Methods using characteristics of urinary and other dna

A method of analyzing a biological sample, the method comprising:

• sequencing a cell-free plurality of nucleic acid molecules from the biological sample of an individual to produce sequence reads, wherein each nucleic acid molecule of the cell-free plurality of nucleic acid molecules is double-stranded with a first strand having a first portion and a second strand, and wherein the first portion of the first strand of at least some of the cell-free plurality of nucleic acid molecules overhangs the second strand;
• aligning the sequence reads to a reference genome to determine genomic locations of the cell-free plurality of nucleic acid molecules;
• identifying a set of nucleic acid molecules of the cell-free plurality of nucleic acid molecules, wherein the genomic location of each nucleic acid molecule of the set of nucleic acid molecules is at a specified distance from a predetermined type of genomic site;
• measuring a characteristic of each nucleic acid molecule of the set of nucleic acid molecules, wherein the characteristic correlates to a length of the first strand that overhangs the second strand;
• determining a jagged index value using the measured characteristics of the set of nucleic acid molecules;
• and
• determining a level of a condition of the individual using the jagged index value.