Table 1 |.

Overview of genetic, epigenetic and transcript features of long-read multi-ome samples

	Sample	HG001	HG002	UDN318336
Sequencing Statistics:	HiFi read yield	98.8 Gb	90.1 Gb	90.3 Gb
	HiFi reads	6,268,744	6,000,613	5,902,290
	Insert length N50	18,932 bp	17,443 bp	17,221 bp
	Median HiFi read QV	Q31	Q32	Q31
Genome:	gDNA reads	5,716,157	5,359,077	5,563,966
	gDNA read length N50	18,785 bp	17,664 bp	16,793 bp
	Median coverage of hg38	30x	26x	28x
	SNVs (F1)	4,416,098 (99.90%)	4,413,305 (99.94%)	4,396,931 (n.a.)
	Indels (F1)	974,414 (98.75%)	973,416 (98.81%)	971,312 (n.a.)
	SVs (F1)	23,458 (n.a.)	23,836 (92.5%)	23,201 (n.a.)
	% of reads haplotype phased	87.0%	90.0%	87.7%
	Assembly size (hap1/hap2)	3,016 Mb / 3,018 Mb	3,010 Mb / 3,010 Mb	3,036 Mb / 3,038 Mb
	Number of contigs (hap1/hap2)	1,129 / 1,131	776 / 919	705 / 762
	Contig N50 (hap1/hap2)	30.6 Mb / 30.7 Mb	36.3 Mb / 28.8 Mb	40.5 Mb / 27.3 Mb
	QV (hap1/hap2)	49.9 / 49.7	50.3 / 50.0	n.a.
mCpG Epigenome:	Methylated CpG sites (%)	12,818,712 (45%)	20,252,720 (70%)	20,301,742 (71%)
	WGBS correlation (Pearson)	0.79	0.92	n.a.
	ONT correlation (Pearson)	0.82	0.93	n.a.
Chromatin Epigenome:	Nucleosome size	146 bp	147 bp	138 bp
	Number of nucleosomes	441,504,701	332,061,724	360,468,819
	FIREs in clusters*	40%	41%	46%
	FIREs in ENCODE peaks	66%	67%	75%
	Number of FIRE peaks†	122,016	84,121	167,752
	% of FIRE peaks in ENCODE peaks	91.6	97.3	96.3
Transcriptome:	MAS-Seq reads	518,921	604,272	297,248
	Transcript reads	2,347,741	3,716,982	2,196,793
	Mean transcript length	2,579 bp	2,041 bp	2,798 bp
	Total unique genes	10,536	11,512	10,383
	Total unique isoforms	40,618	48,967	32,430

FIRE: Fiber-seq Implicated Regulatory Element

^†Number of significant Fiber-seq peaks in the genome

^*Percent of FIREs preferentially clustered along the genome