Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	51.3%	10.4 / 41.0	37	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (11/7);  new base A (0/19);  total (11/26)
Fisher's exact test for biased strand distribution p-value = 3.72e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.33e-03

TAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GG‑TAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAT  >  NC_000913/357744‑358021                                                                                                                                                        |                                                                                                                                       tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAAC‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGc‑aacaa                                                                                                                                      >  1:1144381/1‑149 (MQ=255)            cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTtctc                                                                                                                         >  2:99257/1‑151 (MQ=255)              tCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTtctctc                                                                                                                       >  1:405916/1‑151 (MQ=255)               cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACACAACCGCCGTTCTCTcc                                                                                                                      >  2:1096303/1‑151 (MQ=255)                aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTcc                                                                                                                      >  1:110618/1‑150 (MQ=255)                      ttCCACCCGCAGACTTTTGTCAGCGGCTCCCGTGATTC‑TTTCCCCCAACCACCCGCCCATTTACCCAACGCCAT‑GTGAAAAAAT‑GCTTGCGCGGCGGCTGTCTCCCAGTTTTTTTT‑CCGCCGC‑AAAAAAACCGCCGTTCTCTCCagtag                                                                                                                 <  2:888654/149‑1 (MQ=255)                      ttCAAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCAGCCAA‑CAACCGCGCATTTATCAAACGCCAT‑GTGCAAAAAT‑GCCTTCGCGGCGGATGTCTGACAGCTATTTTT‑CCCCCGC‑AACAAAACCCCCGTTCTAGTCagtagt                                                                                                                >  1:841928/1‑150 (MQ=18)                            cccagccctggtgcCAGCGGCCCCCGTGATTCTTTCCCGCAAA‑CACCCGCGCTTTTACCCACCGCCAT‑GTGAAAAAAT‑GCCTCCGCGGCGGCTGTC‑GCCCGGTTTTTTT‑CCCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑ggg                                                                                                         <  1:1006787/140‑1 (MQ=255)                            ccGCAGCCCTGTTCCGGGGGCTCCCGCGATTCTTTTCCGCCAC‑CACCCCCGCATTTATCCACCCCCGT‑GCGCAAAAAT‑GCCTCGGCGGGGTCTGTCTCCCGGCTTTTTTC‑CCGCCGA‑AACAAACCCGCCGTTCTCTCCAGTAGTGGC‑gggg                                                                                                        <  2:805087/151‑1 (MQ=255)                            ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑ggg                                                                                                         >  1:704239/1‑150 (MQ=255)                                aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gggg                                                                                                        >  2:843782/1‑147 (MQ=255)                                     tgtgccggggcctcccGTAATTCTTTCCCGCCAA‑CACCCGCGCTTTTACCCAACCCCTT‑GTCAAAAAAT‑GCCTTCGGGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCaa                                                                                                     <  2:1125811/131‑1 (MQ=255)                                      gtgtCAGCGGCTCCCGTAATTCTTTCCCCCCAA‑CACCCGCCCATTTCTCCAACGCCTG‑GTGAAAAAAT‑GCTTCCGCGGCGGTTGTCTGCCAGTTTTTTTT‑CCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAAt                                                                                              <  2:634053/151‑1 (MQ=255)                                      gtgtCAGCGGCTACCGTGATTCATTCCCGCCAA‑CACCCGCGCTTTTACCCACCCCCAT‑GTGAAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTTTTTTC‑CCGCCGA‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGaa                                                                                                <  2:683260/149‑1 (MQ=21)                                        gtCAGCGGCTCCCGTGTTTCATTCCCCCAAA‑CACCCGCGCTTTTATCAAACGCCAT‑GTGAAAAAAT‑CCCTTCGGGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAaga                                                                                                   <  2:1116545/144‑1 (MQ=255)                                          cAGGGGCTCCCTTGATTCTTTCCCCCCAA‑CACCCCCTCTTTTCCCCACCCCCAG‑GTAAAAAAAT‑GCCTCCTGGGCGGCTGTCGGCC‑GCTTTTTTTCCCCCCGA‑AAAAAACCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAag                                                                                                    <  1:1095102/141‑1 (MQ=255)                                              ggCTCCCGTGATTCTTTCCCGCCAA‑CACCCGCGCTTTTACCCAACGCCAT‑GTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCttt                                                                                        <  2:1176741/149‑1 (MQ=25)                                              gcctcccGTGTTTCATTCCCCCAAC‑CACCCGCTCATTTACCCACCGCCTT‑GTAAAAAATT‑CCCTTCGCGGCGGCTGTCTGCCAGTTTTTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTaa                                                                                      <  2:686913/146‑1 (MQ=255)                                                   ccGTGATTCATTCCCGCCAA‑CACCCGCGCATTTACCCACCGCCAT‑GTGAAAAAAT‑GCCTCCGCGGCGGCTGTCTGCCAGTTATTTTC‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGc                                                                                    <  2:945958/148‑1 (MQ=37)                                                             ttcccGCCAA‑CACCCGCGCTTTTACCCACCGCCAT‑GTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTTTTTTC‑CCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttgt                                                                        <  2:701447/147‑1 (MQ=37)                                                              tccccccac‑caCCCGCGCATTTACCCACCCCCGT‑‑TGGAAAAATCCCCTCCGGGGGGCCTGTCGGCCAGTTTTTTTC‑CCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtg                                                                       <  1:126139/145‑1 (MQ=255)                                                                cccacaaacccccccgcATTTCACCAACCCCAT‑GTGAAAAATA‑TCCTCCGCGGCGCTTGTCTGCCAGTTTTTTTC‑CCGCCCC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                     <  1:1008498/137‑1 (MQ=255)                                                                   ccac‑caCCCGCGCTTTTA‑CCCACCCCATGGTAAAAAAAT‑GCCTCCGCGGCGGTTTTCTGCCATTTTTTTTC‑CCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCaa                                                                 <  1:1025789/151‑1 (MQ=255)                                                                           ccGCGCTTTTACCAAACCCCAT‑GTGAAAAAAT‑CCCTCCGGGGGGGCTGTCGGCCAGTTTTTTTC‑CCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                            <  1:854908/149‑1 (MQ=255)                                                                                  tttACCCACCGCCTT‑GTAAAAAAAG‑CCTTTCGGGGCGCTTGTCTGCCGGTTTTTTTC‑CCGCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GG‑t                                                    <  1:768967/148‑1 (MQ=255)                                                                                     aTCCAACGCCAT‑GTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGCGAGAAAAAAATTTTAAACCGCCATATTGTGTTGCGGCCGCGGCT‑GG‑GAACa                                                >  2:342821/1‑149 (MQ=21)                                                                                       ccACCGCTAG‑GTGAAAAAAT‑GCTTCCGCGGGGGCTGTCGGCCGGTTATTTTC‑CCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GG‑TAACAAt                                              <  2:240618/149‑1 (MQ=255)                                                                                             ccAT‑GTAAAAAAAT‑GCTTTCGGGGCGGCTTTCTCCCAGTTATTTTC‑CCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GG‑TAACAATGTGGAAAg                                      <  2:997690/151‑1 (MQ=255)                                                                                                 tgtaaaaaaaT‑GCCTTCGCGCCGGCTGTCTCCCACTTTTTTTC‑CCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GG‑TAACAATGTGGAAAggg                                    <  2:984566/145‑1 (MQ=255)                                                                                                   tgaaaaaaT‑CCTTTGGCGGCGGTGTTCTGCCAGTTTTTTTC‑CCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GG‑TAACAATGTGGa                                         <  1:884009/140‑1 (MQ=255)                                                                                                      aaaaaT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCCAG‑GAAAAAGATTTTAACCCGCACTGATTTGTGGGAATCGCCGCG‑GG‑GAACACTTTTGGAAggg                                    >  1:948439/1‑145 (MQ=255)                                                                                                        aaaT‑GCCTTCGGGGCGGTGGTCTGCCAGTTTTTTTT‑CCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GG‑TAACAATGTGGAAAGGGAAGTgcgg                            <  2:878293/151‑1 (MQ=255)                                                                                                             gCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCCAGAGAAAAAACTTTTAACCCCTCATGTTGTTTGGGGATCGCGGGTGGG‑GAACAAT‑TGGGGAGGGAAggggggggg                         >  2:346560/1‑142 (MQ=255)                                                                                                                ttCGGGGCGTCTGTCTGCCTGTTTTTTTC‑CCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GG‑TAACAATGTGGAAAGGGAAGTGCGGCGAAt                       <  2:606904/149‑1 (MQ=255)                                                                                                                              cTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCGAGGGAAAAAAAATTAAAACCGCCATGTTGTTGGGGGAACGCTGCT‑GGTTAAAAATGGGGAAGGGGAGGGGGGGGGAA‑CAGCTCCaaaaaccc        >  1:693010/1‑146 (MQ=255)                                                                                                                               gcctaGCTTTTTTG‑CCCCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GG‑TAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc          <  1:857341/143‑1 (MQ=255)                                                                                                                                   atttATTTTC‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GG‑TAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgcg       <  2:140199/143‑1 (MQ=255)                                                                                                                                        ttttc‑CCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GG‑TAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt  <  1:1153888/146‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                       TAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GG‑TAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAT  >  NC_000913/357744‑358021

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑