Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	436,516	0	C	A	46.2%	61.1 / 25.9	53	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
Reads supporting (aligned to +/- strand):  ref base C (22/6);  new base A (0/24);  total (22/31)
Fisher's exact test for biased strand distribution p-value = 1.60e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.68e-01

CATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTT‑CACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTT  >  NC_000913/436375‑436660                                                                                                                                                  |                                                                                                                                                  cATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTT‑CACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑Accg                                                                                                                                         <  1:764090/151‑1 (MQ=255) cATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTT‑CACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑Accg                                                                                                                                         <  2:204108/151‑1 (MQ=255)                  ggCGCTGCGCTGGGCGCTCTCTGGCGGTAAAGATTACGGGTTGTGTTT‑CACTGTGCGGGAACGGAACCGTGGCGCGCTGGATGTGGCCCTCGGACACC‑TGGGCGTCCCT‑TTTCCCTTTAGCGGG‑AAAATT‑ACCGCCGATATCGAAGGGCt                                                                                                                         <  2:328496/150‑1 (MQ=255)                    cgctgcgcggGGCGCTTTCTGGGGGTGAAGATTACGAGTGGTTTTT‑CACTGTGCCGGAACTGACCCGGGGCGCGTTGGATGTGGCTCTCGGACCCC‑GGGGCGTCCCG‑TTTCCTTGTATGGGG‑AAAATG‑ACCGCCGATATCGAAGGGCttt                                                                                                                       <  2:803773/150‑1 (MQ=255)                     gctgcgcggGGCGCTCTGTGGGGGTAAAGATTACGAGTTGTGTTT‑CACTGTGCCGGAACTGACCGGGGGCGCGTGGGATGTGCCTCTCGGACACC‑GGGGCGTCCCT‑TTTCCCTTTATGGGG‑AAAAGG‑ACCGCCGATATCGAAGGGCTTTg                                                                                                                      <  1:889527/150‑1 (MQ=255)                          gctgGGCGCTCTCTGGCGGTGAATATTACGAGTTGTGTTC‑CAGTGGGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑GGGGCGTCCCT‑TTTCCCTGTATGGGG‑AAAATG‑ACCGCCGATATCGAAGGGCTTTGtttt                                                                                                                  <  2:398763/149‑1 (MQ=255)                          gctgGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTT‑CACTGGGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTAt                                                                                                                >  1:382090/1‑151 (MQ=255)                             gggCCCTCTCTGGGGGGGAAGATTACGTGTT‑TGTTTCCCCTGTGCCGGACCTGACCTGGGGGGGGCTGGATGTGGCCCT‑GGGCACCGTGGCCGTTCCT‑TGTCCCTGTTTCGGA‑AAAATG‑CCCGCCGATATCGAAGGGCTTTGTTTTATTCg                                                                                                             <  2:891604/151‑1 (MQ=255)                                        ggCGGTGAAGATTACGGGTTGTGTTT‑CACGGTGCCGGAACTGAACGGTGGCGCGCGGGATGTGGCTCTCGGACACC‑TGGGCGTCCGG‑TTTCCTTGTATGGGG‑AAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGAc                                                                                                         <  2:139358/144‑1 (MQ=255)                                               aaGATTACGAGTTGTGTTT‑CACTGGGCCGGAACAGAACCGTGGCGGGTGGGTTGTGGCTCTCGGACCCC‑GGGGCGTCCCT‑TTTCCCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGtt                                                                                             <  2:337401/149‑1 (MQ=255)                                                aGATTACGAGTTGTGTTT‑CACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTAc                                                                                           >  2:309458/1‑150 (MQ=255)                                                   ttcggAGTGGTTTTT‑CACTGTGCGGGAACTGAACGGGGGGGCGCTGGTGGTGGCTCTGGGACCCG‑GGGGCGTCCGG‑TTTCCTTGTTTCGGG‑AAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACAtt                                                                                        <  2:717656/146‑1 (MQ=255)                                                    tACGAGTTGTGTTT‑CCCTGTGCCGGAACTGACCCGTGGCGCGCTGGATGTGGCTCTCGGACCCC‑TGGGCGTCCCT‑TTTCCCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTa                                                                                       <  2:256295/150‑1 (MQ=255)                                                      cgtgttgttTTC‑CCCTGTGCCGAAACTGACCCGTGGCGCGTGGGATGTGGCTCTCGGACCCC‑GGGGCTTCCCT‑TTTCCCTGTATGGGC‑AAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAg                                                                                      <  1:100080/146‑1 (MQ=255)                                                          ttGTTTTT‑CACTGCGCGGAACCTGACCCGTGGCGCGCTGGATGTGGCTCTCGGACCCC‑TGGGCGTACCT‑TTTACCTGTATCGGA‑AAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGAc                                                                                    <  1:563452/147‑1 (MQ=255)                                                          ttGTGTTT‑CCCTGTGCGGGAACTGACCCGTGGCGCGCGGGATGTGGCTCTCGGACACC‑TGGGCGTCCCT‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACt                                                                                   <  1:118539/148‑1 (MQ=255)                                                          ttGTGTTT‑CACTGTGCCGGAACTGACCCGTGGCGCGCTGGATGTGGCTCTCGGACCCC‑GGGGCGTCCCG‑TTTCCCTGTATCGGG‑AAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTgg                                                                                 <  2:222038/150‑1 (MQ=255)                                                           tgtgTTT‑CACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGa                                                                                >  2:935618/1‑150 (MQ=255)                                                            gttttt‑CACTGGGCCGGAACTGACCGGGGGCGCGTTGGTTGTGGCTCTCGGACACG‑GGGGCGTCCCT‑TTTCCCTGTAGCGGG‑AAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGaa                                                                               <  2:854242/147‑1 (MQ=255)                                                              gtTT‑CACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAgg                                                                            >  1:387034/1‑151 (MQ=255)                                                                 t‑CACTGTGCCGGAACTGAACCGTGGCGCGCCGGATGTGGCTCTCGGACACC‑TGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGat                                                                          >  2:392110/1‑150 (MQ=255)                                                                       gtgCCGAAACTGACCCGGGGCGCGCTGGATGTGGCTCTCGGACCCC‑TGGGCGTCCCT‑TTTCCCTGTATCGGG‑AAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGAc                                                                     <  1:406307/150‑1 (MQ=255)                                                                           cGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAttt                                                                >  1:434330/1‑151 (MQ=255)                                                                            gaaaCTGAACCGGGGCGCGCTGGATGTGGCTCTCGGACCCC‑GGGGCGTACCG‑TTTCCCTGTTTCGGG‑AAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtttt                                                               <  1:830642/149‑1 (MQ=255)                                                                            gaaaCTAACCCGTGGCGCGTTGGATGTGGCTCTCGGCCCCC‑TGGGCGTACCT‑TTTCCCTGTATGGGG‑AAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtttt                                                               <  1:136213/149‑1 (MQ=255)                                                                             gAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTg                                                              >  1:78489/1‑151 (MQ=255)                                                                              aaCTGACCCGTGGCGCGCTGGATGTGGCTCTCGGACCCC‑GGGGCGTACCT‑TTTCCCTTTATCGGG‑AAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGc                                                             <  2:903056/151‑1 (MQ=255)                                                                              aaCGGAACCGTGGCGCGCTGGTTGGGGCCCTCGGACCCG‑TGGGCGTCCCT‑TTTCCGTGTACCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtttt                                                               <  2:191917/149‑1 (MQ=255)                                                                                      cGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCAt                                                     >  1:631154/1‑151 (MQ=255)                                                                                       gTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCAt                                                     >  1:159166/1‑150 (MQ=255)                                                                                         ggCGCGTTGGAGGGGGCTCGGGGCCCCT‑GGGGCGTCCCT‑TTTCCTTTTTTGGGG‑AAAAGG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATaaa                                                  <  2:21577/151‑1 (MQ=255)                                                                                         ggCGCGCTGGAGGGGCCTCTCGGCCCCC‑TGGGCGTACTT‑TTTCCTTGT‑TCGGGAAAAAGG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATaaa                                                  <  1:389485/151‑1 (MQ=255)                                                                                          gcgcgcTGGTTGTGGCTCTCGGACCCC‑GGGGCGTCCCT‑TTTCCCTGTATCGGG‑AAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATaaa                                                  <  2:653617/150‑1 (MQ=255)                                                                                           cgcgcTGGATGTGGCTCTCGGACACC‑TGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATaa                                                   >  1:929658/1‑148 (MQ=255)                                                                                             cgcTGGATGTGGCTCTCGGACACC‑TGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATg                                              >  2:3032/1‑151 (MQ=255)                                                                                              gcTGGGTGTGCCTCTCGGACGCG‑GGGGCGTCCTG‑TTTCCCTGTAGCGGC‑AAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGa                                                <  2:25636/148‑1 (MQ=255)                                                                                                 ggttgtgCCTCCCGGACCCT‑TGGGGTTCCCG‑TTTCCTTGTA‑CGGG‑GAAATGAACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGa                                                <  2:877189/142‑1 (MQ=255)                                                                                                 ggATGTGGCTCTCGGACACC‑TGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTcgc                                          >  1:589771/1‑151 (MQ=255)                                                                                                 ggATGTGGCTCTCGGACACC‑TGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTcgc                                          >  2:377328/1‑151 (MQ=255)                                                                                                        gCTCTCGGACACC‑TGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAg                                    >  1:15215/1‑150 (MQ=255)                                                                                                           ctcGGACCCG‑TGGGCGTCCCT‑TTTCCTTGTATGGGG‑AAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGaaa                                      <  2:166768/145‑1 (MQ=255)                                                                                                            tcGGACACC‑TGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGcc                               >  2:171264/1‑151 (MQ=255)                                                                                                               ggcccc‑TGGGCGTTCCGTTTTCCCTGTATGGGG‑AAAAGG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCt                              <  2:326888/146‑1 (MQ=255)                                                                                                               gACACC‑TGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTg                             >  1:541674/1‑150 (MQ=255)                                                                                                                  ccccggggCTTCCCT‑TTTCCCTGTAGCGGA‑AAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCt                              <  1:153980/142‑1 (MQ=255)                                                                                                                  acC‑TGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGa                            >  1:902411/1‑148 (MQ=255)                                                                                                                      tGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATg                       >  2:600760/1‑150 (MQ=255)                                                                                                                      tGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATg                       >  2:4528/1‑150 (MQ=255)                                                                                                                       gggCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATg                       >  1:230951/1‑149 (MQ=255)                                                                                                                                  tttACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTgg           >  1:902596/1‑151 (MQ=255)                                                                                                                                      cttttATGGGG‑AAAATG‑CCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCAt        <  2:860376/146‑1 (MQ=255)                                                                                                                                       cTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCt      >  1:130287/1‑151 (MQ=255)                                                                                                                                              ggg‑AAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACtt  <  2:362147/148‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                  CATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTT‑CACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACC‑TGGGCGTACCG‑TTTACCTGTATCGGG‑CAAATG‑ACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTT  >  NC_000913/436375‑436660

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑