Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	51.2%	21.2 / 74.2	43	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (16/5);  new base A (0/22);  total (16/27)
Fisher's exact test for biased strand distribution p-value = 7.67e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.09e-06

TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGA  >  NC_000913/357741‑358024                                                                                                                                                             |                                                                                                                                         tgatgaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑Gcaac                                                                                                                                          >  2:9206/1‑150 (MQ=255) tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑Gcaac                                                                                                                                          >  1:973613/1‑150 (MQ=255)   aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTCCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACaaa                                                                                                                                       <  1:698420/151‑1 (MQ=255)     aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAAc                                                                                                                                     <  2:1119919/151‑1 (MQ=255)        cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAAccgc                                                                                                                                  <  2:1190560/151‑1 (MQ=255)              gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTtct                                                                                                                            >  2:994576/1‑151 (MQ=255)              gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTtct                                                                                                                            >  2:215575/1‑151 (MQ=255)               cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTtctc                                                                                                                           >  2:430983/1‑151 (MQ=255)                aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCA‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGGtct                                                                                                                            >  1:61430/1‑149 (MQ=255)                   aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAAACG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTcc                                                                                                                        >  2:449522/1‑150 (MQ=255)                        aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCagtagt                                                                                                                  >  1:1180567/1‑151 (MQ=255)                          tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                                >  2:412255/1‑151 (MQ=255)                                  cagcccttgtccAGCGGCT‑CCGTGATTTCTTTCCCCCC‑AACACCCC‑CCAATTTACCCACCCCCAGGTAAAAAAATC‑CCTCGGCGGGGGTTG‑TCTGCCAGTTTTTTTC‑CCCCC‑GAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                          <  2:798146/138‑1 (MQ=255)                                           tccAGCGCCTCCCGTGT‑TTCTTCCCCCCC‑AACACCCG‑CTCTTTTCCCCACCGCAATGT‑CAAAAATT‑CCCTCGGGGGCGGTT‑TCCGCCCGGTTTTTTTCCCGCC‑ACAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑Gaaa                                                                                                 <  1:1092899/146‑1 (MQ=255)                                                   gcctcccttatttctttCCCCC‑AAACACCGCCGCATTTCCCCACCGCAATGTGAAAAATTC‑CCTTGGGGGC‑GCTGTTCTCCAAGTTTTTTCC‑CCGCC‑AAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTaa                                                                                       <  1:635475/137‑1 (MQ=255)                                                   cTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGgaaa‑gaaaaaagttt                                                                                          >  2:115766/1‑140 (MQ=25)                                                      ccGTAA‑TTCATTCCCGCC‑AACACCCG‑CTCTTTTACCCACCGCCATGTGAAAAAATC‑CCTCCGGGGCGGCTT‑TCGGCCAGCTTTTTTC‑CCGCC‑GAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCg                                                                                  <  2:837788/151‑1 (MQ=255)                                                       cggggtttCATTCCCCCC‑AACACCCC‑CGCTTTTACCAACCCCCATGTCCAAAAATC‑CCTCCGGGGCGGCTG‑TCGCCCAGCTTTTTTT‑CCCCC‑GCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑tt                                                                                          <  2:425523/137‑1 (MQ=255)                                                       cccttttttctttCCCCCAAACACCCC‑CGCTTTCATCCACCCCTGTGTACAAAAATC‑CCTCCGCGGGGTTTG‑TCGCCCGGCTTTTTTC‑CCCCC‑GAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGcc                                                                                    <  1:522690/140‑1 (MQ=255)                                                                  ttcccccaaacaccCG‑CGCTTTTACCCAACCCAATTTAAAAAAACG‑CCTCCGGGGCGCTTG‑TCTCCCGTTTTTTTTC‑CCGCC‑GCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCAt                                                                              <  2:1080253/137‑1 (MQ=255)                                                                  ttcccccaaacaccCG‑CGCATTTACCCACCCCCTTGTGAAAAAATC‑CCTTCGGGGGGGCTG‑TCTGCCATTTTTTTTC‑CCGCC‑GAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCAtgt                                                                            <  2:592815/139‑1 (MQ=255)                                                                    ccGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGGAAAAACA‑TTTAACCCCgcatttt                                                                            >  2:1092883/1‑139 (MQ=25)                                                                      gCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAAAAAC‑TTTTAAccccgccttttgt                                                                         >  2:210405/1‑135 (MQ=25)                                                                            caacCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGA‑GAAAAAACATTTAAACCC‑CCCTGTTGTGTGGGGATCg                                                               >  2:894792/1‑150 (MQ=25)                                                                               acccgcgaTTTACCCAACCCCATTGTCAAAAACGCCCTCCGGGGGGGTTG‑TTTGCGACTTTTTTGC‑CCCCC‑GCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                             <  2:906168/144‑1 (MQ=255)                                                                                   cgcTTTTACCCACCGCCGTGTAAAAAAATG‑CCTCCGGGGCGGCTG‑TCTCCCATTTTTTTTC‑CCGCC‑AAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGctgctg                                                         <  1:237831/150‑1 (MQ=255)                                                                                   cgcTTTTACCCACCCCCATGGAAAAAAAGC‑CCTCCGGGGCGGCTG‑TCGCCCAGTTTTTTTC‑CCCCC‑GCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                          <  2:1134696/149‑1 (MQ=255)                                                                                              aaCGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGGAAAAAAA‑TTTAA‑CCCCCCCTGGTGTGTGGGGGTCGCCGCTGGtgaaaa                                                  >  1:1047196/1‑141 (MQ=21)                                                                                               aCGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAAA‑GGAAAAAC‑TTTTAAACCCTCCCCTTGTGTGGGGATCACTGCTGGGATCAAagt                                               >  2:1026687/1‑148 (MQ=19)                                                                                               aCGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGG‑GGAAAAAA‑TTTAAATCCGCCCACTTGTGTGGGGAACGCTGCTgggtaaaaaat                                               >  1:759344/1‑139 (MQ=19)                                                                                                cGCCTTGTGAAAAAAGG‑CCTTCGCGGCGGTTG‑TCTGCCAGTTTTTTTC‑CCGCC‑GCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaa                                           <  2:87521/151‑1 (MQ=255)                                                                                                  ccATGGGAAAAAATG‑CTGCGGCGGCGGCTG‑TC‑CCCAGTTTTTTTTCCCCCC‑GAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAg                                         <  1:486005/151‑1 (MQ=255)                                                                                                    cttgagcaaaaTGCCCTCCGCGCGGGCTG‑TCGCCCAGCT‑TTTTT‑CCGCCGGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaaa                                          <  2:238497/142‑1 (MQ=255)                                                                                                       tgCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGCGGCGGA‑GAAAAAAC‑ATTTATCCCCCCACCTTTTGTGGGGATCGCCGCTGGTGACaaaaagg                                             >  1:884031/1‑137 (MQ=255)                                                                                                          aaaaaTC‑CCTTCGCGGCGGCTT‑TCTCCCAGTTTTTTTC‑CCGCC‑CCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                                   <  1:889339/149‑1 (MQ=255)                                                                                                            aaaagcccTCCGCGGCGGCTG‑TCGGCCGGCTATTTTC‑CCGCC‑ACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcg                                <  2:1133552/145‑1 (MQ=255)                                                                                                             aaTG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGA‑GGAAAAAG‑TTTAAACCCCCCCTGTTTGGGGGGAATCACCGCTGGTGAAAAATTGGGAAggggggggggg                               >  1:1180884/1‑142 (MQ=255)                                                                                                                  ccTTCGCGGGGCCGG‑TCTCCCAGCTTTTTTC‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAAt                          <  2:973643/151‑1 (MQ=255)                                                                                                                       ggggggccTG‑TCTCCCAGTTTTTTTC‑CCCCC‑ACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                        <  2:1007016/141‑1 (MQ=255)                                                                                                                         ggcggcTG‑TCTGCCAGTTTTTTTC‑CCCCC‑GAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                        <  2:362243/146‑1 (MQ=255)                                                                                                                             gttG‑TCGGCCACCTTTTTTC‑CCCCC‑ACAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAg                 <  2:1175515/147‑1 (MQ=255)                                                                                                                                tttcgcccAGTTTTTTTC‑CCGCC‑GCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa               <  2:1179468/143‑1 (MQ=255)                                                                                                                                      ccgttttttttc‑CCGCC‑GAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcg            <  1:456846/139‑1 (MQ=255)                                                                                                                                      ccAGTTATTTTC‑CCGCC‑GCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCgcgc         <  1:693054/149‑1 (MQ=255)                                                                                                                                             ttttc‑CCCCC‑GAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGa  <  2:823825/149‑1 (MQ=255)                                                                                                                                                             |                                                                                                                                         TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGA  >  NC_000913/357741‑358024

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑