Fig. 9
From: A cautionary tale of low-pass sequencing and imputation with respect to haplotype accuracy
Imputation discordance relative to sequencing depth and XPEHH score divergence. a–c Mean sequencing depth and discordance were each calculated in 1-Mb windows along all the autosomes. a Genotype discordance was calculated for post-imputation genotypes at each sequencing depth relative to pre-imputation genotypes at 43.5X depth. b–c Haplotype discordance was calculated for each sequencing depth relative to each of the 43.5X haplotypes. The absolute difference in Z(XPEHH) values between those calculated at 43.5X and those calculated at lower depth datasets was plotted against d genotype discordance, e haplotype A discordance, and f haplotype B discordance