Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,112,578	0	T	G	48.1%	23.4 / 12.4	28	G88G (GGT→GGG)	yiiR	DUF805 family putative inner membrane protein
Reads supporting (aligned to +/- strand):  ref base T (3/11);  new base G (13/0);  total (17/11)
Fisher's exact test for biased strand distribution p-value = 3.39e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAGAATCTACTCGATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACTGGGCGATTTTACCGGGTGTCTGGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAGATACTCAGGAT  >  NC_000913/4112429‑4112719                                                                                                                                                       |                                                                                                                                              aaGAATCTACTCGATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTa                                                                                                                                              <  1:239221/151‑1 (MQ=255)         aCTCGATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACTg                                                                                                                                          <  2:235781/147‑1 (MQ=255)         aCTCGATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGGACTggg                                                                                                                                        >  1:331570/1‑149 (MQ=255)                     gACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACTGGGCGATTTTACCGGgt                                                                                                                          <  1:394319/151‑1 (MQ=255)                        cgcgGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAAATGGGGGGTTTTACCggggg                                                                                                                         >  2:137987/1‑147 (MQ=255)                           ggcgTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACTGGGCGATTTTACCGGGTGTCTgg                                                                                                                    <  2:362640/151‑1 (MQ=255)                                   gCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACTGGGCGATTTTACCGGGTGTCTGGCAATggg                                                                                                             <  2:486466/150‑1 (MQ=255)                                       tgtgtgCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACTGGGCGATTTTACCGGGTGTCTGGCAATGGGCGGt                                                                                                         <  1:196219/150‑1 (MQ=255)                                                gctCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACTGGGCGATTTTACCGGGTGTCTGGCAATGGGCGGTGGGGCGtttt                                                                                               <  2:270191/151‑1 (MQ=255)                                                gctCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAACTGGGGGGTTTTTCCGGGGGGCTGGGAATGGGCGGGGGGGGGgttt                                                                                               >  2:579165/1‑151 (MQ=255)                                                        cAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGAC‑GGGTAACTGGGCGATTTTACCGGGTGTCTGGCAATGGGCGGTGGGGCGTTTTGTCCCGAc                                                                                       >  1:599670/1‑151 (MQ=255)                                                              cGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAAATGGGGGAATTTTCCGGGGGGCTGGCAATGGGCGGGGGGGGGTTTTTTCCCCAGGtt                                                                                    >  2:161252/1‑148 (MQ=255)                                                                  aGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAACTGGGCGGTTTTTCCGGGGGTCTGGCAATGGGCGGGGGGGGGTTTTTTCCCGACGGTGAtttt                                                                              >  2:248018/1‑148 (MQ=255)                                                                            aaGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACTGGGCGATTTTACCGGGTGTCTGGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGc                                                                   <  2:233645/151‑1 (MQ=255)                                                                                gcTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAACTGGGGGGTTTTTCCGGGGGGTTGGCAATGGGGGGGGGGGGGTTTTGTTCCGACGTTGGTTTTGGGGATTATGCtt                                                                 >  2:376057/1‑149 (MQ=255)                                                                                gcTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAAATGGGCGGTTTTTCCGGGGGTCTGGCCATGGGCGGGGGGGCGTTTTTTCCCCCCGTTTATTTTGGGGGTGATGCtttt                                                               >  2:490828/1‑149 (MQ=255)                                                                                     cATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACTGGGCGATTTTTCCGGGTGTCTGGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATc                                                          <  1:567583/151‑1 (MQ=255)                                                                                     cATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAAATGGGGGATTTTTCCGGGGGTCTGGCAATGGGGGGGGGGGCGTTTTTTTCCGACGCTGATTCTGGTGATGATGCTTAttgc                                                            >  1:209643/1‑146 (MQ=255)                                                                                                    tCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGCGGGGAAAAGGGGGGTTTTTACCGGG‑GTCTGGGAAAGGGGGGGGGGGGGGTTTTTTCCCCCGTTGGTTTTTGGGGTGGTGGTTTTTGATCTTTGGGGGtttttt                                            >  1:176038/1‑150 (MQ=255)                                                                                                      cGGCGCATGGGCATTTCTGATGATTGTGGCGTGGAAGCTGCTGGC‑GGGGTACTGGGGGATTTTTCCCGGGGTTTGGGAATGGGGGGGGGGGGGTTTTTTCCCGGCGGTGATTCTTGGGATGATGCTTATTGATTTTTGGGGGtttttt                                            >  2:528105/1‑148 (MQ=255)                                                                                                       ggCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAACTGGGCGATTTTTCCGGGGGTCTGGCAATGGGCGGGGGGGGGGTTTTTCCCGACGTTTATTTTGGGGATGATGCTTTTCGATCTTTGTGCGTTTGTTgg                                          >  2:107913/1‑149 (MQ=255)                                                                                                           cATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACTGGGCGATTTTACCGGGTGTCTGGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGcacaca                                    <  1:528102/151‑1 (MQ=255)                                                                                                                  aTTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGGAAACGGGGGGTTTTTCCGGGGGTCTGGGAATGGGGGGGGGGGGGGTTTTTCCCGCCGTTGGTTTTGGGGATGATGCTTTTCGATCTTTGTGGGTTTGTTGGGACACAAGGCg                               >  2:536834/1‑149 (MQ=255)                                                                                                                       tgatgaTTGTGGCGTGGATGCTGCTGGC‑GGGGAACTGGGGGGTTTTTCCGGGGGTCTGGCAAAGGGGGGGGGGGGGGTTTGTCCCGACGGTGATTTTGGGGATGATGCTTATCGATCTTTGTGCGTTTGTTGGCACACAAAGCGaaaa                           >  2:468395/1‑148 (MQ=255)                                                                                                                                  gCGTGGATGCTGCTGGC‑GGGTAACTGGGCGATTTTACCGGGTGTCTGGCAATGGGCGGGGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTaa               >  1:559178/1‑149 (MQ=255)                                                                                                                                    gTGGATGCTGCTGGC‑GGGGAACTGGGCGATTTTACCGGGGGTCTGGGCATGGGCGGGGGGGCGGTTTTTCCCGACGTTGATTCTGGGGATGATGCTTATCGATCTTGGGGCGTTTGTTGGCACACAAGGCGaaaa                           >  1:233023/1‑135 (MQ=255)                                                                                                                                         tgctgcTGGC‑GGGTAACTGGGCGATTTTACCGGGTGTCTGGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGGGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAGATACTc       >  2:126130/1‑150 (MQ=255)                                                                                                                                             gctgGC‑GGGTAACTGGGCGATTTTACCGGGTGTCTGGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAGATACTCAGGAt  <  1:248017/151‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                              AAGAATCTACTCGATATTCAGACCGCGGCGTTTTGCCTTGTGTGCTTGCTCTGGCCAACAGCGGCAGTAACTGTTAAGCGCTTGCATGATCGCGGGCGTTCCGGCGCATGGGCATTTCTGATGATTGTGGCGTGGATGCTGCTGGC‑GGGTAACTGGGCGATTTTACCGGGTGTCTGGCAATGGGCGGTGGGGCGTTTTGTCCCGACGTTGATTCTGGTGATGATGCTTATCGATCTTGGTGCGTTTGTTGGCACACAAGGCGAAAATAAATATGGTAAAGATACTCAGGAT  >  NC_000913/4112429‑4112719

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: ‑