Table 4. Prediction of protein-coding genes.

				Average length (bp)
Methods		Gene number	Exons per gene	Gene	CDS	Exon	Intron
De novo	Augustus	18,318	8.14	16,402.87	1,402.91	172.29	2,099.99
	GlimmerHMM	172,168	2.90	5,695.00	474.06	163.45	2,747.47
	SNAP	61,271	6.31	29,996.61	809.23	128.21	5,495.13
	Geneid	38,214	5.48	20,392.89	1,006.18	183.58	4,326.65
	Genscan	43,335	7.61	19,762.90	1,294.69	170.05	2,792.52
Homologous comparison	Taeniopygia guttata	26,141	5.64	13,827.51	1,049.69	186.24	2,756.00
	Anas platyrhynchos	36,335	4.65	9,142.51	930.19	199.91	2,248.05
	Gallus gallus	25,943	6.03	13,297.66	1,171.56	194.16	2,408.92
	Columba livia	36,315	4.71	9,177.85	913.73	194.05	2,228.25
	Anser cygnoides	34,171	5.14	10,493.05	1,004.18	195.43	2,292.94
	Pseudopodoces humilis	15,498	9.06	21,225.26	1,648.10	181.90	2,428.77
RNA-seq	Cufflinks	48,064	7.93	24,121.46	3,494.75	440.7	2,976.44
	PASA	65,640	6.78	15,650.31	1,168.16	172.35	2,506.53
EVM		24,169	7.12	16,340.12	1,225.82	172.14	2,469.26
PASA-update		24,010	7.20	17,772.08	1,249.46	173.43	2,663.08
Final set		16,428	9.88	25,274.02	1,641.91	166.26	2,662.69