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Table 5 Summary of SNP reliability across species, sections and subgenera of Eucalyptus as measured by the number of SNP meeting the thresholds of call rate and GeneCall50 for two groups of SNPs that differed regarding the flanking sequence constraints during in silico SNP mining and GGGT assay design

From: High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species

  

SNPs selected with no flanking sequence

requirements (N = 372)

SNPs selected with no additional SNPs in

flanking sequence (N = 396)

Subgenera/Section

Species

# SNPs

with

Call rate

% SNPs

with

Call rate

# SNPs

with

GC50

% SNPs

with

GC50

# SNPs

with

Call rate

% SNPs

with

Call rate

# SNPs

with

GC50

% SNPs

with

GC50

  

≥ 95%

≥ 95%

≥ 0.40

≥ 0.40

≥ 95%

≥ 95%

≥ 0.40

≥ 0.40

Symphyomyrtus/Latoangulatae

E. grandis

323

86.8

333

89.5

378

95.5

378

95.5

Symphyomyrtus/Latoangulatae

E. urophylla

310

83.3

335

90.1

369

93.2

377

95.2

Symphyomyrtus/Latoangulatae

E. saligna

279

75.0

328

88.2

343

86.6

376

94.9

Symphyomyrtus/Maidenaria

E. globulus

325

87.4

331

89.0

369

93.2

374

94.4

Symphyomyrtus/Maidenaria

E. nitens

311

83.6

327

87.9

369

93.2

375

94.7

Symphyomyrtus/Maidenaria

E. dunnii

295

79.3

324

87.1

361

91.2

371

93.7

Symphyomyrtus/Maidenaria

E. viminalis

300

80.6

325

87.4

353

89.1

370

93.4

Symphyomyrtus/Exsertaria

E. camaldulensis

289

77.7

336

90.3

339

85.6

376

94.9

Symphyomyrtus/Exsertaria

E. tereticornis

281

75.5

319

85.8

330

83.3

365

92.2

Eucalyptus/Pseudophloius

E. pilularis

194

52.2

271

72.8

246

62.1

325

82.1

Idiogenes/Gympiaria

E. cloeziana

166

44.6

223

59.9

198

50.0

278

70.2