Table 3.

Number of predicted genes with RNA-seq signals

Specimen ID (tissue ID)	Accession number	Tissue	Genotype	Phenotype	RPKM >0		RPKM >1		RPKM >5
					Number	Ratio (%)	Number	Ratio (%)	Number	Ratio (%)
1003347859	ERR753524	Brain	ZZ	Intersex	17,049	87.85	14,403	74.22	11,244	57.94
(AA45100)
1003338787	ERR753525	Brain	ZZ	Male	16,934	87.26	14,467	74.55	11,359	58.53
(AA60463)
1003348364	ERR753526	Brain	ZW	Female	17,121	88.23	14,526	74.85	11,474	59.13
(AA60435)
1003347859	ERR753527	Testes	ZZ	Intersex	16,874	86.95	13,874	71.49	10,784	55.57
(AA45100)
1003347859	ERR753528	Ovary	ZZ	Intersex	16,827	86.71	12,952	66.74	10,421	53.7
(AA45100)
1003338787	ERR753529	Testes	ZZ	Male	17,963	92.56	14,951	77.04	11,311	58.29
(AA60463)
1003348364	ERR753530	Ovary	ZW	Female	17,188	88.57	13,634	70.26	10,946	56.41
(AA60435)
Combined					18,833	97.05	17,646	90.93	15,974	82.31

Gene expression levels were measured as RPKM (reads per kilobase of gene per million mapped reads). Ratios are based on a total of 19,406 annotated protein-coding genes