Table 1. Datasets used for MAGERI benchmark.

Dataset	Source	UMI tagging method	Sequencing method	Control variants
Tru-Q 7	This study	Linear PCR	Illumina HiSeq	27 substitutions, 1 deletion. Variant frequency 1–30%, see S2 Table for details
Tru-Q 7, 1:9 diluted with healthy donor PBMC DNA	This study	Linear PCR	Illumina HiSeq	27 substitutions, 1 deletion. Variant frequency 0.1–3%, see S2 Table for details
Healthy donor PBMC DNA	This study	Linear PCR	Illumina HiSeq	None, all variants are either allelic or erroneous
Tumor and plasma DNA from two cancer patients	This study	Linear PCR	Illumina HiSeq	BRAF V600E in tumor
Duplex sequencing	[43]	Ligation	Illumina HiSeq	ABL1 E279K at 1% frequency
HIV amplicon sequencing	[37]	RT-PCR	Illumina MiSeq	N/A*
Torrent	[38]	PCR	Ion Torrent	N/A**

*—no intrinsic control variants available. Two samples were used: supernatant from 8E5 cell line that should yield unmutated HIV cDNA and HIV cDNA from patient plasma.

**—only sequencing data for a single template with no appropriate variants is publicly available