Table 2.

Sources of alternative ORI positions used in this study

Method	Reference	Comments
OK-seq	[42]	BAM files for hg19 were downloaded from the SRA database, under accession number PRJEB25180. Replication origins were identified using our algorithm described below.
	[31]	BED files with ORI positions for hg19 were provided by the authors of the publication.
SNS-seq	[23]	Genomic coordinates of ORI positions for hg38 were downloaded from the manuscript supplement (Table S1). The coordinates were converted to hg19 using the liftOver function from the rtracklayer Bioconductor library [68]. ORI from Q1 and Q2 were combined into the “core” group, while the remaining Q3–10 into “stochastic”
	[35]	BED files with ORI positions for hg19, for Hela, IMR90, and K562 cell lines were downloaded from http://pbil.univ-lyon1.fr/members/fpicard/oriseq/
	[38]	hg19 ORI positions were downloaded from the DeOri database [8] for both HCT116 and K562 cell lines
Repli-seq	[7]	ENCODE Repli-seq data were downloaded from the GEO dataset GSE34399. We used the peak locations of the wavelet-smoothed signal available as the BED files with the Pk suffix.
Ini-seq	[39]	Genomic coordinates of ORI positions for hg19 were downloaded from the manuscript supplement (Table S3) (determination by SICER at E = 10e−5).
Bubble-seq	[40]	ORI positions for hg18 were downloaded in a bedGraph format from GEO dataset GSE38809 (GM_combined_RD_bubbles file). The coordinates were converted to hg19 using the liftOver function from the rtracklayer Bioconductor library [68].
ORC1-ChIP-seq	[43]	ORI positions for hg18 were downloaded in a BED format from GEO dataset GSM922790 (ChIPseq_Orc1_GradientHela_enrichRegions file). The coordinates were converted to hg19 using the liftOver function from the rtracklayer Bioconductor library [68].
ORC2-ChIP-seq	[44]	Genomic coordinates for hg19 were downloaded from the manuscript supplement (Table S1).
MCM7-ChIP-seq	[45]	Genomic coordinates for hg19 were downloaded from GEO dataset GSE107248 (MCM7ChIP_exp1/2.txt files).
Nucleotide comp. skew	[21]	ORI positions for hg17 were downloaded from the manuscript supplement (N-domain_positions.xls file). The coordinates were converted to hg19 using the liftOver function from the rtracklayer Bioconductor library [68].