Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,111,747	0	G	T	52.0%	26.7 / 40.4	25	N156K (AAC→AAA)	yiiQ	DUF1454 family putative periplasmic protein
Reads supporting (aligned to +/- strand):  ref base G (11/1);  new base T (0/13);  total (11/14)
Fisher's exact test for biased strand distribution p-value = 2.69e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.51e-04

CTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCCGTTGTCCGCGACAACATAACGC‑AGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAGCTTTCGCTTTCGCGGCTTTTTGCTCTGGCCCCTGGATGGGTAGCCA  >  NC_000913/4111608‑4111893                                                                                                                                              |                                                                                                                                                    ctttTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCCGTTGTCCGCGACAACATAACGC‑AGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCccgc                                                                                                                                         >  2:1806015/1‑151 (MQ=255)           tttATTCAACCCTTCAAGCGATTCAGAGAGCGCCAGCTTAATCGTTTAAACAGCGAAGGTCAGCCCTTTTT‑CGCCTTTGTCCGCGAAAACATACCGC‑AGTGCCCCTTCTGTCTCGGTGTAATAACTTTTTTTTTC‑CCCCGCCGTtagt                                                                                                                                  <  1:1737980/148‑1 (MQ=255)                  aacccTTCAAGCGTTACGAATGGCGCCAGTTGAATCGGTAAAACAGCAAGGGTC‑GCCCCTTTTCCGCCTTTGCCCGCGACACAATACCGC‑GGTCCCCCTTCGGTCGGGGT‑AAAAAATGTTTTTTTTTCCCCCGCCGTTAGTAGCGACTg                                                                                                                          <  1:1345148/146‑1 (MQ=255)                   aaCCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCCGTTGTCCGCGACAACATAACGC‑AGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGc                                                                                                                         >  1:2591135/1‑149 (MQ=255)                     ccTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCCGTTGTCCGCGACAACATAACGC‑AGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGtt                                                                                                                     >  1:2581629/1‑151 (MQ=255)                          aaGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCCGTTGTCCGCGACAACATAACGC‑AGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGtttttt                                                                                                                 >  2:2766113/1‑150 (MQ=255)                              gATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCCGTTGTCCGCGACAACATAACGC‑AGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGc                                                                                                            >  2:2114919/1‑151 (MQ=255)                                    gagaGCGCCAGTTTAATCGGTTCAACAGCGAAGGTCACCCCTTTTC‑CGCCGTTGCCCGCAAAAACATAACGC‑AGTGCCCCTTCTGTCTCGGTTTAATACTGTTTTTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTtgt                                                                                                       <  1:2175417/147‑1 (MQ=255)                                                ttAAGCGTTTCAACAGCGAAGGTCACCCCTTTTT‑CGCCGTTGTCCGCAACAACATAACGC‑AGTGCCCCTTCTGTCTCGGTGTAATACCTTTTTTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTg                                                                                                 <  2:1728080/144‑1 (MQ=255)                                                   aTCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCCGTTGTCCGCGACAACATAACGC‑AGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATg                                                                                       >  2:4046026/1‑151 (MQ=255)                                                           aaaagcgagtgcaaGCCCCTTTC‑CCCTTTTGCCCGC‑ACAAAATAACGCGATTCCCCTTTCTGTCGGGTTGTAATAGGTTTTTTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAg                                                                                <  1:2473299/137‑1 (MQ=255)                                                             cAGCGAAGGTCAGCCCCTTTT‑CGCCGTTGTCCGCGACAACATAACGC‑AGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAgtgt                                                                             >  1:2961531/1‑151 (MQ=255)                                                                       cAGCCCCTTTT‑CGCCGTTGTCCGCGACAACATAACGC‑AGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCAcc                                                                   >  2:2651831/1‑151 (MQ=255)                                                                        aGCCCCTTTT‑CGCCGTTGTCCGCGACAACATAACGC‑AGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTTCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCg                                                                  >  2:2827294/1‑151 (MQ=255)                                                                           cccTTTT‑CGCCGTTGTCCGCGACAACATAACGC‑AGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTg                                                               >  1:2009410/1‑151 (MQ=255)                                                                              tttt‑CGCCGTTGTCCGCGAAAACATACCGC‑AGTGCACCTTCTGTCTGGGTGTAATACCTTTTTTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGcc                                                             <  2:3513986/150‑1 (MQ=255)                                                                                tt‑CGCCTTTGCCCGCGAAAAAATAACGC‑AGTGCCCCTTCTGTCTGGGTGTAATAGCTTTTTTTTTC‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCAt                                                           <  2:3810204/150‑1 (MQ=255)                                                                                         tgcccGCGACAACATAACGC‑AGTGCCCCTTCTGTCTGGGTGTAATAACTTTTTTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCt                                                   <  2:3647258/147‑1 (MQ=255)                                                                                              gcgAAAACATACCGC‑ATTGCCCTTTTTGTCTGGGTGTAATATCGTTTTTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAgct                                              <  2:1032108/150‑1 (MQ=255)                                                                                              gaaaaaacaTAACGT‑TGGCCTCCTTCTTGCTCGGTTGAATAATGTTTTTTTCT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTg                                                  <  1:3132373/141‑1 (MQ=255)                                                                                                                  ccctttCTGTCTGGTTTTAATATTTTTTTTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAGCTTTCGCTTTCGCGGCtttt                            <  1:419274/145‑1 (MQ=255)                                                                                                                  ccccTTCTGTCTGGGTGTAATAACTTTTTTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAGCTTTCGCTTTCGCGGCtttt                            <  1:3671127/147‑1 (MQ=255)                                                                                                                  cactttttgtggcGGTGTAATACCTTTTGTTTTC‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAGCTTTCGCTTTCGCGGCtttt                            <  2:968911/137‑1 (MQ=255)                                                                                                                   cccTTCTGTCTCGGTGTAATAACTTTTTTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAGCTTTCGCTTTCGCGGCTTTTTg                          <  2:2084359/149‑1 (MQ=255)                                                                                                                               tttttaaaccctttttttttC‑CCCCTCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTTTGTTTTTTTTTTTTATAGGGTGAGTGCGCACCTCACCTCTGCCATAAATGCCTCACCTTTTGCCCCCACAGCTTTTTGCTCTGTcc                  <  1:3188285/134‑1 (MQ=255)                                                                                                                                       aaCGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAGCTTTCGCTTTCGCGGCTTTTTGCTCTGGCCCCTGGATGGGt       >  1:498195/1‑149 (MQ=255)                                                                                                                                           ttttttttC‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAGCTTTCGCTTTCGCGGCTTTTTGCTCTGGCCCCTGGATGGGTAGCCa  <  1:925159/150‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                    CTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCCGTTGTCCGCGACAACATAACGC‑AGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAGCTTTCGCTTTCGCGGCTTTTTGCTCTGGCCCCTGGATGGGTAGCCA  >  NC_000913/4111608‑4111893

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: ‑