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 36 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,177,255	0	G	T	65.0%	24.4 / 16.7	40	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	454,926	0	G	T	53.8%	3.3 / 13.9	17	intergenic (+137/‑207)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	707,981	0	C	T	53.3%	‑5.9 / 15.7	26	intergenic (+224/‑353)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	3,004,946	0	G	T	52.5%	9.5 / 39.6	40	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV
*	NC_000913	2,177,234	0	C	A	52.2%	‑1.6 / 10.9	35	intergenic (‑30/+278)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,221	0	T	G	47.1%	12.7 / 17.9	34	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,470,405	0	T	G	46.7%	22.1 / 12.8	30	V425V (GTT→GTG)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	1,636,442	0	C	G	45.5%	43.1 / 15.9	34	intergenic (‑75/‑314)	nohA/ynfO	Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO
*	NC_000913	2,470,416	0	A	T	44.8%	18.8 / 10.4	30	Y429F (TAT→TTT)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	3,407,970	0	C	G	42.9%	18.0 / 11.2	21	L122V (CTT→GTT)	panF	pantothenate:Na(+) symporter
*	NC_000913	707,989	0	C	T	42.1%	8.6 / 15.9	28	intergenic (+232/‑345)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	2,470,411	0	A	T	40.0%	25.2 / 10.7	30	L427F (TTA→TTT)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	1,087,697	0	G	C	39.5%	53.5 / 15.6	43	V50V (GTC→GTG)	pgaC	poly‑N‑acetyl‑D‑glucosamine synthase subunit PgaC
*	NC_000913	1,757,170	0	A	T	39.5%	28.0 / 22.3	43	intergenic (+60/‑251)	pykF/lpp	pyruvate kinase I/murein lipoprotein
*	NC_000913	2,177,228	0	C	T	36.0%	7.6 / 18.0	35	intergenic (‑24/+284)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,779,998	0	C	A	35.2%	71.2 / 15.2	54	G910V (GGT→GTT)	ypjA	adhesin‑like autotransporter YpjA
*	NC_000913	1,636,440	0	T	G	35.1%	55.3 / 11.9	37	intergenic (‑73/‑316)	nohA/ynfO	Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO
*	NC_000913	2,570,475	0	A	C	34.2%	31.7 / 11.2	38	L426R (CTG→CGG)	eutE	putative aldehyde dehydrogenase, ethanolamine utilization protein
*	NC_000913	4,236,265	0	A	G	34.2%	51.9 / 14.8	40	K2E (AAG→GAG)	yjbF	lipoprotein YjbF
*	NC_000913	1,297,110	0	A	G	33.3%	59.8 / 18.5	51	S338P (TCC→CCC)	adhE	aldehyde‑alcohol dehydrogenase

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	2068944 =	NA (NA)	6 (0.110)	4/248	4.7	NA	noncoding (1328/1331 nt)	IS2	repeat region
	?	NC_000913	= 2070275	NA (NA)					intergenic (‑95/‑2)	insC‑3/yoeA	CP4‑44 prophage; IS2 insertion element repressor InsA/CP4‑44 prophage; TonB‑dependent receptor plug domain‑containing protein YoeA
*	?	NC_000913	3254133 =	84 (1.540)	3 (0.060)	3/234	5.0	3.6%	coding (82/897 nt)	yhaJ	DNA‑binding transcriptional activator YhaJ
	?	NC_000913	= 3254129	81 (1.610)					coding (86/897 nt)	yhaJ	DNA‑binding transcriptional activator YhaJ
*	?	NC_000913	3471205 =	93 (1.700)	3 (0.060)	3/246	5.2	3.8%	coding (125/1185 nt)	tufA	translation elongation factor Tu 1
	?	NC_000913	4043848 =	60 (1.140)					coding (431/627 nt)	dsbA	thiol:disulfide oxidoreductase DsbA