Fig. 2

A visual representation of the pangenome graph for the gene IGLL1. A IGLL1 contains many SNVs, including one at bGalGal1b#chr15:7,955,357, in its coding sequence. The graph of this SNV shows that although all 30 haplotypes have the same sequence before and after the SNV, 25 haplotypes have G in this position and 5 have A. B The pangenome of IGLL1 contains a ~5 kb deletion compared to bGalGal1b in one haplotype of a single individual, UCD312. At the juncture in the pangenome graph where the deletion haplotype branches from the rest, this haplotype follows edge e1 to skip the sequence in the loop, whereas the other 29 haplotypes follow edge e2 to include the sequence, and then e3 to join back with the deletion haplotype afterwards. C IGLL1 also contains a ~300 bp insertion compared to bGalGal1b in 22 haplotypes. The inserted sequence contains SNVs, so while a linear representation of this insertion considers each version of the insertion as a different allele, the pangenome graph is able to correctly record it as a biallelic variant (i.e., insertion or no insertion) containing additional variable sites. Furthermore, reads can align to this sequence in the pangenome but would be left unmapped when aligning to bGalGal1b as it does not contain this sequence