Switchgrass SNP Browser

How to use

• Search a gene by its AP13 v6.1 locus name (e.g. Pavir.1KG000025), a transcript ID, or an AP13 v5.1 name. Partial names also match.
• Functional names — if the functional-annotation file has been loaded, you can also search by an Arabidopsis/rice homolog symbol or the AtNgNNNNN hit ID. A symbol may match several paralogous switchgrass genes; pick the one you want from the list.
• The gene model shows exons (boxes), CDS (filled), and UTRs. Each SNP is a lollipop colored by region. Hover for position; click for full detail.
• The region counts summarize how many SNPs fall in CDS, 5′/3′ UTR, introns, the promoter (upstream window you set), and downstream.
• Click any SNP (table row or lollipop) to see allele frequency, genotype counts, and a breakdown by ecotype and subpopulation across all 732 samples.
• Download genotype table (CSV) in the gene view exports a sample-by-locus table — one row per sample (with ecotype and subpopulation columns), one column per SNP, each cell the call as nucleotides (A/T…) or - for missing. Opens cleanly in Excel; friendly for non-bioinformatics users.
• The Region browser tab lets you pick a chromosome and a start/end position (up to 5 Mb) and draws a gene track of that window — each gene is an arrow (▶/◀ = strand) at its real position, including genes that only partly overlap. Click a gene (arrow or chip) to open its full view with SNPs. SNPs are not loaded up front (that window can hold many thousands); use Show SNP table for the whole range, or Download CSV/VCF.
• The Samples tab lists the panel metadata; filter by ecotype, subpopulation, or state.
• The Map tab plots each sample at its origin collection site, colored by ecotype (701 of 732 have coordinates). When you click a SNP, its popup also shows a map of the genotype at that site for every sample — 0 hom-ref, 1 het, 2 hom-alt (and grey for missing) — so you can see how the alleles are distributed geographically.

Region definitions

• CDS: inside a coding exon   5′/3′ UTR: annotated UTR
• intron: inside the gene body but not in any exon
• promoter: within the flank window upstream of the gene (strand-aware)
• downstream: within the flank window downstream of the gene