Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	55.6%	16.4 / 60.6	45	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (14/6);  new base A (0/25);  total (14/31)
Fisher's exact test for biased strand distribution p-value = 2.32e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-06

TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGAC  >  NC_000913/357741‑358039                                                                                                                                                            |                                                                                                                                                        tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGcaac                                                                                                                                                         >  1:265116/1‑150 (MQ=255)  gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGcaaca                                                                                                                                                        >  1:546346/1‑150 (MQ=255)      aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                                   <  1:360636/151‑1 (MQ=255)        cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGCAACAAAAccgc                                                                                                                                                 <  2:680720/151‑1 (MQ=255)                       aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                                    >  2:261568/1‑149 (MQ=255)                       aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                                    >  1:86990/1‑149 (MQ=255)                        aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtagt                                                                                                                                 >  2:866926/1‑151 (MQ=255)                           ccggCCGCAGACCTGTGTCGGCGGCTACCGTGATTCATTCCCGCC‑AACACCCGCGCATTTACCC‑AACGCC‑ATGTAAAAAAATGCCTTGGGGGCGGCTG‑T‑CTGCAA‑GTTATTTTTCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                                                <  2:305113/146‑1 (MQ=21)                           cccgCCGAAAACGTGTGTCGGCGGCTACTGTATTTCTTTCCCCCC‑AACACCCGCGCATTTCCCC‑ACCCCC‑TTGTCAAAAAGTGCTTGCGCGGCGGCTG‑T‑CTGCCA‑GTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                                                <  2:466144/146‑1 (MQ=255)                            cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑g                                                                                                                            >  1:1004116/1‑151 (MQ=255)                               ccGCAGCCTTGTGTCGGCGGCTCCCGTGTTTCTTTCCCCCC‑AACACCCGCGCTTTTACCC‑AACGCA‑ATGTGAAAAAATGCCTCCGGGGCGGTTG‑T‑CTGCCA‑GTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑g                                                                                                                            <  2:982347/148‑1 (MQ=255)                               ccGCAGCCTTGTGCCGGGGGCTCCCGTGTTTCTTTCCCCCC‑ACCACCCGCGCATTTACCC‑ACCCCA‑TTGTCCAAAAATCCCTTCGGGGCGGCTG‑T‑CTCCCA‑GCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑g                                                                                                                            <  2:677825/148‑1 (MQ=255)                                  caggcgtgtgtgAGCGGCCACTGTGATACTTTCCCCCC‑ACCACCCGCGCATTTGCCC‑AACCCC‑ATGAAAAAAAAGCCCTTCGGGCCGGCGG‑T‑CGGCCA‑CCTTTTTTCCCGCCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGC‑gggg                                                                                                                         <  2:1005362/142‑1 (MQ=255)                                  cAGACGTGTGTCGGCGGCTCCCGTGATTCATTCCCCCC‑AACACCCGCGCTTTTACCC‑AACGCC‑AGTTAAAAAAATCCCTCCGCGGGGGCTT‑T‑CTCCCA‑GTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGc                                                                                                                        <  2:1096696/149‑1 (MQ=255)                                   aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gggg                                                                                                                         >  2:227735/1‑147 (MQ=255)                                   aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGcg                                                                                                                       >  1:80429/1‑148 (MQ=255)                                     aCCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gggggca                                                                                                                      >  1:637062/1‑145 (MQ=255)                                         gtgtCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAAGAGaa                                                                                                                 >  2:1133716/1‑150 (MQ=255)                                         gtgtCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGaaa                                                                                                                >  2:1143057/1‑150 (MQ=255)                                         gtgccggCGGCTACCGTGTTTCTTTCCCCCC‑AACACCCCCGCTTTTACCC‑ACCCCC‑ATGGAAAAAAATGCTTCCGCGGCGCCGG‑T‑CTGCCA‑GTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGaaa                                                                                                                <  2:513532/144‑1 (MQ=255)                                         ggttcggCGGCTACCGTGATTCATTCCCGCA‑AACACCCGCGCTTTTACCC‑AACCCC‑ATGTGAAAAAATGCCTTCGCGGCGGTTG‑T‑CGCCCA‑GTTTTTTTCCCCCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAgaga                                                                                                                  <  2:492705/142‑1 (MQ=18)                                                      cggtgtTTCATTCCCCCC‑AACACCCGCGCATTTACCC‑AACGCC‑TTGTGAAAAAATGCCTCCGCGGCGGCTG‑T‑CTGCCA‑GCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGccc                                                                                                   <  2:98224/148‑1 (MQ=255)                                                      cggtatttCTTTCCCGCC‑AACACCCGCCTTTTTACCC‑ACCGCC‑AGGTGAAAAATTCCCTCCGGGGC‑GCTGTT‑CTCCCA‑GCTTTTTTCCCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGccc                                                                                                   <  2:546852/144‑1 (MQ=255)                                                      ccgtatttCTTTCCCGCC‑AACACCCGCGCATTTA‑CC‑AACCCCGATTTAAAAAAGTCCCTCCGCGGCGGCTG‑‑‑CCGCCAGGTTATTTTCCCCCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGccc                                                                                                   <  2:1148997/144‑1 (MQ=255)                                                             ttctttCCCCCAAACACCCGCGCTTTTACCC‑ACCGCC‑ATGTCAAAAAATCCTTGCGGGGCGGCTG‑T‑CTGCCA‑TTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTc                                                                                                <  2:812217/144‑1 (MQ=255)                                                                ttcccccc‑AACACCCGCGCTTTTACCC‑ACCGCC‑ATGGGAAAAATTCCCTTCGCGGCGGCTG‑T‑CTGCCA‑GTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttgt                                                                                         <  2:753150/144‑1 (MQ=255)                                                                  cccccc‑AACACCCGCGCTTTTCCCC‑AACGCC‑ATGTG‑AAAAATTCCTTCGGGGCCGCGG‑TCCTGCCA‑GTTTTTTTCCCGCCGAAAAAAATCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGcc                                                                                                    <  1:190522/133‑1 (MQ=255)                                                                   ccccc‑accaCCCGCCCTTTTACCC‑ACCCCC‑ATGTAAAAAAATCCCTCCGGGGGGGCTG‑C‑CTGCCA‑GTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTgg                                                                                     <  1:499703/148‑1 (MQ=255)                                                                    ccccaaacaccCGCCCTTTTACCA‑ACCCCC‑ATGTAAAAAAATGCTTCCGCGGCGGCTG‑T‑CTCCCA‑GCTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTgg                                                                                     <  2:997377/146‑1 (MQ=255)                                                                           acccccgctaTTTATCCAAACGCT‑TTGTGAAAAATGGCCTCCGGGGCGCTGG‑T‑CTGCTA‑TTATTTTTTCCCCCAAAAAAAAGCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAAt                                                                                 <  2:634553/140‑1 (MQ=255)                                                                                 cgcTTTTACCC‑ACCGCA‑ATGTCAAAAAATCCCTTGGCGGGGGCTT‑T‑CTCCCA‑GTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                                          <  2:403464/149‑1 (MQ=255)                                                                                    aTTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAAGAGAAAAAAATTTTAACCCCCCATGTTTTTTGGGGAACGCTGCTgg                                                                        >  2:854884/1‑148 (MQ=25)                                                                                         tCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGAAAAAAAATTTAAAACGTCACGTTTTGTGGGGATCGCTGCGGGGAGCaa                                                                  >  1:890717/1‑149 (MQ=21)                                                                                           cccaccccgagtgaaaaaaaTCCTTCCGGGGGGGCTG‑T‑CGGCCA‑GTTTTTTTCCCGCCAAAAAAAATCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                                                 <  1:573350/135‑1 (MQ=255)                                                                                               cGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAAAAGCTTTTAAACCCTCCTGTTGTGTGGGGATTGGTGCTGGGGACaa                                                                  >  2:1104637/1‑144 (MQ=37)                                                                                                          aaaaaTCCCTCCGGGGCGCCTG‑T‑CGGCCA‑GTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAggg                                                      <  1:737267/145‑1 (MQ=255)                                                                                                           aaatccccTCCGCGGGGGCTT‑T‑CTCCCT‑GTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTgcg                                               <  1:507028/145‑1 (MQ=255)                                                                                                            aaaTGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGGAAAAACATTAAACCCCCCATGTTTGGTGGGGATCGCCGCTGGTTACAAAATGGAGAAGGGagggggg                                               >  2:885772/1‑145 (MQ=255)                                                                                                                        gggggttG‑T‑CTGCCA‑GTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCAGCTc                                   <  2:1032147/144‑1 (MQ=255)                                                                                                                           ggcTT‑T‑CTGCCA‑TTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCa                                       <  2:125857/143‑1 (MQ=255)                                                                                                                                   cTGCCA‑TTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCAg                                      <  2:1017097/138‑1 (MQ=255)                                                                                                                                      ccA‑CCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCAGCTCCAGAACcg                           <  2:865144/146‑1 (MQ=255)                                                                                                                                               tttcCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGt               <  2:505388/150‑1 (MQ=255)                                                                                                                                               ttccccgccaAAAAAAAGCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGt               <  1:1128806/146‑1 (MQ=255)                                                                                                                                                 tccccccgcAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGtt              <  2:541074/144‑1 (MQ=255)                                                                                                                                                      ccgcAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCCAGGGAAAAAAATCTCAAACCCTCCACTTTTGTGGGGATCTCTGCTGGTTACCAAGGGGG‑AAGGGGAGTGGGGGGGGTCAGCCCCCGAAACccgcaccattagatc             >  1:675855/1‑134 (MQ=255)                                                                                                                                                      ccgaAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTc        <  1:868160/150‑1 (MQ=255)                                                                                                                                                           acaaAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGac  <  1:501835/151‑1 (MQ=255)                                                                                                                                                            |                                                                                                                                                        TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGAC  >  NC_000913/357741‑358039

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑