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 141 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	782,311	0	A	C	42.0%	116.2 / 19.1	69	G247G (GGT→GGG)	gpmA	2,3‑diphosphoglycerate‑dependent phosphoglycerate mutase
*	NZ_CP009273	1,264,335	0	G	T	37.1%	67.0 / 10.6	35	E239* (GAA→TAA)	kdsA	3‑deoxy‑8‑phosphooctulonate synthase
*	NZ_CP009273	1,264,332	0	A	T	36.4%	56.3 / 10.1	33	I238F (ATT→TTT)	kdsA	3‑deoxy‑8‑phosphooctulonate synthase
*	NZ_CP009273	3,171,107	0	C	A	35.9%	122.4 / 34.2	78	E55* (GAG→TAG)	nudF	ADP‑ribose diphosphatase
*	NZ_CP009273	3,199,794	0	C	T	35.5%	92.8 / 36.7	76	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha
*	NZ_CP009273	4,049,475	0	A	C	35.2%	107.5 / 15.5	54	G75G (GGT→GGG)	glnL	nitrogen regulation protein NR(II)
*	NZ_CP009273	2,476,733	0	G	A	34.8%	160.7 / 29.0	89	S29L (TCA→TTA)	emrK	multidrug efflux MFS transporter periplasmic adaptor subunit EmrK
*	NZ_CP009273	4,594,167	0	C	T	34.8%	116.0 / 20.0	69	S64F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	883,470	0	T	G	34.2%	162.1 / 10.4	76	intergenic (+55/+120)	rcdA/ybjL	DNA‑binding transcriptional regulator RcdA/aspartate:alanine antiporter
*	NZ_CP009273	1,240,690	0	G	T	33.8%	133.1 / 28.2	71	L25F (TTG→TTT)	BW25113_RS06225	protein YcgY
*	NZ_CP009273	1,820,574	0	C	A	33.3%	93.3 / 11.6	48	G203C (GGC→TGC)	astE	succinylglutamate desuccinylase
*	NZ_CP009273	748,581	0	T	A	32.7%	101.7 / 17.0	55	intergenic (‑330/+60)	ybgD/gltA	fimbrial protein/citrate synthase
*	NZ_CP009273	1,819,313	0	G	A	32.6%	83.6 / 17.3	49	intergenic (‑119/+84)	ves/spy	environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone Spy
*	NZ_CP009273	3,199,805	0	C	A	32.4%	99.4 / 19.2	75	intergenic (‑190/‑17)	ttdR/ttdA	DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha
*	NZ_CP009273	368,096	0	T	G	32.4%	143.6 / 17.0	68	L176V (TTA→GTA)	mhpD	2‑keto‑4‑pentenoate hydratase
*	NZ_CP009273	1,820,636	0	T	C	32.1%	97.0 / 12.0	56	E182G (GAG→GGG)	astE	succinylglutamate desuccinylase
*	NZ_CP009273	2,089,571	0	A	G	31.8%	114.7 / 15.1	63	I83V (ATT→GTT)	hisF	imidazole glycerol phosphate synthase subunit HisF
*	NZ_CP009273	1,041,528	0	A	C	31.1%	183.7 / 15.2	90	V625G (GTA→GGA)	gfcD	YjbH domain‑containing protein
*	NZ_CP009273	341,015	0	G	A	31.1%	143.8 / 33.7	74	intergenic (+313/‑100)	BW25113_RS01680/BW25113_RS01685	protein YahL/protein YahM
*	NZ_CP009273	4,594,161	0	C	T	30.9%	116.0 / 26.3	69	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 1203261	76 (0.860)	26 (0.310)	25/464	5.4	29.5%	coding (305/630 nt)	BW25113_RS05990	protein StfP
	?	NZ_CP009273	= 1205058	53 (0.640)					coding (57/540 nt)	BW25113_RS06005	phage tail protein
*	?	NZ_CP009273	3416618 =	71 (0.800)	5 (0.150) +152 bp	4/192	6.6	15.7%	intergenic (+65/+166)	yhdZ/rrf	amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA
	?	NZ_CP009273	= 3416648	68 (0.770)					intergenic (+95/+136)	yhdZ/rrf	amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA
*	?	NZ_CP009273	1203246 =	71 (0.800)	21 (0.250)	20/464	6.8	25.7%	coding (290/630 nt)	BW25113_RS05990	protein StfP
	?	NZ_CP009273	1205075 =	55 (0.660)					coding (40/540 nt)	BW25113_RS06005	phage tail protein
*	?	NZ_CP009273	= 692197	46 (0.520)	5 (0.080)	5/340	10.7	12.3%	intergenic (‑1/+15)	BW25113_RS03450/BW25113_RS03455	tRNA‑Met/tRNA‑Gln
	?	NZ_CP009273	692591 =	40 (0.660)					intergenic (‑2/+378)	BW25113_RS03470/asnB	tRNA‑Met/asparagine synthase B