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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

From: Identification of low abundance microbiome in clinical samples using whole genome sequencing

 

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

  1. 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