28bfc5e8e4301c0955eac938490458282438cf49 max Tue Nov 4 07:28:44 2025 -0800 adding HGDP and alfa docs page to var freqs track diff --git src/hg/makeDb/trackDb/human/alfa.html src/hg/makeDb/trackDb/human/ALFA.html similarity index 94% rename from src/hg/makeDb/trackDb/human/alfa.html rename to src/hg/makeDb/trackDb/human/ALFA.html index d9815973572..80bea32f2a6 100644 --- src/hg/makeDb/trackDb/human/alfa.html +++ src/hg/makeDb/trackDb/human/ALFA.html @@ -1,75 +1,72 @@ -<html><head> -<meta http-equiv="content-type" content="text/html; charset=UTF-8"></head> - <body> <p><span style="font-size: 12pt;"><strong>Description</strong> </span></p> <p>The NCBI <strong>AL</strong>lele <strong>F</strong>requency <strong>A</strong>ggregator (<a href="https://www.ncbi.nlm.nih.gov/snp/docs/gsr/alfa/">ALFA</a>) pipeline is developed to compute allele frequency for variants in dbGaP across approved un-restricted studies and to provide the data as open-access to the public through dbSNP. The goal of the ALFA project is to make frequency data from over 1M dbGaP subjects open-access in future releases to facilitate discoveries and interpretations of common and rare variants with biological impacts or causing diseases.</p> <p>The R4 release of 408,709 subjects included allele counts and frequency for 15.5 million rs site including 959,966 ClinVar RS IDs. More information about ALFA can be found at https://www.ncbi.nlm.nih.gov/snp/docs/gsr/alfa/ and any questions about ALFA track data should be forwarded to <mailto:snp-admin@ncbi.nlm.nih.gov>.</p> <p><span style="font-size: 12pt;"><strong>Subtracks</strong></span></p> <p>This track contains data from 12 populations:</p> <p>* ALFA data for African population</p> <p>* ALFA data for African American population</p> <p>* ALFA data for African Others population</p> <p>* ALFA data for Asian population</p> <p>* ALFA data for East Asian population</p> <p>* ALFA data for European population</p> <p>* ALFA data for Global population</p> <p>* ALFA data for Latin American 1 population</p> <p>* ALFA data for Latin American 2 population</p> <p>* ALFA data for Other population</p> <p>* ALFA data for Other Asian population</p> <p>* ALFA data for South Asian population</p> <h2> </h2> <h2>Display Conventions and Configuration</h2> <h3>Labels</h3> <p>The variant label is the dbSNP reference SNP ID (rsid).</p> <h3>Mouseover</h3> <p>The mouseover (displayed when the mouse is hovered over a variant) shows the following:</p> <ul> <li>Chromosome</li> <li>position</li> <li>Reference allele and frequency</li> <li>Alternate allele and frequency</li> </ul> <h3> </h3> <h3>Detail Page</h3> <p>The detail page contains the following:</p> <ul> <li><a>link to the dbSNP RS Page of the variation</a></li> <li><a>chromosome position</a></li> <li><a>mouseover label (allele frequencies)</a></li> <li><a>track hub date last updated</a></li> </ul> <p> </p> <h3>Variant Colors</h3> <p><a>The colors indicate the alternate allele frequencies</a><a>. </a></p> <ul> <li style="color: #ff0000;"><strong>red: alternate allele frequency falls in [0.5, 1]<br></strong></li> </ul> <ul> <li style="color: #0000ff;"><strong>blue: alternate allele frequency falls in [0.4, 0.5)<br></strong></li> </ul> <ul> <li style="color: #ee82ee;"><strong>violet: alternate allele frequency falls in [0.3, 0.4)<br></strong></li> </ul> <ul> <li style="color: #9c6597;"><strong>light violet: alternate allele frequency falls in [0.2, 0.3)<br></strong></li> </ul> <ul> <li style="color: #007fff;"><strong>light azure: alternate allele frequency falls in [0.1, 0.2)<br></strong></li> </ul> <ul> <li style="color: #a52a2a;"><strong>brown: alternate alelle frequency falls in [0, 0.1)<br></strong></li> </ul> </body></html>