Long read-based ecDNA reconstructions derived from WGS data in bulk populations and read coverage over the ecDNA fragments across single nuclei in patient no. 2 ( n = 86 nuclei) as detected by long-read or short-read scEC&T-seq. Top to bottom, ecDNA amplicon reconstruction (the SVs on ecDNAs are colored; SV nos. 1-4), gene annotation, read density over the ecDNA region in bulk long-read Nanopore WGS data, read density over the ecDNA region in merged single nuclei and coverage over the ecDNA region in single nuclei (rows) as detected by long-read or short-read scEC&T-seq. The 6-kb deletion is highlighted in red. The single asterisk indicates the unmappable region of the reference genome (hg19).
