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Table 4 Summary of SNP and InDel variations in Prunus species

From: Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Taxon

Genome coverage (%)

Read mapped rate (%)

Variation

SNP in CDS

InDel in CDS

SNP + InDel

Hetero SNPa

Homo SNPb

InDel

Overall

Silence

Nonsense

Missense

Splicing site

Ti/Tv

In-frame

Frame shift

Intron

Intergenic

Pyn-Jeju1

95.4

94.4

2,838,985

1,096,549

895,813

4,831,347

148,300

3661

182,107

1158

1.56

4340

22,281

255,057

4,214,443

Pyn-Jeju2

98.6

95.6

2,596,728

145,287

764,810

3,506,825

99,482

2560

123,473

851

1.52

2967

20,894

180,133

3,076,465

Pyn-Jeju3

95.7

93.9

2,946,741

1,262,874

932,447

5,142,062

153,376

3679

187,285

1259

1.57

4421

22,453

269,721

4,499,868

Pyn-Jeju4

95.3

94.5

2,896,646

1,223,511

916,719

5,036,876

152,756

3652

186,991

1222

1.57

4337

22,262

266,970

4,398,686

Pyn-Jeju5

94.5

93.9

3,378,621

1,657,723

1,063,188

6,099,532

176,065

4532

218,722

1501

1.58

5187

23,776

313,087

5,356,662

Pxy-US1

95.0

94.6

3,464,156

1,629,328

1,072,679

6,166,163

175,976

4596

220,018

1527

1.58

5244

23,717

315,788

5,419,297

Pxy-US2

94.9

94.5

3,445,971

1,626,652

1,068,387

6,141,010

175,718

4600

219,181

1490

1.58

5195

23,653

314,928

5,396,245

Pxy-JP1

94.9

91.3

3,527,140

1,722,941

1,109,412

6,359,493

182,173

4620

225,405

1538

1.58

5329

24,706

324,046

5,591,676

Pxy-JP2

94.9

92.6

3,529,437

1,724,190

1,110,969

6,364,596

182,189

4639

225,537

1557

1.58

5343

24,780

324,679

5,595,872

Ppa-1

82.2

93.3

1,197,274

1,428,540

595,858

3,221,672

87,944

2581

116,320

819

1.60

2857

14,995

165,140

2,831,016

Ppa-2

72.0

94.0

726,505

1,263,932

482,136

2,472,573

74,707

1966

94,308

660

1.56

2216

13,013

136,354

2,149,349

Ppa-3

84.6

96.0

1,883,696

1,522,293

751,829

4,157,818

118,186

3088

148,056

1001

1.59

3340

17,363

218,562

3,648,222

Pjj-1

86.9

93.8

1,975,049

1,823,000

776,618

4,574,667

144,854

3306

173,239

1120

1.55

4011

17,776

238,548

3,991,813

Pjj-2

76.1

94.8

1,139,292

1,592,058

583,439

3,314,789

120,474

2333

138,885

837

1.52

3104

14,767

183,366

2,851,023

Pjq

86.4

94.0

1,946,474

1,769,052

763,036

4,478,562

145,116

3211

172,508

1119

1.55

3924

17,563

233,810

3,901,311

Psa

86.6

93.7

1,960,926

1,823,069

775,824

4,559,819

144,689

3312

173,070

1131

1.55

3957

17,591

240,595

3,975,474

Total

–

–

39,453,641

23,310,999

13,663,164

76,427,804

2,282,005

56,336

2,805,105

18,790

–

65,772

321,590

3,980,784

66,897,422

  1. aHeterozygous SNP rate, proportion of heterozygous SNPs in a genome
  2. bHomozygous SNP rate, proportion of homozygous SNPs in a genome
  3. Ti transition, Tv transversion