Indels are imputed by nearby SNPs. (a) Using SNPTools we imputed low frequency and common indels. For low frequency variants we achieved greater than 50% and 10% concordance for alt/alt and ref/alt imputation, respectively, and near 98% concordance for all common indels. (b) Imputations of ref/alt and alt/alt alleles for LOF variants were marginally harder to impute than non-LOF variants irrespective of SNP panel. Concordance rates were averaged over all populations.