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Table 3 Comparison between the final haplotype solution and the reference haplotype of RPE-1

From: Determination of complete chromosomal haplotypes by bulk DNA sequencing

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
  1. 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
  2. b ≥1 link connecting ref, alt, HapA, and HapB & minor linkage ≤2 or minor linkage/total linkage ≤0.1
  3. cWith both the allele fraction (a) and the linkage (b) filter