Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	43.2%	47.3 / 25.1	44	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (17/8);  new base A (0/19);  total (17/27)
Fisher's exact test for biased strand distribution p-value = 1.61e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAAT  >  NC_000913/357740‑358036                                                                                                                                                        |                                                                                                                                                    cTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                                                     >  1:1009512/1‑151 (MQ=255) cTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                                                     >  1:576329/1‑151 (MQ=255)  tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                                                     >  2:1069036/1‑150 (MQ=255)   gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaaca                                                                                                                                                    <  1:939704/150‑1 (MQ=255)    aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa                                                                                                                                                   >  2:304176/1‑150 (MQ=255)     tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa                                                                                                                                                   <  1:454574/149‑1 (MQ=255)       aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                               <  2:1127919/151‑1 (MQ=255)       aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                               <  1:794532/151‑1 (MQ=255)        gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccg                                                                                                                                              >  1:85311/1‑151 (MQ=255)               gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtct                                                                                                                                       >  1:962491/1‑151 (MQ=255)                 aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctct                                                                                                                                     >  2:988500/1‑151 (MQ=255)                   cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                                   >  2:53154/1‑151 (MQ=255)                    aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                                   >  1:1116803/1‑150 (MQ=255)                     ggaaaTCCCAGCCGCGGACCTGTGTAAGCGGCTACCGTGATTCATTCCCGCCAACACCCGCGCTTTTATCAACCGCCATGTGCAAAAAGGCCTT‑CGCGGCGGCTGTCTGCCAGTTTTTTTTCCGCCGCAACAAAACCGCCGTtc                                                                                                                                        <  2:525226/141‑1 (MQ=18)                       cAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                                >  2:967688/1‑150 (MQ=255)                            ccAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                          >  2:727625/1‑151 (MQ=255)                             cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑g                                                                                                                        >  2:1008111/1‑151 (MQ=255)                                ccgcacccttgtgTCAGCGCCTCCGTTGATTCTTTCCCCCAAACACCCGCATTTTTATCCAACGCCATGAG‑AAAAATTCCTTCCGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑ggg                                                                                                                      <  2:681457/141‑1 (MQ=255)                                ccGAAGCCCTGTGCCGGCGGCTCCCGTGATTCTTTCCCCCCAACACCCGCGCTTTTACCCACCCCCTTGTGAAAAAATCCCTT‑CGGGGCGGCTTTCGGCCAGCTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑ggg                                                                                                                      <  1:177853/150‑1 (MQ=255)                                 cGCAGACCTGTGTCAGCGGCTCCCGTGATTCATTCCCGCAAACACCCCCGCTTTTCCCCAACGCCTTGTGCAAAAAGCCCTC‑CGCGGCGGTTGTCTGCAAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑gg                                                                                                                       <  2:1183906/148‑1 (MQ=255)                                 cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gggg                                                                                                                     >  1:254055/1‑150 (MQ=255)                                 cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑ggg                                                                                                                      >  2:650541/1‑149 (MQ=255)                                  gcaccccTGTGGCGGCGGTTCCTGTTATTTTTTTCCCCAAAAACCCGCGTATTTACCCACCGCATTGTAAAAAATTCCCTT‑CGCGGCGGCTGTCCGCCGCCTTTTTTCCCCCCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGC‑g                                                                                                                        <  1:807857/141‑1 (MQ=255)                                    aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gggg                                                                                                                     >  1:944694/1‑147 (MQ=255)                                     gACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gg                                                                                                                       >  2:1171007/1‑144 (MQ=255)                                              cAGCGGCTCCCGTATTTCTTCCCCCCCAACACCCGCCCTTTTACCCACCGCCATGGAAAAAAATGCCTC‑CGGGGCGGCTTTCTGCCAGCTATTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCt                                                                                                       <  1:68253/151‑1 (MQ=255)                                                  gcctcccGTGTTTCATTCCCCCAAACACCCGCGCTTTTACCCACCGCCATGTGAAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTaa                                                                                                   <  1:267427/146‑1 (MQ=255)                                                   gCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑ggggggaaagga                                                                                                             >  2:916140/1‑132 (MQ=255)                                                   gCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCCACAGaaaaaacatt                                                                                                     >  1:1093397/1‑141 (MQ=255)                                                    cTACCGTGATTCATTTCCGCCAACAAACGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑ggggggtaaaaaa                                                                                                            >  1:1070232/1‑131 (MQ=255)                                                       ccGTGATTCATTTCCCCCAACACCCGCGCATTTACCCACCCCCATGTGAAAAAATGCCTC‑CGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCg                                                                                              <  1:735478/151‑1 (MQ=255)                                                                   ccccccAACACCCGCCCATTTACCCACCCCCATGTAAAAAAATCCCTC‑CGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCAAAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                                  <  2:161365/147‑1 (MQ=255)                                                                       caaacaccCGCGCTTTTCTCCAACGCCATGTGAAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAATCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCaa                                                                              <  1:172020/149‑1 (MQ=255)                                                                          acaccCGCGCATTTACCCACCGCCATGTGAAAAAATGCCTT‑CGCGGCGGCTTTCTGCCAGTTTTTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCaa                                                                              <  1:540394/148‑1 (MQ=255)                                                                              ccgcgtttttccccAACG‑CATGTGGAAAAAAGCCTTCCGCGGCGGTTGCCTGCCACTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgc                                                                       <  1:407940/139‑1 (MQ=255)                                                                                  gcATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGTAGAGAAAAAGCTTTTAAACCCACCTGTTTTGTGGcga                                                                              >  1:581543/1‑138 (MQ=25)                                                                                            accGCCATGTGCAAAAATCCTTG‑CGCGGCGGTTGTCTCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                                          <  1:315443/148‑1 (MQ=255)                                                                                                    gtgAAAAAATCCCTG‑GGGGGGGGCTTTCGGCCATTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAggg                                                   <  2:1083623/149‑1 (MQ=255)                                                                                                             tGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAAAGGAAAAAAATTTAA‑CCCGCCATTTTGTGTGGGGAACGCTGCCGGGGAAAAAGTGggaagggaagggggg                                           >  1:1012188/1‑143 (MQ=255)                                                                                                               ccTC‑CGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAAt                                      <  1:304179/151‑1 (MQ=255)                                                                                                                        gcggtTGTCCGCCATTTTTTTTCCCGCACCAAAAAATCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCa                              <  2:191958/151‑1 (MQ=255)                                                                                                                              tccgcccAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc                          <  2:944672/144‑1 (MQ=255)                                                                                                                               tccgCCAGTTTTTTCCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc                          <  2:596014/145‑1 (MQ=255)                                                                                                                                   caattttttttcCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc                          <  2:787270/137‑1 (MQ=255)                                                                                                                                     agtttttttcCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt                 <  1:419125/146‑1 (MQ=255)                                                                                                                                       cttttttcCCCCCCCAACAAAGCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt                 <  2:299877/146‑1 (MQ=255)                                                                                                                                        ttttttcCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAtt                <  1:1171035/147‑1 (MQ=255)                                                                                                                                          ttttcCCGCGGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAtt                <  1:650558/147‑1 (MQ=255)                                                                                                                                           tttcCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGt            <  1:125976/150‑1 (MQ=255)                                                                                                                                               ccgccgCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc          <  1:1012038/148‑1 (MQ=255)                                                                                                                                                      aacaaAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGCAGAGAAAAAAGTTTTACACCCCCCTGTTGTGGGGGGAAAGCTGCTGGGTAAAAAATGGGAAGGGAAGAGGGGGGGAACAACCCCACAACCCCGCCCATTAAGTTCGGCTcca   >  1:767411/1‑146 (MQ=255)                                                                                                                                                      aacaaAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAAt  <  1:967712/149‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                                    CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAAT  >  NC_000913/357740‑358036

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑