6254a2f3273acb0889ba875ffab273f0099cea16 galt Tue May 21 00:17:23 2019 -0700 Fixe problems found by htmlCheck validate and hgNearTest robot diff --git src/hg/makeDb/trackDb/human/hapmapLdPh.html src/hg/makeDb/trackDb/human/hapmapLdPh.html index 14707d6..08b1bac 100644 --- src/hg/makeDb/trackDb/human/hapmapLdPh.html +++ src/hg/makeDb/trackDb/human/hapmapLdPh.html @@ -9,33 +9,33 @@ <P> This track shows three different measures of linkage disequilibrium — D', r<sup>2</sup>, and LOD (log odds) — between pairs of SNPs as genotyped by the HapMap consortium. LD is useful for understanding the associations between genetic variants throughout the genome, and can be helpful in selecting SNPs for genotyping. </P> <P> By default, the display in full mode shows LOD values. Each diagonal represents a different SNP with each diamond representing a pairwise comparison between two SNPs. Shades are used to indicate linkage disequilibrium between the pair of SNPs, with darker shades indicating stronger LD. For the LOD values, additional colors are used in some cases: <UL> <LI><I>White</I> diamonds indicate pairwise D' values less than 1 - with no statistically significant evidence of LD (LOD < 2).</LI> + with no statistically significant evidence of LD (LOD < 2).</LI> <LI><I>Light blue</I> diamonds indicate high D' values (>0.99) with - low statistical significance (LOD < 2). </LI> + low statistical significance (LOD > 2). </LI> <LI><I>Light pink</I> diamonds are drawn when the statistical significance is high (LOD >= 2) but the D' value is low (less than 0.5). </LI> </UL> </P> <H2>Methods</H2> <P> Phased genotypes from HapMap Phase II release 22 were used with Haploview to calculate LD values for all SNP pairs within 250 kb. The YRI and CEU tracks each use 30 parents+child trios (90 individuals) and the combined JPT+CHB track uses 90 unrelated individuals.</P> <P> Haploview uses a two marker EM (ignoring missing data) to estimate the maximum-likelihood values of the four gamete frequencies, from which