TABLE 2

Phasing accuracy—real data

Familial information (steps I)+ Population information (step III)Overall
TypePhased Het SNPsSwitchesPhased Het SNPsSwitches FPMSwitches LHCMSwitches FPMSwitches LHCM
None0 (0.0%)a0.0 (0.0%)65.22 (100.0%)1.71 (2.6%)0.98 (1.5%)1.71 (2.6%)0.98 (1.5%)
0 (0.0%)b0.0 (0.0%)116.87 (100.0%)1.52 (1.3%)0.86 (0.7%)1.52 (1.3%)0.86 (0.7%)
I35.80 (54,9%)0.0 (0.0%)29.42 (45.1%)0.55 (1.9%)0.45 (1.5%)0.55 (0.8%)0.45 (0.7%)
64.21 (54.9%)0.0 (0.0%)52.66 (45.1%)0.49 (0.9%)0.48 (0.9%)0.49 (0.4%)0.48 (0.4%)
  • Information used for phasing: I, use of Mendelian segregation rules to reconstruct the offspring's phase; III, use of population-wide linkage disequilibrium information.

  • a Low-density segment (256 markers).

  • b High-density map (500 markers). Approximately 67 and 69% of the markers, corresponding to 171.08 and 343.46 markers for the low- and high-density maps, respectively, were homozygous and considered phased de facto. Approximately 8% of the markers, corresponding to 19.71 and 39.66 markers for the low- and high-density maps, respectively, remained unphased after step IIb and were not used for comparison.