Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	436,516	0	C	A	44.2%	59.2 / 21.4	52	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
Reads supporting (aligned to +/- strand):  ref base C (18/11);  new base A (0/23);  total (18/34)
Fisher's exact test for biased strand distribution p-value = 8.80e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.85e-01

CGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTGCTGTC  >  NC_000913/436372‑436666                                                                                                                                                  |                                                                                                                                                       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                                                                                                                               >  2:899611/1‑151 (MQ=255)                    aGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCt                                                                                                                               >  1:262969/1‑151 (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)                                                                                                                                           tATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACt         >  2:537398/1‑151 (MQ=255)                                                                                                                                                 gCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTGCTGt   >  2:57612/1‑151 (MQ=255)                                                                                                                                                  cAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTGCTGTc  >  1:844804/1‑151 (MQ=255)                                                                                                                                                  cAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTGCTGTc  >  1:699779/1‑151 (MQ=255)                                                                                                                                                  cAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTGCTGTc  >  1:560271/1‑151 (MQ=255)                                                                                                                                                  |                                                                                                                                                       CGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACC‑GTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTTGCTGTC  >  NC_000913/436372‑436666

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: ‑