This track is part of the Methylation and 3D Chromatin collection of the zebra finch telomere-to-telomere hub.
Cytosines in a CpG dinucleotide can carry a methyl group, and this mark is copied to the daughter strand after replication, so it is inherited through cell division. Dense methylation is generally associated with silenced DNA, and PacBio reads report it directly, because the polymerase kinetics differ over a modified base. This track shows the estimated fraction of molecules methylated at each CpG. The dip in methylation inside an otherwise heavily methylated satellite array is a well-known signature of the active centromere core.
A bar graph of methylation probability per CpG site, autoscaled to the data in view.
Per-read base modifications were called from the HiFi BAM with the PacBio Jasmine caller (PacBio Jasmine), producing a modBAM with MM and ML tags. HiFi reads were extracted from the CCS output with extracthifi from pbtk, aligned to the reference with pbmm2, and sorted and indexed with SAMtools. Reference-anchored CpG methylation probabilities were then computed with aligned_bam_to_cpg_scores from pb-CpG-tools.
The file was taken from GenomeArk at https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/methylation/bTaeGut7v0.4_MT_rDNA.PBmethylation.v0.1.bw. It is already in a binary indexed format that the browser reads over the network, so the track points at it where it is and no copy is kept in the hub. The hub is reproduced by the commands in src/hg/makeDb/doc/contrib/bTaeGut7.txt of the UCSC kent source tree.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our API, track=methyl5mC.
This track points straight at the file on GenomeArk rather than at a copy in the hub, so no download step is needed to work with it: bigWigToBedGraph reads it over the network, as does the browser.
The original annotation files are on GenomeArk, in the bTaeGut7 annotations directory.
Formenti G, Jain N, Medico JA, Sollitto M, Antipov D, Barcellos S, Biegler M, Borges I, Chang JK, Chen Y et al. The complete genome of a songbird. Cell. 2026 Aug 6;189(16):4922-4945.e12. PMID: 42561917
The assembly and all of these annotations were produced by the Vertebrate Genome Laboratory at The Rockefeller University and their collaborators, and released through GenomeArk. Thanks to Giulio Formenti and Erich D. Jarvis and their co-authors for making the data available before and after publication. The analysis code is at github.com/gf777/T2T-zebra-finch. This hub was assembled at UCSC from the IGV session distributed with the annotations, using hubtools.