Skip to main content

Table 1 Haplotype calls from 454 (run 1) and cloning/Sanger (CS) sequencing.

From: Haplotyping and copy number estimation of the highly polymorphic human beta-defensin locus on 8p23 by 454 amplicon sequencing

Method

454

CS

454

CS

454

CS

454

454

454

454

454

CS

Amplicon

F2

S1

F5

S2

F5

S2

F4

F6

F7

F8

Total

MSV HCs

1-2

#

#

6-8

#

#

7-10a*

#

#

3-5

#

11-15

#

16-18

#

19-24

#

HCs

#

C0140

GA

1.566

112

TCC

664

136

CCGgGc

1.491

81

TAT

582

CCTCG

867

TCG

888

CTACCG

542

  
 

GG

583

36

   

CCGaGc

431

55

CAT

390

CCTAG

816

TTA

288

TCTTTA

195

  
 

CA

528

30

      

TAC

382

      

10.213

450

C0766

GG

1.525

114

TCC

360

140

CCGgGc

1.084

147

TAC

1.679

 

nd

TCG

1.878

CTACCG

876

  
 

CA

842

41

CCC

195

48

CCGgAc

506

41

CAT

601

      

9.546

531

C0913

CA

1.869

113

TCC

680

132

CCGgGc

1.221

145

TAC

1.556

CCTCG

1.195

TCG

1.816

CTACCG

2.153

  
 

GA

1.157

58

CCC

287

54

CCGgAc

617

41

TCC

634

CCTAG

593

    

13.778

543

NA12760

GA

1.750

92

TCC

795

99

CCGgGc

1.566

104

TAC

2.825

CCTCG

1.669

TTA

2.056

TCTTTA

645

  
 

GG

386

20

CCC

181

60

CCGgAc

339

55

TAT

981

CTCAC

599

TCG

1.696

CTACCG

605

  
 

CA

319

19

CTG

184

0

TGGgAc

459

0

TCC

797

CCTAG

499

    

18.351

449

NA15029

GA

1.530

 

TCC

767

nd

CCGgGc

1.046

nd

TCC

1.156

CCTGC

1.785

TTA

1.689

TCTTTA

377

  
 

GG

805

    

CCAgGc

431

 

TAT

882

CTCAT

1.087

TCG

1.115

CTACCG

267

  
    

CTG

475

 

TGGgAc

913

 

TAC

496

        
          

CAT

420

      

15.241

 

NA15213

GA

1.326

 

TCC

665

nd

CCGgGc

1.338

nd

TAC

278

CCTCG

1.178

TCG

1.496

CTACCG

929

  
 

CA

349

 

CTG

171

 

TGGgAc

390

 

TAT

98

CCTAG

577

TTA

866

TCTTTA

551

  
          

TCC

87

CTCAT

473

    

10.772

 

NA15385

GA

985

 

TCC

374

nd

CCGgGc

702

nd

TAC

1.374

CCTCG

1.003

TCG

938

CTACCG

688

  
 

GG

592

 

CCC

169

 

CCGgAc

239

 

TAT

673

CCTAG

322

TTA

782

TCTTTA

483

  
    

CTG

88

 

TGGgAc

188

 

TCC

345

CTCAT

280

    

10.225

 

NA18502

GA

812

80

TCC

182

125

CCGgGc

265

139

TAT

1.453

CCTCG

415

TTA

856

TCTTTA

645

  
 

CA

561

58

CCC

21

15

CCGgGa

56

0

  

TTCAT

65

TCG

418

CTACCG

267

  
    

CCG

(7)

0

CGGgAc

39

0

        

5.995

402

NA18552

CA

3.490

 

TCC

197

nd

CCGgGc

273

nd

TAT

225

CCTCG

1.653

TCG

1.756

CTACCG

1.525

  
    

CCC

328

 

CCGgAc

340

 

TAC

1.058

        
          

CAT

503

      

11.348

 

NA18858

GA

677

97

TCC

1.234

188

CCGgGc

623

124

TAT

1.490

CCTCG

1.327

TTA

1.087

TCTTTA

2.404

  
 

CA

324

45

   

CCGaGc

218

51

TAC

822

  

TCG

404

CTACCG

633

  
 

GG

205

(16)

              

11.448

505

NA19140

GA

314

57

TCC

706

nd

CCGgGc

234

nd

 

nd

CCTCG

504

TTA

281

 

nd

  
 

CA

310

73

   

CCGaGc

42

   

CTCAT

130

TCG

62

    
 

GG

105

24

              

2.688

154

Total

 

22.910

1.069

 

8.702

982

 

15.012

983

 

21.787

 

17.037

 

20.372

 

13.785

119.605

3.034

  1. #: number of HCs; *: alleles in lower cases refer to the 2 additionally identified MSVs 9a and 10a; (): nominally below 10% threshold; nd: no data.