Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	52.8%	15.3 / 57.4	36	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (13/4);  new base A (0/19);  total (13/23)
Fisher's exact test for biased strand distribution p-value = 1.03e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.54e-05

ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCA  >  NC_000913/357743‑358034                                                                                                                                                        |                                                                                                                                                   aTAAGCGTAGCGCATCAGCCAATTCCAGCCGCAGACCTGTGTCAGCGGGTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGTTATTTTT‑CCGCCGcaacaa                                                                                                                                                  <  1:1198493/150‑1 (MQ=255)       gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑ccgcc                                                                                                                                          <  2:672552/151‑1 (MQ=255)              aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTtctct                                                                                                                                   >  1:823140/1‑151 (MQ=255)                cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTcc                                                                                                                                 >  2:201264/1‑151 (MQ=255)                  ggCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTcc                                                                                                                                 >  1:532118/1‑149 (MQ=255)                       ttCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTg                                                                                                                          >  2:822166/1‑151 (MQ=255)                             ccGCAGCCCTGTGTCGGCGCCTCCCGTGTTTCATTCCCCCAAACACCCGCGCTTTTACCCACCGCCATGTGAAAAAAT‑G‑CCTCC‑GCGGCGGCTGTCTGCCAGTTATTTTC‑CCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                    <  2:268130/151‑1 (MQ=255)                               gCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                    >  2:985575/1‑149 (MQ=255)                                cAGACCTGTTTCAGCGGCTCCCGTTTTTCTTTCCCCCCAACACCCCCGCTTTTATCCACCCCCTTGTGAAAAAAT‑G‑CCTTC‑GGGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                                   <  2:571533/149‑1 (MQ=255)                                   aCCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCggggggaggg                                                                                                              >  1:153783/1‑145 (MQ=255)                                      tgtgTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGA‑Gaa                                                                                                           >  2:870932/1‑150 (MQ=255)                                          tcggCGGCTCCCGTGATTCTTTCCCGCCACCACCCGCGCTTTTACCCAACGCCTTGTGAAAAAAT‑G‑CCTCG‑GGGGCGGCTGTCTGCCATTTTTTTTC‑CCGCCCAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATa                                                                                                        <  2:708748/146‑1 (MQ=255)                                            aGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGA‑Gaaaaa                                                                                                        >  2:737081/1‑145 (MQ=255)                                               gccccccGTTATTCTTTCCCCCCAACACCCGCCCATTTACCCACCGCCATG‑GCAAAAAA‑GCCCTCC‑GCGGCGGCTGTCGCCCAGTTTTTTTC‑CCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATa                                                                                                        <  1:1199398/139‑1 (MQ=255)                                                  tACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGG‑Gaaaaaaaatttaaac                                                                                              >  2:99090/1‑139 (MQ=25)                                                    cgttatttaaTTCCCGCCAACACCCGCGCTTTTCCCCACCTCTTTGTAAAAAATC‑G‑CTTTG‑GGGCCGGTTTTCCCCCGGCT‑TTTTT‑CCCCCGAAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTa                                                                                                  <  1:1145831/136‑1 (MQ=255)                                                    ccGTAATTCATTCCCCCCAACACCCGCGCATTTACCCAACGCCATGTGAAAAAAT‑C‑CCTCC‑GGGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCg                                                                                            <  2:292263/151‑1 (MQ=255)                                                      gTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCGCGACGAAAAAGCTTTAAAccacc                                                                                           >  2:951018/1‑148 (MQ=25)                                                          ttCTTTCCCCCCAACACCCCCGCATTTACCCACCGCCTTGTAAAAAAAT‑G‑CCTTC‑GCGGCGGTTGTCTGCCAGTTTTTTTC‑CCGCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGcc                                                                                              <  1:1117506/143‑1 (MQ=255)                                                            cATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGA‑GAAAAAAATTTAAAcccccccccgt                                                                                     >  1:754086/1‑142 (MQ=25)                                                              ttcccccaaacaccCGCGATTTTCGCCACCCCCATGT‑CAAAAATGG‑CCTCG‑GCGGCGGCTTTCGCCGAGTTTTTTTC‑CCGCCGAAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCAtgtt                                                                                     <  2:728455/140‑1 (MQ=255)                                                                cccccaaacaccCGCGCTTTTATCCAACCCCTTG‑GCAAAAAA‑GCCCTTC‑GCGGCGGCTGTCTCCCAGTTTTTTTC‑CCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                                <  2:410661/145‑1 (MQ=255)                                                                cccGCCAACACCCGCCCTTTCCCCCACCCCCATGTAAAAAACC‑C‑CCTTC‑GGGGCGGCTGTCCGCAAGTTTTTTTT‑CCGCAGAAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGccc                                                                                             <  1:56813/137‑1 (MQ=255)                                                                      acaacccGCCCTTTTACCCACCCCCATGTAAAAAAAT‑C‑CCTCC‑GGGGCGGTTGTCTCCCAGTTTTTTTC‑CCGCCCCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                                          <  2:131576/146‑1 (MQ=255)                                                                         acccccgcTTTTACCCACCGCCTTTTGAAAAATT‑G‑CCTCC‑GGGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg                                                                         <  2:1035824/144‑1 (MQ=255)                                                                          cccgctctttcccccACCGCAATGTAAAAAAAG‑G‑CCTGC‑GCGGGGGTTGTCGGCGAGTTTTTTTC‑CCGCCGAAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                                       <  1:397720/137‑1 (MQ=255)                                                                                cATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGCAAA‑GAAAAAAAGTTTAACCCCCCATGTTTTGTggggataggt                                                                       >  1:820411/1‑136 (MQ=25)                                                                                          aCGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGA‑GAAAAAACTTTTAAACCGCCCTTTTTTGGGGGAATCGCTGCCGGGTAAAATGTgg                                                       >  2:1145543/1‑150 (MQ=25)                                                                                             ccttgtgAAAAATT‑G‑CCTCC‑GGGGGGGTTGTCTCCAAGTTTTTTTC‑CCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAg                                                   <  1:805939/148‑1 (MQ=255)                                                                                              aaggtcaaaaatT‑G‑CCTCG‑GGGGCGTCTTTCGGCCGTCTTTTTTC‑CCCCCGCAAAAAAG‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAgg                                                  <  2:972581/144‑1 (MQ=255)                                                                                                    aaaaatT‑G‑CTTTC‑GGGGCGGCTGTCTCCCAGTTTTTTTC‑CCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                                             <  2:1024505/149‑1 (MQ=255)                                                                                                     aaaaaT‑C‑CCTGC‑GGGGGGGTTTTC‑GCCAGTTTTTTTTCCCGCCACAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGa                                                <  1:915469/146‑1 (MQ=255)                                                                                                     aaaaaT‑‑‑CCTTCGGCGGGGGCTGTCGCCCAGTTTTTTTC‑CCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGaa                                               <  2:591194/147‑1 (MQ=255)                                                                                                     aaaaaG‑C‑CCTCC‑GGGGCGGCTGTCGCCCAGTTTTTTTC‑CCGCCCAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTg                                            <  2:1203386/150‑1 (MQ=255)                                                                                                                ttC‑GCGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAAt                                    <  2:50346/149‑1 (MQ=255)                                                                                                                                             tcgcccccaaccaaAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc        <  2:205088/139‑1 (MQ=255)                                                                                                                                                cgccgaAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc        <  2:153785/147‑1 (MQ=255)                                                                                                                                                  ccccaaaaaAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCa  <  2:1078424/148‑1 (MQ=255)                                                                                                                                                   cgcAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCa  <  1:201261/150‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                                   ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCA  >  NC_000913/357743‑358034

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: ‑