Supplemental Material for Serrano Negron, Hansen, and Harbison, 2018

Figure S1. Plot of sequence coverage in SIP lines. Figure S2. Plot of LoFreq score distributions for known and novel variants. Figure S3. Day sleep in The Sleep Inbred Panel. Figure S4. Comparison of SIP night sleep and 24-hour sleep with the longest- and shortest-sleeping lines of the DGRP. Table S1. Analysis of variance of sleep traits. Table S2. Comparison of variant calls between BWA and novoalign alignments. Table S3. Mean sleep parameters for each line.Table S4. Comparison of SIP line sleep phenotypes to progenitor populations by progenitor selection scheme and replicate population. Table S5. Mean sleep <i>CV</i><sub>E </sub>parameters for each line. Table S6. ANOVA of sleep <i>CV</i><sub>E</sub> traits by progenitor selection scheme and replicate population. Table S7. Standard deviation across days for each sleep parameter of each line. Table S8. ANOVA of sleep <i>σ</i> traits by progenitor selection scheme and replicate population. Table S9. Sequence variant categories. Table S10. Comparison of actual versus predicted homozygosity on each chromosome arm of the SIP. File S1. Plot of predicted DGRP founder haplotypes from Hidden Markov Model for Chromosomes <i>X</i>, <i>2L</i>, <i>3L</i>, and <i>3R</i>. File S2. Sleep Inbred Panel list of variants and confidence intervals using BWA alignment. File S3. Sleep Inbred Panel list of variants and confidence intervals using Novoalign alignment. File S4. Sleep Inbred Panel annotated variant call file using BWA alignment. File S5. Sleep Inbred Panel annotated variant call file using Novoalign alignment.