Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,873	0	C	T	42.3%	23.5 / 10.1	26	S273N (AGC→AAC)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (14/1);  new base T (0/11);  total (14/12)
Fisher's exact test for biased strand distribution p-value = 1.55e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTA  >  NC_000913/357723‑358019                                                                                                                                                       |                                                                                                                                                     gCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGc                                                                                                                                                      <  2:158509/151‑1 (MQ=255)      gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAttt                                                                                                                                                 <  2:32083/151‑1 (MQ=255)       aaCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAtttt                                                                                                                                                >  2:107611/1‑151 (MQ=255)                  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)                                                                                                                                                 gcccAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTc               <  1:617789/138‑1 (MQ=255)                                                                                                                                                   ccAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa  <  2:754633/151‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                     GCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTA  >  NC_000913/357723‑358019

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑