Additional file 3: of GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data

The distribution of pre-filtered SNPs across three different depth classes: Low (<4), Acceptable (4–200), and Over-represented (>200). The bar plot in AdditionalFile3.pdf compares the distributions of average read depths for the pre-filtered SNPs called by the five evaluated pipelines. (PDF 43 kb

Additional file 2: of GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data

Bubble plot showing the pair-wise percentage of shared markers called by the different pipelines. AdditionalFile2.pdf complements the visualization in Fig. 3, showing all pair-wise proportions of shared SNPs among the five evaluated pipelines. (PDF 732 kb

Additional file 4: of GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data

List of the 48 A. arguta genotypes used for GBS-SNP-CROP development and analysis. AdditionalFile4.pdf presents the names of the genotypes from the USDA National Clonal Germplasm Repository used in this study, along with their barcodes and the number of parsed GBS reads obtained for each. (PDF 50 kb