Fig. 1

Sequence tube maps. Sequence tube maps [19] of a small region of the human genome with aDNA reads from the Yamnaya individual aligned with abwa aln to a linear reference sequence and bvg map to a graph containing 1000 Genomes variants. The individual is heterozygous for both an indel (GTTTGAG/-) and a SNP (A/C) in this region, with insertion and alternate allele on the same haplotype. The two underlying haplotypes in this region are colored in gray, and red and blue lines indicate forward and reverse reads, respectively. None of the 6 reads across the insertion and only 2 of 12 reads across the SNP were mapped by bwa. Reads were locally realigned with vg map to the graph for the purpose of visualization