Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,755,862	0	C	A	43.6%	47.2 / 24.1	39	S55R (AGC→AGA)	pykF	pyruvate kinase I
Reads supporting (aligned to +/- strand):  ref base C (19/3);  new base A (0/17);  total (19/20)
Fisher's exact test for biased strand distribution p-value = 2.57e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGAAAT  >  NC_000913/1755719‑1756011                                                                                                                                                 |                                                                                                                                                       tGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACt                                                                                                                                                  <  2:156360/150‑1 (MQ=255)      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‑GGTAAAAccgc                                                                                                                                      >  2:426852/1‑151 (MQ=255)                aaaaCCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAACCGCCGCt                                                                                                                                  >  2:680512/1‑150 (MQ=255)                         tCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAACCGCCGCTATCCTGCTTg                                                                                                                        >  1:779418/1‑151 (MQ=255)                           taaaGAGTTGTTAGCTAAAATGGTGGACGCTGGCATGAACTTTATGCGTCTGAACTTCCCTCATGGTAATTATGAAAAAC‑CGGTCCACCGCATTAAAAATCGGCGCAACGTGATGAGAAAATCT‑GAAAAAACCGCCGCTATCCTGCTTGa                                                                                                                       <  1:37042/148‑1 (MQ=255)                              agagATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAACCGCCGCTATCCTGCTTGATAcc                                                                                                                   >  1:448187/1‑151 (MQ=255)                                   ttttaacaaaaaGGCTGGACGCGGGCATGAACTTTGTGCTTCTCTACTTCCCTTAGGGTGCATATGAAAAACACGTA‑CAGCTCATTCAGATTCTCCGCATGGTGAGGAGAAAAACG‑GAAAAAACCGCCGCTATCCTGCTTGATACCAAAg                                                                                                               <  1:123268/142‑1 (MQ=255)                                     ttctatAAAGTGCGGGACGCTGGCATAAACTTTATGCGTTTGATCTTCTCTCAGGGGAACTAGGAAAAACCGGGT‑CAGCTCTCCAAGAATCGCCCCAAGGGGATGAAAAAACCG‑GAAAAAACCGCCGCTATCCTGCTTGa                                                                                                                       <  1:515655/135‑1 (MQ=255)                                     ttaccaaaatTGCTGGCCGCTGGAATGAACGTTAGCCGTCTAACCTTCTCTAATGGTGACTAGGAACACCACGTC‑CGGCCCATCCAGATTCTGCGCAAGGTAAAAACAAAAACG‑GAAAAAACCGCCGCTATCCTGCTTGATACCAAAg                                                                                                               <  1:756087/142‑1 (MQ=255)                                       aGCAAAAAGGCGGGCCGCGGGAATGACCTTTACGCTTCTAATCTCCTCTCATGGTGCCTATGCAAAACCGGGT‑CAGCGCATTCAGAATCTGCGCAACGTGAGGAGAAAAACG‑GAAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTcc                                                                                                           <  2:626020/150‑1 (MQ=255)                                          tAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGa                                                                                                        >  1:709917/1‑150 (MQ=255)                                            aaaTGCTGGGCGCGGACATGAATTTTATGCGTCTAAACTTCTCTCATGGTGAATAGGCAAAACCCGGT‑CAGCCCTTTCAGAATGTGCGCAACGTGATAAACAAAAGT‑GGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCg                                                                                                          <  1:290719/146‑1 (MQ=255)                                               tGCTGGACGCTGGCATAACTGTTTGGCTTCAAACCTTCTTTCAGGGTGACTATGCAAACCCGGGT‑CGGCGAATTAAAATTCTGCGCAACG‑GAGTAACAAAAGTGGGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATcc                                                                                                   <  2:789060/150‑1 (MQ=255)                                                  tGGACGCTGGCATGAACGTTATGCGGCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAACTCCGCAc                                                                                               >  1:185069/1‑151 (MQ=255)                                                   ggcggctgaaaggAACGTTATGCGTCTGACCTCCTCTCATGGTGACTATGAAAAACACGGT‑CAGCGCATTAAGATTCTGCGCACCGTGATGAAAAAACCT‑GAAAAACCCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCAc                                                                                               <  2:786727/138‑1 (MQ=255)                                                    gACGCGGGCAGGAACGTTATGCGTCTGACCTTCTCTCATGGTGACTAGGCAAACCCCGGC‑CAGCGCATTAAGAATCTCCGCACGGTGAGGAAAAAAACG‑GAAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCa                                                                                             <  2:392079/151‑1 (MQ=255)                                                       gCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATg                                                                                           >  1:321881/1‑150 (MQ=255)                                                           gCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACt                                                                                      >  1:774984/1‑151 (MQ=255)                                                              taaaCGTTATGCGTCTGACCTTCTCTCATGGTGACTATGCAAAGCACGTT‑CGGCGCTTTCAAATTCTGCCCAAGGTGATAAAAAAACCT‑GGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTgg                                                                                    <  2:383952/148‑1 (MQ=255)                                                                 actttttGCCTCTAACCTTCTCTCATGGTGACTATGCAAAACCCGGT‑CAGCCCATTAAAAATCGGCGAAACGTGATGAGAAAACTT‑GGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAgg                                                                                <  2:539136/145‑1 (MQ=255)                                                                 acttttggCGTCTAAACTTCTCCCAGGGTAACTAGGAAAAACCCGGT‑CACCCCATCCAAATTCGGGCCAAGGTAAGAAGAAAAAGT‑GAAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTgg                                                                                    <  1:16894/140‑1 (MQ=255)                                                                           tCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAacgac                                                                      >  1:631181/1‑151 (MQ=255)                                                                                 cTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTtct                                                                >  1:49804/1‑151 (MQ=255)                                                                                  ttCTCTCATGGTGATTATGCAGACCACGGT‑CAGCGAATTAAAAATCTGCGCAAGGTGAGGAGAAAACCT‑GAAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAac                                                                         <  2:847543/141‑1 (MQ=255)                                                                                  ttCTCTCATGGTGACTAGGCAAAACGCGGG‑CAGCGCATTCAGAATCGGCGCAAGGTGAGGAAAAAAACT‑GAAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAacga                                                                       <  1:408105/143‑1 (MQ=255)                                                                                                  aagCAGAACACGTT‑CCGCGCATACAGATCCGGCGAAAGGTGATGAAAAAACCT‑GAAAAAGCCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAg                                                 <  1:658408/147‑1 (MQ=255)                                                                                                  aTGAAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGAAAAACT‑GAAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGa                                                <  2:124762/150‑1 (MQ=255)                                                                                                       gAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCttt                                           >  2:760233/1‑150 (MQ=255)                                                                                                        aaCACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTAc                                         >  1:678260/1‑151 (MQ=255)                                                                                                          cgcGGT‑CAGCACATTAAAAGTCTGCCAAACGGGATGAGAAAATGG‑GGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTa                                          <  2:143725/146‑1 (MQ=255)                                                                                                          cacGGT‑CAGCGCATTCAGAATCGGCGAAAGGTGAGGAGAAAATCT‑GAAAAATCCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACtt                                       <  2:414519/151‑1 (MQ=255)                                                                                                                             aacccgccaagtgTGATGACAAAAACG‑GGAAAATCCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTg                              <  2:591149/130‑1 (MQ=255)                                                                                                                              aTCAGCCCAACGTGCTGACCAAAACT‑GGTAAAACCGCCGCTATCCTGCTTGATACCACAGGACCGGCAATCCGCACCATGAAACTCGAAGGTCGCTCCCACGTCTCCCTCACAGCTGGTCAGACCTTTCGTTTCACCCCTGATACCTCTGt                    >  1:505229/1‑151 (MQ=255)                                                                                                                                  gcgcAACGTGATGAGCAAAACT‑GGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATc                >  2:762629/1‑151 (MQ=255)                                                                                                                                         gTGATGAGCAAAACT‑GGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAAc          >  2:144554/1‑150 (MQ=255)                                                                                                                                                gCAAAACT‑GGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGAAAt  >  1:300664/1‑151 (MQ=255)                                                                                                                                                 |                                                                                                                                                       TGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGT‑CAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACT‑GGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGAAAT  >  NC_000913/1755719‑1756011

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑