Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	436,516	0	C	A	55.8%	8.7 / 50.1	43	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
Reads supporting (aligned to +/- strand):  ref base C (13/6);  new base A (1/23);  total (14/29)
Fisher's exact test for biased strand distribution p-value = 8.46e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.23e-04

CCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTG  >  NC_000913/436374‑436661                                                                                                                                                 |                                                                                                                                                  ccATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGAcc                                                                                                                                           >  1:734946/1‑151 (MQ=255)                    gcgctgcgcgGGGCGCTCTCTGGCGGTGAAGATTACGGGTTGTTTTTCACTGTGCCGGAACTGAACCGGGGCGCGCGGGATGTGGCTCTCGGACACCGGGGCGTAC‑CGTTTCCCTG‑TATGGGGAAAATGACCGCCGATATCGAAGGGCttt                                                                                                                        <  2:373885/151‑1 (MQ=255)                              gggCGCTCTCTGGCGGTAAAGATTCCGAGTTTTTTTTCCCTGTGCCGGAACTGACCCGGGGCGCGTTGGATGTGGCTCTCGGACCCCTGGGCGTCC‑CTTTTCCTTG‑TATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTAtt                                                                                                                <  1:930623/149‑1 (MQ=255)                              gggCGCTCTCGGGCGGGGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGGTGGTTGTGGCTCTCGGACCCCTGGGCGTCC‑CGTTTCCCTG‑TATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTc                                                                                                               <  2:633335/150‑1 (MQ=255)                               gggcttttgaggCGGTGAAGTTCAGGGGTTGTTTTTCTCTGTGCCGGAACAGAGCCTGGGCGCGCTGGGTGTGGTTCTCGG‑TACC‑GGGGGTCCACCTTTACCCGATCTCGGTCAAAGGACCGCCGATATCGAAGGGCTTTGTTTTATTc                                                                                                               <  2:245164/139‑1 (MQ=255)                               ggCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGt                                                                                                             >  1:867857/1‑151 (MQ=255)                                         ggCGGTGAAGATTCCGTGTGTTGTTTCCCTGGGCCGGAACTGACCCGTGGCGCGTTGGATGGGGCTCTCGAACACGTGGGCTTCC‑CTTTTCCTTG‑TTTCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGc                                                                                                       <  1:148217/147‑1 (MQ=255)                                           cGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCt                                                                                                 >  1:51071/1‑151 (MQ=255)                                                    ttAGGAGTTGTGTTTCTCTGTGCCGGAACTGACCCGGGGCGCGCGGGTTGTGGCTCTCGGACCCCGGGGCGTCC‑CGTTTCCCTG‑TATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACAtt                                                                                         <  2:502318/150‑1 (MQ=255)                                                     tACGAGTTGTTTTTCACTGTGCCGAAACTGAACCGTGGCGCGTTGGATGTGGCTCTCGGACCCCTGGGCGTCC‑CTTTTCCCTG‑TATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTa                                                                                        <  2:221150/150‑1 (MQ=255)                                                         aGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTg                                                                                   >  1:896529/1‑151 (MQ=255)                                                          gttgttTTCCTCTGTGCCGGAACGGACCCGGGGCGCGGTGGAGGTGGTTGGGGGACCCGGGGGTGTCC‑CGTTTCCCTG‑TCCGGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACt                                                                                    <  2:590375/149‑1 (MQ=255)                                                              tgtTTCCCTGTGCCGGAACTGACCCGTGGCGCGCTGGATGTGGCTCGCGGACCCCTGGGCGTCC‑CTTTTCCCTT‑TATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGaaa                                                                               <  1:268026/150‑1 (MQ=255)                                                               gtTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAgg                                                                             >  1:542789/1‑151 (MQ=255)                                                                   cgcTGTGCGGGAACTGACCGGTGGCGCGCTGGATGTGGCTCTCGGACCCCTGGGCGTCC‑CTTTTACCTT‑TATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTGCATTAGACTGGAAAGGatat                                                                         <  2:585769/149‑1 (MQ=255)                                                                          ccGGACTTGACCCGTGGCGCGCTGGATGTGGCTCTCGGCCACCTGGGCGTCC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGata                                                                          <  2:162625/143‑1 (MQ=255)                                                                           cGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAttt                                                                 >  2:701696/1‑151 (MQ=255)                                                                           cGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAttt                                                                 >  1:134908/1‑151 (MQ=255)                                                                            ggACCTGACCGGGGGCGCGTTGGATGTGGCTCTCGGACACCGGGGCGTCC‑CTTTTCCCTG‑TATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATg                                                                        <  2:312024/143‑1 (MQ=255)                                                                            ggAACTGAACCGTGGCGCGTGGGATGGGGCTCTCGGACCCCGGGGCGTCC‑CGTTTCCCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtt                                                                  <  2:354897/149‑1 (MQ=255)                                                                             gAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTg                                                               >  2:407965/1‑151 (MQ=255)                                                                              aaCTGAACCGGGGCGCGGTGGATGTGGCTCGCGGACCCCTGGGCGTAC‑CGTTTACCTG‑TATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtttt                                                                <  1:925911/149‑1 (MQ=255)                                                                                cggAACGGTGGCGCGTGGGGTGGGGCTCGGGGACGCGTGGGTGTGC‑GTTTTACCTG‑TAGCGGGAAAATGGCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCa                                                            <  2:148442/149‑1 (MQ=255)                                                                                        tGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATa                                                     >  2:507854/1‑150 (MQ=255)                                                                                         ggggcggtggtggtgGCTCTGGCCCCCCGGGGCGTCC‑CTTTTCCTTT‑TATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATaaa                                                   <  1:238175/139‑1 (MQ=255)                                                                                                tGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTcg                                            >  1:68633/1‑151 (MQ=255)                                                                                                  gATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTcgcg                                          >  2:316322/1‑151 (MQ=255)                                                                                                       ggCTCTCGGACACTGGGGCGTCC‑CGTTTCCCTT‑TATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAg                                     <  2:929967/151‑1 (MQ=255)                                                                                                         ctctCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTc                                   >  2:881367/1‑151 (MQ=255)                                                                                                          tctgGGACCCGTGGGCGACC‑GGTTTCCCTG‑TGTGGGGAAATGGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTc                                   <  1:238349/150‑1 (MQ=255)                                                                                                              ggccccgggggCGTCC‑TTTTTCCTTG‑TAGCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAg                                     <  1:689208/136‑1 (MQ=255)                                                                                                              ggACCCCGGGGCTTCC‑CTTTTCCCTG‑TATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGcc                                <  1:438262/149‑1 (MQ=255)                                                                                                                     ggggCTTAC‑TGTTTCCCTT‑TATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGa                       <  1:85990/150‑1 (MQ=255)                                                                                                                      gggCGTCC‑CTTTTCCCTG‑TATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAg                      <  1:736904/151‑1 (MQ=255)                                                                                                                             c‑cGTTTCCTTG‑TAGGGGAAAAAGGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATcc                <  1:881264/150‑1 (MQ=255)                                                                                                                             agcGTTTAAATG‑TATAGGGAAAATGATCGTCGATATAGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTAAATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCGTGAAGATGAGTAATc                 >  1:86501/3‑150 (MQ=255)                                                                                                                                  ttccttG‑TATGGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTgg            <  2:407382/145‑1 (MQ=255)                                                                                                                                     ccttgaacggggCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCAt         <  2:376949/142‑1 (MQ=255)                                                                                                                                       tG‑TATGGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCt       <  2:638257/150‑1 (MQ=255)                                                                                                                                       tG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCt       >  2:636933/1‑150 (MQ=255)                                                                                                                                              gggAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTg  <  2:693492/149‑1 (MQ=255)                                                                                                                                              gggAAAATAACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTg  <  1:689463/149‑1 (MQ=255)                                                                                                                                              gggAAAATAACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTg  <  1:864092/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                  CCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTG  >  NC_000913/436374‑436661

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: ‑