a33a189301f539896d9df28df9008b50f65d757f lrnassar Fri Aug 2 12:09:41 2024 -0700 Fixing up grammar, feedback from CR refs #34174 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 576833b..8c35421 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -225,59 +225,59 @@ target="_blank">(danRer10)</a>, <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 + One or more nucleotides are deleted. The representation in the database is to display one additional nucleotide in both the Reference field (Ref) and the Alternate Allele field (Alt). E.g. a variant that is a deletion of an A maybe be represented as Ref = GA and Alt = G. <li> <b>insertion</b> — - One or more nucleotides is inserted. The representation in the database is to + One or more nucleotides are inserted. The representation in the database is to display one additional nucleotide in both the Reference field (Ref) and the - Alternate Allele field (Alt). E.g. a variant that is an insertion of a T maybe + Alternate Allele field (Alt). E.g. a variant that is an insertion of a T may be represented as Ref = G and Alt = GT <li> <b>delins</b> — - Similar to tandemRepeat, in that the runs of Ref and Alt Alleles are of + Similar to a tandem repeat, in that the runs of Ref and Alt Alleles are of different length, except that there is more than one type of nucleotide, e.g., Ref = CCAAAAACAAAAACA, Alt = ACAAAAAC. <li> <b>multipleNucleotideVariant</b> — More than one nucleotide is substituted by an equal number of different nucleotides, e.g., Ref = AA, Alt = GC. <li> <b>sequence alteration</b> — A parent term meant to signify a deviation from another sequence. Can be assigned to variants that have not been characterized yet. </ul> <p> The variants have also been annotated with our <a href="/cgi-bin/hgVai" target="_blank">Variant Annotation Integrator</a> tool with functional classes such as synonymous variant, missense variant, stop gained, etc. For additional details on the track colors, as well as the filters and metadata on each variant, see the track description page.</p> <p> We would like to thank the <a href="https://www.ebi.ac.uk/eva/" target="_blank">European Variation -Archive</a> making this data publically available. We would also like to thank Luis Nassar, Chris Lee, +Archive</a> for making these data publically available. We would also like to thank Luis Nassar, Chris Lee, and Angie Hinrichs for the creation and release of these tracks. </p> <a name="071224"></a> <h2>Jul. 12, 2024 First update to hg19's UCSC Genes track since 2013</h2> <p> The UCSC Genome Browser is getting ready to update hg19's UCSC Genes dataset for the first time since 2013. In this update, the UCSC Genes track will now use GENCODE v45 gene models lifted to hg19 and replace the old UCSC transcript IDs with the official GENCODE IDs. </p> <p> The anticipated release date for this update is July 31, 2024.</p> <p> As an example of what to expect, here are some GENCODE IDs that will replace the UCSC IDs in the