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Table 2 Comparison between the final haplotype solution and the reference haplotype of NA12878

From: Determination of complete chromosomal haplotypes by bulk DNA sequencing

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
  1. aAll phased variants without any filtering
  2. 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
  3. cFiltered by haplotype linkage: ≥1 link connecting ref, alt, HapA, and HapB, and minor linkage ≤2 or minor linkage/total linkage ≤0.1
  4. 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
  5. eVariants phased by molecular linkage to phased SNVs in the scaffold haplotype solution
  6. fIntersection with phased indel variants in the GIAB data with exactly matching variant genotypes. Total number of phased indels in the GIAB release, 4090
  7. 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
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Genome Biology

ISSN: 1474-760X

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