Table 2. Comparison between statistical phasing.
| Individual | Haplotype concordance (%) | Switch error rate (%) | Flip error rate (%) | Mean interswitch distance (kbp) | Mean length of incorrectly phased haplotype (kbp) |
|---|---|---|---|---|---|
| Fosmid-phased haplotypes vs. SHAPEIT phased haplotypes using the phase one 1000 Genomes reference panel | |||||
| NA19240 | 54.60 | 1.33 | 0.60 | 84.6 | 69.6 |
| HG02799 | 52.46 | 1.84 | 0.79 | 52.2 | 43.3 |
| HG03108 | 53.62 | 1.05 | 0.47 | 94.1 | 78.8 |
| NA12878 | 53.18 | 0.87 | 0.32 | 170.0 | 144.0 |
| NA12878b | 52.82 | 0.85 | 0.31 | 172.0 | 145.0 |
| NA21302 | 52.00 | 2.32 | 1.02 | 43.6 | 37.6 |
| HG03428a | 70.01 | 1.88 | 0.95 | 42.6 | 28.5 |
| NA20847a | 79.30 | 1.83 | 0.97 | 46.5 | 29.5 |
| HGDP01029a | 69.83 | 6.87 | 3.50 | 12.5 | 7.3 |
| HGDP01029a,b | 72.49 | 5.39 | 2.81 | 15.3 | 9.0 |
| HGDP00456a | 78.09 | 4.68 | 2.70 | 16.1 | 8.8 |
| Average | 62.57 | 2.52 | 1.26 | 62.5 | 49.7 |
| Fosmid-phased haplotypes vs. SHAPEIT phased haplotypes using phase three 1000 Genomes reference panel | |||||
| NA19240 | 68.00 | 0.33 | 0.21 | 480.5 | 293.6 |
| HG02799 | 77.10 | 0.63 | 0.27 | 296.5 | 124.4 |
| HG03108 | 69.40 | 0.42 | 0.27 | 346.5 | 208.5 |
| NA12878 | 58.90 | 0.67 | 0.32 | 264.4 | 204.4 |
| NA12878b | 60.86 | 0.66 | 0.33 | 282.9 | 209.4 |
| NA21302 | 53.10 | 2.44 | 1.08 | 41.2 | 32.9 |
| HG03428a | 89.70 | 0.66 | 0.50 | 132.2 | 56.1 |
| NA20847a | 91.50 | 1.00 | 0.73 | 70.0 | 36.9 |
| HGDP01029a | 69.97 | 7.17 | 3.77 | 12.0 | 6.9 |
| HGDP01029a,b | 72.38 | 5.84 | 3.11 | 14.1 | 8.1 |
| HGDP00456a | 77.47 | 5.08 | 2.97 | 14.9 | 8.1 |
| Average | 72.79 | 2.04 | 1.12 | 184.2 | 108.0 |
| Fosmid-phased haplotypes: assign parental alleles using trio data vs. using Prism | |||||
| NA19240 | 54.12 | 0.05 | 0.00 | 1242.6 | 1115.0 |
| HG02799 | 58.18 | 0.02 | 0.00 | 3427.3 | 2821.9 |
| Average | 56.15 | 0.03 | 0.00 | 2335.0 | 1968.5 |
We calculated haplotype concordance, switch error rate, flip error rate, mean interswitch distance, and mean length of incorrectly phased haplotype between haplotypes resolved by fosmid pool sequencing and haplotypes statistically phased using either the phase one or phase three 1000 Genomes reference panels.
a
Indicates that trio data were unavailable to link blocks together and phasing comparison analysis was limited to comparisons within RefHap blocks.
b
Indicates that the sample was phased using a population-specific reference panel (NA12878 used only European populations, and HGDP01029 used only African populations).