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 29 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	1,311,830	0	A	G	42.1%	7.9 / 17.1	19	intergenic (+22/+18)	tonB/yciA	membrane spanning protein in TonB‑ExbB‑ExbD transport complex/acyl‑CoA esterase
*	NC_000913_3_pae_tpiA	1,311,831	0	C	T	42.1%	7.3 / 16.3	19	intergenic (+23/+17)	tonB/yciA	membrane spanning protein in TonB‑ExbB‑ExbD transport complex/acyl‑CoA esterase
*	NC_000913_3_pae_tpiA	1,129,394	0	G	C	41.2%	3.7 / 21.1	17	intergenic (+20/+20)	murJ/flgN	putative lipid II flippase/export chaperone for FlgK and FlgL
*	NC_000913_3_pae_tpiA	922,314	1	.	C	38.9%	11.6 / 31.8	18	intergenic (+21/+52)	macB/cspD	macrolide ABC transporter peremase/ATPase/inhibitor of DNA replication, cold shock protein homolog
*	NC_000913_3_pae_tpiA	922,321	0	G	.	38.9%	33.4 / 26.6	18	intergenic (+28/+45)	macB/cspD	macrolide ABC transporter peremase/ATPase/inhibitor of DNA replication, cold shock protein homolog
*	NC_000913_3_pae_tpiA	3,959,515	0	T	A	31.6%	23.8 / 16.0	19	intergenic (+70/+17)	ilvC/ppiC	ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C)
*	NC_000913_3_pae_tpiA	3,128,138	0	T	.	30.8%	27.1 / 11.4	13	intergenic (‑117/‑134)	glcD/glcC	glycolate oxidase subunit, FAD‑linked/glycolate‑inducible glc operon transcriptional repressor; autorepressor
*	NC_000913_3_pae_tpiA	3,439,588	0	G	C	29.7%	65.3 / 32.3	37	intergenic (‑79/+28)	yhdN/rplQ	DUF1992 family protein/50S ribosomal subunit protein L17
*	NC_000913_3_pae_tpiA	3,439,589	0	G	C	27.8%	67.1 / 30.1	36	intergenic (‑80/+27)	yhdN/rplQ	DUF1992 family protein/50S ribosomal subunit protein L17
*	NC_000913_3_pae_tpiA	601,413	0	T	A	27.3%	37.7 / 12.4	22	I900I (ATT→ATA)	cusA	copper/silver efflux system, membrane component
*	NC_000913_3_pae_tpiA	4,088,091	0	G	C	26.3%	32.2 / 11.9	19	intergenic (+34/+16)	yiiG/frvR	DUF3829 family lipoprotein/putative frv operon regulator; contains a PTS EIIA domain
*	NC_000913_3_pae_tpiA	2,637,444	0	A	G	26.1%	31.2 / 11.3	25	intergenic (‑88/+30)	der/bamB	GTPase; multicopy suppressor of ftsJ/BamABCDE complex OM biogenesis lipoprotein
*	NC_000913_3_pae_tpiA	4,295,976	0	C	T	25.9%	48.4 / 13.0	27	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*	NC_000913_3_pae_tpiA	1,202,957	0	G	.	25.0%	36.5 / 12.0	16	intergenic (‑24/‑67)	cohE/croE	e14 prophage; repressor protein phage e14/e14 prophage; putative DNA‑binding transcriptional regulator
*	NC_000913_3_pae_tpiA	1,202,961	1	.	C	25.0%	35.5 / 15.1	16	intergenic (‑28/‑63)	cohE/croE	e14 prophage; repressor protein phage e14/e14 prophage; putative DNA‑binding transcriptional regulator
*	NC_000913_3_pae_tpiA	3,156,591	0	T	G	25.0%	30.7 / 12.8	20	intergenic (+73/‑32)	yqhD/dkgA	aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A
*	NC_000913_3_pae_tpiA	2,286,311	0	C	G	22.7%	44.1 / 11.9	22	intergenic (+24/+79)	proL/yejO	tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system
*	NC_000913_3_pae_tpiA	2,286,313	0	T	A	22.7%	42.9 / 11.6	22	intergenic (+26/+77)	proL/yejO	tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system
*	NC_000913_3_pae_tpiA	2,375,483	0	A	T	22.7%	42.5 / 11.9	22	L160L (CTT→CTA) ‡	menC	O‑succinylbenzoyl‑CoA synthase
*	NC_000913_3_pae_tpiA	2,375,484	0	A	T	22.7%	45.1 / 10.2	22	L160H (CTT→CAT) ‡	menC	O‑succinylbenzoyl‑CoA synthase

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_3_pae_tpiA	= 4040683	31 (1.990)	5 (0.330)	5/244	1.3	16.3%	intergenic (+47/+223)	rrfA/mobB	5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B
	?	NC_000913_3_pae_tpiA	= 4213078	21 (1.370)					intergenic (+3/‑72)	rrfE/yjaA	5S ribosomal RNA of rrnE operon/stress‑induced protein
*	?	NC_000913_3_pae_tpiA	4542598 =	24 (1.540)	4 (0.280)	4/230	1.4	17.7%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913_3_pae_tpiA	4542912 =	15 (1.040)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913_3_pae_tpiA	= 4542606	24 (1.540)	3 (0.210)	3/230	1.7	13.9%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913_3_pae_tpiA	= 4542902	15 (1.040)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913_3_pae_tpiA	= 238140	13 (0.840)	4 (0.280)	3/230	1.7	24.2%	intergenic (+20/+117)	yafT/ykfM	lipoprotein/lethality reduction protein, putative inner membrane protein
	?	NC_000913_3_pae_tpiA	= 238146	13 (0.900)					intergenic (+26/+111)	yafT/ykfM	lipoprotein/lethality reduction protein, putative inner membrane protein