Figure 7. Imputation results for different SV types.

(a) Histogram on the number of gold standard genotype calls per SV class. (b) Relationship between discordance and fraction of missing genotypes when altering the genotype likelihood (GL) threshold used for filtering the imputed genotypes, ranging from 0.33 (no filter) to 0.999 across SV classes. Thresholds used for further analyses, including panels (c,d), are circled in red. Increasing the minimum GL results in fewer discordant genotypes but increases the number of missing genotypes. Imputation of inversions had the highest rate of discordance and missing genotypes, whereas the tandem duplications and deletions had lower rates of discordant and missing genotypes for those events with a high GL. (c) Discordance rates for deletions, complex indels and MEIs stratified by minor allele frequencies for 20 bins (width=0.025). Bin boundaries are indicated by grey lines. The number of calls per bin are shown by dashed lines. (d) Same as (c), but restricted calls where the gold standard genotype contains at least one copy of the rare allele.