6f00f33a31c1cec74f33b7e408165005f8b87e37 lrnassar Wed Mar 25 13:45:08 2026 -0700 Fix inaccurate alt text in sessions.html per QA feedback. refs #37254 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> diff --git src/hg/htdocs/goldenPath/help/sessions.html src/hg/htdocs/goldenPath/help/sessions.html index 086f1a797f5..05fb4763657 100755 --- src/hg/htdocs/goldenPath/help/sessions.html +++ src/hg/htdocs/goldenPath/help/sessions.html @@ -44,31 +44,31 @@ <!-- Session INFO: This comes from our wiki: http://genomewiki.gi.ucsc.edu/index.php/Genome_Browser_Session_Gallery --> <h3>Premature Stop in the hg18 Reference Assembly</h3> <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/hg18.stop" target="_blank"><center><img width="70%" height="70%" alt="Browser session showing stop codon display in the hg18 assembly" src="../../images/session.hg18.stop.png"></center></a> <p> A premature stop codon was found in the hg18 reference genome and in about half of people of European descent. The UCSC Genes track was forced to skip the codon to indicate a full-length coding region for this gene. The SNP indicated by the G nucleotide in many of the mRNA alignments shows that in many samples from Genbank, the T > G transversion encodes a glutamic acid in the protein, reading through the premature stop predicted by the reference assembly. <a href="../../cgi-bin/hgc?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/hg18.stop&c=chr18&o=59530817&t=59530818&g=hgdpGeo&i=rs4940595" target="_blank"><center><img width="40%" height="40%" -alt="Zoomed view of stop codon coloring in the hg18 gene track" src="../../images/hg18.stop2.png"></center></a> +alt="World map from the Human Genome Diversity Project showing population allele frequencies for SNP rs4940595" src="../../images/hg18.stop2.png"></center></a> <p> Clicking the top highlighted rs4940595 in the <a href="../../cgi-bin/hgTrackUi?db=hg18&g=hgdpGeo" target="_blank">Human Genome Diversity Project SNP Population Allele Frequencies</a> track will display the world frequency image regarding this variant. In the more recent hg38 reference genome this area displays differently. Click into the active session and then into the SNP to read the details. <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/hg38.stop" target="_blank">Link to region in hg38 for comparison</a>. Specifically, in hg38 the T in the previous reference assembly has been replaced by a G, giving the reference a glutamic acid, E, and no longer prematurely truncates the predicted transcript. The SNP at this location, rs4940595, now indicates the G > T transversion in the reverse direction from previously, indicating a premature stop at this location for the T allele.</p> <!-- Session INFO: This comes from https://users.soe.ucsc.edu/~kuhn/workshops/jamesMadison2015/education.html @@ -80,39 +80,39 @@ <p> The above session helps illustrate the display of how one gene can have different transcripts with different start codons, displayed in green in the browser. Here is an example session displaying <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/session.hg19.reverseStart" target="_blank">a start codon on the reverse strand</a>. By clicking the "reverse" button below the browser one can <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/session.hg19.reverseStart2" target="_blank">flip the view</a>.</p> <!-- Session INFO: This comes from https://users.soe.ucsc.edu/~kuhn/workshops/jamesMadison2015/education.html --> <h3>Examples of Split Codons in the hg19 Assembly</h3> <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/session.hg19.split" target="_blank"><center><img width="70%" height="70%" -alt="Browser session showing split screen with two genomic regions side by side" src="../../images/session.hg19.split.png"></center></a> +alt="Browser session showing a split codon between splice sites in the hg19 assembly" src="../../images/session.hg19.split.png"></center></a> <p> The above session helps illustrate how a codon can be split between splice sites. By clicking the little double-headed arrow on the left of one of the transcripts one can see the other part of the codon. Note that there are different AAs (G or R) depending on the different splicing upstream for different isoforms.</p> <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/session.hg19.split2" target="_blank"><center><img width="70%" height="70%" -alt="Browser session showing an alternate split screen configuration" src="../../images/session.hg19.split2.png"></center></a> +alt="Browser session using multi-region exon-only view to show a split codon more clearly" src="../../images/session.hg19.split2.png"></center></a> <p> Using the multi-region exon-only feature available under the top blue menu bar and View selecting "Multi-Region" you can remove introns adjusting padding down to just one base (or none) to more clearly see the split codon above.</p> <!-- Session INFO: This comes from https://users.soe.ucsc.edu/~kuhn/workshops/jamesMadison2015/education.html --> <h3>Examples of Different Codon Numbering in the hg19 Assembly</h3> <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/session.hg19.codonNums" target="_blank"><center><img width="70%" height="70%" alt="Browser session showing codon numbering on gene transcripts" src="../../images/session.hg19.codonNums.png"></center></a> <p> The above session helps illustrate how the same region in an exon can have different codon numbering reflecting different isoforms and that it is important to use caution when reading