Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	298,960	0	A	C	42.6%	75.6 / 25.2	55	Y659D (TAT→GAT)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
Reads supporting (aligned to +/- strand):  ref base A (23/8);  new base C (0/23);  total (23/32)
Fisher's exact test for biased strand distribution p-value = 7.37e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTTATACACCGCGTTGGCGATAGCCGCGCTCACGCCGCACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCATCGGGGAGGATATGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGATTCAGGATGCGTCCTGCAGCACACAC  >  NC_000913/298810‑299107                                                                                                                                                        |                                                                                                                                                    cGTTATACACCGCGTTGGCGATAGCCGCGCTCACGCCGCACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCATCGGGGAGGATATGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATa                                                                                                                                                     <  2:384266/151‑1 (MQ=255)  gTTATACACCGCGTTGGCGATAGCCGCGCTCACGCCGCACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCATCGGGGAGGATATGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATAc                                                                                                                                                    <  2:520772/151‑1 (MQ=255)     ataCACCGCGTTGGCGATAGCCGCGCTCACGCCGCACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCATCGGGGAGGATATGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATAcccc                                                                                                                                                 <  2:393793/151‑1 (MQ=255)       acacCGCGTTGGCGATAGCCGCGCTCACGCCGCACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCATCGGGGAGGATATGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCg                                                                                                                                                <  2:571983/150‑1 (MQ=255)       acacCGCGTTGGCGATAGCCGCGCTCACGCCGCACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCATCGGGGAGGATATGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGc                                                                                                                                               <  2:249870/151‑1 (MQ=255)          ccGCGTTGGCGATAGCCGCGCTCACGCCGCACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCATCGGGGAGGATATGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCat                                                                                                                                            >  2:941644/1‑151 (MQ=255)           cgcgTTGGCGATAGCCGCGCTCACGCCGCACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCATCGGGGAGGATATGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCat                                                                                                                                            >  1:998549/1‑150 (MQ=255)             cgTTGGCGATAGCCGCGCTCACGCCGCACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCATCGGGGAGGATATGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCatat                                                                                                                                          <  2:759705/150‑1 (MQ=255)             cgTTGGCGATAGCCGCGCTCACGCCGCACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCATCGGGGAGGATATGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATc                                                                                                                                         >  1:747921/1‑151 (MQ=255)                  gCGATAGCCGCGCTCACGCCGCACAGCCCCAGCTCCCCGACCCCTTTGG‑CCTTCATCGGGGAGGATAGGGGGTCGGTATCACCCAGAAAAATCCCCTCCTGTTTTGGGATATCCGCATGAACCGGCCCCTCATCCCCCGCCATATCGTGAt                                                                                                                                    <  1:324300/151‑1 (MQ=255)                    gATAGCCGCGCTCACGCCGCACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCATCGGGGAGGATATGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGAtt                                                                                                                                   >  1:656406/1‑150 (MQ=255)                         ccGCGCTCACGCCGCACAGCCCCATCCCCCCGACCCTTGTGC‑CCTTCATCGGGGAGGATATGGGGGCGGTAACTTCCAGAAAAACCCCCCCCTTTTTGGGTATATCCGTATGACCCGGCACCTCATACCCCGCCATATCGTGATTAAc                                                                                                                                <  2:1072980/148‑1 (MQ=255)                          cgcgCTCACGCCGCACGGGCCCAGCCCCCCGACACCTTGGC‑CCTTCATCGGGGAGGATATGGGGTCGGTATCACCCAGAAAAATCCCCCCCTTTTTTGGAATATCCGCATGAACCGGCCCCTCATCCCCCGCCATATCGTGATTAAc                                                                                                                                <  2:873414/147‑1 (MQ=255)                                      gcACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCATCGGGGAGGATATGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACgg                                                                                                                >  1:1255672/1‑151 (MQ=255)                                       cacaGGCCCCGCCCCCCACCACCTTTGC‑CCTTCATGGGGGAGGATGTGGGGTGGTTATCACCAAGGAAAACCCCCCCCTGTTTGGGGATATCCGCAGGACCCGGCACCTCATGCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACgg                                                                                                                <  2:112707/150‑1 (MQ=255)                                         caGGCCCAGCTCACCGACACCTTTGG‑CCCTCATCGGGGAGGATATGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTc                                                                                                              >  1:277690/1‑150 (MQ=255)                                           ggCCCAGCTCCCCGACCCCTTTGG‑CCTTCATCGGGGAGGATATGGGGTCGGTATCACCCAGGAAAATCCCCTCCTTTTTTGGGATACCCGAATGACCCGGCCCCTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACgg                                                                                                                <  2:405318/146‑1 (MQ=255)                                              ccAGCTCACCGACACCTTTGG‑CCTTCATCGGGGAGGATATGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCAc                                                                                                        >  2:126458/1‑151 (MQ=255)                                                   tCACCGACACCTTTGG‑CCTTCATCGGGGAGGATATGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGcc                                                                                                    >  1:1033016/1‑150 (MQ=255)                                                     aCCGACACCTTTGG‑CCTTCATCGGGGAGGATATGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGc                                                                                                 >  1:529126/1‑151 (MQ=255)                                                      ccGACCCCTTTGG‑CCTTCATGGGGGAGGATATGGGGTCGTTATCACCCAGAAAAACCCCCTCCTGTTTGGGGATACCCGCAGAACCCGGCCCCTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCa                                                                                                   <  1:594673/148‑1 (MQ=255)                                                       ccgccccTTTGGCCCTTCATGGGGGAGAATAGGGGGTGGGTATCACCCAGAAAAATCCCCTCTTGTTTGGGAATACCCGAAGAACCCGCCCCCTCACCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCa                                                                                                   <  2:983188/143‑1 (MQ=255)                                                       cGACACCTTTGG‑CCTTCATCGGGGAGGATATGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGctc                                                                                               >  1:464929/1‑151 (MQ=255)                                                              tttGG‑CCTTCATCGGGGAGGATATGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATc                                                                                        >  1:1136066/1‑151 (MQ=255)                                                                 gg‑CCTTCATCGGGGAGGATATGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGt                                                                                     >  2:1218321/1‑151 (MQ=255)                                                                       tCATCGGGGAGGATATGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCcgc                                                                                >  1:201351/1‑151 (MQ=255)                                                                            ggggAGTTTAGGGGGTGGGTATCACCAAGAAAAACCCCCCCCTTTTTGGGAATACCCGAAGAACCCGCCCCCTCACCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCcg                                                                                 <  2:169783/145‑1 (MQ=255)                                                                             gggAGGATAGGGGGTCGTTATCACCCAGAAAAATCCCCTCCTGTTTGGGGATATCCGCAGGACCCGGCCCCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCgcccat                                                                          <  1:1070128/151‑1 (MQ=255)                                                                                     atGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCgcccatgcccat                                                                    >  1:1215735/1‑149 (MQ=255)                                                                                      gggggTCGTTACCACCCAGAAAAACCCCCCCCTGTTGTGGAATACCCGCATCACCCGCCACCTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGt                                                                 <  2:441057/150‑1 (MQ=255)                                                                                            cGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTgc                                                           >  1:787363/1‑151 (MQ=255)                                                                                                 tcaccCAGGAAAACCCCCCCCTGTTTGGGGATACCCCCATGAGCCGGCCCCTAATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTgcgc                                                         <  1:759685/148‑1 (MQ=255)                                                                                                     ccAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGAc                                                  >  2:1263279/1‑151 (MQ=255)                                                                                                           aaaccccctcctTTTTTGGGATACCCGCAGGACCCGCCCCCTCACCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCt                                            <  2:464925/145‑1 (MQ=255)                                                                                                           aaaTCCCCTCCTTTTTGGGAATACCCGGAGGACCCGCCCCCTCACCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCt                                            <  2:701379/151‑1 (MQ=255)                                                                                                            aaTCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTg                                           >  1:946285/1‑151 (MQ=255)                                                                                                               ccccccctGTTTGGGGATACCCGCATGACCCGGCCCCTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTgcg                                         <  1:416940/145‑1 (MQ=255)                                                                                                                ccctcttTTTTGGGGATTCCCGCATAACCCGCCCCCTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTgcgcg                                       <  2:975764/150‑1 (MQ=255)                                                                                                                 ccccctTTTTTGGAATACCCGCATGACCCGCCCCCTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTgcgcgc                                      <  1:41466/148‑1 (MQ=255)                                                                                                                      tGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGttt                                 >  2:472792/1‑151 (MQ=255)                                                                                                                         tttGGGATACCCCAAGTACCCGCCCCCCCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTc                               <  1:42782/150‑1 (MQ=255)                                                                                                                            gggATACCCGATGGACCCGCCCCCTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGAt                           <  1:1141582/151‑1 (MQ=255)                                                                                                                              gATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGATTc                         >  2:3509/1‑151 (MQ=255)                                                                                                                                tatCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGATTc                         >  1:693785/1‑149 (MQ=255)                                                                                                                                 acccGCATGACCCGGCCCCTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGATTCAg                       <  1:1183810/148‑1 (MQ=255)                                                                                                                                  ccctaataacccGGCCCCTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGATTCAGGa                     <  2:1071063/141‑1 (MQ=255)                                                                                                                                  cccGAATGAACCGCCCCCCCCCACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCCCCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGATTCAgg                      <  2:779179/149‑1 (MQ=255)                                                                                                                                   ccGCATGACCCGCCCCCCCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGATTCa                        <  1:761911/147‑1 (MQ=255)                                                                                                                                    cgcagaacccgcccccTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGATTCAGGATg                   <  1:1165984/137‑1 (MQ=255)                                                                                                                                       aTGAACCGCCCCCTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGATTCAGGATGc                  <  1:112553/149‑1 (MQ=255)                                                                                                                                          acccGGCCCCTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGATTCAGGATGCGTcc              <  1:1025279/148‑1 (MQ=255)                                                                                                                                          aaCCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGATTCAGGATGCGTCCt             >  2:872587/1‑151 (MQ=255)                                                                                                                                            ccGGCACCTCACCCCCCGCCATATCGTGACTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGATTCAGGATGCGTCCTg            <  1:516729/150‑1 (MQ=255)                                                                                                                                              gcccccTCATCCCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGATTCAGGATGCGTCCTgcag         <  1:784938/147‑1 (MQ=255)                                                                                                                                                   cTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGATTCAGGATGCGTCCTGCAGcacac    >  2:1239695/1‑151 (MQ=255)                                                                                                                                                      aTACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGATTCAGGATGCGTCCTGCAGcacacac  >  2:825379/1‑150 (MQ=255)                                                                                                                                                        |                                                                                                                                                    CGTTATACACCGCGTTGGCGATAGCCGCGCTCACGCCGCACAGGCCCAGCTCACCGACACCTTTGG‑CCTTCATCGGGGAGGATATGGGGTCGGTATCATCCAGGAAAATCACCTCCTGTTTTGGGATATCCGCATGAACCGGCACCTCATACCCCGCCATATCGTGATTAACGAAGTAGCCCAAACGGTCATCCACCGCCAGCTCCTCCATCAGTGCCGCGCCCATGCCCATAGTCATTGCGCCAATGACCTGGCTGCGCGCAGTTTTCGGATTCAGGATGCGTCCTGCAGCACACAC  >  NC_000913/298810‑299107

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑