Table 2. Statistics of tag mapping against reference gene and genome sequence of the chicken.

	Deformed beak		Normal beak
	Total number	Distinct tag number	Total number	Distinct tag number
Raw data	6,027,921	262,179	5,807,305	251,861
Clean tags	5,864,499	106,180	5,648,877	100,893
All tags mapping to genes	2,935,689	41,530	2,925,791	42,794
Unambiguous tag mapping to genes	2,566,707	38,420	2,452,094	39,666
All tag-mapped genes	10,425	10,425	10,725	10,725
Unambiguous tag-mapped genes	9,096	9,096	9,328	9,328
Mapping to genome	1,444,399	38,761	1,275,093	36,268
Unknown tags	1,484,411	25,889	1,447,993	21,831