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Table 1 The regenotyping results for the different genotyping platforms.

From: Missing call bias in high-throughput genotyping

Platform

rsID

 

Obs.

Seq.

c i

pVal

SNPstream

rs6743724

AA

47

0

1.000

0.231

  

Aa

427

2

0.995

 
  

aa

1009

16

0.984

 
 

rs699512

AA

239

3

0.987

0.0277

  

Aa

1064

3

0.997

 
  

aa

1309

15

0.989

 

Illumina

rs2277632

AA

351

8

0.978

1.42 × 10 -5

  

Aa

1129

1

0.999

 
  

aa

941

2

0.998

 
 

rs1457043

AA

449

1

0.998

0.463

  

Aa

1198

6

0.995

 
  

aa

775

1

0.999

 

TaqMan

rs10109984

AA

111

1

0.991

0.0898

  

Aa

480

9

0.981

 
  

aa

513

20

0.962

 
 

rs11226

AA

242

4

0.984

0.599

  

Aa

568

17

0.971

 
  

aa

298

8

0.974

 

GeneChip 500 K

rs11928855

AA

66

22

0.750

2.26 × 10 -15

  

Aa

243

1

0.996

 
  

aa

133

1

0.992

 
 

rs6855202

AA

59

15

0.797

3.33 × 10 -13

  

Aa

246

0

1.000

 
  

aa

141

0

1.000

 
  1. pVal is the P value calculated by Fisher Exact Test to show whether the genotype counts called by the software provided by the respective platform (Obs.) were significantly different from the no-calls' counts by sequencing (Seq.). c i is the genotypic specific call-rate for AA, Aa and aa.
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BMC Genomics

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