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Table 2 Accuracy of allele frequency estimation for DNA pools.

From: UPDG: U tilities package for data analysis of P ooled D NA G WAS

Correction methoda Allele frequency difference (Pools - Individual samples) Absolute valuesb % of SNPs with over-estimated allele frequencyc
  Sample group Mean difference SD Mean difference SD  
1 Case 0.0726 0.0414 0.0728 0.0411 99.1
2 Case 0.0725 0.0419 0.0725 0.0418 99.1
3 Case 0.0477 0.0435 0.0487 0.0423 94.3
4 Case 0.0690 0.0511 0.0740 0.0435 92.6
1 Control 0.0627 0.0467 0.0630 0.0463 99.1
2 Control 0.0625 0.0465 0.0626 0.0463 99.1
3 Control 0.0352 0.0512 0.0389 0.0484 85.7
4 Control 0.0591 0.0500 0.0637 0.0438 93.5
1 Case - Control 0.0099 0.0276 0.0246 0.0158 70.4
2 Case - Control 0.0100 0.0275 0.0247 0.0157 69.4
3 Case - Control 0.0125 0.0328 0.0298 0.0184 68.6
4 Case - Control 0.0099 0.0293 0.0253 0.0176 69.4
  1. a Correction methods used include those based on (1) Hoogendoorn et al [6], (2) Meaburn et al [7], (3) Craig et al [8] plus Meaburn et al [7], and (4) no adjustment.
  2. b Mean of the absolute values for the differences in allele frequencies between DNA pools and individual samples.
  3. c In total, 108 SNPs were compared for allele frequency differences as estimated for DNA pools and individual DNA samples. However, only 105 SNPs were compared for the correction method (3) (Craig et al [8] plus Meaburn et al [7]) because 3 SNPs were filtered out.