Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	47.9%	48.3 / 21.5	48	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (17/8);  new base C (0/23);  total (17/31)
Fisher's exact test for biased strand distribution p-value = 2.79e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAT  >  NC_000913/357731‑358021                                                                                                                                                       |                                                                                                                                               cTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTc                                                                                                                                               >  1:1051831/1‑151 (MQ=255)   cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTcc                                                                                                                                              >  2:293379/1‑150 (MQ=255)    gTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTccg‑c                                                                                                                                           <  2:994449/151‑1 (MQ=255)     tAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTccg‑cc                                                                                                                                          >  2:926458/1‑151 (MQ=255)     tAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTccg‑cc                                                                                                                                          >  2:1016228/1‑151 (MQ=255)      aGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTccg‑cc                                                                                                                                          <  1:407916/150‑1 (MQ=255)          cTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTCCG‑CCGcaa                                                                                                                                      >  2:204748/1‑150 (MQ=255)            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)                                                                                                                                                       |                                                                                                                                               CTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGC‑TATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAT  >  NC_000913/357731‑358021

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑