Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,036,927	0	T	A	42.0%	74.3 / 22.3	50	L60Q (CTA→CAA)	hyaF	hydrogenase‑1 protein nickel incorporation factor
Reads supporting (aligned to +/- strand):  ref base T (22/7);  new base A (0/21);  total (22/28)
Fisher's exact test for biased strand distribution p-value = 2.63e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGGAACGCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGATGAACCGAGTATGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCGGGGAAGGGGAAGTGTCAGTGCGCATTCAGCAGGCTGACGACAGTGAAAGTGAAATAC  >  NC_000913/1036780‑1037076                                                                                                                                                     |                                                                                                                                                       cAGGAACGCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGATGAACCGAGTATGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTa                                                                                                                                                       >  1:434315/1‑149 (MQ=255)  aGGAACGCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGATGAACCGAGTATGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGc                                                                                                                                                    >  1:575667/1‑151 (MQ=255)   ggAACGCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGATGAACCGAGTATGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGCg                                                                                                                                                   <  1:632750/151‑1 (MQ=255)       cGCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGATGAACCGAGTATGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑Cg                                                                                                                                              >  2:817602/1‑151 (MQ=255)       cGCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGATGAACCGAGTATGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑Cg                                                                                                                                              <  1:468601/151‑1 (MQ=255)        gCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGATGAACCGAGTATGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑CGc                                                                                                                                             >  1:406459/1‑151 (MQ=255)         cAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGATGAACCGAGTATGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑CGcc                                                                                                                                            <  2:28287/151‑1 (MQ=255)           aCCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGATGAACCGAGTATGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑CGCCaa                                                                                                                                          <  1:791160/151‑1 (MQ=255)             cGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGATGAACCGAGTATGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑CGCCAAcc                                                                                                                                        >  1:374469/1‑151 (MQ=255)                 cGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGATGAACCGAGTATGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑CGCCAAccgccg                                                                                                                                    >  2:533678/1‑151 (MQ=255)                                  tggttcctcggCCGATCGCCTCTCAGGTGAGTGATGAGCCGTGTAGGGGTGCCTGGAAACAATTTACTCCCAGCCCGCAGGTGATTGCGCTGTAAAGCGATTTGA‑AACATCAAGAAAGCGAC‑CGCCAACCGCCGTTGGGCGAgg                                                                                                                          <  1:276415/134‑1 (MQ=255)                                    aaTCCACTGCCGATCACCTGTCAGGTGAATGATGAACCGAGTATGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGc                                                                                                                   >  1:426967/1‑149 (MQ=255)                                       ccccTGCCGATCCCCTGTCGGGTAAATGATAAACCGAGTTGGGCGGCCCGGGAGAAATGTGCTCACGGCCCGCGGGTGTTTGCGTTTTTAAACGAGTTAA‑AACATAAACAAGGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTc                                                                                                               <  2:128726/147‑1 (MQ=255)                                         cccgcggacccccTGCCAGGTGAATGATGAACGGATTTGGGCGGCCCGGGACCATTGTCCTCCCAGCCCGCGGGTGTTTCCGTTGTTAAACGATTAAC‑ACCATCAACAAAGAGAG‑CCCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGa                                                                                                             <  2:406470/139‑1 (MQ=255)                                                aTCACCTGTCAGGTGAATGATGAACCGAGTATGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTa                                                                                                      >  1:519923/1‑150 (MQ=255)                                                  cACCTGTCAGGTGAATGATGAACCGAGTATGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAAt                                                                                                   >  2:607213/1‑151 (MQ=255)                                                  cACCGGTCGGGTAAATGATGAACGGAGTAGGGGGGCCCTGGAGAAATGTGCCCACAGCCCGCGGGTGATTGGGTTTTTAAACGAGTAAA‑AACAAC‑ACAAAGGGAACCGCAAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAAt                                                                                                   <  1:393733/151‑1 (MQ=255)                                                        tCAGGTGAATGATGAACCGAGTATGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAAc                                                                                             >  1:15064/1‑151 (MQ=255)                                                               agggaagaACCGAGTGTGCCGCCCCTGGAGAAATGTCCTCACGGCCCGCAGGTGATTGCGCTGTAAAACGAGTTAC‑AACAACACCAAGGCGAC‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCa                                                                                               <  1:918789/136‑1 (MQ=255)                                                                     gaACCGAGTATGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTc                                                                                >  2:687544/1‑151 (MQ=255)                                                                      accggggTATGGGGGCCCTGGAGAAATGTGCTCACCGCCCGCGGGTGTTTGCGCTGTAAAACGATTAAC‑AACATCAACAAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATc                                                                                   <  2:730582/141‑1 (MQ=255)                                                                          gggaaTGGCGCCCCGGGAGCAATGTGCTCAGAGCCCGCGGGTGATTGCGCTGTAAAACGATTAAC‑AACATCAACTAAGCGAA‑CGCAAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACtt                                                                            <  2:461614/146‑1 (MQ=255)                                                                              aTGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATc                                                                        >  2:646520/1‑150 (MQ=255)                                                                                gggggcCCGGGAGAAATGTGCCCACCCCCCGCAGGTGATTGCGCTGTTAAGCGAGATAC‑AACAAAAACAAAGCAAA‑CCCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAAt                                                                     <  1:913653/148‑1 (MQ=255)                                                                                ggcggcCCGGGAGCATTGTGCCCACACCCCGCAGGTGATTGCGTTGTAAAACGATTAAA‑ACCATAAACAAAGCAAC‑CCCAAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCa                                                                       <  2:650795/149‑1 (MQ=255)                                                                                ggcggcCCGGGAGAATTGTGCCCAAAGCCCGCAGGTGTTTGCGCTTTTAAAGGATTAAA‑AACATAAACTAAGCAAC‑CCCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCa                                                                               <  1:98644/141‑1 (MQ=255)                                                                                ggcgccCCTGGAGAATTGTGCTCACAGCCCGCAGGTGATTGCGCTGTAAAACGATTTAA‑AAAACCAACAAAGCGAC‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACt                                                                             <  2:98800/143‑1 (MQ=255)                                                                                ggcgccCCGGGAGAATTGTGCCCACGCCCCGGAGGTGATGCCGCTGTAAAAGGTTTAAA‑AACATCAACAAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCa                                                                       <  1:868875/149‑1 (MQ=255)                                                                                    gcCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGc                                                                 >  1:686213/1‑151 (MQ=255)                                                                                                tggccTCACAGCCCGCGGGTGATTGCGCTTTTAACCGAGTTAC‑AACATAAACTAAGCAAC‑CGCAAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCgggga                                                       <  2:759343/145‑1 (MQ=255)                                                                                                 gtgCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCggggaagg                                                    >  2:14451/1‑151 (MQ=255)                                                                                                 gtgCCCACGGCCCGAAGGTGATTGCGTTGTTAAACGAGTTAC‑AACATCAACAAAGCGAC‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCggggaa                                                      <  2:426978/149‑1 (MQ=255)                                                                                                    cccccaGCCCGCAGGTGATTGCGCTGTAAAACGAGTAAC‑AACATCAACAAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCggggaagggga                                                 <  1:297546/147‑1 (MQ=255)                                                                                                      cacacccggcggtttaTTGCGCTTTAAAACGAGTAAC‑AACATCAACAAAGCAAC‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCGgggaaggggaag                                               <  1:535820/136‑1 (MQ=255)                                                                                                       acaGCCCGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCGgggaaggggaag                                               >  1:184036/1‑150 (MQ=255)                                                                                                           cccGCAGTTGATTGCTTTTTTAAAGGA‑TTACAAACATAAACAAAGCAAC‑CCCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCGGGGAAGGGGAAGTGTCa                                          <  1:607198/151‑1 (MQ=255)                                                                                                           cccGCAGGTGTTGGCGCTGTAAACCGATTTAC‑AACATAACCAAAGGGAC‑CGCAAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCggggaaggggaa                                                <  2:190046/145‑1 (MQ=255)                                                                                                           cccGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCGGGGAAGGGGAAGTGTc                                           >  2:51860/1‑150 (MQ=255)                                                                                                           cccGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCGGGGAAGGGGAAGTGTc                                           >  2:939309/1‑150 (MQ=255)                                                                                                                      ttGCGCTTTAAAACGATTAAC‑AACATCAAAAAAGCGAA‑CCCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCGGGGAAGGGGAAGTGTCAGTGCGCAtt                                 <  2:583641/149‑1 (MQ=255)                                                                                                                        gcgcTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCGGGGAAGGGGAAGTGTCAGTGCGCATTcagc                             >  2:255679/1‑151 (MQ=255)                                                                                                                        gcgcTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCGGGGAAGGGGAAGTGTCAGTGCGCATTcagc                             >  2:315756/1‑151 (MQ=255)                                                                                                                          gcTGTAAAACGATTTAC‑AACATCAAAAAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCGGGGAAGGGGAAGTGTCAGTGCGCATTcag                              <  2:575678/148‑1 (MQ=255)                                                                                                                                 aaCGAGTAAC‑AACATAAACAAAGCAAC‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCGGGGAAGGGGAAGTGTCAGTGCGCATTCAGCAGGCTgacg                    <  1:303351/151‑1 (MQ=255)                                                                                                                                  aCGAGTTAC‑AACATCAACTAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCGGGGAAGGGGAAGTGTCAGTGCGCATTCAGCAGGCTgacg                    >  2:442421/1‑150 (MQ=255)                                                                                                                                            aacaacACCAAAGCAAC‑CCCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCGGGGAAGGGGAAGTGTCAGTGCGCATTCAGCAGGCTgacga                   <  1:750268/142‑1 (MQ=255)                                                                                                                                            aacaTCAATAAAGCAAA‑CCCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCGGGGAAGGGGAAGTGTCAGTGCGCATTCAGCAGGCTGACGACagtgaaa           <  1:538684/150‑1 (MQ=255)                                                                                                                                              caTCAACTAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCGGGGAAGGGGAAGTGTCAGTGCGCATTCAGCAGGCTGACGACagtgaaagtg        >  2:872088/1‑151 (MQ=255)                                                                                                                                                  aaCAAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCGGGGAAGGGGAAGTGTCAGTGCGCATTCAGCAGGCTGACGACagtgaaagtgaa      <  2:807400/149‑1 (MQ=255)                                                                                                                                                    cTAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCGGGGAAGGGGAAGTGTCAGTGCGCATTCAGCAGGCTGACGACAGTGAAAGTGAAATAc  >  2:332228/1‑151 (MQ=255)                                                                                                                                                     |                                                                                                                                                       CAGGAACGCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGATGAACCGAGTATGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGAGTTAC‑AACATCAACTAAGCGAA‑CGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCGGGGAAGGGGAAGTGTCAGTGCGCATTCAGCAGGCTGACGACAGTGAAAGTGAAATAC  >  NC_000913/1036780‑1037076

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑