Table 2.
Summary of the NGS analysis of targeted capture experiments.
| Clone | Target-enrichment method | Library Insert Size (bp) | Total Reads (M) | % Mapped | Mean Coverage | Vector Coverage | Vector Copy No | Fold Enrichment |
|---|---|---|---|---|---|---|---|---|
| AE54SL | RGEN-D (B) | 630 | 22.6 | 98.4 | 2 | 20.1 | ND | 5 |
| AE54SL | xGen | 372 | 32.3 | 99.8 | 3.2 | 14,078* (354,049) | ND | 2,301 |
| AE54SL | WGS | 615/3,985 | 344.7 | 92 | 27 | 46 | 4 | 1 |
| AD49ZG | RGEN-TdT | 641 | 17.3 | 95.2 | 0.5 | 56.8 | ND | 56.8 |
| AD49ZG | RGEN-D (A) | 655 | 18.2 | 94.9 | 0.26 | 16.9 | ND | 16.3 |
| AD49ZG | xGen | 378 | 42.2 | 99.4 | 5 | 8,110* (540,685) | ND | 821 |
| AD49ZG | TLA | 193 | 1.24 | 99.8 | 0.05 | 905* (8,625) | ND | 9,106 |
| AD49ZG | WGS (Illumina) | 450 | 754.9 | 97.9 | 68.3 | 133.1 | 4 | 1 |
| AD49ZG | WGS (PacBio) | 13,200 (N50) | 6.9 | 84.9 | 14.5 | 26.4 | 4 | 1 |
| AD49ZH | RGEN-TdT | 400 | 10 | 94.2 | 0.28 | 82 | ND | 29.2 |
| AD49ZH | xGen | 403 | 44.2 | 99.3 | 5.3 | 98,006* (970,360) | ND | 1,849 |
| AD49ZH | WGS (Illumina) | 454 | 777.4 | 98 | 70.1 | 728.9 | 20 | 1 |
*Vector coverage after removal of PCR duplicates. PCR duplication rates were calculated according to Bansal40. The integrated vector copy numbers were calculated using the WGS Illumina® and PacBio data, as ratios of the vector coverage to the mean chromosome coverage. The fold enrichments were normalized by the corresponding vector copy numbers. Abbreviations used: ND, not determined; WGS, whole genome sequencing; TLA, targeted locus amplification6; xGen, hybridization capture of DNA libraries for NGS target enrichment1; RGEN-D, RGEN-TdT, methods developed in this paper (Figs 1 and 2).