9b60e5505dd8218f538ce44ca13bd4bd86df1d38 jnavarr5 Tue Nov 18 13:22:09 2025 -0800 Fixing typos found in code review, refs #36722 diff --git src/hg/makeDb/trackDb/human/varFreqs.html src/hg/makeDb/trackDb/human/varFreqs.html index dadf9f83ab0..278c10300f4 100644 --- src/hg/makeDb/trackDb/human/varFreqs.html +++ src/hg/makeDb/trackDb/human/varFreqs.html @@ -22,31 +22,31 @@

Simons Genome Diversity Project (SGDP): Funded by the Simons Foundation, the Simons Genome Diversity Project is a large-scale effort that sequenced high-coverage genomes from 300 individuals (279 in this track) representing 142 diverse and often indigenous populations worldwide. Its goal was to capture the full range of human genetic diversity to better understand population history, migration, and adaptation. It is sampling populations in a way that represents as much anthropological, linguistic and cultural diversity as possible, and thus includes many deeply divergent human populations that are not well represented in other datasets. SGDP emphasizes breadth of global representation and population history, whereas HGDP emphasizes continuity and - comparability across major population groups. Not all iits data is + comparability across major population groups. Not all its data is public, so this track contains only 279 genomes. For details, see (Mallick et al, Nature 2016). The hg38 track was lifted from hg19.

Available only on hg38:

Human Genome Diversity Project (HGDP): 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. The Human Genome Diversity Project (HGDP) was launched in the early 1990s to study the genetic variation and evolutionary history of modern humans across global populations. Its goal was to document the full @@ -223,55 +223,55 @@

MCPS: VCFs with summarized allele frequencies are available from the MCPS website.

Regeneron one million exomes: VCFs with summarized allele frequencies are available from the RGC ME website.

TOPMED: VCFs with summarized allele frequencies are available from the TOPMED BRAVO website. They require a login.

-GenomeAsia Pilot: VCFs are available from UCSC and also from the +GenomeAsia Pilot: VCFs are available from UCSC and also from the GenomeAsia 100K website. No license nor login.

Methods

MXB: Genotyping was performed with the Illumina Multi-Ethnic Global Array (MEGA, ~1.8M SNPs), optimized for admixed populations and enriched for ancestry-informative and medically relevant variants. Only autosomal, biallelic SNPs passing quality control are included. Samples were selected from 898 recruitment sites, with prioritization of indigenous language speakers. Data processing included GenomeStudio → PLINK conversion, strand alignment, removal of duplicates, update of map positions using dbSNP Build 151 and low-quality variants/individuals, and relatedness filtering.

SGDP: The version used was https://sharehost.hms.harvard.edu/genetics/reich_lab/sgdp/vcf_variants/, merged with bcftools and lifted to hg38 with CrossMap.

-KOVA: V7 of the TSV.gz was obtained from the KOVA staff and converted to VCF. If it not +KOVA: V7 of the TSV.gz was obtained from the KOVA staff and converted to VCF. It is not available for download from our site but can be requested from the KOVA website.

Credits

MXB: We thank the Center for Research and Advanced Studies (Cinvestav) of Mexico for generating and providing the frequency data, the National Institute of Medical Sciences and Nutrition (INCMNSZ) for DNA extraction, and the Ministry of Health together with the National Institute of Public Health (INSP) for the design and implementation of the National Health Survey 2000 (ENSA 2000). We also thank the ENSA-Genomics Consortium for their contributions to sample collection and data processing that made possible the construction of the MXB genomic resource.

Methods

Credits