Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	231,694	0	C	T	42.2%	60.6 / 17.2	46	F191F (TTC→TTT)	yafD	endo/exonuclease/phosphatase family protein
Reads supporting (aligned to +/- strand):  ref base C (4/22);  new base T (19/0);  total (24/22)
Fisher's exact test for biased strand distribution p-value = 4.26e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCCGCCTGTTGATGGTGGTTAATATACACGCCGTCAACTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATGCCTGGAGCCGTA‑GAAGGATGAACGCGTTATATCGCTTTGCGC‑GGGAAATGTCGCTGCG‑CCAGGTGCGTTTTACCGATGATCAGCGCCGTCGGGCGTTTGGTCGCCCGCTCGATTTTGTTTTCTACCGTGGTCTGAACGTCAGTG  >  NC_000913/231561‑231842                                                                                                                                        |                                                                                                                                                        cccGCCTGTTGATGGTGGTTAATATACACGCCGTCAACTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATGCCTGGAGCCGTa                                                                                                                                         <  1:976417/150‑1 (MQ=255) cccGCCTGTTGATGGTGGTTAATATACACGCCGTCAACTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATGCCTGGAGCCGTa                                                                                                                                         <  2:193875/150‑1 (MQ=255) cccGCCTGTTGATGGTGGTTAATATACACGCCGTCAACTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATGCCTGGAGCCGTA‑g                                                                                                                                       <  1:712383/151‑1 (MQ=255) cccGCCTGTTGATGGTGGTTAATATACACGCCGTCAACTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATGCCTGGAGCCGTA‑g                                                                                                                                       <  1:916080/151‑1 (MQ=255)     ccTGTTGATGGTGGTTAATTTACACGCCGTCAACTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCGCAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATGCCTGGAGCCGTC‑GAAg                                                                                                                                    <  2:406993/150‑1 (MQ=255)     ccTGTTGATGGTGGTTAATATACACGCCGTCAACTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGG‑G‑AATTTAATGCCCGGGGGCGCA‑Gaa                                                                                                                                     >  2:248108/1‑149 (MQ=255)     ccTGTTGATGGTGGTTAATATACACGCCGTCAACTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATGCCTGGAGCCGTA‑GAAgg                                                                                                                                   <  1:954027/151‑1 (MQ=255)        gTTGATGGTGGTTAATATACACGCCGTCAACTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATGCCTGGAGCCGTA‑GAAGGa                                                                                                                                  <  2:489987/149‑1 (MQ=255)           gATGGTGGTTAATATACACGCCGTCAACTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATGCCTGGAGCCGTA‑GAAGGATGAAc                                                                                                                             <  2:868000/151‑1 (MQ=255)             tggtggTTAATATACACGCCGTCAACTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGG‑G‑GTTTCAATGCCCGGAGGCGGaggaaggagaaagg                                                                                                                            >  2:646184/1‑145 (MQ=255)                 ggtTAATATACACGCCGTCAACTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATGCCTGGAGCCGTA‑GAAGGATGAACGCGtt                                                                                                                        <  1:198970/150‑1 (MQ=255)                 ggtTAATATACACGCCGTCAACTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATGCCTGGAGCCGTA‑GAAGGATGAACGCGTta                                                                                                                       <  2:745930/151‑1 (MQ=255)                    tAATATACACGCCGTCAACTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGG‑G‑ATTTTAATTCCTGGGGGCGTA‑GAAGGATGAAAGCGTtat                                                                                                                      >  1:1002879/1‑149 (MQ=255)                      atatACACGCCGTCAACTTCAGTCCGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTTAAAGCCCTGGGGCGGA‑GAAGGATGAACGCGTtat                                                                                                                      >  2:963166/1‑147 (MQ=255)                             cGCCGTCAACTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGG‑G‑AATTTAATTCCCGGGGCCGCA‑GAAGGGAGGAAGGGGTATATTGCttt                                                                                                              >  2:974566/1‑148 (MQ=255)                                cGTCAACTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTTCATTCCTCGGGCCGGA‑GAAAGATGAAAACGGTATTTTGCttt                                                                                                              >  2:285980/1‑145 (MQ=255)                                cGTCAACTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATGCCTGGAGCCGTA‑GAAGGATGAACGCGTTATATCGCTTTGCGC‑gg                                                                                                       <  2:44740/151‑1 (MQ=255)                                cGTCAACTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATGCCTGGAGCCGTA‑GAAGGATGAACGCGTTATATCGCTTTGCGC‑gg                                                                                                       <  2:370488/151‑1 (MQ=255)                                  tCAACTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑GTTTCAAAACCCGGGGCCGGA‑GAAGGAAGAAACCGTTATATACCTTTGCGg‑ggg                                                                                                      >  1:786360/1‑150 (MQ=255)                                  tCAACTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTTAATTCCTGGAGCCGGG‑GAAGGATGAACGCGGTATATTGCTTTGCGC‑gggg                                                                                                     >  2:29595/1‑150 (MQ=255)                                      cTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGAGG‑ATTTAATTTCTTGGGGCCG‑A‑GAAGGGAGAAAGCGGGTTATTGCCTTTCGC‑gggg                                                                                                     >  2:635699/1‑146 (MQ=255)                                          aGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATGACTGGAGGCCGA‑GAAGGGTGAAAGCGGTATATCGCTTTTCGC‑GGGGAATGt                                                                                                >  1:795674/1‑148 (MQ=255)                                          aGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATCCCTGGAGCCGGA‑GAAGGGTGAACGCGTTTTTTCGCTTTTCGC‑GGGGAATGt                                                                                                >  1:913187/1‑148 (MQ=255)                                                  cGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATGCCTGGAGCCGTA‑GAAGGATGAACGCGTTATATCGCTTTGCGC‑GGGAAATGTCGCTGCG‑CCAg                                                                                    <  2:777595/151‑1 (MQ=255)                                                   gTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATGCCTGGAGCCGTA‑GAAGGATGAACGCGTTATATCGCTTTGCGC‑GGGAAATGTCGCTGCG‑CCAgg                                                                                   <  2:676949/151‑1 (MQ=255)                                                     ggATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGG‑GAATTTTAAACCCTGG‑GGCGGA‑GAAGGATGGACGCGGTATATTGCTTTTCGG‑GGGGAAAGGCGCCGCG‑GCAggg                                                                                  >  2:945415/1‑149 (MQ=255)                                                            tataGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGG‑G‑GTTTTAAAGGCTGGGGCCGTA‑GAAGGATGAACGCCGTATATAGCTTTTTGG‑GGGGAATGTCGCCGCG‑CCGGGGGCGttttt                                                                          >  2:242998/1‑150 (MQ=255)                                                               aGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTTAATGCCTGGAGCCGTA‑GAAGGATGAAAGCGTTATATCGCTTTGCGC‑GGGGAAAGTCGCTGCG‑CCCGGGGCGTTTTTcc                                                                        >  1:604387/1‑150 (MQ=255)                                                               aGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATGCCTGGAGCCGTA‑GAAGGATGAACGCGTTATATCGCTTTGCGC‑GGGAAATGTCGCTGCG‑CCAGGTGCGTTTTACCg                                                                       <  2:403606/151‑1 (MQ=255)                                                                 tAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTTAATTCCCGGAGCCGGA‑GAAGGATGAAAGCGGTATATCGCTTTTCGC‑GGGGAAAGTCGCTGCG‑CCCGGGGCGGTTTTcc                                                                        >  1:77437/1‑148 (MQ=255)                                                                  aaGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑AGTTTAATGCCCGGAGCCGGA‑GAAGGATGAACGCGTTATATTGCTTTTCGC‑GGGGAATGGTGCCGCG‑CCCGGGGGGGTTTTCCgatg                                                                    >  2:226874/1‑151 (MQ=255)                                                                  aaGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGATCATTATGGCGGGA‑G‑ATTTTAATGCCTGGAGGCGTA‑GAAGGGTGAAAGCGTTATATCGCTTTTCGC‑GGGGAAAGTCGCTGCG‑CCCGGGGGGGTTTTCCgat                                                                     >  1:196762/1‑150 (MQ=255)                                                                         tACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATGCCTGGAGCCGTA‑GAAGGATGAACGCGTTATATCGCTTTGCGC‑GGGAAATGTCGCTGCG‑CCAGGTGCGTTTTACCGATGATCAgc                                                              <  2:82689/150‑1 (MQ=255)                                                                          aCTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATGCCTGGAGCCGTA‑GAAGGATGAACGCGTTATATCGCTTTGCGC‑GGGAAATGTCGCTGCG‑CCAGGTGCGTTTTACCGATGATCAgcg                                                             <  2:672904/150‑1 (MQ=255)                                                                            ttCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTTAATGCCTGGGGCCGGA‑GAAGGGTGAACGCGGTATATCGCTTTGCGC‑GGGGAAAGTCGCTGCG‑CCAGGTGGGGTTTACCGATGATTAGCGcc                                                           >  1:446811/1‑150 (MQ=255)                                                                                  ttGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGG‑G‑GTTTTAATGCCTGGAGCCGGA‑GAAGGGAGAAAGCGGTATATCGCTTTTCGC‑GGGGAAAGTTGCTGCGCCCGGGGGGGTTTTTCCG‑TGATTAGCGCCGTCggg                                                     >  2:1465/1‑150 (MQ=255)                                                                                         tCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTTAATTCCTGGGGCCGGA‑GAAGGGTGAAAGCGGTTTATTTCTTTGCGCGGGGAAATG‑CGCCGCG‑CCCGGTGGGGTTTTACGGTGATTCGCGCCGGCgggggggt                                                >  2:562114/1‑143 (MQ=255)                                                                                               aGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATGCCTGGAGCCGTA‑GAAGGATGAACGCGTTATATCGCTTTGCGC‑GGGAAATGTCGCTGCG‑CCAGGTGCGTTTTACCGATGATCAGCGCCGTCGGGCGTTTGGTCGccc                                        <  1:885309/150‑1 (MQ=255)                                                                                                      cacaGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTTAATGCCTGGAGGCGGA‑GAAGGGTGAACGCGGTTTATTGCTTTTCGC‑GGGGAATGTCGCTGCG‑CCCGGGGGGGTTTTTCGGTGATCAGCGCCGTCGGGGGGTTGGTCGGCCGCCCGGtt                                >  1:573126/1‑151 (MQ=255)                                                                                                       acaGCGGCCCGGTCATTATGGCGGGA‑G‑AATTTAATGCCTGGAGCCGGA‑GAAGGATGAACGCGGTATATCGCTTTTCGC‑GGGGAATGGCGCTGCG‑CCAGGGGGGGTTTACCCATGATCAGCGCCGTCGGGGGGTTGGGTGCCCGCCCGGttt                               >  1:812438/1‑151 (MQ=255)                                                                                                          gCGGCCCGGTCATTATGGCGGGA‑G‑ATTTTTATGGCTGGGGCCGTA‑GAAGGATGAACGCGGTATATTGCTTTTCGC‑GGGGAATGTCGCTGCG‑CCCGGGGGGGTTTTACGATGATCAGCGCCGTCGGGGGGTTTGGCGCCCGCCCGGTTTTGt                            >  1:805067/1‑151 (MQ=255)                                                                                                             gCCCGGTCATTATGGCGGGA‑G‑ATTTTTATGCCTTGAGCCGGA‑GAAGGGTGGACGCGTTATATTGCCTTGCGG‑GGGGAATGTTGCCGCG‑GCCGGTGGGGTTTTTCGACGAGTAGCGCCGTCGGGGCGTTGGTGCCCCCCCCGACtttttttt                         >  2:840385/1‑151 (MQ=255)                                                                                                                       tATGGCGGGA‑G‑ATTTCAATGCCTGGAGCCGTA‑GAAGGATGAACGCGTTATATCGCTTTGCGC‑GGGAAATGTCGCTGCG‑CCAGGTGCGTTTTACCGATGATCAGCGCCGTCGGGCGTTTGGTCGCCCGCTCGATTTTGTTTTCTACCGTgg                <  1:72621/150‑1 (MQ=255)                                                                                                                          ggCGGGA‑G‑ATTTCAATGCCTGGAGCCGTA‑GAAGGATGAACGCGTTATATCGCTTTGCGC‑GGGAAATGTCGCTGCG‑CCAGGTGCGTTTTACCGATGATCAGCGCCGTCGGGCGTTTGGTCGCCCGCTCGATTTTGTTTTCTACCGTGGTCt             <  1:820870/150‑1 (MQ=255)                                                                                                                           gCGGGA‑G‑ATTTCAATGCCTGGAGCCGTA‑GAAGGATGAACGCGTTATATCGCTTTGCGC‑GGGAAATGTCGCTGCG‑CCAGGTGCGTTTTACCGATGATCAGCGCCGTCGGGCGTTTGGTCGCCCGCTCGATTTTGTTTTCTACCGTGGTCTGa           <  2:388100/151‑1 (MQ=255)                                                                                                                                    aTTTCAATGCCTGGAGCCGTA‑GAAGGATGAACGCGTTATATCGCTTTGCGC‑GGGAAATGTCGCTGCG‑CCAGGTGCGTTTTACCGATGATCAGCGCCGTCGGGCGTTTGGTCGCCCGCTCGATTTTGTTTTCTACCGTGGTCTGAACGTCAg    <  2:786154/151‑1 (MQ=255)                                                                                                                                       acAATGCCTGGAGCCGTA‑GAAGGATGAACGCGTTATATCGCTTTGCGC‑GGGAAATGTCGCTGCG‑CCAGGTGCGTTTTACCGATGATCAGCGCCGTCGGGCGTTTGGTCGCCCGCTCGATTTTGTTTTCTACCGTGGTCTGAACGTCAGTg  >  1:625551/2‑150 (MQ=255)                                                                                                                                        |                                                                                                                                                        CCCGCCTGTTGATGGTGGTTAATATACACGCCGTCAACTTCAGTCTGGGCGTGGATGTCTATAGTAAGCAGTTACTTCCTATTGGCGATCAGATAGCTCACCACAGCGGCCCGGTCATTATGGCGGGA‑G‑ATTTCAATGCCTGGAGCCGTA‑GAAGGATGAACGCGTTATATCGCTTTGCGC‑GGGAAATGTCGCTGCG‑CCAGGTGCGTTTTACCGATGATCAGCGCCGTCGGGCGTTTGGTCGCCCGCTCGATTTTGTTTTCTACCGTGGTCTGAACGTCAGTG  >  NC_000913/231561‑231842

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: ‑