2e3c89f43f3bb9d386178270200d0acce9fc8050 lrnassar Fri Nov 22 17:47:13 2024 -0800 Giving the UI link cronjob some love by fixing all the 301 redirects. These are the bulk of the items listed on the cron. No RM. diff --git src/hg/makeDb/trackDb/human/snpMap.html src/hg/makeDb/trackDb/human/snpMap.html index 4c4cf8e..84614ea 100644 --- src/hg/makeDb/trackDb/human/snpMap.html +++ src/hg/makeDb/trackDb/human/snpMap.html @@ -1,155 +1,155 @@ <H2>Description</H2> <P> This track consolidates all the Simple Nucleotide Polymorphisms into a single track. It is the union of the Overlap SNPs, Random SNPs, Affymetrix 120K SNP, and Affymetrix 10K SNP tracks that previously existed in the Genome Browser. </P> <a name="source"> <B>Variant Sources</B> <UL> <LI> The <B>Random</B> variants were detected by aligning reads from random genomic clones from a diverse pool of human DNA against the genome. <BR> (These were previously located in the Random SNPs track.) <LI> The <B>Mixed</B> variants were detected by both clone overlaps and the random genomic clones. <BR> (These were previously located in the Random SNPs track.) <LI> The <B>BAC Overlaps</B> variants were detected primarily by looking at overlaps between clones that cover the same region of the genome. <BR> (These were previously located in the Overlap SNPs track.) <LI> The <B>Other</B> variants were found using alternative methods. <BR> (These were previously located in the Overlap SNPs track.) <LI> The <B>Affymetrix Genotyping Array 10K</B> variants are those Single Nucleotide Polymorphisms that have been included in the Affymetrix 10K SNP Genotyping Array. <BR> (These were previously located in the Affymetrix 10K SNP track.) <LI> The <B>Affymetrix Genotyping Array 120K</B> variants are those Single Nucleotide Polymorphisms that have been included in the Affymetrix 120K SNP Genotyping Array. <BR> (These were previously located in the Affymetrix 120K SNP track.) </UL> <a name="type"> <B>Variant Types</B> <UL> <LI> <B>Single Nucleotide Polymorphisms:</B> variants where the two alleles are each a single base long. <LI> <B>Insertions and Deletions:</B> variants where one allele contains no bases. <LI> <B>Segmental Mutations:</B> variants with multiple nucleotide differences. </UL> <H2>Filtering</H2> <P> The SNPs in this track include all known polymorphisms that can be mapped against the current assembly. These include known point mutations (Single Nucleotide Polymorphisms), insertions, deletions, and segmental mutations from the current build of <A HREF="https://www.ncbi.nlm.nih.gov/SNP/" TARGET=_blank>dbSnp</A>, which is shown in the Genome Browser <A HREF="/goldenPath/releaseLog.html">release log</A>. </P> <P> There are three major cases that are not mapped and/or annotated: <UL> <LI> Submissions that are completely masked as repetitive elements. These are dropped from any further computations. This set of reference SNPs is can be found in chromosome "rs_chMasked" on the <A HREF="ftp://ftp.ncbi.nih.gov/snp/" TARGET=_blank>dbSNP ftp site</A>. <LI> Submissions that are defined in a cDNA context with extensive splicing. These SNPs are typically annotated on refSeq mRNAs through a separate annotation process. Effort is being made to reverse map these variations back to contig coordinates, but that has not been implemented. For now, you can find this set of variations in "rs_chNotOn" on the <A HREF="ftp://ftp.ncbi.nih.gov/snp/" TARGET=_blank>dbSNP ftp site</A>. <LI> Submissions with excessive hits to the genome. Variations with 3+ hits to the genome are not included in the tracks, but are available in "rs_chMulti" on the <A HREF="ftp://ftp.ncbi.nih.gov/snp/" TARGET=_blank>dbSNP ftp site</A>. </UL> </P> <P>The heuristics for the non-SNP variations (i.e. named elements and STRs) are quite conservative; therefore, some of these are probably lost. This approach was chosen to avoid false annotation of variation in inappropriate locations.</P> <H2>Supporting Details</H2> <P> Positional information can be found in the annotations section of the Genome Browser <A HREF="http://hgdownload.soe.ucsc.edu/downloads.html">downloads</A> page, which is organized by species and assembly. Non-positional information can be found in the <A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/hgFixed/database/">shared data</A> section of the same page, where it is split into tables by organism: <TT><B><FONT size=3>dbSnpRsHg</FONT></B></TT> for Human, <TT><B><FONT size=3>dbSnpRsMm</FONT></B></TT> for Mouse, and <TT><B><FONT size=3>dbSnpRsRn</FONT></B></TT> for Rat. <H2>Credits</H2> <P> Thanks to the <A HREF="http://snp.cshl.org/" TARGET=_blank>SNP Consortium</A> and <A HREF="https://www.ncbi.nlm.nih.gov" TARGET=_blank>NIH</A> for providing the public data, which are available from <A HREF="https://www.ncbi.nlm.nih.gov/SNP" TARGET=_blank>dbSnp</A> at NCBI.</P> <P> Thanks to <A HREF="http://www.perlegen.com" TARGET=_blank>Perlegen Sciences, Inc.</A> for providing additional SNPs from their database. Additional information about the Perlegen SNP discovery process can be found in Patil, N. (2001) <A HREF="http://www.sciencemag.org/cgi/content/abstract/294/5547/1719" TARGET=_blank> Blocks of Limited Haplotype Diversity Revealed by High-Resolution Scanning of Human Chromosome 21</A>. <i>Science</i> 294:1719-1723. </p> <P> Thanks to <A HREF="http://www.affymetrix.com" TARGET=_blank>Affymetrix, Inc.</A> for developing the genotyping arrays. For more details on this genotyping assay, please see the supplemental information on the <A HREF="http://www.affymetrix.com/support/technical/byproduct.affx?product=10k" TARGET=_blank>Affymetrix 10K SNP</A> and <A HREF="http://www.affymetrix.com/support/technical/sample_data/genotyping_data.affx" TARGET=_blank>Affymetrix 120K SNP</A> products. Additional information, including genotyping data, is available from the details pages for the Affymetrix 120K SNP and Affymetrix 10K SNP tracks.</P> <H2>Terms of Use for the Affymetrix data</H2> -<P> Please see the <A HREF="http://www.affymetrix.com/site/terms.affx" +<P> Please see the <A HREF="https://www.affymetrix.com:443/site/terms.affx" TARGET=_blank>Terms and Conditions</A> page on the Affymetrix website for restrictions on the use of their data. <!-- <P>During sample preparation, an <B>enzyme</B> is used to fragment the genomic DNA into smaller pieces. The restriction endonucleases <I><B>HindIII</B></I> and <I><B>XbaI</B></I> have been used to generate this data.</P> <P>Genotypes are reported as pairs of basecalls representing the two observed alleles. Individual genotypes for which no call was made are labeled 'NC'. A minimum of 46 genotype calls in the set of 54 individuals are included for each SNP.</P> <P><B>Allele Frequency</B> for the 'A' allele is two times the number of 'AA' calls plus the number of 'AB' calls, divided by two times the total number of calls. Allele Frequency for the 'B' allele is two times the number of 'BB' calls plus the number of 'AB' calls, divided by two times the total number of calls. The <B>Minimum Allele Frequency</B> is the lesser of these two values. <B>Heterozygosity</B> is two times the product of the two allele frequencies.</P> -->