This track shows DNA methylation across this Human Pangenome Reference Consortium (HPRC) Release 2 assembly, measured from Oxford Nanopore (ONT) long-read sequencing. Methylation is a chemical mark (a methyl group) added to cytosine bases, most often where a C is followed by a G (a "CpG" site). It is a major layer of epigenetic regulation: densely methylated promoters tend to be silenced, while unmethylated CpG islands are typically active. Nanopore sequencing detects these marks directly from the raw signal, so methylation can be read off the same reads used to assemble the genome. The track shows, at each CpG, the fraction of reads that were methylated.
The track is a signal graph. At each position the value is the percentage of reads methylated at that CpG, on a 0 to 100 scale. Taller bars mean a higher fraction of methylated molecules.
Oxford Nanopore reads (R9.4.1 chemistry) were aligned to the assembly with minimap2, per-read 5-methylcytosine calls were summarized to a per-CpG methylation frequency, and the frequencies were stored as a bigWig signal track. See Credits for the HPRC methylation pipeline.
The methylation files were obtained from the HPRC Release 2 data collection on the public s3://human-pangenomics bucket, indexed at the hprc_intermediate_assembly data tables. The per-assembly bigWig files are referenced by this hub directly from that public bucket; the sequence names in them are resolved to the assembly through the GenArk chromAlias.
The methylation signal is stored as a bigWig file hosted on the HPRC S3 bucket (linked above) and can be read with the UCSC tools bigWigInfo and bigWigToBedGraph, or queried by region with bigWigSummary.
Data were generated by the Human Pangenome Reference Consortium. Thanks to the HPRC production team for making these data available.
Method details for the HPRC methylation pipeline are maintained with the HPRC intermediate assembly resources. Data were generated by the Human Pangenome Reference Consortium.