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Table 3 List of medium indels tested by PCR.

From: A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae

Chr

Indel ID

Location

Ultra_contig

AF16 Amplicon (bp)

HK104 Amplicon (bp)

Predicted indel

Validation status

Validation Type

  

(cM)

 

Predicted

Observed

Predicted

Observed

   

1

cb-m142

12.6

cb25.fpc4321

665

700

915

950

250 bp insertion

250 bp insertion

*

 

cb-m2

13.5

cb25.fpc4321

1461

Failed PCR

1125

Failed PCR

336 bp deletion

Failed PCR

 
 

cb-m5

20.0

cb25.fpc4171

774

750

674

Failed PCR

100 bp deletion

Failed PCR

 
 

cb-m5

20.0

cb25.fpc4171

461

500

361

500

100 bp deletion

no indel

 
 

cb-m6

43.9

cb25.fpc4140

930

900

785

1000

145 bp deletion

100 bp insertion

**

 

cb-m13

unknown

cb25.fpc0078

504

420

385

400

119 bp deletion

20 bp deletion

**

 

cb-m14

unknown

cb25.fpc4127

1000

1000

676

710

324 bp deletion

290 bp deletion

*

 

cb-m146

unknown

cb25.fpc4122

406

480

506

530

100 bp insertion

50 bp insertion

**

 

cb-m12

unknown

cb25.fpc4127

921

Failed PCR

416

1000

505 bp deletion

Failed PCR

 

2

cb-m21

24.2

cb25.fpc0058

825

900

670

700

155 bp deletion

200 bp deletion

*

 

cb-m16

37.4

cb25.fpc4071

1097

>1500

687

>1500

410 bp deletion

unclear

 
 

cb-m19

11.9-13.1

cb25.fpc0011

1364

1013

828

750

536 bp deletion

263 bp deletion

**

 

cb-m149

27.9-34.0

cb25.fpc4206

470

490

603

600

133 bp insertion

110 bp insertion

*

 

cb-m26

27.9-34.0

cb25.fpc4206

678

700

407

410

271 bp deletion

290 bp deletion

*

 

cb-m38

unknown

cb25.fpc4131

835

860

544

600

291 bp deletion

260 bp deletion

*

 

bdP4

unknown

cb25.fpc2441

1013

~990

903

~880

110 bp deletion

110 bp deletion

*

3

cb-m46

6.1

cb25.fpc2587

747

1020

574

750

173 bp deletion

270 bp deletion

*

 

cb-m155

6.1

cb25.fpc2587

1169

Failed PCR

1329

Failed PCR

160 bp insertion

Failed PCR

 
 

cb-m48

21.2

cb25.fpc2976

1163

1200

644

1200

519 bp deletion

no indel

 
 

cb-m205

25.8

cb25.fpc4079

671

700

971

1000

300 bp insertion

300 bp insertion

*

 

cb-m159

36.5

cb25.fpc4224

463

500

655

Failed PCR

192 bp insertion

Failed PCR

 
 

cb-m160

28.8-29.3

cb25.fpc2193

821

1000

1053

1200

232 bp insertion

200 bp insertion

*

 

bdP1

31.3

cb25.fpc0002

1723

~1700

~1500

~1500

~200 bp deletion

200 bp deletion

*

4

cb-m172

18.2

cb25.fpc0039

650

700

904

950

254 bp insertion

250 bp insertion

*

 

cb-m170

20.6

cb25.fpc4090

691

720

931

Failed PCR

240 bp insertion

Failed PCR

 
 

cb-m171

25.5

cb25.fpc4132

381

450

476

550

95 bp insertion

100 bp insertion

*

 

cb-m70

25.5

cb25.fpc4132

594

>1600

421

1600

173 bp deletion

very large indel

**

 

cb-m176

37.5-41.2

cb25.fpc3835

732

Failed PCR

1014

Failed PCR

282 bp insertion

Failed PCR

 
 

cb-m74

37.5-41.2

cb25.fpc3835

677

1000

523

700

154 bp deletion

300 bp deletion

**

 

cb-m76

42.4-43.0

cb25.fpc2328

709

900

527

550

182 bp deletion

350 bp deletion

**

 

cb-m177

9.2-9.8

cb25.fpc4118

801

800

946

900

145 bp insertion

100 bp insertion

*

 

cb-m179

unknown

cb25.fpc4331

383

450

500

520

117 bp insertion

70 bp insertion

*

5

cb-m103

19.0

cb25.fpc2220

600

700

454

500

146 bp deletion

200 bp deletion

*

 

cb-m97

46.1

cb25.fpc4109

591

705

392

490

199 bp deletion

215 bp deletion

*

 

cb-m105

37.0-37.7

cb25.fpc4063

692

800

454

520

238 bp deletion

280 bp deletion

*

 

cb-m104

37.0-37.7

cb25.fpc4063

942

Failed PCR

661

Failed PCR

281 bp deletion

Failed PCR

 

x

cb-m197

3.5

cb25.fpc4033

692

700

855

790

163 bp insertion

90 bp insertion

*

 

cb-m204

17.4

cb25.fpc4044

689

750

949

1000

260 bp insertion

250 bp insertion

*

 

cb-m136

30.1

cb25.fpc0829

1440

2000

645

750

795 bp deletion

1250 bp deletion

*

 

cb-m127

34.1

cb25.fpc2334

486

600

349

405

137 bp deletion

195 bp deletion

*

 

cb-m126

34.1

cb25.fpc2334

785

Failed PCR

648

Failed PCR

137 bp deletion

Failed PCR

 
 

cb-m135

27.4-34.1

cb25.fpc0829

720

900

584

Failed PCR

136 bp deletion

Failed PCR

 
  1. The indels are arranged by chromosome and location. The corresponding ultracontigs are also listed. The "unknown" locations refer to unassembled contigs. The predicted indel sizes are based on in silico analysis of AF16 and HK104 amplicons. The validation type column marks indels that were consistent with prediction (*) and those that differed significantly (**).