Table 1. Alignment of sequence reads from various mammals to the human sequence of two ENCODE regions.

		ENCODE region ENm001			ENCODE region ENm005
Species	Distance to human	No. of reads	Aligned to human, %	Correctly aligned to human, %	No. of reads	Aligned to human, %	Correctly aligned to human, %
Cat	0.29	15,152	75.8	97.0	16,143	63.9	97.3
Dog	0.31	11,714	76.7	98.2	17,525	67.5	97.8
Pig	0.34	13,682	76.1	97.7	17,673	58.8	97.5
Cow	0.36	15,511	64.9	98.0	14,404	58.2	98.2
Mouse	0.45	15,847	46.9	98.4	ND	ND	ND
Rat	0.46	19,240	41.1	97.3	12,725	36.9	98.0
Hedgehog	0.44	15,779	35.9	97.3	ND	ND	ND

The sequences of two ENCODE regions, ENm001 and ENm005 [http://genome.ucsc.edu/ENCODE/regions.html (18)], were generated from the indicated seven species (see www.nisc.nih.gov). For each species, the phylogenetic distance relative to human is given in average number of substitutions per base (see Fig. 1). Columns show the total number of high-quality sequence reads processed for alignment to the entire human genome (using blastz and the S1-S2 scoring method; see supporting information), the percentage of reads that aligned to the human genome, and the percentage of aligning reads that correctly aligned to the orthologous region of the human genome. ND, not determined.