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Rice

Table 3 List of significantly associated SNPs in GWAS using antimicrobial activities in the 107 accessions of landraces from WRC and JRC

From: Measurements of Antibacterial Activity of Seed Crude Extracts in Cultivated Rice and Wild Oryza Species

LD block number

Associated SNP number

SNP with highest association in the LD

CHR

Coordinate

− log10(p)

1

1

Yes

1

18,005,951

5.5737002

2

2

 

1

27,878,359

5.8942855

2

3

 

1

27,880,379

5.8942855

2

4

 

1

27,880,453

5.8942855

2

5

 

1

27,881,781

5.8942855

2

6

 

1

27,881,834

5.8942855

2

7

 

1

27,882,081

5.8942855

2

8

 

1

27,882,248

5.8942855

2

9

 

1

27,882,325

5.8942855

2

10

 

1

27,883,352

5.7644463

2

11

 

1

27,885,038

6.0783968

2

12

 

1

27,886,765

6.1436155

2

13

 

1

27,886,937

6.0783968

2

14

 

1

27,887,170

6.0783968

2

15

 

1

27,887,655

6.0783968

2

16

 

1

27,887,678

6.0783968

2

17

 

1

27,887,813

6.0783968

2

18

 

1

27,887,821

6.0783968

2

19

 

1

27,887,894

6.0783968

2

20

 

1

27,889,339

6.0783968

2

21

 

1

27,889,390

6.0783968

2

22

 

1

27,890,608

6.0092839

2

23

 

1

27,891,417

5.8942855

2

24

 

1

27,891,708

6.0783968

2

25

 

1

27,892,211

5.8573603

2

26

 

1

27,893,209

5.8942855

2

27

 

1

27,893,722

5.8573603

2

28

 

1

27,893,863

5.8942855

2

29

 

1

27,894,089

5.8942855

2

30

 

1

27,894,427

5.8573603

2

31

 

1

27,894,659

5.8942855

2

32

 

1

27,894,833

5.8942855

2

33

 

1

27,894,855

5.8942855

2

34

 

1

27,895,567

5.8942855

2

35

 

1

27,895,950

5.8942855

2

36

 

1

27,897,746

5.8942855

2

37

 

1

27,897,749

5.8942855

2

38

 

1

27,905,911

5.8942855

2

39

 

1

27,905,926

5.8942855

2

40

 

1

27,906,578

5.8942855

2

41

 

1

27,906,583

5.8705357

2

42

 

1

27,907,200

5.8942855

2

43

 

1

27,910,437

5.8942855

2

44

 

1

27,916,341

5.8942855

2

45

 

1

27,921,389

5.8942855

2

46

 

1

27,921,462

5.8942855

2

47

 

1

27,921,505

5.8942855

2

48

 

1

27,923,341

5.8942855

2

49

 

1

27,925,445

5.8942855

2

50

 

1

27,925,448

5.8942855

2

51

 

1

27,929,471

5.8942855

2

52

 

1

27,929,485

5.8942855

2

53

 

1

27,936,334

5.8921459

2

54

 

1

27,936,425

5.8921459

2

55

 

1

27,936,624

5.8921459

2

56

 

1

27,938,041

5.8921459

2

57

 

1

27,938,359

5.5031395

2

58

 

1

27,939,515

5.8921459

2

59

 

1

27,949,632

5.8942855

2

60

 

1

27,950,033

5.8942855

2

61

Yes

1

27,950,388

6.1916607

2

62

 

1

27,951,516

5.8942855

2

63

 

1

27,951,520

5.5143779

2

64

 

1

27,951,622

5.8942855

2

65

 

1

27,951,679

5.8942855

2

66

 

1

27,951,730

5.8942855

2

67

 

1

27,951,846

5.8942855

2

68

 

1

27,953,717

5.8921459

2

69

 

1

27,953,871

5.8921459

2

70

 

1

27,953,994

5.8921459

2

71

 

1

27,954,243

5.8921459

2

72

 

1

27,954,363

5.8921459

2

73

 

1

27,954,387

5.8921459

2

74

 

1

27,954,496

5.8921459

2

75

 

1

27,954,743

5.8921459

2

76

 

1

27,955,180

5.8921459

2

77

 

1

27,955,491

5.8921459

2

78

 

1

27,956,227

5.8921459

2

79

 

1

27,956,293

5.8921459

2

80

 

1

27,958,781

5.8921459

2

81

 

1

27,961,451

5.8921459

2

82

 

1

27,961,827

5.793417

2

83

 

1

27,961,979

5.8921459

2

84

 

1

27,962,184

5.8921459

2

85

 

1

27,964,204

5.8921459

2

86

 

1

27,965,101

5.8921459

2

87

 

1

27,965,327

5.8921459

2

88

 

1

27,966,621

5.8921459

2

89

 

1

27,967,087

5.8921459

2

90

 

1

27,968,585

5.8921459

2

91

 

1

27,969,991

5.8921459

2

92

 

1

27,970,071

5.8921459

2

93

 

1

27,972,673

5.8921459

2

94

 

1

27,973,326

5.8921459

2

95

 

1

27,973,533

5.8921459

2

96

 

1

27,980,057

5.8921459

2

97

 

1

27,980,136

5.8921459

2

98

 

1

27,981,282

5.8921459

2

99

 

1

27,981,536

5.8921459

3

100

Yes

2

5,087,458

5.0276583

3

101

 

2

5,102,106

4.7984936

3

102

 

2

5,102,126

4.7984936

4

103

 

2

24,844,697

5.0179777

4

104

 

2

24,880,854

4.9434382

4

105

 

2

24,882,717

4.9434382

4

106

Yes

2

24,884,774

5.2144851

4

107

 

2

24,915,038

4.9434382

4

108

 

2

24,915,059

4.9434382

5

109

Yes

2

31,700,860

4.9846402

5

110

 

2

31,704,278

4.9846402

5

111

 

2

31,704,685

4.9846402

5

112

 

2

31,706,449

4.9846402

5

113

 

2

31,714,007

4.9846402

5

114

 

2

31,714,952

4.9846402

5

115

 

2

31,722,293

4.9846402

5

116

 

2

31,728,246

4.9846402

5

117

 

2

31,728,257

4.9846402

5

118

 

2

31,734,360

4.9846402

5

119

 

2

31,735,654

4.9846402

5

120

 

2

31,736,321

4.9846402

5

121

 

2

31,737,988

4.9846402

5

122

 

2

31,740,565

4.9846402

5

123

 

2

31,742,890

4.9846402

5

124

 

2

31,746,201

4.9846402

5

125

 

2

31,746,203

4.9846402

5

126

 

2

31,757,993

4.9846402

5

127

 

2

31,762,177

4.9846402

5

128

 

2

31,762,204

4.9846402

5

129

 

2

31,773,582

4.9846402

6

130

 

3

23,599,267

5.4185624

6

131

 

3

23,602,834

5.4185624

6

132

 

3

23,602,836

5.4185624

6

133

 

3

23,603,512

5.4185624

6

134

 

3

23,604,571

4.9748581

6

135

 

3

23,604,576

4.9748581

6

136

 

3

23,605,736

5.4185624

6

137

Yes

3

23,619,690

6.2848578

7

138

 

3

23,703,226

5.5702154

7

139

 

3

23,703,283

5.5702154

7

140

 

3

23,705,154

6.9193735

7

141

 

3

23,705,351

6.9085089

7

142

 

3

23,705,455

8.5849765

7

143

 

3

23,705,458

7.3314836

7

144

 

3

23,705,491

7.3314836

7

145

 

3

23,705,652

7.1631128

7

146

 

3

23,705,694

7.9566377

7

147

 

3

23,705,695

7.0222627

7

148

 

3

23,706,631

8.1004531

7

149

 

3

23,706,709

8.3545679

7

150

 

3

23,707,032

5.5702154

7

151

 

3

23,707,299

5.5702154

7

152

 

3

23,708,043

8.1004531

7

153

 

3

23,708,062

8.3545679

7

154

 

3

23,708,620

5.5702154

7

155

 

3

23,710,275

8.1004531

7

156

 

3

23,710,359

8.1004531

7

157

 

3

23,710,419

5.6737461

7

158

 

3

23,710,504

6.9193735

7

159

 

3

23,710,544

8.3545679

7

160

 

3

23,710,576

5.5702154

7

161

 

3

23,711,028

6.0668419

7

162

 

3

23,711,636

8.1004531

7

163

 

3

23,711,749

8.4396629

7

164

 

3

23,712,310

8.3545679

7

165

 

3

23,712,325

8.1004531

7

166

 

3

23,713,421

8.1004531

7

167

 

3

23,713,435

5.5702154

7

168

 

3

23,715,323

7.3879052

7

169

Yes

3

23,715,931

9.3375444

7

170

 

3

23,716,016

9.1989532

7

171

 

3

23,716,745

5.8389016

7

172

 

3

23,716,746

8.3650091

7

173

 

3

23,716,755

8.1796015

7

174

 

3

23,720,991

8.1004531

7

175

 

3

23,721,260

8.3545679

7

176

 

3

23,722,660

5.5702154

7

177

 

3

23,722,804

5.5702154

7

178

 

3

23,723,013

5.5702154

7

179

 

3

23,724,952

5.5702154

7

180

 

3

23,725,905

8.1004531

7

181

 

3

23,725,960

8.3545679

7

182

 

3

23,726,052

8.3545679

7

183

 

3

23,726,144

5.5702154

7

184

 

3

23,726,921

5.5702154

7

185

 

3

23,727,594

5.4542477

7

186

 

3

23,727,607

5.5702154

7

187

 

3

23,729,521

5.5702154

7

188

 

3

23,731,153

5.5702154

7

189

 

3

23,731,242

5.5702154

8

190

Yes

3

23,899,609

5.1917485

9

191

Yes

3

24,212,274

4.796233

10

192

 

3

24,446,000

5.7211321

10

193

 

3

24,446,501

5.7211321

10

194

 

3

24,447,171

5.7211321

10

195

Yes

3

24,447,470

6.2612987

10

196

 

3

24,447,579

6.0825733

11

197

Yes

3

27,810,949

5.0142548

12

198

Yes

3

33,333,544

5.3214088

13

199

 

3

34,199,211

6.3678668

13

200

 

3

34,200,889

6.3678668

13

201

 

3

34,202,851

6.3678668

13

202

 

3

34,207,764

6.292728

13

203

 

3

34,210,099

6.3678668

13

204

 

3

34,210,389

6.3678668

13

205

 

3

34,210,674

6.2748973

13

206

 

3

34,210,690

6.2748973

13

207

 

3

34,210,696

6.2748973

13

208

 

3

34,210,772

6.3678668

13

209

 

3

34,215,449

6.0992343

13

210

 

3

34,217,835

6.3678668

13

211

 

3

34,218,523

6.3678668

13

212

 

3

34,219,544

6.3678668

13

213

 

3

34,229,546

6.3678668

13

214

 

3

34,255,810

6.3678668

13

215

 

3

34,275,277

6.3678668

13

216

 

3

34,278,017

6.3678668

13

217

 

3

34,278,817

6.3678668

13

218

 

3

34,283,349

6.3678668

13

219

Yes

3

34,373,584

6.4472466

13

220

 

3

34,382,599

6.3678668

13

221

 

3

34,385,992

6.3678668

13

222

 

3

34,386,019

6.3678668

13

223

 

3

34,389,605

6.3678668

14

224

Yes

4

2,856,477

5.1343572

15

225

 

4

4,868,339

5.6474895

15

226

 

4

4,914,935

5.5280193

15

227

 

4

5,005,023

4.9696027

15

228

 

4

5,009,730

5.9454252

15

229

 

4

5,010,358

5.9454252

15

230

 

4

5,011,336

4.8936051

15

231

 

4

5,011,658

5.9454252

15

232

 

4

5,013,003

5.9454252

15

233

 

4

5,013,314

6.0225279

15

234

 

4

5,022,565

6.2031621

15

235

 

4

5,025,728

6.2059583

15

236

 

4

5,026,779

6.2059583

15

237

 

4

5,027,101

6.2059583

15

238

 

4

5,027,514

6.2059583

15

239

 

4

5,028,468

6.2059583

15

240

 

4

5,029,403

6.2059583

15

241

 

4

5,031,991

6.2059583

15

242

 

4

5,033,295

6.2059583

15

243

 

4

5,033,475

5.4984068

15

244

 

4

5,033,545

6.2059583

15

245

 

4

5,033,552

6.2059583

15

246

 

4

5,033,624

6.2059583

15

247

 

4

5,034,748

5.9848918

15

248

 

4

5,035,576

6.2059583

15

249

 

4

5,035,806

6.2059583

15

250

 

4

5,037,743

6.2059583

15

251

 

4

5,037,825

6.2059583

15

252

Yes

4

5,038,844

6.310407

15

253

 

4

5,039,716

6.2961758

15

254

 

4

5,045,202

6.2059583

15

255

 

4

5,096,994

6.2059583

15

256

 

4

5,100,290

5.6871248

15

257

 

4

5,128,610

4.9540905

15

258

 

4

5,128,681

4.9540905

15

259

 

4

5,134,602

4.8384224

16

260

Yes

4

30,886,560

5.7629089

16

261

 

4

30,886,994

5.7629089

16

262

 

4

30,920,022

4.8718593

16

263

 

4

30,926,071

5.7629089

16

264

 

4

30,945,182

4.8718593

16

265

 

4

30,948,864

5.7629089

16

266

 

4

30,964,390

4.8718593

16

267

 

4

30,965,051

4.8718593

16

268

 

4

30,965,344

5.7629089

16

269

 

4

30,967,249

4.8718593

16

270

 

4

30,973,636

4.8718593

17

271

Yes

4

31,674,325

8.8057355

18

272

Yes

4

34,786,157

4.8937411

19

273

Yes

6

4,785,418

5.60333

20

274

Yes

6

7,519,840

5.4449539

21

275

Yes

6

25,598,090

6.1028625

22

276

 

7

264,621

5.3368175

22

277

Yes

7

284,003

5.5136829

22

278

 

7

291,471

5.432903

23

279

 

7

6,063,531

6.1889212

23

280

Yes

7

6,064,303

7.2457358

23

281

 

7

6,064,370

7.2457358

23

282

 

7

6,065,094

7.2457358

23

283

 

7

6,065,873

7.2457358

23

284

 

7

6,066,571

7.2457358

23

285

 

7

6,067,391

7.2457358

23

286

 

7

6,070,349

7.2457358

23

287

 

7

6,070,358

7.2457358

23

288

 

7

6,070,366

7.2457358

23

289

 

7

6,070,418

7.2457358

23

290

 

7

6,070,679

7.2457358

23

291

 

7

6,084,536

7.2457358

23

292

 

7

6,084,550

7.2457358

23

293

 

7

6,085,652

5.2117538

23

294

 

7

6,085,690

7.2457358

23

295

 

7

6,085,742

5.2117538

23

296

 

7

6,085,749

5.2117538

23

297

 

7

6,085,763

7.2457358

23

298

 

7

6,085,834

5.2117538

23

299

 

7

6,086,044

5.2117538

23

300

 

7

6,086,074

7.2457358

23

301

 

7

6,086,334

5.2117538

23

302

 

7

6,086,414

7.2457358

23

303

 

7

6,086,726

5.2117538

23

304

 

7

6,086,998

7.2457358

23

305

 

7

6,087,022

7.2457358

23

306

 

7

6,087,080

7.2457358

23

307

 

7

6,087,198

7.2457358

23

308

 

7

6,087,516

7.2457358

23

309

 

7

6,087,526

6.153898

23

310

 

7

6,087,573

7.2457358

23

311

 

7

6,087,600

7.2457358

23

312

 

7

6,087,643

7.2457358

23

313

 

7

6,087,826

7.2457358

23

314

 

7

6,087,834

7.2457358

23

315

 

7

6,088,030

7.2457358

23

316

 

7

6,088,069

7.2457358

23

317

 

7

6,088,359

5.2117538

23

318

 

7

6,090,769

4.768021

23

319

 

7

6,093,126

5.8051805

23

320

 

7

6,093,580

5.2117538

23

321

 

7

6,093,671

5.2117538

23

322

 

7

6,093,908

5.2117538

23

323

 

7

6,094,396

5.8051805

23

324

 

7

6,094,482

5.8051805

23

325

 

7

6,094,801

5.8051805

23

326

 

7

6,094,895

5.8051805

23

327

 

7

6,094,937

5.8051805

23

328

 

7

6,094,964

5.8051805

23

329

 

7

6,095,324

5.8051805

23

330

 

7

6,095,356

5.8051805

23

331

 

7

6,095,484

5.4227381

23

332

 

7

6,095,853

5.3338753

23

333

 

7

6,096,273

5.8051805

23

334

 

7

6,096,485

5.8051805

23

335

 

7

6,096,497

4.9147451

23

336

 

7

6,096,521

5.8051805

23

337

 

7

6,096,547

5.8051805

23

338

 

7

6,096,809

5.9043426

23

339

 

7

6,098,286

5.9043426

23

340

 

7

6,098,386

5.8051805

23

341

 

7

6,098,581

5.8051805

23

342

 

7

6,098,852

5.8051805

23

343

 

7

6,099,226

5.8051805

23

344

 

7

6,099,258

5.8051805

23

345

 

7

6,099,332

5.9043426

23

346

 

7

6,099,594

5.9043426

23

347

 

7

6,099,686

5.9043426

23

348

 

7

6,099,725

5.9043426

23

349

 

7

6,100,039

5.9043426

23

350

 

7

6,100,437

5.9043426

23

351

 

7

6,100,990

5.8051805

23

352

 

7

6,101,657

5.8051805

23

353

 

7

6,102,160

5.7175365

23

354

 

7

6,102,520

5.8051805

23

355

 

7

6,102,592

4.8790972

23

356

 

7

6,102,638

4.8790972

23

357

 

7

6,102,693

4.8790972

23

358

 

7

6,102,735

4.8790972

23

359

 

7

6,102,903

4.8790972

23

360

 

7

6,103,174

5.8051805

23

361

 

7

6,103,463

4.8790972

23

362

 

7

6,103,806

4.8790972

23

363

 

7

6,104,116

4.8790972

23

364

 

7

6,104,228

5.8051805

23

365

 

7

6,104,370

5.8395915

23

366

 

7

6,104,431

4.8790972

23

367

 

7

6,104,667

4.8790972

23

368

 

7

6,104,785

4.8790972

23

369

 

7

6,105,088

4.8790972

23

370

 

7

6,105,180

5.8051805

23

371

 

7

6,105,212

5.8051805

23

372

 

7

6,105,458

4.8790972

23

373

 

7

6,105,479

5.8051805

23

374

 

7

6,105,480

5.8051805

23

375

 

7

6,105,492

5.8051805

23

376

 

7

6,106,134

6.9801363

23

377

 

7

6,108,273

4.8790972

23

378

 

7

6,108,355

5.8051805

23

379

 

7

6,108,654

5.8051805

23

380

 

7

6,109,115

4.8790972

23

381

 

7

6,109,415

5.8051805

23

382

 

7

6,109,443

5.8395915

23

383

 

7

6,109,481

5.8051805

23

384

 

7

6,109,866

5.8051805

23

385

 

7

6,109,868

6.9801363

23

386

 

7

6,109,916

4.8790972

23

387

 

7

6,110,331

4.8790972

23

388

 

7

6,111,183

4.8790972

23

389

 

7

6,111,369

4.8790972

23

390

 

7

6,111,870

4.8790972

23

391

 

7

6,112,133

5.8051805

23

392

 

7

6,112,824

5.8051805

23

393

 

7

6,113,492

4.8790972

23

394

 

7

6,113,568

4.8790972

23

395

 

7

6,114,786

4.8790972

23

396

 

7

6,116,319

4.788826

23

397

 

7

6,116,607

4.788826

23

398

 

7

6,116,670

4.788826

23

399

 

7

6,117,084

4.788826

23

400

 

7

6,117,920

4.788826

23

401

 

7

6,117,951

4.788826

23

402

 

7

6,118,057

4.788826

23

403

 

7

6,119,445

4.788826

23

404

 

7

6,119,850

4.788826

23

405

 

7

6,120,052

4.788826

23

406

 

7

6,122,777

4.7337213

23

407

 

7

6,130,228

4.788826

23

408

 

7

6,130,337

4.788826

23

409

 

7

6,132,970

4.788826

23

410

 

7

6,133,017

4.788826

23

411

 

7

6,133,379

4.788826

23

412

 

7

6,169,691

4.8181564

23

413

 

7

6,199,788

5.0076188

23

414

 

7

6,199,806

5.0076188

24

415

 

7

6,655,446

4.9209635

24

416

Yes

7

6,670,111

5.4666983

25

417

Yes

7

15,950,927

5.0870132

25

418

 

7

15,951,213

5.0870132

25

419

 

7

15,951,648

5.0870132

25

420

 

7

15,952,726

5.0870132

26

421

Yes

8

244,512

4.7358436

26

422

 

8

265,949

4.7358436

26

423

 

8

272,578

4.7358436

26

424

 

8

272,721

4.7358436

27

425

Yes

8

25,340,714

5.2533736

28

426

Yes

8

25,532,049

5.2987689

29

427

Yes

9

7,166,403

9.2837879

29

428

 

9

7,168,080

6.1269237

29

429

 

9

7,168,949

6.1269237

30

430

Yes

9

7,998,198

4.718603

31

431

 

9

9,668,007

5.6750183

31

432

Yes

9

9,668,585

5.7282745

31

433

 

9

9,669,315

5.7282745

31

434

 

9

9,670,051

5.7282745

31

435

 

9

9,670,151

5.7282745

31

436

 

9

9,670,373

5.7282745

32

437

 

9

9,778,486

5.7282745

32

438

 

9

9,778,556

5.7282745

32

439

 

9

9,778,722

4.9079815

32

440

 

9

9,778,764

5.7282745

32

441

 

9

9,778,873

4.9079815

32

442

 

9

9,778,945

4.9079815

32

443

 

9

9,779,063

5.7282745

32

444

 

9

9,779,075

5.7282745

32

445

 

9

9,779,123

5.7282745

32

446

 

9

9,779,138

5.7282745

32

447

 

9

9,779,269

5.7282745

32

448

 

9

9,779,315

5.7282745

32

449

 

9

9,779,351

4.9079815

32

450

 

9

9,779,353

4.9079815

32

451

 

9

9,779,376

5.7282745

32

452

 

9

9,779,470

5.7282745

32

453

 

9

9,779,619

4.9079815

32

454

 

9

9,779,834

4.9079815

32

455

 

9

9,779,839

5.7282745

32

456

 

9

9,779,846

4.9079815

32

457

 

9

9,779,938

4.9079815

32

458

 

9

9,779,996

5.7282745

32

459

 

9

9,780,618

5.7282745

32

460

 

9

9,780,698

5.7282745

32

461

 

9

9,782,756

5.7664962

32

462

 

9

9,783,743

5.7282745

32

463

 

9

9,784,795

6.0492653

32

464

 

9

9,784,952

5.7282745

32

465

 

9

9,785,403

5.9725688

32

466

 

9

9,785,621

5.9725688

32

467

 

9

9,785,899

5.9725688

32

468

Yes

9

9,785,988

6.698189

32

469

 

9

9,786,291

5.9725688

32

470

 

9

9,788,095

5.7282745

32

471

 

9

9,788,526

5.7282745

33

472

 

9

9,925,206

5.6003263

33

473

 

9

9,925,891

5.527741

33

474

 

9

9,926,313

5.1139043

33

475

 

9

9,926,854

5.6642413

33

476

 

9

9,927,170

5.3699792

33

477

 

9

9,927,826

5.3652004

33

478

Yes

9

9,928,848

6.1659864

33

479

 

9

9,929,137

5.6642413

33

480

 

9

9,935,223

5.6642413

33

481

 

9

9,936,891

5.0602412

33

482

 

9

9,939,176

5.6642413

33

483

 

9

9,939,470

5.6642413

33

484

 

9

9,941,053

5.0602412

33

485

 

9

9,941,753

5.6642413

33

486

 

9

9,941,774

5.6642413

33

487

 

9

9,942,709

5.6642413

34

488

Yes

9

14,962,678

4.7118402

35

489

Yes

9

15,900,636

4.7943897

36

490

 

9

20,146,598

4.9416879

36

491

 

9

20,155,748

4.8397716

36

492

Yes

9

20,209,460

5.0262212

37

493

 

10

2,057,109

5.453482

37

494

Yes

10

2,057,364

5.4953117

38

495

Yes

10

21,819,222

5.3096533

39

496

Yes

11

21,990,372

4.7907263

40

497

Yes

11

23,007,993

5.0269461

41

498

Yes

12

19,752,661

4.7299037

42

499

Yes

12

25,568,747

4.8310019

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