Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,001,164	0	A	C	40.0%	89.1 / 10.8	52	T274P (ACC→CCC)	xdhA	xanthine dehydrogenase, molybdenum binding subunit
Reads supporting (aligned to +/- strand):  ref base A (27/3);  new base C (0/20);  total (27/25)
Fisher's exact test for biased strand distribution p-value = 3.76e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATGCGTACGAGTCATCAAACCATTTGTCGGTGGCGGTTTTGGTAATAAACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTG‑ACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCTTCTGCGGGGGGGAATAA  >  NC_000913/3001015‑3001309                                                                                                                                                             |                                                                                                                                                  cATGCGTACGAGTCATCAAACCATTTGTCGGTGGCGGTTTTGGTAATAAACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTG‑ACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCaa                                                                                                                                                   <  1:228459/150‑1 (MQ=255)    gCGTACGAGTCATCAAACCATTTGTCGGTGGCGGTTTTGGTAATAAACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTG‑ACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCAACCCg                                                                                                                                               <  2:699803/151‑1 (MQ=255)      gTACGAGTCATCAAACCATTTGTCGGTGGCGGTTTTGGTAATAAACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTG‑ACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCAACCCGt                                                                                                                                              >  1:532650/1‑150 (MQ=255)         cGAGTCATCAAACCATTTGTCGGTGGCGGTTTTGGTAATAAACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTG‑ACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCATCCCGTAccc                                                                                                                                          <  1:322609/151‑1 (MQ=255)         cGAGTCATCAAACCATTTGTCGGTGGCGGTTTTGGTAATAAACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTG‑ACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCAACCCGTAccc                                                                                                                                          >  2:132838/1‑151 (MQ=255)          gAGTCATCAAACCATTTGTCGGTGGCGGTTTTGGTAATAAACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTG‑ACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCAACCCGTAccc                                                                                                                                          >  1:875224/1‑150 (MQ=255)              catcaAACCATTTGTCGGTGGCGGTTTTGGTAATAAACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTG‑ACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCAACCCGTACCCGCCAc                                                                                                                                     >  2:291252/1‑151 (MQ=255)               atcaAACCATTTGTCGGGGGCGTTTTGGGAAATAAACAGGATGTACTGAAAGAGCCAATGGCGGCATTCCTG‑ACCA‑GCAAGCTGGGCGGCATCCGGGTGAAAGTTC‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTCCCTCGCAACCCGTCCCCGCCa                                                                                                                                      <  1:14027/149‑1 (MQ=255)               accaAACTTTTTGTGGGTGGGGTTTTTTTAAAAAAACGGGTTGTAGTGGAAGAGCCAGTGGCGCCTTCCCTG‑ACGA‑GAAAGCTTGGCGGCATTCCGGTGAAA‑TTT‑CCC‑TT‑TG‑GCATGGAGGTGTTTTCCCCCGCACCCCGTCCCCGCCACg                                                                                                                                    <  1:1042272/149‑1 (MQ=255)                            tCGGTGGCGGTTTTGGTAATAAACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTG‑ACCA‑GCAAGCTTGGCGGCATTCCGGCGAAAGTTT‑CCC‑TT‑AG‑CCGG‑GAAGAGTGTTTCCTCGCCACCCGTACCCGCCACGCTTTTACCATTg                                                                                                                        >  2:1118396/1‑150 (MQ=255)                              ggtggtggtTTGGAAAAAAAACAGGATGTCCGGGAAGACCAAATGGCGGCTTTCCTG‑ACCA‑GAAAGCTGGGCGGCTTTCCGGTAAATTTTT‑CCC‑TT‑GG‑CGGT‑GAAGTGTTTTTCCCCCCACCCCGTACCCGCCACGCTTTTACCATTGAc                                                                                                                      <  2:897210/150‑1 (MQ=255)                              ggTGGGGTTTTTGAAAAAAAACAGGAGGTAGTGAAAG‑GGCAATGGCCGCCTTCCCGAACCA‑CAAGGCTGGGGGGCTTTCGGGTGAAGGTTC‑CCC‑TT‑GG‑CGGT‑AAAGAGTTTTTCCTCGCACCCCGTCCCCGCCACGCTTTTACCATTGa                                                                                                                       <  1:827019/149‑1 (MQ=255)                                 ggCGTTTTTGGAAATAAACAGGATGTAC‑GGAAGGAGCAAGGGGGGCCTTCCCG‑ACCAGGCAAGCTGGGGGCCATTCCGGT‑AAAGTTTCCCC‑TT‑AG‑CGGG‑AAAGTTTGTTCCCCCGAACCCCTTCCCCGCCACGCTTTTACCATTGACggg                                                                                                                   <  1:835222/150‑1 (MQ=255)                                   cGGTTTTGGTAATAAACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTG‑ACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCa                                                                                                                 >  1:513240/1‑150 (MQ=255)                                    ggTTTTGGTAATAAACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTG‑ACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCaa                                                                                                                >  2:665012/1‑150 (MQ=255)                                      tttggaaaaaaaaCAGGATGTACGGGAAGAGCAAGGGGCGGCATTCCTG‑CCCA‑GCAAGCTGGGCGGCTTTCCGGTAAAATTTT‑CCC‑TT‑AG‑CCGT‑GAAGATTTTTCCCCCGCCCCCCGTCCCCGCCACGCTTTTACCATTGACGGGCaaa                                                                                                               <  1:192005/139‑1 (MQ=255)                                             aataaACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTG‑ACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCACCCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGa                                                                                                      <  2:412769/151‑1 (MQ=255)                                             aaaaaaaAGGATGAACGGGAAGGGCC‑GGGGGGGCCTTCCCT‑GCCA‑ACAAGTCTGGGCGCCTTCCGGGAAAAAGTT‑CCC‑TTGAG‑CCGT‑GAAGTGTGTTCCCCCCCACCCCGTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCg                                                                                                         <  1:1085685/145‑1 (MQ=255)                                               taaACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTG‑ACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAAc                                                                                                    >  1:385276/1‑151 (MQ=255)                                                    aGGATGTACTGGAAGAGCCAATGGCGGCATTCCTG‑ACCA‑GCAAGCTTGGCGGCATTCCGGGGAAAGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACcgc                                                                                                 >  1:587617/1‑149 (MQ=255)                                                        tGTACTGGAAGAGCCAATGGCGGCATTCCTG‑ACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACgg                                                                                            >  2:643877/1‑150 (MQ=255)                                                          tACTGGAAGAGCCAATGGCGGCATTCCTG‑ACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAAc                                                                                         >  1:64323/1‑151 (MQ=255)                                                                       aaTGGCGGCTTTCCTA‑ACCA‑GAAAGCTGGGCGGCATCCGGGTAAAATTTT‑CCT‑TT‑AC‑CCGT‑GAAGAGTTTTCCCTCCCACCCCTTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAg                                                                                 <  2:949559/146‑1 (MQ=255)                                                                        aTGGCGGCATTCCTG‑ACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTtat                                                                            >  1:301646/1‑150 (MQ=255)                                                                          ggcgccTTTCCGG‑ACCA‑GCAAGCTGGGCGGCATCCCGGAAAAATTTC‑CCC‑TT‑AC‑CCGT‑GAAGATTTTTCCCCCCCACCCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAg                                                                          <  2:301693/150‑1 (MQ=255)                                                                            cggcATTCCTG‑ACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCt                                                                       >  2:802848/1‑151 (MQ=255)                                                                                  tCCTG‑ACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGt                                                                 >  1:843241/1‑151 (MQ=255)                                                                                   ccTG‑CCCA‑GAAAGCGGGGCGCCATCCGGGTAAAATTTC‑CCC‑TT‑GG‑CGGT‑AAAGAGTTTTCCCCCGCACCCCTCCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGt                                                                 <  1:382441/150‑1 (MQ=255)                                                                                     ccagccaagaaaGTTTGGCGCCTTGCCGGT‑AAATTTT‑CCCTTT‑GG‑CGGT‑AAAGATTTTTCCCCCCCACCCCTTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGtt                                                                <  1:519217/141‑1 (MQ=255)                                                                                         ccA‑GCAAGCTTGGCGGCATTCCGGTGAAAGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTc                                                           >  1:308987/1‑151 (MQ=255)                                                                                            aaaatgttgggcggcTTTCGGGTAAAATTTT‑CCC‑TT‑CG‑CGGT‑GAGGTGTTTTTCCCCCAACCCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATg                                                                  <  1:856111/133‑1 (MQ=255)                                                                                             gCAAGCTTGGCGGCATTCCGGTGAAAGATT‑CCC‑TT‑AG‑CCGC‑GAGGAGTGTTTCCTCGCCACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAACGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTa                                                         >  1:712098/1‑150 (MQ=255)                                                                                              cAAGCTTGGCGGCATTCCGGTGAAAGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGGGTTTCCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTaa                                                        >  1:998765/1‑150 (MQ=255)                                                                                               aggtttGGCGGC‑TTCCGGGTAAAATTT‑CCC‑CT‑AGCCCGT‑AAAGGGTTTTCCCCCGCACCCCTTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAac                                                       <  2:603763/146‑1 (MQ=255)                                                                                                                    aaaTTTC‑CCT‑TT‑AC‑CGGT‑GAAGAGTTTTCCCCCGCACCCCTTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCa                                   <  1:82195/149‑1 (MQ=255)                                                                                                                    aaaGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACg                                 >  2:676033/1‑151 (MQ=255)                                                                                                                     aatgtt‑CCC‑TTGAG‑CGGT‑GAAGGTTTTTCCCCCGCACCCCGTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACg                                 <  1:51039/147‑1 (MQ=255)                                                                                                                     aaGTTC‑CCT‑TT‑GG‑CCGT‑GAGGGGTGTTTCCCCGCACCCCTTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACgg                                <  1:831573/151‑1 (MQ=255)                                                                                                                       gTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGc                              >  2:409946/1‑151 (MQ=255)                                                                                                                                tt‑AG‑CCGT‑GAAGAGTGTTTCCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCAt                       >  2:1003387/1‑151 (MQ=255)                                                                                                                                 t‑AG‑CCGT‑GAAGAGTGTTTCCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATc                      >  1:565407/1‑151 (MQ=255)                                                                                                                                      ccGT‑GAAGGTTTTTCCCCCCCACCCCGCACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCt                   <  1:568993/151‑1 (MQ=255)                                                                                                                                      ccGT‑GAAGAGTGTTTCCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCt                   >  1:252316/1‑151 (MQ=255)                                                                                                                                         t‑GAAGAGTGTTTCCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCTTCt                >  2:441797/1‑151 (MQ=255)                                                                                                                                              gttttttcccTCACACCCCGCCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCTTCTGc              <  1:675934/141‑1 (MQ=255)                                                                                                                                              gagTGTTTCCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCTTCTGCgg            >  2:668714/1‑151 (MQ=255)                                                                                                                                                gtttttCCTCGCAGCCGGCGCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCTTCTGCggg           <  1:1110899/147‑1 (MQ=255)                                                                                                                                                gtgtTTCCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCTTCTGCgggg          >  2:26249/1‑151 (MQ=255)                                                                                                                                                 ttttcccccGCACCCCGTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCTTCt                <  2:346238/136‑1 (MQ=255)                                                                                                                                                 tgtTCCCCCGCACCCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCTTCTGCgg            <  2:1074987/148‑1 (MQ=255)                                                                                                                                                      ccccGCAACCCTTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCTTCTGCGGGGGGGa      <  1:283295/146‑1 (MQ=255)                                                                                                                                                        tCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCTTCTGCGGGGGGGAATa   >  1:1054832/1‑150 (MQ=255)                                                                                                                                                          gCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCTTCTGCGGGGGGGAATaa  >  2:948449/1‑149 (MQ=255)                                                                                                                                                             |                                                                                                                                                  CATGCGTACGAGTCATCAAACCATTTGTCGGTGGCGGTTTTGGTAATAAACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTG‑ACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAGTTT‑CCC‑TT‑AG‑CCGT‑GAAGAGTGTTTCCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCTTCTGCGGGGGGGAATAA  >  NC_000913/3001015‑3001309

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑