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 78 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	454,906	0	G	T	60.0%	3.1 / 22.4	31	intergenic (+117/‑227)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	2,470,427	0	C	A	56.7%	19.3 / 35.7	31	Q433K (CAA→AAA)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	2,177,234	0	C	G	55.2%	12.9 / 41.0	46	intergenic (‑30/+278)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,245	0	G	T	53.2%	‑0.4 / 32.7	50	intergenic (‑41/+267)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	4,378,973	0	G	C	51.8%	‑4.3 / 14.3	27	intergenic (‑29/+34)	ampC/frdD	beta‑lactamase/fumarate reductase membrane protein FrdD
*	NC_000913	3,455,696	0	C	A	51.7%	25.0 / 37.8	29	T40K (ACA→AAA)	gspC	Type II secretion system protein GspC
*	NC_000913	2,177,228	0	C	G	50.0%	8.6 / 25.0	48	intergenic (‑24/+284)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	3,955,616	0	T	G	50.0%	25.4 / 39.8	58	F96V (TTT→GTT)	ilvA	threonine deaminase
*	NC_000913	1,732,646	0	A	.	49.0%	82.8 / 97.2	49	coding (3560/4617 nt)	lhr	putative ATP‑dependent helicase Lhr
*	NC_000913	3,955,620	0	C	G	46.9%	48.5 / 23.1	56	S97C (TCT→TGT)	ilvA	threonine deaminase
*	NC_000913	3,455,680	0	G	T	46.7%	10.6 / 13.5	30	V35L (GTG→TTG)	gspC	Type II secretion system protein GspC
*	NC_000913	707,984	0	C	G	46.2%	19.0 / 10.3	26	intergenic (+227/‑350)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	2,470,411	0	A	T	44.1%	22.9 / 17.8	34	L427F (TTA→TTT)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	3,455,671	0	A	T	43.8%	6.7 / 15.5	32	I32F (ATT→TTT)	gspC	Type II secretion system protein GspC
*	NC_000913	3,455,677	0	A	T	43.8%	8.9 / 11.8	32	N34Y (AAT→TAT)	gspC	Type II secretion system protein GspC
*	NC_000913	2,177,221	0	T	G	43.5%	6.8 / 30.0	46	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	1,879,846	0	T	G	42.9%	30.9 / 18.9	42	T35P (ACG→CCG)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	1,879,848	0	C	G	42.9%	62.5 / 13.8	43	G34A (GGA→GCA)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	2,177,255	0	G	T	42.4%	30.5 / 32.2	59	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	1,879,853	0	A	T	41.9%	44.1 / 19.2	43	D32E (GAT→GAA)	yeaR	DUF1971 domain‑containing protein YeaR

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	1467910 =	NA (NA)	7 (0.110)	6/254	4.9	NA	noncoding (1331/1331 nt)	IS2	repeat region
	?	NC_000913	= 1469242	NA (NA)					intergenic (‑93/‑4)	insC‑2/ydbA	IS2 insertion element repressor InsA/putative outer membrane protein, N‑terminal fragment
*	?	NC_000913	= 2070269	NA (NA)	7 (0.110)	5/250	5.3	NA	noncoding (3/1331 nt)	IS2	repeat region
	?	NC_000913	= 3187430	NA (NA)					intergenic (+15/‑2)	insD‑5/yqiG	IS2 insertion element protein InsB/putative outer membrane usher protein YqiG
*	?	NC_000913	381262 =	NA (NA)	8 (0.120)	4/250	5.7	NA	noncoding (3/1331 nt)	IS2	repeat region
	?	NC_000913	= 382594	NA (NA)					pseudogene (279/282 nt)	yaiX	putative acyltransferase, N‑terminal fragment