Being a lot more accurate at homing in around the chosen locus. Ultimately, to establish if estimating starting allele frequency from the controls introduces bias, we carried out many additional simulations. As above, we simulated 50,000 alleles from every of ten IC87201 manufacturer beginning frequencies, this time working with only two populations to simulate the two control populations. We then deemed only those alleles with an typical ending frequency among 0.40.60: Figure S5A shows that 90 of alleles with these ending frequencies began with frequencies involving 0.20.80. Lastly, given that the ending frequency was 0.40.60, we determined the distribution of differentiation in between the two populations. As shown in Figure S5B, the expected distributions are very equivalent, when conditioned on the exact same average ending frequency, specially for alleles which began above 0.20. As alleles which contributed practically all simulated values that started above 0.20, we conclude that estimating allele frequencies within this way introduces tiny error. Moreover, FDR thresholds have been extremely comparable across allele frequency categories (Tables S2, S3), indicating that FDR thresholds are only slightly sensitive to beginning frequency soon after 110 generations of evolution.Supporting InformationDataset S1 Functional clustering of GO terms generated by DAVID. Located at: doi:10.1371/journal.pgen.1001336.s001 (0.46 MB XLS) Dataset S2 Significant GO Terms, as generated by DAVID. Located at: doi:ten.1371/journal.pgen.1001336.s002 (0.20 MB XLS) Dataset S3 Genes within 1 kb of a peak variant, excluding the Chr. two centromere. Located at: doi:10.1371/journal.pgen.1001336.s003 (0.47 MB TDS) Dataset S4 All peak variants. Located at: doi:10.1371/journal.pgen.1001336.s004 (0.41 MB XLS) Figure S1 Study coverage of genome partitions employing reads with alignment qualities higher than 15. A: Chromosomes X, two, and 3; B: centromeric regions, C: mitochondria, D: Y chromosome, E: UEvolve and Resequence: Body Sizeand Uextra (unplaced regions). Females had been sequenced, so Y coverage is expected to be near zero for exclusive alignments, PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/20025400 although some male DNA may be present if females had been mated and had stored sperm. Found at: doi:10.1371/journal.pgen.1001336.s005 (0.73 MB DOC)Figure Sdifferentiation encompassed multiple genes and lots of polymoprhisms. For the candidate gene at each and every locus, the exons are shown as linked grey boxes; only a single transcript for simplicity. Located at: doi:10.1371/journal.pgen.1001336.s008 (0.86 MB DOC)Figure S5 Low bias introduced by estimating beginning allele frequency. A: the proportion of variants with typical frequency of 0.40.60, according to starting frequency. B: Distribution of anticipated allele frequency differentiation for alleles which have a final average frequency amongst 0.45.50 inside the two control populations; colors indicate beginning allele frequencies, red = 0.50; orange = 0.45, yellow = 0.40; green = 0.35; blue = 0.30; purple = 0.25; fuchsia = 0.20. The distribution is very equivalent until starting allele frequency is 0.25 or significantly less, and couple of alleles with this beginning frequency finish with an typical frequency among 0.400.60, as shown in a. Identified at: doi:ten.1371/journal.pgen.1001336.s009 (0.30 MB DOC) Table S1 Significance of anatomical measurements. Found at: doi:ten.1371/journal.pgen.1001336.s010 (0.04 MB PDF) Table S2 False discovery rates for each and every allele frequency class at several thresholds for autosomes. Located at: doi:ten.1371/journal.pgen.1001336.s011 (0.02 MB PDF) Table S3 False discovery.
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