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 89 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	64.3%	‑1.2 / 18.9	28	Q433K (CAA→AAA)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	2,470,411	0	A	T	62.5%	‑2.3 / 26.5	32	L427F (TTA→TTT)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	2,177,245	0	G	T	59.2%	2.5 / 25.8	50	intergenic (‑41/+267)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	1,636,442	0	C	G	56.2%	17.8 / 43.1	34	intergenic (‑75/‑314)	nohA/ynfO	Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO
*	NC_000913	2,470,405	0	T	G	56.2%	7.1 / 34.2	32	V425V (GTT→GTG)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	3,233,728	0	T	G	55.6%	‑1.7 / 11.8	18	*139Y (TAA→TAC)	higA	antitoxin/DNA‑binding transcriptional repressor HigA
*	NC_000913	454,926	0	G	A	53.3%	‑4.4 / 14.1	27	intergenic (+137/‑207)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	454,906	0	G	T	52.2%	2.3 / 14.9	30	intergenic (+117/‑227)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	4,378,973	0	G	C	50.0%	‑0.3 / 15.2	28	intergenic (‑29/+34)	ampC/frdD	beta‑lactamase/fumarate reductase membrane protein FrdD
*	NC_000913	2,470,416	0	A	T	48.5%	10.2 / 15.3	33	Y429F (TAT→TTT)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	454,934	0	A	C	48.3%	‑3.6 / 15.1	29	intergenic (+145/‑199)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	454,873	0	C	G	46.4%	‑6.2 / 17.4	32	intergenic (+84/‑260)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	2,177,255	0	G	T	45.3%	13.4 / 32.2	53	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	454,877	0	A	T	42.9%	3.4 / 10.8	32	intergenic (+88/‑256)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	2,139,598	0	T	G	42.9%	27.3 / 11.7	49	intergenic (+113/+161)	yegH/asmA	inner membrane protein YegH/putative assembly protein AsmA
*	NC_000913	3,455,677	0	A	T	42.9%	11.0 / 12.5	28	N34Y (AAT→TAT)	gspC	Type II secretion system protein GspC
*	NC_000913	1,708,326	0	G	T	42.4%	67.9 / 15.6	60	E470* (GAA→TAA)	rsxC	SoxR [2Fe‑2S] reducing system protein RsxC
*	NC_000913	1,636,452	0	C	G	41.7%	26.0 / 12.7	35	intergenic (‑85/‑304)	nohA/ynfO	Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO
*	NC_000913	2,177,221	0	T	G	41.7%	50.3 / 12.8	48	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,228	0	C	G	41.2%	44.4 / 14.6	48	intergenic (‑24/+284)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I

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 =	48 (0.780)	4 (0.070)	4/238	5.3	7.1%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	60 (1.050)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	= 4542690	51 (0.830)	4 (0.070)	3/238	5.8	6.9%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	60 (1.050)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit