Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,578,143	0	A	C	46.8%	61.6 / 21.4	48	L79V (TTA→GTA)	maeB	malic enzyme: putative oxidoreductase/phosphotransacetylase
Reads supporting (aligned to +/- strand):  ref base A (23/2);  new base C (0/22);  total (23/25)
Fisher's exact test for biased strand distribution p-value = 2.02e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGACAACTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGCCAGATCGCGCTGTGTTGCC  >  NC_000913/2578008‑2578291                                                                                                                                         |                                                                                                                                                     cgACAACTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGt                                                                                                                                       >  1:572041/1‑151 (MQ=255)   aCAACTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTAc                                                                                                                                     <  1:700834/151‑1 (MQ=255)         tCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGtt                                                                                                                                 >  1:50836/1‑149 (MQ=255)                          gTCGAGTTCGTCACCTTCAATGACAAATACACCAACCCCGGCGAATTTCTAAAACAAAACGCCCTTCCCTCCCACCCCCGTTTTGCCGGCCAGCGCGCAAA‑TGTCGCCTACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAgg                                                                                                              <  2:872653/151‑1 (MQ=255)                          gTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAgg                                                                                                              >  2:97110/1‑151 (MQ=255)                               gTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTAcc                                                                                                         >  1:392199/1‑151 (MQ=255)                               gTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTAcc                                                                                                         >  1:414155/1‑151 (MQ=255)                                ttCGTCATCTTCAATTTAAAATCCACCAATCCGGGCGATTTTCTAAAACAGACCTCCTTTCCCTCCCACCCCCGTTTTGCCTGCCGGGGCGCCAA‑TTTTGCCTACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTAcc                                                                                                         <  2:221377/150‑1 (MQ=255)                                ttCGTCAACTTAAATGAAAAATACATCAACCCCGGCAATTTTCTAAAACAGACCCCCCTTCCCTCCCACCCCCGTTTTCCCTCCCAGCGCCCAAA‑TGTTGCCTACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTAcc                                                                                                         <  2:818591/150‑1 (MQ=255)                                      actttCAATGTAAAATACACCACCCCCGGCGAATTTTTAAAACAGAGCGCCTTTCCTTCCCACCACCGTTTTGCTTCCCAGGGCCCCAA‑TGTTGCCTACCCCCAGCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCg                                                                                                      <  2:181128/144‑1 (MQ=255)                                        cTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGt                                                                                                >  1:241069/1‑151 (MQ=255)                                            aaTGTCAAATACATCAACCCCGGCGAATTTCTAAAACAGACCCCCCTTGCCTCCCACCCCCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGtat                                                                                              <  1:331899/149‑1 (MQ=255)                                            aaTGTCAAATACACCACCCCCGGCAAATTTTTAAAACAGAACGCCCTTCCCTTCCACCCCCGGTTTGCCTGCCAGCGCCCCAA‑TGTTCCCTACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGtata                                                                                             <  2:131166/150‑1 (MQ=255)                                                tCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGt                                                                                        >  1:424657/1‑151 (MQ=255)                                                  aaaTACATCAACCCCGGCAATTTTCTAAAACAGACCGCCTTTGCCTCCCATCCCCGGTTTGCCTGCCAGCGCCCAAA‑TTTTGCCTACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTa                                                                                       <  2:710631/150‑1 (MQ=255)                                                      aCATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCtt                                                                                  >  2:325649/1‑151 (MQ=255)                                                        aTCAATCCCGGAGAATTTCATAAACAAAGCCCCTTTCCCTTCCATCACGGGTTTCCTCGCCGGCGCCCAAA‑TCTCCCCAATCCCCTGCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCtttt                                                                                <  1:277834/151‑1 (MQ=255)                                                        aTCAACCCCGGCGAATTTCTAAAACAGACCCCCCTTGCCTCCCACCCCCGGTTTGCCTGCCAGCGCGCAAT‑TGTTGCCTACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCttt                                                                                 <  1:776673/150‑1 (MQ=255)                                                           acccccGGCGATTTTCTAAAACAGACCGCCTTTCCCTCCCACCCCCGTTTTGCCTGCCAGCGCCCCAT‑TGTTCCCTACCCCCACCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTa                                                                               <  2:221205/146‑1 (MQ=255)                                                           aaccccGGCGAATTTCTAAAACAGACCCCCTTTCCCTCCCACCCCCGTTTTCCCTGCCGGCGCGCCAT‑TGTGCCCTACCCCCACCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCtttt                                                                                <  2:730359/145‑1 (MQ=255)                                                                   caaaTTTCTAAAACAGACCCCCCTTGCTTTCCACCCCCGGTTTGCCTGCCAGCGCCCAAA‑TGTTGCCTACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCtt                                                                      <  1:503459/148‑1 (MQ=255)                                                                     attttCTAAAACAGACCCCCCTTCCCTCCCATCACCGGTTTGCCTCCCAGCGCGCAAA‑TGTTGCCTACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCtt                                                                      <  2:609691/146‑1 (MQ=255)                                                                     attttCTAAAACAG‑ACCCCCTTGCCCTCCCACCCCCGTTTGCCCTCCAGGCCCCCAATTGTTCCCTACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCttttt                                                                   <  2:566869/149‑1 (MQ=255)                                                                      aTTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTc                                                                  >  2:421881/1‑151 (MQ=255)                                                                       tttCTAAAACAGAACGCCTTTCCCTCCCACCCCCGGTTTGCCTGCCAGCGCGCAAA‑TGTTGCCTACCCCCAGCGCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTc                                                                  <  2:719689/150‑1 (MQ=255)                                                                        ttCTAAAACAGAACCCCCTTGCCTCCCACCCCCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCg                                                                 <  1:827047/150‑1 (MQ=255)                                                                          cTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGAtt                                                              >  2:345051/1‑151 (MQ=255)                                                                            tAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTc                                                            >  1:334556/1‑151 (MQ=255)                                                                             aaaCAGAACGCCTTTGCCTCCCACCACCGGTTTCCCTGCCAGCGCGCAAA‑TGTTCCCTACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGAttt                                                             <  1:824269/149‑1 (MQ=255)                                                                              aaCAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCa                                                           >  1:523588/1‑150 (MQ=255)                                                                                cAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCa                                                           >  2:858401/1‑148 (MQ=255)                                                                                 agaccccccTTCCTTCCCACCCCCGTTTTCCCTGCCAGCGCCCCAA‑TGTTCCCAACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGAc                                                       <  2:68836/145‑1 (MQ=255)                                                                                   aaCGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACa                                                      >  1:531725/1‑150 (MQ=255)                                                                                     cGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAgg                                                   >  2:37541/1‑151 (MQ=255)                                                                                      gCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGt                                                  >  1:132346/1‑151 (MQ=255)                                                                                        ccTTGCCTCCCCCCCCCGTTTTGCCGCCGAGCGCGCCAG‑TGTTCCCAACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACa                                                      <  2:883126/145‑1 (MQ=255)                                                                                          tgcccTCCCATCCCCGTTTTCCCGCCCAGCGCGCAAA‑TTTTCCCTACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGt                                                  <  2:846979/144‑1 (MQ=255)                                                                                                tCCATCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGc                                        >  2:961367/1‑151 (MQ=255)                                                                                                 ccacccccGGTTTCCCCGCCAGCGCCCAAA‑TGTTCCCTACCCCCACCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACg                                         <  2:162081/143‑1 (MQ=255)                                                                                                 ccATCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGcc                                       >  1:656201/1‑151 (MQ=255)                                                                                                   aTCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTg                                     >  2:807527/1‑151 (MQ=255)                                                                                                              gcctgccAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGcc                          >  1:431833/1‑151 (MQ=255)                                                                                                               cctgccAGCGCGCAAA‑TTTTGCCTACCCCCAGCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGc                           <  2:336278/149‑1 (MQ=255)                                                                                                                         cgcCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGcc                    >  2:211664/1‑146 (MQ=255)                                                                                                                          ccaaa‑TGTTGCCTACCCCAAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGCCa                   <  1:429550/143‑1 (MQ=255)                                                                                                                            cAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGCCAGATcgcg            >  1:247930/1‑151 (MQ=255)                                                                                                                                 gTTGCCTAACCCCAGCTCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGCCAGATCgcgc           <  1:197237/148‑1 (MQ=255)                                                                                                                                 gTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGCCAGATCGCGCtgt        >  2:737701/1‑151 (MQ=255)                                                                                                                                        aaCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGCCAGATCGCGCTGTGTTGcc  >  2:8181/1‑150 (MQ=255)                                                                                                                                         |                                                                                                                                                     CGACAACTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAA‑TGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGCCAGATCGCGCTGTGTTGCC  >  NC_000913/2578008‑2578291

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑