PAV data dashboard
This dashboard shows the variable gene presence/absence variation (PAV) binary matrix for the Watkins collection in UMAP space. The data is built from the gene PAV matrix for the pangenome, including all new genes found in the Watkins landrace collection.
The dashboard supports basic filtering, allowing users to highlight accessions in UMAP space based on available metadata. After applying filters, a download box will appear at the bottom of the page to export PAV data for the selected accessions.
Users can also search for a specific IWGSC gene using the gene model lookup box to explore its PAV across all accessions in the Watkins Pangenome.
Gene model lookup
PAV matrix filters
Lat / Lon bounding box (optional — leave blank to ignore)
1038 sample(s) — page 1 of 52
| Accession name | Accession name in China (WWWG2B) | GRU StorCode | GRU ID-Plant | Synonym 1 | Synonym 2 | Country of origin | Latitude | Longitude | Growth habit | Ancestral group | Sequencing depth | Mapping rate (%) | Continent |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ability | WWWSC00828 | WGED0562 | 40100.0 | Gediflux ID 562 | W9343 | United Kingdom | -35.3132 | 149.1006 | nan | Modern | 12.32 | 99.69 | Europe |
| Agron | WWWSC00829 | WGED0194 | 39950.0 | Gediflux ID 194 | nan | Austria | 48.2269 | 16.3496 | winter | Modern | 13.95 | 99.88 | Europe |
| Alba | WWWSC00830 | WGED0014 | 39770.0 | Gediflux ID 14 | W0357 | Netherlands | 52.3738 | 4.8969 | winter | Modern | 11.19 | 99.78 | Europe |
| Albatross | WWWSC00831 | WGED0203 | 39959.0 | Gediflux ID 203 | nan | Germany | 52.5159 | 13.3715 | winter | Modern | 13.73 | 99.8 | Europe |
| Alcedo | WWWSC00832 | WGED0077 | 39833.0 | Gediflux ID 77 | W2192 | Germany | 52.5159 | 13.3715 | winter | Modern | 11.09 | 99.76 | Europe |
| Almus | WWWSC00834 | WGED0254 | 40010.0 | Gediflux ID 254 | nan | Germany | 52.5159 | 13.3715 | winter | Modern | 21.81 | 99.71 | Europe |
| Altria | WWWSC00835 | WGED0164 | 39920.0 | Gediflux ID 164 | nan | France | 48.859 | 2.3476 | winter | Modern | 48.44 | 99.88 | Europe |
| Arminda | WWWSC00836 | WGED0097 | 39853.0 | Gediflux ID 97 | W2864 | France | 48.859 | 2.3476 | winter | Modern | 13.7 | 99.4 | Europe |
| Aronde | WWWSC00837 | W0060 | 13682.0 | - | nan | France | 48.859 | 2.3476 | winter | Modern | 12.66 | 92.39 | Europe |
| Avalon | WWWSC00838 | WGED0085 | 39841.0 | Gediflux ID 85 | W2564 | United Kingdom | 51.4934 | -0.2681 | winter | Modern | 11.86 | 99.8 | Europe |
| Avocet | WWWSC00839 | WGED0510 | 40048.0 | Gediflux ID 510 | W4116 | United Kingdom | 51.4934 | -0.2681 | winter | Modern | 26.1 | 99.89 | Europe |
| Aztec | WWWSC00840 | WGED0163 | 39919.0 | Gediflux ID 163 | nan | France | 48.859 | 2.3476 | winter | Modern | 13.35 | 99.88 | Europe |
| Banco | WWWSC00841 | WGED0062 | 39818.0 | Gediflux ID 62 | W1208 | Sweden | 59.3152 | 18.0401 | winter | Modern | 21.21 | 99.88 | Europe |
| Bandit | WWWSC00842 | WGED0568 | 40106.0 | Gediflux ID 568 | W9357 | United Kingdom | 51.4934 | -0.2681 | winter | Modern | 16.51 | 99.9 | Europe |
| Banner | WWWSC00843 | WGED0537 | 40075.0 | Gediflux ID 537 | W6862 | United Kingdom | 51.4934 | -0.2681 | winter | Modern | 19.78 | 99.71 | Europe |
| Beauchamp | WWWSC00844 | WGED0110 | 39866.0 | Gediflux ID 110 | W3598 | France | 48.859 | 2.3476 | winter | Modern | 16.48 | 99.89 | Europe |
| Beaver | WWWSC00845 | WGED0143 | 39899.0 | Gediflux ID 143 | W6955 | United Kingdom | 51.4934 | -0.2681 | winter | Modern | 11.13 | 99.68 | Europe |
| Becard_Kachu | WWWSC00846 | WREN0301 | 45673.0 | - | nan | Mexico | 19.4194 | -99.1308 | nan | Modern | 11.35 | 99.84 | North America |
| Bersee | WWWSC00847 | WGED0002 | 39758.0 | Gediflux ID 2 | W0116 | United Kingdom | 51.4934 | -0.2681 | winter | Modern | 20.95 | 99.88 | Europe |
| Blitz | WWWSC00848 | WGED0657 | 40195.0 | Gediflux ID 657 | nan | United Kingdom | 19.4194 | -99.1308 | spring | Modern | 11.35 | 99.58 | Europe |
CDS and protein sequences for the gene models ids in the PAV matrix are available for public download here.
Accession metadata sourced from: Cheng et al. Nature (2024).