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Table 1 Overview of the sequencing of improved reduced-representation libraries (iRRLs) for the West Alas (WA) and South Kinabatangan (SK) orangutan study populations

From: Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms

  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×
  1. aPredicted by in-silico digest of the orangutan reference genome ponAbe2 (Sumatran) with Hae III. 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 bphiqual.