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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