Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	436,516	0	C	A	50.0%	46.8 / 34.4	54	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
Reads supporting (aligned to +/- strand):  ref base C (19/8);  new base A (0/27);  total (19/35)
Fisher's exact test for biased strand distribution p-value = 2.42e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.64e-01

GTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATC‑GGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTGCTG  >  NC_000913/436378‑436664                                                                                                                                            |                                                                                                                                                     gTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATC‑GGGCAAATGAccgccg                                                                                                                                          <  2:267034/151‑1 (MQ=255)   tGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATC‑GGGCAAATGACCGCCGa                                                                                                                                         <  1:264818/150‑1 (MQ=255)     aaCCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATC‑GGGCAAATGACCGCCGatat                                                                                                                                      >  2:1010139/1‑151 (MQ=255)         ggAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATC‑GGGCAAATGACCGCCGATATCGa                                                                                                                                   >  1:854093/1‑150 (MQ=255)           aaCGGGCGCTGCGCTGGGCGCTCTCGGGGGGTGAAGATTACGAGTTGTTTTTCCCTGGGCCGAAACTGACCCGGGGCGCGGTGGATGTGGCTCCCGGACACCTGGGCGTCCCGTTTACCTGTATC‑GGGAAAATGACCGCCGATATCGAAg                                                                                                                                 <  1:340430/150‑1 (MQ=255)                  gctgcgctgGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATC‑GGGCAAATGACCGCCGATATCGAAGGGCTTTGt                                                                                                                         >  2:941163/1‑151 (MQ=255)                         tgGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATC‑GGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTc                                                                                                                  >  2:60768/1‑151 (MQ=255)                          gggCGCTCTGGGGCGGTGAAGATTAGGGGTTGTTTTTCACTGCGCCGGACCTAACCGGGGGCGCGGGGGTTGTGCCTCCCGCACCCCTGGGCGTCCTTTTTACTTTTAGG‑GGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCg                                                                                                                 <  1:867773/151‑1 (MQ=255)                          gggCGCTCTCGGGGGGTGAAGATCACGGGTTGTTTTTCCCTGTGCCGGAACTGACCGGGGGCGCGGTGGATGTGGCTCTCGGACCCCGGGGCGTACCTTTTCCTTGTATC‑GGGAAAATGACCGCCGATATCGAAGGGCttt                                                                                                                           <  2:901943/141‑1 (MQ=255)                          gggCCCTCTCGGGCGGGGAAGATTAGGAGTTGTTTTTCACTGTGCGGGAACTGACCGGTGGCGCGCTGGATGTGGCTCTCGCACACGGGGGCGTACTTTTTACTTGTATC‑GGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTa                                                                                                                     <  1:443333/147‑1 (MQ=255)                                tctttGGCGGTGAGGATTACGAGTTGTTTTTCTCTGTGCCGGACCGGACCGGTGGGGCGCTGGTTGTGGCTCTCGGACCCTTGGGCTTCCCGTTTCCTTTTATC‑GGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACg                                                                                                            <  2:280584/150‑1 (MQ=255)                                    tGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTTGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATC‑GGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGa                                                                                                        >  2:374946/1‑150 (MQ=255)                                     ggCGGTGAAGATTACGAGTTTTGTTTCACTGTGCCGGAACTAACCCGGGGCGCGCGGGATGTGGCTCCCGGACACCGGGGCGTCCTTTTTTCTTGTAGC‑GGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGa                                                                                                              <  1:70673/143‑1 (MQ=255)                                     ggCGGTGAAGATTACGAGTTGTTTTTCCCTGTGCCGGAACTGACCGGTGGCGCGTTGGATGTGGCTCTCGGACCCCTGGGCTTACCGTTTCCCTGTTTG‑GGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGa                                                                                                        <  2:628676/149‑1 (MQ=255)                                             aGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATC‑GGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTAc                                                                                               >  1:1032159/1‑150 (MQ=255)                                                ttaggggttgttTTTCTCGGGGCCGGAACTGAACGGTGGCGCGCTGGAGGTGGCTCTGGGACCCGTGGGCGTCCCTTTTCCTTGTATG‑GGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACAt                                                                                             <  2:1017567/143‑1 (MQ=255)                                                ttACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATC‑GGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACAtt                                                                                            >  2:741844/1‑150 (MQ=255)                                                 tACGAGTTGTTTTTCACTGTGCCGGAACTGACCCGTGGCGCGTTGGATGGGGCTCTCGGACCCCTGGGCGTCCCGTTTCCCTGTATG‑GGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTa                                                                                           <  2:882539/150‑1 (MQ=255)                                                  aCGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATC‑GGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACAtt                                                                                            >  2:827850/1‑148 (MQ=255)                                                      gTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATC‑GGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTgg                                                                                     >  2:940780/1‑151 (MQ=255)                                                       ttGTTTTCCACTGTGCCGGAACTGACCCGTGGCGCGTTGGATGTGGCTCCCGGCCCCCGGGGCGTCCCTTTTCCCTGTATG‑GGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAg                                                                                          <  1:448956/145‑1 (MQ=255)                                                       ttGTGTTTCCCTGTGCGGGAACTGACCCGGGGCGCGTTGGATGTGCCTCCCGGACCCCGGGGGGTCCCTTTTCCCTGTTGC‑GGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACt                                                                                       <  2:273545/148‑1 (MQ=255)                                                       ttGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATC‑GGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTgg                                                                                     >  1:841985/1‑150 (MQ=255)                                                        tgtgTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATC‑GGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGa                                                                                    >  2:439746/1‑150 (MQ=255)                                                         gtttttCCCTGTCCCGGAACTGAACCGTGGCGCGGTGGTTGTGGCTCTCGGACCCCTGGGCGTCCCTTTTCCCTGTATG‑GGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGaa                                                                                   <  1:499279/147‑1 (MQ=255)                                                            tttCTCTGTGCGGAAACTGACCGGTGGCGGGGTGGAGGGGGTTCTGGGACGCGTGGGCGTCCCGTTTCCCTGTGCC‑GGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAgg                                                                                <  2:889457/150‑1 (MQ=255)                                                             ttCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATC‑GGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGCACCTGTTACATTAGACTGGAAAGGat                                                                              >  1:578398/1‑151 (MQ=255)                                                                   gtgCCGGAACTGACCCGGGGCGCGCTGGATGTGGCTCTCGGACCCCGGGGCGTCCCGTTTCCTTGTATC‑GGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGat                                                                              <  2:244233/145‑1 (MQ=255)                                                                     gCCGGAACTGACCGGGGGCGCGTTGGATGTGGCTCTCGGACCCCGGGGCGTCCCGTTTCCTTGTATC‑GGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCa                                                                       <  2:983817/150‑1 (MQ=255)                                                                     gCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATC‑GGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAt                                                                      >  2:934855/1‑151 (MQ=255)                                                                      ccGGAACGGACCCGTGGGGCGCTGGATGGGGCTCTCGGACACCGGGGCGTACCGTTTACCTGTATC‑GGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGAcc                                                                        <  1:1008328/148‑1 (MQ=255)                                                                        ggaccggaccgggggCGCGTGGGTTTTGGCTCTGGGACCCTTGGGCTTACCGTTACCTTTTATG‑GGGCAAAGGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAttt                                                                    <  2:829475/137‑1 (MQ=255)                                                                        ggAACTGACCCGTGGCGCGTTGGATGTGGCTCTCGGACCCCTGGGCGTCCCTTTTCCCTGTATC‑GGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAttt                                                                    <  2:86163/150‑1 (MQ=255)                                                                        ggAACTAAACCGGGGCGCGTTGGATGTGCCTCTCGGACCCCGGGGCGTTCCTTTTACTTGTAGG‑GGGAAAAGGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCa                                                                       <  1:492638/147‑1 (MQ=255)                                                                        gaaccggacccGGGGGGCGCGGGGTGTGGCTCTCGG‑CCCCGGGGGGGTCCCTTTTCCTTTTTCGGGGAAAAGGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtttt                                                                   <  2:1026434/142‑1 (MQ=255)                                                                          accTGAACGGTGGCGCGCGGGATGTGGCTCGCGGCCCCCGGGGCGTCCCGTTTCCCTTTATG‑GGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGc                                                                 <  2:1036399/149‑1 (MQ=255)                                                                             tGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATC‑GGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCAc                                                              >  1:892612/1‑151 (MQ=255)                                                                               acccGTGGCGCGTGGTGTGTGCCGCTTGAACACTTGGCCGTCCCTTTAACCTGAGTC‑GGTAAAAAGGCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACg                                                             <  2:1066060/148‑1 (MQ=255)                                                                                aCCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATC‑GGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGcc                                                           >  2:513964/1‑151 (MQ=255)                                                                                  cGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATC‑GGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCAt                                                         >  1:978749/1‑151 (MQ=255)                                                                                    gggCGCGGTGGATGTGGCTCGGGGACACGGGGGCGTCCTTTTTACCTGTGCC‑GGAAAAAGGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATaa                                                       <  2:323106/150‑1 (MQ=255)                                                                                             ggagggggCTCGCGGACCCCGGGGCGTCCTTTTTCCTTGTATG‑GGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTcgc                                              <  2:789693/145‑1 (MQ=255)                                                                                                   ggCTCCCGGACCGCTGGGCTTCCCTTTTCCCTGGACG‑GGGAAAATGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGaaaa                                         <  1:1040479/150‑1 (MQ=255)                                                                                                       cgcggacccgggggCGTCCCTTTTCCCTGTATG‑GGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTc                                      <  2:188026/138‑1 (MQ=255)                                                                                                         cggccccgggggCGTCCCTTTTCCCTGTAGG‑GGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTc                                      <  1:67662/138‑1 (MQ=255)                                                                                                               cgtGGGCGTCCCTTTTCCCTGTAGG‑GGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTg                                 <  2:741018/144‑1 (MQ=255)                                                                                                                  gggCGTCCCTTTTCCTTGTATG‑GGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGa                             <  2:117636/147‑1 (MQ=255)                                                                                                                           ttttccttGTATC‑GGCCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAAt                     <  2:391076/139‑1 (MQ=255)                                                                                                                             tttacttttttggggAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATcc                   <  2:326396/135‑1 (MQ=255)                                                                                                                             ttcccTGTTTC‑GGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTg                <  1:835104/146‑1 (MQ=255)                                                                                                                                 cTGTATC‑GGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCt          >  2:999815/1‑151 (MQ=255)                                                                                                                                     tagggggAAAAGGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTa         <  2:854240/145‑1 (MQ=255)                                                                                                                                          ggCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTGCTg  >  1:357935/1‑151 (MQ=255)                                                                                                                                           gCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTGCTg  >  1:72333/1‑150 (MQ=255)                                                                                                                                            |                                                                                                                                                     GTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATC‑GGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTGCTG  >  NC_000913/436378‑436664

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑