Abstract: Fragmentomic features provide various properties of the sample (e.g., urine or plasma) and/or of a subject. Relative contributions or enrichment of clinically-relevant DNA (e.g., type(s) of transrenal and non-transrenal urinary cfDNA) are provided using fragmentomic features of urinary cell-free DNA. Such measurements could be used for reflecting the glomerular permeability and monitoring various diseases, e.g., kidney abnormality. The fragmentomic features can include a corrected urinary DNA concentration, size, end motifs of urinary DNA molecules, and cfDNA molecules from open chromatin regions (OCR) of one or more tissues. In addition, nuclease activities or other fragmentation processes of cfDNA are determined based on relative contributions concerning the different profiles of cfDNA cleavage, which are also used for determining contribution of cfDNA from tissue(s), level of pathology, and gestational age.