Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,755,871	0	T	A	51.2%	28.9 / 65.5	41	G58G (GGT→GGA)	pykF	pyruvate kinase I
Reads supporting (aligned to +/- strand):  ref base T (20/0);  new base A (0/21);  total (20/21)
Fisher's exact test for biased strand distribution p-value = 3.72e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.16e-07

CATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGAAATGGTTGCGGT  >  NC_000913/1755724‑1756020                                                                                                                                                      |                                                                                                                                                       cATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTaa                                                                                                                                                      >  2:93042/1‑150 (MQ=255)  aTCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTaaa                                                                                                                                                     >  2:650439/1‑150 (MQ=255)  aTCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTaaa                                                                                                                                                     >  2:791524/1‑150 (MQ=255)      gACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAA‑ccgc                                                                                                                                               >  2:426852/1‑151 (MQ=255)           aaaaCCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAA‑CCGCCGCt                                                                                                                                           >  2:680512/1‑150 (MQ=255)                    tCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAA‑CCGCCGCTATCCTGCTTg                                                                                                                                 >  1:779418/1‑151 (MQ=255)                      taaaGAGTTGTTAGCTAAAATGGTGGACGCTGGCATGAACTTTATGCGTCTGAACTTCCCTCATGGTAATTATGAAAAAC‑CGGTCCACCGCATTAAAAATCGGCGCAACGTGATGAGAAAATCT‑GAAAAAA‑CCGCCGCTATCCTGCTTGa                                                                                                                                <  1:37042/148‑1 (MQ=255)                         agagATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAA‑CCGCCGCTATCCTGCTTGATAcc                                                                                                                            >  1:448187/1‑151 (MQ=255)                              ttttaacaaaaaGGCTGGACGCGGGCATGAACTTTGTGCTTCTCTACTTCCCTTAGGGTGCATATGAAAAACACGTA‑CAGCTCATTCAGATTCTCCGCATGGTGAGGAGAAAAACG‑GAAAAAA‑CCGCCGCTATCCTGCTTGATACCAAAg                                                                                                                        <  1:123268/142‑1 (MQ=255)                                ttctatAAAGTGCGGGACGCTGGCATAAACTTTATGCGTTTGATCTTCTCTCAGGGGAACTAGGAAAAACCGGGT‑CAGCTCTCCAAGAATCGCCCCAAGGGGATGAAAAAACCG‑GAAAAAA‑CCGCCGCTATCCTGCTTGa                                                                                                                                <  1:515655/135‑1 (MQ=255)                                ttaccaaaatTGCTGGCCGCTGGAATGAACGTTAGCCGTCTAACCTTCTCTAATGGTGACTAGGAACACCACGTC‑CGGCCCATCCAGATTCTGCGCAAGGTAAAAACAAAAACG‑GAAAAAA‑CCGCCGCTATCCTGCTTGATACCAAAg                                                                                                                        <  1:756087/142‑1 (MQ=255)                                  aGCAAAAAGGCGGGCCGCGGGAATGACCTTTACGCTTCTAATCTCCTCTCATGGTGCCTATGCAAAACCGGGT‑CAGCGCATTCAGAATCTGCGCAACGTGAGGAGAAAAACG‑GAAAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTcc                                                                                                                    <  2:626020/150‑1 (MQ=255)                                     tAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGa                                                                                                                 >  1:709917/1‑150 (MQ=255)                                       aaaTGCTGGGCGCGGACATGAATTTTATGCGTCTAAACTTCTCTCATGGTGAATAGGCAAAACCCGGT‑CAGCCCTTTCAGAATGTGCGCAACGTGATAAACAAAAGT‑GGAAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCg                                                                                                                   <  1:290719/146‑1 (MQ=255)                                          tGCTGGACGCTGGCATAACTGTTTGGCTTCAAACCTTCTTTCAGGGTGACTATGCAAACCCGGGT‑CGGCGAATTAAAATTCTGCGCAACG‑GAGTAACAAAAGTGGGAAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATcc                                                                                                            <  2:789060/150‑1 (MQ=255)                                             tGGACGCTGGCATGAACGTTATGCGGCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAACTCCGCAc                                                                                                        >  1:185069/1‑151 (MQ=255)                                              ggcggctgaaaggAACGTTATGCGTCTGACCTCCTCTCATGGTGACTATGAAAAACACGGT‑CAGCGCATTAAGATTCTGCGCACCGTGATGAAAAAACCT‑GAAAAAC‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCAc                                                                                                        <  2:786727/138‑1 (MQ=255)                                               gACGCGGGCAGGAACGTTATGCGTCTGACCTTCTCTCATGGTGACTAGGCAAACCCCGGC‑CAGCGCATTAAGAATCTCCGCACGGTGAGGAAAAAAACG‑GAAAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCa                                                                                                      <  2:392079/151‑1 (MQ=255)                                                  gCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATg                                                                                                    >  1:321881/1‑150 (MQ=255)                                                      gCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACt                                                                                               >  1:774984/1‑151 (MQ=255)                                                         taaaCGTTATGCGTCTGACCTTCTCTCATGGTGACTATGCAAAGCACGTT‑CGGCGCTTTCAAATTCTGCCCAAGGTGATAAAAAAACCT‑GGAAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTgg                                                                                             <  2:383952/148‑1 (MQ=255)                                                            actttttGCCTCTAACCTTCTCTCATGGTGACTATGCAAAACCCGGT‑CAGCCCATTAAAAATCGGCGAAACGTGATGAGAAAACTT‑GGAAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAgg                                                                                         <  2:539136/145‑1 (MQ=255)                                                            acttttggCGTCTAAACTTCTCCCAGGGTAACTAGGAAAAACCCGGT‑CACCCCATCCAAATTCGGGCCAAGGTAAGAAGAAAAAGT‑GAAAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTgg                                                                                             <  1:16894/140‑1 (MQ=255)                                                                      tCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAacgac                                                                               >  1:631181/1‑151 (MQ=255)                                                                            cTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTtct                                                                         >  1:49804/1‑151 (MQ=255)                                                                             ttCTCTCATGGTGATTATGCAGACCACGGT‑CAGCGAATTAAAAATCTGCGCAAGGTGAGGAGAAAACCT‑GAAAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAac                                                                                  <  2:847543/141‑1 (MQ=255)                                                                             ttCTCTCATGGTGACTAGGCAAAACGCGGG‑CAGCGCATTCAGAATCGGCGCAAGGTGAGGAAAAAAACT‑GAAAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAacga                                                                                <  1:408105/143‑1 (MQ=255)                                                                                             aagCAGAACACGTT‑CCGCGCATACAGATCCGGCGAAAGGTGATGAAAAAACCT‑GAAAAAG‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAg                                                          <  1:658408/147‑1 (MQ=255)                                                                                             aTGAAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGAAAAACT‑GAAAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGa                                                         <  2:124762/150‑1 (MQ=255)                                                                                                  gAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCttt                                                    >  2:760233/1‑150 (MQ=255)                                                                                                   aaCACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTAc                                                  >  1:678260/1‑151 (MQ=255)                                                                                                     cgcGGT‑CAGCACATTAAAAGTCTGCCAAACGGGATGAGAAAATGG‑GGAAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTa                                                   <  2:143725/146‑1 (MQ=255)                                                                                                     cacGGT‑CAGCGCATTCAGAATCGGCGAAAGGTGAGGAGAAAATCT‑GAAAAAT‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACtt                                                <  2:414519/151‑1 (MQ=255)                                                                                                                        aacccgccaagtgTGATGACAAAAACG‑GGAAAAT‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTg                                       <  2:591149/130‑1 (MQ=255)                                                                                                                         aTCAGCCCAACGTGCTGACCAAAACT‑GGTAAAA‑CCGCCGCTATCCTGCTTGATACCACAGGACCGGCAATCCGCACCATGAAACTCGAAGGTCGCTCCCACGTCTCCCTCACAGCTGGTCAGACCTTTCGTTTCACCCCTGATACCTCTGt                             >  1:505229/1‑151 (MQ=255)                                                                                                                             gcgcAACGTGATGAGCAAAACT‑GGTAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATc                         >  2:762629/1‑151 (MQ=255)                                                                                                                               cgcaatgagaagaaaaaaCC‑GGAAAAACCCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTa                           <  2:779629/134‑1 (MQ=255)                                                                                                                                    gTGATGAGCAAAACT‑GGTAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAAc                   >  2:144554/1‑150 (MQ=255)                                                                                                                                          acaaaaaCT‑GAAACAT‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGa              <  1:834332/146‑1 (MQ=255)                                                                                                                                           gCAAAACT‑GGTAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGAAAt           >  1:300664/1‑151 (MQ=255)                                                                                                                                                aCT‑GGTAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGAAATGGTTg      >  2:207233/1‑151 (MQ=255)                                                                                                                                                      tAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGAAATGGTTGCGGt  >  1:435062/1‑150 (MQ=255)                                                                                                                                                      |                                                                                                                                                       CATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGAAATGGTTGCGGT  >  NC_000913/1755724‑1756020

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑