Systematic Inference of Copy-Number Genotypes from Personal Genome Sequencing Data Reveals Extensive Olfactory Receptor Gene Content Diversity
Figure 2
Copy-number genotyping results in a chromosome 1 CNV set.
A. Copy-number genotyping concordance between CopySeq- and microarray-based [14] copy-number genotypes inferred for 99 CNVs on chromosome 1 in 118 individuals, using different CNV size cutoffs. Plotted circles represent the total number of high-confidence genotypes, with the largest circle corresponding to >10,000 copy-number genotypes and the smallest to 348 copy-number genotypes. As expected, the genotyping concordance increases with higher CNV size cutoffs. B–C. Copy-number genotyping results for chromosome 1 example CNVs across 150 individuals, i.e., a bi-allelic deletion (chr1:150,822,330–150,853,218; see B) as well as a bi-allelic duplication (chr1:164,451,105–164,460,994; see C). Copy-number genotypes inferred by CopySeq are indicated with different colors: ‘0’, red; ‘1’, orange; ‘2’, grey; ‘3’, blue; ‘4’, purple. Individuals have been arranged according to population: squares, CEU; triangles, CHB+JPT; circles, YRI. The scaled read-depth ratio (indicated on the y-axis) has been calculated by multiplying the read-depth ratio by two.