Table 2.

Comparison between the final haplotype solution and the reference haplotype of NA12878

All SNV sites	Phased from	Reference	Comparable	Agreed	Accuracy	Fraction of
	bulk data	haplotype	sites			completion
2,652,381	2,319,027a	1,861,941b	1,824,401	1,818,042	0.997	0.980
	2,151,642c		1,815,197	1,809,886	0.997	0.975
	2,319,027a	2,183,123d	2,122,256	2,114,548	0.996	0.969
	2,151,642c		2,096,982	2,091,821	0.998	0.958
Indel variants
on Chr.21
9,285	7663e	3618f	3553	3535	0.995	0.982
	4702c		3183	3177	0.998	0.880
	7663e	4581g	4478	4426	0.988	0.978
	4702c		3835	3827	0.998	0.837

^aAll phased variants without any filtering

^bVariants detected in the linked-reads data that are also contained in the GIAB release. Total number of phased SNVs in the GIAB release, 1,867,590

^cFiltered by haplotype linkage: ≥1 link connecting ref, alt, HapA, and HapB, and minor linkage ≤2 or minor linkage/total linkage ≤0.1

^dPhased variants determined from phased de novo assembly of parental chromosomes that are also detected in the linked-reads data. Total number of phased variants from diploid de novo assembly, 2,312,059

^eVariants phased by molecular linkage to phased SNVs in the scaffold haplotype solution

^fIntersection with phased indel variants in the GIAB data with exactly matching variant genotypes. Total number of phased indels in the GIAB release, 4090

^gIntersection with phased indels derived from de novo assembly of parental chromosomes with exactly matching variant genotypes. Total number of phased indels from diploid assembly, 7128