71b87b8f1d09fac9e0a7e1935a11cb52bfd9f65e lrnassar Wed Jul 24 17:22:53 2024 -0700 Forgot to update links to evaSnp6 from 4, oops. Refs #34119 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 388b90b..49c29f0 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -67,109 +67,109 @@ <a name="2024"></a> <a name="072524"></a> <h2>Jul. 25, 2024 EVA SNP release 6 for 37 assemblies</h2> <p> We are pleased to announce the release of the EVA SNP release 6 track for 37 assemblies. These tracks contain mappings of single nucleotide variants and small insertions and deletions (indels) — collectively Simple Nucleotide Variants (SNVs) — from the European Variation Archive (<a href="https://www.ebi.ac.uk/eva/" target="_blank">EVA</a>) Release 6. The full list of assemblies that contain the EVA SNP release 6 track is below:</p> <p> <div class="container"> <div class="row"> <div class="col-sm-4"> <ul> - <li>A. gambiae <a href="../cgi-bin/hgTrackUi?db=anoGam3&g=evaSnp4" + <li>A. gambiae <a href="../cgi-bin/hgTrackUi?db=anoGam3&g=evaSnp6" target="_blank">(anoGam3)</a></li> - <li>C. intestinalis <a href="../cgi-bin/hgTrackUi?db=ci3&g=evaSnp4" + <li>C. intestinalis <a href="../cgi-bin/hgTrackUi?db=ci3&g=evaSnp6" target="_blank">(ci3)</a></li> - <li>Bison <a href="../cgi-bin/hgTrackUi?db=bisBis1&g=evaSnp4" + <li>Bison <a href="../cgi-bin/hgTrackUi?db=bisBis1&g=evaSnp6" target="_blank">(ci3)</a></li> - <li>Cat <a href="../cgi-bin/hgTrackUi?db=felCat8&g=evaSnp4" + <li>Cat <a href="../cgi-bin/hgTrackUi?db=felCat8&g=evaSnp6" target="_blank">(felCat8)</a>, - <a href="../cgi-bin/hgTrackUi?db=felCat9&g=evaSnp4" + <a href="../cgi-bin/hgTrackUi?db=felCat9&g=evaSnp6" target="_blank">(felCat9)</a></li> - <li>Chicken <a href="../cgi-bin/hgTrackUi?db=galGal4&g=evaSnp4" + <li>Chicken <a href="../cgi-bin/hgTrackUi?db=galGal4&g=evaSnp6" target="_blank">(galGal4)</a>, - <a href="../cgi-bin/hgTrackUi?db=galGal5&g=evaSnp4" + <a href="../cgi-bin/hgTrackUi?db=galGal5&g=evaSnp6" target="_blank">(galGal5)</a>, - <a href="../cgi-bin/hgTrackUi?db=galGal6&g=evaSnp4" + <a href="../cgi-bin/hgTrackUi?db=galGal6&g=evaSnp6" target="_blank">(galGal6)</a></li> - <li>Chimp <a href="../cgi-bin/hgTrackUi?db=panTro4&g=evaSnp4" + <li>Chimp <a href="../cgi-bin/hgTrackUi?db=panTro4&g=evaSnp6" target="_blank">(panTro4)</a>, - <a href="../cgi-bin/hgTrackUi?db=panTro5&g=evaSnp4" + <a href="../cgi-bin/hgTrackUi?db=panTro5&g=evaSnp6" target="_blank">(panTro5)</a></li></li> - <li>Cow <a href="../cgi-bin/hgTrackUi?db=bosTau7&g=evaSnp4" + <li>Cow <a href="../cgi-bin/hgTrackUi?db=bosTau7&g=evaSnp6" target="_blank">(bosTau7)</a> - <li>Crab-eating macaque <a href="../cgi-bin/hgTrackUi?db=macFas5&g=evaSnp4" + <li>Crab-eating macaque <a href="../cgi-bin/hgTrackUi?db=macFas5&g=evaSnp6" target="_blank">(macFas5)</a></li> - <li>D. melanogaster <a href="../cgi-bin/hgTrackUi?db=dm6&g=evaSnp4" + <li>D. melanogaster <a href="../cgi-bin/hgTrackUi?db=dm6&g=evaSnp6" target="_blank">(dm6)</a></li> </ul></div> <div class="col-sm-4"> <ul> - <li>Dog <a href="../cgi-bin/hgTrackUi?db=canFam3&g=evaSnp4" + <li>Dog <a href="../cgi-bin/hgTrackUi?db=canFam3&g=evaSnp6" target="_blank">(canFam3)</a></li> - <li>Gorilla <a href="../cgi-bin/hgTrackUi?db=gorGor3&g=evaSnp4" + <li>Gorilla <a href="../cgi-bin/hgTrackUi?db=gorGor3&g=evaSnp6" target="_blank">(gorGor3)</a>, - <a href="../cgi-bin/hgTrackUi?db=gorGor4&g=evaSnp4" + <a href="../cgi-bin/hgTrackUi?db=gorGor4&g=evaSnp6" target="_blank">(gorGor4)</a></li> - <li>Green monkey <a href="../cgi-bin/hgTrackUi?db=chlSab2&g=evaSnp4" + <li>Green monkey <a href="../cgi-bin/hgTrackUi?db=chlSab2&g=evaSnp6" target="_blank">(chlSab2)</a></li> - <li>Horse <a href="../cgi-bin/hgTrackUi?db=equCab3&g=evaSnp4" + <li>Horse <a href="../cgi-bin/hgTrackUi?db=equCab3&g=evaSnp6" target="_blank">(equCab3)</a></li> - <li>Marmoset <a href="../cgi-bin/hgTrackUi?db=calJac3&g=evaSnp4" + <li>Marmoset <a href="../cgi-bin/hgTrackUi?db=calJac3&g=evaSnp6" target="_blank">(calJac3)</a></li> - <li>Mouse <a href="../cgi-bin/hgTrackUi?db=mm10&g=evaSnp4" + <li>Mouse <a href="../cgi-bin/hgTrackUi?db=mm10&g=evaSnp6" target="_blank">(mm10)</a>, - <a href="../cgi-bin/hgTrackUi?db=mm39&g=evaSnp4" + <a href="../cgi-bin/hgTrackUi?db=mm39&g=evaSnp6" target="_blank">(mm39)</a></li> - <li>Nile tilapia <a href="../cgi-bin/hgTrackUi?db=oreNil2&g=evaSnp4" + <li>Nile tilapia <a href="../cgi-bin/hgTrackUi?db=oreNil2&g=evaSnp6" target="_blank">(oreNil2)</a></li> - <li>Orangutan <a href="../cgi-bin/hgTrackUi?db=ponAbe3&g=evaSnp4" + <li>Orangutan <a href="../cgi-bin/hgTrackUi?db=ponAbe3&g=evaSnp6" target="_blank">(ponAbe3)</a></li> </ul></div> <div class="col-sm-4"> <ul> - <li>Pig <a href="../cgi-bin/hgTrackUi?db=susScr11&g=evaSnp4" + <li>Pig <a href="../cgi-bin/hgTrackUi?db=susScr11&g=evaSnp6" target="_blank">(susScr11)</a>, - <a href="../cgi-bin/hgTrackUi?db=susScr3&g=evaSnp4" + <a href="../cgi-bin/hgTrackUi?db=susScr3&g=evaSnp6" target="_blank">(susScr3)</a></li> - <li>Rat <a href="../cgi-bin/hgTrackUi?db=rn5&g=evaSnp4" + <li>Rat <a href="../cgi-bin/hgTrackUi?db=rn5&g=evaSnp6" target="_blank">(rn5)</a>, - <a href="../cgi-bin/hgTrackUi?db=rn7&g=evaSnp4" + <a href="../cgi-bin/hgTrackUi?db=rn7&g=evaSnp6" target="_blank">(rn7)</a></li> - <li>Rhesus <a href="../cgi-bin/hgTrackUi?db=rheMac10&g=evaSnp4" + <li>Rhesus <a href="../cgi-bin/hgTrackUi?db=rheMac10&g=evaSnp6" target="_blank">(rheMac10)</a>, - <a href="../cgi-bin/hgTrackUi?db=rheMac8&g=evaSnp4" + <a href="../cgi-bin/hgTrackUi?db=rheMac8&g=evaSnp6" target="_blank">(rheMac8)</a></li> - <li>S. cerevisiae <a href="../cgi-bin/hgTrackUi?db=sacCer3&g=evaSnp4" + <li>S. cerevisiae <a href="../cgi-bin/hgTrackUi?db=sacCer3&g=evaSnp6" target="_blank">(ponAbe3)</a></li> - <li>Sheep <a href="../cgi-bin/hgTrackUi?db=oviAri3&g=evaSnp4" + <li>Sheep <a href="../cgi-bin/hgTrackUi?db=oviAri3&g=evaSnp6" target="_blank">(oviAri3)</a>, - <a href="../cgi-bin/hgTrackUi?db=oviAri4&g=evaSnp4" + <a href="../cgi-bin/hgTrackUi?db=oviAri4&g=evaSnp6" target="_blank">(oviAri4)</a></li> - <li>Turkey <a href="../cgi-bin/hgTrackUi?db=melGal5&g=evaSnp4" + <li>Turkey <a href="../cgi-bin/hgTrackUi?db=melGal5&g=evaSnp6" target="_blank">(melGal5)</a></li> - <li>Zebra finch <a href="../cgi-bin/hgTrackUi?db=taeGut2&g=evaSnp4" + <li>Zebra finch <a href="../cgi-bin/hgTrackUi?db=taeGut2&g=evaSnp6" target="_blank">(taeGut2)</a></li> - <li>Zebrafish <a href="../cgi-bin/hgTrackUi?db=danRer7&g=evaSnp4" + <li>Zebrafish <a href="../cgi-bin/hgTrackUi?db=danRer7&g=evaSnp6" target="_blank">(danRer7)</a>, - <a href="../cgi-bin/hgTrackUi?db=danRer10&g=evaSnp4" + <a href="../cgi-bin/hgTrackUi?db=danRer10&g=evaSnp6" target="_blank">(danRer10)</a>, - <a href="../cgi-bin/hgTrackUi?db=danRer11&g=evaSnp4" + <a href="../cgi-bin/hgTrackUi?db=danRer11&g=evaSnp6" target="_blank">(danRer11)</a></li> </ul></div> </div> </div></p> <p> These variants are classified by EVA into one of the following <a target="_blank" href="http://www.sequenceontology.org/">sequence ontology</a> terms: </p> <ul> <li> <b>substitution</b> — A single nucleotide in the reference is replaced by another, alternate allele <li> <b>deletion</b> — One or more nucleotides is deleted. The representation in the database is to display one additional nucleotide in both the Reference field (Ref) and the