Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,112,578	0	T	G	45.6%	65.2 / 15.0	47	G88G (GGT→GGG)	yiiR	DUF805 family putative inner membrane protein
Reads supporting (aligned to +/- strand):  ref base T (4/21);  new base G (21/0);  total (26/21)
Fisher's exact test for biased strand distribution p-value = 1.90e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAGAATCTACTCGATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑GGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAGATACTCAGGATGTGA  >  NC_000913/4112429‑4112723                                                                                                                                                       |                                                                                                                                                     aaGAATCTACTCGATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGt                                                                                                                                                      <  1:381330/150‑1 (MQ=255)    aaTCTACTCGATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGaa                                                                                                                                                    >  2:809277/1‑149 (MQ=255)         aCTCGATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACtcatt                                                                                                                                              <  1:537662/150‑5 (MQ=255)             gATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAAAT‑GGGG‑GGttt                                                                                                                                       >  2:646414/1‑151 (MQ=255)                   cAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGC‑GATTTTACCg                                                                                                                                  <  1:757512/150‑1 (MQ=255)                     gACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGC‑GATTTTACCGGgt                                                                                                                               <  2:854216/151‑1 (MQ=255)                             cgTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGCGGGGGAACG‑GGGG‑GTTTTTCCCgg                                                                                                                                 >  1:254114/1‑142 (MQ=255)                             cgTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCa                                                                                                                       <  2:133075/151‑1 (MQ=255)                                tttGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAAAT‑GGGC‑GGTTTTTCCGGGGGTCTgg                                                                                                                         >  2:919871/1‑146 (MQ=255)                                  tGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑gg                                                                                                                  <  2:262604/150‑1 (MQ=255)                                  tGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAACT‑GGGG‑GGTTTTTTCCGGGGGCTGGCCAT‑ggg                                                                                                                 >  2:675665/1‑151 (MQ=255)                                                gctCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑GGGCGGTGGGGCGttt                                                                                                    <  2:130184/150‑1 (MQ=255)                                                     ggCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑GGGCGGTGGGGCGTTTTGt                                                                                                 <  2:820256/148‑1 (MQ=255)                                                        cAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAAAT‑GGGG‑GGTTTTTCCGGGTGGCTGGGAAT‑GGGGGGGGGGGCGGTTTGTtcc                                                                                              >  2:110456/1‑148 (MQ=255)                                                          aCAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑GGGCGGTGGGGCGTTTTGTCCCGACGt                                                                                         <  1:589133/151‑1 (MQ=255)                                                           cAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAACC‑GGGG‑GGTTTTTCCGGGGGGCTGGGAAT‑GGGGGGGGGGGGGGTTTGTCCCCACGtt                                                                                        >  1:420293/1‑151 (MQ=255)                                                            aGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAAAT‑GGGCGGGTTTTTCCGGG‑GGCTTGGAAT‑GGGGGGGGGGGGGtttttttccccc                                                                                           >  2:697507/1‑139 (MQ=255)                                                             gCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑GGGCGGTGGGGCGTTTTGTCCCGACGTTGa                                                                                      <  1:582450/151‑1 (MQ=255)                                                              cGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑GGGCGGTGGGGCGTTTTGTCCCGACGTTGAt                                                                                     <  2:835347/151‑1 (MQ=255)                                                               ggCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑GGGCGGTGGGGCGTTTTGTCCCGACGTTGAtt                                                                                    <  2:704295/151‑1 (MQ=255)                                                                 cAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑GGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCt                                                                                  <  2:570084/151‑1 (MQ=255)                                                                   gTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGAGGCTTCTGGC‑GGGTAAAT‑CGGG‑GAGTTTAAAGGGGGGCTGGGGAT‑GGGCGGGGGGGCGGTTTGTACCGACggt                                                                                        >  2:703969/1‑141 (MQ=255)                                                                     aaCTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAAAT‑GGGG‑GATTTTTCCGGGGGTCTGGCCAT‑GGGGGGGGGGGGGTTTTTTCCCGACGGTGAtttt                                                                                  >  2:272087/1‑145 (MQ=255)                                                                         gTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAACC‑GGGG‑GGTTTTTCCGGGGGGTTGGCAAT‑GGGGGGGGGGGGGGTTTGTCCCGGCGGTGGTTTTgggggt                                                                            >  1:22809/1‑145 (MQ=255)                                                                         gTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GCGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑GGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGtgatga                                                                          <  1:392468/151‑1 (MQ=255)                                                                          ttAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAAAT‑GGGG‑GGTTTTTCCGGGGGGCTGGGAAT‑GGGGGGGGGGGGGGTTTTTCCCCACGGTGGtttttggg                                                                              >  2:655894/1‑140 (MQ=255)                                                                           tAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAAAT‑GGGG‑GGTTTTTCCCGGGGGCTGGGCAT‑GGGGGGGGGGGGGGTTTTTTCCCACGTTGagttttg                                                                                >  2:867575/1‑137 (MQ=255)                                                                                               ggCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAAAT‑GGGG‑GATTTTTCCCGGGGGCTGGCCAT‑GGGCGGGGGGGGGGTTTTTCCCCGCGTTGGTTTTGGTGGTGATGCTTTTCGATCtttgggggtt                                                    >  2:813370/1‑143 (MQ=255)                                                                                                 cGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGGAAA‑GGGG‑GGTTTTACCGGGTGTCTGGGCAA‑GGGGGGGGGGGGGGTTTGTTCCGTGGGTTATTTTGGGGGTTATGCCTATCCAGCTTGGTGCGttt                                                   >  1:331370/1‑150 (MQ=255)                                                                                                 cGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAAATGGGGG‑GTTTTTACCGGG‑GTCTGGCAAT‑TGGGGGGGGGGGGTTTTTTCCCCGCGGTGATTTTGGGGATGGTGCTTTTTGATCTTTGGGCGttt                                                   >  2:163221/1‑150 (MQ=255)                                                                                                       ggCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑GGGCGGTGGGGCGTTGTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGca                                            <  1:751194/151‑1 (MQ=255)                                                                                                           cATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAACA‑GGGG‑GGTTTTTTCCGGGGGCTGGGAATGGGGGGGGGGGGGGTTTTTTCCCG‑CGGTGTTTTTGGGGGTGATGGTTTTCGGTCTTGGGGCGGTTGTTGGgacac                                         >  1:587329/1‑150 (MQ=255)                                                                                                             tGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGCGGGGAAACT‑GGGG‑GTTTTTTCCGGG‑GTGTTGGGAT‑GGGGGGGGGGGGGGTTTTTTCCGCCGGTGTTTTTGGGGGTGATGCTTTTTGGTCTTtgtggggttttt                                                >  1:549553/1‑133 (MQ=255)                                                                                                              gggCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAACC‑GGGC‑GGTTTTTCCGGGGGTCTGGCAAT‑GGGGGGGGGGGCGGTTTGTTCCCACGGTGATTTTGGGGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACaa                                       >  1:469438/1‑149 (MQ=255)                                                                                                               ggCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAAAA‑GGGC‑GGTTTTTTCCGGTGTCTGGCCAT‑GGGCGGGGGGGCGGTTTTTTCCGACGGTGATTCTTGGGGTTGTGGTTATCGGACTTGGGGGGGTTGTTGGCAAACaa                                       >  1:253352/1‑148 (MQ=255)                                                                                                                      cTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAACT‑GGGC‑GGTTTTTCCGGGGGTCTGGGAAT‑GGGGGGGGGGGGGGTTTTTCCCGACGCTGATTTTGGTGGTGGTGGTTTTCGATTTTTGGGCGGTTTTTGGCACACAAGGGGaaaa                               >  1:672308/1‑149 (MQ=255)                                                                                                                        gatgatTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑GGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAaaat                              <  1:609714/148‑1 (MQ=255)                                                                                                                          tgatTGTGGCGTGGATGCTGCTGGC‑GGGTAAAC‑GGGG‑GATTTTTCCGGGGGTCTGGCAAA‑GGGGGGGGGGGGGGTTTTTGCCGGAGGTGGGTTTGGGGATGATGCTTTTTGGTCTTTGGGCGGTTTTTGGGACAAAAAGGGGaaataaa                           >  1:188748/1‑149 (MQ=255)                                                                                                                           gatTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑GGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAaataaata                         <  2:6191/150‑1 (MQ=255)                                                                                                                           gatTGTGGCGTGGATGCTGCTGGC‑GGGGAAAT‑GGGC‑GGTTTTACCGGGGGGCTGGCCATGGGGGGGGGGGGGGTTTTTTCCCGCCG‑TGGTTTTGGGGGTGGTGGTTTTCGATCTTTGGGCGGTTGTTGGCACACAAAGCGGaaaaaaa                           >  2:839464/1‑148 (MQ=255)                                                                                                                                 ggCGTGGATGCTGCTGGC‑GGGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑GGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGt                     <  2:977288/148‑1 (MQ=255)                                                                                                                                  gCGTGGATGCTGCTGGC‑GGGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑GGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAg                 <  1:649788/151‑1 (MQ=255)                                                                                                                                    gTGGATGCTGCTGGC‑GGGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑GGGCGGTGGGGCGTTTTTTCCCGACGGTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGGAAATAAATATGGTaa                   >  2:793594/1‑147 (MQ=255)                                                                                                                                    gTGGATGCTGCTGGC‑GGGGAAAT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑GGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGGGATGATGCTTATCGATCTTGGTGGGTTTGTTGGCACACAAGGCGAAAATAAATATGGTaa                   >  1:114160/1‑147 (MQ=255)                                                                                                                                      ggATGCTGCTGGC‑GGGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑GGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAGATAc             <  1:615997/151‑1 (MQ=255)                                                                                                                                        aTGCTGCTGGC‑GGGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑GGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAGATACTc           <  1:99392/151‑1 (MQ=255)                                                                                                                                            tgctgGC‑GGGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑GGGCGGGGGGGCGTTTTGTCCCGACGTTGGTTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAGATACTCAgg        >  1:877242/1‑150 (MQ=255)                                                                                                                                                 gC‑GGGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑GGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAGATACTCAGGATGTGa  <  1:783686/151‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                     AAGAATCTACTCGATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACT‑GGGC‑GATTTTACCGGGTGTCTGGCAAT‑GGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAGATACTCAGGATGTGA  >  NC_000913/4112429‑4112723

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: ‑