breseq  version 0.32.1  revision aa8f2595a244 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	566,245	0	G	A	47.6%	6.1 / 55.0	42	pseudogene (132/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	566,277	0	C	T	38.3%	55.7 / 59.8	60	pseudogene (100/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	566,205	0	T	C	36.6%	28.1 / 43.3	41	pseudogene (172/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	566,173	0	C	G	30.2%	70.4 / 44.4	43	pseudogene (204/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	4,296,060	0	C	T	25.9%	112.3 / 32.4	54	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*	NC_000913	566,323	0	C	T	20.4%	123.8 / 21.2	54	pseudogene (54/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4373286 =	38 (1.550)	6 (0.240)	3/184	2.4	13.6%	noncoding (90/99 nt)	RIP328 (repetitive extragenic palindromic) element, contains 2 REP sequences and 1 IHF site	RIP328 (repetitive extragenic palindromic) element, contains 2 REP sequences and 1 IHF site
	?	NC_000913	4374508 =	NA (NA)					noncoding (11/99 nt)	RIP329 (repetitive extragenic palindromic) element, contains 2 REP sequences and 1 IHF site	RIP329 (repetitive extragenic palindromic) element, contains 2 REP sequences and 1 IHF site