Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,875	0	A	T	44.9%	67.1 / 18.7	49	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (19/8);  new base T (0/22);  total (19/30)
Fisher's exact test for biased strand distribution p-value = 1.28e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCAGCTCCAGAACCG  >  NC_000913/357727‑358014                                                                                                                                                           |                                                                                                                                              tGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTAtt                                                                                                                                             >  1:515841/1‑151 (MQ=255)    aCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTAttttt                                                                                                                                          >  2:60892/1‑151 (MQ=255)      tCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTAttttt                                                                                                                                          <  2:403400/149‑1 (MQ=255)       cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTc                                                                                                                                         <  1:850657/149‑1 (MQ=255)          aGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTccgcc                                                                                                                                     >  1:505368/1‑150 (MQ=255)            gCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGca                                                                                                                                  <  2:760577/151‑1 (MQ=255)             ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGca                                                                                                                                  >  1:81858/1‑150 (MQ=255)               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)                                                                                                                                                           |                                                                                                                                              TGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCAGCTCCAGAACCG  >  NC_000913/357727‑358014

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: ‑