Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,580,640	0	C	T	45.3%	71.1 / 20.8	54	E275K (GAA→AAA)	hsdS	specificity determinant for hsdM and hsdR
Reads supporting (aligned to +/- strand):  ref base C (9/20);  new base T (24/0);  total (34/20)
Fisher's exact test for biased strand distribution p-value = 5.56e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGAGCTCGAATAAGTTTATCAGGATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTCACTTTCTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTAATTCAGTTAAGATAGATTCAAAATTTAACTT  >  NC_000913/4580492‑4580790                                                                                                                                                     |                                                                                                                                                        cGAGCTCGAATAAGTTTATCAGGATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTCACTTTCt                                                                                                                                                        <  2:697224/150‑1 (MQ=255)        gAATAAGTTTATCAGGATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTTTACCTTTTTAACAtt                                                                                                                                                 >  2:104107/1‑150 (MQ=255)            aaGTTTATCAGGATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTCACTTTCTGAACATTCTAGa                                                                                                                                            <  2:14384/151‑1 (MQ=255)                ttATCAGGATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTCACTTTCTGAACATTCTAGAAAc                                                                                                                                         <  1:196487/150‑1 (MQ=255)                 tATCAGGATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTCACTTTCTGAACATTCTAGAAAcc                                                                                                                                        <  1:613288/150‑1 (MQ=255)                       gATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTTTACTTTTTTAACATTCTTGAAACCCAata                                                                                                                                   >  2:649213/1‑149 (MQ=255)                            aGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTCACTTTCTGAACATTCTAGAAACCGAATATC‑Gtttt                                                                                                                           <  1:112099/151‑1 (MQ=255)                                aaTTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTCACTTTCTGAACATTCTAGAAACCGAATATC‑GTTTTGATc                                                                                                                       <  2:157679/151‑1 (MQ=255)                                aaTTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTCACTTTCTGAACATTCTAGAAACCGAATATC‑GTTTTGATc                                                                                                                       <  2:43408/151‑1 (MQ=255)                                   tttGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTCACTTTCTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTa                                                                                                                     <  2:852523/150‑1 (MQ=255)                                       aTGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTTACTTTTTTAACATTCTTGAAAACGAATATT‑GTTTTTATCTACAttg                                                                                                                >  2:198414/1‑149 (MQ=255)                                       aTGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTCACTTTCTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATgg                                                                                                                <  2:378949/151‑1 (MQ=255)                                        tgttgtAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTTAATTTCTTAAAATTCTATAAAACAAATATC‑Gttttttttt                                                                                                                      >  1:368222/1‑139 (MQ=255)                                                ttttttCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTTACTTTTTTTAAATTTTAAAAACAGAATATA‑GTTTTTTTTTACATGGGCAGCACGt                                                                                                       >  1:18937/1‑151 (MQ=255)                                                      cAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTCACTTTCTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGa                                                                                                  <  2:311469/150‑1 (MQ=255)                                                       aaTAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTTTACTTTTTGAAAAATTTTCAAACCACATATT‑GTTTTGTTTTACAAGGGCCGCACGTACaaaa                                                                                                 >  1:666744/1‑150 (MQ=255)                                                        aTAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTTTACTTTTTTAAAATTCTAAAAAAAGAATATT‑GTTTTTTTTTACATGGCCAGCACGTACAGaaa                                                                                                >  1:279005/1‑149 (MQ=255)                                                          aaCCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTCACTTTCTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTa                                                                                              <  1:978346/150‑1 (MQ=255)                                                           aCCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTTTACTTTTTGTAAATTTTAGAAAACGAATATA‑GTTTTTATTTACATAGCCCACACCCACAGaa                                                                                                 >  1:690417/1‑146 (MQ=255)                                                                     acCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGCTTAGGTCAATTTTTTAATATTCTTGAAAACGAATAAT‑CTTTTTTTCTACATCGCCACCAACCAAAGAACTaaaggcgaggttt                                                                                  >  1:254221/1‑140 (MQ=255)                                                                        aacaaATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTTTACTTTTTTAACATTCTTCAAACCCAATATC‑GTTTTTTTCTACATTGCCCGCACCCACAAAACTAATGCGTAGtttt                                                                                  >  1:64596/1‑148 (MQ=255)                                                                           aaaTTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTTTACTTTTTTAACATTCTAAAAAACGAATATT‑GTTTTTATTTTCATTGCCAGCACGTACAGAAATAATGAGTAGTATTgggt                                                                              >  1:965596/1‑147 (MQ=255)                                                                             aTTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTTCACTTTTTTAAAATTTTTAAAAACCAATATC‑GTTTTTATTTTCATTGCCCACACGTACAGAACTAATACGTAGTATTTGAttaac                                                                          >  1:1108351/1‑147 (MQ=255)                                                                                  aaaCTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTCACTTTCTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAaca                                                                      <  1:262089/150‑1 (MQ=255)                                                                                     cTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTCACTTTTTTAACAATCTAGAAAACGAATAAT‑GTTTTTTTTTACATGGCCAGCACGTACAGAAATAAAGCGGAATATTTGGTGACCAAcaacac                                                                  >  2:1162925/1‑151 (MQ=255)                                                                                        ccGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTTTAATTTTTTAAAAATCTAGAAAACGAAAATC‑GTTTTTTTCTTCATGGCCCGCACGTACAAAAACAATACGTAGTATTTGATGACCAAcaacac                                                                  >  1:619110/1‑148 (MQ=255)                                                                                        ccGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTCACTTTCTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACtt                                                                <  2:1066269/150‑1 (MQ=255)                                                                                           ttATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTATTTACTTTCTTGACAATTTAAAAAACGAAAATT‑GTTTTTATCTACATGGCCAGCACGTACAGAACAAATGTGGAGGATTTGGTGACCAACAACACttt                                                               >  2:1086848/1‑148 (MQ=255)                                                                                           ttATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTTACTTTTTTAAAATTCTTAAAAACCAATATT‑TTTTTGTTTTTCATTGACAGCCCGGACAAAAATAATGCGTAGTATTGGATGAACacaacaacctt                                                               >  1:6785/1‑138 (MQ=255)                                                                                            tataGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTTTACTTTTTTAACATTTTTTAAAACCAATATT‑GTTTTTATTTACATGGCCAGCACCTACAGAACTAATGCGTAGTATTTGGTGACCAACACCACCTTTAtt                                                           >  2:547995/1‑151 (MQ=255)                                                                                            tataGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTATTTCCTTTTTTTACAATCTAAAAAACGAAAAAT‑GTTTTTATTTTCATTGCCAGCACGGACAAAAATAATGGGTTGTATTGGGTGAACAACACCACCTTTAtt                                                           >  2:1138077/1‑151 (MQ=255)                                                                                             ataGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTCACTTTCTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCAttt                                                          <  2:757257/151‑1 (MQ=255)                                                                                                gCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGCTTTGTTTACTTTTTGCAAATTTTCTAAAACGCAAATT‑GTTTTTTTTTTCACAGCCAACACGGACAAAACTAAAGCGGAGTATTTGGTGATCAAACCAACTTTTAttt                                                          >  2:903579/1‑148 (MQ=255)                                                                                                 cGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTCACTTTCTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCt                                                      <  2:30513/151‑1 (MQ=255)                                                                                                  gAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTTTACTTTTTTAAAATTCTAAAAAAACAATATT‑GTTTTGTTTTACATAGCCAGCACCTACAGAAAAAAAGTGGAGTATTGGATGTCCAAAAACACATTTCTTTTGCtt                                                     >  1:517091/1‑151 (MQ=255)                                                                                                     taaataaaAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTTTTCTTTTTTAAAATTCTATAAAACAAATATC‑GTTTTTTTCTACATTGCCCCCACGTACAAAAATAATACGGAATATTGGATGAACAACACCCCCTTTATTTTGtttttt                                                  >  1:624271/1‑149 (MQ=255)                                                                                                      aaataaaAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTCACTTTCTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTtgat                                                 <  1:49864/151‑1 (MQ=255)                                                                                                       aataaaAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTTTACTTTTTTAACATTCTAGAAAACGAATATC‑GTTTTTATCTACATGGCCAGCACGTACAGAAATAATGCGGAGGATTGGATGACCAACACCACTTTTATTTTGCtttttt                                                 >  2:28970/1‑147 (MQ=255)                                                                                                         taaaAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTTACTTTTTGAAAATTCTAGAAAACGAATAAA‑GTTTTTTTCTACATGGCCCGCACGTAAAGAAATAATGCGTAGTATTGGGTGACCAAAACCACCTTTATTTGGGttt                                                    >  2:1128909/1‑145 (MQ=255)                                                                                                            aaGATCTCCATCTTGTAATTTGTGGCGGTGTTGTTCAAATTTTGAAAAATCTTGAAAAAAAAATTCGGTTTTTAT‑TAAATGGCCCACACATACAAAAAAAATGAGAAGGATTTGTTTATCAACACCACCTTTCTTTTGCttt                                                    >  1:136454/1‑142 (MQ=255)                                                                                                             aGATCTCCATCTTGTAATTTGTGGCGGTTTAATTTACTCTTTGAATAATTTAGTAAACGAAAATA‑ATTTTTATTTTCCACGTCAACCCCTACAAAACTAATGTGTAGTAATTGATGACCAAAACCACATTTATTTTGATTTTATGaaata                                           >  2:505412/1‑148 (MQ=255)                                                                                                                   ccATCTTGTAATTTGTGGCGGTTTAGTTCACTTTCTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACGCCACTTTCATTTGGCTTTGATGAAAGAcc                                         <  1:90325/146‑1 (MQ=255)                                                                                                                    cATCTTGTAATTTGTGGCGGTTTAGTTCACTTTCTGAACATTCTAGAATCCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCa                                        <  1:765969/146‑1 (MQ=255)                                                                                                                      tCTTGTAATTTGTGGCGGTTTTGTTTCCTTTTTGAACATTCTTTAAAACACAAATT‑GTTTTTTTTTTAATGGGCAACACGCAAAGAAACAAAACGTAGTATTTGATGAACAACACCACTTTTATTTTGTTTTTTTGaaaaaacaat                                      >  1:1285044/1‑139 (MQ=255)                                                                                                                         tGTAATTTGTGGCGGTTTAGTTCACTTTCTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTAAt                               <  2:1186898/150‑1 (MQ=255)                                                                                                                         tGTAATTTGTGGCGGTTTAGTTCACTTTCTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTAAt                               <  2:845265/150‑1 (MQ=255)                                                                                                                                    gCGGTTTAGTTCACTTTCTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTAATTCAGTTAagat                    >  2:929329/1‑150 (MQ=255)                                                                                                                                    gCGGTTTAGTTCACTTTATGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTAAGTAATTCAGTTAagat                    >  1:148434/1‑150 (MQ=255)                                                                                                                                        tttAGTTCACTTTCTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTAATTCAGTTAAGATAGAtt               >  1:77101/1‑151 (MQ=255)                                                                                                                                           aGTTCACTTTCTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTAATTCAGTTAAGATAGATTCa             >  1:262890/1‑150 (MQ=255)                                                                                                                                             ttCACTTTCTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTAATTCAGTTAAGATAGATTCaaa           >  2:623347/1‑150 (MQ=255)                                                                                                                                               cACTTTCTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTAATTCAGTTAAGATAGATTCAAAAtt        >  2:1258201/1‑151 (MQ=255)                                                                                                                                                  tttCTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTAATTCAGTTAAGATAGATTCAAAATTTa      >  1:966542/1‑150 (MQ=255)                                                                                                                                                   ttCTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTAATTCAGTTAAGATAGATTCAAAATTTAAc    >  1:574731/1‑151 (MQ=255)                                                                                                                                                     cTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTAATTCAGTTAAGATAGATTCAAAATTTAActt  >  2:794677/1‑151 (MQ=255)                                                                                                                                                     cTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTAATTCAGTTAAGATAGATTCAAAATTTAActt  >  2:567057/1‑151 (MQ=255)                                                                                                                                                     |                                                                                                                                                        CGAGCTCGAATAAGTTTATCAGGATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTCACTTTCTGAACATTCTAGAAACCGAATATC‑GTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTAATTCAGTTAAGATAGATTCAAAATTTAACTT  >  NC_000913/4580492‑4580790

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑