Table 3.
PacBio phasing statistics
| Sample | Scaffold SNVs | Assembly SNVs | Phased blocks | Isolated assembly SNVs (%) | Haplotype partitioned SNVs (%) |
|---|---|---|---|---|---|
| PGF + COX | 3090 | 9691 | 16 | 4 (0.04%) | 97.30 |
| EAS-P | 2285 | 6632 | 28 | 9 (0.14%) | 99.77 |
| EUR-P | 1646 | 5500 | 55 | 10 (0.18%) | 99.22 |
| AFA | 2470 | 8174 | 25 | 4 (0.05%) | 99.58 |
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Scaffold SNPs: Number of heterozygous SNVs called using PacBio reads aligned to hg38, restricted to microarray positions. Assembly SNVs: Number of heterozygous SNVs called using the PacBio reads aligned to the collapsed assembly. Phased blocks: Total number of phased blocks generated using assembly SNVs. Isolated assembly SNVs: Number of assembly SNVs that are not phased to another heterozygous variant and are not part of a phased block. Haplotype partitioned SNVs: Percentage of assembly SNVs that intersect with scaffold SNVs and could be used to partition reads by haplotype.
