Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,875	0	A	T	38.2%	77.1 / 17.9	55	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (24/10);  new base T (0/21);  total (24/31)
Fisher's exact test for biased strand distribution p-value = 7.66e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACC  >  NC_000913/357727‑358013                                                                                                                                                     |                                                                                                                                            tGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAtt                                                                                                                                           >  1:661596/1‑151 (MQ=255)  gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAt                                                                                                                                            <  1:1043526/149‑1 (MQ=255)   aaCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAtttt                                                                                                                                         >  2:361906/1‑151 (MQ=255)    aCTAGTATGCCTGATAAGCGTAGCGCATCAGGCAATTCAAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCCTTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAttttt                                                                                                                                        >  2:1041910/1‑151 (MQ=255)       cGTAGGCCTGATAAGCGTAGCGCTTCAGACAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCACCAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑cc                                                                                                                                     <  2:804451/150‑1 (MQ=255)       cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑ccg                                                                                                                                    <  1:190396/151‑1 (MQ=255)         tAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑ccgcc                                                                                                                                  >  1:823977/1‑151 (MQ=255)          aGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑ccgccg                                                                                                                                 <  2:713271/151‑1 (MQ=255)           ggCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑Ccgccgc                                                                                                                                >  2:1116275/1‑151 (MQ=255)            gCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGca                                                                                                                               <  1:288516/151‑1 (MQ=255)              cTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACCACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTGT‑CCGCCGcaa                                                                                                                              >  2:1173707/1‑150 (MQ=255)               tGATAAGCGTAGCGCATAAGGAAATTAAAGCCGCAGAACTGTGTAAGCGGCTACCGTGATTCATTTCAGCCAACAAACGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑TCGCCGcaa                                                                                                                              >  2:441520/1‑149 (MQ=17)                gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCGTACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaaca                                                                                                                            <  2:217570/150‑1 (MQ=255)                   aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACaaaa                                                                                                                         <  2:1237314/150‑1 (MQ=255)                      cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgc                                                                                                                     >  1:892820/1‑151 (MQ=255)                       gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGACTCAATTCCGACAACAACCGCGCATTTATCCAACGCCCTGTTCAAAAATGCCTTCACCGCGGCCGCCAACCAGCTATTTTA‑TCGCCCCAACAAAAcc                                                                                                                       >  2:949243/1‑148 (MQ=17)                        tAGCGCATCAGGCAATTCCGGCCGCAGACCTGTGTCAGAGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCGTGTGCAAAAATGCCTTCGGGGCGGCTGTCTGCAAGCTATTTTT‑CCGCCGCAACAAAAccgcc                                                                                                                    <  2:1241092/150‑1 (MQ=255)                         aGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGt                                                                                                                  >  1:933063/1‑151 (MQ=255)                            gcATCAGGCATTTCCAGCCGCAGACCTGTGTCAGCCGATACCGTGATTCATTTCCGCCAACACCCGCGCCTTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgcc                                                                                                                    <  2:311117/146‑1 (MQ=255)                             cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTtctc                                                                                                              >  1:1407406/1‑151 (MQ=255)                              aTCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACAACCGCGCATTCCTCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTATAGTT‑TATACCCAACAAAAcggccgcgc                                                                                                                >  2:1145147/1‑145 (MQ=14)                              aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTtctct                                                                                                             >  2:276987/1‑151 (MQ=255)                                          cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                 >  2:479428/1‑151 (MQ=255)                                          cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                 >  2:1396181/1‑151 (MQ=255)                                           aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                >  1:210205/1‑151 (MQ=255)                                             ccacagccgtgtgtgAGCGGCTACCGTGTTTCATTCCCCCCAACCCCCGCCATTTTCCCCACCCCCATGTGAAAAAATCCCTTCGCGGGGGTTGTCTCCCATTTTTTTTT‑CCGCCGAAACAAAACCGCCGTTCTCTCCag                                                                                                         <  2:609413/131‑1 (MQ=255)                                             ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCCACAACCGCGCCTTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                >  1:931879/1‑149 (MQ=255)                                             ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                              >  1:859220/1‑151 (MQ=255)                                                    ccTGTGTCGGCGGCTACGGTGATTCATCCCCCCAAACACCCGCCCTTTTCCCCACCCCCATGTCCAAAAGTCCCTCGGCGGCGGCTGTCTCCCGGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                          <  2:780292/148‑1 (MQ=255)                                                    ccTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                              >  2:1098031/1‑144 (MQ=255)                                                         gtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGcggaggaaaaa                                                                                   >  2:495569/1‑140 (MQ=255)                                                          tCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggtagcggaaaa                                                                                   >  2:1097572/1‑138 (MQ=255)                                                           cAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAAAGaaaaa                                                                                   >  1:703277/1‑146 (MQ=255)                                                              cgcctcccttgcttCTTTCCCGCCAACACCCGCGCTTTTATCCAACGCCTGGTGAAAAAAGGCCTTCGGGGCGGTTGTCTCCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAg                                                                                  <  2:1145411/134‑1 (MQ=255)                                                               ggCTACCGTATTTCATTCCCCCAACCACCCGCGCTTTTACCCACCCCCATGTGAAAAAATGCCTTCGCGGCGGTTGTCTGCCAGCTTTTTTC‑CCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCttt                                                                              <  1:319738/149‑1 (MQ=255)                                                               gcctccgttatttCTTTCCCGCCAACACCCGCGCTTTTACCCACCGCCATGTAAAAAAATGCTTCCGGGGGGGCTGTCGGCCAGTTATTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt                                                                                    <  1:762291/132‑1 (MQ=255)                                                               gccacccttaattcattcCCCCCAACAACCGCGATTTTACCAACCGCCATGTAAAAAAATCCCTCCGCGGCGGCTGTCTGCAATTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgaga                                                                                       <  1:879377/130‑1 (MQ=255)                                                                   aCCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGCGAGaaaaaaggttaaatc                                                                         >  2:1370790/1‑138 (MQ=25)                                                                    ccGTGTTTCTTTCCCCCCAACACCCGCGCATTTACCCACCGCCATGTGAAAAAATGCCTCCGCGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAg                                                                           <  1:403947/147‑1 (MQ=255)                                                                       tgtttCTTTCCCCCCAACACCCGCGCATTTACCCAACGCCATGTGCAAAAATGCCTTCGGGGCGGCTTTCGCCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTaa                                                                            <  1:1145486/140‑1 (MQ=25)                                                                           tctttccccccAACACCCGCGCTTTTACCCAACGCCATGCAAAAAAAGCCCTTCGGGGCGGCTGTCTCCCAGTTTTTTTC‑CCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtg                                                                  <  1:958698/140‑1 (MQ=255)                                                                                      accacccGCGCTTTTACCCACCCCCATGGAAAAAAGTCCCTTCGGGGCGGTTTTCGGCCACTTTTTTTC‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAAt                                                      <  1:67082/145‑1 (MQ=255)                                                                                              cgcATTCCTCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCcgtag                                                                                                      >  2:1169958/1‑94 (MQ=255)                                                                                                       caaacccttggtccAAAATTCCCTTGGCGGCGGCTTTCT‑CCAGGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgt                                    <  2:890783/138‑1 (MQ=255)                                                                                                         acccccATGTAAAAAAATGCCTCCGCGGCGGTTGTCTGCCATTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTgg                                  <  1:976498/147‑1 (MQ=255)                                                                                                                     aaaacTTCCTGCGGGGGGGCTGTCTCCGAGTTTTTTTC‑CCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAg                         <  2:377359/148‑1 (MQ=255)                                                                                                                     aaaaaTCCCTTCGCGGGGGCTGTCTCCCATCTTTTTCC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                      <  1:1427178/151‑1 (MQ=255)                                                                                                                     aaaaaGCCCTCCGGGGCGGCTGTCTCCCAGTTTTTTTC‑CCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAg                         <  1:306453/148‑1 (MQ=255)                                                                                                                      aaaaTGCCTCCGCGGCGGCTGTCTCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAg                         <  1:661207/147‑1 (MQ=255)                                                                                                                       aaaccccTGCGGGGCGTCTGTCTCCCAGTTTGTTTC‑CCGCCAAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcgg                    <  2:684453/146‑1 (MQ=255)                                                                                                                        aaTGCTTTCGCGGCGGCTGTCTCCCACCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggc                   <  1:724603/151‑1 (MQ=255)                                                                                                                                   ggggccTGTCGCCCAGTTTTTTTC‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGaa                <  2:532563/138‑1 (MQ=255)                                                                                                                                          tccTGCCAGTTTTTTTC‑CCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa     <  2:932786/145‑1 (MQ=255)                                                                                                                                           tcgcccAGTTTTTTTC‑CCGCCACAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa    <  1:122750/143‑1 (MQ=255)                                                                                                                                               ccAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc  <  1:1320434/145‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                            TGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACC  >  NC_000913/357727‑358013

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑