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Table 4 Concordance between Birdseedv2 and non-redundant HapMap calls of 261,267 genotypes

From: Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays

HapMap Birdseedv2 call
Call Original Spatial normalization
  0 1 2 Missing 0 1 2 Missing
0 27,735
(10.6)
14,592
(5.6)
233
(0.09)
43,806
(16.8)
48,341
(18.5)
9,925
(3.8)
168
(0.06)
27,932
(10.7)
1 6,324
(2.4)
21,250
(8.1)
6,147
(2.4)
38,035
(8.1)
5,483
(2.1)
43,252
(16.6)
5,558
(2.1)
17,463
(6.7)
2 186
(0.07)
15,162
(5.8)
27,250
(10.4)
44,576
(17.1)
169
(0.06)
10,073
(3.9)
48,807
(18.7)
28,125
(10.8)
Missing 2,183
(0.84)
4,287
(1.6)
2,350
(0.90)
7,151
(2.7)
3,007
(1.2)
5,034
(1.9)
3,108
(1.2)
4,822
(1.8)
  1. Entries are frequencies (percentages) out of the 261,267 genotypes from Set 3.