Table 2. Sequencing Statistics.
Summary of sequencing info for all ten sequencing runs. All reads are listed in millions. Accession numbers for.bam files uploaded to European Nucleotide Archive provided, for sarcoma patient all 3 cfDNA runs were combined in a single.bam file separated by read group.
| Cancer Type | Tissue | ENA Accession Number | Input DNA (ng) | Reads (Millions) | Mapped Reads (%) | Paired Reads (%) | On Target Mapped Reads (%) | PCR Duplicates | Mean Sequencing Depth |
|---|---|---|---|---|---|---|---|---|---|
| Sarcoma | Buffy Coat | ERS700862 | 2000 | 392 | 361 (92.3) | 342 (87.4) | 210 (58) | 29% | 226 |
| Sarcoma | Primary Tumor | ERS700863 | 500 | 116 | 114 (98.3) | 113 (96.9) | 93 (81.6) | 31% | 118 |
| Sarcoma | cfDNA 1 | ERS700864 | 750 | 250 | 243 (97.1) | 204 (81.6) | 143 (58.9) | 34% | 160 |
| Sarcoma | cfDNA 2 | ERS700864 | 110 | 155 | 154.8 (99.7) | 147 (94.4) | 124 (80.4) | 12% | 162 |
| Sarcoma | cfDNA 3 | ERS700864 | 110 | 186 | 185 (99.7) | 175 (94.5) | 155 (84.0) | 16% | 203 |
| Sarcoma | Pooled cfDNA 1–3 | ERS700864 | 970 | 591 | 583 (98.62) | 526 (89.0) | 423 (72.6) | n/a | 524 |
| Breast Cancer | Buffy Coat | ERS700858 | 412 | 182 | 181 (99.6) | 180 (98.8) | 154 (84.8) | 20% | 201 |
| Breast Cancer | Primary Tumor | ERS700859 | 301 | 112 | 110.8 (99.2) | 99.1 (88.8) | 92 (82.8) | 52% | 118 |
| Breast Cancer | Metastasis | ERS700860 | 341 | 173 | 171.8 (99.5) | 170 (98.6) | 140 (81.6) | 22% | 183 |
| Breast Cancer | cfDNA | ERS700861 | 155 | 286 | 284.8 (99.5) | 253 (88.5) | 239 (83.8) | 37% | 309 |