Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,112,578	0	T	G	39.6%	87.3 / 10.2	49	G88G (GGT→GGG)	yiiR	DUF805 family putative inner membrane protein
Reads supporting (aligned to +/- strand):  ref base T (3/26);  new base G (19/0);  total (23/26)
Fisher's exact test for biased strand distribution p-value = 1.33e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAGAATCTACTCGATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAGATACTCAGGATGTGAAGTA  >  NC_000913/4112429‑4112727                                                                                                                                                       |                                                                                                                                                         aaGAATCTACTCGATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGt                                                                                                                                                          <  1:472696/150‑1 (MQ=255) aaGAATCTACTCGATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTa                                                                                                                                                         <  1:524922/151‑1 (MQ=255)  aGAATCTACTCGATATTCAGACCGCGGCGTTTTGCCCTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCGTGCATGATCGCGGACGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGATTCTGGC‑AGGt                                                                                                                                                          <  2:147087/149‑1 (MQ=255)       cTACTCGATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAAAT‑ggg                                                                                                                                                  >  2:801722/1‑151 (MQ=255)         aCTCGATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑g                                                                                                                                                    <  2:62892/147‑1 (MQ=255)             gATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAACT‑GGGGG‑Gttt                                                                                                                                           >  1:709039/1‑151 (MQ=255)                atTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTa                                                                                                                                         <  2:562000/150‑1 (MQ=255)                  tCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGGTGCTGCTGGCGGGGAAACT‑GGGcacttt                                                                                                                                            >  1:366320/1‑142 (MQ=255)                  tCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTAcc                                                                                                                                       <  1:619658/150‑1 (MQ=255)                    aGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAAATGGGGGG‑TTTTTACCgg                                                                                                                                     >  1:509783/1‑151 (MQ=255)                           ggcgTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑gg                                                                                                                            <  1:128795/151‑1 (MQ=255)                            gcgTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGc                                                                                                                           <  1:359194/151‑1 (MQ=255)                             cgTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCa                                                                                                                          <  1:203964/151‑1 (MQ=255)                             cgTTTTGCCTTGCGTGCTTGCTCTCGCCAACAGCGGCAGTAACTGTTAAGAGCTTGCATGATCGCGCGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAACA‑GGGCG‑Gttttgtaggggtggtggcc                                                                                                                           >  2:12847/1‑136 (MQ=255)                                          gtgCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAACT‑GGGGG‑GTTTTTCCGGGGGTCT‑GGCAATGgggggggggg                                                                                                             >  1:226427/1‑151 (MQ=255)                                            gcttgctCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCAATGGGCGGTGGGGc                                                                                                            <  2:241587/150‑1 (MQ=255)                                             cttgctCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGGTGCTGCTGGC‑GGGGGAAA‑GGGCG‑GTTTTTCCCGGGGTTT‑GGGGATGGGCGGGGGGGCg                                                                                                           >  2:43065/1‑150 (MQ=255)                                                     ggCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCAATGGGCGGTGGGGCGTTTTGTccc                                                                                                  <  1:790464/151‑1 (MQ=255)                                                        cAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCAATGGGCGGTGGGGCGTTTTGTCCCGAc                                                                                               <  2:490911/151‑1 (MQ=255)                                                           cAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCAATGGGCGGTGGGGCGTTTTGTCCCGACGtt                                                                                            <  1:34982/151‑1 (MQ=255)                                                              cGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGAGTGTGGCGTTGATGTTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTg                                                                                           <  2:69431/149‑1 (MQ=255)                                                                 cAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCt                                                                                      <  1:77011/151‑1 (MQ=255)                                                                   gTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGGTGCTGCTGGC‑GGGGTAAT‑GGGGG‑GTTTTTCCGGGGGGGT‑TGGAATGGGGCGGGGGGCGGTTTTGCCCGCAGTTGActct                                                                                      >  2:189543/1‑149 (MQ=255)                                                                      aCTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAACC‑GGGCG‑ATTTTACCCGGGGTCT‑GGCAAAGGGGGGGGGGGGGGTTTGTGCCGGCGtttgttttgggg                                                                                  >  2:889259/1‑140 (MQ=255)                                                                      aCTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAAAT‑GGGCG‑GTTTTTCCGGGGGTCT‑TGGAATGGGGGGGGGGGGGGTTTTTCCCGCCGGTGATTCTgg                                                                                    >  1:721215/1‑148 (MQ=255)                                                                       cTGTTAAGCGCTTGCATGCTCGCGGGCGCTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAACT‑GGGGGCATTTTCCCGGG‑GTCT‑GGCAAAAGGGGGGGGGGGGTTTTTTACCGACGGTTATTTTggg                                                                                   >  2:470792/1‑147 (MQ=255)                                                                         gTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGtgatg                                                                               <  2:318599/150‑1 (MQ=255)                                                                           tAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTgatgat                                                                             <  1:456869/150‑1 (MQ=255)                                                                           tAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTgatgat                                                                             <  1:877637/150‑1 (MQ=255)                                                                                gcTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAACT‑GGGCG‑ATTTTTCCGGGGGGCT‑GGCAATGGGGGGGGGGGGGGTTTTTTCCGACGGTGATTCTGGGGATGATGCtt                                                                         >  1:363935/1‑149 (MQ=255)                                                                                gcTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAAAC‑GGGGG‑GTTTTTTCGGGGGGCT‑GGGAAAGGGGGGGGGGGGGGTTTTTCCCGACGGTGATTCTgggggtggtggtt                                                                         >  1:644971/1‑138 (MQ=255)                                                                                      aTGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATc                                                                  <  2:105282/150‑1 (MQ=255)                                                                                        gATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTg                                                               <  2:180050/151‑1 (MQ=255)                                                                                         aTCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTgg                                                              <  1:373269/151‑1 (MQ=255)                                                                                            gcgGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAACT‑GGGCG‑GTTTTTACGGGGGTCT‑GGCAATGGGCGGGGGGGGGGTTTTTTCCGACGGTGGTTTTTGGGGTGGTGGTTTTTGATCTTtgtg                                                            >  1:172425/1‑150 (MQ=255)                                                                                                  gTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAAAT‑TGGGG‑ATTTTTCCGGGGGGCT‑GGGCATGGGGGGGGGGGGGGTTTGTCCCGACGGTGATTTTGGTGGTGATGGTTTTTGGTCTTGGGGGGTttgt                                                     >  1:505011/1‑151 (MQ=255)                                                                                                         cgcATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACA‑TGGCG‑GTTTTTACGGGTGTTT‑GGGAATGGGGGGGGGGGGGGTTTGTCCCGGCGGTGGTTTTGGGGATGGTGGTTATCGATCTTTGTGGGGTTTTTgggcc                                               >  2:772503/1‑147 (MQ=255)                                                                                                         cgcATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGGAAT‑TGGGG‑GTTTTTTCGGGGGTCTGGGCAAGGGGGGGGGGGCGGTTTTGTCCCGA‑GTTGTTTTTGGTGGTGGTGCTTATCGAGCTTgggttggtt                                                       >  2:908470/1‑135 (MQ=255)                                                                                                          gcATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑TGGGG‑GTTTTTCCCGGGGTCT‑GGGCATAGGGGGGGGGGCGTTTTTTCCCCAGGTTTGTTTTTGTGATCATGCTTGTCCGTCTTTGGGCCGTTGTTGGcatac                                             >  1:395104/1‑151 (MQ=255)                                                                                                                  aTTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGaa                                     <  1:512458/151‑1 (MQ=255)                                                                                                                    ttCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGaaa                                    <  1:507528/150‑1 (MQ=255)                                                                                                                       tgatgaTTGTGGCGTGGATGCTGCTGGC‑GGGGAACT‑GGGGG‑GTTTTTACGGGTGGCT‑GGCCATGGGGGGGGGGGGGTTTTTTCCCGACGTTGGTTCTGGTGATGATGCTTATCGATCTTTGGGCGTTTTTTTGCACACAAAGCGgaaaaa                                 >  1:668529/1‑148 (MQ=255)                                                                                                                         atgatTGTGGCGTGGATGCTGCTGGC‑GGGGTACT‑GGGGG‑GTTTTAACGGGTGTCT‑GGCAATGGGCGGTGGGGGGGTTTGTCCCGACGTTGATTCTGGGGGTGATGCTTTTCGATCTTTGTGCGTTTGTTGGGACACAAGGCGGaaaaaaa                               >  1:360977/1‑150 (MQ=255)                                                                                                                          tgatTGTGGCGTGGATGCTGCTGGC‑GGGTAAAT‑GGGCG‑GTTTTTCCCGGGGTCT‑GGCAATGGGCGGGGGGGCGGTTTTTCCCGACGGTGATTTTGGTGGTGATGCTTATCGATCTTTGTGCGTTTTTTGGGACACAAAGCGGaaataaa                               >  1:720317/1‑149 (MQ=255)                                                                                                                            atTGTGGCGTGGATGCTGCTGGC‑GGGGGACT‑GGGCG‑ATTTTACCGGGGGTCT‑GGCAAAGGGCGGTGGGGCGGTTTGTCCCGACGGTGATTCTGGTGATGATGCTTATCGATCTTGGGGCGGTTGTTGGGACACAAGGGGaaaaaaaa                               >  2:966424/1‑147 (MQ=255)                                                                                                                            atTGTGGCGTGGATGCTGCTGGC‑GGGGAAAT‑GGGCG‑ATTTTACCGGGTGTCC‑GGGCATGGGCGGGGGGGCGTTTTGTCCCCACGTTGATTTTGGGGATGATGCTTATCTATTTTTGGGGGGTTTTTGGCCCCCAAAGCGaaaaaataatt                            >  2:413924/1‑143 (MQ=255)                                                                                                                               gtgGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTa                        <  1:560587/151‑1 (MQ=255)                                                                                                                                   cGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAg                     <  2:425771/150‑1 (MQ=255)                                                                                                                                             gctgGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAGATACTCAGGa           <  2:172401/150‑1 (MQ=255)                                                                                                                                                    gggTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAGATACTCAGGATGTGaa     <  2:833661/150‑1 (MQ=255)                                                                                                                                                      gTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAGATACTCAGGATGTGAAGta  <  1:479262/151‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                         AAGAATCTACTCGATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGCG‑ATTTTACCGGGTGTCT‑GGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAGATACTCAGGATGTGAAGTA  >  NC_000913/4112429‑4112727

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑