Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,477,840	0	G	C	48.4%	18.6 / 17.6	31	T67T (ACG→ACC)	slyX	phi X174 lysis protein
Reads supporting (aligned to +/- strand):  ref base G (9/7);  new base C (0/15);  total (9/22)
Fisher's exact test for biased strand distribution p-value = 8.16e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.41e-01

GGCTTTTCAGGAAATCACCATTGAAGAACTGAACGTCACGGTGACCGCTCATGAAATGGAGATGGCGAAACTGCGCGATCATCTGCGTCTGCTGACCGAGAAGTTAAAAGCCAGCCAG‑CCGTCGAACATCGCGTCGCAGGCTGAAGAAA‑CGCCACCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTCCCCGCTTTTTTGTCACTTTTTCGGTATTAGTGGCAACCGCAACCGCCGTTGCCTTTACCGCCACAGCAGCCTTCGCCACCGTGTTCATG  >  NC_000913/3477690‑3477969                                                                                                                                                         |                                                                                                                                  ggCTTTTCAGGAAATCACCATTGAAGAACTGAACGTCACGGTGACCGCTCATGAAATGGAGATGGCGAAACTGCGCGATCATCTGCGTCTGCTGACCGAGAAGTTAAAAGCCAGCCAG‑CCGTCGAACATCGCGTCGCAGGCTGAAGAAA‑cg                                                                                                                                   >  1:475274/1‑151 (MQ=255)    ttttCAGGAAATCACCATTGAAGAACTGAACGTCACGGTGACCGCTCATGAAATGGAGATGGCGAAACTGCGCGATCATCTGCGTCTGCTGACCGAGAAGTTAAAAGCCAGCCAG‑CCGTCGAACATCGCGTCGCAGGCTGAAGAAA‑cgcc                                                                                                                                 >  1:378968/1‑150 (MQ=255)         aGGAAATCACCATTGAAGAACTGAACGTCACGGTGACCGCTCATGAAATGGAGATGGCGAAACTGCGCGATCATCTGCGTCTGCTGACCGAGAAGTTAAAAGCCAGCCAG‑CCGTCGAACATCGCGTCGCAGGGTGAAGAAA‑cgccaccgcc                                                                                                                           <  1:558556/151‑1 (MQ=255)             aaTCACCATTGAAGAACTGAACGTCACGGTGACCGCTCATGAAATGGAGATGGCGAAACTGCGCGATCATCTGCGTCTGCTGACCGAGAAGTTAAAAGCCAGCCAG‑CCGTCGAACATCGCGTCGCAGGCTGAAGAAA‑cgccacc                                                                                                                              >  2:434508/1‑144 (MQ=255)             aaTCACCATTGAAGAACTGAACGTCACGGTGACCGCTCATGAAATGGAGATGGCGAAACTGCGCGATCATCTGCGTCTGCTGACCGAGAAGTTAAAAGCCAGCCAG‑CCGTCGAACATCGCGTCGCAGGCTGAAGAAA‑cgccacc                                                                                                                              <  1:434519/144‑1 (MQ=255)              aTCACCATTGAAGAACTGAACGTCACGGTGACCGCTCATGAAATGGAGATGGCGAAACTGCGCGATCATCTGCGTCTGCTGACCGAGAAGTTAAAAGCCAGCCAG‑CCGTCGAACATCGCGTCGCAGGCTGAAGAAA‑CGCCACCGCCACatt                                                                                                                      >  1:623846/1‑151 (MQ=255)                cACCATTGAAGAACTGAACGTCACGGTGACCGCTCATGAAATGGAGATGGCGAAACTGCGCGATCATCTGCGTCTGCTGACCGAGAAGTTAAAAGCCAGCCAG‑CCGTCGAACATCGCGTCGCAGGCTGAAGAAA‑CGCCACCGCCACattat                                                                                                                    >  1:476295/1‑151 (MQ=255)                 aCCATTAAAGAACTGAACGCCACGGGGCCCGCTCATGAAATGGAGAGGGCAAACCTGCGCGATCATCTGCGTCTGCTGACCGAGAATTAAAAACCCAGCCAG‑CCGTCGAACATCGCGTCGCAGGCTAAAGAAC‑CGCCACCGCCACatt                                                                                                                      <  2:380337/148‑1 (MQ=255)                         agaaCGGAACGCCACGGTGACCGCTAATAAAAGGGGGAGGGCGAACCGGCGCAATCTTCTGCGCCTGCTGCCCGAAAATTAAAAAGCCACCCCG‑CCGTCAAACACCGCGCCGCAGGCTGAAAAAC‑CCCCACCGCCACATTATTGAGGCGTa                                                                                                           <  2:476283/151‑1 (MQ=255)                              tGAACGTCACGGTGCCCGCTCATGAAATGGAGATGGCGAACCGGCGCGATCATCTGCGTCTGCTGACCGAGAAGTAAAAAGCCCGCCGG‑CGGTCAAACATCGCGTCGCGGGCTGAAGAAC‑CCCAACCGCCACATTATTGAGGCGTaaaa                                                                                                        <  1:339552/149‑1 (MQ=255)                                accGTCAGGGTGACCGCTAATAAAATGGAGATGGCAAAACGCCGCGATCATCTGCTTCTGCTGCCCGAGAATTTAAAAGCCAGCCGC‑CCGTCAAACATCGCTTCGCAGCCTGAAAAAC‑CCCCACCGCCACATTATTGAGGCGTaaaaa                                                                                                       <  1:95420/146‑1 (MQ=255)                                 aCGTCACGGTGACCGCACATAAAATGGAGATGGCGAAACTGCGCGATCATCTGCGTCTGCTGACCGAGAAGTTAAAAGCCAGCCAG‑CCGTCGAACACCGCGTCGCAGGCTGAAGAAA‑CCCCGCCGCCACATTATTGAGGCGTAAAAAAAGc                                                                                                   <  1:441703/151‑1 (MQ=255)                                  cGTCACGGTGACCGCTCATGAAATGGAGATGGCGAAACTGCGCGATCATCTGCGTCTGCTGACCGAGAAGTTAAAAGCCAGCCAG‑CCGTCGAACATCGCGTCGCAGGCTGAAGAAA‑CGCCACCGCCACATTATTGAGGCGTAAAAAAAGCg                                                                                                  >  1:352650/1‑151 (MQ=255)                                     cccGGTGACCGCTCAAGAAAGGGAGAGGGGAAAACGGCGGGGTCATCTGCGTCCGCTGACCGAGAAGTTAAAACCCAGCCAG‑CCGTCAAACCCCGGAAAGAAGGTTGAAGAAA‑CCCCACCGCCCCATTATTGAGGCGTAAAAAAAg                                                                                                    <  2:454094/144‑1 (MQ=255)                                     cACGGTCACCCCTCAAGAAATGGTGACGGCAAAACTGCCCGACCACCTGCGTCGTGGGACAGAAAAGTAAAAACCCAGCGAG‑CCGTCAAACAGCGCTTCGAGGGGTGAAAACA‑CCCCGCCGCCACATTATTGAGGCGTAAAAAAAGCgg                                                                                                 <  1:540065/149‑1 (MQ=255)                                       cGGTGACCGTTCATAAAGTGGAGATGTCGAAACTGCGCAATCATCTGCGTCTGCTGACCGAAAATTAAAAAGCCAGCCAG‑CCGTCGAACATCGCGTCGGAGGCTGAAAAAA‑CCCCACCGCCACATTATTGAGGCGTAAAAAAAGCGGGGa                                                                                              <  2:631155/150‑1 (MQ=255)                                           gcccGCTCAGAAAAGGGAGAGGGCGAAACTGCGCGATCATCTGCTTCTGCTGCCGGAAAAGTAAAAAGCCACCCAG‑CCGTCGAACATCGCGCCGCAGGCTGAAAAAA‑CGCCACCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTcc                                                                                          <  1:465432/148‑1 (MQ=255)                                             cccctaaaaaaaGGGAGAGGGAAAAACTGCGCGATATTTGGCTTCGGCGGACAGAGAATTAAAAAGCCAGCCAG‑CCGTCGAACACCGGGCCGCAGGTGGAAGAAA‑CCCCACCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTCCCCg                                                                                       <  1:634740/142‑1 (MQ=255)                                                      aaaGGGAGATGGCGAAACGGCGCGATCATCGGCGTCTGCTGACCGAAAAGTAAAAACCCAGCCAG‑CCGTCGAACATGGCGTCGCAGGCGGAAGAAC‑CCCCACCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTCCCCGCTTTTTTg                                                                               <  2:612312/150‑1 (MQ=255)                                                         gggAGATGGCGAACCTGCGCGATCATCTGCGTCTGCTGCCCGAAAAGTAAAAACCCAGCAAG‑CCGTCGAACATCGCGTCGCAGTTTAAAGAAA‑CGCCGCCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTCCCCGCTTTTTTGTCa                                                                            <  1:301994/149‑1 (MQ=255)                                                          ggAGATGGAAAGCCTGCGCTTTCACCTGCGACTGCTGACAGAAAAGTAAAAACCCATCCAG‑CCGTCGAAATCCGCGTCAAAGG‑TGAAAAAACCCCCACCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTCCCCGCTTTTTTGTc                                                                             <  2:238071/148‑1 (MQ=255)                                                              atggaaaaaCTGCGCGACCCTCTGCGTCGGCTGACCGAAAAGTAAAACCCCAGCCAG‑CCGAAGAACATCGCGCCGCGGGCTGAAGAAA‑CGCCCCCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTCCCCGCTTTTTTGTCACtt                                                                         <  2:217760/142‑1 (MQ=255)                                                              aTGGCGAAACTGCGCGATCATCTGCGTCTGCTGACCGAGAAGTTAAAAGCCAGCCAG‑CCGTCGAACATCGCGTCGCAGGCTGAAGAAA‑CGCCACCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTCCCCGCTTTTTTGTCACttttt                                                                      >  2:170902/1‑151 (MQ=255)                                                                ggCGAAACGGCGCGATCATCTGCGTCTGCTGACCGAGAAGTAAAAAGCCAGCCAG‑CCGTCGAACATCGCGTCGCAGGCTGAAAAAA‑CGCCACCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTCCCCGCTTTTTTGTCACTTTTTc                                                                     <  1:277363/150‑1 (MQ=255)                                                                ggCAAAACTGCGCGATCATCTGCGTCTGCGGACCGAAAAGTAAAAAGCCAGCCAG‑CCGTCAAACATCGCGTCGCGGGCTGAAGAAC‑CCCCACCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTCCCCGCTTTTTTGTCACTTTTTCg                                                                    <  1:499674/151‑1 (MQ=255)                                                                   gAAACTGCGCGATCATCTGCGTCTGCTGACCGAGAAGTTAAAAGCCAGCCAG‑CCGTCGAACATCGCGTCGCAGGCTGAAGAAA‑CGCCACCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTCCCCGCTTTTTTGTCACTTTTTCGGt                                                                  >  2:115585/1‑150 (MQ=255)                                                                     aaCTGCGCGATCATCTGCGTCTGCTGACCGAGAAGTAAAAAGCCAGCCAG‑CCGTCGAACACCGCGTCGCAGGCTGAAGAAA‑CCCCACCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTCCCCGCTTTTTTGTCACTTTTTCGGTAtt                                                               <  1:44307/151‑1 (MQ=255)                                                                          cgcgATCATCTGCGTCTGCTGACCGAGAAGTAAAAAGCCACCCAG‑CCGTCAAACATCGCGTCGCGGGCTAAAAAAC‑CGCCCCCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTCCCCGCTTTTTTGTCACTTTTTCGGTATTAGTg                                                           <  2:141400/150‑1 (MQ=255)                                                                                  tcTGCGCCTGCGGACGGAGAAGTAAAAAGCCAGCCAG‑CCGTCGAACATCGCGTCCCAGGCTGAAGAAC‑CCCCTCCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTCCCCGCTTTTTTGTCACTTTTTCGGTATTAGTGgcaacc                                                     <  2:199045/148‑1 (MQ=255)                                                                                     gCGTCTGCTGACCGAGAAGTAAAAAGCCAGCCAG‑CCGTCGAACATCGCGTCGCAGGCTGAAGAAA‑CGCCACCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTCCCCGCTTTTTTGTCACTTTTTCGGTATTAGTGgcaaccgc                                                   <  1:174116/147‑1 (MQ=255)                                                                                         ctgcagACCGAGAAGTAAAAAGCCAGCCAC‑CCGGCGAACACCGCGTCGCAGGCTAAAAAAA‑CCCCACCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTCCCCGCTTTTTTGTCACTTTTTCGGTATTAGTGgcaaccgcaa                                                 <  1:15462/145‑1 (MQ=255)                                                                                             tgACCGAGAAGTTAAAAGCCAGCCAG‑CCGTCGAACATCGCGTCGCAGGCTGAAGAAA‑CGCCACCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTCCCCGCTTTTTTGTCACTTTTTCGGTATTAGTGGCAACCGCAACCGCCGTTGc                                       >  1:186556/1‑151 (MQ=255)                                                                                                 cggaaatgtAAAAACCCGCCCGCCCGTCGAACACCGCGCCGCGGGTAGAAAAAC‑CCCCACCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTCCCCGCTTTTTTGTCACTTTTTCGGTATTAGTGGCAACCGCAAccgcc                                            <  1:385206/135‑1 (MQ=255)                                                                                                                cagccag‑ccGTCGAACATCGCGTCGCAGGCTGAAGAAA‑CGCCACCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTCCCCGCTTTTTTGTCACTTTTTCGGTATTAGTGGCAACCGCAACCGCCGTTGCCTTTACCGCCACAGCAGcc                    >  1:233351/1‑151 (MQ=255)                                                                                                                                cATCGCGTCGCAGGCTGAAGAAA‑CGCCACCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTCCCCGCTTTTTTGTCACTTTTTCGGTATTAGTGGCAACCGCAACCGCCGTTGCCTTTACCGCCACAGCAGCCTTCGCCACCGTGTTc     >  2:499742/1‑151 (MQ=255)                                                                                                                                   cgcgTCGCAGGCTGAAGAAA‑CGCCACCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTCCCCGCTTTTTTGTCACTTTTTCGGTATTAGTGGCAACCGCAACCGCCGTTGCCTTTACCGCCACAGCAGCCTTCGCCACCGTGTTCATg  >  1:254944/1‑151 (MQ=255)                                                                                                                                                         |                                                                                                                                  GGCTTTTCAGGAAATCACCATTGAAGAACTGAACGTCACGGTGACCGCTCATGAAATGGAGATGGCGAAACTGCGCGATCATCTGCGTCTGCTGACCGAGAAGTTAAAAGCCAGCCAG‑CCGTCGAACATCGCGTCGCAGGCTGAAGAAA‑CGCCACCGCCACATTATTGAGGCGTAAAAAAAGCGGGGATTCCCCGCTTTTTTGTCACTTTTTCGGTATTAGTGGCAACCGCAACCGCCGTTGCCTTTACCGCCACAGCAGCCTTCGCCACCGTGTTCATG  >  NC_000913/3477690‑3477969

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑