Methods and processes for non-invasive assessment of genetic variations

A method for estimating a fraction of fetal nucleic acid in a test sample from a pregnant female, comprising:

• (a) obtaining counts of sequence reads mapped to portions of a reference genome, which sequence reads are reads of circulating cell-free nucleic acid from a test sample from a pregnant female,
• (b) selecting a subset of the portions, thereby providing a subset of counts which are derived from a region of the genome that contributes a greater number of counts derived from fetal nucleic acid relative to total counts from the region than counts of fetal nucleic acid relative to total counts of another region of the genome;
• and
• (c) estimating a fraction of fetal nucleic acid for the test sample based on the subset of portions.