Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	436,504	0	A	C	49.1%	58.7 / 19.9	53	T291P (ACC→CCC)	thiL	thiamine monophosphate kinase
Reads supporting (aligned to +/- strand):  ref base A (16/11);  new base C (0/26);  total (16/37)
Fisher's exact test for biased strand distribution p-value = 1.24e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTCTGATGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCG  >  NC_000913/436355‑436648                                                                                                                                                       |                                                                                                                                                 tttCTGATGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTa                                                                                                                                                  <  2:641735/150‑1 (MQ=255)      gATGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGt                                                                                                                                             <  1:656039/150‑1 (MQ=255)         gcgcTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCg                                                                                                                                         <  1:445046/151‑1 (MQ=255)          cgcTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCgg                                                                                                                                        <  1:332759/151‑1 (MQ=255)                  cGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAAt                                                                                                                                  <  1:928075/149‑1 (MQ=255)                    ccATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGAcc                                                                                                                              >  1:715286/1‑151 (MQ=255)                    ccATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGAcc                                                                                                                              <  2:494037/151‑1 (MQ=255)                     cATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAAt                                                                                                                                  <  2:596027/146‑1 (MQ=255)                          tGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGat                                                                                                                        >  2:665964/1‑151 (MQ=255)                             aCCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATc                                                                                                                     >  2:426239/1‑151 (MQ=255)                                ggAACAGGCGCGGCGCTGGGCCCTCTCGGGGGGTGAAGATTACGGGTTGTTTTTCCCTGTGCCGGAACTGAACC‑GTGGCGCGCTGGTTGTGGCTCCCGCACACGTGGGCGTACCTTTTCCTTGTATCGGGAAAATGACCGCCGATATCGaa                                                                                                                  <  1:542973/151‑1 (MQ=255)                                     aGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCt                                                                                                             >  1:262969/1‑151 (MQ=255)                                     aGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCt                                                                                                             >  2:899611/1‑151 (MQ=255)                                                 gggCGTTCTCGGGGGGAGAAGTTTACGGGTTGTTTTTCCCTGTGCGGAAACTGACCG‑GTGGCGCGTTGGATTTGGCTCTCGGACACGTGGGCTTCCCTTTTCCCTGTTTGGGGAAAATGACCGCCGATATCGAAGGGCTTTg                                                                                                          <  2:432959/142‑1 (MQ=255)                                                 gggCGCTTTCGGGGGGGGAAGATTACGATTTGTTTTTCACTGTGCCGGAACTGACCC‑GGGGCGCGCTGGATGTGGCTCTCGGACCCCGGGGCGTCCCGTTTCCCTGTATCGGGAAAATAACCGCCGATATCGAAGGGCTTTGtttt                                                                                                      <  2:555336/146‑1 (MQ=255)                                                 gggCGCTCTCGGGGGGTGAAGATTACGGGTTGTGTTTCACTGTGCCGAAACTGACCC‑GTGGCGGGCGGGATGTGGCTCCCGGCCACCGGGGCGTCCTTTTTACCTGTATCGGGCAAATGCCCGCCGATATCGAAGGGCTTTGTTTTAtt                                                                                                   <  1:262454/149‑1 (MQ=255)                                                 gggCGCTCTCGGGCGGTGAAGATTACGGGTTGTGTTTCACGGTGCCGAAACTGAACC‑GTGGCGCGCGGGATGTGGCTCCGGGCCCCCTGGGGGTACCTTTTCCCTGTATGGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTAt                                                                                                    <  2:154651/148‑1 (MQ=255)                                                            gggggTGAAGTTTACGTGTTGTTTTTCCCTGGGCGGGAACTGACCC‑GTGGCGCGCGGGATGTGGCTCTCGGCCACCGGGGCGTCCTTTTTACTTGTAGGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGa                                                                                        <  1:427419/146‑1 (MQ=255)                                                            gggggTGAAGATTACGAGTTGTGTTTCATTGTCCCGGAAC‑GAACCGGGGGCGCGCTGGATGTGGCTCTCGGACACCGGGGCGTCCTTTTTACCTTTATGGGGAAAAGGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGaa                                                                                       <  2:745410/147‑1 (MQ=255)                                                            gggggTGAAAATTAGGGGTTGTTTTTCCTTGTGCCGGAACTGACCC‑GGGGCGCGGTGGATGTGGCTCTCGGACCCCGGGGCGTCCCTTTTCCCTTTTTCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGc                                                                                          <  2:721620/144‑1 (MQ=255)                                                            ggCGGTGAAGTTTACGAGTTGTTTTTCACTGTGCCGGAACTGACCG‑GTGGCGCGTGGGATGTGGCTCTCGGACCCGGGGGCGTCCCGTTTCCTTGTATCGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGa                                                                                        <  2:1011397/149‑1 (MQ=255)                                                            ggCGGTAAAAATTACGGGTTGTGTTTCACTGTGCCGAAACTGACCG‑GTGGCGCGCTGGATGGGCCTCTCGGACCCGGGGGCGTCCCGTTTCCTTGTATGGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACg                                                                                            <  2:21655/145‑1 (MQ=255)                                                              cGGTGAAGATTACGTGTTGTGTTTCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGTCGTACCGTTTACCTGGATAGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGaagc                                                                                     >  1:728637/1‑148 (MQ=255)                                                              cGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCt                                                                                    >  2:384605/1‑151 (MQ=255)                                                               ggggAAGATTACGAGTTGTGTTCCGCGGTGCCGGACCTGACCC‑GTGGCGCGCTGGAGGGGGCTCTCGGCCCCCGGGGCGCACCTTTTCCCTTTAGCGGACAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTg                                                                                   <  1:412604/148‑1 (MQ=255)                                                               ggTGAAGTTTACGGTTTGTTTTTCACTGTGCCGGAACTGAACG‑GTGGCGCGTGGGATGTGGCTCGCGGACACCGGGGCGTCCCTTTTCCCTGTACCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCt                                                                                    <  2:550911/150‑1 (MQ=255)                                                                 tGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGtt                                                                                 >  1:538226/1‑151 (MQ=255)                                                                   aaaattatgttttttgtTTCACTTTCCCGGATCTAAACC‑TGGCCGCGCTGTTTGTGCCTCTCTAACCCCTGGCCTTCCTTTTTCCTTTTATCGAACAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCTAAcc                                                                                     <  1:398838/131‑1 (MQ=255)                                                                   aaGATTAGGAGTTGTTTTTCACTGGCCCGGAACTGACCG‑GGGGCGCGGTGGTTGTGGCTCTCGGACACGGGGGCGTCCTGTTTACCTGTAGGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGt                                                                                  <  1:33462/148‑1 (MQ=255)                                                                   aaGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTAc                                                                               >  1:746385/1‑151 (MQ=255)                                                                   aaGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACC‑GGGGCGCGCTGGATGTGGCTCTCGGACCCCGGGGCGTCCCGTTTCCCTGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTAc                                                                               <  2:311573/151‑1 (MQ=255)                                                                    aGATTACGTGTTGTTTTTCACTGTGCCGAAACTGACCC‑TGGGCGCGCTGGTTTTGGCTCCCGCCCACCTGGGCGTCCCGTTTCCCTTTACCGGGCAAATGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACa                                                                              <  1:70085/151‑1 (MQ=255)                                                                         aCGGGTTGTTTTTCACTGTGCCGGACCTGACCC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCGGGGCGTCCCGTTTCCCTGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAg                                                                          <  2:196862/150‑1 (MQ=255)                                                                              ttttttttCCCTGGGCGGAAACTAACCC‑GTGGCGCGCTGGTTGTGGCTCTCGGACCCCGGGGCGTACCTTTTACCTTTATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTg                                                                      <  2:316560/144‑1 (MQ=255)                                                                              ttGTTTTTCACTGTGCGGGAACTGAACG‑GGGGGGCGGGGGATGGGGCTCTCGGACACGGGGGCGTCCCGTTTCCCTGTATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTg                                                                      <  2:34951/149‑1 (MQ=255)                                                                                    ttCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGat                                                              >  2:876111/1‑151 (MQ=255)                                                                                         tgtgCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGAc                                                         >  2:791730/1‑151 (MQ=255)                                                                                         ggggcggaaaCTAACCC‑GTGGGGCGTGGGTTGTGCCTCTCGCACCCGTGGGCGTCCTTTTTCCCTGTATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGa                                                          <  1:634341/142‑1 (MQ=255)                                                                                                  aCTGACCC‑GGGGCGCGCTGGATGTGGCTCTGGGACCCGTGGGCGTACCGTTTCCCTGTATCGGACAAAGGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGcc                                                <  2:157087/151‑1 (MQ=255)                                                                                                    tGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCAc                                              >  1:40525/1‑151 (MQ=255)                                                                                                      accc‑GGGGCGGGTTGGATGTGGCTCTCGGCCCCCGGGGCGTCCCGTTTCCGTGTACGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACg                                             <  1:249130/148‑1 (MQ=255)                                                                                                      aaCC‑GTGGCGCGCTGGATGTGGCTCTCGGACCCCTGGGCGTCCCTTTTCCCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCa                                               <  2:860744/148‑1 (MQ=255)                                                                                                       accgggggCGCGCTGTGTGTTGTTCGCGGACCCGGGGGGTTACTTTTTCCTTGTAGCGGGAAAATAACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCAc                                              <  1:673195/143‑1 (MQ=255)                                                                                                        cc‑GGGGCGCGCTGGATGTGGCTCTCGGACCCCTGGGCGTACCGTTTCCTTGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCa                                          <  2:76401/151‑1 (MQ=255)                                                                                                             ggggcgcGGGTTGGGGCTCTGGGCCCCGGGGGCGTCCGTTTTCCCTGTATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATaa                                       <  2:631068/147‑1 (MQ=255)                                                                                                                 cgcTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATg                                  >  2:239527/1‑151 (MQ=255)                                                                                                                      gtggggcctctGGGCCACCGGGGCGTGCGTTTTCCCGGTAGGGGGAAATTGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTcgcg                             <  1:562773/144‑1 (MQ=255)                                                                                                                                 cGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGCCCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCg                     >  1:225548/1‑148 (MQ=255)                                                                                                                                  ggcccccTGGGCGTCCCTTTTCCTTGTATCGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCg                     <  2:464265/142‑1 (MQ=255)                                                                                                                                   accacgggggCGTACGTTTTCCCTTTAGCGGAAAAATGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTg                 <  1:784553/143‑1 (MQ=255)                                                                                                                                       ctggggaaacctttttCCCTGTAGGGGAAAAAGGGCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAg              <  1:987633/136‑1 (MQ=255)                                                                                                                                          gggCGTCCCTTTTCCTTGTATGGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGaa               <  2:667289/145‑1 (MQ=255)                                                                                                                                                aCCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATcc   >  1:382203/1‑151 (MQ=255)                                                                                                                                                 ccGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCg  >  2:692792/1‑151 (MQ=255)                                                                                                                                                       |                                                                                                                                                 TTTCTGATGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCG  >  NC_000913/436355‑436648

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑