The placenta is a temporary organ that develops during pregnancy. Prior work has found that placentas are genetically heterogeneous due to developmental bottlenecks in trophoblast differentiation. The conflicting relationship between confined placental mosaicism and adverse pregnancy outcomes is hypothesized to be from nonuniform mutations throughout the placenta resulting from mosaicism. Retrospective lineage tracing, particularly in trophoblasts, could be key to understanding how derivations of cell fate connect to the development of placental dysfunction. As such, it is important to characterize the relationship between somatic genetic variation, cell types, and lineage tracing in both healthy and diseased placentas. We identified rare, damaging, loss-of-function mutations in placentas with pre-eclampsia and other histopathological lesions that may be clinically relevant. We developed a computational pipeline to perform single cell/nuclei variant calling using STARSolo and GATK Best Practices Workflow for RNA-seq Short Variant Discovery. We also employed VarTrix to perform single-cell genotyping. Using both methodologies, we generated single-nucleotide variant by cell barcode matrices for four 10X Multiome single-nuclei RNA-sequencing samples obtained from different sampling sites in a one human term placenta. Lastly, we performed trajectory inference to determine the relationship between mutational burden and lineage in trophoblasts and find that mutational burden is able to differentiate between different syncytiotrophoblast clusters.