src/hg/makeDb/trackDb/snp131.html 1.2
1.2 2010/05/28 18:47:08 angie
Added new functional annotattion codes cds-indel, coding-synonymy-unknown; added 1000Genomes as validation type. Thanks Mary!
Index: src/hg/makeDb/trackDb/snp131.html
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/snp131.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 4 -r1.1 -r1.2
--- src/hg/makeDb/trackDb/snp131.html 16 Apr 2010 17:36:01 -0000 1.1
+++ src/hg/makeDb/trackDb/snp131.html 28 May 2010 18:47:08 -0000 1.2
@@ -55,9 +55,12 @@
<LI><B>By Frequency</B> - at least one submitted SNP in cluster has frequency data submitted
<LI><B>By Cluster</B> - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
<LI><B>By Submitter</B> - at least one submitter SNP in cluster was validated by independent assay
<LI><B>By 2 Hit/2 Allele</B> - all alleles have been observed in at least 2 chromosomes
- <LI><B>By HapMap</B> - validated by HapMap project
+ <LI><B>By HapMap</B> - submitted by <A HREF="http://hapmap.ncbi.nlm.nih.gov/"
+ TARGET=_BLANK>HapMap</A> project (human only)
+ <LI><B>By 1000Genomes</B> - submitted by <A HREF= "http://1000genomes.org/"
+ TARGET=_BLANK>1000Genomes</A> project (human only)
<LI><B>Unknown</B> - no validation has been reported for this variant
</UL>
</LI>
<LI>
@@ -70,9 +73,9 @@
<LI><B>Coding - Synonymous</B> - no change in peptide for allele with
respect to reference assembly (<TT>coding-synon</TT>)
<LI><B>Coding - Non-Synonymous</B> - change in peptide for allele with
respect to reference assembly (<TT>nonsense</TT>, <TT>missense</TT>,
- <TT>frameshift</TT>)
+ <TT>frameshift</TT>, <TT>cds-indel</TT>, <TT>coding-synonymy-unknown</TT>)
<LI><B>Untranslated</B> - variation in transcript, but not in coding
region interval (<TT>untranslated-3</TT>, <TT>untranslated-5</TT>)
<LI><B>Intron</B> - variation in intron, but not in first two or last two bases of intron
<LI><B>Splice Site</B> - variation in first two or last two bases of