Numbers of homozygous and heterozygous SNPs identified in NA12782 at different sequence coverage thresholds.

<p>Numbers of homozygous and heterozygous SNPs identified in NA12782 at different sequence coverage thresholds.</p

SNPs in the coding sequences of the genes from the target region.

<p>SNPs in the coding sequences of the genes from the target region.</p

Number of sequence reads extracted from intensity files using Illumina and Rolexa analysis.

<p>Number of sequence reads extracted from intensity files using Illumina and Rolexa analysis.</p

Distribution of percentages of a minor variant for SNPs as recovered by Illumina sequencing.

<p>Red: homozygous SNPs, blue: heterozygous SNPs. Solid line: HapMap SNPs, dashed line: new SNPs.</p

Distribution of sequence features of regions and corresponding probes with low (<3 fold) and normal (15-29 fold) sequence coverage.

<p>A,B) Length of the regions/probes. C,D) Percentage of low complexity DNA inside the regions/probes. E,F) GC content of regions/probes. G) Hybridization temperature of the probes.</p

Enrichment of target regions.

<p>All sequencing tags that map uniquely to the reference human genome are displayed in blue. The height of peaks corresponds to the number of tags mapping to the same location. Red circles represent genomic areas plotted on the array. The image was generated using Genome Graphs (<a href="http://genome.ucsc.edu/cgi-bin/hgGenome" target="_blank">http://genome.ucsc.edu/cgi-bin/hgGenome</a>).</p

Comparison of SNPs recovered in this study using different thresholds of sequence coverage (4- and 15-fold) with HapMap SNPs.

<p>Comparison of SNPs recovered in this study using different thresholds of sequence coverage (4- and 15-fold) with HapMap SNPs.</p

Histogram of dbSNP positions coverage on chromosome 21.

<p>Histogram of dbSNP positions coverage on chromosome 21.</p

Proportion of different genomic elements in the captured samples with and without COT-I DNA as compared to their relative abundance in the human genome.

<p>Reads were mapped to the reference human genome using BLAT, allowing 2 mismatches and 1 indel with a minimal perfect match of 30 bp.</p

The overall DNA methylation level at single CpG resolution, and over genomic features.

<p>The probability density distribution and the box-plot of DNA methylation shows differences between the T21 twin and the normal twin at the level of A) single CpG sites, B) promoters, C) CpG islands, D) Exons, E) Introns, F) LADs, and G) iLADs. The red line in the probability plot shows the probability distribution of T21 twin methylome subtracted from the normal twin methylome (T21—N). While, the blue line shows the probability distribution of the normal twin methylome subtracted from T21 twin methylome (N—T21). DNA hyper-methylation in T21 twin (T21 > Normal) is observed at the level of CpGs, and all the genomic features, but the effect is more pronounced in promoters and CpG islands.</p