198c9b8daecc44fbda6a6494c566c723920f030a lrnassar Wed Mar 11 18:25:21 2026 -0700 Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM. diff --git src/hg/makeDb/trackDb/human/hg38/description.html src/hg/makeDb/trackDb/human/hg38/description.html index 1619604923d..30be4c79889 100644 --- src/hg/makeDb/trackDb/human/hg38/description.html +++ src/hg/makeDb/trackDb/human/hg38/description.html @@ -1,234 +1,234 @@ <!-- Display image in righthand corner --> <TABLE ALIGN=RIGHT BORDER=0 WIDTH=415> <TR><TD ALIGN=RIGHT> <A HREF="https://www.ncbi.nlm.nih.gov/genome/51" TARGET=_blank> <IMG SRC="../images/human.jpg" WIDTH=275 HEIGHT=275 ALT="Human"></A> </TD></TR> <TR><TD ALIGN=RIGHT> <FONT SIZE=-1><em>Homo sapiens</em><BR> </FONT> <FONT SIZE=-2> (<A HREF="http://www.cbse.ucsc.edu/" TARGET=_blank>Graphic courtesy of CBSE</A>) </FONT> </TD></TR> </TABLE> <P> <B>UCSC Genome Browser assembly ID:</B> hg38<BR> <B>Sequencing/Assembly provider ID:</B> Genome Reference Consortium Human GRCh38.p14 (GCA_000001405.29)<BR> <B>Assembly date:</B> Dec. 2013 initial release; June 2022 patch release 14<BR> <B>Assembly accession:</B> <A HREF="https://www.ncbi.nlm.nih.gov/assembly/GCA_000001405.29/" TARGET="_blank">GCA_000001405.29</A><BR> <B>NCBI Genome ID:</B> <A HREF="https://www.ncbi.nlm.nih.gov/genome/51" TARGET="_blank">51</A> (Homo sapiens (human))</BR> <B>NCBI Assembly ID:</B> <A HREF="https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.40" TARGET="_blank">GCF_000001405.40</A> (GRCh38.p14, GCA_000001405.29)<BR> <B>BioProject ID:</B></I> <A HREF="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA31257" TARGET="_blank">PRJNA31257</A> </P> <HR> <P> <B>Search the assembly:</B> <UL> <LI> <B>By position or search term: </B> Use the "position or search term" box to find areas of the genome associated with many different attributes, such as a specific chromosomal coordinate range; mRNA, EST, or STS marker names; or keywords from the GenBank description of an mRNA. <A HREF="../goldenPath/help/query.html">More information</A>, including sample queries. <LI> <B>By gene name: </B> Type a gene name into the "search term" box, choose your gene from the drop-down list, then press "submit" to go directly to the assembly location associated with that gene. <A HREF="../goldenPath/help/geneSearchBox.html">More information</A>. <LI> <B>By track type: </B> Click the "track search" button to find Genome Browser tracks that match specific selection criteria. <A HREF="../goldenPath/help/trackSearch.html">More information</A>. </UL> </P> <HR> <P> <B>Download sequence and annotation data:</B> <UL> <LI><A HREF="../goldenPath/help/ftp.html">Using rsync</A> (recommended) <LI><A HREF="http://hgdownload.soe.ucsc.edu/downloads.html#human">Using HTTP</A> <LI><A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg38/">Using FTP</A> <LI><A HREF="../goldenPath/credits.html#human_credits">Data use conditions and restrictions</A> <LI><A HREF="../goldenPath/credits.html#human_credits">Acknowledgments</A> </UL> </P> <hr> <h3>Assembly Details</h3> <p> The GRCh38 assembly is the first major revision of the human genome released in more than four years. As with the previous GRCh37 assembly, the <a href="https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/" target="_blank">Genome Reference Consortium</a> (GRC) is now the primary source for human genome assembly data submitted to GenBank. Beginning with this release, the UCSC Genome Browser version numbers for the human assemblies now match those of the GRC to minimize version confusion. Hence, the GRCh38 assembly is referred to as "hg38" in the Genome Browser datasets and documentation. For a glossary of assembly-related terms, see the GRC <a href="https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/definitions.shtml" target="_blank">Assembly Terminology</a> page. <p> <b>GRCh38 Highlights</b> <ul> <li> <b>Alternate sequences</b> - Several human chromosomal regions exhibit sufficient variability to prevent adequate representation by a single sequence. To address this, the GRCh38 assembly provides alternate sequence for selected variant regions through the inclusion of <em>alternate loci scaffolds</em> (or <em>alt loci</em>). Alt loci are separate accessioned sequences that are aligned to reference chromosomes. The GRCh38 initial assembly contained 261 alt loci, many of which are associated with the LRC/KIR area of chr19 and the MHC region on chr6. Subsequent GRC patch releases have added additional alt loci and fix patches. See the <a href="../cgi-bin/hgTracks?db=hg38&chromInfoPage=">sequences</a> page for the latest list of the reference chromosomes, alternate, and patch sequences in GRCh38. <li> <b>Fix sequences</b> - Fix patches denoted by <em>chr_<accession>_fix</em> represent changes to the existing sequence. These are generally error corrections (such as base changes, component replacements/updates, switch point updates or tiling path changes) or assembly improvements (such as extension of sequence into gaps). These fix patch scaffold sequences are given chromosome context through alignments to the corresponding chromosome regions. A list of all chromosomes including <em>chr_fix</em> sequences can be found in the <a href="../cgi-bin/hgTracks?db=hg38&chromInfoPage=">sequences</a> page. <li> <b>Centromere representation</b> - Debuting in this release, the large megabase-sized gaps that represented centromeric regions in previous assemblies have been replaced by sequences from centromere models created by <a href="http://genome.cshlp.org/content/24/4/697.abstract" target="_blank">Karen Miga et al.</a>, using centromere databases developed during her work in the Willard lab at Duke University (now at the <a href="https://president.uchicago.edu/directory/huntington-willard" target="_blank">University of Chicago</a>) and analysis software developed while working in the <a href="http://cbse.soe.ucsc.edu/people/kent" target="_blank">Kent lab</a> at UCSC. The models, which provide the approximate repeat number and order for each centromere, will be useful for read mapping and variation studies. <li> <b>Mitochondrial genome</b> - The mitochondrial reference sequence included in the GRCh38 assembly (termed "chrM" in the UCSC Genome Browser) is the <a href="http://mitomap.org/bin/view.pl/MITOMAP/HumanMitoSeq" target="_blank">Revised Cambridge Reference Sequence</a> (rCRS) from <a href="http://mitomap.org/MITOMAP" target="_blank">MITOMAP</a> with GenBank accession number J01415.2 and RefSeq accession number NC_012920.1. This differs from the chrM sequence (RefSeq accession number NC_001807) provided by the Genome Browser for hg19, which was not updated when the GRCh37 assembly later transitioned to the new version. <li> <b>Sequence updates</b> - Several erroneous bases and misassembled regions in GRCh37 have been corrected in the GRCh38 assembly, and more than 100 gaps have been filled or reduced. Much of the data used to improve the reference sequence was obtained from other genome sequencing and analysis projects, such as the <a href="http://www.1000genomes.org/" target="_blank">1000 Genomes Project</a>. <li> <b>Analysis set</b> - The GRCh38 assembly offers an "analysis set" that was created to accommodate next generation sequencing read alignment pipelines. To avoid false mapping of reads, duplicate copies of centromeric arrays and WGS on several chromosomes have been hard-masked with Ns. The two PAR regions on chromosome Y have also been hard-masked, and the Epstein-Barr virus sequence has been added as a decoy to attract contamination in samples. Two versions of the analysis set are available on our <a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/" target="_blank">downloads page</a>: one without the alternate chromosomes from this assembly, and one that includes them. </ul> <p> <b>Chromosome naming conventions</b> <br> UCSC has introduced some slight changes to the Genome Browser chromosome naming scheme with this release: <ul> <li>Haplotype chromosome, unplaced contig and unlocalized contig names now include their NCBI accession number (e.g., chr6_GL000256v2_alt)</li> <li>The "v2" at the end of the accession number indicates the NCBI version number</li> <li>Haplotype chromosome names consist of the chromosome number, followed by the NCBI accession number, followed by "alt"</li> - <li>Fix sequence names consist of the chromosomes number, followed by the NCBI accession number, + <li>Fix sequence names consist of the chromosome number, followed by the NCBI accession number, followed by "fix" (e.g., chr7_KQ031388v1_fix)</li> <li>Unlocalized contig names consist of the chromosome number, followed by the NCBI accession number, followed by "random"</li> <li>Unplaced contig names (contigs whose associated chromosome is not known) consist of "chrUn" followed by the NCBI accession number</li> </ul> </p> <p> <b>Pseudoautosomal regions</b> <br> The Y chromosome in this assembly contains two pseudoautosomal regions (PARs) that were taken from the corresponding regions in the X chromosome and are exact duplicates: <blockquote> chrY:10,000-2,781,479 and chrY:56,887,902-57,217,415 <br>chrX:10,000-2,781,479 and chrX:155,701,382-156,030,895 </blockquote> </p> <p> <b>Assembly statistics</b> <br> For a detailed set of statistics about this assembly, see the <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.40/#/st" target="_blank">GRCh38 GenBank record</a>. <br> <TABLE BORDER=1 CELLPADDING=3> <TR><TH>Number</TH><TH>Haplotypes</TH><TH>Fixes</TH><TH>Unlocalized Contigs</TH></TH></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr1</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>22</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>12</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>9</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr2</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>22</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>10</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>2</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr3</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>22</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>10</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>1</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr4</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>17</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>9</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>1</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr5</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>17</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>6</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>1</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr6</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>18</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>6</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>0</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr7</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>12</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>5</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>0</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr8</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>17</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>9</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>0</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr9</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>7</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>5</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>4</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr10</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>5</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>8</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>0</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr11</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>16</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>15</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>1</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr12</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>16</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>9</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>0</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr13</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>8</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>8</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>0</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr14</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>6</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>3</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>8</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr15</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>11</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>6</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>1</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr16</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>10</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>5</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>1</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr17</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>22</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>9</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>3</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr18</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>12</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>3</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>0</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr19</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>59</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>6</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>0</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr20</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>4</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>2</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>0</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr21</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>7</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>4</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>0</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chr22</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>14</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>5</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>9</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chrX</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>7</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>7</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>0</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chrY</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>0</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>4</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>1</FONT></TD></TR> <TR><TD ALIGN="CENTER"><FONT SIZE=-1>chrM</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>0</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>0</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>0</FONT></TD></TR> </TABLE> </p> <p> <TABLE BORDER=1 CELLPADDING=3> <TH ALIGN="LEFT">Type</TH><TH WIDTH=50>Total</TH> <TR><TD><FONT SIZE=-1>chromosomes</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>25</FONT></TD></TR> <TR><TD><FONT SIZE=-1>haplotypes</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>351</FONT></TD></TR> <TR><TD><FONT SIZE=-1>fixes</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>166</FONT></TD></TR> <TR><TD><FONT SIZE=-1>unlocalized contigs</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>42</FONT></TD></TR> <TR><TD><FONT SIZE=-1>unplaced contigs</FONT></TD><TD ALIGN="CENTER"><FONT SIZE=-1>127</FONT></TD></TR> <TR><TD></TD><TD></TD></TR> <TR><TD><B><FONT SIZE=-1>Total</FONT></B></TD><TD ALIGN="CENTER"><FONT SIZE=-1>711</FONT></TD></TR> </TABLE> </p> </p> <p> For more information about the files included in the GRCh38 GenBank submission, see the <a href="https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.29_GRCh38.p14/README.txt" target="_blank">GRCh38 README</a>. Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser <a href="http://hgdownload.soe.ucsc.edu/downloads.html#human">Downloads</a> page or the <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg38/">FTP server</a>. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. </p> <h3>References</h3> <p> Miga KH, Newton Y, Jain M, Altemose N, Willard HF, Kent WJ. <a href="http://genome.cshlp.org/content/24/4/697.abstract" target="_blank">Centromere reference models for human chromosomes X and Y satellite arrays</a>. <em>Genome Res.</em> 2014 Apr;24(4):697-707. Epub 2014 Feb 5. </p>