Fig. 3: Accurate genetic variant calling using the targeted haplotype-resolved assembly.

a An example of a region with newly identified variants. High-confidence HiFi reads with new variants are illustrated below. The colorful lines and dots positioned in the targeted assembly result of the haplotype 1 and HiFi reads indicate four types of nucleotides different from the hg38 reference. The purple character “I” and dots indicate small insertions (<50 bp) compared to the hg38 reference. Black dots indicate small deletions (<50 bp) compared to the hg38 reference. PG: the Illumina Platinum Genomes. b Collapsed region in the assemblies. Blue and red lines represent the coverage of downloaded PacBio HiFi reads of GM12878 cells from the GIAB aligned to the haplotype 1 or haplotype 2 of different assemblies. The dotted lines indicate the threshold of expected coverage (mean + at least three standard deviations) of chromosome 6 excluding the targeted MHC region for the collapsed region. The red bar indicates the collapsed region identified in Supplementary Data 1. c A 2889 bp deletion upstream of the HCP5 gene is illustrated and supported by HiFi reads for both haplotypes.