1eb778792659124aa071876e2c5541bc8e3d6b3d max Tue Nov 4 01:54:21 2025 -0800 adding a link to more updated ancient dna tracks, refs #36592 diff --git src/hg/makeDb/trackDb/human/alfa.html src/hg/makeDb/trackDb/human/alfa.html new file mode 100644 index 00000000000..d9815973572 --- /dev/null +++ src/hg/makeDb/trackDb/human/alfa.html @@ -0,0 +1,75 @@ +<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> \ No newline at end of file