44a568b95d278dc404a42e24c5877b523aa42e50 max Fri Mar 13 07:37:16 2026 -0700 adding a note to gnomad to make it clear that 3.1 should not be used, email from Chris diff --git src/hg/makeDb/trackDb/human/hg38/gnomadV4.1.html src/hg/makeDb/trackDb/human/hg38/gnomadV4.1.html index 4e247d0e706..b1e95fbf2a7 100644 --- src/hg/makeDb/trackDb/human/hg38/gnomadV4.1.html +++ src/hg/makeDb/trackDb/human/hg38/gnomadV4.1.html @@ -1,40 +1,40 @@ <h2>Description</h2> <p> With the gnomAD v4.1 data release, the v4 Pre-Release track has been replaced with the gnomAD v4.1 track. The v4.1 release includes a fix for the allele number <a target="_blank" href="https://gnomad.broadinstitute.org/news/2024-04-gnomad-v4-1/"> issue</a>. The v4.1 track shows variants from 807,162 individuals, including 730,947 exomes and 76,215 genomes. This includes the 76,156 genomes from the gnomAD v3.1.2 release as well as new exome data from 416,555 UK Biobank individuals. For more detailed information on gnomAD v4.1, see the related <a target="_blank" href="https://gnomad.broadinstitute.org/news/2024-04-gnomad-v4-1/">blog post</a>. <p> -The gnomAD v3.1 track shows variants from 76,156 whole genomes (and no exomes), all mapped to the -GRCh38/hg38 reference sequence. 4,454 genomes were added to the number of genomes in the previous -v3 release. For more detailed information on gnomAD v3.1, see the related <a target="_blank" -href="https://gnomad.broadinstitute.org/blog/2020-10-gnomad-v3-1/">blog post</a>.</p> +The gnomAD v3.1.1 track is the current version of gnomAD 3 and shows variants +from 76,156 whole genomes (and no exomes), all mapped to the GRCh38/hg38 +reference sequence. 4,454 genomes were added to the number of genomes in the +previous v3 release. For more detailed information on gnomAD v3.1, see the +related <a target="_blank" href="https://gnomad.broadinstitute.org/blog/2020-10-gnomad-v3-1/">blog post</a>. +A bugfix to v3.1 resulted in gnomAD3.1.1, see +<a target="_blank" href="https://gnomad.broadinstitute.org/news/2021-03-gnomad-v3-1-1/">changelog</a> +</p> <p> -The gnomAD v3.1.1 track contains the same underlying data as v3.1, but -with minor corrections to the VEP annotations and dbSNP rsIDs. On the UCSC side, we have now -included the mitochondrial chromosome data that was released as part of gnomAD v3.1 (but after -the UCSC version of the track was released). For more information about gnomAD v3.1.1, please -see the related -<a target="_blank" href="https://gnomad.broadinstitute.org/news/2021-03-gnomad-v3-1-1/">changelog</a>.</p> +Do not use gnomAD v3.1 anymore, we will remove the track soon. +</p> <p>GnomAD Genome Mutational Constraint is based on v3.1.2 and is available only on hg38. It shows the reduced variation caused by purifying natural selection. This is similar to negative selection on loss-of-function (LoF) for genes, but can be calculated for non-coding regions too. Positive values are red and reflect stronger mutation constraint (and less variation), indicating higher natural selection pressure in a region. Negative values are green and reflect lower mutation constraint (and more variation), indicating less selection pressure and less functional effect. Briefly, for any 1kbp window in the genome, a model based on trinucleotide sequence context, base-level methylation, and regional genomic features predicts expected number of mutations, and compares this number to the observed number of mutations using a Z-score (see preprint in the Reference section for details). The chrX scores were added as received from the authors, as there are no de novo mutation data available on chrX (for estimating the effects of regional