Description
This track shows structural variants (SVs) from the
Consortium of Long-Read Sequencing database (CoLoRSdb).
The sequencing data was contributed by labs and research groups around the world and covers 1,427 individuals in total, all sequenced with PacBio HiFi.
The track contains 426,239 SVs: 232,973 insertions,
192,534 deletions and 732 inversions, with per-site allele frequencies,
genotype counts and Hardy-Weinberg statistics across the cohort.
Note that CoLoRSdb also published short variants, in the Genome Browser,
these can be found in the Variants Frequencies track.
Display Conventions and Configuration
Items are colored by SV type:
- Deletions (DEL) - red
- Insertions (INS) - blue
- Inversions (INV) - purple
Insertions are placed at the insertion site; deletions and inversions span
the affected reference interval. Filters are available for SV type, SV
length and alternate allele count. Mousing over an item shows the SV type,
length, allele frequency, allele counts (homozygous / heterozygous /
hemizygous) and the number of carrier samples.
The detail page additionally shows the total allele number (AN), the
Hardy-Weinberg equilibrium p-value (HWE), the excess-heterozygosity p-value
(ExcHet) and the REF / ALT allele sequences.
Methods
SVs were called on each sample's long-read alignments with
pbsv
and then merged across the CoLoRSdb cohort with
Jasmine
to produce a site-level joint callset. Per-site allele counts, allele
frequencies, HWE and ExcHet p-values were computed from the joint VCF. The
VCF was converted to a bigBed for display in the Genome Browser.
The step-by-step build commands are recorded in the UCSC makeDoc,
doc/hg38/lrSv.txt;
the conversion scripts and autoSql schemas live in
makeDb/scripts/lrSv,
and the track configuration is in
trackDb/human/lrSv.ra.
Data Access
The data can be explored interactively in table format with the
Table Browser or the
Data Integrator, and accessed
programmatically through our API,
track=colorsDbSv.
The bigBed is available from
our
download server as sv.hs1.bb. Example:
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hs1/lrSv/colorsDb/sv.hs1.bb -chrom=chr21 -start=0 -end=100000000 stdout.
The original VCF files and full release documentation are available from
the CoLoRSdb v1.2.0 dataset on Zenodo:
zenodo.org/records/14814308.
Credits
Thanks to Mike Schatz, Evan Eichler, and all
CoLoRSdb investigators
for generating and making the data publicly available.
References
Lake, J. A., & Consortium of Long-Read Sequencing (CoLoRS).
Consortium of Long-Read
Sequencing Database (CoLoRSdb) (v1.2.0) [Data set].
Zenodo. 2025 Feb 5.
DOI: 10.5281/zenodo.14814308
Kirsche M, Prabhu G, Sherman R, Ni B, Battle A, Aganezov S, Schatz MC.
Jasmine and Iris: population-scale structural variant comparison and analysis.
Nat Methods. 2023 Mar;20(3):408-417.
PMID: 36658279;
PMC: PMC10006329
Eisfeldt J, Ameur A, Lenner F, Ten Berk de Boer E, Ek M, Wincent J, Vaz R, Ottosson J, Jonson T,
Ivarsson S et al.
A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities.
Genome Res. 2024 Nov 20;34(11):1774-1784.
PMID: 39472022;
PMC: PMC11610602