Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	535,920	0	C	T	58.5%	90.8 / ‑2.7	54	R71C (CGC→TGC)	hyi	hydroxypyruvate isomerase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (4/27);  minor base G (22/0);  total (27/27)
Fisher's exact test for biased strand distribution p-value = 3.23e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGAGCGCGGTATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAATTAACTGTCTGGTCGGTAAAACGCCGGCTGGTTTCAGCAGTGAACAGATTCACG  >  NC_000913/535774‑536067                                                                                                                                                   |                                                                                                                                                     agaAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGAGTGCgg                                                                                                                                                  <  2:895463/151‑1 (MQ=255)  gaAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGACTGGGGGGGGGGGGAGGGCgg                                                                                                                                                  >  2:325478/1‑150 (MQ=255)     aGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGAGTGCGGTAtt                                                                                                                                              <  1:279669/151‑1 (MQ=255)           gcAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGGCTGGGCGGGGGGGGAGGGGGGGATTggc                                                                                                                                           >  2:604999/1‑146 (MQ=255)              gtgtGGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGAGTGCGGTATTGCCTGTA‑tt                                                                                                                                    <  2:396237/151‑1 (MQ=255)                  ggTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGGCTGGGGGGCGGGGGGGGGCGGGATTGCCTGTA‑t                                                                                                                                     >  2:617930/1‑146 (MQ=255)                             cgTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGAGTGCGGTATTGCCTGTA‑TTCCTGGCCGTgaagaa                                                                                                                     <  1:544950/151‑1 (MQ=255)                             cgTAGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGAGTGCGGTATTGCCTGTA‑TTCCTGGCCGTgaagaa                                                                                                                     <  1:455886/151‑1 (MQ=255)                              gTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGAGTGCGGTATTGCCTGTA‑TTCCTGGCCGTGaagaag                                                                                                                    <  2:272948/151‑1 (MQ=255)                              gTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGACTGGGGGGCGGGGGGGGGCGGGATTTCCTGTA‑TTTCTGGCCggggag                                                                                                                       >  1:523345/1‑143 (MQ=255)                                tGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGGCTGGGCGGCGGGGGGGGGCGGGATTTCCTGTA‑TTGCTGGCCGTGaagaag                                                                                                                    >  1:701745/1‑149 (MQ=255)                                    tttATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGGGGCGGGGGAGTGCGGGAATGCCCGTT‑TTCCTGGCCGTGaagaag                                                                                                                    >  1:513742/1‑145 (MQ=255)                                      tATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGAGTGCGGTATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGTTTCg                                                                                                             <  2:195097/150‑1 (MQ=255)                                         gTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGAGTGCGGTATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGTTTCGGGAt                                                                                                         <  2:70943/151‑1 (MQ=255)                                         gTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGGCTGGGGGGCGGGGGGGGGGGGGATTGCCTGTT‑TTTCTTGCCGGGGAGAAGAGGTTCgggg                                                                                                          >  2:824827/1‑149 (MQ=255)                                            tCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGAGTGGGCGGGGGGGGGGAGGGGGATTGCCTGTA‑TTTCTGGCCGGGAGGAAGAGgttt                                                                                                              >  2:22628/1‑142 (MQ=255)                                              cTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGACTGGGCGGGGGGGGGGGGGGGGATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGGTTTGGGGTGGCg                                                                                                     >  1:422375/1‑150 (MQ=255)                                                 aTGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGAGTGCGGTATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGTTTCGGGATGGCGTagc                                                                                                 <  2:320617/151‑1 (MQ=255)                                                   gACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGAGTGCGGTATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGTTTCGGGATGGCGTagcag                                                                                               <  2:141951/151‑1 (MQ=255)                                                   gACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGAGTGCGGTATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGTTTCGGGATGGCGTagca                                                                                                <  2:471642/150‑1 (MQ=255)                                                        cGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGACTGGGGGGGGGGGGGGGGCGGGATTGCCTGTA‑TTTCTGGCCGGGAAGAAGAGGTTCGGGGTGGCGGagcagca                                                                                             >  1:815093/1‑148 (MQ=255)                                                        cGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGACTGGGCGGCGGGGGGGGGCGGGATTGCCTGTA‑TTTCTTGCCGGGAAGAAGAGGTTCGGGGTgggg                                                                                                     >  1:357081/1‑138 (MQ=255)                                                               gaagaaTTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACCGGGGGGGGGGGGGGGGCGGGATTGCCTGTA‑TTTCTGGCCGGGGAGAAGAGGTTCGGGGGGGGGGAGCAGCAGCGATTCggt                                                                                   >  1:121654/1‑149 (MQ=255)                                                               gaagaaTTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGACTGGGCGGCGGGGGAGTGCGGTATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGTTGCGGGATTGCGTAGCAGCAGCGATTCggt                                                                                   <  2:819541/151‑3 (MQ=255)                                                                aagaaTTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGGGTGCGGGATTGCCTGTA‑TTTCTGGCCGTGAAGAAGAGGTTTGGGATGGCGGAGCAGCAGCGATTCGtt                                                                                   >  1:243191/1‑150 (MQ=255)                                                                  gaaTTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGACTGGGGGGCGGGGGGGGGGGGGATTGGCTGTA‑TTTCTGGGCGTGGAGAAGAGGTTCGGGGGGGCGGAGGAGCAGCGGTTTGTTAt                                                                                 >  1:31758/1‑150 (MQ=255)                                                                     ttAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGGCTGGGGGGCGGGGGGGTGCGGGATTGCCTGTA‑TTTCTGGCCGTGGAGAAGAGTTTTGGGGTGGCGTAGCAGCAGCGATTTGTTATTccc                                                                             >  1:474034/1‑151 (MQ=255)                                                                      tAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGGCTGGGCGGGGGGGGGGGGCGGGATTGCCCGTA‑TTTCCGGGCGGGGAGAAGAGGTTTGGGGGGGGGGAGGAGCAGCGATTCGTTATGgcc                                                                             >  2:756079/1‑150 (MQ=255)                                                                         aaCATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGAGTGCGGTATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTgc                                                                         <  1:459225/151‑1 (MQ=255)                                                                         aaCATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGGCTGGGGGGCGGGGGGGGGCGGGATTTCCTGTA‑TTTCTGGCCGTGAAGAAGAGGTTCGGGATGGGGGAGCAGCAGCGGTTCGTTATGCCCCTg                                                                          >  1:497746/1‑150 (MQ=255)                                                                           cATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGACTGGGCGGCGGGGGGGGGGGGGATTTCCTGTA‑TTTCTGGCCGTGGAGAAGAGGTTTGGGGTGGCGGAGCAGCAGCGATTTGTTATTCCCgcg                                                                          >  1:7136/1‑146 (MQ=255)                                                                            aTGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGATTTGGGGGCGGGGGGGTGTGGGTATGTCTGTA‑TTTTCCGGCGCGGAGAAGAGGGTCGGGGTGGGGTAGCAGCAGCGGCTCGTTATGcccct                                                                           >  1:381405/1‑144 (MQ=255)                                                                              gtgCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGAGTGCGGTATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTgg                                                                    <  2:665389/151‑1 (MQ=255)                                                                                gCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGAGTGCGGTATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGt                                                                  <  1:302186/151‑1 (MQ=255)                                                                                gCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGAGTGCGGTATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGt                                                                  <  1:303159/151‑1 (MQ=255)                                                                                gCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGACTTGGCGGCGGGGGGGGGGGGTATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGGTTCGGGGTGGCGGAGCCGCAGCGATTCGTTATTCCCGTGCGCCggg                                                                   >  1:807096/1‑150 (MQ=255)                                                                                 cTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGGCTGGGGGGCGGGGGGGGGCGGGATTGCCTGTA‑TTTCTGGGCGGGGAGAAGGGGTTTGGGGGGGGGGAGGAGCAGCGATTTGGTTTGGCCGTgcggcggg                                                                   >  2:560869/1‑144 (MQ=255)                                                                                   ggCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGAGTGCGGTATTGCCTGTA‑TTCCTGGTCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGtaa                                                                <  1:636258/150‑1 (MQ=255)                                                                                    gCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGACTGGGCGGCGGGGGGGGGCGGGATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGGTTCGGGGTGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGgaa                                                                >  1:530311/1‑149 (MQ=255)                                                                                       aGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGGATTGGGGGGGGGGGGGGGGGGGATTGCCTGTT‑TTCCTGGCCGGGGAGAAGAGGTTTGGGGGGGGGGAGCAGCCGCGAGTTGTTTTGTCCCTGCGCTGGGGGATaaa                                                            >  2:1057/1‑150 (MQ=255)                                                                                       aGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGGGGCGGGGGGGGGCGGGAGTTACTGTA‑TTCCTGGGCGGGGAGAAGAGTTTTGGGGTGGGGGAGCAGCAGAGATTCGTGATGCCCGTGCGCGGGGGGATaaa                                                            >  2:819716/1‑150 (MQ=255)                                                                                       aGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGAGTGCGGTATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATaaaa                                                           <  1:44787/151‑1 (MQ=255)                                                                                       aGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGAATGGGCGGGGGGGGGAGGGGGGATTTCCTGTATTTCCGGGCCG‑GGAGGAGAGGGTTGGGGTGGCGGTGGAGCAAGGATTCGTTATGACCCTGCGCCGGGGaaaaaa                                                            >  1:188157/1‑150 (MQ=255)                                                                                        gTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGGGGCTGGGAGGCGGGGGAGGGGGGGAATGCCTTTA‑TTCCTGGCCGTGGAGAAGAGGTTCGGGGTGGGGGGGCAGCAGCGATTCGTTTTGGCCCGGGGCTGGGGGATaaaa                                                           >  2:625459/1‑150 (MQ=255)                                                                                                      cATACGCTGCACAATTTACCGGCGGGTGACTGGGGGGCGGGGGGGGGCGGGATTGCCTGTA‑TTTCTGGCCGTGAAGAAGAGTTTCGGGGTGGCGGAGCAGCAGCGATTTGTTTTGCCCGTGCGCTGGGGGATAAAAAAATTAACTGTCTgg                                            >  1:159367/1‑151 (MQ=255)                                                                                                          cGCTGCACAATTTACCGGCGGGTGACTTGGCGTCGGGGGAGTGCGGTATTGCCTGTA‑TTCCTGGCCCTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGTGTAATAAAAAAATTAACTGTCTGGTCgg                                        <  2:333092/151‑1 (MQ=255)                                                                                                          cGCTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGAGTGCGGTATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAATTAACTGTCTGGTCgg                                        <  1:462744/151‑1 (MQ=255)                                                                                                            cTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGAGTGCGGTATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAATTAACTGTCTGGTCGGt                                       <  1:841823/150‑1 (MQ=255)                                                                                                                        ccGGCGGTTGACGGGGCGGCGGGGGAGTGCGGTATGGCCGGTA‑TTCCTGGCCGTGAGAAAGAGTTCCGGAATGCGTTACCAGCAGCGATTCGTTATGCCCGTGGGCTGGGTAAT‑AAAAAATTAACTGTCTGGTCGGTAAAACGCCGGCTgg                         <  2:257477/151‑1 (MQ=255)                                                                                                                                  aCTGGGCGGCGGGGGAGTGCGGTATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAATTAACTGTCTGGTCGGTAAAACGCCGGCTGGTTTcagcag                <  1:834198/151‑1 (MQ=255)                                                                                                                                     gggCGGCGGGGGAGTGCGGTATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAATTAACTGTCTGGTCGGTAAAACGCCGGCTGGTTTCAGCAGTg              <  2:746399/150‑1 (MQ=255)                                                                                                                                       gcggcgGGGGAGTGCGGTATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAATTAACTGTCTGGTCGGTAAAACGCCGGCTGGTTTCAGCAGTGAAc           <  1:101124/151‑1 (MQ=255)                                                                                                                                               ggAGTGCGGTATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAATTAACTGTCTGGTCGGTAAAACGCCGGCTGGTTTCAGCAGTGAACAGATTCAc   <  2:422330/151‑1 (MQ=255)                                                                                                                                                gAGTGCGGTATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAATTAACTGTCTGGTCGGTAAAACGCCGGCTGGTTTCAGCAGTGAACAGATTCACg  <  1:337331/151‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                     AGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGCGGCGGGGGAGCGCGGTATTGCCTGTA‑TTCCTGGCCGTGAAGAAGAGTTTCGGGATGGCGTAGCAGCAGCGATTCGTTATGCCCGTGCGCTGGGTAATAAAAAAATTAACTGTCTGGTCGGTAAAACGCCGGCTGGTTTCAGCAGTGAACAGATTCACG  >  NC_000913/535774‑536067

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑