Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	50.0%	42.6 / 18.0	46	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (17/6);  new base C (0/23);  total (17/29)
Fisher's exact test for biased strand distribution p-value = 1.15e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGT  >  NC_000913/357730‑358026                                                                                                                                                             |                                                                                                                                                     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)                                                                                                                                                          tttcCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGt  <  2:505388/150‑1 (MQ=255)                                                                                                                                                             |                                                                                                                                                     ACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCC‑AACGCC‑ATGTGCAAAAATGCCTTCGCGGCGGCTG‑T‑CTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGT  >  NC_000913/357730‑358026

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑