Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,383,722	0	G	A	41.2%	57.8 / 21.9	51	F80F (TTC→TTT)	ycjW	LacI family putative transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base G (17/13);  new base A (0/21);  total (17/34)
Fisher's exact test for biased strand distribution p-value = 9.75e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAGCATAATAATGCCTTTAATCATTTTCTGCTTAATTTTGCTTTCGCATTTTTGCAGATCTTCTGCCGGATTGTGCGACGTTTGTAATATCACGTCGAAACCTTCTTCTTCAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAGAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAATTCTTCAATGGCCCGTAACACTTTTTCGCGCGCTTCCGG  >  NC_000913/1383578‑1383871                                                                                                                                                 |                                                                                                                                                       gAGCATAATAATGCCTTTAATCATTTTCTGCTTAATTTTGCTTTCGCATTTTTGCAGATCTTCTGCCGGATTGTGCGACGTTTGTAATATCACGTCGAAACCTTCTTCTTCAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAGaaaa                                                                                                                                                    <  1:274210/149‑1 (MQ=255)  aGCATAATAATGCCTTTAATCATTTTCTGCTTAATTTTGCTTTCGCATTTTTGCAGATCTTCTGCCGGATTGTGCGACGTTTGTAATATCACGTCGAAACCTTCTTCTTCAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAGAAAAA‑Cg                                                                                                                                                <  2:658564/151‑1 (MQ=255)     ataataATGCCTTTAATCATTTTCTGCTTAATTTTGCTTTCGCATTTTTGCAGATCTTCTGCCGGATTGTGCGACGTTTGTAATATCACGTCGAAACCTTCTTCTTCAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAGAAAAA‑CGGAt                                                                                                                                             >  2:585619/1‑151 (MQ=255)          aatGCCTTTAATCATTTTCTGCTTAATTTTGCTTTCGCATTTTTGCAGATCTTCTGCCGGATTGTGCGACGTTTGTAATATCACGTCGAAACCTTCTTCTTCAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAGAAAAA‑CGGATTAccc                                                                                                                                        <  2:66194/151‑1 (MQ=255)           atGCCTTTAATCATTTTCTGCTTAATTTTGCTTTCGCATTTTTGCAGATCTTCTGCCGGATTGTGCGACGTTTGTAATATCACGTCGAAACCTTCTTCTTCAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAGAAAAA‑CGGATTACccg                                                                                                                                       <  1:340207/151‑1 (MQ=255)                 ttAATCATTTTCTGCTTAATTTTGCTTTCGCATTTTTGCAGATCTTCTGCCGGATTGTGCGACGTTTGTAATATCACGTCGAAACCTTCTTCTTCAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAGAAAAA‑CGGATTACCCGCCGt                                                                                                                                   >  2:315375/1‑149 (MQ=255)                  tAATCATTTTCTGCTTAATTTTGCTTTCGCATTTTTGCAGATCTTCTGCCGGATTGTGCGACGTTTGTAATATCACGTCGAAACCTTCTTCTTCAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAGAAAAA‑CGGATTACCCGCCGTAGt                                                                                                                                >  2:673468/1‑151 (MQ=255)                    aTCATTTTCTGCTTAATTTTGCTTTCGCATTTTTGCAGATCTTCTGCCGGATTGTGCGACGTTTGTAATATCACGTCGAAACCTTCTTCTTCAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAGAAAAA‑CGGATTACCCGCCGTAGttt                                                                                                                              >  2:347795/1‑151 (MQ=255)                         tttCTGCTTAATTTTGCTTTCGCATTTTTGCAGATCTTCTGCCGGATTGTGCGACGTTTGTAATATCACGTCGAAACCTTCTTCTTCAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAGAAAAA‑CGGATTACCCGCCGTAGTTTTGGTc                                                                                                                         >  2:829516/1‑151 (MQ=255)                                 tatttttGTTTTCGCATTTTTGCAGATCTTCTGCCGTATGGTGCGACGTTTGTAATATCACGTCGAAACCTTCTTCTCCAGCTTTGGCGGTGTTGGCAGGCAAACCTGCAGAAAAAAG‑CGGATTCCCCGCCGTAGTTTTGGTCGAACggg                                                                                                                  <  2:580509/147‑1 (MQ=255)                                     tttGTTTTCGCATTTTTGCAGATCTTCTGCCGTATTGTGCGACGTTTTTAATATCACGTCAAACCCTTCTTCTTCAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAAAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGa                                                                                                              <  1:155490/150‑1 (MQ=255)                                         cTTTCGCATTTTTGCAGATCTTCTGCCGGATTGTGCGACGTTTGTAATATCACGTCGAAACCTTCTTCTTCAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAGAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATc                                                                                                          >  2:745602/1‑150 (MQ=255)                                          tttCGCTTTTTGGGATATCTTCGGCGGGTTGGTGCAAGGTTTTTAAACTCCCGCCAAAACTTTTTTCTCCGGTTTTGGCGGTGTTGGAGTGAAAAACTTCAAAGAAAAC‑CGGATTGCCCGCCGTAGTTTTGGTCGAACGGGTAGaaa                                                                                                            <  1:518436/147‑1 (MQ=255)                                                    ttGCAGTTCTTCTGCCGGATTGTGCGGTTTTTAAAATACCACGTCAAACCTTTCTTCTTCGGTTTTGGCGGTGATGGCATGAAAAACTACAGAAAAAAA‑CGGATTCCCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATgga                                                                                               <  2:536081/150‑2 (MQ=255)                                                    ttGCAGATCTTCTGCCTGATTGTGCGTCTTTTTTAATATCACGTCGAACCCTTCTCCTCCATTTTTGGCGGTGATGGTATACAAACCTCCAGAGAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGc                                                                                               <  1:547926/150‑1 (MQ=255)                                                       cAGATTTTCTGCCGGATTTGGCCACGTTTGAAATATCACGTCAAACCTTTCTTTTTAATCTTTGGCGGTGATGGAATGAAAATTTTCAGAAAAAAT‑GGGATTCCCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCAt                                                                                             <  1:364165/149‑1 (MQ=255)                                                              tctcCCGGATTGTGCGCCTTTTGTAATATCCCTACAAACCCTTCTTCTTCAGTTTTGGCGTTGGTGGCATGAAAACCTTCAGAGAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCaaa                                                                                         <  2:683040/146‑1 (MQ=255)                                                              tctGCCGGATTGTGCGACGTTTGTAATATCACGTCGAAACCTTCTTCTTCAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAGAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCg                                                                                    >  2:834298/1‑151 (MQ=255)                                                               ctGCCGGATTGTGCGACGTTTTAAATATCACGCCGAACCCTTCTTCTTCAGTTTTGGCGGTGATGGCATGAAAACCTTCAGAGAAAAA‑CGAATTCCCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAAccc                                                                                     <  2:336904/149‑1 (MQ=255)                                                                tGCCGGATTGTGCGACGTTTGTAATATCACGTCGAAACCTTCTTCTTCAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAGAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGa                                                                                   >  2:760373/1‑150 (MQ=255)                                                                 gCCGGATTGTGCGACTTTTGTAATACCACGTCAAAACCTTCTTCTTCAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAAAAAAA‑CGGATTCCCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCg                                                                                    <  1:259205/148‑1 (MQ=255)                                                                    ggtttGTGCGACGTTTGTAATATCACGTCGAAACCTTCTTCTTCAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAAAAAAA‑CGGATTCCCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAgg                                                                              <  2:73742/148‑1 (MQ=255)                                                                    ggATGGTGCGACTTTTGTAATATCCCGGCAAATCTTTTTTCTCCAGCTTGGGGGGTGATGGCATGAAAAACTTCAGAAAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAgg                                                                              <  1:877430/151‑1 (MQ=255)                                                                       tttggggACGTTTAAAATACCCCGTCAAACCCTTTTTCTTCATCTTTGGGGGTGATGGCATGAAAAACTTAAGAAAAAAA‑CGGATTCCCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTc                                                                            <  2:537170/144‑1 (MQ=255)                                                                          tgCGACGTTTGTAATATCACGTCAAAACTTTTTTCTTCAGTTTTGGCGGTGATGGCATGAAAAACTTAAGAAAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCa                                                                           <  2:705/148‑1 (MQ=255)                                                                             gtgttttGTAATCTCACTGCAAACCCTTCTTTTTCAGCTTTGGCGGTGATGGCATGCAAAACTTCGGAAAAAAA‑CGAATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAgcgcg                                                                      <  1:332208/146‑1 (MQ=255)                                                                               cGTTTTTAATATCCCGTCGAACCCTTTTTCTCCAGTTTTGGGGGTGTTGGAGTACAAAACTT‑AGAAAAAAACCGAATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCgg                                                                   <  1:103229/151‑1 (MQ=255)                                                                               cGTTTGTAATATCACGTCGAAACCTTCTTCTTCAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAGAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCgg                                                                   >  2:13736/1‑151 (MQ=255)                                                                                gTTTGTAATATCCCGTCGAACCCTTCTTCTTCAGCTTTGGCGGTGAGGGCATGCAAAACTTAAGAAAAAAA‑CGGATTCCCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAgcgcgc                                                                     <  1:859516/148‑1 (MQ=255)                                                                                  ttGTAATATCACGTCGAAACCTTCTTCTTCAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAGAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGcc                                                                >  1:503894/1‑151 (MQ=255)                                                                                      aaTATCACGTCAAAACCTTCTTCTTCAGTTTTGGGGGTGATGGCATGAAAAACTTAAGAAAAAAA‑CGGATTCCCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCa                                                               <  2:863928/148‑1 (MQ=255)                                                                                                  aaaCCTTCTTCTTCAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAGAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGAt                                                >  1:617081/1‑151 (MQ=255)                                                                                                             ttcAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAGAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAAttct                                     >  1:564654/1‑151 (MQ=255)                                                                                                               cAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAAAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAAttct                                     <  1:178725/149‑1 (MQ=255)                                                                                                               cAGCTTGGGCGGTGATGGCATGCAAAACTTCAAAGAAAAA‑GGGATTCCCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAAttcttc                                   <  1:13549/151‑1 (MQ=255)                                                                                                                agttttGGGGGTGATGGCATGCAAAACTTCAGAGAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAAttcttc                                   <  1:697006/147‑1 (MQ=255)                                                                                                                aGCTTTGGCGGTGATGGCATGCAAAACTTCAGAGAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAAttcttc                                   >  1:509514/1‑150 (MQ=255)                                                                                                                aGCTTTGGCGGTGATGGCATGCAAAACTTCAGAGAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAAttctt                                    >  2:687783/1‑149 (MQ=255)                                                                                                                 gCTTTGGCGGTGATGGCATGCAAAACTTCAGAGAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAATTCTTCa                                  <  1:260651/150‑1 (MQ=255)                                                                                                                    ttGGGGGTGATGGCATGCAAACTTACAAAAAAAAA‑CGGATTGCCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAAttcttc                                   <  2:381285/146‑1 (MQ=255)                                                                                                                    ttGGCGGTGATGGCATGCAAAACTTAAGAGAAAAA‑CGGATTCCCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAATTCTTCAATg                               <  2:334978/150‑1 (MQ=255)                                                                                                                       ggggTGAGGGCATGAAAAACTTAAGAGAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAATTCTTCAATGGccc                           <  1:69577/149‑1 (MQ=255)                                                                                                                            gagggCATGCAAAACTTCAGAAAAAAA‑CGGATTCCCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAATTCTTCAATGGCCCGTaa                       <  2:66128/147‑1 (MQ=255)                                                                                                                              tgcaaTGAAAAATTTCAGAAAAAAA‑CGAATTCCCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAATTCTTCAATGGCCCGTaa                       <  2:362847/144‑1 (MQ=255)                                                                                                                                 aaacaaaatCTTCAGAAAAAAA‑CGGTTTCCCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAATTCTTCAATGGCCCGTAACACttt                 <  2:584115/146‑1 (MQ=255)                                                                                                                                      aaaaCTTCAGAAAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAATTCTTCAATGGCCCGTAACACTTTTTc              <  1:699533/149‑1 (MQ=255)                                                                                                                                      aaaaCTTAAGAAAAAAA‑CGGTTTCCCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAATTCTTCAATGGCCCGTAACACTTTTTc              <  2:470957/149‑1 (MQ=255)                                                                                                                                        aaCTTCAGAGAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAATTCTTCAATGGCCCGTAACACTTTTTcgcgc          >  1:184600/1‑151 (MQ=255)                                                                                                                                        aaCTTCAGAAAAAAC‑CGGTTTCCCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAATTCTTCAATGGCCCGTAACACTTTTTcgcgc          <  2:758488/151‑1 (MQ=255)                                                                                                                                          cTTCAGAGAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAATTCTTCAATGGCCCGTAACACTTTTTcgcgcg         >  1:123317/1‑150 (MQ=255)                                                                                                                                           ttCAGAGAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAATTCTTCAATGGCCCGTAACACTTTTTCGCGCGCt       >  2:777829/1‑151 (MQ=255)                                                                                                                                                agaAAAA‑CGGATTCCCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAATTCTTCAATGGCCCGTAACACTTTTTCGCGCGCTTCCgg  <  1:797229/151‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                       GAGCATAATAATGCCTTTAATCATTTTCTGCTTAATTTTGCTTTCGCATTTTTGCAGATCTTCTGCCGGATTGTGCGACGTTTGTAATATCACGTCGAAACCTTCTTCTTCAGCTTTGGCGGTGATGGCATGCAAAACTTCAGAGAAAAA‑CGGATTACCCGCCGTAGTTTTGGTCGAACGGGTAGAAATCACCATAATGGCATCAAAACCCGAAGAGGTCAGCGCGCGGGCCAGCTTGTTTGGCTGATACTGTAATTCTTCAATGGCCCGTAACACTTTTTCGCGCGCTTCCGG  >  NC_000913/1383578‑1383871

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: ‑