Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	50.0%	33.8 / 26.1	46	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (15/8);  new base A (0/23);  total (15/31)
Fisher's exact test for biased strand distribution p-value = 1.92e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01

ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTC  >  NC_000913/357743‑358028                                                                                                                                                           |                                                                                                                                              aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGcaacaa                                                                                                                                             <  2:1144613/150‑1 (MQ=255) aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACaaa                                                                                                                                            <  2:1054938/151‑1 (MQ=255) aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACaaa                                                                                                                                            <  1:646499/151‑1 (MQ=255)  tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACaaa                                                                                                                                            >  2:192340/1‑150 (MQ=255)      cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgc                                                                                                                                       >  1:1171240/1‑151 (MQ=255)      cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccg                                                                                                                                        <  2:1078427/150‑1 (MQ=255)         aGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGt                                                                                                                                    >  1:1037005/1‑151 (MQ=255)          gcgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgccg                                                                                                                                     <  1:768133/149‑1 (MQ=255)                cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                             >  2:408317/1‑151 (MQ=255)                  ggCATTTCCGGCCCCAGCCCTTTGTCGGCGGCTCCCGTTTTTCTTTC‑CCCCA‑AACACCCGCGCTTTTATCCAC‑CCCCA‑TGTCCAAAAATCCCTTC‑GGGGCGGCTG‑TCTCCCAGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCag                                                                                                                           <  1:1198153/151‑1 (MQ=255)                    cattcccAGCCGCAGCGTTGTGTCAGCGGCTACCGTGTTTCTTCC‑CCGCC‑AACAACCGCGCATTTATCCAC‑CGCCA‑TGTGCAAAAATGCCGTC‑GGGGCGGCTG‑TCTGCCATTTTTTTTT‑CCCCCGCAACAAAACCGCCGTtctctc                                                                                                                              <  2:1276174/141‑1 (MQ=255)                      aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCGG‑TCTGCCAGCTATTTTT‑CCACCGCAACAAAACCGCCGTTCTCTCCagta                                                                                                                         >  2:77627/1‑149 (MQ=255)                         ccccccGCAGCCTTGTGTCAGCGGCTCCCGTTTTTCATTC‑CCCCC‑ACCACCCCCCCTTTTCCCCAC‑CCCCA‑TGTAAAAAAATCCCTCC‑GCGGCGGCTG‑CCTGCAAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCagta                                                                                                                         <  2:31752/142‑1 (MQ=255)                           aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                  >  1:768704/1‑151 (MQ=255)                             ccGAAGCCCTGTGACAGCGGCT‑CCGGTATTTATTTCCCCCC‑AACACCCGCCCTTTTACCCAC‑CCCCT‑TGTGAAAAAATGCTTTC‑GGGGGGGCTG‑TCTGCCAGTTTTTTTC‑CCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                  <  1:52819/149‑1 (MQ=255)                                ctgccttgtgTCGGCGGCTTCGGTGATTCATTT‑CCGCC‑AACACCCGCTCTTTTAACCAC‑CGCTA‑TTTAAAAAACTGCCTCG‑GCGGCGCCTC‑TCTGCGATCTATTTTC‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCa                                                                                                              <  1:311717/144‑1 (MQ=255)                                    cttgtgCCAGCGGCCCCCCTGATTCTTTC‑CCCCC‑AACACCCGCGCATTTACCCAC‑CGCCA‑TGTGAAAAAATG‑CTTC‑GGGGGGGCTGTTCGGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCaa                                                                                                             <  2:1081003/145‑1 (MQ=255)                                    ccTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                 >  1:991877/1‑143 (MQ=255)                                       gtgtCGGCGCCTCCCGTGATTCTTTC‑CCCCA‑AACACCCGCGTTTTTACCCAC‑CCCCT‑TGTAAAAAAAGCCCTCC‑GCGGGGGCTG‑TCGGCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgag‑a                                                                                                        <  2:113503/148‑1 (MQ=255)                                       gtgtCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggacgtaga                                                                                                        >  2:327771/1‑141 (MQ=255)                                         gccAGCGGTTCCCGTGATTCTTTC‑CCCCC‑AAAACCCGCCCTTTTACCCAC‑CCCCT‑TGTGAAAAAAGGCTTCC‑GGGGGGGCTT‑TCTGCCAGTTTTTTTC‑CCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgag‑a                                                                                                        <  1:1242738/144‑1 (MQ=255)                                                ggctcccgtttttaTTT‑CCCCCAAACACCCGCGAATTT‑TCCAACCGCCA‑GGTAAAAAAATCCTTCC‑GGGGCGCTTG‑TCTCCCATTTTTTTTC‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                                          <  1:377618/126‑1 (MQ=255)                                                 ctcccgtttttCTTTC‑CCCCC‑ACCACCCGCCCTTTTACCCAC‑CCCCT‑TTTCAAAAAATCCTTCC‑GCGGCGGCTT‑TCTCCAAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGcggg                                                                                               <  1:408735/138‑4 (MQ=255)                                                 cTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAG‑aaaaaaa                                                                                                  >  1:300445/1‑140 (MQ=255)                                                  tACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGTGGAaggaaaaaaacattta                                                                                              >  1:632960/1‑134 (MQ=25)                                                    ccttatttCATTC‑CCGCC‑ACCACCCGCGTTTTTATCCAC‑CCCAA‑TGTGAAAAAAGGCCTGC‑GGGGCGGCTT‑TCGGCCAGCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGccc                                                                                        <  1:1034467/144‑1 (MQ=255)                                                       tttttCTTTC‑CCCCC‑ACCACCCGCTCTTTTACCAAA‑CCCTT‑TGTAAAAAAATGCCTCC‑GCGGGGGTTG‑TCT‑CCAGGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTc                                                                                     <  2:803179/147‑1 (MQ=255)                                                       tGATTCTTTC‑CCCCA‑AACACCCCCGATTTTACCCAC‑CGCAT‑TGT‑CAAAAATTCCCTCGGCGGGGGCTG‑TCGGCAAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGt                                                                                      <  2:1226909/149‑1 (MQ=255)                                                                   ccccaaacaccCGCGCTTTTACCCAC‑CCCCT‑TGTAAAAAAATGCCTTC‑GCGGCGGTTG‑TCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTtgtgtg                                                                           <  1:102361/145‑1 (MQ=255)                                                                       caaacaccccctaTTTAACCAACCGCCA‑TTTAAAAAATTCCCTCC‑GGGGCGGCTT‑TCTGCCAGTTTTTTTC‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCaa                                                                       <  1:562494/139‑1 (MQ=255)                                                                        accacccGCGCTTTTA‑CCAA‑CCCCATTGTAAAAAAAT‑CCTTCGGGGGCGGTTG‑TCTGCCGGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCaa                                                                       <  2:1279175/144‑1 (MQ=255)                                                                               gcgcATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAAAG‑AAAAAAC‑ATTAAAACCCTCCAGTTGTggggggaaag                                                                    >  1:133189/1‑139 (MQ=25)                                                                                cccttttACCCAC‑CCCCA‑TGGAAAAAAATCCTTCC‑GGGGCGGCTG‑TCTCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTgg                                                             <  1:992909/147‑1 (MQ=255)                                                                                          cccaccgcctttagaaaaaaTCCCTTC‑GCGGCGGCTG‑TCCGCCACTTTTTTTC‑CCGCCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGT‑AACAAt                                                     <  1:1711/135‑1 (MQ=255)                                                                                                         aaaaaTGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑AAAAAAC‑TTTTAACCCCTCACGTTTTGTTGGTCTCGCTCCTCGTGAACAA‑GTGGGAAGGGGAgag                                      >  2:167779/1‑148 (MQ=255)                                                                                                          aaaaTGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGCGAGAAAAAAAT‑TTTAAACCCCCCA‑GTTGTGTGGGGAACGCCGCTGGG‑GAAAAAGTGGGAAGGGGAgaggg                                    >  1:240995/1‑147 (MQ=255)                                                                                                           aaaTGCCTCG‑GGGGGGGTTT‑TCGGCCAGTTTTTTTC‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGT‑AACAATGTGGAAAGGGAAGTgcgg                                   <  1:745586/151‑1 (MQ=255)                                                                                                                      gggggggcTG‑TCGGCCGTTTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCa                            <  2:1186843/143‑1 (MQ=255)                                                                                                                      ggggcggcTG‑TCTGCCGTCTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAg                           <  2:376923/147‑1 (MQ=255)                                                                                                                        ggcggcTT‑TCTGCCACTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATc                             <  1:1227983/145‑1 (MQ=255)                                                                                                                           ggcTG‑TCGCCCAGTTATTTTC‑CCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAg                     <  1:364959/150‑1 (MQ=255)                                                                                                                              tG‑TCTGCCATTTTTTTTC‑CCGCCCCAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa                    <  2:509482/148‑1 (MQ=255)                                                                                                                                  cTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAG‑AAAAAAC‑TTTTAACCCCGCCTGTTGTGTGGGAAACGCCGCTGGG‑AAAAAAGTGGGAAGGGGAGGGGGGGGGATCAACTCCCCAAcccc               >  1:812105/1‑148 (MQ=255)                                                                                                                                       attttttttc‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTaa          <  1:1080179/145‑1 (MQ=255)                                                                                                                                               tt‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAG‑AAAAAACATTTAACCCCG‑CACGTTTTGTGGGAAACGCCGCTGGT‑AACAAAGTGGGAAGGGGAGGGGGGGGGAAAAACCCCCGAACCGCGCCAAATGAggt   >  1:413138/1‑147 (MQ=255)                                                                                                                                                  ccgccgCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc  <  1:57540/148‑1 (MQ=255)                                                                                                                                                   ccccgcAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc  <  1:60673/145‑1 (MQ=255)                                                                                                                                                           |                                                                                                                                              ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTC  >  NC_000913/357743‑358028

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: ‑