breseq  version 0.33.1  revision 8505477f25b3 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 30 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	589,934	0	T	G	41.9%	101.0 / 17.6	62	T341P (ACC→CCC)	nfrA	bacteriophage N4 receptor, outer membrane protein
*	NC_000913	589,930	0	A	G	36.2%	92.3 / 24.0	58	L342P (CTC→CCC)	nfrA	bacteriophage N4 receptor, outer membrane protein
*	NC_000913	3,712	0	C	G	32.6%	64.5 / 14.0	44	G304G (GGC→GGG)	thrB	homoserine kinase
*	NC_000913	888,014	0	T	G	32.5%	173.6 / 11.6	83	noncoding (44/81 nt)	rybB	small regulatory RNA RybB
*	NC_000913	3,585,086	0	A	C	32.2%	123.7 / 11.9	59	Y580D (TAC→GAC)	ggt	glutathione hydrolase proenzyme
*	NC_000913	4,296,060	0	C	T	32.0%	279.5 / 219.8	206	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	624,589	0	T	C	29.7%	233.7 / 130.2	138	intergenic (‑79/‑296)	fepB/entC	ferric enterobactin ABC transporter periplasmic binding protein/isochorismate synthase EntC
*	NC_000913	2,029,274	0	C	T	28.8%	110.6 / 22.1	59	K31K (AAG→AAA)	yedI	conserved inner membrane protein YedI
*	NC_000913	599,576	0	T	G	28.1%	130.2 / 14.0	57	V288G (GTG→GGG)	cusA	copper/silver export system RND permease
*	NC_000913	2,096,090	0	A	G	26.3%	185.7 / 11.7	76	I83V (ATT→GTT)	hisF	imidazole glycerol phosphate synthase subunit HisF
*	NC_000913	2,483,268	0	T	A	25.4%	281.0 / 37.8	114	L24F (TTA→TTT)	emrK	tripartite efflux pump membrane fusion protein EmrK
*	NC_000913	4,331,790	0	T	G	25.4%	148.4 / 12.5	67	V430G (GTT→GGT)	proP	osmolyte:H(+) symporter ProP
*	NC_000913	2,548,026	0	A	G	25.3%	174.8 / 17.3	85	I452V (ATT→GTT)	murP	N‑acetylmuramic acid‑specific PTS enzyme IICB component/anhydro‑N‑acetylmuramic acid transporter
*	NC_000913	2,040,075	0	C	G	23.8%	215.6 / 23.6	84	L200V (CTG→GTG)	msrP	periplasmic protein‑L‑methionine sulfoxide reductase catalytic subunit
*	NC_000913	4,223,597	0	C	T	23.4%	147.1 / 22.6	64	R11K (AGA→AAA)	iclR	DNA‑binding transcriptional repressor IclR
*	NC_000913	2,442,586	0	G	T	23.2%	143.9 / 10.9	57	A275S (GCC→TCC)	mnmC	fused 5‑methylaminomethyl‑2‑thiouridine‑forming methyltransferase and FAD‑dependent demodification enzyme
*	NC_000913	121,507	0	A	T	23.0%	249.1 / 28.4	100	L15L (CTT→CTA)	aroP	aromatic amino acid:H(+) symporter AroP
*	NC_000913	2,859,118	0	G	A	22.9%	155.6 / 15.1	62	E676K (GAA→AAA)	mutS	DNA mismatch repair protein MutS
*	NC_000913	3,745,494	0	C	T	22.9%	162.0 / 19.8	70	R231C (CGC→TGC)	yiaN	2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit
*	NC_000913	3,021,774	0	T	A	22.4%	242.0 / 16.3	85	N153K (AAT→AAA)	xdhD	fused putative xanthine/hypoxanthine oxidase: molybdopterin‑binding subunit and Fe‑S binding subunit

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	= 3593298	69 (0.640)	13 (0.120)	12/98	3.3	15.6%	coding (140/714 nt)	livF	branched chain amino acid/phenylalanine ABC transporter ATP binding subunit LivF
	?	NC_000913	3593309 =	72 (0.670)					coding (129/714 nt)	livF	branched chain amino acid/phenylalanine ABC transporter ATP binding subunit LivF
*	?	NC_000913	= 856072	0 (0.000)	8 (0.090) +GGCGGGG	7/84	4.1	21.3%	coding (110/1593 nt)	ybiT	ABC transporter ATP‑binding protein YbiT
	?	NC_000913	= 3593298	69 (0.640)					coding (140/714 nt)	livF	branched chain amino acid/phenylalanine ABC transporter ATP binding subunit LivF