Table 4. Totals and ratios of peaks-genes associations.

	Totals		CAGE peaks annotated		CAGE peaks annotated (%)		Genes covered by CAGE		Genes covered by CAGE (%)
	Rat	Dog	Rat	Dog	Rat	Dog	Rat	Dog	Rat	Dog
Listing of the totals and percentages for the gene models used in this study together with all robust peaks identified in this study in dog and rat.
Ensembl_transcript	39,595	29,881	19,254	10,542	68%	46%	1,0688	6,194	27%	21%
Augustus_gene	29,380	29,165	1,3513	9,829	47%	42%	7,328	5,755	25%	20%
RefSeq_transcript	18,978	2,274	17,188	1,350	60%	6%	9,246	779	49%	34%
Geneid_gene	41,652	32,342	9,399	6,997	33%	30%	5,339	4,155	13%	13%
Genscan_gene	49,319	42,671	8,115	5,779	28%	25%	4,618	3,525	9%	8%
EST_gene	1,270,134	401,654	23,621	13,549	83%	59%	13,718	7,932	1%	2%
All robust CAGE peaks	28,497	23,147	26,208	18,597	92%	80%	28,497	23,147	100%	100%