Visualization of variants in the offspring with intrafamilial contamination. Variant allele frequencies (VAFs) of each variant type in the offspring, based on the parent of origin and parental genotype combinations (GroupA and GroupB), are shown with the total depth plot on the genomic coordinate. Blue and red dots represent maternally and paternally inherited variants, respectively. (A) Offspring without DNA contamination. VAF of GroupA SNPs are at 0.5. VAF of GroupB SNPs are at either 0 or 0.5. (B) Offspring (75%) contaminated by the mother (25%). (C) Offspring (75%) contaminated by the father (25%). (D) Offspring (75%) contaminated by a sibling (25%). The segmented pattern of GroupB SNPs represents meiotic recombination between the parental homologous chromosomes. The gray dashed line on the depth plot represents the mean autosomal depth. The black dashed lines on the VAF plots represent VAF = 0.5. Up and down arrows indicate an increase or decrease in VAF from 0.5. The left arrows indicate the presence of variants with low VAF because of contaminations.
