The proposed framework contains the classical credibility theory as a special case and is based on the idea of varying the trimming threshold level to investigate the sensitivity of the credibility premium.
PEAR was used with default parameter settings with the exception of the Phred scale quality score trimming threshold, which was set to 20.
To eliminate low quality nucleotides, raw Illumina reads were trimmed using a custom Perl script with windowed adaptive trimming (Phred quality threshold of 20 and minimum read length of 20 nt).
The resulting reads were mapped to the baboon genome (Panu2.0) using the efficient short-read aligner bwa 0.5.9 (Li and Durbin, 2009), with a seed length of 25 bases, a maximum edit distance of two mismatches in the seed, a read trimming quality score threshold of 20, and the default maximum edit distance (4% after trimming).
Low quality nucleotide reads trimming (Phred quality threshold of 25 and minimum reads length of 40 nt) was performed with Sickle, a sliding-window, adaptive, quality-based trimming tool for FastQ files (available at [ 95]).
The raw sequencing reads were trimmed at a threshold of 0.01 and the sequences obtained were assembled de novo using CLC Genomics Workbench version 4.9 (CLC bio, Denmark).
For each species, the short reads were trimmed with the threshold of error probability < 0.05 and were de novo assembled using CLC Genomic Workbench 4.9 (CLC Bio, Aarhus, Denmark).
These short reads were trimmed with a threshold of error probability <0.05 and then de novo assembled by use of CLC Genomic Workbench 4.9 (CLC Bio, Aarhus, Denmark).
A genome-wide trimmed standard deviation threshold of 0.25 was used to determine whether a window was within a CNVR, and neighboring windows above this threshold were merged to form the CNVRs.
Pair-end readseads were trimmed with the BWA trimming mode at a threshold of Q13 (P = 0.05) as implemented by SolexaQA version 1.10 [ 24].
