Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	436,516	0	C	A	48.2%	72.4 / 31.1	56	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
Reads supporting (aligned to +/- strand):  ref base C (27/2);  new base A (0/27);  total (27/29)
Fisher's exact test for biased strand distribution p-value = 5.51e-14
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.75e-01

ACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTGCTGT  >  NC_000913/436383‑436665                                                                                                                                       |                                                                                                                                                      aCCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATc                                                                                                                                      >  1:730212/1‑151 (MQ=255)    ggAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGa                                                                                                                                    >  2:576025/1‑150 (MQ=255)        cAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGc                                                                                                                               >  2:977290/1‑151 (MQ=255)                 cgcggGGCCCTCTGGGGCGGTAAATATTAGGTGTTGTTTTTCCCTGTGCCGGAACTGACCCGTGGCGCGCTGGATGTGGCTCCCGGACACC‑TGGGCGTCCTGTTTCCCTTTACCGGGAAAATGACCGCCGATATCGAAGGGCTTTGt                                                                                                                          <  2:359088/147‑1 (MQ=255)                     gggCGTTCTGGGGCGGTGAAGATTGGGTGTTGTGTTTCACTGGGCCGGAACTGACCGGTGGGGGGTTGGATGTGGCTCTGGGCCCCC‑GGGGCGTCCTTTTTACTTGTATGGGCAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCg                                                                                                                  <  2:388993/151‑1 (MQ=255)                     gggCGCTCTCTGGGGGTGAAGATTAGGAGTTTTTTTTCACTGGGCCGGAACGGAACGGTGGCGCGCTGGTTGTGGCTCTCGGACCCC‑TGGGCGTCCCGTTTCCCTGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCg                                                                                                                  <  1:957493/151‑1 (MQ=255)                     gggCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCGGGAACTGACCCGTGGCGCGTTGGATGTGGCTCTCGGACACC‑GGGGCGTACCTTTTCCCTGTAGGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTAtt                                                                                                                    <  1:569646/149‑1 (MQ=255)                     gggCGCTCTCGGGCGGTGAAGATTACGAGTTGTGTTTCTCTGTGCGGGAACTGAACCGTGGCGCGCTGGATGTGGCTCCCGGACACC‑TGGGCGTCCCGTTTCCTTGTATGGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTa                                                                                                                      <  1:286944/147‑1 (MQ=255)                     gggCGCTCTCGGGCGGGGAAGATTCCGGTTTGTGTTTCACTGTGCCGAATGTGACCCGTGGCGGGTTGGATGTGGCTCTCGGACCCC‑GGGGCGTCCCTTTTGCCTTTTTCGGCCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCg                                                                                                                  <  1:490613/151‑1 (MQ=255)                      ggCTCTTTCTGGCGGTAAAAATTCCGAGTTGTTTTTCCCTGCCCCGGACCTGACCGGGGGCGCGCTGGATGTGGCCCTCGGACACC‑GGGGCGTACCGTTTCCTTGTGCCGGGAAAATAGCCGCCGATATCGAAGGGCTTTGTTTTATTCGt                                                                                                                 <  1:790885/151‑1 (MQ=255)                             tctGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCg                                                                                                          >  1:82137/1‑151 (MQ=255)                             tctGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCg                                                                                                          >  2:79782/1‑151 (MQ=255)                             tctGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCg                                                                                                          >  1:671797/1‑151 (MQ=255)                               tGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGa                                                                                                         >  1:406553/1‑150 (MQ=255)                                   ggTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTg                                                                                                    >  1:565023/1‑151 (MQ=255)                                   ggTAAAGTTTACGTGTTGTTTTTCACTGTGCCGGAACTGAACCGTGGCGCGGTGGATGGGGCTCTCGGACCCG‑GGGGCGTCCCTTTTCCCTGTACCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCt                                                                                                     <  1:371956/150‑1 (MQ=255)                                      gAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGtt                                                                                                  >  2:322983/1‑150 (MQ=255)                                        aaatcctttgttgttTTTCCCGGCCCCGGACCTGACCCTAGGCGCGCTGGTGGGGCCTCGCGGAAGCC‑GGGGCTGCCGGTTTACCTGTACCGGCAAAAGGTCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTATTACa                                                                                               <  2:654411/142‑1 (MQ=255)                                         gATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACAt                                                                                              >  1:775703/1‑151 (MQ=255)                                         gATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACAt                                                                                              >  1:329147/1‑151 (MQ=255)                                           tcgcGAGTTTTGTTTCTCTGTGCGGAAGTTGACCGGTGGCGCGCTGGATGGGTCCCTCGGACACC‑GGGGGTTCCCTTTTTCCTGTATCGGGAAAATTACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGtt                                                                                                  <  1:82215/142‑1 (MQ=255)                                               gaattGTCTTTCACTGTGCGGAAATAGACCGGTGGAGCGCTGGGTGTGGCTCTCGGCCACC‑GGGGCGCACCTTTTACCGGTATGGGAAAAATAACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGtt                                                                                                  <  1:330354/138‑1 (MQ=255)                                               gAGTTTTTTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACt                                                                                        >  1:73926/1‑151 (MQ=255)                                               gAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACt                                                                                        >  2:138502/1‑151 (MQ=255)                                                 tttGTGTTTCACTGTGCCGGAACGGACCCGGGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCTTTTCCCTGTATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTg                                                                                       <  1:183952/149‑1 (MQ=255)                                                  ttGTGTTTCTCTGGGCCGGAACTGACCCGGGGCGCTCTGGATGTGCCTC‑CGGCCCCCTTGGGCGTACCTTTTCCCTGTATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTgg                                                                                      <  2:458989/150‑1 (MQ=255)                                                  ttGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTgg                                                                                      >  1:263146/1‑150 (MQ=255)                                                  ttGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTg                                                                                       >  2:183952/1‑149 (MQ=255)                                                   tgtgTTCCCCTGTGCGGGAACTGAGCCGGGGGGGGCTGGTGGTGCCCCTGGGCCACC‑GGGGCGTCCTGTTTCCCTGTCTCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTgg                                                                                      <  2:564424/149‑1 (MQ=255)                                                    gtgtTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGaa                                                                                    >  1:538820/1‑150 (MQ=255)                                                          cACTGTGCCGGAACTGACCCGGGGCGCGTTGGATGTGGCTCTCGGCCCCC‑TGGGCGTCCTTTTTCCCTGTAGGGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGata                                                                              <  1:143686/150‑1 (MQ=255)                                                           cgggtcctgaaatagAACCGCGGCGCCCGGGATGTGACTCTGGGCCCTT‑TGGGCGTCCTTTTTCCCTGTAGGGGGAATCTGTCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGatat                                                                             <  1:42661/136‑1 (MQ=255)                                                              gtgCGGGACCTGACCCGGGGCGCGGGGGTTGTGGCTCCCGGACACG‑GGGGCGTCCTTTTTCCTTTTAGCGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGa                                                                           <  2:545795/149‑1 (MQ=255)                                                                   ggAACTGACCCGTGGCGCGTGGGATGTGCCTCTCGGACCCC‑GGGGCGTCCTGTTTCCCTGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtttt                                                                    <  2:640343/151‑1 (MQ=255)                                                                   ggAACTGACCCGGGGCGCGCTGGATGTGGCTCCCGGCCACC‑GGGGCGTCCCGTTTCCCTGTACCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtttt                                                                    <  2:126763/151‑1 (MQ=255)                                                                   ggAACTGAACGGGGGCGCGGTGGTTGTGGCTCGCGGCCACC‑GGGGCGTCCTTTTTCCCTGTATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtttt                                                                    <  2:839070/151‑1 (MQ=255)                                                                   ggAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtttt                                                                    >  2:905917/1‑151 (MQ=255)                                                                   gaaattaacccGGGGGGCGTTGGTTGTGGCTCGCGGACCCT‑TGGGCGTCCTGTTTCCCTTTATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGAcc                                                                         <  2:881647/137‑1 (MQ=255)                                                                     accTGACCCGTGGCGCGCTGGATGTGGCTCTGGCACACT‑GGGGGGTCCTGTTTCCGTGTATGGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtttt                                                                    <  2:490069/147‑1 (MQ=255)                                                                     aaCTGACCCGTGGCGGGCTGTGTGTGGCTCT‑GGATTCCGGGGGCCCACGTTTTACCTGTCTCGCCAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtt                                                                      <  2:122127/147‑1 (MQ=255)                                                                        tGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCAc                                                               >  1:590960/1‑151 (MQ=255)                                                                         gAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACg                                                              >  2:820739/1‑151 (MQ=255)                                                                                ggggcggggggtgtgCCCCTCGGACACG‑GGGGCGCACGTTTTCCCTTTATGGGCAAAATGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATa                                                         <  2:680582/138‑1 (MQ=255)                                                                                     gcTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGt                                                  >  1:460338/1‑151 (MQ=255)                                                                                     gcTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGt                                                  >  1:528915/1‑151 (MQ=255)                                                                                                 tctcGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCg                                      >  1:878741/1‑151 (MQ=255)                                                                                                         ccc‑TGGGCGTCCCTTTTCCCTGTTTCGGAAAAAGGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAg                               <  1:963966/149‑1 (MQ=255)                                                                                                              gggCGAGCCGTTTCCTTTTACCGGGAAAATGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGa                           <  2:489928/150‑1 (MQ=255)                                                                                                                  gTACCTTTTACCTGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTa                        <  1:699060/149‑1 (MQ=255)                                                                                                                   tACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATc                     >  2:502119/1‑151 (MQ=255)                                                                                                                   tACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATc                     >  2:585219/1‑151 (MQ=255)                                                                                                                      cGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGt                  >  2:62399/1‑151 (MQ=255)                                                                                                                      cGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGt                  >  2:919238/1‑151 (MQ=255)                                                                                                                            cttgtgtggggAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCAt             <  1:784725/142‑1 (MQ=255)                                                                                                                              tGTATGGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCa              <  1:947804/147‑1 (MQ=255)                                                                                                                                  tCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTg      >  1:84096/1‑151 (MQ=255)                                                                                                                                       cAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTGCTGt  >  1:639169/1‑150 (MQ=255)                                                                                                                                       |                                                                                                                                                      ACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTGCTGT  >  NC_000913/436383‑436665

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: ‑