Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,133,302	0	T	G	41.5%	59.6 / 10.2	41	H219P (CAC→CCC)	yghS	putative ATP‑binding protein
Reads supporting (aligned to +/- strand):  ref base T (5/19);  new base G (17/0);  total (22/19)
Fisher's exact test for biased strand distribution p-value = 3.15e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGTAGTTGGGCTGCGGCGCGGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGC‑GATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACGAATCAACAATACG  >  NC_000913/3133155‑3133448                                                                                                                                                    |                                                                                                                                                     tGTAGTTGGGCTGCGGCGCGGCTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCGCTATCCATTTTGGTGATCGGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGgtgt                                                                                                                                                    >  2:223943/1‑150 (MQ=255)    aGTTGGGCTGCGGCGCGGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGcc                                                                                                                                                >  1:77767/1‑151 (MQ=255)       tGGGCTGCGGCGCGGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGccc                                                                                                                                               >  1:673955/1‑149 (MQ=255)        gggCTGCGGCGCGGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATc                                                                                                                                            <  2:772575/151‑1 (MQ=255)             gcggcgCGGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGTCGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCA‑Gtt                                                                                                                                      <  1:136233/151‑1 (MQ=255)               ggcgCGGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCA‑GTTCa                                                                                                                                    <  2:620799/151‑1 (MQ=255)                  gcgGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCA‑GTTCAAgg                                                                                                                                 <  2:522934/151‑1 (MQ=255)                   cgGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCA‑GTTCAAGGa                                                                                                                                <  1:108766/151‑1 (MQ=255)                      ttGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCCTCCAGGTTCAAggtct                                                                                                                              >  1:513779/1‑148 (MQ=255)                          aCTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCA‑GTTCAAGGATCTTTgc                                                                                                                         <  2:277535/151‑1 (MQ=255)                          aCTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCA‑GTTCAAGGATCTTTg                                                                                                                          <  2:146838/150‑1 (MQ=255)                             aTTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCA‑GTTCAAGGATCTTTGCGcc                                                                                                                      <  1:499741/151‑1 (MQ=255)                             aTTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCATCCA‑GTTCAAGGATCTTTGCGcc                                                                                                                      >  2:573785/1‑151 (MQ=255)                                      ttgagtttgTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCA‑GTTCAAGGATCTTTGCGCCATTGAATg                                                                                                              <  1:429635/150‑1 (MQ=255)                                       tgagtttgTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCA‑GTTCAAGGATCTTTGCGCCATTGAATGt                                                                                                             <  2:126854/150‑1 (MQ=255)                                       tgagtttgTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGGTGCCCCTCCA‑GTTCAAGGATCTTTGTGCCATTGAATGTc                                                                                                            >  1:728052/1‑151 (MQ=255)                                              gTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCCTCCC‑GTTCAAGGATCTTTTCGCCCTTTAATGTCAGtt                                                                                                        >  1:398422/1‑148 (MQ=255)                                                 gTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCACCCC‑GGTCCAGGATCTTTTCGCCATTTAATGTAAGTTgccg                                                                                                    >  2:425365/1‑147 (MQ=255)                                                   gCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCATCCA‑GTTTAAGGGTCTTTGTGGCATTTGATGTCGGTTgcggcg                                                                                                  >  2:316653/1‑149 (MQ=255)                                                            cGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCC‑GGTCAAAGAACTTTTCGCCCCTGGATGTCAGTTGCGGCGGAACGGC‑GAtt                                                                                      >  1:674795/1‑151 (MQ=255)                                                             gTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGC‑GAttt                                                                                     <  2:308493/151‑1 (MQ=255)                                                             gTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCACCCC‑GTTCAAAGATCTTTTTGCCCTTGTATGTCAGTTGCGGCGGAACGGC‑GGttt                                                                                     >  1:17416/1‑151 (MQ=255)                                                                aaaTCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGGCGCCCCTCCC‑GTTCAAGGGTTTTTTCGGCCTTGGATGTTAGTTTGGGCGGAACGGC‑GGcttttt                                                                                  >  2:115567/1‑151 (MQ=255)                                                                       ccccTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCATCCA‑GTTCAAGGATCTTTTTGCCATTGAATGTCAGTTGCGGCGTAACGGC‑GGtttttt                                                                                  >  1:577542/1‑144 (MQ=255)                                                                            aTCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCCTCCC‑GTTCAAAGAACTTTGTGCCATTGTATGTCAGTTGCGGCGTAACGGC‑GGTTTTTTTCTGTaa                                                                           >  1:402453/1‑146 (MQ=255)                                                                             tCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGGCGCCCATCCC‑GTTCAAGGATCTTTTCGCCATTGAATGTCAGTTGCGGCGTAACGGC‑GATTTTTTTCTGTAACGCt                                                                       >  1:528776/1‑149 (MQ=255)                                                                               cATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCCTCCA‑GTTCAAAGATCTTTGCGCCCTTGAATGTCAGGTGCGGGGTAACGGC‑GATTTTTTTCTTTAACGCTGcc                                                                    >  1:355426/1‑150 (MQ=255)                                                                                aTTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGC‑GATTTTTTCCTGTAACGCTGCCAg                                                                  <  1:516820/151‑1 (MQ=255)                                                                                  tttGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGC‑GATTTTTTCCTGTAACGCTGCCAGt                                                                 <  2:706792/150‑1 (MQ=255)                                                                                        gATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTGGCCCATCCA‑GGTTAAGGGTCTTTTCGCCAATTAATGTTAGTTGGGGCGGAAAGGG‑GGTTTTTTTCTGTTAAGCCGCCCGGtggggg                                                           >  2:262756/1‑150 (MQ=255)                                                                                             ggAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGC‑GATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGt                                                     <  2:63245/151‑1 (MQ=255)                                                                                                         gTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCTCCCCTCCA‑GTTCCAGGATCTTTTCGCCCTTGAATGTCAGTTGCGGCGGAAAGGC‑GGTTTTTTTCTGTAACGCTGCCAGTTGGGGGTGCGGTTTTCGCGCaaa                                          >  2:354637/1‑150 (MQ=255)                                                                                                           gAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGC‑GATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAAcgc                                       <  2:373232/151‑1 (MQ=255)                                                                                                                        tGACGCTTGCAGAATTTCATCGGCGGGGGTGGGCCCCTCCC‑GTTCAAAGAACTTTGCGCCATTGAATGTCAGTTGCGGGGTAACGGC‑GCTTTTTTTCTGTAACGCTGCCCGGTGGTGGGCCGGGTTTCGGGCCAAAGCGGGTTTTttat                            >  1:794553/1‑149 (MQ=255)                                                                                                                        tGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCATCCA‑GTTCAAAGATCCTTTTGGCATTTAATGTCAGTTGCGGGGCAACGGC‑GCTTTTTTTCTTTTACCCTGCCCGTTGGGGGTCAGGGTTACGCGCAAACGCGGgttgtt                               >  2:206967/1‑146 (MQ=255)                                                                                                                            gCTTGCAGAATTTCATCGGCGGGGGGGCGCCCACCCC‑GTTCAAGGGGCTTTTCGCCATTGAATGTCAGTTGCGGCGGAACGGCGGATTTTTTCTTTTAAC‑CTGCCAGTTGGTGGTCAGGGTTACGCGCAAACGCGGgttgttttt                            >  2:609360/1‑142 (MQ=255)                                                                                                                                   gAATTTCATCGGCGGGGTGTCGCCCATCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGC‑GATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACg               <  2:398380/151‑1 (MQ=255)                                                                                                                                         cATCGGCGGGGTGTCGCCCATCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGC‑GATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACGAATca          <  1:354677/150‑1 (MQ=255)                                                                                                                                            cggcggGGTGTCGCCCATCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGC‑GATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACGAATcaaca       <  1:38435/150‑1 (MQ=255)                                                                                                                                             ggcggGGTGTCGCCCATCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGC‑GATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACGAATcaacaa      >  1:460796/1‑150 (MQ=255)                                                                                                                                               cggGGTGTCGCCCATCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGC‑GATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACGAATCAACAATa    <  1:208807/150‑1 (MQ=255)                                                                                                                                                ggggTGTCGCCCATCCA‑GTTCAAGCATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGC‑GATTTTTTCCTGTAACGCTGCCAGCTGTCGGCCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCCAGACGAATCAACAATACg  >  2:546550/1‑151 (MQ=255)                                                                                                                                                    |                                                                                                                                                     TGTAGTTGGGCTGCGGCGCGGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCATCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGC‑GATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACGAATCAACAATACG  >  NC_000913/3133155‑3133448

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: ‑