Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	436,504	0	A	C	42.0%	80.6 / 13.9	53	T291P (ACC→CCC)	thiL	thiamine monophosphate kinase
Reads supporting (aligned to +/- strand):  ref base A (22/7);  new base C (0/21);  total (22/31)
Fisher's exact test for biased strand distribution p-value = 2.63e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGATGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGG  >  NC_000913/436359‑436651                                                                                                                                                  |                                                                                                                                                    tGATGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGt                                                                                                                                                >  2:338357/1‑151 (MQ=255)   aTGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTAt                                                                                                                                              >  2:71393/1‑151 (MQ=255)    tGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATc                                                                                                                                             >  2:516565/1‑151 (MQ=255)      cgcTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCgg                                                                                                                                           <  1:955908/151‑1 (MQ=255)       gcTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCggg                                                                                                                                          <  1:173304/151‑1 (MQ=255)               gCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGAc                                                                                                                                  <  2:351485/151‑1 (MQ=255)                ccATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGAcc                                                                                                                                 >  2:470130/1‑151 (MQ=255)                 cATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGAccg                                                                                                                                >  1:326869/1‑151 (MQ=255)                           cGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCg                                                                                                                       >  2:355924/1‑150 (MQ=255)                            ggAACAGGCGTGGCGCTGGGCCCTCTCGGGGGGTGAAGATTACGGGTTGTTTTTCCCGGTGCCGGACCTGACCCGGGGCGCGCTGGTTGTGGCCCTCGGCCCCCTGGGCGTACCGTTTCCCTGTAGCGGGCAAATGACCGCCGatat                                                                                                                         <  2:589661/147‑1 (MQ=255)                              aaCAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTTTTTCACTGTGCCGGAACTGACCGGTGGCGCGCTGGATGTGGCTCCCGGACACCGGGGCGTCCCGTTTCCCTGTATCGGGAAAATGACCGCCGATATCGAAgg                                                                                                                   <  1:938654/151‑1 (MQ=255)                                  ggCGCTGCGCTGGGCGCTCTCGGGGGGTGAAGATTACGAGTTGTTTTTCACTGGGCCGAAACTGACCCGGGGGGCGCTGGATGTGGCCCTCGGACACCGGGGCGTCCCTTTTCCCTGTAGGGGGCAAATGACCGCCGATATCGAAGGGCtt                                                                                                               <  2:113788/151‑1 (MQ=255)                                          ggtgGGGGCTCTCGGGGGGTGAAGATTACGAGTTGTTTTTCACTGTGCGGGAACGGAACGGTGGCGCGGTGGTGGTGGCTCTCGGACACCGGGGCGTCCCTTTTCCCTGTTTGGGGCAAATGACCGCCGATATCGAAGGGCttt                                                                                                              <  1:439209/142‑1 (MQ=255)                                            ggggCGCTGTGGGGGGGTGAATATTAGGAGTTTTGTTCCCCTGTGCGGAAACTGAACGGGGCCGCGTGGGTTGTGCCCCTCGGACCCTGGGGGGTCCCGTTTCCTTGTATCGGGAAAAGGACCGCCGATATCGAAGGGCTTTGTTTTATTc                                                                                                     <  1:192148/150‑1 (MQ=255)                                             gggCGCTTTGGGGGGGTGAAGATTACGGGTTGTGTGCCCGTGGGCGGGAAGGGACCCTGGGGGCGTTGGATGGGTTTCTCGGAGATGGGGCCCTACCGTTTTCTTGTTTGGGACAATTGACCGCCGATATCGAAGGGCTTTGTTTTATTc                                                                                                     <  1:775547/150‑1 (MQ=255)                                             gggCGCTCTCTGGGGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACCCCTGGGCGTACCTTTTCCCTGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGt                                                                                                            <  1:51398/143‑1 (MQ=255)                                              ggCGCTCTCTGGGGGTGAAGATTCCGAGTTGTGTTTCACTGTGCCGGAACTGACCGGTGGCGCGCTGGATGTGGCTCTCGGACACCGGGGCGTCCCGTTTCCTTGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGt                                                                                                   <  1:870636/151‑1 (MQ=255)                                                        ggCGGTGAAGATTACGTGTTGTGTTTCCCTGTGCCGGAACTGACCCGTGGCGCGTTGGATGTGGCTCTCGGACCCCTGGGCGTCCCTTTTCCCTGTAGCGGGCAAAGGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAAc                                                                                         <  2:376603/151‑1 (MQ=255)                                                           ggTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTg                                                                                      >  2:966211/1‑151 (MQ=255)                                                            gTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGt                                                                                     >  1:54775/1‑151 (MQ=255)                                                             tGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGtt                                                                                    >  1:355977/1‑151 (MQ=255)                                                                aGATTATGCTTTGTGTTCCACTGTGCGGAAACGAACCCGTGGCGCGCTGGATGTGCCCCTCGCACCGCGGGGCGTCCCTTTTACCGGTTTGGGCAAAATAACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACa                                                                                 <  2:246183/151‑1 (MQ=255)                                                                 gattaggttttGTTTTTCTCTGTGCGGGACCTGAGCGGTGGCGGGTTGGATGTGGCTCTGGACCACGTGGGGGTCCCGTTTGCGTGTTTCGGTTAAAGGGCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACa                                                                                 <  1:864098/141‑1 (MQ=255)                                                                   ttACGTGTTGTTTTTCACTGTGCCGAAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCGGGGCGTCCCTTTTCCCTTTATGGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACa                                                                                 <  2:764433/148‑1 (MQ=255)                                                                   ttACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACAtt                                                                               >  2:669966/1‑150 (MQ=255)                                                                    tACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACAtt                                                                               >  1:91500/1‑149 (MQ=255)                                                                        aGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTg                                                                         >  2:681328/1‑151 (MQ=255)                                                                        aGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTg                                                                         >  1:800822/1‑151 (MQ=255)                                                                           tgtgTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGa                                                                       >  1:85367/1‑150 (MQ=255)                                                                           tggttttctcggggCCGGAACGAACCCGTGGCGCTCTGGATGGGGCTCTCGAACGCTTGGGCGTACCTTTTACCTTTTCCGGGAAATTGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTgg                                                                        <  1:653581/136‑1 (MQ=255)                                                                                  ccttctgCCGAACCTGACCCGTGGCCGGCTGATTGGGGCTCTCGGACACCGGGCCGTACGTTTTCCTTTTAGGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGatat                                                               <  2:352019/146‑1 (MQ=255)                                                                                  cACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGatat                                                               >  1:442889/1‑151 (MQ=255)                                                                                     tgtgCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGAc                                                            >  2:27576/1‑151 (MQ=255)                                                                                         ccGGAACTGAACCGTGGCGGGGTGGATGTGGCTCTCGGACACCGGGGAGTACCTTTTCCCTGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGa                                                             <  2:587458/146‑1 (MQ=255)                                                                                         ccGGAACGAACCCGTGGGGCGCGGGAGGTGGCTCTCGGACTCGGGGGGTTCCCTTTTCCCTTTATGGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCa                                                          <  2:618190/149‑1 (MQ=255)                                                                                         ccGAAACGGACCGGTGGGGCGTTGGATGTGGCTCTCGGACACTGGGGCGTACCTTTTTCCTGTTTGGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGat                                                                 <  1:761858/142‑1 (MQ=255)                                                                                          cGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAttt                                                       >  1:769637/1‑151 (MQ=255)                                                                                          cGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAttt                                                       >  1:437292/1‑151 (MQ=255)                                                                                           ggAACTGAACGGGGGCGCGCTGGATGGGGCTCTCGGCCCCCGGGGCGTCCCGTTTACCTGTATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtttt                                                      <  1:545285/151‑1 (MQ=255)                                                                                             aaCTGAACCGGGGCGCGTTGGATGTGCCTCTCGGACCCCTGGGCGTACCTTTTCCCTGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGc                                                    <  1:855061/151‑1 (MQ=255)                                                                                                     cGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCAt                                            >  1:585826/1‑151 (MQ=255)                                                                                                      ggggCGCGGTGGATGTGGCTCCCGGACCCCGGGGCGTCCCGTTTCCCTTTACGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCAt                                            <  2:768526/148‑1 (MQ=255)                                                                                                                        ctctGGGACCCTGGGGTGTCCTGTTTCCTTGTATGGGGAAATTAACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGaaaa                            <  2:809693/148‑1 (MQ=255)                                                                                                                          ctgggACCCCGGGGCGTCCCTTTTCCTTGTATGGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGt                          <  1:792954/145‑1 (MQ=255)                                                                                                                             ggACCCCTGGGCGTCCCGTTTCCCTGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGc                       <  1:736603/148‑1 (MQ=255)                                                                                                                             ggACCCCGGGGCGTCCCGTTTCCCTTTAGGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTg                    <  1:488062/151‑1 (MQ=255)                                                                                                                                ccccTGGGCGTCCGTTTTCCCTGTAGGGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGaa                  <  2:500338/148‑1 (MQ=255)                                                                                                                                     gggCGTCCCTTTTCCCTGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAg            <  1:186108/151‑1 (MQ=255)                                                                                                                                     gggCGTACTGTTTACCTGTGGGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAg            <  2:18688/151‑1 (MQ=255)                                                                                                                                          tACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATc       >  1:247816/1‑151 (MQ=255)                                                                                                                                          tACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATc       >  1:961592/1‑151 (MQ=255)                                                                                                                                               tttCCCTGTATCGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTg   <  1:475324/150‑1 (MQ=255)                                                                                                                                               tttACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTgg  >  2:452049/1‑151 (MQ=255)                                                                                                                                                  |                                                                                                                                                    TGATGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGG  >  NC_000913/436359‑436651

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: ‑