Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,112,578	0	T	G	43.2%	63.0 / 11.3	46	G88G (GGT→GGG)	yiiR	DUF805 family putative inner membrane protein
Reads supporting (aligned to +/- strand):  ref base T (6/19);  new base G (19/0);  total (27/19)
Fisher's exact test for biased strand distribution p-value = 1.62e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGAATCTACTCGATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGT‑AACT‑GGGCGATTTTACCGGGTGTCTGGCAATGGGC‑GGTGGGGCGTTTTGTCCCGA‑CGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAGATACTCAGGATGTGAAGT  >  NC_000913/4112430‑4112726                                                                                                                                                      |                                                                                                                                                         aGAATCTACTCGATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGT‑aa                                                                                                                                                       <  2:815726/151‑1 (MQ=255)          tCGATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGG‑AACT‑ggggggt                                                                                                                                             >  2:890487/1‑147 (MQ=255)           cGATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGT‑AACT‑GGGCGa                                                                                                                                              <  1:964547/149‑1 (MQ=255)            gATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGT‑AAcatgggggttt                                                                                                                                            >  1:246749/1‑141 (MQ=255)                         cggcgTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGT‑AACT‑GGGCGATTTTACCGGGTGTCTg                                                                                                                              <  1:393891/151‑1 (MQ=255)                           gcgTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGT‑AACT‑GGGCGATTTTACCGGGTGTCTGGc                                                                                                                            <  1:900496/151‑1 (MQ=255)                             gTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGCGGGGG‑AACT‑GGCGGCTTTTTCCggtgggtg                                                                                                                               >  1:420460/1‑141 (MQ=255)                              ttttGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGTTGCTGCTGGC‑GGGA‑GATC‑GGGGGTTTTTTCCGGGGGTTTgggca                                                                                                                          >  2:700026/1‑147 (MQ=255)                               tttGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGT‑AACT‑GGGCGATTTTACCGGGTGTCTGGCAAt                                                                                                                         <  2:985171/150‑1 (MQ=255)                               tttGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGG‑AAAT‑GGGGGGTTTTTACggg                                                                                                                                    >  2:116048/1‑139 (MQ=255)                               tttGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGG‑AAAC‑GGGGGGTTTTTTCggggggttgggca                                                                                                                          >  1:784678/1‑139 (MQ=255)                                ttGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGG‑AACT‑GGGGGGTTTTTCCGGGGGTCTGGGGATgg                                                                                                                       >  2:297728/1‑151 (MQ=255)                                  gCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGG‑AAAC‑GGGGGGTTTTTCCCGGGGGCTGGGAAAgggg                                                                                                                     >  1:372135/1‑150 (MQ=255)                                            cttgctCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGG‑AAATGGGGGGTTTTTACCGGG‑GTCTGGGGATGggg‑ggggggggg                                                                                                           >  1:870809/1‑148 (MQ=255)                                                 tctGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAAATT‑GGGGGCTTTTTCCGGG‑GTCTGGGAATTGGG‑GGGGGGGCGTTTTGt                                                                                                     >  2:213337/1‑151 (MQ=255)                                                        aaCAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGATCCGGCGCATGGGAATTTCTGATGATTGTGGCGTGGATGCTGGTGGC‑GGGG‑AAAA‑GGGGGGTTTTTTCGGGGGGCTTGGGATGGGG‑GGGGGGGGGTTTTGttt                                                                                                   >  1:186781/1‑144 (MQ=255)                                                           aGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGG‑AACT‑GGGGGGTTTTTCCCGGGGGCTGGGCATGGGCGGGGGGGGGGTTTTTTcccaaggt                                                                                             >  1:342902/1‑145 (MQ=255)                                                                    aaCTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGCGGGGA‑AACG‑GGGGGTTTTTACCGGG‑GGCTGGGAATGGGG‑GGGGGGGGGGTTTTTTCCGA‑CGGTGttttttg                                                                                   >  1:400190/1‑145 (MQ=255)                                                                    aaCTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGG‑AACT‑GGGGGGTTTTTACGGGGGTCTGGGAAATGGG‑GGGGGGGGGGTTTGTCCCCA‑CGtttgttttgggg                                                                                 >  2:1061726/1‑141 (MQ=255)                                                                     aCTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGGTGCTGCTGGC‑GGGT‑AAAA‑GGGGGGTTTTAACCGGGGTTTTGCAAATGGC‑GGGGGGGGGCTTTGTGCCCA‑Cggttgttttggg                                                                                  >  1:502403/1‑138 (MQ=255)                                                                     aCTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGG‑AACT‑GGGGGGTTTTTCCCGGGGTCTGGGAATGGGG‑GGGGGGGGGGTTTTTCCCCG‑CGTTGttttt                                                                                     >  2:286975/1‑144 (MQ=255)                                                                         ttAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGG‑AAAT‑GGGGGGTTTTTCCCGGGGTCTTGGCATGGGG‑GGGGGGGGGGTTTTTTCCGA‑CGGTGGtttttggggt                                                                               >  1:531210/1‑140 (MQ=255)                                                                              cgcTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGG‑AAATGGGGGGTTTTTCCCGGGGGCTTGGCAAGGGGG‑GGGGGGGGGTTTTTTCCCG‑‑CGGTGGTTTTGGGGGTGATGCtt                                                                        >  2:844624/1‑150 (MQ=255)                                                                               gcTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGT‑AACT‑GGGCGATTTTACCGGGTGTCTGGCAATGGGC‑GGTGGGGCGTTTTGTCCCGA‑CGTTGATTCTGGTGATGATGCTTAt                                                                      <  2:255820/151‑1 (MQ=255)                                                                                  tGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGT‑AACT‑GGGCGATTTTACCGGGTGTCTGGCAATGGGC‑GGTGGGGCGTTTTGTCCCGA‑CGTTGATTCTGGTGATGATGCTTATCg                                                                    <  2:571866/150‑1 (MQ=255)                                                                                  tGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGT‑AACT‑GGGCGATTTTACCGGGTGTCTGGCAATGGGC‑GGTGGGGCGTTTTGTCCCGA‑CGTTGATTCTGGTGATGATGCTTATCg                                                                    <  1:1012186/150‑1 (MQ=255)                                                                                  tGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGG‑AAAT‑GGGGGGTTTTTTCGGGGGTCTGGGAATGGGG‑GGGGGGGGGGTTTGTCCCGA‑CGGTGGTTTTTGTGGTGGTGGTTTTCg                                                                    >  2:309376/1‑150 (MQ=255)                                                                                     aTGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGT‑AACT‑GGGCGATTTTACCGGGTGTCTGGCAATGGGC‑GGTGGGGCGTTTTGTCCCGA‑CGTTGATTCTGGTGATGATGCTTATCGATCt                                                                <  1:372510/151‑1 (MQ=255)                                                                                       gATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGT‑AACT‑GGGCGATTTTACCGGGTGTCTGGCAATGGGC‑GGTGGGGCGTTTTGTCCCGA‑CGTTGATTCTGGTGATGATGCTTATCGATCtt                                                               <  1:1078506/150‑1 (MQ=255)                                                                                        aTCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGT‑AACT‑GGGCGATTTTACCGGGTGTCTGGCAATGGGC‑GGTGGGGCGTTTTGTCCCGA‑CGTTGATTCTGGTGATGATGCTTATCGATCTTgg                                                             <  2:210662/151‑1 (MQ=255)                                                                                          cgcgGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGT‑AACT‑GGGCGATTTTACCGGGTGTCTGGCAATGGGC‑GGTGGGGCGTTTTGTCCCGA‑CGTTGATTCTGGTGATGATGCTTATCGATCTTGGt                                                            <  1:793634/150‑1 (MQ=255)                                                                                                   tCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGG‑AAAT‑GGGGGATTTTTCCGGGGGGGTGGCGAAGGGG‑GGGGGGGGGGTTTTTTCCGA‑CGGTGTTTTTTGGGAGGGTGGTTATCGGTCTTTGGGGGtttttt                                                   >  1:126951/1‑150 (MQ=255)                                                                                                      ggCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGG‑AACT‑GGGCGGTTTTACCGGGTGTCTGGCAATGGGG‑GGGGGGGGGTTTTTTCCCGA‑CGTTGATTCTTGGGATGATGCTTTTCGATCTTGGTGCGGttttttg                                                 >  2:426555/1‑147 (MQ=255)                                                                                                          cATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGG‑AAAT‑GGGGGGGTTTACCGGGGGTCCGGCAAAGGGG‑GGGGGGGGGGTTTGTCCCGACCGTTGTTTTTGG‑GGTGAAGTTTTTCGGGCTTTGTGGGGTTGTTGGgaca                                             >  2:272149/1‑149 (MQ=255)                                                                                                           aTGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGT‑AACT‑GGGCGATTTTACCGGGTGTCTGGCAATGGGC‑GGTGGGGCGTTTTGTCCCGA‑CGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACaa                                          <  1:286955/151‑1 (MQ=255)                                                                                                           aTGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGT‑AACT‑GGGCGATTTTACCGGGTGTCTGGCAATGGGC‑GGTGGGGCGTTTTGTCCCGA‑CGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACaa                                          <  1:8372/151‑1 (MQ=255)                                                                                                            tGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGG‑AAAT‑GGGGGGTTTTTCCCGGGGGTTTGCGATGGGC‑GGGGGGGGGGTTTTTCCCCA‑CGTTGGTTCTGGTGGTTGTTGTTATCGATCTTGGTGGGGTTTTTGTcaca                                             >  1:179804/1‑147 (MQ=255)                                                                                                             gggCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGT‑AACT‑GGGCGATTTTACCGGGTGTCTGGCAATGGGC‑GGTGGGGCGTTTTGTCCCGA‑CGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAg                                         <  2:776958/150‑1 (MQ=255)                                                                                                                   ttCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGT‑AACT‑GGGCGATTTTACCGGGTGTCTGGCAATGGGC‑GGTGGGGCGTTTTGTCCCGA‑CGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGaaa                                   <  1:970674/150‑1 (MQ=255)                                                                                                                          gatTGTGGCGTGGATGCTGCTGGC‑GGGT‑AACT‑GGGCGGTTTTTCCGGGGGTCTGGCAATGGGG‑GGGGGGGGGTTTTTTTCCGA‑CGTTGGTTCTGGTGGTGATGGTTTTCGATCTTTGTGCGTTTGTTTGGACACAAGGCGGAaataaata                            >  1:789121/1‑150 (MQ=255)                                                                                                                           atTGTGGCGTGGATGCTGCTGGC‑GGGT‑AACT‑GGGCGATTTTACCGGGTGTCTGGCAATGGGC‑GGTGGGGCGTTTTGTCCCGA‑CGTTGGTTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATg                          <  2:189370/151‑1 (MQ=255)                                                                                                                           atTGTGGCGTGGATGCTGCTGGC‑GGGG‑AAAT‑GGGGGGATTTACCGGGGGGGTGGGCATGGGG‑GGGGGGGGGGTTTTTCCCGA‑CGGTTATTTTGGGGGTGATGCTTTTCGGTTTTTGTGGGTTTGGTGGGACACAAAGGGGAaataaata                            >  2:647206/1‑149 (MQ=255)                                                                                                                                         gctgctGGC‑GGGT‑AACT‑GGGCGATTTTACCGGGTGTCTGGCCATGGGC‑GGTGGGGCGGTTTGTCCCGA‑CGTTGATTCTGGGGATGATGCTTATCGATCTTGGTGCGTTTGTTTGCACACAAGGCGAAAATAAATATGGTAAAGATACTc              >  1:821111/1‑149 (MQ=255)                                                                                                                                            gctgGC‑GGGT‑AACT‑GGGCGATTTTACCGGGTGTCTGGCAATGGGC‑GGTGGGGCGTTTTGTCCCGA‑CGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAGATACTCAGGAt         <  2:1069374/151‑1 (MQ=255)                                                                                                                                               ggC‑GGGT‑AACT‑GGGCGATTTTACCGGGTGTCTGGCAATGGGC‑GGTGGGGCGTTTTATCCCGA‑CGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAGATACTCAGGAtgt       <  2:360338/150‑1 (MQ=255)                                                                                                                                                    ggT‑AACT‑GGGCGATTTTACCGGGTGTCTGGCAATGGGC‑GGTGGGGCGTTTTGTCCCGA‑CGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAGATACTCAGGATGTGAAGt  >  1:306549/1‑151 (MQ=255)                                                                                                                                                      |                                                                                                                                                         AGAATCTACTCGATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGT‑AACT‑GGGCGATTTTACCGGGTGTCTGGCAATGGGC‑GGTGGGGCGTTTTGTCCCGA‑CGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAGATACTCAGGATGTGAAGT  >  NC_000913/4112430‑4112726

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: ‑