Genomic Variation in Natural Populations of Drosophila melanogaster

Supporting Information for Langley et al, 2012

Supporting Information

  • Supporting Information - File S1, Figures S1-S13, Figure SA1-SB2, and Tables S1-S26 (PDF, 1.7 MB)
  • Figure S1 - Regions of residual heterozygosity in RAL-335_1 (PDF, 238 KB)
  • Figure S2 - Expected heterozygosity, divergence and HKAl on the chr2R for the North American (RAL), African (MW) and simulans (SIM) samples (PDF, 457 KB)
  • Figure S3 - Expected heterozygosity, divergence and HKAl on the chr3L for the North American (RAL), African (MW) and simulans (SIM) samples (PDF, 525 KB)
  • Figure S4 - Expected heterozygosity, divergence and HKAl on the chr3R for the North American (RAL), African (MW) and simulans (SIM) samples (PDF, 594 KB)
  • Figure S5 - False discovery rates for different HKAl window sizes, chromsome arm and samples of genomes (PDF, 101 KB)
  • Figure S6 - The distributions of expected heterozygosity, divergence and number of sites at various (allele) sampling depths for Q30 data (PDF, 131 KB)
  • Figure S7 - The genomic distribution of theta, an estimate of the population recombination parameter 2Nr along with expected heterozygosity and lineage specific divergence (PDF, 962 KB)
  • Figure S8 - Correlations between recombination rates and HKAl, Piw and TsD (PDF, 129 KB)
  • Figure S9 - Presentation in the UCSC Genome Browser of the distributions across chr2R of the population genomic statistics, Piw, deltaw,^p, HKAl and TsD for the RAL sample as well as HBKl, and WHl (PDF, 461 KB)
  • Figure S10 - Presentation in the UCSC Genome Browser of the distributions in the 260 kbp Hen1 (Pimet) and Cyp6g1 region of the population genomic statistics, Piw, deltaw,^p, HKAl and TsD for the RAL sample as well as HBKl, and WHl (PDF, 257 KB)
  • Figure S11 - Boxplots of the distributions of Piw, deltaw, HKAl, TsD, HBKl and log(^p) in genomic exonic, intronic and intergenic regions annotated as chromatin states 1 through 9 (PDF, 1.2 MB)
  • Figure S12 - ECDFs (epirical cumulative distribution functions) of Piw, deltaw, HKA1, TsD, HKA1 and log(^p) in genomic exonic, intronic and intergenic regions annotated as chromatin states 1 through 9 (PDF, 1.2 MB)
  • Figure S13 - The distribution of recombination rates of genes estimated by loess smoothed genetic maps, ^r15 in bins of 0.25 cM/Mbp (PDF, 163 KB)
  • Figure SA1 - A two dimensional histogram showing the relationship between consensus quality score and read depth (PDF, 64 KB)
  • Figure SB1 - Box plots of G+C content by flow cell lane for all stocks (PDF, 86 KB)
  • Figure SB2 - Empirical and theoretical distributions of read depth illustrating the utility of the negative binomial distribution to model read depth (PDF, 66 KB)
  • File S1 - Demographic simulation methods (PDF, 69 KB)
  • Table S1 - Chromosome segments identified as residually heterozygous in the indicated stock/assembly (PDF, 85 KB)
  • Table S2 - Regions filtered from the genomes RAL-303_1, RAL-304_1 and RAL-306_1 because of apparent IBD with one another (PDF, 80 KB)
  • Table S3 - RAL sampling depth at Q30 plus the total numbers of assembled bp (PDF, 68 KB)
  • Table S4 - MW sampling depth at Q30 plus the total numbers of assembled bp (PDF, 68 KB)
  • Table S5 - SIM sampling depth at Q30 plus the total numbers of assembled bp (PDF, 68 KB)
  • Table S6 - Potential sampling depth after filtering of residually heterozygous regions and those involved in obvious identity by descent (PDF, 69 KB)
  • Table S7 - RAL allelic depth at Q40 plus the total numbers of assembled bp (PDF, 68 KB)
  • Table S8 - MW sampling depth at Q40 plus the total numbers of assembled bp (PDF, 69 KB)
  • Table S9 - SIM sampling depth at Q40 plus the total numbers of assembled bp (PDF, 69 KB)
  • Table S10 - Average sampling depth of coding regions on the X and on the autosomes (PDF, 67 KB)
  • Table S11 - The correlation of divergence or expected heterozygosity in 1000 bp windows across each of the five major chromosome arms for the indicated pair of samples (PDF, 67 KB)
  • Table S13 - Distribution of missing data and statistics of partitions used in the Ldhat-based estimation of recombination (PDF, 82 KB)
  • Table S14 - The centromere proximal and telomere-proximal regions of the 5 major chromosome arms filtered or "trimmed" because of the preponderance of repetitive sequences and strong systematic effects associated with centromeres and telomeres (PDF, 83 KB)
  • Table S15 - The correlations between the logarithm of the estimated rates of recombination ( log(^r15) , log(sup>^p15) , log(^p) ) with Piw, HKA1, TsD, or HBK1 for each chromosome arm in the RAL, MW and SIM samples (PDF, 177 KB)
  • Table S16 - Amino acid replacement FST GO enrichment analysis - biological categories (PDF, 103 KB)
  • Table S17 - Amino acid replacement FST GO enrichment analysis - cellular categories (PDF, 69 KB)
  • Table S18 - Amino acid replacement FST GO enrichment analysis - molecular categories (PDF, 69 KB)
  • Table S12 - Genetic-map-based estimates of the rate of recombination per bp, in "lettered" cytogenetic intervals of the five major chromosome arms (.txt, 16 KB)
  • Table S19 - MW HKA valleys (2.5% lowest quantile, merged if within 10 kbp), and position relative to nearest gene (.txt, 48 KB)
  • Table S20 - Gene ontology analysis of MW HKA low outliers (.txt, 6 KB)
  • Table S21 - MW HKA peaks (2.5% highest quantile, merged if within 10 kbp), and position relative to nearest gene (.txt, 52 KB)
  • Table S22 - Diversity ratio valleys (see text) shared between MW D. melanogaster and the D. simulans data of Begun et al. (2007) (.txt, 4 KB)
  • Table S23 - Gene ontology analysis of MW HKA high outliers (.txt, 5 KB)
  • Table S24 - Diversity ratio valleys (2.5% lowest quantile, merged if within 10 kbp), and position relative to nearest gene (.txt, 34 KB)
  • Table S25 - Gene ontology analysis of heterozygosity ratio outliers (.txt, 22 KB)
  • Table S26 - Diversity valleys (see text) shared between MW D. melanogaster and the D. simulans data of Begun et al. (2007) (.txt, 14 KB)