T (7/21);  new base G (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

TCCGGAGCGCGCCAATATCGGTTTTATGCAAGTGGTTAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAGGGATTCAGCAAGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCCGGCGGTCGTCTTGATATCGCCT‑GGAAAGGTCCGGGTCACCCGTTATATATGACTGGCCCGGCGGTACATGTCTACGACGGATTTATTCATCTATGAAGCAACCAGGGGAAGAACTG  >  NC_000913/3995316‑3995606                                                                                                                                              |                                                                                                                                                       tCCGGAGCGCGCCAATATCGGTTTTATGCAAGTGGTTAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAGGGATTCAGCAAGGTTTGCTGGc                                                                                                                                                <  2:113152/150‑1 (MQ=255)  ccGGAGCGCGCCAATATCGGTTTTATGCAAGTGGTTAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAGGGATTCAGCAAGGTTTGCTGGcc                                                                                                                                               <  1:697402/150‑1 (MQ=255)   cGGAGCGCGCCAATATCGGTTTTATGCAAGTGGTTAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGGAGGGGATTAACAAGGTTCGCTg                                                                                                                                                  >  2:479264/1‑146 (MQ=255)    ggAGCGCGCCAATATCGGTTTTATGCAAGTGGTTAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAGGGATTCAGCAAGGTTTGCTGGCCgaa                                                                                                                                            <  1:655577/151‑1 (MQ=255)     gAGCGCGCCAATATCGGTTTTATGCAAGTGGTTAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAGGGAGTCAGCAAGGGTTGCTGGcc                                                                                                                                               >  2:774332/1‑147 (MQ=255)         gcgcCAATATCGGTTTTATGCAAGTGGTTAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAGGGATTCAGCAAGGTTTGCTGGCCGAAGAAGt                                                                                                                                       <  2:135309/151‑1 (MQ=255)         gcgcCAATATCGGTTTTATGCAAGTGGTTAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAGGGATTCAGCAAGGTTTGCTGGCCGAAGAAGt                                                                                                                                       <  2:584668/151‑1 (MQ=255)          cgcCAATATCGGTTTTATGCAAGTGGTTAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCCGTAGGGATTTAGCAAGGGTTGCTGGCCgaagaa                                                                                                                                         >  2:48208/1‑148 (MQ=255)           gcCAATATCGGTTTTATGCAAGTGGTTAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTGGCAGGAGGGATGTTACAAGGGTTGCCGGCCCgagaag                                                                                                                                        >  2:167368/1‑148 (MQ=255)               atatCGGTTTTATGCAAGTGGTTAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTTGGGGTTTAGCAAGGGTTGCTGGCCCGAGAAGGAcg                                                                                                                                    >  2:547432/1‑148 (MQ=255)                tatCGGTTTTATGCAAGTGGTTAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGGAGTAGGGATTCAGCAAGGGTTGGTGGCCGAAGAAGTAagcggg                                                                                                                                >  1:228008/1‑149 (MQ=255)                      ttttATGCAAGTGGTTAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGGAGGGATTCAGCAAGGGTTGCTGGGCGAAGAAGGACGCGTggga                                                                                                                             >  1:619240/1‑146 (MQ=255)                       tttATGCAAGTGGTTAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAGGGATTCAGCAAGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTc                                                                                                                          <  1:422180/150‑1 (MQ=255)                          aTGCAAGTGGTTAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAGGGATTCAGCAAGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTcccc                                                                                                                       <  2:516066/150‑1 (MQ=255)                            gCAAGTGGTTAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCCGTAGGGAATCAGCAAGGGTTGCTGGCCGAAGAAAGACGCGGGGAACTcccccg                                                                                                                     >  2:86461/1‑148 (MQ=255)                            gCAAGTGGTTAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAGGGATTCAGCAAGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCcgg                                                                                                                     <  1:697686/150‑1 (MQ=255)                             cAAGTGGTTAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGGAGTAGGGGATCAGCAAGGGTTGCTGGCCGGAGAAGGACGCGGGGAAATCCCcggcg                                                                                                                   >  1:152975/1‑151 (MQ=255)                               aGTGGTTAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGGAGGGATTCAGCAAGGGTTGCTGGCCGAAGAAGGACGCGTGGGACTCCCccgcgg                                                                                                                  >  2:260260/1‑150 (MQ=255)                                  ggTTAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAGGGATTCAGCAAGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCCGGCGgtcgt                                                                                                              <  1:674069/151‑1 (MQ=255)                                     tAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGCGTGCGGCGGTTGCGGGCGGGGGTCAGAAAAGGTTCGTGGCGGACGAAGAGGGCCGGGAGGTCCCCGGCGgacg                                                                                                               >  1:15839/1‑147 (MQ=255)                                           cgAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAAGGAGTCAGCAAGGGTTTCTGGCCGAAAAAGTACGCGGGGGAAACCCCCGCGGGCGTCTTGatat                                                                                                      >  1:152102/1‑150 (MQ=255)                                           cgAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGGAGGGGTTTAGCAAGGGTTGCTTGCCGAAGAAGGACGCGGGGAACTCCCCGGCGGGCGTCtttgtat                                                                                                      >  2:546586/1‑145 (MQ=255)                                            gAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTTCAGGAGGGGATCAGCAAGGGTTGCTTGCCGGAGAAGTAAGCGGGGGACTCCCCCGCGGGCGGCTTggtttc                                                                                                     >  1:660915/1‑145 (MQ=255)                                             aGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAGGGAATCAACAAGGGTTGGTGGCCGGAGAAGGAAGCGGGGGAATCCCCGGCGGGCGGCTTTatat                                                                                                      >  1:346344/1‑148 (MQ=255)                                               cATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAGGGATTCAGCAAGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCCGGCGGTCGTCTTGATATCGCCt                                                                                                 <  1:480021/151‑1 (MQ=255)                                               cATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAGGGATTCAGCAAGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCCGGCGGTCGTCTTGATATCGCCt                                                                                                 <  2:706133/151‑1 (MQ=255)                                                  atTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAGGGATTCAGCAAGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCCGGCGGTCGTCTTGATATCGCCT‑gg                                                                                              <  2:200857/150‑1 (MQ=255)                                                    tCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAGGGATTTAGCAAGGGTTGCTGGCCGAAGAAGTACGCGGGGGACTCCCCGGCGGGCGGCTTGATATCGCCC‑GGaa                                                                                            >  2:130222/1‑150 (MQ=255)                                                      gTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGGAGGGATTCAGCAAGGGTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCCCGCGGTCGTCTTGATATTGCCT‑GGaaa                                                                                           >  2:99524/1‑149 (MQ=255)                                                      gTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGGTGGAGTTGGGCGTCAGCAAGGTTTTCCTGGCGAAGGAGGACGCGCGGGACTCCCCGGCGGTCGTGTTTATATctaccg                                                                                                >  1:668300/1‑140 (MQ=255)                                                       tttACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGGAGGGATTTAGCAAGGGTTGCTGGCCGAAGAAGTACGCGTGGGACTCCCCGGCGGTCGTCTTGGTATCGCCC‑GGgaaag                                                                                         >  2:159686/1‑148 (MQ=255)                                                          aCGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGGAGGGATTCAGCAAGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCCGGCGGGCGTCTTGATATCGCCT‑GGGAAGGGcc                                                                                      >  2:696755/1‑150 (MQ=255)                                                             cgTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGGTGAAGATGGGAATCAGCAAAGTTTTCCGGCCGGAGAAGCTAGCGTGGAACTCCCCCCAGGGGGTCTTCATCTTGCCC‑GGAAAAGTCCggg                                                                                   >  1:616536/1‑150 (MQ=255)                                                                ttATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGGAGGGGTTTAGCAAGGGTTTCTGGCCGAAGAAGGACGCGTGGAACTCCCCGGCGGGCGTCTTTATATCGCCT‑GGAAAAGGCCGGGGCAc                                                                               >  2:153295/1‑151 (MQ=255)                                                                          ggggCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAGGGATTCAGCAAGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCCGGCGGTCGTCTTGATATCGCCT‑GGAAAGGTCCGGGTCACCCGTtatata                                                                     <  1:546196/151‑1 (MQ=255)                                                                                    aaaCCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAGGGATTTAGCAAGGGTTGCTGGCCGAAGAAGGACGCCTGGGACTCCCCCGCGGGGGTCTTTGTATTGCCTGGGAAAGGCCCGGG‑CACCCGGTTTATATGACTGGccc                                                           >  2:353444/1‑151 (MQ=255)                                                                                       cccAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAGGGATTCAGCAAGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCCGGCGGTCGTCTTGATATCGCCT‑GGAAAGGTCCGGGTCACCCGTTATATATGACTGGCCcggc                                                        <  1:732968/151‑1 (MQ=255)                                                                                          aGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGGAAGGAATCACCAAGGGTTTCTGGCCGAAGAAGAACGCGTGGAACTCCCCCGCGGGTGGCTTGTTATTGCCC‑CGAAAAGTGCGGGGCGCCCCGTTTATTTTACTGGGCccgcgg                                                      >  1:749337/1‑150 (MQ=255)                                                                                            gCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAGGGATTCAGCAAGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCCGGCGGTCGTCTTGATATCGCCT‑GGAAAGGTCCGGGTCACCCGTTATATATGACTGGCCCGGCGGt                                                     <  2:489910/149‑1 (MQ=255)                                                                                                       cggcgCGTGTGCGGCGGTTGCAGTAGGGATTCAGCAAGGGTTGCTGGCCGCAGAAGTACGCGTGGAACTCCCCGGCGGGCGTCTTGATATCGCCC‑GGGAAGGGCCGGGTCACCCGTTATATATTACTTGCCCGGCGGGGCATGTCTacggc                                        >  1:258723/1‑149 (MQ=255)                                                                                                            cgTGTGCGGCGGTTGCAGTAGGGATTCAGCAAGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCCGGCGGTCGTCTTGATATCGCCT‑GGAAAGGTCCGGGTCACCCGTTATATATGACTGGCCCGGCGGTACATGTCTACGACGGAtt                                   <  2:117960/151‑1 (MQ=255)                                                                                                              tgtgCGGCGGTTGCAGTAGGGATTCAGCAAGGGTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCCGGCGGGCGGCTTTATATCGCCT‑GGAAAGGTCCGGGGCACCCGTTATATATGACTGGCCCGGCGGGACATGTCTACGACGGGttt                                  >  2:574428/1‑150 (MQ=255)                                                                                                                 gcggcgGTTGCAGTAGGGATTCAGCAAGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCCGGCGGTCGTCTTGATATCGCCT‑GGAAAGGTCCGGGTCACCCGTTATATATGACTGGCCCGGCGGTACATGTCTACGACGGATTTAtt                               <  1:666992/150‑1 (MQ=255)                                                                                                                            aGTAGGGATTCAGCAAGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCCGGCGGTCGTCTTGATATCGCCT‑GGAAAGGTCCGGGTCACCCGTTATATATGACTGGCCCGGCGGTACATGTCTACGACGGATTTATTCATCTATGAAGc                   <  2:552821/151‑1 (MQ=255)                                                                                                                            aGTAGGGATTCAGCAAGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCCGGCGGTCGTCTTGATATCGCCT‑GGAAAGGTCCGGGTCACCCGTTATATATGACTGGCCCGGCGGTACATGTCTACGACGGATTTATTCATCTATGAAGc                   <  2:705431/151‑1 (MQ=255)                                                                                                                             gTAGGGATTCAGCAAGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCCGGCGGTCGTCTTGATATCGCCT‑GGAAAGGTCCGGGTCACCCGTTATATATGACTGGCCCGGCGGTACATGTCTACGACGGATTTATTCATCTATGAAGCa                  <  2:333587/151‑1 (MQ=255)                                                                                                                               aGGGATTCAGCAAGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCCGGCGGTCGTCTTGATATCGCCT‑GGAAAGGTCCGGGTCACCCGTTATATATGACTGGCCCGGCGGTACATGTCTACGACGGATTTATTCATCTATGAATCAAc                >  2:181631/1‑151 (MQ=255)                                                                                                                                   aTTCAGCAAGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCCGGCGGTCGTCTTGATATCGCCT‑GGAAAGGTCCGGGTCACCCGTTATATATGACTGGCCCGGCGGTACATGTCTACGACGGATTTATTCATCTATGAAGCAACCAgg            >  1:381166/1‑151 (MQ=255)                                                                                                                                   aTTCAGCAAGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCCGGCGGTCGTCTTGATATCGCCT‑GGAAAGGTCCGGGTCACCCGTTATATATGACTGGCCCGGCGGTACATGTCTACGACGGATTTATTCATCTATGAAGCAACCAgg            >  1:324876/1‑151 (MQ=255)                                                                                                                                          aaGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCCGGCGGTCGTCTTGATATCGCCT‑GGAAAGGTCCGGGTCACCCGTTATATATGACTGGCCCGGCGGTACATGTCTACGACGGATTTATTCATCTATGAAGCAACCAGGGgaagaa     <  2:190182/151‑1 (MQ=255)                                                                                                                                              tttGCTGGCCGAAGAAGTACGCGTGGAACTCCCCGGCGGTCGTCTTGATATCGCCT‑GGAAAGGTCCGGGTCACCCGTTATATATGACTGGCCCGGCGGTACATGTCTACGACGGATTTATTCATCTATGAAGCAACCAGGGGCAGAACTg  >  1:551631/1‑150 (MQ=255)                                                                                                                                              |                                                                                                                                                       TCCGGAGCGCGCCAATATCGGTTTTATGCAAGTGGTTAAGCGCGAGCATATTCGTTTACGCGTTTATGAGCGTGGGGCAGGAGAAACCCAGGCCTGCGGCAGCGGCGCGTGTGCGGCGGTTGCAGTAGGGATTCAGCAAGGTTTGCTGGCCGAAGAAGTACGCGTGGAACTCCCCGGCGGTCGTCTTGATATCGCCT‑GGAAAGGTCCGGGTCACCCGTTATATATGACTGGCCCGGCGGTACATGTCTACGACGGATTTATTCATCTATGAAGCAACCAGGGGAAGAACTG  >  NC_000913/3995316‑3995606

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑