breseq  version 0.29.0  revision 8f9c342918e4 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 280 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,717,671	0	A	C	63.6%	35.5 / 47.8	44	T286T (ACT→ACG)	yfiF	putative methyltransferase
*	NC_000913	1,898,100	0	T	G	63.0%	30.8 / 57.8	46	V390G (GTG→GGG)	sdaA	L‑serine dehydratase 1
*	NC_000913	3,730,927	0	T	G	55.1%	2.9 / 108.3	69	intergenic (‑162/‑204)	xylA/xylF	D‑xylose isomerase/D‑xylose transporter subunit
*	NC_000913	3,593,320	0	T	G	54.7%	‑1.3 / 100.3	64	N40H (AAC→CAC)	livF	branched‑chain amino acid ABC transporter ATPase
*	NC_000913	4,378,802	0	A	C	54.4%	57.8 / 89.3	58	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	357,890	0	C	A	52.5%	11.1 / 50.7	40	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,859,828	0	T	G	51.5%	‑1.6 / 114.6	66	I23M (ATT→ATG)	pphB	serine/threonine‑specific protein phosphatase 2
*	NC_000913	993,917	0	A	C	50.0%	51.0 / 17.9	50	V43G (GTG→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	1,356,201	0	T	G	47.9%	108.3 / 16.8	73	T304P (ACC→CCC)	sapA	antimicrobial peptide transport ABC transporter periplasmic binding protein
*	NC_000913	2,326,450	0	T	G	47.9%	64.6 / 17.3	48	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	941,713	0	T	G	47.4%	61.8 / 23.4	57	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	993,913	0	G	C	47.1%	67.1 / 20.1	52	G44G (GGC→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	1,376,505	0	A	C	46.4%	87.2 / 12.7	57	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	3,042,604	0	A	C	45.9%	104.8 / 15.8	61	V182G (GTG→GGG)	yqfA	hemolysin III family HylIII inner membrane protein
*	NC_000913	357,880	0	T	C	45.7%	33.7 / 11.9	36	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,349,145	0	A	C	45.2%	59.6 / 13.3	42	F110V (TTC→GTC)	inaA	acid‑inducible Kdo/WaaP family putative kinase
*	NC_000913	3,206,435	0	C	T	44.2%	55.4 / 28.4	52	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	987,494	0	T	G	43.1%	83.3 / 15.1	51	intergenic (‑512/+91)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	2,151,589	0	A	T	43.1%	63.7 / 28.4	51	L135F (TTA→TTT)	yegJ	uncharacterized protein
*	NC_000913	2,781,645	0	A	C	42.4%	121.3 / 12.1	67	V361G (GTT→GGT)	ypjA	adhesin‑like autotransporter

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 =	73 (1.220)	4 (0.070)	4/280	10.6	5.0%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	83 (1.470)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	= 4542690	74 (1.230)	3 (0.050)	3/280	11.3	3.8%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	83 (1.470)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)