Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	436,504	0	A	C	43.6%	70.0 / 18.6	55	T291P (ACC→CCC)	thiL	thiamine monophosphate kinase
Reads supporting (aligned to +/- strand):  ref base A (23/8);  new base C (0/24);  total (23/32)
Fisher's exact test for biased strand distribution p-value = 4.74e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCTGATGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGT  >  NC_000913/436357‑436649                                                                                                                                                     |                                                                                                                                                  tCTGATAAGCTTTCTAGCCATGTTGAACCGGAACAGGCGCTGCGCTGCGCGCTCTCTGGCGGTGAAGATTACAAGTTGTGTGTCACTGTGCAGGAACTGAACCCTGTCGGGCTGGATGTGGCTCTCGGA‑CACCTGAGCGTGACGGTTAcc                                                                                                                                                 >  2:915076/1‑150 (MQ=255)    gATGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGt                                                                                                                                              >  1:469700/1‑150 (MQ=255)      tGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATc                                                                                                                                           >  1:184799/1‑151 (MQ=255)       gcgcTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATc                                                                                                                                           <  1:155583/150‑1 (MQ=255)        cgcTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATCgg                                                                                                                                         <  1:128652/151‑1 (MQ=255)             tctcGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATCGGGCaa                                                                                                                                     <  1:676862/150‑1 (MQ=255)                cGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATCGGGCAAATg                                                                                                                                  >  2:856798/1‑150 (MQ=255)                cGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGCGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATCGGGCAAATg                                                                                                                                  >  1:691859/1‑150 (MQ=255)                   cATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGAccg                                                                                                                              >  2:955308/1‑151 (MQ=255)                           aCCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATc                                                                                                                      >  2:231912/1‑151 (MQ=255)                              ggAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGa                                                                                                                    >  1:806632/1‑150 (MQ=255)                                aaCAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAgg                                                                                                                 >  1:398937/1‑151 (MQ=255)                                   aGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCt                                                                                                              >  2:120303/1‑151 (MQ=255)                                     gcgctgcgctGGGCTCTCTCGGGCGGTGAAGATTACGATTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGC‑CCCTGGGGCGTCCCTTTTCCCTGTATCGGGAAAATGACCGCCGATATCGAAGGGCttt                                                                                                            <  1:316728/151‑1 (MQ=255)                                          gcgctgGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGtttt                                                                                                       >  2:564104/1‑151 (MQ=255)                                             ctgGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTAtt                                                                                                    >  2:560170/1‑151 (MQ=255)                                               gggCGCTCTGTGGCGGTGAAGATTACGGGTTTTTTTTCACTGTGCCGGAACTGAACCGTGGCGCGTTGGATGGGGCTCTGGGA‑CCCCGGGGCGTACCGTTTCCCTGTATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTc                                                                                                   <  1:720531/150‑1 (MQ=255)                                               gggCGCTCTCTGGGGTTAAGGTTTAGGTGTTGTTTTTCATTGTGCCGGAACTGACCCGGGGCGCGCTGGGTGTGCCTCTCGGC‑CCCCGGGGCGTCCCGTTTCCTTGTTTCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCg                                                                                                  <  1:429101/151‑1 (MQ=255)                                                ggCGCTCTCGGGGGGTGAAGATTAGGTGTTGTTTTTCCCTGGGCGGAAACTGACCGGGGGCGCGCTGGATGTGGTTCTCGGC‑CACCTGGGGGTCCTTTTTCCCTGTATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGt                                                                                                 <  2:711597/151‑1 (MQ=255)                                                  cgcTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTg                                                                                                >  1:86523/1‑150 (MQ=255)                                                      gtcggggggTGAAGATTCGGGTTTGTTTTTCACGGTGCGGGAACTGACCGGGGGCGGGTTGTTTGTGGTTCGGGGA‑GACTGGGGGTTCCCGTTTCCTTGTATGGGGAAAAGGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACgg                                                                                            <  2:307150/143‑1 (MQ=255)                                                       tctGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTCAACCGTCGCGCGCTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGACATCGAAGGGCTTTGTTTTATTCGTGACGGc                                                                                           >  2:576051/1‑150 (MQ=255)                                                        ctGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCg                                                                                          >  1:912775/1‑150 (MQ=255)                                                          gggggggAAGTTTACGGGTTGTTTTTCGCGGTGCGGAAACTGAACGGGGGCGCGTTGGGTGTGGCTCTGGGC‑CACCGGGGCGTCCTTTTTCCTTTTACCGGACAAATGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAAc                                                                                       <  2:912119/145‑1 (MQ=255)                                                          gggggTGAAGATTCGGGTTTGTTTTTCCCTGTGCCGGAACTGAACCGGGGCGCGCTGGTTGTGTCTCTGGGA‑CCCCGGGGCGTCCCGTTTACCTGTATCGGGAAAAGGACCGCCGATATCGAAGGGCTTTGTTCTATTCGTGACGGCGa                                                                                         <  1:598966/146‑1 (MQ=255)                                                          ggCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGA‑CCCCTGGGCGTCCCGTTTCCCTGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCg                                                                                          <  1:698610/148‑1 (MQ=255)                                                                 aaGATTACGATTTGTTTTTCACTGTGCCGGAACGGAACGGTGGCGCGTTGGTTGTGGCTCCCGGA‑CCCCGGGGCGTCCCTTTTACCTGTATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTa                                                                                 <  1:975510/150‑1 (MQ=255)                                                                    aTTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACAtt                                                                             >  2:407796/1‑151 (MQ=255)                                                                     ttACGAGTTGTGTTTCACTGTGCCGGAACGGAACCGTGGCGCGCTGGAGGTGGCTCTCGGA‑CACCGGGGCGTCCCTTTTCCCTGTATCGGGAAAAGGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACAtt                                                                             <  1:156384/150‑1 (MQ=255)                                                                            ttGTGTTTCACTGTGCCGGACCTGACCCGGGGCGCGCTGGATGGGGCTCTCGGA‑CACTGGGGCGTACCGTTTCCCTGTATCGGGAAATTGTCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTg                                                                       <  1:731735/149‑1 (MQ=255)                                                                                 tttCACTGTGCGGAACCTGACCCGTGGCGCTGTGGATGTGGCTCGCGGA‑CACGGGGGCGTACCTTTTCCCTGTATCGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGaa                                                                    <  2:181981/147‑1 (MQ=255)                                                                                  ttCACTGTGCCGGAACTGACCGGTGGCGCGTTGGATGTGGCTCTCGGA‑CACCGGGGCGTACCGTTTCCCTGTATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGa                                                                <  1:321924/150‑1 (MQ=255)                                                                                      tggcccctgactcgAACCGTGGCGCGATGGGCGTGTTTCTGGGA‑CTCAAGGGCTCCCTGTTCCGCTATATCGGCCAACTGGCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTTGAAAGGATATg                                                            <  1:131652/137‑1 (MQ=255)                                                                                       tgtgCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGa                                                           >  2:461271/1‑150 (MQ=255)                                                                                          gcggaaaCTGACCCGTGGCGCGTTGGATGTGGCTCTCGGA‑CACCGGGGCGTCCCTTTTCCTTTTATGGGGAAAATAACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGAc                                                          <  1:358514/143‑1 (MQ=255)                                                                                             ggACCTGAACCGGGGCGGGTTGGATGGGGCTCCCGGA‑CCCCTGGGGGTCCCGTTTCCTTGTATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAttt                                                     <  2:191405/150‑1 (MQ=255)                                                                                             ggAACTGACCGGTGGCGCGCTGGTTGTGGCTC‑CGGACCTCCTGGGCGTCCCGTTTCCTTGTCTCGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAt                                                       <  1:115008/148‑1 (MQ=255)                                                                                             ggAACTGAACGGTGGCGCGCTGAATGTGGCTCTCGGA‑CACCTGGGCGTCACGATTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGACATGACCAtttt                                                    >  2:776098/1‑151 (MQ=255)                                                                                              gAATTGACCCGTGGCGCGCTGGATGTGCCTCTCGGA‑CACCTGGGCGTCCCTTTTACTTTTATGGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtttt                                                    <  1:620209/150‑1 (MQ=255)                                                                                               acctgaccgggggCGCGTTGGTTGTGCCTCTCGGA‑CCCCTGGGCGTCCCGTTTCCCTGTATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtttt                                                    <  1:514963/138‑1 (MQ=255)                                                                                               aaCTGACCCGGGGCGCGCTGGATGTGGCTCTCGGA‑CCCCTGGGCGTACCGTTTCCCTGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTg                                                   <  1:832243/150‑1 (MQ=255)                                                                                                   gacccGGGGCGCGTGGGGTGGGCCTCTCGGA‑CCCCGGGGCGTACCTTTTCCTTTTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCa                                                <  2:876652/146‑1 (MQ=255)                                                                                                        gTGGCGCGCTGGATGTGGCTCTCGGA‑CCCCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCa                                           <  1:435762/149‑1 (MQ=255)                                                                                                          ggCGGGTTGGTTGTGGCTCTGGGC‑CCCCTGGGCGTCCCTTTTCCCTGTTTCGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCAt                                          <  1:969535/148‑1 (MQ=255)                                                                                                          ggCGCGCTGGATGTGGCTCCCGGA‑CCCTGGGGCGTCCCTTTTCCTTGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATaa                                        <  1:494560/150‑1 (MQ=255)                                                                                                           gcgcgcTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATaa                                        >  1:408912/1‑149 (MQ=255)                                                                                                            cgcgcTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATaa                                        >  2:592314/1‑148 (MQ=255)                                                                                                                 tGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTcg                                >  2:951680/1‑151 (MQ=255)                                                                                                                               ggA‑CACCGGGGCGTCCCGTTTCCCTGTAGGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAg                         <  1:300318/144‑1 (MQ=255)                                                                                                                                  acccgggggCGTCCCTTTTACCTGTATGGGAAAAATGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTc                                 <  2:104015/128‑1 (MQ=255)                                                                                                                                    acCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGa                 >  2:411840/1‑148 (MQ=255)                                                                                                                                       ggggCGTCCCTTTTCCTTGTATGGGGAAAATGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGa           <  2:391925/150‑1 (MQ=255)                                                                                                                                        gggCTTCCCTTTTCCCTGTAGCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATg            <  2:215821/149‑1 (MQ=255)                                                                                                                                        gggCGTCCCTTTTCCCTGTTGCGGAAAAATAACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAg          <  1:683696/151‑1 (MQ=255)                                                                                                                                                cGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGt  >  2:321298/1‑151 (MQ=255)                                                                                                                                                     |                                                                                                                                                  TCTGATGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGA‑CACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGT  >  NC_000913/436357‑436649

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑