Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	46.8%	31.0 / 30.9	47	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (20/5);  new base A (0/22);  total (20/27)
Fisher's exact test for biased strand distribution p-value = 9.41e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAG‑CTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCA  >  NC_000913/357740‑358034                                                                                                                                                          |                                                                                                                                                    cTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                                                     >  1:935568/1‑151 (MQ=255)   gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGCCCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaaca                                                                                                                                                    <  2:667789/150‑1 (MQ=255)   gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaaca                                                                                                                                                    >  2:555429/1‑150 (MQ=255)    aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa                                                                                                                                                   >  2:291608/1‑150 (MQ=255)     tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaa                                                                                                                                                  >  1:395012/1‑150 (MQ=255)      aaGCGGAGATCATCAGGCAATTCCAGCCCCAGGCCTTTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAc                                                                                                                                                <  2:511056/151‑1 (MQ=18)               gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtct                                                                                                                                       >  2:816823/1‑151 (MQ=255)                       cAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCag                                                                                                                                 >  1:1030471/1‑149 (MQ=255)                        attcccccccGCAGCCTTGTCTCGGCGCCTACGGTTTTTCATTCCCCCC‑AACACCCCCCCTTTTACCCACCGCC‑TTTTAAAAAAATCCTTCCGC‑GGCGCCTTTCTCCCATTTTTTTTCCCGCCCCAAAAAAACCGCCGTTCTCTCCag                                                                                                                                 <  2:688152/140‑1 (MQ=255)                            ccAGCCGCGGCCTTTTGTCGGCGCCCCCGGTGATCCTTTTCCCCC‑AACACCCGCTATTTTACCCACCGCG‑ATGGAAAAAAATGCTTCCGC‑GGCGGCTGTCCGCCAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                                            <  2:636503/149‑1 (MQ=255)                            ccAGCCGCAAACTTGTGCCAGGGCCTCCGGTGTTTCTTTCCCGCA‑AAAACCCGCGCATTTA‑CCAACCCCGGTGTGAAAAAATCCCTCCGC‑GGCGGCTGTCTGCAAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCagtagt                                                                                                                             <  1:548180/148‑1 (MQ=255)                              aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                        >  1:811073/1‑151 (MQ=255)                                    aGACCTGTGTCCGCGGCTACCGTGTTTCATTCCCGCC‑AACACCCGCGCTTTTACCCAACCCC‑TTTTAAAAAATTGCCTCCGC‑GGCGGTTGTCTGCCGGCTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgg‑gg                                                                                                                     <  1:829976/147‑1 (MQ=255)                                    aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg‑gg                                                                                                                     >  1:547509/1‑147 (MQ=255)                                     gccttgttTCGGCGGCTCCCGTGTTTCTTTTCCGCA‑ACCACCCGCGATTTTATCCACCTCA‑TTGTTAAAAAGTCCCTCCGG‑GGCGCCGGTCTGCCATTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAag                                                                                                                 <  1:308815/146‑1 (MQ=255)                                      aCCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg‑gg                                                                                                                     >  2:521682/1‑145 (MQ=255)                                         ttttccggcgcCTCCCGTATTTCTTTCCCCCC‑AACACCCCCCCTTTTCCCCACCCCC‑TTGTAAAAAACTCCCTCCGC‑GGCGGTTTTCTCCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAga‑ga                                                                                                             <  2:521458/142‑1 (MQ=255)                                           tttcgggggCTACCGTTATTCTTTCCCCCA‑AACACCCGCGCTTTTCCCCACCGCA‑ATGTCAAAAAACCCCTCGGG‑GGCGGTGGTCGGCCACTTTTTTTCCCGCCACAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑Gaa                                                                                                            <  1:775326/141‑1 (MQ=255)                                           tgtCGGCGGC‑ACCGGTATTTAATTCCCCCAAACACCCGCGTATTTACCCAACCCA‑ATGTACAAAAATGCTTTGGC‑GGCGGCTGTCTGCCATTTTTTTTCCCCCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAAt                                                                                                          <  1:272983/150‑1 (MQ=255)                                            gccggCGGCTACGGTTTTTCTTCCCCCCC‑AACACCCGCCCTTTTACCCACCCCC‑ATGTGAAAAATTCCCTCCGG‑GGGGGCTGTCGGCCAGTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGc                                                                                                                    <  2:451251/136‑1 (MQ=255)                                              cAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGGGAGG‑Gaaa                                                                                                           >  2:355818/1‑146 (MQ=255)                                                   gCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGGGAGG‑Gaaaaaaattt                                                                                                    >  2:1102774/1‑141 (MQ=25)                                                    cTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑AGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGGGAGA‑Gaaaaaaactt                                                                                                    >  1:632429/1‑140 (MQ=25)                                                     tACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGAGGCAaggaacaaaaacttac                                                                                                   >  2:240183/1‑135 (MQ=25)                                                     tACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGGAGGA‑Gaaaaaaactt                                                                                                    >  2:1052696/1‑139 (MQ=255)                                                           gATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGGCAGA‑Gaaaaaaattttaaaccc                                                                                             >  1:591254/1‑133 (MQ=25)                                                             ttcttccccccc‑ATCACCCGCGCATTAATCCAACACC‑ATCTGAAAAAATG‑CTGCGCGGGCGTTTATCACCCATTTTTGTTTCCGCCCCAACAAAGCCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAG‑CTTTAAGCCCGTCAt                                                                                        <  1:704211/139‑1 (MQ=255)                                                                 ttcccGCA‑AACACCCGCGCTTTTACCCACCGCC‑ATGTAAAAAATTGCCTTGGG‑GGCGGCTGTCTGCCGGTTTTTTTCCCGCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAG‑CTTTAAGCCCGTCAtgttg                                                                                    <  1:1086462/146‑1 (MQ=255)                                                                    ccGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGGGAGA‑GAAAAAA‑AATTAAAACCGTCATGTTGTGTgg                                                                               >  2:1031655/1‑151 (MQ=25)                                                                        caaacaccCGCCCTTTAACCCACCCCC‑ATTAGCAAAATTCCCTTCGC‑GGCGGCTTTCTCCCATTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GTAATAG‑CTTTAAGCCCGTCATGTTGTGTGGc                                                                              <  2:388299/147‑1 (MQ=255)                                                                        c‑aacaaCCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GGAAAAGAATTTAGGCCCgcctggt                                                                                      >  2:475887/1‑135 (MQ=25)                                                                             acccGCGATTTTACCCACCGCC‑GTTTAAAAAAGTCCCTCCGC‑GCCGGTTTTCTCCCTGTTATTTTCCCGCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAG‑CTTTAAGCCCGTCATGTtgtg                                                                                  <  1:25973/138‑1 (MQ=255)                                                                               ccgcctttttACCCACCGCC‑ATGGAAAAAAATGCCTGCGG‑GGCGGCTGTCTCCCACTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAG‑CTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                                      <  2:97961/143‑1 (MQ=255)                                                                               ccGCGCATTTACCCACCCCA‑ATGTAAAAAAATCCCTCCGC‑GGGGGCTGTCTCCCAGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAG‑CTTTAAGCCCGTCATGTTGTGTGGCAATCgc                                                                        <  1:1093902/148‑1 (MQ=255)                                                                                  cgcTTTTACCCACCCCC‑ATGTAAAAAAATGCTTCCGC‑GGCGTTTCCCGCCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAG‑CTTTAAGCCCGTCATGTTGTGTGGCAATCgctgc                                                                     <  1:888313/148‑1 (MQ=255)                                                                                     aTTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGGGAGA‑GAAAAAA‑CATTAAAACCCTCCCGTTGTGTGGGGATCgctgcttg                                                                  >  1:16556/1‑146 (MQ=25)                                                                                           ccACCGCC‑TTGGGAAAAATTCCCTCCGC‑GGCGGCTGTTTGCCATTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAG‑CTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                                           <  1:763301/149‑1 (MQ=255)                                                                                             accccc‑ATGTGAAAAAATGCCTTCGG‑GGGGGCTGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAG‑CTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTgg                                                       <  1:291620/147‑1 (MQ=255)                                                                                                 cc‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGGAAGA‑GAAAAAA‑CTTTTAACCCCCCCTGTTGTGTGGGGATCGCCGCTgggtaaaaaatgggaa                                                    >  1:281252/1‑136 (MQ=25)                                                                                                  ccatggaaaaaaaTGCCTCCGC‑GGCGGTTGTCGCCCAGTTTTTTTCCCGCGACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAG‑CTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAg                                                   <  2:729331/143‑1 (MQ=255)                                                                                                   cgatgtaaaaaaaGCCCTCGGGGGCGGTTGTCTCCCATTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAG‑CTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAg                                                   <  2:1101658/144‑1 (MQ=255)                                                                                                     tgtgAAAAAATGCTTTCGG‑GGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAG‑CTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAggg                                                 <  1:281888/150‑1 (MQ=255)                                                                                                          aaaaaTGCCTCCGG‑GGCGGCTGTCTGCAAGTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAG‑CTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGaa                                               <  1:1047391/147‑1 (MQ=255)                                                                                                                                    ccatttttttttcCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAG‑CTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc                       <  1:240193/138‑1 (MQ=255)                                                                                                                                      cAGCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAG‑CTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa                          <  2:287126/141‑1 (MQ=255)                                                                                                                                        gCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCCAGA‑GAAAAAA‑CTTTTAACCCCGCCCGTTGTTTGGGGATTGCCGCTGGGGACAATGTGGGAAGGGGAGGGGGGGGGATAAGCTCCCAAAACgcgcccaat              >  1:1090809/1‑146 (MQ=255)                                                                                                                                          tATTTTCCTCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAG‑CTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAtt              <  2:456992/149‑1 (MQ=255)                                                                                                                                                tCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGGCAAA‑GAAAAAA‑GTTTTAGCCCCTCCTGTTGTGTGGCAATCGCTGCTGGTAAAAATGAGGGAAAGGAAGGGGGGCGGATCAGCACCCGAACCCCGCCAATTGa            >  1:1065843/1‑145 (MQ=255)                                                                                                                                                 ccgccgCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGGAAAAGGAAAAAA‑ATTTAAACCC‑CCCCGTTTTGTGGGGAACGCTTCTGGGAACAATTTGGAAAAGGGAGAGGGGGGGAACAGCTCCCCAAACGCGCCAAttttgtt         >  1:828677/1‑142 (MQ=255)                                                                                                                                                 ccgccgCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAG‑CTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGcc     <  1:684397/151‑1 (MQ=255)                                                                                                                                                     cgcAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGGAAGA‑GAAAAAA‑AATTAAACCCCCCCTGGTGTTGGGGAATCGCTGATGGGGAAAAAGTGGGAAGGGGAGGGGGGGGGAAAAGCCCCCGAACCGCGCCTATTTAGGTTGCCTcc  >  2:724914/1‑149 (MQ=255)                                                                                                                                                          |                                                                                                                                                    CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAG‑CTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCA  >  NC_000913/357740‑358034

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑