Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	52.5%	27.8 / 59.8	40	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (16/3);  new base C (0/21);  total (16/24)
Fisher's exact test for biased strand distribution p-value = 1.54e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.16e-07

CTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTT‑CC‑GCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTT  >  NC_000913/357731‑358027                                                                                                                                                         |                                                                                                                                                         cTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTT‑c                                                                                                                                                        <  2:834693/151‑1 (MQ=255)       ggCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTT‑cc‑gccg                                                                                                                                                  >  2:1009380/1‑150 (MQ=255)       ggCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTT‑ATCCAACGCCATGGGCAAAAATGCCTT‑CGCGGCGG‑CTGACTGCCAGCTATTTTT‑cc‑gccg                                                                                                                                                  >  2:91126/1‑150 (MQ=255)            gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTT‑CC‑GCCGcaacaa                                                                                                                                            >  1:1183309/1‑151 (MQ=255)            gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTT‑CC‑GCCGcaacaa                                                                                                                                            >  1:427360/1‑151 (MQ=255)            gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CCGTCTGCCAGCTATTTTT‑CC‑GCCGccacaa                                                                                                                                            >  2:1144031/1‑151 (MQ=255)                 gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CCGTCTGCCAGCTATTTTT‑CC‑GCCGCAACAAAA‑ccg                                                                                                                                      >  1:1107996/1‑151 (MQ=255)                  cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTT‑CC‑GCCGCAACAAAA‑ccg                                                                                                                                      >  1:649031/1‑150 (MQ=255)                  cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTT‑CC‑GCCGCAACAAAA‑cc                                                                                                                                       <  2:473096/149‑1 (MQ=255)                             aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCAGCCAACAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTT‑CC‑GCCGCAACAAAA‑CCGCCGTTCTCTCCa                                                                                                                          >  2:790800/1‑151 (MQ=255)                                cattcccACCCGCGGCCCTGTGCCGGCGGCTCCGGTGATTCATTCCCCCCAACACCCGCGCTTTT‑ACCCAACGCCATGTACAAAAATGCCTC‑CGGGGGGG‑CTGTCTGCCAGTTTTTTTC‑CC‑CCCGCAAAAAAA‑CCGCCGTTCTCTCCagt                                                                                                                        <  1:1030122/145‑1 (MQ=255)                                 attcccgcccGCAGCCTTGTGCCAGGGGCTCCCGTGTTTCTTTCCCCCCAACACCCCCGCTTTT‑ACCCACCCCCATGTAAAAAAATCCCTT‑CGGGGCGG‑CTGTCTGCCAGCTTTTTTC‑CC‑GCCGAAAAAAAA‑CCGCCGTTCTCTCCagtag                                                                                                                      <  1:662385/143‑1 (MQ=255)                                 attcccACCCGCAGCCCTGTTTCAGCGTTTACTTTGATTCTTTTCCCCCACCACCCGCACTTTT‑ACCCACCGCATTGTAAAAAACTGCCTT‑CGCGGCGG‑CTCTCCCCCATTTTTTTTC‑CC‑GCCACAAAAAAT‑CCGCCGTTCTCTCCagtag                                                                                                                      <  1:1029596/147‑1 (MQ=255)                                 aatcccgcccGCAGCCTTGTGTCGGCGGTTCCGGTGATTCATCCCCCCCACCACCCGCGCATTC‑ACCCACCGCATGGTCCAAAAATCCCTC‑CGGGGCGG‑CGTTCGGCAGGTTATTTTC‑CC‑GCCGAAAAAAAA‑CCGCCGTTCTCTCCagtag                                                                                                                      <  2:504382/143‑1 (MQ=255)                                    tCCACCCGAACACCTTTGCCAGGGGCAACGGTGATTCTTCCCCGCCAACACCCCCTCTTTT‑ACCAAACCCTTTGGGAAAAAATCCCTT‑CGCGCGGG‑TTGCCGCCCAGTTTTTTTC‑CC‑GCCGAAACAAAT‑CCGCCGTTCTCTCCAGTAGTgg                                                                                                                   <  1:249399/151‑1 (MQ=255)                                        gCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTT‑CC‑GCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑gg‑g                                                                                                             >  2:706675/1‑151 (MQ=255)                                              gACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTT‑CC‑GCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑gg‑ggggaga                                                                                                       >  1:1095112/1‑146 (MQ=255)                                               cccTGTGCCGGCGCCTACCGGGATTCATTCCCGCCACCACCCGCGCATTA‑CCCCAACGCCATGTGAAAAAATCCCTT‑CGGGGCGG‑CTGTCCGCCAGTTTTTTTC‑CC‑CCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAagag                                                                                                      <  1:394553/150‑1 (MQ=255)                                                 ctgggctaggcgCTACCGTGATTTCATTCCCCCCACCACCCCGCATTTAACCCAACCCCTTGT‑AAAAAATGCCGT‑CGGGGGGGTGGGTCTCCGGGATTTTTTC‑CC‑GCCG‑AACAAAACCCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAgaga                                                                                                     <  2:90736/140‑1 (MQ=255)                                                   gtgtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTT‑CC‑GCCGCAACAAAA‑CCGCCGTTCTCTCCagtag                                                                                                                      >  1:276445/1‑133 (MQ=255)                                                   gtgtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTT‑CC‑GCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑gg‑ggggaggggaaa                                                                                                  >  1:582705/1‑141 (MQ=255)                                                               aCCGTGATTCATTTCCGCCAACAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTT‑CC‑GCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGTGGCACGGGAAAAAACTTAAAGc                                                                                        >  2:96336/1‑150 (MQ=25)                                                                     aTTCTTTCCCCCCAACACCCGCGAATTT‑ACCCACCCCCTTGTGAAAAAATCCTTT‑CGGGGGGT‑TTGTCTGCCAGTTTTTTTC‑CC‑GCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCAtg                                                                                <  1:803667/151‑1 (MQ=255)                                                                          tccccGCCAACACCCGCGCTTTT‑CCCCACCCCCTTGTAAAAAAGTGCCTT‑CGGGGCGG‑CTTTCTGCCGTTTTTTTTC‑CC‑GCCAAAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCAtgttg                                                                             <  2:913714/146‑1 (MQ=255)                                                                               gCCAACAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTT‑CC‑GCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGGAAGGGAAAAAACATTAAAACCCCCCTGTTTTGTgggg                                                                      >  1:583975/1‑149 (MQ=25)                                                                                              ttt‑ACCCACCGCCATGTAAAAAAATGCCTC‑CGGGGCGG‑CTGTCTCCCAGCTATTTTC‑CC‑CCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAc                                                       <  1:915217/151‑1 (MQ=255)                                                                                              ttt‑ACCCACCGCCATGCGAAAAAGTCCCCT‑GGCGGCGG‑CTGTCGCCCAGTTATTTTC‑CC‑GCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAc                                                       <  2:246797/151‑1 (MQ=255)                                                                                              ttt‑ACCCACCCCCTTGTGAAAAACTCCTTC‑CGCGGCGC‑CTTTCTGCCAGTTTTTTTC‑CC‑CCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAc                                                       <  1:707009/151‑1 (MQ=255)                                                                                                  aTCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTT‑CC‑GCCGCAACAAAA‑CCGCCGTTCTCTCCAGAAGTGGC‑GG‑GGGGAGAGAAAAAACTTTTAAACCCCCCTGTTGTGGGGGGAACGCTTCTggggaaaaa                                                    >  1:67099/1‑144 (MQ=21)                                                                                                       accccATGTGAAAAAAGCCCTG‑CGGGGCGG‑TTGCCTGCAATGTTTTTTC‑CC‑GCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGa                                               <  1:304211/148‑1 (MQ=255)                                                                                                          catggcaaaaaaaTCCCTC‑CGCGCGGG‑CTGCCGGCCGCTTATTTTC‑CC‑GCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAg                                            <  2:248786/143‑1 (MQ=255)                                                                                                           tgtgtgAAAAAGTGCCTG‑GGCGGCGT‑TTTTTTGCCACCTTTTTTC‑CC‑CCGGAAACAAAC‑CCGCCGCTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAgg                                           <  1:665149/149‑1 (MQ=255)                                                                                                             tggcaaaaaaTCCTTT‑CGGGGCGC‑CTTTCTCCAAGCTTTTTTC‑CC‑GCCGAAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGa                                         <  2:1182750/146‑1 (MQ=255)                                                                                                              tttcAAAAATTCCTTCCGCGGGGC‑TTGTCT‑CCCGCTTTTTTTCCC‑CCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGa                                         <  1:748882/148‑1 (MQ=255)                                                                                                                 cAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTT‑CC‑GCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGG‑GGCAAGGAAAAAAACTTTAAACCCCCCCTGTTTGGGGGGAATGCCTGCGGGGAAAAAAGGGGAAAGGGAAgg                                      >  1:405331/1‑150 (MQ=255)                                                                                                                        cccTC‑CGCGGCGG‑CTTTCGGCCACCTTTTTTC‑CC‑GCCACAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGa                               <  1:788099/149‑1 (MQ=255)                                                                                                                                       ttgtcgcccAGTTTTTTTC‑CC‑GCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc                 <  1:991576/144‑1 (MQ=255)                                                                                                                                       ctttctcccattttttttc‑CC‑GCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc                 <  1:234796/137‑1 (MQ=255)                                                                                                                                        ctgcctcccggttttttt‑CCGGCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc                 <  2:487519/138‑1 (MQ=255)                                                                                                                                            tGCCAGTTTTTTTC‑CC‑CCCCCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCgcgc            <  1:315250/151‑1 (MQ=255)                                                                                                                                                  ttATTTTC‑CC‑GCAGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg      <  2:115815/150‑1 (MQ=255)                                                                                                                                                  cttttttc‑CC‑GCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg      <  1:1144561/148‑1 (MQ=255)                                                                                                                                                  cTATTTTC‑CC‑GCCGAAAAAAAG‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg      <  2:885148/151‑1 (MQ=255)                                                                                                                                                    tttttc‑CC‑GCCCCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAg    <  1:246425/150‑1 (MQ=255)                                                                                                                                                      tttc‑CC‑GCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGtt  <  1:46896/151‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                                         CTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTT‑CC‑GCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GG‑GGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTT  >  NC_000913/357731‑358027

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑