Table 2.
Number of reads (in counts per million) mapped to H. pylori or EBV genomes in TCGA samples identified from WGS and RNA-seq data
| Tumor sample-WGS | Tumor sample-RNASeq | Tissue sample-WGS | Tissue sample-RNASeq | |||||
|---|---|---|---|---|---|---|---|---|
| Sample | H. pylori | EBV | H. pylori | EBV | H. pylori | EBV | H. pylori | EBV |
| TCGA-BR-4183 | 0.01 | 0.00 | NA | 0.01 | 0.00 | NA | ||
| TCGA-BR-4184 | 0.00 | 0.00 | NA | 0.01 | 0.00 | NA | ||
| TCGA-BR-4187 | 0.76 | 0.00 | NA | 43.97 | 0.00 | NA | ||
| TCGA-BR-4188 | 0.00 | 0.00 | NA | 0.00 | 0.00 | NA | ||
| TCGA-BR-4191 | 0.04 | 0.00 | NA | 1.65 | 0.01 | NA | ||
| TCGA-BR-4201 | 0.09 | 0.00 | NA | 27.68 | 0.03 | NA | ||
| TCGA-BR-4253 | 0.21 | 6.36 | NA | 0.44 | 0.00 | NA | ||
| TCGA-BR-4255 | 0.00 | 0.00 | NA | 0.04 | 0.00 | NA | ||
| TCGA-BR-4256 | 0.00 | 0.01 | NA | 0.00 | 0.00 | NA | ||
| TCGA-BR-4257 | 0.02 | 0.00 | NA | 11.68 | 0.00 | NA | ||
| TCGA-BR-4267 | 0.01 | 0.00 | NA | 0.40 | 0.00 | NA | ||
| TCGA-BR-4279 | 6.99 | 0.00 | NA | 41.48 | 0.00 | NA | ||
| TCGA-BR-4280 | 0.01 | 0.00 | NA | 0.01 | 0.00 | NA | ||
| TCGA-BR-4292 | 0.04 | 0.00 | NA | 0.00 | 0.00 | NA | ||
| TCGA-BR-4294 | 0.19 | 0.00 | NA | 244.69 | 0.00 | NA | ||
| TCGA-BR-4357 | 0.34 | 0.00 | 0.03 | 0.00 | 64.43 | 0.00 | NA | |
| TCGA-BR-4363 | 0.00 | 0.00 | 0.37 | 0.00 | 0.00 | 0.00 | NA | |
| TCGA-BR-4366 | 0.01 | 0.00 | 0.01 | 0.00 | 0.07 | 0.00 | NA | |
| TCGA-BR-4367 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | NA | |
| TCGA-BR-4368 | 0.01 | 0.00 | 0.01 | 0.02 | 16.97 | 0.00 | NA | |
| TCGA-BR-4369 | 0.00 | 0.00 | 0.00 | 0.17 | 0.03 | 0.00 | NA | |
| TCGA-BR-4370 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | NA | |
| TCGA-BR-6453 | 0.30 | 0.00 | 0.01 | 0.00 | 0.19 | 0.00 | 0.03 | 0.00 |
| TCGA-BR-6454 | 0.01 | 0.00 | 0.00 | 0.00 | 17.95 | 0.00 | 2.72 | 0.00 |
| TCGA-CG-5720 | 3.42 | 0.00 | 1.48 | 0.00 | 12.51 | 0.00 | 2.28 | 0.00 |
| TCGA-CG-5721 | 0.00 | 0.01 | 0.00 | 0.43 | 0.01 | 0.00 | 0.00 | 0.00 |
| TCGA-CG-5722 | 0.13 | 2.55 | 0.04 | 34.13 | 1.83 | 0.00 | 0.00 | 0.22 |
| TCGA-CG-5723 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | NA | |
| TCGA-CG-5724 | 0.03 | 0.00 | 0.00 | 0.00 | 92.65 | 0.00 | NA | |
| TCGA-CG-5725 | 0.00 | 0.01 | 0.00 | 0.61 | 0.01 | 0.00 | NA | |
| TCGA-CG-5726 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | NA | |
| TCGA-CG-5727 | 0.00 | 0.01 | NA | 0.01 | 0.00 | NA | ||
| TCGA-CG-5728 | 0.00 | 0.00 | NA | 2.79 | 0.00 | 0.34 | 0.00 | |
| TCGA-CG-5730 | 0.01 | 0.00 | NA | 0.00 | 0.00 | 0.00 | 0.00 | |
| TCGA-CG-5732 | 0.01 | 0.00 | 0.00 | 0.25 | 0.00 | 0.00 | NA | |
| TCGA-CG-5733 | 0.01 | 0.00 | NA | 2.01 | 0.00 | 0.63 | 0.01 | |
| TCGA-CG-5734 | 1.25 | 0.01 | 0.03 | 0.17 | 0.00 | 0.00 | 0.00 | 0.00 |
Entries in bold are samples that are considered H. pylori-positive and entries in italics EBV-positive by a counts per million (CPM) reads threshold of 0.3. NA not applicable