This track is part of the Structural Variation collection of the zebra finch telomere-to-telomere hub.
Because this genome was assembled as two separate haplotypes, the maternal and paternal copy of each chromosome can be compared directly. This track shows the large differences between them: 38 inversions and 4 translocations. Differences of this size are invisible to short-read resequencing and are one of the practical reasons for building a phased diploid assembly.
Each item is one variant, named by its type, either inversion or translocation.
Maternal and paternal haplotypes were aligned to each other with MashMap and the alignment was inspected as a dotplot in JBrowse2. Every structural variant seen there was confirmed against the Hi-C contact map in PretextView. Genome-wide sequence and structural variation was then quantified with SyRI v1.6.3 using default filtering, and visualized with plotsr v1.1.1.
The file was taken from GenomeArk at https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/large_SVs/bTaeGut7v0.4_MT_rDNA.large_SVs.v0.1.bed. It is a text format that a track hub cannot use directly, so it was converted to a binary indexed file. The conversion, and the whole 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=largeSv.
For automated download and analysis, this annotation is a bigBed file inside the hub. Individual regions or the whole annotation can be obtained with bigBedToBed, which can be compiled from source or downloaded as a precompiled binary; instructions are here. The tool also fetches a range, for example bigBedToBed <hubUrl>/GCF_048771995.1/largeSv.bb -chrom=NC_133024.1 -start=0 -end=100000 stdout, where <hubUrl> is the directory this hub was loaded from.
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
Goel M, Sun H, Jiao WB, Schneeberger K. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol. 2019 Dec 16;20(1):277. PMID: 31842948; PMC: PMC6913012
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.