Skip to main content

Table 4 Number of SNPs in six classes after applying reproducibility, variance and nMinorHom filters

From: Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa

SNP class

No. of SNPs

No. of SNPs in category

  

SNP

mSNP

Indel

SNP-SNP

Indel-SNP

SNP-in-Insertion

F1D

Codon-based

MHR

18,958

9,913

191

2,458

737

286

1,114

1,864

2,395

CRBT

5,876

4,248

0

542

761

96

144

44

41

Other

9,755

6,014

0

1,214

1,387

196

428

150

366

NMH

36,088

25,782

1,050

3,365

979

298

843

1,498

2,273

OTV

1,030

415

1

106

126

21

11

38

312

PHR

23,355

16,891

519

1,843

3,101

280

303

157

261

Reproducibility

3,263

2,568

129

200

182

17

39

55

73

AAvarianceY

491

339

10

38

82

8

8

1

5

ABvarianceX

1,775

1,095

11

221

328

32

32

18

38

ABvarianceY

3,212

2,367

54

279

384

51

34

14

29

BBvarianceY

394

183

6

43

144

7

5

2

4

nMinorHom

1,611

1,153

87

176

53

17

31

33

61

Filtered PHR

12,609

9,186

222

886

1,928

148

154

34

51

No of markers on array

95,063

63,263

1,761

9,528

7,092

1,177

2,843

3,751

5,648

  1. These SNP classes were: MHR (Mono High Resolution), which passed all QC but were monomorphic; CRBT (CallRate Below Threshold), where genotype call rate was under 97%; Other, where the resultant SNP cluster pattern did not fall into any of the other classes; NMH (No Minor Homozygote), which passed all QC but only two clusters were observed; OTV (Off-Target Variant), which had an additional low intensity cluster resulting from mismatches between the probe and the sequences for that group of individuals; and PHR (Poly High Resolution) which were polymorphic and passed all QC. PHR SNPs were subjected to additional filters (reproducibility, variance and nMinorHom).
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us