hCBS SSVS BLA BRR TP FP TP FP TP95  FP95 TP90 FP90 TP95  FP95  TP90  FP90 1 10 0 10 0 10 0 10 0  10  9  10  19 5 10 1 10 0 10 0 10 1  10  2  10  5 20 10 1 10 0 7 0 7 0  6  0  7  1 50 10 1 10 0 0 0 0 0  0  0  0  0

Table 5: True and false positive detections by all methods when applied to the real cattle LD data (4697 SNPs from chromosome 1 and 2) with 10 SNPs outside of LD-blocks used to generate the phenotype. Four different values for the error variance were simulated.