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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.