Table 3.

Comparison between the final haplotype solution and the reference haplotype of RPE-1

Filter	Total variant	Phased from	Phased from	Agreed	Discordant	Fraction of
	sites	bulk data	monosomies			discordance
None	2,475,311	2,242,237	2,320,153	2,101,195	40,006	0.019
Allele fractiona	2,172,689	2,087,188	2,109,589	2,018,906	12,903	0.006
Linkageb	2,156,423	2,156,346	2,071,674	2,054,006	17,616	0.009
Combinedc	2,054,859	2,054,832	2,001,674	1,993,552	8,098	0.004

^aFrom single-cell data: minor allele fraction ≥0.3 in disomic regions and in the [0.18,0.48] range in the trisomic region of Chr.10q

^b ≥1 link connecting ref, alt, HapA, and HapB & minor linkage ≤2 or minor linkage/total linkage ≤0.1

^cWith both the allele fraction (a) and the linkage (b) filter