This container track helps call out sections of the genome that often cause problems or confusion when working with the genome. There are two subtracks for now, Anshul Kundaje's ENCODE Blacklist and the UCSC Unusual Regions track.
The hg19 genome has a track with the same name, but with many more subtracks, as the GeT-RM and Genome-in-a-Bottle artefact variants do not exist yet for hg38, to our knowledge. If you are missing a track here that you know from hg19 and have an idea how to add it hg38, do not hesitate to contact us.
The UCSC Unusual Regions subtrack contains annotations collected at UCSC, -UCSC, put together from other tracks, our experiences and support email list +put together from other tracks, our experiences and support email list requests over the years.
For example, it contains the most well-known gene clusters (IGH, IGL, PAR1/2, TCRA, TCRB, etc) and annotations for the GRC fixed sequences, alternate haplotypes, unplaced contigs, pseudo-autosomal regions, and mitochondria. These loci can yield alignments with low-quality mapping scores and discordant read pairs, especially for short-read sequencing data. This data set was manually curated, based on the Genome Browser's assembly description, the FAQs about assembly, and the NCBI RefSeq "other" annotations track data.The ENCODE Blacklist subtrack contains a comprehensive set of regions which are troublesome for high-throughput Next-Generation Sequencing (NGS) aligners. These regions tend to have a very