b. Second sequencing run and population genetic dataset
The second sequencing run (96 individuals treated with WGA prior to
sequencing) produced a total of 354.9 million sequence reads, which was
reduced to 69.3 million after quality filtering; here, 70.7% of
sequence reads were removed during quality filtering due to adapter
contamination, and 1.1% were discarded due to low quality (Appendix 1:
Table A1). Both the 24 WGA libraries from the WGA test dataset and these
96 libraries were used to create the population genetic dataset, however
14 individuals containing more than 50% missing data were additionally
removed; after filtering, this dataset contained 106 individuals and
1,702 SNPs (Appendix 1: Table A3) and was used for all subsequent SNP
analyses.