Table 1.

Overview of the sequencing of improved reduced-representation libraries (iRRLs) for the West Alas (WA) and South Kinabatangan (SK) orangutan study populations

	Pop_WA	Pop_SK
	(Sumatra)	(Borneo)
No. of individuals	15	16
iRRL stacks per individual (predicted)a	305,574	305,574
Median iRRL target efficiencyb	97%	86%
Total no. of beads per population	675,295,801	762,234,081
Total no. of mapped reads per population	528,081,935	646,922,204
Median no. of mapped reads per individual	32,345,177	43,451,986
% reads mapped F3/F5 (mappability)c	74.9/7.3	67.0/17.0
Mean no. of bphiqual per individuald	10,930,563	18,186,855
Median sequence coverage per individuale	41×	42×

^aPredicted by in-silico digest of the orangutan reference genome ponAbe2 (Sumatran) with HaeIII. ^bPercentage of sequenced sites that were predicted by the in-silico digest. ^cF3/F5 are the sequence read directions of the paired end sequencing mode. ^dNumber of sequenced base pairs passing all high quality filters (sites used for SNP detection). ^eGATK estimates based on bp_hiqual.