Readme file raw sequencing Ð Kooyers et al. 2020 The raw sequence data used in Kooyers et al. 2020 is given in a series of fastq files with .gz compression. This sequence data was generated via a single HiSeqX sequencing lane (PE 150bp) completed by Novogene. Each index is a different fastq file. We only used the first read for the analysis within this paper Ð if you would like the second reads, please email nkooyers@gmail.com. Additionally, two of ten total indexes ran poorly and we did not include those individuals in the manuscript or in this dryad entry. There is also a file labeled MSGkeyfile.txt that lists the relevant lane and barcode for each individual used in this experiment as well as the other information necessary for running the Tassel GBS pipeline. Besides for the header row, each row is a different individual. Below is the description of the relevant columns. The combination of the fastq files and the key file are the relevant inputs for the Tassel GBS pipeline. Column A Ð Flowcell Ð All samples were run on the same flow cell (HMFN7BBXX) Column B Ð Lane Ð While all samples were run on a single lane, this column denotes which index and thus which fastq file the individual is contained in. Column C Ð Barcode Ð The same 40 barcodes are present in each index. Thus each index:barcode combination is unique. Column D - FullSampleName Ð If there is just a number listed, the individual is from the F2 mapping population. If BEL, IM or F1 preceedes a number, the individual is from either the California, Oregon or F1 population. Numbers correspond to the same numbers listed in the phenotype spreadsheet also included in this Dryad entry. Column E Ð Platename Ð Describes which 96-well plate was on when it was sent to Novogene Column F Ð Row Ð Describes the location of the sample in the 96-well plates originally sent to Novogene Column G Ð Column Ð Describes the location of the sample in the 96-well plates originally sent to Novogene Column H Ð Index Ð The index that was used to separate out the different fastq files. Each index:barcode combination is unique.