Table 1. 1000 Genomes Project pilot data used for mobile element insertion discovery.
| Non-reference MEI | Reference MEI | |||||||
| Detection method | Illumina RP | 454 SR | RP+SR | Combined deletion detection algorithms | ||||
| Dataset | Low Cov | Trio | Low Cov | Trio | Total | Low Cov | Trio | Total |
| Number of samples | 138 | 6 | 22 | 2 | 156 | 169 | 6 | 175 |
| Coverage per sample | 2.2x | 16.4x | 2.0x | 7.6x | 3.0x | 3x | 25x | 3.9x |
| Alu insertions | 2882 | 1786 | 2420 | 1284 | 4500 | 1689 | 1420 | 1730 |
| L1 insertions | 345 | 192 | 396 | 172 | 792 | 193 | 170 | 206 |
| SVA insertions | 49 | 35 | 17 | 7 | 79 | 70 | 65 | 74 |
| Loci PCR tested | 193 | 186 | 182 | 185 | 746 | - | - | - |
| Loci validated | 183 | 182 | 173 | 174 | 712 | 1873 | 1615 | 1927 |
| FDR (%) | 5.2±1.6 | 2.2±1.1 | 4.4±1.6 | 5.5±1.1 | 4.5±0.8 | - | - | - |
Number of samples, average read coverage, detected loci, and validation results are shown. Non-reference MEI false detection rates (FDR) were based on validation results at randomly selected loci. In addition to PCR validation, reference MEI were also tested for validation as deletions by local assembly. The FDR for reference MEI, including the additional MEI selection criteria, is estimated to be <10%.