Fragment sizes were calculated using the Fragment Analyser 1.02 computer program (Pharmacia) via comparison with the internal size standards (73, 122, 196, and 231 bp).
The GENOTYPER software was used to analyze the fragment size.
A Bioanalyzer 2100 12 K DNA Chip assay (Agilent Technologies, Santa Clara, USA; p/n 5067 1508) was used to assess the fragment size distribution.
Note that there is a clear correlation between fragment size of the genomic DNA used and the coverage, the larger the fragment size used the lower the target coverage achieved, as more flanking DNA is captured.
For the whole human genome we used the same fragment size as for the horse genome.
Another way to speed-up the pairing phase is to quickly estimate the fragment size distribution using a large-enough sample instead of using the complete set of aligned reads, and then apply this estimate to calculate the mismap probabilities.
We use the mean fragment size, μ, estimated from the data, to calculate p, the probability that the target is fragmented between any given pair of bases, and q = 1-p.
Standard size marker of 100 bp (NEB) was used to determine the fragment sizes for each markers.
As an external size standard, SmaI-digested S. aureus NCTC8325 strain was used to calculate the fragment sizes with BioNumerics version 6.0 software (Applied Maths, Sint-Martens-Latem, Belgium).
PCR products for 81 DNA samples from two varieties were electrophoresed on an ABI PRISM 3100 Genetic Analyzer (Applied Biosystems) and Geneious 7.0.4 software (Biomatters Ltd., Auckland, New Zealand; http://www.geneious.com/) was used to assess the fragment sizes.
