Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	44.8%	25.9 / 14.9	29	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (13/3);  new base A (0/13);  total (13/16)
Fisher's exact test for biased strand distribution p-value = 1.13e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAA  >  NC_000913/357740‑358035                                                                                                                                                       |                                                                                                                                                    cTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                                                     >  2:339433/1‑151 (MQ=255)         cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgc                                                                                                                                             >  2:312477/1‑151 (MQ=255)                   cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                                   >  1:204785/1‑151 (MQ=255)                        attcccAGCCGAGGACCTGGGTCAGCGGCTCCCGTGTTTCTTCCCCCCAAAAAACCGCGATTTTCTCCAACGCCTTGTCAAAAATTCCCTGCGGGGGGGTTTTCTGCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCagta                                                                                                                               <  2:10249/146‑1 (MQ=255)                        aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                                >  2:257113/1‑149 (MQ=255)                            ccgcccccagccttttgtCAGCGCCTCCCGTATTTCTTTCCCGCCAACACCCGCGATTTTCCCCACCCCCTTGTCAAAAAAGGCCTTCGGGGCGGCTGTCGCCAAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                          <  2:110041/136‑1 (MQ=255)                              aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                        >  1:222651/1‑151 (MQ=255)                                    agcccggtgtCAGCGCCACCCGTGATTCATTCCCCCAAACACCCGCGCTTTTACCCACCCCAATGTGAAAAAATGCCTTCGCGGCGGCTGTCTGCAAGTTATTTTCCCGCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                                                  <  2:544873/145‑1 (MQ=255)                                        cTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggtggat                                                                                                                   >  1:630024/1‑141 (MQ=255)                                              cAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑gaaaaa                                                                                                         >  2:647864/1‑146 (MQ=255)                                                                    ccGCCACAACCCGCGCTTTTACCCAACCCCATGTAAAAAATTGCCTCCGGGGCGGCTGTCTGCCATTTTTTTTCCCGCCGCAACAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTgg                                                                                 <  2:45479/151‑1 (MQ=255)                                                                           caacCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAG‑AAACAACTTTTATCCCCCCATGTTTTGTGGGGATCg                                                                           >  1:626781/1‑150 (MQ=25)                                                                            aacCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑AAAAAAATTTTAACCCCCCATGTTTTGTggggatc                                                                            >  2:461572/1‑143 (MQ=25)                                                                                 cgtaTTTACCCACCGCCATGAACAAAAAGCCCTCGGGGGCGGCTGTCGCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTgg                                                                    <  2:478235/148‑1 (MQ=255)                                                                                            acccccatgaaaaaaaaTCCCTGCGGGGCGTCTTCCTCCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgt                                                           <  1:70020/137‑1 (MQ=255)                                                                                            aaCGCCATGTAAAAAAATCCCTCGGGGGCGGTTGTCTGCCAGTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑gg                                                        <  2:366715/151‑1 (MQ=255)                                                                                             aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAG‑AAAAAAATTTTAAACCCCCCCGTTTTGTGGGGATCGCTGCTGGTGACAAAGT‑gg                                                        >  2:502499/1‑150 (MQ=25)                                                                                                caatttcaaaaaaTCCCTTGGGGGGGTTTGTCTGCCACTTTTTTCTCCACCCAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGaaa                                                     <  2:379688/142‑1 (MQ=255)                                                                                                    gtgCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAAAGAAAAAAACTTAAACCCCGCCTTGTT‑TGTGGGGATCGCTGCTggggaaaaaatgg                                                         >  2:485765/1‑132 (MQ=255)                                                                                                       cAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAG‑AAAAAAATTTAAACCCGCCCTGCTGTGTGGGGATCGCCGCTGGGTAAAAAGT‑GGAAAGGGAAggg                                             >  1:34173/1‑149 (MQ=255)                                                                                                        aaaaaTGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAAAATTTAAACCC‑TCCTGTTTTGTGGGAAACCCCGCTTGGTACAAAGTGGGAAAGGGagggg                                             >  2:772309/1‑147 (MQ=255)                                                                                                          aaaCGCCTCCGGGGCGGCTGTCGGCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTgcgg                                          <  1:461521/151‑1 (MQ=255)                                                                                                                         gcccttttgcactttATTTTCCCGCCACAACAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGa                           <  1:105798/137‑1 (MQ=255)                                                                                                                              attgacgcatgttttcCCTCCCCAACAAATCCGCCGTTCGCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGTTCGTCATTTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa                          <  2:642854/136‑1 (MQ=255)                                                                                                                               cggcgagttttttccccgccaAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgcg                     <  1:424972/136‑1 (MQ=255)                                                                                                                                gcccAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTc                               <  1:617789/138‑1 (MQ=255)                                                                                                                                  ccAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa                  <  2:754633/151‑1 (MQ=255)                                                                                                                                  caattttttttcCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGa                           <  2:166096/135‑1 (MQ=255)                                                                                                                                                 ccgcAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTc    <  1:726226/150‑1 (MQ=255)                                                                                                                                                   gcAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAAAG‑AAAAAACTTTAAACCCCGCCTGTTTTGTGGGGAACGCTGCTGGTGACAAAGT‑GGGAAGGGGAGGGGGGCGGAAAAACTCCAGAAACGCGCCAAATTAGTTTGCCTcca  >  2:224491/1‑148 (MQ=255)                                                                                                                                                       |                                                                                                                                                    CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAA  >  NC_000913/357740‑358035

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑