Fig. 1: A deep catalog of TR variation across human populations.

a Overview of EnsembleTR workflow. Aligned reads are input to four TR genotyping tools (GangSTR, HipSTR, adVNTR, and ExpansionHunter). Filtered VCFs are input to EnsembleTR. EnsembleTR first identifies sets of mergeable loci (step 1) and identifies sets of compatible alleles between callers (step 2). Finally, it scores each possible diploid genotype (step 3) and outputs the best genotype and its score. The resulting VCF file is used to generate a phased SNP + TR reference haplotype panel. b Overlap of TRs called by each method. Annotations below the bars indicate the combination of methods a TR was called in. Numbers next to each method indicate the number of unique TRs in each category. Numbers below the plot indicate the Mendelian Inheritance (MI) rate across all calls in each category. Categories with fewer than 10 total TRs were excluded. c Mendelian Inheritance as a function of EnsembleTR quality score. The x-axis gives the EnsembleTR quality score threshold used, and the y-axis gives the percent of genotyped trios that follow MI. Line colors denote repeat unit lengths. Each trio/TR pair was only included in each category if all calls in the trio passed the score threshold. Trio/TR pairs for which all samples were homozygous for the reference allele were excluded from analysis. d Distribution of the fraction of non-reference alleles in individuals by population. Boxplots summarize the distribution of the fraction of variant alleles in each sample. Horizontal lines show median values, boxes span from the 25th percentile (Q1) to the 75th percentile (Q3). Whiskers extend to Q1–1.5*IQR (bottom) and Q3 + 1.5*IQR (top), where IQR gives the interquartile range (Q3-Q1). Homopolymer TRs are excluded. Box colors denote superpopulations. Gray denotes H3Africa. Other colors denote 1000 Genomes superpopulations.