Additional file 2.

Supplementary Tables 1 to 8. Table S1: minimum inclusive segment lengths (bp) calculated for each chromosome for each population and across all populations. Table S2a-d: putative autozygous segment coordinates for YRI, CEU, CHB, and JPT, respectively. Segment coordinates and parameters are listed for segments with a segment length median MAD score greater than 10. Table S3a-d: tables of all detected outlier peaks and derived peak statistics for YRI, CEU, CHB, and JPT, respectively. Outlier peaks by peak height (extAUC) were determined separately for each population and chromosome and statistics extracted for different peak features. Table S4a-d: tables of all detected outlier peak regions and summary of underlying peak statistics for YRI, CEU, CHB, and JPT, respectively. Outlier peaks that were directly adjacent to each other and were not well separated (Valleys > 0.5 × Peak height) were merged to define peak regions, and statistics were summarized across the underlying peaks. Table S5a,b: peaks with high-ranking extAUC and high Fst/θ between CHB and JPT represent extended haplotypes with high frequency differences. Peaks were extracted that had both high-ranking extAUC values and extreme Fst/θ values (autosomes >0.0360 or chromosome X >0.0538) in both/between CHB and JPT. For each peak, approximate haplotype frequencies were estimated using the allele frequencies of the differentiated loci. Table S6a-d: candidate fixed areas: genomic areas of contiguous loci with evidence for fixation. RCL0 were selected using thresholds set as the first quartiles of RCL0 SNP counts and RCL0 centimorgan extent values across all populations. Selected RCL0 were then intersected with a dataset of genes and canonical coding regions as well as data from previous reports by Kimura et al. [27], Sabeti and colleagues [5,28], Tang et al. [29], and O'Reilly et al. [30]. Table S7a-c: outlier peak regions intersecting candidate fixed areas in CEU, CHB, or JPT. Outlier peak regions were intersected with the set of candidate fixed areas presented in Table S6a-d. These peak regions were then intersected with a dataset of genes and canonical coding regions as well as data from previous reports by Kimura et al. [27], Sabeti and colleagues [5,28], Tang et al. [29], and O'Reilly et al. [30]. Table S8: combined candidate fixed regions. Coordinates of candidate fixed peak regions from Table S7a-c that overlapped were merged into a set of combined candidate fixed regions. These regions were annotated with genes that directly intersected any candidate fixed areas as well as the number of overlapping detected regions in each of the previous reports by Kimura et al. [27], Sabeti and colleagues [5,28], Tang et al. [29], and O'Reilly et al. [30].

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Johnson et al. Genome Biology 2011 12:R21   doi:10.1186/gb-2011-12-3-r21