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Popgen Stats from Hufford et al. 2012 Nat. Gen.

dataset
posted on 27.07.2013, 19:22 by Jeffrey Ross-Ibarra

Summary statistics for 10kb windows genome-wide and for genes in the maize v2 filtered gene set.  Data are from Hufford et al. 2012:

http://www.nature.com/ng/journal/v44/n7/full/ng.2309.html

See details in the paper for criteria for calling SNPs, data used for statistics, etc.

 

Columns are: 

locus: GRM name of gene in the filtered gene set

S: number of Segregating sites

ThetaW: Watterson's estimate of theta (per locus)

ThetaPi: nucleotide diversity (per locus)

ThetaH: Fay and Wu (2000) estimator (per locus)

TajD: Tajima's D

seqbp: # of bp sequenced. this should be used as the denominator to calculate per bp. values of the above statistics.

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