breseq  version 0.39.0   mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 26 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,208,132	0	G	A	68.2%	42.3 / 58.5	63	intergenic (‑600/‑15)	purH/rrsE	bifunctional AICAR transformylase/IMP cyclohydrolase/16S ribosomal RNA
*	NC_000913	3,943,634	0	A	G	41.0%	28.0 / 42.6	39	intergenic (+124/‑70)	gltU/rrlC	tRNA‑Glu/23S ribosomal RNA
*	NC_000913	4,622,250	0	A	G	38.5%	56.4 / 10.6	39	E161G (GAG→GGG)	yjjJ	toxin YjjJ
*	NC_000913	2,248,424	0	C	A	37.9%	35.2 / 10.8	29	V37F (GTT→TTT)	lysP	lysine:H(+) symporter
*	NC_000913	2,326,450	0	T	G	37.2%	82.2 / 11.9	52	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	657,676	0	A	C	36.6%	60.9 / 13.5	42	V88G (GTG→GGG)	crcB	F(‑) channel protein
*	NC_000913	3,206,435	0	C	T	36.1%	39.3 / 15.6	37	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	599,576	0	T	G	34.8%	57.8 / 11.8	46	V288G (GTG→GGG)	cusA	copper/silver export system RND permease
*	NC_000913	862,559	0	G	T	33.3%	56.4 / 14.1	39	H16Q (CAC→CAA)	ybiW	putative pyruvate formate lyase
*	NC_000913	2,984,718	0	G	C	32.6%	72.6 / 15.6	45	P292R (CCG→CGG)	yqeF	putative acyltransferase
*	NC_000913	4,056,115	0	A	C	31.5%	83.2 / 12.5	55	G75G (GGT→GGG)	glnL	protein histidine kinase NtrB
*	NC_000913	4,457,105	0	A	G	31.1%	65.0 / 12.9	45	I441V (ATC→GTC)	mpl	UDP‑N‑acetylmuramate‑‑L‑alanyl‑gamma‑D‑glutamyl‑ meso‑2,6‑diaminoheptanedioate ligase
*	NC_000913	4,465,787	0	G	A	30.8%	55.4 / 10.1	39	R132C (CGC→TGC)	treB	trehalose‑specific PTS enzyme IIBC component
*	NC_000913	2,162,120	0	T	G	30.2%	92.2 / 10.7	54	G219G (GGT→GGG)	mdtD	putative multidrug efflux pump MdtD
*	NC_000913	4,296,268	0	T	C	29.6%	40.7 / 17.3	27	intergenic (+474/+168)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	3,786,536	0	A	G	28.8%	141.8 / 12.1	67	E426G (GAA→GGA)	gpmM	2,3‑bisphosphoglycerate‑independent phosphoglycerate mutase
*	NC_000913	3,914,553	0	A	G	28.8%	125.8 / 12.0	66	H216H (CAT→CAC)	glmU	fused N‑acetylglucosamine‑1‑phosphate uridyltransferase and glucosamine‑1‑phosphate acetyltransferase
*	NC_000913	3,556,207	0	T	C	26.4%	113.8 / 15.2	53	S215G (AGT→GGT)	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	3,813,272	0	C	T	26.4%	85.3 / 12.5	53	S181L (TCG→TTG)	dfp	fused 4'‑phosphopantothenoylcysteine decarboxylase and phosphopantothenoylcysteine synthetase
*	NC_000913	2,846,683	0	G	T	25.8%	109.6 / 13.8	63	Q244K (CAA→AAA)	hycD	formate hydrogenlyase subunit HycD

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	= 3653230	NA (NA)	4 (0.090)	4/492	3.6	7.5%	noncoding (1/1195 nt)	IS5	repeat region
	?	NC_000913	= 4161661	49 (1.040)					coding (595/705 nt)	fabR	DNA‑binding transcriptional repressor FabR
*	?	NC_000913	257911 =	NA (NA)	4 (0.090) +CCC	4/486	3.6	100%	noncoding (765/768 nt)	IS1	repeat region
	?	NC_000913	= 323450	0 (0.000)					coding (1113/1428 nt)	ykgF	putative amino acid dehydrogenase with NAD(P)‑binding domain and ferridoxin‑like domain
*	?	NC_000913	1315309 =	21 (0.450)	3 (0.060)	3/492	4.0	12.5%	coding (462/501 nt)	yciF	DUF892 domain‑containing protein YciF
	?	NC_000913	= 1979270	NA (NA)					noncoding (1/768 nt)	IS1	repeat region