low-complexity regions

Cent-Sat - Centromeric satellite repeats - gives the approximate locations of centromeric satellite repeats and acrocentric short arms in T2T-CHM13. It was manually constructed based on the official satellite annotation, the DNA-BRNN satellite annotation and the minigraph pangenome graph from the HPRC year-1 data. Alignment in the BED regions is usually much worse than in the rest of the genome. This file is intended for filtering spurious alignments or variant calls caused by centromeric repeats or acrocentric arms.
PAR regions on chrX, chrY - pseudo-autosomal regions (PARs) on chrX and chrY
low-complexity regions excluding alpha and HSAT2/3 satellites - Column 4: "ldust" for longdust regions 50bp or longer; "mg" for regions overlapping with minigraph LCR SVs. Column 5: longest allele in each LCR.
in LCR AND TRF - intersection of LCR track and the trf/simpleRepeats track
in TRF not LCR - regions in trf/simpleRepeat that are not found in LCR
in LCR not TRF - regions in LCR that are not found in trf/simpleRepeat

Intersections