65091fe6f6487c23d650a144e947fc1c582d3f40 max Tue Apr 21 02:16:16 2026 -0700 abelSv: move under lrSv supertrack as short-read comparison subtrack Move the Abel et al. 2020 CCDG 17,795-genome SV callset from a top-level hg38 track to a subtrack of the lrSv supertrack (parallel to onekg3202Sr) and relabel shortLabel/longLabel to flag Illumina short-read provenance. The same bigBed is now visible on hg38 in the long-read SV browsing context. Also: - Clarify abelSv.html variant counts: 738,624 upstream unique SVs across both callsets, 737,998 after B37->hg38 liftOver (626 unmapped). B38=458,106, B37lift=279,892. - lrSv.html: fix triple-slash https:/// in the Ebert et al. Science reference URL. - bigBed.html: add closing on the extra-fields pipe-separator bullet and tighten a comma in the same sentence. refs #36258, refs #37376 diff --git src/hg/makeDb/trackDb/human/hg38/abelSv.html src/hg/makeDb/trackDb/human/abelSv.html similarity index 91% rename from src/hg/makeDb/trackDb/human/hg38/abelSv.html rename to src/hg/makeDb/trackDb/human/abelSv.html index 82cd0ab81b5..7d5913fffb5 100644 --- src/hg/makeDb/trackDb/human/hg38/abelSv.html +++ src/hg/makeDb/trackDb/human/abelSv.html @@ -1,47 +1,51 @@

Description

Structural variants (SVs) are large changes in DNA — deletions, duplications, inversions, insertions of mobile elements, and translocations — that are at least 50 base pairs in size. They are a major source of genetic variation between individuals and can affect gene dosage, disrupt coding sequence, or rearrange regulatory elements. Because SVs are harder to detect than small variants, population-scale SV maps lag behind single-nucleotide variant resources.

-This track displays site-frequency data for 738,624 SVs identified in 17,795 -deeply sequenced human genomes (mean coverage > 20×) by +This track displays site-frequency data for 737,998 SVs identified in 17,795 +deeply sequenced human genomes (mean coverage > 20×) by Illumina +short-read sequencing by Abel et al., Nature 2020. The samples were sequenced by the four sequencing centers of the NHGRI Centers for Common Disease Genomics (CCDG) program, supplemented with ancestrally diverse samples from the PAGE consortium and the Simons Genome Diversity Project. The composition includes roughly 24% African, 16% Latino, 11% Finnish, 39% non-Finnish European, and 9% other ancestries.

-Two non-overlapping public callsets are displayed as a single track:

+Two non-overlapping public callsets are combined into this track. +The upstream release contains 738,624 unique primary SV records across +the two callsets; 626 B37 records did not lift over to GRCh38, leaving +the 737,998 shown here:

B38 (native GRCh38): 14,623 samples, called directly on the - GRCh38 assembly.
B37lift (GRCh37, lifted): 8,417 samples originally called on - GRCh37, with coordinates lifted to GRCh38 using the standard UCSC - hg19→hg38 liftOver chain. 626 variants could not be lifted.
B38 (native GRCh38): 458,106 SVs from 14,623 samples, called + directly on the GRCh38 assembly.
B37lift (GRCh37, lifted): 279,892 SVs from 8,417 samples + originally called on GRCh37, with coordinates lifted to GRCh38 + using the standard UCSC hg19→hg38 liftOver chain.

Important: the B38 and B37 callsets share 5,245 samples. When inspecting a variant present in both callsets, users should not simply sum the allele counts; the AC/AN reported for each callset reflects that callset's sample set. The callset filter can be used to restrict display to one source.

Display conventions

Items are colored by SV type:

DEL deletion
DUP duplication
INV inversion