Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,285,853	0	G	T	42.5%	67.9 / 20.7	47	A126S (GCC→TCC)	agaD	N‑acetylgalactosamine‑specific enzyme IID component of PTS
Reads supporting (aligned to +/- strand):  ref base G (5/22);  new base T (20/0);  total (25/22)
Fisher's exact test for biased strand distribution p-value = 9.41e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.69e-01

TAATTTCGATGGAAGAAAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCAT‑CATTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCGCAGATGATTG  >  NC_000913/3285710‑3285997                                                                                                                                                 |                                                                                                                                                     taATTTCGATGGAAGAAAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGATTTGCTCTT‑CATTTtccag‑cc                                                                                                                                               >  2:760907/1‑150 (MQ=255)  aaTTTCGATGGAAGAAAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCAT‑CATTTgccag‑cca                                                                                                                                              <  2:413315/150‑1 (MQ=255)  aaTTTCGATGGAAGAAAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCAT‑CATTTGccag‑ccag                                                                                                                                             <  1:377616/151‑1 (MQ=255)      tCGATGGAAGAAAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCAT‑CATTTGCCAG‑CCAGGGa                                                                                                                                          <  1:233034/150‑1 (MQ=255)         aTGGAAGAAAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCAT‑CATTTGCCAG‑CCAAGGAAAcc                                                                                                                                      >  2:224287/1‑151 (MQ=255)            gaagaaAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCAT‑CATTTGCCAG‑CCAGGGAAACctg‑c                                                                                                                                  <  1:496861/151‑1 (MQ=255)             aagaaAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGATTTTTTCCT‑CATTTGTCTG‑CCAGGGAAACctg                                                                                                                                    >  2:685676/1‑149 (MQ=255)                 aaaaGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGATTTTTTCCT‑CATTTTCCAG‑CCCGGGgaaaacgctgg                                                                                                                                >  1:836593/1‑141 (MQ=255)                  aaaGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGTTTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGATTTTCTTCT‑CCTTTTTCAG‑CCAGGGAAAACCG‑CT‑gggg                                                                                                                            >  2:676869/1‑150 (MQ=255)                        gaAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGAATTTTTCAT‑TATTTTTCAG‑CCCGGGGAACCCG‑CT‑GGGGGCGGttt                                                                                                                     >  1:23448/1‑150 (MQ=255)                        gaAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGAATTTATCAT‑CATTTTTCCT‑CCAGGGGAAACTG‑CT‑GGGGCCGGtt                                                                                                                      >  2:179714/1‑150 (MQ=255)                        gaAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGCAATTTGCTCAT‑CATTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGAtt                                                                                                                      >  2:810121/1‑150 (MQ=255)                         aaaaCCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGATTTGTTCAT‑CCTTTTTCAT‑CCCGGGGAACCCG‑CT‑GGGGCCgggttt                                                                                                                    >  1:816098/1‑146 (MQ=255)                                cgACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCAT‑CATTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTc                                                                                                             <  2:859673/151‑1 (MQ=255)                                 gACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCAT‑CATTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTCg                                                                                                            <  2:819531/151‑1 (MQ=255)                                   cacCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCAT‑CATTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTCG‑cc                                                                                                         <  2:776895/151‑1 (MQ=255)                                    acCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCAT‑CATTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTCG‑CCg                                                                                                        <  1:225811/151‑1 (MQ=255)                                      cATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAAATTTCTCCT‑TCTTTTTCAG‑CCCGGGAAAACTC‑CC‑GGGGGCGCTTTTTTTTTTTG‑CCGtt                                                                                                      >  2:768041/1‑151 (MQ=255)                                        ttAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTTGTCAT‑CATTTTTCCG‑CCAGGGGAAACCG‑CT‑GGGGGCGGTTCTttttttttccctttt                                                                                                     >  2:120587/1‑142 (MQ=255)                                            aGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAGTTTGCTCAT‑CATTTGCCGG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTCG‑CCGTTTACCTg                                                                                                <  1:443198/151‑1 (MQ=255)                                                cTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCAT‑CATTTTCCAG‑CCAGGGGAACCTG‑CT‑GGGGGCGGTTCTTTTTTTTG‑CCGTTTTTCTGc                                                                                               >  2:408075/1‑148 (MQ=255)                                                     aGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCAT‑CATTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCttt                                                                                       <  2:666380/151‑1 (MQ=255)                                                        ggCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCAT‑CATTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCttttt                                                                                     <  2:297027/150‑1 (MQ=255)                                                                ttGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGATTTGTTCAT‑CATTTTGCCG‑CCCGGGAAAACTG‑CT‑TGGGGCGGGTCTTTTTTTTC‑CCCTTTTACTGCTTATTTTTTTTCTtcgc                                                                              >  2:865064/1‑149 (MQ=255)                                                                   gCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGATTTGCTTCT‑TATTTTGCAA‑CCCCGGAAACCCG‑CT‑GGGGGCCGTTTTTTTTTTTT‑CCCTTTTCCTTCTTTTCTTTTTTTTGCgcggcg                                                                          >  2:305118/1‑150 (MQ=255)                                                                    cccAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGGTTTTCTCTT‑CATTTTTCAG‑CCCGGGGAAACTG‑CT‑GGGGGCGGGTCTTTTTTTTG‑CCGTTTTCCTCCTTATTTTTTTTCt                                                                                  >  1:4917/1‑141 (MQ=255)                                                                    cccAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGAATTTTTCAT‑CCTTTTGCCG‑CCAGGGGAAACCG‑CT‑GGGGCCGGTTTTTTTTTTTGCCCGTTTCCCT‑CTTTTTTTTTTTCTTCGcggcgg                                                                         >  2:738514/1‑150 (MQ=255)                                                                       aaTCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAAATTGGTCATCCTTTTTCCTC‑CCCGGGAAACC‑G‑AT‑CGGGGCGGCTCTTTTTTTTG‑CCGTTTTCCTCCTTATCTTTTTTCTGCTCCTCgg                                                                         >  2:745395/1‑147 (MQ=255)                                                                        aTCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTTTTTCT‑CATTTTGCAG‑CCCGGGGAACCCGCCT‑GGGGCGGTTTTTTTTTTTTC‑CGGTTTACC‑GCCTTTCttttttc                                                                                   >  2:706190/1‑134 (MQ=255)                                                                                      cgatgcgatTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCCCCT‑TATTTTTCAC‑CCAGCGGGACCTG‑CTCGGGGCGGTTTTTTTTTTTGT‑CCCTTTTCC‑CCTTATTTTTTTTCTTCCCGGCGGCCGGGCCCCCGGCGGtttt                                                      >  1:255155/1‑149 (MQ=255)                                                                                      cgatgcgatTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAAATTTCTCTC‑AATTTTTCAGCCCGGGGAAACCGT‑CT‑‑GGGCCGGTTTTATTTTTTT‑CCGTTTTTCTCCTTTTCTTTTTTTTTCCCGTCGGCTGGGCCCAccccgggttt                                                      >  1:890659/1‑142 (MQ=255)                                                                                          gcgatTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCAT‑CATTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCa                                                   <  2:247879/150‑1 (MQ=255)                                                                                          gcgatTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCAT‑CATTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCa                                                   <  1:594801/150‑1 (MQ=255)                                                                                            gatTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCAT‑CCTTTTCCAG‑CCAGGGAAACCTG‑CT‑GGGGGCGGTTTTTTTTTTTG‑CCGTTTTCCTGCTTATTTTTTTTCTTCGCGGCGGCGGGGCCCACGTCGGTTTTTTAg                                                  >  2:822448/1‑149 (MQ=255)                                                                                                    ggTTTACTTTGTTGCCGATTATGGCGGTAATTTGCTCAT‑CATTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTg                                          <  1:375370/149‑1 (MQ=255)                                                                                                    ggTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCAT‑CATTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGTCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGaa                                        <  2:10800/151‑1 (MQ=255)                                                                                                       ttACTTTGTTGCCGATTATGGCGGGAATTTGTTCAT‑TATTTTCCAA‑CCAGGGGAAACTG‑CT‑GGGGGCGATTCTCTTTTTTT‑CCCTTTTCCTTCTTATCTTTTTTCTTCGCGTCGGCTGGGCCCCCCTCGGTTATTTCGTTGGCGTGGAgg                                      >  2:824855/1‑150 (MQ=255)                                                                                                       ttACTTTGTTGCCGATTATGGCGGGAATTTGCTCAT‑CATTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAgg                                      <  1:614474/150‑1 (MQ=255)                                                                                                       ttACTTTGTTGCCGATTATGGCGGGAATTTGCTCAT‑CATTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAgg                                      <  1:489686/150‑1 (MQ=255)                                                                                                           tttGTTGCCGATTATGGCGGGGAATTTCTCCT‑CATTTTCCCG‑CCCGGGGAAACTG‑CT‑GGGGGCGGGTTTTTTTTTTT‑CCGTTTTCCTTCTTTTCTTTTTTTTTCCCGGCGGCTGGACCCCCCTCGGGTTTTTTTTCGGCGTGTAGGcg                                    >  1:376065/1‑148 (MQ=255)                                                                                                             tgttgCCGATTATGGCGGGAATTTGCTCAT‑CATTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGcgatcg                                <  1:721347/150‑1 (MQ=255)                                                                                                                 gCCGATTATGGCGGGAATTTGCTCAT‑CATTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATaaa                           <  1:310711/151‑1 (MQ=255)                                                                                                                        aTGGCGGGGATTTGCTCAT‑CATTTTCCAG‑CCAGGGAAAACTG‑CT‑GGGGCCGATTCTTTTTTTCT‑CCGTTTACCTGCGTATCTTTTTCCTGCGCGTCGGCTGGGCCCACGTCGGGTATTTAGTCGGCGGGGAAGCGATCGATAAAGTg                        >  1:405013/1‑147 (MQ=255)                                                                                                                          ggCGGGAATTTGCTCAT‑CATTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCgaga                   <  1:592765/150‑1 (MQ=255)                                                                                                                           gCGGGAATTTGCTCAT‑CATTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCgagaga                 <  1:92607/151‑1 (MQ=255)                                                                                                                                       tcat‑caTTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCGCAgatg      >  1:524051/1‑150 (MQ=255)                                                                                                                                        cat‑catTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCGCAgatgat    <  1:583857/151‑1 (MQ=255)                                                                                                                                        cat‑catTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCGCAgatgat    >  1:153957/1‑151 (MQ=255)                                                                                                                                            catTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCGCAGATGATTg  <  1:82071/150‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                     TAATTTCGATGGAAGAAAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCAT‑CATTTGCCAG‑CCAGGGAAACCTG‑CT‑GGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCGCAGATGATTG  >  NC_000913/3285710‑3285997

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑