All .csv files are QTL mapping input files for R/qtl. These files include all genotype and phenotype information for individuals used for mapping
QTL4_GBS_data_processing.txt contains scripts for read processing, read mapping, SNP calling and filtering
QTL4_annotation_script.txt contains scripts for gene prediction, blast, GO annotation and Drosophila candidate gene homolog identification
QTL4_WGS_data_processing.txt contains scripts for WGS read processing, read mapping, variant (SNP+Indel) calling and filtering
QTL4_R/qtl_scripts.rtf contains scripts for QTL mapping for all families in R/qtl
4E_rilf2_snp_stringent_combined_peakscaffolds.xlsx contain all post-filter WGS SNPs on the scaffolds within or flanking the major QTL