Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	436,516	0	C	A	42.5%	63.8 / 23.2	48	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
Reads supporting (aligned to +/- strand):  ref base C (21/6);  new base A (0/20);  total (21/27)
Fisher's exact test for biased strand distribution p-value = 2.41e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.82e-01

TCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCG‑TTTACCTGTATCGGGC‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCA  >  NC_000913/436371‑436653                                                                                                                                                   |                                                                                                                                           tcGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCG‑TTTACCTGTATCGGGC‑AAATg                                                                                                                                      >  2:617257/1‑151 (MQ=255)  cGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCG‑TTTACCTGTATCGGGC‑AAAt                                                                                                                                       <  2:96673/149‑1 (MQ=255)      aTGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCG‑TTTACCTGTATCGGGC‑AAATGAccgc                                                                                                                                 <  1:110105/151‑1 (MQ=255)        gTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCG‑TTTACCTGTATCGGGT‑AAATGAccgcc                                                                                                                                <  2:335869/150‑1 (MQ=255)           gAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCG‑TTTACCTGTATCGGGC‑AAATGACCGCCGat                                                                                                                             >  2:274784/1‑150 (MQ=255)            aaCCGTAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGCAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCG‑TTTACCTGTATCGGGA‑AAATAACCGCCGa                                                                                                                              <  2:423225/148‑1 (MQ=255)                gaaccgggCGCTGCGCGGGCCGCTCTCGGGCGGTGAAGATTACGATTTGTGTTTCCGTGTGCAGGATCTGACCGGGGGCGCGTTGGATGTGCCTCTCGGACCCGTGGACTTCCCT‑TTTCCCTGTTTCGGGC‑AAATGACCGCCGATATCGa                                                                                                                        <  2:893/144‑1 (MQ=255)                         gctgcgctgGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCG‑TTTACCTGTATCGGGC‑AAATGACCGCCGATATCGAAGGGCTTTGt                                                                                                              >  1:275692/1‑151 (MQ=255)                         gctgcgctgGGCGCTCTCGGGGGGTGAAAATTACGGTTTGTTTTTCACTGTGCCGAAACTGACCCGTGGCGCGCTGGTTGTGGCTCTCGGACACCGGGGCGTCCCT‑TTTCCTTGTGTCGGCA‑AAATGACCGCCGATATCGAAGGGCTTTg                                                                                                               <  1:392169/150‑1 (MQ=255)                            gctcggggCCCTCGCGGGCGGTGATGATTGGGGGTTTTTTTTCCCTGCCCCGAACCTGTCCCGTGGCGGGCTGGATGTGGTCCCCGGCCCGCTGGGCGCCCTG‑TTTTCCTAT‑CCGGGCAAAATAGCCGCCGATATCGAAGGGCTTTGtttt                                                                                                           <  2:709365/146‑1 (MQ=255)                                 gggCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCG‑TTTACCTGTATCGGGC‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCg                                                                                                      >  2:417260/1‑151 (MQ=255)                                 gggCGCTCTCGGGGGGTGAAGATTACGAGTTGTTTTTCCCTGTGCCGGAACTGACCCGGGGCGCGCTGGAGGGGGCTCTCGGCCCCGGGGGCTTCCCT‑TTTCCCTGTATCGGGA‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTAt                                                                                                         <  1:109263/148‑1 (MQ=255)                                   gcgcTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCG‑TTTACCTGTATCGGGC‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTg                                                                                                    >  1:173168/1‑151 (MQ=255)                                     gcTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCG‑TTTACCTGTATCGGGC‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGAc                                                                                                  >  2:358343/1‑151 (MQ=255)                                       tctctGGGGGTGAAGTTTAGGATTTGTTTTTCCCTGTGCCGGAACTGACCGGTGGCGCGTTGGTTGTGCCTCTCGGACCCTTGGGCGTCCCT‑TTTCCTTGTATCGGAA‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGa                                                                                                   <  1:584271/148‑1 (MQ=255)                                       tctcgGGCGGTGAAGATTACGGTTTGTGTTTCCCTGTGCGGGAACGGACCGGGGGCGGGGGGGAGGTGCCTCCCGGACACGGGGGCGTCCTT‑TTTCCTTGTAGGGGAA‑AAAGGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGa                                                                                                   <  2:533747/148‑1 (MQ=255)                                         tgtGGCGGTAAAGATTAGGTTTTTTGTTTCGCTGGGCGGGAACTGAGCCGTGGCCCGTTGGATGTGTCCCGCGCACTCCTGGGCTTCCTT‑TTTTCGTTTATCGGAA‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACg                                                                                                 <  2:742424/146‑1 (MQ=255)                                          ctGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCG‑TTTAACTGTATCGGGC‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTTTTCGTGACGGCg                                                                                              >  2:337871/1‑150 (MQ=255)                                             gCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCG‑TTTACCTGTATCGGGC‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAAcc                                                                                          >  2:745303/1‑151 (MQ=255)                                                   aaGATTACGTGTTGTGTTTCCTTGGGCCGAAACTGACCCGTGGCGCGGGGGAGGTGGCTCGGGGACCCCGGGGCGTACCT‑TTTACCTGTATCGGAA‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTAc                                                                                    <  2:334556/151‑1 (MQ=255)                                                    aGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGCACCG‑TTTACCTGTATCGGGC‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTAc                                                                                    >  2:299042/1‑150 (MQ=255)                                                     gattcgggtttGTGTTCCACTGGGCGGAAACGGACCCGGGGCGGGTTGGTTGTGGCTCTCGGACA‑CTGGGGGTTCCGTTTTCCCTGTATGGGGC‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACa                                                                                   <  2:651053/141‑1 (MQ=255)                                                       ttaggggttgttTTTCACGGTGCGGGAACTGACCCGTGGGGCGTTGGTTGTGGCTCTCGGACCCCGGGGCGTCCTG‑TTTACCTGTATCGGCA‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACAt                                                                                  <  2:164137/143‑1 (MQ=255)                                                       ttACGTGTTGTTTTTCCCTGTGCCGAAACTGACCGGGGGCGCGTTGGGGGGGGCTCTGGGACACGGGGGTGTACCG‑TTTACCTGTATGGGAA‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACAtt                                                                                 <  2:246874/150‑1 (MQ=255)                                                            aGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCG‑TTTACCTGTATCGGGC‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTg                                                                           >  1:65064/1‑151 (MQ=255)                                                              ttGTGTTTCTCTGTGCGGGAACTAAACCTGGGCGCGCTGGATGTGCCTCTCGGCCACGGGGGCGTCCCG‑TTTACTTTTAGCGGAA‑AAATAACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTg                                                                           <  1:172069/149‑1 (MQ=255)                                                              ttGTGTTTCACTGTGCCGGAACTGAACCGGGGCGCGCTGGATGTGGATCTCGGACACCTGGGCGTACCG‑TTTACCTGTATCGGGC‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGCGACGGCGAACCTGTTACATTAGACTgg                                                                          >  1:262331/1‑150 (MQ=255)                                                               tgtgTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCG‑TTTACCTGTATCGGGC‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGa                                                                         >  1:643891/1‑150 (MQ=255)                                                                      cccTGTGCGGGAACTGACCGGTGGCGCGTTGGTTGGGGCTCTCGGACCCGTGGGCGTCCCT‑TTTCCTTGTATGGGGA‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGatat                                                                 <  1:159928/149‑1 (MQ=255)                                                                      cACTGTGCCGGAACTGACCCGGGGCGCGCTGGATGTGGCTCTCGGACACCGGGGCGTCCCT‑TTTCCCTGTATGGGGA‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGata                                                                  <  1:350654/150‑1 (MQ=255)                                                                             cgggacctaacccGTGGCGCGTTGGATGTGCCTCTCGGACCCCTGGGCGTCCCT‑TTTCCCTGTACCGGGA‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCa                                                            <  2:353862/138‑1 (MQ=255)                                                                             ccGGAACGGACCCGGGGGGCGTTGGTTGTGCCTCTCGGCCACGGGGGCTTACTT‑TTTCCCTGTATGGGGA‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGa                                                               <  1:4996/146‑1 (MQ=255)                                                                                 aaCTGACCCGTGGCGCGCTGGATGTGGCTCTCGGACACCGGGGCGTCCCG‑TTTCCCTGTATCGGGA‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGc                                                      <  1:226455/151‑1 (MQ=255)                                                                                      acccGGGGCGCGCGGGATGTGGCTCTCGGACCCCGGGGCGTCCCG‑TTTCCCTGTATCGGGA‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCa                                                    <  1:479453/146‑1 (MQ=255)                                                                                      aaCCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCG‑TTTACCTGTATCGGGC‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGc                                                 >  2:103705/1‑151 (MQ=255)                                                                                        cggTGGCGGGCGGGTTGGGGCTCTGGGACACTGGGGCGTCCTT‑TTTCCCGTTAGGGGAA‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCa                                                    <  2:276197/144‑1 (MQ=255)                                                                                          gTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCG‑TTTACCTGTATCGGGC‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCAt                                              >  1:640496/1‑150 (MQ=255)                                                                                            gccgcgcTGGTTGTGGCTCCCGCCCCCCGGGGGGTACCT‑TTTCCTTGTGGGGGAA‑AAATGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATaa                                            <  2:220074/148‑1 (MQ=255)                                                                                                       tgtgGCTCTCGGACACCTGGGCGTACCG‑TTTACCTGTATCGGGC‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGa                                 >  1:197465/1‑150 (MQ=255)                                                                                                             tctcGGACACCTGGGCGTACCG‑TTTACCTGTATCGGGC‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCg                          >  2:237333/1‑151 (MQ=255)                                                                                                             tctcGGACACCTGGGCGTACCG‑TTTACCAGTATTGGGC‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCg                          >  2:129293/1‑151 (MQ=255)                                                                                                                    cccgtGGGCGTCCCT‑TTCCCTTGTATCGGGA‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTg                      <  1:274786/144‑1 (MQ=255)                                                                                                                            cGTACCG‑TTTACCTGTATCGGGC‑AAATGACCGCCGATATCGTAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTa            >  2:766327/1‑150 (MQ=255)                                                                                                                               cctttctttccTTTAGCGGAC‑AAAGGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTaa           <  1:695662/140‑1 (MQ=255)                                                                                                                                ccG‑TTTACCTGTATCGGGC‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCg       >  2:355334/1‑151 (MQ=255)                                                                                                                                 cG‑TTTACCTGTATCGGGC‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGt      >  1:362473/1‑151 (MQ=255)                                                                                                                                      tACCTGTATCGGGC‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTaa           >  2:695656/1‑142 (MQ=255)                                                                                                                                        cttGTATGGGGA‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCa  <  1:256533/147‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                           TCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCG‑TTTACCTGTATCGGGC‑AAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCA  >  NC_000913/436371‑436653

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: ‑