Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	40.0%	70.0 / 12.3	51	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (20/10);  new base C (0/20);  total (21/30)
Fisher's exact test for biased strand distribution p-value = 7.37e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATT  >  NC_000913/357730‑358022                                                                                                                                                       |                                                                                                                                                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                                                                                                          >  2:1396181/1‑151 (MQ=255)                                       cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                          >  2:479428/1‑151 (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)                                                                                                                                              accttttttc‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc         <  1:1278447/140‑1 (MQ=255)                                                                                                                                                 ttttttc‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa     <  1:1033569/144‑1 (MQ=255)                                                                                                                                                 ttttttc‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAtt  <  2:536999/147‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                ACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATT  >  NC_000913/357730‑358022

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: ‑