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ADMIXTURE analysis of 'world' dataset
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ABCDEFGHIJKLMNOPQRST
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Dataset summary
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339populations
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286reported populations; Dodecad populations with less than 5 individuals were included in the ADMIXTURE analysis but population proportions not reported
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4280individuals
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248980SNPs
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Initial processing:Identify common SNPs and intersect with Rutgers recombination map for Illumina chips
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Software used
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Data processing PLINK 1.07
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Admixture analysisADMIXTURE 1.22
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ProcessingCriterionRemaining individualsRemaining SNPs
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Relative removal within populationsPLINK "RATIO" > 2 standard deviations OR "RATIO" > 2.53633248980
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Removal of low genotype individuals--mind 0.013369248980
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Removal of low genotype and low MAF SNPs--geno 0.01 --maf 0.013369246033
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LD-based pruning--indep-pairwise 200 25 0.43369166255
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Behar/Chaubeyhttp://dienekes.blogspot.com/2012/10/relatives-in-admixture.html3362166255
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Notes
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Normalized median proportions are presented in the spreadsheet: these are calculated by taking (for each population) the median of each ancestral component, and then normalizing the sum of components to add up to 100% by multiplying with a constant
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f3-statistics are sorted on increasing Z-score; only negative scores are indicative of admixture (Z<-3); positive scores are consistent with either admixture or not (up to K=11)
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D-statistics, with an African Pop4 are sorted on absolute Z-score; both positive and negative scores (|Z|>3) are significant (up to K=11)
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K#Iterations
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323
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437
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537
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5 (post Paniya)39
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666
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741
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852
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944
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1053
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1186
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1265
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1378
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Calculators
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globe4http://dodecad.blogspot.com/2012/10/globe4-calculator.htmlbased on K=4
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http://dienekes.blogspot.com/2012/10/admixture-tracks-amerindian-like.html
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globe10http://dodecad.blogspot.com/2012/10/globe10-calculator.htmlbased on K=10
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Information
Pairwise f3
K=3
K=3 stats
K=4
K=4 stats
K=5
K=5 stats
K=5 (post Paniya cleanup)
K=5 (post Paniya cleanup) stats
K=6
K=6 stats
K=7
K=7 stats
K=8
K=8 stats
K=9
K=9 stats
K=10
K=10 stats
K=11
K=11 stats
K=12
K=12 stats
K=13
K=13 stats