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 223 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,153,573	0	T	G	60.0%	17.0 / 72.4	50	Y92D (TAC→GAC)	pabC	4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
*	NC_000913	4,538,109	0	A	C	52.1%	60.1 / 83.0	49	G219G (GGT→GGG)	nanM	N‑acetylneuraminic acid mutarotase
*	NC_000913	1,684,712	0	A	C	50.0%	65.0 / 10.7	48	T152P (ACC→CCC)	tus	inhibitor of replication at Ter, DNA‑binding protein
*	NC_000913	2,349,145	0	A	C	49.1%	72.6 / 20.2	55	F110V (TTC→GTC)	inaA	acid‑inducible Kdo/WaaP family putative kinase
*	NC_000913	366,526	0	T	G	48.8%	52.0 / 15.0	44	T329P (ACC→CCC)	lacI	lactose‑inducible lac operon transcriptional repressor
*	NC_000913	1,473,402	0	G	T	48.8%	31.9 / 34.3	43	pseudogene (2886/3497 nt)	ydbA	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
*	NC_000913	266,358	0	T	G	47.8%	53.5 / 20.3	46	T66P (ACC→CCC)	yafY	lipoprotein, inner membrane; degP regulator; CP4‑6 prophage
*	NC_000913	1,649,295	0	T	G	47.5%	56.3 / 11.9	40	intergenic (+254/‑314)	ydfC/dicB	uncharacterized protein, Qin prophage/Qin prophage; cell division inhibition protein
*	NC_000913	73,581	0	A	C	47.5%	90.4 / 15.0	59	V314G (GTA→GGA)	thiP	thiamine/thiamine pyrophosphate ABC transporter permease
*	NC_000913	1,290,716	0	G	A	47.1%	37.9 / 13.9	34	E159K (GAA→AAA)	rssB	PcnB‑degradosome interaction factor; response regulator
*	NC_000913	925,900	0	A	G	46.0%	90.5 / 15.8	64	noncoding (72/88 nt)	serW	tRNA‑Ser
*	NC_000913	4,536,197	0	A	T	45.3%	59.3 / 43.4	53	intergenic (+166/+417)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
*	NC_000913	213,341	0	A	G	44.2%	59.1 / 13.3	43	G337G (GGA→GGG)	tilS	tRNA(Ile)‑lysidine synthetase
*	NC_000913	1,097,581	0	A	G	44.0%	71.1 / 15.6	50	noncoding (72/88 nt)	serX	tRNA‑Ser
*	NC_000913	1,153,569	0	A	G	44.0%	56.9 / 13.3	50	R90R (CGA→CGG)	pabC	4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
*	NC_000913	1,649,300	0	C	T	43.6%	44.0 / 15.7	39	intergenic (+259/‑309)	ydfC/dicB	uncharacterized protein, Qin prophage/Qin prophage; cell division inhibition protein
*	NC_000913	3,035,757	0	A	C	43.4%	87.7 / 11.6	53	G150G (GGT→GGG)	prfB	peptide chain release factor RF‑2
*	NC_000913	1,478,324	0	T	G	42.3%	80.4 / 10.9	52	G33G (GGT→GGG)	ynbB	putative CDP‑diglyceride synthase
*	NC_000913	4,573,500	0	A	G	42.3%	78.8 / 14.7	52	pseudogene (1087/1503 nt)	yjiT	pseudogene
*	NC_000913	646,765	0	G	T	42.1%	38.8 / 18.2	38	Q249K (CAA→AAA)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A 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	= 1207805	38 (0.690)	13 (0.260)	13/266	4.8	25.5%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	42 (0.850)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	39 (0.710)	9 (0.180)	9/266	6.4	18.8%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	43 (0.870)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related