Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,873	0	C	T	45.2%	36.8 / 22.1	42	S273N (AGC→AAC)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (16/7);  new base T (0/19);  total (16/26)
Fisher's exact test for biased strand distribution p-value = 2.01e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAAT  >  NC_000913/357724‑358000                                                                                                                                                         |                                                                                                                                   cACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCt                                                                                                                                   <  2:84348/151‑1 (MQ=38)    tGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTAtt                                                                                                                                >  2:722987/1‑151 (MQ=255)     gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTAtt                                                                                                                                <  1:737238/150‑1 (MQ=255)      aaCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTAtttt                                                                                                                              >  1:1014262/1‑151 (MQ=255)      aaCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTAtttt                                                                                                                              <  2:866277/151‑1 (MQ=255)          cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑c                                                                                                                           <  1:20094/149‑1 (MQ=255)           gTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑ccgc                                                                                                                        >  2:1087905/1‑151 (MQ=255)                    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)                                                                                                                                                         |                                                                                                                                   CACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAAT  >  NC_000913/357724‑358000

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑