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