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Characterization of X-Linked SNP genotypic variation in globally distributed human populations

Amanda M Casto1*, Jun Z Li2, Devin Absher3, Richard Myers3, Sohini Ramachandran4 and Marcus W Feldman5

Author Affiliations

1 Department of Genetics, Stanford University, Mail Stop 5120, Stanford, California 94305, USA

2 Department of Human Genetics, University of Michigan, 4909 Buhl Building, 1241 East Catherine St, Ann Arbor, Michigan 48109, USA

3 HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35806, USA

4 Society of Fellows and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St, Cambridge, Massachusetts 02138, USA

5 Department of Biological Sciences, Stanford University, Gilbert Hall 108, Stanford, California 94305, USA

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Genome Biology 2010, 11:R10  doi:10.1186/gb-2010-11-1-r10

Published: 28 January 2010

Additional files

Additional file 1:

Results of running Frappe on diploid individuals for chromosome 16 and the X chromosome and on individual chromosomes for chromosome 17.

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Additional file 2:

Results of an AMOVA analysis of X-linked and chromosome 16 markers treated as diploid genotypes.

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Additional file 3:

Number of high-delta SNPs and regions contained in various sets of TA/EX values for the Yoruba-French and French-Han population pairs.

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Additional file 4:

Possible effects of a population bottleneck on Nf/N and mf/m values.

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Additional file 5:

Comparison of observed X-linked delta values to TA/EX values using a Wilcoxon test for the Yoruba-French and French-Han population pairs.

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Additional file 6:

Number of high Fst SNPs and regions contained in various sets of TA/EX values and comparison of observed X-linked Fst values to various TA/EX Fst values using a Wilcoxon test for all three population pairs.

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Additional file 7:

Results of one-sided Wilcoxon tests comparing specific sets of TA/EX Fst values to observed X-linked Fst values.

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Additional file 8:

Genic enrichment (relative to the ratio of genic SNPs to all SNPs) of SNPs in different delta bins for all three population pairs.

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Additional file 9:

Sample sets used for different iHS, CLR, and XP-EHH runs.

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Additional file 10:

Raw iHS, CLR, and XP-EHH scores for all 372 X chromosome regions and all 8 continental groups.

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