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	2,470,427	0	C	A	60.0%	12.5 / 30.9	31	Q433K (CAA→AAA)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	2,177,234	0	C	A	59.1%	‑1.6 / 13.2	31	intergenic (‑30/+278)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,470,436	0	C	A	55.6%	9.8 / 26.5	27	Q436K (CAA→AAA)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	2,139,598	0	T	G	50.0%	4.0 / 11.7	32	intergenic (+113/+161)	yegH/asmA	inner membrane protein YegH/putative assembly protein AsmA
*	NC_000913	2,177,255	0	G	T	50.0%	‑1.5 / 21.2	40	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,228	0	C	G	44.0%	16.7 / 14.7	33	intergenic (‑24/+284)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,470,405	0	T	G	43.8%	33.1 / 13.0	32	V425V (GTT→GTG)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	2,470,411	0	A	T	43.8%	23.5 / 18.6	32	L427F (TTA→TTT)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	3,455,677	0	A	T	41.9%	36.0 / 18.1	43	N34Y (AAT→TAT)	gspC	Type II secretion system protein GspC
*	NC_000913	4,220,007	0	T	G	41.7%	8.0 / 10.9	24	V471G (GTG→GGG)	aceK	isocitrate dehydrogenase kinase/phosphatase
*	NC_000913	707,984	0	C	G	40.7%	29.1 / 10.1	29	intergenic (+227/‑350)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	1,231,054	0	G	T	40.0%	44.9 / 10.1	48	V96V (GTG→GTT)	umuD	DNA polymerase V protein UmuD
*	NC_000913	931,029	0	G	C	38.7%	36.9 / 15.8	31	intergenic (‑67/+56)	cydD/trxB	glutathione/L‑cysteine ABC exporter subunit CydD/thioredoxin reductase
*	NC_000913	4,220,016	0	A	T	38.5%	19.3 / 10.2	26	Y474F (TAT→TTT)	aceK	isocitrate dehydrogenase kinase/phosphatase
*	NC_000913	3,004,946	0	G	T	37.0%	48.9 / 21.2	46	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV
*	NC_000913	4,002,320	0	A	T	36.8%	57.7 / 12.7	38	M299L (ATG→TTG)	corA	Ni(2(+))/Co(2(+))/Mg(2(+)) transporter
*	NC_000913	2,470,472	0	G	T	34.5%	27.6 / 10.8	30	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	1,982,994	0	A	C	34.3%	44.0 / 12.8	35	C183G (TGT→GGT)	araH	arabinose ABC transporter membrane subunit
*	NC_000913	4,531,214	0	T	G	34.0%	81.1 / 22.9	54	K146N (AAA→AAC)	sgcX	KpLE2 phage‑like element; putative endoglucanase with Zn‑dependent exopeptidase domain
*	NC_000913	4,296,060	0	C	T	32.3%	85.9 / 59.3	65	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO

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	4542682 =	57 (1.130)	4 (0.090)	4/238	4.5	7.4%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	47 (1.010)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	= 3196551	31 (0.620)	4 (0.080)	4/256	4.7	11.6%	coding (203/1434 nt)	rfaE	fused heptose 7‑phosphate kinase/heptose 1‑phosphate adenyltransferase
	?	NC_000913	3196555 =	30 (0.600)					coding (199/1434 nt)	rfaE	fused heptose 7‑phosphate kinase/heptose 1‑phosphate adenyltransferase
*	?	NC_000913	1467910 =	NA (NA)	3 (0.060)	3/256	5.2	NA	noncoding (1331/1331 nt)	IS2	repeat region
	?	NC_000913	= 1469241	NA (NA)					intergenic (‑92/‑5)	insC‑2/ydbA	IS2 insertion element repressor InsA/putative outer membrane protein, N‑terminal fragment