GC content is the fraction of guanine and cytosine bases in a stretch of DNA. Along a bird chromosome it is far from uniform: it rises with gene density and recombination rate, so the small microchromosomes are considerably more GC rich than the large macrochromosomes, and individual gene-dense regions stand out within a chromosome. This track shows the GC fraction in fixed 200 bp windows.
A bar graph with one value per 200 bp window, autoscaled to the data in view.
GC content was computed with Teloscope, run over the assembly in non-overlapping 200 bp windows (-w 200 -s 200) with the -g flag. Teloscope is a sequence scanner written for this project; see vgl-hub/teloscope. Full parameters are in the manuscript.
The file was taken from GenomeArk at https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/general/bTaeGut7v0.4_MT_rDNA.Teloscope.gc.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=gcPercent.
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.