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 already in bigWig format and are served unchanged, with no conversion step. The sequence names in them follow the HPRC PanSN convention and are resolved to the assembly through the GenArk chromAlias. The steps are described in the makeDoc, the build scripts are in the kent source tree, and the track configuration is in trackDb/contrib/hprc2annot.
The methylation signal is stored as a bigWig file (methylation.bw) that can be read with the UCSC tools bigWigInfo and bigWigToBedGraph, or queried by region with bigWigSummary. The original files are available from the HPRC S3 bucket linked above.
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.