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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
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Genome Biology

ISSN: 1474-760X

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