Documentation PlantQTLdb Assistant Variant Annotation and Local QTL Evidence
Browse Documentation
Getting Started with Assistant Gene Structure and Sequence Extraction Variant Annotation and Local QTL Evidence Functional Enrichment with g:Profiler Network Analysis with STRING Finding Sequencing Data with ENA Sequence Similarity Search with BLAST Plant Motif Analysis with JASPAR and FIMO DNA Analysis with Evo2 External Biological Evidence Sources Troubleshooting and Limitations

PlantQTLdb Assistant

Variant Annotation and Local QTL Evidence

inspect gene-region variants, stored effect annotations and nearby QTL/GWAS evidence with downloadable tables

Requires Research mode

Open PlantQTLdb Assistant

When to use it

Use the KG variant workflow to investigate stored annotations and associations around a candidate gene. Gene structure is checked against the KG coordinates before combining the layers; no new SnpEff annotation or causal inference is run.

How to ask and what you receive

Inspect one exact variant

ask
Show variant annotations for rice MSU7 chr1:14452192:A:G

what you receive

A KG annotation summary for the exact species, assembly, position and alleles, with stored gene effects and available QTL/GWAS context. Missing fields remain unknown; this is not a new SnpEff run or the full gene-window diagram.

Start inside the gene

ask
Show variants inside the gene body of rice LOC_Os01g25484

what you receive

All returned transcripts and local QTL/GWAS tracks, with the table initially filtered to the gene body. Expand a variant to inspect stored effects, transcript/HGVS sets and association context. The verified dataset returned 77 gene-body variants, including 71 SNPs; counts depend on the current KG.

Include upstream and downstream sequence

ask
Show variants for rice LOC_Os01g25484, including flanks of 2 kb on each side and the gene body

what you receive

The evidence window includes the gene plus 2 kb on each side, and the table initially includes that whole window. The prior verification returned 183 variants. These are indexed variants, not every possible mutation.

Read the card and export tables

  • The table starts with 10 rows per page. Use the available region, effect and association filters, and expand individual rows for annotation and source details.
  • Download variants, QTL associations, GWAS matches and nearby GWAS as separate CSVs. Downloads follow the current filters across returned rows, not only the visible page.
  • Gene-specific effect annotations and global variant severity are different fields. Transcript and HGVS lists can be aggregated sets and should not be paired by list position.
  • For a flanks-only analysis, select the corresponding region filter when available or filter the variants CSV to region=flank. The inclusive-window example deliberately also contains the gene body.

What the overlaps and counts mean

A same-position GWAS match has not necessarily been allele-harmonized. It is distinct from a direct KG association and from a nearby locus, and does not establish colocalization or causality.

QTL retrieval is a bounded preview: up to 10 associations per variant and 10,000 overall. Counts with ≥ are lower bounds; qtl_counts_complete and truncation fields in downloaded data record incompleteness. The plot can also be partial. These files are not an unlimited all-target QTL export.

Reference mismatches stop coordinate joins. The gene structure workflow remains unavailable for sorghum and tomato. Missing annotation, a timeout and a successful zero-result query must not be interpreted as the same outcome.