Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	44.7%	27.0 / 20.9	38	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (16/5);  new base A (0/17);  total (16/22)
Fisher's exact test for biased strand distribution p-value = 1.04e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AAC‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGA  >  NC_000913/357742‑358024                                                                                                                                                       |                                                                                                                                           gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aac‑aa                                                                                                                                         <  1:594747/151‑1 (MQ=255)       cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AAC‑AAA‑Accg                                                                                                                                   <  2:872219/150‑1 (MQ=255)         tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AAC‑AAA‑Accgcc                                                                                                                                 <  1:45474/150‑1 (MQ=255)             gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AAC‑AAA‑ACCGCCGTtc                                                                                                                             >  2:396339/1‑150 (MQ=255)               aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AAC‑AAA‑ACCGCCGTtctc                                                                                                                           >  2:417599/1‑150 (MQ=255)               aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AAC‑AAA‑ACCGCCGTtctc                                                                                                                           >  1:190922/1‑150 (MQ=255)                 cgggcattcccgcccGCAGCCCTGGTTCAGCGGCTCCCGTTTTTTTTTCCCGCAACCACCCGCCCATTTACCCACCGCTAGGTGAAAAAATCCTTC‑CGCGGCGTCTGTCGCCCATTTTTTTTCCCGCCGC‑AAC‑AAA‑ACCGCCGTTCTCTcc                                                                                                                        <  2:723090/138‑1 (MQ=255)                            aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AAC‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                             >  1:559360/1‑151 (MQ=255)                               cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AAC‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                             >  1:744489/1‑148 (MQ=255)                                   gACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AAC‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCggggg                                                                                                          >  2:145507/1‑146 (MQ=255)                                           tCAGCGGCTACGGTGTTTCTTTCCCCCCAACACCCGCGATTTCACCCACCGCCTTGTAAAAAATTGCCTT‑CGGGGCGGTTGTCTGCCAGTTATTTTCCCGCCGA‑AAA‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgag‑a                                                                                                   <  1:830295/145‑1 (MQ=255)                                            cAGCGGCTACCGGGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGAGCAAAAATGCCTT‑CGCGGAGGCTGTCTGCCAACTATTTTTCCGCCGC‑AAC‑CAA‑ACCGCCGTTACCTCCAGTAGTGGccgactttctca                                                                                                    >  2:1037042/1‑133 (MQ=255)                                             aGCGCCTCCCGTGATTAATCCCCCCCACAACCCGCACATTTAACCAACGCTTTGTGAAAAAATCCGTT‑CGCGGCGGCTTTCGGCCCGCTTTTTCCCCGCCGC‑AAA‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAAt                                                                                                <  1:389540/146‑1 (MQ=255)                                               cGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AAC‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCgggggggggggaaaaaaa                                                                                             >  2:147055/1‑134 (MQ=255)                                                   tACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCATCTATTTTTCCGCCGC‑AAC‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑aaaaaaagtt                                                                                          >  1:797924/1‑139 (MQ=25)                                                                 ccccccaccccccGCGCTTTTCCCCAACGCTAGGTACAAAATTGCCTC‑CGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGC‑AAA‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtgtt                                                                            <  2:1130441/135‑1 (MQ=255)                                                                  cccccAACACCCGCTCTTTTACCCAACCCCATGTAAAAAAGTCCCTC‑CGCGGCGGCTTTCTCCCTGTTTTTTTCCCGCCGA‑AAA‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTgg                                                                      <  2:1075760/148‑1 (MQ=255)                                                                  cccccAACACCCGCCCTTTTACCCAACGCCAGGTAAAAAAATCCCTC‑CGGGGCGGTTGTCGGCCAGTTTTTTTCCCGCCGA‑AAA‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTtgtgt                                                                        <  1:569854/146‑1 (MQ=255)                                                                  ccaccAACAACGGCGCTTTTACCAACCCCCATGTCCAAAGATGCTTC‑CGCGGCGACTTTCTGCCCGCTATTTTGCCGCCGC‑AAA‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTtgtgt                                                                        <  1:354016/146‑1 (MQ=255)                                                                      caacaaCCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AAC‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑AAAAAAAATTAATCCCCGCACGTtgtg                                                                         >  2:1240381/1‑144 (MQ=25)                                                                       aacaacCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AAC‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑AAAAAAATTTTAACCCGCCCTGTTTTGTggggc                                                                   >  2:500175/1‑146 (MQ=25)                                                                                  aTTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AAC‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGG‑AAAAAAATTTTAGTCCGCCCtgtttttgggcgaactgt                                                              >  2:618553/1‑129 (MQ=25)                                                                                              gctaggtaaaaaaGGCCTTCCGGGGGGGTTGTCTCCAATCTTTTTTCCCGCCAA‑AAA‑AAA‑CCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa                                                   <  2:1214289/135‑1 (MQ=255)                                                                                              cgttgtgCAAAAATCCCTT‑CGGGGCGGCTGTCGGCCGTTTTTTTTCCCGCCCC‑AAA‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAg                                         <  2:7706/148‑1 (MQ=255)                                                                                                       aaaaTGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AAC‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑AAAAAACTTTAAAACCCGCATGGTGTGTGGGAATCGCTGCTGGGGAGAAAGT‑GGGAAGGGGAGTggg                                >  1:459280/1‑149 (MQ=255)                                                                                                       aaaaTCCCTC‑CGCGGCGGCTTTCTGCCAGTTTTTTTCCCCCCGA‑AAC‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTgcg                                <  1:12745/151‑1 (MQ=255)                                                                                                       aaaaCGCTTG‑CGGGGCGCCTGTCCGCCAATTTTTTTCCCGCCAC‑AAA‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTgcg                                <  1:1033073/151‑1 (MQ=255)                                                                                                          atcccTG‑CGCGGCGTCTTTCTCCGATCTTTTTCCCCCCCGC‑AAA‑AAA‑GCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTgcgg                               <  1:268528/146‑1 (MQ=255)                                                                                                          aTGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AAC‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑AAAAAGCATTTAACCCGCCATGTTTTGTGGGGATCGGTGCTGGGAACAAAGT‑GGAAAAGGGAgggggggg                             >  1:594855/1‑144 (MQ=255)                                                                                                            gCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AAC‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAAATTTAATCCC‑TCCTGTTTTGTGGGGATAGCTGCTGGTGAAAAAAT‑GGGAAGGGGAgggggggg                             >  1:105834/1‑142 (MQ=255)                                                                                                               tt‑CGGGGGGGCTGTCTCCCAGTTTTTTTCCCCCCGC‑AAA‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGaacc                         <  1:1222685/150‑3 (MQ=255)                                                                                                                   gggggggcTGTCTCCCAGTTTTTTTCCCGCCGA‑AAA‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAAt                          <  1:733776/141‑1 (MQ=255)                                                                                                                           tgccgccaattttttttcCCCCCGC‑AAA‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCa                  <  2:914308/133‑1 (MQ=255)                                                                                                                                  ccagttattttCCCCCGCAAAC‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa       <  1:1244590/144‑1 (MQ=255)                                                                                                                                  cAGTTATTTTTCCGCCGC‑AAA‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc           <  1:737246/146‑1 (MQ=255)                                                                                                                                   gactttttttCGCCCCC‑AAA‑AAACACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGATCcgc           <  2:174770/141‑1 (MQ=255)                                                                                                                                    gtttttttcCCGCCAA‑AAA‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt     <  1:1074021/146‑1 (MQ=255)                                                                                                                                         ttttCCGCCGC‑AAC‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑AAAAAAATTTTAACCCCCCCTGTTTTTTGGGAAAAGCCTCTGGTAACAATGTGGGAAAGGGAAGGGGGGGGAA‑CAGCTccccaaacccgccaa      >  1:1004520/1‑131 (MQ=255)                                                                                                                                         ttttCCCCCCC‑AAAAAAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGa  <  1:1102594/149‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                           GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AAC‑AAA‑ACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGA  >  NC_000913/357742‑358024

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: ‑