Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,248,424	0	C	A	39.2%	79.7 / 24.8	51	V37F (GTT→TTT)	lysP	lysine transporter
Reads supporting (aligned to +/- strand):  ref base C (29/2);  new base A (0/20);  total (29/22)
Fisher's exact test for biased strand distribution p-value = 2.98e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGTAAGTGGCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGT  >  NC_000913/2248276‑2248571                                                                                                                                                      |                                                                                                                                                    ccGTAAGTGGCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGcaaca                                                                                                                                                    >  1:149634/1‑150 (MQ=255)  cGTAAGTGGCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGcaacaa                                                                                                                                                   >  1:842073/1‑150 (MQ=255)  cGTAAGTGGCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACaaa                                                                                                                                                  <  2:369721/151‑1 (MQ=255)      aGTGGCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACaaaa                                                                                                                                                 >  1:187263/1‑148 (MQ=255)               cGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCg                                                                                                                                     >  1:886445/1‑151 (MQ=255)                gAACCGGAAACCGGCCTATATGCAGCCAGTTCACCGAGAATGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCACCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCg                                                                                                                                     >  2:625981/1‑150 (MQ=255)                     ggAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGa                                                                                                                                >  1:798245/1‑150 (MQ=255)                            ggCATTTATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACAAGAACAATGCCCCGCCCGGACATGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAAgcgc                                                                                                                           >  2:345394/1‑148 (MQ=255)                                     gCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAatc                                                                                                                >  2:270379/1‑150 (MQ=255)                                     gCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAatc                                                                                                                >  1:642104/1‑150 (MQ=255)                                       aGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAatcatc                                                                                                             >  1:384073/1‑151 (MQ=255)                                       aGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAatcatc                                                                                                             >  2:702676/1‑151 (MQ=255)                                         ccATTTCCCCGAGACTGGTCATCAGGAAGAAACCCATCGGCCCAATCAGCATATACGAGAGCAATCCCCCCCCCGGCCCTGCCTGAAAAATC‑TTTGCGCAAGAGGCAAAAAAAAGCCCTGTCCCGATGGAACCGCCAATGGCAATCATCg                                                                                                            <  1:531929/150‑1 (MQ=255)                                                aCCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTg                                                                                                     >  1:470586/1‑150 (MQ=255)                                                 ccGAGACTGGTCATCAGGAAGTAAACCATCAGGCTAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGGGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGAc                                                                                                   >  2:213082/1‑151 (MQ=255)                                                   gagaCTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGAcgc                                                                                                 >  2:757401/1‑151 (MQ=255)                                                    agaCTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGAcgcg                                                                                                >  1:769378/1‑151 (MQ=255)                                                         ggTCACCAGGAAGTAACCCACCAGGCCAATCAGCATAAACGAGAGCACCCCCCCGCCCGGCCCTGCCTGAAAAATC‑GTGGCGCAAGGGCCAAAAAAGACCCCTGCCCCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCt                                                                                             <  2:269647/149‑1 (MQ=255)                                                         ggTAATCAGAAAGAAACCCACCAGGCAAATCAGCATATACGAGAGCAATGCCCCCCCCGGCCCGGCCGGAAAAATC‑GTTGCGCCAGAGGAAAAAAAAAGACCTGTCCCGATGGAACCGCCAATGGCAATCATCGTCAGGTGAcgcg                                                                                                <  1:172612/146‑1 (MQ=255)                                                           tcatcaGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTa                                                                                          >  1:707827/1‑150 (MQ=255)                                                               caGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTc                                                                                      >  2:105041/1‑150 (MQ=255)                                                                      tAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGt                                                                               >  2:459920/1‑150 (MQ=255)                                                                        aaCCATTAGCCCAATCTGCATAAACGGTAGCAAGCCCCCTCCCGCCCCTG‑CGAAAAAATCTGTTGCGCGAGAGCCAAAAAAAATACGTCACCGGATGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGc                                                                                 <  1:582515/146‑1 (MQ=255)                                                                          ccATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGcc                                                                          >  2:638384/1‑151 (MQ=255)                                                                           cATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGCCCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGcc                                                                          >  2:872743/1‑150 (MQ=255)                                                                                    aaccAGAATATACGAGACCAACCCCCCGCCCGGCCCTGCCTAAGAAATC‑TTTGCCCCAGAGGCAAAAAAAAGCCCTGTCCCGATGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCt                                                                <  1:418773/148‑1 (MQ=255)                                                                                     aTCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCtg                                                               >  1:464716/1‑151 (MQ=255)                                                                                        aGCATATACGAGAGCAATCCCCCCCCCGGCCCTGCCTGAGAAATC‑GTTGCGCCAGAGGAAAAAAAAAGCCCTGTCCCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCtgtg                                                             <  1:799095/150‑1 (MQ=255)                                                                                         gCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTgg                                                            >  1:962483/1‑150 (MQ=255)                                                                                          cATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGtt                                                          >  2:863644/1‑151 (MQ=255)                                                                                           ataggggagaCCAACGCCCCGCCCGGCCCTGCCGGAAAAATC‑GTGGCGCAAGAGCAAAAAAAAAGCCCTGTCCCGGGGGAGCCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCtgtg                                                             <  2:159627/141‑1 (MQ=255)                                                                                              taCGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGtttt                                                        >  1:750253/1‑149 (MQ=255)                                                                                                 gagaGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGttt                                                   >  2:194445/1‑151 (MQ=255)                                                                                                   gagCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCg                                                 >  1:946273/1‑151 (MQ=255)                                                                                                    agccaagccccgccccGGACTCCCTGAGAACTC‑GTTCCGCCAGAGGCAACAAAAAGACCCGTACCGATGGAACCGCCACAGGCAACCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGGTTTACGTTCgg                                                >  2:638221/7‑151 (MQ=255)                                                                                                       aaccccccccccGGCCCTGCCTGAAAATTG‑TTTGCCCCAGGGGAAAAAAAAAGCCCTGTCCCGAGGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCg                                                 <  1:141357/143‑1 (MQ=255)                                                                                                       aaTCCCCCGCCGGGCCCTGCCTGAAAAATC‑GTGGCGCGAGAGCCAAAAAAAAGCCCTGTACCGAGGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGa                                               <  1:653503/149‑1 (MQ=255)                                                                                                         tGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAAcc                                           >  1:608584/1‑151 (MQ=255)                                                                                                          cccccGCCCGGCCCTGCCTGAAAAATG‑GTGGCGCAAAGGCCAAAAAAAATCCCGGTCCGGAGGGACCCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGa                                               <  2:723014/145‑1 (MQ=255)                                                                                                               gcccgGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACa                                      >  1:542291/1‑150 (MQ=255)                                                                                                               gcccgGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACa                                      >  1:869863/1‑150 (MQ=255)                                                                                                                      cctccagaaaaagtC‑GTTGCGCAAGAGACAAAAAAACGACCTTCTCGGTTGGACCCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAAt                                 <  2:707421/135‑1 (MQ=255)                                                                                                                          cctgAGAAATC‑GTTGCGCCAGAGGAAAAAAAAACCCCTGTACCGATGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTa                             <  1:189784/148‑1 (MQ=255)                                                                                                                          cctgAAAAATC‑GTTGCGCAAGAGGCAAAAAAAAGCCCTGTCCCGAGGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTAt                            <  1:218033/149‑1 (MQ=255)                                                                                                                              aaaaaTC‑GTTGCGCAAGAGGCAAAAAAAAGCCCTGTACGGATGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCt                      <  1:530530/149‑1 (MQ=255)                                                                                                                              aaaaaTC‑GTGGCGCCAGAGGCAAAAAAAAGCCCTGTCCGGAGGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCt                      <  1:540837/149‑1 (MQ=255)                                                                                                                              aaaaaTC‑GTCGCGCCAGAGGAAAAAAAAACCCCTGTACCGATGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCa                         <  1:26536/146‑1 (MQ=255)                                                                                                                                aaaTC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCtt                     >  2:268777/1‑150 (MQ=255)                                                                                                                                aaaGC‑GTTGCGCCAGGGCCAAAAAAAAGCCCTGTCCCGTGGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCtt                     <  1:819653/150‑1 (MQ=255)                                                                                                                                 aaTC‑GTTGCGCCAGAGGCAAAAAAAAGACCTGTCCCGATGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTaa                   <  1:570040/151‑1 (MQ=255)                                                                                                                                            ccAGAGGCAAAAAAAAGCCCTGTCCCGAGGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGgcg         <  1:396661/151‑1 (MQ=255)                                                                                                                                              agagCCAACAAAAAACCCTATCCCTAAGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGcgcg       <  1:213199/151‑1 (MQ=255)                                                                                                                                                agGCAAAAAAAAGACCTGACCCGATGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGgc          <  1:371875/146‑1 (MQ=255)                                                                                                                                                   caacaaAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGt  >  2:128701/1‑151 (MQ=255)                                                                                                                                                    aacaaAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGt  >  1:648822/1‑150 (MQ=255)                                                                                                                                                    aacaaAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGt  >  2:508768/1‑150 (MQ=255)                                                                                                                                                      |                                                                                                                                                    CCGTAAGTGGCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATC‑GTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGT  >  NC_000913/2248276‑2248571

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑