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Table 1 Results from FDR program QVALUE in 11 replicates

From: Comparison of false-discovery rate for genome-wide and fine mapping regions

  Genome-wide (n = 9187 SNPs) Fine mapping (n = 2094 SNPs)
  Number significant (%)   Number significant (%)  
Replicate p ≤ 0.05 Bonferroni FDR FDR π0 p ≤ 0.05 Bonferroni FDR FDR π0
90 498 (5.4) 21 (0.23) 28 (0.30) 0.982 944 (45.1) 489 (23.4) 1001 (47.8) 0.339
91 483 (5.3) 21 (0.23) 28 (0.30) 0.997 948 (45.3) 448 (21.4) 940 (44.9) 0.464
92 484 (5.3) 23 (0.25) 24 (0.26) 1 939 (44.9) 459 (21.9) 1082 (51.7) 0.248
93 501 (5.5) 18 (0.20) 25 (0.27) 1 914 (43.7) 435 (20.8) 910 (43.5) 0.468
94 526 (5.7) 19 (0.21) 23 (0.25) 0.989 899 (43.0) 444 (21.2) 879 (42.0) 0.471
95 493 (5.4) 20 (0.22) 26 (0.28) 0.992 1010 (48.3) 432 (20.6) 1069 (51.1) 0.355
96 494 (5.4) 18 (0.20) 26 (0.28) 1 945 (45.2) 463 (22.1) 966 (46.1) 0.411
97 533 (5.8) 17 (0.19) 22 (0.24) 0.992 1000 (47.8) 443 (21.2) 1010 (48.2) 0.439
98 500 (5.4) 19 (0.21) 22 (0.24) 0.958 939 (44.9) 437 (20.9) 926 (44.2) 0.467
99 501 (5.5) 21 (0.23) 26 (0.28) 1 923 (44.1) 459 (21.9) 915 (43.7) 0.486
100 528 (5.8) 20 (0.22) 22 (0.24) 0.988 955 (45.6) 428 (20.4) 981 (46.8) 0.366
Average 503.7 (5.5) 19.7 (0.21) 24.7 (0.27) 0.991 946.9 (45.2) 448.8 (21.4) 970.8 (46.4) 0.410