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. -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. +Genomes Project, representing five ancestry groups. This callset was created +primarily for SV imputation. To generate a multi-ancestry SV imputation +reference panel, SVs observed in only one individual (singletons) were excluded, +and the remaining SVs were merged with previously identified short variants from +the same individuals. This panel was used to impute SVs in approximately 500,000 +UK Biobank participants and to 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. -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. +38,459 deletions, 5,729 inversions, 2,696 breakends, and 608 duplications. 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.
-Although the two studies share the same raw sequencing data, they applied +The 888 samples in this dataset are a subset of the 1,019 samples included in +the 1KG Vienna ONT track (Schloissnig et al. +2025). Although the two studies share the same raw sequencing data, they 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) |