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Table 1 Comparison of assigned ancestry using different cutoff value between FastPop and Structure

From: FastPop: a rapid principal component derived method to infer intercontinental ancestry using genetic data

Cutoff value   CEU YRI CHB
  Without prior population information for Hapmap samples
0.9 PCA Scores 17520/16329/16325 64/62/55 740/721/719
0.8 PCA Scores 18016/17928/17928 175/165/159 773/768/767
0.7 PCA Scores 18171/18122/18122 266/263/260 799/796/796
  With prior population information for Hapmap samples
0.9 PCA Scores 17510/16329/16321 69/62/59 743/721/719
0.8 PCA Scores 18017/17928/17928 174/165/159 774/768/768
0.7 PCA Scores 18167/18122/18121 267/263/260 799/796/796
  1. Number in each cell indicates: No. assigned by structure/No. assigned by FastPop/No. common in both methods. Structure analysis was conducted with/without prior population information for Hapmap samples. Structure was run was run under admixture model. Parameter setting “BURNIN 10000 NUMREPS 1000 INFERALPHA 1 POPSPECIFICALMBDA 1”. Without prior population information, the running time is 21:16:00 and 23:30:00 for with prior population information