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 |