Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,270,455	0	G	T	42.5%	46.3 / 20.2	47	intergenic (+853/+170)	yhaC/garK	pentapetide repeats‑related protein/glycerate kinase I
Reads supporting (aligned to +/- strand):  ref base G (10/17);  new base T (20/0);  total (30/17)
Fisher's exact test for biased strand distribution p-value = 5.11e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTTCAGTACGGGCCGTACCTTATGAACCCCTATTTGGCCTTGCTCCGGGTGGAGTTTACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGTTTCCCCCCCAGGCGTTACCTGGCACCCTGCCCTATGGAG‑CCCGGACTTTCCTCCCCTCCGCCCGTCTCCCCCGAAGAGGACGACGACGAAGCGGCGACTGTCTGGTCAGCTTCGGCGCGCAGTA  >  NC_000913/3270305‑3270603                                                                                                                                                       |                                                                                                                                                          gTTCAGTACGGGCCGTACCTTATGAACCCCTATTTGGCCTTGCTCCGGGTGGAGTTTACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTg                                                                                                                                                           <  1:297545/151‑1 (MQ=255)              cGTACCTTATGAACCCCTATTTGGCCTTGCTCCGGGTGGAGTTTACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTCTCTTTTgga                                                                                                                                               >  1:74839/1‑148 (MQ=255)               gTACCTTATGAACCCCTATTTGGCCTTGCTCCGGGTGGAGTTTACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTCTCTGTTGCACt                                                                                                                                             <  1:113165/151‑1 (MQ=255)                tACCTTATGAACCCCTATTTGGCCTTGCTCCGGGTGGAGTTTACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTtctctccttttccccg                                                                                                                                            >  2:519860/1‑141 (MQ=255)                     tATGAACCCCTATTTGGCCTTGCTCCGGGTGGAGTTTACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTTCTCTCTTTTTCACT‑GGGC‑g                                                                                                                                      >  1:883047/1‑150 (MQ=255)                        gAACCCCTATTTGGCCTTGCTCCGGGTGGAGTTTACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTCTCTTTTGCACC‑gggccgggg                                                                                                                                   >  2:323569/1‑144 (MQ=255)                         aaCCCCTATTTGGCCTTGCTCCGGGTGGAGTTTACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGt                                                                                                                               <  2:315010/151‑1 (MQ=255)                                 tttGGCCTTGCTCCGGGTGGAGTTTACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTTCTCTCTGTTGCCCT‑TGGC‑G‑T‑GGGTTTtccccc                                                                                                                       >  1:623935/1‑151 (MQ=255)                                    ggCCTTGCTCCGGGTGGAGTTTACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGTTTCCCCCCCa                                                                                                                     <  1:491707/150‑1 (MQ=255)                                     gCCTTGCTCCGGGTGGAGTTTACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTCTCTTTTGCACT‑GGGC‑G‑T‑GGGGTTcccccccc                                                                                                                     >  1:681752/1‑148 (MQ=255)                                      ccTTGCTCCGGGTGGAGTTTACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTTCCGCACCCTTTCGCCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGTTTCCCCCCCAGGc                                                                                                                  <  2:442151/151‑1 (MQ=255)                                         tGCTCCGGGTGGAGTTTACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGTTTCCCCCCCAGGCg                                                                                                                 <  2:683662/149‑1 (MQ=255)                                              cGGGTGGAGTTTACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGTTTTCCCCCCCGGCggttcc                                                                                                            >  1:421639/1‑144 (MQ=255)                                              cGGGTGGAGTTTACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGCTTTCTCTCTTTTTGCCT‑TGTCGG‑T‑GGTTTTccccccccgcggttcc                                                                                                             >  2:501257/1‑140 (MQ=255)                                                   ggAGTTTACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTTCTCTCTTTTGCACT‑GGTC‑G‑T‑GGGGTTTCCCCCCCCGCGTTACCTCGccc                                                                                                      >  1:153721/1‑148 (MQ=255)                                                    gAGTTTACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTTTTCTCTGTTGCACC‑GGGC‑G‑T‑GGGGTTTCCCCCCCGGCGTTACCTTGCAccc                                                                                                    >  1:833140/1‑151 (MQ=255)                                                    gAGTTTACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGTTTCCCCCCCAGGCGTTACCTGGCAccc                                                                                                    <  1:738108/151‑1 (MQ=255)                                                     aGTTTACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTTCCCTCTGTTTCCCT‑CCGC‑G‑T‑GGGGTTTCCCCCCCGCCGGTTCCTGGcc                                                                                                       >  2:1046542/1‑146 (MQ=255)                                                      gTTTACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGTTTCCCCCCCAGGCGTTACCTGGCACCCTg                                                                                                  <  1:1081465/151‑1 (MQ=255)                                                         tACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTTCTCTCTTTTGCCCC‑GGTC‑G‑T‑GGGGTTTCCCCCCCGGCGTTAccccgcccccccccc                                                                                               >  2:300106/1‑138 (MQ=255)                                                           ccGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGTTTCCCCCCCCGGCGTTACCTGGCACCCTGCCCTa                                                                                             <  2:745166/151‑1 (MQ=255)                                                           ccGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGTTTCCCCCCCAGGCGTTACCTGGCACCCTGCCCTa                                                                                             <  2:696644/151‑1 (MQ=255)                                                            cGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGTTTCCCCCCCAGGCGTTACCTGGCACCCTGCCCTAt                                                                                            <  1:144095/151‑1 (MQ=255)                                                            cGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGTTTCCCCCCCAGGCGTTACCTGGCACCCTGCCCTAt                                                                                            <  2:224064/151‑1 (MQ=255)                                                            cGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGCTTTCTCTCTTTTGCACC‑GGTC‑G‑T‑GGGGTTTCCCCCCCCGCGTTACCCGGGAcccccccc                                                                                               >  2:92944/1‑143 (MQ=255)                                                                ccACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTTCTCTCTTTTGCACT‑GGGC‑GTT‑GGGTTTCCCCCCC‑CGCGTTTCCCGGCccccccccccctgg                                                                                          >  2:64594/1‑139 (MQ=255)                                                                        tGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTTCTCTCTTTTTCACT‑GGTC‑G‑T‑GGGGTTTCCCCCCCCGCGGTTCCTGGCCCCCCGCCCCCTGGAG‑gcc                                                                                    >  2:778107/1‑146 (MQ=255)                                                                                 ccGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGTTTCCCCCCCAGGCGTTACCTGGCACCCTGCCCTATGGAG‑CCCGGACTTTcctcccc                                                                      <  2:1047687/151‑1 (MQ=255)                                                                                        gTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTTCTCTCTTTTGCCCC‑GGTC‑C‑T‑GGGGTTCCCCCCCCCGCGTTTCCCTGCACCCCCCCCCCTTGGG‑GCCGGGCTTTCCTCCCCTcccccc                                                               >  2:863718/1‑151 (MQ=255)                                                                                         tGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTTGTCTCTTTTGGACT‑GGGC‑G‑G‑GGGGTTTCCCCCCCCGCGTGACCTGGGCCCCTGCCCCATGGGGCCCCGGACTTTctaccccccgc                                                                  >  1:335828/1‑144 (MQ=255)                                                                                          gcgcTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGTTTCCCCCCCAGGCGTTACCTGGCACCCTGCCCTATGGAG‑CCCGGACTTTCCTCCCCTCCGCCCg                                                              <  2:462334/150‑1 (MQ=255)                                                                                                 tACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGTTCTCTTTTTCTCT‑GGGC‑C‑TGGGGTTTCCCCCCCCGCCG‑TACCTCGCACCCCTCCCCATGGGG‑CCCGGGCTTTCCCCCCCCCCCCCCGTCcccccc                                                      >  2:1007385/1‑151 (MQ=255)                                                                                                  aCCGCACCCTTTCCCCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGTTTCCCCCCCAGGCGTTACCTGGCACCCTGCCCTATGGAG‑CCCGGACTTTCCTCCCCTCCGCCCGTCTCCCCCg                                                     <  1:38918/151‑1 (MQ=255)                                                                                                           tttCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTTCTCTCTTTTGCACT‑GGTC‑G‑T‑GGGGTTTCCCCCCCGGCGTTACCTGGCACCCCGCCCCATGGAG‑CCCCGACTTTCCTCCCCTCCCCCCCCCTCCCCCCAAGAgg                                               >  1:228190/1‑148 (MQ=255)                                                                                                            ttCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTTCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGTTTTCCCCCCAGGCGGTACCTGGCACCCCGCCCCATGGAG‑CCCGGACTTTCCTCCCCCCCCCCCGCCTCCCCCCCAGAgg                                               >  1:68381/1‑147 (MQ=255)                                                                                                            ttCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTTTTCGTTGCACTCGGCC‑G‑G‑GGGTTCCCCCCCCAGG‑GTTACCTCGCACCCCGCCCCCTTGAG‑CCCGGGGTTTTCTCCCCTCCCCCCCGCTCCCCCGCaggg                                                >  1:207074/1‑144 (MQ=255)                                                                                                               aCCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTTCTCTCTGTTTCACT‑GGTC‑G‑T‑GGGGTTTCCCCCCCCGCGTTACCCGGCACCCCCCCCCATGGGG‑CCCCGGCTTTTCTCCCCCCCCCCCCTCTCCCCCCAAGAGgacga                                           >  1:579280/1‑148 (MQ=255)                                                                                                               aCCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGGTTGCTCTCTTTTTCACT‑TGGC‑G‑T‑GGGGTTCCCCCCCCCGCGGTACCCGGCACCCTCCCCCTTGGGG‑CCCCGGCTTTCCTCCCCCCCCCCCCTCCCCCCCCCAGAGgac                                             >  2:144674/1‑146 (MQ=255)                                                                                                                   ttACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTTCTCTCTGTTTGACT‑GGGC‑G‑T‑GGGGTTTCCCCCCACGCGGTTCCTTGCACCCTTCCCCATGGGG‑GCCCGGCTTTTCTCCCCCCCCCCCCTCTCCCCCCCAGAgg                                               >  1:915312/1‑140 (MQ=255)                                                                                                                   ttACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTTCTCTCTGTTGCACC‑GGTC‑G‑T‑GGGGTTCCCCCCCCGGCGGTTCCTGGCACCCCTCCCCATTGAG‑CCCCGGCTTTCCTCCCCCCCCCCCCCCTCCCCCCCAGAGggagacgac                                       >  1:1024681/1‑148 (MQ=255)                                                                                                                     aCCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGTTTCCCCCCCAGGCGTTACCTGGCACCCTGCCCTATGGAG‑CCCGGACTTTCCTCCCCTCCGCCCGTCTCCCCCGAAGAGGACGACGACGAAgc                                  <  1:1039982/151‑1 (MQ=255)                                                                                                                      ccTGATCCCGCTTGCGCGGGCCATCGGCGGTTTTTACTCCTTTCGACA‑GGGC‑C‑T‑GGGGTTTCCCCCCCGCCCATACCTGGCGCCCTGCCCTATAGAG‑GCCGGGCTTTTCCCCCCTCCCCCCCCGCCCCCCCCAGAGggcgacgac                                       >  1:1051176/1‑145 (MQ=255)                                                                                                                        tGATCCCGCTTGCGCGGGCCATCGGCGGTTTTCTCTCTCTTGAACC‑GGGC‑G‑G‑GGGGTTTCCCCCCCGGCGTTACCTTGCACCCCGCCCTATGGAG‑GCCGGGCTTTCCTCCCCCCCCCCCGGCTCCCCCCGAGAGGAACACGACAAAgccg                                >  1:909007/1‑148 (MQ=255)                                                                                                                           tCCCGCTTGCGCGGGCCATCGGCGGTTTTGTCTCTTTTTCACT‑TGTC‑C‑T‑GGGGTTCCCCCCCCGGCGCTTCCCTGCACCCCGCCCTATTGAG‑GCCGGACTTTCCTCCCCCCCCCCCCTCTCCCCCCCAGAGGAAGACGACCaa                                    >  2:150543/1‑143 (MQ=255)                                                                                                                                              cggcggTTTGCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGTTTCTCCCCCAGGCGTTACCTGGCACCCTGCCCTATGGAG‑CCCGGACTTTCCTCCCCTCCGCCCGTCTCCCCCGAAGAGGACGACGACGAAGCGGCGACTGTCTGGTCAGCTTCGgc          <  2:73902/150‑1 (MQ=255)                                                                                                                                              cggcggTTTGCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGTTTCCCCCCCAGGCGTTACCTGGCACCCTGCCCTATGGAG‑CCCGGACTTTCCTCCCCTCCGCCCGTCTCCCCCGAAGAGGACGACGACGAAGCGGCGACTGTCTGGTCAGCTTCGgc          <  2:158213/150‑1 (MQ=255)                                                                                                                                                   gTTTGCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGTTTCCCCCCCAGGCGTTACCTGGCACCCTGCCCTATGGAG‑CCCGGACTTTCCTCCCCTCCGCCCGTCTCCCCCGAAGAGGACGACGACGAAGCGGCGACTGTCTGGTCAGCTTCGgcgcgc      >  1:297461/1‑149 (MQ=255)                                                                                                                                                     ttGCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGTTTCCCCCCCAGGCGTTACCTGGCACCCTGCCCTATGGAG‑CCCGGACTTTCCTCCCCTCCGCCCGTCTCCCCCGAAGAGGACGACGACGAAGCGGCGACTGTCTGGTCAGCTTCGGCGCGCAGt   >  1:252136/1‑150 (MQ=255)                                                                                                                                                     ttGCTCTCTGCTGCACT‑GGTC‑G‑C‑GCGTTTCCCCCTCAGGCGTTATCTCGCACCCTGCCCTATGCAG‑CCCGGACTTTCCTCCCCTCCGCCCGCCTCCCCCGAAGAGGACGACGACGAAGCGGCGACTGTCTGGGCAGCTTCGGCGCGCAGtc  >  2:967555/1‑150 (MQ=255)                                                                                                                                                       |                                                                                                                                                          GTTCAGTACGGGCCGTACCTTATGAACCCCTATTTGGCCTTGCTCCGGGTGGAGTTTACCGTGCCACGGACTGTTACCAGCCGCGCGGTGCGCTCTTACCGCACCCTTTCACCCTTACCTGATCCCGCTTGCGCGGGCCATCGGCGGTTTGCTCTCTGTTGCACT‑GGTC‑G‑T‑GGGTTTCCCCCCCAGGCGTTACCTGGCACCCTGCCCTATGGAG‑CCCGGACTTTCCTCCCCTCCGCCCGTCTCCCCCGAAGAGGACGACGACGAAGCGGCGACTGTCTGGTCAGCTTCGGCGCGCAGTA  >  NC_000913/3270305‑3270603

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑