Extended Data Fig. 3: Impact of graph normalization on complement component 4 (C4) pangenome graph.

Each bar represents a haplotype and black lines on the bottom represent the graph topology. Paths are colored by using the Spectra color palette with four levels of node depths: white indicates no depth, while gray, red, and yellow indicate depths 1, 2, and greater than or equal to 3, respectively. a) C4 subgraph extracted from the chromosome 6 graph built without SMOOTHXG. b) C4 subgraph extracted from the chromosome 6 graph built without SMOOTHXG and sorted. c). C4 subgraph extracted from the chromosome 6 graph built with SMOOTHXG. The two references present two different allele copies of the C4 genes (red = 2X coverage), both of them including the HERV sequence. The entirely gray paths have one copy of these genes (gray = 1X coverage). HG01071#2 presents three copies of the locus (orange = 3X coverage), of which one contains the HERV sequence (gray in the middle of the orange).