Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	436,516	0	C	A	40.0%	71.5 / 21.4	50	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
Reads supporting (aligned to +/- strand):  ref base C (24/6);  new base A (1/19);  total (25/25)
Fisher's exact test for biased strand distribution p-value = 1.90e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.42e-01

CGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTAC‑GAGTTGTGTTTCACTGTGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTGC  >  NC_000913/436372‑436662                                                                                                                                                     |                                                                                                                                                   cGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTAC‑GAGTTGTGTTTCACTGTGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATg                                                                                                                                               <  1:919832/150‑1 (MQ=255) cGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTAC‑GAGTTGTGTTTCACTGTGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATg                                                                                                                                               <  2:1212098/150‑1 (MQ=255)    cATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGACGGTGAAGATTAC‑GAGTTGTGTTTCACTGTGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGAccg                                                                                                                                           <  2:390903/151‑1 (MQ=255)       gTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTAC‑GAGTTGTGTTTCACTGTGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGAccgcc                                                                                                                                         <  2:654459/150‑1 (MQ=255)        ttGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTAC‑GAGTTGTGTTTCACTGTGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGAccgccg                                                                                                                                        >  2:321592/1‑150 (MQ=255)           aaCCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTAC‑GAGTTGTGTTTCACTGTGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGatat                                                                                                                                    >  2:246926/1‑151 (MQ=255)           aaCCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTAC‑GAGTTGTGTTTCACTGTGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGatat                                                                                                                                    >  2:1104972/1‑151 (MQ=255)           aaCCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTAC‑GAGTTGTGTTTCACTGTGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGatat                                                                                                                                    >  1:60538/1‑151 (MQ=255)               ggAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTAC‑GAGTTGTGTTTCACTGTGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGa                                                                                                                                 >  1:491262/1‑150 (MQ=255)                  acggcggccgggtggggCGCTCTGGGGCGGTAAAGATTAG‑GATTTGTGTTCCGCTTGGCCGGAA‑TGAACCCGTGGGGCGATGGAGGGGCCTCTCGGACCCTG‑GGGCGTCCTGTTTACC‑TGTGCGGGGAAAATGACCGCCGATATCGAAggg                                                                                                                             <  1:1042884/137‑1 (MQ=255)                    aGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTAC‑GAGTTGTGTTTCACTGTGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCt                                                                                                                           >  1:1254583/1‑151 (MQ=255)                         ctgcgctgGGCGCTCTCTGGCGGTGAAGATTAC‑GAGTTGTGTTTCACTGTGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGtt                                                                                                                      >  2:222287/1‑151 (MQ=255)                           gcgctgGGCGCTCTCTGGCGGTGAAGATTAC‑GAGTTGTGTTTCACTGTGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGtttt                                                                                                                    >  2:620977/1‑151 (MQ=255)                            cgctgGCCGCTCTTTGGGGGTAAATTTGAC‑GAGTTTTTTTCCTTTTTGCGGGAGCTGAA‑CGGGGGGGCGCGGGTGGTGCCTCTCGGCCACTG‑GGGCGTCCCTTTTACT‑TTTTAGGGCCAAAGGACCGCCGATATCGAAGGGCTTTGtttt                                                                                                                    <  1:428952/150‑1 (MQ=255)                                gggCGCTCTCTGGGGGGGAAGATTAC‑TTGTTTTGTTCCCCGGGGCCGAAACTGAC‑CCGTGGCGCGCGGGTGGTGGC‑CCCGGAACCCTGGGGGGTGCCTTTTCCT‑TTTGGGGGAAAAAGGCCCGCCGATATCGAAGGGCTTTGtttt                                                                                                                    <  2:359764/146‑1 (MQ=255)                                gggCGCTCTCGGGGGGTGAAGATTGG‑GATTTGTTTTTCACTGTGCCGGAACGGAC‑CGGTGGCGGGTTGGAGGTGCCTCACGCACCCGT‑GGGCGTCCTTTTTCCT‑TGTATGGGAAAAATGCCCGCCGATATCGAAGGGCttt                                                                                                                         <  2:688169/141‑1 (MQ=255)                                   cgcTCTCTGGCGGTGAAGATTAC‑GAGTTGTGTTTCACTGTGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTg                                                                                                             >  2:338485/1‑150 (MQ=255)                                      tctctGGCGGTGAAGATTAC‑GAGTTGTGTTTCACTGTGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACgg                                                                                                         >  2:1268046/1‑151 (MQ=255)                                       ctctGGCGGTGAAGATTAC‑GAGTTGTGTTTCACTGTGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACAACT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGc                                                                                                        >  1:1035473/1‑151 (MQ=255)                                         ctGGCGGTGAAGATTAC‑GAGTTGTGTTTCACTGTGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCg                                                                                                       >  2:97161/1‑150 (MQ=255)                                           ggggggaaaGATTCG‑GTGTTGTTTTTCCCTGGCCGGGAACTGAC‑CTGGGCCGCGTTGGTTGTGCCTCTC‑GCCCCCG‑GGGGGTTCCTTTTTCCTTGTTTGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGa                                                                                                            <  2:618321/136‑1 (MQ=255)                                            ggggTAAAGATTAG‑GTTTTGTTTTTCCCTGGGCCGGAACTGAC‑CGGGGGCGGGTTGGTTGGGGCTCCCGGACCCCG‑GGGCGTCCTGTTTCCT‑TGTATGGGCAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAAcc                                                                                                   <  2:1118543/149‑1 (MQ=255)                                                  aaGATTAC‑GAGTTGTGTTTCACTGGGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGATACCT‑GGGCGAACCGTATACC‑TGTATCGGGCAGATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCCAACCTGTTAc                                                                                             >  2:819162/1‑151 (MQ=255)                                                   aGATTACGGAGTTGTTTTCCACTTTGCCGGAGTGGTC‑CGGTGGGGCGTTGGATGGGGCTCAAGGACTCTT‑GGGCGTACGGTTTCCC‑TGTAGCGGGAAATTGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTa                                                                                              <  1:279580/150‑1 (MQ=255)                                                        aC‑GAGTTGTGTTTCACTGTGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACAtt                                                                                          >  1:380689/1‑148 (MQ=255)                                                         c‑GATTTTTGTTTCCCGGGGCAGTAACGGAA‑CCGGGGCGGGCGGGGTGTGGCTGTGGGCCCCTT‑GGGCTTCCCGTTTCCT‑TGAACGGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTa                                                                                         <  1:471225/148‑1 (MQ=255)                                                               tgtgTTTCACTGTGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGa                                                                                  >  2:1001674/1‑150 (MQ=255)                                                                 tgtTTCACTGTGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGaa                                                                                 >  2:710685/1‑149 (MQ=255)                                                                   tttCCCTGTGCCGGAACTGAC‑CCGTGGCGCGTTGGTTGTGGCTCTCGGACCCTG‑GGGCGTCCCGTTTCCC‑TGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGaa                                                                                 <  2:343759/147‑1 (MQ=255)                                                                       ccggtgCCGAAACTGAG‑CGGTGGCGCGCTGGATGTGGCTCTCGGCCGCGT‑GGGCGTCCTTTTTACC‑TGTAGCGGGAAAAAGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATg                                                                         <  2:492331/148‑1 (MQ=255)                                                                               ggACCTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACGCCG‑GGGCGTACCGTTTCCC‑TGTGCCGGGAAAATGGCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAttt                                                                  <  1:812190/150‑1 (MQ=255)                                                                                agcctaaa‑CCGCGGCGCGGTGGATGTGGCACCCTACCATCT‑GGGGTTCCCTTTTCCT‑TGTATGGGGAAAAGGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGAcc                                                                      <  2:81047/139‑1 (MQ=255)                                                                                    cggaccgggggCGCGTTGGGTGTGGCTCGGGGACCCTT‑GGGCTTACTGTTTCCT‑TGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtttt                                                                 <  1:777600/138‑1 (MQ=255)                                                                                    cggaccggTGGCGCGCTGGAGGTGGCTCTCGCACCCCG‑GGGCGTACCGTTTCCC‑TGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCa                                                             <  1:1002172/144‑1 (MQ=255)                                                                                     gAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACg                                                           >  2:1070303/1‑151 (MQ=255)                                                                                       accgggggCGCGCTGGATGTGGCTCTGGGCCCCCT‑GGGCGTCCCTTTTCCT‑TGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCAc                                                            <  1:1146415/143‑1 (MQ=255)                                                                                        acggTGGCGCGGGGTGTGTGGCTCGCGGACGCGG‑GGGCGTACTTTTTACC‑TGTAGGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACg                                                           <  2:84021/146‑1 (MQ=255)                                                                                             ggCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATaa                                                     >  1:819482/1‑150 (MQ=255)                                                                                               cgcgtgggttgggcctctCGGCCCCGT‑GGGCGT‑CCGTTTTCCTTGTTGCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAg                                                   <  1:275965/136‑1 (MQ=255)                                                                                                     ggttgtgGCTCTCGGACCCGG‑GGGGGTCCCTTTTCCT‑TGTATGGGGAAAAGGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGt                                               <  1:121285/145‑1 (MQ=255)                                                                                                                 cGGACACCT‑GGGCGTACCGGTTACC‑TGTATCGGGAAAATAACCGCCGATATCGAAGGGCTTTGCTTTGTTCGTGACGGAGAGCCTGTTACATAAGACTGTAAAGGATCTGACCGTTTTGCCACCCCATAAAGATGTAGCGAAAAGTCGGCt                                >  2:137791/1‑151 (MQ=255)                                                                                                                   ggccccgggggCGTCCTTTTTCCC‑TGTAGGGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTc                                    <  1:577282/138‑1 (MQ=255)                                                                                                                   gACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTg                               >  2:143522/1‑150 (MQ=255)                                                                                                                    acacCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGa                              >  1:704414/1‑150 (MQ=255)                                                                                                                      cgccggggCGTCCTGTTTCCC‑TGTATGGGAAAAATGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTg                               <  2:667412/143‑1 (MQ=255)                                                                                                                       cgt‑GGGCGTACTTTTTCCC‑TGTACGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGa                           <  1:102078/148‑1 (MQ=255)                                                                                                                               gTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAAt                   >  1:952679/1‑151 (MQ=255)                                                                                                                                      ttACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTTGCGAAAAGTCGCCTGAAGATGAGTCAt                   >  2:55062/1‑144 (MQ=255)                                                                                                                                       tACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGAGTAGATTTAGTCGAGAAGGAGAAAATGAAACATGAGAGTGGAAAGGATAGGAAAAGGTTGCCACGCCAGAAAGATGTCGCGAAAAGTCGCCTGAAGAGGAGGAAACCGTGGc            >  1:817905/1‑150 (MQ=255)                                                                                                                                                 cGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTGc  >  1:69830/1‑151 (MQ=255)                                                                                                                                                    acAAATGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCt        <  2:1066178/141‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                   CGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTAC‑GAGTTGTGTTTCACTGTGCCGGAACTGAA‑CCGTGGCGCGCTGGATGTGGCTCTCGGACACCT‑GGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTGC  >  NC_000913/436372‑436662

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: ‑