Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	44.0%	20.2 / 13.5	25	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (13/1);  new base A (0/11);  total (13/12)
Fisher's exact test for biased strand distribution p-value = 2.69e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTG‑TGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCA  >  NC_000913/357740‑358034                                                                                                                                                        |                                                                                                                                                    cTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                                                     >  2:665833/1‑151 (MQ=255)     tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTCCCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa                                                                                                                                                   >  2:343584/1‑149 (MQ=255)                 aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctct                                                                                                                                     >  1:226266/1‑151 (MQ=255)                  tCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctctc                                                                                                                                    >  2:124125/1‑151 (MQ=255)                   cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                                   >  1:183695/1‑151 (MQ=255)                                ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gggg                                                                                                                     >  1:391880/1‑151 (MQ=255)                                                  gcctccgttttttCTTTCCCGCAAACACCCGCCCTTTTATCCACCGCAATGTGAAAAATTCCTTT‑CGCGGCGGCTGTCGGCCATCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTTa                                                                                                   <  2:194304/139‑1 (MQ=255)                                                    cTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGCAGTTGC‑GGGGCagtataaaaaggt                                                                                                       >  2:291037/1‑133 (MQ=25)                                                          tGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGA‑Gaaaaaaattttaaccc                                                                                              >  2:1295261/1‑134 (MQ=25)                                                                 ttcccccaaacaccCGCGCTTTTACCCACCGCCATGTAAAAAAAGCCCTC‑CGGGGGGGCTGTCGGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTTAAGCCCGTCAtgtt                                                                                      <  2:1037944/140‑1 (MQ=255)                                                                   tCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGGAAAAAGTTTTAAGCCCGCCAggtgt                                                                                     >  2:751547/1‑146 (MQ=25)                                                                        caacaaCCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGG‑GAAAAAAAATTAAACCCGGCCAGGTGTG‑Tgg                                                                               >  1:96808/1‑147 (MQ=25)                                                                                    aTTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGA‑GAAAAAAAATTAAAACCCCCATGTTTTG‑TGGGGATCg                                                                         >  2:85491/1‑141 (MQ=25)                                                                                     tttccccAACCCCGTGTAAAAAAATCCCTC‑GGGGGCGCCTGTCTGCCGGTTTTTTTCCCGCCACAAAAAAGCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTG‑TGGCAATCGCTGCTGGTa                                                                <  1:810775/144‑1 (MQ=255)                                                                                     tttACCCACCCCCTTGAGCAAAATTGCTTC‑CGGGGCGGTTCCCGGCGATCTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTG‑TGGCAATCGCTGCTGGTa                                                                <  1:764871/149‑1 (MQ=255)                                                                                                ccATGTAAAAAAATCCCTC‑CGGGGCGCTTGTCTCCCGGTTTTTTTCCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTG‑TGGCAATCGCTGCTGGTAACAATGTGGa                                                      <  1:641404/148‑1 (MQ=255)                                                                                                     tcaaaaaaGGCCTG‑CGGGGCGGCTGTCTCCCAGTTTTTTTCCCCCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTG‑TGGCAATCGCTGCTGGTAACAATGTGGAAAgg                                                  <  2:308274/144‑1 (MQ=255)                                                                                                        aaaaaTCCCTC‑CGGGGGGGCTGCCTCCCAGTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTG‑TGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                                           <  2:293865/151‑1 (MQ=255)                                                                                                         aaaaCGCCTTCCGCGGCGCCGGTCTCCAAGTTTTTTTCCCGCCCAAAAAAAGCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTG‑TGGCAATCGCTGCTGGTAACAATGTGGAAAGGGaa                                               <  2:361575/147‑1 (MQ=255)                                                                                                               ccTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCGAGAGGAAAAAATTTTAAACCC‑TCATGTTTTG‑TGGGGGTCGCTGGCGGTGACAAAGAGGAGAgggggaggggg                                         >  2:777483/1‑138 (MQ=255)                                                                                                                cTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCGAGA‑GAAAAAAATTTTATACCGCCCCTTTGTGTTGGCAA‑AGCCGGTGGGAACAAAATGGAAAGGGAAgggggg                                         >  1:505318/1‑140 (MQ=255)                                                                                                                     gcggcgGCTGTCTGCAAGTTTTTTTCCCCCCAAAAAAAAGCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTG‑TGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc                                   <  1:1173697/147‑1 (MQ=255)                                                                                                                       ggcggtTGTCGCCCTGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTG‑TGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggc                                        <  1:1295191/140‑1 (MQ=255)                                                                                                                               tctcccattttttttcCCCCCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTG‑TGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc                                   <  2:1298199/126‑1 (MQ=255)                                                                                                                                   ccAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGGG‑GAAAAAACTTTAA‑CCCCCCCTGTTTTG‑TGGGGATCGCTGCTGGGGAAAAAGTGGGAAGGGGAGGGGGGGGGAACAAATCCCGAACcgccc                   >  2:117014/1‑147 (MQ=255)                                                                                                                                         ttttgtcggcccaaccaaAGCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTG‑TGGCAATCGCTGCTGGTAACAATGTGGAAAGTGAATTGCGGCGAATCAGCTCCAGAACCGCGCTAACTGa            <  1:1071812/135‑1 (MQ=255)                                                                                                                                          tttttCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAAGA‑GAAAAAACTTTTAACCCCCCCTGTTGTG‑TGGGGAACGCTGCTGGTGACAAAGTGGGAAGGGGAGGGGGGGGGAACAACTCCACAACCGCGCTCAtt              >  2:405047/1‑147 (MQ=255)                                                                                                                                                  ccgcAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTG‑TGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCa  <  2:391898/151‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                                    CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTG‑TGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCA  >  NC_000913/357740‑358034

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: ‑