This repository contains molecular phenotype data of transposable element (TE) activity within individuals of the species Thlaspi arvense. The raw genomic data used in this study proceeds from 2 different studies: Y. Geng et al. (2021). Genomic Analysis of Field Pennycress (Thlaspi Arvense) Provides Insights into Mechanisms of Adaptation to High Elevation (https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-01079-0). D. Galanti et al. (2022). Genetic and environmental drivers of large-scale epigenetic variation in Thlaspi arvense (https://doi.org/10.1101/2022.03.16.484610). Transposon insertion polymorphisms (TIPS) were detected using SPLITREADER (https://github.com/LeanQ/SPLITREADER) and the initial calls were curated following the steps described in P. Baduel et al. (2021). Efficient Detection of Transposable Element Insertion Polymorphisms Between Genomes Using Short-Read Sequencing Data. J. Cho. Plant Transposable Elements: Methods and Protocols. Springer US. (https://link.springer.com/book/10.1007/978-1-0716-1134-0). We also screen the samples searching for transposon absence polymorphisms (TAPS) using a custom pipeline deposited at https://github.com/weigelworld/popTAP. All TE polymorphisms were detected using as reference genome published by A. Nunn et al. (2021). Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates. (https://pubmed.ncbi.nlm.nih.gov/34990041/). Both datasets and their corresponding metadata are included in this repository.