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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.