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Table 1 Number of SVs called from Illumina data per calling tool, SV type, and size class

From: Combined use of Oxford Nanopore and Illumina sequencing yields insights into soybean structural variation biology

 

[50 bp–100 bp[

[100 bp–1 kb[

[1 kb–10 kb[

≥ 10 kba

Calling program

DELb

INSc

DUPd

INVe

DEL

INS

DUP

INV

DEL

INS

DUP

INV

DEL

DUP

INV

asmvar

11,018

3575

0

0

14,877

2243

0

0

5748

1

0

0

4681

0

0

manta

9664

3358

453

0

12,378

1815

3114

0

11,463

0

4448

0

7325

5034

0

smoove

4168

0

22

45

6489

0

1208

149

4687

0

981

33

1794

975

47

svaba

7288

2284

673

21

6907

215

16,081

292

2969

0

1548

190

512

458

223

mergedf

17,199

5023

656

61

22,980

3165

9810

296

13007

1

4316

135

10,640

4696

178

  1. a Insertions ≥ 10 kb are not shown because none were called
  2. b DEL: deletions
  3. c INS: insertions
  4. d DUP: duplications
  5. e INV: inversions
  6. f merged: the dataset merged using SVmerge