Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,755,871	0	T	A	42.9%	54.3 / 20.5	42	G58G (GGT→GGA)	pykF	pyruvate kinase I
Reads supporting (aligned to +/- strand):  ref base T (19/5);  new base A (0/18);  total (19/23)
Fisher's exact test for biased strand distribution p-value = 1.06e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACA‑CGGTC‑AGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGAAATGGTTGCG  >  NC_000913/1755721‑1756018                                                                                                                                                         |                                                                                                                                                    cACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACA‑CGGTC‑AGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGt                                                                                                                                                     <  2:733773/151‑1 (MQ=255) cACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACA‑CGGTC‑AGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGt                                                                                                                                                     <  2:223306/151‑1 (MQ=255)  aCCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACA‑CGGTC‑AGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTa                                                                                                                                                    <  1:405289/151‑1 (MQ=255)   ccATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACA‑CGGTC‑AGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTaa                                                                                                                                                   <  2:436258/151‑1 (MQ=255)       cGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACA‑CGGTC‑AGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAAc                                                                                                                                                <  2:755141/150‑1 (MQ=255)        ggACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACA‑CGGTC‑AGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAAccg                                                                                                                                              >  2:410909/1‑151 (MQ=255)         gACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACA‑CGGTC‑AGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAAccgc                                                                                                                                             <  2:311733/151‑1 (MQ=255)                                 tGTTAGAAAAAAGGCGGGACGCTGGCATGAACGTTAGGCGTCTAAACTTCTCTCAGGGTGACTATGCAAAACA‑CGGTC‑AGCGCATTCAAATTCTGCGCACCGTGATGAAAAAAACGGGAAAAACCGCCGCTATCCTGCTTGATACCaaa                                                                                                                       <  2:407799/149‑1 (MQ=255)                                   ttaacaaaatTGCGGGCCGCTGGCATGACCTTTATGCTTCGGAACTTCTCTCTTGGTGACTATCCAAAACC‑GGGTC‑AGCGCTTCCAGAATCGCCCCAACGGGAGGAGAAAAACTGAAAAAACCGCCGCTATCCTGCTTGATACCAAAgg                                                                                                                     <  2:159980/143‑1 (MQ=255)                                         aaatggCTGGACGCTGACATGAACTTTAGGGTTCTAAACTTCTCTAAGGGTGACTAGGAAAAACA‑‑GGTCAAGCCCATTAAGATTCTGCGAAAGGTAAGGAGAAAAACGGGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCgg                                                                                                                <  1:643978/143‑1 (MQ=255)                                         aaaaGGCGGGACGCGGGCATAAATTTTATGTGTCGAAATTTCTCTCAGGGTGATTAGGCAAAACA‑GGGTG‑AGCGCATTCAGAACCTGCGAAGCGGGATGGGAAAAACTGGAAAACCCGCCGCTATCCTGCTTGATACCAAAGGTCCGGaaa                                                                                                             <  2:705661/151‑1 (MQ=255)                                           agtGCTGGACGCTGGCATGAACTTTATGCGTCTGAACTACTCTCATGGTGACTATGAAAAACA‑CGGCC‑AGCACATTCAAAATCTGCGCAACGGAATGAGAAAACCTGTAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATc                                                                                                           <  1:519525/149‑1 (MQ=255)                                                  gACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACA‑CGGTC‑AGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCAcc                                                                                                     >  2:102739/1‑150 (MQ=255)                                                        ggaaggaagtttATGCTTTTTAACTTCCCTCGGGGTGAATAGGCA‑AACACCGGCC‑CGCGCTTTCAAATTGTGCCCAACGTGAGGAGCAAAACAGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATg                                                                                                  <  1:5097/137‑1 (MQ=255)                                                            tGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACA‑CGGTC‑AGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTgg                                                                                           >  2:66062/1‑150 (MQ=255)                                                                  ttATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACA‑CGGTC‑AGCGCATTCAGAATCTGCGCAACGTGATGGGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCgg                                                                                    >  2:19926/1‑151 (MQ=255)                                                                  ttATGCGTCTAAACTTCTCTCATGGTGACTATGCAAACCA‑CGGCC‑AGCGCATTCAGAATCTGCGAAAGGTGATGAAAAAAACTGAAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAgg                                                                                       <  2:382846/148‑1 (MQ=255)                                                                    aTGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACA‑CGGTC‑AGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGt                                                                                   >  2:138114/1‑150 (MQ=255)                                                                         tttaactttCTCTCATGGTGACTATGAAAAACA‑CGGCC‑AGCCCATTCAAAATCTGCGCAACGTAAGAAAAAAAACGGGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAacg                                                                               <  1:243720/142‑1 (MQ=255)                                                                             accTTCTCTCATGGTGATTAGGAAAAACC‑CGGTC‑AGCGCATTAAAAATCTGCGAAGCGGGATGAGAAAAACTGAAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGtt                                                                          <  2:390444/148‑1 (MQ=255)                                                                                   tctcATGGTGACTATGCAGAACA‑CGGTC‑AGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTg                                                                    >  2:630468/1‑150 (MQ=255)                                                                                       aTGGTGACTATGCAGAACA‑CGGTC‑AGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGc                                                               >  2:21875/1‑151 (MQ=255)                                                                                           tGACTATGCAGAACA‑CGGTC‑AGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGt                                                           >  1:141411/1‑151 (MQ=255)                                                                                                aTGCAGAACA‑CGGTC‑AGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGAc                                                      >  1:430489/1‑151 (MQ=255)                                                                                                 tgaaGAACA‑CGGAC‑AGCGAATTCAAAATCGGCCAAACGTGAGAAGAAAAACGGAAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGt                                                           <  1:142122/142‑1 (MQ=255)                                                                                                   cggAACA‑CGGTC‑AGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCtt                                                   >  1:148374/3‑151 (MQ=255)                                                                                                      acca‑cGGTC‑AGCGCATCCAAAATCTGCGAAAGGTGATGAAAAAAACTGTAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCttt                                                  <  2:503291/147‑1 (MQ=255)                                                                                                      aaCA‑CGGCC‑AGCGCATTAAAAATCGGCGCAAGGGAAGGAAAAAAACTGGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTa                                                 <  1:27846/150‑1 (MQ=255)                                                                                                            ggcc‑AGCGCTTTCAAATTCTGCGCAACGTAATGAGAAAAACTGAAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACttt                                             <  2:71826/146‑1 (MQ=255)                                                                                                            ggTC‑AGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTc                                            >  2:405960/1‑150 (MQ=255)                                                                                                            ggTC‑AGCGCATCCAGATTCTGCGCAACGTGAGGAAAAAAACTGGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACttt                                             <  2:509530/149‑1 (MQ=255)                                                                                                                      atcaaGAATCGGCGAATGGTAAGGAGAAAACGTGGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACt                                      <  1:546523/143‑1 (MQ=255)                                                                                                                          aaaaTCTGCGCAACGTGAAGAAAAAAACGGAAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAAt                               <  1:700376/148‑1 (MQ=255)                                                                                                                            aaccTGCGCAACGTGATGAGAAAAACTGGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTcacca                                        <  1:603357/136‑1 (MQ=255)                                                                                                                            aaTCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTg                            >  1:58812/1‑151 (MQ=255)                                                                                                                              tCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGtt                          >  1:381088/1‑151 (MQ=255)                                                                                                                                tGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTAt                        >  2:646758/1‑151 (MQ=255)                                                                                                                                   acaaggaaaagaaaaaaaCTGAAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCgg                     <  1:739292/137‑1 (MQ=255)                                                                                                                                     aacgtaaagaaaaaaaCGGGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGtt                          <  1:307475/132‑1 (MQ=255)                                                                                                                                         tgatgaGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAAc                 >  2:165204/1‑149 (MQ=255)                                                                                                                                             gaGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGa            >  1:760321/1‑150 (MQ=255)                                                                                                                                                cAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGAAATg        >  2:510758/1‑151 (MQ=255)                                                                                                                                                 aaaaCTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGAAATgg       >  2:213812/1‑151 (MQ=255)                                                                                                                                                      tGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGAAATGGTTGCg  >  1:14220/1‑151 (MQ=255)                                                                                                                                                         |                                                                                                                                                    CACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACA‑CGGTC‑AGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGAAATGGTTGCG  >  NC_000913/1755721‑1756018

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑