Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	57.8%	4.9 / 52.1	45	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (11/8);  new base A (0/26);  total (11/34)
Fisher's exact test for biased strand distribution p-value = 7.45e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.44e-05

GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGA  >  NC_000913/357742‑358038                                                                                                                                                       |                                                                                                                                                     gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTCCG‑CCGcaaca                                                                                                                                                     <  2:400890/150‑1 (MQ=255) gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTCCG‑CCGcaaca                                                                                                                                                     >  1:27290/1‑150 (MQ=255) gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTCCG‑CCGcaac                                                                                                                                                      <  1:332741/149‑1 (MQ=255)     aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTCCG‑CCGCAACAAAAcc                                                                                                                                                <  1:128263/151‑1 (MQ=255)       cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTCCG‑CCGCAACAAAAccgc                                                                                                                                              >  2:48677/1‑151 (MQ=255)        gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTCCG‑CCGCAACAAAAccgcc                                                                                                                                             <  1:888338/151‑1 (MQ=255)         tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTCCG‑CCGCAACAAAAccgccg                                                                                                                                            >  1:164745/1‑151 (MQ=255)               accAGGCATTCCCACCCGCATACCTGTGTCGGCGGCTCCCGTGTTTCATTCCCGCCAACACCCGCGCATTTATCCACCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTCCCAGT‑TATTTTCCCG‑CCGCAAAAAAAccgccg                                                                                                                                            <  2:80708/143‑1 (MQ=17)                      aaTCCCACCCGCAGCCGTGTGTCGGCGCCTCCTGTAATTCATTCCCGCCAACACCCGCGCTTTTACCCACCGCCATGTAAAAAATTCCCTCCGCGGCGCCTTTCTCCAATT‑TTTTTTCCCG‑CCACAAAAAAACCGCCGTTCTCTCCag                                                                                                                                  <  2:548332/148‑1 (MQ=255)                          ccAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                           >  1:1092446/1‑151 (MQ=255)                           ccgCCGCAGCCCTGTGCCGGGGCCACCCGTAATTCATTCCCCCCAACACCCGCGCTTTTACCCACCCCCTTGGAAAAAATTCCCTCCGGGCCGCCTTTCTCCCAGT‑TTTTTTCCCG‑CCGAAAAAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                                            <  2:743110/147‑1 (MQ=255)                            aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                         >  1:832215/1‑151 (MQ=255)                               cGCAGACTTGTGTCGGCGGCCCCCGTTTTTCTTTCCCCCCAACACCCGCCCTTTTCTCCACCGCCATGTCCAAAAATCCTTCCGCGGCGGCTTCCTCCCAGC‑TTTTTTCCCC‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                         <  2:8854/148‑1 (MQ=255)                                   gccttgttTCGGCGGCTCCCGTGTTTCTTTCCCCCCAACACCCGCGCTTTTCCCCACCGCCTTGTGAAAAAATGCCTTCGGGGCGGCTGTCCGCCAGT‑TATTTTCCCG‑CCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                                                   <  1:358542/146‑1 (MQ=255)                                         tgcaaGCGGTTTCCGTTATTCATTCCCGCAAAAACCCCCGCATTTCCCCAACGCATTGTACAAAAATGCCCTCGGGGCGGCTGCCGGCCAGC‑TATTTTCCCG‑CCACAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt                                                                                                             <  1:996041/146‑1 (MQ=255)                                          gtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGaaaaa                                                                                                            >  1:235059/1‑148 (MQ=255)                                                   tACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGaaaaaaattttaacc                                                                                                  >  1:95400/1‑139 (MQ=255)                                                      cGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGaaaaaagattaaaccc                                                                                                 >  1:103149/1‑136 (MQ=25)                                                               ttccccccAACACCCGCGATTTTACCCAACCCCATGTGCAAAAATCCTTTCGCGGCGGCTGTCTGCCAGC‑TATTTTCCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgt                                                                                          <  1:870541/141‑1 (MQ=255)                                                               ttccccccAACACCCGCCCTTTTACCCACCGCCATGTAAAAAAATCCCTGCGCGGCGGTTTTCTGCCAGT‑TTTTTTCCCG‑CCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTc                                                                                              <  2:511978/137‑1 (MQ=255)                                                                  ccGCCAACACCCGCGCTTTTACCCACCGCCATGTGAAAAAATGCCTTCGCGGCGGCTGTCGGCCAGC‑TATTTTCCCG‑CCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                                    <  1:652512/150‑1 (MQ=255)                                                                  ccGCCAACACCCGCCCTTTTCCCCAACGCCATGTGAAAAAATCCCTTCGGGGCGGCTTTCGCCCAGT‑TTTTTTCCCG‑CCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTgg                                                                                   <  1:79703/151‑1 (MQ=255)                                                                     ccaccaCCCGCTCTTTTACCCACCCCCATGTACAAAACGCCCTCGGGGGCGGCTGCCGGCCAGT‑TTTTTTCCCG‑CCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCaa                                                                                <  2:237136/151‑1 (MQ=255)                                                                        acaccCGCGCATTTACCCAACGCCATGTAAAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTCCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg                                                                             <  1:97659/151‑1 (MQ=255)                                                                          acccGCGCTTTTACCCAACGCCATGTGAAAAAATGCCTTCGCGGCGGCTGTCTCCCAGC‑TTTTTTCCCG‑CCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg                                                                             <  1:248526/147‑1 (MQ=255)                                                                                gcATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAGTTTTAATCCGCCATGTTTTGTggggaatgctgcctgg                                                                     >  1:1096392/1‑137 (MQ=25)                                                                                   tttACCCACCGCCATGTAAAAAAATGCCGTCGCGGCGGCTGTCTGCCAGT‑TATTTTCCCG‑CCAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                                           <  2:820439/142‑1 (MQ=255)                                                                                    ttacccaccccctggtgAAAAATTGCCTCCGCGGCGGCTTTCTCCCAGT‑TTTTTTCCCG‑CCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAc                                                                  <  1:204756/136‑1 (MQ=255)                                                                                    tccccaaccGCTATGTGAAAAAACCCTTCCGCGCGGGTTGTCGCCGAGT‑TTTTTTCCCC‑CCGAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAc                                                                  <  2:775153/142‑1 (MQ=255)                                                                                        ccacctccATGCGAAAAAAGGCCTCCGCGGCGCCTGCCCGCCAGT‑TATTTTCCCG‑CCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa                                                                <  2:380042/142‑1 (MQ=255)                                                                                        caaccccattgtcaaaaaaGGCCTCCGCGGCGGCTTCCTGCCACT‑TATTTTCCCG‑CCACAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                                               <  2:230589/135‑1 (MQ=255)                                                                                            ccccATGAGAAAAATTGCGTTCGCGGCGGTTGTC‑GCCCGCTTTTTTTTCCC‑CCGAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                                            <  1:1063068/146‑1 (MQ=255)                                                                                                  gtgCAAAAATGCCTTCGCGGCGGCTTTCTGCCAGT‑TTTTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGaa                                                   <  1:221313/151‑1 (MQ=255)                                                                                                     cAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGGGGAAAAACTTTTAAACCCCCCTGTTGTGTGGGGATCGCTGCCGGGTACAAAGTGGGAAGGGGAg                                                  >  1:801204/1‑149 (MQ=255)                                                                                                      aaaaaTGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAACCTTTAACCCCCCCTGTTTTGTTGGGATCGCGGCTTGTGAAAAAGTGGGAAGGGGAggg                                                >  1:698260/1‑148 (MQ=255)                                                                                                             ccTTCGCGGCGGTTGTCTGCCAGT‑TTTTTTCCCG‑CCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGa                                          <  1:445040/149‑1 (MQ=255)                                                                                                                       ggcTGTCGCCCAGT‑TTTTTTCCCG‑CCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc                                       <  2:722401/142‑1 (MQ=255)                                                                                                                              ggCCAGT‑TTTTTTCCCG‑CCCAAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc                         <  2:613915/148‑1 (MQ=255)                                                                                                                              cgccaagttttttttCCG‑CCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc                           <  2:53746/138‑1 (MQ=255)                                                                                                                                ccAGT‑TTTTTTCCCG‑CCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa                              <  2:393454/142‑1 (MQ=255)                                                                                                                                ccAGC‑TATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAAAAATTTTAACCCCCCCTGTTTTGTGGGAATCGCTGCTGGGGAAAAAGTGGGAAGGGGAGGGGGGCGGATCAGCCCCCGAAACccgc                       >  1:454821/1‑149 (MQ=255)                                                                                                                                 caagttATTTTCCCG‑CCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCgcgc                       <  1:384909/144‑1 (MQ=255)                                                                                                                                      ttttttcCCGCCCGGAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGGTCCAGAACCGCGCTAAt                   <  2:577142/147‑1 (MQ=255)                                                                                                                                      ttttttcCCG‑CCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt                   <  1:965492/146‑1 (MQ=255)                                                                                                                                        ttttcCCC‑CCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt                   <  2:228237/146‑1 (MQ=255)                                                                                                                                           ttccccctgaaacaaAGCCGCCGTTCTCTCCAGTATTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAGCcgcg                        <  2:466067/129‑1 (MQ=255)                                                                                                                                             ccg‑ccgCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCg           <  1:546643/149‑1 (MQ=255)                                                                                                                                              cg‑ccgaAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTATGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCt        <  1:897414/151‑1 (MQ=255)                                                                                                                                              cccccaaaacaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc            <  1:740703/141‑1 (MQ=255)                                                                                                                                               ccccgcAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCt        <  2:945701/149‑1 (MQ=255)                                                                                                                                                  cccaaaaaACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCa      <  2:103144/148‑1 (MQ=255)                                                                                                                                                     aacaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGa  <  2:1051804/151‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                     GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGA  >  NC_000913/357742‑358038

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑