Identification and summary of putative autozygous segments. (a) High MAD score homozygous segments originate from low frequency haplotypes: for each homozygous segment, a length-based MAD score was calculated and the frequency of haplotypes matching a segment's founder haplotypes estimated within each sample population. A two-dimensional density estimate between the two variables used R's densCols function with nbin = 1,024. (b) Concordance between 1000G data and putative autozygous segments: putative autozygous segments' SNP counts in HapMap Phase 2 compared with heterozygosity in 1000 Genomes Project genotypes. (c,d) Boxplot summaries of putative autozygous segments: (c) genome-wide percent coverage by individual; (d) segment length (outliers not shown). Putative autozygous segments defined as MAD score >10 and founder haplotype frequency = 0.0000. Asterisks mark values that are above the y-axis limit.
Johnson et al. Genome Biology 2011 12:R21 doi:10.1186/gb-2011-12-3-r21