Table 1 Properties of datasets from different sequencing centers
From: Copy Number Variation detection from 1000 Genomes project exon capture sequencing data
| Â | SC | BCM | BI | WU |
|---|---|---|---|---|
Total sample count | 117 | 352 | 161 | 93 |
Sample count after quality control | 106 | 349 | 110 | 82 |
Technology | Illumina | 454 | Illumina | Illumina |
Duplicate rate | 0.21 | 0.30 | 0.50 | 0.72 |
Mapping quality (mean) | 50 | 33 | 45 | 51 |
Base coverage(mean ± standard deviation) | 56 ± 34 | 23 ± 12 | 70 ± 61 | 29 ± 9 |
Read depth per gene(mean ± standard deviation) | 2309 ± 3166 | 106 ± 171 | 1329 ± 2053 | 977 ± 1382 |
MRD(mean ± standard deviation) | 1710 ± 1073 | 97 ± 52 | 1070 ± 803 | 599 ± 164 |
Number of exons | 8174 | 8174 | 8174 | 8174 |
Exons overlapped with segmental duplication regions | 458 (5.6%) | 458 (5.6%) | 458 (5.6%) | 458 (5.6%) |
Number of genes (passing QC) | 862 | 439 | 739 | 1 |
Genes overlapped with segmental duplication regions | 29 (3.3%) | 11(2.5%) | 23(3.1%) | 0(0.0%) |
Over-dispersion factor(mean ± standard deviation) | 7.9 ± 8.2 | 2.1 ± 1.1 | 6.4 ± 5.5 | N/A |
Quality index(mean ± standard deviation) | 9.4 ± 8.8 | 5.5 ± 2.3 | 7.6 ± 5.6 | N/A |
Expected detection sensitivity based on quality index | 0.46 | 0.20 | 0.41 | N/A |
Number of calls h = 0.65 either with or without a neighboring call | 36 | 4 | 56 | N/A |
Number of calls h = 0.1 either with a neighboring call | 17 | 0 | 11 | N/A |