Table 1.
Overview of the 5,734 WGS samples analyzed in this study. Column 4 shows how many reads remained per sample after removing reads that mapped to the GRCh38 human genome. Column 6 shows the number of reads remaining after a second pass further removed reads matching the CHM13 genome. Columns 8 and 10 show the average numbers of reads from column 6 that were identified by Kraken as either human or vector.
| Cancer type | Total # samples | Average read count (millions) | Unmapped reads after mapping to GRCh38 (avg, thousands) | Unmapped reads after mapping to GRCh38+CHM13 (avg, thousands) | Kraken-identified human reads (avg, thousands) | Kraken-identified vector reads (avg, thousands) | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| BLCA | 288 | 284 | 5,983 | (2.10%) | 4,829 | (1.70%) | 199.5 | (0.07%) | 14 | (0.00%) |
| BRCA | 245 | 690 | 1,738 | (0.25%) | 1,532 | (0.22%) | 35.0 | (0.01%) | 418 | (0.06%) |
| CESC | 130 | 375 | 3,347 | (0.89%) | 2,675 | (0.71%) | 113.9 | (0.03%) | 83 | (0.02%) |
| COAD | 262 | 354 | 5,195 | (1.47%) | 4,496 | (1.27%) | 183.9 | (0.05%) | 745 | (0.21%) |
| DLBC | 14 | 926 | 381 | (0.04%) | 381 | (0.04%) | 0.1 | (0.00%) | 363 | (0.04%) |
| ESCA | 115 | 349 | 3,546 | (1.02%) | 2,620 | (0.75%) | 88.2 | (0.03%) | 584 | (0.17%) |
| GBM | 117 | 777 | 898 | (0.12%) | 758 | (0.10%) | 108.6 | (0.01%) | 28 | (0.00%) |
| HNSC | 335 | 388 | 5,334 | (1.38%) | 4,348 | (1.12%) | 235.4 | (0.06%) | 279 | (0.07%) |
| KICH | 100 | 869 | 454 | (0.05%) | 453 | (0.05%) | 0.2 | (0.00%) | 436 | (0.05%) |
| KIRC | 87 | 705 | 1,054 | (0.15%) | 1,054 | (0.15%) | 0.1 | (0.00%) | 400 | (0.06%) |
| KIRP | 77 | 866 | 340 | (0.04%) | 340 | (0.04%) | 0.2 | (0.00%) | 324 | (0.04%) |
| LAML | 110 | 742 | 3,165 | (0.43%) | 2,205 | (0.30%) | 264.0 | (0.04%) | 899 | (0.12%) |
| LGG | 185 | 444 | 3,546 | (0.80%) | 2,804 | (0.63%) | 98.6 | (0.02%) | 2 | (0.00%) |
| LIHC | 108 | 905 | 391 | (0.04%) | 391 | (0.04%) | 0.2 | (0.00%) | 368 | (0.04%) |
| LUAD | 577 | 473 | 4,808 | (1.02%) | 4,185 | (0.88%) | 126.3 | (0.03%) | 1,964 | (0.42%) |
| LUSC | 100 | 906 | 194 | (0.02%) | 194 | (0.02%) | 0.1 | (0.00%) | 2 | (0.00%) |
| OV | 121 | 747 | 454 | (0.06%) | 454 | (0.06%) | 0.3 | (0.00%) | 346 | (0.05%) |
| PRAD | 272 | 304 | 6,680 | (2.20%) | 5,152 | (1.69%) | 305.7 | (0.10%) | 15 | (0.01%) |
| READ | 120 | 283 | 6,620 | (2.34%) | 5,704 | (2.02%) | 230.2 | (0.08%) | 969 | (0.34%) |
| SARC | 82 | 733 | 181 | (0.02%) | 181 | (0.02%) | 0.1 | (0.00%) | 159 | (0.02%) |
| SKCM | 320 | 311 | 3,826 | (1.23%) | 3,134 | (1.01%) | 116.7 | (0.04%) | 632 | (0.20%) |
| STAD | 299 | 368 | 5,292 | (1.44%) | 3,877 | (1.05%) | 284.7 | (0.08%) | 28 | (0.01%) |
| THCA | 1,248 | 784 | 676 | (0.09%) | 527 | (0.07%) | 20.6 | (0.00%) | 43 | (0.01%) |
| UCEC | 320 | 383 | 4,590 | (1.20%) | 3,811 | (1.00%) | 290.7 | (0.08%) | 461 | (0.12%) |
| UVM | 102 | 156 | 3,599 | (2.31%) | 2,548 | (1.64%) | 103.1 | (0.07%) | 2 | (0.00%) |
| Total | 5,734 | 3,099,077 | 18,420,684 | (0.59%) | 14,998,914 | (0.48%) | 713,538 | (0.02%) | 2,444,357 | (0.08%) |
| Average | 229 | 540 | 3,213 | 0.59% | 2,616 | 0.48% | 124 | 0.02% | 426 | 0.08% |