A subset of libraries that exceeded 0.2% human DNA and 10% deamination damage at the terminal end of DNA fragments were subsequently used for two previously published hybridization-based in-solution DNA-enrichment assays: (i) The 1240 k capture (1517, 32), which targets 1,237,207 genome-wide nuclear SNPs. The targeted SNP panel combines the sets reported by Haak et al. (17) and by Fu et al. (16) and is further described by Mathieson et al. (15); and (ii) The “Mitochondrial capture,” which targets the whole human mitochondrial genome (16). Both captures were carried out as described in the SI (supplemental information) text sections 3.2-3.3 of Fu et al. (16) with modified hybridization conditions of 65°C for about 24 hours. Enriched libraries were single-end sequenced on the same platform as the initial shotgun ones.

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