Methods and processes for non-invasive assessment of genetic variations

A system comprising one or more processors and memory,

• which memory comprises instructions executable by the one or more processors and which memory comprises counts of nucleic acid sequence reads mapped to genomic sections of a reference genome, which sequence reads are reads of circulating cell-free nucleic acid from the blood of a pregnant female bearing a male fetus;
• and
• which instructions executable by the one or more processors are configured to:
• (a) access nucleotide sequence reads mapped to a subset of genomic sections of a reference genome, which sequence reads are reads of circulating cell-free nucleic acid from a test sample from a pregnant female, wherein the subset consists essentially of genomic sections to which a significant amount of reads from nucleic acid fragments shorter than about 150 bases are mapped;
• (b) determine the amount of sequence reads mapped to the subset of genomic sections;
• and
• (c) determine the presence or absence of a genetic variation according to the amount determined in (b).