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Table 1 Concordance between Birdseedv2 and consensus HapMap calls of 34,922 genotypes

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

HapMap Call Birdseedv2 call
  Original Spatial normalization
  0 1 2 Missing 0 1 2 Missing
0 3356
(9.6)
2002
(5.7)
19
(0.05)
7045
(20.2)
7451
(21.3)
960
(2.7)
11
(0.03)
4000
(11.5)
1 496
(1.4)
2040
(5.8)
550
(1.6)
4257
(12.2)
393
(1.1)
4340
(12.4)
428
(1.2)
2182
(6.2)
2 17
(0.05)
2157
(6.2)
3470
(9.9)
7343
(21.0)
14
(0.04)
1135
(3.3)
7614
(21.8)
4224
(12.1)
Missing 322
(0.92)
627
(1.8)
323
(0.92)
898
(2.6)
300
(0.86)
575
(1.6)
311
(0.89)
984
(2.8)
  1. Entries are frequencies (percentages) out of the 34,922 genotypes from Set 2 (see Method Section). Spatial bias normalization improved the call rate without inflating the number discordances with the consensus HapMap calls.