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%	72.9 / 35.3	56	G58G (GGT→GGA)	pykF	pyruvate kinase I
Reads supporting (aligned to +/- strand):  ref base T (27/5);  new base A (0/24);  total (27/29)
Fisher's exact test for biased strand distribution p-value = 2.79e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACG‑TTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGAAATGGTTG  >  NC_000913/1755722‑1756016                                                                                                                                                       |                                                                                                                                                   aCCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACG‑TTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGt                                                                                                                                                    >  1:1041720/1‑150 (MQ=255)  ccATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACG‑TTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑aa                                                                                                                                                 <  1:891848/151‑1 (MQ=255)  ccATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACG‑TTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑a                                                                                                                                                  <  1:1030726/150‑1 (MQ=255)    aTCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACG‑TTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑aaaa                                                                                                                                               <  2:68210/151‑1 (MQ=255)     tCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACG‑TTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAAc                                                                                                                                              >  2:826990/1‑151 (MQ=255)         aCCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACG‑TTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAAccgcc                                                                                                                                          >  2:1120412/1‑151 (MQ=255)               aaCCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACG‑TTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATc                                                                                                                                    >  2:1017972/1‑151 (MQ=255)                 ccGAATCTGAAGAGTTGTTAGCAAAAATGCGGGACGCGGGAATGAACT‑TTATGCGTCTGAACTTCTCTCAGGGTGACTATGAAGAACACGGTCAGCGCATTCAAAATCTGCGAAACGTGATGAGAAAAACTGGA‑AAAACCGCCGCTATCCt                                                                                                                                  <  1:457387/151‑1 (MQ=255)                        tGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACG‑TTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGAt                                                                                                                           >  1:629858/1‑151 (MQ=255)                                ttttAGCTAAAATGCTGGACGCGGGCATGAATG‑TTATGCTTCTGACCTTCTCTCATGGTGACTATGCAAAACCCGGTCAGCGCATTCAGAATCTGCGAAACGTGATGAGAAAACCTGAA‑AAAACCGCCGCTATCCTGCTTGATACCAAAg                                                                                                                    <  2:199757/148‑1 (MQ=255)                                tGTTAGAAAAAATGCGGGACGC‑GGGATTAACGTTTTTGCTTCAAACTTTCTCTCAGGGTGACTATGAAAAACGCGGTCACCCCTTTCAAATTCTGCGAAAGGTGATGAAAAAACCTGAA‑AAAACCGCCGCTATCCTGCTTGATAcc                                                                                                                        <  1:331533/146‑1 (MQ=255)                                        aaaaTGCTGGACGCGGGAATGAACT‑TTATGCGTCTAACCTTCTCTCATGGTAATTAGGCAAAACCGGGCCAGCCCATTCAAAATCTGCGAAAGGGAAGGAGAAAAACGGAA‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGaaa                                                                                                           <  1:882445/151‑1 (MQ=255)                                                ggACGCTGGCATGAACG‑TTATGTGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCAcc                                                                                                   >  2:612774/1‑151 (MQ=255)                                                 gcggcgggatttaaCT‑TTATGCGTCTGATCTTCTTTCGTTGTGACTATGGAGAACCGGTTAAGCTAATCCAAAATCTAGGAAACGTAATAAGAAAAACTGAA‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCAcc                                                                                                   <  2:779753/138‑1 (MQ=255)                                                   cccTGGCATGAGGT‑TTTTGCGTCTGCGCTTCTCTCATGGTGCCTAAGAAAACCCGGGTAACCCCTTTAAGATTCAGCGCAGCGTGAGGAAAAAAATTGAA‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATg                                                                                                <  2:827028/149‑1 (MQ=255)                                                     cTGGCATGAACG‑TTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGa                                                                                               >  1:38412/1‑150 (MQ=255)                                                         cATGAACG‑TTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTg                                                                                          >  2:430934/1‑151 (MQ=255)                                                            gAACG‑TTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGa                                                                                        >  2:98178/1‑150 (MQ=255)                                                            gAACG‑TTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGa                                                                                        >  2:870786/1‑150 (MQ=255)                                                             aaCG‑TTATGCGTCTGACCTTCTCTCGTGGTGACTATGCAAAACCCGGCCGGCCAATTAAAAATCGGCGGAACGTGAGGAGCAAAACGGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAg                                                                                      <  1:7424/151‑1 (MQ=255)                                                                  ttATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTcc                                                                                                                >  2:305383/1‑121 (MQ=255)                                                                   taggCGTCTGAACTTCTCTCATGGTGACTATGCAAAACACGCTCAGCGCATTCAGAATCTGCGCAGCGTGATGAGAAAAACTGAA‑AAACCCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCgg                                                                                  <  1:535310/147‑1 (MQ=255)                                                                       cGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAacg                                                                             >  2:42336/1‑151 (MQ=255)                                                                        gTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAacg                                                                             >  2:257689/1‑150 (MQ=255)                                                                         tCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAacgac                                                                           >  2:392651/1‑151 (MQ=255)                                                                           tGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGt                                                                         >  2:414142/1‑151 (MQ=255)                                                                            gAACTCCTCTATTGGTGAATATGAAGAACCCGGTCAGCGCATTAAAAATCTGCGCACCGGGAGAACAAAAACTGGA‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAacgac                                                                           <  2:793265/148‑1 (MQ=255)                                                                               cTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTtct                                                                     >  2:615723/1‑151 (MQ=255)                                                                                ttCTCTAATGGTGACAAGGCAAACCCCGGTCAGCGCATACAGAATCTGCGAAACGTGATAAGAAAAAGTGGA‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTtct                                                                     <  1:1017890/150‑1 (MQ=255)                                                                                      cATGGTGATTAGGCAAAACCCGGTCAGCGAATTCAAAACCTGCGCAACGGGAGAAGAAAAACTGAA‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGa                                                                 <  1:86496/148‑1 (MQ=255)                                                                                       aTGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGc                                                             >  1:1137598/1‑151 (MQ=255)                                                                                             aCTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTc                                                        >  1:402775/1‑150 (MQ=255)                                                                                             aCTATGCAAAACCCGGTCAGCGCATACAAAATCGGCGCAACGTGAGGAGAAAAACGGAA‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTc                                                        <  2:344704/150‑1 (MQ=255)                                                                                               tATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTc                                                        >  2:998119/1‑148 (MQ=255)                                                                                                 acaaaaaCACGATCAGCCCTTTCAGAATCTGCGCAGGGGGATAAACAAAGCTGAA‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGAcc                                                   <  2:54104/146‑1 (MQ=255)                                                                                                    aaaaCCCGGCCAGCGCATTAAAATTCGGCGCAACGTGATGAGAAAAACTGAA‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAg                                                      <  2:340938/143‑1 (MQ=255)                                                                                                    aaaaCACGGCCAGCCCATTAAGAATCGGCGCAACGGGATGAAAAAACCTGAA‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCttt                                                <  1:488674/149‑1 (MQ=255)                                                                                                    aGAACGCGGTCAGCGCATTAAAAATCGGCAAAGCGTGAGGAGAAAAACTGAA‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGa                                                     <  1:78810/146‑1 (MQ=255)                                                                                                      gttctggccggcgcTTTAAGAATCGGCGCAACGGGATAAACAAAACTGAA‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTa                                               <  2:456914/140‑1 (MQ=255)                                                                                                      aaCCCGGCCAGCGCATTAAAAATCGGCGAAAGGTAATAAGAAAAATTGGA‑AAACCCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAg                                                      <  1:12172/143‑1 (MQ=255)                                                                                                       acacGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACt                                             >  1:138560/1‑151 (MQ=255)                                                                                                           ggTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTa                                               >  1:456886/1‑145 (MQ=255)                                                                                                                 cgcATTAAAAATCTGCGAAAGGGAAGGAAAAAACCTGAA‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACt                                    <  1:99738/150‑1 (MQ=255)                                                                                                                    aTTCAGAATCTGCGCAACGTGATGAGAAAAACTGGA‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGAt                                 <  1:329393/150‑1 (MQ=255)                                                                                                                     ttCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATa                                >  1:728926/1‑150 (MQ=255)                                                                                                                     tccAGATTCGGCGCAACGGAATGAGAAAAATGGGA‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTcac                                        <  1:1030580/140‑1 (MQ=255)                                                                                                                         gAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCt                           >  2:809007/1‑151 (MQ=255)                                                                                                                          aaTCTGCGCAACGTGATGAAAAAAACTGAA‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCt                           <  2:1041802/150‑1 (MQ=255)                                                                                                                          aaTCGGCGCAACGGGATGAGAAAAACTGGA‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAAt                             <  1:997702/148‑1 (MQ=255)                                                                                                                           aTCTGCGAAAAGTGATGAGAAAAAGTGTA‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCt                           <  1:459595/149‑1 (MQ=255)                                                                                                                                cgcAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCg                    >  2:533748/1‑151 (MQ=255)                                                                                                                                   aaCGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGc                  >  1:295759/1‑150 (MQ=255)                                                                                                                                    aactgtaggaaaaaaATGGTAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGtt                        <  1:409048/133‑1 (MQ=255)                                                                                                                                           gaGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGa          >  2:487388/1‑150 (MQ=255)                                                                                                                                            aGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGaa         >  2:249524/1‑150 (MQ=255)                                                                                                                                             gCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGAAAt       >  2:158502/1‑151 (MQ=255)                                                                                                                                                    tGGA‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGAAATGGTTg  <  2:483121/149‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                   ACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACG‑TTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGAAATGGTTG  >  NC_000913/1755722‑1756016

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑