Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	436,516	0	C	A	42.9%	63.8 / 21.2	49	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
Reads supporting (aligned to +/- strand):  ref base C (23/5);  new base A (0/21);  total (23/26)
Fisher's exact test for biased strand distribution p-value = 2.87e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.59e-01

TTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTGCTGTC  >  NC_000913/436367‑436666                                                                                                                                                       |                                                                                                                                                       tttCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGc                                                                                                                                                        >  1:682637/1‑150 (MQ=255)        ccATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGAcc                                                                                                                                                >  1:8735/1‑151 (MQ=255)          aTGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGAccgc                                                                                                                                              >  1:355227/1‑151 (MQ=255)                    ggAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGa                                                                                                                                     >  1:298133/1‑150 (MQ=255)                        cAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGc                                                                                                                                >  2:394257/1‑151 (MQ=255)                           gcgctgcgctGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCttt                                                                                                                             >  2:294392/1‑151 (MQ=255)                             ggtgcgttgGGCGCTCGCTGGGGGGAAATATTCCGATTTGTTTTTCACTGTGCCGCAACTAAACCGGGGCGCGCTGTATGTGGCTCTCGGACACTTGGGTGAACCTTTTTCC‑TTTGCAGGGAAAATGACCGCCGATATCGAAGGGCttt                                                                                                                             <  2:522720/147‑1 (MQ=255)                             gctgcgctgGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCGGGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGCAGGGCTTTGt                                                                                                                           >  1:252000/1‑151 (MQ=255)                               tgcgctgGGCGCTCTCTGGCGGCGAAGCTTACGAGTTGTGTTTCACTGTGGCGGTACTGAACCGTGGCGCGCTGGACGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCCGGCAAATGACCGCCCCTATCGAAGGGCTTTGttt                                                                                                                         >  1:517157/1‑151 (MQ=255)                                  gctgGGCGCCCTCGGGCGTTTAAGATTACTAGTTGTTTTTCCTTGGGCCGAAACTGAACCGGGGCGCGTTGGATGTGCCTCTCGGAGCCTTGGGCGTCCTTTTTCCT‑TGTAGCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTAt                                                                                                                      <  2:707551/151‑1 (MQ=255)                                   ctgGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTAtt                                                                                                                     >  1:374815/1‑151 (MQ=255)                                     gggCGCTCTCGGGGGGTGAAGATTCCGATTTGTGTTTCACTGGGCCGGAACTGACCGGGGGCGCGCTGGATGGGGCTCTCGGCCACCGGGGCGTCCCTTTTACC‑TGTATCGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTAtt                                                                                                                     <  2:779570/149‑1 (MQ=255)                                     gggCGCTCTCGGGGGGTGAAGATTAGGTGTTTTTTTTCACTGTGCCGAAACGGACCGGGGGCGCGCTGGATGGGGCCCCCGAACCCGTGGGCGTCCTTTTTCCT‑TGTATGGGAAAAATGACCGCCGATATCGAAGGGCttt                                                                                                                             <  1:409296/141‑1 (MQ=255)                                     gcgcgcTCTCTGGCGGAGCAGATTACGTGTTGCGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGTCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGTTATCGAAGGGCTTTGCTTTATTCg                                                                                                                   >  1:856861/3‑151 (MQ=255)                                           tctctGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACgg                                                                                                             >  2:265054/1‑151 (MQ=255)                                                gggggTGAAGTTTACGGTTTGTTTTCCACGGGGCGGGAACTGACCCGTGGCGCGCGGGAGGTGTCTCTCGGACACGGGGGCTTCCCGTTTACC‑TGTATCGGCAAAATAACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGa                                                                                                          <  1:314712/146‑1 (MQ=255)                                                gggggTGAAGATTACGATTTGTGTTTCACTGTGCCGGAACTGACCGGTGGCGCGTTGGATGTGGCTCTCGGACCCCTGGGCGTACCGTTTCCC‑TGTATCGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAAc                                                                                                        <  2:705741/148‑1 (MQ=255)                                                ggCGGTGAAGATTACGATTTGTGTTTCACTGTGCCGAAACTGACCCGGGGCGCGGTGGAGGTGCCTCCGGGACCCCTGGGCGTCCTTTTTTCC‑TTTATCGGGCAAAGGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGc                                                                                                            <  1:687034/147‑1 (MQ=255)                                                 gCGGAGAGGTTTACGAGTTTTTTTCCCCTGGGCGGGAAGTGACCGGGGGCGCGGGGGATGTGCCTCTGGGACCCGGGGGCGTACCTTTTCCC‑TGTAGGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGa                                                                                                          <  2:787777/148‑1 (MQ=255)                                                       aaaaTTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGGGCGCTGGATGTGGCTCTCGGACCCCGGGGCGTCCCTTTTACC‑TGTATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTa                                                                                                  <  2:44242/147‑1 (MQ=255)                                                           ttgcgtttgttttttCCCTGTGCCGGATCTGACCCGGGGCGCGCTGGATGTGGCTCTCGGACTCGGGGGCGTACTTTTTCCC‑TTTCGCGGGCAAATGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACa                                                                                                <  1:205949/136‑1 (MQ=255)                                                             aCGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACAtt                                                                                              >  2:345196/1‑148 (MQ=255)                                                               gAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACt                                                                                         >  2:494369/1‑151 (MQ=255)                                                                  ttGTGTTTCCTTGTGCCGGAACTGACCCGGGGCGGGCTGGATTGGGATCCGGGACCCCGGGTCGTCCTTTTTACC‑GGTAGGGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTgg                                                                                       <  1:787071/150‑1 (MQ=255)                                                                   tgttTTTCCTTGTCCCGGACCTAAACCGGGGCGCGTTGGATGTGGCTCTCGGCCACGTGGGGGTACCTTTTCCT‑TGTATCGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGa                                                                                      <  2:387422/150‑1 (MQ=255)                                                                     tgtTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGa                                                                                      >  1:314806/1‑148 (MQ=255)                                                                          cccTGTGCGGGAACTAACCCGGGGCGCGCGGGATGTGGCTCGCGAACCCGGGGGTGTACCTTTTCCT‑TGTATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGata                                                                               <  2:478404/148‑1 (MQ=255)                                                                             ggcgCCGGAACGGACCGGGGGCGCGGGGAATGTGGCTTTCGAACCCCTGGCGGTACCTTTTCCT‑TGTAGGGGGAAAATAACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGTGAACCTGTTACATGAGACTGGAAAGGATATg                                                                             <  1:846458/146‑1 (MQ=255)                                                                                gCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAt                                                                        >  1:715209/1‑151 (MQ=255)                                                                                 ccgaaccTGACCCGTGGCGCGCTGGATGTGGCTCTCGGCCCCGTGGGCGTACCTTTTCCC‑TGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtt                                                                       <  1:744944/145‑1 (MQ=255)                                                                                       cTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGcc                                                                  >  2:372717/1‑150 (MQ=255)                                                                                          aaCCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACg                                                               >  1:520740/1‑150 (MQ=255)                                                                                              ggggCGCGTGGGATGTGGCCCTCGGACCCTGGGGCGTACCGTTTCCC‑TGTTTGGGGAAAAGGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCa                                                            <  1:323918/147‑1 (MQ=255)                                                                                              ggggCGCGCTGGATGTGGCTCTCGGCCACCTGGGCGTCCCGTTTCCC‑TGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCa                                                            <  2:582469/147‑1 (MQ=255)                                                                                              gTGGCGCGGTGGATGTGGCTCTCGGACCCCGGGGCGTCCCGTTTCCC‑TGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCa                                                            <  2:603177/149‑1 (MQ=255)                                                                                               tGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGATCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATa                                                          >  1:621053/1‑150 (MQ=255)                                                                                               tGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATa                                                          >  1:793254/1‑150 (MQ=255)                                                                                               tGGCGCGCTGGATGTGGCTCTCGGACACCGGGGCGT‑CCGTTTTCCTTGTCTCGGGAAAATGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCa                                                            <  1:61325/148‑1 (MQ=255)                                                                                                ggCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATaa                                                         >  1:67483/1‑150 (MQ=255)                                                                                                  cgcgcTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATaa                                                         >  2:428509/1‑148 (MQ=255)                                                                                                       tGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCAATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTc                                                  >  1:86044/1‑150 (MQ=255)                                                                                                         gATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTcgcg                                               >  2:198895/1‑151 (MQ=255)                                                                                                                ctcgCGGACCCCGGGGCTTCCTTTTTCCT‑TGTAGCGGGAAAATGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTcgcg                                               <  2:155925/144‑1 (MQ=255)                                                                                                                 tctggaccacgggggAGTCCCTTTTCCC‑TGTGGCGGGAAATTGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGt                                         <  2:564900/137‑1 (MQ=255)                                                                                                                          ccTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGa                                  >  1:262533/1‑147 (MQ=255)                                                                                                                             ggggatccttttttCC‑TTTCTCGGGCAAACGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAg                                <  2:592599/136‑1 (MQ=255)                                                                                                                             gggCGTCCCTTTTCCT‑TTTACGGGGAAAATGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGAt                              <  2:859439/148‑1 (MQ=255)                                                                                                                              ggCGTACCGTTTACC‑TGTATCGGGCAAATGATCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGt                          <  2:621119/151‑1 (MQ=255)                                                                                                                                 gacccttttACT‑TGTGTGGGGAAAAGCACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTaa                        <  1:688317/144‑1 (MQ=255)                                                                                                                                        tttccttGTATGGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTg                  <  2:694471/144‑1 (MQ=255)                                                                                                                                                       cAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTGCTGTc  >  2:261926/1‑151 (MQ=255)                                                                                                                                                       |                                                                                                                                                       TTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACC‑TGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTGCTGTC  >  NC_000913/436367‑436666

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑