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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