Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	64.7%	‑6.3 / 17.4	17	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (5/1);  new base A (0/11);  total (5/12)
Fisher's exact test for biased strand distribution p-value = 9.70e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.63e-03

AAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCC  >  NC_000913/357745‑358031                                                                                                                                                   |                                                                                                                                              aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCTGCTCCCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGCCTGTCTGCCAGCTATTTTTCCGCCGCCACAAAAc                                                                                                                                          <  2:527067/151‑1 (MQ=255)                  cAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCag                                                                                                                           >  2:52717/1‑149 (MQ=255)                         aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                  >  2:202717/1‑151 (MQ=255)                              cAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                >  2:343802/1‑148 (MQ=255)                                             gcctcccGTTATTCTTTC‑CCGCCAACACCCGCGCATTTCCCCACCGCCAGGTAAAAAATTGCCTGCGCGGCGGTTGTCTGCAAGCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTa                                                                                               <  1:520115/145‑1 (MQ=255)                                              ggcttcGTTATTTATTTCCCGCCAACACCCCCTCTTTTTTCCACCACCTGGTAAAAAATTGCCTCCGGGGCGGTTTTTTGCCGGTTTTTTCCCCCCCTAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTaa                                                                                              <  2:235619/146‑1 (MQ=255)                                               ctcccgtttttCTTTC‑CCGCAAACACCCGCGCTTTTACCAACCGCCAGGTCAAAAAATGCTTTGGGGGGGGCTGTCTGCCATTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                                            <  2:281447/126‑1 (MQ=255)                                                  ccGTGTTTCATTC‑CCGCCAACAACCGCGCTTTTACCCACCCCCATGTCAAAAAATCCCTCCGGGGCGGCTGCCTCCCAGTTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTaa                                                                                              <  1:399157/146‑1 (MQ=255)                                                                     aacaccCGCGCATTTACCCACCGCCATGGAAAAAAATCCCTCGGCGGGGGCTGTCCGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                                       <  1:519726/151‑1 (MQ=255)                                                                     aacaacCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGCGAGAAAAAACATTAAAACCGCCCTGTTGTGTggggagg                                                                       >  1:74712/1‑146 (MQ=25)                                                                                            ccATGTAAAAAAGGGCCTCCGCGGCGTCTTTCTGCCAGCTATTTTCCCCCCGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaaa                                                 <  2:134170/150‑1 (MQ=255)                                                                                                                  ggcgcctgccgcccAGTTTTTTTCCCCCCACAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                               <  1:451947/134‑1 (MQ=255)                                                                                                                        tGTCTCCGAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCa                         <  1:266400/146‑1 (MQ=255)                                                                                                                         gccccccAGATGTTTTTCCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc                     <  2:45924/144‑1 (MQ=255)                                                                                                                                     tttttCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAAAGAAAAAAATTTTAACCCGTCTTGTTGTGTGGGAAAAGCCGCTGGGGACAATGTGGGAAGGGGAGGGGGGGGGAACAGCCCCCGAACCccgcccatt           >  2:150347/1‑142 (MQ=255)                                                                                                                                     ttttcCCGCCAAAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAg        <  1:244621/150‑1 (MQ=255)                                                                                                                                          ccgccgAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGcc  <  1:377620/151‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                              AAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCC  >  NC_000913/357745‑358031

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑