Table 1.

Efficiency (proportion of SNPs placed), accuracy (proportion of SNPs placed correctly) and precision (kb location from draft assembly location) of the LODE procedure for placing SNPs with known location in three test runs with varying thresholds of MAF of SNPs to be placed.

Test Run	Number of SNPs	Efficiency (%)	Accuracy (%)	Precision (kb)
Run1 (SNPs with MAF>0.05)	900	96.7	99.9	914 ± 130
Run2 (SNPs with 0.01<MAF ≤ 0.05)	300	30.6	98.9	3137 ± 381
Run3 (SNPs with 0.001<MAF ≤ 0.01)	300	2.0	33.3	6853 ± NA