The structural variants (SVs) in this dataset were identified using Oxford Nanopore long-read whole-genome sequencing of 888 individuals from the 1000 -Genomes Project, representing five ancestry groups. The SVs were merged with +Genomes Project, representing five ancestry groups. +This dataset and the 1KG ONT Vienna track +(Schloissnig et al. 2025) are based on the same underlying Oxford Nanopore +sequencing data; the 888 samples here are a subset of the 1,019 samples in that +track and only SVs that appear in a single sample (singletons) were removed from this track, +so this callset is smaller than the Schloissnig dataset. The reason is that +this callset was created primarily for imputation: The SVs here were merged with previously identified short variants from the same individuals to generate a multi-ancestry SV imputation reference panel. This panel was used to impute SVs in approximately 500,000 UK Biobank participants and test their associations with 32 disease-relevant traits.
The track contains all 107,445 SVs in the reference panel: 59,953 insertions, 38,459 deletions, 5,729 inversions, 2,696 breakends, and 608 duplications. +Variants seen in only a single individual (singletons) were excluded from the +panel, so every SV shown was observed in at least two individuals; the panel is +therefore not exhaustive for very rare variants. Each variant is annotated with its overall allele frequency; allele frequencies across five superpopulations (African, Admixed American, East Asian, European, and South Asian); Hardy-Weinberg equilibrium p-values; and imputation accuracy metrics from internal leave-one-out validation and UK Biobank imputation. For SVs reaching genome-wide significance, the associated traits, p-values, and INFO scores are listed on the corresponding variant details page.
-This dataset is an independent reprocessing of the same Oxford Nanopore reads -used for the 1KG ONT Vienna track -(Schloissnig et al. 2025). The 888 samples in this dataset are a subset of the -1,019 samples included in that track, with both datasets based on the same -underlying sequencing data. -However, the data-processing and SV-calling methods differ between the two -tracks, so the individual calls are only partially concordant. This track has -about 38,000 deletions and the Vienna track about 58,000; at a 50% -reciprocal-overlap threshold roughly 12,000 are shared. That is about a third -of the deletions in this track and, conversely, about a fifth of the Vienna -deletions; requiring at least 90% mutual overlap lowers these shares to roughly -a quarter and a sixth, respectively. A similar fraction (about a quarter) of -the insertions in this track have a size-matched Vienna insertion within -100 bp. The imputation reference panel, UK Biobank imputation results, and -SV-wide association study (SV-WAS) results described here are specific to this -track. +This dataset and the 1KG ONT Vienna track +(Schloissnig et al. 2025) are based on the same underlying Oxford Nanopore +sequencing data; the 888 samples here are a subset of the 1,019 samples in that +track. The two studies applied different data-processing and SV-calling +pipelines to address distinct research objectives, so the individual calls are +only partially concordant. The imputation reference panel, UK Biobank +imputation results, and SV-wide association study (SV-WAS) results described +here are specific to this track.
Items are colored by SV type, matching the other subtracks of the container:
| Deletion (DEL) | |
| Insertion (INS) | |
| Duplication (DUP) | |
| Inversion (INV) |