TABLE 1

Data set descriptions and summary results

Data setMAF classaPopulationsbIndividualsLociFormula%cCC%dCT%eCT%, single locusfFormulag% rare and commonh% fixed and commoniFormulaj% het.k
InsertionsAllDistinct (3)219175100.460561421101832
InsertionsRareDistinct (3)21921475839661257335.77.0
InsertionsCommonDistinct (3)2191549.10.4605514167.12036
InsertionsAllAll (4)259175153.11.2651223111532
InsertionsRareAll (4)25921507646738.362434.37.5
InsertionsCommonAll (4)259154133.10.776412186.51736
MicroarrayAllDistinct (3)1379,922000561526122032
MicroarrayRareDistinct (3)137920177.30651087569.510
MicroarrayCommonDistinct (3)1379,0020005515197.82134
MicroarrayAllAll (8)2789,9223.1101.1821344271832
MicroarrayRareAll (8)27885136721.4848.998887.911
MicroarrayCommonAll (8)2789,0713.38.31.1811339211934
ResequencedAllAll (3)20914,2338.200571340291117
ResequencedRareAll (3)2098,38929450.96599.651434.64.7
ResequencedCommonAll (3)2095,8445.90.9605314238.41934
  • a Sets of loci with MAF < 0.1 (rare), MAF > 0.1 (common), or any MAF (all).

  • b Sets of individuals representing all populations in a data set or only the more distinct populations.

  • c Dissimilarity fraction.

  • d Centroid misclassification rate.

  • e Population trait value misclassification rate.

  • f Trait value misclassification rate based on a single locus, averaged over all loci.

  • g The proportion of variance in allelic frequencies attributable to population differences.

  • h Percentage of loci with MAF < 0.1 in one population and MAF > 0.1 in another.

  • i Percentage of loci that are monomorphic in one population and polymorphic with MAF > 0.1 in another.

  • j Average difference in allele frequency between populations, averaged across alleles, loci, and population pairs.

  • k Percentage of individuals heterozygous at each locus, averaged across all loci.