Table 2. Comparison of sequencing results (N = 17 parameters).

	Parameter	Macrogen-X10	Illumina-X10	Peterhof-HiSeq4000
Sequencing strategy	Library preparation kit	Illumina TruSeq DNA PCR-Free	Illumina TruSeq DNA PCR-Free	Illumina TruSeq DNA PCR-Free
	Insert size	300–400 bp	450 bp	400 bp
	Read length	151bp, paired-end	151bp, paired-end	150bp, paired-end
Raw read QC	Estimated mean coverage	31.685	36	32
	Variance coefficient of coverage	0.245	0.28	0.27
	Fraction of read pairs with both reads retained after filtration	0.989	0.986	0.981
	Fraction of kmers with errors	0.076	0.068	0.069
	Fraction of read pairs without adapters or Ns	0.994	0.994	0.998
Mapping QC	Reads before mapping	812,203,657	834,018,799	912,695,503
	Percentage of mapped reads	97.85%	97.14%	97.43%
Variant QC	Number of SNVs	3956042	3971375	3552604
	% of novel SNVs	2.01%	2.05%	1.64%
	Number of indels	459983	708225	335164
	# Multiallelic sites	30180	122066	14031
	Mendel errors	0.58%	0.30%	0.27%
	Genotype concordance with microarray	96.80%	96.88%	96.67%

Main parameters used for comparison of sequencing centers are presented in this table. These and additional parameters can also be found in S1–S3 Tables. All sequenced samples were used in this comparison.