Imputation performance depends on r
2 of nearby SNPs. (a) For common indels, frequency matched SNP imputation performs similar to imputation using all SNPs. (b) For low frequency indels, imputation performance improves rapidly for heterozygous (ref/alt) imputation with > 90% concordance once r2 between indels and SNPs reaches 0.25. However, imputation of alternative homozygous alleles (alt/alt) remains below 15% even when imputed with SNPs in perfect LD.