Figure 1.
Schematic representation of the pooled libraries used in this study.
Libraries A, B1, B2 and B4 were constructed pooling flies from different number of DGRP strains. Libraries B3, B5 and B6 are the result of merging reads from libraries B1, B2 and B4.
Table 1.
Pooled Libraries.
Table 2.
Library allele frequency estimate comparison to 162 DGRP strains.
Figure 2.
DNA contribution of strains in Library A.
DNA contributions of each strain as observed from representation of unique SNPs in pool. Each vertical line represents pooled frequency estimates of singleton SNPs unique to a single strain. Edges of lines represent values at 2 standard deviations from mean (thick horizontal line). Strain RAL-301 was dropped from analysis due to low unique SNP count. Y-axis: DNA contribution in the form of pool frequency estimate from library A. X-axis: Strains sorted in order of mean DNA contribution.
Figure 3.
Expected and observed pooled frequency estimates.
Correlation coefficients between observed or simulated pooled allele frequency estimates and actual estimates as a function of the number of strains pooled. See Materials and Methods for a description of the libraries. Y-axis: Expected (triangles) and observed (circles) correlation coefficients of the 7 libraries compared to a perfectly binomial library, color-coded by library. X-axis: Libraries ordered by number of strains pooled.
Figure 4.
False positive and false negative rates of novel SNP discovery from pooled library B6. Y-axis: Error rate. Z-axis: Folded allele frequency from DGRP genotypes.