Structural variants contribute substantially to genetic diversity and are important evolutionarily and medically, but they are still understudied. Here we present a comprehensive analysis of structural variation in the Human Genome Diversity panel, a high-coverage dataset of 911 samples from 54 diverse worldwide populations. We identify, in total, 126,018 variants, 78% of which were not identified in previous global sequencing projects. Some reach high frequency and are private to continental groups or even individual populations, including regionally restricted runaway duplications and putatively introgressed variants from archaic hominins. By de novo assembly of 25 genomes using linked-read sequencing, we discover 1,643 breakpoint-resolved unique insertions, in aggregate accounting for 1.9 Mb of sequence absent from the GRCh38 reference. Our results illustrate the limitation of a single human reference and the need for high-quality genomes from diverse populations to fully discover and understand human genetic variation.

结构变异对遗传多样性有很大贡献，在进化和医学上都很重要，但它们的研究仍然不足。在这里，我们对人类基因组多样性面板中的结构变异进行了全面分析，该面板是一个高覆盖率数据集，包含来自全球 54 个不同人群的 911 个样本。我们总共鉴定出 126,018 个变异，其中 78% 在之前的全球测序项目中未发现。有些频率很高，并且是大陆群体甚至个体群体所独有的，包括区域限制的失控复制品和可能来自远古人类的基因渗入变体。通过使用链接读取测序对 25 个基因组进行从头组装，我们发现了 1,643 个断点解析的独特插入，总共占 GRCh38 参考文献中缺失的 1.9 Mb 序列。我们的结果说明了单一人类参考的局限性以及需要来自不同人群的高质量基因组才能充分发现和理解人类遗传变异。