Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,934,995	+C	intergenic (‑308/‑173)	yieP ← / → BW25113_RS19520	FadR/GntR family transcriptional regulator/16S ribosomal RNA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,934,991	1	.	C	87.5%	18.5 / ‑3.7	8	intergenic (‑304/‑177)	yieP/BW25113_RS19520	FadR/GntR family transcriptional regulator/16S ribosomal RNA
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base C (5/2);  total (5/3)
Fisher's exact test for biased strand distribution p-value = 3.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGAT  >  NZ_CP009273/3934930‑3935075                                                               |                                                                                     aCTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagcaaagc                                                           <  2:274772/90‑1 (MQ=255)  cTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCg                                                          >  2:168395/1‑90 (MQ=255)            gaAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagc                                                                <  1:414186/74‑1 (MQ=255)            gaAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagc                                                                >  2:414186/1‑74 (MQ=255)                                           gggAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCa                 >  1:303455/1‑90 (MQ=255)                                             gctggCGTATTATGCACA‑CCACGCGCCGCTGAGAAAAAGCAATGCGGCCCTGCTCTTTAACAATTTATCAAACAATCTGTGTCGGCtctc              <  1:297337/86‑1 (MQ=11)                                                   gTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGa         >  1:29657/1‑90 (MQ=255)                                                          gCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGAt  >  1:361451/1‑90 (MQ=255)                                                               |                                                                                     ACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGAT  >  NZ_CP009273/3934930‑3935075

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑