Table 2.

Summary of RNA-seq filtering/trimming and mapping statistics.

Species	Treatment	RNA-seq library type	Sequencing mode	Mean no. of reads (SE) or pairs (PE)	Mean no. of reads (SE) or pairs (PE) removed	Mean proportion of reads (SE) or pairs (PE) removed	Mean no. of observed fragments*	Mean no. of mapped fragments*	Average mapping rate	Reference source
Homo sapiens	Undepleted	Inward unstranded	PE	40,218,886	8,203,217	20.4%	32,015,669	25,593,239	80.9%	NCBI RefSeq
Homo sapiens	Globin depleted	Inward unstranded	PE	36,874,759	10,704,088	29.0%	26,170,671	20,371,624	75.8%	NCBI RefSeq
Sus scrofa	Undepleted	Inward unstranded	PE	39,036,515	4,613,991	11.8%	28,685,437	25,129,140	87.7%	NCBI RefSeq
Sus scrofa	Globin depleted	Inward unstranded	PE	31,339,886	3,899,427	12.4%	22,867,049	19,959,995	87.3%	NCBI RefSeq
Equus caballus	Undepleted	Unstranded	SE	24,271,141	38,892	0.2%	14,850,797	11,387,774	76.5%	NCBI RefSeq
Bos taurus	Undepleted	Inward stranded forward	PE	20,495,983	3,474,597	17.0%	17,021,386	12,353,147	72.6%	NCBI RefSeq

^*The Salmon tool categorises fragments as single read (for SE RNA-seq libraries) or a read pair (for PE RNA-seq libraries).