Table 1 Quantitative evaluation of CHH methylation detection by DeepPlant and Dorado

From: Accurate cross-species 5mC detection for Oxford Nanopore sequencing in plants with DeepPlant

Species

Tool

Sequencing depth

5×

10×

15×

20×

25×

30×

Training datasets

S. miltiorrhiza

DeepPlant

0.8472

0.8524

0.8601

0.8695

0.8780

–

Dorado

0.7604

0.7500

0.7443

0.7420

0.7441

–

Dorado*

0.8069

0.7975

0.7890

0.7821

0.7784

–

S. tuberosum

DeepPlant

0.8048

0.8173

0.8251

–

–

–

Dorado

0.6964

0.6899

0.6861

–

–

–

Dorado*

0.7453

0.7412

0.7365

–

–

–

R. communis

DeepPlant

0.8340

0.8532

0.8592

0.8663

0.8742

0.8814

Dorado

0.7849

0.7819

0.7752

0.7714

0.7713

0.7735

Dorado*

0.8098

0.8133

0.8085

0.8048

0.8036

0.8041

Testing datasets

A. thaliana

DeepPlant

0.6410

0.6611

0.6733

0.6853

0.6998

0.7139

Dorado

0.5908

0.5828

0.5813

0.5795

0.5789

0.5787

Dorado*

0.6322

0.6324

0.6365

0.6378

0.6394

0.6396

B. vulgaris

DeepPlant

0.7655

0.7740

0.7826

0.7920

0.8006

0.8074

Dorado

0.6385

0.6242

0.6123

0.6062

0.6054

0.6051

Dorado*

0.7253

0.7182

0.7076

0.6996

0.6937

0.6904

O. sativa

DeepPlant

0.6401

0.6535

0.6659

0.6796

0.6937

0.7051

Dorado

0.3266

0.3292

0.3269

0.3247

0.3237

0.3240

Dorado*

0.4833

0.4937

0.4860

0.4728

0.4605

0.4510

V. vinifera

DeepPlant

0.7268

0.7326

0.7445

0.7588

0.7719

0.7832

Dorado

0.6499

0.6360

0.6284

0.6233

0.6201

0.6193

Dorado*

0.7082

0.7026

0.7000

0.6976

0.6949

0.6928

C. sinensis

DeepPlant

0.7616

0.7800

0.7949

0.8064

0.8175

0.8259

Dorado

0.6644

0.6595

0.6563

0.6544

0.6538

0.6533

Dorado*

0.7165

0.7146

0.7090

0.7055

0.7032

0.7017

S. lycopersicum

DeepPlant

0.7808

0.7903

0.8022

0.8157

0.8277

0.8378

Dorado

0.6759

0.6655

0.6569

0.6546

0.6546

0.6577

Dorado*

0.7315

0.7260

0.7195

0.7153

0.7134

0.7133

  1. Note: Each value represents the genome-wide Pearson correlation between the methylation callers and whole-genome BS-seq results at the corresponding sequencing depths of downsampled nanopore datasets. For each species, the same BS-seq dataset (Supplementary Data 2) was used for all tests. The results of applying DeepPlant’s threshold selection method (Supplementary Fig. 2) to Dorado are labeled as “Dorado*”.
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