Performance of the three assays over a range of sequencing depths. For 10 libraries (five double-stranded [DS], and five single-stranded [SS] libraries) with varying percentages of human sequences before enrichment (0.1%–86.7%), we show the number of unique SNPs at different levels of sequencing depth (based on down-sampling). For a typical amount of sequencing of a capture experiment (25 million merged sequences), and after removal of duplicated sequences, the Twist Ancient DNA assay always enriches for more SNPs than the other two assays. For most experiments, more SNPs are retrieved after one round of enrichment than after two. We did not perform the two-enrichment-round Twist Ancient DNA experiment for the two libraries with the highest endogenous content (S1633.E1.L1 and S10871.E1.L6).
