A comparative analysis dataset for improving genuine SNP identification in ancient maize aDNA

Maize is an important subject in the study of ancient DNA (aDNA) due to its profound historical, cultural and economic significance. Studies of maize aDNA can provide insights into the domestication, evolution and gene flow of this important crop plant. During analysis of aDNA samples, it is essential to elucidate the extent of post-mortem damage (PMD) as well as to select optimal tools and read depth criteria for genuine single nucleotide polymorphism (SNP) discovery. Choosing different analytical pipelines can significantly alter SNP calls. To date, standardized approaches to address these issues are lacking. The data in this study was originally collected from previous publications and re-analyzed using two different approaches for solving PMD: Rm5nt and NoChange. The data were processed using three different analysis tools (GATK, angsd and pileupCaller) and analyzed under three read depth criteria (2X, 5X and 10X) for genuine SNP discovery. The dataset in this study is a valuable source for ancient maize research study can also be used to help genetic and archaeological researchers improve the quality of analyses in aDNA maize studies.