apple_leaf

2017-12-03T21:34:11Z (GMT) by Zoë Migicovsky
<p>Contains genetic data and binary images associated with the manuscript "Morphometrics reveals complex and heritable apple leaf shapes" </p><p>####</p><p>Folder: genetic_data</p><p>Contains the genetic data (ped and map files) used in this study.</p><p>File 1: </p><p>ApeKI_PstI-EcoT22I_Malv1.0p_bwa_maf0.01_min2alleles_noIndels_dp5_miss70_imputed_plink_leaf_miss0_maf05_hetero90.ped</p><p>Description: </p><p>Genotype table in PLINK .ped format. Genotypes were obtained using GBS (ApeKI and PstI-EcoT221I). The PED file is a white-space (space or tab) delimited file. the first six columns are:</p><p>Family ID / Individual ID / Paternal ID / Maternal ID / Sex (1=male; 2=female; other=unknown) / Phenotype</p><p>Genotypes (biallelic) are column 7 onwards. </p><p>apple_ids (unique per cultivar) are used for Family ID and Individual ID, these can be linked with the binary images using leaf_binary_image_info.txt </p><p>File 2: </p><p>ApeKI_PstI-EcoT22I_Malv1.0p_bwa_maf0.01_min2alleles_noIndels_dp5_miss70_imputed_plink_leaf_miss0_maf05_hetero90.map</p><p>Description:</p><p>Each line of the .map file describes a single marker and contains 4 columns:</p><p>chromosome (1-18, X, Y or 0 if unplaced) / rs# or snp identifier / Genetic distance (morgans) / Base-pair position (bp units)</p><p>chromosome 18 indicates contigs that are unanchored to the reference genome </p><p>###</p><p>Folder: apple_leaf_binary_images</p><p>Description:</p><p>Contains all binary images of apple leaves used in this study. Files are named after the nursery ID, which is the value before “-“ and can be linked with the apple IDs used in this study through the leaf_binary_image_info.txt info file. </p><p>###</p><p>Folder: leaf_genetic_image_info</p><p>Description:</p><p>Info file (leaf_binary_image_info.txt) which links the name of the images (image_name) with the nursery_id (unique per tree in the orchard) and apple_id (unique per cultivar) for the study. The image_name/nursery_id is used in the leaf images, but the apple IDs are used in the genotype files. </p>