hCBS SSVS BLA BRR TP FP TP FP TP95  FP95 TP90 FP90 TP95  FP95  TP90  FP90 1 18 1 18 2 17 0 19 4 18 22 20 44 5 18 1 19 2 10 0 12 2 12 6 15 15 20 17 4 14 1 5 0 7 0 1 0 7 0 50 13 4 15 2 0 0 2 1 0 0 2 0

Table 4: True and false positive detections by all methods when applied to the real cattle LD data (4697 SNPs from chromosome 1 and 2) with 20 SNPs associated to the phenotype, 10 inside of LD-blocks and 10 non-correlated SNPs outside of LDblocks. Four different values for the error variance were simulated.