Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,133,302	0	T	G	50.0%	42.8 / 24.2	50	H219P (CAC→CCC)	yghS	putative ATP‑binding protein
Reads supporting (aligned to +/- strand):  ref base T (3/21);  new base G (24/0);  total (28/22)
Fisher's exact test for biased strand distribution p-value = 1.81e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTGGGCTGCGGCGCGGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCA‑TCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACGAATCAACAATACGGG  >  NC_000913/3133160‑3133450                                                                                                                                               |                                                                                                                                                       ttGGGCTGCGGCGCGGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGcc                                                                                                                                                  <  1:566508/149‑1 (MQ=255)     gCTGCGGCGCGGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCA‑Tcc                                                                                                                                            <  1:368409/150‑1 (MQ=255)         cggcgCGGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCA‑TCCA‑GTTc                                                                                                                                      <  2:404834/151‑1 (MQ=255)            cgcgGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCA‑TCCA‑GTTCAAg                                                                                                                                   <  1:43400/151‑1 (MQ=255)              cgGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGGCGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCA‑TCCA‑GTTCAAGGa                                                                                                                                 <  1:614301/151‑1 (MQ=255)              cgGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGCCGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCA‑TCCA‑GTTCAAGGa                                                                                                                                 <  2:708582/151‑1 (MQ=255)              cgGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCA‑TCCA‑GTTCAAgg                                                                                                                                  <  1:854873/150‑1 (MQ=255)              cgGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCA‑TCCA‑GTTCAAgg                                                                                                                                  <  1:289710/150‑1 (MQ=255)              cgGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCA‑TCCA‑GTTCAAGGa                                                                                                                                 <  2:627357/151‑1 (MQ=255)              cgGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCA‑TCCA‑GTTCAAGGa                                                                                                                                 <  1:128592/151‑1 (MQ=255)              cgGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCA‑TCCA‑GTTCAAGGa                                                                                                                                 <  1:214718/151‑1 (MQ=255)                     aCTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGGCGCCCC‑TCCC‑GTTCTAAGATCtttt                                                                                                                           >  1:221195/1‑149 (MQ=255)                      cTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGTGTGTCGCCCC‑TCCC‑GTTTTAAGGTCTTTgtg                                                                                                                         >  2:944066/1‑149 (MQ=255)                      cTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGGTGCCCA‑TCCA‑GATCCAGGAACttttgg                                                                                                                         >  2:988487/1‑148 (MQ=255)                               gtttgagtttgTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTTGCCCC‑TCCA‑GTTTAAGGATCTTTGCGCCATTGTAt                                                                                                                >  2:420295/1‑151 (MQ=255)                               gtttgagtttgTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGCGGTGCCCC‑TCCC‑GGTCCAGGGTCTTTTCGCCATTGa                                                                                                                  >  2:726537/1‑149 (MQ=255)                                tttgagtttgTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCA‑TCCA‑GTTCAAGGATCTTTGCGCCATTg                                                                                                                   <  1:177219/147‑1 (MQ=255)                                 ttgagtttgTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCGA‑TCCA‑GTTAAAGTATCTTTGCGCCATTGAAtat                                                                                                              <  2:270693/151‑3 (MQ=255)                                 ttgagtttgTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCA‑TCCA‑GTTCAAGGATCTTTGCGCCATTGAATGt                                                                                                              <  2:290523/151‑1 (MQ=255)                                  tgaggttgGAGTGCAACCATTCGTTGAATCGTCCCCTATCCATTTTGGTGATCAGGAAAGCCCAGCGTGAATTGCGCGTAGTGCCGCTAGCAGAATTTCATCGGCGGGGAGTCGCACA‑TCCA‑GTTCAAGGATCTTTGCGTCATTGAATGtg                                                                                                             <  2:512206/151‑2 (MQ=255)                                   gagtttgTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCC‑TCCC‑CTTCTAGGGTTTTTTGGCCCTTTGATGTCa                                                                                                            >  1:310379/1‑151 (MQ=255)                                      tttgTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCA‑TCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAg                                                                                                           <  2:694334/149‑1 (MQ=255)                                      tttgTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCA‑TCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAg                                                                                                           <  1:213745/149‑1 (MQ=255)                                         gTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCC‑ACCA‑GTTCAAGGGTCTTTTGGCCCTTGAATGTCAGTTgcg                                                                                                      >  1:874284/1‑151 (MQ=255)                                         gTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGGCGCCCC‑TCCC‑GTTCCAGGATCTTTGTGCCATTTTATGTCAGGTgcg                                                                                                      >  2:336026/1‑151 (MQ=255)                                              gCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGGGGCCCC‑ACCA‑GTTCAAGGAACTTTTCGCCCTTGAATGTCCGTTTCGGGGTa                                                                                                 >  2:379912/1‑151 (MQ=255)                                                 tCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGGCCA‑ACCA‑GTTCAAAGAAATTTGTGCCATTGAATGTCCGCTGCGGGGTAACg                                                                                              >  2:476904/1‑151 (MQ=255)                                                 tCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGGCGCCCA‑CCCA‑GTTCAAGGGGCTTTGCGCCATTGAATGTCAGTTGGGGGGGAACg                                                                                              >  1:184968/1‑151 (MQ=255)                                                       cGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTGGGTCC‑CCCC‑GGTCAAGGCGGTTTGTGGCATTGAAGGTCTGTTGCGGGGGAACGGGGaat                                                                                        >  2:164705/1‑149 (MQ=255)                                                       cGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCC‑TCCA‑ATTTCAGGGTCTTTTCGCCCTTGTATTTTAGTTGCGGCGGAAAGGCGGtt                                                                                        >  1:567293/1‑151 (MQ=255)                                                            aaTCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCA‑TCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTc                                                                                   <  1:264904/151‑1 (MQ=255)                                                             atcatcCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCA‑TCCC‑GTTTAAAGATCTTTGTTTCATTGCATGGCCGTTGGCGCGTAACGGCGAgtttttt                                                                                   >  2:513552/1‑149 (MQ=255)                                                                   cccTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCC‑TCCC‑GTTCCAGGATCTTTTGGGCATTTAAAGGTAGTTGCGGCGGAACGGGGGTTTTTTTCTGTaa                                                                             >  2:200004/1‑150 (MQ=255)                                                                     cTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTTGCCCA‑TCCAGGTTAAAGGA‑CTTTGTGCCATTTAATGTCAGTTGGGGGGGAACGGGGGTTTTTTTCTGtgaag                                                                           >  2:687709/1‑146 (MQ=255)                                                                       aTCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCC‑TTCA‑GGTGAAAGATCTTTTCGCCCTTGAAAGTCATGTGCCGGGTAAAGGCGATTTTTTTCTGTAAccgtt                                                                        >  2:415028/1‑147 (MQ=255)                                                                         ccATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCC‑TCCA‑GTTCAAGGGTCTTTTCGCCCTTGAATGTCAGTTGCGGCGGAACGGCGGTTTTTTTCTGTAAcgccgc                                                                       >  1:537946/1‑150 (MQ=255)                                                                                   gATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGGCGCCCC‑CCCC‑GTTCCAGGATTTTTTCGCCCTTTAAATTCTGTTGCGGGGTTACGGCGGTTTTTTTCTTTTACGCTGCCCGGtgggggg                                                            >  1:430182/1‑150 (MQ=255)                                                                                    aTCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCA‑TCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTggtggt                                                            <  1:650199/150‑1 (MQ=255)                                                                                              cgcgGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCA‑TCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTAcgc                                                 <  2:1176531/151‑1 (MQ=255)                                                                                                  gcgTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCA‑TCCA‑GTTCAAGGATCTTTTCGCCCTTGAATGTCAGTTTCGGCGGAACGGCGGTTTTTTTCTTTAACGCTGCCCGTTTGTGGGCAGGGTTTCgcgcca                                             >  2:327884/1‑149 (MQ=255)                                                                                                   cgTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGGGGCCCC‑TCCC‑GGTCCAGGGGCTTTGCGCCCTTGAATGTCAGTTGCGGCGTAAAGGCGGGTTTTTTCTGTAACACCGCCCGCTGGTGGGGAGGTTTACGTGCaaa                                            >  2:439398/1‑151 (MQ=255)                                                                                                      gAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCC‑TCCA‑GTTCAAGGGTCTTTGCGCCATTGAATGTCAGTTGTGGGGTAACGGCGGTTTTTTTCTGTAACGCTGCCCGGTGGGGGGCAGGGTTACGCGCaaaac                                          >  1:781444/1‑148 (MQ=255)                                                                                                           gcgcGTAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCA‑CCCA‑GTTCAAGGGTCTTTGGGCCATTTTATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACTCTGCCAGTTGGGGGCTAGGGTTACCCGCACAAGCGGgtt                                    >  2:132540/1‑151 (MQ=255)                                                                                                              cgTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCC‑TCCC‑GTTCAAGGATCTTTGCGCCCTTTAATGTCAGTTGCGGCGGAACGGCGATTTTTTTCTTTAAACCTGGCCGGTGGGGGGCCGGGTTACGCGCAAAAGCGGGTtttt                                 >  1:908004/1‑151 (MQ=255)                                                                                                                tAGTGACGCTTGCAGAATTTCATCGGCGGGGGGTCGCCCA‑ACCA‑GGTCAAGGATCTTTGCGCCATTTAATGTCAGGTGGGGCGGAAAGGCGATTTTTTTCTTTAACGCTGCCCGTTTGTGGGCAGGGTTTAGCGCCAAAGCGGGTttttta                               >  1:769812/1‑149 (MQ=255)                                                                                                                tAGTGACGCTTGCAGAATTTCATCGCCGGGGGGGTGCCCACACCG‑GTTGAAGG‑TCTTTTCGGCATCTAATGTCAGGTGGGGCGGTCCGACGCTTTTTTTCTGTAACGCTGGCAGTCGTTGGTTTGGGTTAAGCGCAAACGCGGgttagtta                               >  2:749193/1‑146 (MQ=255)                                                                                                                              gAATTTCATCGGCGGGGGGTCGCCCC‑TCCA‑GTTCAAGGATCTTTTCGCCATTGAATGTCAGTTGCGGCGTAACGGCGGTTTTTTTCTGTAAAGCTGCCCGGTGGGGGGCAGGGTTTCGCGCCAAAGCGGGTTGTTTATCCATGCCAAGACg                 >  1:254209/1‑151 (MQ=255)                                                                                                                                      tCGGCGGGGTGTCGCCCA‑TCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACGAATcaaca         <  1:237499/151‑1 (MQ=255)                                                                                                                                          cggGGTGTCGCCCA‑TCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACGAATCAACAATAc     <  1:839244/151‑1 (MQ=255)                                                                                                                                             ggTGTCGCCCA‑TCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACGAATCAACAATACggg  >  2:21623/1‑151 (MQ=255)                                                                                                                                              gtgtCGCCCA‑TCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACGAATCAACAATACggg  >  1:1112074/1‑150 (MQ=255)                                                                                                                                               |                                                                                                                                                       TTGGGCTGCGGCGCGGTTGTACTATTAACAGTTTGAGTTTGTAGTGCATCCATTCGTTAAATCATCCCCTATCCATTTTGGTGATCAGGAAAGCGCGGCGTGAATTGCGCGTAGTGACGCTTGCAGAATTTCATCGGCGGGGTGTCGCCCA‑TCCA‑GTTCAAGGATCTTTGCGCCATTGAATGTCAGTTGCGGCGTAACGGCGATTTTTTCCTGTAACGCTGCCAGTTGGTGGTCAGGTTTACGCGCAAACGCGGTTTGTTCATCAATGCCAAGACGAATCAACAATACGGG  >  NC_000913/3133160‑3133450

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑