breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 27 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,177,221	0	T	G	61.5%	3.9 / 24.2	26	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,470,427	0	C	A	58.1%	10.6 / 30.5	32	Q433K (CAA→AAA)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	126,651	0	A	T	57.1%	6.5 / 20.0	21	E319D (GAA→GAT) ‡	aceF	pyruvate dehydrogenase, E2 subunit
*	NC_000913	126,649	0	G	T	52.6%	12.7 / 22.1	21	E319* (GAA→TAA) ‡	aceF	pyruvate dehydrogenase, E2 subunit
*	NC_000913	2,177,255	0	G	T	51.8%	3.5 / 23.7	27	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,731,439	0	C	G	48.0%	27.5 / 12.2	26	intergenic (‑282/+161)	rrsG/clpB	16S ribosomal RNA/ClpB chaperone
*	NC_000913	707,981	0	C	T	41.2%	10.4 / 13.5	26	intergenic (+224/‑353)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	3,004,946	0	G	T	41.0%	42.6 / 12.3	40	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV
*	NC_000913	2,470,411	0	A	T	39.4%	28.0 / 13.5	33	L427F (TTA→TTT)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	2,470,472	0	G	T	38.5%	21.5 / 10.3	29	intergenic (+10/+605)	yfdI/yfdK	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase/CPS‑53 (KpLE1) prophage; putative tail fiber assembly protein YfdK
*	NC_000913	89,041	0	C	A	36.6%	61.4 / 10.5	41	intergenic (+9/‑593)	cra/mraZ	DNA‑binding transcriptional dual regulator Cra/DNA‑binding transcriptional repressor MraZ
*	NC_000913	350,490	0	T	C	35.7%	33.7 / 11.4	31	I160T (ATC→ACC)	prpC	2‑methylcitrate synthase
*	NC_000913	3,454,069	0	G	T	33.3%	36.0 / 10.8	37	Q444K (CAA→AAA)	gspA	Type II secretion system protein GspA
*	NC_000913	436,805	0	T	G	31.0%	27.4 / 10.6	29	Y73D (TAT→GAT)	pgpA	phosphatidylglycerophosphatase A
*	NC_000913	1,297,110	0	A	G	30.3%	43.5 / 12.6	37	S338P (TCC→CCC)	adhE	aldehyde‑alcohol dehydrogenase
*	NC_000913	1,530,562	0	T	A	28.6%	91.4 / 12.3	56	intergenic (‑58/‑24)	yncO/yncI	protein YncO/putative transposase YncI
*	NC_000913	1,530,570	0	T	A	28.6%	97.1 / 10.9	56	intergenic (‑66/‑16)	yncO/yncI	protein YncO/putative transposase YncI
*	NC_000913	3,441,285	0	T	A	27.8%	78.9 / 11.2	54	N131Y (AAC→TAC)	rpsD	30S ribosomal subunit protein S4
*	NC_000913	931,029	0	G	C	27.0%	72.6 / 13.2	37	intergenic (‑67/+56)	cydD/trxB	glutathione/L‑cysteine ABC exporter subunit CydD/thioredoxin reductase
*	NC_000913	1,530,539	0	C	A	26.8%	115.2 / 17.2	56	intergenic (‑35/‑47)	yncO/yncI	protein YncO/putative transposase YncI

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	847450 =	66 (1.390)	4 (0.090)	4/250	4.5	7.8%	coding (555/747 nt)	glnH	L‑glutamine ABC transporter periplasmic binding protein
	?	NC_000913	= 848212	30 (0.650)					intergenic (‑208/+196)	glnH/dps	L‑glutamine ABC transporter periplasmic binding protein/stationary phase nucleoid protein that sequesters iron and protects DNA from damage
*	?	NC_000913	= 646746	50 (1.060)	3 (0.060)	3/250	5.0	5.2%	coding (764/879 nt)	citG	triphosphoribosyl‑dephospho‑CoA synthase
	?	NC_000913	= 4636636	60 (1.300)					coding (630/690 nt)	creB	DNA‑binding transcriptional regulator CreB