Two cs10 tracks read off the 217-way multiz alignment. Alignment depth is the number of the 216 other assemblies with an aligned base at each cs10 base: high across sequence the panel shares, low where assemblies lack it, cannot place it, or it was masked away. Variant frequency is the share of aligned plants whose base differs from cs10's: a population view of single-base differences against the reference.
Both are bar graphs, hidden by default. Depth runs from 0 to 216. Frequency runs from 0 to 1 and is shown with the maximum over each pixel's bases, so isolated variable sites stay visible when zoomed out. A base no alignment block covers has no value.
Read from the per-chromosome MAFs of the multiz alignment. Depth counts assemblies with A, C, G, T or N aligned (a gap is not aligned). Frequency counts only A, C, G and T, case-blind, and weights each assembly by one over the number of its plant's assemblies in the alignment, so a plant phased into two haplotypes counts once (216 assemblies, 156 plants; plants by BioSample, Lynch et al. 2025's organism IDs and curated pairs). It is written only where cs10 has A, C, G or T and at least 10 plants align; with fewer, one differing base would read as a large frequency. Substitutions only: insertions and deletions are not counted. Built by scripts/build_hub_alignment_tracks.py.
Every track file is a bigBed or bigWig under this hub's directory, named by the track's bigDataUrl, and can be read with UCSC's bigBedToBed and bigWigToBedGraph or downloaded directly.
The HighGen project.
Contact: rcb112@psu.edu
Blanchette M, Kent WJ, Riemer C, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 2004;14:708-715.